bluuebunny/crossref_metadata_2025_split huggingface dataset:
Group Means and Intersubject and Intrasubject Variability Estimates for Absolute and Relative (Categorical) Loudness Judgments of Typical Young Adult Listeners
Authors: Formby Craig , Yang Xin , Payne JoAnne , Parton Jason 
Published: March 2019

Purpose
This brief research note is motivated by an ever-increasing need for typical repeated-measures loudness judgments and variability estimates of the kind necessary to conduct evidence-based treatment studies and clinical trials.

Method

These judgments and variability data, originally collected but not reported by
Formby, Payne, Yang, Wu, and Parton (2017)
, are presented here for relative (categorical) and absolute loudness judgments for typical young adult listeners with normal auditory function.

Results
As shown in this research note, these data may differ appreciably between young and older adult listeners with audiometric pure-tone thresholds within the clinically normal range.

Conclusion

In general, these findings highlight the need for good age-based, repeated-measures data for planning and powering evidence-based treatment studies and, specifically, for clinical trials that rely on categorical loudness judgments (i.e., as measured with the Contour Test of loudness;
Cox, Alexander, Taylor, & Gray, 1997
) as primary and secondary outcome measures.
Patterns of Recovery From Aphasia in the First 2 Weeks After Stroke
Authors: Wilson Stephen M. , Eriksson Dana K. , Brandt Temre H. , Schneck Sarah M. , Lucanie Jillian M. , Burchfield Annie S. , Charney Sara , Quillen Ian A. , de Riesthal Michael , Kirshner Howard S. , Beeson Pélagie M. , Ritter Leslie , Kidwell Chelsea S. 
Published: March 2019

Purpose
Recovery from aphasia after stroke has a decelerating trajectory, with the greatest gains taking place early and the slope of change decreasing over time. Despite its importance, little is known regarding evolution of language function in the early postonset period. The goal of this study was to characterize the dynamics and nature of recovery of language function in the acute and early subacute phases of stroke.

Method
Twenty-one patients with aphasia were evaluated every 2–3 days for the first 15 days after onset of acute ischemic or hemorrhagic stroke. Language function was assessed at each time point with the Quick Aphasia Battery (Wilson, Eriksson, Schneck, & Lucanie, 2018), which yields an overall summary score and a multidimensional profile of 7 different language domains.

Results
On a 10-point scale, overall language function improved by a mean of 1.07 points per week, confidence interval [0.46, 1.71], with 19 of 21 patients showing positive changes. The trajectory of recovery was approximately linear over this time period. There was significant variability across patients, and patients with more impaired language function at Day 2 poststroke experienced greater improvements over the subsequent 2 weeks. Patterns of recovery differed across language domains, with consistent improvements in word finding, grammatical construction, repetition, and reading, but less consistent improvements in word comprehension and sentence comprehension.

Conclusion
Overall language function typically improves substantially and steadily during the first 2 weeks after stroke, driven mostly by recovery of expressive language. Information on the trajectory of early recovery will increase the accuracy of prognoses and establish baseline expectations against which to evaluate the efficacy of interventions.

Supplemental Material

https://doi.org/10.23641/asha.7811876
Multi‐frequency power system for renewable source integration in smart grid
Authors: Chitransh Varun , Veerachary Mummadi 
Published: March 2019

This study presents a new power system enabled by power‐electronic technology for renewable source integration in micro‐grid. The micro‐grid is decoupled into multiple independent power channels. These power channels are used for any source to any load‐independent power transfer over the common power transmission line. This system works on the principle of frequency‐selective orthogonal power transfer and superposition theorem. To demonstrate the proposed power system, a laboratory‐scale prototype of an interconnected two‐source two‐load system is developed. The two sources independently transfer power to their respective loads at power transmission frequencies of 500 and 0 Hz (DC is also a valid frequency for power transmission), respectively, over the common power transmission path. Thus, a two‐source two‐load system is decoupled into two independent power channels. The proposed system is modular and scalable in structure and can be extended for any number of sources and loads. Finally, the effectiveness of the proposed system is verified through simulations and experimental results which demonstrates independent transmission of 100 W power in each of the two power channels of the two source‐two load interconnected system.
Neurovaskuläre Erkrankungen – Ultraschalldiagnostik
Authors: Eicke Martin , Gröschel Klaus , Harrer-Haag Judith 
Published: March 2019

ZusammenfassungNeurovaskuläre Erkrankungen gehören zu den häufigsten Erkrankungen im neurologischen Fachgebiet. Vor dem Hintergrund der immer älter werdenden Gesellschaft spielt der Schlaganfall und damit dessen Diagnostik eine herausragende Rolle. Für den Neurologen in eigener Hand ermöglicht der Ultraschall nicht nur die Einschätzung der Gefäßsituation in der Primärprophylaxe, sondern selbstverständlich v. a. beim akuten Schlaganfall bei Beantwortung der Fragestellung hinsichtlich einer Thrombektomie oder Thrombolyse. Auch im Verlauf hilft der Ultraschall bei der ätiologischen Zuordnung und somit wichtige Therapieentscheidungen zu treffen. Hier sind neben arteriosklerotischen Obstruktionen insbesondere Dissektionen zu nennen. In der Zukunft wird aufgrund der neuen Studienlage pro invasiver Therapie auch die sonografische Detektion eines kardialen Rechts-Links-Shunts mittels transkranieller Doppler- oder Duplexsonografie von noch größerer Bedeutung sein. Nach therapeutischen Eingriffen insbesondere an der extrakraniellen Arteria carotis interna wird die Sonografie zur Beurteilung des Operations- oder Interventionsergebnisses und bei der Verlaufskontrolle genutzt. Ebenso gelingt mit dem Ultraschall auch die Verlaufsbeurteilung intrakranieller Stenosen. Wertvoll ist der transkranielle Ultraschall auch in der Diagnostik auf der Intensivstation, bspw. zur Detektion erhöhten Hirndrucks oder in der Hirntoddiagnostik. Andere Anwendungen sind bspw. die Detektion von intrakraniellen Vasospasmen nach Subarachnoidalblutungen, die Diagnostik von Vaskulitiden der hirnversorgenden Gefäße, und neuerdings auch der transorbitale Ultraschall bei ischämischen Ophthalmopathien. Therapeutisch wird der Ultraschall in der Neurologie bisher überwiegend auf wissenschaftlicher Basis im Rahmen von Studien zur Sonothrombolyse eingesetzt. Die Anwendung transkranieller Sonografie zeigte beim akuten Mediaverschluss eine höhere Rekanalisationsrate, es kam allerdings auch zu etwas häufigeren, statistisch nicht signifikanten symptomatischen Einblutungen. In den meisten Fällen ist bei der alltäglichen Anwendung der Duplexsonografie der Vorzug zu geben, aber auch die einfache Dopplersonografie gehört nach wie vor zum Standardrepertoire der meisten Ultraschallabore. In diesem Artikel möchten wir Ihnen über die wichtigsten Anwendungen des Ultraschalls in der Neurologie einen Überblick geben.
Quality of Life but not Cognition is Impacted by Radiotherapy in Patients with Non-Functioning Pituitary Adenoma
Authors: Crouzeix Genevieve , Morello Rémy , Thariat Juliette , Morera Julia , Joubert Michael , Reznik Yves 
Published: March 2019

AbstractNon-functioning pituitary adenomas (NFPA) are benign neoplasms that are first treated by surgery and secondary radiation therapy in case of residual tumor or regrowth. The consequences of surgery and radiotherapy are still debated. The objective of the work was to assess the impact of surgery, radiotherapy (RT) and pituitary deficiencies on long term health-related quality of life (QoL) and cognitive function among NFPA patients. Forty-six NFPA patients were studied after 9.6±7.5 years follow-up using: i) the MoCA questionnaire to detect mild cognitive disabilities, ii) the McNair and Kahn scale to assess perceived cognitive impairment, iii) the HADS questionnaire to score anxiety and depression, and iv) the SF-36 and QLS-H questionnaires to assess QoL. All NFPA patients had surgery and 54% patients had radiation therapy (RT+). The MoCA score was abnormal in 41% NFPA patients. Neither the type of surgery nor radiotherapy influenced the prevalence of cognitive disabilities. The depression score was higher in RT+than RT– patients. Overall, no alteration in SF-36 and QLS-H QoL scales were observed in NFPA patients when compared with the French reference population. Among NFPA patients, mental composite score, general health and vitality scores were altered in RT+compared to RT– patients. The presence of multiple pituitary axis deficiencies worsened general health and vitality scale scoring. Consistent follow-up had a beneficial impact on psycho-emotional dimensions of health. Surgery and radiotherapy had no adverse effects on cognitive functions, however, QoL was altered in RT+patients. These latter alterations may be partly related to pituitary hormone deficiencies.
Evaluation of Biochemical Conditions Allowing Bypass of Confirmatory Testing in The Workup of Primary Aldosteronism: A Retrospective Study in a French Hypertensive Population
Authors: Vivien Maud , Deberles Emilie , Morello Remy , Haddouche Aimi , Guenet David , Reznik Yves 
Published: March 2019

AbstractThe diagnostic workup for primary aldosteronism includes a screening step using the aldosterone-to-renin ratio (ARR) and a confirmatory step based on dynamic testing of aldosterone secretion autonomy. International guidelines suggest that precise clinical and biochemical conditions may allow the bypassing of the confirmatory step, however, data which validate hormone thresholds defining such conditions are lacking. At our tertiary center, we retrospectively examined a cohort of 173 hypertensive patients screened for PA by the ARR, of whom 120 had positive screening and passed a saline infusion test (SIT) or a captopril challenge test (CCT). Fifty-nine had PA, including 34 Conn adenomas and 25 with idiopathic aldosteronism (IA). Using a threshold of 160 pmol/l, post-SIT plasma aldosterone concentration (PAC) identified PA with 86.4% sensitivity, 94.7% specificity, and a negative predictive value of 92.3%. Of those subjects with a high ARR and a PAC above 550 pmol/l, 93% had a positive SIT, while 100% of subjects with a high ARR, but a PAC under 240 pmol/l had a negative SIT. Our results thus validate the biochemical conditions defined in the French and US guidelines for bypassing the confirmatory step in the workup for PA diagnosis.
Epithelial (E)-Cadherin is a Novel Mediator of Platelet Aggregation and Clot Stability
Authors: Scanlon Vanessa , Teixeira Alexandra , Tyagi Tarun , Zou Siying , Zhang Ping-Xia , Booth Carmen , Kowalska M. , Bao Jialing , Hwa John , Hayes Vincent , Marks Michael , Poncz Mortimer , Krause Diane 
Published: March 2019

AbstractCadherins play a major role in mediating cell–cell adhesion, which shares many parallels with platelet–platelet interactions during aggregate formation and clot stabilization. Platelets express epithelial (E)-cadherin, but its contribution to platelet function and/or platelet production is currently unknown. To assess the role of E-cadherin in platelet production and function in vitro and in vivo, we utilized a megakaryocyte-specific E-cadherin knockout mouse model. Loss of E-cadherin in megakaryocytes does not affect megakaryocyte maturation, platelet number or size. However, platelet dysfunction in the absence of E-cadherin is revealed when conditional knockout mice are challenged with acute antibody-mediated platelet depletion. Unlike wild-type mice that recover fully, knockout mice die within 72 hours post-antibody administration, likely from haemorrhage. Furthermore, conditional knockout mice have prolonged tail bleeding times, unstable clot formation, reduced clot retraction and reduced fibrin deposition in in vivo injury models. Murine platelet aggregation in vitro in response to thrombin and thrombin receptor activating peptide is compromised in E-cadherin null platelets, while aggregation in response to adenosine diphosphate (ADP) is not significantly different. Consistent with this, in vitro aggregation of primary human platelets in response to thrombin is decreased by an inhibitory E-cadherin antibody. Integrin activation and granule secretion in response to ADP and thrombin are not affected in E-cadherin null platelets, but Akt and glycogen synthase kinase 3β (GSK3β) activation are attenuated, suggesting a that E-cadherin contributes to aggregation, clot stabilization and retraction that is mediated by phosphoinositide 3-kinase/Akt/GSK3β signalling. In summary, E-cadherin plays a salient role in platelet aggregation and clot stability.
Toddlers and infants expect individuals to refrain from helping an ingroup victim’s aggressor
Authors: Ting Fransisca , He Zijing , Baillargeon Renée 
Published: March 2019

Significance
Adults are more likely to punish transgressions that do not affect them when these transgressions victimize ingroup members. Such third-party punishment (TPP) often takes an indirect form, such as the withholding of help. Building on these results, we showed 2.5- and 1-year-olds scenarios involving a wrongdoer, a victim, and a bystander, and we manipulated the minimal-group memberships of the wrongdoer and the victim relative to that of the bystander. When the victim belonged to the bystander’s group, children expected TPP: They detected a violation when the bystander chose to help the wrongdoer. When the victim did not belong to the bystander’s group, however, children no longer expected TPP. Young children thus selectively expect indirect TPP for harm to ingroup members.
Analysis of High School Physics National Examination questions based on Bloom Taxonomy and National Examination Question Standard in 2017/2018
Authors: Nurlailiyah A , Deta U A , Ain T N , Haq M S , Lestari N A , Yantidewi M 
Published: March 2019

Abstract
The National Examination is for measuring the success rate of student learning at school and mapping the quality of Education in Indonesia. To fulfill the objectives of the National Examination, an instrument is needed to represent the standards set by the Indonesian government. This research is a qualitative study that aims to analyze National Examination Questions in 2017/2018 based on Bloom’s taxonomy and National Examination Questions Standard. Data collected by analyzing the samples National Examination questions in 2017/2018 using operational verbs in Bloom’s taxonomy and grouping topics based the standard. Based on the research, it was found that most question is in the applying cognitive domain (C3), that is, 35 %, when the least question is in the creating cognitive domain (C6), that is, only 2.5%. According to the National Examination Questions Standard, the most topic in the National Examination in 2017/2018 are “Force and Motion” and “Electric, Magnet and Modern Physics” with the same amount of 22.5%. The National Examination Questions Standard is too general in writing down cognitive levels and the topics that appear on the question.
Behavioral diversity is maintained by a conditional strategy in a freshwater zooplankton
Authors: Meyer G Adam , Nelson William A 
Published: March 2019

AbstractMany populations have intraspecific diversity in phenotype and ecological strategy, but the mechanisms maintaining such diversity are not fully understood. Multiple behaviors can be maintained either as a conditional strategy, where fitness depends on an individual’s phenotype, or as a mixed strategy, where alternative behaviors have similar fitness independent of phenotype. Using high-resolution depth and time sampling, we characterize 2 distinct diel vertical migration behaviors in a population of freshwater zooplankton (Daphnia pulicaria). Individuals in this population differ in their color phenotype and migratory behavior with red morphs upregulating hemoglobin and undergoing a deep migration and pale morphs not producing hemoglobin and undergoing a shallow migration. We experimentally manipulated the behavior of each phenotype in the field and measured population growth in their natural migration behavior as well as population growth in their alternative behaviors. Experimental populations of pale and red morphs under their natural migrations had roughly equal fitness, despite vast differences in environmental conditions. When forced to switch behaviors, pale morphs suffered reduced fitness, whereas red morphs had similar fitness compared with their natural migration. Our results suggest that although behavioral diversity may be promoted by the opportunity for alternative behaviors of equal fitness, the distinct physiological conditions required for survival in alternative behaviors limit the capacity for individual behavioral switching and likely maintain behavioral diversity as a conditional strategy.
100 Years of evolving gene–disease complexities and scientific debutants
Authors: Zeeshan Saman , Xiong Ruoyun , Liang Bruce T , Ahmed Zeeshan 
Published: March 2019

AbstractIt’s been over 100 years since the word `gene’ is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it’s about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene–disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene–disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene–disease data.
Multiresolution correction of GC bias and application to identification of copy number alterations
Authors: Jang Ho , Lee Hyunju 
Published: March 2019

Abstract

Motivation
Whole-genome sequencing (WGS) data are affected by various sequencing biases such as GC bias and mappability bias. These biases degrade performance on detection of genetic variations such as copy number alterations. The existing methods use a relation between the GC proportion and depth of coverage (DOC) of markers by means of regression models. Nonetheless, severity of the GC bias varies from sample to sample. We developed a new method for correction of GC bias on the basis of multiresolution analysis. We used a translation-invariant wavelet transform to decompose biased raw signals into high- and low-frequency coefficients. Then, we modeled the relation between GC proportion and DOC of the genomic regions and constructed new control DOC signals that reflect the GC bias. The control DOC signals are used for normalizing genomic sequences by correcting the GC bias.

Results
When we applied our method to simulated sequencing data with various degrees of GC bias, our method showed more robust performance on correcting the GC bias than the other methods did. We also applied our method to real-world cancer sequencing datasets and successfully identified cancer-related focal alterations even when cancer genomes were not normalized to normal control samples. In conclusion, our method can be employed for WGS data with different degrees of GC bias.

Availability and implementation
The code is available at http://gcancer.org/wabico.

Supplementary information
Supplementary data are available at Bioinformatics online.
CABS-dock standalone: a toolbox for flexible protein–peptide docking
Authors: Kurcinski Mateusz , Pawel Ciemny Maciej , Oleniecki Tymoteusz , Kuriata Aleksander , Badaczewska-Dawid Aleksandra E , Kolinski Andrzej , Kmiecik Sebastian 
Published: March 2019

Abstract

Summary
CABS-dock standalone is a multiplatform Python package for protein–peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein–peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation—it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results.

Availability and implementation
CABS-dock standalone is distributed under the MIT licence, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use and installation instructions for Linux, macOS and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/cabsdock.
GToTree: a user-friendly workflow for phylogenomics
Authors: Lee Michael D 
Published: March 2019

Abstract

Summary
Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required—such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.—can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.

Availability and implementation
GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python.

Supplementary information
Supplementary data are available at Bioinformatics online.