bluuebunny/crossref_metadata_2025 huggingface dataset:
A newt does not change its spots: using pattern mapping for the identification of individuals in large populations of newt species
Authors: Mettouris Onoufrios , Megremis George , Giokas Sinos
Published: February 2016

The correct identification of individuals is a requirement of capture‐mark‐recapture (CMR) methods, and it is commonly achieved by applying artificial marks or by mutilation of study‐animals. An alternative, non‐invasive method to identify individuals is to utilize the patterns of their natural body markings. However, the use of pattern mapping is not yet widespread, mainly because it is considered time consuming, particularly in large populations and/or long‐term CMR studies. Here we explore the use of pattern mapping for the identification of adult individuals in the alpine (Ichthyosaura alpestris) and smooth (Lissotriton vulgaris) newts (Amphibia, Salamandridae), using the freely available, open‐source software Wild‐ID. Our photographic datasets comprised nearly 4000 captured animals’ images, taken during a 3‐year period. The spot patterns of individual newts of both species did not change through time, and were sufficiently varied to allow their individual identification, even in the larger datasets. The pattern‐recognition algorithm of Wild‐ID was highly successful in identifying individual newts in both species. Our findings indicate that pattern mapping can be successfully employed for the identification of individuals in large populations of a broad range of animals that exhibit natural markings. The significance of pattern‐mapping is accentuated in CMR studies that aim in obtaining long‐term information on the demography and population dynamics of species of conservation interest, such as many amphibians facing population declines.
Temporal characterization of serum metabolite signatures in lung cancer patients undergoing treatment
Authors: Hao Desirée , Sarfaraz M. Omair , Farshidfar Farshad , Bebb D. Gwyn , Lee Camelia Y. , Card Cynthia M. , David Marilyn , Weljie Aalim M.
Published: February 2016

Lung cancer causes more deaths in men and women than any other cancer related disease. Currently, few effective strategies exist to predict how patients will respond to treatment. We evaluated the serum metabolomic profiles of 25 lung cancer patients undergoing chemotherapy ± radiation to evaluate the feasibility of metabolites as temporal biomarkers of clinical outcomes. Serial serum specimens collected prospectively from lung cancer patients were analyzed using both nuclear magnetic resonance (1H-NMR) spectroscopy and gas chromatography mass spectrometry (GC–MS). Multivariate statistical analysis consisted of unsupervised principal component analysis or orthogonal partial least squares discriminant analysis with significance assessed using a cross-validated ANOVA. The metabolite profiles were reflective of the temporal distinction between patient samples before during and after receiving therapy (1H-NMR, p < 0.001: and GC–MS p < 0.01). Disease progression and survival were strongly correlative with the GC–MS metabolite data whereas stage and cancer type were associated with 1H-NMR data. Metabolites such as hydroxylamine, tridecan-1-ol, octadecan-1-ol, were indicative of survival (GC–MS p < 0.05) and metabolites such as tagatose, hydroxylamine, glucopyranose, and threonine that were reflective of progression (GC–MS p < 0.05). Metabolite profiles have the potential to act as prognostic markers of clinical outcomes for lung cancer patients. Serial 1H-NMR measurements appear to detect metabolites diagnostic of tumor pathology, while GC–MS provided data better related to prognostic clinical outcomes, possibility due to physiochemical bias related to specific biochemical pathways. These results warrant further study in a larger cohort and with various treatment options.
Physicochemical Properties and ACE‐I Inhibitory Activity of Protein Hydrolysates from a Non‐Genetically Modified Soy Cultivar
Authors: Nguyen Quyen , Hettiarachchy Navam , Rayaprolu Srinivas , Jayanthi Srinivas , Thallapuranam Suresh , Chen Pengyin
Published: February 2016

Arkansas‐grown non‐genetically modified soybean cultivar, R08‐4004, was selected to prepare a protein isolate, which was treated with Alcalase for limited enzymatic hydrolysis. The objective was to optimize the Alcalase hydrolysis condition to produce soy protein hydrolysate (SPH) with high protein yield, low bitterness, and clarity for beverage applications. The degree of hydrolysis ranged between 14 and 52 % during the study at varying incubation times using two different concentrations of Alcalase enzyme. Recovery of soluble protein, between 21 and 53 %, was achieved with a decrease in turbidity. There was an increase in surface hydrophobicity (S0) which is correlated with bitterness of SPH treated with 1.0 AU (3.2 µL/g) of Alcalase 2.4 L. The sodium dodecyl sulfate‐polyacrylamide gel electrophoresis analysis showed a distinct hydrolysis pattern in which 7S globulin and the two acidic sub‐units of 11S globulin were hydrolyzed extensively in comparison to the two basic sub‐units of 11S globulin. Limited enzymatic hydrolysis produced low molecular weight peptides <17 kDa. Among these SPHs, the one derived after 120 min incubation had the highest soluble protein yield (43 %), low S0 value (35.4), low turbidity (0.88), and highest angiotensin‐I converting enzyme (ACE‐I) inhibition activity (66.6 %). This hydrolysate has potential use as protein rich nutraceutical for developing many non‐genetically modified food product applications.
Mismatch negativity: Alterations in adults from the general population who report subclinical psychotic symptoms
Authors: Döring C , Müller M , Hagenmuller F , Ajdacic-Gross V , Haker H , Kawohl W , Rössler W , Heekeren K
Published: February 2016

Background

Deficits of mismatch negativity (MMN) in schizophrenia and individuals at risk for psychosis have been replicated many times. Several studies have also demonstrated the occurrence of subclinical psychotic symptoms within the general population. However, none has yet investigated MMN in individuals from the general population who report subclinical psychotic symptoms.

Methods

The MMN to duration-, frequency-, and intensity deviants was recorded in 217 nonclinical individuals classified into a control group (n = 72) and three subclinical groups: paranoid (n = 44), psychotic (n = 51), and mixed paranoid-psychotic (n = 50). Amplitudes of MMN at frontocentral electrodes were referenced to average. Based on a three-source model of MMN generation, we conducted an MMN source analysis and compared the amplitudes of surface electrodes and sources among groups.

Results

We found no significant differences in MMN amplitudes of surface electrodes. However, significant differences in MMN generation among the four groups were revealed at the frontal source for duration-deviant stimuli (P = 0.01). We also detected a trend-level difference (P = 0.05) in MMN activity among those groups for frequency deviants at the frontal source.

Conclusions

Individuals from the general population who report psychotic symptoms are a heterogeneous group. However, alterations exist in their frontal MMN activity. This increased activity might be an indicator of more sensitive perception regarding changes in the environment for individuals with subclinical psychotic symptoms.
Screening of Egyptian toddlers for autism spectrum disorder using an Arabic validated version of M-CHAT; report of a community-based study (Stage I)
Authors: Mohamed F.E. , Zaky E.A. , Youssef A. , Elhossiny R. , Zahra S. , Khalaf R. , Youssef W. , Wafiq A. , Ibrahim R. , Abd-Elhakim R. , Obada A. , Eldin W.S.
Published: February 2016

Background

Although there is a recommendation that toddlers be screened for Autism spectrum disorder (ASD) during their 18- and 24-month well-care child visits, diagnosis often occurs well after the child turns 4 years old. Such delayed diagnosis hinders the implementation of early intervention thus worsens the long-term prognosis of ASD.

Objectives

The current community-based study in its stage I aimed at early screening of Egyptian toddlers for ASD using an Arabic validated version of Modified Checklist for Autism in Toddlers (M-CHAT).

Methodology

A cross-sectional community-based descriptive study was carried out enrolling 5546 Egyptian toddlers. They were randomly recruited from those attending Primary Health Care Units in six Egyptian governorates with a fair representation of the urban, semi-urban, and rural Egyptian populations. An Arabic validated version of M-CHAT was used as a screening tool for ASD.

Results

The current study revealed failure of M-CHAT (suspected to have ASD and needs further evaluation) in 1320 out of the enrolled 5546 Egyptian toddlers (23.8%).

Conclusions

M-CHAT as a screening tool for ASD has flagged a considerable percent of the enrolled toddlers that necessitates referral for further evaluation (stage II) to settle the diagnosis of ASD in the true positive cases. Perfecting the delicate balance between sensitivity and specificity for ASD screening tools is crucial in order not to miss early detection of ASD cases and at the same time, to avoid over-diagnosis with subsequent abuse of the limited healthcare resources in developing countries.
Spousal resemblance in psychopathology: A comparison of parents of children with and without psychopathology
Authors: Wesseldijk LW , Dieleman GC , Lindauer RJL , Bartels M , Willemsen G , Hudziak JJ , Boomsma DI , Middeldorp CM
Published: February 2016

Background

Spouses resemble each other for psychopathology, but data regarding spousal resemblance in externalizing psychopathology, and data regarding spousal resemblance across different syndromes (e.g. anxiety in wives and attention deficit/hyperactivity disorder [ADHD] in husbands) are limited. Moreover, knowledge is lacking regarding spousal resemblance in parents of children with psychiatric disorders. We investigated and compared spousal resemblance within and across internalizing and externalizing symptom domains in parents of children with and without psychopathology.

Methods

Symptoms of depression, anxiety, avoidant personality, ADHD, and antisocial personality were assessed with the Adult Self Report in 728 mothers and 544 fathers of 778 children seen in child and adolescent psychiatric outpatient clinics and in 2075 mothers and 1623 fathers of 2784 children from a population-based sample. Differences in symptom scores and spousal correlations between the samples were tested.

Results

Parents in the clinical sample had higher symptom scores than in the population-based sample. In both samples, correlations within and across internalizing and externalizing domains of psychopathology were significant. Importantly, correlations were significantly higher in the clinical sample (P = 0.03). Correlations, within and across symptoms, ranged from 0.14 to 0.30 in the clinical sample and from 0.05 to 0.23 in the population-based sample.

Conclusions

This large study shows that spousal resemblance is not only present within but also across symptom domains. Especially in the clinical sample, ADHD symptoms in fathers and antisocial personality symptoms in mothers were correlated with a range of psychiatric symptoms in their spouses. Clinicians need to be alert of these multiple affected families.
Dysfunctional default mode network and executive control network in people with Internet gaming disorder: Independent component analysis under a probability discounting task
Authors: Wang L , Wu L , Lin X , Zhang Y , Zhou H , Du X , Dong G
Published: February 2016

Background

The present study identified the neural mechanism of risky decision-making in Internet gaming disorder (IGD) under a probability discounting task.

Methods

Independent component analysis was used on the functional magnetic resonance imaging data from 19 IGD subjects (22.2 ± 3.08 years) and 21 healthy controls (HC, 22.8 ± 3.5 years).

Results

For the behavioral results, IGD subjects prefer the risky to the fixed options and showed shorter reaction time compared to HC. For the imaging results, the IGD subjects showed higher task-related activity in default mode network (DMN) and less engagement in the executive control network (ECN) than HC when making the risky decisions. Also, we found the activities of DMN correlate negatively with the reaction time and the ECN correlate positively with the probability discounting rates.

Conclusions

The results suggest that people with IGD show altered modulation in DMN and deficit in executive control function, which might be the reason for why the IGD subjects continue to play online games despite the potential negative consequences.
Quantifying Terrestrial Snow from Space
Authors: Kang Do , Kim Edward , Hall Dorothy
Published: February 2016

MicroSnow2 and SnowEx Workshops; Columbia, Maryland, 13–17 July 2015
New Solar Wind Model Could Improve Space Weather Forecasts
Authors: Stanley Sarah
Published: February 2016

Real-world data drive a simulation that successfully predicts Sun structures and interplanetary solar wind dynamics.
Dirty Water: Unintended Consequence of Climate Resiliency
Authors: Wendel JoAnna
Published: February 2016

Scientists testing the quality of floodwater in a Florida city find potentially harmful bacteria.
Quantification of active mitochondrial permeability transition pores using GNX-4975 inhibitor titrations provides insights into molecular identity
Authors: Richardson Andrew P. , Halestrap Andrew P.
Published: February 2016

Inhibition of the mitochondrial permeability transition pore (MPTP) by the novel inhibitor GNX-4975 was characterized. Titration of MPTP activity in de-energized rat liver mitochondria allowed determination of the number of GNX-4975-binding sites and their dissociation constant (Ki). Binding sites increased in number when MPTP opening was activated by increasing [Ca2+], phenylarsine oxide (PAO) or KSCN, and decreased when MPTP opening was inhibited with bongkrekic acid (BKA) or ADP. Values ranged between 9 and 50 pmol/mg of mitochondrial protein, but the Ki remained unchanged at ∼1.8 nM when the inhibitor was added before Ca2+. However, when GNX-4975 was added after Ca2+ it was much less potent with a Ki of ∼140 nM. These data imply that a protein conformational change is required to form the MPTP complex and generate the GNX-4975-binding site. Occupation of the latter with GNX-4975 prevents the Ca2+ binding that triggers pore opening. We also demonstrated that GNX-4975 stabilizes an interaction between the adenine nucleotide translocase (ANT), held in its ‘c’ conformation with carboxyatractyloside (CAT), and the phosphate carrier (PiC) bound to immobilized PAO. No components of the F1Fo-ATP synthase bound significantly to immobilized PAO. Our data are consistent with our previous proposal that the MPTP may form at an interface between the PiC and ANT (or other similar mitochondrial carrier proteins) when they adopt novel conformations induced by factors that sensitize the MPTP to [Ca2+]. We propose that GNX-4975 binds to this interface preventing a calcium-triggered event that opens the interface into a pore.
Local inhibition of elastase reduces EMILIN1 cleavage reactivating lymphatic vessel function in a mouse lymphoedema model
Authors: Pivetta Eliana , Wassermann Bruna , Belluz Lisa Del Bel , Danussi Carla , Modica Teresa Maria Elisa , Maiorani Orlando , Bosisio Giulia , Boccardo Francesco , Canzonieri Vincenzo , Colombatti Alfonso , Spessotto Paola
Published: February 2016

Lymphatic vasculature critically depends on the connections of lymphatic endothelial cells with the extracellular matrix (ECM), which are mediated by anchoring filaments (AFs). The ECM protein EMILIN1 is a component of AFs and is involved in the regulation of lymphatic vessel functions: accordingly, Emilin1−/− mice display lymphatic vascular morphological alterations, leading to functional defects such as mild lymphoedema, lymph leakage and compromised lymph drainage. In the present study, using a mouse post-surgical tail lymphoedema model, we show that the acute phase of acquired lymphoedema correlates with EMILIN1 degradation due to neutrophil elastase (NE) released by infiltrating neutrophils. As a consequence, the intercellular junctions of lymphatic endothelial cells are weakened and drainage to regional lymph nodes is severely affected. The local administration of sivelestat, a specific NE inhibitor, prevents EMILIN1 degradation and reduces lymphoedema, restoring a normal lymphatic functionality. The finding that, in human secondary lymphoedema samples, we also detected cleaved EMILIN1 with the typical bands of an NE-dependent pattern of fragmentation establishes a rationale for a powerful strategy that targets NE inhibition. In conclusion, the attempts to block EMILIN1 degradation locally represent the basis for a novel ‘ECM’ pharmacological approach to assessing new lymphoedema treatments.
Numerical and exact kinetic energy operator using Eckart conditions with one or several reference geometries: Application to HONO
Authors: Lauvergnat David , Luis Josep M. , Kirtman Bernard , Reis Heribert , Nauts André
Published: February 2016

For the computation of rovibrational levels and their spectroscopic intensities, the Eckart conditions are essential to achieve the optimal separation between rotation and vibration. Dymarsky and Kudin [J. Chem. Phys. 122, 124103 (2005)] proposed a procedure for a simplified calculation of the Eckart rotation matrix. In the present work, we have adapted their approach to obtain a kinetic energy operator in curvilinear coordinates using a numerical but exact procedure without resorting to finite differences. Furthermore, we have modified this approach for the study of molecular systems with several minima, for which several Eckart reference geometries are required. The HONO molecular system has been used to show the efficiency of our implementation. Using the Eckart conditions with multi-reference geometries allows for a calculation of the rotational levels as well as frequencies and intensities of the infrared spectra of both HONO isomers with a single calculation.
Pressure drop and thrust predictions for transonic micronozzle flows
Authors: Gomez J. , Groll R.
Published: February 2016

In this paper, the expansion of xenon, argon, krypton, and neon gases through a Laval nozzle is studied experimentally and numerically. The pressurized gases are accelerated through the nozzle into a vacuum chamber in an attempt to simulate the operating conditions of a cold-gas thruster for attitude control of a micro-satellite. The gases are evaluated at several mass flow rates ranging between 0.178 mg/s and 3.568 mg/s. The Re numbers are low (8–256) and the estimated values of Kn number lie between 0.33 and 0.02 (transition and slip-flow regime). Direct Simulation Monte Carlo (DSMC) and continuum-based simulations with a no-slip boundary condition are performed. The DSMC and the experimental results show good agreement in the range Kn > 0.1, while the Navier-Stokes results describe the experimental data more accurately for Kn < 0.05. Comparison between the experimental and Navier-Stokes results shows high deviations at the lower mass flow rates and higher Kn numbers. A relation describing the deviation of the pressure drop through the nozzle as a function of Kn is obtained. For gases with small collision cross sections, the experimental pressure results deviate more strongly from the no-slip assumption. From the analysis of the developed function, it is possible to correct the pressure results for the studied gases, both in the slip-flow and transition regimes, with four gas-independent accommodation coefficients. The thrust delivered by the cold-gas thruster and the specific impulse is determined based on the numerical results. Furthermore, an increase of the thickness of the viscous boundary layer through the diffuser of the micronozzle is observed. This results in a shock-less decrease of the Mach number and the flow velocity, which penalizes thrust efficiency. The negative effect of the viscous boundary layer on thrust efficiency can be lowered through higher values of Re and a reduction of the diffuser length.
Effect of collisions on photoelectron sheath in a gas
Authors: Sodha Mahendra Singh , Mishra S. K.
Published: February 2016

This paper presents a study of the effect of the collision of electrons with atoms/molecules on the structure of a photoelectron sheath. Considering the half Fermi-Dirac distribution of photo-emitted electrons, an expression for the electron density in the sheath has been derived in terms of the electric potential and the structure of the sheath has been investigated by incorporating Poisson's equation in the analysis. The method of successive approximations has been used to solve Poisson's equation with the solution for the electric potential in the case of vacuum, obtained earlier [Sodha and Mishra, Phys. Plasmas 21, 093704 (2014)], being used as the zeroth order solution for the present analysis. The inclusion of collisions influences the photoelectron sheath structure significantly; a reduction in the sheath width with increasing collisions is obtained.
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics
Authors: Petsev Nikolai D. , Leal L. Gary , Shell M. Scott
Published: February 2016

Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.
Inverse period-doubling bifurcations determine complex structure of bursting in a one-dimensional non-autonomous map
Authors: Han Xiujing , Chen Zhenyang , Bi Qinsheng
Published: February 2016

We propose a simple one-dimensional non-autonomous map, in which some novel bursting patterns (e.g., “fold/double inverse flip” bursting, “fold/multiple inverse flip” bursting, and “fold/a cascade of inverse flip” bursting) can be observed. Typically, these bursting patterns exhibit complex structures containing a chain of inverse period-doubling bifurcations. The active states related to these bursting can be period-2n (n = 1, 2, 3,…) attractors or chaotic attractors, which may evolve to quiescence by a chain of inverse period-doubling bifurcations when the slow excitation decreases through period-doubling bifurcation points of the map. This accounts for the complex inverse period-doubling bifurcation structures observed in bursting patterns. Our findings enrich the possible routes to bursting as well as the underlying mechanisms of bursting.
Multifractal analysis of visibility graph-based Ito-related connectivity time series
Authors: Czechowski Zbigniew , Lovallo Michele , Telesca Luciano
Published: February 2016

In this study, we investigate multifractal properties of connectivity time series resulting from the visibility graph applied to normally distributed time series generated by the Ito equations with multiplicative power-law noise. We show that multifractality of the connectivity time series (i.e., the series of numbers of links outgoing any node) increases with the exponent of the power-law noise. The multifractality of the connectivity time series could be due to the width of connectivity degree distribution that can be related to the exit time of the associated Ito time series. Furthermore, the connectivity time series are characterized by persistence, although the original Ito time series are random; this is due to the procedure of visibility graph that, connecting the values of the time series, generates persistence but destroys most of the nonlinear correlations. Moreover, the visibility graph is sensitive for detecting wide “depressions” in input time series.
Local conservative regularizations of compressible magnetohydrodynamic and neutral flows
Authors: Krishnaswami Govind S. , Sachdev Sonakshi , Thyagaraja A.
Published: February 2016

Ideal systems like magnetohydrodynamics (MHD) and Euler flow may develop singularities in vorticity (w=∇×v). Viscosity and resistivity provide dissipative regularizations of the singularities. In this paper, we propose a minimal, local, conservative, nonlinear, dispersive regularization of compressible flow and ideal MHD, in analogy with the KdV regularization of the 1D kinematic wave equation. This work extends and significantly generalizes earlier work on incompressible Euler and ideal MHD. It involves a micro-scale cutoff length λ which is a function of density, unlike in the incompressible case. In MHD, it can be taken to be of order the electron collisionless skin depth c/ωpe. Our regularization preserves the symmetries of the original systems and, with appropriate boundary conditions, leads to associated conservation laws. Energy and enstrophy are subject to a priori bounds determined by initial data in contrast to the unregularized systems. A Hamiltonian and Poisson bracket formulation is developed and applied to generalize the constitutive relation to bound higher moments of vorticity. A “swirl” velocity field is identified, and shown to transport w/ρ and B/ρ, generalizing the Kelvin-Helmholtz and Alfvén theorems. The steady regularized equations are used to model a rotating vortex, MHD pinch, and a plane vortex sheet. The proposed regularization could facilitate numerical simulations of fluid/MHD equations and provide a consistent statistical mechanics of vortices/current filaments in 3D, without blowup of enstrophy. Implications for detailed analyses of fluid and plasma dynamic systems arising from our work are briefly discussed.
Challenges in constraining anthropogenic aerosol effects on cloud radiative forcing using present-day spatiotemporal variability
Authors: Ghan Steven , Wang Minghuai , Zhang Shipeng , Ferrachat Sylvaine , Gettelman Andrew , Griesfeller Jan , Kipling Zak , Lohmann Ulrike , Morrison Hugh , Neubauer David , Partridge Daniel G. , Stier Philip , Takemura Toshihiko , Wang Hailong , Zhang Kai
Published: February 2016

A large number of processes are involved in the chain from emissions of aerosol precursor gases and primary particles to impacts on cloud radiative forcing. Those processes are manifest in a number of relationships that can be expressed as factors dlnX/dlnY driving aerosol effects on cloud radiative forcing. These factors include the relationships between cloud condensation nuclei (CCN) concentration and emissions, droplet number and CCN concentration, cloud fraction and droplet number, cloud optical depth and droplet number, and cloud radiative forcing and cloud optical depth. The relationship between cloud optical depth and droplet number can be further decomposed into the sum of two terms involving the relationship of droplet effective radius and cloud liquid water path with droplet number. These relationships can be constrained using observations of recent spatial and temporal variability of these quantities. However, we are most interested in the radiative forcing since the preindustrial era. Because few relevant measurements are available from that era, relationships from recent variability have been assumed to be applicable to the preindustrial to present-day change. Our analysis of Aerosol Comparisons between Observations and Models (AeroCom) model simulations suggests that estimates of relationships from recent variability are poor constraints on relationships from anthropogenic change for some terms, with even the sign of some relationships differing in many regions. Proxies connecting recent spatial/temporal variability to anthropogenic change, or sustained measurements in regions where emissions have changed, are needed to constrain estimates of anthropogenic aerosol impacts on cloud radiative forcing.
NMRPro: an integrated web component for interactive processing and visualization of NMR spectra
Authors: Mohamed Ahmed , Nguyen Canh Hao , Mamitsuka Hiroshi
Published: February 2016

Summary: The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization.

Availability and implementation: Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/

Contact:  mohamed@kuicr.kyoto-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony
Authors: Jacox Edwin , Chauve Cedric , Szöllősi Gergely J. , Ponty Yann , Scornavacca Celine
Published: February 2016

Summary: A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation, involving sampled and unsampled lineages, within undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation.

Availability and implementation: ecceTERA is freely available under http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA and can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera.

Contact:  celine.scornavacca@umontpellier.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
Authors: Katoh Kazutaka , Standley Daron M.
Published: February 2016

Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction.

Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment.

Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/

Contact:  katoh@ifrec.osaka-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Computational clustering for viral reference proteomes
Authors: Chen Chuming , Huang Hongzhan , Mazumder Raja , Natale Darren A. , McGarvey Peter B. , Zhang Jian , Polson Shawn W. , Wang Yuqi , Wu Cathy H. ,   UniProt Consortium
Published: February 2016

Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.

Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.

Availability and implementation:  http://proteininformationresource.org/rps/viruses/

Contact:  chenc@udel.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules
Authors: Wala Jeremiah , Zhang Cheng-Zhong , Meyerson Matthew , Beroukhim Rameen
Published: February 2016

We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis.

Availability and implementation: VariantBam and full documentation are available at github.com/jwalabroad/VariantBam.

Contact:  rameen@broadinstitute.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
Authors: Elhanati Yuval , Marcou Quentin , Mora Thierry , Walczak Aleksandra M.
Published: February 2016

Motivation: The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events—choices of gene templates, base pair deletions and insertions—described by probability distributions. Not all scenarios are equally likely, and the same receptor sequence may be obtained in several different ways. Quantifying the distribution of these rearrangements is an essential baseline for studying the immune system diversity. Inferring the properties of the distributions from receptor sequences is a computationally hard problem, requiring enumerating every possible scenario for every sampled receptor sequence.

Results: We present a Hidden Markov model, which accounts for all plausible scenarios that can generate the receptor sequences. We developed and implemented a method based on the Baum–Welch algorithm that can efficiently infer the parameters for the different events of the rearrangement process. We tested our software tool on sequence data for both the alpha and beta chains of the T cell receptor. To test the validity of our algorithm, we also generated synthetic sequences produced by a known model, and confirmed that its parameters could be accurately inferred back from the sequences. The inferred model can be used to generate synthetic sequences, to calculate the probability of generation of any receptor sequence, as well as the theoretical diversity of the repertoire. We estimate this diversity to be ≈1023 for human T cells. The model gives a baseline to investigate the selection and dynamics of immune repertoires.

Availability and implementation: Source code and sample sequence files are available at https://bitbucket.org/yuvalel/repgenhmm/downloads.

Contact:  elhanati@lpt.ens.fr or tmora@lps.ens.fr or awalczak@lpt.ens.fr
Mycobacterial r32-kDa antigen-specific T-cell responses correlate with successful treatment and a heightened anti-microbial response in human leprosy patients
Authors: Neela Venkata Sanjeev Kumar , Devalraju Kamakshi Prudhula , Pydi Satya Sudheer , Sunder Sharada Ramaseri , Adiraju Kameswara Rao , Singh Surya Satyanarayana , Anandaraj M. P. J. S. , Valluri Vijaya Lakshmi
Published: February 2016

Background:

Immunological characterization of mycobacterial peptides may help not only in the preparation of a vaccine for leprosy but also in developing in vitro T-cell assays that could perhaps be used as an in vitro correlate for treatment outcome. The main goal of this study was to evaluate the use of Mycobacterium bovis recombinant 32-kDa protein (r32-kDa) antigen-stimulated T-cell assay as a surrogate marker for treatment outcome and monitor vitamin D receptor (VDR)-mediated anti-microbial responses during multidrug therapy (MDT) in leprosy.

Methods:

Newly diagnosed tuberculoid and lepromatous leprosy patients were enrolled and followed up during their course of MDT at 6 and 12 months. IFN-γ, IL-10, IL-17 and IL-23 levels in culture supernatants and expression of VDR, TLR2, LL37 and DEFB in r32-kDa-stimulated PBMCs were measured. Controls comprised household contacts (HHCs) and healthy endemic subjects (HCs).

Results:

Significant differences were observed in the levels of IFN-γ, IL-17, IL-23, VDR and anti-microbial peptides LL37 and DEFB after treatment and when compared with that of HHCs and HCs, respectively.

Conclusions:

These findings suggest that responses to r32-kDa antigen reflect an improved immunological and anti-microbial response in leprosy patients during therapy, thereby indicating its potential use as an immune correlate in the treatment of leprosy patients.
Systematic revision of the pocket gopher genus Orthogeomys
Authors: Spradling Theresa A. , Demastes James W. , Hafner David J. , Milbach Paige L. , Cervantes Fernando A. , Hafner Mark S.
Published: February 2016

Pocket gophers of the genus Orthogeomys show unusually high morphological and ecological diversity compared to other genera in the family Geomyidae. Whereas this diverse group once was divided into 3 genera ( Merriam 1895 ), a revision by Russell (1968) recognized only Orthogeomys , with Merriam’s original genera relegated to subgeneric status as Heterogeomys , Macrogeomys , and Orthogeomys . Recent studies have called into question the monophyly of Orthogeomys , as well as the validity of 4 currently recognized Orthogeomys species. To date, the taxonomic validity of only 1 of these species has been verified ( Hafner et al. 2014 ). In this analysis, the first to include all 11 recognized species of the genus, we examine 3 mitochondrial and 2 nuclear gene sequences (4,352 base pairs) and analyze cranial morphology to explore relationships within the genus. Our data support a taxonomic revision that restricts the genus Orthogeomys to a single species ( O. grandis ) and combines the subgenera Heterogeomys and Macrogeomys into the resurrected genus, Heterogeomys (7 species). In addition, 3 currently recognized species of Orthogeomys are synonymized as follows: O. cuniculus with O. grandis ; H. thaeleri with H. dariensis ; and H. matagalpae with H. cherriei . A synonymy and a key to the species of the genera Orthogeomys and Heterogeomys are provided.

Las tuzas del género Orthogeomys muestran una diversidad morfológica y ecológica inusual en comparación con otros géneros de la familia Geomyidae. Aunque este diverso grupo fue alguna vez dividido en 3 géneros ( Merriam 1895 ), la revisión de Russell (1968) reconoció solo a Orthogeomys , mientras que los géneros originales de Merriam fueron relegados a estatus subgenérico como Heterogeomys , Macrogeomys y Orthogeomys . Estudios recientes han cuestionado la monofilia de Orthogeomys , así como la validez de 4 de las especies actualmente reconocidas. A la fecha, la validez taxonómica de sólo una de estas especies ha sido verificada. En este análisis, el primero en incluir las 11 especies reconocidas en el género, examinamos secuencias de 3 genes mitocondriales y 2 nucleares y analizamos la morfología craneal para explorar las relaciones dentro del género. Nuestras 4,352 pares de bases de secuencias de ADN apoyan una revisión taxonómica que retiene al género Orthogeomys (incluyendo sólo a O. grandis ) y combina los subgéneros Heterogeomys y Macrogeomys en un género recuperado, Heterogeomys (7 especies). Además, 3 especies de Orthogeomys actualmente reconocidas son sinonimizadas de la siguiente forma: O. cuniculus con O. grandis ; H. thaeleri con H. dariensis ; y H. matagalpae con H. cherriei . Se incluye sinonimia y una clave para las especies de los géneros Orthogeomys y Heterogeomys .
Neural Correlates of Phonetic Learning in Postlingually Deafened Cochlear Implant Listeners
Authors: Miller Sharon , Zhang Yang , Nelson Peggy
Published: February 2016

Objective:

The present training study aimed to examine the fine-scale behavioral and neural correlates of phonetic learning in adult postlingually deafened cochlear implant (CI) listeners. The study investigated whether high variability identification training improved phonetic categorization of the /ba/–/da/ and /wa/–/ja/ speech contrasts and whether any training-related improvements in phonetic perception were correlated with neural markers associated with phonetic learning. It was hypothesized that training would sharpen phonetic boundaries for the speech contrasts and that changes in behavioral sensitivity would be associated with enhanced mismatch negativity (MMN) responses to stimuli that cross a phonetic boundary relative to MMN responses evoked using stimuli from the same phonetic category.

Design:

A computer-based training program was developed that featured multitalker variability and adaptive listening. The program was designed to help CI listeners attend to the important second formant transition cue that categorizes the /ba/–/da/ and /wa/–/ja/ contrasts. Nine adult CI listeners completed the training and 4 additional CI listeners that did not undergo training were included to assess effects of procedural learning. Behavioral pre-post tests consisted of identification and discrimination of the synthetic /ba/–/da/ and /wa/–/ja/ speech continua. The electrophysiologic MMN response elicited by an across phoneme category pair and a within phoneme category pair that differed by an acoustically equivalent amount was derived at pre-post test intervals for each speech contrast as well.

Results:

Training significantly enhanced behavioral sensitivity across the phonetic boundary and significantly altered labeling of the stimuli along the /ba/–/da/ continuum. While training only slightly altered identification and discrimination of the /wa/–/ja/ continuum, trained CI listeners categorized the /wa/–/ja/ contrast more efficiently than the /ba/–/da/ contrast across pre-post test sessions. Consistent with behavioral results, pre-post EEG measures showed the MMN amplitude to the across phoneme category pair significantly increased with training for both the /ba/–/da/ and /wa/–/ja/ contrasts, but the MMN was unchanged with training for the corresponding within phoneme category pairs. Significant brain–behavior correlations were observed between changes in the MMN amplitude evoked by across category phoneme stimuli and changes in the slope of identification functions for the trained listeners for both speech contrasts.

Conclusions:

The brain and behavior data of the present study provide evidence that substantial neural plasticity for phonetic learning in adult postlingually deafened CI listeners can be induced by high variability identification training. These findings have potential clinical implications related to the aural rehabilitation process following receipt of a CI device.
Radiological results of treatment using an extensive anterolateral approach for developmental dysplasia of the hip: minimum 5-year follow-up
Authors: Sugawara Ryo , Watanabe Hideaki , Hagiwara Kayo , Inoue Hirokazu , Takeshita Katsushi , Kikkawa Ichiro
Published: February 2016

To investigate the radiological results using the extensive anterolateral approach in patients with developmental dysplasia of the hip. A total of 16 hips with developmental dysplasia of the hip treated by the extensive anterolateral approach were retrospectively reviewed after a minimum follow-up of 5 years. For evaluation, we considered the Severin classification and postoperative complications. At the final follow-up (mean 75.6 months), 14 hips (87.5%) were satisfactory in the Severin classification. Reoperation was performed in only one hip (6.3%) because of redislocation. No femoral head necrosis was observed. Our results were more favorable than those using conventional surgical methods.
The use of percutaneous joystick reduction and limited open reduction techniques in pediatric femoral shaft fractures: a study of 63 cases
Authors: Liu Fei , Ju Li , Tang Kai , Lou Yue
Published: February 2016

Our study aimed to compare the effectiveness and clinical outcomes of percutaneous joystick reduction and limited open reduction for flexible intramedullary nailing in the treatment of pediatric femoral shaft fractures. A total of 63 pediatric femoral shaft fractures were studied: 35 fractures were treated with percutaneous fixation using the K-wire pin as a joystick (group A), whereas 28 fractures were treated with limited open reduction (group B). Clinical and radiographic data at the final follow-up were compared between the surgical groups. Their duration of X-ray exposure, postoperative weight-bearing time, healing time, Harris score, and Hospital for Special Surgery score at the last follow-up did not differ statistically. However, the blood loss, operative time, duration of hospital stay, and postoperative pain at the incision site were considerably lower in group A than in group B. Three and two patients from group A and group B, respectively, reported skin irritation, whereas one patient from group B developed infection. Seven patients in group A and eight patients in group B showed some extremity overgrowth (<2 cm) and no redisplacement or delayed union of fracture, iatrogenic vessel and nerve injury, or osteofascial compartment syndrome was reported in any of the groups. Therefore, we conclude that percutaneous joystick reduction may effectively be used for flexible intramedullary nailing in the treatment of pediatric femoral shaft fractures. Level of Evidence: Level III, retrospective comparative study.