Operational response simulation tool for epidemics within refugee and IDP settlements: A scenario-based case study of the Cox's Bazar settlement.

The spread of infectious diseases such as COVID-19 presents many challenges to healthcare systems and infrastructures across the world, exacerbating inequalities and leaving the world's most vulnerable populations most affected. Given their density and available infrastructure, refugee and internally displaced person (IDP) settlements can be particularly susceptible to disease spread. In this paper we present an agent-based modeling approach to simulating the spread of disease in refugee and IDP settlements under various non-pharmaceutical intervention strategies. The model, based on the June open-source framework, is informed by data on geography, demographics, comorbidities, physical infrastructure and other parameters obtained from real-world observations and previous literature. The development and testing of this approach focuses on the Cox's Bazar refugee settlement in Bangladesh, although our model is designed to be generalizable to other informal settings. Our findings suggest the encouraging self-isolation at home of mild to severe symptomatic patients, as opposed to the isolation of all positive cases in purpose-built isolation and treatment centers, does not increase the risk of secondary infection meaning the centers can be used to provide hospital support to the most intense cases of COVID-19. Secondly we find that mask wearing in all indoor communal areas can be effective at dampening viral spread, even with low mask efficacy and compliance rates. Finally, we model the effects of reopening learning centers in the settlement under various mitigation strategies. For example, a combination of mask wearing in the classroom, halving attendance regularity to enable physical distancing, and better ventilation can almost completely mitigate the increased risk of infection which keeping the learning centers open may cause. These modeling efforts are being incorporated into decision making processes to inform future planning, and further exercises should be carried out in similar geographies to help protect those most vulnerable.

Teaching Instructional Technological Change to Medical School Faculty: A COVID-19 Case Study.

Collaboration between several College of Medicine departments, including the library, resulted in a creation of a new service for faculty during the COVID-19 pandemic crisis. By combining efforts, support for teaching online became a united effort and much less daunting for faculty, who could consult one group for online teaching support, rather than three or four different entities. The resulting endeavor led to a website FAQ and consulting email address that is accessible to all faculty to provide focused and timely technology and education assistance to faculty.

Comparative toxicity and efficacy of engineered anthrax lethal toxin variants with broad anti-tumor activities.

We have previously designed and characterized versions of anthrax lethal toxin that are selectively cytotoxic in the tumor microenvironment and which display broad and potent anti-tumor activities in vivo. Here, we have performed the first direct comparison of the safety and efficacy of three engineered anthrax lethal toxin variants requiring activation by either matrix-metalloproteinases (MMPs), urokinase plasminogen activator (uPA) or co-localized MMP/uPA activities. C57BL/6J mice were challenged with six doses of engineered toxins via intraperitoneal (I.P.) or intravenous (I.V.) dose routes to determine the maximum tolerated dose for six administrations (MTD6) and dose-limiting toxicities. Efficacy was evaluated using the B16-BL6 syngraft model of melanoma; mice bearing established tumors were treated with six I.P. doses of toxin and tumor measurements and immunohistochemistry, paired with terminal blood work, were used to elaborate upon the anti-tumor mechanism and relative efficacy of each variant. We found that MMP-, uPA- and dual MMP/uPA-activated anthrax lethal toxins exhibited the same dose-limiting toxicity; dose-dependent GI toxicity. In terms of efficacy, all three toxins significantly reduced primary B16-BL6 tumor burden, ranging from 32% to 87% reduction, and they also delayed disease progression as evidenced by dose-dependent normalization of blood work values. While target organ toxicity and effective doses were similar amongst the variants, the dual MMP/uPA-activated anthrax lethal toxin exhibited the highest I.P. MTD6 and was 1.5-3-fold better tolerated than the single MMP- and uPA-activated toxins. Overall, we demonstrate that this dual MMP/uPA-activated anthrax lethal toxin can be administered safely and is highly effective in a preclinical model of melanoma. This modified bacterial cytotoxin is thus a promising candidate for further clinical development and evaluation for use in treating human cancers.

Interactive and Visual Prompt Engineering for Ad-hoc Task Adaptation with Large Language Models.

State-of-the-art neural language models can now be used to solve ad-hoc language tasks through zero-shot prompting without the need for supervised training. This approach has gained popularity in recent years, and researchers have demonstrated prompts that achieve strong accuracy on specific NLP tasks. However, finding a prompt for new tasks requires experimentation. Different prompt templates with different wording choices lead to significant accuracy differences. PromptIDE allows users to experiment with prompt variations, visualize prompt performance, and iteratively optimize prompts. We developed a workflow that allows users to first focus on model feedback using small data before moving on to a large data regime that allows empirical grounding of promising prompts using quantitative measures of the task. The tool then allows easy deployment of the newly created ad-hoc models. We demonstrate the utility of PromptIDE (demo: http://prompt.vizhub.ai) and our workflow using several real-world use cases.

Simple, Fast, and Efficient Method for Derivation of Dermal Fibroblasts From Skin Biopsies.

Primary fibroblasts are a precious resource in the field of translational regenerative medicine. Dermal fibroblasts derived from human subject biopsies are being used as donor tissues for the derivation of patient-specific iPSC lines, which in turn are used for disease modeling, drug screening, tissue engineering, and cell transplantation. We developed a fast and simple protocol to grow dermal fibroblasts from skin biopsies. Using this protocol, we simply and firmly fix the biopsy piece on the surface of a tissue culture-treated plate and allow the fibroblasts to grow. This novel method eliminates any need for enzymatic digestion or mechanical dissociation of the biopsy piece. By using this newly developed protocol, we have successfully established around 100 fibroblast lines characterized by the expression of specific markers [Serpin H1 (Hsp-47), F-actin, and Vimentin]. Finally, we have used many of these fibroblast lines as donor tissues to successfully derive iPSC lines. We have developed a method that is simple, fast, convenient, efficient, and gentle on the cells to derive dermal fibroblasts from human skin biopsies. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Skin biopsy collection and fibroblast derivation Support Protocol 1: Culturing, freezing, and thawing dermal fibroblasts derived from a skin biopsy Support Protocol 2: Characterization of dermal fibroblasts by immunocytochemistry.

Insulin action in the brain: cell types, circuits, and diseases.

Since its discovery over 100 years ago, insulin has been recognized as a key hormone in control of glucose homeostasis. Deficiencies of insulin signaling are central to diabetes and many other disorders. The brain is among the targets of insulin action, and insulin resistance is a major contributor to many diseases, including brain disorders. Here, we summarize key roles of insulin action in the brain and how this involves different brain cell types. Disordered brain insulin signaling can also contribute to neuropsychiatric diseases, affecting brain circuits involved in mood and cognition. Understanding of insulin signaling in different brain cell types/circuits and how these are altered in disease may lead to the development of new therapeutic approaches to these challenging disorders.

Extraction of organic chemistry grammar from unsupervised learning of chemical reactions.

Humans use different domain languages to represent, explore, and communicate scientific concepts. During the last few hundred years, chemists compiled the language of chemical synthesis inferring a series of "reaction rules" from knowing how atoms rearrange during a chemical transformation, a process called atom-mapping. Atom-mapping is a laborious experimental task and, when tackled with computational methods, requires continuous annotation of chemical reactions and the extension of logically consistent directives. Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.

Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity.

Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.

An anthrax toxin variant with an improved activity in tumor targeting.

Anthrax lethal toxin (LT) is an A-B type toxin secreted by Bacillus anthracis, consisting of the cellular binding moiety, protective antigen (PA), and the catalytic moiety, lethal factor (LF). To target cells, PA binds to cell-surface receptors and is then proteolytically processed forming a LF-binding competent PA oligomer where each LF binding site is comprised of three subsites on two adjacent PA monomers. We previously generated PA-U2-R200A, a urokinase-activated PA variant with LF-binding subsite II residue Arg200 mutated to Ala, and PA-L1-I210A, a matrix metalloproteinase-activated PA variant with subsite III residue Ile210 mutated to Ala. PA-U2-R200A and PA-L1-I210A displayed reduced cytotoxicity when used singly. However, when combined, they formed LF-binding competent heterogeneous oligomers by intermolecular complementation, and achieved high specificity in tumor targeting. Nevertheless, each of these proteins, in particular PA-L1-I210A, retained residual LF-binding ability. In this work, we screened a library containing all possible amino acid substitutions for LF-binding site to find variants with activity strictly dependent upon intermolecular complementation. PA-I207R was identified as an excellent replacement for the original clockwise-side variant, PA-I210A. Consequently, the new combination of PA-L1-I207R and PA-U2-R200A showed potent anti-tumor activity and low toxicity, exceeding the performance of the original combination, and warranting further investigation.

Reductive methylation and mutation of an anthrax toxin fusion protein modulates its stability and cytotoxicity.

We characterized an anti-cancer fusion protein consisting of anthrax lethal factor (LF) and the catalytic domain of Pseudomonas exotoxin A by (i) mutating the N-terminal amino acids and by (ii) reductive methylation to dimethylate all lysines. Dimethylation of lysines was achieved quantitatively and specifically without affecting binding of the fusion protein to PA or decreasing the enzymatic activity of the catalytic moiety. Ubiquitination in vitro was drastically decreased for both the N-terminally mutated and dimethylated variants, and both appeared to be slightly more stable in the cytosol of treated cells. The dimethylated variant showed greatly reduced neutralization by antibodies to LF. The two described modifications offer unique advantages such as increased cytotoxic activity and diminished antibody recognition, and thus may be applicable to other therapeutic proteins that act in the cytosol of cells.

Increased expression of glutamate transporter GLT-1 in peritumoral tissue associated with prolonged survival and decreases in tumor growth in a rat model of experimental malignant glioma.

OBJECT: Gliomas are known to release excessive amounts of glutamate, inducing glutamate excitotoxic cell death in the peritumoral region and allowing the tumor to grow and to expand. Glutamate transporter upregulation has been shown to be neuroprotective by removing extracellular glutamate in a number of preclinical animal models of neurodegenerative diseases, including amyotrophic lateral sclerosis and Parkinson disease as well as psychiatric disorders such as depression. The authors therefore hypothesized that the protective mechanism of glutamate transporter upregulation would be useful for the treatment of gliomas as well. METHODS: In this study 9L gliosarcoma cells were treated with a glutamate transporter upregulating agent, thiamphenicol, an antibiotic approved in Europe, which has been shown previously to increase glutamate transporter expression and has recently been validated in a human Phase I biomarker trial for glutamate transporter upregulation. Cells were monitored in vitro for glutamate transporter levels and cell proliferation. In vivo, rats were injected intracranially with 9L cells and were treated with increasing doses of thiamphenicol. Animals were monitored for survival. In addition, postmortem brain tissue was analyzed for tumor size, glutamate transporter levels, and neuron count. RESULTS: Thiamphenicol showed little effects on proliferation of 9L gliosarcoma cells in vitro and did not change glutamate transporter levels in these cells. However, when delivered locally in an experimental glioma model in rats, thiamphenicol dose dependently (10-5000 µM) significantly increased survival up to 7 days and concomitantly decreased tumor size from 46.2 mm(2) to 10.2 mm(2) when compared with lesions in nontreated controls. Furthermore, immunohistochemical and biochemical analysis of peritumoral tissue confirmed an 84% increase in levels of glutamate transporter protein and a 72% increase in the number of neuronal cells in the tissue adjacent to the tumor. CONCLUSIONS: These results show that increasing glutamate transporter expression in peritumoral tissue is neuroprotective. It suggests that glutamate transporter upregulation for the treatment of gliomas should be further investigated and potentially be part of a combination therapy with standard chemotherapeutic agents.

RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention.

A hexanucleotide GGGGCC repeat expansion in the noncoding region of the C9ORF72 gene is the most common genetic abnormality in familial and sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The function of the C9ORF72 protein is unknown, as is the mechanism by which the repeat expansion could cause disease. Induced pluripotent stem cell (iPSC)-differentiated neurons from C9ORF72 ALS patients revealed disease-specific (1) intranuclear GGGGCCexp RNA foci, (2) dysregulated gene expression, (3) sequestration of GGGGCCexp RNA binding protein ADARB2, and (4) susceptibility to excitotoxicity. These pathological and pathogenic characteristics were confirmed in ALS brain and were mitigated with antisense oligonucleotide (ASO) therapeutics to the C9ORF72 transcript or repeat expansion despite the presence of repeat-associated non-ATG translation (RAN) products. These data indicate a toxic RNA gain-of-function mechanism as a cause of C9ORF72 ALS and provide candidate antisense therapeutics and candidate human pharmacodynamic markers for therapy.

The receptors that mediate the direct lethality of anthrax toxin.

Tumor endothelium marker-8 (TEM8) and capillary morphogenesis protein-2 (CMG2) are the two well-characterized anthrax toxin receptors, each containing a von Willebrand factor A (vWA) domain responsible for anthrax protective antigen (PA) binding. Recently, a cell-based analysis was used to implicate another vWA domain-containing protein, integrin ß1 as a third anthrax toxin receptor. To explore whether proteins other than TEM8 and CMG2 function as anthrax toxin receptors in vivo, we challenged mice lacking TEM8 and/or CMG2. Specifically, we used as an effector protein the fusion protein FP59, a fusion between the PA-binding domain of anthrax lethal factor (LF) and the catalytic domain of Pseudomonas aeruginosa exotoxin A. FP59 is at least 50-fold more potent than LF in the presence of PA, with 2 µg PA + 2 µg FP59 being sufficient to kill a mouse. While TEM8(-/-) and wild type control mice succumbed to a 5 µg PA + 5 µg FP59 challenge, CMG2(-/-) mice were completely resistant to this dose, confirming that CMG2 is the major anthrax toxin receptor in vivo. To detect whether any toxic effects are mediated by TEM8 or other putative receptors such as integrin ß1, CMG2(-/-)/TEM8(-/-) mice were challenged with as many as five doses of 50 µg PA + 50 µg FP59. Strikingly, the CMG2(-/-)/TEM8(-/-) mice were completely resistant to the 5-dose challenge. These results strongly suggest that TEM8 is the only minor anthrax toxin receptor mediating direct lethality in vivo and that other proteins implicated as receptors do not play this role.