cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24721785
title: Prevalence of uveitis in syphilis patients in Taiwan

description: Few population-based studies have looked at the risk of uveitis among syphilis patients. Our study addresses the knowledge gap by reporting on uveitis risk in syphilis patients through a retrospective cohort study. The Taiwan National Health Insurance database was used for this study, covering the period from January 1st, 2009, to December 31st, 2020. We created a 1:4 propensity score matched cohort between the syphilis patients and controls, which accounted for gender, age, and comorbidities. The primary endpoint was the incidence of newly recorded uveitis. The assessment of uveitis risk in syphilis patients included the use of the Kaplan-Meier method and multivariate Cox proportional hazard model. A total of 31,597 syphilis patients and 126,379 matched comparisons were recruited. The uveitis incidence rate from our syphilis patients was 1.25 per 1000 person-years. The uveitis incidence rate from our non-syphilis group was 0.8 per 1000 person-years. After matching, the syphilis group was found to have a higher risk of developing uveitis (adjusted hazard ratio (aHR) [95% CI]: 1.57 [1.36–1.81], <i>P</i> &lt; .001). Among males and individuals aged 20–34 years, subgroup analysis showed an increased risk of uveitis in the presence of syphilis infection. The Kaplan-Meier survival curve showed a significant difference in uveitis incidence between syphilis and non-syphilis groups (log-rank test <i>P</i> &lt; .001). In summary, our study revealed that Taiwanese syphilis patients were at a higher risk of developing uveitis. These results highlight the need for regular ocular monitoring and screening in individuals with syphilis.
DOI: 10.6084/m9.figshare.24721785.v2
title: Prevalence of uveitis in syphilis patients in Taiwan

description: Few population-based studies have looked at the risk of uveitis among syphilis patients. Our study addresses the knowledge gap by reporting on uveitis risk in syphilis patients through a retrospective cohort study. The Taiwan National Health Insurance database was used for this study, covering the period from January 1st, 2009, to December 31st, 2020. We created a 1:4 propensity score matched cohort between the syphilis patients and controls, which accounted for gender, age, and comorbidities. The primary endpoint was the incidence of newly recorded uveitis. The assessment of uveitis risk in syphilis patients included the use of the Kaplan-Meier method and multivariate Cox proportional hazard model. A total of 31,597 syphilis patients and 126,379 matched comparisons were recruited. The uveitis incidence rate from our syphilis patients was 1.25 per 1000 person-years. The uveitis incidence rate from our non-syphilis group was 0.8 per 1000 person-years. After matching, the syphilis group was found to have a higher risk of developing uveitis (adjusted hazard ratio (aHR) [95% CI]: 1.57 [1.36–1.81], <i>P</i> &lt; .001). Among males and individuals aged 20–34 years, subgroup analysis showed an increased risk of uveitis in the presence of syphilis infection. The Kaplan-Meier survival curve showed a significant difference in uveitis incidence between syphilis and non-syphilis groups (log-rank test <i>P</i> &lt; .001). In summary, our study revealed that Taiwanese syphilis patients were at a higher risk of developing uveitis. These results highlight the need for regular ocular monitoring and screening in individuals with syphilis.
DOI: 10.6084/m9.figshare.26042178
title: Prediction models for COVID-19 disease outcomes

description: SARS-CoV-2 has caused over 6.9 million deaths and continues to produce lasting health consequences. COVID-19 manifests broadly from no symptoms to death. In a retrospective cross-sectional study, we developed personalized risk assessment models that predict clinical outcomes for individuals with COVID-19 and inform targeted interventions. We sequenced viruses from SARS-CoV-2-positive nasopharyngeal swab samples between July 2020 and July 2022 from 4450 individuals in Missouri and retrieved associated disease courses, clinical history, and urban-rural classification. We integrated this data to develop machine learning-based predictive models to predict hospitalization, ICU admission, and long COVID. The mean age was 38.3 years (standard deviation = 21.4) with 55.2% (<i>N</i> = 2453) females and 44.8% (<i>N</i> = 1994) males (not reported, <i>N</i> = 4). Our analyses revealed a comprehensive set of predictors for each outcome, encompassing human, environment, and virus genome-wide genetic markers. Immunosuppression, cardiovascular disease, older age, cardiac, gastrointestinal, and constitutional symptoms, rural residence, and specific amino acid substitutions were associated with hospitalization. ICU admission was associated with acute respiratory distress syndrome, ventilation, bacterial co-infection, rural residence, and non-wild type SARS-CoV-2 variants. Finally, long COVID was associated with hospital admission, ventilation, and female sex. Overall, we developed risk assessment models that offer the capability to identify patients with COVID-19 necessitating enhanced monitoring or early interventions. Of importance, we demonstrate the value of including key elements of virus, host, and environmental factors to predict patient outcomes, serving as a valuable platform in the field of personalized medicine with the potential for adaptation to other infectious diseases. Model summary and motivation. Individuals infected with SARS-CoV-2 experience a wide spectrum of clinical manifestations ranging from no symptoms to death. Using the Virus-Human Outcomes Prediction (ViHOP) algorithm, we aim to utilize the individual’s clinical characteristics, the individual’s location, and the infecting SARS-CoV-2 virus characteristics obtained by whole genome sequencing to determine their likelihood of admission to the hospital, admission to the intensive care unit (ICU), or experiencing long COVID. This model allows clinicians to identify at-risk patients for further monitoring and/or early treatment.
DOI: 10.6084/m9.figshare.26538011
title: Time-resolved scRNA-seq reveals transcription dynamics of polarized macrophages with influenza A virus infection and antigen presentation to T cells

description: Throughout history, the influenza A virus has caused numerous devastating global pandemics. Macrophages, as pivotal innate immune cells, exhibit a wide range of immune functions characterized by distinct polarization states, reflecting their intricate heterogeneity. In this study, we employed the time-resolved single-cell sequencing technique coupled with metabolic RNA labelling to elucidate the dynamic transcriptional changes in distinct polarized states of bone marrow-derived macrophages (BMDMs) upon infection with the influenza A virus. Our approach not only captures the temporal dimension of transcriptional activity, which is lacking in conventional scRNA-seq methods, but also reveals that M2-polarized <i>Arg1</i>_macrophage cluster is the sole state supporting successful replication of influenza A virus. Furthermore, we identified distinct antigen presentation capabilities to CD4<b><sup>+</sup></b> T and CD8<b><sup>+</sup></b> T cells across diverse polarized states of macrophages. Notably, the M1 phenotype, exhibited by (BMDMs) and murine alveolar macrophages (AMs), demonstrated superior conventional and cross-presentation abilities for exogenous antigens, with a particular emphasis on cross-presentation capacity. Additionally, as CD8<b><sup>+</sup></b> T cell differentiation progressed, M1 polarization exhibited an enhanced capacity for cross-presentation. All three phenotypes of BMDMs, including M1, demonstrated robust presentation to CD4<b><sup>+</sup></b> regulatory T cells, while displaying limited ability to present to naive CD4<sup>+</sup> T cells. These findings offer novel insights into the immunological regulatory mechanisms governing distinct polarized states of macrophages, particularly their roles in restricting the replication of influenza A virus and modulating antigen-specific T cell responses through innate immunity.
DOI: 10.6084/m9.figshare.26538011.v1
title: Time-resolved scRNA-seq reveals transcription dynamics of polarized macrophages with influenza A virus infection and antigen presentation to T cells

description: Throughout history, the influenza A virus has caused numerous devastating global pandemics. Macrophages, as pivotal innate immune cells, exhibit a wide range of immune functions characterized by distinct polarization states, reflecting their intricate heterogeneity. In this study, we employed the time-resolved single-cell sequencing technique coupled with metabolic RNA labelling to elucidate the dynamic transcriptional changes in distinct polarized states of bone marrow-derived macrophages (BMDMs) upon infection with the influenza A virus. Our approach not only captures the temporal dimension of transcriptional activity, which is lacking in conventional scRNA-seq methods, but also reveals that M2-polarized <i>Arg1</i>_macrophage cluster is the sole state supporting successful replication of influenza A virus. Furthermore, we identified distinct antigen presentation capabilities to CD4<b><sup>+</sup></b> T and CD8<b><sup>+</sup></b> T cells across diverse polarized states of macrophages. Notably, the M1 phenotype, exhibited by (BMDMs) and murine alveolar macrophages (AMs), demonstrated superior conventional and cross-presentation abilities for exogenous antigens, with a particular emphasis on cross-presentation capacity. Additionally, as CD8<b><sup>+</sup></b> T cell differentiation progressed, M1 polarization exhibited an enhanced capacity for cross-presentation. All three phenotypes of BMDMs, including M1, demonstrated robust presentation to CD4<b><sup>+</sup></b> regulatory T cells, while displaying limited ability to present to naive CD4<sup>+</sup> T cells. These findings offer novel insights into the immunological regulatory mechanisms governing distinct polarized states of macrophages, particularly their roles in restricting the replication of influenza A virus and modulating antigen-specific T cell responses through innate immunity.
DOI: 10.25549/webster-c100-44352
title: Manual of the Los Angeles Police Department, 1992

description: The Los Angeles Police Department's departmental manual, 1992. PART OF SERIES: The series includes materials related to the performance of the LAPD prior to and during the 1992 Los Angeles riots. Included are reports and documents pertaining to the department's tactical planning measures for unusual occurrences and emergencies; riot-related statistics and figures; and arrest logs, incident logs, and activities reports maintained during the riots.
DOI: 10.6084/m9.figshare.25163827
title: Epidemiology and clinical features of Skin and Soft Tissue Infections Caused by PVL-Positive and PVL-Negative Methicillin-Resistant <i>Staphylococcus aureus</i> Isolates in inpatients in China: a single-center retrospective 7-year study

description: Previous studies have mainly focused on outpatient cases of skin and soft tissue infections (SSTIs), with limited attention to inpatient occurrences. Thus, we aimed to compare the clinical parameters of inpatients with SSTIs, performed genomic characterization, and determined the subtypes of Panton-Valentine leucocidin (PVL) bacteriophages of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains isolated from these patients. We found that PVL-positive patients had shorter hospital stays (mean, 9 vs. 24 days; <i>p</i> &lt; 0.001) and abscess resolution durations (mean, 8 vs. 13 days; <i>p</i> &lt; 0.01). PVL-positive MRSA-induced SSTIs were more frequently associated with abscesses [36/55 (65.5%) vs. 15/124 (12.1%), <i>p</i> &lt; 0.001], with 52.7% undergoing incision and drainage; over 80% of PVL-negative patients received incision, drainage, and antibiotics. In PVL-positive patients receiving empirical antibiotics, anti-staphylococcal agents such as vancomycin and linezolid were administered less frequently (32.7%, 18/55) than in PVL-negative patients (74.2%, 92/124), indicating that patients with PVL-positive SSTIs are more likely to require surgical drainage rather than antimicrobial treatment. We also found that the ST59 lineage was predominant, regardless of PVL status (41.3%, 74/179). Additionally, we investigated the linear structure of the <i>lukSF-PV</i> gene, revealing that major clusters were associated with specific STs, suggesting independent acquisition of PVL by different strain types and indicating that significant diversity was observed even within PVL-positive strains detected in the same facility. Overall, our study provides comprehensive insights into the clinical, genetic, and phage-related aspects of MRSA-induced SSTIs in hospitalized patients and contributes to a more profound understanding of the epidemiology and evolution of these pathogens in the Chinese population.
DOI: 10.6084/m9.figshare.25163827.v2
title: Epidemiology and clinical features of Skin and Soft Tissue Infections Caused by PVL-Positive and PVL-Negative Methicillin-Resistant <i>Staphylococcus aureus</i> Isolates in inpatients in China: a single-center retrospective 7-year study

description: Previous studies have mainly focused on outpatient cases of skin and soft tissue infections (SSTIs), with limited attention to inpatient occurrences. Thus, we aimed to compare the clinical parameters of inpatients with SSTIs, performed genomic characterization, and determined the subtypes of Panton-Valentine leucocidin (PVL) bacteriophages of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains isolated from these patients. We found that PVL-positive patients had shorter hospital stays (mean, 9 vs. 24 days; <i>p</i> &lt; 0.001) and abscess resolution durations (mean, 8 vs. 13 days; <i>p</i> &lt; 0.01). PVL-positive MRSA-induced SSTIs were more frequently associated with abscesses [36/55 (65.5%) vs. 15/124 (12.1%), <i>p</i> &lt; 0.001], with 52.7% undergoing incision and drainage; over 80% of PVL-negative patients received incision, drainage, and antibiotics. In PVL-positive patients receiving empirical antibiotics, anti-staphylococcal agents such as vancomycin and linezolid were administered less frequently (32.7%, 18/55) than in PVL-negative patients (74.2%, 92/124), indicating that patients with PVL-positive SSTIs are more likely to require surgical drainage rather than antimicrobial treatment. We also found that the ST59 lineage was predominant, regardless of PVL status (41.3%, 74/179). Additionally, we investigated the linear structure of the <i>lukSF-PV</i> gene, revealing that major clusters were associated with specific STs, suggesting independent acquisition of PVL by different strain types and indicating that significant diversity was observed even within PVL-positive strains detected in the same facility. Overall, our study provides comprehensive insights into the clinical, genetic, and phage-related aspects of MRSA-induced SSTIs in hospitalized patients and contributes to a more profound understanding of the epidemiology and evolution of these pathogens in the Chinese population.
DOI: 10.6084/m9.figshare.25320849
title: H7N6 highly pathogenic avian influenza in Mozambique, 2023

description: On 13 October 2023, the National Directorate for Livestock Development in Mozambique was notified of a suspected outbreak of avian influenza in commercial layers. Samples were screened by real-time and conventional RT–PCR and were positive for both H7 and N6. Full genome sequences were obtained for three representative samples. Sequence analysis of the H7 cleavage site confirmed that the viruses were highly pathogenic (i.e. 333- PEPPKGPRFRR/GLF-346). In addition, the H7 and N6 sequences were highly similar (from 99.4-99.5% and 99.6-99.7% for the HA gene and the NA gene, respectively) to the sequences of a H7N6 virus identified in the Republic of South Africa in May 2023 indicating a similar origin of the viruses. The identification of H7N6 HPAIV in Mozambique has important implications for disease management and food security in the region.
DOI: 10.6084/m9.figshare.25320849.v1
title: H7N6 highly pathogenic avian influenza in Mozambique, 2023

description: On 13 October 2023, the National Directorate for Livestock Development in Mozambique was notified of a suspected outbreak of avian influenza in commercial layers. Samples were screened by real-time and conventional RT–PCR and were positive for both H7 and N6. Full genome sequences were obtained for three representative samples. Sequence analysis of the H7 cleavage site confirmed that the viruses were highly pathogenic (i.e. 333- PEPPKGPRFRR/GLF-346). In addition, the H7 and N6 sequences were highly similar (from 99.4-99.5% and 99.6-99.7% for the HA gene and the NA gene, respectively) to the sequences of a H7N6 virus identified in the Republic of South Africa in May 2023 indicating a similar origin of the viruses. The identification of H7N6 HPAIV in Mozambique has important implications for disease management and food security in the region.
DOI: 10.25549/webster-c100-39700
title: Interviews of city of Los Angeles, Emergency Operations Organization, 1992-08/1992-09

description: Summaries of interviews conducted with personnel from the City of Los Angeles's Emergency Operations Organization, 1992 August - September. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.
DOI: 10.6084/m9.figshare.26538005
title: A nucleoside-modified mRNA vaccine forming rabies virus-like particle elicits strong cellular and humoral immune responses against rabies virus infection in mice

description: Rabies is a lethal zoonotic disease that threatens human health. As the only viral surface protein, the rabies virus (RABV) glycoprotein (G) induces main neutralizing antibody (Nab) responses; however, Nab titre is closely correlated with the conformation of G. Virus-like particles (VLP) formed by the co-expression of RABV G and matrix protein (M) improve retention and antigen presentation, inducing broad, durable immune responses. RABV nucleoprotein (N) can elicit humoral and cellular immune responses. Hence, we developed a series of nucleoside-modified RABV mRNA vaccines encoding wild-type G, soluble trimeric RABV G formed by an artificial trimer motif (tG-MTQ), membrane-anchored prefusion-stabilized G (preG). Furthermore, we also developed RABV VLP mRNA vaccine co-expressing preG and M to generate VLPs, and VLP/N mRNA vaccine co-expressing preG, M, and N. The RABV mRNA vaccines induced higher humoral and cellular responses than inactivated rabies vaccine, and completely protected mice against intracerebral challenge. Additionally, the IgG and Nab titres in RABV preG, VLP and VLP/N mRNA groups were significantly higher than those in G and tG-MTQ groups. A single administration of VLP or VLP/N mRNA vaccines elicited protective Nab responses, the Nab titres were significantly higher than that in inactivated rabies vaccine group at day 7. Moreover, RABV VLP and VLP/N mRNA vaccines showed superior capacities to elicit potent germinal centre, long-lived plasma cell and memory B cell responses, which linked to high titre and durable Nab responses. In summary, our data demonstrated that RABV VLP and VLP/N mRNA vaccines could be promising candidates against rabies.
DOI: 10.6084/m9.figshare.26538005.v1
title: A nucleoside-modified mRNA vaccine forming rabies virus-like particle elicits strong cellular and humoral immune responses against rabies virus infection in mice

description: Rabies is a lethal zoonotic disease that threatens human health. As the only viral surface protein, the rabies virus (RABV) glycoprotein (G) induces main neutralizing antibody (Nab) responses; however, Nab titre is closely correlated with the conformation of G. Virus-like particles (VLP) formed by the co-expression of RABV G and matrix protein (M) improve retention and antigen presentation, inducing broad, durable immune responses. RABV nucleoprotein (N) can elicit humoral and cellular immune responses. Hence, we developed a series of nucleoside-modified RABV mRNA vaccines encoding wild-type G, soluble trimeric RABV G formed by an artificial trimer motif (tG-MTQ), membrane-anchored prefusion-stabilized G (preG). Furthermore, we also developed RABV VLP mRNA vaccine co-expressing preG and M to generate VLPs, and VLP/N mRNA vaccine co-expressing preG, M, and N. The RABV mRNA vaccines induced higher humoral and cellular responses than inactivated rabies vaccine, and completely protected mice against intracerebral challenge. Additionally, the IgG and Nab titres in RABV preG, VLP and VLP/N mRNA groups were significantly higher than those in G and tG-MTQ groups. A single administration of VLP or VLP/N mRNA vaccines elicited protective Nab responses, the Nab titres were significantly higher than that in inactivated rabies vaccine group at day 7. Moreover, RABV VLP and VLP/N mRNA vaccines showed superior capacities to elicit potent germinal centre, long-lived plasma cell and memory B cell responses, which linked to high titre and durable Nab responses. In summary, our data demonstrated that RABV VLP and VLP/N mRNA vaccines could be promising candidates against rabies.
DOI: 10.25549/webster-c100-39850
title: Interviews of city of Los Angeles, Emergency Operations Organization, 1992-08/1992-09

description: Summaries of interviews conducted with personnel from the City of Los Angeles's Emergency Operations Organization, 1992 August - September. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.