Comparative analysis of the value of allogeneic hematopoietic stem-cell transplantation in acute myeloid leukemia with monosomal karyotype versus other cytogenetic risk categories

To determine to what extent allogeneic hematopoietic stem-cell transplantation (alloHSCT) quantitatively reduces relapse in acute myeloid leukemia with monosomal karyotype (MK-AML) compared with alternative postremission therapy and how it compares with other cytogenetic subcategories.

Statistical evaluation of alternative models of human evolution

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species approximately 141 thousand years ago (Kya), an exit out-of-Africa approximately 51 Kya, and a recent colonization of the Americas approximately 10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.

Investigating the structure and form of condom decisional balance in an alternative school sample using confirmatory factor analysis

Teen pregnancy is a continuing problem, bringing with it a host of associated health and social risks. Alternative school students are especially at risk, but are historically under-represented in research. This is especially problematic in that instruments are needed to guide effective intervention development, but psychometrics for these instruments cannot be assumed when used in new populations. Decisional balance from the transtheoretical model offers a framework for understanding condom decision making, but has not been tested with alternative school students. Using responses from 640 subjects from Safer Choices 2 (a school-based HIV/STD/pregnancy prevention program implemented in 10 urban, southwestern alternative schools), a decisional balance scale for condom use was examined. A two-factor, mildly correlated model fit the data well. Tests of invariance examined scale functioning within gender and racial/ethnic groups. The underlying structure varied slightly based on subgroup, but on a practical level the impact on the use of scales was minimal. The structure and loadings were invariant across experimental condition. The pro scale was associated with a lower probability of having engaged in unprotected sexual behavior for sexually active subjects, and this association remained significant while controlling for demographic variables. The con scale did not show a significant association with engagement in unprotected sexual behaviors. Limitations and directions for future research were also discussed.^

Effect of late weaning and use of alternative cages on performance of does, suckling and fattening rabbits under extensive reproductive management

The effects of the combined use of long lactation periods (46 days) with alternative cages on the reproductive and growth performance of 104 rabbit does and their litters during five consecutive reproductive cycles were studied. Half of does were housed in conventional polyvalent cages (39 cm×100 cm×30 cm) and the other half in alternative polyvalent cages (39 cm×100 cm×60 cm), with a raised platform. Half of the rabbit does in each type of cage were weaned at 32 and the other half at 46 days after parturition. Longer lactation negatively affected the body weight (P<0.001), fat and energy content (P<0.05) of rabbit does at the end of the lactation period, but this effect decreased with the number of parturitions. Fertility, prolificacy and doe mortality were not affected by lactation length. Late weaning led to higher litter size (by 8.9%) and litter weight (by 11.3%) at the end of growing period (P<0.001) and lower feed conversion ratio per cage during the experimental period (13.5%) than weaning at 32 day (P<0.001). These results were paralleled by lower mortality (12.6 vs. 17.6%; P<0.01) of young rabbits weaned later during the overall experimental period. Differences in performance as a result of different weaning ages were only observed during cycles with worst health status (third and fifth cycles) in which late weaning decreased mortality. Type of cage did not affect doe body weight and body condition, mortality, fertility, prolificacy and litter size during the five reproductive cycles. Nevertheless, at day 21 litter weight and feed conversion ratio between 3 and 21 day were 4.2% higher (P<0.01) and 5.0% lower (P<0.05), respectively, in animals housed in alternative rather than in conventional cages. Alternative cages also led to heavier litters at 59 days (P<0.01). It was concluded that the combined use of longer lactations and cages with higher available surface with a raised platform could be alternatives to improve animal welfare in farmed rabbit.

Effect of late weaning and use of alternative cages on performance of does, suckling and fattening rabbits under extensive reproductive management

The effects of the combined use of long lactation periods (46 days) with alternative cages on the reproductive and growth performance of 104 rabbit does and their litters during five consecutive reproductive cycles were studied. Half of does were housed in conven- tional polyvalent cages (39 cm x 100 cm x 30 cm) and the other half in alternative polyvalent cages (39 cm x 100 cm x 60 cm), with a raised platform. Half of the rabbit does in each type of cage were weaned at 32 and the other half at 46 days after parturition. Longer lactation negatively affected the body weight ( P o 0.001), fat and energy content ( P o 0.05) of rabbit does at the end of the lactation period, but this effect decreased with the number of parturitions. Fertility, prolificacy and doe mortality were not affected by lactation length. Late weaning led to higher litter size (by 8.9%) and litter weight (by 11.3%) at the end of growing period ( P o 0.001) and lower feed conversion ratio per cage during the experimental period (13.5%) than weaning at 32 day ( P o 0.001). These results were paralleled by lower mortality (12.6 vs. 17.6%; P o 0.01) of young rabbits weaned later during the overall experimental period. Differences in performance as a result of different weaning ages were only observed during cycles with worst health status (third and fifth cycles) in which late weaning decreased mortality. Type of cage did not affect doe body weight and body condition, mortality, fertility, prolificacy and litter size during the five reproductive cycles. Nevertheless, at day 21 litter weight and feed conversion ratio between 3 and 21 day were 4.2% higher ( P o 0.01) and 5.0% lower ( P o 0.05), respectively, in animals housed in alternative rather than in conventional cages. Alternative cages also led to heavier litters at 59 days ( P o 0.01). It was concluded that the combined use of longer lactations and cages with higher available surface with a raised platform could be alternatives to improve animal welfare in farmed rabbit.

The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms

Defects in the XPG DNA repair endonuclease gene can result in the cancer-prone disorders xeroderma pigmentosum (XP) or the XP–Cockayne syndrome complex. While the XPG cDNA sequence was known, determination of the genomic sequence was required to understand its different functions. In cells from normal donors, we found that the genomic sequence of the human XPG gene spans 30 kb, contains 15 exons that range from 61 to 1074 bp and 14 introns that range from 250 to 5763 bp. Analysis of the splice donor and acceptor sites using an information theory-based approach revealed three splice sites with low information content, which are components of the minor (U12) spliceosome. We identified six alternatively spliced XPG mRNA isoforms in cells from normal donors and from XPG patients: partial deletion of exon 8, partial retention of intron 8, two with alternative exons (in introns 1 and 6) and two that retained complete introns (introns 3 and 9). The amount of alternatively spliced XPG mRNA isoforms varied in different tissues. Most alternative splice donor and acceptor sites had a relatively high information content, but one has the U12 spliceosome sequence. A single nucleotide polymorphism has allele frequencies of 0.74 for 3507G and 0.26 for 3507C in 91 donors. The human XPG gene contains multiple splice sites with low information content in association with multiple alternatively spliced isoforms of XPG mRNA.

Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5' splice sites.

Alternative splicing of precursor messenger RNAs (pre-mRNAs) is an important mechanism for the regulation of gene expression. The members of the SR protein family of pre-mRNA splicing factors have distinct functions in promoting alternative splice site usage. Here we show that SR proteins are required for the first step of spliceosome assembly, interaction of the U1 small nuclear ribonucleoprotein complex (U1 snRNP) with the 5' splice site of the pre-mRNA. Further, we find that individual SR proteins have distinct abilities to promote interaction of U1 snRNP with alternative 5' splice junctions. These results suggest that SR proteins direct 5' splice site selection by regulation of U1 snRNP assembly onto the pre-mRNA.

An integer-valued data envelopment analysis model with bounded outputs

Integer-valued data envelopment analysis (DEA) with alternative returns to scale technology has been introduced and developed recently by Kuosmanen and Kazemi Matin. The proportionality assumption of their introduced "natural augmentability" axiom in constant and nondecreasing returns to scale technologies makes it possible to achieve feasible decision-making units (DMUs) of arbitrary large size. In many real world applications it is not possible to achieve such production plans since some of the input and output variables are bounded above. In this paper, we extend the axiomatic foundation of integer-valuedDEAmodels for including bounded output variables. Some model variants are achieved by introducing a new axiom of "boundedness" over the selected output variables. A mixed integer linear programming (MILP) formulation is also introduced for computing efficiency scores in the associated production set. © 2011 The Authors. International Transactions in Operational Research © 2011 International Federation of Operational Research Societies.

Combustion Instability and Active Control: Alternative Fuels, Augmentors, and Modeling Heat Release

Experimental and analytical studies were conducted to explore thermo-acoustic coupling during the onset of combustion instability in various air-breathing combustor configurations. These include a laboratory-scale 200-kW dump combustor and a 100-kW augmentor featuring a v-gutter flame holder. They were used to simulate main combustion chambers and afterburners in aero engines, respectively. The three primary themes of this work includes: 1) modeling heat release fluctuations for stability analysis, 2) conducting active combustion control with alternative fuels, and 3) demonstrating practical active control for augmentor instability suppression. The phenomenon of combustion instabilities remains an unsolved problem in propulsion engines, mainly because of the difficulty in predicting the fluctuating component of heat release without extensive testing. A hybrid model was developed to describe both the temporal and spatial variations in dynamic heat release, using a separation of variables approach that requires only a limited amount of experimental data. The use of sinusoidal basis functions further reduced the amount of data required. When the mean heat release behavior is known, the only experimental data needed for detailed stability analysis is one instantaneous picture of heat release at the peak pressure phase. This model was successfully tested in the dump combustor experiments, reproducing the correct sign of the overall Rayleigh index as well as the remarkably accurate spatial distribution pattern of fluctuating heat release. Active combustion control was explored for fuel-flexible combustor operation using twelve different jet fuels including bio-synthetic and Fischer-Tropsch types. Analysis done using an actuated spray combustion model revealed that the combustion response times of these fuels were similar. Combined with experimental spray characterizations, this suggested that controller performance should remain effective with various alternative fuels. Active control experiments validated this analysis while demonstrating 50-70\% reduction in the peak spectral amplitude. A new model augmentor was built and tested for combustion dynamics using schlieren and chemiluminescence techniques. Novel active control techniques including pulsed air injection were implemented and the results were compared with the pulsed fuel injection approach. The pulsed injection of secondary air worked just as effectively for suppressing the augmentor instability, setting up the possibility of more efficient actuation strategy.

Integrated pest management and the (un)sustainable use of pesticides

Doutoramento em Engenharia Agronómica - Instituto Superior de Agronomia - UL

Harvest-ironman: heavy armature, and not its defensive secretions, protects a harvestman against a spider

Natural selection has caused prey species to evolve distinct defensive mechanisms. One of such mechanisms was the evolution of noxious or distasteful chemicals, which have appeared independently in a number of vertebrates and invertebrates. In detailed analyses of arthropod behaviour, scent gland secretions have consistently been shown to be responsible for repelling specific predators. Because using such chemicals is costly, animals with alternative cheaper defences are expected not to release such secretions when alternative options exist. In this study, we sought to determine the defensive mechanisms of the harvestman Discocyrtus invalidus, a heavy bodied species that bears a pair of repugnatorial glands. The spider Enoploctenus cyclothorax was used as the predator, and the cricket Gryllus sp. was used as a control. In a first set of experiments, the harvestmen were preyed upon significantly less than the crickets. In two other experiments, we found that harvestmen did not use their scent gland secretions to deter the predator. Moreover, results of a fourth experiment revealed that these spiders are not repelled by defensive secretions. Discocyrtus invalidus has a thick cuticle on the entire body: scanning electron micrographs revealed that only the mouth, the articulations of appendages and the tips of the legs are not covered by a hard integument. In a fifth experiment, we found that these spiders had difficulty piercing the harvestmen body. This is the first experimental evidence that a chemically defended arachnid does not use its scent gland secretions to repel a much larger predator but instead relies on its heavily built body. (c) 2010 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (similar to 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

The higher-level phylogeny of Archosauria (Tetrapoda: Diapsida)

Crown group Archosauria, which includes birds, dinosaurs, crocodylomorphs, and several extinct Mesozoic groups, is a primary division of the vertebrate tree of life. However, the higher-level phylogenetic relationships within Archosauria are poorly resolved and controversial, despite years of study. The phylogeny of crocodile-line archosaurs (Crurotarsi) is particularly contentious, and has been plagued by problematic taxon and character sampling. Recent discoveries and renewed focus on archosaur anatomy enable the compilation of a new dataset, which assimilates and standardizes character data pertinent to higher-level archosaur phylogeny, and is scored across the largest group of taxa yet analysed. This dataset includes 47 new characters (25% of total) and eight taxa that have yet to be included in an analysis, and total taxonomic sampling is more than twice that of any previous study. This analysis produces a well-resolved phylogeny, which recovers mostly traditional relationships within Avemetatarsalia, places Phytosauria as a basal crurotarsan clade, finds a close relationship between Aetosauria and Crocodylomorpha, and recovers a monophyletic Rauisuchia comprised of two major subclades. Support values are low, suggesting rampant homoplasy and missing data within Archosauria, but the phylogeny is highly congruent with stratigraphy. Comparison with alternative analyses identifies numerous scoring differences, but indicates that character sampling is the main source of incongruence. The phylogeny implies major missing lineages in the Early Triassic and may support a Carnian-Norian extinction event.

Ultraviolet signals ultra-aggression in a lizard

Understanding the role of multiple colour signals during sexual signalling is a central theme in animal communication. We quantified the role of multiple colour signals (including ultraviolet, UV), measures of body size and testosterone levels in settling disputes between male rivals in an elaborately ornamented, African lizard, played out in a large 'tournament' in the wild. The hue and brightness (total reflectance) of the UV throat in Augrabies flat lizards, Platysaurus broadleyi, as well as body size, were consistent and strong predictors of 'fighting ability'. Males with high fighting ability were larger and displayed a UV throat with low total reflectance. In contrast, males with low fighting ability were smaller and had violet throats with broader spectral reflectance curves (higher total reflectance). As fighting ability is associated with alternative reproductive tactics in this system (territorial versus floater), we also examined the role of colour signals in predicting male reproductive tactic. Territorial males had UV throats with higher chroma but had poorer body condition than floater males, probably because of the energetic costs of maintaining a territory. Although testosterone was not a significant predictor of fighting ability or reproductive tactic, it was correlated with the hue of the UV throat, suggesting that testosterone may impose some constraint on signal expression. Lastly, we show that within the context of the natural signalling environment, UV-reflective throats constitute a conspicuous, effective signal that male Augrabies flat lizards use to advertise their status honestly to rivals. (c) 2006 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

A cost-benefit analysis of hedgerow intercropping in the Philippine uplands using the SCUAF model

Soil erosion in the Philippine uplands is severe. Hedgerow intercropping is widely advocated as an effective means of controlling soil erosion from annual cropping systems in the uplands. However, few farmers adopt hedgerow intercropping even in areas where it has been vigorously promoted. This may be because farmers find hedgerow intercropping to be uneconomic compared to traditional methods of farming. This paper reports a cost-benefit analysis comparing the economic returns from traditional maize farming with those from hedgerow intercropping in an upland community with no past adoption of hedgerows. A simple erosion/productivity model, Soil Changes Under Agroforestry (SCUAF), is used to predict maize yields over 25 years. Economic data were collected through key informant surveys with experienced maize farmers in an upland community. Traditional methods of open-field farming of maize are economically attractive to farmers in the Philippine uplands. In the short term, establishment costs are a major disincentive to the adoption of hedgerow intercropping. In the long term, higher economic returns from hedgerow intercropping compared to open-field farming are realised, but these lie beyond farmers' limited planning horizons.