Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the power spectrum dynamics of the NREM to REM sleep transition

The transition from NREM to REM sleep is considered a transitional or intermediate stage (IS), characterized by high amplitude spindles in the frontal cortex and theta activity in the occipital cortex. Early reports in rats showed an IS lasting from 1 to 5 s, but recent studies suggested a longer duration of this stage. To further characterize the IS, we analyzed its spectral characteristics on electrocorticogram (ECoG) recordings of the olfactory bulb (OB), motor (M1), somato-sensory (S1) and secondary visual cortex (V2) in twelve Wistar male adult rats. By comparing the IS to consolidated NREM/REM epochs, our results reveal that the IS has specific power spectral patterns that statistically differ from both NREM and REM sleep states. Specifically, the main findings were that sigma (11-16 Hz) and beta (17-30 Hz) power in OB, M1, and S1 increased during the IS compared to NREM and REM sleep and began 55 s before REM sleep onset. Additionally, low gamma (31-48 Hz) in the OB started transitioning from NREM levels to REM ones 65 s before its onset. Finally, the high-frequency oscillations (102-198 Hz) in OB, M1, and S1 showed a power increase that began 40 s before REM sleep and reached REM sleep values 10 s after its onset. Thus, we argue that the NREM to REM transition contains its own spectral profile and is more extended than previously described.
The role of Kölliker-Fuse nucleus in breathing variability

The Kölliker-Fuse nucleus (KF), which is part of the parabrachial complex, participates in the generation of eupnea under resting conditions and the control of active abdominal expiration when increased ventilation is required. Moreover, dysfunctions in KF neuronal activity are believed to play a role in the emergence of respiratory abnormalities seen in Rett syndrome (RTT), a progressive neurodevelopmental disorder associated with an irregular breathing pattern and frequent apneas. Relatively little is known, however, about the intrinsic dynamics of neurons within the KF and how their synaptic connections affect breathing pattern control and contribute to breathing irregularities. In this study, we use a reduced computational model to consider several dynamical regimes of KF activity paired with different input sources to determine which combinations are compatible with known experimental observations. We further build on these findings to identify possible interactions between the KF and other components of the respiratory neural circuitry. Specifically, we present two models that both simulate eupneic as well as RTT-like breathing phenotypes. Using nullcline analysis, we identify the types of inhibitory inputs to the KF leading to RTT-like respiratory patterns and suggest possible KF local circuit organizations. When the identified properties are present, the two models also exhibit quantal acceleration of late-expiratory activity, a hallmark of active expiration featuring forced exhalation, with increasing inhibition to KF, as reported experimentally. Hence, these models instantiate plausible hypotheses about possible KF dynamics and forms of local network interactions, thus providing a general framework as well as specific predictions for future experimental testing. Key points The Kölliker-Fuse nucleus (KF), a part of the parabrachial complex, is involved in regulating normal breathing and controlling active abdominal expiration during increased ventilation. Dysfunction in KF neuronal activity is thought to contribute to respiratory abnormalities seen in Rett syndrome (RTT). This study utilizes computational modeling to explore different dynamical regimes of KF activity and their compatibility with experimental observations. By analyzing different model configurations, the study identifies inhibitory inputs to the KF that lead to RTT-like respiratory patterns and proposes potential KF local circuit organizations. Two models are presented that simulate both normal breathing and RTT-like breathing patterns. These models provide plausible hypotheses and specific predictions for future experimental investigations, offering a general framework for understanding KF dynamics and potential network interactions.
Two subtypes of GTPase-activating proteins coordinate tip growth and cell size regulation in Physcomitrium patens

The establishment of cell polarity is a prerequisite for many developmental processes. However, how it is achieved during tip growth in plants remains elusive. Here, we show that the RHO OF PLANTs (ROPs), ROP GUANINE NUCLEOTIDE EXCHANGE FACTORs (RopGEFs), and ROP GTPASE-ACTIVATING PROTEINs (RopGAPs) assemble into membrane domains in tip-growing cells of the moss Physcomitrium patens. The confinement of membrane domains requires redundant global inactivation of ROPs by PpRopGAPs and the PLECKSTRIN HOMOLOGY (PH) domain-containing RenGAP PpREN. Unexpectedly, PpRopGAPs and PpREN exert opposing effects on domain size and cell width upon overexpression. Biochemical and functional analyses indicate that PpRopGAPs are recruited to the membrane by active ROPs to restrict domain size through clustering, whereas PpREN rapidly inactivates ROPs and inhibits PpRopGAP-induced clustering. We propose that the activity- and clustering-based domain organization by RopGAPs and RenGAPs is a general mechanism for coordinating polarized cell growth and cell size regulation in plants. Significance Using the moss Physcomitrium patens, we show that PpRopGAPs and PpRenGAP redundantly regulate tip growth by inactivating ROP GTPases and influencing their membrane organization. They display distinct GAP activities and binding capacities to ROPs and could oppositely regulate cell width when overexpressed. We propose that tip growth and cell size regulation are coordinated by two subtypes of GTPase-activating proteins that act together to maintain an optimal amount of active ROPs but reversely regulate the membrane clustering of ROPs. The involvement of functionally diverged GAPs in modulating ROP activity and localization may represent a general mechanism for cell morphology regulation in plants.
A survey of CIN measures across mechanistic models

Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, 6-centromere FISH, bulk transcriptomics, and single cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples correlated well (R=0.77; p<0.01) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also correlate well (R=0.77; p<0.01) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, single-cell DNA sequencing (scDNAseq) detects CIN with high sensitivity, and correlates very well with imaging methods (R=0.83; p<0.01). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division (MDD). This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting. Significance Cancer relies on genomic changes to drive evolution. One type of change, Chromosomal INstability (CIN), promotes plasticity and heterogeneity of chromosome sets via ongoing errors in mitosis. The rate of these errors informs patient prognosis, drug response, and risk of metastasis. However, measuring CIN in patient tissues is challenging, hindering the emergence of CIN rate as a prognostic and predictive clinical biomarker. To advance clinical measures of CIN, we quantitatively tested the relative performance of several CIN measures in tandem using four well-defined, inducible CIN models. This survey revealed poor sensitivity in several common CIN assays and highlights the primacy of single-cell approaches. Further, we propose a standard, normalized unit of CIN, permitting comparison across methods and studies.
Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV

Older individuals and people with HIV (PWH) were prioritized for COVID-19 vaccination, yet comprehensive studies of the immunogenicity of these vaccines and their effects on HIV reservoirs are not available. We followed 68 PWH aged 55 and older and 23 age-matched HIV-negative individuals for 48 weeks from the first vaccine dose, after the total of three doses. All PWH were on antiretroviral therapy (cART) and had different immune status, including immune responders (IR), immune non-responders (INR), and PWH with low-level viremia (LLV). We measured total and neutralizing Ab responses to SARS-CoV-2 spike and RBD in sera, total anti-spike Abs in saliva, frequency of anti-RBD/NTD B cells, changes in frequency of anti-spike, HIV gag/nef-specific T cells, and HIV reservoirs in peripheral CD4+ T cells. The resulting datasets were used to create a mathematical model for within-host immunization. Various regimens of BNT162b2, mRNA-1273, and ChAdOx1 vaccines elicited equally strong anti-spike IgG responses in PWH and HIV- participants in serum and saliva at all timepoints. These responses had similar kinetics in both cohorts and peaked at 4 weeks post-booster (third dose), while half-lives of plasma IgG also dramatically increased post-booster in both groups. Salivary spike IgA responses were low, especially in INRs. PWH had diminished live virus neutralizing titers after two vaccine doses which were ‘rescued’ after a booster. Anti-spike T cell immunity was enhanced in IRs even in comparison to HIV- participants, suggesting Th1 imprinting from HIV, while in INRs it was the lowest. Increased frequency of viral ‘blips’ in PWH were seen post-vaccination, but vaccines did not affect the size of the intact HIV reservoir in CD4+ T cells in most PWH, except in LLVs. Thus, older PWH require three doses of COVID-19 vaccine to maximize neutralizing responses against SARS-CoV-2, although vaccines may increase HIV reservoirs in PWH with persistent viremia.
Neural manifolds in V1 change with top-down signals from V4 targeting the foveal region

High-dimensional brain activity is often organized into lower-dimensional neural manifolds. However, the neural manifolds of the visual cortex remain understudied. Here, we study large-scale multielectrode electrophysiological recordings of macaque (Macaca mulatta) areas V1, V4 and DP with a high spatio-temporal resolution. We find, for the first time, that the population activity of V1 contains two separate neural manifolds, which correlate strongly with eye closure (eyes open/closed) and have distinct dimensionalities. Moreover, we find strong top-down signals from V4 to V1, particularly to the foveal region of V1, which are significantly stronger during the eyes-open periods, a previously unknown effect. Finally, in silico simulations of a balanced spiking neuron network qualitatively reproduce the experimental findings. Taken together, our analyses and simulations suggest that top-down signals modulate the population activity of V1, causing two distinct neural manifolds. We postulate that the top-down modulation during the eyes-open periods prepares V1 for fast and efficient visual responses, resulting in a type of visual stand-by state.
Demystifying the Visual Word Form Area: Visual and Nonvisual Response Properties of Ventral Temporal Cortex with precision fMRI

The functional nature of the visual word form area (VWFA), a region in left ventrotemporal cortex (VTC), remains debated after over two decades of investigation. Here we use precision fMRI to comprehensively examine the VWFA’s responses to numerous visual and nonvisual stimuli. We find that the VWFA is a distinct region that while showing moderate activation to non-word visual stimuli, its response to words towers above other conditions. Interestingly, the VWFA is also the only VTC region uniquely engaged in auditory language processing, in contrast with the ubiquitous attentional effect within the VTC. However, this language selectivity is dwarfed by its visual responses. This suggests the VWFA primarily functions as a visual look-up orthographic dictionary. Searching within the entire VTC further reveals an additional language cluster in anterior fusiform preferring general visual semantics. Our detailed examination of the VWFA in direct comparison to other VTC regions clarifies the long-standing controversies about its functionality.
Untargeted metabolomics reveals PTI-associated metabolites in tomato

Plants employ a multi-layered innate immune system to detect and fend off invading fungal pathogens. In one such layer, recognition of Pathogen- or Microbe-Associated Molecular Patterns or elicitors, triggers a signaling cascade that leads to defence against the pathogen and ultimately Pattern-Triggered Immunity (PTI). Secondary Metabolites (SMs) are expected to play an important role in this kind of resistance, because they are potentially mycotoxic compounds. Tomato plants inoculated with Alternaria solani show clear symptoms of infection 5 days after inoculation. Whereas plants inoculated with Alternaria alternata remain symptomless. We hypothesized that pattern-triggered induction of resistance-related metabolites in Solanum lycopersicum contribute to the resistance against A. alternata, yet such SMs are suppressed in a compatible interaction. We compared the metabolomic profile (metabolome) of S. lycopersicum at two time points (3 and 24 hours) after treatments with A. alternata, A. solani and the fungal elicitor chitin and identified SMs that are involved in the early defence response of tomato plants. Our study revealed differential metabolome fingerprints and shows that the molecular composition of A. alternata and chitin-induced indeed show larger overlap with each other than with the A. solani-induced metabolome. We identify 65 candidate metabolites possibly associated with pattern-triggered resistance in tomato plants, including the alkaloid, trigonelline, for which we can confirm that it inhibits fungal growth in vitro when supplied at physiological concentrations. Our findings show that a true, pattern-triggered, chemical defence is mounted against A. alternata and that it contains mycotoxin compounds previously unidentified in tomato, that could be interesting for future crop protection strategies.
ScRNA-seq and spatial transcriptomics: exploring the occurrence and treatment of coronary-related diseases starting from development

Single-cell RNA sequencing (scRNA-seq) is a new technology that can be used to explore molecular changes in complex cell clusters at the single-cell level. Single-cell spatial transcriptomic technology complements the cell-space location information lost during single-cell sequencing. Coronary artery disease is an important cardiovascular disease with high mortality rates. Many studies have explored the physiological development and pathological changes in coronary arteries from the perspective of single cells using single-cell spatial transcriptomic technology. This article reviews the molecular mechanisms underlying coronary artery development and diseases as revealed by scRNA-seq combined with spatial transcriptomic technology. Based on these mechanisms, we discuss the possible new treatments for coronary diseases.
Umbilical cord-mesenchymal stem cells induce a memory phenotype in CD4+ T cells

Inflammation is a physiological state where immune cells evoke a response against detrimental insults. Finding a safe and effective treatment for inflammation associated diseases has been a challenge. In this regard, human mesenchymal stem cells (hMSC), exert immunomodulatory effects and have regenerative capacity making it a promising therapeutic option for resolution of acute and chronic inflammation. T cells play a critical role in inflammation and depending on their phenotype, they can stimulate or suppress inflammatory responses. However, the regulatory effects of hMSC on T cells and the underlying mechanisms are not fully elucidated. Most studies focused on activation, proliferation, and differentiation of T cells. Here, we further investigated memory formation and responsiveness of CD4+ T cells and their dynamics by immune-profiling and cytokine secretion analysis. Umbilical cord mesenchymal stem cells (UC-MSC) were co-cultured with either αCD3/CD28 beads, activated peripheral blood mononuclear cells (PBMC) or magnetically sorted CD4+ T cells. The mechanism of immune modulation of UC-MSC were investigated by comparing different modes of action; transwell, direct cell-cell contact, addition of UC-MSC conditioned medium or blockade of paracrine factor production by UC-MSC. We observed a differential effect of UC-MSC on CD4+ T cell activation and proliferation using PBMC or purified CD4+ T cell co-cultures. UC-MSC skewed the effector memory T cells into a central memory phenotype in both co-culture conditions. This effect on central memory formation was reversible, since UC-MSC primed central memory cells were still responsive after a second encounter with the same stimuli. The presence of both cell-cell contact and paracrine factors were necessary for the most pronounced immunomodulatory effect of UC-MSC on T cells. We found suggestive evidence for a partial role of IL-6 and TGFβ in the UC-MSC derived immunomodulatory function. Collectively, our data show that UC-MSCs clearly affect T cell activation, proliferation and maturation, depending on co-culture conditions for which both cell-cell contact and paracrine factors are needed.
Association between delirium and statin use in patients with congestive heart failure: a retrospective propensity score-weighted analysis

Background The relationship between statin use and delirium remains controversial; therefore, we aimed to study the association between statin exposure and delirium and in-hospital mortality in patients with congestive heart failure. Methods In this retrospective study, patients with congestive heart failure were identified from the Medical Information Mart for Intensive Care database. The primary exposure variable was statin use 3 days after admission to the intensive care unit, and the primary outcome measure was the presence of delirium. The secondary outcome measure was in-hospital mortality. Since the cohort study was retrospective, we used inverse probability weighting derived from the propensity score to balance various variables. Results Of 8,396 patients, 5,446 (65%) were statin users. Before matching, the prevalence of delirium was 12.5% and that of in-hospital mortality was 11.8% in patients with congestive heart failure. Statin use was significantly negatively correlated with delirium, with an odds ratio of 0.76 (95% confidence interval: [0.66–0.87]; P < 0.001) in the inverse probability weighting cohort and in-hospital mortality of 0.66 (95% confidence interval: [0.58–0.75]; P < 0.001). Conclusion Statins administered in the intensive care unit can significantly reduce the incidence of delirium and in-hospital mortality in patients with congestive heart failure.
Prevalence of smoking cigarettes and beliefs regarding smoking habits among medical students: a cross-sectional study in Sudan

Background Smoking is a common problem in university students worldwide. Smoking is one of the most dangerous social phenomena and has a significant impact on public health. This study investigated the beliefs and attitudes of medical students toward smoking in Sudan. Methods A cross-sectional study was conducted among medical students at Al Neelain University, Sudan, from March to June 2022 using a web-based questionnaire. The questionnaire consisted of eight items on demographic characteristics and 13 on the beliefs and attitudes toward smoking. Other data included smoking status, smoking habits, the number of cigarettes smoked per day, and smoking duration. Data analysis was performed descriptively, and chi-square test and logistic regression were conducted using SPSS version 24. Statistical significance was set at 0.05. Results A total of 336 students participated in this study, and the smoking prevalence was 48.8% (41.1% in men and 7.7% in women). In total, 76.8% reported smoking daily at a rate of 5–10 cigarettes per day. In terms of students’ beliefs about smoking, 86.8% disagreed with selling cigarettes at the university. Of the respondents, 68.4% did not approve smoking on campus. There was a relationship between smoking habits and the age group of 22–25 years, which was the highest smoking category among students (p-value = 0.01). Conclusion The prevalence of cigarette smoking among medical students is disturbing, particularly as they are future doctors. There is a need to include plans to reduce smoking among students that can be incorporated into courses and special programs.
Shared alterations in hippocampal structural covariance in subjective cognitive decline and migraine

Introduction Subjective cognitive decline (SCD) and migraine are often comorbid. Hippocampal structural abnormalities have been observed in individuals with both SCD and migraine. Given the known structural and functional heterogeneity along the long axis (anterior to posterior) of the hippocampus, we aimed to identify altered patterns of structural covariance within hippocampal subdivisions associated with SCD and migraine comorbidities. Methods A seed-based structural covariance network analysis was applied to examine large-scale anatomical network changes of the anterior and posterior hippocampus in individuals with SCD, migraine and healthy controls. Conjunction analyses were used to identify shared network-level alterations in the hippocampal subdivisions in individuals with both SCD and migraine. Results Altered structural covariance integrity of the anterior and posterior hippocampus was observed in the temporal, frontal, occipital, cingulate, precentral, and postcentral areas in individuals with SCD and migraine compared with healthy controls. Conjunction analysis revealed that, in both SCD and migraine, altered structural covariance integrity was shared between the anterior hippocampus and inferior temporal gyri and between the posterior hippocampus and precentral gyrus. Additionally, the structural covariance integrity of the posterior hippocampus-cerebellum axis was associated with the duration of SCD. Conclusion This study highlighted the specific role of hippocampal subdivisions and specific structural covariance alterations within these subdivisions in the pathophysiology of SCD and migraine. These network-level changes in structural covariance may serve as potential imaging signatures for individuals who have both SCD and migraine.