bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thioesterase superfamily member 2 (Them2)/acyl-CoA thioesterase 13 (Acot13): a homotetrameric hotdog fold thioesterase with selectivity for long-chain fatty acyl-CoAs
Authors: Wei Jie , Kang Hye Won , Cohen David E. 
Published: May 2009

Them2 (thioesterase superfamily member 2) is a 140-amino-acid protein of unknown biological function that comprises a single hotdog fold thioesterase domain. On the basis of its putative association with mitochondria, accentuated expression in oxidative tissues and interaction with StarD2 (also known as phosphatidylcholine-transfer protein, PC-TP), a regulator of fatty acid metabolism, we explored whether Them2 functions as a physiologically relevant fatty acyl-CoA thioesterase. In solution, Them2 formed a stable homotetramer, which denatured in a single transition at 59.3 °C. Them2 exhibited thioesterase activity for medium- and long-chain acyl-CoAs, with Km values that decreased exponentially as a function of increasing acyl chain length. Steady-state kinetic parameters for Them2 were characteristic of long-chain mammalian acyl-CoA thioesterases, with minimal values of Km and maximal values of kcat/Km observed for myristoyl-CoA and palmitoyl-CoA. For these acyl-CoAs, substrate inhibition was observed when concentrations approached their critical micellar concentrations. The acyl-CoA thioesterase activity of Them2 was optimized at physiological temperature, ionic strength and pH. For both myristoyl-CoA and palmitoyl-CoA, the addition of StarD2 increased the kcat of Them2. Enzymatic activity was decreased by the addition of phosphatidic acid/phosphatidylcholine small unilamellar vesicles. Them2 expression, which was most pronounced in mouse heart, was associated with mitochondria and was induced by activation of PPARα (peroxisome-proliferator-activated receptor α). We conclude that, under biological conditions, Them2 probably functions as a homotetrameric long-chain acyl-CoA thioesterase. Accordingly, Them2 has been designated as the 13th member of the mammalian acyl-CoA thioesterase family, Acot13.
Receptor-associated protein (RAP) has two high-affinity binding sites for the low-density lipoprotein receptor-related protein (LRP): consequences for the chaperone functions of RAP
Authors: Jensen Jan K. , Dolmer Klavs , Schar Christine , Gettins Peter G. W. 
Published: May 2009

RAP (receptor-associated protein) is a three domain 38 kDa ER (endoplasmic reticulum)-resident protein that is a chaperone for the LRP (low-density lipoprotein receptor-related protein). Whereas RAP is known to compete for binding of all known LRP ligands, neither the location, the number of binding sites on LRP, nor the domains of RAP involved in binding is known with certainty. We have systematically examined the binding of each of the three RAP domains (D1, D2 and D3) to tandem and triple CRs (complement-like repeats) that span the principal ligand-binding region, cluster II, of LRP. We found that D3 binds with low nanomolar affinity to all (CR)2 species examined. Addition of a third CR domain increases the affinity for D3 slightly. A pH change from 7.4 to 5.5 gave only a 6-fold increase in Kd for D3 at 37 °C, whereas temperature change from 22 °C to 37 °C has a similar small effect on affinity, raising questions about the recently proposed D3-destabilization mechanism of RAP release from LRP. Surprisingly, and in contrast to literature suggestions, D1 and D2 also bind to most (CR)2 and (CR)3 constructs with nanomolar affinity. Although this suggested that there might be three high-affinity binding sites in RAP for LRP, studies with intact RAP showed that only two binding sites are available in the intact chaperone. These findings suggest a new model for RAP to function as a folding chaperone and also for the involvement of YWTD domains in RAP release from LRP in the Golgi.
Inference and sentence comprehension in children with specific or pragmatic language impairments
Authors: Adams Catherine , Clarke Elaine , Haynes Rebecca 
Published: May 2009

Background: Children with language impairments have difficulty in reporting verbal inferences, but it is unclear whether the source of this problem lies in limitations of language comprehension, an inability to access world knowledge, or the integration of information in discourse. Children with pragmatic language impairments (CwPLI) are often described as having disproportionate difficulty with verbal inference, although there is little empirical support for this view.Aims: To examine the performance of children with specific language impairment (CwSLI), CwPLI and a control group with typical language development (CwTLD) on a verbal inferential comprehension task; to explore whether CwPLI's verbal inferential comprehension performance are disproportionate to their sentence comprehension difficulties; and to analyse inferential error types made by the three groups.Methods & Procedures: Sixty‐four children with language impairments (CwLI), aged between 6 and 11 years, participated in an inference comprehension task (IC) and a task of sentence comprehension (SC). For the purpose of analysis, the LI group was then split into two subgroups: CwPLI and CwSLI, using a checklist of pragmatic features. A group of CwTLD were matched to LI children on SC ability and gender; a separate group of CwTLD (CA) was matched to CwLI by age and gender.Outcomes & Results: CwLI had lower raw scores on the IC task than CA‐matched CwTLD, but similar scores to SC‐matched CwTLD. CwPLI produced lower raw IC scores than CwSLI, and this was the same when age and SC performance were controlled for. CwSLI performed similarly to their SC‐matched and CA‐matched control subjects on the IC task. CwPLI scored significantly less on the IC task than both their SC‐matched and CA‐matched control subjects. A regression analysis showed that age and SC ability account for 36% of the variance on the IC task, but group (SLI versus PLI) status accounts for just 5%. A detailed analysis of error types and item performance on the IC task showed a trend for CwPLI to perform more poorly on developmentally more complex inference items, but there was no evidence for a unique pattern of inference errors in CwPLI.Conclusions & Implications: Children with language impairments tend to perform like younger children with matched level of sentence comprehension ability on a verbal inference comprehension task. CwPLI have more difficulty with this task than CwSLI, but the distribution of scores shows considerable overlap exists between clinical groups. Sentence comprehension ability, age and, to a lesser extent, group status contribute to verbal inferencing ability in children with language impairments, but other factors may be important. The implications for assessment and intervention are discussed.
Evaluation of speech and language therapy interventions for pre‐school children with specific language impairment: a comparison of outcomes following specialist intensive, nursery‐based and no intervention
Authors: Gallagher Aoife Lily , Chiat Shula 
Published: May 2009

Background: Clinical services in the UK are increasingly delivering ‘consultative’ methods of intervention rather than ‘direct’ intensive input for children with receptive and expressive language difficulties, yet there has been little systematic evaluation of these different intervention models.Aims: To investigate the effectiveness of different models of therapy provision for children with specific language impairment between the ages of 4;00 and 4;06 years.Methods & Procedures: Twenty‐four children were selected from a specialist waiting list in the London Borough of Lambeth. They were assessed on a range of verbal and non‐verbal skills, and randomly assigned to three different intervention groups. Group 1 received direct intensive speech and language therapy weekly over an 8‐month period at a child development centre; Group 2 received a nursery‐based model of intervention; and Group 3 received review sessions at their local clinic.Outcome & Results: Statistical analysis before the intervention phase revealed no significant differences in scores between the three groups on a range of clinical and parental measures of language, non‐verbal skills, play and behaviour. At the end of the intervention period the Intensive group showed significantly greater improvement than the No Intervention group on all clinical and parental measures, and significantly greater improvement than the Nursery‐based group on all clinical and parental measures except for expressive grammar.Conclusions & Implications: The results of this small‐scale study demonstrate that intensive direct speech and language therapy delivered by speech and language therapists was a more effective model of intervention for this clinical group with severe speech and language impairment.
Speech disruptions in the sentence formulation of school‐age children with specific language impairment
Authors: Finneran Denise A. , Leonard Laurence B. , Miller Carol A. 
Published: May 2009

Background: Many school‐age children with specific language impairment produce sentences that appear to conform to the adult grammar. It may be premature to conclude from this, however, that their language formulation ability is age appropriate.Aims: To determine whether a more subtle measure of language use, speech disruptions during sentence formulation, might serve to distinguish children with specific language impairment from their typically developing peers at an age when grammatical accuracy was high. We analysed the rate of speech disruptions in simple sentence production in school‐age children with specific language impairment and typically developing age‐matched peers. We predicted that: (1) the specific language impairment group would exhibit more speech disruptions than the typically developing group as a result of reduced language proficiency even when grammatical accuracy was high; and (2) the specific language impairment group would demonstrate greater reductions in disruption frequency as compared with the typically developing group when given sentences that model the target syntactic structures.Methods & Procedures: Twenty‐eight children (17 specific language impairment, 11 typically developing, mean = 8;10 years) with no history of stuttering were presented with a series of picture pairs. The examiner described the first picture using a simple sentence and asked the child to repeat the sentence; the child then described the second picture. There were two priming conditions: Matching Syntax condition (paired pictures requiring different syntactic structures) and Different Syntax condition (paired pictures requiring different syntax structures). All testing was audio‐recorded and speech disruptions (repetitions, revisions, fillers, long silent pauses) were transcribed and tabulated for each target response. The data were analysed by analysis of variance (ANOVA).Outcomes & Results: The specific language impairment group demonstrated a significantly greater number of speech disruptions when compared with the typically developing group. There was no effect for priming.Conclusions & Implications: School‐age children with specific language impairment appear to have difficulty with sentence formulation when compared with typically developing peers even when grammatical accuracy is high. We concluded that school‐age children with specific language impairment may demonstrate subtle but persistent language formulation difficulties.
TANDEM: integrating automated allele binning into genetics and genomics workflows
Authors: Matschiner Michael , Salzburger Walter 
Published: May 2009

Abstract
Summary: Computer programs for the statistical analysis of microsatellite data use allele length variation to infer, e.g. population genetic parameters, to detect quantitative trait loci or selective sweeps. However, observed allele lengths are usually inaccurate and may deviate from the expected periodicity of repeats. The common practice of rounding to the nearest whole number frequently results in miscalls and underestimations of allelic richness. Manual sorting of allele lengths into discrete classes, a process called binning, is tedious and error-prone. Here, we present a new program for the automated binning of microsatellite allele lengths to overcome these problems and to facilitate high-throughput allele binning.
Availability: www.evolution.unibas.ch/salzburger/software.htm
Contact: michael.matschiner@unibas.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Repeated autologous bone marrow mononuclear cell therapy in patients with large myocardial infarction
Authors: Yao Kang , Huang Rongchong , Sun Aijun , Qian Juying , Liu Xuebo , Ge Lei , Zhang Yiqi , Zhang Shuning , Niu Yuhong , Wang Qibing , Zou Yunzeng , Ge Junbo 
Published: May 2009

AbstractAimsWe sought to determine whether repeat administration of bone marrow mononuclear cells (BMC) can improve left ventricular function compared with a single infusion in patients with large acute myocardial infarction (AMI).Methods and resultsThirty‐nine patients with a ST‐elevation AMI of the anterior wall and a significantly decreased left ventricular ejection fraction (LVEF 20–39%) were randomly assigned to three groups following primary percutaneous coronary intervention: Group A (n = 12) received a single intracoronary infusion of BMC (1.9 ± 1.2 × 108) at 3–7 days after AMI; Group B (n = 15) received BMC administration both at 3–7 days (2.0 ± 1.4 × 108) and at 3 months (2.1 ± 1.7 × 108); and the control group (CON, n = 12) received one placebo injection at 3–7 days. We noted no severe complications associated with the BMC transfer. The increase in LVEF evaluated by magnetic resonance imaging (MRI) after 12 months in Group B (11.7 ± 2.6%) was significantly greater than that in Group A (7.2 ± 1.6%, P < 0.001) or in CON (2.9 ± 2.0%, P < 0.001). Magnetic resonance imaging‐derived myocardial infarct size decreased significantly in Group B compared with Group A (11.3 ± 2.7% vs. 6.3 ± 1.6%, P < 0.001).ConclusionData from this preliminary study suggest that repeated BMC administration might be a safe and feasible therapeutic strategy for patients with large AMI.
Oil Bodies and Oleosins in Physcomitrella Possess Characteristics Representative of Early Trends in Evolution
Authors: Huang Chien-Yu , Chung Chun-I , Lin Yao-Cheng , Hsing Yue-Ie Caroline , Huang Anthony H.C. 
Published: May 2009

Abstract
Searches of sequenced genomes of diverse organisms revealed that the moss Physcomitrella patens is the most primitive organism possessing oleosin genes. Microscopy examination of Physcomitrella revealed that oil bodies (OBs) were abundant in the photosynthetic vegetative gametophyte and the reproductive spore. Chromatography illustrated the neutral lipids in OBs isolated from the gametophyte to be largely steryl esters and triacylglycerols, and SDS-PAGE showed the major proteins to be oleosins. Reverse transcription-PCR revealed the expression of all three oleosin genes to be tissue specific. This tissue specificity was greatly altered via alternative splicing, a control mechanism of oleosin gene expression unknown in higher plants. During the production of sex organs at the tips of gametophyte branches, the number of OBs in the top gametophyte tissue decreased concomitant with increases in the number of peroxisomes and level of transcripts encoding the glyoxylate cycle enzymes; thus, the OBs are food reserves for gluconeogenesis. In spores during germination, peroxisomes adjacent to OBs, along with transcripts encoding the glyoxylate cycle enzymes, appeared; thus, the spore OBs are food reserves for gluconeogenesis and equivalent to seed OBs. The one-cell-layer gametophyte could be observed easily with confocal microscopy for the subcellular OBs and other structures. Transient expression of various gene constructs transformed into gametophyte cells revealed that all OBs were linked to the endoplasmic reticulum (ER), that oleosins were synthesized in extended regions of the ER, and that two different oleosins were colocated in all OBs.
P‐II‐03  Effect of Platelet Derived Wound Healing Factor (PDWHF) on the Angiogenesis in the Cases of Artificial Dermis Grafts
Authors: Kazutaka Soejima , Chen Xin , Masayuki Yamato , Teruo Okano , Motohiro Nozaki 
Published: May 2009

Aim: The effect of platelet derived wound healing factor (PDWHF) with or without cultured cells on angiogenesis in the cases of artificial dermis grafts was investigated. Methods: Wistar strain rats were used for this study. The PDWHF was prepared from platelets. The endothelial cells and fibroblasts were prepared from thoracic aorta and back skin respectively. Then 2 experimental models were designed. 1) Full‐thickness wounds were created on back of the animals. Artificial dermis (TERUDERMIS®, TERUMO Co, Japan) were grafted to the wounds. 2) Femoral artery and vein were isolated as a vascular pedicle and wrapped with a folded sheet of the AD (1 × 2 cm). Prior to AD grafts, the AD were treated with the PDWHF and/or cultured cells. Results: The combination use of the PDWHF and cultured cells showed best angiogenesis in both experimental models. Conclusions: The result of the present study revealed that treatment with PDWHF combined with cultured cells accelerate the wound angiogenesis.
Cancer stem cell‐like SP cells have a high adhesion ability to the peritoneum in gastric carcinoma
Authors: Nishii Takafumi , Yashiro Masakazu , Shinto Osamu , Sawada Tetsuji , Ohira Masaichi , Hirakawa Kosei 
Published: May 2009

Cancer stem cells (CSCs) are considered to be responsible for cancer metastasis, but the evidence to conclusively prove this hypothesis remains uncertain. The side population (SP), as evaluated by a flow cytometric analysis using Hoechst 33342, has been known as CSC‐rich population. The aim of this study was to clarify the characterization of the SP cells in peritoneal metastasis of gastric carcinoma. Gastric cancer cell lines OCUM‐2M, OCUM‐2D, and OCUM‐2MD3 (a daughter cell line with high potential for peritoneal metastasis) were used. We isolated SP cells from OCUM‐2M and OCUM‐2D using flow cytometry. Serial sorting was performed three times to enrich SP cells, and they were designated as OCUM‐2M/SP and OCUM‐2D/SP cells. Flow cytometric analysis showed 0.46%, 0.29%, 5.24%, 6.49%, and 11.3% of the SP cells to be found in OCUM‐2M, OCUM‐2D, OCUM‐2MD3, OCUM‐2M/SP, and OCUM‐2D/SP cells, respectively. The intraperitoneal inoculation of SP cells and OCUM‐2MD3 cells produced peritoneal metastasis, but parent cells did not. The adhesion ability of SP and OCUM‐2MD3 cells was significantly high in comparison to that of parent cells. The expression level of adhesion molecules α2‐, α5‐, β3‐, and β5‐integrin, and CD44, was high in SP cells compared to parent cells. The expression of stemness markers, Oct3/4 and Sox2, increased in the SP‐cell‐injected tumors. These findings suggested that CSC‐like SP cells expressing α2‐, α5‐, β3‐, and β5‐integrin, and CD44, may play an important role for peritoneal metastasis in gastric carcinoma. Oct3/4 and Sox2 may be associated with CSC in gastric cancer. (Cancer Sci 2009)
Dynamics in the tomato root transcriptome on infection with the potato cyst nematode Globodera rostochiensis
Authors: SWIECICKA MAGDALENA , FILIPECKI MARCIN , LONT DIEUWERTJE , VAN VLIET JOKE , QIN LING , GOVERSE ASKA , BAKKER JAAP , HELDER JOHANNES 
Published: May 2009

SUMMARYPlant parasitic nematodes infect roots and trigger the formation of specialized feeding sites by substantial reprogramming of the developmental process of root cells. In this article, we describe the dynamic changes in the tomato root transcriptome during early interactions with the potato cyst nematode Globodera rostochiensis. Using amplified fragment length polymorphism‐based mRNA fingerprinting (cDNA‐AFLP), we monitored 17 600 transcript‐derived fragments (TDFs) in infected and uninfected tomato roots, 1–14 days after inoculation with nematode larvae. Six hundred and twenty‐four TDFs (3.5%) showed significant differential expression on nematode infection. We employed GenEST, a computer program which links gene expression profiles generated by cDNA‐AFLP and databases of cDNA sequences, to identify 135 tomato sequences. These sequences were grouped into eight functional categories based on the presence of genes involved in hormone regulation, plant pathogen defence response, cell cycle and cytoskeleton regulation, cell wall modification, cellular signalling, transcriptional regulation, primary metabolism and allocation. The presence of unclassified genes was also taken into consideration. This article describes the responsiveness of numerous tomato genes hitherto uncharacterized during infection with endoparasitic cyst nematodes. The analysis of transcriptome profiles allowed the sequential order of expression to be dissected for many groups of genes and the genes to be connected with the biological processes involved in compatible interactions between the plant and nematode.
Definition of progression risk based on combinations of cellular and molecular markers in patients with Binet stage A chronic lymphocytic leukaemia
Authors: Morabito Fortunato , Cutrona Giovanna , Gentile Massimo , Matis Serena , Todoerti Katia , Colombo Monica , Sonaglio Claudia , Fabris Sonia , Reverberi Daniele , Megna Mauro , Spriano Mauro , Lucia Eugenio , Rossi Edoardo , Callea Vincenzo , Mazzone Carla , Festini Gianluca , Zupo Simonetta , Molica Stefano , Neri Antonino , Ferrarini Manlio 
Published: May 2009

Summary IGHV mutational status and ZAP‐70 or CD38 expression correlate with clinical course in B‐cell chronic lymphocytic leukaemia (CLL). The three markers may be discordant in the single case and there is no consensus on their combined use in clinical practise. This multicenter study investigated this issue. Two‐hundred and sixty‐two Binet stage A patients were studied for the three markers. Sixty patients were profiled with HG‐U133A gene expression chips. Disease progression was determined by time from diagnosis to treatment (TTT). The probability of being treatment‐free at 3 years was significantly shorter in patients with unmutated IGHV genes (IGHVunmut 66% vs. 93%, chi square of log‐rank = 30, P < 0·0001), ZAP‐70 positive (ZAP‐70pos 73% vs. 96%, chi square of log‐rank = 8·2, P = 0·004) or CD38‐positive cells (CD38pos 68% vs. 91%, chi square of log‐rank = 21, P < 0·0001). Cox multivariate regression analysis showed that the three markers had an independent predictive value for TTT of similar power. A prognostic system based on presence of none (low‐risk), one (intermediate‐risk) or two or three (high‐risk) markers was generated. Based on such criteria, 56%, 23% and 21% of cases were clustered in low (HR = 1), intermediate [HR = 2·8, 95% confidence interval (CI) 2·4–5·8] and high‐risk group (HR = 8·0, 95% CI 3·9–16·2). Specific transcriptional patterns were significantly associated with risk groups.