Miracle-dz/UniFAR-FTUs huggingface dataset:
On the intersection between data quality and dynamical modelling of large-scale fMRI signals

Large-scale dynamics of the brain are routinely modelled using systems of nonlinear dynamical equations that describe the evolution of population-level activity, with distinct neural populations often coupled according to an empirically measured structural connection matrix. This modelling approach has been used to generate insights into the neural underpinnings of spontaneous brain dynamics, as recorded with techniques such as resting state functional MRI (fMRI). In fMRI, researchers have many degrees of freedom in the way that they can process the data and recent evidence indicates that the choice of pre-processing steps can have a major effect on empirical estimates of functional connectivity. However, the potential influence of such variations on modelling results are seldom considered. Here we show, using three popular whole-brain dynamical models, that different choices during fMRI preprocessing can dramatically affect model fits and interpretations of findings. Critically, we show that the ability of these models to accurately capture patterns in fMRI dynamics is mostly driven by the degree to which they fit global signals rather than interesting sources of coordinated neural dynamics. We show that widespread deflections can arise from simple global synchronisation. We introduce a simple two-parameter model that captures these fluctuations and which performs just as well as more complex, multi-parameter biophysical models. From our combined analyses of data and simulations, we describe benchmarks to evaluate model fit and validity. Although most models are not resilient to denoising, we show that relaxing the approximation of homogeneous neural populations by more explicitly modelling inter-regional effective connectivity can improve model accuracy at the expense of increased model complexity. Our results suggest that many complex biophysical models may be fitting relatively trivial properties of the data, and underscore a need for tighter integration between data quality assurance and model development.
Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis

The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal lineage, and this has demonstrated importance in the specification of piRNA source loci and in silencing of I- and P-elements in the germ cells of daughters. Maternally inherited Piwi protein enters somatic nuclei in early embryos prior to zygotic genome activation and persists therein for roughly half of the time required to complete embryonic development. To investigate the role of the piRNA pathway in the embryonic soma, we created a conditionally unstable Piwi protein. This enabled maternally deposited Piwi to be cleared from newly laid embryos within 30 minutes and well ahead of the activation of zygotic transcription. Examination of RNA and protein profiles over time, and correlation with patterns of H3K9me3 deposition, suggests a role for maternally deposited Piwi in attenuating zygotic transposon expression in somatic cells of the developing embryo. In particular, robust deposition of piRNAs targeting roo, an element whose expression is mainly restricted to embryonic development, results in the deposition of transient heterochromatic marks at active roo insertions. We hypothesize that roo, an extremely successful mobile element, may have adopted a lifestyle of expression in the embryonic soma to evade silencing in germ cells.
Organizations in supramolecular polymers: from the solution to the bulk behavior

We have studied, in solution and in the bulk, a model system consisting of noncrystalline poly(propylene oxide) (PPO) chains end-functionalized with complementary stickers: thymine derivative (Thy) and diaminotrozaine (DAT). This system combines weak (Thy/Thy and DAT/DAT self-associations) and strong (Thy/DAT complementary association) hydrogen bonding, aromaticity of the stickers, strong repulsion between the polar stickers and the PPO spacers, and very different tendency towards crystallization for Thy and DAT. Homoditopic and heteroditopic compounds were synthesized. In solution, the solvent influences the association constants and the organizations observed. In the bulk, all materials show a relatively complex behavior, as three different phenomena concur and compete: hydrogen bonding between the stickers, phase segregation between the polymer backbone (less polar) and the stickers (more polar), and crystallization of thymines into microdomains. These phenomena impact the mesoscopic organization of the materials and thus their mechanical properties. We present the different organizations observed in solution and in the bulk and discuss the new insight our studies bring for understanding the role played respectively by hydrogen bonding, phase segregation, solvation and crystallization.
Modeling Fingerprint Presentation Attack Detection Through Transient Liveness Factor-A Person Specific Approach

A self-learning, secure and independent open-set solution is essential to be explored to characterise the liveness of fingerprint presentation. Fingerprint spoof presentation classified as live (a Type-I error) is a major problem in a high-security establishment. Type-I error are manifestation of small number of spoof sample. We propose to use only live sample to overcome above challenge. We put forward an adaptive ‘fingerprint presentation attack detection’ (FPAD) scheme using interpretation of live sample. It requires initial high-quality live fingerprint sample of the concerned person. It uses six different image quality metrics as a transient attribute from each live sample and record it as ‘Transient Liveness Factor’ (TLF). Our study also proposes to apply fusion rule to validate scheme with three outlier detection algorithms, one-class support vector machine (SVM), isolation forest and local outlier factor. Proposed study got phenomenal accuracy of 100% in terms of spoof detection, which is an open-set method. Further, this study proposes and discuss open issues on person specific spoof detection on cloud-based solutions.
Deciphering Human Leukocyte Antigen Susceptibility Maps From Immunopeptidomics Characterization in Oncology and Infections

Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen [HLA] A, B, and C) may affect susceptibility to many diseases such as cancer, auto-immune or infectious diseases. Individual genetic variation may help to explain different immune responses to microorganisms across a population. HLA typing can be fast and inexpensive; however, deciphering peptides loaded on MHC-I and II which are presented to T cells, require the design and development of high-sensitivity methodological approaches and subsequently databases. Hence, these novel strategies and databases could help in the generation of vaccines using these potential immunogenic peptides and in identifying high-risk HLA types to be prioritized for vaccination programs. Herein, the recent developments and approaches, in this field, focusing on the identification of immunogenic peptides have been reviewed and the next steps to promote their translation into biomedical and clinical practice are discussed.
Development and Validation of a Risk Score for Predicting Post-acute Myocardial Infarction Infection in Patients Undergoing Percutaneous Coronary Intervention: Study Protocol for an Observational Study

Background: Post-acute myocardial infarction (post-AMI) infection is an infrequent but important and serious complication in patients with ST-segment elevation myocardial infarction (STEMI) treated with percutaneous coronary intervention (PCI). Predicting its occurrence is essential for future prevention. However, little is known about the prediction of post-AMI infection in such patients to date. This study aims to develop and validate a new risk score based on risk factors for early prediction of infection in STEMI patients undergoing PCI. Methods: This prospective, multi-center and observational study assesses the predictive value of risk score for post-AMI infection among a cohort of patients hospitalized due to STEMI. The STEMI patients undergoing PCI enrolled between January 1st 2010 and May 31st 2016 were served as a development cohort while those enrolled from June 1st 2016 to May 31st 2018 were served as validation cohort. The primary endpoint was post-AMI infection during hospitalization, defined as infection requiring antibiotics (reflecting the clinical influence of infection compatible with the necessity for additional treatment), and all-cause death and major adverse cardiovascular events (MACE) including all-cause death, recurrent myocardial infarction, target vessel revascularization, and stroke were considered as secondary endpoints. The risk score model based on risk factors was established using stepwise logistic regression, and will be validated in other centers and external patients with non-ST-elevation acute coronary syndrome (NSTE-ACS). Results: This study will provide evidence on prognostic property, reliability of scoring, comparative performance, and suitability of the novel model for screening purpose in order to be recommended for clinical practice. Discussion: Our study is designed to develop and validate a clinical risk score for predicting infection in participants with STEMI who have undergone PCI. This simple tool may therefore improve evaluation of post-AMI infection and enhance future researches into the best practices to prevent or reduce infection in such patients. Clinical Trial Registration: www.chictr. org.cn, identifier: ChiCTR1900028278.
Pulsed Infrared Stimulation of Vertical Semicircular Canals Evokes Cardiovascular Changes in the Rat

A variety of stimuli activating vestibular end organs, including sinusoidal galvanic vestibular stimulation, whole body rotation and tilt, and head flexion have been shown to evoke significant changes in blood pressure (BP) and heart rate (HR). While a role for the vertical semicircular canals in altering autonomic activity has been hypothesized, studies to-date attribute the evoked BP and HR responses to the otolith organs. The present study determined whether unilateral activation of the posterior (PC) or anterior (AC) semicircular canal is sufficient to elicit changes in BP and/or HR. The study employed frequency-modulated pulsed infrared radiation (IR: 1,863 nm) directed via optical fibers to PC or AC of adult male Long-Evans rats. BP and HR changes were detected using a small-animal single pressure telemetry device implanted in the femoral artery. Eye movements evoked during IR of the vestibular endorgans were used to confirm the stimulation site. We found that sinusoidal IR delivered to either PC or AC elicited a rapid decrease in BP and HR followed by a stimulation frequency-matched modulation. The magnitude of the initial decrements in HR and BP did not correlate with the energy of the suprathreshold stimulus. This response pattern was consistent across multiple trials within an experimental session, replicable, and in most animals showed no evidence of habituation or an additive effect. Frequency modulated electrical current delivered to the PC and IR stimulation of the AC, caused decrements in HR and BP that resembled those evoked by IR of the PC. Frequency domain heart rate variability assessment revealed that, in most subjects, IR stimulation increased the low frequency (LF) component and decreased the high frequency (HF) component, resulting in an increase in the LF/HF ratio. This ratio estimates the relative contributions of sympathetic nervous system (SNS) and parasympathetic nervous system (PNS) activities. An injection of atropine, a muscarinic cholinergic receptor antagonist, diminished the IR evoked changes in HR, while the non-selective beta blocker propranolol eliminated changes in both HR and BP. This study provides direct evidence that activation of a single vertical semicircular canal is sufficient to activate and modulate central pathways that control HR and BP.
Mechanisms of Neoantigen-Targeted Induction of Pyroptosis and Ferroptosis: From Basic Research to Clinical Applications

Neoantigens are tumor-specific antigens (TSAs) that are only expressed in tumor cells. They are ideal targets enabling T cells to recognize tumor cells and stimulate a potent antitumor immune response. Pyroptosis and ferroptosis are newly discovered types of programmed cell death (PCD) that are different from apoptosis, cell necrosis, and autophagy. Studies of ferroptosis and pyroptosis of cancer cells are increasing, and strategies to modify the tumor microenvironment (TME) through ferroptosis to inhibit the occurrence and development of cancer, improve prognosis, and increase the survival rate are popular research topics. In addition, adoptive T cell therapy (ACT), including chimeric antigen receptor T cell (CAR-T) technology and T cell receptor engineered T cell (TCR-T) technology, and checkpoint blocking tumor immunotherapies (such as anti-PD- 1 and anti-PD-L1 agents), tumor vaccines and other therapeutic technologies that rely on tumor neoantigens are rapidly being developed. In this article, the relationship between neoantigens and pyroptosis and ferroptosis as well as the clinical role of neoantigens is reviewed.
Experimental and Computational Comparison of Intervertebral Disc Bulge for Specimen-Specific Model Evaluation Based on Imaging

Finite element modelling of the spinal unit is a promising preclinical tool to assess the biomechanical outcome of emerging interventions. Currently, most models are calibrated and validated against range of motion and rarely directly against soft-tissue deformation. The aim of this contribution was to develop an in vitro methodology to measure disc bulge and assess the ability of different specimen-specific modelling approaches to predict disc bulge. Bovine bone-disc-bone sections (N = 6) were prepared with 40 glass markers on the intervertebral disc surface. These were initially magnetic resonance (MR)-imaged and then sequentially imaged using peripheral-qCT under axial compression of 1 mm increments. Specimen-specific finite-element models were developed from the CT data, using three different methods to represent the nucleus pulposus geometry with and without complementary use of the MR images. Both calibrated specimen-specific and averaged compressive material properties for the disc tissues were investigated. A successful methodology was developed to quantify the disc bulge in vitro, enabling observation of surface displacement on qCT. From the finite element model results, no clear advantage was found in using geometrical information from the MR images in terms of the models’ ability to predict stiffness or disc bulge for bovine intervertebral disc.
AutoEncoder-Based Computational Framework for Tumor Microenvironment Decomposition and Biomarker Identification in Metastatic Melanoma

Melanoma is one of the most aggressive cancer types whose prognosis is determined by both the tumor cell-intrinsic and -extrinsic features as well as their interactions. In this study, we performed systematic and unbiased analysis using The Cancer Genome Atlas (TCGA) melanoma RNA-seq data and identified two gene signatures that captured the intrinsic and extrinsic features, respectively. Specifically, we selected genes that best reflected the expression signals from tumor cells and immune infiltrate cells. Then, we applied an AutoEncoder-based method to decompose the expression of these genes into a small number of representative nodes. Many of these nodes were found to be significantly associated with patient prognosis. From them, we selected two most prognostic nodes and defined a tumor-intrinsic (TI) signature and a tumor-extrinsic (TE) signature. Pathway analysis confirmed that the TE signature recapitulated cytotoxic immune cell related pathways while the TI signature reflected MYC pathway activity. We leveraged these two signatures to investigate six independent melanoma microarray datasets and found that they were able to predict the prognosis of patients under standard care. Furthermore, we showed that the TE signature was also positively associated with patients’ response to immunotherapies, including tumor vaccine therapy and checkpoint blockade immunotherapy. This study developed a novel computational framework to capture the tumor-intrinsic and -extrinsic features and identified robust prognostic and predictive biomarkers in melanoma.
Accounting for Natural Uncertainty Within Monitoring Systems for Induced Seismicity Based on Earthquake Magnitudes

To reduce the probability of future large earthquakes, traffic light systems (TLSs) define appropriate reactions to observed induced seismicity depending on each event's range of local earthquake magnitude (ML). The impact of velocity uncertainties and station site effects may be greater than a whole magnitude unit of ML, which can make the difference between a decision to continue (“green” TLS zone) and an immediate stop of operations (“red” zone). We show how to include these uncertainties in thresholds such that events only exceed a threshold with a fixed probability. This probability can be set by regulators to reflect their tolerance to risk. We demonstrate that with the new TLS, a red-light threshold would have been encountered earlier in the hydraulic fracturing operation at Preston New Road, UK, halting operations and potentially avoiding the later large magnitude events. It is therefore critical to establish systems which permit regulators to account for uncertainties when managing risk.
Changes of Periphyton Abundance and Biomass Driven by Factors Specific to Flooding Inflow in a River Inlet Area in Erhai Lake, China

Periphyton is an ecological essential in freshwater lakes and rivers. Its abundance and biomass are very dynamic in various habitats and subject to various factors, for example, nutrient and light. Following flooding events, the transitional area adjacent to a river inlet and the shallow lake generates diverse habitats for periphyton with gradients in current velocity, suspended matters, nutrients, and light, which would strongly shape the growth and community of periphyton. In this study, three sampling sites were established around a river inlet in Erhai Lake, China, and a field survey was conducted in the sites from April to August (flooding seasons) in 2019 to investigate the abundance and biomass of periphyton and explore influential factors. The results showed that three study areas have different gradients of current velocity depending on the distance to the river inlet, thereby regulating the concentrations of nutrients and suspended matters, which strongly affected the periphyton community; to be specific, the biomass of periphyton was inhibited by the concentration of suspended matters and high concentrations of silicate mainly reduced the diversity of periphyton. Our results imply that the study on the driving factors of periphyton could help to understand its community assembly mechanism and biomass and species composition of periphyton can provide some reference for trophic state of the lake.
Creative Thinking and Dyscalculia: Conjectures About a Still Unexplored Link

Research on creativity showed enhanced creative thinking skills in individuals with neurodevelopmental disorders, such as dyslexia (Cancer et al., 2016; Manzoli et al., 2016; Cancer and Antonietti, 2019), autism spectrum disorder (Liu et al., 2011; Kasirer and Mashal, 2014, 2016), and attention-deficit/hyperactivity disorder (ADHD) (White and Shah, 2006, 2011, 2016). In this field the relationships between creativity and dyscalculia are somewhat unexplored. Developmental Dyscalculia (DD) is a specific learning disability affecting the acquisition of numerical-arithmetical abilities in children with normal intelligence and age-appropriate school education (WHO, 2010). It affects 3–6% of the population (Shalev et al., 2001). A literature search of PsychINFO, Scopus, and Pubmed databases–using the following keywords: “Creativity and dyscalculia,” “Divergent thinking and Dyscalculia;” “Creativity andMath Disorders;” “Divergent thinking and Math disorders”–resulted in only one article which met the criteria (Saeidei and Pirkhaefi, 2020). Saeidei and Pirkhaefi (2020) investigated the role of creativity and memory in students with DD. More precisely, performances of this group of students were compared to those of students without any learning disorder, using the Torrance Test of Creative Thinking (TTCT) and the Kim Karad visual memory test. Results showed significantly lower memory and creative performances of students with DD (i.e., lower originality and elaboration scores). In contrast with such results, in a study by Magenes et al.1, who studied a sample of 180 high school students (aged 14–17 years), mathematical skills were found to predict negatively fluency in producing novel ideas, an ability which is often associated to creativity (Guilford, 1967). In accordance with the compensatory hypothesis (Chakravarty, 2009), these findings can suggest that students who fail to acquire a standard way to solve operations or problems tend to look for alternative learning approaches, thus enhancing their creative potential. However, the role of other components of creativity, beside the fluent and divergent production of ideas, have to be taken into account. Considering creativity as a multifaceted construct involving manifold mechanisms (Simonton, 2000), an important role is played by executive functions, defined as higher-order cognitive processes that enable the control of cognitive, behavioral, and emotional activity, including the subprocesses of inhibition, working memory, shifting (Miyake et al., 2000), and cognitive flexibility (Arán Filippetti and Krumm, 2020). Weaknesses in those processes in individuals with DD could potentially hinder their creative potential. The present opinion article aims at exploring the hypotheses of a positive relation between creativity and DD. Neurobiological and cognitive correspondences between DD and creative profiles point to shared characteristics which could support an enhanced creative potential