bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis
Authors: Jiang Xiawei , Liu Wenhong , Zheng Beiwen 
Published: November 2018

AbstractBecause of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) analysis. Protein-coding genes, rRNAs and tRNAs were predicted. Functional annotations of the genome using different databases revealed several genes related to pathogenicity including antibiotic resistance genes and prophages. Our work demonstrates that whole genome sequencing can enhance the resolution of clinical investigations and our data can be used as a reference genome during the rapid diagnosis of C. kerstersii infections in the future.
De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
Authors: Dutreux Fabien , Da Silva Corinne , d’Agata Léo , Couloux Arnaud , Gay Elise J. , Istace Benjamin , Lapalu Nicolas , Lemainque Arnaud , Linglin Juliette , Noel Benjamin , Wincker Patrick , Cruaud Corinne , Rouxel Thierry , Balesdent Marie-Hélène , Aury Jean-Marc 
Published: November 2018

AbstractLeptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing. Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3. The genome annotation was supported by integrating conserved proteins and RNA sequencing from Leptosphaeria-infected samples. The newly produced high-quality assemblies and annotations of those three Leptosphaeria genomes will allow further studies, notably focused on the tripartite interaction between L. maculans, L. biglobosa and oilseed rape. The discovery of as yet unknown effectors will notably allow progress in B. napus breeding towards L. maculans resistance.
Molecular ion abundances in the diffuse ISM: CF+, HCO+, HOC+, and C3H+
Authors: Gerin M. , Liszt H. , Neufeld D. , Godard B. , Sonnentrucker P. , Pety J. , Roueff E. 
Published: November 2018

Aims.The transition between atomic and molecular hydrogen is associated with important changes in the structure of interstellar clouds, and marks the beginning of interstellar chemistry. Most molecular ions are rapidly formed (in ion–molecule reactions) and destroyed (by dissociative recombination) in the diffuse ISM. Because of the relatively simple networks controlling their abundances, molecular ions are usually good probes of the underlying physical conditions including, for instance the fraction of gas in molecular form or the fractional ionization. In this paper we focus on three possible probes of the molecular hydrogen column density, HCO+, HOC+, and CF+.Methods.We presented high-sensitivity ALMA absorption data toward a sample of compact H IIregions and bright QSOs with prominent foreground absorption, in the ground-state transitions of the molecular ions HCO+, HOC+, and CF+and the neutral species HCN and HNC, and from the excited-state transitions of C3H+(4-3) and13CS(2-1). These data are compared withHerschelabsorption spectra of the ground-state transition of HF and p-H2O.Results.We show that the HCO+, HOC+, and CF+column densities are well correlated with each other. HCO+and HOC+are tightly correlated with p-H2O, while they exhibit a different correlation pattern with HF depending on whether the absorbing matter is located in the Galactic disk or in the central molecular zone. We report new detections of C3H+confirming that this ion is ubiquitous in the diffuse matter, with an abundance relative to H2of ~7 × 10−11.Conclusions.We confirm that the CF+abundance is lower than predicted by simple chemical models and propose that the rate of the main formation reaction is lower by a factor of about 3 than usually assumed. In the absence of CH or HF data, we recommend to use the ground-state transitions of HCO+, CCH, and HOC+to trace diffuse molecular hydrogen, with mean abundances relative to H2of 3 × 10−9, 4 × 10−8, and 4 × 10−11, respectively, leading to sensitivityN(H2)/ ∫τdvof 4 × 1020, 1.5 × 1021, and 6 × 1022cm−2/km s−1, respectively.
Predicted Equation for VO2 Based on a 20-Meter Multistage Shuttle Run Test for Children
Authors: Arsa Gisela , Lanza Fernanda , Cambri Lucieli , Antonio Ednei , Murad Neif , de Mello Marco , Santos Alexandra , de Tarso Camillo de Carvalho Paulo , Silva-Junior José , Bocalini Danilo , Mansano Barbara , Tucci Paulo , Serra Andrey 
Published: November 2018

AbstractThis study compared maximum oxygen consumption (VO2max) on a 20-meter multistage shuttle run test (20-Srt) with a cardiopulmonary exercise test (CPET) to determine a VO2max prediction equation for a 20-Srt in children aged 6–10 years. Eighty healthy children performed the CPET on a treadmill, while the 20-Srt took place on a sports court. Heart rate (HR) was measured and the expired gases were continuously measured breath-by-breath using a portable gas analyzer. The VO2max was lower (p<0.05) in CPET than 20-Srt for all, female, and male participants, respectively (46.3±7.9 vs. 48.7±4.6; 42.7±7.8 vs. 46.7±4.8; 49.3±6.8 vs. 50.4±3.9, mL·kg-1·min-1). The standard error estimates were between 3.0 and 3.6 and considered as not clinically relevant if less than 5 mL·kg-1·min-1. The intraclass correlation coefficient between the VO2 in CPET and in 20-Srt was 0.74 (CI95% 0.55–0.84) and considered moderately reliable. The linear multiple regression excluded sex, body mass index and fat-free mass and retained the maximum speed and age in the predictive equation. The 20-Srt estimates the VO2max with moderate reliability and the predictive equation was VO2maxpred=4.302+(maximum speed*5.613)–(age*1.523) for children aged 6–10 years.
Leitlinienadhärenz bei frustran verlaufenden Reanimationen mit automatischen Reanimationsgeräten
Authors: Ondruschka Benjamin , Baier Christina , Hartwig Thomas , Gräwert Stephanie , Böhm Lennert , Dreßler Jan , Bernhard Michael 
Published: November 2018

ZusammenfassungAutomatische externe Reanimationsgeräte, z. B. das LUCAS-Device, werden mehr und mehr im praktischen Alltag zur Sicherstellung einer dauerhaften Thoraxkompression verwendet. Ein besseres neurologisches Outcome oder höhere Überlebenschancen für Patienten mit einem prähospitalen Herz-Kreislauf-Stillstand im Vergleich zur manuellen Herzdruckmassage konnten bisher nicht gezeigt werden. Deswegen wird in den aktuellen nationalen und internationalen Leitlinien zur kardiopulmonalen Reanimation der standardisierte und unkritische Dauereinsatz von Reanimationshilfen nicht empfohlen. Die vorliegende Arbeit sollte an einem Obduktionskollektiv retrospektiv überprüfen, ob die 2015 formulierten Leitlinien zur Anwendung von automatischen externen Reanimationshilfen im Praxisalltag auch Verwendung finden. Grundsätzlich haben sich keine Unterschiede im Reanimationsregime für den Zeitraum vor (2014/2015) bzw. nach (2016/2017) Einführung der Anwendungsleitlinien hinsichtlich der demografischen und klinischen Daten der Patienten ergeben. Es fanden sich nur Einzelfälle mit Abweichungen von der Leitlinie, z. B. eine bereits primär bestehende Asystolie oder prähospitale Sterbefälle ohne Transportbeginn. Die primär korrekte Platzierung des LUCAS-Device am Thorax gelingt nicht permanent. Zusammenfassend kann festgestellt werden, dass für die Verwendung von LUCAS-Reanimationshilfen bei Patienten mit Herz-Kreislauf-Stillstand eine hohe Leitlinienadhärenz bestand und von den Empfehlungen nur in Einzelfällen abgewichen wurde.
Fetal Doppler Parameters at Term in Pregnancies Affected by Gestational Diabetes: Role in the Prediction of Perinatal Outcomes
Authors: Familiari Alessandra , Neri Caterina , Vassallo Chiara , Di Marco Giulia , Garofalo Serafina , Martino Carmelinda , Degennaro Valentina , Lanzone Antonio 
Published: November 2018

Abstract
Objective The timing of delivery for women affected by gestational diabetes (GDM) is still controversial. Good clinical practice often suggests offering induction of labor at term in order to reduce the complications associated with this condition, while recent evidence supports expectant management. Fetal Doppler parameters represent a validated tool for testing fetal well-being at term and can select pregnancies that need increased surveillance. The aim of the present study was to evaluate the role of fetal Doppler parameters at term for the prediction of pregnancy outcomes in patients affected by GDM.
Methods Prospective cohort study in a single center. Evaluation of umbilical artery (UA) PI, middle cerebral artery (MCA) PI, cerebroplacental ratio (CPR) and umbilical-to-cerebral ratio (UCR) at > 37 weeks of gestation in singleton, morphologically normal pregnancies affected by GDM, was performed in order to estimate the association between ultrasound measurements at term and perinatal outcome. Regression linear analysis was used to estimate the association between fetal Doppler parameters and neonatal pH, neonatal Apgar score, neonatal weight and a composite adverse outcome. The receiver operating characteristic (ROC) curve was used to estimate the possible predictive value of the above association.
Results Our results on 130 women showed MCA PI to be the best predictor of perinatal outcomes in terms of low Apgar score at the 1st minute (p = 0.00), pH (p = 0.02) and composite adverse outcome (p = 0.05). UCR showed a significant correlation with neonatal pH (p = 0.02). No significant correlations for UA PI and CPR MoMs have been demonstrated in our population. However, the small sample size is a limitation of the study.
Conclusion Evaluation of MCA Doppler and eventually UCR at term can be a useful tool to discriminate pregnancies affected by GDM that can benefit from IOL before 41 weeks in order to reduce complications related to this condition.
Langzeitbeobachtung ehemaliger krebskranker Kinder und Jugendlicher
Authors: Langer Thorsten , Grabow Desiree , Kaatsch Peter , Creutzig Ursula , Eggert Angelika , Escherich Gabriele , Calaminus Gabriele 
Published: November 2018

ZusammenfassungKrebskranke Kinder und Jugendliche überleben heute dank Heilungsraten von über 80% viel häufiger ihre Krebserkrankung als vor 40 Jahren. Etwa 33 000 geheilte ehemalige krebskranke Kinder und Jugendliche sind in der Langzeitbeobachtung über das Deutsche Kinderkrebsregister (DKKR) bundesweit erfasst. Heißt geheilt aber auch gesund? Beim Vergleich mit der Normalbevölkerung ist festzustellen, dass die Morbidität und Mortalität bei den ehemaligen Patienten deutlich erhöht ist. Die Krebserkrankungen und deren Behandlungen können bei zwei von drei Überlebenden 30 Jahre später zu therapiebedürftigen Spätfolgen führen, bei etwa einem Drittel werden sie als schwer eingestuft. Mittels einer strukturierten Nachbeobachtung können diese frühzeitig erkannt und bei Bedarf behandelt werden. Ziel dieses Positionspapiers ist eine Aktualisierung des ersten Positionspapiers aus dem Jahre 2007. Hierbei werden die aktuellen Entwicklungen beschrieben und dargestellt, wie geeignete Nachsorgestrukturen und Nachsorgeeinrichtungen – unter Berücksichtigung der bestehenden Strukturen und dem steigenden Bedarf – geplant werden sollten.
Outcome Evaluation of Patients with Burst Thoracolumbar Fractures: A Case Series
Authors: Jamali Mohammad , Goorakani Yashar , Solat Niloofar , Taheri Reza , Ghahramani Sulmaz 
Published: November 2018

Objective The aim of the present study was to evaluate the outcome of short segment instrumentation in patients affected by burst thoracolumbar fractures.
Methods A total of 19 patients with unstable burst fractures of the thoracolumbar spine were eligible for short segment instrumentation. Their functional outcome (by using the Oswestry and Denis scales) and back pain (using the visual analog scale) were evaluated after 12 months.
Results The mean age of the patients was 30.7 years old, and most of them were male (n = 15). The mean hospital stay was 4.6 days. The mean ± standard deviation (SD) of the pain score according to the visual analog scale was 1.63 ± 1.25 after 12 months of surgery, and there were no patients classified with grades 4 or 5 on the Denis work scale. The average Oswestry disability index (ODI) was 17% during the follow-ups.
Conclusions The outcome of the studied patients, including the clinical pain and the functional outcome of postsurgical patients, suggested that the short-segment instrumentation could be an appropriate method for patients with unstable thoracolumbar junction fractures. However, a long-term follow-up is recommended.
Cementless versus Cemented Fixation in Total Knee Arthroplasty: Usage, Costs, and Complications during the Inpatient Period
Authors: Gwam Chukwuweike U. , George Nicole E. , Etcheson Jennifer I. , Rosas Samuel , Plate Johannes F. , Delanois Ronald E. 
Published: November 2018

AbstractCemented fixation has been the gold standard in total knee arthroplasty (TKA). However, with younger and more active patients requiring TKA, cementless (press-fit) fixation has sparked renewed interest. Therefore, we investigated differences in (1) patient demographics, (2) inpatient costs, (3) short-term complications, and (4) discharge disposition between patients who underwent TKA with cemented and cementless fixation. The National Inpatient Sample database was queried for TKA patients with cement or cementless fixation between October 1 and December 31, 2015. Primary outcomes of interest included complications, length of stay (LOS), discharge disposition, and inpatient costs. Student's t-test and chi-square analysis were used to assess continuous and categorical data, respectively. Multivariable analysis evaluated the effects of fixation type on the continuous and categorical dependent variables. Patients who received cementless fixation were more often younger (63.5 vs. 65.9 years), male (47.4 vs. 40.3%), Black (10.7 vs. 7.7%), from the Northeast census region (29.1 vs. 17.1%), and under private insurance (49.2 vs. 40.3%; p < 0.001 for all). Cementless fixation involved higher inpatient hospital costs (US$17,357 vs. US$16,888) and charges (US$67,366 vs. US$64,190; p < 0.001 for both), lower mean LOS (2.63 vs. 2.71 days; p < 0.001), and higher odds of being discharged to home (odds ratio = 1.99; p = 0.002). This study revisited the outcomes of TKA with cementless fixation and demonstrated higher inpatient charges and costs, shorter mean LOS, and higher odds of being discharged home. Future studies should investigate patient outcomes and complications past the inpatient period, evaluate long-term survivorship and failure rates, and implement a prospective study design.
Multi-Segment Indexes of Arterial Stiffness Show Lower Repeatability Than Carotid–Femoral Pulse Wave Velocity or Systolic Blood Pressure
Authors: Beltrami Fernando G , Mzee David , Spengler Christina M 
Published: November 2018

Abstract

BACKGROUND
We investigated the inter-day repeatability of newly proposed indexes of cardiovascular health based on the absolute (PWVABS) or relative (PWVRATIO) difference in pulse wave velocity (PWV) between the carotid–femoral (PWVCF) and carotid–radial (PWVCR) segments compared with PWVCF alone and with systolic blood pressure (BPSYST) over multiple days.

METHODS
All variables were measured in triplicates in a group of 16 young, healthy individuals (8 men/8 women, body mass 66 ± 14 kg, height 1.7 ± 0.1 m, age 27 ± 3 years old, all mean ± SD) on 6 different occasions, always at the same time of the day (± 1 hour) and with at least 48 hours between assessments.

RESULTS
Values did not differ significantly over the 6 different visits for any of the parameters (all Ps &gt; 0.08). Intraclass coefficients (ICCs) ranged from 0.52 (PWVRATIO) to 0.8 (PWVCF). The ICC 95% confidence interval of PWVRATIO (0.30–0.77) and PWVABS (0.33–0.78) did not overlap with that of PWVCF (0.79–0.95), indicating lower repeatability. The coefficient of variation (CV) of PWVABS was over 5-fold larger than the next largest one (46.7 vs. 8.1% for PWVABS and PWVRATIO, respectively), whereas PWVCF and BPSYST showed the lowest CVs (4.6 and 4.0%, respectively).

CONCLUSION
Between PWVABS and PWVRATIO, the relative method showed better repeatability and might be more sensitive to longitudinal changes in patients. Nonetheless, indexes of arterial stiffness-based PWV gradients between different segments show lower inter-day repeatability compared with PWVCF or BPSYST, suggesting that the latter are still preferable in clinical practice.
Which Features of Accent affect Understanding? Exploring the Intelligibility Threshold of Diverse Accent Varieties
Authors: Kang Okim , Thomson Ron I , Moran Meghan 
Published: November 2018

Abstract
With the ascendency of English as a global lingua franca, a clearer understanding of what constitutes intelligible speech is needed. However, research systematically investigating the threshold of intelligibility has been very limited. In this article, we provide a brief summary of the literature as it pertains to intelligible and comprehensible speech, and then report on an exploratory study seeking to determine what specific features of accented speech make it difficult for global listeners to process. Eighteen speakers representing six English varieties were recruited to provide speech stimuli for two English listening tests. Sixty listeners from the same six English varieties took part in the listening tests, and their scores were then assessed against measurable segmental, prosodic, and fluency features found in the speech samples. Results indicate that it is possible to identify particular features of English speech varieties that are most likely to lead to a breakdown in communication, and that the number of such features present in a particular speakers’ speech can predict intelligibility.
Measurement error and variant-calling in deep Illumina sequencing of HIV
Authors: Howison Mark , Coetzer Mia , Kantor Rami 
Published: November 2018

Abstract

Motivation
Next-generation deep sequencing of viral genomes, particularly on the Illumina platform, is increasingly applied in HIV research. Yet, there is no standard protocol or method used by the research community to account for measurement errors that arise during sample preparation and sequencing. Correctly calling high and low-frequency variants while controlling for erroneous variants is an important precursor to downstream interpretation, such as studying the emergence of HIV drug-resistance mutations, which in turn has clinical applications and can improve patient care.

Results
We developed a new variant-calling pipeline, hivmmer, for Illumina sequences from HIV viral genomes. First, we validated hivmmer by comparing it to other variant-calling pipelines on real HIV plasmid datasets. We found that hivmmer achieves a lower rate of erroneous variants, and that all methods agree on the frequency of correctly called variants. Next, we compared the methods on an HIV plasmid dataset that was sequenced using Primer ID, an amplicon-tagging protocol, which is designed to reduce errors and amplification bias during library preparation. We show that the Primer ID consensus exhibits fewer erroneous variants compared to the variant-calling pipelines, and that hivmmer more closely approaches this low error rate compared to the other pipelines. The frequency estimates from the Primer ID consensus do not differ significantly from those of the variant-calling pipelines.

Availability and implementation
hivmmer is freely available for non-commercial use from https://github.com/kantorlab/hivmmer.

Supplementary information
Supplementary data are available at Bioinformatics online.
An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein–monosaccharide complexes
Authors: Blanco Capurro Juan I , Di Paola Matias , Gamarra Marcelo Daniel , Martí Marcelo A , Modenutti Carlos P 
Published: November 2018

AbstractUnraveling the structure of lectin–carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and ligand conformational diversity. In the last decade several strategies, such as the inclusion of glycan conformation specific scoring functions or our developed solvent-site biased method, have improved carbohydrate docking performance but significant challenges remain, in particular, those related to receptor conformational diversity. In the present work we have analyzed conventional and solvent-site biased autodock4 performance concerning receptor conformational diversity as derived from different crystal structures (apo and holo), Molecular Dynamics snapshots and Homology-based models, for 14 different lectin–monosaccharide complexes. Our results show that both conventional and biased docking yield accurate lectin–monosaccharide complexes, starting from either apo or homology-based structures, even when only moderate (45%) sequence identity templates are available. An essential element for success is a proper combination of a middle-sized (10–100 structures) conformational ensemble, derived either from Molecular dynamics or multiple homology model building. Consistent with our previous works, results show that solvent-site biased methods improve overall performance, but that results are still highly system dependent. Finally, our results also show that docking can select the correct receptor structure within the ensemble, underscoring the relevance of joint evaluation of both ligand pose and receptor conformation.
Maximum norm error estimates for Neumann boundary value problems on graded meshes
Authors: Apel Thomas , Rogovs Sergejs , Pfefferer Johannes , Winkler Max 
Published: November 2018

AbstractThis paper deals with a priori pointwise error estimates for the finite element solution of boundary value problems with Neumann boundary conditions in polygonal domains. Due to the corners of the domain, the convergence rate of the numerical solutions can be lower than in the case of smooth domains. As a remedy, the use of local mesh refinement near the corners is considered. In order to prove quasi-optimal a priori error estimates, regularity results in weighted Sobolev spaces are exploited. This is the first work on the Neumann boundary value problem where both the regularity of the data is exactly specified and the sharp convergence order $h^{2} \lvert \ln h \rvert $ in the case of piecewise linear finite element approximations is obtained. As an extension we show the same rate for the approximate solution of a semilinear boundary value problem. The proof relies in this case on the supercloseness between the Ritz projection to the continuous solution and the finite element solution.