bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound-Guided Aspiration Does Not Reduce the Recurrence Rate of Ganglion Cysts of the Wrist
Authors: Kurkis Gregory , Anastasio Albert , DeVos Marijke , Gottschalk Michael 
Published: August 2018

Background Ganglion cysts are the most frequent soft tissue tumor encountered in the upper extremity and are commonly treated by aspiration or by surgical excision. Ultrasound is a promising addition to traditional aspiration, as it allows for visualization of the needle within the ganglion before aspiration.
Questions Are ganglion cysts of the wrist less likely to reoccur if they are aspirated under ultrasound guidance versus “blind” aspiration without the use of ultrasound guidance? Does patient functionality change based on whether or not the cyst recurred?
Patients and Methods In total, 52 patients were successfully contacted and recurrence rates were compared between those whose cyst was treated with ultrasound-guided (13 patients) with those whose cyst was treated with blind aspiration (39 patients). Mean follow-up time was 2.9 years.
Results Recurrence rates were 69% (9 patients) and 74% (29 patients) for the ultrasound-guided and blind aspiration groups, respectively (p-value: 0.73), showing no significant difference in recurrences of wrist ganglion between the two groups. A metric of functionality (Quick–DASH [Disabilities of the Arm, Shoulder, and Hand]) revealed worse outcomes in patients who experienced return of ganglion cyst after aspiration versus those who did not.
Conclusion Additional studies with improved sample sizes are needed to demonstrate the superiority of ultrasound-guided aspiration versus blind aspiration. Due to a high recurrence rate following aspiration (both ultrasound-guided and blinded), a lower threshold for surgical intervention is likely reasonable.
Level of Evidence This is a Level IIIb study.
Notfallmedizin abseits schnell erreichbarer medizinischer Infrastruktur
Authors: Leischker Andreas , Holst Fritz 
Published: August 2018

AbstractFor many acute diseases and injuries, treatment does not differ between industrialised environment and wilderness setting. However, for some emergencies, treatment needs to be adapted if advanced medical care facilities cannot be reached within 4 hours.In these situations, dislocated joints and fractures should be reduced quickly. Contaminated wounds should be cleaned carefully, with drinking water being sufficient when no sterile solution is available. A patient with a contaminated wound should receive a systemic antibiotic coverage within one hour. Keeping an injured patient warm is crucial to prevent disseminated coagulation.In most cases in the wilderness, cardiopulmonary resuscitation (CPR) should be stopped after 20 minutes; if no return of spontaneous circulation (ROSC) has occurred. However, in case of severe hypothermia, drowning or cardiac arrest due to lightning, prolonged CPR may be feasible.Handwashing with soap and water and use of alcohol gels are effective measures for the prevention of travellers’ diarrhoea during expeditions.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility
Authors: Kurcinski Mateusz , Oleniecki Tymoteusz , Ciemny Maciej Pawel , Kuriata Aleksander , Kolinski Andrzej , Kmiecik Sebastian 
Published: August 2018

Abstract

Summary
CABS-flex standalone is a Python package for fast simulations of protein structure flexibility. The package combines simulations of protein dynamics using CABS coarse-grained protein model with the reconstruction of selected models to all-atom representation and analysis of modeling results. CABS-flex standalone is designed to allow for command-line access to the CABS computations and complete control over simulation process. CABS-flex standalone is equipped with features such as: modeling of multimeric and large-size protein systems, contact map visualizations, analysis of similarities to the reference structure and configurable modeling protocol. For instance, the user may modify the simulation parameters, distance restraints, structural clustering scheme or all-atom reconstruction parameters. With these features CABS-flex standalone can be easily incorporated into other methodologies of structural biology.

Availability and implementation
CABS-flex standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. CABS-flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS-flex standalone repository at https://bitbucket.org/lcbio/cabsflex.
Clustering of temporal gene expression data with mixtures of mixed effects models with a penalized likelihood
Authors: Lu Darlene , Tripodis Yorghos , Gerstenfeld Louis C , Demissie Serkalem 
Published: August 2018

AbstractMotivationClustering algorithms like K-Means and standard Gaussian mixture models (GMM) fail to account for the structure of variability of replicated data or repeated measures over time. Additionally, a priori cluster number assumptions add an additional complexity to the process. Current methods to optimize cluster labels and number can be inaccurate or computationally intensive for temporal gene expression data with this additional variability.ResultsAn extension to a model-based clustering algorithm is proposed using mixtures of mixed effects polynomial regression models and the EM algorithm with an entropy penalized log-likelihood function (EPEM). The EPEM is used to cluster temporal gene expression data with this additional variability. The addition of random effects in our model decreased the misclassification error when compared to mixtures of fixed effects models or other methods such as K-Means and GMM. Applying our method to microarray data from a fracture healing study revealed distinct temporal patterns of gene expression.Availability and Implementationhttps://github.com/darlenelu72/EPEM-GMM.Supplementary informationSupplementary data are available at Bioinformatics online.
Container-based bioinformatics with Pachyderm
Authors: Novella Jon Ander , Emami Khoonsari Payam , Herman Stephanie , Whitenack Daniel , Capuccini Marco , Burman Joachim , Kultima Kim , Spjuth Ola 
Published: August 2018

AbstractMotivationComputational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages and (iii) a data management layer that tracks data as it moves through the processing pipeline.ResultsPachyderm is an open-source workflow system and data management framework that fulfils these needs by creating a data pipelining and data versioning layer on top of projects from the container ecosystem, having Kubernetes as the backbone for container orchestration. We adapted Pachyderm and demonstrated its attractive properties in bioinformatics. A Helm Chart was created so that researchers can use Pachyderm in multiple scenarios. The Pachyderm File System was extended to support block storage. A wrapper for initiating Pachyderm on cloud-agnostic virtual infrastructures was created. The benefits of Pachyderm are illustrated via a large metabolomics workflow, demonstrating that Pachyderm enables efficient and sustainable data science workflows while maintaining reproducibility and scalability.Availability and implementationPachyderm is available from https://github.com/pachyderm/pachyderm. The Pachyderm Helm Chart is available from https://github.com/kubernetes/charts/tree/master/stable/pachyderm. Pachyderm is available out-of-the-box from the PhenoMeNal VRE (https://github.com/phnmnl/KubeNow-plugin) and general Kubernetes environments instantiated via KubeNow. The code of the workflow used for the analysis is available on GitHub (https://github.com/pharmbio/LC-MS-Pachyderm).Supplementary informationSupplementary data are available at Bioinformatics online.
PrimedRPA: primer design for recombinase polymerase amplification assays
Authors: Higgins Matthew , Ravenhall Matt , Ward Daniel , Phelan Jody , Ibrahim Amy , Forrest Matthew S , Clark Taane G , Campino Susana 
Published: August 2018

Abstract

Summary
Recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification method, is enhancing our ability to detect a diverse array of pathogens, thereby assisting the diagnosis of infectious diseases and the detection of microorganisms in food and water. However, new bioinformatics tools are needed to automate and improve the design of the primers and probes sets to be used in RPA, particularly to account for the high genetic diversity of circulating pathogens and cross detection of genetically similar organisms. PrimedRPA is a python-based package that automates the creation and filtering of RPA primers and probe sets. It aligns several sequences to identify conserved targets, and filters regions that cross react with possible background organisms.

Availability and implementation
PrimedRPA was implemented in Python 3 and supported on Linux and MacOS and is freely available from http://pathogenseq.lshtm.ac.uk/PrimedRPA.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
It’s All in the Details: Relations Between Young Children’s Developing Pattern Separation Abilities and Hippocampal Subfield Volumes
Authors: Canada Kelsey L , Ngo Chi T , Newcombe Nora S , Geng Fengji , Riggins Tracy 
Published: August 2018

Abstract
The ability to keep similar experiences separate in memory is critical for forming unique and lasting memories, as many events share overlapping features (e.g., birthday parties, holidays). Research on memory in young children suggests their memories often lack high-resolution details, i.e., show impoverished pattern separation (PS). Recently developed assessments of PS suitable for children allow us to relate the formation of distinct, detailed memories for the development of the hippocampus, a neural structure critical for this ability in adults. The hippocampus displays a protracted developmental profile and underlies the ability to form detailed memories. This study examined age-related differences in hippocampal subfield volumes in 4- to 8-year-old children and relations with performance on a mnemonic similarity task (MST) designed to index memory specificity. Results revealed age-moderated associations between MST performance and cornu ammonis 2-4/dentate gyrus subfields. Specifically, age-related differences in the ability to form detailed memories tracked with normative patterns of volume increases followed by reductions over this age range. That is, greater volume correlated with better performance in younger children, whereas smaller volume correlated with better performance in older children. These findings support the hypothesis that developmental differences in hippocampal circuitry contribute to age-related improvements in detailed memory formation during this period.
Integrable Stochastic Dualities and the Deformed Knizhnik–Zamolodchikov Equation
Authors: Chen Zeying , de Gier Jan , Wheeler Michael 
Published: August 2018

AbstractWe present a new method for obtaining duality functions in multi-species asymmetric exclusion processes (mASEP), from solutions of the deformed Knizhnik–Zamolodchikov (KZ) equations. Our method reproduces, as a special case, duality functions for the self-dual single species ASEP on the integer lattice.
Astrophysical radio background cannot explain the EDGES 21-cm signal: constraints from cooling of non-thermal electrons
Authors: Sharma Prateek 
Published: August 2018

ABSTRACT
Recently the EDGES experiment has claimed the detection of an absorption feature centred at 78 MHz. When interpreted as a signature of cosmic dawn, this feature appears at the correct wavelength (corresponding to a redshift range of z ≈ 15–20) but is larger by at least a factor of two in amplitude compared to the standard 21-cm models. One way to explain the excess radio absorption is by the enhancement of the diffuse radio background at ν = 1.42 GHz (λ = 21 cm) in the rest frame of the absorbing neutral hydrogen. Astrophysical scenarios, based on the acceleration of relativistic electrons by accretion on to supermassive black holes (SMBHs) and by supernovae (SN) from first stars, have been proposed to produce the enhanced radio background via synchrotron emission. In this letter, we show that either the synchrotron or the inverse-Compton (IC) cooling time for such electrons is at least three orders of magnitude shorter than the duration of the EDGES signal centred at z ≈ 17, irrespective of the magnetic field strength. The synchrotron radio emission at 1.42 GHz due to rapidly cooling electrons is ∼103 times smaller than the non-cooling estimate. Thus astrophysical scenarios for excess radio background proposed to explain the EDGES signal appear very unlikely.
Intratumoral Heterogeneity of Glioblastoma Infiltration Revealed by Joint Histogram Analysis of Diffusion Tensor Imaging
Authors: Li Chao , Wang Shuo , Yan Jiun-Lin , Piper Rory J , Liu Hongxiang , Torheim Turid , Kim Hyunjin , Zou Jingjing , Boonzaier Natalie R , Sinha Rohitashwa , Matys Tomasz , Markowetz Florian , Price Stephen J 
Published: August 2018

Abstract

Background
Glioblastoma is a heterogeneous disease characterized by its infiltrative growth, rendering complete resection impossible. Diffusion tensor imaging (DTI) shows potential in detecting tumor infiltration by reflecting microstructure disruption.

OBJECTIVE
To explore the heterogeneity of glioblastoma infiltration using joint histogram analysis of DTI, to investigate the incremental prognostic value of infiltrative patterns over clinical factors, and to identify specific subregions for targeted therapy.

Methods
A total of 115 primary glioblastoma patients were prospectively recruited for surgery and preoperative magnetic resonance imaging. The joint histograms of decomposed anisotropic and isotropic components of DTI were constructed in both contrast-enhancing and nonenhancing tumor regions. Patient survival was analyzed with joint histogram features and relevant clinical factors. The incremental prognostic values of histogram features were assessed using receiver operating characteristic curve analysis. The correlation between the proportion of diffusion patterns and tumor progression rate was tested using Pearson correlation.

Results
We found that joint histogram features were associated with patient survival and improved survival model performance. Specifically, the proportion of nonenhancing tumor subregion with decreased isotropic diffusion and increased anisotropic diffusion was correlated with tumor progression rate (P = .010, r = 0.35), affected progression-free survival (hazard ratio = 1.08, P < .001), and overall survival (hazard ratio = 1.36, P < .001) in multivariate models.

Conclusion
Joint histogram features of DTI showed incremental prognostic values over clinical factors for glioblastoma patients. The nonenhancing tumor subregion with decreased isotropic diffusion and increased anisotropic diffusion may indicate a more infiltrative habitat and potential treatment target.
The Effects of Tobacco Smoking, and Prenatal Tobacco Smoke Exposure, on Risk of Schizophrenia: A Systematic Review and Meta-Analysis
Authors: Hunter Abby , Murray Rachael , Asher Laura , Leonardi-Bee Jo 
Published: August 2018

AbstractBackgroundThe association between cigarette smoking and schizophrenia is well established. However, up to 90% of people with schizophrenia begin smoking before the onset of their illness; thus, smoking could be an independent risk factor for schizophrenia. Prenatal exposure to maternal cigarette smoke is also associated with psychiatric problems in adolescence. Therefore, our aim was to undertake a systematic review and meta-analysis to explore the effect of smoking, and prenatal smoke exposure, on risk of schizophrenia.MethodWe systematically searched Medline, EMBASE, PsychInfo, Maternity and Infant Care, and Web of Science (from inception to February 2018) to identify comparative observational studies of the risk of schizophrenia in relation to smoking status. Measures of relative risk (RR) were pooled in a meta-analysis with 95% confidence intervals (CI), using random effects model.ResultsTwelve studies (9 cohort, 3 case-control) were included. Odds ratios (OR) and hazard ratios (HR) were pooled together to estimate pooled relative risks and estimates combined in a meta-analysis on an assumption of constant risk over time. Smokers had a significantly increased risk of schizophrenia compared with nonsmokers (RR = 1.99, 95% CI = 1.10% to 3.61%, I2 = 97%, 5 studies). Exposure to prenatal smoke increased the risk of schizophrenia by 29% (95% CI = 1.10% to 1.51%, I2 = 71%, 7 studies). Sensitivity analyses identified no significant differences between the results from studies reporting OR and hazard ratio.ConclusionsOur findings suggest smoking, and prenatal smoke exposure, may be an independent risk factor for schizophrenia. Care should be taken when inferring causation, given the observational nature of the studies.ImplicationsIn this meta-analysis of 12 studies, smokers had a significantly increased risk of schizophrenia compared with nonsmokers. Exposure to prenatal tobacco smoke also increased the risk of schizophrenia by 29% compared with those with no exposure to prenatal tobacco smoke. Our findings suggest that smoking, and prenatal tobacco smoke exposure, may be independent risk factors for schizophrenia. These results may have important public health implications for decreasing the incidence of schizophrenia. The possibility of a causal link between smoking and schizophrenia warrants further investigation.
Missing Children: On the Extent, Patterns, and Correlates of Repeat Disappearances by Young People
Authors: Babuta Alexander , Sidebottom Aiden 
Published: August 2018

AbstractMissing persons investigations are arguably the most common and costly non-crime problem the police are expected to handle, with a large proportion of all cases attributable to young people. This article investigates the prevalence, time course, distance, and correlates of repeat disappearances by children (under the age of 18 years). Using data from one UK police force for the period January 2011 to May 2013 (n = 1,885), we find that (1) nearly two-thirds of all missing child reports are repeat disappearances, (2) a small proportion of children who go missing repeatedly (15%) account for over half of all missing persons incidents, (3) children who go missing repeatedly tend to travel shorter distances than children reported missing once, and (4) the likelihood of a child going missing on multiple occasions is associated with age, being in care, a history of family conflict, and if going missing was judged to be ‘out of character’. The implications of our findings for the prevention of repeat disappearances by young people are discussed.
Different and Not Equal:The Uneven Association of Race, Poverty, and Abortion Laws on Abortion Timing
Authors: Solazzo Alexa L 
Published: August 2018

AbstractThe number of regulations surrounding abortion has increased drastically in recent years. It is important to assess how these laws relate to abortion timing, since the cost, safety, and accessibility of abortion varies by how many weeks pregnant a woman is when the procedure occurs. Research examining how state laws relate to abortion timing generally use rates or data from vital statistics; while informative, such methods do not allow researchers to examine how these laws may be disproportionately associated with abortion timing among select groups of women, including poor and nonwhite women. To fill this research gap, I analyze data from the nationally representative 2008 Abortion Patient Survey, with appended information on state laws regarding abortion in 2008. I find that laws requiring second trimester abortions be performed in a hospital and both in-person counselling and waiting periods have different associations with abortion timing based on race and income-to-poverty status. Predicted abortion timing for black and Hispanic women differs based on state laws and their income-to-poverty status, while for white women, models show that the association between state laws and abortion timing is not dependent on their income-to-poverty status. Overall, this research illustrates the relevance of state-level abortion laws for shaping abortion timing among women, highlighting how these relationships differ across racial and socioeconomic groups in the United States.
Stereoselective Ketamine Metabolism by Genetic Variants of Cytochrome P450 CYP2B6 and Cytochrome P450 Oxidoreductase
Authors: Wang Pan-Fen , Neiner Alicia , Kharasch Evan D. 
Published: August 2018

Abstract

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
Human ketamine N-demethylation to norketamine in vitro at therapeutic concentrations is catalyzed predominantly by the cytochrome P4502B6 isoform (CYP2B6). The CYP2B6 gene is highly polymorphic. CYP2B6.6, the protein encoded by the common variant allele CYP2B6*6, exhibits diminished ketamine metabolism in vitro compared with wild-type CYP2B6.1. The gene for cytochrome P450 oxidoreductase (POR), an obligatory P450 coenzyme, is also polymorphic. This investigation evaluated ketamine metabolism by genetic variants of human CYP2B6 and POR.

Methods
CYP2B6 (and variants), POR (and variants), and cytochrome b
5 (wild-type) were coexpressed in a cell system. All CYP2B6 variants were expressed with wild-type POR and b
5. All POR variants were expressed with wild-type CYP2B6.1 and b
5. Metabolism of R- and S-ketamine enantiomers, and racemic RS-ketamine to norketamine enantiomers, was determined using stereoselective high-pressure liquid chromatography–mass spectrometry. Michaelis–Menten kinetic parameters were determined.

Results
For ketamine enantiomers and racemate, metabolism (intrinsic clearance) was generally wild-type CYP2B6.1 > CYP2B6.4 > CYP2B6.26, CYP2B6.19, CYP2B6.17, CYP2B6.6 > CYP2B6.5, CYP2B6.7 > CYP2B6.9. CYP2B6.16 and CYP2B6.18 were essentially inactive. Activity of several CYP2B6 variants was less than half that of CYP2B6.1. CYP2B6.9 was 15 to 35% that of CYP2B6.1. The order of metabolism was wild-type POR.1 > POR.28, P228L > POR.5. CYP2B6 variants had more influence than POR variants on ketamine metabolism. Neither CYP2B6 nor POR variants affected the stereoselectivity of ketamine metabolism (S > R).

Conclusions
Genetic variants of CYP2B6 and P450 oxidoreductase have diminished ketamine N-demethylation activity, without affecting the stereoselectivity of metabolism. These results suggest candidate genetic polymorphisms of CYP2B6 and P450 oxidoreductase for clinical evaluation to assess consequences for ketamine pharmacokinetics, elimination, bioactivation, and therapeutic effects.