Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for variation of supercoil densities among simian virus 40 nucleoprotein complexes and for higher supercoil density in replicating complexes

The distribution of DNA topoisomers in intracellular simian virus 40 DNA was analyzed by gel electrophoresis. The results suggested that DNA extracted from 70S chromatin had a different superhelical density distribution as compared with the DNA obtained from virions or virion assembly intermediates. The heterogeneity of simian virus 40 viral DNA superhelical density at a late time after infection was partly due to increased virion production and partly due to the intrinsic heterogeneity of the superhelical density of DNA extracted from virions. Using two-dimensional gel electrophoretic analysis we also showed that simian virus 40 DNA templates used for DNA replication have a higher average superhelical density than the bulk of intracellular viral DNA.
Optimization of the Power Output of a Bare Wind Turbine by the Use of a Plain Conical Diffuser

A plain conical diffuser is optimized to augment the wind speed at the throat of the diffuser. The diffuser is used in the construction of a diffuser augmented wind turbine (DAWT) to augment the power output of a bare wind turbine (BWT). Experiments with empty conical diffusers were done to determine optimum geometrical parameters for the diffuser to achieve maximum wind speed augmentation. Using the obtained optimum geometrical parameters, an optimized plain conical DAWT was designed, constructed, and field tested. A twin decentralized wind energy system which comprised a BWT and the optimized plain conical DAWT was erected. The electrical power output from these systems was measured and compared. The optimized plain conical DAWT reduced the cut-in wind speed of a BWT from 2.5 m/s to 1.6 m/s. The power output was increased by a factor of 2.5. This power output is comparable to that of flanged diffusers. However, flanged-DAWTs are more inert due to the addition of the flange. Its response to wind speed and direction is slow as compared to plain conical DAWT. Thus, it cannot fully exploit the potential of the wind. Also, the addition of the flange increases its production cost. Therefore, plain conical DAWT can replace flanged-DAWT in wind power augmentation.
The role of 18F-FDG PET-CT in the detection of unknown primary malignancy: a retrospective study.

BACKGROUND/AIM This study aimed to retrospectively evaluate the role of 18F-FDG PET/CT imaging in the detection of unknown primary tumor sites in patients with a suspicious malignancy. MATERIALS AND METHODS We retrospectively examined the 18F-FDG PET/CT images of 50 unknown primary malignancy patients. The malignancy of the lesions with increased 18F-FDG uptake on PET images was defined by interpreting the nondiagnostic CT images that were obtained with the PET study. The primary tumor site was decided according to the combined PET/CT findings, and the results were subsequently confirmed with a histopathological examination. RESULTS Fifty patients (29 M; 21 F) aged 18-85 years were included in the study. The sample included 32 malignant and 18 benign lesions according to the histopathological evaluation. 18F-FDG PET/CT study accurately identified malignant lesions in 28 (average SUVmax ± SD: 8.27 ± 7.22) and benign lesions in 12 (average SUVmax ± SD: 3.63 ± 3.07) patients; these findings were histopathologically confirmed. PET/CT correctly detected the primary tumor site in 16 (50%) of 32 patients. CONCLUSION 18F-FDG-PET/CT identified the primary tumor site well in 50% of our cases. We propose that 18F-FDG PET/CT imaging may help to accurately detect malignant lesions in patients with unknown primary tumors.
Firm entry, Search and Matching in a Small Open Economy Faced with Uncertainty Shocks: The case of Korea

This paper investigates the impact of uncertainty shocks in a small open economy with search and matching frictions, endogenous job separation and rm entry. We rst develop our empirical analysis in the context of the Korean economy, as all dimensions of the model are relevant in this country. An increase in uncertainty lowers output, consumption, investment and job nding rate, while raising unemployment and job separations. We also supplement the existing empirical evidence by looking at rm dynamics, real exchange rate and current account behavior. Increased uncertainty gen- erates current account surplus, real exchange rate depreciation and reduces the number of rms in the economy. In our theoretical framework, we illustrate new transmissions mechanism that are ignored in the literature. The interaction of search frictions, rm entry and open economy leads to sizable macroeconomic eects of heightened uncer- tainty. Moreover, the model's predictions are consistent with empirical ndings.
PUFAs acutely affect triacylglycerol-derived skeletal muscle fatty acid uptake and increase postprandial insulin sensitivity.

BACKGROUND Dietary fat quality may influence skeletal muscle lipid processing and fat accumulation, thereby modulating insulin sensitivity. OBJECTIVE The objective was to examine the acute effects of meals with various fatty acid (FA) compositions on skeletal muscle FA processing and postprandial insulin sensitivity in obese, insulin-resistant men. DESIGN In a single-blind, randomized, crossover study, 10 insulin-resistant men consumed 3 high-fat mixed meals (2.6 MJ), which were high in SFAs, MUFAs, or PUFAs. Fasting and postprandial skeletal muscle FA processing was examined by measuring differences in arteriovenous concentrations across the forearm muscle. [²H₂]Palmitate was infused intravenously to label endogenous triacylglycerol and FFAs in the circulation, and [U-¹³C]palmitate was added to the meal to label chylomicron-triacylglycerol. Skeletal muscle biopsy samples were taken to assess intramuscular lipid metabolism and gene expression. RESULTS Insulin and glucose responses (AUC) after the SFA meal were significantly higher than those after the PUFA meal (P = 0.006 and 0.033, respectively). Uptake of triacylglycerol-derived FAs was lower in the postprandial phase after the PUFA meal than after the other meals (AUC₆₀₋₂₄₀; P = 0.02). The fractional synthetic rate of the triacylglycerol, diacylglycerol, and phospholipid pool was higher after the MUFA meal than after the SFA meal. PUFA induced less transcriptional downregulation of oxidative pathways than did the other meals. CONCLUSION PUFAs reduced triacylglycerol-derived skeletal muscle FA uptake, which was accompanied by higher postprandial insulin sensitivity, a more transcriptional oxidative phenotype, and altered intramyocellular lipid partitioning and may therefore be protective against the development of insulin resistance.
Sulfated Homologues of Heparin Inhibit Hepatitis C Virus Entry into Mammalian Cells

ABSTRACT The mechanism of entry of hepatitis C virus (HCV) through interactions between the envelope glycoproteins and specific cell surface receptors remains unclear at this time. We have previously shown with the vesicular stomatitis virus (VSV)/HCV pseudotype model that the hypervariable region 1 of the HCV E2 envelope glycoprotein helps in binding with glycosaminoglycans present on the cell surface. In this study, we have examined the binding of HCV envelope glycoproteins with chemically modified derivatives of heparin. Furthermore, we have determined the functional relevance of the interaction of heparin derivatives with HCV envelope glycoproteins for infectivity by using a human immunodeficiency virus (HIV)/HCV pseudotype, a VSV/HCV pseudotype, and cell culture-grown HCV genotype 1a. Taken together, our results suggest that the HCV envelope glycoproteins rely upon O-sulfated esters of a heparin homologue to facilitate entry into mammalian cells.
CT texture analysis can help differentiate between malignant and benign lymph nodes in the mediastinum in patients suspected for lung cancer

Background In patients with non-small-cell lung carcinoma NSCLC the lymph node staging in the mediastinum is important due to impact on management and prognosis. Computed tomography texture analysis (CTTA) is a postprocessing technique that can evaluate the heterogeneity of marked regions in images. Purpose To evaluate if CTTA can differentiate between malignant and benign lymph nodes in a cohort of patients with suspected lung cancer. Material and Methods With tissue sampling as reference standard, 46 lymph nodes from 29 patients were analyzed using CTTA. For each lymph node, CTTA was performed using a research software “TexRAD” by drawing a region of interest (ROI) on all available axial contrast-enhanced computed tomography (CT) slices covering the entire volume of the lymph node. Lymph node CTTA comprised image filtration-histogram analysis undertakes two stages: the first step comprised an application of a Laplacian of Gaussian filter to highlight fine to coarse textures within the ROI, followed by a quantification of textures via histogram analysis using mean gray-level intensity from the entire volume of the lymph nodes. Results CTTA demonstrated a statistically significant difference between the malignant and the benign lymph nodes (P = 0.001), and by binary logistic regression we obtained a sensitivity of 53% and specificity of 97% in the test population. The area under the receiver operating curve was 83.4% and reproducibility was excellent. Conclusion CTTA may be helpful in differentiating between malignant and benign lymph nodes in the mediastinum in patients suspected for lung cancer, with a low intra-observer variance.
The Impact of Oil Prices on ISE Indices

Changes in oil prices, which is one of the major inputs of industrial production has been identified in some surveys as having a significant impact on shares of industrial companies' prices. On the other hand, in the direction of stock prices reacting to changes in oil prices are also a widespread belief. From this point forth, the main aim of this chapter is to research the long-term relationship between oil-prices and ISE 100, ISE Electricity, ISE Industrials, ISE Chemical, Petroleum and plastic index. In this study, Granger cointegration analyzes, and Granger causality test will be applied to determine the relationship of time series.
Assembly of human contact phase proteins and release of bradykinin at the surface of curli‐expressing Escherichia coli

Previous work has demonstrated that most strains of the human pathogen Streptococcus pyogenes bind kininogens through M protein, a fibrous surface protein and virulence determinant. Here we find that strains of several other pathogenic bacterial species, both Gram‐positive and Gram‐negative, isolated from patients with sepsis, also bind kininogens, especially H‐kininogen (HK). The most pronounced interaction was seen between HK and Escherichia coli. Among clinical isolates of E. coli, the majority of the entero‐haemorrhagic, enterotoxigenic, and sepsis strains, but none of the enteroinvasive and enteropathogenic strains, bound HK. Binding of HK to E. coli correlated with the expression of curli, another fibrous bacterial surface protein, and the binding of HK to purified curli was specific, saturable, and of high affinity; Ka = 9 107M‐1. Other contact phase proteins such as factor XI, factor XII, and prekallikrein bound to curliated E. coli, but not to an isogenic curli‐deficient mutant strain, suggesting that contact phase activation may occur at the surface of curliated bacteria. Kininogens are also precursor molecules of the vasoactive kinins. When incubated with human plasma, curli‐expressing bacteria absorbed HK. Addition of purified plasma kallikrein to the HK‐loaded bacteria resulted in a rapid and efficient release of bradykinin from surface‐bound HK. The assembly of contact phase factors at the surface of pathogenic bacteria and the release of the potent proinflammatory and vasoactive peptide bradykinin, should have a major impact on the host‐microbe relationship and may contribute to bacterial pathogencity and virulence.
Business cycles, innovation and growth: welfare analysis

Endogenous growth literature treats deliberate R&D effort as the main engine of long-run growth. It has been already recognized that R&D expenditures are procyclical. This paper builds a microfounded model that generates procyclical aggregate R&D investment as a result of optimizing behavior by heterogeneous monopolistically competitive firms. I find that business cycle fluctuations affect the aggregate endogenous growth rate of the economy so that transitory shocks leave lasting level effects on the economy’s Balanced Growth Path. This result stems from both procyclical R&D expenditures of the incumbents and procyclical firm entry rates. This mechanism generates economically significant hysteresis effects, increasing the welfare cost of business cycles by two orders of magnitude relative to the exogenous growth model. Coupled with potential to affect endogenous growth rates, ample space for welfare improving policy interventions arises. The paper evaluates the effects of selected subsidy schemes and finds some of them welfare improving.
Particulate matter and out-of-hospital coronary deaths in eight Italian cities

Objectives We evaluated the association between PM10 concentration and out-of-hospital coronary deaths in eight Italian cities during 1997–2004. Methods 16 989 subjects aged >35 years who died out-of-hospital from coronary causes were studied and hospital admissions in the previous 2 years identified. We studied the effect of the mean of current and previous day PM10 values (lag 0–1). A city-specific case-crossover analysis was applied using a time-stratified approach considering as confounders weather, holidays, influenza epidemics, and summer decrease in population. The pooled percentage increase (95% CI) in mortality per 10 μg/m3 increase in PM10 was estimated. Results A statistically significant increase in out-of-hospital coronary deaths was related to a 10 μg/m3 increase in PM10: 1.46% (95% CI 0.50 to 2.43). Although no statistically significant effect modification by age was found, the effect was stronger among subjects aged >65 years (1.60%, 0.59 to 2.63), particularly those aged 65–74 (3.01%, 0.74 to 5.34). People in the lowest socio-economic category (3.34%, 1.28 to 5.45) had a stronger effect than those in the highest category. No clear effect modification was seen for gender, season or any specific comorbidity. An indication of negative effect modification was seen for previous admission for cardiac dysrhythmias. Subjects without hospital admissions in the previous 2 years were slightly more affected by PM10 effects (1.91%, 0.28 to 3.47) than those with at least one previous hospital admission (1.44%, 0.09 to 2.82). Conclusions Our results show that short term exposure to PM10 is associated with coronary mortality especially among the elderly and socio-economically disadvantaged. No clear effect modification by previous hospitalisations was detected except for cardiac dysrhythmias, possibly due to protective treatment.
Forelimb proportions and the evolutionary radiation of Neornithes

Analysis of a comprehensive dataset demonstrates that the brachial index (BI = humerus length/ulna length) of modern birds (Neornithes) varies significantly between clades at all taxonomic levels, yet is strongly correlated with recent phylogenetic hypotheses. Variance in BI at the infraclass level is low, but increases rapidly during the proposed major radiation of neornithines in the Palaeocene and Eocene. Although a BI of greater than 1 is primitive for Neornithes, more basal groups of Mesozoic birds (Confuciusornithidae and some members of the diverse Enantiornithidae) had BIs comparable with those of ‘higher’ modern clades. It is possible that occupation of ecological niches by these Mesozoic clades precluded the divergence of some groups of neornithines until after the Cretaceous–Tertiary boundary. We suggest that with further analysis and data collection the relationships between flight behaviour, ecology and BI can be determined. Hence, BI may provide a useful tool for characterizing the ecology of fossil birds.
Southwest Oncology Group studies in bladder cancer

Over 50,000 patients are diagnosed annually with bladder cancer, and approximately 10,000 eventually will die of their disease. Thus, the Southwest Oncology Group (SWOG) Genitourinary Cancer Committee is committed to the study of therapeutic interventions in patients with superficial, invasive, and metastatic bladder cancer. In the past 15 years, SWOG has completed six Phase III, randomized trials. Studies in patients with superficial disease have established the role of bacillus Calmette–Guerin in patient management; and a large, randomized trial has outlined the value of neoadjuvant chemotherapy and cystectomy in patients with advanced disease. SWOG plans to build on this model by evaluating patients with residual disease after chemotherapy for possible bladder preservation while evaluating more chemotherapy for patients with persistent disease. The Genitourinary Cancer Committee will continue to seek new, active agents for metastatic disease and will participate in and support large, Phase III, international trials that seek to improve current regimens. SWOG accomplishments in bladder cancer are highlighted, and future strategies are discussed. Cancer 2003;97(8 Suppl):2099–108. © 2003 American Cancer Society.
Parent-Pediatrician Communication about Complementary and Alternative Medicine Use for Children

Anonymous self-report surveys of a convenience sample of caregivers accompanying children to the pediatrician for acute or well visits at 4 pediatric practices in the Washington, DC area from July through November 1998 were evaluated. Three hundred seventy-eight (85%) of 443 caregivers approached participated. The 348 surveys completed by parents (92%) were analyzed. As previously reported, in this sample 21% of parents used complementary and alternative medicine (CAM) for their child. Overall, 53% of parents expressed the desire to discuss CAM with their pediatrician, increasing to 75% (p<0.001) among those who used CAM themselves and 81% (p<0.01) among those who used CAM for their child. Among parents who used CAM for their child, 36% had discussed it with their pediatrician. Factors associated with increased disclosure to the pediatrician were CAM use in children younger than 6 years (p<0.05), “bioenergetic” CAM use (p<0.02), and parent CAM non-use (p<0.05). Despite parents’ significant interest in discussion about CAM, few factors were associated with adequate parent-pediatrician communication.
Comparison of the antibacterial effect and smear layer removal using photon-initiated photoacoustic streaming aided irrigation versus a conventional irrigation in single-rooted canals: an in vitro study.

OBJECTIVE The Er:YAG laser with photon-induced photoacoustic streaming (PIPS) technique was reported to be effective in root canal disinfection. This study attempted to further investigate the antibacterial efficacy and smear layer removal ability of PIPS in comparison with conventional syringe irrigation in vitro. METHODS For antibacterial analysis, 48 single-rooted human teeth were prepared and inoculated with Enterococcus faecalis, and then divided into six groups of eight roots each. The colony-forming units (CFUs) per milliliter were determined after infection as the baseline. Then, the teeth were subjected to either PIPS plus 3% sodium hypochlorite (PIPS+NaOCl) or conventional syringe irrigation with 0.9% saline, 3% NaOCl, 17% ethylenediaminetetraacetic acid (EDTA), 0.2% chlorhexidine gluconate (CHX), or 3% NaOCl alternating with 17% EDTA. The reduction of CFUs in the individual group was determined. Additionally, scanning electron microscopy (SEM) examination of the canal walls for E. faecalis colonization was performed. For comparing the smear removal efficacy, another 48 single-rooted teeth, assigned to different groups as mentioned, were irrigated after mechanical instrumentation. The presence of a smear layer at different levels of the root canal was scored by SEM examination. RESULTS No significant differences were found in CFU reduction. No bacteria could be observed by SEM in the NaOCl, NaOCl+EDTA, and PIPS+NaOCl groups. The scores of smear layer of the NaOCl+EDTA and PIPS+NaOCl groups were significantly lower than those of the other groups in the coronal and middle third of the root canal. None of the methods can effectively remove smear layer in the apical third. CONCLUSIONS PIPS system supplied with NaOCl and conventional syringe irrigation with NaOCl+EDTA are comparable in their ability to remove E. faecalis and smear layer in single-rooted canals.
Predicting Short-term Mortality in Patients With Pulmonary Embolism: A Simple Model

Background:The aim of the present study was to develop a simple prognostic rule that could classify patients with pulmonary embolism (PE) into categories of increased risk of 30-day mortality. Methods:One hundred patients with PE were enrolled. Clinical and laboratory findings were recorded on admission for each patient. Differences between groups’ survival and death were tested, and the association with the 30-day mortality was determined. Results:Three variables had a significant effect on survival: age, Charlson index and the alveolar to arterial (A-a) gradient. A receiver operating characteristic analysis was performed, and the cut-off points used for the comparison of survival were 67 years of age, A-a gradient over 52.8 mm Hg and Charlson index over 2. By combining these variables, a score was established for distinguishing patients with PE who are at high risk. This score was also validated in a group of 30 consecutive patients admitted to the hospital for PE Additionally, a tree method was applied and showed that for patients with a history of diabetes and Charlson index >3, the expected outcome is death. Conclusions:The results of this study suggest that patients with PE could be stratified into categories of increasing risk of 30-day mortality using a simple score based only on routinely available variables. Future studies are needed to validate our prognostic model in a large cohort of patients with PE.
Comparison of HbA1c analysers: Agilent 1100 HPLC using kits produced by Gordion Diagnostic (Turkey) with Premier Hb9210 using kits produced by Trinity Biotech (USA) in different patient groups.

BACKGROUND The aim of this study was to compare the performance of Agilent 1100 HPLC analyser using HbA1c kits manufactured by Gordion Diagnostic (Turkey) with that of Premier Hb9210 using the original kits for the measurement of HbA1c in different patient groups. METHODS Subjects were divided into four groups: Group 1 included 140 diabetic and non-diabetic subjects with normal urea and haemoglobin levels; Group 2 included 84 diabetic and non-diabetic subjects with high urea levels; Group 3 included 44 diabetic and non-diabetic subjects with iron deficiency anaemia; and Group 4 included 52 diabetic and non-diabetic subjects with high haemoglobin levels. EP Evaluator Release 8 program was used to evaluate the resultant data. RESULTS According to the comparison results of the two methods in all groups, there was an excellent correlation between the two methods (R>0.98). Moderate-low correlation was found between increased urea concentration and the difference of the two methods (R= -0.374, p = 0.0005). The difference between the methods was found to be increased with increased urea concentrations. This difference, although statistically significant, was within the permitted limits. The observed correlation between the difference of the two methods and the low and high haemoglobin concentrations was statistically non-significant (R = 0.149, p = 0.3343; R = 0.263, p = 0.0594). CONCLUSIONS We found that Agilent 1100 HbA1c analyser and Gordions' HbA1c kit comply with the clinical requirements and are suitable for HbA1c analysis at high levels of urea and Hb and low levels of Hb in diabetic and non-diabetic patients.