HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges

High Performance Computing (HPC) clouds are becoming an alternative to on-premise clusters for executing scientific applications and business analytics services. Most research efforts in HPC cloud aim to understand the cost-benefit of moving resource-intensive applications from on-premise environments to public cloud platforms. Industry trends show hybrid environments are the natural path to get the best of the on-premise and cloud resources---steady (and sensitive) workloads can run on on-premise resources and peak demand can leverage remote resources in a pay-as-you-go manner. Nevertheless, there are plenty of questions to be answered in HPC cloud, which range from how to extract the best performance of an unknown underlying platform to what services are essential to make its usage easier. Moreover, the discussion on the right pricing and contractual models to fit small and large users is relevant for the sustainability of HPC clouds. This paper brings a survey and taxonomy of efforts in HPC cloud and a vision on what we believe is ahead of us, including a set of research challenges that, once tackled, can help advance businesses and scientific discoveries. This becomes particularly relevant due to the fast increasing wave of new HPC applications coming from big data and artificial intelligence.Comment: 29 pages, 5 figures, Published in ACM Computing Surveys (CSUR

Macaúba (Acrocomia aculeata) cake from biodiesel processing: a low-cost substrate to produce lipases from Moniliella spathulata R25L270 with potential application in the oleochemical industry

[Background]: Biodiesel industry wastes were evaluated as supplements for lipase production by Moniliella spathulata R25L270, which is newly identified yeast with great lipolytic potential. Macaúba cake (MC), used for the first time in this work as inducer to produce lipases, and residual oil (RO) were mixed to maximise enzyme production. The lipase secreted was biochemically characterised.[Results]: The best ratio for the mixture (MC:RO) was 0.66:0.34 and the fitted values for lipase activity and total protein concentration were 0.98 U mL−1 and 0.356 mg mL−1, respectively. Maximum activity obtained (2.47 U mL−1) was achieved at 31.5°C and pH 6.7, and the enzyme was stable in this condition. A novel enzyme was purified and identified for the first time by mass spectrometry. The lipase efficiently hydrolysed different natural oils and exhibited selectivity in the production of eicosapentaenoic acid from fish oil.[Conclusion]: The use of MC and RO as a supplement to produce the new lipase from M. spathulata R25L270 may be one alternative for reducing lipase production costs and simultaneously adding value to biodiesel industry residues. The potential application of the lipase in the oleochemical industry was demonstrated by its pH and temperature stabilities and selective hydrolysis.This research was supported by Brazilian agencies: CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), INCT (Instituto Nacional de Ciência e Tecnologia) de Nanomateriais de Carbono, FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais), Rede Mineira de Toxinas com Ação Terapêutica and CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior).Peer reviewe

Validação de uma escala de mensuração de atitude em STEM em um contexto brasileiro na Universidade de Pernambuco utilizando análise fatorial confirmatória

O ensino de Ciência, Tecnologia, Engenharia e Matemática (STEM) dentro de todos os níveis educacionais está se tornando de grande importância em escala mundial, mas no Brasil os números indicam um déficit. Neste contexto, o objetivo deste artigo consiste em validar a aplicação de uma escala de atitude em relação a STEM dentro do contexto brasileiro. A amostra é composta por um grupo alunos ingressantes nos cursos de engenharia. A validação da escala foi feita com a utilização de análise fatorial confirmatória, na qual os resultados apontaram que 67% dos itens da escala eram compatíveis a realidade brasileira. Os outros itens foram alterados, gerando uma nova escala, adaptada ao cenário educacional STEM no Brasil

Cationic dyes immobilized on cellulose acetate surface modified with titanium dioxide: factorial design and an application as sensor for NADH

The electrochemical properties of meldola blue and toluidine blue cationic dyes immobilized on cellulose acetate surface modified with titanium dioxide were investigated by cyclic voltammetry. The materials synthesized were employed as carbon paste electrodes. The redox mediator properties of the meldola blue and toluidine blue chemically modified electrodes were optimized using a factorial design, consisting of two levels and four factors with two pseudo-central points (n= 20 experiments). The factorial analysis was carried out by searching for better reversibility of the redox process, such as the lowest separation between anodic and cathodic potential peaks and a current ratio near unity. The factors that presented significant effects on the overall optimization of the system to achieve the best conditions of the reversibility of electron transfer were the main factors scan rate and type of electrode (meldola blue or toluidine blue), besides the interaction factors KCl concentration × type of electrode (B×D) and the pH × [KCl] concentration × scan rate (A×B×C) interaction. The best electrochemical reversibility conditions obtained were: using the CA-TiO2-MB electrode, 1.0 mol L-1 KCl as supporting electrolyte, at scan rate of 10.0 mV s-1. Afterwards, the CA-TiO2-MB modified electrode was tested as an amperometric sensor for the determination of NADH, with a detection limit of 0.1 µmol L-1.As propriedades eletroquímicas dos corantes catiônicos, azul de meldola e azul de toluidina, imobilizados na superfície do acetato de celulose modificado com dióxido de titânio foram investigadas por voltametria cíclica. Os materiais sintetizados foram empregados como eletrodos de pasta de carbono. As propriedades mediadoras redox dos eletrodos modificados quimicamente com azul de meldola e azul de toluidina foram otimizadas utilizando um planejamento fatorial consistindo de dois níveis e quatro fatores com dois pseudo-pontos centrais (n=20 experimentos). A análise fatorial foi realizada para investigar as melhores condições de reversibilidade do processo redox tais como uma diminuição na separação entre os picos de potenciais anódico e catódico e razão de corrente próxima da unidade. Os fatores que apresentaram efeitos significantes na otimização global do sistema e que permitiram alcançar as melhores condições de reversibilidade de transferência de elétrons foram os fatores principais velocidade de varredura e tipo de eletrodo (azul de meldola ou azul de toluidina) além dos fatores de interação concentração do KCl × tipo de eletrodo (B×D) e a interação pH × [KCl] × velocidade de varredura (A×B×C). As melhores condições de reversibilidade eletroquímica obtidas foram: o eletrodo CA-TiO2-MB, KCl 1,0 mol L-1 como eletrólito suporte e velocidade de varredura de 10,0 mV s-1. Adicionalmente, o eletrodo modificado CA-TiO2-MB foi testado como sensor amperométrico para a determinação de NADH com um limite de detecção de 0,1 µmol L-1.14621472Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Associating the Incest and Paternity Index to discriminate sexual aggression among close blood relatives

 A violência sexual no Brasil, além de um crime hediondo, é uma questão de saúde pública. Entre as crianças, parentes destacam-se como agressores. Quando um crime de natureza sexual resulta em gravidez, o exame de paternidade consiste no meio de prova mais fidedigno. Este exame consiste em verificar o compartilhamento de alelos entre o pretenso filho e o suposto pai, de modo a atribuir termos probabilísticos à transmissão dos alelos por parte do suspeito em relação a um homem qualquer na população, não relacionado, o que se denomina índice de paternidade. Porém, em casos cujo suposto pai possui vínculo biológico com a vítima, devem-se considerar alguns parâmetros matemáticos de modo a evitar a superestimativa dos valores atribuídos aos índices de paternidade. Torna-se preciso distinguir Alelos Idênticos por Descendência daqueles Idênticos por Estado. A partir de análise comparativa de 3 casos incestuosos foram efetuados cálculos de Índice de Paternidade da maneira usual, considerando o suspeito como não relacionado à vítima e considerando o suspeito como relacionado à vítima, atribuindo a este cálculo a denominação Índice de Incesto. O Índice de Paternidade Combinado foi superior ao Índice Combinado de Incesto em até 103 vezes, mostrando que as análises usuais podem superestimar os resultados nos exames de vínculo genético. Assim, propõe-se o uso desta metodologia matemática nos cenários incestuosos a fim de evitar a emissão de laudos equivocados ou estatisticamente sobrevalorizados.Sexual violence in Brazil, as well as being a heinous crime, is a public health issue. In the majority of cases of sexually abused children, close relatives are the most common aggressors. When a crime of a sexual nature results in pregnancy, a paternity test is the most reliable form of evidence. The purpose of this test is to verify the sharing of alleles between the child and alleged father, in order to assign probabilistic terms related to the transmission of alleles from the suspect in relation to an unrelated man in population—this is called the Paternity Index. However, in cases where the alleged father has a biological relationship with the victim, some mathematical parameters should be considered, in order to avoid overestimation of the values assigned to the indices of paternity. It becomes necessary to distinguish alleles identical by descent from those identical by state. From a comparative analysis of 3 incestuous cases, calculations of the Paternity Index were performed in the usual way, both considering the suspect as being unrelated to the victim, and considering the suspect as being related to the victim, and this calculation was named the Incest Index. The Combined Paternity Index was higher than the combined ratio of Incest by up to 103 times, showing that the usual analysis may overestimate the results in the exams of genetic link. Thus, the use of this mathematical methodology is proposed for both incestuous scenarios, in order to avoid issuing overrated or erroneous statistical reports of incest

Anandamide Effects in a Streptozotocin-Induced Alzheimer’s Disease-Like Sporadic Dementia in Rats

Alzheimer’s disease (AD) is characterized by multiple cognitive deficits including memory and sensorimotor gating impairments as a result of neuronal and synaptic loss. The endocannabinoid system plays an important role in these deficits but little is known about its influence on the molecular mechanism regarding phosphorylated tau (p-tau) protein accumulation – one of the hallmarks of AD –, and on the density of synaptic proteins. Thus, the aim of this study was to investigate the preventive effects of anandamide (N-arachidonoylethanolamine, AEA) on multiple cognitive deficits and on the levels of synaptic proteins (syntaxin 1, synaptophysin and synaptosomal-associated protein, SNAP-25), cannabinoid receptor type 1 (CB1) and molecules related to p-tau degradation machinery (heat shock protein 70, HSP70), and Bcl2-associated athanogene (BAG2) in an AD-like sporadic dementia model in rats using intracerebroventricular (icv) injection of streptozotocin (STZ). Our hypothesis is that AEA could interact with HSP70, modulating the level of p-tau and synaptic proteins, preventing STZ-induced cognitive impairments. Thirty days after receiving bilateral icv injections of AEA or STZ or both, the cognitive performance of adult male Wistar rats was evaluated in the object recognition test, by the escape latency in the elevated plus maze (EPM), by the tone and context fear conditioning as well as in prepulse inhibition tests. Subsequently, the animals were euthanized and their brains were removed for histological analysis or for protein quantification by Western Blotting. The behavioral results showed that STZ impaired recognition, plus maze and tone fear memories but did not affect contextual fear memory and prepulse inhibition. Moreover, AEA prevented recognition and non-associative emotional memory impairments induced by STZ, but did not influence tone fear conditioning. STZ increased the brain ventricular area and this enlargement was prevented by AEA. Additionally, STZ reduced the levels of p-tau (Ser199/202) and increased p-tau (Ser396), although AEA did not affect these alterations. HSP70 was found diminished only by STZ, while BAG2 levels were decreased by STZ and AEA. Synaptophysin, syntaxin and CB1 receptor levels were reduced by STZ, but only syntaxin was recovered by AEA. Altogether, albeit AEA failed to modify some AD-like neurochemical alterations, it partially prevented STZ-induced cognitive impairments, changes in synaptic markers and ventricle enlargement. This study showed, for the first time, that the administration of an endocannabinoid can prevent AD-like effects induced by STZ, boosting further investigations about the modulation of endocannabinoid levels as a therapeutic approach for AD

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages

Characterization of levan produced by a Paenibacillus sp. isolated from Brazilian crude oil

A levan-type fructooligosaccharide was produced by a Paenibacillus strain isolated from Brazilian crude oil, the purity of which was 98.5% after precipitation with ethanol and dialysis. Characterization by FTIR, NMR spectroscopy, GC-FID and ESI-MS revealed that it is a mixture of linear (26) fructosyl polymers with average degree of polymerization (DP) of 18 and branching ratio of 20. Morphological structure and physicochemical properties were investigated to assess levan microstructure, degradation temperature and thermomechanical features. Thermal Gravimetric Analysis highlighted degradation temperature of 218°C, Differential Scanning Calorimetry (DSC) glass transition at 81.47°C, and Dynamic Mechanical Analysis three frequency-dependent transition peaks. These peaks, corresponding to a first thermomechanical transition event at 86.60°C related to the DSC endothermic event, a second at 170.9°C and a third at 185.2°C, were attributed to different glass transition temperatures of oligo and polyfructans with different DP. Levan showed high morphological versatility and technological potential for the food, nutraceutical, and pharmaceutical industries.São Paulo Research Foundation (FAPESP) within Grants 2020/13271-6 and 2018/25511-1. Additionally, the authors acknowledge the financial support by National Council for Scientific and Technological Development – CNPq and by Coordination for the Improvement of Higher Education Personnel (CAPES), Finance Code 001. In addition, this study was supported by the Portuguese Science Foundation (FCT) under the scope of the strategic funding of UID/BIO/04469/2020 unit and the Project FOSYNBIO (POCI-01-0145-FEDER-029549).info:eu-repo/semantics/publishedVersio

Circulating Senescent T Cells Are Linked to Systemic Inflammation and Lesion Size During Human Cutaneous Leishmaniasis

Leishmania (Viannia) braziliensis induces American tegumentary leishmaniasis that ranges in severity from the milder form, cutaneous (CL) to severe disseminated cutaneous leishmaniasis. Patients with CL develop a cell-mediated Th1 immune response accompanied by production of inflammatory cytokines, which contribute to parasite control and pathogenesis of disease. Here, we describe the accumulation of circulating T cells with multiple features of telomere dependent-senescence including elevated expression of CD57, KLRG-1, and γH2AX that have short telomeres and low hTERT expression during cutaneous L. braziliensis infection. This expanded population of T cells was found within the CD45RA+CD27− (EMRA) subset and produced high levels of inflammatory cytokines, analogous to the senescence-associated secretory profile (SASP) that has been described in senescent non-lymphoid cells. There was a significant correlation between the accumulation of these cells and the extent of systemic inflammation, suggesting that they are involved in the inflammatory response in this disease. Furthermore, these cells expressed high level of the skin homing receptor CLA and there was a highly significant correlation between the number of these cells in the circulation and the size of the Leishmania-induced lesions in the skin. Collectively our results suggest that extensive activation during the early stages of leishmaniasis drives the senescence of T cells with the propensity to home to the skin. The senescence-related inflammatory cytokine secretion by these cells may control the infection but also contribute to the immunopathology in the disease