bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of compound stimulus extinction and inhibition of noradrenaline reuptake on the renewal of alcohol seeking
Authors: Furlong T M , Pan M J , Corbit L H 
Published: September 2015

AbstractAlcohol-related stimuli can trigger relapse of alcohol-seeking behaviors even after extended periods of abstinence. Extinction of such stimuli can reduce their impact on relapse; however, the expression of extinction can be disrupted when testing occurs outside the context where extinction learning took place, an effect termed renewal. Behavioral and pharmacological methods have recently been shown to augment extinction learning; yet, it is not known whether the improved expression of extinction following these treatments remains context-dependent. Here we examined whether two methods, compound–stimulus extinction and treatment with the noradrenaline reuptake inhibitor atomoxetine, would reduce the vulnerability of extinction to a change in context. Following alcohol self-administration, responding was extinguished in a distinct context. After initial extinction, further extinction was given to a target stimulus presented in compound with another alcohol-predictive stimulus intended to augment prediction error (Experiment 1) or after a systemic injection of atomoxetine (1.0 mg kg−1; Experiment 2). A stimulus extinguished as part of a compound elicited less responding than a stimulus receiving equal extinction alone regardless of whether animals were tested in the training or extinction context; however, reliable renewal was not observed in this paradigm. Importantly, atomoxetine enhanced extinction relative to controls even in the presence of a reliable renewal effect. Thus, extinction of alcohol-seeking behavior can be improved by extinguishing multiple alcohol-predictive stimuli or enhancing noradrenaline neurotransmission during extinction training. Importantly, both methods improve extinction even when the context is changed between extinction training and test, and thus could be utilized to enhance the outcome of extinction-based treatments for alcohol-use disorders.
The cytotoxic mechanisms of disulfiram and copper(ii) in cancer cells
Authors: Tawari Patricia Erebi , Wang Zhipeng , Najlah Mohammad , Tsang Chi Wai , Kannappan Vinodh , Liu Peng , McConville Christopher , He Bin , Armesilla Angel L. , Wang Weiguang 
Published: September 2015

Abstract
The anticancer activity of disulfiram (DS) is copper(ii) (Cu)-dependent. This study investigated the anticancer mechanisms of DS/Cu using in vitro cytotoxicity and metabolic kinetic analysis. Our study indicates that DS/Cu targets cancer cells by the combination of two types of actions: (1) instant killing executed by DS/Cu reaction generated reactive oxygen species; (2) delayed cytotoxicity introduced by the end product, DDC-Cu. Nanoencapsulation of DS might shed light on repositioning of DS into cancer treatment.
Building an Inclusive, Accessible, and Responsive Campus at California State University East Bay, 2010-2015
Authors: Woods Dianne Rush , Taylor Sarah , Austin Duke , Beck Julie , Chung Ken , Couch Stephanie , Davis E. Maxwell , Fauth Bryan , Geron Kim , Ireland Dale Katherine , Kupers Eric , Massey Michael S. , Rowley Amy June , Stein Julie , Weiss Jessica 
Published: September 2015

California State University East Bay (CSUEB), opened in 1959 with 300 students on one campus. Since then, it has grown to serve over 14,000 students on three campuses. The motto of our university is “Per Aspera Ad Astra”, or “Through Adversity to the Stars”. This is an apt motto given that our university is the most racially and ethnically diverse campus in the continental United States (The Chronicle of Higher Education, 2014), and 61% of our undergraduate students are the first in their families to earn a college degree (Office of Institutional Research, personal communication, March 9, 2015). Our students are also highly diverse in terms of age, ability status, parenting experience, immigration background, sexual orientation, gender, religion, and much more. Though the diversity of our campus provides ample opportunities for faculty, staff, and students to be exposed to multiple perspectives, we have learned that intentional efforts are required to build an inclusive, accessible, and responsive community.
This article describes strategies we have employed over the past five years across three broad areas: (a) support for student learning, engagement, and retention; (b) professional development; and (c) policies around inclusion and access. Preliminary evaluation of these efforts suggests that we have made significant progress in building an inclusive campus that supports student learning, respects all members of the campus community, and facilitates our continuing engagement in this work.
Dynamic reconfiguration of frontal brain networks during executive cognition in humans
Authors: Braun Urs , Schäfer Axel , Walter Henrik , Erk Susanne , Romanczuk-Seiferth Nina , Haddad Leila , Schweiger Janina I. , Grimm Oliver , Heinz Andreas , Tost Heike , Meyer-Lindenberg Andreas , Bassett Danielle S. 
Published: September 2015

Significance
Cognitive flexibility is hypothesized to require dynamic integration between brain areas. However, the time-dependent nature and distributed complexity of this integration remains poorly understood. Using recent advances in network science, we examine the functional integration between brain areas during a quintessential task that requires executive function. By linking brain regions (nodes) by their interactions (time-dependent edges), we uncover nontrivial modular structure: groups of brain regions cluster together into densely interconnected structures whose interactions change during task execution. Individuals with greater network reconfiguration in frontal cortices show enhanced memory performance, and score higher on neuropsychological tests challenging cognitive flexibility, suggesting that dynamic network reconfiguration forms a fundamental neurophysiological mechanism for executive function.
Parkin loss leads to PARIS-dependent declines in mitochondrial mass and respiration
Authors: Stevens Daniel A. , Lee Yunjong , Kang Ho Chul , Lee Byoung Dae , Lee Yun-Il , Bower Aaron , Jiang Haisong , Kang Sung-Ung , Andrabi Shaida A. , Dawson Valina L. , Shin Joo-Ho , Dawson Ted M. 
Published: September 2015

Significance
Mutations or inactivation of parkin causes Parkinson’s disease (PD) in humans. Recent studies have focused on parkin’s role in mitochondrial quality control in the pathogenesis of PD, including defects in mitophagy, mitochondrial fission, fusion, and transport. This study shows that parkin also controls mitochondrial biogenesis and that defects in mitochondrial biogenesis drive the loss of dopamine (DA) neurons due to the absence of parkin. The findings support the role of parkin in regulating multiple arms of mitochondrial quality control and suggest that maintaining mitochondrial biogenesis is critically important in the survival of DA neurons.
Slowing down of North Pacific climate variability and its implications for abrupt ecosystem change
Authors: Boulton Chris A. , Lenton Timothy M. 
Published: September 2015

Significance
Sea surface temperature (SST) variations in the North Pacific have triggered past abrupt changes in fisheries and other ecosystems. We have discovered that over the last century, fluctuations of North Pacific SSTs have become less frequent and longer-lived. This “reddening” behavior can also be seen in the dominant pattern of climate variability in the region, known as the Pacific Decadal Oscillation index. This fundamental change in climate variability has important implications for ecosystems in the region. It implies that over the last century, ecosystems have become prone to undergoing larger climate-triggered abrupt shifts. Hence our discovery of changing climate variability could have contributed to the large magnitude of well-known abrupt changes in North Pacific ecosystems in 1977 and 1989.
Fluid mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin
Authors: Klein Frieder , Humphris Susan E. , Guo Weifu , Schubotz Florence , Schwarzenbach Esther M. , Orsi William D. 
Published: September 2015

Significance
We provide biogeochemical, micropaleontological, and petrological constraints on a subseafloor habitat at the passive Iberia Margin, where mixing of reduced hydrothermal serpentinization fluids with oxic seawater provided the energy and substrates for metabolic reactions. This mixing zone was inhabited by bacteria and archaea and is comparable to the active Lost City hydrothermal field at the Mid-Atlantic Ridge. Our results highlight the potential of magma-poor passive margins to host Lost City-type hydrothermal systems that support microbial activity in subseafloor environments. Because equivalent systems have likely existed throughout most of Earth's history in a wide range of oceanic environments, fluid mixing may have provided the substrates and energy to support a unique subseafloor community of microorganisms over geological timescales.
A phantom road experiment reveals traffic noise is an invisible source of habitat degradation
Authors: Ware Heidi E. , McClure Christopher J. W. , Carlisle Jay D. , Barber Jesse R. 
Published: September 2015

Significance
Using landscape-scale traffic noise playbacks to create a “phantom road,” we find that noise, apart from other factors present near roads, degrades the value of habitat for migrating songbirds. We found that nearly one third of the bird community avoided the phantom road. For some bird species that remained despite noise exposure, body condition and stopover efficiency (ability to gain body condition over time) decreased compared with control conditions. These findings have broad implications for the conservation of migratory birds and perhaps for other wildlife, because factors driving foraging behavior are similar across animals. For wildlife that remains in loud areas, noise pollution represents an invisible source of habitat degradation.
Fog and rain in the Amazon
Authors: Anber Usama , Gentine Pierre , Wang Shuguang , Sobel Adam H. 
Published: September 2015

Significance
We here demonstrate that we can resolve the seasonality of the hydrologic cycle in the Amazon using an approach, opposite to general circulation models, in which we resolve convection and parameterize large-scale circulation as a function of the resolved convection. The results emphasize the key role of cloud albedo feedback and, in particular, of the morning fog layer in determining the diurnal course of surface heat fluxes and seasonality of the surface and atmospheric heat and water cycles. These results indicate that our understanding of tropical climates over land can be considerably advanced by using coupled land−atmosphere models with explicit convection and parameterized large-scale dynamics.
Evidence integration in model-based tree search
Authors: Solway Alec , Botvinick Matthew M. 
Published: September 2015

SignificanceRecent behavioral research has made rapid progress toward revealing the processes by which we make choices based on judgments of subjective value. A key insight has been that this process unfolds incrementally over time, as we gradually build up evidence in favor of a particular preference. Although the data for this ‟evidence-integration” model are compelling, they derive almost entirely from single-step choices: Would you like chocolate or vanilla ice cream? Decisions in everyday life are typically more complex. In particular, they generally involve choices between sequences of action, with accompanying series of outcomes. We present here results from two experiments, providing the first evidence to our knowledge that the standard integration model of choice can be directly extended to multistep decision making.
Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble
Authors: Zandarashvili Levani , Esadze Alexandre , Vuzman Dana , Kemme Catherine A. , Levy Yaakov , Iwahara Junji 
Published: September 2015

Significance
Many transcription factors and DNA repair/modifying enzymes must first locate the target sites through stochastic scanning of DNA in the vast presence of nonspecific sites. In this work, we demonstrate that target search by these proteins can be accelerated via engineering based on structural dynamic knowledge of the DNA-scanning process. Our biophysical data for the Egr-1 zinc-finger protein and its nuclease derivatives reveal kinetic and thermodynamic roles of the conformational equilibrium between two modes in the DNA-scanning process: one suitable for search and the other for recognition. We found that optimizing the balance between the search and recognition modes improves efficiency in zinc-finger proteins’ target search. This finding can help advance zinc-finger technology for artificial gene regulation and genome editing.
Precursors to morality in development as a complex interplay between neural, socioenvironmental, and behavioral facets
Authors: Cowell Jason M. , Decety Jean 
Published: September 2015

SignificanceResearch in the past decade indicates that the building blocks of morality are present very early in development. However, little is known about the neural and environmental mechanisms underlying their emergence. Here we show, for the first time, to our knowledge, using multiple levels of analysis, the complex integration of bottom–up and top–down processes in sociomoral evaluation. Brain wave differences elicited by witnessing the prosocial and antisocial behaviors of others predicted infants and toddlers’ subsequent attraction to prosocial others and were associated with parental values of justice and fairness. This developmental social neuroscience perspective provides empirical and theoretical clarity to the biological basis and brain–behavior processes involved in moral sensitivity.
Complexity of the human memory B-cell compartment is determined by the versatility of clonal diversification in germinal centers
Authors: Budeus Bettina , Schweigle de Reynoso Stefanie , Przekopowitz Martina , Hoffmann Daniel , Seifert Marc , Küppers Ralf 
Published: September 2015

SignificanceThe complexity of the human memory B-lymphocyte compartment is a key component to depict and understand adaptive immunity. Despite numerous prior investigations, the generation of certain memory B-cell subsets, the dependency on T-cell help, and the composition, size, and diversity of clonal expansions are either poorly understood or debated. Here we provide an extensive and tightly controlled immunoglobulin heavy chain variable (IGHV) gene repertoire analysis of four main human memory B-cell subpopulations, revealing that an ordered diversification in germinal centers determines a highly versatile memory B-cell compartment in humans with surprisingly many very large B-cell clones.
Targeted delivery of liquid microvolumes into the lung
Authors: Kim Jinho , O’Neill John D. , Dorrello N. Valerio , Bacchetta Matthew , Vunjak-Novakovic Gordana 
Published: September 2015

Significance
Systemic drug administrations suffer from inefficient delivery to a specific pathologic region of the lung. Aerosolized drugs, when prepared to display desired transport behavior, can be delivered to selected lung regions by inhalation. We describe an alternative method for delivering drugs directly to a specific lung region in the form of liquid microvolumes based on a mathematical model. Deposition of liquid film on lung epithelium in different target regions of the lung was confirmed in rat lungs using fluorescence imaging. We propose that instilling microvolumes of liquid would enable predictable drug concentrations at the target site, reduce the amount of the drug required for treatment, and minimize systemic side effects for several lung diseases.
Manifestation of axion electrodynamics through magnetic ordering on edges of a topological insulator
Authors: Lee Yea-Lee , Park Hee Chul , Ihm Jisoon , Son Young-Woo 
Published: September 2015

Significance
Interactions between two adjacent surfaces of different surface orientations in a single-crystal topological insulator are investigated. We show that the edge between two surfaces can host nontrivial axion electrodynamics with sizeable experimental signals owing to the unique interaction between the two topological surface states. We find that the large work function difference between facets in a topological insulator can generate strong electric fields around the edges and that, in turn, the electric fields give rise to effective magnetic fields for a given broken time-reversal symmetry. Our theoretical work highlights a route to reveal intriguing axion electrodynamics in a real solid and provides methods to exploit macroscopic topological states.
CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells
Authors: Deng Wulan , Shi Xinghua , Tjian Robert , Lionnet Timothée , Singer Robert H. 
Published: September 2015

Significance
We have derived a new technology for the detection of genes within undisturbed nuclei of fixed cells and tissues. Previous approaches have used fluorescent DNA probes to hybridize to genes of interest, requiring treatment of heat and disruptive chemicals that distort the natural organization of the nucleus. Instead, we have used a bacterial protein, CRISPR (clustered regularly interspaced short palindromic repeats), combined with an RNA sequence as probes to find the genes of interest in the intact genome. This approach preserves the spatial relationships of the genetic elements, which are important for understanding gene expression, and the process is remarkably rapid (15 min), convenient, and can be used directly on tissues for diagnosis of disease.
ACTN3 R577X genotype and athletic performance in a large cohort of Japanese athletes
Authors: Kikuchi Naoki , Miyamoto‐Mikami Eri , Murakami Haruka , Nakamura Tomohiro , Min Seok‐Ki , Mizuno Masuhiko , Naito Hisashi , Miyachi Motohiko , Nakazato Koichi , Fuku Noriyuki 
Published: September 2015

AbstractAim: Recent meta‐analyses of the literature confirmed the association between the RR+RX genotype of the ACTN3 R577X polymorphism and elite sprint/power athletic status in Europeans but not in Asians and Africans, while the association between the R577X genotype and elite endurance athlete status is less convincing. The aim of the present study was to investigate the association between the ACTN3 R577X genotype and elite athlete status in a large Asian (Japanese) cohort of track and field athletes. Methods: One‐thousand fifty‐seven Japanese track and field athletes (627 sprint/power athletes and 430 endurance athletes) and 810 Japanese controls were genotyped for the ACTN3 R577X polymorphism (rs1815739) by using the TaqMan® SNP Genotyping Assay. Results: Elite sprint/power athletes had a higher frequency of the RR+RX genotype than the controls (OR: 1.59, 95% CI: 1.16–2.18; P = .003). A significant linear correlation was found between the RR + RX genotype and athlete status (i.e. regional < national < international) in sprint/power athletes (regional: 71%, national: 81%, international: 84%; P = .001 for trend) and long‐distance runners (regional: 65%, national: 72%, international: 82%; P = .030 for trend). Conclusions: The data obtained for this large Asian (Japanese) cohort of track and field athletes served to confirm the association between the RR + RX genotype of the ACTN3 R577X polymorphism and elite sprint/power athlete status and also the association between the ACTN3 RR + RX genotype and long‐distance running athletic status.
BiopLib and BiopTools—a C programming library and toolset for manipulating protein structure
Authors: Porter Craig T. , Martin Andrew C.R. 
Published: September 2015

Abstract
Summary: We describe BiopLib, a mature C programming library for manipulating protein structure, and BiopTools, a set of command-line tools which exploit BiopLib. The library also provides a small number of functions for handling protein sequence and general purpose programming and mathematics. BiopLib transparently handles PDBML (XML) format and standard PDB files. BiopTools provides facilities ranging from renumbering atoms and residues to calculation of solvent accessibility.
Availability and implementation: BiopLib and BiopTools are implemented in standard ANSI C. The core of the BiopLib library is a reliable PDB parser that handles alternate occupancies and deals with compressed PDB files and PDBML files automatically. The library is designed to be as flexible as possible, allowing users to handle PDB data as a simple list of atoms, or in a structured form using chains, residues and atoms. Many of the BiopTools command-line tools act as filters, taking a PDB (or PDBML) file as input and producing a PDB (or PDBML) file as output. All code is open source and documented using Doxygen. It is provided under the GNU Public Licence and is available from the authors’ web site or from GitHub.
Contact: andrew@bioinf.org.uk
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets
Authors: Guo Zhengyu , Tzvetkova Boriana , Bassik Jennifer M. , Bodziak Tara , Wojnar Brianna M. , Qiao Wei , Obaida Md A. , Nelson Sacha B. , Hu Bo Hua , Yu Peng 
Published: September 2015

Abstract
Summary: Gene targeting is a protocol for introducing a mutation to a specific gene in an organism. Because of the importance of in vivo assessment of gene function and modeling of human diseases, this technique has been widely adopted to generate a large number of mutant mouse models. Due to the recent breakthroughs in high-throughput sequencing technologies, RNA-Seq experiments have been performed on many of these mouse models, leading to hundreds of publicly available datasets. To facilitate the reuse of these datasets, we collected the associated metadata and organized them in a database called RNASeqMetaDB. The metadata were manually curated to ensure annotation consistency. We developed a web server to allow easy database navigation and data querying. Users can search the database using multiple parameters like genes, diseases, tissue types, keywords and associated publications in order to find datasets that match their interests. Summary statistics of the metadata are also presented on the web server showing interesting global patterns of RNA-Seq studies.
Availability and implementation: Freely available on the web at http://rnaseqmetadb.ece.tamu.edu.
Contact: pengyu.bio@gmail.com