Miracle-dz/UniFAR-FTUs huggingface dataset:
Specifying and Verifying the Context-aware Adaptive Behaviour of Software Systems

Context-aware adaptive software systems need to have a model for the system adaptive behaviour. This model decides the system reactions in response to the environment changes. In large scale software systems with high variability, an explosion in the number of system’s sates (i.e. configurations or behaviours) and the transitions between them (i.e. the system adaptive behaviour) is introduced. Therefore, specifying the system adaptive behaviour and assuring its correctness are major challenges. Existing research solves only one of these two challenges where improving one aspect makes the other worse. In this report, we introduce a novel approach to specifying and verifying the context-aware adaptive behaviour of a software system. Our approach explicitly represents the relationships between the context changes and the system variations, so that the system adaptive behaviour is easily captured. We classify the possible system variations into dependent and independent variations for reducing the possible system states and the transition between them. The designed system adaptive behaviour model is transform to a Petri Net model so that it can be verified for detecting the adaptation behaviours errors such as inconsistency, redundancy, circularity, and incompleteness. We generate the system adaptive behaviour implementation from its model. In addition, we illustrate our approach though specifying and verifying the context-aware adaptive behaviour of the vehicle route planning system.
IL-1β Suppresses Innate IL-25 and IL-33 Production and Maintains Helminth Chronicity

Approximately 2 billion people currently suffer from intestinal helminth infections, which are typically chronic in nature and result in growth retardation, vitamin A deficiency, anemia and poor cognitive function. Such chronicity results from co-evolution between helminths and their mammalian hosts; however, the molecular mechanisms by which these organisms avert immune rejection are not clear. We have found that the natural murine helminth, Heligmosomoides polygyrus bakeri (Hp) elicits the secretion of IL-1β in vivo and in vitro and that this cytokine is critical for shaping a mucosal environment suited to helminth chronicity. Indeed in mice deficient for IL-1β (IL-1β−/−), or treated with the soluble IL-1βR antagonist, Anakinra, helminth infection results in enhanced type 2 immunity and accelerated parasite expulsion. IL-1β acts to decrease production of IL-25 and IL-33 at early time points following infection and parasite rejection was determined to require IL-25. Taken together, these data indicate that Hp promotes the release of host-derived IL-1β that suppresses the release of innate cytokines, resulting in suboptimal type 2 immunity and allowing pathogen chronicity.
The Cramér-Rao bound for estimation-after-selection

In many practical parameter estimation problems, a model selection is made prior to estimation. In this paper, we consider the problem of estimating an unknown parameter of a selected population, where the population is chosen from a population set by using a predetermined selection rule. Since the selection step may have an important impact on subsequent estimation, ignoring it could lead to biased-estimation and an invalid Cramér-Rao bound (CRB). In this work, the mean-square-selected-error (MSSE) criterion is used as a performance measure. The concept of Ψ-unbiasedness is introduced for a given selection rule, Ψ, by using the Lehmann-unbiasedness definition. We derive a non-Bayesian Cramér-Rao-type bound on the MSSE of any Ψ-unbiased estimator. The proposed Ψ-CRB is a function of the conditional Fisher information and is a valid bound on the MSSE. Finally, we examine the Ψ-CRB for different selection rules for mean estimation in a linear Gaussian model.
Mechanisms of Growth Plate Maturation and Epiphyseal Fusion

Longitudinal growth occurs within the long bones at the growth plate. During childhood, the growth plate matures, its total width decreases and eventually it disappears at the end of puberty with complete replacement by bone along with cessation of longitudinal growth. The exact mechanism of epiphyseal fusion is still not completely understood and experimental studies are complicated by the fact that there is a species difference between humans and rabbits that do fuse their growth plates and rodents that do not. This mini review summarizes hypotheses and theories postulated in the literature regarding growth plate maturation and epiphyseal fusion. Growth factors, local regulators and hormones involved in growth plate maturation are described as well as four postulated hypotheses and theories regarding the final steps in epiphyseal fusion: apoptosis, autophagy, transdifferentiation and hypoxia. A better insight into the mechanisms of epiphyseal fusion may ultimately help to develop new strategies for the treatment of cartilage and growth disorders.
Antimicrobial Activities and Time-Kill Kinetics of Extracts of Selected Ghanaian Mushrooms

The rapid rise of antimicrobial resistance is a worldwide problem. This has necessitated the need to search for new antimicrobial agents. Mushrooms are rich sources of potential antimicrobial agents. This study investigated the antimicrobial properties of methanol extracts of Trametes gibbosa, Trametes elegans, Schizophyllum commune, and Volvariella volvacea. Agar well diffusion, broth microdilution, and time-kill kinetic assays were used to determine the antimicrobial activity of the extracts against selected test organisms. Preliminary mycochemical screening revealed the presence of tannins, flavonoids, triterpenoids, anthraquinones, and alkaloids in the extracts. Methanol extracts of T. gibbosa, T. elegans, S. commune, and V. volvacea showed mean zone of growth inhibition of 10.00 ± 0.0 to 21.50 ± 0.84, 10.00 ± 0.0 to 22.00 ± 1.10, 9.00 ± 0.63 to 21.83 ± 1.17, and 12.00 ± 0.0 to 21.17 ± 1.00 mm, respectively. The minimum inhibitory concentration of methanol extracts of T. gibbosa, T. elegans, S. commune, and V. volvacea ranged from 4.0 to 20, 6.0 to 30.0, 8.0 to 10.0, and 6.0 to 20.0 mg/mL, respectively. Time-kill kinetics studies showed that the extracts possess bacteriostatic action. Methanol extracts of T. gibbosa, T. elegans, S. commune, and V. volvacea exhibited antimicrobial activity and may contain bioactive compounds which may serve as potential antibacterial and antifungal agents.
Malignant Melanoma of the Nail Apparatus

Background. Malignant melanoma of the nail apparatus is exceedingly rare. Increasingly, genetic studies have been employed to aid in distinguishing between malignant melanoma and benign melanocytic nevi. Methods. Archived nail apparatus melanomas were analyzed by fluorescence in situ hybridization (FISH) using probes targeting the genes at 6p25 (RREB1), 11q13 (CCND1), 8q24.1 (MYC), 6q23 (MYB), 9p21 (CDKN2A) and the centromeres of chromosomes 8 (D8Z2) and 6 (D6Z1). The results were correlated with clinical and demographic information. Results. Mean patient age was 57.8 years (range 23-92 years). In all, 5 of 7 (71%) cases involved the upper extremity digits. RREB1 gain was seen in all cases. CCND1 gain was seen in 6 of 7 (86%) cases, 3 of which were amplified. MYB loss and MYC gain were both seen in 5 of 7 (71%) cases. Homozygous loss of CDKN2A was not observed in any case. Two of 7 (28.6%) patients had lymph node metastasis and died of widely metastatic disease. These 2 patients harbored the most genetic aberrations: gains of RREB1, CCND1, and MYC, and MYB loss. Both benign melanocytic nevi controls showed normal FISH results. Conclusions. RREB1 and CCND1 gains are common in nail apparatus melanoma as in most melanomas, and an increased number of genetic aberrations may be associated with a poorer prognosis, though the limited number of cases precludes definitive correlation. FISH appears to be a useful adjunct in the diagnosis of nail apparatus melanomas and improves diagnostic confidence even in the setting of unambiguous histomorphology.
A Compact Symmetric Microstrip Filter Based on a Rectangular Meandered-Line Stepped Impedance Resonator with a Triple-Band Bandstop Response

This paper presents a symmetric-type microstrip triple-band bandstop filter incorporating a tri-section meandered-line stepped impedance resonator (SIR). The length of each section of the meandered line is 0.16, 0.15, and 0.83 times the guided wavelength (λ g), so that the filter features three stop bands at 2.59 GHz, 6.88 GHz, and 10.67 GHz, respectively. Two symmetric SIRs are employed with a microstrip transmission line to obtain wide bandwidths of 1.12, 1.34, and 0.89 GHz at the corresponding stop bands. Furthermore, an equivalent circuit model of the proposed filter is developed, and the model matches the electromagnetic simulations well. The return losses of the fabricated filter are measured to be −29.90 dB, −28.29 dB, and −26.66 dB while the insertion losses are 0.40 dB, 0.90 dB, and 1.10 dB at the respective stop bands. A drastic reduction in the size of the filter was achieved by using a simplified architecture based on a meandered-line SIR.
Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

To decrypt the regulatory code of the genome, sequence elements must be defined that determine the kinetics of RNA metabolism and thus gene expression. Here we attempt such decryption in an eukaryotic model organism, the fission yeast S. pombe. We first derive an improved genome annotation that redefines borders of 36% of expressed mRNAs and adds 487 non-coding RNAs (ncRNAs). We then combine RNA labeling in vivo with mathematical modeling to obtain rates of RNA synthesis and degradation for 5,484 expressed RNAs and splicing rates for 4,958 introns. We identify functional sequence elements in DNA and RNA that control RNA metabolic rates, and quantify the contributions of individual nucleotides to RNA synthesis, splicing, and degradation. Our approach reveals distinct kinetics of mRNA and ncRNA metabolism, separates antisense regulation by transcription interference from RNA interference, and provides a general tool for studying the regulatory code of genomes.
Inhibition of Endoplasmic Reticulum Stress and Atherosclerosis by 2-Aminopurine in Apolipoprotein E-Deficient Mice

We previously reported that the apolipoprotein (apo) B48-carrying lipoproteins obtained from apoE knockout (apoE −/−) mice, so called E−/B48 lipoproteins, transformed mouse macrophages into foam cells and enhanced the phosphorylation of eukaryotic translation initiation factor 2α (eIF-2α). Furthermore, the eIF-2α phosphorylation inhibitor, 2-aminopurine (2-AP), attenuated E−/B48 lipoprotein-induced foam cell formation. The present report studied the effect of 2-AP on atherosclerosis in apoE −/− mice. Our results showed that the level of food intake, bodyweight, plasma cholesterol, and triglycerides was comparable in apoE −/− mice treated with or without 2-AP. However, the mean size of atherosclerotic lesions in the aorta sinus as well as the surface area of the entire aorta of 2-AP-treated apoE −/− mice were reduced by about 55% and 39%, respectively, compared to samples from untreated control apoE −/− mice. In addition, the 2-AP-treated apoE −/− mice showed a significant decrease in glucose-regulated protein 78 (GRP78) and phosphorylated eIF-2α in their aortic samples as compared to levels in untreated control apoE −/− mice. These observations suggest that endoplasmic reticulum stress is a causal mechanism for the development of atherosclerosis in apoE −/− mice and that therapeutic strategies can be developed for using eIF-2α phosphorylation inhibitors, such as 2-AP, to prevent or treat atherosclerosis.
Conventional versus molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae among males in a sexually transmitted infections clinic.

BACKGROUND Chlamydia trachomatis and Neisseria gonorrhoeae are important bacterial pathogens of sexually transmitted infections (STIs) worldwide. This study sought to compare the analytical sensitivity and specificity of conventional methods against a rapid molecular method in detecting STIs caused by these bacteria. METHODS Ninety five first-time male attendees of the Genito-urinary Medicine Clinic in Hospital Kuala Lumpur were included in this cross-sectional study. The detection of C. trachomatis was achieved through direct fluorescence antibody (DFA) staining of urethral swabs and real-time polymerase chain reaction testing (Xpert® CT/NG assay) on urine specimens. N. gonorrhoeae was detected through Gram staining and culture of urethral swabs and Xpert® CT/ NG assay on urine specimens. RESULTS From the Xpert® CT/NG results, 11 (11.6%) attendees had chlamydia, 23 (24.2%) had gonorrhoea and 8 (8.4%) had both STIs. The sensitivity and specificity of DFA in detecting chlamydia compared to Xpert® CT/NG were 5.3% (95% CI: 0-28) and 94.7% (95% CI: 86-98), respectively. For gonorrhoea, the sensitivity and specificity of Gram staining were 90.3% (95% CI: 73-98) and 95.3% (86-99), respectively, whereas the sensitivity and specificity of culture compared to Xpert® CT/NG were 32.2% (95% CI: 17-51) and 100% (95% CI: 93-100), respectively. CONCLUSION Although Gram-stained urethral swab smears are sensitive enough to be retained as a screening tool for gonorrhoea, culture as well as DFA lack sensitivity and are poorly suited to screen for gonorrhoea and chlamydia, respectively. However, owing to their high specificity, conventional detection methods are still suitable as confirmatory tests for gonorrhoea and chlamydia.
Atmospheric Pressure Photoionization Mass Spectrometry of Oligodeoxyribonucleotides

Small oligonucleotides (di- and trimers) were investigated by atmospheric pressure photoionization (APPI) with focus on the fragmentation mechanisms. The fragmentation patterns of these biomolecular ions have been monitored under dopant-assisted photoionization (DA-APPI) conditions. Our results reveal new aspects of the gas-phase chemistry of ions formed from such biomolecules. They illustrate that the reaction between low-energy electrons released from photoionization processes and di- and trinucleotides lies in dissociative electron attachment processes leading to phosphodiester bond cleavages and to the formation of numerous fragments in the ion source. The conditions of DA-APPI, which involve protic solvents and atmospheric pressure conditions, seem to be relevant for the study of radiation damages to biological molecules
[Studies on chemical constituents in dried buds of Lonicera confusa].

OBJECTIVE To investigate the chemical constituents of the dried buds of Lonicera confusa. METHOD Chromatography and spectral analysis were respectively used to isolate and identify the constituents. RESULT Seven compounds were isolated from the dried buds of L. confusa, and identified as rutin, quercetin, luteilin-7-O-beta-D-galactoside, lonicerin, chlorogenic acid, beta-sitosterol and tetratriacontane. CONCLUSION Rutin was isolated from the genus for the first time, and the others were isolated from the species for the first time.
The Price of Land in the New York Metropolitan Area

The price of vacant land in an urban area is a fundamental indicator of an area’s attractiveness. However, because the value of vacant land is hard to measure, indirect methods are typically used to gauge prices. A more direct approach to measuring land prices, using a unique data set, reveals that the price of unimproved land in the New York area is high, and rose sharply from 1999 to 2006. The rising trend suggests the underlying strength of the area’s economy and the increasing value of the area’s productivity and amenities. Current Issues
The Role of Epigenetic Alterations in Papillary Thyroid Carcinogenesis

Papillary thyroid carcinoma (PTC) accounts for over 80% of all thyroid malignancies. The molecular pathogenesis remains incompletely clarified although activation of the RET fusion oncogenes, and RAS and BRAF oncogenes, has been well characterized. Novel technologies using genome-wide approaches to study tumor genomes and epigenomes have provided great insights into tumor development. Growing evidence shows that acquired epigenetic abnormalities participate with genetic alterations to cause altered patterns of gene expression/function. It has been established beyond doubt that promoter cytosine methylation in CpG islands, and the subsequent gene silencing, is intimately involved in cancer development. These epigenetic events very likely contribute to significant variation in gene expression profiling, phenotypic features, and biologic characteristics seen in PTC. Hypermethylation of promoter regions has also been analyzed in PTC, and most studies have focused on individual genes or a small cohort of genes implicated in tumorigenesis.
Single Cell Analysis

> Automatisation for high throughput image acquisition. > Systems Biology: cell cycle regulatory network of S. meliloti. Outlook > Monitoring the dynamics of proteins implicated in the control of the bacterial cell cycle in individual cells is possible in PDMS chips in face of typical length scales of only 0.5 to 3 microns. > High cell viability visible in the observed division time of about 200 min close to the doubling time of 3 h in liquid cultures during the exponential growth phase [3] demonstrates the exclusion of any harmful influences. > Our method can be easily adapted for investigation of other cell-cycle related proteins, bacteria and other cells. > Quantitative, statistical and standardised in situ data are required for modelling approaches within systems biology that will allow a better understanding of cell proliferation and differentiation in space and time.
Educational Intervention Reduces Complications and Rehospitalizations After Heart Surgery

The effectiveness of in-hospital self-care patient education, delivered to patients following heart surgery, is questionable, as evidence indicates individuals are not able to absorb and/or retain information at this time. In the absence of adequate instruction, individuals will not have the relevant information to engage in specific self-care behaviors, resulting in the onset of complications and/or hospital readmissions. The purpose of this pilot study was to collect preliminary evidence to demonstrate the impact of an individualized education intervention given above and beyond usual care, delivered, at two points in time, following hospital discharge. A randomized controlled trial was used in which 34 patients were randomly assigned to one of two groups. Chi-square analyses to examine differences between groups on complications and hospital readmission rates were conducted. Findings point to the impact of the intervention in reducing the number of hospital readmissions and complications at 3 months following hospital discharge.
Chemical Principles of Textile Conservation

Preface Acknowledgements Introduction Section 1 Fibres Dyes Finishes Binding media Metal threads Case histories Section 2 Soiling on historic textiles Solvents and solubility Solvent cleaning of historic textiles Water Wet cleaning Cleaning by chemical reactions Stain removal Cleaning of metal threads Case histories Section 3 Humidification Drying and freeze drying Disinfestation and disinfection Adhesives and consolidants Storage and display materials Case histories Section 4 Methods of investigation used in textile conservation Investigation of metal threads Case history: Hungarian Coronation Mantle
Prevalence of pulmonary embolism in acute exacerbations of COPD: a systematic review and metaanalysis.

BACKGROUND Nearly 30% of all exacerbations of COPD do not have a clear etiology. Although pulmonary embolism (PE) can exacerbate respiratory symptoms such as dyspnea and chest pain, and COPD patients are at a high risk for PE due to a variety of factors including limited mobility, inflammation, and comorbidities, the prevalence of PE during exacerbations is uncertain. METHODS A systematic review of the literature was performed to determine the reported prevalence of PE in acute exacerbations of COPD in patients who did and did not require hospitalization. The literature search was performed using MEDLINE, CINAHL, and EMBASE, and complemented by hand searches of bibliographies. Only cross-sectional or prospective studies that used CT scanning or pulmonary angiography for PE diagnosis were included. RESULTS Of the 2,407 articles identified, 5 met the inclusion criteria (sample size, 550 patients). Overall, the prevalence of PE was 19.9% (95% confidence interval [CI], 6.7 to 33.0%; p = 0.014). In hospitalized patients, the prevalence was higher at 24.7% (95% CI, 17.9 to 31.4%; p = 0.001) than those who were evaluated in the emergency department (3.3%). Presenting symptoms and signs were similar between patients who did and did not have PE. CONCLUSIONS One of four COPD patients who require hospitalization for an acute exacerbation may have PE. A diagnosis of PE should be considered in patients with exacerbation severe enough to warrant hospitalization, especially in those with an intermediate-to-high pretest probability of PE.
A Puzzle of Card Payment Pricing: Why Are Merchants Still Accepting Card Payments?

This paper presents models that explain why merchants accept payment cards even when the fees they face exceed the transactional benefits they receive from a card transaction. The prevalent assumption  merchants accept cards only when they earn positive net transactional benefits  holds only for a monopoly merchant who faces an inelastic consumer demand. The paper also explores possible explanations for the recent gradual increases in merchant fees in the United States. Three possible explanations are 1) inflexible product price setting by merchants, 2) decreases (increases) in cardholder fees (rebates), and 3) increases in cardholding-customer proportion in a given industry.
Deformation Models for Image Recognition

We present the application of different nonlinear image deformation models to the task of image recognition. The deformation models are especially suited for local changes as they often occur in the presence of image object variability. We show that, among the discussed models, there is one approach that combines simplicity of implementation, low-computational complexity, and highly competitive performance across various real-world image recognition tasks. We show experimentally that the model performs very well for four different handwritten digit recognition tasks and for the classification of medical images, thus showing high generalization capacity. In particular, an error rate of 0.54 percent on the MNIST benchmark is achieved, as well as the lowest reported error rate, specifically 12.6 percent, in the 2005 international ImageCLEF evaluation of medical image specifically categorization.