Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria

Recommendations from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) for interpreting sequence variants specify the use of computational predictors as Supporting level of evidence for pathogenicity or benignity using criteria PP3 and BP4, respectively. However, score intervals defined by tool developers, and ACMG/AMP recommendations that require the consensus of multiple predictors, lack quantitative support. Previously, we described a probabilistic framework that quantified the strengths of evidence (Supporting, Moderate, Strong, Very Strong) within ACMG/AMP recommendations. We have extended this framework to computational predictors and introduce a new standard that converts a tool’s scores to PP3 and BP4 evidence strengths. Our approach is based on estimating the local positive predictive value and can calibrate any computational tool or other continuous-scale evidence on any variant type. We estimate thresholds (score intervals) corresponding to each strength of evidence for pathogenicity and benignity for thirteen missense variant interpretation tools, using carefully assembled independent data sets. Most tools achieved Supporting evidence level for both pathogenic and benign classification using newly established thresholds. Multiple tools reached score thresholds justifying Moderate and several reached Strong evidence levels. One tool reached Very Strong evidence level for benign classification on some variants. Based on these findings, we provide recommendations for evidence-based revisions of the PP3 and BP4 ACMG/AMP criteria using individual tools and future assessment of computational methods for clinical interpretation.
Maintaining hypoxia environment of subchondral bone alleviates osteoarthritis progression

Abnormal subchondral bone remodeling featured by over-activated osteoclastogenesis leads to articular cartilage degeneration and osteoarthritis (OA) progression, but the mechanism is still unclear. In this study, we used lymphocyte cytosolic protein 1 (Lcp1) knock-out mice to suppress subchondral osteoclast formation in mice OA model with anterior cruciate ligament transection (ACLT) and Lcp1-/- mice showed decreased bone remodeling and sensory innervation in subchondral bone accompanied by retarded cartilage degeneration. For mechanisms, in wildtype mice with ACLT the activated osteoclasts in subchondral bone induced type-H vessels and elevated oxygen concentration which ubiquitylated hypoxia-inducible factor 1α (HIF-1α), vital for maintaining chondrocyte homeostasis in articular chondrocytes and led to cartilage degeneration. Deletion of Lcp1 impeded osteoclast-mediated angiogenesis, which maintained the low levels of oxygen partial pressure (pO2) in subchondral bone as well as the whole joint and delayed the OA progression. Stabilization of HIF-1α delayed cartilage degeneration and knockdown of Hif1a abolished the protective effects of Lcp1 knockout. Notably, we identified a novel subgroup of hypertrophic chondrocytes highly associated with OA by single cell sequencing analysis of human articular chondrocytes. Lastly, we showed that Oroxylin A, an Lcp1-encoded protein L-plastin (LPL) inhibitor, could alleviate OA progression. In conclusion, maintaining hypoxic environment in subchondral bone is an attractive strategy for OA treatment. Teaser Inhibiting subchondral osteoclastogenesis alleviates OA progression via maintaining joint hypoxia environment.
A multi-scale fusion CNN model based on adaptive transfer learning for multi-class MI-classification in BCI system

Deep learning-based brain-computer interface (BCI) in motor imagery (MI) has emerged as a powerful method for establishing direct communication between the brain and external electronic devices. However, due to inter-subject variability, inherent complex properties, and low signal-to-noise ratio (SNR) in electroencephalogram (EEG) signal are major challenges that significantly hinders the accuracy of the MI classifier. To overcome this, the present work proposes an efficient transfer learning-based multi-scale feature fused CNN (MSFFCNN) which can capture the distinguishable features of various non-overlapping canonical frequency bands of EEG signals from different convolutional scales for multi-class MI classification. In order to account for inter-subject variability from different subjects, the current work presents 4 different model variants including subject-independent and subject-adaptive classification models considering different adaptation configurations to exploit the full learning capacity of the classifier. Each adaptation configuration has been fine-tuned in an extensively trained pre-trained model and the performance of the classifier has been studied for vast range of learning rates and degrees of adaptation which illustrates the advantages of using an adaptive transfer learning-based model. The model achieves an average classification accuracy of 94.06% (±2.29%) and kappa value of 0.88 outperforming several baseline and current state-of-the-art EEG-based MI classification models with fewer training samples. The present research provides an effective and efficient transfer learning-based end-to-end MI classification framework for designing a high-performance robust MI-BCI system.
Low-toxin Clostridioides difficile RT027 strains exhibit robust virulence

Clostridioides difficile is a leading cause of healthcare-associated infections worldwide. Currently, there is lack of consensus on a single optimal diagnostic method for C. difficile infection (CDI). Nucleic acid amplification tests (NAAT) that detect toxin genes are highly sensitive, but their specificity limitations could inflate CDI rates. Alternate multi-step diagnostic algorithms emphasize the detection of C. difficile toxins TcdA/TcdB, and are premised on the rationale that stool toxin-negative (Tox-) CDI patients have less severe disease, shorter diarrhea duration, and fewer disease complications. There have been no systematic assessments, however, of the virulence of C. difficile strains from Tox-/NAAT+ (discrepant) specimens. In our prospective analysis of 1243 C. difficile-positive patient stool specimens from three Southern Arizona hospitals, 31% were discrepant. Ribotype 027 (RT027) strains were recovered from 221 specimens; of these, 23% were discrepant. Post-culture, RT027 strains produced a range of toxin amounts including levels lower than that of the non-epidemic strain CD630. These low-toxin RT027 (LT-027) strains harbored both tcdA and tcdB genes, and their culture supernatants were cytotoxic to cultured fibroblasts. We confirmed robust colonization and virulence of a subset of LT-027 strains using multiple rodent models; lethality in animals infected with LT-027 strains was comparable to that potentiated by a high-toxin RT027 strain. Comparative genomics and proteomics analyses of several LT-027 strains identified unique genes and altered protein abundances relative to closely-related high-toxin strains. Collectively our data highlight the robust virulence and clinical relevance of low-toxin-producing, RT027 C. difficile isolates.
Frequency-specific neural signatures of perceptual content and perceptual stability

In the natural environment, we often form stable perceptual experiences from ambiguous and fleeting sensory inputs. Which neural activity underlies the content of perception and which neural activity supports perceptual stability remains an open question. We used a bistable perception paradigm involving ambiguous images to behaviorally dissociate perceptual content from perceptual stability, and magnetoencephalography (MEG) to measure whole-brain neural dynamics in humans. Combining multivariate decoding and neural state-space analyses, we found frequency band-specific neural signatures that underlie the content of perception and promote perceptual stability, respectively. Across different types of images, non-oscillatory neural activity in the slow cortical potential (SCP, <5 Hz) range supported the content of perception. By contrast, perceptual stability is influenced by the amplitude of alpha and beta oscillations. In addition, neural activity underlying perceptual memory, which supports perceptual stability when sensory input is temporally removed from view, also encodes elapsed time. Together, these results reveal distinct neural mechanisms that support the content vs. stability of visual perception.
Avatar error in your favor: Embodied avatars can fix users’ mistakes without them noticing

In immersive Virtual Reality (VR), users can experience the subjective feeling of embodiment for the avatar representing them in a virtual world. This is known to be strongly supported by a high Sense of Agency (SoA) for the movements of the avatar that follows the user. In general, users do not self-attribute actions of their avatar that are different from the one they actually performed. The situation is less clear when actions of the avatar satisfies the intention of the user despite distortions and noticeable differences between user and avatar movements. A within-subject experiment was here conducted to determine whether a finger swap helping users achieve a task would be more tolerated than one penalizing them. In particular, in a context of fast-paced finger movements and with clear correct or incorrect responses, we swapped the finger animation of the avatar (e.g. user moves the index finger, the avatar moves the middle one) to either automatically correct for spontaneous mistakes or to introduce incorrect responses. Subjects playing a VR game were asked to report when they noticed the introduction of a finger swap. Results based on 3256 trials (~24% of swaps noticed) show that swaps helping users have significantly fewer odds of being noticed (and with higher confidence) than the ones penalizing users. This demonstrates how the context and the intention for motor action are important factors for the SoA and for embodiment, opening new perspectives on how to design and study interactions in immersive VR.
Dependence on a variable residue limits the breadth of an HIV MPER neutralizing antibody, despite convergent evolution with broadly neutralizing antibodies

Broadly neutralizing antibodies (bNAbs) that target the membrane-proximal external region (MPER) of HIV gp41 envelope, such as 4E10 and VRC42.01, can neutralize >95% of viruses. These two MPER-directed monoclonal antibodies share germline antibody genes (IGHV1-69 and IGKV3-20) and form a bNAb epitope class. Furthermore, convergent evolution within these two lineages towards a 111.2GW111. 3 motif in the CDRH3 is known to enhance neutralization potency. We have previously isolated an MPER neutralizing antibody, CAP206-CH12, that uses these same germline heavy and light chain genes but lacks breadth (neutralizing only 6% of heterologous viruses). Longitudinal sequencing of the CAP206-CH12 lineage over three years revealed similar convergent evolution towards 111.2GW111. 3 among some lineage members. Mutagenesis of CAP206-CH12 from 111.2GL111. 3 to 111.2GW111. 3 modestly improved neutralization breadth (by 9%) and potency (3-fold), but did not reach the levels of breadth and potency of VRC42.01 and 4E10. To explore the lack of potency/breadth, viral mutagenesis was performed to map the CAP206-CH12 epitope. This indicated that CAP206-CH12 is dependent on D674, a highly variable residue at the solvent-exposed elbow of MPER. In contrast, VRC42.01 and 4E10 were dependent on highly conserved residues (W672, F673, T676, and W680) facing the hydrophobic patch of the MPER. Therefore, while CAP206-CH12, VRC42.01, and 4E10 share germline genes and show some evidence of convergent evolution, their dependence on different amino acids, which impacts orientation of binding to the MPER, result in differences in breadth and potency. These data have implications for the design of HIV vaccines directed at the MPER epitope. Author Summary Germline-targeting immunogens are a promising HIV vaccine design strategy. This approach is reliant on the identification of broadly neutralizing antibody (bNAb) classes, which use the same germline antibody genes to target the same viral epitopes. Here, we compare three HIV Envelope MPER-directed antibodies (4E10, VRC42.01 and CAP206-CH12) that despite having shared antibody genes, show distinct neutralization profiles. We show that CAP206-CH12 targets a single highly variable residue in the MPER, which results in low neutralization breadth. In contrast, the 4E10 and VRC42.01 mAbs are dependent on highly conserved residues in the MPER, resulting in exceptional neutralization breadth. Our data suggest that while shared germline genes within bNAb epitope classes are required, in some cases these are not sufficient to produce neutralization breadth, and MPER immunogens will need to trigger responses to conserved sites.
The cGAS-STING Pathway Affects Vertebral Bone but Does Not Promote Intervertebral Disc Cell Senescence or Degeneration

The DNA-sensing cGAS-STING pathway promotes the senescence-associated secretory phenotype (SASP) and mediates type-I interferon inflammatory responses to foreign viral and bacterial DNA as well as self-DNA. Studies of the intervertebral disc in humans and mice demonstrate associations between aging, increased cell senescence, and disc degeneration. Herein we assessed the role of STING in SASP promotion in STING gain- (N153S) and loss-of-function mouse models. N153S mice evidenced elevated circulating levels of proinflammatory markers including IL-1β, IL-6, and TNF-α and exhibited a mild trabecular and cortical bone phenotype in caudal vertebrae. Interestingly, despite systemic inflammation, the structural integrity of the disc and knee articular joint remained intact, and cells did not show a loss of their phenotype or elevated SASP. Transcriptomic analysis of N153S tissues demonstrated an upregulated immune response by disc cells, which did not closely resemble inflammatory changes in human tissues. Interestingly, STING-/- mice also showed a mild vertebral bone phenotype, but the absence of STING did not improve the age-associated disc phenotype or reduce the abundance of SASP markers. Overall, the analyses of N153S and STING-/- mice that the cGAS-STING pathway is not a major contributor to SASP induction and consequent disc aging and degeneration but may play a minor role in the maintenance of trabecular bone in the vertebrae. This work contributes to a growing body of work demonstrating that systemic inflammation is not a key driver of disc degeneration.
In vivo low-intensity magnetic pulses durably alter neocortical neuron excitability and spontaneous activity

Magnetic brain stimulation is a promising treatment for neurological and psychiatric disorders. However, a better understanding of its effects at the individual neuron level is essential to improve its clinical application. We combined focal low-intensity repetitive transcranial magnetic stimulation (LI-rTMS) to the rat somatosensory cortex with intracellular recordings of subjacent pyramidal neurons in vivo. Continuous 10 Hz LI-rTMS reliably evoked firing at ∼4-5 Hz during the stimulation period and induced durable attenuation of synaptic activity and spontaneous firing in cortical neurons, through membrane hyperpolarization and a reduced intrinsic excitability. However, inducing firing in individual neurons by repeated intracellular current injection did not reproduce LI-rTMS effects on neuronal properties. These data provide novel understanding of mechanisms underlying magnetic brain stimulation showing that, in addition to inducing biochemical plasticity, even weak magnetic fields can activate neurons and enduringly modulate their excitability.
The use of pigs vocalisation structure to assess the quality of human-pig relationship

Studying human-animal interactions in domestic species and how they affect the establishment of a positive Human-Animal Relationship (HAR) may help us improve animal welfare and better understand the evolution of interspecific interactions associated with the domestication process. Understanding and describing the quality of an HAR requires information on several aspects of the animal biology and emotional states (social, spatial and postural behaviours, physiological and cognitive states). Growing evidence shows that acoustic features of animal vocalisations may be indicators of emotional states. Here, we tested the hypothesis that vocal structure may indicate the quality of HAR. At weaning, 30 piglets were positively handled by an experimenter who talked to and physically interacted with them three times a day, while 30 other piglets only received the contact necessary for proper husbandry. After two weeks, we recorded the behaviours and vocalisations produced in the presence of the static experimenter for 5 min. We repeated this test two weeks later, after a conditioning period during which human presence with additional positive contacts was used as a reward for all piglets. We hypothesized this conditioning period would lead to a positive human-piglet relationship for all piglets. As expected, piglets that were positively handled at weaning expressed a higher attraction toward the experimenter, and, after the conditioning, piglets that were not positively handled at weaning expressed a similar level of attraction than the positively handled ones. Piglets positively handled at weaning produced shorter grunts than the other ones, regardless of the context of recording, which may indicate a more positive affect. During reunions with the static experimenter, a more positive HAR was associated with a decrease in vocal reactivity to human proximity. However, during reunions with the experimenter providing additional positive contacts and over the conditioning, proximity to the human systematically triggered shorter and higher pitched grunts, indicator of positive a emotional state. Results first show that changes in vocal structure are consistent with indicators of positive states in the presence of a human. Second, these changes are stronger when the human positively interact with the piglets, supposedly emphasizing a higher positive arousal state during these interactions. We show that vocalisation structure may be a promising indicator of the quality of human-pig relationship.
Online learning RBF neural network-based adaptive compensative control scheme for governor system

Control of the governor system has a great impact on the transient stability of power systems.Aiming at improving the control performance of the governor system,an online learning RBF neural network-based adaptive compensative control scheme is proposed in the paper.Firstly,the reversibility of the controlled governor system is analyzed based on the inverse system method,the error between the α-th derivative of the system output and the pseudo-control is deduced,and an online learning RBF neural network is designed to compensate for the error.Then,an online learning algorithm for the RBF neural network is designed based on the Lyapunov principles,and the uniform ultimate boundness of the tracking error of the closed loop system and the weight estimation errors of the RBF neural network are strictly proved.The proposed control scheme does not require the accurately mathematical model of the controlled governor system but only a litter prior knowledge.Moreover,the RBF neural network for adaptive compensative control does not need offline learning phase.Finally,some simulations are conducted for a typical single-machine-infinite-bus governor system and simulation results show that the proposed control scheme can greatly improve the transient control performance of the power system than the conventional nonlinear optimal control scheme.
Progression of AFP SCORE is a Preoperative Predictive Factor of Microvascular Invasion in Selected Patients Meeting Liver Transplantation Criteria for Hepatocellular Carcinoma

Graphical Abstract Microvascular invasion (MVI) is one of the main prognostic factors of hepatocellular carcinoma (HCC) after liver transplantation (LT), but its occurrence is unpredictable before surgery. The alpha fetoprotein (AFP) model (composite score including size, number, AFP), currently used in France, defines the selection criteria for LT. This study’s aim was to evaluate the preoperative predictive value of AFP SCORE progression on MVI and overall survival during the waiting period for LT. Data regarding LT recipients for HCC from 2007 to 2015 were retrospectively collected from a single institutional database. Among 159 collected cases, 34 patients progressed according to AFP SCORE from diagnosis until LT. MVI was shown to be an independent histopathological prognostic factor according to Cox regression and competing risk analysis in our cohort. AFP SCORE progression was the only preoperative predictive factor of MVI (OR = 10.79 [2.35–49.4]; p 0.002). The 5-year overall survival in the progression and no progression groups was 63.9% vs. 86.3%, respectively (p = 0.001). Cumulative incidence of HCC recurrence was significantly different between the progression and no progression groups (Sub-HR = 4.89 [CI 2–11.98]). In selected patients, the progression of AFP SCORE during the waiting period can be a useful preoperative tool to predict MVI.
Whole Genome Sequencing and RNA-seq-Driven Discovery of New Targets That Affect Carotenoid Synthesis in Phaffia rhodozyma

Carotenoids are unsaturated compounds with terpene groups. Among them, astaxanthin has strong antioxidant properties. It is widely used in aquaculture, food, medicine, and cosmetics with a broad market prospect. Phaffia rhodozyma is an important microorganism that synthesizes astaxanthin, but its wild strains have low pigment content, long growth cycle, and low fermentation temperature. Therefore, it is important to research the genetic improvement of the physiological and biochemical properties of P. rhodozyma. In this study, the atmospheric and room temperature plasma mutagenesis technology was adopted, through the functional evolution of the carotenoid production performance; then, through the comparative analysis of the genomics and transcriptomics of the wild strain and evolved strain, the key factor GST1 gene that affects carotenoid synthesis was discovered.
Bio-Inspired Hierarchical Micro/Nanostructured Surfaces for Superhydrophobic and Anti-Ice Applications

We report a scalable and cost-effective fabrication approach for constructing bio-inspired micro/nanostructured surfaces. It involves silicon microstructure etching using a deep reactive ion etch (DRIE) method, nanowires deposition via glancing angle deposition (GLAD) process, and fluorocarbon thin film deposition. Compared with the smooth, microstructured, and nanostructured surfaces, the hierarchical micro/nanostructured surfaces obtained via this method showed the highest water contact angle of ∼161° and a low sliding angle of <10°. It also offered long ice delay times of 2313 s and 1658 s at −5°C and −10°C respectively, more than 10 times longer than smooth surfaces indicating excellent anti-icing properties and offering promising applications in low-temperature environments. These analyses further proved that the surface structures have a significant influence on surface wettability and anti-icing behavior. Hence, the GLAD process which is versatile and cost-effective offers the freedom of constructing nanostructures on top of microstructures to achieve the required objective in the fabrication of micro/nanostructured surfaces when compared to other fabrication techniques.