bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct comparison of performance of single nucleotide variant calling in human genome with alignment-based and assembly-based approaches
Authors: Wu Leihong , Yavas Gokhan , Hong Huixiao , Tong Weida , Xiao Wenming 
Published: September 2017

AbstractComplementary to reference-based variant detection, recent studies revealed that many novel variants could be detected with de novo assembled genomes. To evaluate the effect of reads coverage and the accuracy of assembly-based variant calling, we simulated short reads containing more than 3 million of single nucleotide variants (SNVs) from the whole human genome and compared the efficiency of SNV calling between the assembly-based and alignment-based calling approaches. We assessed the quality of the assembled contig and found that a minimum of 30X coverage of short reads was needed to ensure reliable SNV calling and to generate assembled contigs with a good coverage of genome and genes. In addition, we observed that the assembly-based approach had a much lower recall rate and precision comparing to the alignment-based approach that would recover 99% of imputed SNVs. We observed similar results with experimental reads for NA24385, an individual whose germline variants were well characterized. Although there are additional values for SNVs detection, the assembly-based approach would have great risk of false discovery of novel SNVs. Further improvement of de novo assembly algorithms are needed in order to warrant a good completeness of genome with haplotype resolved and high fidelity of assembled sequences.
Near-optimal integration of facial form and motion
Authors: Dobs Katharina , Ma Wei Ji , Reddy Leila 
Published: September 2017

AbstractHuman perception consists of the continuous integration of sensory cues pertaining to the same object. While it has been fairly well shown that humans use an optimal strategy when integrating low-level cues proportional to their relative reliability, the integration processes underlying high-level perception are much less understood. Here we investigate cue integration in a complex high-level perceptual system, the human face processing system. We tested cue integration of facial form and motion in an identity categorization task and found that an optimal model could successfully predict subjects’ identity choices. Our results suggest that optimal cue integration may be implemented across different levels of the visual processing hierarchy.
The Role of High Frequency Ultrasonography in Diagnosis of Acute Closed Mallet Finger Injury
Authors: Wang Tiezheng , Qi Hengtao , Teng Jianbo , Wang Zengtao , Zhao Bin 
Published: September 2017

AbstractTo evaluate the role of high frequency ultrasonography in diagnosis of acute closed mallet finger injury. 36 patients diagnosed with mallet finger were included in this study. All patients underwent ultrasonography, magnetic resonance imaging(MRI) and X-ray examinations. A new kind of classification of acute mallet finger injury based on ultrasonography findings was described. The difference in terms of extensor tendon injury and bony fragment identification ability among the three types of examinations were described respectively. Either an injury of extensor digital tendon or an avulsion fracture of distal phalangeal base was identified clearly on ultrasonography. Among the 36 cases, avulsion fracture of the distal phalangeal base was found without extensor tendon rupture in Type A, complete rupture of the extensor tendon was found without avulsion fracture in Type B, and contusion of the extensor tendon was found in Type C. Compared with X-ray, ultrasonography and MRI could show the extensor tendon injury clearly. While compared with MRI, ultrasonography and X-ray was more sensitive in showing bony fragment. High frequency ultrasonography could be an accurate, reliable, and non-invasive diagnostic imaging method in diagnosis of acute close mallet finger injury.
The network of plants volatile organic compounds
Authors: Vivaldo Gianna , Masi Elisa , Taiti Cosimo , Caldarelli Guido , Mancuso Stefano 
Published: September 2017

AbstractPlants emission of Volatile Organic Compounds (VOCs) is involved in a wide class of ecological functions, as VOCs play a crucial role in plants interactions with biotic and abiotic factors. Accordingly, they vary widely across species and underpin differences in ecological strategy. In this paper, VOCs spontaneously emitted by 109 plant species (belonging to 56 different families) have been qualitatively and quantitatively analysed in order to provide an alternative classification of plants species. In particular, by using bipartite networks methodology from Complex Network Theory, and through the application of community detection algorithms, we show that is possible to classify species according to chemical classes such as terpenes and sulfur compounds. Such complex network analysis allows to uncover hidden plants relationships related to their evolutionary and adaptation to the environment story.
Hardware emulation of stochastic p-bits for invertible logic
Authors: Pervaiz Ahmed Zeeshan , Ghantasala Lakshmi Anirudh , Camsari Kerem Yunus , Datta Supriyo 
Published: September 2017

AbstractThe common feature of nearly all logic and memory devices is that they make use of stable units to represent 0’s and 1’s. A completely different paradigm is based on three-terminal stochastic units which could be called “p-bits”, where the output is a random telegraphic signal continuously fluctuating between 0 and 1 with a tunable mean. p-bits can be interconnected to receive weighted contributions from others in a network, and these weighted contributions can be chosen to not only solve problems of optimization and inference but also to implement precise Boolean functions in an inverted mode. This inverted operation of Boolean gates is particularly striking: They provide inputs consistent to a given output along with unique outputs to a given set of inputs. The existing demonstrations of accurate invertible logic are intriguing, but will these striking properties observed in computer simulations carry over to hardware implementations? This paper uses individual micro controllers to emulate p-bits, and we present results for a 4-bit ripple carry adder with 48 p-bits and a 4-bit multiplier with 46 p-bits working in inverted mode as a factorizer. Our results constitute a first step towards implementing p-bits with nano devices, like stochastic Magnetic Tunnel Junctions.
On the consistency of seismically imaged lower mantle slabs
Authors: Shephard G. E. , Matthews K. J. , Hosseini K. , Domeier M. 
Published: September 2017

AbstractThe geoscience community is increasingly utilizing seismic tomography to interpret mantle heterogeneity and its links to past tectonic and geodynamic processes. To assess the robustness and distribution of positive seismic anomalies, inferred as subducted slabs, we create a set of vote maps for the lower mantle with 14 global P-wave or S-wave tomography models. Based on a depth-dependent threshold metric, an average of 20% of any given tomography model depth is identified as a potential slab. However, upon combining the 14 models, the most consistent positive wavespeed features are identified by an increasing vote count. An overall peak in the most robust anomalies is found between 1000–1400 km depth, followed by a decline to a minimum around 2000 km. While this trend could reflect reduced tomographic resolution in the middle mantle, we show that it may alternatively relate to real changes in the time-dependent subduction flux and/or a mid-lower mantle viscosity increase. An apparent secondary peak in agreement below 2500 km depth may reflect the degree-two lower mantle slow seismic structures. Vote maps illustrate the potential shortcomings of using a limited number or type of tomography models and slab threshold criteria.
Noble UV protective agent for Bacillus thuringiensis based on a combination of graphene oxide and olive oil
Authors: Maghsoudi Shahab , Jalali Elham 
Published: September 2017

AbstractThe focus of this study is investigating the performance of graphene oxide (GO) in the protective effect of olive oil on Bacillus thuringiensis (Bt) after being exposed to UV radiations. Biological pesticides Bt subsp. Kurstaki is one of the most important biological control agents. We compared the protective effect of two UV protectant; GO and olive oil and also the combination of both, on the stability of the formulation of Bt after exposure to UV radiations. Spore viability was measured for protective effect and bioassay test was performed on the formulations of Bt. The combination of GO and olive oil revealed the highest viabilities of 50.62% after 96 h exposure to UV radiation, while viabilities of free spore, olive oil formulation and GO formulation were 32.54%, 37.19%,and 45.20%, respectively. The mortality of irradiated combination formulation on second-instar larvae Ephestia Kuehniella was 68.89%, while the same parameter for free spore, olive oil formulation and GO formulation were 40%, 46.66%,and 56%, respectively.
Linking primary producer diversity and food quality effects on herbivores: A biochemical perspective
Authors: Marzetz Vanessa , Koussoroplis Apostolos-Manuel , Martin-Creuzburg Dominik , Striebel Maren , Wacker Alexander 
Published: September 2017

AbstractBiodiversity can strongly influence trophic interactions. The nutritional quality of prey communities and how it is related to the prey diversity is suspected to be a major driver of biodiversity effects. As consumer growth can be co-limited by the supply of several biochemical components, biochemically diverse prey communities should promote consumer growth. Yet, there is no clear consensus on how prey specific diversity is linked to community biochemical diversity since previous studies have considered only single nutritional quality traits. Here, we demonstrate that phytoplankton biochemical traits (fatty acids and sterols) can to a large extent explain Daphnia magna growth and its apparent dependence on phytoplankton species diversity. We find strong correlative evidence between phytoplankton species diversity, biochemical diversity, and growth. The relationship between species diversity and growth was partially explained by the fact that in many communities Daphnia was co-limited by long chained polyunsaturated fatty acids and sterols, which was driven by different prey taxa. We suggest that biochemical diversity is a good proxy for the presence of high food quality taxa, and a careful consideration of the distribution of the different biochemical traits among species is necessary before concluding about causal links between species diversity and consumer performance.
Phylogeographic studies of schizothoracine fishes on the central Qinghai-Tibet Plateau reveal the highest known glacial microrefugia
Authors: Liang Yangyang , He Dekui , Jia Yintao , Sun Heying , Chen Yifeng 
Published: September 2017

AbstractPleistocene climatic oscillations have greatly influenced the evolutionary history and distribution pattern of most extant species. However, their effects on species on the Qinghai-Tibet Plateau (QTP) are not well understood. To investigate the effects of past climatic shifts, particularly the Last Glacial Maximum (LGM), on plateau fish, we analysed the phylogeographic structure and demographic history of five closely related taxa of the subfamily Schizothoracinae, a representative endemic taxon of the QTP, from nine endorheic lakes on the central QTP and three peripheral exorheic rivers using the mitochondrial control region (D-loop) sequence and 12 microsatellite (SSR) markers. Phylogram from D-loop haplotypes revealed two well-supported lineages (North and South) separated by the Tanggula Mountains. The results from the D-loop and SSR revealed that endorheic populations possess high genetic diversity and a unique genetic structure. The most recent demographic expansion occurred post-LGM for most endorheic populations and in the last interglacial period for Siling Co and all exorheic populations. Phylogeographic structure, together with species distribution modelling, supports the scenario of multiple glacial refugia on the QTP during the LGM and suggests that Siling Co (4540 m asl) is a cryptic glacial microrefugia for plateau fish, which would be the highest glacial microrefugia known.
Responses of plant species diversity and soil physical-chemical-microbial properties to Phragmites australis invasion along a density gradient
Authors: Uddin MD Nazim , Robinson Randall William 
Published: September 2017

AbstractThe invasion of ecosystems by strongly colonising plants such as Phragmites australis is viewed as one of the greatest threats to plant diversity and soil properties. This study compared a range of diversity measures including soil properties and mycorrhizal potential under different degrees of Phragmites density among three populations in coastal wetland, Victoria, Australia. Species richness, evenness and Shanon-Wiener index had significantly higher values in low degree of Phragmites density in all populations. Higher densities had the lowest diversity, with Shannon-Wiener index = 0 and Simpson’s index = 1 indicating its mono-specificity. Significant alterations in soil properties associated with different degrees of Phragmites density were noticed. These had interactive effects (population × density) on water content, dehydrogenase activity, microbial biomass (C, N and P) but not on pH, electrical conductivity, phenolics, organic carbon, and spore density. Furthermore, the study elucidated decrease of competitive abilities of native plants, by interfering with formation of mycorrhizal associations and biomass. Overall, our results suggest that significant ecological alterations in vegetation and soil variables (including mycorrhizal potential) were strongly dependent on Phragmites density. Such changes may lead to an important role in process of Phragmites invasion through disruption of functional relationships amongst those variables.
Glycosylation-dependent galectin-1/neuropilin-1 interactions promote liver fibrosis through activation of TGF-β- and PDGF-like signals in hepatic stellate cells
Authors: Wu Ming-Heng , Chen Yuh-Ling , Lee Kuen-Haur , Chang Che-Chang , Cheng Tsai-Mu , Wu Szu-Yuan , Tu Chao-Chiang , Tsui Wan-Lin 
Published: September 2017

AbstractConcomitant expressions of glycan-binding proteins and their bound glycans regulate many pathophysiologic processes, but this issue has not been addressed in liver fibrosis. Activation of hepatic stellate cells (HSCs) is a rate-limiting step in liver fibrosis and is an important target for liver fibrosis therapy. We previously reported that galectin (Gal)-1, a β-galactoside-binding protein, regulates myofibroblast homeostasis in oral carcinoma and wound healing, but the role of Gal-1 in HSC migration and activation is unclear. Herein, we report that Gal-1 and its bound glycans were highly expressed in fibrotic livers and activated HSCs. The cell-surface glycome of activated HSCs facilitated Gal-1 binding, which upon recognition of the N-glycans on neuropilin (NRP)-1, activated platelet-derived growth factor (PDGF)- and transforming growth factor (TGF)-β-like signals to promote HSC migration and activation. In addition, blocking endogenous Gal-1 expression suppressed PDGF- and TGF-β1-induced signaling, migration, and gene expression in HSCs. Methionine and choline-deficient diet (MCD)-induced collagen deposition and HSC activation were attenuated in Gal-1-null mice compared to wild-type mice. In summary, we concluded that glycosylation-dependent Gal-1/NRP-1 interactions activate TGF-β and PDGF-like signaling to promote the migration and activation of HSCs. Therefore, targeting Gal-1/NRP-1 interactions could be developed into liver fibrosis therapy.
Lattice light sheet imaging of membrane nanotubes between human breast cancer cells in culture and in brain metastases
Authors: Parker Ian , Evans Katrina T. , Ellefsen Kyle , Lawson Devon A. , Smith Ian F. 
Published: September 2017

AbstractMembrane nanotubes are cytosolic protrusions with diameters <1 µm that extend between cells separated by tens of µm. They mediate several forms of intercellular communication and are upregulated in diverse diseases. Difficulties in visualizing and studying nanotubes within intact tissues have, however, prompted skepticism regarding their in vivo relevance, and most studies have been confined to cell culture systems. Here, we introduce lattice-light sheet imaging of MDA-MB-231 human breast cancer cells genetically engineered to brightly express membrane–targeted GFP as a promising approach to visualize membrane nanotubes in vitro and in situ. We demonstrate that cultured cells form multiple nanotubes that mediate intercellular communication of Ca2+ signals and actively traffic GFP-tagged membrane vesicles along their length. Furthermore, we directly visualize nanotubes in situ, interconnecting breast cancer cells in live acute brain slices from an experimental mouse model of breast cancer brain metastasis. This amenable experimental system should facilitate the transition of the study of intercellular communication by membrane nanotubes from cell culture to the whole animal.
The Chemical Form of Metal Species Released from Corroded Taper Junctions of Hip Implants: Synchrotron Analysis of Patient Tissue
Authors: Di Laura Anna , Quinn Paul D. , Panagiotopoulou Vasiliki C. , Hothi Harry S. , Henckel Johann , Powell Jonathan J. , Berisha Fitim , Amary Fernanda , Mosselmans J. Fred W. , Skinner John A. , Hart Alister J. 
Published: September 2017

AbstractThe mechanisms of metal release from the articulation at the head cup bearing and the tapered junctions of orthopaedic hip implants are known to differ and the debris generated varies in size, shape and volume. Significantly less metal is lost from the taper junction between Cobalt-Chromium-Molybdenum (CoCrMo) and Titanium (Ti) components (fretting-corrosion dominant mechanism), when compared to the CoCrMo bearing surfaces (wear-corrosion dominant mechanism). Corrosion particles from the taper junction can lead to Adverse Reactions to Metal Debris (ARMD) similar to those seen with CoCrMo bearings. We used synchrotron methods to understand the modes underlying clinically significant tissue reactions to Co, Cr and Ti by analysing viable peri-prosthetic tissue. Cr was present as Cr2O3 in the corroded group in addition to CrPO4 found in the metal-on-metal (MoM) group. Interestingly, Ti was present as TiO2 in an amorphous rather than rutile or anatase physical form. The metal species were co-localized in the same micron-scale particles as result of corrosion processes and in one cell type, the phagocytes. This work gives new insights into the degradation products from metal devices as well as guidance for toxicological studies in humans.
Stat3 as a potential therapeutic target for rheumatoid arthritis
Authors: Oike Takatsugu , Sato Yuiko , Kobayashi Tami , Miyamoto Kana , Nakamura Satoshi , Kaneko Yosuke , Kobayashi Shu , Harato Kengo , Saya Hideyuki , Matsumoto Morio , Nakamura Masaya , Niki Yasuo , Miyamoto Takeshi 
Published: September 2017

AbstractRheumatoid arthritis (RA) is a multi-factorial disease characterized by chronic inflammation and destruction of multiple joints. To date, various biologic treatments for RA such as anti-tumor necrosis factor alpha antibodies have been developed; however, mechanisms underlying RA development remain unclear and targeted therapy for this condition has not been established. Here, we provide evidence that signal transducer and activator of transcription 3 (Stat3) promotes inflammation and joint erosion in a mouse model of arthritis. Stat3 global KO mice show early embryonic lethality; thus, we generated viable Stat3 conditional knockout adult mice and found that they were significantly resistant to collagen-induced arthritis (CIA), the most common RA model, compared with controls. We then used anin vitroculture system to screen ninety-six existing drugs to select Stat3 inhibitors and selected five candidate inhibitors. Among them, three significantly inhibited development of arthritis and joint erosion in CIA wild-type mice. These findings suggest that Stat3 inhibitors may serve as promising drugs for RA therapy.
Signatures of the Kondo effect in VSe2
Authors: Barua Sourabh , Hatnean M. Ciomaga , Lees M. R. , Balakrishnan G. 
Published: September 2017

AbstractVSe2 is a transition metal dichaclogenide which has a charge- density wave transition that has been well studied. We report on a low-temperature upturn in the resistivity and, at temperatures below this resistivity minimum, an unusual magnetoresistance which is negative at low fields and positive at higher fields, in single crystals of VSe2. The negative magnetoresistance has a parabolic dependence on the magnetic field and shows little angular dependence. The magnetoresistance at temperatures above the resistivity minimum is always positive. We interpret these results as signatures of the Kondo effect in VSe2. An upturn in the susceptibility indicates the presence of interlayer V ions which can provide the localized magnetic moments required for scattering the conduction electrons in the Kondo effect. The low-temperature behaviour of the heat capacity, including a high value of γ, along with a deviation from a Curie-Weiss law observed in the low-temperature magnetic susceptibility, are consistent with the presence of magnetic interactions between the paramagnetic interlayer V ions and a Kondo screening of these V moments.
Enhancement of extinction memory by pharmacological and behavioral interventions targeted to its reactivation
Authors: Haubrich Josué , Machado Adriano , Boos Flávia Zacouteguy , Crestani Ana P. , Sierra Rodrigo O. , Alvares Lucas de Oliveira , Quillfeldt Jorge A. 
Published: September 2017

AbstractExtinction is a process that involves new learning that inhibits the expression of previously acquired memories. Although temporarily effective, extinction does not erase an original fear association. Since the extinction trace tends to fade over time, the original memory can resurge. On the other hand, strengthening effects have been described in several reconsolidation studies using different behavioral and pharmacological manipulations. In order to know whether an extinction memory can be strengthened by reactivation-based interventions in the contextual fear conditioning task, we began by replicating the classic phenomenon of spontaneous recovery to show that brief reexposure sessions can prevent the decay of the extinction trace over time in a long-lasting way. This fear attenuation was shown to depend both on L-type calcium channels and protein synthesis, which suggests a reconsolidation process behind the reactivation-induced strengthening effect. The extinction trace was also susceptible to enhancement by a post-reactivation infusion of a memory-enhancing drug (NaB), which was also able to prevent rapid fear reacquisition (savings). These findings point to new reactivation-based approaches able to strengthen an extinction memory to promote its persistence. The constructive interactions between extinction and reconsolidation may represent a promising novel approach in the realm of fear-related disorder treatments.