bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs
Authors: Zeng Pan , Cui Qinghua 
Published: January 2016

AbstractNoncoding RNAs (ncRNAs) represent a big class of important RNA molecules. Given the large number of ncRNAs, identifying their functional sites is becoming one of the most important topics in the post-genomic era, but available computational methods are limited. For the above purpose, we previously presented a tertiary structure based method, Rsite, which first calculates the distance metrics defined in Methods with the tertiary structure of an ncRNA and then identifies the nucleotides located within the extreme points in the distance curve as the functional sites of the given ncRNA. However, the application of Rsite is largely limited because of limited RNA tertiary structures. Here we present a secondary structure based computational method, Rsite2, based on the observation that the secondary structure based nucleotide distance is strongly positively correlated with that derived from tertiary structure. This makes it reasonable to replace tertiary structure with secondary structure, which is much easier to obtain and process. Moreover, we applied Rsite2 to three ncRNAs (tRNA (Lys), Diels-Alder ribozyme and RNase P) and a list of human mitochondria transcripts. The results show that Rsite2 works well with nearly equivalent accuracy as Rsite but is much more feasible and efficient. Finally, a web-server, the source codes and the dataset of Rsite2 are available at http://www.cuialb.cn/rsite2.
Effect of Different Mulches under Rainfall Concentration System on Corn Production in the Semi-arid Areas of the Loess Plateau
Authors: Ren Xiaolong , Zhang Peng , Chen Xiaoli , Guo Jingjing , Jia Zhikuan 
Published: January 2016

AbstractThe ridge and furrow farming system for rainfall concentration (RC) has gradually been popularized to improve the water availability for crops and to increase the water use efficiency (WUE), thereby stabilizing high yields. In the RC system, plastic-covered ridges are rainfall harvesting zones and furrows are planting zones. In this study, we optimized the mulching patterns for RC planting to mitigate the risks of drought during crop production in semi-arid agricultural areas. We conducted a four-year field study to determine the effects on corn production of mulching with 0.08-mm plastic film, maize straw, 8% biodegradable film, liquid film, bare furrow and conventional flat (CF) farming. We found that RC significantly increased (P > 0.05) the soil moisture storage in the top 0–100 cm layer and the topsoil temperature (0–10 cm) during the corn-growing season. Combining RC with mulching further improved the rain-harvesting, moisture-retaining and yield-increasing effects in furrows. Compared with CF, the four-year average yield increased by 1497.1 kg ha–1 to 2937.3 kg ha–1 using RC with mulch treatments and the WUE increased by 2.3 kg ha–1 mm–1 to 5.1 kg ha–1 mm–1.
Time series analysis of the association between ambient temperature and cerebrovascular morbidity in the elderly in Shanghai, China
Authors: Zhang Xian-Jing , Ma Wei-Ping , Zhao Nai-Qing , Wang Xi-Ling 
Published: January 2016

AbstractResearch on the association between ambient temperature and cerebrovascular morbidity is scarce in China. In this study, we applied mixed generalized additive model (MGAM) to daily counts of cerebrovascular disease of Shanghai residents aged 65 years or older from 2007–2011, stratified by gender. Weighted daily mean temperature up to lags of one week was smoothed by natural cubic spline and was added into the model to assess both linear and nonlinear effects of temperature. We found that when the mean temperature increased by 1 °C, the male cases of cerebrovascular disease reduced by 0.95% (95% Confidence Interval (CI): 0.80%, 1.10%) or reduced by 0.34% (95% CI: −0.68, 1.36%) in conditions of temperature was below or above 27 °C. However, for every 1 °C increase in temperature, the female cases of cerebrovascular disease increased by 0.34% (95% CI: −0.26%, 0.94%) or decreased by 0.92% (95% CI: 0.72, 1.11%) in conditions of temperature was below or above 8 °C, respectively. Temperature and cerebrovascular morbidity is negatively associated in Shanghai. MGAM is recommended in assessing the association between environmental hazards and health outcomes in time series studies.
Simple and effective exercise design for assessing in vivo mitochondrial function in clinical applications using 31P magnetic resonance spectroscopy
Authors: Sleigh Alison , Lupson Victoria , Thankamony Ajay , Dunger David B. , Savage David B. , Carpenter T. Adrian , Kemp Graham J. 
Published: January 2016

AbstractThe growing recognition of diseases associated with dysfunction of mitochondria poses an urgent need for simple measures of mitochondrial function. Assessment of the kinetics of replenishment of the phosphocreatine pool after exercise using 31P magnetic resonance spectroscopy can provide an in vivo measure of mitochondrial function; however, the wider application of this technique appears limited by complex or expensive MR-compatible exercise equipment and protocols not easily tolerated by frail participants or those with reduced mental capacity. Here we describe a novel in-scanner exercise method which is patient-focused, inexpensive, remarkably simple and highly portable. The device exploits an MR-compatible high-density material (BaSO4) to form a weight which is attached directly to the ankle and a one-minute dynamic knee extension protocol produced highly reproducible measurements of post-exercise PCr recovery kinetics in both healthy subjects and patients. As sophisticated exercise equipment is unnecessary for this measurement, our extremely simple design provides an effective and easy-to-implement apparatus that is readily translatable across sites. Its design, being tailored to the needs of the patient, makes it particularly well suited to clinical applications and we argue the potential of this method for investigating in vivo mitochondrial function in new cohorts of growing clinical interest.
Human Heat shock protein 40 (Hsp40/DnaJB1) promotes influenza A virus replication by assisting nuclear import of viral ribonucleoproteins
Authors: Batra Jyoti , Tripathi Shashank , Kumar Amrita , Katz Jacqueline M. , Cox Nancy J. , Lal Renu B. , Sambhara Suryaprakash , Lal Sunil K. 
Published: January 2016

AbstractA unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins.
Changes in pathogenicity and immunogenicity of Mycoplasma mycoides subsp. mycoides strains revealed by comparative genomics analysis
Authors: Li Yuan , Wang Yang , Wang Rui , Zhu Yongqiang , Liu Suli , Wang Qi , Shao Jiari , Chen Ying , Gao Liping , Zhou Changping , Liu Henggui , Wang Xiumei , Zheng Huajun , Xin Jiuqing 
Published: January 2016

AbstractMycoplasma mycoides subsp. mycoides is the causative agent of contagious bovine pleuropneumonia. A pathogenic strain BEN-1 was isolated from bovine lung and underwent continuous passages in rabbits for 468 generations. During this process, the strain’s strong virulence became weak and, gradually, it lost the ability to confer protective immunity in cattle but developed virulence in rabbits. In order to gain insight into the mechanisms behind the reduction in virulence and the loss of immunogenicity, we sequenced five representative strains of the BEN series, including the original strain (BEN-1), the strain generation that first acquired virulence in rabbits (BEN-50), the two vaccine strain generations (BEN-181 and BEN-326) and the strain generation showing the greatest loss of immunogenicity (BEN-468). The gene mutation rate in the four different propagation stages varied greatly and over half of variations observed in each generation were removed during the propagation process. However, the variation maintained in the BEN-468 generation might contribute to its changes in virulence and immunogenicity. We thus identified 18 genes associated with host adaptation, six genes contributing to virulence in cattle and 35 genes participating in conferring immunity in cattle. These findings might help us optimize the vaccine to obtain more effective immunization results.
CUL2-mediated clearance of misfolded TDP-43 is paradoxically affected by VHL in oligodendrocytes in ALS
Authors: Uchida Tsukasa , Tamaki Yoshitaka , Ayaki Takashi , Shodai Akemi , Kaji Seiji , Morimura Toshifumi , Banno Yoshinori , Nishitsuji Kazuchika , Sakashita Naomi , Maki Takakuni , Yamashita Hirofumi , Ito Hidefumi , Takahashi Ryosuke , Urushitani Makoto 
Published: January 2016

AbstractThe molecular machinery responsible for cytosolic accumulation of misfolded TDP-43 in amyotrophic lateral sclerosis (ALS) remains elusive. Here we identified a cullin-2 (CUL2) RING complex as a novel ubiquitin ligase for fragmented forms of TDP-43. The von Hippel Lindau protein (VHL), a substrate binding component of the complex, preferentially recognized misfolded TDP-43 at Glu246 in RNA-recognition motif 2. Recombinant full-length TDP-43 was structurally fragile and readily cleaved, suggesting that misfolded TDP-43 is cleared by VHL/CUL2 in a step-wise manner via fragmentation. Surprisingly, excess VHL stabilized and led to inclusion formation of TDP-43, as well as mutant SOD1, at the juxtanuclear protein quality control center. Moreover, TDP-43 knockdown elevated VHL expression in cultured cells, implying an aberrant interaction between VHL and mislocalized TDP-43 in ALS. Finally, cytoplasmic inclusions especially in oligodendrocytes in ALS spinal cords were immunoreactive to both phosphorylated TDP-43 and VHL. Thus, our results suggest that an imbalance in VHL and CUL2 may underlie oligodendrocyte dysfunction in ALS and highlight CUL2 E3 ligase emerges as a novel therapeutic potential for ALS.
Multi-decadal trends in global terrestrial evapotranspiration and its components
Authors: Zhang Yongqiang , Peña-Arancibia Jorge L. , McVicar Tim R. , Chiew Francis H. S. , Vaze Jai , Liu Changming , Lu Xingjie , Zheng Hongxing , Wang Yingping , Liu Yi Y. , Miralles Diego G. , Pan Ming 
Published: January 2016

AbstractEvapotranspiration (ET) is the process by which liquid water becomes water vapor and energetically this accounts for much of incoming solar radiation. If this ET did not occur temperatures would be higher, so understanding ET trends is crucial to predict future temperatures. Recent studies have reported prolonged declines in ET in recent decades, although these declines may relate to climate variability. Here, we used a well-validated diagnostic model to estimate daily ET during 1981–2012 and its three components: transpiration from vegetation (Et), direct evaporation from the soil (Es) and vaporization of intercepted rainfall from vegetation (Ei). During this period, ET over land has increased significantly (p < 0.01), caused by increases in Et and Ei, which are partially counteracted by Es decreasing. These contrasting trends are primarily driven by increases in vegetation leaf area index, dominated by greening. The overall increase in Et over land is about twofold of the decrease in Es. These opposing trends are not simulated by most Coupled Model Intercomparison Project phase 5 (CMIP5) models and highlight the importance of realistically representing vegetation changes in earth system models for predicting future changes in the energy and water cycle.
Astragaloside IV inhibits microglia activation via glucocorticoid receptor mediated signaling pathway
Authors: Liu Hong-Shuai , Shi Hai-Lian , Huang Fei , Peterson Karin E. , Wu Hui , Lan Yun-Yi , Zhang Bei-Bei , He Yi-Xin , Woods Tyson , Du Min , Wu Xiao-Jun , Wang Zheng-Tao 
Published: January 2016

AbstractInhibition of microglia activation may provide therapeutic treatment for many neurodegenerative diseases. Astragaloside IV (ASI) with anti-inflammatory properties has been tested as a therapeutic drug in clinical trials of China. However, the mechanism of ASI inhibiting neuroinflammation is unknown. In this study, we showed that ASI inhibited microglia activation both in vivo and in vitro. It could enhance glucocorticoid receptor (GR)-luciferase activity and facilitate GR nuclear translocation in microglial cells. Molecular docking and TR-FRET GR competitive binding experiments demonstrated that ASI could bind to GR in spite of relative low affinity. Meanwhile, ASI modulated GR-mediated signaling pathway, including dephosphorylation of PI3K, Akt, I κB and NF κB, therefore, decreased downstream production of proinflammatory mediators. Suppression of microglial BV-2 activation by ASI was abrogated by GR inhibitor, RU486 or GR siRNA. Similarly, RU486 counteracted the alleviative effect of ASI on microgliosis and neuronal injury in vivo. Our findings demonstrated that ASI inhibited microglia activation at least partially by activating the glucocorticoid pathway, suggesting its possible therapeutic potential for neuroinflammation in neurological diseases.
Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Authors: Guo Qiaoyun , Wei Yu , Xia Bin , Jin Yongxin , Liu Chang , Pan Xiaolei , Shi Jing , Zhu Feng , Li Jinlong , Qian Lei , Liu Xinqi , Cheng Zhihui , Jin Shouguang , Lin Jianping , Wu Weihui 
Published: January 2016

AbstractThe rising antibiotic resistance of bacteria imposes a severe threat on human health. Inhibition of bacterial virulence is an alternative approach to develop new antimicrobials. Molecules targeting antibiotic resistant enzymes have been used in combination with cognate antibiotics. It might be ideal that a molecule can simultaneously suppress virulence factors and antibiotic resistance. Here we combined genetic and computer-aided inhibitor screening to search for such molecules against the bacterial pathogen Pseudomonas aeruginosa. To identify target proteins that control both virulence and antibiotic resistance, we screened for mutants with defective cytotoxicity and biofilm formation from 93 transposon insertion mutants previously reported with increased antibiotic susceptibility. A pyrD mutant displayed defects in cytotoxicity, biofilm formation, quorum sensing and virulence in an acute mouse pneumonia model. Next, we employed a computer-aided screening to identify potential inhibitors of the PyrD protein, a dihydroorotate dehydrogenase (DHODase) involved in pyrimidine biosynthesis. One of the predicted inhibitors was able to suppress the enzymatic activity of PyrD as well as bacterial cytotoxicity, biofilm formation and antibiotic resistance. A single administration of the compound reduced the bacterial colonization in the acute mouse pneumonia model. Therefore, we have developed a strategy to identify novel treatment targets and antimicrobial molecules.
Strong reproductive isolation despite occasional hybridization between a widely distributed and a narrow endemic Rhododendron species
Authors: Ma Yong-Peng , Xie Wei-Jia , Sun Wei-Bang , Marczewski Tobias 
Published: January 2016

AbstractReproductive isolation (RI) plays an important role for speciation, but assessing reproductive barriers at all life-cycle stages remains challenging. In plants, most studies addressing the topic have been focusing on herbs with short generation times. The present study attempted to quantify several reproductive barriers between a hybridizing species pair of long-lived woody rhododendrons. Consistent with findings of previous studies, pre-zygotic reproductive barriers contributed more to total RI than post-zygotic reproductive barriers. Especially in the more widespread species geographic isolation was an important barrier and pollinator constancy contributed exceptionally to RI in both species. Additionally to strong pre-zygotic reproductive barriers, post-zygotic reproductive barriers were considerable and had asymmetric tendencies favoring one of the species as maternal parent. Overall, despite occasional hybridization, the present study provides evidence for strong RI between R. cyanocarpum and R. delavayi.
Control of Surface Segregation in Bimetallic NiCr Nanoalloys Immersed in Ag Matrix
Authors: Bohra Murtaza , Singh Vidyadhar , Grammatikopoulos Panagiotis , Toulkeridou Evropi , Diaz Rosa E. , Bobo Jean-François , Sowwan Mukhles 
Published: January 2016

AbstractCr-surface segregation is a main roadblock encumbering many magneto-biomedical applications of bimetallic M-Cr nanoalloys (where M = Fe, Co and Ni). To overcome this problem, we developed Ni95Cr5:Ag nanocomposite as a model system, consisting of non-interacting Ni95Cr5 nanoalloys (5 ± 1 nm) immersed in non-magnetic Ag matrix by controlled simultaneous co-sputtering of Ni95Cr5 and Ag. We employed Curie temperature (TC) as an indicator of phase purity check of these nanocomposites, which is estimated to be around the bulk Ni95Cr5 value of 320 K. This confirms prevention of Cr-segregation and also entails effective control of surface oxidation. Compared to Cr-segregated Ni95Cr5 nanoalloy films and nanoclusters, we did not observe any unwanted magnetic effects such as presence Cr-antiferromagnetic transition, large non-saturation, exchange bias behavior (if any) or uncompensated higher TC values. These nanocomposites films also lose their unique magnetic properties only at elevated temperatures beyond application requirements (≥800 K), either by showing Ni-type behavior or by a complete conversion into Ni/Cr-oxides in vacuum and air environment, respectively.
Intracoronary Transplantation of Mesenchymal Stem Cells with Overexpressed Integrin-Linked Kinase Improves Cardiac Function in Porcine Myocardial Infarction
Authors: Mu Dan , Zhang Xin-Lin , Xie Jun , Yuan Hui-Hua , Wang Kun , Huang Wei , Li Guan-Nan , Lu Jian-Rong , Mao Li-Juan , Wang Lian , Cheng Le , Mai Xiao-Li , Yang Jun , Tian Chuan-Shuai , Kang Li-Na , Gu Rong , Zhu Bin , Xu Biao 
Published: January 2016

AbstractThe effect of mesenchymal stem cell (MSCs)-based therapy on treating acute myocardial infarction (MI) is limited due to poor engraftment and limited regenerative potential. Here we engineered MSCs with integrin-linked kinase (ILK), a pleiotropic protein critically regulating cell survival, proliferation, differentiation and angiogenesis. We firstly combined ferumoxytol with poly-L-lysine (PLL) and found this combination promisingly enabled MRI visualization of MSCs in vitro and in vivo with good safety. We provided visually direct evidence that intracoronary ILK-MSCs had substantially enhanced homing capacity to infarct myocardium in porcine following cardiac catheterization induced MI. Intracoronary transplantation of allogeneic ILK-MSCs, but not vector-MSCs, significantly enhanced global left ventricular ejection fraction (LVEF) by 7.8% compared with baseline, by 10.3% compared with vehicles and inhibited myocardial remodeling compared with vehicles at 15-day follow-up. Compared with vector-MSCs, ILK-MSCs significantly improved regional LV contractile function, reduced scar size, fibrosis, cell apoptosis and increased regional myocardial perfusion and cell proliferation. This preclinical study indicates that ILK-engineered MSCs might promote the clinical translation of MSC-based therapy in post-MI patients and provides evidence that ferumoxytol labeling of cells combined with PLL is feasible in in vivo cell tracking.
Large Omnivore Movements in Response to Surface Mining and Mine Reclamation
Authors: Cristescu Bogdan , Stenhouse Gordon B. , Boyce Mark S. 
Published: January 2016

AbstractIncreasing global demands have resulted in widespread proliferation of resource extraction. Scientists are challenged to develop environmental mitigation strategies that meet societal expectations of resource supply, while achieving minimal disruption to sensitive “wilderness” species. We used GPS collar data from a 9-year study on grizzly bears (Ursus arctos) (n = 18) in Alberta, Canada to assess movements and associated space use during versus after mining. Grizzly bear home range overlap with mined areas was lower during active mining except for females with cubs, that also had shortest movements on active mines. However, both females with cubs and males made shorter steps when on/close to mines following mine closure and reclamation. Our results show differences in bear movement and space-use strategies, with individuals from a key population segment (females with cubs) appearing most adaptable to mining disturbance. Preserving patches of original habitat, reclaiming the landscape and minimizing the risk of direct human-induced mortality during and after development can help conserve bears and other wildlife on industrially modified landscapes.
El modelo nebrisense delArte de la lengua mexicana(1547) de fray Andrés de Olmos
Authors: Baños Baños José Miguel , Téllez Nieto Heréndira 
Published: January 2016

ResumenTal como se ha señalado reiteradamente, el trabajo gramatical y lexicográfico de los primeros evangelizadores del Nuevo Mundo se vio profundamente influido por la obra de Antonio de Nebrija (1441/44–1522) y, muy especialmente, por susIntroductiones. Es este el caso, también, delArte de la lengua mexicana, la primera gramática conservada del náhuatl. Su autor, Andrés de Olmos (1496/98–1571), un fraile franciscano formado en la Universidad de Valladolid, así lo reconoce: “En el arte de la lengua latina creo que la mejor manera y orden que se ha tenido es la que Antonio de Lebrixa sigue en la suya” (Olmos 2015 [1547] I:1.7–8). Ahora bien, como es sabido, lasIntroductionessufrieron múltiples e importantes cambios de organización y contenido en sus distintas ediciones, sin que hasta ahora se haya determinado con claridad cuál de esas ediciones fue la que tuvo presente Olmos en la redacción de suArte. Este es el objetivo central del artículo: a partir del análisis de determinadas características y contenidos delArte de la lengua mexicana(desde la clasificación misma de las ocho partes de la oración a la mención explícita al libro quinto de Nebrija “sobre el acento” o la inclusión de un capítuloDe nominibus numeralibus) los autores del artículo concluyen que Olmos, en la redacción delArte, utilizó la edición de lasIntroductionesde 1508 o una reedición posterior.