bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anti-Neuraminidase Antibodies Reduce the Susceptibility to and Infectivity of Influenza A/H3N2 Virus
Authors: Hoy Gregory , Cortier Thomas , Maier Hannah E. , Kuan Guillermina , Lopez Roger , Sanchez Nery , Ojeda Sergio , Plazaola Miguel , Stadlbauer Daniel , Shotwell Abigail , Balmaseda Angel , Krammer Florian , Cauchemez Simon , Gordon Aubree 
Published: June 2024

AbstractImmune responses against neuraminidase (NA) are of great interest for developing more robust influenza vaccines, but the role of anti-NA antibodies on influenza infectivity has not been established. We conducted household transmission studies in Managua, Nicaragua to examine the impact of anti-NA antibodies on influenza A/H3N2 susceptibility and infectivity. Analyzing these data with mathematical models capturing household transmission dynamics and their drivers, we estimated that having higher preexisting antibody levels against the hemagglutinin (HA) head, HA stalk, and NA was associated with reduced susceptibility to infection (relative susceptibility 0.67, 95% Credible Interval [CrI] 0.50-0.92 for HA head; 0.59, 95% CrI 0.42-0.82 for HA stalk; and 0.56, 95% CrI 0.40-0.77 for NA). Only anti-NA antibodies were associated with reduced infectivity (relative infectivity 0.36, 95% CrI 0.23-0.55). These benefits from anti-NA immunity were observed even among individuals with preexisting anti-HA immunity. These results suggest that influenza vaccines designed to elicit NA immunity in addition to hemagglutinin immunity may not only contribute to protection against infection but reduce infectivity of vaccinated individuals upon infection.
Assessing knowledge, attitudes, and behaviours toward salt and sugar consumption in the Central Division of Fiji
Authors: Waqa Gade , Bell Colin , Santos Joseph Alvin , Rogers Kris , Silatolu Anasaini Moala , Reeve Erica , Palu Aliyah , Deo Alvina , Webster Jacqui , McKenzie Briar 
Published: June 2024

AbstractBackgroundExcessive salt and sugar intake influence the global burden of non-communicable diseases. This study aimed to describe the knowledge, attitudes and behaviours (KAB) of Fijian adults relating to salt and sugar consumption to inform policy interventions in Fiji.MethodsA randomised stratified sample of 700 adults in the Central Division of Fiji were selected. Questions on salt-related KAB were adapted from the World Health Organization Noncommunicable Disease Risk Factor survey, and questions on sugar were developed following a similar structure. Locally trained research assistants collected data. For analyses, population and sample weights were applied, and difference between predefined subgroups (sex, age, ethnicity and area of residence) were compared using weighted chi-square tests.Results534 adults participated (response rate,76%). Over 80% of participants (82% (95% CI 78.5 to 84.9%)) identified that consuming too much salt or salty sauce can lead to hypertension. More than 90% recognized that consuming too much sugar can lead to diabetes (92.3% (89.7 to 94.3%)). Approximately 80% of participants thought it was somewhat or very important to lower salt and sugar intake in their diet (79.8% (95%CI, 76.1 to 83.0) and 84.2% (80.8 to 87.1%), respectively). However, self-reported behaviours did not align, with almost 40% adding salt or salty sauces as standard practice when cooking (37.3% (32.7 to 42.2%)) and 65% (60.6 to 68.5%) reporting that they add sugar to drinks daily. Younger compared to older individuals (18 to 44 years vs 45 years and older) and men compared to women, had lower levels of KAB.ConclusionDespite having knowledge of the health impacts of consuming excess salt and sugar and positive attitudes towards reducing consumption, many people reported behaviours likely to contribute to high salt and sugar intake. These findings highlight the need for interventions that incentivise healthier choices, through behaviour change communications and the creation of supportive food environments.
Impact of data labeling protocol on the quality of LGE-MRI atrial segmentation
Authors: Berezhnoy A.K. , Kalinin A.S. , Parshin D.A. , Selivanov A.G. , Demin A.G. , Zubov A.G. , Shaidullina R.S. , Aitova A.A. , Slotvitsky M. M. , Kalemberg A.A. , Kirillova V.S. , Syrovnev V.A. , Tsvelaya V.A. 
Published: June 2024

AbstractAtrial fibrillation affects up to 2% of the adult population in developed countries, and ablation as the main method of treatment leads to a high probability of recurrence. For such procedures, the approach of creating an in silico model of the patient’s atrium to be used for navigation during the catheter ablation procedure itself is extremely promising. In this case, the MRI data on which the model is based must be loaded into the system and segmented with high accuracy. This paper describes a new universal protocol for the segmentation of LGE MRI images. This protocol has been used to train state-of-the-art neural networks for automatic MRI segmentation. It is shown that the new data labeling protocol significantly improves the training quality of the network. Using this approach, it is possible to improve the quality of the reproduction of the patient’s atrial parameters and the performance of all related services. The presented protocol is also accompanied by a labeled image dataset. In the future, the data from such labels can be used for predictive modeling and the creation of digital twins of patients’ atria.
A single center retrospective study to examine the effect of concomitant metformin treatment on cisplatin induced nephrotoxicity in adult HNSCC patients between 2015-2021
Authors: Ellayan Dawud 
Published: June 2024

AbstractPurposeExamine the effect of AMPK activation in addition to OCT2 competitive blockage through metformin concomitant treatment on the incidence rate of nephrotoxicity in adult head and neck cancer patients treated with cisplatin-based chemoradiation.MethodsA single center retrospective three to one controlled study in HNSCC patients treated at a single academic health center between January 1st 2015 to December 31st 2021. Patients treated with cisplatin based chemoradiation regimen at a dose of either 40 mg/m2 weekly, or 100 mg/m2 every 3 weeks for a total of 7 weeks were identified and were divided into two cohorts; Cohort A with patients who received concomitant metformin therapy, where concomitant is defined as taken prior to the time of cisplatin start and continued during treatment. And cohort B with a control group of patients who did not receive metformin during cisplatin treatment.Results18 patients were enrolled retrospectively in cohort A and 54 in cohort B. Our data shows a lower incidence of nephrotoxicity than reported in historical controls. However, no statistically significant differences were identified in direct comparison between the two cohorts.ConclusionOur data reaffirms the higher risk of nephrotoxicity for patients on Q3weeks regimen compared to weekly regimen, however, we were unable to show a statistically significant effect in direct comparison between the cohorts due to sample size limitation.
The sexual and gender-diverse face more health challenges during COVID-19: A large-scale social media analysis with natural language processing
Authors: Zhang Zhiyun , Hua Yining , Zhou Peilin , Lin Shixu , Li Minghui , Zhang Yujie , Zhou Li , Liao Yanhui , Yang Jie 
Published: June 2024

AbstractBackground:The COVID-19 pandemic has caused a disproportionate impact on the sex and gender diversity (SGD) community. Compared with non-SGD populations, their social relations and health status are more vulnerable, whereas public health data regarding SGD is scarce.Methods:To analyze the concerns and health status of SGD individuals, this cohort study leveraged 471,371,477 tweets from 251,455 SGD and 22,644,411 non-SGD users, spanning from February 1, 2020, to April 30, 2022. The outcome measures comprised the distribution and dynamics of COVID-related topics, attitudes towards vaccines and the prevalence of symptoms.Results:Topic analysis revealed that SGD users engaged more frequently in discussions related to “friends and family” (20.5% vs 13.1%, P<0.001) and “wear masks” (10.1% vs 8.3%, P<0.001) compared to non-SGD users. Additionally, SGD users exhibited a significantly higher proportion of positive sentiment in tweets about vaccines, including Moderna, Pfizer, AstraZeneca, and Johnson & Johnson. Among 102,464 users who self-reported COVID-19 diagnoses, SGD users disclosed significantly higher frequencies of mentioning 61 out of 69 COVID-related symptoms to non-SGD users, encompassing both physical and mental health challenges.Conclusion:The results provide insights to an understanding of the unique needs and experiences of the SGD community during the pandemic, emphasizing the value of social media data in epidemiological and public health research.
Hybrid adaptive immunity to SARS-CoV-2 protects against breakthrough infection after COVID-19 vaccination in ALSPAC participants
Authors: Baum Holly E. , Santopaolo Marianna , Francis Ore , Milowdowski Emily , Entwistle Katrina , Oliver Elizabeth , Hitchings Benjamin , Diamond Divya , Thomas Amy C. , Mitchell Ruth E. , Kibble Milla , Gupta Kapil , Di Bartolo Natalie , Klenerman Paul , Brown Anthony , Morales-Aza Begonia , Oliver Jennifer , Berger Imre , Toye Ash M. , Finn Adam , Goenka Anu , Davidson Andrew D. , Ring Susan , Molloy Lynn , Lewcock Melanie , Northstone Kate , Roth Firona , Timpson Nicholas J. , Wooldridge Linda , Halliday Alice , Rivino Laura 
Published: June 2024

SUMMARYImmunological memory to vaccination and viral infection involves coordinated action of B and T-cells, thus integrated analysis of these two components is critical for understanding their contributions to protection against breakthrough infections (BI). We investigated cellular and humoral immune responses to SARS-CoV-2 infection and/or COVID-19 vaccination in participants from the Avon Longitudinal Study of Parents and Children (ALSPAC). The magnitude of antibody and T-cell responses following the second vaccine dose was associated with protection against BI in participants with a history of SARS-CoV-2 infection (cases), but not in infection-naïve controls. Youden’s index thresholds for protection against BI were calculated for all immune measures. Anti-Spike IgG (>666.4 BAU/mL) and anti-Nucleocapsid pan Ig (>0.1332 BAU/mL) thresholds combined were 100% specific and 83.3% sensitive for cases without BI over 8-months follow-up. Collectively these results point to the superior protective effect of hybrid immunity and have implications for the design of next-generation COVID-19 vaccines.
Racial Disparities and Trends in Anticoagulant Use among Ambulatory Care Patients with Atrial Fibrillation and Atrial Flutter in the United States from 2007-2019
Authors: Kan Vincent , Lapane Kate , McManus David , Baek Jonggyu , Darling Chad , Alcusky Matthew 
Published: June 2024

ABSTRACTIntroductionAtrial fibrillation (AF) is the most common sustained cardiac arrhythmia, significantly increasing the risk of stroke. The introduction of direct oral anticoagulants (DOACs) since 2010 has transformed anticoagulation therapy, offering an alternative to warfarin with improved safety profiles. Despite the increased adoption of DOACs, disparities in their use among different racial and ethnic groups in the United States remain understudied.MethodsThis study utilized a repeated cross-sectional design, analyzing data from the National Ambulatory Medical Care Survey (NAMCS) from 2007 to 2019. The study population included adults diagnosed with AF or atrial flutter (AFL). We analyzed the temporal trends of DOAC and warfarin use from 2007 to 2019. We examined the prevalence of DOAC versus warfarin use and assessed associations between race/ethnicity, patient characteristics, and DOAC utilization from 2011 to 2019. Multivariable modified Poisson regression models were used to calculate adjusted prevalence ratios (aPR) for the associations.ResultsFrom 2011 to 2019, NAMCS recorded 3,224 visits involving AF or AFL, representing a weighted estimate of 103.6 million visits. DOAC use increased significantly, with apixaban becoming the predominant anticoagulant by 2016. Non-Hispanic Black patients were less likely to use DOACs compared to non-Hispanic White patients over time (aPR 0.75; 95% CI, 0.63-0.90). Patients with Medicaid insurance were also less likely to use DOACs (aPR 0.14; 95% CI: 0.04-0.46).ConclusionDespite the shift from warfarin to DOACs for AF and AFL treatment, significant racial and socioeconomic disparities persist. Non-Hispanic Black patients and those with Medicaid insurance are less likely to use DOACs. These findings highlight the need for targeted strategies to ensure equitable access to advanced anticoagulant therapies.
The expression patterns of different cell types and their interactions in the tumor microenvironment are predictive of breast cancer patient response to neoadjuvant chemotherapy
Authors: Dhruba Saugato Rahman , Sahni Sahil , Wang Binbin , Wu Di , Rajagopal Padma Sheila , Schmidt Yael , Shulman Eldad D. , Sinha Sanju , Sammut Stephen-John , Caldas Carlos , Wang Kun , Ruppin Eytan 
Published: June 2024

ABSTRACTThe tumor microenvironment (TME) is a complex ecosystem of diverse cell types whose interactions govern tumor growth and clinical outcome. While the TME’s impact on immunotherapy has been extensively studied, its role in chemotherapy response remains less explored. To address this, we developed DECODEM (DEcouplingCell-type-specificOutcomes usingDEconvolution andMachine learning), a generic computational framework leveraging cellular deconvolution ofbulk transcriptomicsto associate the gene expression of individual cell types in the TME with clinical response. Employing DECODEM to analyze the gene expression of breast cancer (BC) patients treated with neoadjuvant chemotherapy, we find that the gene expression of specific immune cells (myeloid,plasmablasts,B-cells) and stromal cells (endothelial,normal epithelial,CAFs) are highly predictive of chemotherapy response, going beyond that of the malignant cells. These findings are further tested and validated in a single-cell cohort of triple negative breast cancer. To investigate the possible role of immune cell-cell interactions (CCIs) in mediating chemotherapy response, we extended DECODEM to DECODEMi to identify such CCIs, validated in single-cell data. Our findings highlight the importance of active pre-treatment immune infiltration for chemotherapy success. The tools developed here are made publicly available and are applicable for studying the role of the TME in mediating response from readily available bulk tumor expression in a wide range of cancer treatments and indications.
Top-Down Modulation of Visual Action Perception: Distinct Task Effects in the Action Observation Network
Authors: Eroğlu Aslı , Urgen Burcu A. 
Published: June 2024

AbstractPerceiving others’ actions is essential for survival and social interaction. Cognitive neuroscience research has identified a network of brain regions crucial to visual action perception, known as the Action Observation Network (AON), comprising the posterior superior temporal cortex (pSTS), posterior parietal cortex, and premotor cortex. Recent research highlights the importance of integrating top-down processes, such as attention, to gain a deeper understanding of action perception. This study investigates how attention modulates the AON during human action perception. We conducted a two-session fMRI experiment with 27 participants. They viewed eight videos of pushing actions, varying in actor (female vs. male), effector (hand vs. foot), and target (human vs. object). In the first session, participants focused on specific features of the videos (actor, effector, or target). In the second, they passively viewed the videos. From the passive viewing session data, we defined regions of interest (ROIs) in the pSTS, parietal, and premotor cortices for each hemisphere. We then performed model-based representational similarity analysis (RSA) and decoding analysis. RSA results showed that only the task model, among all tested models, exhibited a significant correlation with neural representational similarity matrices (RDMs) across all ROIs, indicating a specific alignment between AON nodes and the ongoing task. Decoding analysis further showed that different task types uniquely affected each AON node, indicating feature- and region-specific interactions. These findings underscore that top-down attentional processes significantly alter neural representations within the AON, highlighting the dynamic interplay between attention and action perception in the brain.
A type IVB secretion system contributes to the pathogenicity ofYersinia pseudotuberculosisstrains responsible for the Far East scarlet-like fever
Authors: Lemarignier Marion , Savin Cyril , Torres Inés Ruedas , Derbise Anne , Coluzzi Charles , Burlaud-Gaillard Julien , Madej Julien , Beau Rémi , Roingeard Philippe , Lechat Pierre , Rocha Eduardo , Gomez-Laguna Jaime , Pizarro-Cerdá Javier 
Published: June 2024

AbstractYersinia pseudotuberculosisis a food-borne pathogen responsible for a self-limiting gastrointestinal disease in humans known as mesenteric lymphadenitis. A phylogenetically distinctY. pseudotuberculosiscluster from lineages 1 and 8 is associated to a specific syndrome called the Far East scarlet-like fever (FESLF), characterized by skin rash, hyperemic tongue and desquamation. Genome sequencing of FESLF strains previously revealed the presence in the plasmid pVM82 ofdot/icmgenes, homologous to those known to encode a T4BSS in the intracellular pathogensLegionella pneumophilaandCoxiella burnetii.In the present article, we characterized the genomic features and functionality of theY. pseudotuberculosisT4BSS (yT4BSS). We found higherdot/icmgene identity betweenY. pseudotuberculosisandPseudomonas putidagenes than with those ofL. pneumophilaorC. burnetii. We validated the presence of all essentialdot/icmgenes required for the structure of a T4BSS. We then evaluated the conditions required foryT4BSS gene expressionin vitroand identified an influence of temperature, with higher expression at 37°C, which mimicks the mammalian host temperature. TheyT4BSS is also expressedin celluloduring theY. pseudotuberculosisintracellular life cycle andin vivoduring mouse infection. Although T4BSS functions are well characterized in the intracellular life cycle ofL. pneumophilaandC. burnetii, theyT4BSS appears to not be required for the intracellular survival nor for the establishment of a replication niche within cells ofY. pseudotuberculosis. Interestingly, theyT4BSS is implicated inY. pseudotuberculosisFESLF strain pathogenicity when orally inoculated to mice but not during intravenous inoculation. Despite a role in virulence during oral infection, theyT4BSS does not influence organ colonization. However, theyT4BSS appears to be implicated in induction of important necrosis lesions in mesenteric lymph nodes and cæca of mice. Cytokine profil analyses revealed an induction of production of innate immunity related cytokines and chemokines depending on theyT4BSSin cellulousing a mouse bone marrow-derived macrophages infection model. Thus, theyT4BSS modulates cytokine responses of the host innate immune system during oral infection. In conclusion, theyT4BSS is a newly characterized virulence factor implicated in pathogenicity ofY. pseudotuberculosisstrains from lineage 8 responsible for FESLF.
DeMBA: a developmental atlas for navigating the mouse brain in space and time
Authors: Carey Harry , Kleven Heidi , Øvsthus Martin , Yates Sharon C. , Csucs Gergely , Puchades Maja A. , McMullan Simon , Bjaalie Jan G. , Leergaard Trygve B. , Bjerke Ingvild E. 
Published: June 2024

AbstractStudies of the adult mouse brain have benefited from three-dimensional (3D) atlases providing standardised frameworks for data analysis and integration. However, few 3D atlases exist for the developing mouse brain, and none cover more than a few ages. This fails to represent the dynamic nature of development and is insufficient for researchers whose data fall between the ages of existent atlases. Existing atlases also neglect the spatial correspondence between ages, making comparison across ages difficult. We present the Developmental Mouse Brain Atlas (DeMBA), a 4D atlas encompassing every postnatal day from 4 to 56. DeMBA is incorporated in software for spatial registration and analysis, enabling brain-wide quantification of features of interest. Furthermore, we provide a software package, the CCF translator, allowing coordinates or image volumes to be transformed between ages for comparison. These resources provide age-specific spatial frameworks incorporated in accessible analytic pipelines for developmental mouse brain data.
Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells
Authors: Mato-Blanco Xoel , Kim Suel-Kee , Jourdon Alexandre , Ma Shaojie , Tebbenkamp Andrew T.N. , Liu Fuchen , Duque Alvaro , Vaccarino Flora M. , Sestan Nenad , Colantuoni Carlo , Rakic Pasko , Santpere Gabriel , Micali Nicola 
Published: June 2024

ABSTRACTThe implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.One-sentence summaryThe temporal analysis of gene regulatory networks in human neural stem cells reveals multiple early critical phases associated with cortical disorders and neuropsychiatric traits.