A machine learning based framework to identify and classify long terminal repeat retrotransposons

Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-LEARNER, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs) at their boundaries. We evaluate the predictive performance of our framework on the well-annotated genomes of Drosophila melanogaster and Arabidopsis thaliana and we compare our results for three LTR retrotransposon superfamilies with the results of three widely used methods for TE identification or classification: REPEATMASKER, CENSOR and LTRDIGEST. In contrast to these methods, TE-LEARNER is the first to incorporate machine learning techniques, outperforming these methods in terms of predictive performance , while able to learn models and make predictions efficiently. Moreover, we show that our method was able to identify TEs that none of the above method could find, and we investigated TE-LEARNER'S predictions which did not correspond to an official annotation. It turns out that many of these predictions are in fact strongly homologous to a known TE

The effect of a new geometric bicycle saddle on the genital-perineal vascular perfusion of female cyclists

Purpose. — Female cyclists undergo a perineal compression of the pudendal nerve and genitalperineal area, with underexplored effects on genital injuries and sexual dysfunctions. This study tests the effects of a new geometric bicycle saddle (SMP) on perineal compression, blood perfusion, genital sensation and sexual function. Methods. — Thirty-three professional female athletes were monitored when using both the new saddle and a traditional professional saddle, in a randomized order. Short-term effects are estimated by measuring the partial pressure of vagina transcutaneous oxygen (PtcO2) before using the saddle, after 10 minutes of static sitting, after riding 20 minutes. Long-term effects are estimated by measuring athletes Female Sexual Distress Scale (FSDS) before using the new saddle and after 6 months using it. Results. — From an initial average of 70 mmHg, PtcO2 decreases by 30 mmHg after riding on a traditional saddle, 10 mmHg on the new saddle (respectively 20 and 7 after just sitting). When using the traditional saddle all FSDS scores are well over the 12 ‘‘normality’’ threshold, with an average of 41, while after using the new saddle the average falls to 12. All differences between the saddles are strongly significant: paired t-tests > 6; P < 0.001; 95% confidence intervals respectively 13 ± 3 mmHg after sitting, 20 ± 3 mmHg after riding, 29 ± 2 FSDS scores. Conclusion. — Traditional saddles have strong negative effects on the vascular perfusion of the vulva, with possible consequences on female sexual functions. The SMP saddle reduces the compression on the pelvic floor and can help reducing the incidence of urogenital pathologies for female cyclists

Conversion of Cerrado into agricultural land in the south-western amazon: carbon stocks and soil fertility.

Mudanças de uso da terra e práticas de manejo modificam a dinâmica do C e a fertilidade do solo. Este estudo avaliou as implicações dos sistemas de cultivo (NT e CT) nos estoques de C e de nutrientes e identificou inter-relações entre estes estoques e outros atributos da fertilidade do solo em Latossolo após a mudança do uso da terra no cerrado amazônico. Os estoques de C e de nutrientes (P, K, Ca e Mg) ajustados pela massa equivalente do solo sob cerrado (CE), foram maiores principalmente sob NT. Após a adoção do NT, exceto em 2NT, os estoques de C foram maiores em relação às demais áreas avaliadas. Correlações entre estoques de C e de nutrientes revelaram algumas correlações positivas com Ca e Mg nas áreas sob NT, devido ao uso continuo de calcário, à maior quantidade de resíduos culturais e ao não revolvimento do solo, associado à correlações positivas com CTC, saturação por bases e pH. A correlação positiva (r = 0,91, p < 0,05) entre estoques de C e CTC em CE indica a importante contribuição da MOS na CT de solos tropicais, embora os sítios de troca estejam ocupados principalmente por H + Al. Estoques de P e K mostraram correlações positivas com estoques de C em CE (0,81 e 0,82; respectivamente), indicando a alta relação de P e K com a MOS em ecossistemas naturais. A alta variabilidade espacial associada à aplicação de fertilizantes (P e K) no sulco de plantio pode ter mascarado os resultados dos estoques. A principal fonte destes nutrientes para o solo foi o fertilizante aplicado e não a MOS

Estimation de stocks de carbone organique des sols à différentes échelles d'espace et de temps

National audienceCet article traite de l’estimation des stocks de carbone organique des sols à différentes échelles d’espace et de temps. Dans une première partie nous passons en revue les principales échelles de variabilité des stocks de carbone des sols et nous en tirons des recommandations quant aux techniques à utiliser pour leur estimation et des considérations sur les incertitudes associées à ces estimations. Nous analysons ensuite les conséquences de cette variabilité sur la faisabilité de la détection de changements au cours du temps et sur l’optimisation des dispositifs de surveillance in situ. Dans une dernière partie nous comparons différentes techniques analytiques et nous développons l’apport potentiel que pourraient représenter les techniques de spectrométrie infra-rouge

Searches for physics beyond the standard model with the M_(T2) variable in hadronic final states with and without disappearing tracks in proton–proton collisions at √s = 13 TeV

Two related searches for phenomena beyond the standard model (BSM) are performed using events with hadronic jets and significant transverse momentum imbalance. The results are based on a sample of proton–proton collisions at a center-of-mass energy of 13TeV, collected by the CMS experiment at the LHC in 2016–2018 and corresponding to an integrated luminosity of 137fb⁻¹. The first search is inclusive, based on signal regions defined by the hadronic energy in the event, the jet multiplicity, the number of jets identified as originating from bottom quarks, and the value of the kinematic variable M_(T2) for events with at least two jets. For events with exactly one jet, the transverse momentum of the jet is used instead. The second search looks in addition for disappearing tracks produced by BSM long-lived charged particles that decay within the volume of the tracking detector. No excess event yield is observed above the predicted standard model background. This is used to constrain a range of BSM models that predict the following: the pair production of gluinos and squarks in the context of supersymmetry models conserving R-parity, with or without intermediate long-lived charginos produced in the decay chain; the resonant production of a colored scalar state decaying to a massive Dirac fermion and a quark; or the pair production of scalar and vector leptoquarks each decaying to a neutrino and a top, bottom, or light-flavor quark. In most of the cases, the results obtained are the most stringent constraints to date