The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving ‘Functional Association(s) by Response Overlap’ (FARO) between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our results indicate that FARO is more powerful in associating mutants in common pathways than existing methods such as co-expression analysis.

Animal vocalisations are widely used to signal strength or motivation of a caller in competitive interactions, such as in territorial defence. Substantial understanding of signalling functions in territorial conflicts is based on singing by male songbirds. Yet, in many species, both pair members call during territorial conflicts, as well as in predator-induced situations, leading to complex signalling interactions in which calls overlap or alternate. This raises the question as to whether or not variation in how individuals in pairs time their calls is perceived as meaningful by receivers. Here, we tested with playback experiments whether Eurasian magpies (Pica pica), a species producing alarm calls (so-called chatter calls) in territorial defence, respond stronger to simulated pair-intruders who overlap their calls with each other than to those who alternate them. Magpies emitted a significantly longer first chatter in response to playback with overlapping call but tended to more closely approach the loudspeakers playing back alternating (and therefore longer) call sequences. These findings exemplify that the timing of calls by pair members matters, but in more complex ways than we predicted. The overlapping playback appeared to trigger a stronger initial chatter response but a weaker approach response, suggesting that the different ways in which magpies respond reflect different levels of arousal or defence strategies. These findings expand on classical experiments on call function, suggesting that pairs can vary the message by coordinating their alarm calls in different ways, similar to how duetting pairs time their song contributions in advertisement signalling. Methods We conducted playback experiments simulating a territorial intrusion by a pair of magpies were the timing of calls from the pair members differed. Specifically, we used two loudspeakers broadcasting chatter-calls with the calls from the second speaker either alternating or overlapping the calls from the other loudspeaker. The playback trials were conducted in the vicinity of magpie nests. A trial consisted of one minute playback plus two additional minutes observation time. During the trial, we recorded magpie vocal responses and noted the closest approach distance to the loudspeakers of any magpie. Audio recordings were analysed in Audacity® v3.1.3 (Audacity Team, 2023) by setting labels over all chatter calls and overlapping chatter sequences. Those labels were exported as text files and merged with trial data in R v4.3.2 (R Core Team, 2023). We used the packages tidyr v1.2.0 (Wickham & Girlich 2022) and dplyr v1.0.8 (Wickham et al. 2022) to extract for each trial a) the closest approach distance of magpies to the speakers, b) the total number all chatter calls (including those that overlap with another) and total duration of chattering (i.e. total duration of all single chatter calls and overlapping chatter sequences), and c) the number of overlapping chatter sequences. For those trials in which chattering occurred, we further extracted d) the latency between the start of the playback and the first chatter and e) the number of syllables of the first chatter. This dataset contains the resulting summary file per trial. The details of the methods are described in the manuscript itself

Behavioral data Column information: Onset Duration Block Trial: Trial (within a block) Task: task (1:artist, 2:function; task info. of the learning phase for the item repetition and source memory test phases) Stim cat: Stimulus category (1:natural, 2:manmade) Repetition: Repetition (1: repeated, 2: once) Reaction_time: Reaction time (in sec) Response Accuracy: Accuracy (1: correct, 0: incorrect in the source test phase; NaN for the other phases) Confidence_lvl: Confidence level (1: highly unsure, 4: highly sure in the source test phase; n/a for the other phases) RT_confidence: RT of confidence report (n/a for the non-test phases)

Stimulus presentation time Phase 1 (encoding phase): 1s Phase 2 (item repetition phase): 1s Phase 3 (source memory test phase): 6s

How does the increasingly dense network of overlapping institutions in global governance affect the design of intergovernmental organizations (IGOs)? We argue that institutional overlap can unleash mimicking dynamics whereby states design new IGOs using the design of existing organizations that engage in similar issue areas and perform similar governance tasks for similar member states as templates. Using design templates from the reference group of overlapping institutions is a strategy for boundedly rational designers in situations of complexity because it reduces uncertainty and lowers the costs of identifying suitable institutional solutions. Overlap therefore increases the design similarity between new and pre-existing IGOs, specifically where pre-existing organizations have institutional designs that made them endure. Introducing a new measure of institutional overlap in global governance and new data on the design and governance tasks of the 534 IGOs from the Correlates of War Project, we corroborate our argument using regression analyses. Our results hold important lessons for theories of institutional design, regime complexity, and global governance more broadly.

1. Species with different life histories and communities that vary in their seasonal constraints tend to shift their phenology (seasonal timing) differentially in response to climate warming.

2. We investigate how these variable phenological shifts aggregate to influence phenological overlap within communities. Phenological advancements of later-season species and extended durations of early-season species may increase phenological overlap, with implications for species’ interactions such as resource competition.

3. We leverage extensive historic (1958-1960) and recent (2006-2015) weekly survey data for communities of grasshoppers along a montane elevation gradient to assess the impact of climate on shifts in the phenology and abundance distributions of species. We then examine how these responses are influenced by the seasonal timing of species and elevation, and how in aggregate they influence degrees of phenological overlap within communities.

4. In warmer years, abundance d...

To test the lexical overlap heuristic utilization in Reading Comprehension models, we create a new test set: Analyzing Lexically Similar QA (ALSQA). We augment the SQuAD 2.0 dataset (Rajpurkar et al., 2018) by asking crowdworkers to generate questions with high context-overlap from questions with low overlap (These questions are paraphrases of the original questions). In the case of un-answerable questions, annotators were asked to re-write the question without changing its meaning and maintain the unanswerability reason.3 ALSQA contains 365 questions pairs, 190 with an- swer and 174 without answer.

The trophic link between cod (Gadus sp.) and capelin (Mallotus sp.) is important in many panarctic ecosystems. Since the early 2000s, the Northeast Arctic cod stock (G. morhua) in the Barents Sea has increased greatly, and the sea has been exceptionally warm. Such changes have potentially large effects on species distributions and overlap, which in turn could affect the strength of species interactions. Due to its high latitude location, the Barents Sea has strong seasonal variation in physical conditions and interactions. To study drivers of variation in cod-capelin overlap, we use data from two annual surveys run in winter and in autumn of 2004-2015. We first model winter and autumn spatial distributions of mature and immature cod and capelin. We then calculate overlap from model predictions on a grid with similar spatial resolution as the survey data. Our approach allowed us to interpret changes in overlap as species-specific effects of stock size and temperature, while accounting for sampling variation due to sampling time and depth. We found that during winter both species expanded their distribution in response to increased stock sizes, but how strongly and where the expansion occurred varied. The effect of temperature on distributions varied in space, and differed for cod and capelin and for different components of the two species. The results for autumn were clearer and more consistent. Both species expanded their distribution areas as their stock sizes increased. A positive effect of temperature was found in the north-eastern Barents Sea, where temperatures were lowest at the start of the study. Overlap increased and shifted north-eastwards during the study period and remained high despite a decline in the capelin stock. The increased overlap during autumn could mainly be attributed to the shift in cod distribution with increased cod stock biomass. Ecosystem survey 2004-2015Field-collected data on cod and capelin distribution from the Norwegian parts of the ecosystem survey 2004-2015. For details see README file.Norwegian part of ecosystem survey cod-capelin 2004-2015.txtWinter survey 2004-2015Field-collected data on cod and capelin distribution from the Norwegian parts of the winter survey 2004-2015. For details see README file.Norwegian part of winter survey cod-capelin 2004-2015.txt

The overlap of early general stress response genes reported in two previous studies [33], [34] and the repressed genes by NF-YAs (cutoff≤2-fold, p-value≤0.05) is given. Data obtained using the Genesect web tool available through VirtualPlant 1.2 software platform [35]. S, size of intersection. Significant differences (p-value11) are highlighted in bold.

This dataset is flattened and multicounty communities are unsplit by county lines. Flattened means that there are no overlaps; larger shapes like counties are punched out or clipped where smaller communities are contained within them. This allows for choropleth shading and other mapping techniques such as calculating unincorporated county land area. Multicounty cities like Houston are a single feature, undivided by counties. This layer is derived from Census, State of Maine, and National Flood Hazard Layer political boundaries.rnrnThe Community Layer datasets contain geospatial community boundaries associated with Census and NFIP data. The dataset does not contain personal identifiable information (PII). The Community Layer can be used to tie Community ID numbers (CID) to jurisdiction, tribal, and special land use area boundaries.rnrnA geodatabase (GDB) link is Included in the Full Data section below. The compressed file contains a collection of files that can store, query, and manage both spatial and nonspatial data using software that can read such a file. It bcontains all of the community layers/b, not just the layer for which this dataset page describes. rnThis layer can also be accessed from the FEMA ArcGIS viewer online: https://fema.maps.arcgis.com/home/item.html?id=8dcf28fc5b97404bbd9d1bc6d3c9b3cfrnrnrnCitation: FEMA's citation requirements for datasets (API usage or file downloads) can be found on the OpenFEMA Terms and Conditions page, Citing Data section: https://www.fema.gov/about/openfema/terms-conditions.rnrnFor answers to Frequently Asked Questions (FAQs) about the OpenFEMA program, API, and publicly available datasets, please visit: https://www.fema.gov/about/openfema/faq.rnIf you have media inquiries about this dataset, please email the FEMA News Desk at FEMA-News-Desk@fema.dhs.gov or call (202) 646-3272. For inquiries about FEMA's data and Open Government program, please email the OpenFEMA team at OpenFEMA@fema.dhs.gov.

A classical problem in statistics is estimating the expected coverage of a sample, which has had applications in gene expression, microbial ecology, optimization, and even numismatics. Here we consider a related extension of this problem to random samples of two discrete distributions. Specifically, we estimate what we call the dissimilarity probability of a sample, i.e., the probability of a draw from one distribution not being observed in draws from another distribution. We show our estimator of dissimilarity to be a -statistic and a uniformly minimum variance unbiased estimator of dissimilarity over the largest appropriate range of . Furthermore, despite the non-Markovian nature of our estimator when applied sequentially over , we show it converges uniformly in probability to the dissimilarity parameter, and we present criteria when it is approximately normally distributed and admits a consistent jackknife estimator of its variance. As proof of concept, we analyze V35 16S rRNA data to discern between various microbial environments. Other potential applications concern any situation where dissimilarity of two discrete distributions may be of interest. For instance, in SELEX experiments, each urn could represent a random RNA pool and each draw a possible solution to a particular binding site problem over that pool. The dissimilarity of these pools is then related to the probability of finding binding site solutions in one pool that are absent in the other.

Behavioural and eye-movement data gathered from five experiments that examined visual search behaviour/performance in stereoscopic displays. Experiments 1-4 involved examining search of stereoscopic displays under varying levels of overlap (0%, 45%, 90%), and varying task conditions (participants were asked to search for either one or two targets). Each of the first four experiments involved search for a different stimulus type (covering opaque polygons, transparent polygons, household objects and X-ray images respectively). Experiment 5 involved training participants to search through X-ray images for a series of sessions either in the presence of stereoscopic depth, or in flat displays, following by a transfer session to flat displays. Experiments 1-4 involved eye-tracking and Experiment 5 involved eye-tracking every four sessions, as well as in the transfer session.A considerable amount of research has examined the problems associated with searching for multiple target objects, with a particular focus on X-ray baggage screening, where security personnel must search for a number of different objects simultaneously. The goal of this project is to extend the previous research that has been conducted by examining the complexities associated with X-ray images, such as transparency and overlap. Security search for threat items (weapons) within X-ray images of baggage presents a challenge for the visual system because X-ray images do not conform to the conventional rules of solidity, interposition and opacity. In X-ray images, transparency causes colour changes at points of overlap. The colours representing each object interact at areas of overlap in a way that is largely unfamiliar to the visual system. In this project, a series of experiments will be conducted using eye-tracking methodology to understand and explore the complexities involved in searching displays of this type. Furthermore, the displays will be presented in both 2D and 3D, to determine whether any difficulties associated with searching transparent overlapping images can be overcome when the objects are separated into different layers of depth. The data collection was generated by a series of five visual search experiments. Participants viewed displays and were asked to search for pre-specified targets. The nature of the targets being searched for varied depending on the experiment. On each trial, participants were asked to respond 'present' (if they found a target) or 'absent' (if they believed no target to be present). We recorded their responses, the speed of their responses, and participants' eye movement behaviour. Participants were undergraduate/postgraduate students and staff from the University of Southampton in the UK. They were pre-screened for colour vision and an adequate degree of depth perception.

Three-way overlap between: (1) inhibitory-related brain areas according to the ALE meta-analysis (“50/50% Go/NoGo blocks > 100% Go-control blocks”), (2) brain areas with practically equivalent neuronal activity in Go and NoGo trials (“NoGo = Go”) and (3) brain areas activated in equiprobable Go and NoGo trials (“Go + NoGo > Ignore”).

Collection description

Response inhibition is typically considered a brain mechanism selectively triggered by particular “inhibitory” stimuli or events. Based on recent research, an alternative non-selective mechanism was proposed by several authors. Presumably, the inhibitory brain activity may be triggered not only by the presentation of “inhibitory” stimuli but also by any imperative stimuli, including Go stimuli, when the context is uncertain. Earlier support for this notion was mainly based on the absence of a significant difference between neural activity evoked by equiprobable Go and NoGo stimuli. Equiprobable Go/NoGo design with a simple response time task limits potential confounds between response inhibition and accompanying cognitive processes while not preventing prepotent automaticity. However, previous neuroimaging studies used classical null hypothesis significance testing, making it impossible to accept the null hypothesis. Therefore, the current research aimed to provide evidence for the practical equivalence of neuronal activity in the Go and NoGo trials using Bayesian analysis of functional magnetic resonance imaging (fMRI) data. Thirty-four healthy participants performed a cued Go/NoGo task with an equiprobable presentation of Go and NoGo stimuli. To independently localize brain areas associated with response inhibition in similar experimental conditions, we performed a meta-analysis of fMRI studies using equal-probability Go/NoGo tasks. As a result, we observed overlap between response inhibition areas and areas that demonstrate the practical equivalence of neuronal activity located in the right dorsolateral prefrontal cortex, parietal cortex, premotor cortex, and left inferior frontal gyrus. Thus, obtained results favour the existence of non-selective response inhibition, which can act in settings of contextual uncertainty induced by the equal probability of Go and NoGo stimuli.

Subject species

homo sapiens

Modality

fMRI-BOLD

Analysis level

group

Cognitive paradigm (task)

go/no-go task

Map type

R

Expanded dataset will be maintained in the Niwot Ridge LTER Data Catalog via the Environmental Data Initiative (https://nwt.lternet.edu/data-catalog). The subset of the data here, corresponding to that used in the paper, is for residents (common species in both surveys) during 1959-1960 and 2006-2015.

Methods

Study sites

During 2006-2015, we resurveyed the grasshopper (family: Acrididae) communities at four sites in the Front Range of northern Colorado that were originally sampled 60 years prior during the field seasons of 1958 to 1960 (Alexander and Hilliard 1969, Nufio et al. 2009, 2010). These surveyed sites found along an elevational gradient within Boulder County, Colorado, USA, were sampled during both the historic and contemporary surveys on a weekly basis from spring (May-June, depending on elevation) to early fall (August-October). The sites are referred to as Chautauqua Mesa (1752 m; 39.999° N, -105.285° W), A1 (220...

Computational results about networks with overlapping communities.

This dataset was obtained from the OpenfMRI project (http://www.openfmri.org). Accession #: ds000122 Description: Visual Attention Task (block design)

Please cite the following references if you use these data:

J Xu, S Zhang, VD Calhoun, J Monterosso, MN Potenza 2013 Task-related concurrent but opposite modulations of overlapping functional networks as revealed by spatial ICA. NeuroImage 79:62-71 (PMCID: PMC3677796)

04/08/2016: initial release

This dataset is made available under the Public Domain Dedication and License v1.0, whose full text can be found at http://www.opendatacommons.org/licenses/pddl/1.0/. We hope that all users will follow the ODC Attribution/Share-Alike Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); in particular, while not legally required, we hope that all users of the data will acknowledge the OpenfMRI project and NSF Grant OCI-1131441 (R. Poldrack, PI) in any publications.

Events Headings: -ReactionTime: Reaction Time -ResponseButtonCode: Response Button Code (33 is hit, 0 is no response, others were wrong response) -OnsetBlock: Starting time of each block -OnsetTrial: Starting time of each trial -TaskLevel: Task level -TargetNontarget: 1=target; 0=nontarget

This layer shows the percentage of treated POD lines within the northwest region during the last 10 years, starting with the beginning of fiscal year 2013 (10/1/2012) through the publish date. Treatment data came from lands managed by the Department of the Interior or the U.S. Forest Service. Treatments include fuels, timber, and brush. All wildland fire or naturally-caused fire data was not included.Analysis will be rerun when there have been significant updates to the PNW POD layer.PODs are a strategic planning tool developed using local expertise and often advanced spatial analysis. They are meant to identify the safest and most effective control lines used to contain a wildfire and can assist in integrating land management objectives and incident response. Layer used to run the analysis on is a a consolidated layer of PODs from multiple units.Contact the R6 Fire and Aviation and NWCC GIS Coordinator, Desraye Assali, desraye.assali@usda.gov if you have any questions.

Social information transmission is important because it enables horizontal spread of behaviors, not only between conspecifics, but also between individuals of different species. Because interspecific social information use is expected to take place among species with similar resource needs, it may have major consequences for the emergence of local adaptations, resource sharing and community organization. Social information use is expected to be selective, but the conditions promoting it in an interspecific context are not well known. Here, we experimentally test whether pied flycatchers (Ficedula hypoleuca) use the clutch size of great tits (Parus major) in determining the quality of the observed individual and use it as a basis in decision-making. We show that pied flycatchers (Ficedula hypoleuca) copied or rejected a novel nest-site feature preference of great tits (Parus major), experimentally manipulated to exhibit high or low fitness (clutch size), respectively. Our results demonstrate that the social transmission of behaviors across species can be highly selective in response to observed fitness, plausibly making the phenomenon adaptive. In contrast with the current theory of species coexistence, overlap between realized niches of species could dynamically increase or decrease depending on the observed success of surrounding individuals.

Tampere University of Technology (TUT) Sound Events 2018 - Ambisonic, Anechoic, and Synthetic Impulse Response Dataset

This dataset consists of simulated anechoic first order Ambisonic (FOA) format recordings with stationary point sources each associated with a spatial coordinate. The dataset consists of three sub-datasets with a) maximum one temporally overlapping sound events, b) maximum two temporally overlapping sound events, and c) maximum three temporally overlapping sound events. Each of the sub-datasets has three cross-validation splits, that consists of 240 recordings of about 30 seconds long for training split and 60 recordings of the same length for the testing split. For each recording, the metadata file with the same name consists of the sound event name, the temporal onset and offset time (in seconds), spatial location in azimuth and elevation angles (in degrees), and distance from the microphone (in meters).

The isolated sound events were taken from the DCASE 2016 task 2 dataset. This dataset consists of 11 sound event classes such as Clearing throat, Coughing, Door knock, Door slam, Drawer, Human laughter, Keyboard, Keys (put on a table), Page turning, Phone ringing and Speech. The sound events are randomly placed in a spatial grid with 10-degree resolution in full azimuth and [-60 60) degree elevation angles. Additionally, the sound events are placed at a random distance of [1 10] meters from the microphone.

The license of the dataset can be found in the LICENSE file. The rest of the nine zip files consists of datasets for a given split and overlap. For example, the ov3_split1.zip file consists of the audio and metadata folders for the case of maximum three temporally overlapping sound events (ov3) and the first cross-validation split (split1). Within each audio/metadata folder, the filenames for training split have the 'train' prefix, while the testing split filenames have the 'test' prefix.

This dataset was collected as part of the 'Sound event localization and detection of overlapping sources using convolutional recurrent neural network' work.

Predators may alter niche overlap between prey species by eliciting divergent anti-predator behavior. Accordingly, we exploited heterogeneous gray wolf (Canis lupus) presence in Washington, USA, to contrast patterns of resource and dietary overlap between mule (Odocoileus hemionus) and white-tailed deer (O. virginianus) at sites with and without resident packs. Mule deer run (stot) in a way that is less effective as a means of fleeing from predators than the galloping gait of white-tailed deer. Consequently, mule deer manage risk from coursing predators like wolves by avoiding encounters, whereas white-tailed deer respond to such predators by exploiting areas where they are most likely to escape pursuit. Thus, under the "refuge partitioning hypothesis" whereby predators reduce prey niche overlap by eliciting use of different refugia, we predicted wolf exposure to (i) decrease resource and dietary overlap between these ungulates, and (ii) induce segregation consistent with each species using different parts of the landscape to reduce their wolf risk. At the home range scale, the ways in which resource overlap diminished in the wolf areas were consistent with the prey species reducing their respective risks, particularly with respect to slope, with mule deer separating from white-tailed deer by seeking steeper areas where wolf encounters are less likely. At the within-home range scale, the manner in which spatial overlap decreased in relation to forest cover was consistent with species-specific risk management, with mule deer avoiding wolf encounters by shifting toward this resource. Reduced resource overlap between the deer in areas occupied by wolves did not correspond with dietary divergence. Our findings suggest that wolf risk mediates spatial but not necessarily dietary overlap between sympatric ungulates, divergent anti-predator behavior is a non-consumptive pathway by which predators can reduce interspecific competition among prey, and use of disparate refugia by prey may not result in dietary divergence.

This layer shows the percentage of treated POD lines within the northwest region during the last 20 years, starting with the beginning of fiscal year 2003 (10/1/2002) through the publish date. Treatment data came from lands managed by the Department of the Interior or the U.S. Forest Service. Treatments include fuels, timber, and brush. All wildland fire or naturally-caused fire data was not included.Analysis will be rerun when there have been significant updates to the PNW POD layer.PODs are a strategic planning tool developed using local expertise and often advanced spatial analysis. They are meant to identify the safest and most effective control lines used to contain a wildfire and can assist in integrating land management objectives and incident response. Layer used to run the analysis on is a a consolidated layer of PODs from multiple units.Contact the R6 Fire and Aviation and NWCC GIS Coordinator, Desraye Assali, desraye.assali@usda.gov if you have any questions.