bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of Mpox Cases, and Tecovirimat and JYNNEOS Utilization, Alameda County, California, June-October 2022
Authors: Ouyang Megan L. , Marusinec Rachel , Bayard Paul J. , Edmunds Magdalen , Johnson Mark , Lai Sunny , Menker Kaeb , Moore Curtis , Moss Nicholas , Nguyen Mychi , Peña April , Rajagopal Sumanth , Shemsu Munira , Sheppard Ieshia , Slome Sally , Tang Michele , Trivedi Kavita K. , Yette Emily , Dunne Eileen F. , Ayala George , Chitnis Amit 
Published: July 2024

Context:
The 2022 United States mpox outbreak disproportionately affected racial and ethnic minority gay, bisexual, and other men who have sex with men.

Program:
We utilized surveillance data and vaccination registries to determine whether populations most impacted by mpox in Alameda County received JYNNEOS vaccines and tecovirimat (TPOXX) during June 1-October 31, 2022.

Implementation:
Alameda County Public Health Department responded to the mpox epidemic through partnerships with local health care providers who serve communities disproportionately affected by mpox.

Evaluation:
During June 1-October 31, 2022, a total of 242 mpox cases were identified in Alameda County. Mpox incidence rates per 100 000 were highest among Black/African American (35.7; 95% confidence interval [CI], 26.8-46.5) and Hispanic/Latinx (25.1; CI, 20.1-30.9) residents, compared to Asian (3.8; CI, 2.3-5.9) and White (10.5; CI, 7.7-13.9) residents. Most confirmed cases were identified as gay, lesbian, or same-gender-loving (134, 67.3%) and bisexual (31, 15.6%); 226 (93.8%) cases were male. Sixty-nine (28.5%) mpox patients received TPOXX. There were no statistically significant differences in demographic and clinical characteristics of mpox cases when compared by TPOXX receipt status. JYNNEOS vaccine was received by 8277 Alameda County residents. The largest proportion of vaccinees were White residents (40.2%). Administration rates per 100 000 men who have sex with men were lowest among Asian and Hispanic/Latinx individuals, at 8779 (CI, 8283-9296) and 14 953 (CI, 14 156-15 784), respectively. Black/African American and Hispanic/Latinx males had the lowest vaccination-to-case ratios at 16.7 and 14.8, respectively.

Discussion:
Mpox disproportionately affected Black/African American and Hispanic/Latinx men who have sex with men in Alameda County. Strong partnerships with local health care providers ensured that persons with mpox received TPOXX treatment when indicated. However, higher JYNNEOS vaccine uptake in Black and Latinx communities needs improvement through ongoing and meaningful engagement with Black/African American and Hispanic/Latinx gay, bisexual, and transgender communities.
Estimating the Prevalence of Injection Drug Use Among Acute Hepatitis C Cases From a National Surveillance System: Application of Random Forest-Based Multiple Imputation
Authors: Yin Shaoman , Ly Kathleen N. , Barker Laurie K. , Bixler Danae , Thompson Nicola D. , Gupta Neil 
Published: July 2024

Background:
Injection drug use (IDU) is a major contributor to the syndemic of viral hepatitis, human immunodeficiency virus, and drug overdose. However, information on IDU is frequently missing in national viral hepatitis surveillance data, which limits our understanding of the full extent of IDU-associated infections. Multiple imputation by chained equations (MICE) has become a popular approach to address missing data, but its application for IDU imputation is less studied.

Methods:
Using the 2019-2021 National Notifiable Diseases Surveillance System acute hepatitis C case data and publicly available county-level measures, we evaluated listwise deletion (LD) and 3 models imputing missing IDU data through MICE: parametric logistic regression, semi-parametric predictive mean matching (PMM), and nonparametric random forest (RF) (both standard RF [sRF] and fast implementation of RF [fRF]).

Results:
The estimated IDU prevalence among acute hepatitis C cases increased from 63.5% by LD to 65.1% by logistic regression, 66.9% by PMM, 76.0% by sRF, and 85.1% by fRF. Evaluation studies showed that RF-based MICE imputation, especially fRF, has the highest accuracy (as measured by smallest raw bias, percent bias, and root mean square error) and highest efficiency (as measured by smallest 95% confidence interval width) compared to LD and other models. Sensitivity analyses indicated that fRF remained robust when data were missing not at random.

Conclusion:
Our analysis suggested that RF-based MICE imputation, especially fRF, could be a valuable approach for addressing missing IDU data in the context of population-based surveillance systems like National Notifiable Diseases Surveillance System. The inclusion of imputed IDU data may enhance the effectiveness of future surveillance and prevention efforts for the IDU-driven syndemic.
Epidemiology of Chlamydia trachomatis and Repeat Positivity Following Detection in New York State
Authors: Currenti Salvatore , O’Grady Thomas , Bomma Srikanth , Gurram Namratha , Miranda Wilson , Hart-Malloy Rachel 
Published: July 2024

Background:
In New York State, excluding New York City, chlamydia remains a persistent health concern. Our aim was to characterize chlamydia epidemiology and identify groups at higher risk of repeat positivity to inform targeted public health interventions.

Methods:
We analyzed demographic and clinical data of laboratory-confirmed chlamydia cases in New York State from 2015 to 2019. Repeat positivity was defined as a second positive chlamydia test within 31 to 365 days of the initial positive test. We compared characteristics of individuals with single and repeat positivity and evaluated associations with repeat positivity using multivariable logistic regression models.

Results:
During the study period, 176 273 individuals were diagnosed with chlamydia, with 17 253 experiencing repeat positivity. Repeat positivity was more common among individuals assigned female at birth. Key predictors of repeat positivity among females included non-Hispanic Black (adjusted odds ratio [aOR]: 1.33; 95% confidence interval [CI], 1.27-1.40) race/ethnicity, ages 13 to 19 (aOR: 1.62; 95% CI, 1.55-1.69), prior sexually transmitted infection (STI) diagnosis (aOR: 1.24; 95% CI, 1.18-1.31), symptomatic examination (aOR: 1.07; 95% CI, 1.02-1.13), and county/community (aOR: 1.10; 95% CI, 1.05-1.15) or private/public (aOR: 1.18; 95% CI, 1.11-1.25) provider. Among males, predictors included non-Hispanic Black (aOR: 1.57; 95% CI, 1.45-1.70) race/ethnicity, ages 13 to 19 (aOR: 1.27; 95% CI, 1.17-1.38), HIV coinfection (aOR: 1.30; 95% CI, 1.10-1.54), prior STI diagnosis (aOR: 1.31; 95% CI, 1.20-1.43), extragenital infection site (aOR: 2.59; 95% CI, 2.27-2.95), symptomatic examination (aOR: 1.21; 95% CI, 1.12-1.31), and county/community health (aOR: 1.09; 95% CI, 1.02-1.17) provider.

Conclusions:
Our findings provide valuable insights for sexual health interventions to prevent chlamydia transmission and recurrence. Prioritizing resources for prevention interventions and tailored sexual health promotion among non-Hispanic Black individuals is crucial. Additionally, targeted STI prevention efforts are needed for males who have sex with men and those initially diagnosed with extragenital infection. Research is warranted on STI prevention among people living with HIV or at high risk of HIV infection. Strengthening prevention strategies through Expedited Partner Therapy and sexual health education for individuals at risk of repeat positivity could enhance prevention efforts.
Number of Pressurized Intraperitoneal Aerosol Chemotherapy (PIPAC) Treatments is Associated with Longer Survival
Authors: Orgad Ran , Bakrin Naoual , Bonnefoy Isabelle , Villeneuve Laurent , Alyami Mohamad , Alhadeedi Omar , Glehen Olivier , Kepenekian Vahan 
Published: July 2024

Objective:
To analyze the reasons for stopping pressurized intraperitoneal aerosolized chemotherapy (PIPAC) delivered for unresectable peritoneal surface malignancies (PSM) and to determine survival in a large patient cohort of an experienced PIPAC center.

Background:
PIPAC alone or combined with systemic chemotherapy was developed to palliatively treat unresectable PSM. Safety, tolerance and promising survival results were already reported, but the reasons for stopping treatment remain unclear and the influence of the number of PIPAC procedures on prognosis has not been evaluated.

Methods:
A retrospective analysis of PIPAC procedures from a prospectively maintained single institution PSM database was conducted from January 2016 to January 2023.

Results:
A total of 346 patients underwent 1200 PIPAC treatments in the defined time period. Two-thirds of the patients completed 3 or more PIPAC procedures, and 2 patients had more than 15 treatment procedures. Reasons for PIPAC cessation were disease progression or complication (56%), reorientation to a potential curative procedure (19%), surgical complications of the procedure (13%), death between procedures (8%) and patient request (3%). PSM origin and receiving 3 or more PIPAC treatments were independently correlated with better survival in the overall population, in the group of ultimately unresectable PSM and after propensity score weighting.

Conclusion:
The main reason for stopping PIPAC treatment in palliative management of PSM is disease progression. When 3 or more PIPAC procedures can be delivered in combination to systemic chemotherapy, survival is significantly improved. Its use should be validated by prospective studies.
Massive presence of the invasivePolydora websteri(Polychaeta: Spionidae) in the North Adriatic Sea (Mediterranean Sea)
Authors: Lezzi Marco , Mazziotti Cristina 
Published: July 2024

AbstractIn recent decades, the Mediterranean Sea has experienced a marked escalation in the introduction of non-native and invasive marine species.The global expansion of aquaculture, coupled with the increased movement of commercial species, has raised concerns about the potential for introducing parasites into new environments, posing a growing threat to marine ecosystems.Polydora websteriis a shell boring polydorin worm that induces the formation of mud-filled blisters within the shells of molluscs. The annelid is considered indigenous to the Asian coasts and has been documented in various locations across the globe. In the present work, we report a massive presence ofP. websteriin several sites of the North Adriatic costline and we provide some diagnostic features that are useful to identify the species.Polydora websterican be distinguished of a lateral flange on chaetiger 5. Moreover the palps are characterized by continuous black lines along the margins of the ciliated groove.The combined findings of this study provide compelling evidence thatP. websteriis expanding its range within the Mediterranean coast. Given the potential for severe ecological and economic impacts associated with this invasive polychaete, this study serves as an urgent call to action for increased monitoring ofP. websteriin both farmed and wild Pacific oysters in the Mediterranean Sea. Identification key of MediterraneanPolydorais provided.
Unraveling thein plantagrowth of the plant pathogenRalstonia pseudosolanacearumby mathematical modeling
Authors: Baroukh Caroline , Gerlin Léo , Escourrou Antoine , Genin Stéphane 
Published: July 2024

SummaryRalstonia pseudosolanacearum, a plant pathogen responsible for bacterial wilt in numerous plant species, exhibits paradoxical growth in the host by achieving high bacterial densities in xylem sap, an environment traditionally considered nutrient-poor. This study combinedin vitroexperiments and mathematical modeling to elucidate the growth dynamics ofR. pseudosolanacearumstrain GMI1000 within plants. To simulate the xylem environment, a tomato xylem-mimicking medium containing amino acids and sugars was developed to monitor the growth kinetics ofR. pseudosolanacearum. Results indicated that glutamine is the primary metabolite driving bacterial growth, while putrescine is abundantly excreted, and acetate is transiently produced and subsequently consumed. A mathematical model was constructed and calibrated using thein vitrodata. This model was employed to simulate the evolution of bacterial density and xylem sap composition during plant infection. The model accurately reproducedin plantaexperimental observations, including high bacterial densities and the depletion of glutamine and asparagine. Additionally, the model estimated the minimal number of bacteria required to initiate infection, the timing of infection post-inoculation, the bacterial mortality rate within the plant, and the rate at which excreted putrescine is assimilated by the plant. The findings demonstrate that xylem sap is not as nutrient-poor and can sustain high bacterial densities. The study also provides an explanatory framework for the presence of acetate and putrescine in the sap of infected xylem and give clues as to the role of putrescine in the virulence ofR. pseudosolanacearum.
Multi-Omic Analysis Reveals Lipid Dysregulation Associated with Mitochondrial Dysfunction in Parkinson’s Disease Brain
Authors: Hällqvist Jenny , Toomey Christina E , Pinto Rui , Wernick Anna , Sharhani Mesfer Al , Heales Simon , Eaton Simon , Mills Kevin , Gandhi Sonia , Heywood Wendy E 
Published: July 2024

AbstractParkinson’s Disease (PD) is an increasingly prevalent condition within the aging population. PD can be attributed to rare genetic mutations, but most cases are sporadic where the gene-environment interactions are unknown/likely contributory. Age related dysregulation of the glycosphingolipid degradation pathway has been implicated in the development of PD, however, our understanding of how brain lipids vary across different regions of the brain, with age and in disease stages, remains limited.In this study we profiled several phospho- and sphingolipid classes in eight distinct regions of the human brain and investigated the association of lipids with a spatio-temporal pathology gradient, utilising PD samples from early, mid, and late stages of the disease. We performed high-precision tissue sampling in conjunction with targeted LC-MS/MS and applied this to post-mortem samples from PD and control subjects. The lipids were analysed for correlations with untargeted proteomics and mitochondrial activity data, in a multi-omics approach. We concluded that the different brain regions demonstrated their own distinct profiles and also found that several lipids were correlated with age. The strongest differences between PD and controls were identified in ganglioside, sphingomyelin and n-hexosylceramides. Sphingomyelin was also found to correlate with several proteins implicated in Parkinson’s disease pathways. Mitochondrial activity was correlated with the levels of several lipids in the putamen region. Finally, we identified a gradient corresponding to Braak’s disease spread across the brain regions, where the areas closer to the brainstem/substantia nigra showed alterations in PC, LPC and glycosphingolipids, while the cortical regions showed changes in glycosphingolipids, specifically gangliosides, HexCer and Hex2Cer.Graphical Abstract
Effectiveness and equity of vaccination strategies against Rift Valley fever in a heterogeneous landscape
Authors: Tennant Warren S. D. , Cardinale Eric , Moutroifi Youssouf , Spencer Simon E. F. , Charafouddine Onzade , Tildesley Mike J. , Métras Raphaëlle 
Published: July 2024

AbstractSpatio-temporal variations in environment and socio-agricultural factors create heterogeneity in livestock disease transmission risk, raising challenges in identifying populations most at risk and how this risk changes over time. Consequently, prioritising control strategies, such as vaccination, to achieve optimal or equitable outcomes across regions impedes the design of an effective vaccination strategy. We developed a metapopulation model for Rift Valley fever transmission in livestock across the Comoros archipelago which incorporates livestock vaccination in addition to heterogeneity in viral transmission rates and animal movements. We used the model to evaluate three vaccine allocation strategies–proportional allocation, optimal allocation for maximising total infections averted across the archipelago, and optimal allocation for more equitable outcomes across islands—under different vaccination coverage levels and animal identification scenarios. We report that (i) both archipelago-wide and island-specific strategy effectiveness were impacted by vaccination rate, allocation strategy, and animal identification approach, (ii) optimally allocating vaccines improved strategy effectiveness compared with proportional allocation but resulted in inequitable outcomes between islands, and (iii) tagging animals post-vaccination boosted overall strategy effectiveness for all vaccination rates.
TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism
Authors: Feiten Astrid F , Dahm Kilian , van Lengerich Bettina , Suh Jung H , Reifschneider Anika , Wefers Benedikt , Bartos Laura M , Wind-Mark Karin , Schlepckow Kai , Ulas Thomas , De-Domenico Elena , Becker Matthias , Khalin Igor , Davis Sonnet S. , Wurst Wolfgang , Plesnila Nikolaus , Neher Jonas J , Brendel Matthias , Lewcock Joseph W , Di Paolo Gilbert , Capell Anja , Monroe Kathryn M , Schultze Joachim L , Haass Christian 
Published: July 2024

AbstractTriggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA-sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application.
Network-based investigation of petroleum hydrocarbons-induced ecotoxicological effects and their risk assessment
Authors: Sahoo Ajaya Kumar , Madgaonkar Shreyes Rajan , Chivukula Nikhil , Karthikeyan Panneerselvam , Ramesh Kundhanathan , Marigoudar Shambanagouda Rudragouda , Sharma Krishna Venkatarama , Samal Areejit 
Published: July 2024

AbstractPetroleum hydrocarbons (PHs) are compounds composed mostly of carbon and hydrogen, originating from crude oil and its derivatives. PHs are primarily released into the environment through the diffusion of oils, resulting from anthropogenic activities like transportation and offshore drilling, and accidental incidents such as oil spills. Once released, these PHs can persist in different ecosystems and cause long-term detrimental ecological impacts. While the hazards associated with such PH contaminations are often assessed by the concentrations of total petroleum hydrocarbons in the environment, studies focusing on the risks associated with individual PHs are limited. Here, we leveraged different network-based frameworks to explore and understand the adverse ecological effects associated with PH exposure. First, we systematically curated a list of 320 PHs from published reports. Next, we integrated biological endpoint data from toxicological databases, and constructed a stressor-centric adverse outcome pathway (AOP) network linking 75 PHs with 177 ecotoxicologically-relevant high confidence AOPs within AOP-Wiki. Further, we relied on stressor-species network constructions, based on reported toxicity concentrations and bioconcentration factors data for 80 PHs and 28 PHs, respectively, and found that crustaceans are documented to be affected by many of these PHs. Finally, we utilized the aquatic toxicity data within ECOTOX to construct species sensitivity distributions for polycyclic aromatic hydrocarbons (PAHs) prioritized by the US EPA, and derived their corresponding hazard concentrations (HC05) that protect 95% of species in the aquatic ecosystem. Overall, this study highlights the importance of using network-based approaches and risk assessment methods to understand the PH-induced toxicities effectively.
Oestrogen influences B cell class-switching in individuals with an XX sex chromosome complement
Authors: Peckham Hannah , Radziszewska Anna , de Gruijter Nina M , Restuadi Restuadi , Kartawinata Melissa , Robinson George A , Martin-Gutierrez Lucia , Deakin Claire T , Wedderburn Lucy R , Jury Elizabeth C , Butler Gary , Rosser Elizabeth C. , Ciurtin Coziana 
Published: July 2024

ABSTRACTSex differences in humoral immunity are well-documented, though the mechanisms underpinning these differences remain ill-defined. Here, we demonstrate that post-pubertal cisgender females have higher levels of class-switched B cells compared to age-matched cisgender males. However, whilst sex chromosome-encoded genes characterise most of the differences in total B cell transcriptomes between cisgender-females and -males, sex differences in class-switched B cells are only observed post-pubertally. Accordingly, B cells express high levels of oestrogen receptor 2(ESR2)and genes known to regulate B cell class-switching are enriched forESR2-binding sites. Using a gender-diverse cohort of young people, we show that in transgender males (XX chromosomal background), blockade of natal oestrogen reduced the frequency of class-switched B cells, whilst gender-affirming oestradiol treatment in transgender females (XY chromosomal background), did not increase the frequency of class-switched B cells. These data demonstrate that sex hormones and chromosomes work in tandem to impact immune responses, with oestrogen only supporting B cell class-switching on an XX chromosomal background.eTOC summarySex hormones and chromosomes work in tandem to impact immune responses, with oestrogen influencing B cell class-switching exclusively on an XX chromosomal background.