bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the models handling heterotachy in phylogenetic inference
Authors: Zhou Yan , Rodrigue Nicolas , Lartillot Nicolas , Philippe Hervé 
Published: November 2007

AbstractBackgroundThe evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the commonly used models of sequence evolution. These observations have motivated the development of models that explicitly recognize heterotachy, with research directions proposed along two main axes: 1) thecovarionapproach, where sites switch from variable to invariable states; and 2) themixture of branch lengths(MBL) approach, where alignment patterns are assumed to arise from one of several sets of branch lengths, under a given phylogeny.ResultsHere, we report the first statistical comparisons contrasting the performance of covarion and MBL modeling strategies. Using simulations under heterotachous conditions, we explore the properties of three model comparison methods: the Akaike information criterion, the Bayesian information criterion, and cross validation. Although more time consuming, cross validation appears more reliable than AIC and BIC as it directly measures the predictive power of a model on 'future' data. We also analyze three large datasets (nuclear proteins of animals, mitochondrial proteins of mammals, and plastid proteins of plants), and find the optimal number of components of the MBL model to be two for all datasets, indicating that this model is preferred over the standard homogeneous model. However, the covarion model is always favored over the optimal MBL model.ConclusionWe demonstrated, using three large datasets, that the covarion model is more efficient at handling heterotachy than the MBL model. This is probably due to the fact that the MBL model requires a serious increase in the number of parameters, as compared to two supplementary parameters of the covarion approach. Further improvements of the both the mixture and the covarion approaches might be obtained by modeling heterogeneous behavior both along time and across sites.
Patterns of selective constraints in noncoding DNA of rice
Authors: Guo Xingyi , Wang Yu , Keightley Peter D , Fan Longjiang 
Published: November 2007

Abstract

Background
Several studies have investigated the relationships between selective constraints in introns and their length, GC content and location within genes. To date, however, no such investigation has been done in plants. Studies of selective constraints in noncoding DNA have generally involved interspecific comparisons, under the assumption of the same selective pressures acting in each lineage. Such comparisons are limited to cases in which the noncoding sequences are not too strongly diverged so that reliable sequence alignments can be obtained. Here, we investigate selective constraints in a recent segmental duplication that includes 605 paralogous intron pairs that occurred about 7 million years ago in rice (O. sativa).

Results
Our principal findings are: (1) intronic divergence is negatively correlated with intron length, a pattern that has previously been described in Drosophila and mammals; (2) there is a signature of strong purifying selection at splice control sites; (3) first introns are significantly longer and have a higher GC content than other introns; (4) the divergences of first and non-first introns are not significantly different from one another, a pattern that differs from Drosophila and mammals; and (5) short introns are more diverged than four-fold degenerate sites suggesting that selection reduces divergence at four-fold sites.

Conclusion
Our observation of stronger selective constraints in long introns suggests that functional elements subject to purifying selection may be concentrated within long introns. Our results are consistent with the presence of strong purifying selection at splicing control sites. Selective constraints are not significantly stronger in first introns of rice, as they are in other species.
Role of NOD2/CARD15 in coronary heart disease
Authors: El Mokhtari Nour Eddine , Ott Stephan J , Nebel Almut , Schäfer Arne , Rosenstiel Philip , Förster Matti , Nothnagel Michael , Simon Rüdiger , Schreiber Stefan 
Published: November 2007

Abstract

Background:
Bacterial DNA has been repeatedly detected in atheromatous lesions of coronary heart disease (CHD) patients. Phylogenetic signatures in the atheroma lesions that are similar to those of bacterial biofilms on human barrier organs, including the respiratory or gastrointestinal tract, raise the question of a defective barrier function in CHD. NOD2 plays a major role in defense against bacterial invasion. Genetic variation in the CARD15 gene, which encodes NOD2, was previously shown to result in a barrier defect that causes chronic inflammatory disorders (e.g. Crohn disease). In the present study, we investigated the possible involvement of NOD2/CARD15 in the pathology of CHD by i) analyzing the local expression of NOD2 in atherectomy versus healthy tissue (n = 5 each) using histochemical immunofluorescence and ii) by testing the three major functional CARD15 variants (R702W, G908R and 1007fs) for association with early-onset CHD in 900 German patients and 632 healthy controls.

Results:
In atherectomy tissue of CHD patients, NOD2 was detected in inflammatory cells at the luminal sides of the lesions. However, the allele and genotype frequencies of the three major CARD15 polymorphisms did not differ between CHD patients and controls.

Conclusion:
The NOD2 up-regulation in atheroma lesions indicates an involvement of this protein in the pathology of CHD. Although NOD2 could be important in local immune response mechanisms, none of the analyzed CARD15 variants seem to play a significant role in the etiology of CHD.
Cigarette smoking and tooth loss experience among young adults: a national record linkage study
Authors: Ojima Miki , Hanioka Takashi , Tanaka Keiko , Aoyama Hitoshi 
Published: November 2007

Abstract

Background
Various factors affect tooth loss in older age including cigarette smoking; however, evidence regarding the association between smoking and tooth loss during young adulthood is limited. The present study examined the association between cigarette smoking and tooth loss experience among adults aged 20–39 years using linked data from two national databases in Japan.

Methods
Two databases of the National Nutrition Survey (NNS) and the Survey of Dental Diseases (SDD), which were conducted in 1999, were obtained from the Ministry of Health, Labor and Welfare with permission for analytical use. In the NNS, participants received physical examinations and were interviewed regarding dietary intake and health practices including cigarette smoking, whereas in the SDD, participants were asked about their frequency of daily brushing, and received oral examinations by certified dentists. Among 6,805 records electronically linked via household identification code, 1314 records of individuals aged 20 to 39 years were analyzed. The prevalence of 1+ tooth loss was compared among non-, former, and current smokers. Multiple logistic regression models were constructed including confounders: frequency of tooth brushing, body mass index, alcohol consumption, and intake of vitamins C and E.

Results
Smoking rates differed greatly in men (53.3%) and women (15.5%). The overall prevalence of tooth loss was 31.4% (31.8% men and 31.1% women). Tooth loss occurred more frequently among current smokers (40.6%) than former (23.1%) and non-smokers (27.9%). Current smoking showed a significant association with 1+ tooth loss in men (adjusted OR = 2.21 [1.40–3.50], P = 0.0007) and women (1.70 [1.13–2.55], P = 0.0111). A significant positive exposure-related relationship between cigarette smoking status and tooth loss was observed (P for trend < 0.0001 and 0.0004 in men and women, respectively). Current smoking was also associated with the prevalence of decayed teeth (1.67 [1.28–2.20], P = 0.0002).

Conclusion
An association between cigarette smoking and tooth loss was evident among young adults throughout Japan. Due to limitations of the available variables in the present databases, further studies including caries experience and its confounders should be conducted to examine whether smoking is a true risk of premature tooth loss in young adults.
Training pediatric health care providers in prevention of dental decay: results from a randomized controlled trial
Authors: Slade Gary D , Rozier R Gary , Zeldin Leslie P , Margolis Peter A 
Published: November 2007

Abstract
Background
Physicians report willingness to provide preventive dental care, but optimal methods for their training and support in such procedures are not known. This study aimed to evaluate the effect of three forms of continuing medical education (CME) on provision of preventive dental services to Medicaid-enrolled children by medical personnel in primary care physician offices.

Methods
Practice-based, randomized controlled trial. Setting: 1,400 pediatric and family physician practices in North Carolina providing care to an estimated 240,000 Medicaid-eligible children aged 0–3 years. Interventions: Group A practices (n = 39) received didactic training and course materials in oral health screening, referral, counseling and application of fluoride varnish. Group B practices (n = 41) received the same as Group A and were offered weekly conference calls providing advice and support. Group C practices (n = 41) received the same as Group B and were offered in-office visit providing hands-on advice and support. In all groups, physicians were reimbursed $38–$43 per preventive dental visit. Outcome measures were computed from reimbursement claims submitted to NC Division of Medical Assistance. Primary outcome measure: rate of preventive dental services provision per 100 well-child visits. Secondary outcome measure: % of practices providing 20 or more preventive dental visits.

Results
121 practices were randomized, and 107 provided data for analysis. Only one half of Group B and C practices took part in conference calls or in-office visits. Using intention-to-treat analysis, rates of preventive dental visits did not differ significantly among CME groups: GroupA = 9.4, GroupB = 12.9 and GroupC = 8.5 (P = 0.32). Twenty or more preventive dental visits were provided by 38–49% of practices in the three study groups (P = 0.64).

Conclusion
A relatively high proportion of medical practices appear capable of adopting these preventive dental services within a one year period regardless of the methods used to train primary health care providers.

Trial Registration
ClinicalTrials.gov NCT00464009
Regular mosaic pattern development: A study of the interplay between lateral inhibition, apoptosis and differential adhesion
Authors: Podgorski Gregory J , Bansal Mayank , Flann Nicholas S 
Published: November 2007

Abstract

Background
A significant body of literature is devoted to modeling developmental mechanisms that create patterns within groups of initially equivalent embryonic cells. Although it is clear that these mechanisms do not function in isolation, the timing of and interactions between these mechanisms during embryogenesis is not well known. In this work, a computational approach was taken to understand how lateral inhibition, differential adhesion and programmed cell death can interact to create a mosaic pattern of biologically realistic primary and secondary cells, such as that formed by sensory (primary) and supporting (secondary) cells of the developing chick inner ear epithelium.

Results
Four different models that interlaced cellular patterning mechanisms in a variety of ways were examined and their output compared to the mosaic of sensory and supporting cells that develops in the chick inner ear sensory epithelium. The results show that: 1) no single patterning mechanism can create a 2-dimensional mosaic pattern of the regularity seen in the chick inner ear; 2) cell death was essential to generate the most regular mosaics, even through extensive cell death has not been reported for the developing basilar papilla; 3) a model that includes an iterative loop of lateral inhibition, programmed cell death and cell rearrangements driven by differential adhesion created mosaics of primary and secondary cells that are more regular than the basilar papilla; 4) this same model was much more robust to changes in homo- and heterotypic cell-cell adhesive differences than models that considered either fewer patterning mechanisms or single rather than iterative use of each mechanism.

Conclusion
Patterning the embryo requires collaboration between multiple mechanisms that operate iteratively. Interlacing these mechanisms into feedback loops not only refines the output patterns, but also increases the robustness of patterning to varying initial cell states.
Serum epidermal growth factor receptor and HER2 expression in primary and metastatic breast cancer patients
Authors: Asgeirsson Kristjan S , Agrawal Amit , Allen Claire , Hitch Anthony , Ellis Ian O , Chapman Caroline , Cheung Kwok L , Robertson John FR 
Published: November 2007

Abstract
Background
Breast tissue expression of the ERBB proto-oncogene family has been extensively studied. It was recently shown that expression of epidermal growth factor receptor (EGFR; c-erbB-1) and epidermal growth factor receptor (HER)2 (c-erbB-2) can be detected in the serum of breast cancer patients. The clinical relevance of this has not been fully established.

Methods
EGFR and HER2 immunoassays were conducted in blood from 57 patients in whom paired serum samples were available (from the times of primary and metastatic diagnoses), from 96 primary breast cancer patients and from 49 normal individuals. Of the 57 patients with paired serum samples, paired tissue samples for HER2 expression were available for eight.

Results
Serum levels of EGFR serum levels were significantly higher in normal individuals (median 75.3 ng/ml, range 43.2 to 114.2 ng/ml) than in patients with primary breast cancer (median 59.3 ng/ml, range 21.3 to 94.1 ng/ml; P < 0.001). In the paired serum samples, EGFR levels decreased significantly between the time of primary diagnosis (median 56.3 ng/ml, range 29.1 to 142.7 ng/ml) and metastatic diagnosis (median 30.9 ng/ml, range 10.9 to 106.4 ng/ml; P < 0.001). In six (11%) a change occurred from over-expression (>78 ng/ml) to normal expression. In contrast, no significant difference was seen in HER2 serum levels in normal individuals (median 12.2 ng/ml, range 7.8 to 20.9 ng/ml) and primary breast cancer patients (median 12.5 ng/ml, range 6.9 to 122.2 ng/ml; P = 0.511). However, in the paired serum samples, HER2 levels increased significantly between the time of primary (median 12.2 ng/ml, range 5.7 to 85.0 ng/ml) and metastasis (median 17.7 ng/ml, range 6.3 to 3,337.4 ng/ml; P < 0.001). HER2 over-expression (>15 ng/ml) was observed in 16 out of 57 patients (28%) at primary breast cancer diagnosis and in 31 out of 57 (54%) at metastasis. In 18 patients (32%) HER2 expression changed from normal to over-expression.

Conclusion
Decisions regarding the use of targeted therapies in the metastatic setting are often based on the oncogene expression of the primary tumour. Our results suggest that serum oncogene assessments may be complementary to this and could potentially widen the indications for these beneficial therapies.
Identification of the functional role of peroxiredoxin 6 in the progression of breast cancer
Authors: Chang Xin-Zhong , Li Da-Qiang , Hou Yi-Feng , Wu Jiong , Lu Jin-Song , Di Gen-Hong , Jin Wei , Ou Zhou-Luo , Shen Zhen-Zhou , Shao Zhi-Ming 
Published: November 2007

Abstract
Introduction
The molecular mechanisms involved in breast cancer metastasis still remain unclear to date. In our previous study, differential expression of peroxiredoxin 6 was found between the highly metastatic MDA-MB-435HM cells and their parental counterparts, MDA-MB-435 cells. In this study, we investigated the effects of peroxiredoxin 6 on the proliferation and metastatic potential of human breast cancer cells and their potential mechanism.

Methods
Expression of peroxiredoxin 6 in the highly metastatic MDA-MB-231HM cells was investigated by RT-PCR, real-time PCR and western blot. A recombinant expression plasmid of the human peroxiredoxin 6 gene was constructed and transfected into MDA-MB-231 and MDA-MB-435 cells. The effects of peroxiredoxin 6 on the proliferation and invasion of MDA-MB-231 and MDA-MB-435 cells were investigated by the Cell Counting Kit-8 method, colony-formation assay, adhesion assay, flow cytometry and invasion assay in vitro. miRNA was used to downregulate the expression of peroxiredoxin 6. Genes related to the invasion and metastasis of cancer were determined by RT-PCR, real-time PCR and western blot. The tumorigenicity and spontaneously metastatic capability regulated by peroxiredoxin 6 were determined using an orthotopic xenograft tumor model in athymic mice.

Results
Overexpression of peroxiredoxin 6 in MDA-MB-231HM cells compared with their parental counterparts was confirmed. Upregulation of peroxiredoxin 6 enhanced the in vitro proliferation and invasion of breast cancer cells. The enhancement was associated with decreasing levels of tissue inhibitor of matrix metalloproteinase (TIMP)-2 and increasing levels of the urokinase-type plasminogen activator receptor (uPAR), Ets-1 (E26 transformation-specific-1), matrix metalloproteinase (MMP)-9 and RhoC (ras homolog gene family, member C) expression. The results were further demonstrated by RNA interference experiments in vitro. In an in vivo study, we also demonstrated that peroxiredoxin 6-transfected breast cancer cells grew much faster and had more pulmonary metastases than control cells. By contrast, peroxiredoxin 6 knockdown breast cancer cells grew more slowly and had fewer pulmonary metastases. Effects similar to those of peroxiredoxin 6 on the uPAR, Ets-1, MMP-9, RhoC and TIMP-2 expression observed in in vitro studies were found in the in vivo study.

Conclusion
Overexpression of peroxiredoxin 6 leads to a more invasive phenotype and metastatic potential in human breast cancer, at least in part, through regulation of the levels of uPAR, Ets-1, MMP-9, RhoC and TIMP-2 expression.
Determinants of protein function revealed by combinatorial entropy optimization
Authors: Reva Boris , Antipin Yevgeniy , Sander Chris 
Published: November 2007

AbstractWe use a new algorithm (combinatorial entropy optimization [CEO]) to identify specificity residues and functional subfamilies in sets of proteins related by evolution. Specificity residues are conserved within a subfamily but differ between subfamilies, and they typically encode functional diversity. We obtain good agreement between predicted specificity residues and experimentally known functional residues in protein interfaces. Such predicted functional determinants are useful for interpreting the functional consequences of mutations in natural evolution and disease.
Vimentin autoantibodies induce platelet activation and formation of platelet-leukocyte conjugates via platelet-activating factor
Authors: Leong H S , Mahesh B M , Day J R , Smith J D , McCormack A D , Ghimire G , Podor T J , Rose M L 
Published: November 2007

AbstractAnti-vimentin antibodies (AVA) are associated with autoimmunity and solid organ transplantation, conditions associated with vascular disease, but their contribution to disease pathogenesis is unknown. Here, we have examined interactions between AVA (mAb and serum from patients) and various leukocyte populations using whole blood and flow cytometry. Normal blood treated with patient sera containing high AVA-IgM titers or with a vimentin-specific monoclonal IgM led to activation of platelets and other leukocytes, as demonstrated by induced expression of P-selectin, fibrinogen, tissue factor, and formation of platelet:leukocyte (P:L) conjugates and a reduction in platelet counts. This activity was antigen (vimentin)-specific and was not mediated by irrelevant IgM antibodies. Flow cytometry demonstrated that AVA do not bind directly to resting platelets in whole blood, but they bind to ∼10% of leukocytes. Supernatant, derived from AVA-treated leukocytes, induced platelet activation, as measured by the generation of platelet microparticles, when added to platelet-rich plasma. When AVA were added to whole blood in the presence of CV-6209, a platelet-activating factor (PAF) receptor inhibitor, platelet depletion was inhibited. This suggests that PAF is one of the mediators released from AVA-activated leukocytes that leads to P:L conjugation formation and platelet activation. In summary, AVA bind to leukocytes, resulting in release of a PAF and prothrombotic factor that exert a paracrine-activating effect on platelets. Overall, this proposed mechanism may explain the pathogenesis of thrombotic events in autoimmune diseases associated with AVA.
Sound production and spectral hearing sensitivity in the Hawaiian sergeant damselfish, Abudefduf abdominalis
Authors: Maruska Karen P. , Boyle Kelly S. , Dewan Laura R. , Tricas Timothy C. 
Published: November 2007

SUMMARY
Sounds provide important signals for inter- and intraspecific communication in fishes, but few studies examine fish acoustic behavior in the context of coevolution of sound production and hearing ability within a species. This study characterizes the acoustic behavior in a reproductive population of the Hawaiian sergeant fish, Abudefduf abdominalis, and compares acoustic features to hearing ability, measured by the auditory evoked potential (AEP)technique. Sergeant fish produce sounds at close distances to the intended receiver (⩽1–2 body lengths), with different pulse characteristics that are associated primarily with aggression, nest preparation and courtship–female-visit behaviors. Energy peaks of all sounds were between 90 and 380 Hz, whereas courtship–visit sounds had a pulse repetition rate of 125 Hz with harmonic intervals up to 1 kHz. AEP threshold,which is probably higher than the behavioral threshold, indicates best sensitivity at low frequencies (95–240 Hz), with the lowest threshold at 125 Hz (123–127 dBrms re: 1 μPa). Thus, sound production and hearing in A. abdominalis are closely matched in the frequency domain and are useful for courtship and mating at close distances. Measured hearing thresholds did not differ among males and females during spawning or non-spawning periods, which indicates a lack of sex differences and seasonal variation in hearing capabilities. These data provide the first evidence that Abudefduf uses true acoustic communication on a level similar to that of both more derived (e.g. Dascyllus, Chromis) and more basal (e.g. Stegastes) soniferous pomacentrids. This correlation between sound production and hearing ability is consistent with the sensory drive model of signal evolution in which the sender and receiver systems coevolve within the constraints of the environment to maximize information transfer of acoustic signals.