bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lateral compartment osteoarthritis of the knee
Authors: Scott C. E. H. , Nutton R. W. , Biant L. C. 
Published: March 2013

The lateral compartment is predominantly affected in approximately 10% of patients with osteoarthritis of the knee. The anatomy, kinematics and loading during movement differ considerably between medial and lateral compartments of the knee. This in the main explains the relative protection of the lateral compartment compared with the medial compartment in the development of osteoarthritis. The aetiology of lateral compartment osteoarthritis can be idiopathic, usually affecting the femur, or secondary to trauma commonly affecting the tibia. Surgical management of lateral compartment osteoarthritis can include osteotomy, unicompartmental knee replacement and total knee replacement. This review discusses the biomechanics, pathogenesis and development of lateral compartment osteoarthritis and its management.Cite this article: Bone Joint J 2013;95-B:436–44.
Extended venous thromboembolism prophylaxis in patients undergoing hip fracture surgery – the SAVE-HIP3 study
Authors: Fisher W. D. , Agnelli G. , George D. J. , Kakkar A. K. , Lassen M. R. , Mismetti P. , Mouret P. , Turpie A. G. G. 
Published: March 2013

There is currently limited information available on the benefits and risks of extended thromboprophylaxis after hip fracture surgery. SAVE-HIP3 was a randomised, double-blind study conducted to evaluate the efficacy and safety of extended thromboprophylaxis with the ultra-low molecular-weight heparin semuloparin compared with placebo in patients undergoing hip fracture surgery. After a seven- to ten-day open-label run-in phase with semuloparin (20 mg once daily subcutaneously, initiated post-operatively), patients were randomised to once-daily semuloparin (20 mg subcutaneously) or placebo for 19 to 23 additional days. The primary efficacy endpoint was a composite of any venous thromboembolism (VTE; any deep-vein thrombosis and non-fatal pulmonary embolism) or all-cause death until day 24 of the double-blind period. Safety parameters included major and clinically relevant non-major bleeding, laboratory data, and treatment-emergent adverse events (TEAEs). Extended thromboprophylaxis with semuloparin demonstrated a relative risk reduction of 79% in the rate of any VTE or all-cause death compared with placebo (3.9% vs 18.6%, respectively; odds ratio 0.18 (95% confidence interval 0.07 to 0.45), p < 0.001). Two patients in the semuloparin group and none in the placebo group experienced clinically relevant bleeding. TEAE rates were similar in both groups. In conclusion, the SAVE-HIP3 study results demonstrate that patients undergoing hip fracture surgery benefit from extended thromboprophylaxis. Cite this article: Bone Joint J 2013;95-B:459–66.
The long-term clinical outcome after pelvic ring injuries
Authors: Dienstknecht T. , Pfeifer R. , Horst K. , Sellei R. M. , Berner A. , Zelle B. A. , Probst C. , Pape H-C. 
Published: March 2013

We report the functional and socioeconomic long-term outcome of patients with pelvic ring injuries. We identified 109 patients treated at a Level I trauma centre between 1973 and 1990 with multiple blunt orthopaedic injuries including an injury to the pelvic ring, with an Injury Severity Score (ISS) of ≥ 16. These patients were invited for clinical review at a minimum of ten years after the initial injury, at which point functional results, general health scores and socioeconomic factors were assessed. In all 33 isolated anterior (group A), 33 isolated posterior (group P) and 43 combined anterior/posterior pelvic ring injuries (group A/P) were included. The mean age of the patients at injury was 28.8 years (5 to 55) and the mean ISS was 22.7 (16 to 44). At review the mean Short-Form 12 physical component score for the A/P group was 38.71 (22.12 to 56.56) and the mean Hannover Score for Polytrauma Outcome subjective score was 67.27 (12.48 to 147.42), being significantly worse compared with the other two groups (p = 0.004 and p = 0.024, respectively). A total of 42 patients (39%) had a limp and 12 (11%) required crutches. Car or public transport usage was restricted in 16 patients (15%). Overall patients in groups P and A/P had a worse outcome. The long-term outcome of patients with posterior or combined anterior/posterior pelvic ring injuries is poorer than of those with an isolated anterior injury. Cite this article: Bone Joint J 2013;95-B:548–53.
The value of the three-point index in predicting redisplacement of diaphyseal fractures of the forearm in children
Authors: İltar S. , Alemdaroğlu K. B. , Say F. , Aydoğan N. H. 
Published: March 2013

Redisplacement is the most common complication of immobilisation in a cast for the treatment of diaphyseal fractures of the forearm in children. We have previously shown that the three-point index (TPI) can accurately predict redisplacement of fractures of the distal radius. In this prospective study we applied this index to assessment of diaphyseal fractures of the forearm in children and compared it with other cast-related indices that might predict redisplacement. A total of 76 children were included. Their ages, initial displacement, quality of reduction, site and level of the fractures and quality of the casting according to the TPI, Canterbury index and padding index were analysed. Logistic regression analysis was used to investigate risk factors for redisplacement. A total of 18 fractures (24%) redisplaced in the cast. A TPI value of > 0.8 was the only significant risk factor for redisplacement (odds ratio 238.5 (95% confidence interval 7.063 to 8054.86); p < 0.001). The TPI was far superior to other radiological indices, with a sensitivity of 84% and a specificity of 97% in successfully predicting redisplacement. We recommend it for routine use in the management of these fractures in children. Cite this article: Bone Joint J 2013;95-B:563–7.
The Rebirth of Progesterone in the Prevention of Preterm Labor
Authors: Schmouder Vanessa M , Prescott Gina M , Franco Albert , Fan-Havard Patty 
Published: March 2013

OBJECTIVE To evaluate data since 2003 on the efficacy and safety of progesterone supplementation in the prevention of preterm labor. DATA SOURCES A MEDLINE and Ovid database search (January 2003–September 2012) was performed using the search terms preterm, progesterone, and 17α-hydroxyprogesterone caproate. All relevant abstracts were reviewed. STUDY SELECTION For efficacy and safety data, the search was limited to randomized, double-blind, placebo-controlled trials with the primary outcome of preterm delivery, fetal loss, or neonatal morbidity or mortality. Quality of the studies was assessed using the CONSORT (Consolidated Standards of Reporting Trials) guidelines for reporting parallel-group randomized trials. Eleven articles were selected for review. DATA SYNTHESIS Preterm birth, prior to 37 weeks' gestation, remains the leading cause of neonatal morbidity and mortality in the US due to lack of treatment options. Recently, the use of progesterone to prevent preterm labor, deemed decades ago to be ineffective, has been reexamined. Progesterone formulations and dosage regimens varied greatly between studies. In patients with prior preterm birth or shortened cervix shown on transvaginal ultrasound, progesterone appears efficacious in reducing the rate of preterm birth. However, this benefit was not demonstrated in multiple-gestation pregnancies. Overall, progesterone was well tolerated and appeared safe for mother and fetus. More studies are needed to confirm the dosage regimen and population that will benefit most from progesterone. CONCLUSIONS Progesterone appears to be safe and efficacious in reducing the risk of preterm birth in a select group of high-risk women with prior spontaneous preterm births and those with an ultrasound-confirmed short cervix. Women with multiple gestations do not benefit from progesterone supplementation.
Ischemic Colitis with Type I Interferons Used in the Treatment of Hepatitis C and Multiple Sclerosis: An Evaluation from the Food and Drug Administration Adverse Event Reporting System and Review of the Literature
Authors: Salk Allison , Stobaugh Derrick J , Deepak Parakkal , Ehrenpreis Eli D 
Published: March 2013

OBJECTIVE To better characterize the association between type I interferons and ischemic colitis (IC) in patients with the hepatitis C virus (HCV) and multiple sclerosis (MS), by analyzing reports submitted to the Food and Drug Administration (FDA) Adverse Event Reporting System (AERS) and the published literature. DATA SOURCES A total of 2,562,390 reports of adverse events between January 2003 and June 2011 were downloaded from the FDA AERS. A literature review was performed on PubMed (January 1966–August 2012) using the MeSH terms interferon or interferon alfa or interferon beta and ischemic colitis separated by the Boolean operator “and” between the first 3 terms and the last term. Additional literature was identified by conducting a hand search of the reference list of the published literature identified in the initial search. STUDY SELECTION AND DATA EXTRACTION Cases were restricted to those with an indication of HCV or MS, a primary suspect drug of a type I interferon, and a reaction of IC. Full-length reports were requested and organized by type of interferon, age, sex, concomitant drugs, and comorbidities. The Naranjo prob a bility scale was used to define cases as definite, probable, possible, or doubtful drug-induced adverse events. DATA SYNTHESIS Type I interferons, including interferon alfa (IFN-α) and interferon beta (IFN-β), are approved for the treatment of HCV and MS. IFN-α has been shown to induce IC, but a relationship between type I interferons and IC has not been clarified in the medical literature. Fifty-six primary suspect reports of type I interferons associated with IC in patients with HCV or MS were identified from the FDA AERS. Seventeen cases were reported with IFN-α and 39 cases were reported with IFN-β. The majority of the cases were in females (80%) and those between the ages of 50 and 65 years (52%). The Naranjo probability scale identified 13 probable and 4 possible cases of IFN-α–induced IC, and 19 probable and 20 possible cases of IFN-β–induced IC. In the literature, 11 cases of IFN-α–induced IC were reported, while there were no reports with IFN-β. CONCLUSIONS Our study suggests a possible association between treatment with type I interferons and the development of IC. Further research to determine the mechanism of this association is warranted.
Recombinant Activated Factor VII Use in Critically III Patients: Clinical Outcomes and Thromboembolic Events
Authors: Brophy Gretchen M , Candeloro Christina L , Robles Jaime R , Brophy Donald F 
Published: March 2013

BACKGROUND Hemorrhage and coagulopathy are associated with morbidity and mortality in critically ill patients. Recombinant activated factor VII (rFVIIa) is frequently used in these situations to control bleeding; however, few controlled clinical trials have demonstrated clinical benefit and prolonged survival. OBJECTIVE To compare clinical outcomes and thromboembolic events in intensive care unit (ICU) patients who received rFVIIa versus ICU patients who did not between 2000 and 2005. METHODS A total of 2918 nonhemophiliac adult ICU patients, which included 1459 who received at least 1 dose of rFVIIa and 1459 matched controls who did not, were included in a retrospective database study. Data were extracted from the Solucient ACTracker database, which included 550 hospitals across the US. Measures included patient demographics, rFVIIa prescribing, death, thromboembolic events, discharge disposition, length of stay, and transfusion data. RESULTS The most common primary diagnoses for patients receiving rFVIIa included traumatic brain injury, cirrhosis, and nontraumatic intracranial hemorrhage. Patients receiving rFVIIa were more likely to have comorbidities, including mechanical ventilation, acute kidney injury, sepsis, hemodialysis, and gastrointestinal bleeding (p < 0.0001). The average rFVIIa dose was 4.8 mg and 82% of patients received 1 dose. Compared to controls, patients receiving rFVIIa had greater odds of death (OR 2.1, 95% CI 1.8–2.6, p < 0.0001), transfusion (OR 2.1, 95% CI 1.8–2.5, p < 0.0001), and longer length of stay (p < 0.001). There was no significant difference in thromboembolic events between groups. CONCLUSIONS While we cannot show direct causality between rFVIIa and the poor clinical outcomes documented in ICU patients, they provide important insight for critical care clinicians.
An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce
Authors: Truco Maria José , Ashrafi Hamid , Kozik Alexander , van Leeuwen Hans , Bowers John , Wo Sebastian Reyes Chin , Stoffel Kevin , Xu Huaqin , Hill Theresa , Van Deynze Allen , Michelmore Richard W 
Published: March 2013

Abstract
We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.
Reproductive Status Alters Transcriptomic Response to Infection in FemaleDrosophila melanogaster
Authors: Short Sarah M , Lazzaro Brian P 
Published: March 2013

AbstractMating and consequent reproduction significantly reduce the ability of female Drosophila melanogaster to defend against systemic bacterial infection. The goal of the present study was to identify genes likely to inform the mechanism of this post-mating immunosuppression. We used microarrays to contrast genome-wide transcript levels in virgin vs. mated females before and after infection. Because the immunosuppressive effect of mating is contingent on the presence of a germline in females, we repeated the entire experiment by using female mutants that do not form a germline. We found that multiple genes involved in egg production show reduced expression in response to infection, and that this reduction is stronger in virgins than it is in mated females. In germline-less females, expression of egg-production genes was predictably low and not differentially affected by infection. We also identified several immune responsive genes that are differentially induced after infection in virgins vs. mated females. Immune genes affected by mating status and egg production genes altered by infection are candidates to inform the mechanism of the trade-off between mating and immune defense.
A Targeted Genetic Modifier Screen Links the SWI2/SNF2 Protein Domino to Growth and Autophagy Genes inDrosophila melanogaster
Authors: Kwon Matt Hyoung , Callaway Heather , Zhong Jim , Yedvobnick Barry 
Published: March 2013

AbstractTargeted genetic studies can facilitate phenotypic analyses and provide important insights into development and other complex processes. The SWI2/SNF2 DNA-dependent ATPase Domino (Dom) of Drosophila melanogaster, a component of the Tip60 acetyltransferase complex, has been associated with a wide spectrum of cellular processes at multiple developmental stages. These include hematopoiesis, cell proliferation, homeotic gene regulation, histone exchange during DNA repair, and Notch signaling. To explore the wider gene network associated with Dom action, we used RNAi directed against domino (dom) to mediate loss-of-function at the wing margin, a tissue that is readily scored for phenotypic changes. Dom RNAi driven through GAL4-UAS elicited dominant wing nicking that responded phenotypically to the dose of dom and other loci known to function with dom. We screened for phenotypic modifiers of this wing phenotype among 2500 transpositions of the EP P element and found both enhancers and suppressors. Several classes of modifier were obtained, including those encoding transcription factors, RNA regulatory proteins, and factors that regulate cell growth, proliferation and autophagy, a lysosomal degradation pathway that affects cell growth under conditions of starvation and stress. Our analysis is consistent with prior studies, suggesting that Dom acts pleiotropically as a positive effector of Notch signaling and a repressor of proliferation. This genetic system should facilitate screens for additional loci associated with Dom function, and complement biochemical approaches to their regulatory activity.
Genome-Wide Detection of Gene Coexpression Domains Showing Linkage to Regions Enriched with Polymorphic Retrotransposons in Recombinant Inbred Mouse Strains
Authors: Scott-Boyer Marie-Pier , Deschepper Christian F 
Published: March 2013

Abstract
Although gene coexpression domains have been reported in most eukaryotic organisms, data available to date suggest that coexpression rarely concerns more than doublets or triplets of adjacent genes in mammals. Using expression data from hearts of mice from the panel of AxB/BxA recombinant inbred mice, we detected (according to window sizes) 42−53 loci linked to the expression levels of clusters of three or more neighboring genes. These loci thus formed “cis-expression quantitative trait loci (eQTL) clusters” because their position matched that of the genes whose expression was linked to the loci. Compared with matching control regions, genes contained within cis-eQTL clusters showed much greater levels of coexpression. Corresponding regions showed: (1) a greater abundance of polymorphic elements (mostly short interspersed element retrotransposons), and (2) significant enrichment for the motifs of binding sites for various transcription factors, with binding sites for the chromatin-organizing CCCTC-binding factor showing the greatest levels of enrichment in polymorphic short interspersed elements. Similar cis-eQTL clusters also were detected when we used data obtained with several tissues from BxD recombinant inbred mice. In addition to strengthening the evidence for gene expression domains in mammalian genomes, our data suggest a possible mechanism whereby noncoding polymorphisms could affect the coordinate expression of several neighboring genes.
Trans-Lesion DNA Polymerases May Be Involved in Yeast Meiosis
Authors: Arbel-Eden Ayelet , Joseph-Strauss Daphna , Masika Hagit , Printzental Oxana , Rachi Eléanor , Simchen Giora 
Published: March 2013

AbstractTrans-lesion DNA polymerases (TLSPs) enable bypass of DNA lesions during replication and are also induced under stress conditions. Being only weakly dependent on their template during replication, TLSPs introduce mutations into DNA. The low processivity of these enzymes ensures that they fall off their template after a few bases are synthesized and are then replaced by the more accurate replicative polymerase. We find that the three TLSPs of budding yeast Saccharomyces cerevisiae Rev1, PolZeta (Rev3 and Rev7), and Rad30 are induced during meiosis at a time when DNA double-strand breaks (DSBs) are formed and homologous chromosomes recombine. Strains deleted for one or any combination of the three TLSPs undergo normal meiosis. However, in the triple-deletion mutant, there is a reduction in both allelic and ectopic recombination. We suggest that trans-lesion polymerases are involved in the processing of meiotic double-strand breaks that lead to mutations. In support of this notion, we report significant yeast two-hybrid (Y2H) associations in meiosis-arrested cells between the TLSPs and DSB proteins Rev1-Spo11, Rev1-Mei4, and Rev7-Rec114, as well as between Rev1 and Rad30. We suggest that the involvement of TLSPs in processing of meiotic DSBs could be responsible for the considerably higher frequency of mutations reported during meiosis compared with that found in mitotically dividing cells, and therefore may contribute to faster evolutionary divergence than previously assumed.
Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome
Authors: Shanku Alexander G , McPeek Mark A , Kern Andrew D 
Published: March 2013

Abstract
In this paper we present a de novo assembly of the transcriptome of the damselfly (Enallagma hageni) through the use of 454 pyrosequencing. E. hageni is a member of the suborder Zygoptera, in the order Odonata, and Odonata organisms form the basal lineage of the winged insects (Pterygota). To date, sequence data used in phylogenetic analysis of Enallagma species have been derived from either mitochondrial DNA or ribosomal nuclear DNA. This Enallagma transcriptome contained 31,661 contigs that were assembled and translated into 14,813 individual open reading frames. Using these data, we constructed an extensive dataset of 634 orthologous nuclear protein-encoding genes across 11 species of Arthropoda and used Bayesian techniques to elucidate the position of Enallagma in the arthropod phylogenetic tree. Additionally, we demonstrated that the Enallagma transcriptome contains 169 genes that are evolving at rates that differ relative to those of the rest of the transcriptome (29 accelerated and 140 decreased), and, through multiple Gene Ontology searches and clustering methods, we present the first functional annotation of any palaeopteran’s transcriptome in the literature.
PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data
Authors: Ruby J Graham , Bellare Priya , DeRisi Joseph L 
Published: March 2013

Abstract
Low-cost DNA sequencing technologies have expanded the role for direct nucleic acid sequencing in the analysis of genomes, transcriptomes, and the metagenomes of whole ecosystems. Human and machine comprehension of such large datasets can be simplified via synthesis of sequence fragments into long, contiguous blocks of sequence (contigs), but most of the progress in the field of assembly has focused on genomes in isolation rather than metagenomes. Here, we present software for paired-read iterative contig extension (PRICE), a strategy for focused assembly of particular nucleic acid species using complex metagenomic data as input. We describe the assembly strategy implemented by PRICE and provide examples of its application to the sequence of particular genes, transcripts, and virus genomes from complex multicomponent datasets, including an assembly of the BCBL-1 strain of Kaposi’s sarcoma-associated herpesvirus. PRICE is open-source and available for free download (derisilab.ucsf.edu/software/price/ or sourceforge.net/projects/pricedenovo/).