# ent

id: cord-009716-oxahu8nz
type: CHEMICAL
entity:
  Parthenium hysterophorus The small forbs Sida cordifolia Alternanthera bettzikiana Xanthium strumarium


id: cord-022505-17khcmta
type: TAXON
entity:
  Sendai virus coronavirus Streptococcus pneumoniae Corynebacterium kutscheri Bordetella bronchiseptica Klebsiella


id: cord-022505-17khcmta
type: DISEASE
entity:
  BALT hyperplasia neutrophilic bronchopneumonia type II pneumocyte hyperplasia of alveolar epithelium


id: cord-002561-7j43yic1
type: CELL_LINE
entity:
  human HMO strains MAstV 8 and 9 sea lion MAstV 11 unclassified sea lion mink MAstV 21 and bat MAstV 12 strains


id: cord-002561-7j43yic1
type: CHEMICAL
entity:
  Mamastrovirus 1 GI A human Mamastrovirus 2 GI B feline Mamastrovirus 3 GI C porcine Mamastrovirus 4 GI D California sea lion Mamastrovirus 5 GI E


id: cord-002561-7j43yic1
type: CHEMICAL
entity:
  Mamastrovirus 6 GI F human Mamastrovirus 7 GI G bottlenose dolphin Mamastrovirus 8 GII A human Mamastrovirus 9 GII B human Mamastrovirus 10 GII C mink Mamastrovirus 11 GII D California sea lion Mamastrovirus 12 GII E bat Mamastrovirus 13 GII F ovine


id: cord-003838-u8zjzqbr
type: DNA
entity:
  unlinked autosomal nuclear introns ACOX2 intron 3 ACOX2 COPS7A intron 4 COPS7A and ROGDI intron 7 ACOX2 COPS7A ROGDI 31 and STAT5A intron 16


id: cord-003838-u8zjzqbr
type: DNA
entity:
  ACOX2 n 220 ML and BI 219 species tree 420 552 bp COPS7A n 220 ML and BI 219 species tree 581 760 bp ROGDI n 219 ML


id: cord-003838-u8zjzqbr
type: GGP
entity:
  lobatus R cf landeri and d strongly supports all the species group assignments made by Csorba et al 2003 with the exception of R deckenii


id: cord-003838-u8zjzqbr
type: ORG
entity:
  Teaching Collections Texas A M University College Station USA Royal Ontario Museum Toronto Canada National Museums


id: cord-017156-ximzvqbm
type: DNA
entity:
  ATGCTGCGGCTATCGCAGCAT S M 5 I T A G G A G G G G G I T A G C G G G i A 3 3 5 ATGCTG CAG CA T b 3 e e e e e e T 5 A f l ffi iH7 fi F 1 r F F rE fi 3


id: cord-290253-hxxizipk
type: PROTEIN
entity:
  nuclear Adh SOD Amyrel RpL32 A random starting tree was used with a relaxed uncorrelated lognormal molecular clock Each of the partitions used a HKY substitution model


id: cord-021152-6znmkvy9
type: PROTEIN
entity:
  Coronaviridae family 19 20 21 22 Molecular evidence suggests that the Severe Acute Respiratory Syndrome Betacoronavirus SARS CoV beta CoV


id: cord-010305-z5c7zgp7
type: ORG
entity:
  Australian Institute of Urban Studies Greening Western Australia Department of Conservation and Land Management


id: cord-320295-k2i52wgs
type: ORG
entity:
  the International Committee on Taxonomy of Viruses the National Centre for Biotechnology Information the CAB International Bioscience


id: cord-019068-6j42euvc
type: CELL_LINE
entity:
  JT Hoeg M Grygier Y Fujita H Glenner J Olesen 5 8 Ascothoracida Copebarnacles These are uncommon parasites


id: cord-019068-6j42euvc
type: CL
entity:
  algae planktotrophic larvae and metamorphose into myses which look like tiny adults and feed on algae


id: cord-019068-6j42euvc
type: CL
entity:
  pilosus Crustacea Isopoda Gnathiidae from the east coast of South Africa The Salmon Louse Lepeophtheirus salmonis Copepoda Caligidae life cycle has only two chalimus stages The fish parasite Argulus


id: cord-019068-6j42euvc
type: DISEASE
entity:
  embryonic stage Sheina orri Myodocopa Cypridinidae an ostracod parasitic on the gills of the epaulette shark Hemiscyllium ocellatum Elasmobranchii Hemiscyllidae Metazoan parasites


id: cord-276372-q1fzxt3r
type: DNA
entity:
  IUCN Red List A Global Metapopulation Approach to Support Conservation Breeding Programs date 2013 12 11 journal PLoS One DOI 10 1371 journal pone 0080311 sha c4e99c8b861f4457b4a0518860bc9e52f5348e87 doc_id 276372 cord_uid q1fzxt3r


id: cord-010529-c8saxwfj
type: LOC
entity:
  the Northern Tampa Bay Area Hydrologic Evaluation Section Resource Conservation and Development Department


id: cord-263282-a7emso89
type: DNA
entity:
  12S rRNA mitochondrial gene 12Sa forward primer 5 0 CTGGGATTAGATACCCCACTAT 3 0 12Sh reverse primer 5 0 CCTTGACCTGTCTTGTTAGC 3 0 23 Samples


id: cord-304481-yqc8r3ll
type: WORK_OF_ART
entity:
  A Language and Environment for Statistical Computing R Foundation for Statistical Computing Phylogenomic


id: cord-010307-sxh5mq1q
type: DNA
entity:
  Top End i Chalinolobus nigrogriseus Scotorepens greyii and Scotorepens sanborni ii Miniopterus schreibersii


id: cord-005280-a23oy0sz
type: PROTEIN
entity:
  complex III subunit Rieske and complex I subunit NDUFB4 NADH dehydrogenase ubiquinone 1 beta subcomplex subunit 4 respectively Mutants


id: cord-354757-jy47l6zm
type: CELL_LINE
entity:
  Lake Victoria Potential microbial bioinvasions via ships ballast water sediment and biofilm Freshwater biodiversity importance threats status and conservation challenges Responses of invasive species


id: cord-271076-436nxsua
type: ORG
entity:
  the international committee on taxonomy of viruses Virology Division International Union of Microbiological Societies Viral metagenomics


id: cord-024166-t3qxscbp
type: CHEMICAL
entity:
  Polygala vulgaris Centaurea jacea Pimpinella saxifraga Carum carvi Danthonia decumbens Lotus corniculatus


id: cord-312555-qytl2vqt
type: CELL_LINE
entity:
  NE Brazil Boletin Latinoamericano y del Caribe de Plantas Medicinales y Aromáticas Ethnobotany in intermedical spaces the case of the Fulni


id: cord-021013-xvc791wx
type: CL
entity:
  stem and root barks in addition All these plant parts and organs have in common that they are important for the actual fitness or for the reproduction and thus the long term survival of the species Spiny species which invest in mechanical defense accumulate fewer alkaloids than soft bodied ones 15 examples are isoquinoline alkaloids


id: cord-021013-xvc791wx
type: WORK_OF_ART
entity:
  Apocynaceae Celestraceae Elaeocarpaceae Euphorbiaceae Fabaceae Orchidaceae Poaceae Ranunculaceae Rhizo


id: cord-021013-xvc791wx
type: ORG
entity:
  Okologische Biochemie Allelochemicals Role in Agriculture and Forestry Cell Culture and Somatic Cell Genetics of Plants F Constabel


id: cord-021013-xvc791wx
type: CHEMICAL
entity:
  quinolizidine alkaloids cryptopleurine haningtonine homohamngtonine haemanthamine isohamngtonine lycorine


id: cord-021013-xvc791wx
type: CHEMICAL
entity:
  glucosinolates nonproteinogenic amino acids cyanogenic glycosides acids aldehydes saponins triterpenes mono


id: cord-289555-1z4vbldd
type: WORK_OF_ART
entity:
  Diseases and Causes of Death in European Bats Dynamics in Disease Susceptibility and Infection Rates


id: cord-289555-1z4vbldd
type: DISEASE
entity:
  lung liver heart kidney adrenal gland spleen intestine pancreas brain tongue larynx salivary gland and pectoral muscle


id: cord-335915-2apj4qy9
type: PROTEIN
entity:
  1 acid glycoprotein a2 macroglobulin haptoglobin protein C and b C reactive protein fibrinogen complement ferritin globulins


id: cord-335915-2apj4qy9
type: GGP
entity:
  glycoproteins Alpha 1antitrypsin a 1 acid glycoprotein a2 macroglobulin C reactive protein haptoglobin


id: cord-255018-dhkz23co
type: CHEMICAL
entity:
  Berberis microphylla Ribes magellanicum Fragaria chiloensis Ephedra ochreata Aristotelia chilensis Gaultheria mucronata Berberis


id: cord-255018-dhkz23co
type: CHEMICAL
entity:
  Aristotelia chilensis Ribes magellanicum Ephedra ochreata Berberis microphylla Fragaria chiloensis Luma apiculata


id: cord-269505-7g8lio9l
type: ORG
entity:
  Ecosystem Functioning and Human Wellbeing an Ecological and Economic Perspective Ecosystems and Human Well Being Current State


id: cord-301991-n87le8ix
type: ORG
entity:
  the World Health Organization WHO Indian Standard Institution ISI Indian Council of Medical Research ICMR


id: cord-343461-vj6o1b18
type: PROTEIN
entity:
  G Ferisin G Ferreira R J Ferrer A Figueiredo C N Figueiredo Y F Reinoso Fuentealba C G Garrido Benavent I Cañete Gibas C F Gil Durán C Glushakova A M Gonçalves M F M González M Gorczak M Gorton C Guard F E Guarnizo A L Guarro J Gutiérrez M Hamal P Hien L T Hocking A


id: cord-343461-vj6o1b18
type: PROTEIN
entity:
  D Houbraken J Hunter G C Inácio C A Jourdan M Kapitonov V I Kelly L Khanh T N Kisło K Kiss L Kiyashko


id: cord-343461-vj6o1b18
type: PROTEIN
entity:
  N V Liimatainen K Lim H J Lyons M N Maciá Vicente J G Magaña Dueñas V Mahiques R Malysheva E F Marbach P A S Marinho P Matočec N McTaggart A R Mešić A Morin L Muñoz


id: cord-343461-vj6o1b18
type: PROTEIN
entity:
  lactose melibiose raffinose soluble starch inulin D arabinose D ribose L sorbose L rhamnose galactitol erythritol myo inositol 5 keto D gluconate D


id: cord-343461-vj6o1b18
type: CELL_LINE
entity:
  light brown 6C8 6D8 margin smooth fairly undulate Lamellae emarginate crowded greyish when young later greyish orange 6B4 brownish orange 6C5


id: cord-343461-vj6o1b18
type: DNA
entity:
  G kielmeyerae CML3527 T GenBank MN508390 1 was Coryneum heveanum MFLUCC17 0369 GenBank NG_065764 1 99 56 identity and had 99 33 identity


id: cord-343461-vj6o1b18
type: PROTEIN
entity:
  galactitol D mannitol D glucitol methyl alpha D glucoside salicin D gluconate succinic acid citric acid 2 keto D


id: cord-343461-vj6o1b18
type: DNA
entity:
  Identities 1 078 1 099 98 3 gaps 0 Neodevriesia cladophorae GenBank KU578114 Identities 1 076 1 099 98 7 gaps 0 and Neodevriesia strelitziae GenBank GU301810 Identities 1 061 1 091 97 7 gaps 0 Conidia subcylindrical fusoid or ellipsoid to fusoid individually hyaline olivaceous green


id: cord-343461-vj6o1b18
type: CELL_LINE
entity:
  Krông Kmar town N12 23 49 207 E108 20 59 356 h 1 071 m asl on rotten wood 24 May 2019 A A Kiyasko 73 AK 19 holotype LE 323311 ITS


id: cord-343461-vj6o1b18
type: DNA
entity:
  Nectriaceae Pilzkompendium 4 1 793 I XXXVI Mycenae paranaensis Verhandelingen Koninklijke Nederlandse Akademie van Wetenschappen Afdeling Natuurkunde A multi locus backbone tree


id: cord-343461-vj6o1b18
type: CHEBI
entity:
  raffinose Glucose sucrose galactose maltose cellobiose trehalose melezitose methyl alpha D glucoside Dxylose L arabinose D glucosamine ethanol glycerol


id: cord-343461-vj6o1b18
type: GGP
entity:
  inulin D arabinose D ribose L sorbose L rhamnose galactitol erythritol myo inositol 5 keto D gluconate


id: cord-343461-vj6o1b18
type: GGP
entity:
  glucitol methyl alpha D glucoside salicin D gluconate succinic acid citric acid 2 keto D gluconate myo inositol


id: cord-343461-vj6o1b18
type: GGP
entity:
  Mollisiaceae s lat A detailed polyphasic taxonomic analysis in this group is still missing According to our analysis of ITS1 5 8S ITS2 nrDNA


id: cord-343461-vj6o1b18
type: FAC
entity:
  Station Centre for Crop Health Queensland Alliance for Agriculture and Food Innovation Ecosystem Science Department of Biodiversity Conservation


id: cord-343461-vj6o1b18
type: ORG
entity:
  conidia Department of Agriculture and Fisheries Plant Pathology Herbarium Department of Agriculture and Fisheries Centre for Crop Health Benátská


id: cord-343461-vj6o1b18
type: ORG
entity:
  µm Department of Agriculture and Fisheries Plant Pathology Herbarium Department of Agriculture and Fisheries Dense


id: cord-343461-vj6o1b18
type: ORG
entity:
  Naturalis Biodiversity Center Westerdijk Fungal Biodiversity Institute Fungal Planet Mediterranean Quercus


id: cord-343461-vj6o1b18
type: CHEMICAL
entity:
  mannitol D glucitol methyl alpha D glucoside salicin D gluconate succinic acid citric acid 2 keto D gluconate


id: cord-343461-vj6o1b18
type: DISEASE
entity:
  vegetative mycelium margins irregular reverse greenish black diffusible pigments absent On potato carrot agar


id: cord-343461-vj6o1b18
type: CHEMICAL
entity:
  Mediterranean Quercus ilex subsp ballota forest Ascocarps mature ascospores Scale bar 20 μm GTR G selected


# bib

id: cord-002561-7j43yic1
title: The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses
author: Donato, Celeste
date: 2017-05-10
txt: ./txt/cord-002561-7j43yic1.txt
cache: ./cache/cord-002561-7j43yic1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454415/
doi: 10.3390/v9050102
summary:
  Astroviruses within the Mamastrovirus genus are derived from numerous mammalian species in addition to humans (HAstV), including farmed species such as pigs (PAstV), sheep (OAstV), cattle (BoAstV), domesticated animals including cats (FAstV), and dogs (CaAstV), rodents and small mammals including mink (MiAstV), bats (BAstV), rats (RAstV), mice, rabbit (RabAstV), fox, marmot (HHMastV), porcupine, shrew, vole, and larger species including deer (CcAstV), monkeys, water buffalo (BufAstV), yak, camel (DcAstV), and cheetah (ChAstV) (Figure 1a,b) . Viruses from the Avastrovirus genus have been characterized from numerous farmed avian species including turkeys (TAstV), ducks (DAstV), chicken (CAstV), guineafowl (GFAstV), pigeon (PiAstV), goose, as well as wild aquatic and terrestrial birds including heron, doves, penguins, and many other species (Figure 2a) . Astrovirus strains identified from fecal samples of multiple non-human primate species from wild, captive, and peri-urban environments in Bangladesh and Cambodia reveal multiple interspecies transmission events, with viruses closely related to the VA/HMO lineage of human viruses, and non-human mammalian and avian astroviruses (Figure 1a,b) [28] .

abstract:
  Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.


id: cord-003838-u8zjzqbr
author: Demos, Terrence C.
date: 2019-08-22
txt: ./txt/cord-003838-u8zjzqbr.txt
cache: ./cache/cord-003838-u8zjzqbr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6704657/
doi: 10.1186/s12862-019-1485-1
summary:
  CONCLUSIONS: Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. The species limits of morphologically conservative or cryptic lineages of bats have been greatly clarified by an integrative approach using multi-locus genetic delimitation methods as a starting point for identifying candidate species and then testing them using additional, corroborative data from behavioral, morphological, distributional, and/or ecological information ( [4] , cf. Maximum likelihood (ML) and Bayesian inference (BI) inferred trees with similar topologies; the ML gene tree is shown for the 351 sequence cyt-b alignment of 74 Rhinolophus species/clades ( Fig. 3 ; see also Additional file 4 for the phylogeny with all 351 terminals labeled). denti/ simulator; and finally 8 of 8 lineages in the fumigatus group, including three possibly new species as well as support for the recent recognition of R.

title:
  Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics

abstract:
  BACKGROUND: The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. RESULTS: We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. CONCLUSIONS: Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-019-1485-1) contains supplementary material, which is available to authorized users.


id: cord-005280-a23oy0sz
title: ROS and diseases: role in metabolism and energy supply
author: Yang, Shenshu
date: 2019-12-07
txt: ./txt/cord-005280-a23oy0sz.txt
cache: ./cache/cord-005280-a23oy0sz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089381/
doi: 10.1007/s11010-019-03667-9
summary:
  Although ROS play an important role in pathogen resistance and cellular signalling, they are also broadly recognized as harmful reactive particles to cell as they damage intracellular proteins, lipids and nucleic acids. The homeostasis of ROS plays an important role in reducing oxidative damage and fulfil energy demand. Relatively high levels of ROS may cause oxidative damage or induce apoptosis during immunological defences or pathological conditions. However, ROS themselves could activate extracellular signal-regulated kinase (ERK) by targeting proteins Gαi and Gα0 and protect cardiac cell from oxidative damage [18] . Apart from oxidative damage, ROS also serve as signalling molecules and play an important role in homeostasis, metabolism, growth and differentiation [3] . PGC-1α could protect neural cells from oxidative damage by reducing ROS level via antioxidative enzymes GPx1 and SOD2 [15] . ROS regulate vascular cell proliferation and apoptosis with their fundamental role in metabolism.

abstract:
  Researches dedicated to reactive oxygen species (ROS) had been performed for decades, yet the outcomes remain controversial. With the relentless effort of studies, researchers have explored the role of ROS in biosystem and various diseases. ROS are beneficial for biosystem presenting as signalling molecules and enhancing immunologic defence. However, they also have harmful effects such as causing tissue and organ damages. The results are controversial in studies focusing on ROS and ROS-related diseases by regulating ROS with inhibitors or promotors. These competing results hindered the process for further investigation of the specific mechanisms lying behind. The opinions presented in this review interpret the researches of ROS from a different dimension that might explain the competing results of ROS introduced so far from a broader perspective. This review brings a different thinking to researchers, with the neglected features and potentials of ROS, to relate their works with ROS and to explore the mechanisms between their subject and ROS.


id: cord-005845-axrv8zfg
title: Genomic prospecting
author: O''Brien, Stephen J.
date: 1995
txt: ./txt/cord-005845-axrv8zfg.txt
cache: ./cache/cord-005845-axrv8zfg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095837/
doi: 10.1038/nm0895-742
summary:
  When cheetahs became exposed recently to feline infectious peritonitis virus, a coronavirus with low morbidity and mortality in domestic cats (about 1 per cent affected), 100 per cent of infected cheetahs developed symptoms (diarrhea, jaundice, depression, fever) and 60 per cent died 7 • The cheetah''s homogeneous sensitivity to this agent in the face of genetic monomorphism at the MHC provided a rationale for the critical importance of MHC genetic variation in natural populations. Some fascinating insight about lethal infectious disease and natural genetic defences appeared from a wild mouse population in a squab farm near Lake Casitas, forty miles north of Los Angeles'' 0 • Murray Gardner (University of California at Davis) discovered that the mice were suffering a raging epidemic with a retrovirus that caused fatal hindlimb paralysis. Finally, with the recent development of high resolution comparative gene maps of primate, cat, and other mammalian species, the genetic basis of lentivirus resistance can now be approached''".

abstract:
  The importahce of preserving biodiversity extends beyond the discovery of new drugs to understanding how other species have dealt with medical problems we currently face.


id: cord-009716-oxahu8nz
author: Lawes, Roger A.
date: 2006-10-27
txt: ./txt/cord-009716-oxahu8nz.txt
cache: ./cache/cord-009716-oxahu8nz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163630/
doi: 10.1111/j.1472-4642.2006.00291.x
summary:
  A combination of three published weed classification frameworks and multivariate techniques were employed to classify species based on their frequency and cover at a range of spatial scales. (2000) ; Colautti & MacIsaac (2004) ; Davis & Thompson (2000) Introduction Barrier based on three distinct characteristics: dispersal distance (short/ long), uniqueness (novel/common to the region colonized), and impact on the new environment (small/great) ( Table 1 ). The data requirements necessary to implement the frameworks vary, although each draws heavily on frequency and abundance information to classify the invasive characteristics of a species. We propose evaluating weed invasions as part of a larger, existing plant community where invasive species are classified based on their relative abundance, frequency, and cover at local and landscape scales. Colautti & MacIsaac (2004)''s classification system is largely devised around concepts of frequency and abundance and it was a relatively simple process to classify species based on the survey data, where cover provided a surrogate measure of abundance.

title:
  Comparing agglomerative clustering and three weed classification frameworks to assess the invasiveness of alien species across spatial scales

abstract:
  To prioritize weed management at the catchment scale, information is required on the species present, their relatively frequency, abundance, and likely spread and impact. The objective of this study was to classify the invasiveness of alien species that have invaded the Upper Burdekin Catchment in Queensland, Australia, at three spatial scales. A combination of three published weed classification frameworks and multivariate techniques were employed to classify species based on their frequency and cover at a range of spatial scales. We surveyed the Upper Burdekin Catchment for alien species, and for each species determined the following distribution indices — site frequency, total cover, transect frequency per site frequency and quadrat frequency per site frequency, cover per quadrat when present, cover per transect when present, and cover per site when present. These indices capture the effect of species abundance and frequency between sites (site frequency and total cover), within sites (transect frequency per site and cover per transect when present), and within transects (quadrat frequency per site frequency and cover per site). They were used to classify the species into seven groups using a hierarchical cluster analysis. The relationship between the indices was explored to determine how effective the small scale, site‐specific indices were at predicting the broader, landscape‐scale patterns. Strong correlations were observed between transect frequency per site and frequency (r (2) = 0.89) and cover per transect when present and total cover (r (2) = 0.62). This suggests that if a weed is abundant at the site level, it has the potential to occupy large areas of the catchment. The species groupings derived from the application of the three published weed classification frameworks were compared graphically to the groupings derived from the cluster analysis. One of the frameworks classified species into three groups. The other two frameworks classified species into four groups. There was a high degree of subjectivity in applying the frameworks to the survey data. Some of the data were of no relevance to the classification frameworks and were therefore ignored. We suggest that the weed classification frameworks should be used in conjunction with existing multivariate techniques to ensure that classifications capture important natural variations in observed data that may reflect invasion processes. The combined use of the frameworks and multivariate techniques enabled us to aggregate species into categories appropriate for management.


id: cord-010149-zupx8qn1
author: Ni, Yijun
date: 2020-04-21
txt: ./txt/cord-010149-zupx8qn1.txt
cache: ./cache/cord-010149-zupx8qn1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171763/
doi: 10.1186/s12862-020-01608-5
summary:
  title: Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. By analyzing sequence variation in the COI gene, we aimed to explore the species diversity and distribution of copepods among these populations. Based on the haplotype network, seven out of 12 species detected through analysis of the COI gene occurred at more than one locality in Nigeria (Fig. 1b) . Through analysis of COI sequence variation, we explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems, the first such study for West Africa. Our results suggested a high species diversity of Cyclopidae copepods over a small geographic sampling range.

title:
  Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria

abstract:
  BACKGROUND: Copepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography and genetic diversity of copepods in Nigeria is unexplored. RESULTS: Using a mitochondrial cytochrome c oxidase subunit I marker, we preformed phylogenetic and phylogeographic analyses for Cyclopidae copepods in Southeast Nigeria. A high species diversity of Cyclopidae in Nigeria: 5 species of Tropocyclops, 5 species of Mesocyclops and 2 species of Thermocyclops from Cyclopidae were identified in 15 populations. Moreover, we detected 18 unique haplotypes, which fell into two distinct clades. Pairwise genetic distances (uncorrected p-distances) among the species of Cyclopidae ranged from 0.05 to 0.257. Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. Finally, we found that the population genetic diversity for each species of Cyclopidae was low in Nigeria. CONCLUSIONS: Our findings explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems: a high species diversity of Cyclopidae copepods was detected over a small geographic sampling range. Results from this study contribute to a better understanding of copepod diversity of Nigerian freshwater ecosystems.


id: cord-010305-z5c7zgp7
author: GARDEN, JENNI G.
date: 2007-08-06
txt: ./txt/cord-010305-z5c7zgp7.txt
cache: ./cache/cord-010305-z5c7zgp7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175953/
doi: 10.1111/j.1442-9993.2007.01750.x
summary:
  title: Habitat structure is more important than vegetation composition for local‐level management of native terrestrial reptile and small mammal species living in urban remnants: A case study from Brisbane, Australia Patterns in the occurrence of native terrestrial reptile and small mammal species in 59 sites located in remnant urban habitat fragments of Brisbane City were assessed against local‐level environmental characteristics of each site. Investigations were based in urban habitat fragments located within the Brisbane City Council (BCC) local government area, where local government is responsible for setting within-patch management priorities and actions.We applied cluster analysis, multidimensional scaling and principal axis correlation to identify significant habitat attributes and examine their importance for reptile and small mammal assemblages. Our results initially appear to imply that both vegetation composition (weed cover and grass trees) and habitat structure (termite mounds, wood volume and soil compaction) are important for native reptile and small mammal species.

title:
  Habitat structure is more important than vegetation composition for local‐level management of native terrestrial reptile and small mammal species living in urban remnants: A case study from Brisbane, Australia

abstract:
  Abstract As urban areas continue to expand and replace natural and agricultural landscapes, the ability to manage and conserve native wildlife within urban environments is becoming increasingly important. To do so we first need to understand species' responses to local‐level habitat attributes in order to inform the decision‐making process and on‐ground conservation actions. Patterns in the occurrence of native terrestrial reptile and small mammal species in 59 sites located in remnant urban habitat fragments of Brisbane City were assessed against local‐level environmental characteristics of each site. Cluster analysis, multidimensional scaling ordination, and principal axis correlation were used to investigate relationships between species' occurrences and environmental characteristics. Native reptiles were most strongly associated with the presence of termite mounds, a high amount of fallen woody material, and a moderate amount of weed cover. Native small mammals were most strongly associated with the presence of grass trees (Xanthorrhoea spp.), and both reptiles and small mammals were negatively influenced by increased soil compaction. Significant floristic characteristics were considered to be important as structural, rather than compositional, habitat elements. Therefore, habitat structure, rather than vegetation composition, appears to be most important for determining native, terrestrial reptile and small mammal species assemblages in urban forest fragments. We discuss the management implications in relation to human disturbances and local‐level management of urban remnants.


id: cord-010307-sxh5mq1q
author: MILNE, D. J.
date: 2005-11-23
txt: ./txt/cord-010307-sxh5mq1q.txt
cache: ./cache/cord-010307-sxh5mq1q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175956/
doi: 10.1111/j.1442-9993.2005.01535.x
summary:
  Abstract Patterns in the composition of assemblages of microbat species sampled during the late dry season (the ''build‐up'') in north Australian savannas were assessed against a range of environmental factors as well as four a priori defined habitat types (riparian, escarpments, coastal and woodlands). However, we expect this will have a negligible effect on our results as shot sampling at all other sites, used in conjunction with Anabat detectors, enabled us to collect an extensive reference call library for ''high-flying'' bat species for the entire study area (Milne 2002) . Group 5 also had relatively few sites and low species richness, but was associated with the minima or maxima of several environmental variables including long distances to escarpments, flat terrain at low elevations with no rock, low local roost potential, high annual temperatures and low fire frequency.

title:
  Structure and environmental relationships of insectivorous bat assemblages in tropical Australian savannas

abstract:
  Abstract Patterns in the composition of assemblages of microbat species sampled during the late dry season (the ‘build‐up’) in north Australian savannas were assessed against a range of environmental factors as well as four a priori defined habitat types (riparian, escarpments, coastal and woodlands). Distinct species assemblages were most strongly associated with topographic and climatic variables. There were also limited associations with vegetation structure, fire and local roost potential but no associations with insects or water availability. Total species diversity at sample sites was associated with distance to rivers and rainfall. In general, species assemblages were not clearly defined and the number of significant environmental associations was relatively few. We compare these associations with those reported for bat assemblages elsewhere in Australia.


id: cord-010501-kd95xvsg
author: Zenetos, Argyro
date: 2008-06-28
txt: ./txt/cord-010501-kd95xvsg.txt
cache: ./cache/cord-010501-kd95xvsg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192327/
doi: 10.1111/j.1439-0485.1991.tb00247.x
summary:
  Standard multivariate analysis techniques were applied to both ecological (living benthic fauna) and paleoecological data sets in order to distinguish distribution patterns. The species richness, abundance, and diversity per station is given in Table 2 : the number of species ranged from 21 (station A23) to 100 (station A32), and the number of specimens from 152-m-2 (station A 17) to 432.m-2 (station A26 The dendrograms can be truncated at any level, but the areal presentation derived with MDS based on the total living fauna (Fig. 4 a) indicated that the more justified separation in terms of ecological sense was at the 4 groups level (25% similarity) (two dimensional stress = 0.141). The groups are based on the dendrogram of Fig. 2 Table 5 shows the results of the SPEARMAN rank correlation coefficient between the biotic parameters (number of macrofaunal species, number of specimens, and species diversity) and depth and sediment type.

title:
  Analysis of Benthic Communities in the Cyclades Plateau (Aegean Sea) Using Ecological and Paleoecological Data Sets

abstract:
  Abstract. In the Cyclades plateau (Aegean Sea), a qualitative and quantitative analysis of macro‐benthic fauna was carried out in 1986. Standard multivariate analysis techniques were applied to both ecological (living benthic fauna) and paleoecological data sets in order to distinguish distribution patterns. Results showed that caution must prevail in drawing conclusions from a limited data set. The clearest classification was obtained using total living fauna, while the dead molluscan fauna gave a similar pattern; this indicates similar response to the environmental conditions of the area. In the analysis of the living molluscan fauna, the groups failed to show any clusters, probably as an effect of some impoverished sites. In the two groups delineated, depth seems to be the major factor in the distribution of species. The fact that two distinct data sets (subfossil assemblages and living communities), when treated separately, produce similar grouping indicates that the subfossil assemblages could be reliably used as a first approach for determination of the living communities' distribution patterns.


id: cord-010529-c8saxwfj
author: Guzy, Jacquelyn C.
date: 2012-07-17
txt: ./txt/cord-010529-c8saxwfj.txt
cache: ./cache/cord-010529-c8saxwfj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194282/
doi: 10.1111/j.1365-2664.2012.02172.x
summary:
  Our objectives were to (i) conduct a long-term study of cypress domes in south-west Florida to evaluate the potential utility of anurans in providing a quick and reliable assessment of wetland decline resulting from groundwater withdrawal and (ii) to determine whether urbanization interferes with the ability to use anurans as indicators for excessive groundwater withdrawal. These variables included (1) distance to nearest study wetland (indication of possible spatial dependence), (2) distance to nearest natural wetland, (3-5) per cent forest cover within 500, 1000 and 2000 m, and (6-8) mean proximity index (MPX) of forest cover within 500, 1000 and 2000 m; other measured variables included (9) average hydroperiod and (10) water depth at deepest point and (11-13) time (month, year or month plus year) as calling activity of anurans is strongly seasonal.

title:
  Urbanization interferes with the use of amphibians as indicators of ecological integrity of wetlands

abstract:
  1. Wetlands are ecologically and economically important ecosystems but are threatened globally by many forms of human disturbance. Understanding the responses of wetland species to human disturbance is essential for effective wetland management and conservation. 2. We undertook a study to determine (i) whether anurans can be used effectively to assess the ecological integrity of wetlands affected by groundwater withdrawal and, if so, (ii) what effect increasing urbanization might have on the utility of anurans as wetland indicators. We monitored the intensity of anuran calls at 42 wetlands in south‐western Florida throughout 2001–2002 and 2005–2009. 3. We first validated the use of anurans to assess wetland integrity using a small group of wetlands by comparing anuran calling and subsequent tadpole development with an established index employing vegetation composition and structure. We then verified that the results could be expanded to a variety of sites throughout the region. Finally, we focused on urbanized wetlands to determine whether urbanization could interfere with the use of anurans to assess wetland integrity. 4. We used PRESENCE to estimate occupancy and detection probabilities and to examine the relationship between occupancy and five covariates expected to influence individual species occurrence. We used FRAGSTATS to calculate the mean proximity index for urbanized wetlands, which assesses the size and distribution of land use types within a specified area. 5. Our results showed that the group of species including oak toad Anaxyrus quercicus, southern cricket frog Acris gryllus, pinewoods treefrog Hyla femoralis, barking treefrog Hyla gratiosa, and little grass frog Pseudacris ocularis is a reliable indicator of wetland integrity. However, this same group of species, which is sensitive to wetland health, is selectively excluded from urbanized wetlands. 6. Synthesis and applications. Although anurans are effective indicators of wetland health and complement vegetation surveys, the usefulness of this group for monitoring the ecological integrity of wetlands can be substantially reduced, or eliminated, as a consequence of urbanization. We urge for careful consideration of confounding factors in any studies examining the utility of indicator species.


id: cord-010620-4ghzpqct
title: Nitrate reductase activity in vegetation below an arctic bird cliff, Svalbard, Norway
author: Odasz, Ann Marie
date: 2009-02-24
txt: ./txt/cord-010620-4ghzpqct.txt
cache: ./cache/cord-010620-4ghzpqct.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201890/
doi: 10.2307/3236203
summary:
  The aim of this study was to investigate the relationship between the distribution of plant species in bird cliff vegetation and the amount of soil nitrate available in the region of sea-bird guano deposition. In this study I used the maximally induced nitrate reductase activities of species to establish nitrogen indicator figures for arctic plants, thus extending the system of Ellenberg (1991) for central-European plants for different levels of nitrogen, using a scalar system from 1, environments poor in N, through 9, rich in N. Induced NRA values for the dominant species in each zone decreased significantly downslope: Cochlearia groenlandica: 4.35; Oxyria digyna: 6.06; Cerastium arcticum: 4.26; Saxifraga hieracifolia: 1.36; Saxifraga cespitosa: 1.23; and Dryas octopetala representative of the tundra sites: 1.10 (Table 2) .

abstract:
  Abstract. Vegetated sites below bird‐nesting cliffs are uniquely nutrient‐rich habitats in the otherwise nutrient‐poor arctic environment. Plants from six distinct vegetation zones below such a cliff at 79° N, Svalbard, Norway, were collected for analysis under greenhouse conditions. Leaf nitrate reductase activity (NRA) was analysed in 42 species representing 25 % of the Svalbard vascular flora. The species mean NRA values ranged from 0.37 to 8.34 μmols of nitrite ions formed per gram of plant fresh weight per hour. Species in the vegetated zone growing closest to recent guano deposits had the highest NRA values, (mean = 4.47) whereas plants growing farther below the cliff had significantly lower values (mean = 0.55). A similar pattern was detected in a duplicate set of plants induced with 15 mM KNO(3); vegetation zone means for NRA ranged from 5.08 to 0.98 μmols of nitrite ions formed per gram of plant fresh weight per hour. Maximally induced species NRA values were highest in the first zones below the cliff and decreased downslope. This gradient paralleled the steep soil nitrate gradient, which decreased from 13.84 mg/l at the cliffbase to 1.03 mg/l downslope. Correspondingly, soil ammonium ions in the vegetation zones ranged between 1.96 mg/l at the cliff‐base to 0.03 mg/l downslope. Correlations between NRA and soil nitrate provide a systematic basis for assigning scalar ‘nitrogen figures’ as indicators of habitat preference, here for the first time applied to arctic species.


id: cord-016379-lcog1654
title: Plant,Animal, and Microbe Invasive Species in the United States and World
author: Pimentel, David
date: 2007
txt: ./txt/cord-016379-lcog1654.txt
cache: ./cache/cord-016379-lcog1654.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120639/
doi: 10.1007/978-3-540-36920-2_18
summary:
  Calculating the negative economic impacts associated with the invasion of exotic species is difficult.For a few species, there are sufficient data to estimate some impacts on agriculture, forestry, fisheries, public health, and the natural ecosystem in the US and worldwide. Worldwide, an estimated 30,000 species of exotic plants have been intentionally introduced as crops, and have escaped to become established in various natural ecosystems. In the United States, introduced plant species are spreading and invading approximately 700,000 ha of US natural ecosystems per year (Babbitt 1998) . In the Great Lakes, for instance, nearly 50 invasive species are found, and these invaders are causing an estimated $ 5 billion in damages to the fisheries per year (Pimentel 2005) . This investigation reports on various economic damages associated with invasive species in various nations of the world that total more than $ 1.4 trillion per year (Pimentel 2002) .

abstract:
  Approximately 50,000 plant, animal, and microbe invasive species are present in the United States, and an estimated 500,000 plant, animal, and microbe invasive species have invaded other nations of the world. Immediately, it should be pointed out that the US and world agriculture depend on introduced food crops and livestock.Approximately 99 % of all crops and livestock in all nations are intentionally introduced plants, animals, and microbes (Pimentel 2002). Worldwide, the value of agriculture (including beneficial non-indigenous species) is estimated to total $ 30 trillion per year. Other exotic species have been introduced for landscape restoration, biological pest control, sport, and food processing, also contributing significant benefits. Calculating the negative economic impacts associated with the invasion of exotic species is difficult.For a few species, there are sufficient data to estimate some impacts on agriculture, forestry, fisheries, public health, and the natural ecosystem in the US and worldwide. In this article, we estimate the magnitude of the economic benefits, and environmental and economic costs associated with a variety of invasive species that exist in the United States and elsewhere in the world.


id: cord-016717-2twm4hmc
title: How Does Biodiversity Influence the Ecology of Infectious Disease?
author: Vourc’h, Gwenaël
date: 2011-06-28
txt: ./txt/cord-016717-2twm4hmc.txt
cache: ./cache/cord-016717-2twm4hmc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121084/
doi: 10.1007/978-94-007-2114-2_13
summary:
  To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. In this chapter, we investigate how biodiversity influences the ecology of infectious diseases at the intraspecific level (genetic variability of pathogens and hosts) and at the level of communities (species composition). The hypothesis underlying the amplification and dilution effect is that for many diseases, the competence of reservoirs, i.e. the ability to become infected and retransmit the pathogen, varies according to the host species (Haydon et al.

abstract:
  Over the past years, biodiversity has been reduced on an unprecedented scale, while new infectious diseases are emerging at an increasing rate. Greater overall biodiversity could lead to a greater diversity of hosts and thus of pathogens. Yet disease regulation – due to the buffering role of host diversity – is considered to be one of the services provided by biodiversity. In this chapter, we ask how biodiversity is linked to infectious disease. First, we investigate the influence of the biodiversity of pathogens. We highlight that the number of pathogen species is not well known but that new findings are facilitated by the rapid expansion of molecular techniques. We show that, although there is a trend to find higher pathogen richness toward the equator, identifying a global pattern between the richness of all pathogen species and their latitudinal distribution is challenging. We emphasize that pathogen intraspecific diversity is a crucial factor in disease emergence and allows pathogens to adapt to the selective pressures they face. In addition, the selective pressure acting on hosts due to parasite, and reinforced by parasite diversity within hosts seems to be a major evolutionary and ecological force shaping hosts biodiversity. Second, we investigate how the diversity of hosts influences infectious disease ecology. For multi-host diseases, a change in host species richness or abundance can modify the dynamics of local infectious diseases by either reducing (“dilution effect”) or increasing (“amplification effect”) the risk of transmission to the targeted host species. The underlying hypothesis is that, the competence of reservoirs varies according to the host species. The dilution effect has been demonstrated mainly through theoretical work and there have been only few case studies. Regarding the genetic diversity of host, an important issue is: to what extent does a reduction of this diversity impact the ability of the host population to response to infectious diseases? Third, we rapidly examine the role of biodiversity in the treatment of infectious diseases. To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. We highlight that work on multi-host/ ulti-pathogen systems should be fostered and that new approaches, such as metagenomic investigations that does not require a priori assumptions, are promising to describe a community of pathogens and their interactions.


id: cord-017156-ximzvqbm
title: Chargaff’s GC rule
author: Forsdyke, Donald R.
date: 2010-05-18
txt: ./txt/cord-017156-ximzvqbm.txt
cache: ./cache/cord-017156-ximzvqbm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121649/
doi: 10.1007/978-0-387-33419-6_8
summary:
  The model predicts that, for preventing recombination (i.e. creating reproductive isolation), a non-complementarity between the sequences of potentially pairing strands, in itself, might be less important than a noncomplementarity associated with sequence differences that change the pattern of stem-loops. By continuous backcrossing to sylvestris the chromosomes deriv ed from sylvestris can be tested because they form tetrads with the sylvestrisThe surv ival of a duplicate copy of a gene depends on a var iety of factors , including (i) natural selection favouring organisms where a function encoded by the gene is either increased or changed (i.e . Each isochore would have arisen as a random fluctuation in the base composition of a genomic region such that a copy of a duplicated gene that had transposed to that region was able to survive without recombination with the original gene for a sufficient number of generations to allow differentiation between the copy and its original to occur.

abstract:
  Evolutionary selective pressures sometimes act to preserve nucleic acid features at the expense of encoded proteins. That this might occur in the case of nucleic acid secondary structure was noted in Chapter 5. That this might also apply to the species-dependent component of the base composition, (G+C)%, was shown by Sueoka in 1961 [2]. The amino acid composition of the proteins of bacteria is influenced, not only by the demands of the environment on the proteins, but also by the (G+C)% of the genome encoding those proteins.


id: cord-017537-ztdz4a2s
title: Biological Agents and Bioterrorism
author: Bologna, Mauro
date: 2014-09-18
txt: ./txt/cord-017537-ztdz4a2s.txt
cache: ./cache/cord-017537-ztdz4a2s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122122/
doi: 10.1007/978-94-017-9238-7_1
summary:
  For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. In the light of recent concern and interest about the potential for biological terrorism (biofarware) there are several diseases and bacterial toxins that must be considered in particular, like anthrax [ 1 , 2 ] , smallpox [ 3 , 4 ] , plague [ 5 ] , botulinum toxin [ 6 ] , and tularemia [ 7 ] .

abstract:
  For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space.


id: cord-019068-6j42euvc
title: Life Cycle and Life History Strategies of Parasitic Crustacea
author: Williams, Ernest H.
date: 2019-07-05
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124122/
doi: 10.1007/978-3-030-17385-2_5
abstract:
  Different parasitic life strategies are described including four new life cycles: complex rebrooding, micro-male, mesoparasite and prey-predator transfer. Four new life cycle behaviours are named: nursery hiding, mid-moult stage, positive precursor (intraspecific antagonism) and negative precursor (ambush strategy). Further strategies discussed are opossum attack, double parasitism (doubling of the normal reproductive set), duplex arrangement (separated male-female pairs), simple rebrooding, and describing how displaced parasites and superinfections may partly elucidate life cycles. Proportional stunting masks life history effects of parasitism; cuckoo copepods are true parasites and not just associates; burrowing barnacles (acrothoracicans) are not parasites. Further findings based on life cycle information: branchiurans and pentastomes are possibly not related; firefly seed shrimp are not parasites; copepod pre-adult life cycle stages are common in the western pacific but rare in Caribbean; harpacticoids on vertebrates are not parasites; cuckoo copepods are true parasites; explained the importance of pennellid intermediate hosts. Crustacean parasite life cycles are largely unknown (1% of species). Most crustacean life cycles represent minor modifications from the ancestral free-living mode. Crustacean parasites have less complex and less modified life cycles than other major parasite groups. This limits their exploitation of, and effectiveness, in parasitism. However, these life cycles will be an advantage in Global Change. Most metazoan parasites will be eliminated while crustaceans (and nematodes) will inherit the new world of parasites.


id: cord-021013-xvc791wx
title: Chapter 1 Allelochemical Properties or the Raison D'être of Alkaloids
author: Wink, Michael
date: 2008-05-30
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148816/
doi: 10.1016/s0099-9598(08)60134-0
abstract:
  This chapter provides evidence that alkaloids are not waste products or functionless molecules as formerly assumed, but rather defense compounds employed by plants for survival against herbivores and against microorganisms and competing plants. These molecules were developed during evolution through natural selection in that they fit many important molecular targets, often receptors, of cells, which are seen in molecules that mimic endogenous neurotransmitters. The chapter discusses that microorganisms and herbivores rely on plants as a food source. Since both have survived, there must be mechanisms of adaptations toward the defensive chemistry of plants. Many herbivores have evolved strategies to avoid the extremely toxic plants and prefer the less toxic ones. Many herbivores have potent mechanisms to detoxify xenobiotics, which allow the exploitation of at least the less toxic plants. In insects, many specialists evolved that are adapted to the defense chemicals of their host plant, in that they accumulate these compounds and exploit them for their own defense. Alkaloids function as defense molecules against insect predators in the examples studied, and this is further support for the hypothesis that the same compound also serves for chemical defense in the host plant. It needs more experimental data to understand fully the intricate interconnections between plants, their alkaloids, and herbivores, microorganisms, and other plants.


id: cord-021152-6znmkvy9
title: Reproduction of East-African bats may guide risk mitigation for coronavirus spillover
author: Montecino-Latorre, Diego
date: 2020-02-07
txt: ./txt/cord-021152-6znmkvy9.txt
cache: ./cache/cord-021152-6znmkvy9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149079/
doi: 10.1186/s42522-019-0008-8
summary:
  METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. Assuming that higher spillover risk is a function of higher viral shedding [67] and that all coronaviruses with zoonotic potential behave ecologically similarly to coronaviruses detected in this study, managers could target the prevention of human-bat direct (consumption) or indirect (bat droppings) contact specifically during the high-risk season: around and just after weaning, the timing of observable juveniles or individuals smaller than adults. Our proposed risk-driven strategy i) is evidence-based, as it builds upon coronavirus shedding patterns observed across several chiropteran species present around the world; ii) does not require the advanced laboratory capacity often lacking in resource-restricted settings where intense bat-human interfaces usually occur; iii) is a good alternative to the ideal but expensive and resourceintensive longitudinal surveys; and iv) it may prevent the exposure to viruses belonging to other taxa whose observed bat shedding dynamics resemble our findings for coronaviruses (e.g. paramyxoviruses [97] ),

abstract:
  BACKGROUND: Bats provide important ecosystem services; however, current evidence supports that they host several zoonotic viruses, including species of the Coronaviridae family. If bats in close interaction with humans host and shed coronaviruses with zoonotic potential, such as the Severe Acute Respiratory Syndrome virus, spillover may occur. Therefore, strategies aiming to mitigate potential spillover and disease emergence, while supporting the conservation of bats and their important ecological roles are needed. Past research suggests that coronavirus shedding in bats varies seasonally following their reproductive cycle; however, shedding dynamics have been assessed in only a few species, which does not allow for generalization of findings across bat taxa and geographic regions. METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. We assessed, via Bayesian modeling, the hypothesis that chiropterans, across species and spatial domains, experience seasonal trends in coronavirus shedding as a function of the reproductive cycle. RESULTS: We found that, beyond spatial, taxonomic, and life history differences, coronavirus shedding is more expected when pups are becoming independent from the dam and that juvenile bats are prone to shed these viruses. CONCLUSIONS: These findings could guide policy aimed at the prevention of spillover in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding. In these periods, contact with bats should be avoided (for example, by impeding or forbidding people access to caves). Our proposed strategy provides an alternative to culling – an ethically questionable practice that may result in higher pathogen levels – and supports the conservation of bats and the delivery of their key ecosystem services.


id: cord-022505-17khcmta
title: Rodentia
author: Delaney, Martha A.
date: 2018-10-26
txt: ./txt/cord-022505-17khcmta.txt
cache: ./cache/cord-022505-17khcmta.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158172/
doi: 10.1016/b978-0-12-805306-5.00020-1
summary:
  Common microscopic findings in rodents that may be misinterpreted as lesions include: multinucleated, karyomegalic, and cytomegalic hepatocytes are common in several rodent species and can increase with age ( Fig. 20 .1); hepatocellular intranuclear cytoplasmic invaginations (pseudoinclusions) (Fig. 20 .1); eosinophilic cytoplasmic spherical inclusions in renal tubular epithelial cells and hepatocytes seen predominantly male mice, rats, and hamsters; splenic extramedullary hematopoiesis, which is very common in healthy rodents of all ages (Fig. 20 .2); hemosiderin, lipofuscin, ceroid, and melanin (in dark or black coated animals) are commonly detected in various tissues, such as spleen, liver, kidney, and adrenal glands; cardiac muscle in the tunica of pulmonary veins in the lung is a normal finding in mice; male rodents may have refluxed seminal coagula in the urinary bladder and urethra that is thought to occur peri mortem; and adrenal X-zone vacuolation in female mice.

abstract:
  This chapter includes diseases of animals in the order Rodentia, in which there are over 2000 species representing 40% of all mammals. This incredibly diverse order includes members inhabiting every continent, either naturally or in human-made environments. While rodents have been the cause or implicated in disease transmission that has lead to human pandemics, such as the Black Death, and the decimation of certain animal species, like island-dwelling birds; genetically modified rodents have contributed significantly to the advancement of biomedical research and human health. There are more than 50 species of endangered rats, mice, voles, squirrels, and marmots. The recent extinction of the Bramble Cay melomys represents the first human-induced rodent extinction linked to climate change. Rodents are the reservoir host of several human and domestic pathogens of concern listed by OIE. Herein, we highlight those diseases of rodents that lead to clinically important gross and microscopic lesions.


id: cord-022879-j6cecioe
title: Determination and Analysis of Recurrent Groups
author: Fager, Edward W.
date: 1957-10-01
txt: ./txt/cord-022879-j6cecioe.txt
cache: ./cache/cord-022879-j6cecioe.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163427/
doi: 10.2307/1943124
abstract: nan
summary:
  Transformation of the data or the use of rank correlation could overcome this difficulty, but any method which involves a measure of abundance may, in certain cases, not lead to the desired results : two species may always occur together and never separately and yet, unless there is a nearly constant relation between the relative numbers of individuals of the two species, a correlation coefficient will indicate no relationship even though they are a constant part of each other''s biological environment. The following example shows that it is not a satisfactory criterion for grouping if the groups are to be composed of species which form a nearly constant part of each other''s biological environment: Species 1 and 2 show no evidence of association when examined by Cole''s method and yet they nearly always occur together-over 80% of the occurrences of each are in company with the other -and should be considered together in any grouping based on this set of samples.


id: cord-022883-chrxyrls
title: Trophic variety and abundance of hoverflies (Diptera, Syrphidae) in an English suburban garden
author: Owen, Jennifer
date: 2006-06-30
txt: ./txt/cord-022883-chrxyrls.txt
cache: ./cache/cord-022883-chrxyrls.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163471/
doi: 10.1111/j.1600-0587.1981.tb01001.x
summary:
  The trophic composition of the Malaise trap catch varied to some extent from year to year, as shown in Tab, 3, Although hoverflies with aphid-feeding larvae (group 2) constituted the majority of the sample in every year, their relative frequency was considerably lower in 1973 , 1976 . This is not reflected in the relative frequency of group 2 hovertlics in these years (see Tab. 3), largely because the numbers of resident species of Melanostoma and Platycheirus in the catch were far lower than usual; Melanostoma mellinum, for instance, whieh breeds in the garden and is usually common, was represented by only two individuals in 1977, and M. when Eristalis arbustorum and other species with larvae that feed on decaying organic material became particularly abundant in August such that, by September, the relative frequency of aphid-feeders had fallen io38.87o.

abstract:
  28924 hoverflies of 85 species were caught in a Malaise trap in an English suburban garden during the eight‐year period 1972–79, and three additional species were hand‐netted. Hoverfly larvae fall into five trophic categories all of which were represented by adults in the trap sample. 82.71% of the hoverflies trapped have larvae that feed on aphids, 12.04% feed on decaying organic material, 5.14% eat living plants, 0.09% scavenge in Hymcnoptera nests, and 0.02% are associated with tree sap or rotting wood. The relative frequency of the different trophic groups varied annually and seasonally although the aphid‐feeders were nearly always the most abundant. 22 species are believed to breed in the garden, and a further 29 in the surrounding area; 15 species are regarded as casual and 22 as chance visitors. It is suggested that the high plant diversity and spatial heterogeneity of gardens result in them supporting more species than would be found in a natural area.


id: cord-022973-soaz8b74
title: Nestedness of habitat specialists within habitat generalists in a butterfly assemblage
author: Trivellini, Guido
date: 2016-09-25
txt: ./txt/cord-022973-soaz8b74.txt
cache: ./cache/cord-022973-soaz8b74.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165506/
doi: 10.1111/icad.12193
summary:
  Butterflies (Lepidoptera) are a well-studied insect group both taxonomically and ecologically (e.g. Gilbert, 1984; Kocher & Williams, 2000; Ghazoul, 2002; Stefanescu et al., 2004 Stefanescu et al., , 2011 , particularly because they interact with plants both as larval herbivores and adult pollinators (Borges et al., 2003; Hardy et al., 2007) and have different habitat requirements even at each life stage (New et al., 1995; Samways & Lu, 2007; Dennis, 2010) . E-mail: giuseppe.bogliani@unipv.it These largely specialised butterfly-habitat associations are influenced by many physical and biological factors (Leps & Spitzer, 1990; Spitzer et al., 1993) , including temperature, humidity, light levels, rainfall patterns, local microclimate conditions, grassland type and host-plant species richness and distribution (Hill et al., 2001; Meyer & Sisk, 2001; Collinge et al., 2003; Men endez et al., 2007) . To do this, we first defined the requirements, i.e., which habitat types positively or negatively correlate with species abundances, and then used a network-based approach (Bl€ uthgen et al., 2006) to analyse the degree of habitat use overlap within groups of species with similar habitat requirements.

abstract:
  1. The habitat requirements of a species are the resources, conditions and space required for survival and reproduction. The habitat requirements of butterflies have been well studied, but the extent to which individuals within a species and between species utilise and share the habitat is poorly known. 2. In a butterfly assemblage in northern Italy, we found that adults from 30 species avoid deciduous high‐density forests and their ecotones, and they were positively related to open areas and their ecotones. Besides these common features, five groups of species can be discriminated in relation to a gradient from open area to forest, and species within groups were not equally specialised, as observed from a bipartite network analysis. In particular, some species appeared to be specialised and others appeared to be generalist, suggesting a nested pattern of resource use, rather than a clustered pattern in which each species uses a different subset of habitat types. 3. The degree of variation in specialisation among species varied with the number of species falling in each group. Thus, an increased number of species, and thus possibly competition, is more likely to promote the co‐occurrence of generalist and specialised species (nested patterns) rather than an increased niche segregation among species. 4. Ascertaining how species overlap their habitat use at a local scale can be relevant for conservation purposes, because specialised populations are potentially more susceptible to network distortions.


id: cord-023036-rnt6ivcy
title: THE BIRD SUCCESSION IN THE CONIFER PLANTATIONS ON MAT‐GRASS LAND IN SLOVAKIA (CSR).
author: Turc̄ek, F. J.
date: 2008-04-03
txt: ./txt/cord-023036-rnt6ivcy.txt
cache: ./cache/cord-023036-rnt6ivcy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165984/
doi: 10.1111/j.1474-919x.1957.tb03050.x
summary:
  The three groups of areas studied were: (1) bare pastures, with an intermediate number of bird species, few individuals and high biomass of mainly carnivorous and insectivorous birds; (2) conifer plantations 1 to 5 years old, with the smallest number of bird species and the smallest biomass, but an intermediate number of individuals; (3) plantations six to twenty years old, with the highest number of both species and individuals of birds, but only intermediate biomass. The bird species found, their density and biomass per hectare in each group of areas are given in Table 1 . In the plantations studied, mainly of Norway spruce and Scots pine mixed with some European larch and a few deciduous trees, we were able to study the development of the bird community from bare pasture up to a forest of about 20 years of age.

abstract:
  1. The species‐composition, number of individuals and biomass per one‐hectare are given. The three groups of areas studied were: (1) bare pastures, with an intermediate number of bird species, few individuals and high biomass of mainly carnivorous and insectivorous birds; (2) conifer plantations 1 to 5 years old, with the smallest number of bird species and the smallest biomass, but an intermediate number of individuals; (3) plantations six to twenty years old, with the highest number of both species and individuals of birds, but only intermediate biomass. 2. The change from pasture to forest occurs about six to ten years after planting. The last forest birds come in about 20 years after planting. 3. Birds have an important role in establishing the shrub layer and mixing some tree‐species into the plantation, by dissemination. 4. Throughout the entire successional series the bird population seems to have a kernel of species, while other species come or go and/or change in density with the stages.


id: cord-023706-gs3oo3no
title: Veterinary Challenges of Mixed Species Exhibits
author: Kaandorp, Jacques
date: 2011-06-22
txt: ./txt/cord-023706-gs3oo3no.txt
cache: ./cache/cord-023706-gs3oo3no.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173496/
doi: 10.1016/b978-1-4377-1986-4.00004-4
abstract: nan
summary:
  Most often, zoos still show single species exhibits because of lack of space or simply to prevent problems associated with mixing different species. In this chapter, an incomplete listing of diseases and problems is presented to make the reader aware of the broad variety of veterinary challenges of mixed species exhibits. In mixed species exhibits, trauma is the most frequent and serious cause of health problems ( Fig. 4-4) . 6 To prevent trauma, next to appropriate size of the exhibit, pole gates (creeps), where small animals can flee from larger animals, creation of large obstacles in phillipsi) and sable antelope (Hypotrachus niger), or toxicities such as vitamin E toxicity in pelicans or iron storage disease in birds and some primate species, should be avoided when developing feeding protocols for mixed species exhibits. They are responsible for an enormous variety of disease problems, especially in mixed species exhibits.


id: cord-024166-t3qxscbp
author: Losvik, Mary H.
date: 2008-06-28
txt: ./txt/cord-024166-t3qxscbp.txt
cache: ./cache/cord-024166-t3qxscbp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192332/
doi: 10.1111/j.1756-1051.1999.tb01231.x
summary:
  The species group indicators of traditional management was preliminary defined in Losvik (1993b) , and later (Losvik 1996b ) was shown to comprise species occurring in less than 60 YO of 548 plots (1-16 m2) of hay meadow vegetation analysed in western Norway by 6 different authors 1972-1991. The aim of the study was to compare the vegetation and ecology of 4 sites which formed a chronosequence, representing a successional series from a species-rich, old, traditionally managed hay-meadow to sites which had been abandoned for about 10, 20 and 30 years, respectively. Themes of special interest were: how important are the ecological factors years since abandonment and cover of tree canopy in deciding the composition of the vegetation, what differences in species diversity, as measured by species-area curves, are there between the sites, for how long are species which are characteristic for the agricultural landscape able to persist during overgrowing in such sites, and finally, what forest species and additional species are most important in the sites of this series of abandoned haymeadows.

title:
  Plant species diversity in an old, traditionally managed hay meadow compared to abandoned hay meadows in southwest Norway

abstract:
  A chronosequence, representing a successional series, was used for the comparison of a hay meadow site managed in an old traditional way for at least a hundred years, and hay meadow sites abandoned for about 10, 20 and 30 years, respectively. Old traditional management included grazing early and late in the growing season, mowing in August and light or no fertilizing. The tree cover was the most important factor deciding the composition of vegetation. Time since abandonment was not completely correlated to tree cover, as some plots had a dense canopy and others were situated in the open. The total species number decreased with number of years since abandonment in plots > 0.001 m(2)and <100 m(2). The highest species number in 1 m(2) plots was recorded in the managed site, with 38 species of phanerogams. Fourtyeight % of the indicators of traditional management present in the managed site was recorded in the site which had been abandoned for 30 years. Frequency — log area curves made it possible to group species according to persistence in the sward. As a result, a group of functional indicators of rare hay meadows in the region was distinguished.


id: cord-032623-32m3qko4
title: When mycologists describe new species, not all relevant information is provided (clearly enough)
author: Durkin, Louisa
date: 2020-09-10
txt: ./txt/cord-032623-32m3qko4.txt
cache: ./cache/cord-032623-32m3qko4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498475/
doi: 10.3897/mycokeys.72.56691
summary:
  To assess whether fungal species descriptions are attuned to both the wants and needs of a target audience beyond taxonomists and the sign of the times, we explored 10 years'' worth of fungal species descriptions of extant mycological taxa in five major mycological journals (plus one botany journal for reference) for a range of factors pertaining to inter-and intra-scientific terms and concepts, science-demographical aspects, and illustrations and visualisations (Tables 1, 2; Suppl. Dark green -proportion of studies mentioning the word "ecology" or its variations; brown -proportion of studies giving a complete account of the taxonomic affiliation of the new species (family, order, and phylum); purple -proportion of studies with a macroscopic colour photo/illustration of the new species; pink -proportion of studies with macroscopic photos, that also indicate the size of the depicted object through a scale bar or a fiducial marker; light green -proportion of studies with an identification key; yellow -proportion of openly available papers for each year as assessed in 2020 B demographical and publication trends showing the average number of coauthors (dark green), departments (brown), countries (purple), continents (pink), and number of data visualizations (light green) over time.

abstract:
  Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years’ worth (2009–2018) of species descriptions of extant fungal taxa – 1,097 studies describing at most ten new species – in five major mycological journals plus one plant journal. We estimated the frequency at which a range of key words, illustrations, and concepts related to ecology, geography, taxonomy, molecular data, and data availability were provided with the descriptions. We also considered a range of science-demographical aspects such as gender bias and the rejuvenation of taxonomy and taxonomists as well as public availability of the results. Our results show that the target audience of fungal species descriptions appears to be other fungal taxonomists, because many aspects of the new species were presented only implicitly, if at all. Although many of the parameters we estimated show a gradual, and in some cases marked, change for the better over time, they still paint a somewhat bleak picture of mycological taxonomy as a male-dominated field where the wants and needs of an extended target audience are often not understood or even considered. This study hopes to leave a mark on the way fungal species are described by putting the focus on ways in which fungal taxonomy can better anticipate the end users of species descriptions – be they mycologists, other researchers, the public at large, or even algorithms. In the end, fungal taxonomy, too, is likely to benefit from such measures.


id: cord-254713-ghcwfcx2
title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar
author: Razanajatovo, Norosoa H
date: 2015-03-12
txt: ./txt/cord-254713-ghcwfcx2.txt
cache: ./cache/cord-254713-ghcwfcx2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12985-015-0271-y
doi: 10.1186/s12985-015-0271-y
summary:
  RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species.

abstract:
  BACKGROUND: Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island’s chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats. METHODS: Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens. RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages. CONCLUSIONS: Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.


id: cord-255018-dhkz23co
author: Chamorro, Melina Fernanda
date: 2020-05-24
txt: ./txt/cord-255018-dhkz23co.txt
cache: ./cache/cord-255018-dhkz23co.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32448223/
doi: 10.1186/s12906-020-02952-1
summary:
  In this study we focus on native and exotic plants with edible fleshy fruits (PEFF) that grow in Patagonia; that is, species that may be wild, cultivated or in an intermediate state of domestication, which bear fruit that is distinguished by its flavor, preferably sweet, and its use principally as a food resource. In this study we propose a cross-sectional approach which enables exotic and native species richness, local foods, medicines and their use patterns to be evaluated, and which will also help us understand in greater depth, from an ethnobotanical perspective, that diet and health are linked concepts. The principal functional species according to the CIF values were the native Aristotelia chilensis, Ribes magellanicum, Ephedra ochreata, Berberis microphylla, Fragaria chiloensis, Luma apiculata and Amomyrtus luma, and the exotic Sambucus nigra, Rosa rubiginosa and Prunus cerasus ( Table 2) .

title:
  Native and exotic plants with edible fleshy fruits utilized in Patagonia and their role as sources of local functional foods

abstract:
  BACKGROUND: Traditionally part of the human diet, plants with edible fleshy fruits (PEFF) contain bioactive components that may exert physiological effects beyond nutrition, promoting human health and well-being. Focusing on their food-medicine functionality, different ways of using PEFF were studied in a cross-sectional way using two approaches: a bibliographical survey and an ethnobotanical case study in a rural community of Patagonia, Argentina. METHODS: A total of 42 studies were selected for the bibliographical review. The case study was carried out with 80% of the families inhabiting the rural community of Cuyín Manzano, using free listing, interviews, and participant observation. In both cases we analyzed species richness and use patterns through the edible consensus and functional consensus indices. Local foods, ailments, medicines and drug plants were also registered. RESULTS: The review identified 73 PEFF, the majority of which (78%) were native species, some with the highest use consensus. PEFF were used in 162 different local foods, but mainly as fresh fruit. Of the total, 42% were used in a functional way, in 54 different medicines. The principal functional native species identified in the review were Aristotelia chilensis and Berberis microphylla. In the case study 20 PEFF were in current use (50% were native), and consensus values were similar for native and exotic species. These were used in 44 different local foods, mainly as fresh fruit. Only 30% were recognized for their functional value by inhabitants (mainly as gastrointestinal and respiratory treatments). The species with the highest functional consensus were the exotic Sambucus nigra and Rosa rubiginosa, followed by the native A. chilensis, Ribes magellanicum and B. microphylla. Infusions also constituted important local functional foods. CONCLUSIONS: This survey highlights the importance of studying the different local functional foods to depict the biocultural diversity of a human society. The preparation of different beverages and herbal medicines was relevant, and would be a promising subject to investigate in the future. The living heritage of PEFF appears to have undergone hybridization processes, such that exotic species play an increasingly significant role.


id: cord-261466-b9r4cyp7
title: What is the importance of zoonotic trichomonads for human health?
author: Maritz, Julia M.
date: 2014-06-18
txt: ./txt/cord-261466-b9r4cyp7.txt
cache: ./cache/cord-261466-b9r4cyp7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1471492214000919
doi: 10.1016/j.pt.2014.05.005
summary:
  Four species of trichomonad are considered human parasites: Trichomonas vaginalis (found in the urogenital tract) [6] , Trichomonas tenax (localized to the oral cavity) [7] , and Pentatrichomonas hominis and Dientamoeba fragilis (located in the digestive tract) [8, 9] . In addition, several trichomonad species are of veterinary importance, such as the avian pathogens Trichomonas gallinae, Tetratrichomonas gallinarum, and Histomonas meleagridis [16] [17] [18] [19] , and Tritrichomonas foetus, the causative agent of a venereal disease in cattle [20] . Thus, the presence of an increasing number of distinct trichomonads in a broader range of clinical samples from patients with diverse diseases, such as AIDS, rheumatoid arthritis, prostate cancer, pulmonary infections (empyema and pneumonia in addition to PcP and ARDS), and digestive conditions such as diarrhea and IBS [33] [34] [35] , is becoming increasingly apparent.

abstract:
  Trichomonads are common parasites of many vertebrate and invertebrate species, with four species classically recognized as human parasites: Dientamoeba fragilis, Pentatrichomonas hominis, Trichomonas vaginalis, and Trichomonas tenax. The latter two species are considered human-specific; by contrast, D. fragilis and P. hominis have been isolated from domestic and farm mammals, demonstrating a wide host range and potential zoonotic origin. Several new studies have highlighted the zoonotic dimension of trichomonads. First, species typically known to infect birds and domestic mammals have been identified in human clinical samples. Second, several phylogenetic analyses have identified animal-derived trichomonads as close sister taxa of the two human-specific species. It is our opinion, therefore, that these observations prompt further investigation into the importance of zoonotic trichomonads for human health.


id: cord-263282-a7emso89
author: Coghlan, Megan L.
date: 2011-07-07
txt: ./txt/cord-263282-a7emso89.txt
cache: ./cache/cord-263282-a7emso89.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1872497311001323
doi: 10.1016/j.fsigen.2011.06.006
summary:
  Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. In wildlife forensics, DNA species identification is commonly carried out by amplifying and sequencing fragments of the mitochondrial DNA (mtDNA) genes cytochrome oxidase I (COI), cytochrome b (Cytb), or 12S ribosomal RNA (12S) [15, 17, 20, 21] .

title:
  Egg forensics: An appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs

abstract:
  Psittaciformes (parrots and cockatoos) are charismatic birds, their plumage and capacity for learning make them highly sought after pets. The illegal trade in parrots and cockatoos poses a serious threat to the viability of native populations; in addition, species transported to non-endemic areas may potentially vector disease and genetically ‘pollute’ local native avifauna. To reduce the logistical difficulties associated with trafficking live birds, smugglers often transport eggs. This creates a problem for authorities in elucidating accurate species identification without the laborious task of incubation and hand rearing until a morphological identification can be made. Here, we use 99 avian eggs seized from carriers coming into and within Australia, as a result of suspected illegal trade. We investigate and evaluate the use of mitochondrial DNA (mtDNA) to accurately identify eggs to family, genus or species level. However, Identification of a species based on percentage mtDNA similarities is difficult without good representations of the inter- and intra-levels of species variation. Based on the available reference database, we were able to identify 52% of the eggs to species level. Of those, 10 species from eight genera were detected, all of which belong to the parrot (Psittacidae) and cockatoo (Cacatuidae) families. Of the remaining 48%, a further 36% of eggs were identified to genus level, and 12% identified to family level using our assignment criteria. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny.


id: cord-269505-7g8lio9l
title: Impacts of biodiversity on the emergence and transmission of infectious diseases
author: Keesing, Felicia
date: 2010-12-01
txt: ./txt/cord-269505-7g8lio9l.txt
cache: ./cache/cord-269505-7g8lio9l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21124449/
doi: 10.1038/nature09575
summary:
  For hantavirus pulmonary syndrome, a directly transmitted zoonotic disease, correlational and experimental studies have shown that a lower diversity of small mammals increases the prevalence of hantaviruses in their hosts, thereby increasing risk to humans (Box 2). Diversity has a similar effect for plant diseases, with species losses increasing the transmission of two fungal rust pathogens that infect perennial rye grass and other plant species 10 . This is because field studies like those on West Nile virus, hantaviruses and rye grass have typically not controlled for changes in host density that can result from changes in ''species richness'' (the number of species present in a community, which is a measure of taxonomic diversity). In sum, reducing biodiversity can increase disease transmission when the lost species are either not hosts for the pathogen or are suboptimal ones. In several case studies, the species most likely to be lost from ecological communities as diversity declines are those most likely to reduce pathogen transmission.

abstract:
  Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services. Here we evaluate evidence that reduced biodiversity affects the transmission of infectious diseases of humans, other animals and plants. In principle, loss of biodiversity could either increase or decrease disease transmission. However, mounting evidence indicates that biodiversity loss frequently increases disease transmission. In contrast, areas of naturally high biodiversity may serve as a source pool for new pathogens. Overall, despite many remaining questions, current evidence indicates that preserving intact ecosystems and their endemic biodiversity should generally reduce the prevalence of infectious diseases. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature09575) contains supplementary material, which is available to authorized users.


id: cord-271076-436nxsua
title: Emerging diseases, zoonoses and vaccines to control them
author: Paul-Pierre, Pastoret
date: 2009-10-30
txt: ./txt/cord-271076-436nxsua.txt
cache: ./cache/cord-271076-436nxsua.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0264410X0900872X
doi: 10.1016/j.vaccine.2009.06.021
summary:
  In Northern America, the spectacular spread of West Nile virus infection, another vector transmitted disease, in humans and horses, was rapidly followed by the development of several vaccines, including a DNA-based vaccine for horses. To prevent Nipah virus (Henipavirus) infection in pigs a vaccine has recently been developed but, unfortunately, in countries like Bangladesh, humans are directly infected by the reservoir, a fruit bat species. The changes following globalisation, climatic change [6, 7] , and the opening of previously closed ecosystems, have considerably modified the pattern of endemic (or enzootic) infections/diseases, and contributed to the emergence of new agents that are pathogenic for humans and domestic animals. It is even more true when facing a really emerging disease that moreover is zoonotic such as Nipah virus infection [27] for which no vaccine was available yet, because the causative agent was previously unknown; the only solution is once again to kill and destroy the infected and in-contact animals.

abstract:
  Abstract Vaccination, when available, is undoubtedly the most cost-effective means of preventing and controlling, and even eradicating, infectious diseases. In recent years vaccination has also been used for other purposes in animal health, production and welfare, e.g. immunocastration. Vaccination of animals serves many different purposes, such as controlling animal infections and infestations, thus improving animal health and welfare; controlling anthropozoonoses and food poisoning in humans, thereby protecting public health; solving problems associated with antibiotic and anthelmintic resistance; helping to leave food-producing animals free of chemical residues; protecting the environment and biodiversity and ensuring animal farming sustainability. The problem is nevertheless more complex when facing emerging or re-emerging infections particularly zoonotic ones.


id: cord-276372-q1fzxt3r
author: Conde, Dalia A.
date: 2013-12-11
txt: ./txt/cord-276372-q1fzxt3r.txt
cache: ./cache/cord-276372-q1fzxt3r.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0080311
doi: 10.1371/journal.pone.0080311
summary:
  To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. To understand the complexity of maintaining CBPs of threatened species across the ISIS zoo network, we developed a second algorithm to find the optimal radial distance from any given zoo at which the probability of finding a metapopulation size of at least 50, 100 or 250 recruited living individuals was highest relative to that radial distance. As expected, the optimal distance radii and the number of zoos required to maximize the probability of reaching a given population increase with the metapopulation size threshold (.50, .100 and .250 individuals) ( Figure 3) . Therefore, for the zoo community, one of the main challenges of managing their threatened species in CBPs is the complexity of moving individuals across borders and the coordination of conservation efforts among zoos and other institutions at a global level.

title:
  Zoos through the Lens of the IUCN Red List: A Global Metapopulation Approach to Support Conservation Breeding Programs

abstract:
  Given current extinction trends, the number of species requiring conservation breeding programs (CBPs) is likely to increase dramatically. To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. Our results show that 695 of the 3,955 (23%) terrestrial vertebrate species in ISIS zoos are threatened. Only two of the 59 taxonomic orders show a higher proportion of threatened species in ISIS zoos than would be expected if species were selected at random. In addition, for most taxa, the management of a zoo metapopulation of more than 250 individuals will require the coordination of a cluster of 11 to 24 ISIS zoos within a radius of 2,000 km. Thus, in the zoo network, the representation of species that may require CBPs is currently low and the spatial distribution of these zoo populations makes management difficult. Although the zoo community may have the will and the logistical potential to contribute to conservation actions, including CBPs, to do so will require greater collaboration between zoos and other institutions, alongside the development of international agreements that facilitate cross-border movement of zoo animals. To maximize the effectiveness of integrated conservation actions that include CBPs, it is fundamental that the non-zoo conservation community acknowledges and integrates the expertise and facilities of zoos where it can be helpful.


id: cord-276585-m1dkkbq7
title: Viral Host Jumps: Moving toward a Predictive Framework
author: Pulliam, Juliet R. C.
date: 2008-02-13
txt: ./txt/cord-276585-m1dkkbq7.txt
cache: ./cache/cord-276585-m1dkkbq7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10393-007-0149-6
doi: 10.1007/s10393-007-0149-6
summary:
  Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred. Although he makes no attempt to quantitatively determine the relative frequency of emergence for different types of pathogens, Burke claims that recent pandemics in humans and wildlife have mostly been caused by RNA viruses, citing multiple examples (influenza A, HIV-1, enteroviruses 70 and 71, human T-cell lymphoma virus, three paramyxoviruses, porcine respiratory coronavirus, and a calicivirus that causes hemorrhagic disease in rabbits).

abstract:
  In order to predict pathogen emergence, we must distinguish between emergence phenomena that occur via different processes. Focusing on the appearance of viral pathogens in new host species, I outline a framework that uses specific molecular characteristics to rank virus families by their expected a priori ability to complete each of three steps in the emergence process (encounter, infection, and propagation). I then discuss the degree to which the patterns expected, based solely on molecular-level structural characteristics, agree with observations regarding the ability of animal viruses to infect humans. This approach yields predictions consistent with empirical observations regarding the ability of specific viral families to infect novel host species but highlights the need for consideration of other factors, such as the ecology of host interactions and the determinants of cellular susceptibility and permissivity to specific virus groups, when trying to predict the frequency with which a virus will encounter a novel host species or the probability of propagation within a novel host species once infection has occurred.


id: cord-278195-1sle0d1j
title: The Importance of Human Emotions for Wildlife Conservation
author: Castillo-Huitrón, Nathalia M.
date: 2020-06-24
txt: ./txt/cord-278195-1sle0d1j.txt
cache: ./cache/cord-278195-1sle0d1j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32670150/
doi: 10.3389/fpsyg.2020.01277
summary:
  The very diverse and continuous human-wildlife interactions can be seen from three main perspectives: (1) Utilitarian, in which wild species provide goods for human well-being, such as food, clothing, transport, tools, raw materials, and companionship, among others; (2) Affective, where human beings feel sympathy, admiration, and respect for animals because of religious, mystical, or philosophical reasons (Kellert et al., 1996) , which has greatly contributed to cultural development worldwide (Herzog and Galvin, 1992; Alves, 2012) ; and (3) Conflictive, because of the real or potential damage that wild species may inflict on people and their interests (e.g., attacks on humans, livestock predation, damage on crops, and infrastructure, among others; Lescureux and Linnell, 2010) . Emotions such as fear and anger may be induced by predators that are bigger and heavier than persons, as in the case of large carnivores (e.g., bears, wolves, and big cats) (Røskaft et al., 2003) or by those species unattractive for most people, like worms, small carnivores, bats, and reptiles, which are often perceived as harmful (Knight, 2008; Prokop and Tunnicliffe, 2008; Prokop et al., 2009) .

abstract:
  Animals have always been important for human life due to the ecological, cultural, and economic functions that they represent. This has allowed building several kinds of relationships that have promoted different emotions in human societies. The objective of this review was to identify the main emotions that humans show toward wildlife species and the impact of such emotions on animal population management. We reviewed academic databases to identify previous studies on this topic worldwide. An analysis of the emotions on wildlife and factors causing them is described in this study. We identified a controversy about these emotions. Large predators such as wolves, coyotes, bears, big felids, and reptiles, such as snakes and geckos, promote mainly anger, fear, and disgust. This is likely due to the perceptions, beliefs, and experiences that societies have historically built around them. However, in some social groups these animals have promoted emotions such as happiness due to their values for people. Likewise, sadness is an emotion expressed for the threatening situations that animals are currently facing. Furthermore, we associated the conservation status of wildlife species identified in the study with human emotions to discuss their relevance for emerging conservation strategies, particularly focused on endangered species promoting ambiguous emotions in different social groups.


id: cord-289555-1z4vbldd
author: Mühldorfer, Kristin
date: 2011-12-28
txt: ./txt/cord-289555-1z4vbldd.txt
cache: ./cache/cord-289555-1z4vbldd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22216354/
doi: 10.1371/journal.pone.0029773
summary:
  Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats. In this study, we provide new data on infectious diseases in European bat species, considering factors likely to affect the susceptibility of bats to infectious agents including effects of seasonality, individual and species-specific heterogeneities, and possible intra-and inter-species transmission dynamics. Comparative bacteriologic and histo-pathologic analysis identified 22 different bacterial species that were clearly associated with pathological lesions and/or systemic infection, found in 17% (n = 73) of bats investigated bacteriologically ( Table 5) .

title:
  Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates

abstract:
  BACKGROUND: Bats receive increasing attention in infectious disease studies, because of their well recognized status as reservoir species for various infectious agents. This is even more important, as bats with their capability of long distance dispersal and complex social structures are unique in the way microbes could be spread by these mammalian species. Nevertheless, infection studies in bats are predominantly limited to the identification of specific pathogens presenting a potential health threat to humans. But the impact of infectious agents on the individual host and their importance on bat mortality is largely unknown and has been neglected in most studies published to date. METHODOLOGY/PRINCIPAL FINDINGS: Between 2002 and 2009, 486 deceased bats of 19 European species (family Vespertilionidae) were collected in different geographic regions in Germany. Most animals represented individual cases that have been incidentally found close to roosting sites or near human habitation in urban and urban-like environments. The bat carcasses were subjected to a post-mortem examination and investigated histo-pathologically, bacteriologically and virologically. Trauma and disease represented the most important causes of death in these bats. Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate the importance of diseases and infectious agents as cause of death in European bat species. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats.


id: cord-290253-hxxizipk
title: Changes in temperature alter the potential outcomes of virus host shifts
author: Roberts, Katherine E.
date: 2018-10-19
txt: ./txt/cord-290253-hxxizipk.txt
cache: ./cache/cord-290253-hxxizipk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.ppat.1007185
doi: 10.1371/journal.ppat.1007185
summary:
  Susceptibility to infection is known to vary with temperature, due to within individual physiological changes in factors such as the host immune response, metabolic rate or behavioural adaptations [22] [23] [24] [25] . However, if the host phylogeny also explains much of the variation in thermal tolerance, then phylogenetic patterns in virus susceptibility could be due to differences between species'' natural thermal optima and the chosen assay temperatures. We infected 45 species of Drosophilidae with Drosophila C Virus (DCV; Dicistroviridae) at three different temperatures and measured how viral load changes with temperature. We also examine how proxies for thermal optima and cellular function (thermal tolerances and basal metabolic rate) relate to virus susceptibility across temperatures, as increasing temperatures may have broad effects on both host and parasite [43] [44] [45] . To investigate the effect of temperature on virus host shifts we quantified viral load in 12,827 flies over 396 biological replicates, from 45 species of Drosophilidae at three temperatures ( Fig 1) .

abstract:
  Host shifts–where a pathogen jumps between different host species–are an important source of emerging infectious disease. With on-going climate change there is an increasing need to understand the effect changes in temperature may have on emerging infectious disease. We investigated whether species’ susceptibilities change with temperature and ask if susceptibility is greatest at different temperatures in different species. We infected 45 species of Drosophilidae with an RNA virus and measured how viral load changes with temperature. We found the host phylogeny explained a large proportion of the variation in viral load at each temperature, with strong phylogenetic correlations between viral loads across temperature. The variance in viral load increased with temperature, while the mean viral load did not. This suggests that as temperature increases the most susceptible species become more susceptible, and the least susceptible less so. We found no significant relationship between a species’ susceptibility across temperatures, and proxies for thermal optima (critical thermal maximum and minimum or basal metabolic rate). These results suggest that whilst the rank order of species susceptibilities may remain the same with changes in temperature, some species may become more susceptible to a novel pathogen, and others less so.


id: cord-300727-v3spbo5u
title: Biogeography of diseases: a framework for analysis
author: Peterson, A. Townsend
date: 2008-03-05
txt: ./txt/cord-300727-v3spbo5u.txt
cache: ./cache/cord-300727-v3spbo5u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00114-008-0352-5
doi: 10.1007/s00114-008-0352-5
summary:
  The ways in which these differences may influence disease transmission geography are complex; I illustrate their effects by means of worked examples regarding West Nile Virus, plague, filoviruses, and yellow fever. Three example disease systems are illustrated: West Nile Virus, the filoviruses (Ebola and Marburg viruses), and plague: Changes are illustrated as the difference between broken (original) and entire (present) outlines of circles; particular geographic occurrences of the disease are labeled to illustrate points discussed in the text appropriate from both abiotic and biotic perspectives and that are accessible to the species in terms of dispersal. In niche modeling, known occurrences of species (or diseases, in some cases) are related to raster geographic information system (GIS) coverages summarizing relevant environmental parameters in an evolutionary computing environment; the result is a picture of the species'' ecological distribution, which can be projected onto geography to identify a potential distribution for the species (Peterson 2007; Soberón 2007) .

abstract:
  A growing body of literature offers a framework for understanding geographic and ecological distributions of species; a few applications of this framework have treated disease transmission systems and their geography. The general framework focuses on interactions among abiotic requirements, biotic constraints, and dispersal abilities of species as determinants of distributional areas. Disease transmission systems have key differences from other sorts of biological phenomena: Interactions among species are particularly important, interactions may be stable or unstable, abiotic conditions may be relatively less important in shaping disease distributions, and dispersal abilities may be quite variable. The ways in which these differences may influence disease transmission geography are complex; I illustrate their effects by means of worked examples regarding West Nile Virus, plague, filoviruses, and yellow fever.


id: cord-301991-n87le8ix
title: Diatoms recovery from wastewater: Overview from an ecological and economic perspective
author: Saxena, Abhishek
date: 2020-10-16
txt: ./txt/cord-301991-n87le8ix.txt
cache: ./cache/cord-301991-n87le8ix.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S2214714420305833
doi: 10.1016/j.jwpe.2020.101705
summary:
  Because diatoms produce organic matter to a large extent that permits natural inbuilt capacity to withstand toxicity levels in water bodies, extended survival rate, short regeneration time than microalgae, fishes, and other micro invertebrates thus making them one of the best candidate for water quality monitoring, and excellent bioindicators of aquatic biological integrity [12, 13] . Isolation and identification of benthic diatoms are problematic in comparison with planktonic species due to difficulties in sample treatment, sampling, and microscopic observation though benthic diatoms play the main role as bioindicators in the aquatic ecosystem because they attached to the substratum with secreted mucilage from their cell wall [44, 45] . An outline of isolation of pure diatom species getting affected by the surrounding contaminants is challenging since they get heavily occupied with different interfering organisms, which pose a significant threat in obtaining axenic culture, as presented in Fig. 3 .

abstract:
  Alarming water pollution is toxic to the aquatic ecosystem leading to a sharp decline in species diversity. Diatoms have great potency to survive in contaminated water bodies, hence they can be compelling bioindicators to monitor the change in the environmental matrices effectively. Around the globe, researchers are intended to evaluate the impact of pollution on the diatoms recovery and techniques used for the assessment. The diatoms are precious for futuristic need viz. value-added products, energy generation, pharmaceuticals, and aquaculture feedstocks. All these applications led to a significant rise in diatoms research among the scientific community. This review presents different isolation practices, cultivation, and other challenges associated with the diatoms. A precise focus is given to diatoms isolation techniques from highly polluted water bodies with the main thrust towards obtaining an axenic culture to elucidate the significance of pure diatom cultures. Recovery of “jewels of the sea” from polluted water signifies the prospective ecological and economic aspects.


id: cord-304481-yqc8r3ll
author: Luis, Angela D.
date: 2015-08-24
txt: ./txt/cord-304481-yqc8r3ll.txt
cache: ./cache/cord-304481-yqc8r3ll.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26299267/
doi: 10.1111/ele.12491
summary:
  Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. Rodents are a suitable group for comparison because they also host many important zoonotic viruses and share many of the characteristics hypothesised to make bats suitable as viral reservoirs. Host traits that correlated with the highest degree within the bat network (the most connections or viruses shared), in order of importance, were gregariousness and sympatry; diet was marginally important (Fig. 2b, Table S6 and S7). For rodents, sympatry was the most important host trait; species whose distributions overlapped with a greater number of other rodent species had more viruses and higher degree and betweenness (Fig. 2d-f and Table S11-S19).

title:
  Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission

abstract:
  Bats are natural reservoirs of several important emerging viruses. Cross‐species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence.


id: cord-305857-2409me0p
title: Seroprevalence Dynamics of European Bat Lyssavirus Type 1 in a Multispecies Bat Colony
author: López-Roig, Marc
date: 2014-09-04
txt: ./txt/cord-305857-2409me0p.txt
cache: ./cache/cord-305857-2409me0p.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v6093386
doi: 10.3390/v6093386
summary:
  In recent years, bats have been implicated in numerous emerging infectious disease events and have been recognized as important reservoir hosts for viruses that can cross the species barrier to infect humans and other domestic and wild mammals [3] . Persistent viral infections occurring among long-lived bats, coupled with their often gregarious roosting behavior, could greatly increase the potential for intra-and inter-species transmission of viruses [7] , especially in summer and winter periods. To study the variation in EBLV-1-antibody prevalence, we conducted two analyses: first, three explanatory variables (sex, species and year) were first screened using a univariate analysis and a chi-square test to check for statistically significant associations with serological status (0: negative; 1: positive). We report the results of the prevalence of specific EBLV-1 neutralizing antibody analysis from the 2004-2012 period in nine bat species roosting in the same refuge.

abstract:
  We report an active surveillance study of the occurrence of specific antibodies to European Bat Lyssavirus Type 1 (EBLV-1) in bat species, scarcely studied hitherto, that share the same refuge. From 2004 to 2012, 406 sera were obtained from nine bat species. Blood samples were subjected to a modified fluorescent antibody virus neutralization test to determine the antibody titer. EBLV-1-neutralizing antibodies were detected in six of the nine species analyzed (Pipistrellus pipistrellus, P. kuhlii, Hypsugo savii, Plecotus austriacus, Eptesicus serotinus and Tadarida teniotis). Among all bats sampled, female seroprevalence (20.21%, 95% CI: 14.78%–26.57%) was not significantly higher than the seroprevalence in males (15.02%, 95% CI: 10.51%–20.54%). The results showed that the inter-annual variation in the number of seropositive bats in T. teniotis and P. austriacus showed a peak in 2007 (>70% of EBLV-1 prevalence). However, significant differences were observed in the temporal patterns of the seroprevalence modeling of T. teniotis and P. austriacus. The behavioral ecology of these species involved could explain the different annual fluctuations in EBLV-1 seroprevalence.


id: cord-312545-io2jmp7o
title: Ecosystem dynamics, biological diversity and emerging infectious diseases
author: Roche, Benjamin
date: 2011-04-30
txt: ./txt/cord-312545-io2jmp7o.txt
cache: ./cache/cord-312545-io2jmp7o.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1631069111000709
doi: 10.1016/j.crvi.2011.02.008
summary:
  Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective. Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective. This raises two important questions concerning: (i) the effects on local disease transmission of the accidental introduction or biological invasion by exotic vectors, even when they show a low competence to transmit the infection; and (ii) the role of low to very low In species-rich reservoir communities, generally a decrease in the prevalence of disease pathogens in the vectors is observed.

abstract:
  In this article, we summarize the major scientific developments of the last decade on the transmission of infectious agents in multi-host systems. Almost sixty percent of the pathogens that have emerged in humans during the last 30–40 years are of animal origin and about sixty percent of them show an important variety of host species besides humans (3 or more possible host species). In this review, we focus on zoonotic infections with vector-borne transmission and dissect the contrasting effects that a multiplicity of host reservoirs and vectors can have on their disease dynamics. We discuss the effects exerted by host and vector species richness and composition on pathogen prevalence (i.e., reduction, including the dilution effect, or amplification). We emphasize that, in multiple host systems and for vector-borne zoonotic pathogens, host reservoir species and vector species can exert contrasting effect locally. The outcome on disease dynamics (reduced pathogen prevalence in vectors when the host reservoir species is rich and increased pathogen prevalence when the vector species richness increases) may be highly heterogeneous in both space and time. We then ask briefly how a shift towards a more systemic perspective in the study of emerging infectious diseases, which are driven by a multiplicity of hosts, may stimulate further research developments. Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective.


id: cord-312555-qytl2vqt
title: Use of game fauna by Fulni-ô people in Northeastern Brazil: implications for conservation
author: da Silva, Josivan Soares
date: 2020-04-17
txt: ./txt/cord-312555-qytl2vqt.txt
cache: ./cache/cord-312555-qytl2vqt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32303237/
doi: 10.1186/s13002-020-00367-3
summary:
  Also, the use of game meat among the Fulni-ô seems to be actively directed to the preferred species, suggesting that in the case of an urbanized indigenous community, where other sources of income are available, the demand for game meat is lower when compared to other ethnic groups. Thus, this research focused on the hunting of game meat among the Fulni-ô people living in the semi-arid region, being the first study carried out in an ethnic group strongly influenced by urbanization in the Brazilian Northeast. Even when compared to studies of wild animal consumption in the Caatinga region [5, 41] , the number of animals hunted is higher than that reported for the Fulni-ô, which may be indicative of a lower demand for game in relation to other communities in the northeast region [5, 12, 17, 31] .

abstract:
  BACKGROUND: Due to the influence of several factors on the hunting of game meat, we investigated how the seasonality of the environment, the abundance, and the biomass of wild animals, as well as the proximity to these resources, can affect the hunting. METHODS: The research was developed with the Fulni-ô people in the municipality of Águas Belas, Agreste of Pernambuco, Northeast of Brazil. In order to do this, we applied snowball sampling to select the participants. Data from potentially useful game species were obtained from lists and semi-structured interviews to register their particular kind of uses, capture periods (daytime, night, or both), preferences, and perceived abundance. The hunters who allowed their game meat captured to be weighed and identified were followed for 1 year. RESULTS: Our records pointed to a vast repertoire of potentially hunting animals. However, we did not verify relationships between the abundance, seasonality, and biomass of the animals that were hunted by the Fulni-ô. We observed a total of 209,866 (kg) of game meat hunted in the studied group, belonging to 23 species, distributed in three taxonomic groups, the birds being the most representative group with 59% of total reported. CONCLUSION: Such consumption by the group is well below in terms of biomass when compared to other ethnic or local groups in other regions of Brazil, or in Caatinga areas, characterizing an activity much more of cultural character than subsistence. Also, the use of game meat among the Fulni-ô seems to be actively directed to the preferred species, suggesting that in the case of an urbanized indigenous community, where other sources of income are available, the demand for game meat is lower when compared to other ethnic groups.


id: cord-316999-712rit8h
title: Invasive alien species and disease risk: An open challenge in public and animal health
author: Chinchio, Eleonora
date: 2020-10-22
txt: ./txt/cord-316999-712rit8h.txt
cache: ./cache/cord-316999-712rit8h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33091094/
doi: 10.1371/journal.ppat.1008922
abstract: nan
summary:
  To this aim, we provide here an overview of how animal IAS may affect local disease dynamics both directly and indirectly, i.e., acting as pathogen hosts or disrupting the recipient ecosystem structure, through real-case examples from the ecological literature, and, in the last paragraph, we propose future initiatives aimed at improving our capacity for targeted actions toward the IAS most likely to threaten human and animal health, calling for an increased involvement of people working in the fields of animal and public health in a new invasion epidemiology field. IAS may host pathogens that are absent in the area of release and cause their establishment and subsequent spillover to local species, possibly resulting in an increase of disease risk for humans, domestic animals, and native wildlife.


id: cord-320295-k2i52wgs
title: Host Range and Emerging and Reemerging Pathogens
author: Woolhouse, Mark E.J.
date: 2005-12-17
txt: ./txt/cord-320295-k2i52wgs.txt
cache: ./cache/cord-320295-k2i52wgs.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16485468/
doi: 10.3201/eid1112.050997
summary:
  However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population. All the defined host types are potential sources of zoonotic infections, but differences occurred in their importance (ranked by number of pathogen species supported) across viruses, bacteria, fungi, protozoa, and helminths and no 1 type consistently dominates ( Figure 1A) , although ungulates are the most important overall, supporting over 250 species of human pathogen. However, when the fraction of emerging and reemerging species is compared with the breadth of host range (as the number of host types other than humans), a pattern becomes apparent (Figure 2) . Relationship between breadth of host range (as number of nonhuman host types, as listed in Figure 1 ) and the fraction of pathogen species regarded as emerging or reemerging.

abstract:
  An updated literature survey identified 1,407 recognized species of human pathogen, 58% of which are zoonotic. Of the total, 177 are regarded as emerging or reemerging. Zoonotic pathogens are twice as likely to be in this category as are nonzoonotic pathogens. Emerging and reemerging pathogens are not strongly associated with particular types of nonhuman hosts, but they are most likely to have the broadest host ranges. Emerging and reemerging zoonoses are associated with a wide range of drivers, but changes in land use and agriculture and demographic and societal changes are most commonly cited. However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population.


id: cord-335915-2apj4qy9
title: Applications of Serum Protein Electrophoresis in Exotic Pet Medicine
author: Melillo, Alessandro
date: 2013-01-22
txt: ./txt/cord-335915-2apj4qy9.txt
cache: ./cache/cord-335915-2apj4qy9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.cvex.2012.11.002
doi: 10.1016/j.cvex.2012.11.002
summary:
  The main difference between the 2 products is the absence in the serum of fribrinogen, the protein involved in the processes of coagulation; the concentration of total solids of the plasma is thus slightly higher than that of serum (about 5%) and the electrophoretic pattern from it will result in a higher incidence of b-globulin fraction where the fibrinogen normally migrates. In rabbits, the normal Serum Protein Electrophoresis (SPE) pattern lacks a clear distinction between b1-globulins and b2-globulins, as present in dogs and cats, but when gammopathies in the b region occur, usually an extension of the electrophoretic band is seen, with consequent demarcation of the 2 peaks. The first studies of serum proteins in birds were performed on domestic chickens, showing many similarities with the layout of mammals (eg, the production of APPs 18, 19 ), but also several differences: the widespread presence of prealbumin, for example, the lowest concentration of g-globulin, and conversely the more marked response to inflammatory stimuli in the b-globulin field.

abstract:
  Serum Protein Electrophoresis (SPE) is a useful diagnostic and prognostic tool in human and companion animals medicine: several experiences show that it can be useful in exotic practice as well. The fundamentals of SPE interpretation as well as some normal and pathological patterns for the species most commonly seen in practice are provided.


id: cord-343139-19t8g7u7
title: After the Megafires: What Next for Australian Wildlife?
author: Wintle, Brendan A.
date: 2020-07-14
txt: ./txt/cord-343139-19t8g7u7.txt
cache: ./cache/cord-343139-19t8g7u7.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0169534720301713
doi: 10.1016/j.tree.2020.06.009
summary:
  Unfortunately, there was little strategic priority in fire control operations for the protection of key populations of threatened species, critical habitats, and threatened ecological communities. Clear guidance on how to most effectively organise species and ecosystem conservation activities before, during, and immediately following a major fire event can be helpful (Figure 2 ). and extensive control of other threats that can compound fire impacts; and collection of baseline monitoring and survey data to help identify places critical to protect, prioritise emergency responses, and provide clarity around what has been lost immediately following a fire event. Crucial elements in the preparatory phase ''before the fire'' that were not adequately addressed before the 2019-2020 Australian megafires include analysis and synthesis of species sensitivity to fire, monitoring, surveying, and mapping to delineate critical habitats for protection and emergency postfire action.

abstract:
  The 2019–2020 megafires in Australia brought a tragic loss of human life and the most dramatic loss of habitat for threatened species and devastation of ecological communities in postcolonial history. What must be done now to keep impacted species from extinction? What can be done to avoid a repeat of the impacts of such devastating bushfires? Here, we describe hard-won lessons that may also be of global relevance.


id: cord-343461-vj6o1b18
title: Fungal Planet description sheets: 1042–1111
author: Crous, P.W.
date: 2020-06-29
txt: ./txt/cord-343461-vj6o1b18.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.3767/persoonia.2020.44.11
doi: 10.3767/persoonia.2020.44.11
summary:
  Conidia aseptate, hyaline, smooth, guttulate, subcylindrical to fusoid to irregular, straight to somewhat curved, apex subobtuse, base truncate, (9 -) Notes -Coleophoma includes species that are plant pathogenic or saprobic, occurring on a wide range of plant hosts (Crous et al. Based on a megablast search of NCBIs GenBank nucleotide database, the closest hits using the ITS sequence had highest similarity to Helgardia anguioides ( Notes -Pseudopezicula accommodates two species of apothecial ascomycetes that cause angular leaf scorch on Vitis vinifera. Based on a megablast search of NCBIs GenBank nucleotide database, the closest hits using the ITS sequence had highest similarity to Satchmopsis brasiliensis ( Notes -The phylogeny and morphology of Torrendiella and Hymenotorrendiella was discussed in detail by Johnston et al. Culture characteristics -(after 2 wk at 20 °C in the dark): On potato dextrose agar (PDA), colonies reach 44-47 mm diam, round shape, flat, dark olive green, dusty, aerial mycelium absent, profuse sporulation, margin white and glabrous, exudates (blackish droplets) produced mainly on the outermost colony surface; reverse olive green to olive black.

abstract:
  Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects’ frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.


id: cord-354757-jy47l6zm
title: Aquatic invasive species: challenges for the future
author: Havel, John E.
date: 2015-01-25
url: https://www.ncbi.nlm.nih.gov/pubmed/32214452/
doi: 10.1007/s10750-014-2166-0
abstract:
  Humans have effectively transported thousands of species around the globe and, with accelerated trade; the rate of introductions has increased over time. Aquatic ecosystems seem at particular risk from invasive species because of threats to biodiversity and human needs for water resources. Here, we review some known aspects of aquatic invasive species (AIS) and explore several new questions. We describe impacts of AIS, factors limiting their dispersal, and the role that humans play in transporting AIS. We also review the characteristics of species that should be the greatest threat for future invasions, including those that pave the way for invasions by other species (“invasional meltdown”). Susceptible aquatic communities, such as reservoirs, may serve as stepping stones for invasions of new landscapes. Some microbes disperse long distance, infect new hosts and grow in the external aquatic medium, a process that has consequences for human health. We also discuss the interaction between species invasions and other human impacts (climate change, landscape conversion), as well as the possible connection of invasions with regime shifts in lakes. Since many invaders become permanent features of the environment, we discuss how humans live with invasive species, and conclude with questions for future research.


