bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Temporal Bone Dissection Using Self‐Directed Virtual Reality Simulation
Authors: Zhao Yi Chen , Kennedy Gregor , Yukawa Kumiko , Pyman Brian , O’Leary Stephen 
Published: December 2010

ObjectiveA significant benefit of virtual reality (VR) simulation is the ability to provide self‐direct learning for trainees. This study aims to determine whether there are any differences in performance of cadaver temporal bone dissections between novices who received traditional teaching methods and those who received unsupervised self‐directed learning in a VR temporal bone simulator.Study DesignRandomized blinded control trial.SettingRoyal Victorian Eye and Ear Hospital.SubjectsTwenty novice trainees.MethodsAfter receiving an hour lecture, participants were randomized into 2 groups to receive an additional 2 hours of training via traditional teaching methods or self‐directed learning using a VR simulator with automated guidance. The simulation environment presented participants with structured training tasks, which were accompanied by real‐time computer‐generated feedback as well as real operative videos and photos. After the training, trainees were asked to perform a cortical mastoidectomy on a cadaveric temporal bone. The dissection was videotaped and assessed by 3 otologists blinded to participants’ teaching group.ResultsThe overall performance scores of the simulator‐based training group were significantly higher than those of the traditional training group (67% vs 29%; P <. 001), with an intraclass correlation coefficient of 0.93, indicating excellent interrater reliability. Using other assessments of performance, such as injury size, the VR simulator‐based training group also performed better than the traditional group.ConclusionsThis study indicates that self‐directed learning on VR simulators can be used to improve performance on cadaver dissection in novice trainees compared with traditional teaching methods alone.
Orthopaedic In-Training Examination
Authors: Osbahr Daryl C. , Cross Michael B. , Bedi Asheesh , Nguyen Joseph T. , Allen Answorth A. , Altchek David W. , Dines Joshua S. 
Published: December 2010

Background: Since 1963, the Orthopaedic In-Training Examination (OITE) has been administered to orthopaedic residents to assess resident knowledge and measure the quality of teaching within individual programs. The OITE has evolved dramatically over the years and now maintains a standardized format consisting of 275 questions divided among 12 sections. Purpose: To provide a detailed analysis of the OITE sports medicine section to identify patterns in question content, recommended references, and resident performance. Study Design: Cross-sectional study. Methods: All OITE sports medicine questions from 2005 to 2009 were analyzed, and the following data were recorded: resident performance scores, tested topics, type of imaging modalities, tested treatment modalities, taxonomy classification, and recommended references. Results: From 2005 to 2009, the sports medicine section composed 7.8% of the OITE. Mean resident performance on the entire OITE as well as on the sports medicine section improved during each year of training. Imaging modalities typically involved questions on radiographs and magnetic resonance imaging and constituted 27.4% of the OITE sports medicine section. Treatment modalities involved 36.8% of the OITE sports medicine section questions, including most treatment questions relating to ligament reconstruction or rehabilitation. The authors’ assessment of taxonomy classification showed that recall-type questions were most common; however, mean resident performance was minimally affected by type of taxonomy question. Finally, there were trends noted in recommended references; namely, the American Journal of Sports Medicine and Orthopaedic Knowledge Update Sports Medicine were the most commonly and consistently cited journal and review book, respectively. Conclusion: The current study provides some unique information relating to content, recommended references, and resident performance on the OITE sports medicine section. It is hoped this information will provide orthopaedic trainees, orthopaedic residency programs, and the American Academy of Orthopaedic Surgeons Evaluation Committee valuable information relating to improving resident knowledge and performance and optimizing sports medicine educational curricula.
Salvage of Severe Ankle Varus Deformity With Soft Tissue and Bone Rebalancing
Authors: DeCarbo William T. , Granata Angela M. , Berlet Gregory C. , Hyer Christopher F. , Philbin Terrence M. 
Published: December 2010

The etiology of ankle varus is multifactorial. Treatment recommendations after failed conservative care include hindfoot and ankle fusions or total ankle arthroplasty (TAA) with ligament rebalancing. The purpose of this study was to evaluate chronic varus ankle deformities through corrective calcaneal osteotomies and lateral soft tissue reconstruction. All skeletally mature patients with at least 5 degrees of ankle varus were included in the study. Pre and postoperative radiographs were retrospectively reviewed measuring talar tilt. All patients had a lateral closing wedge (Dwyer) calcaneal osteotomy, joint debridement, and lateral ankle ligament reconstruction. Eight feet were included in the study. The average follow-up time was 20.6 months. Six patients (six feet) were asymptomatic and did not have any additional surgery at their most recent follow-up. Two patients failed treatment, requiring surgical intervention for persistent pain and/or deformity. The average postoperative ankle varus correction overall was 4.9 degrees. We found ankle varus on average of less than 10 degrees can be reliably corrected with a combination of lateral ligament reconstruction and calcaneal osteotomy. Approximately 50% of the deformity was corrected when comparing pre and postoperative talar tilt values. In patients with varus deformity greater than 10 degrees preoperatively, persistent varus may occur.
Arthroscopic Ultrasound Assessment of Articular Cartilage in the Human Knee Joint
Authors: Kaleva Erna , Virén Tuomas , Saarakkala Simo , Sahlman Janne , Sirola Joonas , Puhakka Jani , Paatela Teemu , Kröger Heikki , Kiviranta Ilkka , Jurvelin Jukka S. , Töyräs Juha 
Published: December 2010

Objective: We tested whether an intra-articular ultrasound (IAUS) method could be used to evaluate cartilage status arthroscopically in human knee joints in vivo. Design: Seven patients undergoing arthroscopic surgery of the knee were enrolled in this study. An ultrasonic examination was conducted using the same portals as in the arthroscopic surgery. A high-frequency (40-MHz) ultrasound transducer (diameter = 1 mm) was directed to the desired location on the articular surface under arthroscopic control. In addition to ultrasound data, an IAUS video and optical video through the arthroscope were recorded. Classification of cartilage injuries according to International Cartilage Repair Society, as conducted by the orthopedic surgeon, provided reference data for comparison with the IAUS. Results: The IAUS method was successful in imaging different characteristics of the articular surfaces (e.g., intact surface, surface fibrillation, and lesions of varying depth). In some cases, also the subchondral bone and abnormal internal cartilage structure were visible in the IAUS images. Specifically, using the IAUS, a local cartilage lesion of 1 patient was found to be deeper than estimated arthroscopically. Conclusions: The IAUS method provided a novel arthroscopic method for quantitative imaging of articular cartilage lesions. The IAUS provided quantitative information about the cartilage integrity and thickness, which are not available in conventional arthroscopy. The present equipment is already approved by the Food and Drug Administration for intravascular use and might be transferred to intra-articular use. The invasiveness of the IAUS method might restrict its wider clinical use but combined with arthroscopy, ultrasonic assessment may enlarge the diagnostic potential of arthroscopic surgery.
Penetrating Blast Injury to the Knee of a United States Soldier Treated with Allograft Mosaicplasty
Authors: Eichinger Maj. Josef K. , Bluman Eric M. , Arrington Col. Edward D. 
Published: December 2010

Objective: This is the first report of successful allograft mosaicplasty treatment of a large osteochondral lesion of the knee caused by a blast fragment sustained during combat operations. The patient was able to return to active duty following rehabilitation. Methods: An active-duty infantryman sustained an osteochondral lesion of the medial femoral condyle caused by a metallic fragment of an explosively formed projectile. Initial treatment consisted of removal of the foreign body and primary closure. The patient continued to experience pain, mechanical symptoms, and repeated effusions after initial nonoperative treatment. Allograft mosaicplasty of the lesion utilizing two 18-mm-diameter fresh allograft osteochondral plugs was performed at 6 months post-injury. Results: At 2-year follow-up, the patient remains on active duty with marked improvement in symptoms. Two years postoperatively, his outcome scores are 72 of 100 on the Western Ontario and McMaster University osteoarthritis scoring index (WOMAC) and 60 of 100 on the Knee Injury and Osteoarthritis Outcome Score (KOOS). His follow-up x-rays and MRI demonstrate intact articular cartilage and subchondral bone incorporation. Conclusion: Penetrating injuries to joints are commonplace in the battlefield environment. Combat injuries to the knee are frequently associated with articular cartilage injury. While numerous cartilage restoration techniques have been used with success for the treatment of osteochondral injuries to the femoral condyles, no published reports describe the use of allograft mosaicplasty in this location for open, penetrating injuries with focal cartilage loss. This is the first documented use of allograft mosaicplasty for a traumatic osteochondral defect of the medial femoral condyle caused by a metallic projectile. The patient was able to return to active duty following rehabilitation. We demonstrate a high level of functioning is possible following allograft mosaicplasty of a large osteochondral lesion caused by penetrating ballistic trauma.
Postrelapse survival in childhood acute lymphoblastic leukemia is independent of initial treatment intensity: a report from the Children's Oncology Group
Authors: Freyer David R. , Devidas Meenakshi , La Mei , Carroll William L. , Gaynon Paul S. , Hunger Stephen P. , Seibel Nita L. 
Published: December 2010

Abstract
While intensification of therapy has improved event-free survival (EFS) and survival in newly diagnosed children with acute lymphoblastic leukemia (ALL), postrelapse outcomes remain poor. It might be expected that patients relapsing after inferior initial therapy would have a higher retrieval rate than after superior therapy. In the Children's Oncology Group Study CCG-1961, significantly superior EFS and survival were achieved with an augmented (stronger) versus standard intensity regimen of postinduction intensification (PII) for children with newly diagnosed high-risk ALL and rapid day 7 marrow response (EFS/survival 81.2%/88.7% vs 71.7%/83.4%, respectively). This provided an opportunity to evaluate postrelapse survival (PRS) in 272 relapsed patients who had received randomly allocated initial treatment with augmented or standard intensity PII. As expected, PRS was worse for early versus late relapse, marrow versus extramedullary site, adolescent versus younger age and T versus B lineage. However, no difference in 3-year PRS was detected for having received augmented versus standard intensity PII (36.4% ± 5.7% vs 39.2% ± 4.1%; log rank P = .72). Similar findings were noted within subanalyses by timing and site of relapse, age, and immunophenotype. These findings provide insight into mechanisms of relapse in ALL, and are consistent with emergence of a resistant subclone that has acquired spontaneous mutations largely independent of initial therapy. This study is registered at www.clinicaltrials.gov as NCT00002812.
Probabilistic principal component analysis for metabolomic data
Authors: Nyamundanda Gift , Brennan Lorraine , Gormley Isobel Claire 
Published: January 2011

Abstract

Background
Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA is limited by the fact that it is not based on a statistical model.

Results
Here, probabilistic principal component analysis (PPCA) which addresses some of the limitations of PCA, is reviewed and extended. A novel extension of PPCA, called probabilistic principal component and covariates analysis (PPCCA), is introduced which provides a flexible approach to jointly model metabolomic data and additional covariate information. The use of a mixture of PPCA models for discovering the number of inherent groups in metabolomic data is demonstrated. The jackknife technique is employed to construct confidence intervals for estimated model parameters throughout. The optimal number of principal components is determined through the use of the Bayesian Information Criterion model selection tool, which is modified to address the high dimensionality of the data.

Conclusions
The methods presented are illustrated through an application to metabolomic data sets. Jointly modeling metabolomic data and covariates was successfully achieved and has the potential to provide deeper insight to the underlying data structure. Examination of confidence intervals for the model parameters, such as loadings, allows for principled and clear interpretation of the underlying data structure. A software package called MetabolAnalyze, freely available through the R statistical software, has been developed to facilitate implementation of the presented methods in the metabolomics field.
SeqWare Query Engine: storing and searching sequence data in the cloud
Authors: O’Connor Brian D , Merriman Barry , Nelson Stanley F 
Published: January 2011

Abstract

Background
Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands.

Results
In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net).

Conclusions
The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets.
Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes
Authors: Akhunov Eduard D , Akhunova Alina R , Anderson Olin D , Anderson James A , Blake Nancy , Clegg Michael T , Coleman-Derr Devin , Conley Emily J , Crossman Curt C , Deal Karin R , Dubcovsky Jorge , Gill Bikram S , Gu Yong Q , Hadam Jakub , Heo Hwayoung , Huo Naxin , Lazo Gerard R , Luo Ming-Cheng , Ma Yaqin Q , Matthews David E , McGuire Patrick E , Morrell Peter L , Qualset Calvin O , Renfro James , Tabanao Dindo , Talbert Luther E , Tian Chao , Toleno Donna M , Warburton Marilyn L , You Frank M , Zhang Wenjun , Dvorak Jan 
Published: January 2011

Abstract

Background
A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.

Results
Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.

Conclusions
In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.
Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3'UTR-primed SNP detection approach
Authors: Andreassen Rune , Lunner Sigbjørn , Høyheim Bjørn 
Published: January 2011

Abstract

Background
Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest in identification of SNP markers in non-model species and farmed animals. The in silico SNP mining method used for discovery of most known SNPs in Atlantic salmon (Salmo salar) has applied a global (genome-wide) approach. In this study we present a targeted 3'UTR-primed SNP discovery strategy that utilizes sequence data from Salmo salar full length sequenced cDNAs (FLIcs). We compare the efficiency of this new strategy to the in silico SNP mining method when using both methods for targeted SNP discovery.

Results
The SNP discovery efficiency of the two methods was tested in a set of FLIc target genes. The 3'UTR-primed SNP discovery method detected novel SNPs in 35% of the target genes while the in silico SNP mining method detected novel SNPs in 15% of the target genes. Furthermore, the 3'UTR-primed SNP discovery strategy was the less labor intensive one and revealed a higher success rate than the in silico SNP mining method in the initial amplification step. When testing the methods we discovered 112 novel bi-allelic polymorphisms (type I markers) in 88 salmon genes [dbSNP: ss179319972-179320081, ss250608647-250608648], and three of the SNPs discovered were missense substitutions.

Conclusions
Full length insert cDNAs (FLIcs) are important genomic resources that have been developed in many farmed animals. The 3'UTR-primed SNP discovery strategy successfully utilized FLIc data to detect novel SNPs in the partially tetraploid Atlantic salmon. This strategy may therefore be useful for targeted SNP discovery in several species, and particularly useful in species that, like salmonids, have duplicated genomes.
Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice
Authors: Stewart Taryn P , Kim Hyoung Yon , Saxton Arnold M , Kim Jung Han 
Published: January 2011

Abstract
Background
Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.

Results
In order to determine the genetic factors that contribute to these T2D related characteristics in TH mice, we interbred TH mice with C57BL/6J (B6) mice. The parental, F1, and F2 mice were phenotyped at 8, 12, 16, 20, and 24 weeks of age for 4-hour fasting plasma triglyceride, cholesterol, insulin, and glucose levels and body, fat pad and carcass weights. The F2 mice were genotyped genome-wide and used for quantitative trait locus (QTL) mapping. We also applied a genetical genomic approach using a subset of the F2 mice to seek candidate genes underlying the QTLs. Major QTLs were detected on chromosomes (Chrs) 1, 11, 4, and 8 for hypertriglyceridemia, 1 and 3 for hypercholesterolemia, 4 for hyperglycemia, 11 and 1 for body weight, 1 for fat pad weight, and 11 and 14 for carcass weight. Most alleles, except for Chr 3 and 14 QTLs, increased phenotypic values when contributed by the TH strain. Fourteen pairs of interacting loci were detected, none of which overlapped the major QTLs. The QTL interval linked to hypercholesterolemia and hypertriglyceridemia on distal Chr 1 contains Apoa2 gene. Sequencing analysis revealed polymorphisms of Apoa2 in TH mice, suggesting Apoa2 as the candidate gene for the hyperlipidemia QTL. Gene expression analysis added novel information and aided in selection of candidates underlying the QTLs.

Conclusions
We identified several genetic loci that affect the quantitative variations of plasma lipid and glucose levels and obesity traits in a TH × B6 intercross. Polymorphisms in Apoa2 gene are suggested to be responsible for the Chr 1 QTL linked to hypercholesterolemia and hypertriglyceridemia. Further, genetical genomic analysis led to potential candidate genes for the QTLs.