bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biophysical regulation of Chlamydia pneumoniae-infected monocyte recruitment to atherosclerotic foci
Authors: Evani Shankar J. , Ramasubramanian Anand K. 
Published: January 2016

AbstractChlamydia pneumoniaeinfection is implicated in atherosclerosis although the contributory mechanisms are poorly understood. We hypothesize thatC. pneumoniaeinfection favors the recruitment of monocytes to atherosclerotic foci by altering monocyte biophysics. Primary, fresh human monocytes were infected withC. pneumoniaefor 8 h and the interactions between monocytes and E-selectin or aortic endothelium under flow were characterized by video microscopy and image analysis. The distribution of membrane lipid rafts and adhesion receptors were analyzed by imaging flow cytometry. Infected cells rolled on E-selectin and endothelial surfaces and this rolling was slower, steady and uniform compared to uninfected cells. Infection decreases cholesterol levels, increases membrane fluidity, disrupts lipid rafts and redistributes CD44, which is the primary mediator of rolling interactions. Together, these changes translate to higher firm adhesion of infected monocytes on endothelium, which is enhanced in the presence of LDL. Uninfected monocytes treated with LDL or left untreated were used as baseline control. Our results demonstrate that the membrane biophysical changes due to infection and hyperlipidemia are one of the key mechanisms by whichC. pneumoniaecan exacerbate atherosclerotic pathology. These findings provide a framework to characterize the role of ‘infectious burden’ in the development and progression of atherosclerosis.
Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain
Authors: Chou Shen-Ju , Wang Chindi , Sintupisut Nardnisa , Niou Zhen-Xian , Lin Chih-Hsu , Li Ker-Chau , Yeang Chen-Hsiang 
Published: January 2016

AbstractAllen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development.
Experimental investigation of geochemical and mineralogical effects of CO2 sequestration on flow characteristics of reservoir rock in deep saline aquifers
Authors: Rathnaweera T. D. , Ranjith P. G. , Perera M. S. A. 
Published: January 2016

AbstractInteractions between injected CO2, brine and rock during CO2 sequestration in deep saline aquifers alter their natural hydro-mechanical properties, affecting the safety and efficiency of the sequestration process. This study aims to identify such interaction-induced mineralogical changes in aquifers and in particular their impact on the reservoir rock’s flow characteristics. Sandstone samples were first exposed for 1.5 years to a mixture of brine and super-critical CO2 (scCO2), then tested to determine their altered geochemical and mineralogical properties. Changes caused uniquely by CO2 were identified by comparison with samples exposed over a similar period to either plain brine or brine saturated with N2. The results show that long-term reaction with CO2 causes a significant pH drop in the saline pore fluid, clearly due to carbonic acid (as dissolved CO2) in the brine. Free H+ ions released into the pore fluid alter the mineralogical structure of the rock formation, through the dissolution of minerals such as calcite, siderite, barite and quartz. Long-term CO2 injection also creates a significant CO2 drying-out effect and crystals of salt (NaCl) precipitate in the system, further changing the pore structure. Such mineralogical alterations significantly affect the saline aquifer’s permeability, with important practical consequences for the sequestration process.
Plasma extracellular RNA profiles in healthy and cancer patients
Authors: Yuan Tiezheng , Huang Xiaoyi , Woodcock Mark , Du Meijun , Dittmar Rachel , Wang Yuan , Tsai Susan , Kohli Manish , Boardman Lisa , Patel Tushar , Wang Liang 
Published: January 2016

AbstractExtracellular vesicles are selectively enriched in RNA that has potential as disease biomarkers. To systemically characterize circulating extracellular RNA (exRNA) profiles, we performed RNA sequencing analysis on plasma extracellular vesicles derived from 50 healthy individuals and 142 cancer patients. Of ~12.6 million raw reads for each individual, the number of mappable reads aligned to RNA references was ~5.4 million including miRNAs (~40.4%), piwiRNAs (~40.0%), pseudo-genes (~3.7%), lncRNAs (~2.4%), tRNAs (~2.1%) and mRNAs (~2.1%). By expression stability testing, we identified a set of miRNAs showing relatively consistent expression, which may serve as reference control for exRNA quantification. By performing multivariate analysis of covariance, we identified significant associations of these exRNAs with age, sex and different types of cancers. In particular, down-regulation of miR-125a-5p and miR-1343-3p showed an association with all cancer types tested (false discovery rate <0.05). We developed multivariate statistical models to predict cancer status with an area under the curve from 0.68 to 0.92 depending cancer type and staging. This is the largest RNA-seq study to date for profiling exRNA species, which has not only provided a baseline reference profile for circulating exRNA, but also revealed a set of RNA candidates for reference controls and disease biomarkers.
Whole-exome Sequencing Analysis Identifies Mutations in the EYS Gene in Retinitis Pigmentosa in the Indian Population
Authors: Di Yanan , Huang Lulin , Sundaresan Periasamy , Li Shujin , Kim Ramasamy , Ballav Saikia Bibhuti , Qu Chao , Zhu Xiong , Zhou Yu , Jiang Zhilin , Zhang Lin , Lin Ying , Zhang Dingding , Li Yuanfen , Zhang Houbin , Yin Yibing , Lu Fang , Zhu Xianjun , Yang Zhenglin 
Published: January 2016

AbstractRetinitis pigmentosa (RP) is a rare heterogeneous genetic retinal dystrophy disease and despite years of research, known genetic mutations can explain only approximately 60% of RP cases. We sought to identify the underlying genetic mutations in a cohort of fourteen Indian autosomal recessive retinitis pigmentosa (arRP) families and 100 Indian sporadic RP cases. Whole-exome sequencing (WES) was performed on the probands of the arRP families and sporadic RP patients and direct Sanger sequencing was used to confirm the causal mutations identified by WES. We found that the mutations of EYS are likely pathogenic mutations in two arRP families and eight sporadic patients. Specifically, we found a novel pair of compound heterozygous mutations and a novel homozygous mutation in two separate arRP families and found two novel heterozygous mutations in two sporadic RP patients, whereas we found six novel homozygous mutations in six sporadic RP patients. Of these, one was a frameshift mutation, two were stop-gain mutations, one was a splicing mutation and the others were missense mutations. In conclusion, our findings expand the spectrum of EYS mutations in RP in the Indian population and provide further support for the role of EYS in the pathogenesis and clinical diagnosis of RP.
Microarray and whole-exome sequencing analysis of familial Behçet’s disease patients
Authors: Okuzaki Daisuke , Yoshizaki Kazuyuki , Tanaka Toshio , Hirano Toru , Fukushima Kohshiro , Washio Takanori , Nojima Hiroshi 
Published: January 2016

AbstractBehçet’s disease (BD), a chronic systemic inflammatory disorder, is characterized by recurrent oral and genital mucous ulcers, uveitis and skin lesions. We performed DNA microarray analysis of peripheral blood mononuclear cell (PBMC) mRNA from 41 Japanese BD patients and revealed elevated levels of interleukin (IL) 23 receptor (IL23R) mRNA in many BD patients. DNA sequencing around a SNV (Rs12119179) tightly linked to BD revealed an elevated frequency of the C genotype, consistent with a previous report that IL23R is a susceptibility locus for BD. Notably, four of these BD patients are members of familial BD; a whole-exome sequencing (WES) of these BD patients identified 19 novel single-nucleotide variations (SNVs) specific to these patients. They include heterozygous SNVs in the genes encoding IL-1 receptor-associated kinase 4 (IRAK4), nucleotide-binding oligomerization domain (NOD)-like receptor family pyrin domain-containing 14 (NRP14) and melanoma antigen-encoding gene E2 (MAGEE2); IRAK4 harbors a missense mutation, whereas NRP14 and MAGEE2 harbor nonsense mutations. These SNVs may serve as genetic markers that characterize BD.
Skeletal muscle mass adjusted by height correlated better with muscular functions than that adjusted by body weight in defining sarcopenia
Authors: Han Der-Sheng , Chang Ke-Vin , Li Chia-Ming , Lin Yu-Hong , Kao Tung-Wei , Tsai Keh-Sung , Wang Tyng-Grey , Yang Wei-Shiung 
Published: January 2016

AbstractSarcopenia, characterized by low muscle mass and function, results in frailty, comorbidities and mortality. However, its prevalence varies according to the different criteria used in its diagnosis. This cross-sectional study investigated the difference in the number of sarcopenia cases recorded by two different measurement methods of low muscle mass to determine which measurement was better. We recruited 878 (54.2% female) individuals aged over 65 years and obtained their body composition and functional parameters. Low muscle mass was defined as two standard deviations below either the mean height-adjusted (hSMI) or weight-adjusted (wSMI) muscle mass of a young reference group. The prevalence of sarcopenia was 6.7% vs. 0.4% (male/female) by hSMI and 4.0% vs. 10.7% (male/female) by wSMI. The κ coefficients for these two criteria were 0.39 vs. 0.03 (male/female) and 0.17 in all subjects. Serum myostatin levels correlated positively with gait speed (r = 0.142, p = 0.007) after adjustment for gender. hSMI correlated with grip strength, cardiopulmonary endurance, leg endurance, gait speed and flexibility. wSMI correlated with grip strength, leg endurance, gait speed and flexibility. Since hSMI correlated more closely with grip strength and more muscular functions, we recommend hSMI in the diagnosis of low muscle mass.
Curvature-enhanced Spin-orbit Coupling and Spinterface Effect in Fullerene-based Spin Valves
Authors: Liang Shiheng , Geng Rugang , Yang Baishun , Zhao Wenbo , Chandra Subedi Ram , Li Xiaoguang , Han Xiufeng , Nguyen Tho Duc 
Published: January 2016

AbstractWe investigated curvature-enhanced spin-orbit coupling (SOC) and spinterface effect in carbon-based organic spin valves (OSVs) using buckyball C60 and C70 molecules. Since the naturally abundant 12C has spinless nuclear, the materials have negligible hyperfine interaction (HFI) and the same intrinsic SOC, but different curvature SOC due to their distinct curvatures. We fitted the thickness dependence of magnetoresistance (MR) in OSVs at various temperatures using the modified Jullière equation. We found that the spin diffusion length in the C70 film is above 120 nm, clearly longer than that in C60 film at all temperatures. The effective SOC ratio of the C70 film to the C60 film was estimated to be about 0.8. This was confirmed by the magneto-electroluminescence (MEL) measurement in fullerene-based light emitting diodes (LED). Next, the effective spin polarization in C70-based OSVs is smaller than that in C60-based OSVs implying that they have different spinterface effect. First principle calculation study shows that the spin polarization of the dz2 orbital electrons of Co atoms contacted with C60 is larger causing better effective spin polarization at the interface.
Natural HCV variants with increased replicative fitness due to NS3 helicase mutations in the C-terminal helix α18
Authors: Stross Claudia , Shimakami Tetsuro , Haselow Katrin , Ahmad Monazza Q. , Zeuzem Stefan , Lange Christian M. , Welsch Christoph 
Published: January 2016

AbstractHigh replicative fitness is a general determinant of a multidrug resistance phenotype and may explain lower sensitivity to direct-acting antiviral agents (DAAs) in some hepatitis C virus genotypes. Genetic diversity in the molecular target site of peptidomimetic NS3 protease inhibitors could impact variant replicative fitness and potentially add to virologic treatment failure. We selected NS3 helicase residues near the protease natural substrate in the NS3 domain interface and identified natural variants from a public database. Sequence diversity among different genotypes was identified and subsequently analyzed for potential effects of helicase variants on protein structure and function and phenotypic effects on RNA replication and DAA resistance. We found increased replicative fitness in particular for amino acid substitutions at the NS3 helicase C-terminal helix α18. A network of strongly coupled residue pairs is identified. Helix α18 is part of this regulatory network and connects several NS3 functional elements involved in RNA replication. Among all genotypes we found distinct sequence diversity at helix α18 in particular for the most difficult-to-treat genotype 3. Our data suggest sequence diversity with implications for virus replicative fitness due to natural variants in helicase helix α18.
Colorectal Cancer Screening Programme in Spain: Results of Key Performance Indicators After Five Rounds (2000–2012)
Authors: Binefa Gemma , Garcia Montse , Milà Núria , Fernández Esteve , Rodríguez-Moranta Francisco , Gonzalo Núria , Benito Llúcia , Clopés Ana , Guardiola Jordi , Moreno Víctor 
Published: January 2016

AbstractEffective quality assurance is essential in any screening programme. This article provides a unique insight into key quality indicators of five rounds of the first population-based colorectal cancer screening programme implemented in Spain (2000–2012), providing the results according to the type of screening (prevalent or first screen and incident or subsequent screen) and test (guaiac or immunochemical). The total crude participation rate increased from 17.2% (11,011) in the first round to 35.9% (22,988) in the last one. Rescreening rate was very high (88.6% in the fifth round). Positivity rate was superior with the faecal immunochemical test (6.2%) than with the guaiac-based test (0.7%) (p < 0.0001) and detection rates were also better with the immunochemical test. The most significant rise in detection rate was observed for high risk adenoma in men (45.5 per 1,000 screened). Most cancers were diagnosed at an early stage (61.4%) and there was a statistically significant difference between those detected in first or subsequent screening (52.6% and 70.0% respectively; p = 0.024). The availability of these results substantially improves data comparisons and the exchange of experience between screening programmes.
Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis
Authors: Ferguson Tanya M. , Weigel Kris M. , Lakey Becker Annie , Ontengco Delia , Narita Masahiro , Tolstorukov Ilya , Doebler Robert , Cangelosi Gerard A. , Niemz Angelika 
Published: January 2016

AbstractNucleic acid amplification testing (NAAT) enables rapid and sensitive diagnosis of tuberculosis (TB), which facilitates treatment and mitigates transmission. Nucleic acid extraction from sputum constitutes the greatest technical challenge in TB NAAT for near-patient settings. This report presents preliminary data for a semi-automated sample processing method, wherein sputum is disinfected and liquefied, followed by PureLyse® mechanical lysis and solid-phase nucleic acid extraction in a miniaturized, battery-operated bead blender. Sputum liquefaction and disinfection enabled a >104 fold reduction in viable load of cultured Mycobacterium tuberculosis (M.tb) spiked into human sputum, which mitigates biohazard concerns. Sample preparation via the PureLyse® method and a clinically validated manual method enabled positive PCR-based detection for sputum spiked with 104 and 105 colony forming units (cfu)/mL M.tb. At 103 cfu/mL sputum, four of six and two of six samples amplified using the comparator and PureLyse® method, respectively. For clinical specimens from TB cases and controls, the two methods provided 100% concordant results for samples with "Equation missing"1 mL input volume (N = 41). The semi-automated PureLyse® method therefore performed similarly to a validated manual comparator method, but is faster, minimally instrumented and can be integrated into TB molecular diagnostic platforms designed for near-patient low-resource settings.
Ecological opportunity and the evolution of habitat preferences in an arid-zone bird: implications for speciation in a climate-modified landscape
Authors: Norman Janette A. , Christidis Les 
Published: January 2016

AbstractBioclimatic models are widely used to investigate the impacts of climate change on species distributions. Range shifts are expected to occur as species track their current climate niche yet the potential for exploitation of new ecological opportunities that may arise as ecosystems and communities remodel is rarely considered. Here we show that grasswrens of the Amytornis textilis-modestus complex responded to new ecological opportunities in Australia’s arid biome through shifts in habitat preference following the development of chenopod shrublands during the late Plio-Pleistocene. We find evidence of spatially explicit responses to climatically driven landscape changes including changes in niche width and patterns of population growth. Conservation of structural and functional aspects of the ancestral niche appear to have facilitated recent habitat shifts, while demographic responses to late Pleistocene climate change provide evidence for the greater resilience of populations inhabiting the recently evolved chenopod shrubland communities. Similar responses could occur under future climate change in species exposed to novel ecological conditions, or those already occupying spatially heterogeneous landscapes. Mechanistic models that consider structural and functional aspects of the niche along with regional hydro-dynamics may be better predictors of future climate responses in Australia’s arid biome than bioclimatic models alone.
Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest
Authors: Shen Ju-pei , Chen C. R. , Lewis Tom 
Published: January 2016

AbstractEffects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0–10 cm) was significantly higher in the B2 treatment compared with the B0 and B4 treatments. Non-metric multidimensional analysis (NMDS) of bacterial community showed clear separation of the soil bacterial community structure among different fire frequency regimes and between the depths. Different frequency fire did not have a substantial effect on bacterial composition at phylum level or bacterial 16S rRNA gene abundance. Soil pH and C:N ratio were the major drivers for bacterial community structure in the most frequent fire treatment (B2), while other factors (EC, DOC, DON, MBC, NH4+, TC and TN) were significant in the less frequent burning and no burning treatments (B4 and B0). This study suggested that burning had a dramatic impact on bacterial diversity but not abundance with more frequent fire.
High‐voltage gain zero‐current switching push–pull resonant converter for small energy sources
Authors: Bilsalam Anusak , Boonyaroonate Itsda , Chunkag Viboon 
Published: January 2016

This study presents a high‐voltage gain zero‐current switching (ZCS) push–pull resonant converter for small energy sources. The converter provides a high voltage from a 12 VDC battery via isolated transformer and full‐bridge rectifier. The main switches of the push–pull and full‐bridge diode rectifier operate under ZCS condition. The advantage of this technique is the use of leakage inductance for ZCS operation of the power switch and in designing the secondary side of a resonant tank. A prototype high‐voltage gain push–pull resonant converter was built and operated at 110 kHz fixed switching frequency, 350 VDC output voltage, and 200 W output power to analyse the effect of parasitic junction capacitance of the full‐bridge rectifier, which significantly affects the operating point of the resonant tank and the voltage. This study introduces the implementation and design using the data of a single diode to calculate the parameters. The simulation and experimental results verified the proposed and designed circuits. Both results agreed with the theoretical analysis.
Intending, knowing how, infinitives
Authors: Hornsby Jennifer 
Published: January 2016

AbstractIntellectualists tell us that a person who knows how to do something therein knows a proposition. Along with others, they may say that a person who intends to do something intends a proposition. I argue against them. I do so by way of considering ‘know how ——’ and ‘intend ——’ together. When the two are considered together, a realistic conception of human agency can inform the understanding of some infinitives: the argument need not turn on what semanticists have had to say about (what they call) ‘the subjects of infinitival clauses’.
Statistical evaluation of very high cycle fatigue property of high carbon chromium bearing steel under axial loading
Authors: Li W. , Sakai T. , Deng H. 
Published: January 2016

Axial loading test was performed to investigate the S–N characteristics and the failure mechanisms of a high carbon chromium bearing steel under very high cycle fatigue (VHCF). Compared with the experimental results under rotating bending, the bearing steel under axial loading also exhibited two failure modes including surface failure and interior inclusion-induced failure. In the life regime beyond about 106 cycles, the fine granular area can occur around the inclusion. But under the axial loading with the uniform stress distribution on the cross-section of specimen, the duplex S–N characteristics of bearing steel was not so distinct. In view of the limitation of common statistical method, a statistical method based on mixed Weibull distribution and parameter optimisation was proposed to evaluate the VHCF property of bearing steel corresponding to two failure modes. Based on the proposed statistical method, the P–S–N curves of bearing steel under axial loading can be better established. This paper is part of a Themed Issue on Recent developments in bearing steels.