bluuebunny/crossref_metadata_2025_split huggingface dataset:
The obestatin/ghrelin ratio and ghrelin genetics in adult celiac patients before and after a gluten-free diet, in irritable bowel syndrome patients and healthy individuals
Authors: Russo Francesco , Chimienti Guglielmina , Linsalata Michele , Clemente Caterina , Orlando Antonella , Riezzo Giuseppe 
Published: October 2016

BackgroundGhrelin levels and obestatin/ghrelin ratio have been proposed as activity markers in ulcerative colitis, but no data are available in celiac disease (CD) and irritable bowel syndrome (IBS). Our aims were as follows: (a) to assess obestatin and ghrelin concentrations in adult active CD patients, diarrhea-predominant IBS (IBS-d), and healthy controls (HC) in relation to intestinal permeability; (b) to evaluate the ghrelin–obestatin profile in CD patients after a 1-year gluten-free diet (GFD); and (c) to establish the impact of ghrelin genetics.MethodsThe study included 31 CD patients, 28 IBS-d patients, and 19 HC. Intestinal permeability, assayed by high-performance liquid chromatography determination of urinary lactulose (La)/mannitol (Ma), and circulating concentrations of obestatin, ghrelin, and their ratio were evaluated at enrollment and after GFD. The ghrelin single nucleotide polymorphisms Arg51Gln (rs34911341), Leu72Met (rs696217), and Gln90Leu (rs4684677) were analyzed.ResultsIntestinal permeability was impaired in CD patients and ameliorated after GFD. Ghrelin was significantly (P=0.048) higher and the obestatin/ghrelin ratio was significantly (P=0.034) lower in CD patients compared with both IBS-d and HC, and GFD reduced the peptide levels, but without reaching the concentrations in HC. Significant differences (P<0.05) were found in the Leu72Met polymorphism among groups, with the reduction of the GT genotype and the T allele in both CD and IBS-d patients compared with HC.ConclusionIntestinal permeability is altered in CD, but not in IBS-d patients, and ghrelin levels increase in CD patients as observed in other inflammatory conditions. Moreover, a role for ghrelin genetics is hypothesized in sustaining the many pathogenetic components of these different pathologies, but with a similar symptom profile.
Os Odontoideum Discovered After Minor Cervical Trauma
Authors: Kim Tommy Y. , Ratnayake Kristin 
Published: October 2016

Abstract
Minor cervical spine injury is a common cause of pediatric emergency department visits. We present a case of a 10-year-old boy with transient paresthesia after minor cervical trauma found to have a rare cervical spine abnormality requiring surgical fusion. We present and discuss the management options for os odontoideum.
Implementation of the Spanish National Enhanced Recovery Program (ERAS) in Bariatric Surgery: A Pilot Study
Authors: Ruiz-Tovar Jaime , Royo Pablo , Muñoz José L. , Duran Manuel , Redondo Elisabeth , Ramirez Jose M. 
Published: October 2016

Introduction:
The essence of Enhanced Recovery After Surgery (ERAS) programs is the multimodal approach, and many authors have demonstrated safety and feasibility in fast track bariatric surgery. According to this concept, a multidisciplinary ERAS program for bariatric surgery has been developed by the Spanish fast track group (ERAS Spain). The aim of this study was to analyze the initial implementation of this Spanish National ERAS protocol in bariatric surgery.

Patients and Methods:
A multicentric prospective pilot study was performed, including 125 consecutive patients undergoing bariatric surgery at 3 Spanish hospitals between January and June 2015, after the Spanish National ERAS protocol in bariatric surgery. Compliance with the protocol, morbidity, mortality, hospital stay, and readmission were evaluated.

Results:
Bariatric techniques performed included 68 Roux-en-Y gastric bypass (54.4%) and 57 laparoscopic sleeve gastrectomy (45.6%) cases. All surgeries were laparoscopically performed with conversion in only 1 case (0.8%). Median postoperative pain evaluated by visual analogic scale 24 hours after surgery was 2 (range, 0 to 5). Postoperative nausea or vomiting appeared in 7 patients (5.6%). Complications appeared in 6 patients (4.8%). The reoperation rate was 4%. The mortality rate was 0.8%. The median hospital stay was 2 days (range, 2 to 10 d) and readmission rate was 2.4%. The compliance of all the items of the protocol was achieved in 78.4% of the patients.

Conclusions:
The Spanish National ERAS protocol is a safe issue with a high implementation rate. It can be recommended to establish this protocol to other institutions.
Feeling, learning from and being aware of inner states: interoceptive dimensions in neurodegeneration and stroke
Authors: García-Cordero Indira , Sedeño Lucas , de la Fuente Laura , Slachevsky Andrea , Forno Gonzalo , Klein Francisco , Lillo Patricia , Ferrari Jesica , Rodriguez Clara , Bustin Julian , Torralva Teresa , Baez Sandra , Yoris Adrian , Esteves Sol , Melloni Margherita , Salamone Paula , Huepe David , Manes Facundo , García Adolfo M. , Ibañez Agustín 
Published: October 2016

Interoception is a complex process encompassing multiple dimensions, such as accuracy, learning and awareness. Here, we examined whether each of those dimensions relies on specialized neural regions distributed throughout the vast interoceptive network. To this end, we obtained relevant measures of cardiac interoception in healthy subjects and patients offering contrastive lesion models of neurodegeneration and focal brain damage: behavioural variant fronto-temporal dementia (bvFTD), Alzheimer's disease (AD) and fronto-insular stroke. Neural correlates of the three dimensions were examined through structural and functional resting-state imaging, and online measurements of the heart-evoked potential (HEP). The three patient groups presented deficits in interoceptive accuracy, associated with insular damage, connectivity alterations and abnormal HEP modulations. Interoceptive learning was differentially impaired in AD patients, evidencing a key role of memory networks in this skill. Interoceptive awareness results showed that bvFTD and AD patients overestimated their performance; this pattern was related to abnormalities in anterior regions and associated networks sub-serving metacognitive processes, and probably linked to well-established insight deficits in dementia. Our findings indicate how damage to specific hubs in a broad fronto-temporo-insular network differentially compromises interoceptive dimensions, and how such disturbances affect widespread connections beyond those critical hubs. This is the first study in which a multiple lesion model reveals fine-grained alterations of body sensing, offering new theoretical insights into neuroanatomical foundations of interoceptive dimensions.
This article is part of the themed issue ‘Interoception beyond homeostasis: affect, cognition and mental health’.
An active inference theory of allostasis and interoception in depression
Authors: Barrett Lisa Feldman , Quigley Karen S. , Hamilton Paul 
Published: October 2016

In this paper, we integrate recent theoretical and empirical developments in predictive coding and active inference accounts of interoception (including the Embodied Predictive Interoception Coding model) with working hypotheses from the theory of constructed emotion to propose a biologically plausible unified theory of the mind that places metabolism and energy regulation (i.e. allostasis), as well as the sensory consequences of that regulation (i.e. interoception), at its core. We then consider the implications of this approach for understanding depression. We speculate that depression is a disorder of allostasis, whose myriad symptoms result from a ‘locked in’ brain that is relatively insensitive to its sensory context. We conclude with a brief discussion of the ways our approach might reveal new insights for the treatment of depression.This article is part of the themed issue ‘Interoception beyond homeostasis: affect, cognition and mental health’.
Using Machine Learning to Parse Breast Pathology Reports
Authors: Yala Adam , Barzilay Regina , Salama Laura , Griffin Molly , Sollender Grace , Bardia Aditya , Lehman Constance , Buckley Julliette M. , Coopey Suzanne B. , Polubriaginof Fernanda , Garber Judy E. , Smith Barbara L. , Gadd Michele A. , Specht Michelle C. , Gudewicz Thomas M. , Guidi Anthony , Taghian Alphonse , Hughes Kevin S. 
Published: October 2016

1AbstractPurposeExtracting information from Electronic Medical Record is a time-consuming and expensive process when done manually. Rule-based and machine learning techniques are two approaches to solving this problem. In this study, we trained a machine learning model on pathology reports to extract pertinent tumor characteristics, which enabled us to create a large database of attribute searchable pathology reports. This database can be used to identify cohorts of patients with characteristics of interest.MethodsWe collected a total of 91,505 breast pathology reports from three Partners hospitals: Massachusetts General Hospital (MGH), Brigham and Womens Hospital (BWH), and Newton-Wellesley Hospital (NWH), covering the period from 1978 to 2016. We trained our system with annotations from two datasets, consisting of 6,295 and 10,841 manually annotated reports. The system extracts 20 separate categories of information, including atypia types and various tumor characteristics such as receptors. We also report a learning curve analysis to show how much annotation our model needs to perform reasonably.ResultsThe model accuracy was tested on 500 reports that did not overlap with the training set. The model achieved accuracy of 90% for correctly parsing all carcinoma and atypia categories for a given patient. The average accuracy for individual categories was 97%. Using this classifier, we created a database of 91,505 parsed pathology reports.ConclusionsOur learning curve analysis shows that the model can achieve reasonable results even when trained on a few annotations. We developed a user-friendly interface to the database that allows physicians to easily identify patients with target characteristics and export the matching cohort. This model has the potential to reduce the effort required for analyzing large amounts of data from medical records, and to minimize the cost and time required to glean scientific insight from this data.
Genomic plasticity and rapid host switching promote the evolution of generalism in the zoonotic pathogenCampylobacter
Authors: Woodcock Dan J. , Krusche Peter , Strachan Norval J. C. , Forbes Ken J. , Cohan Frederick M. , Méric Guillaume , Sheppard Samuel K. 
Published: October 2016

AbstractHorizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of niche specifying genes and the opportunity for host transition can interact to promote the emergence of host generalist lineages of the zoonotic bacteriumCampylobacter. Using a modelling approach we show that increasing levels of recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with realr/mestimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.
Clear: Composition of Likelihoods for Evolve And Resequence Experiments
Authors: Iranmehr Arya , Akbari Ali , Schlötterer Christian , Bafna Vineet 
Published: October 2016

AbstractThe advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution “in-action” via Evolve-and-Resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, and wide time spans. These assumptions do not hold in many E&R studies.In this article, we propose a method-Composition of Likelihoods for Evolve-And-Resequence experiments (Clear)–to identify signatures of selection in small population E&R experiments. Cleartakes whole-genome sequence of pool of individuals (pool-seq) as input, and properly addresses heterogeneous ascertainment bias resulting from uneven coverage. Clearalso provides unbiased estimates of model parameters, including population size, selection strength and dominance, while being computationally efficient. Extensive simulations show that Clearachieves higher power in detecting and localizing selection over a wide range of parameters, and is robust to variation of coverage. We applied Clearstatistic to multiple E&R experiments, including, data from a study ofD. melanogasteradaptation to alternating temperatures and a study of outcrossing yeast populations, and identified multiple regions under selection with genome-wide significance.
Examining the interaction between TGFBR3 and ESRRA in ovarian cancer prognosis
Authors: Passey Alun , Brown Robert , Wilhelm-Benartzi Charlotte S. 
Published: October 2016

ABSTRACTThe authors found that ESRRA when co-expressed at high levels with TGFβR3 may be prognostic for serous ovarian cancer overall survival in data from the Cancer Genome Atlas; however, this result was not validated in further datasets. A cell line was also identified in this study for future functional investigation of interactions between ESRRA and TGFβR3 in the context of oestrogen signaling in order to further elucidate their potential roles as prognostic biomarkers for serous ovarian cancer.FUNDING SUPPORTThis work was supported by Cancer Research UK program A6689 (RB and CSWB) and the Medical Research Council (AP)CONFLICT OF INTEREST DISCLOSURESThe authors have declared no conflicts of interest.AUTHOR CONTRIBUTIONSCSWB designed the study. AP, CSWB, and RB developed the methodology. AP and CSWB collected the data. AP, CSWB, and RB wrote the manuscript. CSWB is responsible for the overall content.
Using predictive specificity to determine when gene set analysis is biologically meaningful
Authors: Ballouz Sara , Pavlidis Paul , Gillis Jesse 
Published: October 2016

ABSTRACTGene set analysis, which translates gene lists into enriched functions, is among the most common bioinformatic methods. Yet few would advocate taking the results at face value. Not only is there no agreement on the algorithms themselves, there is no agreement on how to benchmark them. In this paper, we evaluate the robustness and uniqueness of enrichment results as a means of assessing methods even where correctness is unknown. We show that heavily annotated (“multifunctional”) genes are likely to appear in genomics study results and drive the generation of biologically non-specific enrichment results as well as highly fragile significances. By providing a means of determining where enrichment analyses report non-specific and non-robust findings, we are able to assess where we can be confident in their use. We find significant progress in recent bias correction methods for enrichment and provide our own software implementation. Our approach can be readily adapted to any pre-existing package.
Multiplexed computations in retinal ganglion cells of a single type
Authors: Deny Stephane , Ferrari Ulisse , Mace Emilie , Yger Pierre , Caplette Romain , Picaud Serge , Tkačik Gašper , Marre Olivier 
Published: October 2016

AbstractIn the early visual system, cells of the same type perform the same computation in di↵erent places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of the same type will extract a single stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code linearly for its position, while distant cells remain largely invariant to the object’s position and, instead, respond non-linearly to changes in the object’s speed. Cells switch between these two computations depending on the stimulus. We developed a quantitative model that accounts for this effect and identified a likely disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems.
Expressing an RbcS Antisense Gene in Transgenic Flaveria bidentis Leads to an Increased Quantum Requirement for CO2 Fixed in Photosystems I and II
Authors: Siebke K. , von Caemmerer S. , Badger M. , Furbank R. T. 
Published: October 2016

Abstract
It was previously shown with concurrent measurements of gas exchange and carbon isotope discrimination that the reduction of ribulose-1,5-bisphosphate carboxylase/oxygenase by an antisense gene construct in transgenic Flaveria bidentis (a C4 species) leads to reduced CO2 assimilation rates, increased bundle-sheath CO2 concentration, and leakiness (defined as the ratio of CO2 leakage to the rate of C4 acid decarboxylation; S. von Caemmerer, A. Millegate, G.D. Farquhar, R.T. Furbank [1997] Plant Physiol 113: 469–477). Increased leakiness in the transformants should result in an increased ATP requirement per mole of CO2 fixed and a change in the ATP-to-NADPH demand. To investigate this, we compared measurements of the quantum yield of photosystem I and II ([phi]PSI and [phi]PSII) with the quantum yield of CO2 fixation ([phi]CO2) in control and transgenic F. bidentis plants in various conditions. Both [phi]PSI/[phi]CO2 and [phi]PSII/[phi]CO2 increased with a decrease in ribulose-1,5-bisphosphate carboxylase/oxygenase content, confirming an increase in leakiness. In the wild type the ratio of [phi]PSI to [phi]PSII was constant at different irradiances but increased with irradiance in the transformants, suggesting that cyclic electron transport may be higher in the transformants. To evaluate the relative contribution of cyclic or linear electron transport to extra ATP generation, we developed a model that links leakiness, ATP/NADP requirements, and quantum yields. Despite some uncertainties in the light distribution between photosystem I and II, we conclude from the increase of [phi]PSII/[phi]CO2 in the transformants that cyclic electron transport is not solely responsible for ATP generation without NADPH production.
Characterization of Blue Light Signal Transduction Chains That Control Development and Maintenance of Sexual Competence in Chlamydomonas reinhardtii
Authors: Pan J. M. , Haring M. A. , Beck C. F. 
Published: October 2016

Abstract
Blue light induces the differentiation of Chlamydomonas reinhardtii pregametes to gametes. The light-induced conversion of pregametes to gametes is protein synthesis dependent and proceeds only after a lag phase. Upon incubation in the dark, gametes lost their mating ability, resulting in dark-inactivated gametes. Reillumination rapidly restored mating competence and this was shown to be independent of protein synthesis. Apparently, differentiation and maintenance of gametic competence are both regulated by light. Whether one or two light-activated signal pathways are involved was investigated using pharmacological compounds that affect signal transduction. Compounds that affected pregamete-to-gamete conversion affected the expression of a gamete-specific gene in a similar fashion. Other drugs affected only dark-inactivated gametes, suggesting that reactivating gametes requires a separate signaling pathway. Combined treatments provided evidence for the consecutive action of a phosphatase and a protein kinase C-like kinase in the light-induced reactivation process.
Evidence for the Presence of a Porin in the Membrane of Glyoxysomes of Castor Bean
Authors: Reumann S. , Bettermann M. , Benz R. , Heldt H. W. 
Published: October 2016

Abstract
Glyoxysomes of endosperm tissue of castor bean (Ricinus communis L.) seedlings were solubilized in a detergent and added to a lipid bilayer. Conductivity measurements revealed that the glyoxysomal preparation contained a porin-like channel. Using an electrophysiological method, which we established for semiquantitative determination of porin activity, we were able to demonstrate that glyoxysomal membranes purified by sucrose density gradient centrifugation contain an integral membrane protein with porin activity. The porin of glyoxysomes was shown to have a relatively small single-channel conductance of about 330 picosiemens in 1 M KCl and to be strongly anion selective. Thus, the glyoxysomal porin differs from the other previously characterized porins in the outer membrane of mitochondria or plastids, but is similar to the porin of spinach (Spinacia oleracea L.) leaf peroxisomes. Our results suggest that, in analogy to the porin of leaf peroxisomes, the glyoxysomal porin facilitates the passage of small metabolites, such as succinate, citrate, malate, and aspartate, through the membrane.
Temporal Changes in State Transitions and Photosystem Organization in the Unicellular, Diazotrophic Cyanobacterium Cyanothece sp. ATCC 51142
Authors: Meunier P. C. , Colon-Lopez M. S. , Sherman L. A. 
Published: October 2016

Abstract
The unicellular Cyanobacterium Cyanothece sp. ATCC 51142, grown under alternating 12-h light/12-h dark conditions, temporally separated N2 fixation from photosynthesis. The regulation of photosynthesis was studied using fluorescence spectra and kinetics to determine changes in state transitions and photosystem organization. The redox poise of the plastoquinone (PQ) pool appeared to be central to this regulation. Respiration supported N2 fixation by oxidizing carbohydrate granules, but reduced the PQ pool. This induced state 2 photosystem II monomers and lowered the capacity for O2 evolution. State 2 favored photosystem I trimers and cyclic electron transport, which could stimulate N2 fixation; the stimulation suggested an ATP limitation to N2 and CO2 fixation. The exhaustion of carbohydrate granules at around 6 h in the dark resulted in reduced respiratory electron flow, which led to a more oxidized PQ pool and produced a sharp transition from state 2 to state 1. This transient state 1 returned to state 2 in the remaining hours of darkness. In the light phase, photosystem II dimerization correlated with increased phycobilisome coupling to photosystem II (state 1) and increased rates of O2 evolution. However, dark adaptation did not guarantee state 2 and left photosystem I centers in a mostly monomeric state at certain times.