bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer of motion through a microelectromechanical linkage at nanometer and microradian scales
Authors: Copeland Craig R. , McGray Craig D. , Geist Jon , Aksyuk Vladimir A. , Stavis Samuel M. 
Published: September 2016

AbstractMechanical linkages are fundamentally important for the transfer of motion through assemblies of parts to perform work. Whereas their behavior in macroscale systems is well understood, there are open questions regarding the performance and reliability of linkages with moving parts in contact within microscale systems. Measurement challenges impede experimental studies to answer such questions. In this study, we develop a novel combination of optical microscopy methods that enable the first quantitative measurements at nanometer and microradian scales of the transfer of motion through a microelectromechanical linkage. We track surface features and fluorescent nanoparticles as optical indicators of the motion of the underlying parts of the microsystem. Empirical models allow precise characterization of the electrothermal actuation of the linkage. The transfer of motion between translating and rotating links can be nearly ideal, depending on the operating conditions. The coupling and decoupling of the links agree with an ideal kinematic model to within approximately 5%, and the rotational output is perfectly repeatable to within approximately 20 microradians. However, stiction can result in nonideal kinematics, and input noise on the scale of a few millivolts produces an asymmetric interaction of electrical noise and mechanical play that results in the nondeterministic transfer of motion. Our study establishes a new approach towards testing the performance and reliability of the transfer of motion through assemblies of microscale parts, opening the door to future studies of complex microsystems.
Inhibition of ROS and upregulation of inflammatory cytokines by FoxO3a promotes survival against Salmonella typhimurium
Authors: Joseph Julie , Ametepe Emmanuelle S. , Haribabu Naveen , Agbayani Gerard , Krishnan Lakshmi , Blais Alexandre , Sad Subash 
Published: September 2016

AbstractVirulent intracellular pathogens, such as the Salmonella species, engage numerous virulence factors to subvert host defence mechanisms to induce a chronic infection that leads to typhoid or exacerbation of other chronic inflammatory conditions. Here we show the role of the forkhead transcription factor FoxO3a during infection of mice with Salmonella typhimurium (ST). Although FoxO3a signalling does not affect the development of CD8+ T cell responses to ST, FoxO3a has an important protective role, particularly during the chronic stage of infection, by limiting the persistence of oxidative stress. Furthermore, FoxO3a signalling regulates ERK signalling in macrophages, which results in the maintenance of a proinflammatory state. FoxO3a signalling does not affect cell proliferation or cell death. Thus, these results reveal mechanisms by which FoxO3a promotes host survival during infection with chronic, virulent intracellular bacteria.
Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data
Authors: Zhang Jianwei , Chen Ling-Ling , Sun Shuai , Kudrna Dave , Copetti Dario , Li Weiming , Mu Ting , Jiao Wen-Biao , Xing Feng , Lee Seunghee , Talag Jayson , Song Jia-Ming , Du Bogu , Xie Weibo , Luo Meizhong , Maldonado Carlos Ernesto , Goicoechea Jose Luis , Xiong Lizhong , Wu Changyin , Xing Yongzhong , Zhou Dao-xiu , Yu Sibin , Zhao Yu , Wang Gongwei , Yu Yeisoo , Luo Yijie , Hurtado Beatriz Elena Padilla , Danowitz Ann , Wing Rod A. , Zhang Qifa 
Published: September 2016

AbstractOver the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.
Surface energies of elemental crystals
Authors: Tran Richard , Xu Zihan , Radhakrishnan Balachandran , Winston Donald , Sun Wenhao , Persson Kristin A. , Ong Shyue Ping 
Published: September 2016

AbstractThe surface energy is a fundamental property of the different facets of a crystal that is crucial to the understanding of various phenomena like surface segregation, roughening, catalytic activity, and the crystal’s equilibrium shape. Such surface phenomena are especially important at the nanoscale, where the large surface area to volume ratios lead to properties that are significantly different from the bulk. In this work, we present the largest database of calculated surface energies for elemental crystals to date. This database contains the surface energies of more than 100 polymorphs of about 70 elements, up to a maximum Miller index of two and three for non-cubic and cubic crystals, respectively. Well-known reconstruction schemes are also accounted for. The database is systematically improvable and has been rigorously validated against previous experimental and computational data where available. We will describe the methodology used in constructing the database, and how it can be accessed for further studies and design of materials.
Discovery of parvovirus-related sequences in an unexpected broad range of animals
Authors: François S. , Filloux D. , Roumagnac P. , Bigot D. , Gayral P. , Martin D. P. , Froissart R. , Ogliastro M. 
Published: September 2016

AbstractOur knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.
Light-induced rotations of chiral birefringent microparticles in optical tweezers
Authors: Donato M. G. , Mazzulla A. , Pagliusi P. , Magazzù A. , Hernandez R. J. , Provenzano C. , Gucciardi P. G. , Maragò O. M. , Cipparrone G. 
Published: September 2016

AbstractWe study the rotational dynamics of solid chiral and birefringent microparticles induced by elliptically polarized laser light in optical tweezers. We find that both reflection of left circularly polarized light and residual linear retardance affect the particle dynamics. The degree of ellipticity of laser light needed to induce rotations is found. The experimental results are compared with analytical calculations of the transfer of angular moment from elliptically polarized light to chiral birefringent particles.
Camouflage and Clutch Survival in Plovers and Terns
Authors: Stoddard Mary Caswell , Kupán Krisztina , Eyster Harold N. , Rojas-Abreu Wendoly , Cruz-López Medardo , Serrano-Meneses Martín Alejandro , Küpper Clemens 
Published: September 2016

AbstractAnimals achieve camouflage through a variety of mechanisms, of which background matching and disruptive coloration are likely the most common. Although many studies have investigated camouflage mechanisms using artificial stimuli and in lab experiments, less work has addressed camouflage in the wild. Here we examine egg camouflage in clutches laid by ground-nesting Snowy Plovers Charadrius nivosus and Least Terns Sternula antillarum breeding in mixed aggregations at Bahía de Ceuta, Sinaloa, Mexico. We obtained digital images of clutches laid by both species. We then calibrated the images and used custom computer software and edge detection algorithms to quantify measures related to three potential camouflage mechanisms: pattern complexity matching, disruptive effects and background color matching. Based on our image analyses, Snowy Plover clutches, in general, appeared to be more camouflaged than Least Tern clutches. Snowy Plover clutches also survived better than Least Tern clutches. Unexpectedly, variation in clutch survival was not explained by any measure of egg camouflage in either species. We conclude that measures of egg camouflage are poor predictors of clutch survival in this population. The behavior of the incubating parents may also affect clutch predation. Determining the significance of egg camouflage requires further testing using visual models and behavioral experiments.
Probing the causal role of prestimulus interregional synchrony for perceptual integration via tACS
Authors: Stonkus Rolandas , Braun Verena , Kerlin Jess R. , Volberg Gregor , Hanslmayr Simon 
Published: September 2016

AbstractThe phase of prestimulus oscillations at 7–10 Hz has been shown to modulate perception of briefly presented visual stimuli. Specifically, a recent combined EEG-fMRI study suggested that a prestimulus oscillation at around 7 Hz represents open and closed windows for perceptual integration by modulating connectivity between lower order occipital and higher order parietal brain regions. We here utilized brief event-related transcranial alternating current stimulation (tACS) to specifically modulate this prestimulus 7 Hz oscillation, and the synchrony between parietal and occipital brain regions. To this end we tested for a causal role of this particular prestimulus oscillation for perceptual integration. The EEG was acquired at the same time allowing us to investigate frequency specific after effects phase-locked to stimulation offset. On a behavioural level our results suggest that tACS did modulate perceptual integration, however, in an unexpected manner. On an electrophysiological level our results suggest that brief tACS does induce oscillatory entrainment, as visible in frequency specific activity phase-locked to stimulation offset. Together, our results do not strongly support a causal role of prestimulus 7 Hz oscillations for perceptual integration. However, our results suggest that brief tACS is capable of modulating oscillatory activity in a temporally sensitive manner.
Quantifying evolutionary dynamics from variant-frequency time series
Authors: Khatri Bhavin S. 
Published: September 2016

AbstractFrom Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.
Low serum magnesium levels are associated with impaired peripheral nerve function in type 2 diabetic patients
Authors: Chu Chen , Zhao Weijing , Zhang Yinan , Li Lu , Lu Jingyi , Jiang Lan , Wang Congrong , Jia Weiping 
Published: September 2016

AbstractThe aim of this study was to explore the relationship between serum magnesium and peripheral nerve function in patients with type 2 diabetes (T2DM). A total of 978 T2DM patients were included in the study. Patients were divided into tertiles according to serum magnesium concentration (low tertile: ≤0.85 mmol/L; medium tertile: 0.85 to 0.92 mmol/L; and high tertile: >0.92 mmol/L). All participants underwent nerve conduction (NC) studies. Composite z scores of conduction velocity, latency, and amplitude were constructed, respectively. The serum magnesium levels were significantly lower in patients with abnormal NC than in those with normal NC (0.87 [0.82, 0.92] vs. 0.88 [0.83, 0.93] mmol/L, P = 0.048). The composite z score of amplitude significantly increased with increasing tertiles of magnesium (−0.60 ± 0.02 vs. −0.57 ± 0.02 vs. −0.48 ± 0.03, P for trend = 0.001). After adjusting for all potential confounders, lower serum magnesium levels were still associated with lower composite z score of amplitude (β = 0.095, P = 0.014). In patients with T2DM, lower serum magnesium levels were significantly associated with lower composite z score of amplitude, indicating magnesium might affect peripheral nerve function through axonal degeneration.
Elucidating the Performance Limitations of Lithium-ion Batteries due to Species and Charge Transport through Five Characteristic Parameters
Authors: Jiang Fangming , Peng Peng 
Published: September 2016

AbstractUnderutilization due to performance limitations imposed by species and charge transports is one of the key issues that persist with various lithium-ion batteries. To elucidate the relevant mechanisms, two groups of characteristic parameters were proposed. The first group contains three characteristic time parameters, namely: (1) te, which characterizes the Li-ion transport rate in the electrolyte phase, (2) ts, characterizing the lithium diffusion rate in the solid active materials, and (3) tc, describing the local Li-ion depletion rate in electrolyte phase at the electrolyte/electrode interface due to electrochemical reactions. The second group contains two electric resistance parameters: Re and Rs, which represent respectively, the equivalent ionic transport resistance and the effective electronic transport resistance in the electrode. Electrochemical modeling and simulations to the discharge process of LiCoO2 cells reveal that: (1) if te, ts and tc are on the same order of magnitude, the species transports may not cause any performance limitations to the battery; (2) the underlying mechanisms of performance limitations due to thick electrode, high-rate operation, and large-sized active material particles as well as effects of charge transports are revealed. The findings may be used as quantitative guidelines in the development and design of more advanced Li-ion batteries.
Deep Networks Can Resemble Human Feed-forward Vision in Invariant Object Recognition
Authors: Kheradpisheh Saeed Reza , Ghodrati Masoud , Ganjtabesh Mohammad , Masquelier Timothée 
Published: September 2016

AbstractDeep convolutional neural networks (DCNNs) have attracted much attention recently, and have shown to be able to recognize thousands of object categories in natural image databases. Their architecture is somewhat similar to that of the human visual system: both use restricted receptive fields, and a hierarchy of layers which progressively extract more and more abstracted features. Yet it is unknown whether DCNNs match human performance at the task of view-invariant object recognition, whether they make similar errors and use similar representations for this task, and whether the answers depend on the magnitude of the viewpoint variations. To investigate these issues, we benchmarked eight state-of-the-art DCNNs, the HMAX model, and a baseline shallow model and compared their results to those of humans with backward masking. Unlike in all previous DCNN studies, we carefully controlled the magnitude of the viewpoint variations to demonstrate that shallow nets can outperform deep nets and humans when variations are weak. When facing larger variations, however, more layers were needed to match human performance and error distributions, and to have representations that are consistent with human behavior. A very deep net with 18 layers even outperformed humans at the highest variation level, using the most human-like representations.
Silver-nanoparticles-modified biomaterial surface resistant to staphylococcus: new insight into the antimicrobial action of silver
Authors: Wang Jiaxing , Li Jinhua , Guo Geyong , Wang Qiaojie , Tang Jin , Zhao Yaochao , Qin Hui , Wahafu Tuerhongjiang , Shen Hao , Liu Xuanyong , Zhang Xianlong 
Published: September 2016

AbstractTitanium implants are widely used clinically, but postoperative implant infection remains a potential severe complication. The purpose of this study was to investigate the antibacterial activity of nano-silver(Ag)-functionalized Ti surfaces against epidemic Staphylococcus from the perspective of the regulation of biofilm-related genes and based on a bacteria-cell co-culture study. To achieve this goal, two representative epidemic Staphylococcus strains, Staphylococcus epidermidis (S. epidermidis, RP62A) and Staphylococcus aureus (S. aureus, USA 300), were used, and it was found that an Ag-nanoparticle-modified Ti surface could regulate the expression levels of biofilm-related genes (icaA and icaR for S. epidermidis; fnbA and fnbB for S. aureus) to inhibit bacterial adhesion and biofilm formation. Moreover, a novel bacteria-fibroblast co-culture study revealed that the incorporation of Ag nanoparticles on such a surface can help mammalian cells to survive, adhere and spread more successfully than Staphylococcus. Therefore, the modified surface was demonstrated to possess a good anti-infective capability against both sessile bacteria and planktonic bacteria through synergy between the effects of Ag nanoparticles and ion release. This work provides new insight into the antimicrobial action and mechanism of Ag-nanoparticle-functionalized Ti surfaces with bacteria-killing and cell-assisting capabilities and paves the way towards better satisfying the clinical needs.
Association between ABCB1 polymorphisms and haplotypes and Alzheimer’s disease: a meta-analysis
Authors: Zhong Xin , Liu Ming-Yan , Sun Xiao-Hong , Wei Min-Jie 
Published: September 2016

AbstractAlthough several epidemiological studies have investigated the association between ATP-binding cassette subfamily B member 1 (ABCB1) gene polymorphisms and Alzheimer’s disease (AD) susceptibility, controversial results exist. Here, we performed a meta-analysis to assess whether ABCB1 polymorphisms 3435C > T (rs1045642), 2677G > T/A (rs2032582), 1236C > T (rs1128503) and haplotypes were associated with AD risk. Nine independent publications were included and analyzed. Crude odds ratio (OR) and 95% confidence interval (CI) were applied to investigate the strength of the association. Sensitivity analysis was conducted to measure the robustness of our analysis. A funnel plot and trim and fill method were used to test and adjust for publication bias. The results showed a significant association between the 3435C > T single nucleotide polymorphism (SNP) and AD susceptibility (CT vs. CC: OR = 1.24, 95% CI = 1.06–1.45, P = 0.01; CT + TT vs. CC: OR = 1.21, 95% CI = 1.04–1.41, P = 0.01) in the total population, as well as in Caucasian subgroup. The 2677G > T/A SNP was related to a decreased AD risk in Caucasian subgroup (TT + TA + AA vs. GT + GA + GG: OR = 0.68, 95% CI = 0.47–0.98, P = 0.04). Moreover, the ABCB1 haplotype analysis showed that the 1236T/2677T/3435C haplotype was associated with a higher risk of AD (OR = 1.99, 95% CI = 1.24–3.18, P = 0.00). Our results suggest that the ABCB1 3435C > T SNP, the 2677G > T/A SNP and 1236T/2677T/3435C haplotype are significantly associated with AD susceptibility.
Origin of the low critical observing temperature of the quantum anomalous Hall effect in V-doped (Bi, Sb)2Te3 film
Authors: Li W. , Claassen M. , Chang Cui-Zu , Moritz B. , Jia T. , Zhang C. , Rebec S. , Lee J. J. , Hashimoto M. , Lu D.-H. , Moore R. G. , Moodera J. S. , Devereaux T. P. , Shen Z.-X. 
Published: September 2016

AbstractThe experimental realization of the quantum anomalous Hall (QAH) effect in magnetically-doped (Bi, Sb)2Te3 films stands out as a landmark of modern condensed matter physics. However, ultra-low temperatures down to few tens of mK are needed to reach the quantization of Hall resistance, which is two orders of magnitude lower than the ferromagnetic phase transition temperature of the films. Here, we systematically study the band structure of V-doped (Bi, Sb)2Te3 thin films by angle-resolved photoemission spectroscopy (ARPES) and show unambiguously that the bulk valence band (BVB) maximum lies higher in energy than the surface state Dirac point. Our results demonstrate clear evidence that localization of BVB carriers plays an active role and can account for the temperature discrepancy.
Clustering drug-drug interaction networks with energy model layouts: community analysis and drug repurposing
Authors: Udrescu Lucreţia , Sbârcea Laura , Topîrceanu Alexandru , Iovanovici Alexandru , Kurunczi Ludovic , Bogdan Paul , Udrescu Mihai 
Published: September 2016

AbstractAnalyzing drug-drug interactions may unravel previously unknown drug action patterns, leading to the development of new drug discovery tools. We present a new approach to analyzing drug-drug interaction networks, based on clustering and topological community detection techniques that are specific to complex network science. Our methodology uncovers functional drug categories along with the intricate relationships between them. Using modularity-based and energy-model layout community detection algorithms, we link the network clusters to 9 relevant pharmacological properties. Out of the 1141 drugs from the DrugBank 4.1 database, our extensive literature survey and cross-checking with other databases such as Drugs.com, RxList, and DrugBank 4.3 confirm the predicted properties for 85% of the drugs. As such, we argue that network analysis offers a high-level grasp on a wide area of pharmacological aspects, indicating possible unaccounted interactions and missing pharmacological properties that can lead to drug repositioning for the 15% drugs which seem to be inconsistent with the predicted property. Also, by using network centralities, we can rank drugs according to their interaction potential for both simple and complex multi-pathology therapies. Moreover, our clustering approach can be extended for applications such as analyzing drug-target interactions or phenotyping patients in personalized medicine applications.