bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni
Authors: Sujatha MS , Balaji Petety V 
Published: April 2006

Abstract

Background
The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs) has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%.

Results
Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs.

Conclusion
The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate specificity, etc. Several studies in literature have focused on the development of tools and/or servers for the large-scale/automated modeling of 3-D structures of proteins. In contrast, the present study focuses on modeling the 3-D structure of a specific protein of interest to a biochemist and illustrates the associated difficulties. It is also able to establish a sequence/structure relationship between sialyltransferases of two distinct families.
Effect of dietary honey on intestinal microflora and toxicity of mycotoxins in mice
Authors: Ezz El-Arab Aly M , Girgis Shenouda M , Hegazy Eman M , Abd El-Khalek Azzat B 
Published: April 2006

Abstract

Background
Bee honey is a functional food which has a unique composition, antimicrobial properties and bifidogenic effect. In order to assess whether honey can inhibit the toxic effect of mycotoxins, the present study was undertaken.

Methods
Production of biomass and toxins by Aspergillus parasiticus and Aspergillus ochraceus were followed in media without and with honey. Although aflatoxins and ochratoxin A. were administrated to male Swiss albino mice up to 1 μg and 10 ng/kg body weight/day respectively. The experimental animals were fed diets without our with 10% honey for two months. The changes in colonic probiotic bacteria, determintal colon enzyme glucuronidases, and genotoxicity were followed.

Results
Addition of 32% in its media increased the biomass of A parasiticus, while the biomass of A. ochraceus decreased and Ochratoxin A. was not produced. When the honey was added at the ratio of 32 and 48% in the medium. No relationship was found between mycelium weight and production of mycotoxins. Oral administration of aflatoxins (mixture of B1, B2, G1 and G2) and Ochratoxin A. induced structural and numerical chromosomal aberrations in bone marrow and germ cells of male mice, whereas, honey treatment reduced the genotoxicity of mycotoxins. Also both toxins induced histopathological changes in liver and kidney. Feeding on diet supplemented with honey improved the histopathological changes in case of aflatoxin group, but not in the case of ochratoxin A. group (except of kidney in two cases). No significant differences were found in the activity of colon β-glucuronidase between group fed diet with or without honey. On the other hand, the colon bifido bacteria and lactobacilli counts were increased markedly in group receiving diet supplemented with honey.

Conclusion
Substituting sugars with honey in processed food can inhibit the harmful and genotoxic effects of mycotoxins, and improve the gut microflora.
NIDDK data repository: a central collection of clinical trial data
Authors: Cuticchia A Jamie , Cooley Philip C , Hall R David , Qin Ying 
Published: April 2006

Abstract

Background
The National Institute of Diabetes and Digestive and Kidney Diseases have established central repositories for the collection of DNA, biological samples, and clinical data to be catalogued at a single site. Here we present an overview of the site which stores the clinical data and links to biospecimens.

Description
The NIDDK Data repository is a web-enabled resource cataloguing clinical trial data and supporting information from NIDDK supported studies. The Data Repository allows for the co-location of multiple electronic datasets that were created as part of clinical investigations. The Data Repository does not serve the role of a Data Coordinating Center, but rather as a warehouse for the clinical findings once the trials have been completed. Because both biological and genetic samples are collected from many of the studies, a data management system for the cataloguing and retrieval of samples was developed.

Conclusion
The Data Repository provides a unique resource for researchers in the clinical areas supported by NIDDK. In addition to providing a warehouse of data, Data Repository staff work with the users to educate them on the datasets as well as assist them in the acquisition of multiple data sets for cross-study analysis. Unlike the majority of biological databases, the Data Repository acts both as a catalogue for data, biosamples, and genetic materials and as a central processing point for the requests for all biospecimens. Due to regulations on the use of clinical data, the ultimate release of that data is governed under NIDDK data release policies. The Data Repository serves as the conduit for such requests.
Evaluation of PROforma as a language for implementing medical guidelines in a practical context
Authors: Sutton David R , Taylor Paul , Earle Kenneth 
Published: April 2006

Abstract

Background
PROforma is one of several languages that allow clinical guidelines to be expressed in a computer-interpretable manner. How these languages should be compared, and what requirements they should meet, are questions that are being actively addressed by a community of interested researchers.

Methods
We have developed a system to allow hypertensive patients to be monitored and assessed without visiting their GPs (except in the most urgent cases). Blood pressure measurements are performed at the patients' pharmacies and a web-based system, created using PROforma, makes recommendations for continued monitoring, and/or changes in medication. The recommendations and measurements are transmitted electronically to a practitioner with authority to issue and change prescriptions.
We evaluated the use of PROforma during the knowledge acquisition, analysis, design and implementation of this system. The analysis focuses on the logical adequacy, heuristic power, notational convenience, and explanation support provided by the PROforma language.

Results
PROforma proved adequate as a language for the implementation of the clinical reasoning required by this project. However a lack of notational convenience led us to use UML activity diagrams, rather than PROforma process descriptions, to create the models that were used during the knowledge acquisition and analysis phases of the project. These UML diagrams were translated into PROforma during the implementation of the project.

Conclusion
The experience accumulated during this study highlighted the importance of structure preserving design, that is to say that the models used in the design and implementation of a knowledge-based system should be structurally similar to those created during knowledge acquisition and analysis. Ideally the same language should be used for all of these models. This means that great importance has to be attached to the notational convenience of these languages, by which we mean the ease with which they can be read, written, and understood by human beings. The importance of notational convenience arises from the fact that a language used during knowledge acquisition and analysis must be intelligible to the potential users of a system, and to the domain experts who provide the knowledge that will be used in its construction.
Predictors of opioid misuse in patients with chronic pain: a prospective cohort study
Authors: Ives Timothy J , Chelminski Paul R , Hammett-Stabler Catherine A , Malone Robert M , Perhac J Stephen , Potisek Nicholas M , Shilliday Betsy Bryant , DeWalt Darren A , Pignone Michael P 
Published: April 2006

Abstract

Background
Opioid misuse can complicate chronic pain management, and the non-medical use of opioids is a growing public health problem. The incidence and risk factors for opioid misuse in patients with chronic pain, however, have not been well characterized. We conducted a prospective cohort study to determine the one-year incidence and predictors of opioid misuse among patients enrolled in a chronic pain disease management program within an academic internal medicine practice.

Methods
One-hundred and ninety-six opioid-treated patients with chronic, non-cancer pain of at least three months duration were monitored for opioid misuse at pre-defined intervals. Opioid misuse was defined as: 1. Negative urine toxicological screen (UTS) for prescribed opioids; 2. UTS positive for opioids or controlled substances not prescribed by our practice; 3. Evidence of procurement of opioids from multiple providers; 4. Diversion of opioids; 5. Prescription forgery; or 6. Stimulants (cocaine or amphetamines) on UTS.

Results
The mean patient age was 52 years, 55% were male, and 75% were white. Sixty-two of 196 (32%) patients committed opioid misuse. Detection of cocaine or amphetamines on UTS was the most common form of misuse (40.3% of misusers). In bivariate analysis, misusers were more likely than non-misusers to be younger (48 years vs 54 years, p < 0.001), male (59.6% vs. 38%; p = 0.023), have past alcohol abuse (44% vs 23%; p = 0.004), past cocaine abuse (68% vs 21%; p < 0.001), or have a previous drug or DUI conviction (40% vs 11%; p < 0.001%). In multivariate analyses, age, past cocaine abuse (OR, 4.3), drug or DUI conviction (OR, 2.6), and a past alcohol abuse (OR, 2.6) persisted as predictors of misuse. Race, income, education, depression score, disability score, pain score, and literacy were not associated with misuse. No relationship between pain scores and misuse emerged.

Conclusion
Opioid misuse occurred frequently in chronic pain patients in a pain management program within an academic primary care practice. Patients with a history of alcohol or cocaine abuse and alcohol or drug related convictions should be carefully evaluated and followed for signs of misuse if opioids are prescribed. Structured monitoring for opioid misuse can potentially ensure the appropriate use of opioids in chronic pain management and mitigate adverse public health effects of diversion.
Monitoring the referral system through benchmarking in rural Niger: an evaluation of the functional relation between health centres and the district hospital
Authors: Bossyns Paul , Abache Ranaou , Abdoulaye Mahaman S , Miyé Hamidou , Depoorter Anne-Marie , Van Lerberghe Wim 
Published: April 2006

Abstract

Background
The main objective of this study is to establish a benchmark for referral rates in rural Niger so as to allow interpretation of routine referral data to assess the performance of the referral system in Niger.

Methods
Strict and controlled application of existing clinical decision trees in a sample of rural health centres allowed the estimation of the corresponding need for and characteristics of curative referrals in rural Niger. Compliance of referral was monitored as well. Need was matched against actual referral in 11 rural districts. The referral patterns were registered so as to get an idea on the types of pathology referred.

Results
The referral rate benchmark was set at 2.5 % of patients consulting at the health centre for curative reasons. Niger's rural districts have a referral rate of less than half this benchmark. Acceptability of referrals is low for the population and is adding to the deficient referral system in Niger. Mortality because of under-referral is highest among young children.

Conclusion
Referral patterns show that the present programme approach to deliver health care leaves a large amount of unmet need for which only comprehensive first and second line health services can provide a proper answer. On the other hand, the benchmark suggests that well functioning health centres can take care of the vast majority of problems patients present with.
Rapid Urban Malaria Appraisal (RUMA) III: epidemiology of urban malaria in the municipality of Yopougon (Abidjan)
Authors: Wang Shr-Jie , Lengeler Christian , Smith Thomas A , Vounatsou Penelope , Cissé Guéladio , Tanner Marcel 
Published: April 2006

Abstract

Background
Currently, there is a significant lack of knowledge concerning urban malaria patterns in general and in Abidjan in particular. The prevalence of malaria, its distribution in the city and the fractions of fevers attributable to malaria in the health facilities have not been previously investigated.

Methods
A health facility-based survey and health care system evaluation was carried out in a peripheral municipality of Abidjan (Yopougon) during the rainy season of 2002, applying a standardized Rapid Urban Malaria Appraisal (RUMA) methodology.

Results
According to national statistics, approximately 240,000 malaria cases (both clinical cases and laboratory confirmed cases) were reported by health facilities in the whole of Abidjan in 2001. They accounted for 40% of all consultations. In the health facilities of the Yopougon municipality, the malaria infection rates in fever cases for different age groups were 22.1% (under one year-olds), 42.8% (one to five years-olds), 42.0% (> five to 15 years-olds) and 26.8% (over 15 years-olds), while those in the control group were 13.0%. 26.7%, 21.8% and 14.6%, respectively. The fractions of malaria-attributable fever were 0.12, 0.22, 0.27 and 0.13 in the same age groups. Parasitaemia was homogenously detected in different areas of Yopougon. Among all children, 10.1% used a mosquito net (treated or not) the night before the survey and this was protective (OR = 0.52, 95% CI 0.29–0.97). Travel to rural areas within the last three months was frequent (31% of all respondents) and associated with a malaria infection (OR = 1.75, 95% CI 1.25–2.45).

Conclusion
Rapid urbanization has changed malaria epidemiology in Abidjan and endemicity was found to be moderate in Yopougon. Routine health statistics are not fully reliable to assess the burden of disease, and the low level of the fractions of malaria-attributable fevers indicated substantial over-treatment of malaria.
Detection of atovaquone-proguanil resistance conferring mutations in Plasmodium falciparum cytochrome b gene in Luanda, Angola
Authors: Pimentel Sónia , Nogueira Fátima , Benchimol Carla , Quinhentos Vatúsia , Bom Joana , Varandas Luís , do Rosário Virgílio , Bernardino Luís 
Published: April 2006

Abstract

Background
The fixed dose combination atovaquone-proguanil is a recently introduced antimalarial for treatment and prophylaxis of Plasmodium falciparum malaria. It is highly effective with a good tolerability profile and a convenient prophylactic regimen. Nevertheless, cases of treatment failure have already been reported, which have been associated to mutations in the cytochrome b gene of the Plasmodium (pfcytb). The presence of atovaquone-proguanil in vivo resistance conferring mutations in pfcytb gene in Luanda, Angola, was investigated, in order to make recommendations on prescribing this antimalarial as prophylaxis for travellers.

Methods
Two hundred and forty nine blood samples from children hospitalized at Luanda Pediatric Hospital for malaria were studied. The PCR-RFLP methodology was used in order to identify pfcytb wild type codon 268 and two point mutations: T802A and A803C.

Results
All samples were identified as wild type for pfcytb gene at codon 268. In the studied population, no mutations associated to atovaquone-proguanil treatment failure were found. Prevalence of the studied mutations in the region was estimated to be less than 0.77% (99% significance level).

Conclusion
Atovaquone-proguanil can be recommended for use by travellers to Luanda with expected high efficacy. This represents an improvement compared to other currently used prophylatic antimalarials in this region. However, it is imperative to continue surveillance.
Biphasic responses of the brachial artery diameter following forearm occlusion: a blunted response in the elderly
Authors: Dobrosielski Devon A , Arce Arturo A , Allen Jason D , Wood Robert H , Welsch Michael A ,   the Louisiana Healthy Aging Study
Published: April 2006

Abstract

Background
The purpose was to examine the temporal response of the brachial artery diameter following 5 minutes of forearm occlusion in young men. A secondary objective was to compare the main features of the temporal pattern between young and old.

Methods
Sixteen young (28 ± 8 yrs) and fifteen older (85 ± 8 yrs) men underwent high-resolution ultrasonography of the brachial artery before and after five minutes of forearm occlusion.

Results
Following release of the pressure cuff the brachial artery diameter exhibits a temporal biphasic response. Initially, there is a significant reduction in brachial diameter (NIL) compared to baseline (BASE), followed by a rapid increase to a PEAK at 41 sec post release. When comparing the magnitude of the decrease in diameter and the Brachial Artery Flow Mediated Dilation (BAFMD) between Young and Old, older subjects demonstrated a blunted response (Magnitude of Decrease: Young: 2.0%; Old: 0.4%, p = 0.015, and BAFMD: Young: 7.7%; Old: 2.3%, p = 0.001). Finally, a significant relationship was noted between the magnitude of decrease and BAFMD (r = -0.44, p = 0.04).

Conclusion
Examination of the temporal response of the brachial artery diameter following 5 minutes of forearm occlusion reveals a biphasic pattern in all participants. Specific features of this pattern are blunted in older adults compared with younger subjects. Finally, the magnitude of the drop in diameter following forearm occlusion correlates with the magnitude of the BAFMD.
CCR3, CCR5, CCR8 and CXCR3 expression in memory T helper cells from allergic rhinitis patients, asymptomatically sensitized and healthy individuals
Authors: Holse Mille , Assing Kristian , Poulsen Lars K 
Published: April 2006

AbstractBackgroundChemokine receptors have been suggested to be preferentially expressed on CD4+ T cells with CCR3 and CCR8 linked to the T helper (Th) 2 subset and CCR5 and CXCR3 to the Th1 subset, however this remains controversial.ObjectiveOur aim was to compare the CCR3, CCR5, CCR8 and CXCR3 expression in memory Th cells from allergic, asymptomatically sensitized and healthy individuals.MethodsPeripheral blood mononuclear cells from 8 pollen allergic rhinitis patients, 10 asymptomatically sensitized and 10 healthy individuals were stimulated for 7 days with allergen or tetanus toxoid. CCR3, CCR5, CCR8, CXCR3, CD4 and CD45RO were detected by flow cytometry.ResultsNo differences in chemokine receptor expression were observed between the three groups on day 0, and seven days of unstimulated culture did not change the expression. Both antigenic stimuli increased the chemokine receptor expression, tetanus toxoid being the most potent. No differences in percentage chemokine receptor positive memory Th cells were observed between the three groups on day 7. Only a change in MFI for CCR5 was significantly different between the three groups after allergen stimulation of the Th cells.ConclusionWe conclude that even though allergen and antigen induced increased chemokine receptor expression, no differences in profiles were identified in memory Th cells from patient groups with different atopic status.
Deconstructing anti-harm-reduction metaphors; mortality risk from falls and other traumatic injuries compared to smokeless tobacco use
Authors: Phillips Carl V , Guenzel Brian , Bergen Paul 
Published: April 2006

AbstractAnti-harm-reduction advocates sometimes resort to pseudo-analogies to ridicule harm reduction. Those opposed to the use of smokeless tobacco as an alternative to smoking sometimes suggest that the substitution would be like jumping from a 3 story building rather than 10 story, or like shooting yourself in the foot rather than the head. These metaphors are grossly inappropriate for several reasons, notably including the fact that they are misleading about the actual risk levels. Based on the available literature on mortality from falls, we estimate that smoking presents a mortality risk similar to a fall of about 4 stories, while mortality risk from smokeless tobacco is no worse than that from an almost certainly non-fatal fall from less than 2 stories. Other metaphors are similarly misleading. These metaphors, like other false and misleading anti-harm-reduction statements are inherently unethical attempts to prevent people from learning accurate health information. Moreover, they implicitly provide bad advice about health behavior priorities and are intended to persuade people to stick with a behavior that is more dangerous than an available alternative. Finally, the metaphors exhibit a flippant tone that seems inappropriate for a serious discussion of health science.
Smad signalling in the ovary
Authors: Kaivo-oja Noora , Jeffery Luke A , Ritvos Olli , Mottershead David G 
Published: April 2006

Abstract
It has now been a decade since the first discovery of the intracellular Smad proteins, the downstream signalling molecules of one of the most important growth factor families in the animal kingdom, the transforming growth factor beta (TGF-beta) superfamily. In the ovary, several TGF-beta superfamily members are expressed by the oocyte, granulosa and thecal cells at different stages of folliculogenesis, and they signal mainly through two different Smad pathways in an autocrine/paracrine manner. Defects in the upstream signalling cascade molecules, the ligands and receptors, are known to have adverse effects on ovarian organogenesis and folliculogenesis, but the role of the individual Smad proteins in the proper function of the ovary is just beginning to be understood for example through the use of Smad knockout models. Although most of the different Smad knockouts are embryonic lethal, it is known, however, that in Smad1 and Smad5 knockout mice primordial germ cell development is impaired and that Smad3 deficient mice harbouring a deletion in exon 8 exhibit impaired folliculogenesis and reduced fertility. In this minireview we discuss the role of Smad structure and function in the ovarian context.