bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of small bowel capsule endoscopy and ileocolonoscopy in patients with nonspecific but suggestive symptoms of Crohn’s disease
Authors: Mitselos Ioannis V. , Christodoulou Dimitrios K. , Katsanos Konstantinos H. , Tatsioni Athina , Rapti Aleksandra , Eliakim Rami , Tsianos Epameinondas V. 
Published: May 2016

Objectives
Ileocolonoscopy (IC) and small bowel capsule endoscopy (SBCE) are essential tools in the investigation of suspected small bowel Crohn’s disease (CD). Overutilization of SBCE should be avoided as it leads to unwanted healthcare expenses; thus, it is recommended when IC is normal and CD is still highly suspected. Our aim was to compare the role of SBCE and IC in the investigation of suspected CD irrespective of its location and assess the additional diagnostic benefit of SBCE over IC.

Methods
This was a retrospective study of 91 patients with chronic abdominal pain and/or diarrhea. All patients were evaluated with both colonoscopy (with terminal ileum intubation where possible) and SBCE. The severity of inflammation on SBCE was assessed using the Lewis Score. Endoscopic findings were analyzed toward CD diagnosis.

Results
The sensitivity of IC and SBCE in the diagnosis of either small bowel or colonic CD was 81.82 and 63.64%, whereas the specificity was 77.50 and 92.50%, respectively. Positive and negative predictive value was 33.33 and 96.88% for IC, as well as 53.85 and 94.87% for SBCE. Area under receiver operating characteristic curve was 0.797 for IC and 0.781 for SBCE. IC was superior to SBCE in diagnosing small and large bowel CD. SBCE showed the true extent of CD in one patient missed by IC. It identified lesions suggestive of CD in three patients with normal IC, one of whom was finally diagnosed with CD.

Conclusion
IC should be the initial diagnostic test in patients with nonspecific, but suggestive symptoms of CD. SBCE offers additional information on small bowel mucosa and disease extent.
Clostridium Difficile Infection in Children
Authors: Borali Elena , De Giacomo Costantino 
Published: May 2016

ABSTRACTClostridium difficile is a sporogenic, anaerobic, Gram‐positive, emerging enteric pathogen. It represents the most common cause of health care‐associated diarrhoea in the United States, with significantly associated morbidity, mortality, and health care costs. Historically regarded as a little more than an innocent coloniser bystander of the gastrointestinal tract of children, C difficile has increasingly demonstrated its behaviour as a true pathogen in the paediatric age groups. This organism may be responsible for a broad spectrum of diseases in children, ranging from self‐limiting secretory diarrhoea to life‐threatening conditions, such as pseudomembranous colitis, toxic megacolon, intestinal perforation, and septic shock. The incidence and severity of C difficile infection are, however, not completely understood in this population. In particular, although asymptomatic carriage remains high among infants, the clinical significance of detecting C difficile in children aged 1 to 3 years is not fully understood. Moreover, recent epidemiological surveillance has demonstrated a rise in the incidence of C difficile infection, particularly in the community and in low‐risk settings. Interestingly, such cases may not show the disease pattern to be associated with typical risk factors, such as recent exposure to antimicrobial drugs or on‐going contacts with the health care system.The purpose of the present review is to present the features of C difficile infection that are unique to paediatric patients and to update paediatricians on information and recommendations regarding C difficile infection in children.
A Qualitative Study Exploring Moral Distress Among Pediatric Resuscitation Team Clinicians: Challenges to Professional Integrity*
Authors: Thomas Tessy A. , Thammasitboon Satid , Balmer Dorene F. , Roy Kevin , McCullough Laurence B. 
Published: May 2016

Objective:
Our study objectives were to explore moral distress among pediatric team clinicians within the context of resuscitation experiences, and determine whether there were any distinctively ethical perspectives on moral distress that could be conceptualized as challenges to professional integrity, rather than to previously described psychological responses of clinicians.

Design:
Descriptive, exploratory qualitative study.

Setting:
A large tertiary pediatric academic hospital in Houston, TX.

Subjects:
Twenty-five PICU resuscitation team clinicians were interviewed from December 2012 to April 2013.

Interventions:
None.

Measurements and Main Results:
All clinicians reported experiencing moral distress during certain resuscitations. Twenty-one of 25 clinicians reflected and acknowledged that their sense of professional integrity had been challenged during those resuscitation events. Four main components of resuscitation experience that induced moral distress were identified: 1) experiences where there was lack of understanding of the big picture; 2) experiences where there was suboptimal team leadership; 3) experiences where there was variable meanings to the word “resuscitation”; and 4) experiences were there was uncertainty of role responsibility.

Conclusions:
The perception of moral distress exists among pediatric clinicians during resuscitations and could be conceptualized as challenges to professional integrity. This ethical framework offers an alternative approach to understanding and investigating the complex layers of moral distress.
The last common ancestor of most bilaterian animals possessed at least 9 opsins
Authors: Ramirez MD , Pairett AN , Pankey MS , Serb JM , Speiser DI , Swafford AJ , Oakley TH 
Published: May 2016

AbstractThe opsin gene family encodes key proteins animals use to sense light and has expanded dramatically since it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in both the last common ancestor of the Nephrozoa (bilaterians excluding Xenoacoelomorpha), and the ancestor of Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 14 animal phyla, especially the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of at least nine opsin paralogs in the bilaterian ancestor and at least four opsin paralogs in the last common ancestor of Cnidaria + Bilateria. Thus, the kernels of extant opsin diversity arose much earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular sensors.
Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
Authors: Mangul Serghei , Yang Harry Taegyun , Strauli Nicolas , Gruhl Franziska , Porath Hagit T. , Hsieh Kevin , Chen Linus , Daley Timothy , Christenson Stephanie , Wesolowska-Andersen Agata , Spreafico Roberto , Rios Cydney , Eng Celeste , Smith Andrew D. , Hernandez Ryan D. , Ophoff Roel A. , Santana Jose Rodriguez , Levanon Erez Y. , Woodruff Prescott G. , Burchard Esteban , Seibold Max A. , Shifman Sagiv , Eskin Eleazar , Zaitlen Noah 
Published: May 2016

AbstractHigh throughput RNA sequencing technologies have provided invaluable research opportunities across distinct scientific domains by producing quantitative readouts of the transcriptional activity of both entire cellular populations and single cells. The majority of RNA-Seq analyses begin by mapping each experimentally produced sequence (i.e., read) to a set of annotated reference sequences for the organism of interest. For both biological and technical reasons, a significant fraction of reads remains unmapped. In this work, we develop Read Origin Protocol (ROP) to discover the source of all reads originating from complex RNA molecules, recombinant T and B cell receptors, and microbial communities. We applied ROP to 8,641 samples across 630 individuals from 54 tissues. A fraction of RNA-Seq data (n=86) was obtained in-house; the remaining data was obtained from the Genotype-Tissue Expression (GTEx v6) project. To generalize the reported number of accounted reads, we also performed ROP analysis on thousands of different, randomly selected, and publicly available RNA-Seq samples in the Sequence Read Archive (SRA). Our approach can account for 99.9% of 1 trillion reads of various read length across the merged dataset (n=10641). Using in-house RNA-Seq data, we show that immune profiles of asthmatic individuals are significantly different from the profiles of control individuals, with decreased average per sample T and B cell receptor diversity. We also show that immune diversity is inversely correlated with microbial load. Our results demonstrate the potential of ROP to exploit unmapped reads in order to better understand the functional mechanisms underlying connections between the immune system, microbiome, human gene expression, and disease etiology. ROP is freely available athttps://github.com/smangul1/ropand currently supports human and mouse RNA-Seq reads.
Parasites and invasions: changes in gastrointestinal helminth assemblages in invasive and native rodents in senegal
Authors: Diagne Christophe , Ribas Alexis , Charbonnel Nathalie , Dalecky Ambroise , Tatard Caroline , Gauthier Philippe , Haukisalmi Voitto , Fossati-Gaschignard Odile , Bâ Khalilou , Kane Mamadou , Niang Youssoupha , Diallo Mamoudou , Sow Aliou , Piry Sylvain , Sembène Mbacké , Brouat Carine 
Published: May 2016

AbstractUnderstanding why some exotic species become widespread and abundant in their colonized range is a fundamental issue that still needs to be addressed. Among many hypotheses, newly established host populations may benefit from a parasite loss (“enemy release” hypothesis) through impoverishment of their original parasite communities or reduced infection levels. Moreover, the fitness of competing native hosts may be affected by the acquisition of exotic taxa from invaders (“parasite spillover”) and/or by an increased transmission risk of native parasites due to their amplification by invaders (“parasite spillback”). We focused on gastrointestinal helminth communities to determine whether these predictions could explain the ongoing invasion success of the commensal house mouse (Mus musculus domesticus) and black rat (Rattus rattus), as well as the associated drop of native Mastomys species, in Senegal. For both invasive species, our results were consistent with the predictions of the enemy release hypothesis. A decrease of helminth overall prevalence and individual species richness was observed along the invasion gradients as well as lower specific prevalence/abundance (Aspiculuris tetraptera in M. m. domesticus, Hymenolepis diminuta in R. rattus) on the invasion fronts. Conversely, we did not find strong evidence of helminth spill-over or spill-back in invasion fronts, where native and invasive rodents co-occurred. Further experimental research is needed to determine whether and how the loss of helminths and reduced infection levels along invasion routes may result in any advantageous effects on invader fitness and competitive advantage.
Blind testing cross-linking/mass spectrometry under the auspices of the 11thcritical assessment of methods of protein structure prediction (CASP11)
Authors: Belsom Adam , Schneider Michael , Fischer Lutz , Brock Oliver , Rappsilber Juri 
Published: May 2016

SummaryDetermining the structure of a protein by any method requires varies contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry data in combination withab initiostructure prediction by conformational space search determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structure of up to 2.53 Å, or 3.38 Å in the context of blood serum. This paper reports the blind test on the readiness of this technology through the help of Critical Assessment of protein Structure Prediction (CASP). We identified between 201-381 unique residue pairs at an estimated 5% FDR (at link level albeit with missing site assignment precision evaluation), for the four proteins that we provided data for. This equates to between 0.63-1.20 proximal residues per residue, which is comparable to that obtained in the HSA study (0.85 links per residue at 5% FDR). Nevertheless, initial results of CASP11 have suggested that improvements in structure prediction using cross-link data are slight. Most significantly, however, CASP11 revealed to us some of the current limitations of cross-linking, spelling out areas in which the method must develop in future: links spread unevenly over sequence and beta sheets both lacked links and suffered from weak definition of observed links over structure. With CASP12 taking place this year and biannually in the future, blind testing low-resolution structure analysis tools is a worthwhile and feasible undertaking. Data are available via ProteomeXchange with identifier PXD003643.The abbreviations used areCLMScross-linking/mass spectrometry;NHSN-hydroxysuccinimide;NMRnuclear magnetic resonance;sulfo-SDAsulfo-NHSdiazirine, sulfosuccinimidyl 4,4’-azipentanoate;FDRfalse discovery rate;MBSmodel-based search;HSAhuman serum albumin;RMSDroot-mean-square deviation;CASPCritical Assessment of protein Structure Prediction;Tristris(hydroxymethyl)aminomethane;PESpolyethersulphone;IAAiodoacetamide;LTQlinear trap quadrupole;MS2tandem MS scan;LC-MSliquid chromatography mass spectrometry;FMfree modelling.
Quantifying the degree of sharing of genetic and non-genetic causes of gene expression variability across four tissues
Authors: Buil Alfonso , Viñuela Ana , Brown Andrew A. , Davies Matthew N. , Padioleau Ismael , Bielser Deborah , Romano Luciana , Glass Daniel , Di Meglio Paola , Small Kerrin S. , Spector Timothy D. , Dermitzakis Emmanouil T. 
Published: May 2016

AbstractGene expression can provide biological mechanisms which underlie genetic associations with complex traits and diseases, but often the most relevant tissue for the trait is inaccessible and a proxy is the only alternative. Here, we investigate shared and tissue specific patterns of variability in expression in multiple tissues, to quantify the degree of sharing of causes (genetic or non-genetic) of variability in gene expression among tissues. Using gene expression in ~800 female twins from the TwinsUK cohort in skin, fat, whole blood and lymphoblastoid cell lines (LCLs), we identified 9166 significant cis-eQTLs in fat, 9551 in LCLs, 8731 in skin and 5313 in blood (1% FDR). We observed up to 80% of cis-eQTLs are shared in pairs of tissues. In addition, the cis genetic correlation between tissues is > 90% for 35% of the genes, indicating for these genes a largely tissue-shared component of cis regulation. However, variance components show that cis genetic signals explain only a small fraction of the variation in expression, with from 67–87% of the variance explained by environmental factors, and 53% of the genetic effects occurring in trans. We observe a trans genetic correlation of 0 for all genes except a few which show correlation between fat and skin expression. The environmental effects are also observed to be entirely tissue specific, despite related tissues largely sharing exposures. These results demonstrate that patterns of gene expression are largely tissue specific, strongly supporting the need to study higher order regulatory interactions in the appropriate tissue context with large samples sizes and diversity of environmental contexts.
Redundancy, feedback, and robustness in theArabidopsis thaliana BZR/BEHgene family
Authors: Lachowiec Jennifer , Mason G. Alex , Schultz Karla , Queitsch Christine 
Published: May 2016

ABSTRACTOrganismal development is remarkably robust, tolerating stochastic errors to produce consistent, so-called canalized adult phenotypes. The mechanistic underpinnings of developmental robustness are poorly understood, but recent studies implicate certain features of genetic networks such as functional redundancy, connectivity, and feedback. Here, we examine theBRZ/BEHgene family, whose function is crucial for embryonic stem development in the plantArabidopsis thaliana, to test current assumptions on functional redundancy and trait robustness. Our analyses ofBRZ/BEHgene mutants and mutant combinations revealed that functional redundancy among gene family members does not contribute to trait robustness. Connectivity is another commonly cited determinant of robustness; however, we found no correlation between connectivity among gene family members or their connectivity with other transcription factors and effects on robustness. Instead, we found that onlyBEH4, the most ancient family member, modulated developmental robustness. We present evidence that regulatory cross-talk among gene family members is integrated byBEH4and promotes wild-type levels of developmental robustness. Further, the chaperone HSP90, a known determinant of developmental robustness, appears to act via BEH4 in maintaining robustness of embryonic stem length. In summary, we demonstrate that even among closely related transcription factors, trait robustness can arise through the activity of a single gene family member, challenging common assumptions about the molecular underpinnings of robustness.
Clinicopathological analysis of 384 cases of poroid neoplasms including 98 cases of apocrine type cases
Authors: Ito Keigo , Ansai Shin‐ichi , Fukumoto Takaya , Anan Takashi , Kimura Tetsunori 
Published: May 2016

AbstractWe examined 384 cases of poroid neoplasms. Most cases (n = 279, 72.7%) exhibited the features of only one subtype. One hundred and ninety‐eight cases (51.6%) showed only the features of poroma (P), 20 (5.2%) hidroacanthoma simplex (HS), five (1.3%) dermal duct tumor (D) and 56 (14.6%) hidradenoma (HA). Composite tumors of those four subtypes were observed in 105 cases (27.3%). In the trunk and lower extremities, lesions with the features of P were observed at higher rates than other sites. Those of HS and D were more frequently observed in the lower extremities. Those of HA were seen at higher rates in the scalp, face, neck and genitalia. Ninety‐eight cases (25.5%) showed decapitation secretion and diagnosed as apocrine type lesion. Apocrine type lesions were frequently observed in the lesions on the genitalia (40.0%), scalp (31.8%) and trunk (31.1%), whereas at lower rates in those on the neck (21.4%) and lower extremities (24.0%). In apocrine type cases, the lesions were located more frequently on the scalp and trunk than non‐apocrine type, whereas were less frequent on extremities. The rate of apocrine type lesions in the cases with only one subtype (19.7%) was lower than that of those with composite tumors (41.0%). In the apocrine type (43.9%), composite tumors are more frequent than in the non‐apocrine type (21.7%). In D (40.8%) and HA (32.3%), apocrine type lesions were more frequently observed than other subtypes. In conclusion, it should be noted that a quarter of poroid neoplasms are composite tumors and/or show apocrine differentiation.
Predator identity influences metacommunity assembly
Authors: Johnston Nicole K. , Pu Zhichao , Jiang Lin 
Published: May 2016

Summary

Predation is among the most important biotic factors influencing natural communities, yet we have a rather rudimentary understanding of its role in modulating metacommunity assembly.

We experimentally examined the effects of two different predators (a generalist and a specialist) on metacommunity assembly, using protist microcosm metacommunities that varied in predator identity, dispersal among local communities and the history of species colonization into local communities.

Generalist predation resulted in reduced α diversity and increased β diversity irrespective of dispersal, likely due to predation‐induced stochastic extinction of different prey species in different local communities. Dispersal, however, induced source–sink dynamics in the presence of specialist predators, resulting in higher α diversity and marginally lower β diversity.

These results demonstrate the distinct effects of different predators on prey metacommunity assembly, emphasizing the need to explore the role of predator diet breadth in structuring metacommunities.
Preventive Action in World Politics
Authors: Garcia Denise , Herz Monica 
Published: May 2016

AbstractIn only a few instances in international relations, states anticipate major problems and address them before they become disastrous: negotiating and creating new international norms to avert human and financial loss. One example is the Protocol banning laser weapons that can permanently blind. It was created in the mid‐1990s before the weapons were fully operational and set a powerful norm that banned their future development. With new evolving technologies that have unparalleled capacity to harm and maim, such as fully autonomous weapons systems (killer robots), it is imperative that states take preventive action and create new multilateral agreements to cope with problems yet to materialize. This article aims to initiate the discussion of when states act preventively to avert major future problems. It advances three initial explanatory propositions on preventive multilateralism in areas of ‘commonly perceived global dimension of future potential harm’ to improve states’ security dilemmas; based upon reputation and humanitarian, material concerns, and national security, and presents the initial discussion toward a world politics of prevention.