bluuebunny/crossref_metadata_2025_split huggingface dataset:
TmaDB: a repository for tissue microarray data
Authors: Sharma-Oates Archana , Quirke Philip , Westhead David R 
Published: September 2005

Abstract
Background
Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations (at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data.

Description
To analyse TMA output a relational database (known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks (from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK).

Conclusion
TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray data.
Expression capable library for studies of Neisseria gonorrhoeae, version 1.0
Authors: Brettin Thomas , Altherr Michael R , Du Ying , Mason Roxie M , Friedrich Alexandra , Potter Laura , Langford Chris , Keller Thomas J , Jens Jason , Howie Heather , Weyand Nathan J , Clary Susan , Prichard Kimberly , Wachocki Susi , Sodergren Erica , Dillard Joseph P , Weinstock George , So Magdalene , Arvidson Cindy Grove 
Published: September 2005

Abstract

Background
The sexually transmitted disease, gonorrhea, is a serious health problem in developed as well as in developing countries, for which treatment continues to be a challenge. The recent completion of the genome sequence of the causative agent, Neisseria gonorrhoeae, opens up an entirely new set of approaches for studying this organism and the diseases it causes. Here, we describe the initial phases of the construction of an expression-capable clone set representing the protein-coding ORFs of the gonococcal genome using a recombination-based cloning system.

Results
The clone set thus far includes 1672 of the 2250 predicted ORFs of the N. gonorrhoeae genome, of which 1393 (83%) are sequence-validated. Included in this set are 48 of the 61 ORFs of the gonococcal genetic island of strain MS11, not present in the sequenced genome of strain FA1090. L-arabinose-inducible glutathione-S-transferase (GST)-fusions were constructed from random clones and each was shown to express a fusion protein of the predicted size following induction, demonstrating the use of the recombination cloning system. PCR amplicons of each ORF used in the cloning reactions were spotted onto glass slides to produce DNA microarrays representing 2035 genes of the gonococcal genome. Pilot experiments indicate that these arrays are suitable for the analysis of global gene expression in gonococci.

Conclusion
This archived set of Gateway® entry clones will facilitate high-throughput genomic and proteomic studies of gonococcal genes using a variety of expression and analysis systems. In addition, the DNA arrays produced will allow us to generate gene expression profiles of gonococci grown in a wide variety of conditions. Together, the resources produced in this work will facilitate experiments to dissect the molecular mechanisms of gonococcal pathogenesis on a global scale, and ultimately lead to the determination of the functions of unknown genes in the genome.
Evidence for proteolytic cleavage of brevican by the ADAMTSs in the dentate gyrus after excitotoxic lesion of the mouse entorhinal cortex
Authors: Mayer Joanne , Hamel Michelle G , Gottschall Paul E 
Published: August 2005

Abstract

Background
Brevican is a member of the lectican family of aggregating extracellular matrix (ECM) proteoglycans that bear chondroitin sulfate (CS) chains. It is highly expressed in the central nervous system (CNS) and is thought to stabilize synapses and inhibit neural plasticity and as such, neuritic or synaptic remodeling would be less likely to occur in regions with intact and abundant, lectican-containing, ECM complexes. Neural plasticity may occur more readily when these ECM complexes are broken down by endogenous proteases, the ADAMTSs (a
disintegrin and metalloproteinase with thrombospondin motifs), that selectively cleave the lecticans. The purpose of these experiments was to determine whether the production of brevican or the ADAMTS-cleaved fragments of brevican were altered after deafferentation and reinnervation of the dentate gyrus via entorhinal cortex lesion (ECL).

Results
In the C57Bl6J mouse, synaptic density in the molecular layer of the dentate gyrus, as measured by synaptophysin levels in ELISA, was significantly attenuated 2 days (nearly 50% of contralateral) and 7 days after lesion and returned to levels not different from the contralateral region at 30 days. Immunoreactive brevican in immunoblot was elevated 2 days after lesion, whereas there was a significant increase in the proteolytic product at 7, but not 30 days post-lesion. ADAMTS activity, estimated using the ratio of the specific ADAMTS-derived brevican fragment and intact brevican levels was increased at 7 days, but was not different from the contralateral side at 2 or 30 days after deafferentation.

Conclusion
These findings indicate that ADAMTS activity in the dentate outer molecular layer (OML) is elevated during the initial synaptic reinnervation period (7 days after lesion). Therefore, proteolytic processing of brevican appears to be a significant extracellular event in the remodeling of the dentate after EC lesion, and may modulate the process of sprouting and/or synaptogenesis.
Soy isoflavone glycitein protects against beta amyloid-induced toxicity and oxidative stress in transgenic Caenorhabditis elegans
Authors: Gutierrez-Zepeda Astrid , Santell Ross , Wu Zhixin , Brown Marishka , Wu YanJue , Khan Ikhlas , Link Christopher D , Zhao Baolu , Luo Yuan 
Published: August 2005

AbstractBackgroundEpidemiological studies have associated estrogen replacement therapy with a lower risk of developing Alzheimer's disease, but a higher risk of developing breast cancer and certain cardiovascular disorders. The neuroprotective effect of estrogen prompted us to determine potential therapeutic impact of soy-derived estrogenic compounds. TransgenicC. elegans, that express human beta amyloid (Aβ), were fed with soy derived isoflavones genistein, daidzein and glycitein (100 μg/ml) and then examined for Aβ-induced paralysis and the levels of reactive oxygen species.ResultsAmong the three compounds tested, only glycitein alleviated Aβ expression-induced paralysis in the transgenicC. elegans. This activity of glycitein correlated with a reduced level of hydrogen peroxide in the transgenicC. elegans.In vitroscavenging effects of glycitein on three types of reactive oxygen species confirmed its antioxidant properties. Furthermore, the transgenicC. elegansfed with glycitein exhibited reduced formation of β amyloid.ConclusionThese findings suggest that a specific soy isoflavone glycitein may suppress Aβ toxicity through combined antioxidative activity and inhibition of Aβ deposition, thus may have therapeutic potential for prevention of Aβ associated neurodegenerative disorders.
Signs and symptoms in children with a serious infection: a qualitative study
Authors: Van den Bruel Ann , Bruyninckx Rudi , Vermeire Etienne , Aerssens Peter , Aertgeerts Bert , Buntinx Frank 
Published: August 2005

Abstract
Background
Early diagnosis of serious infections in children is difficult in general practice, as incidence is low, patients present themselves at an early stage of the disease and diagnostic tools are limited to signs and symptoms from observation, clinical history and physical examination. Little is known which signs and symptoms are important in general practice. With this qualitative study, we aimed to identify possible new important diagnostic variables.

Methods
Semi-structured interviews with parents and physicians of children with a serious infection. We investigated all signs and symptoms that were related to or preceded the diagnosis. The analysis was done according to the grounded theory approach. Participants were recruited in general practice and at the hospital.

Results
18 children who were hospitalised because of a serious infection were included. On average, parents and paediatricians were interviewed 3 days after admittance of the child to hospital, general practitioners between 5 and 8 days after the initial contact.
The most prominent diagnostic signs in seriously ill children were changed behaviour, crying characteristics and the parents' opinion. Children either behaved drowsy or irritable and cried differently, either moaning or an inconsolable, loud crying. The parents found this illness different from previous illnesses, because of the seriousness or duration of the symptoms, or the occurrence of a critical incident. Classical signs, like high fever, petechiae or abnormalities at auscultation were helpful for the diagnosis when they were present, but not helpful when they were absent.

Conclusion
behavioural signs and symptoms were very prominent in children with a serious infection. They will be further assessed for diagnostic accuracy in a subsequent, quantitative diagnostic study.
Health status in older hospitalized patients with cancer or non-neoplastic chronic diseases
Authors: Corsonello Andrea , Pedone Claudio , Carosella Luciana , Corica Francesco , Mazzei Bruno , Antonelli Incalzi Raffaele ,   the Gruppo Italiano di Farmacovigilanza nell'Anziano (GIFA) investigators
Published: August 2005

Abstract
Background
Whether cancer is more disabling than other highly prevalent chronic diseases in the elderly is not well understood, and represents the objective of the present study.

Methods
We used data from the Gruppo Italiano di Farmacovigilanza nell'Anziano (GIFA) study, a large collaborative observational study based in community and university hospitals located throughout Italy. Our series consisted of three groups of patients with non-neoplastic chronic disease (congestive heart failure, CHF, N = 832; diabetes mellitus, N = 939; chronic obstructive pulmonary disease, COPD, N = 399), and three groups of patients with cancer (solid tumors without metastasis, N = 813; solid tumors with metastasis, N = 259; leukemia/lymphoma, N = 326). Functional capabilities were ascertained using the activities of daily living (ADL) scale, and categorical variables for dependency in at least 1 ADL or dependency in 3 or more ADLs were considered in the analysis. Cognitive status was evaluated by the 10-items Hodgkinson Abbreviated Mental Test (AMT).

Results
Cognitive impairment was more prevalent in patients with CHF (28.0%) or COPD (25.8%) than in those with cancer (solid tumors = 22.9%; leukemia/lymphoma = 19.6%; metastatic cancer = 22.8%). Dependency in at least 1 ADL was highly prevalent in patients with metastatic cancer (31.3% vs. 24% for patients with CHF and 22.4% for those with non-metastatic solid tumors, p < 0.001). In people aged 80 years or more, metastatic cancer was not associated with increased prevalence of physical disability. In multivariable analysis, metastatic cancer was associated with a greater prevalence of physical (OR 2.09, 95%CI 1.51–2.90) but not cognitive impairment (OR 1.34, 95%CI 0.94–1.91) with respect to CHF patients. Finally, diabetes was significantly associated with cognitive impairment (OR 1.40, 95%CI 1.11–1.78).

Conclusion
Cancer should not be considered as an ineluctable cause of severe cognitive and physical impairment, at least not more than other chronic conditions highly prevalent in older people, such as CHF and diabetes mellitus.
The relationship between risk factors for falling and the quality of life in older adults
Authors: Ozcan Ayse , Donat Hulya , Gelecek Nihal , Ozdirenc Mehtap , Karadibak Didem 
Published: August 2005

Abstract

Background
Falls are one of the major health problems that effect the quality of life among older adults. The aim of this study was to explore the relationship between quality of life (Short Form-12) and the risk factors of falls (balance, functional mobility, proprioception, muscle strength, flexibility and fear of falling) in older adults.

Methods
One hundred sixteen people aged 65 or older and living in the T.C. Emekli Sandigi Narlidere nursing home participated in the study. Balance (Berg Balance test), functional mobility (Timed Up and Go), proprioception (joint position sense), muscle strength (back/leg dynamometer), flexibility (sit and reach) and fear of falling (Visual Analogue Scale) were assessed as risk factors for falls. The quality of life was measured by Short Form-12 (SF-12).

Results
A strong positive correlation was observed between Physical Health Component Summary of SF-12, General Health Perception and balance, muscle strength. Proprioception and flexibility did not correlated with SF-12 (p > 0.05). There was negative correlation between Physical Health Component Summary of SF-12, General Health Perception and fear of falling, functional mobility (p < 0.05).

Conclusion
We concluded that the risk factors for falls (balance, functional mobility, muscle strength, fear of falling) in older adults are associated with quality of life while flexibility and proprioception are not.
The impact of partial smokefree legislation on health inequalities: Evidence from a survey of 1150 pubs in North West England
Authors: Tocque Karen , Edwards Richard , Fullard Brenda 
Published: September 2005

Abstract

Background
The UK government claims that between 10 and 30% of pubs and bars will be exempt from proposed legislation to achieve smokefree enclosed public places across England. This arises from the contentious inclusion that pubs and bars that do not prepare and serve food and private members clubs, will be able to allow smoking. We aimed to survey pubs and bars across the North West of England to assess smoking policies and the proportion and variations by deprivation level of venues preparing and serving food.

Methods
We carried out a telephone survey of 1150 pubs and bars in 14 local authorities across the North West of England. The main data items were current smoking policy, food preparation and serving status, and intention to change food serving and smoking status in the event of implementation of the proposed English partial smokefree legislation.

Results
29 pubs and bars (2.5%) were totally smoke-free, 500 (44%) had partial smoking restrictions, and 615 (54%) allowed smoking throughout. Venues situated in the most deprived quintiles (4 and 5) of deprivation were more likely to allow unrestricted smoking (62% vs 33% for venues in quintiles 1 and 2). The proportion of pubs and bars not preparing and serving food on the premises was 44% (95% CI 42 to 46%), and ranged from 21% in pubs and bars in deprivation quintile 1 to 63% in quintile 5.

Conclusion
The proportion of pubs and bars which do not serve food was far higher than the 10–30% suggested by the UK government. The proportion of pubs allowing unrestricted smoking and of non-food venues was higher in more disadvantaged areas, suggesting that the proposed UK government policy of exempting pubs in England which do not serve food from smokefree legislation will exacerbate inequalities in smoking and health.
Pride and confidence at work: potential predictors of occupational health in a hospital setting
Authors: Nilsson Kerstin , Hertting Anna , Petterson Inga-Lill , Theorell Töres 
Published: September 2005

AbstractBackgroundThis study focuses on determinants of a healthy work environment in two departments in a Swedish university hospital. The study is based on previously conducted longitudinal studies at the hospital (1994–2001), concerning working conditions and health outcomes among health care personnel in conjunction with downsizing processes. Overall, there was a general negative trend in relation to mental health, as well as long-term sick leave during the study period. The two departments chosen for the current study differed from the general hospital trend in that they showed stable health development. The aim of the study was to identify and analyse experiential determinants of healthy working conditions.MethodsThematic open-ended interviews were carried out with seventeen managers and key informants, representing different groups of co-workers in the two departments. The interviews were transcribed verbatim and an inductive content analysis was made.ResultsIn the two studied departments the respondents perceived that it was advantageous to belong to a small department, and to work in cooperation-oriented care. The management approaches described by both managers and co-workers could be interpreted as transformational, due to a strain of visionary, delegating, motivating, confirmative, supportive attitudes and a strongly expressed solution-oriented attitude. The daily work included integrated learning activities. The existing organisational conditions, approaches and attitudes promoted tendencies towards a work climate characterised by trust, team spirit and professionalism. In the description of the themes organisational conditions, approaches and climate, two core determinants, work-pride and confidence, for healthy working conditions were interpreted. Our core determinants augment the well-established concepts: manageability, comprehensiveness and meaningfulness. These favourable conditions seem to function as a buffer against the general negative effects of downsizing observed elsewhere in the hospital, and in the literature.ConclusionResearch illuminating health-promoting aspects is rather unusual. This study could be seen as explorative. The themes and core dimensions we found could be used as a basis for further intervention studies in similar health-care settings. The result could also be used in future health promotion studies in larger populations. One of the first steps in such a strategy is to formulate relevant questions, and we consider that this study contributes to this.
Influence of condensation temperature on selected exhaled breath parameters
Authors: Goldoni Matteo , Caglieri Andrea , Andreoli Roberta , Poli Diana , Manini Paola , Vettori Maria Vittoria , Corradi Massimo , Mutti Antonio 
Published: September 2005

Abstract

Background
The effects of changes in cooling temperature on biomarker levels in exhaled breath condensate have been little investigated. The aim of the study was to test the effect of condensation temperature on the parameters of exhaled breath condensate and the levels of selected biomarkers.

Methods
Exhaled breath condensate was collected from 24 healthy subjects at temperatures of -10, -5, 0 and +5 C degrees. Selected parameters (condensed volume and conductivity) and biomarkers (hydrogen peroxide, malondialdehyde) were measured.

Results
There was a progressive increase in hydrogen peroxide and malondialdehyde concentrations, and condensate conductivity as the cooling temperature increased; total condensate volume increased as the cooling temperature decreased.

Conclusion
The cooling temperature of exhaled breath condensate collection influenced selected biomarkers and potential normalizing factors (particularly conductivity) in different ways ex vivo. The temperature of exhaled breath condensate collection should be controlled and reported.
Quadriceps force generation in patients with osteoarthritis of the knee and asymptomatic participants during patellar tendon reflex reactions: an exploratory cross-sectional study
Authors: Dixon John , Howe Tracey E 
Published: September 2005

AbstractBackgroundIt has been postulated that muscle contraction is slower in patients with osteoarthritis of the knee than asymptomatic individuals, a factor that could theoretically impair joint protection mechanisms. This study investigated whether patients with osteoarthritis of the knee took longer than asymptomatic participants to generate force during reflex quadriceps muscle contraction. This was an exploratory study to inform sample size for future studies.MethodsAn exploratory observational cross sectional study was carried out. Two subject groups were tested, asymptomatic participants (n = 17), mean (SD) 56.7 (8.6) years, and patients with osteoarthritis of the knee, diagnosed by an orthopaedic surgeon, (n = 16), age 65.9 (7.8) years. Patellar tendon reflex responses were elicited from participants and measured with a load cell. Force latency, contraction time, and force of the reflex response were determined from digitally stored data. The Mann-Whitney U test was used for the between group comparisons in these variables. Bland and Altman within-subject standard deviation values were calculated to evaluate the measurement error or precision of force latency and contraction time.ResultsNo significant differences were found between the groups for force latency (p = 0.47), contraction time (p = 0.91), or force (p = 0.72). The two standard deviation measurement error values for force latency were 27.9 ms for asymptomatic participants and 16.4 ms for OA knee patients. For contraction time, these values were 29.3 ms for asymptomatic participants and 28.1 ms for OA knee patients. Post hoc calculations revealed that the study was adequately powered (80%) to detect a difference between the groups of 30 ms in force latency. However it was inadequately powered (59%) to detect this same difference in contraction time, and 28 participants would be required in each group to reach 80% power.ConclusionPatients with osteoarthritis of the knee do not appear to have compromised temporal parameters or magnitude of force generation during patellar tendon reflex reactions when compared to a group of asymptomatic participants. However, these results suggest that larger studies are carried out to investigate this area further.