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opencc-zeroSep 2020View details →

Spatially anonymized data from: Novel step selection analyses on energy landscapes reveal how linear features alter migrations of soaring birds

This dataset consists of spatially anonymized movement data as well as environmental covariate data to estimate energy landscape step selection selections for migratory golden eagles that summer in Alaska. <ol> <li>Human modification of landscapes includes extensive addition of linear features, such as roads and transmission lines. These can alter animal movement and space use and affect the intensity of interactions among species, including predation and competition. Effects of linear features on animal movement have seen relatively little research in avian systems, despite ample evidence of their effects in mammalian systems and that some types of linear features, including both roads and transmission lines, are substantial sources of mortality.</li> <li>Here, we used satellite telemetry combined with step selection functions designed to explicitly incorporate the energy landscape (el‐SSFs) to investigate the effects of linear features and habitat on movements and space use of a large soaring bird, the golden eagle Aquila chrysaetos, during migration. Our sample consisted of 32 adult eagles tracked for 45 spring and 39 fall migrations from 2014 to 2017.</li> <li>Fitted el‐SSFs indicated eagles had a strong general preference for south‐facing slopes, where thermal uplift develops predictably, and that these areas are likely important aspects of migratory pathways. el‐SSFs also provided evidence that roads and railroads affected movement during both spring and fall migrations, but eagles selected areas near roads to a greater degree in spring compared to fall and at higher latitudes compared to lower latitudes. During spring, time spent near linear features often occurred during slower‐paced or stopover movements, perhaps in part to access carrion produced by vehicle collisions.</li> <li>Regardless of the behavioural mechanism of selection, use of these features could expose eagles and other soaring species to elevated risk via collision with vehicles and/or transmission lines. Linear features have previously been documented to affect the ecology of terrestrial species (e.g. large mammals) by modifying individuals' movement patterns; our work shows that these effects on movement extend to avian taxa.</li> </ol>

opencc-zeroNov 2020View details →

Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

Background: Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2-steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region). Samples included oral wash, protected specimen brushes and protected bronchoalveolar lavage (healthy and obstructive lung disease), and negative controls. Results: The number of sequences and amplicon sequence variants (ASV) decreased in order setup1>setup2>setup3. This trend appeared to be associated with an increased taxonomic resolution when sequencing the V3 V4 region (setup 1) and an increased number of small ASVs in setups 1 and 2. The latter was considered a result of contamination in the two-step PCR protocols as well as sequencing across multiple runs (setup 1). Although genera Streptococcus, Prevotella, Veillonella and Rothia dominated, differences in relative abundance were observed across all setups. Analyses of beta-diversity revealed that while oral wash samples (high biomass) clustered together regardless of number of PCR steps, samples from the lungs (low biomass) separated. The removal of contaminants identified using the Decontam package in R, did not resolve differences in results between sequencing setups. Conclusions: Differences in number of PCR steps will have an impact of final bacterial community descriptions, and more so for samples of low bacterial load. Our findings could not be explained by differences in contamination levels alone, and more research is needed to understand how variations in PCR-setups and reagents may be contributing to the observed protocol bias.

opencc-by-4.0Dec 2020View details →

Python code and experimental data of three-color dynein stepping

This project is described in: Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility (2020) and can be found on BioRxiv: (link to follow) Here, we provide the experimental data of the three-color dynein stepping experiments together with the custom python code used for data analysis. Details on how the code works are given in the script itself.

opencc-zeroDec 2016View details →

Data from: The genetics of egg retention and fertilization success in Drosophila: one step closer to understanding the transition from facultative to obligate viviparity

Oviparous, facultative egg retention enables Drosophila females to withhold fertilized eggs in their reproductive tracts until circumstances favor oviposition. The propensity to retain fertilized eggs varies greatly between species, and is correlated with other reproductive traits, such as egg size and ovariole number. While previous studies have described the phenomenon, no study to date has characterized within-species variation or the genetic basis of the trait. Here, we develop a novel microscope-based method for measuring egg retention in Drosophila females and determine the range of phenotypic variation in mated female egg retention in a subset of 91 Drosophila Genetic Reference Panel (DGRP) lines. We inferred the genetic basis of egg retention using a genome-wide association study (GWAS). Further, the scoring of more than 95,000 stained, staged eggs enabled estimates of fertilization success for each line. We found evidence that ovary- and spermathecae-related genes as well as genes affecting olfactory behavior, male mating behavior, male-female attraction and sperm motility may play a crucial role in post-mating physiology. Based on our findings we also propose potential evolutionary routes towards obligate viviparity. In particular, we propose that the loss of fecundity incurred by viviparity could be offset by benefits arising from enhanced mate discrimination, resource specialization, or modified egg morphology.

Data from: From integrative taxonomy to species description: one step beyond

Integrative taxonomy has emerged as a methodologically sound method for discovering new taxa. By coupling different sources of information (e.g. molecular and morphological data) and by combining analytical approaches (e.g. multivariate analyses, phylogenetics), systematists have the tools to uncover cryptic diversity and draw more reliable species hypotheses. Integratively-delimited taxa may be more prone to formal description compared to taxa delimited with a single source of information, because more detailed species hypotheses can be drawn. Integrative taxonomy has therefore the potential to reduce the so-called "taxonomic impediment" (i.e. the gap between the number of taxa that remain to be described and the number of taxa that are formally named). However, bridging fields such as molecular systematics and morphological taxonomy may remain challenging, as it either requires the training of versatile scientists, or the establishment of collaborations among scientists from these fields. We therefore asked ourselves whether integratively-delimiting species necessarily led to formal taxonomic descriptions. We reviewed the "integrative taxonomy" literature of the past five years to estimate the ratio of studies delimiting species (without describing them) over studies describing species, and tested whether this ratio was dependent on the types and numbers of characters used for delimitation. Based on a sample of 361 studies claiming an integrative approach to species delimitation, 68% used at least two characters for species delimitation, and 32% were based on a single character (most often DNA sequences), restricting their integrative approach to including different types of data analyses. Overall, 46% of studies delimit without describing, and a majority of those do not provide a justification for the absence of formal descriptions. Authors that do provide a justification mention lack of data, forthcoming publications with formal descriptions, or find nomenclatural rules too complex. Integrative taxonomy is, based on our sample, not an efficient solution to the "taxonomic impediment."

Data from: Different effects of paternal trans-generational immune priming on survival and immunity in step and genetic offspring

Paternal trans-generational immune priming, whereby fathers provide immune protection to offspring, has been demonstrated in the red flour beetle Tribolium castaneum exposed to the insect pathogen Bacillus thuringiensis. It is currently unclear how such protection is transferred, as in contrast to mothers, fathers do not directly provide offspring with a large amount of substances. In addition to sperm, male flour beetles transfer seminal fluids in a spermatophore to females during copulation. Depending on whether paternal trans-generational immune priming is mediated by sperm or seminal fluids, it is expected to either affect only the genetic offspring of a male, or also their step offspring that are sired by another male. We therefore conducted a double-mating experiment and found that only the genetic offspring of an immune primed male show enhanced survival upon bacterial challenge, while phenoloxidase activity, an important insect immune trait, and the expression of the immune receptor PGRP were increased in all offspring. This indicates that information leading to enhanced survival upon pathogen exposure is transferred via sperm, and thus potentially constitutes an epigenetic effect, whereas substances transferred with the seminal fluid could have an additional influence on offspring immune traits and immunological alertness.

Data from: PCR duplication: a one-step cloning-free method to generate duplicated chromosomal loci and interference-free expression reporters in yeast

Here, we report on a novel PCR targeting-based strategy called 'PCR duplication' that enables targeted duplications of genomic regions in the yeast genome using a simple PCR-based approach. To demonstrate its application we first duplicated the promoter of the FAR1 gene in yeast and simultaneously inserted a GFP downstream of it. This created a reporter for promoter activity while leaving the FAR1 gene fully intact. In another experiment, we used PCR duplication to increase the dosage of a gene in a discrete manner, from 1× to 2x. Using TUB4, the gene encoding for the yeast γ-tubulin, we validated that this led to corresponding increases in the levels of mRNA and protein. PCR duplication is an easy one-step procedure that can be adapted in different ways to permit rapid, disturbance-free investigation of various genomic regulatory elements without the need for ex vivo cloning.

opencc-by-4.0Jun 2021View details →

DB SMART Step 2

DB SMART , STEP 2

opencc-zeroDec 2018View details →

Data from: Two-step pyrolysis-gas chromatography method with mass spectrometric detection for identification of tattoo ink ingredients and counterfeit products

Tattoo inks are complex mixtures of ingredients. Each of them possesses different chemical properties which have to be addressed upon chemical analysis. In this method for two-step pyrolysis online coupled to gas chromatography mass spectrometry (py-GC-MS) volatile compounds are analyzed during a first desorption run. In the second run, the same dried sample is pyrolyzed for analysis of non-volatile compounds such as pigments and polymers. These can be identified by their specific decomposition patterns. Additionally, this method can be used to differentiate original from counterfeit inks. Easy screening methods for data evaluation using the average mass spectra and self-made pyrolysis libraries are applied to speed up substance identification. Using specialized evaluation software for pyrolysis GS-MS data, a fast and reliable comparison of the full chromatogram can be achieved. Since GC-MS is used as separation technique, the method is limited to volatile substances upon desorption and after pyrolysis of the sample. The method can be applied for quick substance screening in market control surveys since it requires no sample preparation steps.

Data from: Stepping in the direction of the fall: the next foot placement can be predicted from current upper body state in steady-state walking

During human walking, perturbations to the upper body can be partly corrected by placing the foot appropriately on the next step. Here, we infer aspects of such foot placement dynamics using step-to-step variability over hundreds of steps of steady-state walking data. In particular, we infer dependence of the 'next' foot position on upper body state at different phases during the 'current' step. We show that a linear function of the hip position and velocity state (approximating the body center of mass state) during mid-stance explains over 80% of the next lateral foot position variance, consistent with (but not proving) lateral stabilization using foot placement. This linear function implies that a rightward pelvic deviation during a left stance results in a larger step width and smaller step length than average on the next foot placement. The absolute position on the treadmill does not add significant information about the next foot relative to current stance foot over that already available in the pelvis position and velocity. Such walking dynamics inference with steady-state data may allow diagnostics of stability and inform biomimetic exoskeleton or robot design.

opencc-zeroDec 2014View details →

Data from: From steps to home range formation: species-specific movement upscaling among sympatric ungulates

Animals move to interact with the environment in order to find food resources and cover. Intrinsic characteristics affecting feeding and antipredatory strategies likely shape variation in movement patterns and home range formation between individuals, populations and species. Browsing herbivores selectively forage on patchily distributed resources in areas with more canopy cover, whereas mixed feeders and grazers feed on more open grasslands and tend to aggregate as an antipredatory strategy. We therefore predicted that at small temporal scales, browsers will show greater net displacements (i.e. typical of searching patterns) than mixed feeders or grazers; but at larger temporal scales, we expect the opposite pattern, since gregarious species will need to use larger areas to feed the whole herd. We also predicted that the feeding/antipredatory strategy will determine the behavioural responses to other environmental factors. To test this, we compared spatial movement patterns at multiple scales (from 20-min intervals to annual home ranges) of three sympatric, similar-sized, alpine ungulates which differ in their feeding/antipredatory strategy: roe deer (solitary browsers), mouflon (gregarious grazers) and chamois (intermediate feeders in smaller groups). We used location data from GPS-collared females of the three species in the French Alps. As predicted, we found that multi-scale spatial patterns depended on the feeding/antipredatory strategy. Browsers foraged within smaller range areas, searching back and forth. Mixed feeders and, especially, grazers covered larger areas, presumably to satisfy herd needs. The feeding/antipredatory strategies also determined the interspecific variability in behavioural responses to factors such as maternal status, weather, habitat type or human disturbance, supporting our hypothesis. Exploring interspecific variability, we showed how movement behaviour and home range formation vary substantially, even among species within the same guild. This mechanism might be important to maintain intra-guild multi-species associations and increase biodiversity, through contributing to niche segregation and, thus, coexistence.

opencc-zeroDec 2014View details →

Data from: Do humans optimally exploit redundancy to control step variability in walking?

It is widely accepted that humans and animals minimize energetic cost while walking. While such principles predict average behavior, they do not explain the variability observed in walking. For robust performance, walking movements must adapt at each step, not just on average. Here, we propose an analytical framework that reconciles issues of optimality, redundancy, and stochasticity. For human treadmill walking, we defined a goal function to formulate a precise mathematical definition of one possible control strategy: maintain constant speed at each stride. We recorded stride times and stride lengths from healthy subjects walking at five speeds. The specified goal function yielded a decomposition of stride-to-stride variations into new gait variables explicitly related to achieving the hypothesized strategy. Subjects exhibited greatly decreased variability for goal-relevant gait fluctuations directly related to achieving this strategy, but far greater variability for goal-irrelevant fluctuations. More importantly, humans immediately corrected goal-relevant deviations at each successive stride, while allowing goal-irrelevant deviations to persist across multiple strides. To demonstrate that this was not the only strategy people could have used to successfully accomplish the task, we created three surrogate data sets. Each tested a specific alternative hypothesis that subjects used a different strategy that made no reference to the hypothesized goal function. Humans did not adopt any of these viable alternative strategies. Finally, we developed a sequence of stochastic control models of stride-to-stride variability for walking, based on the Minimum Intervention Principle. We demonstrate that healthy humans are not precisely "optimal," but instead consistently slightly over-correct small deviations in walking speed at each stride. Our results reveal a new governing principle for regulating stride-to-stride fluctuations in human walking that acts independently of, but in parallel with, minimizing energetic cost. Thus, humans exploit task redundancies to achieve robust control while minimizing effort and allowing potentially beneficial motor variability.

opencc-zeroJun 2021View details →

Data from: Achieving a step change in the tuberculosis epidemic through comprehensive community-wide intervention: A model-based analysis

Background: Global progress towards reducing tuberculosis (TB) incidence and mortality has consistently lagged behind World Health Organization targets leading to a perception that large reductions in TB burden cannot be achieved. However, several recent and historical trials suggest that intervention efforts that are comprehensive and focused can have substantial epidemiological impact. We aimed to quantify the potential epidemiological impact of an intensive but realistic, community-wide campaign utilizing existing tools, and designed to achieve a "step change" in TB burden. Methods: We developed a compartmental model of tuberculosis transmission in a mid-sized city in India, the country with the greatest absolute burden of TB worldwide. We modeled the impact of a campaign comprising one-time community-wide screening with treatment for TB disease and preventive therapy for latent TB infection (LTBI). This one-time intervention was followed by strengthening of tuberculosis-related health system achieved by leveraging the one-time campaign. We estimated the tuberculosis cases and deaths that could be averted over 10 years using this comprehensive approach and assessed the contributions of individual components of the intervention. Results: A campaign that successfully screened 70% of the adult population for active and latent tuberculosis and subsequently reduced diagnostic and treatment delays and unsuccessful treatment outcomes by 50% was projected to avert 7,800 (95% range: 5,450 – 10,200) cases and 1,710 (1,290 – 2,180) tuberculosis-related deaths per 1 million population over 10 years. Of the total averted deaths, 33.5% (28.2 – 38.3) were attributable to inclusion of preventive therapy and 52.9% (48.4 - 56.9) to health system strengthening. Conclusions: A one-time, community-wide mass campaign, comprehensively designed to detect, treat, and prevent tuberculosis with currently existing tools can have meaningful and long-lasting epidemiological impact. Successful treatment of LTBI is critical to achieving this result. Health system strengthening is essential to any effort to transform the TB response.

opencc-zeroDec 2016View details →

Data from: Silver nanoparticles as a medical device in healthcare settings: a five-step approach for candidate screening of coating agents

Silver nanoparticle-based antimicrobials can promote a long lasting bactericidal effect without detrimental toxic side effects. However, there is not a clear and complete protocol to define and relate the properties of the particles (size, shape, surface charge, ionic content) with their specific activity. In this paper, we propose an effective multi-step approach for the identification of a 'purpose-specific active applicability window' to maximize the antimicrobial activity of medical devices containing silver nanoparticles (Ag NPs) (such as surface coaters), minimizing any consequent risk for human health (safety by design strategy). The antimicrobial activity and the cellular toxicity of four types of Ag NPs, differing in their coating composition and concentration have been quantified. Through the implementation of flow-field flow fractionation, Ag NPs have been characterized in terms of metal release, size and shape. The particles are fractionated in the process while being left unmodified, allowing for the identification of biological particle-specific contribution. Toxicity and inflammatory response in vitro have been assessed on human skin models, while antimicrobial activity has been monitored with both non-pathogenic and pathogenic Escherichia coli. The main benefit associated with such approach is the comprehensive assessment of the maximal effectiveness of candidate nanomaterials, while simultaneously indexing their properties against their safety.

opencc-zeroDec 2017View details →

Data from: Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach

With fossil representatives from the Silurian capable of respiring atmospheric oxygen, millipedes are among the oldest terrestrial animals, and likely the first to acquire diverse and complex chemical defenses against predators. Exploring the origin of complex adaptive traits is critical for understanding the evolution of Earth's biological complexity, and chemical defense evolution serves as an ideal study system. The classic explanation for the evolution of complexity is by gradual increase from simple to complex, passing through intermediate "stepping stone" states. Here we present the first phylogenetic-based study of the evolution of complex chemical defenses in millipedes by generating the largest genomic-based phylogenetic dataset ever assembled for the group. Our phylogenomic results demonstrate that chemical complexity shows a clear pattern of escalation through time. New pathways are added in a stepwise pattern, leading to greater chemical complexity, independently in a number of derived lineages. This complexity gradually increased through time, leading to the advent of three distantly related chemically complex evolutionary lineages, each uniquely characteristic of each of the respective millipede groups.

opencc-by-4.0Mar 2024View details →

Impact of horizontal resolution and model time step on European precipitation extremes in the OpenIFS 43r3 atmosphere model

Python scripts used for GMD paper

opencc-by-4.0Oct 2023View details →

Parameters of RSF law and AE activity for the individual sliding-rate steps

Open the record for dataset details and reuse information.

opencc-by-4.0Nov 2023View details →

Data for: Simulating animal space use from fitted integrated Step-Selection Functions (iSSF)

Open the record for dataset details and reuse information.

opencc-by-4.0Nov 2023View details →

Reduction steps for CPS metrics

Reduction steps for CPS metrics