Publications by authors named "MacKenzie Johnson"

Article Synopsis
  • Somatic hypermutation (SHM) is crucial for antibody diversity and requires probabilistic models for analyzing mutations and understanding affinity maturation.
  • The authors create more efficient "thrifty" models using convolutions on 3-mer embeddings, resulting in fewer parameters yet a wider contextual understanding of SHM compared to traditional 5-mer models.
  • They discover that a per-site effect isn't necessary to explain SHM patterns, and note discrepancies between two current methods for fitting SHM models, which do not improve performance when combined.
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Sex-differential selection (SDS), which occurs when the fitness effects of alleles differ between males and females, can have profound impacts on the maintenance of genetic variation, disease risk, and other key aspects of natural populations. Because the sexes mix their autosomal genomes each generation, quantifying SDS is not possible using conventional population genetic approaches. Here, we introduce a method that exploits subtle sex differences in haplotype frequencies resulting from SDS acting in the current generation.

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Intra-articular corticosteroids are a popular treatment choice for joint-associated pain and inflammation in horses despite recent work on the metabolic effects of these drugs. The goal of this project was to compare metabolic effects between intra-articular (IA) triamcinolone acetonide (TA) and an autologous protein solution (APS). Five mixed-breed geldings (4-9 years) were utilized for this project.

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An 18-year-old female presented to the emergency department after a motor vehicle collision. Initial imaging revealed a liver laceration. Subsequent labs showed significantly elevated prothrombin time, international normalized ratio, and activated partial thromboplastin time.

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The use of dexamethasone to control equine asthma is a common and effective treatment. Although short-term systemic dexamethasone treatment has not been shown to induce systemic immunosuppression in the horse, the goal of this study was to determine whether inhaled ciclesonide, an FDA-approved drug for the treatment of equine asthma, exerts any systemic immunosuppressive effects when compared to dexamethasone-treated and untreated horses. Eighteen light, mixed breed horses, ranging in age from 3 to 8 years of age, were used for this study and randomly assigned to one of three treatment groups: (1) nontreated controls, (2) ciclesonide treatment, or (3) dexamethasone treatment.

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The most highly expressed genes in microbial genomes tend to use a limited set of synonymous codons, often referred to as "preferred codons." The existence of preferred codons is commonly attributed to selection pressures on various aspects of protein translation including accuracy and/or speed. However, gene expression is condition-dependent and even within single-celled organisms transcript and protein abundances can vary depending on a variety of environmental and other factors.

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Background: To evaluate the efficacy of crofelemer, a first in class anti-secretory anti-diarrheal agent, to manage neratinib-induced diarrhea in patients with early-stage breast cancer taking adjuvant neratinib.

Patients And Methods: This single center, open label trial enrolled patients with Stage 2 to 3 HER2+ breast cancer taking adjuvant neratinib. One cohort took prophylactic crofelemer 125 mg bid and loperamide in the first 2 cycles, and as needed in subsequent cycles.

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Accumulating high-speed exercise has been identified as a significant risk factor for catastrophic injuries in racing Thoroughbreds. Injuries, regardless of severity, are a main cause of withdrawal from the racing industry, raising animal welfare concerns and resulting in significant economic losses. While most of the current literature focuses on injuries incurred during racing rather than training, the present study aims to help fill this gap.

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Article Synopsis
  • * Researchers analyzed transcriptomic and proteomic data from *E. coli* and *S. cerevisiae*, finding that gene expression varies significantly based on growth rates, particularly showing that rapid growth enhances codon usage biases.
  • * The findings suggest that understanding gene expression under specific conditions, such as rapid growth, is essential for comprehending the long-term evolution of microbial gene sequences and their translational constraints.
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Background: Intra-articular (IA) corticosteroids are regularly used in equine athletes for the control of joint inflammation.

Objectives: The goal of this study was to use an acute synovitis inflammation model to determine the residual effects of IA betamethasone and triamcinolone acetonide on various inflammatory parameters and lameness.

Study Design: Crossover randomised trial.

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Loss of skeletal muscle mass likely compromises performance and welfare in horses and thus routine monitoring would be valuable. Currently available methods to assess muscle mass require expert knowledge and are often expensive. To provide a simple method, a muscle atrophy scoring system (MASS) was created and tested by three evaluators (raters) in 38 horses of varying age, breed, and health status.

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Protein-protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions can lead to biological changes in an organism. Recent network-based approaches have shown that a phenotype's PPI network's resilience to environmental perturbations is related to its placement in the tree of life; though we still do not know how or why certain intra-cellular factors can bring about this resilience. Here, we explore the influence of gene expression and network properties on PPI networks' resilience.

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In many applications of evolutionary inference, a model of protein evolution needs to be fitted to the amino acid variation at individual sites in a multiple sequence alignment. Most existing models fall into one of two extremes: Either they provide a coarse-grained description that lacks biophysical realism (e.g.

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AMP-activated protein kinase (AMPK) is a member of Ser/Thr kinases that has been shown to regulate energy balance. Although recent studies have demonstrated the function of AMPK in adipose tissue using different fat-specific AMPK knockout mouse models, the results were somewhat inconsistent. For this study, we tested the hypothesis that AMPK in adipose tissue regulates whole body glucose metabolism.

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The complexity of immune responses limits the usefulness of univariate methods in answering complex immunology questions. To demonstrate the utility of a multivariate approach, we employ such approach to compare T cells of African green monkeys (AGMs) and rhesus macaques (RMs). Among the most prominent distinguishing features we found were lower CD3 and higher CD28 surface expression in AGMs compared to RMs.

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Gene duplication is seen as a major source of structural and functional divergence in genome evolution. Under the conventional models of sub or neofunctionalization, functional changes arise in one of the duplicates after duplication. However, we suggest here that the presence of a duplicated gene can result in functional changes to its interacting partners.

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We report on the observation of an unexpected mechanism that controls conductivity at the 100-nm scale on track-etched polycarbonate membranes. Transport measurements of positively charged methyl viologen performed by absorption spectroscopy under various pH conditions demonstrate that for 100-nm-diameter pores at pH 2 conductivity is blocked, while at pH 5 the ions move through the membrane according to diffusion laws. An oppositely charged molecular ion, naphthalene disulfonate, in the same membrane, shows the opposite trend: diffusion of the negative ion at pH 2 and very low conductivity at pH 5.

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