bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors associated with correct vaccination among children aged 24 to 48 months hospitalized in the national hospitals of Bujumbura
Authors: Niyongabo Felix , Butoyi Jean M. , Laetitia Niyoyunguruza , Esperance Kabusoni , Coppieters Yves 
Published: March 2024

IntroductionIn Africa, although vaccines are often available free of charge in health facilities, many children evade various strategies put in place to reach them. In recent years, despite Burundi maintaining high coverage in all antigens (over 80% since the launch of the PEV in 1980), performance has begun to decline. From 2015 to 2017, all coverage rates experienced a slight regression, and the WHO/UNICEF figures for 2018 confirm this downward trend. The objective of this work is to contribute to the reduction of infant morbidity and mortality due to vaccine-preventable diseases by identifying factors associated with correct vaccination among children aged 24 to 48 months hospitalized in national hospitals in Bujumbura.MethodologyA cross-sectional analytical study was conducted in 4 national hospitals in Burundi. A sample of 216 children was selected, and the collected data were entered into Epinfo 7.2 software and transferred to Stata 15 for analysis. Three types of analyses were performed: descriptive analysis, univariate logistic regression, and multivariate logistic regression. After modeling, variables with a p-value <0.05 were considered associated with correct vaccination.ResultsOut of 216 children, correct vaccination was observed in 64.81%. The average age of mothers was 29.4 ± 5.43 years, ranging from 15 to 45 years. Factors significantly associated with correct vaccination after modeling were: husband’s level of education [OR = 15.41; P = 0.021], household income [OR = 10.23; P = 0.021], distance from residence to vaccination facility [OR = 0.12; P = 0.000], and mothers’ knowledge levels of vaccine-preventable diseases [OR = 1.73; P = 0.004]. The model was well-calibrated (the p-value of the Lemeshow test is 0.6697) with a 90% capacity to correctly classify observations.ConclusionThe study’s results indicate that children are not properly vaccinated despite the service being free. Various factors influencing correct vaccination status were identified, including the level of education of the head of the household, income level, distance to vaccination facilities, and mothers’ knowledge of vaccine-preventable diseases. It is essential to implement interventions targeting these factors associated with correct vaccination to reduce morbidity and mortality from vaccine-preventable diseases.
A fatal case of peritonitis caused byDysgonomonas capnocytophagoidesharboring the novel metallo-beta-lactamase geneblaDYB-1
Authors: Imai Kazuo , Kodana Masahiro , Omachi Ryuha , Inoue Tsutomu , Okada Hirokazu , Maeda Takuya 
Published: March 2024

AbstractDysgonomonas capnocytophagoidesshows multidrug resistance to antibiotics and causes opportunistic infections in immunocompromised hosts. We report a fatal case of peritonitis caused byD. capnocytophagoidesin Japan. We identified a novel chromosomally encoded class B1 metallo-beta-lactamase gene designatedblaDYB-1and anermFSgene that contributed to multidrug resistance.
Quantitating SARS-CoV-2 Neutralizing Antibodies from Human Dried Blood Spots
Authors: Berman Katherine , Van Slyke Greta , Novak Hayley , Rock Jean M. , Bievenue Rachel , Damjanovic Amanda K. , DeRosa Kate L. , Mirabile Gianna , Girardin Roxie C. , Dupuis Alan P. , McDonough Kathleen A. , Parker Monica M. , Styer Linda M. , Mantis Nicholas J. 
Published: March 2024

ABSTRACTBackgroundIn the earliest days of COVID-19 pandemic, the collection of dried blood spots (DBS) enabled public health laboratories to undertake population-scale seroprevalence studies to estimate rates of SARS-CoV-2 exposure. With SARS-CoV-2 seropositivity levels now estimated to exceed 94% in the United States, attention has turned to using DBS to assess functional (neutralizing) antibodies within cohorts of interest.MethodsContrived DBS eluates from convalescent, fully vaccinated and pre-COVID-19 serum samples were evaluated in SARS-CoV-2 plaque reduction neutralization titer (PRNT) assays, a SARS-CoV-2 specific 8-plex microsphere immunoassay, a cell-based pseudovirus assay, and two different spike-ACE2 inhibition assays, an in-house Luminex-based RBD-ACE2 inhibition assay and a commercial real-time PCR-based inhibition assay (NAB-Sure™).ResultsDBS eluates from convalescent individuals were compatible with the spike-ACE2 inhibition assays, but not cell-based pseudovirus assays or PRNT. However, the insensitivity of cell-based pseudovirus assays was overcome with DBS eluates from vaccinated individuals with high SARS-CoV-2 antibody titers.ConclusionSARS-CoV-2 neutralizing titers can be derived with confidence from DBS eluates, thereby opening the door to the use of these biospecimens for the analysis of vulnerable populations and normally hard to reach communities.
Autonomic Nervous System activity correlates with peak experiences induced by DMT and predicts increases in wellbeing
Authors: Bonnelle Valerie , Feilding Amanda , Rosas Fernando E. , Nutt David J. , Carhart-Harris Robin L. , Timmermann Christopher 
Published: March 2024

AbstractNon-ordinary states of consciousness induced by psychedelics can be accompanied by so-called ‘peak experiences’, characterized at the emotional level by their intensity and positive valence. These experiences are strong predictors of positive outcomes following psychedelic-assisted therapy, and it is therefore important to better understand their biology. Despite growing evidence that the autonomic nervous system (ANS) plays an important role in mediating emotional experiences, its involvement in the psychedelic experience is poorly understood. The aim of this study was to investigate to what extant changes in the relative influence of the sympathetic (SNS) and parasympathetic nervous systems (PNS) over cardiac activity may reflect the subjective experience induced by the short-acting psychedelic N,N-Dimethyltryptamine (DMT). We derived measures of SNS and PNS activity from the electrocardiogram data of 17 participants (11 males, 6 females, mean age = 33.8 y, SD = 8.3) while they received either DMT or placebo. Results show that the joint influence of SNS and PNS (‘sympatho-vagal coactivation’) over cardiac activity was robustly correlated with participants ratings of ‘Spiritual Experience’ and ‘Insightfulness’ during the DMT experience, while also being related to improved wellbeing scores two weeks after the session. In addition, we found that the state of balance between the two ANS branches (‘sympatho-vagal balance’) before DMT injection predicted scores of ‘Insightfulness’ during the DMT experience. These findings demonstrate the important involvement of the ANS in psychedelic-induced peak experiences and may pave the way to the development of biofeedback-based tools to enhance psychedelic-therapy.Significance statementPsychedelics can give rise to intense positive subjective experiences - aligned with Maslow’s notion of ‘peak experiences’ - that can have a positive and enduring impact on mental health. Understanding how these experiences relate to peripheral physiology before and during the acute effects of psychedelics is an important object of enquiry, as it may help advance the therapeutic use of these compounds. In this study, we demonstrate that specific peripheral states computed from heart rate activity recordings predicted and correlated with acute peak experiences and increases in wellbeing. These findings have implications for the relationship between peripheral physiology and altered states of consciousness. Moreover, they highlight a putative marker of physiological ‘readiness’ prior the psychedelic experience that could predict therapeutically relevant mechanisms that might be modified to improve mental health outcomes in psychedelic-therapy.
Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm
Authors: del Toro-de León Gerardo , van Boven Joram , Santos-González Juan , Jiao Wen-Biao , Schneeberger Korbinian , Köhler Claudia 
Published: March 2024

ABSTRACTGenomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact ofde novoTE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia elementONSENon genomic imprinting inArabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 newONSENcopies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs— both previously identified as promoters ofONSENinsertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.
Parallel Encoding of Speech in Human Frontal and Temporal Lobes
Authors: Hullett Patrick W. , Leonard Matthew K. , Gorno-Tempini Maria Luisa , Mandelli Maria Luisa , Chang Edward F. 
Published: March 2024

ABSTRACTModels of speech perception are centered around a hierarchy in which auditory representations in the thalamus propagate to primary auditory cortex, then to the lateral temporal cortex, and finally through dorsal and ventral pathways to sites in the frontal lobe. However, evidence for short latency speech responses and low-level spectrotemporal representations in frontal cortex raises the question of whether speech-evoked activity in frontal cortex strictly reflects downstream processing from lateral temporal cortex or whether there are direct parallel pathways from the thalamus or primary auditory cortex to the frontal lobe that supplement the traditional hierarchical architecture. Here, we used high-density direct cortical recordings, high-resolution diffusion tractography, and hemodynamic functional connectivity to evaluate for evidence of direct parallel inputs to frontal cortex from low-level areas. We found that neural populations in the frontal lobe show speech-evoked responses that are synchronous or occur earlier than responses in the lateral temporal cortex. These short latency frontal lobe neural populations encode spectrotemporal speech content indistinguishable from spectrotemporal encoding patterns observed in the lateral temporal lobe, suggesting parallel auditory speech representations reaching temporal and frontal cortex simultaneously. This is further supported by white matter tractography and functional connectivity patterns that connect the auditory nucleus of the thalamus (medial geniculate body) and the primary auditory cortex to the frontal lobe. Together, these results support the existence of a robust pathway of parallel inputs from low-level auditory areas to frontal lobe targets and illustrate long-range parallel architecture that works alongside the classical hierarchical speech network model.
Matrix alignment and density modulate YAP-mediated T-cell immune suppression
Authors: Sapudom Jiranuwat , Alatoom Aseel , Tipay Paul , Teo Jeremy CM 
Published: March 2024

AbstractT-cells navigate through various mechanical environments within the body, adapting their behavior in response to these cues. An altered extracellular matrix (ECM) characterized by increased density and enhanced fibril alignment, as observed in cancer tissues, can significantly impact essential T-cell functions critical for immune responses. In this study, we used 3D collagen matrices with controlled density and fibril alignment to investigate T-cell migration, activation, and proliferation. Our results revealed that dense and aligned collagen matrices suppress T-cell activation through enhanced YAP signaling. By inhibiting YAP signaling, we demonstrated that T-cell activation within these challenging microenvironments improved, suggesting potential strategies to enhance the efficacy of immunotherapy by modulating T-cell responses in dense and aligned ECMs. Overall, our study deepens our understanding of T-cell mechanobiology within 3D relevant cellular microenvironments and provides insights into countering ECM-induced T-cell immunosuppression in diseases such as cancer.Graphical abstractDense and aligned extracellular matrices suppress T-cell activation via YAP signaling, affecting immunotherapy efficacy in diseases such as cancer.
Defining phylogenetic relationships: a complete and minimal set of combinatorial properties for triplets
Authors: Valentin Rineau , Stéphane Prin 
Published: March 2024

AbstractTriplets, as minimal informative rooted trees, are fundamental units of information in phylogenetics. Their importance for phylogenetic reconstruction, cladistic biogeography, or supertree methods relies on the fact that any rooted tree can be decomposed into a set of triplets. In order to formalize the tree building from a consistent triplet set, severalk-adic rules of inference, i.e., rules that allow us to deduce at least one new triplet from exactlykother ones, have been identified. However, it remains unclear whether it is possible to reduce all the possiblek-adic rules to a finite set of basic properties. In order to solve this problem, we propose here to define triplets in terms of degree of equivalence relations. Given the axiomatic definition of the latter, we establish a list of the most basic properties for triplets. With such an approach, we finally prove that the closure of any coherent triplet set can be computed uniquely from these basic properties.
Biodiversity impact of the consumption of peat and wood-fired district heating
Authors: Vainio Veera , El Geneidy Sami , Halme Panu , Peura Maiju , Kotiaho Janne S. 
Published: March 2024

AbstractThe use of biofuels is becoming an increasingly important part of national and corporate climate strategies. At the same time, the consumption-based biodiversity impacts of biofuels are generally poorly known. Here we used a consumption-based approach to assess the biodiversity impacts of peat and wood-fired district heating in Finland. We combined the information on the area of impacted ecosystems and their condition before and after the impact to evaluate the impact as habitat hectares, i.e., the loss in the condition of the impacted habitats. The habitat hectare approach has not been used in previous studies on consumption-based biodiversity impacts but could be replicated to assess biodiversity impacts in different contexts around the globe. We present an eight-step general protocol for such assessment and discuss the usability of the protocol in assessing consumption-based biodiversity impacts of district heating systems. Considering different fuel types, peat had the highest biodiversity impact per unit area, followed by chips from roundwood and logging residue chips. If we consider the impacts per unit energy, chips from roundwood had the highest and peat the lowest biodiversity impact. We conclude that it is possible to assess biodiversity impacts of raw material-based consumption, like we did in our example case. This protocol should be further developed and refined in different systems and with different raw materials.
Eye-movement artifact correction in infant EEG: A systematic comparison between ICA and Artifact Blocking
Authors: Srishyla Diksha , Webb Sara Jane , Elsabbagh Mayada , O’Reilly Christian ,   The BASIS Team
Published: March 2024

AbstractBackgroundIndependent Component Analysis (ICA) is a well-established approach to clean EEG and remove the impact of signals of non-neural origin, such as those from muscular activity and eye movements. However, evidence suggests that ICA removes artifacts less effectively in infants than in adults. This study systematically compares ICA and Artifact Blocking (AB), an alternative approach proposed to improve eye-movement artifact correction in infant EEG.MethodsWe analyzed EEG collected from 50 infants between 6 and 18 months of age as part of the International Infant EEG Data Integration Platform (EEG-IP), a longitudinal multi-study dataset. EEG was recorded while infants sat on their caregivers’ laps and watched videos. We used ICA and AB to correct for eye-movement artifacts in the EEG and calculated the proportion of effectively corrected segments, signal-to-noise ratio (SNR), power-spectral density (PSD), and multiscale entropy (MSE) in manually selected EEG segments with and without eye-movement artifacts.ResultsOn the one hand, the proportion of effectively corrected segments indicated that ICA corrected eye-movement artifacts (sensitivity) better than AB. SNR and PSD indicated that both AB and ICA correct eye-movement artifacts with equal sensitivity. MSE gave mixed results. On the other hand, AB caused less distortion to the clean segments (specificity) for SNR, PSD, and MSE.ConclusionsOur results suggest that ICA is more sensitive (i.e., it better removes artifacts) but less specific (it distorts clean signals) than AB for correcting eye-movement artifacts in infant EEG.
Challenges in predicting PROTAC-mediated Protein-Protein Interfaces with AlphaFold
Authors: Pereira Gilberto P. , Gouzien Corentin , Souza Paulo C. T. , Martin Juliette 
Published: March 2024

AbstractIn the last few years, predicting the structure of PROTAC-mediated complexes emerged as a fundamental step toward the design of therapeutic modalities for cancer and other conditions. The development of AlphaFold2 (AF2) caused a paradigm shift in the structural biology community. From then onwards, further developments enabled the prediction of multimeric protein structures while improving calculation efficiency, leading to the widespread usage of AF2 and to the recent release of AF3. However, AF2 does not consider ligands, suggesting that ligand-mediated protein-protein interfaces (PPIs) are challenging to predict. One of the main claims of AF3 is that this limitation has been addressed, but the currently released webserver provides only a few ligands and no PROTACs are available. In this article, we benchmark the performance of AF2 on a test set of 28 PROTAC-mediated dimers, as well as a set of 326 protein hetero-dimers orthogonal to AF2 training set, with a special attention to the interface size and presence of ligand at the interface. We then evaluated whether the newly released AF3 model is able to outperform AF2 on the prediction of PROTAC-mediated complexes, despite not being able to include PROTAC ligands in the prediction. In this letter, we aimed at identifying possible reasons why AF-based methods fail to predict PROTAC-mediated interfaces. Our results show that AF2-multimer predictions are sensitive to the size of the interface to predict, with the majority of models being incorrect for the smallest interfaces. While it performs reasonably well for ligand-mediated interfaces in the absence of the ligand, AF2 is unable to predict PROTAC-mediated interfaces reliably. We also found that AF3 does not significantly improve upon the accuracy of AF2, as it is still unable to correctly predict PROTAC-mediated interfaces for the large majority of cases.
Impact of analytic decisions on test-retest reliability of individual and group estimates in functional magnetic resonance imaging: a multiverse analysis using the monetary incentive delay task
Authors: Demidenko Michael I. , Mumford Jeanette A. , Poldrack Russell A. 
Published: March 2024

AbstractEmpirical studies reporting low test-retest reliability of individual blood oxygen-level dependent (BOLD) signal estimates in functional magnetic resonance imaging (fMRI) data have resurrected interest among cognitive neuroscientists in methods that may improve reliability in fMRI. Over the last decade, several individual studies have reported that modeling decisions, such as smoothing, motion correction and contrast selection, may improve estimates of test-retest reliability of BOLD signal estimates. However, it remains an empirical question whether certain analytic decisionsconsistentlyimprove individual and group level reliability estimates in an fMRI task across multiple large, independent samples. This study used three independent samples (Ns: 60, 81, 119) that collected the same task (Monetary Incentive Delay task) across two runs and two sessions to evaluate the effects of analytic decisions on the individual (intraclass correlation coefficient [ICC(3,1)]) and group (Jaccard/Spearmanrho) reliability estimates of BOLD activity of task fMRI data. The analytic decisions in this study vary across four categories: smoothing kernel (five options), motion correction (four options), task parameterizing (three options) and task contrasts (four options), totaling 240 different pipeline permutations. Across all 240 pipelines, the median ICC estimates are consistently low, with a maximum median ICC estimate of .43 - .55 across the three samples. The analytic decisions with the greatest impact on the median ICC and group similarity estimates are theImplicit Baselinecontrast, Cue Model parameterization and a larger smoothing kernel. Using anImplicit Baselinein a contrast condition meaningfully increased group similarity and ICC estimates as compared to using theNeutralcue. This effect was largest for the Cue Model parameterization; however, improvements in reliability came at the cost of interpretability. This study illustrates that estimates of reliability in the MID task are consistently low and variable at small samples, and a higher test-retest reliability may not always improve interpretability of the estimated BOLD signal.
GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density
Authors: Conery Mitchell , Pippin James A. , Wagley Yadav , Trang Khanh , Pahl Matthew C. , Villani David A. , Favazzo Lacey J. , Ackert-Bicknell Cheryl L. , Zuscik Michael J. , Katsevich Eugene , Wells Andrew D. , Zemel Babette S. , Voight Benjamin F. , Hankenson Kurt D. , Chesi Alessandra , Grant Struan F.A. 
Published: March 2024

ABSTRACTOver 1,100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. Informed by a variant-to-gene mapping strategy implicating 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci, we executed a single-cell CRISPRi screen in human fetal osteoblasts (hFOBs). The BMD relevance of hFOBs was supported by heritability enrichment from stratified LD-score regression involving 98 cell types grouped into 15 tissues. 23 genes showed perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping revealed unexpectedly that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues. Extending our CRISPRi screening approach to these tissues could play a key role in fully elucidating the etiology of BMD.