Find research datasets worth reusing

opencc-by-4.0Aug 2020View details →

Application of spectral library prediction for parallel reaction monitoring of viral peptides_DDA_data

Project description: A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.   Sample processing protocol: A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x106, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 105, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 106, max. injection time of 55 ms and an isolation window of 1.4 m/z. Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x106, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 105, max. injection time of 50 ms and an isolation window of 2 m/z.   To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 106, max. injection time of 100 ms and an isolation window of 1.4 m/z.     Data processing protocol: DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).

opencc-by-4.0Aug 2020View details →

Application of spectral library prediction for parallel reaction monitoring of viral peptides_PRM_NCE_data

opencc-zeroAug 2020View details →

Artificial night light helps account for observer bias in citizen science monitoring of an expanding large mammal population

1. The integration of citizen scientists into ecological research is transforming how, where, and when data are collected, and expanding the potential scales of ecological studies. Citizen-science projects can provide numerous benefits for participants, while educating and connecting professionals with lay audiences, potentially increasing acceptance of conservation and management actions. However, for all the benefits, collection of citizen-science data is often biased towards areas that are easily accessible (e.g. developments and roadways), and thus data are usually affected by issues typical of opportunistic surveys (e.g. uneven sampling effort). These areas are usually illuminated by artificial light at night (ALAN), a dynamic sensory stimulus that alters the perceptual world for both humans and wildlife. 2. Our goal was to test whether satellite-based measures of ALAN could improve our understanding of the detection process of citizen scientist-reported sightings of a large mammal. 3. We collected observations of American black bears (Ursus americanus; n = 1,315) outside their primary range in Minnesota, USA, as part of a study to gauge population expansion. Participants from the public provided sighting locations of bears on a website. We used an occupancy modelling framework to determine how well ALAN accounted for observer metrics when compared to other commonly used metrics (e.g. housing density). 4. Citizen scientists reported 17% of bear sightings were under artificially-lit conditions and monthly ALAN estimates did the best job accounting for spatial bias in detection of all observations, based on AIC values and effect sizes (β ^ = 0.81, 0.71 – 0.90 95% CI). Bear detection increased with elevated illuminance; relative abundance was positively associated with natural cover, closer proximity to primary bear range and lower road density. Although the highest counts of bear sightings occurred in the highly illuminated suburbs of the Minneapolis-St. Paul metropolitan region, we estimated substantially higher bear abundance in another region with plentiful natural cover and low ALAN (up to 275% increased predicted relative abundance) where observations were sparse. 5. We demonstrate the importance of considering ALAN radiance when analyzing citizen scientist-collected data, and we highlight the ways that ALAN data provides a dynamic snapshot of human activity. 31-Jul-2020

opencc-zeroAug 2020View details →

Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of the major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium (mLD) post-LLIN was a positive indicator of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.

opencc-by-4.0Jul 2020View details →

Transcranial Direct Current Stimulation Improves Action-Outcome Monitoring in Schizophrenia Spectrum Disorder

Data set of the publication: Straube, B., van Kemenade, B.M., Kircher, T. & Schülke, R. (2020). Transcranial Direct Current Stimulation Improves Action-Outcome Monitoring in Schizophrenia Spectrum Disorder. Brain Communications. doi: 10.1093/braincomms/fcaa151 Abstract Background: Patients with schizophrenia spectrum disorder (SSD) often demonstrate impairments in action-outcome monitoring. Passivity phenomena and hallucinations, in particular, have been related to impairments of efference copy-based predictions which are relevant for the monitoring of outcomes produced by voluntary action. Frontal transcranial direct current stimulation (tDCS) has been shown to improve action-outcome monitoring in healthy subjects. However, whether tDCS can improve action monitoring in patients with SSD remains unknown. Objective: We investigated whether tDCS can improve the detection of temporal action-outcome discrepancies in patients with SSD. Methods: On 4 separate days, we applied sham or left cathodal/right anodal tDCS in a randomised order to frontal (F3/F4), parietal (CP3/CP4) and frontoparietal (F3/CP4) areas of 19 patients with SSD and 26 healthy control (HC) subjects. Action-outcome monitoring was assessed subsequent to 10 min of sham/tDCS (1.5 mA). After a self-generated (active) or externally generated (passive) key press, subjects were presented with a visual outcome (a dot on the screen), which was presented after various delays (0–417 ms). Participants had to detect delays between the key press and the visual consequence. Symptom subgroups were explored based on the presence or absence of symptoms related to a paranoid-hallucinatory syndrome (SSD phs+/phs-). Results: In general, delay-detection performance was impaired in the SSD compared to the HC group. Interaction analyses showed group-specific (SSD vs HC) and symptom-specific (SSD phs+ vs SSD phs-) tDCS effects. Post-hoc tests revealed that frontal tDCS improved the detection of long delays in active conditions and reduced the proportion of false alarms in undelayed trials of the passive condition in patients. The SSD phs- group benefited especially from frontal tDCS in active conditions, while improvement in the SSD phs+ group was predominantly reflected in reduced false alarm rates in passive conditions. Conclusion: These data provide some first evidence for the potential utility of tDCS in improving efference copy mechanisms and action-outcome monitoring in SSD. Current data indicate that improving efference copy-related processes can be especially effective in patients with no or few positive symptoms, while intersensory matching (i.e. task-relevant in passive conditions) could be more susceptible to improvement in patients with paranoid-hallucinatory symptoms.   Keywords: transcranial direct current stimulation; action-perception; action feedback; delay detection; schizophrenia.

Long-term monitoring of gaseous elementary mercury in background air at the polar station Amderma, Russian Arctic

The  produced  dataset  (in  MS  Excel  format)  contains  time-series  of  concentrations  of  gaseous elementary mercury (GEM, thereafter – mercury) in the background air collected at the Amderma polar station near the Amderma settlement of the Russian Arctic (69,72 deg N; 61,62 deg E; Yugor Peninsula, Russia) from 24th June 2001 until 13th February 2013. The concentrations for mercury are given in ng/m^3. Concentrations were measured in the air at every 30 minute interval using Tekran-2537A instrument. After checking quality of recorded values of the mercury concentration, the average of two consecutive measurements in two channels (average 1 hour measurements) are calculated.  Data (as time-series) are grouped into three blocks covering different time periods and adjacent locations. First block covers period from 24th June 2001 to 13th February 2004 (when the analyzer was located at a distance of about 9 km from the coastline of the Kara Sea). Second block covers period from 3th April 2005 to 12th June 2010 (when the analyzer was placed at 2.5 km from the coast). Third block covers period from 15th June 2010 to 10th October 2013 (the analyzer was set up at a distance of 200 m from the coastline of the sea).

MONITORING AND MODELING OF HYDROLOGICAL PROCESSES IN THE SEMIARID REGION OF BRAZIL: THE CARIRI EXPERIMENTAL BASINS

DATASET DESCRIPTION - Two experimental basins – the Cariri basins – were installed in a typically semiarid region in the State of Paraíba, Brazil, for obtaining reliable estimates of runoff and soil erosion in different scales to evaluate the influence of the human activities and other factors over the processes of runoff and erosion. In the first basin, located in the municipality of Sumé, the field studies were carried out at three different scales: four micro-basins with an area of around 0.5 ha; nine standard Wischmeier-type erosion plots of 100 m2 and seven sample plots of 1 m2. The experimental units had varied vegetal cover and management and, except the sample plots, were subjected to natural rainfall events only, and were monitored from 1982 to 1991. The total runoff and total sediment yield were determined for each of the events of precipitation. The installations of the second basin, in the near municipality of São João do Cariri, were planned for the continuation of the studies initiated at Sumé, and include erosion plots (100 m2), micro-basins, and sub-basins, which are being monitored for runoff and sediment production up to now. Among them, two nested micro-basins were monitored to detect any scale effect at the micro-basin level. Nearly 600 events of natural precipitation, that produced runoff in at least one of the experimental units, have been registered. This bulk of data was utilised to evaluate the influence of various factors, including cultivation practices. The data collected so far has been successfully used to calibrate hydrological models for plots and micro-basins. Parameters have been tested by means of cross validations among micro-basins and sub-basins. FILENAMES – The data files are divided into three categories: Description of the equipment utilized for collecting data and their locations, the data collected from the monitored experimental basins and another with maps, figures and pictures. The file names are designated with the basin name and the content. The files describing the equipment comprise: BASINNAME_DATADESCRIPTION, where BASINNAME could be EBS or EBSJC. The files with the data collected in the experimental basins are denominated like: BASINNAME_DATANAME. The DATANAME will be one of the three that may be, precipitation, runoff and sediment yield, or climatologic data. The file with maps and other information are identified as: BASINNAME_GEOPHYSICDATANAME, and BASINNAME_PICTURES. The geophysical data refer to topographic data, soil data, land cover and the drainage network. Graphs, pictures, etc., are included in the PICTURES file. DATAFORMAT – The data file about equipment and localization as well as the data collected in experimental units are of the type “. csv”, the geophysical data are of either “.dwg” or “.shp”. The figures and picture are in the format: .jpeg, .png or .tif. ACKNOWLEDGEMENTS – SUDENE – the Superintendency for the Development of the Northeast of Brazil with the cooperation of ORSTOM – the French Government Agency for Technical Cooperation Overseas was responsible for implementing the program of Representative and Experimental Basins in the region beginning in the decade of 1970. Pierre Audry, Eric Cadier, Jean Leprun and Michel Molinier, hydrologists and soil scientists from France played key roles in the selection of site, installation of experimental units and beginning the operation of the EBS. Beronildo Freitas was the engineer from SUDENE responsible for technical coordination and administration. The contributions of other researchers and technical people have been listed by Srinivasan and Galvão (2003). The installation of the research catchment at São João de Cariri had the valuable collaboration of GTZ, the cooperation Agency of the Government of Germany. Dr. Ing Ubald Koch was responsible for getting all the equipment, installing them and conducting research work along with the members of the Hydrology Research Group of the Federal Universities of Paraiba and Campina Grande. Late prof. Manoel Gilberto de Barros efficiently coordinated the field work. Eduardo Figueiredo, Celso Santos and Ricardo Aragão have made note worthy contributions. The Ministry of Science and Technology of Brazil has provided the bulk of the financial support needed for the operation of the basins, through its main funding agencies of CNPq (National Council for Development of Science and Technology) and FINEP (Agency for Financing research Studies and Projects).

opencc-zeroOct 2020View details →

Satellite-based habitat monitoring reveals long-term dynamics of deer habitat in response to forest disturbances

Disturbances play a key role in driving forest ecosystem dynamics, but how disturbances shape wildlife habitat across space and time often remains unclear. A major reason for this is a lack of information about changes in habitat suitability across large areas and longer time periods. Here, we use a novel approach based on Landsat satellite image time series to map seasonal habitat suitability annually from 1986 to 2017. Our approach involves characterizing forest disturbance dynamics using Landsat-based metrics, harmonizing these metrics through a temporal segmentation algorithm, and then using them together with GPS telemetry data in habitat models. We apply this framework to assess how natural forest disturbances and post-disturbance salvage logging affect habitat suitability for two ungulates, roe deer (Capreolus capreolus) and red deer (Cervus elaphus), over 32 years in a Central European forest landscape. We found that red and roe deer differed in their response to forest disturbances. Habitat suitability for red deer consistently improved after disturbances, whereas the suitability of disturbed sites was more variable for roe deer depending on season (lower during winter than summer) and disturbance agent (lower in windthrow versus bark-beetle-affected stands). Salvage logging altered the suitability of bark beetle-affected stands for deer, having negative effects on red deer and mixed effects on roe deer, but generally did not have clear effects on habitat suitability in windthrows. Our results highlight long-lasting legacy effects of forest disturbances on deer habitat. For example, bark beetle disturbances improved red deer habitat suitability for at least 25 years. The duration of disturbance impacts generally increased with elevation. Methodologically, our approach proved effective for improving the robustness of habitat reconstructions from Landsat time series: integrating multi-year telemetry data into single, multi-temporal habitat models improved model transferability in time. Likewise, temporally segmenting the Landsat-based metrics increased the temporal consistency of our habitat suitability maps. As the frequency of natural forest disturbances is increasing across the globe, their impacts on wildlife habitat should be considered in wildlife and forest management. Our approach offers a widely applicable method for monitoring habitat suitability changes caused by landscape dynamics such as forest disturbance

opencc-zeroSep 2020View details →

Effects of soil preservation for biodiversity monitoring using environmental DNA

Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guidelines for best practices so far. Here, we assessed the impact of four methods of soil sample preservation commonly used in metabarcoding studies (preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days). For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under optimal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, while the exclusion of rare taxa led to robust results across preservation methods. The differences in community structure among habitats were evident for all treatments, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.

opencc-by-4.0Oct 2020View details →

Towards a method for monitoring the coupling evolution of microservice-based architectures

Backup video for the presentation of the paper "Towards a method for monitoring the coupling evolution of microservice-based architectures", published in SBCARS - CBSoft 2020

opencc-by-4.0Jan 2020View details →

Pilot implementation, monitoring, co-evaluation and validation data_v1

These data have been collected in the context of monitoring and assessing the pilot operation of the INVITE project (H2020 GA 763651) and its OI2lab platform during their 1st deployment round.

opencc-zeroOct 2020View details →

Raw data accompanying: Ground reaction forces in monitor lizards (Varanidae) and the scaling of locomotion in sprawling tetrapods

Geometric scaling predicts a major challenge for legged, terrestrial locomotion. Locomotor support requirements scale identically with body mass (α M1), while force generation capacity should scale α M2/3 as it depends on muscle cross-sectional area. Mammals compensate with more upright limb postures at larger sizes, but it remains unknown how sprawling tetrapods deal with this challenge. Varanid lizards are an ideal group to address this question because they cover an enormous body size range while maintaining a similar bent-limb posture and body proportions. This study reports the scaling of ground reaction forces and duty factor for varanid lizards ranging from 7 g 37 kg. Impulses (force x time) scaled roughly as predicted by the inverted pendulum model (α M0.99-1.34) while peak forces (α M0.73-1.00) scaled higher than expected. Duty factor scaled α M0.04 and was higher for the hindlimb than the forelimb. The proportion of vertical impulse to total impulse increased with body size, and impulses decreased while peak forces increased with speed. These results provide valuable data into how locomotor forces vary with body size and suggest how other, extinct, sprawling tetrapods may have dealt with the biomechanical challenges associated with generating sufficient locomotor forces at larger body sizes.

opencc-zeroAug 2021View details →

Hare's affairs: lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals

Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the five-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex-ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.

Dataset and figures for "Nationwide urban ground deformation monitoring in Japan using Sentinel-1 LiCSAR products and LiCSBAS"

This dataset contains the deformation data for 191 data sets and figures (LOS velocities, amplitude and time offset of the annual deformation, decomposed vertical and EW velocities, rice paddy fields, NDVI, optical images, topography, and SB network) mentioned in the paper “Nationwide urban ground deformation monitoring in Japan using Sentinel-1 LiCSAR products and LiCSBAS” Morishita, Y. Nationwide urban ground deformation monitoring in Japan using Sentinel-1 LiCSAR products and LiCSBAS. Prog Earth Planet Sci 8, 6 (2021). https://doi.org/10.1186/s40645-020-00402-7 View on a web map: https://yumorishita.github.io/gsimaps_S1_Japan_LiCSBAS/#9/35.766572/140.038605/&base=std&base_grayscale=1&ls=std%2C0.5%7Chillshademap%2C0.5%7CallUD%7Clanduse_veg&blend=100&disp=1110&vs=c1j0h0k0l0u0t0z0r0s0m0f2&d=m

Data and code for: Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study

Abstract Previous research has shown diverse vertical space use by various taxa, highlighting the importance of forest canopy. Yet, we often fail to explore how this three-dimensional space use changes over time. Here we use canopy tower systems in French Guiana to monitor neotropical bat activity above and below the forest canopy throughout nine nights in the wet season. We show that different bats use both canopy and understory space differently, and that this can change throughout the night. We find that bats are overall more active in the canopy, but multiple species/acoustic complexes are more active in the understory. We also find that species that do not seem to prefer understory or canopy, when data are aggregated by night, do show temporally changing preferences in hourly activity. This work highlights the need to consider temporal axes in studies of space use, both throughout daily cycles and across seasons.

opencc-by-4.0Nov 2020View details →

EPSRC HEED Data Repository: Individual Appliance Monitoring System

The dataset deposited here was prepared under the EPSRC-funded <a href="http://heed-refugee.coventry.ac.uk/">Humanitarian Engineering and Energy for Displacement</a> research project (EP/P029531/1). The project aimed to understand energy needs of displaced communities, create an evidence base on the usage of different energy interventions and provide recommendations for improved design of future energy interventions to better meet the needs of people.  As part of the project, we deployed an Individual Appliance Monitoring (IAM) System in the Uttargaya settlement in Nepal. The Individual Appliance Monitoring System provides a simple, cost-effective and unobtrusive method of collecting data on the energy usage of connected appliances with the aim to: Evaluate energy consumption of different appliances and Evaluate usage patterns for different appliances. The monitoring system comprises of 2 types of devices – Energenie MiHome Smart Plugs MIHO005 (i.e. Individual Appliance Monitors (IAM)) to sense data relating to power and voltage drawn by the connected appliance, and gateway nodes to collect data from IAM. The unit cost of a MIHO005 adaptor and Raspberry Pi-based gateway is £34.99 and £74.17 respectively. The main component of the gateway node is a Raspberry Pi fitted with an Energenie ENER314-RT (receiver-transmitter) add-on board to allow the Pi to communicate with the smart plugs. The data collected by the gateway is stored locally in an SD card as well as sent to the heed-data server hosted in Coventry University. Post Deployment Challenges: ·         Power outages: These are common in the camp. Data is lost during this time as the devices have no access to power. ·         Internet connectivity: The availability and reliability of Wi-Fi continue to be an issue for the transmission of data to heed-data server.

Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study

This is the code and associated data that was used to generate conclusions for the following manuscript published in Applied and Environmental Microbiology: DOI: 10.1128/AEM.02278-20 Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study Authors: Jonathan H. Sogin(a), Gabriela Lopez Velasco(b), Burcu Yordem(b), Cari K. Lingle(b), John M. David(b), Mario Cobo(a), Randy W. Worobo(a) (a)Department of Food Science, Cornell University, Ithaca, NY, USA (b)3M Company, St. Paul, MN, USA Address correspondence to Jonathan H. Sogin, jhs397@cornell.edu

opencc-by-4.0Nov 2020View details →

Monitoring recent changes in the Beaufort Sea coast using very high resolution remote sensing

Arctic permafrost coasts are major carbon (Schuur et al., 2015) and mercury pools (Schuster et al., 2018). They represent about 34% of the Earth’s coastline, with long sections affected by high erosion rates (Fritz et al, 2017), increasingly threatening coastal communities. Year-round reduction in Arctic sea ice is forecasted and by the end of the 21st century, models indicate a decrease in sea ice area from 43 to 94% in September and from 8 to 34% in February (IPCC, 2014). An increase of the sea-ice free season leads to a longer exposure of coasts to wave action. Further, climate warming is also expected to modify the contribution of terrestrial erosion (Fritz et al., 2015, Ramage et al., 2018, Irrgang et al., 2018). Within the project EU Horizon2020 project NUNATARYUK, we are updating the mapping of the Arctic coast, with the Canadian Beaufort coast as a case-study. The surveying methodology includes: i. a high resolution update of the coastline mapping and change rates using Pleiades (CNES) satellite acquisitions from 2018, ii. a survey using RTK-UAV aerial imagery of long-term monitoring sites from the Canada-US border to King Point, and iii. the experimental use of TerraSAR-X staring spotlight scenes and PAZ at key sites to monitor intraseasonal dynamics of cliff edge retreat. This research is funded by the EC H2020 Project NUNATARYUK. Support on remote sensing imagery access by the WMO Polar Space Task Group.

opencc-zeroDec 2020View details →

Long-term monitoring reveals forest tree community change driven by atmospheric sulfate pollution and contemporary climate change

Aim: Montane environments are sentinels of global change, providing unique opportunities to assess impacts on species diversity. Multiple anthropogenic stressors such as climate change and atmospheric pollution may act concurrently or synergistically in restructuring communities. Thus, a major challenge for conservation is untangling the relative importance of different stressors. Here, we combine long-term monitoring with multivariate community modeling to estimate the anthropogenic drivers shaping forest tree diversity along an elevational gradient. Location: Camels Hump Mountain, Vermont, USA Methods: We used Generalized Dissimilarity Modelling (GDM) to model spatial and temporal turnover in beta diversity along an elevational gradient over a 50-year period, and tested for spatiotemporal shifts in density and elevational distribution of individual species. GDMs were used to predict community turnover as non-linear functions of changes in elevation, climate and atmospheric pollution. Results: We observed significant shifts in elevational range and density of individual species, which contributed to an overall reduction in the elevational gradient in beta diversity through time. GDMs showed the combined effects of sulfate deposition and temperature as drivers of this temporal reduction in beta diversity. Spatiotemporal changes differed among species, with shifts observed both up and downslope. For example, in a reversal of a previous upslope range contraction, red spruce (Picea rubens Sarg.) increased in density and shifted downslope since the 1990's, occupying warmer, drier climates. Main conclusion: Our results demonstrate that global change is impacting the stratification of forest tree diversity along elevational gradients, but the responses of individual species are complex and variable in direction. We suggest abiotic drivers may directly impact individual species while also indirectly altering species interactions along elevational gradients. Our approach modelling the drivers of compositional turnover quantifies the rate and amount of change in beta diversity along environmental gradients, and serves as a powerful complement to studying species-specific responses.