bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of case-parent trios at a locus with a deletion allele: association of GSTM1 with autism
Authors: Buyske Steven , Williams Tanishia A , Mars Audrey E , Stenroos Edward S , Ming Sue X , Wang Rong , Sreenath Madhura , Factura Marivic F , Reddy Chitra , Lambert George H , Johnson William G 
Published: February 2006

AbstractBackgroundCertain loci on the human genome, such as glutathione S-transferase M1 (GSTM1), do not permit heterozygotes to be reliably determined by commonly used methods. Association of such a locus with a disease is therefore generally tested with a case-control design. When subjects have already been ascertained in a case-parent design however, the question arises as to whether the data can still be used to test disease association at such a locus.ResultsA likelihood ratio test was constructed that can be used with a case-parents design but has somewhat less power than a Pearson's chi-squared test that uses a case-control design. The test is illustrated on a novel dataset showing a genotype relative risk near 2 for the homozygous GSTM1 deletion genotype and autism.ConclusionAlthough the case-control design will remain the mainstay for a locus with a deletion, the likelihood ratio test will be useful for such a locus analyzed as part of a larger case-parent study design. The likelihood ratio test has the advantage that it can incorporate complete and incomplete case-parent trios as well as independent cases and controls. Both analyses support (p= 0.046 for the proposed test,p= 0.028 for the case-control analysis) an association of the homozygous GSTM1 deletion genotype with autism.
Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment
Authors: Ricard Guénola , McEwan Neil R , Dutilh Bas E , Jouany Jean-Pierre , Macheboeuf Didier , Mitsumori Makoto , McIntosh Freda M , Michalowski Tadeusz , Nagamine Takafumi , Nelson Nancy , Newbold Charles J , Nsabimana Eli , Takenaka Akio , Thomas Nadine A , Ushida Kazunari , Hackstein Johannes HP , Huynen Martijn A 
Published: February 2006

Abstract

Background
The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium).

Results
A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates.

Conclusion
Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.
Transcriptome analysis of a cnidarian – dinoflagellate mutualism reveals complex modulation of host gene expression
Authors: Rodriguez-Lanetty Mauricio , Phillips Wendy S , Weis Virginia M 
Published: February 2006

Abstract

Background
Cnidarian – dinoflagellate intracellular symbioses are one of the most important mutualisms in the marine environment. They form the trophic and structural foundation of coral reef ecosystems, and have played a key role in the evolutionary radiation and biodiversity of cnidarian species. Despite the prevalence of these symbioses, we still know very little about the molecular modulators that initiate, regulate, and maintain the interaction between these two different biological entities. In this study, we conducted a comparative host anemone transcriptome analysis using a cDNA microarray platform to identify genes involved in cnidarian – algal symbiosis.

Results
We detected statistically significant differences in host gene expression profiles between sea anemones (Anthopleura elegantissima) in a symbiotic and non-symbiotic state. The group of genes, whose expression is altered, is diverse, suggesting that the molecular regulation of the symbiosis is governed by changes in multiple cellular processes. In the context of cnidarian – dinoflagellate symbioses, we discuss pivotal host gene expression changes involved in lipid metabolism, cell adhesion, cell proliferation, apoptosis, and oxidative stress.

Conclusion
Our data do not support the existence of symbiosis-specific genes involved in controlling and regulating the symbiosis. Instead, it appears that the symbiosis is maintained by altering expression of existing genes involved in vital cellular processes. Specifically, the finding of key genes involved in cell cycle progression and apoptosis have led us to hypothesize that a suppression of apoptosis, together with a deregulation of the host cell cycle, create a platform that might be necessary for symbiont and/or symbiont-containing host cell survival. This first comprehensive molecular examination of the cnidarian – dinoflagellate associations provides critical insights into the maintenance and regulation of the symbiosis.
The expansion of the metazoan microRNA repertoire
Authors: Hertel Jana , Lindemeyer Manuela , Missal Kristin , Fried Claudia , Tanzer Andrea , Flamm Christoph , Hofacker Ivo L , Stadler Peter F ,   The Students of Bioinformatics Computer Labs 2004 and 2005
Published: February 2006

AbstractBackgroundMicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript.ResultsWe identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozen ancient microRNA clusters.ConclusionOur results suggest that microRNA innovation is an ongoing process. Major expansions of the metazoan miRNA repertoire coincide with the advent of bilaterians, vertebrates, and (placental) mammals.
Pooled DNA genotyping on Affymetrix SNP genotyping arrays
Authors: Kirov George , Nikolov Ivan , Georgieva Lyudmila , Moskvina Valentina , Owen Michael J , O'Donovan Michael C 
Published: February 2006

Abstract

Background
Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs.

Results
In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5–6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of < 3.2%.

Conclusion
Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.
Sex-dependent gene expression in early brain development of chicken embryos
Authors: Scholz Birger , Kultima Kim , Mattsson Anna , Axelsson Jeanette , Brunström Björn , Halldin Krister , Stigson Michael , Dencker Lennart 
Published: February 2006

AbstractBackgroundDifferentiation of the brain during development leads to sexually dimorphic adult reproductive behavior and other neural sex dimorphisms. Genetic mechanisms independent of steroid hormones produced by the gonads have recently been suggested to partly explain these dimorphisms.ResultsUsing cDNA microarrays and real-time PCR we found gene expression differences between the male and female embryonic brain (or whole head) that may be independent of morphological differentiation of the gonads. Genes located on the sex chromosomes (ZZ in males and ZW in females) were common among the differentially expressed genes, several of which (WPKCI-8,HINT,MHM non-coding RNA) have previously been implicated in avian sex determination. A majority of the identified genes were more highly expressed in males. Three of these genes (CDK7,CCNHandBTF2-P44) encode subunits of the transcription factor IIH complex, indicating a role for this complex in neuronal differentiation.ConclusionIn conclusion, this study provides novel insights into sexually dimorphic gene expression in the embryonic chicken brain and its possible involvement in sex differentiation of the nervous system in birds.
Older adults' beliefs about physician-estimated life expectancy: a cross-sectional survey
Authors: Kistler Christine E , Lewis Carmen L , Amick Halle R , Bynum Debra L , Walter Louise C , Watson Lea C 
Published: February 2006

Abstract

Background
Estimates of life expectancy assist physicians and patients in medical decision-making. The time-delayed benefits for many medical treatments make an older adult's life expectancy estimate particularly important for physicians. The purpose of this study is to assess older adults' beliefs about physician-estimated life expectancy.

Methods
We performed a mixed qualitative-quantitative cross-sectional study in which 116 healthy adults aged 70+ were recruited from two local retirement communities. We interviewed them regarding their beliefs about physician-estimated life expectancy in the context of a larger study on cancer screening beliefs. Semi-structured interviews of 80 minutes average duration were performed in private locations convenient to participants. Demographic characteristics as well as cancer screening beliefs and beliefs about life expectancy were measured. Two independent researchers reviewed the open-ended responses and recorded the most common themes. The research team resolved disagreements by consensus.

Results
This article reports the life-expectancy results portion of the larger study. The study group (n = 116) was comprised of healthy, well-educated older adults, with almost a third over 85 years old, and none meeting criteria for dementia. Sixty-four percent (n = 73) felt that their physicians could not correctly estimate their life expectancy. Sixty-six percent (n = 75) wanted their physicians to talk with them about their life expectancy. The themes that emerged from our study indicate that discussions of life expectancy could help older adults plan for the future, maintain open communication with their physicians, and provide them knowledge about their medical conditions.

Conclusion
The majority of the healthy older adults in this study were open to discussions about life expectancy in the context of discussing cancer screening tests, despite awareness that their physicians' estimates could be inaccurate. Since about a third of participants perceived these discussions as not useful or even harmful, physicians should first ascertain patients' preferences before discussing their life expectancies.
Diagnostic value of biochemical markers (FibroTest-FibroSURE) for the prediction of liver fibrosis in patients with non-alcoholic fatty liver disease
Authors: Ratziu Vlad , Massard Julien , Charlotte Frederic , Messous Djamila , Imbert-Bismut Françoise , Bonyhay Luninita , Tahiri Mohamed , Munteanu Mona , Thabut Dominique , Cadranel Jean François , Le Bail Brigitte , de Ledinghen Victor , Poynard Thierry ,   for the LIDO Study Group and the CYTOL study group
Published: February 2006

Abstract

Background
Liver biopsy is considered as the gold standard for assessing non-alcoholic fatty liver disease (NAFLD) histologic lesions. The aim of this study was to determine the diagnostic utility of non-invasive markers of fibrosis, validated in chronic viral hepatitis and alcoholic liver disease (FibroTest, FT), in patients with NAFLD.

Methods
170 patients with suspected NAFLD were prospectively included in a reference center (Group 1), 97 in a multicenter study (Group 2) and 954 blood donors as controls. Fibrosis was assessed on a 5 stage histological scale validated by Kleiner et al from F0 = none, F1 = perisinusoidal or periportal, F2 = perisinusoidal and portal/periportal, F3 = bridging and F4 = cirrhosis. Histology and the biochemical measurements were blinded to any other characteristics. The area under the ROC curves (AUROC), sensitivity (Se), specificity (Sp), positive and negative predictive values (PPV, NPV) were assessed.

Results
In both groups FT has elevated and not different AUROCs for the diagnosis of advanced fibrosis (F2F3F4): 0.86 (95%CI 0.77–0.91) versus 0.75 (95%CI 0.61–0.83; P = 0.10), and for F3F4: 0.92 (95%CI 0.83–0.96) versus 0.81 (95%CI 0.64–0.91; P = 0.12) in Group1 and Group 2 respectively. When the 2 groups were pooled together a FT cutoff of 0.30 had a 90% NPV for advanced fibrosis (Se 77%); a FT cutoff of 0.70 had a 73% PPV for advanced fibrosis (Sp 98%).

Conclusion
In patients with NAFLD, FibroTest, a simple and non-invasive quantitative estimate of liver fibrosis reliably predicts advanced fibrosis.
Epidemiological trends in nosocomial candidemia in intensive care
Authors: Bassetti Matteo , Righi Elda , Costa Alessandro , Fasce Roberta , Molinari Maria Pia , Rosso Raffaella , Pallavicini Franco Bobbio , Viscoli Claudio 
Published: February 2006

Abstract

Background
Infection represents a frequent complication among patients in Intensive Care Units (ICUs) and mortality is high. In particular, the incidence of fungal infections, especially due to Candida spp., has been increasing during the last years.

Methods
In a retrospective study we studied the etiology of candidemia in critically ill patients over a five-year period (1999–2003) in the ICU of the San Martino University Hospital in Genoa, Italy.

Results
In total, 182 episodes of candidaemia were identified, with an average incidence of 2.22 episodes/10 000 patient-days/year (range 1.25–3.06 episodes). Incidence of candidemia increased during the study period from 1.25 in 1999 to 3.06/10 000 patient-days/year in 2003. Overall, 40% of the fungemia episodes (74/182) were due to C.albicans, followed by C. parapsilosis(23%), C.glabrata (15%), C.tropicalis (9%) and other species (13%). Candidemia due to non-albicans species increased and this was apparently correlated with an increasing use of azoles for prophylaxis or empirical treatment.

Conclusion
The study demonstrates a shift in the species of Candida causing fungemia in a medical and surgical ICU population during a 5 year period. The knowledge of the local epidemiological trends in Candida species isolated in blood cultures is important to guide therapeutic choices.
Patterns of sexually transmitted infections in adolescents and youth in Dar es Salaam, Tanzania
Authors: Chalamilla Guerino , Mbwana Judica , Mhalu Fred , Mmari Eunice , Majigo Mtebe , Swai Andrew , Urassa Willy , Sandstrom Eric 
Published: February 2006

Abstract

Background
Syndromic management of STIs has been advocated as simplified and cheap approach. Youth have been reported to be at increased risk of acquiring STIs which can facilitate HIV transmission. We have investigated the relationship between the syndromic management and specific aetiology diagnosis and its relationship with HIV infection and health seeking behaviour among youth attending a reproductive health clinic in Dar es Salaam, Tanzania.

Methods
Between September 1998 and February 1999 among 1895 adolescents and youth below 25 years seen in the clinic 199 (10.5%) were randomly selected and consented to participate in the study. A standard questionnaire was administered. Blood and vaginal or urethral specimens were taken and investigated for STI causative agents.

Results
Among a total of 199 studied adolescents and youth 22.6 % were teenagers, with fewer females 17.8% than males; 27.5% (p < 0.018). 20.8% of the females compared to 11.5% in males were HIV infected. Genital discharge was the most common complaint which was reported in 54.1% of male and 63.4 % of female patients. All males with gonorrhoea and four out of five with Chlamydia were given appropriate treatment with syndromic management, while 28% women with gonorrhoea or Chlamydia received appropriate treatment by syndromic management. All patients found with active syphilis by serology had not complained of genital ulcers and would not have been assigned to syndromic treatment for syphilis at the initial visit.

Conclusion
The burden of STIs in this youth population is large indicating that youth are at increased risk of STIs and will certainly require youth friendly clinics. There is a need to refine the current syndromic management guidelines.
Diagnostic accuracy of the neurological upper limb examination I: Inter-rater reproducibility of selected findings and patterns
Authors: Jepsen Jorgen R , Laursen Lise H , Hagert Carl-Goran , Kreiner Svend , Larsen Anders I 
Published: February 2006

Abstract

Background
We have previously assessed the reproducibility of manual testing of the strength in 14 individual upper limb muscles in patients with or without upper limb complaints. This investigation aimed at additionally studying sensory disturbances, the mechanosensitivity of nerve trunks, and the occurrence of physical findings in patterns which may potentially reflect a peripheral neuropathy. The reproducibility of this part of the neurological examination has never been reported.

Methods
Two blinded examiners performed a semi-quantitative assessment of 82 upper limbs (strength in 14 individual muscles, sensibility in 7 homonymous territories, and mechanosensitivity of nerves at 10 locations). Based on the topography of nerves and their muscular and cutaneous innervation we defined 10 neurological patterns each suggesting a focal neuropathy. The individual findings and patterns identified by the two examiners were compared.

Results
Strength, sensibility to touch, pain and vibration, and mechanosensitivity were predominantly assessed with moderate to very good reproducibility (median κ-values 0.54, 0.69, 0.48, 0.58, and 0.53, respectively). The reproducibility of the defined patterns was fair to excellent (median correlation coefficient = 0.75) and the overall identification of limbs with/without pattern(s) was good (κ = 0.75).

Conclusion
This first part of a study on diagnostic accuracy of a selective neurological examination has demonstrated a promising inter-rater reproducibility of individual neurological items and patterns. Generalization and clinical feasibility require further documentation: 1) Reproducibility in cohorts of other composition, 2) validity with comparison to currently applied standards, and 3) potential benefits that can be attained by the examination.
How much attention is needed towards men who sell sex to men for HIV prevention in India?
Authors: Dandona Lalit , Dandona Rakhi , Kumar G Anil , Gutierrez Juan Pablo , McPherson Sam , Bertozzi Stefano M ,   the ASCI FPP Study Team
Published: February 2006

Abstract

Background
HIV prevention in India has mostly focussed on heterosexual transmission. Data on homosexual transmission are not readily available from India. We therefore assessed the probability of acquiring and transmitting HIV for men who sell sex to men and compared this with women who sell sex in India.

Methods
Sexual behaviour characteristics of 6661 men who have sex with men and 6648 women who sell sex were obtained in the Indian state of Andhra Pradesh through confidential interviews. These, along with estimates of HIV rates among them and risk of HIV transmission per unprotected sex act from other sources, were used to calculate their annual probability of acquiring and transmitting HIV.

Results
Of 6661 men who have sex with men in this sample, 1776 (26.7%) had sold sex to men. For every 1000 men who sell sex to men, annually 146 (95% confidence interval [CI] 116–179) would acquire HIV and HIV would be transmitted to 55 (95% CI 42–71) men who do not sell sex or women. These estimates were higher by 6.7 (95% CI 4.9–9.2) times for acquiring HIV and 2.5 (95% CI 2.0–3.2) times for transmitting HIV to sex partners outside their group, as compared with similar estimates for women who sell sex. In this sample, the average annual probability of acquiring HIV was higher among men who have sex with men but do not sell sex as compared with women who sell sex.

Conclusion
These data indicate that men who sell sex to men are at much higher risk of acquiring and transmitting HIV than women who sell sex. Therefore, men who sell sex to men and their clients warrant substantial attention for comprehensive HIV prevention in India.