Miracle-dz/UniFAR-FTUs huggingface dataset:
Exposures and Health Outcomes in Relation to Bioaerosol Emissions From Composting Facilities: A Systematic Review of Occupational and Community Studies

The number of composting sites in Europe is rapidly increasing, due to efforts to reduce the fraction of waste destined for landfill, but evidence on possible health impacts is limited. This article systematically reviews studies related to bioaerosol exposures within and near composting facilities and associated health effects in both community and occupational health settings. Six electronic databases and bibliographies from January 1960 to July 2014 were searched for studies reporting on health outcomes and/or bioaerosol emissions related to composting sites. Risk of bias was assessed using a customized score. Five hundred and thirty-six papers were identified and reviewed, and 66 articles met the inclusion criteria (48 exposure studies, 9 health studies, 9 health and exposure studies). Exposure information was limited, with most measurements taken in occupational settings and for limited time periods. Bioaerosol concentrations were highest on-site during agitation activities (turning, shredding, and screening). Six studies detected concentrations of either Aspergillus fumigatus or total bacteria above the English Environment Agency’s recommended threshold levels beyond 250 m from the site. Occupational studies of compost workers suggested elevated risks of respiratory illnesses with higher bioaerosol exposures. Elevated airway irritation was reported in residents near composting sites, but this may have been affected by reporting bias. The evidence base on health effects of bioaerosol emissions from composting facilities is still limited, although there is sufficient evidence to support a precautionary approach for regulatory purposes. While data to date are suggestive of possible respiratory effects, further study is needed to confirm this and to explore other health outcomes.
Interferon Gamma Release Assays for Diagnosis of Pleural Tuberculosis: a Systematic Review and Meta-Analysis

ABSTRACT The role of interferon gamma release assays (IGRAs), although established for identifying latent tuberculosis, is still evolving in the diagnosis of active extrapulmonary tuberculosis. We systematically evaluated the diagnostic performance of blood- and pleural fluid-based IGRAs in tuberculous pleural effusion (TPE). We searched the PubMed and Embase databases for studies evaluating the use of commercially available IGRAs on blood and/or pleural fluid samples for diagnosing TPE. The quality of the studies included was assessed through the QUADAS-2 tool. The pooled estimates of sensitivity and specificity with 95% confidence intervals (95% CI) were generated using a bivariate random-effects model and examined using forest plots and hierarchical summary receiver operating characteristic (HSROC) curves. Indeterminate IGRA results were included for sensitivity calculations. Heterogeneity was explored through subgroup analysis and meta-regression based on prespecified covariates. We identified 19 studies assessing the T.SPOT. TB and/or QuantiFERON assays. There were 20 and 14 evaluations, respectively, of whole-blood and pleural fluid assays, involving 1,085 and 727 subjects, respectively. There was only one good-quality study, and five studies used nonstandard assay thresholds. The pooled sensitivity and specificity for the blood assays were 0.77 (95% CI, 0.71 to 0.83) and 0.71 (95% CI, 0.65 to 0.76), respectively. The pooled sensitivity and specificity for the pleural fluid assays were 0.72 (95% CI, 0.55 to 0.84) and 0.78 (95% CI, 0.65 to 0.87), respectively. There was considerable heterogeneity; however, multivariate meta-regression did not identify any covariate with significant influence. There was no publication bias for blood assays. We conclude that commercial IGRAs, performed either on whole-blood or pleural fluid samples, have poor diagnostic accuracy in patients suspected to have TPE.
Structural and Mechanistic Studies of Escherichia coli Nitroreductase with the Antibiotic Nitrofurazone

The antibiotics nitrofurazone and nitrofurantoin are used in the treatment of genitourinary infections and as topical antibacterial agents. Their action is dependent upon activation by bacterial nitroreductase flavoproteins, including the Escherichia coli nitroreductase (NTR). Here we show that the products of reduction of these antibiotics by NTR are the hydroxylamine derivatives. We show that the reduction of nitrosoaromatics is enzyme-catalyzed, with a specificity constant ∼10,000-fold greater than that of the starting nitro compounds. This suggests that the reduction of nitro groups proceeds through two successive, enzyme-mediated reactions and explains why the nitroso intermediates are not observed. The global reaction rate for nitrofurazone determined in this study is over 10-fold higher than that previously reported, suggesting that the enzyme is much more active toward nitroaromatics than previously estimated. Surprisingly, in the crystal structure of the oxidized NTR-nitrofurazone complex, nitrofurazone is oriented with its amide group, rather than the nitro group to be reduced, positioned over the reactive N5 of the FMN cofactor. Free acetate, which acts as a competitive inhibitor with respect to NADH, binds in a similar orientation. We infer that the orientation of bound nitrofurazone depends upon the redox state of the enzyme. We propose that the charge distribution on the FMN rings, which alters upon reduction, is an important determinant of substrate binding and reactivity in flavoproteins with broad substrate specificity.
Climatology and Forcing of the Quasi-Biennial Oscillation in the MAECHAM5 Model

The quasi-biennial oscillation (QBO) in the equatorial zonal wind is an outstanding phenomenon of the atmosphere. The QBO is driven by a broad spectrum of waves excited in the tropical troposphere and modulates transport and mixing of chemical compounds in the whole middle atmosphere. Therefore, the simulation of the QBO in general circulation models and chemistry climate models is an important issue. Here, aspects of the climatology and forcing of a spontaneously occurring QBO in a middle-atmosphere model are evaluated, and its influence on the climate and variability of the tropical middle atmosphere is investigated. Westerly and easterly phases are considered separately, and 40-yr ECMWF Re-Analysis (ERA-40) data are used as a reference where appropriate. It is found that the simulated QBO is realistic in many details. Resolved large-scale waves are particularly important for the westerly phase, while parameterized gravity wave drag is more important for the easterly phase. Advective zonal wind tendencies are important for asymmetries between westerly and easterly phases, as found for the suppression of the easterly phase downward propagation. The simulation of the QBO improves the tropical upwelling and the atmospheric tape recorder compared to a model without a QBO. The semiannual oscillation is simulated realistically only if the QBO is represented. In sensitivity tests, it is found that the simulated QBO is strongly sensitive to changes in the gravity wave sources. The sensitivity to the tested range of horizontal resolutions is small. The stratospheric vertical resolution must be better than 1 km to simulate a realistic QBO.
A two-dimensional low-sidelobe transmit beampattern synthesis for linear frequency diverse array

Although phased-array beamforming has received much attention, it cannot effectively suppress the interferences that have the same direction angle but different ranges of the targets. More seriously, the targets may be submerged in the strong interferences and can not be identified. In this letter, we propose a range-dependent interference suppression via frequency diverse array (FDA) transmit beamforming based on convex optimization algorithm. The FDA uses a small frequency increment based on phased-array to provide a range-dependent beampattern, which thus offers a beamforming-based solution to suppress range-dependent interferences. The interference suppression performance as compared to phased-array is analyzed by examining the output signal-to-interference ratio (SIR) and signal-to-clutter ratio (SCR). Simulation results show that significant SIR and SCR performance improvements have been achieved by employing the proposed method.
Extensional tectonics in the Jeanne d’Arc Basin, offshore Newfoundland: implications for the timing of break-up between Grand Banks and Iberia

Abstract Using seismic reflection and exploratory well data from the Jeanne d’Arc basin, offshore Newfoundland, we examined the link between unconformity generation and the onset of seafloor spreading between the central Grand Banks and Iberia. A prominent unconformity developed across the entire basin, previously interpreted as a ‘break-up’ unconformity, is reinterpreted as a late Barremian/early Aptian rift-onset unconformity on the basis of the stratal geometry and lithofacies. The rotation and divergence of seismic reflectors above this unconformity attest to differential subsidence documenting an episode of extension and block rotation within the basin at this time. Our seismic sequence analysis suggests that rifting and block rotation continued in the Jeanne d’Arc basin until at least late Aptian/early Albian time. The onset of seafloor spreading between the central Grand Banks and Iberia is uncertain because of limited marine magnetic and drilling data (ODP & DSDP), and the existence of the Cretaceous magnetic quiet zone along the margin. However, recent studies indicate that magnetic anomaly M0 (118 Ma) is not well resolved north of the Newfoundland Seamounts within the Newfoundland basin and is not present north of the Figueiro fracture zone along the conjugate Iberian margin. This suggests that seafloor spreading between the northern portion of the Newfoundland basin and the northern Iberian margin began after the early Aptian. Given that the cessation of rifting marks the onset of seafloor spreading our seismic sequence analysis indicates that the onset of seafloor spreading in the northern Newfoundland basin, north of the Newfoundland Seamounts, began after late Aptian time.
Renal interstitial corticosterone and 11‐dehydrocorticosterone in conscious rats

Genetic or induced abnormalities in the conversion between active and inactive glucocorticoids in the kidney can lead to local glucocorticoid excess and hypertension. It has been difficult, however, to directly assess local glucocorticoid levels in the kidney. We used chronic microdialysis techniques to sample renal cortical and medullary interstitial fluid from conscious rats. The level of corticosterone (compound B, active) and 11‐dehydrocorticosterone (compound A, inactive) was analyzed with liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). Levels of B (ng/ml, n = 13–16) were 0.8 ± 0.1, 1.0 ± 0.1, 66.7 ± 8.1, and 7.9 ± 1.1 in cortical microdialysate, medullary microdialysate, the plasma, and urine, respectively. The B/A ratio, an index of 11 β‐hydroxysteroid dehydrogenase activity, was 0.8 ± 0.1, 0.6 ± 0.1, 10.6 ± 1.4, and 1.7 ± 0.1, respectively, in those four types of sample. Microdialysate levels of B were approximately 55% higher in afternoons than in mornings, while plasma levels differed by 2.8 fold. An increase of dietary salt content from 0.4% to 4% did not significantly alter levels of B or B/A ratios in renal microdialysate. The protein abundance (fold) of 11 β‐hydroxysteroid dehydrogenase type 2, which inactivates B to A, was 1.0 ± 0.2, 1.6 ± 0.4, and 0.7 ± 0.3 in the cortex, the outer medulla, and the inner medulla, respectively. Type 1 of the enzyme, which likely reactivates A to B, was 1.0 ± 0.1, 1.3 ± 0.2, and 2.0 ± 0.3 in the three regions. Renal interstitial levels of active and inactive glucocorticoids provide an important basis for understanding local metabolism of glucocorticoids in the kidney. (NIH R01HL077263)
SLOPE FAILURE OF EMBANKMENT IN SANYO EXPRESSWAY DUE TO PASSAGE OF TYPHOON NO. 14 IN 2005

Typhoon No. 14 in 2005 caused significant rainfall in Yamaguchi Prefecture of Japan, and, due to this, an embankment of Sanyo Expressway at Hataki in Iwakuni city failed. Detailed investigation was conducted after this event in order to identify the mechanism of this failure, which consisted of the field studies as well as laboratory tests and numerical analyses. It was consequently shown that the combined effects of heavy rainfall and the local geological and topographic conditions as well as the reduction of drainage capability due to the breakage of perforated pipe in the underdrainage system were the causes of the failure.
Characteristic intraseasonal oscillation of rainfall and its effect on interannual variability over Bangladesh during boreal summer

Intraseasonal oscillation (ISO) of rainfall during the summer monsoon season (June–August) and its plausible effect on interannual variation (IAV) of total summer monsoon rainfall over Bangladesh are examined using daily rainfall data from 25 rain‐gauge stations for 20 years (1981–2000). Submonthly scale (7–25 days) ISO is a dominant mode of summer rainfall fluctuation over Bangladesh. In the active (suppressed) ISO phases, a cyclonic (anticyclonic) circulation anomaly develops at the low‐level troposphere from northeastern India to Bangladesh, and an anticyclonic (cyclonic) circulation anomaly appears over the Bay of Bengal, accompanied by the enhancement of westerly/southwesterly (easterly/southeasterly) moisture flux anomalies over Bangladesh. The IAV of total summer monsoon rainfall is significantly correlated with that of the rainfall variance, mainly in the submonthly scale, suggesting that the ISO activity controls the IAV of the total summer monsoon rainfall. Moreover, the spatial patterns of atmospheric circulation and convection associated with the ISO and the IAV are quite similar to each other around the monsoon trough, especially from northeastern India to Bangladesh. In wet monsoon years, more frequent strong submonthly scale ISOs and a larger number of rainy days related to the active ISO phase are evident compared with that of dry monsoon years. Climatologically, Bangladesh is one of the most predominant areas of submonthly scale ISO; however, 30–60‐day ISO is not prominent. These characteristic features probably allow the submonthly scale ISO to modulate the total seasonal rainfall and the spatial patterns of circulation and convection over and near Bangladesh. Copyright © 2010 Royal Meteorological Society
Automating spectral unmixing of AVIRIS data using convex geometry concepts

Spectral mixture analysis, or unmixing, has proven to be a useful tool in the semi-quantitative interpretation of AVIRIS data. Using a linear mixing model and a set of hypothesized endmember spectra, unmixing seeks to estimate the fractional abundance patterns of the various materials occurring within the imaged area. However, the validity and accuracy of the unmixing rest heavily on the 'user-supplied' set of endmember spectra. Current methods for emdmember determination are the weak link in the unmixing chain.
Some notes on radial basis functions and thin plate splines

Many methods exist for defining a scalar field f : R → R given N sample values fi ∈ R at N scattered data points xi ∈ R. These methods largely construct the scalar field as the linear combination of N basis functions f(x) = ∑N i=1 aiφi(x). For example, Fourier and wavelet methods transform these data points into a corresponding number of frequencies and amplitudes (and phases). But a theorem of Haar shows that some configurations of data points can lead to ill conditioned and even degenerate linear combinations. A more robust approach arises from so-called data dependent methods whose basis functions depend on the locations of the data points. These basis functions are often radially symmetric and centered at each of the data points, taking the form
Pretreatment of BMSCs with TZD solution decreases the proliferation rate of MCF-7 cells by reducing FGF4 protein expression

The present study aimed to investigate the effects of bone marrow-derived mesenchymal stem cells (BMSCs) that had been pretreated with pioglitazone and/or rosiglitazone on the growth and proliferation rate of MCF-7 cells. The adhesive interaction between the BMSCs and the MCF-7 cancer cells revealed that the pretreatment of BMSCs with a combination of two types of thiazolidinedione drug reduced the growth and proliferation rate of the MCF-7 cells. The proliferation rate of the MCF-7 cells could also be reduced by the non-adhesive interaction of the cancer cells with BMSCs pretreated with pioglitazone and/or rosiglitazone. The growth and proliferation rate reduction effects on the MCF-7 cells may be attributed to the reduction in the protein level of fibroblast growth factor 4 (FGF4) in the conditioned medium of the pretreated BMSCs. The evidence that the low protein level of FGF4 in the conditioned medium of the pretreated BMSCs perturbed the proliferation rate of the MCF-7 cells by reducing the levels of Ki-67 and proliferating cell nuclear antigen transcripts in the cancer cells was also demonstrated in the present study using a FGF4-neutralizing antibody. All the above findings demonstrate that future studies on the correlation between FGF4 and pretreated BMSCs would be beneficial.
Relationship between histology, development and tumorigenesis of mammary gland in female rat

The mammary gland is a dynamic organ that undergoes structural and functional changes associated with growth, reproduction, and post-menopausal regression. The postnatal transformations of the epithelium and stromal cells of the mammary gland may contribute to its susceptibility to carcinogenesis. The increased cancer incidence in mammary glands of humans and similarly of rodents in association with their development is believed to be partly explained by proliferative activity together with lesser degree of differentiation, but it is not completely understood how the virgin gland retains its higher susceptibility to carcinogenesis. During its developmental cycle, the mammary gland displays many of the properties associated with breast cancer. An early first full-term pregnancy may have a protective effect. Rodent models are useful for investigating potential breast carcinogens. The purpose of this review is to help recognizing histological appearance of the epithelium and the stroma of the normal mammary gland in rats, and throughout its development in relation to tumorigenic potential.
Mutation Analysis of 2009 Pandemic Influenza A(H1N1) Viruses Collected in Japan during the Peak Phase of the Pandemic

Background Pandemic influenza A(H1N1) virus infection quickly circulated worldwide in 2009. In Japan, the first case was reported in May 2009, one month after its outbreak in Mexico. Thereafter, A(H1N1) infection spread widely throughout the country. It is of great importance to profile and understand the situation regarding viral mutations and their circulation in Japan to accumulate a knowledge base and to prepare clinical response platforms before a second pandemic (pdm) wave emerges. Methodology A total of 253 swab samples were collected from patients with influenza-like illness in the Osaka, Tokyo, and Chiba areas both in May 2009 and between October 2009 and January 2010. We analyzed partial sequences of the hemagglutinin (HA) and neuraminidase (NA) genes of the 2009 pdm influenza virus in the collected clinical samples. By phylogenetic analysis, we identified major variants of the 2009 pdm influenza virus and critical mutations associated with severe cases, including drug-resistance mutations. Results and Conclusions Our sequence analysis has revealed that both HA-S220T and NA-N248D are major non-synonymous mutations that clearly discriminate the 2009 pdm influenza viruses identified in the very early phase (May 2009) from those found in the peak phase (October 2009 to January 2010) in Japan. By phylogenetic analysis, we found 14 micro-clades within the viruses collected during the peak phase. Among them, 12 were new micro-clades, while two were previously reported. Oseltamivir resistance-related mutations, i.e., NA-H275Y and NA-N295S, were also detected in sporadic cases in Osaka and Tokyo.
High-Sensitivity Cardiac Troponin T: Risk Stratification Tool in Patients with Symptoms of Chest Discomfort

Background Recent studies have demonstrated the association between increased concentrations of high-sensitivity cardiac troponin T (hs-cTnT) and the incidence of myocardial infarction, heart failure, and mortality. However, most prognostic studies to date focus on the value of hs-cTnT in the elderly or general population. The value of hs-cTnT in symptomatic patients visiting the outpatient department remains unclear. The aim of this study was to investigate the prognostic value of hs-cTnT as a biomarker in patients with symptoms of chest discomfort suspected for coronary artery disease and to assess its additional value in combination with other risk stratification tools in predicting cardiac events. Methods We studied 1,088 patients (follow-up 2.2±0.8 years) with chest discomfort who underwent coronary calcium scoring and coronary CT-angiography. Traditional cardiovascular risk factors and concentrations of hs-cTnT, N-terminal pro-brain-type natriuretic peptide (NT-proBNP) and high-sensitivity C-reactive protein (hsCRP) were assessed. Study endpoint was the occurrence of late coronary revascularization (>90 days), acute coronary syndrome, and cardiac mortality. Results Hs-cTnT was a significant predictor for the composite endpoint (highest quartile [Q4]>6.7 ng/L, HR 3.55; 95%CI 1.88–6.70; P<0.001). Survival analysis showed that hs-cTnT had significant predictive value on top of current risk stratification tools (Chi-square change P<0.01). In patients with hs-cTnT in Q4 versus <Q4, a 2- to 3-fold increase in cardiovascular risk was noticed, either when corrected for high or low Framingham risk score, coronary calcium scoring, or CT-angiography assessment (HR 3.11; 2.73; 2.47; respectively; all P<0.01). This was not the case for hsCRP and NT-proBNP. Conclusions Hs-cTnT is a useful prognostic biomarker in patients with chest discomfort suspected for coronary artery disease. In addition, hs-cTnT was an independent predictor for cardiac events when corrected for cardiovascular risk profiling, calcium score and CT-angiography results.
Controlling complexity of web services interfaces through a metrics-driven approach

Metric suites to assess Web Service quality attributes have been proposed recently. In particular, services interfaces in WSDL (Web Service Description Language) have distinct intrinsic aspects (e.g., size or complexity) able to be measured. We present an approach to prevent a high complexity on services interfaces (WSDLs), to ease consumers to reason about services' offered functionality. Mostly, WSDLs are automatically derived from object-oriented (OO) source code, with a likely impact on complexity. In a previous work, we studied the statistical relationships between a metric suite of service interface complexity (by Baski & Misra) and the Chidamber & Kemerer's OO metric suite (onto service implementations). In this work, we extend the study to find out how certain refactorings on services' source codes prior to derive WSDLs might reduce complexity. For this, we conducted a series of experiments on a data-set of 148 real-world services. In this way, our approach exploits OO metrics as indicators at development-time, guiding software developers to achieve less complex service interfaces.