The cooperative parallel: A discussion about run-time schedulers for nested parallelism

Nested parallelism is a well-known parallelization strategy to exploit irregular parallelism in HPC applications. This strategy also fits in critical real-time embedded systems, composed of a set of concurrent functionalities. In this case, nested parallelism can be used to further exploit the parallelism of each functionality. However, current run-time implementations of nested parallelism can produce inefficiencies and load imbalance. Moreover, in critical real-time embedded systems, it may lead to incorrect executions due to, for instance, a work non-conserving scheduler. In both cases, the reason is that the teams of OpenMP threads are a black-box for the scheduler, i.e., the scheduler that assigns OpenMP threads and tasks to the set of available computing resources is agnostic to the internal execution of each team. This paper proposes a new run-time scheduler that considers dynamic information of the OpenMP threads and tasks running within several concurrent teams, i.e., concurrent parallel regions. This information may include the existence of OpenMP threads waiting in a barrier and the priority of tasks ready to execute. By making the concurrent parallel regions to cooperate, the shared computing resources can be better controlled and a work conserving and priority driven scheduler can be guaranteed.Peer ReviewedPostprint (author's final draft

Can an Infectious Disease Genomics Project Predict and Prevent the Next Pandemic?

Infectious diseases need a globally coordinated genomic-based movement linking sequencing efforts to development of response tools to mitigate the impact of existing and emerging threats

25 years of HIV-1 research – progress and perspectives

Twenty-five years after the discovery and isolation of the human immunodeficiency virus by French and American scientists, much progress has been made in basic research, clinical treatment, and public health prevention measures for acquired immunodeficiency syndrome. Here, we summarize, in brief, advances that have been achieved and provide some perspectives on future challenges

Diversity of HIV-1 Subtype B: Implications to the Origin of BF Recombinants

BACKGROUND: The HIV-1 subtype B epidemic in Brazil is peculiar because of the high frequency of isolates having the GWGR tetramer at V3 loop region. It has been suggested that GWGR is a distinct variant and less pathogenic than other subtype B isolates. METHODOLOGY/PRINCIPAL FINDINGS: Ninety-four percent of the HIV-1 subtype B worldwide sequences (7689/8131) obtained from the Los Alamos HIV database contain proline at the tetramer of the V3 loop of the env gene (GPGR) and only 0.74% (60/8131) have tryptophan (GWGR). By contrast, 48.4% (161/333) of subtype B isolates from Brazil have proline, 30.6% (102/333) contain tryptophan and 10.5% (35/333) have phenylalanine (F) at the second position of the V3 loop tip. The proportion of tryptophan and phenylalanine in Brazilian isolates is much higher than in worldwide subtype B sequences (chi-square test, p = 0.0001). The combined proportion of proline, tryptophan and phenylalanine (GPGR+GWGR+GFGR) of Brazilian isolates corresponds to 89% of all amino acids in the V3 loop. Phylogenetic analysis revealed that almost all subtype B isolates in Brazil have a common origin regardless of their motif (GWGR, GPGR, GGGR, etc.) at the V3 tetramer. This shared ancestral origin was also observed in CRF28_BF and CRF29_BF in a genome region (free of recombination) derived from parental subtype B. These results imply that tryptophan substitution (e.g., GWGR-to-GxGR), which was previously associated with the change in the coreceptor usage within the host, also occurs at the population level. CONCLUSIONS/SIGNIFICANCE: Based on the current findings and previous study showing that tryptophan and phenylalanine in the V3 loop are related with coreceptor usage, we propose that tryptophan and phenylalanine in subtype B isolates in Brazil are kept by selective mechanisms due to the distinct coreceptor preferences in target cells of GWGR, GFGR and GFGR viruses

Subtype-associated differences in HIV-1 reverse transcription affect the viral replication

Background: The impact of the products of the pol gene, specifically, reverse transcriptase (RT) on HIV-1 replication, evolution, and acquisition of drug resistance has been thoroughly characterized for subtype B. For subtype C, which accounts of almost 60% of HIV cases worldwide, much less is known. It has been reported that subtype C HIV-1 isolates have a lower replication capacity than B; however, the basis of these differences remains unclear. Results: We analyzed the impact of the pol gene products from HIV-1 B and C subtypes on the maturation of HIV virions, accumulation of reverse transcription products, integration of viral DNA, frequency of point mutations in provirus and overall viral replication. Recombinant HIV-1 viruses of B and C subtypes comprising the pol fragments encoding protease, integrase and either the whole RT or a chimeric RT from different isolates of the C and B subtypes, were used for infection of cells expressing CXCR4 or CCR5 co-receptors. The viruses carrying different fragments of pol from the isolates of B and C subtypes did not reveal differences in Gag and GagPol processing and viral RNA incorporation into the virions. However, the presence of the whole RT from subtype C, or the chimeric RT containing either the polymerase or the connection and RNase H domains from C isolates, caused significantly slower viral replication regardless of B or C viral backbone. Subtype C RT carrying viruses displayed lower levels of accumulation of strong-stop cDNA in permeabilized virions during endogenous reverse transcription, and decreased accumulation of both strong-stop and positive strand reverse transcription products in infected cells and in isolated reverse transcription complexes. This decreased accumulation correlated with lower levels of viral DNA integration in cells infected with viruses carrying the whole RT or RT domains from subtype C isolates. The single viral genome assay analysis did not reveal significant differences in the frequency of point mutations between the RT from B or C subtypes. Conclusions: These data suggest that the whole RT as well as distinct polymerase and connection-RNase H domains from subtype C HIV-1 confer a lower level of accumulation of reverse transcripts in the virions and reverse transcription complexes as compared to subtype B, resulting in a lower overall level of virus replication

COVAD survey 2 long-term outcomes: unmet need and protocol

Vaccine hesitancy is considered a major barrier to achieving herd immunity against COVID-19. While multiple alternative and synergistic approaches including heterologous vaccination, booster doses, and antiviral drugs have been developed, equitable vaccine uptake remains the foremost strategy to manage pandemic. Although none of the currently approved vaccines are live-attenuated, several reports of disease flares, waning protection, and acute-onset syndromes have emerged as short-term adverse events after vaccination. Hence, scientific literature falls short when discussing potential long-term effects in vulnerable cohorts. The COVAD-2 survey follows on from the baseline COVAD-1 survey with the aim to collect patient-reported data on the long-term safety and tolerability of COVID-19 vaccines in immune modulation. The e-survey has been extensively pilot-tested and validated with translations into multiple languages. Anticipated results will help improve vaccination efforts and reduce the imminent risks of COVID-19 infection, especially in understudied vulnerable groups

Ecología acústica y el paisaje sonoro en una comunidad de Huánuco, Perú

The main objective of this research was to establish the relationship or correspondence between noise pollution and the sound landscape. This study is part of descriptive, correlation and cross-sectional research, since through analysis, observation, comparison and description of the variables we have established levels and the relationship between them. The objects of studies were validated by experts in the areas of acoustic ecology, noise pollution and sound landscape. The data that support this research comes from the results obtained by the application of the instruments that do not agree with what is established in the D.S. No. 085-2003 and the weighting of the sound obtained with the sound level meter. Finally, we conclude that despite the results, there is a lack of association between the aspect of noise pollution and the sound landscape, applied for the first time in a Peruvian province.El principal objetivo de esta investigación fue establecer la relación o correspondencia entre la contaminación acústica y el paisaje sonoro. Este estudio se enmarca dentro de las investigaciones descriptivas, correlaciónales y transversales, ya que por medio del análisis, observación, comparación y descripción de las variables hemos establecido niveles y la relación entre ellas. Los objetos de estudios fueron validados por expertos en las áreas de la ecología acústica, contaminación sonora y el paisaje sonoro. Los datos que sostienen esta investigación vienen de los resultados obtenidos por la aplicación de los instrumentos que no concuerdan con lo establecido en el D.S. Nº 085-2003 y la ponderación del sonido obtenido con el sonómetro. Finalmente concluimos que a pesar de los resultados, se muestran una carencia de asociación entre el aspecto de la contaminación acústica y el paisaje sonoro, aplicado por primera vez en una provincia peruana

Guinea pig sperm is capable of fertilising bovine zona-intact oocytes in vitro

Peer reviewe