bluuebunny/crossref_metadata_2025_split huggingface dataset:
Medial Collateral Ligament Injuries and Subsequent Load on the Anterior Cruciate Ligament
Authors: Battaglia Michael J. , Lenhoff Mark W. , Ehteshami John R. , Lyman Stephen , Provencher Matthew T. , Wickiewicz Thomas L. , Warren Russell F. 
Published: December 2008

Background Numerous studies have documented the effect of complete medial collateral ligament injury on anterior cruciate ligament loads; few have addressed how partial medial collateral ligament disruption affects knee kinematics. Purpose To determine knee kinematics and subsequent change in anterior cruciate ligament load in a partial and complete medial collateral ligament injury model. Study Design Controlled laboratory study. Methods Ten human cadaveric knees were sequentially tested by a robot with the medial collateral ligament intact, in a partial injury model, and in a complete injury model with a universal force-moment sensor measuring system. Tibial translation, rotation, and anterior cruciate ligament load were measured under 3 conditions: anterior load (125 N), valgus load (10 N·m), and internal-external rotation torque (4 N·m; all at 0° and 30° of flexion). Results Anterior and posterior translation did not statistically increase with a partial or complete medial collateral ligament injury at 0° and 30° of flexion. In response to a 125 N anterior load, at 0°, the anterior cruciate ligament load increased 8.7% (from 99.5 to 108.2 N; P =. 006) in the partial injury and 18.3% (117.7 N; P <. 001) in the complete injury; at 30°, anterior cruciate ligament load was increased 12.3% (from 101.7 to 114.2 N; P =. 001) in the partial injury and 20.6% (122.7 N; P <. 001) in the complete injury. In response to valgus torque (10 N·m) at 30°, anterior cruciate ligament load was increased 55.3% (30.4 to 47.2 N; P =. 044) in the partial injury model and 185% (86.8 N; P =. 001) in the complete injury model. In response to internal rotation torque (4 N·m) at 30°, anterior cruciate ligament load was increased 29.3% (27.6 to 35.7 N; P =. 001) in the partial injury model and 65.2% (45.6 N; P <. 001) in the complete injury model. The amount of internal rotation at 30° of flexion was significantly increased in the complete injury model (22.8°) versus the intact state (19.5°; P <. 001). Conclusion Partial and complete medial collateral ligament tears significantly increased the load on the anterior cruciate ligament. In a partial tear, the resultant load on the anterior cruciate ligament was increased at 30° of flexion and with valgus load and internal rotation torque. Clinical Relevance Patients may need to be protected from valgus and internal rotation forces after anterior cruciate ligament reconstruction in the setting of a concomitant partial medial collateral ligament tear. This information may help clinicians understand the importance of partial injuries of the medial collateral ligament with a combined anterior cruciate ligament injury complex.
Predictors of Hip Internal Rotation during Running
Authors: Souza Richard B. , Powers Christopher M. 
Published: December 2008

Background Recent studies have suggested that excessive hip internal rotation during dynamic tasks may be associated with patellofemoral pain. Although diminished hip-muscle strength and altered femoral morphologic characteristics have been implicated in abnormal hip rotation in persons with patellofemoral pain, no study has confirmed this hypothesis. Hypothesis Women with patellofemoral pain would demonstrate increased average hip internal rotation, decreased hip-muscle performance, and abnormal femoral shape compared with controls. Furthermore, measures of hip strength and femoral shape are predictive of average hip internal rotation during running. Study Design Cross-sectional study; Level of evidence, 3. Methods Nineteen women with patellofemoral pain and 19 pain-free controls participated. Lower extremity kinematics during running, hip-muscle performance, and femoral morphologic characteristics on magnetic resonance imaging were quantified. Independent t tests were used to assess group differences. Stepwise linear regression was used to determine whether measures of strength and/or structure were predictive of average hip internal rotation during running. Results Participants with patellofemoral pain demonstrated significantly greater average hip internal rotation (8.2° ± 6.6° vs 0.3° ± 3.6°; P <. 001), reduced hip-muscle strength in 8 of 10 hip strength measurements, and greater femoral inclination (132.8° ± 5.2° vs 128.4° ± 5.0°; P =. 011) compared with controls. Stepwise regression revealed that isotonic hip extension endurance was the only predictor of average hip internal rotation (r = −.451; P =. 004). Conclusion Abnormal hip kinematics in women with patellofemoral pain appears to be the result of diminished hip-muscle performance as opposed to altered femoral structure. The results suggest that assessment of hip-muscle performance should be considered in the evaluation and treatment of patellofemoral joint dysfunction.
Identification of a particular HIV-specific CD8+ T-cell subset with a CD27+ CD45RO−/RA+ phenotype and memory characteristics after initiation of HAART during acute primary HIV infection
Authors: Lécuroux Camille , Girault Isabelle , Urrutia Alejandra , Doisne Jean-Marc , Deveau Christiane , Goujard Cécile , Meyer Laurence , Sinet Martine , Venet Alain 
Published: December 2008

AbstractCD8+ T cells play an important role in controlling viral infections. Defective CD8+ T-cell responses during HIV infection could contribute to viral persistence. Early initiation of highly active antiretroviral therapy during acute primary HIV infection helps to preserve HIV-specific immune responses. Here, we describe a particular CD27+ CD45RO−/RA+ HIV-specific CD8+ T cell in participants treated early during the primary infection. These cells, which were present at a very low frequency during primary HIV infection, increased markedly after early treatment, whereas their frequency remained unchanged in untreated participants and in participants treated later. These nonnaive antigen-experienced cells are in a resting state and have characteristics of long-lived memory cells. They also possess direct effector capabilities, such as cytokine production, and are able to proliferate and to acquire cytotoxic functions on reactivation. Our results suggest that these HIV-specific CD27+ CD45RO−/RA+ CD8+ T cells, observed when early viral replication is inhibited, form a pool of resting cells with memory characteristics.
Pathological rate matrices: from primates to pathogens
Authors: Schranz Harold W , Yap Von Bing , Easteal Simon , Knight Rob , Huttley Gavin A 
Published: December 2008

Abstract

Background
Continuous-time Markov models allow flexible, parametrically succinct descriptions of sequence divergence. Non-reversible forms of these models are more biologically realistic but are challenging to develop. The instantaneous rate matrices defined for these models are typically transformed into substitution probability matrices using a matrix exponentiation algorithm that employs eigendecomposition, but this algorithm has characteristic vulnerabilities that lead to significant errors when a rate matrix possesses certain 'pathological' properties. Here we tested whether pathological rate matrices exist in nature, and consider the suitability of different algorithms to their computation.

Results
We used concatenated protein coding gene alignments from microbial genomes, primate genomes and independent intron alignments from primate genomes. The Taylor series expansion and eigendecomposition matrix exponentiation algorithms were compared to the less widely employed, but more robust, Padé with scaling and squaring algorithm for nucleotide, dinucleotide, codon and trinucleotide rate matrices. Pathological dinucleotide and trinucleotide matrices were evident in the microbial data set, affecting the eigendecomposition and Taylor algorithms respectively. Even using a conservative estimate of matrix error (occurrence of an invalid probability), both Taylor and eigendecomposition algorithms exhibited substantial error rates: ~100% of all exonic trinucleotide matrices were pathological to the Taylor algorithm while ~10% of codon positions 1 and 2 dinucleotide matrices and intronic trinucleotide matrices, and ~30% of codon matrices were pathological to eigendecomposition. The majority of Taylor algorithm errors derived from occurrence of multiple unobserved states. A small number of negative probabilities were detected from the Padé algorithm on trinucleotide matrices that were attributable to machine precision. Although the Padé algorithm does not facilitate caching of intermediate results, it was up to 3× faster than eigendecomposition on the same matrices.

Conclusion
Development of robust software for computing non-reversible dinucleotide, codon and higher evolutionary models requires implementation of the Padé with scaling and squaring algorithm.
Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains
Authors: Nelson William , Luo Meizhong , Ma Jianxin , Estep Matt , Estill James , He Ruifeng , Talag Jayson , Sisneros Nicholas , Kudrna David , Kim HyeRan , Ammiraju Jetty SS , Collura Kristi , Bharti Arvind K , Messing Joachim , Wing Rod A , SanMiguel Phillip , Bennetzen Jeffrey L , Soderlund Carol 
Published: December 2008

Abstract

Background
Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR) and methylation spanning linker libraries (MSLL). These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends.

Results
A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the Sal I MSLL libraries being the most highly enriched (31% align to an EST contig), while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%). These two techniques were compared with other gene-enrichment methods, and shown to be complementary.

Conclusion
MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of epigenetic boundaries are barely understood at this time, MSLL technology flags both approximate boundaries and methylated genes that deserve additional investigation. MSLL and HMPR sequences provide a valuable resource for maize genome annotation, and are a uniquely valuable complement to any plant genome sequencing project. In order to make these results fully accessible to the community, a web display was developed that shows the alignment of MSLL, HMPR, and other gene-rich sequences to the BACs; this display is continually updated with the latest ESTs and BAC sequences.
DDESC: Dragon database for exploration of sodium channels in human
Authors: Sagar Sunil , Kaur Mandeep , Dawe Adam , Seshadri Sundararajan Vijayaraghava , Christoffels Alan , Schaefer Ulf , Radovanovic Aleksandar , Bajic Vladimir B 
Published: December 2008

Abstract

Background
Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic disorders such as febrile epilepsy, Brugada syndrome, ventricular fibrillation, long QT syndrome, or channelopathy associated insensitivity to pain. In spite of these significant effects that sodium channel proteins/genes could have on human health, there is no publicly available resource focused on sodium channels that would support exploration of the sodium channel related information.

Results
We report here Dragon Database for Exploration of Sodium Channels in Human (DDESC), which provides comprehensive information related to sodium channels regarding different entities, such as "genes and proteins", "metabolites and enzymes", "toxins", "chemicals with pharmacological effects", "disease concepts", "human anatomy", "pathways and pathway reactions" and their potential links. DDESC is compiled based on text- and data-mining. It allows users to explore potential associations between different entities related to sodium channels in human, as well as to automatically generate novel hypotheses.

Conclusion
DDESC is first publicly available resource where the information related to sodium channels in human can be explored at different levels. This database is freely accessible for academic and non-profit users via the worldwide web http://apps.sanbi.ac.za/ddesc.
Conservation and implications of eukaryote transcriptional regulatory regions across multiple species
Authors: Wan Lin , Li Dayong , Zhang Donglei , Liu Xue , Fu Wenjiang J , Zhu Lihuang , Deng Minghua , Sun Fengzhu , Qian Minping 
Published: December 2008

Abstract

Background
Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs). Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts.

Results
We constructed a hierarchical stochastic language (HSL) model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or OsALYL1, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes.

Conclusion
Our findings indicate that 1) the HSL model can be used to accurately predict core TRRs of transcripts across species and 2) identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.
Assessment of genetic and functional diversity of phosphate solubilizing fluorescent pseudomonads isolated from rhizospheric soil
Authors: Naik Popavath Ravindra , Raman Gurusamy , Narayanan Kannan Badri , Sakthivel Natarajan 
Published: December 2008

Abstract

Background
Phosphorus is an essential macronutrient for the growth of plants. However, in most soils a large portion of phosphorus becomes insoluble and therefore, unavailable to plants. Knowledge on biodiversity of phosphate-solubilizing fluorescent pseudomonads is essential to understand their ecological role and their utilization in sustainable agriculture.

Results
Of 443 fluorescent pseudomonad strains tested, 80 strains (18%) showed positive for the solubilization of tri-calcium phosphate (Ca3(PO4)2) by the formation of visible dissolution halos on Pikovskaya's agar. These phosphate solubilizing strains showed high variability in utilizing various carbon sources. Numerical taxonomy of the phosphate solubilizing strains based on their carbon source utilization profiles resulted into three major phenons at a 0.76 similarity coefficient level. Genotypic analyses of strains by BOX (bacterial repetitive BOX element)-polymerase chain reaction (PCR) resulted into three distinct genomic clusters and 26 distinct BOX profiles at a 80% similarity level. On the basis of phenotypic characterization and 16S rRNA gene phylogenetic analyses strains were identified as Pseudomonas aeruginosa, P. mosselii, P. monteilii, P. plecoglossicida, P. putida, P. fulva and P. fluorescens. These phosphate solubilizing strains also showed the production of plant growth promoting enzymes, hormones and exhibited antagonism against phytopathogenic fungi that attack on various crops. Gene specific primers have identified the putative antibiotic producing strains. These putative strains were grown in fermentation media and production of antibiotics was confirmed by thin layer chromatography (TLC) and high performance liquid chromatography (HPLC).

Conclusion
Present study revealed a high degree of functional and genetic diversity among the phosphate solubilizing fluorescent pseudomonad bacteria. Due to their innate potential of producing an array of plant growth promoting enzymes, hormones and antifungal metabolites these phosphate solubilizing strains are considered to play a vital role in plant growth promotion, disease suppression and subsequent enhancement of yield.
A clarified position for solanum lycopersicum var. cerasiformein the evolutionary history of tomatoes (solanaceae)
Authors: Ranc Nicolas , Muños Stéphane , Santoni Sylvain , Causse Mathilde 
Published: December 2008

Abstract

Background
The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. However it is necessary to consider the genetic structure of the germplasm used to avoid false association. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history. In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. The study focused on the red fruited tomato clade involved in the domestication of tomato and confirmed the admixture status of cherry tomatoes (Solanum lycopersicum var. cerasiforme). We used a nested sample strategy to set-up core collection maximizing the genetic diversity with a minimum of individuals.

Results
Molecular diversity was considerably lower in S. lycopersicum i.e. the domesticated form. Model-based analysis showed that the 144 S. lycopersicum var. cerasiforme accessions were structured into two groups: one close to the domesticated group and one resulting from the admixture of the S. lycopersicum and S. pimpinellifolium genomes. SSR genotyping also indicates that domesticated and wild tomatoes have evolved as a species complex with intensive level of hybridization. We compiled genotypic and phenotypic data to identify sub-samples of 8, 24, 32 and 64 cherry tomato accessions that captured most of the genetic and morphological diversity present in the entire S. lycopersicum var. cerasiforme collection.

Conclusion
The extent and structure of allelic variation is discussed in relation to historical events like domestication and modern selection. The potential use of the admixed group of S. lycopersicum var. cerasiforme for association genetics studies is also discussed. Nested core collections sampled to represent tomato diversity will be useful in diversity studies. Molecular and phenotypic variability of these core collections is defined. These collections are available for the scientific community and can be used as standardized panels for coordinating efforts on identifying novel interesting genes and on examining the domestication process in more detail.
Genetic polymorphisms of RANTES, IL1-A, MCP-1 and TNF-A genes in patients with prostate cancer
Authors: Sáenz-López Pablo , Carretero Rafael , Cózar José Manuel , Romero José Maria , Canton Julia , Vilchez José Ramón , Tallada Miguel , Garrido Federico , Ruiz-Cabello Francisco 
Published: December 2008

Abstract

Background
Inflammation has been implicated as an etiological factor in several human cancers, including prostate cancer. Allelic variants of the genes involved in inflammatory pathways are logical candidates as genetic determinants of prostate cancer risk. The purpose of this study was to investigate whether single nucleotide polymorphisms of genes that lead to increased levels of pro-inflammatory cytokines and chemokines are associated with an increased prostate cancer risk.

Methods
A case-control study design was used to test the association between prostate cancer risk and the polymorphisms TNF-A-308 A/G (rs 1800629), RANTES-403 G/A (rs 2107538), IL1-A-889 C/T (rs 1800587) and MCP-1 2518 G/A (rs 1024611) in 296 patients diagnosed with prostate cancer and in 311 healthy controls from the same area.

Results
Diagnosis of prostate cancer was significantly associated with TNF-A GA + AA genotype (OR, 1.61; 95% CI, 1.09–2.64) and RANTES GA + AA genotype (OR, 1.44; 95% CI, 1.09–2.38). A alleles in TNF-A and RANTES influenced prostate cancer susceptibility and acted independently of each other in these subjects. No epistatic effect was found for the combination of different polymorphisms studied. Finally, no overall association was found between prostate cancer risk and IL1-A or MCP-1 polymorphisms.

Conclusion
Our results and previously published findings on genes associated with innate immunity support the hypothesis that polymorphisms in proinflammatory genes may be important in prostate cancer development.
Antioxidant intervention of smoking-induced lung tumor in mice by vitamin E and quercetin
Authors: Yang Jie , Wang Lu , Chen Zhaoli , Shen Zhi-Qiang , Jin Min , Wang Xin-Wei , Zheng Yufei , Qiu Zhi-Gang , Wang Jing-feng , Li Jun-Wen 
Published: December 2008

Abstract

Background
Epidemiological and in vitro studies suggest that antioxidants such as quercetin and vitamin E (VE) can prevent lung tumor caused by smoking; however, there is limited evidence from animal studies.

Methods
In the present study, Swiss mouse was used to examine the potential of quercetin and VE for prevention lung tumor induced by smoking.

Results
Our results suggest that the incidence of lung tumor and tumor multiplicity were 43.5% and 1.00 ± 0.29 in smoking group; Quercetin has limited effects on lung tumor prevention in this in vivo model, as measured by assays for free radical scavenging, reduction of smoke-induced DNA damage and inhibition of apoptosis. On the other hand, vitamin E drastically decreased the incidence of lung tumor and tumor multiplicity which were 17.0% and 0.32 ± 0.16, respectively (p < 0.05); and demonstrated prominent antioxidant effects, reduction of DNA damage and decreased cell apoptosis (p < 0.05). Combined treatment with quercetin and VE in this animal model did not demonstrate any effect greater than that due to vitamin E alone. In addition, gender differences in the occurrence of smoke induced-lung tumor and antioxidant intervention were also observed.

Conclusion
We conclude that VE might prevent lung tumor induced by smoking in Swiss mice.