bluuebunny/crossref_metadata_2025_split huggingface dataset:
Late Quaternary loss of genetic diversity in muskox (Ovibos)
Authors: MacPhee Ross DE , Tikhonov Alexei N , Mol Dick , Greenwood Alex D 
Published: October 2005

Abstract

Background
The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen.

Results
Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs), closely similar or identical to haplotypes found in modern muskoxen and ranging in age from ~22,000 to ~160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs), dating between ~44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations.

Conclusion
We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval.
Heterotachy and long-branch attraction in phylogenetics
Authors: Philippe Hervé , Zhou Yan , Brinkmann Henner , Rodrigue Nicolas , Delsuc Frédéric 
Published: October 2005

Abstract

Background
Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic.

Results
In this report, we performed more realistic simulations to evaluate the relative performance of MP and ML methods when two kinds of heterogeneities are considered: (i) within-site rate variation (heterotachy), and (ii) rate variation across lineages. Using a similar protocol as Kolaczkowski and Thornton to generate heterotachous datasets, we found that heterotachy, which constitutes a serious violation of existing models, decreases the accuracy of ML whatever the level of rate variation across lineages. In contrast, the accuracy of MP can either increase or decrease when the level of heterotachy increases, depending on the relative branch lengths. This result demonstrates that MP is not insensitive to heterotachy, contrary to the report of Kolaczkowski and Thornton. Finally, in the case of LBA (i.e. when two non-sister lineages evolved faster than the others), ML outperforms MP over a wide range of conditions, except for unrealistic levels of heterotachy.

Conclusion
For realistic combinations of both heterotachy and variation of evolutionary rates across lineages, ML is always more accurate than MP. Therefore, ML should be preferred over MP for analysing real data, all the more so since parametric methods also allow one to handle other types of biological heterogeneities much better, such as among sites rate variation. The confounding effects of heterotachy on tree reconstruction methods do exist, but can be eschewed by the development of mixture models in a probabilistic framework, as proposed by Kolaczkowski and Thornton themselves.
Tracking Alu evolution in New World primates
Authors: Ray David A , Batzer Mark A 
Published: October 2005

Abstract

Background

Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates.

Results
Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; Alu Ta7, Alu Ta10, and Alu Ta15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of Alu Sc- and Alu Sp-type elements. This is a novel mode of origin for new Alu subfamilies.

Conclusion
The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.
The distribution of SNPs in human gene regulatory regions
Authors: Guo Yongjian , Jamison D Curtis 
Published: October 2005

AbstractBackgroundAs a result of high-throughput genotyping methods, millions of human genetic variants have been reported in recent years. To efficiently identify those with significant biological functions, a practical strategy is to concentrate on variants located in important sequence regions such as gene regulatory regions.ResultsAnalysis of the most common type of variant, single nucleotide polymorphisms (SNPs), shows that in gene promoter regions more SNPs occur in close proximity to transcriptional start sites than in regions further upstream, and a disproportionate number of those SNPs represent nucleotide transversions. Additionally, the number of SNPs found in the predicted transcription factor binding sites is higher than in non-binding site sequences.ConclusionCurrent information about transcription factor binding site sequence patterns may not be exhaustive, and SNPs may be actively involved in influencing gene expression by affecting the transcription factor binding sites.
Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes
Authors: Graziano Claudio , Giorgi Massimo , Malentacchi Cecilia , Mattiuz Pier Luigi , Porfirio Berardino 
Published: October 2005

Abstract

Background
The minor histocompatibility antigens (mHags) are self-peptides derived from common cellular proteins and presented by MHC class I and II molecules. Disparities in mHags are a potential risk for the development of graft-versus-host disease (GvHD) in the recipients of bone marrow from HLA-identical donors. Two alleles have been identified in the mHag HA-1. The correlation between mismatches of the mHag HA-1 and GvHD has been suggested and methods to facilitate large-scale testing were afterwards developed.

Methods
We used sequence specific primer (SSP) PCR and direct sequencing to detect HA-1 gene polymorphisms in a sample of 131 unrelated Italian subjects. We then set up a novel melting temperature (Tm) assay that may help identification of HA-1 alleles without oligonucleotide probes.

Results
We report the frequencies of HA-1 alleles in the Italian population and the presence of an intronic 5 base-pair deletion associated with the immunogeneic allele HA-1H. We also detected novel variable sites with respect to the consensus sequence of HA-1 locus. Even though recombination/gene conversion events are documented, there is considerable linkage disequilibrium in the data. The gametic associations between HA-1R/H alleles and the intronic 5-bp ins/del polymorphism prompted us to try the Tm analysis with SYBR® Green I. We show that the addition of dimethylsulfoxide (DMSO) during the assay yields distinct patterns when amplicons from HA-1H homozygotes, HA-1R homozygotes, and heterozygotes are analysed.

Conclusion
The possibility to use SYBR® Green I to detect Tm differences between allelic variants is attractive but requires great caution. We succeeded in allele discrimination of the HA-1 locus using a relatively short (101 bp) amplicon, only in the presence of DMSO. We believe that, at least in certain assets, Tm assays may benefit by the addition of DMSO or other agents affecting DNA strand conformation and stability.
Prevalence of abnormal findings on brain magnetic resonance (MR) examinations in adult participants of brain docking
Authors: Tsushima Yoshito , Taketomi-Takahashi Ayako , Endo Keigo 
Published: October 2005

Abstract

Background
To determine the prevalence of abnormal findings on brain magnetic resonance (MR) examinations in adult participants of brain docking in order to assess its usefulness.

Methods
We analyzed screening brain MR examinations for 1113 adults (age, 52.6+/-8.5 years; range, 22–84; 761 male and 352 female) performed during 6-year period from April 1998 to March 2004. All participants voluntarily sought a brain MR examination at their own expense. All subjects were studied using the same 1.0-T MR scanner, on axial T1-weighted spin echo (SE) images, proton-density-weighted and T2-weighted fast SE images, and intracranial MR angiography (MRA). All abnormal findings were classified into three basic categories: (1) findings with no referral necessary; (2) findings not requiring further evaluation, but which needed to be reported to the referring physician; (3) findings requiring further evaluation.

Results
Participants with abnormal MR findings requiring further evaluation accounted for 1.3 %, but five of seven suspected intracranial aneurysms were not confirmed by other imaging modalities (false positive). No malignant tumors or other life-threatening pathology was detected, and only three participants (0.27 %) with abnormalities underwent surgical treatment. No participant groups were identified from our data as being high risk for MR abnormal findings requiring further evaluation.

Conclusion
Brain-docking participants had a variety of abnormalities on brain MR examinations, but only a small percentage of these findings required further evaluation. The usefulness of the brain docking with MRI and MRA has yet to be proven, and at this time we cannot approve this screening procedure.
Citalopram associated with acute angle-closure glaucoma: case report
Authors: Croos Robert , Thirumalai Srinivasa , Hassan Sabit , Davis Jane Da Roza 
Published: October 2005

AbstractBackgroundAcute angle-closure glaucoma is a rare complication in patients receiving anti-depressant treatment. In the following case, we report the development of acute angle closure glaucoma in a patient who overdosed on Citalopram, an antidepressant, and discuss the possible etiological mechanisms for the condition.Case presentationWe report a 54 year old, Caucasian lady, with depression and alcohol dependence syndrome, who developed acute angle-closure glaucoma after an overdose of Citalopram, along with alcohol. She was treated with medications and had bilateral Yag laser iridotomies to correct the glaucoma and has made complete recovery. In this case, the underlying cause for glaucoma appears to be related to the ingestion of Citalopram.ConclusionThe patho-physiological basis for acute angle closure glaucoma in relation to antidepressant medications remains unclear. The authors suggest Citalopram may have a direct action on the Iris or Ciliary body muscle through serotonergic or anti-cholinergic mechanisms or both. This case highlights the importance of the awareness of the underlying risks, which may predispose an individual to develop acute angle-closure glaucoma, and reminds the clinicians the significance of history taking and examination of the eye before and after starting anti-depressants. This area needs to be further researched.
Chronic koro-like symptoms – two case reports
Authors: Kar Nilamadhab 
Published: October 2005

Abstract

Background
Koro is a culture bound syndrome, which has been reported usually from Asian countries. It has been described as an acute, brief lasting illness, which often occurs in epidemics. There is no description in literature of a chronic form of this syndrome.

Case presentation
Two sporadic cases with koro-like symptoms from East India are presented where the illness had a chronic course with durations spanning more than ten years. In contrast to acute, good prognosis, psycho-education responsive form that is usually seen in epidemics; the chronic form, appeared to be associated with greater morbidity and poorer response to interventions.

Conclusion
There is a possibility of a chronic form of koro syndrome.
Is relatively young age within a school year a risk factor for mental health problems and poor school performance? A population-based cross-sectional study of adolescents in Oslo, Norway
Authors: Lien Lars , Tambs Kristian , Oppedal Brit , Heyerdahl Sonja , Bjertness Espen 
Published: October 2005

Abstract
Background
Several studies have shown that children who are relatively young within a school year are at greater risk for poorer school performance compared with their older peers. One study also reported that relative age within a school year is an independent risk factor for emotional and behavioral problems. The objective of this study was to test the hypothesis that relatively younger adolescents in the multiethnic population of Oslo have poorer school performance and more mental health problems than their relatively older classmates within the same school year.

Methods
This population-based cross-sectional study included all 10th-grade pupils enrolled in 2000 and 2001 in the city of Oslo. The participation rate was 88%. Of the 6,752 pupils in the study sample, 25% had a non-Norwegian background. Mental health problems were quantified using the abbreviated versions of Symptom Check List-25 (SCL-10) and the Strength and Difficulties Questionnaire (SDQ). Information on school performances and mental health problems were self-reported. We controlled for confounding factors including parental educational level, social support, gender, and ethnicity.

Results
The youngest one-third of pupils had significantly lower average school grades than the middle one-third and oldest one-third of their classmates (p < 0.001). Of the mental health problems identified in the questionnaires, the groups differed only on peer problems; the youngest one-third reported significantly more problems than the middle and oldest groups (p < 0.05). Age within a school year and gender showed significant interactions with total SDQ score, SDQ peer problems score, SDQ pro social score, and SCL-10 score. After stratifying for gender, the peer problem scores differed significantly between age groups only among boys. The SCL-10 score was significant, but only in girls and in the opposite direction to that expected, with the oldest pupils having significantly higher scores than the other two groups (p < 0.05).

Conclusion
In adolescents from a multicultural city in Norway, relative age within a school year significantly influenced academic performance. In contrast to data from Great Britain, relative age within a school year was not an important risk factor for mental health problems in adolescents in Oslo.
Work ethics and general work attitudes in adolescents are related to quality of life, sense of coherence and subjective health – a Swedish questionnaire study
Authors: Axelsson Lars , Andersson Ingemar , Håkansson Anders , Ejlertsson Göran 
Published: October 2005

Abstract

Background
Working life is an important arena in most people's lives, and the working line concept is important for the development of welfare in a society. For young people, the period before permanent establishment in working life has become longer during the last two decades. Knowledge about attitudes towards work can help us to understand young people's transition to the labour market. Adolescents are the future workforce, so it seems especially important to notice their attitudes towards work, including attitudes towards the welfare system. The aim of this study was to describe and analyse upper secondary school students' work attitudes, and to explore factors related to these attitudes.

Methods
The sample consisted of 606 upper secondary school students. They all received a questionnaire including questions about quality of life (QOL), sense of coherence (SOC), subjective health and attitudes towards work. The response rate was 91%. A factor analysis established two dimensions of work attitudes. Multivariate analyses were carried out by means of logistic regression models.

Results
Work ethics (WE) and general work attitudes (GWA) were found to be two separate dimensions of attitudes towards work. Concerning WE the picture was similar regardless of gender or study programme. Males in theoretical programmes appeared to have more unfavourable GWA than others. Multivariate analyses revealed that good QOL, high SOC and good health were significantly related to positive WE, and high SOC was positively related to GWA. Being female was positively connected to WE and GWA, while studying on a practical programme was positively related to GWA only. Among those who received good parental support, GWA seemed more favourable.

Conclusion
Assuming that attitudes towards work are important to the working line concept, this study points out positive factors of importance for the future welfare of the society. Individual factors such as female gender, good QOL, high SOC and good health as well as support from both parents, positive experience of school and work contacts related positively to attitudes towards work. Further planning and supportive work have to take these factors into account.
Conventional liquid-based techniques versus Cytyc Thinprep® processing of urinary samples: a qualitative approach
Authors: Piaton Eric , Faÿnel Jacqueline , Hutin Karine , Ranchin Marie-Claude , Cottier Michèle 
Published: October 2005

Abstract

Background
The aim of our study was to objectively compare Cytyc Thinprep® and other methods of obtaining thin layer cytologic preparations (cytocentrifugation, direct smearing and Millipore® filtration) in urine cytopathology.

Methods
Thinprep slides were compared to direct smears in 79 cases. Cytocentrifugation carried out with the Thermo Shandon Cytospin® 4 was compared to Thinprep in 106 cases, and comparison with Millipore filtration followed by blotting was obtained in 22 cases. Quality was assessed by scoring cellularity, fixation, red blood cells, leukocytes and nuclear abnormalities.

Results
The data show that 1) smearing allows good overall results to be obtained, 2) Cytocentrifugation with reusable TPX® chambers should be avoided, 3) Cytocentrifugation using disposable chambers (Cytofunnels® or Megafunnel® chambers) gives excellent results equalling or surpassing Thinprep and 4) Millipore filtration should be avoided, owing to its poor global quality. Despite differences in quality, the techniques studied have no impact on the diagnostic accuracy as evaluated by the rate of abnormalities.

Conclusion
We conclude that conventional methods such as cytocentrifugation remain the most appropriate ones for current treatment of urinary samples. Cytyc Thinprep processing, owing to its cost, could be used essentially for cytology-based molecular studies.
Validity of a self-administered food frequency questionnaire (FFQ) and its generalizability to the estimation of dietary folate intake in Japan
Authors: Ishihara Junko , Yamamoto Seiichiro , Iso Hiroyasu , Inoue Manami , Tsugane Shoichiro ,   the JPHC FFQ Validation Study Group
Published: October 2005

Abstract

Background
In an epidemiological study, it is essential to test the validity of the food frequency questionnaire (FFQ) for its ability to estimate dietary intake. The objectives of our study were to 1) validate a FFQ for estimating folate intake, and to identify the foods that contribute to inter-individual variation of folate intake in the Japanese population.

Methods
Validity of the FFQ was evaluated using 28-day weighed dietary records (DRs) as gold standard in the two groups independently. In the group for which the FFQ was developed, validity was evaluated by Spearman's correlation coefficients (CCs), and linear regression analysis was used to identify foods with large inter-individual variation. The cumulative mean intake of these foods was compared with total intake estimated by the DR. The external validity of the FFQ and intake from foods on the same list were evaluated in the other group to verify generalizability. Subjects were a subsample from the Japan Public Health Center-based prospective Study who volunteered to participate in the FFQ validation study.

Results
CCs for the internal validity of the FFQ were 0.49 for men and 0.29 and women, while CCs for external validity were 0.33 for men and 0.42 for women. CCs for cumulative folate intake from 33 foods selected by regression analysis were also applicable to an external population.

Conclusion
Our FFQ was valid for and generalizable to the estimation of folate intake. Foods identified as predictors of inter-individual variation in folate intake were also generalizable in Japanese populations. The FFQ with 138 foods was valid for the estimation of folate intake, while that with 33 foods might be useful for estimating inter-individual variation and ranking of individual folate intake.