Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey on Deep Learning-Based Short/Zero-Calibration Approaches for EEG-Based Brain–Computer Interfaces

Brain–computer interfaces (BCIs) utilizing machine learning techniques are an emerging technology that enables a communication pathway between a user and an external system, such as a computer. Owing to its practicality, electroencephalography (EEG) is one of the most widely used measurements for BCI. However, EEG has complex patterns and EEG-based BCIs mostly involve a cost/time-consuming calibration phase; thus, acquiring sufficient EEG data is rarely possible. Recently, deep learning (DL) has had a theoretical/practical impact on BCI research because of its use in learning representations of complex patterns inherent in EEG. Moreover, algorithmic advances in DL facilitate short/zero-calibration in BCI, thereby suppressing the data acquisition phase. Those advancements include data augmentation (DA), increasing the number of training samples without acquiring additional data, and transfer learning (TL), taking advantage of representative knowledge obtained from one dataset to address the so-called data insufficiency problem in other datasets. In this study, we review DL-based short/zero-calibration methods for BCI. Further, we elaborate methodological/algorithmic trends, highlight intriguing approaches in the literature, and discuss directions for further research. In particular, we search for generative model-based and geometric manipulation-based DA methods. Additionally, we categorize TL techniques in DL-based BCIs into explicit and implicit methods. Our systematization reveals advances in the DA and TL methods. Among the studies reviewed herein, ~45% of DA studies used generative model-based techniques, whereas ~45% of TL studies used explicit knowledge transferring strategy. Moreover, based on our literature review, we recommend an appropriate DA strategy for DL-based BCIs and discuss trends of TLs used in DL-based BCIs.
Dynamics of Long-Range Temporal Correlations in Broadband EEG During Different Motor Execution and Imagery Tasks

Brain activity is composed of oscillatory and broadband arrhythmic components; however, there is more focus on oscillatory sensorimotor rhythms to study movement, but temporal dynamics of broadband arrhythmic electroencephalography (EEG) remain unexplored. We have previously demonstrated that broadband arrhythmic EEG contains both short- and long-range temporal correlations that change significantly during movement. In this study, we build upon our previous work to gain a deeper understanding of these changes in the long-range temporal correlation (LRTC) in broadband EEG and contrast them with the well-known LRTC in alpha oscillation amplitude typically found in the literature. We investigate and validate changes in LRTCs during five different types of movements and motor imagery tasks using two independent EEG datasets recorded with two different paradigms—our finger tapping dataset with single self-initiated asynchronous finger taps and publicly available EEG dataset containing cued continuous movement and motor imagery of fists and feet. We quantified instantaneous changes in broadband LRTCs by detrended fluctuation analysis on single trial 2 s EEG sliding windows. The broadband LRTC increased significantly (p < 0.05) during all motor tasks as compared to the resting state. In contrast, the alpha oscillation LRTC, which had to be computed on longer stitched EEG segments, decreased significantly (p < 0.05) consistently with the literature. This suggests the complementarity of underlying fast and slow neuronal scale-free dynamics during movement and motor imagery. The single trial broadband LRTC gave high average binary classification accuracy in the range of 70.54±10.03% to 76.07±6.40% for all motor execution and imagery tasks and hence can be used in brain–computer interface (BCI). Thus, we demonstrate generalizability, robustness, and reproducibility of novel motor neural correlate, the single trial broadband LRTC, during different motor execution and imagery tasks in single asynchronous and cued continuous motor-BCI paradigms and its contrasting behavior with LRTC in alpha oscillation amplitude.
Central Regulation of PCOS: Abnormal Neuronal-Reproductive-Metabolic Circuits in PCOS Pathophysiology

Polycystic ovary syndrome (PCOS) is a common reproductive endocrine disease. PCOS patients are characterized by hyperandrogenemia, anovulation, and metabolic dysfunction. Hypothalamus–pituitary–ovary axis imbalance is considered as an important pathophysiology underlying PCOS, indicating that central modulation, especially the abnormal activation of hypothalamic GnRH neurons plays a vital role in PCOS development. Increased GnRH pulse frequency can promote LH secretion, leading to ovarian dysfunction and abnormal sex steroids synthesis. By contrast, peripheral sex steroids can modulate the action of GnRH neurons through a feedback effect, which is impaired in PCOS, thus forming a vicious cycle. Additionally, hypothalamic GnRH neurons not only serve as the final output pathway of central control of reproductive axis, but also as the central connection point where reproductive function and metabolic state inter-regulate with each other. Metabolic factors, such as insulin resistance and obesity in PCOS patients can regulate GnRH neurons activity, and ultimately regulate reproductive function. Besides, gut hormones act on both brain and peripheral organs to modify metabolic state. Gut microbiota disturbance is also related to many metabolic diseases and has been reported to play an essential part in PCOS development. This review concludes with the mechanism of central modulation and the interaction between neuroendocrine factors and reproductive or metabolic disorders in PCOS development. Furthermore, the role of the gut microenvironment as an important part involved in the abnormal neuronal–reproductive–metabolic circuits that contribute to PCOS is discussed, thus offering possible central and peripheral therapeutic targets for PCOS patients.
Establishment of Novel Prostate Cancer Risk Subtypes and A Twelve-Gene Prognostic Model

Prostate cancer (PCa) is the most common malignancy among men worldwide. However, its complex heterogeneity makes treatment challenging. In this study, we aimed to identify PCa subtypes and a gene signature associated with PCa prognosis. In particular, nine PCa-related pathways were evaluated in patients with PCa by a single-sample gene set enrichment analysis (ssGSEA) and an unsupervised clustering analysis (i.e., consensus clustering). We identified three subtypes with differences in prognosis (Risk_H, Risk_M, and Risk_L). Differences in the proliferation status, frequencies of known subtypes, tumor purity, immune cell composition, and genomic and transcriptomic profiles among the three subtypes were explored based on The Cancer Genome Atlas database. Our results clearly revealed that the Risk_H subtype was associated with the worst prognosis. By a weighted correlation network analysis of genes related to the Risk_H subtype and least absolute shrinkage and selection operator, we developed a 12-gene risk-predicting model. We further validated its accuracy using three public datasets. Effective drugs for high-risk patients identified using the model were predicted. The novel PCa subtypes and prognostic model developed in this study may improve clinical decision-making.
Flexible Broadband Terahertz Modulation Based on Strain-Sensitive MXene Material

A flexible broadband terahertz modulator based on a strain-sensitive MXene material is reported. MXene is shown to have high terahertz wave absorption through experimental testing of various substrate samples. Results show that the THz signal transmission increases with increasing stretching degree, which differs obviously from transmission through pure PVAc substrates. Analysis of the terahertz time-domain spectrum and electrical characterization indicate that the sample’s conductivity decreases with increasing stretching degree. The trend and magnitude of the electrical conductivity results are also very similar to those from the time-domain spectrum. MXene is shown to be a simple, efficient terahertz broadband spectrum modulator with transmittance that can be affected by applying external forces.
Metabolomic Characterization of Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS)

Introduction PANS is a controversial clinical entity, consisting of a complex constellation of psychiatric symptoms, adventitious changes, and expression of various serological alterations, likely sustained by an autoimmune/inflammatory disease. Detection of novel biomarkers of PANS is highly desirable for both diagnostic and therapeutic management of affected patients. Analysis of metabolites has proven useful in detecting biomarkers for other neuroimmune-psychiatric diseases. Here, we utilize the metabolomics approach to determine whether it is possible to define a specific metabolic pattern in patients affected by PANS compared to healthy subjects. Design This observational case-control study tested consecutive patients referred for PANS between June 2019 to May 2020. A PANS diagnosis was confirmed according to the PANS working criteria (National Institute of Mental Health [NIMH], 2010). Healthy age and sex-matched subjects were recruited as controls. Methods Thirty-four outpatients referred for PANS (mean age 9.5 years; SD 2.9, 71% male) and 25 neurotypical subjects matched for age and gender, were subjected to metabolite analysis. Serum samples were obtained from each participant and were analyzed using Nuclear Magnetic Resonance (NMR) spectroscopy. Subsequently, multivariate and univariate statistical analyses and Receiver Operator Curves (ROC) were performed. Results Separation of the samples, in line with the presence of PANS diagnosis, was observed by applying a supervised model (R2X = 0.44, R2Y = 0.54, Q2 = 0.44, p-value < 0.0001). The significantly altered variables were 2-Hydroxybutyrate, glycine, glutamine, histidine, tryptophan. Pathway analysis indicated that phenylalanine, tyrosine, and tryptophan metabolism, as well as glutamine and glutamate metabolism, exhibited the largest deviations from neurotypical controls. Conclusion We found a unique plasma metabolic profile in PANS patients, significantly differing from that of healthy children, that suggests the involvement of specific patterns of neurotransmission (tryptophan, glycine, histamine/histidine) as well as a more general state of neuroinflammation and oxidative stress (glutamine, 2-Hydroxybutyrate, and tryptophan-kynurenine pathway) in the disorder. This metabolomics study offers new insights into biological mechanisms underpinning the disorder and supports research of other potential biomarkers implicated in PANS.
Tyrosine Kinase ROR1 as a Target for Anti-Cancer Therapies

Receptor tyrosine kinase ROR1 plays an essential role in embryogenesis and is overexpressed in many types of malignant tumors. Studies have demonstrated that it plays an important role in oncogenesis by activating cell survival signaling events, particularly the non-canonical WNT signaling pathway. Antibody-based immunotherapies targeting ROR1 have been developed and evaluated in preclinical and clinical studies with promising outcomes. However, small molecule inhibitors targeting ROR1 are underappreciated because of the initial characterization of ROR1 as a peusdokinase. The function of ROR1 as a tyrosine kinase remains poorly understood, although accumulating evidence have demonstrated its intrinsic tyrosine kinase activity. In this review, we analyzed the structural and functional features of ROR1 and discussed therapeutic strategies targeting this kinase.
Role of the Ubiquitin System in Chronic Pain

As a significant public health issue, chronic pain, mainly neuropathic pain (NP) and inflammatory pain, has a severe impact. The underlying mechanisms of chronic pain are enigmatic at present. The roles of ubiquitin have been demonstrated in various physiological and pathological conditions and underscore its potential as therapeutic targets. The dysfunction of the component of the ubiquitin system that occurs during chronic pain is rapidly being discovered. These results provide insight into potential molecular mechanisms of chronic pain. Chronic pain is regulated by ubiquitination, SUMOylation, ubiquitin ligase, and deubiquitinating enzyme (DUB), etc. Insight into the mechanism of the ubiquitin system regulating chronic pain might contribute to relevant therapeutic targets and the development of novel analgesics.
Increased Endogenous Activity of the Renin-Angiotensin System Reduces Infarct Size in the Rats with Early Angiotensin II-dependent Hypertension which Survive the Acute Ischemia/Reperfusion Injury

We investigated the role of the interaction between hypertension and the renin-angiotensin system in the pathophysiology of myocardial ischemia/reperfusion injury. We hypothesized that in the early phase of angiotensin II (ANG II)-dependent hypertension with developed left ventricular hypertrophy, cardioprotective mechanism(s) are fully activated. The experiments were performed in transgenic rats with inducible hypertension, noninduced rats served as controls. The early phase of ANG II-dependent hypertension was induced by five-days (5 days) dietary indole-3-carbinol administration. Cardiac hypertrophy, ANG II and ANG 1–7 levels, protein expression of their receptors and enzymes were determined. Separate groups were subjected to acute myocardial ischemia/reperfusion injury, and infarct size and ventricular arrhythmias were assessed. Induced rats developed marked cardiac hypertrophy accompanied by elevated ANG levels. Ischemia/reperfusion mortality was significantly higher in induced than noninduced rats (52.1 and 25%, respectively). The blockade of AT1 receptors with losartan significantly increased survival rate in both groups. Myocardial infarct size was significantly reduced after 5 days induction (by 11%), without changes after losartan treatment. In conclusion, we confirmed improved cardiac tolerance to ischemia/reperfusion injury in hypertensive cardiohypertrophied rats and found that activation of AT1 receptors by locally produced ANG II in the heart was not the mechanism underlying infarct size reduction.
De novo Explorations of Sarcopenia via a Dynamic Model

Background: The cause of sarcopenia has been observed over decades by clinical trials, which, however, are still insufficient to systematically unravel the enigma of how resistance exercise mediates skeletal muscle mass. Materials and Methods: Here, we proposed a minimal regulatory network and developed a dynamic model to rigorously investigate the mechanism of sarcopenia. Our model is consisted of eight ordinary differential equations and incorporates linear and Hill-function terms to describe positive and negative feedbacks between protein species, respectively. Results: A total of 720 samples with 10 scaled intensities were included in simulations, which revealed the expression level of AKT (maximum around 3.9-fold) and mTOR (maximum around 5.5-fold) at 3, 6, and 24 h at high intensity, and non-monotonic relation (ranging from 1.2-fold to 1.7-fold) between the graded intensities and skeletal muscle mass. Furthermore, continuous dynamics (within 24 h) of AKT, mTOR, and other proteins were obtained accordingly, and we also predicted the delaying effect with the median of maximized muscle mass shifting from 1.8-fold to 4.6-fold during a 4-fold increase of delay coefficient. Conclusion: The de novo modeling framework sheds light on the interdisciplinary methodology integrating computational approaches with experimental results, which facilitates the deeper understandings of exercise training and sarcopenia.
CH4/CO2 Ratios and Carbon Isotope Enrichment Between Diet and Breath in Herbivorous Mammals

Breath and diet samples were collected from 29 taxa of animals at the Zurich and Basel Zoos to characterize the carbon isotope enrichment between breath and diet. Diet samples were measured for δ13C and breath samples for CH4/CO2 ratios and for the respired component of δ13C using the Keeling plot approach. Different digestive physiologies included coprophagous and non-coprophagous hindgut fermenters, and non-ruminant and ruminant foregut fermenters. Isotope enrichments from diet to breath were 0.8 ± 0.9‰, 3.5 ± 0.8‰, 2.3 ± 0.4‰, and 4.1 ± 1.0‰, respectively. CH4/CO2 ratios were strongly correlated with isotope enrichments for both hindgut and foregut digestive strategies, although CH4 production was not the sole reason for isotope enrichment. Average CH4/CO2 ratios per taxon ranged over several orders of magnitude from 10–5 to 10–1. The isotope enrichment values for diet-breath can be used to further estimate the isotope enrichment from diet-enamel because Passey et al. (2005b) found a nearly constant isotope enrichment for breath-enamel for diverse mammalian taxa. The understanding of isotope enrichment factors from diet to breath and diet to enamel will have important applications in the field of animal physiology, and possibly also for wildlife ecology and paleontology.
Applying Cryo-X-ray Photoelectron Spectroscopy to Study the Surface Chemical Composition of Fungi and Viruses

Interaction between microorganisms and their surroundings are generally mediated via the cell wall or cell envelope. An understanding of the overall chemical composition of these surface layers may give clues on how these interactions occur and suggest mechanisms to manipulate them. This knowledge is key, for instance, in research aiming to reduce colonization of medical devices and device-related infections from different types of microorganisms. In this context, X-ray photoelectron spectroscopy (XPS) is a powerful technique as its analysis depth below 10 nm enables studies of the outermost surface structures of microorganism. Of specific interest for the study of biological systems is cryogenic XPS (cryo-XPS). This technique allows studies of intact fast-frozen hydrated samples without the need for pre-treatment procedures that may cause the cell structure to collapse or change due to the loss of water. Previously, cryo-XPS has been applied to study bacterial and algal surfaces with respect to their composition of lipids, polysaccharides and peptide (protein and/or peptidoglycan). This contribution focuses onto two other groups of microorganisms with widely different architecture and modes of life, namely fungi and viruses. It evaluates to what extent existing models for data treatment of XPS spectra can be applied to understand the chemical composition of their very different surface layers. XPS data from model organisms as well as reference substances representing specific building blocks of their surface were collected and are presented. These results aims to guide future analysis of the surface chemical composition of biological systems.
A Potential High-Risk Clone of Pseudomonas aeruginosa ST463

Pseudomonas aeruginosa is one of the most common opportunistic pathogens, which causes severe nosocomial infections because of its well-known multidrug-resistance and hypervirulence. It is critical to curate routinely the epidemic P. aeruginosa clones encountered in the clinic. The aim of the present study was to investigate the connection between virulence factors and antimicrobial resistance profiles in epidemic clones. Herein, we found that ST463 (O4), ST1212 (O11), and ST244 (O5) were prevalent in 30 isolates derived from non-cystic fibrosis patients, based on multilocus sequence type (MLST) and serotype analysis. All isolates were multidrug-resistant (MDR) and each was resistance to at least three classes of antibiotics in antimicrobial susceptibility tests, which was consistent with the presence of the abundant resistance genes, such as blaOXA–50, blaPAO, aph(3′), catB7, fosA, crpP, and blaKPC–2. Notably, all blaKPC–2 genes were located between ISKpn6-like and ISKpn8-like mobile genetic elements. In addition, classical exotoxins encoded by exoU, exoS, and pldA were present in 43.44% (13/40), 83.33% (25/30), and 70% (21/30) of the isolates, respectively. The expression of phz operons encoding the typical toxin, pyocyanin, was observed in 60% of isolates (18/30) and was quantified using triple quadrupole liquid chromatograph mass (LC/MS) assays. Interestingly, compared with other MLST types, all ST463 isolates harbored exoU, exoS and pldA, and produced pyocyanin ranging from 0.2 to 3.2 μg/mL. Finally, we evaluated the potential toxicity of these isolates using hemolysis tests and Galleria mellonella larvae infection models. The results showed that ST463 isolates were more virulent than other isolates. In conclusion, pyocyanin-producing ST463 P. aeruginosa, carrying diverse virulence genes, is a potential high-risk clone.
Circulating Plasma miRNA and Clinical/Hemodynamic Characteristics Provide Additional Predictive Information About Acute Pulmonary Thromboembolism, Chronic Thromboembolic Pulmonary Hypertension and Idiopathic Pulmonary Hypertension

Idiopathic pulmonary artery hypertension (IPAH), chronic thromboembolic pulmonary hypertension (CTEPH), and acute pulmonary embolism (APTE) are life-threatening cardiopulmonary diseases without specific surgical or medical treatment. Although APTE, CTEPH and IPAH are different pulmonary vascular diseases in terms of clinical presentation, prevalence, pathophysiology and prognosis, the identification of their circulating microRNA (miRNAs) might help in recognizing differences in their outcome evolution and clinical forms. The aim of this study was to describe the APTE, CTEPH, and IPAH-associated miRNAs and to predict their target genes. The target genes of the key differentially expressed miRNAs were analyzed, and functional enrichment analyses were carried out. The miRNAs were detected using RT-PCR. Finally, we incorporated plasma circulating miRNAs in baseline and clinical characteristics of the patients to detect differences between APTE and CTEPH in time of evolution, and differences between CTEPH and IPAH in diseases form. We found five top circulating plasma miRNAs in common with APTE, CTEPH and IPAH assembled in one conglomerate. Among them, miR-let-7i-5p expression was upregulated in APTE and IPAH, while miRNA-320a was upregulated in CTEP and IPAH. The network construction for target genes showed 11 genes regulated by let-7i-5p and 20 genes regulated by miR-320a, all of them regulators of pulmonary arterial adventitial fibroblasts, pulmonary artery endothelial cell, and pulmonary artery smooth muscle cells. AR (androgen receptor), a target gene of hsa-let-7i-5p and has-miR-320a, was enriched in pathways in cancer, whereas PRKCA (Protein Kinase C Alpha), also a target gene of hsa-let-7i-5p and has-miR-320a, was enriched in KEGG pathways, such as pathways in cancer, glioma, and PI3K-Akt signaling pathway. We inferred that CTEPH might be the consequence of abnormal remodeling in APTE, while unbalance between the hyperproliferative and apoptosis-resistant phenotype of pulmonary arterial adventitial fibroblasts, pulmonary artery endothelial cell and pulmonary artery smooth muscle cells in pulmonary artery confer differences in IPAH and CTEPH diseases form. We concluded that the incorporation of plasma circulating let-7i-5p and miRNA-320a in baseline and clinical characteristics of the patients reinforces differences between APTE and CTEPH in outcome evolution, as well as differences between CTEPH and IPAH in diseases form.