bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abetalipoproteinemia and homozygous hypobetalipoproteinemia: a framework for diagnosis and management
Authors: Lee Jooho , Hegele Robert A. 
Published: November 2013

AbstractAbetalipoproteinemia (ABL; OMIM 200100) and homozygous hypobetalipoproteinemia (HHBL; OMIM 107730) are rare diseases characterized by hypocholesterolemia and malabsorption of lipid‐soluble vitamins leading to retinal degeneration, neuropathy and coagulopathy. Hepatic steatosis is also common. The root cause of both disorders is improper packaging and secretion of apolipoprotein (apo) B‐containing lipoprotein particles due to mutations either in both alleles of the MTP (alias MTTP) gene encoding microsomal triglyceride transfer protein (MTP) or both alleles of the APOB gene itself in the case of ABL and HHBL, respectively. Clinical diagnosis is based on signs and symptoms, acanthocytosis on blood smear, and virtually absent apo B‐containing lipoproteins, including chylomicrons, very low density lipoprotein and low density lipoprotein. Obligate heterozygote parents of ABL patients usually have normal lipids consistent with autosomal recessive inheritance, while heterozygous parents of HHBL patients typically have half normal levels of apo B‐containing lipoproteins consistent with autosomal co‐dominant inheritance. Definitive diagnosis involves sequencing the MTP and APOB genes, for which >30 and >60 mutations have been described for ABL and HHBL, respectively. Follow‐up includes monitoring for ophthalmologic, neurologic, hematologic, and hepatic complications, as well as compliance with treatment. Investigations include lipid profile, serum transaminases, markers for lipid‐soluble vitamins, and periodic instrumental assessment of ocular and neurological function. Mainstays of treatment include adherence to a low‐fat diet, and supplementation with essential fatty acids and high oral doses of fat soluble vitamins. Prognosis is variable, but early diagnosis and strict adherence to treatment can recover normal neurological function and halt disease progression.
Effects of fluctuating energy input on the small scales in turbulence
Authors: Chien Chen-Chi , Blum Daniel B. , Voth Greg A. 
Published: November 2013

AbstractIn the standard cascade picture of three-dimensional turbulent fluid flows, energy is input at a constant rate at large scales. Energy is then transferred to smaller scales by an intermittent process that has been the focus of a vast literature. However, the energy input at large scales is not constant in most real turbulent flows. We explore the signatures of these fluctuations of large-scale energy input on small-scale turbulence statistics. Measurements were made in a flow between oscillating grids, with ${R}_{\lambda } $ up to 262, in which temporal variations in the large-scale energy input can be introduced by modulating the oscillating grid frequency. We find that the Kolmogorov constant for second-order longitudinal structure functions depends on the magnitude of the fluctuations in the large-scale energy input. We can quantitatively predict the measured change with a model based on Kolmogorov’s refined similarity theory. The effects of fluctuations of the energy input can also be observed using structure functions conditioned on the instantaneous large-scale velocity. A linear parametrization using the curvature of the conditional structure functions provides a fairly good match with the measured changes in the Kolmogorov constant. Conditional structure functions are found to provide a more sensitive measure of the presence of fluctuations in the large-scale energy input than inertial range scaling coefficients.
Molecular identification of hookworms in stray and shelter dogs from Guangzhou city, China using ITS sequences
Authors: Liu Y.J. , Zheng G.C. , Zhang P. , Alsarakibi M. , Zhang X.H. , Li Y.W. , Liu T. , Ren S.N. , Chen Z.X. , Liu Y.L. , Li S.J. , Li G.Q. 
Published: November 2013

AbstractCanine hookworm infections are endemic worldwide, with zoonotic transmission representing a potentially significant public health concern. This study aimed to investigate hookworm infection and identify the prevalent species from stray and shelter dogs in Guangzhou city, southern China by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) based on internal transcribed spacer (ITS) sequences. From March 2011 to July 2012, fresh faecal samples from a total of 254 dogs were obtained from five locations, namely Conghua, Baiyun, Liwan, Haizhu and Panyu, in Guangzhou. These samples were screened for the presence of hookworm eggs using light microscopy, with an overall prevalence of 29.53% being recorded. The highest prevalence of 45.28% was found in suburban dogs from Conghua compared with lower values recorded in urban dogs in Haizhu (21.43%), Baiyun (18.97%), Panyu (18.18%) and Liwan (15%). The prevalence in stray dogs was signiﬁcantly higher than that in shelter dogs. PCR-RFLP analysis showed that 57.33% were detected as single hookworm infections withAncyclostoma caninum, and 22.67% asA. ceylanicum, while 20% were mixed infections. This suggests that high prevalences of both hookworm species in stray and shelter dogs in China pose a potential risk of transmission from pet dogs to humans.
White matter microstructural abnormalities in families multiply affected with bipolar I disorder: a diffusion tensor tractography study
Authors: Emsell L. , Chaddock C. , Forde N. , Van Hecke W. , Barker G. J. , Leemans A. , Sunaert S. , Walshe M. , Bramon E. , Cannon D. , Murray R. , McDonald C. 
Published: November 2013

BackgroundWhite matter (WM) abnormalities are proposed as potential endophenotypic markers of bipolar disorder (BD). In a diffusion tensor imaging (DTI) voxel-based analysis (VBA) study of families multiply affected with BD, we previously reported that widespread abnormalities of fractional anisotropy (FA) are associated with both BD and genetic liability for illness. In the present study, we further investigated the endophenotypic potential of WM abnormalities by applying DTI tractography to specifically investigate tracts implicated in the pathophysiology of BD.MethodDiffusion magnetic resonance imaging (MRI) data were acquired from 19 patients with BD type I from multiply affected families, 21 of their unaffected first-degree relatives and 18 healthy volunteers. DTI tractography was used to identify the cingulum, uncinate fasciculus (UF), arcuate portion of the superior longitudinal fasciculus (SLF), inferior longitudinal fasciculus (ILF), corpus callosum, and the anterior limb of the internal capsule (ALIC). Regression analyses were conducted to investigate the effect of participant group and genetic liability on FA and radial diffusivity (RD) in each tract.ResultsWe detected a significant effect of group on both FA and RD in the cingulum, SLF, callosal splenium and ILF driven by reduced FA and increased RD in patients compared to controls and relatives. Increasing genetic liability was associated with decreased FA and increased RD in the UF, and decreased FA in the SLF, among patients.ConclusionsWM microstructural abnormalities in limbic, temporal and callosal pathways represent microstructural abnormalities associated with BD whereas alterations in the SLF and UF may represent potential markers of endophenotypic risk.
Teacher Knowledge and Perceptions of Stuttering and Bullying in School‐Age Children.
Authors: Plexico Laura W. , Plumb Allison M. , Beacham Jillian 
Published: November 2013

Purpose: To evaluate teacher knowledge and perceptions of the development and management of stuttering, as well as bullying.
Method: A 32‐item web‐based survey was created to address the purposes of this investigation. Participants were recruited in 5 states representing diverse geographic regions by sending an e‐mail with an attached information letter and an embedded e‐mail link. A total of 84 teachers completed the survey.
Results: Teachers demonstrated a general understanding of the cause and characteristics associated with stuttering; however, teachers indicated some feelings of discomfort surrounding stuttering and there were some indications that they are not clear on the best ways to manage it, nor do they have access to materials. The majority identified bullying as a problem at their schools and encountered bullying of children who stutter.
Conclusions: The results from this investigation were mixed in that teachers demonstrated insight into some areas of stuttering and bullying, but decreased awareness or misperceptions in others. The findings highlight the critical role of the speech‐language pathologist in the continued need for in‐services and information provision on the nature and management of childhood stuttering as well as bullying.
Correlation Between Frequency and Perceptual Severity of Stuttering in a Clinical Setting
Authors: Irani Farzan , Megan Edge 
Published: November 2013

Purpose: The purpose of this study is to further explore the relationship between the frequency of stuttering measured in percentage of syllables stuttered (%SS) and perceptual ratings of stuttering severity by the clinician and the client in a clinical setting.
Method: Eight adolescent and adult participants attending a stuttering therapy program and their graduate student clinicians perceptually rated stuttering severity using a 9‐point scale. Speech samples were gathered during each therapy session for a total of 167 speech samples. Further, each sample was analyzed for %SS. A Pearson Product Moment Correlation (PPMC) was used to determine the strength and direction of correlations between %SS and perceptual ratings by the clinician and client.
Results: The correlational analysis indicates significant positive correlations between perceptual severity ratings by the clinician and client as well as %SS. Correlation between perceptual ratings was stronger than the correlation between perceptual ratings and %SS.
Conclusion: The strong, positive correlation between the client's self‐measurement and the clinician's perceptual measurement indicates similarities in global severity of stuttering perception. Weaker correlation between %SS and perceptual ratings indicates the need to incorporate a more holistic measure of stuttering severity. Implication and directions for future research are discussed.
Exploring the Frustration of Situational Variability Using Visual Methodology With an Adult Who Stammers
Authors: Bull Claire , Stewart Trudy , Kitchen Joanna 
Published: November 2013

Purpose: Adults who stammer frequently report frustration linked to the variability of stammering (stuttering) across speaking situations, be that in relation to the variability of speech fluency or the underlying emotional response.
The paper will present the case of Tom and the collaborative development of a visual methodology which arose in response to clinical need. Tom is an adult who stammers who experienced high levels of frustration associated with the variability of his speech fluency and speech-associated anxiety (SAA). Exploring this variability was of central importance to the identification stage of therapy.
Method: In the absence of an existing support mechanism for this process, a tool called the Situation Radar was developed. The Situation Radar (SR) provides a unique, visual representation of a client’s individual pattern of situational variability across different speaking situations.
Results: Clinical application of the SR and its associated processes revealed a number of uses within the therapy context, relating to the identification process and throughout therapy.
The client reported that using the SR to explore situational variability supported an increased awareness of his SAA, which in turn guided target setting and led to an expanded comfort zone.
Conclusion: Further study into the use of the SR is indicated.
Neurologic Substrates of Motor Speech Disorders
Authors: Strand Edythe A. 
Published: November 2013

A good clinical understanding of the neurologic substrates of neurologic communicative disorders is important both to diagnosis and treatment. This article briefly reviews neurologic substrates for motor speech disorders (MSD) and how clinicians may identify neurologic signs and symptoms to facilitate differential diagnosis of apraxia of speech (AOS) and the various types of dysarthria.
Students and clinicians have numerous resources regarding general neuroanatomy and neurophysiology (e.g. Benarroch, 2006; Kandel, Schwartz, and Jessel, 1991; Nolte, 2002; Snell, 1997) as well as neuroanatomic correlates of speech-language behavior and disorders (Bhatnagar, 2012; Duffy, 2013). Articles on aspects of neuroimaging (Brown, Petersen and Schlaggar, 2003; Shuster, 2003) and neurologic substrates for MSDs (Farinella-Bocian, Strand, and Benarroch, 2007) are also available in previous editions of Perspectives.
This article begins with an overview of the differing MSDs. A brief overview of neurologic systems is provided, followed by a more detailed description of the neurologic substrates for MSDs. Examples of clinical observations of speech and non-speech characteristics that can aid the clinician in understanding the underlying neural deficit are provided.
Instrumental Assessment in Cleft Palate Care
Authors: Perry Jamie , Schenck Graham 
Published: November 2013

Despite advances in surgical management, it is estimated that 20–30% of children with repaired cleft palate will continue to have hypernasal speech and require a second surgery to create normal velopharyngeal function (Bricknell, McFadden, & Curran, 2002; Härtel, Karsten, & Gundlach, 1994; McWilliams, 1990). A qualitative perceptual assessment by a speech-language pathologist is considered the most important step of the evaluation for children with resonance disorders (Peterson-Falzone, Hardin-Jones, & Karnell, 2010). Direct and indirect instrumental analyses should be used to confirm or validate the perceptual evaluation of an experienced speech-language pathologist (Paal, Reulbach, Strobel-Schwarthoff, Nkenke, & Schuster, 2005).
The purpose of this article is to provide an overview of current instrumental assessment methods used in cleft palate care. Both direct and indirect instrumental procedures will be reviewed with descriptions of the advantages and disadvantages of each. Lastly, new developments for evaluating velopharyngeal structures and function will be provided.
Differential‐fed ultra‐wideband slot‐loaded patch antenna with dual orthogonal polarisation
Authors: Zhang Kai , Zhu Fuguo , Gao Steven 
Published: November 2013

A novel dual‐polarised ultra‐wideband patch antenna is proposed. This antenna consists of a square ring patch and four inclined triangular‐shaped patches. The vertices of the triangular patches are connected to the microstrip lines which are printed on the bottom layer of the grounded FR4 substrate. To realise the differential feed mechanism for reducing the coupling between the two polarisation ports and the cross‐polarisation level, two identical tapered baluns are used to excite the antenna. The antenna prototype can provide two orthogonal polarisations with an impedance bandwidth (|S11| ≤ −10 dB) of 113.2% and isolation of over 28 dB across the whole operating frequency band. The measured antenna gain varies from 2.09 to 7.66 dBi for port 1 and from 0.02 to 6.77 dBi for port 2 with a 3 dB gain bandwidth of 96.3%.
Human autoimmunity after lymphocyte depletion is caused by homeostatic T-cell proliferation
Authors: Jones Joanne L. , Thompson Sara A. J. , Loh Priscilla , Davies Jessica L. , Tuohy Orla C. , Curry Allison J. , Azzopardi Laura , Hill-Cawthorne Grant , Fahey Michael T. , Compston Alastair , Coles Alasdair J. 
Published: November 2013

Significance
This paper identifies the mechanism by which patients with multiple sclerosis develop secondary autoimmunity after treatment with the lymphocyte-depleting humanized monoclonal antibody alemtuzumab (Campath-1H). In identifying this mechanism, it shows that T-cell homeostatic proliferation can lead to autoimmunity in humans. Alemtuzumab is one of the most effective treatments of multiple sclerosis tested to date; it is currently licensed in the European Union and under consideration by the Food and Drug Administration. Understanding what drives its most significant side effect is of clear clinical importance.
Rubella virus capsid protein structure and its role in virus assembly and infection
Authors: Mangala Prasad Vidya , Willows Steven D. , Fokine Andrei , Battisti Anthony J. , Sun Siyang , Plevka Pavel , Hobman Tom C. , Rossmann Michael G. 
Published: November 2013

Significance
Rubella virus (RV) is a human pathogen that causes serious birth defects when contracted during pregnancy. However, due to its variable shape and size, little is known about the RV structure. The RV capsid protein is an essential component of the virus and a key factor for successful replication of the virus in host cells. Here we describe the atomic structure of the RV capsid protein. This structure, along with electron microscopic data on the virus, has provided a three-dimensional picture of the virion. The capsid protein structure has also helped to identify amino acid residues that are required for virus assembly. This information can be used for the development of antiviral therapies that target the viral capsid protein.
Immunoglobulin knockout chickens via efficient homologous recombination in primordial germ cells
Authors: Schusser Benjamin , Collarini Ellen J. , Yi Henry , Izquierdo Shelley Mettler , Fesler Jeffrey , Pedersen Darlene , Klasing Kirk C. , Kaspers Bernd , Harriman William D. , van de Lavoir Marie-Cecile , Etches Robert J. , Leighton Philip A. 
Published: November 2013

Significance
Chickens have been an important animal model in the fields of developmental biology and immunology over the last century and have contributed a number of basic findings in these areas. However, their use has been limited more recently because there has been no way to genetically engineer specific mutations in the chicken. In addition to basic research applications, genetic modification in birds could also be used to mitigate the threat of avian influenza by production of flu-resistant bird stocks in agriculture. Here we describe an efficient way to target genes of interest in the chicken genome and create knockout chickens. We targeted the immunoglobulin heavy chain gene, leading to loss of antibody production and a block in B-cell development.
Flexible analysis of RNA-seq data using mixed effects models
Authors: Turro Ernest , Astle William J. , Tavaré Simon 
Published: November 2013

AbstractMotivation: Most methods for estimating differential expression from RNA-seq are based on statistics that compare normalized read counts between treatment classes. Unfortunately, reads are in general too short to be mapped unambiguously to features of interest, such as genes, isoforms or haplotype-specific isoforms. There are methods for estimating expression levels that account for this source of ambiguity. However, the uncertainty is not generally accounted for in downstream analysis of gene expression experiments. Moreover, at the individual transcript level, it can sometimes be too large to allow useful comparisons between treatment groups.Results: In this article we make two proposals that improve the power, specificity and versatility of expression analysis using RNA-seq data. First, we present a Bayesian method for model selection that accounts for read mapping ambiguities using random effects. This polytomous model selection approach can be used to identify many interesting patterns of gene expression and is not confined to detecting differential expression between two groups. For illustration, we use our method to detect imprinting, different types of regulatory divergence in cis and in trans and differential isoform usage, but many other applications are possible. Second, we present a novel collapsing algorithm for grouping transcripts into inferential units that exploits the posterior correlation between transcript expression levels. The aggregate expression levels of these units can be estimated with useful levels of uncertainty. Our algorithm can improve the precision of expression estimates when uncertainty is large with only a small reduction in biological resolution.Availability and implementation: We have implemented our software in the mmdiff and mmcollapse multithreaded C++ programs as part of the open-source MMSEQ package, available on https://github.com/eturro/mmseq.Contact: et341@cam.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
mCSM: predicting the effects of mutations in proteins using graph-based signatures
Authors: Pires Douglas E. V. , Ascher David B. , Blundell Tom L. 
Published: November 2013

Abstract
Motivation: Mutations play fundamental roles in evolution by introducing diversity into genomes. Missense mutations in structural genes may become either selectively advantageous or disadvantageous to the organism by affecting protein stability and/or interfering with interactions between partners. Thus, the ability to predict the impact of mutations on protein stability and interactions is of significant value, particularly in understanding the effects of Mendelian and somatic mutations on the progression of disease. Here, we propose a novel approach to the study of missense mutations, called mCSM, which relies on graph-based signatures. These encode distance patterns between atoms and are used to represent the protein residue environment and to train predictive models. To understand the roles of mutations in disease, we have evaluated their impacts not only on protein stability but also on protein–protein and protein–nucleic acid interactions.
Results: We show that mCSM performs as well as or better than other methods that are used widely. The mCSM signatures were successfully used in different tasks demonstrating that the impact of a mutation can be correlated with the atomic-distance patterns surrounding an amino acid residue. We showed that mCSM can predict stability changes of a wide range of mutations occurring in the tumour suppressor protein p53, demonstrating the applicability of the proposed method in a challenging disease scenario.
Availability and implementation: A web server is available at http://structure.bioc.cam.ac.uk/mcsm.
Contact: dpires@dcc.ufmg.br; tom@cryst.bioc.cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.