bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
Authors: Ganesan Hamilton , Rakitianskaia Anna S , Davenport Colin F , Tümmler Burkhard , Reva Oleg N 
Published: August 2008

Abstract

Background
Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information for large scale sequence analysis and visualization. The purpose of this research was to make OU statistical analysis available as a novel web-based tool for functional genomics and annotation. The tool is also available as a downloadable package.

Results
The SeqWord Genome Browser (SWGB) was developed to visualize the natural compositional variation of DNA sequences. The applet is also used for identification of divergent genomic regions both in annotated sequences of bacterial chromosomes, plasmids, phages and viruses, and in raw DNA sequences prior to annotation by comparing local and global OU patterns. The applet allows fast and reliable identification of clusters of horizontally transferred genomic islands, large multi-domain genes and genes for ribosomal RNA. Within the majority of genomic fragments (also termed genomic core sequence), regions enriched with housekeeping genes, ribosomal proteins and the regions rich in pseudogenes or genetic vestiges may be contrasted.

Conclusion
The SWGB applet presents a range of comprehensive OU statistical parameters calculated for a range of bacterial species, plasmids and phages. It is available on the Internet at http://www.bi.up.ac.za/SeqWord/mhhapplet.php.
Myosin-Vb functions as a dynamic tether for peripheral endocytic compartments during transferrin trafficking
Authors: Provance D William , Addison Erin J , Wood Patrick R , Chen David Z , Silan Colleen M , Mercer John A 
Published: August 2008

Abstract

Background
Myosin-Vb has been shown to be involved in the recycling of diverse proteins in multiple cell types. Studies on transferrin trafficking in HeLa cells using a dominant-negative myosin-Vb tail fragment suggested that myosin-Vb was required for recycling from perinuclear compartments to the plasma membrane. However, chemical-genetic, dominant-negative experiments, in which myosin-Vb was specifically induced to bind to actin, suggested that the initial hypothesis was incorrect both in its site and mode of myosin-Vb action. Instead, the chemical-genetic data suggested that myosin-Vb functions in the actin-rich periphery as a dynamic tether on peripheral endosomes, retarding transferrin transport to perinuclear compartments.

Results
In this study, we employed both approaches, with the addition of overexpression of full-length wild-type myosin-Vb and switching the order of myosin-Vb inhibition and transferrin loading, to distinguish between these hypotheses. Overexpression of full-length myosin-Vb produced large peripheral endosomes. Chemical-genetic inhibition of myosin-Vb after loading with transferrin did not prevent movement of transferrin from perinuclear compartments; however, virtually all myosin-Vb-decorated particles, including those moving on microtubules, were halted by the inhibition. Overexpression of the myosin-Vb tail caused a less-peripheral distribution of early endosome antigen-1 (EEA1).

Conclusion
All results favored the peripheral dynamic tethering hypothesis.
Cold-inducible RNA binding protein (CIRP), a novel XTcf-3 specific target gene regulates neural development in Xenopus
Authors: van Venrooy Stephanie , Fichtner Dagmar , Kunz Martin , Wedlich Doris , Gradl Dietmar 
Published: August 2008

Abstract

Background
As nuclear mediators of wnt/β-catenin signaling, Lef/Tcf transcription factors play important roles in development and disease. Although it is well established, that the four vertebrate Lef/Tcfs have unique functional properties, most studies unite Lef-1, Tcf-1, Tcf-3 and Tcf-4 and reduce their function to uniformly transduce wnt/β-catenin signaling for activating wnt target genes. In order to discriminate target genes regulated by XTcf-3 from those regulated by XTcf-4 or Lef/Tcfs in general, we performed a subtractive screen, using neuralized Xenopus animal cap explants.

Results
We identified cold-inducible RNA binding protein (CIRP) as novel XTcf-3 specific target gene. Furthermore, we show that knockdown of XTcf-3 by injection of an antisense morpholino oligonucleotide results in a general broadening of the anterior neural tissue. Depletion of XCIRP by antisense morpholino oligonucleotide injection leads to a reduced stability of mRNA and an enlargement of the anterior neural plate similar to the depletion of XTcf-3.

Conclusion
Distinct steps in neural development are differentially regulated by individual Lef/Tcfs. For proper development of the anterior brain XTcf-3 and the Tcf-subtype specific target XCIRP appear indispensable. Thus, regulation of anterior neural development, at least in part, depends on mRNA stabilization by the novel XTcf-3 target gene XCIRP.
Initial validation of the Argentinean Spanish version of the PedsQL™ 4.0 Generic Core Scales in children and adolescents with chronic diseases: acceptability and comprehensibility in low-income settings
Authors: Roizen Mariana , Rodríguez Susana , Bauer Gabriela , Medin Gabriela , Bevilacqua Silvina , Varni James W , Dussel Veronica 
Published: August 2008

Abstract

Background
To validate the Argentinean Spanish version of the PedsQL™ 4.0 Generic Core Scales in Argentinean children and adolescents with chronic conditions and to assess the impact of socio-demographic characteristics on the instrument's comprehensibility and acceptability. Reliability, and known-groups, and convergent validity were tested.

Methods
Consecutive sample of 287 children with chronic conditions and 105 healthy children, ages 2–18, and their parents. Chronically ill children were: (1) attending outpatient clinics and (2) had one of the following diagnoses: stem cell transplant, chronic obstructive pulmonary disease, HIV/AIDS, cancer, end stage renal disease, complex congenital cardiopathy. Patients and adult proxies completed the PedsQL™ 4.0 and an overall health status assessment. Physicians were asked to rate degree of health status impairment.

Results
The PedsQL™ 4.0 was feasible (only 9 children, all 5 to 7 year-olds, could not complete the instrument), easy to administer, completed without, or with minimal, help by most children and parents, and required a brief administration time (average 5–6 minutes). People living below the poverty line and/or low literacy needed more help to complete the instrument. Cronbach Alpha's internal consistency values for the total and subscale scores exceeded 0.70 for self-reports of children over 8 years-old and parent-reports of children over 5 years of age. Reliability of proxy-reports of 2–4 year-olds was low but improved when school items were excluded. Internal consistency for 5–7 year-olds was low (α range = 0.28–0.76). Construct validity was good. Child self-report and parent proxy-report PedsQL™ 4.0 scores were moderately but significantly correlated (ρ = 0.39, p < 0.0001) and both significantly correlated with physician's assessment of health impairment and with child self-reported overall health status. The PedsQL™ 4.0 discriminated between healthy and chronically ill children (72.72 and 66.87, for healthy and ill children, respectively, p = 0.01), between different chronic health conditions, and children from lower socioeconomic status.

Conclusion
Results suggest that the Argentinean Spanish PedsQL™ 4.0 is suitable for research purposes in the public health setting for children over 8 years old and parents of children over 5 years old. People with low income and low literacy need help to complete the instrument. Steps to expand the use of the Argentinean Spanish PedsQL™ 4.0 include an alternative approach to scoring for the 2–4 year-olds, further understanding of how to increase reliability for the 5–7 year-olds self-report, and confirmation of other aspects of validity.
Nuclear import of Avian Sarcoma Virus integrase is facilitated by host cell factors
Authors: Andrake Mark D , Sauter Monica M , Boland Kim , Goldstein Andrew D , Hussein Maryem , Skalka Anna Marie 
Published: August 2008

Abstract

Background
Integration of retroviral DNA into the host cell genome is an obligatory step in the virus life cycle. In previous reports we identified a sequence (amino acids 201–236) in the linker region between the catalytic core and C-terminal domains of the avian sarcoma virus (ASV) integrase protein that functions as a transferable nuclear localization signal (NLS) in mammalian cells. The sequence is distinct from all known NLSs but, like many, contains basic residues that are essential for activity.

Results
Our present studies with digitonin-permeabilized HeLa cells show that nuclear import mediated by the NLS of ASV integrase is an active, saturable, and ATP-dependent process. As expected for transport through nuclear pore complexes, import is blocked by treatment of cells with wheat germ agglutinin. We also show that import of ASV integrase requires soluble cellular factors but does not depend on binding the classical adapter Importin-α. Results from competition studies indicate that ASV integrase relies on one or more of the soluble components that mediate transport of the linker histone H1.

Conclusion
These results are consistent with a role for ASV integrase and cytoplasmic cellular factors in the nuclear import of its viral DNA substrate, and lay the foundation for identification of host cell components that mediate this reaction.
Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus
Authors: Agudelo-Romero Patricia , Carbonell Pablo , de la Iglesia Francisca , Carrera Javier , Rodrigo Guillermo , Jaramillo Alfonso , Pérez-Amador Miguel A , Elena Santiago F 
Published: August 2008

Abstract

Background

Tobacco etch potyvirus (TEV) has been extensively used as model system for the study of positive-sense RNA virus infecting plants. TEV ability to infect Arabidopsis thaliana varies among ecotypes. In this study, changes in gene expression of A. thaliana ecotype Ler infected with TEV have been explored using long-oligonucleotide arrays. A. thaliana Ler is a susceptible host that allows systemic movement, although the viral load is low and syndrome induced ranges from asymptomatic to mild. Gene expression profiles were monitored in whole plants 21 days post-inoculation (dpi). Microarrays contained 26,173 protein-coding genes and 87 miRNAs.

Results
Expression analysis identified 1727 genes that displayed significant and consistent changes in expression levels either up or down, in infected plants. Identified TEV-responsive genes encode a diverse array of functional categories that include responses to biotic (such as the systemic acquired resistance pathway and hypersensitive responses) and abiotic stresses (droughtness, salinity, temperature, and wounding). The expression of many different transcription factors was also significantly affected, including members of the R2R3-MYB family and ABA-inducible TFs. In concordance with several other plant and animal viruses, the expression of heat-shock proteins (HSP) was also increased. Finally, we have associated functional GO categories with KEGG biochemical pathways, and found that many of the altered biological functions are controlled by changes in basal metabolism.

Conclusion
TEV infection significantly impacts a wide array of cellular processes, in particular, stress-response pathways, including the systemic acquired resistance and hypersensitive responses. However, many of the observed alterations may represent a global response to viral infection rather than being specific of TEV.
Brain stimulation modulates driving behavior
Authors: Beeli Gian , Koeneke Susan , Gasser Katja , Jancke Lutz 
Published: August 2008

Abstract

Background
Driving a car is a complex task requiring coordinated functioning of distributed brain regions. Controlled and safe driving depends on the integrity of the dorsolateral prefrontal cortex (DLPFC), a brain region, which has been shown to mature in late adolescence.

Methods
In this study, driving performance of twenty-four male participants was tested in a high-end driving simulator before and after the application of transcranial direct current stimulation (tDCS) for 15 minutes over the left or right DLPFC.

Results
We show that external modulation of both, the left and the right, DLPFC directly influences driving behavior. Excitation of the DLPFC (by applying anodal tDCS) leads to a more careful driving style in virtual scenarios without the participants noticing changes in their behavior.

Conclusion
This study is one of the first to prove that external stimulation of a specific brain area can influence a multi-part behavior in a very complex and everyday-life situation, therefore breaking new ground for therapy at a neural level.
Ketamine analgesia for inflammatory pain in neonatal rats: a factorial randomized trial examining long-term effects
Authors: Rovnaghi Cynthia R , Garg Sarita , Hall Richard W , Bhutta Adnan T , Anand K JS 
Published: August 2008

Abstract

Background
Neonatal rats exposed to repetitive inflammatory pain have altered behaviors in young adulthood, partly ameliorated by Ketamine analgesia. We examined the relationships between protein expression, neuronal survival and plasticity in the neonatal rat brain, and correlated these changes with adult cognitive behavior.

Methods
Using Western immunoblot techniques, homogenates of cortical tissue were analyzed from neonatal rats 18–20 hours following repeated exposure to 4% formalin injections (F, N = 9), Ketamine (K, 2.5 mg/kg × 2, N = 9), Ketamine prior to formalin (KF, N = 9), or undisturbed controls (C, N = 9). Brain tissues from another cohort of rat pups (F = 11, K = 12, KF = 10, C = 15) were used for cellular staining with Fos immunohistochemistry or FluoroJade-B (FJB), followed by cell counting in eleven cortical and three hippocampal areas. Long-term cognitive testing using a delayed non-match to sample (DNMS) paradigm in the 8-arm radial maze was performed in adult rats receiving the same treatments (F = 20, K = 24, KF = 21, C = 27) in the neonatal period.

Results
Greater cell death occurred in F vs. C, K, KF in parietal and retrosplenial areas, vs. K, KF in piriform, temporal, and occipital areas, vs. C, K in frontal and hindlimb areas. In retrosplenial cortex, less Fos expression occurred in F vs. C, KF. Cell death correlated inversely with Fos expression in piriform, retrosplenial, and occipital areas, but only in F. Cortical expression of glial fibrillary acidic protein (GFAP) was elevated in F, K and KF vs. C. No significant differences occurred in Caspase-3, Bax, and Bcl-2 expression between groups, but cellular changes in cortical areas were significantly correlated with protein expression patterns. Cluster analysis of the frequencies and durations of behaviors grouped them as exploratory, learning, preparatory, consumptive, and foraging behaviors. Neonatal inflammatory pain exposure reduced exploratory behaviors in adult males, learning and preparatory behaviors in females, whereas Ketamine ameliorated these long-term effects.

Conclusion
Neuroprotective effects of Ketamine attenuate the impaired cognitive behaviors resulting from pain-induced cell death in the cortical and hippocampal fields of neonatal rats. This cell death was not dependent on the apoptosis associated proteins, but was correlated with glial activation.
Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines
Authors: Cody Neal AL , Zietarska Magdalena , Filali-Mouhim Ali , Provencher Diane M , Mes-Masson Anne-Marie , Tonin Patricia N 
Published: August 2008

Abstract

Background
Expression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease. A possible variable is the influence of growth conditions on discerning candidates. The present study examined the influence of growth conditions on the expression of chromosome 3 genes in the tumorigenic EOC cell lines, OV-90, TOV-21G and TOV-112D using Affymetrix GeneChip® HG-U133A expression microarray analysis.

Methods
Chromosome 3 gene expression profiles (n = 1147 probe sets, representing 735 genes) were extracted from U133A expression microarray analyses of the EOC cell lines OV-90, TOV-21G and TOV-112D that were grown as monolayers, spheroids or nude mouse xenografts and monolayers derived from these tumors. Hierarchical cluster analysis was performed to compare chromosome 3 transcriptome patterns of each growth condition. Differentially expressed genes were identified and characterized by two-way comparative analyses of fold-differences in gene expression between monolayer cultures and each of the other growth conditions, and between the maximum and minimum values of expression of all growth conditions for each EOC cell line.

Results
An overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group. Two-way comparative analysis of each EOC cell line grown in an alternative condition relative to the monolayer culture showed that overall less than 15% of probe sets exhibited at least a 3-fold difference in expression profile. Less than 23% of probe sets exhibited greater than 3-fold differences in gene expression in comparisons of the maximum and minimum value of expression of all growth conditions within each EOC cell line group. The majority of these differences were less than 5-fold. There were 17 genes in common which were differentially expressed in all EOC cell lines. However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.

Conclusion
The various alternative in vivo and in vitro growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the in vitro cell line models are a viable option for testing gene candidates.
Acute myocardial infarction in an 18 year old South Indian girl with familial hypercholesterolemia: a case report
Authors: Kumar Anita A , Shantha Ghanshyam Palamaner Subash , Srinivasan Yadav , Senthil N , Rajkumar K , Paunikar Neeta , Sudhakar MK 
Published: August 2008

AbstractFamilial hypercholesterolemia is a single gene disorder with an autosomal dominant pattern of inheritance. Here we report an 18 year old South Indian girl who presented with myocardial infarction. She had xanthomas and an elevated serum low density lipoprotein cholesterol (LDL-C). Her mother and maternal uncle had died at a young age due to myocardial infarction. Her only sibling, 15 year old younger sister also had xanthomas and an elevated LDL-C. This report is to emphasise the need to clinically recognize xanthomas and its association with elevated LDL-C, premature atherosclerosis and familial inheritance. Early diagnosis and early initiation of treatment will save the affected individual and the other family members.
Continuing trastuzumab beyond disease progression: outcomes analysis in patients with metastatic breast cancer
Authors: Cancello Giuseppe , Montagna Emilia , D'Agostino Diego , Giuliano Mario , Giordano Antonio , Di Lorenzo Giuseppe , Plaitano Monica , De Placido Sabino , De Laurentiis Michele 
Published: August 2008

Abstract
Introduction
We performed a retrospective analysis of HER2-overexpressing metastatic breast cancer patients to describe clinical outcomes of those who, despite progression of the disease (PD), maintained trastuzumab for multiple chemotherapy lines. We also compared survival of these patients with that of those who halted trastuzumab at first PD.

Methods
We identified 101 patients treated between July 2000 and January 2007. Nineteen were still receiving the first-line trastuzumab-based treatment without evidence of PD and were not included in this analysis. Of the remaining 82 patients, 59 retained trastuzumab for one or more additional lines of chemotherapy after PD, according to our institution policy. Twenty-three patients who changed treating institution and stopped trastuzumab at first progression were used as a control group.

Results
For patients retaining trastuzumab, the median follow-up was 39.6 months. Clinical outcomes showed the typical degradation between first and second lines of therapy which we would expect by halting trastuzumab at first progression. Response rates were 35% and 16% and median times to progression were 7.25 and 5.25 months for the first and second lines of trastuzumab therapy, respectively. The median overall survival (OS) rates were 70 months for patients who retained trastuzumab and 56 months for patients who halted the drug (hazard ratio [HR] 0.87, 95% confidence interval [CI] 0.51 to 1.18; P = 0.52). If we consider OS from the start of trastuzumab therapy, the figures are 53.9 and 34.8 months, respectively (HR 0.78, 95% CI 0.58 to 1.32; P = 0.2).

Conclusion
A nonstatistically significant trend of improved survival for patients retaining trastuzumab is observed. This is in line with most retrospective analyses and recent randomized data. Retaining trastuzumab after progression is a reasonable option, but further randomized data are warranted to better define its role in comparison with other available options.