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opencc-zeroJun 2020View details →

Data from: Multi-taxon inventory reveals highly consistent biodiversity responses to ecospace variation

Amidst the global biodiversity crisis, identifying general principles for variation in biodiversity remains a key challenge. Scientific consensus is limited to a few macroecological rules, such as species richness increasing with area, which provide limited guidance for conservation. In fact, few agreed ecological principles apply at the scale of sites or reserve management, partly because most community-level studies are restricted to single habitat types and species groups. We used the recently proposed ecospace framework and a comprehensive data set for aggregating environmental variation to predict multi-taxon diversity. We studied richness of plants, fungi, and arthropods in 130 sites representing the major terrestrial habitat types in Denmark. We found the abiotic environment (ecospace position) to be pivotal for the richness of primary producers (vascular plants, mosses, and lichens) and, more surprisingly, little support for ecospace continuity as a driver. A peak in richness at intermediate productivity adds new empirical evidence to a long-standing debate over biodiversity responses to productivity. Finally, we discovered a dominant and positive response of fungi and insect richness to organic matter accumulation and diversification (ecospace expansion). Two simple models of producer and consumer richness accounted for 77 % of the variation in multi-taxon species richness suggesting a significant potential for generalization beyond individual species responses. Our study widens the traditional conservation focus on vegetation and vertebrate populations unravelling the importance of diversification of carbon resources for diverse heterotrophs, such as fungi and insects.

opencc-by-4.0Jul 2020View details →

Gridded fossil CO2 emissions and related O2 combustion consistent with national inventories 1959-2018

GCP-GridFED (version 2019.1) is a gridded fossil emissions dataset that is consistent with the national CO2 emissions reported by the Global Carbon Project (GCP). GCP-GridFEDv2019.1 provides monthly fossil CO2 emissions for the period 1959-2018 at a spatial resolution of 0.1° × 0.1°. The gridded emissions estimates are provided separately for fossil CO2 emitted by the oxidation of oil, coal and natural gas, with mixed international bunker fuels considered separately, as well as for the calcination of limestone during cement production. GCP-GridFED also includes gridded uncertainties in CO2 emission, incorporating differences in uncertainty across emissions sectors and countries, and gridded estimates of corresponding O2 uptake based on oxidative ratios for oil, coal and natural gas. GCP-GridFED was produced by scaling monthly gridded emissions for the year 2010, from the Emissions Database for Global Atmospheric Research (EDGAR; version 4.3.2; Janssens-Maenhout et al., 2019), to the national annual emissions estimates compiled as part of the 2019 global carbon budget (GCB-NAE) for the years 1959-2018 (Friedlingstein et al., 2019). The data description article is under review.

opencc-by-4.0Jan 2021View details →

Publication rate and consistency of registered trials of motor-based stroke rehabilitation

Table e1 - Eligible records A list of registered randomized controlled trials (RCTs) meeting the following criteria: <ol> <li>RCTs of motor-based interventions in individuals with stroke (including transient ischemic attack);</li> <li>Started on or after 1 July 2005;</li> <li>Completed before 1 April 2017 (actual or expected end date);</li> <li>Included human adult participants (≥18 years old);</li> <li>Included at least one outcome (primary or secondary) related to motor control, mobility, or physical functioning and performance of upper and/or lower extremities or the body as a whole; and</li> <li>Registered in English.</li> </ol> This list was obtained by searching the following registries between 23 November 2017 and 22 February 2018: the International Clinical Trials Registry Platform, Clinicaltrials.gov (USA), Australian New Zealand Clinical Trial Registry, Chinese Clinical Trial Registry, Clinical Research Information Service (Republic of Korea), Clinical Trial Registry of India, Cuban Public Registry of Clinical Trials, European Union Clinical Trials Register, German Clinical Trials Register, Iranian Registry of Clinical Trials, International Standard Randomised Controlled Trials Number registry (UK), Center for Clinical Trials-Japan Medical Association, University Hospital Medical Information Network-Clinical Trial Registry (Japan), Thai Clinical Trials Registry, Netherlands Trials Registry, Pan African Clinical Trials Registry, Peruvian Clinical Trials Registry, and Sri Lanka Clinical Trials Registry.  Variable definitions UIN: Unified identification number (obtained from the trial registry) Status: whether or not a peer-reviewed publication reporting the trial findings for the primary outcome/outcome was found <ul> <li>Paper available: a publication reporting the trial findings for the primary outcome/objective was found</li> <li>Paper available (not English): a publication, published in a language other than English, reporting the trial findings for the primary outcome/objective was found</li> <li>Secondary paper available: a publication reporting study findings is available, but not for the primary objectives/outcome</li> <li>Results available: trial findings for the primary objective/outcome are available in a non-peer reviewed format (e.g., conference publication, non-peer reviewed journal, or uploaded to the trial registry)</li> <li>Discontinued: the trial registry record indicates that the trial was discontinued, so no publication is expected</li> <li>No paper/results: none of the above apply</li> </ul> Source: database or method we used to find the publication reporting the trial findings for the primary objective/outcome <ul> <li>Pubmed: the publication was found by searching for the UIN in Pubmed</li> <li>EMBASE/OVID: the publication was found by searching for the UIN in Embase or OVID Medline</li> <li>Google Scholar: the publication was found by searching for the UIN in Google Scholar</li> <li>Registry: the publication was listed in the trial registry</li> <li>Internet: the publication was found by a superficial internet search for the UIN</li> <li>Protocol: the publication was found through a cited reference search for the published protocol</li> <li>Author: the publication was found by contacting the trial investigators</li> <li>Other: the publication was found by some other means</li> <li>None: no publication reporting the trial findings for the primary objective/outcome was found</li> </ul> Table e2 - Published papers consistency The subset of trials from Table e1 where an English-language publication reporting the trial findings for the primary objective/outcome was found. Variable definitions UIN: Unified identification number (obtained from the trial registry) DOI: digital objective identifier of the publication First_author: last name of the first author of the publication Year: year of the publication Journal: journal of the publication (abbreviated journal names are used, where available) Reg_Trial_End_Date: end date of the trial, as stated in the trial registry (format DD-MMM-YY) Date_Submitted: date when the paper was submitted to the journal for publication (where available; format: DD-MMM-YY) Time_To_Submit: difference, in days, between Reg_Trial_End_Date and Date_Submitted Date_Published: date when the paper was published, either online or in print, whichever is earlier (format: DD-MMM-YY) Time_To_Publish: difference, in days, between Reg_Trial_End_Date and Time_To_Publish UIN_Paper_Location: location of the UIN in the publication Reg_Pilot: whether the trial was defined as a pilot or feasibility study in the registry record (0=no, 1=yes) Paper_Pilot: whether the trial was defined as a pilot or feasibility study in the publication (0=no, 1=yes) Consistency_pilot: whether Reg_Pilot = Paper_Pilot (0=no, 1=yes) Consistency_Primary_Objective: whether the trial registry record and publication were consistent in terms of the primary objective (0=no, 1=yes) Consistency_Primary_Outcome: whether the trial registry record and publication were consistent in terms of the primary outcome (0=no, 1=yes) Target_N: target sample size, as indicated in the trial registry record Paper_N: number of participants recruited to the study, as indicated in the publication Consistency_N: whether the trial registry record and publication were consistent in terms of the sample size (i.e., Paper_N is within +/-10% of Target_N; 0=no, 1=yes) N_direction: for those trials that were inconsistent in terms of the sample size, whether Paper_N was less than (Under) or more then (Over) Target_N Eligibility_Consistency: whether the trial registry record and publication were consistent in terms of the eligibility criteria UIN_in_paper: the UIN that was included in the paper, exactly as it was published UIN_consistency: whether UIN = UIN_in_paper (0=no, 1=yes) Reg_Type: whether the trial was registered before recruiting the first participant (Prospective), after recruiting the first participant but before the trial was completed (Retro - pre-completion), or after the trial was completed (Retro - post-completion) Table e3 - Inconsistency details The subset of trials from Table e2 where the trial registry record and publication were inconsistent on only one of the criteria examined. This table provides further details of these inconsistencies, and details of any explanations for changes to the protocol since registration, if available.

opencc-zeroFeb 2020View details →

Asymmetry in kinematic generalization between visual and passive lead-in movements are consistent with a forward model in the sensorimotor system

In our daily life we often make complex actions comprised of linked movements, such as reaching for a cup of coffee and bringing it to our mouth to drink. Recent work has highlighted the role of such linked movements in the formation of independent motor memories, affecting the learning rate and ability to learn opposing force fields. In these studies, distinct prior movements (lead-in movements) allow adaptation of opposing dynamics on the following movement. Purely visual or purely passive lead-in movements exhibit different angular generalization functions of this motor memory as the lead-in movements are modified, suggesting different neural representations. However, we currently have no understanding of how different movement kinematics (distance, speed or duration) affect this recall process and the formation of independent motor memories. Here we investigate such kinematic generalization for both passive and visual lead-in movements to probe their individual characteristics. After participants adapted to opposing force fields using training lead-in movements, the lead-in kinematics were modified on random trials to test generalization. For both visual and passive modalities, recalled compensation was sensitive to lead-in duration and peak speed, falling off away from the training condition. However, little reduction in force was found with increasing lead-in distance. Interestingly, asymmetric transfer between lead-in movement modalities was also observed, with partial transfer from passive to visual, but very little vice versa. Overall these tuning effects were stronger for passive compared to visual lead-ins demonstrating the difference in these sensory inputs in regulating motor memories. Our results suggest these effects are a consequence of state estimation, with differences across modalities reflecting their different levels of sensory uncertainty arising as a consequence of dissimilar feedback delays.

opencc-by-4.0Dec 2016View details →

Hardware Synthesis of Weakly Consistent C Concurrency

Hardware Synthesis of Weakly Consistency C Concurrency This webpage contains additional material for the paper Hardware Synthesis of Weakly Consistent C Concurrency (FPGA17paper.pdf). Contents <ol> <li>Verifying that our scheduling constraints implement the C11 standard</li> <li>Verifying the lock-free circular buffer</li> <li>Motivating examples</li> <li>Experimental Data</li> </ol> 1. Verifying that our scheduling constraints implement the C11 standard As explained in Section 4.4, we have used the Alloy tool to verify that our scheduling constraints are sufficient to implement the memory consistency model defined by the C11 standard. In alloy.zip, we provide the Alloy model files that we used. The first four are taken from Wickerson et al.'s work on comparing memory consistency models; the fifth is new. <ul> <li>relations.als contains helper functions.</li> <li>exec.als encodes general program executions.</li> <li>exec_C.als encodes C11 program executions.</li> <li>c11.als encodes the constraints imposed by the C11 memory consistency model.</li> <li>question.als encodes our scheduling constraints, and several queries for checking that these scheduling constraints are strong enough to enforce the constraints required by the C11 memory consistency model.</li> </ul> To reproduce our result, save the five files above into the same directory, download Alloy, open question.als in Alloy, and run the queries contained within. 2. Verifying the lock-free circular buffer As explained in Section 5.1, we have used the CppMem tool to verify that our case-study application, a lock-free circular buffer, is free from data races. In order to make the verification feasible, we removed the while-loop, replaced the array variable with a scalar, removed some unimportant local variables, and simplified the increment function. Below, we give the actual code that we verified. int main() { atomic_int tail = 0; atomic_int head = 0; int arr = 0; {{{ { int chead = head.load(memory_order_acquire); int ctail = tail.load(memory_order_relaxed); if (ctail+1 != chead) { arr = 42; tail.store(ctail+1, memory_order_release); } } ||| { int ctail = tail.load(memory_order_acquire); int chead = head.load(memory_order_relaxed); if (ctail != chead) { arr; head.store(chead+1, memory_order_release); } } }}} return 0; } To reproduce our result, paste the code above into CppMem's web interface and click Run. The tool should report (after a couple of minutes) that the code has 92 candidate executions, of which two are consistent, neither of which exhibit data races. 3. Motivating Examples We provide the actual code that displays coherence and message-passing violation in motivating-examples.zip, as described in Section 2 of our paper. These examples have been tested and verified on LegUp's VM. For convenience, we have included the output logs of each experiment for viewing. We include a "transcript" of the execution and a schedule trace, which can be visualised using LegUp's scheduleviewer. 4. Experimental Data We also provide the raw experiment data from Section 5 of our paper. We conduct two experiments, for which we provided raw data on all seven design points. <ul> <li>chaining.csv contains the raw data for the chaining experiment.</li> <li>bursting.csv contains the raw data for the bursting experiment.</li> <li>The version number are from 1 to 7 for Unsound, SC, OMP criticals, SC atomics, Weak atomics, Mutexes and OMP atomics respectively.</li> </ul>

opencc-by-4.0Feb 2016View details →

Shingle example self-consistent source datasets

Self-consistent source datasets for the Shingle project -- an approach and software library for the generation of boundary representation from arbitrary geophysical fields and initialisation for anisotropic, unstructured meshing (see https://www.shingleproject.org for more information).

opencc-by-4.0Nov 2023View details →

Data Set for the Journal Article "Automated Preparation of Nanoscopic Structures: Graph-Based Sequence Analysis, Mismatch Detection, and pH-Consistent Protonation with Uncertainty Estimates"

This repository containes the data generated by ASAP and discussed in the journal article [Csizi, K.-S. and Reiher, M., 2023, arXiv:2307.16344], including Cartesian coordinates of training and test set molecules, and MD trajectories.

opencc-zeroDec 2023View details →

Consistent traffic noise impacts few fitness-related traits in a field cricket

Anthropogenic habitat change is occurring rapidly, and organisms can respond through within-generation responses that improve the match between their phenotype and the novel conditions they encounter. But, plastic responses can be adaptive or maladaptive and are most likely to be adaptive only when contemporary conditions reasonably mimic something experienced historically to which a response has already evolved. Noise pollution is a ubiquitous anthropogenic stressor that accompanies expanding urbanization. We tested whether the amplitude of traffic noise influences a suite of fitness-related traits (e.g. survival, life history, reproductive investment, immunity) and whether that depends on the life stage at which the noise is experienced (juvenile or adult). Our treatments mimic the conditions experienced by animals living in urban roadside environments with variable vehicle types, but continuous movement of traffic. We used the Pacific field cricket, an acoustically communicating insect that was previously shown to experience some negative behavioral and life history responses to very loud, variable traffic noise, as a model system.

opencc-zeroMar 2024View details →

Risk response towards roads is consistent across multiple species in a temperate forest ecosystem

Roads can have diverse impacts on wildlife species, and while some species may adapt effectively, others may not. Studying multiple species' responses to the same infrastructure in a given area can help understand this variation and reveal the effects of disturbance on the ecology of wildlife communities. This study investigates the behavioural responses of four species with distinctive ecological and behavioural traits to roads in the protected Bohemian Forest Ecosystem in Central Europe: European roe deer (Capreolus capreolus), a solitary herbivore; red deer (Cervus elaphus) a gregarious herbivore; wild boar (Sus scrofa), a gregarious omnivore and Eurasian lynx (Lynx lynx), a solitary large carnivore. We used GPS data gathered from each species to study movement behaviour and habitat selection in relation to roads using an integrated step selection analysis. For all species and sexes, we predicted increased movement rates in response to roads, selection of vegetation cover near roads and open areas after road crossings, and increased road avoidance during the day. We found remarkably similar behavioural responses towards roads across species. The behavioural adaptations to road exposure, such as increased movement rates and selection for vegetation cover, were analogous to responses to natural predation risk. Roads were more strongly avoided during daytime, when traffic volume was high. Road crossings were more frequent at twilight and at night within open areas offering food resources. Gregarious animals exposed to roads favoured stronger road avoidance over faster movements. Ungulates crossed roads more at twilight, coinciding with commuter traffic during winter. Despite differences in the ecology and behaviour of the four species, our results showed similar adaptations towards a common threat. These insights can be used by managers to promote safer road crossings where roads interfere with animals' natural behaviour. The continuous expansion of the global transportation network should be accompanied by efforts to understand and minimise the impact of roads on wildlife to assist wildlife management and ensure conservation.

Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs.

Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.

Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation.

Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day.

opengpl-3.0-or-laterJun 2017View details →

GSHHG: Global Self-consistent Hierarchical High-resolution Geography

<a href="http://www.soest.hawaii.edu/pwessel/gshhg/">Global Self-consistent, Hierarchical, High-resolution Geography Database (GSHHG)</a> is a high-resolution geography data set, amalgamated from two databases: World Vector Shorelines (WVS) and CIA World Data Bank II (WDBII). The former is the basis for shorelines while the latter is the basis for lakes, although there are instances where differences in coastline representations necessitated adding WDBII islands to GSHHG. The WDBII source also provides political borders and rivers. GSHHG data have undergone extensive processing and should be free of internal inconsistencies such as erratic points and crossing segments. The shorelines are constructed entirely from hierarchically arranged closed polygons. GSHHG combines the older GSHHS shoreline database with WDBII rivers and borders, available in either ESRI shapefile format or in a native binary format. Geography data are in five resolutions: crude(c), low(l), intermediate(i), high(h), and full(f). Shorelines are organized into four levels: boundary between land and ocean (L1), boundary between lake and land (L2), boundary between island-in-lake and lake (L3), and boundary between pond-in-island and island (L4). Datasets are in WGS84 geographic (simple latitudes and longitudes; decimal degrees). GSHHG is released under the <a title="external link to GNU license" href="http://www.gnu.org/licenses/lgpl.html">GNU Lesser General Public license</a>, and is developed and maintained by Dr. Paul Wessel, SOEST, University of Hawai'i, and Dr. Walter H. F. Smith, NOAA Laboratory for Satellite Altimetry. Please notify Dr. Paul Wessel and Dr. Walter H.F. Smith if any changes are made to the GSHHG data set for commercial use. Processing and assembly of the GSHHG data: Wessel, P., and W. H. F. Smith (1996), A global, self-consistent, hierarchical, high-resolution shoreline database, J. Geophys. Res., 101(B4), 8741–8743, <a href="https://doi.org/10.1029/96JB00104">doi:10.1029/96JB00104.</a>

opencc-by-4.0Sep 2023View details →

Dataset and R code used in "Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes"

Dataset and R code used for the manuscript: Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C., & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. Environmental Microbiology, 26(3), e16607. This dataset and code are also available on GitHub (<a href="https://github.com/jvoneggers/WYLakeSedMicrobes">https://github.com/jvoneggers/WYLakeSedMicrobes</a>).

opencc-by-4.0Sep 2021View details →

Table 1 in Evolution of Impatiens (Balsaminaceae) in the Albertine Rift – The endemic Impatiens purpureoviolacea complex consists of ten species

Table 1. Sequence characterstics of each datamatrix.<table><tbody><tr><th></th><th>Taxa</th><th>Characters</th><th>Parsimony-informative characters</th><th>Variable characters</th><th>Consistency index</th><th>Retention index</th></tr></tbody><tbody><tr><th>atpB-rbcL</th><td>17 + 1*</td><td>729</td><td>2</td><td>15</td><td>1</td><td>1</td></tr><tr><th>ImpDEF1/ImpDEF2</th><td>18 + 2(1)*#</td><td>1023</td><td>43</td><td>145</td><td>0.95</td><td>0.92</td></tr><tr><th>Combined</th><td>18</td><td>1752</td><td>45</td><td>160</td><td>0.95</td><td>0.93</td></tr></tbody></table>Consistency index: Kluge & Farris (1969), retention index: Farris (1989).* indicates inclusion of the hybrid accession, # indicates inclusion of two copies of the nuclear genes ImpDEF1 and ImpDEF2 of the hybrid accession.

opencc-by-4.0Jun 2017View details →

Figure 3 in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

Figure 3. Flow diagram for subspecies delineation using combined quantitative and qualitative standards. The threshold values assume the user is evaluating a case relying on mtDNA control region data. Percent Diagnosable (PD) is the smallest strata-specific correct classification score in a given comparison (e.g., PD50 in two-strata comparisons in Archer et al. 2017). The second box in the second row (other evidence to meet subspecies definition) allows for subspecies delineation when both conditions are not met using mtDNA. This box could be used either for the case when one condition is met and one unmet or when both just barely miss meeting the standards. For example, consider the case with PD <95% and dA> 0.004. Diagnosability could be achieved with morphological data or nuclear data that are sufficient for subspecies but not for full species.