cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/webster-c100-39773
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.25721736
title: Transmission characteristics in Tuberculosis by WGS: nationwide cross-sectional surveillance in China

description: China, with the third largest share of global tuberculosis cases, faces a substantial challenge in its healthcare system as a result of the high burden of multidrug-resistant and rifampicin-resistant tuberculosis (MDR/RR-TB). This study employs a genomic epidemiological approach to assess recent tuberculosis transmissions between individuals, identifying potential risk factors and discerning the role of transmitted resistant isolates in the emergence of drug-resistant tuberculosis in China. We conducted a population-based retrospective study on 5052 <i>Mycobacterium tuberculosis</i> (MTB) isolates from 70 surveillance sites using whole genome sequencing (WGS). Minimum spanning tree analysis identified resistance mutations, while epidemiological data analysis pinpointed transmission risk factors. Of the 5052 isolates, 23% (1160) formed 452 genomic clusters, with 85.6% (387) of the transmissions occurring within the same counties. Individuals with younger age, larger family size, new cases, smear positive, and MDR/RR were at higher odds for recent transmission, while higher education (university and above) and occupation as a non-physical workers emerged as protective factors. At least 61.4% (251/409) of MDR/RR-TB were likely a result of recent transmission of MDR/RR isolates, with previous treatment (crude OR =   2.77), smear-positive (cOR =   2.07) and larger family population (cOR = 1.13) established as risk factors. Our findings highlight that local transmission remains the predominant form of TB transmission in China. Correspondingly, drug-resistant tuberculosis is primarily driven by the transmission of resistant tuberculosis isolates. Targeted interventions for high-risk populations to interrupt transmission within the country will likely provide an opportunity to reduce the prevalence of both tuberculosis and drug-resistant tuberculosis.
DOI: 10.6084/m9.figshare.26823720.v1
title: Clinical Immunological Characteristics of Anti-Interferon-γ Autoantibodies Syndrome: A 3 Year Prospective Cohort Study

description: Anti-interferon-γ autoantibodies (AIGAs) syndrome is susceptible to disseminated opportunistic infections due to increased AIGAs, but its clinical immunological characteristics remain unrecognized. We conducted a prospective cohort study between January 2021 and December 2023, recruiting patients with opportunistic infections who were categorized into AIGAs-positive and AIGAs-negative groups. Clinical immunological data and outcomes were documented. A subset of AIGAs-positive patients received glucocorticoid treatment, and its effectiveness was evaluated. A total of 238 patients were enrolled, with 135 AIGAs-positive and 103 AIGAs-negative patients. AIGAs-positive patients showed higher rates of multiple pathogen dissemination, shorter progression-free survival (PFS), and increased exacerbation frequency. They also showed elevated erythrocyte sedimentation rate (ESR), globulin (GLB), immunoglobulin (Ig)G, IgE, and IgG4 levels. Among the 70 AIGAs-positive patients monitored for at least six months, three subtypes were identified: high AIGAs titer with immune damage, high AIGAs titer without immune damage, and low AIGAs titer without immune damage. Of the 55 patients followed for 1 year, decreasing AIGAs titer and immune indices (GLB, IgG, IgE, IgG4) were observed. Among the 31 patients with high AIGAs titer and immune damage treated with low-dose glucocorticoids at the stable phase, reductions were observed in immune indices and AIGAs titer in 67.74% of cases. AIGAs-positive patients exhibit infectious and immunological characteristics. Elevated AIGAs, IgG, IgG4, and IgE indicate abnormal immune damages. AIGAs titer generally decrease over time. Stable-phase AIGAs-positive patients can be categorized into three subtypes, with those having high AIGAs titer and increased immune indices potentially benefitting from glucocorticoid treatment.
DOI: 10.6084/m9.figshare.27697449
title: Distribution of <i>Clostridioides difficile</i> ribotypes and sequence types across humans, animals and food in 13 European countries

description: <i>Clostridioides difficile</i> is a One Health pathogen found in humans, animals, and the environment, with food representing a potential transmission route. One Health studies are often limited to a single country or selected reservoirs and ribotypes. This study provides a varied and accessible collection of <i>C. difficile</i> isolates and sequencing data derived from human, animal, and food sources across 13 European countries. A total of 441 strains (human hospital- and community-associated cases <i>n</i> = 280, animal <i>n</i> = 96, food <i>n</i> = 65) were analysed by ribotyping, toxinotyping and whole-genome sequencing (WGS). We detected 83 sequence types (STs), with ST11 (<i>n</i> = 80 isolates) and ST1 (<i>n</i> = 54 isolates) being the most represented. Several STs included strains originating from all source combinations. Further genomic analysis confirmed close genetic relatedness in some of the STs. Additionally, the genomic analysis identified 10 strains from cryptic clades (C-I to C-III) and 4 of them were mono-toxigenic possessing only a variant form of <i>tcd</i>A gene. Amongst 106 ribotypes, 10 were shared between all 3 sources and 68 were source-specific. Some ribotypes were only found at the intersection of human and food source (RT023, RT027), or between human and animal source (RT009, RT045, RT046). <i>C. difficile</i> ribotypes and STs in Europe were diverse. In this collection, some ribotypes showed potential association with food or animal transmission routes. <i>C. difficile</i> strains from divergent clades CI-III, currently emerging in the human population, were rare and mostly food-associated. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT03503474.
DOI: 10.6084/m9.figshare.27697449.v2
title: Distribution of <i>Clostridioides difficile</i> ribotypes and sequence types across humans, animals and food in 13 European countries

description: <i>Clostridioides difficile</i> is a One Health pathogen found in humans, animals, and the environment, with food representing a potential transmission route. One Health studies are often limited to a single country or selected reservoirs and ribotypes. This study provides a varied and accessible collection of <i>C. difficile</i> isolates and sequencing data derived from human, animal, and food sources across 13 European countries. A total of 441 strains (human hospital- and community-associated cases <i>n</i> = 280, animal <i>n</i> = 96, food <i>n</i> = 65) were analysed by ribotyping, toxinotyping and whole-genome sequencing (WGS). We detected 83 sequence types (STs), with ST11 (<i>n</i> = 80 isolates) and ST1 (<i>n</i> = 54 isolates) being the most represented. Several STs included strains originating from all source combinations. Further genomic analysis confirmed close genetic relatedness in some of the STs. Additionally, the genomic analysis identified 10 strains from cryptic clades (C-I to C-III) and 4 of them were mono-toxigenic possessing only a variant form of <i>tcd</i>A gene. Amongst 106 ribotypes, 10 were shared between all 3 sources and 68 were source-specific. Some ribotypes were only found at the intersection of human and food source (RT023, RT027), or between human and animal source (RT009, RT045, RT046). <i>C. difficile</i> ribotypes and STs in Europe were diverse. In this collection, some ribotypes showed potential association with food or animal transmission routes. <i>C. difficile</i> strains from divergent clades CI-III, currently emerging in the human population, were rare and mostly food-associated. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT03503474.
DOI: 10.25549/webster-c100-39751
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.24720314
title: Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa

description: The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (<i>Mastomys natalensis</i>), and also in two Guinean multimammate mice (<i>Mastomys erythroleucus</i>) in northern Sierra Leone and two rusty-bellied brush-furred mice (<i>Lophuromys sikapusi</i>) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316–374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.
DOI: 10.6084/m9.figshare.24720314.v2
title: Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa

description: The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (<i>Mastomys natalensis</i>), and also in two Guinean multimammate mice (<i>Mastomys erythroleucus</i>) in northern Sierra Leone and two rusty-bellied brush-furred mice (<i>Lophuromys sikapusi</i>) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316–374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.
DOI: 10.6084/m9.figshare.26107971
title: Transcriptome profiles of organ tissues from pigs experimentally infected with African swine fever virus in early phase of infection

description: African swine fever, caused by African swine fever virus (ASFV), is a highly contagious and fatal disease that poses a significant threat to the global pig industry. The limited information on ASFV pathogenesis and ASFV–host interactions has recently prompted numerous transcriptomic studies. However, most of these studies have focused on elucidating the transcriptome profiles of ASFV-infected porcine alveolar macrophages <i>in vitro</i>. Here, we analyzed dynamic transcriptional patterns <i>in vivo</i> in nine organ tissues (spleen, submandibular lymph node, mesenteric lymph node, inguinal lymph node, tonsils, lungs, liver, kidneys, and heart) obtained from pigs in the early stages of ASFV infection (1 and 3 d after viremia). We observed rapid spread of ASFV to the spleen after viremia, followed by broad transmission to the liver and lungs and subsequently, the submandibular and inguinal lymph nodes. Profound variations in gene expression patterns were observed across all organs and at all time-points, providing an understanding of the distinct defence strategies employed by each organ against ASFV infection. All ASFV-infected organs exhibited a collaborative response, activating immune-associated genes such as <i>S100A8</i>, thereby triggering a pro-inflammatory cytokine storm and interferon activation. Functional analysis suggested that ASFV exploits the PI3K-Akt signalling pathway to evade the host immune system. Overall, our findings provide leads into the mechanisms underlying pathogenesis and host immune responses in different organs during the early stages of infection, which can guide further explorations, aid the development of efficacious antiviral strategies against ASFV, and identify valuable candidate gene targets for vaccine development.
DOI: 10.6084/m9.figshare.26107971.v1
title: Transcriptome profiles of organ tissues from pigs experimentally infected with African swine fever virus in early phase of infection

description: African swine fever, caused by African swine fever virus (ASFV), is a highly contagious and fatal disease that poses a significant threat to the global pig industry. The limited information on ASFV pathogenesis and ASFV–host interactions has recently prompted numerous transcriptomic studies. However, most of these studies have focused on elucidating the transcriptome profiles of ASFV-infected porcine alveolar macrophages <i>in vitro</i>. Here, we analyzed dynamic transcriptional patterns <i>in vivo</i> in nine organ tissues (spleen, submandibular lymph node, mesenteric lymph node, inguinal lymph node, tonsils, lungs, liver, kidneys, and heart) obtained from pigs in the early stages of ASFV infection (1 and 3 d after viremia). We observed rapid spread of ASFV to the spleen after viremia, followed by broad transmission to the liver and lungs and subsequently, the submandibular and inguinal lymph nodes. Profound variations in gene expression patterns were observed across all organs and at all time-points, providing an understanding of the distinct defence strategies employed by each organ against ASFV infection. All ASFV-infected organs exhibited a collaborative response, activating immune-associated genes such as <i>S100A8</i>, thereby triggering a pro-inflammatory cytokine storm and interferon activation. Functional analysis suggested that ASFV exploits the PI3K-Akt signalling pathway to evade the host immune system. Overall, our findings provide leads into the mechanisms underlying pathogenesis and host immune responses in different organs during the early stages of infection, which can guide further explorations, aid the development of efficacious antiviral strategies against ASFV, and identify valuable candidate gene targets for vaccine development.
DOI: 10.6084/m9.figshare.27697449.v1
title: Distribution of <i>Clostridioides difficile</i> ribotypes and sequence types across humans, animals and food in thirteen European countries

description: <i>Clostridioides difficile</i> is a One Health pathogen found in humans, animals, and environment, with food representing a potential transmission route. One Health studies are often limited to single country or selected reservoirs and ribotypes. This study provides a varied and accessible collection of <i>C. difficile</i> isolates and sequencing data derived from human, animal, and food sources across thirteen European countries. A total of 441 strains (human hospital and community associated cases n = 280, animal n = 96, food n = 65) were analysed by ribotyping, toxinotyping and whole genome sequencing (WGS). We detected 83 sequence types (STs), with ST11 (n = 80 isolates) and ST1 (n = 54 isolates) being the most represented. Several STs included strains originating from all source combinations. Further genomic analysis confirmed close genetic relatedness in some of the STs. Additionally, genomic analysis identified ten strains from cryptic clades (C-I to C-III) and four of them were mono-toxigenic possessing only a variant form of <i>tcd</i>A gene. Amongst 106 ribotypes, ten were shared between all three sources and 68 were source specific. Some ribotypes were only found at intersection of human and food source (RT023, RT027), or between human and animal source (RT009, RT045, RT046). <i>C. difficile</i> ribotypes and STs in Europe were diverse. In this collection some ribotypes showed potential association with food or animal transmission routes. <i>C. difficile</i> strains from divergent clades CI-III, currently emerging in human population, were rare and mostly food associated.
DOI: 10.6084/m9.figshare.27165114
title: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

description: A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the properties of antibodies elicited by it is crucial for comprehending the impact of NTD mutations on viral fitness and guiding vaccine design. In this study, we find that most of NTD-targeting antibodies isolated from individuals with BA.5/BF.7 breakthrough infection (BTI) are ancestral (wild-type or WT)-reactive and non-neutralizing. Surprisingly, we identified five ultra-potent neutralizing antibodies (NAbs) that can only bind to Omicron but not WT NTD. Structural analysis revealed that they bind to a unique epitope on the N1/N2 loop of NTD and interact with the receptor-binding domain (RBD) via the light chain. These Omicron-specific NAbs achieve neutralization through ACE2 competition and blockage of ACE2-mediated S1 shedding. However, BA.2.86 and BA.2.87.1, which carry insertions or deletions on the N1/N2 loop, can evade these antibodies. Together, we provided a detailed map of the NTD-targeting antibody repertoire in the post-Omicron era, demonstrating their vulnerability to NTD mutations enabled by its evolutionary flexibility, despite their potent neutralization. These results revealed the function of the indels in the NTD of BA.2.86/JN.1 sublineage in evading neutralizing antibodies and highlighted the importance of considering the immunogenicity of NTD in vaccine design.
DOI: 10.6084/m9.figshare.27165114.v1
title: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

description: A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the properties of antibodies elicited by it is crucial for comprehending the impact of NTD mutations on viral fitness and guiding vaccine design. In this study, we find that most of NTD-targeting antibodies isolated from individuals with BA.5/BF.7 breakthrough infection (BTI) are ancestral (wild-type or WT)-reactive and non-neutralizing. Surprisingly, we identified five ultra-potent neutralizing antibodies (NAbs) that can only bind to Omicron but not WT NTD. Structural analysis revealed that they bind to a unique epitope on the N1/N2 loop of NTD and interact with the receptor-binding domain (RBD) via the light chain. These Omicron-specific NAbs achieve neutralization through ACE2 competition and blockage of ACE2-mediated S1 shedding. However, BA.2.86 and BA.2.87.1, which carry insertions or deletions on the N1/N2 loop, can evade these antibodies. Together, we provided a detailed map of the NTD-targeting antibody repertoire in the post-Omicron era, demonstrating their vulnerability to NTD mutations enabled by its evolutionary flexibility, despite their potent neutralization. These results revealed the function of the indels in the NTD of BA.2.86/JN.1 sublineage in evading neutralizing antibodies and highlighted the importance of considering the immunogenicity of NTD in vaccine design.
DOI: 10.25549/webster-c100-40746
title: Power System Major Emergency Report of Civil Disturbance, 1992-06-24

description: A report issued by the City of Los Angeles Power Operating and Maintenance Division, about major emergencies reported between 1992 April 29 - May 2. 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: Department of Water and Power: Power System Major Emergency Report of Civil Disturbance.