bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germline copy number variation analysis in Finnish families with hereditary prostate cancer
Authors: Laitinen Virpi H. , Akinrinade Oyediran , Rantapero Tommi , Tammela Teuvo L.J. , Wahlfors Tiina , Schleutker Johanna 
Published: November 2015

BACKGROUNDThe inherited factors that predispose individuals to prostate cancer (PrCa) remain largely unknown. The aim of this study was to identify germline copy number variants (CNVs) in Finnish individuals that could contribute to an increased PrCa risk.METHODSGenome‐wide CNV screening was performed by analyzing single nucleotide polymorphisms from 105 PrCa patients and 37 unaffected relatives, representing 31 Finnish hereditary PrCa (HPC) families. The CNVs that aggregated in affected individuals and overlapped with genes implicated in cancer were validated using quantitative PCR in 189 index patients from Finnish HPC families and in 476 controls.RESULTSAn intronic deletion (14.7 kb) in the EPHA3 gene coding for class A ephrin receptor was observed in 11.6% of PrCa patients and in 6.1% of controls. The deletion associated with an increased PrCa risk (P = 0.018, OR = 2.06, 95%CI = 1.18–3.61). Although incomplete segregation with affection status was observed, the results show that the deletion was overrepresented in PrCa patients (56.1%) when compared to unaffected male relatives (31.2%). Interestingly, PrCa‐specific mortality was higher among EPHA3 deletion carriers (24.3%) than among patients with a normal EPHA3 copy number (3.4%).CONCLUSIONSThis study is the first investigation of the contribution of germline CNVs to HPC susceptibility in Finland. A novel association between the EPHA3 deletion and PrCa risk was observed and, if confirmed, screening for this variant may aid in risk stratification among HPC patients. Prostate 76:316–324, 2016. © 2015 Wiley Periodicals, Inc.
Optimization of a large‐volume injection method for compound‐specific isotope analysis of polycyclic aromatic compounds at trace concentrations
Authors: Blessing Michaela , Jochmann Maik A. , Haderlein Stefan B. , Schmidt Torsten C. 
Published: November 2015

RationaleCompound‐specific isotope analysis (CSIA) of persistent organic contaminants can be used for source apportioning in the environment if appropriate sensitivity can be achieved. This paper describes the optimization and validation of a sensitive analytical approach for the determination of the carbon isotope composition of semi‐volatile organic compounds, such as polycyclic aromatic hydrocarbons (PAHs).MethodsAnalyses are based on the introduction of up to 150 μL of organic extracts by means of programmed temperature vaporization–large‐volume injection combined with gas chromatography coupled to isotope ratio mass spectrometry (PTV‐LVI‐GC/IRMS). To allow for the analysis of more volatile, low‐molecular‐weight PAHs, the PTV injector was equipped with a sub‐ambient/cryogenic cooling. Accuracy, precision, linearity and determination limits for application in isotope analysis were evaluated for a set of individual PAHs ranging from two‐ to five‐ring molecular structures. The method was exemplified by determining the δ13C values of individual PAHs in soil samples in a source apportionment study at a contaminated site.ResultsThe choice of PTV injection parameters is crucial to prevent isotope fractionation during injection and largely depends on the analytes to be determined. The observed isotope fractionation effect on semi‐volatiles depends on the applied solvent and injection temperature and demonstrates the importance of performing appropriate tests with given PTV parameters for each of the compounds of interest. The proposed PTV‐LVI‐GC/IRMS method allows the carbon isotope ratio (δ13C value) of individual PAHs to be determined accurately and precisely at concentrations of 0.04–0.1 ng μL−1 even for volatile PAHs such as naphthalene or acenaphthene.ConclusionsLVI with PTV injector cooling allows for the isotopic analysis of volatile and semi‐volatile PAHs at trace concentrations, thus considerably expanding the applicability of CSIA in environmental studies. Copyright © 2015 John Wiley & Sons, Ltd.
Early development of the fetal central sulcus on 7.0T magnetic resonance imaging
Authors: Zhang Haidong , Zhang Zhonghe , Yin Xuntao , Zhan Jinfeng , Zhao Zhenmei , Tang Yuchun , Liu Chao , Liu Shuwei , Zhong Shizhen 
Published: November 2015

AbstractIn the previous studies, the criterion for deciding the occurrence time of the fetal central sulcus (CS) on magnetic resonance imaging (MRI) is based on the observation by the eyes. There have been no existing quantitative standards or numerical criteria in this field. In this study, we reconstructed the three‐dimension (3D) images of the fetal brain based on the 7.0T MR images of 45 Chinese fetal specimens from the 11 to 22 weeks of gestational age (GA). Then we obtained data by measuring the maximum depth and length of the CS so as to analyze the early developmental pattern of it. These measures, especially CS depth, can be used to quantitatively determine the time of emergence of the fetal CS during the development. Statistics show that there are no gender or interhemispheric asymmetries of the CS from GA of 11 to 22 weeks.
A study of an influenza A (H1N1)pdm09 outbreak in pregnant women in Rajasthan, India
Authors: Agrawal Abhishek , Agarwal Sujata , Kumar Vinay , Nawal Chuttan L. , Mital Pradeep , Chejara Radheyshyam 
Published: November 2015

AbstractObjectivesTo describe the clinical and epidemiological factors of influenza A (H1N1)pdm09‐infected patients who were pregnant or in the puerperal period during a recent influenza outbreak in Rajasthan, India.MethodsA retrospective, observational study was performed using hospital records of individuals with confirmed influenza A (H1N1)pdm09 infection admitted to a large tertiary care center in Rajasthan, India, between January 1 and March 15, 2015.ResultsThe study cohort included 44 patients who were pregnant or in the puerperal period. The mean age was significantly lower in the study cohort than in other female patients treated for influenza A (H1N1)pdm09 infection at the hospital during the study period (25.45 ± 3.45 years vs 40.46 ± 13.99 years; P < 0.001). Mortality was significantly higher in the study cohort than in the comparison female patients (36% vs 17%; P = 0.003). Factors found to be associated with mortality were delayed initiation of oseltamivir, poor oxygen saturation at admission, and more than 50% lung involvement under radiographic examination. None of the patients in the study cohort had received a vaccination against seasonal influenza.ConclusionInfluenza A (H1N1)pdm09 infection during pregnancy causes more severe illness. Early recognition and timely administration of antiviral therapy can improve outcomes. The role of influenza vaccination in this high‐risk population cannot be overemphasized.
Trading behavior in S&P 500 index futures
Authors: Smales Lee A. 
Published: November 2015

AbstractThis article examines the determinants of trading decisions and the performance of trader types, in the context of the E‐Mini S&P 500 futures and S&P 500 futures markets. Speculators and small traders tend to follow positive feedback strategies while hedgers dynamically adjust positions in response to market returns. Such strategies apparently reverse during the 2008–09 financial crisis. Investor sentiment and market volatility play an important role in determining the net trading position of traders across the sample period. While all trader types are better at foreseeing market upturns, an out‐of‐sample test suggests that speculators and small traders have some predictive ability for short‐term market returns.
Comparative size evolution of marine clades from the Late Permian through Middle Triassic
Authors: Schaal Ellen K. , Clapham Matthew E. , Rego Brianna L. , Wang Steve C. , Payne Jonathan L. 
Published: November 2015

AbstractThe small size of Early Triassic marine organisms has important implications for the ecological and environmental pressures operating during and after the end-Permian mass extinction. However, this “Lilliput Effect” has only been documented quantitatively in a few invertebrate clades. Moreover, the discovery of Early Triassic gastropod specimens larger than any previously known has called the extent and duration of the Early Triassic size reduction into question. Here, we document and compare Permian-Triassic body size trends globally in eight marine clades (gastropods, bivalves, calcitic and phosphatic brachiopods, ammonoids, ostracods, conodonts, and foraminiferans). Our database contains maximum size measurements for 11,224 specimens and 2,743 species spanning the Late Permian through the Middle to Late Triassic. The Permian/Triassic boundary (PTB) shows more size reduction among species than any other interval. For most higher taxa, maximum and median size among species decreased dramatically from the latest Permian (Changhsingian) to the earliest Triassic (Induan), and then increased during Olenekian (late Early Triassic) and Anisian (early Middle Triassic) time. During the Induan, the only higher taxon much larger than its long-term mean size was the ammonoids; they increased significantly in median size across the PTB, a response perhaps related to their comparatively rapid diversity recovery after the end-Permian extinction. The loss of large species in multiple clades across the PTB resulted from both selective extinction of larger species and evolution of surviving lineages toward smaller sizes. The within-lineage component of size decrease suggests that only part of the size decrease can be related to the end-Permian kill mechanism; in addition, Early Triassic environmental conditions or ecological pressures must have continued to favor small body size as well. After the end-Permian extinction, size decrease occurred across ecologically and physiologically disparate clades, but this size reduction was limited to the first part of the Early Triassic (Induan). Nektonic habitat or physiological buffering capacity may explain the contrast of Early Triassic size increase and diversification in ammonoids versus size reduction and slow recovery in benthic clades.
War on the Home Front: Battle Pieces for the Piano from the American Civil War
Authors: MORGAN ELIZABETH 
Published: November 2015

AbstractDuring the Civil War, countless musical works were written about the conflict and marketed to amateur musicians, especially women. Among them were pieces composed in response to recent conflicts, often published within days or weeks of the relevant event. Popular genres included keyboard battle pieces, which depicted some of the most pivotal battles of the war in musical rhetoric, bringing them alive in the minds and imaginations of drawing room performers and audiences.This essay is the first detailed study of American keyboard battle pieces from the Civil War. It investigates how they mirror many aspects of Civil War life, including the civilian demand for vivid war news, especially eyewitness accounts from the front, the advent of telegraphic reporting, and the fallibility of the media in reporting on the war. The pieces also reflect cultural trends of the mid-nineteenth century not related to war, particularly the popularity of theatrical melodrama on the stage and the prominence of virtuosity in piano repertoire. In investigating the performance of battle pieces as a site where women imagined and experienced the perils of war, this article contributes to scholarship that deepens our understanding of how women at home participated in mass culture.
Scoring The President: Myth and Politics in John Williams'sJFKandNixon
Authors: LEHMAN FRANK 
Published: November 2015

AbstractThroughout his career, John Williams has set the musical tone for the American presidency, most elaborately with his scores for Oliver Stone's controversial filmsJFK(1991) andNixon(1995). While invested in capturing the character of these commanders in chief through musical codes, Williams's soundtracks are equally engaged in the act of the evocation and telling of “history.” Specifically, they construct a tragic myth of 1960s America in which the promise represented by JFK is destroyed from without, and Nixon from within, both by the malevolent forces of the military-industrial complex. In considering the thematic and dramatic means by which Williams paints his orchestral portraits, I reveal the extent to which music supports Stone's paranoiac narratives, especially in cases where the director's collage-like visual aesthetic puts pressure on the otherwise nostalgic traits of Williams's default tonal style.I offer a music-analytical approach toJFKandNixoninformed by interviews, studies of political mythology and paranoia, and musicological appraisals of Williams's music. Stone's 1960s-as-lapsarian-metanarrative positions Kennedy as a romanticized absence, an image of the fabular fallen King, and Williams renders him as a public recollection rather than a human being with interiority. Nixon, by contrast, is a tragic antihero, consumed by dark forces of history and an abundance of ambivalent thematic material. Particular attention is paid to the dismantling of Kennedy's noble leitmotif duringJFK’sprologue and motorcade sequence and to the near-fascistic musical accompaniment of Nixon's speeches. Having demonstrated the active role these scores play, I conclude that Williams's music constitutes an authoring of history in a strong, albeit postmodern, sense, consistent with but independent from Stone's screenplay.
Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Authors: Oyserman Ben O , Noguera Daniel R , del Rio Tijana Glavina , Tringe Susannah G , McMahon Katherine D 
Published: November 2015

Abstract
Previous studies on enhanced biological phosphorus removal (EBPR) have focused on reconstructing genomic blueprints for the model polyphosphate-accumulating organism Candidatus Accumulibacter phosphatis. Here, a time series metatranscriptome generated from enrichment cultures of Accumulibacter was used to gain insight into anerobic/aerobic metabolism and regulatory mechanisms within an EBPR cycle. Co-expressed gene clusters were identified displaying ecologically relevant trends consistent with batch cycle phases. Transcripts displaying increased abundance during anerobic acetate contact were functionally enriched in energy production and conversion, including upregulation of both cytoplasmic and membrane-bound hydrogenases demonstrating the importance of transcriptional regulation to manage energy and electron flux during anerobic acetate contact. We hypothesized and demonstrated hydrogen production after anerobic acetate contact, a previously unknown strategy for Accumulibacter to maintain redox balance. Genes involved in anerobic glycine utilization were identified and phosphorus release after anerobic glycine contact demonstrated, suggesting that Accumulibacter routes diverse carbon sources to acetyl-CoA formation via previously unrecognized pathways. A comparative genomics analysis of sequences upstream of co-expressed genes identified two statistically significant putative regulatory motifs. One palindromic motif was identified upstream of genes involved in PHA synthesis and acetate activation and is hypothesized to be a phaR binding site, hence representing a hypothetical PHA modulon. A second motif was identified ~35 base pairs (bp) upstream of a large and diverse array of genes and hence may represent a sigma factor binding site. This analysis provides a basis and framework for further investigations into Accumulibacter metabolism and the reconstruction of regulatory networks in uncultured organisms.
Sponge-like nanoporous single crystals of gold
Authors: Khristosov Maria Koifman , Bloch Leonid , Burghammer Manfred , Kauffmann Yaron , Katsman Alex , Pokroy Boaz 
Published: November 2015

AbstractSingle crystals in nature often demonstrate fascinating intricate porous morphologies rather than classical faceted surfaces. We attempt to grow such crystals, drawing inspiration from biogenic porous single crystals. Here we show that nanoporous single crystals of gold can be grown with no need for any elaborate fabrication steps. These crystals are found to grow following solidification of a eutectic composition melt that forms as a result of the dewetting of nanometric thin films. We also present a kinetic model that shows how this nano-porous single-crystalline structure can be obtained, and which allows the potential size of the porous single crystal to be predicted. Retaining their single-crystalline nature is due to the fact that the full crystallization process is faster than the average period between two subsequent nucleation events. Our findings clearly demonstrate that it is possible to form single-crystalline nano porous metal crystals in a controlled manner.
Hybrid graphene plasmonic waveguide modulators
Authors: Ansell D. , Radko I. P. , Han Z. , Rodriguez F. J. , Bozhevolnyi S. I. , Grigorenko A. N. 
Published: November 2015

AbstractThe unique optical and electronic properties of graphene make possible the fabrication of novel optoelectronic devices. One of the most exciting graphene characteristics is the tunability by gating which allows one to realize active optical devices. While several types of graphene-based photonic modulators have already been demonstrated, the potential of combining the versatility of graphene with subwavelength field confinement of plasmonic waveguides remains largely unexplored. Here we report fabrication and study of hybrid graphene–plasmonic waveguide modulators. We consider several types of modulators and identify the most promising one for telecom applications. The modulator working at the telecom range is demonstrated, showing a modulation depth of >0.03 dB μm−1 at low gating voltages for an active device area of just 10 μm2, characteristics which are already comparable to those of silicon-based waveguide modulators while retaining the benefit of further device miniaturization. Our proof-of-concept results pave the way towards on-chip realization of efficient graphene-based active plasmonic waveguide devices for optical communications.
Construction, complete sequence, and annotation of a BAC contig covering the silkworm chorion locus
Authors: Chen Zhiwei , Nohata Junko , Guo Huizhen , Li Shenglong , Liu Jianqiu , Guo Youbing , Yamamoto Kimiko , Kadono-Okuda Keiko , Liu Chun , Arunkumar Kallare P. , Nagaraju Javaregowda , Zhang Yan , Liu Shiping , Labropoulou Vassiliki , Swevers Luc , Tsitoura Panagiota , Iatrou Kostas , Gopinathan Karumathil P. , Goldsmith Marian R. , Xia Qingyou , Mita Kazuei 
Published: November 2015

AbstractThe silkmoth chorion was studied extensively by F.C. Kafatos’ group for almost 40 years. However, the complete structure of the chorion locus was not obtained in the genome sequence of Bombyx mori published in 2008 due to repetitive sequences, resulting in gaps and an incomplete view of the locus. To obtain the complete sequence of the chorion locus, expressed sequence tags (ESTs) derived from follicular epithelium cells were used as probes to screen a bacterial artificial chromosome (BAC) library. Seven BACs were selected to construct a contig which covered the whole chorion locus. By Sanger sequencing, we successfully obtained complete sequences of the chorion locus spanning 871,711 base pairs on chromosome 2, where we annotated 127 chorion genes. The dataset reported here will recruit more researchers to revisit one of the oldest model systems which has been used to study developmentally regulated gene expression. It also provides insights into egg development and fertilization mechanisms and is relevant to applications related to improvements in breeding procedures and transgenesis.
Adaptation of H9N2 AIV in guinea pigs enables efficient transmission by direct contact and inefficient transmission by respiratory droplets
Authors: Sang Xiaoyu , Wang Airong , Ding Jie , Kong Huihui , Gao Xiaolong , Li Lin , Chai Tongjie , Li Yuanguo , Zhang Kun , Wang Chengyu , Wan Zhonghai , Huang Geng , Wang Tiecheng , Feng Na , Zheng Xuexing , Wang Hualei , Zhao Yongkun , Yang Songtao , Qian Jun , Hu Guixue , Gao Yuwei , Xia Xianzhu 
Published: November 2015

AbstractH9N2 avian influenza viruses circulate worldwide in poultry and have sporadically infected humans, raising concern whether H9N2 viruses have pandemic potential. Here, we use a guinea pig model to examine whether serial passage results in adaptive viral changes that confer a transmissible phenotype to a wild-type H9N2 virus. After nine serial passages of an H9N2 virus through guinea pigs, productive transmission by direct contact occurred in 2/3 guinea pig pairs. The efficiency of transmission by direct contact increased following the fifteenth passage and occurred in 3/3 guinea pig pairs. In contrast, airborne transmission of the passaged virus was less efficient and occurred in 1/6 guinea pig pairs and 0/6 ferret pairs after the fifteenth passage. Three amino acid substitutions, HA1-Q227P, HA2-D46E and NP-E434K, were sufficient for contact transmission in guinea pigs (2/3 pairs). The two HA amino acid substitutions enhanced receptor binding to α2,3-linked sialic acid receptors. Additionally, the HA2-D46E substitution increased virus thermostability whereas the NP-E434K mutation enhanced viral RNA polymerase activity in vitro. Our findings suggest that adaptive changes that enhance viral receptor binding, thermostability and replicative capacity in mammalian cells can collectively enhance the transmissibility of H9N2 AIVs by direct contact in the guinea pig model.
Synthesis of Hierarchical Nanoporous Microstructures via the Kirkendall Effect in Chemical Reduction Process
Authors: Gao Ling , Pang Chao , He Dafang , Shen Liming , Gupta Arunava , Bao Ningzhong 
Published: November 2015

AbstractA series of novel hierarchical nanoporous microstructures have been synthesized through one-step chemical reduction of micron size Cu2O and Co3O4 particles. By controlling the reduction time, non-porous Cu2O microcubes sequentially transform to nanoporous Cu/Cu2O/Cu dented cubic composites and hollow eightling-like Cu microparticles. The mechanism involved in the complex structural evolution is explained based on oxygen diffusion and Kirkendall effect. The nanoporous Cu/Cu2O/Cu dented cubic composites exhibit superior electrochemical performance as compared to solid Cu2O microcubes. The reduction of nonporous Co3O4 also exhibits a uniform sequential reduction process from nonporous Co3O4 to porous Co3O4/CoO composites, porous CoO, porous CoO/Co composites and porous foam-like Co particles. Nanoscale channels originate from the particle surface and eventually develop inside the entire product, resulting in porous foam-like Co microparticles. The Kirkendall effect is believed to facilitate the formation of porous structures in both processes.