Miracle-dz/UniFAR-FTUs huggingface dataset:
Apoptosis of L929 cells by etoposide: a quantitative and kinetic approach.

Exponentially growing L929 cells were continuously exposed to 1 or 10 microM etoposide (VP-16). The effects of such treatment on cell growth, cycle distribution, morphology, and selected biochemical events were examined. DNA synthesis rates were markedly decreased and the protein/DNA ratio increased (unbalanced growth). Growth was blocked, with most cells being cycle arrested by 24 h in (late S-)G2-M. An asynchronous process of cell death then developed. Cells initially shrank into eosinophilic, trypan blue-excluding bodies, which were then released into the medium, and eventually became permeable to trypan blue. Transmission electron microscopy confirmed that dying cells acquired an apoptotic morphotype, with compaction and margination of chromatin, loss of microvilli, and shrinkage of cytoplasm and nucleus. Tissue transglutaminase activity and intensity of immunostaining rapidly increased in treated cultures. Internucleosomal DNA fragmentation could not be detected by agarose gel electrophoresis, yet flow cytometry revealed that the apoptotic bodies had a very low DNA fluorescence (< or = 10% of the 2n value). In agreement with the microscopic findings, this suggested that extensive DNA degradation had occurred in dead cells. While rates of cell loss from the monolayer amounted to 21 and 57% day(-1) (1 and 10 microM VP-16, respectively), apoptotic indexes largely underestimated the extent of the process. These indexes only measured the accumulation of apoptotic bodies, i.e., the balance between their generation and disposal. The latter occurred by mechanisms similar to those that operate in tissues: "secondary necrosis" or phagocytosis by viable homotypic cells in the monolayer ("homophagy").
Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure

The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.
Author identification in short texts

Most research on author identification considers large texts. Not many research is done on author identification for short texts, while short texts are commonly used since the rise of digital media. The anonymous nature of internet applications offers possibilities to use the internet for illegitimate purposes. In these cases, it can be very useful to be able to predict who the author of a message is. Van der Knaap and Grootjen [28] showed that authors of short texts can be identified using single words (word unigrams) with Formal Concept Analysis. In theory, grammatical information can also be used as an indication of the author of the text. Grammatical information can be captured by word bigrams. Word bigrams are pairs of successive words, so they reveal some information on the sentence structure the author used. For this thesis I performed experiments using word bigrams as features for author identification to determine whether performance increases compared to using word unigrams as features. In most languages many grammatical relations within a sentence are between words that are not successive. The DUPIRA parser, a natural language parser for Dutch, produces dependency triplets that represent relations between non successive words, based on the Dutch grammar. I used these triplets as features, either alone or in combination with unigrams or bigrams. People often use smileys when communicating with someone using digital media. Therefore, I also examined the influence of smileys on author identification. The messages used for the experiments are obtained from the subsection ‘Eurovision Songfestival 2010’ of the fok.nl message board. With these messages the data files for 7 feature sets were constructed: word unigrams excluding smileys, word unigrams including smileys, word bigrams excluding smileys, word bigrams including smileys, only dependency triplets, triplets+word unigrams, triplets+word bigrams. A support vector machine algorithm (SVM) was used as the classification method. This is a commonly used algorithm for author identification. There are different implementations of SVM. In this thesis SMO, LibSVM and LibLINEAR are compared. The LibLINEAR algorithm gave the best results. The results revealed that in all conditions the performance is above chance level. So all reveal some information about the author. The performance for the word unigrams including smileys showed the best results, while the performance using the dependency triplets is the lowest. Results also revealed that when smileys are considered the performance increases, so smileys provide additional information about the author.
Evaluation of a novel monoclonal enzyme immunoassay for detection of Helicobacter pylori antigen in stool from children

Background: Reliable non-invasive methods for detection of Helicobacter pylori infection are required to investigate the incidence, transmission, and clearance of infection in childhood. Aim: To evaluate a new monoclonal enzyme immunoassay (EIA) (FemtoLab H pylori Cnx) for detection of H pylori antigen in stool in a large cohort of children compared with invasive diagnostic methods and the 13C urea breath test. Patients and methods: A total of 302 symptomatic previously untreated children (aged 0.5–18.7 years; 148 girls) were recruited at three centres. H pylori status was defined by results of culture, histology, the rapid urease test, and the 13C urea breath test. Stool samples were investigated locally by the EIA using two different production lots. According to the manufacturer’s recommendations, an optical density (OD) of 0.150 was used as a cut off value. Results: OD values clearly differentiated between the 92 H pylori infected and the 210 non-infected children (median (5th–95th percentiles) 2.729 (0.232–>4.000) v 0.021 (0.009–0.075)). Only two false positive and two false negative results occurred, giving a sensitivity, specificity, positive predictive value, and negative predictive value of 98%, 99%, 98%, and 99%, respectively. No significant relation was found between age and OD values in infected or non-infected children. Conclusions: The monoclonal stool antigen EIA was excellent in diagnosing H pylori infection in symptomatic children. Accuracy was independent of the laboratory, production lot used, or the child’s age. Because only 18/116 children <6 years of age were infected with H pylori, further validation of the test is needed in young infected children.
Excitatory effect of Clostridium perfringens alpha toxin on the rat isolated aorta

1 Clostridium perfringens alpha toxin caused contraction of the isolated aorta of the rat in a dose‐dependent manner. 2 The contractile action caused by the toxin was inhibited or abolished by calcium antagonists such as nifedipine, verapamil and cinnarizine, or a Ca‐free medium, but was not affected by phentolamine, chlorpheniramine, atropine, tetrodotoxin or a low Na medium. 3 The toxin stimulated Ca uptake into the aorta in a dose‐dependent manner. 4 8‐N,N'‐diethylaminooctyl‐3,4,5‐trimethoxybenzoate (TMB‐8) blocked significantly both the toxin‐ and noradrenaline (NA)‐induced contractions. 5 Trifluoperazine (TFP) and N‐(6‐aminohexyl)‐5‐chloro‐l‐naphtharene sulphonamide (W‐7) did not affect the contractile activity of the toxin but blocked the NA‐induced contraction. 6 The toxin also stimulated the 32P phosphate labelling of phosphatidylinositol (PI) and phosphatidic acid (PA) in the preparation. 7 These results indicate that the toxin‐induced contraction, which is different from that induced by NA, is the result of a direct action of the toxin on the aorta and is due to an increased Ca2+ permeability across the smooth muscle membrane. It is suggested that the contractile response to the toxin is associated with activation of phospholipid metabolism and enhanced entry of Ca into the aorta.
Efficient resting-state EEG network facilitates motor imagery performance

Objective. Motor imagery-based brain–computer interface (MI-BCI) systems hold promise in motor function rehabilitation and assistance for motor function impaired people. But the ability to operate an MI-BCI varies across subjects, which becomes a substantial problem for practical BCI applications beyond the laboratory. Approach. Several previous studies have demonstrated that individual MI-BCI performance is related to the resting state of brain. In this study, we further investigate offline MI-BCI performance variations through the perspective of resting-state electroencephalography (EEG) network. Main results. Spatial topologies and statistical measures of the network have close relationships with MI classification accuracy. Specifically, mean functional connectivity, node degrees, edge strengths, clustering coefficient, local efficiency and global efficiency are positively correlated with MI classification accuracy, whereas the characteristic path length is negatively correlated with MI classification accuracy. The above results indicate that an efficient background EEG network may facilitate MI-BCI performance. Finally, a multiple linear regression model was adopted to predict subjects’ MI classification accuracy based on the efficiency measures of the resting-state EEG network, resulting in a reliable prediction. Significance. This study reveals the network mechanisms of the MI-BCI and may help to find new strategies for improving MI-BCI performance.
El real seminario de nobles de Madrid y la formación de las élites en el siglo XVIII

Este trabajo, basado esencialmente en los fondos del Archivo Historico Nacional (seccion Universidad y Clero), consta de tres partes : - ? quienes estudiaban en el seminario ? - ? que ensenanza se daba ? - ? para que empleos, cargos o funciones preparaba a los seminaristas ?
Characterization of a repetitive element detected by NheI in the genomes of Salmo species.

The genomes of the two species in the genus Salmo (Atlantic salmon, S. salar; brown trout, S. trutta) contain a 380-bp repetitive element that is flanked by the recognition sequence of the restriction enzyme NheI. These elements, which comprise approximately 1.2% of the salmon genome, do not exist in long tandem arrays as is typical of satellite DNA. A comparison of the sequences of 16 salmon and 7 trout elements revealed that members of this family of repetitive DNA are closely related to one another (over 95% identity). Subfamily structure exists and there is evidence that members of the same subfamilies are found in both Salmo species. A search of the GenBank database indicated that sequences homologous to the NheI repeat are located within a 1424-bp segment inserted immediately downstream of the 5' end of a Tc1 transposon-like sequence isolated from Atlantic salmon (A.R. Radice, B. Bugaj, D.H. Fitch, and S.W. Emmons, unpublished data; GenBank accession No. L12206).
A numerical method for predicting the bending fatigue life of NiTi and stainless steel root canal instruments.

AIM To evaluate the bending fatigue lifetime of nickel-titanium alloy (NiTi) and stainless steel (SS) endodontic files using finite element analysis. METHODOLOGY The strain-life approach was adopted and two theoretical geometry profiles, the triangular (TR) and the square cross-sections, were considered. Both low-cycle fatigue (LCF) lifetime and high-cycle fatigue (HCF) lifetime were evaluated. RESULTS The bending fatigue behaviour was affected by the material property and the cross-sectional configuration of the instrument. Both the cross-section factor and material property had a substantial impact on fatigue lifetime. The NiTi material and TR geometry profiles were associated with better fatigue resistance than that of SS and square cross-sections. CONCLUSIONS Within the limitations of this study, finite element models were established for endodontic files to prejudge their fatigue lifetime, a tool that would be useful for dentist to prevent premature fatigue fracture of endodontic files.
Exploiting the Natural Diversity in Adenovirus Tropism for Therapy and Prevention of Disease

ABSTRACT Since targeting of recombinant adenovirus vectors to defined cell types in vivo is a major challenge in gene therapy and vaccinology, we explored the natural diversity in human adenovirus tissue tropism. Hereto, we constructed a library of Ad5 vectors carrying fibers from other human serotypes. From this library, we identified vectors that efficiently infect human cells that are important for diverse gene therapy approaches and for induction of immunity. For several medical applications (prenatal diagnosis, artificial bone, vaccination, and cardiovascular disease), we demonstrate the applicability of these novel vectors. In addition, screening cell types derived from different species revealed that cellular receptors for human subgroup B adenoviruses are not conserved between rodents and primates. These results provide a rationale for utilizing elements of human adenovirus serotypes to generate chimeric vectors that improve our knowledge concerning adenovirus biology and widen the therapeutic window for vaccination and many different gene transfer applications.
Toxigenic Vibrio cholerae O1 in Water and Seafood, Haiti

During the 2010 cholera outbreak in Haiti, water and seafood samples were collected to detect Vibrio cholerae. The outbreak strain of toxigenic V. cholerae O1 serotype Ogawa was isolated from freshwater and seafood samples. The cholera toxin gene was detected in harbor water samples.
Towards Unimodular Transformations for Non-perfectly Nested Loops

In this paper we discuss a possibility to extend unimodular transformations to non-perfectly nested loops. The main idea behind this extension is to convert a non-perfectly nested loop into a perfectly nested one by moving code into to innermost loop and properly guarding it to avoid multiple execution. This form of the loop can be viewed as an intermediate form for the transformation. Having obtained a perfectly nested loop, unimodular transformations can be applied in the usual way. The result of this transformation still contains guards. We show how to eliminate these guards. We illustrate our technique by transforming the ijk-version of LU-decomposition to the ikj-version.
Physically Grounded 3D Scene Interpretation with Detailed Object Models

We explore 3D scene reconstruction from a single view building on detailed 3D representations of object classes. These representations allow precise estimation of 3D shape and pose of individual objects, as well as explicit modeling of occlusions. We use the rich detail afforded by these models to reason about physical interactions among multiple object instances, and empirically demonstrate superior performance to models where no such reasoning is performed.
Self-association and Domains of Interactions of an Amphipathic Helix Peptide Inhibitor of HIV-1 Integrase Assessed by Analytical Ultracentrifugation and NMR Experiments in Trifluoroethanol/H2O Mixtures*

EAA26 (VESMNEELKKIIAQVRAQAEHLKTAY) is a better inhibitor of human immunodeficiency virus, type 1, integrase than its parent Lys-159, reproducing the enzyme segment 147–175 with a nonpolar-polar/charged residue periodicity defined by four helical heptads (abcdefg) prone to collapse into a coiled-coil. Circular dichroism, nuclear magnetic resonance, sedimentation equilibrium, and chemical cross-linking were used to analyze EAA26 in various trifluoroethanol/H2O mixtures. In pure water the helix content is weak but increases regularly up to 50–60% trifluoroethanol. In contrast the multimerization follows a bell-shaped curve with monomers in pure water, tetramers at 10% trifluoroethanol, and dimers at 40% trifluoroethanol. All suggest that interhelical interactions between apolar side chains are required for the coiled-coil formation of EAA26 and subsist at medium trifluoroethanol concentration. The NH temperature coefficients measured by nuclear magnetic resonance show that at low trifluoroethanol concentration the amide groups buried in the hydrophobic interior of four α-helix bundles are weakly accessible to trifluoroethanol and are only weakly subject to its hydrogen bond strengthening effect. The increased accessibility of trifluoroethanol to buried amide groups at higher trifluoroethanol concentration entails the reduction of the hydrophobic interactions and the conversion of helix tetramers into helix dimers, the latter displaying a smaller hydrophobic interface. The better inhibitory activity of EAA26 compared with Lys-159 could arise from its better propensity to form a helix bundle structure with the biologically important helical part of the 147–175 segment in integrase.
Shear and Convective Turbulence in a Model of Thermohaline Intrusions

Abstract Thermohaline interleaving is an important mechanism for laterally fluxing salt, heat, and nutrients between water masses. Interleaving is driven by a release of potential energy resulting from the differing diffusivities of heat and salt in seawater. The flows are composed of stacked intrusions that flux more and less buoyant water in opposite directions. In this paper, the role of shear instability caused by this juxtaposed motion is investigated. The model described in Walsh and Ruddick is modified to include both the effects of shear-induced turbulence and an improved convective mixing parameterization. Shear and convective mixing play a similar and significant role in interleaving dynamics. In the absence of either instability, cross-front fluxes are increased by approximately 30%. While in situ observations of horizontal diffusivity resulting from interleaving are not yet precise enough to calibrate the parameterizations independently, parameter values based on independent laboratory and num.
Recherche d'information flexible basée CP-nets

RESUME. Ce papier decrit une approche de recherche d’information (RI) flexible fondee sur l’utilisation des CP-Nets (Conditional Preferences Networks). Le formalisme CP-Net est utilise d’une part, pour la representation graphique de requetes flexibles exprimant des preferences qualitatives et d’autre part pour l’evaluation flexible de la pertinence des documents. Le raisonnement et l’inference sur les preferences qualitatives n’etant pas aises, nous devons quantifier les preferences. Nous proposons alors une approche de ponderation automatique des requetes CP-Nets. Cette ponderation, correspondant a la quantification du CP-Net requete par des valeurs d’utilites, conduit a un UCP-Net. L’UCP-Net correspond a une requete booleenne ponderee. Une utilisation des CP-Nets est egalement proposee pour la representation des documents dans la perspective d’une evaluation flexible des requetes.
Emotional Reactivity during Anticipation and Perception of Affective Pictures

Abstract The focus of the present study was on further exploring anticipatory responses to emotional stimuli by measuring the eyeblink startle reflex in a variation of the picture-picture affective learning procedure. Participants (113 undergraduate women) were not explicitly instructed before the experiment began. Instead, they had to learn the specific relations between cues (geometrical shapes) and emotional pictures based on pairings during the first part of the task. Plausible contingency learning effects were tested afterwards, in a parallel sequence of trials including auditory probes during cues and pictures processing during the second part of the task. Results did show the typical affective startle modulation pattern during perception, linear F(1, 200) = 52.67, p < . 0001, but unexpected inhibition for both pleasant and unpleasant, compared to neutral cues, during anticipation, quadratic F(1, 200) = 7.07, p < . 009. All patterns of startle modulation were independent of cue-picture contingency awareness (all interactions Fs < 1). Skin conductance changes showed the predictable quadratic trend either during picture perception or anticipatory periods (greater activity for emotional vs. neutral; overall quadratic F(1, 224) = 7.04, p < . 01), only for participants fully aware of the cue-picture contingency, quadratic F(1, 158) = 5.86, p < . 02. Overall, our results during anticipation (cues processing) seem to suggest that more resources were allocated to highly arousing pictures that engage attention. Differences between the present results and prior research may be attributed to procedural variations in the sample, cues, or instructions. Future studies should also explore in more detail the role of the contingency awareness during anticipation.
Autolytic activity of human calpain 7 is enhanced by ESCRT‐III‐related protein IST1 through MIT–MIM interaction

Calpain 7, a mammalian ortholog of yeast Cpl1/Rim13 and fungal PalB, is an atypical calpain that lacks a penta‐EF‐hand domain. Previously, we reported that a region containing a tandem repeat of microtubule‐interacting and transport (MIT) domains in calpain 7 interacts with a subset of endosomal sorting complex required for transport (ESCRT)‐III‐related proteins, suggesting involvement of calpain 7 in the ESCRT system. Although yeast and fungal calpains are thought to be involved in alkaline adaptation via limited proteolysis of specific transcription factors, proteolytic activity of calpain 7 has not been demonstrated yet. In this study, we investigated the interaction between calpain 7 and a newly reported ESCRT‐III family member, increased sodium tolerance‐1 (IST1), which possesses two different types of MIT‐interacting motifs (MIM1 and MIM2). We found that glutathione‐S‐transferase (GST)‐fused tandem MIT domains of calpain 7 (calpain 7MIT) pulled down FLAG‐tagged IST1 expressed in HEK293T cells. Coimmunoprecipitation assays with various deletion or point mutants of epitope‐tagged calpain 7 and IST1 revealed that both repetitive MIT domains and MIMs are required for efficient interaction. Direct MIT–MIM binding was confirmed by a pulldown experiment with GST‐fused IST1 MIM and purified recombinant calpain 7MIT. Furthermore, we found that the GST–MIM protein enhances the autolysis of purified Strep‐tagged monomeric green fluorescent protein (mGFP)‐fused calpain 7 (mGFP–calpain 7–Strep). The autolysis was almost completely abolished by 10 mmN‐ethylmaleimide but only partially inhibited by 1 mm leupeptin or E‐64. The putative catalytic Cys290‐substituted mutant (mGFP–calpain 7C290S–Strep) showed no autolytic activity. These results demonstrate for the first time that human calpain 7 is proteolytically active, and imply that calpain 7 is activated in the ESCRT system.