bluuebunny/crossref_metadata_2025_split huggingface dataset:
The antimicrobial peptides pipeline: a bacteria-centric AMP predictor
Authors: Veldsman Werner Pieter , Zhang Qi , Zhao Qian , Zhang Eric Lu 
Published: May 2024

AbstractAntimicrobial peptides (AMPs), unlike antibiotics, are encoded in genomes. AMPs are exported from the cell after expression and translation. In the case of bacteria, the exported peptides target other microbes to give the producing bacterium a competitive edge. While AMPs are sought after for their similar antimicrobial activity to traditional antibiotics, it is difficult to predict which combinations of amino acids will confer antimicrobial activity. Many computer algorithms have been designed to predict whether a sequence of amino acids will exhibit antimicrobial activity, but the vast majority of validated AMPs in databases are still of eukaryotic origin. This defies common sense since the vast majority of life on earth is prokaryotic. The antimicrobial peptides pipeline, presented here, is a bacteria-centric AMP predictor that predicts AMPs by taking design inspiration from the sequence properties of bacterial genomes with the intention to improve detection of naturally occurring bacterial AMPs. The pipeline integrates multiple concepts of comparative biology to search for candidate AMPs at the primary, secondary and tertiary peptide structure level. Results showed that the antimicrobial peptides pipeline identifies known AMPs that are missed by state-of-the-art AMP predictors, and that the pipeline yields more AMP candidates from real bacterial genomes than from fake genomes, with the rate of AMP detection being significantly higher in the genomes of seven nosocomial pathogens than in the fake genomes.
Histone H2B isoformH2bc27is expressed in the developing brain of mouse embryos
Authors: Egashira Saki , Maehara Kazumitsu , Tanaka Kaori , Nakamura Mako , Takemoto Tatsuya , Ohkawa Yasuyuki , Harada Akihito 
Published: May 2024

AbstractHistones bind directly to DNA and play a role in regulating gene expression mediated by chromatin structure. DNA sequences of these histone genes are quite similar, which has hindered individual analyses. The exact function of the 13 different isoforms of histone H2B remains unclear. In this report, a comprehensive gene expression analysis of the H2B isoforms, focusing on tissue specificity, was conducted. We generated mice lacking the H2bc27 gene, which exhibited brain-specific expression of E14.5, and proceeded to characterize the brain tissue. The phenotype ofH2bc27knockout brains was similar to that of wild-type brains, yet transcriptome analysis indicated thatH2bc27is associated with regulating the expression of several functional genes involved in mouse brain development. The methods used in this study may serve to facilitate comprehensive H2B isoform analysis.
Cold exposure transiently increases resistance ofArabidopsis thalianaagainst the fungal pathogenBotrytis cinerea
Authors: Schütte Dominic , Remmo Abdulmalek , Baier Margarete , Griebel Thomas 
Published: May 2024

ABSTRACTA sudden cold exposure (4°C, 24 h) primes resistance ofArabidopsis thalianaagainst the virulent biotrophic pathogenPseudomonas syringaepv.tomatoDC3000 (Pst) for several days. This effect is mediated by chloroplast cold sensing and the activity of stromal and thylakoid-bound ascorbate peroxidases (sAPX/tAPX). In this study, we investigated the impact of such cold exposure on plant defence against the necrotrophic fungusBotrytis cinerea. Plant resistance was transiently enhanced if theB. cinereainfection occurred immediately after the cold exposure, but this cold-enhancedB. cinerearesistance was absent when the cold treatment and the infection were separated by 5 days at normal growth conditions. Plastid ascorbate peroxidases partially contributed to the transient cold-enhanced resistance against the necrotrophic fungus. In response toB. cinerea, the levels of reactive oxygen species (ROS) were significantly higher in cold-pretreated Arabidopsis leaves. Pathogen-triggered ROS levels varied in the absence of sAPX, highlighting the strong capacity for sAPX-dependent ROS regulation in the chloroplast stroma. The cold-enhanced resistance againstB. cinereawas associated with cold-induced plant cell wall modifications, including sAPX-dependent callose formation and significant lignification in cold-treated Arabidopsis leaves.FundingThis work was supported by the German Research Foundation (CRC973/C4) and the FU Berlin.
The global prevalence and genetic spectrum of primary carnitine deficiency
Authors: Sun Liu , Wu Hang-Jing 
Published: May 2024

AbstractBackgroundPrimary carnitine deficiency (PCD) is an autosomal recessive rare disorder of carnitine cycle and carnitine transport caused by mutations in the SLC22A5 gene. The prevalence of PCD is unclear. This study aimed to estimate the carrier frequency and genetic prevalence of PCD using Genome Aggregation Database (gnomAD) data.MethodsThe pathogenicity of SLC22A5 variants was interpreted according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. The minor allele frequency (MAF) of SLC22A5 gene disease-causing variants in 807,162 unique individuals was examined to estimate the global prevalence of PCD in five major ethnicities: African (afr), Admixed American (amr), East Asian (eas), Non-Finnish European (nfe) and South Asian (sas). The global and population-specific carrier frequencies and genetic prevalence of PCD were calculated using the Hardy–Weinberg equation.ResultsIn total, 195 pathogenic/likely pathogenic variants (PV/LPV) were identified according to ACMG standards and guidelines. The global carrier frequency and genetic prevalence of PCD were 1/88 and 1/31,260, respectively.ConclusionsThe prevalence of PCD is estimated to be 1/30,000 globally, with a range of between 1/20,000 and 1/70,000 depending on ethnicity.
Weight Gain Following a Diagnosis of Anti-neutrophil Cytoplasm Antibody-Associated Vasculitis
Authors: Salehi Tania , French Thomas , Farrah Tariq E , Dhaun Neeraj , Hunter Robert W 
Published: May 2024

AbstractObjectivesPatients with anti-neutrophil cytoplasm antibody (ANCA)-associated vasculitis (AAV) are at increased long-term risk of cardiometabolic diseases. The prevalence of obesity in AAV has not been well documented. We aimed to characterise change in body weight following a diagnosis of active AAV and to determine the risk factors for this.MethodsWe examined data from a single-centre registry of patients with AAV, diagnosed between 2003 and 2023. We evaluated changes in body weight and BMI following diagnosis. Using linear regression, we identified factors contributing to an increase in BMI at six-months. Logistic regression was used to define predictors for obesity at six-months.ResultsTwo-hundred and fifteen patients with active AAV were included in the analysis. Patients experienced a mean gain in body weight of 5.2% in the first six-months; this was maintained for at least two-years. 64.1% of patients were overweight or obese at six-months. Weight gain was greater following first presentation of AAV compared to relapsing disease. Baseline factors associated with an increase in BMI at six-months included higher eGFR (β=0.70 [0.36-1.03], P<0.001) and earlier year of presentation (β=0.38 [0.08-0.69], P=0.008). Higher eGFR (aOR=1.36 (1.08-2.72), P<0.001) and baseline BMI (aOR=2.57 (1.81-3.64), P<0.001) were associated with an increased likelihood of obesity at six-months.ConclusionWeight gain is common following a diagnosis of active AAV. This is less pronounced than it was two-decades ago. Better kidney function and higher baseline BMI are associated with a greater risk of being obese at six-months. Management of AAV should include risk mitigation for developing an unhealthy high BMI.Key messagesWeight gain and an unhealthy high BMI are prevalent following diagnosis of active AAV.Higher baseline eGFR is associated with greater weight-gain in the first six-months following diagnosis.Weight gain is less pronounced following treatment of relapsing disease compared to initial presentation.
Prevalence of Depressive symptoms and its associated factors among elderly living in old age homes of Kathmandu Metropolitan City, Nepal
Authors: Maharjan Sanju , Tiwari Nujan , Bista Sita , Basel Prem 
Published: May 2024

AbstractBackgroundDepressive symptoms have become a global public health problem, with a predominant effect on the elderly people. The studies on mental health status of elderly people in Nepal are quite limited. In this study, we aim to assess the prevalence of depressive symptoms and its associated factors among the elderly living in public old age homes of Kathmandu Metropolitan City in Nepal.MethodologyA cross-sectional study was conducted including 142 adults aged 60 years and above recruited through proportional simple random sampling from six old age homes. The 15 item-Geriatric Depression Scale(GDS) was used to assess the depressive symptoms among the participants. Associated factors were tested using Chi-square test; and a p-value of less than 0.05 with a confidence interval of 95% was used for statistical significance.ResultsMore than half of the study participants, 58.5% (95% CI: 49.9%-66.7%) were found to have depressive symptoms. Among them, 38.7% had mild symptoms, 16.2% had moderate symptoms and 3.5% had severe symptoms. Age (OR = 2.25, 95% CI: 1.08-4.66), sex (OR = 2.36, 95% CI: 1.17-4.75), past family type (OR = 0.44, 0.22-0.89), chronic physical health problem (OR = 0.34, 95% CI: 0.12-0.98) and feelings of loneliness were found to have significant association with depressive symptoms among the elderly population.ConclusionThe prevalence of depressive symptoms among the elderly in old age homes in Kathmandu Metropolitan City is quite high and a concerning issue that requires targeted mental health programs and interventions in order to bring about a positive shift in their mental health condition.
Ventricle stimulation as a potential gold-standard control stimulation site for transcranial focused ultrasound stimulation
Authors: Atkinson-Clement Cyril , Kaiser Marcus , Lambon Ralph Matthew A. , Jung JeYoung 
Published: May 2024

AbstractThis research investigates whether ventricular-focused ultrasound stimulation (ventricle-FUS) can serve as an effective control in studies using transcranial FUS, a non-invasive technology for brain modulation. FUS has notable potential for therapeutic applications but requires a robust control to accurately assess its effects. We evaluated the effectiveness of ventricle-FUS, as an active, non-cerebrum control for FUS research, comparing it to sham stimulation. We conducted a comprehensive assessment of ventricle-FUS, employing both questionnaires and multiple neuroimaging metrics such as grey matter and white matter volumes, and functional connectivity. Ventricle-FUS did not alter any of these metrics, thereby successfully retaining the auditory, somatosensory, and experiential elements of FUS without affecting brain structure or function. Importantly, participants were unable to distinguish whether they received ventricle-FUS or sham FUS. Our findings confirm that ventricle-FUS establishes it as a reliable control approach in FUS research, crucial for advancing its therapeutic applications.
Overlapping role of synaptophysin and synaptogyrin family proteins in determining the small size of synaptic vesicles
Authors: Park Daehun , Fujise Kenshiro , Wu Yumei , Luján Rafael , Del Olmo-Cabrera Sergio , Wesseling John F. , De Camilli Pietro 
Published: May 2024

AbstractMembers of the synaptophysin and synaptogyrin family are vesicle proteins with four transmembrane domains. In spite of their abundance in synaptic vesicle (SV) membranes, their role remains elusive and only mild defects at the cellular and organismal level are observed in mice lacking one or more family members. Here, we show that co-expression with synapsin of each of the four brain-enriched members of this family - synaptophysin, synaptoporin, synaptogyrin1 and synaptogyrin3 - in fibroblasts is sufficient to generate clusters of small vesicles in the same size range of SVs. Moreover, mice lacking all these four proteins have larger SVs. We conclude that synaptophysin and synaptogyrin family proteins play an overlapping function in the biogenesis of SVs and in determining their small size.
Unveiling the hidden electroencephalographical rhythms during development: aperiodic and periodic activity in healthy subjects
Authors: Angulo-Ruiz Brenda Y. , Rodríguez-Martínez Elena I. , Muñoz Vanesa , Gómez Carlos M. 
Published: May 2024

AbstractObjectiveThe study analyzes power spectral density (PSD) components, aperiodic (AP) and periodic (P) activity, in resting-state EEG of 240 healthy subjects from 6 to 29 years old, divided into 4 groups.MethodsWe calculate AP and P components using the (Fitting Oscillations and One-Over-f (FOOOF))plugging in EEGLAB. All PSD components were calculated from 1-45Hz. Topography analysis, Spearman correlations, and regression analysis with age were computed for all the components.ResultsAP and P activity show different topography across frequencies and age groups. Age-related decreases in AP exponent and offset parameters lead to reduced power, while P power decreases (1-6Hz) and increases (10-15Hz) with age.ConclusionsWe support the distinction between the AP and P components of the PSD and its possible functional changes with age. AP power is dominant in the configuration of the canonical EEG rhythms topography, although P contribution to topography is embedded in the canonical EEG topography. Some EEG canonical characteristics are similar to those of P component, as topographies of EEG rhythms (embedded) and increases in oscillatory frequency with age.SignificanceWe support that spectral power parameterization improves the interpretation and neurophysiological and functional accuracy of brain processes.HighlightsDifferential topography for aperiodic and periodic EEG components.Power decrease in aperiodic component (exponent and offset) with age.Decrease (lower frequencies) and increase (higher frequencies) of periodic component.
Individual differences in the expression and control of anger are encoded in the same fronto-temporal GM-WM network
Authors: Grecucci Alessandro , Geraci Francesca , Munari Ellyson , Yi Xiaoping , Salvato Gerardo , Messina Irene 
Published: May 2024

AbstractAnger can be deconstructed into distinct components: a temporary emotional state (state anger), a stable personality trait (trait anger), a tendency to outwardly express it (anger-out), or to internally suppress it (anger-in), and the capability to manage it (anger control). These aspects exhibit individual differences that vary across a continuum. Notably, the capacity to express and control anger are of great importance to modulate our reactions in interpersonal situations. The aim of this study was to test the hypothesis that anger expression and control are negatively correlated and that both can be decoded by the same patterns of grey and white matter features of a fronto-temporal brain network. To this aim, a data fusion unsupervised machine learning technique, known as transposed Independent Vector Analysis (tIVA), was used to decompose the brain into covarying GM-WM networks and then backward regression was used to predict both anger expression and control from a sample of 212 healthy subjects. Confirming our hypothesis, results showed that anger control and anger expression are negatively correlated, the more individuals control anger, the less they externalize it. At the neural level, individual differences in anger expression and control can be predicted by the same GM-WM network. As expected, this network included fronto-temporal regions as well as the cingulate, the insula and the precuneus. The higher the concentration of GM-WM in this brain network, the higher level of externalization of anger, and the lower the anger control. These results expand previous findings regarding the neural bases of anger by showing that individual differences in anger control and expression can be predicted by morphometric features.
DENOISING: Dynamic Enhancement and Noise Overcoming in Multimodal Neural Observations via High-density CMOS-based Biosensors
Authors: Hu Xin , Emery Brett Addison , Khanzada Shahrukh , Amin Hayder 
Published: May 2024

AbstractLarge-scale multimodal neural recordings on high-density biosensing microelectrode arrays (HD-MEAs) offer unprecedented insights into the dynamic interactions and connectivity across various brain networks. However, the fidelity of these recordings is frequently compromised by pervasive noise, which obscures meaningful neural information and complicates data analysis. To address this challenge, we introduce DENOISING, a versatile data-derived computational engine engineered to adjust thresholds adaptively based on large-scale extracellular signal characteristics and noise levels. This facilitates the separation of signal and noise components without reliance on specific data transformations. Uniquely capable of handling a diverse array of noise types (electrical, mechanical, and environmental) and multidimensional neural signals, including stationary and non-stationary oscillatory local field potential (LFP) and spiking activity, DENOISING presents an adaptable solution applicable across different recording modalities and brain networks. Applying DENOISING to large-scale neural recordings from mice hippocampal and olfactory bulb networks yielded enhanced signal-to-noise ratio (SNR) of LFP and spike firing patterns compared to those computed from raw data. Comparative analysis with existing state-of-the-art denoising methods, employing SNR and root mean square noise (RMS), underscores DENOISING’s performance in improving data quality and reliability. Through experimental and computational approaches, we validate that DENOISING improves signal clarity and data interpretation by effectively mitigating independent noise in spatiotemporally structured multimodal datasets, thus unlocking new dimensions in understanding neural connectivity and functional dynamics.
Normative evidence weighing and accumulation in correlated environments
Authors: Tardiff Nathan , Kang Jiwon , Gold Joshua I. 
Published: May 2024

AbstractThe brain forms certain deliberative decisions following normative principles related to how sensory observations are weighed and accumulated over time. Previously we showed that these principles can account for how people adapt their decisions to the temporal dynamics of the observations (Glaze et al., 2015). Here we show that this adaptability extends to accounting for correlations in the observations, which can have a dramatic impact on the weight of evidence provided by those observations. We tested online human participants on a novel visual-discrimination task with pairwise-correlated observations. With minimal training, the participants adapted to uncued, trial-by-trial changes in the correlations and produced decisions based on an approximately normative weighing and accumulation of evidence. The results highlight the robustness of our brain’s ability to process sensory observations with respect to not just their physical features but also the weight of evidence they provide for a given decision.
Theoretical proposal for restoration of hand motor function utilizing plasticity of motor-cortical interhemispheric interaction
Authors: Nakano Hideki , Tang Yandi , Morita Tomoyo , Naito Eiichi 
Published: May 2024

AbstractAfter stroke, the poorer recovery of motor function of upper extremities compared to other body parts is a longstanding problem. Based on our recent functional MRI evidence on healthy volunteers, this perspective paper proposes systematic hand motor rehabilitation utilizing the plasticity of interhemispheric interaction between motor cortices and following its developmental rule. We first discuss the effectiveness of proprioceptive intervention on the paralyzed (immobile) hand synchronized with voluntary movement of the intact hand to induce muscle activity in the paretic hand. In healthy participants, we show that this bilateral proprioceptive-motor coupling intervention activates the bilateral motor cortices (= bilaterally active mode), facilitates interhemispheric motor-cortical functional connectivity, and augments muscle activity of the passively-moved hand. Next, we propose training both hands to perform different movements, which would be effective for stroke patients who become able to manage to move the paretic hand. This bilaterally different movement training may guide the motor cortices into left-right independent mode to improve interhemispheric inhibition and hand dexterity, because we have shown in healthy older adults that this training reactivates motor-cortical interhemispheric inhibition (= left-right independent mode) declined with age, and can improve hand dexterity. Transition of both motor cortices from the bilaterally active mode to the left-right independent mode is a developmental rule of hand motor function and a common feature of motor function recovery after stroke. Hence, incorporating the brain’s inherent capacity for spontaneous recovery and adhering to developmental principles may be crucial considerations in designing effective rehabilitation strategies.
Dynamics of EEG Microstates Change Across the Spectrum of Disorders of Consciousness
Authors: Manasova Dragana , Sanz Perl Yonatan , Bruno Nicolas Marcelo , Valente Melanie , Rohaut Benjamin , Tagliazucchi Enzo , Naccache Lionel , Raimondo Federico , Sitt Jacobo D. 
Published: May 2024

AbstractAs a response to the environment and internal signals, brain networks reorganize on a sub-second scale. To capture this reorganization in patients with disorders of consciousness and understand their residual brain activity, we investigated the dynamics of electroencephalography (EEG) microstates. We analyze EEG microstate markers to quantify the periods of semi-stable topographies and the large-scale cortical networks they may reflect. To achieve this, EEG samples are clustered into four groups and then fit back into each time sample. We then obtain a time series of maps with different frequencies of occurrence and duration. One such occurrence of a map with a given duration is called a microstate. The goal of this work is to study the dynamics of these topographical patterns across patients with disorders of consciousness. Using the microstate time series, we calculate static and dynamic markers. In contrast to the static, the dynamic metrics depend on the specific temporal sequences of the maps. The static measure Ratio of Total Time covered (RTT) shows differences between healthy controls and patients, however, no differences were observed between the groups of patients. In contrast, some dynamic markers capture inter-patient group differences. The dynamic markers we investigated are Mean Microstate Durations (MMD), Microstate Duration Variances (MDV), Microstate Transition Matrices (MTM), and Entropy Production (EP). The MMD and MDV decrease with the state of consciousness, whereas the MTM non-diagonal transitions and EP increase. In other words, DoC patients have slower and closer to equilibrium (time-reversible) brain dynamics. In conclusion, static and dynamic EEG microstate metrics differ across consciousness levels, with the latter capturing the subtitler differences between groups of patients with disorders of consciousness.Abbreviated summaryThis study investigates EEG microstate dynamics in patients with disorders of consciousness (DoC) to understand residual brain activity and network reorganization. Entropy production, in addition to static markers, differs between patients and healthy controls, whereas the rest of the dynamic markers show differences across patient groups.