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opencc-zeroNov 2021View details →

Context dependent host-symbiont interactions: shifts along the parasitism-mutualism continuum

Symbiotic interactions can shift along a mutualism to parasitism continuum. While there are many studies examining dynamics typically considered to be mutualistic that sometimes shift towards parasitism, little is known about conditions underlying shifts from parasitism towards mutualism. In lake populations, we observed that infection by a microsporidian gut symbiont sometimes conferred a reproductive advantage and other times a disadvantage to its Daphnia host. We hypothesized that the microsporidian might benefit its host by reducing infection by more virulent parasites, which attack via the gut. In a lab study using field-collected animals, we found that spores of a virulent fungal parasite were much less capable of penetrating the guts of Daphnia harboring the microsporidian gut symbiont. We predicted that this altered gut penetrability could cause differential impacts on host fitness depending on ecological context. Using data from field surveys, we found that microsporidian-infected Daphnia hosts experienced a reproductive advantage when virulent parasites were common and a reproductive disadvantage when resources were scarce and virulent parasites were rare. Our findings highlight the importance of considering multiparasite community context and resource availability in host-parasite studies and open the door for future research into conditions driving shifts along parasitism to mutualism gradients.

opencc-by-4.0Dec 2021View details →

Impairment of aversive episodic memories during Covid-19 pandemic: The impact of emotional context on memory processes

The threatening context of the COVID-19 pandemic provided a unique setting to study the effects of negative psychological symptoms on memory processes. Episodic memory is an essential function of the human being related to the ability to store and remember experiences and anticipate possible events in the future. Studying this function in this context is crucial to understand what effects the pandemic will have on the formation of episodic memories. To study this, the formation of episodic memories was evaluated by free recall, recognition, and episode order tasks for an aversive and neutral content. The results indicated that aversive episodic memory is impaired both in the free recall task and in the recognition task. Even the beneficial effect that emotional memory usually has for the episodic order was undermined as there were no differences between the neutral and aversive condition. The present work adds to the evidence that indicates that the level of activation does not modify memory processes in a linear way, which also depends on the type of recall and the characteristics of the content to be encoded.

opencc-by-4.0Jan 2022View details →

Appendix A - Understanding the application of Handwritten Text Recognition technology in heritage contexts

This appendix lists all the categorised works mentioning the HTR software Transkribus, used in 'Understanding the application of Handwritten Text Recognition technology in heritage contexts: a systematic review of Transkribus in published research'

opencc-zeroFeb 2022View details →

Data from: Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests

Data from: Korhonen, A., Miettinen, O., Kotze, D.J., & Hamberg, L. (2022). Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests. Environmental Microbiology. DOI: 10.1111/1462-2920.15903 This dataset contains occurrence data of 475 fungal ITS2 sequence clusters (OTUs) across 360 sequenced samples originating from dead wood of Norway spruce (Picea abies). Wood samples were collected from 90 downed spruce trunks, at four points from each trunk. Trunks were at intermediate stages of decay and located in spruce-dominated stands in 24 urban forests (66 trunks) and in 8 rural semi-natural forests (24 trunks) in southern Finland. The data consists of an OTU table (sequence read counts in each sample) and sample metadata (locality information, trunk characteristics and environmental variables).

opencc-zeroFeb 2022View details →

Bird predation and landscape context shape arthropod communities on broccoli

Birds increase crop yields via consumption of pests in some contexts but disrupt pest control via intraguild predation in others. Landscape complexity acts as an inconsistent mediator, sometimes increasing, decreasing, or not impacting pest control. Here, we examined how landscape context and seasonal variation mediate the impact of birds on arthropod pests and natural enemies, leaf damage, and yields of broccoli (Brassica oleracea) on highly diversified farms that spanned the USA West Coast. Our study had two complementary components: a bird exclusion experiment and molecular diet analysis of 357 fecal samples collected from the most commonly captured bird species that also foraged in Brassica fields (American Goldfinch, Spinus tristis; American Robin, Turdus migratorius; Savannah Sparrow, Passerculus sandwichensis; Song Sparrow, Melospiza melodia; and White-crowned Sparrow, Zonotrichia leucophrys). Bird access yielded higher, rather than lower, numbers of pest aphids and increased their parasitism, while no other arthropods examined were consistently impacted. Independent of bird presence, percent natural cover in the landscape sometimes increased and sometimes decreased densities of arthropods in the mid-growth period, with diminishing impacts in the late-growth period. Herbivore feeding damage to broccoli leaves decreased with increasing amounts of natural land cover and in the late-growth period. Molecular diet analysis revealed that Brassica pests and predatory arthropods were relatively uncommon prey for birds. Landscape context did not alter the prey items found in bird diets. Altogether, our bird-exclusion experiment and molecular diet analysis suggested that birds have relatively modest impacts on the arthropods associated with broccoli plantings. More broadly, the limited support in our study for net natural pest control services suggests that financial incentives may be required to encourage the adoption of bird friendly farming practices in certain cropping systems.

opencc-by-4.0Jul 2021View details →

Multiple parasitoid species enhance top-down control, but parasitoid performance is context-dependent

<ol> <li>Ecological communities are composed of many species, forming complex networks of interactions. Current environmental changes are altering community composition. We thus need to identify which aspects of species interactions are primarily driven by community structure and which by species identity to predict changes in the functioning of communities. Yet, this partitioning of effects is challenging and thus rarely explored.</li> <li>Here we disentangled the influence of community structure and the identity of co-occurring species on the outcome of consumer-resource interactions using a host-parasitoid system.</li> <li>We used four community modules that are common in host-parasitoid communities to represent community structure (i.e., host-parasitoid, exploitative competition, alternative host, and a combination of both exploitative competition and alternative host). We assembled nine different species combinations per community module in a laboratory experiment using a pool of three Drosophila hosts and three larval parasitoid species. To investigate the potential mechanisms at play, we compared host suppression and parasitoid performance across community modules and species assemblages.</li> <li>We found that multiple parasitoid species enhanced host suppression due to sampling effect, weaker interspecific than intraspecific competition between parasitoids, and synergism. However, the effects of community structure on parasitoid performance were species-specific and dependent on the identity of co-occurring species. Consequently, multiple parasitoid species generally strengthen top down-control, but the performance of the parasitoids depends on the identity of either the co-occurring parasitoid species, the alternative host species, or both. </li> </ol>

opencc-zeroFeb 2022View details →

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Results: Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly-aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 – 56.7] versus 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3] versus 5% [0.9 – 22.9]) compatible with a benefit from treatment-as-prevention. Conclusion: Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies. Funding: This study was supported by the National Institute of General Medical Sciences (U54GM088558); the Fogarty International Center (FIC) of the U.S. National Institutes of Health (D43 TW009610); and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention (CDC) (Cooperative agreements U01 GH000447 and U2G GH001911).

opencc-by-4.0Mar 2022View details →

Burnout and anxiety levels in Human Medicine teachers, COVID-19 context

Introduction: In the COVID-19 context, university teachers have had to face the most complex educational demands, psychosocial risks, and the anxiety of responding to limitations in terms of connectivity and fulfillment of academic objectives. Objective: To identify the levels of burnout and anxiety in the COVID-19 context and determine how these levels are manifested in the participating teachers. Methodology: Analytical-type study; non-experimental, cross-sectional design. The population was 150 teachers of the Human Medicine Program of the University of San Martín de Porres, Chiclayo, Peru; sample: 66 teachers. The survey consisted of three sections: 1. Informed consent, 2. Maslach's Burnout Inventory, 3. Beck's Anxiety Inventory. Data processing was performed using the SPSS V.27 statistical software. All citations and bibliographical references were processed using Mendeley Desktop 1.19.8. Results: in the variable burnout syndrome, 25% of the participants are in the high level downwards; they present anxiety in 30.30% of the total. It was found that 50% of teachers presented mild to moderate anxiety. Conclusions: the largest number of teachers surveyed present anxiety due to burnout syndrome in the COVID-19 context. Finally, it is found that there is a correlation between anxiety and the sociodemographic variables sex, age, and marital status.

opencc-by-4.0Mar 2022View details →

Artifact of Infrastructure and Tools in the Context of Deep Statistical Model Checking

This artifact contains all infrastructure, tools, and additional material used in the context of Deep Statistical Model Checking (DSMC). This includes the DSMC implementation in modes of the Modest Toolset, the infrastructure used to perform case studies on DSMC, the environment and scripts in which the scalability study on DSMC has been performed, the integration of DSMC in MoGym, and also the TraceVis tool. The content has partially been covered in artifacts accompanying individual papers on DSMC, but is combined here based on a single infrastructure. Each folder contains its own readme describing how to use the scripts, tools, and infrastructure, often also with concrete instructions on how to execute exemplary experiments.

opencc-by-4.0Mar 2022View details →

Analysis of Smooth Pursuit Eye Movements in Clinical Context by Tracking the Target and Eyes

Eyemove dataset obtained at Teikyo University. If you use the dataset, please state clearly that you have used our data. The mp4 files are the video of the examination. Excel files are the position of the optic disc analyzed by SSD and the ocular position data analyzed by VOG.

opencc-zeroMar 2022View details →

The causes and ecological context of rapid morphological evolution in birds

Episodic pulses in morphological diversification are a prominent feature of evolutionary history, driven by factors that remain widely disputed. Resolving this question has proved challenging because comprehensive species-level data are generally unavailable at sufficient scale. Combining global phylogenetic and morphological data for birds, we show that pulses of diversification in lineages and traits tend to occur independently and in different contexts. Speciation pulses are preceded by greater differentiation in overall morphology and habitat niche, then followed by increased rates of beak evolution. Contrary to standard hypotheses, pulses of morphological diversification tend to be associated with habitat niche stability rather than adaptation to different diets and habitat types. These patterns suggest that the timing of diversification varies across traits according to their ecological function, and that pulses of morphological evolution may occur when successful lineages subdivide niche space within particular habitat types. Our results highlight the growing potential of functional trait data sets to refine macroevolutionary models.

Data for: The hippocampal representation of context is preserved despite neural drift

The hippocampus is thought to mediate episodic memory through the instantiation and reinstatement of context-specific cognitive maps. However, recent longitudinal experiments have challenged this view, reporting that most hippocampal cells change their tuning properties over days even in the same environment. Often referred to as neural or representational drift, these dynamics raise questions about the capacity and content of the hippocampal code. One such question is whether and how these long-term dynamics impact the hippocampal code for context. To address this, we imaged large CA1 populations over more than a month of daily experience as freely behaving mice participated in an extended geometric morph paradigm. We find that long-timescale changes in population activity occurred orthogonally to the representation of context in network space, allowing for consistent readout of contextual information across weeks. This population-level structure was supported by heterogeneous patterns of activity at the level of individual cells, where we observed evidence of a positive relationship between interpretable contextual coding and long-term stability. Together, these results demonstrate that long-timescale changes to the CA1 spatial code preserve the relative structure of contextual representation.

opencc-by-4.0Apr 2022View details →

Webis-Context-sensitive-Word-Search-Queries-2022

<pre>This is the dataset created for Language Models as Context-sensitive Word Search Engines at the In2Writing workshop at ACL22. </pre>   Cite  <pre><code>@inproceedings{wiegmann:2022, title = "Language Models as Context-sensitive Word Search Engines", author = "Wiegmann, Matti and V{\"{o}}lske, Michael and Potthast, Martin and Stein, Benno", booktitle = "Proceedings of the 1st Workshop on Intelligent and Interactive Writing Assistants (In2Writing 2022)", month = may, year = "2022", address = "Online", publisher = "Association for Computational Linguistics",</code></pre> Datasets This repository contains two datasets with word search queries. Each word search query consists of a token n-gram with one wildcard token ([MASK]). The answers to each query are the most likely token to replace the mask. All queries originate from wikitext-103 and CLOTH, the respected source is annotated for each query. The original-token dataset lists exactly one top answer for each query. The ranked-answers dataset lists multiple, sorted answers in three relevance categories, where 3 is the most relevant. Please refer to the citation for more details.

Host identity matters – up to a point: the community context of Batrachochytrium dendrobatidis transmission

The level of detail on host communities needed to understand multi-host parasite invasions is an unresolved issue in disease ecology. Coarse community metrics that ignore functional differences between hosts, like host species richness, can be good predictors of invasion outcomes. Yet, if host species vary in the extent to which they maintain and transmit infections, then explicitly accounting for those differences may be important. Through controlled mesocosm experiments and modelling, we show that interspecific differences between host species are important for community-wide infection dynamics of the multi-host fungal parasite of amphibians, Batrachochytrium dendrobatidis (Bd), but only up to a point. The most abundant host species in our system, fire salamander larvae (Salamandra salamandra), did not maintain or transmit infections. Rather, two less abundant 'auxiliary' host species, Iberian tree frog (Hyla molleri) and spiny toad (Bufo spinosus) larvae, maintained and transmitted Bd. Frogs had the highest mean rates of Bd shedding, giving them the highest contributions to R0. Toad contributions to R0 were substantial however, and when examining community-level patterns of infection and transmission, the effects of frogs and toads were similar. Specifying more than just host species richness to distinguish salamanders from auxiliary host species was critical for predicting community-level Bd prevalence and transmission. Distinguishing frogs from toads, however, did not improve predictions. These findings demonstrate limitations to the importance of host species identities in multi-host infection dynamics. Host species that exhibit different functional traits, like susceptibility and infectiousness, may play similar epidemiological roles in the broader community.

Data for: Size spectrum model reveals importance of considering species interactions in a freshwater fisheries management context

Inland fisheries have significant cultural and economic value around the globe, providing dietary protein, income, and recreation. Consequently, methods for monitoring and managing these important fisheries are continually being refined. In marine systems, multi-species size spectrum models have been increasingly used to explore management scenarios of important fish stocks within an ecosystem-based fisheries management framework; however, these models have not been applied in freshwater systems. In this study, we developed a multi-species size spectrum model for the fish community of Lake Nipissing, a large, productive lake in Ontario, Canada. To the best of our knowledge, this is the first fully calibrated multi-species size spectrum model for an inland fishery. Using this model, we explored the impacts of different management scenarios on fish community dynamics while taking species interactions into account. Specifically, we examined how changes in fishing mortality affect: (1) species biomass; (2) community size structure; and (3) stock recovery times. We found that community dynamics following changes in fishing mortality were driven by complex interactions among species, including competition and predation. The greatest changes in biomass and community size structure were observed following changes in fishing mortality to top predators, with community size structure most strongly influenced by changes in mortality to the largest species in the community. Counter to predictions based on generation time, the smallest species in our model exhibited the longest time to recovery due to strong competition and predation. Our results demonstrate the importance of taking an ecosystem-based approach and considering species interactions in the management of inland fisheries and highlight the potential of size spectrum model use in freshwater systems.

opencc-by-4.0Apr 2022View details →

A new modulator of cultural transmission: congruence between learning and onward transmission contexts

This study investigated the effects of congruence between two contexts -the one in which we learn variants and the one in which we later transmit them- on cultural transmission.  We hypothesized that when we are placed in a particular context, we will be more likely to produce (and therefore transmit) variants that we learned in that same context. In particular, we tested the effect of a social contextual aspect: the relationship between model and learner. Participants learned two variant methods to solve a puzzle, one from an “expert” (in an expert-to-novice context) and one from a “peer” (in a peer-to-peer context). They were then asked to transmit one variant onward, either to a “novice” (in a new expert-to-novice context) or to another “peer” (in a new peer-to-peer context). We measured whose variant they transmitted onward.

Effects of phenological mismatch under warming are modified by community context

Climate change is altering the relative timing of species interactions by shifting when species first appear in communities and modifying the duration organisms spend in each developmental stage. However, community contexts, such as intraspecific competition and alternative resource species, can prolong shortened windows of availability and may mitigate the effects of phenological shifts on species interactions. Using a combination of laboratory experiments and dynamic simulations, we quantified how the effects of phenological shifts in Drosophila-parasitoid interactions differed with concurrent changes in temperature, intraspecific competition, and the presence of alternative host species. Our study confirmed that warming shortens the window of host susceptibility. However, the presence of alternative host species sustained interaction persistence across a broader range of phenological shifts than pairwise interactions by increasing the degree of temporal overlap with suitable development stages between hosts and parasitoids. Irrespective of phenological shifts, parasitism rates declined under warming due to reduced parasitoid performance, which limited the ability of community context to manage temporally mismatched interactions. These results demonstrate that the ongoing decline in insect diversity may exacerbate the effects of phenological shifts in ecological communities under future global warming temperatures.

opencc-zeroMay 2022View details →

A new phylogeny of Rumex (Polygonaceae) adds evolutionary context to the diversity of reproductive systems present in the genus

Rumex is a unique member of the Polygonaceae family of plants. A source of intrigue for Rumex lies in the diversity of the reproductive systems associated with this genus. Four previously circumscribed subgenera and some two-hundred species comprise the collective Rumex genus. These species exhibit monoecious, dioecious, synoecious (hermaphroditic), and polygamous reproductive systems. Moreover, some of the dioecious species contain heteromorphic sex chromosomes, a phenomenon that is very rare in angiosperms. Apart from these confirmed morphological and phytogeographical distinctions, two of the four described subgenera, Rumex subg. Acetosa and Rumex subg. Acetosella, are distinctive in their sex chromosome systems. For this study, we used three chloroplast markers, rbcL, trnH-psbA, trnL-F, and dense taxon sampling, to reconstruct the most comprehensive molecular phylogeny of Rumex to date. The reconstructed phylogeny for this work resolves six major clades and one large grade in Rumex subg. Rumex. In addition, the species with known dioecious reproductive systems are resolved within a broader clade termed "the dioecious clade". These results suggest that the species with divergent reproductive systems are more closely related to each other than to other species comprising the rest of the Rumex genus. Furthermore, some species with known synoecious reproductive systems are resolved in a single clade which is also nested within "the dioecious clade". These results imply a possible reversal occurring over time which suggests the highly plastic nature of the reproductive systems in Rumex species.

opencc-zeroMay 2022View details →

Ontogeny of risk assessment and escape-hatching performance by red-eyed treefrog embryos in two threat contexts

Arboreal embryos of red-eyed treefrogs, Agalychnis callidryas, hatch prematurely in response to hypoxia when flooded and mechanosensory cues (MC) in snake attacks, but hatching later improves tadpole survival. We studied ontogenetic changes in risk assessment and hatching performance of embryos in response to flooding and physical disturbance. We hypothesized that risk assessment decreases as hatchling survival improves and hatching performance increases as embryos develop. Because snakes eat faster than embryos asphyxiate, we hypothesized that embryos decide to hatch sooner and hatch faster in response to MC. We video-recorded individual embryos hatching in response to each cue type, then compared the incidence and timing of a series of events and behaviors from cue onset to complete hatching across ages and stimuli. Latency from cue to hatching decreased developmentally in both contexts and was shorter with MC, but the elements contributing to those changes differed. Hypoxia-assessment involved position changes, which decreased developmentally along with assessment time. MC-assessment occurred more rapidly, without movement, and decreased with age. The first stages of hatching, membrane rupture and head emergence, were surprisingly age-independent but faster with MC, congruent with greater effort under more immediate risk. In contrast, body emergence and compression showed ontogenetic improvement consistent with morphological constraints but no cue effect. Both appropriate timing and effective performance of hatching are necessary for continued development. Different stages of the process vary with development and environmental context, suggesting combinations of adaptive context- and stage-dependent behavior, cue-related constraints on information acquisition, and ontogenetic constraints on elements of performance.