Brain microstructure and connectivity in COVID-19 patients with olfactory or cognitive impairment.

Introduction: The COVID-19 pandemic has affected millions worldwide, causing mortality and multi-organ morbidity. Neurological complications have been recognized. This study aimed to assess brain structural, microstructural, and connectivity alterations in patients with COVID-19-related olfactory or cognitive impairment using post-acute (time from onset: 264[208-313] days) multi-directional diffusion-weighted MRI (DW-MRI).

Seroprevalence of pathogenic serogroups in asymptomatic domestic dogs and cats: systematic review and meta-analysis.

Leptospirosis is a neglected zoonotic disease transmitted by contact with the urine of animals infected with pathogenic species of the bacteria or by contact with environments contaminated with the bacteria. Domestic dogs and cats may act as reservoirs or as sentinels of environmental contamination with leptospires, posing a public health concern. There is a great diversity of leptospires, and one common way to classify them is into serogroups that provide some information on the host species they are associated with.

Multi-Sensor HR Mass Data Models toward Multi-Temporal-Layered Digital Twins: Maintenance, Design and XR Informed Tour of the Multi-Stratified Appian Way (PAAA).

The article provides an overview of the digitisation project conducted by the Parco Archeologico dell'Appia Antica (PAAA) in Rome, focusing on an 11.7 km section of the Appian Way. This effort is part of the "Appia Regina Viarum" project, supporting the UNESCO heritage site candidacy of the Appian Way.

Brain diffusion alterations in patients with COVID-19 pathology and neurological manifestations.

Background And Objective: COVID-19 neurological manifestations have been progressively recognized. Among available MRI techniques, diffusion weighted imaging (DWI) shows promise to study microstructure, inflammation, and edema. Previous DWI studies reported alterations in brain diffusivity in COVID-19 patients, as assessed by morphologic evaluation of brain DWI scans only.

Leptospiral infection in domestic cats: Systematic review with meta-analysis.

The role of domestic cats in the transmission of Leptospira is controversial, being considered either as a protective factor or a potential source of infection for humans. The aims of this study were to obtain an integrated estimate of the prevalence of leptospiral infection in domestic cats, and to characterize those individuals most susceptible to infection. For this systematic review and meta-analysis, five electronic databases, as well as the reference lists of eligible reports were screened for observational studies published during 1979-2022.

Determining the spatial distribution of environmental and socio-economic suitability for human leptospirosis in the face of limited epidemiological data.

Background: Leptospirosis is among the leading zoonotic causes of morbidity and mortality worldwide. Knowledge about spatial patterns of diseases and their underlying processes have the potential to guide intervention efforts. However, leptospirosis is often an underreported and misdiagnosed disease and consequently, spatial patterns of the disease remain unclear.

Alignment-Free Genotyping of Known Variations with MALVA.

The discovery and characterization of sequence variations in human populations are crucial in genetic studies. Standard methods for addressing this problem are computationally expensive and highly time consuming, thus impractical for clinical applications, where time is often an issue. When the task is to genotype variations that have been previously annotated, alignment-free methods come to the aid.

MALVIRUS: an integrated application for viral variant analysis.

Background: Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in order to track the spread of the viral strains across the globe.

Results: We present MALVIRUS, an easy-to-install and easy-to-use application that assists users in multiple tasks required for the analysis of a viral population, such as the SARS-CoV-2. MALVIRUS allows to: (1) construct a variant catalog consisting in a set of variations (SNPs/indels) from the population sequences, (2) efficiently genotype and annotate variants of the catalog supported by a read sample, and (3) when the considered viral species is the SARS-CoV-2, assign the input sample to the most likely Pango lineages using the genotyped variations.

Emerging hantaviruses in Central Argentina: First case of Hantavirus Pulmonary Syndrome caused by Alto Paraguay virus, and a novel orthohantavirus in Scapteromys aquaticus rodent.

Orthohantaviruses are emerging rodent-borne pathogens that cause Hantavirus Pulmonary Syndrome in humans. They have a wide range of rodent reservoir hosts and are transmitted to humans through aerosolized viral particles generated by the excretions of infected individuals. Since the first description of HPS in Argentina, new hantaviruses have been reported throughout the country, most of which are pathogenic to humans.

Shark: fishing relevant reads in an RNA-Seq sample.

Motivation: Recent advances in high-throughput RNA-Seq technologies allow to produce massive datasets. When a study focuses only on a handful of genes, most reads are not relevant and degrade the performance of the tools used to analyze the data. Removing irrelevant reads from the input dataset leads to improved efficiency without compromising the results of the study.

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.

Motivation: The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies. Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases.

Meta-analysis of risk factors for canine leptospirosis.

Leptospirosis is one of the most widespread zoonotic diseases, with more than one million human cases reported worldwide every year. Dogs could develop infections that range from asymptomatic to severe, and shed leptospires with their urine. Given their close contact with humans, dogs may act both as epidemiological links or as sentinels of pathogenic leptospires in the environment.

Seroprevalence of leptospiral antibodies in rodents from riverside communities of Santa Fe, Argentina.

Background: Leptospirosis is a zoonotic disease that can be transmitted by contact with the urine of infected mammals. Rodents play a mayor role in the transmission of leptospires to humans. The province of Santa Fe reports the greatest number of cases in Argentina.

MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants.

The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure; thus, mapping-free tools have been proposed in recent years. These tools focus on isolated, biallelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels).

[First report on Leptospira interrogans in the sigmodontine rodent Scapteromys aquaticusPrimeiro relato da presença de Leptospira interrogans em roedores sigmodontíneos Scapteromys aquaticus].

Leptospirosis is a globally distributed zoonosis that can be transmitted through direct or indirect contact with the urine or tissues of infected animals. In Argentina, leptospirosis is endemic in the province of Santa Fe and epidemic outbreaks occur during floods. However, very little is known about the role that wild rodents play in the spread of the disease in Argentina.

Orthohantavirus genotype Lechiguanas in Oligoryzomys nigripes (Rodentia: Cricetidae): New evidence of host-switching.

To identify and predict situations of increased risk of orthohantavirus infection in humans, it is necessary to study the relationships between the virus and its rodent hosts. The present study investigated orthohantavirus infection in an assemblage of wild Sigmodontinae rodents of the Paraná Delta, Argentina, and providing new evidence of host-switching events. Rodents belonging to the species Oxymycterus rufus (n = 187), Akodon azarae (n = 82), Oligoryzomys flavescens (n = 80), Oligoryzomys nigripes (n = 47), Scapteromys aquaticus (n = 38), Deltamys kempi (n = 7) and Holochilus brasiliensis (n = 2) were captured at 4 sampling sites during 20 trapping sessions.

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.

Background: While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events from RNA-Seq data and a gene annotation is computationally feasible. This latter task, which is adequate for many transcriptome analyses, is usually achieved by aligning the reads to a reference genome, followed by comparing the alignments with a gene annotation, often implicitly represented by a graph: the splicing graph.

Results: We present ASGAL (Alternative Splicing Graph ALigner): a tool for mapping RNA-Seq data to the splicing graph, with the specific goal of detecting novel splicing events, involving either annotated or unannotated splice sites.

Knowledge, attitudes and practices (KAP) regarding leptospirosis among residents of riverside settlements of Santa Fe, Argentina.

Background: Leptospirosis is a global and re-emerging zoonotic disease caused by Leptospira spirochetes that are shed into the environment by infected animals. Humans can get infected via contact with animal hosts or contaminated environment. In Argentina, the highest annual incidences were reported in the province of Santa Fe, where epidemic outbreaks occurred during flooding events.

FSG: Fast String Graph Construction for De Novo Assembly.

The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this article, we explore a novel approach to compute the string graph, based on the FM-index and Burrows and Wheeler Transform. We describe a simple algorithm that uses only the FM-index representation of the collection of reads to construct the string graph, without accessing the input reads.

Percutaneous mitral valve repair: The last chance for symptoms improvement in advanced refractory chronic heart failure?

Background: The role of percutaneous mitral valve repair (PMVR) in patients with end-stage heart failure (HF) and functional mitral regurgitation (FMR) is unclear.

Methods: Seventy-five consecutive patients with FMR grade≥3+ and severe HF symptoms despite optimal medical therapy and resynchronization therapy underwent PMVR with the MitraClip system (Abbott, Abbott Park, IL, USA) at 3 centers. Clinical evaluation, echocardiography and pro-BNP measurement were performed at baseline and at 6-month.

Optimization of durum wheat bread from a selenium-rich cultivar fortified with bran.

In this work the effect of bran addition (5 %, 10 %, 15 %, 20 %, 25 %, 30 %) on sensory, nutritional and mechanical properties of bread made from a durum wheat semolina enriched with selenium (cultivar PR22D89) was addressed; traditional and whole-meal bread from the same cultivar PR22D89, without any further bran addition, were also investigated for comparative purpose. In order to improve the durum wheat functional bread, different structuring agents (agar agar, gellan gum, guar seed flour, hydroxy-propyl-cellulose, modified food starch-CAPSUL® and tapioca starch) were firstly screened and then optimized. Sensory, textural and nutritional properties of bread were studied in each step.

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly.

The large amount of short read data that has to be assembled in future applications, such as in metagenomics or cancer genomics, strongly motivates the investigation of disk-based approaches to index next-generation sequencing (NGS) data. Positive results in this direction stimulate the investigation of efficient external memory algorithms for de novo assembly from NGS data. Our article is also motivated by the open problem of designing a space-efficient algorithm to compute a string graph using an indexing procedure based on the Burrows-Wheeler transform (BWT).