bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular detection of human immunodeficiency virus: where do we stand? Molekularer Nachweis des humanen Immunschwächevirus: Aktueller Stand
Authors: Kessler Harald H. 
Published: February 2005

Abstract

Abstract Infection with the human immunodeficiency virus (HIV) continues to present diagnostic and therapeutic challenges worldwide. Today, many diagnostic laboratories have implemented assays based on molecular techniques for the detection of HIV. Detection of primary HIV infection, however, still relies on serologic testing, except for the screening of blood and plasma donors, which is done by the use of molecular assays. Additionally, molecular methods are employed for the detection of vertical transmission and monitoring of patients undergoing antiretroviral therapy. Although a continuous improvement in assay performance has been observed during recent years, the lack of comparability of different molecular assays remains a problem. Moreover, a better standardization of molecular assays for the detection of HIV-1 group O and HIV-2 must be addressed in the future.
Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea mays L.)
Authors: Zhang Yuan-Ming , Mao Yongcai , Xie Chongqing , Smith Howie , Luo Lang , Xu Shizhong 
Published: February 2005

Abstract
Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed &gt;80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars.
Elevated Polymorphism and Divergence in the Class C Scavenger Receptors of Drosophila melanogaster and D. simulansSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY865019, AY865135.
Authors: Lazzaro Brian P 
Published: February 2005

Abstract
Scavenger receptor proteins are involved in the cellular internalization of a broad variety of foreign material, including pathogenic bacteria during phagocytosis. I find here that nonsynonymous divergence in three class C scavenger receptors (Sr-C's) between Drosophila melanogaster and D. simulans and between each of these species and D. yakuba is approximately four times the typical genome average. These genes also exhibit unusually high levels of segregating nonsynonymous polymorphism in D. melanogaster and D. simulans populations. A fourth Sr-C is comparatively conserved. McDonald-Kreitman tests reveal a significant excess of replacement fixations between D. melanogaster and D. simulans in the Sr-C's, but tests of polymorphic site frequency spectra do not support models of directional selection. It is possible that the molecular functions of SR-C proteins are sufficiently robust to allow exceptionally high amino acid substitution rates without compromising organismal fitness. Alternatively, SR-Cs may evolve under diversifying selection, perhaps as a result of pressure from pathogens. Interestingly, Sr-CIII and Sr-CIV are polymorphic for premature stop codons. Sr-CIV is also polymorphic for an in-frame 101-codon deletion and for the absence of one intron.
Mutations in the Saccharomyces cerevisiae LSM1 Gene That Affect mRNA Decapping and 3′ End Protection
Authors: Tharun Sundaresan , Muhlrad Denise , Chowdhury Ashis , Parker Roy 
Published: February 2005

AbstractThe decapping of eukaryotic mRNAs is a key step in their degradation. The heteroheptameric Lsm1p–7p complex is a general activator of decapping and also functions in protecting the 3′ ends of deadenylated mRNAs from a 3′-trimming reaction. Lsm1p is the unique member of the Lsm1p–7p complex, distinguishing that complex from the functionally different Lsm2p–8p complex. To understand the function of Lsm1p, we constructed a series of deletion and point mutations of the LSM1 gene and examined their effects on phenotype. These studies revealed the following: (i) Mutations affecting the predicted RNA-binding and inter-subunit interaction residues of Lsm1p led to impairment of mRNA decay, suggesting that the integrity of the Lsm1p–7p complex and the ability of the Lsm1p–7p complex to interact with mRNA are important for mRNA decay function; (ii) mutations affecting the predicted RNA contact residues did not affect the localization of the Lsm1p–7p complex to the P-bodies; (iii) mRNA 3′-end protection could be indicative of the binding of the Lsm1p–7p complex to the mRNA prior to activation of decapping, since all the mutants defective in mRNA 3′ end protection were also blocked in mRNA decay; and (iv) in addition to the Sm domain, the C-terminal domain of Lsm1p is also important for mRNA decay function.
Soft Sweeps
Authors: Hermisson Joachim , Pennings Pleuni S 
Published: February 2005

Abstract
A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario—standing variation vs. new mutations—is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of “soft sweeps,” where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.
Isolation and Characterization of Novel xrs2 Mutations in Saccharomyces cerevisiae
Authors: Shima Hiroki , Suzuki Masakatu , Shinohara Miki 
Published: February 2005

Abstract
The Mre11/Rad50/Xrs2 (MRX) complex is involved in DNA damage repair, DNA damage response, telomere control, and meiotic recombination. Here, we constructed and characterized novel mutant alleles of XRS2. The alleles with mutations in the C-terminal conserved domain of Xrs2 were grouped into the same class. Mutant Xrs2 in this class lacked Mre11 interaction ability. The second class, lacking a C-terminal end, showed defects only in telomere control. A previous study showed that this C-terminal end contains a Tel1-association domain. These results indicate that Xrs2 contains two functional domains, Mre11- and Tel1-binding domains. While the Mre11-binding domain is essential for Xrs2 function, the Tel1-binding domain may be essential only for Tel1 function in telomere maintenance. The third class, despite containing a large deletion in the N-terminal region, showed no defects in DNA damage repair. However, some mutants, which showed a reduced level of Xrs2 protein, were partially defective in formation of meiotic DSBs and telomere maintenance. These defects were suppressed by overexpression of the mutant Xrs2 protein. This result suggests that the total amount of Xrs2 protein is a critical determinant for the function of the MRX complex especially with regard to telomere maintenance and meiotic DSB formation.
Linkage Disequilibrium Grouping of Single Nucleotide Polymorphisms (SNPs) Reflecting Haplotype Phylogeny for Efficient Selection of Tag SNPs
Authors: Takeuchi Fumihiko , Yanai Kazuyuki , Morii Toshiyuki , Ishinaga Yuji , Taniguchi-Yanai Keiko , Nagano Shinobu , Kato Norihiro 
Published: February 2005

Abstract
Single nucleotide polymorphisms (SNPs) have been proposed to be grouped into haplotype blocks harboring a limited number of haplotypes. Within each block, the portion of haplotypes is expected to be tagged by a selected subset of SNPs; however, none of the proposed selection algorithms have been definitive. To address this issue, we developed a tag SNP selection algorithm based on grouping of SNPs by the linkage disequilibrium (LD) coefficient r2 and examined five genes in three ethnic populations—the Japanese, African Americans, and Caucasians. Additionally, we investigated ethnic diversity by characterizing 979 SNPs distributed throughout the genome. Our algorithm could spare 60% of SNPs required for genotyping and limit the imprecision in allele-frequency estimation of nontag SNPs to 2% on average. We discovered the presence of a mosaic pattern of LD plots within a conventionally inferred haplotype block. This emerged because multiple groups of SNPs with strong intragroup LD were mingled in their physical positions. The pattern of LD plots showed some similarity, but the details of tag SNPs were not entirely concordant among three populations. Consequently, our algorithm utilizing LD grouping allows selection of a more faithful set of tag SNPs than do previous algorithms utilizing haplotype blocks.
Effects of Intravenous Midazolam and Diazepam on Patient Response, Percentage of Oxygen Saturation, and Hemodynamic Factors During Periodontal Surgery
Authors: Staretz Lauri R. , Otomo‐Corgel Joan , Lin James I. 
Published: February 2005

Background: The purpose of this double‐masked study was to evaluate effects of intravenous sedation (IVS) using midazolam or diazepam during periodontal procedures on patient recall, psychomotor response, oxygen saturation, and hemodynamic factors.Methods: Seventeen patients received either two or three scheduled periodontal surgeries under IVS with midazolam, diazepam, or placebo control. Patients were monitored throughout the procedure for hemodynamic variables, percent oxygen saturation, level of recall of common objects presented at baseline, and psychomotor function via the perceptual speed test (PST).Results: Fifteen patients completed the study with average titrated dosages of 3.3 and 12.1 mg for midazolam and diazepam, respectively. Within the limitations of the study, there were few differences observed between the drugs with regard to hemodynamic variables, oxygen saturation, and overall percentage of objects recalled by patients sedated with either drug. However, midazolam was found to cause a greater incidence of amnesia lasting up to 30 minutes when compared to placebo. Patients on diazepam required an average of 15 minutes longer to recover accuracy as measured by the PST.Conclusions: The results suggest that diazepam and midazolam each may have advantages for IVS. In procedures lasting over 45 minutes, diazepam appears to be more clinically advantageous including a wider margin of safety during titration and gradual recovery. Midazolam may be used for shorter procedures for faster onset of action, predictable amnesic effects, and relatively rapid recovery. J Periodontol 2004;75:1319‐1326.
Effect of the Interleukin‐1 Genotype on Outcomes of Regenerative Periodontal Therapy With Bone Replacement Grafts
Authors: Weiss Oren I. , Caton Jack , Blieden Timothy , Fisher Susan G. , Trafton Sarah , Hart Thomas C. 
Published: February 2005

Background: Previous studies have shown an association between a specific genotype for the inflammatory cytokine interleukin (IL)‐1 and the severity of periodontal disease. The purpose of this study was to evaluate the effect of the IL‐1 genotype on the outcomes of periodontal surgical regenerative treatment with bone replacement grafts.Methods: Forty‐four patients with interproximal intrabony defects were treated with bone replacement grafts. Probing depths (PD) and clinical attachment levels (CAL) were measured before treatment and at least 9 months post‐treatment. Whole‐mouth plaque index (WMPI) and bleeding index (WMBI) were recorded as well. All patients were tested for the IL‐1 genotype.Results: Thirteen (29.55%) of the patients were IL‐1 genotype positive. There was no statistically significant difference between the genotype‐positive and genotype‐negative groups regarding age, smoking status, gender, WMPI, and WMBI. There was no significant difference in PD or CAL between the genotype‐positive and genotype‐negative groups at baseline. Genotype‐positive patients had a smaller reduction in probing depth (1.86 mm versus 2.13 mm) and a greater gain of clinical attachment (1.20 mm versus 0.65 mm). These differences were not statistically significant (P = 0.70, P = 0.40). Multivariate regression analysis showed that presurgical PD significantly influenced post‐surgical PD and CAL, and only WMPI significantly influenced CAL.Conclusion: In this study, there was no evidence that the IL‐1 genotype influences the clinical treatment outcomes of regenerative periodontal therapy with bone replacement grafts. J Periodontol 2004;75:1335‐1342.
Killing of Periodontopathogenic Bacteria by Photodynamic Therapy
Authors: Pfitzner Anne , Sigusch Bernd W. , Albrecht Volker , Glockmann Eike 
Published: February 2005

Background: The aim of this study was to evaluate a new approach for killing periodontopathogenic bacteria using photodynamic therapy (PDT).Methods: In this study, we investigated the photosensitizers chlorin e6, BLC 1010, and BLC 1014 by three different methods for their effect in PDT on the viability of periodontopathogenic bacterial species. The methods included examination of inhibition zones on agar plates, determination of colony‐forming units (CFU), and the use of a bacterial viability kit.Results: Using the CFU method, we were able to demonstrate that the anaerobic bacteria Porphyromonas gingivalis, Fusobacterium nucleatum, and Capnocytophaga gingivalis can be photoinactivated completely by illumination with an intensity of 5.3 J/cm2 in the presence of 10 µM chlorin e6 and 10 µM BLC 1010. With the photosensitizers chlorin e6 and BLC 1010, we were able to induce zones of inhibition on agar plates. BLC 1014 failed to produce a zone of inhibition. The results of the bacterial viability test also showed that the photosensitizer BLC 1014 provides the lowest photodynamic effect in comparison to the others.Conclusion: The data collected to date suggest that photodynamic therapy with chlorin e6 and BLC 1010 is advantageous for suppressing periodontopathogenic bacteria. J Periodontol 2004; 75:1343‐1349.
Gingival Recession: Epidemiology and Risk Indicators in a Representative Urban Brazilian Population
Authors: Susin Cristiano , Haas Alex N. , Oppermann Rui V. , Haugejorden Ola , Albandar Jasim M. 
Published: February 2005

Background: Gingival recession is a common manifestation of periodontal disease, but it is also associated with other risk factors. A few studies have investigated the epidemiology and risk factors of this condition. This study describes the epidemiology of gingival recession in a representative, urban Brazilian population and assesses various risk indicators.Methods: A representative sample of 1,460 subjects was selected using a multi‐stage, probability, cluster sampling strategy. The subjects were interviewed using a structured questionnaire and had a full‐mouth clinical examination in a mobile examination center.Results: More than half (51.6%) and 22.0% of the individuals and 17.0% and 5.8% of teeth per individual showed gingival recession ≥3 mm and ≥5 mm, respectively. The prevalence, extent, and severity of recession correlated with age. Recession showed a nonlinear relationship with age, with 25 to 50 year olds showing the highest level of recession. Males aged ≥30 years showed significantly higher prevalence and extent of gingival recession than females. The percentage of teeth with recession was significantly higher in the lower socioeconomic groups irrespective of age, and in subjects ≥30 years of age with irregular dental care than in subjects with regular care. Using a multivariable model, cigarette smoking and presence of supragingival calculus were the factors most significantly associated with localized and generalized recession, whereas gender, dental visits, and socioeconomic status were not significant risk indicators.Conclusions: The high level of gingival recession in this Brazilian population may be primarily related to destructive periodontal disease and is significantly associated with a high level of supragingival dental calculus and cigarette smoking. Populationbased programs aimed at the prevention of periodontal diseases may reduce the prevalence of severe gingival recession in this and similar populations. J Periodontol 2004;75:1377‐1386.
Morbidity and Economic Complications Following Mucogingival Surgery in a Hemophiliac HIV‐Infected Patient: A Case Report
Authors: Blanco‐Carrion Juan , Liñares‐Gonzalez Antonio , Batalla‐Vazquez Pilar , Diz‐Dios Pedro 
Published: February 2005

Background: This report describes the surgical treatment of a gingival recession in a hemophiliac HIV‐infected patient. To our knowledge, mucogingival surgery has not been described previously in these patients.Methods: Under the supervision of the patient's hematologist, a subepithelial connective tissue graft procedure was carried out to treat the recession. The treatment was performed after substitution therapy with factor VIII concentrate, supported by local antifibrinolytic treatment with epsilonaminocaproic acid.Results: One week after surgery, the grafted zone showed a normal healing, but an area of necrosis appeared at the donor palatal site with spontaneous bleeding. The administration of factor VIII concentrate had to be prolonged to arrest the hemorrhage. In total, 44,500 units of factor VIII concentrate were used, the cost of which reached around $20,000. After 1 month the donor site had re‐epithelialized by secondary intention. The root coverage was around 85% successful.Conclusions: Because of the surgical risk and the high economic cost in the use of the factor VIII concentrate, we do not recommend performing mucogingival surgery in HIV‐infected hemophiliacs unless it is absolutely necessary. Prevention and early treatment must be the goal in the management of these patients. J Periodontol 2004;75: 1413‐1416.
Patient Evaluation of a Novel Non‐Injectable Anesthetic Gel: A Multicenter Crossover Study Comparing the Gel to Infiltration Anesthesia During Scaling and Root Planing
Authors: van Steenberghe Daniel , Bercy Pierre , De Boever Jan , Adriaens Patrick , Geers Lut , Hendrickx Elke , Adriaenssen Christian , Rompen Eric , Malmenäs Maria , Ramsberg Joakim 
Published: February 2005

Background: Periodontal scaling procedures commonly require some kind of anesthesia. From the patient's perspective, the choice of anesthetic method is a trade‐off between the degree of anesthesia and accepting the side effects. The present study evaluates the preferences for a novel non‐injection anesthetic product (a gel, containing lidocaine 25 mg/g plus prilocaine 25 mg/g and thermosetting agents) versus injection anesthesia (lidocaine 2% adrenaline) in conjunction with scaling and/or root planing (SRP).Methods: In a multicenter, crossover, randomized, open study patients were asked, after they had experienced both products, if they preferred anesthetic gel or injection anesthesia. In addition, the adequacy of anesthesia and occurrence of post‐procedure problems were assessed. The patients were also asked about their willingness to return if they were offered anesthetic gel at their next visit and their maximum willingness to pay (WTP) for this option.Results: One‐hundred seventy (170) patients at eight centers in Belgium were included in the study. There were 157 per protocol (PP) patients. A vast majority of the PP patients (70%) preferred the anesthetic gel to injection anesthesia (22%). The most common reason was less post‐procedure numbness. Eighty percent (80%) of the patients expressed satisfactory anesthesia with the gel and 96% with injection anesthesia (P <0.001). Post‐procedure problems were significantly less with the gel than with injection (P <0.001): numbness 15% versus 66%, unpleasant sensations such as soreness and pain 44% versus 63%, and problems connected with daily activities 19% versus 69%. The majority of patients (60%) who preferred gel were also willing to pay for it. A conservative estimate of the median WTP was $10.00. Furthermore, anesthetic gel would make almost every second patient (45%) more or much more willing to return for the next treatment.Conclusions: The data suggest that a somewhat less profound anesthesia with gel is clearly preferred by the patients because of the low incidence of post‐procedure problems as compared to conventional injection anesthesia. The median WTP is likely in excess of the acquisition cost of the product, which indicates a favorable cost‐benefit ratio for the individual patient. J Periodontol 2004;75:1471‐1478.