Find research datasets worth reusing

opencc-by-4.0Aug 2021View details →

Data for "Unsupervised learning of sequence-specific aggregation behavior for a model copolymer"

These are the data associated with the paper, "Unsupervised learning of sequence-specific aggregation behavior for a model copolymer" (DOI 10.1039/D1SM01012C). Each of the directories contains subdirectories with `GSD` files dumped from HOOMD. Each subdirectory roughly corresponds to one or two of the figures in the paper.

opencc-by-4.0Aug 2021View details →

Visualizing the organization and differentiation of the male-specific nervous system of C. elegans

Image volumes and annotations for male NeuroPAL, flp-3, flp-27, and nlp-51 expression. The following image volumes were annotated by Tessa Tekieli, Chen Wang, and Robert Fernandez for: "Visualizing the organization and differentiation of the male-specific nervous system of C. elegans". The publication is available here: https://journals.biologists.com/dev/article-abstract/doi/10.1242/dev.199687/271902/Visualizing-the-organization-and-differentiation These image files can be viewed with the NeuroPAL ID software, available at: https://www.hobertlab.org/neuropal/ OR https://github.com/amin-nejat/CELL_ID This software was provided for the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans". The publication is available here: https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2 Please cite the NeuroPAL publication when using the software.

opencc-by-4.0Mar 2014View details →

Fig. 39 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters

Fig. 39. Boaedon fuliginosus (Boie), skull of AMNH R-11996, ×3.7.

opencc-by-4.0Mar 2014View details →

Fig. 5 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters

Fig. 5. Eutrachelophis steinbachi (Boulenger). Adult female shown approximately life size (BMNH

opencc-by-4.0Mar 2014View details →

Fig. 17 in New Taxa And Cryptic Species Of Neotropical Snakes (Xenodontinae), With Commentary On Hemipenes As Generic And Specific Characters

Fig. 17. The tips of diverse bilobed hemipenes. A. Apical discs on the hemipenis of Liophis

opencc-by-4.0Mar 2021View details →

Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5

The SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein syntaxin-5 (Stx5) is essential for Golgi transport. In humans, the STX5 mRNA encodes two protein isoforms, Stx5 Long (Stx5L) from the first starting methionine and Stx5 Short (Stx5S) from an alternative starting methionine at position 55. In this study, we identified a novel human disorder caused by a single missense substitution in the second starting methionine (p.M55V), resulting in complete loss of the short isoform. Patients suffer from an early fatal multisystem disease, including severe liver disease, skeletal abnormalities and abnormal glycosylation. Primary human dermal fibroblasts isolated from these patients showed defective glycosylation, altered Golgi morphology as measured by electron microscopy and mislocalization of glycosyltransferases. Measurements of anterograde trafficking, based on biotin-synchronizable forms of Stx5 (the RUSH system), and of cognate binding SNAREs, based on Förster resonance energy transfer (FRET), revealed that the short isoform of Stx5 is essential for intra-Golgi transport. This is the first time a mutation in an alternative starting codon is linked to human disease, demonstrating that the site of translation initiation is an important new layer of regulating protein trafficking.

opencc-by-4.0Dec 2018View details →

Dataset for "Interpreting eddy covariance data from heterogeneous Siberian tundra: land cover-specific methane fluxes and spatial representativeness"

The micrometeorological dataset used in Tuovinen, J.-P., Aurela, M., Hatakka, J., Räsänen, A., Virtanen, T., Mikola, J., Ivakhov, V., Kondratyev, V. and Laurila, T.: Interpreting eddy covariance data from heterogeneous Siberian tundra: land cover-specific methane fluxes and spatial representativeness. Biogeosciences Discussions, https://doi.org/10.5194/bg-2018-155, 2018 (accepted for publication in Biogeosciences).

opencc-zeroOct 2022View details →

Allele‐specific cis‐regulatory methylation of the gene for vasoactive intestinal peptide in white‐throated sparrows

White-throated sparrows (Zonotrichia albicollis) offer a unique opportunity to connect genotype with behavioral phenotype. In this species, a rearrangement of the second chromosome is linked with territorial aggression; birds with a copy of this "supergene" rearrangement are more aggressive than those without it. The supergene has captured the gene VIP, which encodes vasoactive intestinal peptide, a neuromodulator that causes aggression in other songbirds. In white-throated sparrows, VIP expression is higher in the anterior hypothalamus of birds with the supergene than those without it, and expression of VIP in this region predicts the level of territorial aggression regardless of genotype. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of VIP both in breeding adults, which exhibit morph differences in territorial aggression, and in nestlings, before territorial behavior develops. We extracted and bisulfite-converted DNA from samples of the hypothalamus in wild-caught adults and nestlings and used high-throughput sequencing to measure DNA methylation of a region upstream of the VIP start site. We found that the allele inside the supergene was less methylated than the alternative allele in both adults and nestlings. The differential methylation was attributed primarily to CpG sites that were shared between the alleles, not to polymorphic sites, which suggests that epigenetic regulation is occurring independently of the genetic differentiation within the supergene. This work represents an initial step toward understanding how epigenetic differentiation inside chromosomal inversions leads to the development of alternative behavioral phenotypes.

opencc-by-4.0Nov 2022View details →

HLA epitopic mismatch and risk of developing Donor Specific Antibodies in pediatric kidney transplantation

The aim of this study was to evaluate the correlation between epitopic HLA mismatches and the risk of developing DSA in pediatric kidney recipients. There are very few publications concerning epitope HLA mismatch in pediatric kidney transplantation although this topic has been growing in scientific articles in recent years and is promising in adult recipients. The majority of children with chronic renal failure will require multiple kidney transplants during their lifetime and it is therefore important that we can limit the risk of antibody development in order to give them the best chance of survival for their future kidney transplants.

Data for "Boosting propagule transport models with individual-specific data from mobile apps"

<ol> <li>Management of invasive species and pathogens requires information about the traffic of potential vectors. Such information is often taken from vector traffic models fitted to survey data. Here, user-specific data collected via mobile apps offer new opportunities to obtain more accurate estimates and to analyze how vectors' individual preferences affect propagule flows. However, data voluntarily reported via apps may lack some trip records, adding a significant layer of uncertainty. We show how the benefits of app-based data can be exploited despite this drawback.</li> <li>Based on data collected via an angler app, we built a stochastic model for angler traffic in the Canadian province of Alberta. There, anglers facilitate the spread of whirling disease, a parasite-induced fish disease. The model is temporally and spatially explicit and accounts for individual preferences and repeating behaviour of anglers, helping to address the problem of missing trip records.</li> <li>We obtained estimates of angler traffic between all subbasins in Alberta. The model's accuracy exceeds that of direct empirical estimates even when fewer data were used to fit the model. The results indicate that anglers' local preferences and their tendency to revisit previous destinations reduce the number of long inter-waterbody trips potentially dispersing whirling disease. According to our model, anglers revisit their previous destination in 64% of their trips, making these trips irrelevant for the spread of whirling disease. Furthermore, 54% of fishing trips end in individual-specific spatially contained areas with mean radius of 54.7 km. Finally, although the fraction of trips that anglers report was unknown, we were able to estimate the total yearly number of fishing trips in Alberta, matching an independent empirical estimate.</li> <li>We make two major contributions: (1) we provide a model that uses mobile app data to boost the mechanistic accuracy of classic propagule transport models, and (2) we demonstrate the importance of individual-specific behaviour of vectors for propagule transport. Ignoring vectors' local preferences and their tendency to revisit previous destinations can lead to significant overestimates of vector traffic and biased estimates of propagule flows. This has clear implications for the management of invasive species and animal diseases.</li> </ol>

Population-specific responses of an insect herbivore to variation in host-plant quality

Anthropogenic climate change poses a substantial challenge to many organisms, to which they need to respond to avoid fitness reductions. Investigating responses to environmental change is particularly interesting in herbivores, as they are potentially affected by indirect effects mediated via variation in host-plant quality. We here use the herbivorous insect Pieris napi to investigate geographic variation in the response to variation in food quality. We performed a common garden experiment using replicated populations from Germany and Italy, and manipulating host quality by growing host plants at different temperature and water regimes. We found that feeding on plants grown at a higher temperature generally diminished the performance of P. napi, evidenced by a prolonged development time and reduced larval growth rate, body mass, fat content, and phenoloxidase activity. Genotype by environment interactions (G x E) were present in several performance traits, indicating that Italian populations (1) respond more strongly to variation in host-plant quality and (2) are more sensitive to poor food quality than German ones. This may reflect a cost of the rapid lifestyle found in Italian populations. Consequently, German populations may be more resilient against environmental perturbations and may perhaps even benefit from warmer temperatures, while Italian populations will likely suffer from the concomitantly reduced host-plant quality. Our study thus exemplifies how investigating G x E may help to better understand the vulnerability of populations to climate change.

Divergent response and adaptation of specific leaf area to environmental change at different spatio-temporal scales jointly improve plant survival

Specific leaf area (SLA) is one of the most important plant functional traits. It integrates multiple functions and reflects strategies of plants to obtain resources. How plants employ different strategies (e.g., through SLA) to respond to dynamic environmental conditions remains poorly understood.This study aimed to explore the spatial variation in SLA and divergent adaptation of plants by changing SLA through the lens of biogeographic patterns, evolutionary history, and short-term responses. SLA data for 5424 plant species from 76 natural communities in China were systematically measured and integrated with meta-analysis of field experiments (i.e., global warming, drought, and nitrogen addition). The mean value of SLA across all species was 21.8 m2 kg–1, ranging from 0.9 to 110.2 m2 kg–1. SLA differed among different ecosystems, temperature zones, vegetation types, and functional groups. Phylogeny had a weak effect on SLA, but plant species evolved toward higher SLA. Furthermore, plants responded nonlinearly to environmental change by changing SLA. Unexpectedly, radiation was one of the main factors determining the spatial variation in SLA on a large scale. Conversely, short-term manipulative experiments showed that SLA increased with increased resource availability and tended to stabilize with treatment duration. However, different species exhibited varying response patterns. Overall, long-term adaptation of plants to environmental gradients and its short-term response to resource pulses through variation in SLA jointly improve plant adaptability to a changing environment. Overall SLA-environment relationships should be emphasized as a multidimensional strategy for elucidating environmental change in future research.

Validation of Sepsis-3 using survival analysis and clinical evaluation of quick SOFA, SIRS, and burn-specific SIRS for sepsis in burn patients with suspected infection

Purpose: Sepsis-3 is a life-threatening organ dysfunction caused by dysregulated host responses to infection; and defined using the Sepsis-3 criteria, introduced in 2016, however, the criteria need to be validated in specific clinical fields. We investigated mortality prediction and compared the diagnostic performance of quick Sequential Organ Failure Assessment (qSOFA), systemic inflammatory response syndrome (SIRS), and burn-specific SIRS (bSIRS) in burn patients. Methods: This single-center retrospective cohort study examined burn patients in Seoul, Korea during January 2010–December 2020. Overall, 1,391 patients with suspected infection were divided into four sepsis groups using SOFA, qSOFA, SIRS, and burn-specific SIRS. Results: Hazard ratios (HRs) of all unadjusted models were statistically significant; however, the HR (0.726, p = 0.0080.001) in the SIRS ≥2 group is below 1. In the adjusted model, HRs of the SOFA ≥2 (2.426, p < 0.001), qSOFA ≥2 (7.198, p < 0.001), and SIRS ≥2 (0.575, p < 0.001) groups were significant. The diagnostic performance of dichotomized qSOFA, SIRS, and bSIRS for sepsis was defined by the Sepsis-3 criteria. The mean onset day was 4.13±2.97 according to Sepsis-3. The sensitivity of SIRS (0.989, 95% confidence interval [CI]: 0.982–0.994) was higher than that of qSOFA (0.841, 95% CI: 0.819–0.861) and bSIRS (0.803, 95% CI: 0.779–0.825). Specificities of qSOFA (0.929, 95% CI: 0.876–0.964) and bSIRS (0.922, 95% CI: 0.868–0.959) were higher than those of SIRS (0.461, 95% CI: 0.381–0.543). Conclusion: Sepsis-3 is a good alternative diagnostic tool because it reflects sepsis severity without delaying diagnosis. SIRS showed higher sensitivity than qSOFA and bSIRS and may therefore more adequately diagnose sepsis.

Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race

Decades of research have shown that the coevolutionary arms race between avian brood parasites and their hosts can promote phenotypic diversification in hosts and brood parasites. However, relatively little is known about the role of brood parasitism in promoting phenotypic diversification of nestlings. We review field data collected over four decades in Australia, New Caledonia and New Zealand to assess potential for coevolutionary interactions between the shining bronze-cuckoo (Chalcites lucidus) and its hosts, and how diversification at the nestling stage may be generating different subspecies. The shining bronze-cuckoo is a specialist parasite of a few hosts in the family Acanthizidae. It has diversified into subspecies, of which the nestlings closely mimic the respective host nestlings in each region. Additionally, some cuckoo subspecies have polymorphic nestlings. The Acanthizidae hosts have similar breeding and nesting habits and only moderately effective frontline defences against parasitism at cuckoo egg laying or at the egg stages. However, some hosts have developed highly effective defences at the nestling stage by recognising and ejecting cuckoo nestlings from the nest. As with the cuckoo nestlings, some hosts have polymorphic nestlings. The coevolutionary interactions in each region suggest different evolutionary stages of the arms race in which either the parasite or the host is currently in the lead. The presence of moderately effective defences at the egg laying and egg stages might explain why some hosts do not have defences at the nestling stage. The south-Pacific cuckoo – host systems are excellent models to explore the evolutionary mechanisms driving the diversification at the nestling stage in the coevolutionary arms race between avian brood parasites and their hosts.

Global-scale modeling of early factors and country-specific trajectories of COVID-19 incidence: a cross-sectional study of the first 6 months of the pandemic

Studies examining factors responsible for COVID-19 incidence are mostly focused at the national or sub-national level. A global-level characterization of contributing factors and temporal trajectories of disease incidence is lacking. Here we conducted a global-scale analysis of COVID-19 infections to identify key factors associated with early disease incidence. Additionally, we compared longitudinal trends of COVID-19 incidence at a per-country level and classified countries based on COVID-19 incidence trajectories and effects of lockdown responses. Univariate analysis identified eleven variables as independently associated with COVID-19 infections at a global level (p<1e-05). Multivariable analysis identified a 4-variable model as optimal for explaining global variations in COVID-19 (p<0.01). COVID-19 case trajectories for most countries were best captured by a log-logistic model, as determined by AIC estimates. Six predominant country clusters were identified when characterizing the effects of lockdown intervals on variations in COVID-19 new cases per country. Globally, economic and meteorological factors are important determinants of early COVID-19 incidence. Analysis of longitudinal trends and lockdown effects on COVID-19 highlights important nuances in country-specific responses to infections. These results provide valuable insights into disease incidence at a per-country level, possibly allowing for more informed decision making by individual governments in future disease outbreaks.

Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution

Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects of different antibiotics and suggest that these need to be considered in models examining CS-based therapies.

Data from: Temporal change in floral availability leads to periods of resource limitation and affects diet specificity in a generalist pollinator

Generalist species are core components of ecological networks and crucial for the maintenance of biodiversity. Generalised species and networks are expected to be more resilient, therefore understanding the dynamics of specialisation and generalisation in ecological networks is a key focus in a time of rapid global climate change. Whilst diet generalisation is frequently studied, our understanding of how it changes over time is limited. We explore temporal variation in diet specificity in the honeybee (Apis mellifera), using pollen DNA metabarcoding of honey samples, through the foraging season, over two years. We find that overall, honeybees are generalists that visit a wide range of plants, but there is temporal variation in the degree of specialisation. Temporal specialisation of honeybee colonies corresponds to periods of resource limitation, identified as a lack of honey stores. Honeybees experience a lack of preferred resources in June when switching from flowering trees in spring to shrubs and herbs in summer. Investigating temporal patterns in specialisation can identify periods of resource limitation that may lead to species and network vulnerability. Diet specificity must therefore be explored at different temporal scales in order to fully understand species and network stability in the face of ecological change.

Cell-type specific responses to associative learning in the primary motor cortex

The primary motor cortex (M1) is known to be a critical site for movement initiation and motor learning. Surprisingly, it has also been shown to possess reward-related activity, presumably to facilitate reward-based learning of new movements. However, whether reward-related signals are represented among different cell types in M1, and whether their response properties change after cue-reward conditioning remains unclear. Here, we performed longitudinal in vivo two-photon Ca2+ imaging to monitor the activity of different neuronal cell types in M1 while mice engaged in a classical conditioning task. Our results demonstrate that most of the major neuronal cell types in M1 showed robust but differential responses to both cue and reward stimuli, and their response properties undergo cell-type specific modifications after associative learning. PV-INs' responses became more reliable to the cue stimulus, while VIP-INs' responses became more reliable to the reward stimulus. PNs only showed robust response to the novel reward stimulus, and they habituated to it after associative learning. Lastly, SOM-IN responses emerged and became more reliable to both conditioned cue and reward stimuli after conditioning. These observations suggest that cue- and reward-related signals are represented among different neuronal cell types in M1, and the distinct modifications they undergo during associative learning could be essential in triggering different aspects of local circuit reorganization in M1 during reward-based motor skill learning.

Genetic sex determination, sex chromosome size and sex-specific lifespan across tetrapods

Sex differences in lifespan are ubiquitous across the tree of life and exhibit broad taxonomic patterns that remain a puzzle, such as males living longer than females in birds and vice versa in mammals. The prevailing "unguarded-X" hypothesis explains sex differences in lifespan by differential expression of recessive mutations on the X or Z chromosome of the heterogametic sex but has only received indirect support to date. An alternative hypothesis is that the accumulation of deleterious mutations and repetitive elements on the Y or W chromosome might lower the survival of the heterogametic sex ("toxic Y" hypothesis). Here, we use a new database to report lower survival of the heterogametic relative to the homogametic sex across 136 species of birds, mammals, reptiles and amphibians, as expected if sex chromosomes shape sex-specific lifespans, and consistent with previous findings. We also found that the relative sizes of both the X and the Y chromosomes in mammals (but not the Z or the W chromosomes in birds) are associated with sex differences in lifespan, as predicted by the "unguarded-X" and the "toxic Y". Furthermore, we report that the relative size of the Y is negatively associated with male lifespan in mammals, so that small Y size correlates with increased male lifespan. In theory, toxic Y effects are expected to be particularly strong in mammals, and we did not find similar effects in birds. Our results confirm the role of sex chromosomes in explaining sex differences in lifespan across tetrapods and further suggest that, at least in mammals, "toxic Y" effects may play an important part in this role.

Data from: Symbiont-specific responses to environmental cues in a threesome lichen symbiosis

Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We investigated differential gene expression in photosymbiodemes of the lichen Peltigera britannica at different temperatures representing mild and putatively stressful conditions and compared gene expression of thallus sectors containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts. Firstly, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Secondly, we quantified photobiont-mediated differences in fungal gene expression. High temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data. As expected, the expression of genes involved in photosynthesis was increased in both photobiont types at 15 and 25°C. The green algae exhibited thermal stress responses mainly at 25°C, and the fungus and the cyanobacteria already by 15°C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima. Furthermore, photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression.