bluuebunny/crossref_metadata_2025 huggingface dataset:
Treatment for Acquired Apraxia of Speech: A Systematic Review of Intervention Research Between 2004 and 2012
Authors: Ballard Kirrie J. , Wambaugh Julie L. , Duffy Joseph R. , Layfield Claire , Maas Edwin , Mauszycki Shannon , McNeil Malcolm R.
Published: March 2015

Objectives

The aim was for the appointed committee of the Academy of Neurological Communication Disorders and Sciences to conduct a systematic review of published intervention studies of acquired apraxia of speech (AOS), updating the previous committee's review article from 2006.

Method

A systematic search of 11 databases identified 215 articles, with 26 meeting inclusion criteria of (a) stating intention to measure effects of treatment on AOS and (b) data representing treatment effects for at least 1 individual stated to have AOS.

Results

All studies involved within-participant experimental designs, with sample sizes of 1 to 44 (median = 1). Confidence in diagnosis was rated high to reasonable in 18 of 26 studies. Most studies (24/26) reported on articulatory–kinematic approaches; 2 applied rhythm/rate control methods. Six studies had sufficient experimental control for Class III rating according to the
Clinical Practice Guidelines Process Manual
(American Academy of Neurology, 2011), with 15 others satisfying all criteria for Class III except use of independent or objective outcome measurement.

Conclusions

The most important global clinical conclusion from this review is that the weight of evidence supports a strong effect for both articulatory–kinematic and rate/rhythm approaches to AOS treatment. The quantity of work, experimental rigor, and reporting of diagnostic criteria continue to improve and strengthen confidence in the corpus of research.
Asymptomatic Stenosis in the Cervical and Thoracic Spines of Patients with Symptomatic Lumbar Stenosis
Authors: Park Moon Soo , Moon Seong-Hwan , Kim Tae-Hwan , Oh Jae Keun , Lyu Ho Dong , Lee Jae-Hoo , Riew K. Daniel
Published: March 2015

Study Design

Retrospective study.

Objective

Studies on age-related degenerative changes causing concurrent stenoses in the cervical, thoracic, and lumbar spines (triple stenosis) are rare in the literature. Our objectives were to determine: (1) the incidence of asymptomatic radiologic cervical and thoracic stenosis in elderly patients with symptomatic lumbar stenosis, (2) the incidence of concurrent radiologic spinal stenosis in the cervical and thoracic spines, and (3) the radiologic features of cervical stenosis that might predict concurrent thoracic stenosis.

Methods

Whole-spine T2 sagittal magnetic resonance images of patients older than 80 and diagnosed with lumbar spinal stenosis between January 2003 and January 2012 were evaluated retrospectively. We included patients with asymptomatic spondylotic cervical and thoracic stenosis. We measured the anteroposterior diameters of the vertebral body, bony spinal canal, and spinal cord, along with the Pavlov ratio and anterior or posterior epidural stenosis at the level of the disk for each cervical and thoracic level. We compared the radiologic parameters between the subgroups of cervical stenosis with and without thoracic stenosis.

Results

Among the 460 patients with lumbar stenosis, 110 (23.9%) had concurrent radiologic cervical stenosis and 112 (24.3%) had concurrent radiologic thoracic stenosis. Fifty-six patients (12.1%) had combined radiologic cervical and thoracic stenosis in addition to their symptomatic lumbar stenosis (triple stenosis). Anterior epidural stenosis at C7–T1 was associated with a high prevalence of thoracic stenosis.

Conclusions

It appears that asymptomatic radiologic cervical and thoracic stenosis is common in elderly patients with symptomatic lumbar stenosis.
Verification of continuum drift kinetic equation solvers in NIMROD
Authors: Held E. D. , Kruger S. E. , Ji J.-Y. , Belli E. A. , Lyons B. C.
Published: March 2015

Verification of continuum solutions to the electron and ion drift kinetic equations (DKEs) in NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)] is demonstrated through comparison with several neoclassical transport codes, most notably NEO [E. A. Belli and J. Candy, Plasma Phys. Controlled Fusion 54, 015015 (2012)]. The DKE solutions use NIMROD's spatial representation, 2D finite-elements in the poloidal plane and a 1D Fourier expansion in toroidal angle. For 2D velocity space, a novel 1D expansion in finite elements is applied for the pitch angle dependence and a collocation grid is used for the normalized speed coordinate. The full, linearized Coulomb collision operator is kept and shown to be important for obtaining quantitative results. Bootstrap currents, parallel ion flows, and radial particle and heat fluxes show quantitative agreement between NIMROD and NEO for a variety of tokamak equilibria. In addition, velocity space distribution function contours for ions and electrons show nearly identical detailed structure and agree quantitatively. A Θ-centered, implicit time discretization and a block-preconditioned, iterative linear algebra solver provide efficient electron and ion DKE solutions that ultimately will be used to obtain closures for NIMROD's evolving fluid model.
Effects of unsteadiness and non-Newtonian rheology on blood flow through a tapered time-variant stenotic artery
Authors: Zaman A. , Ali N. , Sajid M. , Hayat T.
Published: March 2015

A two-dimensional model is used to analyze the unsteady pulsatile flow of blood through a tapered artery with stenosis. The rheology of the flowing blood is captured by the constitutive equation of Carreau model. The geometry of the time-variant stenosis has been used to carry out the present analysis. The flow equations are set up under the assumption that the lumen radius is sufficiently smaller than the wavelength of the pulsatile pressure wave. A radial coordinate transformation is employed to immobilize the effect of the vessel wall. The resulting partial differential equations along with the boundary and initial conditions are solved using finite difference method. The dimensionless radial and axial velocity, volumetric flow rate, resistance impedance and wall shear stress are analyzed for normal and diseased artery with particular focus on variation of these quantities with non-Newtonian parameters.
Solid-state EPR strategies for the structural characterization of paramagnetic NO adducts of frustrated Lewis pairs (FLPs)
Authors: de Oliveira Marcos , Wiegand Thomas , Elmer Lisa-Maria , Sajid Muhammad , Kehr Gerald , Erker Gerhard , Magon Claudio José , Eckert Hellmut
Published: March 2015

Anisotropic interactions present in three new nitroxide radicals prepared by N,N addition of NO to various borane-phosphane frustrated Lewis pairs (FLPs) have been characterized by continuous-wave (cw) and pulsed X-band EPR spectroscopies in solid FLP-hydroxylamine matrices at 100 K. Anisotropic g-tensor values and 11B, 14N, and 31P hyperfine coupling tensor components have been extracted from continuous-wave lineshape analyses, electron spin echo envelope modulation (ESEEM), and hyperfine sublevel correlation spectroscopy (HYSCORE) experiments with the help of computer simulation techniques. Suitable fitting constraints are developed on the basis of density functional theory (DFT) calculations. These calculations reveal that different from the situation in standard nitroxide radicals (TEMPO), the g-tensors are non-coincident with any of the nuclear hyperfine interaction tensors. The determination of these interaction parameters turns out to be successful, as the cw- and pulse EPR experiments are highly complementary in informational content. While the continuous-wave lineshape is largely influenced by the anisotropic hyperfine coupling to 14N and 31P, the ESEEM and HYSCORE spectra contain important information about the 11B hyperfine coupling and nuclear electric quadrupolar interaction. The set of cw- and pulsed EPR experiments, with fitting constraints developed by DFT calculations, defines an efficient strategy for the structural analysis of paramagnetic FLP adducts.
Molecular dynamics simulation of CO2 hydrates: Prediction of three phase coexistence line
Authors: Míguez J. M. , Conde M. M. , Torré J.-P. , Blas F. J. , Piñeiro M. M. , Vega C.
Published: March 2015

The three phase equilibrium line (hydrate-liquid water-liquid carbon dioxide) has been estimated for the water + carbon dioxide binary mixture using molecular dynamics simulation and the direct coexistence technique. Both molecules have been represented using rigid nonpolarizable models. TIP4P/2005 and TIP4P/Ice were used for the case of water, while carbon dioxide was considered as a three center linear molecule with the parameterizations of MSM, EPM2, TraPPE, and ZD. The influence of the initial guest occupancy fraction on the hydrate stability has been analyzed first in order to determine the optimal starting configuration for the simulations, paying attention to the influence of the two different cells existing in the sI hydrate structure. The three phase coexistence temperature was then determined for a pressure range from 2 to 500 MPa. The qualitative shape of the equilibrium curve estimated is correct, including the high pressure temperature maximum that determines the hydrate re-entrant behaviour. However, in order to obtain quantitative agreement with experimental results, a positive deviation from the classical Lorentz-Berthelot combining rules must be considered.
Free-space reflection method for measuring moisture content and bulk density of particulate materials at microwave frequency
Authors: Li Chenxiao , Han Bing , Zhang Tao
Published: March 2015

A measurement system based on free-space reflection method is designed for simultaneous and independent determination of moisture content and bulk density of particulate materials. The proposed system consists of microwave cavity oscillator, horn antenna, slide rail, sample holder, mixer, and digital meter. Sand and rice with different moisture contents and bulk densities are chosen as samples. Calibration models for moisture content and bulk density are proposed according to the measurement of the position of the minimum of the traveling–standing wave and the ratio of the maximum-to-minimum field strength of the traveling–standing wave at different temperatures. The moisture constant, ranging from 0% to 24.6%, is obtained with a coefficient of determination (R2) greater than 0.982 and a standard error of prediction (SEP) value of less than 0.695%. The bulk density, ranging from 0.501 g/cm3 to 1.822 g/cm3, is determined with a R2 ≥ 0.961 and a SEP value ranging from 0.0144 g/cm3 to 0.0382 g/cm3 for different samples.
Metal-organic vapor-phase epitaxy-grown ultra-low density InGaAs/GaAs quantum dots exhibiting cascaded single-photon emission at 1.3 μm
Authors: Paul Matthias , Kettler Jan , Zeuner Katharina , Clausen Caterina , Jetter Michael , Michler Peter
Published: March 2015

By metal-organic vapor-phase epitaxy, we have fabricated InGaAs quantum dots on GaAs substrate with an ultra-low lateral density (<107 cm−2). The photoluminescence emission from the quantum dots is shifted to the telecom O-band at 1.31 μm by an InGaAs strain reducing layer. In time-resolved measurements, we find fast decay times for exciton (∼600 ps) and biexciton (∼300 ps). We demonstrate triggered single-photon emission (g(2)(0)=0.08) as well as cascaded emission from the biexciton decay. Our results suggest that these quantum dots can compete with their counterparts grown by state-of-the-art molecular beam epitaxy.
Dynamics of charged particle motion in the vicinity of three dimensional magnetic null points: Energization and chaos
Authors: Gascoyne Andrew
Published: March 2015

Using a full orbit test particle approach, we analyse the motion of a single proton in the vicinity of magnetic null point configurations which are solutions to the kinematic, steady state, resistive magnetohydrodynamics equations. We consider two magnetic configurations, namely, the sheared and torsional spine reconnection regimes [E. R. Priest and D. I. Pontin, Phys. Plasmas 16, 122101 (2009); P. Wyper and R. Jain, Phys. Plasmas 17, 092902 (2010)]; each produce an associated electric field and thus the possibility of accelerating charged particles to high energy levels, i.e., > MeV, as observed in solar flares [R. P. Lin, Space Sci. Rev. 124, 233 (2006)]. The particle's energy gain is strongly dependent on the location of injection and is characterised by the angle of approach β, with optimum angle of approach βopt as the value of β which produces the maximum energy gain. We examine the topological features of each regime and analyse the effect on the energy gain of the proton. We also calculate the complete Lyapunov spectrum for the considered dynamical systems in order to correctly quantify the chaotic nature of the particle orbits. We find that the sheared model is a good candidate for the acceleration of particles, and for increased shear, we expect a larger population to be accelerated to higher energy levels. In the strong electric field regime (E0=1500 V/m), the torsional model produces chaotic particle orbits quantified by the calculation of multiple positive Lyapunov exponents in the spectrum, whereas the sheared model produces chaotic orbits only in the neighbourhood of the null point.
Full-range electrical characteristics of WS2 transistors
Authors: Kumar Jatinder , Kuroda Marcelo A. , Bellus Matthew Z. , Han Shu-Jen , Chiu Hsin-Ying
Published: March 2015

We fabricated transistors formed by few layers to bulk single crystal WS2 to quantify the factors governing charge transport. We established a capacitor network to analyze the full-range electrical characteristics of the channel, highlighting the role of quantum capacitance and interface trap density. We find that the transfer characteristics are mainly determined by the interplay between quantum and oxide capacitances. In the OFF-state, the interface trap density (<1012 cm–2) is a limiting factor for the subthreshold swing. Furthermore, the superior crystalline quality and the low interface trap density enabled the subthreshold swing to approach the theoretical limit on a back-gated device on SiO2/Si substrate.
Light emission mechanism of mixed host organic light-emitting diodes
Authors: Song Wook , Lee Jun Yeob
Published: March 2015

Light emission mechanism of organic light-emitting diodes with a mixed host emitting layer was studied using an exciplex type mixed host and an exciplex free mixed host. Monitoring of the current density and luminance of the two type mixed host devices revealed that the light emission process of the exciplex type mixed host was dominated by energy transfer, while the light emission of the exciplex free mixed host was controlled by charge trapping. Mixed host composition was also critical to the light emission mechanism, and the contribution of the energy transfer process was maximized at 50:50 mixed host composition. Therefore, it was possible to manage the light emission process of the mixed host devices by managing the mixed host composition.
Performance and characterization of a MEMS-based device for alignment and manipulation of x-ray nanofocusing optics
Authors: Xu Weihe , Lauer Kenneth , Yan Hui , Milanovic Veljko , Lu Ming , Nazaretski Evgeny
Published: March 2015

X-ray microscopy is a powerful, non-invasive tool used for nanometer-scale resolution imaging, and it is widely applied in various areas of science and technology. To push the spatial resolution of x-ray microscopy studies in the hard x-ray regime below 10 nm, Multilayer Laue Lenses (MLL) can be used as nanofocusing elements. To ensure distortion-free x-ray imaging, high-stability microscopy systems are required. MEMS-based manipulators are a promising route to achieve high stability when used for alignment and manipulation of nanofocusing optics. In this work, we present a tip-tilt MEMS-based device suitable for MLL alignment. We fully characterize the device and demonstrate better-than 10 millidegree angular positioning resolution when utilizing capacitive displacement sensors, and better-than 0.8 millidegree resolution when using laser interferometry.
Damage characterization in plates using singularity of scale mode shapes
Authors: Cao M. S. , Xu H. , Bai R. B. , Ostachowicz W. , Radzieński M. , Chen L.
Published: March 2015

Damage is a prevailing physical phenomenon in in-service structures; accumulation of damage can cause catastrophic structural failure. For damage identification in plates, the concept of scale mode shape with fractal singularity is formulated based on 2D Gabor wavelet transform incorporating fractal dimension analysis of measured mode shapes. With this concept, a scale fractal complexity spectrum is created to reveal mode shape singularities by eliminating noise and interference. The singularity manifests the abnormality of the mode shape, clearly indicating damage. This study develops a philosophy of fusing wavelets and fractals to detect singularities of physical fields in noisy conditions.
Healthcare resource use in patients of the Australian Transition Care Program
Authors: Comans Tracy A. , Peel Nancye M. , Cameron Ian D. , Gray Leonard , Scuffham Paul A.
Published: March 2015

Objective The aim of the present study was to describe, from the perspective of the healthcare funder, the cost components of the Australian Transition Care Program (TCP) and the healthcare resource use and costs for a group of transition care clients over a 6-month period following admission to the program. Methods A prospective cohort observational study of 351 consenting patients entering community-based transition care at six sites in two states in Australia from November 2009 to September 2010 was performed. Patients were followed up 6 months after admission to the TCP to ascertain current living status and hospital re-admissions over the follow-up period. Cost data were collected by transition care teams and from administrative data (hospital and Medicare records). Results The TCP provides a range of services with most costs attributed to provision of personal care support, case management, physiotherapy and occupational therapy. Most healthcare costs up to 6 months after transition care admission were incurred from the hospital admission leading to transition care and from re-admissions. Orthopaedic conditions incurred the highest costs, with many of these for elective procedures and others resulting from falls. Hospital re-admission rates in the present study were 10% lower than in a previous evaluation of the TCP. Over 6 months, approximately 40% of patients in the study were re-admitted to hospital at an average cost of A$7038. Conclusions Although the cost of the TCP is relatively high, it may have some impact on reducing hospital re-admissions and preventing or delaying residential care admissions. What is known about the topic? A majority of healthcare costs occur in older age. What does this paper add? Hospital costs, both initial and re-admissions, are the major contributor to healthcare costs in transition care recipients. Orthopaedic conditions are the most expensive to treat and neurological conditions are the most variable. What are the implications for practitioners? Reducing the length of hospitalisation and reducing re-admissions for older frail people is a key economic concern for health services. Services such as the TCP aim to do both; however, the evidence that this is effective is limited. Streamlining referrals to transition care to enable earlier access and involving the transition care provider in re-admission decisions may help reduce healthcare costs in future.
Can the simple clinical score usefully predict the mortality risk and length of stay for a recently admitted patient?
Authors: Nguyen Minh T. , Woodman Richard J. , Hakendorf Paul , Thompson Campbell H. , Faunt Jeff
Published: March 2015

Objectives
The aim of the present study was to determine whether an aggregate simple clinical score (SCS) has a role in predicting the imminent mortality and in-hospital length of stay (LOS) of newly admitted, acutely unwell General Medical in-patients.

Methods
Data were collected prospectively from adult patients admitted through an Acute Medical Unit between February and August 2013. Using logistic regression analysis before and after adjustment for age, the SCS was assessed for its association with LOS and mortality, including 30-day mortality, just for those patients for full resuscitation. Changes in sensitivity and specificity after adding SCS to age as a predictor, as well as the change in the net reclassification index, were determined using the predicted probabilities from the logistic regression models.

Results
The SCS was superior to age in predicting mortality of any patient within 30 days. It did not assist in predicting 30-day mortality for those patients who were for full resuscitation. The ability of the SCS to predict long stay (>72 h) remained relatively low (64%) and was inferior to published rates achieved by bedside clinician assessment (74%–82%).

Conclusion
There was no useful prospective role for the SCS in predicting LOS and mortality of in-patients newly admitted to a General Medicine service.

What is known about the topic?
After their presentation to the emergency department, care efficiency is improved by the ‘streaming’ of patients according to their risk of imminent deterioration and their likelihood of being a long-stay patient. Although streaming is currently effected by bedside assessment of the patient, an accepted aggregate assessment score may assist disposition decisions.

What does this paper add?
Bedside assessment of each patient still offers the most accurate method for identifying the long-stay patient. The SCS, good at predicting 30-day mortality of all new admissions, is not useful for predicting the death of those admissions who are for full resuscitation.

What are the implications for practitioners?
When deciding admitted patients’ disposition on leaving the emergency department, a simple aggregate score based on patient physiology, comorbidity and functionality has little to offer practitioners beyond knowledge of each patient’s age.
Pre-entry student clinical placement demand: can it be met?
Authors: McBride Liza-Jane , Fitzgerald Cate , Morrison Laura , Hulcombe Julie
Published: March 2015

Objectives The Clinical Education Workload Management Initiative (the Initiative) is a unique, multiprofessional, jurisdiction-wide approach and reform process enshrined within an industrial agreement. The Initiative enabled significant investment in allied health clinical education across Queensland public health services to address the workload associated with providing pre-entry clinical placements. This paper describes the outcomes of a quality review activity to measure the impact of the Initiative on placement capacity and workload management for five allied health professions. Data related to several key factors impacting on placement supply and demand in addition to qualitative perspectives from workforce surveys are reported. Methods Data from a range of quality review actions including collated placement activity data, and workforce and student cohort statistics were appraised. Stakeholder perspectives reported in surveys were analysed for emerging themes. Results Placement offers showed an upward trend in the context of increased university program and student numbers and in contrast with a downward trend in full-time equivalent (FTE) staff numbers. Initiative-funded positions were identified as a major factor in individual practitioners taking more students, and staff and managers valued the Initiative-funded positions’ support before and during placements, in the coordination of placements, and in building partnerships with universities. Conclusions The Initiative enabled a co-ordinated response to meeting placement demand and enhanced collaborations between the health and education sectors. Sustaining pre-entry student placement provision remains a challenge for the future. What is known about the topic? The literature clearly identifies factors impacting on increasing demand for clinical placements and a range of strategies to increase clinical placement capacity. However, reported initiatives have mostly been ad hoc or reactive responses, often isolated within services or professions. What does this paper add? This paper describes implementation of a clinical placement capacity building initiative within public sector health services developed from a unique opportunity to provide funding through an industrial agreement. The Initiative aimed to address the workload associated with clinical education of pre-entry students and new graduates. What are the implications for practitioners? This paper demonstrates that systematic commitment to, and funding of, clinical education across a jurisdiction’s public health services is able to increase placement capacity, even when staffing numbers are in decline.
The future healthcare?
Authors: Charlesworth Kate , Jamieson Maggie , Butler Colin D. , Davey Rachel
Published: March 2015

Background Healthcare systems in Australia and around the world are failing to address the challenges of the modern world. Healthcare leaders are calling for radical, transformational change and entirely new systems of care. However it is unclear what a future, sustainable healthcare system would look like. Methods A narrative review to examine emerging trends in health and social care was conducted. Results and Conclusions Six key trends were identified. Collectively, they suggest that future systems are likely to be characterised by increasingly sophisticated technology, but at the same time greater personal and community responsibility for health and well being, innovative use of social capital, and a new approach to ageing and end-of-life care. What is known about the topic? Health care systems in Australia and around the world are failing to address the key health challenges of modern society. There are calls for radical, transformational change of our health care systems; however it is unclear what a future, sustainable system would look like. What does this paper add? In this narrative review, we identify and examine six key emerging trends in health and social care. Collectively, these trends suggest that future systems are likely to be characterised by increasingly sophisticated technology; but at the same time greater personal and community responsibility for health and well-being, innovative use of social capital, and a new approach to ageing and end-of-life-care. What are the implications for practitioners? It is becoming increasingly clear that radical change is necessary and there are emerging examples of novel and creative initiatives across many areas of practice. Practitioners need to be engaged in, contributing to and in some cases, leading, this transition to a new health and social care system.
Pap smear rates among Australian community-attached lesbian and bisexual women: some good news but disparities persist
Authors: Douglas Catriona , Deacon Rachel , Mooney-Somers Julie
Published: March 2015

Background
Research in the US and UK shows that lesbian women are less likely than their heterosexual peers to attend for routine Pap smear tests. This study examined Pap smear test rates among community-attached lesbian, bisexual and queer (LBQ) women in New South Wales (NSW), to investigate if rates had changed between 2002 and 2012, compare rates to the general NSW population and identify predictive factors for Pap smear test attendance. Methods: Data was taken from the Sydney Women and Sexual Health (SWASH) survey, a self-completed biennial questionnaire of LBQ women’s health and wellbeing. Results: Of the 4083 respondents, 83% had ever had a Pap smear test. Recent attendance rates were similar to the general NSW population. Significant predictors for ever having attended for a Pap smear test were older age, post Year 12 education, ever having had a sexually transmissible infection test, being out about sexuality to a regular doctor and ever having had sex with men. Conclusions: Pap smear rates for LBQ women are encouraging when compared with rates from countries such as the US or UK. A significant proportion of LBQ women are never receiving Pap smear tests. Predictive factors suggest a continued perception that women who have not had sex with men are not at risk of human papillomavirus, and highlight the importance of health providers providing a safe and welcoming environment for LBQ women to openly discuss their health.
DEOD: uncovering dominant effects of cancer-driver genes based on a partial covariance selection method
Authors: Amgalan Bayarbaatar , Lee Hyunju
Published: March 2015

Motivation: The generation of a large volume of cancer genomes has allowed us to identify disease-related alterations more accurately, which is expected to enhance our understanding regarding the mechanism of cancer development. With genomic alterations detected, one challenge is to pinpoint cancer-driver genes that cause functional abnormalities.

Results: Here, we propose a method for uncovering the dominant effects of cancer-driver genes (DEOD) based on a partial covariance selection approach. Inspired by a convex optimization technique, it estimates the dominant effects of candidate cancer-driver genes on the expression level changes of their target genes. It constructs a gene network as a directed-weighted graph by integrating DNA copy numbers, single nucleotide mutations and gene expressions from matched tumor samples, and estimates partial covariances between driver genes and their target genes. Then, a scoring function to measure the cancer-driver score for each gene is applied. To test the performance of DEOD, a novel scheme is designed for simulating conditional multivariate normal variables (targets and free genes) given a group of variables (driver genes). When we applied the DEOD method to both the simulated data and breast cancer data, DEOD successfully uncovered driver variables in the simulation data, and identified well-known oncogenes in breast cancer. In addition, two highly ranked genes by DEOD were related to survival time. The copy number amplifications of MYC (8q24.21) and TRPS1 (8q23.3) were closely related to the survival time with P-values = 0.00246 and 0.00092, respectively. The results demonstrate that DEOD can efficiently uncover cancer-driver genes.

Availability and implementation: DEOD was implemented in Matlab, and source codes and data are available at http://combio.gist.ac.kr/softwares/.

Contact:  hyunjulee@gist.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Halvade: scalable sequence analysis with MapReduce
Authors: Decap Dries , Reumers Joke , Herzeel Charlotte , Costanza Pascal , Fostier Jan
Published: March 2015

Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine.

Results: We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infrastructure in a highly efficient manner. As an example, a DNA sequencing analysis pipeline for variant calling has been implemented according to the GATK Best Practices recommendations, supporting both whole genome and whole exome sequencing. Using a 15-node computer cluster with 360 CPU cores in total, Halvade processes the NA12878 dataset (human, 100 bp paired-end reads, 50× coverage) in <3 h with very high parallel efficiency. Even on a single, multi-core machine, Halvade attains a significant speedup compared with running the individual tools with multithreading.

Availability and implementation: Halvade is written in Java and uses the Hadoop MapReduce 2.0 API. It supports a wide range of distributions of Hadoop, including Cloudera and Amazon EMR. Its source is available at http://bioinformatics.intec.ugent.be/halvade under GPL license.

Contact:  jan.fostier@intec.ugent.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Validation of Diagnostic Groups Based on Health Care Utilization Data Should Adjust for Sampling Strategy
Authors: Cadieux Geneviève , Tamblyn Robyn , Buckeridge David L. , Dendukuri Nandini
Published: March 2015

Objective:

Valid measurement of outcomes such as disease prevalence using health care utilization data is fundamental to the implementation of a “learning health system.” Definitions of such outcomes can be complex, based on multiple diagnostic codes. The literature on validating such data demonstrates a lack of awareness of the need for a stratified sampling design and corresponding statistical methods. We propose a method for validating the measurement of diagnostic groups that have: (1) different prevalences of diagnostic codes within the group; and (2) low prevalence.

Methods:

We describe an estimation method whereby: (1) low-prevalence diagnostic codes are oversampled, and the positive predictive value (PPV) of the diagnostic group is estimated as a weighted average of the PPV of each diagnostic code; and (2) claims that fall within a low-prevalence diagnostic group are oversampled relative to claims that are not, and bias-adjusted estimators of sensitivity and specificity are generated.

Application:

We illustrate our proposed method using an example from population health surveillance in which diagnostic groups are applied to physician claims to identify cases of acute respiratory illness.

Conclusions:

Failure to account for the prevalence of each diagnostic code within a diagnostic group leads to the underestimation of the PPV, because low-prevalence diagnostic codes are more likely to be false positives. Failure to adjust for oversampling of claims that fall within the low-prevalence diagnostic group relative to those that do not leads to the overestimation of sensitivity and underestimation of specificity.
Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase
Authors: Thomsen Maren , Tuukkanen Anne , Dickerhoff Jonathan , Palm Gottfried J. , Kratzat Hanna , Svergun Dmitri I. , Weisz Klaus , Bornscheuer Uwe T. , Hinrichs Winfried
Published: March 2015

Flavonoids represent a large class of secondary metabolites produced by plants. These polyphenolic compounds are well known for their antioxidative abilities, are antimicrobial phytoalexins responsible for flower pigmentation to attract pollinators and, in addition to other properties, are also specific bacterial regulators governing the expression ofRhizobiumgenes involved in root nodulation (Firminet al., 1986). The bacterial chalcone isomerase (CHI) fromEubacterium ramuluscatalyses the first step in a flavanone-degradation pathway by ring opening of (2S)-naringenin to form naringenin chalcone. The structural biology and enzymology of plant CHIs have been well documented, whereas the existence of bacterial CHIs has only recently been elucidated. This first determination of the structure of a bacterial CHI provides detailed structural insights into the key step of the flavonoid-degradation pathway. The active site could be confirmed by co-crystallization with the substrate (2S)-naringenin. The stereochemistry of the proposed mechanism of the isomerase reaction was verified by specific1H/2H isotope exchange observed by1H NMR experiments and was further supported by mutagenesis studies. The active site is shielded by a flexible lid, the varying structure of which could be modelled in different states of the catalytic cycle using small-angle X-ray scattering data together with the crystallographic structures. Comparison of bacterial CHI with the plant enzyme fromMedicago sativareveals that they have unrelated folds, suggesting that the enzyme activity evolved convergently from different ancestor proteins. Despite the lack of any functional relationship, the tertiary structure of the bacterial CHI shows similarities to the ferredoxin-like fold of a chlorite dismutase and the stress-related protein SP1.
Structures of complexes of type 5 17β-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding
Authors: Amano Yasushi , Yamaguchi Tomohiko , Niimi Tatsuya , Sakashita Hitoshi
Published: March 2015

Type 5 17β-hydroxysteroid dehydrogenase (17β-HSD5) is an aldo-keto reductase expressed in the human prostate which catalyzes the conversion of androstenedione to testosterone. Testosterone is converted to 5α-dihydrotestosterone, which is present at high concentrations in patients with castration-resistant prostate cancer (CRPC). Inhibition of 17β-HSD5 is therefore considered to be a promising therapy for treating CRPC. In the present study, crystal structures of complexes of 17β-HSD5 with structurally diverse inhibitors derived from high-throughput screening were determined. In the structures of the complexes, various functional groups, including amide, nitro, pyrazole and hydroxyl groups, form hydrogen bonds to the catalytic residues His117 and Tyr55. In addition, major conformational changes of 17β-HSD5 were observed following the binding of the structurally diverse inhibitors. These results demonstrate interactions between 17β-HSD5 and inhibitors at the atomic level and enable structure-based drug design for anti-CRPC therapy.
The role of monovalent cations in the ATPase reaction of DNA gyrase
Authors: Hearnshaw Stephen James , Chung Terence Tsz-Hong , Stevenson Clare Elizabeth Mary , Maxwell Anthony , Lawson David Mark
Published: March 2015

Four new crystal structures of the ATPase domain of the GyrB subunit ofEscherichia coliDNA gyrase have been determined. One of these, solved in the presence of K+, is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K+ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na+ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.
Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition
Authors: Lin Chien-Chih , Chuankhayan Phimonphan , Chang Wen-Ni , Kao Tseng-Ting , Guan Hong-Hsiang , Fun Hoong-Kun , Nakagawa Atsushi , Fu Tzu-Fun , Chen Chun-Jung
Published: March 2015

10-Formyltetrahydrofolate dehydrogenase (FDH), which is composed of a small N-terminal domain (Nt-FDH) and a large C-terminal domain, is an abundant folate enzyme in the liver and converts 10-formyltetrahydrofolate (10-FTHF) to tetrahydrofolate (THF) and CO2. Nt-FDH alone possesses a hydrolase activity, which converts 10-FTHF to THF and formate in the presence of β-mercaptoethanol. To elucidate the catalytic mechanism of Nt-FDH, crystal structures of apo-form zNt-FDH from zebrafish and its complexes with the substrate analogue 10-formyl-5,8-dideazafolate (10-FDDF) and with the products THF and formate have been determined. The structures reveal that the conformations of three loops (residues 86–90, 135–143 and 200–203) are altered upon ligand (10-FDDF or THF) binding in the active site. The orientations and geometries of key residues, including Phe89, His106, Arg114, Asp142 and Tyr200, are adjusted for substrate binding and product release during catalysis. Among them, Tyr200 is especially crucial for product release. An additional potential THF binding site is identified in the cavity between two zNt-FDH molecules, which might contribute to the properties of product inhibition and THF storage reported for FDH. Together with mutagenesis studies and activity assays, the structures of zNt-FDH and its complexes provide a coherent picture of the active site and a potential THF binding site of zNt-FDH along with the substrate and product specificity, lending new insights into the molecular mechanism underlying the enzymatic properties of Nt-FDH.
Schistosoma mansonivenom allergen-like protein 4 (SmVAL4) is a novel lipid-binding SCP/TAPS protein that lacks the prototypical CAP motifs. Corrigendum
Authors: Kelleher Alan , Darwiche Rabih , Rezende Wanderson C. , Farias Leonardo P. , Leite Luciana C. C. , Schneiter Roger , Asojo Oluwatoyin A.
Published: March 2015

Figure 6(a) of the article by Kelleheret al.[(2014),Acta Cryst.D70, 2186–2196] is corrected.
Crystal structure ofS-octyl (E)-3-(4-methoxybenzylidene)dithiocarbazate
Authors: Begum M. S. , Zangrando E. , Sheikh M. C. , Miyatake R. , Hossain M. M.
Published: March 2015

As already observed in similar molecules, the dithiocarbazate group in the title compound, C17H26N2OS2, adopts anEEconfiguration with respect to the C=N bond of the benzylidene moiety. In the crystal, molecules are connected into inversion dimers by pairs of N—H...S hydrogen bonds. The dimers are linked by weak π–π interactions, with centroid-to-centroid distances of 3.723 (11) Å, forming chains parallel to [110].
Crystal structure of (E)-N-[(2-chloro-6-methoxyquinolin-3-yl)methylidene]-9-ethyl-9H-carbazol-3-amine
Authors: Thirumurthy Kannan , Thirunarayanan Ganesamoorthy , Murugavel S.
Published: March 2015

In the title compound, C25H20ClN3O, the C=N bond of the central imine group adopts anEconformation. The mean planes through the essentially planar carbazole [maximum deviation = 0.052 (2)Å] and quinoline [maximum deviation = 0.050 (2) Å] ring systems form a dihedral angle of 50.2 (1)°. In the crystal, molecules are linked by C—H...π and π—π interactions [centroid–centroid distances ranging from 3.635 (2) to 3.739 (2) Å], forming a three-dimensional supramolecular network.
Crystal structure of heptakis(2,6-dimethylphenyl isocyanide-κC)vanadium(I) iodide
Authors: Minyaev Mikhail E. , Ellis John E.
Published: March 2015

The title salt, [V(C9H9N)7]+I−or [V(CNXyl)7]+I−(Xyl is 2,6-dimethylphenyl), crystallized from tetrahydrofuran at low temperatures after reacting (Et4N)+[V(CO)6]−, excess of CNXyl and iodine. The complex cation and the two crystallographically different iodide anions, each located on a different glide plane, are well separated in the crystal structure. The V(CN)7core of the cation has the form of a distorted monocapped trigonal prism. This compound is of interest as the first isolable homoleptic seven-coordinate vanadium analog of the 18-electron [V(CO)7]+monocation.
Impact of social networking tools on scholarly communication: a cross-institutional study
Authors: Al-Aufi Ali , Fulton Crystal
Published: March 2015

Purpose

– This paper aims to investigate the extent to which social networking tools had an impact on academics’ patterns of informal scholarly communication in humanities and social science disciplines. Social networking tools, reinforced by proliferation and advances in portable computing and wireless technologies, have reshaped how information is produced, communicated and consumed.

Design/methodology/approach

– A cross-institutional quantitative study utilized an online questionnaire survey sent to 382 academics affiliated with humanities and social science disciplines in two different academic institutions: one that belongs to a Western tradition of scholarly communication in Ireland, and the other to a developing country in Oman. Descriptive interpretation of data compared findings from both universities. Frequencies, percentages and means were displayed in tables to enhance the meaning of collected data. Inferential analysis was also conducted to determine statistical significance.

Findings

– Overall findings indicate progressive use of social networking tools for informal scholarly communication. There is perceived usefulness on the impact of social networking tools on patterns of informal scholarly communication. However, nearly one-third of the respondents have never used social networking tools for informal scholarly communication. Institution-based data comparison revealed no significant differences on data except for few activities of informal scholarly communication.

Research limitations/implications

– Given that the number of study subjects was eventually small (total = 382) and that academics by their very nature are disinclined to respond to online surveys, results of the study may suggest non-response errors, and these may impact negatively on the acceptability of inferences and statistical conclusions. The results of the study are, therefore, unlikely to be useful for generalization, but they remain suggestive of a growing tendency among humanities and social sciences’ academics to use social networking tools for informal scholarly communication.

Originality/value

– Empirical findings provide a broad understanding about the potential of social networking tools on informal scholarly communication in areas of humanities and social sciences disciplines. Multi-disciplinary investigation and qualitative studies may further deepen our understanding of the impact of social networking tools on patterns of scholarly communication.
Constructing an e-portfolio-based integrated learning environment supported by library resource
Authors: Chen Zac S.C. , Yang Stephen J.H. , Huang Jeff J.S.
Published: March 2015

Purpose

– The purpose of this study was to present a pilot electronic portfolio (e-portfolio)-integrated learning environment by integrating library resources into an e-portfolio system for its application, and to explore reader’s satisfaction of the integrated system.

Design/methodology/approach

– This study develops a research model by modifying the information success model to explore reader satisfaction to the understanding of the adoption of integrated system. The sample consisted of 289 graduate and undergraduate students. In total, 189 were considered useful and used for analysis. A regression analysis was then conducted to identify key causal relationships.

Findings

– The findings show that reader-perceived benefits, information quality and system quality are critical factors for the reader’s satisfaction. Overall, the model explained 84 per cent of the variance in reader satisfaction. Thus, the results show that the proposed model does satisfactorily explain the reader’s satisfaction of the integrated system.

Originality/value

– There is scant research available in the literature on user satisfaction of pilot e-portfolio-integrated learning environment from a reader perspective. The findings of this research provide some useful insights into a reader’s satisfaction toward adoption of the integrated system. In addition, it will be valuable for better understanding of factors affecting the determinants of reader’s satisfaction, which improve the reader’s satisfaction of the integrated system and thereby boost realization of collaborative learning environment.