bluuebunny/crossref_metadata_2025_split huggingface dataset:
Link Between Celiac Disease and Inflammatory Bowel Disease
Authors: Shah Ayesha , Walker Marjorie , Burger Daniel , Martin Neal , von Wulffen Moritz , Koloski Natasha , Jones Mike , Talley Nicholas J. , Holtmann Gerald J. 
Published: May 2018

Goal:
The aim of this analysis was to assess in patients with inflammatory bowel disease (IBD) the risk of celiac disease and in celiac disease patients the risk of IBD.

Background:
Previous studies report a possible association between IBD and celiac disease; however, this link is controversial.

Study:
Using the search terms “inflammatory bowel disease” and “celiac disease,” we identified initially 1525 publications. In total 27 studies met inclusion criteria. Proportions and 95% confidence intervals (CIs) for the prevalence of IBD in celiac disease and vice versa were compared with published prevalence rates for the respective geographic regions.

Results:
We included 41,482 adult IBD patients (20,357 with Crohn’s disease; 19,791 with ulcerative colitis; and 459 patients with celiac disease). Overall, in IBD patients the prevalence of celiac disease was 1110/100,000 (95% CI, 1010-1210/100,000) as compared with a prevalence of 620/100,000 (95% CI, 610-630/100,000) in the respective populations (odds ratio, 2.23; 95% CI, 1.99-2.50). In contrast, in patients with celiac disease, 2130/100,000 had IBD (95% CI, 1590-2670/100,000) as compared with 260/100,000 (95% CI, 250/100,000-270/100,000) in the respective populations (odds ratio, 11.10; 95% CI, 8.55-14.40). This effect was not different for ulcerative colitis and Crohn’s disease. Although there was no evidence for publication bias for celiac disease in IBD, the funnel plot suggested that the association between IBD in celiac disease might be influenced by publication bias.

Conclusions:
The data are consistent with the notion that celiac disease is a risk factor for IBD and to lesser degree patients with IBD have an increased risk of celiac disease.
History of Acquired Monosaccharide Intolerance in Houston, Texas
Authors: Klish William J. 
Published: May 2018

ABSTRACTIt is appropriate that we begin the clinical part of this conference with a discussion of acquired monosaccharide intolerance. This disease is the most severe form of carbohydrate malabsorption and maldigestion that can afflict an infant. The following article describes the pathophysiology of the disease, as well as its treatment, much of which was based on studies done by the Section of Pediatric Gastroenterology and Nutrition at Baylor College of Medicine. Acquired monosaccharide intolerance has almost disappeared from the United States but remains a problem in the developing world where it is included as part of the diagnosis of environmental enteropathy. Present research on this disease seems to sometimes duplicate what is already known.
Posttranslational Processing and Function of Mucosal Maltases
Authors: Amiri Mahdi , Naim Hassan Y. 
Published: May 2018

ABSTRACTThe final step of carbohydrate digestion in the intestine is performed by 2 major α‐glucosidases of the intestinal mucosa, sucrase‐isomaltase (SI) and maltase‐glucoamylase. Both of these enzymes are type II membrane glycoproteins, which share a significant level of homology in gene and protein structures and yet have differences in the posttranslational processing, substrate specificity and functional capacity. Insufficient activity of these disaccharidases particularly SI as a result of genetic mutations or secondary intestinal pathologies is associated with carbohydrate maldigestion and gastrointestinal intolerances. This review will discuss the maturation profiles of SI and maltase‐glucoamylase relative to their functional capacities and deficiencies.
13C‐Labeled‐Starch Breath Test in Congenital Sucrase‐isomaltase Deficiency
Authors: Robayo‐Torres Claudia C. , Diaz‐Sotomayor Marisela , Hamaker Bruce R. , Baker Susan S. , Chumpitazi Bruno P. , Opekun Antone R. , Nichols Buford L. 
Published: May 2018

ABSTRACTBackground and Hypotheses:Human starch digestion is a multienzyme process involving 6 different enzymes: salivary and pancreatic α‐amylase; sucrase and isomaltase (from sucrose‐isomaltase [SI]), and maltase and glucoamylase (from maltase‐glucoamylase [MGAM]). Together these enzymes cleave starch to smaller molecules ultimately resulting in the absorbable monosaccharide glucose. Approximately 80% of all mucosal maltase activity is accounted for by SI and the reminder by MGAM. Clinical studies suggest that starch may be poorly digested in those with congenital sucrase‐isomaltase deficiency (CSID). Poor starch digestion occurs in individuals with CSID and can be documented using a noninvasive 13C‐breath test (BT).Methods:13C‐Labled starch was used as a test BT substrate in children with CSID. Sucrase deficiency was previously documented in study subjects by both duodenal biopsy enzyme assays and 13C‐sucrose BT. Breath 13CO2 was quantitated at intervals before and after serial 13C‐substrate loads (glucose followed 75 minutes later by starch). Variations in metabolism were normalized against 13C‐glucose BT (coefficient of glucose absorption). Control subjects consisted of healthy family members and a group of children with functional abdominal pain with biopsy‐proven sucrase sufficiency.Results:Children with CSID had a significant reduction of 13C‐starch digestion mirroring that of their duodenal sucrase and maltase activity and 13C‐sucrase BT.Conclusions:In children with CSID, starch digestion may be impaired. In children with CSID, starch digestion correlates well with measures of sucrase activity.
Hemodynamic Shock Caused by Tension Pneumoperitoneum in a 5-Year-Old Girl
Authors: Zentar Marie-Sophie , Berteloot Laureline , Khen Dunlop Naziha , Bustarret Olivier , Pigneur Bénédicte , Cheron Gérard , Angoulvant François 
Published: May 2018

Abstract
Tension pneumoperitoneum is a relatively rare occurrence in the pediatric population. However, tension pneumoperitoneum is associated with significant morbidity and mortality if it is not promptly diagnosed and treated. A 5-year-old girl was admitted to emergency department with abdominal pain. She was in shock, and the radiograph film of the abdomen revealed a voluminous tension pneumoperitoneum. Aggressive fluid challenges were performed in intensive care followed by urgent laparotomy. Primary abdominal compartment due to trapped gas caused a decreased venous return and visceral perfusion. In the absence of hemodynamic improvement after vascular filling, needle decompression was performed before surgery.
Toddler's Paralysis
Authors: Kahne Kimberly Renee , Tay Ee Tein 
Published: May 2018

Abstract
Vegetarian and vegan diets are gaining popularity in the United States. Although appropriately planned vegetarian diets, including vegan diets, are healthful and nutritionally adequate and may provide health benefits in the prevention and treatment of certain diseases, not all families are aware of the nutritional supplements that may be required for their children. We describe a case of a 2-year-old previously healthy child consuming a vegan diet who presented to the pediatric emergency department with an acute inability to move her legs. Ionized calcium was found to be 0.89 mmol/L, and symptoms completely resolved within 2 hours of calcium gluconate infusion.
Temporal Uptake Patterns of 18F-Fluorocholine Among Hyperfunctioning Parathyroid Glands
Authors: Morland David , Richard Capucine , Godard François , Deguelte Sophie , Delemer Brigitte 
Published: May 2018

Abstract
Optimal scan time of 18F-fluorocholine (FCH) PET/CT for localization of hyperfunctioning parathyroid glands is poorly documented. We report a small series of 9 histologically proven hyperfunctioning parathyroid gland with heterogeneous temporal uptake profile. Thirty-minute dynamic acquisition starting just after 18F-fluorocholine administration and delayed acquisition were recorded. Three different uptake patterns are seen (early washout, stable uptake, late increase) indicating the importance of an early (5–10 minutes) acquisition. A late acquisition (60 minutes) could be useful when the early acquisition is negative. No correlations were noted between uptake profile and histological or genetic results.
Quality and Safety in Health Care, Part XLIV
Authors: Harolds Jay A. 
Published: May 2018

Abstract
This article discusses 2 specialized implantable cardioverter defibrillator (ICD) devices. A special type of implantable device is available for cardiac resynchronization therapy, which can also have a defibrillator, in which case it is called a CRT-D device. In patients who meet guidelines for eligibility, a CRT-D will diminish the number of significant cardiac events including death. A subcutaneous ICD device does not need any leads placed in the vascular system and therefore does not have some of the complications that may be seen with transvenous ICDs. Also, there are patients who are not candidates for a typical ICD implantation. On the other hand, there are important disadvantages to the subcutaneous ICD.
IgG4-Related Disease Simulating Carcinoma Colon With Diffuse Peritoneal Carcinomatosis on 18F-FDG PET/CT
Authors: Vadi Shelvin Kumar , Parihar Ashwin Singh , Kumar Rajender , Singh Harmandeep , Mittal Bhagwant Rai , Bal Amanjit , Sinha Saroj Kumar 
Published: May 2018

Abstract
IgG4-related disease (IgG4-RD) continues to be a diagnostic challenge and a great mimicker of malignancies. We report here a case of young man who presented with subacute intestinal obstruction with initial imaging and clinical features suggestive of carcinoma colon. 18F-FDG PET/CT showed diffuse peritoneal carcinomatosis pattern typically seen with abdominal malignancies. However, the histopathology and the raised IgG4 levels diagnosed it to be IgG4-RD. Although 18F-FDG PET/CT has typical patterns corresponding to the multisystemic involvement of IgG4-RD, the index case did not show any such findings.
A Case of Juvenile Psammomatoid Ossifying Fibroma on Skull Base
Authors: Kim Do-Youn , Lee Oh Hyeong , Choi Gyeong Cheol , Cho Jin Hee 
Published: May 2018

Abstract
Juvenile psammomatoid ossifying fibroma (JPOF) is a rare tumor that occurs in maxillary sinus or orbit. Complete removal is required due to the aggressive and locally destructive nature. It is hard to distinguish from psammomatoid meningioma in cranial lesion and to remove completely. The authors are presenting a case of 26-year-old male with JPOF on skull base and report this case with review of literature.
A Giant Congenital Soft Tissue Sinonasal Fibromyxoma of the Nose in a Newborn Baby
Authors: Yucel Ekici Nur , Yucel Gül , Haytoğlu Suheyl , Küllahci Özgür 
Published: May 2018

Abstract
Myxomas of the nose are very rare benign neoplasms. They grow slowly, infiltrate the surrounding bone cortex, and develop multiple local recurrences with no distant metastasis. Almost, even knowing seen at any age, it is very rare in newborn. The authors present a patient with sinonasal soft tissue fibromyxoma in a newborn baby nose followed by the literature.
Endoscopy-Assisted Frontal Sinus Obliteration
Authors: Jaźwiec Anna Maria , Rechner Benjamin , Komorowska-Timek Ewa 
Published: May 2018

Abstract
Comminuted fractures of the anterior table of the frontal sinus involving frontonasal ducts are traditionally treated with sinus obliteration. This technique entails precise mucosa removal which requires unimpeded visualization of the bony recesses. To achieve adequate access to the mucosa, temporary removal of a large part of the frontal bone may often be necessary. This in turn increases fracture comminution requiring placement of additional hardware associated with the risk for bony malalignment, infection, plate palpability, and visibility, especially in thin-skin individuals. Endoscopy, offering magnified visualization and less invasive access, is reported to be beneficial in sinus injury management. Therefore, it may be also considered an adjunct in open-approach management of severely comminuted fractures.
The authors’ patient suffered from comminuted fractures of the anterior and posterior tables of the frontal sinus and nasal bone fractures with involvement of the frontonasal ducts. Due to the extent of the injury he underwent frontal sinus obliteration procedure using the pericranial flap. To avoid additional osteotomy, endoscopic approach was undertaken to achieve the complete removal of the sinus mucosa. The fracture by itself offered an “access port” for the endoscope and electrical cautery. The patient's recovery was uneventful.
Endoscopy employed in frontal sinus obliteration appears to be instrumental in obtaining meticulous mucosa removal, obviating the need for additional osteotomy of the frontal bone.
Extended Release Liposomal Bupivacaine Injection (Exparel) for Early Postoperative Pain Control Following Palatoplasty
Authors: Day Kristopher M. , Nair Narayanan M. , Sargent Larry A. 
Published: May 2018

Introduction:
Liposomal bupivacaine (LB) is a long-acting local anesthetic reported to decrease postoperative pain in adults. The authors demonstrate the safe use of LB in pediatric patients with improved pain control following palatoplasty.

Materials and Methods:
Retrospective patient series of all single-surgeon palatoplasty patients treated at a tertiary craniofacial center from August 2014 to December 2015 were included. All patients received 1.3% LB intraoperatively as greater palatal nerve and surgical field blocks in 2-flap V–Y pushback palatoplasty. Postoperative oral intake, opioids administered, duration of hospitalization, and FLACC (face, legs, activity, cry, consolability) pain scores were measured.

Results:
Twenty-seven patients (16 males and 11 females, average age of 10.8 months, weight 8.8 kg) received 2.9 ± 0.9 mL (2.6 ± 1.9 mg/kg) 1.3% LB. Average FLACC scores were 2.4 ± 2.2/10 in the postanesthesia care unit and 3.8 ± 1.8/10 while inpatients. Oral intake was first tolerated 10.3 ± 11.5 hours postoperatively and tolerated 496.4 ± 354.2 mL orally in the first 24 hours postoperatively. Patients received 8.5 ± 8.4 mg hydrocodone equivalents (0.46 ± 0.45 mg/kg per d hydrocodone equivalents) and were discharged 2.1 ± 1.3 days postoperatively. Opioid-related adverse events included emesis in 7.4% and pruritis in 3.7% of patients.

Conclusions:
The LB may be used safely in pediatric patients. Intraoperative injection of LB during palatoplasty can yield low postoperative opioid use and an early and adequate volume of oral intake over an average hospital stay. Further cost-efficacy studies of LB are needed to assess its value in pediatric plastic surgery.
Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants
Authors: Cho Jungnam , Benoit Matthias , Catoni Marco , Drost Hajk-Georg , Brestovitsky Anna , Oosterbeek Matthijs , Paszkowski Jerzy 
Published: May 2018

AbstractRetrotransposons have played an important role in the evolution of host genomes1,2. Their impact on host chromosomes is mainly deduced from the composition of DNA sequences, which have been fixed over evolutionary time. These studies provide important “snapshots” reflecting historical activities of transposons but do not predict current transposition potential. We previously reported Sequence-Independent Retrotransposon Trapping (SIRT) as a methodology that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active LTR retrotransposons inArabidopsis9. Unfortunately, SIRT cannot be applied to large and transposon-rich genomes of crop plants. We have since developed an alternative approach named ALE-seq (amplification ofLTR ofeclDNAs followed bysequencing). ALE-seq reveals sequences of 5’ LTRs of eclDNAs after two-step amplification:in vitrotranscription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novelCopiafamily LTR retrotransposon,Go-on, which is activated by heat stress. Sequencing of rice accessions revealed thatGo-onhas preferentially accumulated inindicarice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulatedGypsyfamily of retrotransposons. Importantly, a bioinformatic pipeline adapted for ALE-seq data analyses allows the direct and reference-free annotation of new active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are unavailable or are of low quality.
The workings and failings of clustering T-cell receptor beta-chain sequences without a known epitope preference
Authors: Meysman Pieter , De Neuter Nicolas , Gielis Sofie , Bui Thi Danh , Ogunjimi Benson , Laukens Kris 
Published: May 2018

AbstractThe T-cell receptor is responsible for recognizing potentially harmful epitopes presented on cell surfaces. The binding rules that govern this recognition between receptor and epitope is currently an unsolved problem, yet one of great interest. Several methods have been proposed recently to perform supervised classification of T-cell receptor sequences, but this requires known examples of T-cell sequences for a given epitope. Here we study the viability of various methods to perform unsupervised clustering of distinct T-cell receptor sequences and how these clusters relate to their target epitope. The goal is to provide an overview of the performance of various distance metrics on two large independent T-cell receptor sequence data sets. Our results confirm the presence of structural distinct T-cell groups that target identical epitopes. In addition, we put forward several recommendations to perform T-cell receptor sequence clustering.
Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing
Authors: Humphreys David T , Fossat Nicolas , Tam Patrick P L , Ho Joshua W K 
Published: May 2018

ABSTRACTCircular RNAs (circRNAs) are a unique class of transcripts that can only be identified from sequence alignments spanning discordant junctions, commonly referred to as backsplice junctions (BSJ). The challenges of detecting a BSJ from short read high throughput sequencing (HTS) data has steered software development to focus primarily on algorithmic methods to accurately capture BSJs. Here we present Ularcirc, the first software tool that provides a complete circRNA workflow from detection, integrated visualization, quality filtering of BSJ and forward splicing junctions (FSJ), through to sequence retrieval and downstream functional analysis. More importantly, Ularcirc uses an innovative method to filter out false positive circRNAs coined read alignment distribution (RAD) score which allows detection of circRNAs independent of gene annotations. We used Ularcirc to characterise circRNAs from public and in-house generated data sets and demonstrate how to discover (i) novel splicing patterns of parental transcripts, (ii) internal splicing patterns of circRNA, and (iii) the complexity of BSJ formation. Furthermore, we identify circRNAs that have potential open reading frames longer than their linear sequence. Finally, we have identified and validated the presence of a novel class of circRNA generated from ApoA4 transcripts whose BSJ derive from multiple sites within coding exons. Ularcirc can be accessed via https://github.com/VCCRI/Ularcirc.
Marine mammals and sea turtles listed under the U.S. Endangered Species Act are recovering
Authors: Valdivia Abel , Wolf Shaye , Suckling Kieran 
Published: May 2018

AbstractThe U.S. Endangered Species Act (ESA) is the world’s strongest environmental law protecting imperiled plants and animals, and a growing number of marine species have been protected under this law as extinction risk in the oceans has increased. Marine mammals and sea turtles comprise 36% of the 161 ESA-listed marine species, yet analyses of recovery trends after listing are lacking. Here we gather the best available annual population estimates for all marine mammals (n=33) and sea turtles (n=29) listed under the ESA as species. Of these, we quantitatively analyze population trends, magnitude of population change, and recovery status for representative populations of 23 marine mammals and 9 sea turtles, which were listed for more than five years, occur in U.S. waters, and have data of sufficient quality and span of time for trend analyses. Using generalized linear and non-linear models, we found that 78% of marine mammals (n=18) and 78% of sea turtles (n=7) significantly increased after listing; 13% of marine mammals (n=3) and 22% of sea turtles (n=2) showed non-significant changes; while 9% of marine mammals (n=2), but no sea turtles declined after ESA protection. Overall, species with populations that increased in abundance were listed for 20 years or more (e.g., large whales, manatees, and sea turtles). Conservation measures triggered by ESA listing such as ending exploitation, tailored species management, and fishery regulations, among others, appear to have been largely successful in promoting species recovery, leading to the delisting of some species and to increases in most. These findings underscore the capacity of marine mammals and sea turtles to recover from substantial population declines when conservation actions under the ESA are implemented in a timely and effective manner.
DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression
Authors: Yang Laurence , Ebrahim Ali , Lloyd Colton J. , Saunders Michael A. , Palsson Bernhard O. 
Published: May 2018

AbstractGenome-scale models of metabolism and macromolecular expression (ME models) enable systems-level computation of proteome allocation coupled to metabolic phenotype. We develop dynamicME, an algorithm enabling time-course simulation of cell metabolism and protein expression. Our dynamicME correctly predicted the substrate utilization hierarchy on mixed carbon substrate medium. We also found good agreement between predicted and measured time-course expression profiles. ME models involve considerably more parameters than metabolic models (M models). We thus present two methods to calibrate ME models, specifically using time-course measurements such as from a (fed-) batch culture. Overall, dynamicME and the methods presented provide novel methods for understanding proteome allocation and metabolism under complex and transient environments, and to utilize time-course cell culture data for model-based interpretation or model refinement.
11 Million SNP Reference Profiles for Identity Searching Across Ethnicities, Kinship, and Admixture
Authors: Helfer Brian S. , Ricke Darrell O. 
Published: May 2018

AbstractHigh throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) provides additional applications for DNA forensics including identification, mixture analysis, kinship prediction, and biogeographic ancestry prediction. Public repositories of human genetic data are being rapidly generated and released, but the majorities of these samples are de-identified to protect privacy, and have little or no individual metadata such as appearance (photos), ethnicity, relatives, etc. A reference in silico dataset has been generated to enable development and testing of new DNA forensics algorithms. This dataset provides 11 million SNP profiles for individuals with defined ethnicities and family relationships spanning eight generations with admixture for a panel with 39,108 SNPs.