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Henslow's Sparrow shows positive response to prescribed fire rotation data

We examined Henslow's Sparrow (Centronyx henslowii) response to prescribed fire at 32 grasslands at Big Oaks National Wildlife Refuge in southeastern Indiana from 1999–2009. We burned grasslands in the spring between 1999 and 2007 and monitored Henslow's Sparrows for up to 4 years after treatment. We used linear mixed models to analyze our data. Henslow's Sparrow counts were correlated with time since prescribed fire and grassland size. The estimated changes in mean Henslow's Sparrow density relative to pre-burn densities were -0.19, 1.15, 0.74, and -0.68 birds per hectare for 1 to 4 breeding seasons after a spring burn, respectively. We found that Henslow's Sparrows preferred larger grasslands both during the first breeding season after prescribed fire, when vegetation was presumed to possess less litter and structural density, and during the fourth breeding season after fire, when vegetation was presumed to be a more ideal composition, but preferred smaller grasslands in the interim. Thus, grassland size shapes the magnitude of Henslow's Sparrow population response to fire, with populations in smaller grasslands experiencing greater amplitude changes. Larger grasslands might provide more habitat diversity following prescribed fire, attenuating population change. On average, Henslow's Sparrows responded positively to prescribed fire in a network of grasslands and cumulative net change in densities were highest three breeding seasons after a burn, suggesting that maintaining this burn frequency would be beneficial to Henslow's Sparrow abundance.

Divergent responses of grassland productivity and plant diversity to intra-annual precipitation variability across climate regions: A global synthesis

Global warming intensifies the hydrological cycle and may result in changes in the frequency and intensity of precipitation events. Although the effects of changes in precipitation amount and inter-annual precipitation variability on terrestrial plant productivity and carbon sequestration have been well studied, how intra-annual precipitation variability affects terrestrial ecosystem function remains unclear. Here, we synthesized field manipulative experiments from 71 publications to quantify the effects of intra-annual precipitation variability increases (IPVI) on community biomass and plant diversity in grasslands worldwide. At the global scale, we found that IPVI generally increased grassland community aboveground biomass (AGB) by 6%, and decreased grass biomass and soil ammonium nitrogen by 12% and 31%, respectively. IPVI stimulated AGB, belowground biomass, and plant species richness in arid regions, but not changed them in humid regions. Changes in AGB under IPVI were related to changes in the biomass of plant functional groups, species richness, and soil moisture. Structural equation modelling demonstrated that that climate conditions (mean annual temperature and mean annual precipitation) and background soil properties (soil sand content and soil organic carbon content) jointly regulated grassland AGB responses to IPVI across climate types. Synthesis: Overall, our study shows that grassland productivity and diversity may increase under IPVI in arid climates, and that humid grasslands may be highly resistant to the effects of IPVI. These findings have important implications for understanding ecosystem carbon cycling under global precipitation change scenarios.

Comparative transcriptomic analysis reveals coordinated mechanisms of different genotypes of common vetch in response to Al stress

Supplementary Table

The cellular response to extracellular vesicles is dependent on their cell source and dose

Extracellular vesicles (EV) have been established to play important roles in cell-cell communication and have shown promise as therapeutic agents. However, we still lack a basic understanding of how cells respond upon exposure to EVs from different cell sources at various doses. Thus, we treated fibroblasts with EVs from twelve different cell sources at doses between 20 and 200,000 per cell, analyzed their transcriptional effects, and functionally confirmed the findings in various cell types in vitro, and in vivo using single-cell RNA-sequencing. Unbiased global analysis revealed EV dose to have a more significant effect than cell source, such that high doses downregulated exocytosis and upregulated lysozomal activity. However, EV cell source-specific responses were observed at low doses, and these reflected the activities of the EV's source cells. Finally, we assessed EV-derived transcript abundance and found that immune cell-derived EVs were most associated with recipient cells. Together, this study provides important insight into the cellular response to EVs.

Higher predation rate need not and did not lead to higher risk-induced trait responses in related zooplankton species

Predators can directly affect prey populations both through predation (consumption of prey) and risk-induced trait responses (RITRs) that reduce predation risk but are often associated with a fitness cost. Thousands of studies make clear that RITRs (also termed anti-predator or defensive traits) including changes in behavior, morphology, and life history, are employed by numerous taxa across diverse ecological systems, and there is large variation in their magnitude. A natural goal is to elucidate the species and circumstances for which and to what magnitude RITRs are expected. A candidate hypothesis is that prey species that experience higher mortality from a predator will exhibit a higher RITR. This hypothesis is an intuitive extension of the fact that invulnerable animals are not expected to exhibit an RITR, while vulnerable species are. We present an example that clarifies why this relationship is not always expected and when it is expected. Other factors may influence the level of the RITR leading to the possibility that a positive relationship is not expected. We elucidate this problem using a mesocosm experiment with a fish-cladoceran system in which there is large variability in the predation rate on different cladoceran species. Results not only did not show a positive relationship but rather a negative trend between predation rate and the RITR. In fact, highly-preyed-upon taxa did not respond, while the least-preyed-upon taxa had the largest responses. These results clarify how the level of predation risk interacts with many factors to determine the RITR of prey.

Using Formative Assessment and Feedback from Student Response Systems (SRS) to Equitably Revise Statistics Instruction

Instructors are increasingly using interactive student response systems (SRS) to foster active learning and deepen student understanding in statistics education. Yet most studies focus on either the benefits of SRS or on how students can receive and use feedback, rather than on how instructors can use formative assessment data to inform instructional revisions in the pursuit of reaching more learners and creating a more equitable and inclusive classroom. This dataset is being publicly shared to accompany a manuscript submission that draws from a case study of an introductory statistics course to present a framework for how an instructor can engage in what I call a reciprocal formative assessment and feedback cycle using SRS. This cycle includes adopting a structured approach of reflecting on student misconceptions through guided questions like who to reteach, what to reteach, when to reteach, and how to reteach course content – all with the goal of increasing learning for all students.

THE FIELD'S MALL MASS SHOOTING: EMERGENCY MEDICAL SERVICES RESPONSE

Case report describing the mass shooting at the Field's shopping mall in Copenhagen, July 3rd, 2022. Dataset to support the findings of the case report, hopefully to be published after peer-review in Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine.

opencc-by-4.0Jan 2020View details →

Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree

Description of Soil_DataTrees.csv <ul> <li>Tree_label: Label of trees on the field, there are 70 trees</li> <li>Tree_site: Site on which the tree has been sampled; COU: Counami; SPA: Sparouine</li> <li>Descr_date: Date of tree sampling</li> <li>Soil_type: Type of soil; FS: ferralitic soils; WS: white-sand soils</li> <li>Soil_sample: Label of soil sample</li> <li>H2Osoil: Soil water content (g kg-1)</li> <li>Clay: Soil clay content (g kg-1)</li> <li>SiltTh: Soil thin silt content (g kg-1)</li> <li>SiltCo: Soil coarse silt content (g kg-1)</li> <li>SandTh: Soil thin sand content (g kg-1)</li> <li>SandCo: Soil coarse sand content (g kg-1)</li> <li>Csoil: Soil carbon content (g kg-1)</li> <li>Nsoil: Soil nitrogen content (g kg-1)</li> <li>CNsoil: Soil carbon:nitrogen ratio</li> <li>MOsoil: Soil organic matter content (g kg-1)</li> <li>Ptotsoil: Soil total phosphorus content (g 100g-1)</li> <li>Kcec: Soil potassium:CEC[cation-exchange capacity] ratio</li> <li>Cacec: Soil calcium:CEC ratio</li> <li>Mgcec: Soil magnesium:CEC ratio</li> <li>Nacec: Soil sodium:CEC ratio</li> <li>Alcec: Soil aluminum:CEC ratio</li> <li>Fecec: Soil iron:CEC ratio</li> <li>Mncec: Soil manganese:CEC ratio</li> <li>Hcec: Soil hydrogen:CEC ratio</li> <li>pHsoil: Soil pH (cmol kg-1)</li> <li>CECsoil: Soil cation-exchange capacity (cmol kg-1)</li> <li>Indexsoil: Soil index of fertility = (K+Ca+Mg+Na)/CEC</li> </ul> K, Ca, Mg, Na, Al, Fe, Mn, H were initially measured in cmol kg-1   Description of Trait_DataTrees.csv <ul> <li>Tree_label: Label of the tree on the field. There are 70 trees</li> <li>Tree_site: Site of sampling; COU: Counami; SPA: Sparouine</li> <li>Descr_date: Date of tree sampling</li> <li>Calendar_day: Day of the year (between 1 and 365) of tree sampling</li> <li>Soil_type: Type of the soil; FS: ferralitic soils; WS: white-sand soils</li> <li>PCA1_soil: Coordinates of the trees along the first axis of PCA (principal component analysis) with soil data, used as a quantitative soil index on FS-WS soil gradient</li> <li>mesHeight: Measured tree height (m)</li> <li>Height: Tree height based on the sum of all internodes length (m)</li> <li>Dbh: Tree diameter at height breast (cm)</li> <li>Age: Tree age (year)</li> <li>Order: Number of branching order</li> <li>Brtot: Total number of branches branching from the trunk</li> <li>Leaftot: Total number of leaves</li> <li>Fltot: Total number of inflorescences</li> <li>Acrown: Total estimated crown area (m²)</li> <li>INA1: Number of trunk internodes</li> <li>Brbear: Number of A2 bearing branches</li> <li>Brdead: Number of A2 dead branches</li> <li>Br1stH: First branching height</li> <li>Fl1stH: First flowering height</li> <li>Br1stIN: First branching node rank</li> <li>Fl1stIN: First flowering node rank</li> <li>Br1stAge: First branching age</li> <li>Fl1stAge: First flowering age</li> <li>LL: Leaf lifespan (day)</li> <li>Lpet: Petiole length (cm)</li> <li>Apet: Petiole cross-sectional area (mm²)</li> <li>Nlobe: Number of leaf lobes</li> <li>LMA: Leaf mass area (g m-2)</li> <li>Thleaf: Leaf thickness (µm)</li> <li>Aleaf: Estimated individual leaf area (cm²)</li> <li>Chlleaf: Leaf chlorophyll content (mg ml-1)</li> <li>H20resleaf: Leaf residual water content (%)</li> <li>dC13leaf: δ13C content (&permil;)</li> <li>Cleaf: Leaf carbon content (g kg-1)</li> <li>Nleaf: Leaf nitrogen content (g kg-1)</li> <li>CNleaf: Leaf carbon:nitrogen ratio</li> <li>Pleaf: Leaf phosphorus content (g kg-1)</li> <li>Kleaf: Leaf potassium content (g kg-1)</li> <li>WSG: Wood specific gravity (g cm-3)</li> </ul>     <ul> <li>Tree_label: Label of the tree</li> <li>Soil_type: Type of the soil; FS: ferralitic soils; WS: white-sand soils</li> <li>rank_base: Rank of the internode from the base of the tree</li> <li>rank_top: Rank of the internode from the apex of the tree</li> <li>phyllochron: Phyllochron, number of days for the production of one leaf</li> <li>date: Estimated date of tree germination</li> <li>nb_day_base: Number of days since estimated germination</li> <li>nb_day_top: Age of the internode in days at tree sampling</li> <li>AS_rank_base: Rank of the annual shoot from the base of the tree</li> <li>As_rank_top: Rank of the annual shoot from the apex of the tree</li> <li>AS_nodes_base: Number of internodes per annual shoot</li> <li>AS_length_base: Length of the annual shoot (cm)</li> <li>AS_br_base: Number of A2 branches on the annual shoot</li> <li>AS_flo_base: Number of inflorescences on the annual shoot</li> <li>lg_en: Internode length (cm)</li> <li>ht_en: Cumulated height of the tree based on the sum of internode length (cm)</li> <li>ma_lgen: Moving average of internode length</li> <li>resi_lgen: Residuals of internode length</li> </ul>

Data from: Response outcome gates the effect of spontaneous cortical state fluctuations on perceptual decisions

Sensory responses of cortical neurons are more discriminable when evoked on a baseline of desynchronized spontaneous activity, but cortical desynchronization has not generally been associated with more accurate perceptual decisions. Here we show that mice perform more accurate auditory judgements when activity in the auditory cortex is elevated and desynchronized before stimulus onset, but only if the previous trial was an error, and that this relationship is occluded if previous outcome is ignored. We confirmed that the outcome-dependent effect of brain state on performance is neither due to idiosyncratic associations between the slow components of either signal, nor to the existence of specific cortical states evident only after errors. Instead, errors appear to gate the effect of cortical state fluctuations on discrimination accuracy. Neither facial movements nor pupil size during the baseline were associated with accuracy, but they were predictive of measures of responsivity, such as the probability of not responding to the stimulus or of responding prematurely. These results suggest that the functional role of cortical state on behavior is dynamic and constantly regulated by performance monitoring systems. Data/analyses: Mice perform an auditory frequency discrimination task and in the main analyses we predict the outcome of the current or previous trial as a function of different behavioral variables (described in the README file). Different outcomes are predicted depending on the specific analyses. While animals perform the task, we record neuronal activity from the auditory cortex using silicon probes, as well as videos to extract facial movements and pupil size. Electrophysiological data was used to estimate the overall rate and synchrony of the neuronal population before stimulus presentation.

opencc-by-4.0Apr 2023View details →

Generative Machine Learning for Detector Response Modeling with a Conditional Normalizing Flow

The samples are datasets used for testing in the scenarios: baseline (corr0.hdf5), correlation of 0.5 (corr50.hdf5), correlation of 1.0 (corr100.hdf5), and asymmetric detector responses (asymmetric.hdf5). Each file contains the conditional variables, generated and simulated detector responses, and generated and simulated reconstruction-level variables.

Increased importance of cool-water fish at high latitudes emerges from individual level responses to warming

<ol> <li>High-latitude ecosystems are experiencing the most rapid warming on earth, expected to trigger a diverse array of ecological responses. Climate warming affects the ecophysiology of fish, and fish close to the cold end of their thermal distribution are expected to increase somatic growth from increased temperatures and a prolonged growth season, which in turn affects maturation schedules, reproduction and survival, boosting population growth. Accordingly, fish species living in ecosystems close to their northern range edge should increase in relative abundance and importance, and possibly displace cold-water adapted species. </li> <li>We aim to document if and how population-level effects of warming are mediated by individual-level responses to increased temperatures, shifts in community structure and composition in high-latitude ecosystems.</li> <li>We studied 11 cool-water adapted freshwater fish populations in communities dominated by cold-water-adapted species to investigate changes in the relative importance of cool-water fish during the last 30 years of rapid warming in high-latitude lakes. In addition, we studied the individual-level responses to warming to clarify the potential mechanisms underlying the population effects.</li> <li>Our long-term series (1991–2020) reveal a marked increase in numerical importance of the cool-water fish species, perch, in ten out of eleven populations, and in most fish communities the cool-water species is now dominant. Moreover, we show that climate warming affects population-level processes via direct and indirect temperature effects on the individuals. Specifically, the increase in abundance arises from increased recruitment, faster juvenile growth and ensuing earlier maturation, all boosted by climate warming.</li> <li>The speed and magnitude of the response to warming in these high-latitude fish communities strongly suggest that cold-water fish will be displaced by fish adapted to warmer water. Consequently, management should focus on climate adaptation limiting future introductions and invasions of cool-water fish and mitigating harvesting pressure on cold-water fish.</li> </ol>

Oxygen availability and body mass modulate ectotherm responses to ocean warming

Data and analysis scripts for the following publication: Duncan et al. In press. Oxygen availability and body mass regulate ectotherm responses to ocean warming. Nature communications   Analysis_script.R is the R script to carry out the main analysis in the manuscript. data.csv is the physiology data to carry out the main analysis in the manuscript.   current_bottom_oxy_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. current_bottom_salt_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. current_bottom_temp_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. future_bottom_oxy_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. future_bottom_salt_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. future_bottom_temp_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript.   raw respirometry data.zip is the raw respirometry data collected during the experiments for the manuscript. raw_meta_data.xlsx is the meta data related to the respirometry data collected during the experiments. raw_resp_data_script.R is the R script to quantify physiological metrics from experimental data.

opencc-zeroDec 2022View details →

Data for: Repeatable negotiation rules? only females show repeatable response to partner removal in a brood-provisioning songbird

Theoretical models indicate that the evolution of biparental care depends on how parents behaviorally negotiate their level of care in response to those of their partner and whether sexes and individuals consistently vary in their response (compensatory response). While compensatory response has been widely investigated empirically, its repeatability has rarely been assessed. In this study, we used a reaction norm approach to investigate the repeatability of the compensatory offspring provisioning of a parent after temporary removal of its partner in the pied flycatcher (Ficedula hypoleuca) across different breeding seasons and partners. We found that only females partially compensated for the short-term removal of the partner and their response was significantly repeatable across years while breeding with different partners. This study highlights the importance of considering among individual differences in negotiation rules to better understand the role of negotiation mechanisms in the evolution of parental care strategies.

Plant productivity response to inter- and intra-symbiont diversity: mechanisms, manifestations, and meta-analyses

Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality, and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns, and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context-dependency in these relationships.

opencc-by-4.0Jun 2023View details →

Epithelial Micro-Invasion Events by Streptococcus pneumoniae Drives Unique Epithelial Cell Responses

RNA Sequencing dataset for Weight et al Manuscript.

opencc-by-4.0Jun 2022View details →

Code and source data for the paper: "Heat over heritability: increasing body size in response to global warming is not stabilized by genetic effects in Bechstein's bats"

The first two script include code for the model building testing different fixed effect strucutes. The next two script includes all code for the descriptive analysis, all figures, as well as the animal models that compare heritabilty between the different environments (Q1-Q4) as well as between the birth environments differentials of mothers and daughters. Data contain the pedigree ('pedigree_Model_cod.csv'), further information ('pedigree_information_cod.csv) and weather data ('Weather_summer.csv')

opencc-zeroJun 2023View details →

Data for: Variable food alters responses of larval crown-of-thorns starfish to ocean warming but not acidification

We examined whether warming, acidification, and different food availability regimes interacted to affect the survival, development, and growth of larval crown-of-thorns starfish, Acanthaster sp. (CoTS). Larvae were reared in all combinations of two temperatures (26, 30 °C), two pH levels (pH 8.0, 7.6), and three food regimes ('low' ration: 1,000 cells mL-1; 'switch' ration: 1,000 cells mL-1 until day 11, followed by 50,000 cells mL-1; and 'high' ration: 50 000 cells mL-1).

opencc-zeroJun 2023View details →

Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition

Pigs infected with Salmonella may excrete large amounts of Salmonella, increasing the risk of spread of this pathogen in the food chain. Identifying Salmonella high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with Salmonella. Immune response was studied through total blood cell counts, production of anti-Salmonella antibodies and cytokines, and gene expression quantification. Total Salmonella shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences in the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with Salmonella induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to Salmonella modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing Salmonella high shedding in livestock.

opencc-zeroJun 2023View details →

BLM overexpression as a predictive biomarker for CHK1 inhibitor response in PARP inhibitor–resistant BRCA-mutant ovarian cancer

PARP inhibitors (PARPis) have changed the treatment paradigm in BRCA-mutant high-grade serous ovarian carcinoma (HGSC). However, most patients eventually develop resistance to PARPis, highlighting an unmet need for novel therapeutic strategies. Using high-throughput drug screens, we identified ATR/CHK1 pathway inhibitors as cytotoxic, and further validated monotherapy activity of the CHK1 inhibitor (CHK1i), prexasertib, in PARPi-resistant BRCA-mutant HGSC cells and animal models. As a proof-of-concept trial, we conducted a phase II study of prexasertib in BRCA-mutant HGSC patients. The treatment was well-tolerated but yielded an objective response rate of 6% (1/17; 1 PR) in patients with prior PARPi treatment. Exploratory biomarker analyses revealed that replication stress and fork stabilization were associated with clinical benefit to CHK1i. In particular, overexpression of BLM, and CCNE1 overexpression or copy number gain/amplification were seen in patients deriving durable benefit from CHK1i. Our findings suggest replication fork–related biomarkers should be further evaluated for CHK1i sensitivity in HGSC.