Find research datasets worth reusing

opencc-zeroMar 2023View details →

Data for: Kinship, dear enemies, and costly combat: The effects of relatedness on territorial overlap and aggression in a cooperative breeder

Many species maintain territories, but the degree of overlap between territories and the level of aggression displayed in territorial conflicts can vary widely, even within species. Greater territorial overlap may occur when neighbouring territory holders are close relatives. Animals may also differentiate neighbours from strangers, with more-familiar neighbours eliciting less-aggressive responses during territorial conflicts (the "dear enemy" effect). However, research is lacking on how both kinship and overlap affect territorial conflicts, especially in group-living species. Here we investigate kinship, territorial overlap, and territorial conflict in a habituated wild population of group-living cooperatively breeding birds, the southern pied babbler Turdoides bicolor. We find that close kin neighbours are beneficial. Territories overlap more when neighbouring groups are close kin, and these larger overlaps with kin confer larger territories (an effect not seen for overlaps with unrelated groups). Overall, territorial conflict is costly, causing significant decreases in body mass, but conflicts with kin are shorter than those conducted with non-kin. Conflicts with more-familiar unrelated neighbours are also shorter, indicating these neighbours are "dear enemies". However, kinship modulates the "dear enemy" effect; even when kin are encountered less frequently, kin elicit less-aggressive responses, similar to the "dear enemy" effect. Kin selection appears to be a main influence on territorial behaviour in this species. Groups derive kin-selected benefits from decreased conflicts and maintain larger territories when overlapping with kin, though not when overlapping with non-kin. More generally, it is possible that kinship extends the "dear enemy" effect in animal societies.

opencc-by-4.0Mar 2023View details →

International cooperation and Chinese pension reform I: technical assistance, and cooperation projects (1994-2010)

The list provides an overview of international exchange activities relating to Chinese pension reform: exchanges, technical assistance, and cooperation projects in the period 1994 to 2010. Main actors are international organizations, such as the World Bank, Asia Development Bank (ADB), next to the EU and national governments.  Matthias Stepan has compiled the information in the period 2009-2013. It has been part of his dissertation project at VU University Amsterdam.

opencc-zeroJun 2023View details →

Data for: Guppies in large groups cooperate more frequently in an experimental test of the group size paradox

The volunteer's dilemma, in which a single individual is required to produce a public good, predicts that individuals in larger groups will cooperate less frequently. Mechanistically, this could result from trade-offs between costs associated with volunteering and costs incurred if the public good is not produced (nobody volunteers). During predator inspection, one major contributor to the cost of volunteering is likely increased probability of predation; however, a predator also poses a risk to all individuals if nobody inspects. We tested the prediction that guppies in larger groups will inspect a predator less than those in smaller groups. We also predicted that individuals in larger groups would perceive less threat from the predator stimulus because of the protective benefits of larger groups (e.g. dilution). Contrary to prediction, we found that individuals in large groups inspected more frequently than those in smaller groups but (as predicted) spent less time in refuges. There was evidence that individuals in intermediate-sized groups made the fewest inspections and spent the most time in refuges, suggesting that any link between group size, risk and cooperation is not driven by simple dilution. Extensions of theoretical models that capture these dynamics will likely be broadly applicable to risky cooperative behaviour.

opencc-zeroJul 2023View details →

Data from: Phenotypic plasticity of antibiotic resistance, metabolism byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli

Although tag-based donation and recognition have well explained how the cooperative individuals are positively assorted if the cooperative individuals possess some signals and are also able to detect such signals, an additional mechanism is required to explain why some individuals pay the costs of evolving such a tag that may not be rewarded subsequently, and how such tag-based cooperative individuals will meet other similar individuals with a very low mutation rate. Here, we show that many and even all Escherichia coli bacteria cells in the increased antibiotic concentration will plastically evolve to be antibiotic resistant individuals who could protect antibiotic sensitive strain from the attack of antibiotics, and the antibiotic resistant strain could reversibly evolve to be antibiotic sensitive in non-antibiotic supplement medium but in a harsher environment with low glucose. A further experiment showed that antibiotic-sensitive E. coli strain could in turn help reduce the concentration of indole produced by the resistant strain. This metabolic product is harmful to the growth of the antibiotic-resistant strain but benefits the antibiotic-sensitive strain by helping turn on the multi-drug exporter to discharge the antibiotic. The utilization of metabolism byproduct indole produced by antibiotic-resistant cells benefits antibiotic-sensitive cells, while the indole-absorbing service of antibiotic sensitive cells unconsciously help in nullifying the indole side effect on antibiotic resistant strain, and a mutual benefit cooperation could therefore evolve.

opencc-zeroJul 2023View details →

Data for: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly-interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc finger-based TFs. We show that circuits 'wired' using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-termcontinuous culture. Our naturally-inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.

opencc-by-4.0Aug 2023View details →

Raw data for model implementation examples in paper "Incorporating Detected/Undetected Cooperative and Uncooperative Individuals, and Dynamic Transmission Probabilities in Epidemiological Models"

This dataset contains the historical daily new case numbers referenced in the paper titled "Incorporating Detected/Undetected Cooperative and Uncooperative Individuals, and Dynamic Transmission Probabilities in Epidemiological Models." These numbers were utilized to estimate the basic reproduction number R0 and the aggregated epidemic control measure Kr(t) parameters within the model, as shown in the example implementation section of the paper.

opencc-zeroSep 2023View details →

Observation of mHz-level cooperative Lamb shifts in an optical atomic clock

We report on the direct observation of resonant electric dipole-dipole interactions in a cubic array of atoms in the many-excitation limit. The interactions, mediated by single-atom couplings to the shared electromagnetic vacuum, are shown to produce spatially-dependent cooperative Lamb shifts when spectroscopically interrogating the mHz-wide optical clock transition in strontium-87. We show that the ensemble-averaged shifts can be suppressed below the level of evaluated systematic uncertainties for state-of-the-art optical atomic clocks. Additionally, we demonstrate that excitation of the atomic dipoles near a Bragg angle can enhance these effects by nearly an order of magnitude compared to non-resonant geometries. Given the remarkable precision of frequency measurements and the high accuracy of the modeled response, our work demonstrates that such a clock is a novel platform for studies of the quantum many-body physics of spins with long-range interactions mediated by propagating photons.

openother-openSep 2023View details →

Mothers in a cooperatively breeding bird increase investment per offspring at the pre-natal stage when they will have more help with post-natal care

In many cooperative societies, including our own, helpers assist with the post-natal care of breeders’ young and may thereby benefit the post-natal development of offspring. Here, we present evidence of a novel mechanism by which such post-natal helping could also have beneficial effects on pre-natal development: By lightening post-natal maternal workloads, helpers may allow mothers to increase their pre-natal investment per offspring. We present the findings of a decade-long study of cooperatively breeding white-browed sparrow-weaver, Plocepasser mahali, societies. Within each social group, reproduction is monopolized by a dominant breeding pair, and non-breeding helpers assist with nestling feeding. Using a within-mother reaction norm approach to formally identify maternal plasticity, we demonstrate that when mothers have more female helpers, they decrease their own post-natal investment per offspring (feed their nestlings at lower rates) but increase their pre-natal investment per offspring (lay larger eggs, which yield heavier hatchlings). That these plastic maternal responses are predicted by female helper number, and not male helper number, implicates the availability of post-natal helping per se as the likely driver (rather than correlated effects of group size), because female helpers feed nestlings at substantially higher rates than males. We term this novel maternal strategy “maternal front-loading” and hypothesize that the expected availability of post-natal help either allows or incentivizes helped mothers to focus maternal investment on the pre-natal phase, to which helpers cannot contribute directly. The potential for post-natal helping to promote pre-natal development further complicates attempts to identify and quantify the fitness consequences of helping.

opencc-by-4.0Oct 2023View details →

DockGame: Cooperative Games for Multimeric Rigid Protein Docking

Raw datasets used for DB5.5 dataset and DIPS dataset used in DockGame, with associated code at https://github.com/vsomnath/dockgame  These datasets can also be downloaded from https://zlab.umassmed.edu/benchmark (DB5.5) and https://www.dropbox.com/s/sqknqofy58nlosh/DIPS.zip?dl=0 (DIPS). Note that our organization would be slightly different from these downloaded versions. We follow EquiDock (https://github.com/octavian-ganea/equidock_public) for the DB5 dataset splits. Paper Abstract Protein interactions and assembly formation are fundamental to most biological processes. Predicting the assembly structure from constituent proteins -- referred to as the protein docking task -- is thus a crucial step in protein design applications. Most traditional and deep learning methods for docking have focused mainly on binary docking, following either a search-based, regression-based, or generative modeling paradigm. In this paper, we focus on the less-studied multimeric (i.e., two or more proteins) docking problem. We introduce DockGame, a novel game-theoretic framework for docking -- we view protein docking as a cooperative game between proteins, where the final assembly structure(s) constitute stable equilibria w.r.t. the underlying game potential. Since we do not have access to the true potential, we consider two approaches - i) learning a surrogate game potential guided by physics-based energy functions and computing equilibria by simultaneous gradient updates, and ii) sampling from the Gibbs distribution of the true potential by learning a diffusion generative model over the action spaces (rotations and translations) of all proteins. Empirically, on the Docking Benchmark 5.5 (DB5.5) dataset, DockGame has much faster runtimes than traditional docking methods, can generate multiple plausible assembly structures, and achieves comparable performance to existing binary docking baselines, despite solving the harder task of coordinating multiple protein chains.

opencc-zeroOct 2023View details →

Offspring sex ratio is affected by pre-breeding rainfall and hatching order in a cooperative breeding bird

Selection may favour sex ratio adjustment when the fitness benefits of producing male or female offspring vary. In birds, sex ratio bias at hatching has been particularly well-studied in cooperative breeding species, primarily in helper-at-the-nest systems wherein young remain with their parents and help raise subsequent broods. In these systems, breeding females are expected to skew offspring sex ratio in favour of the helping sex if sufficient resources exist. In communal laying systems multiple group members breed and raise the young and offspring dispersal varies, making it difficult to predict whether and how breeders should skew offspring sex ratio. We tested for sex ratio bias in smooth-billed anis (Crotophaga ani), a communal laying cuckoo with low within-group relatedness, high offspring dispersal, and high annual turnover in group membership. One male performs nocturnal incubation and sires more offspring, suggesting these males may have higher reproductive variance and thus that it may be beneficial for his mate to produce more male offspring. We hypothesized that pre-breeding rainfall influences food availability and thus offspring sex ratio, predicting that breeding females skew production towards the more beneficial sex (i.e., males) in high food years, consistent with the Trivers-Willard hypothesis. Females may also adjust sex ratio across the hatching order, so we predicted a male-bias in first hatched chicks in larger broods that should experience greater competition. Contrary to our first prediction, more male chicks hatched when pre-breeding rainfall was lower. In partial support of our second prediction, marginally more first hatched chicks were male in larger broods. Based on these results, we propose the nestling competition hypothesis and predict that when nestling competition is high (i.e., in poor years and in large joint broods), mothers should produce more of the more competitive sex.

opencc-zeroOct 2023View details →

The impact of helping experience on helper life-history and fitness in a cooperatively breeding bird

The data and accompanying .R scripts were used to test whether having experience as a helper affected a number of different breeding and fitness related parameters in the Seychelles warbler (Acrocephalus sechellensis) in the paper "The impact of helping experience on helper life-history and fitness in a cooperatively breeding bird." Datasets statusInfo.xlsx: data collected over a focal individual's lifetime. natalInfo.xlsx: data pertaining to the natal environment of the focal bird. lastSeen.xlsx: data used to calculate when the bird was last seen alive. summerIndex.xlsx: data used to determine whether a particular field period was during a summer or winter season. territoryQuality.xlsx: data used to determine the territory quality of each territory during a particular field period. Statistical analyses experiencePrep.R: the script used to prepare the data and calculate the necessary model variables prior to running the analyses. experienceAnalyses.R: the script used to run the analyses and generate the related graphs. More detailed information regarding the contents of each dataset can be found in the READ.ME From this, we found that helping experience had no significant association with any of the metrics considered, except that individuals with helping experience had an older age at first dominance, and dominant females with helping experience had longer lifespans than those that had never helped. In addition, we found that females with co-breeding experience produced more adult offspring (≥1 year old) after acquiring dominance, and had a higher lifetime reproductive success than females that had never co-bred.

opencc-by-sa-2.5Mar 2021View details →

1790 Cooper's Adze

Modeled from Eric Sloane's [*Museum of Early American Tools*](https://www.amazon.com/Museum-Early-American-Tools-Americana/dp/0486425606/ref=sr_1_1?crid=1MDB8783EQVPS&dchild=1&keywords=museum+of+early+american+tools&qid=1613590281&s=books&sprefix=museum+of+early%2Cstripbooks%2C170&sr=1-1). Textured with [CC0 Textures](https://cc0textures.com) assets. Made with [Blender](https://blender.org). Source: Objaverse 1.0 / Sketchfab

opencc-by-sa-2.5Apr 2019View details →

Cooper Library in Johnson Park, Camden, NJ

One pass DJI Phantom 3 Pro of the Johnson Library in Camden, NJ. Processed in Agisoft Metashape as a test for a custom built computer. Backside of model is due to the lack of data acquisition. From Johnson Library V5 APR2019 project. Source: Objaverse 1.0 / Sketchfab

opencc-zeroAug 2019View details →

Cooper's Apprentice Piece Flask

3D model of a flask made by a cooper at the end of his apprenticeship. He used the same woodworking skills that were required to make herring barrels. Twelve wooden staves were used to make the flask and six brass rings around the outside were used to hold the staves together. Dated. C1880. Physical object held at the Timespan Museum. Part of the Helmsdale Fishing Village reconstruction. A collaborative project between Open Virtual Worlds, a research team within the School of Computer Science, University of St Andrews and Timespan Museum. 3D digitisation was done by Catherine Cassidy and Iain Oliver with archaeological assistance provided by Jacquie Aitken. Digitisation funded by the EU Northern Periphery and Arctic Programme 2014-2020 through the "Connected Culture and Natural Heritage in a Northern Environment" (CINE) project. Source: Objaverse 1.0 / Sketchfab

opencc-bySep 2020View details →

Lottie Cooper

The Lottie Cooper was a three masted schooner built in 1876 which sank in a storm in 1894 in Sheboygan WI, harbor area where the present marina is located. It was removed in 1992 to make room for the marina and parts of the ship made into a display on shore. Unfortunately no preservation was done on the hull and it is probably one of the most at-risk shipwrecks on Lake MIchigan. Source: Objaverse 1.0 / Sketchfab

controlledIPD-YESFeb 2026View details →

A Cooperative Clinical Study of Abatacept in Multiple Sclerosis

ClinicalTrials.gov study NCT01116427. IPD Sharing: YES. Countries: 2. Publications: 2.

closedIPD-NOFeb 2026View details →

Computer Based Treatment for Cognitive Behavioral Therapy and Cooperative Pain Education and Self-Management

ClinicalTrials.gov study NCT05204576. IPD Sharing: NO. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

Cooperative Pain Education and Self-management: Expanding Treatment for Real-world Access (COPES ExTRA)

ClinicalTrials.gov study NCT03469505. IPD Sharing: Not stated. Countries: 1. Publications: 0.

restrictedIPD-UNDECIDEDFeb 2026View details →

RETHINC: REdefining THerapy In Early COPD for the Pulmonary Trials Cooperative

ClinicalTrials.gov study NCT02867761. IPD Sharing: Not stated. Countries: 1. Publications: 1.