Characterization of chaotic dynamics in the human menstrual cycle

Background  

The human menstrual cycle is known to exhibit a significant amount of unexplained variability. This variation is typically dismissed as random fluctuations in an otherwise periodic and predictable system. Given the many delayed nonlinear feedbacks in the multiple levels of the reproductive endocrine system, however, the menstrual cycle can properly be construed as the output of a nonlinear dynamical system, and such a system has the possibility of being in a chaotic trajectory. We hypothesize that this is in fact the case and that it accounts for the observed variability.     

CTAB-urea method purifies RNA from melanin for cDNA microarray analysis

Melanin represents a major problem for the study of melanoma by microarrays since it is retained during RNA extraction and inhibits the enzymatic reactions used for probe preparation. Here we report a new method for cleaning RNA from melanin, based on the use of the cationic detergent cetyl-trimethylammonium bromide (CTAB)-urea for RNA precipitation. This method is easy to perform and has a low cost. Purified RNA is recovered with high quality and good yield. CTAB-urea treated RNA from highly pigmented melanoma cells can be successfully reverse transcribed and labeled to obtain probes which can be subsequently used in cDNA microarray experiments, giving consistent and reproducible results.     

Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (Diptera: Culicidae)

Sequence variation of the ribosomal DNA internal transcribed spacer 2 (ITS2) was examined for populations of the malaria vector Anopheles nuneztovari collected in Colombia, Venezuela, Bolivia, Suriname, and Brazil. Mosquitoes from Colombia and Venezuela had identical ITS2 sequences and were distinguished from sequences in other populations by three insertion/deletion events (indels) and by one transversion. The length of the ITS2 was 363-369 bp, and it had a G+C content of 55.3%- 55.7%. Variation in the length of the ITS2 between and within populations was due to indels in simple repeats. ITS2 consensus sequences were similar or identical for samples from the following three groups: (1) Colombia, Bolivia, and Venezuela; (2) Suriname and northern Brazil; and (3) eastern and central Brazil. The presence of two different consensus sequences from a single location near Manaus, Brazil, suggests that populations from eastern Brazil and those from Suriname converge in this region of the Amazon Basin. These data show that putative cryptic species of An. nuneztovari are distinguished by very minor differences in DNA sequence of the ITS2 region.      

Effect of incorporating probiotics into the diet of matrinxã (Brycon amazonicus) breeders

The aim of the present study was to evaluate the influence of probiotics prepared from Bacillus subtilis (strain C‐3102‐Calsporin^®; Calpis, Tokyo, Japan) as a dietary supplement on several reproductive aspects of female ‘matrinxã’(Brycon amazonicus), including hematological parameters, immunological characteristics and total lipid concentrations in muscle and liver tissue. The broodstock were kept in two ponds of 600 m², at a density of 50 fish per pond, from March to November 2008. The fish were divided into two treatment groups: untreated control fish (T1), and fish fed with 10 g of probiotics per kg of ration (T2). Fish were fed a diet containing 32% crude protein (CP), 7% crude fat (CF), and 6.5% ether extract (EE) twice daily at a rate of 1% of the total biomass per day during the coldest months (May through August) and 3% during the warm season (March, April and September through November). During the reproductive period, 20 individuals from each treatment group were selected for the experiments; two doses of crude carp pituitary extract were given to females in 10‐h intervals, and one dose was given to the males at the same time the females were given the second dose. A total of 20 fish were used for the hematological analyses. After anesthetization, blood samples were withdrawn by caudal puncture to determine the total number of cells, differential and total leukocyte counts, thrombocyte count, hematocrit, hemoglobin rate and plasma cortisol and glucose levels. The hematimetric index mean corpuscular volume (VCM) and mean corpuscular hemoglobin concentration (MHCM) were calculated. Ten other ‘matrinxãs’ from the same groups were used to assess macrophage phagocytic activity and lipid levels. The results showed that females fed a probiotics‐supplemented diet exhibited an increase in numbers of oocytes and, consequently, had higher rates of fertilization and hatching of larvae. Probiotic‐treated fish also exhibited a significant increase in the phagocytic activity of macrophages, indicating an improvement in the immune system of breeders. Hematologic parameters were different in comparison to the time‐zero group, and plasma cortisol and glucose levels were higher in the females. The total lipids levels in muscle and liver tissue were lower in B. amazonicus that received feed supplemented with probiotics.     

CopywriteR: DNA copy number detection from off-target sequence data

Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0617-1) contains supplementary material, which is available to authorized users.     

EuroSCORE Models in a Cohort of Patients with Valvular Heart Disease and a High Prevalence of Rheumatic Fever Submitted to Surgical Procedures

ObjectivesEpidemiological differences can be found between Brazilian and European valvular heart disease patients. The prevalence of heart valve diseases due to rheumatic disease is significantly higher in the Brazilian compared with the European population. Therefore, they could have different risks during and after cardiac surgery. The aim of this study was to evaluate the applicability of the additive and logistic EuroSCORE and EuroSCORE II in a cohort of high-risk patients with valvular heart disease of predominantly rheumatic aetiology submitted to surgery.MethodsBetween 1 February and 30 December 2009, 540 consecutive patients scheduled for valvular heart surgery were included in this study. In this set of patients, we examined the performance of the additive, logistic, and EuroSCORE II models for predicting in-hospital mortality. Calibration of each model was assessed by comparing predicted and observed in-hospital mortality and by the goodness of fit of the Hosmer-Lemeshow chi-square test. Discrimination performance of the model was evaluated with the receiver operating characteristic (ROC) curve analysis.ResultsThe mean age was 56 ± 16 years, 50.6% were female, and the mortality rate was 16.0% (6.0% in elective surgery and 34.0% in emergency/urgency surgery). Mortality rates were estimated according to the additive and logistic EuroSCORE and EuroSCORE II at 6.1%, 8.7%, and 4.3%, respectively. The AUC was 0.76 (95% confidence interval [95% CI] 0.70–0.81) for the additive EuroSCORE, 0.76 (95% CI 0.70–0.81) for the logistic EuroSCORE and 0.81 (95% CI 0.76–0.86) for EuroSCORE II. Hosmer-Lemeshow goodness-of-fit statistics were P = 0.52, P = 0.07, and P = 0.12 for additive, logistic EuroSCORE, and EuroSCORE II.ConclusionsIn this cohort of Brazilian patients with valvular heart disease submitted to surgical procedure, the EuroSCORE models had a good discriminatory capacity; however, the calibration was compromised because of an underestimation of the mortality rate.     

Protein interaction network for Alzheimer's disease using computational approach

Alzheimer''s disease (AD) is the most common form of dementia. It is the sixth leading cause of death in old age people. Despiterecent advances in the field of drug design, the medical treatment for the disease is purely symptomatic and hardly effective. Thusthere is a need to understand the molecular mechanism behind the disease in order to improve the drug aspects of the disease. Weprovided two contributions in the field of proteomics in drug design. First, we have constructed a protein-protein interactionnetwork for Alzheimer''s disease reviewed proteins with 1412 interactions predicted among 969 proteins. Second, the diseaseproteins were given confidence scores to prioritize and then analyzed for their homology nature with respect to paralogs andhomologs. The homology persisted with the mouse giving a basis for drug design phase. The method will create a new drug designtechnique in the field of bioinformatics by linking drug design process with protein-protein interactions via signal pathways. Thismethod can be improvised for other diseases in future.     

Surname as 'cancer risk' in extreme isolates: example from the island of Lastovo, Croatia

The aim of this study was to analyze whether there are surnames which appear more frequently among the ancestors of cancer cases in a small isolate, in comparison to the ancestral surnames of the healthy controls, using the classic case-control design. The chosen setting was the island of Lastovo, Croatia, located more than 100 kilometers from the nearest coastal region. The period of study was 1970-1995, during which a total of 76 cancer cases were recorded in a population of approximately 800. The comparison of surname frequencies was performed in current and in five ancestral generations. The leading hypothesis was that, if inbreeding and common ancestry contributed to the development of the disease, then those phenomena should be reflected in increasing frequency of some surnames among ancestors, identifying the 'hidden' consanguinity, or 'following' cancer-promoting genes on the Y-chromosome. The results imply that there are surnames representing a classic "risk" for cancer, but also those "protecting" from its development, which all underscores the importance of founder effect and genetic predisposition to the disease in a small, reproductively isolated population. All of the results become more evident and increasingly significant when analyzed in more distant ancestral generations.