The impact of genotyping error on haplotype reconstruction and frequency estimation

The choice of genotyping families vs unrelated individuals is a critical factor in any large-scale linkage disequilibrium (LD) study. The use of unrelated individuals for such studies is promising, but in contrast to family designs, unrelated samples do not facilitate detection of genotyping errors, which have been shown to be of great importance for LD and linkage studies and may be even more important in genotyping collaborations across laboratories. Here we employ some of the most commonly-used analysis methods to examine the relative accuracy of haplotype estimation using families vs unrelateds in the presence of genotyping error. The results suggest that even slight amounts of genotyping error can significantly decrease haplotype frequency and reconstruction accuracy, that the ability to detect such errors in large families is essential when the number/complexity of haplotypes is high (low LD/common alleles). In contrast, in situations of low haplotype complexity (high LD and/or many rare alleles) unrelated individuals offer such a high degree of accuracy that there is little reason for less efficient family designs. Moreover, parent-child trios, which comprise the most popular family design and the most efficient in terms of the number of founder chromosomes per genotype but which contain little information for error detection, offer little or no gain over unrelated samples in nearly all cases, and thus do not seem a useful sampling compromise between unrelated individuals and large families. The implications of these results are discussed in the context of large-scale LD mapping projects such as the proposed genome-wide haplotype map.

Sitting time and work patterns as indicators of overweight and obesity in Australian adults

BACKGROUND: Increasing levels of physical inactivity and sedentariness are contributing to the current overweight and obesity epidemic. In this paper, the findings of two recent studies are used to explore the relationships between sitting time ( in transport, work and leisure), physical activity and body mass index (BMI) in two contrasting samples of adult Australians. METHODS: Data on sitting time, physical activity, BMI and a number of demographic characteristics were compared for participants in two studies-529 women who were participants in a preschool health promotion project ('mothers'), and 185 men and women who were involved in a workplace pedometer study ('workers'). Relationships between age, number of children, physical activity, sitting time, BMI, gender and work patterns were explored. Logistic regression was used to predict the likelihood of being overweight or obese, among participants with different physical activity, sitting time and work patterns. RESULTS: The total reported time spent sitting per day ( across all domains) was almost 6 h less among the mothers than the workers (P

Effect of storage time and conditions on the seed coat colour of Australian adzuki beans

Two varieties of adzuki beans (Vigna angularis), Bloodwood and Erimo, were stored at temperatures of 10, 20 or 30degreesC, and relative humidities (RH) 40 or 65%, and samples were analysed at 0, 1.5, 3 and 6 months. Storage at 30degreesC for > 1.5 months caused a significant decrease in the a(star) and b(star) colour values and darkening of the seed coat. Beans stored at 65% RH had lower L-star but higher a(star) and b(star) colour values than those stored at 40% RH. Bloodwood and Erimo samples showed similar trends in colour during storage. The best storage conditions for the preservation of the adzuki colour were 10degreesC and 65% RH. The Australian beans had lower L-star, a(star) and b(star) colour values than Japanese Erimo-shouzu beans and storage increased the difference.

Effect of storage time and conditions on the cotyledon cell wall of the adzuki bean (Vigna angularis)

Two varieties of adzuki grown in Australia, Bloodwood and Erimo, were stored for up to 6 months at three temperatures (10, 20 and 30 degreesC), and two relative humidities (RH; 40 and 65%). The amount of cell wall material increased with time under all storage conditions. This increase was greatest at 30 degreesC and 40% RH. Storage time and conditions did not affect the total pectin levels in the cell wall. Erimo constantly exhibited a higher total pectin level than Bloodwood. The Bloodwood soluble pectin, Ca++ and Mg++ and Erimo Ca++ in the cell wall remained stable during storage, while the Erimo soluble pectin and Mg++ exhibited a slight decrease at 20 and 30 degreesC after 3 months of storage. (C) 2002 Elsevier Science Ltd. All rights reserved.

Beyond time and oblivion : Sir Robert Sidney’s autograph manuscript

Dealing with ancient manuscript or old printed texts often constitutes a difficult task, especially to philologists and editors, for two main reasons: the precarious state of preservation of the documents and the uncertainty regarding their origin, authenticity and authorship. These problems are aggravated by spurious versions, due to the publication of truncated works, poorly supervised miscellanies and non-authorised editions. Sir Robert Sidney’s literary text constitutes an exception amidst such vicissitudes, once the original corpus is wholly contained in a notebook exhibiting the organisation and unity conceived by the author himself. Today, there is no evidence that any loose poems, either autograph or copied by amanuenses, were in circulation among members of the Elizabethan court society. The notebook was kept in private collections for four centuries, which probably explains why it was so well preserved. In fact, only in 1984 would P.J. Croft’s fine edition bring the youngest Sidney’s Poems into light. In this work, I approach Croft’s perceptive, accurate philological study that eventually rescued from oblivion a remarkable piece both of the Elizabethan lyric poetry and of the English Renaissance, and, at the same time, look into Robert Sidney’s peculiar, careful and original formatting of his own autograph manuscript.

Position paper on time and event-triggered communication services in the context of e-manufacturing

Modern factories are complex systems where advances in networking and information technologies are opening new ways towards higher efficiency. Such move is being driven by market rules with ever-increasing competition levels, in search for faster time-to-market, improved process yield, non-stop operations, flexible manufacturing and tighter supply-chain coupling. All these aims present a common requirement, i.e. a realtime flow of information, from the plant-floor up to the management, maintenance, suppliers and clients, to support accurate monitoring and control of the factory. This stresses the importance achieved by the communication infrastructure in modern manufacturing industry. This paper presents the authors view concerning the current trends in modern factory communication systems. It addresses the problems of seamlessly integrating different information flows with diverse requirements, mainly in terms of timeliness. In this aspect, the debate between event-triggered and time-triggered communication is revisited as well as the joint support for both types of traffic. Finally, a view of where factory communication systems are moving to is also presented, showing the impact of open and widely available technologies.

Time domain design of fractional differintegrators using least-squares

In this paper we propose the use of the least-squares based methods for obtaining digital rational approximations (IIR filters) to fractional-order integrators and differentiators of type sα, α∈R. Adoption of the Padé, Prony and Shanks techniques is suggested. These techniques are usually applied in the signal modeling of deterministic signals. These methods yield suboptimal solutions to the problem which only requires finding the solution of a set of linear equations. The results reveal that the least-squares approach gives similar or superior approximations in comparison with other widely used methods. Their effectiveness is illustrated, both in the time and frequency domains, as well in the fractional differintegration of some standard time domain functions.

Multiple Linear Regression and Artificial Neural Networks to Predict Time and Efficiency of Soil Vapor Extraction

The prediction of the time and the efficiency of the remediation of contaminated soils using soil vapor extraction remain a difficult challenge to the scientific community and consultants. This work reports the development of multiple linear regression and artificial neural network models to predict the remediation time and efficiency of soil vapor extractions performed in soils contaminated separately with benzene, toluene, ethylbenzene, xylene, trichloroethylene, and perchloroethylene. The results demonstrated that the artificial neural network approach presents better performances when compared with multiple linear regression models. The artificial neural network model allowed an accurate prediction of remediation time and efficiency based on only soil and pollutants characteristics, and consequently allowing a simple and quick previous evaluation of the process viability.

Design of Digital Fractional-Order Integrators and Differentiators by Least Squares

First IFAC Workshop on Fractional Differentiation and Its Application - 19-21 July 2004, Enseirb, Bordeaux, France - FDA'04

Spectrum and Frequency of GJB2 Mutations in a Cohort of 264 Portuguese Nonsyndromic Sensorineural Hearing Loss Patients

OBJECTIVE: To assess the spectrum and prevalence of mutations in the GJB2 gene in Portuguese nonsyndromic sensorineural hearing loss (NSSHL) patients. DESIGN: Sequencing of the coding region, basal promoter, exon 1, and donor splice site of the GJB2 gene; screening for the presence of the two common GJB6 deletions. STUDY SAMPLE: A cohort of 264 Portuguese NSSHL patients. RESULTS: At least one out of 21 different GJB2 variants was identified in 80 (30.2%) of the 264 patients analysed. Two mutant alleles were found in 53 (20%) of these probands, of which 83% (44/53) harboured at least one c.35delG allele. Twenty-seven (10.2%) of the probands harboured only one mutant allele. Subsequent analysis revealed that the GJB6 deletion del(GJB6-D13S1854) was present in at least 7.4% (2/27) of the patients carrying only one mutant GJB2 allele. Overall, one in five (55/264) of the patients were diagnosed as having DFNB1-related NSSHL, of which the vast majority (53/55) harboured only GJB2 mutations. CONCLUSIONS: This study provides clear demonstration that mutations in the GJB2 gene are an important cause of NSSHL in Portugal, thus representing a valuable indicator as regards therapeutical and rehabilitation options, as well as genetic counseling of these patients and their families.

Carbon prices. Dynamic analysis of European and Californian markets

Dissertação para obtenção do Grau de Doutor em Alterações Climáticas e Políticas de Desenvolvimento Sustentável

Two decades of tuberculosis in a city in Northeastern Brazil: advances and challenges in time and space

Abstract: INTRODUCTION This study presents two decades of epidemiological data on tuberculosis (TB), in order to understanding the disease profile and its spatiotemporal dynamics. METHODS This descriptive study was performed in the City of Olinda/Pernambuco, Brazil, from 1991-2010, and it analyzed new patients with TB living in the city. We used the χ²-test with a p-value <0.05 to identify differences in trends. Incidence and cluster distribution were identified using spatial scan statistics. RESULTS In total, 6202 new cases were recorded during the two decades. The highest incidence occurred in 1995 (110 cases/100,000 inhabitants), and the lowest occurred in 2009 (65 cases/100,000 inhabitants) (β=-1.44; R²=0.43; p=0.0018). The highest mortality occurred in 1998 (16 deaths/100,000 inhabitants), and the lowest occurred in 2008 (5 deaths/100,000 inhabitants) (β=-0.19; R²=0.17; p=0.07). There was a male predominance (65%), and ages ranged from 20-49 years (65%). There was a substantial increase in the number of patients that were cured after treatment (60% to 67%; p<0.001) as well as those tested for HIV (1.9% to 58.5%; p<0.001). During the first decade, clusters with p-values <0.05 included 29% of the total notified cases, and in the second decade, that percentage was 12%. CONCLUSIONS We observed a decreasing trend in incidence, which was significant, and mortality rates, which was not significant. The increased number of laboratory tests performed reflects advances in surveillance, and a reduction in the proportion of cases in primary clusters suggests, among other things, that the disease is spreading across the region.

Heart Rate and Systolic Blood Pressure Variability on Recently Diagnosed Diabetics

Background:Diabetes affects approximately 250 million people in the world. Cardiovascular autonomic neuropathy is a common complication of diabetes that leads to severe postural hypotension, exercise intolerance, and increased incidence of silent myocardial infarction.Objective:To determine the variability of heart rate (HR) and systolic blood pressure (SBP) in recently diagnosed diabetic patients.Methods:The study included 30 patients with a diagnosis of type 2 diabetes of less than 2 years and 30 healthy controls. We used a Finapres® device to measure during five minutes beat-to-beat HR and blood pressure in three experimental conditions: supine position, standing position, and rhythmic breathing at 0.1 Hz. The results were analyzed in the time and frequency domains.Results:In the HR analysis, statistically significant differences were found in the time domain, specifically on short-term values such as standard deviation of NN intervals (SDNN), root mean square of successive differences (RMSSD), and number of pairs of successive NNs that differ by more than 50 ms (pNN50). In the BP analysis, there were no significant differences, but there was a sympathetic dominance in all three conditions. The baroreflex sensitivity (BRS) decreased in patients with early diabetes compared with healthy subjects during the standing maneuver.Conclusions:There is a decrease in HR variability in patients with early type 2 diabetes. No changes were observed in the BP analysis in the supine position, but there were changes in BRS with the standing maneuver, probably due to sympathetic hyperactivity.

A study of the endocervical columnar cells I - morphology and frequency

After the observation of many thousands of histological sections of the endocervical mucosa it became evident that its columnar cells present a great variety of aspects not only those of the surface of the canal but also those of the glands. A classification of these cells was made taking into account the staining affinity, the intensity staining of the cytoplasm, the presence or absence of cilia, the shape and location of the nucleus. The various combinations of these different data made possible the characterization of 26 types of cells which we labelled by the alphabetical letters. Two hundred and fifty cervices obtained by cervical amputation and by hysterectomy were studied. The uteri presented lesions in the course of routine laboratory examination. In each of the 250 histological sections there were specifically counted 2,000 columnar cells which cover the cervical canal and 2,000columnar cells which form the glands. A graphic representation of the frequency of both the superficial and glandular columnar cells was presented; this was given the name EPITHELIOGRAM. The variation of the cellular "composition" of each epithelium is discussed and the frequency of the various cellular types after the count of one million of cells is presented.