Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Statistical Approach for Ocean Colour Estimation of Inherent Optical Properties and Cyanobacteria Abundance in Optically Complex Waters

Eutrophication is an increasing problem in coastal waters of the Baltic Sea. Moreover, algal blooms, which occur every summer in the Gulf of Gdansk can deleteriously impact human health, the aquatic environment, and economically important fisheries, tourism, and recreation industries. Traditional laboratory-based techniques for water monitoring are expensive and time consuming, which usually results in limited numbers of observations and discontinuity in space and time. The use of hyperspectral radiometers for coastal water observation provides the potential for more detailed remote optical monitoring. A statistical approach to develop local models for the estimation of optically significant components from in situ measured hyperspectral remote sensing reflectance in case 2 waters is presented in this study. The models, which are based on empirical orthogonal function (EOF) analysis and stepwise multilinear regression, allow for the estimation of parameters strongly correlated with phytoplankton (pigment concentration, absorption coefficient) and coloured detrital matter abundance (absorption coefficient) directly from reflectance spectra measured in situ. Chlorophyll a concentration, which is commonly used as a proxy for phytoplankton biomass, was retrieved with low error (median percent difference, MPD = 17%, root mean square error RMSE = 0.14 in log10 space) and showed a high correlation with chlorophyll a measured in situ (R = 0.84). Furthermore, phycocyanin and phycoerythrin, both characteristic pigments for cyanobacteria species, were also retrieved reliably from reflectance with MPD = 23%, RMSE = 0.23, R2 = 0.77 and MPD = 24%, RMSE = 0.15, R2 = 0.74, respectively. The EOF technique proved to be accurate in the derivation of the absorption spectra of phytoplankton and coloured detrital matter (CDM), with R2 (? ) above 0.83 and RMSE around 0.10. The approach was also applied to satellite multispectral remote sensing reflectance data, thus allowing for improved temporal and spatial resolution compared with the in situ measurements. The EOF method tested on simulated Medium Resolution Imaging Spectrometer (MERIS) or Ocean and Land Colour Instrument (OLCI) data resulted in RMSE = 0.16 for chl-a and RMSE = 0.29 for phycocyanin. The presented methods, applied to both in situ and satellite data, provide a powerful tool for coastal monitoring and management.
Provitamin A metabolism and functions in mammalian biology 1 – 4

Vitamin A deficiency is a major public health problem in developing countries. Some studies also implicate a suboptimal vitamin A intake in certain parts of the population of the industrialized world. Provitamin A carotenoids such as b-carotene are the major source for retinoids (vitamin A and its derivatives) in the human diet. However, it is still controversial how much b-carotene intake is required and safe. An important contributor to this uncertainty is the lack of knowledge about the biochemical and molecular basis of b-carotene metabolism. Recently, key players of provitamin A metabolism have been molecularly identified and biochemically characterized. Studies in knockout mouse models showed that intestinal b-carotene absorption and conversion to retinoids is under negative feedback regulation that adapts this process to the actual requirement of vitamin A of the body. These studies also showed that in peripheral tissues a conversion of b-carotene occurs and affects retinoid-dependent physiologic processes. Moreover, these analyses provided a possible explanation for the adverse health effects of carotenoids by showing that a pathologic accumulation of these compounds can induce oxidative stress in mitochondria and cell signaling pathways related to disease. Genetic polymorphisms in identified genes exist in humans and also alter carotenoid homeostasis. Here, the advanced knowledge of b-carotene metabolism is reviewed, which provides a molecular framework for understanding the role of this important micronutrient in health and disease. Am J Clin Nutr 2012;96(suppl):1234S–44S.
The millennium water vapour drop in chemistry–climate model simulations

Abstract. This study investigates the abrupt and severe water vapour decline in the stratosphere beginning in the year 2000 (the "millennium water vapour drop") and other similarly strong stratospheric water vapour reductions by means of various simulations with the state-of-the-art Chemistry-Climate Model (CCM) EMAC (ECHAM/MESSy Atmospheric Chemistry Model). The model simulations differ with respect to the prescribed sea surface temperatures (SSTs) and whether nudging is applied or not. The CCM EMAC is able to most closely reproduce the signature and pattern of the water vapour drop in agreement with those derived from satellite observations if the model is nudged. Model results confirm that this extraordinary water vapour decline is particularly obvious in the tropical lower stratosphere and is related to a large decrease in cold point temperature. The drop signal propagates under dilution to the higher stratosphere and to the poles via the Brewer–Dobson circulation (BDC). We found that the driving forces for this significant decline in water vapour mixing ratios are tropical sea surface temperature (SST) changes due to a coincidence with a preceding strong El Nino–Southern Oscillation event (1997/1998) followed by a strong La Nina event (1999/2000) and supported by the change of the westerly to the easterly phase of the equatorial stratospheric quasi-biennial oscillation (QBO) in 2000. Correct (observed) SSTs are important for triggering the strong decline in water vapour. There are indications that, at least partly, SSTs contribute to the long period of low water vapour values from 2001 to 2006. For this period, the specific dynamical state of the atmosphere (overall atmospheric large-scale wind and temperature distribution) is important as well, as it causes the observed persistent low cold point temperatures. These are induced by a period of increased upwelling, which, however, has no corresponding pronounced signature in SSTs anomalies in the tropics. Our free-running simulations do not capture the drop as observed, because a) the cold point temperature has a low bias and thus the water vapour variability is reduced and b) because they do not simulate the appropriate dynamical state. Large negative water vapour declines are also found in other years and seem to be a feature which can be found after strong combined El Nino/La Nina events if the QBO west phase during La Nina changes to the east phase.
Ultrasonography of the metatarsophalangeal joints in rheumatoid arthritis: comparison with magnetic resonance imaging, conventional radiography, and clinical examination.

OBJECTIVE To compare ultrasonography (US) with magnetic resonance imaging (MRI), conventional radiography, and clinical examination in the evaluation of bone destruction and signs of inflammation in the metatarsophalangeal (MTP) joints of patients with rheumatoid arthritis (RA). METHODS Two hundred MTP joints of 40 patients with RA and 100 MTP joints of 20 healthy control subjects were assessed with B-mode US, contrast-enhanced MRI, conventional radiography, and clinical examination for signs of bone destruction and joint inflammation. RESULTS With MRI considered the reference method, the sensitivity, specificity, and accuracy of US for the detection of bone erosions were 0.79, 0.97, and 0.96, respectively, while the corresponding values for radiography were 0.32, 0.98, and 0.93. The sensitivity, specificity, and accuracy of US for the detection of synovitis were 0.87, 0.74, and 0.79, while for clinical examination, the corresponding values were 0.43, 0.89, and 0.71. Erosive disease was identified in 26 patients by US, compared with 20 patients by MRI and 11 patients by radiography. Evaluation by US indicated signs of inflammation in 36 patients, while MRI and clinical examination revealed signs of inflammation in 31 patients and 20 patients, respectively. US and MRI volume-based gradings of synovitis showed intraclass correlation coefficients of 0.56-0.72 (P < 0.0001). The MRI and radiographic visualizations of US-detected bone changes were closely related to their size-based gradings on US. CONCLUSION US enables detection and grading of destructive and inflammatory changes in the MTP joints of patients with RA. By comparison with MRI, US was found to be markedly more sensitive and accurate than clinical examination and conventional radiography. Considering the early and frequent involvement of the MTP joints, evaluation of these joints by US may be of major clinical importance in RA.
Immunohistochemical Detection of the Wilms' Tumor Gene (WT1) in Epithelial Ovarian Tumors

The Wilms' tumor gene WT1 plays multiple roles in the development of the genitourinary organs and Wilms' tumors. The aims of this study were to immunohistochemically evaluate WT1 expression in normal female genital tissues and in epithelial ovarian tumors and to look for correlations between WT1 expression and histologic subtypes and cell proliferation in epithelial ovarian tumors. In normal female genital organs, WT1 expression was recognized in ovarian surface epithelium, the lining of inclusion cysts, and tubal epithelium, but not in the cervical or endometrial epithelium. In epithelial ovarian tumors, serous tumors generally revealed a high WT1 expression. Among adenocarcinomas, serous carcinoma revealed a significantly higher WT1 expression than the other histologic subtypes. There were no significant correlations between the WT1 labeling index and the Ki-67 labeling index, and no significant difference in survival between those showing high and low WT1 expression among the malignant cases. These results suggest that WT1 expression may be related to cell differentiation, and that the histologic subtypes of epithelial ovarian carcinomas may differ considerably in their biological characteristics.
Using Prior Information about Population Quantiles in Nite Population Sampling Using Prior Information about Population Quantiles in Nite Population Sampling

SUMMARY Consider the problem of estimating the population mean when it is known a priori that the population median belongs to some interval. More generally consider the problem of estimating the population mean when it is known a priori that the median of some auxiliary variable belongs to some interval. In this note we show how the Polya posterior, which is useful in problems where little prior information is available, can be adapted to these new situations. The resulting point and interval estimators are shown to have good frequentist properties.
Semantic Place Classification of Indoor Environments with Mobile Robots Using Boosting

Indoor environments can typically be divided into places with different functionalities like kitchens, offices, or seminar rooms. We believe that such semantic information enables a mobile robot to more efficiently accomplish a variety of tasks such as human-robot interaction, path-planning, or localization. This paper presents a supervised learning approach to label different locations using boosting. We train a classifier using features extracted from vision and laser range data. Furthermore, we apply a Hidden Markov Model to increase the robustness of the final classification. Our technique has been implemented and tested on real robots as well as in simulation. The experiments demonstrate that our approach can be utilized to robustly classify places into semantic categories. We also present an example of localization using semantic labeling.
Interpreting prediction markets: a stochastic approach

We strengthen recent connections between prediction markets and learning by showing that a natural class of market makers can be understood as performing stochastic mirror descent when trader demands are sequentially drawn from a fixed distribution. This provides new insights into how market prices (and price paths) may be interpreted as a summary of the market's belief distribution by relating them to the optimization problem being solved. In particular, we show that under certain conditions the stationary point of the stochastic process of prices generated by the market is equal to the market's Walrasian equilibrium of classic market analysis. Together, these results suggest how traditional market making mechanisms might be replaced with general purpose learning algorithms while still retaining guarantees about their behaviour.
Inuvialuit adults in the Canadian Arctic have a high body mass index and self-reported physical activity.

BACKGROUND Inuvialuit in Arctic Canada are undergoing nutrition and lifestyle transitions that encourage decreased physical activity (PA) and increased body mass index (BMI), although data specific to PA and BMI within this unique population are not currently available. The present study aimed to characterise current PA and BMI levels in a sample of Inuvialuit adults. METHODS Inuvialuit adults randomly selected from a cross-sectional survey of three communities in the Northwest Territories, Canada, completed an adapted International Physical Activity Questionnaire (IPAQ) and an anthropometric questionnaire to obtain height and weight. Data were analysed using the standardised IPAQ protocol, and the results are presented by gender and age group (≤50 and >50 years). RESULTS One hundred and ninety-six Inuvialuit adults [148 women, 48 men; mean (standard deviation (SD)) ages 45 (14) and 41 (14) years, respectively; age range 19-84 years] completed the IPAQ (response rates 65-85%). Seventy-one percent of men and 74% of women allowed height measurements, whilst 81% and 84% allowed weight measurements, respectively; the remainder provided self-reported anthropometrics. Mean (SD) BMIs were 28.6 (7.7) kg/m(2) for males and 30.5 (8.8) kg/m(2) for females. The greatest percentage of participants in both gender and age groups fell into the obese BMI category. Self-reported PA was high, with means for men and participants ≤50 years in the high category of PA and means for women and participants >50 years in the medium category. Almost two-thirds (65%) of participants were classified as being overweight or obese, although 89% reported medium or high levels of PA. CONCLUSIONS The results obtained in the present study indicate widespread overweight/obesity accompanying high levels of self-reported PA.
THE APPLICATION OF COMPUTATIONAL FLUID DYNAMICS ( CFD ) SIMULATIONS FOR NASAL DRUG DELIVERY

The Norwegian company OptiNose AS is developing a novel concept that challenges traditional nasal delivery systems. The patented bi-directional delivery system takes advantage of the posterior connection between the nasal passages persisting when the soft palate automatically closes during oral exhalation. The exhalation into the delivery device triggers the release of particles into an airflow, which enters one nostril via a sealing nozzle and exits through the other nostril. During the development process for their drug delivery concept, OptiNose is using Computational Fluid Dynamics (CFD). The simulations are used to visualize and demonstrate the basic features of the bi-directional technique and discuss how its design and functionality could be further optimised. CFD computations thus increase the efficiency of device development and reduce the need for expensive and time consuming laboratory experiments and clinical tests. The simulations are carried out by use of Fluent, using a volume grid generated by Tgrid. To perform successful CFD calculations on the nose, construction of a proper surface grid of the nasal cavity, is mandatory. A high resolution CT-scan was the first part of this process, where after the 3-dimensional surface geometry was created by a pipeline of image segmentation and geometric modification steps. The process of building the surface grid is presented in the paper. Essential for the CFD computations is thorough validation of the simulation results. This paper presents comparisons between experimental and numerical simulations. Simple numerical models are used to verify critical parameters, e.g. airflow and particle size, in the design process, together with in vitro experiments in a human nasal airway model.
Surface modification of electrospun fibre meshes by oxygen plasma for bone regeneration

Plasma treatment is a method to modify the physicochemical properties of biomaterials, which consequently may affect interactions with cells. Based on the rationale that physical cues on the surface of culture substrates and implants, such as surface roughness, have proven to alter cell behaviour, we used electrospinning to fabricate fibrous three-dimensional scaffolds made of a poly (ethylene oxide terephthalate)/poly (butylene terephthalate) copolymer to mimic the physical microenvironment of extracellular matrix and applied radio-frequency oxygen plasma treatment to create nanoscale roughness. Scanning electron microscopy (SEM) analysis revealed a fibre diameter of 5.49 ± 0.96 µm for as-spun meshes. Atomic force microscopy (AFM) measurements determined an exponential increase of surface roughness with plasma treatment time. An increase in hydrophilicity after plasma treatment was observed, which was associated with higher oxygen content in plasma treated scaffolds compared to untreated ones. A more pronounced adsorption of bovine serum albumin occurred on scaffolds treated with plasma for 15 and 30 min compared to untreated fibres. Clinically relevant human mesenchymal stromal cells (hMSCs) were cultured on untreated, 15 and 30 min treated scaffolds. SEM analysis confirmed cell attachment and a pronounced spindle-like morphology on all scaffolds. No significant differences were observed between different scaffolds regarding the amount of DNA, metabolic activity and alkaline phosphatase (ALP) activity after 7 days of culture. The amount of ALP positive cells increased between 7 and 21 days of culture on both untreated and 30 min treated meshes. In addition, ALP staining of cells on plasma treated meshes appeared more pronounced than on untreated meshes after 21 days of culture. Quantitative polymerase chain reaction showed significant upregulation of bone sialoprotein and osteonectin expression on oxygen plasma treated fibres compared to untreated fibres in basic culture medium after 7 days of culture, while no differences were observed in the expression of other osteogenic markers. At 21 days, no osteocalcin protein could be detected by ELISA at any of the substrates. In conclusion, this study shows that oxygen plasma treatment can successfully be applied to modify the nanoscale surface properties of polymeric electrospun fibre meshes, which in turn may positively affect osteogenic differentiation of hMSCs.
The effect of non-surgical periodontal therapy on peroxidase activity in diabetic patients: a case-control pilot study.

OBJECTIVE To evaluate the effect of periodontal therapy on clinical parameters as well as on total salivary peroxidase (TSP) activity and myeloperoxidase (MPO) activity in the gingival crevicular fluid (GCF) of patients with type 2 diabetes mellitus (DM2) and of systemically healthy individuals. MATERIAL AND METHODS Twenty DM2 subjects with inadequate metabolic control (test group) and 20 systemically healthy individuals (control group), both groups with chronic periodontitis, were enrolled. Periodontal clinical parameters, namely periodontal probing depth (PD), clinical attachment level (CAL), visible plaque index (VPI), bleeding on probing (BOP), gingival bleeding index (GBI) and presence of suppuration (SUP), as well as TSP activity and GCF MPO activity, were assessed before and 3 months after non-surgical periodontal therapy. RESULTS At baseline and 3 months post-treatment, the test group presented a higher percentage of sites with VPI and BOP (p<0.01). MPO activity in the GCF presented lower values (p<0.05) for the test group at both baseline and the post-treatment period. The periodontal treatment resulted in a significant improvement of most clinical and enzymatic parameters for both groups (p<0.05). CONCLUSIONS In both groups, the periodontal therapy was effective in improving most clinical parameters and in reducing salivary and GCF enzymatic activity. The diabetic individuals presented lower MPO activity in the GCF.
Differential staining of dead and dying embryonic cells with a simple new technique

A new staining technique with toluidine blue and safranin is described which yields satisfactory results in histological sections of chick embryo tissue fixed in a mixture of glutaraldehyde and formaldehyde and embedded in Spurr's resin. In zones of embryonic cell death, this technique allows the blue‐staining of dying cell pyknotic nuclei to be clearly distinguished from red‐staining healthy cells. The possible factors underlying this differential staining of pyknotic nuclei are discussed.
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations

Functional annotation of unknown proteins is a major goal in proteomics. A key step in this annotation process is the definition of a protein’s subcellular localization. As a consequence, numerous prediction techniques for localization have been developed over the years. These methods typically focus on a single underlying biological aspect or predict a subset of all possible subcellular localizations. There is a clear need for new methods that utilize and represent available protein specific biological knowledge from several sources, in order to improve accuracy and localization coverage for a wide range of organisms. Here we present a novel Support Vector Machine (SVM)-based approach for predicting protein subcellular localization, which integrates information about N-terminal targeting sequences, amino acid composition, and protein sequence motifs. An important step is taken towards emulating the protein sorting process by capturing and bringing together biologically relevant information. Our novel approach has been used to develop two new prediction methods, TargetLoc and MultiLoc. TargetLoc is restricted to analysis of proteins containing N-terminal targeting sequences, whereas MultiLoc covers all major eukaryotic subcellular localizations for animal, plant, and fungal proteins. Compared to similar methods, TargetLoc performs better than these. MultiLoc performs considerably better than comparable prediction methods predicting all major eukaryotic subcellular localizations, and shows better or comparable results to methods that are specialized on fewer localizations or for one organism.
Optimal power consumption based on new power spectral efficiency metric for wireless cellular networks

In this paper, we introduce a new power spectral efficiency (PSE) metric, to quantify the spectral efficiency and the total required power to cover a certain area with a predefined received signal quality. This metric offers the possibility to find the optimal transmission power in each base station to cover the total given area with the minimum total consumed power. We start by deriving the closed-form expression of the maximum transmission range under Rayleigh fading environment. Based on the maximum transmission range, we define and derive the average affected area, the total consumed power and the average ergodic capacity. Then, we introduce the PSE expression, to quantify the power spectral utilization efficiency. After that, we evaluate the new metric for cellular network with 3-cell frequency reuse cluster (3-CFRC), without inter-cell interference (ICI), and the network with 1-cell frequency reuse cluster (1-CFRC) and ICI. Through mathematical analysis and numerical examples, we show that the PSE metric provides a new perspective on the design and optimization of wireless transmissions, especially on the transmission power selection.