bluuebunny/crossref_metadata_2025_split huggingface dataset:
FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform
Authors: Gouret Philippe , Vitiello Vérane , Balandraud Nathalie , Gilles André , Pontarotti Pierre , Danchin Etienne GJ 
Published: August 2005

Abstract
Background
Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps.

Results
Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data.

Conclusion
The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.
Folate system correlations in DNA microarray data
Authors: Radivoyevitch Tomas 
Published: August 2005

Abstract
Background
Gene expression data is abundantly available from the Gene Expression Omnibus (GEO) and various websites. Pathway specific analyses of gene-gene correlations across these datasets remain relatively unexplored, though they could be informative.

Methods
Folate gene expression data is explored here in two ways: (1) directly, using gene-gene scatter plots and gene expression time course plots; and (2) indirectly, using de novo purine synthesis (DNPS) and de novo thymidylate synthesis (DNTS) flux predictions of a folate model perturbed by relative gene expression modulations of its Vmax parameters.

Results
Positive correlations within and between the DNPS and DNTS folate cycles are observed in the folate gene expression data. For steady state measurements across childhood leukemia patients, positive correlations between DNPS and DNTS are consistent with higher proliferative fractions requiring higher levels of both fluxes. For cells exposed to ionizing radiation, transient increases in both pathways are consistent with DNA damage driven dNTP demand, and a steadily decreasing backdrop is consistent with radiation induced cell cycle arrest. By and large, folate model based flux predictions paralleled these findings, the main differences being a gain of correlation information for the TEL-AML1 leukemia data, and the loss of one interesting inference, namely, that RNA repair driven DNPS precedes DNA repair driven DNTS after a 10 gray dose of ionizing radiation.

Conclusion
Pathway focused correlation analyses of DNA microarray data can be informative, with or without a mathematical model. Conceptual models are essential. Mathematical model based analyses should supplement, but should not replace, direct data analyses.
Novel curcumin- and emodin-related compounds identified by in silico 2D/3D conformer screening induce apoptosis in tumor cells
Authors: Füllbeck Melanie , Huang Xiaohua , Dumdey Renate , Frommel Cornelius , Dubiel Wolfgang , Preissner Robert 
Published: August 2005

Abstract

Background
Inhibition of the COP9 signalosome (CSN) associated kinases CK2 and PKD by curcumin causes stabilization of the tumor suppressor p53. It has been shown that curcumin induces tumor cell death and apoptosis. Curcumin and emodin block the CSN-directed c-Jun signaling pathway, which results in diminished c-Jun steady state levels in HeLa cells. The aim of this work was to search for new CSN kinase inhibitors analogue to curcumin and emodin by means of an in silico screening method.

Methods
Here we present a novel method to identify efficient inhibitors of CSN-associated kinases. Using curcumin and emodin as lead structures an in silico screening with our in-house database containing more than 106 structures was carried out. Thirty-five compounds were identified and further evaluated by the Lipinski's rule-of-five. Two groups of compounds can be clearly discriminated according to their structures: the curcumin-group and the emodin-group. The compounds were evaluated in in vitro kinase assays and in cell culture experiments.

Results
The data revealed 3 compounds of the curcumin-group (e.g. piceatannol) and 4 of the emodin-group (e.g. anthrachinone) as potent inhibitors of CSN-associated kinases. Identified agents increased p53 levels and induced apoptosis in tumor cells as determined by annexin V-FITC binding, DNA fragmentation and caspase activity assays.

Conclusion
Our data demonstrate that the new in silico screening method is highly efficient for identifying potential anti-tumor drugs.
Stoichiometric estimates of the biochemical conversion efficiencies in tsetse metabolism
Authors: Custer Adrian V 
Published: August 2005

AbstractBackgroundThe time varying flows of biomass and energy in tsetse (Glossina) can be examined through the construction of a dynamic mass-energy budget specific to these flies but such a budget depends on efficiencies of metabolic conversion which are unknown. These efficiencies of conversion determine the overall yields when food or storage tissue is converted into body tissue or into metabolic energy. A biochemical approach to the estimation of these efficiencies uses stoichiometry and a simplified description of tsetse metabolism to derive estimates of the yields, for a given amount of each substrate, of conversion product, by-products, and exchanged gases. This biochemical approach improves on estimates obtained through calorimetry because the stoichiometric calculations explicitly include the inefficiencies and costs of the reactions of conversion. However, the biochemical approach still overestimates the actual conversion efficiency because the approach ignores all the biological inefficiencies and costs such as the inefficiencies of leaky membranes and the costs of molecular transport, enzyme production, and cell growth.ResultsThis paper presents estimates of the net amounts of ATP, fat, or protein obtained by tsetse from a starting milligram of blood, and provides estimates of the net amounts of ATP formed from the catabolism of a milligram of fat along two separate pathways, one used for resting metabolism and one for flight. These estimates are derived from stoichiometric calculations constructed based on a detailed quantification of the composition of food and body tissue and on a description of the major metabolic pathways in tsetse simplified to single reaction sequences between substrates and products. The estimates include the expected amounts of uric acid formed, oxygen required, and carbon dioxide released during each conversion. The calculated estimates of uric acid egestion and of oxygen use compare favorably to published experimental measurements.ConclusionThis biochemical analysis provides reasonable first estimates of the conversion efficiencies for the major pathways used by tsetse metabolism. These results now enable a deeper analysis of tsetse ecology based on the construction of a dynamic mass-energy budget for tsetse and their populations.
Evaluation of the functional efficacy of an antioxidative probiotic in healthy volunteers
Authors: Songisepp Epp , Kals Jaak , Kullisaar Tiiu , Mändar Reet , Hütt Pirje , Zilmer Mihkel , Mikelsaar Marika 
Published: August 2005

Abstract

Background
In persons without clinical symptom it is difficult to assess an impact of probiotics regarding its effect on health. We evaluated the functional efficacy of the probiotic Lactobacillus fermentum ME-3 in healthy volunteers by measuring the influence of two different formulations on intestinal lactoflora, fecal recovery of the probiotic strain and oxidative stress markers of blood and urine after 3 weeks consumption.

Methods
Two 3-week healthy volunteer trials were performed. Open placebo controlled (OPC) study participants (n = 21) consumed either goat milk or by L. fermentum ME-3 fermented goat milk (daily dose 11.8 log CFU (Colony Forming Units). Double blind randomised placebo controlled (DBRP) study participants (n = 24) received either capsules with L. fermentum ME-3 (daily of dose 9.2 CFU) or placebo capsules.
The faecal lactoflora composition, faecal ME-3 recovery, effect of the consumption on intestinal lactoflora, and oxidative stress markers of blood (total antioxidative activity; total antioxidative status and glutathione red-ox ratio) was measured.

Results
ME-3 was well tolerated and a significant increase in total faecal lactobacilli yet no predominance of ME-3 was detected in all study groups. Faecal recovery of ME-3 was documented by molecular methods only in fermented milk group, however the significant improvement of blood TAA (Total Antioxidative Activity) and TAS (Total Antioxidative Status) indices was seen both in case of fermented goat milk and capsules", yet glutathione re-ox ratio values decreased only in case of fermented by ME-3 goat milk.

Conclusion
The functional efficacy of both consumed formulations of an antioxidative probiotic L. fermentum ME-3 is proved by the increase of the intestinal lactobacilli counts providing putative defence against enteric infections and by reduction of the oxidative stress indices of blood and urine of healthy volunteers. In non-diseased host the probiotic health claims can be assessed by improvement of some measurable laboratory indices of well-established physiological functions of host, e.g. markers of antioxidative defence system.
Cocaine in surface waters: a new evidence-based tool to monitor community drug abuse
Authors: Zuccato Ettore , Chiabrando Chiara , Castiglioni Sara , Calamari Davide , Bagnati Renzo , Schiarea Silvia , Fanelli Roberto 
Published: August 2005

Abstract

Background
Cocaine use seems to be increasing in some urban areas worldwide, but it is not straightforward to determine the real extent of this phenomenon. Trends in drug abuse are currently estimated indirectly, mainly by large-scale social, medical, and crime statistics that may be biased or too generic. We thus tested a more direct approach based on 'field' evidence of cocaine use by the general population.

Methods
Cocaine and its main urinary metabolite (benzoylecgonine, BE) were measured by mass spectrometry in water samples collected from the River Po and urban waste water treatment plants of medium-size Italian cities. Drug concentration, water flow rate, and population at each site were used to estimate local cocaine consumption.

Results
We showed that cocaine and BE are present, and measurable, in surface waters of populated areas. The largest Italian river, the Po, with a five-million people catchment basin, steadily carried the equivalent of about 4 kg cocaine per day. This would imply an average daily use of at least 27 ± 5 doses (100 mg each) for every 1000 young adults, an estimate that greatly exceeds official national figures. Data from waste water treatment plants serving medium-size Italian cities were consistent with this figure.

Conclusion
This paper shows for the first time that an illicit drug, cocaine, is present in the aquatic environment, namely untreated urban waste water and a major river. We used environmental cocaine levels for estimating collective consumption of the drug, an approach with the unique potential ability to monitor local drug abuse trends in real time, while preserving the anonymity of individuals. The method tested here – in principle extendable to other drugs of abuse – might be further refined to become a standardized, objective tool for monitoring drug abuse.
Psychosocial and socioeconomic burden of vasomotor symptoms in menopause: A comprehensive review
Authors: Utian Wulf H 
Published: August 2005

Abstract
Many women experience vasomotor symptoms at or around the time of menopause. Hot flushes and night sweats are considered primary menopausal symptoms that may also be associated with sleep and mood disturbances, as well as decreased cognitive function. All of these symptoms may lead to social impairment and work-related difficulties that significantly decrease overall quality of life. Hot flushes have shown a great deal of variability in their frequency and severity in women. In some women, hot flushes persist for several months; in others, they may last for more than 10 years. Traditionally vasomotor symptoms were reported to begin 5 to 10 years prior to the cessation of the final menstrual cycle, corresponding with the initial decline in circulating gonadal hormones; however, night sweats in particular most often begin in perimenopause. The pathogenesis of hot flushes has not yet been fully elucidated, but the circuitry involving estrogen and neurotransmitters, norepinephrine and serotonin specifically, are hypothesized to play a major role in the altered homeostatic thermoregulatory mechanisms underlying these events.
Menopause-associated vasomotor symptoms are associated with significant direct and indirect costs. Overall costs of traditional pharmacotherapy or complementary and alternative medicine modalities, including over-the-counter treatments and dietary supplements, for managing menopause-related vasomotor symptoms are substantial and include initial and follow-up physician visits and telephone calls. Additional costs include laboratory testing, management of adverse events, loss of productivity at work, and personal and miscellaneous costs. Pharmacoeconomic analyses, including those that consider risks identified by the Women's Health Initiative, generally support the cost-effectiveness of hormonal therapy for menopause-associated vasomotor symptoms, which have been the mainstay for the management of these symptoms for more than 50 years. However, because many women now want to avoid hormone therapy, there is a need for additional targeted therapies, validated by results from controlled clinical trials that are safe, efficacious, cost-effective, and well tolerated by symptomatic menopausal women.
HBx M130K and V131I (T-A) mutations in HBV genotype F during a follow-up study in chronic carriers
Authors: León Bernal , Taylor Lizeth , Vargas Minor , Luftig Ronald B , Albertazzi Federico , Herrero Libia , Visona Kirsten 
Published: August 2005

Abstract

Background
Around 400 million people worldwide are chronically infected with Hepatitis B virus (HBV). An estimated 10% of these chronic patients develop progressive liver damage including cirrhosis and Hepatocellular Carcinoma (HCC). The HBx gene encodes a protein of 154 amino acids which is a transactivator and has been associated with HBV pathogenesis. A change in the amino acid sequences at positions 130 and 131 in the HBV-X protein (M130K and V131I) produced by T-A point mutations at the nucleic acids level has been associated with severe liver damage and HCC in patients from China and Africa. Further, such changes have been proposed as a prognostic marker for progressive liver damage and HCC. The purpose of this study was to determine if T-A mutations are present in HBV chronic carriers with genotype F (the major genotype in Costa Rica) and further, if these mutations are associated with HBV disease progression in Costa Rica HBV patients from 1972 to 1985.

Results
Serum samples from 50 HBV positive individuals were amplified and directly sequenced, 48 belonged to genotype F, 1 from genotype D and another was classified as D or E.
T-;A mutations were absent in 17 acute patients who recovered, but was present in 12 of 29 chronic carrier samples (42.8%), in one sample the T-A mutations were detected as early as 29 days after clinical onset of disease. In 17 carriers with available liver biopsies, T-;A mutations were found in 8 sera of 13 (61.5%) classified as moderate or severe, and none in 4 biopsies with mild liver damage. However, it was not possible to demonstrate a statistical association between the presence of T-A mutations and moderate/severe liver damage, using a Fischer exact test, 1 tail, p = 0.05.
In 4 patients HCC was diagnosed, and 2 of them presented the T-A mutations in their sera.

Conclusion
T-A mutations were found in HBV genotype F in chronic carriers but not in patients who recovered from acute infection. These mutations could be developing early during infection although the possibility of infection with the mutant virus could not be excluded.
More studies are necessary to establish if the T-A mutation can be used as a prognostic marker for severity of liver disease in patients infected with HBV.
Effect of stroke location on the laryngeal cough reflex and pneumonia risk
Authors: Addington W Robert , Stephens Robert E , Widdicombe John G , Rekab Kamel 
Published: August 2005

AbstractBackgroundThe purpose of this study was to evaluate the risk of developing pneumonia in acute stroke patients comparing the early anatomical stroke location and laryngeal cough reflex (LCR) testing.MethodsA prospective study of 818 consecutive acute stroke patients utilizing a reflex cough test (RCT), which assesses the neurological status of the LCR compared to magnetic resonance imaging or computerized tomography for stroke location and subsequent pneumonia outcome. Stroke diagnosis and stroke location were made by a neurologist and clinical radiologist, respectively; both were blinded to the RCT results.ResultsBrainstem (p-value < .007) and cerebral strokes (p-value < .005) correlated with the RCT results and pneumonia outcome. Of the 818 patients, 35 (4.3%) developed pneumonia. Of the 736 (90%) patients who had a normal RCT, 26 (3.5%) developed pneumonia, and of the 82 (10%) patients with an abnormal RCT, 9 (11%) developed pneumonia despite preventive interventions (p-value < .005). The RCT had no serious adverse events.ConclusionThe RCT acted as a reflex hammer or percussor of the LCR and neurological airway protection and indicated pneumonia risk. Despite stroke location, patients may exhibit "brainstem shock," a global neurological condition involving a transient or permanent impairment of respiratory drive, reticular activating system or LCR. Recovery of these functions may indicate emergence from brainstem shock, and help predict morbidity and mortality outcome.
Organic compatible solutes of halotolerant and halophilic microorganisms
Authors: Roberts Mary F 
Published: August 2005

Abstract
Microorganisms that adapt to moderate and high salt environments use a variety of solutes, organic and inorganic, to counter external osmotic pressure. The organic solutes can be zwitterionic, noncharged, or anionic (along with an inorganic cation such as K+). The range of solutes, their diverse biosynthetic pathways, and physical properties of the solutes that effect molecular stability are reviewed.
HIV-1 gp120-induced TNF-α production by primary human macrophages is mediated by phosphatidylinositol-3 (PI-3) kinase and mitogen-activated protein (MAP) kinase pathways
Authors: Lee Chuhee , Tomkowicz Brian , Freedman Bruce D , Collman Ronald G 
Published: August 2005

AbstractHuman immunodeficiency virus type 1 (HIV-1) infection is initiated by binding of the viral envelope glycoprotein gp120 to CD4 followed by a chemokine receptor, but these interactions may also take place independently from infection. gp120 stimulation of primary human macrophages is known to trigger production of cytokines implicated in pathogenesis, particularly tumor necrosis factor α (TNF-α), but the mechanisms have not been determined. We sought to define the pathways responsible for TNF-α secretion by monocyte-derived macrophages (MDM) following HIV-1 gp120 stimulation. MDM exposure to recombinant macrophage-tropic (R5) gp120 led to dose- and donor-dependent release of TNF-α, which was cyclohexamide-sensitive and associated with up-regulated message. Pretreatment with specific inhibitors of the mitogen-activated protein kinases (MAPK) extracellular signal-regulated kinase 1/2 (ERK-1/2; PD98059, U0126) and p38 (SB202190, PD169316) inhibited the secretion of TNF-α. gp120-elicited TNF-α production was also blocked by phosphatidylinositol-3 kinase (PI-3K) inhibitors (wortmannin, LY294002). Moreover, PI-3K inhibition ablated gp120-induced phosphorylation of p38 and ERK-1/2. The response was inhibited by a CC chemokine receptor 5 (CCR5)-specific antagonist, indicating that CCR5 was in large part responsible. These results indicate that gp120-elicited TNF-α production by macrophages involves chemokine receptor-mediated PI-3K and MAPK activation, that PI-3K is an upstream regulator of MAPK in this pathway, and that p38 and ERK-1/2 independently regulate TNF-α production. These gp120-triggered signaling pathways may be responsible for inappropriate production of proinflammatory cytokines by macrophages, which are believed to play a role in immunopathogenesis and in neurological sequelae of AIDS.
The effects of CpG DNA on HMGB1 release by murine macrophage cell lines
Authors: Jiang Weiwen , Li Jianhua , Gallowitsch-Puerta Margot , Tracey Kevin J , Pisetsky David S 
Published: August 2005

AbstractDNA containing cytosine-guanine dinucleotide (CpG) motifs (CpG DNA) has potent immunostimulatory activities that resemble those of lipopolysaccharide (LPS) in its effects on the innate immune system. Among its activities, LPS can induce the release of high mobility group protein (HMGB1) by macrophages, a dual function molecule that can mediate the late effects of LPS. To determine whether CpG DNA can also induce HMGB1 release, the effects of a synthetic CpG oligonucleotide (ODN) on HMGB1 release from RAW 264.7 and J774A.1 cells were assessed by Western blotting of culture supernatants. Under conditions in which the CpG ODN activated the cell lines, as assessed by stimulation of tumor necrosis factor α and interleukin-12, it failed to cause HMGB1 release into the media. Although unable to induce HMGB1 release by itself, the CpG ODN nevertheless potentiated the action of LPS. With RAW 264.7 cells, lipoteichoic acid and polyinosinic-polycytidylic acid, like LPS, stimulated HMGB1 release as well as cytokine production. These results indicate that the effects of CpG DNA on macrophages differ from other ligands of Toll-like receptors and may lead to a distinct pattern of immune cell activation in the context of infection or its use as an immunomodulatory agent.