Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Analysis of Non-coding RNA Profiles of Exosome-Like Vesicles From the Protoscoleces and Hydatid Cyst Fluid of Echinococcus granulosus

Cystic echinococcosis is a worldwide chronic zoonotic disease that threatens human health and animal husbandry. Exosome-like vesicles (ELVs) have emerged recently as mediators in the parasite–parasite intercommunication and parasite–host interactions. Exosome-like vesicles from parasites can transfer non-coding RNAs (ncRNAs) into host cells to regulate their gene expression; however, the ncRNAs profiles of the ELVs from Echinococcus granulosus remain unknown. Here, we isolated protoscolece (PSC)–ELVs and hydatid fluid (HF)–ELVs from the culture medium for E. granulosus PSCs in vitro and the HF of fertile sheep cysts, respectively. The microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) profiles of the two types of ELVs were analyzed using high-throughput sequencing, and their functions were predicted using Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. In PSC–ELVs and HF–ELVs, 118 and 58 miRNAs were identified, respectively, among which 53 miRNAs were present in both ELVs, whereas 65 and 5 miRNAs were unique to PSC–ELVs and HF–ELVs, respectively; 2,361 and 1,254 lncRNAs were identified in PSC–ELVs and HF–ELVs, respectively, among which 1,004 lncRNAs were present in both ELVs, whereas 1,357 and 250 lncRNAs were unique to PSC–ELVs and HF–ELVs, respectively. Intriguingly, the spilled PSCs from cysts excrete ELVs with higher numbers of and higher expression levels of miRNAs and circRNAs than HF–ELVs. The miRNA sequencing data were validated by quantitative reverse transcription–polymerase chain reaction. Furthermore, the target lncRNAs and mRNAs regulated by the 20 most abundant miRNAs were screened, and a ceRNA regulatory network containing 5 miRNAs, 41 lncRNAs, and 23 mRNAs was constructed, which provided new ideas and the molecular basis for further clarification of the function and mechanism of E. granulosus ELVs ncRNAs in the parasite–host interactions. Egr-miR-125-5p and egr-miR-10a-5p, sharing identical seed sites with host miRNAs, were predicted to mediate inflammatory response, collagen catabolic process, and mitogen-activated protein kinase cascade during parasite infections. In conclusion, for the first time, we identified the ncRNAs profiles in PSC–ELVs and HF–ELVs that might be involved in host immunity and pathogenesis, and enriched the ncRNAs data of E. granulosus. These results provided valuable resources for further analysis of the regulatory potential of ncRNAs, especially miRNAs, in both types of ELVs at the parasite–host interface.
Countering cross-technology jamming attack

Internet-of-things (IoT) devices are sharing the radio frequency band (e.g., 2.4 GHz ISM band). The exponentially increasing number of IoT devices introduces potential security issues at the gateway in IoT networks. In this paper, we introduce a set of new attacks through concealed jamming - an adversary pretends to be (or compromises) a legitimate WiFi device, then sends out WiFi packets to prevent ZigBee devices' communication or collide with ZigBee's packets. By doing this, concealed jamming has the potential to severely delay the reception of ZigBee packets that may contain important information (e.g., critical health data from wearables, fire alarms, and intrusion alarms). To defend against these attacks, we designed a novel ZigBee data extraction technique that can recover ZigBee data from the ZigBee packets that were collided with WiFi packets. We extensively evaluated our design in different real-world settings. The results show that ZigBee devices (protected by our proposed methods) achieve similar performance as those that are not under the concealed jamming attack. Moreover, compared with unprotected devices, their throughput is more than 15 times higher than the unprotected one that is under concealed jamming attacks.
Phase transition behaviour in yeast and bacterial populations under stress

Non-equilibrium phase transitions from survival to extinction have recently been observed in computational models of evolutionary dynamics. Dynamical signatures predictive of population collapse have been observed in yeast populations under stress. We experimentally investigate the population response of the budding yeast Saccharomyces cerevisiae to biological stressors (temperature and salt concentration) in order to investigate the system's behaviour in the vicinity of population collapse. While both conditions lead to population decline, the dynamical characteristics of the population response differ significantly depending on the stressor. Under temperature stress, the population undergoes a sharp change with significant fluctuations within a critical temperature range, indicative of a continuous absorbing phase transition. In the case of salt stress, the response is more gradual. A similar range of response is observed with the application of various antibiotics to Escherichia coli, with a variety of patterns of decreased growth in response to antibiotic stress both within and across antibiotic classes and mechanisms of action. These findings have implications for the identification of critical tipping points for populations under environmental stress.
Cancer Cell Metabolism Bolsters Immunotherapy Resistance by Promoting an Immunosuppressive Tumor Microenvironment

Immune checkpoint inhibitors (ICIs) targeting immune checkpoint proteins, such as CTLA-4 and PD-1/PD-L1, have demonstrated remarkable and durable clinical responses in various cancer types. However, a considerable number of patients receiving ICIs eventually experience a relapse due to diverse resistance mechanisms. As a result, there have been increasing research efforts to elucidate the molecular mechanisms behind resistance to ICIs and improve patient outcomes. There is growing evidence that the dysregulated metabolic activity of tumor cells generates an immunosuppressive tumor microenvironment (TME) that orchestrates an impaired anti-tumor immune response. Notably, the immunosuppressive TME is characterized by nutrient shortage, hypoxia, an acidic extracellular milieu, and abundant immunosuppressive molecules. A detailed understanding of the TME remains a major challenge in mounting a more effective anti-tumor immune response. Herein, we discuss how tumor cells reprogram metabolism to modulate a pro-tumor TME, driving disease progression and immune evasion; in particular, we highlight potential approaches to target metabolic vulnerabilities in the context of anti-tumor immunotherapy.
Communications collectives et ordonnancement en régime permanent sur plates-formes hétérogènes. (Collective communications and steady-state-scheduling on heterogeneous platforms)

Les travaux presentes dans cette these concernent l'ordonnancement pour les plates-formes heterogenes a grande echelle. Nous nous interessons principalement aux operations de communications collectives comme la diffusion de donnees, la distribution de donnees ou la reduction. Nous etudions ces problemes dans le cadre de leur regime permanent, en optimisant le debit d'une serie d'operations de communications, en vue d'obtenir un ordonnancement asymptotiquement optimal du point de vue du temps d'execution total. Apres avoir presente un cadre general d'etude qui nous permet de connaitre la complexite du probleme pour chaque primitive, nous developpons, pour le modele de communication un-port bidirectionnel, une methode de resolution pratique fondee sur la resolution d'un programme lineaire en rationnels. Cette etude du regime permanent est illustree par des experimentations sur Grid5000 et se prolonge vers l'ordonnancement d'applications multiples sur des grilles de calcul.
Redox priming promotes Aurora A activation during mitosis

CoAlation of the kinase Aurora A induces an open dimer conformation that facilitates its activation. Structurally primed by CoA The mitotic kinase Aurora A promotes tumor growth. Redox modification of an evolutionarily conserved cysteine residue in the activation loop of Aurora A may be exploitable therapeutically. Lim et al. identified Cys-binding redox compounds and elucidated how such adducts may conformationally affect Aurora A activation. One such compound, coenzyme A, resulted in two types of dimers—one that was Cys290-coAlated in which the active site was in an open conformation that showed how covalent modification of the activation loop can promote dimerization and the other one that lacked CoAlation but showed how dimerization can lead to a catalytically active conformation that promotes autophosphorylation. The findings suggest that CoAlation may promote Aurora A activation through an intermediate conformation. Hence, compounds that block CoAlation may suppress Aurora A activation in tumors. Cell cycle–dependent redox changes can mediate transient covalent modifications of cysteine thiols to modulate the activities of regulatory kinases and phosphatases. Our previously reported finding that protein cysteine oxidation is increased during mitosis relative to other cell cycle phases suggests that redox modifications could play prominent roles in regulating mitotic processes. The Aurora family of kinases and their downstream targets are key components of the cellular machinery that ensures the proper execution of mitosis and the accurate segregation of chromosomes to daughter cells. In this study, x-ray crystal structures of the Aurora A kinase domain delineate redox-sensitive cysteine residues that, upon covalent modification, can allosterically regulate kinase activity and oligomerization state. We showed in both Xenopus laevis egg extracts and mammalian cells that a conserved cysteine residue within the Aurora A activation loop is crucial for Aurora A activation by autophosphorylation. We further showed that covalent disulfide adducts of this residue promote autophosphorylation of the Aurora A kinase domain. These findings reveal a potential mechanistic link between Aurora A activation and changes in the intracellular redox state during mitosis and provide insights into how novel small-molecule inhibitors may be developed to target specific subpopulations of Aurora A.
Same Standards, Different Decisions: A Study of QUIC and HTTP/3 Implementation Diversity

The QUIC and HTTP/3 protocols are quickly maturing together with their implementations, though many of their low-level behaviours are not yet well-understood. To help improve this, we empirically compare 15 IETF QUIC+HTTP/3 implementations for advanced features like Flow and Congestion Control, 0-RTT, Multiplexing, and Packetization. We find a large heterogeneity between stacks, discuss uncovered bugs and conclude that most implementations are not fully optimized or validated yet. We argue that future work must prioritize rigorous root-cause analysis of observed behaviours, and show this is possible by employing our qlog and qvis tools.
Bearings degradation monitoring indicators based on discarded projected space information and piecewise linear representation

Condition-based maintenance of rotating mechanics requests efficient bearings degradation monitoring. The accuracy of bearings degradation measure depends largely on degradation indicators. To extract efficient indicators, in this paper we propose a method based on the discarded projected space information and piecewise linear representation (PLR) to build three bearings degradation monitoring indicators which are named SDHT2, VSDHT2 and NVSDHT2. The discarded projected space information is measured by the segmented discarded Hotelling T square we propose in this paper. For illustration, the IEEE PHM 2012 benchmark dataset is used in this paper. The results show that the three new indicators are all sensitive and monotonic during the bearings whole lifecycle. They describe the whole degradation process history and carry the real-time information of bearings degradation. And NVSDHT2 is the generalised version of VSDHT2, which is promising to monitor bearings degradation.
Joint Recursive Beam and Channel Tracking for 2-dimensional Phased Antenna Arrays

Millimeter wave (mmWave) is an attractive candidate for high-speed wireless communication in the future. However, due to the propagation characteristics of mmWave, beam alignment becomes a key challenge in mobile environments. In this paper, we develop a joint 3D recursive beam and channel tracking algorithm that can achieve low tracking error. We discuss the special challenges in optimazing the beamforming matrix of 3D tracking. A general asymptotically optimal beamforming matrix is given to obtain the minimum Cramer-Rao lower bound (CRLB) of beam and channel tracking. The beamforming matrix can be used in different channel environments when antenna number is large enough. In static scenarios, three theorems are developed to prove that the algorithm converges to the minimum CRLB. Simulation results show that our algorithm outperforms several existing algorithms.
Sticking With It: ER-PM Membrane Contact Sites as a Coordinating Nexus for Regulating Lipids and Proteins at the Cell Cortex

Membrane contact sites between the cortical endoplasmic reticulum (ER) and the plasma membrane (PM) provide a direct conduit for small molecule transfer and signaling between the two largest membranes of the cell. Contact is established through ER integral membrane proteins that physically tether the two membranes together, though the general mechanism is remarkably non-specific given the diversity of different tethering proteins. Primary tethers including VAMP-associated proteins (VAPs), Anoctamin/TMEM16/Ist2p homologs, and extended synaptotagmins (E-Syts), are largely conserved in most eukaryotes and are both necessary and sufficient for establishing ER-PM association. In addition, other species-specific ER-PM tether proteins impart unique functional attributes to both membranes at the cell cortex. This review distils recent functional and structural findings about conserved and species-specific tethers that form ER-PM contact sites, with an emphasis on their roles in the coordinate regulation of lipid metabolism, cellular structure, and responses to membrane stress.
Extracting and Analyzing Deep Learning Features for Discriminating Historical Art: Deep Learning Features and Art

Art historians are interested in possible methods and visual criteria for determining the style and authorship of artworks. One approach, developed by Giovanni Morelli in the late nineteenth century, focused on abstracting, extracting and comparing details of recognizable human forms, although he never prescribed what exactly to look for. In this work, we asked what could a contemporary method like convolution networks contribute or reveal about such a humanistic method that is not fully determined, but that is also so clearly aligned with computation? Convolution networks have become very successful in object recognition because they learn general features to distinguish and classify large sets of objects. Thus, we wanted to explore what features are present in these networks that have some discriminatory power for distinguishing paintings. We input the digitized art into a large-scale convolutional network that was pre-trained for object recognition from naturalistic images. Because we do not have labels, we extracted activations from the network and ran K-means clustering. We contrasted and evaluated discriminatory power between shallow and deeper layers. We also compared predetermined features from standard computer vision techniques of edge detection. It turns out that the deep network individual feature maps are highly generic and do not easily map onto obvious authorship interpretations, but in the aggregate can have strong discriminating power that are intuitive. Although this does not directly test issues of attribution, the application can inform humanistic perspectives regarding what counts as features that make up visual elements of paintings.
Disentangling inflammatory from fibrotic disease activity by fibroblast activation protein imaging

Objectives To date, there is no valuable tool to assess fibrotic disease activity in humans in vivo in a non-invasive way. This study aims to uncouple inflammatory from fibrotic disease activity in fibroinflammatory diseases such as IgG4-related disease. Methods In this cross-sectional clinical study, 27 patients with inflammatory, fibrotic and overlapping manifestations of IgG4-related disease underwent positron emission tomography (PET) scanning with tracers specific for fibroblast activation protein (FAP; 68Ga-FAP inhibitor (FAPI)-04), 18F-fluorodeoxyglucose (FDG), MRI and histopathological assessment. In a longitudinal approach, 18F-FDG and 68Ga-FAPI-04 PET/CT data were evaluated before and after immunosuppressive treatment and correlated to clinical and MRI data. Results Using combination of 68Ga-FAPI-04 and 18F-FDG-PET, we demonstrate that non-invasive functional tracking of IgG4-related disease evolution from inflammatory towards a fibrotic outcome becomes feasible. 18F-FDG-PET positive lesions showed dense lymphoplasmacytic infiltration of IgG4 + cells in histology, while 68Ga-FAPI-04 PET positive lesions showed abundant activated fibroblasts expressing FAP according to results from RNA-sequencing of activated fibroblasts. The responsiveness of fibrotic lesions to anti-inflammatory treatment was far less pronounced than that of inflammatory lesions. Conclusion FAP-specific PET/CT permits the discrimination between inflammatory and fibrotic activity in IgG4-related disease. This finding may profoundly change the management of certain forms of immune-mediated disease, such as IgG4-related disease, as subtypes dominated by fibrosis may require different approaches to control disease progression, for example, specific antifibrotic agents rather than broad spectrum anti-inflammatory treatments such as glucocorticoids.
Study on Quality Response to Environmental Factors and Geographical Traceability of Wild Gentiana rigescens Franch

Gentiana rigescens Franch. ex Hemsl. is an important medicinal plant in China and the over exploitation of wild resources has affected its quality and clinical efficacy. The accumulation of plant secondary metabolites is not only determined by their genetic characteristics but also influenced by environmental factors. At present, many studies on evaluating the environmental conditions of its planting area are still in the qualitative stage. Therefore, it is necessary to establish a systematic evaluation method to deeply analyze the impact of environmental factors on the quality of medicinal materials and quickly verify the geographical origin. In this study, the contents of five iridoids (loganic acid, swertiamarin, sweroside, gentiopicroside and 6'-O-β-D-glucopyranosylgentiopicroside) of G. rigescens from 45 different origins (including 441 individuals) of Yunnan Province in China were analyzed by high performance liquid chromatography. Analytical procedures of one-way analysis of variance, correlation analysis, principal components analysis, and hierarchical cluster analysis were employed to interpret the correlation of iridoid content and environmental factors. Fourier transform infrared spectroscopy (FT-IR) combined with two multivariate analysis methods (partial least squares discriminant analysis; support vector machines, SVM) was used to discriminate four major producing areas (158 individuals). The combination of SVM with grid search algorithm achieved an accuracy of 100% in the test set. One-way analysis of variance showed that the contents of five iridoids in root tissues of G. rigescens varied significantly among different origins, which was also verified by the chemometrics analysis results of hierarchical cluster analysis. The results of correlation analysis indicated that the high value of altitude and precipitation were unfavorable for the accumulation of these five iridoids. A correlation between increase of temperature and iridoid accumulation was observed. This study provided a certain theoretical basis for the resource protection and development of G. rigescens based on the correlation analysis between the ecological environment factors and quality.
Analyzing the Adoption of QUIC From a Mobile Development Perspective

First introduced in 2013, QUIC protocol has been in constant development and it has gained great importance over time, currently being standardized by the Internet Engineering Task Force (IETF). Previous experiments have shown that the performance of QUIC can be of particular interest for lossy wireless networks. Thus, it becomes relevant to measure and profile QUIC traffic from mobile devices in the wild. This paper analyzes the adoption of QUIC from a mobile development perspective, by using crowdsourced data from real Android users during the normal use of their mobile devices. The results obtained show a significant increase in the number of Android apps using QUIC and evidence newer efforts of companies to adopt this protocol. To the best of the authors' knowledge, this is the first work focused on analyzing and profiling QUIC traffic from crowdsourced network measurements taken by mobile end-user devices.
Testing QUIC with packetdrill

A secure transport protocol like QUIC has extensive state machines and algorithms to ensure secure, reliable and in-order delivery of multiple byte streams. Testing these mechanisms is at the heart of a successful deployment of QUIC. While interop-testing, fuzzing and performance tests allow to explore a large part of these algorithms, concrete issues are hard to reproduce reliably with those methods. packetdrill has emerged as an effective tool for exercising the TCP stack by generating events like incoming packets or system calls at precise timings. In this paper, we present how we extended packetdrill for testing QUIC. This involves a special grammar to express the QUIC packet format and integration of TLS 1.3 into packetdrill. We integrated our own QUIC library and show that it is easy to include any QUIC library into packetdrill, and even reuse test cases across different libraries. This illustrates that using packetdrill is a useful approach for testing QUIC implementations.