bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic variant in IL-33 is associated with idiopathic recurrent miscarriage in Chinese Han population
Authors: Yue Jun , Tong Yu , Xie Lan , Ma Tao , Yang Jiyun 
Published: March 2016

AbstractRecurrent miscarriage (RM) is the occurrence of repeated pregnancies that end in miscarriage of the fetus before 20 weeks of gestation. At least 50% of the RM patients are considered idiopathic. High IL-33 levels are critical in early pregnancy and impact the outcome of subsequent pregnancies. However, the association of polymorphisms of IL-33 with idiopathic RM is still unclear. The present study was initiated to investigate whether IL-33 polymorphisms are risk factors for idiopathic RM in Chinese Han population. Study subjects comprised of 321 cases and 384 controls. Five polymorphisms (rs10435816, rs16924159, rs16924171, rs1929992, rs1332290) in IL-33 and serum IL-33 concentrations were assessed. rs16924159 variant exhibits significant association with RM in additive and recessive genetic model (additive model P = 0.015, recessive model P = 0.007). In contrast, rs10435816, rs16924171, rs1929992 and rs1332290 are not significantly associated with RM. Serum IL-33 levels are significantly lower in RM cases than in control (173.51 ± 94.12 versus. 200.97 ± 110.06 (pg/ml), P = 4.57 × 10−4). There are lower levels of serum IL-33 in rs16924159 homozygous mutant (AA) than homozygous wild-type (GG) in this study population, including cases and control groups (172.18 ± 103.01 versus. 205.82 ± 119.01 (pg/ml), P = 0.006). Reduced IL-33 levels and rs16924159 IL-33 variant may contribute to the pathogenesis of idiopathic RM in Chinese Han population.
X-ray Absorption Spectroscopy Study of the Effect of Rh doping in Sr2IrO4
Authors: Sohn C. H. , Cho Deok-Yong , Kuo C.-T. , Sandilands L. J. , Qi T. F. , Cao G. , Noh T. W. 
Published: March 2016

AbstractWe investigate the effect of Rh doping in Sr2IrO4 using X-ray absorption spectroscopy (XAS). We observed appearance of new electron-addition states with increasing Rh concentration (x in Sr2Ir1−xRhxO4) in accordance with the concept of hole doping. The intensity of the hole-induced state is however weak, suggesting weakness of charge transfer (CT) effect and Mott insulating ground states. Also, Ir Jeff = 1/2 upper Hubbard band shifts to lower energy as x increases up to x = 0.23. Combined with optical spectroscopy, these results suggest a hybridisation-related mechanism, in which Rh doping can weaken the (Ir Jeff = 1/2)–(O 2p) orbital hybridisation in the in-planar Rh-O-Ir bond networks.
Wireless power transfer technology using full‐bridge current‐fed topology for medium power applications
Authors: Samanta Suvendu , Rathore Akshay Kumar 
Published: March 2016

This paper studies, explores and analyses a wireless power transfer (WPT) system using current‐fed power electronics topology for electric vehicles and battery charging applications. The main contribution is analysis, design, and implementation of a current‐fed technology for WPT application. The required resonance in both the transmitter and receiver coils is parallel (L)(C) and series (LC) type, respectively. A detailed mathematical analysis and design have been reported. Stiff DC current at the input of the inverter limits the inverter switch current stress. Also, the inductor in DClink provides natural short‐circuit protection during inverter fault. It is quite important in such application. Resonant converter facilitates soft‐switching at turn‐off of the transmitter side switches. Also, soft‐commutation of rectifier diodes reduces reverse recovery loss. Mathematical analysis is verified by simulation results using PSIM 9.3. A 420 W proof‐of‐concept lab hardware prototype is developed and the experimental results are demonstrated to validate the mathematical analysis and simulation results. The maximum efficiency of DC–DC WPT stage obtained from the proof‐of‐concept lab‐prototype is close to 90% with a coefficient of coupling 18%. It is suitable for solar‐to‐vehicle and single‐phase residential slow charging.
Magnetic field design for optimal wireless power transfer to multiple receivers
Authors: Huang Xiaoyan , Gao Yuqing , Zhou Jing , Ma Jien , Zhang Jian , Fang Youtong 
Published: March 2016

This study proposes a model of multiple receivers in resonant wireless power transmission. Based on the dual‐load series‐resonant wireless power transfer system, the expression of system efficiency and its calculation model is achieved using the coupled mode theory. Considering the mutual coupling between loads, the system transmission efficiency is analysed against the intrinsic decay rate and coupling coefficient by Matlab simulation. The diversity effects of introducing aluminium material are analysed by electromagnetic field analysis through JMAG. Base on the principles of the eddy current loss, the laminated aluminium structure is adopted to restore the transmission characteristics effectively. Finally, 96 kHz magnetic resonant wireless power transfer test platform is established to verify the correctness of theoretical analysis.
On the global attractivity and asymptotic stability for autonomous systems of differential equations on the plane
Authors: Hatvani László 
Published: March 2016

The autonomous system of differential equations
\[

x
′

=
f
(
x
)
,

(
x
=
(

x
1

,

x
2

)
T

∈

R

2

,

f
(
x
)
=
(

f
1

(
x
)
,

f
2

(
x
)

)
T

)
,

x’=f(x),\qquad (x=(x_1,x_2)^T\in \mathbb {R}^2,\ f(x)=(f_1(x),f_2(x))^T),

\]
is considered, and sufficient conditions are given for the global attractivity of the unique equilibrium

x
=
0

x=0

. This property means that all solutions tend to the origin as

t
→
∞

t\to \infty

. The two cases (a)

div
⁡
f
(
x
)
≤
0

\operatorname {div} f(x)\le 0

(

x
∈

R

2

x\in \mathbb {R}^2

) and (b)

div
⁡
f
(
x
)
≥
0

\operatorname {div} f(x)\ge 0

(

x
∈

R

2

x\in \mathbb {R}^2

) are treated, where

div
⁡
f
(
x
)
:=
∂

f
1

(
x
)

/

∂

x
1

+
∂

f
2

(
x
)

/

∂

x
2

\operatorname {div} f(x):=\partial f_1(x)/\partial x_1+\partial f_2(x)/\partial x_2

. Earlier results of N. N. Krasovskiĭ and C. Olech about case (a) are improved and generalized to case (b). Three types of assumptions are required: certain stability properties of the origin (local attractivity, stability), boundedness above in some sense for

div
⁡
f
(
x
)

\operatorname {div} f(x)

, and assumptions that

|

f
(
x
)

|

|f(x)|

is not as small as

|

x

|

→
∞

|x|\to \infty

. The conditions of the second and third types are connected with each other.
HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials
Authors: Mukherjee Sumanta , Bhattacharyya Chiranjib , Chandra Nagasuma 
Published: March 2016

Abstract
Motivation: T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics and are critically dependent on experimentally obtained training data. Analysis of a training set from Immune Epitope Database (IEDB) for several alleles indicates that the sampling of the peptide space is extremely sparse covering a tiny fraction of the possible nonamer space, and also heavily skewed, thus restricting the range of epitope prediction.
Results: We present a new epitope prediction method that has four distinct computational modules: (i) structural modelling, estimating statistical pair-potentials and constraint derivation, (ii) implicit modelling and interaction profiling, (iii) feature representation and binding affinity prediction and (iv) use of graphical models to extract peptide sequence signatures to predict epitopes for HLA class I alleles.
Conclusions: HLaffy is a novel and efficient epitope prediction method that predicts epitopes for any Class-1 HLA allele, by estimating the binding strengths of peptide-HLA complexes which is achieved through learning pair-potentials important for peptide binding. It relies on the strength of the mechanistic understanding of peptide-HLA recognition and provides an estimate of the total ligand space for each allele. The performance of HLaffy is seen to be superior to the currently available methods.
Availability and implementation: The method is made accessible through a webserver http://proline.biochem.iisc.ernet.in/HLaffy.
Contact: nchandra@biochem.iisc.ernet.in
Supplementary information: Supplementary data are available at Bioinformatics online.
A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes
Authors: Cheng Feixiong , Zhao Junfei , Fooksa Michaela , Zhao Zhongming 
Published: March 2016

AbstractObjective Development of computational approaches and tools to effectively integrate multidomain data is urgently needed for the development of newly targeted cancer therapeutics.Methods We proposed an integrative network-based infrastructure to identify new druggable targets and anticancer indications for existing drugs through targeting significantly mutated genes (SMGs) discovered in the human cancer genomes. The underlying assumption is that a drug would have a high potential for anticancer indication if its up-/down-regulated genes from the Connectivity Map tended to be SMGs or their neighbors in the human protein interaction network.Results We assembled and curated 693 SMGs in 29 cancer types and found 121 proteins currently targeted by known anticancer or noncancer (repurposed) drugs. We found that the approved or experimental cancer drugs could potentially target these SMGs in 33.3% of the mutated cancer samples, and this number increased to 68.0% by drug repositioning through surveying exome-sequencing data in approximately 5000 normal-tumor pairs from The Cancer Genome Atlas. Furthermore, we identified 284 potential new indications connecting 28 cancer types and 48 existing drugs (adjusted P &lt; .05), with a 66.7% success rate validated by literature data. Several existing drugs (e.g., niclosamide, valproic acid, captopril, and resveratrol) were predicted to have potential indications for multiple cancer types. Finally, we used integrative analysis to showcase a potential mechanism-of-action for resveratrol in breast and lung cancer treatment whereby it targets several SMGs (ARNTL, ASPM, CTTN, EIF4G1, FOXP1, and STIP1).Conclusions In summary, we demonstrated that our integrative network-based infrastructure is a promising strategy to identify potential druggable targets and uncover new indications for existing drugs to speed up molecularly targeted cancer therapeutics.
Patients, care partners, and shared access to the patient portal: online practices at an integrated health system
Authors: Wolff Jennifer L , Berger Andrea , Clarke Deserae , Green Jamie A , Stametz Rebecca , Yule Christina , Darer Jonathan D 
Published: March 2016

AbstractObjective To describe the characteristics and online practices of patients and “care partners” who share explicit access to a patient portal account at a large integrated health system that implemented shared access functionality in 2003.Materials and Methods Survey of 323 patients and 389 care partners at Geisinger Health System with linked information regarding access and use of patient portal functionality.Results Few (0.4%) registered adult patient portal users shared access to their account. Patients varied in age (range: 18–102); more than half had a high school education or less (53.6%). Patient motivations for sharing access included: to help manage care (41.9%), for emergency reasons (29.7%), lack of technology experience (18.4%), or care partner request (10.0%). Care partners were parents (39.8%), adult children (27.9%), spouses (26.2%), and other relatives (6.1%). Patients were more likely than care partners to have inadequate health literacy (54.8% versus 8.8%, P &lt; .001) and less confident in their ability to manage their care (53.0% versus 88.1%; P &lt; .001). Care partners were more likely than patients to perform health management activities electronically (95.5% versus 48.4%; P &lt; .001), access the patient portal (89.2% versus 30.3%; P &lt; .001), and use patient portal functionality such as secure messaging (39.6% versus 13.9%; P &lt; .001). Care partners used their own credentials (89.1%) and patient credentials (23.3%) to access the patient portal.Discussion and Conclusion Shared access is an underused strategy that may bridge patients’ health literacy deficits and lack of technology experience and that helps but does not fully resolve concerns regarding patient and care partner identity credentials.
Developing knowledge resources to support precision medicine: principles from the Clinical Pharmacogenetics Implementation Consortium (CPIC)
Authors: Hoffman James M , Dunnenberger Henry M , Kevin Hicks J , Caudle Kelly E , Whirl Carrillo Michelle , Freimuth Robert R , Williams Marc S , Klein Teri E , Peterson Josh F 
Published: March 2016

Abstract
To move beyond a select few genes/drugs, the successful adoption of pharmacogenomics into routine clinical care requires a curated and machine-readable database of pharmacogenomic knowledge suitable for use in an electronic health record (EHR) with clinical decision support (CDS). Recognizing that EHR vendors do not yet provide a standard set of CDS functions for pharmacogenetics, the Clinical Pharmacogenetics Implementation Consortium (CPIC) Informatics Working Group is developing and systematically incorporating a set of EHR-agnostic implementation resources into all CPIC guidelines. These resources illustrate how to integrate pharmacogenomic test results in clinical information systems with CDS to facilitate the use of patient genomic data at the point of care. Based on our collective experience creating existing CPIC resources and implementing pharmacogenomics at our practice sites, we outline principles to define the key features of future knowledge bases and discuss the importance of these knowledge resources for pharmacogenomics and ultimately precision medicine.
PhredEM: A Phred-Score-Informed Genotype-Calling Approach for Next-Generation Sequencing Studies
Authors: Liao Peizhou , Satten Glen A. , Hu Yi-juan 
Published: March 2016

ABSTRACTA fundamental challenge in analyzing next-generation sequencing data is to determine an individual’s genotype correctly as the accuracy of the inferred genotype is essential to downstream analyses. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates fromphredscores or recalibrated base quality scores. Others, such as SeqEM, estimate error rates from the read data without using any quality scores. It is also a common quality control procedure to filter out reads with lowphredscores. However, choosing an appropriatephredscore threshold is problematic as a too-high threshold may lose data while a too-low threshold may introduce errors. We propose a new likelihood-based genotype-calling approach that exploits all reads and estimates the per-base error rates by incorporatingphredscores through a logistic regression model. The algorithm, which we call PhredEM, uses the Expectation-Maximization (EM) algorithm to obtain consistent estimates of genotype frequencies and logistic regression parameters. We also develop a simple, computationally efficient screening algorithm to identify loci that are estimated to be monomorphic, so that only loci estimated to be non-monomorphic require application of the EM algorithm. We evaluate the performance of PhredEM using both simulated data and real sequencing data from the UK10K project. The results demonstrate that PhredEM is an improved, robust and widely applicable genotype-calling approach for next-generation sequencing studies. The relevant software is freely available.
dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Authors: Sayols Sergi , Scherzinger Denise , Klein Holger 
Published: March 2016

AbstractBackgroundPCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed genes. Especially when working with little input material or single cells assessing the fraction of duplicate reads is an important quality control step for NGS data sets. Up to now there are only tools to calculate the global duplication rates that do not take into account the effect of gene expression levels which leaves them of limited use for RNA-Seq data.ResultsHere we present the tool dupRadar, which provides an easy means to distinguish artefactual from natural duplicate reads in RNA-Seq data. dupRadar assesses the fraction of duplicate reads per gene dependent on the expression level. Apart from the Bioconductor package dupRadar we provide shell scripts for easy integration into processing pipelines.ConclusionsThe Bioconductor package dupRadar offers straight-forward methods to assess RNA-Seq datasets for quality issues with PCR duplicates. It is aimed towards simple integration into standard analysis pipelines as a default QC metric that is especially useful for low-input and single cell RNA-Seq data sets.
A review of recommendations for medical undergraduate intellectual disability psychiatry teaching from UK reports
Authors: Spackman Ross , Qureshi Adnan , Rai Dheeraj 
Published: March 2016

Purpose– The purpose of this paper is to amalgamate recommendations from contemporary national reports on healthcare provision and needs of people with intellectual disabilities. The paper combines these with recommendations for undergraduate curricula of medical students from the GMC and Royal College of Psychiatrists (RCPsych).Design/methodology/approach– National reports from Mencap, Department of Health, Disability rights commission, NHS Executive, the GMC and RCPsych were searched for relevant recommendations to undergraduate medical education in ID psychiatry. Recommendations were collated and grouped to form a single list for use when planning future curricula or auditing existing teaching.Findings– In total, 13 relevant recommendations were identified in nine groups. These included that people with intellectual disabilities and their carers should be involved in the teaching. That teaching should include the ethical, moral and legal obligations and should include the mental capacity act and equality act. Institutional and individual discrimination should be highlighted as a problem and diagnostic overshadowing should be covered.Originality/value– This paper has collated in a single document the combined recommendations of multiple reports. These are relevant to medical undergraduate teaching and may also be of use to other undergraduate healthcare courses. They are a useful template for others wishing to examine or benchmark the content of their medical undergraduate ID psychiatry teaching against an amalgamated list.
Making older workers happy to carry on
Authors: Beal Brian 
Published: March 2016

Purpose
The paper aims to examine the influences of the competencies, social skills and continuous learning ability on career success and career satisfaction among workers aged 50 and over.

Design/methodology/approach
A mixed methods approach consisted of 920 surveys and 11 semi-structured interviews with working individuals aged 50 or above, registered at a job agency specialized in older employees in The Netherlands. Multiple regression and content analysis were used to analyze the findings.

Findings
The survey showed a positive relationship between the competencies and career success and career satisfaction. However, the interviews revealed that not all older workers perceived the need to continuously stay up-to-date as positive, pushing them into retirement.

Originality/value
The influence of competencies on career success and career satisfaction of older workers has received only little attention from researchers.
Taking the outsider route to learning
Authors: Cole Graham 
Published: March 2016

Findings
When it comes to identifying key factors to organizational success, leadership is invariably uppermost in many minds. It is thus hardly surprising that firms afford leadership development as the top priority. Expert in the field Morgan McCall perfectly articulated its importance when commenting on the imprudence of leaving leadership development to chance. Leadership development comes in an array of shapes and sizes. Mentoring, action learning, case studies, job assignments and experiential learning are just some of the methodologies commonly utilized. Transfer of knowledge, team building, raising self-awareness and increasing the ability to interact with others are core objectives typically pursued.
Investigating a best practice model of microfinance for poverty alleviation
Authors: Toindepi Joseph 
Published: March 2016

Purpose– The purpose of this paper is to establish what constitutes best practice models of microfinance for poverty alleviation. It argues that the new microfinance phenomenon characterized by two camps; commercial and developmental players should be recognized as legitimate separate microfinance approaches with different aims and motives. This paper aims to establish strong foundational argument for developing parallel thinking and separate best practice models for effective engagement with each approach.Design/methodology/approach– Rapid evidence assessment methodology was used to systematically identify and analyze a comprehensive list of relevant literature on best practice models of microfinance for poverty alleviation from both online and offline publications. Over 40 publications on microfinance best practice were critically reviewed with a specific attention to how the two approaches to microfinance (commercial and developmental) were dealt with in relation to impact on poverty and best practice approaches.Findings– The paper argues that, business priorities of commercial microfinance providers differ significantly to those of development microfinance providers and this impacts on the program design which means clients of each regardless of coming from the same target group may have different experiences. The microfinance concept evolved far beyond any single philosophical or ideological confinement that there is now need for formal recognition and acknowledgment that commercial and developmental microfinance paradigms are parallel models of approaches whose continuous evolution is less likely to converge in the near future, so should be treated separately.Research limitations/implications– Because the purpose, challenges and requirements of commercial and developmental microfinance approaches are different, continued lack of purposeful distinction between the two will continue to cause confusion and lack of precision in policy response on specific sector challenges. Further work and discourse on the impact of both commercial and developmental approach to microfinance on service delivery to the poor is required to test the implications on best practice.Originality/value– The paper highlights the fundamental flaw in the current perspective of microfinance sector which fails to recognize irreconcilable parallel approaches underpinned by different motives.