bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weak SARS-CoV-2-specific responses of TIGIT-expressing CD8+ T cells in people living with HIV after a third dose of a SARS-CoV-2 inactivated vaccine
Authors: Jin Junyan , Wang Xiuwen , Li Yongzheng , Yang Xiaodong , Wang Hu , Han Xiaoxu , Sun Jin , Ma Zhenglai , Duan Junyi , Zhang Guanghui , Huang Tao , Zhang Tong , Wu Hao , Zhang Xin , Su Bin 
Published: November 2023

Abstract

Background:
T-cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibition motif domains (TIGIT), an inhibitory receptor expressed on T cells, plays a dysfunctional role in antiviral infection and antitumor activity. However, it is unknown whether TIGIT expression on T cells influences the immunological effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inactivated vaccines.

Methods:
Forty-five people living with HIV (PLWH) on antiretroviral therapy (ART) for more than two years and 31 healthy controls (HCs), all received a third dose of a SARS-CoV-2 inactivated vaccine, were enrolled in this study. The amounts, activation, proportion of cell subsets, and magnitude of the SARS-CoV-2-specific immune response of TIGIT+CD4+ and TIGIT+CD8+ T cells were investigated before the third dose but 6 months after the second vaccine dose (0W), 4 weeks (4W) and 12 weeks (12W) after the third dose.

Results:
Compared to that in HCs, the frequency of TIGIT+ CD8+ T cells in the peripheral blood of PLWH increased at 12W after the third dose of the inactivated vaccine, and the immune activation of TIGIT+CD8+ T cells also increased. A decrease in the ratio of both T naïve (TN) and central memory (TCM) cells among TIGIT+CD8+ T cells and an increase in the ratio of the effector memory (TEM) subpopulation were observed at 12W in PLWH. Interestingly, particularly at 12W, a higher proportion of TIGIT+CD8+ T cells expressing CD137 and CD69 simultaneously was observed in HCs than in PLWH based on the activation-induced marker assay. Compared with 0W, SARS-CoV-2-specific TIGIT+CD8+ T-cell responses in PLWH were not enhanced at 12W but were enhanced in HCs. Additionally, at all time points, the SARS-CoV-2-specific responses of TIGIT+CD8+ T cells in PLWH were significantly weaker than those of TIGIT–CD8+ T cells. However, in HCs, the difference in the SARS-CoV-2-specific responses induced between TIGIT+CD8+ T cells and TIGIT–CD8+ T cells was insignificant at 4W and 12W, except at 0W.

Conclusions:
TIGIT expression on CD8+ T cells may hinder the T-cell immune response to a booster dose of an inactivated SARS-CoV-2 vaccine, suggesting weakened resistance to SARS-CoV-2 infection, especially in PLWH. Furthermore, TIGIT may be used as a potential target to increase the production of SARS-CoV-2-specific CD8+ T cells, thereby enhancing the effectiveness of vaccination.
Exposure to ultrafine particles and the incidence of asthma in children
Authors: da Silveira Fleck Alan , Vachon Julien , Buteau Stéphane , Laouan-Sidi Elhadji Anassour , Hatzopoulou Marianne , Weichenthal Scott , Smargiassi Audrey 
Published: November 2023

Background:
Asthma is the most prevalent chronic respiratory disease in children. The role of ultrafine particles (UFPs) in the development of the disease remains unclear. We used a population-based birth cohort to evaluate the association between prenatal and childhood exposure to low levels of ambient UFPs and childhood-onset asthma.

Methods:
The cohort included all children born and residing in Montreal, Canada, between 2000 and 2015. Children were followed for asthma onset from birth until <13 years of age. Spatially resolved annual mean concentrations of ambient UFPs were estimated from a land use regression model. We assigned prenatal exposure according to the residential postal code at birth. We also considered current exposure during childhood accounting for time-varying residence location. We estimated hazard ratios (HRs) using Cox proportional hazards models adjusted for age, sex, neighborhood material and social deprivation, calendar year, and coexposure to ambient nitrogen dioxide (NO2) and fine particles (PM2.5).

Results:
The cohort included 352,966 children, with 30,825 children developing asthma during follow-up. Mean prenatal and childhood UFP exposure were 24,706 particles/cm3 (interquartile range [IQR] = 3,785 particles/cm3) and 24,525 particles/cm3 (IQR = 3,427 particles/cm3), respectively. Both prenatal and childhood UFP exposure were not associated with childhood asthma onset in single pollutant models (HR per IQR increase of 0.99 [95% CI = 0.98, 1.00]). Estimates of association remained similar when adjusting for coexposure to ambient NO2 and PM2.5.

Conclusion:
In this population-based birth cohort, childhood asthma onset was not associated with prenatal or childhood exposure to low concentrations of UFPs.
Baseline Quality of Life in Low-Flow Head and Neck Vascular Malformations in Children
Authors: Evans Sean S. , Goudy Steven L. , Siong Tey Ching , Swerdlin Rachel F. , Hawkins C. Matthew 
Published: November 2023

Objective:
To determine baseline quality of life characteristics in patients with low-flow head and neck vascular malformations.

Study Design:
Retrospective review of prospectively collected data.

Setting:
Tertiary Pediatric Hospital.

Methods:
Patients with low-flow head and neck vascular malformations (age 0–18 years) evaluated through our vascular anomalies clinic from 2016 to 2019 were reviewed. Patients with completed PedsQL surveys using parent-proxy reports for children 2–7 years old and both patient and parent-proxy data for patients ≥8 years old were included.

Results:
In total 94 consecutive patients were included, with a mean age of 9.2 ± 4.7 years. Diagnoses included lymphatic malformations (n = 50), venous malformations (n = 41), and combined venolymphatic malformations (n = 3). Total parental quality of life scores were lower than their children’s (84.23 vs 87.45; P = .037), with lower emotional scores as age at presentation increased (d = −0.60; P < .01). Lower parental scores were also noted across multiple domains for submandibular/sublingual, oropharyngeal, hypopharyngeal, and orbital involvement. (g = −0.68 to −1.10; P < .05). Increasing subsite number involvement affected parents and children similarly (−0.30 vs −0.35; P ≤ .02). Higher physical function scores were noted in venous versus lymphatic malformations (d =−1.07; P = .01). The child-reported school function scores were lower in African-American versus Caucasian children (P = .04). Prior treatment was associated with lower parental scores (d = 0.59; P = .04).

Conclusion:
The parent and patient’s quality of life is reduced across multiple domains for low-flow head and neck vascular malformations based on age, lesion location and type, disease burden, race, and prior treatment.
COVID-19 Vaccine Policy Implementation and Differential Vaccine Uptake Trajectories in Chicago Communities
Authors: Kim Sage J. , McWhirter Noah , Duong Kelly , Khare Manorama M. , Giles Wayne H. , Basu Sanjib , Hershow Ronald C. , Stiehl Emily 
Published: November 2023

Background:
Since the onset of the COVID-19 pandemic, multiple public health interventions have been implemented to respond to the rapidly evolving pandemic and community needs. This article describes the scope, timing, and impact of coordinated strategies for COVID-19 vaccine uptake in Chicago for the first year of vaccine distribution.

Methods:
Using a series of interviews with public health officials and leaders of community-based organizations (CBOs) who participated in the implementation of the citywide COVID-19 vaccine outreach initiatives, we constructed a timeline of vaccine outreach initiatives. The timeline was matched to the vaccine uptake rates to explore the impact of the vaccine outreach initiatives by community area. Finally, we discussed the nature of policy initiatives and the level of vaccine uptake in relation to community characteristics.

Results:
The Chicago Department of Public Health (CDPH) implemented myriad vaccine outreach strategies, including mass vaccination sites, improved access, and community-level vaccine campaigns. Protect Chicago+ was the primary vaccine outreach effort initiated by the CDPH, which identified 15 highly vulnerable community areas. More than 2.7 million (67%) Chicagoans completed the vaccine regimen by December 2021. Black (51.3%) Chicagoans were considerably less likely to be vaccinated than Asian (77.6%), White (69.8%), and Hispanic (63.6%) Chicago residents. In addition, there were significant spatial differences in the rate of COVID-19 vaccine completion: predominantly White and Hispanic communities, compared with Black communities, had higher rates of vaccine completion.

Conclusions:
The community outreach efforts to improve COVID-19 vaccine uptake in Chicago have shown the importance of community-engaged approaches in pandemic responses. Despite citywide efforts to build community infrastructure, Black communities had relatively lower levels of vaccine uptake than other communities. Broader social restructuring to mitigate disinvestment and residential segregation and to ameliorate medical mistrust will be needed to prepare for future pandemics and disasters.
SillyPutty: Improved clustering by optimizing the silhouette width
Authors: Bombina Polina , Tally Dwayne , Abrams Zachary B. , Coombes Kevin R. 
Published: November 2023

AbstractUnsupervised clustering is an important task in biomedical science. We developed a new clustering method, called SillyPutty, for unsupervised clustering. As test data, we generated a series of datasets using the Umpire R package. Using these datasets, we compared SillyPutty to several existing algorithms using multiple metrics (Silhouette Width, Adjusted Rand Index, Entropy, Normalized Within-group Sum of Square errors, and Perfect Classification Count). Our findings revealed that SillyPutty is a valid standalone clustering method, comparable in accuracy to the best existing methods. We also found that the combination of hierarchical clustering followed by SillyPutty has the best overall performance in terms of both accuracy and speed.AvailabilityThe SillyPutty R package has been submitted to the Comprehensive R Archive Network (CRAN). Code to perform and analyze the simulations described here can be found in a Git project hosted athttps://gitlab.com/krcoombes/sillyputty.
The change of lymphocyte subsets and inflammatory cytokine in BK viruria
Authors: Jiang Yu Huan , Yuan Lei , Chen Qiang , He Hui Min , Liu Yang , Lai Lan Min 
Published: November 2023

BackgroundPolyomavirus BK (BKV) infection as a serious complication after kidney transplantation. The process of infections in kidney transplant recipients is viruria, viremia, and BKVAN. The difference between BK negative and BK viruria in kidney recipients has not been defined.Patients and MethodsWe compared post-transplant lymphocyte subsets 、blood cytokines、urine cytokines levels of 19 renal transplant outpatients with (BK-positive) or without BK viruria (BK-negative, n=20), and 20 healthy controls (HCs). Group of BK-positive divide into low-(n=4) and high-level (n=15) According to BK viral load (VL).Immune cells including T cells, B cells, and natural killer (NK) cells、interleukin-2(IL-2),IL-5,IL-6, IL-1β, IL-10, IL-8, IL-17A,IL-4,IL-12P70, interferon-α(IFN-α), IFN-γ,and tumor necrosis factor-α (TNF-α)were determined by flow cytometry.ResultsBK-positive patients showed higher urine IL-1β (P=0.040), IL-10 (P=0.010), IFN-γ (P=0.002), and TNF-α (P=0.027) than BK-negative patients. Compared with HCs, BK-negative patients had lower urine IL-1β (P=0.04), IL-10 (P=0.01), TNF-α (P=0.027) and IFN-γ (P=0.004),suggesting that cytokine expression regulation BK-infection.ConclusionBK-positive renal transplant recipients, especially those with high VL, showed strong inflammatory cytokine responses with increases of urine IL-1β, IL-10, IFN-γ, and TNF-α. Our data suggest that monocyte- and Th-2-induced cytokines are involved in the pathogenesis of BKV-associated nephropathy.
Design and fabrication of flexible biodegradable microelectrode array for recording electrocorticography signals
Authors: Chatterjee Suman , Joshi Rathin K. , Bhaskara Sreenivas , Hari RS , Datta Shubham , Shabari Girishan KV , Pandya Hardik J. 
Published: November 2023

AbstractConventional flexible implantable microelectrode arrays, used for real-time brain activity monitoring, incur minimal tissue damage due to their flexibility; however, these require retrieval surgery, causing trauma to subjects. Implants, fabricated using biodegradable materials, dissolve gradually in body fluid, eliminating the necessity for retrieval surgery. This work reports designing and developing a 10-channel flexible biodegradable microelectrode array to acquire electrocorticography signals from rats’ brains. The array was fabricated using tungsten, a transient metal, and PLLA:PCL (80:20), a biodegradable composite polymer. The subdural implantation of the array on the somatosensory cortex of rats (n=3) facilitated electrical biopotentials acquisition using OpenBCI Cyton Boards. The baseline activities, the induced epileptic discharges after peripheral electrical stimulation, and the recovered baseline activities after antiepileptic drug administration were recorded from sedated rats. The chronic baselines and evoked activities were also acquired from awake rats. The gradual decline of chronic baselines was evident, suggesting a possible dissolution of electrodes. Furthermore, the time-frequency analyses demonstrate the differences between baselines and induced epileptic activities. The signals recorded from microelectrode arrays demonstrate their potential to monitor brain activities in a chronic study. Histology of the harvested vital organs from the euthanized rats confirmed minimal tissue damage due to implantation.
Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome
Authors: Oesterle Ian , Ayeni Kolawole I. , Ezekiel Chibundu N. , Berry David , Rompel Annette , Warth Benedikt 
Published: November 2023

AbstractEarly-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 byin silicofragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin were elevated when complementary foods were introduced to the infants’ diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genusBlautia. Moreover, vulgaxanthin negatively correlated withEscherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.Highlights-Suspect screening of exposure biomarkers in human breast milk and infant stool.-542 features in breast milk and 864 in stool were identified or annotated.-Consumption of complementary foods influenced the chemical exposure of infants.-Correlations between xenobiotics in both biological matrices evaluated.-Dietary exposure correlated to the stool microbiome composition.Graphical abstract
In vivoscreening for toxicity-modulating drug interactions identifies antagonism that protects against ototoxicity in zebrafish
Authors: Bustad Ethan , Mudrock Emma , Nilles Elizabeth M. , McQuate Andrea , Bergado Monica , Gu Alden , Galitan Louie , Gleason Natalie , Ou Henry C. , Raible David W. , Hernandez Rafael E. , Ma Shuyi 
Published: November 2023

AbstractOtotoxicity is a debilitating side effect of over 150 medications with diverse mechanisms of action, many of which could be taken concurrently to treat multiple conditions. Approaches for preclinical evaluation of drug interactions that might impact ototoxicity would facilitate design of safer multi-drug regimens and mitigate unsafe polypharmacy by flagging combinations that potentially cause adverse interactions for monitoring. They may also identify protective agents that antagonize ototoxic injury. To address this need, we have developed a novel workflow that we call Parallelized Evaluation of Protection and Injury for Toxicity Assessment (PEPITA), which empowers high-throughput, semi-automated quantification of ototoxicity and otoprotection in zebrafish larvae. By applying PEPITA to characterize ototoxic drug interaction outcomes, we have discovered antagonistic interactions between macrolide and aminoglycoside antibiotics that confer protection against aminoglycoside-induced damage to lateral line hair cells in zebrafish larvae. Co-administration of either azithromycin or erythromycin in zebrafish protected against damage from a broad panel of aminoglycosides, at least in part via inhibiting drug uptake into hair cells via a mechanism independent from hair cell mechanotransduction. Conversely, combining macrolides with aminoglycosides in bacterial inhibition assays does not show antagonism of antimicrobial efficacy. The proof-of-concept otoprotective antagonism suggests that combinatorial interventions can potentially be developed to protect against other forms of toxicity without hindering on-target drug efficacy.
Genomic architecture of nestmate recognition cues in the desert ant
Authors: Cohen Pnina , Inbar Shani , Privman Eyal 
Published: November 2023

AbstractNestmate recognition is the basis for cooperation within social insect colonies. Quantitative variation in cuticle hydrocarbons (CHCs) is used for nestmate recognition in ants and other social insects. We carried out a Genome Wide Association Study (GWAS) of CHCs in the desert antCataglyphis nigerby sampling 47 colonies, fully sequencing six workers from each colony, and measuring the relative amounts of their CHCs. Under the Gestalt colony odour model, social interactions between nestmates, in which CHCs are being transferred and mixed, are essential in creating a uniform colony CHC profile.Therefore, we carried out a second GWAS between the colonies and their uniform Gestalt odour by averaging nestmate genotypes and comparing them to their averaged CHC amounts. Our results are in line with the Gestalt model. Together, the two analyses identified 99 candidate QTLs associated with 18 of the CHCs. Thirteen clusters of two to four QTLs located within 10cM from each other were identified, seven of which contained QTLs from both analyses. We conclude that nestmate recognition cues are a complex quantitative colony-level trait with a significant genetic component to their phenotypic variation and a highly polygenic architecture.
Physiological variability in mitochondrial rRNA predisposes to metabolic syndrome
Authors: Pecina Petr , Čunátová Kristýna , Kaplanová Vilma , Puertas-Frias Guillermo , Šilhavý Jan , Tauchmannová Kateřina , Vrbacký Marek , Čajka Tomáš , Gahura Ondřej , Pravenec Michal , Houštěk Josef , Mráček Tomáš , Pecinová Alena 
Published: November 2023

AbstractMetabolic syndrome is a growing concern in developed societies, and due to its polygenic nature, the genetic component is only slowly being elucidated. Common mitochondrial DNA sequence variants have been associated with symptoms of metabolic syndrome and may be relevant players in the genetics of metabolic syndrome.We investigate the effect of mitochondrial sequence variation on the metabolic phenotype in conplastic rat strains with identical nuclear but unique mitochondrial genomes, challenged by high-fat diet. We find that the variation in mitochondrial rRNA sequence represents a risk factor in insulin resistance development, which is caused by diacylglycerols accumulation induced by tissue-specific reduction of the oxidative capacity. These metabolic perturbations stem from the 12S rRNA sequence variation affecting mitochondrial ribosome assembly and translation. Our work demonstrates that physiological variation in mitochondrial rRNA might represent a relevant underlying factor in the progression of metabolic syndrome.Competing interestsThe authors declare that no competing interests exist.
Structure of scavenger receptor SCARF1 and its interaction with lipoproteins
Authors: Wang Yuanyuan , Xu Fan , Li Guangyi , Cheng Chen , Yu Bowen , Zhang Ze , Kong Dandan , Chen Fabao , Liu Yali , Fang Zhen , Cao Longxing , Yu Yang , Gu Yijun , He Yongning 
Published: November 2023

AbstractSCARF1 (Scavenger receptor class F member 1, SREC-1 or SR-F1) is a type I transmembrane protein that recognizes multiple endogenous and exogenous ligands such as modified low-density lipoproteins (LDL) and is important for maintaining homeostasis and immunity. But the structural information and the mechanisms of ligand recognition of SCARF1 are largely unavailable. Here we solve the crystal structures of the N-terminal fragments of human SCARF1, which show that SCARF1 forms homodimers and its epidermal growth factor (EGF)-like domains adopt a long-curved conformation. Then we examine the interactions of SCARF1 with lipoproteins and are able to identify a region on SCARF1 for recognizing modified LDLs. The mutagenesis data show that the positively charged residues in the region are crucial for the interaction of SCARF1 with modified LDLs, which is confirmed by making chimeric molecules of SCARF1 and SCARF2. In addition, teichoic acids, a cell wall polymer expressed on the surface of gram-positive bacteria, are able to inhibit the interactions of modified LDLs with SCARF1, suggesting the ligand binding sites of SCARF1 might be shared for some of its scavenging targets. Overall, these results provide mechanistic insights into SCARF1 and its interactions with the ligands, which are important for understanding its physiological roles in homeostasis and the related diseases.