Optimizing automated photo identification for population assessments.

Several legal acts mandate that management agencies regularly assess biological populations. For species with distinct markings, these assessments can be conducted noninvasively via capture-recapture and photographic identification (photo-ID), which involves processing considerable quantities of photographic data. To ease this burden, agencies increasingly rely on automated identification (ID) algorithms.

phylotypr: an R package for classifying DNA sequences.

The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.

Pulmonary granuloma formation during latent infection in C3HeB/FeJ mice involves progression through three immunological phases.

is a fungal pathogen that can cause lethal disease in immunocompromised patients. Immunocompetent host immune responses, such as formation of pulmonary granulomas, control the infection and prevent disseminated disease. Little is known about the immunological conditions establishing the latent infection granuloma in the lungs.

Near-complete genome sequence of a type-A deformed wing virus discovered from in Mississippi, USA.

Deformed wing virus (DWV) can cause a major disease in honeybees worldwide and has been detected in many other arthropods (S. J. Martin and L.

Virulence factor discovery identifies associations between the Fic gene family and Fap2 fusobacteria in colorectal cancer microbiomes.

is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2.

Emerging themes in microbial stress response and mechanistic insights: key findings from the fall 2024 ASM Theobald Smith Society meeting.

The annual fall meeting for the Theobald Smith Society was held in November 2024 on the campus of Rutgers University-New Brunswick. Eighty-six branch members from across New Jersey attended the meeting, composed of undergraduate, graduate, and postdoctoral trainees, faculty members, and government and industry professionals. This report highlights the breadth and diversity of research conducted by American Society for Microbiology members in the Theobald Smith Society and celebrates their groundbreaking discoveries.

Reverse transcriptase inhibitors diminish systemic proinflammatory responses to bacterial pathogens.

Bacterial infections can induce exuberant immune responses that can damage host tissues. Previously, we demonstrated that systemic infection in mice causes tissue damage in the liver. This liver necrosis is associated with the expression of endogenous retroviruses, chromosomally integrated retroviruses that encode a reverse transcriptase.

Single-cell phenotyping of extracellular electron transfer via microdroplet encapsulation.

Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes via extracellular electron transfer (EET). Unfortunately, developing genotype-phenotype relationships for electroactive organisms is challenging because EET is necessarily removed from the cell of origin. Microdroplet emulsions, which encapsulate individual cells in aqueous droplets, have been used to study a variety of extracellular phenotypes but have not been applied to investigate EET.

Faculty rewards from course-based undergraduate research experiences (CURE) in biochemistry.

In recent years, there has been an increase in the number of course-based undergraduate research experience (CURE) courses. These courses provide research opportunities for many more students than are typically exposed to traditional independent research experiences, including women, historically underrepresented groups in science, and non-traditional students. However, the benefits for faculty who teach CURE courses have been less well documented, potentially discouraging faculty from offering such courses.

A course-based undergraduate research experience (CURE) embedded within a summer undergraduate research experience demonstrates value-added benefits.

We hosted a nine-week NIH-funded summer undergraduate research experience in Environmental Health Sciences, the New College Environmental Health Science Scholars program, in which undergraduate students who were rising sophomores, juniors, and seniors receive both professional development and mentored research opportunities. In addition to this standard model of a summer research program, we added an additional professional development and skill-building activity, a course-based undergraduate research experience (CURE) performed by the whole group. Students designed and carried out an experiment in the CURE research project looking at the relationship between soil elemental content and sampling site location.

Benchmarking the Efficacy of Salvage Systemic Therapies for Recurrent Meningioma: A RANO Group Systematic Review and Meta-analysis to Guide Clinical Trial Design.

Background: Despite advances in our understanding of the molecular underpinnings of meningioma progression and innovations in systemic and local treatments, recurrent meningiomas remain a substantial therapeutic challenge. The objective of this systematic review and meta-analysis is to provide a historical baseline, contemporary analysis, and propose a "rate of probable interest" to inform future clinical trial design and development on behalf of the RANO meningioma group.

Methods: PubMed, ClinicalTrials.

Kifunensine-sensitive ADP-ribosylation factor A1EG69R mutant revealed coordination of protein glycosylation and vesicle transport pathways.

Complex N-glycans are asparagine (N)-linked branched sugar chains attached to secretory proteins in eukaryotes. They are produced by modification of N-linked oligosaccharide structures in the endoplasmic reticulum (ER) and Golgi apparatus. Complex N-glycans formed in the Golgi apparatus are often assigned specific roles unique to the host organism, with their roles in plants remaining largely unknown.

Stanniocalcin 1 in patients with refractory colorectal cancer treated with regorafenib: A post-hoc biomarker analysis of the TEXCAN and CORRECT trials.

Biomarkers for anti-angiogenic drugs in chemo-refractory metastatic colorectal cancer (mCRC) are lacking. We investigated the relationship between stanniocalcin 1 (STC1) and outcomes in patients treated with regorafenib in the TEXCAN and CORRECT trials. Baseline plasma STC1 protein levels were measured by ELISA from patients with chemo-refractory mCRC enrolled in TEXCAN (regorafenib n=48) and CORRECT (placebo n=211; regorafenib n=435).

Real-World Incidence of Anaplastic Lymphoma Kinase alterations in Hispanics with Non-Small Cell Lung Cancer at a Large Academic Institution in Los Angeles.

Race and ethnicity affect the distribution of molecular alterations seen in patients with non-small cell lung cancer (NSCLC). While anaplastic lymphoma kinase (ALK) alterations are known to occur in 4-5% of the population, data specific to the Hispanic population remains limited. This study describes the real-world incidence of ALK alterations in Hispanic patients with NSCLC treated at a large academic institution in Los Angeles, California, USA to further elucidate the underlying factors that shape differences in mutational profiles.

Advancing Principled Pharmacoepidemiologic Research to Support Regulatory and Healthcare Decision Making: The Era of Real-World Evidence.

A compilation of factors over the past decade-including the availability of increasingly large and rich healthcare datasets, advanced technologies to extract unstructured information from health records and digital sources, advancement of principled study design and analytic methods to emulate clinical trials, and frameworks to support transparent study conduct-has ushered in a new era of real-world evidence (RWE). This review article describes the evolution of the RWE era, including pharmacoepidemiologic methods designed to support causal inferences regarding treatment effects, the role of regulators and other health authorities in establishing distributed real-world data networks enabling analytics at scale, and the many global guidance documents on principled methods of producing RWE. This article also highlights the growing opportunity for RWE to support decision making by regulators, health technology assessment groups, clinicians, patients, and other stakeholders and provides examples of influential RWE studies.

Graphene-based single-atom catalysts for electrochemical CO reduction: unraveling the roles of metals and dopants in tuning activity.

Discovering electrocatalysts that can efficiently convert carbon dioxide (CO) to valuable fuels and feedstocks using excess renewable electricity is an emergent carbon-neutral technology. A single metal atom embedded in doped graphene, , single-atom catalyst (SAC), possesses high activity and selectivity for electrochemical CO reduction (COR) to CO, yet further reduction to hydrocarbons is challenging. Here, using density functional theory calculations, we investigate stability and reactivity of a broad SAC chemical space with various metal centers (3d transition metals) and dopants (2p dopants of B, N, O; 3p dopants of P, S) as electrocatalysts for COR to methane and methanol.

A computational study on the effect of structural isomerism on the excited state lifetime and redox energetics of archetype iridium photoredox catalyst platforms [Ir(ppy)2(bpy)]+ and Ir(ppy)3.

This study investigates the impact of structural isomerism on the excited state lifetime and redox energetics of heteroleptic [Ir(ppy)2(bpy)]+ and homoleptic Ir(ppy)3 photoredox catalysts using ground-state and time-dependent density functional theory methods. While the ground- and excited-state reduction potentials differ only slightly among the isomers of these complexes, our findings reveal significant variations in the radiative and non-radiative decay rates of the reactivity-controlling triplet 3MLCT states of these closely related species. The observed differences in radiative decay rates could be traced back to variations in the transition dipole moment, vertical energy gaps, and spin-orbit coupling of the isomers.

Accurate machine learning of rate coefficients for state-to-state transitions in molecular collisions.

We present an algorithm that combines quantum scattering calculations with probabilistic machine-learning models to predict quantum dynamics rate coefficients for a large number of state-to-state transitions in molecule-molecule collisions much faster than with direct solutions of the Schrödinger equation. By utilizing the predictive power of Gaussian process regression with kernels, optimized to make accurate predictions outside of the input parameter space, the present strategy reduces the computational cost by about 75%, with an accuracy within 5%. Our method uses temperature dependences of rate coefficients for transitions from the isolated states of initial rotational angular momentum j, determined via explicit calculations, to predict the temperature dependences of rate coefficients for other values of j.

Navigating the Challenges of Cyclosporine as an Alternative to Rifampicin as an OATP1B Index Inhibitor.

Rifampicin is a widely employed index inhibitor to assess the impact of organic anion transporting polypeptide 1B (OATP1B) inhibition on investigational drugs. The observation of nitrosamines in certain drug products, including rifampicin, has impacted the conduct of clinical drug-drug interaction (DDI) studies with rifampicin drug products. Cyclosporine is a recommended alternative to assess in vivo OATP1B activity; however, challenges exist in its use due to pharmacokinetic (PK) variability and non-selective inhibition of other drug disposition mechanisms.

Environmental drivers of monomethylmercury photodegradation along the land-to-ocean aquatic continuum.

In surface waters, photodegradation is a major abiotic removal pathway of the neurotoxin monomethylmercury (MMHg), acting as a key control on the amounts of MMHg available for biological uptake. Different environmental factors can alter the rate of MMHg photodegradation. However, our understanding of how MMHg photodegradation pathways in complex matrixes along the land-to-ocean aquatic continuum respond to changes in salinity, dissolved organic carbon (DOC) concentration and dissolved organic matter (DOM) composition is incomplete.

Circadian rhythm of heart rate and activity: A cross-sectional study.

Circadian rhythms are governed by a biological clock, and are known to occur in a variety of physiological processes. We report results on the circadian rhythm of heart rate observed using a wrist-worn wearable device (Fitbit), consisting of over 17,000 individuals over the course of 30 days. We obtain an underlying heart rate circadian rhythm from the time series heart rate by modeling the circadian rhythm as a sum over the first two Fourier harmonics.

TRIB1 facilitates the proliferation and migration of ovarian cancer cells by inducing EMT progression.

Aim: Ovarian cancer (OC) is a fatal female malignant tumor that severely impacts the health of women worldwide. Due to the lack of diagnostic biomarkers, 70% of OC patients are considered in the advanced stage at the first diagnosis. Exploring novel biomarkers for OC diagnosis has become an urgent clinical need to address.

Pump-controlled retrograde trial off extracorporeal membrane oxygenation.

Venoarterial extracorporeal membrane oxygenation weaning strategies are not standardized. When dealing with patients with complex physiologies and borderline haemodynamics, it is prudent to have a fail-safe method of approaching decannulation from extracorporeal membrane oxygenation. Standardizing the extracorporeal membrane oxygenation weaning strategy with a pump-controlled retrograde trial off protocol seems a feasible alternative to traditional venoarterial extracorporeal membrane oxygenation weaning approaches.