Miracle-dz/UniFAR-FTUs huggingface dataset:
Articulating Socially Aware Design Artifacts and User Stories in the Conception of the OpenDesign Platform

Gathering and understanding requirements and features in a system play a central role in its acceptance and proper use. Unconventional systems involving uncertainties about their requirements demand methods that adequately support the capture of stakeholder’s needs, desires and objectives. The OpenDesign project aims at supporting the design of computational solutions to wide-ranging problems under a holistic and socially-aware perspective through an open and collaborative platform. Designing this platform with a proper understanding of the desired features is for sure a hard task. In this paper, we investigate and characterize an ideation process to be used in situations involving uncertainties about requirements, as experienced in the OpenDesign Project. This process involves the collaborative construction of user stories, articulated with Socially Aware Design artifacts, created through participatory practices, as part of the platform design and prospection of potential uses of it. Based on the results, we organize the core concepts permeating the OpenDesign proposal, expressed in a map synthesizing its features.
Alternate Hosts of Puccinia striiformis f. sp. tritici and Their Role

Understanding the interactions between the host and the pathogen is important in developing resistant cultivars and strategies for controlling the disease. Since the discovery of Berberis and Mahonia spp. as alternate hosts of the wheat stripe rust pathogen, Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), their possible role in generating new races of Pst through sexual reproduction has become a hot topic. To date, all the investigations about the role of alternate hosts in the occurrence of the wheat stripe rust epidemics revealed that it depends on alternate host species and environmental conditions. In this review, we summarized the current status of alternate hosts of Pst, their interactions with the pathogen, their importance in genetic diversity and disease epidemics. Most importantly, the recent research progress in understanding the role of alternate hosts of Pst is provided.
Incremental cost-effectiveness analysis of tyrosine kinase inhibitors in advanced non-small cell lung cancer with mutations of the epidermal growth factor receptor in Colombia

ABSTRACT Objective To estimate the cost-effectiveness of sequences starting with tyrosine kinase inhibitors (TKI), afatinib and osimertinib, for the treatment of epidermal growth factor receptor (EGFR) mutation-positive (Exon 19 deletion or L858R) non-small cell lung cancer (NSCLC), stages IIIB – IV in Colombia. Methods A partitioned survival model was designed, using information from global and progression-free survival curves. For first and second-generation TKI, second line treatment was assumed according to the presence of T790M mutation to define the use of osimertinib or chemotherapy. The cost of the states without progression and post-progression was estimated using the base case approach, identified through consultation with clinical experts. Results The cost of treatment starting with afatinib in the first line was of 222,247 USD (1 USD = 3171.99 COP) and produced 1.36 QALYs. The strategy with afatinib was dominant with respect to that of first line TKI (227,289 USD and 1.34 QALY). The strategy with osimertinib resulted in more QALYs and higher costs, with ICERs of 35,062 USD, exceeding the current willingness to pay threshold for Colombia. Conclusions Treatment starting with afatinib in the first line is dominant with respect to the strategy with first line TKI. The ICER of osimertinib sequence exceeds the threshold when compared with afatinib one.
A trimeric metazoan Rab7 GEF complex is crucial for endocytosis and scavenger function

ABSTRACT Endosome biogenesis in eukaryotic cells is critical for nutrient uptake and plasma membrane integrity. Early endosomes initially contain Rab5, which is replaced by Rab7 on late endosomes prior to their fusion with lysosomes. Recruitment of Rab7 to endosomes requires the Mon1–Ccz1 guanine-nucleotide-exchange factor (GEF). Here, we show that full function of the Drosophila Mon1–Ccz1 complex requires a third stoichiometric subunit, termed Bulli (encoded by CG8270). Bulli localises to Rab7-positive endosomes, in agreement with its function in the GEF complex. Using Drosophila nephrocytes as a model system, we observe that absence of Bulli results in (i) reduced endocytosis, (ii) Rab5 accumulation within non-acidified enlarged endosomes, (iii) defective Rab7 localisation and (iv) impaired endosomal maturation. Moreover, longevity of animals lacking bulli is affected. Both the Mon1–Ccz1 dimer and a Bulli-containing trimer display Rab7 GEF activity. In summary, this suggests a key role for Bulli in the Rab5 to Rab7 transition during endosomal maturation rather than a direct influence on the GEF activity of Mon1–Ccz1. Summary: Bulli forms a trimeric complex with Mon1–Ccz1 and is crucial for endosomal maturation in nephrocytes.
Oxygen consumption in the Baltic proper1

Total oxygen consumption rate, averaged over 1957-1982, and its variations with salinity in the deep water of the Baltic proper are calculated by a system of diagnostic advection-diffusion equations in a "natural" coordinate frame of reference. Although the data set used is not ideal for a more thorough investigation of the sensitivity of the model, an oxygen budget is formulated. A gross consumption rate of 3 x 10-9 mol m-3 s-1 is obtained. Further, a total consumption of about 0.14 x 10-6 mol m-2 s-1 is found, which is equivalent to an annual carbon input of 10 g C m-2 yr-1.
Mutations causing Friedreich ataxia

Friedreich ataxia (FRDA) is an autosomal recessive degenerative disease primarily affecting the nervous system and the heart. The identification of the FRDA gene (FXN) encoding the mitochondrial protein frataxin allowed to better define the clinical and pathological spectrum of the disease, to investigate pathogenesis and to eventually propose novel treatments for this so far incurable disease. Frataxin has homologs in all eukaryotes and in gram-negative bacteria. Studies in yeast and mouse models and biochemical investigations indicate a role in the assembly of iron–sulfur clusters in the mitochondrion. Frataxin deficiency leads to abnormal mitochondrial iron metabolism, decreased activities of iron–sulfur cluster-containing enzymes, reduced oxidative phosphorylation and possibly increased oxidative stress. Complete absence of frataxin is lethal at an embryonic level in all investigated multicellular organisms, in yeast it leads to loss of mitochondrial function and mitochondrial DNA. Patients with FRDA .
High‐throughput, microscope‐based sorting to dissect cellular heterogeneity

Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking these phenotypes to genotype or RNA expression at scale remains challenging. Here, we present Visual Cell Sorting, a method that physically separates hundreds of thousands of live cells based on their visual phenotype. Automated imaging and phenotypic analysis directs selective illumination of Dendra2, a photoconvertible fluorescent protein expressed in live cells; these photoactivated cells are then isolated using fluorescence‐activated cell sorting. First, we use Visual Cell Sorting to assess hundreds of nuclear localization sequence variants in a pooled format, identifying variants that improve nuclear localization and enabling annotation of nuclear localization sequences in thousands of human proteins. Second, we recover cells that retain normal nuclear morphologies after paclitaxel treatment, and then derive their single‐cell transcriptomes to identify pathways associated with paclitaxel resistance in cancers. Unlike alternative methods, Visual Cell Sorting depends on inexpensive reagents and commercially available hardware. As such, it can be readily deployed to uncover the relationships between visual cellular phenotypes and internal states, including genotypes and gene expression programs.
Classifying Big Data Taxonomies: A Systematic Literature Review

: As big data is a rather young, but growing discipline, lots of confusion about the general nature of this term exists. Consequently, multiple research endeavours to discover unique characteristics, technologies, techniques and their interconnections were conducted, resulting in comprehensive classification approaches. For this purpose, various taxonomies on big data exist in literature. However, due to the multitude of approaches and partial contradictions, no real clarification is achieved. To overcome this issue, a systematic literature review was conducted, which identifies and analyses big data taxonomies. As a result, a classification of those taxonomies is proposed, which additionally tracks sub-domains that are not yet covered by the existing taxonomies so far. Eventually, the publication at hand serves as a starting point for further taxonomy related research endeavours in the big data domain.
Detection and Replication of Moku Virus in Honey Bees and Social Wasps

Transmission of honey bee viruses to other insects, and vice versa, has previously been reported and the true ecological importance of this phenomenon is still being realized. Members of the family Vespidae interact with honey bees via predation or through the robbing of brood or honey from colonies, and these activities could result in virus transfer. In this study we screened Vespa velutina and Vespa crabro collected from Europe and China and also honey bees and Vespula vulgaris from the UK for Moku virus (MV), an Iflavirus first discovered in the predatory social wasp Vespula pensylvanica in Hawaii. MV was found in 71% of Vespula vulgaris screened and was also detected in UK Vespa crabro. Only seven percent of Vespa velutina individuals screened were MV-positive and these were exclusively samples from Jersey. Of 69 honey bee colonies screened, 43% tested positive for MV. MV replication was confirmed in Apis mellifera and Vespidae species, being most frequently detected in Vespula vulgaris. MV sequences from the UK were most similar to MV from Vespula pensylvanica compared to MV from Vespa velutina in Belgium. The implications of the transfer of viruses between the Vespidae and honey bees are discussed.
Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity

ABSTRACT SARS-CoV-2, the causative agent of the COVID-19 pandemic, may be transmitted via airborne droplets or contact with surfaces onto which droplets have deposited. In this study, the ability of SARS-CoV-2 to survive in the dark, at two different relative humidity values and within artificial saliva, a clinically relevant matrix, was investigated. SARS-CoV-2 was found to be stable, in the dark, in a dynamic small particle aerosol under the four experimental conditions we tested and viable virus could still be detected after 90 minutes. The decay rate and half-life was determined and decay rates ranged from 0.4 to 2.27 % per minute and the half lives ranged from 30 to 177 minutes for the different conditions. This information can be used for advice and modelling and potential mitigation strategies.
Antithrombotic Therapy in Hereditary Hemorrhagic Telangiectasia: Real-World Data from the Gemelli Hospital HHT Registry

Although Hereditary Hemorrhagic Telangiectasia (HHT) is characterized by an overwhelming bleeding propensity, patients with this disease may also present medical conditions that require antithrombotic therapy (AT). However, precise information on indications, dosage, duration, effectiveness, and safety of AT in HHT patients is lacking. We performed a retrospective analysis of the HHT Registry of our University Hospital and found 26 patients who received AT for a total of 30 courses (19 courses of anticoagulant therapy and 11 courses of antiplatelet therapy). Indications to treatments included: atrial fibrillation, venous thrombosis and pulmonary embolism, heart valve replacement, retinal artery occlusion, secondary prevention after either stroke or myocardial infarction, and thromboprophylaxis for surgery. The total time of exposure to antiplatelet therapy was 385 months and to anticoagulant therapy 169 months. AT was generally well tolerated, with no fatal bleedings and no significant changes in hemoglobin levels. However, we found three major bleedings, with an incidence rate of 6.5 per 100 patients per year. When only patients treated with anticoagulants were considered, the incidence rate of major bleedings increased to 21.6 per 100 patients per year. Our study indicates that major bleeding may occur in HHT patients receiving AT, with a substantially increased rate in those treated with anticoagulants. Further studies are needed to fully estimate the tolerability of antithrombotic drugs in HHT.
Implementation of Improved Association Rule Mining Algorithms for Fast Mining with Efficient Tree Structures on Large Datasets

ARM is a significant area of knowledge mining which enables association rules which are essential for decision making. Frequent itemset mining has a challenge against large datasets. As going on the dataset size increases the burden and time to discover rules will increase. In this paper the ARM algorithms with tree structures like FP-tree, FIN with POC tree and PPC tree are discussed for reducing overheads and time consuming. These algorithms use highly competent data structures for mining frequent itemsets from the database. FIN uses nodeset a unique and novel data structure to extract frequent itemsets and POC tree to store frequent itemset information. These techniques are extremely helpful in the marketing fields. The proposed and implemented techniques reveal that they have improved about performance by means of time and efficiency
Epistemological Dualism between Einstein's Relativity and Quantum Mechanics in the Five-Dimensional Continuum for Universe

The article is an answer to the call of Dr. Stefano Veneroni, the Catholic University of the Sacred Heart explain the relationship between the continuum and discreteness in the epistemological model of the classical theory and explain how can Quantum Mechanics explain the connection between matter, antimatter, and gravitation, while being respectful of the (phoronomic) rules of general relativity? To answer the Dr. Stefano Veneroni questions, I first propose to recognize that Minkowski's space-time, as well as an attempt Einstein in General Relativity Theory to generalize it to the case of accelerated motion, cannot be accepted as the basic model for describing the Universe. As such a basic model, the author sees the Finsler space of projective geometry, which allows combining the coordinate space and the space of impulses into a single continuum. In the article emphasized the role of the theory of global resonance in the birth of particles and the self-organization of matter in the five-dimensional continuum of
Genetic Algorithm Dependent Qos Aware Adaptive Subcarrier Allocation Scheme in Cognitive Radio Networks

Cognitive Radio Network technology is an efficient and intelligent system with the intention of detecting automatically about the availability of channels in a wireless spectrum and changing transmission parameters to facilitate more communication.In Quality of Service aware spectrum decision making system is locating the spectrum bands all the way through in view of the application necessities by means of the self-motivated nature of the spectrum bands.Here, an innovative adaptive sub-carrier allocation mechanism is proposed for Cognitive Radio Networks by rearranging the functional parameters anchored in the Proportional Resource Algorithm and Genetic Algorithm.This proposed scheme is designed to achieve a divergent performance standard for subcarrier allocation and power allocation system of the Cognitive Radio Network users. The suggested scheme is proven to be effective by maximizing the allocation of data rate for each subcarrier. Moreover, by increasing the overall network throughput, the numbers of satisfied users within bandwidth limits are maintained with the quality of service. In fact, it locates the maximum channel availability
Characterization of the glycogen branching enzyme from Pectobacterium carotovorum subsp. carotovorum LY34

A branching enzyme (EC 2.4.1.18) gene was isolated from Pectobacterium carotovorum subsp. carotovorum LY34. The branching enzyme gene, glgB, consists of an open reading frame (ORF) of 2,178 bp encoding a protein of 725 amino acids (calculated molecular weight of 83,891 Da). The ORF of the glgB gene starts with an ATG codon and ends with a TAA stop codon 3 bp upstream of glgX. The deduced amino acid sequence of GlgB has 40 to 95% similarity to known bacterial branching enzyme sequences. The enzyme is most similar to GlgB of Escherichia coli and contains the four regions conserved in the α-amylase family. The enzyme GlgB was purified and the molecular weight of the enzyme is estimated to be about 84 kDa. The glycogen branching enzyme is optimally active at pH 7 and 40°C.
Complete exclusion of nonsires in an analysis of paternity in a natural plant population using amplified fragment length polymorphism (AFLP)

The utility of the new polymerase chain reaction (PCR)‐based multilocus DNA fingerprinting technique amplified fragment length polymorphism (AFLP) for paternity analysis in natural plant populations was assessed. In a natural population of 25 plants of Persoonia mollis (Proteaceae), three AFLP primer pairs generated 147 dominant loci. Of these, 125 (85%) were polymorphic, with a mean recessive allele frequency of 0.735. The theoretical expected percentage of offspring for which all males except the true father can be excluded (PET) was 99.9% for this population. The estimates of PET drop marginally to 99.6% and 97.6% for larger populations of 100 and 1000 individuals, respectively. A preliminary investigation confirmed the power of AFLP for paternity analysis by assigning paternity, or excluding all known potential sires, for 242 of 252 (96.0%) naturally pollinated seeds. Ambiguous paternity for the remaining 10 seeds was quickly resolved by utilizing two further AFLP primer pairs, ultimately generating over 200 polymorphic loci and resulting in the exclusion of all nonsires for all 252 (100%) seeds. This study highlights the utility of AFLP for paternity analysis because: (i) it generates sufficiently large numbers of highly reproducible polymorphic loci, that are (ii) quickly and accurately scored using an automated DNA sequencer and dedicated software, and (iii) unlike microsatellites, requires no sequence knowledge so it is more easily applied to new study species.
Basis Optimisation for Multiscale Recurrent Pattern Coding

- The Multidimensional Multiscale Parser (MMP) was recently proposed has a generic lossy data compression method. As a compression algorithm, MMP combines ideas from the adaptive vector quantisation and pattern matching theories with a new and important principle: approximate pattern matching with scales. In spite of this, it will be shown here that the coding process of MMP can also be regarded as a decomposition of the original signal into a set of orthogonal, non overlapping, bases functions. In the original method, the initial dictionary uses a set of pulses with different amplitudes and scales, that correspond to the scaling function of the Haar’s wavelet. The approximation of the input signal can be regarded has a combination of these pulses, using appropriate amplitudes, shifts and scales, that are determined by the MMP’s rate-distortion controlled coding (or analysis) algo-rithm. The decoding (or synthesis) process uses the same basis functions to reconstruct the approximated signal. The proposed problem is related to whether the use of base functions other than the Haar’s scaling functions can be applied in the MMP’s framework and what should be the characteristics of these base functions (orthogonality, perfect reconstruction, etc.), that allow their use and an increased performance of the method.
Mixed-Technique, Maliciously-Secure, and Composed Multi-Party Computations

Efficient multi-party protocols are commonly composed of different sub-protocols, combining techniques such as homomorphic encryption, secret or Boolean sharing, and garbled circuits. To ensure security of the composed protocol against malicious adversaries, one needs to prove in zero-knowledge that conversions between individual techniques are correct. However, efficient ZK proofs for conversion between fully homomorphic encryption and garbled circuits are still an open problem. In this paper, we design new efficient proofs and apply them to a new class of multi-party protocols which themselves are composed out of two-party protocols. We integrate both types of compositions, compositions of fully homomorphic encryption with garbled circuits and compositions of multi-party protocols from two-party protocols. As a result, we can construct communication-efficient protocols for special problems with malicious security. To show the usefulness of this approach, we give an example scheme for private set analytics, i.e., private set disjointness. This scheme enjoys lower communication complexity than a solution based on generic multi-party protocols and lower computation cost than fully homomorphic encryption. So, our de-sign is more suitable for deployments in wide-area networks, such as the Internet, with many participants or problems with circuits of moderate or high multiplicative depth.
Mapping QTLs with additive effects and additive × additive epistatic interactions for harvest index in wheat (Triticum aestivum L.)

To map quantitative trait loci (QTL) for harvest index, 148 recombinant inbred lines and their parents, Yecora Rojo and an Iranian landrace line (No. 49), were evaluated under normal and terminal water deficit stress conditions in the research stations of Mahabad University and Miyandoab Agricultural Research Center, Iran, during 2014 and 2015. The experiment was carried out as design alpha lattice design with two replications. A linkage map of 51 retrotransposon and 177 microsatellite markers was used in this investigation. Quantitative trait loci (QTL) for additive effects and additive × additive interactions were determined by QTL Network 2.0 software using CIM and mixed-linear methods. QTL analysis revealed that under normal condition, six QTLs (R2A= 0.04 to 12.0%), two QTL × environment (E) interactions (R2AE= 6.28%), five additive × additive epistatic effects (R2AA= 0.7 to 8.68%) and 12 additive × additive × E (R2AAE= 3.76 to 11.4%) were significant. Under water deficit stress conditions, two QTLs (R2A= 5.0 to 7.0%), two additive × additive interactions (R2AA= 3.72 to 5.48%) and seven additive × additive × E interactions (R2AAE= 8.04 to 9.58) were identified. Among the eight QTLs identified, three QTLs were located on chromosome 2D, suggesting the importance of this chromosome in controlling harvest index, which may be used for marker assisted selection in breeding programs.