bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitchell’s Osteotomy With Mini-Plate and Screw Fixation for Hallux Valgus
Authors: Kalender Ali Murat , Uslu Mustafa , Bakan Betul , Ozkan Fuat , Erturk Cemil , Altay Mehmet Akif , Guner Savas , Kalender Mahmut 
Published: January 2013

Background: The aim of this study was to evaluate the use of mini-plate and screw fixation to stabilize the first metatarsal osteotomy in patients undergoing Mitchell bunionectomy, with the outcomes of interest being radiological alignment and the time to bony union. Methods: We used mini-plates and screws in 43 feet of 25 patients to avoid cast immobilization and prevent osteotomy displacement. The mean age at operation was 45.4 ± 13.4 years (range, 17.0-65.0 years). The mean follow-up was 16.9 ± 3.6 months (range, 12.0-30.0 months). The hallux valgus angles, intermetatarsal angles, and American Orthopaedic Foot and Ankle Society (AOFAS) forefoot scores were evaluated preoperatively and at postoperative month 12. Results: The mean preoperative value for the hallux valgus angle was 35.9 ± 4.4 degrees (range, 26.0-45.0 degrees) and for the intermetatarsal angle was 12.1 ± 1.4 degrees (range, 10.0-15.0 degrees). The mean postoperative value for the hallux valgus angle was 16.0 ± 2.12 degrees (range, 12.0-20.0 degrees) and for the intermetatarsal angle was 7.7 ± 1.2 degrees (range, 5.0-10.0 degrees). The mean AOFAS score was 50.5 ± 12.8 points (range, 30.1-76.0 points) preoperatively and 75.9 ± 11.3 points (range, 43.3-92.3 points) at postoperative month 12. Improvement of range of motion of the metatarsophalangeal joint, pain relief, and satisfactory alignment of the first ray were achieved in 41 feet (95.3%). Conclusions: We recommend this fixation for Mitchell’s bunionectomy because it provided stable fixation without the need for casting. Level of Evidence: Level IV, retrospective case series.
The Spectrum of Open Fractures of the Foot in Adults
Authors: Court-Brown Charles , Honeyman Calum , Bugler Kate , McQueen Margaret 
Published: January 2013

Background: Open foot fractures are rare, and few surgeons see the whole spectrum of these injuries. There has been no previous study of the epidemiology and severity of open foot fractures. Methods: A 23-year study of the epidemiology of open fractures was undertaken in a hospital with a catchment area of about 530 000 adults. The results were used to calculate the incidences of open foot fractures and to study their epidemiology and severity. Results: In 23 years, 348 open foot fractures were treated. Analysis showed 3 levels of severity with the least severe fractures being isolated open forefoot fractures, which occurred in 69% of the patients. Patients with multiple forefoot fractures had a higher Injury Severity Score (ISS), prevalence of Gustilo type III fractures, and amputation rate. The most severely injured patients presented with open hindfoot and midfoot fractures. They had an average ISS of 12, and 65.9% had Gustilo type III fractures. In patients with open hindfoot fractures, the amputation rate was 17.1%. This rose to 30% in patients with open midfoot fractures. Open foot fractures tended to occur in younger patients, and only 13% were in patients aged at least 65 years. Conclusions: Open foot fractures are uncommon. There were 3 levels of injury. Level 1 injuries were isolated fractures of the forefoot. Level 2 injuries were multiple forefoot fractures, and level 3 injuries were open fractures of the midfoot and hindfoot. These were severe injuries with a high amputation rate. They should be treated in level 1 trauma centers. Level of Evidence: Level III, retrospective comparative series.
Tarsal Tunnel Syndrome in Hemodialysis Patients
Authors: Imai Kan , Ikoma Kazuya , Imai Ryo , Fujiwara Hiroyoshi , Kido Masamitsu , Hara Yusuke , Ono Toshihiko , Kubo Toshikazu 
Published: January 2013

Background: The purpose of our study was to investigate tarsal tunnel syndrome (TTS) arising in patients who have undergone maintenance dialysis at our facility and to evaluate the frequency, pathological characteristics, and diagnosis of TTS. Methods: We evaluated 1011 patients (mean age 65.1 years) undergoing maintenance dialysis from 2000 to 2006 at our hospital. In patients diagnosed with TTS, we examined clinical symptoms and imaging findings. In addition, we evaluated intraoperative findings in patients who had undergone surgery. A follow-up study was conducted for at least 1 year. Results: Five patients (7 ankles) (mean age 57.8 years) were diagnosed as have TTS, with a mean dialysis duration of 23.4 years (range, 7-30 years). With conservative treatment consisting of rest and a steroid injection, 4 ankles showed improvement. Surgery was performed on 3 ankles. Amyloidoma, nodular tumor fragile deposits in the soft tissue or thecal surface, proliferation of the synovial tendon sheath, and thickened joint capsule were recognized in 3 ankles, and a concomitant ganglion was recognized in 1 ankle. Histologically, the deposition of hyaline material was recognized in all tissues, including the walls of the ganglion or joint capsule, by staining to a pale red color using Congo red stain. An immunohistochemical study indicated positive staining by β-2 microglobulin staining. The flexor retinaculum was thin in all cases, with retinaculum-like thickness not found in carpal tunnel syndrome. Conclusions: We believe that the occurrence of TTS in dialysis patients was 0.5%, with a tendency to be more prevalent among patients undergoing maintenance dialysis for 5 or more years. The pathological process of TTS may be different from that of carpal tunnel syndrome. Level of Evidence: Level IV, retrospective case series.
RETRACTED: Effects of High-Frequency Repetitive Transcranial Magnetic Stimulation on Motor and Gait Improvement in Incomplete Spinal Cord Injury Patients
Authors: Kumru Hatice , Benito Jesus , Murillo Narda , Valls-Sole Josep , Valles Margarita , Lopez-Blazquez Raquel , Costa Ursula , Tormos Josep M. , Pascual-Leone Alvaro , Vidal Joan 
Published: January 2013

Kumru H, Benito J, Murillo N, et al. Effects of high-frequency repetitive transcranial magnetic stimulation on motor and gait improvement in incomplete spinal cord injury patients. Neurorehabil & Neural Repair. 2013;27:421-429. Original DOI: 10.1177/1545968312471901. The above article has been retracted because of substantial overlap with a previously published article in another journal.
SOX11 regulates PAX5 expression and blocks terminal B-cell differentiation in aggressive mantle cell lymphoma
Authors: Vegliante Maria Carmela , Palomero Jara , Pérez-Galán Patricia , Roué Gaël , Castellano Giancarlo , Navarro Alba , Clot Guillem , Moros Alexandra , Suárez-Cisneros Helena , Beà Sílvia , Hernández Luis , Enjuanes Anna , Jares Pedro , Villamor Neus , Colomer Dolors , Martín-Subero José Ignacio , Campo Elias , Amador Virginia 
Published: January 2013

Key Points
SOX11 silencing promotes the shift from a mature B cell into the initial plasmacytic differentiation phenotype in MCL. SOX11 promotes tumor growth of MCL cells in vivo, highlighting its implication in the aggressive behavior of conventional MCL.
B-cell deficiency and severe autoimmunity caused by deficiency of protein kinase C δ
Authors: Salzer Elisabeth , Santos-Valente Elisangela , Klaver Stefanie , Ban Sol A. , Emminger Wolfgang , Prengemann Nina Kathrin , Garncarz Wojciech , Müllauer Leonhard , Kain Renate , Boztug Heidrun , Heitger Andreas , Arbeiter Klaus , Eitelberger Franz , Seidel Markus G. , Holter Wolfgang , Pollak Arnold , Pickl Winfried F. , Förster-Waldl Elisabeth , Boztug Kaan 
Published: January 2013

Key Points
PRKCD deficiency causes a novel primary immunodeficiency with B-cell deficiency and severe autoimmunity. Protein kinase C δ may represent a key factor controlling immune homeostasis and autoimmunity.
Prospective evaluation of gene mutations and minimal residual disease in patients with core binding factor acute myeloid leukemia
Authors: Jourdan Eric , Boissel Nicolas , Chevret Sylvie , Delabesse Eric , Renneville Aline , Cornillet Pascale , Blanchet Odile , Cayuela Jean-Michel , Recher Christian , Raffoux Emmanuel , Delaunay Jacques , Pigneux Arnaud , Bulabois Claude-Eric , Berthon Céline , Pautas Cécile , Vey Norbert , Lioure Bruno , Thomas Xavier , Luquet Isabelle , Terré Christine , Guardiola Philippe , Béné Marie C. , Preudhomme Claude , Ifrah Norbert , Dombret Hervé 
Published: January 2013

Key PointsIn adult patients with core binding factor AML, intensified induction is not associated with a better outcome in the context of intensive postremission therapy. Minimal residual disease, rather than KIT or FLT3 gene mutations, should be used to identify core binding factor AML patients at higher risk of relapse.
GSVA: gene set variation analysis for microarray and RNA-Seq data
Authors: Hänzelmann Sonja , Castelo Robert , Guinney Justin 
Published: January 2013

AbstractBackgroundGene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets.ResultsTo address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments.ConclusionsGSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded athttp://www.bioconductor.org.
Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing
Authors: Wang Junwen , Xia Yudong , Li Lili , Gong Desheng , Yao Yu , Luo Huijuan , Lu Hanlin , Yi Na , Wu Honglong , Zhang Xiuqing , Tao Qian , Gao Fei 
Published: January 2013

Abstract

Background
Reduced representation bisulfite sequencing (RRBS) was developed to measure DNA methylation of high-CG regions at single base-pair resolution, and has been widely used because of its minimal DNA requirements and cost efficacy; however, the CpG coverage of genomic regions is restricted and important regions with low-CG will be ignored in DNA methylation profiling. This method could be improved to generate a more comprehensive representation.

Results
Based on in silico simulation of enzyme digestion of human and mouse genomes, we have optimized the current single-enzyme RRBS by applying double enzyme digestion in the library construction to interrogate more representative regions. CpG coverage of genomic regions was considerably increased in both high-CG and low-CG regions using the double-enzyme RRBS method, leading to more accurate detection of their average methylation levels and identification of differential methylation regions between samples. We also applied this double-enzyme RRBS method to comprehensively analyze the CpG methylation profiles of two colorectal cancer cell lines.

Conclusion
The double-enzyme RRBS increases the CpG coverage of genomic regions considerably over the previous single-enzyme RRBS method, leading to more accurate detection of their average methylation levels. It will facilitate genome-wide DNA methylation studies in multiple and complex clinical samples.
Comparative genome analysis of Spiroplasma melliferumIPMB4A, a honeybee-associated bacterium
Authors: Lo Wen-Sui , Chen Ling-Ling , Chung Wan-Chia , Gasparich Gail E , Kuo Chih-Horng 
Published: January 2013

Abstract

Background
The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic ‘Candidatus Phytoplasma’, all characterized Spiroplasma species were found to be associated with eukaryotic hosts. While most of the Spiroplasma species appeared to be harmless commensals of insects, a small number of species have evolved pathogenicity toward various arthropods and plants. In this study, we isolated a novel strain of honeybee-associated S. melliferum and investigated its genetic composition and evolutionary history by whole-genome shotgun sequencing and comparative analysis with other Mollicutes genomes.

Results
The whole-genome shotgun sequencing of S. melliferum IPMB4A produced a draft assembly that was ~1.1 Mb in size and covered ~80% of the chromosome. Similar to other Spiroplasma genomes that have been studied to date, we found that this genome contains abundant repetitive sequences that originated from plectrovirus insertions. These phage fragments represented a major obstacle in obtaining a complete genome sequence of Spiroplasma with the current sequencing technology. Comparative analysis of S. melliferum IPMB4A with other Spiroplasma genomes revealed that these phages may have facilitated extensive genome rearrangements in these bacteria and contributed to horizontal gene transfers that led to species-specific adaptation to different eukaryotic hosts. In addition, comparison of gene content with other Mollicutes suggested that the common ancestor of the SEM (Spiroplasma, Entomoplasma, and Mycoplasma) clade may have had a relatively large genome and flexible metabolic capacity; the extremely reduced genomes of present day Mycoplasma and ‘Candidatus Phytoplasma’ species are likely to be the result of independent gene losses in these lineages.

Conclusions
The findings in this study highlighted the significance of phage insertions and horizontal gene transfer in the evolution of bacterial genomes and acquisition of pathogenicity. Furthermore, the inclusion of Spiroplasma in comparative analysis has improved our understanding of genome evolution in Mollicutes. Future improvements in the taxon sampling of available genome sequences in this group are required to provide further insights into the evolution of these important pathogens of humans, animals, and plants.
Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis
Authors: Affara Muna , Sanders Debbie , Araki Hiromitsu , Tamada Yoshinori , Dunmore Benjamin J , Humphreys Sally , Imoto Seiya , Savoie Christopher , Miyano Satoru , Kuhara Satoru , Jeffries David , Print Cristin , Charnock-Jones D Stephen 
Published: January 2013

Abstract

Background
Apoptosis is a critical process in endothelial cell (EC) biology and pathology, which has been extensively studied at protein level. Numerous gene expression studies of EC apoptosis have also been performed, however few attempts have been made to use gene expression data to identify the molecular relationships and master regulators that underlie EC apoptosis. Therefore, we sought to understand these relationships by generating a Bayesian gene regulatory network (GRN) model.

Results
ECs were induced to undergo apoptosis using serum withdrawal and followed over a time course in triplicate, using microarrays. When generating the GRN, this EC time course data was supplemented by a library of microarray data from EC treated with siRNAs targeting over 350 signalling molecules.
The GRN model proposed Vasohibin-1 (VASH1) as one of the candidate master-regulators of EC apoptosis with numerous downstream mRNAs. To evaluate the role played by VASH1 in EC, we used siRNA to reduce the expression of VASH1. Of 10 mRNAs downstream of VASH1 in the GRN that were examined, 7 were significantly up- or down-regulated in the direction predicted by the GRN.Further supporting an important biological role of VASH1 in EC, targeted reduction of VASH1 mRNA abundance conferred resistance to serum withdrawal-induced EC death.

Conclusion
We have utilised Bayesian GRN modelling to identify a novel candidate master regulator of EC apoptosis. This study demonstrates how GRN technology can complement traditional methods to hypothesise the regulatory relationships that underlie important biological processes.
Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus
Authors: Yan Xiaohong , Dong Caihua , Yu Jingyin , Liu Wanghui , Jiang Chenghong , Liu Jia , Hu Qiong , Fang Xiaoping , Wei Wenhui 
Published: January 2013

Abstract

Background
The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants.

Results
In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data.

Conclusions
A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specifically expressed in Fer will help to explore desirable agronomic traits from wild species.
Clinical utility and tolerability of JSPH-1 wireless esophageal pH monitoring system
Authors: Li Jun-Nan , Liu Chun-Lun , Tao Xiao-Hong 
Published: January 2013

Abstract

Background
Wireless esophageal pH monitoring system is an important approach for diagnosis of gastroesophageal reflux disease (GERD), the aim of this study is to test the tolerability and utility of the first wireless esophageal pH monitoring system made in China, and evaluate whether it is feasible for clinical application to diagnose GERD.

Methods
Thirty patients from Department of Gastroenterology of The First Affiliated Hospital of Chongqing Medical University who were suspected GERD underwent JSPH-1 pH capsule. The capsule was placed 5 cm proximal to the squamocolumnar junction (SCJ) by endoscopic determination, the data was recorded consecutively for 48 hours. Then all pH data was downloaded to a computer for analysis. The discomforts reported by patients were recorded.

Results
30 patients were placed JSPH-1 pH capsule successfully and completed 24-hour data recording, 29 patients completed 48-hour data recording. One patient complained of chest pain and required endoscopic removal. No complications and interference of daily activities were reported during data monitoring or follow-up period. 48-hour pH monitoring detected 15 patients of abnormal acid exposure, on day1 detected 9 patients, the difference had statistical significance (P<0.01). Positive symptom index (SI) was identified in 3 patients with normal pH data in both 24-hours. In total, 48-hour monitoring increased diagnosis of GERD in 9 patients.

Conclusion
48-hour esophageal pH monitoring with JSPH-1 wireless pH monitoring system is safe, well tolerated and effective. It can be feasible for clinical application to diagnose GERD.
GERD assessment including pH metry predicts a high response rate to PPI standard therapy
Authors: Kandulski Arne , Peitz Ulrich , Mönkemüller Klaus , Neumann Helmut , Weigt Jochen , Malfertheiner Peter 
Published: January 2013

Abstract

Background
Inadequate response to proton pump inhibitor (PPI) therapy in patients with gastroesophageal reflux disease (GERD) is reported in up to 40%. Patients with non erosive reflux disease (NERD) have lower response rates compared to patients with erosive reflux disease (ERD); pH metry contributes to GERD diagnosis and is critical for proper diagnosis of NERD.
Aim of the study was to assess the need for doubling esomeprazole standard dose (40 mg) for 4 weeks in PPI naive patients with typical reflux symptoms and diagnosis of GERD based on endoscopy and 48 hours, wireless pH metry.

Methods
All patients underwent upper GI endoscopy. Symptoms were recorded with a structured questionnaire (RDQ) and acid exposure was determined by 48 hours, wireless pH monitoring (BRAVO). In case of abnormal acid exposure, patients received a short term treatment with esomeprazole 40 mg q.d. for 4 weeks. If symptoms persisted, patients underwent a second pH metry on PPI and the dose was increased to 40 mg b.i.d.

Results
31 consecutive patients with typical reflux symptoms underwent 48 hours pH monitoring. 22 patients (71%) had abnormal acid exposure, 9 patients had normal pH metry (29%). Of the 9 patients with normal pH metry, 2 were found with erosive esophagitis and 7 without endoscopic abnormalities.
24 patients with documented GERD received esomeprazole treatment. 21 patients achieved complete symptom resolution with 40 mg q.d. after 4 weeks (88%). Only 2 patients required doubling the dose of esomeprazole for complete symptom resolution, 1 patient remained with symptoms.

Conclusions
Patients with typical reflux symptoms and abnormal acid exposure have a high response rate to standard dose esomeprazole regardless of whether they have ERD or NERD.