bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Authors: Navarange Mahendra , Game Laurence , Fowler Derek , Wadekar Vihar , Banks Helen , Cooley Nicola , Rahman Fatimah , Hinshelwood Justin , Broderick Peter , Causton Helen C 
Published: November 2005

Abstract
Background
The generation of large amounts of microarray data presents challenges for data collection, annotation, exchange and analysis. Although there are now widely accepted formats, minimum standards for data content and ontologies for microarray data, only a few groups are using them together to build and populate large-scale databases. Structured environments for data management are crucial for making full use of these data.

Description
The MiMiR database provides a comprehensive infrastructure for microarray data annotation, storage and exchange and is based on the MAGE format. MiMiR is MIAME-supportive, customised for use with data generated on the Affymetrix platform and includes a tool for data annotation using ontologies. Detailed information on the experiment, methods, reagents and signal intensity data can be captured in a systematic format. Reports screens permit the user to query the database, to view annotation on individual experiments and provide summary statistics. MiMiR has tools for automatic upload of the data from the microarray scanner and export to databases using MAGE-ML.

Conclusion
MiMiR facilitates microarray data management, annotation and exchange, in line with international guidelines. The database is valuable for underpinning research activities and promotes a systematic approach to data handling. Copies of MiMiR are freely available to academic groups under licence.
Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
Authors: Ye Ping , Peyser Brian D , Spencer Forrest A , Bader Joel S 
Published: November 2005

Abstract
Background
In a genetic interaction, the phenotype of a double mutant differs from the combined phenotypes of the underlying single mutants. When the single mutants have no growth defect, but the double mutant is lethal or exhibits slow growth, the interaction is termed synthetic lethality or synthetic fitness. These genetic interactions reveal gene redundancy and compensating pathways. Recently available large-scale data sets of genetic interactions and protein interactions in Saccharomyces cerevisiae provide a unique opportunity to elucidate the topological structure of biological pathways and how genes function in these pathways.

Results
We have defined congruent genes as pairs of genes with similar sets of genetic interaction partners and constructed a genetic congruence network by linking congruent genes. By comparing path lengths in three types of networks (genetic interaction, genetic congruence, and protein interaction), we discovered that high genetic congruence not only exhibits correlation with direct protein interaction linkage but also exhibits commensurate distance with the protein interaction network. However, consistent distances were not observed between genetic and protein interaction networks. We also demonstrated that congruence and protein networks are enriched with motifs that indicate network transitivity, while the genetic network has both transitive (triangle) and intransitive (square) types of motifs. These results suggest that robustness of yeast cells to gene deletions is due in part to two complementary pathways (square motif) or three complementary pathways, any two of which are required for viability (triangle motif).

Conclusion
Genetic congruence is superior to genetic interaction in prediction of protein interactions and function associations. Genetically interacting pairs usually belong to parallel compensatory pathways, which can generate transitive motifs (any two of three pathways needed) or intransitive motifs (either of two pathways needed).
The yeast kinome displays scale free topology with functional hub clusters
Authors: Lee Robin EC , Megeney Lynn A 
Published: November 2005

Abstract
Background
The availability of interaction databases provides an opportunity for researchers to utilize immense amounts of data exclusively in silico. Recently there has been an emphasis on studying the global properties of biological interactions using network analysis. While this type of analysis offers a wide variety of global insights it has surprisingly not been used to examine more localized interactions based on mechanism. In as such we have particular interest in the role of key topological components in signal transduction cascades as they are vital regulators of healthy and diseased cell states.

Results
We have used publicly available databases and a novel software tool termed Hubview to model the interactions of a subset of the yeast interactome, specifically protein kinases and their interaction partners. Analysis of the connectivity distribution has inferred a fat-tailed degree distribution with parameters consistent with those found in other biological networks. In addition, Hubview identified a functional clustering of a large group of kinases, distributed between three separate groupings. The complexity and average degree for each of these clusters is indicative of a specialized function (cell cycle propagation, DNA repair and pheromone response) and relative age for each cluster.

Conclusion
Using connectivity analysis on a functional subset of proteins we have evidence that reinforces the scale free topology as a model for protein network evolution. We have identified the hub components of the kinase network and observed a tendency for these kinases to cluster together on a functional basis. As such, these results suggest an inherent trend to preserve scale free characteristics at a domain based modular level within large evolvable networks.
Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains
Authors: Giuntini Elisa , Mengoni Alessio , De Filippo Carlotta , Cavalieri Duccio , Aubin-Horth Nadia , Landry Christian R , Becker Anke , Bazzicalupo Marco 
Published: November 2005

Abstract

Background

Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region.

Results
From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function.

Conclusion
The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.
Prevalence of physical and verbal aggressive behaviours and associated factors among older adults in long-term care facilities
Authors: Voyer Philippe , Verreault René , Azizah Ginette M , Desrosiers Johanne , Champoux Nathalie , Bédard Annick 
Published: November 2005

Abstract

Background
Verbal and physical aggressive behaviours are among the most disturbing and distressing behaviours displayed by older patients in long-term care facilities. Aggressive behaviour (AB) is often the reason for using physical or chemical restraints with nursing home residents and is a major concern for caregivers. AB is associated with increased health care costs due to staff turnover and absenteeism.

Methods
The goals of this secondary analysis of a cross-sectional study are to determine the prevalence of verbal and physical aggressive behaviours and to identify associated factors among older adults in long-term care facilities in the Quebec City area (n = 2 332).

Results
The same percentage of older adults displayed physical aggressive behaviour (21.2%) or verbal aggressive behaviour (21.5%), whereas 11.2% displayed both types of aggressive behaviour. Factors associated with aggressive behaviour (both verbal and physical) were male gender, neuroleptic drug use, mild and severe cognitive impairment, insomnia, psychological distress, and physical restraints. Factors associated with physical aggressive behaviour were older age, male gender, neuroleptic drug use, mild or severe cognitive impairment, insomnia and psychological distress. Finally, factors associated with verbal aggressive behaviour were benzodiazepine and neuroleptic drug use, functional dependency, mild or severe cognitive impairment and insomnia.

Conclusion
Cognitive impairment severity is the most significant predisposing factor for aggressive behaviour among older adults in long-term care facilities in the Quebec City area. Physical and chemical restraints were also significantly associated with AB. Based on these results, we suggest that caregivers should provide care to older adults with AB using approaches such as the progressively lowered stress threshold model and reactance theory which stress the importance of paying attention to the severity of cognitive impairment and avoiding the use of chemical or physical restraints.
Bright light treatment of depression for older adults [ISRCTN55452501]
Authors: Loving Richard T , Kripke Daniel F , Elliott Jeffrey A , Knickerbocker Nancy C , Grandner Michael A 
Published: November 2005

Abstract

Background
The incidence of insomnia and depression in the elder population is significant. It is hoped that use of light treatment for this group could provide safe, economic, and effective rapid recovery.

Methods
In this home-based trial we treated depressed elderly subjects with bright white (8,500 Lux) and dim red (<10 Lux) light for one hour a day at three different times (morning, mid-wake and evening). A placebo response washout was used for the first week. Wake treatment was conducted prior to the initiation of treatment, to explore antidepressant response and the interaction with light treatment. Urine and saliva samples were collected during a 24-hour period both before and after treatment and assayed for aMT6s and melatonin respectively to observe any change in circadian timing. Subjects wore a wrist monitor to record light exposure and wrist activity. Daily log sheets and weekly mood (GDS) and physical symptom (SAFTEE) scales were administered. Each subject was given a SCID interview and each completed a mood questionnaire (SIGH-SAD-SR) before and after treatment. Also, Hamilton Depression Rating (SIGH-SAD version) interviews were conducted by a researcher who was blind to the treatment condition. A control group of healthy, age-matched, volunteers was studied for one day to obtain baseline data for comparison of actigraphy and hormone levels.

Results
Eighty-one volunteers, between 60 and 79 years old, completed the study. Both treatment and placebo groups experienced mood improvement. Average GDS scores improved 5 points, the Hamilton Depression Rating Scale (HDRS) 17 scores (extracted from the self-rated SIGH-SAD-SR) improved 6 points. There were no significant treatment effects or time-by-treatment interactions. No significant adverse reactions were observed in either treatment group. The assays of urine and saliva showed no significant differences between the treatment and placebo groups. The healthy control group was active earlier and slept earlier but received less light than the depressed group at baseline.

Conclusion
Antidepressant response to bright light treatment in this age group was not statistically superior to placebo. Both treatment and placebo groups experienced a clinically significant overall improvement of 16%.
Prevalence of mental disorders and torture among Tibetan refugees: A systematic review
Authors: Mills Edward J , Singh Sonal , Holtz Timothy H , Chase Robert M , Dolma Sonam , Santa-Barbara Joanna , Orbinski James J 
Published: November 2005

Abstract

Background
Many Tibetan refugees flee Tibet in order to escape physical and mental hardships, and to access the freedoms to practice their culture and religion. We aimed to determine the prevalence of mental illnesses within the refugee population and determine the prevalence of previous torture reported within this population.

Methods
We performed a systematic literature search of 10 electronic databases from inception to May 2005. In addition, we searched the internet, contacted all authors of located studies, and contacted the Tibetan Government-in-exile, to locate unpublished studies. We included any study reporting on prevalence of mental illness within the Tibetan refugee populations. We determined study quality according to validation, translation, and interview administration. We calculated proportions with exact confidence intervals.

Results
Five studies that met our inclusion criteria (total n = 410). All studies were conducted in North India and 4 were specifically in adult populations. Four studies provided details on the prevalence of torture and previous imprisonment within the populations. The prevalence of post-traumatic stress disorder ranged from 11–23%, anxiety ranged from 25–77%, and major depression ranged from 11.5–57%.

Conclusion
Our review indicates that the prevalence of serious mental health disorders within this population is elevated. The reported incidence of torture and imprisonment is a possible contributor to the illnesses. Non-government organizations and international communities should be aware of the human rights abuses being levied upon this vulnerable population and the mental health outcomes that may be associated with it.
Role of cultivation media in the development of yeast strains for large scale industrial use
Authors: Hahn-Hägerdal Bärbel , Karhumaa Kaisa , Larsson Christer U , Gorwa-Grauslund Marie , Görgens Johann , van Zyl Willem H 
Published: November 2005

Abstract
The composition of cultivation media in relation to strain development for industrial application is reviewed. Heterologous protein production and pentose utilization by Saccharomyces cerevisiae are used to illustrate the influence of media composition at different stages of strain construction and strain development. The effects of complex, defined and industrial media are compared. Auxotrophic strains and strain stability are discussed. Media for heterologous protein production and for bulk bio-commodity production are summarized.
Cross-cultural validation and analysis of responsiveness of the QUALIOST®: QUAlity of Life questionnaire In OSTeoporosis
Authors: de la Loge Christine , Sullivan Kate , Pinkney Robert , Marquis Patrick , Roux Christian , Meunier Pierre Jean 
Published: November 2005

Abstract

Background
The QUALIOST® was designed for use with the SF-36 to measure established osteoporosis-specific quality of life (QoL). The reliability (internal consistency and test-retest) and validity of the questionnaire were established in a stand-alone psychometric validation study. The objective of this paper is to provide additional information on the instrument's responsiveness using clinical trial data, along with the reliability and validity of translated versions.

Methods
The Spinal Osteoporosis Therapeutic Intervention (SOTI) was an international clinical trial comparing strontium ranelate to placebo on the occurrence of new vertebral fracture in patients with postmenopausal osteoporosis. QoL was a secondary endpoint, assessed using the SF-36 and QUALIOST® at baseline and every six months, with the main analysis at 3-year follow-up. Questionnaire acceptability, analysis of the hypothesised structure, internal consistency reliability and responsiveness to clinical change over time were assessed at the 3-year follow up.

Results
1592 patients from 11 countries completed at least one QoL questionnaire. The psychometric properties of the questionnaires were assessed on cross-sectional (N = 1486) and longitudinal (N = 1288) data. Item discriminant validity of the QUALIOST® was excellent, as was item convergent validity, with 100% of item-scale correlations being above the 0.40 level. Internal consistency reliability was also extremely good, with high Cronbach's alpha scores above the 0.70 benchmark. Responsiveness results were consistent for all QUALIOST® scores, indicating that greater decreases in QoL corresponded to greater numbers of fractures experienced. QUALIOST® scores also differed according to the type of fracture suffered. This was demonstrated by increased effect sizes for more severe vertebral fractures (clinical vertebral and painful vertebral). In comparing responsiveness, the QUALIOST® scores were generally more consistent than those of the SF-36. Most notably, the QUALIOST® was more responsive with regard to painful vertebral fractures than the SF-36.

Conclusion
The QUALIOST® is a reliable and valid tool for measuring QoL in postmenopausal osteoporotic women. Being available in several validated language versions, it is ready to be used in a variety of settings, including international clinical trials.
The impact of compliance with 6-hour and 24-hour sepsis bundles on hospital mortality in patients with severe sepsis: a prospective observational study
Authors: Gao Fang , Melody Teresa , Daniels Darren F , Giles Simon , Fox Samantha 
Published: November 2005

Abstract
Introduction
Compliance with the ventilator care bundle affects the rate of ventilator-associated pneumonia. It was not known, however, whether compliance with sepsis care bundles has an impact on outcome. The aims of the present study were to determine the rate of compliance with 6-hour and 24-hour sepsis bundles and to determine the impact of the compliance on hospital mortality in patients with severe sepsis or septic shock.

Methods
We conducted a prospective observational study on 101 consecutive adult patients with severe sepsis or septic shock on medical or surgical wards, or in accident and emergency areas at two acute National Health Service Trust Teaching hospitals in England. The main outcome measures were: the rate of compliance with 6-hour and 24-hour sepsis care bundles adapted from the Surviving Sepsis Campaign guidelines on patients' clinical care; and the difference in hospital mortality between the compliant and the non-compliant groups.

Results
The median age of the patients was 69 years (interquartile range 51 to 78), and 53% were male. The sources of infection were sought and confirmed in 87 of 101 patients. The chest was the most common source (50%), followed by the abdomen (22%). The rate of compliance with the 6-hour sepsis bundle was 52%. Compared with the compliant group, the non-compliant group had a more than twofold increase in hospital mortality (49% versus 23%, relative risk (RR) 2.12 (95% confidence interval (CI) 1.20 to 3.76), P = 0.01) despite similar age and severity of sepsis. Compliance with the 24-hour sepsis bundle was achieved in only 30% of eligible candidates (21/69). Hospital mortality was increased in the non-compliant group from 29% to 50%, with a 76% increase in risk for death, although the difference did not reach statistical significance (RR 1.76 (95% CI 0.84 to 3.64), P = 0.16).

Conclusion
Non-compliance with the 6-hour sepsis bundle was associated with a more than twofold increase in hospital mortality. Non-compliance with the 24-hour sepsis bundle resulted in a 76% increase in risk for hospital death. All medical staff should practise these relatively simple, easy and cheap bundles within a strict timeframe to improve survival rates in patients with severe sepsis and septic shock.
Sedative clearance during extracorporeal membrane oxygenation
Authors: Bhatt-Mehta Varsha , Annich Gail 
Published: November 2005

The effects of polyvinyl chloride (PVC) tubing and membrane oxygenator (MO) on the concentrations of lorazepam and morphine in the neonatal extracorporeal membrane oxygenation (ECMO) circuit were evaluated using an in vitro model that included a closed ECMO circuit with a MO, heat exchanger, bladder and PVC tubing. The circuit was primed with blood, electrolytes, albumin and heparin and maintained at physiologic pH and temperature throughout by frequent measurement of blood gas pH and a temperature probe. Lorazepam and morphine were each studied separately in three separate, but identical circuits for 6 h on the day of circuit prime (new circuit) and then again for 6 h at 24 h (old circuit). Each circuit (new and old) was spiked once with lorazepam to a final concentration of 250 ng/mL or with morphine to a final concentration of 70 ng/mL in the circuit. Serial samples were drawn at baseline and every 30/60 min for 6 h at the site of injection and pre- and post-MO for each circuit. Lorazepam and morphine concentrations were analysed using gas chromatography with electron capture and gas chromatography with mass spectrometry, respectively. The concentrations of morphine and lorazepam at various sample sites and time points were expressed as a percentage of the original concentration. This single-dose study shows that up to 50% of a dose of lorazepam and 40% of a dose of morphine may be extracted by PVC and MO during bypass, depending on the age of the circuit. As the circuits become older, this amount could increase. These data may explain, in part, the higher doses of lorazepam and morphine required to sedate patients during ECMO.
PVC-plasticizer DEHP in medical products: do thin coatings really reduce DEHP leaching into blood?
Authors: Hildenbrand Sibylle L , Lehmann Hans-Dieter , Wodarz Roman , Ziemer Gerhard , Wendel Hans P 
Published: November 2005

The hemocompatibility of artificial surfaces in extracorporeal blood circulation systems can be improved by coatings. According to the literature, heparin coatings should avoid the leaching of the plasticizer di(2-ethylhexyl) phthalate (DEHP) into the blood from components made from plasticized polyvinyl chloride (PVC). DEHP and its metabolites are known to impair the fertility of male rodents; effects on human fertility are assumed. Three different surface coatings with and without heparin were examined in a Chandler Loop model at 37°C using fresh human blood to evaluate their hemocompatibility and barrier property to plasticizer. The levels of toxic oxidation products of DEHP generated in the blood, particularly, were found as high as in the uncoated tubing. The coatings improved the hemocompatibility, but are not safe protection against the hazardous metabolites of DEHP. For pregnant women, neonates and children, we would recommend using the available surface-coated plasticized PVC tubing sets, but free of DEHP.