Design of a flexible, user friendly feature matrix generation system and its application on biomedical datasets

© The Author(s) 2020. The generation of a feature matrix is the first step in conducting machine learning analyses on complex data sets such as those containing DNA, RNA or protein sequences. These matrices contain information for each object which have to be identified using complex algorithms to interrogate the data. They are normally generated by combining the results of running such algorithms across various datasets from different and distributed data sources. Thus for non-computing experts the generation of such matrices prove a barrier to employing machine learning techniques. Further since datasets are becoming larger this barrier is augmented by the limitations of the single personal computer most often used by investigators to carry out such analyses. Here we propose a user friendly system to generate feature matrices in a way that is flexible, scalable and extendable. Additionally by making use of The Berkeley Open Infrastructure for Network Computing (BOINC) software, the process can be speeded up using distributed volunteer computing possible in most institutions. The system makes use of a combination of the Grid and Cloud User Support Environment (gUSE), combined with the Web Services Parallel Grid Runtime and Developer Environment Portal (WS-PGRADE) to create workflow-based science gateways that allow users to submit work to the distributed computing. This report demonstrates the use of our proposed WS-PGRADE/gUSE BOINC system to identify features to populate matrices from very large DNA sequence data repositories, however we propose that this system could be used to analyse a wide variety of feature sets including image, numerical and text data

Functional diversity of marine ecosystems after the Late Permian mass extinction event

Article can be accessed from http://www.nature.com/ngeo/journal/v7/n3/full/ngeo2079.htmlThe Late Permian mass extinction event was the most severe such crisis of the past 500 million years and occurred during an episode of global warming. It is assumed to have had significant ecological impact, but its effects on marine ecosystem functioning are unknown and the patterns of marine recovery are debated. We analysed the fossil occurrences of all known Permian-Triassic benthic marine genera and assigned each to a functional group based on their inferred life habit. We show that despite the selective extinction of 62-74% of marine genera there was no significant loss of functional diversity at the global scale, and only one novel mode of life originated in the extinction aftermath. Early Triassic marine ecosystems were not as ecologically depauperate as widely assumed, which explains the absence of a Cambrian-style Triassic radiation in higher taxa. Functional diversity was, however, significantly reduced in particular regions and habitats, such as tropical reefs, and at these scales recovery varied spatially and temporally, probably driven by migration of surviving groups. Marine ecosystems did not return to their pre-extinction state, however, and radiation of previously subordinate groups such as motile, epifaunal grazers led to greater functional evenness by the Middle Triassic

Environmental differences between sites control the diet and nutrition of the carnivorous plant Drosera rotundifolia

Background and aims: Carnivorous plants are sensitive to small changes in resource availability, but few previous studies have examined how differences in nutrient and prey availability affect investment in and the benefit of carnivory. We studied the impact of site-level differences in resource availability on ecophysiological traits of carnivory for Drosera rotundifolia L. Methods: We measured prey availability, investment in carnivory (leaf stickiness), prey capture and diet of plants growing in two bogs with differences in N deposition and plant available N: Cors Fochno (0.62 g m−2 yr.−1, 353 μg l−1), Whixall Moss (1.37 g m−2 yr.−1, 1505 μg l−1). The total N amount per plant and the contributions of prey/root N to the plants’ N budget were calculated using a single isotope natural abundance method. Results: Plants at Whixall Moss invested less in carnivory, were less likely to capture prey, and were less reliant on prey-derived N (25.5% compared with 49.4%). Actual prey capture did not differ between sites. Diet composition differed – Cors Fochno plants captured 62% greater proportions of Diptera. Conclusions: Our results show site-level differences in plant diet and nutrition consistent with differences in resource availability. Similarity in actual prey capture may be explained by differences in leaf stickiness and prey abundance

Use of the internet for sexual health among sexually experienced persons aged 16 to 44 years: evidence from a nationally representative survey of the British population

BACKGROUND: Those who go online regarding their sexual health are potential users of new Internet-based sexual health interventions. Understanding the size and characteristics of this population is important in informing intervention design and delivery. OBJECTIVE: We aimed to estimate the prevalence in Britain of recent use of the Internet for key sexual health reasons (for chlamydia testing, human immunodeficiency virus [HIV] testing, sexually transmitted infection [STI] treatment, condoms/contraceptives, and help/advice with one's sex life) and to identify associated sociodemographic and behavioral factors. METHODS: Complex survey analysis of data from 8926 sexually experienced persons aged 16-44 years in a 2010-2012 probability survey of Britain's resident population. Prevalence of recent (past year) use of Internet sources for key sexual health reasons was estimated. Factors associated with use of information/support websites were identified using logistic regression to calculate age-adjusted odds ratios (AORs). RESULTS: Recent Internet use for chlamydia/HIV testing or STI treatment (combined) was very low (men: 0.31%; women: 0.16%), whereas 2.35% of men and 0.51% of women reported obtaining condoms/contraceptives online. Additionally, 4.49% of men and 4.57% of women reported recent use of information/support websites for advice/help with their sex lives. Prevalence declined with age (men 16-24 years: 7.7%; 35-44 years: 1.84%, P<.001; women 16-24 years: 7.8%; 35-44 years: 1.84%, P<.001). Use of information/support websites was strongly associated with men's higher socioeconomic status (managerial/professional vs semiroutine/routine: AOR 1.93, 95% CI 1.27-2.93, P<.001). Despite no overall association with area-level deprivation, those in densely populated urban areas were more likely to report use of information/support websites than those living in rural areas (men: AOR 3.38, 95% CI 1.68-6.77, P<.001; women: AOR 2.51, 95% CI 1.34-4.70, P<.001). No statistically significant association was observed with number of sex partners reported after age adjustment, but use was more common among men reporting same-sex partners (last 5 years: AOR 2.44, 95% CI 1.27-4.70), women reporting sex with multiple partners without condoms (last year: AOR 1.90, 95% CI 1.11-3.26), and, among both sexes, reporting seeking sex online (last year, men: AOR 1.80, 95% CI 1.16-2.79; women: AOR 3.00, 95% CI 1.76-5.13). No association was observed with reporting STI diagnosis/es (last 5 years) or (after age adjustment) recent use of any STI service or non-Internet sexual health seeking. CONCLUSIONS: A minority in Britain used the Internet for the sexual health reasons examined. Use of information/support websites was reported by those at greater STI risk, including younger people, indicating that demand for online STI services, and Internet-based sexual health interventions in general, may increase over time in this and subsequent cohorts. However, the impact on health inequalities needs addressing during design and evaluation of online sexual health interventions so that they maximize public health benefit

Neuroinflammation and structural injury of the fetal ovine brain following intra-amniotic Candida albicans exposure.

BackgroundIntra-amniotic Candida albicans (C. Albicans) infection is associated with preterm birth and high morbidity and mortality rates. Survivors are prone to adverse neurodevelopmental outcomes. The mechanisms leading to these adverse neonatal brain outcomes remain largely unknown. To better understand the mechanisms underlying C. albicans-induced fetal brain injury, we studied immunological responses and structural changes of the fetal brain in a well-established translational ovine model of intra-amniotic C. albicans infection. In addition, we tested whether these potential adverse outcomes of the fetal brain were improved in utero by antifungal treatment with fluconazole.MethodsPregnant ewes received an intra-amniotic injection of 10(7) colony-forming units C. albicans or saline (controls) at 3 or 5 days before preterm delivery at 0.8 of gestation (term ~ 150 days). Fetal intra-amniotic/intra-peritoneal injections of fluconazole or saline (controls) were administered 2 days after C. albicans exposure. Post mortem analyses for fungal burden, peripheral immune activation, neuroinflammation, and white matter/neuronal injury were performed to determine the effects of intra-amniotic C. albicans and fluconazole treatment.ResultsIntra-amniotic exposure to C. albicans caused a severe systemic inflammatory response, illustrated by a robust increase of plasma interleukin-6 concentrations. Cerebrospinal fluid cultures were positive for C. albicans in the majority of the 3-day C. albicans-exposed animals whereas no positive cultures were present in the 5-day C. albicans-exposed and fluconazole-treated animals. Although C. albicans was not detected in the brain parenchyma, a neuroinflammatory response in the hippocampus and white matter was seen which was characterized by increased microglial and astrocyte activation. These neuroinflammatory changes were accompanied by structural white matter injury. Intra-amniotic fluconazole reduced fetal mortality but did not attenuate neuroinflammation and white matter injury.ConclusionsIntra-amniotic C. albicans exposure provoked acute systemic and neuroinflammatory responses with concomitant white matter injury. Fluconazole treatment prevented systemic inflammation without attenuating cerebral inflammation and injury

Uncertainties in projecting climate-change impacts in marine ecosystems

Projections of the impacts of climate change on marine ecosystems are a key prerequisite for the planning of adaptation strategies, yet theyare inevitablyassociated withuncertainty.Identifying,quantifying,andcommunicatingthisuncertaintyis keytobothevaluatingtherisk associated with a projection and building confidence in its robustness. Wereview howuncertainties in such projections are handled in marine science. We employan approach developedin climatemodelling by breaking uncertainty down into(i) structural (model) uncertainty,(ii) initialization and internalvariabilityuncertainty,(iii)parametricuncertainty,and(iv)scenariouncertainty.Foreachuncertaintytype,wethenexaminethecurrent state-of-the-art in assessing and quantifying its relative importance. We consider whether the marine scientific community has addressed these types of uncertainty sufficiently and highlight the opportunities and challenges associated with doing a better job. We find that even within a relatively small field such as marine science, there are substantial differences between subdisciplines in the degree of attention given to each type of uncertainty. We find that initialization uncertainty is rarely treated explicitly and reducing this type of uncertainty may deliver gainsontheseasonal-to-decadaltime-scale.Weconcludethatallpartsofmarinesciencecouldbenefitfromagreaterexchangeofideas,particularly concerningsuchauniversalproblemsuchasthetreatmentofuncertainty.Finally,marinescienceshouldstrivetoreachthepointwherescenario uncertainty is the dominant uncertainty in our projections

Influence of molecular imaging on patient selection for treatment intensification prior to salvage radiation therapy for prostate cancer: a post hoc analysis of the PROPS trial.

BACKGROUND: The impact of molecular imaging (MI) on patient management after biochemical recurrence (BCR) following radical prostatectomy has been described in many studies. However, it is not known if MI-induced management changes are appropriate. This study aimed to determine if androgen deprivation therapy (ADT) management plan is improved by MI in patients who are candidates for salvage radiation therapy. METHODS: Data were analyzed from the multicenter prospective PROPS trial evaluating PSMA/Choline PET in patients being considered for salvage radiotherapy (sRT) with BCR after prostatectomy. We compared the pre- and post-MI ADT management plans for each patient and cancer outcomes as predicted by the MSKCC nomogram. A higher percentage of predicted BCR associated with ADT treatment intensification after MI was considered as an improvement in a patient's management. RESULTS: Seventy-three patients with a median PSA of 0.38 ng/mL were included. In bivariate analysis, a positive finding on MI (local or metastatic) was associated with decision to use ADT with an odds ratio of 3.67 (95% CI, 1.25 to 10.71; p = 0.02). No factor included in the nomogram was associated with decision to use ADT. Also, MI improved selection of patients to receive ADT based on predicted BCR after sRT : the predicted nomogram 5-year biochemical-free survivals were 52.5% and 43.3%, (mean difference, 9.2%; 95% CI 0.8 to 17.6; p = 0.03) for sRT alone and ADT±sRT subgroups, while there was no statistically significant difference between subgroups before MI. CONCLUSIONS: PSMA and/or Choline PET/CT before sRT can potentially improve patient ADT management by directing clinicians towards more appropriate intensification

Inter-annual decrease in pulse rate and peak frequency of Southeast Pacific blue whale song types

The decrease in the frequency of two southeast Pacific blue whale song types was examined over decades, usingacoustic data from several different sources ranging between the Equator and Chilean Patagonia. The pulse rate ofthe song units as well as their peak frequency were measured using two different methods (summed auto-correlationand Fourier transform). The sources of error associated with each measurement were assessed. There was a lineardecline in both parameters for the more common song type (southeast Pacific song type n ◦ 2). An abbreviated analysisalso showed a frequency decline in the scarcer southeast Pacific song type n ◦ 1 between 1970 to 2014, revealing thatboth song types are declining at similar rates. We discussed the use of measuring both pulse rate and peak frequencyto examine the frequency decline. Finally, a comparison of the rates of frequency decline with other song typesreported in the literature is presented.La décroissance en fréquence des deux chants de baleine bleue de l'océan pacifique sud est est examiné sur plusieurs décennies en utilisant comme source des données acoustiques de l'Equateur à la Patagonie chilienne. La fréquence de pulsation et la fréquence pic des signaux sont mesurés en utilisant deux méthodes distinctes (auto-corrélation sommée et transformée de Fourier rapide). Les sources d'erreur associées à chaque mesure sont estimées. Il y a un déclin linéaire de ces deux fréquences pour le chant le plus commun de cette zone (chant du Pacifique Sud Est n°2, SEP2). Un analyse plus rapide montre aussi une baisse linéaire, entre 1970 et 2014, de la fréquence du chant SEP1, plus rarement enregistré dans cette zone. Ces deux baisses ont des amplitudes similaires. L'intérêt de mesurer la fréquence de pulsation et la fréquence pic de façon concomitante est estimé. Enfin, une comparaison globale des déclins en fréquence de tous les types de chants de baleines bleues est fournie

Temperature, Viral Genetics, and the Transmission of West Nile Virus by Culex pipiens Mosquitoes

The distribution and intensity of transmission of vector-borne pathogens can be strongly influenced by the competence of vectors. Vector competence, in turn, can be influenced by temperature and viral genetics. West Nile virus (WNV) was introduced into the United States of America in 1999 and subsequently spread throughout much of the Americas. Previously, we have shown that a novel genotype of WNV, WN02, first detected in 2001, spread across the US and was more efficient than the introduced genotype, NY99, at infecting, disseminating, and being transmitted by Culex mosquitoes. In the current study, we determined the relationship between temperature and time since feeding on the probability of transmitting each genotype of WNV. We found that the advantage of the WN02 genotype increases with the product of time and temperature. Thus, warmer temperatures would have facilitated the invasion of the WN02 genotype. In addition, we found that transmission of WNV accelerated sharply with increasing temperature, T, (best fit by a function of T4) showing that traditional degree-day models underestimate the impact of temperature on WNV transmission. This laboratory study suggests that both viral evolution and temperature help shape the distribution and intensity of transmission of WNV, and provides a model for predicting the impact of temperature and global warming on WNV transmission