bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation by Inflammatory Stimuli Increases Neutrophil Binding of Human Immunodeficiency Virus Type 1 and Subsequent Infection of Lymphocytes
Authors: Gabali Ali M. , Anzinger Joshua J. , Spear Gregory T. , Thomas Larry L. 
Published: September 2004

ABSTRACT
Resting neutrophils bind human immunodeficiency virus type 1 (HIV-1) and efficiently transfer infection to lymphocytes. The present study shows that a brief activation by inflammatory stimuli increases the neutrophil binding levels of both R5 and X4 isolates of HIV-1 at least twofold. The binding occurs independently of CD4, gp120, and incubation temperature and is observed with HIV-1 propagated either in lymphocytes or in HEK293 cells. Significantly, HIV-1 bound to the activated neutrophils accelerates the infection of activated lymphocytes compared to free HIV-1 or to HIV-1 bound to resting neutrophils. It is proposed that these events may contribute to the increased risk of HIV-1 transmission at sites of mucosal infection.
Handling multiple testing while interpreting microarrays with the Gene Ontology Database
Authors: Osier Michael V , Zhao Hongyu , Cheung Kei-Hoi 
Published: September 2004

Abstract
Background
The development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally.

Results
We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database.

Conclusions
We found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.
Functionally specified protein signatures distinctive for each of the different blue copper proteins
Authors: Giri Anuradha Vivekanandan , Anishetty Sharmila , Gautam Pennathur 
Published: September 2004

Abstract
Background
Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance of using patterns or signatures to retrieve out related sequences. Blue copper proteins are found in the electron transport chain of prokaryotes and eukaryotes. The signatures already existing in the databases like the type 1 copper blue, multiple copper oxidase, cyt b/b6, photosystem 1 psaA&B, psaG&K, and reiske iron sulphur protein are not specified signatures for blue copper proteins as the name itself suggests. Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. This work describes the signatures designed based on the copper metal binding motifs in blue copper proteins. The common feature in all blue copper proteins is a trigonal planar arrangement of two nitrogen ligands [each from histidine] and one sulphur containing thiolate ligand [from cysteine], with strong interactions between the copper center and these ligands.

Results
Sequences that share such conserved motifs are crucial to the structure or function of the protein and this could provide a signature of family membership. The blue copper proteins chosen for the study were plantacyanin, plastocyanin, cucumber basic protein, stellacyanin, dicyanin, umecyanin, uclacyanin, cusacyanin, rusticyanin, sulfocyanin, halocyanin, azurin, pseudoazurin, amicyanin and nitrite reductase which were identified in both eukaryotes and prokaryotes. ClustalW analysis of the protein sequences of each of the blue copper proteins was the basis for designing protein signatures or peptides. The protein signatures and peptides identified in this study were designed involving the active site region involving the amino acids bound to the copper atom. It was highly specific for each kind of blue copper protein and the false picks were minimized. The set of signatures designed specifically for the BCP's was entirely different from the existing broad spectrum signatures as mentioned in the background section.

Conclusions
These signatures can be very useful for the annotation of uncharacterized proteins and highly specific to retrieve blue copper protein sequences of interest from the non redundant databases containing a large deposition of protein sequences.
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
Authors: Sinha Saurabh , Schroeder Mark D , Unnerstall Ulrich , Gaul Ulrike , Siggia Eric D 
Published: September 2004

Abstract
Background
The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. It is important to quantify how comparative genomics can improve computational detection of such modules.

Results
We run the Stubb software on the entire D. melanogaster genome, to obtain predictions of modules involved in segmentation of the embryo. Stubb uses a probabilistic model to score sequences for clustering of transcription factor binding sites, and can exploit multiple species data within the same probabilistic framework. The predictions are evaluated using publicly available gene expression data for thousands of genes, after careful manual annotation. We demonstrate that the use of a second genome (D. pseudoobscura) for cross-species comparison significantly improves the prediction accuracy of Stubb, and is a more sensitive approach than intersecting the results of separate runs over the two genomes. The entire list of predictions is made available online.

Conclusion
Evolutionary conservation of modules serves as a filter to improve their detection in silico. The future availability of additional fruitfly genomes therefore carries the prospect of highly specific genome-wide predictions using Stubb.
Development of real-time PCR for detection of Mycoplasma hominis
Authors: Baczynska Agata , Svenstrup Helle F , Fedder Jens , Birkelund Svend , Christiansen Gunna 
Published: September 2004

Abstract
Background
Mycoplasma hominis is associated with pelvic inflammatory disease, bacterial vaginosis, post partum fever, sepsis and infections of the central nervous system often leading to serious conditions. Association with development of female infertility has also been suggested, but different publications present different results. We developed a sensitive and fast diagnostic real-time PCR to test clinical samples from women undergoing laparoscopic examination before fertility treatment. To develop a test for the detection and quantification of M. hominis we selected a housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (gap), as a target.

Results
Real-time PCR was optimized to detect 10 copies of M. hominis PG21 genomic DNA. A fluorescence signal was measured for all 20 other M. hominis isolates, and melting curves analysis showed variations in the melting temperature in agreement with sequence variation in the region of the probes. There was no amplification of other mycoplasmal DNA and human DNA. Eighty-three patient cervical swab samples from infertile women were cultured for M. hominis in the BEa medium. Two of the samples (2.4%) were positive after 48 hours of incubation. The real-time PCR detected the same two samples positive, and the DNA concentrations in the clinical specimens were calculated to 37.000 copies/ml and 88.500 copies/ml, respectively.

Conclusion
The results demonstrate that real-time PCR may prove to be a rapid alternative to the traditional cultivation method. Information on bacterial load in genital swabs can be obtained. The assay allowed detection of M. hominis in a closed system reducing the risk of contamination by amplicon carry-over.
The relationship between educational level and bone mineral density in postmenopausal women
Authors: Gur Ali , Sarac Ayşegül Jale , Nas Kemal , Cevik Remzi 
Published: September 2004

Abstract
Background
This study describes the influence of educational level on bone mineral density (BMD) and investigating the relationship between educational level and bone mineral density in postmenopausal women.

Methods
A total of 569 postmenopausal women, from 45 to 86 years of age (mean age of 60.43 ± 7.19 years) were included in this study. A standardized interview was used at the follow-up visit to obtain information on demographic, life-style, reproductive and menstrual histories such as age at menarche, age at menopause, number of pregnancies, number of abortions, duration of menopause, duration of fertility, and duration of lactation. Patients were separated into four groups according to the level of education, namely no education (Group 1 with 209 patients), elementary (Group 2 with 222 patients), high school (Group 3 with 79 patients), and university (Group 4 with 59 patients).

Results
The mean ages of groups were 59.75 ± 7.29, 61.42 ± 7.50, 60.23 ± 7.49, and 58.72 ± 7.46, respectively. Spine BMD was significant lower in Group 1 than that of other groups (p < 0.05). Trochanter and ward's triangle BMD were the highest in Group 4 and there was a significant difference between Group 1 and 4 (p < 0.05). The prevalence of osteoporosis showed an inverse relationship with level of education, ranging from 18.6% for the most educated to 34.4% for the no educated women (p < 0.05). Additionally, there was a significant correlation between educational level and spine BMD (r = 0.20, p < 0.01), trochanter BMD (r = 0.13, p < 0.01), and ward's BMD (r = 0.14, p < 0.01).

Conclusions
The results of the study suggest that there is a significant correlation between educational level and BMD. Losses in BMD for women of lower educational level tend to be relatively high, and losses in spine and femur BMD showed a decrease with increasing educational level.
Good physicians from the perspective of their patients
Authors: Schattner Ami , Rudin Dan , Jellin Navah 
Published: September 2004

Abstract
Background
It is not currently known what is the patient's viewpoint of a "good" physician. We set out to define patient's priorities regarding different physician's attributes in 3 domains important in medical care.

Methods
Patients hospitalized or attending clinics at a large teaching hospital selected the 4 attributes that they considered most important out of 21 listed arbitrarily in a questionnaire. The questionnaire included 7 items each in the domains of patient autonomy, professional expertise and humanism.

Results
Participating patients (n = 445, mean age 57.5 ± 16 years) selected professional expertise (50%), physician's patience and attentiveness (38% and 30%, respectively), and informing the patient, representing the patient's interests, being truthful and respecting patient's preferences (25–36% each) as the most essential attributes. Patient's selections were not significantly influenced by different demographic or clinical background. Selections of attributes in the domain of patient's autonomy were significantly more frequent and this was the preferred domain for 31% and as important as another domain for 16% – significantly more than the domain of professional expertise (P = 0.008), and much more than the domain of humanism and support (P < 0.0005).

Conclusions
Patients studied want their physicians to be highly professional and expert clinicians and show humaneness and support, but their first priority is for the physician to respect their autonomy.
History of opioid allergy: what significance?
Authors: Gilbar Peter J , Ridge Alison M 
Published: September 2004

Objective. To assess how health professionals would manage a patient’s pain when the patient is labelled as allergic to opioid analgesics. Methods. A clinical case scenario, describing a patient obviously requiring opioid pain management but reporting a morphine allergy, was designed and pretested. This was distributed to medical (students, interns/residents, registrars, consultants) and nursing staff of Toowoomba Health Service District. All staff had some experience in pain management, though this varied widely. Respondents were asked to review the history and briefly comment on how the patient’s pain should be managed. Results. Overall response rate was 46%. Doctors returned 47% (39/83) of scenarios, with 53% requesting further information on the nature of the allergy before using opioids. Nurses response rate was 45.2% (42/93), with only 21.4% requesting more information. Eighty three per cent (15/18) of doctors and 60% (20/33) of nurses, who didn’t query the nature of the morphine allergy, recommended opioid medication. No one specifically suggested using structurally dissimilar opioids to morphine if an allergy really existed. Conclusion. Many health care staff either missed or ignored the allergy or assumed it was really an adverse effect and not significant, potentially placing the patient at risk of serious consequences, including anaphylaxis. Despite the low incidence of true opioid allergy, health professionals must fully investigate purported allergies to determine their validity. Patients should never be administered medications until their likelihood of experiencing a true allergy is determined.
Inappropriate labelling of patients as opioid allergic
Authors: Gilbar Peter J , Ridge Alison M 
Published: September 2004

Objectives. To investigate the incidence of patients being inappropriately labelled as allergic to opioid medications and to assess the effect that this label may have had on the subsequent prescribing of opioids. Methods. A study was conducted on patients admitted to Toowoomba Hospital over a three month period as to their perceived opioid allergy status. In addition to medication history interview, pharmacists recorded data on any claimed drug allergy attributed to opioid medications. Events were classified depending on the probability of the event being an allergic or immunological drug reaction. Medical records and medication charts of identified patients were checked to determine if allergy status had any effect on opioid prescribing. Results. Thirty patients reported an opioid allergy. Morphine and codeine were most commonly implicated, with nausea and vomiting the most likely adverse events. Six patients were classified as high probability of allergic reaction, although anaphylaxis wasn’t reported. Most allergy documentation was incomplete, with the nature of reaction seldom recorded. Despite a ‘supposed’ opioid allergy, 70% of patients were prescribed subsequent opioids. Of the six patients in the high probability group, four were prescribed opioids. Three received alternate opioids without incident, while nurses refused to administer the same previously implicated drug to the fourth patient. Conclusion. Opioid prescribing did not appear to be influenced by a reported allergy. Ignoring ‘real’ allergies, however rare, may put patients at risk of severe consequences. Staff must be educated regarding the importance of recording accurately and thoroughly the specifics of patients’ medication allergies and its importance in future safe prescribing.
Assimilation of Meteosat radiance data within the 4D‐Var system at ECMWF: Data quality monitoring, bias correction and single‐cycle experiments
Authors: Munro Rosemary , Köpken Christina , Kelly Graeme , Thépaut Jean‐Noël , Saunders Roger 
Published: September 2004

AbstractThis paper describes the direct assimilation of water vapour (WV) clear‐sky radiance (CSR) data from geostationary satellites within the context of the ECMWF four‐dimensional variational assimilation (4D‐Var) system. The assimilation of Meteosat–7 WV CSR data became operational on 9 April 2002. As 4D‐Var includes a time dimension, the high temporal resolution of the geostationary radiance data can be exploited to provide information not only on the upper‐tropospheric humidity but also on the upper‐tropospheric wind field. The data assimilated have a spatial resolution of approximately 80 km and a time resolution of 1 hour. Extensive pre‐operational monitoring of the CSR data has been carried out, showing a systematic warm bias of approximately 2–3 K in the Meteosat WV CSR data compared to radiances simulated from model first‐guess fields. The systematic biases between the brightness temperatures derived from the model and the observations are investigated and compared to other satellite radiance data. For assimilation purposes this is accounted for by using a bias correction based on a statistical regression. The monitoring also shows contamination of certain time slots caused by intruding solar stray light and a certain degree of residual cloud contamination present in the CSR. Data quality control is introduced to exclude affected data. Initial single‐cycle 3D‐Var with first guess at appropriate time and 4D‐Var experiments demonstrate both the direct and indirect effects of the Meteosat WV CSR data on the model fields, particularly of humidity and wind. The operational implementation of the assimilation of the Meteosat WV CSR data, including results from pre‐operational experiments and forecast impacts, is discussed in a companion paper. Copyright © 2004 Royal Meteorological Society
The dependence of retrieved cirrus ice‐crystal effective dimension on assumed ice‐crystal geometry and size‐distribution function at solar wavelengths
Authors: Baran A. J. , Havemann S. 
Published: September 2004

AbstractThe dependence of retrieved ice‐crystal effective dimension on assumed ice‐crystal shape and size‐distribution function is investigated at solar wavelengths (0.87, 1.6 and 3.7 µm). The dual viewing Along Track Scanning Radiometer is used to retrieve ice‐crystal effective dimension using a method of Optimal Estimation over semi‐transparent cirrus located in the tropics and mid‐latitudes. The ice‐crystal effective dimension is defined in terms of the effective diameter and it is retrieved assuming roughened hexagonal ice aggregates, pristine hexagonal ice columns, and four‐branched bullet rosettes. It is shown that if a phase function that well represents the scattering properties of cirrus is applied to each crystal type then the retrieved ice‐crystal effective diameter is only weakly dependent on ice‐crystal shape and size‐distribution function. Absolute differences between retrieved ice‐crystal effective diameter assuming hexagonal ice columns and ice aggregates combined with a representative phase function are generally well within ±5 µm. The findings of this paper have the important implication that, in climate models, simulation of cirrus cloudy radiances at solar wavelengths might be made to be independent of assumed ice‐crystal shape and size‐distribution function. © Crown copyright, 2004.
Evaluation and optimization of sampling errors for the Monte Carlo Independent Column Approximation
Authors: Räisänen Petri , Barker Howard W. 
Published: September 2004

AbstractThe Monte Carlo Independent Column Approximation (McICA) method for computing domain‐average broadband radiative fluxes is unbiased with respect to the full ICA, but its flux estimates contain conditional random noise. McICA's sampling errors are evaluated here using a global climate model (GCM) dataset and a correlated‐k distribution (CKD) radiation scheme. Two approaches to reduce McICA's sampling variance are discussed. The first is to simply restrict all of McICA's samples to cloudy regions. This avoids wasting precious few samples on essentially homogeneous clear skies. Clear‐sky fluxes need to be computed separately for this approach, but this is usually done in GCMs for diagnostic purposes anyway. Second, accuracy can be improved by repeated sampling, and averaging those CKD terms with large cloud radiative effects. Although this naturally increases computational costs over the standard CKD model, random errors for fluxes and heating rates are reduced by typically 50% to 60%, for the present radiation code, when the total number of samples is increased by 50%. When both variance reduction techniques are applied simultaneously, globally averaged flux and heating rate random errors are reduced by a factor of ∼3. Copyright © 2004 Royal Meteorological Society
Stochastic generation of subgrid‐scale cloudy columns for large‐scale models
Authors: Räisänen Petri , Barker Howard W. , Khairoutdinov Marat F. , Li Jiangnan , Randall David A. 
Published: September 2004

AbstractTo use the Monte Carlo Independent Column Approximation method for computing domain‐average radiative fluxes in large‐scale atmospheric models (LSAMs), a method is needed for generating cloudy subcolumns within LSAM columns. Here, a stochastic cloud generator is introduced to produce the subcolumns. The generator creates a cloud field on a column‐by‐column basis using information about layer cloud fraction, vertical overlap of cloud fraction and cloud condensate for adjacent layers, and density functions describing horizontal variations in cloud water content. The performance of the generator is assessed using a single day's worth of data from an LSAM simulation that employed a low‐resolution two‐dimensional cloud‐resolving model (CRM) within each LSAM column (a total of ∼59 000 cloudy domains). Statistical characteristics of generated cloud fields are compared against original CRM data, and radiative‐transfer biases associated with the generator are evaluated. When the generator is initialized to the greatest extent possible with information obtained from the CRM fields, overall biases are small. For example, global‐mean total cloud fraction exhibits a bias of −0.004, as compared with −0.024 for maximum‐random overlap (MRO) and 0.047 for random overlap. Biases in radiative fluxes and heating rates are in general ¼ to ½ those for MRO with horizontally homogeneous clouds. Copyright © 2004 Royal Meteorological Society
Analytical Validation of the Tag-It High-Throughput Microsphere-Based Universal Array Genotyping Platform: Application to the Multiplex Detection of a Panel of Thrombophilia-Associated Single-Nucleotide Polymorphisms
Authors: Bortolin Susan , Black Margot , Modi Hemanshu , Boszko Ihor , Kobler Daniel , Fieldhouse Dan , Lopes Eve , Lacroix Jean-Michel , Grimwood Rebecca , Wells Philip , Janeczko Richard , Zastawny Roman 
Published: September 2004

AbstractBackground: We have developed a novel, microsphere-based universal array platform referred to as the Tag-It™ platform. This platform is suitable for high-throughput clinical genotyping applications and was used for multiplex analysis of a panel of thrombophilia-associated single-nucleotide polymorphisms (SNPs).Methods: Genomic DNA from 132 patients was amplified by multiplex PCR using 6 primer sets, followed by multiplex allele-specific primer extension using 12 universally tagged genotyping primers. The products were then sorted on the Tag-It array and detected by use of the Luminex xMAP™ system. Genotypes were also determined by sequencing.Results: Empirical validation of the universal array showed that the highest nonspecific signal was 3.7% of the specific signal. Patient genotypes showed 100% concordance with direct DNA sequencing data for 736 SNP determinations.Conclusions: The Tag-It microsphere-based universal array platform is a highly accurate, multiplexed, high-throughput SNP-detection platform.