cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/webster-c100-39873
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.25676559
title: Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events

description: H6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.
DOI: 10.6084/m9.figshare.25676559.v2
title: Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events

description: H6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.
DOI: 10.6084/m9.figshare.25151901
title: Detecting and genotyping high-risk human papillomavirus among male patients during 2015–2023 in Beijing, China

description: Few studies focused on human papillomavirus (HPV) in male patients. This study aimed to explore the detection rate and genotyping of HPV among male patients in Beijing to provide a reference for formulating prevention strategies for HPV infection. The cross-sectional study was conducted in Beijing Chaoyang Hospital from November 2015 to March 2023. It covered male patients from the urology and dermatology departments. Fifteen high-risk HPV genotypes were detected by the multiplex real-time polymerase chain reaction method. The overall detection rate of HPV was 25.19% (1288/5114, 95% confidence interval [CI] 24.00%−26.38%), of which the single infection rate was 16.99% (869/5114, 95% CI 15.97%−18.05%) and the co-infection rate was 8.19% (419/5114, 95% CI 7.46%−8.98%). The detection rate of HPV was 40.77% (521/1278), 35.58% (58/163), 32.69% (101/309), 31.91% (60/188), 12.63% (299/2367), and 32.35% (131/405) among male patients with balanitis, warts, rash, urethritis, prostatitis, and other urinary inflammation, respectively (<i>P</i> &lt; 0.001). The top five HPV genotypes were HPV-52, HPV-58, HPV-16, HPV-51, and HPV-66. After the first positive HPV test, the proportion of male patients who turned negative was 22.47% within 3 months, 26.40% within 3−6 months, 24.72% within 6−12 months, 17.98% within 12−24 months, and 8.43% more than 24 months. The detection rate of HPV was high among male patients from the urology and dermatology departments in Beijing, which should be considered to develop HPV vaccines with better prevention effects.
DOI: 10.6084/m9.figshare.25151901.v2
title: Detecting and genotyping high-risk human papillomavirus among male patients during 2015–2023 in Beijing, China

description: Few studies focused on human papillomavirus (HPV) in male patients. This study aimed to explore the detection rate and genotyping of HPV among male patients in Beijing to provide a reference for formulating prevention strategies for HPV infection. The cross-sectional study was conducted in Beijing Chaoyang Hospital from November 2015 to March 2023. It covered male patients from the urology and dermatology departments. Fifteen high-risk HPV genotypes were detected by the multiplex real-time polymerase chain reaction method. The overall detection rate of HPV was 25.19% (1288/5114, 95% confidence interval [CI] 24.00%−26.38%), of which the single infection rate was 16.99% (869/5114, 95% CI 15.97%−18.05%) and the co-infection rate was 8.19% (419/5114, 95% CI 7.46%−8.98%). The detection rate of HPV was 40.77% (521/1278), 35.58% (58/163), 32.69% (101/309), 31.91% (60/188), 12.63% (299/2367), and 32.35% (131/405) among male patients with balanitis, warts, rash, urethritis, prostatitis, and other urinary inflammation, respectively (<i>P</i> &lt; 0.001). The top five HPV genotypes were HPV-52, HPV-58, HPV-16, HPV-51, and HPV-66. After the first positive HPV test, the proportion of male patients who turned negative was 22.47% within 3 months, 26.40% within 3−6 months, 24.72% within 6−12 months, 17.98% within 12−24 months, and 8.43% more than 24 months. The detection rate of HPV was high among male patients from the urology and dermatology departments in Beijing, which should be considered to develop HPV vaccines with better prevention effects.
DOI: 10.6084/m9.figshare.25676559.v1
title: Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events

description: H6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.
DOI: 10.25549/webster-c100-45863
title: Incident and deployment data, 1992-04/1992-05

description: Unusual Occurrence Situation Report summaries for the period between 1992 April 29 - May 3. 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.26212880
title: A novel small RNA PhaS contributes to polymyxin B-heteroresistance in carbapenem-resistant <i>Klebsiella pneumoniae</i>

description: In recent years, polymyxin has been used as a last-resort therapy for carbapenem-resistant bacterial infections. The emergence of heteroresistance (HR) to polymyxin hampers the efficacy of polymyxin treatment by amplifying resistant subpopulation. However, the mechanisms behind polymyxin HR remain unclear. Small noncoding RNAs (sRNAs) play an important role in regulating drug resistance. The purpose of this study was to investigate the effects and mechanisms of sRNA on polymyxin B (PB)-HR in carbapenem-resistant <i>Klebsiella pneumoniae</i>. In this study, a novel sRNA PhaS was identified by transcriptome sequencing. PhaS expression was elevated in the PB heteroresistant subpopulation. Overexpression and deletion of PhaS were constructed in three carbapenem-resistant <i>K. pneumoniae</i> strains. Population analysis profiling, growth curve, and time-killing curve analysis showed that PhaS enhanced PB-HR. In addition, we verified that PhaS directly targeted <i>phoP</i> through the green fluorescent protein reporter system. PhaS promoted the expression of <i>phoP</i>, thereby encouraging the expression of downstream genes <i>pmrD</i> and <i>arnT</i>. This upregulation of <i>arnT</i> promoted the 4-amino-4-deoxyL-arabinosaccharide (L-Ara4N) modification of lipid A in PhaS overexpressing strains, thus enhancing PB-HR. Further, within the promoter region of PhaS, specific PhoP recognition sites were identified. ONPG assays and RT-qPCR analysis confirmed that PhaS expression was positively modulated by PhoP and thus up-regulated by PB stimulation. To sum up, a novel sRNA enhancing PB-HR was identified and a positive feedback regulatory pathway of sRNA-PhoP/Q was demonstrated in the study. This helps to provide a more comprehensive and clear understanding of the underlying mechanisms behind polymyxin HR in carbapenem-resistant <i>K. pneumoniae</i>.
DOI: 10.6084/m9.figshare.26212880.v2
title: A novel small RNA PhaS contributes to polymyxin B-heteroresistance in carbapenem-resistant <i>Klebsiella pneumoniae</i>

description: In recent years, polymyxin has been used as a last-resort therapy for carbapenem-resistant bacterial infections. The emergence of heteroresistance (HR) to polymyxin hampers the efficacy of polymyxin treatment by amplifying resistant subpopulation. However, the mechanisms behind polymyxin HR remain unclear. Small noncoding RNAs (sRNAs) play an important role in regulating drug resistance. The purpose of this study was to investigate the effects and mechanisms of sRNA on polymyxin B (PB)-HR in carbapenem-resistant <i>Klebsiella pneumoniae</i>. In this study, a novel sRNA PhaS was identified by transcriptome sequencing. PhaS expression was elevated in the PB heteroresistant subpopulation. Overexpression and deletion of PhaS were constructed in three carbapenem-resistant <i>K. pneumoniae</i> strains. Population analysis profiling, growth curve, and time-killing curve analysis showed that PhaS enhanced PB-HR. In addition, we verified that PhaS directly targeted <i>phoP</i> through the green fluorescent protein reporter system. PhaS promoted the expression of <i>phoP</i>, thereby encouraging the expression of downstream genes <i>pmrD</i> and <i>arnT</i>. This upregulation of <i>arnT</i> promoted the 4-amino-4-deoxyL-arabinosaccharide (L-Ara4N) modification of lipid A in PhaS overexpressing strains, thus enhancing PB-HR. Further, within the promoter region of PhaS, specific PhoP recognition sites were identified. ONPG assays and RT-qPCR analysis confirmed that PhaS expression was positively modulated by PhoP and thus up-regulated by PB stimulation. To sum up, a novel sRNA enhancing PB-HR was identified and a positive feedback regulatory pathway of sRNA-PhoP/Q was demonstrated in the study. This helps to provide a more comprehensive and clear understanding of the underlying mechanisms behind polymyxin HR in carbapenem-resistant <i>K. pneumoniae</i>.
DOI: 10.6084/m9.figshare.26762543
title: Insights into the evolution, virulence and speciation of <i>Babesia MO1</i> and <i>Babesia divergens</i> through multiomics analyses

description: Babesiosis, caused by protozoan parasites of the genus <i>Babesia</i>, is an emerging tick-borne disease of significance for both human and animal health. <i>Babesia</i> parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of new <i>Babesia</i> species underscores the ongoing risk of zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental changes. One such pathogen, <i>Babesia MO1</i>, previously implicated in severe cases of human babesiosis in the United States, was initially considered a subspecies of <i>B. divergens</i>, the predominant agent of human babesiosis in Europe. Here we report comparative multiomics analyses of <i>B. divergens</i> and <i>B. MO1</i> that offer insight into their biology and evolution. Our analysis shows that despite their highly similar genomic sequences, substantial genetic and genomic divergence occurred throughout their evolution resulting in major differences in gene functions, expression and regulation, replication rates and susceptibility to antiparasitic drugs. Furthermore, both pathogens have evolved distinct classes of multigene families, crucial for their pathogenicity and adaptation to specific mammalian hosts. Leveraging genomic information for <i>B. MO1</i>, <i>B. divergens</i>, and other members of the Babesiidae family within Apicomplexa provides valuable insights into the evolution, diversity, and virulence of these parasites. This knowledge serves as a critical tool in preemptively addressing the emergence and rapid transmission of more virulent strains.
DOI: 10.6084/m9.figshare.26762543.v2
title: Insights into the evolution, virulence and speciation of <i>Babesia MO1</i> and <i>Babesia divergens</i> through multiomics analyses

description: Babesiosis, caused by protozoan parasites of the genus <i>Babesia</i>, is an emerging tick-borne disease of significance for both human and animal health. <i>Babesia</i> parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of new <i>Babesia</i> species underscores the ongoing risk of zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental changes. One such pathogen, <i>Babesia MO1</i>, previously implicated in severe cases of human babesiosis in the United States, was initially considered a subspecies of <i>B. divergens</i>, the predominant agent of human babesiosis in Europe. Here we report comparative multiomics analyses of <i>B. divergens</i> and <i>B. MO1</i> that offer insight into their biology and evolution. Our analysis shows that despite their highly similar genomic sequences, substantial genetic and genomic divergence occurred throughout their evolution resulting in major differences in gene functions, expression and regulation, replication rates and susceptibility to antiparasitic drugs. Furthermore, both pathogens have evolved distinct classes of multigene families, crucial for their pathogenicity and adaptation to specific mammalian hosts. Leveraging genomic information for <i>B. MO1</i>, <i>B. divergens</i>, and other members of the Babesiidae family within Apicomplexa provides valuable insights into the evolution, diversity, and virulence of these parasites. This knowledge serves as a critical tool in preemptively addressing the emergence and rapid transmission of more virulent strains.
DOI: 10.25549/webster-c100-78461
title: After-action reporting for April/May riots, 1992

description: After-action reporting for April/May riots, Operations - Bureau of Special Investigation, 1992. PART OF SERIES: Included in the series are internal documents produced by the LAPD, which aided the Webster Commission in its assessment of the Department's operations. Materials include copies of the Watch Commander's Daily Reports between October, 1991 and May, 1992; critiques and after-action reports on the riots issued by each LAPD bureau; and correspondence regarding personnel and budget matters, crime statistics, and several Department-initiated programs. Also included are several documents, including schedules, press releases, and memoranda, that were issued by the office of Los Angeles Mayor Tom Bradley regarding the verdicts in the Rodney King case.
DOI: 10.6084/m9.figshare.26042178.v1
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.26762543.v1
title: Insights Into the Evolution, Virulence and Speciation of <i>Babesia MO1</i> and <i>Babesia divergens</i> Through Multiomics Analyses

description: Babesiosis, caused by protozoan parasites of the genus <i>Babesia</i>, is an emerging tick-borne disease of significance for both human and animal health. <i>Babesia</i> parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of new <i>Babesia</i> species underscores the ongoing risk of zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental changes. One such pathogen, <i>Babesia MO1</i>, previously implicated in severe cases of human babesiosis in the United States, was initially considered a subspecies of <i>B. divergens</i>, the predominant agent of human babesiosis in Europe. Here we report comparative multiomics analyses of <i>B. divergens</i> and <i>B. MO1</i> that offer insight into their biology and evolution. Our analysis shows that despite their highly similar genomic sequences, substantial genetic and genomic divergence occurred throughout their evolution resulting in major differences in gene functions, expression and regulation, replication rates and susceptibility to antiparasitic drugs. Furthermore, both pathogens have evolved distinct classes of multigene families, crucial for their pathogenicity and adaptation to specific mammalian hosts. Leveraging genomic information for <i>B. MO1</i>, <i>B. divergens</i>, and other members of the Babesiidae family within Apicomplexa provides valuable insights into the evolution, diversity, and virulence of these parasites. This knowledge serves as a critical tool in preemptively addressing the emergence and rapid transmission of more virulent strains.