Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling plant species distribution in alpine grasslands using airborne imaging spectroscopy

Remote sensing using airborne imaging spectroscopy (AIS) is known to retrieve fundamental optical properties of ecosystems. However, the value of these properties for predicting plant species distribution remains unclear. Here, we assess whether such data can add value to topographic variables for predicting plant distributions in French and Swiss alpine grasslands. We fitted statistical models with high spectral and spatial resolution reflectance data and tested four optical indices sensitive to leaf chlorophyll content, leaf water content and leaf area index. We found moderate added-value of AIS data for predicting alpine plant species distribution. Contrary to expectations, differences between species distribution models (SDMs) were not linked to their local abundance or phylogenetic/functional similarity. Moreover, spectral signatures of species were found to be partly site-specific. We discuss current limits of AIS-based SDMs, highlighting issues of scale and informational content of AIS data.
Black carbon solar absorption suppresses turbulence in the atmospheric boundary layer

Significance The cooling effect of aerosols on climate and the modification of clouds by aerosols have been widely debated, because quantifying their effects is important for constraining current climate change. Here we present measurements of turbulence from unmanned aerial vehicles. We find that absorption of sunlight by black carbon (BC) aerosols suppresses turbulence in the lower atmosphere, with important consequences for the environmental impacts of BC emissions from anthropogenic fossil fuel and biomass burning. A mechanism is proposed that links the suppressed turbulence to taller clouds. These results highlight the importance of understanding and observing the role of turbulence in studies of aerosol impacts on clouds. Suppressed turbulence also exacerbates the visibility and human health impacts of pollution. The introduction of cloud condensation nuclei and radiative heating by sunlight-absorbing aerosols can modify the thickness and coverage of low clouds, yielding significant radiative forcing of climate. The magnitude and sign of changes in cloud coverage and depth in response to changing aerosols are impacted by turbulent dynamics of the cloudy atmosphere, but integrated measurements of aerosol solar absorption and turbulent fluxes have not been reported thus far. Here we report such integrated measurements made from unmanned aerial vehicles (UAVs) during the CARDEX (Cloud Aerosol Radiative Forcing and Dynamics Experiment) investigation conducted over the northern Indian Ocean. The UAV and surface data reveal a reduction in turbulent kinetic energy in the surface mixed layer at the base of the atmosphere concurrent with an increase in absorbing black carbon aerosols. Polluted conditions coincide with a warmer and shallower surface mixed layer because of aerosol radiative heating and reduced turbulence. The polluted surface mixed layer was also observed to be more humid with higher relative humidity. Greater humidity enhances cloud development, as evidenced by polluted clouds that penetrate higher above the top of the surface mixed layer. Reduced entrainment of dry air into the surface layer from above the inversion capping the surface mixed layer, due to weaker turbulence, may contribute to higher relative humidity in the surface layer during polluted conditions. Measurements of turbulence are important for studies of aerosol effects on clouds. Moreover, reduced turbulence can exacerbate both the human health impacts of high concentrations of fine particles and conditions favorable for low-visibility fog events.
Risk of infection is associated more with drain duration than daily drainage volume in prosthesis-based breast reconstruction

Abstract In prosthesis-based breast reconstruction, drains are used to prevent seroma formation and to reduce the risk of infection. However, prolonged drainage increases the risk of ascending infection. Although the volume often accepted for drain removal is ⩽30 mL per day, the optimal timing to remove the drain for best clinical outcome remains controversial. We did a retrospective cohort study of 569 patients of prosthesis-based breast reconstruction with infection rate as the outcome variable; drain duration and last daily drainage volume as the main independent variables. Data on age, smoking history, diabetes mellitus history, body mass index, breast weight, tissue expander size, drain size, number of retrieved lymph nodes, tumor size, number of metastatic lymph nodes, tumor stage, mastectomy type, reconstruction type, submuscular implantation, skin defect, operative time, duration of antibiotics use, chemotherapy, and radiotherapy were collected as covariates. Multivariable logistic regression analysis was used to control for confounding. The total infection rate was 5.1% (29/569). The daily drainage volume ≥30 mL/d at the time of drain removal was not found associated with increased infection rate (P = 0.32). Of the various cutoff values of last daily drainage volume, none was found to be a determinant for drain removal where the risk of infection was concerned. By contrast, drain duration over 21 days significantly increased infection rate (P = 0.001). The multivariable logistic regression analysis showed an increase of 76.2% in the infection rate with each additional week of drain retention (P = 0.001). Breast weight also had a significant influence on risk of infection. Chemotherapy and drain size showed borderline effect on risk of infection whereas the last daily drainage volume was not associated with risk of infection In summary, our study revealed that drain duration, rather than the last daily drainage volume, significantly affects the infection rate in prosthesis-based breast reconstruction. We recommend that the drain is better removed no longer than 3 weeks postoperatively and can be removed as early as postoperative day 7, even when the drainage is over 30 mL in a 24-hour period.
Comparison of long‐chain alcohols and other volatile compounds emitted from food‐borne and related Gram positive and Gram negative bacteria

Numerous reports have been published on the antimicrobial activity of synthetic volatile long chain alcohols, such as 1‐decanol and 1‐dodecanol, against bacteria and fungi. The objective of the present study was to survey microorganisms for emission patterns of naturally occurring long chain alcohols and other volatile components to determine if these compounds are associated with certain groups of bacteria. Cultures were grown in trypticase soy broth overnight and volatile compounds were trapped on a porous polymer and identified by mass spectrometry. Subsequently, volatile compounds were collected from 26 strains of food associated bacteria using solid‐phase microextraction and analyzed by gas chromatography. Alcohols comprising 1‐octanol, 1‐decanol, and 1‐dodecanol occurred as products from enteric Gram negative bacteria, which included Citrobacter, Enterobacter, Klebsiella, Salmonella, and Shigella. However, the long chain alcohols were not detected as products from the nonenteric Gram negative species studied which included Acinetobacter, Pseudomonas, and Shewanella. Among Gram positive bacteria, including Bacillus, Enterococcus, Lactococcus, Leuconostoc, Listeria, Staphylococcus, and Streptococcus, the only long chain alcohol detected was 1‐decanol and, if present, it occurred in relatively small amounts. Other classes of compounds emitted by bacteria included methylketones and sulfides. The methylketones were found as products from Gram positive and Gram negative bacteria, whereas the sulfides were closely associated with Gram positive bacteria. In summary, the emission patterns of volatile compounds from bacteria showed many trends including the association of long chain alcohols with enteric Gram negative bacteria. The results provide a basis for future in vivo studies to determine if volatile compounds such as natural long chain alcohols function in the ecology of food‐borne Gram negative bacterial pathogens.
Beam tracing polygonal objects

Ray tracing has produced some of the most realistic computer generated pictures to date. They contain surface texturing, local shading, shadows, reflections and refractions. The major disadvantage of ray tracing results from its point-sampling approach. Because calculation proceeds ab initio at each pixel it is very CPU intensive and may contain noticeable aliasing artifacts. It is difficult to take advantage of spatial coherence because the shapes of reflections and refractions from curved surfaces are so complex. In this paper we describe an algorithm that utilizes the spatial coherence of polygonal environments by combining features of both image and object space hidden surface algorithms. Instead of tracing infinitesimally thin rays of light, we sweep areas through a scene to form “beams. ” This technique works particularly well for polygonal models since for this case the reflections are linear transformations, and refractions are often approximately so. The recursive beam tracer begins by sweeping the projection plane through the scene. Beam-surface intersections are computed using two-dimensional polygonal set operations and an occlusion algorithm similar to the Weiler-Atherton hidden surface algorithm. For each beam-polygon intersection the beam is fragmented and new beams created for the reflected and transmitted swaths of light. These sub-beams are redirected with a 4×4 matrix transformation and recursively traced. This beam tree is an object space representation of the entire picture. Since the priority of polygons is pre-determined, the final picture with reflections, refractions, shadows, and hidden surface removal is easily drawn. The coherence information enables very fast scan conversion and high resolution output. Image space edge and texture antialiasing methods can be applied.
Things aren't what they seem to be: innovation through technology inspiration

How does designing for novel experiences with largely untried technologies get its inspiration? Here we report on a project whose goal was to promote learning through novel, playful visions of technologies. To this end, we experimented with a diversity of ambient and pervasive technologies to inspire and drive our design. Working as a large multi-disciplinary group of researchers and designers we developed novel and imaginative experiences for children. To crystallise our ideas we designed, implemented and experimented with a mixed reality adventure game, where children had to hunt an elusive, virtual creature called the Snark, in a large interactive environment. We describe our experiences, reflecting on the process of design inspiration in an area where so much remains unknown.
Promoter methylation in circadian genes of endometrial cancers detected by methylation‐specific PCR

Methylation of CpG dinucleotides in the promoter sequence of a gene can lead to deregulated and suppressed gene expression. In this study, we have developed procedures for methylation‐specific polymerase chain reaction (MSP) and sequencing analysis to determine CpG methylation status of the promoter sequences of nine circadian genes in 35 endometrial cancers (EC) and paired noncancerous endometrial tissues. DNA methylation was found in the promoter sequences of PER1, PER2, and CRY1, but not of other six circadian genes in the ECs and normal tissues examined. Eleven of the 35 EC tissues showed CpG methylation in the promoter sequences of PER1, PER2, or CRY1. Of these 11 cases, 1 had promoter methylation in all the three genes, 1 in PER1 and PER2, 3 in PER1 and CRY1, and 6 in PER1, respectively. In comparison, promoter CpG methylation of PER1, PER2, or CRY1 was found in only 7 of 35 paired noncancerous tissues including 2 in PER1 and PER2, 2 in PER1, and 3 in CRY1. In summary, promoter methylation in the PER1, PER2, or CRY1 circadian genes was detected in about one‐third of EC and one‐fifth of noncancerous endometrial tissues of 35 paired specimens indicating possible disruption of the circadian clock in the development of EC. © 2006 Wiley‐Liss, Inc.
Use of an in vivo biotinylated single-chain antibody as capture reagent in an immunometric assay to decrease the incidence of interference from heterophilic antibodies.

BACKGROUND Heterophilic antibodies are a common source of interference in immunometric assays. We tested the hypothesis that the incidence of such interference could be decreased by use of a recombinant in vivo-biotinylated single-chain antibody (scFv) as the capture reagent. METHODS We established three assays for carcinoembryonic antigen (CEA) with the capture antibody either chemically biotinylated whole monoclonal T84.66 immunoglobulin, a corresponding F(ab')2 fragment, or a site-specifically biotinylated T84.66-derived single-chain antibody (scFv). Antibodies were attached to streptavidin-coated microplates. A common europium-labeled anti-CEA tracer monoclonal antibody was used. The F(ab')2 assay used a buffer that contained bovine immunoglobulin and aggregated irrelevant monoclonal antibody MAK33 as blocking agents. The whole T84.66 immunoglobulin and scFv assays were performed without addition of blocking agents. From a previous study of 11 261 sera, we tested 390 samples that had displayed heterophilic antibody interference and 179 samples that had not. RESULTS After correction for bias and analytical variation [2.56 x SD (from the precision profile)], 383 samples displayed significantly different values (>1 microg/L) in the whole T84.66-based assay and the F(ab')2 assay. In contrast, only nine samples showed falsely high CEA concentrations in the scFv assay. After blocking agents were added to the assay buffer, eight of the nine samples displayed results equivalent to those of the F(ab')2 assay, and sample dilution produced equivalent results for the remaining sample. CONCLUSION Their ability to be site-specifically biotinylated and their relative resistance to heterophilic antibody interference indicate that single-chain antibodies may be useful solid-phase reagents in immunometric assays.
Purified Adult Ensheathing Glia Fail to Myelinate Axons under Culture Conditions that Enable Schwann Cells to Form Myelin

Several studies have suggested that olfactory ensheathing glia (EG) can form Schwann cell (SC)-like myelin. Because of possible misinterpretation attributable to contaminating SCs, the capacity of EG to produce myelin needs to be explored further. Therefore, we compared the abilities of adult EG, purified by immunopanning with p75 antibody, and adult SCs to produce myelin when cocultured with purified dorsal root ganglion neurons (DRGNs) in serum-free and serum-containing media. In both media formulations, the number of myelin sheaths in SC/DRGN cultures was far higher than in EG/DRGN cultures; the number of sheaths in EG/DRGN cultures was equal to that in purified DRGN cultures without added cells. The latter result demonstrates that myelination by a few SCs remaining in purified DRGN cultures may occur, suggesting that myelin in EG/DRGN cultures could be SC myelin. Striking differences in the relationship of EG and SC processes to axons were observed. Whereas SCs displayed relatively short, thick processes that engulfed axons in small bundles or in individual cytoplasmic furrows and segregated larger axons into one-to-one relationships, EG extended flattened sheets that partitioned or only partially encircled fascicles of axons, sometimes spanning the entire culture. SCs exhibited behavior typical of SCs in peripheral nerves, whereas EG exhibited characteristics resembling those of EG in olfactory nerves. In sum, p75-selected EG from adult animals did not exhibit an SC-like relationship to axons and did not form myelin.
Dependability Modeling and Evaluation of Software Fault-Tolerant Systems

Dependability modeling and evaluation (encompassing reliability and safety issues) of the two major fault tolerance software approaches-recovery blocks (RBs) and N version programming (NVP)-are presented. The study is based on the detailed analysis of software fault-tolerance architectures able to tolerate a single fault (RB: two alternates and an acceptance test; NVP: three versions and a decider). For each approach a detailed model based on the software production process is established and then simplified by assuming that only a single fault type may manifest during execution of the fault-tolerant software and that no error compensation may take place within the software. The analytical results obtained make it possible to identify the improvement, compared to a non-fault-tolerant software, that could result from the use of RB (the acceptance test has to be more reliable from the alternates) and NVP (related faults among the versions and the decider have to be minimized) and to determine the most critical types of related faults. Nested RBs are studied, showing that the proposed analysis approach can be applied to such realistic software structures and that when an alternate is itself an RB, the results are analogous to the case of the addition of a third alternate. The reliability analysis shows that only a small improvement can be expected. >
Protective Effects of Cannabidiol against Seizures and Neuronal Death in a Rat Model of Mesial Temporal Lobe Epilepsy

The present study reports the behavioral, electrophysiological, and neuropathological effects of cannabidiol (CBD), a major non-psychotropic constituent of Cannabis sativa, in the intrahippocampal pilocarpine-induced status epilepticus (SE) rat model. CBD was administered before pilocarpine-induced SE (group SE+CBDp) or before and after SE (group SE+CBDt), and compared to rats submitted only to SE (SE group), CBD, or vehicle (VH group). Groups were evaluated during SE (behavioral and electrophysiological analysis), as well as at days one and three post-SE (exploratory activity, electrophysiological analysis, neuron density, and neuron degeneration). Compared to SE group, SE+CBD groups (SE+CBDp and SE+CBDt) had increased SE latency, diminished SE severity, increased contralateral afterdischarge latency and decreased relative powers in delta (0.5–4 Hz) and theta (4–10 Hz) bands. Only SE+CBDp had increased vertical exploratory activity 1-day post SE and decreased contralateral relative power in delta 3 days after SE, when compared to SE group. SE+CBD groups also showed decreased neurodegeneration in the hilus and CA3, and higher neuron density in granule cell layer, hilus, CA3, and CA1, when compared to SE group. Our findings demonstrate anticonvulsant and neuroprotective effects of CBD preventive treatment in the intrahippocampal pilocarpine epilepsy model, either as single or multiple administrations, reinforcing the potential role of CBD in the treatment of epileptic disorders.
Timing Results Using an FPGA-Based TDC with Large Arrays of 144 SiPMs

Silicon photomultipliers (SiPMs) have become an alternative to traditional tubes due to several features. However, their implementation to form large arrays is still a challenge especially due to their relatively high intrinsic noise, depending on the chosen readout. In this contribution, two modules composed of 12 ×12 SiPMs with an area of roughly 50 mm×50 mm are used in coincidence. Coincidence resolving time (CRT) results with a field-programmable gate array, in combination with a time to digital converter, are shown as a function of both the sensor bias voltage and the digitizer threshold. The dependence of the CRT on the sensor matrix temperature, the amount of SiPM active area and the crystal type is also analyzed. Measurements carried out with a crystal array of 2 mm pixel size and 10 mm height have shown time resolutions for the entire 288 SiPM two-detector set-up as good as 800 ps full width at half maximum (FWHM).
The Effects of Adiantum capillus-veneris on Wound Healing: An Experimental In Vitro Evaluation

Background: A lot of remedies, mostly plant based, were mentioned in the Persian old pharmacopoeias for promoting of burn and wound healing and tissue repairing. The efficacy of most of these old remedies is unexplored till now. Adiantum capillus-veneris from Adiantaceae family is one of them that was used to treating of some kinds of chronic wounds. Methods: Methanol extract was fractionated to four different partitions that is, hexane, ethyl acetate, n-butanol, and aqueous. The potential of A. capillus-veneris fractions in wound healing or prevention of chronic wounds were evaluated through angiogenesis and fibroblast proliferation, in addition to in vitro tests for protection against damage to fibroblasts by oxygen free radicals. Results: The aqueous part of A. capillus-veneris promoted significant angiogenesis (P < 0.05) through both capillary-like tubular formations and proliferation of endothelial cells in vitro. In addition, in the tests for protection against damage to fibroblasts by oxygen free radicals, aqueous and butanol fractions showed significant protective effects in the concentrations 50, and 500 μg/ml (P < 0.05) in comparison with a control group. In the toxicity testing, it showed weak irritation in the Hen's egg test chorioallantoic membrane (CAM) bioassay at the vascular level on the CAM of the chicken and no significant cytotoxicity in the MTT assays on normal human dermal fibroblasts. Conclusions: Angiogenic effects and protective effects against oxygen free radicals suggested aqueous partition of A. capillus-veneris local application for prevention of late-radiation-induced injuries after radiation therapy and healing of external wounds similar to bedsores and burns.
Edinburgh Research Explorer Detection of Abnormal Fish Trajectories Using a Clustering Based Hierarchical Classifier

We address the analysis of fish trajectories in unconstrained underwater videos to help marine biologist to detect new/rare fish behaviours and to detect environmental changes which can be observed from the abnormal behaviour of fish. The fish trajectories are separated into normal and abnormal classes which indicate the common behaviour of fish and the behaviours that are rare/ unusual respectively. The proposed solution is based on a novel type of hierarchical classifier which builds the tree using clustered and labelled data based on similarity of data while using different feature sets at different levels of hierarchy. The paper presents a new method for fish trajectory analysis which has better performance compared to state-of-the-art techniques while the results are significant considering the challenges of underwater environments, low video quality, erratic movement of fish and highly imbalanced trajectory data that we used. Moreover, the proposed method is also powerful enough to classify highly imbalanced real-world datasets.