National Greenhouse Gas Emission Reduction Potential from Adopting Anaerobic Digestion on Large-Scale Dairy Farms in the United States.

Waste-to-energy systems can provide a functional demonstration of the economic and environmental benefits of circularity, innovation, and reimagining existing systems. This study offers a robust quantification of the greenhouse gas (GHG) emission reduction potential of the adoption of anaerobic digestion (AD) technology on applicable large-scale dairy farms in the contiguous United States. GHG reduction estimates were developed through a robust life cycle modeling framework paired with sensitivity and uncertainty analyses.

Utilizing logistic regression to compare risk factors in disease modeling with imbalanced data: a case study in vitamin D and cancer incidence.

Imbalanced data, a common challenge encountered in statistical analyses of clinical trial datasets and disease modeling, refers to the scenario where one class significantly outnumbers the other in a binary classification problem. This imbalance can lead to biased model performance, favoring the majority class, and affecting the understanding of the relative importance of predictive variables. Despite its prevalence, the existing literature lacks comprehensive studies that elucidate methodologies to handle imbalanced data effectively.

Global Life Cycle and Techno-Economic Assessment of Algal-Based Biofuels.

Techno-economic analyses (TEAs) and life cycle assessments (LCAs) of algal biofuels often focus on locations in suboptimal latitudes for algal cultivation, which can under-represent the sustainability potential of the technology. This study identifies the optimal global productivity potential, environmental impacts, and economic viability of algal biofuels by using validated biophysical and sustainability modeling. The biophysical model simulates growth rates of based on temperature, photoinhibition, and respiration effects at 6685 global locations.

The emergence of lines of hierarchy in collective motion of biological systems.

The emergence of large-scale structures in biological systems, and in particular the formation of lines of hierarchy, is observed at many scales, from collections of cells to groups of insects to herds of animals. Motivated by phenomena in chemotaxis and phototaxis, we present a new class of alignment models that exhibit alignment into lines. The spontaneous formation of such 'fingers' can be interpreted as the emergence of leaders and followers in a system of identically interacting agents.

Using simulations to explore the potential effect of disease and inflammation on the frequency of violative flunixin residues in cattle.

The US Food and Drug Administration (FDA) assigns a tolerance and withdrawal period when evaluating new drugs for use in food-producing species. Because withdrawal periods are determined from data generated in normal, healthy animals, questions have been raised regarding whether disease and inflammation can be a factor associated with some residue violations. We explored this question using flunixin liver concentrations as a model situation.

Regionalized Life-Cycle Water Impacts of Microalgal-Based Biofuels in the United States.

While algal biofuels have the potential to reduce the national reliance on fossil fuels, high water consumption associated with algal biomass cultivation represents a major concern potentially compromising the sustainable commercialization of this technology. This study focuses on quantifying the water footprint (WF) and water scarcity footprint (WSF) of renewable diesel derived from algal biomass and provides insights into where algal cultivation is less water-intensive than traditional ethanol and biodiesel feedstocks. Results are generated with an engineering process model developed to predict the life-cycle water consumption, considering green, blue, and gray water, of algae facilities across the United States at a high spatiotemporal resolution.

Reimagining drug manufacturing paradigm in today's pharmacy landscape.

The coronavirus disease 2019 pandemic has escalated the ongoing problem of critical medication shortages, which has serious implications for the health of our patients. Currently, active pharmaceutical ingredients (APIs) are synthesized in large-scale batch operations and shipped to drug product manufacturers, where they are produced on a large scale at centralized facilities. In the centralized drug manufacturing process, the formulation components, operations, and packaging are structured to favor long-term storage and shipment of resultant medicines to the point of care, making this process vulnerable to supply chain disruptions.

Suppression of human and simian immunodeficiency virus replication with the CCR5-specific antibody Leronlimab in two species.

The CCR5-specific antibody Leronlimab is being investigated as a novel immunotherapy that can suppress HIV replication with minimal side effects. Here we studied the virological and immunological consequences of Leronlimab in chronically CCR5-tropic HIV-1 infected humans (n = 5) on suppressive antiretroviral therapy (ART) and in ART-naïve acutely CCR5-tropic SHIV infected rhesus macaques (n = 4). All five human participants transitioned from daily combination ART to self-administered weekly subcutaneous (SC) injections of 350 mg or 700 mg Leronlimab and to date all participants have sustained virologic suppression for over seven years.

Identification and Characterization of Antigen-Specific CD8 T Cells Using Surface-Trapped TNF-α and Single-Cell Sequencing.

CD8 T cells are key mediators of antiviral and antitumor immunity. The isolation and study of Ag-specific CD8 T cells, as well as mapping of their MHC restriction, has practical importance to the study of disease and the development of therapeutics. Unfortunately, most experimental approaches are cumbersome, owing to the highly variable and donor-specific nature of MHC-bound peptide/TCR interactions.

Antibody-based CCR5 blockade protects Macaques from mucosal SHIV transmission.

In the absence of a prophylactic vaccine, the use of antiretroviral therapy (ART) as pre-exposure prophylaxis (PrEP) to prevent HIV acquisition by uninfected individuals is a promising approach to slowing the epidemic, but its efficacy is hampered by incomplete patient adherence and ART-resistant variants. Here, we report that competitive inhibition of HIV Env-CCR5 binding via the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges of CCR5-tropic SHIV. Injection of Leronlimab weekly at 10 mg/kg provides significant but partial protection, while biweekly 50 mg/kg provides complete protection from SHIV acquisition.

Influence of age, sex and respiratory viruses on the rates of emergency department visits and hospitalisations with respiratory tract infections, asthma and COPD.

Background: The importance of age, sex and respiratory virus prevalence in emergency department (ED) visits and hospitalisations for respiratory tract infections (RTIs), asthma and COPD in a whole population over time is not well established.

Methods: This study retrospectively analysed data for daily ED visits and hospitalisations from 2003 to 2013 in Ontario, Canada and the daily number of virus positive tests. Daily numbers of ED visits and hospitalisations with RTIs, asthma and COPD listed as a primary diagnosis were collected from the Canadian Institute for Health Information.

Universal features of epidemic models under social distancing guidelines.

Social distancing as a form of nonpharmaceutical intervention has been enacted in many countries as a form of mitigating the spread of COVID-19. There has been a large interest in mathematical modeling to aid in the prediction of both the total infected population and virus-related deaths, as well as to aid government agencies in decision making. As the virus continues to spread, there are both economic and sociological incentives to minimize time spent with strict distancing mandates enforced, and/or to adopt periodically relaxed distancing protocols, which allow for scheduled economic activity.

Cytomegaloviral determinants of CD8 T cell programming and RhCMV/SIV vaccine efficacy.

Simian immunodeficiency virus (SIV) insert-expressing, 68-1 rhesus cytomegalovirus (RhCMV/SIV) vectors elicit major histocompatibility complex E (MHC-E)- and MHC-II-restricted, SIV-specific CD8 T cell responses, but the basis of these unconventional responses and their contribution to demonstrated vaccine efficacy against SIV challenge in the rhesus monkeys (RMs) have not been characterized. We show that these unconventional responses resulted from a chance genetic rearrangement in 68-1 RhCMV that abrogated the function of eight distinct immunomodulatory gene products encoded in two RhCMV genomic regions ( and ), revealing three patterns of unconventional response inhibition. Differential repair of these genes with either RhCMV-derived or orthologous human CMV (HCMV)-derived sequences (; ) leads to either of two distinct CD8 T cell response types-MHC-Ia-restricted only or a mix of MHC-II- and MHC-Ia-restricted CD8 T cells.

Emergency department visits and hospitalisations for asthma, COPD and respiratory tract infections: what is the role of respiratory viruses, and return to school in September, January and March?

Background: Asthma exacerbations increase in September coinciding with children returning to school. The aim of this study was to investigate whether this occurs 1) for COPD and respiratory tract infections (RTIs); 2) after school resumes in January and March; and 3) identify which viruses may be responsible.

Methods: Emergency department (ED) visits and admissions for asthma, COPD and RTIs and the prevalence of viruses in Ontario, Canada were analysed daily between 2003 and 2013.

A novel COVID-19 epidemiological model with explicit susceptible and asymptomatic isolation compartments reveals unexpected consequences of timing social distancing.

Motivated by the current COVID-19 epidemic, this work introduces an epidemiological model in which separate compartments are used for susceptible and asymptomatic "socially distant" populations. Distancing directives are represented by rates of flow into these compartments, as well as by a reduction in contacts that lessens disease transmission. The dynamical behavior of this system is analyzed, under various different rate control strategies, and the sensitivity of the basic reproduction number to various parameters is studied.

Terumo spectra optia leukapheresis of cynomolgus macaques for hematopoietic stem cell and T cell collection.

Macaques are physiologically relevant animal models of human immunology and infectious disease that have provided key insights and advanced clinical treatment in transplantation, vaccinology, and HIV/AIDS. However, the small size of macaques is a stumbling block for studies requiring large numbers of cells, such as hematopoietic stem cells (HSCs) for transplantation, antigen-specific lymphocytes for in-depth immunological analysis, and latently-infected CD4+ T-cells for HIV cure studies. Here, we provide a detailed protocol for collection of large numbers of HSCs and T-cells from cynomolgus macaques as small as 3 kg using the Terumo Spectra Optia apheresis system, yielding an average of 5.

Mathematical Details on a Cancer Resistance Model.

One of the most important factors limiting the success of chemotherapy in cancer treatment is the phenomenon of drug resistance. We have recently introduced a framework for quantifying the effects of induced and non-induced resistance to cancer chemotherapy (Greene et al., 2018a, 2019).

Prospective, randomized, single-blinded, multi-center phase II trial of two HER2 peptide vaccines, GP2 and AE37, in breast cancer patients to prevent recurrence.

Purpose: AE37 and GP2 are HER2 derived peptide vaccines. AE37 primarily elicits a CD4+ response while GP2 elicits a CD8+ response against the HER2 antigen. These peptides were tested in a large randomized trial to assess their ability to prevent recurrence in HER2 expressing breast cancer patients.

Prevalence and contribution of respiratory viruses in the community to rates of emergency department visits and hospitalizations with respiratory tract infections, chronic obstructive pulmonary disease and asthma.

Background: The individual and combined contribution of viral prevalence in the community to Emergency Department (ED) visits and hospitalizations with respiratory tract infections (RTIs), chronic obstructive pulmonary disease (COPD) and asthma is unclear.

Methods: A retrospective analysis on daily viral positive tests and daily ED visits and hospitalizations between 01/01/2003 to 31/12/2013 in Ontario, Canada. Viral data was collected from the Centre for Immunization and Respiratory Infectious Diseases (CIRID).

A neonatal nonhuman primate model of gestational Zika virus infection with evidence of microencephaly, seizures and cardiomyopathy.

Zika virus infection during pregnancy is associated with miscarriage and with a broad spectrum of fetal and neonatal developmental abnormalities collectively known as congenital Zika syndrome (CZS). Symptomology of CZS includes malformations of the brain and skull, neurodevelopmental delay, seizures, joint contractures, hearing loss and visual impairment. Previous studies of Zika virus in pregnant rhesus macaques (Macaca mulatta) have described injury to the developing fetus and pregnancy loss, but neonatal outcomes following fetal Zika virus exposure have yet to be characterized in nonhuman primates.

Final analysis of a phase I/IIa trial of the folate-binding protein-derived E39 peptide vaccine to prevent recurrence in ovarian and endometrial cancer patients.

Background: E39, an HLA-A2-restricted, immunogenic peptide derived from the folate-binding protein (FBP), is overexpressed in multiple malignancies. We conducted a phase I/IIa trial of the E39 + GM-CSF vaccine with booster inoculations of either E39 or E39' (an attenuated version of E39) to prevent recurrences in disease-free endometrial and ovarian cancer patients(pts). Here, we present the final 24-month landmark analysis.

Mathematical Approach to Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.

Purpose: Drug resistance is a major impediment to the success of cancer treatment. Resistance is typically thought to arise from random genetic mutations, after which mutated cells expand via Darwinian selection. However, recent experimental evidence suggests that progression to drug resistance need not occur randomly, but instead may be induced by the treatment itself via either genetic changes or epigenetic alterations.