bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the landscape of focal amplifications in cancer using AmpliconArchitect
Authors: Deshpande Viraj , Luebeck Jens , Nguyen Nam-Phuong D. , Bakhtiari Mehrdad , Turner Kristen M. , Schwab Richard , Carter Hannah , Mischel Paul S. , Bafna Vineet 
Published: January 2019

AbstractFocal oncogene amplification and rearrangements drive tumor growth and evolution in multiple cancer types. We present AmpliconArchitect (AA), a tool to reconstruct the fine structure of focally amplified regions using whole genome sequencing (WGS) and validate it extensively on multiple simulated and real datasets, across a wide range of coverage and copy numbers. Analysis of AA-reconstructed amplicons in a pan-cancer dataset reveals many novel properties of copy number amplifications in cancer. These findings support a model in which focal amplifications arise due to the formation and replication of extrachromosomal DNA. Applying AA to 68 viral-mediated cancer samples, we identify a large fraction of amplicons with specific structural signatures suggestive of hybrid, human-viral extrachromosomal DNA. AA reconstruction, integrated with metaphase fluorescence in situ hybridization (FISH) and PacBio sequencing on the cell-line UPCI:SCC090 confirm the extrachromosomal origin and fine structure of a Forkhead box E1 (FOXE1)-containing hybrid amplicon.
Unveiling coherently driven hyperpolarization dynamics in signal amplification by reversible exchange
Authors: Lindale Jacob R. , Eriksson Shannon L. , Tanner Christian P. N. , Zhou Zijian , Colell Johannes F. P. , Zhang Guannan , Bae Junu , Chekmenev Eduard Y. , Theis Thomas , Warren Warren S. 
Published: January 2019

AbstractSignal amplification by reversible exchange (SABRE) is an efficient method to hyperpolarize spin-1/2 nuclei and affords signals that are orders of magnitude larger than those obtained by thermal spin polarization. Direct polarization transfer to heteronuclei such as 13C or 15N has been optimized at static microTesla fields or using coherence transfer at high field, and relies on steady state exchange with the polarization transfer catalyst dictated by chemical kinetics. Here we demonstrate that pulsing the excitation field induces complex coherent polarization transfer dynamics, but in fact pulsing with a roughly 1% duty cycle on resonance produces more magnetization than constantly being on resonance. We develop a Monte Carlo simulation approach to unravel the coherent polarization dynamics, show that existing SABRE approaches are quite inefficient in use of para-hydrogen order, and present improved sequences for efficient hyperpolarization.
Importance of Experimental Environmental Conditions in Estimating Risks and Associated Uncertainty of Transgenic Fish Prior to Entry into Nature
Authors: Vandersteen Wendy E. , Leggatt Rosalind , Sundström L. Fredrik , Devlin Robert H. 
Published: January 2019

AbstractSalmonids show a high degree of phenotypic plasticity that can differ among genotypes, and this variation is one of the major factors contributing to uncertainty in extrapolating laboratory-based risk assessment data to nature. Many studies have examined the relative growth and survival of transgenic and non-transgenic salmonids, and the results have been highly variable due to genotype × environment interactions. The relative survival of fast- and slow-growing strains can reverse depending on the environment, but it is not clear which specific environmental characteristics are driving these responses. To address this question, two experiments were designed where environmental conditions were varied to investigate the contribution of rearing density, food amount, food type, habitat complexity, and risk of predation on relative growth and survival of fast-growing transgenic and slow-growing wild-type coho salmon. The first experiment altered density (high vs. low) and food amount (high vs. low). Density impacted the relative growth of the genotypes, where transgenic fish grew more than non-transgenic fish in low density streams, regardless of food level. Density also affected survival, with high density causing increased mortality for both genotypes, but the mortality of transgenic relative to non-transgenic fish was lower within the high-density streams, regardless of food level. The second experiment altered habitat complexity (simple vs. complex), food type (artificial vs. natural), amount of food (normal vs. satiation), and risk of predation (present vs. absent). Results from this experiment showed that genotype affected growth and survival, but genotype effects were modulated by one or more environmental factors. The effect of genotype on survival was influenced by all examined environmental factors, such that no predictable trend in relative survival of transgenic versus non-transgenic fry emerged. This was primarily due to variations in survival of non-transgenic fish under different environmental conditions (non-transgenic fry had highest survival in hatchery conditions, and lowest survival in complex conditions with natural food fed at a normal level with or without predators). Transgenic fry survival was only significantly influenced by predator presence. The effects of genotype on mass and length were significantly modulated by food type only. Transgenic fry were able to gain a large size advantage over non-transgenic fish when fed artificial food under all habitat types. These experiments support the observations of dynamic responses in growth and survival depending on the environment, and demonstrate the challenge of applying laboratory-based experiments to risk assessment in nature.
Risk factors of stillbirth in rural China: A national cohort study
Authors: Qu Yimin , Chen Shi , Pan Hui , Zhu Huijuan , Yan Chengsheng , Zhang Shikun , Jiang Yu 
Published: January 2019

AbstractPeople living in rural China are more frequently exposed to some specific risk factors which made stillbirth rate higher than urban areas. National Free Preconception Health Examination Project was launched to investigate these risk factors and collected a representative sample of 248501 participants from 31 provinces in China from 2010 to 2013. Parental risk factors were ascertained twice before and during pregnancy respectively by questionnaires. Stillbirth or live birth were recorded by trained physicians. In the analysis, nested case-control study was conducted, and propensity score matching method was used to adjust the confounding. Multi-level logistic regression was used to fit for multi-level sampling. The overall stillbirth rate was 0.35% in rural China, it was higher in North (0.42%) and West (0.64%) areas. Maternal exposure to pesticide (OR (95%CI 1.06, 3.39)), hypertension (OR = 1.58 (95%CI 1.07, 2.34)), lack of appetite for vegetables (OR = 1.99 (95%CI 1.00, 3.93)), stress (compared with no pressure, OR of a little pressure was 1.34(95% CI 1.02, 1.76)); paternal exposure to smoking (OR = 1.22 (95% CI 1.02, 1.46)), organic solvents (OR = 1.64 (95% CI 1.01, 2.69)) were found independent risk factors of stillbirth. Folacin intake 3 months before pregnancy (OR = 0.72 (95%) CI 0.59, 0.89), folacin intake 1-2 months before pregnancy (OR = 0.71 (95% CI 0.55, 0.92)), folacin intake after pregnancy (OR = 0.81 (95% CI 0.65, 1.02) for) were protect factors of stillbirth. Maternal pesticide exposure, lack of vegetables, stress, paternal smoking and exposure to organic solvents were risk factors of stillbirth. Folic acid intake was protective factor of stillbirth, no matter when the intake began.
Large Scale Mapping of Fractures and Groundwater Pathways in Crystalline Hardrock By AEM
Authors: Chandra Subash , Auken Esben , Maurya Pradip K. , Ahmed Shakeel , Verma Saurabh K. 
Published: January 2019

AbstractIn hardrocks that cover about 20% of the Earth’s surface, it is difficult to locate steady sources for groundwater due to inadequate understanding of the fracture networks. A comprehensive knowledge of fracture distribution at the regional scale is necessary to delineate sustainable aquifers and manage them efficiently. The resistivity maps derived from the airborne electromagnetic (AEM) survey over the Ankasandra watershed in Karnataka, India, reveal sharp and deep zones of low formation resistivity, which indicate groundwater-bearing zones. It is found that some of these zones are hydrogeologically connected through fracture networks resulting in augmented yield. AEM results in combination with an in-depth understanding of the geological structures successfully map these groundwater-saturated fracture networks (or hydrogeological lineaments) that we term as ‘Hydrolins’. As groundwater occurrence is generally associated with lineaments, we analyzed the drilling and geophysical logs from 21 wells within a 380 sq.km area to study the relationships of various lineaments with ‘Hydrolins’, particularly in respect of their groundwater potential. AEM results, though calibrated and correlated with a limited number of well data, revealed a threshold groundwater horizon (TGWH), found to be at 80 m depth for Ankasandra watershed, beyond which a strong correlation exists between the depth of a well and its yield. While the TGWH may differ for different watersheds, the approach presented here can be readily adopted to map sustainable groundwater sources in hardrocks worldwide.
A novel approach for assessing neuromodulation using phase-locked information measured with TMS-EEG
Authors: Miyauchi Eri , Ide Masayuki , Tachikawa Hirokazu , Nemoto Kiyotaka , Arai Tetsuaki , Kawasaki Masahiro 
Published: January 2019

AbstractNeuromodulation therapies such as electroconvulsive therapy (ECT) are used to treat several neuropsychiatric disorders, including major depressive disorder (MDD). Recent work has highlighted the use of combined transcranial magnetic stimulation and electroencephalography (TMS-EEG) to evaluate the therapeutic effects of neuromodulation; particularly, the phase locking factor (PLF) and phase locking value (PLV) can reportedly assess neuromodulation-induced functional changes in cortical networks. To examine changes in TMS-induced PLV and PLF before and after ECT, and their relationship with depression severity in patients with MDD, TMS-EEG and the Montgomery–Åsberg Depression Rating Scale (MADRS; depression severity) were implemented before and after ECT in 10 patients with MDD. Single-pulse TMS was applied to the visual and motor areas to induce phase propagation in the visuo-motor network at rest. Functional changes were assessed using PLF and PLV data. Pre-ECT TMS-induced alpha band (9–12 Hz) PLV was negatively correlated with depression severity, and increments of post-ECT from pre-ECT TMS-induced alpha band PLV were positively correlated with the reduction in depression severity. Moreover, we found a negative correlation between pre-ECT TMS-induced PLF at TMS-destination and depression severity. Finally, differences in post-ECT TMS-induced PLF peak latencies between visual and motor areas were positively correlated with depression severity. TMS-EEG-based PLV and PLF may be used to assess the therapeutic effects of neuromodulation and depressive states, respectively. Furthermore, our results provide new insights about the neural mechanisms of ECT and depression.
Defects and dopant properties of Li3V2(PO4)3
Authors: Kuganathan Navaratnarajah , Chroneos Alexander 
Published: January 2019

AbstractPolyanion phosphate based Li3V2(PO4)3 material has attracted considerable attention as a novel cathode material for potential use in rechargeable lithium ion batteries. The defect chemistry and dopant properties of this material are studied using well-established atomistic scale simulation techniques. The most favourable intrinsic defect process is the Li Frenkel (0.45 eV/defect) ensuring the formation of Li vacancies required for Li diffusion via the vacancy mechanism. Long range lithium paths via the vacancy mechanism were constructed and it is confirmed that the lowest activation energy of migration (0.60 eV) path is three dimensional with curved trajectory. The second most stable defect energy process is calculated to be the anti-site defect, in which Li and V ions exchange their positions (0.91 eV/defect). Tetravalent dopants were considered on both V and P sites in order to form Li vacancies needed for Li diffusion and the Li interstitials to increase the capacity respectively. Doping by Zr on the V site and Si on the P site are calculated to be energetically favourable.
Forming social impressions from voices in native and foreign languages
Authors: Baus Cristina , McAleer Phil , Marcoux Katherine , Belin Pascal , Costa Albert 
Published: January 2019

AbstractWe form very rapid personality impressions about speakers on hearing a single word. This implies that the acoustical properties of the voice (e.g., pitch) are very powerful cues when forming social impressions. Here, we aimed to explore how personality impressions for brief social utterances transfer across languages and whether acoustical properties play a similar role in driving personality impressions. Additionally, we examined whether evaluations are similar in the native and a foreign language of the listener. In two experiments we asked Spanish listeners to evaluate personality traits from different instances of the Spanish word “Hola” (Experiment 1) and the English word “Hello” (Experiment 2), native and foreign language respectively. The results revealed that listeners across languages form very similar personality impressions irrespective of whether the voices belong to the native or the foreign language of the listener. A social voice space was summarized by two main personality traits, one emphasizing valence (e.g., trust) and the other strength (e.g., dominance). Conversely, the acoustical properties that listeners pay attention to when judging other’s personality vary across languages. These results provide evidence that social voice perception contains certain elements invariant across cultures/languages, while others are modulated by the cultural/linguistic background of the listener.
Synthetic CpG-ODN rapidly enriches immune compartments in neonatal chicks to induce protective immunity against bacterial infections
Authors: Gunawardana Thushari , Ahmed Khawaja Ashfaque , Goonewardene Kalhari , Popowich Shelly , Kurukulasuriya Shanika , Karunarathna Ruwani , Gupta Ashish , Lockerbie Betty , Foldvari Marianna , Tikoo Suresh K. , Willson Philip , Gomis Susantha 
Published: January 2019

AbstractOligodeoxynucleotides containing CpG motifs (CpG-ODN) induce innate immunity against bacterial infections. Despite recent advances, how CpG-ODN alone protects against bacterial infections remained elusive. Here, we report for the first time, to our knowledge, that CpG-ODN orchestrates anti-microbial protective immunity by inducing a rapid enrichment of various immune compartments in chickens. In this study, eighteen-day-old embryonated eggs were injected with either 50 µg of CpG-ODN or saline (~n = 90 per group). In the first experiment, four days after CpG-ODN treatment, chicks were challenged subcutaneously with a virulent strain ofEscherichia coli(E.coli) and mortality was monitored for 8 days. We found significant protection, and reduced clinical scores in CpG-ODN treated chicks. To gain insights into mechanisms of protection induced by CpG-ODN, first we investigated cytokine expression kinetics elicited by CpG-ODN. The spleen and lung were collected from embryos or chicks (n = 3–4 per group) at 10 time points post-CpG-ODN inoculation. Multiplex gene analysis (interleukin (IL)-1, IL-4, IL-6, IL-10, IL-18, interferon (IFN)-γ, IFN-α, and lipopolysaccharide induced tumor necrosis factor (LITAF), revealed a significantly higher expression of pro-inflammatory cytokines following CpG-ODN treatment compared to the saline controls. In our study, LITAF stands out in the cytokine profiles of spleen and lungs, underscoring its role in CpG-ODN-induced protection. The third experiment was designed to examine the effects of CpG-ODN on immune cell populations in spleen, lungs, and thymus. Flow cytometry analysis was conducted at 24, 48 and 72 hrs (thymus only collected at 72 hr) after CpG-ODN administration to examine the changes in CD4+and CD8+T-cell subsets, monocyte/macrophage cell populations and their expression of maturation markers (CD40 and CD86). Flow cytometry data indicated a significant enrichment of macrophages, CD4+and CD8+T-cell subsets in both spleen and lungs of CpG-ODN treated embryos and chicks. Macrophages in spleen and lungs showed an upregulation of CD40 but not CD86, whereas thymocytes revealed significantly high CD4 and CD8 expression. Overall, the present study has demonstrated that CpG-ODN provides protection in neonatal chicks againstE.coliinfection not only by eliciting cytokine responses and stimulating immune cells but also through enriching immunological niches in spleen and lungs.
Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers
Authors: Ali Ahmad , Pan Yong-Bao , Wang Qin-Nan , Wang Jin-Da , Chen Jun-Lü , Gao San-Ji 
Published: January 2019

AbstractIn order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus, 79 accessions from five species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense), six accessions of E. arundinaceus, and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis (CE) detection system. A total of 167 polymorphic SSR alleles were identified by CE with a mean value of polymorphic information content (PIC) of 0.92. Genetic diversity parameters among these 115 accessions revealed that Saccharum spp. hybrids were more diverse than those of Saccharum and Erianthus species. Based on the SSR data, the 115 accessions were classified into seven main phylogenetic groups, which corresponded to the Saccharum and Erianthus genera through phylogenetic analysis and principle component analysis (PCA). We propose that seven core SSR primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, SMC24DUQ, mSSCIR3, and mSSCIR43, may have a wide appicability in genotype identification of Saccharum species and Saccharum spp. hybrids. Thus, the information from this study contibites to manage sugarcane genetic resources.
Parieto-frontal mechanisms underlying observation of complex hand-object manipulation
Authors: Errante Antonino , Fogassi Leonardo 
Published: January 2019

AbstractThe observation of actions performed by others is believed to activate the Action Observation Network (AON). Previous evidence suggests that subjects with a specific motor skill show increased activation of the AON during observation of the same skill. The question arises regarding which modulation of the AON occurs during observation of novel complex manipulative actions that are beyond the personal motor repertoire. To address this issue, we carried out a functional MRI study in which healthy volunteers without specific hand motor skills observed videos displaying hand-object manipulation executed by an expert with high manual dexterity, by an actor with intermediate ability or by a naïve subject. The results showed that the observation of actions performed by a naïve model produced stronger activation in a dorso-medial parieto-premotor circuit including the superior parietal lobule and dorsal premotor cortex, compared to observation of an expert actor. Functional connectivity analysis comparing the observation of the naïve model with that of the expert model, revealed increased connectivity between dorsal areas of the AON. This suggests a possible distinction between ventral and dorsal brain circuits involved in the processing of different aspects of action perception, such as kinematics and final action goal.
Towards Remote Lightning Manipulation by Meters-long Plasma Channels Generated by Ultra-Short-Pulse High-Intensity Lasers
Authors: Papeer Jenya , Dey Indranuj , Botton Moti , Henis Zohar , Lad Amit D. , Shaikh Moniruzzaman , Sarkar Deep , Jana Kamalesh , Tata Sheroy , Roy Sudipta Lodh , Ved Yash M. , Kumar G. Ravindra , Zigler Arie 
Published: January 2019

AbstractRemote manipulation (triggering and guiding) of lightning in atmospheric conditions of thunderstorms has been the subject of intense scientific research for decades. High power, ultrashort-pulse lasers are considered attractive in generating plasma channels in air that could serve as conductors/diverters for lightning. However, two fundamental obstacles, namely the limited length and lifetime of such plasma channels prevented their realization to this date. In this paper, we report decisive experimental results of our multi-element broken wire concept that extends the generated plasma channels to the required tens of meters range. We obtain 13-meter-long plasma wire, limited only by our current experimental setup, with plasma conditions that could be sufficient for the leader initiation. This advance, coupled with our demonstrated method of laser heating for long time sustenance of the plasma channel, is a major, significant step towards controlling lightning.
Expression of NOTCH3 exon 16 differentiates Diffuse Large B-cell Lymphoma into molecular subtypes and is associated with prognosis
Authors: Jespersen Ditte Starberg , Schönherz Anna A. , Due Hanne , Bøgsted Martin , Sondergaard Teis Esben , Dybkær Karen 
Published: January 2019

AbstractDiffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with diverse clinical presentation and outcome. Bio-clinical prognostic models including oncogene expression and cell-of-origin phenotyping has been developed, however, approximately 30% of all patients still die from their disease, illustrating the need for additional prognostic biomarkers associating oncogenesis and phenotypic subclasses. Hence, we tested if alternative splice variations have biomarker potential. Initial alternative splicing analysis of human exon array from clinical DLBCL samples identified candidate genes. Experimental validation by ddPCR was performed in a DLBCL cohort classified into ABC/GCB subclasses, B-cell associated gene signatures (BAGS: naive, centroblast, centrocyte, memory, and plasmablast), and vincristine resistant gene signatures. Prognostic potential was assessed for aberrantly spliced transcripts. Thus, NOTCH3 was identified as alternatively spliced, with differential exon 16 depletion (−exon 16) between differentiation associated BAGS subtypes. Predicted vincristine resistant patients of the GCB subclass had significantly downregulated NOTCH3 −exon 16 transcript expression and tended to display adverse overall survival for R-CHOP treated patients. In conclusion, we have identified a specific alternatively spliced NOTCH3 event that differentiate molecular subtypes of DLBCL and display prognostic and predictive biomarker potential in GCB DLBCL.
Injection-Locked, Single Frequency, Multi-core Yb-doped Phosphate Fiber Laser
Authors: Demir V. , Akbulut M. , Nguyen D. T. , Kaneda Y. , Neifeld M. , Peyghambarian N. 
Published: January 2019

AbstractFor the first time, we demonstrate injection locking and single frequency operation of a multi-core Yb-doped phosphate fiber laser (MCF). The 19 MCF laser cores operated in CW mode at 1030 nm. Each laser core was locked to the frequency and polarization of the single-frequency master laser, and produced milliwatts of power with similar lasing thresholds. The pump beam was homogenized with a simple technique to increase uniform lasing behavior of the cores. This behavior was verified using a MCF laser model developed in-house. This unique MCF laser can be useful for applications of coherent, coupled oscillator networks, for example in an all-optical coherent Ising machine configuration.