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opencc-zeroOct 2020View details →

Irisin directly stimulates osteoclastogenesis and bone resorption in vitro and in vivo: RNAseq dataset

Irisin, a skeletal-muscle secreted myokine, facilitates muscle-bone crosstalk and skeletal remodeling in part by its action on osteoblasts and osteocytes. In this study, we investigated whether irisin directly regulates osteoclasts. In vitro, irisin (2–10 ng/mL) increased osteoclast differentiation in C57BL/6J mouse bone marrow progenitors; however, this increase was blocked by a neutralizing antibody to integrin αVβ5. Irisin also increased bone resorption on several substrates in situ. RNAseq revealed differential gene expression induced by irisin including upregulation of markers for osteoclast differentiation and resorption, as well as osteoblast-stimulating 'clastokines'. Forced expression of the irisin precursor Fndc5 in transgenic C57BL/6J mice resulted in lower bone mass at three ages and greater in vitro osteoclastogenesis from Fndc5-transgenic bone marrow progenitors. This study demonstrates that irisin acts directly on osteoclast progenitors to increase differentiation and promote bone resorption, supporting the tenet that irisin not only stimulates bone remodeling but may also be an important counter-regulatory hormone.

opencc-by-4.0Nov 2020View details →

Data, analysis scripts, and simulations files for "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"

Measured data and analysis script, as well as, simulated data, and input scripts for our publication "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"

Signalling adjustments to direct and indirect environmental effects on signal perception in meerkats

The efficiency of communication between animals is determined by the perception range of signals. With changes in the environment, signal transmission between a sender and a receiver can be affected both directly, where the signal's propagation quality itself is affected, and indirectly, where for example the spacing between signaller and receiver is impacted. Here we investigated how meerkats (Suricata suricatta) in the Kalahari Desert adjust to these challenges in the context of maintaining group cohesion through contact calls. We found that meerkats changed their calling rate when signal transmission was affected indirectly due to increased dispersion of group members as during a drought, but not under typical wet conditions, when signal transmission was directly affected due to higher vegetation density. Instead under these wetter conditions, meerkats remained within proximity to each other. Overall, both direct and indirect environmental effects on signal perception resulted in an increased probability of groups splitting. In conclusion, we provide evidence that social animals can flexibly adjust their vocal coordination behaviour to cope with direct and indirect effects of the environment on signal perception, but that these adjustments have limitations.

Direct oral anticoagulants in atrial fibrillation patients with concomitant hyperthyroidism

Objective Patients with hyperthyroidism were excluded from randomized clinical trials of direct oral anticoagulants(DOACs) for stroke prevention in patients with non-valvular atrial fibrillation (NVAF). Methods We performed a nationwide retrospective cohort study using data from the Taiwan National Health Insurance Research Database. We enrolled 3,213 and 1,181 NVAF patients with hyperthyroidism taking DOACs and warfarin, respectively, from June 1, 2012 to December 31, 2017. We also enrolled 53,591 and 16,564 NVAF patients without hyperthyroidism taking DOACs and warfarin, respectively. We used propensity score-based stabilized weights (PSSWs) to balance covariates across the study groups. We also used 1:4 matching on both taking DOACs, with (n=3,213) and without hyperthyroidism (n=12,852); and both taking warfarin, with (n=1,181) and without hyperthyroidism (n=4,724). Results After PSSW, DOAC had a comparable risk of ischemic stroke/systemic embolism (IS/SE) and a lower risk of major bleeding (hazard ratio (HR):0.65; [95% confidential interval (CI):0.44-0.96]; P=0.0295) than warfarin among patients with hyperthyroidism. There were comparable risks of IS/SE and major bleeding between those patients with and without hyperthyroidism. However, patients taking warfarin with hyperthyroidism had a lower risk of IS/SE than those without hyperthyroidism (HR:0.61; [95%CI:0.43-0.86]; P=0.0050). Conclusion Among NVAF Asian patients with concomitant hyperthyroidism, DOACs may be an effective and safer alternative to warfarin. Thromboprophylaxis with DOACs may be considered for such patients, and it is important to validate this finding in further prospective study.

Direct and indirect effects of island size and wave exposure on shoreline arthropod diversity

Aim: Available theories suggest that the species number increases with island size, but the relationship between island size and species density, the number of species per unit area, is less understood. Moreover, mechanisms connecting island size and species density are not always evident because small and large islands differ in physical characteristics other than island size. The purpose here was to disentangle direct and indirect effects of island size and wave exposure on the species density of arthropods from herb-dominated shore habitats. Location: Islands in the Stockholm Archipelago, Sweden Taxon: Spiders (Araneae) and beetles (Coleoptera) Methods: We collected spiders and beetles on vegetated shores on islands of varying sizes, and used structural equation models to disentangle direct and indirect island size and wave exposure effects on species density. Results: Island size affected diversity of web-building spiders, predatory beetles and other beetles (detritivores and omnivores), direct and indirectly. Indirect effects arose because large islands have more trees and steeper slopes than small islands, both of which affected species occurrence. Because height above the sea level reduces the effect of wave exposure, there were effects of these variables on the forest cover and on the diversity of web-building spiders. Finally, surrounding forest cover and diversity of flowering plants within sites increased diversity of herbivore beetles and cursorial spiders, likely because these sites provide more diverse resources. Main conclusions: The result that predictors for species density vary between functional groups, with mechanisms that may or may not relate to island size, suggest potential developments in island biogeography theories. Future studies of island size effects should also attempt to quantify indirect effects, and not only total effects.

Separating direct and indirect effects of rising temperatures on biogenic volatile emissions in the Arctic

Volatile organic compounds (VOCs) are released from biogenic sources in a temperature-dependent manner. Consequently, Arctic ecosystems are expected to greatly increase their VOC emissions with ongoing climate warming, which is proceeding at twice the rate of global temperature rise. Here, we show that ongoing warming has strong, increasing effects on Arctic VOC emissions. Using a combination of statistical modelling on data from several warming experiments in the Arctic tundra and dynamic ecosystem modelling, we separate the impacts of temperature and soil moisture into direct effects and indirect effects through vegetation composition and biomass alterations. The indirect effects of warming on VOC emissions were significant, but smaller than the direct effects. Furthermore, vegetation changes also cause shifts in the chemical speciation of the emissions. Both direct and indirect effects result in large geographic differences in VOC emission responses in the warming Arctic, depending on the local vegetation cover and the climate dynamics. Our results outline complex links between local climate, vegetation, and ecosystem-atmosphere interactions, with likely local-to-regional impacts on the atmospheric composition.

opencc-by-4.0Nov 2020View details →

Direct Observational Evidence of the Simultaneous Excitation of Electromagnetic Ion Cyclotron Waves and Magnetosonic Waves by an Anisotropic Ring Distribution

dataset of "Direct Observational Evidence of the Simultaneous Excitation of Electromagnetic Ion Cyclotron Waves and Magnetosonic Waves by an Anisotropic Proton Ring Distribution"

Tomato Plants Treated with Systemin Peptide Show Enhanced Levels of Direct and Indirect Defense Associated with Increased Expression of Defense-Related Genes

Numerical data that underlies tables, graphs and statistics of the Plants article from Coppola et al., 2019: "Tomato Plants Treated with Systemin Peptide Show Enhanced Levels of Direct and Indirect Defense Associated with Increased Expression of Defense-Related Genes".

Helicos direct RNA sequencing of FPA mutants and overexpressors

Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat receptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, controlling their functional expression and impacting immunity. Using long-read nanopore direct RNA sequencing we resolve the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism

Current global warming trends are expected to have direct effects on species through their sensitivity to temperature, as well as on their biotic interactions, with cascading indirect effects on species, communities, and entire ecosystems. To predict the community-level consequences of global change we need to understand the relative roles of both the direct and indirect effects of warming. We used a laboratory experiment to investigate how warming affects a tropical community of three species of Drosophila hosts interacting with two species of parasitoids over a single generation. Our experimental design allowed us to distinguish between the direct effects of temperature on host species performance, and indirect effects through altered biotic interactions (competition among hosts and parasitism by parasitoid wasps). Although experimental warming significantly decreased parasitism for all host-parasitoid pairs, the effects of parasitism and competition on host communities did not vary across temperatures. Instead, effects on host relative abundances were species-specific, with one host species dominating the community at warmer temperatures, independently of parasitism and competition treatments. Our results show that temperature shaped a Drosophila host community directly through differences in species’ thermal performance, and not via its influences on biotic interactions.

opencc-zeroDec 2020View details →

Effect of vitamin D supplementation in patients with chronic hepatitis C after direct-acting antiviral treatment: a randomized, double-blind, placebo-controlled trial

Background: Replacement of vitamin D (VD) among patients with chronic hepatitis C (CHC) before viral eradication has demonstrated a protective effect on serum markers associated with hepatic fibrogenesis. We therefore hypothesized that VD may facilitate further fibrosis amelioration following curative treatment with direct-acting antivirals (DAA). Methods: This study was a randomized, double-blind, placebo-controlled trial conducted between February 2018 and August 2018. Patients with CHC and VD deficiency were randomized in a 1:1 ratio to either receive ergicalciferol or placebo over 6 weeks. Biochemical analysis indicators, including 25-hydroxyvitamin D (25(OH)D), fibrogenic markers [(transforming growth factor beta 1 (TGF-β1) and tissue inhibitors of matrix metalloproteinases 1 (TIMP-1)], and fibrolytic markers [matrix metalloproteinase 9 (MMP-9) and amino terminal type III procollagen peptide (P3NP)], were assessed at baseline and at 6 weeks. Serum 25(OH)D was analyzed by a chemiluminescence immunoassay. Serum hepatic fibrogenesis markers were measured using a quantitative sandwich enzyme-linked immunosorbent assay. Results: Seventy-five patients with CHC and VD deficiency were randomly assigned to VD (n=37) and placebo (n=38) groups. At the end of the study, the mean serum 25(OH)D level had risen to a normal level in the VD group, but was still deficient in the placebo group (41.8±9.1 vs. 18.1±4.6 ng/mL, p<0.001). Upon restoration of the VD level, there were no significant mean differences in the change from baseline for TGF-β1 (-0.6 ng/mL (95% confidence interval (95%CI) -2.8 – 1.7), p=0.63), TIMP-1 (-5.5 ng/mL (95%CI -26.4 – 15.3), p=0.60), MMP-9 (122.9 ng/mL (95%CI -69.0 – 314.8), p=0.21), and P3NP (-0.1 ng/mL (95%CI -2.4 – 2.2), p=0.92) between the VD and placebo groups. Conclusion: Short-term VD supplementation after DAA treatment in patients with CHC does not improve serum fibrogenesis markers and may not expedite the residual liver fibrosis healing process. Future studies are warranted to evaluate the long-term effect of VD supplementation on hepatic fibrosis regression.

Experimental Data for "Seismic wave attenuation and dispersion due to partial fluid saturation: Direct measurements and numerical simulations based on X-Ray CT"

Experimental Data from a Berea sandstone sample. Includes X-ray CT scans and mechanical response of sample. Abstract Quantitatively assessing seismic attenuation caused by fluid pressure diffusion (FPD) in partially saturated rocks is challenging because of its sensitivity to the spatial fluid distribution. To address this challenge we performed depressurisation experiments to induce the exsolution of carbon dioxide from water in a Berea sandstone sample. In a first set of experiments we used medical X-ray computed tomography (CT) to characterise the fluid distribution. At an equilibrium pressure of ~1 MPa and applying a fluid pressure decline rate of ~0.6 MPa per minute, we allowed a change in saturation of less than 1 %. The gas was heterogeneously distributed along the length of the sample, with most of the gas exsolving near the sample outlet. In a second set of experiments, at the same pressure and temperature, following a very similar exsolution protocol, we measured the frequency dependent attenuation and modulus dispersion between 0.1 and 1000 Hz using the forced oscillation method. We observed significant attenuation and dispersion in the extensional and bulk deformation modes, however not in the shear mode. Lastly, we use the fluid distribution derived from the X-ray CT as an input for numerical simulations of FPD to compute the attenuation and modulus dispersion. The numerical solutions are in close agreement with the attenuation and modulus dispersion measured in the laboratory. Our methodology allows for accurately relating attenuation and dispersion to the fluid distribution, which can be applied to improving the seismic monitoring of the subsurface.

opencc-by-4.0Jan 2021View details →

Automatic Method of Flow Direction Reasoning for Bridging Tributaries

Please see the detailed description of the data in the Read me.txt file.

opencc-by-4.0Jan 2021View details →

Dataset for Direct field evidence of autocatalytic iodine release from atmospheric aerosol

The datasets generated and/or analyzed for the publication of Tham et al., 'Direct field evidence of autocatalytic iodine release from  atmospheric aerosol' in PNAS (https://doi.org/10.1073/pnas.2009951118). Data are also available from the corresponding authors upon request.

opencc-zeroJan 2021View details →

Direct oral anticoagulants in treatment of cerebral venous thrombosis: systematic review

Objectives Current guidelines do not recommend direct oral anticoagulants (DOAC) to treat cerebral venous thrombosis (CVT) despite their benefits over standard therapy. We performed a systematic review to summarize the published experience of DOAC therapy in CVT. Data sources MEDLINE, EMBASE, and COCHRANE databases up to November 18, 2020. Eligibility criteria All published articles of patients with CVT treated with DOAC were included. Studies without follow-up information were excluded. Data extraction and synthesis Two independent reviewers screened articles and extracted data. A risk of bias analysis was performed. Primary and secondary outcome measures Safety data included mortality, intracranial hemorrhage (ICH), or other adverse events. Efficacy data included recurrent CVT, recanalization rates, and disability by modified Rankin Scales (mRS). Results 33 studies met inclusion criteria. One randomized controlled trial, 5 observational cohorts, and 27 case series or studies reported 279 patients treated with DOAC for CVT: 41% dabigatran, 47% rivaroxaban, 10% apixaban, and 2% edoxaban, in addition to 315 patients treated with standard therapy. The observational cohorts showed a similar risk of death in DOAC and standard therapy arms (RR 2.12, 95%CI 0.29-15.59). New ICH was reported in 2 (0.7%) DOAC-treated patients and recurrent CVT occurred in 4 (1.5%). A favourable mRS between 0 and 2 was reported in 94% of DOAC-treated patients, more likely than standard therapy in observational cohorts (RR 1.13, 95% CI: 1.02-1.25). Conclusion The evidence for DOAC use in CVT is limited although suggests sufficient safety and efficacy despite variability in timing and dose of treatment. This systematic review highlights that further rigorous trials are needed to validate these findings and to determine optimal treatment regimens. PROSPERO ID: CRD42017078398

opencc-zeroDec 2015View details →

Data from: Behavioral adaptations imply a direct link between ecological specialization and reproductive isolation in a sympatrically diverging ground beetle

Adaptation to a previously unoccupied niche within a single population is one of the most contentious topics in evolutionary biology as it assumes the simultaneous evolution of ecologically selected and preference traits. Here, we demonstrate behavioral adaptation to contrasting hydrological regimes in a sympatric mosaic of Pogonus chalceus beetle populations, and argue that this adaptation may result in nonrandom gene flow. When exposed to experimental inundations, individuals from tidal marshes, which are naturally subjected to frequent but short floods, showed a higher propensity to remain submerged compared to individuals from seasonal marshes that are inundated for several months. This adaptive behavior is expected to decrease the probability that individuals will settle in the alternative habitat, resulting in spatial sorting and reproductive isolation of both ecotypes. Additionally, we show that this difference in behavior is induced by the environmental conditions experienced by the beetles during their nondispersive larval stages. Hence, accidental or forced ovipositioning in the alternative habitat may induce both an increased performance and preference to the natal habitat type. Such plastic traits could play an important role in the most incipient stages of divergence with gene flow.

opencc-zeroDec 2016View details →

Data from: The effect of atomoxetine on random and directed exploration in humans

The adaptive regulation of the trade-off between pursuing a known reward (exploitation) and sampling lesser-known options in search of something better (exploration) is critical for optimal performance. Theory and recent empirical work suggest that humans use at least two strategies for solving this dilemma: a directed strategy in which choices are explicitly biased toward information seeking, and a random strategy in which decision noise leads to exploration by chance. Here we examined the hypothesis that random exploration is governed by the neuromodulatory locus coeruleus-norepinephrine system. We administered atomoxetine, a norepinephrine transporter blocker that increases extracellular levels of norepinephrine throughout the cortex, to 22 healthy human participants in a double-blind crossover design. We examined the effect of treatment on performance in a gambling task designed to produce distinct measures of directed exploration and random exploration. In line with our hypothesis we found an effect of atomoxetine on random, but not directed exploration. However, contrary to expectation, atomoxetine reduced rather than increased random exploration. We speculate that our results may be due to interactions with other neuromodulators that are also affected by atomoxetine, or that the reduction in random exploration was driven by a drug-related increase in phasic norepinephrine activity rather than in baseline norepinephrine levels.

opencc-zeroDec 2014View details →

Data from: Crown asymmetry in high latitude forests: disentangling the directional effects of tree competition and solar radiation

Light foraging by trees is a fundamental process shaping forest communities. In heterogeneous light environments this behavior is expressed as plasticity of tree growth and the development of structural asymmetries. We studied the relative influence of neighborhood structure and directional solar radiation on horizontal asymmetry of tree crowns in late-successional high latitude (67–68°N) forests in northern Fennoscandia. We described crown asymmetries as crown vectors (i.e. horizontal vectors from stem center to crown center), which we obtained from canopy maps based on crown perimeter measurements in the field. To disentangle the influence of the two main determinants, inter-tree competition and directionality of above-canopy solar radiation at high latitudes, we applied circular statistical models, utilizing cylindrical distributions, to these data consisting of orientations and intensities of crown asymmetry. At the individual tree level, our model predicted crown asymmetry vectors from the current stand structure, and the predictions became better when the intensity of asymmetry (i.e. crown vector length) was higher. Competition was the main determinant of crown asymmetry for 2/3 of trees, and the model predictions improved when we incorporated the directionality of solar radiation. At the stand-level, these asymmetries had resulted in a small increment of the projected canopy area and an increased regularity of spatial structure. Our circular statistical modelling approach provided a quantitative evaluation of the relative importance of directionality of solar radiation and neighborhood stand structure, showing how both of these factors play a role in formation of crown asymmetries in high latitude forests. This approach further demonstrated the applicability of circular statistical modeling in ecological studies where the response variable has both orientation and intensity.

opencc-zeroDec 2015View details →

Data from: Energy and lipid metabolism during direct and diapause development in a pierid butterfly

Diapause is a fundamental component of the life-cycle in the majority of insects living in environments characterized by strong seasonality. The present study addresses poorly understood associations and trade-offs between endogenous diapause duration, thermal sensitivity of development, energetic cost of development and cold tolerance. Diapause intensity, metabolic rate trajectories and lipid profiles of directly developing and diapausing animals were studied using pupae and adults of Pieris napi butterflies from a population for which endogenous diapause is well studied. Endogenous diapause was terminated after 3 months and termination required chilling. Metabolic and postdiapause development rates increased with diapause duration, while the metabolic cost of postdiapause development decreased, indicating that once diapause is terminated development proceeds at a low rate even at low temperature. Diapausing pupae had larger lipid stores than the directly developing pupae and lipids constituted the primary energy source during diapause. However, during diapause lipid stores did not decrease. Thus, despite lipid catabolism meeting the low energy costs of the diapausing pupae, primary lipid store utilization did not occur until the onset of growth and metamorphosis in spring. In line with this finding, diapausing pupae contained low amounts of mitochondria-derived cardiolipins, which suggests a low capacity for fatty acid β-oxidation. While ontogenic development had a large effect on lipid and fatty acid profiles, only small changes in these were seen during diapause. The data therefore indicate that the diapause lipidomic phenotype is built early, when pupae are still at high temperature, and retained until diapause post-diapause development.