Miracle-dz/UniFAR-FTUs huggingface dataset:
Receiver function method in reflection seismology

The receiver function method was originally developed to analyse earthquake data recorded by multicomponent (3C) sensors and consists in deconvolving the horizontal component by the vertical component. The deconvolution process removes travel path effects from the source to the base of the target as well as the earthquake source signature. In addition, it provides the possibility of separating the emergent P and PS waves based on adaptive subtraction between recorded components if plane waves of constant ray parameters are considered. The resulting receiver function signal is the local PS wave's impulse response generated at impedance contrasts below the 3C receiver.We propose to adapt this technique to the wide‐angle multi‐component reflection acquisition geometry. We focus on the simplest case of land data reflection acquisition. Our adapted version of the receiver function approach consists in a multi‐step procedure that first removes the P wavefield recorded on the horizontal component and next removes the source signature. The separation step is performed in the τ−p domain while the source designature can be achieved in either the τ−p or the t−x domain. Our technique does not require any a priori knowledge of the subsurface. The resulting receiver function is a pure PS‐wave reflectivity response, which can be used for amplitude versus slowness or offset analysis. Stack of the receiver function leads to a high‐quality S wave image.
Hypothalamic tanycytes—masters and servants of metabolic, neuroendocrine, and neurogenic functions

There is a resurgent interest in tanycytes, a radial glial-like cell population occupying the floor and ventro-lateral walls of the third ventricle (3V). Tanycytes reside in close proximity to hypothalamic neuronal nuclei that regulate appetite and energy expenditure, with a subset sending projections into these nuclei. Moreover, tanycytes are exposed to 3V cerebrospinal fluid and have privileged access to plasma metabolites and hormones, through fenestrated capillaries. Indeed, some tanycytes act as conduits for trafficking of these molecules into the brain parenchyma. Tanycytes can also act as neural stem/progenitor cells, supplying the postnatal and adult hypothalamus with new neurons. Collectively, these findings suggest that tanycytes regulate and integrate important trophic and metabolic processes and possibly endow functional malleability to neuronal circuits of the hypothalamus. Hence, manipulation of tanycyte biology could provide a valuable tool for modulating hypothalamic functions such as energy uptake and expenditure in order to tackle prevalent eating disorders such as obesity and anorexia.
Blinking Phase-Change Nanocapsules Enable Background-Free Ultrasound Imaging

Microbubbles are widely used as contrast agents to improve the diagnostic capability of conventional, highly speckled, low-contrast ultrasound imaging. However, while microbubbles can be used for molecular imaging, these agents are limited to the vascular space due to their large size (> 1 μm). Smaller microbubbles are desired but their ultrasound visualization is limited due to lower echogenicity or higher resonant frequencies. Here we present nanometer scale, phase changing, blinking nanocapsules (BLInCs), which can be repeatedly optically triggered to provide transient contrast and enable background-free ultrasound imaging. In response to irradiation by near-infrared laser pulses, the BLInCs undergo cycles of rapid vaporization followed by recondensation into their native liquid state at body temperature. High frame rate ultrasound imaging measures the dynamic echogenicity changes associated with these controllable, periodic phase transitions. Using a newly developed image processing algorithm, the blinking particles are distinguished from tissue, providing a background-free image of the BLInCs while the underlying B-mode ultrasound image is used as an anatomical reference of the tissue. We demonstrate the function of BLInCs and the associated imaging technique in a tissue-mimicking phantom and in vivo for the identification of the sentinel lymph node. Our studies indicate that BLInCs may become a powerful tool to identify biological targets using a conventional ultrasound imaging system.
Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation

Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother’s old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother’s old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington’s genetic assimilation. Our model is able to quantify the evolution of the assimilation because it characterizes the fitness consequences of variation.
Oil-Spill Pollution Remote Sensing by Synthetic Aperture Radar

Oil-spill, one of the major marine ecological disasters, can result in enormous damage to the marine environment and great difficulties to clean-up operations. In 2002, oil leaked from the sunken tanker Prestige off the coast of Galicia, polluted thousands of kilometers’ coastline. In April 2010, the explosion of British Petrol’s drilling rig Deepwater Horizion (DWH) in Mexico Gulf caused the largest accidental oil-spill throughout history. During 87 days of oil leaking from a sea–floor gusher, approximately 780,000 m3 of oil, methane or other petro products was flowed into the Atlantic Ocean. In 2011, Bohai Sea, oil-spill was caused by the crack of submarine fault, triggered by the over pressure caused by oil extraction operation of Conoco‐ phillips Petro, China. Approximately 700 barrels of crude oil was leaked into the sea, and there were also about 2500 barrels of mineral oil-based mud deposited on the sea bed. Besides, a large proportion of oil-spills were caused by deliberate discharges form tankers or cargos, for the reason that there are still some vessels used to clean their tanks or engines before entering into the harbor. All these accidents and illegal acts caused huge damage to the costal ecosystem and marine environment. As a result, early warning of oil-spill accidents by remote sensing is very important for costal environmental protection and has become a vital task for maritime surveillance.
Terahertz analysis of stratified wall plaster at buildings of cultural importance across Europe

Terahertz (THz) radiation is being developed as a tool for the analysis of cultural heritage, and due to recent advances in technology is now available commercially in systems which can be deployed for field analysis. The radiation is capable of penetrating up to one centimetre of wall plaster and is delivered in ultrafast pulses which are reflected from layers within this region. The technique is non-contact, non-invasive and non-destructive. While sub-surface radar is able to penetrate over a metre of wall plaster, producing details of internal structures, infrared and ultraviolet techniques produce information about the surface layers of wall plaster. THz radiation is able to provide information about the interim region of up to approximately one centimetre into the wall surface. Data from Chartres Cathedral, France, Riga Dome Cathedral, Latvia, and Chartreuse du Val de Bénédiction, France is presented each with different research questions. The presence of sub-surface paint layers was expected from documentary evidence, dating to the 13th Century, at Chartres Cathedral. In contrast, at the Riga Dome Cathedral surface painting had been obscured as recently as 1941 during the Russian occupation of Latvia using white lead-based paint. In the 13th Century, wall paintings at the Chapel of the Frescos, Chartreuse du Val de Benediction in Villeneuve les Avignon were constructed using sinopia under-painting on plaster covering uneven stonework. This paper compares and contrasts the ability of THz radiation to provide information about sub-surface features in churches and Cathedrals across Europe by analysing depth based profiles gained from the reflected signal.
Formulation of a cattle feed from co-products of the sugarcane industry of Sri Lanka.

G. CHANDRASENA, A.P. KEERTHIPALA, V.P. JAYAWARDENA, W.A.M.J.S.B. ABEYSINGHE and A. NIMAL PERERA Sugarcane Research Institute, Uda Walawe, Sri Lanka. Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Sri Lanka. sri@bellmail.lk
Usefulness of two SCAR markers for marker-assisted selection of seedless grapevine cultivars

A PCR-specific marker, SCP18, was developed from a RAPD marker linked to a major locus involved in seedlessness, sdI . A preliminary study of the usefulness of SCP18 and SCC8 (a marker linked to sdI previously developed by LAHOGUE et al. 1998) for the marker assisted selection of seedless varieties was realized using various strategies: a posteriori test in seedless x seedless and seeded x seeded progenies and test of their allelic diversity in a set of 81 seedless and seeded varieties. In contrast to SCP18, SSC8 was found to be a useful marker at least in the seedless x seedless progenies and to show a good linkage disequilibrium with seedlessness in our set of varieties.
Earthquake Forecasting System Based on Sequential Data Assimilation of Slip on the Plate Boundary

We are constructing an earthquake forecasting system based on sequential data assimilation of the slip on the plate boundary. We use SIS, a kind of particle ﬁlter for the data assimilation. The forward calculation is done using earthquake generation cycle simulation. From the simulation results, we estimate crustal deformation that can be compared to the observation of GEONET on land and DONET on the seaﬂoor. We demonstrate numerical test of this system using synthetic data of seaﬂoor deformation before virtual Tonankai or Nankai earthquakes. We also use real data set of GEONET to compare the results of earthquake generation cycles.
OpenCL-Based Mobile GPGPU Benchmarking: Methods and Challenges

Benchmarking general-purpose computing on graphics processing unit (GPGPU) aims to profile and compare performance across different devices. Due to the low-level nature of most GPGPU APIs, GPGPU benchmarks are also useful for architectural exploration and program optimization. This can be challenging in mobile devices due to lack of underlying hardware details and limited profiling capabilities in some platforms. Measuring the performance of mobile GPU by executing benchmarks covering major hardware and software features can reveal the strength and weakness of a GPGPU system, enable better program optimization and make automatic performance tuning possible. In this paper, we will describe several design methods of OpenCL-based mobile GPGPU benchmarking, and discuss key issues that one may encounter during development. We will also present design tips and guidelines to achieve more "fair" and accurate benchmarking results.
A Thorough Accuracy Estimation of DTM Produced From Airborne Full-Waveform Laser Scanning Data of Unmanaged Eucalypt Plantations

A digital terrain model (DTM) is needed to extract forest variables. Its accuracy affects that of these variables, and thus it has to be known. Airborne laser scanning (ALS) is being increasingly used to produce DTM. The potential of full-waveform ALS (FWALS), however, for DTM production in forest areas has not been thoroughly evaluated, particularly under adverse conditions of heterogeneous forest stands, such as the typically extensively managed eucalypt plantations of north-central Portugal studied here. In the study area of 900 ha, an exhaustive assessment of FWALS-derived DTM accuracy was carried out based on the field survey of 43 plots. In each of these circular plots of roughly 400 m2, the coordinates were measured for all trees and all prominent terrain points using Global Navigation Satellite Systems receivers and total station. In addition, the quality of the FWALS data was assessed by surveying 1 m × 1 m grids of points on three bare areas. The accuracy assessment measures are computed by assuming normal and nonnormal distributions of the differences between the h values of FWALS terrain points and those of control points at the same planimetric locations. While the accuracy of the FWALS data is as expected, around 3 cm, that of the DTM of the forested area exceeds expectations. In fact, the DTM accuracy of 12 cm is higher than that obtained in prior ALS studies carried out in less adverse conditions than those studied here. Thus, the current FWALS-based methodology to derive DTM appears highly suitable to extracting forest variables.
Phenotype Switching in Melanoma: Implications for Progression and Therapy

Epithelial–mesenchymal transition (EMT) is a key process associated with the progression of epithelial cancers to metastatic disease. In melanoma, a similar process of phenotype switching has been reported and EMT-related genes have been implicated in promotion to a metastatic state. This review examines recent research on the role of signaling pathways and transcription factors regulating EMT-like processes in melanoma and their association with response to therapy in patients, especially response to BRAF inhibition, which is initially effective but limited by development of resistance and subsequent progression. We highlight studies implicating specific roles of various receptor tyrosine kinases (RTKs) in advancing melanoma progression by conferring a proliferative advantage and through promoting invasive phenotypes and metastasis. We also review the current knowledge of the mechanisms underlying resistance to BRAF inhibition and the potential role of melanoma phenotype switching in this process. In particular, we discuss how these important new insights may significantly enhance our ability to predict patterns of melanoma progression during treatment, and may facilitate rational development of combination therapies in the future.
Modulation of intercellular communication in macrophages: possible interactions between GAP junctions and P2 receptors

Gap junctions are connexin-formed channels that play an important role in intercellular communication in most cell types. In the immune system, specifically in macrophages, the expression of connexins and the establishment of functional gap junctions are still controversial issues. Macrophages express P2X7 receptors that, once activated by the binding of extracellular ATP, lead to the opening of transmembrane pores permeable to molecules of up to 900 Da. There is evidence suggesting an interplay between gap junctions and P2 receptors in different cell systems. Thus, we used ATP-sensitive and -insensitive J774.G8 macrophage cell lines to investigate this interplay. To study junctional communication in J774-macrophage-like cells, we assessed cell-to-cell communication by microinjecting Lucifer Yellow. Confluent cultures of ATP-sensitive J774 cells (ATP-s cells) are coupled, whereas ATP-insensitive J774 cells (ATP-i cells), derived by overexposing J774 cells to extracellular ATP until they do not display the phenomenon of ATP-induced permeabilization, are essentially uncoupled. Western-blot and reverse-transcription polymerase chain reaction assays revealed that ATP-s and ATP-i cells express connexin43 (Cx43), whereas only ATP-s cells express the P2X7 receptor. Accordingly, ATP-i cells did not display any detectable ATP-induced current under whole-cell patch-clamp recordings. Using immunofluorescence microscopy, Cx43 reactivity was found at the cell surface and in regions of cell-cell contact of ATP-s cells, whereas, in ATP-i cells, Cx43 immunoreactivity was only present in cytosolic compartments. Using confocal microscopy, it is shown here that, in ATP-s cells as well as in peritoneal macrophages, Cx43 and P2X7 receptors are co-localized to the membrane of ATP-s cells and peritoneal macrophages.
Consensus for multi-agent systems with random link failures

This paper investigates the second-order consensus problem for multi-agent systems with random link failures between each agent. The discrete-time multi-agent systems are described by the second-order dynamics, and the communication network is assumed to be directed with fixed topology. Since each link between the agents can be subject to failure with a certain probability, the control protocol is designed by considering the random link failures. The random link failures are presented by a Bernoulli probability sequence, that is, the control protocol for failure occurrence is designed by using the one step previous data that is sent by its neighbors' agents. The control protocol for second-order multi-agent systems is designed by using Lyapunov method. The mean square stability is shown for leaderless and leader-following multi-agent systems in terms of a set of linear matrix inequality (LMI), and some simulation results are provided to verify the effectiveness of the proposed methods.
A New Evolutionary Algorithm Based on Decomposition for Multi-Objective Optimization Problems

For multi-objective optimization problems (MOPs), the diversity of obtained solutions is of great importance for multi-objective evolutionary algorithms (MOEAs). To this end, in this paper, a new MOEA based on decomposition of a MOP into a number of constrained single-objective sub-problems (MOEA/D-MCS) is proposed. A MOP is firstly decomposed into a set of simple single-objective optimization sub-problems, and the objective space of the MOP is also decomposed into some number of sub-objective spaces. Then, each sub-objective space is considered as the feasible region of the corresponding single-objective problem. For each sub-problem, solutions of the feasible region are better than solutions of the infeasible region, which can maintain quite well the diversity of obtained solutions. Moreover, MOEA/D-MCS compares with MOEA/D UMOEA/D, GDRE3 d NSGAIII on six multi-objective benchmark functions. Simulation results show that the proposed algorithm is able to obtain a set of solutions with better diversity and convergence.
Automatic Support for Usability Evaluation

The main goal of the work is to propose a method to evaluate user interfaces using task models and logs generated from a user test of an application. The method can be incorporated into an automatic tool which gives the designer information useful to evaluate and improve the user interface. These results include an analysis of the tasks which have been accomplished, those which failed and those never tried, user errors and their type, time related information, task patterns among the accomplished tasks, and the available tasks from the current state of the user session. This information is also useful to an evaluator checking whether the specified usability goals have been accomplished.
View context based 2D sketch-3D model alignment

2D sketch-3D model alignment is important for many applications such as sketch-based 3D model retrieval, sketch-based 3D modeling as well as model-based vision and recognition. In this paper, we propose a 2D sketch-3D model alignment algorithm using view context and shape context matching. A sketch consists of a set of curves. A 3D model is typically a 3D triangle mesh. It includes two main steps: precomputation and actual alignment. In the precomputation, we extract the view context features of a set of sample views for a 3D model to be aligned. To speed up the precomputation, two computationally efficient and rotation-invariant features, Zernike moments and Fourier descriptors are used to represent a view. In the actual alignment, we prune most sample views which are dissimilar to the sketch very quickly based on their view context similarities. Finally, to find an approximate pose, we only compare the sketch with a very small portion (e.g. 5% in our experiments) of the sample views based on shape context matching. Experiments on two types of datasets show that the algorithm can align 2D sketches with 3D models approximately.
Fundoplication eliminates chronic cough due to non-acid reflux identified by impedance pH monitoring

The symptoms of extra-oesophageal gastro-oesophageal reflux disease (GORD) (such as chronic cough and hoarseness) are traditionally more difficult to treat than typical GORD symptoms (heartburn and regurgitation). Patients with extra-oesophageal manifestations may require longer and higher doses of acid suppressive therapy. In patients not responding to acid suppressive therapy the physician faces a dilemma as to whether the symptoms are due to ongoing acid reflux, non-acid reflux, or not associated with reflux. We report the case of a 45 year old woman with a history of a chronic cough referred for fundoplication after documenting her symptoms were associated with non-acid reflux using multichannel intraluminal impedance and pH (MII-pH).
Mechanism Design for Cost Optimal PAC Learning in the Presence of Strategic Noisy Annotators

We consider the problem of Probably Approximate Correct (PAC) learning of a binary classifier from noisy labeled examples acquired from multiple annotators (each characterized by a respective classification noise rate). First, we consider the complete information scenario, where the learner knows the noise rates of all the annotators. For this scenario, we derive sample complexity bound for the Minimum Disagreement Algorithm (MDA) on the number of labeled examples to be obtained from each annotator. Next, we consider the incomplete information scenario, where each annotator is strategic and holds the respective noise rate as a private information. For this scenario, we design a cost optimal procurement auction mechanism along the lines of Myer-son's optimal auction design framework in a non-trivial manner. This mechanism satisfies incentive compatibility property, thereby facilitating the learner to elicit true noise rates of all the annotators.