bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steady-state mechanical squeezing in a double-cavity optomechanical system
Authors: Wang Dong-Yang , Bai Cheng-Hua , Wang Hong-Fu , Zhu Ai-Dong , Zhang Shou 
Published: December 2016

AbstractWe study the physical properties of double-cavity optomechanical system in which the mechanical resonator interacts with one of the coupled cavities and another cavity is used as an auxiliary cavity. The model can be expected to achieve the strong optomechanical coupling strength and overcome the optomechanical cavity decay, simultaneously. Through the coherent auxiliary cavity interferences, the steady-state squeezing of mechanical resonator can be generated in highly unresolved sideband regime. The validity of the scheme is assessed by numerical simulation and theoretical analysis of the steady-state variance of the mechanical displacement quadrature. The scheme provides a platform for the mechanical squeezing beyond the resolved sideband limit and solves the restricted experimental bounds at present.
Latent curing systems stabilized by reaction equilibrium in homogeneous mixtures of benzoxazine and amine
Authors: Wang Jun , Xu Ya Zhen , Fu Ya Fei , Liu Xiang Dong 
Published: December 2016

AbstractLatent curing systems are widely used in industrial thermosets in applications such as adhesion, coating, and composites. Despite many attempts to improve the practicality of this dormant reaction system, the majority of commercially available latent products still use particulate hardeners or liquid compounds with blocked active groups. These formulations generally lack fluidity or rapid reaction characteristics and thus are problematic in some industry applications. Here we describe a novel concept that stabilizes highly reactive benzoxazine/amine mixtures by reaction equilibrium. These new latent benzoxazine curing systems have a long storable lifetime but very short gel time at 150 °C. The reversible reaction between benzoxazine and amine is further demonstrated by FT-IR spectral measurements and rheological experiments, and it is shown that the overall characteristics of the latent system are promising for many industrial applications.
Black carbon radiative forcing at TOA decreased during aging
Authors: Wu Yu , Cheng Tianhai , Zheng Lijuan , Chen Hao 
Published: December 2016

AbstractDuring aging processing, black carbon (also called soot) particles may tend to be mixed with other aerosols, and highly influence their radiative forcing. In this study, freshly emitted soot particles were simulated as fractal aggregates composed of small spherical primary monomers. After aging in the atmosphere, soot monomers were coated by a thinly layer of sulfate as thinly coated soot particles. These soot particles were entirely embedded into large sulfate particle by further aging, and becoming heavily coated soot particles. In clear-sky conditions, black carbon radiative forcing with different aging states were investigated for the bottom and top of atmosphere (BOA and TOA). The simulations showed that black carbon radiative forcing increased at BOA and decreased at TOA after their aging processes. Thinly and heavily coated states increased up to ~12% and ~35% black carbon radiative forcing at BOA, and black carbon radiative forcing at TOA can reach to ~20% and ~100% smaller for thinly and heavily coated states than those of freshly emitted states, respectively. The effect of aging states of black carbon radiative forcing was varied with surface albedo, aerosol optical depth and solar zenith angles. These findings would be helpful for the assessments of climate change.
A high-throughput fluorimetric microarray with enhanced fluorescence and suppressed “coffee-ring” effects for the detection of calcium ions in blood
Authors: Ding Yanjun , Ling Jiang , Qiao Yuchun , Li Zhengjian , Sun Zongzhao , Cai Jifeng , Guo Yadong , Wang Hua 
Published: December 2016

AbstractA rapid, ultrasensitive, and high-throughput fluorimetric microarray method has been developed using hydrophobic pattern as the microarray substrate and 3-aminopropyltriethoxysilane-coupled carboxylic acid calcium (APS-CCA) as the fluorescent probes for sensing Ca2+ ions in blood. The hydrophobic pattern of the developed Ca2+ analysis microarray could largely suppress the “coffee-ring” effects to facilitate the better distribution density of testing microspots toward the high-throughput detections, and especially prevent the cross-contamination of the multiple samples between adjacent microspots. Moreover, the use of APS matrix could endow the CCA probe the enhanced environmental stability and fluorescence intensity, which is about 2.3-fold higher than that of free CCA. The interactions between APS-CCA and Ca2+ ions were systematically characterized by UV-vis and fluorescence measurements including microscopy imaging. It was demonstrated that the fluorimetric microarray could display the strong capacity of specifically sensing Ca2+ ions with the minimal interferences from blood backgrounds. Such an APS-CCA-based fluorimetric microarray can allow for the analysis of Ca2+ ions down to 0.0050 mM in blood, promising a highly sensitive and selective detection candidate for Ca2+ ions to be applied in the clinical laboratory.
Biodiversity in models of cyclic dominance is preserved by heterogeneity in site-specific invasion rates
Authors: Szolnoki Attila , Perc Matjaž 
Published: December 2016

AbstractGlobal, population-wide oscillations in models of cyclic dominance may result in the collapse of biodiversity due to the accidental extinction of one species in the loop. Previous research has shown that such oscillations can emerge if the interaction network has small-world properties, and more generally, because of long-range interactions among individuals or because of mobility. But although these features are all common in nature, global oscillations are rarely observed in actual biological systems. This begets the question what is the missing ingredient that would prevent local oscillations to synchronize across the population to form global oscillations. Here we show that, although heterogeneous species-specific invasion rates fail to have a noticeable impact on species coexistence, randomness in site-specific invasion rates successfully hinders the emergence of global oscillations and thus preserves biodiversity. Our model takes into account that the environment is often not uniform but rather spatially heterogeneous, which may influence the success of microscopic dynamics locally. This prevents the synchronization of locally emerging oscillations, and ultimately results in a phenomenon where one type of randomness is used to mitigate the adverse effects of other types of randomness in the system.
Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea
Authors: Wang Kai , Ye Xiansen , Zhang Huajun , Chen Heping , Zhang Demin , Liu Lian 
Published: December 2016

AbstractKnowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies.
Normally‐off AlGaN/GaN‐on‐Si MOS‐HFET with a monolithically integrated single‐stage inverter as a gate driver
Authors: Han S.‐W. , Park S.‐H. , Kim H.‐S. , Jo M.‐G. , Cha H.‐Y. 
Published: December 2016

A normally‐off AlGaN/GaN‐on‐Si metal–oxide–semiconductor‐heterojunction field‐effect transistor (MOS‐HFET) with an integrated single‐stage inverter is developed. The integrated single‐stage GaN inverter consisted of an AlGaN/GaN driver MOS‐HFET and a resistive load. With the monolithically integrated gate driver, the gate charging current was boosted from 10 to 170 mA, which reduced the charging and discharging times from 626 to 107 ns and 553 to 196 ns, respectively.
Comparison of zero‐sequence injection methods in cascaded H‐bridge multilevel converters for large‐scale photovoltaic integration
Authors: Yu Yifan , Konstantinou Georgios , Townsend Christopher D. , Agelidis Vassilios G. 
Published: December 2016

Photovoltaic (PV) power generation levels in the three phases of a multilevel cascaded H‐bridge (CHB) converter can be significantly unbalanced, owing to different irradiance levels and ambient temperatures over a large‐scale solar PV power plant. Injection of a zero‐sequence voltage is required to maintain three‐phase balanced grid currents with unbalanced power generation. This study theoretically compares power balance capabilities of various zero‐sequence injection methods based on two metrics which can be easily generalised for all CHB applications to PV systems. Experimental results based on a 430 V, 10 kW, three‐phase, seven‐level cascaded H‐bridge converter prototype confirm superior performance of the optimal zero‐sequence injection technique.
Catheter-Associated Blood Stream Infections in Intracardiac Lines
Authors: Pye Sherry , Tang Xinyu , Gossett Jeffrey , Prodhan Parthak , Bhutta Adnan , Garcia Xiomara 
Published: December 2016

Purpose Right atrial (RA) or intracardiac lines are commonly used for hemodynamic monitoring in children undergoing cardiac surgery. In some institutions, these lines are used as the preferred long-term access line due to concerns for catheter-associated blood stream infections (CABSI) and catheter-related venous thrombosis with central lines in other locations. However, the rates and risk factors for CABSI and other complications are not known for RA lines. We undertook this study to estimate CABSI rates for RA lines in comparison with central catheters of various types and locations and to evaluate the incidence of other complications associated with the use of RA lines.
Methods After approval from the Institutional Review Board, a retrospective review of all patients undergoing cardiac surgery at Arkansas Children's Hospital between the dates of January 1, 2006 and December 31, 2011 was performed. Demographic data, clinical features, and outcomes were summarized on a per-patient level. Type, location of placement, and duration of all centrally placed catheters as well as associated complications were recorded. Central venous lines (CVL) used in our unit include peripherally inserted central catheters (PICC) lines, and antibiotic and heparin coated double or triple lumen lines placed in internal jugular (IJ), femoral (Fem), or RA positions. The data were analyzed using statistical software STATA/MP.
Results A total of 2,736 central lines were used in 1,537 patients. Data on line duration, alteplase use, and percentage of lines developing CABSI are described in the study. Disease severity as assessed by risk-adjusted classification for congenital heart surgery (RACHS) score (p < 0.046), year of placement (p < 0.001), and line type adjusted for thrombolytic (alteplase) use are significantly associated with risk of any CABSI. Overall, IJ and RA lines had least risk of CABSI while PICC lines had the highest CABSI rates. RA lines are also associated with other medically significant complications.
Conclusion The CABSI rates associated with RA lines are lower than those seen with PICC lines. However, RA line use is associated with other, potentially significant complications. RA lines may be used cautiously as long-term access lines in cardiac patients in whom it is important to preserve venous patency for future interventions.
Homozygosity mapping and CDH23 mutation analysis in Iranian deaf families
Authors: Davoudi-Dehaghani Elham , Bagherian Hamideh , DabbaghBagheri Samira , Mahdieh Nejat , Shirkavand Atefeh , Zeinali Sirous 
Published: December 2016

Objective:
Cadherin-related 23 (CDH23) gene encodes a cell–cell adhesion protein which is required for the proper development of hair cells. Previous studies have shown that different mutations in this gene are associated with Usher syndrome, autosomal recessive nonsyndromic deafness (DFNB12) and age-related hearing loss. In this study the contribution of CDH23 mutations in hearing loss has been investigated.

Study design:
The homosygosity mapping, using microsatellite markers linked to DFNB12 locus was performed for a population of 45 GJB2 negative Iranian families with autosomal recessive non-syndromic form of hearing loss. Coding region and exon-intron boundaries of all 69 exons of the CDH23 gene were investigated using Sanger sequencing.

Results:
The homozygosity mapping showed co-segregation of the hearing loss with four STR markers linked to the DFNB12 locus in one family. Assessing pathogenicity of identified variations in this gene showed that previously reported mutation c.2968G > A (p.Asp990Asn) can be the cause of hearing loss in this family.

Conclusion:
This study suggests that CDH23 mutations may have a significant role in causing hearing loss in Iran. More studies should be performed to determine frequency of this gene in the Iranian population.
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes
Authors: Jung Inuk , Jo Kyuri , Kang Hyejin , Ahn Hongryul , Yu Youngjae , Kim Sun 
Published: December 2016

Abstract

Motivation
Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i.e. gene-time-condition. Computational complexity for analyzing such data is very high, compared to the already difficult NP-hard two dimensional biclustering algorithms. Because of this challenge, traditional time series clustering algorithms are designed to capture co-expressed genes with similar expression pattern in two sample conditions.

Results
We present a triclustering algorithm, TimesVector, specifically designed for clustering three-dimensional time series data to capture distinctively similar or different gene expression patterns between two or more sample conditions. TimesVector identifies clusters with distinctive expression patterns in three steps: (i) dimension reduction and clustering of time-condition concatenated vectors, (ii) post-processing clusters for detecting similar and distinct expression patterns and (iii) rescuing genes from unclassified clusters. Using four sets of time series gene expression data, generated by both microarray and high throughput sequencing platforms, we demonstrated that TimesVector successfully detected biologically meaningful clusters of high quality. TimesVector improved the clustering quality compared to existing triclustering tools and only TimesVector detected clusters with differential expression patterns across conditions successfully.

Availability and Implementation
The TimesVector software is available at http://biohealth.snu.ac.kr/software/TimesVector/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Diagnostic difficulty identifying Apophysomyces trapeziformis septic arthritis in a patient with multiple myeloma
Authors: Bertumen J. Bradford , Schell Wiley A. , Joyce Maria , Alley Christopher , Woods Christopher W. 
Published: December 2016

Introduction:
Mucormycosis is a rare fungal infection, but can cause substantial morbidity and mortality in both immunocompromised and immunocompetent patients. Apophysomyces is a mucormycetes species ubiquitous in nature, particularly in soil, decaying wood and other organic matter. Apophysomyces is known to cause cutaneous fungal infections, particularly after penetrating trauma. Septic arthritis is a rare clinical manifestation.

Case presentation:
We describe a case of Apophysomyces trapeziformis causing septic arthritis of the knee of a patient with multiple myeloma. He was treated multiple times for bacterial septic arthritis with minimal improvement. Surgical tissue specimens finally grew mucoraceous mould, and DNA sequencing and morphological assessment of spores identified the mould as A. trapeziformis. The patient was treated with amphotericin B and posaconazole, but ultimately required an above-the-knee amputation for definitive treatment.

Conclusion:
This case illustrates the need to evaluate for fungal infection in a persistent septic arthritis that is culture negative and refractory to empiric antibiotics, particularly in an immunocompromised individual. It also shows the importance of a thorough social history and adequate tissue specimens for culture.
mRNA destabilisation through CDS-targeting is the primary role of endogenous miRNA in the green algaChlamydomonas
Authors: Chung Betty Y-W. , Deery Michael J. , Groen Arnoud J. , Howard Julie , Baulcombe David 
Published: December 2016

AbstractMicroRNAs regulate gene expression as part of the RNA-induced silencing complex, where the sequence identity of the miRNA provides the specificity to the target messenger RNA, and the result is target repression. The mode of repression can be through target cleavage, RNA destabilization and/or decreased translational efficiency. Here, we provide a comprehensive global analysis of the evolutionarily distant unicellular green algaChlamydomonas reinhardtiito quantify the effects of miRNA on protein synthesis and RNA abundance. We show that, similar to metazoan systems, miRNAs inChlamydomonasregulate gene-expression primarily by destabilizing mRNAs. However, unlike metazoan miRNA where target site utilization localizes mainly to 3’UTRs, inChlamydomonasutilized target sites lie predominantly within coding regions. These results demonstrate that destabilization of mRNA is the main evolutionarily conserved mode of action for miRNAs, but details of the mechanism diverge between plant and metazoan kingdoms.
Monozygotic twin pairs discordant for amyotrophic lateral sclerosis carry both common and unique epigenetic differences relevant to disease
Authors: Young Paul E , Kum Jew Stephen , Buckland Michael E , Pamphlett Roger , Suter Catherine M 
Published: December 2016

AbstractAmyotrophic lateral sclerosis (ALS) is a devastating late-onset neurodegenerative disorder in which only a small proportion of patients carry an identifiable causative genetic lesion. Despite high heritability estimates, a genetic etiology for most sporadic ALS remains elusive. Here we report the epigenetic profiling of five monozygotic twin pairs discordant for ALS in whom previous genome sequencing excluded a genetic basis for their disease discordance. By studying cytosine methylation patterns in peripheral blood DNA we identified thousands of large between-twin differences at individual CpGs. While the specific sites of difference were largely idiosyncratic to a twin pair, a proportion (involving GABA signalling) were common to all affected individuals. In both instances the differences occurred within genes and pathways related to neurobiological function and dysfunction. Our findings reveal widespread changes in epigenetic marks in ALS patients, consistent with an epigenetic contribution to disease. These findings may be exploited to develop blood-based biomarkers of ALS and develop further insight into disease pathogenesis. We expect that our findings will provide a useful point of reference for further large scale studies of sporadic ALS.
Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean
Authors: Matthew S. Leslie , Frederick I. Archer , Phillip A. Morin 
Published: December 2016

AbstractSpinner dolphins (Stenella longirostris) and spotted dolphins (S. attenuata) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA (mtDNA) have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical levels. Our results showed significant differences between subspecies of spotted (FST: 0.0125;P =0.0402) and spinner dolphins (FST: 0.0133;P= 0.034), but no support for the division of existing offshore stocks of spotted dolphins or Tres Marias spinner dolphins. We compare these results to previous results of genome-wide nuclear SNP data and suggest high haplotype diversity, female dispersal, male philopatry, or relative power of the two datasets explains the differences observed. Our results further support a genetic basis for biologically meaningful management units at the subspecies level, and provide a critical component to mitigating historical and continued fishery interactions.