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Neonatal 3T PRESS Basis Sets (MARBLE)

Neonatal 3T basis sets used for the multi-site MARBLE study, simulated using Vespa. These correspond to the vendor-provided PRESS sequences used on Siemens, Philips and GE scanners, as described in Lally PJ, Montaldo P et al. Lancet Neuro 2019. For each vendor, a basis set is provided for each of TE=60ms and TE=288ms. File types: <ul> <li>.RAW files (compressed into RAW.zip) - includes additional metabolites which were not included in the final basis set, but could still be useful for other neonatal MRS studies. *In GSH, glycine component has an additional 10Hz Gaussian broadening applied, following Kaiser LG. et al. JMR 202.2 (2010): 259-266*</li> <li>.in files - makebasis input file used to generate the fitting basis set from .RAW files</li> <li>.basis files - fitting basis set. *For MARBLE, the following metabolites were omitted from the fit with 'CHOMIT' control parameters: AcAc, Acn, Etm, Ser. The following metabolites were also combined with 'CHCOMB' due to their strong correlation during fitting: Thr+Lac, Asc+GSH*</li> <li>.pdf files - visualisation of the basis set components</li> </ul> Some specific details: <ul> <li>Narrow FWHM (1Hz Gaussian broadening) to allow accurate quantification of sharp linewidth neonatal spectra and undoped MRS phantoms.</li> <li>Two versions of each basis set: i) each metabolite has a single component in the basis set (as usual); ii) singlet peaks of NAA, Cho, Cr are separated from other resonances to allow two-point T2 relaxometry between TEs (as used for MARBLE)</li> <li>Ideal RF pulses are assumed</li> <li>TE1,TE2 are adjusted according to vendor/TE</li> <li>Reference singlet at 0ppm</li> </ul> If using this to calculate peak area ratios at TE=288ms, multiply the LCModel provided 'concentrations' by a factor of the number of protons that contribute to each peak (i.e. 3 for NAA singlet @ 2.0ppm, 3 for Cr singlet @ 3.0ppm, 3 for Lac+Thr doublet @ 1.3ppm, 9 for Cho singlet @ 3.2ppm) - this will give you relative peak areas which are consistently scaled. Contact: p.lally [at] imperial.ac.uk

Data sets used in the study "To supplement estuaries turbidity theory: An investigation of low turbidity zones in estuaries "

This is the data sets used in the study "To supplement estuaries turbidity theory: An investigation of low turbidity zones in estuaries "

opencc-by-4.0Mar 2020View details →

Data set for all Bifurcation diagrams of 'Two-dimensional patterns in dip coating - first steps on the continuation path'

Data set for all bifurcation diagrams of  'Two-dimensional patterns in dip coating - first steps on the continuation path' by Phong-Minh Timmy Ly, Kevin David Joachim Mitas, Uwe Thiele, Svetlana V. Gurevich published as Physica D 409, 132485 (2020).  DOI: <a href="http://doi.org/10.1016/j.physd.2020.132485">10.1016/j.physd.2020.132485</a> Specifically: Figures 1, 2, 5, 6 and 7

BRIR data set for interactive listener translation in two rooms

This BRIR data set was measured with a Kemar 45BA at 9 different positions along a defined translation line with a length of 2m in two different rooms,  a listening laboratory (T60 = 0.27s) and a seminar room (T60 = 1.0s). At each position BRIRs for a full 360° head rotation with an azimuth resolution of 4° were captured. Two Genelec 1030A loudspeakers served as the sound sources, one place in the fron of the line, one at the side. In addition, omni-directional room impulse responses were determined of the 9 positions at the center the head in both rooms. The data set is of interest to study dynamic binaural synthesis for walking towards or past a sound source in two different room acoustical settings. The same source and receiver setup was used in both rooms, therefore the direct sound and its progress along the given translation line is similar.

opencc-zeroJun 2020View details →

Data from: ClinicNet: machine learning for personalized order set recommendations

Objective This study assesses whether neural networks trained on electronic health record (EHR) data can anticipate what individual clinical orders and existing institutional order set templates clinicians will use more accurately than existing decision support tools. Materials and Methods We process 57,624 patients-worth of clinical event EHR data from 2008-2014. We train a feed-forward neural network (ClinicNet) and logistic regression applied to the traditional problem structure of predicting individual clinical items as well as our proposed workflow of predicting existing institutional order set template usage. Results ClinicNet predicts individual clinical orders (precision=0.32, recall=0.47) better than existing institutional order sets (precision=0.15, recall=0.46). The ClinicNet model predicts clinician usage of existing institutional order sets (avg. precision=0.31) with higher average precision than a baseline of order set usage frequencies (avg. precision=0.20) or a logistic regression model (avg. precision=0.12). Discussion Machine learning methods can predict clinical decision-making patterns with greater accuracy and less manual effort than existing static order set templates. This can streamline existing clinical workflows, but may not fit if historical clinical ordering practices are incorrect. For this reason, manually authored content such as order set templates remain valuable for purposeful design of care pathways. ClinicNet's capability of predicting such personalized order set templates illustrates the potential of combining both top-down and bottom-up approaches to delivering clinical decision support content. Conclusion ClinicNet illustrates the capability for machine learning methods applied to the EHR to anticipate both individual clinical orders and existing order set templates, which has the potential to improve upon current standards of practice in clinical order entry.

opencc-zeroJul 2020View details →

Data from: Neural dysfunction correlates with heat coma and CTmax in Drosophila but does not set the boundaries for heat stress survival

When heated, insects lose coordinated movement followed by the onset of heat coma (critical thermal maximum, CTmax). These traits are popular measures to quantify interspecific and intraspecific differences in insect heat tolerance, and CTmax correlates well with current species distributions of insects, including Drosophila. Here, we examined the function of the central nervous system (CNS) in five species of Drosophila with different heat tolerances, while they were exposed to either constant high temperature or a gradually increasing temperature (ramp). Tolerant species were able to preserve CNS function at higher temperatures and for longer durations than sensitive species, and similar differences were found for the behavioural indices (loss of coordination and onset of heat coma). Furthermore, the timing and temperature (constant and ramp exposure, respectively) for loss of coordination or complete coma coincided with the occurrence of spreading depolarisation (SD) events in the CNS. These SD events disrupt neurological function and silence the CNS, suggesting that CNS failure is the primary cause of impaired coordination and heat coma. Heat mortality occurs soon after heat coma in insects; to examine whether CNS failure could also be the proximal cause of heat death, we used selective heating of the head (CNS) and abdomen (visceral tissues). When comparing the temperature causing 50% mortality (LT50) of each body part versus that of the whole animal, we found that the head was not particularly heat sensitive compared with the abdomen. Accordingly, it is unlikely that nervous failure is the principal/proximate cause of heat mortality in Drosophila.

opencc-zeroJul 2020View details →

Data from: Pollination and fruit set in two rewardless slipper orchids and their hybrids (Cypripedium, Orchidaceae): large yellow flowers outperform small white flowers in the northern tall grass prairie

• Species with rewardless flowers often have low fruit to flower ratios, although wide temporal and spatial variation in fruiting success can occur. We compared floral phenotypes, insect visitors, and fruiting success in four populations of the small white (Cypripedium candidum) and yellow lady's slipper orchids (C. parviflorum) and their hybrids near the northern extent of North America's tall grass prairie. • Flower and fruit numbers were observed for two seasons on marked individuals (n = 1811). Floral traits were measured on 82-140 individuals per taxon, and analyzed in relation to fruiting success. All insects found inside flowers were collected, inspected for pollen smears, and measured for comparison to floral features. • Among orchid taxa, C. candidum had the smallest flowers, lowest number and variety of insect visitors, and lowest fruit to flower ratios. These measures were intermediate in hybrids and highest in C. parviflorum, despite low flower numbers in the latter. Within orchid taxa, fruit number was positively related to flower number, but fruit to flower ratios decreased slightly, as would be expected if pollinators left unrewarding patches. Potential pollinators included the dipteran Odontomyia pubescens and hymenopterans Andrena spp., Apis mellifera, and Lasioglossum zonulum. • Cypripedium parviflorum had a reproductive advantage over C. candidum across multiple populations and years. Hybrids showed segregation for floral traits, and hybrid fruiting success increased with a deeper intensity of yellow pigment and larger escape routes for floral visitors. These same attributes likely contributed to the relatively high fruit set in C. parviflorum in the study region.

opencc-zeroJul 2020View details →

Data from: Agri-environment conservation set-asides have co-benefits for connectivity

Widespread declines in farmland biodiversity have led to state-funded schemes which take land out of production to create (semi-)natural habitats for biodiversity (e.g. EU agri-environment schemes; US Conservation Reserve Program). Common features of such schemes are grassland strips at the edges of agricultural fields, and we examine potential co-benefits of these biodiversity set-asides for contributing to grassland connectivity. Although set-aside strips had negligible impact on landscape-scale species persistence (using metapopulation models parameterized for flying insects run on 267 landscapes of ~30 000 ha across England), they nonetheless improved connectivity in 74% (198/267) of landscapes (comparing landscapes with and without set-asides), as shown by range expansion rates increasing by up to 100%. Benefits of set-aside strips varied according to species type (high/low dispersal, high/low population density), but had little benefit for species with low dispersal and small population sizes, which enerally failed to expand. High dispersal/high density species were already successful expanders regardless of set-asides (> 75% of simulations were successful without set-sides) although expansion rates were still improved when set-asides were added. Whilst alternative strategies for placement of set-aside strips (more/less aggregated), revealed no consensus 'better' strategy across species types, set-aside benefits were generally greatest in landscapes with intermediate availability of semi-natural grassland (0.5-4% over). We conclude that small-scale set-asides have the potential to improve connectivity, which we expect to help some species track climate change, and connect habitat patches within existing climate space for others. However, set-asides are unlikely to benefit low dispersal species which are probably at greatest risk from agricultural intensification.

Result Set_Desarrollo, reuso, y resignificación de artefactos de software en Ciencia Ciudadana. ¿Reinventando la rueda?

String de Búsqueda y resultados analizados.

Domain-specific Language for Data-driven Design Time Analyses and Result Mappings for Logic Programs - Data Set

This data set contains additional information to the master thesis of Sebastian Hahner. This includes the prototypical implementation of the domain-specific language (DSL) as well as sample scenarios and mapping results.

opencc-zeroAug 2020View details →

Data set for: Behavioral traits that define social dominance are the same that reduce social influence in a consensus task

Dominant individuals are often most influential in their social groups, affecting movement, opinion, and performance across species and contexts. Yet behavioral traits like aggression, intimidation, and coercion, which are associated with and in many cases define dominance, can be socially aversive. The traits that make dominant individuals influential in one context may therefore reduce their influence in other contexts. Here we examine this association between dominance and influence using the cichlid fish Astatotilapia burtoni, comparing the influence of dominant and subordinate males during normal social interactions and in a more complex group-consensus association task. We find that phenotypically dominant males are aggressive, socially central, and that these males have a strong influence over normal group movement, whereas subordinate males are passive, socially peripheral, and have little influence over normal movement. However, subordinate males have the greatest influence in generating group-consensus during the association task. Dominant males are spatially distant and have lower signal-to-noise ratios of informative behavior in the association task, potentially interfering with their ability to generate group-consensus. In contrast, subordinate males are physically close to other group members, have a high signal-to-noise ratio of informative behavior, and equivalent visual connectedness to their group as dominant males. The behavioral traits that define effective social influence are thus highly context-specific and can be dissociated with social dominance. Thus, processes of hierarchical ascension in which the most aggressive, competitive, or coercive individuals rise to positions of dominance may be counter-productive in contexts where group-performance is prioritized.

The insertion of a mitochondrial selfish element into the nuclear genome and its consequences: supporting data sets and scripts

Supplementary data sets and script for the article "The insertion of a mitochondrial selfish element into the nuclear genome and its consequences". The original source code with versioning is available at https://gitlab.gwdg.de/molsysevol/umag_11064 .

Data Set for Consumer Electronics MFA in Althaf et al 2020 JIE manuscript

This data set includes all the data used in the MFA model and the figures presented in JIE manuscript ' The evolution of consumer electronic waste in the U.S' by Althaf et al (2020).

Neural and subjective effects of inhaled DMT in natural settings

Raw EEG data (DMT, eyes open and eyes closed) and psychometric scales for the 35 participants of "Neural and subjective effects of inhaled DMT in natural settings".

Data set and software for 2020JC016485

This is data set in support of publication in JGR 2020JC016485

GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 1

This dataset contains 50 Hz GPS data to explore JAVAD and Leica receivers quality to reconstruct slant TEC. GNSS receiver is to some extent a “black box” when its data is used for ionospheric studies. The results based on Javad, Septentrio, Trimble and Leica GNSS receivers (which is placed in this data set) proved that the accuracy of the slant Total Electron Content (TEC) calculation can differ significantly if data used for its calculation is from different GNSS receiver make/type. This is because TEC measurements depend on the carrier phase tracking technique applied in a receiver. Based on this data it was found that: 1) Correlation coefficient between carrier phase noises in L1 and L2 channel outputs may be considered as an indicator showing whether the L1-aided tracking technique or independent tracking is applied. 2) The empirical model of TEC noise component was provided to determine TEC noise value in GNSS receivers of different make/type.

opencc-zeroAug 2020View details →

Didimosphenia geminata: sequences and morphology data set

Microalgae and their invasiveness are recurrent themes in aquatic environments and many invasions by microalgae are linked to eutrophication. However the diatom Didymosphenia geminata has gained notoriety in forming thick mucilaginous mats in pristine, rocky-bottomed rivers with no obvious connection to elevated levels of nutrients. This species is native to freshwaters of the circumboreal region of the Northern Hemisphere and blooms in the Southern Hemisphere have been attributed to recent introductions of the species to these regions. Although regional population genetic analyses have suggested multiple recent introduction of this species, the gene flow and the spatial genetic diversity distribution on a global scale remains unknown. We develop a phylogeographic analysis to investigate the genetic diversity of D. geminata populations around the globe. Our results indicate two distinct genetic lineages geographically distributed that remain spatially isolated. One lineage is exclusively found in Europe, the other is distributed in North America, New Zealand and South America. Since blooms of D. geminata commenced in North America and in Europe simultaneously, these data support the idea that factors associated with global environmental change and possibly the associated biome are the cause of blooms globally. We further discuss the role of human mediated-dispersal.

Raw Project Data Set: Uncovering the Hidden Dangers:Finding Unsafe Go Code in the Wild

Raw project source code data from Git used to create our data set for our paper "Uncovering the Hidden Dangers: Finding Unsafe Go Code in the Wild". For more information, please read the README.md file and check out our data set repository at https://github.com/stg-tud/unsafe_go_study_results

opencc-zeroFeb 2021View details →

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of STRUCTURE-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates, impact the estimation of the optimal number of population clusters Kopt that best describe the observed data. Domestic horses are suited as a test case as there is extensive knowledge of the history of many breeds, extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (DAPC, FLOCK, PCoA and STRUCTURE with different run scenarios) all revealed the general, broad-scale relationships among the breeds that largely reflect known breed histories but diverged largely how they characterized small-scale patterns. STRUCTURE failed to consistently identify Kopt using the most widespread approach, the ΔK method, despite very large numbers of MCMCs (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a Kopt, was consistent with known breed histories. The over-reliance on Kopt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.