bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Outer Membrane Protein Involved in the Uptake of Glucose Is Essential for Cytophaga hutchinsonii Cellulose Utilization
Authors: Zhou Hong , Wang Xia , Yang Tengteng , Zhang Weixin , Chen Guanjun , Liu Weifeng 
Published: January 2016

ABSTRACT

Cytophaga hutchinsonii
specializes in cellulose digestion by employing a collection of novel cell-associated proteins. Here, we identified a novel gene locus, CHU_1276, that is essential for
C. hutchinsonii
cellulose utilization. Disruption of CHU_1276 in
C. hutchinsonii
resulted in complete deficiency in cellulose degradation, as well as compromised assimilation of cellobiose or glucose at a low concentration. Further analysis showed that CHU_1276 was an outer membrane protein that could be induced by cellulose and low concentrations of glucose. Transcriptional profiling revealed that CHU_1276 exerted a profound effect on the genome-wide response to both glucose and Avicel and that the mutant lacking CHU_1276 displayed expression profiles very different from those of the wild-type strain under different culture conditions. Specifically, comparison of their transcriptional responses to cellulose led to the identification of a gene set potentially regulated by CHU_1276. These results suggest that CHU_1276 plays an essential role in cellulose utilization, probably by coordinating the extracellular hydrolysis of cellulose substrate with the intracellular uptake of the hydrolysis product in
C. hutchinsonii
.
TBES
Authors: Corre Youenn , Diguet Jean-Philippe , Heller Dominique , Blouin Dominique , Lagadec Loïc 
Published: January 2016

This article describes TBES, a software end-to-end environment for synthesizing multitask applications on FPGAs. The implementation follows a template-based approach for creating heterogeneous multiprocessor architectures. Heterogeneity stems from the use of general-purpose processors along with custom accelerators. Experimental results demonstrate substantial speedup for several classes of applications.
Furthermore, this work allows for reducing development costs and saving development time for the software architect, the domain expert, and the optimization expert. This work provides a framework to bring together various existing tools and optimisation algorithms. The advantages are manifold: modularity and flexibility, easy customization for best-fit algorithm selection, durability and evolution over time, and legacy preservation including domain experts' know-how.
In addition to the use of architecture templates for the overall system, a second contribution lies in using high-level synthesis for promoting exploration of hardware IPs. The domain expert, who best knows which tasks are good candidates for hardware implementation, selects parts of the initial application to be potentially synthesized as dedicated accelerators. As a consequence, the HLS general problem turns into a constrained and more tractable issue, and automation capabilities eliminate the need for tedious and error-prone manual processes during domain space exploration.
The automation only takes place once the application has been broken down into concurrent tasks by the designer, who can then drive the synthesis process with a set of parameters provided by TBES to balance tradeoffs between optimization efforts and quality of results.
The approach is demonstrated step by step up to FPGA implementations and executions with an MJPEG benchmark and a complex Viola-Jones face detection application. We show that TBES allows one to achieve results with up to 10 times speedup to reduce development times and to widen design space exploration.
Target Identification in Small Cell Lung Cancer via Integrated Phenotypic Screening and Activity-Based Protein Profiling
Authors: Li Jiannong , Fang Bin , Kinose Fumi , Bai Yun , Kim Jae-Young , Chen Yian A. , Rix Uwe , Koomen John M. , Haura Eric B. 
Published: January 2016

Abstract
To overcome hurdles in identifying key kinases in small cell lung cancer (SCLC), we integrated a target-agnostic phenotypic screen of kinase inhibitors with target identification using activity-based protein profiling (ABPP) in which a desthiobiotin-ATP probe was used. We screened 21 SCLC cell lines with known c-MYC amplification status for alterations in viability using a chemical library of 235 small-molecule kinase inhibitors. One screen hit compound was interrogated with ABPP, and, through this approach, we reidentified Aurora kinase B as a critical kinase in MYC-amplified SCLC cells. We next extended the platform to a second compound that had activity in SCLC cell lines lacking c-MYC amplification and identified TANK-binding kinase 1, a kinase that affects cell viability, polo-like kinase-1 signaling, G2–M arrest, and apoptosis in SCLC cells lacking MYC amplification. These results demonstrate that phenotypic screening combined with ABPP can identify key disease drivers, suggesting that this approach, which combines new chemical probes and disease cell screens, has the potential to identify other important targets in other cancer types. Mol Cancer Ther; 15(2); 334–42. ©2016 AACR.
Modelling of Polarity Change in a Nonlinear Internal Wave Train in Laoshan Bay
Authors: Grimshaw Roger , Wang Caixia , Li Lan 
Published: January 2016

AbstractThere are now several observations of internal solitary waves passing through a critical point where the coefficient of the quadratic nonlinear term in the variable coefficient Korteweg–de Vries equation changes sign, typically from negative to positive as the wave propagates shoreward. This causes a solitary wave of depression to transform into a train of solitary waves of elevation riding on a negative pedestal. However, recently a polarity change of a different kind was observed in Laoshan Bay, China, where a periodic wave train of elevation waves converted to a periodic wave train of depression waves as the thermocline rose on a rising tide. This paper describes the application of a newly developed theory for this phenomenon. The theory is based on the variable coefficient Korteweg–de Vries equation for the case when the coefficient of the quadratic nonlinear term undergoes a change of sign and predicts that a periodic wave train will pass through this critical point as a linear wave, where a phase change occurs that induces a change in the polarity of the wave, as observed. A two-layer model of the density stratification and background current shear is developed to make the theoretical predictions specific and quantitative. Some numerical simulations of the variable coefficient Korteweg–de Vries equation, and also the extended variable coefficient Korteweg–de Vries equation, are reported that confirm the theoretical predictions and are in good agreement with the observations.
Use of Geostationary Super Rapid Scan Satellite Imagery by the Storm Prediction Center*
Authors: Line William E. , Schmit Timothy J. , Lindsey Daniel T. , Goodman Steven J. 
Published: January 2016

Abstract
The Geostationary Operational Environmental Satellite-14 (GOES-14) Imager was operated by the National Oceanic and Atmospheric Administration (NOAA) in an experimental rapid scan 1-min mode during parts of 2012, 2013, 2014, and 2015. This scan mode, known as the Super Rapid Scan Operations for GOES-R (SRSOR), emulates the high-temporal-resolution sampling that will be provided by the Advanced Baseline Imager on the next-generation GOES-R series. NOAA/National Weather Service/Storm Prediction Center (SPC) forecasters utilized the 1-min imagery extensively in operations when available over convectively active regions. They found it provided them with unique insight into relevant features and processes before, during, and after convective initiation. This paper introduces how the SRSOR datasets from GOES-14 were used by SPC forecasters and how these data are likely to be applied when available operationally from GOES-R. Several animations, included as supplemental material, showcase the rapid change of severe weather–related phenomena observed during the 2014 and 2015 SRSOR campaigns from the GOES-14 Imager.
B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel
Authors: Almaden Jonathan V. , Liu Yi C. , Yang Edward , Otero Dennis C. , Birnbaum Harry , Davis-Turak Jeremy , Asagiri Masataka , David Michael , Goldrath Ananda W. , Hoffmann Alexander 
Published: January 2016

Key PointsNF-κB family members RelB and cRel are coordinately activated by BAFF and provide distinct survival signals. In vivo and in vitro B-cell developmental defects are observed when both RelB and cRel are deleted.
Dicer1-mediated miRNA processing shapes the mRNA profile and function of murine platelets
Authors: Rowley Jesse W. , Chappaz Stéphane , Corduan Aurélie , Chong Mark M. W. , Campbell Robert , Khoury Amanda , Manne Bhanu Kanth , Wurtzel Jeremy G. T. , Michael James V. , Goldfinger Lawrence E. , Mumaw Michele M. , Nieman Marvin T. , Kile Benjamin T. , Provost Patrick , Weyrich Andrew S. 
Published: January 2016

Key PointsDicer1 deletion in MKs alters platelet miRNA and mRNA profiles. Dicer1-deficient platelets display increased integrins αIIb and β3 levels and enhanced in vitro and in vivo functional responses.
The impact of multiple low-level BCR-ABL1 mutations on response to ponatinib
Authors: Parker Wendy T. , Yeung David T. O. , Yeoman Alexandra L. , Altamura Haley K. , Jamison Bronte A. , Field Chani R. , Hodgson J. Graeme , Lustgarten Stephanie , Rivera Victor M. , Hughes Timothy P. , Branford Susan 
Published: January 2016

Key Points
The association between multiple BCR-ABL1 mutations and inferior response to nilotinib/dasatinib was not seen with ponatinib therapy. However, chronic phase patients with T315I plus additional mutation(s) did have poorer responses to ponatinib than those with T315I only.
N-linked glycan stabilization of the VWF A2 domain
Authors: Lynch Christopher J. , Lane David A. 
Published: January 2016

Key Points
Glycosylation at N1574 stabilizes the VWF A2 domain against unfolding and proteolysis by ADAMTS13, and its first GlcNAc is the critical element. Y1544 is a likely interacting residue with N1574-GlcNAc, and its mutation to aspartic acid stabilizes the domain in the absence of the glycan.
A lymphomagenic role for HIV beyond immune suppression?
Authors: Dolcetti Riccardo , Gloghini Annunziata , Caruso Arnaldo , Carbone Antonino 
Published: January 2016

AbstractDespite the immune reconstitution promoted by combined antiretroviral therapy (cART), lymphomas still represent the most common type of cancer in HIV-infected individuals. Cofactors related to immunodeficiency such as oncogenic viruses, chronic antigenic stimulation, and cytokine overproduction are thought to be the main drivers of HIV lymphomagenesis, although the current scenario does not convincingly explain the still-high incidence of lymphomas and the occurrence of peculiar lymphoma histotypes in HIV-infected patients under cART. Recent findings are challenging the current view of a mainly indirect role of HIV in lymphoma development and support the possibility that HIV may directly contribute to lymphomagenesis. In fact, mechanisms other than immune suppression involve biologic effects mediated by HIV products that are secreted and accumulate in lymphoid tissues, mainly within lymph node germinal centers. Notably, HIV-infected patients with lymphomas, but not those not affected by these tumors, were recently shown to carry HIV p17 protein variants with enhanced B-cell clonogenic activity. HIV p17 protein variants were characterized by the presence of distinct insertions at the C-terminal region of the protein responsible for a structural destabilization and the acquisition of novel biologic properties. These data are changing the current paradigm assuming that HIV is only indirectly related to lymphomagenesis. Furthermore, these recent findings are consistent with a role of HIV as a critical microenvironmental factor promoting lymphoma development and pave the way for further studies that may lead to the design of more effective strategies for an early identification and improved control of lymphomas in the HIV setting.
A computational method for genotype calling in family-based sequencing data
Authors: Chang Lun-Ching , Li Bingshan , Fang Zhou , Vrieze Scott , McGue Matt , Iacono William G. , Tseng George C. , Chen Wei 
Published: January 2016

Abstract
Background
As sequencing technologies can help researchers detect common and rare variants across the human genome in many individuals, it is known that jointly calling genotypes across multiple individuals based on linkage disequilibrium (LD) can facilitate the analysis of low to modest coverage sequence data. However, genotype-calling methods for family-based sequence data, particularly for complex families beyond parent-offspring trios, are still lacking.

Results
In this study, first, we proposed an algorithm that considers both linkage disequilibrium (LD) patterns and familial transmission in nuclear and multi-generational families while retaining the computational efficiency. Second, we extended our method to incorporate external reference panels to analyze family-based sequence data with a small sample size. In simulation studies, we show that modeling multiple offspring can dramatically increase genotype calling accuracy and reduce phasing and Mendelian errors, especially at low to modest coverage. In addition, we show that using external panels can greatly facilitate genotype calling of sequencing data with a small number of individuals. We applied our method to a whole genome sequencing study of 1339 individuals at ~10X coverage from the Minnesota Center for Twin and Family Research.

Conclusions
The aggregated results show that our methods significantly outperform existing ones that ignore family constraints or LD information. We anticipate that our method will be useful for many ongoing family-based sequencing projects. We have implemented our methods efficiently in a C++ program FamLDCaller, which is available from http://www.pitt.edu/~wec47/famldcaller.html.
Deciphering transcriptional regulations coordinating the response to environmental changes
Authors: Acuña Vicente , Aravena Andrés , Guziolowski Carito , Eveillard Damien , Siegel Anne , Maass Alejandro 
Published: January 2016

Abstract
Background
Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless, the prediction of TRNs based on the affinity of transcription factors (TFs) with binding sites (BSs) generally produces an over-estimation of the observable TF/BS relations within the network and therefore many of the predicted relations are spurious.

Results
We present Lombarde, a bioinformatics method that extracts from a TRN determined from a set of predicted TF/BS affinities a subnetwork explaining a given set of observed co-expressions by choosing the TFs and BSs most likely to be involved in the co-regulation. Lombarde solves an optimization problem which selects confident paths within a given TRN that join a putative common regulator with two co-expressed genes via regulatory cascades. To evaluate the method, we used public data of Escherichia coli to produce a regulatory network that explained almost all observed co-expressions while using only 19 % of the input TF/BS affinities but including about 66 % of the independent experimentally validated regulations in the input data. When all known validated TF/BS affinities were integrated into the input data the precision of Lombarde increased significantly. The topological characteristics of the subnetwork that was obtained were similar to the characteristics described for known validated TRNs.

Conclusions
Lombarde provides a useful modeling scheme for deciphering the regulatory mechanisms that underlie the phenotypic responses of an organism to environmental challenges. The method can become a reliable tool for further research on genome-scale transcriptional regulation studies.
Lactic acidosis and severe septic shock in metformin users: a cohort study
Authors: Doenyas-Barak Keren , Beberashvili Ilia , Marcus Ronit , Efrati Shai 
Published: January 2016

Abstract
Background
High serum lactate is associated with increased mortality in septic shock patients. Metformin alters lactate metabolism, and may affect its prognostic value. We compared, between metformin users and nonusers, the prognosis of extremely elevated plasma lactate levels in patients with septic shock.

Methods
The electronic medical records (EMR) of patients admitted to the emergency room between January 2011 and June 2013 were reviewed. The study cohort comprised patients with an initial diagnosis of septic shock and blood lactate higher than 10 mmol/L. The selected population was divided into two groups: metformin users (exposed) and metformin nonusers (unexposed). The primary outcome measured was inhospital mortality.

Results
The study included 44 metformin users and 118 nonusers. Metformin users were similar to nonusers with respect to levels of lactate, HCO3, and blood pH; however, they were older and had higher incidence rates of cardiovascular disease and acute kidney injury at admission, compared to nonusers. Inhospital mortality rates were significantly lower in the metformin-treated group, 56.8 % vs. 88.1 %, p <0.0001.

Conclusions
Though high lactate concentration indicates poor prognosis in septic patients, mortality rate was found to be significantly lower in those who were treated with metformin. This finding may help clinicians in deciding treatment for these patients, who could otherwise be considered too ill for real treatment benefit.
Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1
Authors: Horn Hannes , Keller Alexander , Hildebrandt Ulrich , Kämpfer Peter , Riederer Markus , Hentschel Ute 
Published: January 2016

AbstractThe Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the Arabidopsis thaliana phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus Williamsia and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.
The Gly16 Allele of the Gly16Arg Single-Nucleotide Polymorphism in the β2-Adrenergic Receptor Gene Augments Perioperative Use of Vasopressors: A Retrospective Cohort Study
Authors: Nielsen Morten , Staalsoe Jonatan M. , Ullum Henrik , Secher Niels H. , Nielsen Henning B. , Olsen Niels V. 
Published: January 2016

BACKGROUND:
Arterial hypotension is frequent in patients undergoing anesthesia and may aggravate the outcome. Common genetic variations may influence the cardiovascular response to anesthesia. In this retrospective cohort study, we tested whether variation in the gene encoding the β2-adrenergic receptor (ADRB2) influences perioperative arterial blood pressure and consequently the use of vasopressors.

METHODS:
Five hundred seventy-one Danish Caucasians undergoing neurosurgery were genotyped for 5 marker single-nucleotide polymorphisms (SNPs) within ADRB2 (Gly16Arg, Gln27Glu, Thr164Ile, Arg175Arg, and Gly351Gly). A pairwise tagging principle was used to identify ADRB2 haplotypes. Mean arterial blood pressure (MAP) was recorded in the supine awake state and, together with administration of vasopressors (ephedrine and/or phenylephrine), for 30 minutes after induction of general anesthesia (sevoflurane/remifentanil or propofol/remifentanil).

RESULTS:
Four hundred thirteen (72%) patients received ephedrine and/or phenylephrine. Only baseline MAP (P < 0.001) and the Arg175Arg SNP (P = 0.01) were associated with nadir perioperative MAP. The Gly16Arg SNP but no other SNPs showed a trend toward an association with the amount of vasopressors used during anesthesia with Arg16 homozygotes receiving less ephedrine equivalents. The Arg16-Gln27-Thr164-Arg175-Gly351 haplotype was associated with approximately 13% lower vasopressor requirements than the most common Gly16-Glu27-Thr164-Arg175-Gly351 haplotype (P = 0.01).

CONCLUSIONS:

Gly16 carriers received larger amounts of vasopressor compared with Arg16 homozygotes. This corresponds to previous studies demonstrating that the Gly16 allele in ADRB2 is associated with vasodilation and high cardiac output.
Thyroid bud morphogenesis requires CDC42- and SHROOM3-dependent apical constriction
Authors: Loebel David A. F. , Plageman Timothy F. , Tang Theresa L. , Jones Vanessa J. , Muccioli Maria , Tam Patrick P. L. 
Published: January 2016

ABSTRACTEarly development of the gut endoderm and its subsequent remodeling for the formation of organ buds are accompanied by changes to epithelial cell shape and polarity. Members of the Rho-related family of small GTPases and their interacting proteins play multiple roles in regulating epithelial morphogenesis. In this study we examined the role of Cdc42 in foregut development and organ bud formation. Ablation of Cdc42 in post-gastrulation mouse embryos resulted in a loss of apical-basal cell polarity and columnar epithelial morphology in the ventral pharyngeal endoderm, in conjunction with a loss of apical localization of the known CDC42 effector protein PARD6B. Cell viability but not proliferation in the foregut endoderm was impaired. Outgrowth of the liver, lung and thyroid buds was severely curtailed in Cdc42-deficient embryos. In particular, the thyroid bud epithelium did not display the apical constriction that normally occurs concurrently with the outgrowth of the bud into the underlying mesenchyme. SHROOM3, a protein that interacts with Rho GTPases and promotes apical constriction, was strongly expressed in the thyroid bud and its sub-cellular localization was disrupted in Cdc42-deficient embryos. In Shroom3 gene trap mutant embryos, the thyroid bud epithelium showed no apical constriction, while the bud continued to grow and protruded into the foregut lumen. Our findings indicate that Cdc42 is required for epithelial polarity and organization in the endoderm and for apical constriction in the thyroid bud. It is possible that the function of CDC42 is partly mediated by SHROOM3.
Uma Análise de Técnicas de Ensino em Ciências Sociais e Características Sociodemográficas dos Discentes
Authors: Pereira Felipe Augusto , Lins Daniel , Picarte Ronei , Castellan Rita Rovai 
Published: January 2016

Este artigo é o resultado de uma pesquisa que teve como objetivo principal identificar a existência de associação entre a preferência por técnicas de ensino e as características sociodemográficas de estudantes de cursos de ciências sociais. Para tanto, foi realizado um estudo de caráter bibliográfico exploratório, para a identificação das técnicas a serem pesquisadas, seguido de uma análise quantitativa com 89 discentes, com o intuito de identificar as preferências e as relações. Foram identificadas tanto as técnicas preferidas quanto as menos apreciadas pelos alunos. Posteriormente, as técnicas foram agrupadas em 08 fatores através de análise fatorial e descobriu-se que alguns dos fatores estão associados a características sociodemográficas dos discentes. Desse modo, os docentes podem lançar mão de técnicas que têm maior aceitação, adaptando-se às contingências e potencializando assim a aprendizagem.