Avoidance of Long Mononucleotide Repeats in Codon Pair Usage

Protein is an essential component for life, and its synthesis is mediated by codons in any organisms on earth. While some codons encode the same amino acid, their usage is often highly biased. There are many factors that can cause the bias, but a potential effect of mononucleotide repeats, which are known to be highly mutable, on codon usage and codon pair preference is largely unknown. In this study we performed a genomic survey on the relationship between mononucleotide repeats and codon pair bias in 53 bacteria, 68 archaea, and 13 eukaryotes. By distinguishing the codon pair bias from the codon usage bias, four general patterns were revealed: strong avoidance of five or six mononucleotide repeats in codon pairs; lower observed/expected (o/e) ratio for codon pairs with C or G repeats (C/G pairs) than that with A or T repeats (A/T pairs); a negative correlation between genomic GC contents and the o/e ratios, particularly for C/G pairs; and avoidance of C/G pairs in highly conserved genes. These results support natural selection against long mononucleotide repeats, which could induce frameshift mutations in coding sequences. The fact that these patterns are found in all kingdoms of life suggests that this is a general phenomenon in living organisms. Thus, long mononucleotide repeats may play an important role in base composition and genetic stability of a gene and gene functions.

Usage of complementary medicine across Switzerland. Results of the Swiss Health Survey 2007

QUESTIONS UNDER STUDY: This study investigated the use among the Swiss adult population and regional dissemination of various methods of complementary medicine (CM) provided by physicians or therapists in Switzerland. METHODS: Data of the Swiss Health Survey 2007 were used, which comprised a telephone interview followed by a written questionnaire (18,760 and 14,432 respondents, respectively) and included questions about people's state of health, health insurance and usage of health services. Users and non-users of CM were compared using logistic regression models. RESULTS: The most popular CM methods were homeopathy, osteopathy, acupuncture and shiatsu/foot reflexology. 30.5% of women and 15.2% of men used at least one CM method in the 12 months preceding the survey. Lake Geneva region and central Switzerland had more CM users than the other regions. Women, people between 25 and 64 years of age and people with higher levels of education were more likely to use CM. 53.5% of the adult population had a supplemental health insurance for CM treatments. 32.9% of people with such an insurance used CM during the 12 months preceding the survey, and so did 12.0% of people without additional insurance. CONCLUSIONS: Almost one fourth of the Swiss adult population had used CM within the past 12 months. User profiles were comparable to those in other countries. Despite a generally lower self-perceived health status, elderly people were less likely to use CM.

HIV-1 coreceptor usage and CXCR4-specific viral load predict clinical disease progression during combination antiretroviral therapy

BACKGROUND: Although combination antiretroviral therapy (cART) dramatically reduces rates of AIDS and death, a minority of patients experience clinical disease progression during treatment. OBJECTIVE: To investigate whether detection of CXCR4(X4)-specific strains or quantification of X4-specific HIV-1 load predict clinical outcome. METHODS: From the Swiss HIV Cohort Study, 96 participants who initiated cART yet subsequently progressed to AIDS or death were compared with 84 contemporaneous, treated nonprogressors. A sensitive heteroduplex tracking assay was developed to quantify plasma X4 and CCR5 variants and resolve HIV-1 load into coreceptor-specific components. Measurements were analyzed as cofactors of progression in multivariable Cox models adjusted for concurrent CD4 cell count and total viral load, applying inverse probability weights to adjust for sampling bias. RESULTS: Patients with X4 variants at baseline displayed reduced CD4 cell responses compared with those without X4 strains (40 versus 82 cells/microl; P = 0.012). The adjusted multivariable hazard ratio (HR) for clinical progression was 4.8 [95% confidence interval (CI) 2.3-10.0] for those demonstrating X4 strains at baseline. The X4-specific HIV-1 load was a similarly independent predictor, with HR values of 3.7 (95% CI, 1.2-11.3) and 5.9 (95% CI, 2.2-15.0) for baseline loads of 2.2-4.3 and > 4.3 log10 copies/ml, respectively, compared with < 2.2 log10 copies/ml. CONCLUSIONS: HIV-1 coreceptor usage and X4-specific viral loads strongly predicted disease progression during cART, independent of and in addition to CD4 cell count or total viral load. Detection and quantification of X4 strains promise to be clinically useful biomarkers to guide patient management and study HIV-1 pathogenesis.

Gender-specific usage of intramyocellular lipids and glycogen during exercise

PURPOSE: Gender-specific differences in substrate utilization during exercise have been reported, typically such that women rely more on fat than men. This study investigated whether gender differences exist in the utilization of intramyocellular lipids (IMCL) and glycogen. METHODS: IMCL and glycogen, as well as total fat and carbohydrate (CHO) oxidation were measured in nine males and nine females before, during, and after an endurance exercise. The trained subjects exercised on a bicycle ergometer at 50% maximal workload for 3 h. IMCL and glycogen were determined in the thigh by magnetic resonance spectroscopy. Oxygen uptake (VO(2)) and carbon dioxide production were determined by open circuit spirometry to calculate total fat and CHO oxidation. Relative power output, percent of maximum heart rate, VO(2peak), and respiratory exchange ratio were the same. RESULTS: Average fat oxidation was the same, whereas CHO oxidation was significantly higher in males compared with females. The relative contribution of these fuels to total energy used were similar in males and females. Males and females depleted IMCL and glycogen significantly (P < 0.001) during the 3-h exercise. IMCL levels at rest (P < 0.05) and its depletion during exercise (P < 0.001) were significantly higher in males compared with females, whereas glycogen was stored and used in the same range by both genders. CONCLUSION: During this 3-h exercise, energy supplies from fat and CHO were similar in both genders, and males as well as females reduced their IMCL stores significantly. The larger contribution of IMCL during exercise in males compared with females could either be a result of gender-specific substrate selection, or different long-term training habit.

Current trends in hormone replacement therapy: perceptions and usage

OBJECTIVE: To determine whether physicians' confidence in the use of hormone replacement therapy (HRT) for climacteric symptoms has been affected by the negative media interpretation of data from landmark studies investigating HRT usage such as the Women's Health Initiative (WHI) study. METHODS: A structured questionnaire was completed via the internet by European and US gynecologists, obstetrician/gynecologists and general practitioners - all experienced in treating women with climacteric symptoms. RESULTS: Six hundred physicians completed the survey in six countries. Overall, 98% agreed that the menopause significantly affects quality of life and 97% considered that the majority/all of their patients experienced positive benefits from HRT. Most physicians (90%) believed the benefits of HRT outweigh the risks in suitable patients, and 92% would prescribe HRT for themselves/spouse/family. For treatment of atrophic vaginitis, 86% agreed that local estrogen was the most effective course of action. While 82% of participants were aware of the latest recommendations on low-dose HRT, and estrogen dose in particular, 67% cited lowering the progestogen dose as important. With regard to the recent negative media coverage on HRT, 78% of physicians felt this was unjustified. CONCLUSIONS: These results provide reassurance that health-care professionals in Europe and the US, experienced in treating women with climacteric symptoms, have not lost confidence in HRT. Despite a consensus on the importance of lowering the dose of HRT and a focus on estrogen, there remains a need to heighten prescribers' awareness on the pivotal role that a lower progestogen dose plays in optimizing the risk-benefit profile.

Simulator Network project report: a tool for improvement of teaching materials and targeted resource usage in Skills Labs

During the last decade, medical education in the German-speaking world has been striving to become more practice-oriented. This is currently being achieved in many schools through the implementation of simulation-based instruction in Skills Labs. Simulators are thus an essential part of this type of medical training, and their acquisition and operation by a Skills Lab require a large outlay of resources. Therefore, the Practical Skills Committee of the Medical Education Society (GMA) introduced a new project, which aims to improve the flow of information between the Skills Labs and enable a transparent assessment of the simulators via an online database (the Simulator Network).

Temporary anchorage device usage: a survey among Swiss orthodontists.

BACKGROUND The aim of the survey was to obtain information on the treatment plan preferences, mechanics and characteristics of temporary anchorage device (TAD) application using a single case presented to orthodontists in Switzerland. METHODS A structured questionnaire to be completed by all study participants with case-specific (treatment plan including mechanics and TAD usage) and general questions (general fixed appliance and TAD usage as well as professional, educational and demographic questions) together with an orthodontic borderline case was utilised. The case was a female adult with dental Class II/2, deep bite and maxillary anterior crowing, who had been treated in childhood with extraction of four premolars and fixed appliance followed by wisdom tooth extraction. RESULTS The response rate was 24.4% (108 out of 443). The majority (96.3%, 104) proposed comprehensive treatment, while 3.7% (4) planned only alignment of maxillary teeth. 8.3% (9) included a surgical approach in their treatment plan. An additional 0.9% (1) combined the surgical approach with Class II mechanics. 75.1% (81) decided on distalization on the maxilla using TADs, 7.4% (8) planned various types of Class II appliances and 3.7% (4) combined distalization using TADs or headgear with Class II appliances and surgery. Palatal implants were the most popular choice (70.6%, 60), followed by mini-screws (22.4%, 19) and mini-plates on the infrazygomatic crests (7.0%, 6). The preferred site of TAD insertion showed more variation in sagittal than in transversal dimension, and the median size of mini-screws used was 10.0-mm long (interquartile range (IQR) 2.3 mm) and 2.0-mm wide (IQR 0.3 mm). CONCLUSIONS Distalization against palatal implants and then distalization against mini-screws were the most popular treatment plans. Preferred site for TAD insertion varied depending on type and size but varied more widely in the sagittal than in the transversal dimension.

Should the standard dimethyl sulfoxide concentration be reduced? Results of a European Group for Blood and Marrow Transplantation prospective noninterventional study on usage and side effects of dimethyl sulfoxide.

BACKGROUND Dimethyl sulfoxide (DMSO) is essential for the preservation of liquid nitrogen-frozen stem cells, but is associated with toxicity in the transplant recipient. STUDY DESIGN AND METHODS In this prospective noninterventional study, we describe the use of DMSO in 64 European Blood and Marrow Transplant Group centers undertaking autologous transplantation on patients with myeloma and lymphoma and analyze side effects after return of DMSO-preserved stem cells. RESULTS While the majority of centers continue to use 10% DMSO, a significant proportion either use lower concentrations, mostly 5 or 7.5%, or wash cells before infusion (some for selected patients only). In contrast, the median dose of DMSO given (20 mL) was much less than the upper limit set by the same institutions (70 mL). In an accompanying statistical analysis of side effects noted after return of DMSO-preserved stem cells, we show that patients in the highest quartile receiving DMSO (mL and mL/kg body weight) had significantly more side effects attributed to DMSO, although this effect was not observed if DMSO was calculated as mL/min. Dividing the myeloma and lymphoma patients each into two equal groups by age we were able to confirm this result in all but young myeloma patients in whom an inversion of the odds ratio was seen, possibly related to the higher dose of melphalan received by young myeloma patients. CONCLUSION We suggest better standardization of preservation method with reduced DMSO concentration and attention to the dose of DMSO received by patients could help reduce the toxicity and morbidity of the transplant procedure.