bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interior permanent magnet motor‐based isolated on‐board integrated battery charger for electric vehicles
Authors: Abdel‐Khalik Ayman S. , Massoud Ahmed , Ahmed Shehab 
Published: September 2017

This study proposes an isolated on‐board integrated battery charger using an interior permanent magnet (IPM) machine with a nine‐slot/eight‐pole combination or its multiples, and equipped with a non‐overlapped fractional slot concentrated winding. The proposed winding layout comprises three three‐phase winding sets that are connected in such a way as to provide six motor terminals. Hence, a six‐phase or two three‐phase converters will be required for propulsion. Under motoring mode, the machine can be effectively regarded as a six‐phase machine, which provides a high fault‐tolerant capability, and allows for a ‘limp home’ mode of operation. Additionally, all magneto motive force subharmonics are eliminated, which significantly reduces the induced rotor eddy current losses, when compared with a conventional three‐phase motor having the same slot/pole combination. In battery charging mode, the winding is reconfigured, so that the machine is considered as a three‐phase to six‐phase rotating transformer. A 40 kW IPM machine is designed and simulated under different modes of operation using two‐dimensional finite element analysis to validate the proposed concept. A small‐scale prototype machine is also used for experimental validation.
Improved component compensation for geomagnetic field vector measurement using Lagrange multiplier method
Authors: Wan Chengbiao , Pan Mengchun , Zhang Qi , Pang Hongfeng , Zhu Xuejun , Pan Long , Sun Xiaoyong , Wu Fenghe 
Published: September 2017

Owing to the ferromagnetism and stray fields of inertial navigation system, component compensation of magnetic field distortion is significant for geomagnetic field vector measurement system. However, traditional scalar compensation methods cannot be used for component compensation of magnetic field distortion, so some improvement works have been researched for component compensation in the study, the major of which is estimating compensation parameters using the Lagrange multiplier method. Experiment results show that the performance of the component compensation method is much better than traditional scalar compensation method. After compensation, the maximal measurement errors of north, vertical, east components and total intensity caused by magnetic field distortion are reduced to 10.4 nT (0.91% of the raw error), 32.5 nT (5.20%), 12.9 nT (1.27%), and 18.4 nT (2.02%), respectively. In addition, compared with previous component compensation method, the proposed method has three advantages: (i) simplified equipment, (ii) easier operation process, and (iii) better generality.
Provider and Patient Knowledge and Views of Office Practices on Weight Gain and Exercise during Pregnancy
Authors: Delgado Arlin , Stark Lauren , Macri Charles , Power Michael , Schulkin Jay 
Published: September 2017

Objective This study sought to assess provider and patient knowledge and beliefs on gestational weight gain (GWG) and exercise during pregnancy, outline current clinical practices and the perceived value of educational tools.
Study Design Providers and patients at the George Washington Medical Faculty Associates Obstetricians and Gynecologists clinic were recruited for a voluntary survey. Descriptive statistics of responses were compared and chi-square analysis tested for significant associations.
Results A total of 461 patient and 36 provider questionnaires were analyzed. Providers recommended GWG consistent with the Institute of Medicine guidelines for a “normal” body mass index (82.9%); however, a majority (52.8%) recommended GWG below guidelines for obese women. All providers reported counseling patients on GWG, but only 53.4% of patients reported discussing personal recommendations. About half of providers reported distributing educational materials for GWG (60.0%); however, only 30.6% of patients reported receiving them. African American patients self-reported receiving the highest rates of counseling and educational materials, though a lower rate of recommendations to exercise. Patients perceived educational tools to be more useful than did providers.
Conclusion Our findings suggest a gap between provider–patient perceptions regarding counseling and provision of informational materials. Future research should study whether implementing various educational tools might increase the efficacy of current practices.
Organinteraktionen: Herz und Lunge – Management des akuten Rechtsherzversagens
Authors: Michels Guido , Pfister Roman 
Published: September 2017

AbstractThe pathophysiology and the management of patients with acute right heart failure are very complex. The bed-side focused echocardiography is the basis of differential diagnosis and acute diagnosis. Individual therapy monitoring is complex due to the strong preload dependence of the right ventricle and the limitation of non-invasive estimation of pulmonary-vascular hemodynamics, so that the indication for a pulmonary artery catheter should be liberal in acute right heart failure. The treatment goals of acute right heart failure are the treatment of the underlying disease or triggering factors in combination with individualized optimization of hemodynamic tailored to current right-ventricular function.
Niereninsuffizienz und Dialyse
Authors: Stracke Sylvia 
Published: September 2017

ZUSAMMENFASSUNGGeschlechtsspezifische Unterschiede spielen bei vielen Erkrankungen eine Rolle, so auch bei der chronischen Niereninsuffizienz (CKD). Frauen
und Männer unterscheiden sich hinsichtlich der zugrunde liegenden Pathophysiologie der Erkrankungen, die zur CKD geführt haben und auch
hinsichtlich der Ausprägung der Urämie assoziierten Zweiterkrankungen sowie hinsichtlich des Therapieansprechens und der
Krankheitsbewältigung. Auch beim Outcome und dem Management der Dialysetherapie gibt es Unterschiede zwischen Frauen und Männern. Es muss
unterschieden werden, ob es sich um biologische, psychosoziale oder ökonomische Faktoren handelt. In den Leitlinien wird bislang nicht auf
geschlechtsspezifische Unterschiede bei CKD und/oder Dialyse eingegangen. Generelle Schwierigkeiten umfassen neben einem „Neglect“ oben
genannter Umstände auch die Tatsache, dass in großen randomisierten, nephrologischen Studien Frauen oftmals nicht eingeschlossen wurden. In
einigen Fällen haben neue Erkenntnisse auf dem Gebiet der geschlechtsspezifischen Unterschiede bei CKD zur Entdeckung neuer
pathophysiologischer Zusammenhänge und zu Verbesserungen in der Therapie geführt.
Neurografie ist mehr als die Nervenleitgeschwindigkeit
Authors: Lieba-Samal Doris 
Published: September 2017

ZusammenfassungIm deutschen Sprachgebrauch wird „Nervenleitgeschwindigkeitsuntersuchung“ oder überhaupt nur „das NLG“ häufig synonym verwendet für die Neurografie. Der Artikel ruft in Erinnerung, dass die berühmte NLG zwar eine wichtige Größe ist, aber bei weitem nicht die einzige, die es im Rahmen dieser Untersuchung zu beurteilen gilt. Für jede Messgröße der Neurografie wird die mögliche Aussagekraft sowie die Grenzen der Methodik beleuchtet und im Zusammenhang mit existierender Literatur besprochen.
E46K α-synuclein pathological mutation causes cell-autonomous toxicity without altering protein turnover or aggregation
Authors: Íñigo-Marco Ignacio , Valencia Miguel , Larrea Laura , Bugallo Ricardo , Martínez-Goikoetxea Mikel , Zuriguel Iker , Arrasate Montserrat 
Published: September 2017

Significance
α-Synuclein (aSyn) plays a key role in neurodegenerative disorders known as “synucleinopathies.“ By tracking individual primary neurons overexpressing wild-type and mutant aSyn versions we have determined how pathological hallmarks like alterations in aSyn expression and stability, aggregation, or serine 129 phosphorylation (PS129) contribute to neuronal death. We have found that the E46K mutant displayed the highest toxicity. Neurotoxicity was independent of aggregation but correlated with PLK2-dependent PS129. Surprisingly, inhibiting PS129 did not affect neuronal survival, suggesting that this modification is an epiphenomenon. Finally, we set up an assay to score for cell-autonomous and nonautonomous toxicity. While we identified a minor non–cell-autonomous component restricted to proximal neurons, E46K toxicity was mostly cell autonomous.
Prior expectations induce prestimulus sensory templates
Authors: Kok Peter , Mostert Pim , de Lange Floris P. 
Published: September 2017

Significance
The way that we perceive the world is partly shaped by what we expect to see at any given moment. However, it is unclear how this process is neurally implemented. Recently, it has been proposed that the brain generates stimulus templates in sensory cortex to preempt expected inputs. Here, we provide evidence that a representation of the expected stimulus is present in the neural signal shortly before it is presented, showing that expectations can indeed induce the preactivation of stimulus templates. Importantly, these expectation signals resembled the neural signal evoked by an actually presented stimulus, suggesting that expectations induce similar patterns of activations in visual cortex as sensory stimuli.
The development of iconicity in children’s co-speech gesture and homesign
Authors: Cartmill Erica A. , Rissman Lilia , Novack Miriam A. , Goldin-Meadow Susan 
Published: September 2017

AbstractGesture can illustrate objects and events in the world by iconically reproducing elements of those objects and events. Children do not begin to express ideas iconically, however, until after they have begun to use conventional forms. In this paper, we investigate how children’s use of iconic resources in gesture relates to the developing structure of their communicative systems. Using longitudinal video corpora, we compare the emergence of manual iconicity in hearing children who are learning a spoken language (co-speech gesture) to the emergence of manual iconicity in a deaf child who is creating a manual system of communication (homesign). We focus on one particular element of iconic gesture – the shape of the hand (handshape). We ask how handshape is used as an iconic resource in 1–5-year-olds, and how it relates to the semantic content of children’s communicative acts. We find that patterns of handshape development are broadly similar between co-speech gesture and homesign, suggesting that the building blocks underlying children's ability to iconically map manual forms to meaning are shared across different communicative systems: those where gesture is produced alongside speech, and those where gesture is the primary mode of communication.
Developing communicative postures
Authors: Beaupoil-Hourdel Pauline , Debras Camille 
Published: September 2017

AbstractThis article analyses the development of a composite communicative posture, the shrug (which can combine palm-up flips, lifted shoulders and a head tilt), in a video corpus of spontaneous interactions between a typically developing British girl, Ellie, and her mother, filmed at home one hour each month from Ellie’s tenth month to her fourth birthday. The systematic coding of every shrug yields a total of 124 tokens (Ellie: 98; her mother: 26), providing results in terms of forms, functions and input. Ellie’s first shrug components emerge from non-linguistic actions and she acquires them one at a time starting with the hands: these features recall the development of complex signs among deaf children of the same age (Reilly & Anderson, 2002for ASL). The functions of Ellie’s shrugs gradually diversify from the expression of absence at 1;04 to other epistemic and non-epistemic meanings (affective and dynamic). Adult intervention plays a crucial role as adults recurrently equate Ellie’s physical movements with speech, thereby contributing to the emergence of their communicative functions as gestural emblems (Ekman & Friesen, 1969).
JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts
Authors: Chatzinakos Chris , Lee Donghyung , Webb Bradley T , Vladimirov Vladimir I , Kendler Kenneth S , Bacanu Silviu-Alin 
Published: September 2017

AbstractMotivationTo increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our Gene-level Joint Analysis of functional SNPs in Cosmopolitan Cohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals.ResultsWe propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q-values based on Holm adjustment of P-values.Availability and implementationhttps://github.com/Chatzinakos/JEPEGMIX2.Supplementary informationSupplementary data are available at Bioinformatics online.
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants
Authors: Basile Anna O , Byrska-Bishop Marta , Wallace John , Frase Alexander T , Ritchie Marylyn D 
Published: September 2017

Abstract

Motivation
BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements.

Results
In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool.

Availability and implementation
The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download

Supplementary information
Supplementary data are available at Bioinformatics online.
PySCeSToolbox: a collection of metabolic pathway analysis tools
Authors: Christensen Carl D , Hofmeyr Jan-Hendrik S , Rohwer Johann M 
Published: September 2017

Abstract

Summary
PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalized supply–demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects of enzyme-catalyzed reactions. Each tool addresses a different aspect of metabolic behaviour, control, and regulation; the tools complement each other and can be used in conjunction to better understand higher level system behaviour.

Availability and implementation
PySCeSToolbox is available on Linux, Mac OS X and Windows. It is licensed under the BSD 3-clause licence. Code, setup instructions and a link to documentation can be found at https://github.com/PySCeS/PyscesToolbox.

Supplementary information
Supplementary data are available at Bioinformatics online.
Applying family analyses to electronic health records to facilitate genetic research
Authors: Huang Xiayuan , Elston Robert C , Rosa Guilherme J , Mayer John , Ye Zhan , Kitchner Terrie , Brilliant Murray H , Page David , Hebbring Scott J 
Published: September 2017

Abstract

Motivation
Pedigree analysis is a longstanding and powerful approach to gain insight into the underlying genetic factors in human health, but identifying, recruiting and genotyping families can be difficult, time consuming and costly. Development of high throughput methods to identify families and foster downstream analyses are necessary.

Results
This paper describes simple methods that allowed us to identify 173 368 family pedigrees with high probability using basic demographic data available in most electronic health records (EHRs). We further developed and validate a novel statistical method that uses EHR data to identify families more likely to have a major genetic component to their diseases risk. Lastly, we showed that incorporating EHR-linked family data into genetic association testing may provide added power for genetic mapping without additional recruitment or genotyping. The totality of these results suggests that EHR-linked families can enable classical genetic analyses in a high-throughput manner.

Availability and implementation
Pseudocode is provided as supplementary information

Supplementary information
Supplementary data are available at Bioinformatics online.
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling
Authors: Boloc Daniel , Rodríguez Natalia , Gassó Patricia , Abril Josep F , Bernardo Miquel , Lafuente Amalia , Mas Sergi 
Published: September 2017

Abstract

Motivation
The selection of a single nucleotide polymorphism (SNP) using bibliographic methods can be a very time-consuming task. Moreover, a SNP selected in this way may not be easily visualized in its genomic context by a standard user hoping to correlate it with other valuable information. Here we propose a web form built on top of Circos that can assist SNP-centered screening, based on their location in the genome and the regulatory modules they can disrupt. Its use may allow researchers to prioritize SNPs in genotyping and disease studies.

Results
SiNoPsis is bundled as a web portal. It focuses on the different structures involved in the genomic expression of a gene, especially those found in the core promoter upstream region. These structures include transcription factor binding sites (for promoter and enhancer signals), histones and promoter flanking regions. Additionally, the tool provides eQTL and linkage disequilibrium (LD) properties for a given SNP query, yielding further clues about other indirectly associated SNPs. Possible disruptions of the aforementioned structures affecting gene transcription are reported using multiple resource databases. SiNoPsis has a simple user-friendly interface, which allows single queries by gene symbol, genomic coordinates, Ensembl gene identifiers, RefSeq transcript identifiers and SNPs. It is the only portal providing useful SNP selection based on regulatory modules and LD with functional variants in both textual and graphic modes (by properly defining the arguments and parameters needed to run Circos).

Availability and implementation
SiNoPsis is freely available at https://compgen.bio.ub.edu/SiNoPsis/

Supplementary information
Supplementary data are available at Bioinformatics online.
Kfits: a software framework for fitting and cleaning outliers in kinetic measurements
Authors: Rimon Oded , Reichmann Dana 
Published: September 2017

Abstract

Motivation
Kinetic measurements have played an important role in elucidating biochemical and biophysical phenomena for over a century. While many tools for analysing kinetic measurements exist, most require low noise levels in the data, leaving outlier measurements to be cleaned manually. This is particularly true for protein misfolding and aggregation processes, which are extremely noisy and hence difficult to model. Understanding these processes is paramount, as they are associated with diverse physiological processes and disorders, most notably neurodegenerative diseases. Therefore, a better tool for analysing and cleaning protein aggregation traces is required.

Results
Here we introduce Kfits, an intuitive graphical tool for detecting and removing noise caused by outliers in protein aggregation kinetics data. Following its workflow allows the user to quickly and easily clean large quantities of data and receive kinetic parameters for assessment of the results. With minor adjustments, the software can be applied to any type of kinetic measurements, not restricted to protein aggregation.

Availability and implementation
Kfits is implemented in Python and available online at http://kfits.reichmannlab.com, in source at https://github.com/odedrim/kfits/, or by direct installation from PyPI (`pip install kfits`)

Supplementary information
Supplementary data are available at Bioinformatics online.
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC
Authors: Liu Bin , Yang Fan , Huang De-Shuang , Chou Kuo-Chen 
Published: September 2017

Abstract

Motivation
Being responsible for initiating transaction of a particular gene in genome, promoter is a short region of DNA. Promoters have various types with different functions. Owing to their importance in biological process, it is highly desired to develop computational tools for timely identifying promoters and their types. Such a challenge has become particularly critical and urgent in facing the avalanche of DNA sequences discovered in the postgenomic age. Although some prediction methods were developed, they can only be used to discriminate a specific type of promoters from non-promoters. None of them has the ability to identify the types of promoters. This is due to the facts that different types of promoters may share quite similar consensus sequence pattern, and that the promoters of same type may have considerably different consensus sequences.

Results
To overcome such difficulty, using the multi-window-based PseKNC (pseudo K-tuple nucleotide composition) approach to incorporate the short-, middle-, and long-range sequence information, we have developed a two-layer seamless predictor named as ‘iPromoter-2 L’. The first layer serves to identify a query DNA sequence as a promoter or non-promoter, and the second layer to predict which of the following six types the identified promoter belongs to: σ24, σ28, σ32, σ38, σ54 and σ70.

Availability and implementation
For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the powerful new predictor has been established at http://bioinformatics.hitsz.edu.cn/iPromoter-2L/. It is anticipated that iPromoter-2 L will become a very useful high throughput tool for genome analysis.

Supplementary information
Supplementary data are available at Bioinformatics online.