POPREP: a generic report for population management

Genetic variation provides a basis upon which populations can be genetically improved. Management of animal genetic resources in order to minimize loss of genetic diversity both within and across breeds has recently received attention at different levels, e. g., breed, national and international levels. A major need for sustainable improvement and conservation programs is accurate estimates of population parameters, such as rate of inbreeding and effective population size. A software system (POPREP) is presented that automatically generates a typeset report. Key parameters for population management, such as age structure, generation interval, variance in family size, rate of inbreeding, and effective population size form the core part of this report. The report includes a default text that describes definition, computation and meaning of the various parameters. The report is summarized in two pdf files, named Population Structure and Pedigree Analysis Reports. In addition, results (e. g., individual inbreeding coefficients, rate of inbreeding and effective population size) are stored in comma-separate-values files that are available for further processing. Pedigree data from eight livestock breeds from different species and countries were used to describe the potential of POPREP and to highlight areas for further research.

Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a ""flipflop'' phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Simulation of sugarcane residue decomposition and aboveground growth

Due to the worldwide increase in demand for biofuels, the area cultivated with sugarcane is expected to increase. For environmental and economic reasons, an increasing proportion of the areas are being harvested without burning, leaving the residues on the soil surface. This periodical input of residues affects soil physical, chemical and biological properties, as well as plant growth and nutrition. Modeling can be a useful tool in the study of the complex interactions between the climate, residue quality, and the biological factors controlling plant growth and residue decomposition. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of aboveground phytomass and litter decomposition, and to validate the model through field experiment data. When studying aboveground growth, burned and unburned harvest systems were compared, as well as the effect of mineral fertilizer and organic residue applications. The simulations were performed with data from experiments with different durations, from 12 months to 60 years, in Goiana, TimbaA(0)ba and Pradpolis, Brazil; Harwood, Mackay and Tully, Australia; and Mount Edgecombe, South Africa. The differentiation of two pools in the litter, with different decomposition rates, was found to be a relevant factor in the simulations made. Originally, the model had a basically unlimited layer of mulch directly available for decomposition, 5,000 g m(-2). Through a parameter optimization process, the thickness of the mulch layer closer to the soil, more vulnerable to decomposition, was set as 110 g m(-2). By changing the layer of mulch at any given time available for decomposition, the sugarcane residues decomposition simulations where close to measured values (R (2) = 0.93), contributing to making the CENTURY model a tool for the study of sugarcane litter decomposition patterns. The CENTURY model accurately simulated aboveground carbon stalk values (R (2) = 0.76), considering burned and unburned harvest systems, plots with and without nitrogen fertilizer and organic amendment applications, in different climates and soil conditions.

Simulation of Soil Carbon Dynamics under Sugarcane with the CENTURY Model

Currently there is a trend for the expansion of the area cropped with sugarcane (Saccharum officinarum L.), driven by an increase in the world demand for biofuels, due to economical, environmental, and geopolitical issues. Although sugarcane is traditionally harvested by burning dried leaves and tops, the unburned, mechanized harvest has been progressively adopted. The use of process based models is useful in understanding the effects of plant litter in soil C dynamics. The objective of this work was to use the CENTURY model in evaluating the effect of sugarcane residue management in the temporal dynamics of soil C. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of soil C, validating the model through field experiment data, and finally to make predictions in the long term regarding soil C. The main focus of this work was the comparison of soil C stocks between the burned and unburned litter management systems, but the effect of mineral fertilizer and organic residue applications were also evaluated. The simulations were performed with data from experiments with different durations, from 1 to 60 yr, in Goiana and Timbauba, Pernambuco, and Pradopolis, Sao Paulo, all in Brazil; and Mount Edgecombe, Kwazulu-Natal, South Africa. It was possible to simulate the temporal dynamics of soil C (R(2) = 0.89). The predictions made with the model revealed that there is, in the long term, a trend for higher soil C stocks with the unburned management. This increase is conditioned by factors such as climate, soil texture, time of adoption of the unburned system, and N fertilizer management.

Access and Affordability of Electricity in Developing Countries

A key objective of developing countries is to provide affordable access to modern energy services in order to support economic and social development. The paper presents a number of arguments for why and in which way energy access and affordability can play a key role in national development programs and in achieving the Millennium Development Goals. Approaches for measuring accessibility and affordability are presented, drawing on case studies of Bangladesh. Brazil, and South Africa, countries with different rates of electrification. Affordability of using electricity is examined in relation to the energy expenditure burden for households and time consumption. Conclusions focus on lessons learned and recommendations for implementing policies, instruments, and regulatory measures to tackle the challenge of affordability. (C) 2011 Elsevier Ltd. All rights reserved.

Effects of Varenicline in Adult Smokers: A Multinational, 24-Week, Randomized, Double-Blind, Placebo-Controlled Study

Background: Prevalence rates of smoking are rising in developing countries. Previous trials evaluating the efficacy and tolerability of the smoking-cessation medication varenicline have used largely participants of Caucasian origin. Objective: This study was conducted to evaluate the efficacy and tolerability of varenicline in populations of participants from Latin America, Africa, and the Middle East to investigate potential differences in the therapeutic response to varenicline. Methods: This multinational, randomized, double-blind, placebo-controlled trial was conducted at 42 centers in 11 countries (Latin America: Brazil, Colombia, Costa Rica, Mexico, and Venezuela; Africa: Egypt and South Africa; Middle East: Jordan, Lebanon, Saudi Arabia, and the United Arab Emirates). Participants were male and female smokers aged 18 to 75 years who were motivated to stop smoking; smoked >= 10 cigarettes/d, with no cumulative period of abstinence >3 months in the previous year; and who had no serious or unstable disease within the previous 6 months. Subjects were randomized in a 2:1 ratio to receive varenicline 1 mg or placebo, BID for 12 weeks, with a 12-week nontreatment follow-up. Brief smoking-cessation counseling was provided. The main outcome measures were carbon monoxide confirmed continuous abstinence rate (CAR) at weeks 9 to 12 and weeks 9 to 24. Adverse events (AEs) were recorded for tolerability assessment. Results: Overall, 588 subjects (varenicline, 390; placebo, 198) were randomized and treated. The mean (SD) ages of subjects in the varenicline and placebo groups were 43.1 (10.8) and 43.9 (10.8) years, respectively; 57.7% and 65.7% were male; and the mean (SD) weights were 75.0 (16.0) and 76.7 (16.3) kg (range, 40.0-130.0 and 45.6-126.0 kg). CAR at weeks 9 to 12 was significantly higher with varenicline than with placebo (53.59% vs 18.69%; odds ratio [OR] = 5.76; 95% CI, 3.74-8.88; P < 0.0001), and this rate was maintained during weeks 9 to 24 (39.74% vs 13.13%; OR = 4.78; 95% CI, 2.97-7.68; P < 0.0001). Nausea, headache, and insomnia were the most commonly reported AEs with varenicline and were reported numerically more frequently in the varenicline group compared with the placebo group. Serious AEs (SAEs) were reported in 2.8% of varenicline recipients compared with 1.0% in the placebo group, with 6 subjects reporting psychiatric SAEs compared with none in the placebo group. Conclusion: Based on these data, varenicline was apparently efficacious and generally well tolerated as a smoking-cessation aid in smokers from selected sites in Latin America, Africa, and the Middle East. ClinicalTrials. gov identifier: NCT00594204. (Clin Ther. 2011;33:465-477) (C) 2011 Published by Elsevier HS Journals, Inc.

Postharvest harpin or Bacillus thuringiensis treatments suppress citrus black spot in `Valencia` oranges

Citrus black spot (CBS) caused by Guignardia citricarpa represents an important threat to citriculture in Brazil. Limited information is available regarding potential biological control agents and new alternative compounds that may provide protection of orange fruits against the disease. In this study, the effects of commercial products based on Bacillus thuringiensis var. kurstaki (Bt) bacterium, Bt pure isolates and Harpin protein (Messenger (R)) on the postharvest control of CBS, were evaluated in `Valencia` sweet orange fruits harvested for three consecutive years in a citrus grove. The fruits were sprayed with the following products: DiPel (R) WP (Bt, subspecies, kurstaki strain HD-1,16,000 International Units mg(-1), 32 g active ingredient kg(-1)) (1, 20 and 50 mg ml(-1)), Dimy Pel (R) WP (Bt, subspecies, kurstaki, strain HD-1, 17,600 IU mg(-1), 26 g active ingredient l(-1)) (2, 20 and 50 mg ml(-1)), Messenger (R) (3% harpin protein) (1 and 2 mg ml(-1)) and fungicide Tecto (R) Flowable SC (thiabendazole, 485 gl(-1)) (0.8g active ingredient l(-1)), besides the Bt isolates, Bt- HD-567, Bt- DiPel and Bt- Dimy (9 x 10(8) CFU ml(-1)). Ten days after treatment, the number of newly developed CBS lesions and pycnidia produced were evaluated using fifty fruits per treatment. The Dimy Pel (R) and Messenger (R) reduced the number of new developed CBS lesions on fruits in up to 67% and 62%, respectively. All applied treatments drastically decreased the number of pycnidia produced in the CBS lesions on orange fruits with 85% to 96% reductions compared to the untreated control. Volatile compounds produced by the isolates Bt- HD-567, Bt- Dimy and Bt- DiPel, reduced the number of lesions on treated fruits by 70%, 65% and 71% compared to the control, respectively. In addition, the survival of Bt isolates on orange fruit surfaces were evaluated by recovering and quantifying the number of CFU every seven days for up to 28 days. The declines in survival rates on orange fruit surfaces were drastic for the three strains of Bt in the first week. The CFU numbers of all applied isolates declined by 4 to 5 orders of magnitude after storage at room temperature for 28 days. In vitro assays revealed that the Bt isolates significantly reduced the mycelial growth of the pathogen, ranging from 32% to 51%, compared to the control, whereas no inhibitory effect was observed in the presence of Messenger (R). (C) 2010 Elsevier Ltd. All rights reserved.

The Anglo Cluster: Legacy of the British Empire

The Anglo cluster comprises Australia, Canada, England, Ireland, New Zealand, South Africa (White sample), and the United States of America. These countries are all developed nations, predominantly English speaking, and were all once British colonies. Today, they are amongst the wealthiest countries in the world. The GLOBE results show that the Anglo cluster is characterized by an individualistic performance orientation. Further, although they value gender equality, the Anglo cluster countries tend to be male-dominated in practice. Effective leadership in the Anglo cultures is affected by a combination of charismatic inspiration and a articipative style.

Leadership in the Asian Century: Lessons from GLOBE

In this paper, based on the results of the Global Leadership and Organizational Behavior Effectiveness (GLOBE) 61-nation study of culture and leadership, we present findings related to three ‘clusters’ of countries. These clusters are: (1) the ‘Anglo culture’ cluster (Australia, Canada, Ireland, New Zealand, white South Africa, UK, and USA), the ‘Southern Asia’ cluster (Iran, India, Thailand, Malaysia, Indonesia, and the Philippines), and the ‘Confucian Asia’ cluster (China, Hong Kong, Japan, Singapore, South Korea, and Taiwan). Data from the GLOBE study, reporting middle managers’ perceptions of societal practices and values, and of the factors that facilitate and inhibit effective leadership will be compared across the three clusters. Results demonstrate that, despite differences in cultures, especially cultural values, perceptions of effective leadership vary substantially only in respect of the extent that participation is seen to facilitate leadership. In the Anglo cluster, participative leadership is seen as much more facilitative of leadership, than in either of the Asian clusters. Results are discussed in terms of effective leadership styles suitable for management in the twenty-first century, where Asian economies are likely to play a more dominant role than they have in recent history.

Isotopes, wool, and rangeland monitoring: Let the sheep do the sampling

Stable carbon isotope analyses of wool staples provided insight into the vegetation consumed by sheep at a temporal resolution not previously studied. Contemporary Australian and historic South African samples dating back to 1916 were analyzed for their stable carbon isotope ratio, a proxy for the proportion of C-3 and C-4 plant species consumed by animals. Sheep sample vegetation continuously throughout a year, and as their wool grows it integrates and stores information about their diet. In subtropical and tropical rangelands the majority of grass species are C-4. Since sheep prefer to graze, and their wool is an isotopic record of their diet, we now have the potential to develop a high resolution index to the availability of grass from a sheep's perspective. Isotopic analyses of wool suggest a new direction for monitoring grazing and for the reconstruction of past vegetation changes, which will make a significant contribution to traditional rangeland ecology and management. It is recommended that isotopic and other analyses of wool be further developed for use in rangeland monitoring programs to provide valuable feedback for land managers.

Identification of two novel mutations in the hydroxymethylbilane synthase gene in three patients from two unrelated families with acute intermittent porphyria

We have screened the hydroxymethylbilane synthase cDNAs of 3 patients from 2 families suffering from acute intermittent porphyria (AIP) from Scotland and South Africa using heteroduplex and chemical cleavage of mismatch analyses, Direct sequencing was used to characterise the mutations, The two novel mutations identified were a missense mutation at nucleotide position 64 in exon 3 (R22C) and a single base-pair deletion in exon 15, These mutations are predicted to affect the normal function of the enzyme and, therefore, are expected to be the primary cause of disease in these patients.

Distinguishing species and populations of Rhipicephaline ticks with its 2 ribosomal RNA

Most populations and some species of ticks of the genera Boophilus (5 spp.) and Rhipicephalus (ca. 75 spp.) cannot be distinguished phenotypically. Moreover, there is doubt about the validity of species in these genera. I studied the entire second internal transcribed spacer (ITS 2) rRNA of 16 populations of rhipicephaline ticks to address these problems: Boophilus,microplus from Australia, Kenya, South Africa and Brazil (4 populations); Boophilus decoloratus from Kenya; Rhipicephalus appendiculatus from Kenya, Zimbabwe and Zambia (7 populations); Rhipicephalus zambesiensis from Zimbabwe (3 populations); and Rhipicephalus evertsi from Kenya. Each of the 16 populations had a unique ITS 2, but most of the nucleotide variation occurred among species and genera. ITS 2 rRNA can be used to distinguish the populations and species of Boophilus and Rhipicephalus studied here. Little support was found for the hypothesis that B. microplus from Australia and South Africa are different species. ITS 2 appears useful for phylogenetic inference in the Rhipicephalinae because in genetic distance, maximum likelihood, and maximum parsimony analyses, most branches leading to species had >95% bootstrap support. Rhipicephalus appendiculatus and R, zambeziensis are closely related, yet their ITS 2 sequences could be distinguished unambiguously. This lends weight to a previous proposal that Rhipicephalus sanguineus and Rhipicephalus turanicus, and Rhipicephalus pumlilio and Rhipicephalus camicasi, respectively, are conspecific, because each of these pairs of species had identical sequences for ca. 250 bp of ITS 2 rRNA.

STD syndrome packets: Improving syndromic management of sexually transmitted diseases in developing countries

Objective: To design, introduce, and evaluate STD syndrome packets containing recommended drugs for each syndrome, four condoms, a partner treatment card, and a patient information leaflet, with the goal of improving sexually transmitted disease (STD) case management. Methods: Packet design evolved around available packaging technology, informed by pilot testing with nurses working in primary care clinics, doctors in private medical practices, and patients with an STD, in Hlabisa, South Africa. Evaluation 1 year later included analysis of distribution records and interviews with 16 nurses and 61 patients. Results: A cheap packet (2 U, S, cents each, excluding contents) compatible with current legislation was designed and introduced to six public sector clinics and as a short pilot to five private medical practices, Four thousand eighty-five packets were distributed to the clinics, equivalent to approximately 115% of the STDs reported over that period. All 16 nurses reported using the packets, but only 63% did so all the time because of occasional supply problems, All believed the packets improved treatment by saving time (75%), improving supply of condoms and partner cards (44%), and making treatment easier (56%), Patients also responded positively, and most said they would buy a packet (up to $5) at a pharmacy (84%) or store (63%) if available. Conclusions: The STD syndrome packets have the potential to improve STD syndromic management by standardizing therapy and improving the supply of condoms, partner cards, and information leaflets. Packets are popular with practitioners and patients, but consistent supply is essential for maximal impact, There may be scope for social marketing of the packets, which could further increase use.

Effects of data characteristics on the results of reserve selection algorithms

We tested the effects of four data characteristics on the results of reserve selection algorithms. The data characteristics were nestedness of features (land types in this case), rarity of features, size variation of sites (potential reserves) and size of data sets (numbers of sites and features). We manipulated data sets to produce three levels, with replication, of each of these data characteristics while holding the other three characteristics constant. We then used an optimizing algorithm and three heuristic algorithms to select sites to solve several reservation problems. We measured efficiency as the number or total area of selected sites, indicating the relative cost of a reserve system. Higher nestedness increased the efficiency of all algorithms (reduced the total cost of new reserves). Higher rarity reduced the efficiency of all algorithms (increased the total cost of new reserves). More variation in site size increased the efficiency of all algorithms expressed in terms of total area of selected sites. We measured the suboptimality of heuristic algorithms as the percentage increase of their results over optimal (minimum possible) results. Suboptimality is a measure of the reliability of heuristics as indicative costing analyses. Higher rarity reduced the suboptimality of heuristics (increased their reliability) and there is some evidence that more size variation did the same for the total area of selected sites. We discuss the implications of these results for the use of reserve selection algorithms as indicative and real-world planning tools.

Traditional healers as tuberculosis treatment supervisors: precedent and potential

SETTING: Hlabisa, South Africa. OBJECTIVE: To determine precedent and potential for traditional healers to act as tuberculosis (TB) treatment supervisors. METHODS: Literature review to describe precedent for the involvement of traditional healers in TB treatment supervision. Interviews with 100 TB patients to determine use of healers and their acceptability as supervisors. Interviews with 24 healers in the project sub-district to determine willingness to act as supervisors. RESULTS: Despite extensive literature on the interaction between traditional healers and conventional health services, including descriptions of traditional understandings of TB, no published work was identified that reported supervision of TB patients by traditional healers. Of 100 patients interviewed, only 10% had used a healer as the first health provider for their illness, but 40% had attended a healer at some time prior to diagnosis. Although only 4% believe healers can cure TB, 84% would consider choosing a healer as a treatment supervisor. Of the 24 healers, 15 (63%) distinguished between two types of diagnosis made among patients with. symptoms suggestive of TB: TB and idliso. Idliso is poisoning or bewitching, and is said to be best cured by healers, while TB is infectious and cannot be cured by healers. Most healers (88%) reported having referred patients with possible TB to hospital in the past; all were keen to negotiate collaboration with health services, and 92% were willing to act as treatment supervisors. CONCLUSIONS: While there is little reported precedent for traditional healers to interact formally with tuberculosis treatment services, the potential for collaboration seems to be high, at least in our setting.