bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiclass relevance units machine: benchmark evaluation and application to small ncRNA discovery
Authors: Menor Mark , Baek Kyungim , Poisson Guylaine 
Published: February 2013

Abstract

Background
Classification is the problem of assigning each input object to one of a finite number of classes. This problem has been extensively studied in machine learning and statistics, and there are numerous applications to bioinformatics as well as many other fields. Building a multiclass classifier has been a challenge, where the direct approach of altering the binary classification algorithm to accommodate more than two classes can be computationally too expensive. Hence the indirect approach of using binary decomposition has been commonly used, in which retrieving the class posterior probabilities from the set of binary posterior probabilities given by the individual binary classifiers has been a major issue.

Methods
In this work, we present an extension of a recently introduced probabilistic kernel-based learning algorithm called the Classification Relevance Units Machine (CRUM) to the multiclass setting to increase its applicability. The extension is achieved under the error correcting output codes framework. The probabilistic outputs of the binary CRUMs are preserved using a proposed linear-time decoding algorithm, an alternative to the generalized Bradley-Terry (GBT) algorithm whose application to large-scale prediction settings is prohibited by its computational complexity. The resulting classifier is called the Multiclass Relevance Units Machine (McRUM).

Results
The evaluation of McRUM on a variety of real small-scale benchmark datasets shows that our proposed Naïve decoding algorithm is computationally more efficient than the GBT algorithm while maintaining a similar level of predictive accuracy. Then a set of experiments on a larger scale dataset for small ncRNA classification have been conducted with Naïve McRUM and compared with the Gaussian and linear SVM. Although McRUM's predictive performance is slightly lower than the Gaussian SVM, the results show that the similar level of true positive rate can be achieved by sacrificing false positive rate slightly. Furthermore, McRUM is computationally more efficient than the SVM, which is an important factor for large-scale analysis.

Conclusions
We have proposed McRUM, a multiclass extension of binary CRUM. McRUM with Naïve decoding algorithm is computationally efficient in run-time and its predictive performance is comparable to the well-known SVM, showing its potential in solving large-scale multiclass problems in bioinformatics and other fields of study.
Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
Authors: Koo HyunJo , McDowell Eric T , Ma Xiaoqiang , Greer Kevin A , Kapteyn Jeremy , Xie Zhengzhi , Descour Anne , Kim HyeRan , Yu Yeisoo , Kudrna David , Wing Rod A , Soderlund Carol A , Gang David R 
Published: February 2013

AbstractBackgroundGinger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric.ResultsIn order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols.ConclusionA significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expression, suggesting that gene expression itself may play an important role in regulating metabolite production in these plants.
Family burden in inherited ichthyosis: creation of a specific questionnaire
Authors: Dufresne Hélène , Hadj-Rabia Smail , Méni Cécile , Sibaud Vincent , Bodemer Christine , Taïeb Charles 
Published: February 2013

AbstractBackgroundThe concept of individual burden, associated with disease, has been introduced recently to determine the “disability” caused by the pathology in the broadest sense of the word (psychological, social, economic, physical). Inherited ichthyosis belong to a large heterogeneous group of Mendelian Disorders of Cornification. Skin symptoms have a major impact on patients’ Quality of Life but little is known about the burden of the disease on the families of patients.ObjectivesTo develop and validate a specific burden questionnaire for the families of patients affected by ichthyosis.MethodsTwo steps were required. First, the creation of the questionnaire which followed a strict methodological process involving a multidisciplinary team and families. Secondarily, the validation of the questionnaire, including the assessment of its reliability, external validity, reproducibility and sensitivity, was carried out on a population of patients affected by autosomal recessive congenital ichthyosis. A population of parents of patients affected by ichthyosis was enrolled to answer the new questionnaire in association with the Short Form Q12 questionnaire (SF-12) and a clinical severity score was filled for each patient.ResultsNinety four families were interviewed to construct the verbatim in order to create the questionnaire and a cognitive debriefing was realized. The concept of burden could be structured around five components: “economic”, “daily life”, “familial and personal relationship”, “work”, and “psychological impact”. As a result, “Family Burden Ichthyosis” (FBI) reproducible questionnaire of 25 items was created.Forty two questionnaires were analyzable for psychometric validation. Reliability (Cronbach’s alpha coefficient = 0.89), reflected the good homogeneity of the questionnaire. The correlation between mental dimensions of the SF-12 and the FBI questionnaire was statistically significant which confirmed the external validity. The mean FBI score was 71.7 ± 18.8 and a significant difference in the FBI score was shown between two groups of severity underlining a good sensitivity of the questionnaire.ConclusionsThe internal and external validity of the “FBI” questionnaire was confirmed and it is correlated to the severity of ichtyosis. Ichthyoses, and other chronic pathologies, are difficult to assess by clinical or Quality of Life aspects alone as their impact can be multidimensional. “FBI” takes them all into consideration in order to explain every angle of the handicap generated.
Role of p73 in Alzheimer disease: lack of association in mouse models or in human cohorts
Authors: Vardarajan Badri , Vergote David , Tissir Fadel , Logue Mark , Yang Jing , Daude Nathalie , Ando Kunie , Rogaeva Ekaterina , Lee Joseph , Cheng Rong , Brion Jean-Pierre , Ghani Mahdi , Shi Beipei , Baldwin Clinton T , Kar Satyabrata , Mayeux Richard , Fraser Paul , Goffinet André M , George-Hyslop Peter St , Farrer Lindsay A , Westaway David 
Published: February 2013

AbstractBackgroundP73 belongs to the p53 family of cell survival regulators with the corresponding locusTrp73producing the N-terminally distinct isoforms, TAp73 and DeltaNp73. Recently, two studies have implicated the murineTrp73in the modulation in phospho-tau accumulation in aged wild type mice and in young mice modeling Alzheimer’s disease (AD) suggesting thatTrp73, particularly the DeltaNp73 isoform, links the accumulation of amyloid peptides to the creation of neurofibrillary tangles (NFTs). Here, we reevaluated tau pathologies in the same TgCRND8 mouse model as the previous studies.ResultsDespite the use of the same animal models, ourin vivostudies failed to demonstrate biochemical or histological evidence for misprocessing of tau in young compound Trp73+/-+ TgCRND8 mice or in aged Trp73+/-mice analyzed at the ages reported previously, or older. Secondly, we analyzed an additional mouse model where the DeltaNp73 was specifically deleted and confirmed a lack of impact of the DeltaNp73 allele, either in heterozygous or homozygous form, upon tau pathology in aged mice. Lastly, we also examined humanTP73for single nucleotide polymorphisms (SNPs) and/or copy number variants in a meta-analysis of 10 AD genome-wide association datasets. No SNPs reached significance after correction for multiple testing and no duplications/deletions inTP73were found in 549 cases of AD and 544 non-demented controls.ConclusionOur results fail to support P73 as a contributor to AD pathogenesis.
De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes
Authors: Weimann Aaron , Trukhina Yulia , Pope Phillip B , Konietzny Sebastian GA , McHardy Alice C 
Published: February 2013

AbstractBackgroundUnderstanding the biological mechanisms used by microorganisms for plant biomass degradation is of considerable biotechnological interest. Despite of the growing number of sequenced (meta)genomes of plant biomass-degrading microbes, there is currently no technique for the systematic determination of the genomic components of this process from these data.ResultsWe describe a computational method for the discovery of the protein domains and CAZy families involved in microbial plant biomass degradation. Our method furthermore accurately predicts the capability to degrade plant biomass for microbial species from their genome sequences. Application to a large, manually curated data set of microbial degraders and non-degraders identified gene families of enzymes known by physiological and biochemical tests to be implicated in cellulose degradation, such as GH5 and GH6. Additionally, genes of enzymes that degrade other plant polysaccharides, such as hemicellulose, pectins and oligosaccharides, were found, as well as gene families which have not previously been related to the process. For draft genomes reconstructed from a cow rumen metagenome our method predicted Bacteroidetes-affiliated species and a relative to a known plant biomass degrader to be plant biomass degraders. This was supported by the presence of genes encoding enzymatically active glycoside hydrolases in these genomes.ConclusionsOur results show the potential of the method for generating novel insights into microbial plant biomass degradation from (meta-)genome data, where there is an increasing production of genome assemblages for uncultured microbes.
Room-temperature Sinterable Silver Nanoparticle Ink with Low-molecular-weight Poly(N-vinylpyrrolidone) Ligand
Authors: Lee Mi Yeon , Lee Won Jin , Roy Arup Kumer , Lee Kang Seok , Park Sung Young , Lee Ji-Hoon , In Insik 
Published: February 2013

Abstract
A highly conductive silver (Ag) film or pattern was prepared on a poly(ethylene terephthalate) (PET) substrate by using room-temperature sinterable silver nanoparticle (AgNP) ink without any thermal treatment. The most critical factor in the room-temperature sintering of the AgNP ink was the molecular weight of the poly(N-vinylpyrrolidone) (PVP) ligand. AgNP-10 ink having a PVP ligand with the lowest molecular weight of 10000 Da produced a conductive Ag film with 6.3% of the conductivity of bulk silver without any post-treatment such as heating.
Comparison of natural and recombinant tissue factor proteins: new insights
Authors: Butenas Saulius 
Published: February 2013

Abstract
Tissue factor (TF), an initiator of blood coagulation in vivo, is expressed in a variety of cells. Sufficient natural TF has been isolated to clone and express recombinant proteins ranging from full-length TF to its extracellular domain. Because of the limited availability of natural TF, recombinant proteins have been used as surrogates. Despite the differences in their post-translational modifications, it has been accepted that membrane-anchored recombinant TFs are quite similar to the natural TF. Recent studies, however, have shown that post-translational modifications play an important role in TF-triggered thrombin generation.
Towards a Representative Bureaucracy: Promoting Linguistic Representation and Diversity in the Swiss and Canadian Federal Public Services
Authors: Kübler Daniel , Kobelt Émilienne , Andrey Stephanie 
Published: February 2013

AbstractDrawing on the concept of representative bureaucracy, this article examines how two multilingual states – Canada and Switzerland – deal with issues related to the participation of different linguistic communities in the federal public service. Following a political mobilization of the linguistic cleavage, strategies to promote multilingualism in the public service have been adopted in both countries. The Canadian strategy focuses on equal treatment of Anglophones and Francophones in the public service. In Switzerland, adequate representation of the linguistic communities is the primary goal. These differences are explained by the characteristics of the linguistic regimes in each of the two countries as well as by the peculiarities of consociational democracy in Switzerland. In both countries, the linguistic origins of public administration staff, overall, mirrors the proportions of the linguistic communities in the wider society. Within administrative units, however, linguistic diversity is hampered by the logics of language rationalization, where minorities are under pressure to communicate in the language of the majority.
The Protein Chaperone HSP90 Can Facilitate the Divergence of Gene Duplicates
Authors: Lachowiec Jennifer , Lemus Tzitziki , Thomas James H , Murphy Patrick J M , Nemhauser Jennifer L , Queitsch Christine 
Published: February 2013

Abstract
The heat-shock protein 90 (HSP90) acts as a chaperone by ensuring proper maturation and folding of its client proteins. The HSP90 capacitor hypothesis holds that interactions with HSP90 allow proteins to accumulate mutations while maintaining function. Following this logic, HSP90 clients would be predicted to show relaxed selection compared with nonclients. In this study, we identify a new HSP90 client in the plant steroid hormone pathway: the transcription factor BES1. Its closest paralog, BZR1, is not an HSP90 client. This difference in HSP90 client status in two highly similar proteins enabled a direct test of the capacitor hypothesis. We find that BES1 shows relaxed selection compared to BZR1, hallmarks of neo- and subfunctionalization, and dynamic HSP90 client status across independent evolutionary paths. These results suggested that HSP90’s influence on gene evolution may be detectable if we compare gene duplicates because duplicates share most other properties influencing evolutionary rate that might otherwise conceal the chaperone’s effect. We test this hypothesis using systematically identified HSP90 clients in yeast and observe a significant trend of HSP90 clients evolving faster than their nonclient paralogs. This trend was not detected when yeast clients and nonclients were compared without considering paralog status. Our data provide evidence that HSP90 influences selection on genes encoding its clients and facilitates divergence between gene duplicates.
Clinical Correlates of Ambulatory BP Monitoring among Patients with CKD
Authors: Iimuro Satoshi , Imai Enyu , Watanabe Tsuyoshi , Nitta Kosaku , Akizawa Tadao , Matsuo Seiichi , Makino Hirofumi , Ohashi Yasuo , Hishida Akira 
Published: February 2013

Summary

Background and objectives
Ambulatory BP monitoring (ABPM) allows a better risk stratification than office BP in hypertensive patients. However, the clinical relevance of ABPM has not been extensively investigated in the CKD population.

Design, setting, participants, & measurements
Within the Chronic Kidney Disease Japan Cohort study, 2977 patients enrolled (62% men, aged 60.8±11.6 years) and ABPM was conducted in a subgroup of patients from September 2007 to April 2010. Data from 1075 patients (682 men) were analyzed to determine BP control and factors associated with the ABPM parameters.

Results
The prevalence of masked hypertension was 30.9%, whereas that of white-coat hypertension was 5.6%. With advancing CKD stage, the percentage of persistent hypertension increased from 21.7% to 36.1%. Diabetes, antihypertensive medicine use, and low estimated GFR (eGFR) were significantly associated with the difference between office BP and ambulatory BP (1.7 mmHg, 2.6 mmHg, and 0.6 mmHg per 10 ml/min per 1.73 m2, respectively). There tended to be fewer nondippers and risers in stage 3 than in stages 4 and 5. In the nocturia-negative group, low eGFR, diabetes, and summer season were identified as factors associated with lower nocturnal BP change (−0.5 mmHg, −2.0 mmHg, and −2.8 mmHg, respectively). Morning BP change was greater with older age (0.2 mmHg per 10 years) and higher body mass index (0.6 mmHg per 1 kg/m2), and in winter (4.5 mmHg) versus summer.

Conclusions
Various factors including eGFR, diabetes, antihypertensive medication use, and season are associated with higher BP and abnormal BP patterns in CKD patients.
Stability of the Two-parameter Set of Nonlocal Difference Schemes
Authors: GULIN A. , MOROZOVA V. 
Published: February 2013

Abstract The paper deals with difference schemes for the heat-conduction equa-
tion with nonlocal boundary conditions containing two real parameters. Such
schemes have been investigated for some special parameter values, but the general case
was not considered previously. The eigenvalue problem arises as a result of variable
division and is solved here explicitly. The so-called reality domains were selected on
the plane for which all eigenvalues and eigenfunctions are real. It was demon-
strated that the difference schemes in question are symmetrizable in reality domains,
that is their transition operators are similar to self-adjoint ones. The necessary and
sufficient stability conditions for difference schemes under consideration are obtained
with respect to the initial data in the specially constructed norm. The equivalence of
the above-mentioned norm to the grid L2-norm has been proved.
Numerical Method for Singularly Perturbed Parabolic Equations in Unbounded Domains in the Case of Solutions Growing at Infinity
Authors: Shishkin G. I. 
Published: February 2013

AbstractAn initial-boundary value problem is considered in an unbounded do-
main on the x-axis for a singularly perturbed parabolic reaction-diffusion equation. For small values of the
parameter ε, a parabolic boundary layer arises in a neighbourhood of the lateral part
of the boundary. In this problem, the error of a discrete solution in the maximum
norm grows without bound even for fixed values of the parameter ε. In
the present paper, the proximity of solutions of the initial-boundary value problem
and of its numerical approximations is considered. Using the method of special grids condensing
in a neighbourhood of the boundary layer, a special finite difference scheme converging
ε-uniformly in the weight maximum norm has been constructed.
The English Pronunciation Teaching in Europe Survey: Selected Results
Authors: Henderson Alice , Frost Dan , Tergujeff Elina , Kautzsch Alexander , Murphy Deirdre , Kirkova-Naskova Anastazija , Waniek-Klimczak Ewa , Levey David , Cunnigham Una , Curnick Lesley 
Published: February 2013

This paper provides an overview of the main findings from a European-wide on-line survey of English pronunciation teaching practices. Both quantitative and qualitative data from seven countries (Finland, France, Germany, Macedonia, Poland, Spain and Switzerland) are presented, focusing on teachers' comments about:
● their own pronunciation,
● their training,
● their learners’ goals, skills, motivation and aspirations,
● their preferences for certain varieties (and their perception of their students' preferences).
The results of EPTiES reveal interesting phenomena across Europe, despite shortcomings in terms of construction and distribution. For example, most respondents are non-native speakers of English and the majority of them rate their own mastery of English pronunciation favourably. However, most feel they had little or no training in how to teach pronunciation, which begs the question of how teachers are coping with this key aspect of language teaching. In relation to target models, RP remains the variety of English which teachers claim to use, whilst recognizing that General American might be preferred by some students. Differences between countries are explored, especially via replies to open-ended questions, allowing a more nuanced picture to emerge for each country. Other survey research is also referred to, in order to contextualise the analyses and implications for teaching English and for training English teachers.
Enhancement of the pool boiling heat transfer coefficient using the gas injection into the water
Authors: Sarafraz M.M. , Peyghambarzadeh S.M. , Alavi Fazel S.A. 
Published: February 2013

Abstract
In this paper, a new method for enhancing the pool boiling heat transfer coefficient of pure liquid, based on the gas injection through the liquids has been introduced. Hence, the effect of gas dissolved in a stagnant liquid on pool boiling heat transfer coefficient, nucleation site density, and bubble departure diameter has experimentally been investigated for different mole fractions of SO2 and various heat fluxes up to 114 kW/ m2. The presence of SO2 in captured vapor inside the bubbles, particularly around the heat transfer surface increases the pool boiling heat transfer coefficient. The available predicted correlations are unable to obtain the reasonable values for pool boiling heat transfer coefficient in this particular case. Therefore, to predict the pool boiling heat transfer coefficient accurately, a new modified correlation based on Stephan-Körner relation has been proposed. Also, during the experiments, it is found that nucleation site density is a strictly exponential function of heat flux. Accordingly, a new correlation has been obtained to predict the nucleation site density. The major application of the nucleation site density is in the estimating of mean bubble diameters as well as local agitation due to the rate of bubble frequency.