Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxytetracycline induces DNA damage and epigenetic changes: a possible risk for human and animal health?

Background Oxytetracycline (OTC), which is largely employed in zootechnical and veterinary practices to ensure wellness of farmed animals, is partially absorbed within the gastrointestinal tract depositing in several tissues. Therefore, the potential OTC toxicity is relevant when considering the putative risk derived by the entry and accumulation of such drug in human and pet food chain supply. Despite scientific literature highlights several OTC-dependent toxic effects on human and animal health, the molecular mechanisms of such toxicity are still poorly understood. Methods Here, we evaluated DNA damages and epigenetic alterations by quantitative reverse transcription polymerase chain reaction, quantitative polymerase chain reaction, chromatin immuno-precipitation and Western blot analysis. Results We observed that human peripheral blood mononuclear cells (PBMCs) expressed DNA damage features (activation of ATM and p53, phosphorylation of H2AX and modifications of histone H3 methylation of lysine K4 in the chromatin) after the in vitro exposure to OTC. These changes are linked to a robust inflammatory response indicated by an increased expression of Interferon (IFN)-γ and type 1 superoxide dismutase (SOD1). Discussion Our data reveal an unexpected biological in vitro activity of OTC able to modify DNA and chromatin in cultured human PBMC. In this regard, OTC presence in foods of animal origin could represent a potential risk for both the human and animal health.
Using Case Studies in the Methods Classroom

T he use of case s tudies as a m e a n s of t r a i n i n g y o u n g professionals has had a long tradition in fields such as law and m e d i c i n e . In the las t decade, the teacher education profession has also discovered the benefits of t ra in ing wi th case s tudies and now regularly uses them in teacher education courses at both elementary and secondary levels . 1 Although it is not yet common practice, case studies are beginning to be used in undergraduate music methods classes. 2 One particular ly fruitful approach is the use of case studies as a means of nurturing reflective practice through cooperative activities. Cooperative activities help students hear a variety of viewpoints, compare their responses with those of their peers, and understand how their ideas compare to the ideas of others in the classroom. This self-knowledge is e s s e n t i a l i f s t u d e n t s are to m a k e progress in learning to assess their own teaching skills.
Working Towards Professionalism: A Pathway Into The Post-Compulsory Community Of Practice

It is a particularly volatile and unpredictable time in UK Further Education (FE). This article aims to give an insightful and honest account of one pre-service trainee’s post-compulsory PGCE (1 year; full-time) experience with close reference to various aspects of professionalism within the FE community of practice, looking at the degree to which the Lifelong Learning UK (LLUK) professional standards have been met throughout the year. The paper sheds some light on the positive and negative aspects of Initial Teacher Education (ITE) in FE, concluding that professionalism can be defined using both subjective and objective measurements, that individual conceptions of professionalism may or may not overlap with others, and that it is felt some of the LLUK standards have been met more than others in the author’s own teaching practice. The training provider was in central London; the teaching placement was in an FE college in south-west London.
A measure for the batting performance of cricket players : research article

A single measure that can be used to assess the performance of batsmen in cricket is defined. This study shows how it can be used to rank batsmen. The batting ability of a batsman is generally measured by means of his average. His strike rate is, however, also very important and is often looked at as well. It will furthermore be motivated that a batsman's consistency is also of great importance. The consistency coefficient will be discussed and it's importance will be illustrated by showing that a batsman with a high consistency coefficient has a better chance to get a good score than one with a low consistency coefficient. It will also be shown how the consistency curve can be used to assess the present form of a batsman. By making use of a data set consisting of the statistics of a large group of one-day international players, these three measures will be combined into a single measure that can be used to assess the performance of a batsman and to compare different batsmen with each other. A classification scheme with ten classes according to which batsmen can be classified will be given. The best batsmen are those who fall into class one. The same procedure will be used to find a formula for batting performance and a classification table for Test players. Keywords: Batting performance, Consistency, Cricket, Present form of a batsman, Rating of batsmen South African Journal for Research in Sport, Physical Education and Recreation Vol.26(1) 2004: 55-64
Base Substitutions, Targeted Single-Base Deletions, and Chromosomal Translocations Induced by Bleomycin in Plateau-Phase Mammary Epithelial Cells

Abstract Yu, Y. , Inamdar, K. V. , Turner, K. , Jackson-Cook, C. K. and Povirk, L. F. Base Substitutions, Targeted Single-Base Deletions, and Chromosomal Translocations Induced by Bleomycin in Plateau-Phase Mammary Epithelial Cells. Radiat. Res. 158, 327–338 (2002). Previous work showed that treatment of plateau-phase Chinese hamster ovary cells with the radiomimetic double-strand cleaving agent bleomycin induced very small deletions as well as interchromosomal reciprocal translocations, both of which could be ascribed to errors in end joining of DNA double-strand breaks. In an attempt to assess the possible role of TP53 in suppressing such repair errors, bleomycin-induced mutagenesis at the HPRT locus was examined in immortalized 184B5 human mammary epithelial cells (TP53+), and in a TP53-defective derivative, 184B5-E6tfxc6. For both cell lines, the most frequent bleomycin-induced mutations were base substitutions, with no apparent targeting to major bleomycin lesions. However, both lines also sustained single-base deletions that were targeted to expected sites of double-strand breaks, suggesting that they arose by end-joining repair of the breaks. Surprisingly, only a few large deletions or rearrangements, and no interchromosomal events involving the HPRT locus were detected among the mutants. The results suggest that in both cell lines, errors in double-strand break repair resulting in heritable large deletions and rearrangements are rare. Spectral karyotyping of bleomycin-treated 184B5 cells showed that a significant number of translocations were present shortly after bleomycin exposure, but their frequency decreased upon continued culture of the cells. Thus, for these cells, the lack of induced interchromosomal rearrangements can be explained in part by selection against such events as the cells proliferate.
Subsurface Cycling of Nitrogen and Anaerobic Aromatic Hydrocarbon Biodegradation Revealed by Nucleic Acid and Metabolic Biomarkers

ABSTRACT Microbial processes are crucial for ecosystem maintenance, yet documentation of these processes in complex open field sites is challenging. Here we used a multidisciplinary strategy (site geochemistry, laboratory biodegradation assays, and field extraction of molecular biomarkers) to deduce an ongoing linkage between aromatic hydrocarbon biodegradation and nitrogen cycling in a contaminated subsurface site. Three site wells were monitored over a 10-month period, which revealed fluctuating concentrations of nitrate, ammonia, sulfate, sulfide, methane, and other constituents. Biodegradation assays performed under multiple redox conditions indicated that naphthalene metabolism was favored under aerobic conditions. To explore in situ field processes, we measured metabolites of anaerobic naphthalene metabolism and expressed mRNA transcripts selected to document aerobic and anaerobic microbial transformations of ammonia, nitrate, and methylated aromatic contaminants. Gas chromatography-mass spectrometry detection of two carboxylated naphthalene metabolites and transcribed benzylsuccinate synthase, cytochrome c nitrite reductase, and ammonia monooxygenase genes indicated that anaerobic metabolism of aromatic compounds and both dissimilatory nitrate reduction to ammonia (DNRA) and nitrification occurred in situ. These data link formation (via DNRA) and destruction (via nitrification) of ammonia to in situ cycling of nitrogen in this subsurface habitat, where metabolism of aromatic pollutants has led to accumulation of reduced metabolic end products (e.g., ammonia and methane).
Electronic and Optical Properties of Arsenene Under Uniaxial Strain

The electronic and optical properties of strained monolayer arsenene were calculated based on first-principle density functional theory. Our theoretical calculations demonstrated that monolayer arsenene was transformed from indirect to direct band gap semiconductor by inducing uniaxial tensile strain along armchair and zigzag directions. Compared to the biaxial tensile strain of 0.04, this transformation occurred at the strain of 0.06 and 0.10 along armchair and zigzag direction, respectively. Spin-orbital coupling is available to tune the bandgaps. The spin-orbit interaction opens a 0.2 eV bandgap in the Γ-point on the unstrained monolayer arsenene. The absorption properties were calculated and a clear red shift was observed with the increasing strain.
The analysis of measurement equivalence in international studies using the Rasch model

When comparing data derived from tests or questionnaires in cross-national studies, researchers commonly assume measurement invariance in their underlying scaling models. However, different cultural contexts, languages, and curricula can have powerful effects on how students respond in different countries. This article illustrates how the application of the Rasch item response theory (IRT) model (Rasch, 1960) can be used for assessing differences in measurement properties of tests and questionnaires with reference to examples from the field trial analyses for the International Association for the Evaluation of Educational Achievement (IEA) International Civic and Citizenship Education Study (ICCS). It also discusses the general scope and limitations of the analyses undertaken in the context of this study.
Sliding-mode control of coordinated nonholonomic mobile manipulators

Coordinated systems of multiple mobile manipulators can be much more flexible than single mobile manipulator in order to accomplish complex and changeable tasks. In this paper, sliding-mode control strategies are used to control the coordinated multiple mobile manipulators which carry a common object. The control ensures that the output tracking errors of the system converge to zero. Simulation studies show the effectiveness of the proposed scheme.
Entrepreneurial mindset of information and communication technology firms

Limited research focuses on the entrepreneurial mindset of information and communication technology (ICT) firms, despite the opportunities in and importance of this sector for economic growth. In this article, the entrepreneurial mindset of ICT firms is described by using three indicators: entrepreneurial orientation, e-business initiatives and a supportive organizational climate. Data were obtained using structured telephone interviews with 144 ICT firms. The findings indicate that the three indicators of an entrepreneurial mindset are associated and can be linked to performance. It is recommended that managers create a supportive climate for entrepreneurship by offering rewards, empowering employees and providing leadership and support for initiatives.
Transmembrane signalling by the T cell antigen receptor. Perturbation of the T3-antigen receptor complex generates inositol phosphates and releases calcium ions from intracellular stores

Antibodies against the T3-antigen receptor complex can activate the human T cell line, Jurkat, to produce interleukin 2 (2-5). This activation is initiated by a receptor-mediated increase in the concentration of free cytoplasmic calcium ions [Ca2+]i (3, 4). In this communication, we investigate the mechanism by which the receptor complex increases [Ca2+ )i in Jurkat cells. The initial receptor- mediated change in [Ca2+]i can occur when extracellular Ca2+ is depleted by EGTA. Perturbation of the T cell antigen receptor, therefore, generates a signal which mobilizes Ca2+ from intracellular stores. As inositol trisphosphate appears to function as such a signal for certain hormone receptors, we measured the levels of inositol trisphosphate and of the other inositol phosphate compounds in Jurkat. Antibodies to either the antigen receptor heterodimer or T3 determinants result in marked elevations of all three inositol phosphates. These changes in inositol phosphates are not secondary to the receptor-mediated increases in [Ca2+]i as demonstrated by the inability of the Ca2+ ionophore, ionomycin, to affect the levels of any of these compounds. In concentrations between 0.1 and 1 microM, purified inositol trisphosphate releases Ca2+ from permeabilized Jurkat cells. Taken together, these data indicate that, during activation, perturbation of the T3-antigen receptor complex generates inositol trisphosphate. This compound functions as an intracellular signal to release Ca2+ from intracellular stores, leading to increases in [Ca2+]i.
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma

Glioblastoma multiforme (GBM) is the most common and lethal brain tumor in humans. Recent studies revealed that patterns of microRNA (miRNA) expression in GBM tissue samples are different from those in normal brain tissues, suggesting that a number of miRNAs play critical roles in the pathogenesis of GBM. However, little is yet known about which miRNAs play central roles in the pathology of GBM and their regulatory mechanisms of action. To address this issue, in this study, we systematically explored the main regulation format (feed-forward loops, FFLs) consisting of miRNAs, transcription factors (TFs) and their impacting GBM-related genes, and developed a computational approach to construct a miRNA-TF regulatory network. First, we compiled GBM-related miRNAs, GBM-related genes, and known human TFs. We then identified 1,128 3-node FFLs and 805 4-node FFLs with statistical significance. By merging these FFLs together, we constructed a comprehensive GBM-specific miRNA-TF mediated regulatory network. Then, from the network, we extracted a composite GBM-specific regulatory network. To illustrate the GBM-specific regulatory network is promising for identification of critical miRNA components, we specifically examined a Notch signaling pathway subnetwork. Our follow up topological and functional analyses of the subnetwork revealed that six miRNAs (miR-124, miR-137, miR-219-5p, miR-34a, miR-9, and miR-92b) might play important roles in GBM, including some results that are supported by previous studies. In this study, we have developed a computational framework to construct a miRNA-TF regulatory network and generated the first miRNA-TF regulatory network for GBM, providing a valuable resource for further understanding the complex regulatory mechanisms in GBM. The observation of critical miRNAs in the Notch signaling pathway, with partial verification from previous studies, demonstrates that our network-based approach is promising for the identification of new and important miRNAs in GBM and, potentially, other cancers.
Exploiting both local and global constraints for multi-span statistical language modeling

A new framework is proposed to integrate the various constraints, both local and global, that are present in the language. Local constraints are captured via n-gram language modeling, while global constraints are taken into account through the use of latent semantic analysis. An integrative formulation is derived for the combination of these two paradigms, resulting in several families of multi-span language models for large vocabulary speech recognition. Because of the inherent complementarity in the two types of constraints, the performance of the integrated language models, as measured by the perplexity, compares favorably with the corresponding n-gram performance.
Reliability estimation for component-based software product lines

The objective of the software product line engineering paradigm is to enhance the largescale reuse of common core assets within a target domain. Reuse is facilitated by systematically organizing and modeling the core assets and the relationships between them. One of the main core assets of a domain is the model for representing the available functional aspects, often known as features, within structured forms such as feature models. The selection and composition of the most suitable or desirable set of features for a given purpose allows the rapid development of new final products from the software product line. Product developers are, in most cases, not only interested in building applications that possess certain functional characteristics but are also concerned with nonfunctional properties of the final product, such as reliability. To this end, we propose a component based software product line reliability estimation model that is able to provide lower and upper reliability bounds guarantees for a software product line feature model, its specializations and configurations. Our model builds on top of the reliability of the individual features that are present in the product line and provides best- and worst-case estimates. Our work is based on an essential and widely used assumption that features are implemented using self-contained software components or services whose reliability can be determined independently. We also propose reliability-aware configuration methods that ensure the satisfaction of both functional and reliability requirements during the application development process. We offer our observations and insight into the performance of our reliability estimation model and provide analysis of its advantages and shortcomings.
Multi-label Subspace Ensemble

A challenging problem of multi-label learning is that both the label space and the model complexity will grow rapidly with the increase in the number of labels, and thus makes the available training samples insufficient for training a proper model. In this paper, we eliminate this problem by learning a mapping of each label in the feature space as a robust subspace, and formulating the prediction as finding the group sparse representation of a given instance on the subspace ensemble. We term this approach as “multi-label subspace ensemble (MSE)”. In the training stage, the data matrix is decomposed as the sum of several low-rank matrices and a sparse residual via a randomized optimization, where each low-rank part defines a subspace mapped by a label. In the prediction stage, the group sparse representation on the subspace ensemble is estimated by group lasso. Experiments on several benchmark datasets demonstrate the appealing performance of MSE.
Consciousness, explanatory inversion, and cognitive science

Abstract Cognitive science typically postulates unconscious mental phenomena, computational or otherwise, to explain cognitive capacities. The mental phenomena in question are supposed to be inaccessible in principle to consciousness. I try to show that this is a mistake, because all unconscious intentionality must be accessible in principle to consciousness; we have no notion of intrinsic intentionality except in terms of its accessibility to consciousness. I call this claim the “Connection Principle. ” The argument for it proceeds in six steps. The essential point is that intrinsic intentionality has aspectual shape: Our mental representations represent the world under specific aspects, and these aspectual features are essential to a mental state's being the state that it is. Once we recognize the Connection Principle, we see that it is necessary to perform an inversion on the explanatory models of cognitive science, an inversion analogous to the one evolutionary biology imposes on preDarwinian animistic modes of explanation. In place of the original intentionalistic explanations we have a combination of hardware and functional explanations. This radically alters the structure of explanation, because instead of a mental representation (such as a rule) causing the pattern of behavior it represents (such as rule-governed behavior), there is a neurophysiological cause of a pattern (such as a pattern of behavior), and the pattern plays a functional role in the life of the organism. What we mistakenly thought were descriptions of underlying mental principles in, for example, theories of vision and language were in fact descriptions of functional aspects of systems, which will have to be explained by underlying neurophysiological mechanisms. In such cases, what looks like mentalistic psychology is sometimes better construed as speculative neurophysiology. The moral is that the big mistake in cognitive science is not the overestimation of the computer metaphor (though that is indeed a mistake) but the neglect of consciousness.
Teaching Data Science and Cloud Computing in Low and Middle Income Countries

Large, publicly available data sets present a challenge and an opportunity for researchers based in Low and Middle Income Countries (LMIC). The challenge for these researchers is how they can make use of such data sets given their poor connectivity and infrastructure. The opportunity is the ability to perform leading edge research using these data sets and hence avoid having to invest substantial resources in generating the data sets. The offshoot of this will be to generate solutions to the substantial local problems encountered in these countries and create an educated workforce in data science. Cloud computing in particular may well close the infrastructural gap here. In this paper we discuss our experiences of teaching a variety of summer schools on data intensive analysis in bioinformatics in China, Namibia and Malaysia. On the basis of these experiences we propose that a larger series of summer schools in data science and cloud computing in LMIC would create a cadre of data scientists to start this process. We finally discuss the possibility of the provision of cloud computing resources where the usage costs are controlled so that it is affordable for LMIC researchers.
Large Einstein radii: a problem for ΛCDM

The Einstein radius of a cluster provides a relatively model-independent measure of the mass density of a cluster within a projected radius of ∼150 kpc, large enough to be relatively unaffected by gas physics. We show that the observed Einstein radii of four well-studied massive clusters, for which reliable virial masses are measured, lie well beyond the predicted distribution of Einstein radii in the standard A cold dark matter (ACDM) model. Based on large samples of numerically simulated cluster-sized objects with virial masses ∼10 15 M O , the predicted Einstein radii are only 15-25 arcsec, a factor of 2 below the observed Einstein radii of these four clusters. This is because the predicted mass profile is too shallow to exceed the critical surface density for lensing at a sizable projected radius. After carefully accounting for measurement errors as well as the biases inherent in the selection of clusters and the projection of mass measured by lensing, we find that the theoretical predictions are excluded at a 4σ significance. Since most of the free parameters of the ACDM model now rest on firm empirical ground, this discrepancy may point to an additional mechanism that promotes the collapse of clusters at an earlier time thereby enhancing their central mass density.