Miracle-dz/UniFAR-FTUs huggingface dataset:
COEUS: a semantic web application framework

As the "omics" revolution unfolds, the growth in data quantity and diversity is pushing forward the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging Semantic Web technologies that better suit the life sciences domain. The latter complex innate relationships are easily mapped into Semantic Web graphs, enabling a superior understanding of collected knowledge. Despite the increased awareness regarding Semantic Web technologies in bioinformatics, its usage is still diminished. With COEUS, we introduce a new Semantic Web framework, aiming at a streamlined application development cycle. COEUS follows a "Semantic Web in a box" approach, with a package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. The platform, targeted at life sciences developers, provides a complete application skeleton ready for rapid application deployment, and is available free as open source at http://bioinformatics.ua. pt/coeus/.
The Classification of Artifacts in Archaeology

Abstract Analytic classification consists of forming successive series of classes, referring to different features of artifacts. Each class is characterized by one or more attributes which indicate a custom to which the artisan conformed, for example, a technique of manufacture, or a concept which he expressed in the artifacts, such as a design. These customs and concepts constitute modes. They are “procedural modes” when they refer to behavior of artisans and “conceptual modes” when they consist of ideas which artisans have expressed in artifacts. Taxonomic classification consists of formulating a single set of classes, one for each kind of artifact in the collection. Each class is characterized by two or more modes, selected from among the total number of modes obtainable by means of analytic classification. The modes diagnostic of each class constitute its type. If diagnostic modes are selected for their time-space significance, the resultant types are “historical. ” If the diagnostic modes are selected for what they indicate about the intrinsic nature of the artifacts, the types are “descriptive. ” The situations under which it is best to use either procedural or conceptual modes or historical or descriptive types are discussed and it is concluded that all four kinds of units are essential for the complete interpretation of archaeological remains.
Results from the UK NHS breast screening programme 2000–05

Objective: To present results from the UK NHS breast screening programme (NHSBSP) for the six-year period from 1 April 1999 to 31 March 2005, and to compare these with targets. Methods: Data are collected annually from all UK screening units on standard KC62 return forms. Results: The prevalence of screen-positive cancer (cancer detection rate) has increased at both rounds during the six-year period. At the incident round, cancer detection rates increased by 24%, from 5.4 per 1000 in 2000 to 6.7 per 1000 in 2005 and the detection of small cancers (≤ 10 mm) has increased by 40%. Generally, quality measures in the programme continue to improve. However, while rates of recall at the incident screen decreased from 3.8% in 2000 to 3.6% in 2005, at the prevalent round, in 2005, 22% of units continued to recall more than 10% of women to assessment. Conclusions: The results suggest that the performance of the programme continues to improve. In the future, analysis of data on interval cancers will assist the interpretation of cancer detection rates.
Hospitalization Effects on Physical Performance and Muscle Strength in Hospitalized Elderly Subjects

Background: Hospitalization is a stressful event, potentially dangerous for older people. In fact, it worsens and accelerates muscle mass loss associated with bed rest, increasing the risk of loss of autonomy, rehospitalization and mortality. The aim of this study was to evaluate in an acute care setting handgrip and physical performance in patients at hospital admission and discharge, and detect changes related to hospitalization. Methods: Between June 2011 and January 2012 we were recruited 355 patients of which about 255 it was possible to perform at least Handgrip both at admission and at discharge. Of these, 38.8% were female. Handgrip strength and physical performance by using the short physical performance battery (SPPB) were assessed at admission and before the discharge. In all subjects Barthel index and mini nutritional assessment (MNA) were also evaluated. Results: A significant worsening in walking speed, chair stands test and handgrip strength performance was observed. On the contrary the study population showed an improvement in the Barthel index. No significant differences between males and females in performance and muscle strength loss were observed. The chair stand test performance worsens further in malnourished patients. Conclusion: our data suggests that during hospitalization elderly patients experience a loss of performance and muscle strength, with no differences between males and females. Subjects with score indicative of malnutrition or at risk for malnutrition presented a chair stand test performance worsening significantly greater than subjects with normal nutritional status.
The parasitoid complex of Parthenolecanium corni Bouché in the city of Tbilisi and its surroundings and comparison with some other European countries

Abstract The European fruit lecanium (EFL), Parthenolecanium corni Bouché (Hemiptera: Coccoidea), is a common and harmful soft scale, which attacks Fraxinus oxycarpa Willd. and other ornamental and orchard plants in Tbilisi, Georgia. This study investigates the phenology, degree of plant damage and effect of parasitoids on this scale in Tbilisi, a densely populated area. We present data on the 32 species of chalcidoid parasitoids recorded from EFL in Georgia and south-eastern Europe. The scale is heavily parasitized in Tbilisi, but we did not find any variation in seasonal abundance. The most common parasitoid of EFL was Blastothrix longipennis (Hymenoptera: Encyrtidae).
Swearing in the ‘Tradie’ Environment as a Tool for Solidarity

Swearing within a social interaction is often considered obscene and offensive, however swear words have many other functions within society that are rarely noted. The social meaning of swear words, such as fuck and cunt, have over time shifted from their offensive nature to having a more rapport‐building function within certain contexts. This paper will analyse this meaning shift and the social motivations behind the use of the words fuck and cunt in the Australian trade workplace. It has been observed that Australian ‘tradies’ insult and swear at each other as a means of building and maintaining rapport amongst co‐ workers, as well as a means of differentiating themselves from the rest of society. In order to demonstrate this, ten conversations were recorded between five tradies on their lunchbreaks, with these interactions subsequently being analysed. It is hoped that this study will expose the need for further research in this area of linguistics and demonstrate how words may serve different functions within different cultures.
Mutational specificity: Mutation frequencies but not mutant frequencies in Big Blue® mice fit a Poisson distribution

Transgenic mutation assays generally use mutant frequencies to estimate mutation frequencies but the degree to which clonal expansion inflates mutant frequencies is largely unknown. Mutant frequency is defined as the fraction of cells carrying mutations in the gene of interest and, according to the standard Big Blue® protocol, is determined by dividing the number of mutant plaques by the total number of plaques screened. Mutation frequency is determined as the fraction of cells carrying definitely independent mutations and therefore requires correction for clonal expansion. Mutant and mutation frequencies were determined for brain, thymus and male germ cells of four mice from two age groups (3‐ versus 10‐month old). The mutant frequency in thymus differed significantly between 3‐ and 10‐month old mice (P < 0.05). By sequencing all mutants, the mutation frequency (i.e., corrected for jackpot mutations) in thymus was determined and was not significantly different between 3‐ and 10‐month old mice. Mutant frequency does not fit a Poisson distribution, but mutation frequency corrected for jackpot mutations is substantially less variable and does fit a Poisson distribution. © 1996 Wiley‐Liss, Inc.
Case‐only gene–environment interaction between ALAD tagSNPs and occupational lead exposure in prostate cancer

Black men have historically had higher blood lead levels than white men in the U.S. and have the highest incidence of prostate cancer in the world. Inorganic lead has been classified as a probable human carcinogen. Lead (Pb) inhibits delta‐aminolevulinic acid dehydratase (ALAD), a gene recently implicated in other genitourinary cancers. The ALAD enzyme is involved in the second step of heme biosynthesis and is an endogenous inhibitor of the 26S proteasome, a master system for protein degradation and a current target of cancer therapy.
BODY FAT DISTRIBUTION , AND SERUM LEPTIN IN YOUNG MEN WITH UNDIAGNOSED OBSTRUCTIVE SLEEP APNEA SYNDROME

Background and Purpose: Little is known about influences of obstructive sleep apnea syndrome (OSAS) on dietary intake and body composition. The purpose of this study was to evaluate dietary status, body fat distribution and leptin in overweight young men with and without OSAS in comparison to published values for normal weight counterparts. Methods: Groups were comprised of 24 sedentary overweight young men with and without OSAS, who had a body mass index (BMI) greater than 25 kg/m. Serum leptin concentration was measured in the 24 subjects using radioimmunoassay, while OSAS assessment was done using nighttime home somnography. Analysis of 4-day diet recalls was performed using Nutritionist Pro (First DataBank, Inc., San Bruno, CA). A Healthy Eating Index (HEI) score was calculated for the 24 overweight subjects. Results: There were no differences between the two overweight groups for total fat mass, central abdominal fat, BMI, waist circumference, leptin, or the HEI. The HEI was not predictive of overall OSAS severity; however, BMI was moderately related to OSAS severity (r = 0.39; p=0.05). The normal weight group did have a 50% higher report of carbohydrate intake, and consumed on average, 500 more kilocalories per day. The normal weight group consumed 50% less sodium, and 50% more Vitamin’s C and E including a 13% increase in the HEI. Conclusions: Regulation of eating behavior and related influences on diet composition may be affected by a number of neurohormonal disturbances associated with OSAS and/or obesity, itself. Further research is needed to quantify these possible differences on dietary status and the underlying mechanism involved.
Discovering Author Groups using a B-compact graph-based Clustering

Identifying the authorship either of an anonymous or a doubtful document constitutes a cornerstone for automatic forensic applications. Moreover, it is a challenging task for both humans and computers. Clustering documents according to the linguistic style of the authors who wrote them has been a task little studied by the research community. In order to address this problem, PAN Evaluation Framework has become the first effort to promote the development of the author clustering. This article proposes a graph-based method, specifically βcompact clustering, for discovering the groups of documents written by the same author. The β-compact algorithm is based on the analysis of the similarity between documents and they belong to the same group as long as the similarity between them exceeds the threshold β and it is the maximum similarity with respect to other documents. In our proposal we evaluated different linguistic features and similarity measures presented in previous works of authorship analysis task. The training dataset was used to determine the best value of β parameter for each language. The result of the experiments was encouraging.
Monoclonal Antibodies Neutralize Bacillus cereus Nhe Enterotoxin by Inhibiting Ordered Binding of Its Three Exoprotein Components

ABSTRACT The Nhe enterotoxin from Bacillus cereus is known to induce cytotoxicity on Vero and CaCo-2 cells by ordered binding of its single components NheA, NheB, and NheC. This study aimed to elucidate functional sites on NheB by identifying the epitopes of the neutralizing monoclonal antibodies 1E11 and 2B11. The binding regions of both antibodies were determined by using recombinant NheB fragments and synthetic peptides. The antigenic site of antibody 1E11 was located within the amino acids 321 to 341 of NheB, whereas reactivity of antibody 2B11 was dependent on the presence of amino acids 122 to 150 and on conformation. Both antibodies were able to bind simultaneously to NheB and did not interfere with target cell binding as shown by immunofluorescence microscopy. A set of neutralization assays revealed that antibody 2B11 most likely interfered with the interaction between NheB and NheC both on the epithelium cell surface and in solution. In contrast, antibody 1E11 inhibited association between NheA and cell-bound NheB in a competitive manner, and effectively neutralized Nhe cytotoxicity on a variety of human cell lines. This distinct mechanism further supports that NheA is the key component during the Nhe mode of action and the C-terminal epitope recognized by antibody 1E11 points to an important functional region of NheB.
Digital-domain chromatic dispersion compensation for different pulse shapes: Practical considerations

We infer, by computer simulations, practical values of the overlap length for frequency-domain chromatic dispersion compensation in long and ultra-long-haul coherent optical systems. The overlap length has a direct impact on computational complexity and the receive-side DSP power consumption. The NRZ, RZ, and Nyquist-shaped signals are investigated. The presented results may be used as guidelines for trading off OSNR margin and computational complexity. In a sufficiently high OSNR scenario, these trade-offs may reduce computational complexity by 10-25%, depending on the particular filter implementation.
Early growth response gene-1 and hypoxia-inducible factor-1α affect tumor metastasis via regulation of tissue factor

Abstract Background. Hypoxia up-regulated expression of tissue factor (TF) may facilitate tumor cell metastasis, but transcriptional mechanisms remain undefined. Material and methods. To verify the role of Egr-1 in hypoxia-induced TF expression in breast cancer cells, quantitative PCR and Western blot analysis were performed. The secretion of VEGF under hypoxia was detected by enzyme-linked immunosorbent assay (ELISA). Egr-1 and HIF-1α siRNA were transiently transfected into breast cancer cells to evaluate their specific roles. Results. The increased Egr-1 expression occurring in hypoxic breast cancer cells can up-regulate TF expression and stimulating protein 1(Sp1) was not responsible for the hypoxia-induced expression of TF. HIF-1α mediated the hypoxia-induced up-regulation of TF expression through vascular endothelial growth factor (VEGF). The regulatory effects of Egr-1 on TF under hypoxia were independent of HIF-1α. Either Egr-1 or HIF-1α was responsible for hypoxic induction of tumor cells adhesion. HIF-1α, but not Egr-1, had a pivotal role in human breast cancer cells invasion. Both Egr-1 and HIF-1α were critical to angiogenesis induced by hypoxic conditions in MDA-MB-231 and HUVEC co-cultures. In nude mice, both Egr-1 and HIF-1α small interfering RNA (siRNA) could decrease extravasation of MDA-MB-435 cells in the lung after tail vein injection. Conclusions. Hypoxia-induced expression of TF in human breast cancer cells depends on Egr-1 and HIF-1α, and both of these proteins may play an important role in breast cancer metastasis, either directly or indirectly through the TF pathway.
Condición física relacionada con la salud y hábitos de alimentación en niños y adolescentes: propuesta de addendum al informe de salud escolar

Objetivo: Aplicar, en el ambito escolar, la bateria de test ALPHA-fitness (desarrollada y estandarizada en el proyecto europeo: ALPHA-Assessing Levels of Physical Activity and Fitness) para evaluar la condicion fisica, complementandola con un estudio de habitos alimentarios y, asi, estudiar su viabilidad en el contexto escolar. En base a ello, disenar y proponer un addendum al Informe de Salud Escolar. Metodo: Los profesores de Educacion Fisica, de forma autonoma y previamente instruidos, evaluaron a 138 alumnos (6-18 anos). Resultados y conclusion: La medida de la condicion fisica relacionada con la salud y los habitos alimentarios es factible de ser evaluada en el ambito escolar e incorporada al Informe de Salud Escolar. Esta informacion es relevante para la salud basandose en la reciente evidencia cientifica.
Folding energetics in thin ̄ thin ̄ thin ̄ lm diaphragms

By G. Gioia1, A. DeSimone2, M. Ortiz3 a n d A. M. C u i t i ~ n o4 1Theoretical and Applied Mechanics, University of Illinois, Urbana, IL 61801, USA (ggioia@uiuc.edu) 2Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany Graduate Aeronautical Laboratories, California Institute of Technology, Pasadena, CA 91125, USA 4Mechanical and Aerospace Engineering, Rutgers University, Piscataway, NJ 08854, USA
Comparison of four different vascular occlusion tests for assessing reactive hyperemia using near-infrared spectroscopy

Objective:To compare data gathered via four different types of vascular occlusion test (VOT) by using near-infrared spectroscopy. The data may support a standardized method to appropriately measure the postischemic recovery slope, which is currently emphasized as a quantitative marker of the microvascular reserve in septic patients. Design:Prospective study. Setting:Medical intensive care unit of a university hospital. Patients and Measurements:In 20 healthy volunteers and in 20 septic shock patients, we measured muscle tissue oxygen saturation at the thenar eminence by using near-infrared spectroscopy and performed four different vascular occlusion tests in a random order. A pneumatic cuff was placed around either the upper arm (A) or the forearm (FA). Cuff inflation was maintained either during 3 mins (VOTA3min and VOTFA3min) or until muscle tissue oxygen saturation decreased to 40% (VOTA40% and VOTFA40%). Results:In volunteers: 1) During VOTA3min and VOTFA3min, the minimal muscle tissue oxygen saturation was significantly higher than 40% (52% ± 10% and 54% ± 6%, respectively), and 2) the muscle tissue oxygen saturation recovery slopes were steeper with VOTA40% and VOTFA40% than with VOTA3min and VOTFA3min, respectively. Considering the pooled data obtained during VOTA3min and VOTFA3min (n = 40), recovery slope negatively correlated with minimal muscle tissue oxygen saturation in volunteers (r2 = .46, p < .0001) as in septic patients (r2 = .34, p = .0001). Considering the pooled data obtained during 40% VOTs, the recovery slope did not correlate with ischemic time in either group. The overlap of recovery slopes between volunteers and septic patients was small for both 40% VOTs but large for both 3-min occlusion VOTs. Conclusion:The comparison of recovery slopes between volunteers and septic patients and the fact that the recovery slope was influenced by the extent of muscle tissue oxygen saturation decrease during ischemia and not by the ischemic time both support the use of a fixed minimal muscle tissue oxygen saturation target (40%) over the use of a fixed ischemic time (3 mins) for assessing reactive hyperemia by using near-infrared spectroscopy.
Perturbations of Plasmodium Puf2 expression and RNA‐seq of Puf2‐deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility

Malaria's cycle of infection requires parasite transmission between a mosquito vector and a mammalian host. We here demonstrate that the Plasmodium yoelii Pumilio‐FBF family member Puf2 allows the sporozoite to remain infectious in the mosquito salivary glands while awaiting transmission. Puf2 mediates this solely through its RNA‐binding domain (RBD) likely by stabilizing or hastening the degradation of specific mRNAs. Puf2 traffics to sporozoite cytosolic granules, which are negative for several markers of stress granules and P‐bodies, and disappear rapidly after infection of hepatocytes. In contrast to previously described Plasmodium berghei pbpuf2− parasites, pypuf2− sporozoites have no apparent defect in host infection when tested early in salivary gland residence, but become progressively non‐infectious and prematurely transform into EEFs during prolonged salivary gland residence. The premature overexpression of Puf2 in oocysts causes striking deregulation of sporozoite maturation and infectivity while extension of Puf2 expression in liverstages causes no defect, suggesting that the presence of Puf2 alone is not sufficient for its functions. Finally, by conducting the first comparative RNA‐seq analysis of Plasmodium sporozoites, we find that Puf2 may play a role in directly or indirectly maintaining the homeostasis of specific transcripts. These findings uncover requirements for maintaining a window of opportunity for the malaria parasite to accommodate the unpredictable moment of transmission from mosquito to mammalian host.
On Duality-Based A Posteriori Error Estimation in Various Norms and Linear Functionals for Large Eddy Simulation

We derive a posteriori error estimates for the filtered velocity field in a large eddy simulation in various norms and linear functionals. The a posteriori error estimates take the form of an integral in space-time of a discretization residual and a modeling residual times a dual weight. The discretization residual is directly computable, and the modeling residual is estimated by a scale similarity model. We approximate the dual weight by solving an associated linearized dual problem numerically. Computational examples from transition to turbulence in Couette flow are presented.
Diabetic nephropathy: leveraging mouse genetics

Purpose of reviewAdvances in mouse genetics have made this species particularly useful as a model for human disease. This review will summarize recent advances regarding the pathogenesis of diabetic nephropathy discovered in mice. Recent findingsDiabetic nephropathy has been characterized in novel genetic models of murine diabetes including the Akita, Ove26, and ICER-Iγ mice. Mutagenesis resources targeting every gene of the genome and the importance of inbred genetic background are discussed. SummaryThrough the use of these resources mouse models should provide new insight into the pathogenesis of diabetic nephropathy, and complement human studies and validate the identity of candidate genes contributing to diabetic nephropathy.