bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects and Results of Omentopexy During Laparoscopic Sleeve Gastrectomy
Authors: Arslan Ergin , Banli Oktay , Sipahi Mesut , Yagci Gokhan 
Published: April 2018

Purpose:
The aim of this study was to demonstrate that gastric volvulus can be prevented by omentopexy and sleeve gastrectomy without increasing other complication rates.

Materials and Methods:
A total of 1385 patients who underwent omentopexy and sleeve gastrectomy between April 2013 and September 2017 were included this study. Body mass index, age, sex, comorbidities, and postoperative complications of the patients were recorded as data.

Results:
A total of 1385 patients underwent sleeve gastrectomy and omentopexy. There were 999 female and 386 male patients. The mean age of the patients was 36 years (14 to 71 y). The mean body mass index was 42.74 kg/m2 (35 to 73 kg/m2). Twenty-one patients had previously undergone gastric banding and the other 80 patients had previous abdominal operation. The number of patients undergoing simultaneous cholecystectomy was 98. Three patients had hemorrhage due to hypertension and anticoagulant treatment in the postoperative period and the patients were treated medically. One staple-line leakage was observed. Twist, and stricture were not observed and no mortalities were noted.

Conclusions:
Sleeve gastrectomy and omentopexy can prevent the gastric twist, which is a functional cause of gastric stenosis, by stabilizing the posterior stomach wall.
The role of four-factor prothrombin complex concentrate in coagulopathy of trauma: A propensity matched analysis
Authors: Jehan Faisal , Aziz Hassan , O'Keeffe Terence , Khan Muhammad , Zakaria El Rasheid , Hamidi Mohammad , Zeeshan Muhammad , Kulvatunyou Narong , Joseph Bellal 
Published: April 2018

BACKGROUND
Coagulopathy is a common complication after severe trauma. The efficacy of 4-factor prothrombin complex concentrate (4-PCC) as an adjunct to fresh frozen plasma (FFP) in reversal of coagulopathy of trauma (COT) has not been studied. The aim of our study is to compare 4-PCC + FFP versus FFP alone for the treatment of COT.

METHODS
We reviewed all trauma patients older than 18 years who received PCC + FFP or FFP alone at our Level I trauma center from 2015 to 2016. We excluded patients on preinjury oral anticoagulants. Patients were divided into two groups (4-PCC + FFP: FFP alone) and were matched in a 1:2 ratio using propensity score matching for demographics, vital and injury parameters, and initial international normalized ratio (INR). COT was defined as admission INR > 1.5. Corrected INR was defined as an INR of 1.5 or less. Outcome measures were time to correction of INR, packed red blood cells units transfused, thromboembolic complications, and mortality.

RESULTS
We analyzed 516 trauma patients, of which 120 patients (4-PCC + FFP: 40, FFP: 80) were matched. Mean age was 58 ± 20 years; 60% were male, median Injury Severity Score was 29 (14–38). Mechanism of injury was blunt in 87% patients. 4-PCC + FFP was associated with an accelerated correction of INR (373 minutes vs. 955 minutes; p = 0.001), a decrease in packed red blood cells units (7 units vs. 9 units; p = 0.04), and FFP units (5 units vs. 7 units; p = 0.03) transfused compared to FFP alone. 4-PCC + FFP was associated with a lower mortality (25% vs. 33% p = 0.04) compared with FFP alone; however, there was no difference in the thromboembolic complications (2.5% vs. 1.2%, p = 0.5) between the two groups. Administration of PCC + FFP led to an earlier correction of the INR compared with FFP alone.

CONCLUSION
Results of our study demonstrated that the use of 4-PCC in conjunction with FFP is associated with the rapid reversal of INR and reduction in transfusion requirements as compared with FFP alone. Four-factor PCC as a component therapy along with FFP is superior to FFP alone for the reversal of COT.

LEVEL OF EVIDENCE
Therapeutic studies, level IV.
Transfer status: A significant risk factor for mortality in emergency general surgery patients requiring colon resection
Authors: DeWane Michael P. , Davis Kimberly A. , Schuster Kevin M. , Erwin Scott P. , Maung Adrian A. , Becher Robert D. 
Published: April 2018

BACKGROUND
Patients requiring emergency surgery have increased rates of morbidity and mortality. Transfer from outside institution delays effective control of ongoing infection and has been linked with worse outcomes. Previous research suggests transfer status negatively impacts survival but has not examined the effect of location and type of institution prior to transfer. This study aims to characterize the effect of type of transferring institution on postoperative outcomes after emergency colon surgery.

METHODS
Data originated from the American College of Surgeons National Surgical Quality Improvement Program database from 2010 to 2012. Patients undergoing emergent colectomy were stratified based on location: not transferred, transferred from outside emergency department (ED), transferred from outside hospital inpatient unit, or transferred from a nursing home. Patient variables were stratified and compared via χ2 and analysis of variance. A backward-multivariable logistic regression and adjusted multivariate Cox regression analysis were performed to determine factors predicting 30-day mortality.

RESULTS
A total of 14,245 patients were identified, of whom 22% (3,203) were transfer patients. Among transfers, 48% (1,531) came from outside hospital inpatient units. Thirty-day mortality varied significantly (p < 0.001) among transfer location: 12.8% when not transferred, 19.4% from outside EDs, 25.7% from outside hospital inpatient units, and 34.2% from nursing homes. Hazard ratios were 1.30 (p < 0.001) after transfer from outside hospital inpatient ward and 1.50 (p < 0.001) after transfer from nursing home. Patients transferred from nursing homes were more likely to have septic shock (26.9% vs. 11.6%, p < 0.001) and longer hospitalizations (13 days vs. 10 days, p < 0.001) versus those not transferred.

CONCLUSION
Transfer status is an independent contributor to death in emergency general surgery patients undergoing colectomy. Patients transferred from an outside hospital ED, nursing home or chronic care facility have the poorest outcomes. These results reinforce the importance of rapid triage and transfer of patients with early physiologic decompensation to ensure timely surgical evaluation and intervention.

LEVEL OF EVIDENCE
Prognostic, level III; Therapeutic, level IV.
Developing and Implementing a Quality Assurance Strategy for Electroconvulsive Therapy
Authors: Hollingsworth Jessa , Baliko Beverly , McKinney Selina , Rosenquist Peter 
Published: April 2018

Background
The literature provides scant guidance in effective quality assurance strategies concerning the use of electroconvulsive therapy (ECT) for the treatment of psychiatric conditions. Numerous guidelines are published that provide guidance in the delivery of care; however, little has been done to determine how a program or facility might ensure compliance to best practice for safety, tolerability, and efficacy in performing ECT.

Objective
The objective of this project was to create a quality assurance strategy specific to ECT. Determining standards for quality care and clarifying facility policy were key outcomes in establishing an effective quality assurance strategy.

Methods
An audit tool was developed utilizing quality criteria derived from a systematic review of ECT practice guidelines, peer review, and facility policy. All ECT procedures occurring over a 2-month period of May to June 2017 were retrospectively audited and compared against target compliance rates set for the facility’s ECT program. Facility policy was adapted to reflect quality standards, and audit findings were used to inform possible practice change initiatives, were used to create benchmarks for continuous quality monitoring, and were integrated into regular hospital quality meetings.

Results
Clarification on standards of care and the use of clinical auditing in ECT was an effective starting point in the development of a quality assurance strategy. Audit findings were successfully integrated into the hospital’s overall quality program, and recognition of practice compliance informed areas for future quality development and policy revision in this small community-based hospital in the southeastern United States.

Conclusions
This project sets the foundation for a quality assurance strategy that can be used to help monitor procedural safety and guide future improvement efforts in delivering ECT. Although it is just the first step in creating meaningful quality improvement, setting clear standards and identifying areas of greatest clinical need were crucial beginning for this hospital’s growing program.
A method for RNA structure prediction shows evidence for structure in lncRNAs
Authors: ponti Riccardo Delli , Armaos Alexandros , Marti Stefanie , Tartaglia Gian Gaetano 
Published: April 2018

AbstractTo compare the secondary structures of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure at single-nucleotide resolution using sequence information, and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modelling. CROSSalign can be applied to perform pair-wise comparisons and is able to find homologues between thousands of matches identifying the exact regions of similarity between profiles of different lengths. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/CROSSalign.
Multimodal evidence on shape and surface information in individual face processing
Authors: Nemrodov Dan , Behrmann Marlene , Niemeier Matthias , Drobotenko Natalia , Nestor Adrian 
Published: April 2018

AbstractThe significance of shape and surface information for face perception is well established, yet their relative contribution to recognition and their neural underpinnings await clarification. Here, we employ image reconstruction to retrieve, assess and visualize such information using behavioral, electroencephalography and functional magnetic resonance imaging data.Our results indicate that both shape and surface information can be successfully recovered from each modality but that the latter is better recovered than the former, consistent with its key role for face representations. Further, shape and surface information exhibit similar spatiotemporal profiles, rely on the extraction of specific visual features, such as eye shape or skin tone, and reveal a systematic representational structure, albeit with more cross-modal consistency for shape than surface.Thus, the present results help elucidate the representational basis of individual face recognition while, methodologically, they showcase the utility of image reconstruction and clarify its reliance on diagnostic visual information.
Early Exposure to Polycyclic Aromatic Hydrocarbons (PAHs) and Cardiac Toxicity in a Species (Xenopus laevis) with Low Aryl Hydrocarbon Receptor (AHR) Responsiveness
Authors: Sestak Madison C. , Pinette Julia A. , Lamoureux Caithlin M. , Whittemore Susan L. 
Published: April 2018

AbstractPolycyclic aromatic hydrocarbons (PAHs) are ubiquitous, persistent environmental contaminants, of which 16 are EPA-designated priority pollutants. Cardiotoxicity is observed in fish with developmental exposures to certain PAHs; however, the mechanism of toxicity can differ. Phenanthrene (PHE) and benzo(a)pyrene (BaP) are both cardiotoxic to fish, but PHE acts independently of aryl hydrocarbon receptor (AHR) activation while BaP-associated cardiotoxicity is AHR-dependent. To further understanding of mechanisms of toxicity, we compared the effects of early exposure to the priority PAHs pyrene (PYR), fluoranthene (FLA), PHE and BaP on cardiac function andcytochrome P450 type 1A(cyp1a) mRNA expression, an indicator of AHR activation, in a model system with lower AHR sensitivity than that of fish, the embryos and larvae ofXenopus laevis.Exposure to PYR, PHE, and FLA (0.25 – 25 μM) caused ventricular tachycardia early in heart development, but bradycardia and atrioventricular (AV) block in later stages. Elevatedcyp1amRNA levels indicate that FLA and BaP, but not PHE or PYR, are AHR agonists. The finding of FLA-induced cardiotoxicity andcyp1aexpression (35-fold) is particularly surprising as FLA inhibits CYP1A activity in fish and, as a single compound, is not cardiotoxic. Our results suggest that early exposure to PHE, PYR, and FLA, but not to BaP, compromises cardiac function by altering normal pacemaker activity and conduction inXenopus, effects associated with increased mortality. Our findings also reveal a considerable degree of species specificity between fish and frog regarding cardiac sensitivity to developmental PAH exposures and have implications for the cardiovascular health of PAH-exposed humans and wild amphibians.
Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty
Authors: Landis Michael J. , Freyman William A. , Baldwin Bruce. G. 
Published: April 2018

AbstractThe Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation of 33 species. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade’s age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. In lieu of fossils, paleo-geographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the silversword clade and test biogeographic hypotheses about its radiation across the Hawaiian Archipelago by modeling interactions between species relationships, molecular evolution, biogeographic scenarios, divergence times, and island origination times using the Bayesian phylogenetic framework, RevBayes. The ancestor of living silverswords most likely colonized the modern Hawaiian Islands once from the mainland approximately 5.1 Ma, with early surviving silversword lineages first appearing approximately 3.5 Ma. In testing the progression rule of island biogeography, we found strong positive evidence of the dispersal process preferring old-to-young directionality, but strong negative evidence for speciation occurring on islands during their young growth phase. This work serves as a general example for how diversification studies benefit from incorporating biogeographic and paleogeographic components.
Structural variants and selective sweep foci contribute to insecticide resistance in theDrosophila melanogastergenetic reference panel
Authors: Battlay Paul , Green Llewellyn , Leblanc Pontus B. , Schmidt Joshua M. , Fournier-Level Alexandre , Robin Charles 
Published: April 2018

AbstractPatterns of nucleotide polymorphism within populations ofDrosophila melanogastersuggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweep loci to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome wide association studies map ‘survival-on-malathion’ to two of the largest sweeps in theD. melanogastergenome;AceandCyp6g1. Malathion survivorship also correlates with lines which have high levels ofCyp12d1andJheh1andJheh2transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived state seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes:Cyp6g1exhibits copy number variation and transposable element insertions,Cyp12d1is tandemly duplicated, theJhehloci are associated with aBari1transposable element insertion, and aCyp6a17deletion is associated with susceptibility.
NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells
Authors: Becker-Kettern Julia , Paczia Nicole , Conrotte Jean-François , Zhu Chenchen , Fiehn Oliver , Jung Paul P. , Steinmetz Lars M. , Linster Carole L. 
Published: April 2018

ABSTRACTNADHX and NADPHX are hydrated and redox inactive forms of the NADH and NADPH cofactors, known to inhibit several dehydrogenasesin vitro. A metabolite repair system that is conserved in all domains of life and that comprises the two enzymes NAD(P)HX dehydratase and NAD(P)HX epimerase, allows reconversion of both theS- andR-epimers of NADHX and NADPHX to the normal cofactors. An inherited deficiency in this system has recently been shown to cause severe neurometabolic disease in children. Although evidence for the presence of NAD(P)HX has been obtained in plant and human cells, little is known about the mechanism of formation of these derivativesin vivoand their potential effects on cell metabolism. Here, we show that NAD(P)HX dehydratase deficiency in yeast leads to an important, temperature-dependent NADHX accumulation in quiescent cells with a concomitant depletion of intracellular NAD+and serine pools. We demonstrate that NADHX potently inhibits the first step of the serine synthesis pathway in yeast. Human cells deficient in the NAD(P)HX dehydratase also accumulated NADHX and showed decreased viability. In addition, those cells consumed more glucose and produced more lactate, potentially indicating impaired mitochondrial function. Our results provide first insights into how NADHX accumulation affects cellular functions and pave the way for a better understanding of the mechanism(s) underlying the rapid and severe neurodegeneration leading to early death in NADHX repair deficient children.
Structural insights into DNA sequence recognition by Arabidopsis ETHYLENE RESPONSE FACTOR 96
Authors: Chen Chun-Yen , Lin Pei-Hsuan , Chen Kun-Hung , Cheng Yi-Sheng 
Published: April 2018

ABSTRACTThe phytohormone ethylene is widely involved in many developmental processes and is a crucial regulator of defense responses against biotic and abiotic stresses in plants. Ethylene-responsive element binding protein (EREBP), a member of the APETALA2/ethylene response factor (AP2/ERF) superfamily, is a transcription factor that regulates stress-responsive genes by recognizing a specific cis-acting element of target DNA. A previous study showed only the NMR structure of the AP2/ERF domain of AtERF100 in complex with a GCC box DNA motif. In this report, we determined the crystal structure of AtERF96 in complex with a GCC box at atomic resolution. We analyzed the binding residues of the conserved AP2/ERF domain in the DNA recognition sequence. In addition to the AP2/ERF domain, an N-terminal α-helix of AtERF96 participates in DNA interaction in the flanking region. We also demonstrated the structure of AtERF96 EDLL motif, a unique conserved motif in the group IX of AP2/ERF family, is critical for the transactivation of defense-related genes. Our study establishes the structural basis of the AtERF96 transcription factor in complex with the GCC box, as well as the DNA binding mechanisms of the N-terminal α-helix and AP2/ERF domain.
Rare non-synonymous germline mutations systematically define the risk of triple negative breast cancer
Authors: Yang Mei , Fan Yanhui , Wu Zhi-Yong , Feng Zhendong , Zhang Qiangzu , Han Shunhua , Li Xiaoling , Zhu Teng , Cheng Minyi , Xu Juntao , Yang Ciqiu , Gao Hongfei , Zhang Chunming , Tan Guangming , Zhang Michael Q. , Song You-Qiang , Niu Gang , Wang Kun 
Published: April 2018

AbstractEarly identification of the risk for triple-negative breast cancer (TNBC) at the asymptomatic phase could lead to better prognosis. Here we developed a machine learning method to quantify systematic impact of all rare germline mutations on each pathway. We collected 106 TNBC patients and 287 elder healthy women controls. The spectra of activity profiles in multiple pathways were mapped and most pathway activities exhibited globally suppressed by the portfolio of individual germline mutations in TNBC patients. Accordingly, all individuals were delineated into two types: A and B. Type A patients could be differentiated from controls (AUC = 0.89) and sensitive to BRCA1/2 damages; Type B patients can be also differentiated from controls (AUC = 0.69) but probably being protected from BRCA1/2 damages. Further we found that Individuals with the lowest activity of selected pathways had extreme high relative risk (up to 21.67 in type A) and increased lymph node metastasis in these patients. Our study showed that genomic DNA contains information of unimaginable pathogenic factors. And this information is in a distributed form that could be applied to risk assessment for more cancer types.SignificanceWe identified individuals who are more susceptible to triple negative breast cancer. Our method performs much better than previous assessments based on BRCA1/2 damages, even polygenic risk scores. We disclosed previously unimaginable pathogens in a distributed form on genome and extended risk prediction to scenarios for other cancers.
Inferring Population Structure and Admixture Proportions in Low Depth NGS Data
Authors: Meisner Jonas , Albrechtsen Anders 
Published: April 2018

ABSTRACTWe here present two methods for inferring population structure and admixture proportions in low depth next generation sequencing data. Inference of population structure is essential in both population genetics and association studies and is often performed using principal component analysis or clustering-based approaches. Next-generation sequencing methods provide large amounts of genetic data but are associated with statistical uncertainty for especially low depth sequencing data. Models can account for this uncertainty by working directly on genotype likelihoods of the unobserved genotypes. We propose a method for inferring population structure through principal component analysis in an iterative approach of estimating individual allele frequencies, where we demonstrate improved accuracy in samples with low and variable sequencing depth for both simulated and real datasets. We also use the estimated individual allele frequencies in a fast non-negative matrix factorization method to estimate admixture proportions. Both methods have been implemented in the PCAngsd framework available at http://www.popgen.dk/software/.