Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling atmospheric wet refractivity profile using ground and space-based global positioning system

Precise measurement of atmospheric water vapour has been very challenging due to some limitations of the conventional meteorological systems. Hence, there is a need for Global Positioning System (GPS) for meteorology or GPS meteorology. Therefore, the ground-based GPS meteorology and the space-based GPS Radio Occultation (GPS RO) techniques have been used. The major challenges of groundbased GPS meteorology approach include the lack of surface meteorological data collocating with the location of the ground-based GPS receivers as well as its inability to profile the atmosphere. Whereas the GPS RO technique has a problem of generating profile for the lower tropospheric region which holds the largest amount of water vapour. This research investigates an approach for estimating wet refractivity profile using GPS data. Three specific objectives were set for the study which was conducted in three phases. The first objective assessed GPS Integrated Water Vapour (GPS IWV) in which GPS IWV from interpolated meteorological data and the applicability of Global Pressure and Temperature (GPT2w) model for GPS meteorology was evaluated. The results revealed that the GPS IWV from Automatic Weather Station (AWS) presents good correlation with the radiosonde IWV, the standard deviation of the biases vary spatially from 3.162kg/m2 to 3.878 kg/m2. The actual influence of the errors of GPT2w meteorological parameters on GPT2w-based GPS IWV lies between 2kg/m2 and 3kg/m2, translating to an average relative accuracy of 1.2%. Meanwhile, the sensitivity of the GPS RO data to equatorial water vapour trend was evaluated to achieve second objective. It was found that the GPS RO IWV is highly comparable with the ground-based GPS IWV, having average bias of 1.8kg/m2. Finally, a methodology for GPS wet refractivity retrieval was developed towards achieving the third objective of this research. The Modified Single Exponential Function (MSEF) model for retrieving wet refractivity profile from ground-based GPS Zenith Wet Delay (ZWD) was realised. The output validation using profile from radiosonde and GPS RO observations showed high correlation in each case. In order to improve the performance of the MSEF model, an approach for integrating the ground-based and the space-based GPS data (GIWRef) was formulated. The GIWRef profile is highly correlated with the GPS RO profile, which showed an average improvement of 41% over the initial MSEF method with average correlation coefficient of 0.99. It can be concluded from the foregoing results of the study that the MSEF and GIWREF concepts developed in this work, presents a potential for augmenting weather forecasting and monitoring water vapour system.
Spatial and spectral analysis of corneal epithelium injury using hyperspectral images

Eye assessment is essential in preventing blindness. Currently, the existing methods to assess corneal epithelium injury are complex and require expert knowledge. Hence, we have introduced a non-invasive technique using hyperspectral imaging (HSI) and an image analysis algorithm of corneal epithelium injury. Three groups of images were compared and analyzed, namely healthy eyes, injured eyes, and injured eyes with stain. Dimensionality reduction using principal component analysis (PCA) was applied to reduce massive data and redundancies. The first 10 principal components (PCs) were selected for further processing. The mean vector of 10 PCs with 45 pairs of all combinations was computed and sent to two classifiers. A quadratic Bayes normal classifier (QDC) and a support vector classifier (SVC) were used in this study to discriminate the eleven eyes into three groups. As a result, the combined classifier of QDC and SVC showed optimal performance with 2D PCA features (2DPCA-QDSVC) and was utilized to classify normal and abnormal tissues, using color image segmentation. The result was compared with human segmentation. The outcome showed that the proposed algorithm produced extremely promising results to assist the clinician in quantifying a cornea injury.
RIM2, MSI1 and PGI1 and located within an 8 kb segment of Saccharomyces cerevisiae chromosome II, which also contains the putative ribosomal gene L21 and a new putative essential gene with a leucine zipper motif

We report the DNA sequence of an 8 kb segment localized on the right arm of chromosome II from Saccharomyces cerevisiae. The sequence reveals the presence of eight open reading frames (ORFs). Three of them, YBR1402, YBR1405 and YBR1406 are previously sequenced genes, respectively the RIM2 (replication in mitochondria), MSI1 (multicopy suppressor of IRA1 gene) and PGI1 (phosphoglucoisomerase) genes. The predicted product of the ORF YBR1401 could be the putative yeast ribosomal protein L21. A new essential gene, YBR1403, has been identified by disruption; it possesses a leucine zipper motif.
TWO DISTINCT-ABSORPTION X-RAY COMPONENTS FROM TYPE IIn SUPERNOVAE: EVIDENCE FOR ASPHERICITY IN THE CIRCUMSTELLAR MEDIUM

We present multi-epoch X-ray spectral observations of three Type IIn supernovae (SNe), SN 2005kd, SN 2006jd, and SN 2010jl, acquired with Chandra, XMM-Newton, Suzaku, and Swift. Previous extensive X-ray studies of SN 2010jl have revealed that X-ray spectra are dominated by thermal emission, which likely arises from a hot plasma heated by a forward shock propagating into a massive circumstellar medium (CSM). Interestingly, an additional soft X-ray component was required to reproduce the spectra at a period of ∼1–2 years after the SN explosion. Although this component is likely associated with the SN, its origin remained an open question. We find a similar, additional soft X-ray component from the other two SNe IIn as well. Given this finding, we present a new interpretation for the origin of this component; it is thermal emission from a forward shock essentially identical to the hard X-ray component, but directly reaches us from a void of the dense CSM. Namely, the hard and soft components are responsible for the heavily and moderately absorbed components, respectively. The co-existence of the two components with distinct absorptions as well as the delayed emergence of the moderately absorbed X-ray component could be evidence for asphericity of the CSM. We show that the X-ray spectral evolution can be qualitatively explained by considering a torus-like geometry for the dense CSM. Based on our X-ray spectral analyses, we estimate the radius of the torus-like CSM to be on the order of ∼5 × 1016 cm.
Hantaan Virus Infection Induces CXCL10 Expression through TLR3, RIG-I, and MDA-5 Pathways Correlated with the Disease Severity

Hantaan virus (HTNV) is a major agent causing hemorrhagic fever with renal syndrome (HFRS). Although the pathogenesis of HFRS is unclear, some reports have suggested that the abundant production of proinflammatory cytokines and uncontrolled inflammatory responses may contribute to the development of HFRS. CXCL10 is one of these cytokines and is found to be involved in the pathogenesis of many virus infectious diseases. However, the role of CXCL10 in the pathogenesis of HFRS and the molecular regulation mechanism of CXCL10 in HTNV infection remain unknown. In this study, we report that CXCL10 expresses highly in the HFRS patients' sera and the elevated CXCL10 is positively correlated with the severity of HFRS. We find that HTNV, a single-strand RNA virus, can act as a double-strand RNA to activate the TLR3, RIG-I, and MDA-5 signaling pathways. Through the downstream transcription factors of these pathways, NF-κB and IRF7, which bind directly to the CXCL10's promoter, the expression of CXCL10 is increased. Our results may help to better understand the role of CXCL10 in the development of HFRS and may provide some novel insights into the immune response of HTNV infection.
Pentavalent Single-Domain Antibodies Reduce Campylobacter jejuni Motility and Colonization in Chickens

Campylobacter jejuni is the leading cause of bacterial foodborne illness in the world, with symptoms ranging from acute diarrhea to severe neurological disorders. Contaminated poultry meat is a major source of C. jejuni infection, and therefore, strategies to reduce this organism in poultry, are expected to reduce the incidence of Campylobacter-associated diseases. We have investigated whether oral administration of C. jejuni-specific single-domain antibodies would reduce bacterial colonization levels in chickens. Llama single-domain antibodies specific for C. jejuni were isolated from a phage display library generated from the heavy chain IgG variable domain repertoire of a llama immunized with C. jejuni flagella. Two flagella-specific single-domain antibodies were pentamerized to yield high avidity antibodies capable of multivalent binding to the target antigen. When administered orally to C. jejuni-infected two-day old chicks, the pentabodies significantly reduced C. jejuni colonization in the ceca. In vitro, the motility of the bacteria was also reduced in the presence of the flagella-specific pentabodies, suggesting the mechanism of action is through either direct interference with flagellar motility or antibody-mediated aggregation. Fluorescent microscopy and Western blot analyses revealed specific binding of the anti-flagella pentabodies to the C. jejuni flagellin.
Regionalizing time of concentration using landscape structural patterns of catchments

Abstract There is an emerging challenge within water resources on how, and to what extent, borrowing concepts from landscape ecology might help re-define traditional concepts in hydrology in a more tangible manner. A stepwise regression model was adopted in this study to assess whether the time of concentration of catchments could be explained by five landscape structure-representing metrics for land use/land cover, soil and geological patches, using spatial data from 39 catchments. The models suggested that the times of concentration of the catchments could be predicted using the measures of four landscape structure-representing metrics, which include contiguity index (r2 = 0.46, p ≤0.05), fractal dimension index (r2 = 0.51, p ≤0.05), related circumscribing circle (r2 = 0.52, p ≤0.05), and shape index (r2 = 0.47, p ≤0.05). The models indicated that the regularity or irregularity in land use/land cover patch shape played a key role in affecting catchment hydrological response. Our findings revealed that regularity and irregularity in the shape of a given patch (e.g., urban and semi-urban, rangeland and agricultural patches) can affect patch functions in retarding and/or increasing flow accumulation at the catchment scale, which can, in turn, decrease or increase the times of concentration in the catchments.
Ineffectiveness of the 2014-2015 H3N2 influenza vaccine

The seasonal influenza vaccine is currently the most effective preventive modality against influenza infection. Nasopharyngeal samples of vaccinated and non-vaccinated patients presenting with Influenza-like-illness (ILI) were collected from over 20 outpatient clinics located in different geographic parts of Israel and were tested for the presence of influenza viruses (influenza A and influenza B). Here we show, that in the 2014-2015 season, the vaccine that included the A/Texas/50/2012 H3N2 virus was ineffective. Significant numbers of individuals vaccinated with the 2014-2015 vaccine, of all ages, were infected with influenza A (H3N2), manifesting similar symptoms as the non-vaccinated group. We further demonstrate that the Israeli circulating influenza A(H3N2) virus was different than that included in the 2014-2015 northern hemisphere vaccine, and that antibodies elicited by this vaccine were significantly less efficient in neutralizing influenza A(H3N2) infection.
FOXP3-stained image analysis for follicular lymphoma: optimal adaptive thresholding with maximal nucleus coverage

Immunohistochemical detection of FOXP3 antigen is a usable marker for detection of regulatory T lymphocytes (TR) in formalin fixed and paraffin embedded sections of different types of tumor tissue. TR plays a major role in homeostasis of normal immune systems where they prevent auto reactivity of the immune system towards the host. This beneficial effect of TR is frequently “hijacked” by malignant cells where tumor-infiltrating regulatory T cells are recruited by the malignant nuclei to inhibit the beneficial immune response of the host against the tumor cells. In the majority of human solid tumors, an increased number of tumor-infiltrating FOXP3 positive TR is associated with worse outcome. However, in follicular lymphoma (FL) the impact of the number and distribution of TR on the outcome still remains controversial. In this study, we present a novel method to detect and enumerate nuclei from FOXP3 stained images of FL biopsies. The proposed method defines a new adaptive thresholding procedure, namely the optimal adaptive thresholding (OAT) method, which aims to minimize under-segmented and over-segmented nuclei for coarse segmentation. Next, we integrate a parameter free elliptical arc and line segment detector (ELSD) as additional information to refine segmentation results and to split most of the merged nuclei. Finally, we utilize a state-of-the-art super-pixel method, Simple Linear Iterative Clustering (SLIC) to split the rest of the merged nuclei. Our dataset consists of 13 region-ofinterest images containing 769 negative and 88 positive nuclei. Three expert pathologists evaluated the method and reported sensitivity values in detecting negative and positive nuclei ranging from 83-100% and 90-95%, and precision values of 98-100% and 99-100%, respectively. The proposed solution can be used to investigate the impact of FOXP3 positive nuclei on the outcome and prognosis in FL.
Comparing Internet Assistance for Smoking Cessation: 13-Month Follow-Up of a Six-Arm Randomized Controlled Trial

Background Although many smokers seek Internet-based cessation assistance, few studies have experimentally evaluated long-term cessation rates among cigarette smokers who receive Internet assistance in quitting. Objective The purpose of this study is to describe long-term smoking cessation rates associated with 6 different Internet-based cessation services and the variation among them, to test the hypothesis that interactive and tailored Internet services yield higher long-term quit rates than more static Web-posted assistance, and to explore the possible effects of level of site utilization and a self-reported indicator of depression on long-term cessation rates. Method In 2004-05, a link was placed on the American Cancer Society (ACS) website for smokers who wanted help in quitting via the Internet. The link led smokers to the QuitLink study website, where they could answer eligibility questions, provide informed consent, and complete the baseline survey. Enrolled participants were randomly assigned to receive emailed access to one of five tailored interactive sites provided by cooperating research partners or to a targeted, minimally interactive ACS site with text, photographs, and graphics providing stage-based quitting advice and peer modeling. Results 6451 of the visitors met eligibility requirements and completed consent procedures and the baseline survey. All of these smokers were randomly assigned to one of the six experimental groups. Follow-up surveys done online and via telephone interviews at approximately 13 months after randomization yielded 2468 respondents (38%) and found no significant overall quit rate differences among those assigned to the different websites (P = .15). At baseline, 1961 participants (30%) reported an indicator of depression. Post hoc analyses found that this group had significantly lower 13-month quit rates than those who did not report the indicator (all enrolled, 8% vs 12%, P < .001; followed only, 25% vs 31%, P = .003). When the 4490 participants (70%) who did not report an indicator of depression at baseline were separated for analysis, the more interactive, tailored sites, as a whole, were associated with higher quitting rates than the less interactive ACS site: 13% vs 10% (P = .04) among 4490 enrolled and 32% vs 26% (P = .06) among 1798 followed. Conclusions These findings show that Internet assistance is attractive and potentially cost-effective and suggest that tailored, interactive websites may help cigarette smokers who do not report an indicator of depression at baseline to quit and maintain cessation.
Hough Transform: Underestimated Tool In The Computer Vision Field

We discuss Hough Transform, some of its key properties, a scheme of fast and complete calculation of the Hough Transform (similar to the Fast Fourier Transform), and an efficient implementation of this scheme on SIMD processors. We also demonstrate an application of the Fast Hough Transform in computer vision by the example of an automatic page orientation detection unit incorporated in an intelligent character recognition system. Both 2D (scanner) and 3D (camera) cases of page acquisition are considered.
Kernel-based nonparametric anomaly detection

An anomaly detection problem is investigated, in which there are totally n sequences, with s anomalous sequences to be detected. Each normal sequence contains m independent and identically distributed (i.i.d.) samples drawn from a distribution p, whereas each anomalous sequence contains m i.i. d. samples drawn from a distribution q that is distinct from p. The distributions p and q are assumed to be unknown a priori. The scenario with a reference sequence generated by p is studied. Distribution-free tests are constructed using maximum mean discrepancy (MMD) as the metric, which is based on mean embeddings of distributions into a reproducing kernel Hilbert space (RKHS). It is shown that as the number n of sequences goes to infinity, if the value of s is known, then the number m of samples in each sequence should be of order O(log n) or larger in order for the developed tests to consistently detect s anomalous sequences. If the value of s is unknown, then m should be of order strictly larger than O(log n). The computational complexity of all developed tests is shown to be polynomial. Numerical results demonstrate that these new tests outperform (or perform as well as) tests based on other competitive traditional statistical approaches and kernel-based approaches under various cases.
A Functional Interaction between Sprouty Proteins and Caveolin-1*

Growth factor-mediated signal transduction cascades can be regulated spatio-temporally by signaling modulators, such as Sprouty proteins. The four mammalian Sprouty family members are palmitoylated phosphoproteins that can attenuate or potentiate numerous growth factor-induced signaling pathways. Previously, we have shown that Sprouty-1 and Sprouty-2 associate with Caveolin-1, the major structural protein of caveolae. Like Sprouty, Caveolin-1 inhibits growth factor-induced mitogen-activated protein kinase activation. Here, we demonstrate that all four mammalian Sprouty family members physically interact with Caveolin-1. The C terminus of Caveolin-1 is the major Sprouty-binding site, whereas Sprouty binds Caveolin-1 via its conserved C-terminal domain. A single point mutation in this domain results in loss of Caveolin-1 interaction. Moreover, we demonstrate that the various Sprouty isoforms differ dramatically in their cooperation with Caveolin-1-mediated inhibition of mitogen-activated protein kinase activation and that such cooperation is also highly dependent on the type of growth factor investigated and on cell density. Together, the data suggest that the Sprouty/Caveolin-1 interaction modulates signaling in a growth factor- and Sprouty isoform-specific manner.
Ad Hoc Network Measurement Based on Network Tomography: Theory, Technique, and Application

Owing to the inherent characteristic of Ad Hoc network, a multi-hops , self-organiz ed wireless network, it is difficult to adopt traditional measurement technique in Ad Hoc network. Based on the analysis of the dynamic characteristic of Ad Hoc network topology, the paper brings forth an Ad Hoc network measurement model, and presents in detail the functions and implementation of each elements in this model. The simulation results show that the Ad Hoc network measurement model in this paper has the universality characteristic , since it could be used for all d ifferent mobility models in Ad Hoc network s . Besides, it could effectively resolve the problem of me a surability, because it could not only obtain the performance parameters of path in Ad Hoc networks , but also infer the link performance parameters based on network tomography .
Improvement of Glucose Tolerance and Hepatic Insulin Sensitivity by Oligofructose Requires a Functional Glucagon-Like Peptide 1 Receptor

Nondigestible fermentable dietary fibers such as oligofructose (OFS) exert an antidiabetic effect and increase the secretion of glucagon-like peptide 1 (GLP-1). To determine the importance of GLP-1 receptor-dependent mechanisms for the actions of OFS, we studied high-fat-fed diabetic mice treated with OFS for 4 weeks in the presence or absence of the GLP-1 receptor antagonist exendin 9-39 (Ex-9). OFS improved glucose tolerance, fasting blood glucose, glucose-stimulated insulin secretion, and insulin-sensitive hepatic glucose production and reduced body weight gain. Ex-9 totally prevented the beneficial effects of OFS. Furthermore, GLP-1 receptor knockout mice (GLP-1R−/−) were completely insensitive to the antidiabetic actions of OFS. At the molecular level, the effects of OFS on endogenous glucose production correlated with changes of hepatic IRS (insulin receptor substrate)-2 and Akt phosphorylation in an Ex-9-dependent manner. As inflammation is associated with diabetes and obesity, we quantified nuclear factor-κB and inhibitor of κB kinase β in the liver. The activity of both intracellular inflammatory effectors was reduced by OFS but, importantly, this effect could not be reverted by Ex-9. In summary, our data show that the antidiabetic actions of OFS require a functional GLP-1 receptor. These findings highlight the therapeutic potential of enhancing endogenous GLP-1 secretion for the treatment of type 2 diabetes.
Gravitational energy, dS/CFT correspondence and cosmic no-hair

The gravitational energy is examined in asymptotically de Sitter space-times. The positivity will be shown for certain cases. The de Sitter/CFT(dS/CFT) correspondence recently proposed and cosmic no-hair conjecture are testified in the aspect of the gravitational energy. From the holographic renormalization group point of view, the two conjectures are deeply connected with each other.
Quantifying Geoacoustic Uncertainty and Seabed Variability for Propagation Uncertainty

Abstract : Propagation and reverberation of acoustic fields in shallow waters depend strongly on the spatial variability of seabed geoacoustic parameters, and lack of knowledge of seabed variability is often a limiting factor in acoustic modeling applications. However, direct sampling (e.g., coring)of vertical and lateral variability is expensive and laborious, and matched-field and other long-range inversion methods fail to provide sufficient resolution. The long-term goal of this work is to use a Bayesian inversion approach in combination with seabed reflectivity data to investigate and quantify spatial variability of seabed sediments in two and three dimensions. For proper quantitative examination of spatial variability, it is important to differentiate between parameter estimate uncertainty, model parameterization effects, and actual spatial variability.