bluuebunny/crossref_metadata_2025_split huggingface dataset:
Who are Non-Resident Fathers?: A British Socio-Demographic Profile
Authors: POOLE ELOISE , SPEIGHT SVETLANA , O’BRIEN MARGARET , CONNOLLY SARA , ALDRICH MATTHEW 
Published: November 2015

AbstractDespite international growth of, and policy interest in, divorce and separation since the 1970s, there is still surprisingly little known about non-residential fatherhood. This paper presents a ‘father-centric’ analysis and provides one of the first profiles of non-residential fatherhood in early millennium UK. Using data from Understanding Society Wave 1, a nationally representative survey of over 30,000 households in the UK, we found 1,070 men self-identifying as having a non-resident child under 16 years old (https://www.understandingsociety.ac.uk). We estimate a prevalence of 5 per cent of British men having a non-resident dependent child. Through latent class analysis, four distinct groups of non-resident fathers are identified: ‘Engaged’ fathers, ‘Less Engaged’ fathers, ‘Disengaged’ fathers and ‘Distance’ fathers. Our analysis finds that non-resident fathers form a heterogeneous group in terms of their socio-demographic profile and family behaviour. It is recommended that legislation and policy concerning fathers in post-separation families are sensitive to variation as well as commonality in socio-economic conditions and family lives and situations.
Good Holders, Bad Shufflers: An Examination of Working Memory Processes and Modalities in Children with and without Attention-Deficit/Hyperactivity Disorder
Authors: Simone Ashley N. , Bédard Anne-Claude V. , Marks David J. , Halperin Jeffrey M. 
Published: November 2015

AbstractThe aim of this study was to examine working memory (WM) modalities (visual-spatial and auditory-verbal) and processes (maintenance and manipulation) in children with and without attention-deficit/hyperactivity disorder (ADHD). The sample consisted of 63 8-year-old children with ADHD and an age- and sex-matched non-ADHD comparison group (N=51). Auditory-verbal and visual-spatial WM were assessed using the Digit Span and Spatial Span subtests from the Wechsler Intelligence Scale for Children Integrated - Fourth Edition. WM maintenance and manipulation were assessed via forward and backward span indices, respectively. Data were analyzed using a 3-way Group (ADHD vs. non-ADHD)×Modality (Auditory-Verbal vs. Visual-Spatial)×Condition (Forward vs. Backward) Analysis of Variance (ANOVA). Secondary analyses examined differences between Combined and Predominantly Inattentive ADHD presentations. Significant Group×Condition (p=.02) and Group×Modality (p=.03) interactions indicated differentially poorer performance by those with ADHD on backward relative to forward and visual-spatial relative to auditory-verbal tasks, respectively. The 3-way interaction was not significant. Analyses targeting ADHD presentations yielded a significant Group×Condition interaction (p=.009) such that children with ADHD-Predominantly Inattentive Presentation performed differentially poorer on backward relative to forward tasks compared to the children with ADHD-Combined Presentation. Findings indicate a specific pattern of WM weaknesses (i.e., WM manipulation and visual-spatial tasks) for children with ADHD. Furthermore, differential patterns of WM performance were found for children with ADHD-Predominantly Inattentive versus Combined Presentations. (JINS, 2016, 22, 1–11)
Glycogen synthase kinase-3-mediated phosphorylation of serine 73 targets sterol response element binding protein-1c (SREBP-1c) for proteasomal degradation
Authors: Dong Qingming , Giorgianni Francesco , Beranova-Giorgianni Sarka , Deng Xiong , O'Meally Robert N. , Bridges Dave , Park Edwards A. , Cole Robert N. , Elam Marshall B. , Raghow Rajendra 
Published: November 2015

Sterol regulatory element binding protein-1c (SREBP-1c) is a key transcription factor that regulates genes involved in the de novo lipid synthesis and glycolysis pathways. The structure, turnover and transactivation potential of SREBP-1c are regulated by macronutrients and hormones via a cascade of signalling kinases. Using MS, we have identified serine 73 as a novel glycogen synthase kinase-3 (GSK-3) phosphorylation site in the rat SREBP-1c purified from McA-RH7777 hepatoma cells. Our site-specific mutagenesis strategy revealed that the turnover of SREBP-1c, containing wild type, phospho-null (serine to alanine) or phospho-mimetic (serine to aspartic acid) substitutions, was differentially regulated. We show that the S73D mutant of pSREBP-1c, that mimicked a state of constitutive phosphorylation, dissociated from the SREBP-1c–SCAP complex more readily and underwent GSK-3-dependent proteasomal degradation via SCFFbw7 ubiquitin ligase pathway. Pharmacologic inhibition of GSK-3 or knockdown of GSK-3 by siRNA prevented accelerated degradation of SREBP-1c. As demonstrated by MS, SREBP-1c was phosphorylated in vitro by GSK-3β at serine 73. Phosphorylation of serine 73 also occurs in the intact liver. We propose that GSK-3-mediated phosphorylation of serine 73 in the rat SREBP-1c and its concomitant destabilization represents a novel mechanism involved in the inhibition of de novo lipid synthesis in the liver.
Reliable ABC model choice via random forests
Authors: Pudlo Pierre , Marin Jean-Michel , Estoup Arnaud , Cornuet Jean-Marie , Gautier Mathieu , Robert Christian P. 
Published: November 2015

Abstract
Motivation: Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques.
Results: We propose a novel approach based on a machine learning tool named random forests (RF) to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with RF and postponing the approximation of the posterior probability of the selected model for a second stage also relying on RF. Compared with earlier implementations of ABC model choice, the ABC RF approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least 50) and (iv) it includes an approximation of the posterior probability of the selected model. The call to RF will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets.
Availability and implementation: The proposed methodology is implemented in the R package abcrf available on the CRAN.
Contact: jean-michel.marin@umontpellier.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
hybridSPAdes: an algorithm for hybrid assembly of short and long reads
Authors: Antipov Dmitry , Korobeynikov Anton , McLean Jeffrey S. , Pevzner Pavel A. 
Published: November 2015

Abstract
Motivation: Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost.
Results: We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads.
Availability and implementation: hybridSPAdes is implemented in C++ as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades
Contact: d.antipov@spbu.ru
Supplementary information: supplementary data are available at Bioinformatics online.
ParTIES: a toolbox for Paramecium interspersed DNA elimination studies
Authors: Denby Wilkes Cyril , Arnaiz Olivier , Sperling Linda 
Published: November 2015

Abstract
Motivation: Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available.
Results: We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.
Availability and implementation: ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3.
Contact: linda.sperling@i2bc.paris-saclay.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Effects of elevated CO2 on early life history development of the yellowtail kingfish, Seriola lalandi, a large pelagic fish
Authors: Munday Philip L. , Watson Sue-Ann , Parsons Darren M. , King Alicia , Barr Neill G. , Mcleod Ian M. , Allan Bridie J. M. , Pether Steve M. J. 
Published: November 2015

Abstract
An increasing number of studies have examined the effects of elevated carbon dioxide (CO2) and ocean acidification on marine fish, yet little is known about the effects on large pelagic fish. We tested the effects of elevated CO2 on the early life history development and behaviour of yellowtail kingfish, Seriola lalandi. Eggs and larvae were reared in current day control (450 µatm) and two elevated CO2 treatments for a total of 6 d, from 12 h post-fertilization until 3 d post-hatching (dph). Elevated CO2 treatments matched projections for the open ocean by the year 2100 under RCP 8.5 (880 µatm CO2) and a higher level (1700 µatm CO2) relevant to upwelling zones where pelagic fish often spawn. There was no effect of elevated CO2 on survival to hatching or 3 dph. Oil globule diameter decreased with an increasing CO2 level, indicating potential effects of elevated CO2 on energy utilization of newly hatched larvae, but other morphometric traits did not differ among treatments. Contrary to expectations, there were no effects of elevated CO2 on larval behaviour. Activity level, startle response, and phototaxis did not differ among treatments. Our results contrast with findings for reef fish, where a wide range of sensory and behavioural effects have been reported. We hypothesize that the absence of behavioural effects in 3 dph yellowtail kingfish is due to the early developmental state of newly hatched pelagic fish. Behavioural effects of high CO2 may not occur until larvae commence branchial acid–base regulation when the gills develop; however, further studies are required to test this hypothesis. Our results suggest that the early stages of kingfish development are tolerant to rising CO2 levels in the ocean.
Geographic variation in subantarctic fur seal pup growth: linkages with environmental variability and population density
Authors: Oosthuizen W. Chris , de Bruyn P. J. Nico , Wege Mia , Bester Marthán N. 
Published: November 2015

Abstract
Marine predator populations are sensitive to temporal variation in prey availability, but prey dynamics are often difficult to quantify. Long-term measures of offspring growth is a useful performance attribute to gauge the potential demographic direction for such predator populations, especially where other metrics (e.g., population size estimates) are lacking. Subantarctic fur seal ( Arctocephalus tropicalis ) females are central place foragers during a protracted lactation period, and their foraging success determines the growth and vitality of their offspring. Using data spanning over 2 decades, we assessed geographic and temporal variation in growth rates and weaning mass of subantarctic fur seal pups at 2 of the species’ principal populations (Gough and Marion islands) and identified environmental conditions that may, through assumed bottom-up mechanisms, affect body mass at weaning. While Marion Island pups grew at an average rate of between 0.040 and 0.067kg/day early in lactation (comparable to conspecific growth at Amsterdam Island), the mean growth rate at Gough Island (approximately 0.030kg/day) was lower than the growth rate represented by the bottom 5% of the body mass distribution at Marion Island. Notwithstanding substantial interannual variability, we found support for a negative trend in weaning mass at both populations, suggesting a rise in limiting factors that is hypothesized to relate to concurrent local population size increases. Weaning mass tended to be higher when sea surface temperatures were warmer (with a stronger positive effect at Gough Island) and during positive phases of the Southern Oscillation Index (La Niña events), with a stronger positive effect in males. Given the low weaning mass of Gough Island fur seal pups, continued population growth here seems unlikely. While density-dependent regulation appears to have increased in strength at Marion Island, terminating rapid population growth, current weaning weights remain above the physiological limits of growth in subantarctic fur seals.
On the use of the number count of blue horizontal branch stars to infer the dominant building blocks of the Milky Way halo
Authors: Chung Chul , Lee Young-Wook , Pasquato Mario 
Published: November 2015

Abstract
The formation of the Milky Way stellar halo is thought to be the result of merging and accretion of building blocks such as dwarf galaxies and massive globular clusters. Recently, Deason et al. suggested that the Milky Way outer halo formed mostly from big building blocks, such as dwarf spheroidal galaxies, based on the similar number ratio of blue straggler (BS) stars to blue horizontal branch (BHB) stars. Here we demonstrate, however, that this result is seriously biased by not taking into detailed consideration on the formation mechanism of BHB stars from helium-enhanced second-generation population. In particular, the high BS-to-BHB ratio observed in the outer halo fields is most likely due to a small number of BHB stars provided by globular clusters (GCs) rather than to a large number of BS stars. This is supported by our dynamical evolution model of GCs which shows preferential removal of first-generation stars in GCs. Moreover, there are a sufficient number of outer halo GCs which show very high BS-to-BHB ratio. Therefore, the BS-to-BHB number ratio is not a good indicator to use in arguing that more massive dwarf galaxies are the main building blocks of the Milky Way outer halo. Several lines of evidence still suggest that GCs can contribute a significant fraction of the outer halo stars.
Carbon production on accreting neutron stars in a new regime of stable nuclear burning
Authors: Keek L. , Heger A. 
Published: November 2015

Abstract
Accreting neutron stars exhibit Type I X-ray bursts from both frequent hydrogen/helium flashes as well as rare carbon flashes. The latter (superbursts) ignite in the ashes of the former. Hydrogen/helium bursts, however, are thought to produce insufficient carbon to power superbursts. Stable burning could create the required carbon, but this was predicted to only occur at much larger accretion rates than where superbursts are observed. We present models of a new steady-state regime of stable hydrogen and helium burning that produces pure carbon ashes. Hot CNO burning of hydrogen heats the neutron star envelope and causes helium to burn before the conditions of a helium flash are reached. This takes place when the mass accretion rate is around 10  per cent of the Eddington limit: close to the rate where most superbursts occur. We find that increased heating at the base of the envelope sustains steady-state burning by steepening the temperature profile, which increases the amount of helium that burns before a runaway can ensue.
The disappearance of the progenitor of SN 2012aw in late-time imaging
Authors: Fraser Morgan 
Published: November 2015

Abstract
We present new late-time near-infrared imaging of the site of the nearby core-collapse supernova SN 2012aw, confirming the disappearance of the point source identified by Fraser et al. and Van Dyk et al. as a candidate progenitor in both J and Ks filters. We remeasure the progenitor photometry, and find that both the J and Ks magnitudes of the source are consistent with those quoted in the literature. We also recover a marginal detection of the progenitor in H-band, for which we measure H = 19.67 ± 0.40 mag. Comparing the luminosity of the progenitor to stellar evolutionary models, SN 2012aw appears to have resulted from the explosion of a 12.5 ± 1.5 M⊙ red supergiant.
West Nile Virus Population Structure, Injury, and Interferon-Stimulated Gene Expression in the Brain From a Fatal Case of Encephalitis
Authors: Grubaugh Nathan D. , Massey Aaron , Shives Katherine D. , Stenglein Mark D. , Ebel Gregory D. , Beckham J. David 
Published: November 2015

Abstract
Background.  West Nile virus (WNV) infection in humans can result in severe, acute encephalitis typically involving subcortical gray matter brain regions. West Nile virus replication within specific human brain regions from a human case of acute encephalitis has not been studied.
Methods.  We describe a fatal case of WNV encephalitis in which we obtained tissue from specific brain regions at autopsy to evaluate viral-host interactions using next-generation sequencing and immunohistochemistry analysis.
Results.  We found that WNV populations in the injured subcortical brain regions exhibited increased amino acid variation and increased expression of specific interferon genes compared with cortical tissues despite similar viral burden.
Conclusions.  These observational, patient-based data suggest that neuronal injury and the strength of viral selection pressure may be associated with the level of the innate immune responses. Further studies in human and animal models evaluating the role of innate immune responses on injury patterns and viral selection pressure are needed.
Three-dimensional distribution of the ISM in the Milky Way galaxy. III. The total neutral gas disk
Authors: Nakanishi Hiroyuki , Sofue Yoshiaki 
Published: November 2015

Abstract
We present newly obtained three-dimensional gaseous maps of the Milky Way Galaxy: H i, H2, and total-gas (H i plus H2) maps, which were derived from the H i and 12CO(J = 1–0) survey data and rotation curves based on the kinematic distance. The H i and H2 face-on maps show that the H i disk is extended to a radius of 15–20 kpc and its outskirts are asymmetric to the Galactic center, while most of the H2 gas is distributed inside the solar circle. The total gas mass within a radius of 30 kpc amounts to 8.0 × 109 M⊙, 89% and 11% of which are H i and H2, respectively. The vertical slices show that the outer H i disk is strongly warped and the inner H i and H2 disks are corrugated. The total gas map is advantageous for tracing spiral structures from the inner to outer disk. Spiral structures such as the Norma–Cygnus, the Perseus, the Sagittarius–Carina, the Scutum–Crux, and the Orion arms are more clearly traced in the total gas map than ever. All the spiral arms are well explained by logarithmic spiral arms with pitch angles of 11°–15°. The molecular fraction of the total gas is high near the Galactic center and decreases with Galactocentric distance. The molecular fraction is also locally enhanced at the spiral arms compared with the inter-arm regions.
Signs of active galactic nucleus quenching in a merger remnant with radio jets
Authors: Ichikawa Kohei , Ueda Junko , Shidatsu Megumi , Kawamuro Taiki , Matsuoka Kenta 
Published: November 2015

Abstract
We investigate optical, infrared, and radio active galactic nucleus (AGN) signs in the merger remnant Arp 187, which hosts luminous jets launched in the order of 105 yr ago but whose present-day AGN activity is still unknown. We find AGN signs from the optical Baldwin–Phillips–Telervich diagram and infrared [O iv] 25.89 μm line, originating from the narrow line regions of AGN. On the other hand, Spitzer/IRS show host galaxy dominated spectra, suggesting that the thermal emission from the AGN torus is considerably small or already diminished. Combining the black hole mass, the upper limit of radio luminosity of the core, and the fundamental plane of the black hole enables us to estimate X-ray luminosity, which gives &lt;1040 erg s−1. Those results suggest that the AGN activity of Arp 187 has already been quenched, but the narrow line region is still alive owing to the time delay of emission from the past AGN activity.
Polarized Cortical Tension drives Zebrafish Epiboly Movements
Authors: Hernández-Vega Amayra , Marsal María , Pouille Philippe-Alexandre , Tosi Sebastien , Colombelli Julien , Luque Tomás , Navajas Daniel , Pagonabarraga Ignacio , Martín-Blanco Enrique 
Published: November 2015

SUMMARYThe physical principles underlying the biomechanics of morphogenetic processes are largely unknown. Epiboly is an essential embryonic event in which three distinct tissues coordinate to direct the expansion of the blastoderm. How and where forces are generated during epiboly and how these are globally coupled remains elusive. Here we first develop a method, Hydrodynamic Regression (HR), to infer 3D dynamic pressure fields, mechanical power densities and cortical surface tension profiles within living organisms. HR is based on velocity measurements retrieved from 2D+T microscopy time-lapses and their hydrodynamic modeling. We then applied this method to identify biomechanically active structures during epiboly in the zebrafish and the changes in the distribution of cortex local tension as epiboly progresses. Based on these results, we propose a novel simple physical description for epiboly, where tissue movements are directed by a polarized gradient of cortical tension. We found that this tensional gradient relies on local contractile forces at the cortex, differences in the elastic properties of cortex components and force passive transmission within the incompressible yolk cell. All in all, our work identifies a novel way to physically regulate concerted cellular movements that will be fundamental for the mechanical control of many morphogenetic processes.
Conjecture: Some auto-immune diseases are caused by the tissue, not a problem with the immune system
Authors: Robins Harlan 
Published: November 2015

AbstractApplying highly sensitive modern immune profiling techniques to the blood or inflamed tissue of auto-immune patients with one of the common T-cell mediated diseases fails to detect large clonal expansions or other signs of a dysregulated immune system. Additionally, these new methods have shown that self-reactive T-cells are found in the periphery (and are not completely negatively selected in the thymus as previously believed). Combining these new data with well-established studies in auto-immunity leads to the conjecture that certain auto-immune diseases are likely to be caused by defects in tissue, not by dysregulation of the adaptive immune system. In particular, one hypothesis is that specific tissues up-regulate HLA class 2 genes, presenting epitopes that are bound by CD4+helper T cells, which facilitates an immune response against the tissue specific cells.