Molecular phylogeny: pitfalls and progress

Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects

Recurrent urinary tract infections in healthy and nonpregnant women

AbstractRecurrent urinary tract infections (RUTI) are prevalent and pose significant clinical challenges. Although the term RUTI has long been vaguely defined, a consensus definition has emerged in recent years. The exact etiology behind RUTI remains under debate, with valid arguments for both ascending reinfections as well as persistent infection inside the bladder. These persistent infections exist in the form of quiescent intracellular reservoirs in the mouse model and may represent a novel concept to explain UTI recurrence in humans. Manageable risk factors such as behavioral patterns alongside nonmanageable risk factors including genetic susceptibility are growing fields of investigation. Acute UTI have been studied through two model bacterial strains: Escherichia coli UTI89 and CFT073. However, the clinical relevance to RUTI of these two strains has not been firmly established. Current treatment strategies for RUTI are limited and remain dominated by antibiotic usage despite variable efficacy. The majority of studies in humans have focused on younger groups of women with little information available about the postmenopausal population despite a heightened risk of RUTI in this age group

Secondary Plastids of Euglenids and Chlorarachniophytes Function with a Mix of Genes of Red and Green Algal Ancestry

International audienceEndosymbiosis has been common all along eukaryotic evolution, providing opportunities for genomic and organellar innovation. Plastids are a prominent example. After the primary endosymbiosis of the cyanobacterial plastid ancestor, photosynthesis spread in many eukaryotic lineages via secondary endosymbioses involving red or green algal endosymbionts and diverse heterotrophic hosts. However, the number of secondary endosymbioses and how they occurred remain poorly understood. In particular, contrasting patterns of endosymbiotic gene transfer (EGT) have been detected and subjected to various interpretations. In this context, accurate detection of EGTs is essential to avoid wrong evolutionary conclusions. We have assembled a strictly selected set of markers that provides robust phylogenomic evidence suggesting that nuclear genes involved in the function and maintenance of green secondary plastids in chlorarachniophytes and euglenids have unexpected mixed red and green algal origins. This mixed ancestry contrasts with the clear red algal origin of most nuclear genes carrying similar functions in secondary algae with red plastids

Investigating memory prefetcher performance over parallel applications: from real to simulated

In recent years, there have been significant advances in the performance of processors, exemplified by the reduction of transistor size and the increase in the number of cores in a processor. Conversely, the memory subsystem did not advance as significantly as processors, not being able to deliver data at the required rate, and creating what is known as the memory wall [1]. An example of a technology used to mitigate the memory latency is the prefetcher, a technique that identifies access patterns from each core, creates speculative memory requests, and fetches data that can be potentially useful to the cache beforehand. In High-Performance Computing (HPC) systems, many other problems arise with parallelism. Since HPC applications are highly parallel, with many threads communicating with one another mainly through shared memory, it becomes necessary to keep data coherence in the several cache levels. Moreover, the memory interactions among different threads may also unpredictably change the data path through the memory hierarchy. When considering the memory hierarchy complexity along with prefetcher action, the behavior of the processor’s memory subsystem reaches a new level of complexity. In this work, we seek to shed light on how the prefetcher affects the processing performance of parallel HPC applications, and how accurately state-of-the-art multicore architecture simulators are simulating the execution of such applications, with and without prefetcher. We identify that an L2 cache prefetcher is more efficient in comparison with an L1 prefetcher, since avoiding excessive L3 cache accesses better contributes to performance, when comparing to accessing the L2 cache. Moreover, we show evidence that the prefetchers’ contribution to performance is limited by the memory contention that emerges when the level of parallelism increases

Manual de educação jurídica antirracista: direito, justiça e transformação social

Divulgação dos SUMÁRIOS das obras recentemente incorporadas ao acervo da Biblioteca Ministro Oscar Saraiva do STJ. Em respeito à Lei de Direitos Autorais, não disponibilizamos a obra na íntegra.Localização na estante: 34:378.4(81) M838

Reliability Study of Thin-Oxide Zero-Ionization, Zero-Swing FET 1T-DRAM Memory Cell

The experimental time-dependent dielectric breakdown and ON voltage reliability of advanced FD-SOI Z2-FET memory cells are characterized for the first time. The front-gate stress time is shown to significantly modulate the ON voltage and, hence, the memory window. The Weibull slope, β, indicating the device variability to breakdown, and the time to soft breakdown, α, present different trends depending on the cell geometry. This fact highlights the tradeoff between variability and reliability to account for in Z2-FET designs.H2020 REMINDER project (grant agreement No 687931) and TEC2017-89800-R are thanked for financial support

Comparative genomics suggests primary homothallism of Pneumocystis species

This work was supported by the Swiss National Science Foundation grant 310030-146135 to P.M.H. and M.P. O.H.C. is supported by the Swiss National Science Foundation fellowship grant 151780.Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two different MAT loci on separate DNA molecules would have been detected, nor with secondary homothallism, because the latter involves generally more MAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identical MAT genes in P. jirovecii isolates from six patients. A strong synteny of the genomic region surrounding the putative MAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. deformans. IMPORTANCE: Sexual reproduction among fungi can involve a single partner (homothallism) or two compatible partners (heterothallism). We investigated the issue in three pathogenic fungal relatives: Pneumocystis jirovecii, which causes severe pneumonia in immunocompromised humans; Pneumocystis carinii, which infects rats; and the plant pathogen Taphrina deformans. The nature, the number, and the organization within the genome of the genes involved in sexual reproduction were determined. The three species appeared to harbor a single genomic region gathering only three genes involved in sexual differentiation, an organization which is compatible with sexual reproduction involving a single partner. These findings illuminate the strategy adopted by fungal pathogens to infect their hosts.publishersversionpublishe

Uterine ruptures during labor: a study of 26 cases at Nabil Choucair Medical Center, in the suburbs of Dakar

Background: This study aims to clarify the epidemiological profile of patients and describe the diagnostic, therapeutic and prognostic aspects of uterine ruptures at Nabil Choucair Health Center, in the suburbs of Dakar.Methods: This was a retrospective and prospective, descriptive and analytical study conducted over a period of 112 months, from July 31, 2005 and March 31, 2015; it concerned all diagnosed cases with uterine rupture, managed at Nabil Health Center Choucair Dakar. Data were collected from antenatal notebooks, delivery records, surgical reports and anesthetic records. The following parameters were studied: socio-demographic characteristics (frequency, chracteristics of patient), the course of pregnancy, diagnostic, prognostic, and therapeutic aspects. Data analysis was performed using SPSS software (version 11.0).Results: During the study period, we recorded 26 uterine ruptures from a total of 34,097 deliveries, that is a frequency of 8 out of 10,000 births. The epidemiological profile of the patients was that of a 30-year old woman, on average, few previous deliveries with an average parity of 3, who received on average 3 antenatal and evacuated in 50% of cases. Uterine rupture occurred in 17 patients on a new uterus (65, 4%) and in 9 patients on a scarred uterus (34.6%). Two patients (7%) were in hemorrhagic shock. A laparotomy aimed at specifying the place of rupture and making the treatment was performed in all patients. It was 18 uterine segmento-corporeal ruptures (69.2%), 5 segmental ruptures (19.2%) and 2 corporeal ruptures (7.6%). We recorded 9 uterine ruptures with living fetus (38.5%). Twenty-three patients (88.5%) underwent conservative suture against only 3 hemostasis hysterectomy (11.5%). The postoperative courses were uneventful in 57.7% of cases. Eleven patients (42.3%) had anemia and we recorded maternal deaths, which is a maternal mortality of 3.84%.Conclusions: Uterine rupture is a serious complication that is still responsible for significant maternal and fetal mortality. Prevention is based on careful monitoring of pregnancy and delivery

Compensação Fuzzy Proporcional-Derivativa de Incertezas no Controle de Vibrações de Treliças com Memória de Forma / Proportional-Derivative Fuzzy Compensation of Uncertainties in the Control of Shape Memory Trusses Vibrations

Neste trabalho, um controlador por modos deslizantes com compensação fuzzy proporcional-derivativa de incertezas é empregado no controle ativo de vibrações de uma treliça de duas barras de liga com memória de forma. Esse sistema possui uma dinâmica bastante rica e complexa, podendo apresentar comportamentos caóticos dependendo dos parâmetros da perturbação externa. No intuito de facilitar o projeto do controlador, dois modelos constitutivos são utilizados: um polinomial, para o desenvolvimento da lei de controle, e um outro mais sofisticado, para simular o comportamento termomecânico dos elementos da estrutura, o qual apresenta resultados compatíveis com experimentos. Dessa forma, esta abordagem tem como vantagem a obtenção de uma lei de controle mais simples, inteligente, e permite que a sua robustez seja evidenciada. Simulações numéricas são apresentadas para comprovar a eficácia da estratégia proposta