A signal-detection account of item-based and ensemble-based visual change detection: A reply to Harrison, McMaster, and Bays.

Growing empirical evidence shows that ensemble information (e.g., the average feature or feature variance of a set of objects) affects visual working memory for individual items. Recently, Harrison, McMaster, and Bays (2021) used a change detection task to test whether observers explicitly rely on ensemble representations to improve their memory for individual objects. They found that sensitivity to simultaneous changes in all memorized items (which also globally changed set summary statistics) rarely exceeded a level predicted by the so-called optimal summation model within the signal-detection framework. This model implies simple integration of evidence for change from all individual items and no additional evidence coming from ensemble. Here, we argue that performance at the level of optimal summation does not rule out the use of ensemble information. First, in two experiments, we show that, even if evidence from only one item is available at test, the statistics of the whole memory set affect performance. Second, we argue that optimal summation itself can be conceptually interpreted as one of the strategies of holistic, ensemble-based decision. We also redefine the reference level for the item-based strategy as the so-called "minimum rule," which predicts performance far below the optimum. We found that that both our and Harrison et al. (2021)'s observers consistently outperformed this level. We conclude that observers can rely on ensemble information when performing visual change detection. Overall, our work clarifies and refines the use of signal-detection analysis in measuring and modeling working memory.

A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences.

In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.

HLA Genotypes in Patients with Infection Caused by Different Strains of SARS-CoV-2.

The aggressive infectious nature of SARS-CoV-2, its rapid spread, and the emergence of mutations necessitate investigation of factors contributing to differences in SARS-CoV-2 susceptibility and severity. The role of genetic variations in the human HLA continues to be studied in various populations in terms of both its effect on morbidity and clinical manifestation of illness. The study included 484 COVID-19 convalescents (northwest Russia residents of St. Petersburg). Cases in which the responsible strain was determined were divided in two subgroups: group 1 (n = 231) had illness caused by genovariants unrelated to variant of concern (VOC) strains; and group 2 (n = 80) had illness caused by the delta (B.1.617.2) VOC; and a control group (n = 1456). DNA typing (HLA-A, B, DRB1) was performed at the basic resolution level. HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants only but not against infection caused by delta strains. HLA-A*03 was associated with protection against infection caused by delta strains; and allele groups associated with infection by delta strains were HLA-A*30, B*49, and B*57. Thus, in northwest Russia, HLA-A*02 was associated with protection against infection caused by non-VOC SARS-CoV-2 genetic variants but not against delta viral strains. HLA-A*03 was associated with a reduced risk of infection by delta SARS-CoV-2 strains. HLA-A*30, HLA-B*49, and HLA-B*57 allele groups were predisposing factors for infection by delta (B.1.617.2) strains.

Consortium of Indigenous Fecal Bacteria in the Treatment of Metabolic Syndrome.

The features of gut microbiota in metabolic syndrome (MS) and ways to correct it using autoprobiotics, based on indigenous bacteria obtained from fecal samples of the host, remain unexplored. The aim of the study was to investigate the effectiveness of an indigenous consortium (IC) of fecal bacteria in treatment of patients with MS. The study was carried out on 36 patients with MS, manifested with abdominal obesity, eating disorders, dyslipidemia, and hypertension. The control group was formed by 20 healthy volunteers. Samples of IC and gut microbiota content were examined by qPCR and metagenome (16S rRNA) analysis before and after therapy. The decrease in anthropometric parameters of obesity, liver enzyme level correction, reduction in C reactive protein and triglyceride concentrations were revealed after IC usage. The decrease in genera Bifidobacterium, Enterobacter, Paraprevotella, and Prevotella, as well as an increase in Bacteroides fragilis and Oscillospira spp. populations were shown after consumption of IC. A negative correlation between the quantity of B. fragilis and the anthropometric parameters of obesity (r = -0.48) and C reactive protein level (r = -0.36) in serum was established. Thus, IC can be considered as a potential functional personified product for the therapy of MS.

Two Novel Lytic Bacteriophages Infecting Enterococcus spp. Are Promising Candidates for Targeted Antibacterial Therapy.

The rapid emergence of antibiotic resistance is of major concern globally. Among the most worrying pathogenic bacteria are vancomycin-resistant enterococci. Phage therapy is a highly promising method for controlling enterococcal infections. In this study, we described two virulent tailed bacteriophages possessing lytic activity against Enterococcus faecalis and E. faecium isolates. The SSsP-1 bacteriophage belonged to the Saphexavirus genus of the Siphoviridae family, and the GVEsP-1 bacteriophage belonged to the Schiekvirus genus of Herelleviridae. The genomes of both viruses carried putative components of anti-CRISPR systems and did not contain known genes coding for antibiotic-resistance determinants and virulence factors. The conservative arrangement of protein-coding sequences in Saphexavirus and Schiekvirus genomes taken together with positive results of treating enterococcal peritonitis in an animal infection model imply the potential suitability of GVEsP-1 and SSsP-1 bacteriophages for clinical applications.

Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism.

BACKGROUND: The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T rubrum sensu stricto and T violaceum, as well as other less well-established or debatable taxa like T soudanense, T kuryangei and T megninii. Our previous study provided limited evidence in favour of the existence of two genetic lineages in the Russian T rubrum sensu stricto population. OBJECTIVES: We aimed to study the genetic structure of the Russian population of T rubrum and to identify factors shaping this structure. METHODS: We analysed the polymorphism of 12 simple sequence repeat (SSR or microsatellite) markers and single nucleotide polymorphism in the TERG_02941 protein-coding gene in 70 T rubrum isolates and performed a phylogenomic reconstruction. RESULTS: All three types of data provided conclusive evidence that the population consists of two genetic lineages. Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5'-area of the fructose-1,6-bisphosphate aldolase gene. Analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22%-48% of the variability was among groups within T rubrum. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity. CONCLUSION: Our results suggest that the Russian population of T rubrum consists of two cosmopolitan genetic lineages.

Whole genome sequence of first Candida auris strain, isolated in Russia.

Candida auris is an emergent yeast pathogen, easily transmissible between patients and with high percent of multidrug resistant strains. Here we present a draft genome sequence of the first known Russian strain of C. auris, isolated from a case of candidemia. The strain clustered within South Asian C. auris clade and seemingly represented an independent event of dissemination from the original species range. Observed fluconazole resistance was probably due to F105L and K143R mutations in ERG11.

Species boundaries in the Trichophyton mentagrophytes / T. interdigitale species complex.

The fungi Trichophyton mentagrophytes and T. interdigitale are closely related species, causing superficial infections in humans and other mammals. The status of these taxa is a field of long-lasting debates. To clarify their phylogenetic relationships within the genus Trichophyton and sharpen the species boundaries, we performed sequencing of four T. mentagrophytes genomes and also evaluated three previously published multilocus data sets. We performed computational species delimitation analysis on all available in GenBank internal transcribed spacer region (ITS) sequences of Trichophyton spp. Phylogenomic data, phylogenetic network, and species delimitation analyses implied that T. mentagrophytes and T. interdigitale belong to the same phylogenetic species. However, we argue that taxonomic status quo should be retained, from the perspective of epidemiological data and the principle of taxonomic stability. Since there is a correlation between ITS genotype and epidemiological source of an isolate, restriction of T. interdigitale to purely anthropophilic ITS genotypes seems to be reasonable.

Single-nucleotide polymorphism in a local population of Trichophyton rubrum.

Trichophyton rubrum is an important causative agent of superficial mycoses worldwide. To uncover a genetic composition of a local population of this fungus, we sequenced A7C99_6411 and A7C99_6714 loci, coding for hypothetical proteins and revealed two complex genotypes, differing by a single missense mutation in each locus. One of the two A7C99_6411/6714 genotypes was not found in tinea pedis cases and demonstrated mostly longer TRS-1 elements when compared to another genotype. Thus, we present a description of nucleotide polymorphism in protein-coding loci in T. rubrum and provide evidence for ecological preferences of T. rubrum genotypes at a local scale.

Draft Genome Sequence of a Multidrug-Resistant Nosocomial Serratia marcescens Strain That Persisted in a Hospital in Kemerovo, Russian Federation.

Serratia marcescens is a frequent cause of health care-associated infections and has led to multiple outbreaks. Here, we report the draft genome of a multidrug-resistant S. marcescens strain 189 which was isolated in 2012 as a predominant clone in a neonatal hospital in Kemerovo.

Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius.

Enterococcus faecium 58m is a putative ancient nonpathogenic strain isolated from the intestinal content of an adult woolly mammoth (Mammuthus primigenius). Here, we report its draft genome sequence, consisting of 60 contigs. In silico genomic analysis was performed to determine the genetic features and pathogenic potential of this microorganism.