The mask (which we need so much is the one we would have needed)☆☆☆ La mascarilla (que tanto necesitamos es la que hubieramos necesitado)
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ABSTRACT:
SUBMITTER: Torres L
PROVIDER: S-EPMC7255161 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: Not available
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Project description:Scientific investigations in medicine and beyond increasingly require observations to be described by more features than can be simultaneously visualized. Simply reducing the dimensionality by projections destroys essential relationships in the data. Similarly, traditional clustering algorithms introduce data bias that prevents detection of natural structures expected from generic nonlinear processes. We examine how these problems can best be addressed, where in particular we focus on two recent clustering approaches, Phenograph and Hebbian learning clustering, applied to synthetic and natural data examples. Our results reveal that already for very basic questions, minimizing clustering bias is essential, but that results can benefit further from biased post-processing.This article is part of the themed issue 'Mathematical methods in medicine: neuroscience, cardiology and pathology'.
| S-EPMC5434083 | biostudies-literature
Project description:Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in developing new methods to construct rooted phylogenetic networks, that is, networks whose internal vertices correspond to hypothetical ancestors, whose leaves correspond to sampled taxa, and in which vertices with more than one parent correspond to taxa formed by reticulate evolutionary events such as recombination or hybridization. Several methods for constructing evolutionary trees use the strategy of building up a tree from simpler building blocks (such as triplets or clusters), and so it is natural to look for ways to construct networks from smaller networks. In this article, we shall demonstrate a fundamental issue with this approach. Namely, we show that even if we are given all of the subnetworks induced on all proper subsets of the leaves of some rooted phylogenetic network, we still do not have all of the information required to completely determine that network. This implies that even if all of the building blocks for some reticulate evolutionary history were to be taken as the input for any given network building method, the method might still output an incorrect history. We also discuss some potential consequences of this result for constructing phylogenetic networks.
| S-EPMC4265143 | biostudies-literature
Project description:The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.
| S-EPMC3278447 | biostudies-literature
Project description:Recent trials show 5-year survival rates >95% for ETV6::RUNX1 Acute Lymphoblastic Leukemia (ALL). Since treatment has many side effects, an overview of cumulative drug doses and intensities between eight international trials is presented to characterize therapy needed for cure. A meta-analysis was performed as a comprehensive summary of survival outcomes at 5 and 10 years. For drug dose comparison in non-high risk trial arms, risk group distribution was applied to split the trials into two groups: trial group A with ~70% (range: 63.5-75%) of patients in low risk (LR) (CCLSG ALL2004, CoALL 07-03, NOPHO ALL2008, UKALL2003) and trial group B with ~45% (range: 38.7-52.7%) in LR (AIEOP-BFM ALL 2000, ALL-IC BFM ALL 2002, DCOG ALL10, JACLS ALL-02). Meta-analysis did not show evidence of heterogeneity between studies in trial group A LR and medium risk (MR) despite differences in treatment intensity. Statistical heterogeneity was present in trial group B LR and MR. Trials using higher cumulative dose and intensity of asparaginase and pulses of glucocorticoids and vincristine showed better 5-year event-free survival but similar overall survival. Based on similar outcomes between trials despite differences in therapy intensity, future trials should investigate, to what extent de-escalation is feasible for ETV6::RUNX1 ALL.
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Project description:16S sequencing data from skin microbiota samples derived from female volunteers
| PRJEB45035 | ENA
Project description:Data from the memory training arm (n = 629) of the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) trial were examined to characterize change in memory performance through 5 years of follow-up as a function of memory training, booster training, adherence to training, and other characteristics.Latent growth model analyses revealed that memory training was associated with improved memory performance through Year 5 but that neither booster training nor training adherence significantly influenced this effect. Baseline age was associated with change in memory performance attributable to the passage of time alone (i.e., to aging). Higher education and better self-rated health were associated with greater change in memory performance after training.These findings confirm that memory training can aid in maintaining long-term improvements in memory performance. Booster training and adherence to training do not appear to attenuate rates of normal age-related memory decline.
| S-EPMC3825774 | biostudies-literature
Project description:The D-A-CH reference value (D-A-CH arises from the initial letters of the common country identification for the countries Germany (D), Austria (A) and Switzerland (CH)) for folate equivalents had been set at 400 μg/d for adults in the year 2000. By that time, the prevention of cardiovascular diseases through reduction of homocysteine was considered an important target of the reference value. Since that time a number of research papers revealed that in spite of an inverse association between folate-rich diet and chronic diseases, a preventive effect of folic acid intake on cardiovascular events was not supported by randomized controlled trials, and the reduction of plasma homocysteine levels to around 10-12 μmol/l did not reduce the risk for thromboembolic and cardiovascular diseases in persons already affected by these diseases. These results together with the observation that folate intakes below 400 μg/d result in a sufficient folate status justified a review of the current literature and-consequently-a reduction of the reference value to 300 μg/d for adults. This reference value is expressed as dietary folate equivalents that take into account the difference in bioavailability between folic acid and all types of folates in food. The recommendation to take a daily supplement of 400 μg of synthetic folic acid for women who intend to get pregnant and until the end of the first trimester of pregnancy is maintained.
| S-EPMC4050524 | biostudies-other
Project description:Conflict-driven clause learning (CDCL) is a remarkably successful paradigm for solving the satisfiability problem of propositional logic. Instead of a simple depth-first backtracking approach, this kind of solver learns the reason behind occurring conflicts in the form of additional clauses. However, despite the enormous success of CDCL solvers, there is still only a limited understanding of what influences the performance of these solvers in what way. Considering different measures, this paper demonstrates, quite surprisingly, that clause learning (without being able to get rid of some clauses) can not only help the solver but can oftentimes deteriorate the solution process dramatically. By conducting extensive empirical analysis, we furthermore find that the runtime distributions of CDCL solvers are multimodal. This multimodality can be seen as a reason for the deterioration phenomenon described above. Simultaneously, it also gives an indication of why clause learning in combination with clause deletion is virtually the de facto standard of SAT solving, in spite of this phenomenon. As a final contribution, we show that Weibull mixture distributions can accurately describe the multimodal distributions. Thus, adding new clauses to a base instance has an inherent effect of making runtimes long-tailed. This insight provides an explanation as to why the technique of forgetting clauses is useful in CDCL solvers apart from the optimization of unit propagation speed.
| S-EPMC9417043 | biostudies-literature