bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive–linguistic deficit and speech intelligibility in chronic progressive multiple sclerosis
Authors: Mackenzie Catherine , Green Jan 
Published: March 2009

Background: Multiple sclerosis is a disabling neurological disease with varied symptoms, including dysarthria and cognitive and linguistic impairments. Association between dysarthria and cognitive–linguistic deficit has not been explored in clinical multiple sclerosis studies.Aims: In patients with chronic progressive multiple sclerosis, the study aimed to investigate the presence and nature of cognitive–linguistic deficit, the association between levels of cognitive–linguistic ability and speech intelligibility, and of both of these with functional disability and time since onset of multiple sclerosis symptoms.Methods & Procedures: The Arizona Battery for Communication Disorders of Dementia (ABCD) (Bayles and Tomoeda 1993), The Assessment of Intelligibility of Dysarthric Speech (AIDS) Sentence Intelligibility Task (Yorkston and Beukelman 1984), and the Modified Barthel Activities of Daily Living Index (MBADLI) (Shah 1998) were administered to 24 chronic progressive multiple sclerosis participants with dysarthria. A total of 24 non‐neurologically impaired participants, matched for gender, age and education, formed a control group.Outcomes & Results: For multiple sclerosis participants, linear regression analysis showed a strong association between ABCD and AIDS (β = 0.89, p = 0.005), no association between ABCD and either MBADLI or time since onset, a strong association between AIDS and MBADLI (β = 0.60, p = 0.001), and a trend towards an association between AIDS and time since onset (β = −0.29, p = 0.08). Correlations between the four included ABCD construct scores and between these and the total ABCD score were significant (r>0.60, p<0.01). For each of the 15 included ABCD measures and for the four construct scores and the overall ABCD score, multiple sclerosis and control group performances were significantly different (p<0.01) and effect sizes were large (d>0.80).Conclusions & Implications: The results revealed a strong association between dysarthria, as measured by connected speech intelligibility testing, and cognitive–linguistic deficit, in people with chronic progressive‐type multiple sclerosis. While some of the impairments that are associated with multiple sclerosis, including motor speech disorder, may influence performance on the ABCD, the data support the conclusion that marked cognitive–linguistic deficit is present in chronic progressive‐type multiple sclerosis patients with dysarthria. Deterioration was global, rather than being indicative of a construct specific deficit, and encompassed language, both expression and comprehension. Episodic memory and linguistic expression were especially affected. Speech and language therapists who work with dysarthric patients with chronic progressive multiple sclerosis should monitor cognitive–linguistic impairment. An awareness of this might influence assessment, intervention and management, including the information and advice given to patients and their relatives.
Determinants of “optimal” cadence during cycling
Authors: Ansley Les , Cangley Patrick 
Published: March 2009

AbstractCadence is one of the only variables cyclists can adjust to manage their performance and fatigue during an event. Not surprisingly, cadence has received a great deal of attention from the scientific community in an effort to identify the cadence that optimizes power output while minimizing the fatigue that is incurred. The literature appears to present conflicting results with little consensus as regards the optimal pedalling cadence. This is in large part due to the inconsistent definition of the term “optimal” cadence, which has been used to describe energetic cost, muscular stress, and perception of effort. The issue is further confounded by the workload‐dependent nature of the “optimal” cadence – that is, at higher power outputs, the optimized cadence is different from that at lower power outputs. Although the optimal cadence is different for energetic, muscular, and perceptual definitions, the curves that describe the effect of changes in cadence on these variables consistently exhibit a J‐shaped response. This suggests that there is an underlying principle that is common to each of the definitions. Indeed, it would appear that the response of both the cardio‐respiratory system (energetic cost) and the muscular system (muscular stress) is determined by the types of muscle motor units that are recruited during the exercise. Furthermore, although part of the response may be due to the inherent differences in the characteristics between the different motor units, the absolute contraction velocity relative to fibre type optimum may be of greater significance. Even when the power output is increased, the shape of the response curves to changes in cadence remains constant, although the nadir of the curve does shift to the right for increasing power outputs. We propose that the point at which the energetic vs. power and the muscular stress vs. power curves intercept is defined by the cadence at which the perceived effort is minimized (i.e. the preferred cadence). However, cadence fluctuations occur under field conditions that are unrelated to physiological factors and, therefore, the ability to identify an “optimal” cadence is limited to the laboratory environment and specific field conditions.
TopHat: discovering splice junctions with RNA-Seq
Authors: Trapnell Cole , Pachter Lior , Salzberg Steven L. 
Published: March 2009

Abstract
Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites.
Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development.
Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu
Contact: cole@cs.umd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Long‐term left ventricular reverse remodelling with cardiac resynchronization therapy: results from the CARE‐HF trial
Authors: Ghio Stefano , Freemantle Nick , Scelsi Laura , Serio Alessandra , Magrini Giulia , Pasotti Michele , Shankar Aparna , Cleland John G.F. , Tavazzi Luigi 
Published: March 2009

AimsThe aim of the present study was to assess the long‐term effects of cardiac resynchronization therapy (CRT) on the reverse remodelling of the left ventricle (LV).Methods and resultsThe effects of CRT compared with controls on LV dimensions and function were assessed at 3, 9, and 18 months and at the end of study (average 29 months) in 735 (90%) patients with adequate echocardiographic examinations, randomized in the CARE‐HF trial. Echocardiographic recordings were submitted to a core laboratory to ensure consistent quantitative analysis. LV volume decreased and ejection fraction increased substantially in the CRT group by 3 months and improved further at each assessment when compared with the control group. Effects were less marked in patients with ischaemic heart disease and those with right ventricular dysfunction, but not in patients with a restrictive LV filling pattern. The extent of reverse remodelling at 18 months showed a modest relationship with baseline interventricular mechanical delay (IVMD).ConclusionCRT induces sustained LV reverse remodelling with the most marked effects occurring within the first 3–9 months. The extent of remodelling in response to CRT is related to the aetiology of heart failure and, to a lesser extent, to the IVMD.
Non‐radioisotope method for diagnosing photosensitive genodermatoses and a new marker for xeroderma pigmentosum variant
Authors: HASHIMOTO Satoru , EGAWA Kiyofumi , IHN Hironobu , TATEISHI Satoshi 
Published: March 2009

ABSTRACTXeroderma pigmentosum (XP) is an autosomal recessive disorder characterized by photo‐induced deterioration of the skin, which often leads to the early development of skin cancers. To diagnose patients with XP and the related disorder Cockayne syndrome (CS), our laboratory has established a simple autoradiographic method that examines three cellular markers of DNA repair: unscheduled DNA synthesis (UDS), recovery of RNA synthesis (RRS) and recovery of replicative DNA synthesis (RDS). However, it is very laborious to measure the three markers using tritiated thymidine or uridine; therefore, we developed a non‐isotope method for diagnosing XP and CS. Fibroblasts from the patient were labeled with bromodeoxyuridine (BrdU) instead of tritiated thymidine to measure UDS and RDS, or were labeled with bromouridine (BrU) instead of tritiated uridine to measure RRS. Incorporated BrdU or BrU could be detected using the immunofluorescence method. Moreover, we discovered a new useful marker for XP variant based on checkpoint activity. The non‐radioisotope method and the new marker described here comprise an easy way to diagnose XP and CS.
Venous insufficiency in patients with necrobiosis lipoidica
Authors: NAKAJIMA Takeshi , TANEMURA Atsushi , INUI Shigeki , KATAYAMA Ichiro 
Published: March 2009

ABSTRACTThe pretibial area is the most frequently affected site in necrobiosis lipoidica (NL), but proposed mechanisms of NL cannot fully explain this high frequency. Although a few case reports indicate NL patients are complicated with venous insufficiency, no accurate assessment of the relationship between these two conditions has been performed. By using color Doppler ultrasonographic screening of four NL patients for venous insufficiency, we detected venous insufficiency in at least one leg of each patient. NL lesions were observed on all legs with venous insufficiency, and laboratory examination findings revealed that all the patients had hypercholesterolemia. The skin lesions did not respond satisfactorily to 6‐month use of anticholesterolemic medication and elastic stockings. However, these results indicate that both hyperlipidemia and venous reflux, in addition to other pathogenic factors, can trigger tissue damage in the lower legs and lead to the onset of NL.
Carcinogenicity of acetaldehyde in alcoholic beverages: risk assessment outside ethanol metabolism
Authors: Lachenmeier Dirk W. , Kanteres Fotis , Rehm Jürgen 
Published: March 2009

ABSTRACTAims In addition to being produced in ethanol metabolism, acetaldehyde occurs naturally in alcoholic beverages. Limited epidemiological evidence points to acetaldehyde as an independent risk factor for cancer during alcohol consumption, in addition to the effects of ethanol. This study aims to estimate human exposure to acetaldehyde from alcoholic beverages and provide a quantitative risk assessment.Methods The human dietary intake of acetaldehyde via alcoholic beverages was estimated based on World Health Organization (WHO) consumption data and literature on the acetaldehyde contents of different beverage groups (beer, wine, spirits and unrecorded alcohol). The risk assessment was conducted using the European Food Safety Authority's margin of exposure (MOE) approach with benchmark doses obtained from dose–response modelling of animal experiments. Life‐time cancer risk was calculated using the T25 dose descriptor.Results The average exposure to acetaldehyde from alcoholic beverages was estimated at 0.112 mg/kg body weight/day. The MOE was calculated to be 498, and the life‐time cancer risk at 7.6 in 10 000. Higher risk may exist for people exposed to high acetaldehyde contaminations, as we have found in certain unrecorded alcohol beverages in Guatemala and Russia, for which we have demonstrated possible exposure scenarios, with risks in the range of 1 in 1000.Conclusions The life‐time cancer risks for acetaldehyde from alcoholic beverages greatly exceed the usual limits for cancer risks from the environment set between 1 : 10 000 and 1 : 1 000 000. Alcohol consumption has thus been identified as a direct source of acetaldehyde exposure, which in conjunction with other sources (food flavourings, tobacco) results in a magnitude of risk requiring intervention. An initial public health measure could be to reduce the acetaldehyde content in alcoholic beverages as low as technologically possible, and to restrict its use as a food flavour additive.
Seasonal cycles of assortative mating and reproductive behaviour in polymorphic populations ofHarmonia axyridisin China
Authors: SU WANG , MICHAUD J. P. , RUNZHI ZHANG , FAN ZHANG , SHUANG LIU 
Published: March 2009

Abstract1. We observed native populations ofHarmonia axyridis(Pallas) around Beijing, China, over 2 years and performed choice and no‐choice mating tests between melanic and succinic (non‐melanic) beetles in the laboratory.2. Succinic phenotypes outnumbered melanics by 5:1 in autumn, but melanics became equally abundant in spring, supporting previous inferences that melanism is advantageous in winter, but costly in summer.3. FemaleH. axyridisexpressed mate preference overtly, by rejecting less‐preferred phenotypes, and cryptically, by retaining their eggs for longer periods after matings with less‐preferred males, ostensibly to replace their sperm.4. Succinic pairs formed more quickly in the spring generation, and melanic pairs in the autumn, and the time to copula was affected by both male and female phenotype. The strength of mate preference was contingent on female phenotype, suggesting melanic alleles had pleiotropic effects.5. Whereas pair formation was under female control, the duration of copula was under male control and lasted longer in the autumn generation than in the spring. Copulations in the choice test tended to be shorter between similar phenotypes, suggesting that males invested more in dissimilar females when alternative mates were available.6. Although spring and autumn generations were raised under identical conditions, significant contrasts were observed in their reproductive behaviour.7. Two alternative hypotheses are advanced to explain why gender‐specific reproductive behaviours might vary between generations: maternally‐mediated epigenetic factors that influence the expression of genes in progeny as a function of maternal environment, and linkage disequilibria among alleles that cycle in frequency seasonally as a function of assortative mating.
Larval food stress differentially affects flight morphology in male and female speckled woods (Pararge aegeria)
Authors: PELLEGROMS BORIS , VAN DONGEN STEFAN , VAN DYCK HANS , LENS LUC 
Published: March 2009

Abstract 1. Adaptive plasticity in flight morphology can be of great importance for organisms, in order to deal with changing environments. When different demands are imposed to this morphology, different responses to environmental changes can be expected.2. The aim of this study is to examine whether males and females of Pararge aegeria, which show different flight behaviours, respond differently to larval food stress.3. In a food‐stress experiment, larvae of 35 families were reared on host plants subjected to a drought‐stress treatment with three groups: a control group, a low‐stress group and a high‐stress group.4. Individuals from stress treatments significantly differed in wing morphology; they had lower wing loadings, and stressed females tended to have more pointed wings than females of the control group.5. The difference in phenotypic response to food stress between both sexes may indicate that males and females benefit from different changes in morphology. In females, an increase in dispersal capacity may entail fitness benefits, whereas male morphology is mainly shaped by mate‐location strategy.
Morphological development and nutritive value of herbage in five temperate grass species during primary growth: analysis of time dynamics
Authors: Čop J. , Lavrenčič A. , Košmelj K. 
Published: March 2009

AbstractIn a 2‐year field experiment, morphological development and measures of the nutritive value of herbage for livestock during primary growth in Meadow foxtail, Tall oatgrass, Cocksfoot, Perennial ryegrass and Yorkshire fog were investigated. All measured variables were affected significantly by both species and sampling date, and their interaction (P < 0·001), in the period of primary growth. Changes with time in mean stage weight for Meadow foxtail and Cocksfoot were different from the other species due to their indeterminate growth habits. Mean stage weight of Tall oatgrass and Yorkshire fog increased more rapidly than that of Perennial ryegrass with time. Changes in mean stage weight with time were described by linear, parabolic and sigmoid relationships. Crude protein (CP) concentration of herbage was higher for Cocksfoot and Meadow foxtail than for Perennial ryegrass. A parabolic relationship of CP concentration with time was typical for all the species. Concentrations of neutral‐detergent fibre (NDF) and acid‐detergent fibre (ADF) in herbage of the species differed most during the mid‐period of primary growth. Their increases with time showed curvilinear (sigmoid and parabolic) relationships. Perennial ryegrass had lower concentrations of both NDF and ADF in herbage than the other species. Differences between thein vitrodry matter (DM) digestibility among the grasses increased in mid‐ and late periods of primary growth. Perennial ryegrass had higher values forin vitroDM digestibility but the difference from other species was small in the early period of primary growth and from cocksfoot in the late period of primary growth.In vitroDM digestibility showed, in most cases, a sigmoid and, in others, a linear decrease with time. Principal component analysis showed that perennial ryegrass and meadow foxtail were the most distinctive of the species in characteristics relating to morphological development and the nutritive value of herbage to livestock.
A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two‐component system
Authors: Mandin Pierre , Gottesman Susan 
Published: March 2009

SummaryIn Escherichia coli, the largest class of small regulatory RNAs binds to the RNA chaperone Hfq and regulates the stability and/or translation of specific mRNAs. While recent studies have shown that some mRNAs could be subject to post‐transcriptional regulation by sRNAs (e.g. mRNAs found by co‐immunoprecipitation with Hfq), no method has yet been described to identify small RNAs that regulate them. We developed a method to easily make translational fusions of genes of interest to the lacZ reporter gene, under the control of a PBAD‐inducible promoter. A multicopy plasmid library of the E. coli genome can then be used to screen for small RNAs that affect the activity of the fusion. This screening method was first applied to the dpiB gene from the dpiBA operon, which encodes a two‐component signal transduction system involved in the SOS response to β‐lactams. One small RNA, RybC, was found to negatively regulate the expression of dpiB. Using mutants in the dpiB–lacZ fusion and compensatory mutations in the RybC sRNA, we demonstrate that RybC directly base pairs with the dpiBA mRNA.
Counter point bar deposits: lithofacies and reservoir significance in the meandering modern Peace River and ancient McMurray Formation, Alberta, Canada
Authors: SMITH DERALD G. , HUBBARD STEPHEN M. , LECKIE DALE A. , FUSTIC MILOVAN 
Published: March 2009

AbstractCounter point bar deposits in the meandering Peace River, North‐central Alberta, Wood Buffalo National Park, are distinct from point bar deposits in terms of morphology, lithofacies and reservoir potential for fluids. Previously referred to as the distal‐most parts of point bars, point bar tails and concave bank‐bench deposits, counter point bar deposits have concave morphological scroll patterns rather than convex as with point bars. The Peace is a large river (bankfull discharge 11 700 m3 sec−1, width 375 to 700 m, depth 15 m, gradient 0·00004 or 4 cm km−1) in which counter point bar deposits are dominated by silt (80% to 90%), which contrasts with sand‐dominant (90% to 100%) point bar deposits. Beginning at the meander inflection (transition from convex to concave), counter point bar deposit stratigraphy thickens as a wedge‐like architecture in the distal direction until the deposit is nearly as thick as the point bar deposits. The low permeability silt‐dominant lithofacies in counter point bar deposits will limit reservoir extent and movement of fluids in both modern and ancient subsurface fluvial deposits. In the exploration and extraction of bitumen and heavy oil in subsurface fluvial rocks, identification and mapping of reservoir potential of point bar deposits and counter point bar deposits is now possible in the fluvial‐dominated tidal estuarine Lower Cretaceous Middle McMurray Formation, North‐east Alberta. Recent geophysical advances have facilitated imaging of some ancient buried point bar deposits and counter point bar deposits which, on the basis of morphological shape of sedimentary bodies observed from seismic amplitude, can be interpreted and mapped as depositional elements or blocks that contain associated sandstone or siltstone dominant lithofacies, respectively. As counter point bar deposits exhibit poor permeability and thus limit reservoir potential for water, natural gas, light crude, heavy oil and bitumen, counter point bar deposits should be avoided in resource developments. Geophysical imaging, interpretation and mapping of point bar deposit and counter point bar deposit elements provide new opportunities to improve recovery of bitumen and heavy oil and reduce development costs in subsurface cyclic steam stimulation and steam‐assisted gravity drainage projects by not drilling into counter point bar deposits.