Estimating and evaluating the statistics of gapped local-alignment scores

We present a novel maximum-likelihood-based algorithm for estimating the distribution of alignment scores from the scores of unrelated sequences in a database search. Using a new method for measuring the accuracy of p-values, we show that our maximum-likelihood-based algorithm is more accurate than existing regression-based and lookup table methods. We explore a more sophisticated way of modeling and estimating the score distributions (using a two-component mixture model and expectation maximization), but conclude that this does not improve significantly over simply ignoring scores with small E-values during estimation. Finally, we measure the classification accuracy of p-values estimated in different ways and observe that inaccurate p-values can, somewhat paradoxically, lead to higher classification accuracy. We explain this paradox and argue that statistical accuracy, not classification accuracy, should be the primary criterion in comparisons of similarity search methods that return p-values that adjust for target sequence length.

H�� salva����o para a ��frica? Thabo Mbeki e seu New Partnership for African development

O NEPAD - New Partnership for African Development - tem seus prim��rdios em 1996, proposto pelo atual presidente da ��frica do Sul, Thabo Mbeki e outros l��deres africanos, para erradicar a marginaliza����o e o subdesenvolvimento africanos e promover o crescimento econ��mico, atrav��s da integra����o continental. Seus objetivos, inseridos no contexto da globaliza����o e do African Renaissance, incorpora valores da luta antiapartheid sul-africana, restaura����o da auto-estima e resgate de valores pr��-coloniais. O que o difere de outros planos que n��o deram certo na ��frica �� o v��nculo insepar��vel entre democracia, direitos humanos, paz, governabilidade e o desenvolvimento econ��mico, as responsabilidades assumidas pelos participantes e a propriedade africana do plano.

Property and age organisation among an East African pastoralist group

Estudos sobre sistemas et��rios na ��frica Oriental t��m focado principalmente as regras que regulam recrutamento, com ��nfase ao modo em que se mant��m a autoridade e os cargos pol��ticos, assim como �� natureza n��o-militar e n��o-pol��tica dos sistemas et��rios. Apesar de contribu��rem enormemente para a nossa compreens��o das organiza����es et��rias na regi��o, esses estudos n��o lidam explicitamente com a quest��o da propriedade e com o modo em que ela constitui um dos principais focos para atividades de organiza����es et��rias. De fato, quando se menciona a propriedade, ela �� vista em fun����o das fam��lias e, portanto, do parentesco. Apresentando e discutindo uma variedade de casos envolvendo o modo em que a propriedade �� tratada por lideran��as de um conjunto et��rio/geracional e residentes Hor e n��o-Hor do territ��rio Hor, este estudo conclui que a posse, o uso e controle de recursos n��o constitui um assunto que pertence exclusivamente �� esfera de grupos de parentesco; trata-se tamb��m de uma quest��o central para organiza����es et��rias. Apesar de haver, aparentemente, alguma ambig��idade decorrente da ��nfase equilibrada que os Hor dedicam ao parentesco e ��s categorias et��rias e suas complementaridades em assuntos relacionados �� economia, �� religi��o e ao direito, dados referentes aos Hor revelam uma tend��ncia a tratar quest��es referentes ao uso de recursos cruciais em termos de organiza����o et��ria. Trata-se de um estudo sobre os Hor (Arbore), um povo pastoril do Sudoeste da Eti��pia.

Portuguese-Americans in the East Coast: is ���crystallization��� a myth?

In the last but one census of the population in the US, I had to respond as a foreigner resident, and when I was asked about my race, I chose to answer the ways I had heard the activists of the civil rights movement used to do in the US, when color blindness was an important thing to fight for ��� to ���RACE��� I added ���HUMAN���...

Difficulties in the Learning of Statistics by the Students of the Primary Education

The present study, covering students from public schools and a private school on the island of S��o Miguel (Azores, Portugal), aims to meet the difficulties of the students of the 3rd and 4th years of the primary education in solving tasks involving construction, reading and interpreting tables and statistical graphs, in the context of Organization and Data Handling (ODH). We present the main results obtained from statistical methods, among which we highlight some non-parametric hypothesis tests and the Categorical Principal Component Analysis (CatPCA), given the nature of the variables included in the questionnaire (mostly nominal and ordinal variables).

Transnational Migrants and Transnational Spirits: An African Religion in Lisbon

Journal of Ethnic and Migration Studies, Vol.34, n.2,pp. 253 ��� 269

Probability and statistics: selected problems

Probability and Statistics���Selected Problems is a unique book for senior undergraduate and graduate students to fast review basic materials in Probability and Statistics. Descriptive statistics are presented first, and probability is reviewed secondly. Discrete and continuous distributions are presented. Sample and estimation with hypothesis testing are presented in the last two chapters. The solutions for proposed excises are listed for readers to references.

Ambient noise tomography of the East African Rift in Mozambique

Seismic ambient noise tomography is applied to central and southern Mozambique, located in the tip of the East African Rift (EAR). The deployment of MOZART seismic network, with a total of 30 broad-band stations continuously recording for 26 months, allowed us to carry out the first tomographic study of the crust under this region, which until now remained largely unexplored at this scale. From cross-correlations extracted from coherent noise we obtained Rayleigh wave group velocity dispersion curves for the period range 5���40 s. These dispersion relations were inverted to produce group velocity maps, and 1-D shear wave velocity profiles at selected points. High group velocities are observed at all periods on the eastern edge of the Kaapvaal and Zimbabwe cratons, in agreement with the findings of previous studies. Further east, a pronounced slow anomaly is observed in central and southern Mozambique, where the rifting between southern Africa and Antarctica created a passive margin in the Mesozoic, and further rifting is currently happening as a result of the southward propagation of the EAR. In this study, we also addressed the question concerning the nature of the crust (continental versus oceanic) in the Mozambique Coastal Plains (MCP), still in debate. Our data do not support previous suggestions that the MCP are floored by oceanic crust since a shallow Moho could not be detected, and we discuss an alternative explanation for its ocean-like magnetic signature. Our velocity maps suggest that the crystalline basement of the Zimbabwe craton may extend further east well into Mozambique underneath the sediment cover, contrary to what is usually assumed, while further south the Kaapval craton passes into slow rifted crust at the Lebombo monocline as expected. The sharp passage from fast crust to slow crust on the northern part of the study area coincides with the seismically active NNE-SSW Urema rift, while further south the Mazenga graben adopts an N-S direction parallel to the eastern limit of the Kaapvaal craton. We conclude that these two extensional structures herald the southward continuation of the EAR, and infer a structural control of the transition between the two types of crust on the ongoing deformation.

African histoplasmosis: report of the first case in Brazil and treatment with itraconazole

We report the first case of African histoplasmosis diagnosed in Brazil. The patient was an immigrant from Angola who had come to Brazil six months after the appearance of the skin lesion. The skin of the right retroauricular area was the only site of involvement. The diagnosis was established by direct mycologic examination, culture and by histopathologic examination of the lesion. The patient was successfully treated with Itraconazole 100mg a day for 52 days. No recurrent skin lesions were observed during the ten month follow-up period.

Neutralization of bitis parviocula (Ethiopian mountain adder) venom by the south african institute of medical research (SAIMR) antivenom

BACKGROUND: The Ethiopian mountain adder (Bitis parviocula) is a viperid known only from a few locations in southwestern Ethiopia. METHODS: a total of 30 ��g of B. arietans and B. parviocula venoms were run on a 10-20% Tricine gel. To assay lethality dose fifty (LD50), five groups of eight mice for each venom were used. Hemorrhagic activity for crude venom was tested. Fibrinogenolytic activity of crude venom was measured using (2.5 mg/mL) of fibrinogen solution and (0.03 mg/mL) of crude venom. Gelatinase activity of the venom was tested on a Kodak X-OMAT TM film. Crude venoms of B. parviocula and B. arietans were tested for their abilities to affect clotting time, clotting rate and platelet function on whole human blood. RESULTS: The (SAIMR) antivenom was confirmed in this study to neutralize the lethal activity of venom from Bitis parviocula. The ED50s of SAIMR antivenom on B. parviocula and B. arietans neutralized half of 18.2 and 66.7 mg of venom, respectively. The hemorrhagic activities (MHDs) of B. parviocula and B. arietans were 0.88 and 1.7 ��g, respectively. Bitis arietans and B. parviocula venoms degradated α and β chains at different times. The γ chains remained unaffected. Bitis parviocula venom did not exhibit gelatinase activity, while B. arietans had a MGD of 6.9 ��g. At 3 mg/mL, the crude venoms of B. parviocula and B. arietans did not significantly affect clotting time or clotting rate. CONCLUSIONS: The SAIMR antivenom is very effective in neutralizing the venom of B. parviocula and should be considered in treating envenomations by these snakes.

Strategies of the African swine fever virus to manipulate innate immunity

Dissertation presented to obtain the Ph.D degree in Biology

Effect of Efavirenz on High-Density Lipoprotein Antioxidant Properties in HIV-Infected Patients

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT: * In previous work, we showed a long-term and concentration-dependent beneficial effect of the non-nucleoside reverse transcriptase inhibitor efavirenz (EFV) on high-density lipoproteins (HDL) in human immunodeficiency virus (HIV)-infected patients. * Furthermore, it has been suggested that instead of the current practice of only measuring HDL-chelesterol values, the evaluation of HDL function, namely its antioxidant properties, might be an improved tool for identifying subjects at increased risk for cardiovascular events. * Paraoxonase-1 (PON-1) is an enzyme associated with HDL that is responsible for HDL antioxidant function. WHAT THIS STUDY ADDS: * In the present work, we studied the effect of EFV on the activity of PON-1 and showed, for the first time, that EFV-based antiretroviral therapy is associated with a better antioxidant function, i.e. with a higher PON-1 activity. AIMS: A long-term and concentration-dependent beneficial effect of efavirenz (EFV) on cholesterol associated with high-density lipoprotein (HDL-c) in human immunodeficiency virus (HIV)-infected patients has been documented. Furthermore, it has been suggested that, instead of the current practice of only measuring HDL-c values, the evaluation of HDL quality might be an improved tool for identifying subjects at increased risk of cardiovascular events. Paraoxonase-1 (PON-1) is an enzyme associated with HDL that is involved in the onset of cardiovascular disease and responsible for HDL antioxidant function. The aim of the present study was to investigate the effect of EFV on the circulating activity of PON-1 in HIV-infected patients. METHODS: The patients included were adults with a documented HIV-1 infection, nontreated or treated with antiretroviral regimens including EFV 600 mg once daily as first therapeutic regimen for at least 3 months. The influence of treatment with EFV, HDL-c and CD4 cell count on PON-1 activity was analysed. RESULTS: HIV-infected White patients treated with EFV had higher PON-1 activity [77.35 U l(-1) (65.66, 89.04)] (P < 0.05) and higher PON-1 activity : HDL-c ratio [1.88 (1.49, 2.28)] (P < 0.01) than untreated patients. PON-1 activity was higher in Black patients (P < 0.001) and in patients with a CD4 cell count >500 cells ml(-1) (P= 0.0120). CONCLUSIONS: EFV-based antiretroviral regimens are associated with HDL particles with a better antioxidant function, i.e. with a higher PON-1 activity. The PON-1 activity of Black patients is higher than that found in Whites regardless of treatment. Ethnicity should be taken into consideration when studying drug effects on PON-1 activity.

The African studies course of the Instituto de Estudos Superiores Militares. An analysis of the correlations and conflictive character inside the triangle - Development, environment and security - in Africa���s Nigeria

Relat��rio de Est��gio de Mestrado em Ci��ncia Pol��tica e Rela����es Internacionais Globaliza����o e Ambiente

Under-Report and Underdiagnosis of Chronic Respiratory Diseases in an African Country

BACKGROUND: Chronic respiratory diseases (CRD) are greatly underestimated. The aim of this study was to assess the burden associated with reported CRD and chronic obstructive pulmonary disease, as defined on the basis of various standardized criteria, by estimating their point prevalence in a sample of individuals attending the Primary Health Care (PHC) level and Emergency Room (ER) Departments in Cape Verde (CV) archipelago. The second aim of the study was to identify factors related to airways obstruction and reported CRD in this population. METHODS: A cross-sectional study was carried out in CV during 2 weeks. Outpatients aged more than 20 years seeking care at PHC level and ER answered a standardized questionnaire and were subjected to spirometry, independently of their complaint. Two criteria for airways obstruction were taken into account: forced expiratory volume (FEV(1)) <80% of the predicted value and FEV(1)/forced vital capacity (FVC) ratio <0.70. RESULTS: A total of 274 individuals with a satisfactory spirometry were included. 22% of the individuals had a FEV(1) < 80%. Individuals older than 46 years had a higher risk of having airways obstruction. Asthma diagnosis (11%) had a clear association with airways obstruction. Smoking was a risk factor for a lower FEV(1). Working in a dust place and cooking using an open fire were both related to chronic bronchitis and asthma diagnosis. CONCLUSION: Under-report and underdiagnosis of chronic respiratory conditions seem to be a reality in CV just as in other parts of the world. To improve diagnosis, our results reinforce the need of performing a spirometry