Fiberoptic characteristics for extreme operating environments

Fiberoptics could offer several major benefits for cryogenic liquid-fueled rocket engines, including lightning immunity, weight reduction, and the possibility of implementing a number of new measurements for engine condition monitoring. The technical feasibility of using fiberoptics in the severe environments posed by cryogenic liquid-fueled rocket engines was determined. The issues of importance and subsequent requirements for this use of fiberoptics were compiled. These included temperature ranges, moisture embrittlement succeptability, and the ability to withstand extreme shock and vibration levels. Different types of optical fibers were evaluated and several types of optical fibers' ability to withstand use in cryogenic liquid-fueled rocket engines was demonstrated through environmental testing of samples. This testing included: cold-bend testing, moisture embrittlement testing, temperature cycling, temperature extremes testing, vibration testing, and shock testing. Three of five fiber samples withstood the tests to a level proving feasibility, and two of these remained intact in all six of the tests. A fiberoptic bundle was also tested, and completed testing without breakage. Preliminary cabling and harnessing for fiber protection was also demonstrated. According to cable manufacturers, the successful -300 F cold bend, vibration, and shock tests are the first instance of any major fiberoptic cable testing below roughly -55 F. This program has demonstrated the basic technical feasibility of implementing optical fibers on cryogenic liquid-fueled rocket engines, and a development plan is included highlighting requirements and issues for such an implementation

HIV Research Year in Review in Haiti

Introduction For this issue of the Epidemiologic Surveillance Bulletin, we summarize the prior year’s research on populations living with HIV (PLWH) in Haiti for World AIDS Day 2020. Methods We retrieved 50 articles from PubMed (pubmed.gov) for articles written in English using the search term [Haiti* AND (HIV OR human immunodeficiency virus OR AIDS)] from December 2019 to November 19, 2020 (approximately 1 year). We included studies that of cohorts of people living with HIV in Haiti, patients enrolled from Haiti in multi-country clinical studies and studies involving populations at substantial risk of HIV in Haiti. We excluded studies of Haitian populations in other countries, study protocols, perspectives, and opinion articles. The final review contains summaries of 28 studies. We grouped into relevant themes when possible and summarized each paper

OBSERVAÇÕES INTRODUTÓRIAS BEM-ESTAR ANIMAL: UM CONCEITO APLICÁVEL AOS ANIMAIS SELVAGENS NA LEGISLAÇÃO DA UNIÃO EUROPEIA?

Associar a noção de bem-estar animal com animais selvagens não é necessariamente evidente, pois geralmente ela só se aplica aos animais sob cuidados humanos. Numa visão ambientalista, o ser humano pode ser considerado responsável pelas ameaças que as suas atividades representam para as espécies. A isto pode ser acrescentada uma abordagem "bem-estarista", no sentido de uma obrigação negativa de não prejudicar os animais selvagens. Podendo ser considerados como mercadorias,estes animais dificilmente estão sujeitos a uma estrutura jurídica destinada a protegê-los como indivíduos, na medida em que a União Europeia só tem competência imperfeita nesta área. Mas o direito da União Europeia poderia ser mobilizado , em primeiro lugar, através da lógica ambientalista de conservação (particularmente de habitats), que, por sua vez, asseguraria, por ricochete, a proteção do bem-estar animal; em seguida, mobilizando a visão “bem-estarista”, em consonância com a proibição do uso de armadilhas de mandíbulas na UE em 1991. Uma extensão da abrangência do Artigo 13 do TFUE através de sua revisão pode ser essencial para uma ação integral da UE neste aspecto. &nbsp

Efficient decoding algorithms for generalized hidden Markov model gene finders

BACKGROUND: The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity. RESULTS: As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN. CONCLUSIONS: In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques

Obstetrician-Gynecologist Perceptions and Utilization of Prescription Drug Monitoring Programs: A Survey Study

Query of Prescription Drug Monitoring Programs (PDMPs) is recommended before prescribing opioids by the US Centers for Disease Control and Prevention, to inform clinical practice and aid diversion prevention. Many states mandate prescriber PDMP use; however, little is known about PDMP perception of utility and use among Obstetricians-Gynecologists (OB/GYN), who are the primary provider for most women during pregnancy. This study examined OB/GYN perceptions and utilization of their state PDMP. Survey items were developed by expert consensus. A voluntary anonymous survey was emailed to a random sample of 5000 OB/GYNs (adjusted participants n = 1470, minus unread/refusals). Responses were stratified by state policy environment, where response frequency distributions were compared for OB/GYNs practicing in states with mandatory vs voluntary PDMP query. Adjusted response rate was 27% (n = 397). Most OB/GYNs (78%) were registered with their PDMP. The majority agreed that “…mandating physician use of the PDMP was a good idea” (51.4% mandatory state vs 58.3% voluntary state). Respondents in mandatory states reported that the primary purpose of the PDMP was “to allow the physician to verify medications that the patient is being prescribed” less frequently than those in voluntary states (38.3% vs 52.8%). Several report speaking with patients about controlled substance prescriptions after viewing PDMP reports (27.8% in mandatory vs 26.3% in voluntary states). In qualitative responses, reported frustration with PDMPs was evident. OB/GYNs are diverse in their perceptions regarding the utility and purpose of PDMPs. Tailored education is needed regarding clinical utility of PDMPs for OB/GYN practice

Minimus: a fast, lightweight genome assembler

BACKGROUND: Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. RESULTS: We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. CONCLUSION: We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge

Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure