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Metabolic rate data and code for: Intra-specific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis)
<p>Metabolic rate data and code for: Intra-specific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis)</p> <p> </p> <p>The raw data and R-code used to calculate SMR used in the analysis. </p>
Towards resolving the complex paramagnetic NMR spectrum of small laccase: Assignments of resonances to residue specific nuclei
<p>NMR dataset as TopSpin (Bruker Corporation) files for the article titled "Towards resolving the complex paramagnetic NMR spectrum of small laccase: Assignments of resonances to residue specific nuclei" (https://doi.org/10.5194/mr-2020-31).</p>
A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease
<p><strong>Background:</strong> Chagas disease caused by Trypanosoma cruzi (T. cruzi) affects approximately six million individuals worldwide. Clinical manifestations are expected to occur due to the parasite persistence and host immune response. Herein we investigated potential associations between IL1B, IL6, IL17A or IL18 polymorphism profiles and cardiomyopathy or T. cruzi parasitemia, as well as the impact of HIV infection on cardiopathy.</p> <p><strong>Methods:</strong> 206 patients and 90 control individuals were analyzed. IL1B rs1143627 T>C, IL6 rs1800795 C>G, IL17A rs2275913 G>A, IL18 rs187238 C>G, and IL18 rs1946518 C>A SNVs were analyzed by real-time PCR and T. cruzi parasitemia by PCR.</p> <p><strong>Results: </strong>Our data revealed association between a cytokine gene polymorphism and parasitemia never previously reported. The IL6 rs1800795 CG genotype lowered the risk of positive parasitemia (OR=0.45, 95% CI 0.24–0.86, P=0.015). Original findings included associations between IL17A rs2275913 AA and IL18 s1946518 AA genotypes with decreased risk of developing cardiomyopathy (OR=0.27, 95% CI 0.07-0.97, P=0.044; and OR=0.35, 95% CI 0.14-0.87, P=0.023, respectively). IL18 rs1946518 AA and IL1B rs1143627 TC were associated with reduced risk for cardiomyopathy severity, including NYHA (New York Heart Association) class≥ 2 (OR=0.21, 95% CI 0.06-0.68, P=0.009; and OR=0.48, 95% CI 0.24-0.95, P=0.036, respectively) and LVEF (Left Ventricular Ejection Fraction) <45% for IL18 rs1946518 AA (OR=0.22, 95% CI 0.05-0.89, P=0.034). A novel, unexpected protective effect of HIV infection against development/progression of cardiomyopathy was identified, based on a lower risk of developing cardiopathy (OR=0.48, 95% CI 0.23‐0.96, P=0.039), NYHA class≥2 (OR=0.15, 95% CI 0.06‐0.39, P<0.001) and LVEF<45% (OR=0.03, 95% CI 0.00‐0.25, P=0.001). Digestive involvement was negatively associated with NYHA ≥2 and LVEF<45% (OR=0.20, 95% CI 0.09‐0.47, P<0.001; and OR=0.24, 95% CI 0.09-0.62, P=0.004, respectively).</p> <p><strong>Conclusions: </strong>Our data support a protective role of IL17A AA, IL18 AA and IL1B TC genotypes against development/progression of cardiomyopathy and a modulatory effect of the IL6 CG genotype on the risk of parasitemia in Chagas disease. Notably, HIV infection was shown to protect against development/progression of cardiopathy, potentially associated with a synergistic effect of HIV and HAART, attenuating a Th1-mediated response in the myocardium. This proposed hypothesis requires confirmation, however, in larger and more comprehensive future studies.</p>
The growth of COVID-19 scientific literature: A forecast analysis of different daily time series in specific settings
<p>Submitted to The ISSI 2021 Conference. The conference is organised by KU Leuven in close collaboration with the university of Antwerp under the auspices of ISSI – the International Society for Informetrics and Scientometrics (<a href="http://www.issi-society.org/">http://www.issi-society.org/</a>). </p> <p>We present a forecasting analysis on the growth of scientific literature related to COVID-19 expected for 2021. Considering the paramount scientific and financial efforts made by the research community to find solutions to end the COVID-19 pandemic, an unprecedented volume of scientific outputs is being produced. This questions the capacity of scientists, politicians and citizens to maintain infrastructure, digest content and take scientifically informed decisions. A crucial aspect is to make predictions to prepare for such a large corpus of scientific literature. Here we base our predictions on the ARIMA model and use two different data sources: the Dimensions and World Health Organization COVID-19 databases. These two sources have the particularity of including in the metadata information on the date in which papers were indexed. We present global predictions, plus predictions in three specific settings: by type of access (Open Access), by NLM source (PubMed and PMC), and by domain-specific repository (SSRN and MedRxiv). We conclude by discussing our findings.</p>
Food quality effects on instar-specific life histories of a holometabolous insect
<ol> <li><span><span>It is a long-standing challenge to understand how changes in food resources impact consumer life history traits and, in turn, impact how organisms interact with their environment. To characterize food quality effects on life history, most studies follow organisms throughout their life cycle and quantify major life events, such as age at maturity or fecundity. From these studies, we know that food quality generally impacts body size, juvenile development, and life span. Importantly, throughout juvenile development, many organisms develop through several stages of growth that can have different interactions with their environment. For example, parasitoids typically attack larger instars, whereas larval insect predators typically attack smaller instars. Interestingly, most studies lump all juvenile stages together, which ignores these ecological changes over juvenile development. </span></span></li> <li><span><span>We combine a cross-sectional experimental approach with a stage-structured population model to estimate instar-specific vital rates in the bean weevil, <i>Callosobruchus maculatus</i> across a food quality gradient. We characterize food quality effects on the bean weevil's life history traits throughout its juvenile ontogeny to test how food quality impacts instar-specific vital rates. </span></span></li> <li><span><span>Vital rates differed across food quality treatments within each instar; however, their effect differed with instar. Weevils consuming low quality food spent 38%, 37% and 18% more time, and were 1%, 8% and 60% smaller than weevils consuming high quality food in the second, third and fourth instars, respectively. Overall, our results show that consuming poor food quality means slower growth, but that food quality effects on vital rates, growth and development are not equal across instars. Differences in life history traits over juvenile ontogeny in response to food quality may impact how organisms interact with their environment, including how susceptible they are to predation, parasitism, and their competitive ability.</span></span></li> </ol>
Data from: Species-specific variation in germination rates contributes to spatial coexistence more than adult plant water use in four closely-related annual flowering plants
1. Spatial partitioning is a classic hypothesis to explain plant species coexistence, but evidence linking local environmental variation to spatial sorting, demography, and species' traits is sparse. If co-occurring species' performance is optimized differently along environmental gradients because of trait variation, then spatial variation might facilitate coexistence. 2. We used a system of four naturally co-occurring species of Clarkia (Onagraceae) to ask if distribution patchiness corresponds to variation in two environmental variables that contribute to hydrological variation. We then reciprocally sowed Clarkia into each patch type and measured demographic rates in the absence of congeneric competition. Species sorted in patches along one or both gradients, and in three of the four species, germination rate in the "home" patch was higher than all other patches. 3. Spatially variable germination resulted in the same three species exhibiting the highest population growth rates in their home patches. 4. Species' trait values related to plant water use, as well as indicators of water stress in home patches, differed among species and corresponded to home patch attributes. However, post-germination survival did not vary among species or between patch types, and fecundity did not vary spatially. 5. Synthesis Our research demonstrates the likelihood that within-community spatial heterogeneity affects plant species coexistence, and presents novel evidence that differential performance in space is explained by what happens in the germination stage. Despite the seemingly obvious link between adult plant water-use and variation in the environment, our results distinguish the germination stage as important for spatially variable population performance.
Data from: Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones.
Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus Symbiodinium. Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular Symbiodinium types are poorly known. Here we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama. Patterns of anemone abundance and symbiont diversity were consistent with specialization of holobionts for particular habitats, with Exaiptasia pallida/S. minutum (ITS2 type B1) abundant on vertical substrate in thermally stable, shaded environments but E. brasiliensis/Symbiodinium sp. (ITS2 clade A) more common in shallow areas subject to high temperature and irradiance. Population genomic sequencing revealed a novel E. pallida population from the Bocas del Toro Archipelago that only harbors S. minutum. Loci most strongly associated with divergence of the Bocas-specific population were enriched in genes with putative roles in cnidarian symbiosis, including activators of the complement pathway of the innate immune system, thrombospondin-type-1 repeat domain proteins, and coordinators of endocytic recycling. Our findings underscore the importance of unmasking cryptic diversity in natural populations and the role of long-term evolutionary history in mediating interactions with Symbiodinium.
Data from: Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank
Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.
Data from: Serotonin differentially affects morph-specific behavior in divergent populations of a horned beetle
Associations between animal weapons and corresponding aggressive behaviors are among the most characteristic features of species, yet at the same time their co-expression is itself often strongly dependent on context, such as male condition or population ecology. Yet the mechanisms that modulate associations between aggression, morphology, and biological context remain poorly understood. The biogenic amine serotonin has been shown to regulate a wide range of aggressive and morph-specific behaviors in diverse insect species. However, the extent to which serotonin may coordinate the expression of behavior with morphology across biological contexts remains unclear. In this study, we pharmacologically increased serotonin biosynthesis in males of the polyphenic beetle, Onthophagus taurus, and assessed how this manipulation affects both aggressive and non-aggressive behaviors in alternative fighter and sneaker morphs, as well as in males derived from rapidly diverging populations characterized by disparate levels of competition for mates. We find (i) that enhancing serotonin biosynthesis increases most measures of aggressive behaviors, but influences only a subset of non-aggressive behaviors, (ii) that similar serotonin-mediated behavioral changes manifest in both morphs within populations more often than just a single morph, and (iii) that males derived from populations subject to disparate levels of competition for mates have diverged in their behavioral responsiveness to serotonin up-regulation. Collectively, our study suggests that serotonin signaling plays a critical role in the regulation of male behavior and its evolution, including in the context of rapid, short term population divergence.
Data from: Species-specific spatiotemporal patterns of leopard, lion and tiger attacks on humans
1. Large carnivores of the genus Panthera can pose serious threats to public safety. Although the annual number of attacks on humans is rare compared to livestock depredation, such incidents undermine popular support for wildlife conservation and require immediate responses to protect human life. 2. We used a space-time scan method to perform a novel spatiotemporal analysis of 908 attacks on humans by lions, leopards and tigers to estimate the risks of further attacks in the same locales. 3. We found that a substantial proportion of attacks were clustered in time and space, but the dimension of these outbreaks varied between species. Lion outbreaks included more human fatalities, persisted for longer periods of time, and extended over larger areas than tiger or leopard outbreaks. 4. These techniques could be used by relevant agencies to warn local people of risks from further attacks within a certain time and distance following an initial incident by each species, as well as identify areas that require management interventions to address these threats.31-Oct-2018
Data from: Sex- and tissue-specific differences in telomere length in a reptile
The usage of telomere length (TL) in blood as a proxy for the TL of other tissues relies on the assumption that telomere dynamics across all tissues are similar. However, telomere attrition can be caused by reactive oxygen species (ROS) which may vary with metabolic rate, which itself varies across organs depending upon the life history strategy of an organism. Thus we chose to measure the telomeres of various cell types in juvenile painted dragon lizards, Ctenophorus pictus, given their unusual life history strategy. Individuals typically only experience a single mating season. We measured the TL of male and female dragons using qPCR and observed that TL varied with tissue type and sex. Telomeres of blood cells were longer than those of liver, heart, brain, and spleen, and females had longer telomeres than males. Brain telomeres in males were approximately half the length of those in females. Telomeric attrition in the male brain may be due to the need for rapid learning of reproductive tactics (territory patrol and defence, mate-finding). Significant correlations between the TL of tissue types suggest that blood TL may be a useful proxy for the TL of other tissues. Our comparison of organ-specific telomere dynamics, the first in a reptile, suggests that the usage of blood TL as a proxy requires careful consideration of the life history strategy of the organism.
Data from: On the specificity of avian blood parasites: revealing specific and generalist relationships between haemosporidians and biting midges
The study of host-parasite relationships involving vector-borne parasites requires understanding interactions between parasites and vectors. The capacity of haemosporidians to infect insects has clear evolutionary consequences for the transmission of diseases. Here we investigated (1) the associations between blood parasites, biting midges and birds and (2) the potential specificity between biting midge and haemosporidian haplotypes. A total of 629 parous biting midges Culicoides and 224 wild birds (belonging to seven species) from a locality of central Spain were examined individually to detect the presence of Haemoproteus and Plasmodium parasites by sequencing a fragment of the cytochrome B gene. Biting midges were identified morphologically and characterised on the basis of a fragment of the cytocrome c oxidase (COI) gene. Overall 12 Haemoproteus and 3 Plasmodium haplotypes were isolated and sequenced. Among them, 10 haplotypes were exclusively isolated from biting midges, three haplotypes only from birds and two haplotypes from both biting midges and birds. Biting midge haplotypes showed both specific and generalist relationships with Haemoproteus haplotypes but only generalist relationships with Plasmodium haplotypes. Several C. festivipennis and C. kibunesis haplotypes established significant coevolutionary links with Haemoproteus haplotypes. These results help to understand the specificity of vector-blood parasite interactions.
Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ~3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
Condition-specific gene coexpression in ATTED-II (LS index)
<p>The coexpression index has changed in recent versions of ATTED-II.</p> <ul> <li>ATTED-II ver 11: z-score of LS index (larger value indicates stronger coexpression)</li> <li>ATTED-II ver 10: LS index (larger value indicates stronger coexpression)</li> <li>ATTED-II ver 4 to ver 9: MR index (smaller value indicates stronger coexpression)</li> </ul> <p>To continue providing the condition-specific gene coexpression data, they were converted to z-score of the LS index. </p> <ul> <li>ATTED-II ver 6.0 (September 2010): MR index. AGI (Arabidopsis Genome Initiative) code.</li> <li>ATTED-II ver 11.0 (February 2021): z-score of the LS index. EGI (Entrez Gene ID)code.</li> </ul> <p><strong>Reference of condition-specific gene coexpression data in ATTED-II</strong><br> Obayashi et al. (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol. 52. 213-9.<br> https://pubmed.ncbi.nlm.nih.gov/21217125/</p> <p><strong>Detail of the condition-specific gene coexpression data</strong><br> The condition-specific gene coexpression data are based on the following AtGenExpress expression data.<br> https://www.arabidopsis.org/portals/expression/microarray/ATGenExpress.jsp</p> <ul> <li>bio: AtGenExpress biotic treatment <ul> <li>ME00341 (Carine Denoux , Fred Ausubel , Julia Dewdney , Simone Ferrari)</li> <li>ME00353 (Xinnian Dong)</li> <li>ME00331 (Birgit Kemmerling , Thorsten Nürnberger)</li> <li>ME00332 (Frederic Brunner , Thorsten Nürnberger)</li> <li>ME00342 (Dierk Scheel , Frederic Brunner , Lore Westphal)</li> <li>ME00354 (Fred Ausubel , Julia Dewdney)</li> </ul> </li> <li>hor: AtGenExpress hormone treatment <ul> <li>ME00333 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00334 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00335 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00336 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00337 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00343 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00344 (Hideki Goda , Shigeo Yoshida , Yukihisa Shimada)</li> <li>ME00352 (Hideki Goda , Yukihisa Shimada)</li> <li>ME00356 (Takatoshi Kiba , Takeshi Mizuno)</li> <li>ME00357 (Hideki Goda , Shigeo Yoshida , Tadao Asami , Yukihisa Shimada)</li> <li>ME00358 (Hideki Goda , Shigeo Yoshida , Tadao Asami , Yukihisa Shimada)</li> <li>ME00359 (Hideki Goda , Shigeo Yoshida , Tadao Asami , Yukihisa Shimada)</li> <li>ME00360 (Hideki Goda , Shigeo Yoshida , Tadao Asami , Yukihisa Shimada)</li> </ul> </li> <li>lig: AtGenExpress light treatment <ul> <li>ME00345 (Thomas Kretsch)</li> </ul> </li> <li>str: AtGenExpress stress series <ul> <li>ME00325 (Cecilia D`Angelo , Joachim Kilian , Joerg Kudla , Oliver Batistic , Stefan Weinl)</li> <li>ME00326 (Holger Puchta , I-Peng Chen)</li> <li>ME00327 (Cecilia D`Angelo , Joachim Kilian , Joerg Kudla , Oliver Batistic , Stefan Weinl)</li> <li>ME00328 (Cecilia D`Angelo , Joachim Kilian , Joerg Kudla , Oliver Batistic , Stefan Weinl)</li> <li>ME00329 (Jakub Horak , Klaus Harter)</li> <li>ME00330 (Dierk Wanke , Klaus Harter)</li> <li>ME00338 (Cecilia D`Angelo , Joachim Kilian , Joerg Kudla , Oliver Batistic , Stefan Weinl)</li> <li>ME00339 (Lutz Nover , Pascal von Koskull-Döring)</li> <li>ME00340 (Andrea Ditzer , Dorothea Bartels , Hans-Hubert Kirch)</li> </ul> </li> <li>tis: AtGenExpress development <ul> <li>ME00319 (Detlef Weigel , Jan Lohmann , Markus Schmid)</li> </ul> </li> </ul>
Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression
<p>While it is well-established that distal hypoxia response elements (HREs) regulate hypoxia-inducible factor (HIF) target genes such as erythropoietin (Epo), an interplay between multiple distal and proximal (promoter) HREs has not been described so far. Hepatic Epo expression is regulated by a HRE located downstream of the <i>EPO</i> gene, but this 3' HRE is dispensable for renal <i>EPO</i> gene expression. We previously identified a 5' HRE and could show that both HREs direct exogenous reporter gene expression. Here, we show that whereas in hepatic cells the 3' but not the 5' HRE is required, in neuronal cells both the 5' and 3' HREs contribute to endogenous Epo induction. Moreover, two novel putative HREs were identified in the <i>EPO</i> promoter. In hepatoma cells HIF interacted mainly with the distal 3' HRE, but in neuronal cells HIF most strongly bound the promoter, to a lesser extent the 3' HRE, and not at all the 5' HRE. Interestingly, mutation of either of the two distal HREs abrogated HIF binding to the 3' and promoter HREs. These results suggest that a canonical functional HRE can recruit multiple, not necessarily HIF, transcription factors to mediate HIF binding to different distant HREs in an organ-specific manner.</p>
Bridging the flux gap: sap flow measurements reveal species-specific patterns of water-use in a tallgrass prairie
<p>Predicting the hydrological consequences following changes in grassland vegetation type (i.e., woody encroachment) requires an understanding of water flux dynamics at high spatiotemporal resolution for predominant species within grassland communities. However, grassland fluxes are typically measured at the leaf or landscape scale, which inhibits our ability to predict how individual species contribute to changing ecosystem fluxes. We used external heat balance sap flow sensors and a hierarchical Bayesian state-space modeling approach to bridge this "flux-gap" and estimate continuous species-level water flux in common tallgrass prairie species. Specifically, we asked: 1) How do diurnal and nocturnal water fluxes differ among woody and herbaceous plants? (2) How sensitive are woody and herbaceous species to environmental drivers of diurnal and nocturnal water flux? We highlight three results: (1) <i>Cornus drummondii</i>, the primary woody encroacher in this grassland, exhibited the greatest canopy-level water loss, (2) nocturnal transpiration was a large component of the water lost in this ecosystem and was driven primarily by C<sub>4</sub> grasses and <i>C. drummondii</i>, and (3) the sensitivity of canopy transpiration to environmental drivers varies among plant functional types and throughout a 24-hour period. Our data reveal important insights regarding the water-use strategies of woody versus herbaceous species in tallgrass prairies, and about the potential hydrological consequences of ongoing woody encroachment. We suggest that the high, static flux rates observed in woody species will likely deplete deep water stores over time, potentially creating hydrological deficits in grasslands experiencing woody encroachment and concomitantly increasing the vulnerability of these ecosystems to drought.</p>
Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii) interpret the community composition of this region within the emerging global biogeography of Geosmithia. Geosmithia was detected in 87% of 126 beetle samples obtained from 39 plant species. Twenty-nine species of Geosmithia were distinguished, of which 13 may be new species. Bark beetles from hardwoods, Cupressus, and Sequoia appear to be regular vectors, with Geosmithia present in all beetle gallery systems examined. Other subcortical insects appear to vector Geosmithia at lower frequencies. Overall, most Geosmithia have a distinct level of vector specificity (mostly high, sometimes low) enabling their separation to generalists and specialists. Plant pathogenic Geosmithia morbida was not found in association with any other beetle besides Pityophthorus juglandis. However, four additional Geosmithia species were found in P. juglandis galleries. When integrated with recent data from other continents, a global pattern of Geosmithia distribution across continents, latitudes, and vectors is emerging: of the 29 Geosmithia species found in the western USA, 12 have not been reported outside of the USA. The most frequently encountered species with the widest global distribution also had the broadest range of beetle vectors. Several Geosmithia spp. with very narrow vector ranges in Europe exhibited the similar degree of specialization in the USA. Such strong canalization in association could reflect an ancient origin of each individual association, or a recent origin and a subsequent diversification in North America.
Development of a genus-specific antigen capture ELISA for orthopoxviruses. Target selection and optimized screening
<p><strong>Raw data for quantification of anti surface protein antibody binding to vaccinia virus.</strong></p> <p>Method description</p> <p>Immuno-negative staining and electron microscopy were performed as described elsewhere (Laue, 2010). Briefly, purified VACV<sub>NYCBOH</sub> particles were inactivated by incubation in freshly prepared 2% PFA in 0.05 M HEPES (pH 7.2), sonicated and immobilized on sample supports for transmission electron microscopy. Biotinylated pAbs were titrated on BSA coated grids, until detection with 5 nm gold nanoparticle coupled streptavidin (British Biocell, Cardiff, United Kingdom) resulted in the same mean background labelling density of ~10 particles per view field at a, 87,000-fold magnification (anti-A27: 0.7 µg/mL; anti-D8: 2 µg/mL; anti-H3: 0.9 µg/mL; anti-L1: 1.9 µg/mL). Negative staining was performed with either 0.1 or 0.5% uranyl acetate solution. For quantification, only IMV particles of the mulberry form, which were found isolated from other particles, were analyzed. Randomized sampling was done in 22 evenly distributed mesh areas with five viral particles analyzed per area. Imaging was done with a Tecnai 12 BioTwin (FEI Corp.) at 120 kV and a 1k digital CCD camera (Megaview III, Olympus Soft Imaging Solutions).</p>
Prostate specific antigen density values among patients with symptomatic prostatic enlargement in Nigeria
<p><strong>Background</strong></p> <p>This study aims to estimate the prostate specific antigen density(PSAD) cut off level for detecting prostate cancer( CAP) in Nigerian men with “grey zone PSA’’(4-10ng/ml) and normal digital rectal examination findings . We addressed this research question: Is the international PSAD cut off of 0.15 ideal for detecting CAP in our symptomatic patients with “grey zone PSA’’?</p> <p><strong> Methods</strong></p> <p>Aim: To estimate the prostate specific antigen density(PSAD) cut off level for detecting prostate cancer( CAP) in Nigerian men with “grey zone PSA’’(4-10ng/ml) and normal digital rectal examination findings .</p> <p>Design: prospective</p> <p>Setting: A tertiary medical center in Enugu Nigeria</p> <p> Participants: Two hundred and fifty four men with either benign prostatic hyperplasia (BPH) or prostate cancer (CAP) were recruited. </p> <p> Intervention: Patients with PSA above 4ng/ml or abnormal digital rectal examination or hypoecoic lesion in the prostate were biopsied.</p> <p>Outcome measures: PSAD and histology report of BPH or CAP</p> <p><strong>Results</strong></p> <p>Ninety seven patients had cancer of the prostate (CAP) while 157 has benign prostatic hyperplasia (BPH). Seventy two patients had their serum PSA value within the range of 4.0 and 10ng/ml . PSAD cut off level to detect CAP was 0.04(sensitivity 95.88 %; specificity 28.7 %).</p> <p> </p> <p><strong>CONCLUSION</strong> </p> <p>The PSAD cut off level generated for Nigerian men in this study is 0.04 which is relatively different from international consensus. This PSAD cut off level has a positive correlation with histology and could detect patients with CAP who have “grey zone PSA’’.</p>
WESSBAS: Extraction of Probabilistic Workload Specifications for Load Testing and Performance Prediction - A Model-Driven Approach for Session-Based Application Systems.
<p>Supplementary material for the paper: "WESSBAS: Extraction of Probabilistic Workload Specifications for Load Testing and Performance Prediction".</p> <p>Included in the supplementary material are the evaluation results.</p> <p>The WESSBAS software relevant to the paper is available via https://github.com/Wessbas/</p> <p>The WESSBAS UI is available as a password-protected (password: wessbasui) ZIP file:</p> <p>https://dl.dropboxusercontent.com/u/81621779/wessbas.ui.zip (--- WESSBAS GUI (license confirmation pending, i.e., not on GitHub, yet))</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.