bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate variability and trends at a national scale
Authors: Xu Zhenci , Tang Ying , Connor Thomas , Li Dapeng , Li Yunkai , Liu Jianguo 
Published: June 2017

AbstractClimate variability and trends have significant environmental and socioeconomic impacts. Global challenges such as food security, biodiversity loss, water scarcity and human health are affected by reference evapotranspiration, temperature, solar radiation, and precipitation together, but nonlinear dynamics of these four climatic factors have not been assessed simultaneously at the national scale. This leads to unclear climatic dynamics and limited applications. To address this knowledge gap, we analyzed the daily variability and trends of four climatic factors (reference evapotranspiration, temperature, solar radiation, and precipitation) in China simultaneously using high spatial resolution data from 1960 to 2013. The results indicate that the daily variability of climate system dynamics (quantified by multiplying fractal dimensions of the four climatic factors) in north China was higher than that in south China. For example, the climate system dynamics were more chaotic and with higher nonlinear variation in north China, most notably in Heilongjiang Province, the major grain base of China, posing threats to food security in the context of growing national population. Spatial distribution of variability varies among different climatic factors. Our study highlights the need for a more holistic study of climate variability and trends in other countries with multiple climate types to address challenges of sustainable development.
Non-iterative Directional Dark-field Tomography
Authors: Schaff Florian , Prade Friedrich , Sharma Yash , Bech Martin , Pfeiffer Franz 
Published: June 2017

AbstractDark-field imaging is a scattering-based X-ray imaging method that can be performed with laboratory X-ray tubes. The possibility to obtain information about unresolvable structures has already seen a lot of interest for both medical and material science applications. Unlike conventional X-ray attenuation, orientation dependent changes of the dark-field signal can be used to reveal microscopic structural orientation. To date, reconstruction of the three-dimensional dark-field signal requires dedicated, highly complex algorithms and specialized acquisition hardware. This severely hinders the possible application of orientation-dependent dark-field tomography. In this paper, we show that it is possible to perform this kind of dark-field tomography with common Talbot-Lau interferometer setups by reducing the reconstruction to several smaller independent problems. This allows for the reconstruction to be performed with commercially available software and our findings will therefore help pave the way for a straightforward implementation of orientation-dependent dark-field tomography.
A translational approach to capture gait signatures of neurological disorders in mice and humans
Authors: Broom Lauren , Ellison Brian A. , Worley Audrey , Wagenaar Lara , Sörberg Elina , Ashton Christine , Bennett David A. , Buchman Aron S. , Saper Clifford B. , Shih Ludy C. , Hausdorff Jeffrey M. , VanderHorst Veronique G. 
Published: June 2017

AbstractA method for capturing gait signatures in neurological conditions that allows comparison of human gait with animal models would be of great value in translational research. However, the velocity dependence of gait parameters and differences between quadruped and biped gait have made this comparison challenging. Here we present an approach that accounts for changes in velocity during walking and allows for translation across species. In mice, we represented spatial and temporal gait parameters as a function of velocity and established regression models that reproducibly capture the signatures of these relationships during walking. In experimental parkinsonism models, regression curves representing these relationships shifted from baseline, implicating changes in gait signatures, but with marked differences between models. Gait parameters in healthy human subjects followed similar strict velocity dependent relationships which were altered in Parkinson’s patients in ways that resemble some but not all mouse models. This novel approach is suitable to quantify qualitative walking abnormalities related to CNS circuit dysfunction across species, identify appropriate animal models, and it provides important translational opportunities.
An Advanced Deep Learning Approach for Ki-67 Stained Hotspot Detection and Proliferation Rate Scoring for Prognostic Evaluation of Breast Cancer
Authors: Saha Monjoy , Chakraborty Chandan , Arun Indu , Ahmed Rosina , Chatterjee Sanjoy 
Published: June 2017

AbstractBeing a non-histone protein, Ki-67 is one of the essential biomarkers for the immunohistochemical assessment of proliferation rate in breast cancer screening and grading. The Ki-67 signature is always sensitive to radiotherapy and chemotherapy. Due to random morphological, color and intensity variations of cell nuclei (immunopositive and immunonegative), manual/subjective assessment of Ki-67 scoring is error-prone and time-consuming. Hence, several machine learning approaches have been reported; nevertheless, none of them had worked on deep learning based hotspots detection and proliferation scoring. In this article, we suggest an advanced deep learning model for computerized recognition of candidate hotspots and subsequent proliferation rate scoring by quantifying Ki-67 appearance in breast cancer immunohistochemical images. Unlike existing Ki-67 scoring techniques, our methodology uses Gamma mixture model (GMM) with Expectation-Maximization for seed point detection and patch selection and deep learning, comprises with decision layer, for hotspots detection and proliferation scoring. Experimental results provide 93% precision, 0.88% recall and 0.91% F-score value. The model performance has also been compared with the pathologists’ manual annotations and recently published articles. In future, the proposed deep learning framework will be highly reliable and beneficial to the junior and senior pathologists for fast and efficient Ki-67 scoring.
Motor errors lead to enhanced performance in older adults
Authors: Levy-Tzedek S. 
Published: June 2017

AbstractYoung individuals make larger and faster forearm movements when visual feedback about the movement is not available, compared to when it is. We set out to test whether this behavior persists with aging. We tested 40 participants, 20 in each age group – young and old, on a task that required making rhythmic movements of the forearm with and without visual feedback. Surprisingly, we found that older adults increased the speed and the amplitude of their movements to an even greater extent than did the young adults. Furthermore, we found that the increase in speed and amplitude during the non-vision trial segments improved their performance on the task, and they were able to leverage the change in these movement parameters (speed and amplitude) to improve their performance during subsequent trial segments that did include visual feedback. The improvement in accuracy on the task was accompanied by a decrease in path variability. The results indicate that older adults can adapt their movement parameters to enhance performance following a motor perturbation. They further suggest that motor variability in old age can be advantageous under certain circumstances.
Role of the stability of charge ordering in exchange bias effect in doped manganites
Authors: Dasgupta Papri , Das Kalipada , Pakhira Santanu , Mazumdar Chandan , Mukherjee S. , Mukherjee S. , Poddar A. 
Published: June 2017

AbstractIn this work we have carried out an elaborate study on the magnetic properties and investigated the exchange bias phenomena of some charge-ordered (CO) manganites. The detailed study of Sm1−xCaxMnO3(x = 0.5, 0.55, 0.6, 0.65, 0.7) compounds shows that Sm0.4Ca0.6MnO3, which is the most robust charge ordered material studied here, shows significantly large exchange bias field (HE) as compared to the other compounds. Our experimental results and analysis indicate that TCO, which reflects the stability of the charge-ordered state, is one of the key parameters for the exchange bias effect. Similar behaviour is found in other rare-earth analogues,viz., La1−xCaxMnO3and Pr1−xCaxMnO3compounds as well. We also found that with increasing stability of CO states in Sm1−xCaxMnO3compounds, HEenhances due to increase in number and reduction in size of ferromagnetic clusters.
Chronic vitamin D deficiency induces lung fibrosis through activation of the renin-angiotensin system
Authors: Shi Yongyan , Liu Tianjing , Yao Li , Xing Yujiao , Zhao Xinyi , Fu Jianhua , Xue Xindong 
Published: June 2017

AbstractPulmonary fibrosis, which influences lung function and exacerbates a patient’s condition, is the ultimate stage of many lung diseases. Vitamin D deficiency is associated with pulmonary fibrosis and impaired lung function, but the underlying mechanism has not yet been fully elucidated. Moreover, vitamin D deficiency may cause over-activation of the renin-angiotensin system (RAS), which aggravates extracellular matrix (ECM) deposition and lung fibrosis. This study aims to investigate the effect of chronic vitamin D deficiency on lung fibrosis in otherwise healthy mice and to explore the role of RAS in this process. Mice were depleted of vitamin D through diet control and were compared with healthy subjects. Chronic vitamin D deficiency destructs lung structures, impairs lung development and stimulates ECM deposition. RAS components are also found to increase. These effects seem to worsen with prolonged vitamin D deficiency. By giving RAS blockers, these changes can be largely rescued. However, a smooth muscle relaxant whose regulatory effect on blood pressure is independent of RAS does not show similar effects. This study demonstrated that chronic vitamin D deficiency may induce RAS activation, which subsequently stimulates the expression of profibrotic factors and activates the fibrotic cascade. This profibrotic effect of RAS is independent of elevated blood pressure.
Effect of hydrogen on semiconductive properties of passive film on ferrite and austenite phases in a duplex stainless steel
Authors: Guo L. Q. , Qin S. X. , Yang B. J. , Liang D. , Qiao L. J. 
Published: June 2017

AbstractHydrogen effect on semiconductivity and compositions of passive films formed on ferrite and austenite phases in a duplex stainless steel were investigated by current sensing atomic force microscopy and X-ray photoelectron spectroscopy. It is demonstrated that hydrogen significantly increases the conductivity of passive film due to the increase of OH−/O2− ratio. The passive film on austenite has higher conductivity than that on ferrite after hydrogen charging due to more hydrogen in austenite. The presence of hydrogen causes an inversion of conductivity type of passive film from p-type to n-type, attributed to the chemical composition change.
Visuotactile integration modulates motor performance in a perceptual decision-making task
Authors: Grechuta Klaudia , Guga Jelena , Maffei Giovanni , Rubio Ballester Belen , Verschure Paul F. M. J. 
Published: June 2017

AbstractBody ownership is critically dependent on multimodal integration as for instance revealed in the Rubber Hand Illusion (RHI) and a number of studies which have addressed the neural correlates of the processes underlying this phenomenon. Both experimental and clinical research have shown that the structures underlying body ownership seem to significantly overlap with those of motor control including the parietal and ventral premotor cortices, Temporal Parietal Junction (TPJ) and the insula. This raises the question of whether this structural overlap between body ownership and motor control structures is of any functional significance. Here, we investigate the specific question of whether experimentally induced ownership over a virtual limb can modulate the performance of that limb in a simple sensorimotor task. Using a Virtual reality (VR) environment we modulate body ownership in three experimental conditions with respect to the (in)congruence of stimulus configurations. Our results show that the degree of ownership directly modulates motor performance. This implies that body ownership is not exclusively a perceptual and/or subjective multimodal state but that it is tightly coupled to systems for decision-making and motor control.
Single-stranded RNA viruses infecting the invasive Argentine ant, Linepithema humile
Authors: Gruber Monica A. M. , Cooling Meghan , Baty James W. , Buckley Kevin , Friedlander Anna , Quinn Oliver , Russell Jessica F. E. J. , Sébastien Alexandra , Lester Philip J. 
Published: June 2017

AbstractSocial insects host a diversity of viruses. We examined New Zealand populations of the globally widely distributed invasive Argentine ant (Linepithema humile) for RNA viruses. We used metatranscriptomic analysis, which identified six potential novel viruses in the Dicistroviridae family. Of these, three contigs were confirmed by Sanger sequencing as Linepithema humile virus-1 (LHUV-1), a novel strain of Kashmir bee virus (KBV) and Black queen cell virus (BQCV), while the others were chimeric or misassembled sequences. We extended the known sequence of LHUV-1 to confirm its placement in the Dicistroviridae and categorised its relationship to closest relatives, which were all viruses infecting Hymenoptera. We examined further for known viruses by mapping our metatranscriptomic sequences to all viral genomes, and confirmed KBV, BQCV, LHUV-1 and Deformed wing virus (DWV) presence using qRT-PCR. Viral replication was confirmed for DWV, KBV and LHUV-1. Viral titers in ants were higher in the presence of honey bee hives. Argentine ants appear to host a range of’ honey bee’ pathogens in addition to a virus currently described only from this invasive ant. The role of these viruses in the population dynamics of the ant remain to be determined, but offer potential targets for biocontrol approaches.
Enhanced derivation of human pluripotent stem cell-derived cortical glutamatergic neurons by a small molecule
Authors: Cao Shi-Ying , Hu Yao , Chen Cheng , Yuan Fang , Xu Min , Li Qi , Fang Kai-Heng , Chen Yaoyu , Liu Yan 
Published: June 2017

AbstractHuman pluripotent stem cells (hPSCs) play important role in studying the function of human glutamatergic neurons and related disease pathogenesis. However, the current hPSC-derived cortical system produced a significant number of inhibitory GABAergic neurons that reduced the purity of excitatory neurons. In this study, we established a robust hPSC-derived cortical neurogenesis system by applying the SHH inhibitor cyclopamine. Cyclopamine specified the dorsal cortical fate in a dose-dependent manner and enhanced the generation of cortical glutamatergic neurons, expressing PAX6, TBR1, TBR2, CTIP2, SATB2, and vesicular glutamate transporters (vGLUT). In contrast, the ventral patterning was inhibited and the GABAergic neurons were significantly reduced to 12% with the treatment of cyclopamine. In addition, we applied our current method to generate trisomy 21 iPSC-derived glutamatergic neurons that showed a robust reduction of vesicular glutamate transporters in the glutamatergic neurons with trisomy 21, revealing the developmental deficits in cortical glutamatergic neurons. Our method enriched the generation of cortical glutamatergic neurons which may facilitate the study of human neurological diseases and cell therapy.
Effective Adsorption and Removal of Phosphate from Aqueous Solutions and Eutrophic Water by Fe-based MOFs of MIL-101
Authors: Xie Qiying , Li Yan , Lv Zhaoling , Zhou Hang , Yang Xiangjun , Chen Jing , Guo Hong 
Published: June 2017

AbstractAlthough many efforts have been devoted to the adsorptive removal of phosphate from aqueous solutions and eutrophic water, it is still highly desirable to develop novel adsorbents with high adsorption capacities. In this study, Fe-based metal-organic frameworks (MOFs), MIL-101 and NH2-MIL-101, are fabricated through a general facile strategy. Their performance as an adsorbent for phosphate removal is investigated. Experiments are performed to study the effects of various factors on the phosphate adsorption, including adsorbent dosage, contact time and co-existing ions. Both MIL-101(Fe) and NH2-MIL-101(Fe) show highly effective removal of phosphates from aqueous solutions, and the concentration of phosphates decrease sharply from the initial 0.60 mg·L−1 to 0.045 and 0.032 mg·L−1, respectively, within just 30 min of exposure. The adsorption kinetics and adsorption isotherms reveal that NH2-MIL-101(Fe) has higher adsorption capacity than MIL-101(Fe) possibly due to the amine group. Furthermore, the Fe-based MOFs also exhibit a high selectivity towards phosphate over other anions such as chloride, bromide, nitrate and sulfate. Particularly, the prepared Fe-based MIL-101 materials are also capable of adsorbing phosphate in an actual eutrophic water sample and display better removal effect.
Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China
Authors: Zhou Jing , Jiang Xin , Wei Dan , Zhao Baisuo , Ma Mingchao , Chen Sanfeng , Cao Fengming , Shen Delong , Guan Dawei , Li Jun 
Published: June 2017

AbstractLong-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.
Differences in pharmacodynamic responses to rocuronium in normal or injured orbicularis oris are associated with expression of acetylcholine receptor subunits
Authors: Huang Yong , Xing Yian , Wang Hong , Chen Lianhua , Li Shitong 
Published: June 2017

AbstractPrevious research has indicated that differences in sensitivities to muscle relaxants exist between facial nerve- and somatic nerve-innervated muscles. Here, we report that the 50% inhibitory concentration (IC50) values for rocuronium were significantly larger in the normal orbicularis oris than those in the gastrocnemius. Increased IC50 values and reduced twitch tension were observed after facial nerve injury. The normal orbicularis oris had a smaller muscle fiber cross-sectional area (CSA) and a larger ratio of endplate surface area (ESA) to muscle fiber CSA (ESA/CSA), but no difference was found in the density of nicotinic acetylcholine receptor (nAChR) subunits on endplates between normal orbicularis oris and gastrocnemius. Expression of the nAChR α1, β1, δ, ε, and γ subunits increased significantly on the postsynaptic membranes of endplates and extra-junctional muscle membranes after facial nerve injury. Our results suggest that facial nerve-innervated muscle was less sensitive than somatic nerve-innervated muscle, and the mechanisms underlying this result may be related to muscle fiber CSA and the ESA/CSA ratio, but not to the density of nAChR subunits on endplates. Facial nerve injury caused the resistance to neuromuscular blockers and reduced twitch tension, which was related to qualitative, quantitative, and locational changes in nAChR subunits.
WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data
Authors: Zhang Hongbo , Zhu Lin , Huang De-Shuang 
Published: June 2017

AbstractAlthough discriminative motif discovery (DMD) methods are promising for eliciting motifs from high-throughput experimental data, due to consideration of computational expense, most of existing DMD methods have to choose approximate schemes that greatly restrict the search space, leading to significant loss of predictive accuracy. In this paper, we propose Weakly-Supervised Motif Discovery (WSMD) to discover motifs from ChIP-seq datasets. In contrast to the learning strategies adopted by previous DMD methods, WSMD allows a “global” optimization scheme of the motif parameters in continuous space, thereby reducing the information loss of model representation and improving the quality of resultant motifs. Meanwhile, by exploiting the connection between DMD framework and existing weakly supervised learning (WSL) technologies, we also present highly scalable learning strategies for the proposed method. The experimental results on both real ChIP-seq datasets and synthetic datasets show that WSMD substantially outperforms former DMD methods (including DREME, HOMER, XXmotif, motifRG and DECOD) in terms of predictive accuracy, while also achieving a competitive computational speed.
MatureP: prediction of secreted proteins with exclusive information from their mature regions
Authors: Orfanoudaki Georgia , Markaki Maria , Chatzi Katerina , Tsamardinos Ioannis , Economou Anastassios 
Published: June 2017

AbstractMore than a third of the cellular proteome is non-cytoplasmic. Most secretory proteins use the Sec system for export and are targeted to membranes using signal peptides and mature domains. To specifically analyze bacterial mature domain features, we developed MatureP, a classifier that predicts secretory sequences through features exclusively computed from their mature domains. MatureP was trained using Just Add Data Bio, an automated machine learning tool. Mature domains are predicted efficiently with ~92% success, as measured by the Area Under the Receiver Operating Characteristic Curve (AUC). Predictions were validated using experimental datasets of mutated secretory proteins. The features selected by MatureP reveal prominent differences in amino acid content between secreted and cytoplasmic proteins. Amino-terminal mature domain sequences have enhanced disorder, more hydroxyl and polar residues and less hydrophobics. Cytoplasmic proteins have prominent amino-terminal hydrophobic stretches and charged regions downstream. Presumably, secretory mature domains comprise a distinct protein class. They balance properties that promote the necessary flexibility required for the maintenance of non-folded states during targeting and secretion with the ability of post-secretion folding. These findings provide novel insight in protein trafficking, sorting and folding mechanisms and may benefit protein secretion biotechnology.