bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differentiating vascular parkinsonism from idiopathic Parkinson's disease: A systematic review
Authors: Kalra Seema , Grosset Donald G. , Benamer Hani T.S. 
Published: January 2010

AbstractVascular parkinsonism (VP) remains a loose constellation of various clinical features. We systematically reviewed studies comparing clinical, neuroimaging and other investigations that might distinguish VP from idiopathic Parkinson's disease (PD). Medline, Embase, Cinahl (R), and PsycINFO were searched by querying appropriate key words. Reports were included if the study population contained comparative findings between patients with VP and PD. Twenty‐five articles fulfilled the selection criteria. Patients with VP were older, with a shorter duration of illness, presented with symmetrical gait difficulties, were less responsive to levodopa, and were more prone to postural instability, falls, and dementia. Pyramidal signs, pseudobulbar palsy, and incontinence were more common in VP. Tremor was not a main feature of VP. Structural neuroimaging was more likely to be abnormal in VP (90–100% of cases) than in PD (12–43% of cases), but there was no specific abnormal structural imaging pattern for VP. Two studies of presynaptic striatal dopamine transporters (using single photon emission computed tomography) showed a significant reduction in striatal uptake ratios in PD but not in VP, whereas another study found that only the mean asymmetry index was significantly lower in VP. Various other investigations, including alternative imaging techniques, electrophysiological, and neuropsychological studies, are reported, but the diverse diagnostic criteria used makes it difficult to reach any firm conclusions. The development of accepted international diagnostic criteria for VP is urgently needed to facilitate further studies. © 2010 Movement Disorder Society
Progressive supranuclear palsy syndrome presenting as progressive nonfluent aphasia: A neuropsychological and neuroimaging analysis
Authors: Rohrer Jonathan D. , Paviour Dominic , Bronstein Adolfo M. , O'Sullivan Sean S. , Lees Andrew , Warren Jason D. 
Published: January 2010

AbstractThere is currently considerable interest in the clinical spectrum of progressive nonfluent aphasia (PNFA) and progressive supranuclear palsy (PSP) and the intersection of these two entities. Here, we undertook a detailed prospective clinical, neuropsychological, and neuroimaging analysis of 14 consecutive patients presenting with PNFA to identify cases meeting clinical criteria for PSP. These patients had further detailed assessment of extrapyramidal and oculomotor functions. All patients had high‐resolution MR brain volumetry and a cortical thickness analysis was undertaken on the brain images. Four patients presenting with PNFA subsequently developed features of a PSP syndrome, including a typical oculomotor palsy. The neuropsychological profile in these cases was similar to other patients with PNFA, however, with more marked reduction in propositional speech, fewer speech errors, less marked impairment of literacy skills but more severe associated deficits of episodic memory and praxis. These PSP‐PNFA cases had less prominent midbrain atrophy but more marked prefrontal atrophy than a comparison group of five patients with pathologically confirmed PSP without PNFA and more prominent midbrain atrophy but less marked perisylvian atrophy than other PNFA cases. In summary, although the PSP‐PNFA syndrome overlaps with PNFA without PSP, certain neuropsychological and neuroanatomical differences may help predict the development of a PSP syndrome. © 2010 Movement Disorder Society
Aberrant branches of the radial digital nerve in the index and middle finger: Two case‐reports
Authors: Nguyen D. Thuan , Harries Iwan B. , Fessas Christian , Dickson William A. , Meek Marcel F. 
Published: January 2010

AbstractThis report describes two incidental findings of aberrant branches of the radial digital nerves in the middle finger of a 52‐year‐old man who cut himself with a grinding machine, and in the index finger of a 45‐year‐old female who sustained a flexor sheath infection following a dog bite. In both patients, two equally sized radial digital nerves were found and both nerves originated from one common digital nerve. © 2010 Wiley‐Liss, Inc. Microsurgery, 2010.
The influence of dietary status on the cognitive performance of children
Authors: Benton David 
Published: January 2010

AbstractThe rapid rate of growth of the brain during the last third of gestation and the early postnatal stage makes it vulnerable to an inadequate diet, although brain development continues into adulthood and micronutrient status can influence functioning beyond infancy. Certain dietary deficiencies during the first 2 years of life, for example iodine and iron, create problems that are not reversed by a later adequate diet. It is important that the intake of micronutrients varies greatly between individuals as they are essential for metabolism in general and in particular cell division and hence growth. In developing countries, there is consistent evidence that the adequacy of diet has lasting implications for cognitive development. In particular, attention has been directed to protein–calorie malnutrition and more specifically the intake of iron, iodine and vitamin A, a deficiency of which damages eyesight. In industrialized countries variations in diet are less influential, although a few well‐designed studies have reported that multivitamin and mineral supplementations influence anti‐social behaviour and intelligence. In the short term, there is increasing evidence that the missing of breakfast has negative consequences late in the morning. A working hypothesis is that meals of a low rather than high glycaemic load are beneficial.
Significance of vitamin A to brain function, behavior and learning
Authors: Olson Christopher R. , Mello Claudio V. 
Published: January 2010

AbstractRetinoid acid, the bioactive metabolite of vitamin A, is a potent signaling molecule in the brains of growing and adult animals, regulates numerous gene products, and modulates neurogenesis, neuronal survival and synaptic plasticity. Vitamin A deficiency (VAD) is a global health problem, yet our knowledge of its effects on behavior and learning is still emerging. Here we review studies that have implicated retinoids in learning and memory deficits of post‐embryonic and adult rodent and songbird models. Dietary vitamin A supplementation improves learning and memory in VAD rodents and can ameliorate cognitive declines associated with normal aging. Songbird studies examine the effects of retinoid signaling on vocal/auditory learning and are uniquely suited to study the behavioral effects of VAD because the neural circuitry of the song system is discrete and well understood. Similar to human speech acquisition, avian vocal learning proceeds in well‐defined stages of template acquisition, rendition and maturation. Local blockade of retinoic acid production in the brain or excess dietary retinoic acid results in the failure of song maturation, yet does not affect prior song acquisition. Together these results yield significant insights into the role of vitamin A in maintaining neuronal plasticity and cognitive function in adulthood.
Hypolipidemic effect of dietary pea proteins: Impact on genes regulating hepatic lipid metabolism
Authors: Rigamonti Elena , Parolini Cinzia , Marchesi Marta , Diani Erika , Brambilla Stefano , Sirtori Cesare R. , Chiesa Giulia 
Published: January 2010

AbstractControversial data on the lipid‐lowering effect of dietary pea proteins have been provided and the mechanisms behind this effect are not completely understood. The aim of the study was to evaluate a possible hypolipidemic activity of a pea protein isolate and to determine whether pea proteins could affect the hepatic lipid metabolism through regulation of genes involved in cholesterol and fatty acid homeostasis. Rats were fed Nath's hypercholesterolemic diets for 28 days, the protein sources being casein or a pea protein isolate fromPisum sativum. After 14 and 28 days of dietary treatment, rats fed pea proteins had markedly lower plasma cholesterol and triglyceride levels than rats fed casein (p<0.05). Pea protein‐fed rats displayed higher hepatic mRNA levels of LDL receptorversusthose fed casein (p<0.05). Hepatic mRNA concentration of genes involved in fatty acids synthesis, such as fatty acid synthase and stearoyl‐CoA desaturase, was lower in pea protein‐fed rats than in rats fed casein (p<0.05). In conclusion, the present study demonstrates a marked cholesterol and triglyceride‐lowering activity of pea proteins in rats. Moreover, pea proteins appear to affect cellular lipid homeostasis by upregulating genes involved in hepatic cholesterol uptake and by downregulating fatty acid synthesis genes.
Thermal contact conductance characterization via computational contact homogenization: A finite deformation theory framework
Authors: Temizer İ. , Wriggers P. 
Published: January 2010

AbstractIn order to predict the macroscopic thermal response of contact interfaces between rough surface topographies, a computational contact homogenization technique is developed at the finite deformation regime. The overall homogenization framework transfers macroscopic contact variables, such as surfacial stretch, pressure and heat flux, as boundary conditions on a test sample within a micromechanical interface testing procedure. An analysis of the thermal dissipation within the test sample reveals a thermodynamically consistent identification for the macroscopic thermal contact conductance parameter that enables the solution of a homogenized thermomechanical contact boundary value problem based on standard computational approaches. The homogenized contact response effectively predicts a temperature jump across the macroscale contact interface. The strong dependence of this homogenized response on macroscale solution variables of interest is demonstrated via representative three‐dimensional numerical investigations. The proposed contact homogenization framework is suitable for the analysis of similar energy transport phenomena across heterogeneous contact interfaces where the investigation of the sources for energy dissipation is of concern. Copyright © 2010 John Wiley & Sons, Ltd.
School psychologists' perceptions regarding the practice of identifying reading disabilities: Cognitive assessment and response to intervention considerations
Authors: Machek Greg R. , Nelson Jason M. 
Published: January 2010

AbstractThis study surveyed a national sample of school psychologists with respect to the identification of reading disabilities (RD). It covers school psychologists' opinions regarding perceived benefits of the use of cognitive assessment in RD identification, both within and outside of an IQ–achievement discrepancy model. The survey also solicited opinions about the nature of RD, particularly conceptions of general slow learners (and readers) versus those evidencing a discrepancy. Results related to school psychologists' concerns about job security, should IQ testing be reduced, are presented. Furthermore, the perceived benefits of a Response to Intervention (RTI) model, how school psychologists see themselves contributing to an RTI effort, as well as possible hurdles to RTI implementation are covered. Measurement of these perceptions may be beneficial in informing current and future service delivery models for RD identification as well as possible training needs of currently practicing school psychologists. Finally, the current work represents an effort to measure assessment acceptability for RD identification techniques. © 2010 Wiley Periodicals, Inc.
Teaching social skills to children with autism spectrum disorders using tiers of support: A guide for school‐based professionals
Authors: Sansosti Frank J. 
Published: January 2010

AbstractThe quintessential characteristic of autism spectrum disorders (ASD) is having difficulty with basic social interactions. Due to the pervasiveness of their social skills difficulties, it is necessary that supports for increasing social skills of children with ASD are included as part of the educational plan within schools. The purpose of this article is to provide educators with a framework for using multiple tiers of instruction to teach social skills to children with ASD. Specifically, a number of evidence‐based strategies for teaching social skills are summarized within a systemic, multitiered approach. It is anticipated that such a model proves helpful as educators address issues related to service delivery provisions for students with ASD. © 2010 Wiley Periodicals, Inc.
Teenage girls' perceptions of the functions of relationally aggressive behaviors
Authors: Reynolds Bridget M. , Repetti Rena L. 
Published: January 2010

AbstractAdolescent girls reported on their experiences both as perpetrators and as victims of several distinct forms of relational aggression. Details of these incidents were gathered from 114 ethnically diverse ninth and tenth graders via a secure online survey. The frequency with which girls perpetrated or were targeted for particular acts of relational aggression was assessed and, based on the responses, a computer program randomly selected one item (i.e., gossip, ignoring, or exclusion) for which each girl was asked to recall a specific experience and answer follow‐up questions. Perceptions of the goals and functions of specific relationally aggressive acts were assessed, as well as how the perpetrator or victim felt at the time of the incident. Ignoring or “giving the silent treatment” appeared to be a unique form of relational aggression inasmuch as the girls perceived different motives, or functions, for ignoring compared with gossip and exclusion and felt worse at the time of the ignoring incident, both when they were reporting as aggressors and as victims. © 2010 Wiley Periodicals, Inc.
Missing values in gel‐based proteomics
Authors: Albrecht Daniela , Kniemeyer Olaf , Brakhage Axel A. , Guthke Reinhard 
Published: January 2010

AbstractGel‐based proteomics is a widely applied technique to measure abundances of proteins in various biological systems. Comparison of two or more biological groups involves matching of 2‐D gels. Depending on the software, this can result in spots showing missing values on several gels. Most studies ignore this fact or substitute all missing data by zero. Since a couple of years, scientists have realized that this is not the optimal way of analyzing their data and several studies were published presenting methods of imputing missing proteomics data. Most of these methods have already been applied to microarray data before; the phenomenon of missing data is well known in this field, too. With this review, we intend to further raise awareness of the problem of missing values in gel‐based proteomics. We summarize reasons for missing values and explore their distribution in data sets. We also provide a comparison and evaluation of hitherto proposed imputation methods for gel‐based proteomics data.
From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets
Authors: Malik Rainer , Dulla Kalyan , Nigg Erich A. , Körner Roman 
Published: January 2010

AbstractMS has become a method‐of‐choice for proteome analysis, generating large data sets, which reflect proteome‐scale protein–protein interaction and PTM networks. However, while a rapid growth in large‐scale proteomics data can be observed, the sound biological interpretation of these results clearly lags behind. Therefore, combined efforts of bioinformaticians and biologists have been made to develop strategies and applications to help experimentalists perform this crucial task. This review presents an overview of currently available analytical strategies and tools to extract biologically relevant information from large protein lists. Moreover, we also present current research publications making use of these tools as examples of how the presented strategies may be incorporated into proteomic workflows. Emphasis is placed on the analysis of Gene Ontology terms, interaction networks, biological pathways and PTMs. In addition, topics including domain analysis and text mining are reviewed in the context of computational analysis of proteomic results. We expect that these types of analyses will significantly contribute to a deeper understanding of the role of individual proteins, protein networks and pathways in complex systems.
Free computational resources for designing selected reaction monitoring transitions
Authors: Cham (Mead) Jennifer A. , Bianco Luca , Bessant Conrad 
Published: January 2010

AbstractSelected reaction monitoring (SRM) is a technique for quantifying specific proteins using triple quadrupole MS. Proteins are digested into peptides and fed into MS following HPLC separation. The stream of ionized peptides is filtered by m/z ratio so only specific peptide targets enter the collision cell, where they are fragmented into product ions. A specific product ion is then filtered from the cell and its intensity measured. By spiking an isotopically labeled version of each target peptide into a sample, both native and surrogate peptides enter MS, pass the filters and transition into product ions in tandem; thus the quantity of the native peptide may be calculated by examining the relative intensities of the native and surrogate signals. The choice of precursor‐to‐product ion transitions is critical for SRM, but predicting the best candidates is challenging and time‐consuming. To alleviate this problem, software tools for designing and optimizing transitions have recently emerged, predominantly driven by data from public proteomics repositories, such as the Global Proteome Machine and PeptideAtlas. In this review, we provide an overview of the state‐of‐the‐art in automated SRM transition design tools in the public domain, explaining how the systems work and how to use them.
Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome
Authors: Weiss Manuel , Schrimpf Sabine , Hengartner Michael O. , Lercher Martin J. , von Mering Christian 
Published: January 2010

AbstractGenome‐wide, absolute quantification of expressed proteins is not yet within reach for most eukaryotes. However, large numbers of MS‐based protein identifications have been deposited in databases, together with information on the observation frequencies of each peptide spectrum (“spectral counts”). We have conducted a meta‐analysis using several million peptide observations from five model eukaryotes, establishing a consistent, semi‐quantitative analysis pipeline. By inferring and comparing protein abundances across orthologs, we observe: (i) the accuracy of spectral counting predictions increases with sampling depth and can rival that of direct biochemical measurements, (ii) the quantitative makeup of the consistently observed core proteome in eukaryotes is remarkably stable, with abundance correlations exceeding RS=0.7 at an evolutionary distance greater than 1000 million years, and (iii) some groups of proteins are more constrained than others. We argue that our observations reveal stabilizing selection: central parts of the eukaryotic proteome appear to be expressed at well‐balanced, near‐optimal abundance levels. This is consistent with our further observations that essential proteins show lower abundance variations than non‐essential proteins, and that gene families that tend to undergo gene duplications are less well constrained than families that keep a single‐copy status.
Scaffold: A bioinformatic tool for validating MS/MS‐based proteomic studies
Authors: Searle Brian C. 
Published: January 2010

AbstractOver‐reporting of unreliable protein identifications has reduced the accuracy and reproducibility of MS/MS‐based proteomic studies. In this work, we demonstrate the analysis workflow used by a bioinformatic tool called Scaffold, which attempts to increase the confidence in protein identification reports through the use of several statistical methods. In addition, this work describes an advanced protein grouping method used by Scaffold to further reduce falsely reported protein identifications, particularly when using large or otherwise sequence redundant protein databases.
Investigating protein isoforms via proteomics: A feasibility study
Authors: Blakeley Paul , Siepen Jennifer A. , Lawless Craig , Hubbard Simon J. 
Published: January 2010

AbstractAlternative splicing (AS) and processing of pre‐messenger RNAs explains the discrepancy between the number of genes and proteome complexity in multicellular eukaryotic organisms. However, relatively few alternative protein isoforms have been experimentally identified, particularly at the protein level. In this study, we assess the ability of proteomics to inform on differently spliced protein isoforms in human and four other model eukaryotes. The number of Ensembl‐annotated genes for which proteomic data exists that informs on AS exceeds 33% of the alternately spliced genes in the human and worm genomes. Examining AS in chicken via proteomics for the first time, we find support for over 600 AS genes. However, although peptide identifications support only a small fraction of alternative protein isoforms that are annotated in Ensembl, many more variants are amenable to proteomic identification. There remains a sizeable gap between these existing identifications (10–52% of AS genes) and those that are theoretically feasible (90–99%). We also compare annotations between Swiss‐Prot and Ensembl, recommending use of both to maximize coverage of AS. We propose that targeted proteomic experiments using selected reactions and standards are essential to uncover further alternative isoforms and discuss the issues surrounding these strategies.
An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunneling
Authors: Kamerlin Shina C. L. , Warshel Arieh 
Published: January 2010

AbstractEnzymatic reactions are crucial toward controlling and performing most life processes, and, as such, understanding how they really work has both fundamental and practical importance. Thus, one of the major current challenges of biophysics involves understanding the origin of the enormous catalytic power of enzymes, an issue that is still not widely understood and remains controversial within the scientific community. Several proposals have been put forth to try to explain the origin of enzyme catalysis, one of which is the idea that enzyme catalysis involves special factors such as nuclear quantum mechanical (NQM) effects, and, in particular, nuclear tunneling. Here, we will discuss both the factors for and against this proposition, and demonstrate that an analysis of all the relevant facts and arguments seems to establish that enzyme catalysis does not involve large contributions from nuclear tunneling. Copyright © 2010 John Wiley & Sons, Ltd.