Miracle-dz/UniFAR-FTUs huggingface dataset:
An Approach to Perform Local Analysis on Multidimensional Projection

In the context of Visualization, Multidimensional Projection techniques are employed to show similarity relations among instances of a multidimensional dataset. Distinct projection techniques use different approaches to perform the dimensionality reduction and, consequently, different metrics are employed to assess projection quality according to similarity and structures preservation. Usually, quality measures are computed from the whole projection, what can impair a specific evaluation. This work presents a novel approach to perform evaluation on multidimensional projections, in which clusters of instances are selectively evaluated and compared to the whole projection. The proposed approach has shown to be effective on evaluating projections and it offers a way to apply techniques to enhance poor projected areas.
Changes in the nuclear deposition of histone H2A variants during pre-implantation development in mice

Histone H2A has several variants, and changes in chromatin composition associated with their replacement might involve chromatin structure remodeling. We examined the dynamics of the canonical histone H2A and its three variants, H2A.X, H2A.Z and macroH2A, in the mouse during oogenesis and pre-implantation development when genome remodeling occurs. Immunocytochemistry with specific antibodies revealed that, although H2A and all variants were deposited in the nuclei of full-grown oocytes, only histone H2A.X was abundant in the pronuclei of one-cell embryos after fertilization, in contrast with the low abundance of histone H2A and the absence of H2A.Z. The decline in H2A and the depletion of H2A.Z and macroH2A after fertilization were confirmed using Flag epitope-tagged H2A, H2A.Z and macroH2A transgenic mouse lines. Microinjection experiments with mRNA encoding the Flag-tagged proteins revealed a similar pattern of nuclear incorporation of the H2A variants. Fusion protein experiments using H2A, H2A.Z and macroH2A fused with the C-terminal 23 amino acids of H2A.X showed that the C-terminal amino acids of H2A.X function specifically to target this variant histone into chromatin in embryos after fertilization and that the absence of H2A.Z and macroH2A from the chromatin is required for normal development. These results suggest that global changes in the composition of histone H2A variants in chromatin play a role in genome remodeling after fertilization.
Tag Recommendation Using Probabilistic Topic Models

Tagging systems have become major infrastructures on the Web. They allow users to create tags that annotate and categorize content and share them with other users, very helpful in particular for searching multimedia content. However, as tagging is not constrained by a controlled vocabulary and annotation guidelines, tags tend to be noisy and sparse. Especially new resources annotated by only a few users have often rather idiosyncratic tags that do not reect a common perspective useful for search. In this paper we introduce an approach based on Latent Dirichlet Allocation (LDA) for recommending tags of resources. Resources annotated by many users and thus equipped with a fairly stable and complete tag set are used to elicit latent topics represented as a mixture of description tokens and tags. Based on this, new resources are mapped to latent topics based on their content in order to recommend the most likely tags from the latent topics. We evaluate recall and precision for the bibsonomy benchmark provided within the ECML PKDD Discovery Challenge 2009.
Secure privacy-preserving protocols for outsourcing continuous authentication of smartphone users with touch data

We introduce new secure privacy-preserving protocols for outsourcing continuous authentication of smartphone users. Our protocols allow a smartphone to privately perform continuous and unobtrusive authentication using touch behaviors. Through our protocols, the smartphone does not need to disclose touch information to the authentication server. Further, neither the server nor the smartphone have access to the content of the user's template. We present formal proofs to substantiate security claims on our protocols. We then perform experiments on publicly available touch data, collected from forty-one users. Our experiments on a commodity Android smartphone show that our protocols incur an overhead between 263ms and 2.1s.
Epidemic cholera in Guatemala, 1993: transmission of a newly introduced epidemic strain by street vendors

SUMMARY Epidemic cholera reached Guatemala in July 1991. By mid-1993, Guatemala ranked third in the hemisphere in reported cases of cholera. We conducted a case-control study with two age-, sex-, and neighbourhood-matched controls per patient in periurban Guatemala City. Twenty-six patients hospitalized for cholera and 52 controls were enrolled. Seven (47%) of 15 stool cultures obtained after admission yielded toxigenic Vibrio cholerae Ol. All seven were resistant to furazolidone, sulfisoxazole, and streptomycin, and differed substantially by pulsed-field gel electrophoresis from the Latin American epidemic strain dominant in the hemisphere since 1991. In univariate analysis, illness was associated with consumption of left-over rice (odds ratio [OR] = 7·0, 95% confidence interval [CI] = 1·4–36), flavored ices (‘helados’) (OR = 3·6, CI = 1·1–12), and street-vended non-carbonated beverages (OR = 3·8, CI = 1·2–12) and food items (OR = 11·0, CI = 2·3–54). Street-vended food items remained significantly associated with illness in multivariate analysis (OR = 6·5, CI = 1·4–31). Illness was not associated with drinking municipal tap water. Maintaining water safety is important, but slowing the epidemic in Guatemala City and elsewhere may also require improvement in street vendor food handling and hygiene.
Geo-locating the knowledge transfer in StackOverflow

Stack Overflow can be seen as an information market for software engineering knowledge in which the goods that are exchanged are answers to questions and the rewards are score points and badges that contribute to a users reputation. By analyzing the transactions in Stack Overflow we can get a glimpse of the way in which the different geographical regions in the world contribute to the knowledge market represented by the website. In this paper we aggregate the knowledge transfer from the level of the users to the level of geographical regions and learn that Europe and North America are the principal and virtually equal contributors; Asia comes as a distant third, mainly represented by India; and Oceania contributes less than Asia but more than South America and Africa together.
Determinants of Microdamage in Elderly Human Vertebral Trabecular Bone

Previous studies have shown that microdamage accumulates in bone as a result of physiological loading and occurs naturally in human trabecular bone. The purpose of this study was to determine the factors associated with pre-existing microdamage in human vertebral trabecular bone, namely age, architecture, hardness, mineral and organic matrix. Trabecular bone cores were collected from human L2 vertebrae (n = 53) from donors 54–95 years of age (22 men and 30 women, 1 unknown) and previous cited parameters were evaluated. Collagen cross-link content (PYD, DPD, PEN and % of collagen) was measured on surrounding trabecular bone. We found that determinants of microdamage were mostly the age of donors, architecture, mineral characteristics and mature enzymatic cross-links. Moreover, linear microcracks were mostly associated with the bone matrix characteristics whereas diffuse damage was associated with architecture. We conclude that linear and diffuse types of microdamage seemed to have different determinants, with age being critical for both types.
Aggrephagy: Selective Disposal of Protein Aggregates by Macroautophagy

Protein aggregation is a continuous process in our cells. Some proteins aggregate in a regulated manner required for different vital functional processes in the cells whereas other protein aggregates result from misfolding caused by various stressors. The decision to form an aggregate is largely made by chaperones and chaperone-assisted proteins. Proteins that are damaged beyond repair are degraded either by the proteasome or by the lysosome via autophagy. The aggregates can be degraded by the proteasome and by chaperone-mediated autophagy only after dissolution into soluble single peptide species. Hence, protein aggregates as such are degraded by macroautophagy. The selective degradation of protein aggregates by macroautophagy is called aggrephagy. Here we review the processes of aggregate formation, recognition, transport, and sequestration into autophagosomes by autophagy receptors and the role of aggrephagy in different protein aggregation diseases.
An evolutionary multi-objective approach for prototype generation

k-NN is one of the most popular and effective models for pattern classification. However, it has two main drawbacks that hinder the application of this method for large data sets: (1) the whole training set has to be stored in memory, and (2) for classifying a test pattern it has to be compared to all other training instances. In order to overcome these shortcomings, prototype generation (PG) methods aim to reduce the size of the training set while maintaining or increasing the classification performance of k-NN. Accordingly, most PG methods aim to generate instances that try to maximize classification performance. Nevertheless, in most cases, the reduction objective is only implicitly optimized. This paper introduces EMOPG, a novel approach to PG based on multi-objective optimization that explicitly optimizes both objectives: accuracy and reduction. Under EMOPG, prototypes are initialized with a subset of training instances selected through a tournament, according to a weighting term. A multi-objective evolutionary algorithm, PAES (Pareto Archived Evolution Strategy), is implemented to adjust the position of the initial prototypes. The optimization process aims to simultaneously maximize the classification performance of prototypes while reducing the number of instances with respect to the training set. A strategy for selecting a single solution from the set of non-dominated solutions is proposed. We evaluate the performance of EMOPG using a suite of benchmark data sets and compare the performance of our proposal with respect to the one obtained by alternative techniques. Experimental results show that our proposed method offers a better trade-off between accuracy and reduction than other methods.
Bacterial Adherence on Fabrics by a Radioisotope Labeling Method

A radioisotope labeling technique was used to quantify the adherence of Staphy lococcus aureus, Staphylococcus epidermidis, and Escherichia coli on eight fabrics. The extent of bacterial adherence depends on the bacterial type, the fiber content, and the contact condition. Staphylococci adhered more than Escherichia coli, and Staph. epidermidis adhered more than Staph. aureus on all fabrics. There were apparently different degrees of bacterial adherence in the eight fabrics, but the ranking orders of adherence depended to a great extent on the contact condition. Bacterial adherence was increased by both agitation and saturated wetting due to increasing bacterial cell- fiber contact. There was an increasing trend in bacterial adherence on all fabrics as contact time increased up to 24 hours, with occasional zig-zag patterns. On most fabrics, cleaning and autoclaving did significantly influence the extent of bacterial adherence to the fabrics. The quantitative data along with the morphology of bacterial adherence by SEM suggested that factors other than hydrophilicity, water absorbency, and surface roughness may affect the extent of bacterial adherence to the fibers.
Steady-state simulation of queueing processes: survey of problems and solutions

For years computer-based stochastic simulation has been a commonly used tool in the performance evaluation of various systems. Unfortunately, the results of simulation studies quite often have little credibility, since they are presented without regard to their random nature and the need for proper statistical analysis of simulation output data. This paper discusses the main factors that can affect the accuracy of stochastic simulations designed to give insight into the steady-state behavior of queuing processes. The problems of correctly starting and stopping such simulation experiments to obtain the required statistical accuracy of the results are addressed. In this survey of possible solutions, the emphasis is put on possible applications in the sequential analysis of output data, which adaptively decides about continuing a simulation experiment until the required accuracy of results is reached. A suitable solution for deciding upon the starting point of a steady-state analysis and two techniques for obtaining the final simulation results to a required level of accuracy are presented, together with pseudocode implementations.
The Conserved nhaAR Operon Is Drastically Divergent between B2 and Non-B2 Escherichia coli and Is Involved in Extra-Intestinal Virulence

The Escherichia coli species is divided in phylogenetic groups that differ in their virulence and commensal distribution. Strains belonging to the B2 group are involved in extra-intestinal pathologies but also appear to be more prevalent as commensals among human occidental populations. To investigate the genetic specificities of B2 sub-group, we used 128 sequenced genomes and identified genes of the core genome that showed marked difference between B2 and non-B2 genomes. We focused on the gene and its surrounding region with the strongest divergence between B2 and non-B2, the antiporter gene nhaA. This gene is part of the nhaAR operon, which is in the core genome but flanked by mobile regions, and is involved in growth at high pH and high sodium concentrations. Consistently, we found that a panel of non-B2 strains grew faster than B2 at high pH and high sodium concentrations. However, we could not identify differences in expression of the nhaAR operon using fluorescence reporter plasmids. Furthermore, the operon deletion had no differential impact between B2 and non-B2 strains, and did not result in a fitness modification in a murine model of gut colonization. Nevertheless, sequence analysis and experiments in a murine model of septicemia revealed that recombination in nhaA among B2 strains was observed in strains with low virulence. Finally, nhaA and nhaAR operon deletions drastically decreased virulence in one B2 strain. This effect of nhaAR deletion appeared to be stronger than deletion of all pathogenicity islands. Thus, a population genetic approach allowed us to identify an operon in the core genome without strong effect in commensalism but with an important role in extra-intestinal virulence, a landmark of the B2 strains.
Essential Fatty Acids and the Brain

Objective: To review the role of essential fatty acids in brain membrane function and in the genesis of psychiatric disease. Method: Medline databases were searched for published articles with links among the following key words: essential fatty acids, omega-3 fatty acids, docosahexanoic acid, eicosapentanoic acid, arachidonic acid, neurotransmission, phospholipase A2, depression, schizophrenia, mental performance, attention-deficit hyperactivity disorder, and Alzheimer's disease. Biochemistry textbooks were consulted on the role of fatty acids in membrane function, neurotransmission, and eicosanoid formation. The 3-dimensional structures of fatty acids were obtained from the Web site of the Biochemistry Department, University of Arizona (2001). Results: The fatty acid composition of neuronal cell membrane phospholipids reflects their intake in the diet. The degree of a fatty acid's desaturation determines its 3-dimensional structure and, thus, membrane fluidity and function. The ratio between omega-3 and omega-6 polyunsaturated fatty acids (PUFAs), in particular, influences various aspects of serotoninergic and catecholaminergic neurotransmission, as shown by studies in animal models. Phospholipase A2 (PLA2) hydrolyzes fatty acids from membrane phospholipids: liberated omega-6 PUFAs are metabolized to prostaglandins with a higher inflammatory potential, compared with those generated from the omega-3 family. Thus the activity of PLA2 coupled with membrane fatty acid composition may play a central role in the development of neuronal dysfunction. Intervention trials in human subjects show that omega-3 fatty acids have possible positive effects in the treatment of various psychiatric disorders, but more data are needed to make conclusive directives in this regard. Conclusion: The ratio of membrane omega-3 to omega-6 PUFAs can be modulated by dietary intake. This ratio influences neurotransmission and prostaglandin formation, processes that are vital in the maintenance of normal brain function.
Synergistic cytotoxic effects of inorganic phosphate and chemotherapeutic drugs on human osteosarcoma cells

Novel therapeutic approaches are required for the treatment of osteosarcoma. Combination chemotherapy is receiving increased attention in order to identify compounds that may increase the therapeutic index of clinical anticancer drugs. In this regard, naturally occurring molecules with antitumor activity and with limited toxicity to normal tissues have been suggested as possible candidates for investigation of their synergistic efficacy in combination with antineoplastic drugs. Inorganic phosphate (Pi) is an essential nutrient for living organisms. Relevantly, Pi has emerged as an important signaling molecule capable of modulating multiple cellular functions by altering signal transduction pathways, gene expression and protein abundance in many cell types. Previously, we showed that Pi inhibits proliferation and aggressiveness of U2OS human osteosarcoma cells and that Pi is capable of inducing sensitization of osteosarcoma cells to doxorubicin in a p53-dependent manner. In this study, we extended the role of Pi in the chemosensitivity of osteosarcoma cells to other anticancer drugs. Specifically, we report and compare the antiproliferative effects of a combination between Pi and doxorubicin, Taxol® and 5-fluorouracil (5-FU) treatments. We found that Pi increases the antiproliferative response to both Taxol and doxorubicin to a similar extent. On the other hand, Pi did not potentiate the anticancer effects induced by 5-FU. These effects were paralleled by apoptosis induction and were cell cycle-dependent. The clinical significance of our data and their potential therapeutic applications for improving osteosarcoma treatment are discussed.
PREVALENCE OF PSEUDOEXFOLIATION OF THE LENS CAPSULE IN INDIA

The condition of Pseudoexfoliation of the lens capsule has been reported the world over in Ophthalmic literature but the reports published in different countries differ with regard to its incidence. Rehsteiner (1929) in Zurich found four cases of exfoliation in 238 patients over the age of sixty years 'an incidence of 1.7 0 / 0 . Baumgart (1933) in Italy found an incidence of 7.50/0 in 611 subjects over the age of 50 years. Horven (1937) in Norway found an incidence of 12.00/0 in 154 subjects over the age of 52 years. Irvine (1940) found an incidence of 310/0 in U.S.A. in a total of 276 cases. Laderkarl (1965) amongst 800 Danes, over sixty years found an incidence of 21/80/0. An incidence of 1.30/0 in persons over the age of 50 years and 1.9'0/0 over the age of 60 years has been reported by Backhaus and Lorentzen from D'enmark (1966). The assessment of incidence in India is based on the report of Irvine (1940) who examined two hundred and thirty five elderly patients in Madras, South India, admitted for cataract extraction. He found an incidence of 8 0/0 in these patients. The object of present investigation has been an attempt to estimate the incidence of pseudoexfolation of the lens capsule in India in patients over the age of 50 years. Clinically the exfoliation syndrome or pseudoexfoliation of lens capsule consists of flakes on the pupillary margin, a central disc and the peripheral band on the lens capsule. The pheripheral band is the most constant feature and we, therefore, cannot preclude the absence of exfoliation syndrome unless the peripheral band is shown to be absent (Horven, 1937). Further in patients
Dissociations Among Direct and Indirect Indicators of Adiposity in Young Wrestlers

Abstract Cochrane, KC, Housh, TJ, Bergstrom, HC, Jenkins, NDM, Johnson, GO, Housh, DJ, Traylor, DA, Lewis, RW Jr, Schmidt, RJ, and Cramer, JT. Dissociations among direct and indirect indicators of adiposity in young wrestlers. J Strength Cond Res 29(2): 408–415, 2015—The purposes of this study were to: (a) examine the age-related patterns of differences in height (HT), body mass (BM), percent body fat (% fat), body mass index (BMI), and skinfolds (SF) in 11- to 18-year-old wrestlers; (b) determine the coherence of direct (% fat) and indirect (BMI and SFs) indicators of adiposity in the wrestlers; and (c) compare the age-related patterns and mean values for HT, BM, BMI, subscapular, and triceps SF for the wrestlers to those of national samples of boys from the National Health and Nutrition Examination Survey (NHANES) database. One hundred thirty wrestlers were divided into 8 independent yearly age groups (AG): AG11–AG18 years. Height, BM, BMI, subscapular SF, triceps SF, medial calf SF, thigh SF, sum of SFs, and % fat were assessed. There were no differences between the wrestlers and NHANES samples for age-related patterns of BMI (0.61 and 0.63 kg·m−2·y−1), subscapular SF (0.47 and 0.37 mm·y−1), or triceps SF (−0.31 and −0.39 mm·y−1). Furthermore, the wrestlers displayed no differences in % fat between age groups. The results indicated that: (a) dissociations existed between the direct and indirect indicators of adiposity; (b) the wrestlers were similar in height but had smaller upper-body SFs when compared with NHANES samples; and (c) participation in wrestling (1–8 years) had no adverse effects on the normal age-related growth patterns for HT, but favorable effects on measures of adiposity.
Aquaporin-1 Expression in Proliferative Vitreoretinopathy and in Epiretinal Membranes

Purpose. Aquaporin-1 (AQP1) is involved in cell migration and proliferation; therefore, the purpose of the study was to investigate its expression in proliferative vitreoretinopathy (PVR) and epiretinal membranes (ERM). Methods. 19 membranes from PVR and ERM were collected following eye surgery. AQP1 mRNA and protein expressions were determined by RT-qPCR and immunofluorescence in the membranes from PVR and ERM. Results. AQP1 mRNA and protein were expressed in both PVR and ERM as shown by RT-qPCR and immunofluorescence. AQP1 protein expression was heterogeneous among and between PVR and ERM and colocalized with alpha-smooth muscle actin (αSMA) and with glial fibrillary acidic protein (GFAP). There were a higher percentage of cells coexpressing AQP1 and αSMA than AQP1 and GFAP. GFAP and αSMA did not colocalize. Conclusion. Our data show for the first time AQP1 expression in both PVR and ERM. AQP1 is expressed mostly by the αSMA-positive cells, presumably myofibroblasts, but also by GFAP-positive cells, assumed to be glial cells. These original findings warrant further functional investigations aiming at studying the potential role of AQP1 in cell migration and proliferation occurring during the development of PVR and ERM.