Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on new guinea moths. 1. Introduction (Lepidoptera)

This is the first in a series of papers providing taxonomic data in support of ecological and biogeographic studies of moths in New Guinea. The primary study is an extensive inventory of the caterpillar fauna of a lowland rainforest site near Madang, Papua New Guinea, from 1994-2001. The inventory focused on the Lepidoptera com- munity on 71 woody plant species representing 45 genera and 23 families. During the study, 46,457 caterpillars representing 585 species were sampled, with 19,660 caterpillars representing 441 species reared to adults. This introductory contribution is intended to provide background on the project, including descriptions of the study site, sampling methods, and taxonomic methods.
Non linear image analysis for fuzzy classification of breast cancer

Non linear image processing proves to be a powerful tool for segmenting images preserving only the interesting regions; those are the cells's nucleous (CN) in this application. All CN are preserved and identified even if the are in a cluster, while the rest of image is considered to be a part of the background. The morphological segmentation makes it possilbe to calculate outstanding feature that could not be obtain by simple observation. These are passed to a fuzzy classifier which decides the probability of the biopsy to belong to a high or low cancer level. Obtaining these measures by human observation is a hard, and nonprecise task. The extracted features will make it possible to reach a parametric classification that is more efficient than the subjective classification made by a human observation
The long life of birds: an examination of the oxidative stress theory of aging

iv TABLE OF CONTENTS . viii LIST OF FIGURES . xii LIST OF TABLES . xv Acknowledgements . xvi Abbreviations . xviii Preface . xx PART A: Introduction and Methodology Chapter 1: Introduction. 25 1.1 Early theories of aging – The 19 th century . 25 1.2 Evolutionary and ecological reasons for aging . 26 1.3 The long life of birds and their metabolic rate . 26 1.4 Principles of the oxidative stress theory of aging . 28 1.4. 1 Mitochondrial respiration and ROS production . 29 1.4. 2 Resistance to oxidative stress: Antioxidant Systems . 33 1.4. 3 The membrane pacemaker theory of aging . 36 1.4. 4 Oxidative Stress Biomarkers . 41 1.5 Oxidative stress in disease and ‘healthy’ aging . 48 1.6 The Rat-Pigeon comparison . 49 1.7 The Parrot-Fowl comparison . 54 Chapter 2: Methodology . 58 2.1 Animals and Tissue Sampling . 58 2.2 Materials . 61 2.3 Whole Animal Metabolic Rate . 61
Botulinum Toxin-A and Scar Reduction: A Review

Pathologic scars remain a therapeutic enigma. Several therapeutic modalities have been described for the prevention and treatment of hypertrophic and keloid scars, but the optimal management approach has not yet been defined. This article reviews the newly emerging, off-label treatment, botulinum toxin-A (BTXA) for scar reduction. Eight in vitro, 9 in vivo animal, and 23 human clinical studies were deemed relevant to this review. Studies were conducted between 2000 and 2018. Clinical studies were of various methodologic qualities and comprised of 8 blinded randomized control trials, 7 cohort studies, and 7 case series/reports. Across all 23 human clinical studies, 521 patients were recruited, 20 studies were in favor of BTXA to reduce scars, 2 studies had equivocal results, and 1 study showed no benefit. The efficacy of BTXA to reduce scars appears promising and the clinical literature currently favors its use over placebo controls as a safe scar reduction alternative. The efficacy of this modality in comparison with other more widely accepted scar reduction methods is less clear. Further understanding of the molecular mechanism of action of BTXA upon scars and treatment modality cost-effectiveness comparisons remain to be explored. Large-scale randomized control trials of high methodologic quality, using objective measurement scales, must be produced to truly determine the efficacy of this innovative treatment.
The effect of dietary fatty acid on breast cancer lipidome

Phospholipids, dietary fatty acids, breast cancer, mass spectrometry, lipidomics Breast cancer is a complex heterogeneous disease and one of the leading causes of death among women. Many studies have tried to determine if saturated, monounsaturated and polyunsaturated fatty acids (FA) have different effects on the development of breast cancer. However, the role of different dietary FAs in lipidome of breast cancer cells is not completely understood. The aim of this work was to establish if lipidome of breast cancer T47-D cell line differs with different dietary FAs and correlate this findings to effects in proliferation and apoptosis. The lipid changes in lipidome induced by the presence of 1 μg/mL oleic acid (OA1) or 1 or 2 μg/mL linoleic (LA1 or LA2, respectively) acid in vitro were study through a lipidomic analysis, based on techniques such as TLC and GC-MS. TLC allowed the separation and quantification of Phospholipid (PL) classes and GC –MS allowed the separation and quantification of FAs. TGs and CHL were quantified. Also, cell viability and apoptosis were evaluated. PL class analysis showed significant alterations in phosphatidylethanolamine (PE), phosphatidylserine (PS) in the medium with LA1 or LA2, respectively and lysophosphatidylcholine (LPC) in the medium with OA1. GC-MS showed an increase of 18:2 in the treatment with LA. Further TG showed a decrease on LA2 treatment and viability and apoptosis assays showed that LA1 and LA2 stimulate cell growth and OA2 stimulated apoptosis, respectively. This work contributes to a better understanding of the influence of dietary FAs on the lipidome of T-47D cells and shows that alterations in cellular lipidome are associated to changes in cell number and apoptosis. These findings may lead to new perspectives in the identification of specific targets that may be helpful to understand the process behind breast cancer growth. However, more studies are necessary to conclude about how different lipid molecules promote these effects.
Role of Liver Stiffness Measurement in Prediction of Esophageal Varices in Chronic Hepatitis C Virus Infected Egyptian Patients

Background; Hepatitis C virus (HCV) infection is a public health problem worldwide. It is estimated more than 185 million people around the world have been infected with it according to the world health organization (WHO). The highest prevalence is in Egypt and constitute about 10-20% of the general population. Bleeding from esophago-gastric varices is the most important complication of cirrhosis. Fibro Scan is a non-invasive device that assesses stiffness of the liver via the technique of transient Elastography. Objective; to evaluate the role of fibro scan in prediction of esophageal varices in chronic HCV infected patients. Patients and methods; A cross sectional prospective study was conducted on 100 Egyptian patients with chronic HCV infection, Studied patients were subjected to full medical history, Routine laboratory investigations, Hepatitis markers including HBsAg, HCV antibody and HCV RNA by real time polymerase chain reaction (PCR), an Abdominal ultrasonography, upper gastrointestinal endoscopy and assessment of liver fibrosis by fibroscan which, was obtained using fibroscan device (Echosens, Paris, France) by an expert fibroscan operator who was not aware by patients data, abdominal ultrasound and upper gastrointestinal endoscopy results were done for all studied patients. Results: liver stiffness measurement revealed patients with values (2-33 kPa with mean ± SD of 8.40 ± 6.82) had no esophageal varices (EV) and patients with values of (11-68 kPa) had EV. And disturbed as the following; (11-54 kPa with mean ±SD of 26.071 ±15.606) for patients with grade I, (13-43 kPa with mean ±SD of 32.625 ±10.716) for patients with grade II, (32-64 kPa with mean ± SD of 43.188 ± 10.232) for patients with grade III and (22-68KPa with mean ±SD of 51.875 ±17.374) for patients with grade IV esophageal varices respectively (P 21 kPa have an accuracy of presence of EV.
T-bet and Eomesodermin are required for adaptive immunity against cancer (101.27)

Cell-mediated adaptive immunity is very important in tumor immune surveillance and tumor vaccination. However, the genetic program underlying an effective adaptive anti-tumor immunity is elusive. T-bet and Eomes have been suggested to be master regulators of Th1 cells and CD8+ T cells. Whether they are important for anti-tumor immunity is controversial. Here we show that lack of T-bet and Eomes has resulted in profound defects in adaptive anti-tumor immune responses in both prophylactic and therapeutic settings. T-bet and Eomes are also important for CD8+ T cell activation without affecting T cell clonal expansion, the gaining of effector phenotype and cytolytic function. Unexpectedly, T-bet and Eomes are dispensable for IFNg production by CD8+ T cells under optimal Th1 differentiation conditions. However, they are necessary for suppressing alternative fates of CD8+ T cells. They drive Tc1 differentiation by preventing alternative CD8+ T cell differentiation to Tc17 or Tc2 cells. Surprisingly, T-bet and Eomes are not critical for the generation of systemic CTL activities against tumor cells. Instead, T-bet and Eomes are crucial for T cell migration and retention in the tumor site and elimination of solid tumors by CD8+ T cells through regulating chemokine receptors such as CXCR3 and IFNg expression in tumor microenvironment. Therefore, our study establishes T-bet and Eomes as key regulators of adaptive cell-mediated immunity against cancer.
Towards More Robust Saccharomyces cerevisiae Strains for Lignocellulosic Bioethanol Production: Lessons from process concepts and physiological investigations

Dwindling oil reserves and the negative impacts of fossil fuels on the environment call for more sustainable energy sources. First-generation bioethanol produced from sugar cane and corn has met some of these needs, but it competes with the food supply for raw materials. Lignocellulosic biomass is an abundant non-edible raw material that can be converted to ethanol using the yeast Saccharomyces cerevisiae. However, due to the inherent recalcitrance to degradation of lignocellulosic raw materials, harsh pretreatment methods must be used to liberate fermentable sugars, resulting in the release of compounds such as acetic acid, furan aldehydes and phenolics, that inhibit yeast metabolism. This thesis research aimed to identify bottlenecks in terms of inhibitory compounds related to ethanol production from two lignocellulosic raw materials, Arundo donax and spruce, and furthermore to harness the physiological responses to these inhibitors to engineer more robust yeast strains. A comparative study of separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) revealed that acetic acid limits xylose utilization in pretreated Arundo donax, whereas the furan aldehydes furfural and 5-hydroxymethyl-2-furaldehyde (HMF) were hypothesized to be key inhibitors in pretreated spruce. The impacts of furfural and HMF on the redox and energy metabolism of S. cerevisiae were studied in detail in chemostat and batch cultivations. After adding the inhibitors to the feed medium of chemostat cultivations, the intracellular levels of NADH, NADPH, and ATP were found to decrease by 40, 75, and 19%, respectively, suggesting that furan aldehydes drain the cells of reducing power. A strong effect on redox metabolism was also observed after pulsing furfural and HMF in the xylose consumption phase in batch cultures. The drainage of reducing power was also observed in a genome-wide study of transcription that found that genes related to NADPH-requiring processes, such as nitrogen and sulphur assimilation, were significantly induced. The redox metabolism was engineered by overproducing the protective metabolite and antioxidant glutathione. Strains with an increased intracellular level of reduced glutathione were found to sustain ethanol production for longer duration in SSF of pretreated spruce, yielding 70% more ethanol than did the wild type strain.
Novel findings from a beta coronavirus outbreak on an American Miniature Horse breeding farm in upstate New York

Summary This case report describes an outbreak and novel findings associated with a beta coronavirus (BCoV) infection that occurred on an American Miniature Horse (AMH) breeding farm in upstate New York, in January and February of 2013. Twenty‐nine AMH and one donkey were present on the farm when the outbreak occurred. One 10‐year‐old Quarter Horse mare, stabled at a separate location and owned by an employee of the farm, also tested positive. A polymerase chain reaction (PCR) assay for the detection of BCoV was performed at the Animal Health Diagnostic Center (AHDC) at Cornell on all faecal samples. The PCR assay used detects multiple beta coronaviruses, including, but not limited to, equine enteric coronavirus (ECoV). Novel findings regarding this BCoV infection in horses were recognised in this outbreak study. To the authors’ knowledge, this is the largest outbreak of BCoV described thus far in a closed herd on a single premise. The case fatality rate was 0% unlike that described in a previous outbreak of ECoV involving miniature horses and a miniature donkey (Fielding et al. 2015). The morbidity rate was lower in this outbreak than in previously described studies (Oue et al. 2013; Pusterla et al. 2013). This outbreak also demonstrated the potential for BCoV transmission via farm personnel. The duration of shedding of virus in the faeces among some asymptomatic horses in this outbreak was longer than previously described clinical cases of ECoV (Pusterla et al. 2013; Nemoto et al. 2014). This study suggests that asymptomatic animals may play a role in the maintenance of BCoV during an outbreak; therefore, the need for diagnostic testing of both clinically affected and apparently clinically normal horses on a premises followed by appropriate biosecurity and control measures.
A functional analysis of a signaling center of the insect head

Most of our knowledge on embryonic development comes from the fruit y Drosophila melanogaster. An elaborate genetic model explains the segmentation process in the trunk. However, the anterior head region is patterned in a di erent way, and many details are not well understood so far. This work analyzes the genetic regulations that govern anterior head patterning in the the red our beetle Tri- bolium castaneum. Especially, functional analysis with RNAi against crucial components of the Wnt and hedgehog signaling pathways is used to reveal the genetic interactions of these. In addition, the combination of reverse genetics with next generation sequencing is applied to identify downstream genetic components of these signaling pathways and to discriminate between anterior and posterior targets in the early germ band. With this work I propose a new model for the patterning of the antennal segment in Tribolium based on the cross regulation of head-gap genes, gap-genes and segment polarity genes. The RNAseq approach successfully identi ed target genes of the Wnt and hedgehog pathways, as con rmed via in situ hybridization, showing the great potential of this method. Finally, this study reveals an unexpected essential role of Tc-senseless in hindgut establishment.
Regulation of ryanodine receptor by nitric oxide

The control of redox state of free thiols on ryanodine receptor (RyR) has been implicated as an important mechanism to regulate RyR channel activity and tune its responses to the physiological modulators. Both the skeletal and cardiac RyRs have been shown to be activated by S-nitrosylation of free thiols on them by a chemical process analogous to the oxidation of i°criticali± or i°hyperreactivei± thiols on RyR proteins. Inositol 1,4,5-triphophate receptors (IP3Rs) that control Ca2+ release from internal stores in non-excitable cells were found to be activated by oxidation, which emphasizes the redox reaction as a common mechanism to regulate intracellular Ca2+ channels. Therefore, the study on nitric oxide-mediated regulation of these ion channels will be important to understand the regulation of Ca2+ homeostasis in all cells including excitable and non-excitable cells since it regulates internal Ca2+ stores via RyR and /or IP3 receptors.The aims were to investigate the chemical reaction underlying the thiol-oxidation and activation of ryanodine receptors (RyRs) by various types of NO donors namely authentic NOi¤, S-nitrosothiols and other NOi¤ species such as nitroxyl anions (i.e. HNO). The different actions of these various NOi¤ species were used to better evaluate the physiological significance of RyR activation by biologically relevant forms of NO, to investigate the role of oxygen on these chemical reactions and to identify the critical cysteine residues involved in redox mediated regulation of RyRs. The main findings are that RyRs are direct targets of S-nitrosothiols which trans-nitrosate hyper-reactive thiols and activate RyRs at biologically relevant concentration. In contrast, NOi¤ gas cannot modify RyRs at biological circumstances found in cells. HNO is considerably more potent activator of RyR1 than NOi¤, activates RyRs at nM concentrations. The study with truncated RyR1 indicated that all of transmembrane domains are located close to the C-terminus of the protein and the i®criticali¯ regulatory thiols are part of conserved cysteines residing in it.Further studies will be required to elucidate the interplay of oxidants and reductants found in the cytosolic milieu of all cells and how these activators and inhibitors act to regulate the opening and closure of Ca2+ release channels.
Comparison of 18F-FDG-PET/CT and CT Tumour Volume Delineation in Head and Neck Cancer Patients

Introduction: Aim of the current study was to compare gross tumour volume delineation for radiation therapy planning by PET/CT and CT scan in head and neck tumour patients. Methods: 70 oncological patients with primary head and neck cancer were enrolled in the study. CT and 18F-FDGPET/ CT scans were performed within 3 weeks of enrolment in the planned irradiation position. For radiation therapy planning delineation of the target volumes was performed manually both in conventional topometric CT slides and in FDG-PET/CT images. Gross tumour target volume was calculated (GTVcm3) using both modalities. Numerical and geometrical (intersection divided union ratio) comparisons were assessed. Intraobserver, interobserver, and intermodality variation analyses were performed. Results: Intra- and interobserver agreement (intraclass correlation coefficients: 0.99 and 0.97) of tumour volume delineation with 18F-FDG-PET/CT was excellent. Radiotherapy target volume as assessed by FDG-PET/ CT differed in 98% (69/70) from target volumes calculated by the CT scans. According to the metabolic information, the target volume was larger in 12 cases (18%) and smaller in 58 cases (82%). Significant differences were found between CT and PET/CT based tumour volume (paired t-test, p<0.0001). Intersection divided union ratio showed low overlap (0.32). Conclusions: Tumour delineation for radiation therapy planning with PET/CT shows good reproducibility in patients with head and neck cancer. CT based morphologic information compared to PET/CT overestimates the tumour volume in larger lesions and may underestimate it in smaller target lesions. Differences are not only evident in tumour volume, but in geometry: Morphology of tumour volume and position.
Etude du metabolisme azote d'Acyrthosiphon Pisum (Harris) (Homoptera : Aphididae), : intervention des bacteries symbiotiques

Aphids are highly specialized insects that feed on the phloem-sap of plants, the amino acid composition of which is unbalanced. Nevertheless, on such a diet, aphids complete bath high development rates and fast reproduction. This adaptive response suppose that aphids display an important amino acid metabolism. In this context, free amino acid pool was analyzed in Acyrthosiphon pisum reared on Vicia faba and on three artificial diets with different amino acid profiles: the two first diets (name "luzerne" and "feve diets) copying the unbalanced profiles of phloem saps of alfalfa and broad bean respectively, the last one, diet AP2, deriving from aphid carcass analysis. Whatever the food source was, the free amino acid pool of aphids displayed roughly similar patterns. The role played by the symbionts in this homeostasis was investigated with aposymbiotic aphids reared on the same diets. The treated aphids had significantly higher free amino acid content than control ones. In contrast to the symbiotic situation, the well balanced free amino acid pool were not maintained in aposymbiotic aphids. Then, the metabolism of sixteen amino acids was studied on diets AP2 and "luzerne" using metabolic radio-tracers in the pea aphid. The most amino acids were subject to substantial catabolism as measured by high 14C02 production. For the first time in an aphid, we directly demonstrated the synthesis of three essential amino-acids (threonine, isoleucine and lysine) from carbons of common amino acids. The synthesis of these three compounds was only observed from amino acids that were previously converted into glutamate. To explain the quantitative results of interconversion between amino acids, we propose a compartmentalization model with the intervention of bacterial endosymbiotes for the synthesis of essential amino-acids. According to our results, glutamate is the only amino acid provided by the insect to its symbiotic bacteria. It would be used for synthesis of the essential amino acids, they would then be used by the aphid.
Don’t Give Me the Details, Just the Summary! Topic-Aware Convolutional Neural Networks for Extreme Summarization

We introduce “extreme summarization”, a new single-document summarization task which does not favor extractive strategies and calls for an abstractive modeling approach. The idea is to create a short, one-sentence news summary answering the question “What is the article about? ”. We collect a real-world, large-scale dataset for this task by harvesting online articles from the British Broadcasting Corporation (BBC). We propose a novel abstractive model which is conditioned on the article’s topics and based entirely on convolutional neural networks. We demonstrate experimentally that this architecture captures long-range dependencies in a document and recognizes pertinent content, outperforming an oracle extractive system and state-of-the-art abstractive approaches when evaluated automatically and by humans.
DYCI2 agents: merging the ”free”, ”reactive”, and ”scenario-based” music generation paradigms

The collaborative research and development project DYCI2, Creative Dynamics of Improvised Interaction, focuses on conceiving, adapting, and bringing into play efﬁcient models of artiﬁcial listening, learning, interaction, and generation of musical contents. It aims at developing creative and autonomous digital musical agents able to take part in various human projects in an interactive and artistically credible way; and, in the end, at contributing to the perceptive and communicational skills of embedded artiﬁcial intelligence. The concerned areas are live performance, production, pedagogy, and active listening. This paper gives an overview focusing on one of the three main research issues of this project: conceiving multi-agent architectures and models of knowledge and decision in order to explore scenarios of music co-improvisation involving human and digital agents. The objective is to merge the usually exclusive “free”, “reactive”, and “scenario-based” paradigms in interactive music generation to adapt to a wide range of musical contexts involving hybrid temporality and multimodal interactions.