Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyrosequencing: applicability for studying DNA damage‐induced mutagenesis

Site‐specifically modified DNAs are routinely used in the study of DNA damage‐induced mutagenesis. These analyses involve the creation of DNA vectors containing a lesion at a pre‐determined position, DNA replication, and detection of mutations at the target site. The final step has previously required the isolation of individual DNA clones, hybridization with radioactively labeled probes, and verification of mutations by Sanger sequencing. In the search for an alternative procedure that would allow direct quantification of sequence variants in a mixed population of DNA molecules, we evaluated the applicability of pyrosequencing to site‐specific mutagenesis assays. The progeny DNAs were analyzed that originated from replication of N6‐(deoxy‐D‐erythro‐pentofuranosyl)‐2,6‐diamino‐3,4‐dihydro‐4‐oxo‐5‐N‐methylformamidopyrimidine (MeFapy‐dG)‐containing vectors in primate cells, with the lesion being positioned in the 5′‐GCNGG‐3′ sequence context. Pyrosequencing detected ∼8% G to T transversions and ∼3.5% G to A transitions, a result that was in excellent agreement with frequencies previously measured by the standard procedure (Earley LF et al. [2013]: Chem Res Toxicol 26:1108–1114). However, ∼3.5% G to C transversions and ∼2.0% deletions could not be detected by pyrosequencing. Consistent with these observations, the sensitivity of pyrosequencing for measuring the single deoxynucleotide variants differed depending on the deoxynucleotide identity, and in the given sequence contexts, was determined to be ∼1–2% for A and T and ∼5% for C. Pyrosequencing of other DNA isolates that were obtained following replication of MeFapy‐dG‐containing vectors in primate cells or Escherichia coli, identified several additional limitations. Collectively, our data demonstrated that pyrosequencing can be used for studying DNA damage‐induced mutagenesis as an effective complementary experimental approach to current protocols. Environ. Mol. Mutagen. 55:601–608, 2014. © 2014 Wiley Periodicals, Inc.
Efficient Message Passing Methods With Fully Connected Models for Early Vision

Fully connected Markov random fields and conditional random fields have recently been shown to be advantageous in many early vision tasks being formulated as multi-labeling problems, such as stereo matching and image segmentation. The maximum posterior marginal (MPM) inference method in solving fully connected models uses a hybrid framework of mean-field (MF) method and a filtering like approach, and yields excellent results. In this paper, we extend this framework in several aspects. First, we provide an alternative inference method employing fractional belief propagation based method instead of MF. Second, we reformulate the MPM problem into a maximum a posterior (MAP) problem and provide efficient algorithms for solving this. Third, we extend the fully connected model into a multi-resolution approach. Finally, we propose an integral image based approach which makes it possible for efficiently integrating the local linear regression technique into this framework. Comparisons are carried out among different algorithms and different formulations to find the best combination. We demonstrate that the use of our multi-resolution approach with MAP formulation substantially outperforms the ordinary MF-based inference scheme.
Molecular signatures in systemic lupus erythematosus: distinction between disease flare and infection

The clinical scenario of a febrile, acutely ill, immunocompromised patient with immunocompromised lupus remains challenging despite advances in technology and improved understanding of pathogenic mechanisms. Infection is a major contributor to morbidity and mortality in systemic lupus erythematosus (SLE); infection-related hospitalisation rates range from 10% to 35%1–4 and mortality rates range from 29% to 53%. 5 ,6 The disease itself and most treatment strategies are immunosuppressive, rendering patients with SLE more susceptible to severe infection with common organisms and opportunistic pathogens. Both infection and lupus flare can incite clinically indistinguishable inflammatory responses. Consequently, appropriate therapy may be delayed or patients are treated for both conditions while awaiting results of time-consuming investigations for bacterial and viral infections. The potential consequences of treating infection with immunosuppression are obvious and may contribute to the high mortality rates. Antibiotics given unnecessarily also have potential toxicities. A biomarker that would accurately and rapidly differentiate between flare and infection would provide an extremely valuable guide to more directed, precise therapy, likely leading to significantly decreased morbidity and mortality. Microarray technology offers an unbiased, systems biology approach to study the expression level of thousands of genes simultaneously and genome-wide transcriptional studies have emerged as a powerful investigational tool to study complex diseases as well as infection.7 The objective of this exploratory study was to use whole blood gene expression profiling to identify specific RNA expression profiles that would differentiate systemic inflammation related to SLE disease flare from infection in acutely ill patients with lupus. We hypothesised that the molecular signature associated with active disease and no infection in patients with SLE will differ from the molecular signature in patients with SLE with infection. Comparison groups consisted of SLE subjects with inactive disease and healthy controls. ### Study design Blood samples for microarray analysis were obtained from two …
Influence of the Global Financial Crisis on Fiscal Burden in the EU Economies

The main aim of the article is to assess an influence of the last global financial crisis on the level of fiscal burden in Central European countries compared to old member states of the EU. In the research the fiscal burden was treated as multidimensional phenomenon, which should be analyzed with application of multiple criteria analysis tools. In the research zero unitatization method was applied, which allowed to create synthetic measure of the fiscal burden in the EU countries in the years 2004-2015. The measure allowed to propose rankings of the countries and assess the changes of the level of the fiscal burden during and after the crisis. The research was based on the Eurostat data.
Do fiscal decentralization and income inequality affect the size of the shadow economy? A panel data analysis for OECD countries

ABSTRACT In this article, we study fiscal decentralization and inequality as driving forces of the shadow economy in advanced economies. Our empirical analysis suggests that a reduction in income inequality will contain the shadow economy, whereas expenditure and tax decentralization do not significantly impact it. As decentralization is generally believed to increase government efficiency, this result is indicative of already highly efficient public administrations. Our results further indicate that redistributive policies positively affect the size of the shadow economy, whereas the tax burden does not have any discernible effect on the shadow economy in our sample.
Adherence to montelukast versus inhaled corticosteroids in children with asthma

Our objective was to compare adherence to montelukast with adherence to inhaled corticosteroids (ICS) in children with persistent asthma. In this retrospective study, we obtained data from a computerized hospital pharmacy database and medical records on 14l patients, 3–18 years of age, who received care for asthma at a military medical center. For each patient, we collected fill/refill data from a consecutive 6‐month period and calculated an adherence rate, i.e., (# doses filled/# doses prescribed) × 100. We then determined whether the patient had “good adherence” (adherence rate, ≥70%) or “very poor adherence” (adherence rate, <50%). Eighty‐one children were prescribed montelukast, and 104 took ICS; 44 of these children took both. The majority of patients had mild or moderate persistent asthma. There was no significant difference between mean adherence rates: 71% (95% CI, 65–77%) for montelukast vs. 67% (95% CI, 61–73%) for ICS. Fifty‐one percent of patients taking montelukast had good adherence, compared to 41% in the ICS group (P = 0.27). Nineteen percent of the montelukast group and 26% of the ICS group had very poor adherence (P = 0.31). Using pharmacy refill data, we found that children with asthma were no more likely to take montelukast than inhaled corticosteroids. Adherence to both medications was suboptimal, even in a system that provides free and easy access to medications. Pediatr Pulmonol. 2003; 36:. 301–304. Published 2003 Wiley‐Liss, Inc.
Immunohistochemical analysis of receptor tyrosine kinase signal transduction activity in chordoma

Aims: Currently, there are no effective chemotherapeutic protocols for chordoma. Reports of receptor tyrosine kinase (RTK) expression in chordoma suggest that these tumours may respond to kinase inhibitor therapy. However, RTK signalling activity has not been extensively investigated in chordoma. Methods: A tissue microarray containing 21 cases of chordoma was analysed for expression of a number of proteins involved in signal transduction from RTKs by immunohistochemistry. Results: Platelet‐derived growth factor receptor‐β, epidermal growth factor receptor (EGFR), KIT and HER2 were detected in 100%, 67%, 33% and 0% of cases, respectively. Platelet‐derived growth factor receptor‐β staining was of moderate‐to‐strong intensity in 20 of 21 cases. In contrast, KIT immunoreactivity was weak and focal in each of the seven positive cases. Total EGFR staining was variable; weak staining for phosphorylated EGFR was detected in nine cases. Phosphorylated isoforms of p44/42 mitogen‐activated protein kinase, Akt and STAT3, indicative of tyrosine kinase activity, were detected in 86%, 76% and 67% of cases, respectively. Conclusions: Chordomas commonly express RTKs and activated signal transduction molecules. Although there were no statistically significant correlations between the expression of any of the markers studied and disease‐free survival or tumour location, the results nonetheless indicate that chordomas may respond to RTK inhibitors or modulators of other downstream signalling molecules.
Abnormal hippocampal shape in offenders with psychopathy

Posterior hippocampal volumes correlate negatively with the severity of psychopathy, but local morphological features are unknown. The aim of this study was to investigate hippocampal morphology in habitually violent offenders having psychopathy. Manual tracings of hippocampi from magnetic resonance images of 26 offenders (age: 32.5 ± 8.4), with different degrees of psychopathy (12 high, 14 medium psychopathy based on the Psychopathy Checklist Revised), and 25 healthy controls (age: 34.6 ± 10.8) were used for statistical modelling of local changes with a surface‐based radial distance mapping method. Both offenders and controls had similar hippocampal volume and asymmetry ratios. Local analysis showed that the high psychopathy group had a significant depression along the longitudinal hippocampal axis, on both the dorsal and ventral aspects, when compared with the healthy controls and the medium psychopathy group. The opposite comparison revealed abnormal enlargement of the lateral borders in both the right and left hippocampi of both high and medium psychopathy groups versus controls, throughout CA1, CA2‐3 and the subicular regions. These enlargement and reduction effects survived statistical correction for multiple comparisons in the main contrast (26 offenders vs. 25 controls) and in most subgroup comparisons. A statistical check excluded a possible confounding effect from amphetamine and polysubstance abuse. These results indicate that habitually violent offenders exhibit a specific abnormal hippocampal morphology, in the absence of total gray matter volume changes, that may relate to different autonomic modulation and abnormal fear‐conditioning. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
Self-Determination Theory and Diminished Functioning

Drawing from self-determination theory, three studies explored the social-environmental conditions that satisfy versus thwart psychological needs and, in turn, affect psychological functioning and well-being or ill-being. In cross-sectional Studies 1 and 2, structural equation modeling analyses supported latent factor models in which need satisfaction was predicted by athletes’ perceptions of autonomy support, and need thwarting was better predicted by coach control. Athletes’ perceptions of need satisfaction predicted positive outcomes associated with sport participation (vitality and positive affect), whereas need thwarting more consistently predicted maladaptive outcomes (disordered eating, burnout, depression, negative affect, and physical symptoms). In addition, athletes’ perceptions of psychological need thwarting were significantly associated with perturbed physiological arousal (elevated levels of secretory immunoglobulin A) prior to training. The final study involved the completion of a diary and supported the relations observed in the cross-sectional studies at a daily level. These findings have important implications for the operationalization and measurement of interpersonal styles and psychological needs.
Mandatory IFRS adoption: the trade-off between accrual-based and real earnings management

This paper examines whether firms substituted real earnings management for accrual-based earnings management after the International Financial Reporting Standards (IFRS) became mandatory. Using a sample of 101,331 firm-year observations from 33 countries between 2000 and 2010, we show that IFRS adoption came with the unintended consequence of certain firms substituting real earnings management for accrual-based earnings management, especially among firms in countries with strict enforcement regimes. Furthermore, we document that the trade-off is confined to EU countries in which strong firm-level characteristics (i.e. the firm-level mechanism of control, the market’s level of scrutiny, and firm-specific incentives to provide transparency) are coupled with strong enforcement. We also show that IFRS had an effect in countries outside the EU, albeit at a different time. Overall, the results suggest that accounting regulators’ efforts to increase earnings quality might have had the unintended consequence of increasing real earnings management activities.
Effects of chronic treatment with a low dose of nicorandil on the function of the rat aorta during ageing

1. It is known that ATP‐sensitive potassium (KATP) channels regulate the membrane potential of smooth muscle cells and vascular tone. Because their activity is altered during ageing, many pharmacological treatments aimed at improving KATP channel and cardiovascular functions have been evaluated. Nicorandil, a KATP channel opener, nitric oxide (NO) donor and anti‐oxidant, induces vasodilation, decreases blood pressure and exhibits cardioprotection in ageing, as well as after ischaemia–reperfusion.
Dieulafoy lesions: a review of 6 years of experience at a tertiary referral center

Dieulafoy lesions are uncommon sources of GI hemorrhage and predominantly occur in the proximal stomach. At one time a pathological diagnosis made postoperatively, Dieulafoy lesions are now routinely diagnosed and treated endoscopically. Their true incidence is unclear as quiescent Dieulafoy lesions are easily overlooked on endoscopy and bleeding lesions are occasionally misidentified. Over 6 yr (June 1993–November 1999), 40 Dieulafoy lesions were identified on upper endoscopy at our institution, of which seven were located in the duodenum and one in the right colon. Forty-seven percent of patients were hospitalized for other causes before onset of bleeding, and 17 of 40 were found to have other abnormal findings at endoscopy. In 90% of the cases, endoscopic treatment was successful. Seven patients died, but none as a result of hemorrhage. In 24 endoscopically-treated patients in whom follow-up data are available, Dieulafoy bleeding recurred in one patient. Dieulafoy lesions are rare and often difficult to diagnose, but must be considered in the evaluation of upper and lower GI tract hemorrhage, as they can usually be managed endoscopically.
Job strain, hypoxia and risk of amyotrophic lateral sclerosis: Results from a death certificate study

Abstract Amyotrophic lateral sclerosis (ALS) most likely results from a multifactorial gene-environment interaction. Strenuous physical activity and occupational exposures have been suggested to play a role, and an abnormal response to hypoxia has been proposed in ALS pathogenesis. To test the hypothesis of an excess risk in occupations typically leading to intermittent hypoxia at the tissue level, we accessed a large publicly available database, including death certificates from 24 U.S. states in 1984–1998. We conducted a case-control analysis of 14,628 deaths due to ALS therein reported and 58,512 controls deceased from other selected causes of death, frequency matched by age, gender and broad geographic area. ALS risk associated with physical activity, and occupations leading to intermittent hypoxia, such as fire fighters and professional athletes, were calculated with unconditional logistic regression, adjusting by age, marital status, residence, and socioeconomic status. Physical activity in general did not show an association with ALS risk. Risk associated with occupation as a professional athlete was elevated (OR = 1.81, 99% CI 0.69–4.78), but not significantly so. Fire fighters showed a significant two-fold excess ALS risk (OR = 2.0; 99% CI 1.2–3.2). Based on our findings and the current clinical, epidemiological and experimental evidence, we suggest that occupational conditions typically leading to intermittent hypoxia, such as fire fighting, might be an ALS risk factor in subjects genetically prone to an abnormal response to hypoxia.
Cardiac autonomic modulation adjustments in isometric exercise

OBJECTIVE: Isometric exercise is characterized by promoting an overload on the cardiovascular system due to pulsatile contraction followed by a significant increase in muscle blood flow. The hemodynamic responses during exercise and during recovery from endurance exercise are well documented. However, there are few studies with hard data regarding the influence of isometric exercise on autonomic control, which can be obtained by analysis of heart rate variability. Thus, the object of this study was to analyze reports on cardiac autonomic regulation in isometric exercise. METHODS: The articles used in this study were selected fromPubmed, PEDro,Medline, Lilacs and SciELO. The search wasmade by crossing the following keywords: isometric exercise, autonomic nervous system, cardiovascular system, and heart rate variability, which were defined based on descriptors of Health Headings (MeSH). RESULTS: The search provided 17 articles in isometric exercise autonomic modulation characterized by decreased vagalmodulation followedby increased sympatheticmodulation and its reversal shortly after the endof the activity. CONCLUSION: During isometric exercise, increased sympathetic modulation and reduced vagal modulation of the sinus node have been reported.
Specific amplification of Aspergillus fumigatus DNA by polymerase chain reaction.

We have developed a specific and sensitive method to detect the human pathogen Aspergillus fumigatus by polymerase chain reaction (PCR) with an objective of detecting the organism in peripheral blood and urine which can be obtained by non-invasive procedures. A pair of oligonucleotide primers for PCR were designed based on the published partial protein sequences of an 18 KD IgE-binding protein of A. fumigatus Asp f1 and the ribotoxins mitogillin and restrictocin of A. restrictus, and alpha-sarcin of A. giganteus. The primers were specific in amplifying an expected 315 bp region of the homologous genes in A. fumigatus and A. restrictus but not in A. giganteus. Also, there was no amplification of human DNA or DNA of A. flavus, A. niger, A. fischeri, Penicillium sp. , Candida albicans and Pneumocystis carinii. The sensitivity of the PCR detection of A. fumigatus DNA is about 20 pg on an ethidium bromide gel and 0.6 pg by Southern analysis using a 32P-labelled internal oligonucleotide. In preliminary analysis of 13 urine specimens of patients suspected of invasive aspergillosis (IA), two were PCR positive, one of whom died of IA with brain lesion. Further analyses of both urine and blood specimens of IA are in progress to determine the comparative utility of PCR over the conventional antigen tests.
Human Papillomavirus Vaccination Counseling in Pediatric Training

Objective Demonstrate the need for increased education regarding otolaryngology-related manifestations of human papillomavirus (HPV). Highlight a need to incorporate otolaryngology-related manifestations of HPV in vaccine counseling. Study Design Survey. Setting Tertiary care academic children’s hospital. Subjects Pediatric residents, fellows, and staff. Methods An online survey was made available regarding HPV education and vaccination. Results Participants (N = 348) initiated the survey representing 28.4%, 25.6%, and 19.0% postgraduate year 1, 2, and 3 residents, respectively, as well as 17.5% chief residents/fellows and 9.5% attendings. Participants rated their prior education as none or fair regarding recurrent respiratory papillomatosis (63.8%) and oropharyngeal squamous cell carcinoma (68.3%). In contrast, 60.6% and 70.9% rated their education on genital warts and cervical cancer correspondingly as good or excellent. When asked what was routinely discussed during HPV vaccine counseling, 63.3% reported “never” discussing recurrent respiratory papillomatosis and 52.9% “never” discussing oropharyngeal squamous cell carcinoma. A range from 92.7% to 95.5% responded that there was a need for increased education regarding HPV and its role in recurrent respiratory papillomatosis and oropharyngeal squamous cell carcinoma. Conclusions Increased education about HPV and its otolaryngology-related manifestations should be undertaken to increase provider, patient, and parent awareness of recurrent respiratory papillomatosis and oropharyngeal squamous cell carcinoma. We propose that discussing the risks of otolaryngology-related disease be routinely included in HPV vaccination counseling.
Improving Proceeding Test Case Prioritization with Learning Software Agents

Test case prioritization is an important technique to improve the planning and management of a system test. The system test itself is an iterative process, which accompanies a software system during its whole life cycle. Usually, a software system is altered and extended continuously. Test case prioritization algorithms find and order the most important test cases to increase the test efficiency in the limited test time. Generally, the knowledge about a systemâs characteristics grows throughout the development. With better experience and more empirical data, the test case prioritization can be optimized to rise the test efficiency. This article introduces a learning agent-based test case prioritization system, which improves the prioritization automatically by drawing conclusions from actual test results.
Effects of stepped psychooncological care on referral to psychosocial services and emotional well‐being in cancer patients: A cluster‐randomized phase III trial

Emotional distress in cancer patients often goes unnoticed in daily routine; therefore, distress screening is now recommended in many national guidelines. However, screening alone does not necessarily translate into better well‐being. We examined whether stepped psychooncological care improves referral to consultation‐liaison (CL) services and improves well‐being.