bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insufficient quality of sputum submitted for tuberculosis diagnosis and associated factors, in Klaten district, Indonesia
Authors: Sakundarno Mateus , Nurjazuli Nurjazuli , Jati Sutopo Patria , Sariningdyah Retna , Purwadi Sumarsono , Alisjahbana Bachti , van der Werf Marieke J 
Published: May 2009

Abstract

Background
Sputum smear microscopy is the standard diagnostic method for detection of smear positive pulmonary tuberculosis (TB). Insufficient quality of sputum might result in missing cases. In this study we aimed at assessing the quality of sputum in a district in Central Java and determining patient and health worker factors associated with submission of three good quality sputum samples.

Methods
In 16 health centers information was collected on the quality of sputum submitted by TB suspects, i.e. volume, color, and viscosity. TB suspects were interviewed to assess their knowledge of TB, motivation to provide sputum and whether they were informed why and how to produce a sputum sample. Health workers were interviewed to assess what information they provided to TB suspects about the reason for sputum examination, methods to produce sputum and characteristics of a good quality sputum sample. All health worker and patient factors were evaluated for association with sputum quality.

Results
Of 387 TB suspects, 294 (76.0%) could be traced and interviewed, and of 272 (70.3%) information about sputum quality was available. Of those 203 (74.6%) submitted three samples, 90 (33.1%) provided at least one good sample, and 37 (13.6%) provided three good quality sputum samples. Of the 272 TB suspects, 168 (61.8%) mentioned that information on the reason for sputum examination was provided, 66 (24.3%) remembered that they were informed about how to produce sputum and 40 (14.7%) recalled being informed about the characteristics of good quality sputum. Paramedics reported to provide often/always information on the importance of sputum examination, and when to produce sputum. Information on how to produce sputum and characteristics of a good sputum sample was less often provided. None of the studied patient characteristics or health worker factors was associated with providing good quality sputum.

Conclusion
A considerable number of TB suspects did not provide three sputum samples and a large number of sputum samples were of insufficient quality. Training of health workers in providing health education to the TB suspect about the reason for sputum examination and how to produce a good quality sputum sample should be a priority of the TB program.
Maternal and perinatal guideline development in hospitals in South East Asia: results from the SEA-ORCHID project
Authors: Thinkhamrop Jadsada , Turner Tari , Subramaniam Sivasangari ,   The SEA-ORCHID Study Group
Published: May 2009

Abstract

Background
Recognising the potential of clinical practice guidelines (CPGs) to improve practice, one of the strategies of the SEA-ORCHID project was to facilitate the development of evidence-based CPGs, and to support clinical staff in each of the four countries to build their skills in development of CPGs in the nine participating hospitals in Thailand, Malaysia, Philippines and Indonesia. This study was undertaken to investigate the impact of the SEA-ORCHID project on development of evidence-based CPGs.

Methods
Data on the CPGs available to support maternal and perinatal healthcare were collected by SEA-ORCHID team members at each hospital before and after the intervention period of the project.

Results
There were only a few evidence-based CPGs available in the SEA-ORCHID hospitals before the intervention period. After the intervention period, in the SEA-ORCHID hospitals in Malaysia and Indonesia there was no change in evidence-based CPG development activity in maternal and perinatal care. In Thailand and The Philippines there was a small increase in evidence-based CPG development activity in maternal and perinatal care.

Conclusion
Despite the wide range of interventions to support evidence-based CPG development implemented in the hospitals participating in the SEA-ORCHID, very little change was seen in the development of evidence-based CPGs.
The receptor RAGE: Bridging inflammation and cancer
Authors: Riehl Astrid , Németh Julia , Angel Peter , Hess Jochen 
Published: May 2009

AbstractThe receptor for advanced glycation end products (RAGE) is a single transmembrane receptor of the immunoglobulin superfamily that is mainly expressed on immune cells, neurons, activated endothelial and vascular smooth muscle cells, bone forming cells, and a variety of cancer cells. RAGE is a multifunctional receptor that binds a broad repertoire of ligands and mediates responses to cell damage and stress conditions. It activates programs responsible for acute and chronic inflammation, and is implicated in a number of pathological diseases, including diabetic complications, stroke, atheriosclerosis, arthritis, and neurodegenerative disorders. The availability ofRageknockout mice has not only advanced our knowledge on signalling pathways within these pathophysiological conditions, but also on the functional importance of the receptor in processes of cancer. Here, we will summarize molecular mechanisms through which RAGE signalling contributes to the establishment of a pro-tumourigenic microenvironment. Moreover, we will review recent findings that provide genetic evidence for an important role of RAGE in bridging inflammation and cancer.
Phylogenetic analysis of three genes of Penguinpox virus corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L reveals that it is most closely related to Turkeypox virus, Ostrichpox virus and Pigeonpox virus
Authors: Carulei Olivia , Douglass Nicola , Williamson Anna-Lise 
Published: May 2009

AbstractPhylogenetic analysis of three genes of Penguinpox virus, a novel Avipoxvirus isolated from African penguins, reveals its relationship to other poxviruses. The genes corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L were sequenced and phylogenetic trees (Neighbour-Joining and UPGMA) constructed from MUSCLE nucleotide and amino acid alignments of the equivalent sequences from several different poxviruses. Based on this analysis, PEPV was confirmed to belong to the genus Avipoxvirus, specifically, clade A, subclade A2 and to be most closely related to Turkeypox virus (TKPV), Ostrichpox virus (OSPV)and Pigeonpox virus (PGPV).
Dietary fatty acid intake affects the risk of developing bone marrow lesions in healthy middle-aged adults without clinical knee osteoarthritis: a prospective cohort study
Authors: Wang Yuanyuan , Davies-Tuck Miranda L , Wluka Anita E , Forbes Andrew , English Dallas R , Giles Graham G , O'Sullivan Richard , Cicuttini Flavia M 
Published: May 2009

Abstract
Introduction
Fatty acids have been implicated in osteoarthritis (OA), yet the mechanism by which fatty acids affect knee structure and consequently the risk of knee OA has not been fully elucidated. Higher intakes of fatty acids have been shown to be associated with the risk of bone marrow lesions (BMLs) in a healthy population. The aim of this study was to examine the association between fatty acid consumption and the incidence of BMLs in healthy middle-aged adults without clinical knee OA.

Methods
Two hundred ninety-seven middle-aged adults without clinical knee OA underwent magnetic resonance imaging (MRI) of their dominant knee at baseline. BMLs were assessed. Of the 251 participants with no BMLs in their knee at baseline, 230 underwent MRI of the same knee approximately 2 years later. Intakes of fatty acids were estimated from a food frequency questionnaire.

Results
Increased consumption of saturated fatty acids was associated with an increased incidence of BMLs over 2 years after adjusting for energy intake, age, gender, and body mass index (odds ratio of 2.56 for each standard deviation increase in dietary intake, 95% confidence interval 1.03 to 6.37, P = 0.04). Intake of monounsaturated or polyunsaturated fatty acids was not significantly associated with the incidence of BMLs.

Conclusions
Increased fatty acid consumption may increase the risk of developing BMLs. As subchondral bone is important in maintaining joint integrity and the development of OA, this study suggests that dietary modification of fatty acid intake may be one strategy in the prevention of knee OA which warrants further investigation.
Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression
Authors: Williams Cecilia , Helguero Luisa , Edvardsson Karin , Haldosén Lars-Arne , Gustafsson Jan-Åke 
Published: May 2009

Abstract
Introduction
Mammary stem cells are bipotential and suggested to be the origin of breast cancer development, but are elusive and vaguely characterized. Breast tumors can be divided into subgroups, each one requiring specific treatment. To determine a possible association between mammary stem cells and breast cancer, a detailed characterization of the transcriptome in mammary stem cells is essential.

Methods
We have used a murine mammary epithelial stem-like cell line (HC11) and made a thorough investigation of global gene-expression changes during stepwise differentiation using dual-color comparative microarray technique. Subsequently, we have performed a cross-species comparison to reveal conserved gene expression between stem cells and subtype-specific and prognosis gene signatures, and correlated gene expression to in vivo mammary gland development.

Results
Our analysis of mammary stem-like and stepwise cell differentiation, and an in-depth description of our findings in a breast cancer perspective provide a unique map of the transcriptomic changes and a number of novel mammary stem cell markers. We correlate the alterations to in vivo mammary gland differentiation, and describe novel changes in nuclear receptor gene expression. Interestingly, our comparisons show that specific subtypes of breast cancers with poor prognosis and metastasizing capabilities show resemblance to stem-like gene expression.

Conclusions
The transcriptional characterization of these mammary stem-like cells and their differentiation-induced gene expression patterns is here made widely accessible and provides a basis for research on mammary stem-like cells. Our comparisons suggest that some tumors are more stem-like than others, with a corresponding worse prognosis. This information would, if established, be important for treatment decisions. We also suggest several marker candidates valuable to investigate further.
p54nrb Is a Transcriptional Corepressor of the Progesterone Receptor that Modulates Transcription of the Labor-Associated Gene, Connexin 43 (Gja1)
Authors: Dong Xuesen , Yu Celeste , Shynlova Oksana , Challis John R. G. , Rennie Paul S. , Lye Stephen J. 
Published: May 2009

Abstract
The progesterone receptor (PR) plays important roles in the establishment and maintenance of pregnancy. By dynamic interactions with coregulators, PR represses the expression of genes that increase the contractile activity of myometrium and contribute to the initiation of labor. We have previously shown that PTB-associated RNA splicing factor (PSF) can function as a PR corepressor. In this report, we demonstrated that the PSF heterodimer partner, p54nrb (non-POU-domain-containing, octamer binding protein), can also function as a transcription corepressor, independent of PSF. p54nrb Interacts directly with PR independent of progesterone. In contrast to PSF, p54nrb neither enhances PR protein degradation nor blocks PR binding to DNA. Rather, p54nrb recruits mSin3A through its N terminus to the PR-DNA complex, resulting in an inhibition of PR-mediated transactivation of the progesterone-response element-luciferase reporter gene. PR also repressed transcription of the connexin 43 gene (Gja1), an effect dependent on the presence of an activator protein 1 site within the proximal Gja1 promoter. Mutation of this site abolished PR-mediated repression and decreased the recruitment of PR and p54nrb onto the Gja1 promoter. Furthermore, knockdown p54nrb expression by small interfering RNA alleviated PR-mediated repression on Gja1 transcription, whereas overexpression of p54nrb enhanced it. In the physiological context of pregnancy, p54nrb protein levels decrease with the approach of labor in the rat myometrium. We conclude that p54nrb is a transcriptional corepressor of PR. Decreased expression of p54nrb at the time of labor may act to derepress PR-mediated inhibition on connexin 43 expression and contribute to the initiation of labor.
Managing the impact of psychosis: A grounded theory exploration of recovery processes in psychosis
Authors: Dilks Sarah , Tasker Fiona , Wren Bernadette 
Published: May 2009

Objectives. There has been little conceptual bridge building between what individuals report as helpful in recovery and how psychological therapy might impact on recovery in psychosis. This study explores the links between therapy and recovery in psychosis.Design. Grounded theory was chosen as an appropriate methodology to distil an explanatory account across the qualitative data collected.Methods. An initial sample of 19 therapy session tapes and 23 interviews with psychologists and clients engaged in psychological therapy in psychosis was collected and analysed using grounded theory. This data set was extended through the additional sampling and analysis of 31 published personal accounts of the experience of psychosis.Results. The study reports on specific elements of a larger grounded theory study that particularly relate to recovery processes in psychosis. Specific categories of activity were conceptualised to theorise the key activities involved in managing the impact of psychosis.Conclusions. Therapy in psychosis appeared to be aimed at enhancing clients' functioning in the social world. In an effort to achieve this, it seemed that clients engaged in an ongoing effort to manage the impact of psychosis on both their subjective experience and on day to day life. The conceptualisation of this effort as an active, ongoing, and individually‐directed process was consistent with other examinations of service user accounts.
Cognitive behavioural therapy and psycho‐education for chronic fatigue syndrome in young people: Reflections from the families' perspective
Authors: Dennison Laura , Stanbrook Rachel , Moss‐Morris Rona , Yardley Lucy , Chalder Trudie 
Published: May 2009

ObjectivesRecent trials have produced optimistic results for family‐focussed cognitive behavioural therapy (CBT) for chronic fatigue syndrome (CFS) in young people. This study sought to examine the under‐researched question of the views and experiences of patients and families who take part.DesignSemi‐structured interviews and qualitative analysis were chosen in order to address clients' perspectives in depth.MethodsSixteen young people and sixteen parents who participated in a trial of CBT versus psycho‐education (PE) for CFS were interviewed. Key themes were discerned using inductive thematic analysis.ResultsMost families had low expectations of a cure but hope for improvement. Generally speaking, participants found both CBT and PE acceptable and helpful. Behavioural aspects of CBT (e.g. goal‐setting, graded activity) were found helpful. The opportunity to gain support, recognition and validation was important. Cognitive elements of therapy were sometimes deemed inappropriate and some felt emotional aspects of CFS were not adequately addressed. Participants were ambivalent towards the extent of family involvement. Negative experiences related to the therapy setting and feeling inappropriately labeled. Most participants felt therapy was a stepping‐stone towards normal life, although many felt recovery was incomplete. Very few differences were found between themes from CBT and PE participants. A notable exception was that every young person who experienced CBT described therapy as helpful, whereas the participants who strongly opposed the therapy approach had all experienced PE.ConclusionsThe detailed insights regarding families' therapy experiences suggest areas of improvement for service delivery and topics for further investigation.
Molecular Species of the Alcohol Biomarker Phosphatidylethanol in Human Blood Measured by LC-MS
Authors: Helander Anders , Zheng Yufang 
Published: May 2009

AbstractBackground: The alcohol biomarker phosphatidylethanol (PEth) comprises a group of ethanol-derived phospholipids formed from phosphatidylcholine by phospholipase D. The PEth molecular species have a common phosphoethanol head group onto which 2 fatty acid moieties are attached. We developed an electrospray ionization (ESI) LC-MS method for qualitative and quantitative measurement of different PEth species in human blood.Methods: We subjected a total lipid extract of whole blood to HPLC gradient separation on a C4 column and performed LC-ESI-MS analysis using selected ion monitoring of deprotonated molecules for the PEth species and phosphatidylpropanol (internal standard). Identification of individual PEth species was based on ESI–tandem mass spectrometry (MS/MS) analysis of product ions.Results: The fatty acid moieties were the major product ions of PEth, based on comparison with PEth-16:0/16:0, 18:1/18:1, and 16:0/18:1 reference material. For LC-MS analysis of different PEth species in blood, we used a calibration curve covering 0.2–7.0 μmol/L PEth-16:0/18:1. The lower limit of quantitation of the method was &lt;0.1 μmol/L, and intra- and interassay CVs were &lt;9% and &lt;11%. In blood samples collected from 38 alcohol patients, the total PEth concentration ranged between 0.1 and 21.7 μmol/L (mean 8.9). PEth-16:0/18:1 and 16:0/18:2 were the predominant molecular species, accounting for approximately 37% and 25%, respectively, of total PEth. PEth-16:0/20:4 and mixtures of 18:1/18:1 plus 18:0/18:2 (not separated using selected ion monitoring because of identical molecular masses) and 16:0/20:3 plus 18:1/18.2 made up approximately 13%, 12%, and 8%.Conclusions: This LC-MS method allows simultaneous qualitative and quantitative measurement of several PEth molecular species in whole blood samples.
Unbound (Free) Bilirubin: Improving the Paradigm for Evaluating Neonatal Jaundice
Authors: Ahlfors Charles E , Wennberg Richard P , Ostrow J Donald , Tiribelli Claudio 
Published: May 2009

AbstractBackground: The serum or plasma total bilirubin concentration (BT) has long been the standard clinical laboratory test for evaluating neonatal jaundice, despite studies showing that BT correlates poorly with acute bilirubin encephalopathy (ABE) and its sequelae including death, classical kernicterus, or bilirubin-induced neurological dysfunction (BIND). The poor correlation between BT and ABE is commonly attributed to the confounding effects of comorbidities such as hemolytic diseases, prematurity, asphyxia, or infection. Mounting evidence suggests, however, that BT inherently performs poorly because it is the plasma non–protein-bound (unbound or free) bilirubin concentration (Bf), rather than BT, that is more closely associated with central nervous system bilirubin concentrations and therefore ABE and its sequelae.Content: This article reviews (a) the complex relationship between serum or plasma bilirubin measurements and ABE, (b) the history underlying the limited use of Bf in the clinical setting, (c) the peroxidase method for measuring Bf and technical and other issues involved in adapting the measurement to routine clinical use, (d) clinical experience using Bf in the management of newborn jaundice, and (e) the value of Bf measurements in research investigating bilirubin pathochemistry.Summary: Increasing evidence from clinical studies, clinical experience, and basic research investigating bilirubin neurotoxicity supports efforts to incorporate Bf expeditiously into the routine evaluation of newborn jaundice. .
Development of a Multiplex Ligation-Dependent Probe Amplification Assay for Diagnosis and Estimation of the Frequency of Spinocerebellar Ataxia Type 15
Authors: Ganesamoorthy Devika , Bruno Damien L , Schoumans Jacqueline , Storey Elsdon , Delatycki Martin B , Zhu Danqing , Wei Morgan K , Nicholson Garth A , McKinlay Gardner R J , Slater Howard R 
Published: May 2009

Abstract
Background: Spinocerebellar ataxia type 15 (SCA15) is a slowly progressive neurodegenerative disorder characterized by cerebellar ataxia. Mutation of the ITPR1 gene (inositol 1,4,5-triphosphate receptor, type 1) has been identified recently as the underlying cause, and in most cases the molecular defect is a multiexon deletion. To date, 5 different SCA15 families have been identified with ITPR1 gene deletion.
Methods: We have designed a synthetic, dual-color multiplex ligation-dependent probe amplification (MLPA) assay that measures copy number with high precision in selected exons across the entire length of ITPR1 and the proximal region of the neighboring gene, SUMF1 (sulfatase modifying factor 1). We screened 189 idiopathic ataxic patients with this MLPA assay.
Results: We identified ITPR1 deletion of exons 1–10 in the previously reported AUS1 family (4 members) and deletion of exons 1–38 in a new family (2 members). In addition to the multiexon deletions, apparent single-exon deletions identified in 2 other patients were subsequently shown to be due to single-nucleotide changes at the ligation sites.
Conclusions: The frequency of ITPR1 deletions is 2.7% in known familial cases. This finding suggests that SCA15 is one of the “less common” SCAs. Although the deletions in the 5 families identified worldwide thus far have been of differing sizes, all share deletion of exons 1–10. This region may be important, both in terms of the underlying pathogenetic mechanism and as a pragmatic target for an accurate, robust, and cost-effective diagnostic analysis.
Designing a System to Apply an Assessment Method of Buildings for All Lifecycle Stages Based on the Concept of Eco-Efficiency
Authors: Endo Junko , Murakami Shuzo , Ikaga Toshiharu 
Published: May 2009

Abstract
CASBEE (Comprehensive Assessment System for Building Environmental Efficiency) is an environmental labeling method for buildings, based on assessment of the environmental performance of buildings. In CASBEE, BEE (Building Environmental Efficiency) was developed as a new indicator for assessment following the concept of eco-efficiency. With the increasing BEE value, the total environmental performance of buildings is labeled from the highest performance. The framework of basic and extended CASBEE tools as a structured assessment system is called the “CASBEE family.” CASBEE consists of a set of four basic assessment tools; namely, “CASBEE for Pre-design” (CASBEE-PD), “CASBEE for New Construction” (CASBEE-NC), “CASBEE for Existing Building” (CASBEE-EB), and “CASBEE for Renovation” (CASBEE-RN). These correspond to the individual stages of the building’s lifecycle. There are also needs for detailed assessment targeting specific environmental aspects. “CASBEE-HI,” as an extended tool, assesses efforts made in buildings to alleviate the heat island effect. A new tool called “CASBEE for Urban Development” (CASBEE-UD) is developed for assessment of a group of buildings. Some local authorities introduced CASBEE into their building administration as assessment methods for their sustainable building reporting systems. This requires building owners to submit a planning document assessing the environmental performance of their buildings to the authorities. In April 2004, the city of Nagoya introduced “CASBEE Nagoya.” Introduction of CASBEE followed in the city of Osaka, Yokohama, Kyoto, and other municipals. These local systems require some modification in CASBEE to reflect their local characteristics, such as climate and prioritized policies.