bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalizations of Markov model to characterize biological sequences
Authors: Wang Junwen , Hannenhalli Sridhar 
Published: September 2005

AbstractBackgroundThe currently usedkthorder Markov models estimate the probability of generating asinglenucleotide conditional upon the immediately preceding (gap= 0)kunits. However, this neither takes into account the joint dependency ofmultipleneighboring nucleotides, nor does it consider the long range dependency withgap>0.ResultWe describe a configurable tool to explore generalizations of the standard Markov model. We evaluated whether the sequence classification accuracy can be improved by using an alternative set of model parameters. The evaluation was done on four classes of biological sequences – CpG-poor promoters, all promoters, exons and nucleosome positioning sequences. Using di- and tri-nucleotide as the model unit significantly improved the sequence classification accuracy relative to the standard single nucleotide model. In the case of nucleosome positioning sequences, optimal accuracy was achieved at agaplength of 4. Furthermore in the plot of classification accuracy versus the gap, a periodicity of 10–11 bps was observed which might indicate structural preferences in the nucleosome positioning sequence. The tool is implemented in Java and is available for download atftp://ftp.pcbi.upenn.edu/GMM/.ConclusionMarkov modeling is an important component of many sequence analysis tools. We have extended the standard Markov model to incorporate joint and long range dependencies between the sequence elements. The proposed generalizations of the Markov model are likely to improve the overall accuracy of sequence analysis tools.
No evidence for the association of DRD4 with ADHD in a Taiwanese population within-family study
Authors: Brookes Keeley-Joanne , Xu Xiaohui , Chen Chih-Ken , Huang Yu-Shu , Wu Yu-Yu , Asherson Philip 
Published: September 2005

AbstractBackgroundAttention Deficit Hyperactivity Disorder (ADHD) is a prevalent and highly heritable childhood disorder. The dopamine D4 receptor (DRD4) gene has shown a genetic association with ADHD in Caucasian populations with meta-analysis indicating a small but significant effect across datasets. It remains uncertain whether this association can be generalised to non-Caucasian ethnic groups. Here we investigate two markers within the DRD4 gene in a Taiwanese population, the exon 3 variable number tandem repeat (VNTR) and a 5' 120 base-pair duplication.MethodsWithin-family transmission disequilibrium tests of association of the 5' 120 base-pair duplication, and exon 3 VNTR in a Taiwanese population.ResultsNo evidence of association of ADHD with either polymorphism in this population was observed.ConclusionThe DRD4 gene markers investigated were not found to be associated with ADHD in this Taiwanese sample. Further work in Taiwanese and other Asian populations will therefore be required to establish whether the reports of association of DRD4 genetic variants in Caucasian samples can be generalised to Asian populations.
Equal antipyretic effectiveness of oral and rectal acetaminophen: a randomized controlled trial [ISRCTN11886401]
Authors: Nabulsi Mona , Tamim Hala , Sabra Ramzi , Mahfoud Ziyad , Malaeb Shadi , Fakih Hadi , Mikati Mohammad 
Published: September 2005

Abstract

Background
The antipyretic effectiveness of rectal versus oral acetaminophen is not well established. This study is designed to compare the antipyretic effectiveness of two rectal acetaminophen doses (15 mg/kg) and (35 mg/kg), to the standard oral dose of 15 mg/kg.

Methods
This is a randomized, double-dummy, double-blind study of 51 febrile children, receiving one of three regimens of a single acetaminophen dose: 15 mg/kg orally, 15 mg/kg rectally, or 35 mg/kg rectally. Rectal temperature was monitored at baseline and hourly for a total of six hours. The primary outcome of the study, time to maximum antipyresis, and the secondary outcome of time to temperature reduction by at least 1°C were analyzed by one-way ANOVA. Two-way ANOVA with repeated measures over time was used to compare the secondary outcome: change in temperature from baseline at times1, 2, 3, 4, 5, and 6 hours among the three groups. Intent-to-treat analysis was planned.

Results
No significant differences were found among the three groups in the time to maximum antipyresis (overall mean = 3.6 hours; 95% CI: 3.2–4.0), time to fever reduction by 1°C or the mean hourly temperature from baseline to 6 hours following dose administration. Hypothermia (temperature < 36.5°C) occurred in 11(21.6%) subjects, with the highest proportion being in the rectal high-dose group.

Conclusion
Standard (15 mg/kg) oral, (15 mg/kg) rectal, and high-dose (35 mg/kg) rectal acetaminophen have similar antipyretic effectiveness.
Ensuring safety of DNA vaccines
Authors: Glenting Jacob , Wessels Stephen 
Published: September 2005

Abstract
In 1990 a new approach for vaccination was invented involving injection of plasmid DNA in vivo, which elicits an immune response to the encoded protein. DNA vaccination can overcome most disadvantages of conventional vaccine strategies and has potential for vaccines of the future. However, today 15 years on, a commercial product still has not reached the market. One possible explanation could be the technique's failure to induce an efficient immune response in humans, but safety may also be a fundamental issue. This review focuses on the safety of the genetic elements of DNA vaccines and on the safety of the microbial host for the production of plasmid DNA. We also propose candidates for the vaccine's genetic elements and for its microbial production host that can heighten the vaccine's safety and facilitate its entry to the market.
Mining for diagnostic information in body surface potential maps: A comparison of feature selection techniques
Authors: Finlay Dewar D , Nugent Chris D , McCullagh Paul J , Black Norman D 
Published: September 2005

Abstract

Background
In body surface potential mapping, increased spatial sampling is used to allow more accurate detection of a cardiac abnormality. Although diagnostically superior to more conventional electrocardiographic techniques, the perceived complexity of the Body Surface Potential Map (BSPM) acquisition process has prohibited its acceptance in clinical practice. For this reason there is an interest in striking a compromise between the minimum number of electrocardiographic recording sites required to sample the maximum electrocardiographic information.

Methods
In the current study, several techniques widely used in the domains of data mining and knowledge discovery have been employed to mine for diagnostic information in 192 lead BSPMs. In particular, the Single Variable Classifier (SVC) based filter and Sequential Forward Selection (SFS) based wrapper approaches to feature selection have been implemented and evaluated. Using a set of recordings from 116 subjects, the diagnostic ability of subsets of 3, 6, 9, 12, 24 and 32 electrocardiographic recording sites have been evaluated based on their ability to correctly asses the presence or absence of Myocardial Infarction (MI).

Results
It was observed that the wrapper approach, using sequential forward selection and a 5 nearest neighbour classifier, was capable of choosing a set of 24 recording sites that could correctly classify 82.8% of BSPMs. Although the filter method performed slightly less favourably, the performance was comparable with a classification accuracy of 79.3%. In addition, experiments were conducted to show how (a) features chosen using the wrapper approach were specific to the classifier used in the selection model, and (b) lead subsets chosen were not necessarily unique.

Conclusion
It was concluded that both the filter and wrapper approaches adopted were suitable for guiding the choice of recording sites useful for determining the presence of MI. It should be noted however that in this study recording sites have been suggested on their ability to detect disease and such sites may not be optimal for estimating body surface potential distributions.
What parameters affect left ventricular diastolic flow propagation velocity? in vitro studies using color m-mode doppler echocardiography
Authors: Ogawa Toshihiro , Scotten Lawrence N , Walker David K , Yoganathan Ajit P , Bess Renee L , Nordstrom Cheryl K , Gardin Julius M 
Published: September 2005

Abstract

Background
Insufficient data describe the relationship of hemodynamic parameters to left ventricular (LV) diastolic flow propagation velocity (Vp) measured using color M-mode Doppler echocardiography.

Methods
An in vitro LV model used to simulate LV diastolic inflow with Vp measured under conditions of varying: 1) Stroke volume, 2) heart rate (HR), 3) LV volume, 4) LV compliance, and 5) transmitral flow (TMF) waveforms (Type 1: constant low diastasis flow and Type 2: no diastasis flow).

Results
Univariate analysis revealed excellent correlations of Vp with stroke volume (r = 0.98), LV compliance (r = 0.94), and HR with Type 1 TMF (r = 0.97). However, with Type 2 TMF, HR was not associated with Vp. LV volume was not related to Vp under low compliance, but inversely related to Vp under high compliance conditions (r = -0.56).

Conclusion
These in vitro findings may help elucidate the relationship of hemodynamic parameters to early diastolic LV filling.
Peptidylarginine deiminase (PAD) is a mouse cortical granule protein that plays a role in preimplantation embryonic development
Authors: Liu Min , Oh Andrea , Calarco Patricia , Yamada Michiyuki , Coonrod Scott A , Talbot Prue 
Published: September 2005

Abstract

Background
While mammalian cortical granules are important in fertilization, their biochemical composition and functions are not fully understood. We previously showed that the ABL2 antibody, made against zona free mouse blastocysts, binds to a 75-kDa cortical granule protein (p75) present in a subpopulation of mouse cortical granules. The purpose of this study was to identify and characterize p75, examine its distribution in unfertilized oocytes and preimplantation embryos, and investigate its biological role in fertilization.

Results
To identify p75, the protein was immunoprecipitated from ovarian lysates with the ABL2 antibody and analyzed by tandem mass spectrometry (MS/MS). A partial amino acid sequence (VLIGGSFY) was obtained, searched against the NCBI nonredundant database using two independent programs, and matched to mouse peptidylarginine deiminase (PAD). When PAD antibody was used to probe western blots of p75, the antibody detected a single protein band with a molecular weight of 75 kDa, confirming our mass spectrometric identification of p75. Immunohistochemistry demonstrated that PAD was present in the cortical granules of unfertilized oocytes and was released from activated and in vivo fertilized oocytes. After its release, PAD was observed in the perivitelline space, and some PAD remained associated with the oolemma and blastomeres' plasma membranes as a peripheral membrane protein until the blastocyst stage of development. In vitro treatment of 2-cell embryos with the ABL2 antibody or a PAD specific antibody retarded preimplantation development, suggesting that cortical granule PAD plays a role after its release in preimplantation cleavage and early embryonic development.

Conclusion
Our data showed that PAD is present in the cortical granules of mouse oocytes, is released extracellularly during the cortical reaction, and remains associated with the blastomeres' surfaces as a peripheral membrane protein until the blastocyst stage of development. Our in vitro study supports the idea that extracellular PAD functions in preimplantation development.
Perceived environment and physical activity: a meta-analysis of selected environmental characteristics
Authors: Duncan Mitch J , Spence John C , Mummery W Kerry 
Published: September 2005

Abstract

Background
Several narrative reviews have been conducted on the literature examining environmental correlates of physical activity (PA). To date these reviews have been unable to provide definitive summaries of observed associations. This study utilizes meta-analytical techniques to calculate summaries of associations between selected environmental characteristics and PA.

Methods
Published studies were identified from electronic databases and searches of personal files. Studies were examined to determine the environmental constructs most frequently studied. Included studies (N = 16) examined at least one identified construct and determined associations between perceived environmental constructs and PA using logistic regression. Data were analyzed separately for crude and adjusted ORs using general-variance based fixed effect models.

Results
No significant associations emerged between environmental characteristics and PA using crude OR. The perceived presence of PA facilities (OR 1.20, 95% 1.06–1.34), sidewalks (OR 1.23, 95% 1.13–1.32), shops and services (OR 1.30, 95% 1.14–1.46) and perceiving traffic not to be a problem (OR 1.22, 95% 1.08–1.37) were positively associated with activity using adjusted ORs. Variance in PA accounted for by significant associations ranged from 4% (heavy traffic not a problem) to 7% (presence of shops and services).

Conclusion
Results of the meta-analysis support the relevance of perceived environmental characteristics for understanding population PA. These results should encourage the use of comprehensive ecological models that incorporate variables beyond basic demographic information.
Phobic memory and somatic vulnerabilities in anorexia nervosa: a necessary unity?
Authors: Myslobodsky Michael 
Published: September 2005

AbstractAnorexia nervosa is a clinically significant illness that may be associated with permanent medical complications involving almost every organ system. The paper raises a question whether some of them are associated with premorbid vulnerability such as subcellular ion channel abnormalities ('channelopathy') that determines the clinical expression of the bodily response to self-imposed malnutrition. Aberrant channels emerge as a tempting, if rather speculative alternative to the notion of cognitively-driven neurotransmitter modulation deficit in anorexia nervosa. The concept of channelopathies is in keeping with some characteristics of anorexia nervosa, such as a genetically-based predisposition to hypophagia, early onset, cardiac abnormalities, an appetite-enhancing efficacy of some antiepileptic drugs, and others. The purpose of this article is to stimulate further basic research of ion channel biophysics in relation to restrictive anorexia.
Management of chest pain: exploring the views and experiences of chiropractors and medical practitioners in a focus group interview
Authors: Smith Monica , Lawrence Dana J , Rowell Robert M 
Published: September 2005

AbstractBackgroundWe report on a multidisciplinary focus group project related to the appropriate care of chiropractic patients who present with chest pain. The prevalence and clinical management, both diagnosis and treatment, of musculoskeletal chest pain in ambulatory medical settings, was explored as the second dimension of the focus group project reported here.MethodsThis project collected observational data from a multidisciplinary focus group composed of both chiropractic and medical professionals. The goals of the focus group were to explore the attitudes and experiences of medical and chiropractic clinicians regarding their patients with chest pain who receive care from both medical and chiropractic providers, to identify important clinical or research questions that may inform the development of 'best practices' for coordinating or managing care of chest pain patients between medical and chiropractic providers, to identify important clinical or research questions regarding the diagnosis and treatment of chest pain of musculoskeletal origin, to explore various methods that might be used to answer those questions, and to discuss the feasibility of conducting or coordinating a multidisciplinary research effort along this line of inquiry. The convenience-sample of five focus group participants included two chiropractors, two medical cardiologists, and one dual-degreed chiropractor/medical physician. The focus group was audiotaped and transcripts were prepared of the focus group interaction. Content analysis of the focus group transcripts were performed to identify key themes and concepts, using categories of narratives.ResultsSix key themes emerged from the analysis of the focus group interaction, including issues surrounding (1) Diagnosis; (2) Treatment and prognosis; (3) Chest pain as a chronic, multifactorial, or comorbid condition; (4) Inter-professional coordination of care; (5) Best practices and standardization of care; and (6) Training and education.ConclusionThis study carries implications for chiropractic clinical training relative to enhancing diagnostic competencies in chest pain, as well as the need to ascertain and improve those skills, competencies, and standards for referrals and sharing of clinical information that may improve cross-disciplinary coordination of care for chest pain patients.
Strain driven fast osseointegration of implants
Authors: Joos Ulrich , Büchter Andre , Wiesmann Hans-Peter , Meyer Ulrich 
Published: September 2005

Abstract

Background
Although the bone's capability of dental implant osseointegration has clinically been utilised as early as in the Gallo-Roman population, the specific mechanisms for the emergence and maintenance of peri-implant bone under functional load have not been identified. Here we show that under immediate loading of specially designed dental implants with masticatory loads, osseointegration is rapidly achieved.

Methods
We examined the bone reaction around non- and immediately loaded dental implants inserted in the mandible of mature minipigs during the presently assumed time for osseointegration. We used threaded conical titanium implants containing a titanium2+ oxide surface, allowing direct bone contact after insertion. The external geometry was designed according to finite element analysis: the calculation showed that physiological amplitudes of strain (500–3,000 ustrain) generated through mastication were homogenously distributed in peri-implant bone. The strain-energy density (SED) rate under assessment of a 1 Hz loading cycle was 150 Jm-3 s-1, peak dislocations were lower then nm.

Results
Bone was in direct contact to the implant surface (bone/implant contact rate 90%) from day one of implant insertion, as quantified by undecalcified histological sections. This effect was substantiated by ultrastructural analysis of intimate osteoblast attachment and mature collagen mineralisation at the titanium surface. We detected no loss in the intimate bone/implant bond during the experimental period of either control or experimental animals, indicating that immediate load had no adverse effect on bone structure in peri-implant bone.

Conclusion
In terms of clinical relevance, the load related bone reaction at the implant interface may in combination with substrate effects be responsible for an immediate osseointegration state.
Focusing on the ethnobotanical uses of plants in Mersin and Adana provinces (Turkey)
Authors: Everest Ayse , Ozturk Ersin 
Published: September 2005

Abstract
This paper presents the result of a study on the herbal drugs in the herbal markets in Mersin and Adana. The data were collected through direct interviews with herbalists and customers between 2002–2005 and the popular medicinal plants were investigated. A total of 107 species belonging to 56 families were investigated and the samples were listedwith their local and Latin names. The investigation includes cross-checking the disorders and their herbal cures and their recommended use stated by the local herbalists, by the parts used, and by the preparations. The cultivated species and their ethno botanical uses, are documented and extensive inventory is presented.
As a result, we observed that these plants are used especially for intestinal digestive disorders of the gastrointestinal tract, (21.68%), respiratory tract system disorders (10.43%), heart-blood circulatory system disorders (8.48%), urinary tract system disorders (7.70%), skin disorders (6.48%) and others.
The estrogen receptor-α A908G (K303R) mutation occurs at a low frequency in invasive breast tumors: results from a population-based study
Authors: Conway Kathleen , Parrish Eloise , Edmiston Sharon N , Tolbert Dawn , Tse Chiu-Kit , Geradts Joseph , Livasy Chad A , Singh Harsharan , Newman Beth , Millikan Robert C 
Published: September 2005

Abstract
Introduction
Evidence suggests that alterations in estrogen signaling pathways, including estrogen receptor-α (ER-α), occur during breast cancer development. A point mutation in ER-α (nucleotide A908G), producing an amino acid change from lysine to arginine at codon 303 (K303R) results in receptor hypersensitivity to estrogen. This mutation was initially reported in one-third of hyperplastic benign breast lesions, although several recent studies failed to detect it in benign or malignant breast tissues.

Methods
We screened 653 microdissected, newly diagnosed invasive breast tumors from patients in the Carolina Breast Cancer Study, a population-based case-control study of breast cancer in African American and white women in North Carolina, for the presence of the ER-α A908G mutation by using single-strand conformational polymorphism (SSCP) analysis and 33P-cycle sequencing.

Results
We detected the ER-α A908G mutation in 37 of 653 (5.7%) breast tumors. The absence of this mutation in germline DNA confirmed it to be somatic. Three tumors exhibited only the mutant G base at nucleotide 908 on sequencing, indicating that the wild-type ER-α allele had been lost. The ER-α A908G mutation was found more frequently in higher-grade breast tumors (odds ratio (OR) 2.83; 95% confidence interval (CI) 1.09 to 7.34, grade II compared with grade I), and in mixed lobular/ductal tumors (OR 2.10; 95% CI 0.86 to 5.12) compared with ductal carcinomas, although the latter finding was not statistically significant.

Conclusion
This population-based study, the largest so far to screen for the ER-α A908G mutation in breast cancer, confirms the presence of the mutant in invasive breast tumors. The mutation was associated with higher tumor grade and mixed lobular/ductal breast tumor histology.
Entropy diagnosis for phase transitions occurring in functional materials
Authors: Sorai Michio 
Published: September 2005

Abstract
Functionalities of materials manifest themselves as the result of a concerted effect among molecular structure, intermolecular interactions, and molecular motions. Since the entropy of substance directly reflects the degree of molecular motions, the entropy plays a crucial role when one discusses the stability of a given phase at finite temperatures. When a delicate balance of these three factors is broken, the condensed state faces a catastrophe and is transformed into another phase. Therefore, phase transition is a good probe for elucidation of the interplay between these three factors. As there is no selection rule in thermodynamics, the entropy gain at the phase transition is a good tool to diagnose the mechanism of phase transition. In this presentation, calorimetric investigations aimed at the elucidation of the mechanisms governing phase transitions occurring in molecule-based functional materials are reviewed.