Single-cell Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper (preprint)

High-throughput single-cell cytometry data are crucial for understanding immune system\'s involvement in diseases and responses to treatment. Traditional methods for annotating cytometry data, specifically manual gating and clustering, face challenges in scalability, robustness, and accuracy. In this study, we propose a single-cell masked autoencoder (scMAE), which offers an automated solution for immunophenotyping tasks including cell type annotation. The scMAE model is designed to uphold user-defined cell type definitions, thereby facilitating easier interpretation and cross-study comparisons. The scMAE model operates on a pre-train and fine-tune approach. In the pre-training phase, scMAE employs Masked Single-cell Modelling (MScM) to learn relationships between protein markers in immune cells solely based on protein expression, without relying on prior information such as cell identity and cell type-specific marker proteins. Subsequently, the pre-trained scMAE is fine-tuned on multiple specialized tasks via task-specific supervised learning. The pre-trained scMAE addresses the shortcomings of manual gating and clustering methods by providing accurate and interpretable predictions. Through validation across multiple cohorts, we demonstrate that scMAE effectively identifies co-occurrence patterns of bound labeled antibodies, delivers accurate and interpretable cellular immunophenotyping, and improves the prediction of subject metadata status. Specifically, we evaluated scMAE for cell type annotation and imputation at the cellular-level and SARS-CoV-2 infection prediction, secondary immune response prediction against COVID-19, and prediction the infection stage in the COVID-19 progression at the subject-level. The introduction of scMAE marks a significant step forward in immunology research, particularly in large-scale and high-throughput human immune profiling. It offers new possibilities for predicting and interpretating cellular-level and subject-level phenotypes in both health and disease.

COVID pandemic impact on hypertension management in North-East London: an observational cohort study using electronic health records (preprint)

Background: The COVID19 pandemic had a major impact on primary care management of long-term conditions such as hypertension. This observational cohort study of adults with hypertension registered in 193 primary care practices in North-East London between January 2019 and October 2022 investigated the impact of the COVID19 pandemic on the treatment and control of blood pressure including demographic and social inequities. Method and findings: In 224,329 adults with hypertension, the proportion with a blood pressure (BP) recorded within the preceding 1 year fell from a 91% pre-pandemic peak to 62% at the end of the pandemic lock-down phase and improved to 77% by the end of the study. The proportion with controlled hypertension (<80 years old, BP <=140/90mmHg; 80 or more years old: <=150/90mmHg) for the same time points was 81%, 50% and 60% respectively. Using 'blood pressure control' (which considered only patients with a valid blood pressure recording) as the indicator attenuated the reduction to 83%, 80% and 78% respectively. The study used multivariable logistic analysis at four representative time points (Pre-pandemic: April 2019; Pre lockdown: April 2020; Lockdown: April 2021; Post-lockdown: April 2022) to identify temporal, clinical and demographic influences on blood pressure monitoring and control. Pre-pandemic inequities in the management of hypertension were not significantly altered by the pandemic. Throughout the pandemic phases, in comparison to the White ethnic group, the Black ethnic group was less likely to achieve blood pressure control (ORs 0.81 [95% CI = 0.78 to 0.85, p-value<0.001] to 0.87 [95% CI = 0.84 to 0.91, p-value<0.001]). Conversely, the Asian ethnic group was more likely to have controlled blood pressure (ORs 1.09 [95% CI = 1.05 to 1.14, p-value<0.001] to 1.28 [95% CI = 1.23 to 1.32, p-value<0.001]). Younger, male, more affluent individuals, individuals with unknown or unrecorded ethnicity or those untreated were less likely to have blood pressure controlled to target throughout the study. Conclusion: The COVID pandemic had a greater impact on blood pressure recording than on blood pressure control. Although recording and control have improved, these had not returned to pre-pandemic levels by the end of the study period. Ethnic inequalities in blood pressure control persisted during the pandemic and remain outstanding.

Telemedicine in a spine clinic setting: a large survey of patient preferences and experiences.

BACKGROUND: Coronavirus Disease 2019 (COVID-19) has greatly disturbed healthcare and the practice of neurosurgery. As healthcare systems evolve in the face of COVID-19, the use of telehealth platforms has expanded. We present the results of a large survey of patient perspectives on the role of telehealth in the care of spine clinic patients. METHODS: All patients at the spine clinic of a large, tertiary, academic medical center were surveyed at their clinic visit from 5/30/20-6/30/20. All responses were anonymous and results were analyzed with standard statistical techniques. RESULTS: 176 surveys were returned and 164 were entirely completed. 56.8% of patients were new while 24.4% were post-operative follow-up visits. 54.9% had lumbar symptoms. 85% had pain while more than half also reported weakness. 58% traveled greater than twenty-five miles for their appointment. 96% had transportation readily available. Of all respondents, only 15.3% preferred the appointment via video telehealth while 4% had no preference between in-person appointment or virtual visit. Preference for telehealth appointment was not associated with factors such as new or established in the practice, spinal region of symptoms, pain, weakness, comfort with technology, age or duration of symptoms. There was a significant difference between how far the patient traveled for the clinic appointment and their preference for a telehealth appointment, with patients traveling further distances favoring telehealth (p=0.04). This effect remained significant when stratifying based on 25 miles (p=0.03) or 50 miles (p=0.03) but not when stratifying based on 100 miles (p=0.32). However, the sample size of patients traveling >100 miles was small, limiting any inference regarding that subgroup. Access to transportation was associated with preference for telehealth (88.89% vs. 97.18%, p=0.08) but did not reach statistical significance. CONCLUSIONS: Most spine patients prefer in-person clinic appointments to virtual appointments. These preferences should be considered when arranging patient encounters.

Television News Media Consumption and Misperceptions about COVID-19 among US Populations at High Risk for Severe Health Outcomes Early in the Pandemic.

Research indicates that misperceptions that become part of people's initial mental models about an issue tend to persist and influence their attitudes even after the misperception has been corrected. Recent work on evolving mental models suggests that communication efforts about the ongoing COVID-19 pandemic and its aftermath may be improved by crafting messages that acknowledge biases and misunderstandings about the virus and other infectious diseases that may remain among members of the target audience. This study was designed to provide insight into such biases by: (1) establishing salient categories of COVID-related misperceptions in the earliest months of the pandemic in the United States among (a) the general population, and (b) demographic sub-populations at high risk of severe health outcomes; (2) identifying demographic predictors of misperceptions; and (3) examining the relationship between consumption of different television news outlets and agreement with misperceptions about COVID-19. A national sample of 1,000 adults in the United States (48.1% male; M age = 47.32, SD = 18.01; 72.9% White/Caucasian, 14.3% Black/African American, 15.9% Hispanic/Latinx) completed a survey between March 19 and March 25, 2020. Results identify prevalent classes of salient early COVID-19 misperceptions. Adjusting for numerous covariates, data indicated individuals over the age of 60 held the fewest COVID-related misperceptions among various demographic sub-populations, misperceptions were most prevalent among Black respondents, and increased consumption of television network news was associated with lower levels of misperception. Consumption of some 24-hour news networks (FOX and MSNBC) were significant positive correlates of misperceptions.

Changes in Mental Health and Well-Being Are Associated With Living Arrangements With Parents During COVID-19 Among Sexual Minority Young Persons in the U.S.

Sexual minority young persons may be at risk for compounding mental health effects of the COVID-19 pandemic due to their existing vulnerabilities for psychological inequities. Indeed, recent research has documented that sexual minority young persons are experiencing compounding psychiatric effects associated with the COVID-19 pandemic. Further, researchers and practitioners hypothesized that sexual minority youth and young adults may experience unique hardships related to their sexual and gender identities and familial conflict as a result of the COVID-19 pandemic and living arrangement changes with their parents and families. This study aims to investigate whether there are changes in sexual minority (and non-sexual minority) young adults' (SMYAs) mental health and wellbeing among those living with and living without their parents before and after the start of COVID-19. Among a cross-sectional sample of SMYAs (n=294; Mage=22 years; age range=18-26) and non-SMYAs (n=874; Mage=22 years; age range=18-26) defined by whether they were living with or living without their parents before and after the start of COVID-19, we retrospectively analyzed changes in psychological distress and wellbeing. SMYAs who returned to their parents' homes during post-onset of COVID-19 reported greater mental distress and lower wellbeing, followed by those who were living with their parents both before and after the start of COVID-19. Patterns were not consistent among non-SMYAs, and lower magnitudes of change were seen. There is a significant public health need for mental health services and family education resources for supporting SMYAs in the context of COVID-19 and beyond.

Global report on COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities: Results from secondary analyses of Special Olympics' program planning.

The COVID-19 pandemic has disproportionately affected people with intellectual disabilities worldwide. The objective of this study was to identify global rates of COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities (ID) associated with country economic income levels. The Special Olympics COVID-19 online survey was administered in January-February 2022 to adults with ID from 138 countries. Descriptive analyses of survey responses include 95% margins of error. Logistic regression and Pearson Chi-squared tests were calculated to assess associations with predictive variables for vaccination using R 4.1.2 software. Participants (n = 3560) represented 18 low (n = 410), 35 lower-middle (n = 1182), 41 upper-middle (n = 837), and 44 high (n = 1131) income countries. Globally, 76% (74.8-77.6%) received a COVID-19 vaccination while 49.5% (47.9-51.2%) received a COVID-19 booster. Upper-middle (93% (91.2-94.7%)) and high-income country (94% (92.1-95.0%)) participants had the highest rates of vaccination while low-income countries had the lowest rates (38% (33.3-42.7%)). In multivariate regression models, country economic income level (OR = 3.12, 95% CI [2.81, 3.48]), age (OR = 1.04, 95% CI [1.03, 1.05]), and living with family (OR = 0.70, 95% CI [0.53, 0.92]) were associated with vaccination. Among LLMICs, the major reason for not vaccinating was lack of access (41.2% (29.5-52.9%)). Globally, concerns about side effects (42%, (36.5-48.1%)) and parent/guardian not wanting the adult with ID to vaccinate (32% (26.1-37.0%)) were the most common reasons for not vaccinating. Adults with ID from low and low-middle income countries reported fewer COVID-19 vaccinations, suggesting reduced access and availability of resources in these countries. Globally, COVID-19 vaccination levels among adults with ID were higher than the general population. Interventions should address the increased risk of infection for those in congregate living situations and family caregiver apprehension to vaccinate this high-risk population.

Electronic Nose Development and Preliminary Human Breath Testing for Rapid, Non-Invasive COVID-19 Detection.

We adapted an existing, spaceflight-proven, robust "electronic nose" (E-Nose) that uses an array of electrical resistivity-based nanosensors mimicking aspects of mammalian olfaction to conduct on-site, rapid screening for COVID-19 infection by measuring the pattern of sensor responses to volatile organic compounds (VOCs) in exhaled human breath. We built and tested multiple copies of a hand-held prototype E-Nose sensor system, composed of 64 chemically sensitive nanomaterial sensing elements tailored to COVID-19 VOC detection; data acquisition electronics; a smart tablet with software (App) for sensor control, data acquisition and display; and a sampling fixture to capture exhaled breath samples and deliver them to the sensor array inside the E-Nose. The sensing elements detect the combination of VOCs typical in breath at parts-per-billion (ppb) levels, with repeatability of 0.02% and reproducibility of 1.2%; the measurement electronics in the E-Nose provide measurement accuracy and signal-to-noise ratios comparable to benchtop instrumentation. Preliminary clinical testing at Stanford Medicine with 63 participants, their COVID-19-positive or COVID-19-negative status determined by concomitant RT-PCR, discriminated between these two categories of human breath with a 79% correct identification rate using "leave-one-out" training-and-analysis methods. Analyzing the E-Nose response in conjunction with body temperature and other non-invasive symptom screening using advanced machine learning methods, with a much larger database of responses from a wider swath of the population, is expected to provide more accurate on-the-spot answers. Additional clinical testing, design refinement, and a mass manufacturing approach are the main steps toward deploying this technology to rapidly screen for active infection in clinics and hospitals, public and commercial venues, or at home.

Coronary microvascular health in symptomatic patients with prior COVID-19 infection: an updated analysis.

AIMS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with endothelial dysfunction. We aimed to determine the effects of prior coronavirus disease 2019 (COVID-19) on the coronary microvasculature accounting for time from COVID-19, disease severity, SARS-CoV-2 variants, and in subgroups of patients with diabetes and those with no known coronary artery disease. METHODS AND RESULTS: Cases consisted of patients with previous COVID-19 who had clinically indicated positron emission tomography (PET) imaging and were matched 1:3 on clinical and cardiovascular risk factors to controls having no prior infection. Myocardial flow reserve (MFR) was calculated as the ratio of stress to rest myocardial blood flow (MBF) in mL/min/g of the left ventricle. Comparisons between cases and controls were made for the odds and prevalence of impaired MFR (MFR < 2). We included 271 cases matched to 815 controls (mean ± SD age 65 ± 12 years, 52% men). The median (inter-quartile range) number of days between COVID-19 infection and PET imaging was 174 (58-338) days. Patients with prior COVID-19 had a statistically significant higher odds of MFR <2 (adjusted odds ratio 3.1, 95% confidence interval 2.8-4.25 P < 0.001). Results were similar in clinically meaningful subgroups. The proportion of cases with MFR <2 peaked 6-9 months from imaging with a statistically non-significant downtrend afterwards and was comparable across SARS-CoV-2 variants but increased with increasing severity of infection. CONCLUSION: The prevalence of impaired MFR is similar by duration of time from infection up to 1 year and SARS-CoV-2 variants, but significantly differs by severity of infection.

Remote Monitoring for Heart Failure Management at Home.

Early telemonitoring of weights and symptoms did not decrease heart failure hospitalizations but helped identify steps toward effective monitoring programs. A signal that is accurate and actionable with response kinetics for early re-assessment is required for the treatment of patients at high risk, while signal specifications differ for surveillance of low-risk patients. Tracking of congestion with cardiac filling pressures or lung water content has shown most impact to decrease hospitalizations, while multiparameter scores from implanted rhythm devices have identified patients at increased risk. Algorithms require better personalization of signal thresholds and interventions. The COVID-19 epidemic accelerated transition to remote care away from clinics, preparing for new digital health care platforms to accommodate multiple technologies and empower patients. Addressing inequities will require bridging the digital divide and the deep gap in access to HF care teams, who will not be replaced by technology but by care teams who can embrace it.

An evolutionarily conserved strategy for ribosome binding and inhibition by β-coronavirus non-structural protein 1 (preprint)

An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Nsp1, which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs through an unknown mechanism. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from beta-CoV inhibits translation through ribosome binding. The C-terminal domain of all beta-CoV Nsp1s confers high-affinity ribosome-binding despite low sequence conservation. Modeling of interactions of four Nsp1s to the ribosome identified few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the beta-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal effector domain. Finally, we show that a viral cis-acting RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aide future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2, but also related human-pathogenic beta-coronaviruses. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.

Die Kämpfe únd schláchten-the struggles and battles of innate-like effector T lymphocytes with microbes.

The large majority of lymphocytes belong to the adaptive immune system, which are made up of B2 B cells and the αß T cells; these are the effectors in an adaptive immune response. A multitudinous group of lymphoid lineage cells does not fit the conventional lymphocyte paradigm; it is the unconventional lymphocytes. Unconventional lymphocytes-here called innate/innate-like lymphocytes, include those that express rearranged antigen receptor genes and those that do not. Even though the innate/innate-like lymphocytes express rearranged, adaptive antigen-specific receptors, they behave like innate immune cells, which allows them to integrate sensory signals from the innate immune system and relay that umwelt to downstream innate and adaptive effector responses. Here, we review natural killer T cells and mucosal-associated invariant T cells-two prototypic innate-like T lymphocytes, which sense their local environment and relay that umwelt to downstream innate and adaptive effector cells to actuate an appropriate host response that confers immunity to infectious agents.

Long-Term Care Resident Health and Quality of Care During the COVID-19 Pandemic: A Synthesis Analysis of Canadian Institute for Health Information Data Tables.

Objective: Long-term care (LTC) homes ("nursing homes") were challenged during the first year of the COVID-19 pandemic in Canada. The objective of this study was to measure the impact of the COVID-19 pandemic on resident admission and discharge rates, resident health attributes, treatments, and quality of care. Design: Synthesis analysis of "Quick Stats" standardized data table reports published yearly by the Canadian Institute for Health Information. These reports are a pan-Canadian scorecard of LTC services rendered, resident health characteristics, and quality indicator performance. Setting and participants: LTC home residents in Alberta, British Columbia, Manitoba, and Ontario, Canada that were assessed with the interRAI Minimum Data Set 2.0 comprehensive health assessment in fiscal years 2018/2019, 2019/2020 (pre-pandemic period), and 2020/2021 (pandemic period). Methods: Risk ratio statistics were calculated to compare admission and discharge rates, validated interRAI clinical summary scale scores, medication, therapy and treatment provision, and seventeen risk-adjusted quality indicator rates from the pandemic period relative to prior fiscal years. Results: Risk of dying in the LTC home was greater in all provinces (risk ratio [RR] range 1.06-1.18) during the pandemic. Quality of care worsened substantially on 6 of 17 quality indicators in British Columbia and Ontario, and 2 quality indicators in Manitoba and Alberta. The only quality indicator where performance worsened during the pandemic in all provinces was the percentage of residents that received antipsychotic medications without a diagnosis of psychosis (RR range 1.01-1.09). Conclusions and implications: The COVID-19 pandemic has unveiled numerous areas to strengthen LTC and ensure that resident's physical, social, and psychological needs are addressed during public health emergencies. Except an increase in potentially inappropriate antipsychotic use, this provincial-level analysis indicates that most aspects of resident care were maintained during the first year of the COVID-19 pandemic.

Researching COVID to enhance recovery (RECOVER) adult study protocol: Rationale, objectives and design (preprint)

Importance: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or other health effects after the acute phase of infection; termed post-acute sequelae of SARS-CoV-2 infection (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are ill-defined. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Multi-site Observational Study of PASC in Adults (RECOVER-Adult) are to: (1) characterize PASC prevalence; (2) characterize the symptoms, organ dysfunction, natural history, and distinct phenotypes of PASC; (3) identify demographic, social and clinical risk factors for PASC onset and recovery; and (4) define the biological mechanisms underlying PASC pathogenesis. Methods: RECOVER-Adult is a combined prospective/retrospective cohort currently planned to enroll 14,880 adults aged [≥]18 years. Eligible participants either must meet WHO criteria for suspected, probable, or confirmed infection; or must have evidence of no prior infection. Recruitment occurs at 86 sites in 33 U.S. states, Washington, DC and Puerto Rico, via facility- and community-based outreach. Participants complete quarterly questionnaires about symptoms, social determinants, vaccination status, and interim SARS-CoV-2 infections. In addition, participants contribute biospecimens and undergo physical and laboratory examinations at approximately 0, 90 and 180 days from infection or negative test date, and yearly thereafter. Some participants undergo additional testing based on specific criteria or random sampling. Patient representatives provide input on all study processes. The primary study outcome is onset of PASC, measured by signs and symptoms. A paradigm for identifying PASC cases will be defined and updated using supervised and unsupervised learning approaches with cross-validation. Logistic regression and proportional hazards regression will be conducted to investigate associations between risk factors, onset, and resolution of PASC symptoms. Discussion: RECOVER-Adult is the first national, prospective, longitudinal cohort of PASC among US adults. Results of this study are intended to inform public health, spur clinical trials, and expand treatment options.

Review article: Food safety culture from the perspective of the Australian horticulture industry

Foodborne illness outbreaks associated with fresh produce suggest a focus on food safety culture within food safety management systems throughout supply chains would benefit the horticulture industry. The recent inclusion of food safety culture in horticulture standards will drive the need for better understanding, integration into business activities, and monitoring, to help mitigate foodborne incidents in horticulture.The purpose of this review was to identify definitions of food safety culture and methods of measuring its performance in the context of the Australian horticulture industry. Investigation of how to better apply and integrate a positive food safety culture into existing food safety management systems was conducted. A roadmap for food safety culture improvement in Australian horticulture is presented, highlighting the challenges and opportunities.To guide the development of a mature culture of food safety, mixed-method approaches to performance assessment were found to be the most comprehensive, valid, and offer the most potential for use by horticulture businesses. Food safety culture can be developed by using feedback from regular culture assessments that identify weaknesses and opportunities for improvement, leading to increased knowledge, alignment of attitudes, and better food safety and hygiene behaviour. To this end, the development of measurement tools specific to horticulture operations would be beneficial. Despite unforeseen challenges like the COVID-19 pandemic, the Australian horticulture industry continues to investigate the efficacy of its food safety management.

Validating a Proteomic Signature of Severe COVID-19.

COVID-19 is a heterogenous disease. Biomarker-based approaches may identify patients at risk for severe disease, who may be more likely to benefit from specific therapies. Our objective was to identify and validate a plasma protein signature for severe COVID-19. DESIGN: Prospective observational cohort study. SETTING: Two hospitals in the United States. PATIENTS: One hundred sixty-seven hospitalized adults with COVID-19. INTERVENTION: None. MEASUREMENTS AND MAIN RESULTS: We measured 713 plasma proteins in 167 hospitalized patients with COVID-19 using a high-throughput platform. We classified patients as nonsevere versus severe COVID-19, defined as the need for high-flow nasal cannula, mechanical ventilation, extracorporeal membrane oxygenation, or death, at study entry and in 7-day intervals thereafter. We compared proteins measured at baseline between these two groups by logistic regression adjusting for age, sex, symptom duration, and comorbidities. We used lead proteins from dysregulated pathways as inputs for elastic net logistic regression to identify a parsimonious signature of severe disease and validated this signature in an external COVID-19 dataset. We tested whether the association between corticosteroid use and mortality varied by protein signature. One hundred ninety-four proteins were associated with severe COVID-19 at the time of hospital admission. Pathway analysis identified multiple pathways associated with inflammatory response and tissue repair programs. Elastic net logistic regression yielded a 14-protein signature that discriminated 90-day mortality in an external cohort with an area under the receiver-operator characteristic curve of 0.92 (95% CI, 0.88-0.95). Classifying patients based on the predicted risk from the signature identified a heterogeneous response to treatment with corticosteroids (p = 0.006). CONCLUSIONS: Inpatients with COVID-19 express heterogeneous patterns of plasma proteins. We propose a 14-protein signature of disease severity that may have value in developing precision medicine approaches for COVID-19 pneumonia.

Transparency in infectious disease research: meta-research survey of specialty journals.

BACKGROUND: Infectious diseases carry large global burdens and have implications for society at large. Therefore, reproducible, transparent research is extremely important. METHODS: We evaluated transparency indicators (code and data sharing, registration, conflict and funding disclosures) in the 5340 PubMed Central Open Access articles published in 2019 or 2021 in the 9 most-cited specialty journals in infectious disease using the text-mining R package, rtransparent. RESULTS: 5340 articles were evaluated (1860 published in 2019 and 3480 in 2021 (of which 1828 on COVID-19)). Text-mining identified code sharing in 98 (2%) articles, data sharing in 498 (9%), registration in 446 (8%), conflict of interest disclosures in 4209 (79%) and funding disclosures in 4866 (91%). There were substantial differences across the 9 journals: 1-9% for code sharing, 5-25% for data sharing, 1-31% for registration, 7-100% for conflicts of interest, and 65-100% for funding disclosures. Validation-corrected imputed estimates were 3%, 11%, 8%, 79% and 92%, respectively. There were no major differences between articles published in 2019 and non-COVID-19 articles in 2021. In 2021, non-COVID-19 articles had more data sharing (12%) than COVID-19 articles (4%). CONCLUSIONS: Data sharing, code sharing, and registration are very uncommon in infectious disease specialty journals. Increased transparency is required.

The COVID-19 pandemic and its impacts on mass shootings in six major US cities.

BACKGROUND: The COVID-19 pandemic has significant impacts on the US socioeconomic structure. Gun violence is a major public health issue and the effects on this area have not been well-elucidated. The objective of this study was to determine the impacts of the pandemic on mass shootings in six major United States cities with historically high rates of gun violence. METHODS: Mass shooting data were extracted from an open-source database, Gun Violence Archive. Mass shooting was defined as four or more people shot at a single event. Data from six cities with the highest incidence of mass shootings were analyzed in 2019 versus 2020 (Baltimore, Chicago, Detroit, New Orleans, Philadelphia, and St. Louis). Geographic data were examined to assess changes in each city's mass shooting geographic distribution over time. Quantitative changes were assessed using the Area Deprivation Index (ADI), and qualitative data were assessed using ArcGIS. RESULTS: In 2020, the overall percentage of mass shootings increased by 46.7% though there was no change in the distribution of these events when assessed quantitatively (no change in average ADI) nor qualitatively (using ArcGIS). In the six cities analyzed, the total proportion of mass shooting events was unchanged during the pandemic (21.8% vs 20.6%, p = 0.64). Chicago, the US city with the highest incidence of mass shootings, did not experience a significant change in 2020 (n = 34/91, 37.3% vs. n = 53/126, 42.1%, p = 0.57). Baltimore had a significant decrease in mass shooting events (n = 18/91, 19.8% vs. 10/126, 7.9%, p = 0.01). The other four cities had no significant change in the number of mass shootings (p>0.05). CONCLUSION: This study is the first to use ArcGIS technology to describe the patterns of mass shooting in six major US cities during the COVID-19 pandemic. The number of mass shootings in six US cities remained largely unchanged which suggests that changes in mass shootings is likely occurring in smaller cities. Future studies should focus on the changing patterns of homicides in at-risk communities and other possible social influences.