Miracle-dz/UniFAR-FTUs huggingface dataset:
Convolving Pre-Trained Convolutional Neural Networks at Various Magnifications to Extract Diagnostic Features for Digital Pathology

Deep learning is an area of artificial intelligence that has received much attention in the past few years due to both an increase in computational power with the increased use of graphics processing units (GPU’s) for computational analyses and the performance of these class of algorithms on visual recognition tasks. They have found utility in applications ranging from image search to facial recognition for security and social media purposes. Their continued success has propelled their use across many new domains including the medical field, in areas of radiology and pathology in particular, as these fields are thought to be driven by visual recognition tasks. In this paper, we present an application of deep learning, termed ‘transfer learning’, using ResNet50, a pre-trained convolutional neural network (CNN) to act as a ‘feature-detector’ at various magnifications to identify low and high level features in digital pathology images of various breast lesions for the purpose of classifying them correctly into the labels of normal, benign, in-situ, or invasive carcinoma as provided in the ICIAR 2018 Breast Cancer Histology Challenge (BACH).
Towards the assessment of human-relevant repeated dose toxicity using an in vitro systems toxicological approach

7 Chapter 1 General introduction 9 Part I Metabolic characterization of HepaRG cells 35 Chapter 2 Carbon metabolism in HepaRG cells and its alterations upon drug exposure in a comparative study with primary human hepatocytes and HepG2 cells 37 Part II Optimization of HepaRG culture conditions for shortand longterm toxicity studies 59 Chapter 3 Hepatotoxicity assessment in 3D and 2D high-throughput systems using HepaRG cells 61 Chapter 4 Long-term maintenance of HepaRG cells in serum-free conditions and application in a repeated dose study 73 Part III Application of HepaRG cells in repeated dose toxicity studies 87 Chapter 5 In silico modeling for the prediction of dose and pathway related adverse effects in human from in vitro repeated dose studies 89 Chapter 6 Systems toxicological evaluation of valproic acid-induced toxicity in HepaRG cells 105 Chapter 7 Summary, conclusion and outlook 133 Supplementary material 139
CaCO3 nanoparticles as the tags for potentiometric detection of a cardiac biomarker using a calcium ion-selective electrode

A novel potentiometric immunosensing protocol was developed for the detection of myoglobin (a cardiac biomarker for acute myocardial infarction), using bovine serum albumin (BSA)-functionalized calcium carbonate (CaCO3) nanoparticles as the signal-generation tags and using a calcium ion-selective electrode.
A fish mortality episode reveals the expansion of invasive mummichog Fundulus heteroclitus (L., 1766) in southern Spain

The mummichog Fundulus heteroclitus , a cyprinodontiform species native to the Atlantic coast of North America, was apparently introduced to southern Iberian Pen-insula in the early 1970s, if not earlier. Until now, the Barbate marshes constituted the southern limit of the species in the Iberian Peninsula. However, a fish mortality event promoted by an anoxia episode in the Cachón River (July 31 st -August 4 th 2016) revealed a southward expansion of the species from its known southern limit. It is not known whether the mummichog has already occupied other potentially suitable habitats south to the Cachón River, but this should be of concern, since it could threaten the unique populations of some native fish species in the area.
Efficacy of AM fungi against drought stress on sweet corn cultivars with special reference to biochemical contents

This study was carried out to investigate the effect of drought stress on biochemical contents of sweet corn cultivars. The plants of sweet corn were grown in pots without mycorrhiza and with mycorrhiza i.e. control and experimental. The pots were placed under shade net and watered with normal water for one month at an interval of 4 days. The water stress treatment was started after one month at an interval of 4, 8 and 12 days. The biochemical analysis was carried out from leaves and kernels of sweet corn plants. The amount of chlorophyll, protein and starch has been decreased significantly due to increase in drought stress. The amount of proline and carbohydrates has been increased significantly with the increase in drought stress. However, these contents were more in mycorrhizal plants as compared to control plants. The results indicated that AM symbiosis alleviates the toxic effect of drought stress via improving water status of plants.
Fully unsupervised online spike sorting based on an artificial spiking neural network

Spike sorting is a crucial step of neural data processing widely used in neuroscience and neuroprosthetics. However, current methods remain not fully automatic and require heavy computations making them not embeddable in implantable devices. To overcome these limitations, we propose a novel method based on an artificial spiking neural network designed to process neural data online and completely automatically. An input layer continuously encodes the data stream into artificial spike trains, which are then processed by two further layers to output artificial trains of spikes reproducing the real spiking activity present in the input signal. The proposed method can be adapted to process several channels simultaneously in the case of tetrode recordings. It outperforms two existing algorithms at low SNR and has the advantage to be compatible with neuromorphic computing and the perspective of being embedded in very low-power analog systems for future implantable devices serving neurorehabilitation applications.
Biecheleria tirezensis sp. nov. (Dinophyceae, Suessiales), a new halotolerant dinoflagellate species isolated from the athalassohaline Tirez natural pond in Spain

ABSTRACT A new euryhaline and eurythermal dinoflagellate species, Biecheleria tirezensis sp. nov., is described based on samples taken from an extreme environment, the athalassohaline and particularly sulphate-rich Tirez natural pond (Spain). This species is able to survive in salinities from almost fresh water up to 56 and over a 5–25°C temperature range. Thus, the ecological characteristics of this isolate differentiate it from other species of the same genus. Its morphology, as examined by light, scanning and transmission electron microscopy, shows that the cells are almost spherical, with several series of amphiesmal vesicles. It also has a single elongate amphiesmal vesicle (EAV) observed by SEM and the eyespot has a type E structure, typical of Biecheleria. Spherical and smooth cysts were observed in old cultures. The pigment composition is typical of a peridinin-containing dinoflagellate. Phylogeny inferred from nuclear rDNA SSU, ITS and LSU sequences showed the isolate belongs to the genus Biecheleria, closest to B. cincta and B. brevisulcata. Modelling and analysis of the secondary structure of its ITS2 region, and that of other species of the same genus and some representatives of the most closely related genera, indicated that the isolate represents a new species clearly separated from but related to B. cincta. The criterion of the presence of Compensatory Base Changes (CBCs) in the secondary structure of the ITS2 region as an indicator of species differentiation confirmed this, supporting the establishment of the Tirez pond isolate as a new species of Biecheleria.
First Record of Myelobia smerintha (Hübner) (Lepidoptera: Pyralidae: Crambinae) in Sugarcane in Colombia1

Sugarcane (Saccharum officinarum L.) cultivation occupies approximately 474,559 ha in Colombia (Cenicaña 2011). The Hoya del Río Suárez region (Boyacá and Santander Departments in north-central Colombia) produced 100,799 tons of sugar, which accounted for 40% of the total volume of sugarcane grown for the production of panela (MADR-CCI 2012). Other major production areas are the Departments of Cundinamarca (24%), Antioquia (20%), Huila (6%), and Nariño (11%) (MADR-CCI 2012). Panela is a molded rectangular block of sugar produced by heating and concentrating sugarcane juice. Colombia is the second largest producer of panela in the world after India (Rodríguez 2000). Production of sugarcane is affected by different insect pests, and borers in the genusDiatraea (Lepidoptera: Pyralidae: Crambinae) are considered the most damaging and commonly encountered (Bustillo-Pardey 2013). Larvae of Crambinae feed upon roots and leaves of sugarcane. They bore into grasses, sedges, and rushes (Stehr 1987, Landry 1995). Larvae of Myelobia smerintha (Hübner) (Lepidoptera: Pyralidae: Crambinae) are known to bore inside stem internodes of bamboo (Guadua aculeateRupr. Ex E. Fourn.) and taquara (Bambusa tuldoides Munro) (both Poaceae), two species closely related to sugarcane (Neto & Ramos-Elorduy 2006, Landry et al. 2015). In this paper, we report the detection of M. smerintha using sugarcane as a developmental host. This is not the first record of M. smerintha in Colombia (Bleszynski 1967), but it is the first record of sugarcane as a host plant for this giant Crambinae species. In November 2015 and February 2016, a total of 10 unidentified borer larvae were collected manually from sugarcane plants in the municipality of Villeta, Cundinamarca Department. The sugarcane plants were grown near a corridor of guadua, Guadua angustifolia Kunth (Poaceae). The larvae were taken to the
Eradication of Multidrug‐Resistant Staphylococcal Infections by Light‐Activatable Micellar Nanocarriers in a Murine Model

Bacterial infections are mostly due to bacteria in their biofilm mode‐of‐growth, making them recalcitrant to antibiotic penetration. In addition, the number of bacterial strains intrinsically resistant to available antibiotics is alarmingly growing. This study reports that micellar nanocarriers with a poly(ethylene glycol) shell fully penetrate staphylococcal biofilms due to their biological invisibility. However, when the shell is complemented with poly(β‐amino ester), these mixed‐shell micelles become positively charged in the low pH environment of a biofilm, allowing not only their penetration but also their accumulation in biofilms without being washed out, as do single‐shell micelles lacking the pH‐adaptive feature. Accordingly, bacterial killing of multidrug resistant staphylococcal biofilms exposed to protoporphyrin IX‐loaded mixed‐shell micelles and after light‐activation is superior compared with single‐shell micelles. Subcutaneous infections in mice, induced with vancomycin‐resistant, bioluminescent staphylococci can be eradicated by daily injection of photoactivatable protoporphyrin IX‐loaded, mixed‐shell micelles in the bloodstream and light‐activation at the infected site. Micelles, which are not degraded by bacterial enzymes in the biofilm, are degraded in the liver and spleen and cleared from the body through the kidneys. Thus, adaptive micellar nanocarriers loaded with light‐activatable antimicrobials constitute a much‐needed alternative to current antibiotic therapies.
Internalisation des leucotoxines de S. aureus dans les cellules cibles et conséquences cellulaires associées

S. aureus secrete de nombreux facteurs de virulence qui lui permettent de lutter efficacement contre le systeme immunitaire, afin de favoriser la dissemination de la bacterie dans l’organisme hote. Parmi ces molecules, les leucotoxines ciblent principalement les cellules myeloides comme les neutrophiles, les macrophages ou encore les monocytes, et sont formees par deux sous-unites : une de classe S et une de classe F. La Leucodine de Panton et Valentine (LPV) et l’Hemolysine γ HlgC/HlgB sont deux leucotoxines dont le composant de classe S se fixe sur l’un des recepteurs du systeme du complement, le C5aR. Naturellement active par l’anaphylatoxine C5a, le C5aR voit son activite modifiee lors d’une interaction avec la LPV ou HlgC/HlgB, tout du moins pour la liberation du calcium intracellulaire. Ces deux leucotoxines, a l’instar du C5a, sont internalisees dans le neutrophile humain et utilisent le transport retrograde pour atteindre l’appareil de Golgi. Elles peuvent rester dans la cellule jusqu’a 3h sans susciter la mort pour le neutrophile. Plus tard, a 6h, seule la LPV induit de l’apoptose et de la NETose.
Ecología y reproducción de Opsanus beta (Actinopterygii: Batrachoididae) en la Laguna de Alvarado, Veracruz, México

Opsanus beta is a permanent species in the Alvarado Lagoon System (ALS), Veracruz, and eventhough it is not of economic importance, it might be actively involved in the energy transfer of the system. Currently, there is no information about the reproductive and ecological characteristics of this common fish, so this work aimed to evaluate those aspects, and to contribute with some ecological features. For this, a total of six sampling sites were selected and studied from April 2008 to December 2012. Per site, we determined fish seasonality, feeding, sex ratio, gonadosomatic index, hepatosomatic and condition factors for both sexes, as well as the fecundity and length-weight relationships. We also considered some environmental parameters such as temperature, water temperature, depth, salinity and pH. Our results on the environmental parameters analysis did not show significant differences for the study period; besides, salinity data confirmed an oligohaline environment, and the rest of the physico-chemical parameters, varied in accordance with the climatic pattern in the area. We captured a total of 519 fishes, 311 (59.9 %) males and 208 (41.1 %) females; the proportion of males resulted favorable against females throughout the study. The standard length found along the study period showed that the average was higher in males than in females. The trophic spectrum was composed of 13 food items, principally crustaceans, molluscs and fishes; in addition, cannibalism was observed over young individuals during March and April. The most advanced stages of gonadal maturation were recorded from November to March for males, and from November to February in females; generally, the Gonadosomatic index (IGS) recorded the highest values from November to April. The Hepatosomatic Index (IHS) and the Condition Factor (FC) presented an inverse relationship with the Gonadosomatic index (IGS). The fecundity of this species ranged from 96 to 428 oocytes per female. The weight-length relationship by sexes and seasons, showed a higher growth rate for males than for females, and an allometric growth type. The biological and ecological information of O. beta in ALS evidenced the importance of this species and its ecological role in the structure and dynamics of these aquatic communities. This species may be used as a model for future proposals dealing with the management and sustainable use of this ecosystem.
Eichhoria crassipes (Mart.) Solms. Application of Macrophyte in Heavy Metals Removal

The present study tested the remediation potential of Eichhornia crassipes (water hyacinth), for the removal of chromium (Cr) and Zinc (Zn) and Nickel (Ni). Fresh and young plants of equal size were grown in hydroponic medium and supplemented with 300, 600, 1200 and 2400μg/L of Cr and 600, 1200, 2400 and 6000 μg/L of Zn and 300, 600, 1200 and 2400 μg/L of Ni individually for 15 days. The bioaccumulation pattern was reported high in Zn culture. Metal toxicity in the floating macrophyte showed a significant reduction (P <0.001) on phytomass, chlorophyll, NO3-N and PO4-P uptake inhibition in comparison to control. The rate and amount of Cr uptake were minimum as compared to Zn and Ni. The rate of uptake increased with concentration and decreased with increasing time duration. The uptake and accumulation of Cr in the root were always higher than that of shoot except between 2 h to 72 h period at an initial concentration of test metal. The lowest and the highest tolerance indices in Eichhornia crassipes were recorded for Cr and Zn respectively. Bioconcentration factor (BCF) for Zn, Ni, and Cr were 14.6, 12.5 and 10.2 respectively, indicates that Eichorrnia crassipes can be a moderate accumulator of heavy metals and the ubiquitous weed could be used to clean aquatic bodies threatened with pollutants.
The 3D genome organization of Drosophila melanogaster through data integration

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of 3D genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete 3D genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our 3D geome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about the genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of differnet chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. To our knowledge our approach is the first that allows systematic integration of Hi-C and lamina DamID data for complete 3D genome structure calculation, while also explicitly considering genome structural variability.
Selection for antibiotic resistance in the aquatic environment : novel assays to detect effect concentrations of micropollutants

2 List of tables . 9 List of figures . 12 Author’s declaration . 21 Acknowledgements . 22 Definitions . 23 Abbreviations . 28 Chapter one: Literature review . 29 1.1. Background . 29 1.2. Environmental resistome . 30 1.3. Selection for resistance . 31 1.4. Costs of resistance . 33 1.5. Antibiotic uses and discharge to the environment . 35 1.6. What is driving environmental prevalence of AMR – discharge of antibiotics or resistant bacteria? 38 1.7. Mobilisation of resistance genes . 41 1.8. Issues with current research methods aiming to study resistance in the environment . 45 1.9. Problems for risk assessment of antibiotics using current methods . 48 1.10. New microbiological methods to inform risk assessment . 51 1.11. Thesis overview . 53 1.11.1. Co-authored papers . 54 Chapter two: Selection and co-selection for antibiotic resistance in a complex community, at low antibiotic concentrations . 56 2.
Potential of carapeba, Eugerres brasilianus, for culture

The Eugerres brasilianus is a commercial species appreciated in markets in the Northeastern region of Brazil . This study had as objective to evaluate and get to know the feed diet, reproductive period and management of carapeba fish in tanks in a recirculation system for intensive raising. The fish were caught with a gill net at two different places near the mouth of the Sao Francisco River. The stomach content was analyzed according to the occurrence frequency method, applying on it the Important Index of relative food, evaluating and calculating the degree of the stomach repletion. The reproductive period was established by determining the gonadosomatic indexes and gonad maturation stages. The behavior and management of the fish were observed in captivity being submitted to artificial diets in cultivation tanks. The striped carapeba feeds around dusk, having as its main feedings: Crustacea Amphipoda, Insecta Chironomidea and Crustacea Tanaidacea. The spawning happened at different moments from February to March and from July to September. The morphological differences between males and females, especially in the urogenital papilla, are the average standard length and color. In confinement, the the best fish density was from seven to eight fish/m3, showing a good indexes of centesimal composition, adapting well to the supplied diet.
Species traits and shoot–root biomass allocation in 20 dry-grassland species

A plant has a limited amount of resources at any time and it allocates them to different structures. In spite of the large number of previous studies on allocation patterns within single species, knowledge of general patterns in species allocation is still very limited. This is because each study was done in different conditions using different methodology, making generalization difficult. We investigate intraspecific above- versus below-ground biomass allocation among individuals across a spectrum of dry-grassland plant species at two different developmental stages and ask whether allocation is age- and species specific, and whether differences among species can be explained by their life-history traits and phylogeny. We collected data on above- and below-ground biomass of seedlings and adult plants of 20 species from a common garden experiment. We analysed data on shoot–root biomass allocation allometrically and studied the relationship between the allometric exponents (slopes on log–log scale), species life-history traits and phylogenetic distances. We found isometric as well as allometric patterns of biomass allocation in the studied species. Seedlings and adult individuals of more than half of the species differed in their above- versus below-ground biomass allometric exponents. Seedlings and adult individuals of the remaining species differed in their allometric coefficients (intercepts). Annual species generally allocated proportionally more to above- than below-ground biomass as seedlings than as adults, whereas perennial species showed the opposite pattern. Plant life-history traits, such as plant life span, age of first flowering, month in which the species begin flowering and specific leaf area were much more important in explaining differences in shoot–root allometry among species than were phylogenetic relationships. This suggests that allocation patterns vary greatly among closely related species but can be predicted based on species life-history traits.
Enteric infection meets intestinal function: how bacterial pathogens cause diarrhoea

V. K. Viswanathan* § , Kim Hodges ‡§ and Gail Hecht ‡ Abstract | Infectious diarrhoea is a significant contributor to morbidity and mortality worldwide. In bacterium-induced diarrhoea, rapid loss of fluids and electrolytes results from inhibition of the normal absorptive function of the intestine as well as the activation of secretory processes. Advances in the past 10 years in the fields of gastrointestinal physiology, innate immunity and enteric bacterial virulence mechanisms highlight the multifactorial nature of infectious diarrhoea. This Review explores the various mechanisms that contribute to loss of fluids and electrolytes following bacterial infections, and attempts to link these events to specific virulence factors and toxins.