A neural tracking and motor control approach to improve rehabilitation of upper limb movements

<p>Abstract</p> <p>Background</p> <p>Restoration of upper limb movements in subjects recovering from stroke is an essential keystone in rehabilitative practices. Rehabilitation of arm movements, in fact, is usually a far more difficult one as compared to that of lower extremities. For these reasons, researchers are developing new methods and technologies so that the rehabilitative process could be more accurate, rapid and easily accepted by the patient. This paper introduces the proof of concept for a new non-invasive FES-assisted rehabilitation system for the upper limb, called smartFES (sFES), where the electrical stimulation is controlled by a biologically inspired neural inverse dynamics model, fed by the kinematic information associated with the execution of a planar goal-oriented movement. More specifically, this work details two steps of the proposed system: an <it>ad hoc </it>markerless motion analysis algorithm for the estimation of kinematics, and a neural controller that drives a synthetic arm. The vision of the entire system is to acquire kinematics from the analysis of video sequences during planar arm movements and to use it together with a neural inverse dynamics model able to provide the patient with the electrical stimulation patterns needed to perform the movement with the assisted limb.</p> <p>Methods</p> <p>The markerless motion tracking system aims at localizing and monitoring the arm movement by tracking its silhouette. It uses a specifically designed motion estimation method, that we named Neural Snakes, which predicts the arm contour deformation as a first step for a silhouette extraction algorithm. The starting and ending points of the arm movement feed an Artificial Neural Controller, enclosing the muscular Hill's model, which solves the inverse dynamics to obtain the FES patterns needed to move a simulated arm from the starting point to the desired point. Both position error with respect to the requested arm trajectory and comparison between curvature factors have been calculated in order to determine the accuracy of the system.</p> <p>Results</p> <p>The proposed method has been tested on real data acquired during the execution of planar goal-oriented arm movements. Main results concern the capability of the system to accurately recreate the movement task by providing a synthetic arm model with the stimulation patterns estimated by the inverse dynamics model. In the simulation of movements with a length of ± 20 cm, the model has shown an unbiased angular error, and a mean (absolute) position error of about 1.5 cm, thus confirming the ability of the system to reliably drive the model to the desired targets. Moreover, the curvature factors of the factual human movements and of the reconstructed ones are similar, thus encouraging future developments of the system in terms of reproducibility of the desired movements.</p> <p>Conclusion</p> <p>A novel FES-assisted rehabilitation system for the upper limb is presented and two parts of it have been designed and tested. The system includes a markerless motion estimation algorithm, and a biologically inspired neural controller that drives a biomechanical arm model and provides the stimulation patterns that, in a future development, could be used to drive a smart Functional Electrical Stimulation system (sFES). The system is envisioned to help in the rehabilitation of post stroke hemiparetic patients, by assisting the movement of the paretic upper limb, once trained with a set of movements performed by the therapist or in virtual reality. Future work will include the application and testing of the stimulation patterns in real conditions.</p

The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains

The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date. Rigorous analysis of our data-excluding false-positives due to background contamination or incorrect index assignments-indicated a lack of endogenous DNA in nearly all samples, except for one lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely to be spurious. We suggest these technologies are not suitable for use with charred archaeobotanicals and urge great caution when interpreting data obtained by HTS of these remains

Climate Change, Coral Reef Ecosystems, and Management Options for Marine Protected Areas

Marine protected areas (MPAs) provide place-based management of marine ecosystems through various degrees and types of protective actions. Habitats such as coral reefs are especially susceptible to degradation resulting from climate change, as evidenced by mass bleaching events over the past two decades. Marine ecosystems are being altered by direct effects of climate change including ocean warming, ocean acidification, rising sea level, changing circulation patterns, increasing severity of storms, and changing freshwater influxes. As impacts of climate change strengthen they may exacerbate effects of existing stressors and require new or modified management approaches; MPA networks are generally accepted as an improvement over individual MPAs to address multiple threats to the marine environment. While MPA networks are considered a potentially effective management approach for conserving marine biodiversity, they should be established in conjunction with other management strategies, such as fisheries regulations and reductions of nutrients and other forms of land-based pollution. Information about interactions between climate change and more “traditional” stressors is limited. MPA managers are faced with high levels of uncertainty about likely outcomes of management actions because climate change impacts have strong interactions with existing stressors, such as land-based sources of pollution, overfishing and destructive fishing practices, invasive species, and diseases. Management options include ameliorating existing stressors, protecting potentially resilient areas, developing networks of MPAs, and integrating climate change into MPA planning, management, and evaluation

Seasonal variation in environmental DNA detection in sediment and water samples

The use of aquatic environmental DNA (eDNA) to detect the presence of species depends on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments for longer than it does in water, and analysing sediment could potentially extend the seasonal window for species assessment. Using the great crested newt as a model, we compare how detection probability changes across the seasons in eDNA samples collected from both pond water and pond sediments. Detection of both aquatic and sedimentary eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter (January): in all seasons, detection probability of eDNA from water exceeded that from sediment. Detection probability of eDNA also varied between study areas, and according to great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA show the same seasonal fluctuations, the patterns observed in both sample types likely reflect current or recent presence of the target species. However, given the low detection probabilities found in the autumn and winter we would not recommend using either aquatic or sedimentary eDNA for year-round sampling without further refinement and testing of the methods

Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens

Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies

Planktic foraminiferal stable oxygen isotopes of Globigerinoides ruber and Mg/Ca sea surface temperature reconstructions of sediment core RAPID-21-12B from Gardar Drift over the last 230 years

The subpolar North Atlantic Ocean (SPNA) is of key importance for modulating the climate of NW Europe because of heat loss to the atmosphere from the North Atlantic Current. Although hydrographic properties of the surface SPNA vary on interannual to multidecadal timescales, hydrographic time series scarcely extend back beyond the 1950s. We present a 230 year long record of SPNA surface conditions reconstructed from a very high accumulation rate core that also registers changes in deep flow speed in the Iceland Basin. A lagged correlation is observed between the records of deep flow speed and stable oxygen isotopic composition of the surface SPNA (δ18Ow), with strongest correlation when the paleoflow speed record leads by 15–20 years. This offset may to some extent reflect size‐selective biological mixing of the sediment. Nonetheless, these records reveal a decadal‐scale coupling between surface and deep ocean variability over the past 230 years, possibly driven by the North Atlantic Oscillation, with implications for North Atlantic circulation and climate

Monitoring study of chemical and isotopic composition of lake water and ostracods in the high Andes of SE Peru.

We present the results of a years monitoring study (September 2002 to September 2003) of temperature and chemistry from both lake water and ostracods (bivalved Crustacea) from Lake Huacarpay (Lucre Basin), in the Cusco region of Peru. The project was carried out to provide a modern baseline for Holocene palaeoenvironmental reconstructions based on sequences obtained from a series of lakes in the high Andes of SE Peru. Terrestrial palaeoenvironmental reconstructions are often based on the chemical composition (e.g. [delta]18O, [delta]13C, Mg/Ca) of ostracod valves in lacustrine sediments. In controlled experiments, several authors have investigated the chemical composition of ostracod valves in relation to separate environmental parameters such as temperature or salinity. However, these relationships have only been established for a limited number of ostracod taxa. Hence, this monitoring study was carried out to determine the link between the chemical composition of ostracod valves and environmental parameters in their natural habitat. Water and ostracod samples were taken monthly from the northern side of Lake Huacarpay (71 4324"W; 13 3636"S; 3100 m a.s.l.), adjacent to a reed marsh, dominated by Typha dominguensis vegetation; water temperature was recorded every hour using a StarmonMini temperature logger. The climate of the research area is strongly seasonal: most precipitation falls between December and March, while dry and cold conditions (causing occasional freezing at night) occur from May-August. The chemical composition of the monthly water samples has been analysed, while the taxonomy of the ostracods is currently being resolved. Almost all measured major and trace elements show a clear annual trend with highest values between September and December. Stable oxygen isotopes in at least one common species of ostracod roughly follow this pattern. This is the first study of its kind from Peru integrating ostracod chemistry and annual temperature variability, and such investigations will be invaluable for interpreting palaeoecological records from this area

Surface and deep ocean coupling in the subpolar North Atlantic during the last 230 years

The subpolar North Atlantic Ocean (SPNA) is of key importance for modulating the climate of NW Europe because of heat loss to the atmosphere from the North Atlantic Current. Although hydrographic properties of the surface SPNA vary on interannual to multidecadal timescales, hydrographic time series scarcely extend back beyond the 1950s. We present a 230 year long record of SPNA surface conditions reconstructed from a very high accumulation rate core that also registers changes in deep flow speed in the Iceland Basin. A lagged correlation is observed between the records of deep flow speed and stable oxygen isotopic composition of the surface SPNA (delta(18)O(w)), with strongest correlation when the paleoflow speed record leads by 15-20 years. This offset may to some extent reflect size-selective biological mixing of the sediment. Nonetheless, these records reveal a decadal-scale coupling between surface and deep ocean variability over the past 230 years, possibly driven by the North Atlantic Oscillation, with implications for North Atlantic circulation and climate

Surface and deep ocean coupling in the subpolar North Atlantic during the last 230 years

The subpolar North Atlantic Ocean (SPNA) is of key importance for modulating the climate of NW Europe because of heat loss to the atmosphere from the North Atlantic Current. Although hydrographic properties of the surface SPNA vary on interannual to multidecadal timescales, hydrographic time series scarcely extend back beyond the 1950s. We present a 230 year long record of SPNA surface conditions reconstructed from a very high accumulation rate core that also registers changes in deep flow speed in the Iceland Basin. A lagged correlation is observed between the records of deep flow speed and stable oxygen isotopic composition of the surface SPNA (d 18 O w ), with strongest correlation when the paleoflow speed record leads by 15–20 years. This offset may to some extent reflect size‐selective biological mixing of the sediment. Nonetheless, these records reveal a decadal‐scale coupling between surface and deep ocean variability over the past 230 years, possibly driven by the North Atlantic Oscillation, with implications for North Atlantic circulation and climate