bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel method for high accuracy sumoylation site prediction from protein sequences
Authors: Xu Jialin , He Yun , Qiang Boqin , Yuan Jiangang , Peng Xiaozhong , Pan Xian-Ming 
Published: January 2008

Abstract

Background
Protein sumoylation is an essential dynamic, reversible post translational modification that plays a role in dozens of cellular activities, especially the regulation of gene expression and the maintenance of genomic stability. Currently, the complexities of sumoylation mechanism can not be perfectly solved by experimental approaches. In this regard, computational approaches might represent a promising method to direct experimental identification of sumoylation sites and shed light on the understanding of the reaction mechanism.

Results
Here we presented a statistical method for sumoylation site prediction. A 5-fold cross validation test over the experimentally identified sumoylation sites yielded excellent prediction performance with correlation coefficient, specificity, sensitivity and accuracy equal to 0.6364, 97.67%, 73.96% and 96.71% respectively. Additionally, the predictor performance is maintained when high level homologs are removed.

Conclusion
By using a statistical method, we have developed a new SUMO site prediction method – SUMOpre, which has shown its great accuracy with correlation coefficient, specificity, sensitivity and accuracy.
AI-2-dependent gene regulation in Staphylococcus epidermidis
Authors: Li Min , Villaruz Amer E , Vadyvaloo Viveka , Sturdevant Daniel E , Otto Michael 
Published: January 2008

Abstract

Background
Autoinducer 2 (AI-2), a widespread by-product of the LuxS-catalyzed S-ribosylhomocysteine cleavage reaction in the activated methyl cycle, has been suggested to serve as an intra- and interspecies signaling molecule, but in many bacteria AI-2 control of gene expression is not completely understood. Particularly, we have a lack of knowledge about AI-2 signaling in the important human pathogens Staphylococcus aureus and S. epidermidis.

Results
To determine the role of LuxS and AI-2 in S. epidermidis, we analyzed genome-wide changes in gene expression in an S. epidermidis luxS mutant and after addition of AI-2 synthesized by over-expressed S. epidermidis Pfs and LuxS enzymes. Genes under AI-2 control included mostly genes involved in sugar, nucleotide, amino acid, and nitrogen metabolism, but also virulence-associated genes coding for lipase and bacterial apoptosis proteins. In addition, we demonstrate by liquid chromatography/mass-spectrometry of culture filtrates that the pro-inflammatory phenol-soluble modulin (PSM) peptides, key virulence factors of S. epidermidis, are under luxS/AI-2 control.

Conclusion
Our results provide a detailed molecular basis for the role of LuxS in S. epidermidis virulence and suggest a signaling function for AI-2 in this bacterium.
Validity of self-reported criminal justice system involvement in substance abusing women at five-year follow-up
Authors: Jansson Irene , Hesse Morten , Fridell Mats 
Published: January 2008

Abstract

Background
Few studies have compared self-reported criminal behaviour with high-quality databases of criminal offences and judicial sanctions. Self-reported problems from drug abusers are generally believed to be valid. We assessed the validity of self-reported theft, drug offences and prison sentences from a five-year follow-up of female substance abusers who were originally treated in a compulsory care unit in Lund, run by the Swedish Board of Institutional Care.

Methods
Data from a total of 106 of a consecutive sample of 132 women inter-viewed in a five-year follow-up. All were thoroughly assessed for somatic complaints, psychiatric and psychological problems, background factors with standardized instruments. Data over the five years were linked to official records of judicial sanctions, retrieved from The National Council for Crime Prevention, Stockholm, Sweden. Register data have a full cover for the whole cohort. The current data base contain full data back to 1975 up to 2004.

Results
Agreement was assessed for each year, as well as for the total period. Statistical control was performed for other types of crimes and prison. Although statistically significant, agreement was modest, and in contrast to previous studies, patients under-reported violence charges.

Conclusion
The findings suggest that self-reports of criminal behaviour from women can be used with some caution, and that the validity of self-report may vary between types of criminal justice system involvement.
Presentations of patients of poisoning and predictors of poisoning-related fatality: Findings from a hospital-based prospective study
Authors: Lee Hsin-Ling , Lin Hung-Jung , Yeh Steve Ting-Yuan , Chi Chih-Hsien , Guo How-Ran 
Published: January 2008

Abstract

Background
Poisoning is a significant public health problem worldwide and is one of the most common reasons for visiting emergency departments (EDs), but factors that help to predict overall poisoning-related fatality have rarely been elucidated. Using 1512 subjects from a hospital-based study, we sought to describe the demographic and clinical characteristics of poisoning patients and to identify predictors for poisoning-related fatality.

Methods
Between January 2001 and December 2002 we prospectively recruited poisoning patients through the EDs of two medical centers in southwest Taiwan. Interviews were conducted with patients within 24 hours after admission to collect relevant information. We made comparisons between survival and fatality cases, and used logistic regressions to identify predictors of fatality.

Results
A total of 1512 poisoning cases were recorded at the EDs during the study period, corresponding to an average of 4.2 poisonings per 1000 ED visits. These cases involved 828 women and 684 men with a mean age of 38.8 years, although most patients were between 19 and 50 years old (66.8%), and 29.4% were 19 to 30 years. Drugs were the dominant poisoning agents involved (49.9%), followed by pesticides (14.5%). Of the 1512 patients, 63 fatalities (4.2%) occurred. Paraquat exposure was associated with an extremely high fatality rate (72.1%). The significant predictors for fatality included age over 61 years, insufficient respiration, shock status, abnormal heart rate, abnormal body temperature, suicidal intent and paraquat exposure.

Conclusion
In addition to well-recognized risk factors for fatality in clinical settings, such as old age and abnormal vital signs, we found that suicidal intent and ingestion of paraquat were significant predictors of poisoning-related fatality. Identification of these predictors may help risk stratification and the development of preventive interventions.
Oxaliplatin retains HMGB1 intranuclearly and ameliorates collagen type II-induced arthritis
Authors: Östberg Therese , Wähämaa Heidi , Palmblad Karin , Ito Norimasa , Stridh Pernilla , Shoshan Maria , Lotze Michael T , Harris Helena Erlandsson , Andersson Ulf 
Published: January 2008

Abstract
Introduction
High mobility group box chromosomal protein 1 (HMGB1) is a nuclear protein that acts as a pro-inflammatory mediator following extracellular release. The protein is aberrantly expressed extracellularly in the settings of clinical and experimental synovitis. Therapy based on HMGB1 antagonists has shown encouraging results in experimental arthritis and warrants further scientific exploration using independent methods. In the present study we asked whether nuclear sequestration of HMGB1 preventing HMGB1 release would be beneficial for synovitis treatment.

Methods
Oxaliplatin-based therapy was evaluated in collagen type II-induced arthritis in DBA/1 mice by clinical scoring and immunostaining of articular tissue. Oxaliplatin is an antineoplastic platinum-based compound that generates DNA adducts which tightly bind HMGB1. Secretion and intracellular location of HMGB1 were assessed by a novel HMGB1-specific ELISPOT assay and immunofluorescent staining.

Results
Intraperitoneal injections of oxaliplatin in early collagen type II-induced arthritis trapped HMGB1 with a distinct biphasic response pattern. Oxaliplatin therapy showed beneficial results for approximately 1 week. Microscopic evaluation of synovitis during this period showed strong nuclear HMGB1 staining in the oxaliplatin treated animals with much lower quantities of extracellular HMGB1 when compared to control treated animals. Furthermore, cellular infiltration, as well as cartilage and bone damage, were all reduced in the oxaliplatin treated group. A dramatic and as yet unexplained clinical relapse occurred later in the oxaliplatin exposed animals, which coincided with a massive synovial tissue expression of extracellular HMGB1 in all treated animals. This rebound-like reaction was also accompanied by a significantly increased incidence of arthritis in the oxaliplatin treated group. These results indicate a distinct temporal and spatial relationship between the clinical course of disease and the cellular localization of HMGB1. Beneficial effects were noted when extracellular HMGB1 expression was low, while severe inflammation coincided with substantial extracellular synovial HMGB1 expression.

Conclusion
Therapeutic compounds like oxaliplatin and gold salts share a capacity to inhibit nuclear HMGB1 release and to ameliorate the course of synovial inflammation. These observations support the hypothesis that HMGB1 plays an important functional role in the pathogenesis of arthritis and may represent a novel target molecule for therapy.
Circulating RANKL is inversely related to RANKL mRNA levels in bone in osteoarthritic males
Authors: Findlay David , Chehade Mellick , Tsangari Helen , Neale Susan , Hay Shelley , Hopwood Blair , Pannach Susan , O'Loughlin Peter , Fazzalari Nicola 
Published: January 2008

Abstract
Introduction
The relationship of circulating levels of receptor activator of nuclear factor-κB ligand (RANKL) and osteoprotegerin (OPG) with the expression of these molecules in bone has not been established. The objective of this study was to measure, in humans, the serum levels of RANKL and OPG, and the corresponding levels in bone of mRNA encoding these proteins.

Methods
Fasting blood samples were obtained on the day of surgery from patients presenting for hip replacement surgery for primary osteoarthritis (OA). Intraoperatively, samples of intertrochanteric trabecular bone were collected for analysis of OPG and RANKL mRNA, using real time RT-PCR. Samples were obtained from 40 patients (15 men with age range 50 to 79 years, and 25 women with age range 47 to 87 years). Serum total RANKL and free OPG levels were measured using ELISA.

Results
Serum OPG levels increased over the age range of this cohort. In the men RANKL mRNA levels were positively related to age, whereas serum RANKL levels were negatively related to age. Again, in the men serum RANKL levels were inversely related (r = -0.70, P = 0.007) to RANKL mRNA levels. Also in the male group, RANKL mRNA levels were associated with a number of indices of bone structure (bone volume fraction relative to bone tissue volume, specific surface of bone relative to bone tissue volume, and trabecular thickness), bone remodelling (eroded surface and osteoid surface), and biochemical markers of bone turnover (serum alkaline phosphatase and osteocalcin, and urinary deoxypyridinoline).

Conclusion
This is the first report to show a relationship between serum RANKL and the expression of RANKL mRNA in bone.
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novogene prediction
Authors: Gross Samuel S , Do Chuong B , Sirota Marina , Batzoglou Serafim 
Published: January 2008

AbstractWe describe CONTRAST, a gene predictor which directly incorporates information from multiple alignments rather than employing phylogenetic models. This is accomplished through the use of discriminative machine learning techniques, including a novel training algorithm. We use a two-stage approach, in which a set of binary classifiers designed to recognize coding region boundaries is combined with a global model of gene structure. CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art method, misses 46% fewer exons and displays comparable gains in specificity.
Picoeukaryotic sequences in the Sargasso Sea metagenome
Authors: Piganeau Gwenael , Desdevises Yves , Derelle Evelyne , Moreau Herve 
Published: January 2008

Abstract
Background
With genome sequencing becoming more and more affordable, environmental shotgun sequencing of the microorganisms present in an environment generates a challenging amount of sequence data for the scientific community. These sequence data enable the diversity of the microbial world and the metabolic pathways within an environment to be investigated, a previously unthinkable achievement when using traditional approaches. DNA sequence data assembled from extracts of 0.8 μm filtered Sargasso seawater unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. Serendipitously, many sequences representing picoeukaryotes (cell size <2 μm) were also present within this dataset. We investigated the picoeukaryotic diversity of this database by searching sequences containing homologs of eight nuclear anchor genes that are well conserved throughout the eukaryotic lineage, as well as one chloroplastic and one mitochondrial gene.

Results
We found up to 41 distinct eukaryotic scaffolds, with a broad phylogenetic spread on the eukaryotic tree of life. The average eukaryotic scaffold size is 2,909 bp, with one gap every 1,253 bp. Strikingly, the AT frequency of the eukaryotic sequences (51.4%) is significantly lower than the average AT frequency of the metagenome (61.4%). This represents 4% to 18% of the estimated prokaryotic diversity, depending on the average prokaryotic versus eukaryotic genome size ratio.

Conclusion
Despite similar cell size, eukaryotic sequences of the Sargasso Sea metagenome have higher GC content, suggesting that different environmental pressures affect the evolution of their base composition.
The cytoplasmic domain of tissue factor in macrophages augments cutaneous delayed-type hypersensitivity
Authors: Apostolopoulos Jim , Hickey Michael J , Sharma Laveena , Davenport Piers , Moussa Leon , James Will G , Gregory Julia L , Kitching A Richard , Li Ming , Tipping Peter G 
Published: January 2008

AbstractIn addition to its procoagulant role, tissue factor (TF) has important coagulation-independent roles, including in inflammation. The cytoplasmic domain of TF has been implicated in some of these coagulation-independent roles, particularly cell signaling. To assess the contribution of the cytoplasmic domain of TF to cell-mediated adaptive immunity, the development of cutaneous delayed-type hypersensitivity (DTH) was studied in mice lacking the cytoplasmic domain of TF (TFδCT/δCT mice). DTH responses in sensitized mice were significantly attenuated in TFδCT/δCT mice, and leukocyte-endothelial cell interactions, assessed by intravital microscopy, were impaired significantly. Studies in chimeric mice, created by bone marrow transplantation, showed that the absence of the cytoplasmic domain of TF in leukocytes rather than endothelial cells was responsible for reduced DTH and leukocyte recruitment. DTH responses to OVA could be induced in wild-type mice but not in TFδCT/δCT mice by transfer of activated CD4+ OVA-specific TCR transgenic T cells, demonstrating that the defective DTH response in TFδCT/δCT mice was independent of any defect in T cell activation. Macrophage and neutrophil accumulation and expression of TNF-α mRNA and phospho-p38-MAPK were reduced significantly in TFδCT/δCT mice, and their macrophages had reduced P-selectin-binding capacity and reduced in vivo emigration in response to MCP-1. These results indicate that leukocyte expression of the cytoplasmic domain of TF contributes to antigen-specific cellular adaptive immune responses via effects on leukocyte recruitment and activation.
Long-Term Results of the AIEOP-ALL-95 Trial for Childhood Acute Lymphoblastic Leukemia: Insight on the Prognostic Value of DNA Index in the Framework of Berlin-Frankfurt-Muenster–Based Chemotherapy
Authors: Aricò Maurizio , Valsecchi Maria Grazia , Rizzari Carmelo , Barisone Elena , Biondi Andrea , Casale Fiorina , Locatelli Franco , Lo Nigro Luca , Luciani Matteo , Messina Chiara , Micalizzi Concetta , Parasole Rosanna , Pession Andrea , Santoro Nicola , Testi Anna Maria , Silvestri Daniela , Basso Giuseppe , Masera Giuseppe , Conter Valentino 
Published: January 2008

Purpose Between May 1995 and August 2000 the Associazione Italiana di Ematologia Oncologia Pediatrica conducted the ALL-95 study for risk-directed, Berlin-Frankfurt-Muenster (BFM) –oriented therapy of childhood acute lymphoblastic leukemia, aimed at exploring treatment reduction in standard-risk patients (SR) and intensification during continuation therapy in intermediate-risk patients (IR) as randomized questions and treatment intensification in high-risk patients (HR). The prognostic value of DNA index was explored in this setting. Patients and Methods A total of 1,744 patients were enrolled (115, SR; 1,385, IR; and 244, HR). SR patients (DNA index ≥ 1.16 and < 1.60; age, 1 to 5 years; and WBC < 20,000, non–T-immunophenotype, with no high-risk features) received a reduced induction therapy (no anthracyclines); IR patients were randomly assigned to receive or not receive vincristine and dexamethasone pulses during maintenance; HR therapy was based on a conventional BFM schedule intensified with three chemotherapy blocks followed by a double reinduction phase. Results The event-free survival and overall survival probabilities at 10 years for the entire group were 72.5% (SE, 1.3) and 83.6% (SE, 0.9); 85.0% (SE, 3.4) and 95.5% (SE, 2.0) in SR, 75.1% (SE, 1.5) and 87.5% (SE, 0.9) in IR, and 51.0% (SE, 3.2) and 57.2% (SE, 3.3) in HR patients, respectively. Patients with a favorable DNA index had superior EFS in both IR (83.8% [2.7%] v 73.9% [1.7%]) and in HR (67.8% [9.4%] and 49.6% [3.5%]). Of the six patients with DNA index less than 0.8, only one remained in remission. Conclusion Favorable DNA index was associated with a better prognosis in IR and HR patients defined by presenting clinical criteria and treatment with a BFM-oriented chemotherapy.
Modeling the Cost Effectiveness of Secondary Febrile Neutropenia Prophylaxis During Standard-Dose Chemotherapy
Authors: Timmer-Bonte Johanna N.H. , Adang Eddy M.M. , Termeer Evelien , Severens Johan L. , Tjan-Heijnen Vivianne C.G. 
Published: January 2008

Purpose Current guidelines (ie, by the American Society of Clinical Oncology and the European Organisation for Research and Treatment of Cancer) do not recommend secondary infection prophylaxis, whereas, in contrast, caregivers prefer secondary prophylaxis to chemotherapy dose reduction after an episode of febrile neutropenia (FN). Because granulocyte colony-stimulating factor (G-CSF) is expensive, this study investigates the economic consequences of secondary prophylactic use of different prophylactic strategies (antibiotics, antibiotics plus G-CSF, and a combined sequential approach) in a population at risk of FN, using a Markov model. Methods The input for the model is mainly based on the clinical outcome and patient-based cost data set (adopting the health care payer's perspective for the Netherlands) derived from a randomized study on primary prophylaxis in small-cell lung cancer (SCLC) patients; establishing mean cost of an episode FN of €3,290 and prophylaxis of €79 (antibiotics) ± €1,616 (G-CSF) per cycle. The economic analysis was analyzed probabilistically using first- and second-order Monte Carlo simulation. The incremental cost-effectiveness ratio (ICER) was defined as cost per FN-free cycle. Results Secondary prophylaxis with antibiotics was the least expensive strategy (mean, €4,496/patient). The strategy antibiotics plus G-CSF was most expensive (mean, € 8,998/patient). Comparison of these two strategies resulted in an unacceptably high ICER (€343,110 per FN-free cycle) in the Dutch context. In scenarios using higher FN-related costs (as found in the United States), the strategies are less distinct in their monetary effects, but still favor antibiotics. Conclusion This model-based economic analysis demonstrates that in the Netherlands and most likely also in the United States, if secondary prophylaxis is preferred, the strategy with antibiotics is recommended.
Is There an Association Between Meningioma and Hormone Replacement Therapy?
Authors: Blitshteyn Svetlana , Crook Julia E. , Jaeckle Kurt A. 
Published: January 2008

Purpose Molecular and clinical observations suggest a role of sex steroid hormones in the occurrence of meningioma. However, there is limited and often conflicting data on the use of hormone replacement therapy (HRT) as a possible risk factor for meningioma. The goal of this study was to investigate whether there is an association between a diagnosis of meningioma and either current or past HRT use in women. Methods We retrospectively reviewed records in the Mayo Clinic Jacksonville electronic patient database between 1993 and 2003 to identify women with a diagnosis of either symptomatic or incidentally discovered, clinically silent meningioma. Records were also searched to identify women with a documented history of either current or past HRT use. Results Of the 355,318 women, ages 26 to 86, evaluated for any medical issue, 18,037 (5%) were documented as current or past HRT users. A total of 1,390 women with a history of symptomatic or incidentally discovered meningiomas were identified, 156 (11%) of whom were either current or past HRT users. A logistic regression analysis, adjusted for age, demonstrated a positive association between a diagnosis of meningioma and HRT use, with an odds ratio of 2.2 (95% CI, 1.9 to 2.6; P < .0001). The frequency of meningioma in women with either current or past HRT use was 865 in 100,000, whereas the frequency of meningioma in women without the history of HRT use was 366 in 100,000. Conclusion The study provides evidence of a positive association between HRT use and diagnosis of meningioma, and therefore, HRT use may be a risk factor for meningioma.
Professional Standards Review Organizations and Confidentiality: The Question of Public Access to Medical Peer Review Data Through the Freedom of Information Act
Authors: Hastings Douglas A. 
Published: January 2008

The degree of confidentiality to be accorded data gathered and analyzed by Professional Standards Review Organizations (PSROs) in the course of their medical peer review activities is a crucial and controversial issue in health policy. In late 1977, a consumer organization in Washington, D.C. sought access to data in the hands of the local PSRO through a lawsuit under the Freedom of Information Act, touching off a continuing debate throughout the country. That lawsuit is now on appeal.
The courts, the Congress, and the Department of Health and Human Services have all been involved in the ongoing controversy. PSROs, practicing physicians, and health care consumers all have an interest in the outcome. This article analyzes the PSRO program and its data confidentiality problems, examines in detail the lawsuit that sparked the controversy, and assesses the overall impact of this case on the PSRO program and on federal regulation of the health care system in general.