Miracle-dz/UniFAR-FTUs huggingface dataset:
The Science and Application of Cloning

The report in February 1997 that scientists in Scotland had cloned a sheep, Dolly, led to much public discussion of "cloning" of animals and speculation about the possibility of cloning humans. The term "cloning" is used by scientists to describe many different processes that involve making duplicates of biological material. In most cases isolated genes or cells are duplicated for scientific study, and no new animal results. This type of cloning, using genes and cells, has led to many medical advances such as providing insulin to treat diabetes and therapies for hemophilia. The sheep experiment was different; it used a cloning technique called "somatic cell nuclear transfer" and resulted in an animal that was a genetic twin—although delayed in time—of an adult sheep. This technique of transferring a nucleus from a somatic cell into an egg that produced Dolly was an extension of experiments that had been ongoing for over 40 years. These experiments were aimed at understanding how development of an animal from a single fertilized egg is carried out. In recent years the agricultural industry has been trying to improve nuclear transplantation cloning to facilitate the breeding of desirable livestock and some biotechnology companies are exploring ways to use nuclear transfer cloning to improve the production of therapeutic drugs. In addition to drug production, understanding the details of nuclear transplantation cloning might lead to new therapies to treat human disease. For instance it might be possible to grow human cells and tissues for transplantation and grafts that would not be rejected after transfer, as they often are today. These kinds of benefits are currently only hypothetical and much additional research will be needed in animal systems. Although the birth of Dolly was lauded as an amazing success, in fact the procedure is not perfected. Only one sheep was produced from over two hundred nuclear transfers. In addition, it is not yet clear whether Dolly is normal or whether she could have subtle problems that might lead to serious diseases. Using this technique to produce a human child might result in, for example, malformations or disease due to problems inherent in the technique. Thus, while using animals to understand the biological process that produced Dolly holds great promise for future medical advances, there is no current scientific justification for attempting to produce a human child at this time with this technique.
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform

We present KnowEnG, a free-to-use computational system for analysis of genomics data sets, designed to accelerate biomedical discovery. It includes tools for popular bioinformatics tasks such as gene prioritization, sample clustering, gene set analysis and expression signature analysis. The system offers ‘knowledge-guided’ data-mining and machine learning algorithms, where user-provided data are analyzed in light of prior information about genes, aggregated from numerous knowledge-bases and encoded in a massive ‘Knowledge Network’. KnowEnG adheres to ‘FAIR’ principles: its tools are easily portable to diverse computing environments, run on the cloud for scalable and cost-effective execution of compute-intensive and data-intensive algorithms, and are interoperable with other computing platforms. They are made available through multiple access modes including a web-portal, and include specialized visualization modules. We present use cases and re-analysis of published cancer data sets using KnowEnG tools and demonstrate its potential value in democratization of advanced tools for the modern genomics era.
Multi-electron processes in atoms and molecules - Experimental investigations by coincidence spectroscopy

This thesis presents studies on multi-electron processes in atoms and molecules initiated by single-photon absorption. The experimental techniques used for these studies rely on synchrotron radiation offered at large scale user facilities, and a magnetic bottle spectrometer. The magnetic bottle spectrometer is a versatile time-of-flight instrument that collects charged particles emitted from an ionization event using a characteristic magnetic field. The experiments were carried out in a coincidence detection mode, which allows selective analysis of correlated ionization processes. The work in this thesis includes detailed analyses of Auger decay processes leading to triply ionized final states in atomic Cd and Hg. The experimental data were compared with numerical calculations to identify the triply ionized final states and the Auger cascades leading to these states. The Auger cascade analyses identified important intermediate inner-states involved in the formation of triply ionized final states, and demonstrated the strong influence of Coster-Kronig transitions when energetically allowed. The studies on Cd also demonstrated the involvement of shake-up transitions in reaching the triply ionized ground state from photoionization using 200 eV photons. A new instrument for multi-electron and multi-ion coincidence studies was developed and used in experimental studies on Auger cascades in atomic Xe and on Coulomb explosion of molecular ICN. We studied the final charge state distributions from photoionization of different subshells in Xe, by measuring the ion mass spectra recorded in coincidence with specific photoelectrons. These results were compared with experimental results on Coulomb explosion of ICN from photoionization of similar subshells in I. The results suggest that the overall degree of ionization in Coulomb explosion of ICN is similar to the charge state distributions from photoionization of the related subshells in Xe. Furthermore, experimental results on energy sharing distributions of the two emitted electrons from single-photon direct double photoionization of He are presented. Energy sharing distributions were measured by recording the kinetic energies of both electrons in coincidence for excess energies ranging from 11-221 eV. An empirical model was introduced to parametrize the shapes of the distributions and to form benchmarks for future studies on other direct double ionization processes. The experimental distributions were used to extract indirect information on the knock-out mechanism, thought to be partly responsible for the direct double photoionization process. Theoretical shake-off distributions and the experimentally estimated knock-out distributions were parametrized using the same empirical model, and the results are found to be in agreement with numerical simulations.
Automated information foraging for sensemaking

In preparations for Multi-Domain Operations and Battles, All-Source and OSINT intelligence analysts gather, assess, and extract relevant information from operational databases as well as publicly available information. This data, often unstructured text documents, is noisy with relevant snippets buried within the document corpus. The costs of exploratory search and exploitive document analysis required to find these hidden snippets of information often drive searches toward a small subset of documents. Additionally, modern search tools may reinforce the confirmation bias of analysts by providing only those documents that closely match their search query. Due to the potentially high tempo of multi-domain battle, the end result is a decision or hypothesis that is ill-considered and substantiated by potentially biased information. An automated information foraging framework can mitigate these challenges by automatically identifying a wide breadth of topics for the user, extracted directly from a document corpus. A semantic network formed from the constituent entities within a document corpus contains inherently valuable topological structures that can be used to generate topics and also guide the analyst? s information exploration. Leveraging a suite of information retrieval and graph analysis algorithms that analyze the semantic network, a framework is defined for assisting analysts in both exploring and exploiting relevant information from a corpus to support the sensemaking process.
Efficient Distributed Outlier Detection in Data Streams

Anomaly detection is one of the major data mining tasks in modern applications. An element that shows significant deviation from the "usual" behavior is marked as an outlier. This means that this element either corresponds to noise or it requires more careful examination because it may be important. Also, many clustering algorithms are very sensitive to outliers. In any case, outliers must be identified and explored further, meaning that efficient outlier mining techniques are required. In this paper, we focus on distributed density-based outlier detection over multi-dimensional data streams. In particular, we focus on the approximation method for computing the Local Correlation Integral (LOCI) of multi-dimensional points. Each object p is assigned a score score(p) which represents the outlier score of p. Thus, one can select the top-k elements from the dataset that have the highest outlier scores. Our proposal has been implemented in Apache Spark using Scala and experiments have been conducted in a physical cluster running Apache Hadoop 2.7 and Apache Spark 2.4. 0. Performance evaluation results demonstrate that the proposed algorithm is efficient and scalable and therefore it can be used to mine outliers in large distributed datasets.
Inferência de idade utilizando o LIWC: identificando potenciais predadores sexuais

Predadores sociais utilizam a internet para explorar criancas ou adolescentes com propositos abusivos ou sexuais. Cada vez mais esses predadores utilizam as redes sociais para ter acesso as suas vitimas, muitas vezes fornecendo perfis falsos para se passarem por adolescentes. Nesse cenario, o presente trabalho tem o objetivo de analisar os textos em portugues do Brasil para inferir a idade dos usuarios. Para esse proposito, foi utilizada uma ferramenta denominada LIWC em sua versao do portugues do Brasil. Como estudo de caso, foi utilizada uma rede social brasileira para realizar os experimentos. O referido estudo concentrou-se na analise de textos de adolescentes e homens entre 25 e 45 anos, que representam a grande maioria dos predadores sexuais. Os resultados alcancados foram relevantes e abrem lacunas para trabalhos futuros.
Load Aware Provisioning of IoT Services on Fog Computing Platform

To support the drastically increasing traffic generated by devices at the edge of the network, 5G players are urged to rethink their infrastructure design. Unfortunately, conventional Cloud infrastructures struggle to adapt to the huge volume of traffic. In this context, Fog computing has been developed to bridge Cloud data centers and edge devices servicing a multitude of heterogeneous devices. These nearby nodes offer analytics and data storage capabilities increasing considerably the capacity of the infrastructure. However, provisioning IoT applications on such a heterogeneous infrastructure, while meeting their stringent requirements is extremely challenging. In this paper, we study the Fog service provisioning issue in a practical manner. In this regard, we propose a novel strategy, which we call GO-FSP. GO-FSP optimizes the placement of IoT application components while coping with their strict performance requirements. To do so, we first propose an Integer Linear Programming (ILP) formulation for the IoT application provisioning problem. The latter targets to minimize the deployment cost while ensuring a load balancing between heterogeneous devices. Then, a GRASP-based approach is proposed to achieve the aforementioned objectives. Finally, we make use of the FITOR orchestration system to evaluate the performance of our solution under real conditions. Obtained results show that our scheme outperforms the related strategies.
Lean Agile Integration for the Development of Large Size Projects

Scrum is a well-known agile model due to its strong management practices. It can be mingled with many software development models such as extreme programming (XP), Agile Unified Process, and Feature Driven Development (FDD). Lean is a very popular known process in the automobile industry due to its effective practices such as Kanban bard and smooth workflow. Lean development is gaining popularity in the software industry from the last few years. Lean development is rational, convenient, responsive, and team-based and it adds value to the enterprise. Scrum is useable and practical for small and medium projects but it does not render positive support for the large size projects. In order to adopt Scrum for large size projects, there is a need to integrate Lean and Scrum. It is required to inherit some properties of the Lean into Scrum, without compromising the speed, quality, efficiency, and standards, to accomplish large size projects successfully such as enterprise resource planning (ERP) systems. It is anticipated that the proposed Lean Scrum integration will make it suitable to develop large size projects. The same is accomplished by purposing an integrated LScrum model in this research. The proposed model is validated using a survey to conclude the results. The results of the survey support the proposed integration of Lean and Scrum for the development of large size projects.
ION MOBILITY SPECTROMETRY: HISTORY, CHARACTERISTICS AND APPLICATIONS

Ion mobility spectrometry (IMS) is an analytical technique that separates ions in the gas phase. Ions are separated at atmospheric pressure under the influence of an electric field, according to their size and shape. IMS is the best choice for detection of narcotics, chemical and biological warfare agents and explosives in airports and customs. IMS can detect almost anything that can be ionized and has been applied to the analysis from the lightest elements such as helium to the most complex mixtures such as proteomes, metabolomes and complete organisms such as bacteria, chiral separations, and structure determination. Although since 2000 there have been approximately fifty reviews of IMS, this review is probably the only general valuation of this technique since then.
Heat Flux Estimation at Pool Boiling Processes with Computational Intelligence Methods

It is difficult to manually process and analyze large amounts of data. Therefore, to solve a given problem, it is easier to reach the solution by studying the data obtained from the environment of the problem with computational intelligence methods. In this study, pool boiling heat flux was estimated in the isolated bubble regime using two optimization methods (genetic and artificial bee colony algorithm) and three machine learning algorithms (decision tree, artificial neural network, and support vector machine). Six boiling mechanisms containing eighteen different parameters in the genetic and the artificial bee colony (ABC) algorithms were used to calculate overall heat flux of the isolated bubble regime. Support vector machine regression (SVMReg), alternating model tree (ADTree), and multilayer perceptron (MLP) regression only used the heat transfer equation input parameters without heat transfer equations for prediction of pool boiling heat transfer over a horizontal tube. The performance of computational intelligence methods were determined according to the results of error analysis. Mean absolute error (MAE), root mean square error (RMSE), and mean absolute percentage error (MAPE) error were used to calculate the validity of the predictive model in genetic algorithm, ABC algorithm, SVMReg, MLP regression, and alternating model tree. According to the MAPE error analysis, the accuracy values of MLP regression (0.23) and alternating model tree (0.22) methods were the same. The SVMReg method used for pool boiling heat flux estimation performed better than the other methods, with 0.17 validation error rate of MAPE.
Chromosome synapsis, recombination and epigenetic modification in rams heterozygous for metacentric chromosome 3 of the domestic sheep Ovis aries and acrocentric homologs of the argali Ovis ammon

Hybridization of domestic animal breeds with their wild relatives is a promising method for increasing the genetic diversity of farm animals. Resource populations derived from the hybridization of various breeds of domestic sheep with mouflon and argali are an important source of breeding material. The karyotypes of argali and domestic sheep differ for a Robertsonian translocation, which occurred in the common ancestor of mouflon and domestic sheep (Ovis aries) due to the centric fusion of chromosomes 5 and 11 of the argali (O. ammon) into chromosome 3 of sheep. It is known that heterozygosity for translocation can lead to synapsis, recombination and chromosome segregation abnormalities in meiosis. Meiosis in the heterozygotes for translocation that distinguishes the karyotypes of sheep and argali has not yet been studied. We examined synapsis, recombination, and epigenetic modification of chromosomes involved in this rearrangement in heterozygous rams using immunolocalization of key proteins of meiosis. In the majority of cells, we observed complete synapsis between the sheep metacentric chromosome and two argali acrocentric chromosomes with the formation of a trivalent. In a small proportion of cells at the early pachytene stage we observed delayed synapsis in pericentromeric regions of the trivalent. Unpaired sites were subjected to epigenetic modification, namely histone H2A.X phosphorylation. However, by the end of the pachytene, these abnormalities had been completely eliminated. Asynapsis was replaced by a nonhomologous synapsis between the centromeric regions of the acrocentric chromosomes. By the end of the pachytene, the γH2A.X signal had been preserved only at the XY bivalent and was absent from the trivalent. The translocation trivalent did not differ from the normal bivalents of metacentric chromosomes for the number and distribution of recombination sites as well as for the degree of centromeric and crossover interference. Thus, we found that heterozygosity for the domestic sheep chromosome 3 and argali chromosomes 5 and 11 does not cause significant alterations in key processes of prophase I meiosis and, therefore, should not lead to a decrease in fertility of the offspring from interspecific sheep hybridization.
Copper (II) Ions Activate Ligand-Independent Receptor Tyrosine Kinase (RTK) Signaling Pathway

Receptor tyrosine kinase (RTK) is activated by its natural ligand, mediating multiple essential biological processes. Copper (II) ions are bioactive ions and are crucial in the regulation of cell signaling pathway. However, the crosstalk between copper (II) ions and RTK-mediated cellular signaling remains unclear. Herein, we reported the effect of copper (II) ions on the ligand-independent RTK cellular signaling pathway. Our results indicate that both EGFR and MET signaling were activated by copper (II) in the absence of the corresponding ligands, EGF and HGF, respectively. Consequently, copper (II) ions initiate two RTK-mediated downstream signal transductions, including AKT and ERK. Moreover, copper (II) significantly increased proliferation and cellular migration. Our study proposes a novel role of copper in RTK-mediated signaling for growth factor-independent cancer cell proliferation and migration, implying that targeting both the copper (II) and growth factor in tumor microenvironments may be necessary for cancer treatment.
Skill Needs for Early Career Researchers—A Text Mining Approach

Research and development activities are one of the main drivers for progress, economic growth and wellbeing in many societies. This article proposes a text mining approach applied to a large amount of data extracted from job vacancies advertisements, aiming to shed light on the main skills and demands that characterize first stage research positions in Europe. Results show that data handling and processing skills are essential for early career researchers, irrespective of their research field. Also, as many analyzed first stage research positions are connected to universities, they include teaching activities to a great extent. Management of time, risks, projects, and resources plays an important part in the job requirements included in the analyzed advertisements. Such information is relevant not only for early career researchers who perform job selection taking into account the match of possessed skills with the required ones, but also for educational institutions that are responsible for skills development of the future R&D professionals.
Examining Users’ Understanding of Security Failures in EMV Smart Card Payment Systems

New credit cards containing Europay, MasterCard and Visa (EMV) chips for enhanced security, and for in-store purchases (rather than online purchases) have been adopted considerably in recent years. EMV supposedly protects the payment cards in such a way that the computer chips in a card referred to as chip-and-pin cards generate a unique one-time code each time the card is used. The one-time code is designed such that if it is copied or stolen from the merchant system or from the system terminal, it cannot be useful for creating a counterfeit copy of that card or counterfeit chip of the transaction. However, in spite of this design, EMV technology is not entirely foolproof from failure. This paper dis-cusses the issues, failures and fraudulent cases associated with EMV Chip-And-Card technology. The work also evaluates people’s understanding of these issues and the consequential precautions they take to safeguard their information while using the EMV cards for transactions.
On a burning plasma low recycling regime with PDT = 23–26 MW, QDT = 5–7 in a JET-like tokamak

The recent invention of a continuously flowing liquid lithium system, called 24/7-FLiLi, opens the opportunity to design a plasma pumping divertor which can significantly suppress plasma edge cooling by recycling. The paper describes the expected performance of deuterium–tritium burning plasma with low recycling using a tokamak of JET size, magnetic field and plasma current as an example. So far, only the technological aspects of flowing lithium have been tested on the HT-7 and EAST tokamaks (ASIPP, Hefei, China) with no attempts to create the low recycling regime. The compatibility of 24/7-FLiLi with tokamak plasma was confirmed and some mistakes in the design were revealed, thus, requiring another fabrication approach. Now, with the proper design of the Li system, recycling as low as 0.5 seems to be achievable. The suppression of plasma cooling by recycling in combination with neutral beam injection (NBI) for core plasma fueling by energetic particles automatically leads to ‘the best possible confinement regime’, uniquely compatible with burning plasma. This paper outlines the conceptual details of the 24/7-FLiLi divertor for a JET size tokamak. The main focus is in regard to the physics of the low recycling regime as well as to the expected performance of the burning plasma. In comparison with the results of 1994 on TFTR and 1997 on JET, the projected performance is astonishing: fusion power –26 MW, fusion efficiency , tritium burn up 7.8%–8.7% with modest NBI power MW, and energy keV. This new regime could resolve the outstanding plasma physics issues related to burning plasma that are unsolvable with the currently dominant approach.