Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change.

The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled.

ProvenanceWidgets: A Library of UI Control Elements to Track and Dynamically Overlay Analytic Provenance.

We present ProvenanceWidgets, a Javascript library of UI control elements such as radio buttons, checkboxes, and dropdowns to track and dynamically overlay a user's analytic provenance. These in situ overlays not only save screen space but also minimize the amount of time and effort needed to access the same information from elsewhere in the UI. In this paper, we discuss how we design modular UI control elements to track how often and how recently a user interacts with them and design visual overlays showing an aggregated summary as well as a detailed temporal history.

Long-Read-Based Genome Assembly Reveals Numerous Endogenous Viral Elements in the Green Algal Bacterivore Cymbomonas tetramitiformis.

The marine tetraflagellate Cymbomonas tetramitiformis has drawn attention as an early diverging green alga that uses a phago-mixotrophic mode of nutrition (i.e., the ability to derive nourishment from both photosynthesis and bacterial prey).

The VA National TeleNeurology Program implementation: a mixed-methods evaluation guided by RE-AIM framework.

Introduction: The Veteran Affairs (VA) Office of Rural Health (ORH) funded the Veterans Health Administration (VHA) National TeleNeurology Program (NTNP) as an Enterprise-Wide Initiative (EWI). NTNP is an innovative healthcare delivery model designed to fill the patient access gap for outpatient neurological care especially for Veterans residing in rural communities. The specific aim was to apply the RE-AIM framework in a pragmatic evaluation of NTNP services.

One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade.

Mantamonads were long considered to represent an "orphan" lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the "CRuMs" supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes.

The VA National Teleneurology Program (NTNP): Implementing Teleneurology to Improve Equitable Access to Outpatient Neurology Care.

Background: Telehealth is increasingly utilized in many healthcare systems to improve access to specialty care and better allocate limited resources, especially for rurally residing persons who face unique barriers to care.

Objectives: The VHA sought to address critical gaps in access to neurology care by developing and implementing the first outpatient National Teleneurology Program (NTNP).

Design: Pre-post evaluation of intervention and control sites.

Multiple outgroups can cause random rooting in phylogenomics.

Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods.

Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil.

We typed 600 methicillin-resistant Staphylococcus aureus (MRSA) isolates collected in 51 hospitals in the Rio de Janeiro, Brazil, metropolitan area during 2014-2017. We found that multiple new clonal complex (CC) 5 sequence types had replaced previously dominant MRSA lineages in hospitals. Whole-genome analysis of 208 isolates revealed an emerging sublineage of multidrug-resistant MRSA, sequence type 105, staphylococcal cassette chromosome mec II, spa t002, which we designated the Rio de Janeiro (RdJ) clone.

Left, Right, and Gender: Exploring Interaction Traces to Mitigate Human Biases.

Human biases impact the way people analyze data and make decisions. Recent work has shown that some visualization designs can better support cognitive processes and mitigate cognitive biases (i.e.

Lumos: Increasing Awareness of Analytic Behavior during Visual Data Analysis.

Visual data analysis tools provide people with the agency and flexibility to explore data using a variety of interactive functionalities. However, this flexibility may introduce potential consequences in situations where users unknowingly overemphasize or underemphasize specific subsets of the data or attribute space they are analyzing. For example, users may overemphasize specific attributes and/or their values (e.

VITALITY: Promoting Serendipitous Discovery of Academic Literature with Transformers & Visual Analytics.

There are a few prominent practices for conducting reviews of academic literature, including searching for specific keywords on Google Scholar or checking citations from some initial seed paper(s). These approaches serve a critical purpose for academic literature reviews, yet there remain challenges in identifying relevant literature when similar work may utilize different terminology (e.g.

Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus.

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar.

Genetic variation of staphylococcal LukAB toxin determines receptor tropism.

Staphylococcus aureus has evolved into diverse lineages, known as clonal complexes (CCs), which exhibit differences in the coding sequences of core virulence factors. Whether these alterations affect functionality is poorly understood. Here, we studied the highly polymorphic pore-forming toxin LukAB.

Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans.

Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. () is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the , the lineage that includes Old World monkeys (OWM) and humans.

SafetyLens: Visual Data Analysis of Functional Safety of Vehicles.

Modern automobiles have evolved from just being mechanical machines to having full-fledged electronics systems that enhance vehicle dynamics and driver experience. However, these complex hardware and software systems, if not properly designed, can experience failures that can compromise the safety of the vehicle, its occupants, and the surrounding environment. For example, a system to activate the brakes to avoid a collision saves lives when it functions properly, but could lead to tragic outcomes if the brakes were applied in a way that's inconsistent with the design.

NL4DV: A Toolkit for Generating Analytic Specifications for Data Visualization from Natural Language Queries.

Natural language interfaces (NLls) have shown great promise for visual data analysis, allowing people to flexibly specify and interact with visualizations. However, developing visualization NLIs remains a challenging task, requiring low-level implementation of natural language processing (NLP) techniques as well as knowledge of visual analytic tasks and visualization design. We present NL4DV, a toolkit for natural language-driven data visualization.

Genomic variant-identification methods may alter transmission inferences.

Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach on transmission inferences for we conducted an experiment in which five genomic epidemiology groups applied variant-identification pipelines to the same outbreak sequence data.

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets.

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters).

Antimicrobial sensing coupled with cell membrane remodeling mediates antibiotic resistance and virulence in .

Bacteria have developed several evolutionary strategies to protect their cell membranes (CMs) from the attack of antibiotics and antimicrobial peptides (AMPs) produced by the innate immune system, including remodeling of phospholipid content and localization. Multidrug-resistant an opportunistic human pathogen, evolves resistance to the lipopeptide daptomycin and AMPs by diverting the antibiotic away from critical septal targets using CM anionic phospholipid redistribution. The LiaFSR stress response system regulates this CM remodeling via the LiaR response regulator by a previously unknown mechanism.

Understanding Failure Mode Effect Analysis Data Using Interactive Visual Analytics.

Providing actionable insights through interactive visual analytics is essential to effective decision making. Yet, many complex systems engineering (SE) domains still lack such tools. Design reviews are often still based on static snapshots of data, without any dynamic interaction, data curation, and view creation capabilities to answer salient analysis questions.

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa.

Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant () strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment.

Strains of Staphylococcus aureus that Colonize and Infect Skin Harbor Mutations in Metabolic Genes.

Staphylococcus aureus is the most common cause of skin and soft tissue infections, yet the bacterial genetic changes associated with adaptation to human skin are not well characterized. S. aureus strains isolated from patients with chronic skin colonization and intermittent infection were used to determine the staphylococcal genotypes or phenotypes associated with adaptation to human skin.

CFTR-PTEN-dependent mitochondrial metabolic dysfunction promotes airway infection.

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor suppressor best known for regulating cell proliferation and metabolism. PTEN forms a complex with the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) at the plasma membrane, and this complex is known to be functionally impaired in CF. Here, we demonstrated that the combined effect of PTEN and CFTR dysfunction stimulates mitochondrial activity, resulting in excessive release of succinate and reactive oxygen species.