bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of a national outbreak of STEC Escherichia coli O157 using online consumer panel control methods: Great Britain, October 2014
Authors: SINCLAIR C. , JENKINS C. , WARBURTON F. , ADAK G. K. , HARRIS J. P. 
Published: December 2016

SUMMARYIn October 2014, Public Health England (PHE) identified cases of Shiga toxin-producing Escherichia coli (STEC) serogroup O157 sharing a multiple locus variable-number tandem repeat analysis (MLVA) profile. We conducted a case-control study using multivariable logistic regression to calculate adjusted odds ratios (aOR) and 95% confidence intervals (CI) testing a range of exposures. Cases were defined as laboratory-confirmed STEC O157 with the implicated MLVA profile, were UK residents aged ⩾18 years with symptom onset between 25 September and 30 October 2014, and had no history of travel abroad within 5 days of symptom onset. One hundred and two cases were identified. Cases were mostly female (65%; median age 49, range 2–92 years). It was the second largest outbreak seen in England, to date, and a case-control study was conducted using market research panel controls and online survey methods. These methods were instrumental in the rapid data collection and analysis necessary to allow traceback investigations for short shelf-life products. This is a new method of control recruitment and this is the first in which it was a standalone recruitment method. The case-control study suggested a strong association between consumption of a ready-to-eat food and disease (aOR 28, 95% CI 5·0–157) from one retailer. No reactive microbiological testing of food items during the outbreak was possible due to the short shelf-life of the product. Collaboration with industrial bodies is needed to ensure timely traceback exercises to identify contamination events and initiate appropriate and focused microbiological testing and implement control measures.
Evaluation of Hospitals’ Disaster Preparedness Plans in the Holy City of Makkah (Mecca): A Cross-Sectional Observation Study
Authors: Al-Shareef Ali S. , Alsulimani Loui K. , Bojan Hattan M. , Masri Taha M. , Grimes Jennifer O. , Molloy Michael S. , Ciottone Gregory R. 
Published: December 2016

AbstractBackgroundMakkah (Mecca) is a holy city located in the western region of the Kingdom of Saudi Arabia. Each year, millions of pilgrims visit Makkah. These numbers impact both routine health care delivery and disaster response. This study aimed to evaluate hospitals’ disaster plans in the city of Makkah.MethodsStudy investigators administered a questionnaire survey to 17 hospitals in the city of Makkah. Data on hospital characteristics and three key domains of disaster plans (general evaluation of disaster planning, structural feasibility of the hospitals, and health care worker knowledge and training) were collated and analyzed.ResultsA response rate of 82% (n=14) was attained. Ten (71%) of the hospitals were government hospitals, whereas four were private hospitals. Eleven (79%) hospitals had a capacity of less than 300 beds.Only nine (64%) hospitals reviewed their disaster plan within the preceding two years. Nine (64%) respondents were drilling for disasters at least twice per year. The majority of hospitals did not rely on a hazard vulnerability analysis (HVA) to develop their Emergency Operations Plan. Eleven (79%) hospitals had the Hospital Incident Command Systems (HICS) present in their plans.All hospitals described availability of some supplies required for the first 24 hours of a disaster response, such as: N95 masks, antidotes for nerve agents, and antiviral medications. Only five (36%) hospitals had a designated decontamination area. Nine (64%) hospitals reported ability to re-designate inpatient wards into an intensive care unit (ICU) format. Only seven (50%) respondents had a protocol for increasing availability of isolation rooms to prevent the spread of airborne infection. Ten (71%) hospitals had a designated disaster-training program for health care workers.ConclusionsMakkah has experienced multiple disaster incidents over the last decade. The present research suggests that Makkah hospitals are insufficiently prepared for potential future disasters. This may represent a considerable threat to the health of both residents and visitors to Makkah. This study demonstrated that there is significant room for improvement in most aspects of hospital Emergency Operations Plans, in particular: reviewing the plan and increasing the frequency of multi-agency and multi-hospital drills. Preparedness for terrorism utilizing chemical, biologic, radiation, nuclear, explosion (CBRNE) and infectious diseases was found to be sub-optimal and should be assessed further.Al-ShareefAS, AlsulimaniLK, BojanHM, MasriTM, GrimesJO, MolloyMS, CiottoneGR. Evaluation of hospitals’ disaster preparedness plans in the holy city of Makkah (Mecca): a cross-sectional observation study. Prehosp Disaster Med. 2017;32
(1):33–45.
Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism
Authors: Mehrmohamadi Mahya , Mentch Lucas K. , Clark Andrew G. , Locasale Jason W. 
Published: December 2016

AbstractAltered DNA methylation is common in cancer and often considered an early event in tumorigenesis. However, the sources of heterogeneity of DNA methylation among tumours remain poorly defined. Here we capitalize on the availability of multi-platform data on thousands of human tumours to build integrative models of DNA methylation. We quantify the contribution of clinical and molecular factors in explaining intertumoral variability in DNA methylation. We show that the levels of a set of metabolic genes involved in the methionine cycle is predictive of several features of DNA methylation in tumours, including the methylation of cancer genes. Finally, we demonstrate that patients whose DNA methylation can be predicted from the methionine cycle exhibited improved survival over cases where this regulation is disrupted. This study represents a comprehensive analysis of the determinants of methylation and demonstrates the surprisingly large interaction between metabolism and DNA methylation variation. Together, our results quantify links between tumour metabolism and epigenetics and outline clinical implications.
Evaluating the convergence between eddy-covariance and biometric methods for assessing carbon budgets of forests
Authors: Campioli M. , Malhi Y. , Vicca S. , Luyssaert S. , Papale D. , Peñuelas J. , Reichstein M. , Migliavacca M. , Arain M. A. , Janssens I. A. 
Published: December 2016

AbstractThe eddy-covariance (EC) micro-meteorological technique and the ecology-based biometric methods (BM) are the primary methodologies to quantify CO2 exchange between terrestrial ecosystems and the atmosphere (net ecosystem production, NEP) and its two components, ecosystem respiration and gross primary production. Here we show that EC and BM provide different estimates of NEP, but comparable ecosystem respiration and gross primary production for forest ecosystems globally. Discrepancies between methods are not related to environmental or stand variables, but are consistently more pronounced for boreal forests where carbon fluxes are smaller. BM estimates are prone to underestimation of net primary production and overestimation of leaf respiration. EC biases are not apparent across sites, suggesting the effectiveness of standard post-processing procedures. Our results increase confidence in EC, show in which conditions EC and BM estimates can be integrated, and which methodological aspects can improve the convergence between EC and BM.
Continuous-variable quantum computing on encrypted data
Authors: Marshall Kevin , Jacobsen Christian S. , Schäfermeier Clemens , Gehring Tobias , Weedbrook Christian , Andersen Ulrik L. 
Published: December 2016

AbstractThe ability to perform computations on encrypted data is a powerful tool for protecting a client’s privacy, especially in today’s era of cloud and distributed computing. In terms of privacy, the best solutions that classical techniques can achieve are unfortunately not unconditionally secure in the sense that they are dependent on a hacker’s computational power. Here we theoretically investigate, and experimentally demonstrate with Gaussian displacement and squeezing operations, a quantum solution that achieves the security of a user’s privacy using the practical technology of continuous variables. We demonstrate losses of up to 10 km both ways between the client and the server and show that security can still be achieved. Our approach offers a number of practical benefits (from a quantum perspective) that could one day allow the potential widespread adoption of this quantum technology in future cloud-based computing networks.
Differential protein expression in metallothionein protection from depleted uranium-induced nephrotoxicity
Authors: Hao Yuhui , Huang Jiawei , Liu Cong , Li Hong , Liu Jing , Zeng Yiping , Yang Zhangyou , Li Rong 
Published: December 2016

AbstractThe purpose of this study was to investigate the underlying mechanism of metallothionein (MT) protection from depleted uranium (DU) using a proteomics approach to search for a DU toxicity-differential protein. MT−/− and MT+/+ mice were administrated with a single dose of DU (10 mg/kg, i.p.) or equal volume of saline. After 4 days, protein changes in kidney tissues were evaluated using a proteomics approach. A total of 13 differentially expressed proteins were identified using two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The validating results showed that the expression of aminoacylase-3 (ACY-3) and the mitochondrial ethylmalonic encephalopathy 1 (ETHE1) decreased significantly after DU exposure; in addition, the reduction in MT−/− mice was more significant than that in MT+/+ mice. The results also showed that exogenous ETHE1 or ACY-3 could increase the survival rate of human embryonic kidney 293 (HEK293) cells after DU exposure. A specific siRNA of ETHE1 significantly increased cell apoptosis rates after DU exposure, whereas exogenous ETHE1 significantly decreased cell apoptosis rates. In summary, ACY-3 and ETHE1 might involve in protection roles of MT. ETHE1 could be a new sensitive molecular target of DU-induced cell apoptosis.
Microarray analysis of long noncoding RNA and mRNA expression profiles in human macrophages infected with Mycobacterium tuberculosis
Authors: Yang Xiaofan , Yang Jiahui , Wang Jinli , Wen Qian , Wang Hui , He Jianchun , Hu Shengfeng , He Wenting , Du Xialin , Liu Sudong , Ma Li 
Published: December 2016

AbstractMacrophages play a crucial role in the control and elimination of invading Mycobacterium tuberculosis (Mtb), and also serve as the major residence for Mtb. However, the interaction between macrophages and Mtb remains to be clearly determined. Although long noncoding RNAs (lncRNAs) have emerged as key regulators in many biological processes, their roles in anti-mycobacterial responses of macrophages remain to be elucidated. Here, we applied microarray analysis to examine lncRNA and mRNA expression profiles in human primary macrophages after 72 h of infection with H37Ra or H37Rv. Our results revealed that many lncRNAs were differentially expressed in macrophages after H37Ra or H37Rv infection, indicating a possible role for lncRNAs in immune responses induced by Mtb infection and providing important cues for further functional studies. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis of the differentially expressed mRNAs showed the potential functions and pathways related to the pathogenesis of Mtb infection. Finally, two lncRNAs, MIR3945HG V1 and MIR3945HG V2, were identified as novel candidate diagnostic markers for tuberculosis. Our results provide novel insight into the mechanisms of the pivotal Mtb-macrophage interactions, and reveal potential targets for diagnostics and the treatment of tuberculosis.
Cumulative release characteristics of controlled-release nitrogen and potassium fertilizers and their effects on soil fertility, and cotton growth
Authors: Yang Xiuyi , Geng Jibiao , Li Chengliang , Zhang Min , Tian Xiaofei 
Published: December 2016

AbstractTo investigate the interacting effects of polymer coated urea (PCU) and polymer coated potassium chloride (PCPC) on cotton growth, an experiment was conducted with containerized plants in 2014 and 2015. There were two kinds of nitrogen fertilizer, PCU and urea, which were combined with PCPC at three application rates (40, 80 and 120 kg ha−1). The kinds of nitrogen fertilizer formed the main plot, while individual rates of PCPC were the subplots. The results suggested N and K release patterns for PCU and PCPC in the soil were closely matched to the N and K requirements by cotton. Soil inorganic nitrogen contents significantly increased by using PCU instead of urea, and the same trend was observed with soil available potassium contents, which also had increased rates. Meanwhile, the number of bolls and lint yields of cotton in the PCU treatments were 4.9–35.3% and 2.9–40.7% higher than from urea treatments. Lint yields also increased by 9.1–12.7% with PCPC80 and PCPC120 treatments compared with PCPC40 treatment at the same nitrogen type. Hence, application of PCU combined with 80 kg ha−1 of PCPC fertilizer on cotton increased the yields and fertilizer use efficiencies in addition to improving fiber quality and delaying leaf senescence.
Resilin microjoints: a smart design strategy to avoid failure in dragonfly wings
Authors: Rajabi H. , Shafiei A. , Darvizeh A. , Gorb S. N. 
Published: December 2016

AbstractDragonflies are fast and manoeuvrable fliers and this ability is reflected in their unique wing morphology. Due to the specific lightweight structure, with the crossing veins joined by rubber-like resilin patches, wings possess strong deformability but can resist high forces and large deformations during aerial collisions. The computational results demonstrate the strong influence of resilin-containing vein joints on the stress distribution within the wing. The presence of flexible resilin in the contact region of the veins prevents excessive bending of the cross veins and significantly reduces the stress concentration in the joint.
Symbiont-derived sphingolipids modulate mucosal homeostasis and B cells in teleost fish
Authors: Sepahi Ali , Cordero Héctor , Goldfine Howard , Esteban Maria Ángeles , Salinas Irene 
Published: December 2016

AbstractSymbiotic bacteria and mucosal immunoglobulins have co-evolved for millions of years in vertebrate animals. Symbiotic bacteria products are known to modulate different aspects of the host immune system. We recently reported that Flectobacillus major is a predominant species that lives in the gill and skin mucosal surfaces of rainbow trout (Oncorhynchus mykiss). F. major is known to produce sphingolipids of a unique molecular structure. Here we propose a role for F. major and its sphingolipids in the regulation of B cell populations in rainbow trout, as well as an essential role for sphingolipids in trout mucosal homeostasis. We found that F. major-specific IgT titers are confined to the gill and skin mucus, whereas F. major-specific IgM titers are only detected in serum. Live F. major cells are able to stimulate sustained IgT expression and secretion in gills. F. major sphingolipids modulate the growth of trout total skin and gill symbiotic bacteria. In vivo systemic administration of F. major sphingolipids changes the proportion of IgT+ to IgM+ B cells in trout HK. These results demonstrate the key role of the symbiont F. major and its sphingolipids in mucosal homeostasis via the modulation of mucosal and systemic Igs and B cells.
Validated methodology for quantifying infestation levels of dreissenid mussels in environmental DNA (eDNA) samples
Authors: Peñarrubia Luis , Alcaraz Carles , Vaate Abraham bij de , Sanz Nuria , Pla Carles , Vidal Oriol , Viñas Jordi 
Published: December 2016

AbstractThe zebra mussel (Dreissena polymorpha Pallas, 1771) and the quagga mussel (D. rostriformis Deshayes, 1838) are successful invasive bivalves with substantial ecological and economic impacts in freshwater systems once they become established. Since their eradication is extremely difficult, their detection at an early stage is crucial to prevent spread. In this study, we optimized and validated a qPCR detection method based on the histone H2B gene to quantify combined infestation levels of zebra and quagga mussels in environmental DNA samples. Our results show specific dreissenid DNA present in filtered water samples for which microscopic diagnostic identification for larvae failed. Monitoring a large number of locations for invasive dreissenid species based on a highly specific environmental DNA qPCR assay may prove to be an essential tool for management and control plans focused on prevention of establishment of dreissenid mussels in new locations.
Structure-based activity prediction of CYP21A2 stability variants: A survey of available gene variations
Authors: Bruque Carlos D. , Delea Marisol , Fernández Cecilia S. , Orza Juan V. , Taboas Melisa , Buzzalino Noemí , Espeche Lucía D. , Solari Andrea , Luccerini Verónica , Alba Liliana , Nadra Alejandro D. , Dain Liliana 
Published: December 2016

AbstractCongenital adrenal hyperplasia due to 21-hydroxylase deficiency accounts for 90–95% of CAH cases. In this work we performed an extensive survey of mutations and SNPs modifying the coding sequence of the CYP21A2 gene. Using bioinformatic tools and two plausible CYP21A2 structures as templates, we initially classified all known mutants (n = 343) according to their putative functional impacts, which were either reported in the literature or inferred from structural models. We then performed a detailed analysis on the subset of mutations believed to exclusively impact protein stability. For those mutants, the predicted stability was calculated and correlated with the variant’s expected activity. A high concordance was obtained when comparing our predictions with available in vitro residual activities and/or the patient’s phenotype. The predicted stability and derived activity of all reported mutations and SNPs lacking functional assays (n = 108) were assessed. As expected, most of the SNPs (52/76) showed no biological implications. Moreover, this approach was applied to evaluate the putative synergy that could emerge when two mutations occurred in cis. In addition, we propose a putative pathogenic effect of five novel mutations, p.L107Q, p.L122R, p.R132H, p.P335L and p.H466fs, found in 21-hydroxylase deficient patients of our cohort.
Identification of Development-Related Genes in the Ovaries of Adult Harmonia axyridis (Pallas) Lady Beetles Using a Time- Series Analysis by RNA-seq
Authors: Du Wenxiao , Zeng Fanrong 
Published: December 2016

AbstractAdults of the lady beetle species Harmonia axyridis (Pallas) are bred artificially en masse for classic biological control, which requires egg-laying by the H. axyridis ovary. Development-related genes may impact the growth of the H. axyridis adult ovary but have not been reported. Here, we used integrative time-series RNA-seq analysis of the ovary in H. axyridis adults to detect development-related genes. A total of 28,558 unigenes were functionally annotated using seven types of databases to obtain an annotated unigene database for ovaries in H. axyridis adults. We also analysed differentially expressed genes (DEGs) between samples. Based on a combination of the results of this bioinformatics analysis with literature reports and gene expression level changes in four different stages, we focused on the development of oocyte reproductive stem cell and yolk formation process and identified 26 genes with high similarity to development-related genes. 20 DEGs were randomly chosen for quantitative real-time PCR (qRT-PCR) to validate the accuracy of the RNA-seq results. This study establishes a robust pipeline for the discovery of key genes using high-throughput sequencing and the identification of a class of development-related genes for characterization.
DkXTH8, a novel xyloglucan endotransglucosylase/hydrolase in persimmon, alters cell wall structure and promotes leaf senescence and fruit postharvest softening
Authors: Han Ye , Ban Qiuyan , Li Hua , Hou Yali , Jin Mijing , Han Shoukun , Rao Jingping 
Published: December 2016

AbstractFruit softening is mainly associated with cell wall structural modifications, and members of the xyloglucan endotransglucosylase/hydrolase (XTH) family are key enzymes involved in cleaving and re-joining xyloglucan in the cell wall. In this work, we isolated a new XTH gene, DkXTH8, from persimmon fruit. Transcriptional profiling revealed that DkXTH8 peaked during dramatic fruit softening, and expression of DkXTH8 was stimulated by propylene and abscisic acid but suppressed by gibberellic acid and 1-MCP. Transient expression assays in onion epidermal cells indicated direct localization of DkXTH8 to the cell wall via its signal peptide. When expressed in vitro, the recombinant DkXTH8 protein exhibited strict xyloglucan endotransglycosylase activity, whereas no xyloglucan endohydrolase activity was observed. Furthermore, overexpression of DkXTH8 resulted in increased leaf senescence coupled with higher electrolyte leakage in Arabidopsis and faster fruit ripening and softening rates in tomato. Most importantly, transgenic plants overexpressing DkXTH8 displayed more irregular and twisted cells due to cell wall restructuring, resulting in wider interstitial spaces with less compact cells. We suggest that DkXTH8 expression causes cells to be easily destroyed, increases membrane permeability and cell peroxidation, and accelerates leaf senescence and fruit softening in transgenic plants.
Pt-Bi decorated nanoporous gold for high performance direct glucose fuel cell
Authors: Guo Hong , Yin Huiming , Yan Xiuling , Shi Shuai , Yu Qingyang , Cao Zhen , Li Jian 
Published: December 2016

AbstractBinary PtBi decorated nanoporous gold (NPG-PtBi) electrocatalyst is specially designed and prepared for the anode in direct glucose fuel cells (DGFCs). By using electroless and electrochemical plating methods, a dense Pt layer and scattered Bi particles are sequentially coated on NPG. A simple DGFC with NPG-PtBi as anode and commercial Pt/C as cathode is constructed and operated to study the effect of operating temperatures and concentrations of glucose and NaOH. With an anode noble metal loading of only 0.45 mg cm−2 (Au 0.3 mg and Pt 0.15 mg), an open circuit voltage (OCV) of 0.9 V is obtained with a maximum power density of 8 mW cm−2. Furthermore, the maximum gravimetric power density of NPG-PtBi is 18 mW mg−1, about 4.5 times higher than that of commercial Pt/C.
Transportation dynamics on coupled networks with limited bandwidth
Authors: Li Ming , Hu Mao-Bin , Wang Bing-Hong 
Published: December 2016

AbstractThe communication networks in real world often couple with each other to save costs, which results in any network does not have a stand-alone function and efficiency. To investigate this, in this paper we propose a transportation model on two coupled networks with bandwidth sharing. We find that the free-flow state and the congestion state can coexist in the two coupled networks, and the free-flow path and congestion path can coexist in each network. Considering three bandwidth-sharing mechanisms, random, assortative and disassortative couplings, we also find that the transportation capacity of the network only depends on the coupling mechanism, and the fraction of coupled links only affects the performance of the system in the congestion state, such as the traveling time. In addition, with assortative coupling, the transportation capacity of the system will decrease significantly. However, the disassortative coupling has little influence on the transportation capacity of the system, which provides a good strategy to save bandwidth. Furthermore, a theoretical method is developed to obtain the bandwidth usage of each link, based on which we can obtain the congestion transition point exactly.