bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide Asian genetic map and ethnic comparison: The GENDISCAN study
Authors: Ju Young Seok , Park Hansoo , Lee Mi Kyeong , Kim Jong-Il , Sung Joohon , Cho Sung-Il , Seo Jeong-Sun 
Published: November 2008

Abstract

Background
Genetic maps provide specific positions of genetic markers, which are required for performing genetic studies. Linkage analyses of Asian families have been performed with Caucasian genetic maps, since appropriate genetic maps of Asians were not available. Different ethnic groups may have different recombination rates as a result of genomic variations, which would generate misspecification of the genetic map and reduce the power of linkage analyses.

Results
We constructed the genetic map of a Mongolian population in Asia with CRIMAP software. This new map, called the GENDISCAN map, is based on genotype data collected from 1026 individuals of 73 large Mongolian families, and includes 1790 total and 1500 observable meioses. The GENDISCAN map provides sex-averaged and sex-specific genetic positions of 1039 microsatellite markers in Kosambi centimorgans (cM) with physical positions. We also determined 95% confidence intervals of genetic distances of the adjacent marker intervals.
Genetic lengths of the whole genome, chromosomes and adjacent marker intervals are compared with those of Rutgers Map v.2, which was constructed based on Caucasian populations (Centre d'Etudes du Polymorphisme Humain (CEPH) and Icelandic families) by mapping methods identical to those of the GENDISCAN map, CRIMAP software and the Kosambi map function. Mongolians showed approximately 1.9 fewer recombinations per meiosis than Caucasians. As a result, genetic lengths of the whole genome and chromosomes of the GENDISCAN map are shorter than those of Rutgers Map v.2. Thirty-eight marker intervals differed significantly between the Mongolian and Caucasian genetic maps.

Conclusion
The new GENDISCAN map is applicable to the genetic study of Asian populations. Differences in the genetic distances between the GENDISCAN and Caucasian maps could facilitate elucidation of genomic variations between different ethnic groups.
New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides
Authors: Salse Jérome , Chagué Véronique , Bolot Stéphanie , Magdelenat Ghislaine , Huneau Cécile , Pont Caroline , Belcram Harry , Couloux Arnaud , Gardais Soazic , Evrard Aurélie , Segurens Béatrice , Charles Mathieu , Ravel Catherine , Samain Sylvie , Charmet Gilles , Boudet Nathalie , Chalhoub Boulos 
Published: November 2008

Abstract

Background
Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the Sitopsis section, having Aegilops speltoides (SS, 2n = 14) as the closest identified relative. However molecular relationships based on genomic sequence comparison, including both coding and non-coding DNA, have never been investigated. In an attempt to clarify these relationships, we compared, in this study, sequences of the Storage Protein Activator (SPA) locus region of the S genome of Ae. speltoides (2n = 14) to that of the A, B and D genomes co-resident in the hexaploid wheat species (Triticum aestivum, AABBDD, 2n = 42).

Results
Four BAC clones, spanning the SPA locus of respectively the A, B, D and S genomes, were isolated and sequenced. Orthologous genomic regions were identified as delimited by shared non-transposable elements and non-coding sequences surrounding the SPA gene and correspond to 35 268, 22 739, 43 397 and 53 919 bp for the A, B, D and S genomes, respectively. Sequence length discrepancies within and outside the SPA orthologous regions are the result of non-shared transposable elements (TE) insertions, all of which inserted after the progenitors of the four genomes divergence.

Conclusion
On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, Ae speltoides appears to be more evolutionary related to the B genome of T. aestivum than the A and D genomes. However, the differential insertions of TEs, none of which are conserved between the two genomes led to the conclusion that the S genome of Ae. speltoides has diverged very early from the progenitor of the B genome which remains to be identified.
Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)
Authors: Danzmann Roy G , Davidson Evelyn A , Ferguson Moira M , Gharbi Karim , Koop Ben F , Hoyheim Bjorn , Lien Sigbjorn , Lubieniecki Krzysztof P , Moghadam Hooman K , Park Jay , Phillips Ruth B , Davidson William S 
Published: November 2008

Abstract

Background
Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12–13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD) in their ancestry (2R duplication). Salmonids have experienced one additional WGD (4R duplication event) compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates. We describe the organization of the 4R chromosomal segments of the proto-ray-finned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes.

Results
Evidence is presented for the retention of large whole-arm affinities between the ancestral linkage groups of the ray-finned fishes, and the 50 homeologous chromosomal segments in Atlantic salmon and rainbow trout. In the comparisons between the two salmonid species, there is also evidence for the retention of large whole-arm homeologous affinities that are associated with the retention of duplicated markers. Five of the 7 pairs of chromosomal arm regions expressing the highest level of duplicate gene expression in rainbow trout share homologous synteny to the 5 pairs of homeologs with the greatest duplicate gene expression in Atlantic salmon. These regions are derived from proto-Actinopterygian linkage groups B, C, E, J and K.

Conclusion
Two chromosome arms in Danio rerio and Oryzias latipes (descendants of the 3R duplication) can, in most instances be related to at least 4 whole or partial chromosomal arms in the salmonid species. Multiple arm assignments in the two salmonid species do not clearly support a 13 proto-linkage group model, and suggest that a 12 proto-linkage group arrangement (i.e., a separate single chromosome duplication and ancestral fusion/fissions/recombination within the putative G/H/I groupings) may have occurred in the more basal soft-rayed fishes. We also found evidence supporting the model that ancestral linkage group M underwent a single chromosome duplication following the 3R duplication. In the salmonids, the M ancestral linkage groups are localized to 5 whole arm, and 3 partial arm regions (i.e., 6 whole arm regions expected). Thus, 3 distinct ancestral linkage groups are postulated to have existed in the G/H and M lineage chromosomes in the ancestor of the salmonids.
Tolerance induced via TLR2 and TLR4 in human dendritic cells: role of IRAK-1
Authors: Albrecht Valerie , Hofer Thomas PJ , Foxwell Brian , Frankenberger Marion , Ziegler-Heitbrock Loems 
Published: November 2008

AbstractBackgroundWhile dendritic cells (DCs) can induce tolerance in T cells, little is known about tolerance induction in DCs themselves. We have analysed tolerance induced in humanin-vitrogenerated DCs by repeated stimulation with ligands for TLR4 and TLR2.ResultsDCs stimulated with the TLR4 ligand LPS did show a rapid and pronounced expression of TNF mRNA and protein. When DCs were pre-cultured for 2 days with 5 ng LPS/ml then the subsequent response to stimulation with a high dose of LPS (500 ng/ml) was strongly reduced for both TNF mRNA and protein. At the promoter level there was a reduced transactivation by the -1173 bp TNF promoter and by a construct with a tetrameric NF-κB motif. Within the signalling cascade leading to NF-κB activation we found an ablation of the IRAK-1 adaptor protein in LPS-tolerant DCs. Pre-culture of DCs with the TLR2 ligand Pam3Cys also led to tolerance with respect to TNF gene expression and IRAK-1 protein was ablated in such tolerant cells as well, while IRAK-4 protein levels were unchanged.ConclusionThese data show that TLR-ligands can render DCs tolerant with respect to TNF gene expression by a mechanism that likely involves blockade of signal transduction at the level of IRAK-1.
Comparative analysis of Mycobacterium avium subsp. paratuberculosis isolates from cattle, sheep and goats by short sequence repeat and pulsed-field gel electrophoresis typing
Authors: Sevilla Iker , Li Lingling , Amonsin Alongkorn , Garrido Joseba M , Geijo Maria V , Kapur Vivek , Juste Ramón A 
Published: November 2008

Abstract

Background

Mycobacterium avium subsp. paratuberculosis (Map) causes the chronic enteritis called paratuberculosis mainly in cattle, sheep and goats. Evidences that point out an association between Map and Crohn's Disease in humans are increasing. Strain differentiation among Map isolates has proved to be difficult and has limited the study of the molecular epidemiology of paratuberculosis. In order to asses the usefulness of the PCR based short sequence repeat (SSR) analysis of locus 1 and locus 8 in the epidemiological tracing of paratuberculosis strains we here compare for the first time the results of SSR and Sna BI-Spe I pulsed-field gel electrophoresis (PFGE) typing methods in a set of 268 Map isolates from different hosts (cattle, sheep, goats, bison, deer and wild boar).

Results
A total of nineteen different multi-locus SSR (SSR1_SSR8) types were identified amongst the 268 isolates compared to the 37 multiplex profiles differentiated by the Sna BI-Spe I PFGE. SSR type 7_4 was the predominant genotype (51.2% of all isolates and 54.3% of cattle isolates), but combined with PFGE results the abundance of the most prevalent genotype (7_4&{2-1}) dropped down to 37.7%. SSR types 7_3 and 14_3 were significantly spread amongst isolates recovered from small ruminants. The comparison of SSR1_SSR8 and Sna BI-Spe I PFGE typing of these isolates has shown that both methods perform at similar discriminatory level. These were 0.691 and 0.693, respectively for SSR and PFGE as indicated Simpson's Index of Diversity, and 0.82 when calculated for combined SSR and PFGE genotypes. Overall, SSR1_SSR8 analysis seemed to detect higher levels of within-farm strain diversity and seemed to give higher year-related information. Combination of both typing methods revealed 20 multi-type farms out of the 33 bovine farms studied with more than one isolate.

Conclusion
The particular SSR and PFGE typing approaches described here are in general agreement but they showed some discrepancies that might reflect differing evolutionary processes of Map strains. Both methods are able to reciprocally complement their results and neither should be replaced with the other if sufficient material and time is available. Overall, the results of our comparative analyses suggest that, based on current methodologies available, a combined approach that includes SSR and PFGE seems to provide the highest level of discrimination for Map strain typing with meaningful epidemiological information.
A comparison of two methods for estimating odds ratios: Results from the National Health Survey
Authors: Bakhshi Enayatollah , Eshraghian Mohammad R , Mohammad Kazem , Seifi Behjat 
Published: November 2008

Abstract

Background
The practice of dichotomizing a continuous outcome variable does not make use of within-category information. That means the loss of information. This study compared two approaches in the modelling of the association between sociodemographic and smoking with obesity in adult women in Iran.

Methods
We conducted a comparative study between two methods via an illustrative example, using data from the "National Health Survey in Iran (NHSI)" database. It included 14176 women aged 20–69 years. At first, body mass index(BMI) was treated as a continuous variable, ORs and 95 per cent confidence intervals were calculated using the "without dichotomizing" method. Then subjects were classified into obese (BMI ≥ 30 kg/m2) and nonobese (BMI < 30 kg/m2) and logistic regression model was used to estimate ORs and 95 per cent confidence intervals.

Results
The odds ratio estimates changed only slightly over the two methods. But the "without dichotomizing" method provided shorter confidence intervals on the odds ratio parameters than dichotomizing method. All relative confidence interval lengths were greater than 1.15.

Conclusion
If responses are continuous then the "without dichotomizing" method is certainly more useful than the "dichotomizing" method and leads to more precise estimation of odds ratios.
Legionella species colonization of water distribution systems, pools and air conditioning systems in cruise ships and ferries
Authors: Goutziana Georgia , Mouchtouri Varvara A , Karanika Maria , Kavagias Antonios , Stathakis Nikolaos E , Gourgoulianis Kostantinos , Kremastinou Jenny , Hadjichristodoulou Christos 
Published: November 2008

Abstract

Background
Legionnaires' disease continues to be a public health concern in passenger ships. This study was scheduled in order to investigate Legionella spp. colonization of water distribution systems (WDS), recreational pools, and air-conditioning systems on board ferries and cruise ships in an attempt to identify risk factors for Legionella spp. colonization associated with ship water systems and water characteristics.

Methods
Water systems of 21 ferries and 10 cruise ships including WDS, air conditioning systems and pools were investigated for the presence of Legionella spp.

Results
The 133 samples collected from the 10 cruise ships WDS, air conditioning systems and pools were negative for Legionella spp. Of the 21 ferries WDS examined, 14 (66.7%) were legionellae-positive. A total of 276 samples were collected from WDS and air conditioning systems. Legionella spp. was isolated from 37.8% of the hot water samples and 17.5% of the cold water samples. Of the total 96 positive isolates, 87 (90.6%) were L. pneumophila. Legionella spp. colonization was positively associated with ship age. The temperature of the hot water samples was negatively associated with colonization of L. pneumophila serogroup (sg) 1 and that of L. pneumophila sg 2 to 14. Increases in pH ≥7.8 and total plate count ≥400 CFU/L, correlated positively with the counts of L. pneumophila sg 2 to 14 and Legionella spp. respectively. Free chlorine of ≥0.2 mg/L inhibited colonization of Legionella spp.

Conclusion
WDS of ferries can be heavily colonized by Legionella spp. and may present a risk of Legionnaires' disease for passengers and crew members. Guidelines and advising of Legionnaires' disease prevention regarding ferries are needed, in particular for operators and crew members.
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction
Authors: Agarwal Vatsal , Remmert Michael , Biegert Andreas , Söding Johannes 
Published: November 2008

Abstract

Background
During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When no homologs can be found in the protein structure database (PDB), the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available.

Results
PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models.

Conclusion
PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest.
"They all work...when you stick to them": A qualitative investigation of dieting, weight loss, and physical exercise, in obese individuals
Authors: Thomas Samantha L , Hyde Jim , Karunaratne Asuntha , Kausman Rick , Komesaroff Paul A 
Published: November 2008

Abstract
Background
To explore the extent to which people living with obesity have attempted to lose weight, their attitudes towards dieting, physical exercise and weight loss solutions, why their weight loss attempts have failed, and their opinions about what would be most beneficial to them in their struggle with their weight.

Method
Qualitative study, using open-ended interviews, of 76 people living with obesity in Victoria, Australia in 2006/7. Individuals with a BMI of 30 or over were recruited using articles in local newspapers, convenience sampling, and at a later stage purposive sampling techniques to diversify the sample. Data analysis was conducted by hand using a constant, comparative method to develop and test analytical categories. Data were interpreted both within team meetings and through providing research participants the chance to comment on the study findings.

Results
Whilst participants repeatedly turned to commercial diets in their weight loss attempts, few had used, or were motivated to participate in physical activity. Friends or family members had introduced most individuals to weight loss techniques. Those who took part in interventions with members of their social network were more likely to report feeling accepted and supported. Participants blamed themselves for being unable to maintain their weight loss or 'stick' to diets. Whilst diets did not result in sustained weight loss, two thirds of participants felt that dieting was an effective way to lose weight.

Conclusion
Individuals with obesity receive numerous instructions about what to do to address their weight, but very few are given appropriate long term guidance or support with which to follow through those instructions. Understanding the positive role of social networks may be particularly important in engaging individuals in physical activity. Public health approaches to obesity must engage and consult with those currently living with obesity, if patterns of social change are to occur.
No evidence of enhanced oxidant production in blood obtained from patients with obstructive sleep apnea
Authors: Grabska-Kobylecka Izabela , Kobylecki Andrzej , Bialasiewicz Piotr , Krol Maciej , Ehteshamirad Golsa , Kasielski Marek , Nowak Dariusz 
Published: November 2008

Abstract

Background
Obstructive sleep apnea syndrome (OSAS) is a recognized risk factor for cardiovascular morbidity and mortality, perhaps due to causative exacerbations of systemic oxidative stress. Putative oxidative stress related to numerous episodes of intermittent hypoxia, may be an oxidants chief driving force in OSAS patients.

Methods
We assessed the resting and n-formyl-methionyl-leucyl-phenylalanine (fMLP)- induced whole blood chemiluminescence (as a measure of oxidant production by polymorphonuclear leukocytes and monocytes), ferric reducing ability of plasma (FRAP) and H2O2 generation in the whole blood of 27 untreated OSAS patients, 22 subjects after a night of CPAP therapy and 11 controls without OSAS. All of them were matched to age, BMI (body mass index) and smoking habits. All parameters were measured before and after polysomnography-controlled sleep, individual results were obtained as a mean from duplicated experiments.

Results
No significant differences were distinguished between evening and morning blood chemiluminescence, H2O2 activity and FRAP within and between all three study groups.
For instance patients with untreated OSAS had similar morning and evening resting whole blood chemiluminescence (2.3 +/- 2.2 vs. 2.4 +/- 2.2 [aU·10-4 phagocytes]), total light emission after stimulation with fMLP (1790 +/- 1371 vs. 1939 +/- 1532 [aU·s·10-4 phagocytes]), as well as FRAP after 3 min. plasma incubation (602 +/- 202 vs. 671 +/- 221 [uM]). Although, in the subgroup of 11 patients with severe OSAS (apnea/hypopnea index 58 +/- 18/h and oxygen desaturation index 55 +/- 19/h), the morning vs. evening resting chemiluminescence and total light emission after stimulation with fMLP observed a propensity to elevate 2.5 +/- 2.7 vs. 1.9 +/- 1.8 [aU·10-4 phagocytes] and 1778 +/- 1442 vs. 1503 +/- 1391 [aU·s·10-4 phagocytes], respectively, these did not attain statistical significance (p > 0.05).

Conclusion
Our investigation exposed no evidence in the overproduction of oxidants via circulating phagocytes, once considered a culprit in the oxidative stress of OSAS patients.
Diets high in selenium and isoflavones decrease androgen-regulated gene expression in healthy rat dorsolateral prostate
Authors: Legg Russell L , Tolman Jessica R , Lovinger Cameron T , Lephart Edwin D , Setchell Kenneth DR , Christensen Merrill J 
Published: November 2008

AbstractBackgroundHigh dietary intake of selenium or soybean isoflavones reduces prostate cancer risk. These components each affect androgen-regulated gene expression. The objective of this work was to determine the combined effects of selenium and isoflavones on androgen-regulated gene expression in rat prostate.MethodsMale Noble rats were exposed from conception until 200 days of age to diets containing an adequate (0.33-0.45 mg/kg diet) or high (3.33-3.45 mg/kg) concentration of selenium as Se-methylselenocysteine and a low (10 mg/kg) or high (600 mg/kg) level of isoflavones in a 2 × 2 factorial design. Gene expression in the dorsolateral prostate was determined for the androgen receptor, for androgen-regulated genes, and for Akr1c9, whose product catalyzes the reduction of dihydrotestosterone to 5alpha-androstane-3alpha, 17beta-diol. Activity of hepatic glutathione peroxidise 1 and of prostatic 5alpha reductase were also assayed.ResultsThere were no differences due to diet in activity of liver glutathione peroxidase activity. Total activity of 5alpha reductase in prostate was significantly lower (p= 0.007) in rats fed high selenium/high isoflavones than in rats consuming adequate selenium/low isoflavones. High selenium intake reduced expression of the androgen receptor, Dhcr24 (24-dehydrocholesterol reductase), and Abcc4 (ATP-binding cassette sub-family C member 4). High isoflavone intake decreased expression of Facl3 (fatty acid CoA ligase 3), Gucy1a3 (guanylate cyclase alpha 3), and Akr1c9. For Abcc4 the combination of high selenium/high isoflavones had a greater inhibitory effect than either treatment alone. The effects of selenium on gene expression were always in the direction of chemopreventionConclusionThese results suggest that combined intake of high selenium and high isoflavones may achieve a greater chemopreventive effect than either compound supplemented individually.