bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of copy number variation detection for a SNP array platform
Authors: Zhang Xin , Du Renqian , Li Shilin , Zhang Feng , Jin Li , Wang Hongyan 
Published: February 2014

Abstract

Background
Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the performance of these software packages; it is therefore difficult to select one or several software packages for CNV detection based on the SNP array platform.
We selected four publicly available software packages designed for CNV calling from an Affymetrix SNP array, including Birdsuite, dChip, Genotyping Console (GTC) and PennCNV. The publicly available dataset generated by Array-based Comparative Genomic Hybridization (CGH), with a resolution of 24 million probes per sample, was considered to be the “gold standard”. Compared with the CGH-based dataset, the success rate, average stability rate, sensitivity, consistence and reproducibility of these four software packages were assessed compared with the “gold standard”. Specially, we also compared the efficiency of detecting CNVs simultaneously by two, three and all of the software packages with that by a single software package.

Results

Simply from the quantity of the detected CNVs, Birdsuite detected the most while GTC detected the least. We found that Birdsuite and dChip had obvious detecting bias. And GTC seemed to be inferior because of the least amount of CNVs it detected. Thereafter we investigated the detection consistency produced by one certain software package and the rest three software suits. We found that the consistency of dChip was the lowest while GTC was the highest. Compared with the CNVs detecting result of CGH, in the matching group, GTC called the most matching CNVs, PennCNV-Affy ranked second. In the non-overlapping group, GTC called the least CNVs. With regards to the reproducibility of CNV calling, larger CNVs were usually replicated better. PennCNV-Affy shows the best consistency while Birdsuite shows the poorest.

Conclusion
We found that PennCNV outperformed the other three packages in the sensitivity and specificity of CNV calling. Obviously, each calling method had its own limitations and advantages for different data analysis. Therefore, the optimized calling methods might be identified using multiple algorithms to evaluate the concordance and discordance of SNP array-based CNV calling.
Evaluation of an early step-down strategy from intravenous anidulafungin to oral azole therapy for the treatment of candidemia and other forms of invasive candidiasis: results from an open-label trial
Authors: Vazquez Jose , Reboli Annette C , Pappas Peter G , Patterson Thomas F , Reinhardt John , Chin-Hong Peter , Tobin Ellis , Kett Daniel H , Biswas Pinaki , Swanson Robert 
Published: February 2014

Abstract

Background
Hospitalized patients are at increased risk for candidemia and invasive candidiasis (C/IC). Improved therapeutic regimens with enhanced clinical and pharmacoeconomic outcomes utilizing existing antifungal agents are still needed.

Methods
An open-label, non-comparative study evaluated an intravenous (IV) to oral step-down strategy. Patients with C/IC were treated with IV anidulafungin and after 5 days of IV therapy had the option to step-down to oral azole therapy (fluconazole or voriconazole) if they met prespecified criteria. The primary endpoint was the global response rate (clinical + microbiological) at end of treatment (EOT) in the modified intent-to-treat (MITT) population (at least one dose of anidulafungin plus positive Candida within 96 hours of study entry). Secondary endpoints included efficacy at other time points and in predefined patient subpopulations. Patients who stepped down early (≤ 7 days’ anidulafungin) were identified as the "early switch" subpopulation.

Results
In total, 282 patients were enrolled, of whom 250 were included in the MITT population. The MITT global response rate at EOT was 83.7% (95% confidence interval, 78.7–88.8). Global response rates at all time points were generally similar in the early switch subpopulation compared with the MITT population. Global response rates were also similar across multiple Candida species, including C. albicans, C. glabrata, and C. parapsilosis. The most common treatment-related adverse events were nausea and vomiting (four patients each).

Conclusions
A short course of IV anidulafungin, followed by early step-down to oral azole therapy, is an effective and well-tolerated approach for the treatment of C/IC.

Trial registration
ClinicalTrials.gov: NCT00496197
Functional modelling of a novel mutation in BBS5
Authors: Al-Hamed Mohamed H , van Lennep Charles , Hynes Ann Marie , Chrystal Paul , Eley Lorraine , Al-Fadhly Fatimah , El Sayed Riham , Simms Roslyn J , Meyer Brian , Sayer John A 
Published: February 2014

AbstractBackgroundBardet-Biedl syndrome (BBS) is an autosomal recessive ciliopathy disorder with 18 known causative genes (BBS1-18). The primary clinical features are renal abnormalities, rod-cone dystrophy, post-axial polydactyly, learning difficulties, obesity and male hypogonadism.ResultsWe describe the clinical phenotype in three Saudi siblings in whom we have identified a novel mutation in exon 12 ofBBS5(c.966dupT; p.Ala323CysfsX57). This single nucleotide duplication creates a frame shift results in a predicted elongated peptide. Translation blocking Morpholino oligonucleotides were used to create zebrafishbbs5morphants. Morphants displayed retinal layering defects, abnormal cardiac looping and dilated, cystic pronephric ducts with reduced cilia expression. Morphants also displayed significantly reduced dextran clearance via the pronephros compared to wildtype embryos, suggesting reduced renal function in morphants. The eye, kidney and heart defects reported in morphant zebrafish resemble the human phenotype ofBBS5mutations. The pathogenicity of the novelBBS5mutation was determined. Mutant mRNA was unable to rescue pleiotropic phenotypes ofbbs5morphant zebrafish and in cell culture we demonstrate a mislocalisation of mutant BBS5 protein which fails to localise discretely with the basal body.ConclusionsWe conclude that this novelBBS5mutation has a deleterious function that accounts for the multisystem ciliopathy phenotype seen in affected human patients.
Cross-country variation in additive effects of socio-economics, health behaviors, and comorbidities on subjective health of patients with diabetes
Authors: Assari Shervin 
Published: February 2014

Abstract
Purpose
This study explored cross-country differences in the additive effects of socio-economic characteristics, health behaviors and medical comorbidities on subjective health of patients with diabetes.

Methods
The study analyzed data from the Research on Early Life and Aging Trends and Effects (RELATE). The participants were 9,179 adults with diabetes who were sampled from 15 countries (i.e. China, Costa Rica, Puerto Rico, United States, Mexico, Argentina, Barbados, Brazil, Chile, Cuba, Uruguay, India, Ghana, South Africa, and Russia). We fitted three logistic regressions to each country. Model I only included socio-economic characteristics (i.e. age, gender, education and income). In Model II, we also included health behaviors (i.e. smoking, drinking, and exercise). Model III included medical comorbidities (i.e. hypertension, respiratory disease, heart disease, stroke, and arthritis), in addition to the previous blocks.

Results
Our models suggested cross-country differences in the additive effects of socio-economic characteristics, health behaviors and comorbidities on perceived health of patients with diabetes. Comorbid heart disease was the only condition that was consistently associated with poor subjective health regardless of country.

Conclusion
Countries show different profiles of social and behavioral determinants of subjective health among patients with diabetes. Our study suggests that universal programs that assume that determinants of well-being are similar across different countries may be over-simplistic. Thus instead of universal programs that use one protocol for health promotion of patients in all countries, locally designed interventions should be implemented in each country.
Implementation of Ramadan-specific diabetes management recommendations: a multi-centered prospective study from Pakistan
Authors: Ahmedani Muhammad Yakoob , Alvi Syed Faraz Danish , haque Muhammad Saif Ul , Fawwad Asher , Basit Abdul 
Published: February 2014

Abstract
Background
To observe the outcome of implementation of Ramadan-specific diabetes management recommendations in fasting individuals with diabetes through health care providers.

Methods
This multi-centered prospective study was conducted at nine diabetes specialist centers in four provinces of Pakistan. The study was carried out in two phases; pre-Ramadan recruitment interview (visit A) and post-Ramadan follow up interview (visit B) of the same patients. Pre-Ramadan individual counseling was given and educational material provided to each patient by health care providers during visit A.

Results
Out of 388 patients with diabetes, blood glucose level was checked by all patients with type 1 and 71.43% patients with type 2 diabetes when they developed hypoglycemic symptoms during Ramadan. Of patients with type 1 and type 2 diabetes, 33.33% and 48% discontinued their fast when they felt hypoglycemic symptoms, respectively. None of the patient with type 1, while 18.87% patients with type 2 diabetes discontinued fast on the development of hyperglycemic symptoms. Drug dosage and timing were altered in 80% patients with type 1 and 90.5% patients with type 2 diabetes during Ramadan. Majority of the patients with type 2 diabetes changed from moderate/severe levels of physical activity before Ramadan to light physical activity during Ramadan (p<0.000). None of the patients required hospitalization when they developed symptomatic hypoglycemia or hyperglycemia and none developed diabetic ketoacidosis and hyperglycemic hyperosmolar state during Ramadan.

Conclusion
We observed that it is practicable to implement Ramadan-specific diabetes management recommendations through health care providers.
Remission in rheumatoid arthritis: benefit over low disease activity in patient-reported outcomes and costs
Authors: Radner Helga , Smolen Josef S , Aletaha Daniel 
Published: February 2014

Abstract
Introduction
Rheumatoid arthritis (RA) is a chronic inflammatory disease that causes a considerable burden for the patient and society. It is not clear yet whether aiming for remission (REM) is worthwhile, especially when compared with low disease activity (LDA).

Methods
In 356 consecutive RA patients, we obtained data on physical function (health assessment questionnaire (HAQ)), health-related quality of life (HRQoL: Short Form 36 (SF36), Short Form 6 dimensions (SF-6D), Euro QoL 5D (EQ-5D)), work productivity (work productivity and activity impairment questionnaire (WPAI)), as well as estimation of direct and indirect costs. Cross-sectionally, data were compared in patients within different levels of disease activity according to the simplified disease activity index (SDAI; remission (REM ≤3.3); n = 87; low disease activity (LDA: 3.3 < SDAI ≤11); n = 103; moderate to high disease activity (MDA/HDA) >11 n = 119) by using analyses of variance (ANOVA). Longitudinal investigations assessed patients who changed from LDA to REM and vice versa.

Results
We found differences in patients achieving REM compared with LDA for HAQ (0.39 ± 0.58 versus 0.72 ± 68), WPAI (percentage impairment while working 11.8% ± 18.7% versus 26.8% ± 23.9%; percentage of overall activity impairment, 10.8% ± 14.1% versus 29.0% ± 23.6%)), EQ-5D (0.89 ± 0.12 versus 0.78 ± 0.6) and SF-36 (physical component score (PCS): 46.0 ± 8.6 versus 38.3 ± 10.5; mental component score (MCS): 49.9 ± 11.1 versus 47.9 ± 12.3) (P < 0.01 for all, except for SF36 MCS). Regarding costs, we found significant differences of direct and indirect costs (P < 0.05) within different levels of disease activity, with higher costs in patients with higher states of disease activity. Longitudinal evaluations confirmed the main analyses.

Conclusion
Patients with REM show better function, HRQoL, and productivity, even when compared with another good state, such as LDA. Also from a cost perspective, REM appears superior to all other states.
A yeast-based assay identifies drugs that interfere with Epstein-Barr virus immune evasion
Authors: Voisset Cécile , Daskalogianni Chrysoula , Contesse Marie-Astrid , Mazars Anne , Arbach Hratch , Le Cann Marie , Soubigou Flavie , Apcher Sébastien , Fåhraeus Robin , Blondel Marc 
Published: February 2014

AbstractEpstein-Barr virus (EBV) is tightly associated to certain human cancers but there is of today no specific treatment against EBV-related diseases. The EBV-encoded EBNA1 protein is essential to maintain viral episomes and for viral persistence. EBNA1 is expressed in all EBV infected cells and is highly antigenic. All infected individuals, including cancer patients, have CD8+ T cells directed towards EBNA1 epitopes, yet the immune system fails to detect and destroy cells harboring the virus. EBV's immune evasion depends on the capacity of the Gly-Ala repeat (GAr) domain of EBNA1 to inhibit the translation of its own mRNA in cis, thereby limiting the production of EBNA1-derived antigenic peptides presented by the Major Histocompatibility Complex (MHC) class I pathway. Here we establish a yeast-based assay for monitoring GAr-dependent inhibition of translation. Using this assay we identify doxorubicin (DXR) as a compound that specifically interferes with the GAr effect on translation in yeast. DXR targets the topoisomerase II/DNA complexes and thereby causes genomic damage. We show, however, that the genotoxic effect of DXR and various analogues thereof is uncoupled from the effect on GAr-mediated translation control. This is further supported by the observation that etoposide and teniposide, representing another class of topoisomerase II/DNA targeting drugs, have no effect on GAr-mediated translation control. DXR and active analogues stimulate in a GAr-dependent manner EBNA1 expression in mammalian cells and overcome GAr-dependent restriction of MHC class I antigen presentation. These results validate our approach as an effective high-throughput screening assay to identify drugs that interfere with EBV immune evasion and, thus, constitute candidates for treating EBV-related diseases, in particular EBV-associated cancers.
Wax plants (Hoya, Apocynaceae) evolution: Epiphytism drives successful radiation
Authors: Wanntorp Livia , Grudinski Melanie , Forster Paul I. , Muellner-Riehl Alexandra N. , Grimm Guido W. 
Published: February 2014

AbstractHoya, a species‐rich, mostly epiphytic genus within tribe Marsdenieae (Apocynaceae), occurs in tropical and subtropical forests of the Indo‐Australian Archipelago (IAA). Previous molecular phylogenetic studies based on a restricted taxon sample have provided a first phylogenetic framework for the genus. Questions remain, however, about the evolution and relationships among the over 300 species of the genus. Here, we (1) present the first well‐resolved phylogenetic tree based on sequences of the plastid spacer regions trnH‐psbA, trnT‐trnL, and of the nuclear‐encoded ITS and 5′‐ETS regions, for 154 species covering all proposed sections and (2) we discuss the evolution of epiphytism and its possible role in the successful radiation of Hoya in the tropical forests of the IAA in light of the new phylogenetic results. According to our results, species of Hoya group into six major lineages (Clades I–VI) with widespread geographic distribution. The earliest‐diverging epiphytic lineages of Clade I are restricted to subtropical continental Asia or tropical to subtropical Australasia (Clade IV), whereas their non‐epiphytic relatives are limited to the tropical Indomalayan (Clade II/III) and Australasian (Clade II) parts of the IAA. Clade V (tropical Indomalaya and Australasia) and Clade VI, with outposts in the Himalayas, Japan, and throughout Australasia, represent the second phase of diversification within Hoya. We hypothesise that Hoya is of tropical to subtropical Indo‐Burma/Himalayan origin and that the common trait epiphytism is connected with the onset of monsoon climates during the Himalayan uplift. The subsequent dispersal of Hoya into the many subareas of the IAA region and eventually Australia and the Southwest Pacific, and its success‐ ful radiation there, are proposed to be linked to its epiphytic life style, a trait that is today only found in 10% of angiosperms.
The nomenclatural history of Salsola sedoides L. and Salsola sedoides Pall. (Suaedoideae and Camphorosmoideae, Chenopodiaceae/Amaranthaceae)
Authors: Sennikov Alexander , Freitag Helmut 
Published: February 2014

AbstractThe original circumscriptions and nomenclatural history of the homonyms Salsola sedoides L. 1759 and Salsola sedoides Pall. 1771 are discussed, and lectotypes or neotypes are designated for both names and their synonyms. Two species were involved in the protologue of Salsola sedoides L.; its earliest history, the latest material and the proposed lectotype correspond to its current interpretation as Suaeda maritima from the North Sea coasts, whereas its validating statement is referable to Suaeda splendens from the Mediterranean. The unused name Salsola cinerea Waldst. & Kit. is the earliest legitimate name for the later homonym Salsola sedoides Pall. To avoid creating a new transfer of this epithet to Sedobassia, the name Salsola sedoides Pall. is proposed for conservation against its earlier homonym S. sedoides L.
Risk Preferences Around the World
Authors: Rieger Marc Oliver , Wang Mei , Hens Thorsten 
Published: February 2014

We present results from a large-scale international survey on risk preferences conducted in 53 countries. In all countries, we find, on average, an attitude of risk aversion in gains and of risk seeking in losses. The degree of risk aversion shows significant cross-country differences. Moreover, risk attitudes in our sample depend not only on economic conditions but also on cultural factors, as measured by the Hofstede dimensions individualism and uncertainty avoidance. The data may also serve as an interesting starting point for further research on cultural differences in behavioral economics. Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2013.1869 . This paper was accepted by Peter Wakker, decision analysis.
Analytic Investigation of a Reaction-diffusion Brusselator Model with the Time-space Fractional Derivative
Authors: Aslan İsmail 
Published: February 2014

Abstract
It is well known that many models in nonlinear science are described by fractional differential equations in which an unknown function appears under the operation of a derivative of fractional order. In this study, we propose a reaction-diffusion Brusselator model from the viewpoint of the Jumarie's modified Riemann-Liouville fractional derivative. Based on the (G′/G)-expansion method, various kinds of exact solutions are obtained. Our results could be used as a starting point for numerical procedures as well.
The Fate of Chromosomes and Alleles in an AllohexaploidBrassicaPopulation
Authors: Mason Annaliese S , Nelson Matthew N , Takahira Junko , Cowling Wallace A , Alves Gustavo Moreira , Chaudhuri Arkaprava , Chen Ning , Ragu Mohana E , Dalton-Morgan Jessica , Coriton Olivier , Huteau Virginie , Eber Frédérique , Chèvre Anne-Marie , Batley Jacqueline 
Published: February 2014

AbstractProduction of allohexaploid Brassica (2n = AABBCC) is a promising goal for plant breeders due to the potential for hybrid heterosis and useful allelic contributions from all three of the Brassica genomes present in the cultivated diploid (2n = AA, 2n = BB, 2n = CC) and allotetraploid (2n = AABB, 2n = AACC, and 2n = BBCC) crop species (canola, cabbages, mustards). We used high-throughput SNP molecular marker assays, flow cytometry, and fluorescent in situ hybridization (FISH) to characterize a population of putative allohexaploids derived from self-pollination of a hybrid from the novel cross (B. napus × B. carinata) × B. juncea to investigate whether fertile, stable allohexaploid Brassica can be produced. Allelic segregation in the A and C genomes generally followed Mendelian expectations for an F2 population, with minimal nonhomologous chromosome pairing. However, we detected no strong selection for complete 2n = AABBCC chromosome complements, with weak correlations between DNA content and fertility (r2 = 0.11) and no correlation between missing chromosomes or chromosome segments and fertility. Investigation of next-generation progeny resulting from one highly fertile F2 plant using FISH revealed general maintenance of high chromosome numbers but severe distortions in karyotype, as evidenced by recombinant chromosomes and putative loss/duplication of A- and C-genome chromosome pairs. Our results show promise for the development of meiotically stable allohexaploid lines, but highlight the necessity of selection for 2n = AABBCC karyotypes.
Association of Simvastatin and Hyperlipidemia With Periodontal Status and Bone Metabolism Markers
Authors: Magán‐Fernández Antonio , Papay‐Ramírez Lara , Tomás Juan , Marfil‐Álvarez Rafael , Rizzo Manfredi , Bravo Manuel , Mesa Francisco 
Published: February 2014

Background: The objective of this study is to determine whether simvastatin consumption and hyperlipidemia are associated with a worse periodontal condition and specific bone activity biomarkers.Methods: This cross‐sectional and analytic study includes 73 patients divided into three groups: 1) simvastatin‐treated patients with hyperlipidemia (n = 29); 2) patients with hyperlipidemia treated by diet alone (n = 28); and 3) normolipidemic patients (controls, n = 16). The periodontal clinical variables of all participants were gathered, a blood sample was drawn from each to determine the lipid profile (total cholesterol, triglycerides, low‐density lipoprotein, and high‐density lipoprotein), serum levels of acute‐phase reactants (C‐reactive protein), erythrocyte sedimentation rate, and bone metabolism markers (osteoprotegerin [OPG], osteocalcin, procollagen type I N‐terminal propeptide, and C‐terminal telopeptide of type I collagen).Results: The mean ESR was higher in the diet‐treated patients with hyperlipidemia than in the normolipidemic controls (P = 0.04). Serum OPG concentrations were significantly higher in the simvastatin‐treated patients with hyperlipidemia than in the diet‐treated patients with hyperlipidemia (P = 0.05). Multivariable linear regression analysis adjusted for age, sex, tobacco, and alcohol revealed that, compared with the normolipidemic patients, the simvastatin‐treated patients with hyperlipidemia showed a mean reduction of 0.8 mm (95% confidence interval = −1.5 to 0.0, P = 0.05) in clinical attachment loss.Conclusions: Within the limits of this study, the findings suggest that the intake of simvastatin is associated with increasing serum OPG concentrations, and this could have a protective effect against bone breakdown and periodontal attachment loss. The baseline systemic inflammatory state of patients with hyperlipidemia is indicated by their increased erythrocyte sedimentation rate.