bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zinc disrupts central carbon metabolism and capsule biosynthesis in Streptococcus pyogenes
Authors: Ong Cheryl-lynn Y. , Walker Mark J. , McEwan Alastair G. 
Published: June 2015

AbstractNeutrophils release free zinc to eliminate the phagocytosed bacterial pathogen Streptococcus pyogenes (Group A Streptococcus; GAS). In this study, we investigated the mechanisms underpinning zinc toxicity towards this human pathogen, responsible for diseases ranging from pharyngitis and impetigo, to severe invasive infections. Using the globally-disseminated M1T1 GAS strain, we demonstrate that zinc stress impairs glucose metabolism through the inhibition of the glycolytic enzymes phosphofructokinase and glyceraldehyde-3-phosphate dehydrogenase. In the presence of zinc, a metabolic shift to the tagatose-6-phosphate pathway allows conversion of D-galactose to dihydroxyacetone phosphate and glyceraldehyde phosphate, partially bypassing impaired glycolytic enzymes to generate pyruvate. Additionally, zinc inhibition of phosphoglucomutase results in decreased capsule biosynthesis. These data indicate that zinc exerts it toxicity via mechanisms that inhibit both GAS central carbon metabolism and virulence pathways.
Ultraviolet photoconductive devices with an n-GaN nanorod-graphene hybrid structure synthesized by metal-organic chemical vapor deposition
Authors: Kang San , Mandal Arjun , Chu Jae Hwan , Park Ji-Hyeon , Kwon Soon-Yong , Lee Cheul-Ro 
Published: June 2015

AbstractThe superior photoconductive behavior of a simple, cost-effective n-GaN nanorod (NR)-graphene hybrid device structure is demonstrated for the first time. The proposed hybrid structure was synthesized on a Si (111) substrate using the high-quality graphene transfer method and the relatively low-temperature metal-organic chemical vapor deposition (MOCVD) process with a high V/III ratio to protect the graphene layer from thermal damage during the growth of n-GaN nanorods. Defect-free n-GaN NRs were grown on a highly ordered graphene monolayer on Si without forming any metal-catalyst or droplet seeds. The prominent existence of the undamaged monolayer graphene even after the growth of highly dense n-GaN NRs, as determined using Raman spectroscopy and high-resolution transmission electron microscopy (HR-TEM), facilitated the excellent transport of the generated charge carriers through the photoconductive channel. The highly matched n-GaN NR-graphene hybrid structure exhibited enhancement in the photocurrent along with increased sensitivity and photoresponsivity, which were attributed to the extremely low carrier trap density in the photoconductive channel.
Hexagonal-structured ε-NbN: ultra-incompressibility, high shear rigidity and a possible hard superconducting material
Authors: Zou Yongtao , Wang Xuebing , Chen Ting , Li Xuefei , Qi Xintong , Welch David , Zhu Pinwen , Liu Bingbing , Cui Tian , Li Baosheng 
Published: June 2015

AbstractExploring the structural stability and elasticity of hexagonal ε-NbN helps discover correlations among its physical properties for scientific and technological applications. Here, for the first time, we measured the ultra-incompressibility and high shear rigidity of polycrystalline hexagonal ε-NbN using ultrasonic interferometry and in situ X-ray diffraction, complemented with first-principles density-functional theory calculations up to 30 GPa in pressure. Using a finite strain equation of state approach, the elastic bulk and shear moduli, as well as their pressure dependences are derived from the measured velocities and densities, yielding BS0 = 373.3(15) GPa, G0 = 200.5(8) GPa, ∂BS/∂P = 3.81(3) and ∂G/∂P = 1.67(1). The hexagonal ε-NbN possesses a very high bulk modulus, rivaling that of superhard material cBN (B0 = 381.1 GPa). The high shear rigidity is comparable to that for superhard γ-B (G0 = 227.2 GPa). We found that the crystal structure of transition-metal nitrides and the outmost electrons of the corresponding metals may dominate their pressure dependences in bulk and shear moduli. In addition, the elastic moduli, Vickers hardness, Debye temperature, melting temperature and a possible superconductivity of hexagonal ε-NbN all increase with pressures, suggesting its exceptional suitability for applications under extreme conditions.
Remote p-type Doping in GaSb/InAs Core-shell Nanowires
Authors: Ning Feng , Tang Li-Ming , Zhang Yong , Chen Ke-Qiu 
Published: June 2015

AbstractBy performing first-principles calculation, we investigated the electronic properties of remotely p-type doping GaSb nanowire by a Zn-doped InAs shell. The results show that for bare zinc-blende (ZB) [111] GaSb/InAs core-shell nanowire the Zn p-type doped InAs shell donates free holes to the non-doped GaSb core nanowire without activation energy, significantly increasing the hole density and mobility of nanowire. For Zn doping in bare ZB [110] GaSb/InAs core-shell nanowire the hole states are compensated by surface states. We also studied the behaviors of remote p-type doing in two-dimensional (2D) GaSb/InAs heterogeneous slabs and confirmed that the orientation of nanowire side facet is a key factor for achieving high efficient remote p-type doping.
Switched photocurrent direction in Au/TiO2 bilayer thin films
Authors: Chen Hongjun , Liu Gang , Wang Lianzhou 
Published: June 2015

AbstractSwitched photocurrent direction in photoelectrodes is a very interesting phenomenon and has demonstrated their potentials in important applications including photodiodes, phototransistors, light-driven sensors and biosensors. However, the design and mechanism understanding of such photoelectrodes remain challenging to date. Here we report a new phenomenon of sequence-driven the photocurrent direction on a simple bilayer structure of 5 nm thick Au and 10 nm TiO2 under visible-light irradiation. It is found that when Au layer are deposited as the outer layer on TiO2 coated fluorine doped tin oxide (FTO) substrate (designated as FTO/TiO2/Au), anodic photocurrent is obtained due to the band bending formed at the electrode-electrolyte interface. Interestingly, simply swapping the deposition sequence of Au and TiO2 leads to cathodic photocurrent on FTO/Au/TiO2 electrode. Characterization and calculations on the photoelectrode reveals that the photogenerated electrons can be easily trapped in the energy well formed between the band bending and the Schottky contact, which allows electronic tunnelling through the 1.6 nm thick space charge layer, resulting in a unique anodic to cathodic photocurrent conversion. The understanding of this new phenomenon can be important for designing new generation optoelectronic converting devices in a low-cost and facile manner.
The Serum Profile of Hypercytokinemia Factors Identified in H7N9-Infected Patients can Predict Fatal Outcomes
Authors: Guo Jing , Huang Fengming , Liu Jun , Chen Yu , Wang Wei , Cao Bin , Zou Zhen , Liu Song , Pan Jingcao , Bao Changjun , Zeng Mei , Xiao Haixia , Gao Hainv , Yang Shigui , Zhao Yan , Liu Qiang , Zhou Huandi , Zhu Jingdong , Liu Xiaoli , Liang Weifeng , Yang Yida , Zheng Shufa , Yang Jiezuan , Diao Hongyan , Su Kunkai , Shao Li , Cao Hongcui , Wu Ying , Zhao Min , Tan Shuguang , Li Hui , Xu Xiaoqing , Wang Chunmei , Zhang Jianmin , Wang Li , Wang Jianwei , Xu Jun , Li Dangsheng , Zhong Nanshan , Cao Xuetao , Gao George F. , Li Lanjuan , Jiang Chengyu 
Published: June 2015

AbstractThe novel avian origin influenza A (H7N9) virus has caused severe diseases in humans in eastern China since the spring of 2013. Fatal outcomes of H7N9 infections are often attributed to the severe pneumonia and acute respiratory distress syndrome (ARDS). There is urgent need to discover biomarkers predicting the progression of disease and fatal outcome of potentially lethal flu infections, based on sound statistical analysis. We discovered that 34 of the 48 cytokines and chemokines examined in this study were significantly elevated in the plasma samples from patients infected with H7N9. We report for the first time that the levels of MIF, SCF, MCP-1, HGF and SCGF-β are highly positively linked to disease severity and the profile of mediators MIF, SCF, MCP-1, HGF, SCGF-β, IP-10, IL-18 and IFN-γ is an independent outcome predictor.
Oral Vaccination of Channel Catfish against Enteric Septicemia of Catfish Using a Live Attenuated Edwardsiella ictaluri Isolate
Authors: Wise David J. , Greenway Terrence E. , Byars Todd S. , Griffin Matt J. , Khoo Lester H. 
Published: June 2015

Abstract
Enteric septicemia of catfish (ESC), caused by Edwardsiella ictaluri, is the most problematic bacterial disease affecting catfish aquaculture in the southeastern United States. Efforts to develop an effective ESC vaccine have had limited industrial success. In commercial settings, ESC vaccines are typically administered by immersion when fry are transferred from the hatchery to rearing ponds. While this approach is a practical method of mass delivery, this strategy administers vaccines to very young fish, which lack a fully developed immune system. To circumvent this limitation, an oral vaccination strategy was evaluated as a means of immunizing catfish at the fingerling stage of production, when fish possess a more complete immune arsenal. A virulent E. ictaluri isolate (S97-773) was attenuated by successive passage on media containing increasing concentrations of rifamycin. In laboratory trials, cultured vaccine was diluted and mixed with feed (100 mL diluted vaccine/454 g feed). This mixture was then fed to Channel Catfish Ictalurus punctatus fingerlings. Two separate dilutions of cultured vaccine (1:10 and 1:100) were used to create the vaccine–feed mixture, equating to estimated doses of 5 × 107 and 5 × 106 CFU/g of feed, respectively. After 30 d, catfish were exposed by immersion (1 × 106 CFU/mL) to the virulent parental strain of E. ictaluri. The target dose (1:100 dilution, ∼5 × 106 CFU/g of feed) offered exceptional protection (relative percent survival = 82.6–100%). In addition, negligible deaths occurred in fish vaccinated at 10 times the target dose (1:10 dilution, ∼5 × 107 CFU/g of feed). In pond trials, antibody production increased 18-fold in orally vaccinated fish. When compared with nonvaccinated controls, vaccination significantly improved survival, feed fed, feed conversion, biomass produced, and total harvest. This research demonstrates Channel Catfish can be successfully immunized in a commercial setting against E. ictaluri with a single dose of an orally delivered, live attenuated, E. ictaluri vaccine.
Received July 31, 2014; accepted March 2, 2015
ACE: accurate correction of errors using K-mer tries
Authors: Sheikhizadeh Siavash , de Ridder Dick 
Published: May 2015

Abstract
Summary: The quality of high-throughput next-generation sequencing data significantly influences the performance and memory consumption of assembly and mapping algorithms. The most ubiquitous platform, Illumina, mainly suffers from substitution errors. We have developed a tool, ACE, based on K-mer tries to correct such errors. On real MiSeq and HiSeq Illumina archives, ACE yields higher gains in terms of coverage depth, outperforming state-of-the-art competitors in the majority of cases.
Availability and implementation: ACE is licensed under the GPL license and can be freely obtained at https://github.com/sheikhizadeh/ACE/. The program is implemented in C++ and runs on most Unix-derived operating systems.
Contact: siavash.sheikhizadehanari@wur.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative outcomes of β-lactam antibiotics in outpatient parenteral antibiotic therapy: treatment success, readmissions and antibiotic switches
Authors: Lee Boeun , Tam Idy , Weigel Bernard , Breeze Janis L. , Paulus Jessica K. , Nelson Jason , Allison Genève M. 
Published: May 2015

Abstract

Objectives
β-Lactam antibiotics are commonly used in outpatient parenteral antimicrobial therapy (OPAT), but data regarding outcomes of long-term therapy are limited. The purpose of this study was to compare treatment success, readmission and antibiotic switch rates in patients treated with β-lactam antibiotics as OPAT.

Methods
We carried out a retrospective review of all patients, discharged from Tufts Medical Center with cefazolin, ceftriaxone, ertapenem or oxacillin, between January 2009 and June 2013. A competing risks analysis was used to compare the cumulative incidence of first occurrence of treatment success, antibiotic switch and 30 day readmission for each drug.

Results
Four hundred patients were identified (cefazolin n = 38, ceftriaxone n = 104, ertapenem n = 128 and oxacillin n = 130). Baseline demographics were similar. Treatment success rates were higher for ceftriaxone and ertapenem (cefazolin 61%, ceftriaxone 81%, ertapenem 73% and oxacillin 58%; P &lt; 0.001). Thirty-day all-cause readmissions were similar (cefazolin 21%, ceftriaxone 14%, ertapenem 20% and oxacillin 15%; P = 0.46). In 400 OPAT courses, 37 out of 50 antibiotic switches were accomplished without readmission. Adverse drug events (ADEs) were the most common reason for outpatient antibiotic switches (31/37, 84%). The ADE rate was higher for the oxacillin group (cefazolin 2.0 versus ceftriaxone 1.5 versus ertapenem 2.9 versus oxacillin 8.4 per 1000 OPAT days; P &lt; 0.001).

Conclusions
OPAT with β-lactam antibiotics is effective, but antibiotic switches for adverse events were more frequent with oxacillin use. Clinicians should be cognizant of the risk of readmissions and ADEs in OPAT patients, as the value of OPAT lies in reducing patient morbidity and readmissions by managing ADEs and preventing clinical failures.
SAM/BAM format v1.5 extensions forde novoassemblies
Authors: Cock Peter J. A. , Bonfield James , Chevreux Bastien , Li Heng 
Published: May 2015

ABSTRACTSummary:The plain text Sequence Alignment/Map (SAM) file format and its companion binary form (BAM) are a generic alignment format for storing read alignments against reference sequences (and unmapped reads) together with structured meta-data (Liet al., 2009). Driven by the needs of the 1000 Genomes Project which sequenced many individual human genomes, early SAM/BAM usage focused on pairwise alignments of reads to a reference. However, through the CIGAR P operator multiple sequence alignments can also be preserved. Herein we describe clarifications and additions in version 1.5 of the specification to facilitate storingde novosequence alignments: Padded reference sequences (with gap characters), annotation of reads or regions of the reference, and the option of embedding the reference sequence within the file.Availability:The latest public release of the specification is athttp://samtools.sourceforge.net/SAM1.pdf, with in development drafts athttps://github.com/samtools/hts-specs/under version control.Contact:peter.cock@hutton.ac.uk
A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary
Authors: May Michael R. , Höhna Sebastian , Moore Brian R. 
Published: June 2015

AbstractThe paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting mass-extinction events from phylogenies estimated from molecular sequence data. We develop our approach in a Bayesian statistical framework, which enables us to harness prior information on the frequency and magnitude of mass-extinction events. The approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between rate-shift events. We model three types of events: (1) instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events is described by a separate compound Poisson process (CPP) model, where the waiting times between each event are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-type specific prior distribution. Parameters of the model are then estimated using a reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events, provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e.,below 5%) false discovery rate even in the case of background diversification rate variation. Finally, we provide an empirical application of this approach to conifers, which reveals that this group has experienced two major episodes of mass extinction. This new approach—the CPP on Mass Extinction Times (CoMET) model—provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate.
Learning quantitative sequence-function relationships from high-throughput biological data
Authors: Atwal Gurinder S. , Kinney Justin B. 
Published: June 2015

AbstractUnderstanding the transcriptional regulatory code, as well as other types of information encoded within biomolecular sequences, will require learning biophysical models of sequence-function relationships from high-throughput data. Controlling and characterizing the noise in such experiments, however, is notoriously difficult. The unpredictability of such noise creates problems for standard likelihood-based methods in statistical learning, which require that the quantitative form of experimental noise be known precisely. However, when this unpredictability is properly accounted for, important theoretical aspects of statistical learning which remain hidden in standard treatments are revealed. Specifically, one finds a close relationship between the standard inference method, based on likelihood, and an alternative inference method based on mutual information. Here we review and extend this relationship. We also describe its implications for learning sequence-function relationships from real biological data. Finally, we detail an idealized experiment in which these results can be demonstrated analytically.
Impact of service quality, corporate image and customer satisfaction towards customers’ perceived value in the banking sector in Pakistan
Authors: Zameer Hashim , Tara Anam , Kausar Uzma , Mohsin Aisha 
Published: June 2015

Purpose
– The purpose of this paper is to explore the impact of services quality, customer satisfaction and corporate image on customer perceived value in the banking sector of Pakistan.

Design/methodology/approach
– A model is developed to show the relationship between dependent and independent variables taken from the existing literature. The data are collected from 200 respondents taken from the five major cities of Pakistan using structured questionnaire. Correlation and regression are applied to estimate the relationship between variables and find out the extent to which the independent variables have impact on the dependent variable.

Findings
– Results show that there is a positive relation between the service quality, customer satisfaction and corporate image. It is also analyzed by the results that service quality and customer satisfaction have high impact on the customer perceived value where corporate image also effect the customer perceived value.

Originality/value
– This paper identified the impact of service quality, customer satisfaction and corporate image on the customer perceived value that helps the services sector especially banks how they can improve the customer perceived value through improving their service quality, customer satisfaction and corporate image.
The impact of Islamic beliefs on consumers’ attitudes and purchase intentions of life insurance
Authors: Souiden Nizar , Jabeur Yosr 
Published: June 2015

Purpose
– The purpose of this paper is to investigate the role of Islamic beliefs in moderating consumers’ attitudes and purchase intentions of conventional and Islamic life insurance. Second, it investigates the role of Islamic beliefs in moderating the relationship between the attitude toward conventional/Islamic life insurance and purchase intentions of these types of services.

Design/methodology/approach
– A questionnaire was administered online in a Muslim liberal country where both types of insurance are offered. Based on a total sample of 207 responses, ANOVA tests and a structural Equation Modeling were used to test the research hypotheses.

Findings
– Results show that: the higher (lower) the Islamic beliefs of individuals, the less (more) favorable their attitude will be toward conventional life insurance and the more (less) favorable their attitude will be toward Islamic life insurance; the higher (lower) the Islamic beliefs of individuals, the weaker (stronger) their purchase intentions for conventional life insurance will be and the stronger (weaker) their purchase intentions for Islamic life insurance will be; and Islamic beliefs moderate the relationships between attitudes and purchase intentions of life insurance.

Practical implications
– Because they play a significant role in moderating consumers’ attitudes and purchase intentions of conventional and Islamic life insurance, Islamic beliefs can be used as a meaningful criterion to segment the life insurance markets in (less conservative) Muslim countries. This would help insurance companies to better target their services. In a case where two segments coexist (i.e. individuals scoring low on Islamic beliefs vs individuals scoring high on Islamic beliefs), insurers should weigh different strategic options by targeting one of the two segments or both of them. Perhaps the main issue occurs when an insurer attempts to target both segments. In this case, managers should be aware of the confusion that they might create in the mind of their clients (or potential clients). Concurrently offering two types of life insurance (conventional and Islamic) may put the insurers’ credibility at stake.

Originality/value
– Earlier studies report that in Muslim countries, the demand for life insurance is weak or negatively correlated with religion. The majority of these studies consider religion as a macro indicator (i.e. at the country level) when explaining the demand for such services. The present study further clarifies the nature of the relationship between religion and the demand for life insurance by: examining the role of Islamic beliefs (as one of the main dimensions of Muslims’ religiosity) at the micro level (i.e. at the consumer level); and investigating the moderating role of Islamic beliefs in explaining attitudes and purchase intentions of conventional and Islamic life insurance in a less conservative Muslim country.