Miracle-dz/UniFAR-FTUs huggingface dataset:
Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts

We discuss and clarify several aspects of applying Felsenstein's (1985, Am. Nat. 125: 1n15) procedures to test for correlated evolution of continuous traits. This is one of several available comparative methods that maps data for phenotypic traits onto an existing phylogenetic tree (derived from independent information). Application of Felsenstein's method does not require an entirely dichotomous topology. It also does not require an assumption of gradual, clocklike character evolution, as might be modeled by Brownian motion. Almost any available information can be used to estimate branch lengths (e.g., genetic distances, divergence times estimated from the fossil record or from molecular clocks, numbers of character changes from a cladistic analysis). However, the adequacy for statistical purposes of any proposed branch lengths must be verified empirically for each phytogeny and for each character. We suggest a simple way of doing this, based on graphical analysis of plots of standardized independent contrasts versus their standard deviations (i.e., the square roots of the sums of their branch lengths). In some cases, the branch lengths and/or the values of traits being studied will require transformation. An example involving the scaling of mammalian home range area is presented. Once adequately standardized, sets of independent contrasts can be analyzed using either linear or nonlinear (multiple) regression. In all cases, however, regressions (or correlations) must be computed through the origin. We also discuss ways of correcting for body size effects and how this relates to making graphical representations of relationships of standardized independent contrasts. We close with a consideration of the types of traits that can be analyzed with independent contrasts procedures and conclude that any (continuous) trait that is inherited from ancestors is appropriate for analysis, regardless of the mechanism of inheritance (e.g., genetic or cultural).
Aggregating predictions vs. aggregating features for relational classification

Relational data classification is the problem of predicting a class label of a target entity given information about features of the entity, of the related entities, or neighbors, and of the links. This paper compares two fundamental approaches to relational classification: aggregating the features of entities related to a target instance, or aggregating the probabilistic predictions based on the features of each entity related to the target instance. Our experiments compare different relational classifiers on sports, financial, and movie data. We examine the strengths and weaknesses of both score and feature aggregation, both conceptually and empirically. The performance of a single aggregate operator (e.g., average) can vary widely across datasets, for both feature and score aggregation. Aggregate features can be adapted to a dataset by learning with a set of aggregate features. Used adaptively, aggregate features outperformed learning with a single fixed score aggregation operator. Since score aggregation is usually applied with a single fixed operator, this finding raises the challenge of adapting score aggregation to specific datasets.
Usability analysis with Markov models

How hard to users to find interactive devices to use to achieve their goals, and how can we get this information early enough to influence design? We show that Markov modeling can obtain suitable measures, and we provide formulas that can be used for a large class of systems. We analyze and consider alternative designs for various real examples. We introduce a “knowledege/usability graph,” which shows the impact of even a smaller amount of knowledge for the user, and the extent to which designers' knowledge may bias their views of usability. Markov models can be built into design tools, and can therefore be made very convenient for designers to utilize. One would hope that in the future, design tools would include such mathematical analysis, and no new design skills would be required to evaluate devices. A particular concern of this paper is to make the approach accessible. Complete program code and all the underlying mathematics are provided in appendices to enable others to replicate and test all results shown.
Wnt Activation of Immortalized Brain Endothelial Cells as a Tool for Generating a Standardized Model of the Blood Brain Barrier In Vitro

Reproducing the characteristics and the functional responses of the blood–brain barrier (BBB) in vitro represents an important task for the research community, and would be a critical biotechnological breakthrough. Pharmaceutical and biotechnology industries provide strong demand for inexpensive and easy-to-handle in vitro BBB models to screen novel drug candidates. Recently, it was shown that canonical Wnt signaling is responsible for the induction of the BBB properties in the neonatal brain microvasculature in vivo. In the present study, following on from earlier observations, we have developed a novel model of the BBB in vitro that may be suitable for large scale screening assays. This model is based on immortalized endothelial cell lines derived from murine and human brain, with no need for co-culture with astrocytes. To maintain the BBB endothelial cell properties, the cell lines are cultured in the presence of Wnt3a or drugs that stabilize β-catenin, or they are infected with a transcriptionally active form of β-catenin. Upon these treatments, the cell lines maintain expression of BBB-specific markers, which results in elevated transendothelial electrical resistance and reduced cell permeability. Importantly, these properties are retained for several passages in culture, and they can be reproduced and maintained in different laboratories over time. We conclude that the brain-derived endothelial cell lines that we have investigated gain their specialized characteristics upon activation of the canonical Wnt pathway. This model may be thus suitable to test the BBB permeability to chemicals or large molecular weight proteins, transmigration of inflammatory cells, treatments with cytokines, and genetic manipulation.
Techreport Ncrg/97/025. under Review for Neural Computation Computation with Innnite Neural Networks

For neural networks with a wide class of weight priors, it can be shown that in the limit of an innnite number of hidden units the prior over functions tends to a Gaussian process. In this paper analytic forms are derived for the covariance function of the Gaussian processes corresponding to networks with sigmoidal and Gaussian hidden units. This allows predictions to be made eeciently using networks with an innnite number of hidden units, and shows that, somewhat paradoxically, it may be easier to carry out Bayesian prediction with innnite networks rather than nite ones.
Efficient authenticated encryption schemes with public verifiability

An authenticated encryption scheme allows messages to be encrypted and authenticated simultaneously. C. Ma and K. Chen proposed such a scheme with public verifiability (see Electronics Letters, vol.39, no.3 p.281-2, 2003). That is, in their scheme, the receiver can efficiently prove to a third party that a message has indeed originated from a specific sender. We first identify two security weaknesses in the Ma-Chen authenticated encryption scheme. Then, based on the Schnorr signature, we proposed an efficient and secure improved scheme such that all the desired security requirements are satisfied.
Process for enhanced acid leaching of laterite ores

a) preparing a nickel containing laterite ores and ore screening prepared with low magnesium and high magnesium limonite part of the new Take the light part; b) the main high pressure leaching step of preparing a primary leach slurry was treated in the acid solution, the limonite portion; c) in addition to a new Take the light part to the primary leach slurry containing sub atmospheric leaching stage to release acid further from the needle iron ore and at the same time for producing a part leach slurry / or causing a precipitate to hematite, iron precipitation of the iron a method for the nickel and cobalt is recovered from the nickel-containing lateritic ore, the ore slurry, and / or all of the water is a nickel and cobalt recovery characterized in that with the ion components to prevent site formed substantially as used to prepare an acid solution Way. Nickel and cobalt recovery, laterite, limonite, Take the new light, jarosite
In the absence of a “landscape of fear”: How lions, hyenas, and cheetahs coexist

Abstract Aggression by top predators can create a “landscape of fear” in which subordinate predators restrict their activity to low‐risk areas or times of day. At large spatial or temporal scales, this can result in the costly loss of access to resources. However, fine‐scale reactive avoidance may minimize the risk of aggressive encounters for subordinate predators while maintaining access to resources, thereby providing a mechanism for coexistence. We investigated fine‐scale spatiotemporal avoidance in a guild of African predators characterized by intense interference competition. Vulnerable to food stealing and direct killing, cheetahs are expected to avoid both larger predators; hyenas are expected to avoid lions. We deployed a grid of 225 camera traps across 1,125 km2 in Serengeti National Park, Tanzania, to evaluate concurrent patterns of habitat use by lions, hyenas, cheetahs, and their primary prey. We used hurdle models to evaluate whether smaller species avoided areas preferred by larger species, and we used time‐to‐event models to evaluate fine‐scale temporal avoidance in the hours immediately surrounding top predator activity. We found no evidence of long‐term displacement of subordinate species, even at fine spatial scales. Instead, hyenas and cheetahs were positively associated with lions except in areas with exceptionally high lion use. Hyenas and lions appeared to actively track each, while cheetahs appear to maintain long‐term access to sites with high lion use by actively avoiding those areas just in the hours immediately following lion activity. Our results suggest that cheetahs are able to use patches of preferred habitat by avoiding lions on a moment‐to‐moment basis. Such fine‐scale temporal avoidance is likely to be less costly than long‐term avoidance of preferred areas: This may help explain why cheetahs are able to coexist with lions despite high rates of lion‐inflicted mortality, and highlights reactive avoidance as a general mechanism for predator coexistence.
Dissecting the Structural Determinants of the Stability of Cholesterol Oxidase Containing Covalently Bound Flavin*

Cholesterol oxidase from Brevibacterium sterolicum is a monomeric flavoenzyme catalyzing the oxidation and isomerization of cholesterol to cholest-4-en-3-one. This protein is a class II cholesterol oxidases, with the FAD cofactor covalently linked to the enzyme through the His69 residue. In this work, unfolding of wild-type cholesterol oxidase was compared with that of a H69A mutant, which does not covalently bind the flavin cofactor. The two protein forms do not show significant differences in their overall topology, but the urea-induced unfolding of the H69A mutant occurred at significant lower urea concentrations than wild-type (∼3 versus ∼5 m, respectively), and the mutant protein had a melting temperature ∼10–15 °C lower than wild-type in thermal denaturation experiments. The different sensitivity of the various spectroscopic features used to monitor protein unfolding indicated that in both proteins a two-step (three-state) process occurs. The presence of an intermediate was more evident for the H69A mutant at 2 m urea, where catalytic activity and tertiary structure were lost, and new hydrophobic patches were exposed on the protein surface, resulting in protein aggregation. Comparative analysis of the changes occurring upon urea and thermal treatment of the wild-type and H69A protein showed a good correlation between protein instability and the elimination of the covalent link between the flavin and the protein. This covalent bond represents a structural device to modify the flavin redox potentials and stabilize the tertiary structure of cholesterol oxidase, thus pointing to a specific meaning of the flavin binding mode in enzymes that carry out the same reaction in pathogenic versus non-pathogenic bacteria.
Generative Adversarial Networks-based solution for improving medical data quality and insufficiency

As big data brings intelligent solutions and innovations to various fields, the goal of this research is to solve the problem of poor-quality and insufficient datasets in the medical field, to help poor areas can access to high quality and rich medical datasets as well. This study focuses on solving the current problem by utilizing variants of generative adversarial network, Super Resolution Generative Adversarial Network (SRGAN) and Deep Convolutional Generative Adversarial Network (DCGAN). In this study, OpenCV is employed to introduce fuzziness to the Brain Tumor MRI Dataset, resulting in a blurred dataset. Subsequently, the research utilizes both the unaltered and blurred datasets to train the SRGAN model, which is then applied to enhance the low-quality dataset through inpainting. Moving forward, the original dataset, low-quality dataset, and the improved dataset are each used independently to train the DCGAN model. In order to compare the difference between the produced image datasets and the real dataset, the FID Score is separately computed. The results of the study found that by training DCGAN with SRGAN repaired medical dataset, the naked eye can observe that the medical image dataset is significantly clearer and there is a reduction in Frchet Inception Distance (FID) Score. Therefore, by using SRGAN and DCGAN the current problem of low quality and small quantity of datasets in the medical field can be solved, which increase the potential possibilities of big data in artificial intelligence filed of medicine.
Transforming information systems development through computer‐aided systems engineering (CASE): lessons from practice

In dealing with the challenges posed by the ongoing problem of developing and integrating an evermore complex and diverse range of information systems in a timely manner, practitioners continue to grapple with important issues such as increasing developer productivity and bringing quality improvements to the process and product of systems development. Many organizations have adopted computer‐aided systems engineering (CASE) tools with such outcomes in mind. With few exceptions, previous research into the phenomenon of CASE adoption and use has been survey based in the main, and has resulted in some confusion over the benefits to be derived from the use of CASE tools within the systems development process. This paper extends previous work as part of an interpretive, case‐based research strategy to examine the adoption and use of integrated CASE (I‐CASE) in a single organization. Such an approach facilitates a deeper understanding of the impact that CASE exerts on the process and product of systems development. Based on the experience of practitioners in the organization studied, a set of recommendations is presented. The findings of this study also lend support to the view that an I‐CASE development platform does indeed have the potential to exert a positive impact on the development process and its product.
Hexokinase II gene transfer protects against neurodegeneration in the rotenone and MPTP mouse models of Parkinson's disease

A typical feature of Parkinson's disease is the progressive loss of dopaminergic neurons in the substantia nigra, in which inhibition of mitochondrial complex I activity may play an important role. Rotenone or 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) inhibit the mitochondrial complex I and they cause the death of substantia nigra dopaminergic neurons, thereby providing acute murine models of Parkinson's disease. We have found that increasing mitochondrial hexokinase II activity can prevent cell death in neuronal cultures treated with rotenone. As a result, we have studied the effects of hexokinase II gene transfer in vivo using a herpes simplex virus type 1 (HSV‐1) amplicon vector. The placHK2 amplicon vector was injected into substantia nigra of mice that were subsequently administered rotenone or MPTP. Overexpression of hexokinase II prevented both rotenone and MPTP‐induced dopaminergic neuronal cell death, as well as reducing the associated motor defects. Our results provide the first proof‐of‐principle that hexokinase II protects against dopaminergic neurodegeneration in vivo, emphasizing the role of this enzyme in promoting neuronal survival. Thus, the increase of hexokinase II expression by gene transfer or other means represents a promising approach to treat Parkinson's and other neurodegenerative diseases. © 2010 Wiley‐Liss, Inc.
Simple and Secure Electronic Voting with Prêt á Voter

Prêt à Voter is an electronic voting system with very high security properties. We aim to make the system truly usable and applicable in elections with many races and candidates by allowing the vote to be formed using a voting machine and printing a minimalistic receipt. We also introduce the procedure/technology mix concept to describe the use of procedures, people and technology to secure electronic voting systems.
Hypertableau Reasoning for Description Logics

We present a novel reasoning calculus for the description logic SHOIQ+--a knowledge representation formalism with applications in areas such as the SemanticWeb. Unnecessary nondeterminism and the construction of large models are two primary sources of inefficiency in the tableau-based reasoning calculi used in state-of-the-art reasoners. In order to reduce nondeterminism, we base our calculus on hypertableau and hyperresolution calculi, which we extend with a blocking condition to ensure termination. In order to reduce the size of the constructed models, we introduce anywhere pairwise blocking. We also present an improved nominal introduction rule that ensures termination in the presence of nominals, inverse roles, and number restrictions--a combination of DL constructs that has proven notoriously difficult to handle. Our implementation shows significant performance improvements over state-of-the-art reasoners on several well-known ontologies.
Biohydrology—Walking on drylands and swimming through pores

Biology and hydrology are closely linked in nature, with human influences from land management, water use, and climate change having a massive impact (Vogel et al., 2015). This special issue of Ecohydrology provides a range of papers on these complex interactions, ranging in scale from the hydrophobicity of biopore surfaces up to landscape vegetation structure affected by soil hydrological characteristics. The papers were first presented at the 4th Biohydrology Conference, held in Almeria, Spain, in 2016. These conferences have provided a forum to bridge between a reductionist understanding of the underpinning interactions between biological and hydrological processes, and a systems understanding of the impacts to ecology, plant productivity and hydrology. This is the second Ecohydrology special issue from the Biohydrology conferences: the first one (Ecohydrology, 3, 379–508) published 12 papers from the 2nd Biohydrology Conference held in Bratislava, Slovakia, in 2009. Included in that special issue are well‐cited papers on hydraulic redistribution by tree roots (Nadezhdina et al., 2010) and ecological versus topographical drivers of run‐off in the Ethiopian highlands (Bayabil et al., 2010). The 4th Biohydrology conference had the theme “walking on drylands,” which was appropriate for its location in southern Spain and addressed a major hydrological challenge. Drylands cover about 45% of the global land area (Prăvălie, 2016), containing more than 38% of the human population and a high biodiversity that plays an essential role in maintaining the multiple functions of these ecosystems. Although an emerging body of literature in the last decades has focused on researching dryland ecosystems, there is a surprisingly weak understanding of biohydrological processes. One of the processes is groundwater access by vegetation, which Guirado et al. (2018) studied using a non‐destructive low‐cost remote‐sensing‐ based approach. This approach combined object‐based image analysis of high‐resolution orthoimages to map shrub individuals with geomorphometric analysis of a lidar‐derived terrain model to map fractures that roots use to access groundwater. Further research on the establishment of vegetation in drylands by Fan et al. (2018) explored shrub patches along a precipitation gradient on the Inner Mongolia Plateau of Northwest China. While they found shrub cover and height to be affected most by climate, shrub density was mainly affected by soil properties and the size of patches by vegetation. They discussed how the complex interactions between climate, vegetation, and soil drove the structure of the observed ecosystems along the precipitation gradient. This included biology influencing the capacity of soils to transport and retain water. Biology
Fueling Wireless Networks perpetually: A case of multi-hop wireless power distribution∗

Inspired by the recent invention of a high efficiency Wireless Power Transfer (WPT) technique, we propose in this paper the Perpetual Wireless Networks (PWNs) as a novel wireless networking paradigm. Similar to the conventional wireless (data) access point, a PWN has a power access point, from which electrical power is injected and distributed into the network in a form of multi-hop transfer. Consequently, we lay our focus on this new type of multi-hop flow problems concerning not data but power. We formulate and analyze a set of such power flow problems (some are joint with data flow), and we devise algorithms to solve them. The intriguing insights obtained from solving these optimization problems offer instructive guidance for future studies on real PWN constructions.
Electron microscope localization of acetylcholinesterase and butyrylcholinesterase in the superior cervical ganglion of the cat. I. Normal ganglion

The distributions of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) in the superior cervical ganglion (SCG) of the cat were determined by electron microscopy (EM) with the bis- (thioacetoxy)aurate (I), or Au(TA)2, method. Before the infusion of fixative, one of the enzymes was selectively, irreversibly inactivated in vivo, as confirmed by light microscope (LM) examination of sections of the stellate ganglion stained by the more specific copper thiocholine method. Physostigmine-treated controls, for inhibition of AChE or BuChE, were stained concomitantly with tissue for enzyme localization by the Au(TA)2 method for EM examination in each experiment. It was concluded that most of the AChE of the cat SCG is present in the plasma membranes of the preganglionic axons and their terminals, and in the dendritic and perikaryonal plasma membranes of the postsynaptic ganglion cells. BuChE is confined largely to the postsynaptic neuronal plasma membranes. Reasons for the discrepancies between the localizations found by the present direct EM observations and those deduced earlier from LM comparisons of normal and denervated SCG are discussed. It is proposed that a trophic factor released by the preganglionic terminals is probably required for the synthesis of postsynaptic neuronal AChE, and that BuChE may serve as a precursor of AChE at that site.