bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function
Authors: McNutt Markey C , Tongbai Ron , Cui Wenwu , Collins Irene , Freebern Wendy J , Montano Idalia , Haggerty Cynthia M , Chandramouli GVR , Gardner Kevin 
Published: October 2005

Abstract
Background
The purpose of this study is to determine whether or not there exists nonrandom grouping of cis-regulatory elements within gene promoters that can be perceived independent of gene expression data and whether or not there is any correlation between this grouping and the biological function of the gene.

Results
Using ProSpector, a web-based promoter search and annotation tool, we have applied an unbiased approach to analyze the transcription factor binding site frequencies of 1400 base pair genomic segments positioned at 1200 base pairs upstream and 200 base pairs downstream of the transcriptional start site of 7298 commonly studied human genes. Partitional clustering of the transcription factor binding site composition within these promoter segments reveals a small number of gene groups that are selectively enriched for gene ontology terms consistent with distinct aspects of cellular function. Significance ranking of the class-determining transcription factor binding sites within these clusters show substantial overlap between the gene ontology terms of the transcriptions factors associated with the binding sites and the gene ontology terms of the regulated genes within each group.

Conclusion
Thus, gene sorting by promoter composition alone produces partitions in which the "regulated" and the "regulators" cosegregate into similar functional classes. These findings demonstrate that the transcription factor binding site composition is non-randomly distributed between gene promoters in a manner that reflects and partially defines general gene class function.
Novel splice variants associated with one of the zebrafish dnmt3genes
Authors: Smith Tamara HL , Dueck Christine C , Mhanni Aizeddin A , McGowan Ross A 
Published: October 2005

Abstract

Background
DNA methylation and the methyltransferases are known to be important in vertebrate development and this may be particularly true for the Dnmt3 family of enzymes because they are thought to be the de novo methyltransferases. Mammals have three Dnmt3 genes; Dnmt3a, Dnmt3b, and Dnmt3L, two of which encode active enzymes and one of which produces an inactive but necessary cofactor. However, due to multiple promoter use and alternative splicing there are actually a number of dnmt3 isoforms present. Six different dnmt3 genes have recently been identified in zebrafish.

Results
We have examined two of the dnmt3 genes in zebrafish that are located in close proximity in the same linkage group and we find that the two genes are more similar to each other than they are to the other zebrafish dnmt3 genes. We have found evidence for the existence of several different splice variants and alternative splice sites associated with one of the two genes and have examined the relative expression of these genes/variants in a number of zebrafish developmental stages and tissues.

Conclusion
The similarity of the dnmt3-1 and dnmt3-2 genes suggests that they arose due to a relatively recent gene duplication event. The presence of alternative splice and start sites, reminiscent of what is seen with the human DNMT3s, demonstrates strong parallels between the control/function of these genes across vertebrate species. The dynamic expression levels of these genes/variants suggest that they may well play a role in early development and this is particularly true for dnmt3-2-1 and dnmt3-1. dnmt3-2-1 is the predominantly expressed form prior to zygotic gene activation whereas dnmt3-1 predominates post zygotic gene activation suggesting a distinct developmental role for each.
Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters
Authors: Pavy Nathalie , Paule Charles , Parsons Lee , Crow John A , Morency Marie-Josee , Cooke Janice , Johnson James E , Noumen Etienne , Guillet-Claude Carine , Butterfield Yaron , Barber Sarah , Yang George , Liu Jerry , Stott Jeff , Kirkpatrick Robert , Siddiqui Asim , Holt Robert , Marra Marco , Seguin Armand , Retzel Ernest , Bousquet Jean , MacKay John 
Published: October 2005

Abstract

Background
The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss).

Results
We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations.

Conclusion
This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.
Pseudouridine modification in Caenorhabditis elegans spliceosomal snRNAs: unique modifications are found in regions involved in snRNA-snRNA interactions
Authors: Patton Jeffrey R , Padgett Richard W 
Published: October 2005

AbstractBackgroundPseudouridine (Ψ) is an abundant modified nucleoside in RNA and a number of studies have shown that the presence of Ψ affects RNA structure and function. The positions of Ψ in spliceosomal small nuclear RNAs (snRNAs) have been determined for a number of species but not for the snRNAs fromCaenorhabditis elegans(C. elegans), a popular experimental model system of development.ResultsAs a prelude to determining the function of or requirement for this modification in snRNAs, we have mapped the positions of Ψ in U1, U2, U4, U5, and U6 snRNAs from worms using a specific primer extension method. As with other species,C. elegansU2 snRNA has the greatest number of Ψ residues, with nine, located in the 5' half of the U2 snRNA. U5 snRNA has three Ψs, in or near the loop of the large stem-loop that dominates the structure of this RNA. U6 and U1 snRNAs each have one Ψ, and two Ψ residues were found in U4 snRNA.ConclusionThe total number of Ψs found in the snRNAs ofC. elegansis significantly higher than the minimal amount found in yeasts but it is lower than that seen in sequenced vertebrate snRNAs. When the actual sites of modification onC. eleganssnRNAs are compared with other sequenced snRNAs most of the positions correspond to modifications found in other species. However, two of the positions modified onC. eleganssnRNAs are unique, one at position 28 on U2 snRNA and one at position 62 on U4 snRNA. Both of these modifications are in regions of these snRNAs that interact with U6 snRNA either in the spliceosome or in the U4/U6 small nuclear ribonucleoprotein particle (snRNP) and the presence of Ψ may be involved in strengthening the intermolecular association of the snRNAs.
A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study
Authors: Chung Grace TY , Chiu Rossa WK , Cheung Jo LK , Jin Yongjie , Chim Stephen SC , Chan Paul KS , Lo YM Dennis 
Published: October 2005

AbstractBackgroundThe Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002–2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination.MethodsThirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing.ResultsGenotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort.ConclusionWe have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak.
Diet induced weight loss accelerates onset of negative alliesthesia in obese women
Authors: Frankham Patrick , Gosselin Caroline , Cabanac Michel 
Published: October 2005

Abstract

Background
The physiological and behavioral responses to hypocaloric diet are to increase energy intake to defend a steady body weight. We utilized the method of "negative alliesthesia" for measuring the hedonic reponse to sweet stimulus before (Initial session) and 3 months after entering a weight loss program. The negative alliesthesia test is known by physiologists but few clinical data exist. It is based on the observation that repeated pleasant gustatory stimuli turn into unpleasantness in the process of alliesthesia. At first visit participants repeatedly ingested sweet stimuli until they found them unpleasant and rated quantitatively on a linear analogue scale their hedonic experience. This procedure was repeated every 3 min until participants felt displeasure to end the session. The same protocol was followed after three months of following a weight loss diet. Dieting energy intake was from 1400 – 2000 kcal/d for 8 wk. Energy composition was 50% carb:25% prot: 25% lipid. After 8 wk caloric intake increased by 50 kcal/wk, to reach daily intake of 1800 – 2400 kcal/d. Energy composition was 50% carb:22% prot: 27% lipid. We report results on the effect of slow weight loss on negative alliesthesia in ten obese female participants enrolled in a commercial diet program based on Canada's Food Guide (Mincavi®).

Results
Results showed that diet lowered the mean BMI (Initial session 36.8 +/- 1.8 vs. 3 mo 34.9 +/- 1.8 kg/m2). At 3 mo the onset of negative alliesthesia, time to abandon experimental session, was shortened (Initial session 33 vs. 3 mo 24 min). The same trend was observed in the time to reach indifference (Initial session 21.9 +/- 3.8 vs. 3 mo 16.2 +/-2.4 min). There was no observed difference in maximum (Initial session +79.5 +/- 11.7; 3 mo +94.5 +/- 9.9 mm) and minimum (Initial session -90.0 +/- 14.4; 3 mo -106 +/- 11.1 mm) hedonic rating.

Conclusion
Earlier onset of negative alliesthesia, as seen in our participants, is not consistent with previous hedonic studies that showed delayed or absent negative alliesthesia in participants when below their initial body weight. Therefore, it is hypothesized that the accelerated onset of negative alliesthesia observed in our obese participants after weight loss is suggestive of a lowered body weight set-point. Factors inherent to the weight loss diet studied here, such as mild energetic restriction, lowered palatability, and diet composition, may have played a role in this experimental outcome.
Mistreatment of university students most common during medical studies
Authors: Rautio Arja , Sunnari Vappu , Nuutinen Matti , Laitala Marja 
Published: October 2005

Abstract

Background
This study concerns the occurrence of various forms of mistreatment by staff and fellow students experienced by students in the Faculty of Medicine and the other four faculties of the University of Oulu, Finland.

Methods
A questionnaire with 51 questions on various forms of physical and psychological mistreatment was distributed to 665 students (451 females) after lectures or examinations and filled in and returned. The results were analysed by gender and faculty. The differences between the males and females were assessed statistically using a test for the equality of two proportions. An exact two-sided P value was calculated using a mid-P approach to Fisher's exact test (the null hypothesis being that there is no difference between the two proportions).

Results
About half of the students answering the questionnaire had experienced some form of mistreatment by staff during their university studies, most commonly humiliation and contempt (40%), negative or disparaging remarks (34%), yelling and shouting (23%), sexual harassment and other forms of gender-based mistreatment (17%) and tasks assigned as punishment (13%). The students in the Faculty of Medicine reported every form of mistreatment more commonly than those in the Faculties of Humanities, Education, Science and Technology. Experiences of mistreatment varied, but clear messages regarding its patterns were to be found in each faculty. Female students reported more instances of mistreatment than males and were more disturbed by them. Professors, lecturers and other staff in particular mistreated female students more than they mistreated males. About half of the respondents reported some form of mistreatment by their fellow students.

Conclusion
Students in the Faculty of Medicine reported the greatest amount of mistreatment. If a faculty mistreats its students, its success in the main tasks of universities, research, teaching and learning, will be threatened. The results challenge university teachers, especially in faculties of medicine, to evaluate their ability to create a safe environment conducive to learning.
A suite of methods for representing activity space in a healthcare accessibility study
Authors: Sherman Jill E , Spencer John , Preisser John S , Gesler Wilbert M , Arcury Thomas A 
Published: October 2005

Abstract

Background
"Activity space" has been used to examine how people's habitual movements interact with their environment, and can be used to examine accessibility to healthcare opportunities. Traditionally, the standard deviational ellipse (SDE), a Euclidean measure, has been used to represent activity space. We describe the construction and application of the SDE at one and two standard deviations, and three additional network-based measures of activity space using common tools in GIS: the road network buffer (RNB), the 30-minute standard travel time polygon (STT), and the relative travel time polygon (RTT). We compare the theoretical and methodological assumptions of each measure, and evaluate the measures by examining access to primary care services, using data from western North Carolina.

Results
Individual accessibility is defined as the availability of healthcare opportunities within that individual's activity space. Access is influenced by the shape and area of an individual's activity space, the spatial distribution of opportunities, and by the spatial structures that constrain and direct movement through space; the shape and area of the activity space is partly a product of how it is conceptualized and measured. Network-derived measures improve upon the SDE by incorporating the spatial structures (roads) that channel movement. The area of the STT is primarily influenced by the location of a respondent's residence within the road network hierarchy, with residents living near primary roads having the largest activity spaces. The RNB was most descriptive of actual opportunities and can be used to examine bypassing. The area of the RTT had the strongest correlation with a healthcare destination being located inside the activity space.

Conclusion
The availability of geospatial technologies and data create multiple options for representing and operationalizing the construct of activity space. Each approach has its strengths and limitations, and presents a different view of accessibility. While the choice of method ultimately lies in the research question, interpretation of results must consider the interrelated issues of method, representation, and application. Triangulation aids this interpretation and provides a more complete and nuanced understanding of accessibility.
Differential effect sizes of growth hormone replacement on quality of life, well-being and health status in growth hormone deficient patients: a meta-analysis
Authors: Deijen Jan Berend , Arwert Lucia I , Witlox Joost , Drent Madeleine L 
Published: October 2005

Abstract

Background
Patients with growth hormone deficiency (GHD) frequently report to suffer from an impaired Quality of Life (QoL) and growth hormone (GH) substitution is found to improve this. However, the same test may be used for measuring QoL, well-being or health status in different studies. QoL has been defined as the subjective appraisal of one's current life based primarily on psychological function. The most important in the appraisal of well-being is mental function and concerning health status patients evaluate physical function as most important. To differentiate the effects of GH replacement on psychological variables in patients with GHD we carried out a number of meta-analyses, classifying questionnaires into instruments measuring QoL, psychological well-being and health status.

Methods
We searched the electronic databases PUBMED and PiCarta from 1985 to 2004. Studies were included that evaluated the effect of GH on patient-reported outcomes in adults with GHD (aged 18 years and above). According to generally accepted definitions we classified the questionnaires as instruments measuring QoL, well-being and health status. By means of meta-analyses the average effect size (d) for QoL, well-being and health status was calculated.

Results and Discussion
Based on open studies GH replacement is found to improve QoL with a small effect size (d = 0.18), well-being with a medium effect size (d = 0.47) and health status with a small effect size (d = 0.26). As the effect size of well-being is most pronounced the generally reported effects of GH replacement on QoL may be overestimated and actually reflect the effect on well-being.

Conclusion
To get more insight in the specific psychological effects of GH treatment it is recommended that instruments selected for these studies should be more consistently classified as instruments measuring QoL, well-being or health status.
Injection of colorectal cancer cells in mesenteric and antimesenteric sides of the colon results in different patterns of metastatic diffusion: An experimental study in rats
Authors: Boni Luigi , Benevento Angelo , Dionigi Gianlorenzo , Rovera Francesca , Diurni Mario , Dionigi Renzo 
Published: October 2005

Abstract

Background
This experimental study was designed to investigate the differences in pattern of local growth and diffusion of colorectal cancer cells injected into either mesenteric (M) or antimesenteric (AM) sides of the colon.

Methods
A total of 1 × 106 colonic adenocarcinoma cells (line DHD/K12-TRb) were injected into the cecal wall of BDIX syngeneic male rats at an M or AM site of the colon. At six weeks after injection, all animals were sacrificed and the presence or absence of tumor in the cecum as well as regional metastasis and peritoneal carcinomatosis were determined.

Results
Six weeks after injection, macroscopic tumor growth was observed in 27/37 (72%) animals in group M and 21/32 (65%) in group AM (P = 0.98). In group AM, diffuse peritoneal carcinomatosis was present in 19/21 rats (90.4%) versus 3/27 rats (11%) in group M; this difference was statistically significant (P = 0.025). Regional mesenteric lymph nodes were the only location in which tumor was detected in 23/27 rats (85%) in group M versus 2/21 (9.5%) in group AM; this difference too was statistically significant (P = 0.031)

Conclusion
The patterns of diffusion of tumors implanted in mesenteric and antimesenteric sites of the colon appear to be different, although the reason for this is not clear.
The natural history of EGFR and EGFRvIII in glioblastoma patients
Authors: Heimberger Amy B , Suki Dima , Yang David , Shi Weiming , Aldape Kenneth 
Published: October 2005

AbstractBackgroundThe epidermal growth factor receptor (EGFR) is over expressed in approximately 50–60% of glioblastoma (GBM) tumors, and the most common EGFR mutant, EGFRvIII, is expressed in 24–67% of cases. This study was designed to address whether over expressed EGFR or EGFRvIII is an actual independent prognostic indicator of overall survival in a uniform body of patients in whom gross total surgical resection (GTR; ≥ 95% resection) was not attempted or achieved.MethodsBiopsed or partially/subtotally resected GBM patients (N = 54) underwent adjuvant conformal radiation and chemotherapy. Their EGFR and EGFRvIII status was determined by immunohistochemistry and Kaplan-Meier estimates of overall survival were obtained.ResultsIn our study of GBM patients with less than GTR, 42.6% (n = 23) failed to express EGFR, 25.9% (n = 14) had over expression of the wild-type EGFR only and 31.5 % (n = 17) expressed the EGFRvIII. Patients within groups expressing the EGFR, EGFRvIII, or lacking EGFR expression did not differ in age, Karnofsky Performance Scale (KPS) score, extent of tumor resection. They all had received postoperative radiation and chemotherapy. The median overall survival times for patients with tumors having no EGFR expression, over expressed EGFR only, or EGFRvIII were 12.3 (95% CI, 8.04–16.56), 11.03 (95% CI, 10.18–11.89) and 14.07 (95% CI, 7.39–20.74) months, respectively, log rank test p > 0.05). Patients with tumors that over expressed the EGFR and EGFRvIII were more likely to present with ependymal spread, 21.4% and 35.3% respectively, compared to those patients whose GBM failed to express either marker, 13.0%, although the difference was not statistically significant. There was no significant difference in multifocal disease or gliomatosis cerebri among EGFR expression groups.ConclusionThe over expressed wild-type EGFR and EGFRvIII are not independent predictors of median overall survival in the cohort of patients who did not undergo extensive tumor resection.