cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13187859.v1
title: Mapping of aetiologies of gastroenteritis: a systematic review and meta-analysis of pathogens identified using a multiplex screening array

description: Emergence of molecular methods to screen stools could provide a more complete picture of pathogens causing gastroenteritis, allowing to adequately treat patients whenever required but, so far, no aggregate data have been released. Our objective was to report pathogens identified in patients suffering from gastroenteritis using a multiplex molecular array. Medline and Embase were searched for original publications reporting pathogens identified with FilmArray GI panel in patients suffering from gastroenteritis. Proportions of pathogens were extracted and pooled using a model with random effects. Fourteen studies (17,815 patients) were included in the analysis. Among the 7,071 patients (39.7%) with positive FilmArray, identified pathogens were <i>EPEC</i> (27.5%), <i>Clostridium difficile</i> (19.3%), <i>Norovirus</i> (15.1%), <i>EAEC</i> (15%), <i>Campylobacter spp</i> (11.8%), <i>Salmonella spp</i> (8.1%), <i>ETEC</i> (7.3%), <i>Rotavirus</i> (7.3%), <i>Sapovirus</i> (7.1%), <i>STEC</i> (5.2%), <i>Shigella/EIEC</i> (4.9%), <i>Giardia lamblia</i> (4%), <i>Adenovirus</i> (3.8%), <i>Cryptosporidium spp</i> (3.8%), <i>Astrovirus</i> (2.8%), <i>Yersinia enterocolitica</i> (1.7%), <i>Escherichia coli</i> O157 (1.1%), <i>Plesiomonas shigelloides</i> (1.1%), <i>Cyclospora cayetanensis</i> (0.7%), <i>Vibrio spp</i> (0.5%), <i>Vibrio cholerae</i> (0.3%) and <i>Entamoeba histolytica</i> (0.3%). When considering only studies with control group (microbiological examination of the stools performed by other methods), FilmArray identified at least one pathogen in 48.2% of patients versus 16.7% when using comparative diagnostic methods. FilmArray GI panel was positive in 39.7% of patients suffering from gastroenteritis. This proportion has to be mitigated by the carriage rates of identified organisms. Ultimately, restricted ordering of molecular panels to those patients who might benefit from specific treatment could provide medical value by swift identification of the pathogen and more targeted therapy.
DOI: 10.6084/m9.figshare.13187859
title: Mapping of aetiologies of gastroenteritis: a systematic review and meta-analysis of pathogens identified using a multiplex screening array

description: Emergence of molecular methods to screen stools could provide a more complete picture of pathogens causing gastroenteritis, allowing to adequately treat patients whenever required but, so far, no aggregate data have been released. Our objective was to report pathogens identified in patients suffering from gastroenteritis using a multiplex molecular array. Medline and Embase were searched for original publications reporting pathogens identified with FilmArray GI panel in patients suffering from gastroenteritis. Proportions of pathogens were extracted and pooled using a model with random effects. Fourteen studies (17,815 patients) were included in the analysis. Among the 7,071 patients (39.7%) with positive FilmArray, identified pathogens were <i>EPEC</i> (27.5%), <i>Clostridium difficile</i> (19.3%), <i>Norovirus</i> (15.1%), <i>EAEC</i> (15%), <i>Campylobacter spp</i> (11.8%), <i>Salmonella spp</i> (8.1%), <i>ETEC</i> (7.3%), <i>Rotavirus</i> (7.3%), <i>Sapovirus</i> (7.1%), <i>STEC</i> (5.2%), <i>Shigella/EIEC</i> (4.9%), <i>Giardia lamblia</i> (4%), <i>Adenovirus</i> (3.8%), <i>Cryptosporidium spp</i> (3.8%), <i>Astrovirus</i> (2.8%), <i>Yersinia enterocolitica</i> (1.7%), <i>Escherichia coli</i> O157 (1.1%), <i>Plesiomonas shigelloides</i> (1.1%), <i>Cyclospora cayetanensis</i> (0.7%), <i>Vibrio spp</i> (0.5%), <i>Vibrio cholerae</i> (0.3%) and <i>Entamoeba histolytica</i> (0.3%). When considering only studies with control group (microbiological examination of the stools performed by other methods), FilmArray identified at least one pathogen in 48.2% of patients versus 16.7% when using comparative diagnostic methods. FilmArray GI panel was positive in 39.7% of patients suffering from gastroenteritis. This proportion has to be mitigated by the carriage rates of identified organisms. Ultimately, restricted ordering of molecular panels to those patients who might benefit from specific treatment could provide medical value by swift identification of the pathogen and more targeted therapy.
DOI: 10.6084/m9.figshare.13138744.v1
title: Lactose after Roux-en-Y gastric bypass for morbid obesity, is it a problem?

description: Roux-en-Y gastric bypass (RYGB) can cause multiple food intolerances and gastrointestinal complaints are frequently reported after dairy consumption. We aimed to determine the prevalence of lactose malabsorption and intolerance, and complaints associated with dairy consumption in daily life, before and after RYGB. The lactose breath test (LBT) and lactose tolerance test (LTT) was performed in 84 patients awaiting RYGB surgery and 84 patients after surgery. Gastrointestinal symptoms at baseline and after testing were recorded. Lactose malabsorption was defined as a positive LBT and/or LTT. Lactose intolerance as a positive test combined with an increase of gastrointestinal complains. Dairy consumption in daily life and successive gastrointestinal complaints were registered <i>via</i> a questionnaire. Results of preoperative and postoperative patients were compared. Lactose malabsorption was present in 15 (17.9%) of the preoperative patients and in 25 (29.8%) of the postoperative patients (OR 2.46; 95%CI: 1.08–5.59; <i>p</i> = .03). Of the preoperative patients 6 (7.1%) patients met the criteria for lactose intolerance, compared to 8 (9.5%) patients in the postoperative group (OR 1.48; 95%CI 0.48–4.57; <i>p</i> = .50). Twelve (14.3%) preoperative patients indicated to have gastrointestinal complaints after dairy consumption in daily life versus 45 (53.6%) postoperative patients (<i>p</i> This study shows no increase in patients with proven lactose intolerance after RYGB compared to preoperative patients. Gastrointestinal complaints after dairy consumption in daily life were far more frequently reported by RYGB patients. It is unlikely that all reported gastrointestinal complaints are actually caused by lactose. Other ingredients in dairy, like fat, are possibly contributory.
DOI: 10.6084/m9.figshare.12859609
title: Validation of ulcerative colitis and Crohn’s disease and their phenotypes in the Danish National Patient Registry using a population-based cohort

description: The Danish National Patient Registry (DNPR) has been the source of several epidemiological studies of inflammatory bowel disease (IBD). However, the validation dates back to 1996 and lacks outpatient records and disease classification. The aim of this study was to update the validation and assess the validity and reliability of using the registry in disease classification. Validation of the registry was done using a population-based inception cohort of IBD patients from 2003 to 2011 consisting of 513 patients. Specificity and sensitivity were calculated for the diagnoses of Crohn’s disease (CD) and ulcerative colitis (UC), age at diagnosis and disease classification according to the Montreal Classification at both time of diagnosis and end of follow-up. The registry showed high validity and reliability in identifying CD and UC patients concerning correct age classification and identifying perianal disease. The registry showed inconsistent, unreliable results in further disease classification. The DNPR has good validity and reliability in identifying patients with CD and UC, and defining the age of patients at diagnosis. However, categorising IBD patients according to the Montreal Classification should not be carried out using DNPR data in their current form, except when identifying CD patients with perianal disease.
DOI: 10.6084/m9.figshare.13138744
title: Lactose after Roux-en-Y gastric bypass for morbid obesity, is it a problem?

description: Roux-en-Y gastric bypass (RYGB) can cause multiple food intolerances and gastrointestinal complaints are frequently reported after dairy consumption. We aimed to determine the prevalence of lactose malabsorption and intolerance, and complaints associated with dairy consumption in daily life, before and after RYGB. The lactose breath test (LBT) and lactose tolerance test (LTT) was performed in 84 patients awaiting RYGB surgery and 84 patients after surgery. Gastrointestinal symptoms at baseline and after testing were recorded. Lactose malabsorption was defined as a positive LBT and/or LTT. Lactose intolerance as a positive test combined with an increase of gastrointestinal complains. Dairy consumption in daily life and successive gastrointestinal complaints were registered <i>via</i> a questionnaire. Results of preoperative and postoperative patients were compared. Lactose malabsorption was present in 15 (17.9%) of the preoperative patients and in 25 (29.8%) of the postoperative patients (OR 2.46; 95%CI: 1.08–5.59; <i>p</i> = .03). Of the preoperative patients 6 (7.1%) patients met the criteria for lactose intolerance, compared to 8 (9.5%) patients in the postoperative group (OR 1.48; 95%CI 0.48–4.57; <i>p</i> = .50). Twelve (14.3%) preoperative patients indicated to have gastrointestinal complaints after dairy consumption in daily life versus 45 (53.6%) postoperative patients (<i>p</i> This study shows no increase in patients with proven lactose intolerance after RYGB compared to preoperative patients. Gastrointestinal complaints after dairy consumption in daily life were far more frequently reported by RYGB patients. It is unlikely that all reported gastrointestinal complaints are actually caused by lactose. Other ingredients in dairy, like fat, are possibly contributory.
DOI: 10.6084/m9.figshare.12859609.v1
title: Validation of ulcerative colitis and Crohn’s disease and their phenotypes in the Danish National Patient Registry using a population-based cohort

description: The Danish National Patient Registry (DNPR) has been the source of several epidemiological studies of inflammatory bowel disease (IBD). However, the validation dates back to 1996 and lacks outpatient records and disease classification. The aim of this study was to update the validation and assess the validity and reliability of using the registry in disease classification. Validation of the registry was done using a population-based inception cohort of IBD patients from 2003 to 2011 consisting of 513 patients. Specificity and sensitivity were calculated for the diagnoses of Crohn’s disease (CD) and ulcerative colitis (UC), age at diagnosis and disease classification according to the Montreal Classification at both time of diagnosis and end of follow-up. The registry showed high validity and reliability in identifying CD and UC patients concerning correct age classification and identifying perianal disease. The registry showed inconsistent, unreliable results in further disease classification. The DNPR has good validity and reliability in identifying patients with CD and UC, and defining the age of patients at diagnosis. However, categorising IBD patients according to the Montreal Classification should not be carried out using DNPR data in their current form, except when identifying CD patients with perianal disease.
DOI: 10.6084/m9.figshare.12935283
title: 3D analysis of the myenteric plexus of the human bowel by X-ray phase-contrast tomography – a future method?

description: Light microscopical analysis in two dimensions, combined with immunohistochemistry, is presently the gold standard to describe the enteric nervous system (ENS). Our aim was to assess the usefulness of three-dimensional (3D) imaging by X-ray phase-contrast tomography in evaluating the ENS of the human bowel. Myenteric ganglia were identified in full-thickness biopsies of the ileum and colon by hematoxylin & eosin staining. A1-mm biopsy punch was taken from the paraffin blocks and placed into a Kapton<sup>®</sup> tube for subsequent tomographic investigation. The samples were scanned, without further preparation, using phase-contrast tomography at two different scales: overview scans (performed with laboratory setups), which allowed localization of the nervous tissue (∼1µm effective voxel size); and high-resolution scans (performed with a synchrotron endstation), which imaged localized regions of 320x320x320 µm<sup>3</sup> (176 nm effective voxel size). The contrast allowed us to follow the shape and the size changes of the ganglia, as well as to study their cellular components together with the cells and cellular projections of the periganglional space. Furthermore, it was possible to show the 3D network of the myenteric plexus and to quantify its volume within the samples. Phase-contrast X-ray tomography can be applied for volume analyses of the human ENS and to study tissue components in unstained paraffin-embedded tissue biopsies. This technique could potentially be used to study disease mechanisms, and to compare healthy and diseased tissues in clinical research.
DOI: 10.6084/m9.figshare.12859606.v1
title: Diagnostic accuracy of faecal calprotectin in a symptom-based algorithm for early diagnosis of inflammatory bowel disease adjusting for differential verification bias using a Bayesian approach

description: Diagnostic delay in IBD is a major problem and diagnosis is frequently arrived when irreversible damage has already occurred. This study evaluated accuracy of faecal calprotectin (fCAL) integrated with diagnostic criteria for early diagnosis of IBD in a primary care setting. General practitioners (GPs) were trained to recognize alarm symptoms for IBD classified as major and minor criteria. Fulfilment of one major or at least two minor criteria was followed by free fCAL testing and a visit by an IBD specialist and follow-up over 12 months. All patients with positive fCAL testing, i.e., ≥70 μg/g underwent colonoscopy. The diagnostic accuracy of fCAL was estimated after adjusting for differential-verification bias following a Bayesian approach. Thirty-four GPs participated in the study and 133 patients were tested for fCAL between July 2016 and August 2017. Positivity of fCAL was seen in 45/133 patients (34%) and a final IBD diagnosis was made in 10/45 (22%). According to the threshold of 70 μg/g, fCAL achieved a sensitivity of 74.8% (95%CI: 39.10–96.01%), a specificity of 70.4% (95%CI: 61.76–78.16%) and an overall diagnostic accuracy of 70.6% (95%CI: 61.04–78.37%). As for prognostic accuracy, despite positive predictive value being low, 21.9% (95%CI: 11.74–35.18%), the negative predictive value was definitely higher: 96.2% (95%CI: 84.96–99.51%). fCAL with a threshold set at 70 μg/g seems to represent a potentially reliable negative test to be used in primary care settings for patients with symptoms suggestive of IBD.
DOI: 10.6084/m9.figshare.12935283.v1
title: 3D analysis of the myenteric plexus of the human bowel by X-ray phase-contrast tomography – a future method?

description: Light microscopical analysis in two dimensions, combined with immunohistochemistry, is presently the gold standard to describe the enteric nervous system (ENS). Our aim was to assess the usefulness of three-dimensional (3D) imaging by X-ray phase-contrast tomography in evaluating the ENS of the human bowel. Myenteric ganglia were identified in full-thickness biopsies of the ileum and colon by hematoxylin & eosin staining. A1-mm biopsy punch was taken from the paraffin blocks and placed into a Kapton<sup>®</sup> tube for subsequent tomographic investigation. The samples were scanned, without further preparation, using phase-contrast tomography at two different scales: overview scans (performed with laboratory setups), which allowed localization of the nervous tissue (∼1µm effective voxel size); and high-resolution scans (performed with a synchrotron endstation), which imaged localized regions of 320x320x320 µm<sup>3</sup> (176 nm effective voxel size). The contrast allowed us to follow the shape and the size changes of the ganglia, as well as to study their cellular components together with the cells and cellular projections of the periganglional space. Furthermore, it was possible to show the 3D network of the myenteric plexus and to quantify its volume within the samples. Phase-contrast X-ray tomography can be applied for volume analyses of the human ENS and to study tissue components in unstained paraffin-embedded tissue biopsies. This technique could potentially be used to study disease mechanisms, and to compare healthy and diseased tissues in clinical research.
DOI: 10.6084/m9.figshare.12859606
title: Diagnostic accuracy of faecal calprotectin in a symptom-based algorithm for early diagnosis of inflammatory bowel disease adjusting for differential verification bias using a Bayesian approach

description: Diagnostic delay in IBD is a major problem and diagnosis is frequently arrived when irreversible damage has already occurred. This study evaluated accuracy of faecal calprotectin (fCAL) integrated with diagnostic criteria for early diagnosis of IBD in a primary care setting. General practitioners (GPs) were trained to recognize alarm symptoms for IBD classified as major and minor criteria. Fulfilment of one major or at least two minor criteria was followed by free fCAL testing and a visit by an IBD specialist and follow-up over 12 months. All patients with positive fCAL testing, i.e., ≥70 μg/g underwent colonoscopy. The diagnostic accuracy of fCAL was estimated after adjusting for differential-verification bias following a Bayesian approach. Thirty-four GPs participated in the study and 133 patients were tested for fCAL between July 2016 and August 2017. Positivity of fCAL was seen in 45/133 patients (34%) and a final IBD diagnosis was made in 10/45 (22%). According to the threshold of 70 μg/g, fCAL achieved a sensitivity of 74.8% (95%CI: 39.10–96.01%), a specificity of 70.4% (95%CI: 61.76–78.16%) and an overall diagnostic accuracy of 70.6% (95%CI: 61.04–78.37%). As for prognostic accuracy, despite positive predictive value being low, 21.9% (95%CI: 11.74–35.18%), the negative predictive value was definitely higher: 96.2% (95%CI: 84.96–99.51%). fCAL with a threshold set at 70 μg/g seems to represent a potentially reliable negative test to be used in primary care settings for patients with symptoms suggestive of IBD.
DOI: 10.5517/ccrkzlv
title: CCDC 702478: Experimental Crystal Structure Determination

description: Related Article: G.J.Gainsford, M.D.H.Bhuiyan, A.J.Kay, W.T.Robinson|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1715|doi:10.1107/S1600536808024719
DOI: 10.5517/ccrkzmw
title: CCDC 702479: Experimental Crystal Structure Determination

description: Related Article: Xiao-Hong Geng, Li-Chun Kong, Yun-Long Feng|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1716|doi:10.1107/S1600536808020515
DOI: 10.5517/ccrkznx
title: CCDC 702480: Experimental Crystal Structure Determination

description: Related Article: N.Muhammad, M.N.Tahir, Zia-ur-Rehman, S.Ali|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1717|doi:10.1107/S1600536808024999
DOI: 10.5517/ccrkzqz
title: CCDC 702482: Experimental Crystal Structure Determination

description: Related Article: H.-K.Fun, S.Chantrapromma, P.S.Patil, S.M.Dharmaprakash|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1720|doi:10.1107/S1600536808024872
DOI: 10.5517/ccrkzr0
title: CCDC 702483: Experimental Crystal Structure Determination

description: Related Article: H.-K.Fun, R.Kia|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1722|doi:10.1107/S1600536808024926
DOI: 10.5517/ccrkzt2
title: CCDC 702485: Experimental Crystal Structure Determination

description: Related Article: Wei-Jin Gu, Bing-Xiang Wang|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1725|doi:10.1107/S1600536808025026
DOI: 10.5517/ccr4yjb
title: CCDC 689952: Experimental Crystal Structure Determination

description: Related Article: W.-K.Dong, X.-N.He, Y.-X.Sun, L.Xu, J.-F.Tong|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1726|doi:10.1107/S1600536808024902
DOI: 10.5517/ccrkzv3
title: CCDC 702486: Experimental Crystal Structure Determination

description: Related Article: I.N.Hassan, B.M.Yamin, M.B.Kassim|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1727|doi:10.1107/S1600536808024896
DOI: 10.5517/ccrkzx5
title: CCDC 702488: Experimental Crystal Structure Determination

description: Related Article: Yin-Hong Liu, Fang-Shi Li, Yi Li, Da-Sheng Yu, Chui Lu|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1729|doi:10.1107/S1600536808024987
DOI: 10.5517/ccrkzy6
title: CCDC 702489: Experimental Crystal Structure Determination

description: Related Article: Jian-Gang Wang, Fang-Fang Jian, Yu-Feng Ding|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1730|doi:10.1107/S1600536808025105
DOI: 10.5517/ccrkzz7
title: CCDC 702490: Experimental Crystal Structure Determination

description: Related Article: K.Nakaema, A.Okamoto, S.Maruyama, K.Noguchi, N.Yonezawa|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1731|doi:10.1107/S1600536808025178
DOI: 10.5517/ccrl00b
title: CCDC 702491: Experimental Crystal Structure Determination

description: Related Article: Zheng-Ping Chen, Song-Pei Wang, Xiao-Min Li, Jie Tang, Jian-Guo Lin|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1732|doi:10.1107/S1600536808025002
DOI: 10.5517/ccrl01c
title: CCDC 702492: Experimental Crystal Structure Determination

description: Related Article: Su-Qing Wang, Fang-Fang Jian, Huan-Qiang Liu|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1733|doi:10.1107/S160053680802518X
DOI: 10.5517/ccrl03f
title: CCDC 702494: Experimental Crystal Structure Determination

description: Related Article: M.-H.Xie, P.Zou, Y.-J.He, Y.-L.Liu, B.Huang|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1736|doi:10.1107/S1600536808024938
DOI: 10.5517/ccrl04g
title: CCDC 702495: Experimental Crystal Structure Determination

description: Related Article: Chen-Xia Yu, Pei-Li Qian, Jia-Jing Ping, Chang-Sheng Yao|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1737|doi:10.1107/S1600536808024835
DOI: 10.5517/ccr6l8s
title: CCDC 691525: Experimental Crystal Structure Determination

description: Related Article: R.M.Jarraya, A.Bouaziz, B.Hamdi, A.B.Salah, M.Damak|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1739|doi:10.1107/S1600536808025324
DOI: 10.5517/ccrl06j
title: CCDC 702497: Experimental Crystal Structure Determination

description: Related Article: H.-K.Fun, R.Kia, P.R.Raithby|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1741|doi:10.1107/S1600536808025269
DOI: 10.5517/ccrl07k
title: CCDC 702498: Experimental Crystal Structure Determination

description: Related Article: Yu-Feng Li, Fang-Fang Jian|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1743|doi:10.1107/S1600536808025142
DOI: 10.5517/ccrl6yg
title: CCDC 702706: Experimental Crystal Structure Determination

description: Related Article: Yu-Feng Li, Fang-Fang Jian|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1744|doi:10.1107/S1600536808025166
DOI: 10.5517/ccrl08l
title: CCDC 702499: Experimental Crystal Structure Determination

description: Related Article: Dongmei Cui, Qian Wang, Chen Zhang, Jianming Gu|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1745|doi:10.1107/S1600536808025063
DOI: 10.5517/ccrl09m
title: CCDC 702500: Experimental Crystal Structure Determination

description: Related Article: An-Le Xie, Tong-Jian Ding, Xiao-Ping Cao|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1746|doi:10.1107/S1600536808025014
DOI: 10.5517/ccrl6zh
title: CCDC 702707: Experimental Crystal Structure Determination

description: Related Article: Li Shen, Qi Liu, Hai-Jun Shen|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1747|doi:10.1107/S1600536808025464
DOI: 10.5517/ccrl0bn
title: CCDC 702501: Experimental Crystal Structure Determination

description: Related Article: Bin Zhu, Xiang-Wei Cheng|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1748|doi:10.1107/S1600536808024434
DOI: 10.5517/ccrl0cp
title: CCDC 702502: Experimental Crystal Structure Determination

description: Related Article: Lihua Mao, Yan Chen|2008|Acta Crystallogr.,Sect.E:Struct.Rep.Online|64|o1749|doi:10.1107/S1600536808024847