A novel algorithm can generate data to train machine learning models in conditions of extreme scarcity of real world data

Training machine learning models requires large datasets. However, collecting, curating, and operating large and complex sets of real world data poses problems of costs, ethical and legal issues, and data availability. Here we propose a novel algorithm to generate large artificial datasets to train machine learning models in conditions of extreme scarcity of real world data. The algorithm is based on a genetic algorithm, which mutates randomly generated datasets subsequently used for training a neural network. After training, the performance of the neural network on a batch of real world data is considered a surrogate for the fitness of the generated dataset used for its training. As selection pressure is applied to the population of generated datasets, unfit individuals are discarded, and the fitness of the fittest individuals increases through generations. The performance of the data generation algorithm was measured on the Iris dataset and on the Breast Cancer Wisconsin diagnostic dataset. In conditions of real world data abundance, mean accuracy of machine learning models trained on generated data was comparable to mean accuracy of models trained on real world data (0.956 in both cases on the Iris dataset, p = 0.6996, and 0.9377 versus 0.9472 on the Breast Cancer dataset, p = 0.1189). In conditions of simulated extreme scarcity of real world data, mean accuracy of machine learning models trained on generated data was significantly higher than mean accuracy of comparable models trained on scarce real world data (0.9533 versus 0.9067 on the Iris dataset, p < 0.0001, and 0.8692 versus 0.7701 on the Breast Cancer dataset, p = 0.0091). In conclusion, this novel algorithm can generate large artificial datasets to train machine learning models, in conditions of extreme scarcity of real world data, or when cost or data sensitivity prevent the collection of large real world datasets.Comment: 4 figures, 3 tables, 12 references, 3850 word

A Boolean Model of Molecular Signaling Pathways

7 pages, 6 figuresNational audienceThe usual representation of signaling pathways in molecular biology consists of diagrams. These diagrams are often unclear and confusing, thus making global understanding, prediction and computerization of the signaling pathways impossible. Here we propose a novel representation of signaling pathways, based on a mathematical model. This model associates a simple equation with any signaling pathway. We used this model to study several pathways, such as Akt, leading to strong predictions and powerful in silico experiments

Long-term antibody persistence after vaccination with a 2-dose Havrix™ (inactivated hepatitis A vaccine): 20 years of observed data, and long-term model-based predictions

AbstractAntibody persistence in two cohorts of adults, who received inactivated hepatitis A (HAV) vaccine (1440El.U; Havrix™; GSK Vaccines) according to a 0–6 or 0–12 month schedule in 1992–1993, has been measured annually. After 20 years, >97% of the subjects in both studies were seropositive for anti-HAV antibodies. Geometric mean concentrations in the according-to-protocol cohorts were 312mIU/ml in 34/36 subjects vaccinated initially at 0–6 months (NCT00289757) and 317mIU/ml in 85/86 subjects vaccinated at 0–12 months (NCT00291876). Over the whole follow-up period, seven subjects (2+5, respectively) lost circulating anti-HAV antibodies but mounted a strong response after HAV booster administration (1440El.U). Mathematical modelling, which was applied to assess true persistence at Year 20 (accounting for drop-outs and missing data), and to predict longer-term persistence confirmed previous estimates that seropositive anti-HAV levels would persist in ≥95% vaccinees at Year 30 and ≥90% at Year 40.ClinicalTrials.Gov number: NCT00289757/NCT0029187

Factors influencing risky sexual behaviour among Mozambican miners : a socio-epidemiological contribution for HIV prevention framework in Mozambique

Background: Information dealing with social and behavioural risk factors as well as their mechanisms among Mozambican migrants working in South African mines remains undocumented. This study aims to understand the various factors influencing HIV-related risk behaviours and the resulting HIV positive status of Mozambican miners employed by South African mines. This analysis was undertaken in order to inform a broader and more effective HIV preventive framework in Mozambique. Method: This study relied upon data sourced from the first Integrated Biological and Behavioural Survey among Mozambican miners earning their living in South African mines. It employs quantitative techniques using standard statistical tools to substantiate the laid-down objectives. The primary technique applied in this paper is the multivariable statistical method used in the formulation and application of a proximate determinants framework. Results: The odds of reporting one sexual partner were roughly three times higher for miners working as perforators as opposed to other types of occupation. As well, the odds of condom use - always or sometimes - for miners in the 31-40 age group were three times higher than the odds of condom use in the 51+ age group. Miners with lower education levels were less likely to use condoms. The odds of being HIV positive when the miner reports use of alcohol or drugs (sometimes/always) is 0.32 times lower than the odds for those reporting never use of alcohol or drugs. And finally, the odds of HIV positive status for those using condoms were 2.16 times that of miners who never used condoms, controlling for biological and other proximate determinants. Conclusion: In Mozambique, behavioural theory emphasising personal behavioural changes is the main strategy to combat HIV among miners. Our findings suggest there is a need to change thinking processes about how to influence safer sexual behaviour. This is viewed to be the result of a person's individual decision, due to of the complexity of social and contextual factors that may also influence sexual behaviours. This only stresses the need for HIV prevention strategies to exclusively transcend individual factors while considering the broader social and contextual phenomena influencing HIV risk among Mozambican miners

The lack of star formation gradients in galaxy groups up to z~1.6

In the local Universe, galaxy properties show a strong dependence on environment. In cluster cores, early type galaxies dominate, whereas star-forming galaxies are more and more common in the outskirts. At higher redshifts and in somewhat less dense environments (e.g. galaxy groups), the situation is less clear. One open issue is that of whether and how the star formation rate (SFR) of galaxies in groups depends on the distance from the centre of mass. To shed light on this topic, we have built a sample of X-ray selected galaxy groups at 0<z<1.6 in various blank fields (ECDFS, COSMOS, GOODS). We use a sample of spectroscopically confirmed group members with stellar mass M >10^10.3 M_sun in order to have a high spectroscopic completeness. As we use only spectroscopic redshifts, our results are not affected by uncertainties due to projection effects. We use several SFR indicators to link the star formation (SF) activity to the galaxy environment. Taking advantage of the extremely deep mid-infrared Spitzer MIPS and far-infrared Herschel PACS observations, we have an accurate, broad-band measure of the SFR for the bulk of the star-forming galaxies. We use multi-wavelength SED fitting techniques to estimate the stellar masses of all objects and the SFR of the MIPS and PACS undetected galaxies. We analyse the dependence of the SF activity, stellar mass and specific SFR on the group-centric distance, up to z~1.6, for the first time. We do not find any correlation between the mean SFR and group-centric distance at any redshift. We do not observe any strong mass segregation either, in agreement with predictions from simulations. Our results suggest that either groups have a much smaller spread in accretion times with respect to the clusters and that the relaxation time is longer than the group crossing time.Comment: Accepted for publication in MNRA

Lack of involvement of CD63 and CD9 tetraspanins in the extracellular vesicle content delivery process

Extracellular vesicles (EVs) are thought to mediate intercellular communication by transferring cargoes from donor to acceptor cells. The EV content-delivery process within acceptor cells is still poorly characterized and debated. CD63 and CD9, members of the tetraspanin family, are highly enriched within EV membranes and are respectively enriched within multivesicular bodies/endosomes and at the plasma membrane of the cells. CD63 and CD9 have been suspected to regulate the EV uptake and delivery process. Here we used two independent assays and different cell models (HeLa, MDA-MB-231 and HEK293T cells) to assess the putative role of CD63 and CD9 in the EV delivery process that includes uptake and cargo delivery. Our results suggest that neither CD63, nor CD9 are required for this function

Systèmes agraires et changement climatique au Sud

À partir de l’étude détaillée et de la comparaison d’une douzaine de situations locales contrastées en Afrique sub-saharienne et en Asie du Sud-Est, les auteurs mettent en évidence les processus et les trajectoires qui expliquent la forte exposition aux aléas des différents groupes d’agriculteurs, ainsi que leur inégale capacité d’adaptation. Ils expliquent les ressorts de cette vulnérabilité et illustrent le poids des choix passés et actuels en matière de politiques agricole, environnementale et commerciale. Enfin, ils présentent les modalités d’ajustement et les transformations passées et en cours des pratiques paysannes allant dans le sens d’une réduction de l’exposition à l’aléa, d’une atténuation de la vulnérabilité, et d’une meilleure adaptation aux changements globaux : dérèglement climatique bien sûr, mais aussi accroissement démographique, compétition accrue pour l’accès aux ressources, évolution des prix relatifs et fluctuations des marchés, dérégulation et baisse des soutiens publics, etc. Ils esquissent en conclusion les chemins possibles en matière d’adaptation et des propositions de mesures politiques pour accompagner les producteurs.Pour des raisons de différences de fabrication, les figures et photos en couleurs de la présente version sont disséminées au sein des différents chapitres, mais sont réunies à la fin du chapitre 4 de la version PDF

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly