bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gender differences in respiratory symptoms in 19-year-old adults born preterm
Authors: Vrijlandt Elianne JLE , Gerritsen Jorrit , Boezen H Marike , Duiverman Eric J ,   the Dutch POPS-19 Collaborative Study Group*
Published: October 2005

AbstractObjectiveTo study the prevalence of respiratory and atopic symptoms in (young) adults born prematurely, differences between those who did and did not develop Bronchopulmonary Disease (BPD) at neonatal age and differences in respiratory health between males and females.MethodsDesign: Prospective cohort study.Setting:Nation wide follow-up study, the Netherlands.Participants:690 adults (19 year old) born with a gestational age below 32 completed weeks and/or with a birth weight less than 1500 g. Controls were Dutch participants of the European Community Respiratory Health Survey (ECRHS).Main outcome measures:Presence of wheeze, shortness of breath, asthma, hay fever and eczema using the ECRHS-questionnaireResultsThe prevalence of doctor-diagnosed asthma was significantly higher in the ex-preterms than in the general population, whereas eczema and hay fever were significant lower. Women reported more symptoms than men. Preterm women vs controls: asthma 13% vs 5% (p < 0.001); hay fever 8% vs 20% (p < 0.001); eczema 10% vs 42% (p < 0.001). Preterm men vs controls: asthma 9% vs 4% (p = 0.007); hay fever 8% vs 17% (p = 0.005); eczema 9% vs 31% (p < 0.001) Preterm women reported more wheeze and shortness of breath during exercise (sob) than controls: wheeze 30% vs 22% (p = 0.009); sob 27% vs 16% (p < 0.001); 19-year-old women with BPD reported a higher prevalence of doctor diagnosed asthma compared to controls (24% vs 5% p < 0.001) and shortness of breath during exercise (43% vs 16% p = 0.008). The prevalence of reported symptoms by men with BPD were comparable with the controls.ConclusionOur large follow-up study shows a higher prevalence of asthma, wheeze and shortness of breath in the prematurely born young adults. 19-year-old women reported more respiratory symptoms than men. Compared to the general population atopic diseases as hay fever and eczema were reported less often.
Nonnatural amino acid incorporation into the methionine 214 position of the metzincin Pseudomonas aeruginosa alkaline protease
Authors: Walasek Paula , Honek John F 
Published: October 2005

AbstractBackgroundThe alkaline protease fromPseudomonas aeruginosa(AprA) is a member of the metzincin superfamily of metalloendoproteases. A key feature of these proteases is a conserved methionine-containing 1,4-tight β turn at the base of the active site zinc binding region.ResultsTo explore the invariant methionine position in this class of protease, incorporation of a nonnatural fluorinated methionine, L-difluoromethionine (DFM), into this site was accomplished. Although overproduction of the N-terminal catalytic fragment of AprA resulted in protein aggregates which could not be resolved, successful heterologous production of the entire AprA was accomplished in the presence and absence of the nonnatural amino acid. DFM incorporation was found to only slightly alter the enzyme kinetics of AprA. In addition, differential scanning calorimetry indicated no significant alteration in the thermal stability of the modified enzyme.ConclusionAlthough invariant in all metzincin proteases, the methionine 214 position in AprA can be successfully replaced by the nonnatural amino acid DFM resulting in little effect on protein structure and function. This study indicates that the increased size of the methyl group by the introduction of two fluorines is still sufficiently non-sterically demanding, and bodes well for the application of DFM to biophysical studies of protein structure and function in this class of protease.
MASQOT: a method for cDNA microarray spot quality control
Authors: Bylesjö Max , Eriksson Daniel , Sjödin Andreas , Sjöström Michael , Jansson Stefan , Antti Henrik , Trygg Johan 
Published: October 2005

Abstract
Background
cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

Results
A novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies.

Conclusion
The proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process.
Polyamine stress at high pH in Escherichia coli K-12
Authors: Yohannes Elizabeth , Thurber Amy E , Wilks Jessica C , Tate Daniel P , Slonczewski Joan L 
Published: October 2005

Abstract

Background
Polyamines such as spermine and spermidine are required for growth of Escherichia coli; they interact with nucleic acids, and they bind to ribosomes. Polyamines block porins and decrease membrane permeability, activities that may protect cells in acid. At high concentrations, however, polyamines impair growth. They impair growth more severely at high pH, probably due to their increased uptake as membrane-permeant weak bases. The role of pH is critical in understanding polyamine stress.

Results
The effect of polyamines was tested on survival of Escherichia coli K-12 W3110 in extreme acid or base (pH conditions outside the growth range). At pH 2, 10 mM spermine increased survival by 2-fold, and putrescine increased survival by 30%. At pH 9.8, however, E. coli survival was decreased 100-fold by 10 mM spermine, putrescine, cadaverine, or spermidine. At pH 8.5, spermine decreased the growth rate substantially, whereas little effect was seen at pH 5.5. Spermidine required ten-fold higher concentrations to impair growth. On proteomic 2-D gels, spermine and spermidine caused differential expression of 31 different proteins. During log-phase growth at pH 7.0, 1 mM spermine induced eight proteins, including PykF, GlpK, SerS, DeaD, OmpC and OmpF. Proteins repressed included acetate-inducible enzymes (YfiD, Pta, Lpd) as well as RapA (HepA), and FabB. At pH 8.5, spermine induced additional proteins: TnaA, OmpA, YrdA and NanA (YhcJ) and also repressed 17 proteins. Four of the proteins that spermine induced (GlpK, OmpA, OmpF, TnaA) and five that were repressed (Lpd, Pta, SucB, TpiA, YfiD) show similar induction or repression, respectively, in base compared to acid. Most of these base stress proteins were also regulated by spermidine, but only at ten-fold higher concentration (10 mM) at high pH (pH 8.5).

Conclusion
Polyamines increase survival in extreme acid, but decrease E. coli survival in extreme base. Growth inhibition by spermine and spermidine requires neutral or higher pH. At or above pH 7, spermine and spermidine regulate specific proteins, many of which are known to be regulated by base stress. High pH amplifies polyamine stress; and naturally occurring polyamines may play an important role in base stress.
Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705
Authors: Guy Lionel , Karamata Dimitri , Moreillon Philippe , Roten Claude-Alain H 
Published: October 2005

AbstractBackgroundAnalysis of the first reported complete genome sequence ofBifidobacterium longumNCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness toStreptomyces coelicolorandMycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes.ResultsGenerally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of theB. longumNCC2705 chromosome yielded six, instead of two, linear segments, while itsdnaAlocus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low.Comparison with closely related actinobacteria strongly suggested that the chromosome ofB. longumwas misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10AB. longumstrain. Recently, a corrected sequence ofB. longumNCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions.ConclusionGenometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.
Methods for confidence interval estimation of a ratio parameter with application to location quotients
Authors: Beyene Joseph , Moineddin Rahim 
Published: October 2005

AbstractBackgroundThe location quotient (LQ) ratio, a measure designed to quantify and benchmark the degree of relative concentration of an activity in the analysis of area localization, has received considerable attention in the geographic and economics literature. This index can also naturally be applied in the context of population health to quantify and compare health outcomes across spatial domains. However, one commonly observed limitation of LQ is its widespread use as only a point estimate without an accompanying confidence interval.MethodsIn this paper we present statistical methods that can be used to construct confidence intervals for location quotients. The delta and Fieller's methods are generic approaches for a ratio parameter and the generalized linear modelling framework is a useful re-parameterization particularly helpful for generating profile-likelihood based confidence intervals for the location quotient. A simulation experiment is carried out to assess the performance of each of the analytic approaches and a health utilization data set is used for illustration.ResultsBoth the simulation results as well as the findings from the empirical data show that the different analytical methods produce very similar confidence limits for location quotients. When incidence of outcome is not rare and sample sizes are large, the confidence limits are almost indistinguishable. The confidence limits from the generalized linear model approach might be preferable in small sample situations.ConclusionLQ is a useful measure which allows quantification and comparison of health and other outcomes across defined geographical regions. It is a very simple index to compute and has a straightforward interpretation. Reporting this estimate with appropriate confidence limits using methods presented in this paper will make the measure particularly attractive for policy and decision makers.
Serum hyaluronate as a non-invasive marker of hepatic fibrosis and inflammation in HBeAg-negative chronic hepatitis B
Authors: Montazeri Ghodrat , Estakhri Arezoo , Mohamadnejad Mehdi , Nouri Negin , Montazeri Farhad , Mohammadkani Ashraf , Derakhshan Mohammad Hossain , Zamani Farhad , Samiee Shahram , Malekzadeh Reza 
Published: October 2005

Abstract

Background
HBV infection is a serious global heath problem. It is crucial to monitor this disease more closely with a non-invasive marker in clinical trials. We aimed to evaluate the predictive value of serum hyaluronate for the presence of extensive liver fibrosis and inflammation.

Methods
28 healthy volunteers and 65 patients with HBeAg negative chronic hepatitis B were enrolled. Liver biopsies scored according to Ishak system. Association of serum hyaloronate with liver fibrosis and inflammation were assessed, and cut off points for serum hyaluronate levels were identified by receiver operating characteristics (ROC) curves and their values for prediction of fibrosis and inflammation were assessed.

Results
In patients with CHB serum hyaluronate had the most significant correlation and predictive values for the liver fibrosis and inflammation comparing to the other variables. At the cut off point of 126.4 ngm/ml it could discriminate extensive fibrosis from milder ones with sensitivity of 90.9% and specificity of 98.1%. With the same value it could discriminate extensive inflammation from their milder counterparts with sensitivity of 63.6% and specificity of 92.6%.

Conclusion
Serum hyaluronate was the best predictor of extensive liver fibrosis and inflammation and it could discriminate subgroups of patients with chronic hepatitis B. It could be used as a non-invasive test to monitor these patients more closely with developing anti viral agents in clinical trials.
The McKenzie method for the management of acute non-specific low back pain: design of a randomised controlled trial [ACTRN012605000032651]
Authors: Machado Luciana AC , Maher Chris G , Herbert Rob D , Clare Helen , McAuley James 
Published: October 2005

Abstract

Background
Low back pain (LBP) is a major health problem. Effective treatment of acute LBP is important because it prevents patients from developing chronic LBP, the stage of LBP that requires costly and more complex treatment.
Physiotherapists commonly use a system of diagnosis and exercise prescription called the McKenzie Method to manage patients with LBP. However, there is insufficient evidence to support the use of the McKenzie Method for these patients. We have designed a randomised controlled trial to evaluate whether the addition of the McKenzie Method to general practitioner care results in better outcomes than general practitioner care alone for patients with acute LBP.

Methods/design
This paper describes the protocol for a trial examining the effects of the McKenzie Method in the treatment of acute non-specific LBP. One hundred and forty eight participants who present to general medical practitioners with a new episode of acute non-specific LBP will be randomised to receive general practitioner care or general practitioner care plus a program of care based on the McKenzie Method. The primary outcomes are average pain during week 1, pain at week 1 and 3 and global perceived effect at week 3.

Discussion
This trial will provide the first rigorous test of the effectiveness of the McKenzie Method for acute non-specific LBP.
Laparoscopic repair of high rectovaginal fistula: Is it technically feasible?
Authors: Kumaran Saravanan S , Palanivelu Chinnusamy , Kavalakat Alfie J , Parthasarathi Ramakrishnan , Neelayathatchi Murugayyan 
Published: October 2005

Abstract

Background
Rectovaginal fistula (RVF) is an epithelium-lined communication between the rectum and vagina. Most RVFs are acquired, the most common cause being obstetric trauma. Most of the high RVFs are repaired by conventional open surgery. Laparoscopic repair of RVF is rare and so far only one report is available in the literature.

Methods
We present a case of high RVF repaired by laparoscopy. 56-year-old female who had a high RVF following laparoscopic assisted vaginal hysterectomy was successfully operated laparoscopically. Here we describe the operative technique and briefly review the literature.

Results
The postoperative period of the patient was uneventful and after a follow up of 6 months no recurrence was found.

Conclusion
Laparoscopic repair of high RVF is feasible in selected patients but would require proper identification of tissue planes and good laparoscopic suturing technique.
Development and validation of a quality of life questionnaire for patients with colostomy or ileostomy
Authors: Prieto Luis , Thorsen Hanne , Juul Kristian 
Published: October 2005

Abstract

Background
Quality of life of stoma patients is increasingly being addressed in clinical trials. However, the instruments used in the majority of these studies have not been validated specifically for stoma patients. The aim of this paper is to describe the development and validation of a quality-of-life instrument, "Stoma-QOL", specifically for patients with colostomy or ileostomy.

Methods
Potential items were formulated in English on the basis of the results of a series of semi-structured interviews with 169 adult stoma patients. The process resulted in a preliminary 37-item version, which was translated into French, German, Spanish and Danish, and administered repeatedly to 182 patients with colostomy or ileostomy. A psychometric selection of items was performed through Rasch Analysis. The measurement properties of the final questionnaire version were subsequently tested.

Results
The 20 items in the final questionnaire covered four domains – sleep, sexual activity, relations to family and close friends, and social relations to other than family and close friends. These items were found to define a unidimensional variable according to Rasch specifications (Infit MNSQ < 1.3). Internal consistency reliability calculated as Cronbach's alpha was 0.92, i.e., highly reliable. Spearman's correlation coefficients of scores across times of administration was >0.88 (p < 0.01), indicating a high test-retest reliability. Item calibrations by country calculated as ICC were 0.81 (0.67–0.91 95% CI), confirming cross-cultural comparability across the European countries included in the study.

Conclusion
Given the adequacy of the metric properties of the Stoma-QOL suggested by the psychometric analyses, this study confirms the suitability of the instrument in clinical practice and in clinical research.
Kapillarelektrophorese in der Urin-Diagnostik Urine diagnostics by capillary electrophoresis
Authors: Marti Ulrich 
Published: October 2005

Zusammenfassung
Die Kapillarelektrophorese wird in einigen medizinischen Laboratorien seit mehreren Jahren zur Serumprotein-Elektrophorese verwendet. Der Einsatz der Kapillarelektrophorese in der Urindiagnostik beschränkt sich hingegen bis heute auf einige wenige Machbarkeitsstudien und Forschungsanwendungen. Diese Arbeit zeigt die Entwicklung der Kapillarelektrophorese bis zu einer gerade kürzlich erschienenen neuen Version einer kommerziellen Urinelektrophorese von Beckman Coulter. Man kann gespannt sein auf die ersten Berichte zu dieser Anwendung.
FISH-Diagnostik bei hämatologischen Neoplasien FISH diagnostics in hematological malignancies
Authors: Schoch Claudia , Kern Wolfgang , Schnittger Susanne , Haferlach Torsten 
Published: October 2005

Zusammenfassung
Die Technik der Fluoreszenz-in-situ-Hybridisierung (FISH) ist eine wichtige Methode, mit welcher Nukleinsäuresequenzen im Zellkern nachgewiesen werden können. Sie hat inzwischen in der Diagnostik und Klassifikation von hämatologischen Neoplasien einen festen Stellenwert. Die Durchführung eines diagnostischen FISH-Assays setzt voraus, dass die Sequenz der zu untersuchenden genetischen Region bekannt ist. Durch das zunehmende Wissen über die genetischen Veränderungen bei Tumoren konnten FISH-Assays für viele klinisch relevante Fragestellungen entwickelt werden. Grundsätzlich können für diverse Fragestellungen Sonden für eine FISH-Untersuchung hergestellt werden, sofern die zu untersuchende genetische Veränderung molekular aufgeklärt und prinzipiell mit FISH erfassbar ist, wie dies bei Deletionen, Translokationen, Duplikationen, Inversionen sowie Zugewinnen und Verlusten ganzer Chromosomen der Fall ist. Kleine Mutationen innerhalb eines einzelnen Gens sind nicht erfassbar. Viele für die Diagnostik wichtige Sonden sind bereits kommerziell erhältlich. Eine Empfehlung zum Einsatz der FISH-Diagnostik bei Leukämien wird zur Zeit im Rahmen des Europäischen Leukämie-Netzes erarbeitet (www.leukemia-net.org).
Differentiation of anti-platelet antibodies using microspheres and flow cytometry Einsatz von Mikrosphären und Durchflusszytometrie für die Differenzierung von Antithrombozyten-Antikörpern
Authors: Woetzel Michael , Schroeder Sabine , Sack Ulrich 
Published: October 2005

Abstract
Background: Allo- and autoantibodies against membrane structures of human platelets cause different types of immune thrombocytopenic disorders and require a sensitive and specific assay. The well-established monoclonal antibody immobilization of platelet antigens (MAIPA) test is able to distinguish between specifically bound immunoglobulins and coating of membrane-associated immune complexes; but MAIPA is rather time consuming and requires 2×107 platelets or more. For patients with very low platelet count and for little children with small blood volume, this may present a serious limitation.
Methods: The advantages of flow cytometry and of modern microsphere technology were combined with the selectivity of MAIPA to overcome the disadvantages of this assay. In order to compare different types of beads, i) goat anti-mouse Ig-labelled magnetic beads, ii) dyed polymeric beads designed for multiplexed assays, and iii) blanc polymeric beads have been studied. After loading with glycoprotein-specific or anti-β2-microglobulin-specific antibodies, these beads could be stored for months at 4°C without substantial loss of sensitivity.
Glycoproteins from platelet membranes, loaded with platelet-specific auto-/alloantibodies, have been immobilized on the bead surfaces during detergent solubilization of platelets prior to labelling with anti-human IgG-Biotin and Extravidin® R-Phycoerythrin.
Results: Magnetic beads are very easy to handle, show strong signals and low nonspecific binding, but have stronger autofluorescence compared to polymeric beads. Polymeric beads have low autofluorescence but stronger tendency to nonspecific binding. All types of beads tested in this study can be used to detect antibodies against platelet antigens, even against glycoproteins with low frequency such as anti-HPA-5 autoantibodies and with as few as 106 platelets or less. In multiplexed settings, they are suitable for simultaneous detection of multiple antibodies.
Conclusions: Flow cytometry is a fast and sensitive method for a bead-based MAIPA assay and is especially useful for low platelet counts and for pediatric patients. It is further improved by the use of multiplexed beads.