Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted Nanomaterials for Phototherapy

Phototherapies involve the irradiation of target tissues with light. To further enhance selectivity and potency, numerous molecularly targeted photosensitizers and photoactive nanoparticles have been developed. Active targeting typically involves harnessing the affinity between a ligand and a cell surface receptor for improved accumulation in the targeted tissue. Targeting ligands including peptides, proteins, aptamers and small molecules have been explored for phototherapy. In this review, recent examples of targeted nanomaterials used in phototherapy are summarized.
Foil and leaf gilding on cultural artifacts: forming and adhesion

The process used to obtain foils of more and more thin thickness and coat them on artefacts varied during centuries. It started from thick foils of the first ages mechanically assembled and evolved until the rolled and beaten leaves, a few hundred nanometres thick. This paper will develop, through examples taken from laboratory studies on museum objects, the main evolution steps of gold leaf forming. It will discuss the present knowledge about processes used by hand-workers of different origins and periods: antic Egypt, Roman Empire, western and oriental Middle-Age, South America, modern Europe. A recent mechanical modelling work about gold forming by beating will be exposed. Then will be described, still through recent examples, some of the non-destructive and destructive laboratory methods used to characterise ancient and modern gildings, their composition, thickness and adhesion modes. The different coating process will be discussed, owing to the presently available knowledge. These depend on the substrate nature and the possible necessity to treat its surface before and during the gilding process. Such treatment varies from the "white preparation" found on antic Egyptian artefacts and also on wooden decoration of baroque Brazilian churches, to "oil gilding" used for the recent restoration of the Invalides roof in Paris. It may also include a high temperature firing, as for gilding with powder issued from leaf grinding on Middle-Age Syria glass. The paper will end with a listing of the numerous research perspectives open for the presently poorly developed study of the adhesion mechanisms between gold leaf and its substrate, to understand fully the gilding process.
Shape Neutral Analysis of Graph-based Data-structures

Abstract Malformed data-structures can lead to runtime errors such as arbitrary memory access or corruption. Despite this, reasoning over data-structure properties for low-level heap manipulating programs remains challenging. In this paper we present a constraint-based program analysis that checks data-structure integrity, w.r. t. given target data-structure properties, as the heap is manipulated by the program. Our approach is to automatically generate a solver for properties using the type definitions from the target program. The generated solver is implemented using a Constraint Handling Rules (CHR) extension of built-in heap, integer and equality solvers. A key property of our program analysis is that the target data-structure properties are shape neutral, i.e., the analysis does not check for properties relating to a given data-structure graph shape, such as doubly-linked-lists versus trees. Nevertheless, the analysis can detect errors in a wide range of data-structure manipulating programs, including those that use lists, trees, DAGs, graphs, etc. We present an implementation that uses the Satisfiability Modulo Constraint Handling Rules (SMCHR) system. Experimental results show that our approach works well for real-world C programs.
Convergence guarantees for a class of non-convex and non-smooth optimization problems

We consider the problem of finding critical points of functions that are non-convex and non-smooth. Studying a fairly broad class of such problems, we analyze the behavior of three gradient-based methods (gradient descent, proximal update, and Frank-Wolfe update). For each of these methods, we establish rates of convergence for general problems, and also prove faster rates for continuous sub-analytic functions. We also show that our algorithms can escape strict saddle points for a class of non-smooth functions, thereby generalizing known results for smooth functions. Our analysis leads to a simplification of the popular CCCP algorithm, used for optimizing functions that can be written as a difference of two convex functions. Our simplified algorithm retains all the convergence properties of CCCP, along with a significantly lower cost per iteration. We illustrate our methods and theory via applications to the problems of best subset selection, robust estimation, mixture density estimation, and shape-from-shading reconstruction.
Recursive Clustering Using Different Features Sets for Metagenomic Data

Metagenomics binning process is a step prior to the taxonomic assignment of metagenomic reads of contigs, which helps to group genome sequences belonging to the same species. In this paper we propose a clustering method that is executed recursively to cluster contigs into groups of same taxa. In each step the method increases the taxonomic level, beginning with a domain and ending with a group that represents the species. The method uses a previous rule-based system to separate virus from the rest of the organism and feature selection algorithms to select different features in each step of the clustering. The clustering is based on k-means++ using Cosine and Jaccard distance, and feature selection on gain information. The proposed method outperforms classic k-means++, achieving 88.15% of purity in clusters.
BomJi at SemEval-2018 Task 10: Combining Vector-, Pattern- and Graph-based Information to Identify Discriminative Attributes

This paper describes BomJi, a supervised system for capturing discriminative attributes in word pairs (e.g. yellow as discriminative for banana over watermelon). The system relies on an XGB classifier trained on carefully engineered graph-, pattern- and word embedding-based features. It participated in the SemEval-2018 Task 10 on Capturing Discriminative Attributes, achieving an F1 score of 0.73 and ranking 2nd out of 26 participant systems.
The roles of FGF10 in vasculogenesis and angiogenesis

Vasculogenesis and angiogenesis are of physiological and pathological importance during the process of development. In this study we address that FGF10 affects both vasculogenesis and angiogenesis in vitro and in vivo. Evidence indicates FGF10 does not alter the proliferation of HUVECs in vitro, but FGF10 stimulates HUVECs cultured on Matrigel to form capillary-like structures. In chick embryo chorioallantoic membrane assay, evidence shows FGF10 induces strong angiogenesis responses in vivo. Together, our studies provide novel insights into the functions of FGF10 during the formation of newborn blood vessels.
An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods

Abstract Evolutionary morphological and physiological differences between browsers and grazers contribute to species‐specific digestion efficiency of food resources. Rumen microbial community structure of browsers is supposedly adapted to characteristic nutrient composition of the diet source. If this assumption is correct, domesticated ruminants, or grazers, are poor model animals for assessing the nutritional value of food consumed by browsing game species. In this study, typical spring and summer foods of the European moose (Alces alces) were combined with rumen fluid collected from both dairy cows (Bos taurus) and from moose, with the aim of comparing fermentation efficiency and microbial community composition. The nutritional value of the food resources was characterized by chemical analysis and advanced in vitro measurements. The study also addressed whether or not feed evaluation based on in vitro techniques with cattle rumen fluid as inoculum could be a practical alternative when evaluating the nutritional value of plants consumed by wild browsers. Our results suggest that the fermentation characteristics of moose spring and summer food are partly host‐specific and related to the contribution of the bacterial phyla Firmicutes and Bacteriodetes to the rumen microbial community. Host‐specific adaptations of the ruminal microbial community structure could be explained from the evolutionary adaptations related to feeding habitats and morphophysiological differences between browsers and grazers. However, the observed overall differences in microbial community structure could not be related to ruminal digestion parameters measured in vitro. The in vitro evaluation of digestion efficiency reveals that equal amounts of methane were produced across all feed samples regardless of whether the ruminal fluid was from moose or dairy cow. The results of this study suggested that the nutritional value of browsers' spring and summer food can be predicted using rumen fluid from domesticated grazers as inoculum in in vitro assessments of extent of digestion when excluding samples of the white water lily root, but not of fermentation characteristics as indicated by the proportions of individual fermentation fatty acids to the total of volatile fatty acids.
The PMIP4 contribution to CMIP6 – Part 1: Overview and over-arching analysis plan

Abstract. This paper is the first of a series of four GMD papers on the PMIP4-CMIP6 experiments. Part 2 (Otto-Bliesner et al., 2017) gives details about the two PMIP4-CMIP6 interglacial experiments, Part 3 (Jungclaus et al., 2017) about the last millennium experiment, and Part 4 (Kageyama et al., 2017) about the Last Glacial Maximum experiment. The mid-Pliocene Warm Period experiment is part of the Pliocene Model Intercomparison Project (PlioMIP) – Phase 2, detailed in Haywood et al. (2016). The goal of the Paleoclimate Modelling Intercomparison Project (PMIP) is to understand the response of the climate system to different climate forcings for documented climatic states very different from the present and historical climates. Through comparison with observations of the environmental impact of these climate changes, or with climate reconstructions based on physical, chemical, or biological records, PMIP also addresses the issue of how well state-of-the-art numerical models simulate climate change. Climate models are usually developed using the present and historical climates as references, but climate projections show that future climates will lie well outside these conditions. Palaeoclimates very different from these reference states therefore provide stringent tests for state-of-the-art models and a way to assess whether their sensitivity to forcings is compatible with palaeoclimatic evidence. Simulations of five different periods have been designed to address the objectives of the sixth phase of the Coupled Model Intercomparison Project (CMIP6): the millennium prior to the industrial epoch (CMIP6 name: past1000); the mid-Holocene, 6000 years ago (midHolocene); the Last Glacial Maximum, 21 000 years ago (lgm); the Last Interglacial, 127 000 years ago (lig127k); and the mid-Pliocene Warm Period, 3.2 million years ago (midPliocene-eoi400). These climatic periods are well documented by palaeoclimatic and palaeoenvironmental records, with climate and environmental changes relevant for the study and projection of future climate changes. This paper describes the motivation for the choice of these periods and the design of the numerical experiments and database requests, with a focus on their novel features compared to the experiments performed in previous phases of PMIP and CMIP. It also outlines the analysis plan that takes advantage of the comparisons of the results across periods and across CMIP6 in collaboration with other MIPs.
4D Temporally Coherent Light-Field Video

Light-field video has recently been used in virtual and augmented reality applications to increase realism and immersion. However, existing light-field methods are generally limited to static scenes due to the requirement to acquire a dense scene representation. The large amount of data and the absence of methods to infer temporal coherence pose major challenges in storage, compression and editing compared to conventional video. In this paper, we propose the first method to extract a spatio-temporally coherent light-field video representation. A novel method to obtain Epipolar Plane Images (EPIs) from a spare lightfield camera array is proposed. EPIs are used to constrain scene flow estimation to obtain 4D temporally coherent representations of dynamic light-fields. Temporal coherence is achieved on a variety of light-field datasets. Evaluation of the proposed light-field scene flow against existing multi-view dense correspondence approaches demonstrates a significant improvement in accuracy of temporal coherence.
The decrease of glycolytic enzyme hexokinase 1 accelerates tumor malignancy via deregulating energy metabolism but sensitizes cancer cells to 2-deoxyglucose inhibition

Malignant tumors often display an aberrant energy metabolism that relies primarily on glycolysis to produce adenosine triphosphate (ATP) the so-called Warburg effect or aerobic glycolysis. Thus, the elucidation of this energetic alteration in malignant tumors is important in the search for more effective therapeutics against malignant cancers, the most deadly human disease. To investigate whether attenuated glycolytic activity modulates tumor progression, the effects of silencing the first and rate-limiting glycolytic enzyme hexokinase (HK) isozymes HK1 and HK2 were examined. There was an inverse correlation between the expression of HK1 and HK2 in human cancer cells. In cervical carcinoma cells, the HK1 but not HK2 knockdown induced a phenotypic change characteristic of epithelial-mesenchymal transition, which accelerated tumor growth and metastasis both in vitro and in vivo analyses. Notably, the silencing of HK1 disrupted aerobic respiration and increased glycolysis, but it had no effect on ATP generation. These metabolic changes were associated with higher HK2 and lactate dehydrogenase 1 expression but a lower citrate synthase level. Particularly, the HK1 knockdown induced aberrant energy metabolism that was almost recapitulated by HK2 overexpression. Moreover, the HK1-silenced cells showed strong glucose-dependent growth and 2-deoxyglucose (2-DG) induced cell proliferation inhibition. These results clearly indicate that the silencing of HK1, but not HK2, alters energy metabolism and induces an EMT phenotype, which enhances tumor malignancy, but increases the susceptibility of cancer cells to 2-DG inhibition. In addition, this work also suggests that the glycolytic inhibitors should be used only to treat cancers with elevated glycolytic activity.
Voltage and power regulators guaranteeing stability of dc-links between DERs and the electricity grid

An alternative control design for dc-links used to connect distributed energy resources (DERs) with the main power grid, is proposed and studied for its stability. As DERs are considered to be weak, unpredictable power sources, ac voltage regulation is applied at the side of DER connection while at the grid side, dc voltage and reactive power control is implemented. The challenging issue of achieving these tasks effectively through the design of a rather simple control scheme is examined in this paper. While the traditionally proposed techniques involve parameter-dependent controllers in order to make possible simple linear designs, in this paper, the proposed controllers are clearly simpler ones, parameter-free of proportional-integral (PI) type, but require a more complicated and advanced nonlinear analysis. To that end, incorporating the controllers into the nonlinear dc-link model, the closed-loop system is analyzed by applying advanced Lyapunov techniques combined with input to state stability notions. As shown in the paper, stability and convergence to the equilibrium is guaranteed while the extended simulations presented, fully verify the theoretical analysis.
Changing attitudes and emotions toward coyotes with experiential education

ABSTRACT An experiential education program was designed to target risk perceptions and preventative measures that make people feel comfortable in human-coyote interactions. The research was conducted in a Canadian national park where a coyote caused a human fatality in 2009. Based on previous research, we explored the effects of an experience-based coyote education program on people's (a) attitudes toward, (b) fear of, (c) likelihood of, and (d) control over coming into contact with coyotes. A pre-post-test experiment (n = 150; 96% completion rate) was conducted. The experiential education approach to wildlife safety and coexistence communication had a significant positive effect on people's attitudes, significantly decreased their sense of fear toward coyotes, significantly decreased their sense of likelihood, and increased their sense of control in human-coyote interactions.
Mammalian Mat1 subunit of Transcription Factor IIH in gene-specific and general transcription

9 REVIEW OF THE LITERATURE 10 1. RNA Polymerase II-mediated transcription 10 The chromatin template 11 Phosphorylation of the C-terminal domain of RNAPII 13 TFIIH and Mat1 16 Cotranscriptional mRNA processin 19 Regulation of mRNA stability and decay 21 Chromatin modifications 23 2. Transcriptional regulation of energy metabolism 26 The transcriptional cascade of adipocyte differentiation 26 The PPAR coactivator-1 family members and fatty acid oxidation 29 Transcriptional control of hepatic lipogenesis 30 TFIIH: linking general and gene-specific transcription 33 AIMS OF THE STUDY 35 MATERIALS AND METHODS 36 1. Materials 36 2. Methods 37 RESULTS 44 1. Mat1 is required for phosphorylation of RNA Polymerase II C-terminal domain, transcription and efficient mRNA turnover 44 2. The Cdk7 kinase submodule of TFIIH acts as a physiological roadblock to adipogenesis through inhibitory phosporylation of PPARγ 46 3. Mat1 is critical for cardiac energy metabolism in vivo via regulation of PGC1 48 4. Hepatic-specific deletion of Mat1 in mice results in fatty liver through activation of SREBP-1c target genes via loss of DMAP1 and Dnmt1 49 DISCUSSION & PERSPECTIVES 52 1. Mat1, Cdk7 and RNA Polymerase II CTD phosphorylation 52 2. Tissue-specific functions of Mat1 54 3. mRNA stabilization: linking transcription progression to mRNA turnover 55 ACKNOWLEDGEMENTS 58 REFERENCES 60
The BundleExplorer: A Focus and Context Rendering Framework for Complex Fiber Distributions

Advanced diffusion imaging enables the reconstruction of complex fiber configurations such as crossings or fannings. However, resulting visualizations often suffer from visual clutter which makes exploration challenging. This paper presents the BundleExplorer as a GPU-based focus and context rendering framework for diffusion data. A combination of a fiber encompassing hull and line rendering is proposed to provide insight into inner-bundle fiber configurations as well as to enable bundle crossing exploration. Visual clutter is reduced and information about the global bundle geometry is provided by using fiber encompassing hulls. At the same time important characteristics, such as individual trajectory courses, which are conventionally neglected when using hull visualizations, are revealed by cutaway techniques and enhanced line renderings. In addition, spatial features, the distance to the fiber hull, as well as functional features, i.e., the degree of anisotropy, are visualized using fiber color encoding. Different cutaway techniques using marker and view-dependent clippings are implemented in order to reveal focus information. Visual enhancements are used to indicate bundle intersections.
Evaluation of document binarization using eigen value decomposition

A necessary step for the recognition of scanned documents is binarization, which is essentially the segmentation of the document. In order to binarize a scanned document, we can find several algorithms in the literature. What is the best binarization result for a given document image? To answer this question, a user needs to check different binarization algorithms for suitability, since different algorithms may work better for different type of documents. Manually choosing the best from a set of binarized documents is time consuming. To automate the selection of the best segmented document, either we need to use ground-truth of the document or propose an evaluation metric. If ground-truth is available, then precision and recall can be used to choose the best binarized document. What is the case, when ground-truth is not available? Can we come up with a metric which evaluates these binarized documents? Hence, we propose a metric to evaluate binarized document images using eigen value decomposition. We have evaluated this measure on DIBCO and H-DIBCO datasets. The proposed method chooses the best binarized document that is close to the ground-truth of the document.
Bioluminescent fungi for real-time monitoring of fungal infections

Novel luciferase reporters have been developed that allow real-time monitoring of infections by the fungal pathogens Candida albicans and Aspergillus fumigatus. Although these reporters still suffer limitations in the context of invasive infections, they provide unprecedented tools to monitor superficial infections and the efficacy of antifungal drugs or vaccines. In particular, the sensitivity and ease of detection of the cell-surface Gaussia princeps luciferase developed for C. albicans should make it a powerful tool for functional genomics studies in this and other pathogenic fungi.
Boltzmann Encoded Adversarial Machines

Restricted Boltzmann Machines (RBMs) are a class of generative neural network that are typically trained to maximize a log-likelihood objective function. We argue that likelihood-based training strategies may fail because the objective does not sufficiently penalize models that place a high probability in regions where the training data distribution has low probability. To overcome this problem, we introduce Boltzmann Encoded Adversarial Machines (BEAMs). A BEAM is an RBM trained against an adversary that uses the hidden layer activations of the RBM to discriminate between the training data and the probability distribution generated by the model. We present experiments demonstrating that BEAMs outperform RBMs and GANs on multiple benchmarks.
Space Filling Approach for Distributed Processing of Top-k Dominating Queries

A top-k dominating query returns <inline-formula><tex-math notation="LaTeX">$k$</tex-math><alternatives> <inline-graphic xlink:href="amagata-ieq1-2790387.gif"/></alternatives></inline-formula> data objects that dominate the highest number of data objects in a given dataset. This query provides us with a set of intuitively preferred data, thus can support a wide variety of multi-criteria decision-making applications, e.g., e-commerce and web search. Due to the growth of data centers and cloud computing infrastructures, the above applications are increasingly being operated in distributed environments. These motivate us to address the problem of distributed top-k dominating query processing. We propose an efficient decentralized algorithm that exploits virtual points and returns the exact answer. The virtual points are utilized to focus on the data space to be preferentially searched and also to limit the search space to prune unnecessary computation and data forwarding. We also propose two other algorithms, which return an approximate answer set while further reducing query processing time. Extensive experiments on both real and synthetic data demonstrate the efficiency and scalability of our algorithms.