Strategic assessment of research priorities for sweetpotato.

The following report presents an ex‐ante evaluation of priority research options for sweetpotato carried out in the scope of the strategic assessment of research priorities for the CGIAR Research Program on Roots, Tubers, and Bananas (RTB). It contains the results from the economic surplus model used for the assessment, which are extended to include estimations of the number of beneficiaries and poverty reduction effects. The report identifies and describes the sweetpotato research options taken into consideration for and included into the assessment. The socioeconomic and technological parameters used as input data for the analysis are described and information on the elicitation process and data sources is provided. Results are presented so as to explain the outputs obtained and interpreted with respect to the relevant differences between research option

Effects of immersive and non-immersive virtual reality on the static and dynamic balance of stroke patients: A systematic review and meta-analysis

(1) Background: The development of new technologies means that the use of virtual reality is increasingly being implemented in rehabilitative approaches for adult stroke patients. Objective: To analyze the existing scientific evidence regarding the application of immersive and non-immersive virtual reality in patients following cerebrovascular incidents and their efficacy in achieving dynamic and static balance. (2) Data sources: An electronic search of the databases Medline, Cochrane Library, PEDro, Scopus, and Scielo from January 2010 to December 2020 was carried out using the terms physiotherapy, physical therapy, virtual reality, immersive virtual reality, non-immersive virtual reality, stroke, balance, static balance, and dynamic balance. Selection of studies: Randomized controlled trials in patients older than 18 developed with an adult population (>18 years old) with balance disorders as a consequence of suffering a stroke in the previous six months before therapeutic intervention, including exercises harnessing virtual reality in their interventions and evaluations of balance and published in English or Spanish, were included. A total of two hundred twenty-seven articles were found, ten of which were included for review and of these, nine were included in the subsequent meta-analysis. (3) Data extraction: Two authors selected the studies and extracted their characteristics (participants, interventions, and validation instruments) and results. The methodological quality of the studies was evaluated using the PEDro scale, and the risk of bias was determined using the Cochrane risk-of-bias tool. Data synthesis: Of the selected studies, three did not show significant improvements and seven showed significant improvements in the intervention groups in relation to the variables. (4) Conclusions: Non-immersive virtual reality combined with conventional rehabilitation could be considered as a therapeutic option. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

There are currently more than 150.000 sequenced genomes available from which considerable amounts of information can be extracted. However, annotation information is often not interoperable, static, lacks provenance and is quickly outdated. Keeping these datasets up-to-date, and interoperable is a challenging ..

Changes in cannabinoid receptor binding and mRNA levels in several brain regions of aged rats

AbstractWe have recently found that cannabinoid receptor binding and gene expression markedly decreased in extrapyramidal structures of aged rats. The present study was designed to analyze the possible existence of similar aging-induced changes in cannabinoid receptor binding and gene expression in brain regions other than extrapyramidal areas, but that also contain a significant population of cannabinoid receptors, such as the cerebellum, hippocampal structures, limbic and hypothalamic nuclei, the cerebral cortex and others. To this end, we analyzed cannabinoid receptor binding, using autoradiography, and cannabinoid receptor mRNA levels, using in situ hybridization, in slide-mounted brain sections obtained from young (3 month old) and aged (>2 year old) rats. Results were as follows. In the cerebellum, aged rats exhibited a marked decrease in cannabinoid receptor binding in the molecular layer (−33.3%), although accompanied by no changes in mRNA levels in the granular layer. In the cerebral cortex, a small, although statistically significant, decrease in binding was found in the deep layer (VI) (−18.3%) of aged rats, whereas no changes were found in the superficial layer (I). As in the case of the cerebellum, mRNA levels did not change in the cerebral cortex layers (II–III and V–VI). The different regions of the Ammon’s horn of the hippocampus exhibited similar cannabinoid receptor binding levels in aged and young rats. Interestingly, mRNA levels decreased in aged rats to a small, but statistically significant, extent (CA1: −26.1%; CA2: −21.6%; CA3: −14.4%). This was also seen in another hippocampal structure, the dentate gyrus (−14.6%), although in this region binding levels increased in aged rats (+28.4%). Two hypothalamic structures, the arcuate nucleus and the ventromedial hypothalamic nucleus, exhibited decreased cannabinoid receptor binding in aged rats (−31.1% and −30.3%, respectively), but this was not seen in the medial preoptic area. This was accompanied by no changes in mRNA levels in the ventromedial hypothalamic nucleus. In the limbic structures, aged rats exhibited similar binding levels to young rats. This was seen in the nucleus accumbens, septum nuclei and basolateral amygdaloid nucleus. However, mRNA levels slightly decreased in the basolateral amygdaloid nucleus (−13.4%), whereas they were not altered in the septum nuclei. Finally, other brain structures, such as the central gray substance and the brainstem, exhibited similar binding levels in aged and young rats. However, it is important to note that mRNA levels increased significantly (+211.2%) in the brainstem of aged rats, an area where the levels of binding and mRNA were very low in young rats. This marked increase may be related to an increase in the presence of glial elements in this region, as revealed by the increase in the immunoreactivity for glial fibrillary acidic protein observed in the brainstem of aged rats as compared to young animals. In summary, senescence was associated with changes in cannabinoid receptors in the cerebellum, the cerebral cortex, limbic and hypothalamic structures, the hippocampus and other brain regions. However, the changes observed (i) were not as marked and relevant as those early reported in extrapyramidal areas, and (ii) exhibited regional differences that might be attributed to the different roles played by these receptors in each region. Of particular relevance by their magnitude were the aging-induced decrease in binding found in the cerebellum and the hypothalamus, and the increase in mRNA levels observed in the brainstem. The latter might be related to an increase in the presence of glial cells which might contain cannabinoid receptor mRNA

Does exposure to inflammatory particles modify the pattern of anion in exhaled breath condensate?

Exposure to environmental and occupational particulate matter (PM) induces health effects on the cardio-pulmonary system. In addition, associations between exposure to PM and metabolic syndromes like diabetes mellitus or obesity are now emerging in the literature. Collection of exhaled breath condensate (EBC) is an appealing non-invasive technique to sample pulmonary fluids. This hypothesis-generating study aims to (1) validate an ion chromatography method allowing the robust determination of different metabolism-related molecules (lactate, formate, acetate, propionate, butyrate, pyruvate, nitrite, nitrate) in EBC; (2) apply this method to EBC samples collected from workers exposed to quartz (a known inflammatory particle), to soapstone (a less inflammatory particle than quartz), as well as to controls. A multi-compound standard solution was used to determine the linearity range, detection limit, repeatability and bias from spiked EBC. The biological samples were injected without further treatment into an ion chromatograph with a conductivity detector. RTube <sup>®</sup> were used for field collection of EBC from 11 controls, 55 workers exposed to soapstone and 12 volunteers exposed to quartz dust. The analytical method used proved to be adequate for quantifying eight anions in EBC samples. Its sub-micromolar detection limits and repeatability, combined with a very simple sample preparation, allowed an easy and fast quantification of different glycolysis or nitrosative stress metabolites. Using multivariate discriminant analysis to maximize differences between groups, we observed a different pattern of anions with a higher formate/acetate ratio in the EBC samples for quartz exposed workers compared to the two other groups. We hypothesize that a modification of the metabolic signature could be induced by exposure to inflammatory particles like quartz and might be observed in the EBC via a change in the formate/acetate ratio

Dynamics of Excited Electrons in Copper and Ferromagnetic Transition Metals: Theory and Experiment

Both theoretical and experimental results for the dynamics of photoexcited electrons at surfaces of Cu and the ferromagnetic transition metals Fe, Co, and Ni are presented. A model for the dynamics of excited electrons is developed, which is based on the Boltzmann equation and includes effects of photoexcitation, electron-electron scattering, secondary electrons (cascade and Auger electrons), and transport of excited carriers out of the detection region. From this we determine the time-resolved two-photon photoemission (TR-2PPE). Thus a direct comparison of calculated relaxation times with experimental results by means of TR-2PPE becomes possible. The comparison indicates that the magnitudes of the spin-averaged relaxation time \tau and of the ratio \tau_\uparrow/\tau_\downarrow of majority and minority relaxation times for the different ferromagnetic transition metals result not only from density-of-states effects, but also from different Coulomb matrix elements M. Taking M_Fe > M_Cu > M_Ni = M_Co we get reasonable agreement with experiments.Comment: 23 pages, 11 figures, added a figure and an appendix, updated reference

Association of Systemic Lupus Erythematosus Clinical Features with European Population Genetic Substructure

Systemic Lupus Erythematosus (SLE) is an autoimmune disease with a very varied spectrum of clinical manifestations that could be partly determined by genetic factors. We aimed to determine the relationship between prevalence of 11 clinical features and age of disease onset with European population genetic substructure. Data from 1413 patients of European ancestry recruited in nine countries was tested for association with genotypes of top ancestry informative markers. This analysis was done with logistic regression between phenotypes and genotypes or principal components extracted from them. We used a genetic additive model and adjusted for gender and disease duration. Three clinical features showed association with ancestry informative markers: autoantibody production defined as immunologic disorder (P = 6.8×10(-4)), oral ulcers (P = 6.9×10(-4)) and photosensitivity (P = 0.002). Immunologic disorder was associated with genotypes more common in Southern European ancestries, whereas the opposite trend was observed for photosensitivity. Oral ulcers were specifically more common in patients of Spanish and Portuguese self-reported ancestry. These results should be taken into account in future research and suggest new hypotheses and possible underlying mechanisms to be investigated. A first hypothesis linking photosensitivity with variation in skin pigmentation is suggested

A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)

Motivation: We address the following question: Does inhibition of the expression of a gene X in a cellular assay affect the expression of another gene Y? Rather than inhibiting gene X experimentally, we aim at answering this question computationally using as the only input observational gene expression data. Recently, a new statistical algorithm called Intervention calculus when the Directed acyclic graph is Absent (IDA), has been proposed for this problem. For several biological systems, IDA has been shown to outcompete regression-based methods with respect to the number of true positives versus the number of false positives for the top 5000 predicted effects. Further improvements in the performance of IDA have been realized by stability selection, a resampling method wrapped around IDA that enhances the discovery of true causal effects. Nevertheless, the rate of false positive and false negative predictions is still unsatisfactorily high. Results: We introduce a new resampling approach for causal discovery called accumulation IDA (aIDA). We show that aIDA improves the performance of causal discoveries compared to existing variants of IDA on both simulated and real yeast data. The higher reliability of top causal effect predictions achieved by aIDA promises to increase the rate of success of wet lab intervention experiments for functional studies

Molecular Dynamics for Fermions

The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. Keywords: Many-body theory; Fermion system; Molecular dynamics; Wave-packet dynamics; Time-dependent variational principle; Statistical properties; Canonical ensemble; Ergodicity; Time averagingComment: 97 pages, 13 postscript figures. To be published in July 2000 issue of Reviews of Modern Physics. More information at http://www-aix.gsi.de/~fmd

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

Prokaryotes use a mechanism called priming to update their CRISPR immunological memory to rapidly counter revisiting, mutated viruses, and plasmids. Here we have determined how new spacers are produced and selected for integration into the CRISPR array during priming. We show that Cas3 couples CRISPR interference to adaptation by producing DNA breakdown products that fuel the spacer integration process in a two-step, PAM-associated manner. The helicase-nuclease Cas3 pre-processes target DNA into fragments of about 30–100 nt enriched for thymine-stretches in their 3′ ends. The Cas1-2 complex further processes these fragments and integrates them sequence-specifically into CRISPR repeats by coupling of a 3′ cytosine of the fragment. Our results highlight that the selection of PAM-compliant spacers during priming is enhanced by the combined sequence specificities of Cas3 and the Cas1-2 complex, leading to an increased propensity of integrating functional CTT-containing spacers.</p