Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling radiative transfer in molecular clouds. 1: HCO(+) in the star-forming region W49A North

A new general multilevel, non-Local Thermodynamic Equilibrium (LTE) radiative transfer code, valid for any velocity field, is applied to HCO(+) observations of W49A North. Three classes of collapse models are considered: free-fall collapse (v proportional to 1/sq. root of r), rho proportional to r(exp -3/2) throughout the molecular cloud, successfully reproduces the features of the observations and gives the best fit to the J = 1-0 and J = 3-2 profiles both toward the prominent H II component G of W49A North and off the center. In addition to a slow radial fall-off of density, the theoretical modeling implies the following for the molecular cloud: the large line widths result from motions occurring within the inner 1 pc, and there are probably one or more fragments with peculiar velocities within this same region.
Shear rheology of a cell monolayer

We report a systematic investigation of the mechanical properties of fibroblast cells using a novel cell monolayer rheology (CMR) technique. The new technique provides quantitative rheological parameters averaged over ∼106 cells making the experiments highly reproducible. Using this method, we are able to explore a broad range of cell responses not accessible using other present day techniques. We perform harmonic oscillation experiments and step shear or step stress experiments to reveal different viscoelastic regimes. The evolution of the live cells under externally imposed cyclic loading and unloading is also studied. Remarkably, the initially nonlinear response becomes linear at long timescales as well as at large amplitudes. Within the explored rates, nonlinear behaviour is only revealed by the effect of a nonzero average stress on the response to small, fast deformations. When the cell cytoskeletal crosslinks are made permanent using a fixing agent, the large amplitude linear response disappears and the cells exhibit a stress stiffening response instead. This result shows that the dynamic nature of the cross-links and/or filaments is responsible for the linear stress-strain response seen under large deformations. We rule out the involvement of myosin motors in this using the inhibitor drug blebbistatin. These experiments provide a broad framework for understanding the mechanical responses of the cortical actin cytoskeleton of fibroblasts to different imposed mechanical stimuli.
Integrative Analysis Identified CD38 As a Key Node That Correlates Highly with Immunophenotype, Chemoradiotherapy Resistance, And Prognosis of Head and Neck Cancer

Head and neck cancer (HNC) is mainly treated by surgery, radiotherapy, and adjuvant chemotherapy; however, the prognosis of some patients with HNC is poor because of radiotherapy and chemotherapy resistance. In recent years, anti‑PD‑1 monoclonal antibodies have shown certain efficacy, and a change of the tumor immune microenvironment is the main reason for the failure of HNC immunotherapy. The present study aimed to identify and verify that CD38, which is closely related to the prognosis of HNC, is a potential biological marker of radiotherapy and chemotherapy resistance and PD-L1 immunotherapy resistance via a comprehensive bioinformatic analysis in The Cancer Genome Atlas and Gene Expression Omnibus databases. According to the UALCAN database, the transcript level of CD38 in HNC was analyzed using cluster analysis, and the expression of CD38 mRNA in HNC was detected using the Oncomine database. The characteristics of CD38-related oncogenes were identified by gene cluster enrichment analysis in LinkedOmics. The R2 and SEER databases were used to further evaluate the prognostic significance of the CD38 gene in HNC using receiver operating characteristic curve analysis of Kaplan-Meier (KM) survival and the clinical characteristics of the subjects. The protein-protein interaction network of the top 50 genes showing significant positive correlations with CD38 in HNC was analyzed using STRING. Finally, we used a nasopharyngeal carcinoma (NPC) cell line to verify the biological function. The results showed that the levels of CD38 mRNA expression in patients with HNC were significantly higher than those in healthy controls. The levels of CD38 mRNA expression in patients with HNC of different ages, sexes, and races were significantly higher than those in the healthy controls. CD38 is an independent prognostic factor for HNC, and high expression of CD38 indicates poor prognosis. CD38 expression correlated positively with the markers of many kinds of immune cells, and correlated significantly with the expression of PD-L1. We found that the high expression of CD38 suggested a poor prognosis in the subgroup of tumors treated with chemotherapeutic drugs in the G1/S phase. We used HNC cell lines to verify that the high expression of CD38 promoted the proliferation of NPC cells and produced radiotherapy tolerance. Through comprehensive bioinformatics analysis, we suggested that CD38 is a key gene involved in radiotherapy, chemotherapy, and immune drug resistance in HNC. This study provides a reliable biomarker to predict the prognosis of patients with HNC and a reference for clinical comprehensive treatment of HNC. Individualization combined with CD38 monoclonal antibodies might provide a promising treatment strategy for this fatal disease, and this comprehensive treatment might reduce the damage to normal tissue and improve the prognosis and quality of life of patients with HNC.
Assimilation of radar and satellite data in mesoscale models: A physical initialization scheme

The quality of numerical precipitation prediction depends on the accuracy with which the model reproduces the true initial state of the atmosphere prior to the fo recast. Typically a numerical model needs a spin-up time of several hours until its hydrological cycle is establ ished. Assimilation of precipitation data can reduce the spin-up time significantly and consequently opens the po ssibility of nowcasting with Numerical Weather Prediction (NWP) models. We further enhanced the physical i nitialisation scheme (PIB, Physical Initialisation Bonn) by HAASE (2002) in order to improve quantitative precipitation nowc asting with a high-resolution NWP model. The assimilation scheme takes as input a radar bas ed precipitation product and a cloud top height field retrieved from satellite observations. During the assimilation window, PIB adjusts the vertical wind, humidity, cloud water, and cloud ice to force the model state towards the measurements. The most distinctive feature of the algorithm is the adjustment of th e vertical wind profile in the framework of a simple precipitation generation scheme. In this paper, we present an identical twin experiment, which reveals how the model variables are adjusted during the assimilation windo w, and which demonstrates the consistency of PIB with the physics of the NWP model. Three case studies with rea l m surements demonstrate that the scheme improves the forecast of the precipitation patterns, as wel l as the dynamics of the events. These improvements are found both during the assimilation window and for the firs t hours of the free forecast.
Interaction between Nanoparticles, Membranes and Proteins: A Surface Plasmon Resonance Study

Regardless of the promising use of nanoparticles (NPs) in biomedical applications, several toxic effects have increased the concerns about the safety of these nanomaterials. Although the pathways for NPs toxicity are diverse and dependent upon many parameters such as the nature of the nanoparticle and the biochemical environment, numerous studies have provided evidence that direct contact between NPs and biomolecules or cell membranes leads to cell inactivation or damage and may be a primary mechanism for cytotoxicity. In such a context, this work focused on developing a fast and accurate method to characterize the interaction between NPs, proteins and lipidic membranes by surface plasmon resonance imaging (SPRi) technique. The interaction of gold NPs with mimetic membranes was evaluated by monitoring the variation of reflectivity after several consecutive gold NPs injections on the lipidic membranes prepared on the SPRi biochip. The interaction on the membranes with varied lipidic composition was compared regarding the total surface concentration density of gold NPs adsorbed on them. Then, the interaction of gold and silver NPs with blood proteins was analyzed regarding their kinetic profile of the association/dissociation and dissociation constants (koff). The surface concentration density on the membrane composed of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine and cholesterol (POPC/cholesterol) was 2.5 times higher than the value found after the injections of gold NPs on POPC only or with dimethyldioctadecylammonium (POPC/DDAB). Regarding the proteins, gold NPs showed preferential binding to fibrinogen resulting in a value of the variation of reflectivity that was 8 times higher than the value found for the other proteins. Differently, silver NPs showed similar interaction on all the tested proteins but with a variation of reflectivity on immunoglobulin G (IgG) 2 times higher than the value found for the other tested proteins.
Tropical Cyclogenesis Associated with Rossby Wave Energy Dispersion of a Preexisting Typhoon. Part I: Satellite Data Analyses*

The structure and evolution characteristics of Rossby wave trains induced by tropical cyclone (TC) energy dispersion are revealed based on the Quick Scatterometer (QuikSCAT) and Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) data. Among 34 cyclogenesis cases analyzed in the western North Pacific during 2000–01 typhoon seasons, six cases are associated with the Rossby wave energy dispersion of a preexisting TC. The wave trains are oriented in a northwest–southeast direction, with alternating cyclonic and anticyclonic vorticity circulation. A typical wavelength of the wave train is about 2500 km. The TC genesis is observed in the cyclonic circulation region of the wave train, possibly through a scale contraction process. The satellite data analyses reveal that not all TCs have a Rossby wave train in their wakes. The occur- rence of the Rossby wave train depends to a certain extent on the TC intensity and the background flow. Whether or not a Rossby wave train can finally lead to cyclogenesis depends on large-scale dynamic and thermodynamic conditions related to both the change of the seasonal mean state and the phase of the tropical intraseasonal oscillation. Stronger low-level convergence and cyclonic vorticity, weaker vertical shear, and greater midtropospheric moisture are among the favorable large-scale conditions. The rebuilding process of a conditional unstable stratification is important in regulating the frequency of TC genesis.
Extraction of centre line from curvilinear objects

This tutorial paper surveys three methods designed to detect the centre line in curvilinear structures. These are the iterative thinning, Steger’s and derivatives’ methods. We aim to illustrate the effectivness of the chosen methods for processing laser-trace images and magnetic resonance slices of human head. The essence of each three methods is presented and important parameters are discussed. Experiments have been carried out and results are discussed in the light of the quality of the centre line produced and work time of all three methods.
Variational motion segmentation based on discontinuity-preserving optical flow estimation

In this paper, a variational method for motion segmentation has been proposed, which is realized by first estimate discontinuity-preserving optical flow field and then segmenting. Specifically, the complementarity between estimation and segmentation was emphasized, so two main improvements were presented: firstly, a segmentation-oriented diffusion tensor has been suggested in the optical flow model, which combines the image and flow information and determine the boundaries more effectively; Secondly, according to the characteristic of vector field, a motion segmentation model with considerations of both motion boundaries and region information were established. The results were illustrated with examples of sequence images which show the usefulness of the proposed approach for various problems.
Characteristics of noise and resolution on image reconstruction in cone-beam computed tomography

The cone-beam computed tomography (CBCT) is a useful modality in diagnostic imaging due to the properties of fast volume coverage, lower radiation dose, easy hardware implementation, and higher spatial resolution. Recently, attention is being paid to address the noise and resolution relationship for CBCT. In CBCT system, image noise and spatial resolution play important roles in image quality. However, there has not been done many works for evaluating the relationship of image noise and the spatial resolution in CBCT. In this study, we evaluated the image noise and spatial resolution as a function of filter, number of projections, and voxel size on reconstructed images in CBCT. The simulated projection data of Catphan 600 phantom were reconstructed using the FDK algorithm. To evaluate the image noise and spatial resolution, the coefficient of variation (COV) of attenuation coefficient and the modulation transfer function (MTF) in axial images were calculated, respectively. The filters used for reconstruction were Ram-lak, Shepp-logan, Cosine, Hamming, and Hann. A number of projections were 161, 321, 481 and 642 acquired from scanning of 360 degree and the voxels with sizes of 0.10 mm, 0.15 mm, 0.20 mm, 0.25 mm and 0.30 mm were used. The image noise given by Hann filter was the lowest and decreased as functions of number of projections and voxel size. The spatial resolution given by Ram-lak filter was the highest and increased as a function of number of projections, decreased as a function of voxel size. The results of this study show the relationship of image noise and spatial resolution in CBCT and the characteristics of reconstruction factors for trade-off between the image noise and spatial resolution. It can also provide information of image noise and spatial resolution for adaptive image.
A simple formula to calculate the x-ray flux after a double-crystal monochromator

We present a very simple formula for calculating the total number of photons of an x-ray beam after being monochromatized by a double crystal monochromator. This is a typical case for most synchrotron radiation beamlines. The derivation of the formula and its numerical benchmarking by ray-tracing simulations are also presented.
Data Augmentation and Dynamic Linear Models

We define a subclass of dynamic linear models with unknown hyperparameters called d-inverse-gamma models. We then approximate the marginal p.d. f.s of the hyperparameter and the state vector by the data augmentation algorithm of Tanner/Wong. We prove that the regularity conditions for convergence hold. A sampling based scheme for practical implementation is discussed. Finally, we illustrate how to obtain an iterative importance sampling estimate of the model likelihood. (author's abstract)
A Proportional Hazards Model for the Subdistribution of a Competing Risk

Abstract With explanatory covariates, the standard analysis for competing risks data involves modeling the cause-specific hazard functions via a proportional hazards assumption. Unfortunately, the cause-specific hazard function does not have a direct interpretation in terms of survival probabilities for the particular failure type. In recent years many clinicians have begun using the cumulative incidence function, the marginal failure probabilities for a particular cause, which is intuitively appealing and more easily explained to the nonstatistician. The cumulative incidence is especially relevant in cost-effectiveness analyses in which the survival probabilities are needed to determine treatment utility. Previously, authors have considered methods for combining estimates of the cause-specific hazard functions under the proportional hazards formulation. However, these methods do not allow the analyst to directly assess the effect of a covariate on the marginal probability function. In this article we pro.
A new dynamic-grooming algorithm for IP over WDM optical networks

Efficiently grooming low-rate traffic flows into high-capacity lightpaths will improve the network throughput and resource utilization. In this paper, we study the traffic -grooming algorithm for WDM mesh networks. A novel dynamic grooming graph is proposed, which models the number of transceivers per node and the number of wavelength per fiber in addition to the combined information of IP layer and WDM layer, while taking into account the constraints of wavelength continuity in optical domain. Based on the grooming graph, a new dynamic traffic-grooming algorithm, namely Integrated Grooming Algorithm (IGA), is developed to provide an efficient solution to the traffic-grooming problem in WDM optical mesh networks. This algorithm is evaluated via simulations and results reveal that satisfactory performance of the proposed algorithms can be achieved.
OPTIMIZATION OF A MICROSTRIP ANTENNA WITH A GENETIC ALGORITHM FOR USE AS A GROUND PENETRATING RADAR

In this paper we present an optimization technique for microstrip antennas based on combining a genetic algorithm (GA) and a Mixed Potential based Method of Moments technique. The GA optimizes the shape of the metallisation pattern in order to obtain a specific frequency response. Recalculation of the MoM interaction matrix for each individual in the GA is avoided. The technique is applied to design a broad-band antenna which can be used as a Ground Penetrating Radar. In order to detect the 'Vampire Signature' of the buried objects and in order to minimize the effect of ground reflections at the ground air interface, an antenna which detects cross-polarization is used. It is shown by measurements on the designed antenna that the optimization procedure is able to significantly reduce the return loss in a wide frequency band. The broadband characteristics of the antenna proved to be sufficient to detect buried objects and their vampire signature.
SPH without a Tensile Instability

The tensile instability in smoothed particle hydrodynamics results in a clustering of smoothed particle hydrodynamics (SPH) particles. The clustering is particularly noticeable in materials which have an equation of state which can give rise to negative pressures, but it can occur in gases where the pressure is always positive and in magnetohydrodynamics (MHD) problems. It is a particular problem in solid body computations where the instability may corrupt physical fragmentation by numerical fragmentation which, in some cases, is so severe that the dynamics of the system is completely wrong. In this paper it is shown how the instability can be removed by using an artificial stress which, in the case of fluids, is an artificial pressure. The method is analyzed by examining the dispersion relation for small oscillations in a fluid with a stiff equation of state. The short and long wavelength limits of the dispersion relation indicate appropriate parameters for the artificial pressure and, with these parameters, the errors in the long wavelength limit are small. Numerical studies of the dispersion relation for a wide range of parameters confirm the approximate analytical results for the dispersion relation. Applications to several test problems show that the artificial stress works effectively. These problems include the evolution of a region with negative pressure, extreme expansion in one dimension, and the collision of rubber cylinders. To study this latter problem the artificial pressure is generalized to an artificial stress. The results agree well with the calculations of other stable codes.
CCD mosaic images of the supernova remnant 3C 400.2

We have constructed CCD mosaic images of the old Galactic supernova remnant 3C 400.2 in lines of H-alpha + forbidden N II, forbidden S II, and forbidden O III, plus a continuum band. These are the first CCD images covering the full extent of this remnant, and they reveal significantly more nebulosity than the deepest photographic plates. Comparison with radio and X-ray images indicates dramatically different morphology in the three regimes. The optical images both in H-alpha + forbidden N II and in forbidden S II show an almost complete, irregular shell of emission, with a diameter of about 16 arcmin, little over half that of the radio shell, while the X-ray structure is a centrally peaked ellipsoid. Approximate values for optical line fluxes are obtained; we estimate L(H-alpha) about 3 x 10 exp 35 ergs/s, roughly three times the X-ray luminosity. We also report a previously uncataloged planetary nebula southwest of 3C 400.2.
Inspection and Correction Error in Data Processing

Abstract It is common practice to assume that inspectors of sample items and correctors of items in rejected work lots carry out their job without error and invariably classify defectives and nondefectives correctly. This assumption does not agree with experience in data processing activities, especially those requiring interpretation and judgment as well as clerical or machine skills. This paper emphasizes the error of classifying defectives as nondefectives (Type II) made by inspectors called “verifiers” and by correctors to prepare data for machine readability. The following activities are included: (1) verification of card punching, (2) proofreading of typed data, (3) verification of codes clerically assigned to written responses on questionnaires, (4) matching of codes assigned independently by three coders to the same item, and (5) proofreading of the output of special typing combined with coding and rounding figures for input to optical scanning.
High current-induced degradation of AlGaN ultraviolet light emitting diodes

Degradation under high current stress of AlGaN quantum well based light emitting diodes emitting at 285 and 310 nm has been studied using electroluminescence, time-resolved photoluminescence and current-voltage experimental techniques. The measurements have revealed that during aging decrease of the emission intensity is accompanied by increase of the tunneling current, increase of the nitrogen vacancy concentration and partial compensation of the p-doping. The main role in the device degradation has been ascribed to formation of tunneling conductivity channels, probably, via activation of the closed core screw dislocations with the help of nitrogen vacancies. Carrier lifetimes in the quantum wells and the p-cladding were found to be unaffected by the aging process, suggesting that the nonradiative recombination has a lesser influence on the device degradation.