Deep learning-based parameter mapping for joint relaxation and diffusion tensor MR Fingerprinting

Magnetic Resonance Fingerprinting (MRF) enables the simultaneous quantification of multiple properties of biological tissues. It relies on a pseudo-random acquisition and the matching of acquired signal evolutions to a precomputed dictionary. However, the dictionary is not scalable to higher-parametric spaces, limiting MRF to the simultaneous mapping of only a small number of parameters (proton density, T1 and T2 in general). Inspired by diffusion-weighted SSFP imaging, we present a proof-of-concept of a novel MRF sequence with embedded diffusion-encoding gradients along all three axes to efficiently encode orientational diffusion and T1 and T2 relaxation. We take advantage of a convolutional neural network (CNN) to reconstruct multiple quantitative maps from this single, highly undersampled acquisition. We bypass expensive dictionary matching by learning the implicit physical relationships between the spatiotemporal MRF data and the T1, T2 and diffusion tensor parameters. The predicted parameter maps and the derived scalar diffusion metrics agree well with state-of-the-art reference protocols. Orientational diffusion information is captured as seen from the estimated primary diffusion directions. In addition to this, the joint acquisition and reconstruction framework proves capable of preserving tissue abnormalities in multiple sclerosis lesions

Keyframe-based visual–inertial odometry using nonlinear optimization

Combining visual and inertial measurements has become popular in mobile robotics, since the two sensing modalities offer complementary characteristics that make them the ideal choice for accurate visual–inertial odometry or simultaneous localization and mapping (SLAM). While historically the problem has been addressed with filtering, advancements in visual estimation suggest that nonlinear optimization offers superior accuracy, while still tractable in complexity thanks to the sparsity of the underlying problem. Taking inspiration from these findings, we formulate a rigorously probabilistic cost function that combines reprojection errors of landmarks and inertial terms. The problem is kept tractable and thus ensuring real-time operation by limiting the optimization to a bounded window of keyframes through marginalization. Keyframes may be spaced in time by arbitrary intervals, while still related by linearized inertial terms. We present evaluation results on complementary datasets recorded with our custom-built stereo visual–inertial hardware that accurately synchronizes accelerometer and gyroscope measurements with imagery. A comparison of both a stereo and monocular version of our algorithm with and without online extrinsics estimation is shown with respect to ground truth. Furthermore, we compare the performance to an implementation of a state-of-the-art stochastic cloning sliding-window filter. This competitive reference implementation performs tightly coupled filtering-based visual–inertial odometry. While our approach declaredly demands more computation, we show its superior performance in terms of accuracy

Neutrinos below 100 TeV from the southern sky employing refined veto techniques to IceCube data

Many Galactic sources of gamma rays, such as supernova remnants, are expected to produce neutrinos with a typical energy cutoff well below 100 TeV. For the IceCube Neutrino Observatory located at the South Pole, the southern sky, containing the inner part of the Galactic plane and the Galactic Center, is a particularly challenging region at these energies, because of the large background of atmospheric muons. In this paper, we present recent advancements in data selection strategies for track-like muon neutrino events with energies below 100 TeV from the southern sky. The strategies utilize the outer detector regions as veto and features of the signal pattern to reduce the background of atmospheric muons to a level which, for the first time, allows IceCube searching for point-like sources of neutrinos in the southern sky at energies between 100 GeV and several TeV in the muon neutrino charged current channel. No significant clustering of neutrinos above background expectation was observed in four years of data recorded with the completed IceCube detector. Upper limits on the neutrino flux for a number of spectral hypotheses are reported for a list of astrophysical objects in the southern hemisphere.Comment: 19 pages, 17 figures, 2 table

Neutrinos below 100 TeV from the southern sky employing refined veto techniques to IceCube data

Many Galactic sources of gamma rays, such as supernova remnants, are expected to produce neutrinos with a typical energy cutoff well below 100 TeV. For the IceCube Neutrino Observatory located at the South Pole, the southern sky, containing the inner part of the Galactic plane and the Galactic Center, is a particularly challenging region at these energies, because of the large background of atmospheric muons. In this paper, we present recent advancements in data selection strategies for track-like muon neutrino events with energies below 100 TeV from the southern sky. The strategies utilize the outer detector regions as veto and features of the signal pattern to reduce the background of atmospheric muons to a level which, for the first time, allows IceCube searching for point-like sources of neutrinos in the southern sky at energies between 100 GeV and several TeV in the muon neutrino charged current channel. No significant clustering of neutrinos above background expectation was observed in four years of data recorded with the completed IceCube detector. Upper limits on the neutrino flux for a number of spectral hypotheses are reported for a list of astrophysical objects in the southern hemisphere

The Mid-Pleistocene Transition induced by delayed feedback and bistability

The Mid-Pleistocene Transition, the shift from 41 kyr to 100 kyr glacial-interglacial cycles that occurred roughly 1 Myr ago, is often considered as a change in internal climate dynamics. Here we revisit the model of Quaternary climate dynamics that was proposed by Saltzman and Maasch (1988). We show that it is quantitatively similar to a scalar equation for the ice dynamics only when combining the remaining components into a single delayed feedback term. The delay is the sum of the internal times scales of ocean transport and ice sheet dynamics, which is on the order of 10 kyr. We find that, in the absence of astronomical forcing, the delayed feedback leads to bistable behaviour, where stable large-amplitude oscillations of ice volume and an equilibrium coexist over a large range of values for the delay. We then apply astronomical forcing. We perform a systematic study to show how the system response depends on the forcing amplitude. We find that over a wide range of forcing amplitudes the forcing leads to a switch from small-scale oscillations of 41 kyr to large-amplitude oscillations of roughly 100 kyr without any change of other parameters. The transition in the forced model consistently occurs near the time of the Mid-Pleistocene Transition as observed in data records. This provides evidence that the MPT could have been primarily a forcing-induced switch between attractors of the internal dynamics. Small additional random disturbances make the forcing-induced transition near 800 kyr BP even more robust. We also find that the forced system forgets its initial history during the small-scale oscillations, in particular, nearby initial conditions converge prior to transitioning. In contrast to this, in the regime of large-amplitude oscillations, the oscillation phase is very sensitive to random perturbations, which has a strong effect on the timing of the deglaciation events

Robust and flexible multi-scale medial axis computation

The principle of the multi-scale medial axis (MMA) is important in that any object is detected at a blurring scale proportional to the size of the object. Thus it provides a sound balance between noise removal and preserving detail. The robustness of the MMA has been reflected in many existing applications in object segmentation, recognition, description and registration. This thesis aims to improve the computational aspects of the MMA. The MMA is obtained by computing ridges in a “medialness” scale-space derived from an image. In computing the medialness scale-space, we propose an edge-free medialness algorithm, the Concordance-based Medial Axis Transform (CMAT). It not only depends on the symmetry of the positions of boundaries, but also is related to the symmetry of the intensity contrasts at boundaries. Therefore it excludes spurious MMA branches arising from isolated boundaries. In addition, the localisation accuracy for the position and width of an object, as well as the robustness under noisy conditions, is preserved in the CMAT. In computing ridges in the medialness space, we propose the sliding window algorithm for extracting locally optimal scale ridges. It is simple and efficient in that it can readily separate the scale dimension from the search space but avoids the difficult task of constructing surfaces of connected maxima. It can extract a complete set of MMA for interfering objects in scale-space, e.g. embedded or adjacent objects. These algorithms are evaluated using a quantitative study of their performance for 1-D signals and qualitative testing on 2-D images

POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization

Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increasingly used to map protein–chromatin interactions at global scale. The comparison of ChIP-seq profiles for RNA polymerase II (PolII) established in different biological contexts, such as specific developmental stages or specific time-points during cell differentiation, provides not only information about the presence/accumulation of PolII at transcription start sites (TSSs) but also about functional features of transcription, including PolII stalling, pausing and transcript elongation. However, annotation and normalization tools for comparative studies of multiple samples are currently missing. Here, we describe the R-package POLYPHEMUS, which integrates TSS annotation with PolII enrichment over TSSs and coding regions, and normalizes signal intensity profiles. Thereby POLYPHEMUS facilitates to extract information about global PolII action to reveal changes in the functional state of genes. We validated POLYPHEMUS using a kinetic study on retinoic acid-induced differentiation and a publicly available data set from a comparative PolII ChIP-seq profiling in Caenorhabditis elegans. We demonstrate that POLYPHEMUS corrects the data sets by normalizing for technical variation between samples and reveal the potential of the algorithm in comparing multiple data sets to infer features of transcription regulation from dynamic PolII binding profiles

Proportional bandwidth distribution in IP networks implementing the assured forwarding PHB

Recent demands for new applications are giving rise to an increasing need of Quality of Service (QoS). Nowadays, most IP-based networks tend to use the DiffServ architecture to provide end-to-end QoS. Traffic conditioners are a key element in the deployment of DiffServ. In this paper, we introduce a new approach for traffic conditioning based on feedback signaling among boundary nodes and traffic conditioners. This new approach is intended to provide a poportional distribution of excess bandwidth to endusers. We evaluate through extensive simulations the performance of our proposal in terms of final throughput, considering contracted target rates and distribution of spare bandwidth. Results show a high level of fairness in the excess bandwidth allocation among TCP sources under different network conditions

Vegetation responses to variations in climate: A combined ordinary differential equation and sequential Monte Carlo estimation approach

Vegetation responses to variation in climate are a current research priority in the context of accelerated shifts generated by climate change. However, the interactions between environmental and biological factors still represent one of the largest uncertainties in projections of future scenarios, since the relationship between drivers and ecosystem responses has a complex and nonlinear nature. We aimed to develop a model to study the vegetation’s primary productivity dynamic response to temporal variations in climatic conditions as measured by rainfall, temperature and radiation. Thus, we propose a new way to estimate the vegetation response to climate via a non-autonomous version of a classical growth curve, with a time-varying growth rate and carrying capacity parameters according to climate variables. With a Sequential Monte Carlo Estimation to account for complexities in the climate-vegetation relationship to minimize the number of parameters. The model was applied to six key sites identified in a previous study, consisting of different arid and semiarid rangelands from North Patagonia, Argentina. For each site, we selected the time series of MODIS NDVI, and climate data from ERA5 Copernicus hourly reanalysis from 2000 to 2021. After calculating the time series of the a posteriori distribution of parameters, we analyzed the explained capacity of the model in terms of the linear coefficient of determination and the parameters distribution variation. Results showed that most rangelands recorded changes in their sensitivity over time to climatic factors, but vegetation responses were heterogeneous and influenced by different drivers. Differences in this climate-vegetation relationship were recorded among different cases: (1) a marginal and decreasing sensitivity to temperature and radiation, respectively, but a high sensitivity to water availability; (2) high and increasing sensitivity to temperature and water availability, respectively; and (3) a case with an abrupt shift in vegetation dynamics driven by a progressively decreasing sensitivity to water availability, without any changes in the sensitivity either to temperature or radiation. Finally, we also found that the time scale, in which the ecosystem integrated the rainfall phenomenon in terms of the width of the window function used to convolve the rainfall series into a water availability variable, was also variable in time. This approach allows us to estimate the connection degree between ecosystem productivity and climatic variables. The capacity of the model to identify changes over time in the vegetation-climate relationship might inform decision-makers about ecological transitions and the differential impact of climatic drivers on ecosystems.Estación Experimental Agropecuaria BarilocheFil: Bruzzone, Octavio Augusto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Bruzzone, Octavio Augusto. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; ArgentinaFil: Perri, Daiana Vanesa. Instituto Nacional de Tecnologia Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Área de Recursos Naturales; ArgentinaFil: Perri, Daiana Vanesa. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; ArgentinaFil: Easdale, Marcos Horacio. Instituto Nacional de Tecnologia Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Área de Recursos Naturales; ArgentinaFil: Easdale, Marcos Horacio. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentin