bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guidelines for the standardization of preanalytic variables for blood‐based biomarker studies in Alzheimer's disease research
Authors: O'Bryant Sid E. , Gupta Veer , Henriksen Kim , Edwards Melissa , Jeromin Andreas , Lista Simone , Bazenet Chantal , Soares Holly , Lovestone Simon , Hampel Harald , Montine Thomas , Blennow Kaj , Foroud Tatiana , Carrillo Maria , Graff-Radford Neill , Laske Christoph , Breteler Monique , Shaw Leslie , Trojanowski John Q. , Schupf Nicole , Rissman Robert A. , Fagan Anne M. , Oberoi Pankaj , Umek Robert , Weiner Michael W. , Grammas Paula , Posner Holly , Martins Ralph ,   STAR-B and BBBIG working groups
Published: October 2014

AbstractThe lack of readily available biomarkers is a significant hindrance toward progressing to effective therapeutic and preventative strategies for Alzheimer's disease (AD). Blood‐based biomarkers have potential to overcome access and cost barriers and greatly facilitate advanced neuroimaging and cerebrospinal fluid biomarker approaches. Despite the fact that preanalytical processing is the largest source of variability in laboratory testing, there are no currently available standardized preanalytical guidelines. The current international working group provides the initial starting point for such guidelines for standardized operating procedures (SOPs). It is anticipated that these guidelines will be updated as additional research findings become available. The statement provides (1) a synopsis of selected preanalytical methods utilized in many international AD cohort studies, (2) initial draft guidelines/SOPs for preanalytical methods, and (3) a list of required methodological information and protocols to be made available for publications in the field to foster cross‐validation across cohorts and laboratories.
Psychometric evaluation of the Work Readiness Questionnaire in schizophrenia
Authors: Potkin Steven G. , Bugarski-Kirola Dragana , Edgar Chris J. , Soliman Sherif , Le Scouiller Stephanie , Kunovac Jelena , Miguel Velasco Eugenio , Garibaldi George M. 
Published: October 2014

Objective/IntroductionUnemployment can negatively impact quality of life among patients with schizophrenia. Employment status depends on ability, opportunity, education, and cultural influences. A clinician-rated scale of work readiness, independent of current work status, can be a valuable assessment tool. A series of studies were conducted to create and validate a Work Readiness Questionnaire (WoRQ) for clinicians to assess patient ability to engage in socially useful activity, independent of work availability.MethodsContent validity, test–retest and inter-rater reliability, and construct validity were evaluated in three separate studies.ResultsContent validity was supported. Cronbach’s α was 0.91, in the excellent range. Clinicians endorsed WoRQ concepts, including treatment adherence, physical appearance, social competence, and symptom control. The final readiness decision showed good test–retest reliability and moderate inter-rater reliability. Work readiness was associated with higher function and lower levels of negative symptoms. Low positive and high negative predictive values confirmed the concept validity.DiscussionThe WoRQ has suitable psychometric properties for use in a clinical trial for patients with a broad range of symptom severity. The scale may be applicable to assess therapeutic interventions. It is not intended to assess eligibility for supported work interventions.ConclusionsThe WoRQ is suitable for use in schizophrenia clinical trials to assess patient work functional potential.
Model‐Based Assessment of Dosing Strategies in Children for Monoclonal Antibodies Exhibiting Target‐Mediated Drug Disposition
Authors: Zheng S , Gaitonde P , Andrew M A , Gibbs M A , Lesko L J , Schmidt S 
Published: October 2014

Body weight/body surface area–based and/or tiered fixed dosing strategies are widely utilized for monoclonal antibodies with linear clearance to scale adult clinical doses to children. However, there is limited knowledge on whether or not body weight–based dosing strategies also yield comparable dose‐concentration‐response relationships in adults and children for monoclonal antibodies that exhibit target‐mediated drug disposition. Our findings indicate that it is important to interpret pharmacokinetics information in a pharmacokinetics/pharmacodynamics context as similar systemic drug exposure in adults and children may not be reflective of the corresponding target occupancy. They further indicate that BW‐based dosing is superior to fixed dosing for the same target concentration, whereas the opposite holds true for the same target amount in adults and children. Michaelis‐Menten approximations yielded similar profiles compared to the full target‐mediated drug disposition model for all simulation scenarios and may be used to guide the selection of appropriate dosing regimens in children.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e138; doi:10.1038/psp.2014.38; published online 01 October 2014
The disease-associated mutation of the mitochondrial thiol oxidase Erv1 impairs cofactor binding during its catalytic reaction
Authors: Ceh-Pavia Efrain , Ang Swee Kim , Spiller Michael P. , Lu Hui 
Published: October 2014

Erv1 (essential for respiration and viability 1) is an FAD-dependent thiol oxidase of the Erv/ALR (augmenter of liver regeneration) sub-family. It is an essential component of the mitochondrial import and assembly (MIA) pathway, playing an important role in the oxidative folding of the mitochondrial intermembrane space (IMS) proteins and linking the MIA pathway to the mitochondrial respiratory chain via cytochrome c (cyt c). The importance of the Erv/ALR enzymes was also demonstrated in a recent study where a single mutation in the human ALR (R194H) leads to autosomal recessive myopathy [Di Fonzo, Ronchi, Lodi, Fassone, Tigano, Lamperti, Corti, Bordoni, Fortunato, Nizzardo et al. (2009) Am. J. Hum. Genet. 84, 594–604]. However, the molecular mechanism of the disease is still unclear. In the present study, we use yeast Erv1 as a model to provide clear evidence for a progressive functional defect in the catalytic activity of the corresponding Erv1 R182H mutant. We show that the FAD cofactor was released from Erv1 R182H during its catalytic cycle, which led to the inactivation of the enzyme. We also characterized the effects of the mutation on the folding and stability of Erv1 and tested our in vitro findings in vivo using a yeast genetic approach. The results of the present study allow us to provide a model for the functional defect in Erv1 R182H, which could potentially be extended to human ALR R194H and provides insights into the molecular basis of autosomal recessive myopathy.
Tsc1 promotes the differentiation of memory CD8
+
T cells via orchestrating the transcriptional and metabolic programs
Authors: Shrestha Sharad , Yang Kai , Wei Jun , Karmaus Peer W. F. , Neale Geoffrey , Chi Hongbo 
Published: October 2014

Significance
Enhancing the generation and function of memory T cells represents a crucial strategy to improve protective immunity against pathogens and tumors. The signaling pathway via mechanistic target of rapamycin (mTOR) has been implicated in the regulation of the differentiation of effector and memory T cells, but the upstream regulators or downstream mechanisms remain unclear. In this study, we provide insight into the mechanistic basis that controls mTOR signaling and memory T-cell responses. The deficiency of tuberous sclerosis 1 (Tsc1) in antigen-experienced T cells impairs the differentiation of memory T-cell precursors and the formation of memory T cells, associated with excessive mTOR activity and dysregulated cell metabolism. Our study establishes a molecular mechanism that links mTOR signaling and cell metabolism for memory T-cell development.
Modulation of age-related insulin sensitivity by VEGF-dependent vascular plasticity in adipose tissues
Authors: Honek Jennifer , Seki Takahiro , Iwamoto Hideki , Fischer Carina , Li Jingrong , Lim Sharon , Samani Nilesh J. , Zang Jingwu , Cao Yihai 
Published: October 2014

Significance
The etiology and mechanisms underlying the age-related high incidence of metabolic diseases such as type 2 diabetes are not fully understood. In this paper, we show that blood vasculatures in the adipose tissues experience continuous changes during aging and VEGF is a key angiogenic factor controlling microvessel numbers and functions. Surprisingly, targeting VEGF and VEGF receptor 2 by specific blocking drugs produces different and sometimes opposing effects on white adipocytes, resulting in marked differences in insulin sensitivity in different age groups. These findings demonstrate that vascular changes in white adipose tissues are the key determinant for modulation of adipocyte metabolism and insulin sensitivity and provide valuable information for treatment of obesity and diabetes by targeting the vasculature.
A historical examination of the Corps of Engineers and natural valley storage protection: the economics and politics of ‘green’ flood control
Authors: Kousky Carolyn 
Published: October 2014

Abstract
Between 1972 and 1994, the US Army Corps of Engineers undertook five studies in New England evaluating the benefits and costs of protecting natural valley storage (NVS) areas—natural reservoirs—for flood mitigation. Only along the Charles River did benefits outweigh costs. Analysis of the studies finds that the costs of large-scale land acquisition will often exceed the sole benefits of avoided flood damages. To generate net benefits, there must be significant amounts of NVS lands still undeveloped, development pressure on those lands, and downstream areas that would sustain large damages. The NVS studies also raised questions of whether the Corps should be involved in land acquisition, and whether regulating land use could substitute for purchasing land. Note, these findings do not apply to other forms of natural flood-risk reduction, such as levee setbacks, green infrastructure for stormwater management, and multi-purpose projects, which have different economic and institutional contexts.
Nonlinear equations for fractional Laplacians II: Existence, uniqueness, and qualitative properties of solutions
Authors: Cabré Xavier , Sire Yannick 
Published: October 2014

This paper, which is the follow-up to part I, concerns the equation

(
−
Δ

)

s

v
+

G
′

(
v
)
=
0

(-\Delta )^{s} v+G’(v)=0

in

R

n

\mathbb {R}^{n}

, with

s
∈
(
0
,
1
)

s\in (0,1)

, where

(
−
Δ

)

s

(-\Delta )^{s}

stands for the fractional Laplacian—the infinitesimal generator of a Lévy process.

When

n
=
1

n=1

, we prove that there exists a layer solution of the equation (i.e., an increasing solution with limits

±
1

\pm 1

at

±
∞

\pm \infty

) if and only if the potential

G
G

has only two absolute minima in

[
−
1
,
1
]

[-1,1]

, located at

±
1

\pm 1

and satisfying

G
′

(
−
1
)
=

G
′

(
1
)
=
0

G’(-1)=G’(1)=0

. Under the additional hypotheses

G
(
−
1
)
>
0

G(-1)>0

and

G
(
1
)
>
0

G(1)>0

, we also establish its uniqueness and asymptotic behavior at infinity. Furthermore, we provide with a concrete, almost explicit, example of layer solution.

For

n
≥
1

n\geq 1

, we prove some results related to the one-dimensional symmetry of certain solutions—in the spirit of a well-known conjecture of De Giorgi for the standard Laplacian.
Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes
Authors: Trubetskoy Vassily , Rodriguez Alex , Dave Uptal , Campbell Nicholas , Crawford Emily L. , Cook Edwin H. , Sutcliffe James S. , Foster Ian , Madduri Ravi , Cox Nancy J. , Davis Lea K. 
Published: October 2014

Abstract
Motivation : The development of cost-effective next-generation sequencing methods has spurred the development of high-throughput bioinformatics tools for detection of sequence variation. With many disparate variant-calling algorithms available, investigators must ask, ‘Which method is best for my data?’ Machine learning research has shown that so-called ensemble methods that combine the output of multiple models can dramatically improve classifier performance. Here we describe a novel variant-calling approach based on an ensemble of variant-calling algorithms, which we term the Consensus Genotyper for Exome Sequencing (CGES). CGES uses a two-stage voting scheme among four algorithm implementations. While our ensemble method can accept variants generated by any variant-calling algorithm, we used GATK2.8, SAMtools, FreeBayes and Atlas-SNP2 in building CGES because of their performance, widespread adoption and diverse but complementary algorithms.
Results : We apply CGES to 132 samples sequenced at the Hudson Alpha Institute for Biotechnology (HAIB, Huntsville, AL) using the Nimblegen Exome Capture and Illumina sequencing technology. Our sample set consisted of 40 complete trios, two families of four, one parent–child duo and two unrelated individuals. CGES yielded the fewest total variant calls ( NCGES=139°897 ), the highest Ts/Tv ratio (3.02), the lowest Mendelian error rate across all genotypes (0.028%), the highest rediscovery rate from the Exome Variant Server (EVS; 89.3%) and 1000 Genomes (1KG; 84.1%) and the highest positive predictive value (PPV; 96.1%) for a random sample of previously validated de novo variants. We describe these and other quality control (QC) metrics from consensus data and explain how the CGES pipeline can be used to generate call sets of varying quality stringency, including consensus calls present across all four algorithms, calls that are consistent across any three out of four algorithms, calls that are consistent across any two out of four algorithms or a more liberal set of all calls made by any algorithm.
Availability and implementation : To enable accessible, efficient and reproducible analysis, we implement CGES both as a stand-alone command line tool available for download in GitHub and as a set of Galaxy tools and workflows configured to execute on parallel computers.
Contact : trubetskoy@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Powdery Mildew Caused by Erysiphe platani on Platanus × acerifolia in Rio Grande do Sul, Brazil
Authors: de Oliveira T. S. , Dallagnol L. J. , de Araujo Filho J. V. , de Castro Moretti F. R. , Camargo L. E. A. 
Published: October 2014

Platanus × acerifolia (Aiton) Willd. (London planetree) is a tree commonly used as an ornamental and in the furniture industry. In the summer of 2013, powdery mildew was observed on shoots of P. × acerifolia plants in the cities of Pelotas and Canela (State of Rio Grande do Sul, Brazil). Voucher specimens (n = 2) were deposited in the Phytopathological Museum Manoel Alves Oliveira at Federal University of Pelotas. Dense white powdery masses of conidia and mycelium were observed on leaves (abaxial and adaxial surfaces), petioles, and young stems. Leaves with high disease severities (≥70%) were deformed with curved edges to the adaxial side, and they often died. Mycelia were superficial with lobed appressoria. Conidiophores were straight, sometimes curved at the base, unbranched, cylindrical, 98 to 236 μm long (137.3 ± 41.2 μm) and composed of a cylindrical foot cell 49 to 102 μm long (66.9 ± 19.5 μm) and 4.4 to 6.4 μm wide (5.3 ± 0.8 μm) followed by two to four cells. Conidia were produced singly or in short chains (two to three), without distinct fibrosin bodies, ellipsoid to ovoid and measuring 24 to 37 μm long (29.5 ± 3.2 μm) and 12 to 19 μm wide (15.2 ± 1.4 μm), often with a wrinkled appearance. Primary conidia had truncate bases and rounded apex while both base and apex were truncated in secondary conidia. Germ tubes were produced apically (pseudoidium type). Chasmothecia were not observed. Genomic DNA was used to amplify the internal transcribed spacer (ITS) region using the ITS1 and ITS4 primers. The resulting sequence (602 bp) was deposited (Accession No. KF499270) in GenBank. BLASTn searches revealed similarity of 100 and 99% with Erysiphe platani from P. orientalis L. (Accession No. JQ365943.1) and P. occidentalis L. (Accession No. JX997805.1), respectively. Phylogenetic analysis placed our sequence in a clade (99% bootstrap support) which included only other E. plantani sequences. In short, morphological and molecular approaches allowed us to identify the infecting fungus as E. platani. For Koch's postulates, 10 detached leaves were inoculated (10 to 15 conidia cm2) on their adaxial surface using an eyelash brush. Non-inoculated leaves served as control. All leaves were kept inside trays with petiole immersed in humidified cotton and maintained at 25 ± 1°C. Symptoms identical to those of the original leaves were observed 6 to 8 days after inoculation, whereas the control leaves remained symptomless. Although E. platani has been previously reported on P. × acerifolia in the city of Poços de Calda, state of Minas Gerais, Brazil (1) and on P. occidentalis in Korea (2), to our knowledge, this is the first record of E. platani on P. × acerifolia in Rio Grande do Sul, Brazil. References: (1) E. M. Inokuti et al. New Dis. Rep. 15:38, 2007. (2) Y. J. La and H. D. Shin. Plant Dis. 97:843, 2013.
Spatio-Temporal Dynamics of Fructan Metabolism in Developing Barley Grains
Authors: Peukert Manuela , Thiel Johannes , Peshev Darin , Weschke Winfriede , Van den Ende Wim , Mock Hans-Peter , Matros Andrea 
Published: October 2014

Abstract
Barley (Hordeum vulgare) grain development follows a series of defined morphological and physiological stages and depends on the supply of assimilates (mainly sucrose) from the mother plant. Here, spatio-temporal patterns of sugar distributions were investigated by mass spectrometric imaging, targeted metabolite analyses, and transcript profiling of microdissected grain tissues. Distinct spatio-temporal sugar balances were observed, which may relate to differentiation and grain filling processes. Notably, various types of oligofructans showed specific distribution patterns. Levan- and graminan-type oligofructans were synthesized in the cellularized endosperm prior to the commencement of starch biosynthesis, while during the storage phase, inulin-type oligofructans accumulated to a high concentration in and around the nascent endosperm cavity. In the shrunken endosperm mutant seg8, with a decreased sucrose flux toward the endosperm, fructan accumulation was impaired. The tight partitioning of oligofructan biosynthesis hints at distinct functions of the various fructan types in the young endosperm prior to starch accumulation and in the endosperm transfer cells that accomplish the assimilate supply toward the endosperm at the storage phase.
Computer literacy competencies among Indian students: the digital divide
Authors: Sampath Kumar B.T. , Basavaraja M.T. , Gagendra R. 
Published: October 2014

Purpose
– The purpose of this paper is to investigate computer literacy competencies among rural and urban students in India and its prime objectives are to find out: how rural and urban students use computers, what is the purpose of computers for these students and what problems have the students encountered while using computers.

Design/methodology/approach
– Scheduled interviews were conducted to collect necessary data from rural and urban students. The interview schedules consisted of various questions designed to elicit details about the students’ use of computers. A total of 600 interview schedules were collected and data were analyzed using Statistical Package for the Social Sciences for windows to test the formulated hypothesis.

Findings
– The findings of the study indicate that the infrastructural facilities varied among rural and urban schools. Another notable finding of the study was that majority (91.33 percent) of urban students used computers compared to a significantly less percentage of rural students (32.33 percent). Most rural students have not used computers mainly because they do not know how to (49.75 percent) followed by lack of support from teachers (48.76 percent) and non-availability of computers in their schools (48.27 percent). Electrical power failure was another major problem faced by both urban students (31.75 percent) and rural students (40.20 percent).

Originality/value
– This study attempted to learn about the computer literacy competencies among the students and the digital divide in Indian schools. On the basis of the findings, the study has recommended guidelines to bridge the digital gap. These findings and recommendations will potentially be helpful to school authorities and the government in order to take the necessary measurements to bridge the digital gap between the rural and urban students.
Guinea-Bissau 2014 elections
Authors: A. Berlie Jean 
Published: October 2014

Purpose
– The West African Republic of Guinea-Bissau has been unstable since gaining its independence in 1974. The 2014 presidential and parliamentary elections are being closely analyzed to study how the United Nations and the Guinean people have reacted to the outcomes of these elections. The paper aims to discuss these issues.

Design/methodology/approach
– Sociological methodologies and a comparative approach have been used in this paper to understand why the elections in 2014 were so important in this country.

Findings
– The author finds that stability is possible in Guinea-Bissau after years of political uncertainties.

Originality/value
– Particular focus has been paid to studying the responses of specific aspects of society, including the youth population, the political elite, the main political party, the African Party for the Independence of Guinea and Cape Verde, the opposition parties and the army and whether these different groups will be able to cooperate after electing a sustainable and relatively wide-ranging government.
Police legitimacy and protest policing: a case study of Hong Kong
Authors: Lai Hang Hui Dennis , Chi Yan Au Ryan 
Published: October 2014

Purpose
– The purpose of this paper is to examine the interplay between police legitimacy and protest policing with reference to the case of Hong Kong.

Design/methodology/approach
– This study will review the concepts of police legitimacy and protest policing and examine the evolving policing practices in Hong Kong since 2010.

Findings
– The study argues that the increasing polarisation of society could render policing protest a potential source of problem for sustaining police legitimacy.

Originality/value
– This is a pioneering study that looks at the interplay between police legitimacy and protest policing.
Police powers and accountability in China and Hong Kong: a comparative perspective
Authors: Chan Ray 
Published: October 2014

Purpose
– The purpose of this paper is to study police powers and accountability from a comparative perspective in both China and Hong Kong.

Design/methodology/approach
– This paper compares and contrasts police powers and accountability.

Findings
– The implications are many, including different political systems in which China is more authoritarian or paternalistic whereas Hong Kong is more pluralistic; checks and balances mechanisms in Hong Kong are far greater than in China; and the concept of accountability to the public is different in that Hong Kong police are accountable to members of the public but the mainland Chinese police force has a limited and top-down concept of accountability.

Originality/value
– An original comparative approach to policing in Hong Kong and China.