Miracle-dz/UniFAR-FTUs huggingface dataset:
FR3: A Fuzzy Rule Learner for Inducing Reliable Classifiers

This paper introduces a fuzzy-rule-based classification method called fuzzy round robin [repeated incremental pruning to produce error reduction (RIPPER)] (FR3). As the name suggests, FR3 builds upon the RIPPER algorithm, a state-of-the-art rule learner. More specifically, in the context of polychotomous classification, it uses a fuzzy extension of RIPPER as a base learner within a round robin scheme, and thus, can be seen as a fuzzy variant of the R3 learner that has recently been introduced in the literature. A key feature of FR3, in comparison with its nonfuzzy counterpart, is its ability to represent different facets of uncertainty involved in a classification decision in a more faithful way. FR3 thus provides the basis for implementing ldquoreliable classifiersrdquo that may abstain from a decision when not being sure enough, or at least indicate that a classification is not fully supported by the empirical evidence at hand. Besides, our experimental results show that FR3 outperforms R3 in terms of classification accuracy, and therefore, suggest that it produces predictions that are not only more reliable but also more accurate. The superb classification performance of FR3 is furthermore confirmed by comparing it to other state-of-the-art (fuzzy) rule learners.
Estimating Time to the Common Ancestor for a Beneficial Allele

The haplotypes of a beneficial allele carry information about its history that can shed light on its age and putative cause for its increase in frequency. Specifically, the signature of an allele’s age is contained in the pattern of local ancestry that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to approaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to provide a global perspective on the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.
Hydrogel-Electrospun Fiber Mat Composite Materials for the Neuroprosthetic Interface

ii Dedication . iv Acknowledgments. v Vita . vii List of Tables . xv List of Figures . xvi Chapter 1: Introduction . 1 1.1 Overview of the central nervous system (CNS) and CNS injury . 2 1.2 Limitations of neuron-electronic device interfaces . 6 1.3 Current strategies and clinical demands . 10 1.3. 1 Development of microelectrode array technology . 10 1.3. 2 Investigations on electrode geometry and implantation techniques . 11 1.3. 3 Haptotactic and chemotactic cues for electrode biocompatibility improvement . 12 1.4 Dissertation overview . 14 Chapter 2: Hydrogels, Electrospun Fibrous Scaffolds and Their Applications in Neural Engineering . 19 2.1 Hydrogels . 20 2.1.1 Hydrogel structure, design and material selection . 20 2.1.1.1 Synthetic hydrogels . 23 2.1.1.2 Natural hydrogels . 26 2.1.1.3 Hybrid hydrogels . 28 2.1.2 Hydrogels in neural engineering . 29 2.1.2.1 Hydrogels’ scaffold architecture in neural engineering . 29
Improvement of the sterile insect technique for codling moth Cydia pomonella (Linnaeus) (Lepidoptera Tortricidae) to facilitate expansion of field application

The codling moth Cydia pomonella (L.) (Lepidoptera Tortricidae) is a key pest of pome fruit (apple, pear and quince) and walnut orchards in most temperate regions of the world. Efforts to control the codling moth in the past mostly relied on the use of broad spectrum insecticide sprays, which has resulted in the development of insecticide resistance, and the disruption of the control of secondary pests. In addition, the frequent reliance and use of these insecticides are a constant threat to the environment and human health. Consequently, there have been increased demands from the growers for the development of codling moth control tactics that are not only effective but also friendly to the environment. In that respect, the sterile insect technique (SIT) and its derivative, inherited sterility (IS), are, together with mating disruption and granulosis virus, among the options that offer great potential as cost‐effective additions to available control tactics for integration in area‐wide integrated pest‐management approaches. In support of the further development of the SIT/IS for codling moth control, the Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture implemented a 5‐year Coordinated Research Project (CRP) entitled ‘Improvement of codling moth SIT to facilitate expansion of field application’. Research focussed on sterile codling moth quality and management (e.g. mobility and life‐history traits in relation to rearing strategy, dispersal, flight ability, radiosensitivity and mating compatibility) and a better understanding of the basic genetics of codling moth to assist the development of genetic sexing strains (e.g. cytogenetics, the development of dominant conditional lethal mutations, molecular characterization of the sex chromosomes, sex identification in embryos and cytogenetic markers). The results of the CRP are presented in this special issue.
Immediate effect of transcranial direct current stimulation combined with functional electrical stimulation on activity of the tibialis anterior muscle and balance of individuals with hemiparesis stemming from a stroke

[Purpose] The aim of the present study was to evaluate the immediate effects of transcranial direct current stimulation (tDCS) and functional electrical stimulation (FES) on activity of the tibialis anterior muscle (TA) and static balance of individuals with hemiparesis stemming from stroke. [Subjects and Methods] A randomized, double-blind, crossover, clinical trial conducted with 30 individuals with chronic post-stroke hemiparesis. Median frequency of electrical activity of the TA were determined using electromyography in five contractions concentrics and Static balance (body sway velocity and frequency), both before and immediately after the intervention. The participants were submitted to four 20-minute intervention protocols with 48-hour interval: anodal tDCS + sham FES; sham tDCS + active FES; anodal tDCS + active FES and sham tDCS + sham FES. Anodal tDCS was administered over C3 or C4, the cathode was positioned in the supraorbital region on the contralateral side and FES was administered to the affected TA. [Results] No significant differences among the protocols were found regarding electrical activity of the TA and static balance. [Conclusion] The results demonstrate that tDCS alone or in combination with FES had no immediate effect on electrical activity of the TA and static balance of the 30 individuals analyzed.
Genome‐based evolutionary history of Pseudomonas spp

Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.
Poly-Spline Finite-Element Method

We introduce an integrated meshing and finite-element method pipeline enabling solution of partial differential equations in the volume enclosed by a boundary representation. We construct a hybrid hexahedral-dominant mesh, which contains a small number of star-shaped polyhedra, and build a set of high-order bases on its elements, combining triquadratic B-splines, triquadratic hexahedra, and harmonic elements. We demonstrate that our approach converges cubically under refinement, while requiring around 50% of the degrees of freedom than a similarly dense hexahedral mesh composed of triquadratic hexahedra. We validate our approach solving Poisson’s equation on a large collection of models, which are automatically processed by our algorithm, only requiring the user to provide boundary conditions on their surface.
First Principles Study of Fe based Full Heusler Alloy

The electronic structure of Fe-based quaternary Heusler compounds Fe 2 CoZ (Z=Ga, Ge) is calculated by first-principles density functional theory. Structural optimization is performed for two possible structures: Hg 2 CuTi-type and Cu 2 MnAl-type structures of Fe 2 CoZ. We found that Hg 2 CuTi-type structure is energetically more favorable than Cu 2 MnAl-type structure. The calculated equilibrium lattice constant is 5.812A and 5.75A respectively for Ga and Ge based alloy. The calculations reveal that Fe 2 CoGa material exhibit 100% spin-polarization whereas Fe 2 CoGe has 62% spin-polarization. The value of magnetic moment for Fe 2 CoGa and Fe 2 CoGe is 5.72m B , 4.96m B respectively
Noncoding RNAs and Stroke

Over many years, extensive efforts have focused on the development and improvement of diagnostic and therapeutic strategies to reduce stroke-associated neurovascular damage, such as blood-brain barrier dysfunction, brain edema, parenchymal inflammation, and neural cell death. However, the only clinically applied pharmacological therapy to date for the treatment of acute ischemic stroke is thrombolysis. Because of the short therapeutic window of current thrombolytic therapy and the activation of various pathophysiological signaling cascades triggered after ischemic stroke, the development of new therapies is urgently required. Noncoding RNAs (ncRNAs) are defined as untranslated regulatory RNA molecules. Although ncRNAs with biological roles have been known for almost 60 years, they have within the past decade emerged as key mediators of posttranscriptional gene expression/function in pathological aspects of ischemic stroke. With properties of relative stability, specificity, and reproducibility, ncRNAs are considered to be promising as biomarkers and better candidates than proteins and genes for early recognition of the onset of disease. In this update, we summarized the current knowledge for three groups of ncRNAs in stroke, focusing on the role of long noncoding RNAs and circular RNAs as biomarkers for stroke and as targets for regulating large sets of genes in related pathways after ischemic stroke.
Elevated serum MFG‐E8 level is possibly associated with the presence of high‐intensity cerebral lesions on magnetic resonance imaging in patients with systemic lupus erythematosus

Human milk fat globule‐EGF factor 8 (MFG‐E8), also known as lactadherin, is a secreted glycoprotein that plays essential roles in the clearance of apoptotic cells and angiogenesis. It has been reported that serum MFG‐E8 levels are higher in systemic lupus erythematosus (SLE) patients compared with in healthy controls; however, a previous study reported no correlation between serum MFG‐E8 levels and SLE disease activity. The objective of this study was to assess serum MFG‐E8 levels and their clinical associations in patients with SLE. Serum MFG‐E8 levels in 49 Japanese patients with SLE, eight with cutaneous LE, and 28 healthy controls were examined. Serum MFG‐E8 levels in SLE patients were significantly higher than those in cutaneous LE patients and healthy individuals. In addition, serum MFG‐E8 levels were positively correlated with the SLE Disease Activity Index score, which reflects the disease activity of SLE. Notably, the frequency of the presence of high‐intensity cerebral lesions on MRI in the SLE patients with elevated serum MFG‐E8 levels was significantly higher than that in SLE patients with normal serum MFG‐E8 levels. These findings suggest that elevated serum MFG‐E8 levels may be associated with cerebrovascular diseases or neuropsychiatric SLE in patients with SLE, and that the measurement of serum MFG‐E8 levels in SLE patients is useful for risk stratification of cerebrovascular disease or cerebrovascular disease‐related neuropsychiatric SLE.
Pharmacological and genetic inhibition of downstream targets of p38 MAPK in experimental nephrotic syndrome.

Nie X, Chanley MA, Pengal R, Thomas DB, Agrawal S, Smoyer WE. Pharmacological and genetic inhibition of downstream targets of p38 MAPK in experimental nephrotic syndrome. Am J Physiol Renal Physiol 314: F602-F613, 2018. First published November 29, 2017; doi: 10.1152/ajprenal.00207. 2017 . -The p38 MAPK pathway plays a crucial role in various glomerulopathies, with activation being associated with disease and inhibition being associated with disease amelioration. We hypothesized that the downstream targets of p38 MAPK, MAPK-activated protein kinase 2 and/or 3 (MK2 and/or MK3), play an important role in mediating injury in experimental nephrotic syndrome via their actions on their downstream substrates heat shock protein B1 (HSPB1) and cyclooxygenase-2 (COX-2). To test this hypothesis, the effects of both pharmacological and genetic inhibition of MK2 and MK3 were examined in mouse adriamycin (ADR) and rat puromycin aminonucleoside (PAN) nephropathy models. MK2-/-, MK3-/-, and MK2-/-MK3-/- mice were generated in the Sv129 background and subjected to ADR-induced nephropathy. MK2 and MK3 protein expression was completely abrogated in the respective knockout genotypes, and massive proteinuria and renal histopathological changes developed after ADR treatment. Furthermore, renal cortical HSPB1 was induced in all four genotypes by day 21, but HSPB1 was activated only in the wild-type and MK3-/- mice. Expression of the stress proteins HSPB8 and glucose-regulated protein 78 (GRP78) remained unaltered across all genotypes. Finally, while MK2 and/or MK3-knockout downregulated the proinflammatory enzyme COX-2, ADR significantly induced renal cortical COX-2 only in MK2-/- mice. Additionally, pharmacological MK2 inhibition with PF-318 during PAN-induced nephropathy did not result in significant proteinuria reduction in rats. Together, these data suggest that while the inhibition of MK2 and/or MK3 regulates the renal stress response, our currently available approaches are not yet able to safely and effectively reduce proteinuria in experimental nephrotic syndrome and that other p38MAPK downstream targets should also be considered to improve the future treatment of glomerular disease.
Bond Characteristics of Strengthened and Retrofitted Steel by Smart CFRP Technique

Usage of new smart materials in retrofitting of structures has become popular within last decade. Carbon fiber reinforced polymer (CFRP) has been widely used in retrofitting and strengthening of concrete structures and its usage in metallic structures is still in the developing stage. The variation of mechanical properties of CFRP and the consequent effects on strengthening and retrofitting CFRP systems are yet to be investigated under different loading and environmental conditions. This paper presents the results of CFRP strengthened and retrofitted corroded steel plate double strap joints under tension. An accelerated corrosion cell has been developed to accelerate the corrosion of the steel samples and CFRP strengthened samples. The results show a direct comparison of bond characteristics of CFRP strengthened and retrofitted steel double strap joints.
Heat treatment influence on rheological properties of pork meat.

During the heating of meat, meat proteins are denaturizing, which causes various changes in the structure of the meat, such as the destruction of cell membranes, tearing of muscle fibbers, tearing and dissolution of the connective tissue proteins, coagulation and gel formation of the myofibrillar and sarcoplasmic proteins. The aim of the study presented in this paper was to investigate the effect of heat treatment by roasting and cooking at atmospheric pressure on the rheological properties of M. longissimus dorsi of pork in the temperature range between 51 0C and 100 0C. Consequently, the TPA and Warner Bratzler tests were conducted, for both processes of heat treatment, after each of the observed temperature in a given temperature range. By TPA test were determined hardness (g), elasticity, cohesiveness, plasticity and chewiness. Warner Bratzler test determined the change of strength (N) and shear test (Ns). The observed parameters during rheological tests showed constant statistically significant change (P < 0.001) of observed values with temperature increasing during the both heat treatment processes in the given temperature range. The most optimal temperature in the centre of the sample during thermal processing of pork meat is in the temperature range between 71 0C and 81 0C. Heat treatment by cooking gave products with more desirable rheological properties, as seen in relation to the thermal treatment by roasting.
Service level agreement and provisioning in optical networks

This article proposes a service level agreement applied to the optical domain (O-SLA), which is expected to be the near- and long-term network technology of the great bandwidth capacity offered by optical devices. After an exposition of the rationale behind an optical SLA, parameters that could be included in this O-SLA, as well as their values for four classes of services are proposed. Different client (wavelength or subwavelength) and service types (from leased wavelength to bandwidth on demand) are distinguished when necessary. The last part of this article presents issues related to the provisioning of services emanating from this O-SLA.
Conjunctival Lesions: When Should We Perform Biopsy?

INTRODUCTION The conjunctiva is a thin and flexible mucus membrane that provides a protective barrier for the eye. Very few histopathologic studies have been conducted on biopsies from conjunctival lesions (CL) in central India. OBJECTIVE To study the spectrum of CL and define those lesions that need attention with regard to need of biopsy in order to prevent grave sequelae and ocular morbidity. RESULTS Degenerative conditions such as pterygium followed by pinguicula were the commonest lesions seen in conjunctiva. Out of 129 subjects, youngest in the series was 3 years old while oldest patient was 72 years of age. Commonest age interval for involvement was 35 to 50 years. In children below 8 years, cystic lesions (infective or inclusion), limbal dermoid and choristoma were seen. Vascular lesions were noticed by patients for the first time between mid-teens to 25 years age. Premalignant lesions were dysplasia, actinic keratosis and PAM with or without XP. Malignant lesions in this series were squamous cell carcinoma, basal cell carcinoma and sebaceous carcinoma; which were observed in the age interval 25 to 75 years. In none of the malignant conditions there was deeper penetration into the globe or orbit. Though diagnosed within two weeks duration (by incisional biopsy) from appearance of nodule, unfavourable outcome was seen only in one malignant CL; a case having sebaceous carcinoma. In all pediatric cases outcome was good, except in child having choristoma, where amblyopia ensued before a diagnosis was made. Response to sclerotherapy was excellent as all the epibulbar vascular malformations regressed. All degenerative lesions regressed except one recurrence in a recurred pterygium. Case diagnosed as large B cell lymphoma recurred after one year. Dysplastic changes were seen to occur at limbus on followup in one XP, but in all cases of naevi, neither cellular atypia was seen nor melanoma developed. CONCLUSION An overview of various CL disclosed that clinician has to differentiate benign from premalignant and malignant lesions. Early diagnosis, proper histological study and patient education, all are equally important for achieving good outcome.
Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology

Abstract Sirtuins are NAD+-dependent protein deacylases/ADP-ribosyltransferases that have emerged as candidate targets for new therapeutics to treat metabolic disorders and other diseases, including cancer. The sirtuin SIRT5 resides primarily in the mitochondrial matrix and catalyzes the removal of negatively charged lysine acyl modifications; succinyl, malonyl, and glutaryl groups. Evidence has now accumulated to document the roles of SIRT5 as a significant regulator of cellular homeostasis, in a context- and cell-type specific manner, as has been observed previously for other sirtuin family members. SIRT5 regulates protein substrates involved in glycolysis, the TCA cycle, fatty acid oxidation, electron transport chain, ketone body formation, nitrogenous waste management, and ROS detoxification, among other processes. SIRT5 plays pivotal roles in cardiac physiology and stress responses and is involved in the regulation of numerous aspects of myocardial energy metabolism. SIRT5 is implicated in neoplasia, as both a tumor promoter and suppressor in a context-specific manner, and may serve a protective function in the setting of neurodegenerative disorders. Here, we review the current understanding of functional impacts of SIRT5 on its metabolic targets, and its molecular functions in both normal and pathological conditions. Finally, we will discuss the potential utility of SIRT5 as a drug target and also summarize the current status, progress, and challenges in developing small molecule compounds to modulate SIRT5 activity with high potency and specificity.