Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of rural landscapes from low-density lidar data: is it theoretically possible?

Lidar technology has become an important data source in 3D terrain modelling. In Spain, the National Plan for Aerial Orthophotography will soon release public low-density lidar data (0.5–1 pulses/m2) for most of the country territory. Taking advantage of this fact, this article experimentally assesses the possibility of classifying a rural landscape into eight classes using multitemporal and multidensity lidar data and analyses the effect of point density on classification accuracy. Two statistical methods (transformed divergence and the Jeffries–Matusita distance) were used to assess the possibility of discriminating the eight classes and to determine which data layers were best suited for classification purposes. The results showed that ‘dirt road’ cannot be discriminated from ‘bare earth’ and that the possibility of discriminating ‘bare earth’, ‘pavement’, and ‘low vegetation’ decreases when using densities below 4 pulses/m2. Two non-parametric tests, the Kruskal–Wallis test and the Friedman test, were used to strengthen the results by assessing their statistical significance. According to the results of the Kruskal–Wallis test, lidar point density does not significantly affect the classification, whereas the results of the Friedman test show that bands could be considered as the only parameter affecting the possibility of discriminating some of the classes, such as ‘high vegetation’. Finally, the J48 algorithm was used to perform cross-validation in order to obtain the most familiar quantitative values in the international literature (e.g. overall accuracy). Mean overall accuracy was around 85% when the eight classes were considered and increased up to 95% when ‘dirt road’ was disregarded.
Ccn2a is an injury-induced matricellular factor that promotes cardiac regeneration in zebrafish

: The ability of zebrafish to heal their heart after injury makes them an attractive model for investigating the mechanisms governing the regenerative process. In this study, we show that the gene cellular communication network factor 2a (ccn2a), previously known as ctgfa, is induced in endocardial cells in the injured tissue and regulates CM proliferation and repopulation of the damaged tissue. We find that, whereas in wild-type animals, CMs track along the newly formed blood vessels that revascularize the injured tissue, in ccn2a mutants CM proliferation and repopulation are disrupted, despite apparently unaffected revascularization. In addition, we find that ccn2a overexpression enhances CM proliferation and improves the resolution of transient collagen deposition. Through loss- and gain-of-function as well as pharmacological approaches, we provide evidence that Ccn2a is necessary for and promotes heart regeneration by enhancing the expression of pro-regenerative extracellular matrix genes, and by inhibiting the chemokine receptor gene cxcr3.1 through a mechanism involving Tgf฀/pSmad3 signaling. Thus, Ccn2a positively modulates the innate regenerative response of the adult zebrafish heart. ABSTRACT The ability of zebrafish to heal their heart after injury makes them an attractive model for investigating the mechanisms governing the regenerative process. In this study, we show that the gene cellular communication network factor 2a ( ccn2a ), previously known as ctgfa , is induced in endocardial cells in the injured tissue and regulates CM proliferation and repopulation of the damaged tissue. We find that, whereas in wild-type animals, CMs track along the newly formed blood vessels that revascularize the injured tissue, in ccn2a mutants CM proliferation and repopulation are disrupted, despite apparently unaffected revascularization. In addition, we find that ccn2a overexpression enhances CM proliferation and improves the resolution of transient collagen deposition. Through loss- and gain-of-function as well as pharmacological approaches, we provide evidence that Ccn2a is necessary for and promotes heart regeneration by enhancing the expression of pro-regenerative extracellular matrix genes, and by inhibiting the chemokine receptor gene cxcr3.1 through a mechanism involving Tgf β /pSmad3 signaling. Thus, Ccn2a positively modulates the innate regenerative response of the adult zebrafish heart.
Mucosal Toll-like receptor 3-dependent synthesis of complement factor B and systemic complement activation in inflammatory bowel disease Short title: complement activation in IBD

1Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway, Department of Laboratory Medicine, Children and Women`s Health, Norwegian University of Science and Technology, Trondheim, Norway, Department of Gastroenterology and Hepatology, St. Olav`s University Hospital, Trondheim, Norway, Department of Pathology and Medical Genetics, St. Olav`s University Hospital, Trondheim, Department of Infectious Diseases, St. Olav`s University Hospital, Trondheim, Norway, Research Laboratory, Nordland Hospital, Bodø, University of Tromsø, Tromsø, Norway, Department of Immunology, Oslo University Hospital Rikshospitalet, and K.G. Jebsen IRC, University of Oslo, Oslo, Norway.
Ultrafast single-photon detection based on optical Kerr gates at GHz rates

The ultrafast detection of single photons is currently restricted by the limited time resolution (a few picoseconds) of the available single-photon detectors. Optical gates offer a faster time resolution, but so far they have been mostly applied to ensembles of emitters. Here, we demonstrate through a semi-analytical model that the ultrafast time-resolved detection of single quantum emitters can be possible using an optical-Kerr-shutter (OKS) at GHz rates under focused illumination. This technique provides sub-picosecond time resolution, while keeping a gate efficiency at around 85 \%. These findings lay the ground for future experimental investigations on the ultrafast dynamics of single quantum emitters, with implications for quantum nanophotonics and molecular physics
Principal component analysis applied to feature-oriented band ratios of hyperspectral data: A tool for vegetation studies

This paper presents a simple but effective method to identify and map the distribution of vegetation using hyperspectral data, which involves band ratios and principal component analysis (PCA). Using spectral data from the literature, we devised spectral indices focused on specific vegetation constituents (band positions are in nm): chlorophyll-a (461/422 and 807/638); chlorophyll-b (520/470 and 807/648); @-carotene (520/442); carotenoids (539/490 and 807/490); anthocyanin (510/530); phytochrome P730 (845/730), phytochrome P660 (778/658); lignin (1028/2101); cellulose (2211/2400); nitrogen (1731/1691); and leaf water content (1066/1452). In a second step, these indices were submitted to PCA. PCA eigenvector loadings were examined to decide which of the principal component (PC) images concentrate information directly related to the spectral signatures of specific vegetation constituents. An important aspect of this approach was that it predicted whether the target surface type would be highlighted by dark or bright pixels in the relevant PC image. Finally, the optimal PCs are selected and combined in a colour composite. In this study, we applied this method to atmospherically corrected Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data collected in the Alto Paraíso de Goiás (APG) region of central Brazil. The results from identifying and mapping the distribution of vegetation in the APG region were very encouraging. Photosynthetic and non-photosynthetic vegetation or a mixture of both were mapped on the basis of feature-oriented PC loadings. Discriminations between vegetation types were made, including identifying riparian forests, burn grasslands and resurgence zones, crops and several types of savannah and pastures.
Ebf Activates Expression of a Cholinergic Locus in a Multipolar Motor Ganglion Interneuron Subtype in Ciona

Conserved transcription factors termed “terminal selectors” regulate neuronal sub-type specification and differentiation through combinatorial transcriptional regulation of terminal differentiation genes. The unique combinations of terminal differentiation gene products in turn contribute to the functional identities of each neuron. One well-characterized terminal selector is COE (Collier/Olf/Ebf), which has been shown to activate cholinergic gene batteries in C. elegans motor neurons. However, its functions in other metazoans, particularly chordates, is less clear. Here we show that the sole COE ortholog in the non-vertebrate chordate Ciona robusta, Ebf, controls the expression of the cholinergic locus VAChT/ChAT in a single dorsal interneuron of the larval Motor Ganglion, which is presumed to be homologous to the vertebrate spinal cord. We propose that, while the function of Ebf as a regulator of cholinergic neuron identity conserved across bilaterians, its exact role may have diverged in different cholinergic neuron subtypes (e.g., interneurons vs. motor neurons) in chordate-specific motor circuits.
Four Decades of Progress in Monitoring and Modeling of Processes in the Soil-Plant- Atmosphere System: Applications and Challenges Characterization of the heterogeneous flow and pollutant transfer in the unsaturated zone in the fluvio-glacial deposit.

Infiltration basins are part of the best management practices. They are aimed at infiltrating stormwater to prevent additional collection and treatment through rainwater systems. In the suburbs of Lyon (France), many of these infiltration basins were built over fluvio-glacial deposit. These bhave been the subject of research programs on vadose zone flow and fate of pollutants. This study focuses on the impact of the heterogeneity of the fluvio-glacial deposit on both flow pattern and solute transfer. A proper geological and sedimentological description is first proposed to characterize the efficient water transfer properties of the fluvio-glacial deposit at the work scale (1 ha). The local geological and sedimentological architecture of the deposit and its lithofacies were investigated locally through trenches using both particle size analysis and sedimentological approach. This information was extended to the whole work by combining several geophysical techniques, i.e. GPR, electric resistivity and seismic refraction tomography (data not shown). Then water infiltration experiments were performed on each lithofacies to derive the hydrodynamic properties through BEST algorithm (Beerkan estimation of Soil Transfer properties), leading to the corresponding hydrofacies. In addition, soil-column and batch experiments were performed to estimate hydrodispersive parameters by tracer experiments and the geochemical properties of lithofacies for a model pollutant, copper (Cu). All these data were implemented into Hydrus to model flow and solute transfer through a 2D soil profile with a precise description of the hydrofacies at the basin scale (flow domain 14x2 m2). The results are highly relevant because they emphasize different types of preferential flow due to either the presence of capillary barriers, drainage layers or pipe flow, which may be responsible for the enhancement of pollutant transfer. In particular, they show that sand lenses may play an important role whereas unconnected gravels may have insignificant effect on flow. This methodology may help in understanding the mechanisms which that are responsible for preferential solute transfer. A sensitivity analysis combining the distribution of lithofacies, the soil initial water content and unsaturated hydraulic properties allows bettering understanding the development of preferential flows across the vadose zone underneath the basin. This data is of great interest in terms of the optimization of basin infiltration monitoring.
Ground Penetrating Radar (GPR) Data Enhancement Using Seismic Techniques

Ground penetrating radar (GPR) data from three sites are processed using seismic analysis techniques. Processing operations performed include: gain recovery, spiking deconvolution, bandpass filtering, velocity analysis, elevation and static corrections, NMO corrections, and f‐k migration. In the first example, we analyze 0.5 km lines of 50 MHz and 100 MHz, single‐fold data and a common receiver (CR) gather from the William River delta, Lake Athabasca, Saskatchewan. Next, a 100 MHz, single‐fold, 120 m line from the Slave River delta, Ft. Smith, N.W. T. is processed using the previous steps. Finally, 100 m of 100 MHz, single‐fold data (also with a CR gather) from Brigham City, Utah are analyzed.Filter bands chosen for the 50 MHz and 100 MHz data were 10/20–75/100 MHz and 20/30–150/180 MHz respectively. Velocity spectra for William River delta and Brigham City are based on CR gather velocity semblances and interpreted arrivals. Velocities range from 0.3 m/ns (air) to about 0.07 m/ns (wet sand). Dry sands at B.
Cox-nnet v2.0: improved neural-network based survival prediction extended to large-scale EMR dataset

Cox-nnet is a neural-network based prognosis prediction method, originally applied to genomics data. Here we propose the version 2 of Cox-nnet, with significant improvement on efficiency and interpretability, making it suitable to predict prognosis based on large-scale electronic medical records (EMR) datasets. We also add permutation-based feature importance scores and the direction of feature coefficients. Applying on an EMR dataset of OPTN kidney transplantation, Cox-nnet v2.0 reduces the training time of Cox-nnet up to 32 folds (n=10,000) and achieves better prediction accuracy than Cox-PH (p<0.05). Availability and implementation: Cox-nnet v2.0 is freely available to the public at this https URL
Simulation of Snow on Arctic Sea Ice Using a Coupled Snow–Ice Model

Abstract The new Recherche Prevision Numerique (NEW-RPN) model, a coupled system including a multilayer snow thermal model (SNTHERM) and the sea ice model currently used in the Meteorological Service of Canada (MSC) operational forecasting system, was evaluated in a one-dimensional mode using meteorological observations from the Surface Heat Budget of the Arctic Ocean (SHEBA)’s Pittsburgh site in the Arctic Ocean collected during 1997/98. Two parameters simulated by NEW-RPN (i.e., snow depth and ice thickness) are compared with SHEBA’s observations and with simulations from RPN, MSC’s current coupled system (the same sea ice model and a single-layer snow model). Results show that NEW-RPN exhibits better agreement for the timing of snow depletion and for ice thickness. The profiles of snow thermal conductivity in NEW-RPN show considerable variability across the snow layers, but the mean value (0.39 W m−1 K−1) is within the range of reported observations for SHEBA. This value is larger than 0.31 W m−1 K−1, .
Tectonic history from vitrinite reflectance

Summary. The degree of organic metamorphism of carbonaceous matter is expressed in terms of the reflectance of vitrinite. Vitrinite reflectance is a function of temperature and time. A model relating vitrinite reflectance to temperature and time is proposed from published vitrinite reflectance—temperature—time nomograms. A plot of the logarithm of vitrinite reflectance versus depth gives a linear curve (for vitrinite reflectance greater than 0.3 per cent) in a sedimentary basin which has had a constant geothermal gradient throughout its tectonic history; the geothermal gradient (°C km−1) is equal to the slope of the curve multiplied by 194.8. The model is also applied to sedimentary basins with decreasing geothermal gradient with time (i.e. cooling continental-margin basins). The vitrinite reflectance model is demonstrated to be consistent with observed reflectance data and tectonic information from the Sydney, Bowen-Surat and Gippsland basins in eastern Australia.
The overall plant-based diet index during pregnancy and risk of gestational diabetes mellitus: a prospective cohort study in China

Abstract The high overall plant-based diet index (PDI) is considered to protect against type 2 diabetes in the general population. However, whether the PDI affects gestational diabetes mellitus (GDM) risk among pregnant women is still unclear. We evaluated the association between PDI and GDM risk based on a Chinese large prospective cohort – the Tongji Maternal and Child Health Cohort. Dietary data were collected at 13–28 weeks of pregnancy by a validated semi-quantitative FFQ. The PDI was obtained by assigning plant food groups positive scores while assigning animal food groups reverse scores. GDM was diagnosed by a 75 g 2-h oral glucose tolerance test at 24–28 weeks of gestation. Logistic regression models were fitted to estimate OR of GDM, with associated 95 % CI, comparing women in different PDI quartiles. Among the total 2099 participants, 169 (8·1 %) were diagnosed with GDM. The PDI ranged from 21·0 to 52·0 with a median of 36·0 (interquartile range (IQR) 33·0–39·0). After adjusting for social-demographic characteristics and lifestyle factors etc., the participants with the highest quartile of PDI were associated with 57 % reduced odds of GDM compared with women in the lowest quartile of PDI (adjusted OR 0·43; 95 % CI 0·24, 0·77; P for trend = 0·005). An IQR increment in PDI was associated with 29 % decreased odds of GDM (adjusted OR 0·71; 95 % CI 0·56, 0·90). Findings suggest that adopting a plant-based diet during pregnancy could reduce GDM risk among Chinese women, which may be valuable for dietary counselling during pregnancy.
Design of an Instrumented Flat Dilatometer

To better understand the mechanics of the flat plate dilatometer expansion, a probe has been developed to measure the continuous pressure-displacement soil response during the test. This paper presents details of a specially designed Marchetti dilatometer with sensors to record the continuous displacement of the membrane, unload-reload cycles, the pore water pressure, the total pressure, and the penetration thrust. With minimal impact on the original blade design, the resulting instrumented dilatometer was tested at the University of Massachusetts-Amherst National Geotechnical Experimentation Site.
Predicting incident radiographic knee osteoarthritis in middle-aged women within 4 years

Objective Develop and internally validate risk models and a clinical risk score tool to predict incident radiographic knee osteoarthritis (RKOA) in middle-aged women. Methods We analysed 649 women in the Chingford 1000 Women study. The outcome was incident RKOA, defined as Kellgren/Lawrence grade 0-1 at baseline and ≥2 at year 5. We estimated predictors’ effects on the outcome using logistic regression models. Two models were generated. The clinical model considered patient characteristics, medication, biomarkers, and knee symptoms. The radiographic model considered the same factors, plus radiographic factors (e.g., angle between the acetabular roof and ilium’s vertical cortex (hip α-angle)). The models were internally validated. Model performance was assessed using calibration and discrimination (area under the receiver characteristic curve, AUC). Results The clinical model contained age, quadriceps circumference, and a cartilage degradation marker (CTX-II) as predictors (AUC = 0.692). The radiographic model contained older age, greater quadriceps circumference, knee pain, knee baseline Kellgren/Lawrence 1 (versus 0), greater hip α-angle, greater spinal bone mineral density, and contralateral RKOA at baseline as predictors (AUC = 0.797). Calibration tests showed good agreement between the observed and predicted incident RKOA. A clinical risk score tool was developed from the clinical model. Conclusion Two models predicting incident RKOA within 4 years were developed; including radiographic variables improved model performance. First-time predictor hip α-angle and contralateral RKOA suggest osteoarthritis origins beyond the knee. The clinical tool has the potential to help physicians identify patients at risk of RKOA in routine practice, but should be externally validated.
Extraction of Energy Resources—Exploitation of the Canadian Oil Sands

Considerable reserves of oil sands are located in northernAlberta. Exploitation of these reserves has been instrumental in the development of theAlbertaeconomy. Mining and processing techniques, including “in situ” processing and surface mining/aqueous treatment, are presented. Oil assisted flotation and solvent extraction are discussed as possible future processing alternatives. Subsequent froth treatment and refining methods are described. The rapid expansion of bitumen processing in theFort McMurrayarea has drastically affectedAlberta’s economic, political and social policy. Corresponding strain has been placed on the regional ecosystem. A comparison between wind and bitumen as sources of energy is offered.
Imperialism and Primitive Accumulation: Notes on the New Scramble for Africa

This article recuperates the links between imperialism and primitive accumulation, arguing that the two are inherently connected. It undertakes a review of the literature to show that the links are deeper than is often recognized, as in the work of David Harvey. It also maps the stages of imperialism, their logics and characteristics, from the initial expansion of merchant capitalism, through monopoly capitalism and its financialization, which is now leading a ‘new scramble’. The article shows how the various scrambles for Africa have evolved, including past and present land grabs, as well as the nature of resistance.
Active earth pressure of retaining wall considering wall movement

The coulomb’s limit equilibrium theory is employed for the active earth pressure calculation of retaining wall considering translational wall movement. It is considered that the earth pressure against the back of the wall is due to the thrust exerted by a wedge of soil between the wall and a plane passing through the heel of the wall. The soil–wall friction angle and internal soil friction angle are obtained via the simulation of the unloading triaxial test. The basic equations are established by considering the force equilibrium of a partial soil wedge. The lateral earth pressure coefficient is achieved through the moment equilibrium of the whole soil wedge. Comparisons illustrating the accuracy of the proposed approach are made with solutions available in the literature.
Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes

Glucansucrases are large enzymes belonging to glycoside hydrolase family 70, which catalyze the cleavage of sucrose into fructose and glucose, with the concomitant transfer of the glucose residue to a growing α-glucan polymer. Among others, plaque-forming oral bacteria secrete these enzymes to produce α-glucans, which facilitate the adhesion of the bacteria to the tooth enamel. We determined the crystal structure of a fully active, 1,031-residue fragment encompassing the catalytic and C-terminal domains of GTF180 from Lactobacillus reuteri 180, both in the native state, and in complexes with sucrose and maltose. These structures show that the enzyme has an α-amylase-like (β/α)8-barrel catalytic domain that is circularly permuted compared to the catalytic domains of members of glycoside hydrolase families 13 and 77, which belong to the same GH-H superfamily. In contrast to previous suggestions, the enzyme has only one active site and one nucleophilic residue. Surprisingly, in GTF180 the peptide chain follows a “U”-path, such that four of the five domains are made up from discontiguous N- and C-terminal stretches of the peptide chain. Finally, the structures give insight into the factors that determine the different linkage types in the polymeric product.