bluuebunny/crossref_metadata_2025_split huggingface dataset:
Operative Versus Conservative Management of Displaced Tibial Shaft Fracture in Adolescents
Authors: Kinney Matthew C. , Nagle David , Bastrom Tracey , Linn Michael S. , Schwartz Alexandra K. , Pennock Andrew T. 
Published: May 2015

Background:
Displaced tibial shaft fractures are common in adolescent patients, yet there is no standardized management strategy. We compared surgical fixation and closed reduction and casting (CRC) of these fractures to assess treatment outcomes and determine predictors of failure.

Methods:
We retrospectively reviewed all patients aged 12 to 18 who presented with a displaced tibial shaft fracture that required reduction over an 8-year period. Exclusion criteria included open fractures and lack of follow-up to radiographic union or to 6 months from the index procedure. Fractures were initially treated based on surgeon preference either with CRC or with immediate intramedullary nailing. Seventy-four patients met inclusion criteria: 57 were initially managed with CRC and 17 with operative fixation. Radiographic healing was defined as bridging of 3 cortices and adequacy of final alignment was defined as <5 degrees of angular deformity in both planes and <1.0 cm of shortening. Outcomes were analyzed both on intent-to-treat principles and by definitive treatment method.

Results:
Although all fractures in both groups achieved bony healing, 23 of the 57 patients who underwent CRC failed closed treatment and ultimately required surgery (40.3%). Multivariate analysis of patient and fracture characteristics revealed fracture displacement of >20% (odds ratio=7.8, P<0.05) and the presence of a fibula fracture (odds ratio=5.06, P=0.05) as predictors of closed treatment failure. Patients ultimately managed with intramedullary nailing trended toward increased adequacy of final alignment (92.5% vs. 72.4%, P=0.10) but required longer hospitalization (5.4 vs. 1.9 d, P<0.001) and had a higher incidence of anterior knee pain (20% vs. 0%, P<0.01). There was no significant difference between groups with respect to time to healing.

Conclusions:
Treatment outcomes between initial operative fixation and closed reduction of displaced tibia fractures in adolescents are similar, but patients must be counseled about the high failure rates with CRC. Predictors of CRC failure include initial fracture displacement and the presence of a fibula fracture—these variables should be considered when selecting a treatment method.

Level of Evidence:
Level III—Therapeutic study.
Mirror bisulfite sequencing — a method for single-base resolution of hydroxymethylcytosine
Authors: Tan Darany , Chung Tzu Hung , Sun Xueguang , Jia Xi-Yu 
Published: May 2015

ABSTRACTWhile the role of 5-methylcytosine has been well studied, the biological role of 5- hydroxymethylcytosine still remains unclear due to the limited methods available for single-base detection of 5-hydroxymethylcytosine (5hmC). Here, we present Mirror bisulfite sequencing detects 5-hydroxymethylcytosines at a single CpG site by synthesizing a DNA strand to mirror the parental strand. This semi-conservative duplex is sequentially treated with β- glucosyltransferase and M.SssI methylase. A glucosyl-5hmCpG in the parental strand inhibits methylation of the mirroring CpG site, and after bisulfite conversion, a thymine in the mirroring strand indicates a 5hmCpG site in the parental strand whereas a cytosine indicates a non-5hmC site. Using this method, the 5hmC levels of various human tissues and paired liver tissues were mapped genome-wide.
Environmental complexity favors the evolution of learning
Authors: Dridi Slimane , Lehmann Laurent 
Published: May 2015

AbstractLearning is a fundamental biological adaptation that is widespread throughout the animal kingdom. According to previous research, two conditions are necessary for learning to be adaptive: between-generation environmental variability and within-generation environmental predictability. In this paper, we show that between-generation variability is not necessary, and that instrumental learning can provide a selective advantage in complex environments, where an individual is exposed to a large number of different challenges during its lifespan. We construct an evolutionary model where individuals have a memory with limited storage capacity, and an evolving trait determines the fraction of that memory that should be allocated to innate responses to the environment versus learning these responses. The evolutionarily stable level of learning depends critically on the environmental process, but generally increases with environmental complexity. Overall, our work sheds light on the importance of global structural properties of the environment in shaping the evolution of learning.
Expression ofE. coliglycogen branching enzyme in anArabidopsismutant devoid of endogenous starch branching enzymes induces the synthesis of starch-like polyglucans
Authors: Boyer Laura , Roussel Xavier , Courseaux Adeline , Ndjindji Ofilia Mvundza , Lancelon-Pin Christine , Putaux Jean-Luc , Tetlow Ian , Emes Michael , Pontoire Bruno , D’Hulst Christophe , Wattebled Fabrice 
Published: May 2015

ABSTRACTStarch synthesis requires several enzymatic activities including branching enzymes (BEs) responsible for the formation ofα(1→6) linkages. Distribution and number of these linkages are further controlled by debranching enzymes (DBEs) that cleave some of them, rendering the polyglucan water-insoluble and semi-crystalline. Although the activity of BEs and DBEs is mandatory to sustain normal starch synthesis, the relative importance of each in the establishment of the plant storage polyglucan (i.e. water-insolubility, crystallinity, presence of amylose) is still debated. Here, we have substituted the activity of BEs inArabidopsiswith that of theEscherichia coliglycogen branching enzyme (GlgB). The latter is the BE counterpart in the metabolism of glycogen, a highly branched water-soluble and amorphous storage polyglucan. GlgB was expressed in thebe2 be3double mutant ofArabidopsisthat is devoid of BE activity and consequently free of starch. The synthesis of a water-insoluble, partly crystalline, amylose-containing starch-like polyglucan was restored in GlgB-expressing plants, suggesting that BEs origin only have a limited impact on establishing essential characteristics of starch. Moreover, the balance between branching and debranching is crucial for the synthesis of starch, as an excess of branching activity results in the formation of highly branched, water-soluble, poorly crystalline polyglucan.
The GL Service: Web Service to Exchange GL String Encoded HLA & KIR Genotypes With Complete and Accurate Allele and Genotype Ambiguity
Authors: Milius Robert P. , Heuer Michael , George Mike , Pollack Jane , Hollenbach Jill A. , Mack Steven J. , Maiers Martin 
Published: May 2015

AbstractGenotype List (GL) Strings use a set of hierarchical character delimiters to represent allele and genotype ambiguity in HLA and KIR genotypes in a complete and accurate fashion. A RESTful web service called Genotype List Service was created to allow users to register a GL String and receive a unique identifier for that string in the form of a URI. By exchanging URIs and dereferencing them through the GL Service, users can easily transmit HLA genotypes in a variety of useful formats. The GL Service was developed to be secure, scalable, and persistent. An instance of the GL Service is configured with a nomenclature and can be run in strict or non-strict modes. Strict mode requires alleles used in the GL String to be present in the allele database using the fully qualified nomenclature. Non-strict mode allows any GL String to be registered as long as it is syntactically correct. The GL Service source code is free and open source software, distributed under the GNU Lesser General Public License (LGPL) version 3 or later.AbbreviationsAPIApplication Program InterfaceAWSAmazon Web ServicesCDISCClinical Data Interchange Standards ConsortiumDaSHData Standard HackathonEMBLEuropean Molecular Biology LaboratoryEMDISEuropean Marrow Donor Information SystemENAEuropean Nucleotide ArchiveFDAFood and Drug AdministrationFHIRFast Healthcare Interoperability ResourcesGLGenotype ListGNUGNU’s Not UnixHL7Health Level Seven, InternationalHLAHuman Leucocyte AntigenHMLHistoimmunogenetics Markup LanguageHTMLHypertext Markup LanguageHTTPHypertext Transfer ProtocolIMGTImMunoGeneTicsISOInternational Organization for StandardizationJDBCJava Database ConnectivityJSONJavascript Object NotationKIRKiller-cell Immunoglobulin-like ReceptorLGPLLesser General Public LicenseLSDAMLife Sciences Domain Analysis ModelMHCMajor Histocompatibility ComplexMIRINGMinimum Information for Reporting Immunogenomic NGS GenotypingMUGMultilocus Unphased GenotypeN3Notation 3NCINational Cancer InstituteNGSNext Generation SequencingNMDPNational Marrow Donor ProgramOIDObject IdentifierOWLWeb Ontology LanguagePNGPortable Network GraphicsQR CodeQuick Response CodeRAMRandom Access MemoryRDBMSRelational Database Management SystemRDFResource Description LanguageRESTRepresentational State TransferSBTSequence Based TypingSDKSoftware Development KitSQLStructured Query LanguageSSOSequence Specific OligonucleotideSSPSequence Specific PrimerURIUniform Resource IdentifierURLUniform Resource LocatorXMLExtensible Markup LanguageAbbreviationsGL ServiceA web service to exchange GL Strings
Mixed Models for Meta-Analysis and Sequencing
Authors: Bulik-Sullivan Brendan 
Published: May 2015

AbstractMixed models are an effective statistical method for increasing power and avoiding confounding in genetic association studies. Existing mixed model methods have been designed for “pooled” studies where all individual-level genotype and phenotype data are simultaneously visible to a single analyst. Many studies follow a “meta-analysis” design, wherein a large number of independent cohorts share only summary statistics with a central meta-analysis group, and no one person can view individual-level data for more than a small fraction of the total sample. When using linear regression for GWAS, there is no difference in power between pooled studies and meta-analyses [1]; however, we show that when using mixed models, standard meta-analysis is much less powerful than mixed model association on a pooled study of equal size. We describe a method that allows meta-analyses to capture almost all of the power available to mixed model association on a pooled study without sharing individual-level genotype data. The added computational cost and analytical complexity of this method is minimal, but the increase in power can be large: based on the predictive performance of polygenic scoring reported in [2] and [3], we estimate that the next height and BMI studies could see increases in effective sample size of ≈15% and ≈8%, respectively. Last, we describe how a related technique can be used to increase power in sequencing, targeted sequencing and exome array studies.Note that these techniques are presently only applicable to randomly ascertained studies and will sometimes result in loss of power in ascertained case/control studies. We are developing similar methods for case/control studies, but this is more complicated.
Optimizing error correction of RNAseq reads
Authors: MacManes Matthew D. 
Published: May 2015

ABSTRACTMotivation:The correction of sequencing errors contained in Illumina reads derived from genomic DNA is a common pre-processing step in manyde novogenome assembly pipelines, and has been shown to improved the quality of resultant assemblies. In contrast, the correction of errors in transcriptome sequence data is much less common, but can potentially yield similar improvements in mapping and assembly quality. This manuscript evaluates several popular read-correction tool’s ability to correct sequence errors commonplace to transcriptome derived Illumina reads.Results:I evaluated the efficacy of correction of transcriptome derived sequencing reads using using several metrics across a variety of sequencing depths. This evaluation demonstrates a complex relationship between the quality of the correction, depth of sequencing, and hardware availability which results in variable recommendations depending on the goals of the experiment, tolerance for false positives, and depth of coverage. Overall, read error correction is an important step in read quality control, and should become a standard part of analytical pipelines.Availability:Results are non-deterministically repeatable using AMI:ami-3dae4956 (MacManes_EC_2015) and the Makefile available here:https://goo.gl/oVIuE0Contact:matthew.macmanes@unh.eduand @PeroMHC
Lipid Peroxide-Derived Short-Chain Carbonyls Mediate Hydrogen Peroxide-Induced and Salt-Induced Programmed Cell Death in Plants
Authors: Biswas Md. Sanaullah , Mano Jun’ichi 
Published: May 2015

AbstractLipid peroxide-derived toxic carbonyl compounds (oxylipin carbonyls), produced downstream of reactive oxygen species (ROS), were recently revealed to mediate abiotic stress-induced damage of plants. Here, we investigated how oxylipin carbonyls cause cell death. When tobacco (Nicotiana tabacum) Bright Yellow-2 (BY-2) cells were exposed to hydrogen peroxide, several species of short-chain oxylipin carbonyls [i.e. 4-hydroxy-(E)-2-nonenal and acrolein] accumulated and the cells underwent programmed cell death (PCD), as judged based on DNA fragmentation, an increase in terminal deoxynucleotidyl transferase dUTP nick end labeling-positive nuclei, and cytoplasm retraction. These oxylipin carbonyls caused PCD in BY-2 cells and roots of tobacco and Arabidopsis (Arabidopsis thaliana). To test the possibility that oxylipin carbonyls mediate an oxidative signal to cause PCD, we performed pharmacological and genetic experiments. Carnosine and hydralazine, having distinct chemistry for scavenging carbonyls, significantly suppressed the increase in oxylipin carbonyls and blocked PCD in BY-2 cells and Arabidopsis roots, but they did not affect the levels of ROS and lipid peroxides. A transgenic tobacco line that overproduces 2-alkenal reductase, an Arabidopsis enzyme to detoxify α,β-unsaturated carbonyls, suffered less PCD in root epidermis after hydrogen peroxide or salt treatment than did the wild type, whereas the ROS level increases due to the stress treatments were not different between the lines. From these results, we conclude that oxylipin carbonyls are involved in the PCD process in oxidatively stressed cells. Our comparison of the ability of distinct carbonyls to induce PCD in BY-2 cells revealed that acrolein and 4-hydroxy-(E)-2-nonenal are the most potent carbonyls. The physiological relevance and possible mechanisms of the carbonyl-induced PCD are discussed.
Time to diagnosis of Type I or II invasive epithelial ovarian cancers: a multicentre observational study using patient questionnaire and primary care records
Authors: Lim AWW , Mesher D , Gentry‐Maharaj A , Balogun N , Widschwendter M , Jacobs I , Sasieni P , Menon U 
Published: May 2015

ObjectiveTo compare time to diagnosis of the typically slow‐growing Type I (low‐grade serous, low‐grade endometrioid, mucinous, clear cell) and the more aggressive Type II (high‐grade serous, high‐grade endometrioid, undifferentiated, carcinosarcoma) invasive epithelial ovarian cancer (iEOC).DesignMulticentre observational study.SettingTen UK gynaecological oncology centres.PopulationWomen diagnosed with primary EOC between 2006 and 2008.MethodsSymptom data were collected before diagnosis using patient questionnaire and primary‐care records. We estimated patient interval (first symptom to presentation) using questionnaire data and diagnostic interval (presentation to diagnosis) using primary‐care records. We considered the impact of first symptom, referral and stage on intervals for Type I and Type II iEOC.Main outcome measuresPatient and diagnostic intervals.ResultsIn all, 78% of 60 Type I and 21% of 134 Type II iEOC were early‐stage. Intervals were comparable and independent of stage [e.g. median patient interval for Type I: early‐stage 0.3 months (interquartile range 0.3–3.0) versus late‐stage 0.3 months (interquartile range 0.3–4.5), P = 0.8]. Twenty‐seven percent of women with Type I and Type II had diagnostic intervals of at least 9 months. First symptom (questionnaire) was also similar, except for the infrequent abnormal bleeding (Type I 15% versus Type II 4%, P = 0.01). More women with Type I disease (57% versus 41%, P = 0.04) had been referred for suspected gynaecological cancer. Median time from referral to diagnosis was 1.4 months for women with iEOC referred via a 2‐week cancer referral to any specialty compared with 2.6 months (interquartile range 2.0–3.7) for women who were referred routinely to gynaecology.ConclusionOverall, shorter diagnostic delays were seen when a cancer was suspected, even if the primary tumour site was not recognised to be ovarian. Despite differences in carcinogenesis and stage for Type I and Type II iEOC, time to diagnosis and symptoms were similar. Referral patterns were different, implying subtle symptom differences. If symptom‐based interventions are to impact on ovarian cancer survival, it is likely to be through reduced volume rather than stage‐shift. Further research on histological subtypes is needed.Tweetable abstractNo difference in time to diagnosis for Type I versus Type II invasive epithelial ovarian cancers.
Gestational weight gain and the risk of offspring obesity at 10 and 16 years: a prospective cohort study in low‐income women
Authors: Diesel JC , Eckhardt CL , Day NL , Brooks MM , Arslanian SA , Bodnar LM 
Published: May 2015

ObjectiveTo study the association between gestational weight gain (GWG) and offspring obesity risk at ages chosen to approximate prepuberty (10 years) and postpuberty (16 years).DesignProspective pregnancy cohort.SettingPittsburgh, PA, USA.SampleLow‐income pregnant women (n = 514) receiving prenatal care at an obstetric residency clinic and their singleton offspring.MethodsGestational weight gain was classified based on maternal GWG‐for‐gestational‐age Z‐score charts and was modelled using flexible spline terms in modified multivariable Poisson regression models.Main outcome measuresObesity at 10 or 16 years, defined as body mass index (BMI) Z‐scores ≥95th centile of the 2000 CDC references, based on measured height and weight.ResultsThe prevalence of offspring obesity was 20% at 10 years and 22% at 16 years. In the overall sample, the risk of offspring obesity at 10 and 16 years increased when GWG exceeded a GWG Z‐score of 0 SD (equivalent to 30 kg at 40 weeks); but for gains below a Z‐score of 0 SD there was no relationship with child obesity risk. The association between GWG and offspring obesity varied by prepregnancy BMI. Among mothers with a pregravid BMI <25 kg/m2, the risk of offspring obesity increased when GWG Z‐score exceeded 0 SD, yet among overweight women (BMI ≥25 kg/m2), there was no association between GWG Z‐scores and offspring obesity risk.ConclusionsAmong lean women, higher GWG may have lasting effects on offspring obesity risk.Tweetable abstractMaternal weight gain is associated with offspring obesity at 10 and 16 years in a prospective study.
Previous caesarean delivery and the risk of unexplained stillbirth: retrospective cohort study and meta‐analysis
Authors: Moraitis AA , Oliver‐Williams C , Wood AM , Fleming M , Pell JP , Smith GCS 
Published: May 2015

ObjectiveTo determine whether caesarean delivery in the first pregnancy is a risk factor for unexplained antepartum stillbirth in a second pregnancy.DesignA population‐based retrospective cohort study and meta‐analysis.SettingAll maternity units in Scotland.ParticipantsA cohort of 128 585 second births, 1999–2008.MethodsTime‐to‐event analysis and random‐effects meta‐analysis.Main outcome measureRisk of unexplained antepartum stillbirth in a second pregnancy.ResultsThere were 88 stillbirths among 23 688 women with a previous caesarean delivery (2.34 per 10 000 women per week) and 288 stillbirths in 104 897 women who had previously delivered vaginally (1.67 per 10 000 women per week, P = 0.002). When analysed by cause, women with a previous caesarean delivery had an increased risk of unexplained stillbirth (hazard ratio, HR 1.47; 95% confidence interval, 95% CI 1.12–1.94; P = 0.006) and, as previously observed, the excess risk was apparent from 34 weeks of gestation onwards. The risk did not differ in relation to the indication of the caesarean delivery, and was independent of maternal characteristics and previous obstetric complications. We identified three other comparable studies (two in North America and one in Europe), and meta‐analysis of these studies showed a statistically significant association between previous caesarean delivery and the risk of antepartum stillbirth in the second pregnancy (pooled HR 1.40; 95% CI 1.10–1.77; P = 0.006).ConclusionsWomen who have had a previous caesarean delivery are at increased risk of unexplained stillbirth in the second pregnancy.Tweetable abstractCaesarean first delivery is associated with an increased risk of unexplained stillbirth in the next pregnancy.
Effectiveness of Rinse Water during In‐Place Cleaning of Stainless Steel Pipe Lines
Authors: Fan Mengyuan , Phinney David M. , Heldman Dennis R. 
Published: May 2015

AbstractThe 1st step of any Clean‐In‐Place (CIP) operation is a prerinse with water. The purpose of this step is to remove the bulk of food material remaining in the processing lines after production period has ended. It is known that this prerinse step can be a very water intensive process. The objective of this investigation was to measure the influence of CIP parameters (flow characteristics, water temperature, and contact time) on the effectiveness of prerinse water in removing dairy‐based deposits from stainless steel pipe surfaces and to compare the rinse effectiveness of unused to reused rinse water. A pilot‐scale CIP system was operated to rinse 304 stainless steel pipe sections of 3 different pipe diameters. The velocity of the rinse water was varied from 0.72 to 2.26 m/s. The rinse water temperatures were 22 °C, 45 °C, and 67 °C. The contact times between rinse water and deposited film were 20 and 60 s. Rinse effectiveness was expressed as the ratio of the amount of protein residue removed from the pipe surface during rinsing, as compared to the magnitude of the initial protein deposit. The rinse effectiveness varied from 73.1% to 94.9% for the range of the CIP parameters investigated. High velocities of rinse water provided a higher level of rinse effectiveness. Increasing the rinse water temperature from 23 °C to 45 °C improved rinse effectiveness significantly (P < 0.05). This impact was not significant when the water temperature was increased from 45 °C to 67 °C and at higher rinse water velocities. Similarly, longer contact time provided less improvement in rinse effectiveness at higher temperatures and velocities as compared to lower temperatures and velocities. There were no significant differences in rinse effectiveness when comparing reused and unused water (normal tap water) within the range of velocities evaluated.