Trees of tangles in infinite separation systems

We present infinite analogues of our splinter lemma for constructing nested sets of separations. From these we derive several tree-of-tangles-type theorems for infinite graphs and infinite abstract separation systems.

Algorithm for Solving Problem of Designing Regional Logistics Infrastructure

The paper considers an algorithm for solving the problem of finding the optimal location of key objects of transport and warehouse infrastructures within the framework of a methodological approach to designing logistics infrastructure in the territory of the region of the countries. The methodological approach includes three stages. At the first stage, areas are determined where it is advisable to locate key objects of the regional logistics infrastructure. Further, using the models developed by the authors, the linking of warehouse infrastructure objects on the ground has been carried out and, taking into account the designed warehouse network, the optimal dislocation of transport infrastructure objects has been determined. To find the optimal locations for the objects for regional logistics infrastructure facilities, the authors propose an algorithm that is applicable both for building warehouse and transport infrastructures due to the similarity of the models. The algorithm is based on the method of constructing a sequence of plans. At the initial stage, the final expansion is constructed for the set of plans under consideration. For a given set, a minorant has been determined for the cost function associated with the placement and maintenance of infrastructure facilities, the movement of goods, and the haul of an empty vehicle. After that, an iterative algorithm has been formed that determines the sequence of optima of the minorant on a sequence of nested sets. At the first step, an element of the set of plans has been found that minimizes the minorant, at the next step, the found element is excluded from the set under consideration, and a new optimum is sought on the remaining set for which the minorant takes the minimum value. To eliminate multiple plans, it is advisable to use dynamic programming procedures. The limits of applicability of the method for constructing a sequence of plans are determined by the ability to construct an extension of the set of plans for placing objects, select a minorant on it, and build an algorithm for ordering optima.

Error curves for evaluating the quality of feature rankings

In this article, we propose a method for evaluating feature ranking algorithms. A feature ranking algorithm estimates the importance of descriptive features when predicting the target variable, and the proposed method evaluates the correctness of these importance values by computing the error measures of two chains of predictive models. The models in the first chain are built on nested sets of top-ranked features, while the models in the other chain are built on nested sets of bottom ranked features. We investigate which predictive models are appropriate for building these chains, showing empirically that the proposed method gives meaningful results and can detect differences in feature ranking quality. This is first demonstrated on synthetic data, and then on several real-world classification benchmark problems.

Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells

ABSTRACTUnderstanding and eliciting protective immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent priority. To facilitate these objectives, we have profiled the repertoire of human leukocyte antigen class II (HLA-II)-bound peptides presented by HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein. We identify 209 unique HLA-II-bound peptide sequences, many forming nested sets, which map to sites throughout S including glycosylated regions. Comparison of the glycosylation profile of the S protein to that of the HLA-II-bound S peptides revealed substantial trimming of glycan residues on the latter, likely introduced during antigen processing. Our data also highlight the receptor-binding motif in S1 as a HLA-DR-binding peptide-rich region. Results from this study have application in vaccine design, and will aid analysis of CD4+ T cell responses in infected individuals and vaccine recipients.

TreeBASEdmp: A Toolkit for Phyloinformatic Research

Over the last 20 years, TreeBASE has acquired a substantial body of phylogenetic data, including more than 20,000 published phylogenies. Given latency issues and limited options when it comes to querying the database remotely, a simplified and consolidated version of the database, here called TreeBASEdmp, is made available for download, allowing biologists to design custom analyses of the data on their local computers. The database is indexed to support searching for phylogenetic topologies using nested sets and closure tables. Here we propose a new approach to find broadly-defined phylogenetic patterns, a method we call Generic Topological Querying, which allows the user to find hypotheses of relationship without being constrained to use particular sets of specific taxa. Additionally, we normalize as many leaf nodes as possible to an equivalent species rank identifier to assist in supertree synthesis. Our example script rapidly assembles sets of trees and generates a matrix representation of them for subsequent supertree generation.

Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses

ABSTRACTDespite the critical role of epitope presentation for immune recognition, we still lack a comprehensive definition of HIV peptides presented by HIV-infected cells. Here we identified 107 major histocompatibility complex (MHC)-bound HIV peptides directly from the surface of live HIV-transfected 293T cells, HIV-infected B cells, and primary CD4 T cells expressing a variety of HLAs. The majority of peptides were 8 to 12 amino acids (aa) long and mostly derived from Gag and Pol. The analysis of the total MHC-peptidome and of HLA-A02-bound peptides identified new noncanonical HIV peptides of up to 16 aa that could not be predicted by HLA anchor scanning and revealed an heterogeneous surface peptidome. Nested sets of surface HIV peptides included optimal and extended HIV epitopes and peptides partly overlapping or distinct from known epitopes, revealing new immune responses in HIV-infected persons. Surprisingly, in all three cell types, a majority of Gag peptides derived from p15 rather than from the most immunogenic p24. The cytosolic degradation of peptide precursors in corresponding cells confirmed the generation of identified surface-nested peptides. Cytosolic degradation revealed peptides commonly produced in all cell types and displayed by various HLAs, peptides commonly produced in all cell types and selectively displayed by specific HLAs, and peptides produced in only one cell type. Importantly, we identified areas of proteins leading to common presentations of noncanonical peptides by several cell types with distinct HLAs. These peptides may benefit the design of immunogens, focusing T cell responses on relevant markers of HIV infection in the context of HLA diversity.IMPORTANCEThe recognition of HIV-infected cells by immune T cells relies on the presentation of HIV-derived peptides by diverse HLA molecules at the surface of cells. The landscape of HIV peptides displayed by HIV-infected cells is not well defined. Considering the diversity of HLA molecules in the human population, it is critical for vaccine design to identify HIV peptides that may be displayed despite the HLA diversity. We identified 107 HIV peptides directly from the surface of three cell types infected with HIV. They corresponded to nested sets of HIV peptides of canonical and novel noncanonical lengths not predictable by the presence of HLA anchors. Importantly, we identified areas of HIV proteins leading to presentation of noncanonical peptides by several cell types with distinct HLAs. Including such peptides in vaccine immunogen may help to focus immune responses on common markers of HIV infection in the context of HLA diversity.