Tailored vs. General COVID-19 prevention for adults with mental disabilities residing in group homes: a randomized controlled effectiveness-implementation trial.

Background: People with serious mental illness (SMI) and people with intellectual disabilities/developmental disabilities (ID/DD) are at higher risk for COVID-19 and more severe outcomes. We compare a tailored versus general best practice COVID-19 prevention program in group homes (GHs) for people with SMI or ID/DD in Massachusetts (MA).

Methods: A hybrid effectiveness-implementation cluster randomized control trial compared a four-component implementation strategy (Tailored Best Practices: TBP) to dissemination of standard prevention guidelines (General Best-Practices: GBP) in GHs across six MA behavioral health agencies.

Predictors of COVID-19 infection and hospitalization in group homes for individuals with intellectual and/or developmental disabilities.

Background: More than seven million people with intellectual and/or developmental disabilities (ID/DD) live in the US and may face an elevated risk for COVID-19.

Objective: To identify correlates of COVID-19 and related hospitalizations among people with ID/DD in group homes in Massachusetts.

Methods: We collected data during March 1, 2020-June 30, 2020 (wave 1) and July 1, 2020-March 31, 2021 (wave 2) from the Massachusetts Department of Public Health and six organizations administering 206 group homes for 1035 residents with ID/DD.

On forensic likelihood ratios from low-coverage sequencing.

Advances in sequencing technology are allowing forensic scientists to access genetic information from increasingly challenging samples. A recently published computational approach, IBDGem, analyzes sequencing reads, including from low-coverage samples, in order to arrive at likelihood ratios for human identification. Here, we show that likelihood ratios produced by IBDGem are best interpreted as testing a null hypothesis different from the traditional one used in a forensic genetics context.

COVID-19-Related Outcomes Among Group Home Residents with Serious Mental Illness in Massachusetts in the First Year of the Pandemic.

This study examined COVID-19 infection and hospitalizations among people with serious mental illness who resided in residential care group homes in Massachusetts during the first year of the COVID-19 pandemic. The authors analyzed data on 2261 group home residents and COVID-19 data from the Massachusetts Department of Public Health. Outcomes included positive COVID-19 tests and COVID-19 hospitalizations March 1, 2020-June 30, 2020 (wave 1) and July 1, 2020-March 31, 2021 (wave 2).

The house is a machine for everything: the role of the built environment in group homes during the COVID-19 pandemic.

Objectives: Individuals living in group homes during the COVID-19 pandemic faced unique challenges and health risks related to living in shared spaces. This study aimed to assess the experiences of living and working in a group home during the pandemic and to explore the role of the built environment.

Study Design And Methods: We conducted longitudinal working groups with group home residents with intellectual and developmental disabilities and serious mental illness, group home staff, and families/caregivers of residents from December 2020 through December 2022.

Group Home Staff Experiences With Work and Health in the COVID-19 Pandemic in Massachusetts.

Importance: Direct reports of the experiences of staff working in group homes for people with serious mental illness (SMI) and/or intellectual or developmental disabilities (ID/DD) are rarely reported. Hearing from workers about their experiences in the COVID-19 pandemic may inform future workforce and public policy.

Objective: To gather baseline data on worker experience with the perceived effects of COVID-19 on health and work in the pandemic prior to initiating an intervention to mitigate the spread of COVID-19 and to measure differences in worker experience by gender, race, ethnicity, education, and resident population served (persons with SMI and/or IDD/DD).

Best practices to reduce COVID-19 in group homes for individuals with serious mental illness and intellectual and developmental disabilities: Protocol for a hybrid type 1 effectiveness-implementation cluster randomized trial.

Background: People with serious mental illness (SMI) and intellectual disabilities and/or developmental disabilities (ID/DD) living in group homes (GHs) and residential staff are at higher risk for COVID-19 infection, hospitalization, and death compared with the general population.

Methods: We describe a hybrid type 1 effectiveness-implementation cluster randomized trial to assess evidence-based infection prevention practices to prevent COVID-19 for residents with SMI or ID/DD and the staff in GHs. The trial will use a cluster randomized design in 400 state-funded GHs in Massachusetts for adults with SMI or ID/DD to compare effectiveness and implementation of "Tailored Best Practices" (TBP) consisting of evidence-based COVID-19 infection prevention practices adapted for residents with SMI and ID/DD and GH staff; to "General Best Practices" (GBP), consisting of required standard of care reflecting state and federal standard general guidelines for COVID-19 prevention in GHs.

Simulation-assisted machine learning.

Motivation: In a predictive modeling setting, if sufficient details of the system behavior are known, one can build and use a simulation for making predictions. When sufficient system details are not known, one typically turns to machine learning, which builds a black-box model of the system using a large dataset of input sample features and outputs. We consider a setting which is between these two extremes: some details of the system mechanics are known but not enough for creating simulations that can be used to make high quality predictions.

The value of prior knowledge in machine learning of complex network systems.

Motivation: Our overall goal is to develop machine-learning approaches based on genomics and other relevant accessible information for use in predicting how a patient will respond to a given proposed drug or treatment. Given the complexity of this problem, we begin by developing, testing and analyzing learning methods using data from simulated systems, which allows us access to a known ground truth. We examine the benefits of using prior system knowledge and investigate how learning accuracy depends on various system parameters as well as the amount of training data available.

8-Halo-substituted naphtho[2,3-b]thiophene-4,9-diones as redox-active inhibitors of keratinocyte hyperproliferation with reduced membrane-damaging properties.

A series of 8-chloronaphtho[2,3-b]thiophene-4,9-diones and also some 8-bromo analogues were prepared. The compounds were evaluated for their potencies to suppress keratinocyte hyperproliferation using the human keratinocyte line HaCaT as the primary test system. Structure-activity relationship studies revealed that replacement of the phenolic group of an earlier series with an 8-halogen atom retained the inhibitory potency against keratinocyte hyperproliferation with IC50 values in the submicromolar range.

Synthesis and structure-activity relationships of lapacho analogues. 2. Modification of the basic naphtho[2,3-b]furan-4,9-dione, redox activation, and suppression of human keratinocyte hyperproliferation by 8-hydroxynaphtho[2,3-b]thiophene-4,9-diones.

The basic structure of linearly anellated lapacho quinones, naphtho[2,3-b]furan-4,9-dione (7), was modified in the search for novel agents against keratinocyte hyperproliferation. The synthesis and structure-activity relationships of several heterocycle-fused naphthoquinones as well as a full range of 2- and 7-substituted derivatives of one of these, 8-hydroxynaphtho[2,3-b]thiophene-4,9-dione (8a), are described. Out of a total of 71 analogues, particularly 2-thenoyl-substituted 26l, 2-nicotinoyl-substituted 26m, and 2-oxadiazole-substituted 35a compared favorably with the antipsoriatic agent anthralin.

Metabolic and translational efficiency in microbial organisms.

Metabolic efficiency, as a selective force shaping proteomes, has been shown to exist in Escherichia coli and Bacillus subtilis and in a small number of organisms with photoautotrophic and thermophilic lifestyles. Earlier attempts at larger-scale analyses have utilized proxies (such as molecular weight) for biosynthetic cost, and did not consider lifestyle or auxotrophy. This study extends the analysis to all currently sequenced microbial organisms that are amenable to these analyses while utilizing lifestyle specific amino acid biosynthesis pathways (where possible) to determine protein production costs and compensating for auxotrophy.

Amino acid biosynthetic cost and protein conservation.

Protein products of highly expressed genes tend to favor amino acids that have lower average biosynthetic costs (i.e., they exhibit metabolic efficiency).

Inferring the number of contributors to mixed DNA profiles.

Forensic samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors to the sample can be challenging. These uncertainties can dramatically reduce the statistical weight attached to evidentiary samples.

A genetic optimization approach for isolating translational efficiency bias.

The study of codon usage bias is an important research area that contributes to our understanding of molecular evolution, phylogenetic relationships, respiratory lifestyle, and other characteristics. Translational efficiency bias is perhaps the most well-studied codon usage bias, as it is frequently utilized to predict relative protein expression levels. We present a novel approach to isolating translational efficiency bias in microbial genomes.

Automated isolation of translational efficiency bias that resists the confounding effect of GC(AT)-content.

Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons are preferred.

Magnitude-dependent variation in peak height balance at heterozygous STR loci.

When the smaller of two peaks at an STR locus is less than 70% the magnitude of the larger peak at that locus, the disparity is typically taken to be an indication that there is more than one contributor of template DNA to the sample being tested. An analysis of 1,763 heterozygous allele pairs suggests that a peak height imbalance threshold that varies with the magnitude of the peaks being evaluated at a locus is superior to a fixed threshold. Identifying samples that are likely to be mixtures and those that are likely to have arisen from a single source is accomplished more reliably when a statistically based, magnitude-dependent peak height imbalance threshold is used.

Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?

Prokaryotic organisms preferentially utilize less energetically costly amino acids in highly expressed genes. Studies have shown that the proteome of Saccharomyces cerevisiae also exhibits this behavior, but only in broad terms. This study examines the question of metabolic efficiency as a proteome-shaping force at a finer scale, examining whether trends consistent with cost minimization as an evolutionary force are present independent of protein function and amino acid physicochemical property, and consistently with respect to amino acid biosynthetic costs.