bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time feedback reduces participant motion during task-based fMRI
Authors: Rogers Chad S. , Jones Michael S. , McConkey Sarah , McLaughlin Drew J. , Peelle Jonathan E. 
Published: January 2023

AbstractThe potential negative impact of head movement during fMRI has long been appreciated. Although a variety of prospective and retrospective approaches have been developed to help mitigate these effects, reducing head movement in the first place remains the most appealing strategy for optimizing data quality. Real-time interventions, in which participants are provided feedback regarding their scan-to-scan motion, have recently shown promise in reducing motion during resting state fMRI. However, whether feedback might similarly reduce motion during task-based fMRI is an open question. In particular, it is unclear whether participants can effectively monitor motion feedback while attending to task-related demands. Here we assessed whether a combination of real-time and between-run feedback could reduce head motion during task-based fMRI. During an auditory word repetition task, 78 adult participants (aged 19–81) were pseudorandomly assigned to receive feedback or not. Feedback was provided FIRMM software that used real-time calculation of realignment parameters to estimate participant motion. We quantified movement using framewise displacement (FD). We found that motion feedback resulted in a statistically significant reduction in participant head motion, with a small-to-moderate effect size (reducing average FD from 0.347 to 0.282). Reductions were most apparent in high-motion events. We conclude that under some circumstances real-time feedback may reduce head motion during task-based fMRI, although its effectiveness may depend on the specific participant population and task demands of a given study.
The neural activity of auditory conscious perception
Authors: Christison-Lagay Kate L. , Freedman Noah C. , Micek Christopher , Khalaf Aya , Kronemer Sharif I. , Gusso Mariana M. , Kim Lauren , Forman Sarit , Ding Julia , Aksen Mark , Abdel-Aty Ahmad , Kwon Hunki , Markowitz Noah , Yeagle Erin , Espinal Elizabeth , Herrero Jose , Bickel Stephan , Young James , Mehta Ashesh , Wu Kun , Gerrard Jason , Damisah Eyiyemisi , Spencer Dennis , Blumenfeld Hal 
Published: January 2023

AbstractAlthough recent work has made significant headway in understanding the temporal and spatial dynamics of the neural mechanisms of conscious perception, much of that work has focused on visual paradigms. To determine whether there are shared mechanisms for perceptual consciousness across sensory modalities, here we developed a task to test within the auditory domain. Participants (n=31) completed an auditory perceptual threshold task while undergoing intracranial electroencephalography (icEEG) for intractable epilepsy. Intracranial recordings from over 2,800 grey matter electrodes representing widespread cortical coverage were analyzed for power in the high gamma range (40–115 Hz)—a frequency range that reflects local neural activity. For trials that were perceived, we find activity in early auditory regions which is accompanied by activity in the right caudal middle frontal gyrus, and shortly thereafter by activity in non-auditory thalamus. This is followed by a wave of activity that sweeps through the higher auditory association regions and into parietal and frontal cortices, similar to the wave observed in our visual conscious perception paradigm. However, for not perceived trials, we find that significant activity is restricted to early auditory regions (and areas immediately adjacent to the Sylvian fissure). These findings show that the broad anatomical regions of cortical and subcortical networks involved in auditory perception are similar to the networks observed with vision, suggesting shared general mechanisms for conscious perception.
Interaction of FlhF, SRP-like GTPase with FliF, MS ring component assembling the initial structure of flagella in marineVibrio
Authors: Fukushima Yuria , Homma Michio , Kojima Seiji 
Published: January 2023

ABSTRACTVibrio alginolyticusforms a single flagellum at its cell pole. FlhF and FlhG are known to be the main proteins responsible for the polar formation of single flagellum. FlhF, which belongs to the signal recognition particle (SRP)-type GTPase family, localizes at the cell pole and initiates flagellar generation. In contrast, FlhG negatively regulates flagellar numbers. Furthermore, MS-ring formation in the flagellar basal body appears to be an initiation step for flagellar assembly. The MS-ring is formed by a single protein, FliF, which has two transmembrane (TM) segments and a large periplasmic region. We had shown that FlhF was required for the polar localization ofVibrioFliF, and FlhF facilitated MS-ring formation when FliF was overexpressed inE. colicells. These results suggest that FlhF interacts with FliF to facilitate MS-ring formation. Here, we attempted to detect this interaction usingVibrioFliF fragments fused to a tag of Glutathione S-transferase (GST) inE. coli. We found that the N-terminal 108 residues of FliF, including the first TM segment and the periplasmic region, could pull FlhF down. In the first step, the SRP and its receptor are involved in the transport of membrane proteins to target them, which delivers them to the translocon. FlhF may have a similar or enhanced function as SRP, which binds to a region rich in hydrophobic residues.IMPORTANCEVibrio alginolyticusforms only a single flagellum at the cell pole by regulators of FlhF and FlhG. FlhF regulates positively the formation of flagella and is required for polar positioning of the flagellum. FliF, the two transmembrane (TM) segments and a large periplasmic region, forms the MS ring of flagellar basal body in the membrane. Previous studies suggest that FlhF interacts with FliF to facilitate MS ring formation at the cell pole, but the interaction has not been detected. Here, we show the evidence that FlhF interacts with FliF at residues including the first TM segment and following periplasmic region. The hydrophobic residues of this region seem to be important for the interaction.
Redox-active compound generated by bacterial crosstalk induces hypha branching inStreptomycesspecies
Authors: Kato Manami , Asamizu Shumpei , Onaka Hiroyasu 
Published: January 2023

AbstractChemical cross talks betweenMycolicibacterium septicumHEK138M andBacillus subtilis168 affect the bacterial morphology ofStreptomyces variegatusHEK138A. We found thatS. variegatusexhibits unusual hyphae branching by the bacterial interaction. We aimed to elucidate the mechanism by performing activity guided purification of substances that induce the unusual cell morphology. We found that pyrogallol, a redox active aromatic small molecule induced significant hyphae branching inS. variegatusand the activity was also observed in some of otherStreptomycesspecies. Interestingly, the pyrogallol activity was diminished by adding catalase, which broke down H2O2. To further confirm the involvement, H2O2was tested and similar activity which induced hyphal branching was observed. This indicates that reactive oxygen species (ROS) generated by redox-active compound (RAC) is the inducing factor of hyphae branching. Further investigation revealed that pyrogallol was generated by NahG enzyme homolog ofM. septicumusing 2,3-dihydroxybenzoic acid as substrate by heterologous expression inE. coli. Moreover, co-culture with gene knock-out mutants revealed that 2,3-dihydroxybenzoic acid was supplied byB. subtilisproduced as intermediate of bacterial siderophore bacillibactin. Since the hyphae branching of vegetative mycelium can increase the density of filamentous network and consequently help secure the milieu in soil, our results suggested that those filamentous soil bacteria use ROS which can be supplied from plant derived RAC as a signal. As those RAC ubiquitously exist in soil environment, the system will be beneficial for sensing the nutrient sources in addition to the generally considered defensive response to oxidative stress.ImportanceThe characterization of interactions between three or more bacteria are lacking as these interactions are visually imperceptible in general. Our current study revealed changes of morphological behavior by the bacterial interaction. This study showed that hydrogen peroxide generated by redox-active compound derived from a breakdown product of siderophore can significantly increase the number of hyphae tip extension in filamentous bacteria. Our result implies the existence of oxidative response system using a low amount of reactive oxygen species as an integrated signal to sense the plant-derived carbon source by the filamentous soil bacteria. As a result of sensing, filamentous soil bacteria may decide whether the hypha tip should be extended to further explore the area or increase the tips to densify filamentous network to monopolize the nutrients in the milieu.
Gait event prediction from surface electromyography in parkinsonian patients
Authors: Haufe Stefan , Isaias Ioannis U. , Pellegrini Franziska , Palmisano Chiara 
Published: January 2023

AbstractGait disturbances are common manifestations of Parkinson’s disease (PD), with unmet therapeutic needs. Inertial measurement units (IMU) are capable of monitoring gait, but they lack neurophysiological information that may be crucial for studying gait disturbances in these patients. Here, we present a machine-learning approach to approximate IMU angular velocity profiles, and subsequently gait events from electromyographic (EMG) channels. We recorded six parkinsonian patients while walking for at least three minutes. Patient-agnostic regression models were trained on temporally-embedded EMG time series of different combinations of up to five leg muscles bilaterally (i.e., tibialis anterior, soleus, gastrocnemius medialis, gastrocnemius lateralis, and vastus lateralis). Gait events could be detected with high temporal precision (median displacement <50 msec), low numbers of missed events (<2%), and next to no false positive event detections (<0.1%). Swing and stance phases could thus be determined with high fidelity (median F1 score ∼0.9). Interestingly, the best performance was obtained using as few as two EMG probes placed on the left and right vastus lateralis. Our results demonstrate the practical utility of the proposed EMG-based system for gait event prediction while allowing the simultaneous acquisition of an electromyographic signal. This gait analysis approach has the potential to make additional measurement devices such as IMU and force plates less essential, and thereby to reduce financial and preparation overheads and discomfort factors in gait studies.
Differences in site-specific cancer incidence by individual- and area-level income in Canada from 2006-2015
Authors: Tope Parker , Morais Samantha , El-Zein Mariam , Franco Eduardo L. , Malagón Talía 
Published: January 2023

ABSTRACTIntroductionIncome, a component of socioeconomic status, influences cancer risk as a social determinant of health. We evaluated the independent associations between individual- and area-level income, and site-specific cancer incidence in Canada.MethodsWe used data from the 2006 and 2011 Canadian Census Health and Environment Cohorts, which are probabilistically linked datasets constituted by 5.9 million and 6.5 million respondents of the 2006 Canadian long-form census and 2011 National Household Survey, respectively. Individuals were linked to the Canadian Cancer Registry through 2015. Individual-level income was derived using after-tax household income adjusted for household size. Annual tax return postal codes were used to assign area-level household income quintiles to individuals for each year of follow-up. We calculated age-standardized incidence rates (ASIR) and rate ratios for cancers overall and by site. We conducted multivariable negative binomial regression to adjust these rates for other demographic and socioeconomic variables.ResultsIndividuals of lower individual- and area-level income had higher ASIRs compared to those in the wealthiest income quintile for head and neck, oropharyngeal, esophageal, stomach, colorectal, anal, liver, pancreas, lung, cervical, and kidney and renal pelvis cancers. Conversely, individuals of wealthier individual- and area-level income had higher ASIRs for melanoma, leukemia, Hodgkin’s lymphoma, and non-Hodgkin’s lymphoma, breast, uterine, prostate, and testicular cancers. Most differences in site-specific incidence by income quintile remained after adjustment.ConclusionsAlthough Canada’s publicly funded healthcare system provides universal coverage, inequalities in cancer incidence persist across individual- and area-level income gradients. Our estimates suggest that individual- and area-level income affect cancer incidence through independent mechanisms.
Long-term systemic and mucosal SARS-CoV-2 IgA response and its association with persistent smell and taste disorders
Authors: Denis Jessica , Garnier Annabelle , Cheutin Laurence , Ferrier Audrey , Timera Hawa , Jarjaval Fanny , Hejl Carine , Billon-Denis Emmanuelle ,   Percy ImmunoCovid group, Ricard Damien , Tournier Jean-Nicolas , Trignol Aurélie , Mura Marie 
Published: January 2023

AbstractCurrent approved COVID-19 vaccines, notably mRNA and adenoviral vectored technologies, still fail to fully protect against infection and transmission of various SARS-CoV-2 variants. The mucosal immunity at the upper respiratory tract represents the first line of defense against respiratory viruses such as SARS-CoV-2 and is thus critical to develop vaccine blocking human-to-human transmission. We measured systemic and mucosal Immunoglobulin A (IgA) response in serum and saliva from 133 healthcare workers from Percy teaching military hospital following a mild infection (SARS-CoV-2 Wuhan strain, n=58) or not infected (n=75), and after SARS-CoV-2 vaccination (Vaxzevria®/Astrazeneca and/or Comirnaty®/Pfizer). While serum anti-SARS-CoV-2 Spike IgA response lasted up to 16 months post-infection, IgA response in saliva had mostly fallen to baseline level at 6 months post-infection. Vaccination could reactivate the mucosal response generated by prior infection, but failed to induce a significant mucosal IgA response by itself. As breakthrough infections have been correlated with IgA levels, other vaccine platforms inducing a better mucosal immunity are needed to control COVID-19 infection in the future. Early post-COVID-19 serum anti-Spike-NTD IgA titer correlated with seroneutralization titers. Interestingly, its saliva counterpart positively correlated with persistent smell and taste disorders more than one year after mild COVID-19, and could potentially be used as an early prognosis biomarker.
Coverage of primary and booster vaccination against COVID-19 by socioeconomic level: A nationwide cross-sectional registry study
Authors: Hansen Bo T , Labberton Angela S , Kour Prabhjot , Kraft Kristian B 
Published: January 2023

AbstractHigh and equitable COVID-19 vaccination coverage is important for pandemic control and prevention of health inequity. However, little is known about socioeconomic correlates of booster vaccination coverage. In this cross-sectional study of all Norwegian adults in the national vaccination program (N = 4,190,655), we use individual-level registry data to examine coverage by levels of household income and education of primary (≥2 doses) and booster (≥3 doses) vaccination against COVID-19. We stratify the analyses by age groups with different booster recommendations and report relative risk ratios (RR) for vaccination by 25 August 2022. In the 18-44 years group, individuals with highest vs. lowest education had 94% vs. 79% primary coverage (adjusted RR (adjRR) 1.15, 95%CI 1.14-1.15) and 67% vs. 38% booster coverage (adjRR 1.55, 95% CI 1.55-1.56), while individuals with highest vs. lowest income had 94% vs. 81% primary coverage (adjRR 1.10, 95%CI 1.10-1.10) and 60% vs. 43% booster coverage (adjRR 1.23, 95%CI 1.22-1.24). In the≥45 years group, individuals with highest vs. lowest education had 96% vs. 92% primary coverage (adjRR 1.02, 95%CI 1.02-1.02) and 88% vs. 80% booster coverage (adjRR 1.09, 95%CI 1.09-1.09), while individuals with highest vs. lowest income had 98% vs. 82% primary coverage (adjRR 1.16, 95%CI 1.16-1.16) and 92% vs. 64% booster coverage (adjRR 1.33, 95%CI 1.33-1.34). In conclusion, we document large socioeconomic inequalities in COVID-19 vaccination coverage, especially for booster vaccination, even though all vaccination was free-of-charge. The results highlight the need to tailor information and to target underserved groups for booster vaccination.
Automated Prognosis of Renal Function Decline in ADPKD Patients using Deep Learning
Authors: Raj Anish , Tollens Fabian , Caroli Anna , Nörenberg Dominik , Zöllner Frank G. 
Published: January 2023

AbstractThe prognosis of renal function decline in Autosomal Dominant Polycystic Kidney Disease (ADPKD) is vital for early intervention. Currently, the accepted biomarkers are height-adjusted total kidney volume (HtTKV) with estimated glomerular filtration rate (eGFR) and patient age. However, kidney volume delineation is time-consuming and prone to observer variability. Furthermore, improvement in prognosis can be achieved by incorporating automatically generated features of kidney MRI images in addition to the conventional biomarkers. Hence, to improve prediction we develop two deep learning algorithms. At first, we create an automated kidney volume segmentation model that can accurately calculate HtTKV. Secondly, we use the segmented kidney volumes with the predicted HtTKV, age, and eGFR at the baseline visit. Here, we use a combination of convolutional neural network (CNN) and multi-layer perceptron (MLP) for the prediction of chronic kidney disease (CKD) stages >=3A, >=3B, and a 30% decline in eGFR after 8 years from the baseline visit. We obtain AUC scores of 0.96, 0.96, and 0.95 for CKD stages >=3A, >=3B, and 30% decline in eGFR, respectively. Moreover, our algorithm achieves a Pearson correlation coefficient of 0.81 between predicted and measured eGFR decline. We further extend our approach to predict distinct CKD stages after eight years with high accuracy. The proposed approach might improve monitoring and support the prognosis of ADPKD patients from the earliest disease stages.
Variations in COVID-19 impacts by social vulnerability in Philadelphia, June 2020-December 2022
Authors: Strelau Katherine M. , Feuerstein-Simon Rachel , Naseer Nawar , Lang Megan , Rix Kevin , Murray Eleanor J , Morris Jeffrey S. , Wiebe Douglas J. , Nelson Hillary C.M. , Collman Ronald G. , Rodino Kyle G. , Bushman Frederic D. , Kelly Brendan J. , Cannuscio Carolyn C. 
Published: January 2023

AbstractIntroductionThe study objective was to elucidate the relationship between social vulnerability and COVID-19 impacts in Philadelphia over a 2.5-year period, between June 2020 and December 2022.MethodsUsing publicly available COVID-19 case, test, hospitalization, and mortality data for Philadelphia (June 7, 2020-December 31, 2022) and area-level social vulnerability data, we compared the incidence, test positivity, hospitalization, and mortality rates in high and low vulnerability neighborhoods of Philadelphia, characterized as scoring above or below the national median score on the social vulnerability index. We used linear mixed effects models to test the association between social vulnerability and COVID-19 incidence, test positivity, hospitalization, and mortality rates, adjusting for time and age distribution.Results90.4% of Philadelphians (n= 1,430,153) live in neighborhoods classified as socially vulnerable, based on scoring above the national median score on the social vulnerability index. COVID-19 incidence, hospitalization, and mortality rates were significantly elevated in the more vulnerable communities, withp< 0.05,p< 0.005, andp< 0.001, respectively. The relative risks of COVID-19-related incidence, hospitalization, and death, comparing the more vulnerable neighborhoods to the less vulnerable neighborhoods, were 1.11 (95%CI: 1.10-1.12), 2.07 (95%CI: 1.93-2.20), and 2.06 (95%CI: 1.78-2.38), respectively. Thus, between June 7, 2020 and December 31, 2022, 32,573 COVID-19 cases, 9,409 hospitalizations, and 1,967 deaths would have been avoided in Philadelphia’s more vulnerable communities had they experienced the same rates of incidence, hospitalization, and death as the less vulnerable Philadelphia communities.ConclusionsThese results highlight the disparate morbidity and mortality experienced by people living in more vulnerable neighborhoods in a large US city. Importantly, our findings illustrate the importance of designing public health policies and interventions with an equity-driven approach, with greater resources and more intensive prevention strategies applied in socially vulnerable communities.
Speos: An ensemble graph representation learning framework to predict core genes for complex diseases
Authors: Ratajczak Florin , Joblin Mitchell , Hildebrandt Marcel , Ringsquandl Martin , Falter-Braun Pascal , Heinig Matthias 
Published: January 2023

ABSTRACTUnderstanding phenotype-to-genotype relationships is a grand challenge of 21st century biology with translational implications. The recently proposed “omnigenic” model postulates that effects of genetic variation on traits are mediated bycore-genes and -proteins whose activities mechanistically influence the phenotype, whereasperipheralgenes encode a regulatory network that indirectly affects phenotypes via core gene products. We have developed a positive-unlabeled graph representation-learning ensemble-approach to predict core genes for diverse diseases using Mendelian disorder genes for training. Employing mouse knockout phenotypes for external validation, we demonstrate that our most confident predictions validate at rates on par with the Mendelian disorder genes, and all candidates exhibit core-gene properties like transcriptional deregulation in diseases and loss-of-function intolerance. Predicted candidates are enriched for drug targets and druggable proteins and, in contrast to Mendelian disorder genes, also for druggable but yet untargeted gene products. Model interpretation suggests key molecular mechanisms and physical interactions for core gene predictions. Our results demonstrate the potential of graph representation learning and pave the way for studying core gene properties and future drug development.