Intelligent Motion Planning and Analysis with Probabilistic Roadmap Methods for the Study of Complex and High-Dimensional Motions

At first glance, robots and proteins have little in common. Robots are commonly thought of as tools that perform tasks such as vacuuming the floor, while proteins play essential roles in many biochemical processes. However, the functionality of both robots and proteins is highly dependent on their motions. In order to study motions in these two divergent domains, the same underlying algorithmic framework can be applied. This method is derived from probabilistic roadmap methods (PRMs) originally developed for robotic motion planning. It builds a graph, or roadmap, where configurations are represented as vertices and transitions between configurations are edges. The contribution of this work is a set of intelligent methods applied to PRMs. These methods facilitate both the modeling and analysis of motions, and have enabled the study of complex and high-dimensional problems in both robotic and molecular domains. In order to efficiently study biologically relevant molecular folding behaviors we have developed new techniques based on Monte Carlo solution, master equation calculation, and non-linear dimensionality reduction to run simulations and analysis on the roadmap. The first method, Map-based master equation calculation (MME), extracts global properties of the folding landscape such as global folding rates. On the other hand, another method, Map-based Monte Carlo solution (MMC), can be used to extract microscopic features of the folding process. Also, the application of dimensionality reduction returns a lower-dimensional representation that still retains the principal features while facilitating both modeling and analysis of motion landscapes. A key contribution of our methods is the flexibility to study larger and more complex structures, e.g., 372 residue Alpha-1 antitrypsin and 200 nucleotide ColE1 RNAII. We also applied intelligent roadmap-based techniques to the area of robotic motion. These methods take advantage of unsupervised learning methods at all stages of the planning process and produces solutions in complex spaces with little cost and less manual intervention compared to other adaptive methods. Our results show that our methods have low overhead and that they out-perform two existing adaptive methods in all complex cases studied

PRM-RL: Long-range Robotic Navigation Tasks by Combining Reinforcement Learning and Sampling-based Planning

We present PRM-RL, a hierarchical method for long-range navigation task completion that combines sampling based path planning with reinforcement learning (RL). The RL agents learn short-range, point-to-point navigation policies that capture robot dynamics and task constraints without knowledge of the large-scale topology. Next, the sampling-based planners provide roadmaps which connect robot configurations that can be successfully navigated by the RL agent. The same RL agents are used to control the robot under the direction of the planning, enabling long-range navigation. We use the Probabilistic Roadmaps (PRMs) for the sampling-based planner. The RL agents are constructed using feature-based and deep neural net policies in continuous state and action spaces. We evaluate PRM-RL, both in simulation and on-robot, on two navigation tasks with non-trivial robot dynamics: end-to-end differential drive indoor navigation in office environments, and aerial cargo delivery in urban environments with load displacement constraints. Our results show improvement in task completion over both RL agents on their own and traditional sampling-based planners. In the indoor navigation task, PRM-RL successfully completes up to 215 m long trajectories under noisy sensor conditions, and the aerial cargo delivery completes flights over 1000 m without violating the task constraints in an environment 63 million times larger than used in training.Comment: 9 pages, 7 figure

Creación de un cibermedio sobre periodismo: "Académica_mente”

Depto. de Periodismo y Comunicación GlobalDepto. de Periodismo y Nuevos MediosFac. de Ciencias de la InformaciónFALSEsubmitte

Updating the National Baseline of Non-Indigenous Species in Spanish Marine Waters

The introduction of new non-indigenous species (NIS) in Spanish marine waters is addressed under Descriptor 2 of the European Union’s Marine Strategy Framework Directive. National baseline inventories of NIS have been compiled and updated for the three subregions (Western Mediterranean Sea, WMED; Bay of Biscay–Iberian Coast, ABI; Macaronesia, AMA) with data from 1800 to 2021. An overall of 574 species were identified with an alien, cryptogenic, crypto-expanding, or debatable status, mostly invertebrates (~65%) and primary producers (~22%). Of 412 alien species, 80.51% were reported in ABI, 67.82% in WMED, and 66.67% in AMA. Cryptogenic species are more abundant in the WMED (25.25%), compared to AMA (19.77%) and ABI (18.46%). ABI harbors more established species (62.56%) than AMA (45.2%) and WMED (43.56%), contrary to casual records (AMA 31.64%, WMED 23.76%, ABI 13.85%). Invasive species are more abundant (14.36%) in WMED. The ‘transport-stowaway’ pathway accounted for 142 (79.33%), 123 (67.58%), and 169 (85.21%) records in WMED, ABI, and AMA, respectively. The second most common pathway was ‘transport-contaminant’ related to mariculture (~10% of the total), prevalently in ABI with 42 species (23.08%). The Canary Islands stand out for species introduced through oil platforms from throughout the world. ‘Unaided’ was a relevant pathway of secondary introduction into the WMED, particularly of Lessepsian species progressing westwards. Temporal trends in newly introduced species show similar behavior among subregions.This research was funded by Ministerio para la Transición Ecológica y el Reto Demográfico, grant number 11_MM_ESMARES2. The APC was funded by the ESMARES2-C3 project

San Adrian: Brontze Aroko aztarnategi berria Iberiar penintsulako iparraldean San Adrian: a new site of the Bronze Age in the north of the Iberian peninsula

Resumen: La investigación sobre la Edad del Bronce en la región cantábrica se ha centrado tradicionalmente en el estudio de objetos de prestigio y de contextos funerarios, dando lugar a un estado de la cuestión con importantes lagunas acerca del poblamiento, las actividades cotidianas y las estrategias de subsistencia de los grupos humanos durante este período. En este artículo presentamos las evidencias recuperadas en el yacimiento de San Adrian (Sierra de Aizkorri, Gipuzkoa), cuya excavación ha permitido reconstruir aspectos relativos a los modos de vida, la base económica, la cultura material y el contexto medioambiental de una serie de ocupaciones de la Edad del Bronce. Los resultados preliminares revelan la existencia de ocupaciones de hábitat periódicas y la explotación de recursos procedentes del Valle del Ebro y de la costa atlántica, contribuyendo a reconstruir los modos de vida y la circulación de bienes cotidianos en el norte de la península ibérica.Abstract: Bronze Age studies carried out in the Cantabrian Region have traditionally focused on prestige goods and funerary contexts. As a result of this, the lack of information about daily activities, subsistence strategies, and human settlement on a regional scale is evident in the state of art. However, current research has achieved new discoveries in recent years, allowing a reconstruction of some aspects of the economic structure, settlements, material culture and the palaeoenvironment during the Bronze Age. Indeed, besides the funerary practices discovered in 1983 in San Adrian (Parztuergo Nagusia, Gipuzkoa), research has now revealed the presence of Upper Palaeolithic and Early Bronze Age occupations. This paper presents a first characterization of the retrieved evidence and a preliminary evaluation of the archaeological site and its environment. San Adrian is a tunnel-shaped cave located at 1,000 meters a.s.l. in the Aizkorri mountain range, opening a passage beneath the Atlantic-Mediterranean watershed in northern Iberia. The strategic character of this mountain site is demonstrated by the presence of Upper Palaeolithic and Bronze Age occupations, and by the construction of a road passing through it and the fortification of both its entrances in the Middle Ages. The aim of the archaeological survey started in 2008 was to identify, describe and evaluate the heritage potential of the cave, because previous fieldwork had only managed to make surface finds in the side galleries, including a medieval hoard and Bronze Age human remains. The work carried out by our research group at San Adrian includes a series of test pits and the excavation of an area nine square metres in size following stratigraphic criteria. In the current state, we identified at least two contexts corresponding to Late Upper Palaeolithic and Bronze Age occupations in the cave. Fieldwork included the sieving and flotation of sediment and the collection of samples for different types of analysis: palynology, carpology, sedimentology, and radiocarbon dating. The evidence is being studied by a multidisciplinary team according to expertise requirements for each topic: palaeobotany and environment, archaeozoology, sedimentology, geology, physical anthropology, prehistoric industries (lithics, pottery and bone) and archaeological and historical documentation. Because of its recent discovery, Upper Palaeolithic evidence remains still under study, but first results on Bronze Age layers can be presented. The ongoing archaeobotanical and archaeozoological studies reveal the exploitation of domestic plants and fauna complemented by hunting and foraging of wild species. At the same time, the archaeological artefacts and their production sequences show the exploitation of nearby resources on both sides of the mountain range, while prestige goods are absent. This evidence is also used to estimate the regularity of cave occupations and to propose a model of seasonal exploitation of the mountain environment. The results obtained reveal the exploitation of resources from both the Mediterranean and Atlantic basins, and contribute towards an understanding of the daily activities of Bronze Age societies. In addition, the evidence shows the exchange and circulation of quotidian products between the Cantabrian region and inland Iberia in other networks than those of prestige goods

3D Reconstruction of VZV Infected Cell Nuclei and PML Nuclear Cages by Serial Section Array Scanning Electron Microscopy and Electron Tomography

Varicella-zoster virus (VZV) is a human alphaherpesvirus that causes varicella (chickenpox) and herpes zoster (shingles). Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML) in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D) distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM) and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity), what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency) and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the single cell level