cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24720416.v2
title: Viral diversity in wild and urban rodents of Yunnan Province, China

description: Rodents represent over 40% of known mammal species and are found in various terrestrial habitats. They are significant reservoirs for zoonotic viruses, including harmful pathogens such as arenaviruses and hantaviruses, yet knowledge of their hosts and distributions is limited. Therefore, characterizing the virome profile in these animals is invaluable for outbreak preparedness, especially in potential hotspots of mammal diversity. This study included 681 organs from 124 rodents and one Chinese tree shrew collected from Yunnan Province, China, during 2020-2021. Metagenomic analysis revealed unique features of mammalian viruses in rodent organs across habitats with varying human disturbances. <i>R. tanezumi</i> in locations with high anthropogenic disturbance exhibited the highest mammal viral diversity, with spleen and lung samples showing the highest diversities for these viruses at the organ level. Mammal viral diversity for both commensal and non-commensal rats was identified to positively correlate with landscape disturbance. Some virus families were associated with particular organs or host species, suggesting tropism for these pathogens. Notably, known and novel viral species that are likely to infect humans were identified. <i>R. tanezumi</i> was identified as a reservoir and carrier for various zoonotic viruses, including porcine bocavirus, hantavirus, cardiovirus, and lyssavirus. These findings highlight the influence of rodent community composition and anthropogenic activities on diverse virome profiles, with <i>R. tanezumi</i> as an important reservoir for zoonotic viruses.
DOI: 10.6084/m9.figshare.26196892.v1
title: Mycolyltransferase is important for biofilm formation and pathogenesis of <i>Tsukamurella</i> keratitis

description: <i>Tsukamurella</i>, a group of multi-drug resistant, Gram-positive, aerobic, and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the pathogenesis of <i>Tsukamurella</i> keratitis is largely unknown. To address this, we used New Zealand White rabbits to develop the first eye infection model and conducted <i>in vitro</i> tests to study the pathogenesis mechanisms of <i>Tsukamurella</i>. There is increasing evidence that biofilms play a significant role in ocular infections, leading us to hypothesize that biofilm formation is crucial for effective <i>Tsukamurella</i> infection. In order to look for potential candidate genes which are important in biofilm formation and <i>Tsukamurella</i> keratitis. We performed genome sequencing of two ocular isolates, <i>T. pulmonis</i>-PW1004 and <i>T. tyrosinosolvens</i>-PW899, to identify potential virulence factors. Through <i>in vitro</i> and <i>in vivo</i> studies, we characterized their biological roles in mediating <i>Tsukamurella</i> keratitis. Our findings confirmed that <i>Tsukamurella</i> is an ocular pathogen by fulfilling Koch's postulates, and using genome sequence data, we identified <i>tmytC,</i> encoding a mycolyltransferase, as a crucial gene in biofilm formation and causing <i>Tsukamurella</i> keratitis in the rabbit model. This is the first report demonstrating the novel role of mycolyltransferase in causing ocular infections. Overall, our findings contribute to a better understanding of <i>Tsukamurella</i> pathogenesis and provide a potential target for treatment. Specific inhibitors targeting TmytC could serve as an effective treatment option for <i>Tsukamurella</i> infections.
DOI: 10.6084/m9.figshare.27629318
title: The dissemination of multidrug-resistant and hypervirulent <i>Klebsiella pneumoniae</i> clones across the Kingdom of Saudi Arabia

description: <i>Klebsiella pneumoniae</i> is a Gram-negative bacterium associated with a wide range of community- and hospital-acquired infections. The emergence of clonal hypervirulent strains resistant to last-resort antimicrobial agents has become a global concern. The Kingdom of Saudi Arabia (KSA), with its diverse population and high tourism traffic, serves as a platform where the spread of multidrug-resistant (MDR) strains are facilitated. However, the knowledge of epidemiology and population diversity of MDR <i>K. pneumoniae</i> in KSA is scarce. We conducted a comprehensive genomic survey on 352 MDR <i>K. pneumoniae</i> isolates systematically collected from bloodstream and urinary tract infections in 34 hospitals across 15 major cities in KSA during 2022 and 2023. Whole-genome sequencing on the isolates was performed, followed by genomic epidemiology and phylodynamic analysis. Our study revealed a dynamic population characterized by the rapid expansion of several dominant clones, including, ST2096, ST147, and ST231, which were estimated to have emerged within the past decade. These clones exhibited widespread dissemination across hospitals and were genetically linked to global strains, particularly from the Middle East and South Asia. All major clones harboured plasmid-borne ESBLs and carbapenemase genes, with plasmidome analysis identifying multiple IncH, IncA/C and IncL plasmids underlying the MDR-hypervirulent phenotype. These plasmids were shared between major clones and became acquired on the same time scales as the expansion of the dominant clones. Our results report ST2096 as an emerging MDR-hypervirulent clone, emphasizing the need for monitoring of the circulating clones and their plasmid content in the KSA and broader West Asia.
DOI: 10.6084/m9.figshare.27629318.v2
title: The dissemination of multidrug-resistant and hypervirulent <i>Klebsiella pneumoniae</i> clones across the Kingdom of Saudi Arabia

description: <i>Klebsiella pneumoniae</i> is a Gram-negative bacterium associated with a wide range of community- and hospital-acquired infections. The emergence of clonal hypervirulent strains resistant to last-resort antimicrobial agents has become a global concern. The Kingdom of Saudi Arabia (KSA), with its diverse population and high tourism traffic, serves as a platform where the spread of multidrug-resistant (MDR) strains are facilitated. However, the knowledge of epidemiology and population diversity of MDR <i>K. pneumoniae</i> in KSA is scarce. We conducted a comprehensive genomic survey on 352 MDR <i>K. pneumoniae</i> isolates systematically collected from bloodstream and urinary tract infections in 34 hospitals across 15 major cities in KSA during 2022 and 2023. Whole-genome sequencing on the isolates was performed, followed by genomic epidemiology and phylodynamic analysis. Our study revealed a dynamic population characterized by the rapid expansion of several dominant clones, including, ST2096, ST147, and ST231, which were estimated to have emerged within the past decade. These clones exhibited widespread dissemination across hospitals and were genetically linked to global strains, particularly from the Middle East and South Asia. All major clones harboured plasmid-borne ESBLs and carbapenemase genes, with plasmidome analysis identifying multiple IncH, IncA/C and IncL plasmids underlying the MDR-hypervirulent phenotype. These plasmids were shared between major clones and became acquired on the same time scales as the expansion of the dominant clones. Our results report ST2096 as an emerging MDR-hypervirulent clone, emphasizing the need for monitoring of the circulating clones and their plasmid content in the KSA and broader West Asia.
DOI: 10.25549/webster-c100-39585
title: Inter-agency team, final report, 1992

description: Inter-Agency Team Final Report, Appendix: Local police departments, materials collected by the Inter-Agency Team regarding the policies, procedures, and operations of several local police departments aside from the Los Angeles Police Department, 1992. 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.26196892
title: Mycolyltransferase is important for biofilm formation and pathogenesis of <i>Tsukamurella</i> keratitis

description: <i>Tsukamurella</i>, a group of multi-drug resistant, Gram-positive, aerobic, and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the pathogenesis of <i>Tsukamurella</i> keratitis is largely unknown. To address this, we used New Zealand White rabbits to develop the first eye infection model and conducted <i>in vitro</i> tests to study the pathogenesis mechanisms of <i>Tsukamurella</i>. There is increasing evidence that biofilms play a significant role in ocular infections, leading us to hypothesize that biofilm formation is crucial for effective <i>Tsukamurella</i> infection. In order to look for potential candidate genes which are important in biofilm formation and <i>Tsukamurella</i> keratitis. We performed genome sequencing of two ocular isolates, <i>T. pulmonis</i>-PW1004 and <i>T. tyrosinosolvens</i>-PW899, to identify potential virulence factors. Through <i>in vitro</i> and <i>in vivo</i> studies, we characterized their biological roles in mediating <i>Tsukamurella</i> keratitis. Our findings confirmed that <i>Tsukamurella</i> is an ocular pathogen by fulfilling Koch's postulates, and using genome sequence data, we identified <i>tmytC,</i> encoding a mycolyltransferase, as a crucial gene in biofilm formation and causing <i>Tsukamurella</i> keratitis in the rabbit model. This is the first report demonstrating the novel role of mycolyltransferase in causing ocular infections. Overall, our findings contribute to a better understanding of <i>Tsukamurella</i> pathogenesis and provide a potential target for treatment. Specific inhibitors targeting TmytC could serve as an effective treatment option for <i>Tsukamurella</i> infections.
DOI: 10.6084/m9.figshare.26946026.v1
title: Genetic microevolution of clinical <i>Candida auris</i> with reduced Amphotericin B sensitivity in China

description: The global rate of Amphotericin B (AmB) resistance in <i>Candida auris</i> has surpassed 12%. However, there is limited data on available clinical treatments and microevolutionary analyses concerning reduced AmB sensitivity. In this study, we collected 18 <i>C. auris</i> isolates from five patients between 2019 and 2022. We employed clinical data mining, genomic, and transcriptomic analyses to identify genetic evolutionary features linked to reduced AmB sensitivity in these isolates during clinical treatment. We identified six isolates with a minimum inhibitory concentration (MIC) of AmB below 0.5 µg/mL (AmB<sup>0.5</sup>) and 12 isolates with an AmB-MIC of 1 µg/mL (AmB<sup>1</sup>) or ≥ 2 µg/mL (AmB<sup>2</sup>). All five patients received 24-hour AmB (5 mg/L) bladder irrigation treatment. Evolutionary analyses revealed an <i>ERG3</i> (c923t) mutation in AmB<sup>1</sup> <i>C. auris</i>. Additionally, AmB<sup>2</sup> <i>C. auris</i> was found to contain a t2831c mutation in the <i>RAD2</i> gene. In the AmB<sup>1</sup> group, membrane lipid-related gene expression (<i>ERG1, ERG2, ERG13,</i> and <i>ERG24</i>) was upregulated, while in the AmB<sup>2</sup> group, expression of DNA-related genes (e.g. <i>DNA2</i> and <i>PRI1</i>) was up-regulated. In a series of <i>C.auris</i> strains with reduced susceptibility to AmB, five key genes were identified: two upregulated (<i>IFF9</i> and <i>PGA6)</i> and three downregulated (<i>HGT7, HGT13,</i>and <i>PRI32)</i>. In this study, we demonstrate the microevolution of reduced AmB sensitivity in vivo and further elucidate the relationship between reduced AmB sensitivity and low-concentration AmB bladder irrigation. These findings offer new insights into potential antifungal drug targets and clinical markers for the “super fungus”, <i>C. auris</i>.
DOI: 10.6084/m9.figshare.25379339
title: Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China

description: In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a “long-tailed” shape in the COVID-19  outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work. HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV First long-term monitoring of SARS-CoV-2 in wastewater in Mainland China COVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containment Wastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methods Triple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV
DOI: 10.6084/m9.figshare.25379339.v1
title: Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China

description: In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a “long-tailed” shape in the COVID-19  outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work. HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV First long-term monitoring of SARS-CoV-2 in wastewater in Mainland China COVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containment Wastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methods Triple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV
DOI: 10.6084/m9.figshare.26058913
title: Deciphering lung granulomas in HIV & TB co-infection: unveiling macrophages aggregation with IL6R/STAT3 activation

description: Tuberculosis (TB) remains a leading cause of mortality among individuals coinfected with HIV, characterized by progressive pulmonary inflammation. Despite TB’s hallmark being focal granulomatous lung lesions, our understanding of the histopathological features and regulation of inflammation in HIV & TB coinfection remains incomplete. In this study, we aimed to elucidate these histopathological features through an immunohistochemistry analysis of HIV & TB co-infected and TB patients, revealing marked differences. Notably, HIV & TB granulomas exhibited aggregation of CD68 + macrophage (Mφ), while TB lesions predominantly featured aggregation of CD20+ B cells, highlighting distinct immune responses in coinfection. Spatial transcriptome profiling further elucidated CD68+ Mφ aggregation in HIV & TB, accompanied by activation of IL6 pathway, potentially exacerbating inflammation. Through multiplex immunostaining, we validated two granuloma types in HIV & TB versus three in TB, distinguished by cell architecture. Remarkably, in the two types of HIV & TB granulomas, CD68 + Mφ highly co-expressed IL6R/pSTAT3, contrasting TB granulomas’ high IFNGRA/SOCS3 expression, indicating different signaling pathways at play. Thus, activation of IL6 pathway may intensify inflammation in HIV & TB-lungs, while SOCS3-enriched immune microenvironment suppresses IL6-induced over-inflammation in TB. These findings provide crucial insights into HIV & TB granuloma formation, shedding light on potential therapeutic targets, particularly for granulomatous pulmonary under HIV & TB co-infection. Our study emphasizes the importance of a comprehensive understanding of the immunopathogenesis of HIV & TB coinfection and suggests potential avenues for targeting IL6 signaling with SOCS3 activators or anti-IL6R agents to mitigate lung inflammation in HIV & TB coinfected individuals.
DOI: 10.6084/m9.figshare.26058913.v1
title: Deciphering lung granulomas in HIV & TB co-infection: unveiling macrophages aggregation with IL6R/STAT3 activation

description: Tuberculosis (TB) remains a leading cause of mortality among individuals coinfected with HIV, characterized by progressive pulmonary inflammation. Despite TB’s hallmark being focal granulomatous lung lesions, our understanding of the histopathological features and regulation of inflammation in HIV & TB coinfection remains incomplete. In this study, we aimed to elucidate these histopathological features through an immunohistochemistry analysis of HIV & TB co-infected and TB patients, revealing marked differences. Notably, HIV & TB granulomas exhibited aggregation of CD68 + macrophage (Mφ), while TB lesions predominantly featured aggregation of CD20+ B cells, highlighting distinct immune responses in coinfection. Spatial transcriptome profiling further elucidated CD68+ Mφ aggregation in HIV & TB, accompanied by activation of IL6 pathway, potentially exacerbating inflammation. Through multiplex immunostaining, we validated two granuloma types in HIV & TB versus three in TB, distinguished by cell architecture. Remarkably, in the two types of HIV & TB granulomas, CD68 + Mφ highly co-expressed IL6R/pSTAT3, contrasting TB granulomas’ high IFNGRA/SOCS3 expression, indicating different signaling pathways at play. Thus, activation of IL6 pathway may intensify inflammation in HIV & TB-lungs, while SOCS3-enriched immune microenvironment suppresses IL6-induced over-inflammation in TB. These findings provide crucial insights into HIV & TB granuloma formation, shedding light on potential therapeutic targets, particularly for granulomatous pulmonary under HIV & TB co-infection. Our study emphasizes the importance of a comprehensive understanding of the immunopathogenesis of HIV & TB coinfection and suggests potential avenues for targeting IL6 signaling with SOCS3 activators or anti-IL6R agents to mitigate lung inflammation in HIV & TB coinfected individuals.
DOI: 10.6084/m9.figshare.27629318.v1
title: The Dissemination of Multidrug-Resistant and Hypervirulent <i>Klebsiella pneumoniae</i> Clones Across the Kingdom of Saudi Arabia

description: <i>Klebsiella pneumoniae</i> is a Gram-negative bacterium associated with a wide range of community- and hospital-acquired infections. The emergence of clonal hypervirulent strains resistant to last-resort antimicrobial agents has become a global concern. The Kingdom of Saudi Arabia (KSA), with its diverse population and high tourism traffic, serves as a platform where the spread of multidrug-resistant (MDR) strains are facilitated. However, the knowledge of epidemiology and population diversity of MDR <i>K. pneumoniae</i> in KSA is scarce. We conducted a comprehensive genomic survey on 352 MDR <i>K. pneumoniae</i> isolates systematically collected from bloodstream and urinary tract infections in 34 hospitals across 15 major cities in KSA during 2022 and 2023. Whole-genome sequencing on the isolates was performed, followed by genomic epidemiology and phylodynamic analysis. Our study revealed a dynamic population characterized by the rapid expansion of several dominant clones, including, ST2096, ST147, and ST231, which were estimated to have emerged within the past decade. These clones exhibited widespread dissemination across hospitals and were genetically linked to global strains, particularly from the Middle East and South Asia. All major clones harbored plasmid-borne ESBLs and carbapenemase genes, with plasmidome analysis identifying multiple IncH, IncA/C and IncL plasmids underlying the MDR-hypervirulent phenotype. These plasmids were shared between major clones and became acquired on the same time scales as the expansion of the dominant clones. Our results report ST2096 as an emerging MDR-hypervirulent clone, emphasizing the need for monitoring of the circulating clones and their plasmid content in the KSA and broader West Asia.
DOI: 10.25549/webster-c100-32897
title: Roundtable 5, discussion, 1992-06-03

description: Roundtable discussion between Deputy Commissioner Dwight ("Spike") Helmick Jr., Assistant Commissioner for Field Operations Bob Rengstorff, and Chief Edward Gomez of the California Highway Patrol. The discussion centers on the Highway Patrol's tactical planning measures for emergency situations, and the planning measures it undertook for the civil disturbance, 1992 June 3. PART OF SERIES: After the violence had subsided, the Webster Commission met of a variety of public officials, law enforcement personnel, activists, and community leaders to discuss the rioting, its root causes, and the adequacy of the LAPD's response. The series includes summaries of these meetings, including questions and comments along of the interviewers' own mental impressions, conclusions, and opinions. Materials are arranged in alphabetical order, according to the last name of the interviewee.