bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional genomics of human brain development and implications for autism spectrum disorders
Authors: Ziats M N , Grosvenor L P , Rennert O M 
Published: October 2015

AbstractTranscription of the inherited DNA sequence into copies of messenger RNA is the most fundamental process by which the genome functions to guide development. Encoded sequence information, inherited epigenetic marks and environmental influences all converge at the level of mRNA gene expression to allow for cell-type-specific, tissue-specific, spatial and temporal patterns of expression. Thus, the transcriptome represents a complex interplay between inherited genomic structure, dynamic experiential demands and external signals. This property makes transcriptome studies uniquely positioned to provide insight into complex genetic–epigenetic–environmental processes such as human brain development, and disorders with non-Mendelian genetic etiologies such as autism spectrum disorders. In this review, we describe recent studies exploring the unique functional genomics profile of the human brain during neurodevelopment. We then highlight two emerging areas of research with great potential to increase our understanding of functional neurogenomics—non-coding RNA expression and gene interaction networks. Finally, we review previous functional genomics studies of autism spectrum disorder in this context, and discuss how investigations at the level of functional genomics are beginning to identify convergent molecular mechanisms underlying this genetically heterogeneous disorder.
Frequency stability and phase noise performance of X‐band to Ka‐band active multiplier
Authors: Bara‐Maillet R. , Creedon D.L. , Parker S.R. , Le Floch J.‐M. , Tobar M.E. 
Published: October 2015

The performance of an active frequency doubler used to generate a pump signal for a solid‐state microwave amplification by stimulated emission of radiation (MASER) based on paramagnetic impurity ions in sapphire is reported. The frequency doubler has been characterised in terms of phase noise, power dependence and frequency stability (Allan variance) for an output frequency range between 20 and 40 GHz. With the measurement system referenced to a 10 MHz hydrogen MASER, the doubler exhibits a single sideband phase noise of ∼−108 dBc/Hz at 1 Hz offset frequency, from which an upper limit fractional frequency instability of about 2 × 10−16 at 1 s integration time is estimated.
Rail‐to‐rail regulating voltage‐controlled oscillator with low supply and ground noise sensitivity
Authors: Ko Jaehong , An Chang‐Ho , Kwon Chan‐Keun , Kim Soo‐Won , Kim Chulwoo 
Published: October 2015

A rail‐to‐rail (R‐to‐R) regulating voltage‐controlled oscillator (VCO) is employed to generate multiple‐phase clocks for clock and data recovery in a display driver IC (DDI). To achieve a low supply and ground noise sensitivity, the proposed R‐to‐R regulating method generates VSP and VSN as the supply and the ground of the VCO instead of VDD and VSS. By applying the proposed method, the frequency–VDD variation rate of the VCO (%−fVCO/%−VDD) changes from 3.5%−fVCO/1%−VDD to 0.0073%−fVCO/1%−VDD within the Vctrl range of 0.5–1.2 V. The DDI is fabricated in a 1P6M 0.18 μm 1.8 V CMOS technology for the interface block and in a 1.6 μm 18 V CMOS technology for the DAC. The R‐to‐R regulating VCO has a tuning range of 140–240 MHz with linear and small gain (KVCO) characteristics, and is suitable for the phase‐locked loop used in flat‐panel display interfaces that operate from 0.3 to 2 Gbits/s.
Enhanced efficiency for wireless power transmission using an auxiliary loop on ferrite in metallic environment
Authors: Park Byung‐Chul , Lee Jeong‐Hae 
Published: October 2015

An enhanced magnetic shield consisting of an auxiliary loop on a ferrite in a metallic environment at 6.78 MHz is described. Utilising an in‐phase current of the auxiliary loop on the ferrite, the performances such as power transfer efficiency and the coupling coefficient are improved. The conventional shielding method that uses high‐permeability ferrites has a limitation on the utilisation because of their high magnetic loss tangent. However, the proposed method using the auxiliary loop coated on the ferrite can provide better efficiency than the conventional method. In particular, at distance of 20 cm, the measured efficiency is improved by 30% after applying the auxiliary loop to the ferrite. The proposed method is considered to be useful to wireless power transmission systems having a ground plane.
High step‐down interleaved buck converter with low voltage stress
Authors: Esteki Morteza , Poorali Behzad , Adib Ehsan , Farzanehfard Hosein 
Published: October 2015

This study presents a four‐phase interleaved buck converter with low voltage stress and high step‐down conversion ratio. The proposed converter provides an extended duty cycle and low voltage stress for switches and diodes, in high step‐down applications. This makes it possible to use switches with lower voltage rating and thus reduce both switching and conduction losses to improve the overall efficiency. Extremely low output current ripple and continuous input current are two other advantages of the proposed converter. Also, the output current can be shared between interleaved modules without using additional current sharing control technique due to charge balance of input and blocking capacitors. All these benefits are obtained without adding any active auxiliary component or using transformers. The experimental results from a prototype of the proposed converter designed for 400–24 V, operating at 0.5 kW, verify the theoretical analysis.
Convenient and green soft chemical route to cuprous oxide films and their visible‐light photocatalytic properties
Authors: Zheng Haiyan , Li Qing , Zhang Yongping , Qin Lizhao , Lin Hua , Nie Ming 
Published: October 2015

Cuprous oxide (Cu2O) films have been synthesised by a convenient and green soft chemical route at room temperature. The films were obtained through the chemical reduction of copper acetate by ascorbic acid in solutions with ethylene glycol and deionised water. X‐ray diffraction, energy‐dispersive X‐ray spectrometry, scanning electron microscopy (SEM), atomic force microscopy, as well as UV–Vis spectroscopy (UV‐Vis) were used to characterise the resulting films. It was obvious from the SEM image that the obtained films were composed of nanosphere particles with a size of 100–400 nm. The photocatalytic activity of degradation of methyl orange (MO) of the obtained Cu2O films, H2O2 and H2O2/Cu2O films system under visible light irradiation was also investigated. The results have shown that the system exhibits high catalytic ability under visible light irradiation. Also, there was a strong synergistic effect between the obtained Cu2O films and H2O2 when the system was used to degrade MO.
Size‐tunable synthesis of mono‐disperse wastewater‐derived carbon spheres with polyacrylamide as a directing agent
Authors: Tang Chuanqiu , Zhang Pingping , Sun Yong , Bai Li 
Published: October 2015

Highly mono‐disperse carbon spheres (CSs) with a tunable diameter of 300–4000 nm are shown to be successfully synthesised using sugar‐rich wastewater as carbon sources and polyacrylamide (PAM) as a size‐controlling agent. The effects of PAM and pH on the morphology and size were also investigated. Experimental results showed that PAM acted as a size‐directing agent which directs the self‐assembly of sugar from wastewater to form the spheroidal particles. The size of CSs could be increased from 300 to 600 nm without any alteration in the morphologies by altering the solution pH from 7 to 12. Furthermore, the size of spheroidal carbon particles can be easily controlled by increasing the concentration of PAM from 0.05 to 0.1% (w/v) at pH 12. The largest sizes of CSs grew nearly 4000 nm without damage to their morphology or broadening of their size distribution with the addition of 0.1% PAM. On the basis of the experimental results, a mechanism is proposed to elucidate the formation of CSs with a wide diameter range. It is believed that this work not only provides a novel potential way to utilise wastewater, but also puts forward a facile sustainable approach to synthesise size‐controllable CSs.
Investigation of thermal effects in a resonance condition of microfibre double‐knot resonators as high‐order filter
Authors: Nodehi Somayeh , Mohammed Waleed Soliman , Ahmad Harith , Harun Sulaiman Wadi 
Published: October 2015

Theoretical and experimental investigations are conducted into the thermal effect on resonance conditions of microfibre double‐knot resonators. A double‐knot microfibre resonator which utilises heat for optical path correction is introduced to increase the finesse. The proposed resonator consists of two knots with radii of 357.66 and 357.73 µm which are placed in series. Each individual knot has a finesse of 5 and an extinction ratio of 6 dB. When placed in series, the extinction ratio of the comb spectrum varies from 3.5 to 15 dB by controlling the resonance wavelength of both knots through optical correction. Optical path correction is implemented by placing a hot metal bar with a temperature of 30°C close to the smallest knot. This path resulted in a flat comb spectrum with a high extinction ration of 15 dB. The produced resonance has an unchanged free spectral range of 715 pm, a quality factor of 20 000, FWHD of 85 pm and a finesse of 9.5.
Global nutrient transport in a world of giants
Authors: Doughty Christopher E. , Roman Joe , Faurby Søren , Wolf Adam , Haque Alifa , Bakker Elisabeth S. , Malhi Yadvinder , Dunning John B. , Svenning Jens-Christian 
Published: October 2015

Significance
Animals play an important role in the transport of nutrients, but this role has diminished because many of the largest animals have gone extinct or experienced massive population declines. Here, we quantify the movement of nutrients by animals in the land, sea, rivers, and air both now and prior to their widespread reductions. The capacity to move nutrients away from hotspots decreased to 6% of past values across land and ocean. The vertical movement of phosphorus (P) by marine mammals was reduced by 77% and movement of P from sea to land by seabirds and anadromous fish was reduced by 96%, effectively disrupting an efficient nutrient distribution pump that once existed from the deep sea to the continental interiors.
College football, elections, and false-positive results in observational research
Authors: Fowler Anthony , Montagnes B. Pablo 
Published: October 2015

Significance
We reassess the surprising finding that college football games influence incumbent support in subsequent elections. Because independent replication is impossible for such nonexperimental findings, we proceed by testing multiple independent hypotheses that should hold if college football games indeed influence elections. In each case, the evidence suggests that the original finding was a false positive. For example, if college football games indeed influence elections, this effect should be greatest in places where the public is most interested in college football. However, we find the opposite. We conclude with general recommendations for evaluating surprising research findings and avoiding similar false-positive results—particularly for nonexperimental work in the social sciences where independent replication is impossible.
Test of Martin’s overkill hypothesis using radiocarbon dates on extinct megafauna
Authors: Surovell Todd A. , Pelton Spencer R. , Anderson-Sprecher Richard , Myers Adam D. 
Published: October 2015

SignificanceCoincident with the human colonization of the Western Hemisphere, dozens of genera of Pleistocene megafauna were lost to extinction. Following Martin, we argue that declines in the record of radiocarbon dates of extinct genera may be used as an independent means of detecting the first presence of humans in the New World. Our results, based on analyses of radiocarbon dates from Eastern Beringia, the contiguous United States, and South America, suggest north to south, time, and space transgressive declines in megafaunal populations as predicted by the overkill hypothesis. This finding is difficult to reconcile with other extinction hypotheses. However, it remains to be determined whether these findings will hold with larger samples of radiocarbon dates from all regions.
Impacts of high-latitude volcanic eruptions on ENSO and AMOC
Authors: Pausata Francesco S. R. , Chafik Leon , Caballero Rodrigo , Battisti David S. 
Published: October 2015

Significance
In the model simulations analyzed here, large high-latitude volcanic eruptions have global and long-lasting effects on climate, altering the spatiotemporal characteristic of the El Niño–Southern Oscillation (ENSO) on both short (<1 y) and long timescales and affecting the strength of the Atlantic Meridional Overturning Circulation (AMOC). In the first 8–9 mo following the start of the eruption, El Niño-like anomalies develop over the equatorial Pacific. The large high-latitude eruptions also trigger a strengthening of the AMOC in the first 25 y after the eruption, which is associated with an increase in ENSO variability. This is then followed by a weakening of the AMOC lasting another 30–35 y, associated with decreased ENSO variability.
Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia
Authors: Tackney Justin C. , Potter Ben A. , Raff Jennifer , Powers Michael , Watkins W. Scott , Warner Derek , Reuther Joshua D. , Irish Joel D. , O’Rourke Dennis H. 
Published: October 2015

Significance
Beringia gave rise to the first Western Hemisphere colonists, although the genetic characterization of that source population has remained obscure. We report two mitogenomes from human remains within Beringia, with an age (∼11,500 cal B.P.) that postdates the end of the initial colonization by only a few millennia. The mitochondrial lineages identified (B2, C1b) are rare to absent in modern northern populations, indicating greater genetic diversity in early Beringia than in modern populations of the region. The antiquity and geographic location of these two burials, and the combined genomic and archaeological analyses, provide new perspectives on the link between Asia and the Americas, and the genetic makeup of the first Americans.
Purkinje cell activity during classical conditioning with different conditional stimuli explains central tenet of Rescorla–Wagner model
Authors: Rasmussen Anders , Zucca Riccardo , Johansson Fredrik , Jirenhed Dan-Anders , Hesslow Germund 
Published: October 2015

Significance
The Rescorla–Wagner model of associative learning has guided research in behavioral and neural sciences for several decades. Although phenomena associated with the model have previously been linked to nucleo-olivary inhibition, many questions regarding the neural mechanisms underlying the model still remain. In this paper, we present evidence from our eyeblink conditioning setup, indicating that the variables used in Rescorla and Wagner's model have physiological correlates.
Liver X receptor β controls thyroid hormone feedback in the brain and regulates browning of subcutaneous white adipose tissue
Authors: Miao Yifei , Wu Wanfu , Dai Yubing , Maneix Laure , Huang Bo , Warner Margaret , Gustafsson Jan-Åke 
Published: October 2015

Significance
Liver X receptors (LXRs) are nuclear receptors vital in controlling lipid and glucose metabolism through direct or indirect mechanisms. Here, we demonstrate for the first time, to our knowledge, that, in addition to changing the activity of classic brown adipose tissue, LXRs, especially LXRβ, are able to regulate the browning of white adipose tissue (WAT), activation of mitochondria, and increased energy expenditure. Deletion of LXRs removed their suppressive effect on thyrotropin releasing hormone expression in brain, thus activating the hypothalamic–pituitary–thyroid (HPT) axis and inducing the browning of WAT. Altogether, the data confirm the importance on LXRs in ameliorating obesity through a previously unidentified mechanism (i.e., increasing browning of WAT and energy dissipation).
Toroidal mode number transition of the edge localized modes in the KSTAR plasmas
Authors: Lee J.E. , Yun G.S. , Kim M. , Lee J. , Lee W. , Park H.K. , Domier C.W. , Luhmann N.C. , Ko W.H. 
Published: October 2015

Abstract
Rapid transitions of the toroidal mode number (

) have been often detected during the evolution of the edge localized modes (ELMs) in the inter-ELM-crash periods of the KSTAR tokamak plasmas. The mode number transitions accompany changes of the mode frequency (

) (e.g.

changed from 8 to 5 while

changed from ~32 to 9 kHz). The observed transition phenomena have been diverse including small and large increase (or decrease) in the mode number and multiple transitions during a single inter-ELM-crash period. Two classes of the mode transitions were identified: non-overlapping transition and overlapping transition. The former case is characterized by the absence of coherent filamentary structure during the transition and the latter case is characterized by co-existence of two coherent filamentary structures with different mode numbers. Each transition process typically lasts a few hundreds to thousands of μs.
MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues
Authors: Lewin Alex , Saadi Habib , Peters James E. , Moreno-Moral Aida , Lee James C. , Smith Kenneth G. C. , Petretto Enrico , Bottolo Leonardo , Richardson Sylvia 
Published: October 2015

Abstract
Motivation: Analysing the joint association between a large set of responses and predictors is a fundamental statistical task in integrative genomics, exemplified by numerous expression Quantitative Trait Loci (eQTL) studies. Of particular interest are the so-called ‘hotspots’, important genetic variants that regulate the expression of many genes. Recently, attention has focussed on whether eQTLs are common to several tissues, cell-types or, more generally, conditions or whether they are specific to a particular condition.
Results: We have implemented MT-HESS, a Bayesian hierarchical model that analyses the association between a large set of predictors, e.g. SNPs, and many responses, e.g. gene expression, in multiple tissues, cells or conditions. Our Bayesian sparse regression algorithm goes beyond ‘one-at-a-time’ association tests between SNPs and responses and uses a fully multivariate model search across all linear combinations of SNPs, coupled with a model of the correlation between condition/tissue-specific responses. In addition, we use a hierarchical structure to leverage shared information across different genes, thus improving the detection of hotspots. We show the increase of power resulting from our new approach in an extensive simulation study. Our analysis of two case studies highlights new hotspots that would remain undetected by standard approaches and shows how greater prediction power can be achieved when several tissues are jointly considered.
Availability and implementation: C++ source code and documentation including compilation instructions are available under GNU licence at http://www.mrc-bsu.cam.ac.uk/software/.
Contact: sylvia.richardson@mrc-bsu.cam.ac.uk or lb664@cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Pycellerator: an arrow-based reaction-like modelling language for biological simulations
Authors: Shapiro Bruce E. , Mjolsness Eric 
Published: October 2015

Abstract
Motivation: We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales–Menten–Henri (MMH) and Gene-Regulation (GRN) to Monod–Wyman–Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface.
Results: Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica.
Availability and implementation: All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases. Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information.
Contact: bruce.e.shapiro@csun.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation
Authors: Lu Qiongshi , Yao Xinwei , Hu Yiming , Zhao Hongyu 
Published: October 2015

Abstract
Motivation: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks. Under such circumstances, a computational approach that may increase signal replication rate and identify potential functional sites among correlated markers is urgently needed.
Results: We describe GenoWAP, a GWAS signal prioritization method that integrates genomic functional annotation and GWAS test statistics. The effectiveness of GenoWAP is demonstrated through its applications to Crohn’s disease and schizophrenia using the largest studies available, where highly ranked loci show substantially stronger signals in the whole dataset after prioritization based on a subset of samples. At the single nucleotide polymorphism (SNP) level, top ranked SNPs after prioritization have both higher replication rates and consistently stronger enrichment of eQTLs. Within each risk locus, GenoWAP may be able to distinguish functional sites from groups of correlated SNPs.
Availability and implementation: GenoWAP is freely available on the web at http://genocanyon.med.yale.edu/GenoWAP
Contact: hongyu.zhao@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
IsoMIF Finder: online detection of binding site molecular interaction field similarities
Authors: Chartier Matthieu , Adriansen Etienne , Najmanovich Rafael 
Published: October 2015

Abstract
Summary: IsoMIF Finder is an online server for the identification of molecular interaction field (MIF) similarities. User defined binding site MIFs can be compared to datasets of pre-calculated MIFs or against a user-defined list of PDB entries. The interface can be used for the prediction of function, identification of potential cross-reactivity or polypharmacological targets and drug repurposing. Detected similarities can be viewed in a browser or within a PyMOL session.
Availability and Implementation: IsoMIF Finder uses JSMOL (no java plugin required), is cross-browser and freely available at bcb.med.usherbrooke.ca/imfi.
Contact: Rafael.Najmanovich@Usherbrooke.ca
Supplementary information: Supplementary data are available at Bioinformatics online.