bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between metabolic syndrome and knee osteoarthritis: data from the Korean National Health and Nutrition Examination Survey (KNHANES)
Authors: Han Chang Dong , Yang Ik Hwan , Lee Woo Suk , Park Yoo Jung , Park Kwan Kyu 
Published: June 2013

Abstract

Background
This study was designed to investigate the correlations of knee osteoarthritis (OA) with metabolic syndrome (MetS) and MetS parameters in Korean subjects.

Methods
This study included data from 270 subjects with knee OA and 1964 control subjects with a mean age of 54.56 (SD 11.53) years taken from the Korean National Health and Nutritional Examination Survey (KNHANES) 2008. Multivariate logistic regression analysis was conducted to examine possible associations for knee OA with MetS and MetS parameters.

Results
MetS was shown to be associated with an increased risk of knee OA in female subjects in unadjusted analysis (OR 1.798, 95% CI 1.392, 2.322), but this significance disappeared when adjusted for confounding factors (OR 1.117, 95% CI 0.805, 1.550). No significant association between MetS and knee OA was found in male subjects. Among parameters of MetS, only high waist circumference (WC) in female subjects was significantly associated with an increased prevalence of knee OA, even after adjusting for confounding factors, while no other significant associations were found in both male and female subjects.

Conclusion
We found that WC was associated with knee OA in female subjects, but neither MetS nor any parameters thereof were shown to be associated with knee OA in the Korean subjects of this study. Although we found no relationship between a pre-inflammatory state of MetS and knee OA, we believe further investigation of this relationship in various aspects is warranted, as MetS may also be a risk factor for complications in knee OA related procedures.
Reactivation of immune responses against Mycobacterium tuberculosis by boosting with the CpG oligomer in aged mice primarily vaccinated with Mycobacterium bovis BCG
Authors: Taniguchi Keiichi , Takii Takemasa , Yamamoto Saburo , Maeyama Jun-ichi , Iho Sumiko , Maruyama Mitsuo , Iizuka Narushi , Ozeki Yuriko , Matsumoto Sohkichi , Hasegawa Tomohiro , Miyatake Yuuji , Itoh Saotomo , Onozaki Kikuo 
Published: June 2013

Abstract

Background

Mycobacterium bovis bacillus Calmette Guérin (BCG) vaccine, which has been inoculated to more than one billion people world-wide, has significant effect in preventing tuberculous meningitis and miliary tuberculosis (TB) in neonate and early childhood. However, BCG fails to adequately protect against pulmonary TB and reactivation of latent infections in adults. To overcome this problem, adequate booster is urgently desired in adult who received prior BCG vaccination, and appropriate animal models that substitute human cases would be highly valuable for further experimentation.

Findings
The booster effect of the synthesized CpG oligomer (Oligo-B) on aged mice which had been primarily vaccinated with BCG at the age of 4-week old. The specific Th1 type reaction, production of interferon-γ, in response to TB antigens, purified protein derivatives (PPD) and protection against challenge with Mycobacterium tuberculosis (MTB) H37Rv decreased with increasing age and were not observed in 89-week old mice. In order to rejuvenate the Th1 type response against PPD and protection activity against MTB infection, Oligo-B, which is known to augment Th1 responses, was administered as a booster to 81-90-week old mice (late 50’s in human equivalent) vaccinated with BCG at 4-week old. The boosting with Oligo-B increased the number of CD4+ CD44high CD62Lhigh, central memory type T cell. Furthermore, the Oligo-B boosting rejuvenated the ability of mice to protect against infection with MTB H37Rv.

Conclusions
Th1-adjuvant CpG oligo DNA, such as Oligo-B, may be a promising booster when coupled with BCG priming.
First Report on Circulation of Echinococcus ortleppi in the one Humped Camel (Camelus dromedaries), Sudan
Authors: Ahmed Mohamed E , Eltom Kamal H , Musa Nasreen O , Ali Ibtisam A , Elamin Fatima M , Grobusch Martin P , Aradaib Imadeldin E 
Published: June 2013

Abstract

Background

Echinococcus granulosus (EG) complex, the cause of cystic echinococcosis (CE), infects humans and several other animal species worldwide and hence the disease is of public health importance. Ten genetic variants, or genotypes designated as (G1-G10), are distributed worldwide based on genetic diversity. The objective of this study was to provide some sequence data and phylogeny of EG isolates recovered from the Sudanese one-humped camel (Camelus dromedaries). Fifty samples of hydatid cysts were collected from the one- humped camels (Camelus dromedaries) at Taboul slaughter house, central Sudan. DNAs were extracted from protoscolices and/or associated germinal layers of hydatid cysts using a commercial kit. The mitochondrial NADH dehydrogenase subunit 1 (NADH1) gene and the cytochrome C oxidase subunit 1 (cox1) gene were used as targets for polymerase chain reaction (PCR) amplification. The PCR products were purified and partial sequences were generated. Sequences were further examined by sequence analysis and subsequent phylogeny to compare these sequences to those from known strains of EG circulating globally.

Results
The identity of the PCR products were confirmed as NADH1 and cox1 nucleotide sequences using the Basic Local Alignment Search Tool (BLAST) of NCBI (National Center for Biotechnology Information, Bethesda, MD). The phylogenetic analysis showed that 98% (n = 49) of the isolates clustered with Echinococcus canadensis genotype 6 (G6), whereas only one isolate (2%) clustered with Echinococcus ortleppi (G5).

Conclusions
This investigation expands on the existing sequence data generated from EG isolates recovered from camel in the Sudan. The circulation of the cattle genotype (G5) in the one-humped camel is reported here for the first time.
Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle
Authors: Jupe Julietta , Stam Remco , Howden Andrew JM , Morris Jenny A , Zhang Runxuan , Hedley Pete E , Huitema Edgar 
Published: June 2013

Abstract
Background
Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome sequences of both hosts and microbes, little is known about the signal interplay between them during infection. In particular, accurate descriptions of coordinate relationships between host and microbe transcriptional programs are lacking.

Results
Here, we explore the molecular interaction between the hemi-biotrophic broad host range pathogen Phytophthora capsici and tomato. Infection assays and use of a composite microarray allowed us to unveil distinct changes in both P. capsici and tomato transcriptomes, associated with biotrophy and the subsequent switch to necrotrophy. These included two distinct transcriptional changes associated with early infection and the biotrophy to necrotrophy transition that may contribute to infection and completion of the P. capsici lifecycle

Conclusions
Our results suggest dynamic but highly regulated transcriptional programming in both host and pathogen that underpin P. capsici disease and hemi-biotrophy. Dynamic expression changes of both effector-coding genes and host factors involved in immunity, suggests modulation of host immune signaling by both host and pathogen. With new unprecedented detail on transcriptional reprogramming, we can now explore the coordinate relationships that drive host-microbe interactions and the basic processes that underpin pathogen lifestyles. Deliberate alteration of lifestyle-associated transcriptional changes may allow prevention or perhaps disruption of hemi-biotrophic disease cycles and limit damage caused by epidemics.
A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Authors: Philippe Romain , Paux Etienne , Bertin Isabelle , Sourdille Pierre , Choulet Fréderic , Laugier Christel , Šimková Hana , Šafář Jan , Bellec Arnaud , Vautrin Sonia , Frenkel Zeev , Cattonaro Federica , Magni Federica , Scalabrin Simone , Martis Mihaela M , Mayer Klaus FX , Korol Abraham , Bergès Hélène , Doležel Jaroslav , Feuillet Catherine 
Published: June 2013

Abstract
Background
As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

Results
Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

Conclusions
Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
Separating homeologs by phasing in the tetraploid wheat transcriptome
Authors: Krasileva Ksenia V , Buffalo Vince , Bailey Paul , Pearce Stephen , Ayling Sarah , Tabbita Facundo , Soria Marcelo , Wang Shichen ,   IWGS Consortium, Akhunov Eduard , Uauy Cristobal , Dubcovsky Jorge 
Published: June 2013

Abstract
Background
The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs.

Results
A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing.

Conclusions
Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.
Conditionally immortalized stem cell lines from human spinal cord retain regional identity and generate functional V2a interneurons and motorneurons
Authors: Cocks Graham , Romanyuk Nataliya , Amemori Takashi , Jendelova Pavla , Forostyak Oksana , Jeffries Aaron R , Perfect Leo , Thuret Sandrine , Dayanithi Govindan , Sykova Eva , Price Jack 
Published: June 2013

Abstract
Introduction
The use of immortalized neural stem cells either as models of neural development in vitro or as cellular therapies in central nervous system (CNS) disorders has been controversial. This controversy has centered on the capacity of immortalized cells to retain characteristic features of the progenitor cells resident in the tissue of origin from which they were derived, and the potential for tumorogenicity as a result of immortalization. Here, we report the generation of conditionally immortalized neural stem cell lines from human fetal spinal cord tissue, which addresses these issues.

Methods
Clonal neural stem cell lines were derived from 10-week-old human fetal spinal cord and conditionally immortalized with an inducible form of cMyc. The derived lines were karyotyped, transcriptionally profiled by microarray, and assessed against a panel of spinal cord progenitor markers with immunocytochemistry. In addition, the lines were differentiated and assessed for the presence of neuronal fate markers and functional calcium channels. Finally, a clonal line expressing eGFP was grafted into lesioned rat spinal cord and assessed for survival, differentiation characteristics, and tumorogenicity.

Results
We demonstrate that these clonal lines (a) retain a clear transcriptional signature of ventral spinal cord progenitors and a normal karyotype after extensive propagation in vitro, (b) differentiate into relevant ventral neuronal subtypes with functional T-, L-, N-, and P/Q-type Ca2+ channels and spontaneous calcium oscillations, and (c) stably engraft into lesioned rat spinal cord without tumorogenicity.

Conclusions
We propose that these cells represent a useful tool both for the in vitro study of differentiation into ventral spinal cord neuronal subtypes, and for examining the potential of conditionally immortalized neural stem cells to facilitate functional recovery after spinal cord injury or disease.
Performance characteristics of consensus approaches for small and minor paroxysmal nocturnal hemoglobinuria clone determination by flow cytometry
Authors: Marinov Iuri , Kohoutová Martina , Tkáčová Vlasta , Pešek Adam , Čermák Jaroslav , Cetkovský Petr 
Published: June 2013

AbstractBackground:Evaluation of paroxysmal nocturnal hemoglobinuria (PNH) clones by flow cytometry (FCM) is not standardized and is associated with consistent inter-laboratory variability.Methods:In order to rule out the influence of particular approach in generating final results, we analyzed the performance characteristics of individual consensus strategies for small to intermediate (1%–20%) and minor (<1%) PNH clones within the white blood cell (WBC) and red blood cell (RBC) compartments with sensitivity up to 0.1%.Results:Coefficient of variation (CV) for precision/reproducibility analysis ranged from 0.67%/1.49% to 2.56%/3.09% for granulocytes, from 0.93%/3.09% to 7.76%/12.06% for monocytes and from 0.41%/4.73% to 6.53%/5.1% for RBCs. Coefficient of determination (r2) for linear regression analysis ranged from 0.95 to 0.99, Wilcoxon ranks test showed no statistically significant differences (p>0.05), Bland-Altman analysis demonstrated performance agreement with mean bias ranging from −0.18 to 1.24.Conclusions:Our results confirmed very good performance characteristics for precision and reproducibility analysis, excellent correlation and favorable agreement between strategies, suggesting that reported inter-laboratory variability is related mainly to incorrect performance and/or insufficient experience with PNH testing by flow cytometry, rather than to relevant limitations of any particular approach.
Two-Dimensional Modeling of an Externally Irradiated Slurry Photoreactor
Authors: Palmisano Giovanni , Loddo Vittorio , Augugliaro Vincenzo 
Published: June 2013

AbstractA batch cylindrical photocatalytic reactor, externally irradiated by 1–6 UV fluorescent lamps and containing a stirred slurry of polycrystalline TiO2, was modeled by coupling a modified Langmuir–Hinshelwood kinetics together with a two-dimensional light intensity field. The radiation field has been determined on the main assumptions of diffuse radiation, isotropic scattering and negligible backward reflected photon flow. The model has been applied to the photocatalytic oxidation of organic substrates which do not undergo homogeneous photochemical degradation. The model is characterized by the following four parameters: the kinetic constants of substrate adsorption, desorption and degradation and the exponent of the power law expressing the kinetics dependence on the light intensity. The model constants may be determined by applying a simple least-squares best fitting procedure.
Effects of Feed Powder Quantity and Compression Pressure on the Tensile Strength of Eurycoma longifolia Jack Tablets Using Different Binders
Authors: Abdul Hamid Aziana Azlin , Yusof Yus Aniza , Chin Nyuk L. , Mohamed Suhaila , Salleh Faiqa 
Published: June 2013

Abstract
This study investigated the direct compression properties of Eurycoma longifolia Jack tablets using binary mixtures such as microcrystalline cellulose (mcc) and κ-carrageenan (carr). The mixtures were compacted to various compression pressures ranging from 7.5 to 74 MPa at a constant compression speed of 5 mm/min. The tensile strengths of the tablets were determined by a diametral compression test. A linear relationship between the tensile strength and the compression pressure was observed under the conditions of the test; hence, the slopes of the data were obtained by fitting linear trend lines. This paper shows that binary mixtures of 30% mcc and 70% Eurycoma longifolia Jack give the highest values for constant (a slope) compared with the other binary mixtures of both binders. Thus, this approach can be used to develop formulations for Eurycoma longifolia Jack tablets.
Interactive Learning Research: Application of Cognitive Load Theory to Nursing Education
Authors: Hessler Karen L. , Henderson Ann M. 
Published: June 2013

AbstractThe purpose of this research was to investigate the effectiveness of interactive self-paced computerized case study compared to traditional hand-written paper case study on the outcomes of student knowledge, attitude, and retention of the content delivered. Cognitive load theory (CLT) provided the theoretical framework for the study. A quasi-experimental pre-test post-test design with random group assignment was used to measure by self-report survey student cognitive load and interactivity level of the intervention. Student scores on quizzes in semester 1 and post-test follow-up quizzes in semester 3 were assessed for the intervention’s effects on knowledge retention. While no significant statistical differences were found between groups, the students in the interactive case study group rated their case study as more fun and interactive. These students also scored consistently higher on the post-test quiz items in their third semester, showing the viability of using CLT to improve student retention of nursing curricula information.
The Relevance of Indigenous Knowledge for Nursing Curriculum
Authors: Stansfield Della , Browne Annette J. 
Published: June 2013

AbstractIndigenous knowledge (IK) has the potential to complement the dominant epistemologies central to nursing curricula. Acknowledging IK as a thriving set of worldviews, we discuss how nursing educators might access and integrate IK in ways that are respectful and sustainable. IK is highlighted as an entry point for understanding concepts such as cultural safety, ethical space, and relational practice and as a strength-based approach to learning about Aboriginal people’s health. As with any use of knowledge, consideration must be given to issues of ownership, misappropriation, institutional responsibility, Indigenous protocol, and the creation of partnerships. Recommendations are provided for educators wishing to explore how to incorporate IK into nursing curriculum. With appropriate partnerships, protocols, and processes in place, the incorporation of IK may provide educators and students an opportunity to explore divergent epistemologies, philosophies, and worldviews, thereby encouraging broader perspectives about the world, ways of being, various types of knowledge, and nursing care.
Texture Inpainting Using Covariance in Wavelet Domain
Authors: Biradar Rajkumar L. , Kohir Vinayadatt V. 
Published: June 2013

AbstractIn this article, the covariance of wavelet transform coefficients is used to obtain a texture inpainted image. The covariance is obtained by the maximum likelihood estimate. The integration of wavelet decomposition and maximum likelihood estimate of a group of pixels (texture) captures the best-fitting texture used to fill in the inpainting area. The image is decomposed into four wavelet coefficient images by using wavelet transform. These wavelet coefficient images are divided into small square patches. The damaged region in each coefficient image is filled by searching a similar square patch around the damaged region in that particular wavelet coefficient image by using covariance.
Knowledge-Based Features for Place Classification of Unvoiced Stops
Authors: Karjigi Veena , Rao Preeti 
Published: June 2013

AbstractThe classification of unvoiced stops in consonant–vowel (CV) syllables, segmented from continuous speech, is investigated by features related to speech production. As burst and vocalic transitions contribute to identification of stops in the CV context, features are computed from both regions. Although formants are the truly discriminating articulatory features, their estimation from the speech signal is a challenge especially in unvoiced regions like the release burst of stops. This may be compensated partially by sub-band energy-based features. In this work, formant features from the vocalic region are combined with features from the burst region comprising sub-band energies, as well as features from a formant tracking method developed for unvoiced regions. The overall combination of features at the classifier level obtains an accuracy of 84.4%, which is significantly better than that obtained with solely sub-band features on unvoiced stops in CV syllables of TIMIT.
Building an Academic Community: Minority Serving Institutions and How They Influence Students Pursuing Undergraduate Degrees in STEM
Authors: Flower III Alonzo M. 
Published: June 2013

Abstract
Scientific and technological innovation, according to a report by the National Academy of Sciences (2007), can only be secured with individuals’ success in science, technology, engineering, and mathematics (STEM). Because STEM remains White and male-dominated, programs that focus on increasing the participation of female and minority students has been of great interest to organizations, universities, and national agencies (e.g., National Science Foundation [NSF]) alike. Ways to increase students’ interest, participation, matriculation, and completion of STEM undergraduate degrees have been discussed throughout the scholarly community – from primary to secondary to postsecondary school officials and researchers.