Characterization of Patients with COVID-19 Admitted to a Community Hospital of East Harlem in New York City.

Background New York City was the epicenter for the coronavirus disease 2019 (COVID-19) in the United States. Accordingly, the aim of this study was to characterize the population of patients admitted with this condition to a community hospital in East Harlem located in the northeast part of the city. Methods A retrospective review of medical records of patients at least 18 years of age, admitted to the hospital with COVID-19 disease from March 14 to April 30 of 2020. Results Three hundred and seventy-one patients were identified. The majority was comprised of men. Obesity, hypertension, and hyperlipidemia were the most prevalent comorbidities. Most patients were treated with a combination of hydroxychloroquine, azithromycin, zinc, and vitamin C. Twenty-three percent of the patients died from the disease during the study period. Conclusion Morbidity and mortality were substantial in patients with COVID-19 admitted to a community hospital in East Harlem.

MEK1 regulates pulmonary macrophage inflammatory responses and resolution of acute lung injury.

The MEK1/2-ERK1/2 pathway has been implicated in regulating the inflammatory response to lung injury and infection, and pharmacologic MEK1/2 inhibitor compounds are reported to reduce detrimental inflammation in multiple animal models of disease, in part through modulation of leukocyte responses. However, the specific contribution of myeloid MEK1 in regulating acute lung injury (ALI) and its resolution remain unknown. Here, the role of myeloid Mek1 was investigated in a murine model of LPS-induced ALI (LPS-ALI) by genetic deletion using the Cre-floxed system (LysMCre × Mekfl), and human alveolar macrophages from healthy volunteers and patients with acute respiratory distress syndrome (ARDS) were obtained to assess activation of the MEK1/2-ERK1/2 pathway. Myeloid Mek1 deletion results in a failure to resolve LPS-ALI, and alveolar macrophages lacking MEK1 had increased activation of MEK2 and the downstream target ERK1/2 on day 4 of LPS-ALI. The clinical significance of these findings is supported by increased activation of the MEK1/2-ERK1/2 pathway in alveolar macrophages from patients with ARDS compared with alveolar macrophages from healthy volunteers. This study reveals a critical role for myeloid MEK1 in promoting resolution of LPS-ALI and controlling the duration of macrophage proinflammatory responses.

Transcriptional and functional diversity of human macrophage repolarization.

BACKGROUND: Macrophage plasticity allows cells to adopt different phenotypes, a property with important implications in disorders such as cystic fibrosis (CF) and asthma. OBJECTIVE: We sought to examine the transcriptional and functional significance of macrophage repolarization from an M1 to an M2 phenotype and assess the role of a common human genetic disorder (CF) and a prototypical allergic disease (asthma) in this transformation. METHODS: Monocyte-derived macrophages were collected from healthy subjects and patients with CF and polarized to an M2 state by using IL-4, IL-10, glucocorticoids, apoptotic PMNs, or azithromycin. We performed transcriptional profiling and pathway analysis for each stimulus. We assessed the ability of M2-repolarized macrophages to respond to LPS rechallenge and clear apoptotic neutrophils and used murine models to determine conserved functional responses to IL-4 and IL-10. We investigated whether M2 signatures were associated with alveolar macrophage phenotypes in asthmatic patients. RESULTS: We found that macrophages exhibit highly diverse responses to distinct M2-polarizing stimuli. Specifically, IL-10 activated proinflammatory pathways and abrogated LPS tolerance, allowing rapid restoration of LPS responsiveness. In contrast, IL-4 enhanced LPS tolerance, dampening proinflammatory responses after repeat LPS challenge. A common theme observed across all M2 stimuli was suppression of interferon-associated pathways. We found that CF macrophages had intact reparative and transcriptional responses, suggesting that macrophage contributions to CF-related lung disease are primarily shaped by their environment. Finally, we leveraged in vitro-derived signatures to show that allergen provocation induces distinct M2 state transcriptional patterns in alveolar macrophages. CONCLUSION: Our findings highlight the diversity of macrophage polarization, attribute functional consequences to different M2 stimuli, and provide a framework to phenotype macrophages in disease states.

Matrix metalloproteinase 28 is regulated by TRIF- and type I IFN-dependent signaling in macrophages.

Matrix metalloproteinases (MMPs) are transcriptionally regulated proteases that have multiple roles in modifying the extracellular matrix (ECM) and inflammatory response. Our previous work identified Mmp28 as a key regulator of inflammation and macrophage polarization during experimental models of pulmonary infection, fibrosis, and chronic smoke exposure. However, the signaling pathways responsible for regulation of macrophage Mmp28 expression remain undefined. This study utilized murine macrophages obtained from wild type, Tlr2-/-, Tlr4-/-, MyD88-/-, Ticam1 Lps2 ( Trifmutant), and Ifnar1-/- mice to test the hypothesis that macrophage Mmp28 expression was dependent on TRIF and type I IFN. Our results support the hypothesis, demonstrating that increased macrophage Mmp28 expression was dependent on type I IFN after LPS and poly(I:C) stimulation. To gain further insight into the function of MMP28, we explored the inflammatory response of macrophages derived from wild type or Mmp28-/- mice to stimulation with poly(I:C). Our data support a role for MMP28 in regulating the macrophage inflammatory response to poly(I:C) because expression of Ccl2, Ccl4, Cxcl10, and Il6 were increased in Mmp28-/- macrophages. Together, these data support a model in which macrophages integrate TRIF- and type I IFN-dependent signaling to coordinate regulation of proteins with the capacity to modify the ECM.

Reduced feeding activity of soil detritivores under warmer and drier conditions.

Anthropogenic warming is projected to trigger positive feedbacks to climate by enhancing carbon losses from the soil1. While such losses are, in part, owing to increased decomposition of organic matter by invertebrate detritivores, it is unknown how detritivore feeding activity will change with warming2, especially under drought conditions. Here, using four year manipulation experiments in two North American boreal forests, we investigate how temperature (ambient, +1.7 °C, +3.4 °C) and rainfall (ambient, -40% summer precipitation) perturbations influence detritivore feeding activity. In contrast to general expectations1,3, warming had negligible net effects on detritivore feeding activity at ambient precipitation. However, when combined with precipitation reductions, warming decreased feeding activity by ~14%. As across all plots and dates, detritivore feeding activity was positively associated to bulk soil microbial respiration, our results suggest slower rates of decomposition of soil organic matter, and thus reduced positive feedbacks to climate under anthropogenic climate change.

Frontiers in alley cropping: Transformative solutions for temperate agriculture.

Annual row crops dominate agriculture around the world and have considerable negative environmental impacts, including significant greenhouse gas emissions. Transformative land-use solutions are necessary to mitigate climate change and restore critical ecosystem services. Alley cropping (AC)-the integration of trees with crops-is an agroforestry practice that has been studied as a transformative, multifunctional land-use solution. In the temperate zone, AC has strong potential for climate change mitigation through direct emissions reductions and increases in land-use efficiency via overyielding compared to trees and crops grown separately. In addition, AC provides climate change adaptation potential and ecological benefits by buffering alley crops to weather extremes, diversifying income to hedge financial risk, increasing biodiversity, reducing soil erosion, and improving nutrient- and water-use efficiency. The scope of temperate AC research and application has been largely limited to simple systems that combine one timber tree species with an annual grain. We propose two frontiers in temperate AC that expand this scope and could transform its climate-related benefits: (i) diversification via woody polyculture and (ii) expanded use of tree crops for food and fodder. While AC is ready now for implementation on marginal lands, we discuss key considerations that could enhance the scalability of the two proposed frontiers and catalyze widespread adoption.

A Fully Automatic Method for Comparing Cartridge Case Images.

When a gun is fired, it leaves marks on cartridge cases that are thought to be unique to the gun. In current practice, firearms examiners inspect cartridge cases for "sufficient agreement," in which case they conclude that they come from the same gun, testifying in courts as such. A 2016 President's Council of Advisors on Science and Technology report questioned the scientific validity of such analysis (President's Committee of Advisors on Science and Technology, Washington, DC, Executive Office of the President). One recommendation was to convert firearms analysis to an objective method. We propose a fully automated, open-source method for comparing breechface marks on cartridge cases using 2D optical images. We improve on existing methodology by automating the selection of marks, and removing the effects of circular symmetry. We propose an empirical computation of a "random match probability" given a known database, which can be used to quantify the weight of evidence. We demonstrate an improvement in accuracy on images from controlled test fires.

Pharmacologic inhibition of MEK1/2 reduces lung inflammation without impairing bacterial clearance in experimental Pseudomonas aeruginosa pneumonia.

This study was designed to test the therapeutic potential of a MEK1/2 inhibitor (MEKi) in an experimental model of Pseudomonas aeruginosa pneumonia. The study found that treatment with MEKi reduced alveolar neutrophilic inflammation and led to faster recovery of weight compared to carrier-treated mice, without impairing bacterial clearance. Alveolar macrophages isolated from MEKi-treated mice also had increased M2 gene and protein expression, supporting the concept that MEKi modulates in vivo macrophage inflammatory responses. In summary, this report demonstrates the potential of MEKi to promote the resolution of inflammation in vivo during a primary lung infection without impairing bacterial clearance.

Stat5 Is Required for CD103+ Dendritic Cell and Alveolar Macrophage Development and Protection from Lung Injury.

We tested the role of Stat5 in dendritic cell and alveolar macrophage (AM) homeostasis in the lung using CD11c-cre mediated deletion (Cre+5f/f). We show that Stat5 is required for CD103+ dendritic cell and AM development. We found that fetal monocyte maturation into AMs was impaired in Cre+5f/f mice, and we also confirmed impaired AM development of progenitor cells using mixed chimera experiments. In the absence of Stat5 signaling in AMs, mice developed alveolar proteinosis with altered lipid homeostasis. In addition, loss of Stat5 in CD11c+ cells was associated with exaggerated LPS-induced inflammatory responses and vascular leak. In Cre+5f/f mice, there was loss of immune-dampening effects on epithelial cells, a key source of CCL2 that serves to recruit monocytes and macrophages. These findings demonstrate the critical importance of Stat5 signaling in maintaining lung homeostasis, and underscore the importance of resident macrophages in moderating tissue damage and excess inflammation.

Matrix Metalloproteinase-28 Is a Key Contributor to Emphysema Pathogenesis.

Chronic obstructive pulmonary disease (COPD) comprises chronic bronchitis and emphysema, and is a leading cause of morbidity and mortality. Because tissue destruction is the prominent characteristic of emphysema, extracellular proteinases, particularly those with elastolytic ability, are often considered to be key drivers in this disease. Several human and mouse studies have implicated roles for matrix metalloproteinases (MMPs), particularly macrophage-derived proteinases, in COPD pathogenesis. MMP-28 is expressed by the pulmonary epithelium and macrophage, and we have found that it regulates macrophage recruitment and polarization. We hypothesized that MMP-28 has contributory roles in emphysema via alteration of macrophage numbers and activation. Because of the established association of emphysema pathogenesis to macrophage influx, we evaluated the inflammatory changes and lung histology of Mmp28-/- mice exposed to 3 and 6 months of cigarette smoke. At earlier time points, we found altered macrophage polarization in the smoke-exposed Mmp28-/- lung consistent with other published findings that MMP-28 regulates macrophage activation. At both 3 and 6 months, Mmp28-/- mice had blunted inflammatory responses more closely resembling nonsmoked mice, with a reduction in neutrophil recruitment and CXCL1 chemokine expression. By 6 months, Mmp28-/- mice were protected from emphysema. These results highlight a previously unrecognized role for MMP-28 in promoting chronic lung inflammation and tissue remodeling induced by cigarette smoke and highlight another potential target to modulate COPD.

MEK1/2 Inhibition Promotes Macrophage Reparative Properties.

Macrophages have important functional roles in regulating the timely promotion and resolution of inflammation. Although many of the intracellular signaling pathways involved in the proinflammatory responses of macrophages are well characterized, the components that regulate macrophage reparative properties are less well understood. We identified the MEK1/2 pathway as a key regulator of macrophage reparative properties. Pharmacological inhibition of the MEK1/2 pathway by a MEK1/2 inhibitor (MEKi) significantly increased expression of IL-4/IL-13 (M2)-responsive genes in murine bone marrow-derived and alveolar macrophages. Deletion of the MEK1 gene using LysMCre+/+Mek1fl/fl macrophages as an alternate approach yielded similar results. MEKi enhanced STAT6 phosphorylation, and MEKi-induced changes in M2 polarization were dependent on STAT6. In addition, MEKi treatment significantly increased murine and human macrophage efferocytosis of apoptotic cells, independent of macrophage polarization and STAT6. These phenotypes were associated with increased gene and protein expression of Mertk, Tyro3, and Abca1, three proteins that promote macrophage efferocytosis. We also studied the effects of MEKi on in vivo macrophage efferocytosis and polarization. MEKi-treated mice had increased efferocytosis of apoptotic polymorphonuclear leukocytes instilled into the peritoneum. Furthermore, administration of MEKi after LPS-induced lung injury led to improved recovery of weight, fewer neutrophils in the alveolar compartment, and greater macrophage M2 polarization. Collectively, these results show that MEK1/2 inhibition is capable of promoting the reparative properties of murine and human macrophages. These studies suggest that the MEK1/2 pathway may be a therapeutic target to promote the resolution of inflammation via modulation of macrophage functions.

Temperature response of soil respiration largely unaltered with experimental warming.

The respiratory release of carbon dioxide (CO2) from soil is a major yet poorly understood flux in the global carbon cycle. Climatic warming is hypothesized to increase rates of soil respiration, potentially fueling further increases in global temperatures. However, despite considerable scientific attention in recent decades, the overall response of soil respiration to anticipated climatic warming remains unclear. We synthesize the largest global dataset to date of soil respiration, moisture, and temperature measurements, totaling >3,800 observations representing 27 temperature manipulation studies, spanning nine biomes and over 2 decades of warming. Our analysis reveals no significant differences in the temperature sensitivity of soil respiration between control and warmed plots in all biomes, with the exception of deserts and boreal forests. Thus, our data provide limited evidence of acclimation of soil respiration to experimental warming in several major biome types, contrary to the results from multiple single-site studies. Moreover, across all nondesert biomes, respiration rates with and without experimental warming follow a Gaussian response, increasing with soil temperature up to a threshold of ∼25 °C, above which respiration rates decrease with further increases in temperature. This consistent decrease in temperature sensitivity at higher temperatures demonstrates that rising global temperatures may result in regionally variable responses in soil respiration, with colder climates being considerably more responsive to increased ambient temperatures compared with warmer regions. Our analysis adds a unique cross-biome perspective on the temperature response of soil respiration, information critical to improving our mechanistic understanding of how soil carbon dynamics change with climatic warming.

Inhibition of endoplasmic reticulum glucosidases is required for in vitro and in vivo dengue antiviral activity by the iminosugar UV-4.

The antiviral activity of UV-4 was previously demonstrated against dengue virus serotype 2 (DENV2) in multiple mouse models. Herein, step-wise minimal effective dose and therapeutic window of efficacy studies of UV-4B (UV-4 hydrochloride salt) were conducted in an antibody-dependent enhancement (ADE) mouse model of severe DENV2 infection in AG129 mice lacking types I and II interferon receptors. Significant survival benefit was demonstrated with 10-20 mg/kg of UV-4B administered thrice daily (TID) for seven days with initiation of treatment up to 48 h after infection. UV-4B also reduced infectious virus production in in vitro antiviral activity assays against all four DENV serotypes, including clinical isolates. A set of purified enzyme, in vitro, and in vivo studies demonstrated that inhibition of endoplasmic reticulum (ER) α-glucosidases and not the glycosphingolipid pathway appears to be responsible for the antiviral activity of UV-4B against DENV. Along with a comprehensive safety package, these and previously published data provided support for an Investigational New Drug (IND) filing and Phases 1 and 2 clinical trials for UV-4B with an indication of acute dengue disease.

CD8+ T Cells Can Mediate Short-Term Protection against Heterotypic Dengue Virus Reinfection in Mice.

UNLABELLED: Dengue virus (DENV) is a major public health threat worldwide. Infection with one of the four serotypes of DENV results in a transient period of protection against reinfection with all serotypes (cross-protection), followed by lifelong immunity to the infecting serotype. While a protective role for neutralizing antibody responses is well established, the contribution of T cells to reinfection is less clear, especially during heterotypic reinfection. This study investigates the role of T cells during homotypic and heterotypic DENV reinfection. Mice were sequentially infected with homotypic or heterotypic DENV serotypes, and T cell subsets were depleted before the second infection to assess the role of DENV-primed T cells during reinfection. Mice primed nonlethally with DENV were protected against reinfection with either a homotypic or heterotypic serotype 2 weeks later. Homotypic priming induced a robust neutralizing antibody response, whereas heterotypic priming elicited binding, but nonneutralizing antibodies. CD8(+) T cells were required for protection against heterotypic, but not homotypic, reinfection. These results suggest that T cells can contribute crucially to protection against heterotypic reinfection in situations where humoral responses alone may not be protective. Our findings have important implications for vaccine design, as they suggest that inducing both humoral and cellular responses during vaccination may maximize protective efficacy across all DENV serotypes. IMPORTANCE: Dengue virus is present in more than 120 countries in tropical and subtropical regions. Infection with dengue virus can be asymptomatic, but it can also progress into the potentially lethal severe dengue disease. There are four closely related dengue virus serotypes. Infection with one serotype results in a transient period of resistance against all serotypes (cross-protection), followed by lifelong resistance to the infecting serotype, but not the other ones. The duration and mechanisms of the transient cross-protection period remain elusive. This study investigates the contribution of cellular immunity to cross-protection using mouse models of DENV infection. Our results demonstrate that cellular immunity is crucial to mediate cross-protection against reinfection with a different serotype, but not for protection against reinfection with the same serotype. A better understanding of the mediators responsible for the cross-protection period is important for vaccine design, as an ideal vaccine against dengue virus should efficiently protect against all serotypes.

Voxel Level Survival Analysis of Grey Matter Volume and Incident Mild Cognitive Impairment or Alzheimer's Disease.

The purpose of this study was to identify, at the voxel level, brain regions associated with the time to develop mild cognitive impairment (MCI) or Alzheimer's disease (AD) from normal cognition. We analyzed incident MCI (n = 58) or AD (n = 151) in 292 cognitively normal participants in the Cardiovascular Health Study-Cognition Study (mean age = 79.2 ± 3.6 years). We used segmented, modulated grey matter maps from 3D (spoiled gradient echo) MRI scans obtained in 1998/99 (with clinical follow-up through 2012) that were smoothed with a 3-D 4 mm Gaussian filter. We fit approximately 1.92 million voxel-level Cox proportional hazard models to examine the grey matter volume effect on time to event, adjusting for age, sex, and diabetes. We used the significance threshold of p <  0.005 with contiguity threshold of at least 68 voxels (false detection probability <2.5×10 -8). Areas within the mesial temporal lobe (MTL), anterior temporal lobe, hippocampus, and posterior cingulate gyrus were associated with time to MCI or AD. The presence of white matter lesions (a marker of small vessel disease in the brain) was associated with the volumes of the MTL and precuneus; MRI-identified infarcts also predicted MTL volume. These findings are important because we identified critical brain regions that predict a person's increased likelihood of developing MCI or AD over a decade prior to the onset of clinical symptoms; these critical brain regions were themselves affected by the presence of vascular disease.

CD8+ T cells prevent antigen-induced antibody-dependent enhancement of dengue disease in mice.

Dengue virus (DENV) causes pathologies ranging from the febrile illness dengue fever to the potentially lethal severe dengue disease. A major risk factor for developing severe dengue disease is the presence of subprotective DENV-reactive Abs from a previous infection (or from an immune mother), which can induce Ab-dependent enhancement of infection (ADE). However, infection in the presence of subprotective anti-DENV Abs does not always result in severe disease, suggesting that other factors influence disease severity. In this study we investigated how CD8(+) T cell responses influence the outcome of Ab-mediated severe dengue disease. Mice were primed with aluminum hydroxide-adjuvanted UV-inactivated DENV prior to challenge with DENV. Priming failed to induce robust CD8(+) T cell responses, and it induced nonneutralizing Ab responses that increased disease severity upon infection. Transfer of exogenous DENV-activated CD8(+) T cells into primed mice prior to infection prevented Ab-dependent enhancement and dramatically reduced viral load. Our results suggest that in the presence of subprotective anti-DENV Abs, efficient CD8(+) T cell responses reduce the risk of Ab-mediated severe dengue disease.

Role of humoral versus cellular responses induced by a protective dengue vaccine candidate.

With 2.5 billion people at risk, dengue is a major emerging disease threat and an escalating public health problem worldwide. Dengue virus causes disease ranging from a self-limiting febrile illness (dengue fever) to the potentially fatal dengue hemorrhagic fever/dengue shock syndrome. Severe dengue disease is associated with sub-protective levels of antibody, which exacerbate disease upon re-infection. A dengue vaccine should generate protective immunity without increasing severity of disease. To date, the determinants of vaccine-mediated protection against dengue remain unclear, and additional correlates of protection are urgently needed. Here, mice were immunized with viral replicon particles expressing the dengue envelope protein ectodomain to assess the relative contribution of humoral versus cellular immunity to protection. Vaccination with viral replicon particles provided robust protection against dengue challenge. Vaccine-induced humoral responses had the potential to either protect from or exacerbate dengue disease upon challenge, whereas cellular immune responses were beneficial. This study explores the immunological basis of protection induced by a dengue vaccine and suggests that a safe and efficient vaccine against dengue should trigger both arms of the immune system.

Bootstrapping GEE models for fMRI regional connectivity.

An Alzheimer's fMRI study has motivated us to evaluate inter-regional correlations during rest between groups. We apply generalized estimating equation (GEE) models to test for differences in regional correlations across groups. Both the GEE marginal model and GEE transition model are evaluated and compared to the standard pooling Fisher-z approach using simulation studies. Standard errors of all methods are estimated both theoretically (model-based) and empirically (bootstrap). Of all the methods, we find that the transition models have the best statistical properties. Overall, the model-based standard errors and bootstrap standard errors perform about the same. We also demonstrate the methods with a functional connectivity study in a healthy cognitively normal population of ApoE4+ participants and ApoE4- participants who are recruited from the Adult Children's Study conducted at the Washington University Knight Alzheimer's Disease Research Center.

Potential utility of resting-state magnetoencephalography as a biomarker of CNS abnormality in HIV disease.

There is a lack of a neuroimaging biomarker for HIV-Associated Neurocognitive Disorder. We report magnetoencephalography (MEG) data from patients with HIV disease and risk-group appropriate controls that were collected to determine the MEG frequency profile during the resting state, and the stability of the profile over 24 weeks. 17 individuals (10 HIV+, 7 HIV-) completed detailed neurobehavioral evaluations and 10min of resting-state MEG acquisition with a 306-channel whole-head system. The entire evaluation and MEG measurement were repeated 24 weeks later. Relative MEG power in the delta (0-4Hz), theta (4-7Hz), alpha (8-12Hz), beta (12-30Hz) and low gamma (30-50Hz) bands was computed for 8 predefined sensor groups. The median stability of resting-state relative power over 24 weeks of follow-up was .80 with eyes closed, and .72 with eyes open. The relative gamma power in the right occipital (t(15)=1.99, p<.06, r=-.46) and right frontal (t(15)=2.15, p<.05, r=-.48) regions was associated with serostatus. The effect of age on delta power was greater in the seropositive subjects (r(2)=.51) than in the seronegative subjects (r(2)=.11). Individuals with high theta-to-gamma ratios tended to have lower cognitive test performance, regardless of serostatus. The stability of the wide-band MEG frequency profiles over 24 weeks supports the utility of MEG as a biomarker. The links between the MEG profile, serostatus, and cognition suggest further research on its potential in HAND is needed.

A generalized estimating equations approach for resting-state functional MRI group analysis.

An Alzheimer's fMRI study has motivated us to evaluate inter-regional correlations between groups. The overall objective is to assess inter-regional correlations at a resting-state with no stimulus or task. We propose using a generalized estimating equation (GEE) transition model and a GEE marginal model to model the within-subject correlation for each region. Residuals calculated from the GEE models are used to correlate brain regions and assess between group differences. The standard pooling approach of group averages of the Fisher-z transformation assuming temporal independence is a typical approach used to compare group correlations. The GEE approaches and standard Fisher-z pooling approach are demonstrated with an Alzheimer's disease (AD) connectivity study in a population of AD subjects and healthy control subjects. We also compare these methods using simulation studies and show that the transition model may have better statistical properties.