bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in opioid seizure data and their association with opioid mortality
Authors: McBrien Heather , Alexander Monica 
Published: October 2022

AbstractBackgroundThe opioid epidemic remains an emergent health issue in the United States, as opioid-related deaths continue to rise in the second year of COVID-19. The introduction of synthetic opioids into the illicit supply began causing deaths in 2015, however, data describing the illicit opioid supply is scarce.MethodsWe used a newly available national dataset of drug seizure reports, aggregated from law enforcement agencies across the United States, to describe changes in fentanyl, heroin, and other opioid presence in the national illicit supply from 2011-2017, by state and geographic region. We assessed the relationship between drug seizures and opioid-related deaths at the state level using linear regression.ResultsNational and state increases in opioid seizure rates from 2011-2017 were entirely due to increased fentanyl and heroin seizures, as other opioid seizure rates remained constant. Most increases in seizures occurred in the Northeast, Midwest, and Appalachia, where fentanyl seizures and heroin seizures were highest and increased most sharply along with opioid deaths. The composition of drugs seized was similar within geographic regions, but did vary across regions. State opioid seizures of all types were strongly associated with state opioid deaths. The strongest relationship was between fentanyl seizures and fentanyl deaths.ConclusionsThe association between opioid seizures and deaths means seizure data has potential as an early-warning system to predict overdose, although national level data requires quality improvement. Regional variation in seizure rates supports existing evidence that illicit fentanyl and heroin supplies differ between regions, producing distinct regional risk environments, causing varying mortality rates.
RNetDys: identification of disease-related impaired regulatory interactions due to SNPs
Authors: Barlier Céline , Ribeiro Mariana Messias , Jung Sascha , del Sol Antonio 
Published: October 2022

AbstractThe dysregulation of regulatory mechanisms due to Single Nucleotide Polymorphisms (SNPs) can lead to diseases and does not affect all cell (sub)types equally. Current approaches to study the impact of SNPs in diseases lack mechanistic insights. Indeed, they do not account for the regulatory landscape to decipher cell (sub)type specific regulatory interactions impaired due to disease-related SNPs. Therefore, characterizing the impact of disease-related SNPs in cell (sub)type specific regulatory mechanisms would provide novel therapeutical targets, such as promoter and enhancer regions, for the development of gene-based therapies directed at preventing or treating diseases. We present RNetDys, a pipeline to decipher cell (sub)type specific regulatory interactions impaired by disease-related SNPs based on multi-OMICS data. RNetDys leverages the information obtained from the generated cell (sub)type specific GRNs to provide detailed information on impaired regulatory elements and their regulated genes due to the presence of SNPs. We applied RNetDys in five disease cases to study the cell (sub)type differential impairment due to SNPs and leveraged the GRN information to guide the characterization of dysregulated mechanisms. We were able to validate the relevance of the identified impaired regulatory interactions by verifying their connection to disease-related genes. In addition, we showed that RNetDys identifies more precisely dysregulated interactions linked to disease-related genes than expression Quantitative Trait Loci (eQTL) and provides additional mechanistic insights. RNetDys is a pipeline available athttps://github.com/BarlierC/RNetDys.git
Patients with ACPA-positive and ACPA-negative Rheumatoid Arthritis Show Different Serological Autoantibody Repertoires and Autoantibody Associations with Disease Activity
Authors: Cunningham Kevin Y. , Hur Benjamin , Gupta Vinod K. , Arment Courtney A. , Wright Kerry A. , Mason Thomas G. , Peterson Lynne S. , Bekele Delamo I. , Schaffer Daniel E. , Bailey Marissa L. , Delger Kara E. , Crowson Cynthia S. , Myasoedova Elena , Zeng Hu , Rodriguez Moses , Weyand Cornelia M. , Davis John M. , Sung Jaeyun 
Published: October 2022

AbstractObjectivesPatients with rheumatoid arthritis (RA) can test either positive or negative for anti-citrullinated protein antibodies (ACPA), and are thereby ACPA-positive (ACPA+) or ACPA-negative (ACPA–), respectively. Through comprehensive profiling of autoantibodies in serum, we aimed to identify autoantibodies that are differentially abundant between patients with ACPA+ RA and ACPA– RA, and also those that are significantly associated with clinical disease activity.MethodsSerum was collected from patients with ACPA+ RA (n= 32), ACPA– RA (n= 30), and healthy controls (n= 30). Sengenics Immunome™protein microarray was used to screen for over 1,600 IgG autoantibodies against native, unmodified human proteins from each serum sample. Autoantibody profiles were compared between each RA subgroup and controls to identify differentially abundant autoantibodies (P< 0.05, Mann–WhitneyUtest; |Cliff’s delta (d)| > 0.33). Additionally, the relationship between RA patients’ autoantibody abundances and Clinical Disease Activity Index (CDAI) was examined for correlations between serum autoantibodies and disease activity (|Spearman’sρ| > 0.4 andP< 0.01).ResultsWe identified differences in serum autoantibodies between patients with ACPA+ RA and ACPA– RA compared with healthy controls. Specifically, we found 22 and 19 autoantibodies higher in ACPA+ RA patients and ACPA– RA patients, respectively. Among these two sets of autoantibodies, only one autoantibody (anti-GTF2A2) was common in both comparisons. On the other hand, we found 30 and 25 autoantibodies lower in ACPA+ RA and ACPA– RA, respectively, of which eight autoantibodies were common in both comparisons. Functional enrichment analysis of the protein antigens targeted by these autoantibodies showed an over-representation of a range of essential biological processes, including programmed cell death, metabolism, and signal transduction. Lastly, we found that autoantibodies correlate with CDAI, but associate differently depending on the presence or absence of ACPA.ConclusionsACPA status in patients with RA determines not only the composition of the serum autoantibody repertoire, but also the correlative relationships between autoantibodies and disease activity. Notably, many of the autoantibodies identified herein were reported for the first time. Our findings warrant further investigation into the immunological differences between these two RA subgroups, and shed new light on the possible need for different treatment approaches.
Accessibility of covariance information creates vulnerability in Federated Learning frameworks
Authors: Huth Manuel , Arruda Jonas , Gusinow Roy , Contento Lorenzo , Tacconelli Evelina , Hasenauer Jan 
Published: October 2022

AbstractFederated Learning (FL) is gaining traction in various fields as it enables integrative data analysis without sharing sensitive data, such as in healthcare. However, the risk of data leakage caused by malicious attacks must be considered. In this study, we introduce a novel attack algorithm that relies on being able to compute sample means, sample covariances, and construct known linearly independent vectors on the data owner side. We show that these basic functionalities, which are available in several established FL frameworks, are sufficient to reconstruct privacy-protected data. Additionally, the attack algorithm is robust to defense strategies that involve adding random noise. We demonstrate the limitations of existing frameworks and propose potential defense strategies analyzing the implications of using differential privacy. The novel insights presented in this study will aid in the improvement of FL frameworks.
Cell type catalog of middle turbinate epithelium
Authors: Mathews Fasil , Keng Tung Victoria Sook , Foronjy Robert , Boruk Marina , Knowles James A , Evgrafov Oleg V 
Published: October 2022

AbstractImportanceElucidation of the cellular makeup of the middle turbinate provides a foundation for future studies of pathogenesis of sinonasal disease. Neural progenitors and pluripotent basal cells found in middle turbinate mucosa potentially can be used to develop cellular models to study brain disorders or in regenerative medicine to substitute neuronal tissues.ObjectiveSingle cell RNA-sequencing (scRNA-seq) of middle turbinate mucosa was performed to create the first single cell transcriptome catalog of this part of the human body.DesignSamples were obtained from the head of the middle turbinate from healthy volunteers. After the specimen was prepared per lab protocol, cells were dissociated, suspended, and counted. Single cell libraries were then prepared according to the 10x Genomics protocol and sequenced using NovaSeq 6000 (Illumina). Sequencing data were processed using Cell Ranger, and clustering and gene expression analysis was performed using Seurat. Cell types were annotated using known markers and data from other single cell studies.SettingSingle center, tertiary care centerParticipantsHealthy volunteerIntervention(s) (for clinical trials) or Exposure(s) (for observational studies)NoneMain Outcome(s) and Measure(s)Identification of cell types of middle turbinate mucosa through expression profiling of single cells using known markersResults14 unique cell types were identified, including serous, goblet, club, basal, ciliated, endothelial, and neural progenitor cells, as well as multiple types of blood cells.Conclusions and RelevanceThis catalog provides a comprehensive depiction of the cellular composition of middle turbinate mucosa. By uncovering the cellular stratification of gene expression profiles in healthy middle turbinate epithelium, the groundwork has been laid for further investigation into the molecular pathogenesis and targeted therapy of sinonasal disease.Key PointsQuestionWhat is the cellular makeup of human middle turbinate mucosa?FindingsSingle-cell RNA sequencing revealed 14 cell types in middle turbinate epithelium, including neural progenitors, a previously unrecognized component of middle turbinate epithelium.MeaningGene expression profiles of middle turbinate mucosa cell types are concordant with other respiratory mucosa transcriptomic data with notable heterogeneity in serous and basal cells.□
A Cross-sectional Analysis of Food Perceptions, Food Preferences, Diet Quality, and Health in a Food Desert Campus
Authors: Aldaz Kaitlyn J. , Ortiz Sigry , Ortiz Rudy M. , Diaz Rios L. Karina , Dhillon Jaapna 
Published: October 2022

AbstractThe sensory properties of foods guide food choices and intake, importantly determining nutritional and health status. In communities that have inconsistent access to nutritious foods, such as food deserts, the food taste perceptions and preferences have yet to be explored. The paucity of data pertaining to food perceptions, preferences, and choices and the complex relationship of socioeconomic status (SES), race/ethnicity, and sex on cardiometabolic and cognitive health warrants further examination. Two hundred fifty participants (aged 18-24 years) living in a food desert campus were recruited for this cross-sectional study where participants underwent taste tests on selected fruits, vegetables, and nuts, and clinical tests (anthropometrics, blood glucose, blood pressure, and endothelial function), cognitive function tests (memory and attention), diet quality assessment (HEI), and food preference and perception assessments. Food taste intensities were influenced by sex with bitter and umami taste intensities of several foods being perceived more intensely by males. Moreover, food liking was largely influenced by ethnicity with Hispanics having higher liking ratings for several foods compared with non-Hispanics. Both, Hispanics and females, had higher total fruit HEI scores and lower attention scores than non-Hispanics and males respectively. Females also had lower blood pressure, reactive hyperemia index, and fasting blood glucose. Food-insecure individuals rated cost and convenience as more important factors for overall food consumption and had lower attention scores than those with higher food-security status. Future research should consider the complex interactions of factors such as taste and flavor perception, sex, ethnicity, prior exposure to foods, and other environmental factors when studying food preferences and health in young adults.
Epidemic graph diagrams as analytics for epidemic control in the data-rich era
Authors: Valdano Eugenio , Colombi Davide , Poletto Chiara , Colizza Vittoria 
Published: October 2022

AbstractCOVID-19 highlighted how modeling is an integral part of pandemic response. But it also exposed fundamental methodological challenges. As high-resolution data on disease progression, epidemic surveillance, and host behavior are now available, can models turn them into accurate epidemic estimates and reliable public health recommendations? Take the epidemic threshold, which estimates the potential for an infection to spread in a host population, quantifying epidemic risk throughout epidemic emergence, mitigation, and control. While models increasingly integrated realistic host contacts, no parallel development occurred with matching detail in disease progression and interventions. This narrowed the use of the epidemic threshold to oversimplified disease and control descriptions. Here, we introduce the epidemic graph diagrams (EGDs), novel representations to compute the epidemic threshold directly from arbitrarily complex data on contacts, disease and control efforts. We define a grammar of diagram operations to decompose, compare, simplify models, extracting new theoretical understanding and improving computational efficiency. We test EGDs on two public health challenges, influenza and sexuallytransmitted infections, to (i) explain the emergence of resistant influenza variants in the 2007-2008 season, and (ii) demonstrate that neglecting non-infectious prodromic stages biases the predicted epidemic risk, compromising control. EGDs are however general, and increase the performance of mathematical modeling to respond to present and future public health challenges.
Persisting low skin prick test prevalence among children receiving periodic anthelminthic treatment after recurrent soil-transmitted helminth infections: a one-year observation
Authors: Lubis Inke Nadia D. , Nasution Masitah , Nasution Rizky Keumala Ansari , Lubis Aridamuriany D. , Yanni Gema Nazri , Trisnawati Yunnie , Sofyan Ferryan 
Published: October 2022

AbstractBackgroundThe immune system in human develops when they are exposed to severe helminth infections. Chronic soil-transmitted helminth (STH) infection can modulate and suppress allergic reactions particularly by changing the responses from the immune effector. This study observed how STH infections are correlated with allergic reactions as determined by skin prick test (SPT).MethodologyFourty-five primary school children with recurrent STH infections (determined by at least two positive results in 4-monthly Kato Katz examination over a year period) who received periodic treatment from Mandailing Natal, were classified as case, and 45 primary school students with no history of STH infections from Medan were classified as control in this study. Positive SPT occurred among 27% and 89% of children in the case and control groups (OR 22, 95% CI 7.032-68.827), respectively. No history of helminthiasis, history of allergy, history of parent’s allergies, and history of sibling’s allergies were associated with increased risks of positive SPT.ConclusionOur findings supported the hygiene hypothesis, where decreased exposure to infectious disease pathogens and decreased diversity of microbial exposures in the environment increases the prevalence of allergies, and anthelminthic treatment show limited effect in reversing the protective effect of STH infections to allergies.
Structural snapshots uncover a lock-and-key type conserved activation mechanism of β-arrestins by GPCRs
Authors: Maharana Jagannath , Sarma Parishmita , Yadav Manish K. , Saha Sayantan , Singh Vinay , Saha Shirsha , Chami Mohamed , Banerjee Ramanuj , Shukla Arun K. 
Published: October 2022

AbstractAgonist-induced phosphorylation of G protein-coupled receptors (GPCRs) is a key determinant for the binding and activation of multifunctional regulatory proteins known as β-arrestins (βarrs). Although the primary sequence and phosphorylation pattern of GPCRs are poorly conserved, the downstream functional responses mediated by βarrs such as receptor desensitization, endocytosis and signaling are broadly applicable across GPCRs. A conserved principle of βarr activation, if any, upon their interaction with different GPCRs harboring divergent phosphorylation patterns remains to be visualized, and it represents a major knowledge gap in our current understanding of GPCR signaling and regulatory paradigms. Here, we present four structural snapshots of activated βarrs, in complex with distinct phosphorylation patterns derived from the carboxyl-terminus of three different GPCRs, determined using cryogenic-electron microscopy (cryo-EM). These structures of activated βarrs elucidate a “lock-and-key” type conserved mechanism of βarr activation wherein a P-X-P-P phosphorylation pattern in GPCRs interacts with a spatially organized K-K-R-R-K-K sequence in the N-domain of βarrs. Interestingly, the P-X-P-P pattern simultaneously engages multiple structural elements in βarrs responsible for maintaining the basal conformation, and thereby, leads to efficient βarr activation. The conserved nature of this lock-and-key mechanism is further illustrated by a comprehensive sequence analysis of the human GPCRome, and demonstrated in cellular context with targeted mutagenesis including “loss-of-function” and “gain-of-function” experiments with respect to βarr activation measured by an intrabody-based conformational sensor. Taken together, our findings uncover previously lacking structural insights, which explain the ability of distinct GPCRs to activate βarrs through a common mechanism, and a key missing link in the conceptual framework of GPCR-βarr interaction and resulting functional outcomes.
Structure-first identification of conserved RNA elements that regulate dengue virus genome architecture and replication
Authors: Boerneke Mark A. , Gokhale Nandan S. , Horner Stacy M. , Weeks Kevin M. 
Published: October 2022

AbstractThe genomes of RNA viruses encode the information required for replication in host cells in both their linear sequence and in complex higher-order structures. A subset of these complex functional RNA genome structures show clear sequence conservation. However, the extent to which viral RNA genomes contain conserved structural elements – that cannot be detected by sequence alone – that nonetheless are critical to viral fitness is largely unknown. Here, we take a structure-first approach to identify motifs conserved across the coding sequences of the RNA genomes for the four dengue virus (DENV) serotypes. We used SHAPE-MaP to identify 22 candidate motifs with conserved RNA structures, but no prior association with viral replication. At least ten of these motifs are important for viral fitness, revealing a significant unnoticed extent of RNA structure-mediated regulation within viral coding sequences. These conserved viral RNA structures promote a compact global genome architecture, interact with proteins, and regulate the viral replication cycle. These motifs are constrained at the levels of both RNA structure and protein sequence and are potential resistance-refractory targets for antivirals and live-attenuated vaccines. Structure-first identification of conserved RNA structure is poised to guide efficient discovery of RNA-mediated regulation in viral genomes and other cellular RNAs.
Fusion event-triggered model predictive control based on shrinking prediction horizon
Authors: Cao Qun , Xia Yuanqing , Sun Zhongqi , Dai Li 
Published: October 2022

Purpose
This paper aims to design an algorithm which is used to deal with non-linear discrete systems with constraints under the lower computation burden. As a result, we solve the non-holonomic vehicle tracking problem with the lower computational load and the convergence performance.

Design/methodology/approach
A fusion event-triggered model predictive control version is developed in this paper. The authors designed a shrinking prediction strategy.

Findings
The fusion event-triggered model predictive control scheme combines the strong points of event triggered and self-triggered methods. As the practical state approaches the terminal set, the computational complexity of optimal control problem (OCP) decreases.

Originality/value
The proposed strategy has proven to stabilize the system and also guarantee a reproducible solution for the OCP. Also, it is proved to be effected by the performance of the simulation results.
Impression management tactics in Covid-19 related disclosures: a study on the annual reports of Bangladeshi listed insurance companies
Authors: Hossain Dewan Mahboob , Alam Md. Saiful , Mazumder Mohammed Mehadi Masud 
Published: October 2022

PurposeThe purpose of this article is to explore the impression management practices in Covid-19 related discourses in the annual reports of the insurance companies in Bangladesh.Design/methodology/approachTo fulfil this objective, the authors have conducted a discourse analysis of the Covid-19 related corporate narratives in the latest annual reports of listed insurance companies. The findings are then interpreted through the lens of impression management theory, following the impression management strategies identified by Caliskan et al. (2021).FindingsIt is found that companies tried to manage the impression of the stakeholders through the strategic use of language. There is evidence that the companies used assertive and performance-oriented tactics to impress their stakeholders. In few cases, defensive strategies were applied.Practical implicationsThis study will facilitate improving the understanding of corporate communication during the Covid-19 crisis. Policymakers will be able to understand the current status of Covid-19 related disclosures and consider the necessity to provide guidance that may lead to better accountability during the crisis.Originality/valueThis study will contribute to the limited literature on Covid-19 related disclosure from the context of developing economies. This research is methodologically novel as it applies discourse analysis and interprets the findings through the lens of impression management.