Miracle-dz/UniFAR-FTUs huggingface dataset:
PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5′ region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.
Assessing scientists for hiring, promotion, and tenure

Assessment of researchers is necessary for decisions of hiring, promotion, and tenure. A burgeoning number of scientific leaders believe the current system of faculty incentives and rewards is misaligned with the needs of society and disconnected from the evidence about the causes of the reproducibility crisis and suboptimal quality of the scientific publication record. To address this issue, particularly for the clinical and life sciences, we convened a 22-member expert panel workshop in Washington, DC, in January 2017. Twenty-two academic leaders, funders, and scientists participated in the meeting. As background for the meeting, we completed a selective literature review of 22 key documents critiquing the current incentive system. From each document, we extracted how the authors perceived the problems of assessing science and scientists, the unintended consequences of maintaining the status quo for assessing scientists, and details of their proposed solutions. The resulting table was used as a seed for participant discussion. This resulted in six principles for assessing scientists and associated research and policy implications. We hope the content of this paper will serve as a basis for establishing best practices and redesigning the current approaches to assessing scientists by the many players involved in that process.
Successful Human Infection with P. falciparum Using Three Aseptic Anopheles stephensi Mosquitoes: A New Model for Controlled Human Malaria Infection

Controlled human malaria infection (CHMI) is a powerful method for assessing the efficacy of anti-malaria vaccines and drugs targeting pre-erythrocytic and erythrocytic stages of the parasite. CHMI has heretofore required the bites of 5 Plasmodium falciparum (Pf) sporozoite (SPZ)-infected mosquitoes to reliably induce Pf malaria. We reported that CHMI using the bites of 3 PfSPZ-infected mosquitoes reared aseptically in compliance with current good manufacturing practices (cGMP) was successful in 6 participants. Here, we report results from a subsequent CHMI study using 3 PfSPZ-infected mosquitoes reared aseptically to validate the initial clinical trial. We also compare results of safety, tolerability, and transmission dynamics in participants undergoing CHMI using 3 PfSPZ-infected mosquitoes reared aseptically to published studies of CHMI using 5 mosquitoes. Nineteen adults aged 18–40 years were bitten by 3 Anopheles stephensi mosquitoes infected with the chloroquine-sensitive NF54 strain of Pf. All 19 participants developed malaria (100%); 12 of 19 (63%) on Day 11. The mean pre-patent period was 258.3 hours (range 210.5–333.8). The geometric mean parasitemia at first diagnosis by microscopy was 9.5 parasites/µL (range 2–44). Quantitative polymerase chain reaction (qPCR) detected parasites an average of 79.8 hours (range 43.8–116.7) before microscopy. The mosquitoes had a geometric mean of 37,894 PfSPZ/mosquito (range 3,500–152,200). Exposure to the bites of 3 aseptically-raised, PfSPZ-infected mosquitoes is a safe, effective procedure for CHMI in malaria-naïve adults. The aseptic model should be considered as a new standard for CHMI trials in non-endemic areas. Microscopy is the gold standard used for the diagnosis of Pf malaria after CHMI, but qPCR identifies parasites earlier. If qPCR continues to be shown to be highly specific, and can be made to be practical, rapid, and standardized, it should be considered as an alternative for diagnosis. Trial Registration ClinicalTrials.gov NCT00744133 NCT00744133
Gravity and Heater Size Effects on Pool Boiling Heat Transfer

The current work is based on observations of boiling heat transfer over a continuous range of gravity levels between 0g to 1.8g and varying heater sizes with a fluorinert as the test liquid (FC-72/n-perfluorohexane). Variable gravity pool boiling heat transfer measurements over a wide range of gravity levels were made during parabolic flight campaigns as well as onboard the International Space Station. For large heaters and-or higher gravity conditions, buoyancy dominated boiling and heat transfer results were heater size independent. The power law coefficient for gravity in the heat transfer equation was found to be a function of wall temperature under these conditions. Under low gravity conditions and-or for smaller heaters, surface tension forces dominated and heat transfer results were heater size dependent. A pool boiling regime map differentiating buoyancy and surface tension dominated regimes was developed along with a unified framework that allowed for scaling of pool boiling over a wide range of gravity levels and heater sizes. The scaling laws developed in this study are expected to allow performance quantification of phase change based technologies under variable gravity environments eventually leading to their implementation in space based applications.
PIVET rFSH dosing algorithms for individualized controlled ovarian stimulation enables optimized pregnancy productivity rates and avoidance of ovarian hyperstimulation syndrome

The first PIVET algorithm for individualized recombinant follicle stimulating hormone (rFSH) dosing in in vitro fertilization, reported in 2012, was based on age and antral follicle count grading with adjustments for anti-Müllerian hormone level, body mass index, day-2 FSH, and smoking history. In 2007, it was enabled by the introduction of a metered rFSH pen allowing small dosage increments of ~8.3 IU per click. In 2011, a second rFSH pen was introduced allowing more precise dosages of 12.5 IU per click, and both pens with their individual algorithms have been applied continuously at our clinic. The objective of this observational study was to validate the PIVET algorithms pertaining to the two rFSH pens with the aim of collecting ≤15 oocytes and minimizing the risk of ovarian hyperstimulation syndrome. The data set included 2,822 in vitro fertilization stimulations over a 6-year period until April 2014 applying either of the two individualized dosing algorithms and corresponding pens. The main outcome measures were mean oocytes retrieved and resultant embryos designated for transfer or cryopreservation permitted calculation of oocyte and embryo utilization rates. Ensuing pregnancies were tracked until live births, and live birth productivity rates embracing fresh and frozen transfers were calculated. Overall, the results showed that mean oocyte numbers were 10.0 for all women <40 years with 24% requiring rFSH dosages <150 IU. Applying both specific algorithms in our clinic meant that the starting dose was not altered for 79.1% of patients and for 30.1% of those receiving the very lowest rFSH dosages (≤75 IU). Only 0.3% patients were diagnosed with severe ovarian hyperstimulation syndrome, all deemed avoidable due to definable breaches from the protocols. The live birth productivity rates exceeded 50% for women <35 years and was 33.2% for the group aged 35–39 years. Routine use of both algorithms led to only 11.6% of women generating >15 oocytes, significantly lower than recently published data applying conventional dosages (38.2%; P<0.0001). When comparing both specific algorithms to each other, the outcomes were mainly comparable for pregnancy, live birth, and miscarriage rate. However, there were significant differences in relation to number of oocytes retrieved, but the mean for both the algorithms remained well below 15 oocytes. Consequently, application of both these algorithms in our in vitro fertilization clinic allows the use of both the rFSH products, with very similar results, and they can be considered validated on the basis of effectiveness and safety, clearly avoiding ovarian hyperstimulation syndrome.
Effect of roasting, boiling and microwaving cooking method on doxycline residues in edible tissues of poultry by microbial method

The purpose of this study was to determine the effects of different cooking processes like boiling, roasting and microwaving on doxycline residues in chicken muscle, liver and gizzard tissues of broiler chickens. Each chick was fed by water and food with 0.1% of Doxycline in their drinking water for 5 consecutive days. Then, three locations were sampled aseptically from each carcass: Breast muscle, liver and gizzard. doxcycline residue was analysed using microbial inhibition method by plates seeded with Escherichia coli. After doing different phases of the test on raw samples, the positive raw samples were cooked by various cooking procedures and we surveyed the cooked samples with a similar method again for the detection of residue. The results showed a reduction in the concentration of doxycline residue after different cooking processes and a part of the residue in the boiling process were excreted from the tissue to the cooking fluid. Between the various agents affecting antibiotics residue after the cooking process, cooking time and temperature can play a major role in antibiotic residue reduction while cooking food. Regarding the results of this study, we can conclude that cooking processes do not guarantee a full elimination of these drugs present in condemned animals and it can only decrease its amounts. Key words: Cooking, doxycline, residue, poultry, edible, tissue.
Mental Workload and ARL Workload Modeling Tools.

Abstract : The author of this report provides an overview of mental workload theory and mental workload measurement. She also describes the development, application, and validation of the mental workload modeling tools developed by the Human Research and Engineering Directorate of the U.S. Army Research Laboratory (ARL). These ARL tools, VACP (visual, auditory, cognitive, psychomotor) option in the improved performance research integration tool (IMPRINT) and WinCrew, can help the designers of military systems to assess the mental workload associated with different configurations of soldiers and equipment involved in the performance of a mission. System designers can conduct this assessment in the concept development phase of system design and reduce the need to build costly system mock-ups.
In fl uence of ruthenium on microstructural evolution in a model

The effect of 2 at. % Ru addition on the elemental partitioning and microstructural evolution of a base Co8.8Al-7.3W at. % superalloy, consisting of a g-(fcc) matrix with g’-(L12 structure) precipitates is studied using scanning electron microscopy and atom-probe tomography. Ruthenium partitions to the g’-precipitates in the Co-9.4Al-7.5W-2.1Ru at. % alloy with a partitioning coefficient, K 0=g Ru 1⁄4 1.27, after aging at 900 C for 16 h, in contrast to the behavior observed in Ni-base superalloys and theoretically predicted for Co-base superalloys, for which Ru partitions preferentially to the g-phase. The addition of ruthenium does not significantly affect the g0 volume-fraction or the coarsening kinetics of the g0 precipitates compared to the base ternary alloy. The addition of Ru also leads, however, to a rapid discontinuous transformation of (g plus g0), which initiates at the grain boundaries after 128 h aging at 900 C; (g plus g0) is transformed into a lamellar phase mixture containing Co3W (D019), fcc solid-solution (g), and Co(Al,W) (B2). After 256 h aging at 900 C in the Ru-containing alloy, some grains have completely transformed, although regions of g plus g0 persist. The base ternary CoeAleW alloy does not exhibit a discontinuous transformation and contains a (g plus g0) microstructure up to 1024 h of aging at 900 C. © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, and is associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a dataset of 22 mitochondrial and nuclear markers from 92% of species in the tribe to re-examine the phylogeny of Heliconiini with both supermatrix and multi-species coalescent approaches, characterise the patterns of conflicting signal and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach fails to reflect the underlying variation in the history of individual loci. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Amazonia over the past 23 million years, or changes caused by diversity-dependent effects on the rate of diversification. We find that the tribe Heliconiini had doubled its rate of speciation around 11 Ma and that the presently most speciose genus Heliconius started diversifying rapidly at 10 Ma, likely in response to the recent drastic changes in topography of the region. Our study provides comprehensive evidence for a rapid adaptive radiation among an important insect radiation in the most biodiverse region of the planet.
High-resolution 7-Tesla fMRI data on the perception of musical

Here we present an extension to the dataset – a versatile studyforrest resource for studying the behavior of the human brain in situations of real-life complexity ( ). This release adds more http://studyforrest.org high-resolution, ultra high-field (7 Tesla) functional magnetic resonance imaging (fMRI) data from the same individuals. The twenty participants were repeatedly stimulated with a total of 25 music clips, with and without speech content, from five different genres using a slow event-related paradigm. The data release includes raw fMRI data, as well as precomputed structural alignments for within-subject and group analysis. In addition to fMRI, simultaneously recorded cardiac and respiratory traces, as well the complete implementation of the stimulation paradigm, including stimuli, are provided. An initial quality control analysis reveals distinguishable patterns of response to individual genres throughout a large expanse of areas known to be involved in auditory and speech processing. The present data can be used to, for example, generate encoding models for music perception that can be validated against the previously released fMRI data from stimulation with the “Forrest Gump” audio-movie and its rich musical content. In order to facilitate replicative and derived works, only free and open-source software was utilized.
Web Recommendation System Based on a Markov-Chainmodel

This work presents some general procedures for computing dissimilarities between nodes of a weighted, undirected, graph. It is based on a Markov-chain model of random walk through the graph. This method is applied on the architecture of a Multi Agent System (MAS), in which each agent can be considered as a node and each interaction between two agents as a link. The model assigns transition probabilities to the links between agents, so that a random walker can jump from agent to agent. Two quantities, called the average commute time and the pseudoinverse of the Laplacian matrix of the graph, provide proximity measures between any pair of agents. The model is applied on a collaborative filtering task where suggestions are made about which movies people should watch based upon what they watched in the past. For the experiments, we build a MAS architecture and instantiated the agents belief set from a real movie database.
Modification of Precipitation by Coastal Orography in Storms Crossing Northern California

Abstract This study compiles and interprets three-dimensional Weather Surveillance Radar-1988 Doppler (WSR-88D) data during a 2.5-yr period and examines the typical orographic effects on precipitation mainly associated with winter storms passing over coastal northern California. The three-dimensional mean reflectivity patterns show echo structure that was generally stratiform from over the ocean to inland over the mountains. The flow above the 1-km level was strong enough to be unblocked by the terrain, and the mean echo pattern over land had certain characteristics normally associated with an unblocked cross-barrier flow, both on the broad scale of the windward slopes of the coastal mountains and on the scale of individual peaks of the terrain on the windward side. Upward-sloping echo contours on the scale of the overall region of coastal mountains indicated broadscale upslope orographic enhancement. On a smaller scale, the mean stratiform echo pattern over the mountains contained a strong embedded core .
The Effect of Temperature on the Strength of Wood

Impact bending tests were carried out on specimens of Spruce and Plywood between the range of temperatures from +66°C to -60°C. The testing machine used was an Amsler's 4 ton universal machine for testing wood. When this machine is used for impact bending, it is possible to measure the maximum pressure on the supports besides the energy required to break the test pieces, so that the equivalent modulus of rupture can also be computed.Results show that both Spruce and Plywood change in their mechanical properties with variation of temperatures. Thus the absorbed energy shows a minimum between 6°C and -10°C, and the equivalent modulus of rupture increases almost linearly with decrease in temperature.Moreover prolonged cooling produced no difference in the results as compared with those cooled for a short time. And it was observed that test pieces which were first cooled and then brought back to the normal temperature regained their initial properties.
Leptospirosis: risk factors and management challenges in developing countries

Leptospirosis is a widespread bacterial zoonosis with highest burden in low-income populations living in tropical and subtropical regions, both in urban and in rural environments. Rodents are known as the main reservoir animals, but other mammals may also significantly contribute to human infections in some settings. Clinical presentation of leptospirosis is nonspecific and variable, and most of the early signs and symptoms point to the so-called “acute fever of unknown origin”, a major diagnostic challenge in tropical and subtropical areas. However, leptospirosis can rapidly evolve to life-threatening complications, especially if left untreated. There is a need for good awareness of leptospirosis and rapid antibiotic treatment based on clinical and epidemiological suspicion. Severe leptospirosis cases include renal and/or respiratory failure and shock, necessitating intensive care, also seldom available or with limited capacity. Confirmation of leptospirosis relies on biological diagnosis, which unfortunately uses tricky methods seldom available. This biological confirmation, however, is essential for surveillance and public health purpose. A good knowledge of leptospirosis epidemiology (eg, the reservoir animals involved, the Leptospira strains circulating, the seasonal and geographical patterns, and specific populations at risk) can be achieved through adequate surveillance and diagnosis. This can pave the way to prevention and intervention strategies and in turn alleviate the toll leptospirosis takes on affected populations. Over the past few years, leptospirosis has been increasingly recognized, as the need for multidisciplinary approaches in a One-Health perspective has been acknowledged, raising hope to successfully tackle the challenges of this zoonosis.
Exercise training alone or with the addition of activity counseling improves physical activity levels in COPD: a systematic review and meta-analysis of randomized controlled trials

Background Physical inactivity is associated with poor outcomes in COPD, and as a result, interventions to improve physical activity (PA) are a current research focus. However, many trials have been small and inconclusive. Objective The aim of this systematic review and meta-analysis was to study the effects of randomized controlled trials (RCTs) targeting PA in COPD. Methods Databases (Physiotherapy Evidence Database [PEDro], Embase, MEDLINE, CINAHL and the Cochrane Central Register for Controlled Trials) were searched using the following keywords: “COPD”, “intervention” and “physical activity” from inception to May 20, 2016; published RCTs that aimed to increase PA in individuals with COPD were included. The PEDro scale was used to rate study quality. Standardized mean differences (effect sizes, ESs) with 95% confidence intervals (CIs) were determined. Effects of included interventions were also measured according to the minimal important difference (MID) in daily steps for COPD (599 daily steps). Results A total of 37 RCTs with 4,314 participants (mean forced expiratory volume in one second (FEV1) % predicted 50.5 [SD=10.4]) were identified. Interventions including exercise training (ET; n=3 studies, 103 participants) significantly increased PA levels in COPD compared to standard care (ES [95% CI]; 0.84 [0.44–1.25]). The addition of activity counseling to pulmonary rehabilitation (PR; n=4 studies, 140 participants) showed important effects on PA levels compared to PR alone (0.47 [0.02–0.92]), achieving significant increases that exceeded the MID for daily steps in COPD (mean difference [95% CI], 1,452 daily steps [549–2,356]). Reporting of methodological quality was poor in most included RCTs. Conclusion Interventions that included ET and PA counseling during PR were effective strategies to improve PA in COPD.