bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acellular Fetal Bovine Dermal Matrix for Treatment of Chronic Ulcerations of the Midfoot Associated With Charcot Neuroarthropathy
Authors: Kavros Steven J. 
Published: June 2012

Background. Gross deformity of the foot in Charcot neuroarthropathy can lead to collapse and subsequent ulceration, infection, amputation, or premature death. This study evaluated healing of midfoot ulcerations of Charcot neuroarthropathy using PriMatrix, a novel acellular fetal bovine dermal matrix. Methods. In this retrospective analysis, 20 patients with ulcerations of the midfoot associated with Charcot neuroarthropathy were treated with either PriMatrix in addition to standard wound care (PriMatrix group,n = 12) or standard wound care alone (control group, n = 8). All patients had chronic, nonhealing foot ulcerations of at least 2250 mm3 for a minimum of 30 days duration. All foot ulcerations were full thickness with subcutaneous involvement. Ankle brachial index ≥0.90 and/or transcutaneous oximetry (TcPo2) ≥40 mm Hg at the periulcer site was necessary for inclusion. Patients were excluded if they had acute or chronic osteomyelitis of the foot. Results. Demography, risk factors, baseline severity of Charcot neuroarthropathy, and wound volume (control 4078 mm3, PriMatrix 3737.5 mm3, P = nonsignificant) were similar between treatment groups. Mean time to healing in the PriMatrix group (116 days, 95% CI = 109-123) was significantly shorter than in the control group (180 days, 95% confidence interval [CI] = 171-188); P < .0001. A significantly faster rate of healing was observed with PriMatrix (87.9 mm3/wk, 95% CI = 115.2% to 60.6%) compared with control (59.0 mm3/wk, 95% CI = 72.8% to 45.3%); P < .0001). Conclusions. The significantly faster rate of healing and steeper slope of volume reduction in the PriMatrix group warrants further investigation into its effects on healing of neuropathic ulcerations and potential limb salvage. Levels of Evidence: Therapeutic, Level IV
Clinical Efficacy of the Pan Metatarsal Head Resection as a Curative Procedure in Patients with Diabetes Mellitus and Neuropathic Forefoot Wounds
Authors: Armstrong David G. , Fiorito Joseph L. , Leykum Brian J. , Mills Joseph L. 
Published: June 2012

Objective. To evaluate the safety and efficacy of the pan metatarsal head resection (PMHR) compared with nonsurgical management of wounds in the forefoot in people with diabetes. Methods. The authors evaluated 92 patients with diabetes (66.3% male), with ulcers classified as University of Texas grade 1A or 2A at the plantar aspect of the forefoot using a case-control model. Cases were patients treated with multiple metatarsal head resections for multiple metatarsal head wounds, and controls received standard nonsurgical care. Both groups received standard off-loading and wound care. Outcomes included time to healing, reulceration, infection, and amputation. Results. Patients in the surgery group (SG) healed significantly faster than those in the standard therapy group (ST; 84.2 ± 39.9 days for the ST vs 60.1 ± 27.9 days for the SG; P = .003) and had fewer recurrent ulcers (39.1% for the ST vs 15.2% for the SG; P = .02; odds ratio [OR] = 3.6; 95% confidence interval [CI] = 1.3-9.7) and infections during 1 year of follow-up (64.5% for the ST vs 35.5% for the SG; P = .047; OR = 2.4; 95% CI = 1.0-6.0). There was no significant difference in the proportion of patients receiving an incident amputation in the follow-up period (13.0% for the ST vs 6.5% for the SG; P = .5). Conclusion. The results of this study suggest that the PMHR may be associated with shorter times to healing and lower morbidity compared with standard care alone in patients without digital gangrene and with multiple plantar forefoot ulcers. Levels of Evidence: Therapeutic Level III
Subcaptial Oblique Fifth Metatarsal Osteotomy Versus Distal Chevron Osteotomy for Correction of Bunionette Deformity
Authors: Cooper Minton Truitt , Coughlin Michael J. 
Published: June 2012

The aim of this study was to compare a distal subcapital oblique fifth metatarsal with a distal chevron osteotomy for correction of bunionette deformity. Materials and methods. Twenty cadaveric feet were randomly assigned to undergo either a subcapital oblique or chevron osteotomy of the distal fifth metatarsal. Radiographic measurements, including 4–5 intermetatarsal angle (IMA), fifth metatarsophalangeal angle (5-MPA) and foot width, were compared between the 2 groups. Results. Foot width and 5-MPA was significantly decreased in both groups with no difference between the groups. The 4–5 IMA was not significantly altered in either group. Conclusion. Decrease in foot width and 5-MPA was similarly achieved with either distal chevron or subcapital oblique osteotomy of the fifth metatarsal in normal cadaveric specimens. No significant difference was found between the 2 techniques in any of the radiographic parameters measured. Levels of Evidence: Cadaveric, Level V
Tenodesis Reconstruction for Chronic Ankle Instability
Authors: Meacham Benjamin P. , Granata Jaymes D. , Berlet Gregory C. 
Published: June 2012

Lateral ankle ligament surgical reconstruction can take many forms, including anatomic and nonanatomic reconstructions. The nonanatomic reconstructions require the use of autograft or allograft tendons to recreate the vectors of the injured anterior talofibular ligament (ATFL) and the calcaneofibular ligament (CFL). The purpose of this study was to determine the minimum, maximum, and average graft length requirements for a modified Chrisman–Snook procedure. The structures at risk during drilling of the bone tunnels were documented to guide recommendations for tunnel placement. Modified Chrisman–Snook lateral ligament reconstructions were performed on 10 cadaveric below-the-knee specimens, with no known pathology. Transosseus tunnels were placed through and through the fibula, talus, and calcaneus at the origin and insertion sites of the ATFL and CFL. The minimum, maximum, and average graft length requirements were 91 mm, 170 mm, and 120.7 ± 23.84 mm, respectively. The overall average graft requirement was approximately 120 mm. The length of graft was correlated with the height of the patient. Medial structures that were directly encountered, in at least one specimen, with the transosseus tunnels included the tibial nerve, tibial artery and flexor hallucis longus tendon. The posterior tibial nerve was the structure at greatest risk. The length of the graft, when performing the modified Chrisman–Snook, should measure approximately 120 mm, but considerable variability exists depending on the size of the patient. To avoid injury to medial structures, the transosseus tunnels should be made using either a blind hole technique or guide wire to avoid perforating the medial cortex. Levels of Evidence: Cadaveric, Level V
Muscle Impairments in Patients With Knee Osteoarthritis
Authors: Alnahdi Ali H. , Zeni Joseph A. , Snyder-Mackler Lynn 
Published: June 2012

Context: Muscle impairments associated with knee osteoarthritis (OA) are the primary underlying cause of functional limitations. Understanding the extent of muscle impairments, its relationship with physical function and disease progression, and the evidence behind exercise therapy that targets muscle impairments is crucial. Evidence Acquisition: An electronic search for relevant articles using MEDLINE and CINHAL databases up to September 2011 was performed. In addition to the electronic search, retrieved articles were searched manually for relevant studies. Results: Quadriceps, hamstrings, and hip muscles are significantly impaired in subjects with knee OA compared with age-matched controls. Muscle strength, especially quadriceps, is a major determinant of both performance-based and self-reported physical function. Whether stronger quadriceps is protective against knee OA onset and progression is not clear. Exercise therapy, including global and targeted resistance training, is effective in reducing pain and improving function in subjects with knee OA. Conclusions: Subjects with knee OA have significant muscle impairments. These muscle impairments affect physical function and should be targeted in therapy. Further research is needed to explore the relationship between quadriceps strength and knee OA initiation and progression and to determine the optimal exercise prescription that augments outcomes in this patient population.
Therapeutic Exercise for Athletes With Nonspecific Neck Pain
Authors: Durall Christopher J. 
Published: June 2012

Context: Benign neck pain is common in athletes and is usually the result of minor sprains, strains, or contusions. Athletes with neck pain may have deficits in cervical and/or upper thoracic mobility, muscle recruitment, strength and endurance, repositioning acuity, postural stability, and oculomotor control. Evidence Acquisition: A Medline search was performed via PubMed to locate articles of any publication date through December 2011 using the search terms cervical pain, neck pain, athlete, athletic, therapeutic exercise, and rehabilitation. Reference lists of retrieved articles were searched for additional relevant references. Results: Therapeutic exercise has promise as an intervention for individuals with neck pain, although reports on isolated athletic populations are lacking. To date, recommendations for specific therapeutic exercises have been derived largely from anecdotal or uncontrolled level IV or V evidence. Conclusion: Clinicians should consider deficits, functional limitations, irritability level, and the sport’s cervical spine stress profile when selecting exercises for athletes with neck pain.
A Segmental Approach to Imaging of Sports-Related Injuries of the Pediatric Elbow
Authors: Dwek Jerry R. 
Published: June 2012

Context: The imaging of pediatric sports injuries of the elbow requires an understanding of the interaction between biomechanical forces common in sports and the developing skeleton. Evidence Acquisition: A PubMed search was performed using the terms elbow, radiology, and sports with the search limited to children up to 18 years of age. No limits were set on the range of years searched. Articles were reviewed for relevance with an emphasis of the changing nature of sports injuries about the pediatric elbow. Results: A clear progression of injuries about the elbow can be identified as the skeleton matures. Sports most commonly associated with injuries in the pediatric age group were baseball and gymnastics. Conclusions: Most pediatric sports injuries result from overhand throwing, especially in baseball or gymnastics. The manifestation of the injuries shifts as the physes progress toward closure.
A new hybrid general iterative algorithm for common solutions of generalized mixed equilibrium problems and variational inclusions
Authors: Wattanawitoon Kriengsak , Jitpeera Thanyarat , Kumam Poom 
Published: June 2012

Abstract
In this article, we introduce a new general iterative method for finding a common element of the set of solutions generalized for mixed equilibrium problems, the set of solution for fixed point for nonexpansive mappings and the set of solutions for the variational inclusions for β
1, β
2-inverse-strongly monotone mappings in a real Hilbert space. We prove that the sequence converges strongly to a common element of the above sets under some suitable conditions. Our results improve and extend the corresponding results of Marino and Xu, Su et al., Tan and Chang and some authors.

Mathematics subject Classification: 46C05; 47H09; 47H10.
Transcriptome analysis of microRNAs in developing cerebral cortex of rat
Authors: Yao Mao-jin , Chen Gang , Zhao Ping-ping , Lu Ming-hua , Jian Jiang , Liu Mo-fang , Yuan Xiao-bing 
Published: June 2012

Abstract

Background
The morphogenesis of the cerebral cortex depends on the precise control of gene expression during development. Small non-coding RNAs, including microRNAs and other groups of small RNAs, play profound roles in various physiological and pathological processes via their regulation of gene expression. A systematic analysis of the expression profile of small non-coding RNAs in developing cortical tissues is important for clarifying the gene regulation networks mediating key developmental events during cortical morphogenesis.

Results
Global profiling of the small RNA transcriptome was carried out in rat cerebral cortex from E10 till P28 using next-generation sequencing technique. We found an extraordinary degree of developmental stage-specific expression of a large group of microRNAs. A group of novel microRNAs with functional hints were identified, and brain-enriched expression and Dicer-dependent production of high-abundant novel microRNAs were validated. Profound editing of known microRNAs at “seed” sequence and flanking sequence was observed, with much higher editing events detected at late postnatal stages than embryonic stages, suggesting the necessity of microRNA editing for the fine tuning of gene expression during the formation of complicated synaptic connections at postnatal stages.

Conclusion
Our analysis reveals extensive regulation of microRNAs during cortical development. The dataset described here will be a valuable resource for clarifying new regulatory mechanisms for cortical development and diseases and will greatly contribute to our understanding of the divergence, modification, and function of microRNAs.
Identification of metagenes and their Interactions through Large-scale Analysis of Arabidopsis Gene Expression Data
Authors: Wilson Tyler J , Lai Liming , Ban Yuguang , Ge Steven X 
Published: June 2012

Abstract

Background
Many plant genes have been identified through whole genome and deep transcriptome sequencing and other methods; yet our knowledge on the function of many of these genes remains limited. The integration and analysis of large gene-expression datasets gives researchers the ability to formalize hypotheses concerning the functionality and interaction between different groups of correlated genes.

Results
We applied the non-negative matrix factorization (NMF) algorithm to the AtGenExpress dataset which consists of 783 microarray samples (29 separate experimental series) conducted on the model plant Arabidopsis thaliana. We identified 15 metagenes, which are groups of genes with correlated expression. Functional roles of these metagenes are established by observing the enriched gene ontology (GO) categories using gene set enrichment analyses (GSEA). Activity levels of these metagenes in various experimental conditions are also analyzed to associate metagenes with stimuli/conditions. A metagene correlation network, constructed based on the results of NMF analysis, revealed many new interactions between the metagenes. Comparison of these metagenes with an earlier large-scale clustering analysis indicates many statistically significant overlaps.

Conclusions
This study identifies a network of correlated metagenes composed of Arabidopsis genes acting in a highly correlated fashion across a broad spectrum of experimental stimuli, which may shed some light on the function of many of the un-annotated genes.
Analyses of the sucrose synthase gene family in cotton: structure, phylogeny and expression patterns
Authors: Chen Aiqun , He Shae , Li Feifei , Li Zhao , Ding Mingquan , Liu Qingpo , Rong Junkang 
Published: June 2012

Abstract

Background
In plants, sucrose synthase (Sus) is widely considered as a key enzyme involved in sucrose metabolism. Several paralogous genes encoding different isozymes of Sus have been identified and characterized in multiple plant genomes, while limited information of Sus genes is available to date for cotton.

Results
Here, we report the molecular cloning, structural organization, phylogenetic evolution and expression profiles of seven Sus genes (GaSus1 to 7) identified from diploid fiber cotton (Gossypium arboreum). Comparisons between cDNA and genomic sequences revealed that the cotton GaSus genes were interrupted by multiple introns. Comparative screening of introns in homologous genes demonstrated that the number and position of Sus introns are highly conserved among Sus genes in cotton and other more distantly related plant species. Phylogenetic analysis showed that GaSus1, GaSus2, GaSus3, GaSus4 and GaSus5 could be clustered together into a dicot Sus group, while GaSus6 and GaSus7 were separated evenly into other two groups, with members from both dicot and monocot species. Expression profiles analyses of the seven Sus genes indicated that except GaSus2, of which the transcripts was undetectable in all tissues examined, and GaSus7, which was only expressed in stem and petal, the other five paralogues were differentially expressed in a wide ranges of tissues, and showed development-dependent expression profiles in cotton fiber cells.

Conclusions
This is a comprehensive study of the Sus gene family in cotton plant. The results presented in this work provide new insights into the evolutionary conservation and sub-functional divergence of the cotton Sus gene family in response to cotton fiber growth and development.
Molecular interactions between the olive and the fruit fly Bactrocera oleae
Authors: Corrado Giandomenico , Alagna Fiammetta , Rocco Mariapina , Renzone Giovanni , Varricchio Paola , Coppola Valentina , Coppola Mariangela , Garonna Antonio , Baldoni Luciana , Scaloni Andrea , Rao Rosa 
Published: June 2012

Abstract

Background
The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively.

Results
We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures.

Conclusions
This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.
The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization
Authors: Lo Fang-Yi , Chang Jer-Wei , Chang I-Shou , Chen Yann-Jang , Hsu Han-Shui , Huang Shiu-Feng Kathy , Tsai Fang-Yu , Jiang Shih Sheng , Kanteti Rajani , Nandi Suvobroto , Salgia Ravi , Wang Yi-Ching 
Published: June 2012

Abstract

Background
Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis.

Methods
Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients.

Results
We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68% in Asian and 70% in Caucasian.

Conclusions
Our study provides an invaluable database revealing common and differential imbalance regions at specific chromosomes among Asian and Caucasian lung cancer patients. Four validation methods confirmed our database, which would help in further studies on the mechanism of lung tumorigenesis.