Comparing new tools of artificial intelligence to the authentic intelligence of our global health students.

Introduction: The transformative feature of Artificial Intelligence (AI) is the massive capacity for interpreting and transforming unstructured data into a coherent and meaningful context. In general, the potential that AI will alter traditional approaches to student research and its evaluation appears to be significant. With regard to research in global health, it is important for students and research experts to assess strengths and limitations of GenAI within this space.

A generative artificial intelligence approach for antibiotic optimization.

Antimicrobial resistance (AMR) poses a critical global health threat, underscoring the urgent need for innovative antibiotic discovery strategies. While recent advances in peptide design have yielded numerous antimicrobial agents, optimizing these molecules experimentally remains challenging due to unpredictable and resource-intensive trial-and-error approaches. Here, we introduce APEX Generative Optimization (APEX ), a generative artificial intelligence (AI) framework that integrates a transformer-based variational autoencoder with Bayesian optimization to design and optimize antimicrobial peptides.

Active mutual conjoint estimation of multiple contrast sensitivity functions.

Recent advances in nonparametric contrast sensitivity function (CSF) estimation have yielded a new tradeoff between accuracy and efficiency not available to classical parametric estimators. An additional advantage of this new framework is the ability to independently tune multiple aspects of the estimator to seek further improvements. Machine learning CSF estimation with Gaussian processes allows for design optimization in the kernel, acquisition function, and underlying task representation, to name a few.

The evolution and ecology of gigantism in terror birds (Aves, Phorusrhacidae).

Terror birds (Aves, Phorusrhacidae) were large flightless apex predators in South America during the Cenozoic. Here, we estimate a new phylogeny for phorusrhacids using Bayesian inference. We demonstrate phylogenetic evidence for a monophyletic Patagornithinae and find significant support for a distinct crown group associated with the quintessential 'terror bird' characteristics.

Global latitudinal gradients and the evolution of body size in dinosaurs and mammals.

Global climate patterns fundamentally shape the distribution of species and ecosystems. For example, Bergmann's rule predicts that homeothermic animals, including birds and mammals, inhabiting cooler climates are generally larger than close relatives from warmer climates. The modern world, however, lacks the comparative data needed to evaluate such macroecological rules rigorously.

Active Mutual Conjoint Estimation of Multiple Contrast Sensitivity Functions.

Recent advances in nonparametric Contrast Sensitivity Function (CSF) estimation have yielded a new tradeoff between accuracy and efficiency not available to classical parametric estimators. An additional advantage of this new framework is the ability to independently tune multiple aspects of the estimator to seek further improvements. Machine Learning CSF (MLCSF) estimation with Gaussian processes allows for design optimization in the kernel, acquisition function and underlying task representation, to name a few.

The coevolution of rostral keratin and tooth distribution in dinosaurs.

Teeth evolved early in vertebrate evolution, and their morphology reflects important specializations in diet and ecology among species. The toothless jaws (edentulism) in extant birds likely coevolved with beak keratin, which functionally replaced teeth. However, extinct dinosaurs lost teeth multiple times independently and exhibited great variation in toothrow distribution and rhamphotheca-like keratin structures.

Contrast response function estimation with nonparametric Bayesian active learning.

Multidimensional psychometric functions can typically be estimated nonparametrically for greater accuracy or parametrically for greater efficiency. By recasting the estimation problem from regression to classification, however, powerful machine learning tools can be leveraged to provide an adjustable balance between accuracy and efficiency. Contrast sensitivity functions (CSFs) are behaviorally estimated curves that provide insight into both peripheral and central visual function.

Filling in the white space: Spatial interpolation with Gaussian processes and social media data.

Full national coverage below the state level is difficult to attain through survey-based data collection. Even the largest survey-based data collections, such as the CDC's Behavioral Risk Factor Surveillance System or the Gallup-Healthways Well-being Index (both with more than 300,000 responses p.a.

Contrast Response Function Estimation with Nonparametric Bayesian Active Learning.

Unlabelled: Multidimensional psychometric functions can typically be estimated nonparametrically for greater accuracy or parametrically for greater efficiency. By recasting the estimation problem from regression to classification, however, powerful machine learning tools can be leveraged to provide an adjustable balance between accuracy and efficiency. Contrast Sensitivity Functions (CSFs) are behaviorally estimated curves that provide insight into both peripheral and central visual function.

wenda_gpu: fast domain adaptation for genomic data.

Motivation: Domain adaptation allows for the development of predictive models even in cases with limited sample data. Weighted elastic net domain adaptation specifically leverages features of genomic data to maximize transferability but the method is too computationally demanding to apply to many genome-sized datasets.

Results: We developed wenda_gpu, which uses GPyTorch to train models on genomic data within hours on a single GPU-enabled machine.

Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China.

Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin.

Ancient DNA reveals the maternal genetic history of East Asian domestic pigs.

Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ∼7500- to 2750-year-old individuals from the Yellow River basin.

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM.

Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample.

Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity.

Xinjiang is a key region in northwestern China, connecting East and West Eurasian populations and cultures for thousands of years. To understand the genetic history of Xinjiang, we sequenced 237 complete ancient human mitochondrial genomes from the Bronze Age through Historical Era (41 archaeological sites). Overall, the Bronze Age Xinjiang populations show high diversity and regional genetic affinities with Steppe and northeastern Asian populations along with a deep ancient Siberian connection for the Tarim Basin Xiaohe individuals.

Evolutionary Sample Size and Consilience in Phylogenetic Comparative Analysis.

Phylogenetic comparative methods (PCMs) are commonly used to study evolution and adaptation. However, frequently used PCMs for discrete traits mishandle single evolutionary transitions. They erroneously detect correlated evolution in these situations.

Lower-limb joint reaction forces and moments during modified cycling in healthy controls and individuals with knee osteoarthritis.

Background: Osteoarthritis (OA) is a clinical problem affecting an estimated 27 million adults in the United States, with the only clear treatment options being pain management. Cycling is an integral component of exercise for individuals with knee osteoarthritis, while the joint reaction forces during cycling remain unknown.

Methods: Thirteen subjects with medial compartment knee osteoarthritis and eleven healthy subjects performed a cycling protocol with a neutral pedal and four pedal modifications.

Is sarcopenia and sarcopenic obesity associated with clinical and pathological outcomes in patients undergoing radical nephroureterectomy?

Purpose: To investigate the association between sarcopenia and sarcopenic obesity on clinical, perioperative, and oncologic outcomes in patients with upper-tract urothelial carcinoma (UTUC) undergoing radical nephroureterectomy (RNU).

Methods: Retrospective review of our institutional UTUC database was performed to identify all patients who underwent radical nephroureterectomy from 2002-2016. Skeletal Muscle Index (SMI) was measured at the L3 vertebral level and standardized according to patient height (cm/m).

Intraoperative Frontal Alpha-Band Power Correlates with Preoperative Neurocognitive Function in Older Adults.

Each year over 16 million older Americans undergo general anesthesia for surgery, and up to 40% develop postoperative delirium and/or cognitive dysfunction (POCD). Delirium and POCD are each associated with decreased quality of life, early retirement, increased 1-year mortality, and long-term cognitive decline. Multiple investigators have thus suggested that anesthesia and surgery place severe stress on the aging brain, and that patients with less ability to withstand this stress will be at increased risk for developing postoperative delirium and POCD.

Role of proteasome-dependent protein degradation in long-term operant memory in Aplysia.

We investigated the in vivo role of protein degradation during intermediate (ITM) and long-term memory (LTM) in Aplysia using an operant learning paradigm. The proteasome inhibitor MG-132 inhibited the induction and molecular consolidation of LTM with no effect on ITM. Remarkably, maintenance of steady-state protein levels through inhibition of protein synthesis using either anisomycin or rapamycin in conjunction with proteasome inhibition permitted the formation of robust 24 h LTM.

Differential role of calpain-dependent protein cleavage in intermediate and long-term operant memory in Aplysia.

In addition to protein synthesis, protein degradation or protein cleavage may be necessary for intermediate (ITM) and long-term memory (LTM) to remove molecular constraints, facilitate persistent kinase activity and modulate synaptic plasticity. Calpains, a family of conserved calcium dependent cysteine proteases, modulate synaptic function through protein cleavage. We used the marine mollusk Aplysia californica to investigate the in vivo role of calpains during intermediate and long-term operant memory formation using the learning that food is inedible (LFI) paradigm.

Acute effects of lateral shoe wedges on joint biomechanics of patients with medial compartment knee osteoarthritis during stationary cycling.

Cycling is commonly prescribed for individuals with knee osteoarthritis (OA) but very little biomechanical research exists on the topic. Individuals with OA may be at greater risk of OA progression or other knee injuries because of their altered knee kinematics. This study investigated the effects of lateral wedges on knee joint biomechanics and pain in patients with medial compartment knee OA during stationary cycling.

Vertebral Adaptations to Large Body Size in Theropod Dinosaurs.

Rugose projections on the anterior and posterior aspects of vertebral neural spines appear throughout Amniota and result from the mineralization of the supraspinous and interspinous ligaments via metaplasia, the process of permanent tissue-type transformation. In mammals, this metaplasia is generally pathological or stress induced, but is a normal part of development in some clades of birds. Such structures, though phylogenetically sporadic, appear throughout the fossil record of non-avian theropod dinosaurs, yet their physiological and adaptive significance has remained unexamined.

Effects of Workloads and Cadences on Frontal Plane Knee Biomechanics in Cycling.

Unlabelled: Although effects of workload and cadence on sagittal plane knee biomechanics in cycling have been widely studied, few studies have examined their impact on the frontal plane.

Purpose: The purpose of this study was to investigate the effects of different workloads and cadences on knee sagittal and frontal plane biomechanics.

Methods: Eighteen healthy participants (age, 55.