dataesr/scientific-paragraphs-categorization huggingface dataset:
The glucooligosaccharides produced and purified as previously described were dissolved at 40 mM  (39). Soaking of crystals with isomaltotriose (Sigma-Aldrich Chemie S. a. r. l. , Saint Quentin-Fallavier, France) was performed at 50 mM ligand. The concentration of PEG 3,350 was increased to 28. 5% (w/v) for cryoprotection. D-Glucose (Sigma) was dissolved at 100 mM. Soaking solutions of dextran T1 were prepared at concentrations varying from 50 mM to saturation. No cryo-protectant was necessary for those two last ligands. Crystals were then cryo-cooled in a flux of nitrogen gas at 100 K. Data Collection, Phasing, and Refinement-Diffraction data were collected at the ESRF (Grenoble, France). Intensities were indexed and integrated using iMOSFLM or XDS and scaled using SCALA or XSCALE  (40 -42).
Crystals belong to space group P2 1 2 1 2 1 with one molecule per asymmetric unit, which corresponds to a solvent content of 52. 5% and Matthews coefficient of 2. 59 Å 3 Da Ϫ1. Structures were solved using molecular replacement with Phaser (43) and the atomic coordinates of the apo-form of ⌬N 123 -GBD-CD2 (PDB entry 3TTQ (9)) as a search model. Models were manually constructed in A weighted 2F o Ϫ F c electron density maps using Coot and refined using Refmac5  (44, 45). Carbohydrate fitting in electron density maps was also guided by simulated annealing (F o Ϫ F c ) omit maps were calculated with PHENIX  (46). Data collection and refinement statistics are shown in Table  1. Structural Analysis-Electrostatic potential of the ⌬N 123 -GBD-CD2 surface, without any ligand, was calculated via the PDB2PQR server using the program APBS, specifying the pH at 5.
75, which is the optimum pH for activity  (47). From complex B, the groove search from subsite Ϫ1 was done using CAVER 3. 01 as a PyMOL plugin  (48). Molecular Dynamics-The starting point for the molecular dynamics (MD) simulation was the crystal structure of complex A, composed of the protein and 10 D-glucose molecules. The calculations were performed with the Amber 14 software (49 -51) using the FF03 force field for the protein, the GAFF force field for the ligands, and the TIP3P water model for the solvent (52). The complex was placed at the center of a periodic box. To hydrate the system, the volume occupied by the complex was extended by 10 Å on each side, and 40,251 water molecules were added to the box. To neutralize the charge of the system, 37 Na ϩ ions were added by random replacement of the equivalent number of solvent molecules.
22 ns/day. To obtain a detailed view of the studied system, nine simulations of this type have been performed, for the total time length of 450 ns. The resulting MD trajectories were analyzed with the Amber-Tools 14 programs as well as with in-house software. The last 20 ns of each equilibrated trajectory were used to calculate intermolecular interaction energy for all protein-ligand pairs with the MM-GBSA approach  (55). Identification of Glucan Binding Pockets by Multiple Sequence Alignments-Sequence alignment of the three repeats forming the sugar-binding pockets, V-J, V-K, and V-L in domain V of ⌬N 123 -GBD-CD2, was first performed using Clustal Omega  (56). This alignment was inspected and corrected using the structural superimposition of each of the three binding pockets. Then, the primary structure of the full-length GBD of DSR-E (57) was analyzed using the online repeat detection tool TRUST  (58) , and this allowed detecting 12 sequence repeats in this domain.
from 3. 35 to 2. 60 Å, the three-dimensional structures obtained from crystals soaked with 1-kDa dextran did not reveal any clear electron density attributable to a ligand. Structure of the Complex of ⌬N 123 -GBD-CD2 with D-Glucose-The crystal structure of ⌬N 123 -GBD-CD2 in complex with D-glucose has been solved at 2. 3-Å resolution and superimposed with the apo structure (PDB entry 3TTQ) with a r. m. s. deviation on C␣ atoms of 0. 6 Å. Nine D-glucose molecules are observed at the enzyme surface (Figs. 3A  and 4 ). Four of them are found in domain A in sites A-1, A2, A3, and A4. Additionally, two glucose molecules were bound in domain IV (sites IV1 and IV2). Two others are at the interface of domains IV and V (site IV-V) or domains B, IV, and V (site B-IV-V) and one glucose unit is bound to the domain V (site V-L).
Residues framed in dashed line on the LOGO sequence correspond to YG repeats. In the repeats of GBD1A, residues circled in white, were mutated by Shah et al. (25) (see "Discussion"). Secondary structure elements, as determined by DSSP from PDB entries 3TTQ, 3KLK, and 4AMC, are displayed below the LOGO sequence. ␤-Strands, numbered according to Fig. 8, linked by dashed lines represent either ␤-hairpins or three-stranded ␤-sheets.
Data analysis Tanks (n = 3) were used as experimental unit for data on body mineral composition and mineral balance. Individual fish was the experimental unit for data on gene expression (n = 9), on enzyme analyses (n = 9, except for SOD activities, n = 6) and on plasma parameters (n = 6). The analysis of gene expression data was performed after eliminating outliers according to the Grubbs test followed by replacing missing values with estimates using the Yates procedure. Two-way ANOVA was performed after transformation of raw data in ranks to analyse the main effects of the basal diet, micro-mineral premix inclusion and their interactions. The statistical significance was set at P<0. 05. In the case of a significant interaction, group means were compared by Tukey's multiple comparison test as indicated by different superscript letters.
Acknowledgments This work was part of a PhD thesis funded by  INRA , under the  INRA-WUR aquaculture platform. This work received funds from the  EU seventh Framework Programmes ARRAINA (Advanced Research Initiatives for Nutrition & Aquaculture , FP7/2007-2013; grant agreement  n°288925 ) and  AQUAEXCEL (Aquaculture Infrastructures for Excellence in European Fish Research ,  FP7/2007-2012 ; grant agreement  n°262336 ). The views expressed in this work are the sole responsibility of the authors and do not necessarily reflect the views of the  European Commission. The efforts of  Frederic Terrier  and other staff at the  INRA experimental fish  farm are acknowledged.
This work was part of a PhD thesis funded by  INRA , under the  INRA-WUR aquaculture platform. This work received funds from the  EU seventh Framework Programmes ARRAINA (Advanced Research Initiatives for Nutrition & Aquaculture , FP7/ 2007-2013; grant agreement  n°288925 ) and  AQUAEXCEL (Aquaculture Infrastructures for Excellence in European Fish Research ,  FP7/2007-2012 ; grant agreement  n°262336 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
1371/journal. pone. 0149378. t003 *GenBank accession number; F, forward primer; R, reverse primer; EF1α, elongation factor 1α; HAMP, Hepcidin anti-microbial peptide; HO1, heme oxygenase 1; FPN1, ferroportin1; Nramp-β, Natural resistance associated macrophage protein beta polypeptide; Nramp-γ, Natural resistance associated.
We aimed to develop and describe a classification scheme of esophageal motility based on parameters generated with a novel analysis paradigm: FLIP topography. Methods: 100 patients (ages 19-82, 50 female) presenting with dysphagia that underwent upper endoscopy with a 16-cm FLIP and high-resolution manometry (HRM) were included. HRMs were analyzed according to the Chicago Classification of esophageal motility disorders. A customized MATLAB program generated FLIP topography plots of diameter by axial position over time. EGJ-distensibility index (DI) was measured by dividing the narrowest EGJ cross-sectional area by the median intra-bag pressure at a 60-mL distension volume. Esophageal contractions were identified by noting periods of reduced diameter and contractility patterns including repetitive antegrade contractions © 2 0 1 6 T H E AU T H O R S N E U R O G A S T R O E N T E R O L O G Y & MO T I L I T Y © 2 0 1 6 J O H N W I L E Y & S O N S L T D N E U R O G AS T R O E N T E R O L.
44 Evaluating the safety and efficacy of eluxadoline for treating diarrhea-predominant irritable bowel syndrome: A Meta-analysis E. SHAH* and P. SCHOENFELD † *University of Michigan, Ann Arbor, MI, USA Background: Eluxadoline is an opioid receptor agonist/ antagonist recently approved by the FDA for therapy of diarrhea-predominant irritable bowel syndrome (IBS-D). We evaluated the safety and efficacy of eluxadoline in treating IBS-D based on controlled clinical trial data. Methods: We searched the literature (PubMed and Cochrane database) and abstract books since 2005 from ACG, DDW, and UEGW to identify relevant randomized placebo-controlled trials. Study eligibility was independently evaluated by ES and MP. Consistent with recent FDA methodology, data were pooled based on similarities in population characteristics and trial design.
gov no: NCT01252550). The properties of hypothesized brain regions in large-scale functional networks were quantified with local centrality measures indexing a region's contribution to the network's structural integrity and information flow. Tripartite network analysis was performed for integrative analysis. The nodes of the network were the bacterial genera comprising the IBS severity signature, psychophysiological data and the morphometry and functional network metrics characterizing insula, somatosensory cortex, basal ganglia, and thalamus. The edges (or links) between nodes were based on significant correlations (p < 0. 05) between nodes. Results: There were several significant interactions between the relative abundance of Bacteriodetes (Bacteroides, Parabacteroides, Alistipes) and Firmicutes associated genera (Clostridium sensu stricto, Clostridium XlVa, Clostridium XlVb, Clostridium IV, Oscillibacter, Clostridium XVIII) with physiological (oroanal transit times) and behavioral (self-reports of sensitivity, urgency, pain and discomfort during rectal distension, and pain rating during the lactulose challenge) measures, and the morphometry and functional connectivity (centrality) of insula and sensorimotor region.
Conclusion: The antagonistic ability of ibodutant appeared agonist-dependent in females, indicating that the NK2 receptor is of ligand bias property, which involves ligand-dependent conformations. This may underlie the gender-related effectiveness of ibodutant in the treatment of IBS. References: 1. https://clinicaltrials. gov/ct2/show/results/NCT01303224?sect=X01256#all (Menarini Group). Validated questionnaires were used to assess the severity of symptoms (patient assessment of constipation symptoms (PAC-SYM)), somatic symptoms (patient health questionnaire-12 (PHQ-12-SS)), anxiety/ depression and the personality traits of neuroticism and extroversion (big five inventory-neuroticism or extroversion scale (BFI-N and BFI-E)). Patients were excluded if they did not wish to complete the questionnaires.
Methods: All adult patients who presented to the Flinders Medical Centre anorectal laboratory for investigation of faecal incontinence between January 1998 and July 2015 were collated into a database for analysis. Investigation included endoanal ultrasound, anorectal manometry, rectal sensation, rectoanal inhibitory reflex, pudendal nerve latency, and completed a Wexner symptom score for incontinence. Patients with a previous history of trauma, anorectal or perineal surgery, anorectal pathology, or radiotherapy to the pelvis and anorectum were excluded (n = 256). Multivariate analyses were undertaken to explore correlations between structure, function, and symptom severity. Results: 353 patients were included in the analysis. 45. 9% of the cohort had intact an anal sphincter on sonography.
Conclusion: We have shown that discomfort scores are higher and fecal SCFA concentrations are decreased in female vs male IBS patients. Differences in intestinal microbiota composition and colonic metabolism may underlie these gender differences in IBS and deserve further evaluation. Method: We reviewed our esophageal high-resolution manometry database to identify studies where AN was given to assess possible EOR. Patients with history of surgery and chronic opioid intake were excluded. EGJ pressure, along with integrated relaxation pressure (IRP) before and after AN administration were recorded. Patients were considered to have EOR unresponsive to AN when the difference between EGJ pressure following deglutitive relaxation and AN-induced relaxation was <8 mmHg. Manometric and clinical characteristics in this group were compared to those in patients with normal esophageal motility (N = 10) and achalasia (N = 22).
© 2 0 1 6 T H E AU T H O R S N E U R O G A S T R O E N T E R O L O G Y & MO T I L I T Y © 2 0 1 6 J O H N W I L E Y & S O N S L T D N E U R O G AS T R O E N T E R O L. MO T I L. 2 0 Methods: High-resolution impedance manometry (MMS, Unisensor) was conducted in fourteen healthy volunteers (8M, 30 AE 5 years), seven each with and without bolus perception (visual analogue scale) during solid bolus. Data were exported and analyzed via Matlab TM for characterization of neuromechanical states, and compared between perceived and nonperceived swallows, with p-value < 0. 05 considered significant. Results: Neuromechanical analyses were consistent with bolus presence in the transition zone (TZ) during the majority, but not all perceived swallows. Specifically, there was evidence of states not routinely observed in healthy swallowing: increased passive isometric pressure increase -PIPI (4% vs <1%), passive isometric pressure decrease -PIPD (6% vs 1%), and distended quiescence -DQ (21% vs 7%) in the TZ during perceived swallows.
Results Aim: To study the relationship between GA, transient lower esophageal sphincter relaxations (TLESRs) and reflux events in healthy volunteers (HV) and patients with overlapping GERD and FD symptoms. Methods: Twenty HV (10 m, 23 years (range 19-36)) with no prior history of digestive disease and 9 patients with both GERD and FD symptoms (2 m, 34 years (range 20-54)) underwent combined high resolution impedance and manometry (HRiM) monitoring, with the catheter placed into the stomach. Recordings were made 30 min before and 60 min after a high carbohydrate and high fat solid meal (1000 kcal). Medical Measurement System (MMS) software was used for  2 0 1 6 , 2 8  , S U P P L E M E NT 1 , 5 --1 0 8 78 analysis. TLESRs and reflux events were quantified. In sensors 5 cm below the lower border of the lower esophageal sphincter (LES), the intra-gastric pressure (IGP) before, during and after the meal was measured.
282 Postprandial intragastric pH levels are elevated for significantly longer on reflux monitoring in patients with confirmed gastroparesis to a median of 4. 5 during a meal, and gradually returns to fasting-state as the buffer (i. e. ingested food) leaves the stomach  (Gardner et al. , 2002). We aimed to establish if reflux monitoring, where intragastric pH is recorded routinely, could also detect longer periods of high pH postprandially in subjects with confirmed gastroparesis compared to those with normal gastric emptying. Methods: From our database of patients seen in our tertiary referral gastrointestinal physiology unit, we identified patients with confirmed delayed gastric emptying on 13C-octanoic acid breath test from 2009 to 2015 who had also undergone 24-h reflux monitoring off PPI.
A solid-state catheter with 36 sensors (at 3 cm intervals), was placed in a prepared colon with the aid of colonoscopy or intervention radiology via the anus (retrograde) or through a cecostomy (anterograde). Recordings included 2 h before and after a meal, followed by 1 hr of recording after infusion of bisacodyl through the central lumen of the catheter. These data were compared with; (i) 18 children (median age 15 years, 2 male) with intractable FC studied in Amsterdam, the Netherlands (water-perfused manometry, 36 channels, at 1. 5 cm intervals); and; (ii) 12 healthy adults (median age 51 years, 5 male) studied in Adelaide, Australia (fiber-optic manometry; 72 sensors at 1 cm intervals). The dominant frequencies of contractile activity were quantified for pre-and post-prandial recordings.
317 Abnormal autonomic function testing suggests chronic globus sensation is a functional disorder in teenage females T. CEICEIREGA* and N. A. TIPNIS † *Weil-Cornell Medical Center, New York, NY, USA and † University of Mississippi Medical Center, Jackson, MS, USA Background: Globus sensation is a condition described a feeling of a foreign body stuck in the throat. It is a troubling symptom for many, and a specific cause for the symptom can be difficult to elucidate. Aim: We describe a series of consecutive patients referred for the evaluation of globus sensation to a tertiary care, academic medical center. Methods: The Investigation Review Board at the University of Mississippi Medical Center approved the case series. From September 2013-February 2016, consecutive cases of globus sensation were reviewed and demographic, clinical, radiographic, endoscopic, manometric and autonomic testing data extracted.
Research funding was provided by Ironwood Pharmaceuticals. 85 Distribution of monoamine oxidase in human colon and its alteration in 6-hydroxydopamine-induced Parkinson's disease rats C. Z. LIU*, L. S. LI*, Y. LI † , X. L. ZHANG* and J. X. ZHU* *Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China and † Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.
This study was supported by a grant of the Korea Healthcare Technology R & D Project, Ministry of Health & Welfare, Republic of Korea (nos'. HI14C2206, HI06C0868 and HI15C3078), and the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MEST) (no. 2011-0019632). 166 BGP-15 co-treatment protects against oxaliplatininduced neuronal loss and alleviates gastrointestinal dysfunction R. M. MCQUADE*, V. STOJANOVSKA*, J. C. SORENSEN*, J. C. BORNSTEIN † , A. C. PETERSEN ‡, § ,.
Efficacy and tolerability of linaclotide and plecanatide in treating Irritable Bowel Syndrome with constipation (IBS-C) and chronic idiopathic constipation (CIC): A meta-analysis E. SHAH*, M. PIMENTEL † , H. KIM* and P. SCHOENFELD* *University of Michigan, Ann Arbor, MI, USA and † Cedars-Sinai Medical Center, Los Angeles, CA, USA Background: In this study, we contrast the rates of diarrhea adverse events (AE) and efficacy of the guanylate cyclase-C agonists linaclotide and plecanatide in treating IBS-C and CIC. Methods: Literature search: PubMED and Cochrane databases, abstracts from UEGW, DDW, and ACG since 2005, and SEC filings. Study selection: double-blind, placebo-controlled RCTs of IBS-C or CIC patients treated for at least 14 days using dosages that are FDAapproved (linaclotide) or evaluated in Phase III RCTs (plecanatide).
345 Efficacy and tolerability of linaclotide and plecanatide in treating Irritable Bowel Syndrome with constipation (IBS-C) and chronic idiopathic constipation (CIC): A meta-analysis E. SHAH*, M. PIMENTEL † , H. KIM* and P. SCHOENFELD* *University of Michigan, Ann Arbor, MI, USA and † Cedars-Sinai Medical Center, Los Angeles, CA, USA Background: In this study, we contrast the rates of diarrhea adverse events (AE) and efficacy of the guanylate cyclase-C agonists linaclotide and plecanatide in treating IBS-C and CIC. Methods: Literature search: PubMED and Cochrane databases, abstracts from UEGW, DDW, and ACG since 2005, and SEC filings. Study selection: double-blind, placebo-controlled RCTs of IBS-C or CIC patients treated for at least 14 days using dosages that are FDAapproved (linaclotide) or evaluated in Phase III RCTs (plecanatide).
Acknowledging this common comorbidity may facili- tate recognition and treatment, and opens new ques- tions as to the pathways and mechanisms of the association. 190 Reflux finding score for laryngopharygeal reflux observed by esophagogastroduodenoscopy H. KIM and J. LEE Yonsei University Wonju College of Medicine, Wonju, Korea Backgrounds: Esophagogastroduodenoscopy (EGD) can observe laryngopharynx more precisely than laryn- goscopy. This study aimed to investigate the association between laryngopharygeal reflux and gastroesophageal reflux disease (GERD) scoring by EGD and question- naires. Methods: The patients diagnosed with erosive esophagitis by EGD were enrolled. They were requested to fill three questionnaires, such as GERDQ, QUEST and reflux symptom index (RSI) for laryngopharygeal reflux.
This supplement contains three articles that aim to disseminate the major findings from these meetings and to align these findings with data available from a systematic review of the published literature base. Electronic database searches (NCBI PubMed) formed the basis of the literature search within the time frame (1952 to December 2014). Key search terms included 'transthyretin familial amyloid polyneuropathy,' 'familial amyloid polyneuropathy,' 'transthyretin amyloidosis,' 'TTR-FAP,' 'TTR-FAP and Europe,' and 'TTR-FAP and Bulgaria/Cyprus/France/Germany/Italy/the Netherlands/Portugal/Spain/Sweden/Turkey. ' Essentially, this supplement lays the foundations for expert recommendations on the current epidemiology, genetic basis, diagnosis, management, and followup of TTR-FAP, highlighting the need for genetic counselling and early detection of TTR-FAP among asymptomatic carriers.
Acknowledgements Members of the ATTReuNET who provided countryspecific information for this article were  David Adams  [ CHU Bicetre (APHP), Universite´Paris-Sud, Paris, France ];  Juan Buades  ( Servicio de Medicina Interna, Hospital Son Llatzer, Palma de Mallorca, Spain );  Josep M. Campistol  ( Instituto Clı ´nico de Nefrologı ´a y Urologı ´a ICNU, Barcelona, Spain );  Teresa Coelho  ( Hospital Santo Antonio, Centro Hospitalar do Porto, Porto, Portugal );  Lucı ´a Galan  ( Servicio de Neurologı ´a, Hospital Clı ´nico San Carlos, Madrid, Spain );  Ivailo Tournev  ( Department of Neurology, Medical University -Sofia , and  Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria) ;  Velina Guergueltcheva  ( University Hospital Sofiamed, Sofia, Bulgaria );  Bouke P.
In Situ hybridization All solutions were made using diethylpyrocarbonate (DEPC, Sigma, St. Louis, MO, USA) treated water. Stomach sections were fixed with 4% paraformaldehyde in PBS, pH 7. 5. After washing with PBS for 5 min, the sections were incubated with 0. 5M HCl in DEPC water for 5 min and then washed in PBS twice for 3 min. Further, the sections were treated with 0. 25% acetic anhydride in 0. 1M triethanolamine, pH 8. 0, for 20 min. The sections were washed in PBS twice for 3 min, and immersed in a graded ethanol series (70, 80, and 99. 5%) for 2 min each. Finally, sections were dried for 30 min and then stored at -80°C. RNA probes specific to preproghrelin mRNA (Accession number: NM_021669. 2, National Center for Biotechnology Information, Bethesda, MD, USA) were prepared from rat stomach mRNA.
Then, between injections of each dilution, the binding surface was regenerated with 10 mM NaOH resulting in the return of the sensorgram to the same baseline. The affinity kinetic data were analysed using BiaEvaluation 4. 1. 1 programme (GE Healthcare). For fitting kinetic data, the Langmuir's 1:1 model was used, and the sample values were corrected by subtracting the blank values resulting from the injection of HBS-EP buffer.
statistical analysis Group differences were statistically analyzed using GraphPad Prism 5. 02 (GraphPad software Inc. , San Diego, CA, USA). Differences in daily food intake, body weight, and water intake were analyzed by a two-way repeated measurements (RM) ANOVA taking in account effects of time and treatment followed by the Bonferroni post-tests. Individual groups were compared using the Student's t-test or Mann-Whitney test according to the Kolmogorov-Smirnov (KS) normality test, and p < 0. 05 was considered as significant.