bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of Subsequent Respiratory Virus Detection After Primary Virus Detection in a Community Household Study—King County, Washington, 2019–2021
Authors: Heimonen Jessica , Chow Eric J , Wang Yongzhe , Hughes James P , Rogers Julia , Emanuels Anne , O’Hanlon Jessica , Han Peter D , Wolf Caitlin R , Logue Jennifer K , Ogokeh Constance E , Rolfes Melissa A , Uyeki Timothy M , Starita Lea , Englund Janet A , Chu Helen Y 
Published: August 2023

Abstract

Background
The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described.

Methods
From October 2019 to June 2021, enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swab specimens; after April 2020, participants with ARI or laboratory-confirmed severe acute respiratory syndrome coronavirus 2 and their household members self-collected nasal swab specimens. Specimens were tested using multiplex reverse-transcription polymerase chain reaction for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection.

Results
Rhinovirus was the most frequently detected pathogen in study specimens (406 [9.5%]). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8 [14.8%]) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03–2.06-fold increase in risk of subsequent virus detection in the 90 days after primary detection; risk varied by primary virus: human parainfluenza virus, rhinovirus, and respiratory syncytial virus were statistically significant.

Conclusions
Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection.
P25 Healthcare associated candiduria in ICU patients: experience from a surveillance network in India, 2017–22
Authors: Vedachalam Srividya K , Thakur Arpan Kumar , Parveen Rasna , Puraswani Mamta , Srivastav Sharad , Ningombam Aparna , Walia Kamini , Siromany Valan A , VanderEnde Daniel , Malpiedi Paul A , Vasquez Amber M , Mathur Purva ,   Indian Healthcare Associated Infection Surveillance Network Collaborators
Published: August 2023

Abstract

Background
Urinary tract infections (UTI) are common healthcare associated infections (HAI) in low-and-middle-income countries including India, with limited information on Candida UTI. An ICU-based HAI surveillance network of tertiary care hospitals across India, coordinated by the All-India Institute of Medical Sciences, New Delhi and the Indian Council of Medical Research, modified the US CDC’s National Healthcare Safety Network (NHSN) case definitions to record UTI. Unlike NHSN, India surveillance includes fungal pathogens, such as Candida spp., as eligible pathogens causing HAI-UTI. We describe the epidemiology, microbiology and antimicrobial resistance (AMR) profile of candiduria cases reported to this network to address the knowledge gap on Candida UTI in India.

Methods
Patients with at least one UTI symptom and a positive urine culture with Candida sp. who had spent at least 2 calendar days in a participating ICU were included as candiduria events. All candiduria events reported by participating sites from 1 November 2017 to 31 May 2022 were extracted from overall UTI reported for all pathogens. The distribution of events by age, gender, ICU type, urinary catheterization, pathogen and drug resistance profile were performed. UTI rate and device utilization ratio (DUR) were calculated. Network sites performed antifungal susceptibility testing (AST) on Candida isolates using MIC-based method as per CLSI guidelines.

Results
Data was reported by 131 ICUs in 39 hospitals. Overall network UTI events including all pathogens were 3600; UTI rates were 2.6 (adult ICUs) and 1.3 (paediatric ICUs); DUR was 0.8 (adult ICUs) and 0.4 (paediatric ICUs). There were 1111 candiduria events, 95% were classified as catheter-associated UTI (CAUTI), and the median age of patients was 65 years (IQR 32–74 years) and 58% were male. Among 739 Candida isolates speciated, Candida tropicalis (37%), Candida albicans (36%), Candida glabrata (6%) and Candida auris (6%) were the top four species isolated. Among 220 C. tropicalis isolates tested with AST, 6.9% were fluconazole resistant and 2% of 140 were caspofungin resistant; 7% of 177 C. albicans isolates were fluconazole resistant and 6.5% of 92 isolates were caspofungin resistant; and 48% of 28 C. glabrata isolates were fluconazole resistant and 44% of 18 isolates were caspofungin resistant.

Conclusions
Candiduria events reported from ICUs to the HAI surveillance network-India are common and the majority are classified as CAUTI. Most of the species isolated are susceptible to fluconazole and caspofungin. Additional work is needed to understand the clinical significance of candiduria events reported to the network.
Two complementary AI approaches for predicting UMLS semantic group assignment: heuristic reasoning and deep learning
Authors: Mao Yuqing , Miller Randolph A , Bodenreider Olivier , Nguyen Vinh , Fung Kin Wah 
Published: August 2023

Abstract

Objective
Use heuristic, deep learning (DL), and hybrid AI methods to predict semantic group (SG) assignments for new UMLS Metathesaurus atoms, with target accuracy ≥95%.

Materials and Methods
We used train-test datasets from successive 2020AA–2022AB UMLS Metathesaurus releases. Our heuristic “waterfall” approach employed a sequence of 7 different SG prediction methods. Atoms not qualifying for a method were passed on to the next method. The DL approach generated BioWordVec and SapBERT embeddings for atom names, BioWordVec embeddings for source vocabulary names, and BioWordVec embeddings for atom names of the second-to-top nodes of an atom’s source hierarchy. We fed a concatenation of the 4 embeddings into a fully connected multilayer neural network with an output layer of 15 nodes (one for each SG). For both approaches, we developed methods to estimate the probability that their predicted SG for an atom would be correct. Based on these estimations, we developed 2 hybrid SG prediction methods combining the strengths of heuristic and DL methods.

Results
The heuristic waterfall approach accurately predicted 94.3% of SGs for 1 563 692 new unseen atoms. The DL accuracy on the same dataset was also 94.3%. The hybrid approaches achieved an average accuracy of 96.5%.

Conclusion
Our study demonstrated that AI methods can predict SG assignments for new UMLS atoms with sufficient accuracy to be potentially useful as an intermediate step in the time-consuming task of assigning new atoms to UMLS concepts. We showed that for SG prediction, combining heuristic methods and DL methods can produce better results than either alone.
Northeast Regional Center for Excellence in Vector-Borne Diseases’ Master of Science training program: a curriculum to support future capacity in public health entomology
Authors: Harrington Laura C , Mader Emily M 
Published: August 2023

Abstract
A major lack of expertise in vector biology, surveillance, and control for public health professionals has been acknowledged over the past several decades, especially in light of the introduction of West Nile and Zika viruses to the United States. To address this growing need, the Northeast Regional Center for Excellence in Vector-Borne Diseases (NEVBD) designed a unique educational program to cross-train students in the fundamentals of vector biology and public health. Here, we summarize the formation, evaluation, and outcomes of NEVBD’s Master of Science in Entomology: Vector-Borne Disease Biology program and provide details on core competencies to enable adoption and adaptation of the program to other institutions and contexts. A discussion of major barriers to filling the nation’s need for public health personnel with medical entomology training, such as financial barriers and recruitment of underrepresented students, is presented. We conclude with considerations for administering these training programs.
Racial and ethnic and socioeconomic disparities in childhood cancer incidence trends in the United States, 2000-2019
Authors: Monterroso Pablo S , Li Zhaoheng , Domingues Allison M , Sample Jeannette M , Marcotte Erin L 
Published: August 2023

Abstract

Background
Population-based surveillance of pediatric cancer incidence trends is critical to determine high-risk populations, drive hypothesis generation, and uncover etiologic heterogeneity. We provide a comprehensive update to the current understanding of pediatric cancer incidence trends by sex, race and ethnicity, and socioeconomic status (SES).

Methods
The Surveillance, Epidemiology, and End Results 22 data (2000-2019) was used to summarize age-adjusted incidence rates for children and adolescents aged 0-19 years at diagnosis. The annual percentage change (APC) and 95% confidence interval (CI) were estimated to evaluate incidence trends by sex, race and ethnicity, and SES overall and for cancer subtypes. Tests of statistical significance were 2-sided.

Results
Substantial variation was observed overall and for several histologic types in race and ethnicity– and SES–specific rates. Overall, we observed a statistically significant increase in incidence rates (APC = 0.8%, 95% CI = 0.6% to 1.1%). All race and ethnic groups saw an increase in incidence rates, with the largest occurring among non-Hispanic American Indian and Alaska Native children and adolescents (APC = 1.7%, 95% CI = 0.5% to 2.8%) and the smallest increase occurring among non-Hispanic White children and adolescents (APC = 0.7%, 95% CI = 0.5% to 1.0%). The lowest SES quintiles saw statistically significant increasing trends, while the highest quintile remained relatively stable (quintile 1 [Q1] APC = 1.6%, 95% CI = 0.6% to 2.6%; quintile 5 [Q5] APC = 0.3%, 95% CI = –0.1% to 0.7%).

Conclusions
Childhood cancer incidence is increasing overall and among every race and ethnic group. Variation by race and ethnicity and SES may enable hypothesis generation on drivers of disparities observed.
Wasserstein barycenter for link prediction in temporal networks
Authors: Spelta Alessandro , Pecora Nicolò 
Published: August 2023

Abstract
We propose a flexible link forecast methodology for weighted temporal networks. Our probabilistic model estimates the evolving link dynamics among a set of nodes through Wasserstein barycentric coordinates arising within the optimal transport theory. Optimal transport theory is employed to interpolate among network evolution sequences and to compute the probability distribution of forthcoming links. Besides generating point link forecasts for weighted networks, the methodology provides the probability that a link attains weights in a certain interval, namely a quantile of the weights distribution. We test our approach to forecast the link dynamics of the worldwide Foreign Direct Investments network and of the World Trade Network, comparing the performance of the proposed methodology against several alternative models. The performance is evaluated by applying non-parametric diagnostics derived from binary classifications and error measures for regression models. We find that the optimal transport framework outperforms all the competing models when considering quantile forecast. On the other hand, for point forecast, our methodology produces accurate results that are comparable with the best performing alternative model. Results also highlight the role played by model constraints in the determination of future links emphasising that weights are better predicted when accounting for geographical rather than economic distance.
Spectropolarimetric study of 4U 1630−47 in steep power-law state with IXPE and NICER
Authors: Rawat Divya , Garg Akash , Méndez Mariano 
Published: August 2023

ABSTRACT
We probe the spectropolarimetric properties of the black hole binary source 4U 1630−47 in the steep power-law state. We detect a significant polarization fraction of ∼7 per cent at a polarization angle of ∼21°. The 2–12 keV NICER spectrum can be fitted with a combination of a thermal and a Comptonization component, the latter characterized by a spectral index, Γ ∼ 2.1, along with a reflection feature at ∼7.0 keV. In the 2–8 keV band, the degree of polarization of 4U 1630−47 in the steep power-law state is 4.4σ different from the value previously measured in the high-soft state. In the steep power-law state, the polarization fraction increases as a function of energy but exhibits an overall drop in each energy band compared to that of the high-soft state. We propose that the decrease in the polarization fraction in the steep power-law state could be attributed to the presence of a corona. The observed polarization properties in both states can be explained by the self-irradiation of the disc around a Kerr black hole, likely influenced by the frame dragging effect.
Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells
Authors: Zanin Irene , Ruggiero Emanuela , Nicoletto Giulia , Lago Sara , Maurizio Ilaria , Gallina Irene , Richter Sara N 
Published: August 2023

Abstract
i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions in vitro. Their formation in cells is still under debate. We performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs form within the human genome in live cells. We mapped iMs in two human cell lines and recovered C-rich sequences that were confirmed to fold into iMs in vitro. We found that iMs in cells are mainly present at actively transcribing gene promoters, in open chromatin regions, they overlap with R-loops, and their abundance and distribution are specific to each cell type. iMs with both long and short C-tracts were recovered, further extending the relevance of iMs. By simultaneously mapping G-quadruplexes (G4s), which form at guanine-rich regions, and comparing the results with iMs, we proved that the two structures can form in independent regions; however, when both iMs and G4s are present in the same genomic tract, their formation is enhanced. iMs and G4s were mainly found at genes with low and high transcription rates, respectively. Our findings support the in vivo formation of iM structures and provide new insights into their interplay with G4s as new regulatory elements in the human genome.
Isocitrate dehydrogenase wt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2’O-methylation of ribosomal RNA
Authors: Paraqindes Hermes , Mourksi Nour-El-Houda , Ballesta Samantha , Hedjam Jordan , Bourdelais Fleur , Fenouil Tanguy , Picart Thiébaud , Catez Frédéric , Combe Théo , Ferrari Anthony , Kielbassa Janice , Thomas Emilie , Tonon Laurie , Viari Alain , Attignon Valéry , Carrere Marjorie , Perrossier Jessie , Giraud Stéphane , Vanbelle Christophe , Gabut Mathieu , Bergeron Danny , Scott Michelle S , Castro Vega Luis , Magne Nathalie , Huillard Emmanuelle , Sanson Marc , Meyronet David , Diaz Jean-Jacques , Ducray François , Marcel Virginie , Durand Sébastien 
Published: August 2023

Abstract

Background
High-grade adult-type diffuse gliomas (HGGs) constitute a heterogeneous group of aggressive tumors that are mostly incurable. Recent advances highlighting the contribution of ribosomes to cancer development have offered new clinical perspectives. Here, we uncovered that isocitrate dehydrogenase (IDH)wt and IDHmut HGGs display distinct alterations of ribosome biology, in terms of rRNA epitranscriptomics and ribosome biogenesis, which could constitute novel hallmarks that can be exploited for the management of these pathologies.

Methods
We analyzed (1) the ribosomal RNA 2’O-ribose methylation (rRNA 2’Ome) using RiboMethSeq and in-house developed bioinformatics tools (https://github.com/RibosomeCRCL/ribomethseq-nfandrRMSAnalyzer) on 3 independent cohorts compiling 71 HGGs (IDHwt n = 30, IDHmut n = 41) and 9 non-neoplastic samples, (2) the expression of ribosome biogenesis factors using medium throughput RT-qPCR as a readout of ribosome biogenesis, and (3) the sensitivity of 5 HGG cell lines to RNA Pol I inhibitors (CX5461, BMH-21).

Results
Unsupervised analysis demonstrated that HGGs could be distinguished based on their rRNA 2’Ome epitranscriptomic profile, with IDHwt glioblastomas displaying the most significant alterations of rRNA 2’Ome at specific sites. In contrast, IDHmut HGGs are largely characterized by an overexpression of ribosome biogenesis factors compared to non-neoplastic tissues or IDHwt glioblastomas. Finally, IDHmut HGG-derived spheroids display higher cytotoxicity to CX5461 than IDHwt glioblastoma, while all HGG spheroids display a similar cytotoxicity to BMH-21.

Conclusions
In HGGs, IDH mutational status is associated with specific alterations of the ribosome biology and with distinct sensitivities to RNA Pol I inhibitors.
Long-term outcomes with reduced-dose whole-brain radiotherapy and a stereotactic radiosurgery boost for primary central nervous system lymphoma
Authors: Foreman Bronwen E , Mullikin Trey C , Floyd Scott R , Kelsey Chris R , Patel Mallika P , Peters Katherine B , Kirkpatrick John P , Reitman Zachary J , Vaios Eugene J 
Published: August 2023

AbstractBackgroundPrimary central nervous system lymphoma (PCNSL) is an aggressive diffuse large B-cell lymphoma. Treatment approaches are historically associated with neurotoxicity, particularly with high-dose whole-brain radiotherapy (WBRT). We hypothesized that reduced dose-WBRT (rd-WBRT) followed by a stereotactic radiosurgery (SRS) boost could provide durable disease control without significant adverse effects.MethodsWe retrospectively reviewed PCNSL patients treated with rd-WBRT plus an SRS boost at Duke University between 2008 and 2021. Progression-free survival and overall survival (OS) were estimated using competing risk and Kaplan–Meier methods.ResultsWe identified 23 patients with pathologically confirmed PCNSL. Median age at diagnosis was 69 years (Q1Q3: 52–74) and median Karnofsky Performance Scale (KPS) was 80 (Q1Q3: 70–80). Median follow-up was 21 months. Median doses for rd-WBRT and SRS were 23.4 Gy (Q1Q3: 23.4–23.4) and 12 Gy (Q1Q3: 12–12.5), respectively. The cumulative incidence of intracranial progression at 2 years was 23% (95% CI: 8–42). Six patients (26%) developed distant radiographic progression while 2 patients (9%) developed both distant and local progression. Ten patients (44%) were alive without progression at last follow-up. By Kaplan–Meier estimate, the 2-year OS was 69% (95% CI: 46–84). There were no reported grade 3 + radiation-induced toxicities.ConclusionsThe combination of rd-WBRT with an SRS boost appears well-tolerated with durable intracranial control. This approach may represent a treatment option for select patients, such as those with progressive or refractory disease. Further prospective studies are needed to validate these findings and determine whether this approach could be incorporated into consolidation strategies.
The Impact of High or Low Doses of Nicotine in a Mouse Model of Vapor Self-Administration
Authors: Cooper Skylar Y , Olszewski Nathan A , Tetteh-Quarshie Samuel , Hill Sean P , Ghodsi Saaman , González-Castro Astrid , Willis Clay V , Henderson Brandon J 
Published: August 2023

Abstract

Introduction
A wide variety of nicotine concentrations and formulations are available to users of electronic nicotine delivery systems (ENDS). This is increasingly true when considering the many flavors available with ENDS products. To date, there have been few preclinical investigations into the impact of nicotine doses, with and without flavors, on vaping-related behaviors. This present study evaluated how nicotine concentrations relevant to tank-based and pod-based ENDS, with and without flavors, impact reinforcement-related behavior in a mouse model.

Aims and Methods
Adult male and female C57/BL6J mice were used in vapor-inhalation self-administration assays. Mice were assigned e-liquids containing 6 mg/mL or 60 mg/mL nicotine. Additional mice were assigned these nicotine doses with green apple or menthol flavorants. Mice were trained on fixed-ratio 1 for 10, 2-hour sessions, then five sessions at FR3, three progressive ratio sessions, and two FR3 sessions.

Results
We observed male mice exhibited higher reinforcement-related behavior to menthol-flavored 6 mg/mL nicotine when compared to female mice. Males were only observed to have a menthol-induced enhancement of self-administration at 6 mg/mL nicotine and not 60 mg/mL nicotine. However, female mice exhibited significant menthol-induced increases in reinforcement-related behaviors with 60 mg/mL nicotine.

Conclusions
These data provide evidence that males and females exhibit different dose sensitivities to nicotine. These sex-dependent differences in nicotine sensitivity also indicate that flavor-induced enhancement in nicotine intake is dependent on the different doses for each sex.

Implications
There has been much discussion recently regarding the impact of flavors on vaping-related behavior. Our current study may support prior investigations that suggest flavors enhance the palatability of nicotine-containing products. However, this current study provides evidence that males and females exhibit different sensitivities to nicotine.
Potential Implications for Tobacco Industry Transformation of the Acquisition of Swedish Match by Philip Morris International
Authors: Levy David T , Warner Kenneth E , Liber Alex C , Travis Nargiz , Sweanor David T , Meza Rafael , Cummings K Michael 
Published: August 2023

Abstract
Philip Morris International’s recent purchase of Swedish Match may prove to be a vital tobacco industry development. We focus on PMIs potential progress in moving from primarily selling cigarettes toward primarily selling noncombustible nicotine delivery products (NCNDPs). We also consider the potential contribution of the acquisition to industry transformation whereby other cigarette firms may potentially move toward primarily selling NCNDPs. We examine the potential impact on noncombustible nicotine delivery product use, including nicotine pouches (a major Swedish Match product), e-cigarettes, heated tobacco products, and, most importantly, on sales of the industry’s staple, combustible cigarettes. We focus on the United States as a special case, where PMI is limited from entering the cigarette market.
Implications: Philip Morris International’s purchase of Swedish Match and policies regarding nicotine pouches (NPs) have been overlooked in the tobacco control literature. The acquisition indicates the importance of the NP market to the largest nonstate-owned tobacco company. The acquisition has the potential through pricing and marketing tactics to either encourage or discourage the use of NPs, e-cigarettes, heated tobacco products, and most importantly cigarettes. Due to its inability to sell cigarettes in the United States, PMI will have incentives to use its alternative nicotine delivery products, including its newly acquired NPs, to reduce the sale of cigarettes by other companies. However, the potential effects in other countries, where PMI does sell cigarettes, are less clear. Monitoring and analyzing tobacco company acquisitions is essential to studying future transitions in using different kinds of tobacco products, especially from cigarettes to lower-risk alternative nicotine delivery products.