Simple implementation of complex functionals: scaled selfconsistency

We explore and compare three approximate schemes allowing simple implementation of complex density functionals by making use of selfconsistent implementation of simpler functionals: (i) post-LDA evaluation of complex functionals at the LDA densities (or those of other simple functionals); (ii) application of a global scaling factor to the potential of the simple functional; and (iii) application of a local scaling factor to that potential. Option (i) is a common choice in density-functional calculations. Option (ii) was recently proposed by Cafiero and Gonzalez. We here put their proposal on a more rigorous basis, by deriving it, and explaining why it works, directly from the theorems of density-functional theory. Option (iii) is proposed here for the first time. We provide detailed comparisons of the three approaches among each other and with fully selfconsistent implementations for Hartree, local-density, generalized-gradient, self-interaction corrected, and meta-generalized-gradient approximations, for atoms, ions, quantum wells and model Hamiltonians. Scaled approaches turn out to be, on average, better than post-approaches, and unlike these also provide corrections to eigenvalues and orbitals. Scaled selfconsistency thus opens the possibility of efficient and reliable implementation of density functionals of hitherto unprecedented complexity.Comment: 12 pages, 1 figur

Systematic investigation of a family of gradient-dependent functionals for solids

Eleven density functionals are compared with regard to their performance for the lattice constants of solids. We consider standard functionals, such as the local-density approximation and the Perdew-Burke-Ernzerhof (PBE) generalized-gradient approximation (GGA), as well as variations of PBE GGA, such as PBEsol and similar functionals, PBE-type functionals employing a tighter Lieb-Oxford bound, and combinations thereof. Several of these variations are proposed here for the first time. On a test set of 60 solids we perform a system-by-system analysis for selected functionals and a full statistical analysis for all of them. The impact of restoring the gradient expansion and of tightening the Lieb-Oxford bound is discussed, and confronted with previous results obtained from other codes, functionals or test sets. No functional is uniformly good for all investigated systems, but surprisingly, and pleasingly, the simplest possible modifications to PBE turn out to have the most beneficial effect on its performance. The atomization energy of molecules was also considered and on a testing set of six molecules, we found that the PBE functional is clearly the best, the others leading to strong overbinding

Exome and Tissue-Associated Microbiota as Predictive Markers of Response to Neoadjuvant Treatment in Locally Advanced Rectal Cancer

The clinical and pathological responses to multimodal neoadjuvant therapy in locally advanced rectal cancers (LARCs) remain unpredictable, and robust biomarkers are still lacking. Recent studies have shown that tumors present somatic molecular alterations related to better treatment response, and it is also clear that tumor-associated bacteria are modulators of chemotherapy and immunotherapy efficacy, therefore having implications for long-term survivorship and a good potential as the biomarkers of outcome. Here, we performed whole exome sequencing and 16S ribosomal RNA (rRNA) amplicon sequencing from 44 pre-treatment LARC biopsies from Argentinian and Brazilian patients, treated with neoadjuvant chemoradiotherapy or total neoadjuvant treatment, searching for predictive biomarkers of response (responders, n = 17; non-responders, n = 27). In general, the somatic landscape of LARC was not capable to predict a response; however, a significant enrichment in mutational signature SBS5 was observed in non-responders (p = 0.0021), as well as the co-occurrence of APC and FAT4 mutations (p < 0.05). Microbiota studies revealed a similar alpha and beta diversity of bacteria between response groups. Yet, the linear discriminant analysis (LDA) of effect size indicated an enrichment of Hungatella, Flavonifractor, and Methanosphaera (LDA score ≥3) in the pre-treatment biopsies of responders, while non-responders had a higher abundance of Enhydrobacter, Paraprevotella (LDA score ≥3) and Finegoldia (LDA score ≥4). Altogether, the evaluation of these biomarkers in pre-treatment biopsies could eventually predict a neoadjuvant treatment response, while in post-treatment samples, it could help in guiding non-operative treatment strategies.Fil: Takenaka, Isabella Kuniko T. M.. No especifíca;Fil: Bartelli, Thais F.. No especifíca;Fil: Defelicibus, Alexandre. No especifíca;Fil: Sendoya, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Golubicki, Mariano. Gobierno de la Ciudad de Buenos Aires. Hospital de Gastroenterología "Dr. Carlos B. Udaondo"; ArgentinaFil: Robbio, Juan. No especifíca;Fil: Serpa, Marianna S.. No especifíca;Fil: Branco, Gabriela P.. No especifíca;Fil: Santos, Luana B. C.. No especifíca;Fil: Claro, Laura C. L.. No especifíca;Fil: Oliveira dos Santos, Gabriel. No especifíca;Fil: Kupper, Bruna E. C.. No especifíca;Fil: da Silva, Israel T.. No especifíca;Fil: Llera, Andrea Sabina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: de Mello, Celso A. L.. No especifíca;Fil: Riechelmann, Rachel P.. No especifíca;Fil: Dias Neto, Emmanuel. Universidade de Sao Paulo; BrasilFil: Iseas, Soledad. Gobierno de la Ciudad de Buenos Aires. Hospital de Gastroenterología "Dr. Carlos B. Udaondo"; ArgentinaFil: Aguiar, Samuel. No especifíca;Fil: Nunes, Diana Noronha. No especifíca

17-AAG-induced activation of the autophagic pathway in Leishmania is associated with parasite death

The heat shock protein 90 (Hsp90) is thought to be an excellent drug target against parasitic diseases. The leishmanicidal effect of an Hsp90 inhibitor, 17-N-allylamino-17-demethoxygeldanamycin (17-AAG), was previously demonstrated in both in vitro and in vivo models of cutaneous leishmaniasis. Parasite death was shown to occur in association with severe ultrastructural alterations in Leishmania, suggestive of autophagic activation. We hypothesized that 17-AAG treatment results in the abnormal activation of the autophagic pathway, leading to parasite death. To elucidate this process, experiments were performed using transgenic parasites with GFP-ATG8-labelled autophagosomes. Mutant parasites treated with 17-AAG exhibited autophagosomes that did not entrap cargo, such as glycosomes, or fuse with lysosomes. ATG5-knockout (Δatg5) parasites, which are incapable of forming autophagosomes, demonstrated lower sensitivity to 17-AAG-induced cell death when compared to wild-type (WT) Leishmania, further supporting the role of autophagy in 17-AAG-induced cell death. In addition, Hsp90 inhibition resulted in greater accumulation of ubiquitylated proteins in both WT- and Δatg5-treated parasites compared to controls, in the absence of proteasome overload. In conjunction with previously described ultrastructural alterations, herein we present evidence that treatment with 17-AAG causes abnormal activation of the autophagic pathway, resulting in the formation of immature autophagosomes and, consequently, incidental parasite death

Synthesis of the land carbon fluxes of the Amazon region between 2010 and 2020

The Amazon is the largest continuous tropical forest in the world and plays a key role in the global carbon cycle. Human-induced disturbances and climate change have impacted the Amazon carbon balance. Here we conduct a comprehensive synthesis of existing state-of-the-art estimates of the contemporary land carbon fluxes in the Amazon using a set of bottom-up methods (i.e., dynamic vegetation models and bookkeeping models) and a top-down inversion (atmospheric inversion model) over the Brazilian Amazon and the whole Biogeographical Amazon domain. Over the whole biogeographical Amazon region bottom-up methodologies suggest a small average carbon sink over 2010-2020, in contrast to a small carbon source simulated by top-down inversion (2010-2018). However, these estimates are not significantly different from one another when accounting for their large individual uncertainties, highlighting remaining knowledge gaps, and the urgent need to reduce such uncertainties. Nevertheless, both methodologies agreed that the Brazilian Amazon has been a net carbon source during recent climate extremes and that the south-eastern Amazon was a net land carbon source over the whole study period (2010-2020). Overall, our results point to increasing human-induced disturbances (deforestation and forest degradation by wildfires) and reduction in the old-growth forest sink during drought

Limited effect of chronic valproic acid treatment in a mouse model of Machado-Joseph disease

Machado-Joseph disease (MJD) is an inherited neurodegenerative disease, caused by a CAG repeat expansion within the coding region of ATXN3 gene, and which currently lacks effective treatment. In this work we tested the therapeutic efficacy of chronic treatment with valproic acid (VPA) (200mg/kg), a compound with known neuroprotection activity, and previously shown to be effective in cell, fly and nematode models of MJD. We show that chronic VPA treatment in the CMVMJD135 mouse model had limited effects in the motor deficits of these mice, seen mostly at late stages in the motor swimming, beam walk, rotarod and spontaneous locomotor activity tests, and did not modify the ATXN3 inclusion load and astrogliosis in affected brain regions. However, VPA chronic treatment was able to increase GRP78 protein levels at 30 weeks of age, one of its known neuroprotective effects, confirming target engagement. In spite of limited results, the use of another dosage of VPA or of VPA in a combined therapy with molecules targeting other pathways, cannot be excluded as potential strategies for MJD therapeuticsPM received funding from Ataxia UK Grant (Project: Pharmacologic therapy for Machado-Joseph disease: from a C. elegans drug screen to a mouse model validation). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

CO2 emissions in the Amazon: are bottom-up estimates from land use and cover datasets consistent with top-down estimates based on atmospheric measurements?

Amazon forests are the largest forests in the tropics and play a fundamental role for regional and global ecosystem service provision. However, they are under threat primarily from deforestation. Amazonia's carbon balance trend reflects the condition of its forests. There are different approaches to estimate large-scale carbon balances, including top-down (e.g., CO2 atmospheric measurements combined with atmospheric transport information) and bottom-up (e.g., land use and cover change (LUCC) data based on remote sensing methods). It is important to understand their similarities and differences. Here we provide bottom-up LUCC estimates and determine to what extent they are consistent with recent top-down flux estimates during 2010 to 2018 for the Brazilian Amazon. We combine LUCC datasets resulting in annual LUCC maps from 2010 to 2018 with emissions and removals for each LUCC, and compare the resulting CO2 estimates with top-down estimates based on atmospheric measurements. We take into account forest carbon stock maps for estimating loss processes, and carbon uptake of regenerating and mature forests. In the bottom-up approach total CO2 emissions (2010 to 2018), deforestation and degradation are the largest contributing processes accounting for 58% (4.3 PgCO2) and 37% (2.7 PgCO2) respectively. Looking at the total carbon uptake, primary forests play a dominant role accounting for 79% (−5.9 PgCO2) and secondary forest growth for 17% (−1.2 PgCO2). Overall, according to our bottom-up estimates the Brazilian Amazon is a carbon sink until 2014 and a source from 2015 to 2018. In contrast according to the top-down approach the Brazilian Amazon is a source during the entire period. Both approaches estimate largest emissions in 2016. During the period where flux signs are the same (2015–2018) top-down estimates are approximately 3 times larger in 2015–2016 than bottom-up estimates while in 2017–2018 there is closer agreement. There is some agreement between the approaches–notably that the Brazilian Amazon has been a source during 2015–2018 however there are also disagreements. Generally, emissions estimated by the bottom-up approach tend to be lower. Understanding the differences will help improve both approaches and our understanding of the Amazon carbon cycle under human pressure and climate change