Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved automatic impact crater detection on Mars based on morphological image processing and template matching

ABSTRACT Impact craters help scientists to understand the geological history of planetary bodies. The aim of this paper is to improve the existing methodology for impact craters detection in images of planetary surfaces using a new approach based on morphological image processing (MIP). The improved methodology uses MIP followed by template matching based on fast Fourier transform (FFT). In this phase, a probability volume is generated based on the correlation between templates and images. The analysis of this probability volume allows the detection of different size of impact craters. We have applied the improved methodology to detect impact craters in a set of images from Thermal Emission Imaging System onboard the 2001 Mars Odyssey Space probe. The improved methodology has achieved a crater detection rate of 92.23% which can be considered robust, since results were obtained based on geomorphological features, different illumination conditions and low spatial resolution. The achieved results proved the viability of using MIP and template matching by FFT, to detect impact craters from planetary surfaces.
Biologically inspired intelligent decision making

Artificial neural networks (ANNs) are a class of powerful machine learning models for classification and function approximation which have analogs in nature. An ANN learns to map stimuli to responses through repeated evaluation of exemplars of the mapping. This learning approach results in networks which are recognized for their noise tolerance and ability to generalize meaningful responses for novel stimuli. It is these properties of ANNs which make them appealing for applications to bioinformatics problems where interpretation of data may not always be obvious, and where the domain knowledge required for deductive techniques is incomplete or can cause a combinatorial explosion of rules. In this paper, we provide an introduction to artificial neural network theory and review some interesting recent applications to bioinformatics problems.
SIFT Implementation and Optimization for General-Purpose GPU

With the addition of free programmable components to modern graphics hardware, graphics processing units (GPUs) become increasingly interesting for general purpose computations, especially due to utilizing parallel buffer processing. In this paper we present methods and techniques that take advantage of modern graphics hardware for real-time tracking and recognition of feature-points. The focus lies on the generation of feature vectors from input images in the various stages. For the generation of feature-vectors the Scale Invariant Feature Transform (SIFT) method [Low04a] is used due to its high stability against rotation, scale and lighting condition changes of the processed images. We present results of the various stages for feature vector generation of our GPU implementation and compare it to the CPU version of the SIFT algorithm. The approach works well on Geforce6 series graphics board and above and takes advantage of new hardware features, e.g. dynamic branching and multiple render targets (MRT) in the fragment processor [KF05]. With the presented methods feature-tracking with real time frame rates can be achieved on the GPU and meanwhile the CPU can be used for other tasks.
Non-linear magnetic field decay in neutron stars Theory and observations

There exists both theoretical and observational evidence that the magnetic field decay in neutron stars may proceed in a pronounced non-linear way during a certain episode of the neutron star's life. In the presence of a strong magnetic field the Hall-drift dominates the field evolution in the crust and/or the superfluid core of neutron stars. Analysing observations of P and ˙ P for suciently old isolated pulsars we gain strong hints for a significantly non-linear magnetic field decay. Under certain conditions with respect to the geometry and strength of a large-scale magnetic background field an instability is shown to occur which rapidly raises small-scale magnetic field modes. Their growth rates increase with the background field strength and may reach10 4 times the ohmic decay rate. Consequences for the rotational and thermal evolution as well as for the cracking of the crust of neutron stars are discussed.
Early bison remains from Mygdonia Basin (Northern Greece)

ABSTRACT The continuous enrichment of the European Pleistocene mammal fossil record leads inevitably to a comprehensive forthcoming review of the biogeographic and evolutionary history of bisons on the continent. New and revised data from the post-Olduvai (<1.8 Ma)-pre-Jaramillo (>1.0 Ma) time span of the Mygdonia basin (N. Greece), exposed here, indicate the presence of a small bison referred to as Bison cf. degiulii (Masini, Palombo & Rozzi, 2013) due to its similarities with the contemporaneous type material from the Italian Peninsula. A series of minor morphometrical changes detected across chronologically successive Mygdonia bison populations is interpreted as local adaptations to harsher environmental conditions. A re-evaluation of several morphological and biometrical features of the European early bison populations in comparison with later and extant taxa leads to the reconfirmation of some characters as taxonomically and phylogenetically important, while questioning others. The results allow recognizing B. degiulii as most likely member of the true bison clade Bison (Bison) Hamilton Smith, 1827 and reconsidering the current B. (Eobison) Flerov, 1972 concept. The data from Mygdonia basin and Northern Greece confirm the short co-occurrence of Bison Hamilton Smith, 1827 and Leptobos Rütimeyer, 1877-1878 in the Balkans and suggest the appearance of at least two bison lineages in Southern Europe between 1.7-1.5 Ma.
Conserved Endonuclease Function of Hantavirus L Polymerase

Hantaviruses are important emerging pathogens belonging to the Bunyaviridae family. Like other segmented negative strand RNA viruses, the RNA-dependent RNA polymerase (RdRp) also known as L protein of hantaviruses lacks an intrinsic “capping activity”. Hantaviruses therefore employ a “cap snatching” strategy acquiring short 5′ RNA sequences bearing 5′cap structures by endonucleolytic cleavage from host cell transcripts. The viral endonuclease activity implicated in cap snatching of hantaviruses has been mapped to the N-terminal domain of the L protein. Using a combination of molecular modeling and structure–function analysis we confirm and extend these findings providing evidence for high conservation of the L endonuclease between Old and New World hantaviruses. Recombinant hantavirus L endonuclease showed catalytic activity and a defined cation preference shared by other viral endonucleases. Based on the previously reported remarkably high activity of hantavirus L endonuclease, we established a cell-based assay for the hantavirus endonuclase function. The robustness of the assay and its high-throughput compatible format makes it suitable for small molecule drug screens to identify novel inhibitors of hantavirus endonuclease. Based on the high degree of similarity to RdRp endonucleases, some candidate inhibitors may be broadly active against hantaviruses and other emerging human pathogenic Bunyaviruses.
Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium

CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.
Motor Simulation during Action Word Processing in Neurosurgical Patients

The role that human motor areas play in linguistic processing is the subject of a stimulating debate. Data from nine neurosurgical patients with selective lesions of the precentral and postcentral sulcus could provide a direct answer as to whether motor area activation is necessary for action word processing. Action-related verbs (face-, hand-, and feet-related verbs plus neutral verbs) silently read were processed for (i) motor imagery by vividness ratings and (ii) frequency ratings. Although no stimulus- or task-dependent modulation was found in the RTs of healthy controls, patients showed a task × stimulus interaction resulting in a stimulus-dependent somatotopic pattern of RTs for the imagery task. A lesion affecting a part of the cortex that represents a body part also led to slower RTs during the creation of mental images for verbs describing actions involving that same body part. By contrast, no category-related differences were seen in the frequency judgment task. This task-related dissociation suggests that the sensorimotor area is critically involved in processing action verbs only when subjects are simulating the corresponding movement. These findings have important implications for the ongoing discussion regarding the involvement of the sensorimotor cortex in linguistic processing.
Molecular Basis of Light Harvesting and Photoprotection in CP24

CP24 is a minor antenna complex of Photosystem II, which is specific for land plants. It has been proposed that this complex is involved in the process of excess energy dissipation, which protects plants from photodamage in high light conditions. Here, we have investigated the functional architecture of the complex, integrating mutation analysis with time-resolved spectroscopy. A comprehensive picture is obtained about the nature, the spectroscopic properties, and the role in the quenching in solution of the pigments in the individual binding sites. The lowest energy absorption band in the chlorophyll a region corresponds to chlorophylls 611/612, and it is not the site of quenching in CP24. Chlorophylls 613 and 614, which are present in the major light-harvesting complex of Photosystem appear to be absent in CP24. In contrast to all other light-harvesting complexes, CP24 is stable when the L1 carotenoid binding site is empty and upon mutations in the third helix, whereas mutations in the first helix strongly affect the folding/stability of the pigment-protein complex. The absence of lutein in L1 site does not have any effect on the quenching, whereas substitution of violaxanthin in the L2 site with lutein or zeaxanthin results in a complex with enhanced quenched fluorescence. Triplet-minus-singlet measurements indicate that zeaxanthin and lutein in site L2 are located closer to chlorophylls than violaxanthin, thus suggesting that they can act as direct quenchers via a strong interaction with a neighboring chlorophyll. The results provide the molecular basis for the zeaxanthin-dependent quenching in isolated CP24.
Temporal distance metrics for social network analysis

The analysis of social and technological networks has attracted a lot of attention as social networking applications and mobile sensing devices have given us a wealth of real data. Classic studies looked at analysing static or aggregated networks, i.e., networks that do not change over time or built as the results of aggregation of information over a certain period of time. Given the soaring collections of measurements related to very large, real network traces, researchers are quickly starting to realise that connections are inherently varying over time and exhibit more dimensionality than static analysis can capture. In this paper we propose new temporal distance metrics to quantify and compare the speed (delay) of information diffusion processes taking into account the evolution of a network from a local and global view. We show how these metrics are able to capture the temporal characteristics of time-varying graphs, such as delay, duration and time order of contacts (interactions), compared to the metrics used in the past on static graphs. As a proof of concept we apply these techniques to two classes of time-varying networks, namely connectivity of mobile devices and e-mail exchanges.
Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population

HIV-1 is subject to immune pressure exerted by the host, giving variants that escape the immune response an advantage. Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure. Nevertheless, there is increasing evidence that virus displaying a signal of latency survives in patient plasma despite having reduced fitness due to long-term immune memory. We investigated the survival of virus with latent envelope genomic fragments by simulating within-host HIV-1 sequence evolution and the cycling of viral lineages in and out of the latent reservoir. Our model incorporates a detailed mutation process including nucleotide substitution, recombination, latent reservoir dynamics, diversifying selection pressure driven by the immune response, and purifying selection pressure asserted by deleterious mutations. We evaluated the ability of our model to capture sequence evolution in vivo by comparing our simulated sequences to HIV-1 envelope sequence data from 16 HIV-infected untreated patients. Empirical sequence divergence and diversity measures were qualitatively and quantitatively similar to those of our simulated HIV-1 populations, suggesting that our model invokes realistic trends of HIV-1 genetic evolution. Moreover, reconstructed phylogenies of simulated and patient HIV-1 populations showed similar topological structures. Our simulation results suggest that recombination is a key mechanism facilitating the persistence of virus with latent envelope genomic fragments in the productively infected cell population. Recombination increased the survival probability of latent virus forms approximately 13-fold. Prevalence of virus with latent fragments in productively infected cells was observed in only 2% of simulations when we ignored recombination, while the proportion increased to 27% of simulations when we allowed recombination. We also found that the selection pressures exerted by different fitness landscapes influenced the shape of phylogenies, diversity trends, and survival of virus with latent genomic fragments. Our model predicts that the persistence of latent genomic fragments from multiple different ancestral origins increases sequence diversity in plasma for reasonable fitness landscapes.
Immunoglobulin adsorption in patients with idiopathic dilated cardiomyopathy.

BACKGROUND Idiopathic dilated cardiomyopathy (IDC) frequently is a progressive disease without causative therapy options. Following the hypothesis that in certain patients autoantibodies against cardiac structures may induce, maintain, or promote the progression of the disease, we investigated whether the elimination of these autoantibodies through immunoadsorption would improve cardiac function. METHODS AND RESULTS This prospective case-control study included 34 patients with IDC. Each patient presented with moderate to severe heart failure and evidence of autoantibodies directed against beta(1)-adrenoceptors (beta(1)-AABs). Seventeen patients received standard medical therapy (control group), whereas 17 were also treated with immunoadsorption (treatment group) to eliminate beta(1)-AABs. A 1-year follow-up included echocardiographic assessment of left ventricular ejection fraction and internal diameters, beta(1)-AAB levels, and clinical status every 3 months. Within 1 year, the mean+/-SD left ventricular ejection fraction rose from 22.3+/-3.3% to 37.9+/-7.9% (P=0.0001) in the treatment group, with a relative increase of 69.9%. However, in the control group, no overall increase was seen (from 23.8+/-3.0% to 25.2+/-5.9%, P=0. 3154). Left ventricular diameter in diastole decreased by 14.5% from 74.5+/-7.1 to 63.7+/-6.0 mm in the treatment group (P=0.0001) and by 3.8% (P=0.2342) in the control group. In the treatment group, the NYHA functional rating improved after immunoadsorption (P=0.0001). beta(1)-AABs did not increase anew. CONCLUSIONS In IDC, the use of immunoadsorption is superior to the use of standard medical therapy. It significantly improves cardiac performance and clinical status.
Accuracy of 64-Multidetector-Row Computed Tomography in the Diagnosis of Coronary Artery Disease

Objectives: The aim of this prospective study was to assess the accuracy of 64-multidetector-row computed tomography coronary angiography (CTA) in the diagnosis of coronary artery disease (CAD). Patients and Methods: Ninety-two patients suspected of having CAD underwent CTA using a 64-slice CT scanner before a scheduled, conventional coronary angiogram (CCA). Blinded assessment of CTA to detect CAD was performed. The accuracy of CTA in detecting significant stenoses (≥50%) was compared to CCA. Data analysis was performed on 73 patients because the scans were nondiagnostic in 5 patients and 14 refused to undergo coronary angiography. Results: The CTAs of 21 of these 73 patients were considered as normal; 19 were confirmed on CCA. For the remaining 52 diagnosed as abnormal, 51 were confirmed on CCA. For patient-based analysis, CTA had a sensitivity of 95%, a specificity of 96%, a positive predictive value of 98% and a negative predictive value of 90%. For the whole vessel, the sensitivity of CTA was 60–100%, for all vessels and the specificity was 82–100%. Pooled sensitivity was 92% and pooled specificity was 98%. For the segments, the sensitivity of CTA was 64% or above for all vessels except for the distal left anterior descending artery (40%), mid circumflex artery (50%) and posterior descending artery (60%); the pooled sensitivity was 79%. The specificity for the segments was 82–100% for all vessels and pooled specificity was 94%. Conclusion: The sensitivity and specificity for patient-based analysis and for the main coronary vessels were high whereas for the segments, the sensitivity was moderately good, but the specificity was high, confirming that a negative CTA is useful to rule out significant CAD. A coordinated classification system between radiologists and cardiologists is required to eliminate errors in segment classification.
Towards MR-navigable nanorobotic carriers for drug delivery into the brain

Magnetic Resonance Navigation (MRN) relies on Magnetic Nanoparticles (MNPs) embedded in microcarriers or microrobots to allow the induction of a directional propelling force by 3-D magnetic gradients. These magnetic gradients are superposed on a sufficiently high homogeneous magnetic field (e.g. the Bo field of a MR scanner) to achieve maximum propelling force through magnetization saturation of the MNPs. As previously demonstrated by our group, such technique was successful at maintaining microcarriers along a planned trajectory in the blood vessels based on tracking information gathered using Magnetic Resonance Imaging (MRI) sequences from artifacts caused by the same MNPs. Besides propulsion and tracking, the same MNPs can be synthesized with characteristics that can allow for the diffusion of therapeutic cargo carried by these MR-navigable carriers through the Blood Brain Barrier (BBB) using localized hyperthermia without compromising the MRN capabilities. In the present study, localized hyperthermia induced by an alternating magnetic field (AC field) is investigated for the purpose of transient controlled disruption of the BBB and hence local delivery of therapeutic agents into the brain. Here, an external heating apparatus was used to impose a regional heat shock on the skull of a living mouse model. The effect of heat on the permeability of the BBB was assessed using histological observation and tissue staining by Evans blue dye. Results show direct correlation between hyperthermia and BBB leakage as well as its recovery from thermal damage. Therefore, in addition to on-command propulsion and remote tracking, the proposed navigable agents could be suitable for controlled opening of the BBB by hyperthermia and selective brain drug delivery.
Viticulture and ecosystem services : from myths to reality with Chilean vine-growers

This thesis work was led in the context of the Wine, Climate Change and Biodiversity program, coordinated since 2008 by Chilean researchers in cooperation with the biggest wine-making firms of the country and aiming at protecting the chilean native biodiversity from the chilean central mediterranean climate biomes from the agro-industry expansion. It aimed at gathering and comparing the existing scientific and experiential knowledge about the Ecosystem Services concept and its application in interactions with the different viticulture practices identified in the Chilean vineyards context. A literature review of thirty articles from the whole world and 21 semi-structured interviews were led with the viticulturists from the partner firms of the host program. Results analysis were structured around the hypotheses that 1) a knowledge gap separates the scientific knowledge collected in the articles from the experiential knowledge gathered throughout the interviews and 2) the variation of experiential knowledge between the viticulturists could potentially be explained by their management paradigm, defined as their personal qualification of the practices they apply on the vineyards they are managing. Results were compared using a conceptual diagram where the number of mentions to each ES and interaction were emphasized. Both approaches most valued the same ES. If the management paradigm defines clear differences in the viticulturists’ choices for some practices, like fertilization and weeds management, it has a reduced influence on many other practices. The global perception that viticulturists have of their vineyards doesn’t necessarily rely on their management paradigm, while it highly influences the way they integrate natural ecosystems and the ES in their practices. The complementarity of the two approaches also permitted to identify several potential research topics for the Wine, Climate Change and Biodiversity program to generate locally appropriate knowledge with direct impact on the viticulturists’ behaviour towards native ecosystems and further involvement in native biodiversity conservation. Table of content