The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.

Transcriptional Profiling of Filovirus-Infected Nonhuman Primate Samples.

Transcriptional analysis is a powerful tool to help decipher the host response to filovirus infections. In this chapter, we describe how transcriptional analysis can be performed on samples obtained from nonhuman primates infected with filoviruses, specifically Marburg virus, for assessment of the RNA changes over the course of the infection and disease.

The IBEX Knowledge-Base: Achieving more together with open science.

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to empower innovation.

Rebalancing Viral and Immune Damage versus Tissue Repair Prevents Death from Lethal Influenza Infection.

Maintaining tissue function while eliminating infected cells is fundamental to host defense. Innate inflammatory damage contributes to lethal influenza and COVID-19, yet other than steroids, immunomodulatory drugs have modest effects. Among more than 50 immunomodulatory regimes tested in mouse lethal influenza infection, only the previously reported early depletion of neutrophils showed efficacy, suggesting that the infected host passes an early tipping point in which limiting innate immune damage alone cannot rescue physiological function.

Causality Bounds on Dissipative General-Relativistic Magnetohydrodynamics.

We derive necessary and sufficient conditions under which a large class of relativistic generalizations of Braginskii's magnetohydrodynamics with shear, bulk, and heat diffusion effects is causal and strongly hyperbolic in the fully nonlinear regime in curved spacetime. We find that causality severely constrains the size of nonideal effects and the onset of kinetic instabilities. Our results are crucial for assessing the regime of validity of fluid dynamical simulations of plasmas near supermassive black holes.

Preservation of scRNA-Seq Libraries Using Existing Inactivation Protocols.

Single-cell RNA sequencing has soared in popularity in recent years. The ability to deeply profile the states of individual cells during the course of disease or infection has helped to expand our knowledge of coordinated responses. However, significant challenges arise when performing this analysis in high containment settings such as biosafety level 3 (BSL-3), BSL-3+ and BSL-4.

Virology-the path forward.

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases.

Spatial Patterning Analysis of Cellular Ensembles (SPACE) discovers complex spatial organization at the cell and tissue levels.

Spatial patterns of cells and other biological elements drive both physiologic and pathologic processes within tissues. While many imaging and transcriptomic methods document tissue organization, discerning these patterns is challenging, especially when they involve multiple elements in complex arrangements. To address this challenge, we present Spatial Patterning Analysis of Cellular Ensembles (SPACE), an R package for analysis of high-plex spatial data.

Understanding virus-host interactions in tissues.

Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to understanding how an infected cell behaves in a tissue, organ or whole organism. Infections occur in complex tissue environments, which contain a host of factors that can alter the course of the infection, including immune cells, non-immune cells and extracellular-matrix components. These factors affect how the host responds to the virus and form the basis of the protective response.

Initial assessment of multi-compound antineoplastic drug surface contamination in Argentinean healthcare centers: Insights into occupational exposures in South America.

Introduction: Antineoplastic drug contamination can result in severe health effects for healthcare workers exposed to them. Despite the worldwide growing concern regarding these drugs and sustained monitoring efforts in developed countries, there is almost no data about surface contamination levels in Argentina, in particular, and South America, in general.

Methods: Antineoplastic drug contamination was measured in three Argentinean public hospitals (pharmacy and daycare center areas) by surface wiping and liquid chromatography coupled with tandem mass spectrometry.

High-resolution multivariate analysis of the hydrochemical signature of water corridors in the upper Río de la Plata estuary, Argentina.

Major world river-estuaries integrate the hydrochemical characteristics of the basin with specific signatures which are maintained until complete mixing or discharge to the sea. The chemical signature of distinct water masses and the anthropogenic impact in the Upper Río de la Plata estuary (RLP) were evaluated by high-resolution continuous monitoring (i.e.

Evaluation of the Nutritional Status of Gaucher Disease Type I Patients under Enzyme Replacement Treatment.

(1) Background: Gaucher disease (GD) is a rare lysosomal storage disease. The few studies analyzing Resting Energy Expenditure (REE) in GD involved mainly untreated patients and supported a hypermetabolic condition possibly due to the associated inflammatory state. Definitive conclusions could not be drawn also because of the heterogeneity and the small size of the samples investigated.

Transient Relativistic Fluid Dynamics in a General Hydrodynamic Frame.

We propose a new theory of second-order viscous relativistic hydrodynamics which does not impose any frame conditions on the choice of the hydrodynamic variables. It differs from Mueller-Israel-Stewart theory by including additional transient degrees of freedom, and its first-order truncation reduces to Bemfica-Disconzi-Noronha-Kovtun theory. Conditions for causality and stability are explicitly given in the conformal regime.

Prevalence of Sarcopenia in Women with Breast Cancer.

Sarcopenia is a common finding in patients with cancer and potentially influences the patient’s outcome. The aim of this study was to evaluate the prevalence of sarcopenia, according to the European Working Group on Sarcopenia in Older People, in a sample of women with breast cancer (BC) and a BMI lower than 30 kg/m2. This cross-sectional study was conducted in patients with BC, stage 0-III, and receiving therapy for BC; the women were recruited at the Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.

Nutritional Screening and Anthropometry in Patients Admitted From the Emergency Department.

Background: Due to the high prevalence of malnutrition among hospitalized patients, screening and assessment of nutritional status should be routinely performed upon hospital admission. The main objective of this observational study was to evaluate the prevalence of and the risk for malnutrition, as identified by using three nutritional screening tests, and to observe whether some anthropometric and functional parameters used for nutritional evaluation were related to these test scores.

Methods: This single-center observational study included 207 patients admitted from the emergency department for hospitalization in either the internal medicine or surgery units of our institution from September 2017 to December 2018.

Age-related differences in immune dynamics during SARS-CoV-2 infection in rhesus macaques.

Advanced age is a key predictor of severe COVID-19. To gain insight into this relationship, we used the rhesus macaque model of SARS-CoV-2 infection. Eight older and eight younger macaques were inoculated with SARS-CoV-2.

IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues.

High-content imaging is needed to catalog the variety of cellular phenotypes and multicellular ecosystems present in metazoan tissues. We recently developed iterative bleaching extends multiplexity (IBEX), an iterative immunolabeling and chemical bleaching method that enables multiplexed imaging (>65 parameters) in diverse tissues, including human organs relevant for international consortia efforts. IBEX is compatible with >250 commercially available antibodies and 16 unique fluorophores, and can be easily adopted to different imaging platforms using slides and nonproprietary imaging chambers.

Metabolic Disrupting Effects of Polychlorinated Biphenyls Revealed by Long-Term Temporal Variations of Lipids in Detritivorous Fish from the Rio de la Plata Basin.

The long-term covariation (2002-2017) of lipids, polychlorinated biphenyls (PCBs), and sewage tracers was studied in the detritivorous fish () and settling detritus from the Rio de la Plata. Fatty fish from polluted Buenos Aires area (BA) exhibited a significant decrease of muscle lipids (71 ± 12 to 29 ± 8.6% dry weight; < 0.

Pulmonary infection induces persistent, pathogen-specific lipidomic changes influencing trained immunity.

Resolution of infection results in development of trained innate immunity which is typically beneficial for defense against unrelated secondary infection. Epigenetic changes including modification of histones via binding of various polar metabolites underlie the establishment of trained innate immunity. Therefore, host metabolism and this response are intimately linked.

Model of Care for Microelimination of Hepatitis C Virus Infection among People Who Inject Drugs.

Background: People who inject drugs (PWID) are the largest group at risk for HCV infection. Despite the direct acting antivirals (DAA) advancements, HCV elimination has been hindered by real-life difficulties in PWID.

Aims: This study aimed to assess the impact of a multidisciplinary intervention strategy where HCV screening, treatment and follow-up were performed at the same location on efficacy and safety of DAA-therapy in real-life PWID population.

Generating Spin Polarization from Vorticity through Nonlocal Collisions.

We derive the collision term in the Boltzmann equation using the equation of motion for the Wigner function of massive spin-1/2 particles. To next-to-lowest order in ℏ, it contains a nonlocal contribution, which is responsible for the conversion of orbital into spin angular momentum. In a proper choice of pseudogauge, the antisymmetric part of the energy-momentum tensor arises solely from this nonlocal contribution.