Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution-driven attenuation of alphaviruses highlights key glycoprotein determinants regulating viral infectivity and dissemination

Understanding the fundamental mechanisms of arbovirus transmission and pathogenesis is essential to develop new strategies for treatment and prevention. We previously took an in vivo evolution-based approach and identified the chikungunya virus E1 glycoprotein residue 80 to play a critical role in viral transmission and pathogenesis. In this study, we address the genetic robustness and function of position 80 and demonstrate that this highly conserved residue is a key determinant in alphavirus infectivity and dissemination through modulation of viral fusion and cholesterol dependence. In addition, in studying the evolution of position 80, we identified a network of glycoprotein residues, including epidemic determinants, that regulate virus dissemination and infectivity. These studies underscore the importance of taking evolution-based approaches to not only identify key viral determinants driving arbovirus transmission and pathogenesis but also to uncover fundamental aspects of arbovirus biology.
An adaptive clocking control circuit with 7.5% frequency gain for SPARC processors

This paper presents an adaptive clocking control circuit to mitigate the processor performance degradation due to on-die supply voltage droops. The circuit utilizes multi-path TDC to reduce quantization errors and thermometer code-based data processing to eliminate latches, which shortens frequency modulation latency. This results in faster frequency/supply tracking. A test chip including the adaptive clocking control circuit with SPARC processor cores was fabricated in a 20-nm CMOS process. Experimental measurements demonstrated that the adaptive clocking control circuit achieved the state-of-the-art frequency gain of 7.5%, resulting in the operating frequency as high as 5 GHz.
[Multicomponent physical exercise program: Vivifrail].

Los beneficios del ejercicio físico en el envejecimiento, y específicamente en la fragilidad, se asocian con una disminución del riesgo de mortalidad, enfermedades crónicas, institucionalización y deterioro cognitivo y funcional. El tipo de ejercicio físico más beneficioso en el anciano frágil es el denominado entrenamiento multicomponente. Este tipo de programas combina entrenamiento de fuerza, resistencia, equilibrio y marcha y es el que más ha demostrado mejorías en la capacidad funcional y que es un elemento fundamental para el mantenimiento de la independencia en las actividades básicas de la vida diaria (ABVD) de los ancianos. Los objetivos deberían centrarse, por lo tanto, en mejorar dicha capacidad funcional a través de mejorías en el equilibrio y la marcha y la disminución del riesgo y del número de caídas. El Programa Multicomponente de Ejercicio Físico Vivifrail (www.vivifrail.com) intenta proporcionar los conocimientos necesarios para la prescripción de ejercicio físico en la prevención de la fragilidad y el riesgo de caídas en ancianos.
Deep-water agglutinated foraminifera in Paleogene hemipelagic sediments of the Magura Basin in the Sucha Beskidzka area : variegated shales of the Łaboa Shwale Formation

Sedimentation of the variegated shales of the Łabowa Shale Formation in the Siary Zone of the Magura Basin commenced during the late Paleocene and lasted up to the middle Eocene. Quiet sedimentation of shales, mostly from a free fall suspension regime below the CCD, was favorable for the development of agglutinated foraminiferal communities. The Paleocene shales contain characteristic rich assemblages of the Rzehakina fissistomata Zone, followed by poor Recurvoides and Glomospira assemblages of the latest Paleocene and earliest Eocene connected with the LPTM crisis interval. These are followed by post-crisis Karrerulina assemblages, as well as assemblages of the Saccamminoides carpathicus Zone (Early Eocene) and the Reticulophragmium amplectens Zone (middle Eocene). Numerous very thin bentonite layers in the upper variegated shales subdivision of the Łabowa Shale Formation are found. The foraminiferal assemblages from these bentonite intercalations show low taxonomic diversity with numerous juvenile forms and increased numbers of Glomospira charoides (Jones & Parker).
Chemical environment of water molecules adsorbed on the anatase surface: quantum chemical study

Theoretical studies of the interactions of an oxygen molecule with the surface of a solid phase are of great importance for understanding the mechanisms of reactions involving oxygen on a solid surface. In this work, the spatial and electronic structure of oxygen defects and nitrogen impurity centers of the anatase surface and their manifestation in water adsorption are investigated. The anatase surface was simulated for by clusters of the composition Ti14H22O39 (defect-free face (001)), Ti14H22O38 (surface with oxygen vacancy), and Ti14H22N2O36 (surface with both oxygen vacancy and incorporated nitrogen), terminated with boundary hydrogen atoms. Calculations on the total energy of the optimized geometric structures of the model TiO2 clusters and on the corresponding theoretical XPS spectra were performed using the density functional theory (DFT) method and the B3LYP hybrid functional with an extended valence-split basis set 6-31G (d, p). In the XPS spectra of O1s, each peak can be attributed to a specific type of oxygen atoms in the initial structure, dependent on their coordination environment. The substitution of nitrogen atoms for oxygen ones leads to a complication of the spectrum. Simultaneous replacement of nitrogen atoms for oxygen ones and presence of an oxygen vacancy leads to further complication of the XPS spectrum. The different structure of the adsorption complexes of water molecules on the anatase surface formed due to the HOH···O hydrogen bond (this displaces by 0.05 eV all the peaks in the XPS spectrum) or the coordination bond Ti···OH2 has been also considered. Based on the analysis of theoretical results, the role of various forms of defects in the adsorption of water on the anatase surface is considered. The results of quantum chemical studies of molecular models simulated for the bulk and surface of titanium dioxide are compared with the literature data available.
Investigation of rare earth upconversion fluorescent nanoparticles in biomedical field

Abstract Rare earth upconversion nanoparticles (UCNPs) with the superior performance in the biomedical field have attracted great attention. Due to the good light stability, low toxicity, deep tissue penetration and excellent bio-compatibility, UCNPs display great potential for development in the biomedical field. Excellent related reports are increasing year by year, like molecular sensing, bioimaging and therapeutics. In this paper, the preparation, modification, application of upconversion fluorescent nanoparticles and the latest research results in the field of biomedical materials have been reported in detail. Graphical abstract: In this paper, we systematically summarize and describe the preparation, modification, application and latest discovery in biomedical field of rare earth upconversion nanoparticles (UCNP). Due to the good light stability, low toxicity, deep tissue penetration and excellent biocompatibility, UCNPs display superior performance for the development of biomedical field in cancer therapy. Our work will certainly inspire researchers in related fields to create more meaningful upconversion nanomaterials and do more contributions to human cancer treatment research.
Micro-Patterning Cells on Polyacrylamide Hydrogels

II ACKNOWLEDGEMENTS III AUTHORSHIP IV CHAPTER 1—INTRODUCTION 9 CHAPTER 2—LITERATURE REVIEW 11 2.1 THE EXTRACELLULAR MATRIX 11 2.2 ECM STIFFNESS 11 2.3 COLLAGEN & THE ECM 12 2.4 HYDROGELS & POLYACRYLAMIDE 13 2.5 NIH/3T3 CELLS 13 2.6 CELL SIGNALING 15 2.7 MICRO-PATTERNING 18 2.8 TUMORS 20 3— PROJECT STRATEGY 21 3.1 INITIAL CLIENT STATEMENT 22 3.2 DESIGN REQUIREMENTS 23 3.3 REVISED CLIENT STATEMENT 28 3.4 PROJECT APPROACH 29 CHAPTER 4— DESIGN PROCESS 31 4.1 NEEDS ANALYSIS 322 4.2 ALTERNATIVE DESIGNS 37 4.3 SELECTION OF FINAL DESIGNS 47 4.4 FINAL DESIGN CONSIDERATIONS 52 CHAPTER 5— FINAL DESIGN 57 5.1 METHODOLOGY 57 5.2 VERIFICATION 65 CHAPTER 6— FINAL DESIGN VALIDATION 67 6.1 RESULTS 67 6.2 CELL MEASUREMENTS 77 CHAPTER 7— DISCUSSION 79
Privacy in microblogging online social networks: issues and metrics

Samia Oukemeni Internet Interdisciplinary Institute (IN3) Universitat Oberta de Catalunya CYBERCAT Center for Cybersecurity Research of Catalonia Barcelona, Spain soukemeni@uoc.edu Helena Rifà-Pous Internet Interdisciplinary Institute (IN3) Universitat Oberta de Catalunya CYBERCAT Center for Cybersecurity Research of Catalonia Barcelona, Spain hrifa@uoc.edu Joan Manuel Marquès Puig Internet Interdisciplinary Institute (IN3) Universitat Oberta de Catalunya Barcelona, Spain jmarquesp@uoc.edu
Multi-Stage Stochastic Programming to Joint Economic Dispatch for Energy and Reserve With Uncertain Renewable Energy

To address the uncertain renewable energy in the day-ahead optimal dispatch of energy and reserve, a multi-stage stochastic programming model is established in this paper to minimize the expected total costs. The uncertainties over the multiple stages are characterized by a scenario tree and the optimal dispatch scheme is cast as a decision tree which guarantees the flexibility to decide the reasonable outputs of generation and the adequate reserves accounting for different realizations of renewable energy. Most importantly, to deal with the “Curse of Dimensionality” of stochastic programming, stochastic dual dynamic programming (SDDP) is employed, which decomposes the original problem into several sub-problems according to the stages. Specifically, the SDDP algorithm performs forward pass and backward pass repeatedly until the convergence criterion is satisfied. At each iteration, the original problem is approximated by creating a linear piecewise function. Besides, an improved convergence criterion is adopted to narrow the optimization gaps. The results on the IEEE 118-bus system and real-life provincial power grid show the effectiveness of the proposed model and method.
Ecological Revelations: Recovering the Unseen

Chet Bowers’ contributions to education are numerous and provocatively persistent. Using the title Ecological Revelations: Recovering the Unseen to frame my examination, I explore four concepts central to Bowers’ work: oikos, intelligence, language, and cultural maps. First, I reflect on the ways in which Bowers’ conceptualization of the concepts created ecological meaning and discursive relevance in education over the course of his scholarship, which spanned more than four decades. I highlight how Bowers’ development of the ideas, each on their own and collectively as a coherent whole, not only challenged assumed cultural ways of being for educators, but importantly, provided an alternative theoretical framework to make new sense of how education (re)produces culture. I examine these concepts in relation to Bowers’ critique of STEM (science, technology, engineering, mathematics), the theoretical dilemmas they raise, and the ecological questions that emerge. Finally, I inquire into how the four featured ideas, STEM, and STEM education play out in the context of a community commons. Here, additional concepts such as collaboration, innovation, renewal, and relationality expand Bowers’ theory, which, in turn, not only give rise to ecological alternatives for STEM and STEM education but for the cultural commons as well.
Improving the precision and accuracy of animal population estimates with aerial image object detection

Animal population sizes are often estimated using aerial sample counts by human observers, both for wildlife and livestock. The associated methods of counting remained more or less the same since the 1970s, but suffer from low precision and low accuracy of population estimates. Aerial counts using cost‐efficient Unmanned Aerial Vehicles or microlight aircrafts with cameras and an automated animal detection algorithm can potentially improve this precision and accuracy. Therefore, we evaluated the performance of the multi‐class convolutional neural network RetinaNet in detecting elephants, giraffes and zebras in aerial images from two Kenyan animal counts. The algorithm detected 95% of the number of elephants, 91% of giraffes and 90% of zebras that were found by four layers of human annotation, of which it correctly detected an extra 2.8% of elephants, 3.8% giraffes and 4.0% zebras that were missed by all humans, while detecting only 1.6 to 5.0 false positives per true positive. Furthermore, the animal detections by the algorithm were less sensitive to the sighting distance than humans were. With such a high recall and precision, we posit it is feasible to replace manual aerial animal count methods (from images and/or directly) by only the manual identification of image bounding boxes selected by the algorithm and then use a correction factor equal to the inverse of the undercounting bias in the calculation of the population estimates. This correction factor causes the standard error of the population estimate to increase slightly compared to a manual method, but this increase can be compensated for when the sampling effort would increase by 23%. However, an increase in sampling effort of 160% to 1,050% can be attained with the same expenses for equipment and personnel using our proposed semi‐automatic method compared to a manual method. Therefore, we conclude that our proposed aerial count method will improve the accuracy of population estimates and will decrease the standard error of population estimates by 31% to 67%. Most importantly, this animal detection algorithm has the potential to outperform humans in detecting animals from the air when supplied with images taken at a fixed rate.
Cooperativity between the 3’ untranslated region microRNA binding sites is critical for the virulence of eastern equine encephalitis virus

Eastern equine encephalitis virus (EEEV), a mosquito-borne RNA virus, is one of the most acutely virulent viruses endemic to the Americas, causing between 30% and 70% mortality in symptomatic human cases. A major factor in the virulence of EEEV is the presence of four binding sites for the hematopoietic cell-specific microRNA, miR-142-3p, in the 3’ untranslated region (3’ UTR) of the virus. Three of the sites are “canonical” with all 8 seed sequence residues complimentary to miR-142-3p while one is “non-canonical” and has a seed sequence mismatch. Interaction of the EEEV genome with miR-142-3p limits virus replication in myeloid cells and suppresses the systemic innate immune response, greatly exacerbating EEEV neurovirulence. The presence of the miRNA binding sequences is also required for efficient EEEV replication in mosquitoes and, therefore, essential for transmission of the virus. In the current studies, we have examined the role of each binding site by point mutagenesis of seed sequences in all combinations of sites followed by infection of mammalian myeloid cells, mosquito cells and mice. The resulting data indicate that both canonical and non-canonical sites contribute to cell infection and animal virulence, however, surprisingly, all sites are rapidly deleted from EEEV genomes shortly after infection of myeloid cells or mice. Finally, we show that the virulence of a related encephalitis virus, western equine encephalitis virus, is also dependent upon miR-142-3p binding sites. Author Summary Eastern equine encephalitis virus (EEEV) is one of the most acutely virulent mosquito-borne viruses in the Americas. A major determinant of EEEV virulence is a mammalian microRNA (miRNA) that is primarily expressed in myeloid cells, miR-142-3p. Like miRNA suppression of host mRNA, miR-142-3p binds to the 3’ untranslated region (UTR) of the EEEV genome only in myeloid cells suppressing virus replication and the induction of the innate immune response. In this study, we used point mutations in all four miR-142-3p binding sites in the EEEV 3’ UTR to understand the mechanism behind this miRNA suppression. We observed that decreasing the number of miR-142-3p binding sites leads to virus escape and ultimately attenuation in vivo. Furthermore, another virus, western equine encephalitis virus, also encodes miR-142-3p binding sites that contribute to virulence in vivo. These results provide insight into the mechanism of how cell-specific miRNAs can mediate suppression of virus replication.
Path planning and re-planning of lane change manoeuvres in dynamic traffic environments

Automatic lane change is of utmost importance in designing autonomous vehicles and driver assistant systems. In this study, a novel path for lane change manoeuvres, based on mathematical functions, is introduced. To obtain a suitable path for lane change manoeuvres, four functions, namely quintic, septic, sinusoidal, and tangent functions, were examined. The analysis revealed that, according to the ISO Standards and peak acceleration criterion, a quintic function has the advantage of passenger comfort over other path functions. After choosing the appropriate path, an algorithm for re-planning the lane change path, based on dynamic traffic conditions, was proposed. The simulation results show that the proposed algorithm is capable of designing the path in various traffic conditions. Moreover, the algorithm can navigate the vehicle to the initial lane, if the manoeuvre is not possible. Our analytical results showed that the designed paths are suitable, comfortable, and safe.
Phytophthora ramorum and Phytophthora gonapodyides Differently Colonize and Contribute to the Decomposition of Green and Senesced Umbellularia californica Leaves in a Simulated Stream Environment

Plant pathogenic as well as saprotrophic Phytophthora species are now known to inhabit forest streams and other surface waters. How they survive and function in aquatic ecosystems, however, remains largely uninvestigated. Phytophthora ramorum, an invasive pathogen in California forests, regularly occurs in forest streams, where it can colonize green leaves shed in the stream but is quickly and largely succeeded by saprotrophically competent clade 6 Phytophthora species, such as Phytophthora gonapodyides. We investigated, using controlled environment experiments, whether leaf litter quality, based on senescence, affects how P. ramorum and P. gonapodyides compete in leaf colonization and to what extent each species can contribute to leaf decomposition. We found that both Phytophthora species effectively colonized and persisted on green or yellow (senescing) bay leaves, but only P. gonapodyides could also colonize and persist on brown (fully senesced and dried) leaves. Both Phytophthora species similarly accelerated the decomposition of green leaves and yellow leaves compared with non-inoculated controls, but colonization of brown leaves by P. gonapodyides did not affect their decomposition rate.
Investigate the Performance of WordNet and Association Rules for Hard Clustering Web Document

A powerful technique that has been widely used to organizing a large number of web documents into a small number of general and meaningful clusters is Document Clustering. High dimensionality, scalability, accuracy, extracting semantics relations from texts and meaningful cluster labels are the major challenges for document clustering. To improve the document clustering quality, we intend to introduce an effective methodological system using association rules instead of frequent term sets for clustering web documents into different topical groups called Hard Document Clustering using Association Rules (HDCAR). HDCAR characterized by high performance in the organization of web documents and navigates them effectively in order to keep up with the explosive growth of the number and size of web documents. Association Rule has the equally important advantage of having a higher descriptive power compared to single words (frequent term sets). Moreover, the external knowledge from both WordNet synonym and hypernyms will be used to enhance the ‘‘bag of words’’ used before the clustering process and to assist the label generation procedure following the clustering process. Then, Multi-Hash Tire Association Rule (MHTAR) algorithm is
Heart Rate Variability Biofeedback Stress Relief Program for Depression*. A Replicated Single-Subject Design.

BACKGROUND Depressive disorders often have a chronic course and the efficacy of evidence-based treatments may be overestimated. OBJECTIVE To examine the effectiveness of the Heart Rate Variability Stress Reduction Program (SRP) as a supplement to standard treatment in patients with depressive disorders. METHODS The SRP was individually administered in eight weekly sessions. Seven participants completed the full protocol and were enrolled in a single-subject ABA multiple baseline experimental design. To perform interrupted time-series analyses, daily measures were completed in a diary (depression, resilience, happiness, heart coherence and a personalized outcome measure). RESULTS Five out of seven patients improved in depressed mood and/or a personalized outcome measure. The effect of treatment was reversed in four patients during the withdrawal phase. One patient reliably improved on depression, whereas two patients recovered on autonomy and one on social optimism. No consistent relationship was found between the heart rate variability-related level of coherence and self-reported mood levels. CONCLUSIONS The SRP is beneficial in some domains and for some patients. A prolonged treatment or continued home practice may be required for enduring effects. The intervention had more clinical impact on resilience-related outcome measures than on symptoms. The small sample size does not permit generalization of the results. We recommend future investigation of the underlying mechanisms of the SRP.
A Bag of Concepts Approach for Biomedical Document Classification Using Wikipedia Knowledge

Summary Objectives: The ability to efficiently review the existing literature is essential for the rapid progress of research. This paper describes a classifier of text documents, represented as vectors in spaces of Wikipedia concepts, and analyses its suitability for classification of Spanish biomedical documents when only English documents are available for training. We propose the cross-language concept matching (CLCM) technique, which relies on Wikipedia interlanguage links to convert concept vectors from the Spanish to the English space. Methods: The performance of the classifier is compared to several baselines: a classifier based on machine translation, a classifier that represents documents after performing Explicit Semantic Analysis (ESA), and a classifier that uses a domain-specific semantic an- notator (MetaMap). The corpus used for the experiments (Cross-Language UVigoMED) was purpose-built for this study, and it is composed of 12,832 English and 2,184 Spanish MEDLINE abstracts. Results: The performance of our approach is superior to any other state-of-the art classifier in the benchmark, with performance increases up to: 124% over classical machine translation, 332% over MetaMap, and 60 times over the classifier based on ESA. The results have statistical significance, showing p-values < 0.0001. Conclusion: Using knowledge mined from Wikipedia to represent documents as vectors in a space of Wikipedia concepts and translating vectors between language-specific concept spaces, a cross-language classifier can be built, and it performs better than several state-of-the-art classifiers.