bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel DNA-damage tolerance genes reveals regulation of translesion DNA synthesis by nucleophosmin
Authors: Ziv Omer , Zeisel Amit , Mirlas-Neisberg Nataly , Swain Umakanta , Nevo Reinat , Ben-Chetrit Nir , Martelli Maria Paola , Rossi Roberta , Schiesser Stefan , Canman Christine E. , Carell Thomas , Geacintov Nicholas E. , Falini Brunangelo , Domany Eytan , Livneh Zvi 
Published: November 2014

AbstractCells cope with replication-blocking lesions via translesion DNA synthesis (TLS). TLS is carried out by low-fidelity DNA polymerases that replicate across lesions, thereby preventing genome instability at the cost of increased point mutations. Here we perform a two-stage siRNA-based functional screen for mammalian TLS genes and identify 17 validated TLS genes. One of the genes, NPM1, is frequently mutated in acute myeloid leukaemia (AML). We show that NPM1 (nucleophosmin) regulates TLS via interaction with the catalytic core of DNA polymerase-η (polη), and that NPM1 deficiency causes a TLS defect due to proteasomal degradation of polη. Moreover, the prevalent NPM1c+ mutation that causes NPM1 mislocalization in ~30% of AML patients results in excessive degradation of polη. These results establish the role of NPM1 as a key TLS regulator, and suggest a mechanism for the better prognosis of AML patients carrying mutations in NPM1.
Deletion of α-neurexin II results in autism-related behaviors in mice
Authors: Dachtler J , Glasper J , Cohen R N , Ivorra J L , Swiffen D J , Jackson A J , Harte M K , Rodgers R J , Clapcote S J 
Published: November 2014

AbstractAutism is a common and frequently disabling neurodevelopmental disorder with a strong genetic basis. Human genetic studies have discovered mutations disrupting exons of theNRXN2gene, which encodes the synaptic adhesion protein α-neurexin II (Nrxn2α), in two unrelated individuals with autism, but a causal link betweenNRXN2and the disorder remains unclear. To begin to test the hypothesis that Nrxn2α deficiency contributes to the symptoms of autism, we employed Nrxn2α knockout (KO) mice that genetically model Nrxn2α deficiencyin vivo. We report that Nrxn2α KO mice displayed deficits in sociability and social memory when exposed to novel conspecifics. In tests of exploratory activity, Nrxn2α KO mice displayed an anxiety-like phenotype in comparison with wild-type littermates, with thigmotaxis in an open field, less time spent in the open arms of an elevated plus maze, more time spent in the enclosure of an emergence test and less time spent exploring novel objects. However, Nrxn2α KO mice did not exhibit any obvious changes in prepulse inhibition or in passive avoidance learning. Real-time PCR analysis of the frontal cortex and hippocampus revealed significant decreases in the mRNA levels of genes encoding proteins involved in both excitatory and inhibitory transmission. Quantification of protein expression revealed that Munc18-1, encoded byStxbp1, was significantly decreased in the hippocampus of Nrxn2α KO mice, which is suggestive of deficiencies in presynaptic vesicular release. Our findings demonstrate a causal role for the loss of Nrxn2α in the genesis of autism-related behaviors in mice.
Effective Identification of Functional Hearing Loss Using Behavioral Threshold Measures
Authors: Schlauch Robert S. , Koerner Tess K. , Marshall Lynne 
Published: November 2014

Purpose
Four functional hearing loss protocols were evaluated.

Method
For each protocol, 30 participants feigned a hearing loss first on an audiogram and then for a screening test that began a threshold search from extreme levels (–10 or 90 dB HL). Two-tone and 3-tone protocols compared thresholds for ascending and descending tones for 2 (0.5 and 1.0 kHz) and 3 (0.5, 1.0, and 2.0 kHz) frequencies, respectively. A noise-band protocol compared an ascending noise-band threshold with that for 2 descending tones (0.5 and 1.0 kHz). A spondee protocol compared an ascending spondee threshold with that for 2 descending tones (0.5 and 1.0 kHz). These measures were repeated without the participants feigning losses.

Results
With nonfeigning participants, ascending and descending threshold differences were minimal for all protocols. When the participants feigned a loss, the spondee protocol produced the largest average threshold difference (30.8 dB), whereas the other protocols produced smaller differences (19.6–22.2 dB).

Conclusions
Using both the screening test and a comparison of the initial audiogram with the screening test, the spondee and 3-tone protocols resulted in 100% true positives and 0% false positives for functional hearing loss. Either of these protocols could be used clinically or in occupational hearing conservation programs.
A general construction for parallelizing Metropolis−Hastings algorithms
Authors: Calderhead Ben 
Published: November 2014

Significance
Many computational problems in modern-day statistics are heavily dependent on Markov chain Monte Carlo (MCMC) methods. These algorithms allow us to evaluate arbitrary probability distributions; however, they are inherently sequential in nature due to the Markov property, which severely limits their computational speed. We propose a general approach that allows scalable parallelization of existing MCMC methods. We do so by defining a finite-state Markov chain on multiple proposals in a way that ensures asymptotic convergence to the correct stationary distribution. In example simulations, we demonstrate up to two orders of magnitude improvement in overall computational performance.
Evolutionary tipping points in the capacity to adapt to environmental change
Authors: Botero Carlos A. , Weissing Franz J. , Wright Jonathan , Rubenstein Dustin R. 
Published: November 2014

SignificanceEnvironmental variation is becoming more frequent and unpredictable as a consequence of climate change, yet we currently lack the tools to evaluate the extent to which organisms may adapt to this phenomenon. Here we develop a model that explores these issues and use it to study how changes in the timescale and predictability of environmental variation may ultimately affect population viability. Our model indicates that, although populations can often cope with fairly large changes in these environmental parameters, on occasion they will collapse abruptly and go extinct. We characterize the conditions under which these evolutionary tipping points occur and discuss how vulnerability to such cryptic threats may depend on the genetic architecture and life history of the organisms involved.
Signals from the surface modulate differentiation of human pluripotent stem cells through glycosaminoglycans and integrins
Authors: Wrighton Paul J. , Klim Joseph R. , Hernandez Brandon A. , Koonce Chad H. , Kamp Timothy J. , Kiessling Laura L. 
Published: November 2014

Significance
Human pluripotent stem (hPS) cells possess the extraordinary capacity to self-renew indefinitely and differentiate into specialized cell types. Elucidating the signaling pathways that underlie hPS cell differentiation is important for understanding human development and advancing regenerative medicine. Growth factors and small molecules can influence hPS cell differentiation. Many protocols rely on these soluble cues while using substrata composed of numerous biomolecules (e.g. Matrigel). Complex substrata engage multiple types of cellular receptors, thereby obscuring the influence of distinct signals on hPS cell fate. Modular peptide-modified surfaces that interact with specific targets can selectively activate signaling pathways, thereby facilitating hPS cell differentiation. This strategy can be used to dissect how cross-talk between soluble and insoluble signals influences cell fate.
Body ownership causes illusory self-attribution of speaking and influences subsequent real speaking
Authors: Banakou Domna , Slater Mel 
Published: November 2014

Significance
Under normal circumstances we consciously attribute authorship of our actions to ourselves, the sensation of agency. We describe an experiment where participants observed a virtual human character speak and falsely attributed the speaking to themselves. They later shifted the FF of their own voice toward the stimulus voice. This only occurred when the life-sized VB substituted their own and moved with their own movements. A further contribution to the effect was vibrotactile stimulation on the thyroid cartilage synchronized with the speaking. This suggests that agency can be self-attributed even in the absence of prior intention, feed-forward prediction, priming, and cause preceding effect. A critical contributor is the illusion of ownership over the VB that spoke.
Engineering the shape and structure of materials by fractal cut
Authors: Cho Yigil , Shin Joong-Ho , Costa Avelino , Kim Tae Ann , Kunin Valentin , Li Ju , Lee Su Yeon , Yang Shu , Han Heung Nam , Choi In-Suk , Srolovitz David J. 
Published: November 2014

Significance
Most materials can be stretched to a small degree, depending on their elastic limits and failure properties. For most materials the maximum elastic dilatation is very small, implying that the macroscopic shapes to which an elastic body can be deformed is severely limited. The present work addresses the simple modification of any material via hierarchical cut patterns to allow for extremely large strains and shape changes and a large range of macroscopic shapes. This is an important step in the development of shape-programmable materials. We provide the mathematical foundation, simulation results, and experimental demonstrations of the concept of fractal cut. This approach effectively broadens the design space for engineered materials for applications ranging from flexible/stretchable devices and photonic materials to bioscaffolds.
GABAρ subunits confer a bicuculline-insensitive component to GFAP
+
cells of cerebellum
Authors: Pétriz Adriana , Reyes-Haro Daniel , González-González María Alejandra , Miledi Ricardo , Martínez-Torres Ataúlfo 
Published: November 2014

Significance
Early postnatal development of the cerebellum involves a number of events that require signaling via the neurotransmitter GABA, which acts on specific receptors anchored in the plasma membrane. GABAergic transmission regulates the proliferation and migration of neuronal precursors of astrocytic lineage. Glial cells are known to express GABA-A receptors that include GABAρ subunits, but their expression pattern, functional properties, and trafficking dynamics remain unknown. This study found that a large number of glial cells express GABAρ in the cerebellum. Functional properties and intracellular trafficking of GABA-A receptors in glial cells grown in vitro suggest a different mechanism of GABAergic control of extrasynaptic transmission.
Transforming professional learning and practice in assessment for learning
Authors: Poskitt Jenny 
Published: November 2014

Assessing student learning is a complex process requiring teachers to have deep knowledge of the curriculum, assessment, and pedagogy. Changing political climates mean that teachers are expected to respond to new approaches or systems and adjust their classroom practice accordingly. Teachers often engage in professional learning (PL) to assist their knowledge and classroom practice, but what impact does PL have on their assessment practice as well as student learning and achievement?This paper examines optimal PL principles, the New Zealand assessment policy context, and application of assessment for learning principles in a nation‐wide PL programme. Empirical data presented in relation to the five levels of Guskey%s (2002) model evaluating PL indicate successful outcomes at the classroom level. However, application of Carless’ (2005) theoretical framework on embedding PL changes in schools reveals an area of neglect: attending to system (macro) level needs. Collaborative partnerships between schools and the wider community are posited as essential determinants of assessment literacies and transformational PL in times of political change.
Estimating Proxy Economic Target Reference Points in Data Poor Single Species Fisheries
Authors: Pascoe Sean , Thebaud Olivier , Vieira Simon 
Published: November 2014

Abstract
Bioeconomic models have been developed and applied to a range of fisheries around the world. However, an even greater number of fisheries are relatively data poor, and development of traditional bioeconomic models is not feasible. For small scale fisheries, the cost of data collection and model development may exceed the additional value these models may generate. Fisheries biologists have grappled with similar issues and have developed a range of data poor methods for estimating reference points related to fishing mortality based on life history characteristics and other indicators. In other cases, catch and effort data may be sufficient to estimate sustainable biomass levels. However, model derived economic target reference points require robust biological models as well as appropriate economic information, both of which are often unavailable. In this paper, we extend the data poor work to move from biological to economic target reference points for single species fisheries. We show that the relationship between economic (maximum economic yield) and biological (maximum sustainable yield) reference points depends primarily on the cost : revenue ratio, and that, where unavailable, these can be inferred from fisheries characteristics. We show that good estimates of biomass and effort based economic target reference points can be achieved with limited data.
Received September 4, 2013; accepted August 10, 2014
Ductile compaction of partially molten rocks: the effect of non-linear viscous rheology on instability and segregation
Authors: Veveakis E. , Regenauer-Lieb K. , Weinberg R.F. 
Published: November 2014

Abstract
The segregation of melt from a linear viscous matrix is traditionally described by McKenzie's compaction theory. This classical solution overlooks instabilities that arise when non-linear solid matrix behaviour is considered. Here we report a closed form 1-D solution obtained by extending McKenzie's theory to non-linear matrix behaviours. The new solution provides periodic stress singularities, acting as high porosity melt channels, to be the fundamental response of the compacted matrix. The characteristic length controlling the periodicity is still McKenzie's compaction length $\bar{\delta }_{\rm c}$, adjusted for non-linear rheologies.
Macrozooplankton predation impact on anchovy (Engraulis encrasicolus) eggs mortality at the Bay of Biscay shelf break spawning centre
Authors: Albaina Aitor , Irigoien Xabier , Aldalur Unai , Boyra Guillermo , Santos María , Estonba Andone 
Published: November 2014

Abstract
A real-time PCR based method involving a species-specific probe was applied to detect Engraulis encrasicolus eggs predation by the macrozooplankton community during the 2011 spawning season. Three locations along the shelf break presenting contrasting but high prey densities were sampled. A total of 840 individuals from 38 taxa of potential macrozooplankton predators were assayed for E. encrasicolus DNA presence and 27 presented at least one positive signal. Carnivorous copepods were responsible for the most predation events (66%) followed by euphausiids (16%), chaetognaths (5%), and myctophid fish (4%). Macrozooplankton predation on anchovy eggs followed a type-I functional response with daily mortalities &lt;4% of available prey abundance suggesting a negligible impact on the species recruitment at the shelf break spawning centre.
The colours of satellite galaxies in the Illustris simulation
Authors: Sales Laura V. , Vogelsberger Mark , Genel Shy , Torrey Paul , Nelson Dylan , Rodriguez-Gomez Vicente , Wang Wenting , Pillepich Annalisa , Sijacki Debora , Springel Volker , Hernquist Lars 
Published: November 2014

Abstract
Observationally, the fraction of blue satellite galaxies decreases steeply with host halo mass, and their radial distribution around central galaxies is significantly shallower in massive (M* ≥ 1011 M⊙) than in Milky Way-like systems. Theoretical models, based primarily on semi-analytical techniques, have had a long-standing problem with reproducing these trends, instead predicting too few blue satellites in general but also estimating a radial distribution that is too shallow, regardless of primary mass. In this Letter, we use the Illustris cosmological simulation to study the properties of satellite galaxies around isolated primaries. For the first time, we find good agreement between theory and observations. We identify the main source of this success relative to earlier work to be a consequence of the large gas contents of satellites at infall, a factor ∼5–10 times larger than in semi-analytical models. Because of their relatively large gas reservoirs, satellites can continue to form stars long after infall, with a typical time-scale for star-formation to be quenched ∼2 Gyr in groups but more than ∼5 Gyr for satellites around Milky Way-like primaries. The gas contents we infer are consistent with z = 0 observations of H i gas in galaxies, although we find large discrepancies among reported values in the literature. A testable prediction of our model is that the gas-to-stellar mass ratio of satellite progenitors should vary only weakly with cosmic time.
Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
Authors: Tuerk Andreas , Wiktorin Gregor , Güler Serhat 
Published: November 2014

AbstractQuantification of RNA transcripts with RNA-Seq is inaccurate due to positional fragment bias, which is not represented appropriately by current statistical models of RNA-Seq data. This article introduces the Mix2(rd. ”mixquare”) model, which uses a mixture of probability distributions to model the transcript specific positional fragment bias. The parameters of the Mix2model can be efficiently trained with the Expectation Maximization (EM) algorithm resulting in simultaneous estimates of the transcript abundances and transcript specific positional biases. Experiments are conducted on synthetic data and the Universal Human Reference (UHR) and Brain (HBR) sample from the Microarray quality control (MAQC) data set. Comparing the correlation between qPCR and FPKM values to state-of-the-art methods Cufflinks and PennSeq we obtain an increase in R2value from 0.44 to 0.6 and from 0.34 to 0.54. In the detection of differential expression between UHR and HBR the true positive rate increases from 0.44 to 0.71 at a false positive rate of 0.1. Finally, the Mix2model is used to investigate biases present in the MAQC data. This reveals 5 dominant biases which deviate from the common assumption of a uniform fragment distribution. The Mix2software is available athttp://www.lexogen.com/fileadmin/uploads/bioinfo/mix2model.tgz.
Identification of a Buried Cadaver Based on Finger Ridge Characteristics of a Hand Protected by a Latex Glove
Authors: Klemczak Krzysztof , Szczepański Tomasz M. , Więckiewicz Urszula , Kulczyk Tomasz 
Published: November 2014

AbstractThis paper presents the case of a cadaver buried in a pine grove, in loamy soil at a depth of about 1.8 m. The case is quite interesting due to the fact that one hand of the victim was bare and the other one was clad in a latex glove. In the laboratory, the severed hands were gently washed with water. The left palm exhibited signs of advanced decomposition. The ridges were visible only on the thumb. The gloved hand was found to be in much better condition. There were signs of saponification on the palm. Ridges on both the palm and all fingers were visible. The fingers of the right hand, palm prints, and the thumb of the left hand were successfully matched against a ten‐print card. The match provided the police with a positive identification of the missing person.
Arg972 insulin receptor substrate‐1 polymorphism and risk and severity of rheumatoid arthritis
Authors: Zhao Hongjun , Liu Shiqing , Long Mei , Peng Lijuan , Deng Hongxiang , You Yunhui 
Published: November 2014

AbstractAimTo explore the association between the Arg972 insulin receptor substrate (IRS)‐1 polymorphism (rs1801278) and the risk and disease activity/severity of rheumatoid arthritis (RA).MethodWe genotyped the Arg972 IRS‐1 polymorphism in 871 pairs of age‐, sex‐, body mass index‐, residence area‐ and current smoking status‐matched RA patients and controls. We assessed RA severity using the disease activity score of 28 joints (DAS28).ResultsThe AA (homozygous Arg972 IRS‐1) and GA (heterozygous Arg972 IRS‐1) genotypes were significantly associated with high risk of RA with or without adjustment for comorbidities (P < 0.001). The A allele was significantly associated with high risk of RA (P < 0.001). The AA genotype was significantly associated with high/severe RA activity (P < 0.001), while the GG genotype (wild type IRS‐1) had protective effects.ConclusionThe Arg972 IRS‐1 polymorphism is associated with increased risk and disease activity/severity of RA, and therefore may be a potential prognostic factor for RA. This study adds novel insights into the pathogenesis of RA.
Corticosterone: effects on feather quality and deposition into feathers
Authors: Jenni‐Eiermann Susanne , Helfenstein Fabrice , Vallat Armelle , Glauser Gaétan , Jenni Lukas 
Published: November 2014

Summary

The concentration of the glucocorticoid hormone corticosterone (CORT) is increasingly used in ecology and conservation biology as an integrated measure of the historical record of an individual's hypothalamo–pituitary–adrenal (HPA) activity during feather growth. However, where and how CORT is incorporated in feathers is incompletely known.

We therefore examined whether CORT is reliably measured with an enzyme immunoassay, where CORT is incorporated in the feather and where it affects feather quality, and whether CORT incorporation is related to plasma CORT levels, feather growth rate and melanin pigmentation.

During the regrowth of plucked tail feathers, we injected pigeons with tritium‐labelled CORT, and implanted a CORT‐releasing pellet to increase plasma CORT concentration for about 3 days. In feather segments, we measured labelled CORT (DPM3H) and we quantified CORT with an enzyme immunoassay EIA (CORTEIA) and double‐checked the results with ultra‐high performance liquid chromatography–tandem mass spectrometry (LCMS) (CORTMS).

Administered CORT affected feather structure and colour at the very base of the feather (epidermal collar, ramogenic zone) and reduced growth rate. In contrast, incorporation of CORT into the feather happened mainly in the blood quill, as shown with all three methods (DPM3H, CORTEIA and CORTMS).

Incorporation of CORT into feathers was only roughly proportional to plasma concentration, proportional to feather growth rate and increased with melanin pigmentation.

Measuring CORT in feather is a way to reveal past events of increased stress during feather growth in birds.
Acquiring Competence in Oncology Nursing Skills Through the Use of Film: A Study Protocol
Authors: Raga‐Chardi Rosa , Iglesias‐Parra Maria R. , García‐Mayor Silvia , Kaknani Shakira , García‐Guerrero Alfonso , Morales‐Asencio Jose M. 
Published: November 2014

PurposeTo determine the influence of movies as a teaching resource with nursing students to improve their ability to cope with challenging scenarios in oncology nursing, as well as their competence to identify nursing diagnoses in these patients.MethodsCluster, randomized controlled trial with nursing students at the University of Málaga (Spain).MeasuresAccuracy of nursing diagnoses, perceived stressors, death anxiety, empathy, level of decision making, and cognitive closure.ConclusionsThis study will provide information about the efficacy of movies to improve the competence in nursing students for the care of oncology patients, as well as their diagnostic reasoning.Implications for Nursing PracticeIf significant modifications are obtained, this approach can be an important resource applicable to other contexts of patient care.