bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eight-minute self-regulation intervention raises educational attainment at scale in individualist but not collectivist cultures
Authors: Kizilcec René F. , Cohen Geoffrey L. 
Published: April 2017

SignificanceHigh attrition from educational programs is a major obstacle to social mobility and a persistent source of economic inefficiency. Over two-thirds of students entering a 2-y institution fail to earn a credential in the United States. In online courses, attrition rates are even higher. In two large field experiments, we tested the conditions under which a writing activity that facilitates goal commitment and goal-directed behavior reduces attrition in online courses. The activity raised completion rates by up to 78% for members of individualist cultures and primarily for those who contended with predictable and surmountable obstacles in the form of everyday obligations, but it was ineffective in collectivist cultures and for people contending with other types of obstacles.
Tectonic controls on the long-term carbon isotope mass balance
Authors: Shields Graham A. , Mills Benjamin J. W. 
Published: April 2017

Significance
The carbon isotope record has played a major role in reconstructing the oxygen and carbon dioxide content of the ancient atmosphere. However, known oxygenation events are not always reflected in the isotopic record of marine carbonate rocks, while conventional interpretations imply that less organic matter is buried when erosion rates are high, which is hard to explain. Here we show that both issues can be resolved if limestone weathering makes up a proportionately greater fraction of the global carbon cycle at high erosion rates. We argue that the link between carbon isotopes and oxygenation is more tenuous than commonly assumed, and propose a case-by-case reexamination of earth’s oxygenation history.
Formation of neurodegenerative aggresome and death-inducing signaling complex in maternal diabetes-induced neural tube defects
Authors: Zhao Zhiyong , Cao Lixue , Reece E. Albert 
Published: April 2017

SignificanceNeural tube defects in infants of women with diabetes are associated with disrupted protein folding and increased programmed cell death in embryonic cells. Misfolded proteins are ubiquitinylated and form aggregates that contain the neurodegenerative disease-associated proteins α-Synuclein, Parkin, and Huntingtin (Htt). Aggregation of Htt leads to formation of a Hip1–Hippi–Caspase-8 complex to activate Caspase-8. Treatment with chemical chaperones alleviates protein aggregation and decreases neural tube defects in the embryos of diabetic mice. Targeting misfolded proteins could be a potential approach to preventing birth defects in diabetic pregnancies.
Structural basis of Tie2 activation and Tie2/Tie1 heterodimerization
Authors: Leppänen Veli-Matti , Saharinen Pipsa , Alitalo Kari 
Published: April 2017

Significance
Tie1 and Tie2 receptor tyrosine kinases are key regulators of blood and lymphatic vessel development and of pathological processes including tumor angiogenesis, atherosclerosis, and vascular leakage, e.g., in sepsis. Tie1 is essential for the Tie2 agonist activity of angiopoietins, and the activated receptors form heteromeric complexes in endothelial cell–cell junctions. However, little is known about the activation mechanisms of the Tie receptors. Here we demonstrate that the membrane-proximal domains of Tie2 mediate homotypic interactions, which occur via intermolecular β-sheet formation and are necessary for Tie2 activation. The structural analysis suggests that Tie2/Tie1 heterodimerization occurs by the same mechanism. The crystal structures provide a model for angiopoietin-stimulated Tie2 ectodomain dimerization, clustering, and activation and insights into therapeutic targeting.
Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance
Authors: Wu Yixuan , Albrecht Todd R. , Baillat David , Wagner Eric J. , Tong Liang 
Published: April 2017

Significance
The Integrator complex (INT) has important functions in the 3′-end processing of noncoding RNAs and RNA polymerase II transcription. The INT contains at least 14 subunits, but its molecular mechanism of action is still poorly understood. The endonuclease activity of INT is mediated by its subunit 11 (IntS11), which forms a stable complex with Integrator complex subunit 9 (IntS9) through their C-terminal domains (CTDs). Here, we report the crystal structure of the IntS9–IntS11 CTD complex at 2.1-Å resolution and detailed, structure-based biochemical and functional studies. Highly conserved residues are located in the extensive interface between the two CTDs. Yeast two-hybrid assays and coimmunoprecipitation experiments confirm the structural observations. Functional studies demonstrate that the IntS9–IntS11 interaction is crucial for INT in snRNA 3′-end processing.
Selective entrainment of gamma subbands by different slow network oscillations
Authors: Zhong Weiwei , Ciatipis Mareva , Wolfenstetter Thérèse , Jessberger Jakob , Müller Carola , Ponsel Simon , Yanovsky Yevgenij , Brankačk Jurij , Tort Adriano B. L. , Draguhn Andreas 
Published: April 2017

Significance
Theta-gamma coupling has been largely documented in hippocampal and neocortical areas and hypothesized to constitute a network mechanism for information processing. However, we identify here another global slow rhythm at near-theta frequency that also couples to gamma. By simultaneously recording respiration, we could distinguish actual theta oscillations from a respiration-entrained rhythm (RR) in the local field potential whose peak frequency may overlap with theta. We demonstrate a robust specificity for the coupling of different gamma subbands to either theta or RR depending on brain state and region. The results suggest that the brain uses different frequency channels for transferring different types of information.
Automated glycan assembly using the Glyconeer 2.1 synthesizer
Authors: Hahm Heung Sik , Schlegel Mark K. , Hurevich Mattan , Eller Steffen , Schuhmacher Frank , Hofmann Johanna , Pagel Kevin , Seeberger Peter H. 
Published: April 2017

Significance
Rapid access to defined, pure biomacromolecules is key to biochemical and biophysical investigations as evidenced by the impact automated solid-phase synthesis of oligonucleotides and oligopeptides had on basic research. Here, a strategy as well as a new instrument to routinely access oligosaccharides by automated synthesis is reported. The method produces glycans quickly and reliably to accelerate fundamental advances in glycobiology.
Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike
Authors: Cai Yongfei , Karaca-Griffin Selen , Chen Jia , Tian Sai , Fredette Nicholas , Linton Christine E. , Rits-Volloch Sophia , Lu Jianming , Wagh Kshitij , Theiler James , Korber Bette , Seaman Michael S. , Harrison Stephen C. , Carfi Andrea , Chen Bing 
Published: April 2017

Significance
A vaccine against HIV-1 should elicit antibodies that prevent infection (“neutralize”) by binding the viral envelope glycoprotein (Env). The extraordinary genetic diversity of Env means that protective antibodies must recognize one of a few broadly conserved sites (“epitopes”). The trimeric Env protein fluctuates among a range of conformations: Closed conformations expose only the conserved epitopes, whereas various open conformations expose many other, more variable epitopes. The latter dominate immune responses and restrict protection to a narrow range of viral strains. We describe here the properties of Env from an extremely neutralization-resistant HIV-1 variant. We find that it binds only antibodies that recognize conserved epitopes, consistent with a tightly closed conformation, and suggest that it might be a suitable vaccine template.
Intranasal MSC-derived A1-exosomes ease inflammation, and prevent abnormal neurogenesis and memory dysfunction after status epilepticus
Authors: Long Qianfa , Upadhya Dinesh , Hattiangady Bharathi , Kim Dong-Ki , An Su Yeon , Shuai Bing , Prockop Darwin J. , Shetty Ashok K. 
Published: April 2017

SignificanceThis study demonstrated that intranasal (IN) administration of A1-exosomes alleviates multiple adverse changes that typically emerge after status epilepticus (SE), a medical crisis that presents a high propensity to evolve into chronic hippocampus dysfunction. Specifically, A1-exosome treatment after SE led to reduced neuron loss and inflammation, maintenance of normal neurogenesis, and preservation of cognitive and memory function. The results have significance for clinical application of A1-exosomes for curbing the evolution of SE-induced injury into chronic hippocampus dysfunction. The results also imply that IN administration of A1-exosomes is therapeutic for other neurological conditions that present with significant neuroinflammation.
Non-local effects on pedestal kinetic ballooning mode stability
Authors: Saarelma S , Martin-Collar J , Dickinson D , McMillan B F , Roach C M 
Published: April 2017

Abstract
The H-mode pedestal height plays an important role in determining the global confinement of the tokamak plasma. In type I ELMy H-mode the ultimate limit for the pedestal pressure at constant width is set by the ideal MHD peeling-ballooning modes (PBMs) that are thought to be the trigger for the ELMs. However, the PBM criterion does not uniquely determine the pedestal. Increasing the width of the pedestal, the marginally peeling-ballooning stable pedestal height increases as well. The second criterion for the pedestal is set by the transport processes in the pedestal that limit the gradient between the ELMs. One candidate for driving this transport is the kinetic ballooning mode (KBM) that is driven by the pressure gradient (Snyder et al 2009 Nucl. Fusion
49 085035). The KBM growth rate increases very rapidly after the critical pressure gradient is exceeded leading to very stiff profiles with the pressure gradient clamped near to the stability limit. In the local linear gyrokinetic analysis of experimental MAST and JET plasmas we have found that, like the

n

=
∞

ideal MHD ballooning modes, the KBMs can access locally so called second stability if the magnetic shear becomes low enough (Dickinson et al 2011 Plasma Phys. Control. Fusion
53 115010; Saarelma et al 2013 Nucl. Fusion
53 123012). However, in the pedestal region the local assumption that the equilibrium can be considered radially constant for the investigated modes is no longer justified. In this paper we revisit the KBM analysis using a global code ORB5 to investigate whether second stability access exists for KBMs. We find that counter to the local analysis, the global KBM stability is not sensitive to the magnetic shear in the pedestal region. At sufficiently high β (but still below the ideal peeling-ballooning limit) the pedestal region becomes KBM unstable regardless of the amount of bootstrap current assumed in the equilibrium reconstruction. However, just as in local analysis, the mode is stabilised by reducing the pressure gradient. This suggests that KBMs can regulate the pedestal pressure gradient during the ELM cycle even when local analysis finds them stable due to high bootstrap current.
Global stability analysis of axisymmetric boundary layer over a circular cone
Authors: Bhoraniya Ramesh , Vinod Narayanan 
Published: April 2017

Abstract
This paper presents linear biglobal stability analysis of axisymmetric boundary layer over a circular cone. An incompressible flow over a sharp circular cone is considered with zero angle of attack. The base flow velocity profile is fully non-parallel and non-similar. Linearized Navier-Stokes (LNS) equations are derived for disturbance flow quantities using the standard procedure. The LNS equations are discretized using Chebyshev spectral collocation method. The governing equations along with boundary conditions form a general eigenvalues problem. The numerical solution of general eigenvalues problem is obtained using ARPACK subroutine, which uses Arnoldis iterative algorithm. The global temporal modes are computed for the range of Reynolds number and semi-cone angles(α)for the axisymmetric mode(N=0). The flow is found temporally and spatially stable for 1° semi-cone angle and the range of Reynolds numbers considered. However, flow becomes temporally unstable and spatially stable with the increase in semi-cone angle(α). The wave-like behaviour of the disturbances is found at small semi-cone angles (α).
Network module-based model in the differential expression analysis for RNA-seq
Authors: Lei Mingli , Xu Jia , Huang Li-Ching , Wang Lily , Li Jing 
Published: April 2017

Abstract

Motivation
RNA-seq has emerged as a powerful technology for the detection of differential gene expression in the transcriptome. The commonly used statistical methods for RNA-seq differential expression analysis were designed for individual genes, which may detect too many irrelevant significantly genes or too few genes to interpret the phenotypic changes. Recently network module-based methods have been proposed as a powerful approach to analyze and interpret expression data in microarray and shotgun proteomics. But the module-based statistical model has not been adequately addressed for RNA-seq data.

Result
we proposed a network module-based generalized linear model for differential expression analysis of the count-based sequencing data from RNA-seq. The simulation studies demonstrated the effectiveness of the proposed model and the improvement of the statistical power for identifying the differentially expressed modules in comparison to the existing methods. We also applied our method to tissue datasets and identified 207 significantly differentially expressed kidney-active or liver-active modules. For liver cancer datasets, significantly differentially expressed modules, including Wnt signaling pathway and VEGF pathway, were found to be tightly associated with liver cancer. Besides, in comparison with the single gene-level analysis, our method could identify more significantly biological modules, which related to the liver cancer.

Availability and Implementation
The R package SeqMADE is available at https://cran.r-project.org/web/packages/SeqMADE/.

Supplementary information
Supplementary data are available at Bioinformatics online.
SubCons: a new ensemble method for improved human subcellular localization predictions
Authors: Salvatore M , Warholm P , Shu N , Basile W , Elofsson A 
Published: April 2017

Abstract

Motivation
Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein. Unfortunately large-scale experimental studies are limited in their accuracy. Therefore, the development of prediction methods has been limited by the amount of accurate experimental data. However, recently large-scale experimental studies have provided new data that can be used to evaluate the accuracy of subcellular predictions in human cells. Using this data we examined the performance of state of the art methods and developed SubCons, an ensemble method that combines four predictors using a Random Forest classifier.

Results
SubCons outperforms earlier methods in a dataset of proteins where two independent methods confirm the subcellular localization. Given nine subcellular localizations, SubCons achieves an F1-Score of 0.79 compared to 0.70 of the second best method. Furthermore, at a FPR of 1% the true positive rate (TPR) is over 58% for SubCons compared to less than 50% for the best individual predictor.

Availability and Implementation
SubCons is freely available as a webserver (http://subcons.bioinfo.se) and source code from https://bitbucket.org/salvatore_marco/subcons-web-server. The golden dataset as well is available from http://subcons.bioinfo.se/pred/download.

Supplementary information
Supplementary data are available at Bioinformatics online.
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly
Authors: Huang Shengfeng , Kang Mingjing , Xu Anlong 
Published: April 2017

Abstract

Summary
De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity.

Availability and Implementation
Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Domain prediction with probabilistic directional context
Authors: Ochoa Alejandro , Singh Mona 
Published: April 2017

Abstract

Motivation
Protein domain prediction is one of the most powerful approaches for sequence-based function prediction. Although domain instances are typically predicted independently of each other, newer approaches have demonstrated improved performance by rewarding domain pairs that frequently co-occur within sequences. However, most of these approaches have ignored the order in which domains preferentially co-occur and have also not modeled domain co-occurrence probabilistically.

Results
We introduce a probabilistic approach for domain prediction that models ‘directional’ domain context. Our method is the first to score all domain pairs within a sequence while taking their order into account, even for non-sequential domains. We show that our approach extends a previous Markov model-based approach to additionally score all pairwise terms, and that it can be interpreted within the context of Markov random fields. We formulate our underlying combinatorial optimization problem as an integer linear program, and demonstrate that it can be solved quickly in practice. Finally, we perform extensive evaluation of domain context methods and demonstrate that incorporating context increases the number of domain predictions by ∼15%, with our approach dPUC2 (Domain Prediction Using Context) outperforming all competing approaches.

Availability and Implementation
dPUC2 is available at http://github.com/alexviiia/dpuc2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Comment on “Bioerosion: the other ocean acidification problem”: on field studies and mechanisms
Authors: Silbiger Nyssa J , DeCarlo Thomas M 
Published: April 2017

Abstract
In a recent review, “Bioerosion: the other ocean acidification problem,” Schönberg et al. claim that studies of bioerosion across natural chemical gradients are “flawed” or “compromised” by co-variation among environmental factors. Their discussion falls largely on two publications, Silbiger et al. and DeCarlo et al. Here, we demonstrate that critical errors in plotting, statistical analysis, and data selection in Schönberg et al.’s reanalysis, result in a gross misrepresentation of these studies. Further, we argue three key points regarding field-based studies that require broader discussion within the bioerosion community and marine scientists in general: (1) that natural variability in field studies is not a flaw, (2) interpretations must be supported by mechanistic understanding, and (3) field-based studies play an essential role in elucidating interactions between OA and natural variability that is not captured by laboratory CO2-manipulation experiments. Our goal with this comment is to encourage open discussion of the advantages and caveats of field-based studies in general, and ultimately, advance our understanding of bioerosion patterns observed in nature.
Intraoperative Computed Tomography Angiography: A Novel Completion Imaging Modality for Carotid Endarterectomy
Authors: Sen Anish N , Fridley Jared , Sebastian Sherly , Duckworth Edward A M 
Published: April 2017

Abstract

BACKGROUND
Intraoperative computed tomography angiography (ICTA) is a novel completion imaging modality for carotid endarterectomy (CEA). No studies exist in the literature describing ICTA use in CEA.

OBJECTIVE
To evaluate the feasibility and efficacy of ICTA as a method of immediately evaluating the technical results of CEA.

METHODS
Twenty-three consecutive CEAs were performed by a single neurosurgeon over an 8-month period. Of this series, 12 utilized ICTA for completion imaging, 10 utilized duplex ultrasonography (US), and 1 utilized no intraoperative completion imaging. Electronic medical records were reviewed to assess demographics, CTA results, US results, and need for revisions.

RESULTS
Patients included 13 men (62%) and 8 women (38%). All patients had symptomatic internal carotid artery stenosis. Polytetrafluoroethylene (PTFE) patch angioplasty was used in 16 cases (70%). Average operative times were comparable between cases that utilized CTA and US, 180 and 175 min, respectively. Major technical defects were identified in one of the 12 cases utilizing ICTA and none of the 10 cases utilizing intraoperative US. The technical defect was revised without subsequent neurological complication. One patient had a postoperative intracerebral hemorrhage requiring surgical evacuation. Fifteen patients were followed for up to 3 months with no postoperative stroke or transient ischemic attacks.

CONCLUSION
ICTA is a potentially safe and effective completion imaging modality compared to traditional alternatives, enabling the identification of technical deficits intraoperatively. While no statistically significant difference in operative times were noted between intraoperative CTA and US use, numerous steps must be taken to maximize the efficiency of ICTA.
Equilibrium configuration of a stratus floating above accretion disks: Full-disk calculation
Authors: Itanishi Yusuke , Fukue Jun 
Published: April 2017

Abstract
We examine floating strati above a luminous accretion disk, supported by the radiative force from the entire disk, and calculate the equilibrium locus, which depends on the disk luminosity and the optical depth of the stratus. Due to the radiative transfer effect (albedo effect), the floating height of the stratus with a finite optical depth generally becomes high, compared with the particle case. In contrast to the case of the near-disk approximation, moreover, the floating height becomes yet higher in the present full-disk calculation, since the intense radiation from the inner disk is taken into account. As a result, when the disk luminosity normalized by the Eddington luminosity is ∼0.3 and the stratus optical depth is around unity, the stable configuration disappears at around r ∼ 50 rg, rg being the Schwarzschild radius, and the stratus would be blown off as a cloudy wind consisting of many strati with appropriate conditions. This luminosity is sufficiently smaller than the Eddington one, and the present results suggest that the radiation-driven cloudy wind can be easily blown off from the sub-Eddington disk, and this can explain various outflows observed in ultra-fast outflow objects as well as in broad-absorption-line quasars.