bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognosis of Traumatic Ulnar Nerve Injuries
Authors: Lan Ching-Yu , Tien Huey-Yuan , Lin Yu-Te , Hsu Chun-Cheng , Lin Cheng-Hung , Chen Shih-Heng 
Published: December 2018

Abstract
Ulnar nerve injury (UNI) is not uncommon and often results in incomplete motor recovery after the initial nerve repair and requires secondary functional reconstruction. To clarify the prognosis and predicting factor of UNI, and if it is reasonable to wait after the initial repair, a systematic literature review from PubMed computerized literature database and Google scholar was performed. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) checklist and guidelines were followed to develop the search protocol for this literature review. Two reviewers independently assessed titles, abstracts, and full-text articles, and a third reviewer resolved any disagreements. Seventeen articles with 260 cases were found with sufficient data and enough follow-up. After multiple logistic regression, age, injury level, gap of lesion, and delayed time to surgery were significant prognostic factors in UNI. If considering only high-level injuries (injury at or above proximal forearm), age became the only predicting factor. In cases with likely poor prognosis, their motor recovery tends to be unsatisfactory, and observation for months after the initial repair might not be reasonable. Other surgical interventions such as early nerve transfer may be an option to improve the outcome.
Using Simulation to Teach Echocardiography
Authors: Rambarat Cecil A. , Merritt Justin M. , Norton Hannah F. , Black Erik , Winchester David E. 
Published: December 2018

Summary Statement
We identified 24 studies of high-fidelity simulation being used to teach echocardiography. A variety of study designs were used with outcomes ranging from reports of learner self-confidence up to improvement in organizational practice. Most studies were carried out in graduate medical populations, specifically in anesthesia trainees. The substantial majority of studies (91.6%) concluded that simulation has positive outcomes for teaching echocardiography. Future investigations would benefit from application of educational theory and should focus on demonstrating whether simulation can improve care delivery and patient outcomes.
Is it Necessary to Send the Sleeve Gastrectomy Specimens to Pathology?
Authors: Demirbas Baha Tolga , Erdim Aylin , Celikel Cigdem , Akbas Gamze , Cingi Asim 
Published: December 2018

Background:
Laparoscopic sleeve gastrectomy (LSG) has become more popular among other bariatric procedures. The histopathologic changes in the sleeve gastrectomy specimens have not been widely investigated among the Turkish population.

Objective:
The purpose of this study was to delineate these histopathologic findings of the LSG specimens of morbidly obese patients from a single center.

Materials and Methods:
A prospective database of all patients who have undergone LSG at a single center was reviewed. Demographic parameters, that is, sex, age, and body mass index were examined. The incidence of Helicobacter pylori, and other pathologic findings in the specimens were studied.

Results:
In total, 253 patients who had undergone LSG between the period spanning from April 2012 to January 2017 were included in the study. The 183 patients were female individuals and 70 patients were male individuals. The mean age at the time of operation was 38.5 years (range, 18 to 65 y). The mean body mass index was 47.7 kg/m2. The pathologic findings were H. pylori positivity in 69 patients (27%), chronic active gastritis in 52 patients (20.5%), chronic gastritis in 135 patients (53.4%), and intestinal metaplasia in 5 patients (2%), whereas normal histopathologic findings were observed in 65 patients (25.7%). As regards surgical complications, the mortality rate was 0%, the staple-line leak was observed in 2 patients (0.8%), and intra-abdominal hemorrhage occurred in 2 patients (0.8%).

Conclusions:
The majority of patients who underwent LSG had pathologic findings in the resected specimens. With regard to the high incidence of pathologic findings in this study, we conclude that it is essential to send the gastrectomy materials for pathologic investigation after sleeve gastrectomy.
Symptomatic, Radiological, and Quality of Life Outcome of Paraesophageal Hernia Repair With Urinary Bladder Extracellular Surgical Matrix: Comparison With Primary Repair
Authors: Wang Chloe Q. , Tran Thanh , Montera Beth , Karlnoski Rachel , Feldman John , Albrink Michael H. , Velanovich Vic 
Published: December 2018

Introduction:
Paraesophageal hernia repairs are prone to recurrence and mesh reinforcement is common. Both biologic and prosthetic meshes have been used. We report a comparison of a new type of biologically derived graft, Gentrix Surgical Urinary Bladder Matrix (UBM).

Methods:
The medical records of 65 patients who underwent paraesophageal hernia repair (PEHR) were reviewed. Primary data points included demographics, first-time or recurrent hernia, operative approach, graft or primary repair, operative time, and postoperative complications. Patients then underwent upper gastrointestinal series, completed the GERD-HRQL symptom severity questionnaire, and the SF-36 generic quality of life instrument.

Results:
A total of 32 patients underwent graft-reinforced repair, 33 underwent primary repair. More patients in the UBM group were being treated for recurrent PEH. Demographic data and postoperative complications were similar. There was no difference in recurrence rates, size of recurrence, postoperative symptomatic or quality of life improvement. Patients who suffered recurrence in the primary repair group had more severe symptoms and a higher rate of dissatisfaction. Of the 3 patients with recurrences after Gentrix placement, reoperation demonstrated anterior failure where no reinforcement had occurred because of the posteriorly placed U-shaped graft.

Conclusions:
The use of UBM was not associated with an increased complications despite use in more difficult patients. Although there appeared to be no difference in recurrence rate or size, it was associated with less severe symptomatic recurrences. The U-shape configuration is prone to recurrence at the site of the repair not covered by the graft, suggesting that a keyhole configuration may be superior.
Computational tools to detect signatures of mutational processes in DNA from tumours: a review and empirical comparison of performance
Authors: Hanane Omichessan , Gianluca Severi , Vittorio Perduca 
Published: December 2018

AbstractMutational signatures refer to patterns in the occurrence of somatic mutations that reflect underlying mutational processes. To date, after the analysis of tens of thousands of genomes and exomes from about 40 different cancers types, 30 mutational signatures characterized by a unique probability profile across the 96 mutation types have been identified, validated and listed on the COSMIC (Catalogue of Somatic Mutations in Cancer) website. Simultaneously with this development, the last few years saw the publication of several concurrent methods (mathematical algorithms implemented in publicly available software packages) for either the quantification of the contribution of prespecified signatures (e.g. COSMIC signatures) in a given cancer genome or the identification of new signatures from a sample of cancer genomes. A review about existing computational tools has been recently published to guide researchers and practitioners in conducting their mutational signatures analysis, however, other tools have been introduced since its publication and, to date, there has not been a systematic evaluation and comparison of the performance of such tools. In order to fill this gap, we carry on an empirical evaluation study of all available packages to date, using both real and simulated data.
Reconciling biodiversity conservation, food production and farmers’ demand
Authors: Montoya Daniel , Gaba Sabrina , de Mazancourt Claire , Bretagnolle Vincent , Loreau Michel 
Published: December 2018

AbstractAgricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee the provision of ecosystem services that reaches stakeholders’ demands, especially considering the observed biodiversity decline and the current global change predictions that may affect food security. Here, we use a model to examine how landscape composition – fraction of semi-natural habitat (SNH) – affects biodiversity and crop production services in intensively-managed agricultural systems. We analyse three groups of stakeholders assumed to value different ecosystem services most – individual farmers (crop yield per area), agricultural unions (landscape production) and conservationists (biodiversity). We find that trade-offs among stakeholders’ demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder, i.e. function thresholds. Intermediate amounts of SNH can allow for the delivery of relatively high levels of the three ecosystem services. Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, these results suggest ways of managing landscapes to reconcile the demands of several actors and ensure for biodiversity conservation and food production.
De novoassembly of thePasteuria penetransgenome reveals high plasticity, host dependency, and BclA-like collagens
Authors: Orr Jamie N , Mauchline Tim H , Cock Peter J , Blok Vivian C , Davies Keith G 
Published: December 2018

1.ABSTRACTPasteuria penetransis a gram-positive endospore forming bacterial parasite ofMeloidogynespp. the most economically damaging genus of plant parasitic nematodes globally. The obligate antagonistic nature ofP. penetransmakes it an attractive candidate biological control agent. However, deployment ofP. penetransfor this purpose is inhibited by a lack of understanding of its metabolism and the molecular mechanics underpinning parasitism of the host, in particular the initial attachment of the endospore to the nematode cuticle. Several attempts to assemble the genomes of species within this genus have been unsuccessful. Primarily this is due to the obligate parasitic nature of the bacterium which makes obtaining genomic DNA of sufficient quantity and quality which is free from contamination challenging. Taking advantage of recent developments in whole genome amplification, long read sequencing platforms, and assembly algorithms, we have developed a protocol to generate large quantities of high molecular weight genomic DNA from a small number of purified endospores. We demonstrate this method via genomic assembly ofP. penetrans. This assembly reveals a reduced genome of 2.64Mbp estimated to represent 86% of the complete sequence; its reduced metabolism reflects widespread reliance on the host and possibly associated organisms. Additionally, apparent expansion of transposases and prediction of partial competence pathways suggest a high degree of genomic plasticity. Phylogenetic analysis places our sequence within the Bacilli, and most closely related toThermoactinomycesspecies. Seventeen predicted BclA-like proteins are identified which may be involved in the determination of attachment specificity. This resource may be used to developin vitroculture methods and to investigate the genetic and molecular basis of attachment specificity.
Anatomical basis and physiological role of cerebrospinal fluid transport through the murine cribriform plate
Authors: Norwood Jordan N. , Zhang Qingguang , Card David , Craine Amanda , Ryan Timothy M. , Drew Patrick J. 
Published: December 2018

AbstractCerebrospinal fluid (CSF) flows through the brain, transporting chemical signals and removing waste. CSF production in the brain is balanced by a constant outflow of CSF, the anatomical basis of which is poorly understood. Here we characterized the anatomy and physiological function of the CSF outflow pathway along the olfactory sensory nerves through the cribriform plate, and into the nasal epithelia. Chemical ablation of olfactory sensory nerves greatly reduced outflow of CSF through the cribriform plate. The reduction in CSF outflow did not cause an increase in intracranial pressure (ICP), consistent with an alteration in the pattern of CSF drainage or production. Our results suggest that damage to olfactory sensory neurons (such as from air pollution) could contribute to altered CSF turnover and flow, providing a potential mechanism for neurological diseases.
Glendonite occurrences in the Tremadocian of Baltica: first Early Palaeozoic evidence of massive ikaite precipitation at temperate latitude
Authors: Popov Leonid E. , Álvaro J. Javier , Holmer Lars E. , Bauert Heikki , Pour Mansoureh Ghobadi , Dronov Andrei V. , Lehnert Oliver , Hints Olle , Männik Peep , Zhang Zhifei , Zhang Zhiliang 
Published: December 2018

AbstractThe Tremadocian (Early Ordovician) is currently considered a time span of greenhouse conditions with tropical water surface temperature estimates, interpolated from oxygen isotopes, approaching 40°C. In the high-latitude Baltoscandian Basin, these data are in contrast with the discovery of glendonite, a pseudomorph of ikaite (CaCO3·6H2O) and valuable indicator of near-freezing bottom-water conditions. The massive precipitation of this climatically sensitive mineral is associated with transgressive conditions and high organic productivity. Surprisingly, the precipitation of glendonite is contemporaneous with the record of conodonts displaying low δ18O values, which would suggest high temperatures (>40°C) in the water column. Therefore, the early Tremadocian sediments of Baltoscandia contain both “greenhouse” pelagic signals and near-freezing substrate indicators. This apparent paradox suggests both the influence of isotopically depleted freshwater yielded by fluvial systems, and the onset of sharp thermal stratification patterns in a semi-closed basin, which should have played an important role in moderating subpolar climates and reducing latitudinal gradients.
Anthropogenic risk factors as the major cause of cancer driver events
Authors: Belikov Aleksey V. 
Published: December 2018

AbstractBackgroundI have recently shown that the number of rate-limiting driver events per tumor can be estimated from the age distribution of cancer incidence using the gamma/Erlang probability distribution. It is important to understand how these predictions relate to established risk factors.MethodsThe number of rate-limiting driver events per tumor was estimated using the gamma/Erlang distribution and correlated to the percentage of cancer cases attributable to modifiable risk factors.ResultsThe predicted number of rate-limiting driver events per tumor strongly correlates with the proportion of cancer cases attributable to modifiable risk factors for all cancers except those induced by infection or ultraviolet radiation. The correlation was confirmed for three countries, three corresponding incidence databases and risk estimation studies, as well as for both sexes: USA, males [r=0.80, P=0.002], females [r=0.81, P=0.0003]; England, males [r=0.90, P<0.0001], females [r=0.67, P=0.002]; Australia, males [r=0.90, P=0.0004], females [r=0.68, P=0.01].ConclusionsIt is thus confirmed that predictions based on interpreting the age distribution of cancer incidence as the gamma/Erlang probability distribution have biological meaning, validating the underlying Poisson process as the law governing the development of the majority of cancer types, especially those driven by chemical mutagens. Importantly, this study suggests that the majority of driver events (60-80% in males, 50-70% in females) are induced by anthropogenic carcinogens, and not by cell replication errors or other internal processes.
Persister Cells Resuscitate Using Membrane Sensors that Activate Chemotaxis, Lower cAMP Levels, and Revive Ribosomes
Authors: Yamasaki Ryota , Song Sooyeon , Benedik Michael J. , Wood Thomas K. 
Published: December 2018

ABSTRACTPersistence, the stress-tolerant state, is arguably the most vital phenotype since nearly all cells experience nutrient stress, which causes a sub-population to become dormant. However, how persister cells wake to reconstitute infections is not understood well. Here, using single-cell observations, we determined thatEscherichia colipersister cells resuscitate primarily when presented with specific carbon sources, rather than spontaneously. In addition, we found that the mechanism of persister cell waking is through sensing nutrients by chemotaxis and phosphotransferase membrane proteins. Furthermore, nutrient transport reduces the level of secondary messenger cAMP through enzyme IIA; this reduction in cAMP levels leads to ribosome resuscitation and rescue. Resuscitating cells also immediately commence chemotaxis toward nutrients, although flagellar motion is not required for waking. Hence, persister cells wake by perceiving nutrients via membrane receptors which relay the signal to ribosomes via the secondary messenger cAMP, and persisters wake and utilize chemotaxis to acquire nutrients.
Schizotypy-related magnetization of cortex in healthy adolescence is co-located with expression of schizophrenia-related genes
Authors: Romero-Garcia Rafael , Seidlitz Jakob , Whitaker Kirstie J , Morgan Sarah E , Fonagy Peter , Dolan Raymond J , Jones Peter B , Goodyer Ian M , Suckling John ,   the NSPN Consortium, Vértes Petra E , Bullmore Edward T 
Published: December 2018

AbstractBackgroundGenetic risk is thought to drive clinical variation on a spectrum of schizophrenia-like traits but the underlying changes in brain structure that mechanistically link genomic variation to schizotypal experience and behaviour are unclear.MethodsWe assessed schizotypy using a self-reported questionnaire, and measured magnetization transfer (MT), as a putative micro-structural MRI marker of intra-cortical myelination, in 68 brain regions, in 248 healthy young people (aged 14-25 years). We used normative adult brain gene expression data, and partial least squares (PLS) analysis, to find the weighted gene expression pattern that was most co-located with the cortical map of schizotypy-related magnetization (SRM).ResultsMagnetization was significantly correlated with schizotypy in bilateral posterior cingulate cortex and precuneus (and for disorganized schizotypy also in medial prefrontal cortex; all FDR-corrected P < 0.05), which are regions of the default mode network specialized for social and memory functions. The genes most positively weighted on the whole genome expression map co-located with SRM were enriched for genes that were significantly down-regulated in two prior case-control histological studies of brain gene expression in schizophrenia. Conversely, the most negatively weighted genes were enriched for genes that were transcriptionally up-regulated in schizophrenia. Positively weighted (down-regulated) genes were enriched for neuronal, specifically inter-neuronal, affiliations and coded a network of proteins comprising a few highly interactive “hubs” such as parvalbumin and calmodulin.ConclusionsMicrostructural MRI maps of intracortical magnetization can be linked to both the behavioural traits of schizotypy and to prior histological data on dysregulated gene expression in schizophrenia.
Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites
Authors: Colonna Vincenza , D’Agostino Nunzio , Garrison Erik , Meisner Jonas , Albrechtsen Anders , Facchiano Angelo , Cardi Teodoro , Tripodi Pasquale 
Published: December 2018

AbstractBackgroundCapsicum is one of the major vegetable crops grown world-wide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Fruits broad variability has been driven by breeding programs and has been mainly studied by linkage analysis.ResultsWe discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known subdivision of C. annuum in two groups separates large and bulky fruits form small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080).ConclusionsOur collection covers all the economically important species of Capsicum widely used in breeding programs, and represent the widest and largest study so far in terms of the number of species and genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results foster fine genetic association studies and foresee genomic variability at population-level.
Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage
Authors: Murphy Chelsea L. , Youssef Noha H. , Hanafy Radwa A. , Couger MB , Stajich Jason E. , Wang Y. , Baker Kristina , Dagar Sumit S. , Griffith Gareth W. , Farag Ibrahim F. , Callaghan TM , Elshahed Mostafa S. 
Published: December 2018

AbstractSurvival and growth of the anaerobic gut fungi (AGF, Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. Patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 283 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. The majority of HGT events were AGF specific (91.5%) and wide (70.7%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This work strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.ImportanceThe anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryotes dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. This manuscript assesses the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota post sequestration in the herbivorous gut. Analysis of twenty-seven transcriptomes that represent the broad Neocallimastigomycota diversity identified 283 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This work represents a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.