bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology
Authors: Wang Shi-Bo , Feng Jian-Ying , Ren Wen-Long , Huang Bo , Zhou Ling , Wen Yang-Jun , Zhang Jin , Dunwell Jim M. , Xu Shizhong , Zhang Yuan-Ming 
Published: January 2016

AbstractGenome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large. To address this concern, we proposed a random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) for GWAS. The RMLM simply treats the SNP-effect as random, but it allows a modified Bonferroni correction to be used to calculate the threshold p value for significance tests. The MRMLM is a multi-locus model including markers selected from the RMLM method with a less stringent selection criterion. Due to the multi-locus nature, no multiple test correction is needed. Simulation studies show that the MRMLM is more powerful in QTN detection and more accurate in QTN effect estimation than the RMLM, which in turn is more powerful and accurate than the EMMA. To demonstrate the new methods, we analyzed six flowering time related traits in Arabidopsis thaliana and detected more genes than previous reported using the EMMA. Therefore, the MRMLM provides an alternative for multi-locus GWAS.
Distinct mutation accumulation rates among tissues determine the variation in cancer risk
Authors: Hao Dapeng , Wang Li , Di Li-jun 
Published: January 2016

AbstractCancer is believed to be a result of accumulated mutations. However, this concept has not been fully confirmed owing to the impossibility of tracking down the ancestral somatic cell. We sought to verify the concept by exploring the correlation between cancer risk and mutation accumulation among different tissues. We hypothesized that the detected mutations through bulk tumor sequencing are commonly shared in majority, if not all, of tumor cells and are therefore largely a reflection of the mutations accumulated in the ancestral cell that gives rise to tumor. We collected a comprehensive list of mutation frequencies revealed by bulk tumor sequencing and investigated its correlation with cancer risk to mirror the correlation between mutation accumulation and cancer risk. This revealed an approximate 1:1 relationship between mutation frequency and cancer risk in 41 different cancer types based on the sequencing data of 5,542 patients. The correlation strongly suggests that variation in cancer risk among tissues is mainly attributable to distinct mutation accumulation rates. Moreover, the correlation establishes a baseline to evaluate the effect of non-mutagenic carcinogens on cancer risk. Finally, our mathematic modeling provides a reasonable explanation to reinforce that cancer risk is predominantly determined by the first rate-limiting mutation.
Transient nature of cooperation by pay-it-forward reciprocity
Authors: Horita Yutaka , Takezawa Masanori , Kinjo Takuji , Nakawake Yo , Masuda Naoki 
Published: January 2016

AbstractHumans often forward kindness received from others to strangers, a phenomenon called the upstream or pay-it-forward indirect reciprocity. Some field observations and laboratory experiments found evidence of pay-it-forward reciprocity in which chains of cooperative acts persist in social dilemma situations. Theoretically, however, cooperation based on pay-it-forward reciprocity is not sustainable. We carried out laboratory experiments of a pay-it-forward indirect reciprocity game (i.e., chained gift-giving game) on a large scale in terms of group size and time. We found that cooperation consistent with pay-it-forward reciprocity occurred only in a first few decisions per participant and that cooperation originated from inherent pro-sociality of individuals. In contrast, the same groups of participants showed persisting chains of cooperation in a different indirect reciprocity game in which participants earned reputation by cooperating. Our experimental results suggest that pay-it-forward reciprocity is transient and disappears when a person makes decisions repeatedly, whereas the reputation-based reciprocity is stable in the same situation.
Stress Induced Mechano-electrical Writing-Reading of Polymer Film Powered by Contact Electrification Mechanism
Authors: Goswami Sumita , Nandy Suman , Calmeiro Tomás R. , Igreja Rui , Martins Rodrigo , Fortunato Elvira 
Published: January 2016

AbstractMechano-electrical writing and reading in polyaniline (PANI) thin film are demonstrated via metal-polymer contact electrification mechanism (CEM). An innovative conception for a non-destructive self-powered writable-readable data sheet is presented which can pave the way towards new type of stress induced current harvesting devices. A localized forced deformation of the interface has been enacted by pressing the atomic force microscopic probe against the polymer surface, allowing charge transfer between materials interfaces. The process yields a well-defined charge pattern by transmuting mechanical stress in to readable information. The average of output current increment has been influenced from 0.5 nA to 15 nA for the applied force of 2 nN to 14 nN instead of electrical bias. These results underscore the importance of stress-induced current harvesting mechanism and could be scaled up for charge patterning of polymer surface to writable-readable data sheet. Time evolutional current distribution (TECD) study of the stress-induced patterned PANI surface shows the response of readability of the recorded data with time.
Metabolomic Profiling of Mice Serum during Toxoplasmosis Progression Using Liquid Chromatography-Mass Spectrometry
Authors: Zhou Chun-Xue , Zhou Dong-Hui , Elsheikha Hany M. , Zhao Yu , Suo Xun , Zhu Xing-Quan 
Published: January 2016

AbstractBetter understanding of the molecular changes associated with disease is essential for identifying new routes to improved therapeutics and diagnostic tests. The aim of this study was to investigate the dynamic changes in the metabolic profile of mouse sera during T. gondii infection. We carried out untargeted metabolomic analysis of sera collected from female BALB/c mice experimentally infected with the T. gondii Pru strain (Genotype II). Serum samples were collected at 7, 14 and 21 day post infection (DPI) from infected and control mice and were subjected to liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS)-based global metabolomics analysis. Multivariate statistical analysis identified 79 differentially expressed metabolites in ESI+ mode and 74 in ESI− mode in sera of T. gondii-infected mice compared to the control mice. Further principal component analysis (PCA) and partial least squares-discrimination analysis (PLS-DA) identified 19 dysregulated metabolites (5 in ESI+ mode and 14 in ESI− mode) related to the metabolism of amino acids and energy metabolism. The potential utility of these metabolites as diagnostic biomarkers was validated through receiver operating characteristic (ROC) curve analysis. These findings provide putative metabolite biomarkers for future study and allow for hypothesis generation about the pathophysiology of toxoplasmosis.
Programmable SERS active substrates for chemical and biosensing applications using amorphous/crystalline hybrid silicon nanomaterial
Authors: Powell Jeffery Alexander , Venkatakrishnan Krishnan , Tan Bo 
Published: January 2016

AbstractWe present the creation of a unique nanostructured amorphous/crystalline hybrid silicon material that exhibits surface enhanced Raman scattering (SERS) activity. This nanomaterial is an interconnected network of amorphous/crystalline nanospheroids which form a nanoweb structure; to our knowledge this material has not been previously observed nor has it been applied for use as a SERS sensing material. This material is formed using a femtosecond synthesis technique which facilitates a laser plume ion condensation formation mechanism. By fine-tuning the laser plume temperature and ion interaction mechanisms within the plume, we are able to precisely program the relative proportion of crystalline Si to amorphous Si content in the nanospheroids as well as the size distribution of individual nanospheroids and the size of Raman hotspot nanogaps. With the use of Rhodamine 6G (R6G) and Crystal Violet (CV) chemical dyes, we have been able to observe a maximum enhancement factor of 5.38 × 106 and 3.72 × 106 respectively, for the hybrid nanomaterial compared to a bulk Si wafer substrate. With the creation of a silicon-based nanomaterial capable of SERS detection of analytes, this work demonstrates a redefinition of the role of nanostructured Si from an inactive to SERS active role in nano-Raman sensing applications.
The role of off-equatorial surface temperature anomalies in the 2014 El Niño prediction
Authors: Zhu Jieshun , Kumar Arun , Huang Bohua , Balmaseda Magdalena A. , Hu Zeng-Zhen , Marx Lawrence , Kinter III James L. 
Published: January 2016

AbstractThe 2014 El Niño, anticipated to be a strong event in early 2014, turned out to be fairly weak. In early 2014, the tropical Pacific exhibited persistent negative SST anomalies in the southeastern Pacific and positive SST anomalies in north, following the pattern of the Southern Pacific Meridional Mode. In this study, we explored the role of the off-equatorial SST anomalies in the 2014 prediction. Our experiments show that 40% of the amplitude error at the peak phase could be attributed to the lack of prediction of negative SST anomalies in the southeastern Pacific. However, the impact of this model error is partially compensated by the absence of the positive SST anomalies in the tropical western North Pacific in the model. The model response to the amplitude of negative southeastern Pacific SST anomalies is nonlinear in terms of equatorial warming, because the enhanced meridional pressure gradient forces very strong meridional winds without accelerating the zonal wind component near the equator. Our study suggests that reliable forecasts of ENSO strongly rely on correctly modeling the meridional SST gradient, as well as its delicate feedback with the zonal (ENSO) mode.
Charge transport through one-dimensional Moiré crystals
Authors: Bonnet Roméo , Lherbier Aurélien , Barraud Clément , Rocca Maria Luisa Della , Lafarge Philippe , Charlier Jean-Christophe 
Published: January 2016

AbstractMoiré superlattices were generated in two-dimensional (2D) van der Waals heterostructures and have revealed intriguing electronic structures. The appearance of mini-Dirac cones within the conduction and valence bands of graphene is one of the most striking among the new quantum features. A Moiré superstructure emerges when at least two periodic sub-structures superimpose. 2D Moiré patterns have been particularly investigated in stacked hexagonal 2D atomic lattices like twisted graphene layers and graphene deposited on hexagonal boron-nitride. In this letter, we report both experimentally and theoretically evidence of superlattices physics in transport properties of one-dimensional (1D) Moiré crystals. Rolling-up few layers of graphene to form a multiwall carbon nanotube adds boundaries conditions that can be translated into interference fringes-like Moiré patterns along the circumference of the cylinder. Such a 1D Moiré crystal exhibits a complex 1D multiple bands structure with clear and robust interband quantum transitions due to the presence of mini-Dirac points and pseudo-gaps. Our devices consist in a very large diameter (>80 nm) multiwall carbon nanotubes of high quality, electrically connected by metallic electrodes acting as charge reservoirs. Conductance measurements reveal the presence of van Hove singularities assigned to 1D Moiré superlattice effect and illustrated by electronic structure calculations.
Quantum Criticality in the Biased Dicke Model
Authors: Zhu Hanjie , Zhang Guofeng , Fan Heng 
Published: January 2016

AbstractThe biased Dicke model describes a system of biased two-level atoms coupled to a bosonic field and is expected to produce new phenomena that are not present in the original Dicke model. In this paper, we study the critical properties of the biased Dicke model in the classical oscillator limits. For the finite-biased case in this limit, We present analytical results demonstrating that the excitation energy does not vanish for arbitrary coupling. This indicates that the second order phase transition is avoided in the biased Dicke model, which contrasts to the original Dicke model. We also analyze the squeezing and the entanglement in the ground state and find that a finite bias will strongly modify their behaviors in the vicinity of the critical coupling point.
Dual surface sliding mode controller for photovoltaic systems enhanced by a ripple domain search maximum power point tracking algorithm for fast changing environmental conditions
Authors: Ghaffarzadeh Navid , Bijani Sepehr 
Published: January 2016

In this research, a dual surface sliding mode controller is proposed and implemented to increase robustness and speed of boost converter, its asymptotic response is proved in the presence of disturbances. In addition, a filtered mapping pulse width modulation technique is developed to attenuate the chattering problem caused by finite frequency switching. Ripple domain search (RDS), a precise maximum power point tracking (MPPT) algorithm, is suggested to find the maximum power point (MPP) in photovoltaics. RDS uses the inherent ripple problem of the converter as a tool for finding MPP. By combining the proposed fast controller and the RDS algorithm, a fast and robust MPPT technique is obtained, which is simple to implement, eliminates the need for initial parameter tuning and is free from oscillations. Moreover, the proposed controlling method and MPPT algorithm are tested using Mitsubishi Electric MF170W module and their efficiency is compared with conventional methods (including P & O) in fast irradiation changing conditions. The proposed method harvests a 6% higher power than P & O and constant voltage. Compared with incremental conductance 24% more power is harvested. Finally, the practicality of the controller and algorithm was experimentally validated with a prototype system using a 5 W Evergreen module.
Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling
Authors: Serra François , Baù Davide , Filion Guillaume , Marti-Renom Marc A. 
Published: January 2016

AbstractBackgroundThe sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its threedimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights on the spatial organization of genomes. However, inferring structures from raw contact data is a tedious process for shortage of available tools.ResultsHere we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition.ConclusionsTADbit provides three-dimensional built from 3C-based experiments, which are ready for visualization and for characterizing their relation to gene expression and epigenetic states. TADbit is open-source and available for download fromhttp://www.3DGenomes.org.
Cell freezing protocol optimized for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Authors: Milani Pamela , Escalante-Chong Renan , Shelley Brandon C. , Patel-Murray Natasha L. , Xin Xiaofeng , Adam Miriam , Mandefro Berhan , Sareen Dhruv , Svendsen Clive N. , Fraenkel Ernest 
Published: January 2016

AbstractIn recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it has proven difficult to perform this technique on frozen samples because freezing cells before extracting nuclei impairs nuclear integrity and alters chromatin structure. We describe a protocol for freezing cells that is compatible with ATAC-Seq, producing results that compare well with those generated from fresh cells. We found that while flash-frozen samples are not suitable for ATAC-Seq, the assay is successful with slow-cooled cryopreserved samples. Using this method, we were able to isolate high quality, intact nuclei, and we verified that epigenetic results from fresh and cryopreserved samples agree quantitatively. We developed our protocol on a disease-relevant cell type, namely motor neurons differentiated from induced pluripotent stem cells from a patient affected by spinal muscular atrophy.
A convex optimization approach for identification of human tissue-specific interactomes
Authors: Mohammadi Shahin , Grama Ananth 
Published: January 2016

AbstractMotivation:Analysis of organism-specific interactomes has yielded novel insights into cellular function and coordination, understanding of pathology, and identification of markers and drug targets. Genes, however, can exhibit varying levels of cell-type specificity in their expression, and their coordinated expression manifests in tissue-specific function and pathology. Tissue-specific/ selective interaction mechanisms have significant applications in drug discovery, as they are more likely to reveal drug targets. Furthermore, tissue-specific transcription factors (tsTFs) are significantly implicated in human disease, including cancers. Finally, disease genes and protein complexes have the tendency to be differentially expressed in tissues in which defects cause pathology. These observations motivate the construction of refined tissue-specific interactomes from organism-specific interactomes.Results:We present a novel technique for constructing human tissue-specific interactomes. Using a variety of validation tests (ESEA, GO Enrichment, Disease-Gene Subnetwork Compactness), we show that our proposed approach significantly outperforms state of the art techniques. Finally, using case studies of Alzheimer’s and Parkinson’s diseases, we show that tissue-specific interactomes derived from our study can be used to construct pathways implicated in pathology and demonstrate the use of these pathways in identifying novel targets.Availability:http://www.cs.purdue.edu/homes/mohammas/projects/ActPro.html
A frameshift mutation inGON4Lis associated with proportionate dwarfism in Fleckvieh cattle
Authors: Schwarzenbacher Hermann , Wurmser Christine , Flisikowski Krzysztof , Misurova Lubica , Jung Simone , Langenmayer Martin C. , Schnieke Angelika , Knubben-Schweizer Gabriela , Fries Ruedi , Pausch Hubert 
Published: January 2016

AbstractBackgroundLow birth weight and postnatal growth restriction are the most evident symptoms of dwarfism. Accompanying skeletal aberrations may compromise the general condition and locomotion of affected individuals. Several paternal half sibs with low birth weight and size were born in 2013 in the Fleckvieh cattle population.ResultsAffected calves were strikingly underweight at birth despite a normal gestation length and had craniofacial abnormalities such as elongated narrow heads and brachygnathia inferior. Despite a normal general condition, their growth remained restricted during rearing. We genotyped 27 affected and 10,454 unaffected animals at 44,672 SNPs and performed association testing followed by homozygosity mapping to map the growth failure to a 1.85 Mb segment on bovine chromosome 3. Analysis of whole-genome re-sequencing data from one affected and 289 unaffected animals revealed a 1bp deletion (g.15079217delC, rs723240647) in the coding region of the GON4L gene that segregated with the dwarfism-associated haplotype. We show that the deletion introduces intron retention and premature termination of translation, putatively resulting in a severely truncated protein that lacks domains that are likely essential to normal protein function. The widespread use of an unnoticed carrier bull for artificial insemination has resulted in a tenfold increase in the frequency of the deleterious allele in the female population.ConclusionsA frameshift mutation inGON4Lis associated with autosomal recessive proportionate dwarfism in Fleckvieh cattle. The mutation has segregated in the population for more than fifty years without being recognized as a genetic disorder. However, the widespread use of an unnoticed carrier bull for artificial insemination caused a sudden accumulation of homozygous calves with dwarfism. Our findings provide the basis for genome-based mating strategies to avoid the inadvertent mating of carrier animals and thereby prevent the birth of homozygous calves with impaired growth.
The prognostic potential of alternative transcript isoforms across human tumors
Authors: Trincado Juan L. , Sebestyén E. , Pagés A. , Eyras E. 
Published: January 2016

AbstractBackgroundPhenotypic changes during cancer progression are associated to alterations in gene expression, which can be exploited to build molecular signatures for tumor stage identification and prognosis. However, it is not yet known whether the relative abundance of transcript isoforms may be informative for clinical stage and survival.MethodsUsing information theory and machine learning methods, we integrated RNA sequencing and clinical data from The Cancer Genome Atlas project to perform the first systematic analysis of the prognostic potential of transcript isoforms in 12 solid tumors to build new predictive signatures for stage and prognosis. This study was also performed in breast tumors according to estrogen receptor status and melanoma tumors with proliferative and invasive phenotypes.ResultsTranscript isoform signatures accurately separate early from late stage and metastatic from non-metastatic tumors, and are predictive of the survival of patients with undetermined lymph node invasion or metastatic status. These signatures show similar, and sometimes better, accuracies compared with known gene expression signatures, and are largely independent of gene expression changes. Furthermore, we show frequent transcript isoform changes in breast tumors according to estrogen receptor status, and in melanoma tumors according to the invasive or proliferative phenotype, and derive accurate predictive models of stage and survival within each patient subgroup.ConclusionsOur analyses reveal new signatures based on transcript isoform abundances that characterize tumor phenotypes and their progression independently of gene expression. Transcript isoform signatures appear especially relevant to determine lymph node invasion and metastasis, and may potentially contribute towards current strategies of precision cancer medicine.