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Weintraub, A.

Publications and source records attributed to Weintraub, A..

2 recordsLinked to original sources

RUSBoost: A suitable species distribution method for imbalanced records of presence and absence. A case study of twenty-five species of Iberian bats

O_LITraditional Species Distribution Models (SDMs) may not be appropriate when examples of one class (e.g. absence or pseudo-absences) greatly outnumber examples of the other class (e.g. presences or observations), because they tend to favor the learning of observations more frequently. C_LIO_LIWe present an ensemble method called Random UnderSampling and Boosting (RUSBoost), which was designed to address the case where the number of presence and absence records are imbalanced, and we opened the "black-box" of the algorithm to interpret its results and applicability in ecology. C_LIO_LIWe applied our methodology to a case study of twenty-five species of bats from the Iberian Peninsula and we build a RUSBoost model for each species. Furthermore, in order to improve to build tighter models, we optimized their hyperparameters using Bayesian Optimization. In particular, we implemented a objective function that represents the cross-validation loss: [Formula], with [Formula] representing the hyper-parameters Maximum Number of Splits, Number of Learners and Learning Rate. C_LIO_LIThe models reached average values for Area Under the ROC Curve (AUC), specificity, sensitivity, and overall accuracy of 0.84 {+/-} 0.05%, 79.5 {+/-} 4.87%, 74.9 {+/-} 6.05%, and 78.8 {+/-} 5.0%, respectively. We also obtained values of variable importance and we analyzed the relationships between explanatory variables and bat presence probability. C_LIO_LIThe results of our study showed that RUSBoost could be a useful tool to develop SDMs with good performance when the presence/absence databases are imbalanced. The application of this algorithm could improve the prediction of SDMs and help in conservation biology and management. C_LI

ecology

Loss of heterochromatin and retrotransposon silencing constitute an early phase in oocyte aging

Mammalian oocyte quality reduces with female age. A well-studied aspect of this deterioration is an age-associated rise in oocyte aneuploidy. We show that prior to the occurrence of significant aneuploidy (at the age of 9 months in mouse females), epigenetic changes occur and impact oocyte quality and maturation ability. At this age- we observe a reduction in heterochromatin marks in mouse oocytes. This decrease is apparent in both constitutive heterochromatin and facultative heterochromatin marks but is absent in active euchromatic marks which remain constant. A decrease of heterochromatin marks with age is also observed in human GV oocytes from IVF treatments. Heterochromatin loss with age is associated with an elevation in retrotransposon RNA transcription and processing, an elevation in retrotransposon protein expression, elevation in DNA repair proteins nuclear localization and oocyte maturation defects. Artificial inhibition of the heterochromatin machinery in young oocytes causes an elevation in retrotransposon expression and processing and oocyte maturation defects. Collectively, our work demonstrates an early stage of oocyte aging, characterized by the loss of heterochromatin associated chromatin marks and activation of retrotransposons which cause DNA damage and impair oocyte maturation. We hypothesize that this heterochromatin loss serves as an oocyte associated "epigenetic clock" and is exploited by the cell as an oocyte QC mechanism. One Sentence SummaryOocyte aging includes an early pre-aneuploidy phase when loss of repressive chromatin marks occurs as well as retrotransposon activation and egg maturation defects.

cell biology