bluuebunny/crossref_metadata_2025 huggingface dataset:
Multilevel inverter for interfacing renewable energy sources with low/medium‐ and high‐voltage grids
Authors: Agrawal Rekha , Jain Shailendra
Published: September 2017

This study presents a new multilevel inverter (MLI) with reduced devices, for low/medium‐ and high‐voltage applications. The proposed MLI is evolved from existing cross‐connected source‐based multilevel inverter (CCS‐MLI), results in reduced switches, driver circuits, diodes, and DC voltage sources when compared with the classical CHB, CCS‐MLI, and other MLIs. Owing to reduced device numbers, the complexity, size, cost, and maintenance of the proposed topology are greatly reduced. The detailed analysis and working of the proposed topology is presented along with its comparison with classical, CCS‐MLI, and other MLIs. Different algorithms are presented for selecting appropriate magnitudes of DC voltage sources to generate different voltage levels in the output. The proposed MLI is suitable for grid integration of renewable energy sources. The concept is presented through modelling and simulation in MATLAB/Simulation environment and validated through real‐time simulator OPAL‐RT (OP‐4500).
Efficient SPF approach based on regression and correction models for active distribution systems
Authors: Mahmoud Karar , Abdel‐Nasser Mohamed
Published: September 2017

This study proposes efficient methods for sequential power flow (SPF) analysis of distribution systems with intermittent photovoltaic (PV) units and fluctuated loads. The proposed methods are based on machine learning techniques; more specifically, they use a regression trees (RTs) algorithm to construct a model for voltage estimation. This model is trained using synthetic data generated by a number of PV generation and load demand scenarios. The SPF methods that utilise iterative techniques have a high computational burden. In turn, the proposed method, which is called SPF‐RT, is fast and accurate. Furthermore, the authors combine SPF‐RT with a correction method to develop a new method, called SPF‐RTC, which significantly reduces the estimation error of the RT model. The proposed methods are tested using a 33‐bus distribution test system interconnected with two PV units. To assess the performance of the proposed methods, they conducted several experiments at different resolutions of day/year data. The proposed methods are compared with the iterative SPF methods and validated using the OpenDSS software. The simulation results demonstrate that the proposed methods outperform the other methods in terms of the computational speed. The SPF‐RT and SPF‐RTC methods are useful for real‐time assessment of distribution systems with PV units.
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

The 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

Geschlechtsspezifische 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

Im 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.
Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs
Authors: Liu Kuan-Yu , Herbert John M.
Published: September 2017

Papers I and II in this series [R. M. Richard et al., J. Chem. Phys. 141, 014108 (2014); K. U. Lao et al., ibid. 144, 164105 (2016)] have attempted to shed light on precision and accuracy issues affecting the many-body expansion (MBE), which only manifest in larger systems and thus have received scant attention in the literature. Many-body counterpoise (CP) corrections are shown to accelerate convergence of the MBE, which otherwise suffers from a mismatch between how basis-set superposition error affects subsystem versus supersystem calculations. In water clusters ranging in size up to (H2O)37, four-body terms prove necessary to achieve accurate results for both total interaction energies and relative isomer energies, but the sheer number of tetramers makes the use of cutoff schemes essential. To predict relative energies of (H2O)20 isomers, two approximations based on a lower level of theory are introduced and an ONIOM-type procedure is found to be very well converged with respect to the appropriate MBE benchmark, namely, a CP-corrected supersystem calculation at the same level of theory. Results using an energy-based cutoff scheme suggest that if reasonable approximations to the subsystem energies are available (based on classical multipoles, say), then the number of requisite subsystem calculations can be reduced even more dramatically than when distance-based thresholds are employed. The end result is several accurate four-body methods that do not require charge embedding, and which are stable in large basis sets such as aug-cc-pVTZ that have sometimes proven problematic for fragment-based quantum chemistry methods. Even with aggressive thresholding, however, the four-body approach at the self-consistent field level still requires roughly ten times more processors to outmatch the performance of the corresponding supersystem calculation, in test cases involving 1500–1800 basis functions.
Resonant tunneling and multiple negative differential conductance features in long wavelength interband cascade infrared photodetectors
Authors: Lei Lin , Li Lu , Huang Wenxiang , Massengale Jeremy A. , Ye Hao , Lotfi Hossein , Yang Rui Q. , Mishima Tetsuya D. , Santos Michael B. , Johnson Matthew B.
Published: September 2017

We report on an investigation of multiple negative differential conductance (NDC) features in long wavelength interband cascade infrared photodetectors (ICIPs) at and above 300 K. Using ICIPs with various structures and carrier concentrations, we employ several approaches to demonstrate that the observed multiple NDC features and their unusual temperature dependence are related to the sequential turn off of resonant tunneling of minority carriers through the electron barriers at high temperatures.
Photo-physical properties of He-related color centers in diamond
Authors: Prestopino G. , Marinelli M. , Milani E. , Verona C. , Verona-Rinati G. , Traina P. , Moreva E. , Degiovanni I. P. , Genovese M. , Ditalia Tchernij S. , Picollo F. , Olivero P. , Forneris J.
Published: September 2017

Diamond is a promising platform for the development of technological applications in quantum optics and photonics. The quest for color centers with optimal photo-physical properties has led in recent years to the search for novel impurity-related defects in this material. Here, we report on a systematic investigation of the photo-physical properties of two He-related (HR) emission lines at 535.2 nm and 559.7 nm (as measured at a temperature of 25 K) created in three different diamond substrates upon implantation with 1.3 MeV He+ ions and subsequent annealing. The spectral features of the HR centers were studied in an “optical grade” diamond substrate as a function of several physical parameters, namely, the measurement temperature, the excitation wavelength, and the intensity of external electric fields. The emission lifetimes of the 535.2 nm and 559.7 nm lines were also measured by means of time-gated photoluminescence measurements. The Stark shifting of the HR centers under the application of an external electrical field was observed in a CVD diamond film equipped with buried graphitic electrodes, suggesting the lack of inversion symmetry in the defects' structure. Furthermore, the photoluminescence mapping under 405 nm excitation of a “detector grade” diamond sample implanted at a He+ ion fluence of 1 × 1010 cm−2 enabled us to identify the spectral features of both the HR emission lines from the same localized optical spots. The reported results provide an insight into the structure of He-related defects in diamond and their possible utilization in practical applications.
Plasma sheath: An equivalent nonlinear mirror between electron density and transmitted electromagnetic signal
Authors: Yao Bo , Li Xiaoping , Shi Lei , Liu Yanming , Lei Fan , Zhu Congying
Published: September 2017

An experiment on the propagation of electromagnetic (EM) signals in continuous time-varying plasma is designed to establish the nonlinear mirror between electron density and transmission coefficient. The nonlinearity is confirmed from the theoretical and experimental results. The amplitude and phase can be considered nonlinear functions of electron density when the complex interaction between plasma and EM waves is ignored. Results show that amplitude and phase distributions are asymmetrical when electron density follows symmetric distribution. The skewness of amplitude is positive, whereas the skewness of phase is negative. The nonlinear degree is closely related to the ratio of plasma frequency to the incident wave frequency and the range of electron density. The conclusions are crucial to the modeling of plasma sheath channels and understanding the blackout problem.
Polaronic transport in Ag-based quaternary chalcogenides
Authors: Wei Kaya , Khabibullin Artem R. , Stedman Troy , Woods Lilia M. , Nolas George S.
Published: September 2017

Low temperature resistivity measurements on dense polycrystalline quaternary chalcogenides Ag2+xZn1-xSnSe4, with x = 0, 0.1, and 0.3, indicate polaronic type transport which we analyze employing a two-component Holstein model based on itinerant and localized polaron contributions. Electronic structure property calculations via density functional theory simulations on Ag2ZnSnSe4 for both energetically similar kesterite and stannite structure types were also performed in order to compare our results to those of the compositionally similar but well known Cu2ZnSnSe4. This theoretical comparison is crucial in understanding the bonding that results in polaronic type transport for Ag2ZnSnSe4, as well as the structural and electronic properties of both crystal structure types. In addition to possessing this unique electronic transport, the thermal conductivity of Ag2ZnSnSe4 is low and decreases with increasing silver content. This work reveals unique structure-property relationships in materials that continue to be of interest for thermoelectric and photovoltaic applications.
Index finger motor imagery EEG pattern recognition in BCI applications using dictionary cleaned sparse representation-based classification for healthy people
Authors: Miao Minmin , Zeng Hong , Wang Aimin , Zhao Fengkui , Liu Feixiang
Published: September 2017

Electroencephalogram (EEG)-based motor imagery (MI) brain-computer interface (BCI) has shown its effectiveness for the control of rehabilitation devices designed for large body parts of the patients with neurologic impairments. In order to validate the feasibility of using EEG to decode the MI of a single index finger and constructing a BCI-enhanced finger rehabilitation system, we collected EEG data during right hand index finger MI and rest state for five healthy subjects and proposed a pattern recognition approach for classifying these two mental states. First, Fisher’s linear discriminant criteria and power spectral density analysis were used to analyze the event-related desynchronization patterns. Second, both band power and approximate entropy were extracted as features. Third, aiming to eliminate the abnormal samples in the dictionary and improve the classification performance of the conventional sparse representation-based classification (SRC) method, we proposed a novel dictionary cleaned sparse representation-based classification (DCSRC) method for final classification. The experimental results show that the proposed DCSRC method gives better classification accuracies than SRC and an average classification accuracy of 81.32% is obtained for five subjects. Thus, it is demonstrated that single right hand index finger MI can be decoded from the sensorimotor rhythms, and the feature patterns of index finger MI and rest state can be well recognized for robotic exoskeleton initiation.
New radiographic image processing for fusion experiments
Authors: Kim Meeri
Published: September 2017

Researchers present a radiographic image processing method that removes the backlighter contribution in laser shock-tube experiments.
Laser-Assisted Stark Deceleration of Polar Molecules HC2n+1N (n=2, 3, 4) in High-Field-Seeking State
Authors: Chen Kai , Huang Yun-xia , Yang Xiao-hua
Published: September 2017

Laser-assisted Stark deceleration scheme was proposed to decelerate the high-field-seeking molecule ICl in its rovibronic ground state. However, the laser intensity of 1.0×1010 W/cm2 is hard to realize in experiment. The time-of-flight signals of HC2n+1N (n=2, 3 and 4) by three-dimensional Monte-Carlo simulation suggest that deceleration of such molecules is more feasible experimentally as only one-tenth laser intensity is needed.
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

Gesture 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

This 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).
Dating violence in young Mexican couples: a dyadic analysis / Agresiones en el noviazgo de universitarios mexicanos: un análisis diádico
Authors: Rojas-Solís José-Luis , Fuertes-Martín José-Antonio , Orgaz-Baz María-Begoña
Published: September 2017

This study analyses the frequency, perception, bidirectionality and degree of agreement in the occurrence of aggression committed and suffered in 100 heterosexual couples. The selection of the sample was non-probabilistic, with 100 Mexican male-and-female dyads (age range 18 to 25). We used a virtual questionnaire which evaluated the frequency of psychological, mild physical and sexual aggression committed and suffered by each member of the dyads. Psychological aggression was the most frequent, and no significant differences were found by sex except in sexual aggression committed by men. The women more often underestimated both the aggression they suffered from and that which they committed, primarily sexual aggression. Bidirectionality was found in all three kinds of aggression, and there was greater agreement between couples when the women were the aggressors than when the men were the perpetrators. More studies are needed on couple violence that include the perspective of both members of the dyad.
The Volterra Principle Generalized
Authors: Räz Tim
Published: September 2017

Michael Weisberg and Kenneth Reisman argue that the Volterra Principle can be derived from multiple predator-prey models and that, therefore, the Volterra Principle is a prime example for robustness analysis. In the current article, I give new results regarding the Volterra Principle, extending Weisberg’s and Reisman’s work, and I discuss the consequences of these results for robustness analysis. I argue that we do not end up with multiple, independent models but rather with one general model. I identify the kind of situation in which this generalization approach may occur, and I analyze the generalized Volterra Principle from an explanatory perspective.
Values and Data Collection in Social Research
Authors: Zahle Julie
Published: September 2017

In this article, I offer a partial analysis of the role of values in qualitative data collection in social research. The partial analysis shows that nonepistemic values have both required and permissible roles to play during this phase of research. By appeal to the analysis, I reject the ideal of value-free science as applied to qualitative data collection, and I demonstrate why two alternative ideals should likewise be dismissed as standards for values in qualitative data collection. Also, I briefly discuss the extent to which the partial analysis carries over to quantitative data collection in social research.
Inductive Risk and Regulatory Toxicology: A Comment on de Melo-Martín and Intemann
Authors: Hicks Daniel J.
Published: September 2017

Inmaculada de Melo-Martín and Kristen Intemann consider whether, from the perspective of the argument from inductive risk, ethical and political values might be logically, epistemically, pragmatically, or ethically necessary in the “core” of scientific reasoning. In each case, they argue that there are significant conceptual problems. In this comment, employing regulatory uses of high-throughput toxicology at the US Environmental Protection Agency as a case study, I respond to some of their claims about the notion of “pragmatic necessity.” I conclude that, while an inductive risk framework has some significant limitations, it is still conceptually and rhetorically valuable.
Letting Go of “Natural Kind”: Toward a Multidimensional Framework of Nonarbitrary Classification
Authors: Ludwig David
Published: September 2017

This article uses the case study of ethnobiological classification to develop a positive and a negative thesis about the state of natural kind debates. On the one hand, I argue that current accounts of natural kinds can be integrated in a multidimensional framework that advances understanding of classificatory practices in ethnobiology. On the other hand, I argue that such a multidimensional framework does not leave any substantial work for the notion “natural kind” and that attempts to formulate a general account of naturalness have become an obstacle to understanding classificatory practices.
Bayes, Bounds, and Rational Analysis
Authors: Icard Thomas F.
Published: September 2017

While Bayesian models have been applied to an impressive range of cognitive phenomena, methodological challenges have been leveled concerning their role in the program of rational analysis. The focus of the current article is on computational impediments to probabilistic inference and related puzzles about empirical confirmation of these models. The proposal is to rethink the role of Bayesian methods in rational analysis, to adopt an independently motivated notion of rationality appropriate for computationally bounded agents, and to explore broad conditions under which (approximately) Bayesian agents would be rational. The proposal is illustrated with a characterization of costs inspired by thermodynamics.
Evolution of polymer formation within the actin superfamily
Authors: Stoddard Patrick R. , Williams Tom A. , Garner Ethan , Baum Buzz
Published: September 2017

While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes. It is not known whether these polymers descended from a single ancestral polymer or arose multiple times by convergent evolution from monomeric actin-like proteins. In this work, we provide an overview of the structures, dynamics, and functions of this diverse set. Then, using a phylogenetic analysis to examine actin evolution, we show that the actin-related protein families that form polymers are more closely related to one another than they are to other nonpolymerizing members of the actin superfamily. Thus all the known actin-like polymers are likely to be the descendants of a single, ancestral, polymer-forming actin-like protein.
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

Motivation

To 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.

Results

We 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 implementation

https://github.com/Chatzinakos/JEPEGMIX2.

Supplementary information

Supplementary 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

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

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

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

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

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

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.
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome
Authors: Alvarez Roberto Vera , Li Shan , Landsman David , Ovcharenko Ivan
Published: September 2017

Addressing deleterious effects of noncoding mutations is an essential step towards the identification of disease-causal mutations of gene regulatory elements. Several methods for quantifying the deleteriousness of noncoding mutations using artificial intelligence, deep learning and other approaches have been recently proposed. Although the majority of the proposed methods have demonstrated excellent accuracy on different test sets, there is rarely a consensus. In addition, advanced statistical and artificial learning approaches used by these methods make it difficult porting these methods outside of the labs that have developed them. To address these challenges and to transform the methodological advances in predicting deleterious noncoding mutations into a practical resource available for the broader functional genomics and population genetics communities, we developed SNPDelScore, which uses a panel of proposed methods for quantifying deleterious effects of noncoding mutations to precompute and compare the deleteriousness scores of all common SNPs in the human genome in 44 cell lines. The panel of deleteriousness scores of a SNP computed using different methods is supplemented by functional information from the GWAS Catalog, libraries of transcription factor-binding sites, and genic characteristics of mutations. SNPDelScore comes with a genome browser capable of displaying and comparing large sets of SNPs in a genomic locus and rapidly identifying consensus SNPs with the highest deleteriousness scores making those prime candidates for phenotype-causal polymorphisms.

Availability and implementation

https://www.ncbi.nlm.nih.gov/research/snpdelscore/

Supplementary information

Supplementary data are available at Bioinformatics online.
Marriage, Cohabitation, and Divorce in Later Life
Authors: Brown Susan L , Wright Matthew R
Published: September 2017

Older adults are at the forefront of family change as a declining share experiences lifelong marriage and rates of cohabitation and divorce in later life continue to rise. The goal of this article is to review recent scholarship on marriage, cohabitation, and divorce among older adults and identify directions for future research. The varied family experiences characterizing the later life course demonstrate the importance of moving beyond marital status to capture additional dimensions of the marital biography, including transitions, timing, duration, and sequencing. Cohabitation operates as an alternative to marriage for older adults and is increasingly replacing remarriage following divorce or widowhood. The gray divorce rate has doubled in recent decades as older adults abandon marriage in favor of unmarried partnerships or singlehood. The retreat from marriage among older adults raises important questions about the ramifications of family change for health and well-being as well as access to caregivers given that spouses historically have been the primary source of care.
Experience with Kaposi Sarcoma Herpesvirus Inflammatory Cytokine Syndrome in a Large Urban HIV Clinic in the United States: Case Series and Literature Review
Authors: Cantos Valeria D , Kalapila Aley G , Ly Nguyen Minh , Adamski Marylyn , Gunthel Clifford J
Published: September 2017

In 2010, a new entity, characterized by the classical signs and symptoms of Kaposi sarcoma herpesvirus–associated multicentric Castleman’s disease (KSHV-MCD) in the absence of pathologic evidence of MCD, was described in individuals living with HIV. This syndrome was named KSHV inflammatory cytokine syndrome (KICS). It carries mortality rates of up to 60%. To date, there are no standard therapies. Treatment regimens studied in clinical trials for MCD disease are used in cases of KICS.
The detection rates of merging binary black holes originating from star clusters and their mass function
Authors: Fujii Michiko S. , Tanikawa Ataru , Makino Junichiro
Published: September 2017

Advanced LIGO (Laser Interferometer Gravitational Wave Observatory) observations achieved the first detection of the gravitational wave, which was from a merging binary black hole (BBH). In the near future, more merger events will be observed, and the mass distribution of them will become available. The mass distribution of merger events reflects the evolutionary path of BBHs: dynamical formation in dense star clusters or common envelope evolution from primordial binaries. In this paper, we estimate the detection rate of merging BBHs which dynamically formed in dense star clusters by combining the results of N-body simulations, modeling of globular clusters, and cosmic star-cluster formation history. We estimate that the merger rate density in the local universe within the redshift of 0.1 is 13–57 Gpc−3 yr−1. We find that the detection rate is 0.23–4.6 per year for the current sensitivity limit and that it would increase to 5.1–99 per year for the designed sensitivity which will be achieved in 2019. The distribution of merger rate density in the local universe as a function of redshifted chirp mass has a peak close to the low-mass end. The chirp mass function of the detected mergers, on the other hand, has a peak at the high-mass end, but is almost flat. This difference is simply because the detection range is larger for more massive BBHs.
Reliability of a Skin Diagnostic Device in Assessing Hydration and Erythema
Authors: Huimin Koh , Rowledge Alexandra M. , Borzdynski Caroline J. , Miller Charne , Frescos Nicoletta , McKenzie Gayle , Perry Elizabeth , McGuiness William
Published: September 2017

OBJECTIVE:

To examine the reliability of a skin diagnostic device, the SD202 (Courage+Khazaka GmBH, Cologne, Germany), in assessing hydration and erythema of periwound skin and pressure injury-prone areas.

DESIGN:

Intrarater reliabilities from 3 cross-sectional and prospective studies are reported.

SETTING AND PARTICIPANTS:

Patients attending an outpatient, nurse-led wound dressing clinic (n = 16), a podiatrist-led high-risk foot clinic (n = 17), and residents (n = 38) at a single residential aged-care facility.

MAIN OUTCOME MEASURE:

Skin hydration and erythema levels assessed using the SD202.

MAIN RESULTS:

High internal consistency was maintained for consecutive skin hydration and erythema measures at a single point on the venous leg ulcer periwound (α > .996 and α > .970 for hydration and erythema, respectively) and for the pressure-prone areas of the sacrum (α > .916), right (α > .994) and left (α > .967) ischium, right (α > .989) and left (α > .916) trochanter, right (α > .985) and left (α > .992) calcaneus, and right (α > .991) and left (α > .990) lateral malleolus. High consistency was also found for the measures obtained at 4 different locations around the periwound for the venous leg ulcer (α > .935 and α > .870 for hydration and erythema, respectively). In diabetic foot ulcer assessment, acceptable internal consistency of hydration measures around the periwound was observed (α > .634). Internal consistency of erythema measures was variable, ranging from low to high reliability, particularly among predebridement measures.

CONCLUSIONS:

Using the protocols outlined in this study, the SD202 demonstrates high reliability for assessing skin hydration and erythema levels. It is possible that the SD202 can be used in clinical practice as an appropriate tool for skin hydration and erythema assessment.