bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum oscillations from generic surface Fermi arcs and bulk chiral modes in Weyl semimetals
Authors: Zhang Yi , Bulmash Daniel , Hosur Pavan , Potter Andrew C. , Vishwanath Ashvin 
Published: April 2016

AbstractWe re-examine the question of quantum oscillations from surface Fermi arcs and chiral modes in Weyl semimetals. By introducing two tools - semiclassical phase-space quantization and a numerical implementation of a layered construction of Weyl semimetals - we discover several important generalizations to previous conclusions that were implicitly tailored to the special case of identical Fermi arcs on top and bottom surfaces. We show that the phase-space quantization picture fixes an ambiguity in the previously utilized energy-time quantization approach and correctly reproduces the numerically calculated quantum oscillations for generic Weyl semimetals with distinctly curved Fermi arcs on the two surfaces. Based on these methods, we identify a ‘magic’ magnetic-field angle where quantum oscillations become independent of sample thickness, with striking experimental implications. We also analyze the stability of these quantum oscillations to disorder and show that the high-field oscillations are expected to persist in samples whose thickness parametrically exceeds the quantum mean free path.
Mechanism of Paroxetine (Paxil) Inhibition of the Serotonin Transporter
Authors: Davis Bruce A. , Nagarajan Anu , Forrest Lucy R. , Singh Satinder K. 
Published: April 2016

AbstractThe serotonin transporter (SERT) is an integral membrane protein that exploits preexisting sodium-, chloride- and potassium ion gradients to catalyze the thermodynamically unfavorable movement of synaptic serotonin into the presynaptic neuron. SERT has garnered significant clinical attention partly because it is the target of multiple psychoactive agents, including the antidepressant paroxetine (Paxil), the most potent selective serotonin reuptake inhibitor known. However, the binding site and orientation of paroxetine in SERT remain controversial. To provide molecular insight, we constructed SERT homology models based on the Drosophila melanogaster dopamine transporter and docked paroxetine to these models. We tested the predicted binding configurations with a combination of radioligand binding and flux assays on wild-type and mutant SERTs. Our data suggest that the orientation of paroxetine, specifically its fluorophenyl ring, in SERT’s substrate binding site directly depends on this pocket’s charge distribution and thereby provide an avenue toward understanding and enhancing high-affinity antidepressant activity.
Serotonin modulates glutamatergic transmission to neurons in the lateral habenula
Authors: Xie Guiqin , Zuo Wanhong , Wu Liangzhi , Li Wenting , Wu Wei , Bekker Alex , Ye Jiang-Hong 
Published: April 2016

AbstractThe lateral habenula (LHb) is bilaterally connected with serotoninergic raphe nuclei, and expresses high density of serotonin receptors. However, actions of serotonin on the excitatory synaptic transmission to LHb neurons have not been thoroughly investigated. The LHb contains two anatomically and functionally distinct regions: lateral (LHbl) and medial (LHbm) divisions. We compared serotonin’s effects on glutamatergic transmission across the LHb in rat brains. Serotonin bi-directionally and differentially modulated glutamatergic transmission. Serotonin inhibited glutamatergic transmission in higher percentage of LHbl neurons but potentiated in higher percentage of LHbm neurons. Magnitude of potentiation was greater in LHbm than in LHbl. Type 2 and 3 serotonin receptor antagonists attenuated serotonin’s potentiation. The serotonin reuptake blocker, and the type 2 and 3 receptor agonists facilitated glutamatergic transmission in both LHbl and LHbm neurons. Thus, serotonin via activating its type 2, 3 receptors, increased glutamate release at nerve terminals in some LHb neurons. Our data demonstrated that serotonin affects both LHbm and LHbl. Serotonin might play an important role in processing information between the LHb and its downstream-targeted structures during decision-making. It may also contribute to a homeostatic balance underlying the neural circuitry between the LHb and raphe nuclei.
Effect of alternating bioremediation and electrokinetics on the remediation of n-hexadecane-contaminated soil
Authors: Wang Sa , Guo Shuhai , Li Fengmei , Yang Xuelian , Teng Fei , Wang Jianing 
Published: April 2016

AbstractThis study demonstrated the highly efficient degradation of n-hexadecane in soil, realized by alternating bioremediation and electrokinetic technologies. Using an alternating technology instead of simultaneous application prevented competition between the processes that would lower their efficiency. For the consumption of the soil dissolved organic matter (DOM) necessary for bioremediation by electrokinetics, bioremediation was performed first. Because of the utilization and loss of the DOM and water-soluble ions by the microbial and electrokinetic processes, respectively, both of them were supplemented to provide a basic carbon resource, maintain a high electrical conductivity and produce a uniform distribution of ions. The moisture and bacteria were also supplemented. The optimal DOM supplement (20.5 mg·kg−1 glucose; 80–90% of the total natural DOM content in the soil) was calculated to avoid competitive effects (between the DOM and n-hexadecane) and to prevent nutritional deficiency. The replenishment of the water-soluble ions maintained their content equal to their initial concentrations. The degradation rate of n-hexadecane was only 167.0 mg·kg−1·d−1 (1.9%, w/w) for the first 9 days in the treatments with bioremediation or electrokinetics alone, but this rate was realized throughout the whole process when the two technologies were alternated, with a degradation of 78.5% ± 2.0% for the n-hexadecane after 45 days of treatment.
Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel
Authors: Bravo-Gil Nereida , Méndez-Vidal Cristina , Romero-Pérez Laura , González-del Pozo María , Rodríguez-de la Rúa Enrique , Dopazo Joaquín , Borrego Salud , Antiñolo Guillermo 
Published: April 2016

AbstractNext-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management.
Inherently-Forced Tensile Strain in Nanodiamond-Derived Onion-like Carbon: Consequences in Defect-Induced Electrochemical Activation
Authors: Ko Young-Jin , Cho Jung-Min , Kim Inho , Jeong Doo Seok , Lee Kyeong-Seok , Park Jong-Keuk , Baik Young-Joon , Choi Heon-Jin , Lee Seung-Cheol , Lee Wook-Seong 
Published: April 2016

AbstractWe analyzed the nanodiamond-derived onion-like carbon (OLC) as function of synthesis temperature (1000~1400 °C), by high-resolution electron microscopy, electron energy loss spectroscopy, visible-Raman spectroscopy, ultraviolet photoemission spectroscopy, impedance spectroscopy, cyclic voltammetry and differential pulse voltammetry. The temperature dependences of the obtained properties (averaged particle size, tensile strain, defect density, density of states, electron transfer kinetics, and electrochemical oxidation current) unanimously coincided: they initially increased and saturated at 1200 °C. It was attributed to the inherent tensile strains arising from (1) the volume expansion associated with the layer-wise diamond-to-graphite transformation of the core, which caused forced dilation of the outer shells during their thermal synthesis; (2) the extreme curvature of the shells. The former origin was dominant over the latter at the outermost shell, of which the relevant evolution in defect density, DOS and electron transfer kinetics determined the electrochemical performances. In detection of dopamine (DA), uric acid (UA) and ascorbic acid (AA) using the OLC as electrode, their oxidation peak currents were enhanced by factors of 15~60 with annealing temperature. Their limit of detection and the linear range of detection, in the post-treatment-free condition, were as excellent as those of the nano-carbon electrodes post-treated by Pt-decoration, N-doping, plasma, or polymer.
Effectiveness of the Young-Laplace equation at nanoscale
Authors: Liu Hailong , Cao Guoxin 
Published: April 2016

AbstractUsing molecular dynamics (MD) simulations, a new approach based on the behavior of pressurized water out of a nanopore (1.3–2.7 nm) in a flat plate is developed to calculate the relationship between the water surface curvature and the pressure difference across water surface. It is found that the water surface curvature is inversely proportional to the pressure difference across surface at nanoscale and this relationship will be effective for different pore size, temperature and even for electrolyte solutions. Based on the present results, we cannot only effectively determine the surface tension of water and the effects of temperature or electrolyte ions on the surface tension, but also show that the Young-Laplace (Y-L) equation is valid at nanoscale. In addition, the contact angle of water with the hydrophilic material can be further calculated by the relationship between the critical instable pressure of water surface (burst pressure) and nanopore size. Combining with the infiltration behavior of water into hydrophobic microchannels, the contact angle of water at nanoscale can be more accurately determined by measuring the critical pressure causing the instability of water surface, based on which the uncertainty of measuring the contact angle of water at nanoscale is highly reduced.
Effects of Perfluorooctanoic Acid on Metabolic Profiles in Brain and Liver of Mouse Revealed by a High-throughput Targeted Metabolomics Approach
Authors: Yu Nanyang , Wei Si , Li Meiying , Yang Jingping , Li Kan , Jin Ling , Xie Yuwei , Giesy John P. , Zhang Xiaowei , Yu Hongxia 
Published: April 2016

AbstractPerfluorooctanoic acid (PFOA), a perfluoroalkyl acid, can result in hepatotoxicity and neurobehavioral effects in animals. The metabolome, which serves as a connection among transcriptome, proteome and toxic effects, provides pathway-based insights into effects of PFOA. Since understanding of changes in the metabolic profile during hepatotoxicity and neurotoxicity were still incomplete, a high-throughput targeted metabolomics approach (278 metabolites) was used to investigate effects of exposure to PFOA for 28 d on brain and liver of male Balb/c mice. Results of multivariate statistical analysis indicated that PFOA caused alterations in metabolic pathways in exposed individuals. Pathway analysis suggested that PFOA affected metabolism of amino acids, lipids, carbohydrates and energetics. Ten and 18 metabolites were identified as potential unique biomarkers of exposure to PFOA in brain and liver, respectively. In brain, PFOA affected concentrations of neurotransmitters, including serotonin, dopamine, norepinephrine and glutamate in brain, which provides novel insights into mechanisms of PFOA-induced neurobehavioral effects. In liver, profiles of lipids revealed involvement of β-oxidation and biosynthesis of saturated and unsaturated fatty acids in PFOA-induced hepatotoxicity, while alterations in metabolism of arachidonic acid suggesting potential of PFOA to cause inflammation response in liver. These results provide insight into the mechanism and biomarkers for PFOA-induced effects.
A female-biased sex ratio reduces the twofold cost of sex
Authors: Kobayashi Kazuya , Hasegawa Eisuke 
Published: April 2016

AbstractThe evolution of sexual reproduction remains a fascinating enigma in biology. Theoretically, populations of sexual organisms investing half of their resources into producing male offspring that don’t contribute to reproduction should grow at only half the rate of their asexual counterparts. This demographic disadvantage due to male production is known as the twofold cost of sex. However, the question of whether this cost is truly twofold for sexual females remains unanswered. The cost of producing males should decrease when the number of male offspring is reduced. Here, we report a case where the cost of males is actually less than twofold. By measuring the numbers of sexual strain coexisting with asexual strain among thrips, our survey revealed that the sexual strain showed female-biased sex ratios and that the relative frequency of sexual strain is negatively correlated with the proportion of males in the sexual strain. Using computer simulations, we confirmed that a female-biased sex ratio evolves in sexual individuals due to the coexistence of asexual individuals. Our results demonstrate that there is a cost of producing males that depends on the number of males. We therefore conclude that sexual reproduction can evolve with far fewer benefits than previously assumed.
Somatic Mutations and Genetic Variants of NOTCH1 in Head and Neck Squamous Cell Carcinoma Occurrence and Development
Authors: Liu Yu-Fan , Chiang Shang-Lun , Lin Chien-Yu , Chang Jan-Gowth , Chung Chia-Min , Ko Albert Min-Shan , Lin You-Zhe , Lee Chien-Hung , Lee Ka-Wo , Chen Mu-Kuan , Hua Chun-Hung , Tsai Ming-Hsui , Chen Yuan-Chien , Ko Ying-Chin 
Published: April 2016

AbstractA number of genetic variants have been associated with cancer occurrence, however it may be the acquired somatic mutations (SMs) that drive cancer development. This study investigates the potential SMs and related genetic variants associated with the occurrence and development of head and neck squamous cell carcinoma (HNSCC). We identified several SMs in NOTCH1 from whole-exome sequencing and validated them in a 13-year cohort of 128 HNSCC patients using a high-resolution melting analysis and resequencing. Patients who have NOTCH1 SMs show higher 5-year relapse-free recurrence (P = 0.0013) and lower survival proportion (P = 0.0447) when the risk-associated SMs were analysed by Cox proportional hazard models. Interestingly, the NOTCH1 gene rs139994842 that shares linkage with SMs is associated with HNSCC risk (OR = 3.46), increasing when SMs in NOTCH1 are involved (OR = 7.74), and furthermore when there are SMs in conjunction to betel quid chewing (OR = 32.11), which is a related independent environmental risk factor after adjusting for substances use (alcohol, betel quid, cigarettes) and age. The findings indicate that betel quid chewing is highly associated with NOTCH1 SMs (especially with changes in EGF-like domains), and that rs139994842 may potentially serve as an early predictive and prognostic biomarker for the occurrence and development of HNSCC.
Tenascin-C promotes migration of hepatic stellate cells and production of type I collagen
Authors: Ma Jian-Cang , Huang Xin , Shen Ya-Wei , Zheng Chen , Su Qing-Hua , Xu Jin-Kai , Zhao Jun 
Published: April 2016

Abstract
Tenascin-C (TN-C) is an extracellular matrix glycoprotein markedly upregulated during liver fibrosis. The study is performed to explore the role of TN-C during the growth and activation of hepatic stellate cells (HSCs). We found that TN-C was accumulated accompanying with the HSC activation. Our data on cell migration assay revealed that the rTN-C treatment enhanced HSC migration in a dose- and time-dependent manner, but did not influence their proliferation. HSCs transfected with pTARGET-TN-C overexpression vector displayed increased the type I collagen (Col I) production. TN-C overexpression enhanced the process of HSC activation through TGF-β1 signaling. Moreover, the anti-α9β1 integrin antibody treatment blocked the TN-C-driven Col I increase in rat HSCs. Collectively, TN-C had a positive role in activation of HSCs mediated by TGF-β1 and α9β1 integrin, manifesting elevation of Col I production and promotion of cell migration. Our results provide a potential insight for the therapy of hepatic fibrosis.
The interaction between fishbone modes and shear Alfvén waves in tokamak plasmas
Authors: He Hongda , Liu Yueqiang , Dong J.Q. , Hao G.Z. , Wu Tingting , He Zhixiong , Zhao K. 
Published: April 2016

Abstract
The resonant interaction between the energetic particle triggered fishbone mode and the shear Alfvén waves is computationally investigated and firmly demonstrated based on a tokamak plasma equilibrium, using the self-consistent MHD-kinetic hybrid code MARS-K (Liu et al 2008 Phys. Plasmas

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112503). This type of continuum resonance, occurring critically due to the mode’s toroidal rotation in the plasma frame, significantly modifies the eigenmode structure of the fishbone instability, by introducing two large peaks of the perturbed parallel current density near but offside the q  =  1 rational surface (q is the safety factor). The self-consistently computed radial plasma displacement substantially differs from that being assumed in the conventional fishbone theory.
Comparison of acoustic structures between heads of a narrow-ridged finless porpoise fetus and its mother
Authors: Song Zhongchang , Zhang Yu , Wang Xianyan , Wei Chong , Berggren Per 
Published: April 2016

AbstractComputed tomography (CT) was used to compare the tissue structures involved in sound production and reception in a fetus and its maternal body of a female finless porpoise (Neophocaena asiaorientalis sunameri) found stranded at Huian, Fujian Province, China, in April 2014. Qualitative assessment of the CT images revealed the physical development of main acoustic tissues including melon, blubber, mandibular fat, muscle, and connective tissue in a 10-month old fetus. Compared to the maternal body, the cranium of the fetus was not enclosed, air sacs and nasal meatus were both absent, and the maxilla was much thinner. Furthermore, Hounsfield unit (HU) measurements from CT scanning were used to quantify the difference between the fetus and its maternal body for melon, blubber, mandibular fat, muscle, and connective tissue. Statistical analyses revealed significant differences in HU between all 5 structures melon, blubber, mandibular fat, muscle, and connective tissue (P &lt; 0.001) both in the fetus and maternal body. The median HU values of melon, blubber, mandibular fat, and muscle in the fetus (−61.0, −74.0, −24.0, and 25.0, respectively) were higher than those recorded in the maternal body (−85.0, −85.0, −69.0, and 12.0, respectively). However, the median HU value of connective tissue (50.0) in the fetus was lower than that recorded in the maternal body (60.0). The results show that the acoustic tissue structures were not fully developed in the fetus and depending on the actual age of the fetus the structures may not be fully formed by the time of birth. Further studies are needed to determine at what age finless porpoise calves have fully developed the tissue structures needed to produce and use ultrasound beams for echolocation.
FOCUS2: agile and sensitive classification of metagenomics data using a reduced database
Authors: Silva Genivaldo Gueiros Z. , Dutilh Bas E. , Edwards Robert A. 
Published: April 2016

ABSTRACTSummaryMetagenomics approaches rely on identifying the presence of organisms in the microbial community from a set of unknown DNA sequences. Sequence classification has valuable applications in multiple important areas of medical and environmental research. Here we introduce FOCUS2, an update of the previously published computational method FOCUS. FOCUS2 was tested with 10 simulated and 543 real metagenomes demonstrating that the program is more sensitive, faster, and more computationally efficient than existing methods.AvailabilityThe Python implementation is freely available athttps://edwards.sdsu.edu/FOCUS2.Supplementary informationavailable at Bioinformatics online.
Multi-Connection Pattern Analysis: Decoding the Representational Content of Neural Communication
Authors: Li Yuanning , Richardson R. Mark , Ghuman Avniel Singh 
Published: April 2016

AbstractThe lack of multivariate methods for decoding the representational content of interregional neural communication has left it difficult to know what information is represented in distributed brain circuit interactions. Here we present Multi-Connection Pattern Analysis (MCPA), which works by learning mappings between the activity patterns of the populations as a factor of the information being processed. These maps are used to predict the activity from one neural population based on the activity from the other population. Successful MCPA-based decoding indicates the involvement of distributed computational processing and provides a framework for probing the representational structure of the interaction. Simulations demonstrate the efficacy of MCPA in realistic circumstances. Applying MCPA to fMRI data shows that interactions between visual cortex regions are sensitive to information that distinguishes individual natural images, suggesting that image individuation occurs through interactive computation across the visual processing network. MCPA-based representational similarity analyses (RSA) results support models of error coding in interactions among regions of the network. Further RSA analyses relate the non-linear information transformation operations between layers of a computational model (HMAX) of visual processing to the information transformation between regions of the visual processing network. Additionally, applying MCPA to human intracranial electrophysiological data demonstrates that the interaction between occipital face area and fusiform face area contains information about individual faces. Thus, MCPA can be used to assess the information represented in the coupled activity of interacting neural circuits and probe the underlying principles of information transformation between regions.