bluuebunny/crossref_metadata_2025_split huggingface dataset:
CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis
Authors: Tang Yong , Chen Yingfeng , Lichti Cheryl F , Hall Roger A , Raney Kevin D , Jennings Steven F 
Published: July 2005

Abstract

Background
Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies.

Result
We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides.

Conclusion
Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites.
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis
Authors: Metpally Raghu Prasad Rao , Sowdhamini Ramanathan 
Published: July 2005

Abstract

Background
The G-protein-coupled receptors (GPCRs) constitute one of the largest and most ancient superfamilies of membrane proteins. They play a central role in physiological processes affecting almost all aspects of the life cycle of an organism. Availability of the complete sets of putative members of a family from diverse species provides the basis for cross genome comparative studies.

Results
We have defined the repertoire of GPCR superfamily of Tetraodon complement with the availability of complete sequence of the freshwater puffer fish Tetraodon nigroviridis. Almost all 466 Tetraodon GPCRs (Tnig-GPCRs) identified had a clear human homologue. 189 putative human and Tetraodon GPCR orthologous pairs could be identified. Tetraodon GPCRs are classified into five GRAFS families, by phylogenetic analysis, concurrent with human GPCR classification.

Conclusion
Direct comparison of GPCRs in Tetraodon and human genomes displays a high level of orthology and supports large-scale gene duplications in Tetraodon. Examples of lineage specific gene expansions were also observed in opsin and odorant receptors. The human and Tetraodon GPCR sequences are analogous in terms of GPCR subfamilies but display disproportionate numbers of receptors at the subfamily level. The teleost genome with its expanded set of GPCRs provides additional and interesting comparators to study both evolution and function of these receptors.
Sirolimus increases tissue factor expression but not activity in cultured human vascular smooth muscle cells
Authors: Zhu Shengsi , Viswambharan Hema , Gajanayake Thusitha , Ming Xiu-Fen , Yang Zhihong 
Published: July 2005

Abstract

Background
Sirolimus-eluting stents (CYPHER stents) demonstrated remarkable efficacy in reducing restenosis rates in patients with coronary artery disease. There is a concern of sub-acute and late stent thrombosis. Tissue factor (TF) is critical in thrombosis. This study investigated the effect of sirolimus on TF expression and activity in cultured human vascular smooth muscle cells (SMCs).

Methods
SMCs were cultured from human saphenous veins and aortas. Quiescent cells were stimulated with sirolimus (0.1 – 20 ng/ml) over 24 hours. Cellular TF expression and activity released into culture medium were measured. The effect of sirolimus on activation of
m
ammalian
t
arget
o
f rapamycin (mTOR) was measured by phosphorylation of the substrate p70s6k at T389, and activation of RhoA was measured by pull-down assay.

Results
Sirolimus increased TF protein level in cultured human SMCs in a concentration and time-dependent manner (about 2-fold, p < 0.01) reaching maximal effect at 5 ng/ml. The stimulation of TF expression by sirolimus was associated with inhibition of basal activity of mTOR. No effects of sirolimus on RhoA or p38mapk activation that are positive regulators of TF in vascular wall cells were observed. The stimulation of TF expression by sirolimus (20 ng/ml) was prevented by the HMG-CoA reductase inhibitor fluvastatin (1 μmol/L). However, no increase in TF activity released from SMC into culture medium was observed after sirolimus treatment.

Conclusion
Although sirolimus stimulates TF protein expression in human SMC associated with inhibition of mTOR, it does not enhance TF activity released from the cells, suggesting a relatively safe profile of CYPHER stents. The inhibition of TF expression by fluvastatin favors clinical use of statins in patients undergoing coronary stenting.
Bacteriophage- based tests for the detection of Mycobacterium tuberculosis in clinical specimens: a systematic review and meta- analysis
Authors: Kalantri Shriprakash , Pai Madhukar , Pascopella Lisa , Riley Lee , Reingold Arthur 
Published: July 2005

AbstractBackgroundSputum microscopy, the most important conventional test for tuberculosis, is specific in settings with high burden of tuberculosis and low prevalence of non tuberculous mycobacteria. However, the test lacks sensitivity. Although bacteriophage-based tests for tuberculosis have shown promising results, their overall accuracy has not been systematically evaluated.MethodsWe did a systematic review and meta-analysis of published studies to evaluate the accuracy of phage-based tests for the direct detection ofM. tuberculosisin clinical specimens. To identify studies, we searched Medline, EMBASE, Web of science and BIOSIS, and contacted authors, experts and test manufacturers. Thirteen studies, all based on phage amplification method, met our inclusion criteria. Overall accuracy was evaluated using forest plots, summary receiver operating (SROC) curves, and subgroup analyses.ResultsThe data suggest that phage-based assays have high specificity (range 0.83 to 1.00), but modest and variable sensitivity (range 0.21 to 0.88). The sensitivity ranged between 0.29 and 0.87 among smear-positive, and 0.13 to 0.78 among smear-negative specimens. The specificity ranged between 0.60 and 0.88 among smear-positive and 0.89 to 0.99 among smear-negative specimens. SROC analyses suggest that overall accuracy of phage-based assays is slightly higher than smear microscopy in direct head-to-head comparisons.ConclusionPhage-based assays have high specificity but lower and variable sensitivity. Their performance characteristics are similar to sputum microscopy. Phage assays cannot replace conventional diagnostic tests such as microscopy and culture at this time. Further research is required to identify methods that can enhance the sensitivity of phage-based assays without compromising the high specificity.
Recovery of NIS expression in thyroid cancer cells by overexpression of Pax8 gene
Authors: Presta Ivan , Arturi Franco , Ferretti Elisabetta , Mattei Tiziana , Scarpelli Daniela , Tosi Emanuele , Scipioni Angela , Celano Marilena , Gulino Alberto , Filetti Sebastiano , Russo Diego 
Published: July 2005

Abstract

Background
Recovery of iodide uptake in thyroid cancer cells by means of obtaining the functional expression of the sodium/iodide symporter (NIS) represents an innovative strategy for the treatment of poorly differentiated thyroid cancer. However, the NIS gene expression alone is not always sufficient to restore radioiodine concentration ability in these tumour cells.

Methods
In this study, the anaplastic thyroid carcinoma ARO cells were stably transfected with a Pax8 gene expression vector. A quantitative RT-PCR was performed to assess the thyroid specific gene expression in selected clones. The presence of NIS protein was detected by Western blot and localized by immunofluorescence. A iodide uptake assay was also performed to verify the functional effect of NIS induction and differentiation switch.

Results
The clones overexpressing Pax8 showed the re-activation of several thyroid specific genes including NIS, Pendrin, Thyroglobulin, TPO and TTF1. In ARO-Pax8 clones NIS protein was also localized both in cell cytoplasm and membrane. Thus, the ability to uptake the radioiodine was partially restored, associated to a high rate of efflux. In addition, ARO cells expressing Pax8 presented a lower rate of cell growth.

Conclusion
These finding demonstrate that induction of Pax8 expression may determine a re-differentiation of thyroid cancer cells, including a partial recovery of iodide uptake, fundamental requisite for a radioiodine-based therapeutic approach for thyroid tumours.
Otitis media in young Aboriginal children from remote communities in Northern and Central Australia: a cross-sectional survey
Authors: Morris Peter S , Leach Amanda J , Silberberg Peter , Mellon Gabrielle , Wilson Cate , Hamilton Elizabeth , Beissbarth Jemima 
Published: July 2005

Abstract
Background
Middle ear disease (otitis media) is common and frequently severe in Australian Aboriginal children. There have not been any recent large-scale surveys using clear definitions and a standardised middle ear assessment. The aim of the study was to determine the prevalence of middle ear disease (otitis media) in a high-risk population of young Aboriginal children from remote communities in Northern and Central Australia.

Methods
709 Aboriginal children aged 6–30 months living in 29 communities from 4 health regions participated in the study between May and November 2001. Otitis media (OM) and perforation of the tympanic membrane (TM) were diagnosed by tympanometry, pneumatic otoscopy, and video-otoscopy. We used otoscopic criteria (bulging TM or recent perforation) to diagnose acute otitis media.

Results
914 children were eligible to participate in the study and 709 were assessed (78%). Otitis media affected nearly all children (91%, 95%CI 88, 94). Overall prevalence estimates adjusted for clustering by community were: 10% (95%CI 8, 12) for unilateral otitis media with effusion (OME); 31% (95%CI 27, 34) for bilateral OME; 26% (95%CI 23, 30) for acute otitis media without perforation (AOM/woP); 7% (95%CI 4, 9) for AOM with perforation (AOM/wiP); 2% (95%CI 1, 3) for dry perforation; and 15% (95%CI 11, 19) for chronic suppurative otitis media (CSOM). The perforation prevalence ranged from 0–60% between communities and from 19–33% between regions. Perforations of the tympanic membrane affected 40% of children in their first 18 months of life. These were not always persistent.

Conclusion
Overall, 1 in every 2 children examined had otoscopic signs consistent with suppurative ear disease and 1 in 4 children had a perforated tympanic membrane. Some of the children with intact tympanic membranes had experienced a perforation that healed before the survey. In this high-risk population, high rates of tympanic perforation were associated with high rates of bulging of the tympanic membrane.
Mass ivermectin treatment for Onchocerciasis: Lack of evidence for collateral impact on transmission of Wuchereria bancroftiin areas of co-endemicity
Authors: Richards FO , Eigege A , Pam D , Kal A , Lenhart A , Oneyka JOA , Jinadu MY , Miri ES 
Published: July 2005

AbstractThere has long been interest in determining if mass ivermectin administration for onchocerciasis has 'unknowingly' interrupted lymphatic filariasis (LF) transmission where the endemicity of the two diseases' overlaps. We studied 11 communities in central Nigeria entomologically for LF by performing mosquito dissections on Anopheline LF vectors. Six of the communities studied were located within an onchocerciasis treatment zone, and five were located outside of that zone. Communities inside the treatment zone had been offered ivermectin treatment for two-five years, with a mean coverage of 81% of the eligible population (range 58–95%). We found 4.9% of mosquitoes were infected with any larval stage of W. bancrofti in the head or thorax in 362 dissections in the untreated villages compared to 4.7% infected in 549 dissections in the ivermectin treated villages (Mantel-Haenszel ChiSquare 0.02, P = 0.9). We concluded that ivermectin annual therapy for onchocerciasis has not interrupted transmission of Wuchereria bancrofti (the causative agent of LF in Nigeria).
Telomerase inhibition by siRNA causes senescence and apoptosis in Barrett's adenocarcinoma cells: mechanism and therapeutic potential
Authors: Shammas Masood A , Koley Hemanta , Batchu Ramesh B , Bertheau Robert C , Protopopov Alexei , Munshi Nikhil C , Goyal Raj K 
Published: July 2005

AbstractBackgroundIn cancer cells, telomerase induction helps maintain telomere length and thereby bypasses senescence and provides enhanced replicative potential. Chemical inhibitors of telomerase have been shown to reactivate telomere shortening and cause replicative senescence and apoptotic cell death of tumor cells while having little or no effect on normal diploid cells.ResultsWe designed siRNAs against two different regions of telomerase gene and evaluated their effect on telomere length, proliferative potential, and gene expression in Barrett's adenocarcinoma SEG-1 cells. The mixture of siRNAs in nanomolar concentrations caused a loss of telomerase activity that appeared as early as day 1 and was essentially complete at day 3. Inhibition of telomerase activity was associated with marked reduction in median telomere length and complete loss of detectable telomeres in more than 50% of the treated cells. Telomere loss caused senescence in 40% and apoptosis in 86% of the treated cells. These responses appeared to be associated with activation of DNA sensor HR23B and subsequent activation of p53 homolog p73 and p63 and E2F1. Changes in these gene regulators were probably the source of observed up-regulation of cell cycle inhibitors, p16 and GADD45. Elevated transcript levels of FasL, Fas and caspase 8 that activate death receptors and CARD 9 that interacts with Bcl10 and NFKB to enhance mitochondrial translocation and activation of caspase 9 were also observed.ConclusionThese studies show that telomerase siRNAs can cause effective suppression of telomerase and telomere shortening leading to both cell cycle arrest and apoptosis via mechanisms that include up-regulation of several genes involved in cell cycle arrest and apoptosis. Telomerase siRNAs may therefore be strong candidates for highly selective therapy for chemoprevention and treatment of Barrett's adenocarcinoma.
Validation of a patient-administered questionnaire to measure the activity impairment experienced by women with uncomplicated urinary tract infection: the Activity Impairment Assessment (AIA)
Authors: Wild Diane J , Clayson Darren J , Keating Karen , Gondek Kathleen 
Published: July 2005

Abstract

Background
To validate a questionnaire to assess the activity impairment associated with uncomplicated urinary tract infection (uUTI).

Methods
The Activity Impairment Assessment (AIA) assesses the amount of time an individual's work or regular activities have been impaired as a result of their UTI. The measure was completed by 276 women with uUTI who had participated in a prospective, open-label, non-comparative multi-centre clinical trial of CIPRO® XR (extended-release ciprofloxacin). Baseline scores on the King's Health Questionnaire (KHQ) and clinical symptom evaluations were collected for validation purposes.

Results
An exploratory factor analysis showed that all items loaded >0.84 on a single component. This uni-dimensional structure was supported by Rasch analysis. The AIA was found to have excellent levels of internal consistency (Cronbach's alpha = 0.93), convergent validity (all rs >.70) and divergent validity (rs = .078). The AIA displayed excellent discriminant validity in relation to clinical evaluations, and was found to be responsive to change across all clinical evaluations.

Conclusion
The unidimensional AIA shows high levels of internal reliability, convergent and divergent validity, discriminant validity and responsiveness. It is an excellent tool for measuring activity impairment in UTI.
Extent of lymphadenectomy in radical cystectomy for bladder cancer
Authors: Ather M Hammad , Fatima Sadaf , Sinanoglu Orhun 
Published: July 2005

Abstract

Background
The benefit of pelvic lymphadenectomy in patients with cancer of the urinary bladder remains controversial. Though the inclusion of lymph node dissection in conjunction with radical cystectomy for patients with clinically negative nodes is well accepted, however, the extent of the nodal dissection remains contentious, particularly in patients with gross disease and T1G3 cancer. The extent of the primary bladder tumor, number of lymph nodes removed and the lymph node tumor burden are important prognostic variables in patients undergoing cystectomy. We analyzed the impact of the extent of lymphadenectomy during radical cystectomy on survival in the contemporary literature.

Methods
A Pubmed search was carried out for the literature published over the last 15 years using bladder cancer, radical cystectomy, survival, lymphadenectomy and complications as the key words. We have discussed the extent of lymphadenectomy on survival and its anatomical basis to determine the optimal number of lymph nodes to be removed and the concept of node density.

Results
Evidence from contemporary literature indicate significantly increased survival rates after cystectomy in patients with bladder cancer diagnosed with stages III or IV disease who have had relatively more lymph nodes examined, suggesting that even some patients with higher stage disease may benefit from extended pelvic lymphadenectomy at the time of cystectomy. Studies also indicate that more extensive lymphadenectomy significantly improved the prognosis of patients with bladder cancer, not only by providing prognostic information but perhaps it is also due to its inherent therapeutic value.

Conclusion
Extended lymph node dissection improves local control and survival. However, in the absence of controlled randomized trial this remains a dubitable issue.
Occult solitary submucosal jejunal metastasis from esophageal carcinoma
Authors: Lindenmann Joerg , Gollowitsch Franz , Matzi Veronika , Porubsky Christian , Maier Alfred , Smolle-Juettner Freyja Maria 
Published: July 2005

Abstract

Background
Metastatic tumors of the intestinal tract from extra-abdominal sites are rare. In esophageal cancer, the liver, lung and the bones are the most common sites of metastases. Metastasis to intestines are very rare.

Case presentation
A 54-year old male was admitted with esophageal squamous cell carcinoma (SCC) associated with dysphagia II-III and weight loss of 20 kg. Preoperative routine staging failed to detect any metastases. A transthoracic esophagectomy and orthotopic gastric pull-up with collar esophago-gastrostomy, associated with 2-field lymphadenectomy was perfromed. During the digital placement of the naso-jejunal feeding catheter a submucosal jejunal nodule with a diameter of 1 cm, about 40 cm distal to the duodeno-jejunal fold was detected which was completely resected by jejunotomy. Histopathology of jejunal nodule showed metastasis from esophageal squamous cell carcinoma.

Conclusion
Because of the extensic esophageal lymphatic system, an occult widespread dissemination of the tumor cells into the abdominal cavity is possible. Additional intraoperative evaluation of the small intestine and the complete abdominal cavity should be performed in every operation of esophageal carcinoma to detect possible occult intraabdominal metastases.
Comparison of incidence/risk of venous thromboembolism (VTE) among selected clinical and hereditary risk markers: A community-based cohort study
Authors: Spannagl Michael , Heinemann Lothar AJ , DoMinh Thai , Assmann Anita , Schramm Wolfgang , Schürmann Rolf 
Published: July 2005

Abstract

Background
Little information is available from community-based long-term VTE cohort studies to compare the absolute thrombosis risk of established clinical and genetic risk factors.

Materials and methods
The occurrence of venous thromboembolism (VTE) was observed during a 10-year observation period in the BAvarian ThromboEmbolic Risk (BATER) study, a cohort study of 4337 women (age 18–55 years). We collected data on demographics, reproductive life, lifestyle, conditions/diseases, and particularly potential risk factors for VTE with a self-administered questionnaire. The objective was to present incidence rates of VTE and to show relative risk estimated associated with different clinical and genetic risk factors.

Results
34 new, by diagnostic means confirmed VTE events occurred during the observation time of 32,656 women-years (WY). The overall incidence of VTE was 10.4 per 104 WY. The incidence rates varied markedly among different risk cohorts. The highest incidence was observed in women with previous history of VTE, followed by family history of VTE. None of the measured "genetically-related risk markers" (antithrombin, protein C, FVL, prothrombin mutation, or MTHFR) showed a significant VTE risk.

Conclusion
Most of the discussed VTE risk factors showed no significant association with the occurrence of new VTEs due to smallness of numbers. Only first-degree family history of VTE and own history of a previous VTE event depicted a significant association with future VTE. Clinical information seems to be more important to determine future VTE risk than genetically related laboratory tests.
Increasing weight-bearing physical activity and calcium-rich foods to promote bone mass gains among 9–11 year old girls: outcomes of the Cal-Girls study
Authors: French Simone A , Story Mary , Fulkerson Jayne A , Himes John H , Hannan Peter , Neumark-Sztainer Dianne , Ensrud Kristine 
Published: July 2005

Abstract
Background
A two-year, community-based, group-randomized trial to promote bone mass gains among 9–11 year-old girls through increased intake of calcium-rich foods and weight-bearing physical activity was evaluated.

Methods
Following baseline data collection, 30 5th-grade Girl Scout troops were randomized to a two-year behavioral intervention program or to a no-treatment control group. Evaluations were conducted at baseline, one year, and two years. Measures included bone mineral content, density, and area (measured by DXA), dietary calcium intake (24-hour recall), and weight-bearing physical activity (physical activity checklist interview). Mixed-model regression was used to evaluate treatment-related changes in bone mineral content (g) for the total body, lumbar spine (L1-L4), proximal femur, one-third distal radius, and femoral neck. Changes in eating and physical activity behavioral outcomes were examined.

Results
Although the intervention was implemented with high fidelity, no significant intervention effects were observed for total bone mineral content or any specific bone sites. Significant intervention effects were observed for increases in dietary calcium. No significant intervention effects were observed for increases in weight-bearing physical activity.

Conclusion
Future research needs to identify the optimal dosage of weight-bearing physical activity and calcium-rich dietary behavior change required to maximize bone mass gains in pre-adolescent and adolescent girls.