Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing an in Vivo Based CRISPR-Induced Genetic Screen to Identify Novel Regulators of T- Cell Dysfunction in the Context of Tumors

T-cell dysfunction is a central characteristic of the immune system’s response to cancer, and one of the primary mechanisms that allows tumors to escape the immune response and thrive. Within the last decade, there has been rapid progress in immunotherapy treatments that are capable of manipulating the immune system to target and attack cancer cells. Two immunotherapy treatments in particular, antibody checkpoint blockade and chimeric antigen receptor (CAR) modified T-cells, have been especially effective in preventing or reversing T-cell dysfunction in the context of tumors. However, these immunotherapies are not without their limitations, as only certain subsets of patients have robust responses to these treatments and many show no response at all. It is therefore imperative that we discover novel therapeutic targets of T-cell dysfunction in the context of tumors, and this can best be achieved through large-scale loss-of-function genetic screens. The efficiency and affordability of the recently developed CRISPR-Cas9 genomic DNA editing technology makes it an ideal method for performing large scale genetic screens. The primary goal of this thesis was to develop the tools necessary to create an in vivo based CRISPR-mediated system that could be used to generate a genetic screen to discover novel negative regulators of T-cell dysfunction in the tumor microenvironment. Targets discovered in such a screen will be useful to identify novel therapeutic targets for use in both checkpoint blockade and CAR T-cell therapies.
A Trajectory Clustering Framework to Analyse Air Traffic Flows

This paper describes a framework to automatically identify air traffic flows from a set of trajectories by using a clustering algorithm. The framework offers two methods to cluster trajectories, each one using a different distance/similarity measure between trajectories. Results and performance characteristics of both methods are compared by applying them to real trajectories over a French Area Control Center. The framework can output statistics and figures for flow analysis and its use is facilitated by the relatively low number of parameters to be provided by the user. Its aim is to help support the SESAR vision of flow-centric operations by being integrated into Air Traffic Management tools, e.g. for airspace design/management or for analysis of traffic patterns in a free route environment.
Multi-Spectral Convolutional Neural Networks for Biometric Presentation Attack Detection

Nowadays, reliable and automatic subject authentication has become of the utmost importance in multiple application scenarios. Over the last decades, biometric recognition has shown to be a good alternative to password based systems. In spite of their numerous advantages, biometric systems are vulnerable to presentation attacks (PAs), i.e., attempts to log into the system with a fake biometric characteristic or presentation attack instrument (PAI). These attacks pose a severe threat to the security of the authentication system: any person could eventually fabricate or order a gummy finger to impersonate someone else. Therefore, the development of accurate presentation attack detection (PAD) schemes is key to the wider deployment of secure biometric systems. In this paper, we present a novel approach for fingerprint PAD based on short wave infrared (SWIR) images and multi-spectral convolutional neural networks (CNNs). In particular, four samples are acquired at different SWIR wavelengths, which are subsequently fed to five different CNN models. These networks first pre-process the multi-spectral information to obtain images with three channels, and then apply regular CNN models. The approach is evaluated on a database comprising over 4700 samples, stemming from 562 different subjects and 35 different PAI species. The results show the soundness of the proposed approach with a detection equal error rate (D-EER) as low as 0.5%, outperforming the state-of-the-art D-EER of 1.4%. In addition, fusing the SWIR information with laser speckle contrast imaging (LSCI) sequences leads to an even lower D-EER of 0.2%.
Recent Developments on 1,3-Dipolar Cycloaddition Reactions by Catalysis in Green Solvents

The use of eco-compatible synthetic procedures in organic reactions and, in particular, in 1,3-dipolar cycloaddition reactions, has recently received a great deal of attention and considerable progress has been achieved in this area in the last years. This review summarizes the approaches currently employed to synthesize heterocyclic compounds by catalyzed 1,3-dipolar cycloadditions in green solvents in the last six years. Our choice to do a selection of the literature from 2014 to 2019 was made considering the absence of a recent review about this period, to our knowledge. Several examples to construct heterocycles by 1,3-dipolar cycloadditions will be discussed in this work subdivided in function of the most important class of non-conventional and green solvents, i.e., ionic liquids (ILs), deep eutectic solvents (DES), and water.
Benefits of Integrated Seismic and Gravity Exploration: An example from Norman Wells, NWT

Interpretation of a gravity survey was integrated with processing of reflection seismic data acquired across the Norman Range, near Norman Wells, NWT. Previous geological mapping had led to the development of three structural models for this area: (1) A low angle thrust fault in the Upper Cambrian Saline River Formation, causing repetition of dense Palaeozoic dolomites and anhydrites, with no involvement of sub-Saline River sediments. (2) A high-angle reverse fault thrusting Proterozoic sediments into the core of the Norman Range. (3) A vertical block fault model with a horst of Proterozoic and basement rocks coring the Norman Range, with no horizontal shortening. We modelled the theoretical gravity field for each case, constrained by outcrop data, well data and density measurements, and thus determined that the first model is most likely to represent the structure of the Norman Range. This preferred gravity-derived model was then used effectively to assist in the construction of a velocity model for depth migration of the seismic data, which was collected in a difficult data area where carbonates outcrop at surface. Integrated analysis of the two data sets supports a thin-skinned deformational model for the Norman Range.
The Symmetry of Lower and Upper Approximations, Determined by a Cyclic Hypergroup, Applicable in Control Theory

In the first part of our paper, we construct a cyclic hypergroup of matrices using the Ends Lemma. Its properties are then, in the second part of the paper, used to describe the symmetry of lower and upper approximations in certain rough sets with respect to invertible subhypergroups of this cyclic hypergroup. Since our approach is widely used in autonomous robotic systems, we suggest an application of our results for the study of detection sensors, which are used especially in mobile robot mapping.
Animal Origin Bioactive Hydroxyapatite Thin Films Synthesized by RF-Magnetron Sputtering on 3D Printed Cranial Implants

Ti6Al4V cranial prostheses in the form of patterned meshes were 3D printed by selective laser melting in an argon environment; using a CO2 laser source and micron-sized Ti6Al4V powder as the starting material. The size and shape of prostheses were chosen based on actual computer tomography images of patient skull fractures supplied in the framework of a collaboration with a neurosurgery clinic. After optimizations of scanning speed and laser parameters, the printed material was defect-free (as shown by metallographic analyses) and chemically homogeneous, without elemental segregation or depletion. The prostheses were coated by radio-frequency magnetron sputtering (RF-MS) with a bioactive thin layer of hydroxyapatite using a bioceramic powder derived from biogenic resources (Bio-HA). Initially amorphous, the films were converted to fully-crystalline form by applying a post-deposition thermal-treatment at 500 °C/1 h in air. The X-ray diffraction structural investigations indicated the phase purity of the deposited films composed solely of a hexagonal hydroxyapatite-like compound. On the other hand, the Fourier transform infrared spectroscopic investigations revealed that the biological carbonatation of the bone mineral phase was well-replicated in the case of crystallized Bio-HA RF-MS implant coatings. The in vitro acellular assays, performed in both the fully inorganic Kokubo’s simulated body fluid and the biomimetic organic–inorganic McCoy’s 5A cell culture medium up to 21 days, emphasized both the good resistance to degradation and the biomineralization capacity of the films. Further in vitro tests conducted in SaOs-2 osteoblast-like cells showed a positive proliferation rate on the Bio-HA RF-MS coating along with a good adhesion developed on the biomaterial surface by elongated membrane protrusions.
Entrepreneurship Education and Employability: Insights from UK

This article aims to provide insights into how employability skills, career development and entrepreneurial mind-sets are embedded into entrepreneurship education to enhance graduate employability in tertiary education. Recent initiatives in United Kingdom universities respond to the calls from The Association of Business Schools to incorporate more practice into the teaching, learning and assessment of entrepreneurship curricular. The calls aim to encourage the development of entrepreneurial skills and mind sets relevant for graduate employability. One of the most appropriate approaches for designing such practice-based curricular is Problem-based learning (PBL). The authors reviewed the literature on entrepreneurship education and also drew on constructivist theories of teaching and learning based on two case studies to demonstrate how entrepreneurship curricular development could enhance graduate employability. Case story approach was used to accurately report the full extent of the knowledge of entrepreneurship educators. The findings showed a critique and rethinking of current university education in the United Kingdom. Instead of the traditional teaching and learning methods, entrepreneurship educators use a portfolio of practicebased pedagogies including starting businesses, design thinking and reflective practice to embed practice into learning and assessment. The findings therefore show how the choice of teaching, learning and assessment focus on enhancing the development of entrepreneurial mind-sets and employability skills in learners. The article analysed practices and techniques for embedding entrepreneurial skills, mind-sets and employability in entrepreneurship education. It therefore highlights the processes through which practice-based curricular design enhance entrepreneurial and employability skills among university graduates.
Analysis of U.S. Patents Network: Development of Patents over Time

The NBER network of U.S. patents from 1963 to 1999 (Hall, Jaffe, Tratjenberg 2001, USPTO) is an example of a very large citation network (3774768 vertices and 16522438 arcs). Using islands algorithm (Zaver šnik, Batagelj, 2004) for the Search Path Count (SPC) weights (Hummon and Doreian 1989; Batagelj 2003) the most powerful theme in the entire network was determined. From this we selected a group of companies and categories that appeared and split the entire network into subnetworks according to selected companies and technological categories. We study the general trends and features of the subnetworks over the past thirty-seven years. We propose another approach for studying patents’ network as a temporal network. Vertices from the same category in the same time slice are shrunk and then the obtained smaller networks over time are studied. By studying development patterns of the network over time we are trying to determine the general trends in the research and development for the selected companies and categories over the past three decades.
Force-Locking Attack on Sync Hotstuff

Blockchain, which realizes state machine replication (SMR), is a fundamental building block of decentralized systems, such as cryptocurrencies and smart contracts. These systems require a consensus protocol in their global-scale, public, and trustless networks. In such an environment, consensus protocols require high resiliency, which is the ability to tolerate a fraction of faulty replicas, and thus synchronous protocols have been gaining significant research attention recently. Abraham et al. proposed a simple and practical synchronous SMR protocol called Sync Hotstuff (to be presented in IEEE S&P 2020). Sync Hotstuff achieves 2∆ latency, which is near optimal in a synchronous protocol, and its throughput without lock-step execution is comparable to that of partially synchronous protocols. Sync Hotstuff was presented under a standard synchronous model as well as under a weaker, but more realistic, model called mobile sluggish model. Sync Hotstuff also adopts an optimistic responsive mode, in which the latency is independent of ∆. However, Sync Hotstuff has a critical security vulnerability with which an adversary can conduct double spending or denial-of-service attack. In this paper, we present an attack we call force-locking attack on Sync Hotstuff. This attack violates the safety, i.e., consistency of agreements, of the protocol under the standard synchronous model and the liveness, i.e., progress of agreements, of all versions of the protocol, including the mobile sluggish model and responsive mode. The force-locking attack is not only a specific attack on Sync Hotstuff but also on some general blockchain protocols. After describing the attack, we will present some refinements to prevent this attack. Our refinements remove the security vulnerability on Sync Hotstuff without any performance compromises. We will also provide formal proofs of the security for each model.
CORP: Coreference Resolution for Portuguese

We are building an open-source off-the-shelf system, which solves Portuguese noun phrase coreference, using plain texts as input. Our tool goes beyond basic syntactic heuristics, such as string matching, copular, juxtaposition. We consider semantics. In other words, string matching heuristics serve to deal with cases such as “Miguel Guerra” and “Guerra”, in which both NPs share some identical part. Copular constructions are used to link two mentions as in “Miguel Guerra is the agronomist”. Juxtaposition refers to cases of appositive constructions such as “Miguel Guerra, the agronomist”. So far, it may seem a simple problem, but refined syntactic knowledge must be taken into account even in those cases. For instance, we do not want to find that “mushrooms found in Brazil” is coreferent with “mushrooms found in France”. In other situations, establishing a coreference relation is even more difficult. In cases such as “the boy” and “the kid”, there is a semantic relation which is usually part of the readers’ common sense knowledge. We are currently dealing with this sort of problem. The current version of the system is available through a web interface and is detailed below.
A Methodology for Obtaining Primary and Secondary Creep Characteristics from Indentation Experiments, Using a Recess

Abstract A procedure is described for Indentation Creep Plastometery (using a spherical indenter), which is analogous to that developed previously for Indentation Plastometry. As in that case, it is based on iterative numerical simulation of the indentation process, with repeated comparison between an experimental outcome and the corresponding model prediction, systematically varying the values of parameters in a constitutive law until optimal agreement is achieved. The constitutive law used here is the Miller–Norton relationship, which covers both primary and secondary creep regimes (although the transition between them is not well-defined). The experimental outcome is the penetration depth as a function of time, under a constant applied load. An important feature of the procedure is the prior creation of a spherical recess in the sample, having a pre-selected depth and a curvature radius equal to that of the indenter. This allows control over the stress levels created during the indentation creep testing and can be used to ensure that no (time-independent) plastic deformation is stimulated during the test. In the absence of such a recess, this is virtually unavoidable, since the stress levels created during initial contact between a spherical indenter and a flat surface tend to be very high. Such plasticity introduces unwanted complications into creep testing. Confirmation of the viability of the procedure is provided via comparisons between the creep characteristics of pure nickel samples at 750 °C, obtained in this way and via conventional uniaxial tensile testing.
Simulation and the Finite-Difference Stochastic Approximation Method

An important application of stochastic optimization – simulation optimization, where the objective function can be evaluated only by computer simulation, is considered. We examined some difficulties arised in solving these problems applying the finite-difference stochastic approximation (FDSA) method. Also, we investigated efficiency of the FDSA algorithm depending on the coefficients that generate the step length in optimization algorithm and the perturbation value of gradient approximation of objective function. Efficiency is measured by the mean values of the objective function at the final estimates of the algorithm, over the specified number of replications.
The Role of ß-Mannanase (Hemicell) in Improving Poultry Productivity, Health and Environment

I Department of Poultry Science, Cholistan University of Veterinary and Animal Sciences Bahawalpur 63100, Pakistan. II Osmaniye Korkut Ata University, Kadirli Applied Science School, Department of Organic Farming Business Management, Osmaniye/Turkey. III Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt. IV Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22516, Egypt. V Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, Kolkata, India.
NAIR: A novel automated intrusion response system based on decision making approach

In recent years, automated intrusion response has become a promising research problem in network security. Several approaches have been proposed to perform an effective automated response policy. However, these approaches have some limitations, i.e., heavily depending on attack alerts and not taking in account uncertainty of system runtime state. In this paper, we present a comprehensive sequential decision-making based automated intrusion response approach. We utilize different decision approaches and models to respectively represent and reason about attack activities and system runtime state in view of their different dynamic nature. We perform some experiments to validate proposed approach and the results show that our approach has good performance in response accuracy to different attack scenarios and robustness against false alerts.
Normal Distribution Transform with Point Projection for 3D Point Cloud Registration

Normal Distribution Transform (NDT) is a registration algorithm very used in many fields. Its main idea consists in modeling clouds (points sets) with a set of Gaussian distributions generated by discretizing each points set into voxels. This algorithm gives a good transformation estimation if a point and its neighbors represent a planar and linear patch. In light of this fact, this paper presents a new way to apply NDT on 3D registration problem. Our approach consists in applying NDT onto projected clouds instead of the original ones. The new point clouds are determined by taking into consideration the shape topology. The proposed approach uses a statistical method to find the best plane that represents each point cloud. An experimental study ,carried out on several clouds, shows that the proposed approach is better than the original NDT in terms of accuracy and runtime performance.
Tactical prediction of the number of control positions with softmax regression and tree search

In the tactical phase, ATC supervisors and Flow Management Positions (FMP) foresee the number of control po-sitions to be deployed in the next few hours through the analysis of traffic counts, the update of the daily sector configuration plan, and their capacity to anticipate the probable evolution of the traffic demand. We present in this paper a method based on softmax regression and tree search to predict the number of control positions based on the latest traffic count previsions for a given time period. This method is inspired by some of the current operational techniques: first a multinomial logistic regression is applied to compute an approximate value by analyzing the traffic count values of the whole Area Control Center (ACC). Then a tree search algorithm identifies all the sector configurations that could be deployed during this period, without generating an overloaded sector. The configuration with the minimal number of sectors is finally used to estimate the minimum number of control positions to be deployed. Results obtained on the French ACC of Bordeaux show that the predictions are close to the results obtained by operational expert assessment and could hence be used as a decision support tool to alleviate FMP and ATC supervisor workload.
Paroxysmal nocturnal hemoglobinuria revisited: news on pathophysiology, clinical course and treatment

Abstract Paroxysmal nocturnal hemoglobinuria (PNH) is a rare benign clonal disorder of hematopoiesis. Its etiologic basis is the clonal dominance of a PIGA-mutated hematopoietic progenitor that gives rise to GPI-deficient blood cells that are unable to express complement inhibitors like CD55 or CD59. These cells are prone to complement-induced hemolysis. In classic hemolytic PNH, granulocyte clone sizes can be up to 90% or more. Much progress has been made during the last years in understanding the interrelations of complement-dependent hemolysis; its consequences like thrombosis, renal failure or pulmonal hypertension; and possible treatment strategies. To gain clinical relevance, the PNH clone has to make a relevant contribution to blood cell generation; however, a minimal clone size as a threshold for the occurrence of symptoms such as thrombosis, dyspnea, chest or abdominal pain cannot be given. Such symptoms can be seen in a relevant proportion of patients with clone size smaller than 10%. The driver for the clonal dominance of the PIGA-mutated hematopoiesis is still not clear. Recently, data about coexisting mutations in cancer genes have been published and new mechanisms for autoimmunity have been presented. The success of eculizumab in the treatment of PNH patients has stimulated the development of a variety of new strategies for complement inhibition. This review will focus on the most important findings in pathophysiology, clinical course and treatments during the last years.