Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthetic smectite colloids: Characterization of nanoparticles after co-precipitation in the presence of lanthanides and tetravalent elements (Zr, Th)

The magnesian smectite hectorite is a corrosion product frequently detected in nuclear waste glass alteration experiments. The structural incorporation of a single trivalent lanthanide was previously demonstrated. Hectorite was presently synthesized, for the first time, in the presence of several lanthanides (La, Eu, Yb) following a multi-step synthesis protocol. The smallest-sized particles (nanoparticles, NPs) were isolated by centrifugation and analyzed by asymmetrical flow field-flow fractionation (AsFlFFF) coupled to ICP-MS, in order to obtain information on the elemental composition and distribution as a function of the size. Nanoparticles can be separated from the bulk smectite phase. The particles are able to accommodate even the larger-sized lanthanides such as La, however, with lower efficiency. We, therefore, assume that the incorporation proceeds by substitution for octahedral Mg accompanied by a concomitant lattice strain that increases with the size of the lanthanides. The presence of a mixture does not seem to affect the incorporation extent of any specific element. Furthermore, syntheses were performed where in addition the tetravalent zirconium or thorium elements were admixed, as this oxidation state may prevail for many actinide ions in a nuclear waste repository. The results show that they can be incorporated as well.
Onset Pattern and Long-Term Prognosis in Schizophrenia: 10-Year Longitudinal Follow-Up Study

Background Although the duration of untreated psychosis (DUP) plays an important role in the short-term prognosis of patients with schizophrenia, their long-term prognosis generally is not determined by DUP alone. It is important to explore how other clinical factors in the early stage are related to DUP and consequent disease courses. Methods A total of 664 patients with untreated psychosis were surveyed for this study. At the first examination, we divided them into the severe positive symptoms cases (SC) or the less severe cases (NonSC) and compared the prognosis among the two groups after a 10-year follow-up. In all, 113 patients in the SC group and 43 patients in the NonSC group were follow-up completers. Results Whereas DUP was not different between the two groups, patients with nonacute onset in both groups had significantly longer DUP than those in patients with acute onset. For all clinical measures, there was no difference in prognosis between the two groups or among the four groups classified by mode of onset (MoO) and initial severity of positive symptoms. However, the degree of improvement of global assessment of functioning (GAF) was significantly smaller in the NonSC-nonacute group than in the SC-acute and SC-nonacute groups. Conclusions These results suggest that neither DUP nor MoO alone necessarily affects the initial severity of positive symptoms. Moreover, it is possible that patients with low impetus of positive symptoms onset within long DUP experience profound pathologic processes. Therefore, the current study results indicated that long DUP and nonacute onset were related to poor long-term prognosis, regardless of initial positive symptoms.
Travelling kinks in discrete ϕ4 models

In recent years, three exceptional discretizations of the ϕ4 theory have been discovered (by Speight and Ward, Bender and Tovbis, and Kevrekidis) which support translationally invariant kinks, i.e. families of stationary kinks centred at arbitrary points between the lattice sites. It has been suggested that the translationally invariant stationary kinks may persist as sliding kinks, i.e. discrete kinks travelling at nonzero velocities without experiencing any radiation damping. The purpose of this study is to check whether this is indeed the case. By computing the Stokes constants in beyond-all-order asymptotic expansions, we prove that the three exceptional discretizations do not support sliding kinks for most values of the velocity—just like the standard, one-site discretization. There are, however, isolated values of velocity for which radiationless kink propagation becomes possible. There is one such value for the discretization of Speight and Ward and three sliding velocities for the model of Kevrekidis.
Block Buying and Choice of Issue Method in UK Seasoned Equity Offers

Much of the new equity declined by existing shareholders in UK SEOs is bought in a few large blocks, both by other existing holders and by new investors. The paper argues that a placing process via negotiation with investors facilitates the purchase of large blocks better than the alternative method of selling rights on the market, and that this helps to explain the decline of rights issues in the UK. Other explanations for use of the placing method appear to be of limited relevance, except perhaps certificaton of issuer value. Copyright (c) 2010 Blackwell Publishing Ltd.
Disruption of six Saccharomyces cerevisiae ORFs on chromosome XII results in three lethal disruptants

Six ORFs of unknown function from the left arm of chromosome XII of Saccharomyces cerevisiae were chosen for a reverse genetic approach to provide materials to assist in assignment of function. A two‐step PCR using long‐flanking homology was employed to amplify disruption cassettes consisting of a kanMX gene as selectable marker flanked by 250–350 bp long regions homologous to the target gene. The diploid strains FY1679 and CEN.PK2 were transformed with the replacement cassettes and transformants were selected for geneticin (G418) resistance. Correct targeting of the replacement cassettes at the genomic locus was verified by Southern blot analysis with the kanMX gene as a probe. Disruption cassettes were cloned in pUG7 plasmid for systematic gene inactivation in other yeast strains and the cognate genes were cloned in pRS416 plasmid for gene complementation studies. Sporulation and tetrad analysis of heterozygous disruptants showed that three of the six ORFs [YLR141w (RRN5), YLR145w and YLR147c (SMD3)] were essential genes that were complemented by their cognate genes. ylr146cΔ (spe4) homozygous diploids showed enhanced sporulation efficiency, whereas ylr147cΔ heterozygous diploids failed to sporulate in the FY1679 but not in the CEN.PK2 genetic background. The other two disruptants [ylr143w and ylr144c (acf2)] gave no phenotype. Copyright © 2002 John Wiley & Sons, Ltd.
Is cross-validation valid for small-sample microarray classification?

MOTIVATION Microarray classification typically possesses two striking attributes: (1) classifier design and error estimation are based on remarkably small samples and (2) cross-validation error estimation is employed in the majority of the papers. Thus, it is necessary to have a quantifiable understanding of the behavior of cross-validation in the context of very small samples. RESULTS An extensive simulation study has been performed comparing cross-validation, resubstitution and bootstrap estimation for three popular classification rules-linear discriminant analysis, 3-nearest-neighbor and decision trees (CART)-using both synthetic and real breast-cancer patient data. Comparison is via the distribution of differences between the estimated and true errors. Various statistics for the deviation distribution have been computed: mean (for estimator bias), variance (for estimator precision), root-mean square error (for composition of bias and variance) and quartile ranges, including outlier behavior. In general, while cross-validation error estimation is much less biased than resubstitution, it displays excessive variance, which makes individual estimates unreliable for small samples. Bootstrap methods provide improved performance relative to variance, but at a high computational cost and often with increased bias (albeit, much less than with resubstitution).
A quantification of prospect theory in the health domain

It is well-known that expected utility (EU) has empirical deficiencies. Prospect theory (PT) has developed as an alternative with more descriptive validity. However, PT’s full function had not yet been quantified in the health domain. This paper is therefore the first to simultaneously measure utility of life duration, probability weighting, and loss aversion in the health domain. We observe loss aversion and risk aversion for gains and losses, which for gains can be explained by probabilistic pessimism. Utility for gains is almost linear. For losses, we find less weighting of probability 1/2 and concave utility. This contrasts with the common finding of convex utility for monetary losses. However, PT was proposed to explain choices among lotteries involving small outcomes. Life years are arguably not ‘small’ and need not generate convex utility for losses. Moreover, utility of life duration reflects discounting, causing concave utility. These results are a first step in fitting non-EU models for health-related decisions.
Reconfigurable Nets, a Class of High Level Petri Nets Supporting Dynamic Changes

We introduce a class of high level Petri nets, called reconfigurable nets, that can dynamically modify their own structure by rewriting some of their components. Boundedness of a reconfigurable net can be decided by constructing its coverability tree. Moreover such a net can be simulated by a self-modifying Petri net. The class of reconfigurable nets thus provide a subclass of self-modifying Petri nets for which boundedness can be decided. Delayed dynamic changes within workflow systems in the sense of [7] can then be handled in an extension of van der Aalst's workflow nets [2]. For this class (the reconfigurable workflow nets), a notion of soundness has been defined that can also be verified using the coverability tree construction.
Ventilation–Perfusion Scintigraphy Is More Sensitive than Multidetector CTPA in Detecting Chronic Thromboembolic Pulmonary Disease as a Treatable Cause of Pulmonary Hypertension

Pulmonary hypertension (PH) is a progressive disease with a poor prognosis. Identifying chronic thromboembolic pulmonary disease as a cause of PH has major clinical implications as these patients could be potentially offered a surgical cure. Ventilation–perfusion (V/Q) scintigraphy has a high sensitivity to detect embolic disease but its value has been challenged with the emergence of multidetector CT pulmonary angiography (CTPA). We compared the value of V/Q scintigraphy with CTPA in detecting chronic thromboembolic pulmonary disease. Methods: We retrospectively reviewed the results of V/Q scintigraphy and CTPA performed on patients who had been referred to the Pulmonary Hypertension Service at Hammersmith Hospital between 2000 and 2005. A total of 227 patients (85 males, 142 females; age range, 18–81 y; mean age, 42 y) had all tests done at Hammersmith Hospital and were included in the study. Interpretation of scans was according to the modified PIOPED (Prospective Investigation of Pulmonary Embolism Diagnosis) criteria. CTPA was considered as suggestive of chronic thromboembolic pulmonary disease if it showed visualization of the thrombus or webs, recanalization, perfusion abnormalities, stenosis, or strictures. Standard pulmonary angiography was performed via femoral approach. In 90% of the cases, CTPA and V/Q scintigraphy were performed within 10 d. Results: Seventy-eight patients (group A) had a final diagnosis of chronic thromboembolic pulmonary hypertension (CTEPH) and 149 (group B) had non-CTEPH etiology. Among group A, V/Q scintigraphy was reported as high probability in 75 patients, intermediate probability in 1 patient, and low probability in 2 patients. CTPA was positive in 40 patients and negative in 38 patients. Among group B, V/Q scintigraphy was reported as low probability in 134, intermediate probability in 7, and high probability in 8 patients. CTPA was negative in 148 patients and false-positive in 1 patient. Statistical analysis showed V/Q scintigraphy to have a sensitivity of 96%–97.4% and a specificity of 90%–95%. CTPA showed a sensitivity of 51% and a specificity of 99%. Conclusion: Our results demonstrate that V/Q scintigraphy has a higher sensitivity than CTPA in detecting CTEPH as a potential curable cause of PH.
Docosahexaenoic Acid Induces Apoptosis in the Human PaCa-44 Pancreatic Cancer Cell Line by Active Reduced Glutathione Extrusion and Lipid Peroxidation

Abstract: We investigated the ability of fatty acids to induce growth inhibition and apoptosis in the human PaCa-44 pancreatic cancer cell line and the mechanism(s) underlying apoptosis. Butyric acid, α-linoleic acid, and docosahexaenoic acid (DHA) were supplemented at 200 μM concentration in the medium of cell cultures. Our results showed that all fatty acids inhibited cell growth, whereas only DHA induced cell apoptosis. An oxidative process was implicated in apoptosis induced by DHA because butylated hydroxytoluene and vitamin E prevented lipid peroxidation and reversed apoptosis. Intracellular and extracellular glutathione [reduced glutathione (GSH) and oxidized glutathione (GSSG)] concentrations were measured following DHA treatment in the presence or in the absence of GSH extrusion inhibitors such as cystathionine or methionine. DHA induced intracellular GSH depletion without affecting intracellular GSSG concentration and increased extracellular GSH and GSSG levels. Intracellular GSH depletion and extracellular GSH increase were both reversed by cystathionine. Inhibition of active GSH extrusion from the cell by cystathionine or methionine completely reversed lipid peroxidation and apoptosis. These data document the antiproliferative and apoptotic activities of DHA. The date provide evidence that intracellular GSH depletion represents an active extrusion process rather than a consequence of an oxidative stress, suggesting a causative role of GSH depletion in DHA-induced apoptosis.
From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data

Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites for protein of interest. Most conventional approaches to ChIP-seq data analysis involve the detection of the absolute presence (or absence) of a binding site. However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB). This may yield more relevant results than conventional analyses, as changes in binding can be associated with the biological difference being investigated. The aim of this article is to facilitate the implementation of DB analyses, by comprehensively describing a computational workflow for the detection of DB regions from ChIP-seq data. The workflow is based primarily on R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, from alignment of read sequences to interpretation and visualization of putative DB regions. In particular, detection of DB regions will be conducted using the counts for sliding windows from the csaw package, with statistical modelling performed using methods in the edgeR package. Analyses will be demonstrated on real histone mark and transcription factor data sets. This will provide readers with practical usage examples that can be applied in their own studies.
Critical Analysis of Various Known Methods for Approximate Reasoning in Fuzzy Logic Control

:In this paper a rewiev and a critical analysis of various, soft computing based, approximate reasoning methods is given, studied in the Phd thesis of the author. Since Mamdani first implemented a fuzzy logic controller it has also gone trough substantial theoretical developments and serious discussions about place of this method in theory of computational rule of inference. The paper gives a review of these notes.
Do Pursuit Movement Tasks Lead to Differential Changes in Early Somatosensory Evoked Potentials Related to Motor Learning in Comparison to Typing Tasks? Affiliation

35 36 Central nervous system (CNS) plasticity is essential for development; however recent research 37 has demonstrated its role in pathology, particularly following overuse and repetition. Previous 38 studies investigating changes in sensorimotor integration (SMI) have used relatively simple 39 paradigms resulting in minimal changes in neural activity, as determined through the use of 40 somatosensory evoked potentials (SEPs). This study sought to utilize complex tasks and compare 41 separate motor paradigms to determine which one best facilitates long-term learning. Spinal, 42 brainstem and cortical SEPs were recorded following median nerve stimulation at the wrist pre 43 and post interventions. 18 participants performed the same paradigms, a control condition of 10 44 minutes of mental recitation, and two interventions, one consisting of 10 minutes of tracing and 45 the other, 10 minutes of repetitive typing. Significant increases in the N13, N20, P25 and N30 46 SEP peaks were seen for both interventions. A significant decrease in the N24 SEP peak was 47 observed for both interventions. Significant improvements in accuracy were seen for both 48 interventions post-acquisition but only for tracing during retention. The changes seen following 49 motor learning were congruent with those associated with long-term learning which was also 50 reflected by significant increases in accuracy during retention. Tracing or the pursuit movement 51 paradigm was shown to be a more effective learning tool. The identification of a task which is 52 sufficiently novel and complex, leading to robust changes in SEP peaks indicates a task which 53 can be utilized in future work to study clinical populations and the effect of experimental 54 interventions on SMI. 55
Organizational knowledge assets and innovation capability

Purpose – Organizational knowledge assets are key organizational factors responsible for firm innovation, as well as effective management. Traditionally, a good piece of research takes the innovation processes from an external perspective, leaving aside the internal complexity that characterizes innovation dynamics. Nevertheless, the innovation capability of a certain firm depends very closely on the intellectual assets and organizational knowledge that it possesses, as well as on its ability to deploy them. In this sense, this paper aims to test empirically the relationships between organizational knowledge assets and the innovation capability of the firm.Design/methodology/approach – The data collection was carried out through a questionnaire on a sample of 251 Spanish high and medium‐high manufacturing firms. Exploratory and confirmatory factor analyses and multiple linear regressions were also used.Findings – Based on the literature review, this work explores the nature and measurement of organization.
Effect of Long Term Reverse Feeding on the Reproductive and Non-reproductive Tissues in Male Mice

Previously, we demonstrated that the shift and/or restriction of feeding time during relatively short-term period (4 weeks) could alter the pituitary gonadotropin expression and the weights of seminal vesicle and prostate in rats. We also found that the reverse feeding (RF) schedule (up to 8 weeks) might induce an adaptable metabolic stress and cause impairment of androgen-dependent reproductive tissues. In the present study, we extended the RF time regimen up to 12 weeks, and measured the reproductive tissue weights. After 4 and 8 weeks of RF, the weights of epididymis were not significantly different. After 12 weeks, however, epididymis weights of RF animals were significantly different (CON 12W : RF 12W = 48.26±0.62 mg : 44.05±1.57 mg, p<0.05). After 4 and 12 weeks of feeding, seminal vesicle weights of RF animals were significantly decreased (CON 4W : RF 4W = 79.36±8.34 mg : 46.28±2.43 mg, p<0.001; CON 12W : RF 12W = 72.04±3.76 mg : 46.71±2.27 mg, p<0.001, respectively). Prostate weights were not changed by RF. Kidney and spleen weights of RF animals were significantly different on weeks 4 and 12 (Kidney, CON 4W : RF 4W = 249.72±4.20 mg : 228.41±3.03 mg, p<0.001; CON 12W : RF 12W = 309.15±7.49 mg : 250.72±6.13 mg, p<0.001, respectively, Spleen, CON 4W : RF 4W = 111.26±3.76 mg : 96.88±4.69 mg, p<0.05; CON 12W : RF 12W = 123.93±10.72 mg : 94.68±5.65 mg, p<0.05, respectively). Histology analysis of seminal vesicle revealed that the thinner epithelial cell layers, reduced complexities of swollen papilla folding in the exocrine glands on weeks 4 and 12 of RF. There was no histological difference between control and RF group on week 8. The present study indicates that up to 12 weeks RF induced differential changes in tissue weights of male mice. In particular, seminal vesicle, kidney and spleen seemed to temporarily adapted to the RF-induced metabolic stress on week 8 of feeding schedule. These results confirmed the our previous study that the RF might induce an adaptable metabolic stress and cause impairment of androgen-dependent reproductive tissues such as epididymis and seminal vesicle as well as non-reproductive tissues such as kidney and spleen. Further studies will be needed to achieve a better understanding of the how does mealtime shift affect the reproductive function and exact nature of adaptation.
H(div) conforming and DG methods for incompressible Euler’s equations

H(div) conforming and discontinuous Galerkin (DG) methods are designed for incompressible Euler’s equation in two and three dimension. Error estimates are proved for both the semi-discrete method and fully-discrete method using backward Euler time stepping. Numerical examples exhibiting the performance of the methods are given.
Unique Roles of Phosphorus in Endochondral Bone Formation and Osteocyte Maturation

The mechanisms by which inorganic phosphate (Pi) homeostasis controls bone biology are poorly understood. Here we used Dmp1 null mice, a hypophosphatemic rickets/osteomalacia model, combined with a metatarsal organ culture and an application of neutralizing fibroblast growth factor 23 (FGF‐23) antibodies to gain insight into the roles of Pi in bone biology. We showed (1) that abnormal bone remodeling in Dmp1 null mice is due to reduced osteoclast number, which is secondary to a reduced ratio of RANKL/OPG expressed by osteoclast supporting cells and (2) that osteoblast extracellular matrix mineralization, growth plate maturation, secondary ossification center formation, and osteoblast differentiation are phosphate‐dependent. Finally, a working hypothesis is proposed to explain how phosphate and DMP1 control osteocyte maturation. © 2011 American Society for Bone and Mineral Research.
THE EXTENDED NARROW-LINE REGION OF TWO TYPE-I QUASI-STELLAR OBJECTS

We investigate the narrow-line region (NLR) of two radio-quiet QSOs, PG1012+008 and PG1307+085, using high signal-to-noise spatially resolved long-slit spectra obtained with FORS1 at the Very Large Telescope. Although the emission is dominated by the point-spread function of the nuclear source, we are able to detect extended NLR emission out to several kiloparsec scales in both QSOs by subtracting the scaled central spectrum from outer spectra. In contrast to the nuclear spectrum, which shows a prominent blue wing and a broad line profile of the [O iii] line, the extended emission reveals no clear signs of large-scale outflows. Exploiting the wide wavelength range, we determine the radial change of the gas properties in the NLR, i.e., gas temperature, density, and ionization parameter, and compare them with those of Seyfert galaxies and type-II QSOs. The QSOs have higher nuclear temperature and lower electron density than Seyferts, but show no significant difference compared to type-II QSOs, while the ionization parameter decreases with radial distance, similar to the case of Seyfert galaxies, For PG1012+008, we determine the stellar-velocity dispersion of the host galaxy. Combined with the black hole mass, we find that the luminous radio-quiet QSO follows the local MBH–σ* relation of active galactic nuclei.