bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology study of HBV genotypes and antiviral drug resistance in multi-ethnic regions from Western China
Authors: Zhang Qi , Liao Yun , Chen Jie , Cai Bei , Su Zhenzhen , Ying Binwu , Lu Xiaojun , Tao Chuanmin , Wang Lanlan 
Published: November 2015

AbstractHepatitis B virus (HBV) infection is a critical global health issue and moderately epidemic in Western China, but HBV molecular epidemiology characteristics are still limited. We conducted this study to investigate HBV genotypes and antiviral resistant mutations in this multi-ethnic area. A total of 1316 HBV patients were recruited from four ethnic groups from 2011 to 2013. Genotypes and resistant mutations were determined by Sanger sequencing. Four genotypes (B, C, D and C/D) were identified. Genotype B and C were common in Han population, while genotype D was predominant in Uygurs. Genotype C was the major genotype in both Tibetans and Yis and recombinant C/D was found in Tibetans only. Lamivudine resistance was common in all populations, especially in Hans with prevalence of 42.8%. Entecavir resistance was barely observed regardless of ethnicity. Genotype C isolates had higher rates of rtA181T/V than genotype B (13.5% vs. 5.1%, P < 0.001), in accordance with higher prevalence of resistance to adefovir (20.0% vs. 9.5%, P < 0.001). While incidence of resistant mutations to other drugs and clinical factors showed no difference among different genotypes. HBV genotypes and resistance-conferring mutations had different geographic and demographic distributions in Western China, which provided molecular epidemiology data for clinical management.
The mitotic regulator Hec1 is a critical modulator of prostate cancer through the long non-coding RNA BX647187 in vitro
Authors: Wang Haifeng , Gao Xu , Lu Xin , Wang Yan , Ma Chunfei , Shi Zhenkai , Zhu Feng , He Biming , Xu Chuanliang , Sun Yinghao 
Published: November 2015

Hec1 (highly expressed in cancer) is a member of a conserved Ndc80 (nuclear division cycle 80) complex that regulates mitotic processes. Its overexpression is seen in various tumours and is associated with cancer progression. However, its expression pattern and role inhuman prostate cancer (PCa) still not clear. The aim of our study is to investigate the expression and functional role of Hec1 in human PCa. Hec1 expression was measured in 10 pairs of PCa cancerous and non-cancerous tissue samples by quantitative real-time (qRT)-PCR. The effects of Hec1 on PCa cells were studied by RNAi approach. Apoptosis and cell cycle were analysed by flow cytometry. Cells viability was evaluated using cell counting Kit-8. Cyclin B1–Cdc2 (cell division cycle 2) activity was measured by ELISA assay. Long non-coding (Lnc)RNAs regulated by Hec1 were gained from bioinformatics analysis. The role of LncRNA BX647187, regulated by Hec1, was finally characterized in PCa cells by siRNA. Our results showed that Hec1 mRNA and protein were significantly overexpressed in Human PCa tissues and several PCa cell lines. Silencing Hec1 markedly suppressed proliferation, promoted apoptosis and induced cell-cycle arrest in G2/M-phase in PCa cells. Through bioinformatics analysis and knockdown Hec1 in PCa cells, we found LncRNA BX647187 was positively regulated by Hec1. We further demonstrated that suppression of BX647187 in PCa cells significantly reduced cell proliferation and promoted apoptosis. Thus, we conclude that Hec1 is consistently overexpressed in human PCa and Hec1 is closely linked with human PCa progression through the meditator LncRNA BX647187. Our studies may contribute to understand the molecular mechanism of PCa pathogenesis and clinical therapy.
Hierarchical decomposition of metabolic networks using k-modules
Authors: Reimers Arne C. 
Published: November 2015

The optimal solutions obtained by flux balance analysis (FBA) are typically not unique. Flux modules have recently been shown to be a very useful tool to simplify and decompose the space of FBA-optimal solutions. Since yield-maximization is sometimes not the primary objective encountered in vivo, we are also interested in understanding the space of sub-optimal solutions. Unfortunately, the flux modules are too restrictive and not suited for this task. We present a generalization, called k-module, which compensates the limited applicability of flux modules to the space of sub-optimal solutions. Intuitively, a k-module is a sub-network with low connectivity to the rest of the network. Recursive application of k-modules yields a hierarchical decomposition of the metabolic network, which is also known as branch decomposition in matroid theory. In particular, decompositions computed by existing methods, like the null-space-based approach, introduced by Poolman et al. [(2007) J. Theor. Biol. 249, 691–705] can be interpreted as branch decompositions. With k-modules we can now compare alternative decompositions of metabolic networks to the classical sub-systems of glycolysis, tricarboxylic acid (TCA) cycle, etc. They can be used to speed up algorithmic problems [theoretically shown for elementary flux modes (EFM) enumeration] and have the potential to present computational solutions in a more intuitive way independently from the classical sub-systems.
Modelling metabolism of the diatomPhaeodactylum tricornutum
Authors: Singh Dipali , Carlson Ross , Fell David , Poolman Mark 
Published: November 2015

Marine diatoms have potential as a biotechnological production platform, especially for lipid-derived products, including biofuels. Here we introduce some features of diatom metabolism, particularly with respect to photosynthesis, photorespiration and lipid synthesis and their differences relative to other photosynthetic eukaryotes. Since structural metabolic modelling of other photosynthetic organisms has been shown to be capable of representing their metabolic capabilities realistically, we briefly review the main approaches to this type of modelling. We then propose that genome-scale modelling of the diatom Phaeodactylum tricornutum, in response to varying light intensity, could uncover the novel aspects of the metabolic potential of this organism.
Double resonant output filter to eliminating the tradeoff between bandwidth and switching ripple in shunt active power filters
Authors: Xu Yong , Yu Jingrong , Cao Yijia , Lu Xiaonan , Yu Jiaqi 
Published: November 2015

Since shunt active power filters (SAPFs) are designed to inject harmonic current, its bandwidth should be much wider compared to regular inverters. LCL filters are commonly employed in regular inverters. However, it cannot completely meet the requirements of SAPF due to its filtering performance and the impact on system stability. This study proposes a novel double resonant LCL (DR‐LCL) filter for SAPFs. Derived from the conventional LCL filters, one RC damping circuit and two LC resonant circuits are employed in the proposed filter. Meanwhile, a resistor is connected in parallel with the grid‐side inductor. The mutual impact among different components of the filter is discussed, and the stability of SAPF with DR‐LCL filter is studied. This DR‐LCL filter can not only inherit the advantages of LCL filters, but also eliminate the tradeoff between bandwidth and switching ripple in SAPFs. Finally, the design principle of the proposed output filter is presented and the parameters of the filter are applied to a 66 kW three‐phase three‐wire SAPF prototype. Simulation and experimental results verify the feasibility of DR‐LCL filter.
Effects of high pCO2 on Tanner crab reproduction and early life history—Part I: long-term exposure reduces hatching success and female calcification, and alters embryonic development
Authors: Swiney Katherine M. , Long William Christopher , Foy Robert J. 
Published: November 2015

Abstract
Ocean acidification, a decrease in ocean pH due to absorption of anthropogenic atmospheric CO2, has variable effects on different species. To examine the effects of long-term exposure on Tanner crab (Chionoecetes bairdi) embryonic development, hatching success, and calcification, ovigerous females were reared in one of three treatments: ambient pH (∼8.1), pH 7.8, and pH 7.5 for 2 years. Embryos and larvae in year 1 were from oocytes developed in the field and appear resilient to high pCO2. Embryos and larvae in year 2 were from oocytes developed under high pCO2 conditions. Oocyte development appears sensitive to high pCO2, effects carryover and altered embryonic development, and reduced hatching success with on average 71% fewer viable larvae hatched in the pH 7.5 treatment than in the other treatments. Per cent calcium was reduced among females exposed to pH 7.5 waters, and their carapaces were noticeably more pliable than those in the other treatments. Softer carapaces may result in reduced defences against predators, and a reduction in the ability to feed on prey with hard parts such as shells. The results from this long-term study suggest that projected ocean pH levels within the next two centuries will likely have a pronounced impact on Tanner crab populations unless the crab are able to acclimatize or adapt to changing conditions.
Octodon degus kin and social structure
Authors: Davis Garrett T. , Vásquez Rodrigo A. , Poulin Elie , Oda Esteban , Bazán-León Enrique A. , Ebensperger Luis A. , Hayes Loren D. 
Published: November 2015

AbstractA growing body of evidence showing that individuals of some social species live in non-kin groups suggests kin selection is not required in all species for sociality to evolve. Here, we investigate 2 populations of Octodon degus , a widespread South American rodent that has been shown to form kin and non-kin groups. We quantified genetic relatedness among individuals in 23 social groups across 2 populations as well as social network parameters (association, strength, and clustering coefficient) in order to determine if these aspects of sociality were driven by kinship. Additionally, we analyzed social network parameters relative to ecological conditions at burrow systems used by groups, to determine if ecological characteristics within each population could explain variation in sociality. We found that genetic relatedness among individuals within social groups was not significantly higher than genetic relatedness among randomly selected individuals in both populations, suggesting that non-kin structure of groups is common in degus. In both populations, we found significant relationships between the habitat characteristics of burrow systems and the social network characteristics of individuals inhabiting those burrow systems. Our results suggest that degu sociality is non-kin based and that degu social networks are influenced by local conditions.Es creciente la evidencia que apoya la ocurrencia de especies sociales donde los individuos no están emparentados genéticamente, lo que sugiere que la selección de parentesco no es indispensable para la evolución de la sociabilidad. En este estudio se examinaron dos poblaciones de Octodon degus , un roedor sudamericano donde los grupos sociales pueden o no incluir individuos cercanamente emparentados. Se cuantificó el parentesco genético entre individuos en 23 grupos sociales y en redes sociales de dos poblaciones para determinar si estos aspectos de la sociabilidad dependen del grado de parentesco. Además, se examinaron asociaciones entre los parámetros cuantificados de las redes sociales (asociación, fuerza, coeficiente de anidamiento) y las condiciones ecológicas a nivel de los sistemas de madriguera usados por cada grupo. El grado de parentesco genético dentro de los grupos no fue distinto del grado de parentesco entre individuos de la población tomados al azar, lo que apoya que una estructura de grupos no emparentada es la regla en Octodon degus . En ambas poblaciones se registró una asociación entre características ecológicas de los sistemas de madriguera y atributos de las redes sociales de los individuos que usan estas estructuras. Nuestros resultados indican que la sociabilidad en Octodon degus no está basada en relaciones de parentesco y que las redes sociales de estos animales dependen de las condiciones ecológicas.
Is the baryon acoustic oscillation peak a cosmological standard ruler?
Authors: Roukema Boudewijn F. , Buchert Thomas , Fujii Hirokazu , Ostrowski Jan J. 
Published: November 2015

Abstract
In the standard model of cosmology, the Universe is static in comoving coordinates; expansion occurs homogeneously and is represented by a global scale factor. The baryon acoustic oscillation (BAO) peak location is a statistical tracer that represents, in the standard model, a fixed comoving-length standard ruler. Recent gravitational collapse should modify the metric, rendering the effective scale factor, and thus the BAO standard ruler, spatially inhomogeneous. Using the Sloan Digital Sky Survey, we show to high significance (P &lt; 0.001) that the spatial compression of the BAO peak location increases as the spatial paths’ overlap with superclusters increases. Detailed observational and theoretical calibration of this BAO peak location environment dependence will be needed when interpreting the next decade's cosmological surveys.
Exopolysaccharide biosynthetic glycoside hydrolases can be utilized to disrupt and preventPseudomonas aeruginosabiofilms
Authors: Baker Perrin , Hill Preston J. , Snarr Brendan D. , Alnabelseya Noor , Pestrak Mathew J. , Lee Mark J. , Jennings Laura K. , Tam John , Melnyk Roman , Parsek Matthew R. , Sheppard Donald C. , Wozniak Daniel J. , Howell P. Lynne 
Published: November 2015

AbstractBacterial biofilms are a significant medical challenge as they are recalcitrant to current therapeutic regimes. A key component of biofilm formation in the opportunistic human pathogenPseudomonas aeruginosais the biosynthesis of the exopolysaccharides Pel and Psl, which are involved in the formation and maintenance of the structural biofilm scaffold and protection against antimicrobials and host defenses. Given that the glycoside hydrolases – PelAhand PslGh– encoded in thepelandpslbiosynthetic operons, respectively, are utilized forin vivoexopolysaccharide processing, we reasoned that these would provide specificity to targetP. aeruginosabiofilms. Evaluating these enzymes as potential therapeutics, we demonstrate that these glycoside hydrolases selectively target and degrade the exopolysaccharide component of the biofilm matrix and that nanomolar concentrations of these enzymes can both prevent biofilm formation as well as rapidly disrupt preexisting biofilmsin vitro. This treatment was effective against clinical and environmentalP. aeruginosaisolates and reduced biofilm biomass by 58–94%. These non-cytotoxic enzymes potentiated antibiotics as the addition of either enzyme to a sub-lethal concentration of colistin reduced viable bacterial counts by 2.5 orders of magnitude. Additionally, PelAhwas able to increase neutrophil killing by ~50%. This work illustrates the feasibility and benefits of using bacterial exopolysaccharide biosynthetic glycoside hydrolases and synthetic biology to develop novel anti-biofilm therapeutics.
A quantitative interaction between signal detection in attention and reward/aversion behavior
Authors: Viswanathan V , Kim BW , Sheppard JP , Ying H , Raman K , Lee MJ , Lee S , Mulhern F , Block M , Calder B , Mortensen D , Blood AJ , Breiter HC ,   Phenotype Genotype Project in Addiction and Mood Disorders
Published: November 2015

AbstractThis study examines how processes such as reward/aversion and attention, which are often studied as independent processes, in fact interact at a systems level. We operationalize attention with a continuous performance task and variables from signal detection theory, and reward/aversion with a keypress task using variables from relative preference theory. We find that while the relationship between reward/aversion and attention is functionally invariant, a power law formulation akin to the Cobb-Douglas production function in economics provides the best model fit and theoretical explanation for the interaction. These results indicate that a decreasing signal-to-noise with signal detection results in higher loss aversion. Furthermore, the estimated exponents for the multiplicative power law suggest capacity constraints to processing for attention and reward/aversion. These results demonstrate a systemic interaction of attention and reward/aversion across subjects, with a quantitative schema raising the hypothesis that mechanistic inference may be possible at the level of behavior alone.
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases
Authors: Queralt Rosinach Núria , Piñero Janet , Bravo Serrano Àlex , Sanz Ferran , Furlong Laura I. 
Published: November 2015

AbstractMotivationDisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web (SW). Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected Linked Open Data (LOD).Availabilityhttp://rdf.disgenet.org/Contactsupport@disgenet.org
The limitations ofin vitroexperimentation in understanding biofilms and chronic infection
Authors: Roberts Aled E. L. , Kragh Kasper N. , Bjarnsholt Thomas , Diggle Stephen P. 
Published: November 2015

AbstractWe have become increasingly aware that during infection, pathogenic bacteria often grow in multicellular biofilms which are often highly resistant to antibacterial strategies. In order to understand how biofilms form and contribute to infection,in vitrobiofilm systems such as microtitre plate assays and flow cells, have been heavily used by many research groups around the world. Whilst these methods have greatly increased our understanding of the biology of biofilms, it is becoming increasingly apparent that many of ourin vitromethods do not accurately representin vivoconditions. Here we present a systematic review of the most widely usedin vitrobiofilm systems, and we discuss why they are not always representative of thein vivobiofilms found in chronic infections. We present examples of methods that will help us to bridge the gap betweenin vitroandin vivobiofilm work, so that our bench-side data can ultimately be used to improve bedside treatment.
The experiences of mothers caring for a child with developmental disabilities: a cross cultural perspective
Authors: Heer Kuljit , Rose John , Larkin Michael , Singhal Nidhi 
Published: November 2015

Purpose
– India has one of the more progressive disability frameworks in the developing world which tends to adopt western philosophies and principles (e.g. parent participation and advocacy) which to some degree mirrors the type of service delivery in the UK. The purpose of this paper is to adopt a cross-cultural perspective to explore caregiving amongst parents caring for a child with intellectual/developmental disabilities in India.

Design/methodology/approach
– Three focus groups were used to interview parents at Action for Autism (AFA) located in Delhi, India. The focus groups explored how disability is encountered within an Indian context.

Findings
– Two main themes were identified in the parents narratives which were “making the decision to get help” and “seeing disabilities in from a new perspective”. Family members played an important role in the decision to get help and acted as a platform for mothers to explore their own concerns. Seeing disability from a new perspective was a four stage process which included initially accepting the diagnosis and their child; regaining control through parenting skills training; witnessing positive changes in their children and themselves and reaping personal benefits as a result of their involvement with AFA.

Research limitations/implications
– The research is very small scale and focused on parents in a specific organisation, as a consequence the results cannot be generalised.

Originality/value
– The discourses of these individuals do provide a useful insight into the provision of services to children in India and provide a starting point for cross-cultural understanding of parenting children with disabilities.
Multi-modular design optimization and multidisciplinary design optimization
Authors: Adami Amirhossein , Mortazavi Mahda , Nosratollahi Mehran 
Published: November 2015

Purpose
– For complex engineering problems, multidisciplinary design optimization (MDO) techniques use some disciplines that need to be run several times in different modules. In addition, mathematical modeling of a discipline can be improved for each module. The purpose of this paper is to show that multi-modular design optimization (MMO) improves the design performances in comparison with MDO technique for complex systems.

Design/methodology/approach
– MDO framework and MMO framework are developed to optimum design of a complex system. The nonlinear equality and inequality constrains are considered. The system optimizers included Genetic Algorithm and Sequential Quadratic Programming.

Findings
– As shown, fewer design variables (optimization variables) are needed at the system level for MMO. Unshared variables are optimized in the related module when shared variables are optimized at the system level. The results of this research show that MMO has lower elapsed times (14 percent) with lower F-count (16 percent).

Practical implications
– The monopropellant propulsion upper-stage is selected as a case study. In this paper, the efficient model of the monopropellant propulsion system is proposed. According to the results, the proposed model has acceptable accuracy in mass model (error
<
2 percent), performance estimation (error
<
6 percent) and geometry estimation (error
<
10 percent).

Originality/value
– The monopropellant propulsion system is broken down into the three important modules including propellant tank (tank and propellant), pressurized feeding (tank and gas) and thruster (catalyst, nozzle and catalysts bed) when chemical decomposition, aerothermodynamics, mass and configuration, catalyst and structure have been considered as the disciplines. The both MMO and MDO frameworks are developed for the monopropellant propulsion system.