Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying the response of the ORAC aerosol optical depth retrieval for MSG SEVIRI to aerosol model assumptions

[1] We test the response of the Oxford-RAL Aerosol and Cloud (ORAC) retrieval algorithm for Meteosat Second Generation Spinning Enhanced Visible and InfraRed Imager (MSG SEVIRI) to changes in the aerosol properties used in the dust aerosol model, using data from the Dust Outflow and Deposition to the Ocean (DODO) flight campaign in August 2006. We find that using the observed DODO free tropospheric aerosol size distribution and refractive index increases simulated top of the atmosphere radiance at 0.55 μm assuming a fixed aerosol optical depth of 0.5 by 10–15%, reaching a maximum difference at low solar zenith angles. We test the sensitivity of the retrieval to the vertical distribution of the aerosol and find that this is unimportant in determining simulated radiance at 0.55 μm. We also test the ability of the ORAC retrieval when used to produce the GlobAerosol data set to correctly identify continental aerosol outflow from the African continent, and we find that it poorly constrains aerosol speciation. We develop spatially and temporally resolved prior distributions of aerosols to inform the retrieval which incorporates five aerosol models: desert dust, maritime, biomass burning, urban, and continental. We use a Saharan Dust Index and the GEOS-Chem chemistry transport model to describe dust and biomass burning aerosol outflow and compare AOD using our speciation against the GlobAerosol retrieval during January and July 2006. We find AOD discrepancies of 0.2–1 over regions of intense biomass burning outflow, where AOD from our aerosol speciation and GlobAerosol speciation can differ by as much as 50–70%.
What Is Wrong with Criterion FN‐Lines for Judging the Tolerability of Risk?

This paper is concerned with the intellectual framework in which judgments are made about the tolerability of so‐called societal risk. The current practical approach is based on the position of the FN‐curves representing the risks from hazardous systems in relation to criterion FN‐lines. The objections to FN‐criteria are that they can give unreasonable conclusions and that they are inconsistent. Statistical decision theory suggests an alternative and preferable rule of minimising the expected disutility, that is average harm, from accidents.
Nasal Cytology as a Marker of Atopy in Children

The aim of this study was to evaluate the cytological picture of nasal mucosa in children with atopic diseases and to determine the diagnostic value of the test for the diagnosis of atopic diseases. The study included 140 children from 4 months to 17 years old. Among children with a history of atopy, there were 30 children with atopic dermatitis, 30 children with asthma, and 46 children with allergic rhinitis. The control group consisted of 34 healthy children. The nasal scraping technique has been used to collect samples from the nasal cavity. The samples were evaluated under light microscope. Epithelial cells as well as infiltrating cells were assessed. The only statistically significant group of cells differentiating children with atopic disease and without atopy were eosinophils, which in children with atopy were significantly more common. Assuming a significant eosinophilia value of at least 5% of all cells in cytogram, the sensitivity of nasal cytology in allergic rhinitis was 52.2%, in asthma 33.3%, and in atopic dermatitis 13.3%. The specificity of the test in atopic diseases was 94.1%. It can be concluded that nasal cytology with eosinophilia assessment can be a useful tool for an early diagnosis of atopic disease in children.
Label-Free Imaging of Lipid Depositions in C. elegans Using Third-Harmonic Generation Microscopy

Elucidation of the molecular mechanisms regulating lipid storage and metabolism is essential for mitigating excess adiposity and obesity, which has been associated with increased prevalence of severe pathological conditions such as cardiovascular disorders and type II diabetes, worldwide. However, imaging fatty acid distribution and dynamics in vivo, at the cellular or organismal level is challenging. We developed a label-free method for visualizing lipid depositions in vivo, based on third harmonic generation (THG) microscopy. THG imaging requires a single pulsed-laser light source, alleviating the technical challenges of implementing coherent anti-Stokes Raman scattering spectroscopy (CARS) to detect fat stores in living cells. We demonstrate that THG can be used to efficiently and reliably visualize lipid droplets in Caenorhabditis elegans. Thus, THG microscopy offers a versatile alternative to fluorescence and dye-based approaches for lipid biology research.
TGF-&bgr;1 Limits Plaque Growth, Stabilizes Plaque Structure, and Prevents Aortic Dilation in Apolipoprotein E–Null Mice

Objective—Impairment of transforming growth factor (TGF)-&bgr;1 signaling accelerates atherosclerosis in experimental mice. However, it is uncertain whether increased TGF-&bgr;1 expression would retard atherosclerosis. The role of TGF-&bgr;1 in aneurysm formation is also controversial. We tested whether overexpression of active TGF-&bgr;1 in hyperlipidemic mice affects atherogenesis and aortic dilation. Methods and Results—We generated apolipoprotein E–null mice with transgenes that allow regulated overexpression of active TGF-&bgr;1 in their hearts. Compared to littermate controls, these mice had elevated cardiac and plasma TGF-&bgr;1, less aortic root atherosclerosis (P≤0.002), fewer lesions in the thoracic and abdominal aortae (P≤0.01), less aortic root dilation (P<0.001), and fewer pseudoaneurysms (P=0.02). Mechanistic studies revealed no effect of TGF-&bgr;1 overexpression on plasma lipids or cytokines, or on peripheral lymphoid organ cells. However, aortae of TGF-&bgr;1–overexpressing mice had fewer T-lymphocytes, more collagen, less lipid, lower expression of inflammatory cytokines and matrix metalloproteinase-13, and higher expression of tissue inhibitor of metalloproteinase-2. Conclusions—When overexpressed in the heart and plasma, TGF-&bgr;1 is an antiatherogenic, vasculoprotective cytokine that limits atherosclerosis and prevents aortic dilation. These actions are associated with significant changes in cellularity, collagen and lipid accumulation, and gene expression in the artery wall.
Adiposity and human regional body temperature.

BACKGROUND Human obesity is associated with increased heat production; however, subcutaneous adipose tissue provides an insulating layer that impedes heat loss. To maintain normothermia, therefore, obese individuals must increase their heat dissipation. OBJECTIVE The objective was to test the hypothesis that temperature in a heat-dissipating region of the hand is elevated in obese adults. DESIGN Obese [body mass index (in kg/m(2)) > or = 30] and normal-weight (NW; body mass index = 18-25) adults were studied under thermoneutral conditions at rest. Core body temperature was measured by using ingested telemetric capsules. The temperatures of the third fingernail bed of the right hand and of abdominal skin from an area 1.5 cm inferior to the umbilicus were determined by using infrared thermography. Abdominal skin temperatures were also measured via adhesive thermistors that were placed over a prominent skin-surface blood vessel and over an adjacent nonvessel location. The groups were compared by analysis of covariance with age, sex, race, and room temperature as covariates. RESULTS Core temperature did not differ significantly between the 23 obese and 13 NW participants (P = 0.74). However, infrared thermography-measured fingernail-bed temperature was significantly higher in obese subjects than in NW subjects (33.9 +/- 0.7 degrees C compared with 28.6 +/- 0.9 degrees C; P < 0.001). Conversely, infrared thermography-measured abdominal skin temperature was significantly lower in obese subjects than in NW subjects (31.8 +/- 0.2 degrees C compared with 32.8 +/- 0.3 degrees C; P = 0.02). Nonvessel abdominal skin temperatures measured by thermistors were also lower in obese subjects (P = 0.04). CONCLUSIONS Greater subcutaneous abdominal adipose tissue in obese adults may provide a significant insulating layer that blunts abdominal heat transfer. Augmented heat release from the hands may offset heat retention in areas of the body with greater adiposity, thereby helping to maintain normothermia in obesity. This trial was registered at clinicaltrials.gov as NCT00266500.
MicroRNA-382 induced by HIF-1α is an angiogenic miR targeting the tumor suppressor phosphatase and tensin homolog

Recent studies have revealed that microRNAs (miRs) play important roles in the regulation of angiogenesis. In this study, we have characterized miR-382 upregulation by hypoxia and the functional relevance of miR-382 in tumor angiogenesis. miRs induced by hypoxia in MKN1 human gastric cancer cells were investigated using miRNA microarrays. We selected miR-382 and found that the expression of miR-382 was regulated by HIF-1α. Conditioned media (CM) from MKN1 cells transfected with a miR-382 inhibitor (antagomiR-382) under hypoxic conditions significantly decreased vascular endothelial cell (EC) proliferation, migration and tube formation. Algorithmic programs (Target Scan, miRanda and cbio) predicted that phosphatase and tensin homolog (PTEN) is a target gene of miR-382. Deletion of miR382-binding sequences in the PTEN mRNA 3′-untranslated region (UTR) diminished the luciferase reporter activity. Subsequent study showed that the overexpression of miR-382 or antagomiR-382 down- or upregulated PTEN and its downstream target AKT/mTOR signaling pathway, indicating that PTEN is a functional target gene of miR-382. In addition, PTEN inhibited miR-382-induced in vitro and in vivo angiogenesis as well as VEGF secretion, and the inhibition of miR-382 expression reduced xenograft tumor growth and microvessel density in tumors. Taken together, these results suggest that miR-382 induced by hypoxia promotes angiogenesis and acts as an angiogenic oncogene by repressing PTEN.
Vascular Health and Risk Management Dovepress Blood and Urine Levels of Heavy Metal Pollutants in Female and Male Patients with Coronary Artery Disease

Background: Heavy metal pollutants such as cadmium (Cd), lead (Pb), and mercury (Hg) are rarely the subjects of cardiovascular research although they have been suspected for decades to negatively impact the circulatory system. Methods: Apart from detailed anamnestic data, urinary levels of Cd and full blood levels of Pb and Hg were measured in 53 female (mean age: 68.04±7.03 years) and 111 male (mean age: 60.68±11.43 years) nonsmoking or never-smoking patients with angiographically verified and precisely quantified coronary artery disease (CAD). Results: Although Cd was quantifiable in 68.3% of subjects, only 34.1% of these patients exceeded the critical 1 µg/L Human Biomonitoring (HBM)-I level. Median Pb (20 µg/L) and Hg (0.55 µg/L) levels were lower than the HBM-I, as well as reference levels of Pb. Wine consumption was the main source for Pb, fish and wine consumption for Hg, and previous nicotine abuse for Cd. There was no correlation between Cd, Pb, or Hg and severity of CAD although severity correlated positively with atherosclerosis parameters (uric acid, creatinine, triglycerides, blood urea nitrogen, C-reactive protein) and negatively with high density lipoprotein cholesterol. Conclusion: Cd levels detected in CAD patients were high compared to German and European reference levels but it could not be proven that urine levels of Cd and blood levels of Hg or Pb played a major role in the genesis of CAD, particularly when compared to well-known biomarkers such as blood pressure, glucose, and lipids.
Antibodies against Early Proteins of Human Papillomaviruses as Diagnostic Markers for Invasive Cervical Cancer

ABSTRACT Cervical cancer is the most prevalent tumor in developing countries and the second most frequent cancer among females worldwide. Specific human papillomaviruses (HPVs) and, most notably, HPV types 16 and 18 are recognized as being causally associated with this malignancy. Antibodies against early HPV proteins E6 and E7 have been found more often in patients with tumors than in controls. Existing peptide enzyme-linked immunosorbent assays (ELISAs) for the detection of anti-E6 and anti-E7 antibodies in human sera have low levels of sensitivity and specificity and thus are not suitable for use as diagnostic tools. Based on highly purified recombinant native proteins, we developed four sandwich ELISAs for the detection of antibodies against HPV type 16 and 18 E6 and E7 proteins. We demonstrate their sensitivities and high degrees of specificity for cervical cancer. Among a total of 501 serum specimens from unselected patients with invasive cervical cancer, 52.9% reacted positively in at least one of the four assays. In contrast, among 244 serum specimens from control subjects without cervical cancer, only 2 reactive serum specimens (0.8%) were found. For 19 of 19 antibody-positive patients, the HPV type indicated by seroreactivity was identical to the HPV DNA type found in the tumor, which also indicates a high degree of specificity for antibody detection with respect to HPV type. In a direct comparison of 72 serum specimens from patients with cervical cancer, 56% of the specimens reacted in at least one of the four protein ELISAs, whereas 40% reacted in at least one of seven peptide ELISAs covering the four antigens. These assays could be of value for the detection of invasive cervical cancer in settings in which cytology-based early tumor screening is not available, for the clinical management of patients diagnosed with cervical cancer, and for the immunological monitoring of E6 and E7 vaccination trials.
Epidemiological Evidence for Dormant Cryptococcus neoformans Infection

ABSTRACT To date, the time of acquisition of a Cryptococcus neoformans infectious strain has never been studied. We selected a primer, (GACA)4, and a probe, CNRE-1, that by randomly amplified polymorphic DNA (RAPD) analysis and restriction fragment length polymorphism (RFLP), respectively, regrouped strains from control samples of C. neoformans var. grubiienvironmental isolates according to their geographical origins. The two typing techniques were then used to analyze 103 isolates from 29 patients diagnosed with cryptococcosis in France. Nine of the 29 patients lived in Africa a median of 110 months prior to moving to France; 17 of the patients originated from Europe. Results showed a statistically significant clustering of isolate subtypes from patients originating from Africa compared to those from Europe. We conclude that the patients had acquired the C. neoformans infectious strain long before their clinical diagnoses were made.
Does the EUA institutional evaluation programme contribute to quality improvement

Purpose – This paper aims to reflect on the relevance of the Institutional Evaluation Programme (IEP) of the European University Association (EUA) to universities' quality improvement. It aims to analyse IEP follow‐up reports to determine whether the programme contributes to the development of a quality improvement culture.Design/methodology/approach – The structure and contents of 22 follow‐up reports were analysed to assess the IEP programme. All reports were subject to content analysis using adequate software (NVivo 8 with a 242 nodes tree), the main goal being to evaluate progress made since the original evaluation.Findings – The reports analysed and the work by other authors show that IEP can constitute a useful approach towards the universities' quality improvement. IEP evaluations generally give a precise account of problems faced by each university, identifying its strong and weak points, opportunities and threats, and presenting clear recommendations and suggestions for improvement. If properly d.
A New Parameterization of Cloud Droplet Activation Applicable to General Circulation Models

Abstract A new parameterization is proposed to link the droplet number concentration to the size distribution and chemical composition of aerosol and updraft velocity. Except for an empirical assumption of droplet growth, the parameterization is formulated almost entirely on first principles to allow for satisfactory performance under a variety of conditions. For a series of updraft velocity ranging from 0.03 to 10.0 m s−1, the droplet number concentrations predicted with the parameterization are in good agreement with the detailed parcel model simulations with an average error of −4 ± 26% (one standard deviation). The accuracy is comparable to or better than some existing parameterizations. The parameterization is able to account for the effects of droplet surface tension and mass accommodation coefficient on activation without adjusting the empirical parameter. These desirable attributes make the parameterization suitable for being used in the prognostic determination of the cloud droplet number concent.
Learning a Distance Metric from a Network

Many real-world networks are described by both connectivity information and features for every node. To better model and understand these networks, we present structure preserving metric learning (SPML), an algorithm for learning a Mahalanobis distance metric from a network such that the learned distances are tied to the inherent connectivity structure of the network. Like the graph embedding algorithm structure preserving embedding, SPML learns a metric which is structure preserving, meaning a connectivity algorithm such as k-nearest neighbors will yield the correct connectivity when applied using the distances from the learned metric. We show a variety of synthetic and real-world experiments where SPML predicts link patterns from node features more accurately than standard techniques. We further demonstrate a method for optimizing SPML based on stochastic gradient descent which removes the running-time dependency on the size of the network and allows the method to easily scale to networks of thousands of nodes and millions of edges.
Outcomes of stereotactic body radiotherapy for unresectable primary or recurrent cholangiocarcinoma

Purpose To report the results of stereotactic body radiotherapy (SBRT) for unresectable primary or recurrent cholangiocarcinoma. Materials and Methods From January 2005 through August 2013, 58 patients with unresectable primary (n = 28) or recurrent (n = 30) cholangiocarcinoma treated by SBRT were retrospectively analyzed. The median prescribed dose was 45 Gy in 3 fractions (range, 15 to 60 Gy in 1-5 fractions). Patients were treated by SBRT only (n = 53) or EBRT + SBRT boost (n = 5). The median tumor volume was 40 mL (range, 5 to 1,287 mL). Results The median follow-up duration was 10 months (range, 1 to 97 months). The 1-year, 2-year overall survival rates, and median survival were 45%, 20%, and 10 months, respectively. The median survival for primary group and recurrent group were 5 and 13 months, respectively. Local control rate at 1-year and 2-year were 85% and 72%, respectively. Disease progression-free survival rates at 1-year and 2-year were 26% and 23%, respectively. In univariate analysis, ECOG performance score (0-1 vs. 2-3), treatment volume (<50 vs. ≥50 mL), and pre-SBRT CEA level (<5 vs. ≥5 ng/mL) were significant in overall survival rate. In multivariate analysis, ECOG score (p = 0.037) and tumor volume (p = 0.030) were statistically significant. In the recurrent tumor group, patients with >12 months interval from surgery to recurrence showed statistically significant higher overall survival rate than those with ≤12 months (p = 0.026). Six patients (10%) experienced ≥grade 3 complications. Conclusion SBRT can be considered as an effective local modality for unresectable primary or recurrent cholangiocarcinoma.
High RAD54B expression: an independent predictor of postoperative distant recurrence in colorectal cancer patients

We recently reported a specific mechanism that RAD54B, an important factor in homologous recombination, promotes genomic instability via the degradation of p53 protein in vitro. However, clinical significance of RAD54Bin colorectal cancer (CRC) remains unclear. Thus we analyzed RAD54B geneexpression in CRC patients. Using the training set (n = 123), the optimal cut-off value for stratification was determined, and validated in another cohort (n = 89). Kaplan–Meier plots showed that distant recurrence free survival was significantly lesser in high RAD54B expression group compared with that of low expression group in both training (P = 0.0013) and validation (P = 0.024) set. Multivariate analysis using Cox proportional-hazards model showed that high RAD54B expression was an independent predictor in both training (hazard ratio, 4.31; 95% CI, 1.53–13.1; P = 0.0060) and validation (hazard ratio, 3.63; 95% CI, 1.23–10.7; P = 0.021) set. In addition, a negative significant correlation between RAD54B and CDKN1A, a target gene of p53, was partially confirmed, suggesting that RAD54B functions via the degradation of p53 protein even in clinical samples. This study first demonstrated RAD54B expression has potential to serve as a novel prognostic biomarker, particularly for distant recurrence in CRC patients.
Can item response theory reduce patient burden when measuring health status in neurological disorders? Results from Rasch analysis of the SF-36 physical functioning scale (PF-10)

BACKGROUND Indices of physical function may have a hierarchy of items. In cases where this can be demonstrated it may be possible to reduce patient burden by asking them to complete only those items which relate directly to their own level of ability. OBJECTIVES To determine whether statistical procedures, operationalising what is known as item response theory (IRT), can be used to assess the unidimensionality of the 10 item physical functioning domain of the SF-36 in patients with Parkinson's disease and motor neuron disease, and, secondly, to determine whether it would be possible to administer subsets of items to certain patients, on the basis of their replies to other items in the scale, thereby reducing patient burden. METHODS Rasch analysis, a form of IRT methodology, of the 10 item physical functioning domain (PF-10) in two neurological patient samples was undertaken and the results compared with results of a Rasch analysis of data gained from a population survey (the third Oxford healthy lifestyles survey). RESULTS Evidence from the analyses suggests that the PF-10 does not form a perfect hierarchy on a unidimensional scale. However, certain items seem to form a hierarchy, and responses to some of them are contingent on responses to the other items. CONCLUSIONS Rasch analysis of the PF-10 in neurological patients has indicated that certain items of the scale are hierarchically ordered, and consequently not all respondents would need to complete them all: indeed those most severely ill would be required to complete less items than those with only limited disabilities. The implications of this are discussed.
Improved M-FOCUSS Algorithm With Overlapping Blocks for Locally Smooth Sparse Signals

The focal underdetermined system solver (FOCUSS) algorithm has already found many applications in signal processing and data analysis, whereas the regularized M-FOCUSS algorithm has been recently proposed by Cotter for finding sparse solutions to an underdetermined system of linear equations with multiple measurement vectors. In this paper, we propose three modifications to the M-FOCUSS algorithm to make it more efficient for sparse and locally smooth solutions. First, motivated by the simultaneously autoregressive (SAR) model, we incorporate an additional weighting (smoothing) matrix into the Tikhonov regularization term. Next, the entire set of measurement vectors is divided into blocks, and the solution is updated sequentially, based on the overlapping of data blocks. The last modification is based on an alternating minimization technique to provide data-driven (simultaneous) estimation of the regularization parameter with the generalized cross-validation (GCV) approach. Finally, the simulation results demonstrating the benefits of the proposed modifications support the analysis.