bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV/Sexually Transmitted Infection Screening and Eligibility for HIV Preexposure Prophylaxis Among Women Incarcerated in an Urban County Jail
Authors: Desai Jui , Krakower Douglas , Harris Barry-Lewis , Culp Sophia , Nijhawan Ank E. 
Published: September 2023

Background
Incarcerated women experience high rates of HIV and sexually transmitted infections (STIs); few are offered HIV preexposure prophylaxis (PrEP). We aimed to examine HIV/STI screening rates in this population and identify PrEP eligibility.

Methods
Results of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) urine and HIV/syphilis screening in cisgender women in the Dallas County Jail were compiled from January to October 2020. An electronic health record review was conducted for a subgroup in March 2020 to identify PrEP eligibility.

Results
Overall, 4398 of 13,292 women were screened for CT and 4389 of 13,292 for GC, and among them, 479 (11%) screened for HIV and 562 (13%) for syphilis. Furthermore, 462 of 4398 (11%) were positive for CT, 323 of 4389 (7%) were positive for GC, 10 of 479 (2%) had positive HIV test results, of whom 6 (1.3%) were new diagnoses and 75 (13%) had a reactive rapid plasma reagin test. In March 2020, of 541 women screened, 90 tested positive for CT or GC. Of these 90, 70 (78%) did not receive HIV or syphilis screening, including women with these risk factors: 10 (14%) were homeless, 11 (16%) reported heroin use, and 10 (14%) reported methamphetamine use. Based on the presence of an acute bacterial STI, 17% (96 of 541) were PrEP eligible.

Conclusions
Incarcerated women had high STI rates and other risk factors for HIV acquisition, although only 1 in 5 with acute STIs (11% overall) was also screened for HIV or syphilis. HIV prevention efforts should include comprehensive STI/HIV screening, linkage to treatment, and identification of PrEP candidates.
Spinning Through History: Evolution of the Concept of Vestibular Migraine
Authors: Cha Yoon-Hee 
Published: September 2023

Vestibular migraine represents a growing public health problem, imposing enormous societal burdens in the form of patient suffering, loss of productivity, and direct healthcare costs. This raises the question of how we developed our ideas about vestibular migraine and how these ideas shape how we treat it.
This review walks through the history of how our conceptualization of migraine and vestibular symptoms evolved, starting with clinical observations in ancient times, inclusion under the umbrella of Meniere’s disease, and then separation from Meniere’s disease with its own identity. Tradition, clinical observations, and diagnostic criteria developed by professional societies have played prominent roles in building our current concept of vestibular migraine. A review of the ideas that have shaped our current conception of vestibular migraine may help us to see which ones have stood the test of time and which ones should continue to evolve. As in other disciplines, we study history in medicine to be inspired, warned, and sometimes, to be freed.
Micro-heterogeneity of transmission shapes the submicroscopic malaria reservoir in coastal Tanzania
Authors: Rapp Tyler , Amagai Kano , Sinai Cyrus , Basham Christopher , Loya Mwajabu , Ngasala Sifa , Said Hamza , Muller Meredith S. , Chhetri Srijana B. , Yang Guozheng , François Ruthly , Odas Melic , Mathias Derrick , Juliano Jonathan J. , Lin Feng-Chang , Ngasala Billy , Lin Jessica T. 
Published: September 2023

AbstractBackgroundAsymptomatic malaria may be patent (visible by microscopy) and detectable by rapid malaria diagnostic tests (RDTs), or it may be submicroscopic and only detectable by polymerase chain reaction (PCR).MethodsTo characterize the submicroscopic reservoir in an area of declining malaria transmission, asymptomatic persons >5 years of age in Bagamoyo District, Tanzania, were screened using RDT, microscopy, and PCR. We investigated the size of the submicroscopic reservoir across villages, determined factors associated with submicroscopic parasitemia, and assessed the natural history of submicroscopic malaria over four weeks.ResultsAmong 6,076 participants,Plasmodium falciparumprevalence by RDT, microscopy, and PCR was 9%, 9%, and 28%, respectively, with roughly two-thirds of PCR-positive individuals harboring submicroscopic infection. Adult status, female gender, dry season months, screened windows, and bednet use were associated with submicroscopic carriage. Among 15 villages encompassing 80% of participants, the proportion of submicroscopic carriers increased with decreasing village-level malaria prevalence. Over four weeks, 23% (61/266) of submicroscopic carriers became RDT-positive and were treated, with half exhibiting symptoms. This occurred more frequently in villages with higher malaria prevalence.ConclusionsMicro-heterogeneity in transmission impacts the size of the submicroscopic reservoir and the likelihood of submicroscopic carriers developing patent malaria in coastal Tanzania.
Malaria Stratification Mapping in Thailand to Support Prevention of Re-establishment
Authors: Bisanzio Donal , Sudathip Prayuth , Kitchakarn Suravadee , Kanjanasuwan Jerdsuda , Gopinath Deyer , Pinyajeerapat Niparueradee , Sintasath David , Shah Jui A. 
Published: September 2023

AbstractThailand aims to eliminate malaria by 2026, with 46 of the country’s 77 provinces already verified as malaria free. However, these provinces remain susceptible to the re-establishment of indigenous transmission that would threaten the national goal. Thus, the country is prioritizing national and subnational prevention of re-establishment (POR) planning while considering the spatial heterogeneity of the remaining malaria caseload. To support POR efforts, a novel non-modeling method produced a malaria stratification map at the tambon (subdistrict) level, incorporating malaria case data, environmental factors, and demographic data. The stratification analysis categorized 7,425 tambons into the following four risk strata: Local Transmission (2.9%), At Risk for Transmission (3.1%), High Risk for Reintroduction (2.9%), and Low Risk for Reintroduction (91.1%). The stratification map will support the national program to target malaria interventions in remaining hotspots and mitigate the risk of transmission in malaria-free areas.
Microbe-induced plant resistance against insect pests depends on timing of inoculation, but is consistent across climatic conditions
Authors: Sanchez-Mahecha Oriana , Klink Sophia , Rothballer Michael , Sturm Sarah , Weisser Wolfgang W. , Zytynska Sharon , Heinen Robin 
Published: September 2023

AbstractTo cope with abiotic and biotic stressors, plants have developed mutualistic associations with beneficial soil microbes, but little is known about how (extreme) abiotic conditions impact on microbe-induce resistance to insect herbivores.Extreme temperatures are often accompanied by extremes in plant water availability, which together reduce plant growth and change plant physiology. There are potential consequences for increasing plant susceptibility to biotic stresses, and this poses a real challenge for plant productivity.We evaluated how the effects of beneficial soil bacteria (Acidovorax radicis) on barley plant growth and resultant resistance against aphid infestation (Sitobion avenae) were impacted by a single heatwave event across a plant water availability gradient. We also tested if timing of bacterial inoculation (before or after the heatwave) affected bacteria-plant interactions on aphids.We found that heatwaves affected plant biomass allocation from aboveground to belowground tissues. Inoculation withA. radicisled to reduction of aphid numbers, but depended on timing of inoculation, and led to stronger resistance when inoculations occurred closer to aphid infestation. Remarkably, microbe-induced resistance against aphids was consistent across heatwave and water availability treatments.This study provides evidence that beneficial plant-bacteria interactions may represent a potential solution for sustainable agricultural practices to enhance plant growth and response to insect pests under climate change. Future field trials should investigate the consistency of beneficial effects reported here for a better understanding of multispecies interactions in the context of global change.
Untargeted Metabolomics to Expand the Chemical Space of the Marine DiatomSkeletonema marinoi
Authors: Zulfiqar Mahnoor , Stettin Daniel , Schmidt Saskia , Nikitashina Vera , Pohnert Georg , Steinbeck Christoph , Peters Kristian , Sorokina Maria 
Published: September 2023

AbstractDiatoms (Bacillariophyceae) are aquatic photosynthetic microalgae with an ecological role as primary producers in the aquatic food web. They account substantially for global carbon, nitrogen, and silicon cycling. Elucidating the chemical space of diatoms is crucial to understanding their physiology and ecology. To expand the known chemical space of a cosmopolitan marine diatom,Skeletonema marinoi, we performed High-Resolution Liquid Chromatography-Tandem Mass Spectrometry (LC-MS2) for untargeted metabolomics data acquisition. The spectral data from LC-MS2was used as input for the Metabolome Annotation Workflow (MAW) to obtain putative annotations for all measured features. A suspect list of metabolites previously identified in theSkeletonemaspp. was generated to verify the results. These known metabolites were then added to the putative candidate list from LC-MS2data to represent an expanded catalogue of 1970 metabolites estimated to be produced byS. marinoi. The most prevalent chemical superclasses, based on the ChemONT ontology in this expanded dataset, were “Organic acids and derivatives”, “Organoheterocyclic compounds”, “Lipids and lipid-like molecules”, and “Organic oxygen compounds”. The metabolic profile from this study can aid the bioprospecting of marine microalgae for medicine, biofuel production, agriculture, and environmental conservation. The proposed analysis can be applicable for assessing the chemical space of other microalgae, which can also provide molecular insights into the interaction between marine organisms and their role in the functioning of ecosystems.ImportanceDiatoms are abundant marine phytoplankton members and have great ecological importance and biochemical potential. The cosmopolitan diatomSkeletonema marinoihas become an ecological and environmental research model organism. In this study, we used untargeted metabolomics to acquire a general metabolic profile ofS. marinoito assess its chemical diversity and expand the known metabolites produced by this diatom.S. marinoiproduces a chemically diverse set of secondary metabolites with potential therapeutic properties, such as anti-cancer, antioxidant, and anti-inflammatory. Such metabolites are highly significant due to their potential role in drug discovery and bioeconomy. Lipids fromS. marinoialso have potential in the biofuel industry. Furthermore, the environmental fluctuations in the water bodies directly affect the production of different secondary metabolites from diatoms, which can be key indicators of climate change.
“Invisible Killer”: Seasonal Allergies and Accidents
Authors: Akesaka Mika , Shigeoka Hitoshi 
Published: September 2023

AbstractAlthough at least 400 million people suffer from seasonal allergies worldwide, the adverse effects of pollen on “non-health” outcomes, such as cognition and productivity, are relatively understudied. Using ambulance archives from Japan, we demonstrate that high pollen days are associated with increased accidents and injuries— one of the most extreme consequences of cognitive impairment. We find some evidence of avoidance behavior in buying allergy products but limited evidence in curtailing outdoor activity, implying that the cognitive risk of pollen exposure is discounted. Our results call for governmental efforts to raise public awareness of the risks and promote widespread behavioral change.
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification
Authors: Ryu Jayoung , Barkal Sam , Yu Tian , Jankowiak Martin , Zhou Yunzhuo , Francoeur Matthew , Phan Quang Vinh , Li Zhijian , Tognon Manuel , Brown Lara , Love Michael I. , Lettre Guillaume , Ascher David B. , Cassa Christopher A. , Sherwood Richard I. , Pinello Luca 
Published: September 2023

AbstractCRISPR base editing screens are powerful tools for studying disease-associated variants at scale. However, the efficiency and precision of base editing perturbations vary, confounding the assessment of variant-induced phenotypic effects. Here, we provide an integrated pipeline that improves the estimation of variant impact in base editing screens. We perform high-throughput ABE8e-SpRY base editing screens with an integrated reporter construct to measure the editing efficiency and outcomes of each gRNA alongside their phenotypic consequences. We introduce BEAN, a Bayesian network that accounts for per-guide editing outcomes and target site chromatin accessibility to estimate variant impacts. We show this pipeline attains superior performance compared to existing tools in variant classification and effect size quantification. We use BEAN to pinpoint common variants that alter LDL uptake, implicating novel genes. Additionally, through saturation base editing ofLDLR, we enable accurate quantitative prediction of the effects of missense variants on LDL-C levels, which aligns with measurements in UK Biobank individuals, and identify structural mechanisms underlying variant pathogenicity. This work provides a widely applicable approach to improve the power of base editor screens for disease-associated variant characterization.
Ventilation during COVID-19 in a school for students with intellectual and developmental disabilities (IDD)
Authors: Zand Martin S. , Spallina Samantha , Ross Alexis , Zandi Karen , Pawlowski Anne , Seplaki Christopher L. , Herington Jonathan , Corbett Anthony M. , Kaukeinen Kimberly , Holden-Wiltse Jeanne , Freedman Edward G. , Alcantara Lisette , Li Dongmei , Cameron Andrew , Beaumont Nicole , Dozier Ann , Dewhurst Stephen , Foxe John J. 
Published: September 2023

AbstractBackgroundThis study examined the correlation of classroom ventilation (air exchanges per hour (ACH)) and exposure to CO2≥1,000 ppm with the incidence of SARS-CoV-2 over a 20-month period in a specialized school for students with intellectual and developmental disabilities (IDD). These students were at a higher risk of respiratory infection from SARS-CoV-2 due to challenges in tolerating mitigation measures (e.g. masking). One in-school measure proposed to help mitigate the risk of SARS-CoV-2 infection in schools is increased ventilation.MethodsWe established a community-engaged research partnership between the University of Rochester and the Mary Cariola Center school for students with IDD. Ambient CO2levels were measured in 100 school rooms, and air changes per hour (ACH) were calculated. The number of SARS-CoV-2 cases for each room was collected over 20 months.Results97% of rooms had an estimated ACH≤4.0, with 7% having CO2levels≥2,000 ppm for up to 3 hours per school day. A statistically significant correlation was found between the time that a room had CO2levels ≥1,000 ppm and SARS-CoV-2 PCR tests normalized to room occupancy, accounting for 43% of the variance. No statistically significant correlation was found for room ACH and per-room SARS-CoV-2 cases. Rooms with ventilation systems using MERV-13 filters had lower SARS-CoV-2-positive PCR counts. These findings led to ongoing efforts to upgrade the ventilation systems in this community-engaged research project.ConclusionsThere was a statistically significant correlation between the total time of room CO2concentrations ≥1,000 and SARS-CoV-2 cases in an IDD school. Merv-13 filters appear to decrease the incidence of SARS-CoV-2 infection. This research partnership identified areas for improving in-school ventilation.
DIMR Score: A Tool for Determining the Destination of LVO Patients After Thrombolysis
Authors: Rao Rahul , Ali Aizaz , Zoghi Zeinab , Shawver Julie , Burgess Richard , Zaidi Syed , Jumaa Mouhammad 
Published: September 2023

AbstractBackgroundStroke patients with large vessel occlusion (LVO) benefit from thrombolysis (tPA) and mechanical thrombectomy (MT). We aim to characterize triaging patterns in these patients, specifically those who go to perfusion-based imaging first or direct to angio in the drip-and-ship model. Furthermore, we propose that select patients may benefit from CTP prior to MT.MethodsA total of 270 patients with acute ischemic stroke secondary to LVO/MeVO were retrospectively evaluated from January 2018 to June 2022. These patients received intravenous tPA from the outside hospital and were transferred for the intention of MT. We compared baseline characteristics between those who received CTP upon arrival and those who went either directly to the angiography suite (DTA) along with logistic regression and functional outcomes.ResultsPredictors of CTP utilization over DTA was the presence of an M3 occlusion (11.3% vs. 1.7%, p=0.005) and PCA occlusion (12.9% vs. 3.4%, p=0.015). The DTA approach was higher in M1 MCA occlusions (43.2% vs. 27.4%, p=0.038) and basilar occlusions (7.6% vs. 0, p=0.026). DTA patients had a higher NIHSS at the spoke (median NIHSS 15 [9-21] vs. 9 [4.75-14], p<0.001) and the hub (14 [7-20] vs. 7 [3-15.75], p<0.001). There was no significant difference between the DTA and CTP groups in regards to mRS at 90 days (39% vs. 48.4%, p=0.101).ConclusionIn the drip-and-ship model, NIHSS and location of an occlusion on initial CTA guide CTP utilization in LVO/ MeVO patients. Long term functional outcomes are not significantly affected by arrival at CTP over DTA. Patients whose transfer is delayed, improve after thrombolysis, present with a MeVO, or are limited by resources at the CSC may benefit from transfer to CT over a DTA approach. We propose this DIMR score may help guide triaging of patients who have an intracranial occlusion and receive thrombolysis.
Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation ofCa.Methanoglobus hypatiae from a Yellowstone hot spring
Authors: Lynes Mackenzie M. , Jay Zackary J. , Kohtz Anthony J. , Hatzenpichler Roland 
Published: September 2023

AbstractOver the past decade, environmental metagenomics and PCR-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic euryarchaeotes that have long been considered to live non-methanogenic lifestyles. Here, we enrichedCandidatusMethanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64-70 °C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine.Ca.M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescencein situhybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate thatCa.M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related toCa.M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.
A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match
Authors: Verheyden Nikita A. , Klostermann Melina , Brüggemann Mirko , Steede Hanna M. , Scholz Anica , Amr Shady , Lichtenthaeler Chiara , Münch Christian , Schmid Tobias , Zarnack Kathi , Krueger Andreas 
Published: September 2023

AbstractMicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3’ untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T-cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules.Key Points• Deep profiling identifies novel targets of miR-181 associated with global gene regulation.• miR-181 MREs in repeat elements in the coding sequence act through translational inhibition.• High-resolution analysis reveals an alternative seed match in functional MREs.
Encoding the Space of Protein-protein Binding Interfaces by Artificial Intelligence
Authors: Su Zhaoqian , Dhusia Kalyani , Wu Yinghao 
Published: September 2023

ABSTRACTThe physical interactions between proteins are largely determined by the structural properties at their binding interfaces. It was found that the binding interfaces in distinctive protein complexes are highly similar. The structural properties underlying different binding interfaces could be further captured by artificial intelligence. In order to test this hypothesis, we broke protein-protein binding interfaces into pairs of interacting fragments. We employed a generative model to encode these interface fragment pairs in a low-dimensional latent space. After training, new conformations of interface fragment pairs were generated. We found that, by only using a small number of interface fragment pairs that were generated by artificial intelligence, we were able to guide the assembly of protein complexes into their native conformations. These results demonstrate that the conformational space of fragment pairs at protein-protein binding interfaces is highly degenerate. Our study illustrates how artificial intelligence can be used to understand and characterize protein-protein binding interfaces. The method will be potentially useful to search for the conformation of unknown protein-protein interactions. This result demonstrated that the structural space of protein-protein interactions is highly degenerate under the representation of interface fragment pairs. Features in this degenerate space can be well characterized by artificial intelligence. In summary, our machine learning method will be potentially useful to search for and predict the conformations of unknown protein-protein interactions.