bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive Effects of Lung function test on Postoperative Pneumonia in Squamous Esophageal Cancer
Authors: Wei Ran , Dong Wei , Shen Hongchang , Ni Yang , Zhang Tiehong , Wang Yibing , Du Jiajun 
Published: March 2016

AbstractPulmonary function tests had prospective implications for postoperative pneumonia, which occurred frequently after esophagectomy. Understanding factors that were associated with pulmonary infection may help in patient selection and postoperative management. We performed a retrospective review of 2 independent cohorts including 216 patients who underwent esophagectomy between November 2011 and May 2014, aiming at identifying predictors of primary pneumonia. Univariate analysis was used to identify potential covariates for the development of primary pneumonia. Adjustments for multiple comparisons were made using False Discovery Rate (FDR) (Holm-Bonferroni method). Multivariable logistic regression analysis was used to identify independent predictors and construct a regression model based on a training cohort (n = 166) and then the regression model was validated using an independent cohort (n = 50). It showed that low PEF (hazard ratio 0.97, P = 0.009) was independent risk factors for the development of primary pneumonia in multivariate analyses and had a predictive effect for primary pneumonia (AUC = 0.691 and 0.851 for training and validation data set, respectively). Therefore, PEF has clinical value in predicting postoperative pneumonia after esophagectomy and it may serve as an indicator of preoperative lung function training.
„Mein Haus, mein Auto, mein Boot“. Zufriedenheit mit dem Lebensstandard als geschlechtsspezifischer Mortalitätsprädiktor
Authors: Arnold L. , Keller B. , Lange A. , Szagun B. 
Published: March 2016

Zusammenfassung
Hintergrund: Männer haben ein höheres Mortalitätsrisiko als Frauen und reagieren wesentlich sensibler auf statusbezogene Stressbelastungen. Mögliche Erklärungen für die stärker ausgeprägte männliche Empfindlichkeit liefert der über die HPA-Achse vermittelte Zusammenhang zwischen hierarchischem Rang und Gesundheit. Viel Aufmerksamkeit hat in diesem Zusammenhang das Konstrukt des Statusunbehagens erfahren, wonach soziale Vergleichsprozesse das generelle Wohlbefinden senken und als wesentliche Risikofaktoren für verschiedene Erkrankungen angesehen werden.
Methodik: Mittels Sekundärdatenanalyse des sozio-ökonomischen Panels (SOEP) soll analysiert werden, inwiefern die subjektive Unzufriedenheit mit dem eigenen Lebensstandard mit einem erhöhten geschlechtsabhängigen Mortalitätsrisiko assoziiert werden kann. Zur statistischen Modellierung der Fragestellung werden geschlechtsdifferenzierte Cox-Regressionsmodelle berechnet. Die unbalancierte Teilstichprobe umfasst 6 963 Männer (764 Todesfälle) und 7 461 Frauen (663 Todesfälle).
Ergebnisse: Unzufriedenheit mit dem eigenen Lebensstandard hat einen signifikanten Einfluss auf das Mortalitätsrisiko von Männern nicht jedoch von Frauen. Unzufriedene Männer weisen ein nahezu doppelt so hohes Mortalitätsrisiko auf als die Referenzgruppe (HR=1,95, 95% KI 1,48–2,58), Männer mit mittlerer Zufriedenheit ein um 25% höheres Mortalitätsrisiko (HR=1,26, 95% KI 1,08–1,49). Außerdem zeigt der subjektive Statusindikator stärkere Dosis-Wirkungs-Beziehungen als die klassischen objektiven Statusparameter.
Schlussfolgerung: Unzufriedenheit mit dem eigenen Lebensstandard kann mit einem erhöhten geschlechtsabhängigen Mortalitätsrisiko in Verbindung gebracht werden und erweist sich als klarer Prädiktor insbesondere für die männliche Mortalität. Eine zentrale Ursache können über die HPA-Achse vermittelte Stressreaktionen aufgrund von herabsetzenden sozialen Vergleichsprozessen zu sein. Die Ergebnisse sprechen für eine standardisierte Einbeziehung subjektiver Statusindikatoren; der ausgeprägte Geschlechterunterschied legt darüber hinaus eine geschlechtergerechte epidemiologische Datenanalyse nahe.
Sleeping Beautytransposon mutagenesis identifies genes that cooperate with mutantSmad4in gastric cancer development
Authors: Takeda Haruna , Rust Alistair G. , Ward Jerrold M. , Yew Christopher Chin Kuan , Jenkins Nancy A. , Copeland Neal G. 
Published: March 2016

SignificanceGastric cancer is the third leading cause of cancer mortality, with an overall 5-y survival rate of <25%. Although sequencing and comprehensive molecular profiling of human gastric cancer have identified a wide spectrum of genes that drive gastric cancer development, we are still far from understanding the complete pathophysiology of this disease. Here, we usedSleeping Beautytransposon mutagenesis to identify genes and evolutionary forces driving gastric cancer development. This study identified pathways driving gastric cancer development, including WNT, TGF-β, PI3K signaling, ubiquitin-mediated proteolysis, adherens junctions, RNA degradation, and chromatin modification, and discovered many previously unidentified genes, such as the LDL receptor-related protein 1B (LRP1B) tumor suppressor gene, with potential clinical importance in human gastric cancer.
Aureolysin of Staphylococcus warneri M accelerates its proteolytic cascade, and participates in biofilm formation
Authors: Yokoi Ken-ji , Kuzuwa Shinya , Iwasaki Shu-Ichi , Yamakawa Ayanori , Taketo Akira , Kodaira Ken-Ichi 
Published: March 2016

Abstract
The aureolysin (Aur) gene of S. warneri M (aurWM) was cloned and sequenced. Analyses of the aurWM-inactivated mutant (S. warneri Mau) suggested that AurWM was probably associated with efficient processing of the PROM protease (homolog of V8/SspA serine protease), whereas considerable amount of mature-PROC protease (homolog of SspB cysteine protease) accumulated without AurWM. Additionally, AurWM appeared to affect biofilm formation in an uncertain suppressive way.
Signaling pathways for stress responses and adaptation in Aspergillus species: stress biology in the post-genomic era
Authors: Hagiwara Daisuke , Sakamoto Kazutoshi , Abe Keietsu , Gomi Katsuya 
Published: March 2016

Abstract
Aspergillus species are among the most important filamentous fungi in terms of industrial use and because of their pathogenic or toxin-producing features. The genomes of several Aspergillus species have become publicly available in this decade, and genomic analyses have contributed to an integrated understanding of fungal biology. Stress responses and adaptation mechanisms have been intensively investigated using the accessible genome infrastructure. Mitogen-activated protein kinase (MAPK) cascades have been highlighted as being fundamentally important in fungal adaptation to a wide range of stress conditions. Reverse genetics analyses have uncovered the roles of MAPK pathways in osmotic stress, cell wall stress, development, secondary metabolite production, and conidia stress resistance. This review summarizes the current knowledge on the stress biology of Aspergillus species, illuminating what we have learned from the genomic data in this “post-genomic era.”
Artificial Rearing of Endemic Red-tailed Barb Hypselobarbus kurali: A First Report
Authors: Williams Sherly E , Vijayalekshmi P , Benziger Allen , Karim Razeena , Nair Vishnu 
Published: March 2016

Abstract
Hypselobarbus kurali, a freshwater ray-finned fish (class Actinopterigii, order Cyprinidae), inhabits large streams and rivers of South Western Ghats of Kerala, India. The present work aims to create a breakthrough in the captive breeding technology of H. kurali and thereby successfully accomplish the goal of restocking resources. While both induced and artificial breeding were performed, the success rate for induced breeding was negligible when compared with that of artificial breeding. Artificial breeding was successfully carried out in the laboratory by dry stripping berried females (weight, 20–250 g; length, 25–28 cm) and matured milting males (weight, 180–200 g; length, 20–25 cm). Fertilized eggs were incubated in filtered source water (collected from the study site [Kulathupuzha region, Kallada River, Kollam district, Kerala]), at a temperature of 22–25°C and pH 7.5–7.8. The rate of fertilization was 92%, and the average hatching rate was 83.5%. The eggs hatched by 48 h after fertilization. After the yolk sac stage, the 7-d-old larvae were fed with cladocerans and rotifers.
Large-volume flux closure during plasmoid-mediated reconnection in coaxial helicity injection
Authors: Ebrahimi F. , Raman R. 
Published: March 2016

Abstract
A large-volume flux closure during transient coaxial helicity injection (CHI) in NSTX-U is demonstrated through resistive magnetohydrodynamics (MHD) simulations. Several major improvements, including the improved positioning of the divertor poloidal field coils, are projected to improve the CHI start-up phase in NSTX-U. Simulations in the NSTX-U configuration with constant in time coil currents show that with strong flux shaping the injected open field lines (injector flux) rapidly reconnect and form large volume of closed flux surfaces. This is achieved by driving parallel current in the injector flux coil and oppositely directed currents in the flux shaping coils to form a narrow injector flux footprint and push the injector flux into the vessel. As the helicity and plasma are injected into the device, the oppositely directed field lines in the injector region are forced to reconnect through a local Sweet–Parker type reconnection, or to spontaneously reconnect when the elongated current sheet becomes MHD unstable to form plasmoids. In these simulations for the first time, it is found that the closed flux is over 70% of the initial injector flux used to initiate the discharge. These results could work well for the application of transient CHI in devices that employ super conducting coils to generate and sustain the plasma equilibrium.
Effect of plasma response on the fast ion losses due to ELM control coils in ITER
Authors: Varje Jari , Asunta Otto , Cavinato Mario , Gagliardi Mario , Hirvijoki Eero , Koskela Tuomas , Kurki-Suonio Taina , Liu Yueqiang , Parail Vassili , Saibene Gabriella , Sipilä Seppo , Snicker Antti , Särkimäki Konsta , Äkäslompolo Simppa 
Published: March 2016

Abstract
Mitigating edge localized modes (ELMs) with resonant magnetic perturbations (RMPs) can increase energetic particle losses and resulting wall loads, which have previously been studied in the vacuum approximation. This paper presents recent results of fusion alpha and NBI ion losses in the ITER baseline scenario modelled with the Monte Carlo orbit following code ASCOT in a realistic magnetic field including the effect of the plasma response. The response was found to reduce alpha particle losses but increase NBI losses, with up to 4.2% of the injected power being lost. Additionally, some of the load in the divertor was found to be shifted away from the target plates toward the divertor dome.
Strategies for reducing ocean plastic debris should be diverse and guided by science
Authors: Rochman Chelsea M 
Published: March 2016

Abstract
Studies suggest that trillions of microplastic particles are floating on the surface of the global oceans and that the total amount of plastic waste entering the ocean will increase by an order of magnitude by 2025. As such, this ever-increasing problem demands immediate mitigation and reduction. Diverse solutions have been proposed, ranging from source reduction to ocean-based cleanup. These solutions are most effective when guided by scientific evidence. A study published in Environmental Research Letters (Sherman and van Sebille 2016 Environ. Res. Lett.

11 014006) took a closer look at the potential effectiveness of ocean-based cleanup. They conclude that it will be most cost-effective and ecologically beneficial if clean-up efforts focus on the flux of microplastics from the coasts rather than in the center of the oceans where plastic accumulates in so called ‘garbage patches’. If followed, this example may become one of a series of examples where science has informed a solution to the complex problem of plastic pollution.
Similarities in perceived predation risk prevent temporal partitioning of food by rodents in an African grassland
Authors: Banasiak Natalia , Shrader Adrian M. 
Published: March 2016

AbstractOne way in which animals coexist is through temporal separation of feeding activities. This separation directly reduces interference competition, but potentially not exploitive competition. To reduce exploitive competition, coexisting species tend to utilize different microhabitats and/or achieve different feeding efforts across microhabitats. However, 1 factor that has generally not been considered with regards to its impacts on competition, and thus coexistence, is predation risk. As different predators are active during the day and at night, the location of safe areas across the landscape can vary temporally. If so, then temporally separated prey species would likely forage in different areas thus reducing exploitive competition. However, if predation risk across the landscape is similar for nocturnal and diurnal species, then both could restrict their foraging to the same microhabitats, thus increasing exploitive competition. To explore these alternative possibilities, we manipulated grass height in an African grassland to create microhabitats that varied in predation risk. We then estimated perceived predation risk of both nocturnal and diurnal rodents in these microhabitats by recording giving-up densities (GUDs) in artificial resource patches. We found that despite differences in predators, both nocturnal and diurnal rodents preferred feeding in the same microhabitats, and they achieved similar feeding efforts within these microhabitats. This suggests that despite the prevention of interference competition through temporal partitioning, the spatial similarities in perceived predation risk in relation to cover likely increase exploitive competition between these rodents. However, as both nocturnal and diurnal rodents were present in the study area, it is likely that some other mechanism (e.g., varied diets) allows them to coexist.
Supported Standing in Boys With Duchenne Muscular Dystrophy
Authors: Townsend Elise L. , Bibeau Christine , Holmes Tara M. 
Published: March 2016

Purpose:
To evaluate the safety, tolerability, and efficacy of supported standing in a small sample of boys with Duchenne muscular dystrophy (DMD).

Methods:
Four 12- to 15-year-old boys with DMD engaged in a home-based supported standing program for 6 to 12 months. A single-subject design was employed to examine muscle length. Bone mineral density was assessed at 4-month intervals using dual-energy x-ray absorptiometry.

Results:
Upright, sustained supported standing was tolerated in 3 of the 4 boys. Mean weekly stand times ranged from 1.3 to 3.3 hours. Improved hip or knee flexor muscle length was seen in 3 of the 4 boys. No boys showed improved plantar flexor muscle length or increased lumbar bone mineral density.

Conclusions:
Findings offer preliminary empirical evidence addressing the safety, tolerability, and efficacy of standing in boys with DMD. Additional research with an emphasis on better program adherence is indicated.
Performance Evaluation of the New HIV-1 Quantification Assay, Xpert HIV-1 Viral Load, on a Wide Panel of HIV-1 Variants
Authors: Gueudin Marie , Baron Adeline , Alessandri-Gradt Elodie , Lemée Véronique , Mourez Thomas , Etienne Manuel , Plantier Jean-Christophe 
Published: March 2016

Objective:
To evaluate the quantification performance of the new Cepheid GeneXpert HIV-1 viral load assay, on a wide panel of HIV-1 variants.

Methods:
Clinical performance was evaluated relative to the Abbott RealTime HIV-1 assay on 285 HIV-1 seropositive samples selected to cover the assays quantification range (40 copies/mL–10,000,000 copies/mL), and included RNA undetectable or detected seropositive samples. The panel comprised 120 subtype B, 150 non-B, and 15 nontypable clinical samples; serial dilutions of 18 viral supernatants representative of the divergent viruses of HIV-1 groups N, O, and P were also tested.

Results:
Based on samples selected according to the Abbott assay viral loads (VL), the Cepheid assay detected or quantified 222/285 (78%) samples and the Abbott assay 240/285 (84%). Xpert yielded VLs for 162 (76%) of the 213 quantifiable samples with Abbott. This difference corresponded to 51 samples with VL >40 copies/mL by the Abbott assay (all below 200 copies/mL) but detected (n = 40) or undetectable (n = 11) by the Cepheid assay. VL of samples quantifiable by both assays (n = 162) showed very strong correlation, with a Spearman correlation coefficient of 0.985 and a Bland–Altman's mean of differences of −0.01. Performance for quantification of the non-M samples showed very good correlation, with significantly higher values with Cepheid for the group N and 2 group O samples.

Conclusions:
Our study showed that the Xpert HIV-1 VL assay offered very good performance for detection and quantification of the current HIV-1 genetic diversity; differences reported at the threshold could be an issue and requires further evaluations. The practicability of this new assay makes it suitable for low-income countries, where it could facilitate and improve follow-up of patients, as well as for high-income regions.
Balanced excitation and inhibition decorrelates visual feature representation in the mammalian inner retina
Authors: Franke Katrin , Berens Philipp , Schubert Timm , Bethge Matthias , Euler Thomas , Baden Tom 
Published: March 2016

SUMMARYThe retina extracts visual features for transmission to the brain. Different types of bipolar cell split the photoreceptor input into parallel channels and provide the excitatory drive for downstream visual circuits. Anatomically, mouse bipolar cell types have been described down to the ultrastructural level, but a similarly deep understanding of their functional diversity is lacking. By imaging light-driven glutamate release from more than 11,000 bipolar cell axon terminals in the intact retina, we here show that bipolar cell functional diversity is generated by the balanced interplay of dendritic excitatory inputs and axonal inhibitory inputs. The resultant centre and surround components of bipolar cell receptive fields interact to decorrelate bipolar cell output in the spatial and temporal domain. Our findings highlight the importance of inhibitory circuits in generating functionally diverse excitatory pathways and suggest that decorrelation of parallel visual pathways begins already at the second synapse of the mouse visual system.
A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses
Authors: Chen Chih-yu , Shi Wenqiang , Matthews Allison M. , Li Yifeng , Arenillas David J. , Mathelier Anthony , Itoh Masayoshi , Kawaji Hideya , Lassmann Timo ,   FANTOM Consortium, Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R. R. , Brown Carolyn J. , Wasserman Wyeth W. 
Published: March 2016

AbstractSex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted analyses of the sexes using human datasets to gain perspectives in such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study elucidated the importance of YY1 on transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.
Evaluation of SNP-based genotyping to monitor tuberculosis control in a high MDR-TB setting
Authors: Tukvadze N , Bergval I , Bablishvili N , Bzekalava N , Schuitema ARJ , de Beer J , de Zwaan R , Alba S , van Soolingen D , Aspindzelashvili R , Anthony RM , Sengstake S 
Published: March 2016

ABSTRACTMycobacterium tuberculosis(Mtb) lineage identification and typing of clinical isolates in general is performed only retrospectively. The results are rarely linked to drug susceptibility testing (DST) or patient data. Consequently, the association between Mtb lineage, (multi)drug resistance and treatment history is not fully explored at the local level. Here we evaluated a new SNP based typing assay. We furthermore assessed the added value of genotyping of Mtb isolates for epidemiological purposes and guidance of tuberculosis (TB) control.Mtblineage, DST profile and treatment history were determined for 399 samples at the National TB Reference Laboratory (NRL) in Tbilisi, Georgia by local staff. Data was shared electronically and analysis was performed remotely. Out of 399 isolates, 74 (74/399, 18.5%) were at least multidrug resistant (MDR)-TB, of which 63 (63/74, 85.1%) were members of three differentMtbBeijing lineages. Previous treatment was reported in 38/74 (51.4%) MDR(+) patients. The availability of this data allows associations with lineages. Notably, multidrug resistant TB was more strongly associated with the Beijing lineage than treatment history. Of all MDR-TB Beijing strains 56.7% (42/74) were members of a genetic cluster. This is most easily explained by (ongoing) MDR-TB transmission rather than drug resistance amplification. This knowledge is useful when designing intervention strategies for MDR-TB. Our study provides an example that on-site integratedMtbgenotyping is realistic and could support TB control activities.
RNA Synthesis is Associated with Multiple TBP-Chromatin Binding Events
Authors: Zaidi Hussain A. , Auble David T. , Bekiranov Stefan 
Published: March 2016

AbstractCompetition chip is an experimental method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a genome. We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction rate theory and derive the physical half-life or residence time for TATA-binding protein (TBP) across the yeast genome from competition ChIP data. Using our physical modeling approach where we explicitly include the induction profile of the competitor in the model, we are able to estimate yeast TBP-chromatin residence time as short as 1.3 minutes, demonstrating that competition ChIP is a relatively high temporal-resolution approach. Strikingly, we find a median value of ~5 TBP-chromatin binding events associated with the synthesis of one RNA molecule across Pol II genes, suggesting multiple rounds of pre-initiation complex assembly and disassembly before productive elongation of Pol II is achieved at most genes in the yeast genome.