Sustained Input Research Articles

Readout Software for the Alice Integrated Online-Offline (O2) System

ALICE (A Large Ion Collider Experiment) is a heavy -ion detector studying the physics of strongly interacting matter and the quarkgluon plasma at CERN’s LHC (Large Hadron Collider). During the second long shutdown of the LHC, the ALICE detector will be upgraded to cope with an interaction rate of 50 kHz in Pb–Pb collisions, producing in the online computing system (O2) a sustained input throughput of 3 TB/s. The readout software is in charge of the first step of data-acquisition, handling the data transferred from over 8000 detector links to PC memory by dedicated PCI boards, formatting and buffering incoming traffic until sent to the next components in the processing pipeline. On the 250 readout nodes where it runs, the software has to sustain a throughput which can locally exceed 100 Gb/s. We present the modular design used to cope with various data sources (hardware devices and software emulators), integrated with the central O2 components (logging, configuration, monitoring, data sampling, transport) and initiating the online data flow using the standard O2 messaging system. Performance considerations and measurements are also discussed.

Design of recombinase and terminator-based genetic switches for cell state control

Various genetic switches have been developed to let engineered cells perform designed functions. However, a sustained input is often needed to maintain the on/off state, which is energy-consuming and sensitive to perturbation. Therefore, we developed a set of transcriptional switches for cell states control that were constructed by the inversion effect of site-specific recombinases on terminators. Such a switch could respond to a pulse signal and maintain the new state by itself until the next input. With a bottom-up design principle, we first characterized the terminators and recombinases. Then the mutual interference was studied to select compatible pairs, which were used to achieve one-time and two-time state transitions. Finally, we constructed a biological seven-segment display as a demonstration to prove such switch's immense potential for application.

Challenging local realism with human choices.

A Bell test is a randomized trial that compares experimental observations against the philosophical worldview of local realism 1 , in which the properties of the physical world are independent of our observation of them and no signal travels faster than light. A Bell test requires spatially distributed entanglement, fast and high-efficiency detection and unpredictable measurement settings2,3. Although technology can satisfy the first two of these requirements4-7, the use of physical devices to choose settings in a Bell test involves making assumptions about the physics that one aims to test. Bell himself noted this weakness in using physical setting choices and argued that human 'free will' could be used rigorously to ensure unpredictability in Bell tests 8 . Here we report a set of local-realism tests using human choices, which avoids assumptions about predictability in physics. We recruited about 100,000 human participants to play an online video game that incentivizes fast, sustained input of unpredictable selections and illustrates Bell-test methodology 9 . The participants generated 97,347,490 binary choices, which were directed via a scalable web platform to 12 laboratories on five continents, where 13 experiments tested local realism using photons5,6, single atoms 7 , atomic ensembles 10 and superconducting devices 11 . Over a 12-hour period on 30 November 2016, participants worldwide provided a sustained data flow of over 1,000 bits per second to the experiments, which used different human-generated data to choose each measurement setting. The observed correlations strongly contradict local realism and other realistic positions in bipartite and tripartite 12 scenarios. Project outcomes include closing the 'freedom-of-choice loophole' (the possibility that the setting choices are influenced by 'hidden variables' to correlate with the particle properties 13 ), the utilization of video-game methods 14 for rapid collection of human-generated randomness, and the use of networking techniques for global participation in experimental science.

Developing a spinal cord injury rehabilitation service in Madagascar.

Rehabilitation for people with spinal cord injury in many low- and middle-income countries is not avail-able or is in the early stages of development. However, rehabilitation is recognized as crucial in order to optimize functional recovery and outcomes for patients with spinal cord injury. With an increasing incidence of spinal cord injury, the unmet need for rehabilitation is huge. This report describes the early development of a specialist rehabilitation service for spinal cord injury in Madagascar, one of the poorest countries in the world. The sustained input to an expanding rehabilitation team has led to reductions in avoidable complications. The input of the rehabilitation team has been welcomed by the neurosurgery department, which has recognized fewer delays in patients undergoing surgical treatments. Cost, lack of resources and trained staff, and poor understanding of disability continue to provide challenges. However, the development of the rehabilitation service using low technology, but with a high level of knowledge and systematic management, is a source of considerable pride. This development in Madagascar can be regarded as a model for spinal cord injury rehabilitation in other low-resource settings.

Online monitoring of a photocatalytic reaction by real-time high resolution FlowNMR spectroscopy.

We demonstrate how FlowNMR spectroscopy can readily be applied to investigate photochemical reactions that require sustained input of light and air to yield mechanistic insight under realistic conditions. The Eosin Y mediated photo-oxidation of N-allylbenzylamine is shown to produce imines as primary reaction products from which undesired aldehydes form after longer reaction times. Facile variation of reaction conditions during the reaction in flow allows for probe experiments that give information about the mode of action of the photocatalyst.

03 Data linkage across ambulance services and acute trusts: challenges and opportunities

BackgroundMost callers to 999 ambulance services are transported to hospital emergency departments (EDs), but ambulance services receive no information on patient outcomes. PHED Data is a two-year mixed-methods observational study...

Comparison of USDA Forest Service and Stakeholder Motivations and Experiences in Collaborative Federal Forest Governance in the Western United States.

In the United States, over 191 million acres of land is managed by the United States Department of Agriculture Forest Service, a federal government agency. In several western U.S. states, organized collaborative groups have become a de facto governance approach to providing sustained input on management decisions on much public land. This is most extensive in Oregon, where at least 25 "forest collaboratives" currently exist. This affords excellent opportunities for studies of many common themes in collaborative governance, including trust, shared values, and perceptions of success. We undertook a statewide survey of participants in Oregon forest collaboratives to examine differences in motivations, perceptions of success, and satisfaction among Forest Service participants ("agency participants"), who made up 31% of the sample, and other respondents ("non-agency") who represent nonfederal agencies, interest groups, citizens, and non-governmental groups. We found that agency participants differed from non-agency participants. They typically had higher annual incomes, and were primarily motivated to participate to build trust. However, a majority of all respondents were similar in not indicating any other social or economic motivations as their primary reason for collaborating. A majority also reported satisfaction with their collaborative-despite not ranking collaborative performance on a number of specific potential outcomes highly. Together, this suggests that collaboration in Oregon is currently perceived as successful despite not achieving many specific outcomes. Yet there were significant differences in socioeconomic status and motivation that could affect the ability of agency and nonagency participants to develop and achieve mutually-desired goals.

Regional and seasonal variability in planktonic photosynthesis and planktonic community respiration in Amazon floodplain lakes

Results from two regional surveys and multi-lake seasonal studies were used to investigate the variability of phytoplankton photosynthesis and planktonic community respiration in central Amazon floodplain lakes. Hypothesized effects of optical and chemical variables on planktonic photosynthesis and respiration were examined statistically. Changes in dissolved oxygen in light and dark bottles distributed along light-gradients in a shipboard incubator or in situ were used to calculate volumetric community respiration (Rc), volumetric gross photosynthesis (P), daily integral gross photosynthesis (Π), and daily integral community respiration rates (Λ). Π varied significantly among all lakes with source-water river stage and source-water river type. Λ also varied significantly with source-water river stage. Variation in maximum depth linked to source-water river stage was a key factor controlling seasonal variations in Π through its influence on total suspended solids and total phosphorus concentrations which affected light extinction and light-saturated photosynthesis, respectively. The predominance of sub-saturated dissolved O2 in the pelagic surface waters of Amazon floodplain lakes was attributed to high integral Rc:P ratios, indicating the existence of large sustained inputs of non-phytoplankton organic carbon to these environments.

Speeded saccadic and manual visuo-motor decisions: Distinct processes but same principles

Action decisions are considered an emergent property of competitive response activations. As such, decision mechanisms are embedded in, and therefore may differ between, different response modalities. Despite this, the saccadic eye movement system is often promoted as a model for all decisions, especially in the fields of electrophysiology and modelling. Other research traditions predominantly use manual button presses, which have different response distribution profiles and are initiated by different brain areas. Here we tested whether core concepts of action selection models (decision and non-decision times, integration of automatic and selective inputs to threshold, interference across response options, noise, etc.) generalise from saccadic to manual domains. Using two diagnostic phenomena, the remote distractor effect (RDE) and ‘saccadic inhibition', we find that manual responses are also sensitive to the interference of visual distractors but to a lesser extent than saccades and during a shorter time window. A biologically-inspired model (DINASAUR, based on non-linear input dynamics) can account for both saccadic and manual response distributions and accuracy by simply adjusting the balance and relative timings of transient and sustained inputs, and increasing the mean and variance of non-decisional delays for manual responses. This is consistent with known neurophysiological and anatomical differences between saccadic and manual networks. Thus core decision principles appear to generalise across effectors, consistent with previous work, but we also conclude that key quantitative differences underlie apparent qualitative differences in the literature, such as effects being robustly reported in one modality and unreliable in another.

PP116 Data Linkage Across Ambulance Services And Emergency Departments

INTRODUCTION:Most callers to emergency ambulance services are transported to hospital emergency departments (EDs), but ambulance services receive no information on patient outcomes. Pre-Hospital and Emergency Department (PHED) Data is a two-year mixed-methods observational study of the process and potential benefits of linking ambulance and ED data to allow analysis of patient outcomes. We report on our first aim, to examine the potential opportunities and challenges of this data linkage initiative.METHODS:We approached six hospital trusts in an English metropolitan area. We used a structured learning log to collect data on the process, time input and reflections. We analyzed these data with descriptive statistics, and qualitatively for themes.RESULTS:All six trusts agreed to participate. We used an algorithm based on date, time and patient demographics to link data. We achieved a dataset of 775,018 records covering 2012 – 2016, and a linkage rate of 81 percent.Initial set up tasks within the ambulance service took 30 hours 20 minutes. We then identified five stages of tasks with each hospital trust: negotiating senior approval; exploring data availability; information governance agreement; data transfer; and linking. Mean time spent by the research team on these processes was 30 hours 30 minutes per trust (range: 17 hours 20 minutes to 43 hours 10 minutes), plus additional time from staff of hospital trusts. The most intensive phases were: negotiating senior approval (mean: 8 hours 5 minutes), and data linking (mean: 12 hours 40 minutes). The stage which took the longest was information governance (mean: 19 weeks).Key themes included the positive attitudes of trusts to participating, the range of decision makers involved, and the need for sustained input from the research team.CONCLUSIONS:We found the process of data linkage was feasible, but requires dedicated time from research and trust staff, over a prolonged period, to achieve set up. Linked data are now being analyzed.

Making the transition to post-secondary education: opportunities and challenges experienced by students with ASD in the Republic of Ireland

Internationally there are increasing numbers of young people on the ASD spectrum attending higher education. Early transition planning is essential and students with ASD often require support to articulate their post-school educational goals and actively participate in transition planning meetings. Services within higher education are primarily designed to provide academic supports however, non-academic supports may be an even more crucial factor in enabling successful transitions for young people on the ASD spectrum who often experience heightened anxiety within an unfamiliar environment. Within this paper, the results of a small-scale exploratory study of the transition experiences of six young people on the ASD spectrum to post-secondary education will be shared. There was limited evidence that transition planning had been initiated as a formal process for the six students. Accessing support in higher education proved to be a complex process for some students who required sustained input from parents to ensure that they would utilise the supports available. Encouraging the development of self-determination skills, a key predictor of success in higher education, needs to begin in secondary school. It is anticipated insights from this study can contribute to the development of an embedded infrastructure to support effective transitions for students with ASD to post-secondary education.

MATRIX: a 15 ps resistive interpolation TDC ASIC based on a novel regular structure

This paper presents a 4-channel TDC ASIC with the following features: 15-ps LSB (9.34 ps after calibration), 10-ps jitter, < 4-ps time resolution, up to 10 MHz of sustained input rate per channel, 45 mW of power consumption and very low area (910×215 μm2) in a commercial 180 nm technology. The main contribution of this work is the novel design of the clock interpolation circuitry based on a resistive interpolation mesh circuit (patented), a two-dimensional regular structure with very good properties in terms of power consumption, area and low process variability.

Processing Oscillatory Signals by Incoherent Feedforward Loops.

From the timing of amoeba development to the maintenance of stem cell pluripotency, many biological signaling pathways exhibit the ability to differentiate between pulsatile and sustained signals in the regulation of downstream gene expression. While the networks underlying this signal decoding are diverse, many are built around a common motif, the incoherent feedforward loop (IFFL), where an input simultaneously activates an output and an inhibitor of the output. With appropriate parameters, this motif can exhibit temporal adaptation, where the system is desensitized to a sustained input. This property serves as the foundation for distinguishing input signals with varying temporal profiles. Here, we use quantitative modeling to examine another property of IFFLs—the ability to process oscillatory signals. Our results indicate that the system’s ability to translate pulsatile dynamics is limited by two constraints. The kinetics of the IFFL components dictate the input range for which the network is able to decode pulsatile dynamics. In addition, a match between the network parameters and input signal characteristics is required for optimal “counting”. We elucidate one potential mechanism by which information processing occurs in natural networks, and our work has implications in the design of synthetic gene circuits for this purpose.

Sediment trap efficiency of paddy fields at the watershed scale in a mountainous catchment in northwest Vietnam

Abstract. Composite agricultural systems with permanent maize cultivation in the uplands and irrigated rice in the valleys are very common in mountainous southeast Asia. The soil loss and fertility decline of the upland fields is well documented, but little is known about reallocation of these sediments within the landscape. In this study, a turbidity-based linear mixed model was used to quantify sediment inputs, from surface reservoir irrigation water and from direct overland flow, into a paddy area of 13 ha. Simultaneously, the sediment load exported from the rice fields was determined. Mid-infrared spectroscopy was applied to analyze sediment particle size. Our results showed that per year, 64 Mg ha−1 of sediments were imported into paddy fields, of which around 75 % were delivered by irrigation water and the remainder by direct overland flow during rainfall events. Overland flow contributed one-third of the received sandy fraction, while irrigated sediments were predominantly silty. Overall, rice fields were a net sink for sediments, trapping 28 Mg ha−1 a−1 or almost half of total sediment inputs. As paddy outflow consisted almost exclusively of silt- and clay-sized material, 24 Mg ha−1 a−1 of the trapped amount of sediment was estimated to be sandy. Under continued intensive upland maize cultivation, such a sustained input of coarse material could jeopardize paddy soil fertility, puddling capacity and ultimately food security of the inhabitants of these mountainous areas. Preventing direct overland flow from entering the paddy fields, however, could reduce sand inputs by up to 34 %.

Motor facilitation during action observation: The role of M1 and PMv in grasp predictions

Recent theories propose that movement observation is not a “passive mirror” of ongoing actions but might induce anticipatory activity when predictable movements are observed, e.g., because the action goal is known. Here we investigate this mechanism in a series of 3 experiments, by applying transcranial magnetic stimulation (TMS) to primary motor cortex (M1) while subjects observed either whole hand or precision grasping performed by an actor. We show that corticomotor excitability changes in a grip-specific manner but only once the grip can be decoded based on the observed kinematic cues (Exp. 1). By contrast, presenting informative contextual precues evokes anticipatory modulations in M1 already during the reach phase, i.e., well before the grip type could be observed, a finding in line with a predictive coding account (Exp. 2). Finally, we used paired-pulse (PP) TMS to show that ventral premotor cortex (PMv) facilitates grip-specific representations in M1 but only while grip formation is observed. These findings suggest that PMv and M1 interact temporarily and mainly when motor aspects of hand-object interactions are extracted from visual information. By contrast, no sustained input from PMv to M1 seems to be required to maintain action representations that are anticipated based on contextual information or once the grip is formed (Exp. 3).

The 2014 water release into the arid Colorado River delta and associated water losses by evaporation

For the first time in history, water was intentionally released for environmental purposes into the final, otherwise dry, 160-km stretch of the Colorado River basin, south of the Mexican border. Between March and May 2014 three pulses of water with a total volume of 132×106m3 were released to assess the restoration potential of endemic flora along its course and to reach its estuary. The latter had not received a sustained input of fresh water and nutrients from its main fluvial source for over 50years because of numerous upstream dam constructions. During this pulse flow large amounts of water were lost and negligible amounts reached the ocean. While some of these water losses can be attributed to plant uptake and infiltration, we were able to quantify evaporation losses between 16.1 to 17.3% of the original water mass % within the first 80km after the Morels Dam with water stable isotope data. Our results showed no evidence for freshwater reaching the upper Colorado River estuary and it is assumed that the pulse flow had only negligible influences on the coastal ecosystem. Future water releases that aim on ecological restoration need to become more frequent and should have larger volumes if more significant effects are to be established on the area.

Physiologically informed dynamic causal modeling of fMRI data

The functional MRI (fMRI) signal is an indirect measure of neuronal activity. In order to deconvolve the neuronal activity from the experimental fMRI data, biophysical generative models have been proposed describing the link between neuronal activity and the cerebral blood flow (the neurovascular coupling), and further the hemodynamic response and the BOLD signal equation. These generative models have been employed both for single brain area deconvolution and to infer effective connectivity in networks of multiple brain areas. In the current paper, we introduce a new fMRI model inspired by experimental observations about the physiological underpinnings of the BOLD signal and compare it with the generative models currently used in dynamic causal modeling (DCM), a widely used framework to study effective connectivity in the brain. We consider three fundamental aspects of such generative models for fMRI: (i) an adaptive two-state neuronal model that accounts for a wide repertoire of neuronal responses during and after stimulation; (ii) feedforward neurovascular coupling that links neuronal activity to blood flow; and (iii) a balloon model that can account for vascular uncoupling between the blood flow and the blood volume. Finally, we adjust the parameterization of the BOLD signal equation for different magnetic field strengths. This paper focuses on the form, motivation and phenomenology of DCMs for fMRI and the characteristics of the various models are demonstrated using simulations. These simulations emphasize a more accurate modeling of the transient BOLD responses — such as adaptive decreases to sustained inputs during stimulation and the post-stimulus undershoot. In addition, we demonstrate using experimental data that it is necessary to take into account both neuronal and vascular transients to accurately model the signal dynamics of fMRI data. By refining the models of the transient responses, we provide a more informed perspective on the underlying neuronal process and offer new ways of inferring changes in local neuronal activity and effective connectivity from fMRI.

Development of recent chronologies and evaluation of temporal variations in Pb fluxes and sources in lake sediment and peat cores in a remote, highly radiogenic environment, Cairngorm Mountains, Scottish Highlands

The use of stable Pb isotope analyses in conjunction with recent (210Pb and anthropogenic radionuclide) chronologies has become a well-established method for evaluating historical trends in depositional fluxes and sources of atmospherically deposited Pb using archival records in lake sediment or peat cores. Such studies rely upon (i) simple radioactive disequilibrium between unsupported 210Pb and longer-lived members of the 238U decay series and (ii) well-defined values for the isotopic composition of contaminant Pb and indigenous Pb in the study area. However, areas of high natural radioactivity can present challenging environments for such studies, with potential complications arising from more complex disequilibria in the 238U decay series and the occurrence, at local or regional level, of anomalous, ill-defined stable isotope ratios due to the presence of elevated levels of radiogenic Pb.Results are presented here for a study of a sediment core from a freshwater lake, Loch Einich, in the high natural radioactivity area of the Cairngorm Mountains of Scotland. 238U decay series disequilibria revealed recent diagenetic re-deposition of both U and 226Ra, the latter resulting in a requirement to use a modified calculation to derive a 210Pb chronology for the core. Confidence in the chronology was provided by good agreement with the independent 241Am chronology, but the 137Cs distribution was affected by significant post-depositional mobility in the organic-rich sediment. The systematics of variations in 230Th, 232Th and stable Pb isotope ratio distributions were used to establish the indigenous Pb characteristics of the sediment. The relatively high radiogenic content of the indigenous Pb resulted in complications in source apportionment, in particular during the 20th century, with multiple natural and anthropogenic sources precluding the use of a simple binary mixing model. Consequently, 206Pb/207Pb ratios in Scottish moss samples from an archive collection were used to provide the input term for atmospheric deposition in order to establish historical trends in indigenous and anthropogenic Pb fluxes.A test of the accuracy of the derived Pb fluxes was provided by analysis of a core from a nearby blanket peat deposit, Great Moss. Independent atmospheric and basal inputs gave a complex distribution of 210Pb in the peat, but this did not affect calculation of a 210Pb chronology. Once again, the 210Pb chronology was supported by the 241Am distribution.Temporal trends in anthropogenic Pb deposition derived for the Loch Einich sediment core were in generally good agreement with those for the Great Moss peat core, other peat cores and some other lake sediment cores from northern Scotland, providing confidence in the use of the archive moss data to characterise atmospheric deposition. However, sustained input of Pb to Loch Einich sediment at relatively high levels in the late 20th century, after the regional decline in atmospheric Pb deposition, suggested that catchment-derived Pb is now a significant component of the depositional flux for Loch Einich.

Changes in soil phosphorus fractions after 9 years of continuous nitrogen addition in a Larix gmelinii plantation

N addition decreased soil inorganic P availability, microbial biomass P, and acid phosphatase activity in the larch plantation. Soil inorganic P availability decreased after N addition due to the changes in both microbial properties and plant uptake. Soil phosphorus (P) availability is considered an important factor in influencing the biomass production of plants. Sustained inputs of nitrogen (N) through atmospheric deposition or N fertilizers, particularly in temperate forests, may change the composition and availability of P and thus affect long-term forest productivity. The objective of this study was to assess soil P availability, P fractions, and microbial properties including microbial biomass P and acid phosphatase activity after 9 consecutive years of N addition in a larch (Larix gmelinii) plantation, northeastern China. From 2003 to 2011, NH4NO3 was added to replicate plots (three 20 m × 30 m plots) in the larch plantation each year at a rate of 100 kg N ha−1 year−1. Soil samples from 0–10-cm and 10–20-cm depths were collected in N addition plots and control (no N addition) plots. N addition significantly decreased soil NaHCO3-Pi (Pi is inorganic P), microbial biomass P, and acid phosphatase activity but increased the NaOH-Pi concentration. N addition appeared to induce a decrease in soil inorganic P availability by changing pH and P uptake by trees. In addition, N addition significantly decreased the NaOH-Po (Po is organic P) concentration, possibly because of increased P mineralization. However, the total P and other P fractions were unaffected by N fertilization. Our results suggested that N addition enhanced P uptake by trees, whereas it reduced soil inorganic P availability as well as microbial biomass and activity related to soil P cycling in the larch plantation.

Performance of a temperate-zone channel catfish biofloc technology production system during winter

Channel catfish (Ictalurus punctatus) have been grown successfully in an outdoor biofloc technology production system. Outdoor biofloc production systems in the tropics are operated year-round, whereas the channel catfish studies were conducted only during the growing season and biofloc production tanks were harvested and idled for the winter. If an outdoor biofloc production system is to be adopted by farmers at temperate latitudes, then data gaps related to system and fish performance over the winter must be addressed. The present study was conducted to address these data gaps for channel catfish culture. Waters from a recently completed biofloc production experiment that contained low (153.3mg/L) and high (790.0mg/L) total suspended solids were retained for this study. Three 15.7-m3 tanks per water type each were stocked (8kg/m3) with market size channel catfish from that same study for a 152-day study from November to April. Mean chlorophyll a concentrations were similar in both treatments during the first 55 days, after which treatments diverged and chlorophyll a concentration increased linearly (P<0.001, R2=0.721) to a mean final concentration of 2251.7mg/m3 in the low solids treatment. Ammonia from ammonium chloride spikes (1.25–1.5mg TAN) added on three occasions during the experiment was biotransformed completely, putatively by algal uptake and nitrification. Ammonia biotransformation rate was linearly related to mean water temperature in the high solids (P<0.001, R2=0.920) and low solids (P=0.002, R2=0.761) treatments. Catfish survival through the winter was high (99.75%) in biofloc tanks and did not differ significantly between treatments. Net fish yield did not differ significantly between treatments. However, net fish yields were 1–4% less than initial fish biomasses. Water in the biofloc production tanks appeared to retain through the winter the ability to biotransform ammonia regardless of whether phytoplankton or suspended solids predominate and despite sustained input of ammonia-nitrogen. Having an active biofloc in the spring obviates the start-up time required to establish a new, fully functional biofloc and the associated TAN and nitrite spikes.