bluuebunny/crossref_metadata_2025 huggingface dataset:
Neonatal Onset of Epilepsy of Infancy with Migrating Focal Seizures Associated with a Novel GABRB3 Variant in Monozygotic Twins
Authors: Štěrbová Katalin , Vlčková Markéta , Klement Petr , Neupauerová Jana , Staněk David , Zůnová Hana , Seeman Pavel , Laššuthová Petra
Published: February 2018

Background Recently, a study providing insight into GABRB3 mutational spectrum was published (Møller et al 2017). The authors report considerable pleiotropy even for single mutations and were not able to identify any genotype–phenotype correlations.

Methods The proband (twin B) was referred for massively parallel sequencing of epilepsy-related gene panel because of hypotonia and neonatal seizures. The revealed variant was confirmed with Sanger sequencing in the proband and the twin A, and both parents were tested for the presence of the variant.

Results We report a case of epilepsy of infancy with migrating focal seizures (EIMFS) of neonatal onset in monozygotic twins with a de novo novel GABRB3 variant p.Thr281Ala. The variant has a uniform presentation on an identical genomic background. In addition, early seizure-onset epilepsy associated with GABRB3 mutation has been until now described only for the p.Leu256Gln variant in the GABRB3 (Møller et al 2017, Myers et al 2016) located in the transmembrane domain just as the p.Thr281Ala variant described here.

Conclusion De novo GABRB3 mutations may cause neonatal-onset EIMFS with early-onset hypotonia, respiratory distress, and severe developmental delay.
Line-to-Line Reaming of Highly Porous Acetabular Components Improves Position and Reduces Variability of Component Placement
Authors: Antioch Valentin , Heaven Sebastian , Bedair Hany
Published: February 2018

Accurate and precise acetabular component position in total hip arthroplasty remains challenging even for experienced, high-volume surgeons. Some variability may result from the press-fit technique of cementless components and maybe magnified by the use of highly porous cups with high-friction surfaces. The purpose of this study is to investigate the acetabular component positioning of a hemispherical, highly porous cup with line-to-line reaming compared with press-fit techniques. A retrospective cohort study was performed of 110 consecutive primary total hip arthroplasties performed by a single surgeon using a highly porous acetabular component. Half of the patients had the component implanted with a line-to-line reaming technique and the other half were implanted using a 1 mm press-fit technique. Postoperative radiographs were evaluated for component positioning and loosening at a minimum of 1 year postoperatively by two independent surgeons. Records were reviewed for subsequent surgery. There were no differences between the groups with respect to age, sex, body mass index, operative side, or acetabular component size. The press-fit group had an average abduction angle of 49.4 ± 5° and anteversion of 20.6 ± 7°. The line-to-line group had an average abduction angle of 45.02° [standard deviation (SD) 4.58] and anteversion of 25.42° (SD 4.44) and were statistically different from the press-fit group (p < 0.01). There was significantly less variability in the line-to-line group with respect to anteversion (F-test, p < 0.01) compared with the press-fit group. At most recent follow-up, there were no dislocations, revisions for any reason, or radiographic evidence of loosening in either group. Line-to-line reaming for highly porous cups can improve component positioning and reduce variability compared with press-fit techniques with no difference in fixation or other clinical outcome parameters.
Pediatric Transjugular Intrahepatic Portosystemic Shunts
Authors: Shin David , Shivaram Giridhar , Koo Kevin , Monroe Eric
Published: February 2018

Transjugular intrahepatic portosystemic shunt (TIPS) creation offers potentially life-saving portal decompression regardless of patient age or size, but has been underutilized in pediatric patients to date. Experience has therefore been limited, and the full clinical benefit in this population is yet to be realized. Those wishing to embark on pediatric TIPSs would benefit not only from significant experience in adult TIPSs, but also from an awareness of challenges posed by the unique pediatric population. We herein review the etiologies and manifestations of portal hypertension more common in children, highlight some of the technical nuances of creating TIPSs in smaller anatomy, and summarize the existing literature on the topic. As extrahepatic portal vein occlusion (EHPVO) occurs with greater frequency in pediatric patients, special attention is paid to this condition and its associated challenges.
Subject and Academic Setting of Pre-residency Publications as Potential Predictors of Post-residency Academic Productivity in a Cohort of Ophthalmology Residents
Authors: Cruz Franz , Wang Jiangxia , Joseph Shannon , Miller Neil
Published: February 2018

Objective This study aimed to determine if there is any association between the subject of pre-residency research publications (PRPs) and the academic settings in which they are produced with post-residency academic productivity among graduates from an academic ophthalmology residency program.

Design, Setting, Participants This is a cross-sectional study involving graduates of the Wilmer Eye Institute Residency Training Program from 1990 to 1999. An electronic survey was conducted and each participant was asked to submit his/her curriculum vitae, including a list of peer-reviewed publications. Publications were validated and then classified according to the academic setting in which the research was performed, and whether or not the research was related to ophthalmology.

Outcome Measures The primary outcome measure was the post-residency academic productivity score. The secondary outcome measures were the relationships of academic productivity with the settings in which PRPs were performed and the topics of the PRPs.

Results Fifty-one individuals were included. Regression analysis showed a positive association between the number of PRPs generated during undergraduate studies and medical school and the academic productivity score (ratio = 1.17, p = 0.006) but not during an advanced degree program, research fellowship, or a year off to perform research. Regardless of the setting in which it was performed, the subject of a PRP was not associated with academic productivity.

Conclusion It may be appropriate for ophthalmology residency programs whose mission is to train future academicians to place increased weight on applicants who have published articles related to projects performed during undergraduate years or in medical school and less weight on publications related to research performed during a more structured research period, such as an advanced degree program, regardless of the subject(s) of the publication(s).
Kinematically Aligned Total Knee Arthroplasty or Mechanically Aligned Total Knee Arthroplasty
Authors: Ansari Juned , Pandit Hemant , Takahashi Tsuneari
Published: February 2018

Kinematically aligned total knee arthroplasty (KATKA) was developed to more anatomically align the knee prosthesis to restore the native alignment of the knee and promote physiological kinematics. Even though there are concerns with implant survival, and follow-up at 10 years or more after KATKA has not been reported, there is a negligible incidence of failure of a tibial component at 2 to 9 years. Early clinical results with this technique are encouraging and demonstrate better functional outcomes compared with mechanically aligned TKA (MATKA). The purpose of this study is to perform a systematic review and meta-analysis of the literature to determine whether there are any clinical differences between KATKA and MATKA. The authors conducted a systematic review of the English literature. Five randomized controlled trials (RCTs) which compared clinical outcomes of KATKA and MATKA were finally included. Four RCTs used patient-specific instrument, and one RCT used navigation. Data were extracted and meta-analysis was conducted. KATKA patients had better outcomes: Mean difference between KATKA and MATKA and p-value are presented in brackets after each variable: the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) (–12.5; p < 0.0001), Oxford Knee Score (OKS) (2.3; p = 0.030), combined Knee Society Score (C-KSS) (13.1; p < 0.0001), Knee Function Score (KFS) (6.4; p = 0.0070), and postoperative range of motion (ROM) (4.1°; p = 0.0010). There was no significant difference concerning the complication rates which needed reoperations or revision surgery (odds ratio, 1.01; p = 0.99). KATKA components had a more femoral valgus (–1.8°; p < 0.0001), more tibial varus (1.2°; p = 0.0001), and more tibial slope (1.2°; p = 0.0001), all being statistically significantly different. Better clinical outcomes were obtained in KATKA and component placement in KATKA is significantly different from that in MATKA. There was no increase of patients with poor clinical results due to implant position especially for varus placement of tibial component. This systematic review of five RCTs suggests that KATKA is of potential alternative method to MATKA since the risk of revision for tibial loosening is negligible compared with MATKA for the same follow-up period.
Effekte eines judospezifischen Messplatztrainings auf kinetische und elektromyografische Parameter des Anreißens bei Wurfeingangsbewegungen von Judoka
Authors: Helm Norman , Prieske Olaf , Muehlbauer Thomas , Krüger Tom , Granacher Urs
Published: February 2018

Hintergrund Schnellkräftige Wurfeingangsbewegungen stellen im Judo entscheidende Voraussetzungen für den Wettkampferfolg dar, weshalb das Training der Anrissbewegung ein zentrales Element des judospezifischen Trainings darstellt. Das Ziel der Studie bestand darin, die Effekte eines Anrisstrainings mit einem Judoergometer-System (ATJ) gegenüber einem tradierten Anrisstraining mit Partner (ATP) auf kinetische und elektromyografische Parameter des Anreißens bei Wurfeingangsbewegungen von Judoka zu untersuchen. Methode Männliche leistungsorientierte Judoka (N = 24, Alter: 22 ± 4 Jahre; Trainingserfahrung: 15 ± 3 Jahre) wurden randomisiert in zwei Gruppen aufgeteilt. Im Crossover-Design absolvierte die erste Gruppe über vier Wochen ein ATJ gefolgt von vier Wochen ATP (je 3x/ Woche). Die zweite Gruppe führte beide Trainingsvarianten in umgekehrter Reihenfolge durch. ATJ und ATP wurden zusätzlich zum bestehenden Training absolviert. Vor dem Training sowie nach vier und nach acht Wochen Training wurden Tests zur Erfassung kinetischer Parameter (dynamisch-realisierte Maximalkraft, Explosivkraft, mechanische Arbeit) und elektromyografischer (EMG) Schulter-/ Rumpfmuskelaktivitäten (M. biceps brachii, M. deltoideus, M. trapezius, M. erector spinae) für die Hub- und Zugarmseite bei Wurfeingangsbewegungen am Judoergometer sowie sportartunspezifische Krafttests (d. h. Liegend-Anreißen, Klimmziehen) durchgeführt.

Ergebnisse Die Ergebnisse der statistischen Analyse ergaben über den gesamten Interventionszeitraum (8 Wochen) für beide Trainingsgruppen signifikante Verbesserungen der kinetischen Parameter (p <,05; 0,83 ≤d≤ 1,77) und EMG-Aktivitäten (p <,05; 1,07 ≤d≤ 2,25). Darüber hinaus zeigten sich größere Zuwachsraten in der Explosivkraft, der mechanischen Arbeit und den Schulter-/Rumpfmuskelaktivitäten (M. deltoideus, M. erector spinae, M. trapezius) zugunsten von ATJ im Vergleich zu ATP (p <,05; 1,25 ≤d≤ 2,79). Für die sportartunspezifischen Kraftwerte wurden keine signifikanten Veränderungen festgestellt.

Schlussfolgerung Die vorliegenden Ergebnisse zeigen, dass ATJ gegenüber ATP größere Steigerungsraten von kinetischen und elektromyografischen Parametern des Anreißens bei Wurfeingangsbewegungen von Judoka bewirkt. Die trainingsbedingten Leistungssteigerungen scheinen zumindest teilweise auf neuronalen Anpassungen zu beruhen.
Aerodynamics of a translating comb-like plate inspired by a fairyfly wing
Authors: Lee Seung Hun , Kim Daegyoum
Published: February 2018

Unlike the smooth wings of common insects or birds, micro-scale insects such as the fairyfly have a distinctive wing geometry, comprising a frame with several bristles. Motivated by this peculiar wing geometry, we experimentally investigated the flow structure of a translating comb-like wing for a wide range of gap size, angle of attack, and Reynolds number, Re = O(10) − O(103), and the correlation of these parameters with aerodynamic performance. The flow structures of a smooth plate without a gap and a comb-like plate are significantly different at high Reynolds number, while little difference was observed at the low Reynolds number of O(10). At low Reynolds number, shear layers that were generated at the edges of the tooth of the comb-like plate strongly diffuse and eventually block a gap. This gap blockage increases the effective surface area of the plate and alters the formation of leading-edge and trailing-edge vortices. As a result, the comb-like plate generates larger aerodynamic force per unit area than the smooth plate. In addition to a quasi-steady phase after the comb-like plate travels several chords, we also studied a starting phase of the shear layer development when the comb-like plate begins to translate from rest. While a plate with small gap size can generate aerodynamic force at the starting phase as effectively as at the quasi-steady phase, the aerodynamic force drops noticeably for a plate with a large gap because the diffusion of the developing shear layers is not enough to block the gap.
Soil organic layer combustion in boreal black spruce and jack pine stands of the Northwest Territories, Canada
Authors: Walker Xanthe J. , Baltzer Jennifer L. , Cumming Steven G. , Day Nicola J. , Johnstone Jill F. , Rogers Brendan M. , Solvik Kylen , Turetsky Merritt R. , Mack Michelle C.
Published: February 2018

Increased fire frequency, extent and severity are expected to strongly affect the structure and function of boreal forest ecosystems. In this study, we examined 213 plots in boreal forests dominated by black spruce (Picea mariana) or jack pine (Pinus banksiana) of the Northwest Territories, Canada, after an unprecedentedly large area burned in 2014. Large fire size is associated with high fire intensity and severity, which would manifest as areas with deep burning of the soil organic layer (SOL). Our primary objectives were to estimate burn depth in these fires and then to characterise landscapes vulnerable to deep burning throughout this region. Here we quantify burn depth in black spruce stands using the position of adventitious roots within the soil column, and in jack pine stands using measurements of burned and unburned SOL depths. Using these estimates, we then evaluate how burn depth and the proportion of SOL combusted varies among forest type, ecozone, plot-level moisture and stand density. Our results suggest that most of the SOL was combusted in jack pine stands regardless of plot moisture class, but that black spruce forests experience complete combustion of the SOL only in dry and moderately well-drained landscape positions. The models and calibrations we present in this study should allow future research to more accurately estimate burn depth in Canadian boreal forests.
Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice
Authors: Koide Yohei , Ogino Atsushi , Yoshikawa Takanori , Kitashima Yuki , Saito Nozomi , Kanaoka Yoshitaka , Onishi Kazumitsu , Yoshitake Yoshihiro , Tsukiyama Takuji , Saito Hiroki , Teraishi Masayoshi , Yamagata Yoshiyuki , Uemura Aiko , Takagi Hiroki , Hayashi Yoriko , Abe Tomoko , Fukuta Yoshimichi , Okumoto Yutaka , Kanazawa Akira
Published: February 2018

Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The
S

1

locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species,
Oryza sativa
and
Oryza glaberrima
. The
O. glaberrima
-derived allele (denoted

S
1

g
) on the
S

1

locus causes preferential abortion of gametes with its allelic alternative (denoted

S
1

s
) in
S

1

g
/
S

1

s
heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele,
S

1

mut
, which does not confer sterility in the
S

1

mut
/
S

1

g
and
S

1

mut
/
S

1

s
hybrids. We found that the causal mutation of the
S

1

mut
allele was a deletion in the peptidase-coding gene (denoted “
SSP
”) in the
S

1

locus of
O. glaberrima
. No orthologous genes of
SSP
were found in the
O. sativa
genome. Transformation experiments indicated that the introduction of
SSP
in carriers of the
S

1

s
allele did not induce sterility. In
S

1

mut
/
S

1

s
heterozygotes, the insertion of
SSP
led to sterility, suggesting that
SSP
complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the
SSP
gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a “neutral” allele, which facilitates interspecific hybridization for breeding programs.
Doubly hybrid density functionals that correctly describe both density and energy for atoms
Authors: Su Neil Qiang , Zhu Zhenyu , Xu Xin
Published: February 2018

Significance

It was commented that some modern density functional theory functionals may be giving the correct energies for the wrong reason and functionals that produce “right” energies from “wrong” densities fail twice. However, the route to the “heaven” of the “Jacob’s ladder” is incomplete in Medvedev et al. [Medvedev MG, et al. (2017)Science355:49–52], as the authors did not provide any information on the top fifth-rung functionals. We fill the gap to show here that the XYG3 type of doubly hybrid density functionals (xDHs) can correctly describe both density and energy for the same atomic set used by Medvedev et al., such that electronic structure calculations for molecular sciences of the main group elements can be carried out reliably by using xDHs.
Targeted DNA demethylation of the
Arabidopsis
genome using the human TET1 catalytic domain
Authors: Gallego-Bartolomé Javier , Gardiner Jason , Liu Wanlu , Papikian Ashot , Ghoshal Basudev , Kuo Hsuan Yu , Zhao Jenny Miao-Chi , Segal David J. , Jacobsen Steven E.
Published: February 2018

DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is
fwa
, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the
FLOWERING WAGENINGEN
(
FWA
) gene, causing up-regulation of
FWA
and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the
FWA
promoter can cause highly efficient targeted demethylation,
FWA
up-regulation, and a heritable late-flowering phenotype. Additional ZF–TET1cd fusions designed to target methylated regions of the
CACTA1
transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCas9-based targeted demethylation system using the TET1cd and a modified SunTag system. Similar to the ZF–TET1cd fusions, the SunTag–TET1cd system is able to target demethylation and activate gene expression when directed to the
FWA
or
CACTA1
loci. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.
Evolutionary stability of antibiotic protection in a defensive symbiosis
Authors: Engl Tobias , Kroiss Johannes , Kai Marco , Nechitaylo Taras Y. , Svatoš Aleš , Kaltenpoth Martin
Published: February 2018

The increasing resistance of human pathogens severely limits the efficacy of antibiotics in medicine, yet many animals, including solitary beewolf wasps, successfully engage in defensive alliances with antibiotic-producing bacteria for millions of years. Here, we report on the in situ production of 49 derivatives belonging to three antibiotic compound classes (45 piericidin derivatives, 3 streptochlorin derivatives, and nigericin) by the symbionts of 25 beewolf host species and subspecies, spanning 68 million years of evolution. Despite a high degree of qualitative stability in the antibiotic mixture, we found consistent quantitative differences between species and across geographic localities, presumably reflecting adaptations to combat local pathogen communities. Antimicrobial bioassays with the three main components and in silico predictions based on the structure and specificity in polyketide synthase domains of the piericidin biosynthesis gene cluster yield insights into the mechanistic basis and ecoevolutionary implications of producing a complex mixture of antimicrobial compounds in a natural setting.
Role of glutathione metabolism in host defense against
Borrelia burgdorferi
infection
Authors: Kerstholt Mariska , Vrijmoeth Hedwig , Lachmandas Ekta , Oosting Marije , Lupse Mihaela , Flonta Mirela , Dinarello Charles A. , Netea Mihai G. , Joosten Leo A. B.
Published: February 2018

Significance

Inflammation plays a crucial role in the pathogenesis of Lyme disease, caused by the spirochete
Borrelia burgdorferi
. Intracellular metabolism is increasingly being recognized as a major determinant of inflammation. In this study, we investigated how
B. burgdorferi
affects host cell metabolism by analyzing the intracellular metabolome in vitro, as well as the circulating metabolome in patients with early-onset Lyme disease. We identify glutathione metabolism as the most important target of
B. burgdorferi
infection and discover that this pathway is essential for cytokine production, likely through glutathionylation. These findings not only provide more insight into the pathogenesis of Lyme disease but also underline how host–pathogen interactions in metabolism can play crucial roles in host defense against pathogens.
Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast
Authors: Gibney Patrick A. , Schieler Ariel , Chen Jonathan C. , Bacha-Hummel Jessie M. , Botstein Maxim , Volpe Matthew , Silverman Sanford J. , Xu Yifan , Bennett Bryson D. , Rabinowitz Joshua D. , Botstein David
Published: February 2018

Toxicity resulting from accumulation of sugar-phosphate molecules is an evolutionarily conserved phenomenon, observed in multiple bacterial and eukaryotic systems, including a number of human diseases. However, the molecular mechanisms involved in sugar-phosphate toxicity remain unclear. Using the model eukaryote Saccharomyces cerevisiae, we developed two systems to accumulate human disease-associated sugar-phosphate species. One system utilizes constitutive expression of galactose permease and galactose kinase to accumulate galactose-1-phosphate, while the other system utilizes constitutive expression of a mammalian ketohexokinase gene to accumulate fructose-1-phosphate. These systems advantageously dissociate sugar-phosphate toxicity from metabolic demand for downstream enzymatic products. Using them, we characterized the pathophysiological effects of sugar-phosphate accumulation, in addition to identifying a number of genetic suppressors that repair sugar-phosphate toxicity. By comparing the effects of different sugar-phosphates, and examining the specificity of genetic suppressors, we observed a number of striking similarities and significant differences. These results suggest that sugar-phosphates exert toxic effects, at least in part, through isomer-specific mechanisms rather than through a single general mechanism common to accumulation of any sugar-phosphate.
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry
Authors: Lux Markus , Brinkman Ryan Remy , Chauve Cedric , Laing Adam , Lorenc Anna , Abeler-Dörner Lucie , Hammer Barbara
Published: February 2018

Motivation

Identification of cell populations in flow cytometry is a critical part of the analysis and lays the groundwork for many applications and research discovery. The current paradigm of manual analysis is time consuming and subjective. A common goal of users is to replace manual analysis with automated methods that replicate their results. Supervised tools provide the best performance in such a use case, however they require fine parameterization to obtain the best results. Hence, there is a strong need for methods that are fast to setup, accurate and interpretable.

Results

flowLearn is a semi-supervised approach for the quality-checked identification of cell populations. Using a very small number of manually gated samples, through density alignments it is able to predict gates on other samples with high accuracy and speed. On two state-of-the-art datasets, our tool achieves median(F1)-measures exceeding 0.99 for 31%, and 0.90 for 80% of all analyzed populations. Furthermore, users can directly interpret and adjust automated gates on new sample files to iteratively improve the initial training.

Availability and implementation

FlowLearn is available as an R package on https://github.com/mlux86/flowLearn. Evaluation data is publicly available online. Details can be found in the Supplementary Material.

Supplementary information

Supplementary data are available at Bioinformatics online.
Combining co-evolution and secondary structure prediction to improve fragment library generation
Authors: de Oliveira Saulo H P , Deane Charlotte M
Published: February 2018

Motivation

Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co-evolution constraints to generate better fragment libraries for fragment-based protein structure prediction.

Results

We have compared five different fragment library generation programmes on three different datasets encompassing over 400 unique protein folds. We show that considering the secondary structure of the fragments when assembling these libraries provides a critical way to assess their usefulness to structure prediction. We then use co-evolution constraints to improve the fragment libraries by enriching them with fragments that satisfy constraints and discarding those that do not. These improved libraries have better precision and lead to consistently better modelling results.

Availability and implementation

Data is available for download from: http://opig.stats.ox.ac.uk/resources. Flib-Coevo is available for download from: https://github.com/sauloho/Flib-Coevo.

Supplementary information

Supplementary data are available at Bioinformatics online.
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier
Authors: Cao Zhen , Pan Xiaoyong , Yang Yang , Huang Yan , Shen Hong-Bin
Published: February 2018

Motivation

The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date.

Results

In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset.

Availability and implementation

The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator.

Supplementary information

Supplementary data are available at Bioinformatics online.
Message Pretesting Using Assessments of Expected or Perceived Persuasiveness: Evidence About Diagnosticity of Relative Actual Persuasiveness
Authors: O’Keefe Daniel J
Published: February 2018

Do formative assessments of the expected or perceived effectiveness of persuasive messages provide a good guide to the relative actual effectiveness of those messages? The correlational evidence usually invoked on this question is less than ideal. The most relevant evidence compares two messages’ relative standing on perceived message effectiveness (PME) and actual message effectiveness (AME) as assessed in separate samples. Across 151 such comparisons, the direction of difference in PME matched that of AME in 58% of cases (ns). Diagnostic accuracy did not differ significantly depending on the size or significance of the PME difference, the size of the PME sample, whether PME assessments came from experts or target-audience representatives, the referent of the PME assessment, or whether the PME assessment involved comparing messages.
Flow Diversion of Posterior Circulation Cerebral Aneurysms: A Single-Institution Series of 59 Cases
Authors: Bender Matthew T , Colby Geoffrey P , Jiang Bowen , Lin Li-Mei , Campos Jessica K , Xu Risheng , Westbroek Erick M , Vo Chau D , Zarrin David A , Caplan Justin M , Huang Judy , Tamargo Rafael J , Coon Alexander L
Published: February 2018

BACKGROUND

Posterior circulation cerebral aneurysms are at higher risk of rupture and are more symptomatic than those in the anterior circulation. Existing treatments carry significant morbidity. Early reports of flow diversion for posterior circulation aneurysms have suggested high complication and low occlusion rates.

OBJECTIVE

To report safety and efficacy of flow diversion with the pipeline embolization device (ev3, Medtronic Inc, Dublin, Ireland) for aneurysms located throughout the posterior circulation.

METHODS

A prospective, institutional review board-approved database was analyzed for all patients with posterior circulation aneurysms treated by flow diversion at our institution.

RESULTS

Fifty-nine embolization procedures were performed on 55 patients. Average aneurysm size was 9.4 mm. Morphology was saccular (45%), fusiform (29%), or dissecting/pseudo-aneurysms (25%). Sixty-two percent of aneurysms arose along the vertebral artery. There were 7 mid-basilar (13%) and 7 basilar apex (13%) aneurysms. Procedural success was 98%; 1 Pipeline embolization device was placed in 85%; and coiling was performed in 17% of cases. There were 5 major complications (8%), all strokes. Patients with major stroke had modified Rankin Scale score at last follow-up of 1, 3, 4, 6, and 6 (2 mortalities). There were zero intracerebral or subarachnoid hemorrhages. No variable predicted complications on univariate or multivariate analysis. Follow-up digital subtraction angiography was performed for 43 patients (78%). Complete occlusion was 68% at 6 mo and 78% at 12 mo. Average follow-up was 11.8 mo. Fusiform or dissecting morphology and large or giant aneurysm size were predictors of aneurysm persistence at 6 mo on multivariate logistic regression.

CONCLUSION

This is a large single-institution series of Pipeline (Medtronic Inc) for posterior circulation aneurysms and demonstrates acceptable safety and effectiveness in these challenging cases.
Effects of a Home-Based Telephone-Supported Physical Activity Program for Older Adult Veterans With Chronic Low Back Pain
Authors: Goode Adam P , Taylor Shannon Stark , Hastings Susan N , Stanwyck Catherine , Coffman Cynthia J , Allen Kelli D
Published: February 2018

Background

Chronic low back pain (CLBP) is highly prevalent in older adults, leading to functional decline.

Objective

The objective of this study was to evaluate physical activity (PA) only and PA plus cognitive-behavioral therapy for pain (CBT-P) among older adult veterans with CLBP.

Design

This study was a pilot randomized trial comparing a 12-week telephone–supported PA-only intervention group (PA group) or PA plus CBT-P intervention group (PA + CBT-P group) and a wait-list control group (WL group).

Setting

The study setting was the Durham Veterans Affairs Health Care System.

Participants

The study participants were 60 older adults with CLBP.

Interventions

The PA intervention included stretching, strengthening, and aerobic activities; CBT-P covered activity pacing, relaxation techniques, and cognitive restructuring.

Measurements

Feasibility measures included enrollment and completion metrics; acceptability was measured by completed phone calls. Primary outcomes included the Timed “Up & Go” Test and the PROMIS Health Assessment Questionnaire. Generalized linear mixed models were used to estimate changes within and between groups. Effect sizes were calculated with the Cohen d. Adverse effects were measured by self-report.

Results

The mean participant age was 70.3 years; 53% were not white, and 93% were men. Eighty-three percent of participants completed the study, and the mean number of completed phone calls was 10 (of 13). Compared with the results for the WL group, small to medium treatment effects were found for the intervention groups in the Timed “Up & Go” Test (PA group: −2.94 [95% CI = −6.24 to 0.35], effect size = −0.28; PA + CBT-P group: –3.26 [95% CI = −6.69 to 0.18], effect size = −0.31) and the PROMIS Health Assessment Questionnaire (PA group: −6.11 [95% CI = −12.85 to 0.64], effect size = −0.64; PA + CBT-P group: –4.10 [95% CI = –11.69 to 3.48], effect size = −0.43). Small treatment effects favored PA over PA + CBT-P. No adverse effects were noted.

Limitations

This was a pilot study, and a larger study is needed to verify the results.

Conclusions

This pilot trial demonstrated that home-based telephone-supported PA interventions were feasible, acceptable, and safe for older adult veterans. The results provide support for a larger trial investigating these interventions.
Characterization and Genetic Structure of aTospovirusCausing Chlorotic Ring Spots and Chlorosis Disease on Peanut; Comparison with Iranian and Polish Populations of Tomato yellow fruit ring virus
Authors: Golnaraghi A. , Shahraeen N. , Nguyen H. D.
Published: February 2018

A Tospovirus species was isolated from peanut plants showing chlorotic ring spots and chlorosis, and identified as Tomato yellow fruit ring virus (TYFRV) on the basis of its biological, serological, and molecular properties. In host range studies, a broad range of indicator plants was infected by the five isolates studied; all the isolates systemically infected Nicotiana tabacum cultivars and, thus, they were classified into the N-host-infecting type isolates of the virus. These isolates strongly reacted with TYFRV antibodies but not with the specific antibodies of other tospoviruses tested. Recombination analyses showed that the nucleoprotein gene of the peanut isolates and other isolates studied were nonrecombinant. In phylogenetic trees, the virus isolates were clustered in three genogroups: IRN-1, IRN-2, and a new group, POL; the peanut isolates fell into IRN-2 group. Multiple sequence alignments showed some genogroup-specific amino acid substitutions among the virus isolates studied. The results revealed the presence of negative selection in TYFRV populations. Also, the Iranian populations had higher nucleotide diversity compared with the Polish population. Genetic differentiation and gene flow analyses indicated that the populations from Iran and Poland and those belonging to different genogroups were partially differentiated populations. Our findings seem to suggest that there has been frequent gene flow between some populations of the virus in the mid-Eurasian region of Iran.
Distinct Trophic Specializations Affect How Phytophthora ramorum and Clade 6 Phytophthora spp. Colonize and Persist on Umbellularia californica Leaves in Streams
Authors: Aram Kamyar , Rizzo David M.
Published: February 2018

Phytophthora spp. are regularly recovered from streams but their ecology in aquatic environments is not well understood. Phytophthora ramorum, invasive in California forests, persists in streams at times when sporulation in the canopy is absent, suggesting that it reproduces in the water. Streams are also inhabited by resident, clade 6 Phytophthora spp., believed to be primarily saprotrophic. We conducted experiments to determine whether differences of trophic specialization exist between these two taxa, and investigated how this may affect their survival and competition on stream leaf litter. P. ramorum effectively colonized fresh (live) rhododendron leaves but not those killed by freezing or drying, whereas clade 6 species colonized all leaf types. However, both taxa were recovered from naturally occurring California bay leaf litter in streams. In stream experiments, P. ramorum colonized bay leaves rapidly at the onset; however, colonization was quickly succeeded by clade 6 species. Nevertheless, both taxa persisted in leaves over 16 weeks. Our results confirm that clade 6 Phytophthora spp. are competent saprotrophs and, though P. ramorum could not colonize dead tissue, early colonization of suitable litter allowed it to survive at a low level in decomposing leaves.
Grover Disease With Epidermal Dysmaturation Pattern: A Common Histopathologic Finding
Authors: Aljarbou Ohoud Z. , Asgari Masoud , Al-Saidi Nagla , Silloca-Cabana Elizabeth O. , Alathamneh Mamoun , P. Sangueza Omar
Published: February 2018

Background:

Grover disease is an entity whose diagnosis is based on clinicopathologic correlation. Histopathologically, focal acantholysis is the most common finding. In some cases, there is prominent squamous atypia which can prove to be very challenging and the lesion may be confused with an epidermal neoplasm.

Objective:

To report on atypical histopathological changes in Grover disease and to provide helpful clues to differentiate between the epidermal atypia seen in some cases of Grover disease and epithelial neoplasms.

Material and Methods:

We analyzed 33 cases of Grover disease histologically diagnosed at Wake Forest Baptist Medical Center, NC, between 2011 and 2017. Atypical changes in keratinocytes were defined as epithelial buds, nuclear pleomorphism, and dyskeratosis in all layers of epidermis or altered granular layer.

Results:

Twenty cases (64%) showed foci with alteration of the normal keratinocytic maturation, whereas 18 cases demonstrated nuclear pleomorphism. Buds of epithelial cells emanating from the basal layer of the epidermis and granular cell alteration was present in 19 cases.

Conclusions:

The findings especially the presence of an altered granular layer may represent a diagnostic clue in cases of Grover disease with atypical changes.
CLINICAL FEATURES, IMAGING, AND NATURAL HISTORY OF MYELINATED RETINAL NERVE FIBER LAYER
Authors: Rao Raksha , Turkoglu Elif B. , Say Emil A. T. , Shields Carol L.
Published: February 2018

Purpose:

To evaluate the natural history of myelinated retinal nerve fiber layer (MRNFL) through clinical features and enhanced depth imaging optical coherence tomography.

Methods:

This is a retrospective, noncomparative, case series of patients who underwent thorough clinical examination to document associated ocular and systemic features. Enhanced depth imaging optical coherence tomography was performed when MRNFL was located posteriorly and accessible to imaging.

Results:

Seventy-two eyes of 62 patients had a total of 86 MRNFL lesions. Enhanced depth imaging optical coherence tomography (n = 42 eyes) showed that all lesions originated in the nerve fiber layer with preservation of the vascular structures. Mean thickness by enhanced depth imaging optical coherence tomography was 255 μm (median, 182 μm; range, 61–717 μm). Natural history was obtainable in 58 lesions with a mean follow-up duration of 57 months (median, 37 months; range, 2–253 months) with no significant change overall in largest basal diameter (2.5 vs. 2.5 mm; P = 0.361) or thickness (255 vs. 240 μm; P = 0.053). However, evidence of lesion change included growth in base only (≥0.5 mm) (3 of 58; 5%), growth in base (≥0.5 mm) and thickness (≥50 μm) (3 of 58; 5%), and reduction in base (≥0.5 mm) after plaque radiotherapy for choroidal melanoma (3 of 58; 5%).

Conclusion:

In general, MRNFL is a rare, benign retinal finding with a potential for growth in 10% of cases. This supports previous histopathological reports that MRNFL represents accumulation of both myelin and oligodendrocytes and could be an oligodendrocytic choristoma.
NITINOL FLEX LOOP–ASSISTED RETRIEVAL AND SUTURELESS INTRASCLERAL REFIXATION OF A DISLOCATED INTRAOCULAR LENS IMPLANT
Authors: Hsu Jason
Published: February 2018

Background/Purpose:

To describe a novel use of the flexible nitinol loop membrane scraper (FINESSE Flex loop; Alcon, Fort Worth, TX) for rescue and refixation of a dislocated intraocular lens (IOL).

Methods:

A 27-gauge nitinol flex loop was used to lasso each haptic of a dislocated 3-piece IOL. By retracting the loop, the haptic could be effectively locked to the instrument and externalized through a scleral tunnel, thereby fixating it to the sclera in a sutureless fashion.

Results:

A 50-year-old man presented with a posteriorly dislocated Sensar AR40e IOL (Abbott Medical Optics, Inc; Santa Barbara, CA) and retained lens material after a complicated cataract surgery in the left eye. His visual acuity was counting fingers at face. The patient underwent 27-gauge pars plana vitrectomy with successful rescue and refixation of the IOL using the nitinol flex loop. One week postoperatively, his visual acuity had improved to 20/40.

Conclusion:

The nitinol flex loop may be used to lasso the haptics of a dislocated IOL and refixate it using a sutureless intrascleral fixation technique. This instrument may be a safer alternative compared with forceps for retrieving posteriorly dislocated IOLs that are sitting on the retinal surface.
FULL-THICKNESS MACULAR HOLE WITH MACULAR INTRACHOROIDAL CAVITATION IN A PATIENT WITH PATHOLOGIC MYOPIA
Authors: Örnek Nurgül , Örnek Kemal
Published: February 2018

Purpose:

To describe a full-thickness macular hole (MH) opening to macular intrachoroidal cavitation in a patient with pathologic myopia.

Methods:

Full ophthalmologic examination, fundus camera (Topcon TRC; Topcon Co, Tokyo, Japan), optical coherence tomography (RetinaScan Advanced RS-3000; NIDEK, Gamagori, Japan) imaging, and cataract surgery.

Results:

A 61-year-old woman admitted with decreased vision in the left eye. Visual acuity was counting fingers from 30 cm. Anterior segment examination showed advanced cataract. Fundus examination revealed pathologic myopia. There was full-thickness MH opening to macular intrachoroidal cavitation in contact with the anterior surface of the sclera subfoveally. Except for the communicating part of MH and macular intrachoroidal cavitation, outer retina, ellipsoid zone, and retinal pigment epithelium were intact. Choroid was intact except for a small part at subfoveal area. The patient received an uncomplicated cataract surgery. Visual acuity improved to 5/10. Because she was satisfied, MH surgery was postponed to a later date.

Conclusion:

Full-thickness MH may occur within the area of macular intrachoroidal cavitation in pathologic myopia.
Robotic Transthoracic Primary Repair of a Diaphragmatic Hernia and Reduction of an Intrathoracic Liver
Authors: Counts Sarah J. , Saffarzadeh Areo G. , Blasberg Justin D. , Kim Anthony W.
Published: February 2018

This case involves a 70-year-old woman who presented after a low-speed motor vehicle collision with a traumatic right hemidiaphragm rupture and herniation of the liver into the right chest. She was brought to the operating room for a robotic-assisted minimally invasive transthoracic repair of this hernia with diaphragm plication. The case and video described in this report highlight the utility of the robotic platform in performing a transthoracic diaphragm repair and plication after a right-sided traumatic diaphragm rupture in a patient without concomitant abdominal injuries.
Maternal Influenza Immunization and Prevention of Severe Clinical Pneumonia in Young Infants
Authors: Omer Saad B. , Clark Dayna R. , Aqil Anushka R. , Tapia Milagritos D. , Nunes Marta C. , Kozuki Naoko , Steinhoff Mark C. , Madhi Shabir A. , Wairagkar Niteen
Published: February 2018

Background:

To evaluate the effect of antenatal influenza vaccination on all-cause severe infant pneumonia, we performed pooled analysis of 3 randomized controlled trials conducted in Nepal, Mali and South Africa.

Methods:

The trials were coordinated from the planning phase. The follow-up period was 0–6 months postpartum in Nepal and Mali and 0–24 weeks in South Africa. Pregnant women with gestational age 17–34 weeks in Nepal, ≥28 weeks in Mali and 20–36 weeks in South Africa were enrolled. Trivalent inactivated influenza vaccine (IIV) was compared with either saline placebo (Nepal and South Africa) or quadrivalent meningococcal conjugate vaccine (Mali). In South Africa, cases were hospitalized and were therefore considered to have severe pneumonia. In Nepal and Mali, severe infant pneumonia diagnosis was based on the WHO Integrated Management of Childhood Illness definition.

Results:

A total of 10,002 mothers and 9801 live-born eligible infants were included in the present analysis. There was a 31% lower incidence rate of severe pneumonia in the IIV group compared with the control group in Nepal [incidence rate ratio (IRR): 0.69; 95% CI: 0.50–0.94; Table 1]. In South Africa, there was a 43% lower incidence rate of severe pneumonia in the IIV group versus the control group (IRR: 0.57; 95% CI: 0.33–1.0). There was no difference in incidence rates between the IIV group and the control group in Mali. Overall, incidence rate of severe pneumonia was 20% lower in the IIV group compared with the control group (IRR: 0.80; 95% CI: 0.66–0.99; P = 0.04). Protection was highest in the high influenza circulation period (IRR: 0.44; 95% CI: 0.23–0.84).

Conclusions:

Maternal influenza immunization may reduce severe pneumonia episodes among infants—particularly those too young to be completely vaccinated against Streptococcus pneumoniae and influenza.
Retained Guidewires in the Veterans Health Administration: Getting to the Root of the Problem
Authors: Cherara Leila , Sculli Gary L. , Paull Douglas E. , Mazzia Lisa , Neily Julia , Mills Peter D.
Published: February 2018

Objectives

The aims of this study were to investigate the demographics, causes, and contributing factors of retained guidewires (GWs) and to make specific recommendations for their prevention.

Methods

The Veterans Administration patient safety reporting system database for 2000–2016 was queried for cases of retained GWs (RGWs). Data extracted for each case included procedure location, provider experience, insertion site, urgency, time to discovery, root causes, and corrective actions taken.

Results

There were 101 evaluable cases of RGWs. Resident trainee (36%), critical care unit (38%), femoral vein (44%), and nonemergent placement (79%) were the conditions most frequently associated with a RGW. While discovery occurred almost immediately (30%) or in next 24 hours (31%), there were instances of RGWs found months (2%) or years (3%) later. Common root causes included inexperience (46%), lack of standardization (35%), distractions (25%), and lack of a checklist (23%).

Conclusions

The results demonstrate the result of human factors–based errors such as posttask completion errors. We recommend human factor–based interventions such as checklists and devices employing forcing functions that do not allow clinicians to complete the insertion process without first removing the GW.