bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
Authors: Perez-Iratxeta Carolina , Andrade Miguel A 
Published: July 2005

Abstract
Background
DNA microarray probes are designed to match particular mRNA transcripts, often based on expressed sequences like ESTs, or cDNAs, many times incomplete. As a result, the relations between probes and genes can change as the sequence data are updated. However, it is frequent that the reported results of microarray analyses are given just as lists of genes without any reference to the underlying probes.

Results
We show for a particular commercial microarray design that the number of probes associated to some genes change with time. These changes concern approximately 5% of the probe sets across the history of annotation releases over a two year span.

Conclusion
We recommend to report probe set identifiers when publishing microarray results, and to submit those analyses to microarray public databases to ensure that the interpretation of the data is updated with the latest set of annotations.
A computational approach for identifying pathogenicity islands in prokaryotic genomes
Authors: Yoon Sung Ho , Hur Cheol-Goo , Kang Ho-Young , Kim Yeoun Hee , Oh Tae Kwang , Kim Jihyun F 
Published: July 2005

Abstract
Background
Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs.

Results
We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs.

Conclusion
Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
Authors: Margelevičius Mindaugas , Venclovas Česlovas 
Published: July 2005

Abstract
Background
Protein sequence alignments have become indispensable for virtually any evolutionary, structural or functional study involving proteins. Modern sequence search and comparison methods combined with rapidly increasing sequence data often can reliably match even distantly related proteins that share little sequence similarity. However, even highly significant matches generally may have incorrectly aligned regions. Therefore when exact residue correspondence is used to transfer biological information from one aligned sequence to another, it is critical to know which alignment regions are reliable and which may contain alignment errors.

Results
PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins. The software is freely available at: http://www.ibt.lt/bioinformatics/iss.

Conclusion
PSI-BLAST-ISS is an effective reliability assessment tool that can be useful in applications such as comparative modelling or analysis of individual sequence regions. It favorably compares with the existing similar software both in the performance and functional features.
Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments
Authors: Gao Xin , Song Peter XK 
Published: July 2005

AbstractBackgroundNumerous nonparametric approaches have been proposed in literature to detect differential gene expression in the setting of two user-defined groups. However, there is a lack of nonparametric procedures to analyze microarray data with multiple factors attributing to the gene expression. Furthermore, incorporating interaction effects in the analysis of microarray data has long been of great interest to biological scientists, little of which has been investigated in the nonparametric framework.ResultsIn this paper, we propose a set of nonparametric tests to detect treatment effects, clinical covariate effects, and interaction effects for multifactorial microarray data. When the distribution of expression data is skewed or heavy-tailed, the rank tests are substantially more powerful than the competing parametric F tests. On the other hand, in the case of light or medium-tailed distributions, the rank tests appear to be marginally less powerful than the parametric competitors.ConclusionThe proposed rank tests enable us to detect differential gene expression and establish interaction effects for microarray data with various non-normally distributed expression measurements across genome. In the presence of outliers, they are advantageous alternative approaches to the existing parametric F tests due to the robustness feature.
Lectin binding profiles of SSEA-4 enriched, pluripotent human embryonic stem cell surfaces
Authors: Venable Alison , Mitalipova Maisam , Lyons Ian , Jones Karen , Shin Soojung , Pierce Michael , Stice Steven 
Published: July 2005

Abstract

Background
Pluripotent human embryonic stem cells (hESCs) have the potential to form every cell type in the body. These cells must be appropriately characterized prior to differentiation studies or when defining characteristics of the pluripotent state. Some developmentally regulated cell surface antigens identified by monoclonal antibodies in a variety of species and stem cell types have proven to be side chains of membrane glycolipids and glycoproteins. Therefore, to examine hESC surfaces for other potential pluripotent markers, we used a panel of 14 lectins, which were chosen based on their specificity for a variety of carbohydrates and carbohydrate linkages, along with stage specific embryonic antigen-4 (SSEA-4), to determine binding quantitation by flow cytometry and binding localization in adherent colonies by immunocytochemistry.

Results
Enriching cells for SSEA-4 expression increased the percentage of SSEA-4 positive cells to 98–99%. Using enriched high SSEA-4-expressing hESCs, we then analyzed the binding percentages of selected lectins and found a large variation in binding percentages ranging from 4% to 99% binding. Lycopersicon (tomato)esculetum lectin (TL), Ricinus communis agglutinin (RCA), and Concanavalin A (Con A) bound to SSEA-4 positive regions of hESCs and with similar binding percentages as SSEA-4. In contrast, we found Dolichos biflorus agglutinin (DBA) and Lotus tetragonolobus lectin (LTL) did not bind to hESCs while Phaseolus vulgaris leuco-agglutinin (PHA-L), Vicia villosa agglutinin (VVA), Ulex europaeus agglutinin (UEA), Phaseolus vulgaris erythro-agglutinin (PHA-E), and Maackia amurensis agglutinin (MAA) bound partially to hESCs. These binding percentages correlated well with immunocytochemistry results.

Conclusion
Our results provide information about types of carbohydrates and carbohydrate linkages found on pluripotent hESC surfaces. We propose that TL, RCA and Con A may be used as markers that are associated with the pluripotent state of hESCs because binding percentages and binding localization of these lectins are similar to those of SSEA-4. Non-binding lectins, DBA and LTL, may identify differentiated cell types; however, we did not find these lectins to bind to pluripotent SSEA-4 positive hESCs. This work represents a fundamental base to systematically classify pluripotent hESCs, and in future studies these lectins may be used to distinguish differentiated hESC types based on glycan presentation that accompanies differentiation.
Characterization of Pseudomonas aeruginosa isolated from chronically infected children with cystic fibrosis in India
Authors: Agarwal Gunjan , Kapil Arti , Kabra Susheel Kumar , Das Bimal Kumar , Dwivedi Sada Nand 
Published: July 2005

Abstract

Background

Pseudomonas aeruginosa is the leading cause of morbidity and mortality in patients with cystic fibrosis (CF). With chronicity of infection, the organism resides as a biofilm, shows multi-drug resistance, diversifies its colony morphology and becomes auxotrophic. The patients have been found to be colonized with multiple genotypes. The present work was carried out to characterize P. aeruginosa isolated from children with cystic fibrosis using phenotypic and genotypic methods.

Results
We studied 56 patients with CF attending the Pediatric Chest clinic at All India Institute of Medical Sciences, New Delhi, India during August 1998-August 2001. These patients were regularly followed up at the clinic. Out of 56 patients, 27 were culture positive for P. aeruginosa where 8 were chronically infected (Group1) and 19 were intermittently colonized with the organism (Group2). Patients under Group1 had significantly higher rates of hospitalization, death and colonization with different colony morphotypes (p < 0.05). The isolates from Group1 patients were the positive producers of extended spectrum beta lactamase. A total of 5 auxotrophs were recovered from 2 patients where one was chronically infected with P. aeruginosa and the other was a recently enrolled patient. The auxotrophs had the specific requirement for methionine and arginine. Molecular typing revealed 33 ERIC-PCR (E1-E33) and 5 PCR-ribotyping (P1-P5) patterns. By ERIC-PCR, 4 patients were colonized with 2–4 genotypes and the remaining 23 patients were colonized with the single genotype.

Conclusion
With chronicity of infection, P. aeruginosa becomes multidrug resistant, diversifies its colony morphology, acquires mucoidity and shows auxotrophy for amino acids. The chronically infected patients can be colonized with multiple genotypes. Thus in a particular clinical set up, high index of suspicion should be there for diagnosis of CF patients so as to prevent the delay in diagnosis and management of CF patients.
Antenatal screening for Group B Streptococcus: A diagnostic cohort study
Authors: Hiller Janet E , McDonald Helen M , Darbyshire Philip , Crowther Caroline A 
Published: July 2005

Abstract

Background
A range of strategies have been adopted to prevent early onset Group B Streptococcal (EOGBS) sepsis, as a consequence of Group B Streptococcal (GBS) vertically acquired infection. This study was designed to provide a scientific basis for optimum timing and method of GBS screening in an Australian setting, to determine whether screening for GBS infection at 35–37 weeks gestation has better predictive values for colonisation at birth than screening at 31–33 weeks, to examine the test characteristics of a risk factor strategy and to determine the test characteristics of low vaginal swabs alone compared with a combination of perianal plus low vaginal swabs per colonisation during labour.

Methods
Consented women received vaginal and perianal swabs at 31–33 weeks gestation, 35–38 weeks gestation and during labour. Swabs were cultured on layered horse blood agar and inoculated into selective broth prior to analysis. Test characteristics were calculated with exact confidence intervals for a high risk strategy and for antenatal screening at 31–33 and 35–37 weeks gestation for vaginal cultures alone, perianal cultures alone and combined low vaginal and perianal cultures.

Results
The high risk strategy was not informative in predicting GBS status during labour. There is an unequivocal benefit for the identification of women colonised with GBS during labour associated with delaying screening until 36 weeks however the results for method of screening were less definitive with no clear advantage in using a combined low vaginal and perianal swabbing regimen over the use of a low vaginal swab alone.

Conclusion
This study can contribute to the development of prevention strategies in that it provides clear evidence for optimal timing of swabs. The addition of a perianal swab does not confer clear benefit. The quantification of advantages and disadvantages provided in this study will facilitate communication with clinicians and pregnant women alike.
HIF1-alpha overexpression indicates a good prognosis in early stage squamous cell carcinomas of the oral floor
Authors: Fillies Thomas , Werkmeister Richard , van Diest Paul J , Brandt Burkhard , Joos Ulrich , Buerger Horst 
Published: July 2005

AbstractBackgroundHypoxia-inducible factor 1 (HIF-1) is a transcription factor, which plays a central role in biologic processes under hypoxic conditions, especially concerning tumour angiogenesis. HIF-1α is the relevant, oxygen-dependent subunit and its overexpression has been associated with a poor prognosis in a variety of malignant tumours. Therefore, HIF-1α expression in early stage oral carcinomas was evaluated in relation to established clinico-pathological features in order to determine its value as a prognostic marker.Methods85 patients with histologically proven surgically treated T1/2 squamous cell carcinoma (SCC) of the oral floor were eligible for the study. Tumor specimens were investigated by means of tissue micro arrays (TMAs) and immunohistochemistry for the expression of HIF-1. Correlations between clinical features and the expression of HIF-1 were evaluated by Kaplan-Meier curves, log-rank tests and multivariate Cox regression analysis.ResultsHIF-1α was frequently overexpressed in a probably non-hypoxia related fashion. The expression of HIF-1α was related with a significantly improved 5-year survival rate (p < 0.01) and a significantly increased disease free period (p = 0.01) independent from nodal status and tumour size. In primary node negative T1/T2 SCC of the oral floor, absence of HIF-1α expression specified a subgroup of high-risk patients (p < 0.05).ConclusionHIF-1α overexpression is an indicator of favourable prognosis in T1 and T2 SCC of the oral floor. Node negative patients lacking HIF-1α expression may therefore be considered for adjuvant radiotherapy.
Zollinger-Ellison syndrome associated with neurofibromatosis type 1: a case report
Authors: Lee Wan-Sik , Koh Yang-Seok , Kim Jung-Chul , Park Chang-Hwan , Joo Young-Eun , Kim Hyun-Soo , Cho Chol-Kyoon , Choi Sung-Kyu , Rew Jong-Sun , Kim Sei-Jong 
Published: July 2005

AbstractBackgroundNeurofibromatosis type 1 is an autosomal dominant neurocutaneous disorder with characteristic features of skin and central nervous system involvement. Gastrointestinal involvement is rare, but the risk of malignancy development is considerable. Zollinger-Ellison syndrome is caused by gastrin-secreting tumors called gastrinomas. Correct diagnosis is often difficult, and curative treatment can only be achieved surgically.Case presentationA 41-year-old female affected by neurofibromatosis type 1 presented with a history of recurrent epigastric soreness, diarrhea, and relapsing chronic duodenal ulcer. Her serum fasting gastrin level was over 1000 pg/mL. An abdominal CT scan revealed a 3 × 2-cm, well-enhanced mass adjacent to the duodenal loop. She was not associated with multiple endocrine neoplasia type 1. Operative resection was performed and gastrinoma was diagnosed by immunohistochemical staining. The serum gastrin level decreased to 99.1 pg/mL after surgery, and symptoms and endoscopic findings completely resolved without recurrences.ConclusionGastrinoma is difficult to detect even in the general population, and hence symptoms such as recurrent idiopathic peptic ulcer and diarrhea in neurofibromatosis type 1 patients should be accounted for as possibly contributing to Zollinger-Ellison syndrome.
Risk of cardio-respiratory abnormalities in preterm infants placed in car seats: a cross-sectional study
Authors: Ojadi Vallier C , Petrova Anna , Mehta Rajeev , Hegyi Thomas 
Published: July 2005

Abstract
Background
Little is known about the factors that predispose to the occurrence and severity of cardio-respiratory symptoms during the placement of a prematurely born infant in a car seat. The impact of gestational age, weight at discharge and infant's pre-existing cardio-respiratory status (in the supine position) on cardio-respiratory function during pre-discharge testing in a car seat (semi-upright position) has not been investigated.

Methods
The cardio-respiratory function of 42 preterm neonates with gestational age 24 to 35 weeks and discharge weight 1790 to 2570 grams were monitored for 45 minutes before, during, and after placement in a car seat. The occurrence of periodic breathing, apnea, bradycardia, or decreased oxygen saturation (SaO2) was analyzed.

Results
Prior to the car seat testing, 15 (35.7%) infants displayed one or more abnormalities of cardio-respiratory function. During the car seat testing, 25 (59.6%) infants had periodic breathing, 33 (78.2%) had oxygen saturation <90%, 14 (33.3%) had bradycardia less than 80 beats per minute, and 35 (83.3%) had a combination of these symptoms. Infants, both with and without pre-existing cardio-respiratory abnormalities, had an almost equal probability (80% vs. 83.3%) for the development of cardio-respiratory symptoms during placement in the car seat. Weight at discharge ([less than or equal to] 2,000 grams) but not the gestational age (<28 weeks or [greater than or equal to] 28<37 weeks), was associated with either increased episodes of oxygen desaturation or the combination of cardio-respiratory symptoms that were seen during the placement of these infants in the car seat. Repositioning from the car seat to the supine position showed normalization of cardio-respiratory function in the majority (83%) of the tested infants. None of the tested clinical factors were associated with the severity of the cardio-respiratory symptoms.

Conclusion
Pre-discharge testing of the cardio-respiratory function of preterm infants during placement in a car seat is important for the prevention of cardio-respiratory symptoms during their transportation. However, the high risk for developing cardio-respiratory symptoms will require the consideration of an alternative mode of safe home transportation for preterm infants; especially those with a discharge weight less than 2,000 grams.
Severely disabling chronic pain in young adults: prevalence from a population-based postal survey in North Staffordshire
Authors: Mallen Christian , Peat George , Thomas Elaine , Croft Peter 
Published: July 2005

Abstract

Background
Severely disabling chronic pain in the adult population is strongly associated with a range of negative health consequences for individuals and high health care costs, yet its prevalence in young adults is less clear.

Methods
All adults aged 18–25 years old registered with three general practices in North Staffordshire were invited to complete a postal questionnaire containing questions on pain within the last 6 months, pain location and duration. Severity of chronic pain was assessed by the Chronic Pain Grade. Severely disabling chronic pain was defined as pain within the last six months that had lasted for three months or more and was highly disabling-severely limiting (Grade IV).

Results
858 responses from 2,389 were received (adjusted response = 37.0%). The prevalence of any pain within the previous six months was 66.9% (95%CI: 63.7%, 70.1%). Chronic pain was reported by 14.3% (95%CI: 12.0%, 16.8%) of respondents with severely disabling chronic pain affecting 3.0% (95%CI: 2.0%, 4.4%) of this population. Late responders were very similar to early responders in their prevalence of pain. Cross-checking the practice register against the electoral roll suggested register inaccuracies contributed to non-response.

Conclusion
Pain is a common phenomenon encountered by young adults, affecting 66.9% of this study population. Previously observed age-related trends in severely disabling chronic pain in older adults extend to younger adults. Although a small minority of younger adults are affected, they are likely to represent a group with particularly high health care needs. High levels of non-response in the present study means that these estimates should be interpreted cautiously although there was no evidence of non-response bias.
Variation in gene expression patterns in effusions and primary tumors from serous ovarian cancer patients
Authors: Schaner Marci E , Davidson Ben , Skrede Martina , Reich Reuven , Flørenes Vivi Ann , Risberg Björn , Berner Aasmund , Goldberg Iris , Givant-Horwitz Vered , Tropè Claes G , Kristensen Gunnar B , Nesland Jahn M , Børresen-Dale Anne-Lise 
Published: July 2005

Abstract

Background
While numerous studies have characterized primary ovarian tumors, little information is available regarding expression patterns of metastatic sites of this cancer. To define sets of genes that distinguish primary and metastatic ovarian tumors, we used cDNA microarrays to characterize global gene expression patterns in 38 effusions (28 peritoneal, 10 pleural) and 8 corresponding primary ovarian tumors, and searched for associations between expression patterns and clinical parameters.

Results
We observed multidimensional variation in expression patterns among the cancers. Coordinate variation in expression of genes from two chromosomal regions, 8q and 19q, was seen in subsets of the cancers indicating possible amplifications in these regions. A set of 112 unique genes of known function was differentially expressed between primary tumors and effusions using supervised analysis. Relatively few differences were seen between effusions isolated from the pleural and peritoneal cavities or between effusions from patients diagnosed with stage III and stage IV cancers. A set of 84 unique genes was identified that distinguished high from lower grade ovarian cancers. The results were corroborated using immunocytochemistry, mRNA in situ hybridization, and immunoblotting.

Conclusion
The extensive variation in expression patterns observed underscores the molecular heterogeneity of ovarian cancer, but suggests a similar molecular profile for ovarian carcinoma cells in serosal cavities.