Miracle-dz/UniFAR-FTUs huggingface dataset:
Oncogenic Transformation of Dendritic Cells and Their Precursors Leads to Rapid Cancer Development in Mice

Dendritic cells (DCs) are powerful APCs that can induce Ag-specific adaptive immune responses and are increasingly recognized as important players in innate immunity to both infection and malignancy. Interestingly, although there are multiple described hematological malignancies, DC cancers are rarely observed in humans. Whether this is linked to the immunogenic potential of DCs, which might render them uniquely susceptible to immune control upon neoplastic transformation, has not been fully investigated. To address the issue, we generated a genetically engineered mouse model in which expression of Cre recombinase driven by the C-type lectin domain family 9, member a (Clec9a) locus causes expression of the Kirsten rat sarcoma viral oncogene homolog (Kras)G12D oncogenic driver and deletion of the tumor suppressor p53 within developing and differentiated DCs. We show that these Clec9aKras-G12D mice rapidly succumb from disease and display massive accumulation of transformed DCs in multiple organs. In bone marrow chimeras, the development of DC cancer could be induced by a small number of transformed cells and was not prevented by the presence of untransformed DCs. Notably, activation of transformed DCs did not happen spontaneously but could be induced upon stimulation. Although Clec9aKras-G12D mice showed altered thymic T cell development, peripheral T cells were largely unaffected during DC cancer development. Interestingly, transformed DCs were rejected upon adoptive transfer into wild-type but not lymphocyte-deficient mice, indicating that immunological control of DC cancer is in principle possible but does not occur during spontaneous generation in Clec9aKras-G12D mice. Our findings suggest that neoplastic transformation of DCs does not by default induce anti-cancer immunity and can develop unhindered by immunological barriers.
Mito-seek Enables Deep Analysis of Mitochondrial Dna, Revealing Ubiquitous, Stable Heteroplasmy Maintained by Intercellular Exchange

Eukaryotic cells carry two genomes, nuclear (nDNA) and mitochondrial (mtDNA), which are ostensibly decoupled in their replication, segregation and inheritance. It is increasingly appreciated that heteroplasmy, the occurrence of multiple mtDNA haplotypes in a cell, plays an important biological role, but its features are not well understood. Until now, accurately determining the diversity of mtDNA has been difficult due to the relatively small amount of mtDNA in each cell (< 1% of the total DNA), the intercellular variability of mtDNA content and copies of mtDNA pseudogenes in nDNA. To understand the nature of heteroplasmy, we developed Mito-seek, a novel technique that purifies and sequences mtDNA. Mito-seek yields high purity (> 98%) mtDNA and its ability to detect rare variants is limited only by sequencing depth, providing unprecedented sensitivity and specificity. Using Mito-seek, we confirmed the ubiquity of heteroplasmy by analyzing mtDNA from a diverse set of cell lines and human samples. By applying Mito-seek to colonies derived from single cells, we showed that heteroplasmy is stably maintained in individual daughter cells over multiple cell divisions. Our simulations indicate that the stability of heteroplasmy can be facilitated by the exchange of mtDNA between cells. We also explicitly demonstrate this exchange by co-culturing cell lines with distinct mtDNA haplotypes. Our results shed new light on the maintenance of heteroplasmy and provide a novel platform to investigate various features of heteroplasmy in normal and diseased tissues.
GyroWand: IMU-based Raycasting for Augmented Reality Head-Mounted Displays

We present GyroWand, a raycasting technique for 3D interactions in self-contained augmented reality (AR) head-mounted displays. Unlike traditional raycasting which requires absolute spatial and rotational tracking of a user's hand or controller to direct the ray, GyroWand relies on the relative rotation values captured by an inertial measurement unit (IMU) on a handheld controller. These values cannot be directly mapped to the ray direction due to the phenomenon of sensor drift and the mismatch between the orientations of the physical controller and the virtual content. To address these challenges GyroWand 1) interprets the relative rotational values using a state machine which includes an anchor, an active, an out-of-sight and a disambiguation state; 2) handles drift by resetting the default rotation when the user moves between the anchor and active states; 3) does not initiate raycasting from the user's hand, but rather from other spatial coordinates (e.g. chin, shoulder, or chest); and 4) provides three new disambiguation mechanisms: Lock&Twist, Lock&Drag, and AutoTwist. In a series of controlled user studies we evaluated the performance and convenience of different GyroWand design parameters. Results show that a ray originating from the user's chin facilitates selection. Results also show that Lock&Twist is faster and more accurate than other disambiguation mechanisms. We conclude with a summary of the lessons learned for the adoption of raycasting in mobile augmented reality head-mounted displays.
Learning to Rank Binary Codes

Binary codes have been widely used in vision problems as a compact feature representation to achieve both space and time advantages. Various methods have been proposed to learn data-dependent hash functions which map a feature vector to a binary code. However, considerable data information is inevitably lost during the binarization step which also causes ambiguity in measuring sample similarity using Hamming distance. Besides, the learned hash functions cannot be changed after training, which makes them incapable of adapting to new data outside the training data set. To address both issues, in this paper we propose a flexible bitwise weight learning framework based on the binary codes obtained by state-of-the-art hashing methods, and incorporate the learned weights into the weighted Hamming distance computation. We then formulate the proposed framework as a ranking problem and leverage the Ranking SVM model to offline tackle the weight learning. The framework is further extended to an online mode which updates the weights at each time new data comes, thereby making it scalable to large and dynamic data sets. Extensive experimental results demonstrate significant performance gains of using binary codes with bitwise weighting in image retrieval tasks. It is appealing that the online weight learning leads to comparable accuracy with its offline counterpart, which thus makes our approach practical for realistic applications.
NON-SYNCHRONOUS TILTING PAD BEARING CHARACTERISTICS

The characteristics of fluid film bearings are speed- dependent. Recently it is discussed more and more, that the characteristics may also be frequency dependent, especially in case of tilting pad bearings. In the present paper a model for tilting pad bearings including the pad inertias and coordinates for the pad rotational angles and their rotational velocities is created. Dynamic bearing coefficients are calculated including these coordinates by solving the Reynolds equation for the perturbed equilibrium position. The perturbation includes the rotor displacements and velocities as well as the pad tilting angles and angular velocities. Thus a system of linear 2+Np differential equations with Np as the number of pads is created for the bearing. From these equations transfer functions for the bearing force / rotor displacement relation can be determined. These transfer functions clearly yield frequency dependent stiffness and damping coefficients, although all coefficients of the complete system with 2+Np equations are only speed dependent. The tilting pad bearing model with the 2+Np equations is included into a rotor model by means of the rotor dynamic program MADYN 2000 (1). The rotor dynamic stability of the rotor considering the non-synchronous behaviour of the tilting pad bearings is presented for different bearing geometries showing cases with strong and weak frequency dependence.
A novel frequency-selective metamaterial to improve helix antenna

A novel frequency-selective metamaterial with negative permittivity and permeability for improving directivity and gain of a helix antenna is presented in this paper. The proposed metamaterial is composed of two Z-shape resonators printed on opposite sides of a dielectric substrate. Two forms of multilayered cells are found to be suitable for antennas and waveguides applications. In addition, a new method of designing a metamaterial-based helix antenna is presented with high directivity and gain. A comparison on radiation properties is given between the conventional and the new metamaterial-based helix antennas. Two comparisons on radiation properties are performed: (1) the effect of proposed Z-structure on monopole, dipole, and helix antennas; (2) the effect of OE3, split-ring resonator (SRR), and proposed Z-structure unit cells on the performance of helix antennas. The results show improvement of parameters such as directivity, gain, and radiation power of the new metamaterial-based helix antenna. Therefore, the combination of Z-structure with the helix antenna shows the best performance.
Unsettling the taken (for granted)

Histories of colonial plunder produced geographies that settler societies take for granted as settled. While some aspects of the conqueror/settler imaginary have been unsettled in specific cases, and through the negotiation of new instruments such as the United Nations Declaration on the Rights of Indigenous Peoples, various national apologies and modern treaties, much unsettling remains to be done. New geographies of plunder, violence and abuse reinstate geographies of various kleptocracies across the planet, reinforcing the unnatural disasters of displacement, disfigurement and loss on many people, places and communities. This paper uses the framing offered by emergent discourses of Indigenous geographies to reconsider the task of unsettling the taken-for-granted privilege of settler dominance in Indigenous domains.
Police Initial Responses to Domestic Abuse A systematic review

Key findings A systematic review of the available literature found very little evidence relating to actions police officers should take when attending a domestic abuseincident . Specifically, there is a paucity of evaluative evidence in relation to alternatives to arrest. There is evidence from one data source that police attendance in and of itself is effective in reducing victimisation. Arrest also appears to result in modest reductions in revictimisation, though the effect of arrest over and above police attendance is not clear. There is emerging evidence that the use of technology may help to secure more convictions for domestic abuse.
Note on the power law of forgetting

Power functions (e.g., f(t) = at−b) describe the relationships among many variables observed in nature. One example of this is the power law of forgetting: The decline in memory performance with time or intervening events is well fit by a power function. This simple functional relationship accounts for a great deal of accumulated data. In this note, we consider a simple yet general memory model in which all items decay monotonically in strength, but at different rates. To translate between continuous changes in strength and actual memory for events we assume a simple strength threshold for remembering. We prove a limit theorem for this model: as time grows large and memories decay, the empirical forgetting function approaches a power function under very general conditions. Power forgetting emerges for almost any monotonically decreasing strength function (including linear and exponential cases). We also illustrate by way of simulations that the power function provides an excellent fit to the entire time-course of the forgetting function, not just its limiting behavior.
Spherical Perfectly Matched Absorber for Finite-Volume 3-D Domain Truncation

The theory of 2-D radial perfectly matched Maxwellian absorber is extended to 3-D domain truncation problems using a generalized approximate formulation of a spherical finite-volume absorber. The mathematical modeling of the spherical absorber is presented and update equations are derived. The performance of the absorber is characterized with numerical experiments. As practical application of the technique, a complex problem considering the coupling between two spiral antennas is simulated using the finite-volume time-domain method. The comparison of the results to measured data demonstrates the excellent performance of the spherical absorber.
Calpain 6 Is Involved in Microtubule Stabilization and Cytoskeletal Organization

ABSTRACT The calpains are a family of Ca2+-dependent cysteine proteases implicated in various biological processes. In this family, calpain 6 (Capn6) is unique in that it lacks the active-site cysteine residues requisite for protease activity. During the search for genes downstream of the endothelin 1 (ET-1) signaling in pharyngeal-arch development, we identified Capn6. After confirming that the expression of Capn6 in pharyngeal arches is downregulated in ET-1-null embryos by in situ hybridization, we investigated its function. In Capn6-transfected cells, cytokinesis was retarded and was often aborted to yield multinucleated cells. Capn6 overexpression also caused the formation of microtubule bundles rich in acetylated α-tubulin and resistant to the depolymerizing activity of nocodazole. Green fluorescent protein-Capn6 overexpression, immunostaining for endogenous Capn6, and biochemical analysis demonstrated interaction between Capn6 and microtubules, which appeared to be mainly mediated by domain III. Furthermore, RNA interference-mediated Capn6 inactivation caused microtubule instability with a loss of acetylated α-tubulin and induced actin reorganization, resulting in lamellipodium formation with membrane ruffling. Taken together, these results indicate that Capn6 is a microtubule-stabilizing protein expressed in embryonic tissues that may be involved in the regulation of microtubule dynamics and cytoskeletal organization.
A ) Research-related Topics with possible internships in research centers

Context: Development of algorithms and tools for the veri fication of reactive systems and the synthesis of such systems Reactive systems are computer systems that maintain a continuous interaction with an environment in order to control it and to ensure that some properties are enforced. The controller of a lift system is a typical reactive system: it reacts to stimuli from the environment (e.g. an user push a bottom to call the lift) and it controls the lift in order to ful fill a given speci fication (e.g. whenever a user asks for the lift at floor i, the lift eventually reach floor i). Reactive systems are notoriously difficult to develop correctly. Difficulties arise because of concurrency, real-time constraints, parallelism, etc. Because they are difficult to develop and often used in safety critical situations (e.g. control of automatic transportation devices, embedded systems in plane or aeronautics, etc), a large research effort has been devoted to the development of computer aided methods able to certify the correctness of reactive systems. The most successful of those techniques are based on the so-called model-checking approach. Model-checking relies on algorithms that receive as inputs mathematical models (for example in the form of a finite state automaton) of the behaviours of the reactive system and the environment in which it is embedded, a logical formula defining the expected correct behaviour of the system within its environment. Then the algorithm verify that all the possible executions of the model are satisfying the formula. A more ambitious goal is to synthesis correct reactive systems directly from their speci fications. Our research group at ULB has done signi ficant progress recently on this problem (see http://www.antichains.be/). Those techniques are based on ideas coming from automata theory, temporal logics and two-player games on graphs. In this context, we propose the three following master's thesis topics. Please note that:-all the proposed master's thesis can be coupled to an internship in a research center abroad-all the topics are proposed by JF Raskin and G. Geeraerts. In practice, the students will be either co-supervised, or supervised by either of them. Asynchronous distributed systems (such as client/server applications) are notoriously difficult to design correctly. This is due to the complex (and sometimes unforeseen) interactions resulting from the asynchronous communication. Therefore, there is a growing need for automatic veri fication tools capable of analyzing such systems. This project considers asynchronous distributed systems that are …
STIM and ORAI proteins in the nervous system

Stromal interaction molecules (STIM) 1 and 2 are sensors of the calcium concentration in the endoplasmic reticulum. Depletion of endoplasmic reticulum calcium stores activates STIM proteins which, in turn, bind and open calcium channels in the plasma membrane formed by the proteins ORAI1, ORAI2, and ORAI3. The resulting store-operated calcium entry (SOCE), mostly controlled by the principal components STIM1 and ORAI1, has been particularly characterized in immune cells. In the nervous system, all STIM and ORAI homologs are expressed. This review summarizes current knowledge on distribution and function of STIM and ORAI proteins in central neurons and glial cells, i.e. astrocytes and microglia. STIM2 is required for SOCE in hippocampal synapses and cortical neurons, whereas STIM1 controls calcium store replenishment in cerebellar Purkinje neurons. In microglia, STIM1, STIM2, and ORAI1 regulate migration and phagocytosis. The isoforms ORAI2 and ORAI3 are candidates for SOCE channels in neurons and astrocytes, respectively. Due to the role of SOCE in neuronal and glial calcium homeostasis, dysfunction of STIM and ORAI proteins may have consequences for the development of neurodegenerative disorders, such as Alzheimer's disease.
Membrane lipids in Agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis

Many cellular processes critically depend on the membrane composition. In this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen Agrobacterium tumefaciens. The major components of A. tumefaciens membranes are the phospholipids (PLs), phosphatidylethanolamine (PE), phosphatidylglycerol, phosphatidylcholine (PC) and cardiolipin, and ornithine lipids (OLs). Under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipids like glycolipids, OLs and a betaine lipid. Remarkably, PC and OLs have opposing effects on virulence of A. tumefaciens. OL-lacking A. tumefaciens mutants form tumors on the host plant earlier than the wild type suggesting a reduced host defense response in the absence of OLs. In contrast, A. tumefaciens is compromised in tumor formation in the absence of PC. In general, PC is a rare component of bacterial membranes but amount to ~22% of all PLs in A. tumefaciens. PC biosynthesis occurs via two pathways. The phospholipid N-methyltransferase PmtA methylates PE via the intermediates monomethyl-PE and dimethyl-PE to PC. In the second pathway, the membrane-integral enzyme PC synthase (Pcs) condenses choline with CDP-diacylglycerol to PC. Apart from the virulence defect, PC-deficient A. tumefaciens pmtA and pcs double mutants show reduced motility, enhanced biofilm formation and increased sensitivity towards detergent and thermal stress. In summary, there is cumulative evidence that the membrane lipid composition of A. tumefaciens is critical for agrobacterial physiology and tumor formation.
Molecular dynamics simulation study of the ejection and transport of polymer molecules in matrix-assisted pulsed laser evaporation

The physical mechanisms and molecular-level picture of laser-induced material ejection from frozen solutions of polymer molecules in a volatile matrix are investigated in a series of coarse-grained molecular dynamics simulations. The simulations are performed for polymer concentrations up to 6wt% and laser fluences covering the range from the regime where molecular ejection is limited to matrix evaporation from the surface up to more than twice the threshold fluence for the onset of the collective molecular ejection or ablation. The results of the simulations are related to experimental observations obtained in matrix-assisted pulsed laser evaporation (MAPLE) thin film depositions and are used to address unresolved research questions that are of direct relevance to MAPLE performance. Contrary to the original picture of the ejection and transport of individual polymer molecules in MAPLE, the simulations indicate that polymer molecules are only ejected in the ablation regime and are always incorporated into.
Applying Phenomenology and Hermeneutics in IS Design: A Report on Field Experiences

Phenomenology and hermeneutics have long been promoted as sources of inspiration for better information system (IS) design. Practical approaches to applying these philosophical ideas have been awaited for just as long. This paper offers a review of one practitioner’s experience in devising a theoretical and methodological ‘toolkit’ via which these disciplines’ principles have been applied in actual IS design practice.
Shape-from-Shading by Fast Marching

Shape-from-Shading (SfS) is a fundamental problem in Computer Vision. At its basis lies the image irradiance equation. Recently, the authors proposed to base the image irradiance equation on the assumption of perspective projection rather than the common orthographic one. The current paper presents a greatly-improved reconstruction method based on the perspective formulation. The proposed model is solved efficiently via a modification of the Fast Marching method of Kimmel and Sethian. We compare the two versions of the Fast Marching method (orthographic vs. perspective) on medical images. The perspective algorithm outperformed the orthographic one. This shows that the more realistic hypothesis of perspective projection improves reconstruction significantly. The comparison also demonstrates the usability of perspective SfS for real-life applications such as medical endoscopy.