Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Detection and Classification of Tumor Infiltrating Lymphocytes

The latest global statistics from 2008 show that 12.7 million new cancer cases and 7.6 million cancer deaths occurred worldwide1. This accounts for 13% of all deaths for that year, making cancer a common threat to all families. As technology becomes more efficient, a trend towards computer aided diagnostic (CAD) tools for identification, prognosis prediction and reoccurrence likelihood is becoming a reality. A cornerstone of CAD systems is the field of digital histopathology, where analyzing large quantities of cellular images can leverage the research from the mature field of computer vision. In this thesis we present two novel general theories, one focusing on homogeneity and one which quantifies heterogeneity. From these theoretical roots, we explain our two algorithms, Hierarchical Normalized Cuts (HNCuts) and Local Morphologic Scale (LMS), which when used together, create a system which can automatically segment (via homogeneity) and classify (via heterogeneity) lymphocytes from digital histology images as either tumoral or stromal. There is strong evidence that this laborious task is a valuable prognostic indicator, motivating the development of algorithms for its automation. The first algorithm, HNCut, is responsible for segmenting the stained lymphocytes from the digital image. By using a hierarchical data structure with a novel frequency weighted mean shift for clustering, our approach is able to perform segmentation with very high throughput in a reproducible robust manner. We take our theory which contributes a general approach towards segmenting colors of interest defined by a user specified swatch and apply it to the aforementioned histology task, which previously took a pathologist a day to complete. Using our algorithm it can be completed in a matter of seconds. The second algorithm, LMS, classifies the lymphocytes identified by HNCut as either tumoral or stromal based on their local morphology. While available theories tend to focus on quantifying homogeneity, our theory contributes a general approach towards quantifying 1World Heath Organization, GLOBOCAN 2008
Lattice-Boltzmann simulation of coaxial jet noise generation

A Lattice-Boltzmann model for high-speed non-isothermal subsonic flows is used to simulate the unsteady jet exhausting from a short-cowl axisymmetric coaxial nozzle and the associated noise. The primary and secondary jet exit Mach numbers are 0.87 and 0.90, respectively, the secondary jet Reynolds number is 2.8 · 10, and the primary to secondary temperature ratio is 2.7. The far-field is computed through a Ffowcs-Williams and Hawkings analogy applied to a fluid surface encompassing the plume. Numerical results are presented for one exhaust condition and for one grid resolution only; in this respect, the main achievements of the present effort are a sanity check of the simulation setup and a first stage of a grid resolution study. The presented nearand far-field results confirm that the underlying flow features are reasonably represented by the numerical solution. Areas of required improvements have been clearly identified in the growth rate of the shear-layer turbulent fluctuations and will be the main objective of future studies. More in general, the sensitivity of the jet turbulent properties to the mesh resolution will be investigated and published in the future as a completing part of the present work.
Mechanically reconfigurable waveguide-slot single element using tuning screws

A mechanically reconfigurable waveguide-slot single radiating element is presented. The tuning mechanism consists on three metallic screws introduced through the bottom wall of the feeding waveguide. The insertion length of the tuning screws and the distance to the slot are used to control the radiated signal as well as to maintain a good input matching response. Several prototypes with different slot lengths have been manufactured to experimentally validate the reconfigurable performance. The proposed triple tuning screw waveguide-slot radiator provides a low cost and simple mechanism to conform a reconfigurable array antenna.
Analysis of helminth communities of the pine marten, Martes martes, in Spain: Mainland and insular data

The present study analyses the helminth communities found in one hundred and two specimens of Martes martes from the Iberian Peninsula and the Balearic Archipelago. The component community is constituted by seventeen helminth species, which frequency and mean abundance show a bimodal pattern. The set of core species is constituted by the trichurids Pearsonema plica, Eucoleus aerophilus and Aonchotheca putorii (72.2% of total helminth individuals found), while the remaining can be considered satellite species. Significant co-occurrences were found among E. aerophilus/A. putorii and E. aerophilus/P. plica. These results demonstrate the great importance of earthworms within the diet of pine marten and contribute to the knowledge of the pine marten’s food ethology, since this kind of prey normally goes undetected in diet studies. Several helminth species, as Sobolevingylus petrowi, Centrorhynchus aluconis, Uncinaria criniformis, Mastophorus muris and Spirura rytipleurites seurati seem to show geographical distributions limited to insular ecosystems. Moreover, helminth communities of M. martes among four Spanish territories, including mainland and insular areas, are characterized and compared.
Protective effect of a new C5a receptor antagonist against ischemia-reperfusion injury in the rat small intestine.

BACKGROUND The complement system is a major contributor to the pathogenesis of intestinal ischemia-reperfusion (I/R) injury. We have studied the action of an orally active complement factor 5a (C5a) receptor antagonist, the cyclic peptide AcF-(OPdChaWR) [Ac-Phe(Orn-Pro-d-cyclohexylalanine-Trp-Arg)] against local and remote intestinal I/R injuries in rats. MATERIALS AND METHODS Anesthetized rats were administered with AcF-(OPdChaWR) at doses of 1 mg/kg intravenously or 0.3, 1, or 10 mg/kg orally with pyrogen-free saline for sham control animals. The superior mesenteric artery was occluded for 30 min and the intestine reperfused for 120 min. Changes associated with tissue injury were assessed by neutropenia, intestinal edema, serum tumor necrosis factor-alpha, serum haptoglobin, plasma aspartate aminotransferase, and histopathology. RESULTS Pretreatment with either a single intravenous dose (1 mg/kg), or a single oral dose (10 mg/kg) of AcF-(OPdChaWR) significantly inhibited I/R induced neutropenia, the elevated serum levels of tumor necrosis factor-alpha, haptoglobin, and plasma aspartate aminotransferase, as well as intestinal edema. Histological analysis of AcF-(OPdChaWR)-treated I/R animals showed markedly reduced mucosal layer damage compared to that of untreated rats. CONCLUSIONS These results indicate that a potent antagonist of C5a receptors on human cells protects the rat small intestine from I/R injury after oral or intravenous administration. Small molecule C5a antagonists may have some therapeutic utility in reperfusion injury.
The cost-effectiveness of interleukin-1 genetic testing for periodontal disease.

BACKGROUND A genetic test for a composite interleukin-1 (IL-1) genotype is being marketed to predict risk for progression of periodontal disease. The objective of this study was to determine the clinical scenario required to produce cost-effective results with the use of IL-1 testing to identify high-risk patients. METHODS A disease simulation model was developed using decision-analytic techniques and a 30-year time frame. RESULTS Using different modeling scenarios, the genetic test produced results ranging from cost savings of $830,140 and 52.8 fewer cases of severe periodontitis to increased costs of $300,430 and 3.6 additional cases of severe periodontitis (per 1,000 patients). Three parameters in the analysis were highly influential: 1) the compliance rate for maintenance therapy in test positive versus non-tested patients; 2) the effectiveness of non-surgical therapy; and 3) the relative risk of disease progression for test positive patients. CONCLUSION The model produced a wide range of outcomes reflecting our incomplete understanding of the biology, optimal treatment, and genetic susceptibility of periodontal diseases. However, the model demonstrates that three clinical parameters are highly influential in determining if IL-1 testing can be implemented in a primary care setting in a cost-effective manner.
New Mesochria species (Diptera: Anisopodidae) from Fiji, with notes on the classification of the family

Two new species of Mesochria from Fiji are described and illustrated: M. schlingeri Thompson, n. sp. and M. vulgaris Thompson, n. sp. A key to genera of Aniso- podidae and key to the species of Mesochria species are provided, along with notes on the classification of the family.
Lipopolysaccharides of Helicobacter pylori strains P466 and MO19: structures of the O antigen and core oligosaccharide regions.

Lipopolysaccharides (LPS) from phenol-water extraction of dyspeptic (P466) and asymptomatic (MO19) strains of Helicobacter pylori were each isolated as water-soluble material of high relative molecular mass (high M(r)) and as water-insoluble gels of low M(r). Chemical and spectroscopic analyses of the soluble LPS and oligosaccharides liberated from the water-insoluble gels led to proposed structures for chains comprising the O antigen, intervening, and core regions. As in the LPS from the type strain NCTC 11637 [Aspinall, G. O. , et al. (1996) Biochemistry 35, 2489-2497], the O antigen region of the P466 LPS is characterized by the presence of extended chains with fucosylated and nonfucosylated N-acetyllactosamine units, the former carrying alpha-L-fucopyranose units at O-3 of beta-D-GlcNAc residues. This structure differs from that of the type strain in termination of the O chain by a Lewis(y) (Le(y)) antigenic determinant [alpha-L-Fuc(1-->2)beta-D-Gal(1-->4)[alpha-L-Fuc(1-->3)]beta-D-GlcNAc] but also has internal Lewis(x) (Le(x)) units. The inner core region of the P466 LPS is indistinguishable from that in the type strain. In contrast, the O antigen region of the LPS from strain MO19 consists of a single Le(y) epitope linked via a 3-linked beta-D-Gal to an intervening region on the basis of a sequence of 3-linked D-glycero-alpha-D-manno-heptose residues which is in turn linked to an inner core identical to that in the type strain and the P466 strain. Results in this and the preceding paper show that LPS from the three H. pylori strains display molecular mimicry of human cell surface glycoconjugates but may vary in the expression of Le(x) or Le(y) determinants, the degree of O antigen chain extension, or in the presence of an additional region between the inner core and the O antigen.
Poly(ADP-ribose) Polymerase and Ku Autoantigen Form a Complex and Synergistically Bind to Matrix Attachment Sequences*

Genomic sequences with a cluster of ATC sequence stretches where one strand consists exclusively of well mixed As, Ts, and Cs confer high base unpairing propensity under negative superhelical strain. Such base unpairing regions (BURs) are typically found in scaffold or matrix attachment regions (SARs/MARs) that are thought to contribute to the formation of the loop domain structure of chromatin. Several proteins, including cell type-specific proteins, have been identified that bind specifically to double-stranded BURs either in vitro or in vivo. By using BUR-affinity chromatography to isolate BUR-binding proteins from breast cancer SK-BR-3 cells, we almost exclusively obtained a complex of poly(ADP-ribose) polymerase (PARP) and DNA-dependent protein kinase (DNA-PK). Both PARP and DNA-PK are activated by DNA strand breaks and are implicated in DNA repair, recombination, DNA replication, and transcription. In contrast to the previous notion that PARP and Ku autoantigen, the DNA-binding subunit of DNA-PK, mainly bind to free ends of DNA, here we show that both proteins individually bind BURs with high affinity and specificity in an end-independent manner using closed circular BUR-containing DNA substrates. We further demonstrate that PARP and Ku autoantigen form a molecular complexin vivo and in vitro in the absence of DNA, and as a functional consequence, their affinity to the BURs are synergistically enhanced. ADP-ribosylation of the nuclear extract abrogated the BUR binding activity of this complex. These results provide a mechanistic link toward understanding the functional overlap of PARP and DNA-PK and suggest a novel role for these proteins in the regulation of chromatin structure and function.
An Open-Source Engine for the Processing of Electron Backscatter Patterns: EBSD-Image

Abstract An open source software package dedicated to processing stored electron backscatter patterns is presented. The package gives users full control over the type and order of operations that are performed on electron backscatter diffraction (EBSD) patterns as well as the results obtained. The current version of EBSD-Image (www.ebsd-image.org) offers a flexible and structured interface to calculate various quality metrics over large datasets. It includes unique features such as practical file formats for storing diffraction patterns and analysis results, stitching of mappings with automatic reorganization of their diffraction patterns, and routines for processing data on a distributed computer grid. Implementations of the algorithms used in the software are described and benchmarked using simulated diffraction patterns. Using those simulated EBSD patterns, the detection of Kikuchi bands in EBSD-Image was found to be comparable to commercially available EBSD systems. In addition, 24 quality metrics were evaluated based on the ability to assess the level of deformation in two samples (copper and iron) deformed using 220 grit SiC grinding paper. Fourteen metrics were able to properly measure the deformation gradient of the samples.
Authentication Protocol for Healthcare Services over Wireless Body Area Networks

Ubiquitous healthcare service is one of the major fields of research for wireless body area networks (WBANs). Ensuring complete and a good level of security for such types of WBANs, is not a trivial task. It is practically impossible to deal with all sorts of security threats with a single mechanism. This paper reviews Khan et al.’s authentication protocol for healthcare service over WBANs and shows that it does not provide forward secrecy. Furthermore, this paper proposes a remedy protocol for Khan et al.’s authentication protocol and the previous related protocols. The proposed protocol could be utilized as a basic security building block for healthcare applications based on WBANs.
Brucella ceti Infection in Harbor Porpoise (Phocoena phocoena)

We describe Brucella sp. infection and associated lesions in a harbor porpoise (Phocoena phocoena) found on the coast of Belgium. The infection was diagnosed by immunohistochemistry, transmission electron microscopy, and bacteriology, and the organism was identified as B. ceti. The infection’s location in the porpoise raises questions of abortion and zoonotic risks.
Effects of topography on structure and composition of the understorey herpetofauna of a lowland rainforest in the Golfo Dulce Region, Costa Rica

Topographische Faktoren konnen die Biodiversitat auf kleinster raumlicher Ebene beeinflussen und daher einen entscheidenden Einfluss auf Artenreichtum, -zusammensetzung und –abundanz haben. In unserer Studie haben wir diesen Effekt auf die Biodiversitat der Herpetofauna in einem Tiefland-Regenwald in Costa Rica untersucht. Amphibien und Reptilien wurden auf jeweils 6 verschiedenen Transekten im Kammwald (RF), Hangwald (SF) und Schluchtwald (CF) zwischen November 2015 und Januar 2016 erfasst. Wahrend insgesamt 252 Transektbegehungen konnten 58 verschiedene Arten gefunden werden, 26 Amphibien- und 33 Reptilienarten. Es wurden 1580 Individuen dokumentiert, 840 Reptilien und 740 Amphibien. Die Abundanz der gesamten Herpetofauna variiert zwischen den drei Waldtypen, wobei die meisten Individuen an CF-Standorten gefunden wurden. Fur den Artenreichtum konnten solche signifikanten Unterschiede nicht festgestellt werden. Im Detail konnte auch fur Reptilien (jedoch nicht fur Amphibien) alleine eine signifikant hohere Abundanz an CF-Transekten nachgewiesen werden. Auch zeichnete sich CF durch eine signifikant unterschiedliche Artenzusammensetzungen im Vergleich zu den beiden anderen Waldtypen SF und RF aus. so konnte an CF-Standorten eine erhohte Anzahl an von Fliesgewassern abhangigen Arten gefunden werden. Dies zeigt eindeutig, dass aufgrund unterschiedlicher biotischer und abiotischer Bedingungen artspezifische Praferenzen fur einzelne durch die Topografie bedingte Waldtypen bestehen. Unsere Ergebnisse betonen die Bedeutung von kleinraumiger topographischer Heterogenitat fur den lokalen Artenreichtum der Herpetofauna. Daher muss kleinraumige Topographie bei Schutzbemuhungen fur den gesamten Artenreichtum von Amphibien und Reptilien in tropischen Tieflandregenwaldern berucksichtigt werden.
Flexpoint: An Adaptive Numerical Format for Efficient Training of Deep Neural Networks

Deep neural networks are commonly developed and trained in 32-bit floating point format. Significant gains in performance and energy efficiency could be realized by training and inference in numerical formats optimized for deep learning. Despite advances in limited precision inference in recent years, training of neural networks in low bit-width remains a challenging problem. Here we present the Flexpoint data format, aiming at a complete replacement of 32-bit floating point format training and inference, designed to support modern deep network topologies without modifications. Flexpoint tensors have a shared exponent that is dynamically adjusted to minimize overflows and maximize available dynamic range. We validate Flexpoint by training AlexNet, a deep residual network and a generative adversarial network, using a simulator implemented with the neon deep learning framework. We demonstrate that 16-bit Flexpoint closely matches 32-bit floating point in training all three models, without any need for tuning of model hyperparameters. Our results suggest Flexpoint as a promising numerical format for future hardware for training and inference.
Rôle des fluides extrapalléaux des bivalves dans la défense immunitaire : cas de la maladie de l'anneau brun chez la palourde d'élevage Ruditapes philippinarum

Pour contrer les pathogenes, le systeme de defense interne des bivalves est base sur l'hemolymphe, fluide circulant, engendrant l'immunite a mediation cellulaire assuree par les hemocytes et une panoplie de facteurs humoraux. Le modele de la maladie de l'anneau brun (mab) a ete utilise afin de mieux comprendre la strategie de defense mise en oeuvre par l'hote (la palourde d'elevage ruditapes philippinarum) pour contrer le pathogene (vibrio tapetis). Cette maladie coquilliere est caracterisee par la presence d'un depot organique sur la face interne des valves. L'agent infectieux etant principalement associe a la lame periostracale et au depot organique, tous deux baignes par les fluides extrapalleaux, le role de ces fluides dans le processus de defense a ete particulierement considere. Nos resultats montrent la presence, chez des palourdes saines, de facteurs de defense, hemocytes, enzymes lytiques et activite antibacterienne, dans les fluides extrapalleaux. Une augmentation de la concentration en hemocytes, de l'activite du lysozyme et de l'activite antibacterienne a ete observee dans l'hemolymphe et dans les fluides extrapalleaux de palourdes malades. Une mobilisation de cellules immunocompetentes vers les fluides extrapalleaux, siege du principal site d'infection, a ete observee. La reaction de defense des palourdes permet de surmonter la maladie et de presenter un phenomene de guerison traduit par une baisse de la charge en pathogene et un recouvrement du depot organique par des nouvelles couches calcifiees. Une faible activite phagocytaire a ete mesuree chez les animaux fortement atteints en comparaison des palourdes saines. Les experiences menees au laboratoire ont demontre un effet considerable de la temperature sur les parametres de defense et sur le developpement de la maladie, des resultats qui vont dans le meme sens que les observations epidemiologiques sur le terrain concernant l'absence de la mab dans les pays ayant une tres forte temperature estivale. De fortes mortalites ont ete reproduites apres inoculation du pathogene dans la cavite extrapalleale ou dans la chair des palourdes. Ces resultats soulignent la pathogenicite de v. Tapetis et pourraient expliquer les mortalites d'animaux malades sur les parcs d'elevage suite a la penetration du pathogene dans les tissus d'individus affaiblis.
Computer Simulations of Membrane-Lytic peptides: Perspectives in Drug Design

Structure activity relationships were investigated for membrane-lytic peptides (MLP) Ltc1 and Ltc2a from the latarcin family. The peptides were studied via long-term molecular dynamics (MD) simulations in different membrane environments (detergent micelles, mixed lipid bilayers mimiking eukaryotic and bacterial membranes). The calculated structure of Ltc2a in sodium dodecyl sulfate micelle agrees well with the data obtained by (1)H-NMR spectroscopy. This validates the applied modeling approach. The binding mode of MLPs is governed by several factors: (i) the membrane surface curvature; (ii) the conformational plasticity and hydrophobic organization of the peptide, which depend on the arrangement of charged, non-polar and helix-breaking residues in the amino acid sequence. In contrast to Ltc1, insertion of Ltc2a into model membranes induces significant changes in dynamic behavior of lipids in the contact region. Such a prominent membrane destabilization correlates with high membrane-lytic activity of Ltc2a. In all cases the "membrane response" has a local character and is caused by formation of specific peptide-lipid contacts. Results of MD simulations of Ltc2a in model membranes were used to develop a number of its analogs with predefined activity.
Effects of Dietary Vitamin C Supplementation on Some Serum Biochemical Parameters of Laying Japanese Quails Exposed To Heat Stress (34.8°C)

SUMMARY This experiment was conducted to evaluate the effects of vitamin C (Lascorbic acid) on some biochemical serum parameters such as albumin, globulin, creatinine, cholesterol, VLDL, calcium, triglyceride, glucose concentrations and alkaline phosphatase (ALP) activity. Forty eight laying Japanese quails were divided into four groups and exposed to heat stress (34.8 ± 1.25°C) for 75 days. Animals in control group were fed with a basal diet, whereas experimental animals were fed with a basal diet supplemented with either 150, 250, 500 mg of L-ascorbic acid/kg of diet. Compared to controls, the serum concentrations of cholesterol, VLDL, triglyceride and the ALP activity in birds supplemented with vitamin C decreased significantly (p<0.01, p<0.001 for cholesterol), whereas albumin concentrations showed significant (p<0.01) elevations. Serum concentrations of creatinine, globuline, calcium and glucose were not statistically significantly altered. On the other hand, the variations of serum biochemical marker concentrations or activities were not correlated with the dietary vitamin C doses. As a consequence, dietary vitamin C supplementation reduces the biochemical adverse effects of heat stress on laying Japanese quails. Furthermore, 150 mg vitamin C/kg diet would be enough to prevent the damaging effects of heat stress on laying Japanese quails.