Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous protein and RNA analysis in single extracellular vesicles, including viruses: SPIRFISH

Interest in using nanoparticles for delivery of therapeutic RNA has been steadily growing, provoking a need to precisely understand their structure and contents. Single-particle and single-molecule analysis techniques provide snapshots of single biological nanoparticles, including viruses, liposomes, and extracellular vesicles (EVs). While existing methods primarily focus on protein detection, RNA delivery is becoming increasingly prevalent. A method to simultaneously detect protein and internal RNA in the same particle would reveal variability in size, structure, and RNA packaging efficiency, enabling optimization of nanoparticle delivery. Here, we introduce SPIRFISH, a high-throughput method for single-particle protein and RNA analysis, combining single particle interferometric reflectance imaging sensor (SP-IRIS) with single-molecule fluorescence in-situ hybridization (smFISH). Using SPIRFISH, we detect HIV-1 envelope protein and genomic RNA within single infectious virions, allowing resolution against EV background and noninfectious virions. We further show that SPIRFISH can be used to detect specific RNA within EVs. SPIRFISH should enable single particle analysis of a broad class of RNA-containing nanoparticles. Teaser: A new single particle analysis technique simultaneously detects specific RNA and protein in biological nanoparticles.
Generic rules of lumen nucleation and fusion in epithelial organoids

Many internal organs in the body harbor a fluid-filled lumen. The mechanisms of lumens initiation and fusion have been reported as dependent on organ-type during organogenesis. In contrast, the physics of lumen suggests that force balance between luminal pressure and cell mechanics could lead to conserved rules which may unify their self-organisation. However, this hypothesis lacks experimental evidence. Here we show that lumens share similar dynamics for three different systems (MDCK cysts, pancreatic spheres, and epiblast cysts) by using quantitative cell biology, microfabrication and theory. We report that initial cell number determines the maximum number of lumens but does not impact the steady state which is a final single lumen. In addition, lumens numbers exhibit two phases over time, a nucleation phase followed by a fusion phase. In the nucleation phase, lumens form between two cells in pancreatic and MDCK cysts whereas they form at the rosette stage between ten cells in epiblasts. In the second phase, lumens fuse by an increase in lumen volume for pancreatic spheres and MDCK cysts, whereas cell convergent directional motion leads to lumens fusion in epiblasts. We support these results by reproducing numerically lumens dynamics using a phase field model with simple rules for cell proliferation, cell adhesion and lumen growth. We finally use MDCK cysts to manipulate cell adhesion and lumen volume and we successfully reproduce the fusion dynamics of pancreatic spheres and epiblasts. Our results reveal self-organisation rules of lumens across systems with relevance for morphogenesis during development and for the design of synthetic organs.
The Role of Soil and Site Conditions in the Vulnerability and Risk Assessment of Lifelines and Infrastructures. The Case of Thessaloniki (Greece).

Soil conditions and site effects play an important role in the vulnerability assessment of lifelines and infrastructures under strong seismic excitation. Due to the spatial extent of these networks, they are subjected to non-uniform and incoherent ground motion as a result of the variability of soil and geological conditions; consequently their vulnerability assessment depends entirely on the variability of soil conditions and ground motion, known as site effects, for a given seismic scenario. Fragility functions for the exposed elements at risk, composing the different lifelines and infrastructure systems, play an equally important role. The paper presents some selected results of a recent application of a comprehensive methodology assessing the vulnerability of several lifeline systems in Thessaloniki in Greece. The work is part of a large research program, aiming to the development of a general methodology for the assessment of the seismic risk for the building stock, lifeline systems and infrastructures at urban scale. Key factors of the methodology are the inventory, the typology, the specific characteristics and the importance (global value) of the elements at risk, the development of seismic scenarios (seismic hazard) and the geotechnical characterization, with the detailed site response analysis. The methodology and the role of soil and site conditions are highlighted with representative examples of the application in Thessaloniki.
Real-time verification of network properties using Atomic Predicates

Network management will benefit from automated tools based upon formal methods. Several such tools have been published in the literature. We present a new formal method for a new tool, Atomic Predicates (AP) Verifier, which is much more time and space efficient than existing tools. Given a set of predicates representing packet filters, AP Verifier computes a set of atomic predicates, which is minimum and unique. The use of atomic predicates dramatically speeds up computation of network reachability. We evaluated the performance of AP Verifier using forwarding tables and ACLs from three large real networks. The atomic predicate sets of these networks were computed very quickly and their sizes are surprisingly small. Real networks are subject to dynamic state changes over time as a result of rule insertion and deletion by protocols and operators, failure and recovery of links and boxes, etc. In a software-defined network, the network state can be observed in real time and thus may be controlled in real time. AP Verifier includes algorithms to process such events and check compliance with network policies and properties in real time. We compare time and space costs of AP Verifier with NetPlumber using datasets from the real networks.
SELF _ MOTION COLLABORATION CONDUCTGoalManner Partner _ 1 Partner _ 2 Manner Agent Self _ mover

We present a novel technique for jointly predicting semantic arguments for lexical predicates. The task is to find the best matching between semantic roles and sentential spans, subject to structural constraints that come from expert linguistic knowledge (e.g., in the FrameNet lexicon). We formulate this task as an integer linear program (ILP); instead of using an off-the-shelf tool to solve the ILP, we employ a dual decomposition algorithm, which we adapt for exact decoding via a branch-and-bound technique. Compared to a baseline that makes local predictions, we achieve better argument identification scores and avoid all structural violations. Runtime is nine times faster than a proprietary ILP solver.
A polynomial-time algorithm for deciding the Hilbert Nullstellensatz in P Z 2 n . A proof of P = NP hypothesis

In this paper we prove the following: There is a constructive algorithm for deciding the Hilbert Nullstellensatz over Z 2 , where Z 2 is the space of all complex numbers with integer real and imaginary parts. The number s ( n, m σ ) of basic steps of the algorithm, where n is the number of variables and m σ is the total length of input polynomials, satisﬁes the inequality where c is an absolute constant and the variables z n , z n − 1 and z n − 2 are chosen so, that the major ( n − 1) -sub-monomial is a ( z 1 , z 2 , . . . , z n − 1 ) -monomial with highest exponent of z n − 1 in it and the major ( n − 2) -sub-monomial is a ( z 1 , z 2 , . . . , z n − 2 ) -monomial with highest exponent of z n − 2 in it. The natural numbers N ( ℓ ) are the serial numbers of the major ( z 1 , z 2 , . . . , z ℓ ) -sub-monomials, ℓ = n − 2 , n − 1 , respectively, in the natural order of monomials. This statement proves the hypothesis P = NP , or more precisely, the class of polynomial-time decision problems P is equivalent to the nondeterministic polynomial time class NP . MSC(2020) : 32A08, 68Q15, 68Q25,
A polynomial-time algorithm for deciding the Hilbert Nullstellensatz in P Z 2 n . A proof of NP hypothesis

The main result of this paper is the resolving of the P versus NP problem by answering the question asked by Cook [3], with Yes . It is done by using the following theorem. Theorem 1 . There is a constructive algorithm for deciding the Hilbert Nullstellensatz over Z 2 , where Z 2 is the space of all complex numbers with integer real and imaginary parts. The number s ( n, m σ ) of basic steps of the algorithm, where n is the number of variables and m σ is the total length of input polynomials, satisﬁes the inequality where c is an absolute constant and the variables z n − 1 and z n − 2 are chosen so, that the major ( n − 1) -sub-monomial is a ( z 1 , z 2 , . . . , z n − 1 ) -monomial such that the highest exponent in it is that of z n − 1 and the major ( n − 2) -sub-monomial is a ( z 1 , z 2 , . . . , z n − 2 ) monomial such that the highest exponent in it is that of z n − 2 . The natural numbers N ( ℓ ) , ℓ = n − 2 , n − 1 , are the numbers of the same monomials in the natural order of monomials.
Improving TCP/IP Performance over Third-Generation Wireless Networks

As third-generation (3G) wireless networks with high data rate get widely deployed, optimizing the transmission control protocol (TCP) performance over these networks would have a broad and significant impact on data application performance. In this paper, we make two main contributions. First, one of the biggest challenges in optimizing the TCP performance over the 3G wireless networks is adapting to the significant delay and rate variations over the wireless channel. We present window regulator algorithms that use the receiver window field in the acknowledgment (ACK) packets to convey the instantaneous wireless channel conditions to the TCP source and an ACK buffer to absorb the channel variations, thereby maximizing long-lived TCP performance. It improves the performance of TCP selective ACK (SACK) by up to 100 percent over a simple drop-tail policy, with small buffer sizes at the congested router. Second, we present a wireless channel and TCP-aware scheduling and buffer sharing algorithm that reduces the latency of short flows while still exploiting user diversity for a wide range of user and traffic mix.
A Simulation Environment for Job Scheduling Distributed Systems

In this paper we present a simulation environment for the study of hierarchical job scheduling on distributed systems. The environment provides a multi-level mechanism to simulate various types of jobs. An execution model of jobs is implemented to simulate the behaviour of jobs to obtain an accurate performance prediction. For parallel jobs, two execution models have been implemented: one in which the tasks of the job frequently synchronise and effectively run in lock step and a second in which the tasks only synchronise at beginning and end. The simulator is based on an object approach and on process oriented simulation. Our model supports an unlimited number of workstations, grouped into clusters with their own local resource manager (RM). Work is distributed over these clusters by a global RM. To validate the model, we use two approaches, analysing the main queueing systems and experimenting with real jobs to obtain the actual performance as a reference.
Pulsed Multi-Layered Image Filtering : A VLSI Implementation

Image convolution similar to the receptive fields found in mammalian visual pathways has long been used in conventional image processing in the form of Gabor masks. However, no VLSI implementation of parallel, multi-layered pulsed processing has been brought forward which would emulate this property. We present a technical realization of such a pulsed image processing scheme. The discussed IC also serves as a general testbed for VLSI-based pulsed information processing, which is of interest especially with regard to the robustness of representing an analog signal in the phase or duration of a pulsed, quasi-digital signal, as well as the possibility of direct digital manipulation of such an analog signal. The network connectivity and processing properties are reconfigurable so as to allow adaptation to various processing tasks. Keywords—Neural image processing, pulse computation application, pulsed Gabor convolution, VLSI pulse routing.
DraculR: A web based application for in silico haemolysis detection in high throughput small RNA sequencing data

Motivation: The search for novel microRNA (miRNA) biomarkers in plasma is hampered by haemolysis, the lysis and subsequent release of red blood cell (RBC) contents, including miRNAs, into surrounding fluid. The biomarker potential of miRNAs comes in part from their multi-compartment origin, and the long-lived nature of miRNA transcripts in plasma, giving researchers a functional window for tissues that are otherwise difficult or disadvantageous to sample. The inclusion of RBC derived miRNA transcripts in downstream analysis introduces a source of error that is difficult to identify post hoc and may lead to spurious results. Where access to a physical specimen is not possible, our tool will provide an in silico approach to haemolysis prediction. Results: We present DraculR, an interactive Shiny/R application that enables a user to upload microRNA expression data from short read sequencing of human plasma as a raw read counts table and interactively calculate a metric that indicates the degree of haemolysis contamination. Availability and implementation: DraculR and its tutorial are freely available from (https://mxhp75.shinyapps.io/shinyVamp/). Code is available from (https://github.com/mxhp75/shinyVamp.git).
VendingMachine v CancelPurchase c Beverages b FreeDrinks f Currency cur Soda s Tea

Test Case Generation for Behavioural Testing of Software Product Lines Xavier Devroey, Gilles Perrouin ⇤ and Pierre-Yves Schobbens PReCISE Research Center, Faculty of Computer Science, University of Namur, Belgium xavier.devroey@unamur.be, gilles.perrouin@unamur.be, pierre-yves.schobbens@unamur.be
Author's Accepted Manuscript High Order Plsa for Indexing Tagged Images High Order Plsa for Indexing Tagged Images

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Abstract This work presents a method for the efficient indexing of tagged images. Tagged images are a common resource of social networks and occupy a large portion of the social media stream. Their basic characteristic is the coexistence of two heterogeneous information modalities i.e. visual and tag, which refer to the same abstract meaning. This multi-modal nature of tagged images makes their efficient indexing a challenging task that apart from dealing with the hetero-geneity of modalities, it needs to also exploit their complementary information capacity. Towards this objective, we propose the extension of probabilistic Latent Semantic Analysis to higher order, so as to become applicable for more than two observable variables. Then, by treating images, visual features and tags as the three observable variables of an aspect model, we learn a space of latent topics that incorporates the semantics of both visual and tag information. Our novelty is on using the cross-modal dependencies learned from a corpus of images to approximate the joint distribution of the observable variables. By penalizing the coexistence of visual content and tags that are known from experience to exhibit low dependency, we manage to filter out the effect of noisy content in the resulting latent space.
Size Scaling of Tensile Failure Stress in a Soda-Lime-Silicate Float Glass

The (tensile) strength-size scaling of a float soda-lime silicate glass was studied using biaxial flexure and Hertzian ring crack initiation testing. The examined Weibull effective areas spanned ~ 0.4 to 48,000 mm2. Both the air- and tin-sides were tested. The air side was stronger than the tin side as others have observed; however, the differences in their characteristic strengths decreased with decreasing effective area, and their strengths converged for effective areas smaller than ~ 100 mm2. The failure stress at the smallest effective area examined for the tin-side was ~ 500% greater than that at the largest effective area while that difference was ~ 250% for the air- side. A Weibull modulus change at ~ 100 mm2 suggests different strength-limiting flaw types were dominant below and above that effective area. These results reinforce the importance to interpret and use tensile strength of glass in context to how much of its area is being tensile stressed.
Automatic Web Page Categorization by Link and Context Analysis

Assistance in retrieving documents on the World Wide Web is provided either by search engines, through keyword-based queries, or by catalogues, which organize documents into hierarchical collections. Maintaining catalogues manually is becoming increasingly difficult, due to the sheer amount of material on the Web; it is thus becoming necessary to resort to techniques for the automatic classification of documents. Automatic classification i s traditionally performed by extracting the information for representing a document (“indexing”) from the document itself. The paper describes the novel technique of categorization by context, which instead extracts useful information for classifying a document from the context where a URL referring to it appears. We present the results of experimenting with Theseus, a classifier that exploits this technique.
Task 5: Applications of state-of-the-art techniques to current problems in multimedia understanding

—We present an automatic focus area estimation method, working with a single image without a priori information about the image, the camera, or the scene. It produces relative focus maps by localized blind deconvolution and a new residual error-based classification. Evaluation and comparison is performed and applicability is shown through image indexing.
Informationswissenschaft zwischen virtueller Infrastruktur und materiellen Lebenswelten

The dramatic increase in information on the World Wide Web makes it more difficult for web users using web search engines to effectively satisfy their information needs. The users’ lack of knowledge regarding the searched topics creates a complicated problem when formulating an effective query. Query expansion can play an essential role in overcoming such a deficit. However, because they lack sufficient knowledge about the searched topics, users sometimes find it difficult to evaluate the relatedness of the system’s automatically expanded terms. This problem arises mostly in domain-specific areas, e.g. Social Science. In this paper, we expand the queries based on a structured, open knowledge resource on the Web (Wikipedia). We link the entities from a domain-specific corpus (qualitative journals in social science) to Wikipedia entities. With Wikipedia serving as background knowledge, we help users with their selections by providing the most likely related terms. Furthermore, users are provided with contextual information that describes each expanded term in order to give users a clearer idea about the meaning of each expanded term. By utilizing 10 test queries chosen by experts who also evaluated the results, we compared the results of using Wikipedia with the results achieved by using a qualitative journal.
Modular Strategies : B 2 B Technologies and Architectural Knowledge

Business-to-business information technology systems (B2B technologies) are becoming increasingly important in B2B markets. Utilizing the concept of modularity, this paper clarifies the strategic implications of B2B technology and develops a theoretical structure to explain these outcomes. Five firms are studied in detail: Eastman Chemical, Cemex, Li & Fung, Agribuys and Dell. Our findings point to the existence of two generic B2B strategies: ‘modularization’, which allows a firm to rent out its internal capabilities to other firms in its industry, and ‘architectural entrepreneurship’, which alters the supply chain by allowing a central coordinating firm to facilitate arrangements that trust issues and information asymmetries had previously made impossible. Which modular strategy is appropriate is influenced by the role the focal firm plays in the supply chain; we characterize this as their ‘supply chain indispensability’. Theory and evidence suggest that only firms with deep architectural knowledge can take full advantage of these modular strategies.
Lateral Mixing Processes in the Hadean

Samples of ancient Eoarchean volcanism suggest the existence of isotopically distinct mantle domains. 142Nd evidence suggests that these domains formed within the first several hundred million years of Earth's history and were preserved until circa 3.7 Ga—a span of almost 800 Myr. Here we explore evolving mantle convection models under Hadean conditions to constrain mantle mixing dynamics and in particular focus on the generation, or preservation, of upper mantle hemispheric compositional anomalies. We find that initially radially homogenous models fail to produce hemispheric anomalies spontaneously due to mixing processes and that rheological and buoyancy effects, or asymmetric processes such as plate tectonics or meteorite impacts, do not generate long‐lived heterogeneities in upper mantle composition from homogenous initial conditions. In contrast, models initiated with compositional variations can preserve these hemispheric differences of periods >800 Myr despite vigorous internal convection, as a function of the proclivity of these models to exhibit stagnant‐lid behavior, resulting in isolated convection cells with restricted lateral transport.
Long‐Lived Tsunami Edge Waves and Shelf Resonance From the M8.2 Tehuantepec Earthquake

The 8 September 2017 M8.2 Tehuantepec, Mexico, earthquake ruptured an ~150‐km‐long high‐angle normal fault below the subduction zone megathrust. A tsunami was generated by the event with surveyed runup as large as 3 m. Tide gauges in the region show a remarkably long duration of the tsunami with oscillations within the very wide and shallow Tehuantepec shelf lasting as long as 3 days. Here we produce a model of the tsunami and validate it by comparing it to the tsunami survey and to the time and frequency domain features of regional tide gauges. We analyze the model results and show that the long‐lived oscillations are a result of wholesale resonance of the shelf as well as very efficient trapping of edge waves at the shore. These resonant features are the result of the Tehuantepec shelf morphology and illuminate a previously unidentified tsunami hazard for the region.