The Naïve Bayes classifier++ for metagenomic taxonomic classification-query evaluation.

Motivation: This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

Neurodegeneration in the cortical sulcus is a feature of chronic traumatic encephalopathy and associated with repetitive head impacts.

Neurodegeneration is a seminal feature of many neurological disorders. Chronic traumatic encephalopathy (CTE) is caused by repetitive head impacts (RHI) and is characterized by sulcal tau pathology. However, quantitative assessments of regional neurodegeneration in CTE have not been described.

SHARD: an improved method for staining and visualizing multiplex immunofluorescence in optically cleared postmortem human brain tissue.

Postmortem human brain tissue is a critical resource for studying neurodegenerative disease, providing critical insights into cellular morphology, pathology, and network connectivity. To improve standard microscopy and enable high-resolution, three-dimensional (3D) images of tissues at the subcellular level, tissue-clearing methods have been developed. These 3D images allow for the analysis of large regions of interest and can be used to study structural and spatial changes that occur during neurodegeneration.

Escaping the benthos with Coral Reef Arks: effects on coral translocation and fish biomass.

Anthropogenic stressors like overfishing, land based runoff, and increasing temperatures cause the degradation of coral reefs, leading to the loss of corals and other calcifiers, increases in competitive fleshy algae, and increases in microbial pathogen abundance and hypoxia. To test the hypothesis that corals would be healthier by moving them off the benthos, a common garden experiment was conducted in which corals were translocated to midwater geodesic spheres (hereafter called Coral Reef Arks or Arks). Coral fragments translocated to the Arks survived significantly longer than equivalent coral fragments translocated to Control sites (.

The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain.

Purpose Of Review: This review aims to explore the interface between artificial intelligence (AI) and chronic pain, seeking to identify areas of focus for enhancing current treatments and yielding novel therapies.

Recent Findings: In the United States, the prevalence of chronic pain is estimated to be upwards of 40%. Its impact extends to increased healthcare costs, reduced economic productivity, and strain on healthcare resources.

Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening.

Recent advances in computational methods provide the promise of dramatically accelerating drug discovery. While mathematical modeling and machine learning have become vital in predicting drug-target interactions and properties, there is untapped potential in computational drug discovery due to the vast and complex chemical space. This paper builds on our recently published computational fragment-based drug discovery (FBDD) method called fragment databases from screened ligand drug discovery (FDSL-DD).

Using hypnotic suggestion in the rehabilitation of working memory capacity after acquired brain injury: study protocol for a randomized controlled trial.

Objectives: Establishment of effective evidence-based interventions in rehabilitation of working memory (WM) deficits after acquired brain injury (ABI) is sorely needed. Despite robust evidence for the efficiency of clinical hypnosis in a wide range of clinical conditions, and improved understanding of mechanisms underlying its effects, the potential of clinical hypnosis in cognitive rehabilitation is underexplored. A recent study has shown large effects of hypnotic suggestion on WM capacity following ABI.

Advance Care Planning in Primary Care: A Step toward Normalizing the Conversation.

Despite the number of advance care planning (ACP) conversation guides and tools, ACP conversations are not common in healthcare. In this quality improvement project, we took a different approach and applied complex adaptive systems theory to develop an intervention that emerged from the users (family physicians) themselves - a standardized e-form with prompts. By listening to the users, we were able to integrate ACP best practices, including shifting the focus of ACP conversations from treatment decisions to patient values, in a way that met both users' and patients' needs, addressed barriers and will help normalize ACP conversations in primary care.

Fragment databases from screened ligands for drug discovery (FDSL-DD).

Fragment-based drug design (FBDD) is one major drug discovery method employed in computer-aided drug discovery. Due to its inherent limitations, this process experiences long processing times and limited success rates. Here we present a new Fragment Databases from Screened Ligands Drug Design method (FDSL-DD) that intelligently incorporates information about fragment characteristics into a fragment-based design approach to the drug development process.

Caveat emptor: Mental health specialty certifications and the public's preferences for clinical care.

Appropriate training and continuing education for mental health professionals are designed to ensure that clinicians provide effective and ethical care. Mental health consumers may depend upon these credentials to judge the level of a professional's competence, but whether these activities and credentials provide a valid indicator of knowledge and skills is subject to debate. The present study was designed to examine preferences for mental health clinicians among potential consumers and factors that may inform these preferences, specifically comparing preferences for doctoral-level mental health clinicians and masters-level clinicians with and without specialty certification for treating anxiety symptoms.

Sediment recontamination potential and biological impacts of hydrophobic organics from stormwater in a mixed-use watershed.

This study focused on understanding the influence of stormwater on sediment recontamination and biota bioaccumulation. Stormwater and sediment sampling was conducted at Paleta Creek San Diego, CA, a mixed-use urban watershed. Stormwater samples were size fractioned into clay, silt, sand, and filtered fractions to better understand the association of PAHs and PCBs with different particle sizes.

Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants.

While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication.

Three dimensional evaluation of cerebrovascular density and branching in chronic traumatic encephalopathy.

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts (RHI) and characterized by perivascular accumulations of hyperphosphorylated tau protein (p-tau) at the depths of the cortical sulci. Studies of living athletes exposed to RHI, including concussive and nonconcussive impacts, have shown increased blood-brain barrier permeability, reduced cerebral blood flow, and alterations in vasoreactivity. Blood-brain barrier abnormalities have also been reported in individuals neuropathologically diagnosed with CTE.

Randomized Controlled Trial of Single-dose Perioperative Pregabalin in Ureteroscopy.

Purpose: Ureteroscopy is a commonly performed procedure, with postoperative pain that can lead to revisits and opioid prescribing. Perioperative gabapentinoids have shown promise in decreasing pain and opioid use. We hypothesized that single-dose perioperative pregabalin would be safe and efficacious for decreasing pain after ureteroscopy.

Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.

Background: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.

Methods: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.