Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 69 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 11669 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 47 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 68 IBD 18 COVID-19 17 SARS 15 patient 6 cat 5 study 5 disease 5 covid-19 5 PCR 4 group 4 dog 4 University 4 Crohn 3 dna 3 CKD 3 CHF 2 treatment 2 protein 2 infection 2 figure 2 concentration 2 cell 2 Veterinary 2 TNF 2 RNA 2 HLA 2 Fig 2 FIP 2 ELISA 2 ACE2 1 western 1 time 1 th2 1 th1 1 test 1 ssh 1 small 1 sign 1 sample 1 risk 1 result 1 response 1 prevalence 1 polyp 1 pancreatic 1 mouse 1 microbiota 1 microbe 1 liver 1 intestinal Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 5616 cell 4223 dog 4111 % 3878 patient 3538 disease 3389 cat 2965 study 1889 p 1686 infection 1565 group 1528 treatment 1416 response 1330 expression 1316 case 1253 result 1200 protein 1132 concentration 1128 level 1086 time 1069 t 1068 sample 1032 analysis 1017 day 994 gene 980 effect 975 blood 928 serum 913 therapy 904 mouse 894 bowel 892 risk 867 control 823 datum 812 n 809 diagnosis 794 test 759 role 733 year 729 activity 718 age 709 colitis 694 factor 654 sign 650 antigen 646 b 633 antibody 629 difference 619 change 613 function 596 cytokine Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 2458 IBD 1083 T 884 COVID-19 620 SARS 587 mg 477 CoV-2 470 AE 391 Crohn 378 CD4 377 TNF 376 IFN 374 CD8 367 PCR 257 L 251 C 246 GI 242 ELISA 239 University 235 HLA 233 kg 229 UC 219 ACE2 216 g 212 CD 211 C. 205 al 195 MHC 189 E. 183 B 179 China 177 TCR 169 II 167 Disease 163 A 159 et 155 DC 154 RNA 143 M. 142 • 139 IL-10 138 Group 138 . 135 S. 134 gd 132 Fig 125 CI 125 CHF 124 CKD 122 NKT 121 TG Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 2299 we 1229 it 475 they 313 i 146 them 58 us 41 one 29 itself 23 he 22 you 18 themselves 15 yϕ 15 she 5 ourselves 3 mg 2 interleukin-15 2 igmcic 2 himself 2 euthanasia 2 esat-6 2 e2f2-/-mice 2 crx-527 1 Ò 1 yourself 1 turns 1 thbs1 1 srd)dogs 1 s 1 rab3b 1 pi3kg 1 pep005 1 mtecs 1 il-1β 1 il)-2r 1 igg1 1 ifnl4 1 idc 1 hrgal3 1 gate16 1 esat6 1 cd5.h449stop 1 caspase-1 1 3de Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 29156 be 4773 have 2670 use 1363 associate 1358 increase 1346 include 1323 show 1222 compare 1124 report 899 do 857 induce 837 find 816 suggest 799 perform 771 follow 770 evaluate 718 determine 701 base 694 identify 604 treat 578 occur 578 consider 555 assess 551 observe 544 affect 528 present 519 reduce 515 require 513 describe 500 express 497 measure 495 cause 484 demonstrate 475 obtain 464 develop 461 result 457 provide 453 investigate 438 involve 436 indicate 436 detect 433 see 417 remain 399 decrease 394 receive 377 lead 376 infect 367 confirm 362 test 355 know Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2590 not 2128 - 1679 clinical 1581 high 1376 inflammatory 1292 also 1076 other 986 more 895 specific 879 most 878 low 862 significant 859 significantly 841 however 795 immune 774 human 769 only 751 such 747 different 707 well 669 healthy 658 normal 647 non 622 severe 613 anti 607 positive 591 canine 576 intestinal 574 small 564 further 542 chronic 528 respectively 498 gastrointestinal 495 as 492 important 482 common 481 present 458 first 437 large 437 feline 434 therefore 427 acute 398 viral 393 median 381 long 366 many 360 primary 357 available 353 respiratory 351 negative Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 264 most 153 least 125 Most 81 high 68 good 35 low 23 large 20 great 8 late 7 early 6 strong 6 small 6 close 5 bad 4 near 4 long 4 easy 4 big 2 ≤3 2 young 2 common 2 B27 1 simple 1 severe 1 safe 1 poor 1 p=0.016 1 outermost 1 old 1 new 1 narrow 1 hexose 1 hard 1 fit 1 few 1 fast 1 dirty 1 deep 1 clean 1 af33e711bd3232fa1242e428523e769d22b9ad25 1 VEGFR-1 1 Least 1 Gly908Arg 1 CFP10 1 -low 1 -V Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 615 most 107 least 26 well 2 worst 2 highest 2 hard 1 strongest 1 shortest 1 lowest 1 -v Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 2 wpsites.ucalgary.ca 2 covidibd.org 1 youtu.be 1 www.worldometers.info 1 www.vetcancerregistry.com 1 www.naspghan.org 1 vetmed.tamu.edu 1 qiime2.org 1 orcid.org 1 ibdregistry.org 1 creat 1 adz.cf.ac.uk Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://wpsites.ucalgary.ca/ 1 http://youtu.be/6Cp7TAcc8XM 1 http://www.worldometers.info/coronavirus/ 1 http://www.vetcancerregistry.com 1 http://www.naspghan.org/content/59/en/Continuing-Medical-Educa 1 http://vetmed.tamu.edu/gilab/ 1 http://qiime2.org 1 http://orcid.org/0000-0001-5767-5541 1 http://ibdregistry.org 1 http://creat 1 http://covidibd.org/map/ 1 http://covidibd.org/ 1 http://AdZ.cf.ac.uk Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 ewilson@gastro.org Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 17 concentrations were significantly 10 expression was significantly 10 levels were not 9 concentration was significantly 9 concentrations were higher 8 ibd do not 8 study was therefore 7 cats did not 6 concentrations were not 6 expression was higher 5 cat was positive 5 cats do not 5 cells are not 5 cells were positive 5 dogs did not 5 dogs had normal 5 dogs were male 5 dogs were prospectively 5 expression is not 5 expression was not 5 groups were not 5 infection is not 5 levels were significantly 5 patients required hospitalization 5 studies are necessary 5 study did not 4 cats are more 4 cells including plasma 4 cells is not 4 cells was significantly 4 cells were significantly 4 concentrations did not 4 concentrations increased significantly 4 dogs had lower 4 dogs had significantly 4 dogs were clinically 4 dogs were more 4 dogs were negative 4 dogs were retrospectively 4 expression did not 4 samples were negative 4 study was partially 4 treatment was not 3 % were female 3 % were males 3 cases are best 3 cases were positive 3 cats are often 3 cats had normal 3 cats had only Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 4 levels were not significantly 3 treatment had no effect 2 analysis showed no significant 2 concentrations were not different 2 expression was not different 2 groups were not significantly 2 groups were not statistically 2 treatment is not useful 1 % had no detectable 1 analysis showed no correlation 1 blood identified no mutations 1 cases had no effect 1 cases had no respiratory 1 cases suggesting no major 1 cat has no weight 1 cat was no longer 1 cats are not well 1 cats do not commonly 1 cats had no clinical 1 cats had no evidence 1 cats has no protective 1 cats is not well 1 cats showed no significant 1 cats were not completely 1 cells are not necessary 1 cells are not preponderant 1 cells do no longer 1 cells is not available 1 cells is not due 1 cells is not essential 1 cells was not relative 1 cells was not statistically 1 concentration is not clinically 1 concentration was not significantly 1 concentrations are not ideally 1 concentrations have not yet 1 concentrations is not predictive 1 disease has not yet 1 disease is not yet 1 diseases are not well 1 dogs had no alterations 1 dogs had no intrinsic 1 dogs is not just 1 dogs were not neutered 1 effect was not significant 1 expression did not significantly 1 expression is not essential 1 expression is not fully 1 gene was not significantly 1 genes is not signifi A rudimentary bibliography -------------------------- id = cord-013370-gktnz644 author = Abreu, Maria T title = Providing Guidance During a Global Viral Pandemic for the Care of Patients With Inflammatory Bowel Disease date = 2020-10-21 keywords = IBD; patient summary = We have partnered closely with the European Crohn''s and Colitis Organisation because of our shared desire to provide the best guidance to patients with inflammatory bowel disease at a global level, as well as to the physicians that are caring for these patients. The process is called a RAND panel wherein the members of IOIBD, as well as other very knowledgeable practitioners of IBD, voted on a series of statements largely having to do with the risk of infection with the SARS-CoV-2 virus and the development of COVID-19 in patients who have IBD. We urge you to continue to check the IOIBD or the ECCO websites for the most up-to-date information, and we hope to keep updating the guidance in all of the various dimensions of IBD care. doi = 10.1093/ecco-jcc/jjaa116 id = cord-276267-77903fld author = Al‐Ani, Aysha H. title = Review article: prevention, diagnosis and management of COVID‐19 in the IBD patient date = 2020-05-26 keywords = COVID-19; IBD; SARS; patient; risk summary = 6 Consequently, there is a concern that IBD patients are at greater risk of developing COVID-19 and at increased risk of progressing to a more severe clinical course or even death compared to the general population. 18 Furthermore, there is a recent case report of a possible SARS-CoV-2 gastrointestinal infection causing acute haemorrhagic colitis and signalling COVID-19 disease. Clinical assessment of risk factors for infection in inflammatory bowel disease patients Protection of 318 inflammatory bowel disease patients from the outbreak and rapid spread of COVID-19 infection in Wuhan Risk of infection with methotrexate therapy in inflammatory diseases: a systematic review and meta-analysis Comparative risk of serious infections with biologic and/or immunosuppressive therapy in patients with inflammatory bowel diseases: a systematic review and meta-analysis Infection-related hospitalizations are associated with increased mortality in patients with inflammatory bowel diseases Respiratory tract infections in patients with inflammatory bowel disease: safety analyses from vedolizumab clinical trials doi = 10.1111/apt.15779 id = cord-310042-9z8rkzq8 author = Aysha, Al‐Ani title = Practical management of inflammatory bowel disease patients during the COVID‐19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty date = 2020-07-12 keywords = COVID-19; IBD; SARS; infection summary = This review aims to summarise the current literature and provide guidance on the management of inflammatory bowel disease (IBD) patients in the context of the COVID‐19 pandemic in the Australasian setting. A significant proportion of IBD patients are treated with long-term immunomodulator/immunosuppressive therapy which potentially places them at increased risk of infections and associated complications. Practitioners and patients alike are therefore concerned about the risk and implications of COVID-19 infection in the IBD patient, despite a paucity of evidence supporting an altered predisposition to disease or more severe disease course. Despite concerns regarding immunosuppression and consequent predisposition to infection, there is no evidence to suggest increased infection rates of COVID-19 in IBD patients to date. 8, 9 Hence, expert consensus currently is that patients with IBD do not appear to be at increased risk of SARS-CoV-2 infection compared with the general population. 2 • Reducing disease activitythere is evidence that moderate to severe disease activity increases the risk of infection in IBD patients. doi = 10.1111/imj.14889 id = cord-283279-1qcdnd1y author = Barberio, Brigida title = The Adherence to Infusible Biologic Therapies in Inflammatory Bowel Disease Patients During COVID-19 Pandemic: Is It Really a Problem? date = 2020-07-17 keywords = IBD summary = title: The Adherence to Infusible Biologic Therapies in Inflammatory Bowel Disease Patients During COVID-19 Pandemic: Is It Really a Problem? 1 a evaluating the adherence to infusible biologic therapies, defined as receiving an infusion within ten weeks of the prior infusion, in patients with Inflammatory Bowel Disease (IBD) during the current Coronavirus disease 2019 (COVID-19) pandemic. 4, 5 For instance, at our Center, one week before the infusion, patients were contacted by email to reassure about the lack of risk in moving to the Hospital and the benefit of continuing medical therapy. We should explain to our patients with chronic diseases why it is important that they adhere to therapies which are relative safe and manageable despite the COVID-19 pandemic. Adherence of infusible biologics during the time of COVID-19 among patients with Inflammatory Bowel Disease: A nationwide VA cohort study doi = 10.1053/j.gastro.2020.07.017 id = cord-307201-keec6fzo author = Barberio, Brigida title = Should IBD Patients Be Tested for Active COVID-19 Prior Starting a Biological Treatment? date = 2020-08-30 keywords = IBD summary = title: Should IBD Patients Be Tested for Active COVID-19 Prior Starting a Biological Treatment? aimed to provide recommendations regarding the management of patients with inflammatory bowel disease (IBD) in the era of COVID-19 pandemic. The AGA suggests that IBD patients should not stop their current treatments in order to prevent infection or adverse outcome with COVID-19. However, there was no specific international guidance with respect to COVID-19 testing in patients starting immunosuppressive treatment, particularly if they are asymptomatic, and the article by Rubin et al did not cover this topic either. 6 Overall, we believe that screening for active COVID-19 infection should be performed in order to avoid potential complications and to adjust therapy accordingly prior starting biological treatment. Viral screening before initiation of biologics in patients with inflammatory bowel disease during the COVID-19 outbreak Are patients with inflammatory bowel disease at increased risk for COVID-19 infection ? doi = 10.1053/j.gastro.2020.08.049 id = cord-302717-hn3airxq author = Bayoumy, Ahmed B. title = Efficacy, safety and drug survival of thioguanine as maintenance treatment for inflammatory bowel disease: a retrospective multi-centre study in the United Kingdom date = 2020-09-11 keywords = AZA; IBD; NRH summary = title: Efficacy, safety and drug survival of thioguanine as maintenance treatment for inflammatory bowel disease: a retrospective multi-centre study in the United Kingdom BACKGROUND: Thioguanine (TG) is a thiopurine which has been used for patients with inflammatory bowel disease (IBD), who have failed azathioprine (AZA) or mercaptopurine (MP) due to adverse events or suboptimal response. The aim of this study was to investigate the long-term efficacy and safety of low-dose TG therapy in IBD patients failing AZA and MP. METHODS: A retrospective multicentre study was performed in IBD patients who failed prior treatment with conventional thiopurines with or without following immunomodulation (thiopurine-allopurinol, biologicals, methotrexate, tacrolimus) and were subsequently treated with TG as rescue monotherapy between 2003 and 2019 at three hospitals in the United Kingdom. They reported results of 11 studies, comprising of 353 patients who were treated with a median TG starting dose of 20 mg/day after failing prior conventional thiopurine therapy. doi = 10.1186/s12876-020-01441-6 id = cord-311162-kbqh7beq author = Behzad, Catherine title = Establishing Safe Out-of-Hospital Infusion Centers May Improve the Quality of Care in Patients With IBD During the COVID-19 Pandemic date = 2020-09-09 keywords = IBD summary = title: Establishing Safe Out-of-Hospital Infusion Centers May Improve the Quality of Care in Patients With IBD During the COVID-19 Pandemic We read with great interest the article by Occhipinti and Pastorelli 1 about the challenges in the care of patients with inflammatory bowel disease (IBD) during the COVID-19 pandemic. However, 2 medical wards were maintained COVID-19-free to provide care for patients with urgent situations and essential services. In addition, we gave special consideration to patients with IBD who were on immunosuppressive therapy and decided to continue biologic infusions in the hospital''s COVID-19-free wards. In our experience, 92% of the patients whose scheduled biologic infusion dates were during the peak of the outbreak in early February through March refused to come to the hospital to receive their infusions. Challenges in the care of IBD patients during the CoViD-19 pandemic: report from a "Red Zone" area in Northern Italy doi = 10.1093/ibd/izaa246 id = cord-345786-1o9nx7z9 author = Bernstein, Charles N title = Worldwide Management of Inflammatory Bowel Disease During the COVID-19 Pandemic: An International Survey date = 2020-08-14 keywords = China; IBD; covid-19 summary = METHODS: Members of the World Gastroenterology Organization (WGO) IBD Task Force contacted colleagues in countries largely beyond North America and Europe, inviting them to review the WGO website for IBD and COVID-19 introduction, with links to guideline documents, and then to respond to 9 ancillary open-ended management questions. [1] [2] [3] The management of IBD may differ by geography with economically more advanced countries having greater access to health care resources such as endoscopy and expensive therapies like biologics. 8 Recommendations include continuing all immunomodulatory medications in patients with IBD, reducing steroid doses as much as possible, limiting elective endoscopies, and encouraging telemedicine in place of in-person clinic visits. Respondents from 8 countries, both low and high resource regions, reported that they routinely tested persons with IBD with new gastrointestinal symptoms. However, even with reports from 1 or 2 clinicians from each country, it allows insight into the uniformity or key differences in the practice of IBD around the world during the COVID-19 pandemic. doi = 10.1093/ibd/izaa202 id = cord-351566-z6onmkrn author = Bezzio, Cristina title = SEVERE IBD FLARES AND COVID-19: EXPAND THE GASTROENTEROLOGY-SURGERY TEAM TO INCLUDE AN INFECTIOUS DISEASE SPECIALIST date = 2020-06-16 keywords = IBD summary = title: SEVERE IBD FLARES AND COVID-19: EXPAND THE GASTROENTEROLOGY-SURGERY TEAM TO INCLUDE AN INFECTIOUS DISEASE SPECIALIST Perhaps because of the lack of empirical evidence, these guidelines did not specifically address the challenging case of IBD patients hospitalized due to a severe flare of disease with subsequent or concomitant pneumonia due to SARS-CoV-2. Especially in ulcerative colitis, a severe flare of disease is a life-threatening emergency that requires prompt recognition, hospitalization, early initiation of treatment and close monitoring (4). However, in the COVID-19 pandemic, this professional pair may not be enough to effectively manage the infection in an IBD patient with a severe disease flare. Nonetheless, we think that the issues raised by this case are of great interest to physicians managing IBD patients during the COVID-19 pandemic. In particular, we suggest that an infectious disease specialist join the gastroenterologist and surgeon on the team managing IBD patients hospitalized for a severe flare of disease. doi = 10.1053/j.gastro.2020.05.082 id = cord-295066-76se8mxq author = Botti, Fiorenzo title = URGENT SURGERY FOR INFLAMMATORY BOWEL DISEASES DURING THE COVID-19 OUTBREAK IN A HIGH INCIDENCE AREA - EXPERIENCE FROM A HIGH-VOLUME CENTRE date = 2020-08-31 keywords = IBD; covid-19 summary = [4] As a tertiary referral centre for the surgical management of IBD patients, it was important to clearly define which complicated IBD cases were to be operated, by taking into account several variables including disease severity and quality of life, presence of comorbidities, feasibility of an alternative procedure. According to the British Society of Gastroenterology (BSG) guidelines on the IBD management during the COVID-19 pandemic, [5] routine elective operations should be deferred, while emergency procedures (e.g. colectomy in acute severe ulcerative colitis [UC] or intestinal resection in septic complications of penetrating Crohn''s disease [CD]) should continue. Complex surgical IBD cases should also be deferred when possible and its timing must be regularly reviewed at multidisciplinary meetings, trying to optimize medical treatment (e.g. using partial or exclusive enteral nutrition regimens or draining abscesses in combination with antibiotic therapy) and to avoid surgery or change the timing from emergency to urgent or semi-urgent. doi = 10.1016/j.dld.2020.08.039 id = cord-266392-bayabroa author = Brenner, Erica J. title = BENIGN EVOLUTION OF SARS-CoV2 INFECTIONS IN CHILDREN WITH INFLAMMATORY BOWEL DISEASE: RESULTS FROM TWO INTERNATIONAL DATABASES date = 2020-10-12 keywords = COVID-19; IBD summary = 2 Since highest ACE2 expression is in the terminal ileum and colon, further upregulated during inflammation, and many COVID-19 patients experience gastrointestinal symptoms, longitudinal data are necessary determine whether inflammatory bowel diseases (IBD) patients are at risk for severe or complicated COVID-19. A recent analysis in IBD patients from the SECURE-IBD registry revealed older age, steroid medication and comorbidities as risk factors for severe evolution, while the same study showed that the 29 IBD patients less 20 years had only mild disease courses. Factors associated with hospitalization included comorbid conditions other than IBD (50% hospitalized vs 12% not; p value <0.01), moderate/severe IBD disease activity (64% vs 15%; p value <0.01 overall), gastrointestinal symptoms (71% vs 19%, p value <0.01), sulfasalazine/mesalamine use (57% vs 21%; p value 0.01), and steroid use (29% vs 8%, p value 0.03). The six-year-old colitis patient requiring ICU care in this series is in line with the recent reports of multi-systemic inflammatory (Kawasaki-like) syndrome temporarily related to SARS-CoV-2 infection in children. doi = 10.1016/j.cgh.2020.10.010 id = cord-267260-8l831mre author = Brenner, Erica J. title = Corticosteroids, but not TNF Antagonists, are Associated with Adverse COVID-19 Outcomes in Patients With Inflammatory Bowel Diseases: Results from an International Registry date = 2020-05-18 keywords = IBD; covid-19 summary = Risk factors for severe COVID-19 among IBD patients included increasing age (adjusted odds ratio [aOR] 1.04, 95% CI 1.01-1.02), ≥2 comorbidities (aOR 2.9, 95% CI 1.1-7.8), systemic corticosteroids (aOR 6.9, 95% CI 2.3-20.5), and sulfasalazine or 5-aminosalicylate use (aOR 3.1, 95% CI 1.3-7.7). To understand the impact of IBD on case fatality, we computed expected and observed deaths and age-standardized mortality ratios (SMR) utilizing published agestratified COVID-19 case fatality rates from China and Italy 2, 23 and publically available data from the U.S. 24, 25 Multivariable logistic regression estimated the independent effects of age, sex, disease (CD vs UC/IBD-U), disease activity, smoking, BMI ≥30, and number of comorbidities (0, 1, ≥2) on the primary outcome of severe COVID-19, defined as a composite of ICU admission, ventilator use, and/or death, consistent with existing COVID-19 literature. In our exploratory analyses, we found that TNF antagonist combination therapy, compared to monotherapy, was positively associated with the outcome of hospitalization or death (aOR 5.0, 95% CI 2.0-12.3), after adjusting for clinical and demographic variables and use of systemic corticosteroids and 5-ASA/sulfasalazine. doi = 10.1053/j.gastro.2020.05.032 id = cord-306859-aqfgl9cm author = Clough, Jennie N title = Managing an IBD Infusion Unit During the COVID-19 Pandemic: Service Modifications and the Patient Perspective date = 2020-06-27 keywords = IBD summary = title: Managing an IBD Infusion Unit During the COVID-19 Pandemic: Service Modifications and the Patient Perspective The COVID-19 pandemic has posed significant challenges to the provision of inflammatory bowel disease (IBD) unit infusion services in terms of the redeployment of specialist staff and reduced capacity because of social distancing. Given the recommendation for patients to remain on their usual biologic medication wherever possible, 1 we modified our service to ensure that our patients were adequately protected on the unit and surveyed attenders regarding their views and concerns. Patients were telephoned 24 hours before their infusion to screen for COVID-19 symptoms and were advised to attend the unit unaccompanied. In addition, 25.2% of patients felt "very" or "somewhat uncomfortable" at the prospect of attending hospital for their usual infusion, but 80.2% felt on attending that the measures taken to reduce the risk of contact with COVID-19 were "completely adequate." doi = 10.1093/ibd/izaa171 id = cord-322957-clf8f90t author = Crespo, Javier title = Resumption of activity in gastroenterology departments. Recommendations by SEPD, AEEH, GETECCU and AEG date = 2020-04-28 keywords = COVID-19; CoV-2; IBD; SARS; patient summary = The general objectives of these recommendations include: • To protect our patients against the risks of infection with SARS-CoV-2 and to provide them with high-quality care. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. These recommendations are based on the sparse, changing evidence available, and will be updated in the future according to daily needs and the availability of expendable materials to suit them; in each department they will be implemented depending upon the cumulative incidence of SARS-CoV-2 infection in each region, and the burden the pandemic has represented for each hospital. doi = 10.1016/j.gastre.2020.04.001 id = cord-287885-1jwwmoys author = D''Amico, Ferdinando title = Views of patients with inflammatory bowel disease on the COVID-19 pandemic: a global survey date = 2020-05-13 keywords = IBD summary = title: Views of patients with inflammatory bowel disease on the COVID-19 pandemic: a global survey Therefore, we did an anonymous web survey with the support of the European Federation of Crohn''s and Ulcerative Colitis Associations (EFCCA) between March 30 and April 16, 2020, to investigate the concerns, fears, and behaviours of patients with IBD during the early phase of the COVID-19 pandemic. The European Crohn''s and Colitis Organisation, the British Society of Gastroenterology, and the International Organization for the Study of Inflammatory Bowel Diseases have responded to this request, providing practical guidelines for the management of patients with IBD during the pandemic, focusing not only on drug treatment but also on advice for daily life (eg, social distancing, use of masks, and travel avoidance). Prevention of COVID-19 in patients with inflammatory bowel disease in Wuhan, China British Society of Gastroenterology guidance for management of inflammatory bowel disease during the COVID-19 pandemic doi = 10.1016/s2468-1253(20)30151-5 id = cord-290750-85731og8 author = Danese, Silvio title = Management of IBD during the COVID-19 outbreak: resetting clinical priorities date = 2020-03-25 keywords = IBD; patient summary = Because of the very high transmission capacity, the WHO declared the outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection a public health emergency of international concern. Additional recommendations for patients with IBD from the IOIBD: • Medicines such as mesalamine are safe • If possible, withdraw from steroid use • Biologic agents used to treat IBD (e.g. anti-TNF agents, ustekinumab and vedolizumab) are generally safe; there are no recommendations to stop taking these medications and the effects of these drugs are present for many months • Thiopurines and tofacitinib tend to inhibit the immune response to viral infections, but stopping these agents in the short-term will not help • Get the influenza vaccination • Stay at home and minimize social contact c | Strategies to enable maintenance of our biologic agent clinic during the COVID-19 outbreak in Italy include checkpoints at hospital entrances for symptom screening and use of surgical masks for clinical staff and patients. doi = 10.1038/s41575-020-0294-8 id = cord-297768-tjqpiyp1 author = Day, Alice S. title = Practical guidance for dietary management of patients with inflammatory bowel disease during the SARS-CoV2 pandemic date = 2020-07-20 keywords = IBD summary = Coronavirus disease (COVID-19) has resulted in considerable morbidity and mortality along with major disruption to global financial markets and social function with mandated social isolation precautions in many countries. 6, 7 It must 55 be acknowledged that it is unlikely any high quality evidence will allow timely production of 56 guidelines specific for IBD patients during the COVID-19 pandemic, so observational data 57 and anecdotal lessons learned from the first countries affected by the novel coronavirus are 58 providing direction for the rest of the world. 2 59 60 Despite reassuring registry data and published guidelines, many patients with IBD and their 61 treating clinicians alike may be reticent to persist with immunosuppressive therapy in the 62 setting of the COVID-19 pandemic. 8 Moreover, EEN has been shown to delay or avoid IBD surgery, 70 which is critical at a time when hospitalization increases risk of COVID-19 exposure as well 71 as in the setting of stretched health care resources. doi = 10.1016/j.jand.2020.07.019 id = cord-280023-r3qgdgeu author = Dipasquale, Valeria title = Challenges in paediatric inflammatory bowel diseases in the COVID-19 time date = 2020-04-08 keywords = IBD summary = The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first reported in China in December 2019, now involves the whole world [1 , 2] . Currently no cases of IBD patients infected by SARS-CoV-2 have been reported. As the risk of infections is generally higher in case of combination therapy (biologics plus immunomodulators) in adult and paediatric patients with IBD [6 , 7] , caution should be used with this therapeutic strategy during the COVID-19 epidemic. In conclusion, while waiting for more specific data concerning the risk of COVID-19 in children with IBD and, more generally, in paediatric patients on immunosuppressive therapy, it seems reasonable to carefully weigh the risks/benefits ratio of treatment with immunomodulators and biologics, especially in areas of high infection rate or outbreaks. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China doi = 10.1016/j.dld.2020.03.015 id = cord-285238-bpk3xl8x author = Dong, Xiuli title = Intestinal and Peripheral Fibrinogen-Like Protein 2 Expression in Inflammatory Bowel Disease date = 2013-11-28 keywords = FGL2; IBD summary = AIM: The purpose of this work was to investigate intestinal and peripheral expression of FGL2 in patients with inflammatory bowel disease (IBD), mainly ulcerative colitis (UC) and Crohn''s disease (CD). Correlations of FGL2 expression with disease type, activity, and location, and with measured laboratory data, including C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), were examined. However, our study demonstrated that intestinal and peripheral expression of FGL2 was significantly higher in UC and CD patients with active disease, and decreased in inactive disease. Reduced FGL2 expression in patients with inactive disease may be because successful treatment, including immune modifiers, anti-TNF-a therapy, and other anti-inflammatory treatment, made up for the deficiency of Treg cells, or reversed the deficiency to exert sufficient suppression against other subsets of T lymphocytes through multiple other suppression molecules. doi = 10.1007/s10620-013-2962-9 id = cord-258930-60yn4hg7 author = D’Amico, Ferdinando title = Inflammatory bowel diseases and COVID-19: the invisible enemy date = 2020-04-16 keywords = IBD; patient summary = All biological and immunosuppressive treatments were discontinued, visits in person were replaced by online consultations, and 318 patients were daily recommended to wash their hands frequently, to reduce the time spent outside the home and to use masks outside the home 7 . It is important to underline that a relevant percentage of evaluated patients had risk factors of infection: chronic diseases (15.4%), immunosuppressive agent therapy (11.0%), elderly (10.4%), high-risk professional categories (7.5%), and biological therapy (6.3%) 7 . Telemedicine has also been associated with a reduction in gastroenterological consultations and hospitalizations and could be a valid alternative to improve the quality of IBD patient care during the COVID-19 outbreak 23 . Comparative Risk of Serious Infections With Biologic and/or Immunosuppressive Therapy in Patients With Inflammatory Bowel Diseases: A Systematic Review and Meta-Analysis Protection of 318 inflammatory bowel disease patients from the outbreak and rapid spread of COVID-19 infection in Wuhan doi = 10.1053/j.gastro.2020.04.032 id = cord-275447-nx45kwn6 author = Ehrenpreis, Eli D. title = Rapid Review: Nonsteroidal Anti-inflammatory Agents and Aminosalicylates in COVID-19 Infections date = 2020-06-10 keywords = COVID-19; IBD summary = Since 5-ASAs are a mainstay treatment for inflammatory bowel disease, the authors review the pharmacology of both classes of drugs and discuss the potential relevance of 5-ASAs in the ongoing discussion of medication use in patients infected with COVID-19. T here has been recent controversy regarding the risk that ibuprofen (and possibly other nonsteroidal antiinflammatory drugs, NSAIDs) may worsen the clinical course of patients that are infected with COVID-19. It is therefore the purpose of this brief review to inform practitioners treating patients with 5-ASAs about the potential relationships between 5-ASAs and NSAIDs. At the time of this writing, both the World Health Organization (WHO) and the Food and Drug Administration (FDA) have not recommended the avoidance of ibuprofen in patients with known or suspected COVID-19 infections. doi = 10.1097/mcg.0000000000001371 id = cord-263419-qeo6qn0d author = Fiorino, Gionata title = Protecting patients with IBD during the COVID-19 pandemic date = 2020-05-20 keywords = IBD summary = An and colleagues stopped biologics (infliximab infusions) and immunosuppressive treatments for all patients with IBD. Indeed, a systematic review 4 showed that the risk of hospital admission (odds ratio 0·48, 95% CI 0·29-0·80) and surgery (0·67, 0·46-0·97) is significantly reduced by use of biologics for patients with IBD. The probability of relapse after stopping effective immunomodulators or biological therapy is about 50% and is associated with an increased need for steroids, and risk of hospital admission and surgery. Thus, the risk and benefits of continuing or stopping biologics should be carefully balanced and should not be assumed to be a general rule for all patients with IBD, especially given the length of time the pandemic is likely to last. Prevention of COVID-19 in patients with inflammatory bowel disease in Wuhan, China Systematic review of effects of withdrawal of immunomodulators or biologic agents from patients with inflammatory bowel disease doi = 10.1016/s2468-1253(20)30152-7 id = cord-312663-hhd5f823 author = Fiorino, Gionata title = Inflammatory Bowel Disease Care in the COVID-19 Pandemic Era: The Humanitas, Milan, Experience date = 2020-03-24 keywords = IBD; SARS summary = The outbreak of the COVID-19 caused by coronavirus SARS-CoV2, is rapidly spreading worldwide. IBD patients are severely worried about the impact of their disease and medications on the risk and the prognosis of COVID-19, and many of them are forced to come to hospital because of active disease, complications and drug administration. Patients scheduled for a follow-up visit are required to stay at home and to complete a questionnaire about IBD symptoms and quality of life, together with their routine laboratory tests, to the nurse and the dedicated doctor, who give recommendations and information about therapy and follow-up procedures. Based on the assumption that the risk of coronavirus infection is not different between the general population and IBD patients, but that IBD flares are difficult to manage in this situation, we advise all patients to continue their therapies, especially if in remission. doi = 10.1093/ecco-jcc/jjaa058 id = cord-269835-mz7i66qp author = Furfaro, Federica title = SFED recommendations for IBD endoscopy during COVID-19 pandemic: Italian and French experience date = 2020-06-11 keywords = COVID-19; Crohn; IBD; SARS; patient summary = The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has required a complete change in the management of patients with inflammatory bowel disease (IBD) who need to undergo endoscopic procedures. In particular, recommendations regarding the use of personal protective equipment to prevent COVID-19 transmission, both for patients and health-care professionals, are proposed and different scenarios in endoscopic IBD management are evaluated to suggest when endoscopy could be rescheduled and replaced by alternative biomarkers. The panel of experts con sidered possible aerosolization during colonoscopy, in particular during the insertion and removal of instruments through the biopsy channel and the presence of the virus in the stool and advised on the use of N95 masks for lower gastrointestinal procedures as a precautionary measure to protect the endoscopist from the risk of possible COVID-19 transmission from the patient if infected by SARS-CoV-2 (ref. doi = 10.1038/s41575-020-0319-3 id = cord-300963-1n1f8mf2 author = Gajendran, Mahesh title = Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date = 2020-10-12 keywords = COVID-19; IBD; RNA; SARS; patient summary = Previous studies based on SARS-CoV-1 showed that the "cytokine storm" was strongly associated with viral sepsis, inflammation-induced lung injury, and acute respiratory distress syndrome (ARDS) [32, 34] . With regard to IBD-specific risk factors, it is speculated that patients on immunosuppressive agents, those with active IBD symptoms, malnutrition, and frequent visits to clinics or hospitals are at greater risk of acquiring SARS-CoV-2 infection [50] . The International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) maintains a registry for reporting COVID-19 in IBD patients called SECURE-IBD registry. Hence, all the societies have recommended that patients continue their IBD medications to sustain remission, because the risk of disease flare-up outweighs the chance of contracting SARS-CoV-2 infection. The management strategy will depend on multiple factors, such as the patient''s age, the severity of the COVID-19 infection, the clinical status of the IBD, and the presence of other comorbid conditions. doi = 10.20524/aog.2020.0547 id = cord-306325-9alfvda1 author = Galmozzi, E. title = Letter: does the IFNL4 gene discovery really provide a causal role for the IL28B haplotype blocks? date = 2014-02-04 keywords = IBD summary = 1 The authors have evaluated and discussed current evidence regarding the roles of vitamin D deficiency in the pathogenesis and progression of inflammatory bowel disease (IBD). [4] [5] [6] It is therefore interesting that vitamin D deficiency has been shown to play a role in both psychological 7 and sleep disorders 8 in non-IBD populations, although the underlying mechanisms are still unknown. There is no study till now evaluating the effects of vitamin D deficiency on psychological health or sleep quality in IBD patients. Although several factors can affect psycho-logical health and sleep quality in IBD patients including demographic-and disease-related factors, 2, 4 a role for vitamin D deficiency is also plausible. 1, 2 We agree that our study does not provide insights on the causal relationship between IFNL4 and treatment response in patients with chronic hepatitis C virus (HCV) infection. doi = 10.1111/apt.12615 id = cord-285426-iyl12ber author = Ghavami, Shaghayegh Baradaran title = IBD Patients Could Be Silent Carriers for Novel Coronavirus and Less Prone to its Severe Adverse Events: True or False? date = 2020-09-08 keywords = IBD; SARS summary = Interestingly, in the recent pandemic of coronavirus disease (COVID19) , and the SARS-CoV epidemic in 2003, while the fecal samples of these patients were positive for the virus, they did not present any severe respiratory distress syndrome (4). Remarkably, the angiotensin-converting enzyme-2 (ACE2) is the receptor for SARS-CoV-2 and it is expressed in different organs including the lungs, testis and ileum. showed that when rheumatoid arthritis patients were treated with anti-TNF-α biologicals (infliximab, adalimumab, and certolizumab pegol), the expression of IFN-α-regulated genes was increased in the peripheral blood mononuclear cell (PBMC) compared to the control group. Besides, in IBD patients, particularly those who are under anti-TNF-α treatment, the host innate immune system interferes more efficiently with viral replication cycle and the clinical presentations are more moderate (9, 12) . Are patients with inflammatory bowel disease at increased risk for Covid-19 infection? doi = 10.22074/cellj.2020.7603 id = cord-256143-9u5a0jqz author = Grassia, Roberto title = Inflammatory Bowel Diseases and Biological Treatment in SARS-CoV-2 Era. Why Not? date = 2020-05-09 keywords = IBD summary = title: Inflammatory Bowel Diseases and Biological Treatment in SARS-CoV-2 Era. Why Not? 1 In this setting, the initial indication from the inflammatory bowel disease (IBD) center in Wuhan was to discontinue all biological and immunosuppressive treatments. 3 In an Italian observational study, among 522 IBD patients (89% adults), 16% under biological therapy, none was hospitalized for COVID-19. Further studies are needed to investigate if IBD patients under biological treatment could be protected against the COVID-19 pneumonia, whereas those under immunosuppressive therapy (ie, thiopurines) could remain at higher risk of developing the disease due to the different mechanism of action. Protection of 318 Inflammatory Bowel Disease Patients from the Outbreak and Rapid Spread of COVID-19 Infection in Wuhan Uneventful course in IBD patients during SARS-CoV-2 outbreak in northern Italy Are patients with inflammatory bowel disease at increased risk for Covid-19 infection? doi = 10.1093/ibd/izaa110 id = cord-266648-962r0vm8 author = Grossberg, Laurie B title = Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic date = 2020-07-03 keywords = COVID-19; IBD; SARS summary = title: Review of Societal Recommendations Regarding Management of Patients With Inflammatory Bowel Disease During the SARS-CoV-2 Pandemic Although data in patients with IBD contracting COVID-19 are still limited, both providers and patients have particular concerns regarding the risk of infection with SARS-CoV-2 and how to manage their medications during the COVID-19 pandemic. Information regarding risk factors, prevention, routine care (including office visits, testing, endoscopy, and surgery), and medication management of patients with IBD in the setting of COVID-19 was collected from each reference and is summarized in the Results. 10, 11 Other organizations, including the American Gastroenterological Association doi: 10.1093/ibd/izaa174 Published online 3 July 2020 (AGA), the Gastroenterological Society of Australia, and the European Crohn''s and Colitis Organisation (ECCO), agree that there are no data to support an increased risk of infection among patients with IBD. doi = 10.1093/ibd/izaa174 id = cord-255930-2bobmkvu author = Kaplan, Gilaad G. title = The four epidemiological stages in the global evolution of inflammatory bowel disease date = 2020-10-08 keywords = Crohn; IBD; Incidence; prevalence; western summary = Inflammatory bowel disease (IBD) is a global disease; its evolution can be stratified into four epidemiological stages: Emergence, Acceleration in Incidence, Compounding Prevalence and Prevalence Equilibrium. Western regions will eventually transition to the Prevalence Equilibrium stage, in which the accelerating prevalence levels off as the IBD population ages and possibly as a result of an unexpected rise in mortality during the COVID-19 pandemic. The evolution of IBD occurs within Omran''s Degenerative and Human-Influenced Diseases age and has occurred across three distinct epidemiological stages ( Fig. 1) : Emergence, Acceleration in Incidence and Compounding Prevalence. In the meantime, developing, newly industrialized regions and countries of the Western world all need to innovate their current health-care delivery to address the evolving demographics of their IBD populations as they transition across epidemiological stages. doi = 10.1038/s41575-020-00360-x id = cord-316354-pix0hmpj author = Kennedy, Nicholas A title = Organisational changes and challenges for inflammatory bowel disease services in the UK during the COVID-19 pandemic date = 2020-06-15 keywords = COVID-19; IBD; IQR summary = ► Essential services for inflammatory bowel disease (IBD) patients including outpatient care, advice lines, endoscopy and infusion units may be affected. The number of whole-time equivalent gastroenterologists and IBD nurses providing elective outpatient care decreased significantly between baseline (median 4, IQR 4-7.5 and median 3, IQR 2-4) to the point of survey (median 2, IQR 1-4.8 and median 2, IQR 1-3) in the 6-week period following the onset of the COVID-19 pandemic (p<0.001 for both comparisons). The number of whole-time equivalent gastroenterologists and IBD nurses providing elective outpatient care decreased significantly between baseline (median 4, IQR 4-7.5 and median 3, IQR 2-4) to the point of survey (median 2, IQR 1-4.8 and median 2, IQR 1-3) in the 6-week period following the onset of the COVID-19 pandemic (p<0.001 for both comparisons). doi = 10.1136/flgastro-2020-101520 id = cord-337896-mct29erg author = Kornbluth, Asher title = Management of Inflammatory Bowel Disease and COVID-19 in New York City 2020: The Epicenter of IBD in the First Epicenter of the Global Pandemic date = 2020-09-03 keywords = COVID-19; IBD; NYC; SARS; patient summary = A number of the major GI societies, the Crohn''s & Colitis Foundation, 3 British Society of Gastroenterology, 4 European Crohn''s and Colitis Organization, 5 The American Gastroenterology Association, 6 and the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) 7 have published guidelines regarding treating the IBD patient with SARS-CoV-2 and COVID-19. 8 The key features are that the patient without proven or suspected SARS-CoV-2 should continue on their current medications with aggressive attempts to reduce steroid usage because this is the only single agent that has been associated with increased poor outcomes with COVID-19, defined in the SECURE registry as a composite score of hospitalization, intubation, or death. 14 We are now participating in the development of a database that will follow patients after clearance of the SARS-CoV-2 virus to determine the courses and outcomes of the IBD and of any sequelae or recurrence of COVID-19 after any drug therapy has been suspended. doi = 10.1093/ibd/izaa212 id = cord-286912-cww4ha3j author = Manolakis, Anastassios C title = α2-Heremans-schmid glycoprotein (fetuin A) downregulation and its utility in inflammatory bowel disease date = 2017-01-21 keywords = AHSG; IBD summary = METHODS: AHSG serum levels were determined in treatment-naïve newly-diagnosed patients, 96 with ulcerative colitis (UC), 84 with Crohn''s disease (CD), 62 with diarrhea-predominant or mixed irritable bowel syndrome (IBS, Dand Mtypes) and 180 healthy controls (HC), by an enzyme linked immunosorbent assay (ELISA). Low levels of AHSG have been recorded in patients on hemodialysis, those with cirrhosis, hepatoma or rheumatoid arthritis (RA), an entity sharing common inflammatory pathways with IBD, and have been linked to vascular -excessive valvular and coronary artery calcification, ischemic events-and skeletal disorders -osteopenia [14, 17, 18] . In order to perform additional testing of the link between lower AHSG levels and complicated disease behavior, logistic regression was applied, while considering penetrating or stricturing CD, as dependent, and AHSG concentrations, in quartiles -lowest, low, high, highest -as independent variables. After multivariate analysis -also considering age, sex, activity, duration, smoking status-the inverse association between AHSG and need for anti-TNFα therapy or surgery remained statistically significant (partial correlation coefficients: -0.33 and -0.41, respectively -P < 0.05, in both cases). doi = 10.3748/wjg.v23.i3.437 id = cord-312374-gu9tq48n author = Martin Arranz, Eduardo title = Management of COVID-19 Pandemic in Spanish Inflammatory Bowel Disease Units: Results From a National Survey date = 2020-06-04 keywords = COVID-19; IBD summary = The survey included items in 5 sections asking about the structure of IBD units, structural changes adopted because of the current pandemic, recommendations regarding immunosuppressive and biologic treatments during the SARS-CoV-2 pandemic, adopted measures regarding suspected COVID-19 in patients with IBD, and management of patients with IBD with confirmed COVID-19. During the COVID-19 crisis, 100% of hospitals surveyed have cancelled elective onsite consultation and changed to phone assistance, 40% have also attended patients via e-mail, and 13% have used social media to inform patients about the latest updates regarding IBD and SARS-CoV-2. The COVID-19 pandemic has severely affected Spain, with 205,905 cases confirmed by polymerase chain reaction and 22,902 deaths registered up to April 24, 2020, and has forced all hospitals to change their clinical practice, suspending all ambulatory procedures to minimize the risk of infection and relocating doctors and nurses to attend COVID-19 patients. doi = 10.1093/ibd/izaa142 id = cord-032753-icteg34y author = Namai, Fu title = Microbial therapeutics for acute colitis based on genetically modified Lactococcus lactis hypersecreting IL-1Ra in mice date = 2020-09-28 keywords = Fig; IBD; IL-1 summary = Oral administration of these gmLAB suppressed body weight reduction and exacerbation of the disease activity index score in mice with acute colitis and decreased the number of CD4(+) IL-17A(+) cells in the mesenteric lymph nodes. HE staining of colon sections removed on the last day revealed a decrease in immune cell infiltration in the NZ-IL1Ra administration group and a significant decrease in the total mucosal tissue area (Fig. 5e-g) . Production of IL-2 by EL4.NOB-1 cells stimulated with IL-1β was suppressed by increasing the concentration of rmIL-1Ra purified from NZ-IL1Ra supernatant, commercially available mIL-1Ra, or hIL-1Ra. These results indicate that rmIL-1Ra produced by gmLAB can play an effective role as an endogenous antagonist of IL-1. In conclusion, we successfully constructed gmLAB that hypersecrete bioactive mIL-1Ra. Oral administration of NZ-IL1Ra to acute colitis mice alleviated colitis symptoms and suppressed excessive immune reactions in the intestinal tract and MLNs. These results suggest that rmIL-1Ra reaches the colon via NZ-IL1Ra and inhibits IL-1 signaling. doi = 10.1038/s12276-020-00507-5 id = cord-017342-qsfykh1k author = Nedelsky, Natalia B. title = Inflammatory Bowel Disease at the Intersection of Autophagy and Immunity: Insights from Human Genetics date = 2013-06-21 keywords = ATG16L1; ATG8; Crohn; IBD; IRGM; autophagy summary = Although historically considered to be a relatively nonselective process of degradation of cytosolic contents, autophagy has recently been revealed to have several selective and immune-specific functions that are relevant to the maintenance of intestinal homeostasis, including xenophagy, mitophagy, antigen presentation, secretion, and inflammasome regulation. We summarize the basic molecular events underlying general and selective autophagy and present evidence suggesting possible pathogenic mechanisms revealed by studies of IBD-associated risk alleles of ATG16L1 and IRGM. As mentioned above, autophagy has been implicated in several immune-related processes that infl uence IBD pathogenesis, including xenophagy, mitophagy, antigen presentation, secretion and vesicular traffi cking, and cytokine-based regulation of infl ammasome activity. In epithelial cells, bacteria become ubiquitinated and targeted for autophagic degradation in a process that requires the CD-associated genes ATG16L1 and IRGM appears to have different effects on these functions depending on the cell type examined [ 42 , 67 ] . doi = 10.1007/978-1-4614-8256-7_12 id = cord-349500-603v8lfb author = Neurath, Markus F title = Covid-19 and immunomodulation in IBD date = 2020-04-16 keywords = ACE2; IBD; SARS; covid-19; patient summary = Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Although covid-19 leads to little or mild flu-like symptoms in the majority of affected patients, the disease may cause severe, frequently lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infects ACE2 expressing epithelial cells in the lung and/or the intestine. The covid-19 receptor ACE2 is particularly highly expressed in intestinal epithelial cells from the terminal ileum and to a lesser extent in the colon, where mucosal inflammation in patients with IBD (Crohn''s disease (CD); UC) is frequently detected. doi = 10.1136/gutjnl-2020-321269 id = cord-259585-mjtxiu0t author = Occhipinti, Vincenzo title = Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a “Red Zone” Area in Northern Italy date = 2020-04-21 keywords = IBD; SARS; patient summary = Every possible effort was made to quickly increase the capacity of intensive care units (ICUs) to accommodate the alarming numbers of very sick CoViD-19 patients, including constructing new units in unused areas of the hospital or converting surgical rooms into ICUs. These drastic measures were implemented in a very short period of time, and although necessary to counteract the devastation brought about by the outbreak, they also posed tremendous challenges to the care of patients with GI conditions, including those with inflammatory bowel diseases (IBD). However, for patients on biologic therapies, we have implemented a mandatory phone call-in the day before any planned hospital visit to screen for possible CoViD-19 symptoms or contact with infected individuals and to reassure patients that all possible precautions are being taken by the IBD center to reduce the risk of infection. doi = 10.1093/ibd/izaa084 id = cord-331703-4hwmajt3 author = Occhipinti, Vincenzo title = Impact of COVID-19 outbreak on the management of patients with severe IBD: a domino effect date = 2020-05-12 keywords = IBD summary = The International Organization for the study of Inflammatory Bowel Diseases (IOIBD) recently published on Gastroenterology a consensus 1 about the management of IBD patients during the coronavirus disease 19 (COVID-19) pandemic, addressing several topics of interest such as the risk of infection in IBD patients, how to manage therapies and how to safely provide continuity of biological therapy. Thus, we decided to transfer the patient to a COVID-free hospital with IBD-specialized gastroenterologists and surgeons (Rho Hospital, in the Northern area of Milan) for further management. This case clearly highlights some unanticipated difficulties in providing adequate care to patients with severe IBD in a high-prevalence area of COVID-19. Management of Patients with Crohn''s Disease and Ulcerative Colitis During the COVID-19 Pandemic: Results of an International Meeting Challenges in the Care of IBD Patients During the CoViD-19 Pandemic: Report From a "Red Zone" Area in Northern Italy doi = 10.1053/j.gastro.2020.05.027 id = cord-026025-xqj877en author = PETRAS, ROBERT E. title = Large Intestine (Colon) date = 2009-10-30 keywords = Crohn; Fig; Hirschsprung; IBD; Jeghers; Lynch; MSI; carcinoma; cell; colitis; colon; colorectal; disease; dna; dysplasia; patient; polyp summary = 27, 28 These guidelines consider colonoscopic polypectomy definitive treatment for a patient with a malignant polyp if the following criteria are fulfilled: (1) the polyp is considered completely excised at endoscopy, (2) the specimen is properly processed by the pathology laboratory, (3) the cancer is not poorly differentiated, (4) no histologic evidence of vascular or lymphatic involvement exists, and (5) the resection margin is not involved by carcinoma. Pathologic features of colorectal cancer that suggest MSI/Lynch''s syndrome include right-sided location, synchronous or metachronous large bowel cancers, large and bulky polypoid tumors with circumscribed pushing margins, tumors showing prominent lymphoid infiltrate, and cancers of poor differentiation (medullary or undifferentiated carcinoma) or mucinous and signet ring cell histologic pattern (Figs. [352] [353] [354] [355] The trauma-type histologic features can be seen in the solitary rectal ulcer syndrome, localized colitis cystica profunda, inflammatory cloacogenic polyp, the mucosa adjacent to orifices of colonic diverticula, 356 and inflammatory cap polyposis 357 and are frequent findings adjacent to neoplasia and in the vicinity of the ileocecal valve. doi = 10.1016/b978-1-4160-3966-2.00023-0 id = cord-253001-xmcwuuk4 author = Papa, Alfredo title = Epidemiology and the Impact of Therapies on the Outcome of COVID-19 in Patients With Inflammatory Bowel Disease date = 2020-08-19 keywords = IBD summary = A retrospective study from the United States including a large cohort of patients with IBD reported that the use of antitumor necrosis factor (TNF)-a agents or thiopurines was not associated with an increased risk of developing COVID-19 (9) . In the Surveillance Epidemiology of Coronavirus Under Research Exclusion-IBD database, we found evidence of greater prevalence of milder COVID-19 cases in patients treated with anti-TNF-a than that in patients undergoing steroid treatments (3) . Further support to this theory comes from the results of the Italian Group for the Study of Inflammatory Bowel Disease study, which reported a 60% reduction in mortality among patients receiving anti-TNF-a antibodies (although not statistically significant); however, corticosteroid use was associated, with a trend toward statistical significance, with COVID-19-related pneumonia (P 5 0.05) and death (P 5 0.064) (4). Furthermore, anti-TNF-a agents could achieve effective control of inflammatory mediators, which makeup the "cytokine storm" that occurs in severe COVID-19-related pneumonia, thereby mitigating the course of the disease. doi = 10.14309/ajg.0000000000000830 id = cord-317151-cxx5pcln author = Papa, Alfredo title = Covid-19 and the management of patients with inflammatory bowel disease: a practical decalogue for the post-pandemic phase date = 2020-10-24 keywords = COVID-19; IBD; SARS; patient summary = 14 Since the beginning of the pandemic, the World Health Organization has provided general recommendations for the prevention of They include: to wash hands frequently and properly with soap or alcohol-based sanitizer, to maintain social distancing (at least 1 m of distance), to avoid touching eyes, nose and mouth, to cover mouth and nose when coughing or sneezing, to seek medical care early when fever, cough or difficulty in breathing are recorded, to wear personal protective equipment (PPE), in particular the facial mask when social distancing is not possible to maintain or in closed places, to stay informed and follow any advice provided by own healthcare providers. This may require further changes in the planning of healthcare activities, both by using different prioritization criteria for outpatient visits, diagnostic tests and surgical interventions and by continuing to use treatment strategies that have worked well during the pandemic such as telemedicine, psychological support to patients and the educational function of patient associations (Table 1) . doi = 10.1177/1756284820968747 id = cord-337204-14gxpeaf author = Piciucchi, Matteo title = Preliminary considerations regarding the risk of COVID-19 and disease severity in chronic gastrointestinal conditions date = 2020-05-25 keywords = COVID-19; IBD summary = Since the discovery of SARS-CoV-2 at the end of 2019, several studies of the epidemiology, risk factors, clinical findings, therapy and virological features of this infection have become available and are totally free to clinicians via a PubMed search [1, 2] . In particular, several risk factors that are involved in acquiring the infection and that affect the clinical course and severity of COVID-19related diseases have been identified (Figure 1 ), but conclusive data are still lacking [2, 4] . As far as inflammatory bowel disease (IBD) is concerned, there are no data to suggest a higher risk of SARS-CoV-2 infection or a higher severity of related diseases in these patients, compared to the general population. More specifically, prospective studies to analyze the risk of the infection and its possible course in patients with IBD, pancreatitis and liver diseases are needed in order to improve care for these patients. doi = 10.20524/aog.2020.0498 id = cord-343832-xg3swuzs author = Pugliese, Daniela title = The management of Inflammatory Bowel Diseases in the era of COVID-19 pandemic: when “non-urgent” does not mean “deferrable” date = 2020-06-18 keywords = IBD; patient summary = authors: Pugliese, Daniela; Papi, Claudio; Privitera, Giuseppe; Aratari, Annalisa; Festa, Stefano; Armuzzi, Alessandro Accordingly, Inflammatory Bowel Disease (IBD) Units throughout the country had to re-organize their own agenda, limiting the accesses to 3 categories of outpatients: 1) patients undergoing biological therapies, for whom the risk of disease relapse is considered more worrying than the risk of COVID-19 infection; 2) patients enrolled in clinical trials in order to guarantee the prosecution of therapies and 3) patients complaining of acute symptoms, not manageable with telemedicine. 1-2 Examples of "non deferrable" visits are for patients complaining of moderate-to-severe IBD symptoms, new onset/relapse of extra-intestinal manifestations, active perianal disease or sub-acute obstruction symptoms requiring surgery. 4 Accordingly, highly suspect CD patients should be promptly investigated in order to start early and effective treatment strategies, aimed to impact the long-term clinical course and to reduce the risk of complications. doi = 10.1016/j.dld.2020.05.053 id = cord-027386-23exaaik author = Rao, Vishwas title = A Machine-Learning-Based Importance Sampling Method to Compute Rare Event Probabilities date = 2020-05-25 keywords = IBD; bayesian summary = title: A Machine-Learning-Based Importance Sampling Method to Compute Rare Event Probabilities We develop a novel computational method for evaluating the extreme excursion probabilities arising from random initialization of nonlinear dynamical systems. The method uses excursion probability theory to formulate a sequence of Bayesian inverse problems that, when solved, yields the biasing distribution. To alleviate the computational cost, we build machine-learning-based surrogates to solve the Bayesian inverse problems that give rise to the biasing distribution. The most commonly used method to determine the probability of rare and extreme events is Monte Carlo simulation (MCS). In this paper, we build on our recent algorithm [25] , which we used to construct an importance biasing distribution (IBD) to accelerate the computation of extreme event probabilities. IS, instead, uses problem-specific information to construct an IBD; computing the rare event probability using the IBD requires fewer samples. doi = 10.1007/978-3-030-50433-5_14 id = cord-269390-4yn8c34i author = Rimondi, Alessandro title = Fogging IBD Management: An Unusual Case of IBD Flare-up During the COVID-19 Outbreak date = 2020-07-28 keywords = IBD summary = We have read with interest the article by Occhipinti and Pastorelli, with particular reference to the management of inflammatory bowel diseases (IBD) relapse during the COVID-19 outbreak. 1 Diagnostic challenges may arise in the presence of symptoms that overlap between active IBD and COVID-19, and concerns about the use of immunosuppressive drugs, mainly corticosteroids, which potentially lead to an increased risk for infections. We hereby report on a representative case of how COVID-19 has redefined priorities and changed our clinical approach to active IBD patients. 3 Therefore, the differential diagnosis between IBD relapse and SARS-CoV-2 infection has possibly proved challenging at the peak of the COVID-19 outbreak. Ageusia, as reported by our patient, contributed to increase the suspicion of SARS-CoV-2 infection and made the differential diagnosis trickier. Challenges in the care of IBD patients during the CoViD-19 pandemic: report from a "Red Zone" area in Northern Italy doi = 10.1093/ibd/izaa184 id = cord-026792-jsqa4pmu author = Samanta, Jayanta title = 2019 Novel Coronavirus Infection: Gastrointestinal Manifestations date = 2020-05-16 keywords = IBD; SARS; covid-19 summary = The modern world is facing a major public health crisis due to novel corona virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) which has caused a pandemic involving at least 210 countries. The extrapulmonary effects and modes of transmission gained attention when the first confirmed case of SARS-CoV-2 reported from the United States had gastrointestinal (GI) complaints of nausea and vomiting followed later by diarrhea and patient''s fecal specimen tested positive on day 7 of illness. This review aims to comprehensively outline the GI manifestations of this virus, its potential to spread via the feco-oral route and its implications and an overview of management strategies for other GI diseases, such as inflammatory bowel disease (IBD) coexisting with coronavirus-19 disease (COVID-19) infection. doi = 10.1055/s-0040-1712077 id = cord-281275-i9920nvm author = Schlabitz, Franziska title = Inflammatory Bowel Disease and COVID-19—“Preventive” Sick Certificates as a Frequent Coping Strategy in the Face of the Pandemic date = 2020-06-12 keywords = IBD summary = title: Inflammatory Bowel Disease and COVID-19—"Preventive" Sick Certificates as a Frequent Coping Strategy in the Face of the Pandemic 1 The authors report their experiences and challenges in managing patients with inflammatory bowel disease (IBD) during the COVID-19 pandemic. We complement this important information by presenting a survey conducted among German patients with IBD regarding their personal evaluation of their work-related risk of contracting SARS-CoV-2. However, during the COVID-19 pandemic, the survey participants have used this coping strategy frequently. Clearly, the ability to work is very important to most patients with IBD. Therefore, straightforward recommendations stating clearly who is at risk and who should avoid which type of work are very important for managing the daily life of our patients. Niels Teich: acquisition of data, analysis, critical revision of the manuscript for important intellectual content. Challenges in the care of IBD patients during the CoViD-19 pandemic: report from a "Red Zone" area in Northern Italy doi = 10.1093/ibd/izaa155 id = cord-284234-9cd2v6bt author = Sebastian, S title = Safety of drugs during previous and current coronavirus pandemics: Lessons for IBD date = 2020-06-10 keywords = COVID-19; IBD; MERS; SARS summary = Understandable concerns have been raised on the safety of steroids, immunosuppressive drugs, and biologics used in patients for a variety of indications including immune mediated inflammatory disease such as inflammatory bowel diseases (IBD), which do increase the risk of opportunistic bacterial, viral and fungal infections (5) . Therefore, continuing concerns remain both from IBD patients and the A c c e p t e d M a n u s c r i p t clinicians managing them, regarding the potential of IBD related drugs causing more frequent infections by SARS-CoV2, and increased risk of severe complications from COVID-19 (13) . Corticosteroids are thought to have a divergent effect on viral infections including SARS COV viruses; on one hand they inhibit host immune response acting on migration and chemokines production leading to impaired viral clearance and the resultant prolonged Moreover, a prospective, randomized double-blinded, placebo-controlled trial compared early hydrocortisone treatment (before day seven of the illness) with a placebo and found that early hydrocortisone therapy was associated with a higher subsequent plasma viral load (61) . doi = 10.1093/ecco-jcc/jjaa120 id = cord-303942-77nbi3ws author = Segal, Jonathan P title = Prevention of COVID-19 in patients with IBD date = 2020-05-20 keywords = IBD summary = We read with interest the Correspondence from Ping An and colleagues 1 describing their efforts to prevent coronavirus disease 2019 in patients with inflammatory bowel disease (IBD) in Wuhan, China. Indeed, the National Health Service, in conjunction with the British Society of Gastroenterology (BSG), relied on individual health-care trusts to highlight patients at high risk with IBD so advice could be delivered by post regarding shielding and stringent physical distancing. BSG guidance suggests that patients should continue on their current medications, including infliximab, as active disease remains the biggest risk to a patient with IBD. As further evidence accumulates, our understanding of COVID-19-related risks in IBD populations globally will improve. Prevention of COVID-19 in patients with inflammatory bowel disease in Wuhan, China BSG COVID-19 Guidance on IBD patient risk groups British Society of Gastroenterology guidance for management of inflammatory bowel disease during the COVID-19 pandemic doi = 10.1016/s2468-1253(20)30153-9 id = cord-288439-srzysoqy author = Segal, Jonathan P. title = Mechanisms underpinning the efficacy of faecal microbiota transplantation in treating gastrointestinal disease date = 2020-09-03 keywords = CDI; IBD; clostridium; fmt; microbiota summary = Faecal microbiota transplantation (FMT) is currently a recommended therapy for recurrent/ refractory Clostridioides difficile infection (CDI). Faecal microbiota transplantation (FMT) is currently a recommended therapy for recurrent/ refractory Clostridioides difficile infection (CDI). Rodent studies supported the concept that restoration of bacterial bile-metabolising capacity to the gut microbiota was protective against CDI, 39 prompting interest into whether this could also be a mechanism of efficacy of FMT. difficile; administration of an FXR agonist in a mouse model of colitis resulted in significantly reduced colonic inflammation and a more intact intestinal barrier, 44 while microbially mediated production of particular secondary bile acids exhibit anti-inflammatory effects on intestinal epithelial cells 45 and have been recently recognised as promoting generation of peripheral regulatory T cells. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection doi = 10.1177/1756284820946904 id = cord-307769-rjseio5s author = Sim, Winnie H title = Expression profile of genes involved in pathogenesis of pediatric Crohn''s disease date = 2012-05-24 keywords = MMP2; gene; ibd; ssh summary = Methods: We used suppressive subtractive hybridization (SSH) and differential screening analysis to profile the mRNA expression patterns of children with CD and age‐ and sex‐matched controls without inflammatory bowel disease (IBD). The real-time RT-PCR results validated that genes represented by > 10 clones enriched by subtractive hybridization were expressed in higher abundance in CD as compared with non-IBD ileal biopsies. To contextualize our SSH findings, we compared our results with the data tables from seven microarray studies published previously, that had reported differential expression of genes between inflamed biopsies of CD and non-inflamed biopsies of non-IBD controls. The antigen presentation, inflammatory response and cancer gene network (Network 1) comprise one-third Figure 1 The relative expression levels of REG1A, MMP2 and ANPEP in ileal biopsies from 13 Crohn''s disease (CD) and nine non-inflammatory bowel disease (IBD) patients. Primers used for real-time reverse transcription polymerase chain reaction quantification of ANPEP, REG1A, MMP2 and RPL32 Table S2 Differentially expressed genes specific to Crohn''s Disease (CD) ileum. doi = 10.1111/j.1440-1746.2011.06973.x id = cord-021852-o0k2r0yo author = Simpson, Kenneth W. title = The Role of the Microbiota in Feline Inflammatory Bowel Disease date = 2015-12-04 keywords = IBD; cat summary = The only culture-independent study of the duodenal mucosal bacteria in cats to date employed FISH analysis to evaluate the numbers and types of bacteria associated with the duodenal mucosa and their relationship to clinical signs, histopathology, and mucosal cytokines. This study shows that changes in the number and type of mucosa-associated bacteria are related to the presence and severity of IBD in cats and raises the possibility that abnormal mucosal flora are involved in the etiopathogenesis of feline IBD. 13 For example, FISH analysis enabled the identification of invasive spiral bacteria in the ileum, colon, and regional lymph nodes of a cat with pyogranulomatous ileocolitis associated with recurrent episodes of fever and leukocytosis whose inflammatory process was considered sterile on the basis of histopathology (see Figure 10 -4C). doi = 10.1016/b978-0-323-22652-3.00010-4 id = cord-323553-bukm9m9q author = Song, Woo-Jin title = Canine adipose tissue-derived mesenchymal stem cells pre-treated with TNF-alpha enhance immunomodulatory effects in inflammatory bowel disease in mice date = 2019-08-31 keywords = IBD; TNF; TSG-6 summary = title: Canine adipose tissue-derived mesenchymal stem cells pre-treated with TNF-alpha enhance immunomodulatory effects in inflammatory bowel disease in mice Mesenchymal stem cells (MSCs), which release immunomodulatory factors such as tumor necrosis factor-α (TNF-α)-induced gene/protein 6 (TSG-6) and prostaglandin E2 (PGE2), have been suggested as an alternative therapeutic option for IBD treatment in veterinary medicine. (C) Canine adipose tissue-derived mesenchymal stem cells (cAT-MSCs) stimulated with TNF-α released higher concentrations of immunomodulatory factors such as TSG-6 and PGE2 compared to levels released by naive cAT-MSCs. Results are shown as the mean ± standard deviation of three independent experiments. Canine adipose tissue-derived mesenchymal stem cells (cAT-MSCs) stimulated with TNF-α showed enhanced therapeutic effects on mice with dextran sodium sulfate (DSS)-induced colitis. Canine adipose tissue-derived mesenchymal stem cells (cAT-MSCs) stimulated with TNF-α showed enhanced therapeutic effects on mice with dinitrobenzene sulfonic acid (DNBS)-induced colitis. doi = 10.1016/j.rvsc.2019.06.012 id = cord-347607-ydbyonbg author = Spagnuolo, Rocco title = COVID-19 and Inflammatory Bowel Disease: Patient Knowledge and Perceptions in a Single Center Survey date = 2020-08-13 keywords = COVID-19; IBD; patient summary = The aim of this survey is to evaluate knowledge about clinical importance of COVID-19, disease management, prevention measures, and anxiety level during pandemic among patients with IBD. The questionnaire consisted of five sections: (1) anthropometric, demographic and clinical characteristics, (2) knowledge about clinical importance of COVID-19, (3) IBD management, (4) prevention measures, (5) anxiety level during pandemic. Taken together with findings that an active disease status compromises knowledge of IBD management and the high level of anxiety related to increasing age, these data suggest the need of further supporting patient-oriented strategies in IBD during Covid-19 pandemic. The aim of this study is to perform a survey about knowledge about clinical importance of COVID-19, knowledge of disease management, prevention measures, and anxiety level during the pandemic among patients with IBD. The questionnaire was defined and organized into five sections, dealing with: (1) demographic and clinical characteristic, (2) knowledge about clinical importance of COVID-19, (3) knowledge about management of IBD, (4) knowledge of prevention measures, (5) anxiety level during pandemic, respectively. doi = 10.3390/medicina56080407 id = cord-261029-befymalm author = Sultan, Keith title = Review of inflammatory bowel disease and COVID-19 date = 2020-10-07 keywords = COVID-19; IBD; SARS summary = Early reports of the virus, now known as severe acute respiratory syndrome coronavirus 2, and its clinical disease coronavirus disease 2019 (COVID-19), has shown higher rates of morbidity and mortality in the elderly and those with pre-existing medical conditions. The authors also reported that there had been no cases of IBD/SARS-CoV-2 infected patients in the three largest tertiary IBD centers in Wuhan (Tongji Hospital, Union Hospital, and Zhongnan Hospital) at the time their manuscript was prepared, March 8, 2020. Rodriguez-Lago et al [29] reported on 40 cases of IBD (21 hospitalized) with confirmed positive tests for SARS-CoV-2 from 5 sites in the Basque Country (Spain), median age 59 years, 60% male, 32% Crohn''s disease (CD), with 28% on immune therapy, 18% biologic, and 10% systemic corticosteroids. To date, the largest national case reporting has come from a combined 24 IBD referral centers in Italy, affiliated with the Italian Group for the Study of Inflammatory Bowel Disease (IG-IBD) [32] . doi = 10.3748/wjg.v26.i37.5534 id = cord-275199-y7b12vml author = Suárez-Fariñas, Mayte title = Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease date = 2020-09-25 keywords = ACE2; IBD; SARS; TMPRSS2; figure summary = The RISK cohort 18 : ACE2 and TMPRSS2 in treatment-free pediatric CD (<17 years of age) patients was studied using RNA-seq expression profiles from GSE57945, which includes ileal biopsies from endoscopically defined inflamed samples (n=160), non-inflamed (n=53) and non-IBD controls (n=42). Genes differentially expressed in blood 22 , lung NHBE/A549 23 or human small intestinal organoids 24 (hSIO) following SARS-CoV-2 infection; IBD inflammation; or response to medications were separately projected onto various BGRNs allowing for 1 or 2 nearest neighbors depending on the signature sizes. The expression of ACE2 and TMPRSS2 was similar when comparing active smokers to non-smokers, either between healthy controls or IBD patients (data not shown) and no significant interactions with inflammation status, region or other covariates were found. We observed that genes: up-regulated with inflammation, or positively associated with macroscopic or microscopic measures of disease, or associated with the risk of IBD, were significantly enriched with genes up-regulated by SARS-CoV2 infection of lung epithelial cells ( Figure S10e ). doi = 10.1053/j.gastro.2020.09.029 id = cord-285820-g8b7u3yf author = Taxonera, Carlos title = Innovation in IBD Care During the COVID-19 Pandemic: Results of a Cross-Sectional Survey on Patient-Reported Experience Measures date = 2020-08-19 keywords = COVID-19; IBD summary = We evaluated the feasibility of a strategy based on the conversion of face-to-face visits to telephone consultations to manage IBD outpatients during the COVID-19 pandemic. 8, 9 The aim of this study was to assess the feasibility of a strategy based on the conversion of face-to-face visits to remote telephone consultations to improve care of patients with IBD during the COVID-19 pandemic, and to evaluate satisfaction of patients with telephone consultations. 10 Here, we report the outcomes and patient perception of a strategy based on the conversion of face-to-face visits to remote telephone consultations to improve care of outpatients with IBD during the COVID-19 pandemic. Results of a global telemedicine survey among gastroenterologists by the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) demonstrated the shift from face-to face clinics to remote telemedicine during COVID-19, with telephone consultations increasing the most, currently accounting for over half of all IBD visits. doi = 10.1093/ibd/izaa223 id = cord-306760-05my504t author = Turner, Dan title = Corona Virus Disease 2019 and Paediatric Inflammatory Bowel Diseases: Global Experience and Provisional Guidance (March 2020) from the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology, and Nutrition date = 2020-03-31 keywords = COVID-19; IBD; Porto; SARS summary = METHODS: An electronic reporting system of children with IBD infected with SARS-CoV-2 has been circulated among 102 PIBD centres affiliated with the Porto and Interest-group of ESPGHAN. Standard IBD treatments including biologics should continue at present through the pandemic, especially in children who generally have more severe IBD course on one hand, and milder SARS-CoV-2 infection on the other. In light of the hyperinflammatory immune response seen in patients with COVID-19 it is highly relevant that blockade of IL-6R with tocilizumab resulted in clinical improvement associated with normalisation of fever, lymphocyte counts, and CRP in a retrospective group of 21 adults with severe SARS-CoV-2 infection (20) . Therefore, uninfected children should generally continue their medical treatment, including immunomodulators and biologic therapies, as the risk of a disease flare outweighs any estimated risk of SARS-CoV2 infection. doi = 10.1097/mpg.0000000000002729 id = cord-031937-qhlatg84 author = Verma, Anukriti title = Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date = 2020-09-15 keywords = HLA; IBD; KYNU; host; microbe; protein summary = In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. The contributions of the microorganisms in the co-evolved IBD and ReA as part of the disease network was created through the interactive maps of the essential host interaction proteins (verified using literature survey) and the information processed through gene expression data analysis 64 . The pathways of the above host interacting proteins were found out using KEGG database that provides ontologies for proteins related to biological processes 67 www.nature.com/scientificreports/ Subsequently, the role of drugs or inhibitors used to suppress the effect of IBD and ReA such as indomethacin, prednisone, ciprofloxacin, sulfasalazine, azathioprine, methotrexate and hydroxychloroquine was scored in the disease network through their docking studies against the potential targets (both host as well microbial targets) as per published methodologies 68, 69 . doi = 10.1038/s41598-020-71674-8 id = cord-288014-rrr4x755 author = Wang, Hong-Gang title = Excessive anxiety in IBD patients is unnecessary for COVID-19 date = 2020-05-12 keywords = IBD summary = To the editor, Currently, 2019 novel coronavirus (SARS-CoV-2) infection disease (COVID-19) broke out in Wuhan, China and spread worldwide [1, 2] . Inflammatory bowel disease (IBD) is a chronic non-specific intestinal disease, including ulcerative colitis (UC) and Crohn''s disease (CD), and many of these patients have anxiety [3] . Analysis of the transcriptome data of these samples, we found that the expression of ACE2 in the terminal ileum was significantly higher than that in the rectal colon, with a fold change of 9.8 times (P < 0.001). The expression of ACE2 in the UC rectum was not significantly higher than that in non-IBD. In the terminal ileum of CD, ACE2 expression was also not higher than that of non-IBD. These results indicate that the expression of ACE2 does not show a significant difference between IBD and non-IBD patients. Compared with non-IBD, there was no significant difference in TMPRSS2 expression in the rectum and terminal ileum of patients with IBD. doi = 10.1016/j.clinre.2020.03.001 id = cord-311804-39mu0tdr author = Zingone, Fabiana title = Screening for Active COVID-19 Infection and Immunization Status Prior to Biologic Therapy in IBD Patients at the Time of the Pandemic Outbreak date = 2020-04-10 keywords = IBD summary = title: Screening for Active COVID-19 Infection and Immunization Status Prior to Biologic Therapy in IBD Patients at the Time of the Pandemic Outbreak When clinical conditions and the disease activity do not allow a treatment delay, before starting a biological therapy, screening of IBD patients for COVID-19 active infection by RT-PCR should be advisable, even in absence of clinical suspicion. When clinical conditions and the disease activity do not allow a treatment delay, before starting a biological therapy, screening of IBD patients for COVID-19 active infection by RT-PCR should be advisable, even in absence of clinical suspicion. Accumulating evidence shows that patients with COVID-19 infection may also experience gastrointestinal symptoms, including diarrhea, nausea, vomiting and abdominal discomfort prior to the common respiratory symptoms Current recommendation suggests postponing the start of treatment with immunosuppressive drugs and biologics, whenever possible, based on an individual risk assessment during the COVID19 pandemic (5-7). doi = 10.1016/j.dld.2020.04.004 id = cord-014516-r59usk02 author = nan title = Research Communications of the 24th ECVIM‐CA Congress date = 2015-01-10 keywords = Animal; CHF; CRP; FCV; IBD; Ltd; PCR; SBP; University; cat; concentration; disease; dog; group; study summary = Serum prolactin concentration measured in 22/23 dogs at time zero, 6 weeks and 6 months was 3.35 ng/ml (range, 1.4-6.36), 3.57 ng/ml (range, 1.87-7.39) and 3.92 ng/ml (range, 2.01-12.92) and did not differ significantly in either time period when compared with time zero (P = 0.99 and P = 0.52).Altogether, results of this study failed to demonstrate a significant role of thyroid supplementation on the majority of evaluated behavioural symptoms as well as neurohormonal status of hypothyroid dogs during 6 months of therapy. The aims of the present study were (1) to describe a clinical series of recent autochtonous cases and (2) to retrospectively assess Angiostrongylus vasorum qPCR in bronchoalveolar lavage fluid (BALF) samples, collected over the last 7 years from a larger series of dogs, healthy or with other respiratory conditions, in order to investigate the past prevalence of the disease in Belgium. doi = 10.1111/jvim.12491 id = cord-014527-nvzfpntu author = nan title = Research Communications of the 25th ECVIM‐CA Congress date = 2015-11-09 keywords = BCS; CHF; CIPF; CKD; FIP; HCM; IBD; PCR; Staphylococcus; University; VEGF; Veterinary; cat; disclosure; dog; group; study summary = A negative outcome was associated with higher fecal S100A12 concentrations in CE dogs, but the response to different forms of treatment and fecal S100A12 has not been reported, and this information will be important to further evaluate the utility of fecal S100A12 as a biomarker for gastrointestinal disease. Statistical analysis was performed using non-parametric 2-or multiple-group comparisons, the likelihood ratio to evaluate the association between groups of dogs and response to treatment, and a receiver operating characteristic curve to calculate sensitivity and specificity at the optimum cut-off concentration. The objectives of this study were to describe pulmonary transit time and myocardial perfusion normalized to heart rate (nPTT and nMP, respectively), evaluated by means of contrast echocardiography, in dogs with stable stage C ACVIM myxomatous mitral valve disease (MMVD), and to assess short-term effects of pimobendan on these parameters. doi = 10.1111/jvim.13647 id = cord-022555-a7ie82fs author = nan title = Digestive System, Liver, and Abdominal Cavity date = 2011-12-05 keywords = EPI; FIP; Giardia; IBD; cat; cause; clinical; diarrhea; disease; feline; figure; gastrointestinal; infection; intestinal; liver; pancreatic; sign; small; treatment summary = One study found that, of cats investigated for gastrointestinal disease, 9 of 33 cats (27%) had no pathology recognized proximal to the jejunum (i.e., the effective length of diagnostic endoscopes would have precluded diagnosis), and other organs were affected in 9 of 10 cats with inflammatory bowel diseases and 7 of 8 cats with intestinal small cell lymphoma. 60, 64 Quantification of serum cobalamin levels is recommended in cats with clinical signs of small bowel diarrhea, ones suspected to have an infiltrative disease of the small intestine (inflammatory bowel disease or gastrointestinal lymphoma), or ones with pancreatic dysfunction. Survey radiographs may be normal in cats with esophagitis and strictures, but are useful to rule out other causes for the clinical signs, such as a foreign body, or to detect related problems, such as aspiration pneumonia. 8, 29 Other non-neoplastic causes reported for gastric or gastroduodenal ulceration in cats include parasites (e.g., Ollulanus tricuspis, Toxocara cati, Aonchotheca putorii, Gnathostoma spp.), bacterial infections, toxins, inflammatory bowel disease, and foreign bodies. doi = 10.1016/b978-1-4377-0660-4.00023-5 id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 keywords = APC; BCR; CD14; CD4; CD8; CMV; CTL; EBV; ELISA; Germany; HCV; HIV; HLA; IBD; IFN; IL-10; IL-2; IL-4; IL-6; Immunology; Institute; LPS; MHC; NKT; PCR; RNA; SLE; TCR; TGF; TLR; TLR4; TNF; University; antigen; cell; dna; expression; immune; mouse; patient; protein; response; result; study; th1; th2 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. doi = 10.1002/eji.200990224 id = cord-023095-4dannjjm author = nan title = Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date = 2011-05-03 keywords = ACTH; CHF; CKCS; CKD; DMVD; ECG; ELISA; IBD; PCR; TLR5; University; Veterinary; blood; cat; concentration; day; disease; dna; dog; group; horse; sample; study; test; time; treatment summary = The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] ! doi = 10.1111/j.1939-1676.2011.0726.x id = cord-023134-y665agnh author = nan title = Oral Research Communications of the 22(nd) ECVIM‐CA Congress date = 2012-11-20 keywords = BEM; CKD; DCM; IBD; IPF; PCR; SAM; cat; disease; dog; group; study summary = Doppler echocardiographic indices of diastolic function of the right ventricle are good prognostic markers during left ventricular (LV) failure secondary to ischemic and dilated cardiomyopathy.The aims of the present study were: to assess LV and RV diastolic function by conventional Doppler and pulsed-wave tissue Doppler imaging (PW-TDI) in dogs with mitral valve disease (MVD), with or without pulmonary hypertension (PH); to test if echocardiographic parameters of LV and RV diastolic dysfunction correlate to the Doppler-estimated pulmonary artery systolic pressure (PASP).114 dogs were prospectively evaluated, including 86 dogs with MVD. The aims of the present study were to assess whether diabetic cats have pathological evidence of islet inflammation or pancreatitis and to define islet lesions in comparison to a well-matched control population.Formalin-fixed, paraffin-embedded pancreatic samples were collected from post-mortem examination performed on diabetic and control cats died due to any disease at the Clinic for Small Animal Internal Medicine, University of Zurich (Switzerland) between 1997 and 2009. doi = 10.1111/jvim.12000 id = cord-258066-ncuegrq7 author = nan title = Inflammatory Bowel Disease date = 2013-12-31 keywords = IBD summary = Inflammatory bowel disease (IBD) is a poorly defined and often incorrectly used term in ferrets and other small animals for a systemic inflammatory disease primarily involving the gastrointestinal tract. The umbrella term IBD used in ferrets and other small animals for a variety of gastrointestinal diseases is not the same disease that is seen in humans. • Ferrets are susceptible to several gastrointestinal inflammatory conditions that have erroneously been placed under the umbrella term of IBD. Endoscopic biopsies are often done early, after symptomatic medical therapy (see Acute General Treatment) has failed to control clinical signs. • It is not appropriate for a pathologist to issue a diagnosis of "inflammatory bowel disease." It is more appropriate to list the histologic findings, and to indicate that the changes could be "compatible with" a clinical diagnosis of that syndrome. • Chronic gastrointestinal inflammatory disease in ferrets is not always cured. Treatment of inflammatory bowel disease (IBD) in dogs and cats doi = 10.1016/b978-1-4160-3969-3.00215-8