bluuebunny/crossref_metadata_2025_split huggingface dataset:
pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks
Authors: Budach Stefan , Marsico Annalisa 
Published: April 2018

Abstract

Summary
Convolutional neural networks (CNNs) have been shown to perform exceptionally well in a variety of tasks, including biological sequence classification. Available implementations, however, are usually optimized for a particular task and difficult to reuse. To enable researchers to utilize these networks more easily, we implemented pysster, a Python package for training CNNs on biological sequence data. Sequences are classified by learning sequence and structure motifs and the package offers an automated hyper-parameter optimization procedure and options to visualize learned motifs along with information about their positional and class enrichment. The package runs seamlessly on CPU and GPU and provides a simple interface to train and evaluate a network with a handful lines of code. Using an RNA A-to-I editing dataset and cross-linking immunoprecipitation (CLIP)-seq binding site sequences, we demonstrate that pysster classifies sequences with higher accuracy than previous methods, such as GraphProt or ssHMM, and is able to recover known sequence and structure motifs.

Availability and implementation
pysster is freely available at https://github.com/budach/pysster.

Supplementary information
Supplementary data are available at Bioinformatics online.
PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles
Authors: Tran Ngoc-Vinh , Greshake Tzovaras Bastian , Ebersberger Ingo 
Published: April 2018

Abstract

Summary
Phylogenetic profiles form the basis for tracing proteins and their functions across species and through time. Novel genome sequences nowadays often represent species from the remotest corner of the tree of life. Thus, phylogenetic profiling becomes increasingly important for functionally annotating this data and to integrate it into a comprehensive view on organismal evolution. To strengthen the link between the sharing of a gene across species and of the corresponding function, it is meanwhile common to complement phylogenetic profiles with additional information, such as domain architecture similarities between orthologs, or pairwise similarities of other protein features. However, there are few visualization tools that facilitate an intuitive integration of these various information layers. Here, we present PhyloProfile, an R-based tool to visualize, explore and analyze multi-layered phylogenetic profiles.

Availability and implementation
PhyloProfile is available as open source code under the MIT license at https://github.com/BIONF/phyloprofile. An online version for testing PhyloProfile and for small to medium-scale analyses is available at http://applbio.biologie.uni-frankfurt.de/phyloprofile.
Uncovering Susceptibility Risk to Online Deception in Aging
Authors: Ebner Natalie C , Ellis Donovan M , Lin Tian , Rocha Harold A , Yang Huizi , Dommaraju Sandeep , Soliman Adam , Woodard Damon L , Turner Gary R , Spreng R Nathan , Oliveira Daniela S 
Published: April 2018

Abstract

Objectives
Fraud in the aged is an emerging public health problem. An increasingly common form of deception is conducted online. However, identification of cognitive and socioemotional risk factors has not been undertaken yet. In this endeavor, this study extended previous work suggesting age effects on susceptibility to online deception.

Methods
Susceptibility was operationalized as clicking on the link in simulated spear-phishing emails that young (18−37 years), young-old (62−74 years), and middle-old (75−89 years) Internet users received, without knowing that the emails were part of the study. Participants also indicated for a set of spear-phishing emails how likely they would click on the embedded link (susceptibility awareness) and completed cognitive and socioemotional measures to determine susceptibility risk profiles.

Results
Higher susceptibility was associated with lower short-term episodic memory in middle-old users and with lower positive affect in young-old and middle-old users. Greater susceptibility awareness was associated with better verbal fluency in middle-old users and with greater positive affect in young and middle-old users.

Discussion
Short-term memory, verbal fluency, and positive affect in middle-old age may contribute to resilience against online spear-phishing attacks. These results inform mechanisms of online fraud susceptibility and real-life decision-supportive interventions toward fraud risk reduction in aging.
Resolution of biodiversity and assemblage structure in demersal fisheries surveys: the role of tow duration
Authors: Moriarty M , Sell A F , Trenkel V M , Lynam C P , Burns F , Clarke E D , Greenstreet S P R , McGonigle C 
Published: April 2018

AbstractAn experiment during a fisheries independent survey in the North Sea was conducted to test whether sampling effort could be reduced without a significant loss in data precision. To examine potential effects of reducing tow duration from the standard 30 min to a proposed 15 min estimates of species encounter rates, species richness, and estimates of abundance, biomass, and body size were analysed. Results show species richness estimates are lower in the short tow category. While biomass and abundance at length and body size are significantly affected by the change in tow duration, estimates of Large Fish Indicator, the Typical length and Mean-max length are not significantly affected by the regime change. The results presented here suggest that a reduction of tow duration did not optimize the resolution of biodiversity, and it may affect other survey objectives, such as, providing estimates of abundance or biomass for assessment of commercial species.
Adherence to recommended electronic health record safety practices across eight health care organizations
Authors: Sittig Dean F , Salimi Mandana , Aiyagari Ranjit , Banas Colin , Clay Brian , Gibson Kathryn A , Goel Ashutosh , Hines Robert , Longhurst Christopher A , Mishra Vimal , Sirajuddin Anwar M , Satterly Tyler , Singh Hardeep 
Published: April 2018

AbstractObjectiveThe Safety Assurance Factors for EHR Resilience (SAFER) guides were released in 2014 to help health systems conduct proactive risk assessment of electronic health record (EHR)- safety related policies, processes, procedures, and configurations. The extent to which SAFER recommendations are followed is unknown.MethodsWe conducted risk assessments of 8 organizations of varying size, complexity, EHR, and EHR adoption maturity. Each organization self-assessed adherence to all 140 unique SAFER recommendations contained within 9 guides (range 10–29 recommendations per guide). In each guide, recommendations were organized into 3 broad domains: “safe health IT” (total 45 recommendations); “using health IT safely” (total 80 recommendations); and “monitoring health IT” (total 15 recommendations).ResultsThe 8 sites fully implemented 25 of 140 (18%) SAFER recommendations. Mean number of “fully implemented” recommendations per guide ranged from 94% (System Interfaces—18 recommendations) to 63% (Clinical Communication—12 recommendations). Adherence was higher for “safe health IT” domain (82.1%) vs “using health IT safely” (72.5%) and “monitoring health IT” (67.3%).ConclusionsDespite availability of recommendations on how to improve use of EHRs, most recommendations were not fully implemented. New national policy initiatives are needed to stimulate implementation of these best practices.
‘African Curiosities’ from the voyage of HMS Avon, 1845–1846: historiographical notes on a forgotten collection
Authors: Coote Jeremy 
Published: April 2018

Abstract
Thanks to the detailed nature of the sketches accompanying an article published in the Illustrated London News in 1846, it has proved possible recently to trace the history of some objects in the University of Oxford’s Pitt Rivers Museum to the voyage of HMS Avon (Commander Henry Mangles Denham) to the coast of West Africa in 1845–6. Drawing on archival materials that survive at the Pitt Rivers Museum, the British Museum, the National Archives, and the United Kingdom Hydrographic Office, historiographical notes are provided on the nature and content of the collection, along with an account of its post-voyage history, including its recent ‘rediscovery’.
Reoperation for Medulloblastoma Prior to Adjuvant Therapy
Authors: Patel Prayash , Wallace David , Boop Frederick A , Vaughn Brandy , Robinson Giles W , Gajjar Amar , Klimo Paul 
Published: April 2018

Abstract

BACKGROUND
Surgery remains an integral part of the treatment of medulloblastoma. We present our experience with repeat surgery for this tumor before initiation of adjuvant therapy.

OBJECTIVE
To report what was found intraoperatively and where at time of second-look surgery and detail any postoperative events or readmissions within 90 days of surgery.

METHODS
Two separate institutional databases were queried to identify patients who underwent repeat resection of suspected residual medulloblastoma from January 2003 to January 2017.

RESULTS
We identified 51 patients (36 male, 15 female) who underwent repeat surgery. Average age at diagnosis was 8.31 years (range, 1.3-21.2). Imaging prior to repeat surgery demonstrated unequivocal residual tumor in 37 patients, but indeterminate in 14 patients. All but 1 patient had histopathologically confirmed residual tumor (50/51, 98%). The fourth ventricle was the primary site in 39 (76%) cases, compared with hemispheric in 12 cases (24%). Thirty (59%) tumors were non-WNT/non-SHH. All indeterminate cases (except for 1 patient) had residual tumor. Hemostatic agents were found within the resection cavity in 80% of indeterminate cases. The most common sites of residual tumor were lateral (26/39, 67%, lateral recess and/or foramen of Luschka) and roof (25/39, 64%); the superior medullary velum was the most common region of the roof (19/25, 76%). Eight (16%) patients developed new neurological deficits: cranial nerve palsies in 5 patients and posterior fossa syndrome in 3 patients.

CONCLUSION
Meticulous inspection of the resection cavity is necessary, paying particular attention to the roof and lateral recess. Hemostatic agents can conceal residual tumor.
The Voltage-Dependent Sodium Channel Family
Authors: Zaleska Mariola , Salvage Samantha C. , Thompson Andrew J. , Namadurai Sivakumar , Huang Christopher L.-H. , Wilkinson Trevor , Cusdin Fiona S. , Jackson Antony P. 
Published: April 2018

Abstract
In neurones and other electrically excitable tissues, voltage-dependent sodium (Nav) channels play an essential role in initiating and propagating the action potential. High-resolution structures of sodium channels have revealed new details concerning these macromolecules that provide insights into their ion-specificity and the conformational changes they undergo during the action potential. Nav channels typically exist in vivo as multicomponent macromolecular assemblies, containing auxiliary proteins that modulate channel gating and trafficking. The properties of some of these auxiliary proteins raise the possibility that Nav channels may exist as functionally coupled complexes. The close similarity between different Nav channel subtypes has frustrated attempts to develop isoform-specific inhibitors. However, the combination of new structural insights, together with antibody-based reagents and site-directed mutagenesis of protein-based toxin inhibitors, raises the possibility of higher target specificities than previously possible. Such reagents may form the basis for a new generation of Nav channel drugs.
Changes in the Inferior Colliculus Associated with Hearing Loss
Authors: Palmer Alan R. , Berger Joel I. 
Published: April 2018

Abstract
The inferior colliculus is an important auditory relay center that undergoes fundamental changes following hearing loss, whether noise induced (NIHL) or age related (ARHL). These changes may contribute to the induction or maintenance of phenomena such as tinnitus (phantom auditory sensations) and hyperacusis (increased sensitivity to sound). Here, we outline changes that can occur in the inferior colliculus following damage to the periphery and/or as a result of the ageing process, both immediate and long-term, and attempt to disentangle which changes relate to either tinnitus or hyperacusis, as opposed to solely hearing loss. Understanding these changes is ultimately important to reversing the underlying pathology and treating these conditions.
The Postauricular Reflex as a Measure of Attention and Positive Emotion
Authors: Benning Stephen D. 
Published: April 2018

Abstract
The postauricular reflex is a muscular reaction that occurs behind the ear in response to short, abrupt sounds. Its magnitude increases with louder eliciting sounds, rotating the eyes in the direction of the eliciting sound, and flexing the head forward. The reflex exhibits prepulse inhibition, especially during attention to complex foreground stimuli. Its magnitude is larger (or potentiated) during pleasant than during neutral pictures, sounds, and videos that are highly arousing. This pattern is particularly evident for erotic, food, and nurturant scenes, suggesting it assesses more than just appetitive processing. This reflex’s potentiation varies across development; positively correlates with personality traits associated with well-being; and negatively correlates with such psychopathologies as depression, schizophrenia, and opioid dependence. It appears distinct from and uncorrelated with the startle blink reflex. New data suggest that activity in left frontal areas generates postauricular reflex potentiation during pleasant versus neutral pictures.
Immediate Effects of a Single Session of Motor Skill Training on the Lumbar Movement Pattern During a Functional Activity in People With Low Back Pain: A Repeated-Measures Study
Authors: Marich Andrej V , Lanier Vanessa M , Salsich Gretchen B , Lang Catherine E , Van Dillen Linda R 
Published: April 2018

Abstract

Background
People with low back pain (LBP) may display an altered lumbar movement pattern of early lumbar motion compared to people with healthy backs. Modifying this movement pattern during a clinical test decreases pain. It is unknown whether similar effects would be seen during a functional activity.

Objective
The objective of this study was to examine the lumbar movement patterns before and after motor skill training, effects on pain, and characteristics that influenced the ability to modify movement patterns.

Design
The design consisted of a repeated-measures study examining early-phase lumbar excursion in people with LBP during a functional activity test.

Methods
Twenty-six people with chronic LBP received motor skill training, and 16 people with healthy backs were recruited as a reference standard. Twenty minutes of motor skill training to decrease early-phase lumbar excursion during the performance of a functional activity were used as a treatment intervention. Early-phase lumbar excursion was measured before and after training. Participants verbally reported increased pain, decreased pain, or no change in pain during performance of the functional activity test movement in relation to their baseline pain. The characteristics of people with LBP that influenced the ability to decrease early-phase lumbar excursion were examined.

Results
People with LBP displayed greater early-phase lumbar excursion before training than people with healthy backs (LBP: mean = 11.2°, 95% CI = 9.3°–13.1°; healthy backs: mean = 7.1°, 95% CI = 5.8°–8.4°). Following training, the LBP group showed a decrease in the amount of early-phase lumbar excursion (mean change = 4.1°, 95% CI = 2.4°–5.8°); 91% of people with LBP reported that their pain decreased from baseline following training. The longer the duration of LBP (β = − 0.22) and the more early-phase lumbar excursion before training (β = − 0.82), the greater the change in early-phase lumbar excursion following training.

Limitations
The long-term implications of modifying the movement pattern and whether the decrease in pain attained was clinically significant are unknown.

Conclusions
People with LBP were able to modify their lumbar movement pattern and decrease their pain with the movement pattern within a single session of motor skill training.
Bibliometric analysis of the trends of Zika related research from 2015 to 2017
Authors: Gwon Yong-Dae , Evander Magnus 
Published: April 2018

AbstractBackgroundZika virus (ZIKV) is a mosquito-borne disease discovered in 1947, which did not cause public concern for the next 68 years. However, when ZIKV emerged in Brazil 2015 the attention increased rapidly. The announcement by Brazilian authorities, that ZIKV infection was associated with severe congenital disease e.g. microcephaly, surged public interest. Because of the accumulation of evidence that showed the magnitude of the ZIKV outbreak in the Americas, the World Health Organization declared a Public Health Emergency of International Concern February 1, 2016.ResultsDuring 2015-2017, we witnessed one of the most active and cooperated research responses against an emerging disease. To investigate the impact of ZIKV research during those years we decided to perform a bibliometric analysis of ZIKV research. The search for research articles on ZIKV was performed by bibliometric analysis from the scientific databases PubMed and Scopus. We found that the number of ZIKV related publications increased 38-41 times in 2016-2017 compared to 2015. During the three years there was a temporal shift in ZIKV research trends, from reports of ZIKV case studies and diagnostic methods, to development of ZIKV prevention and treatment. In addition, the number of countries involved in ZIKV research increased from 25 in 2015 to 111 in 2016 and 139 in the following year, showing that ZIKV research became global during three years.ConclusionsThe results from our study highlighted the importance of gathering public interest to global health issues, and how it can act as a powerful catalyzer to trigger the research field. However, despite the progress in ZIKV research, many questions remain to be addressed to accelerate the development of effective ZIKV countermeasures. Nevertheless, as long as we remember the importance of support and collaboration that we have experienced during the multidisciplinary effort against the current ZIKV outbreak, we will have an idea on how to handle the next inevitable and yet unknown infectious disease threat.
Proteomic and Evolutionary Analyses of Sperm Activation Identify Uncharacterized Genes inCaenorhabditisNematodes
Authors: Kasimatis Katja R. , Moerdyk-Schauwecker Megan J. , Timmermeyer Nadine , Phillips Patrick C. 
Published: April 2018

AbstractBackgroundNematode sperm have unique and highly diverged morphology and molecular biology. In particular, nematode sperm contain subcellular vesicles known as membranous organelles that are necessary for male fertility, yet play a still unknown role in overall sperm function. Here we take a novel proteomic approach to characterize the functional protein complement of membranous organelles in twoCaenorhabditisspecies:C. elegansandC. remanei.ResultsWe identify distinct protein compositions between membranous organelles and the activated sperm body. Two particularly interesting and undescribed gene families—the Nematode-Specific Peptide family, group D and the here designated Nematode-Specific Peptide family, group F—localize to the membranous organelle. Both multigene families are nematode-specific and exhibit patterns of conserved evolution specific to theCaenorhabditisclade. These data suggest gene family dynamics may be a more prevalent mode of evolution than sequence divergence within sperm. Using a CRISPR-based knock-out of the NSPF gene family, we find no evidence of a male fertility effect of these genes, despite their high protein abundance within the membranous organelles.ConclusionsOur study identifies key components of this unique subcellular sperm component and establishes a path toward revealing their underlying role in reproduction.
Influence of pathway topology and functional class on the molecular evolution of human metabolic genes
Authors: Montanucci Ludovica , Laayouni Hafid , Dobón Begoña , Keys Kevin L. , Bertranpetit Jaume , Peretó Juli 
Published: April 2018

AbstractMetabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways during the divergence of primates and rodents. Then, we related those selective pressures to the functional and topological characteristics of the pathways. We have used DNA sequences of all enzymes (956) of the metabolic pathways comprised in the HumanCyc database, using genome data for humans and five other mammalian species.We have found that the evolution of metabolic genes is primarily constrained by the layer of the metabolism in which the genes participate: while genes encoding enzymes of the inner core of metabolism are much conserved, those encoding enzymes participating in the outer layer, mediating the interaction with the environment, are evolutionarily less constrained and more plastic, having experienced faster functional evolution. Genes that have been targeted by adaptive selection are endowed by higher out-degree centralities than non-adaptive genes, while genes with high in-degree centralities are under stronger purifying selection. When the position along the pathway is considered, a funnel-like distribution of the strength of the purifying selection is found. Genes at bottom positions are highly preserved by purifying selection, whereas genes at top positions, catalyzing the first steps, are open to evolutionary changes.These results show how functional and topological characteristics of metabolic pathways contribute to shape the patterns of evolutionary pressures driven by natural selection and how pathway network structure matters in the evolutionary process that shapes the evolution of the system.