Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Microarray Expression Data and Phylogenetic Profiles to Learn Gene Functional Categories Using Support Vector Machines

A primary goal in biology is to understand the molecular machinery of the cell. The sequencing projects currently underway provide one view of this machinery. A complementary view is provided by data from DNA microarray hybridization experiments. Synthesizing the information from these disparate types of data requires the development of improved computational techniques. We demonstrate how to apply a machine learning algorithm called support vector machines to a heterogeneous data set consisting of expression data as well as phylogenetic pro les derived from sequence similarity searches against a collection of complete genomes. The two types of data provide accurate pictures of overlapping subsets of the gene functional categories present in the cell. Combining the expression data and phylogenetic pro les within a single learning algorithm frequently yields superior classication performance compared to using either data set alone. However, the improvement is not uniform across functional classes. For the data sets investigated here, 23-element phylogenetic pro les typically provide more information than 79-element expression vectors. Often, adding expression data to the phylogenetic pro les introduces more noise than information. Thus, these two types of data should only be combined when there is evidence that the functional classi cation of interest is clearly re ected in both data sets.
Non-Contact PIM Evaluation Method using a Standing-Wave Coaxial-Tube

A non-contact PIM measurement method is introduced into the standing wave transmission line method. DUT is tested inside the inner conductor of an opened-coaxial line which is excited in standing wave field. The electromagnetic excitation of DUT realizes non-contact measurement and eliminates electrical contacts such as soldering connection. Employment of wire with the resonant length enables low-power testing. It is also shown that PIM has a relation with its source size and position, and is less produced in small sample compared with operating wavelength.
Optimization in Cooperative Spectrum Sensing Techniques of CRN

An encouraging technology that grabs the clash between spectrum scarcity and underutilization is cognitive radio (CR), spectrum sensing is the main task of cognitive radio . Cooperative spectrum sensing overcome the adverse effect of shadowing and multipath.In this paper we are focusing on the optimization of cooperative spectrum sensing. Optimization strategy is proposed in order to optimize the overall performance by variation of SNR.In this technique we consider three parameters, spectrum sensing technique used locally ,SNRand the number of users . Decision made by all the users is sent to the fusion centerwhich estimate the final presence or absence of primary user .
Colony-level impacts of parasitoid èies on ére ants

The red imported  re ant is becoming a global ecological problem, having invaded the United States, Puerto Rico, New Zealand and, most recently, Australia. In its established areas, this pest is devastating natural biodiversity. Early attempts to halt  re ant expansion with pesticides actually enhanced its spread. Phorid  y parasitoids from South America have now been introduced into the United States as potential biological control agents of the red imported  re ant, but the impact of these  ies on  re ant populations is currently unknown. In the laboratory, we show that an average phorid density of as little as one attacking  y per 200 foraging ants decreased colony protein consumption nearly twofold and signi cantly reduced numbers of large-sized workers 50 days later. The high impact of a single phorid occurred mainly because ants decreased foraging rates in the presence of the  ies. Our experiments, the  rst (to our knowledge) to link indirect and direct effects of phorids on  re ants, demonstrate that colonies can be stressed with surprisingly low parasitoid densities. We interpret our  ndings with regard to the more complex  re ant– phorid interactions in the  eld.
Fast Transform for Decoding Both Errors and Erasures of Reed – Solomon Codes Over GF ( 2 m ) for 8 m 10

In this letter, it is shown that a fast, prime-factor discrete Fourier transform (DFT) algorithm can be modified to compute Fourier-like transforms of long sequences of 2 1 points over GF(2 ), where 8 10. Using these transforms, together with the Berlekamp–Massey algorithm, the complexity of the transform-domain decoder for correcting both errors and erasures of the Reed–Solomon codes of block length 2 1 over GF(2 ) for 8 10 is reduced substantially from the previous time-domain decoder. A computer simulation verifies these new results.
1 Identification of a novel RNA virus , lethal to Tilapia 1 2

Identification of a novel RNA virus, lethal to Tilapia 1 2 Marina Eyngor, Rachel Zamostiano, Japhette Esther Kembou Tsofack, Asaf 3 Berkowitz, Hillel Bercovier, Simon Tinman, Menachem Lev, Avshalom Hurvitz, 4 Marco Galeotti, Eran Bacharach, and Avi Eldar 5 § Equal contributors 6 7 Department of Poultry and Fish Diseases, The Kimron Veterinary Institute, Bet Dagan 8 50250, Israel, Department of Cell Research and Immunology, The George S. Wise 9 Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel, The Hebrew 10 University-Hadassah Medical School, Jerusalem 91120, Israel, Department of Animal 11 Facility, Faculty of Life sciences, Bar Ilan University, Ramat Gan 52900, Israel, Ein Gev 12 Fisheries, Kibbutz Ein Gev 14940, Israel, Dan Fish Farms, Kibbutz Dan, Upper Galilee 13 12245, Israel, Department of Food Science, Section of Veterinary Pathology, University 14 of Udine, Udine 33100, Italy 15 16 Running head: Novel RNA virus of tilapines. 17
Diagnostyka i leczenie padaczki u osób dorosłych — rekomendacje Polskiego Towarzystwa Neurologicznego

W ostatnich latach zmienily sie w Polsce zasady refundacji lekow stosowanych w padaczce. Umozliwiają one wybor terapii zgodnie z regulami opracowanymi przez miedzynarodowe grupy ekspertow. Skuteczne leczenie padaczki zalezy od prawidlowego zdefiniowania typu napadow padaczkowych lub określonego zespolu padaczkowego. W artykule przedstawiono aktualne zalecenia diagnostyczne i terapeutyczne w leczeniu padaczki. Dokonano rowniez adaptacji rekomendacji miedzynarodowych do warunkow systemu opieki medycznej w Polsce.
ITLS-WP-1707 Smartphone-based Travel Surveys : A Review

Interest continues to grow in the use of smartphones for travel survey purposes. Their locational and interactive potential combined with their ubiquity and pragmatism as something people are likely to keep with them and charged, makes them particularly appealing. However, several challenges remain, particularly around battery life, user acceptance as an instrument for tracking mobility and a fundamental lack of concordance on how travel survey apps should be designed. The current paper provides a review of smartphone-based travel survey apps focusing on issues around functionality, participant burden, processing requirements, data quality and costs. We identify a typology of smartphone apps, that all passively collect route information but vary in the level of automation and user interaction required. All of the apps reviewed report reasonable levels of participant satisfaction irrespective of the levels of automation and user-app interaction required. However, the accuracy with which information is accurately inferred appears to vary markedly, largely a function of the quality of data collected, which in turn is heavily influenced by the make/model of phone, and the processing algorithms employed. One common issue is battery drain, which continues to be an issue for both highly automated apps and those requiring significant user interaction. Looking forward, while the intuitive appeal of smartphones will continue to grow, we argue that developments have been constrained by attempts to integrate existing survey approaches within a smartphone environment. More attention needs to be given to the design of apps that engage users to start and finish the survey, focusing on ‘smart’ use of the sensors and processing routines to minimise battery consumption and on providing additional benefits for users.
Reflections from Pre-Service Teachers Mathematics Teaching Process

Pedagogical Content Knowledge (PCK) has been considered to be the most important factor for identifying the role of the teacher in carrying out effective teaching. This paper examines, with respect to the components of PCK, the types of difficulties that a group of pre-service teachers encountered during the process of designing teaching activities. For this purpose, 8 pre-service teachers (4 elementary mathematics and 4 classroom teachers) are observed whilst teaching mathematics during the Teaching Practicum course and are interviewed. The study reveals that both groups of pre-service teachers had similar problems in teaching practices. Pre-service teachers experienced difficulties in determining the activities with regard to prior knowledge of the students, deciding the difficulty level of the activities and sorting them, informing students about the purpose of the activities, conducting activities according to their perceived purposes and making transitions between activities.
Validation of SRTM Elevations Over Vegetated and Non-vegetated Terrain Using Medium-Footprint Lidar

The Shuttle Radar Topography Mission (SRTM) generated one of the most-complete high-resolution digital topographic data sets of the world to date. The elevations generated by the on-board C-band sensor represent surface elevations in “bare earth” regions, and the elevations of various scatterers such as leaves and branches in other regions. Elevations generated by a medium-footprint (� 10 m diameter) laser altimeter (lidar) system known as NASA’s Laser Vegetation Imaging Sensor (LVIS) were used to assess the accuracy of SRTM elevations at study sites of variable relief, and landcover. Five study sites in Maine, Massachusetts, Maryland, New Hampshire, and Costa Rica were chosen where coincident LVIS and SRTM data occur. Both ground and canopy top lidar elevations were compared to the SRTM elevations. In “bare earth” regions, the mean vertical offset between the SRTM elevations and LVIS ground elevations varied with study site and was approximately 0.0 m, 0.5 m, 3.0 m, 4.0 m, and 4.5 m at the Maine, Maryland, Massachusetts, New Hampshire, and Costa Rica study sites, respectively. In vegetated regions, the mean vertical offset increased, implying the phase center fell above the ground, and the offset varied by region. The SRTM elevations fell on average approximately 14 m below the LVIS canopy top elevations, except in Costa Rica where they were approximately 8 m below the canopy top. At all five study sites, SRTM elevations increased with increasing vertical extent (i.e., the difference between the LVIS canopy top and ground elevations and analogous to canopy height in vegetated regions). A linear relationship was found sufficient to describe the relationship between the SRTM-LVIS elevation difference and canopy vertical extent.
Towards entanglement of purification for conformal field theories

We argue that the entanglement of purification for two dimensional holographic CFT can be obtained from conformal blocks with internal twist operators. First, we explain our formula from the view point of tensor network model of holography. Then, we apply it to bipartite mixed states dual to subregion of AdS${}_3$ and the static BTZ blackhole geometries. The formula in CFT agrees with the entanglement wedge cross section in the bulk, which has been recently conjectured to be equivalent to the entanglement of purification.
An Interoperability System for User Models in Adaptive Educational Hypermedia

The integration of adaptive educational systems is changing from an interesting research problem into an important practical task. One of the major challenges that need to be accepted on the way is the development of mechanisms for student model integration. In this paper we propose an approach for aligning overlay models of students’ knowledge collected by different educational tools relying on different domain representations. The approach is based on common protocols for evidence communication and manual mapping of underlying domain models. This approach has been applied for integration of two existing educational systems in the framework of undergraduate Java course.
NFκB is an Essential Intermediate in the Activation of Endothelial Cells by Anti-β2-Glycoprotein 1 Antibodies

Summary Antiphospholipid antibodies (aPLA) are associated with thrombophilia and recurrent pregnancy loss. They bind directly to anionic phospholipids or via phospholipid-binding proteins such as β2-glycoprotein 1 (β2GP1). The underlying mechanisms by which aPLA induce a thrombophilic phenotype are not well understood. The present work was done to determine whether antibodies to β2GP1 activate endothelial cells (EC) and whether NFκB is involved in this activation. Incubation of EC with these antibodies resulted in a redistribution of NFκB from the cytoplasm to the nucleus after a delay of several hours. This was accompanied by an increased expression of tissue factor and of the leukocyte adhesion molecules ICAM-1, VCAM-1 and E-selectin. Inhibition of the nuclear translocation of NFκB abolished the response to these antibodies. In comparison to anti-β2GP1 antibodies, incubation of EC with TNF resulted in a more rapid (within 30 minutes) redistribution of NFκB and a more pronounced expression of tissue factor and of the leukocyte adhesion molecules. The slower response to the antibodies as compared to TNF suggests that the NFκB response to anti-β2GP1 antibodies is indirect. Taken together our results imply that NFκB is an essential intermediate in the activation of EC by anti-β2GP1 antibodies.
Data Hallucination , Falsification and Validation using Generative Models and Formal Methods by

Data Hallucination, Falsification and Validation using Generative Models and Formal Methods by José Rafael Valle Gomes da Costa Doctor of Philosophy in Machine Listening and Improvisation and Designated Emphasis in Computational and Data Science and Engineering University of California, Berkeley Professor Edmund Campion, Chair Professor Sanjit Seshia, Co-Chair The increasing pervasiveness and fast-paced development of deep learning (DL) systems with human-like perception, agency and creativity has brought concern related to information reliability: the generative models that have surprised and confused humans with their high quality media hallucinations can be used to fool other computer systems and humans to believe that the generated media is real. In addition to developing strategies to increase the quality of the data produced with generative models, specially generative adversarial networks (GANs), our research community has been exploring mechanisms to better understand and control the data they generate. In the context of data falsification, formal methods (FM) and formal specifications (FS) can be used to prevent adversarial attacks by verifying that some potentially adversarial data follows the specifications of the real data. Formal methods and formal specifications can also be used to guide the output of a generator such that, as much as possible, the generated data fulfills the specifications of the real data. Although formal methods have been largely and sucessfuly used in the field of software and hardware engineering, their interaction with Artificial Neural Networks (ANNs) poses many challenges that are yet to be solved. In this thesis, we address challenges related to hallucination, falsification and validation of data using generative models and formal methods. We start by focusing on artistic applications related to music by developing an automata-based system for machine improvisation with formal specifications. We briefly describe the Control Improvisation framework and describe its application to machine improvisation with formal specifications. We propose data abstractions derived from symbolic music data and describe strategies for mining specifications from them. We then use the mined specification to summarize a musical style and guide the improvisation of a generative model. Next, we focus on security applications in speech synthesis and investigate the efficiency of generative models such as WaveNet, SampleRNN and our own GAN
MODELING FOR SOIL AND WATER RESEARCH AND MANAGEMENT : CURRENT STATUS AND NEEDS FOR THE 21 ST CENTURY

Quantitative system approaches, provided by process‐based models of agricultural systems, are essential for optimizing the use of increasingly limited water and soil resources, guiding tactical management, and addressing the environmental concerns and global issues of the 21st century. Agricultural engineers have made significant contributions in the past to model development and applications in soil and water research, irrigation design, and water management, and they are uniquely capable of making the much‐needed and exciting further model enhancements. In this brief review, we present: (1) the current status of system model development and applications in soil and water research and management, with examples from the USDA‐ARS Root Zone Water Quality Model (RZWQM); (2) lessons learned from RZWQM development and applications; and (3) future needs and directions in system model enhancements and applications to make them more effective. We make a strong case for international collaborations among modelers and experimentalists and for a common development/applications protocol and platform for the future.
Movement Patterns and Population Genetics of the American Horseshoe Crab in Relation to Long Island Sound Conservation Strategies.

The Connecticut Department of Environmental Protection (CTDEP) established three no-harvest zones for the horseshoe crab ( Limulus polyphemus ) population as part of a conservation plan for the species. Data from a long-term mark/recapture study of horseshoe crabs in conjunction with a microsatellite-based genetic survey of the population were analyzed to determine if this plan was appropriate to conserve genetic diversity and broaden our knowledge of movement patterns of Limulus in Long Island Sound (LIS). To date, ~53,000 crabs have been tagged over a 10 year period through the Project Limulus program with an annual average recapture rate of 12 to 15%. In addition to the ongoing tagging study, 187 horseshoe crabs collected from 5 distinct sites spanning the geographic extent of Long Island Sound (Rye and Mt. Sinai, NY; Milford, New Haven, and Groton, CT) were genotyped for 11 microsatellite loci to determine the overall genetic health of the LIS population and determine if regional genetic differentiation was sufficient to identify sub-populations within this region. The genetic data indicates that the LIS Limulus population is genetically homogenous with no signs of inbreeding and substantially similar to other Mid-Atlantic populations. Data from the mark-recapture study indicate significant migration east and west along the north shore of LIS relative to the original tag site and in addition cross LIS migrations have also been observed. Therefore, the locations of the established no-harvest zones are appropriate to conserve genetic diversity. However, based on their tri-state migration patterns, a multi-state management strategy is needed for the LIS horseshoe crab population.
EFFECT OF EXTERNAL FIELD ON THE VARIATION OF MAGNETIC MEMORY SIGNALS

Tensile-tensile fatigue tests of 16MnR steel sheet specimens with prefabricated flaws were carried out to measure spontaneous stray field signals of stress concentration zones by GMR sensor, and excitation device was used to make external field excitation for sheet specimens. The results showed that the tangential component of stray field signals can still be considered as generalized magnetic memory signals when tests were conducted in external field without load. Magnetic memory signals were strengthened due to external magnetic excitation, improving sensitivity of detection system. The tangential component of stray field signals presented the maximum value at the stress concentration zones, which increased as cycle number increase, and the growth rate isn’t identical in different stages of fatigue damage.
Natural products as antioxidants.

The addition of synthetic antioxidants to oils and/or foods is one of the most efficient ways to prevent lipid oxidation. However, the safety of synthetic additives has been questioned stimulating the evaluation of naturally occurring compounds with antioxidative properties. Although there is no assurance of the safety of natural antioxidants, there is some comfort knowing that such antioxidants are purified from natural products that have been consumed for generations. Correspondence/Reprint request: Dr. Zygadlo J.A, Instituto Multidisciplinario de Biología Vegetal CONICET UNC. , Cátedra de Química Orgánica, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Avenida Velez Sarsfield 1611, X5016 GCA Córdoba, Argentina. E-mail. jzygadlo@efn.uncor. edu Maestri D.M. et al. 106 Phenolic compounds in plants are recognized as important compounds in conferring stability against oxidation. Natural antioxidant phenolics can be classified into a lipophilic group, tocopherols, and a hydrophilic group, including simple phenolics, phenolic acids, anthocyanins, flavonoids and tannins. Even though chemists have elucidated the structures of thousands of phenolics, there are still many compounds that have not yet been fully characterized and they are referred as phenolic extracts. In this ways berry extracts, aromatic plant extracts, essential oils and their components are gaining interest because of their relatively safe and wide acceptance by consumers. Many authors have reported antioxidant and radical-scavenging properties by berries, spices and essential oils. In this work we reviewed the most important groups of natural antioxidants, with some peculiarities related to chemical composition.
Bounds of efficiency at maximum power for linear, superlinear and sublinear irreversible Carnot-like heat engines

The efficiency at maximum power (EMP) of irreversible Carnot-like heat engines is investigated based on the weak endoreversible assumption and the phenomenologically irreversible thermodynamics. It is found that the weak endoreversible assumption can reduce to the conventional one for the heat engines working at maximum power. Carnot-like heat engines are classified into three types (linear, superlinear, and sublinear) according to different characteristics of constitutive relations between the heat transfer rate and the thermodynamic force. The EMPs of Carnot-like heat engines are proved to be bounded between ηC/2 and ηC/(2−ηC) for the linear type, 0 and ηC/(2−ηC) for the superlinear type, and ηC/2 and ηC for the sublinear type, respectively, where ηC is the Carnot efficiency.