cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3886/e192023
title: Data and Code for: Intertemporal Altruism

description: Most prosocial decisions involve intertemporal tradeoffs. Yet, the timing of prosocial utility flows is ambiguous and bypassed by most models of other-regarding preferences. We study the behavioral implications of the time structure of prosocial utility, leveraging a conceptual distinction between consequence-dated and choice-dated utility flows. We<br>conduct a high-stakes donation experiment that comprehensively characterizes discounting behavior in self-other tradeoffs and allows us to identify different prosocial motives from their distinct time profiles. Our data can only be explained by a combination of choice- and consequence-dated prosocial utility. Both motives are pervasive and negatively correlated at the individual level.
DOI: 10.3886/e192023v1
title: Data and Code for: Intertemporal Altruism

description: Most prosocial decisions involve intertemporal tradeoffs. Yet, the timing of prosocial utility flows is ambiguous and bypassed by most models of other-regarding preferences. We study the behavioral implications of the time structure of prosocial utility, leveraging a conceptual distinction between consequence-dated and choice-dated utility flows. We<br>conduct a high-stakes donation experiment that comprehensively characterizes discounting behavior in self-other tradeoffs and allows us to identify different prosocial motives from their distinct time profiles. Our data can only be explained by a combination of choice- and consequence-dated prosocial utility. Both motives are pervasive and negatively correlated at the individual level.
DOI: 10.5525/gla.researchdata.1576
title: Example code for article titled "Tutorial: Shaping the Spatial Correlations of Entangled Photon Pairs”

description: Example code and associated example data for tutorial paper on quantum imaging and shaping.
DOI: 10.15454/qstxwf/1fp5fy
title: RNA_caecum.csv

description: provide qPCR normalize data regarding gene expression in the caecal mucosa
DOI: 10.15454/qstxwf/tlo8bn
title: Pellet_consumption.csv

description: Consumption of pellets per rabbits before weaning (from d15 to d36)
DOI: 10.15454/qstxwf/2jixs7
title: Rabbits_weight.tab

description: Weights of all the rabbit litters before weaning and all the individuals raised after weaning
DOI: 10.15454/qstxwf/ck8bsw
title: Gel_consumption.csv

description: Consumption of gel foods (starter food made from pellets mash mixed with water and gelling agent) by suckling rabbits (in addition with the doe's milk) from 7 to 17 days of age after correction for water loss by evaporation
DOI: 10.15454/qstxwf/co5zaw
title: Metabolites_caecum.csv

description: Metabolites present in the caecal luminal milieu of rabbit from 18 to 58 days of age quantified with H1 NMR spectra
DOI: 10.15454/qstxwf/m4kotm
title: Milk_consumption.csv

description: Milk consumption by suckling rabbits from 3 to 21 days of age in controlled nursing conditions (suckling once a day)
DOI: 10.15454/qstxwf/th4vp3
title: RNA_ileon.csv

description: provide qPCR normalize data regarding gene expression in the ileal mucosa
DOI: 10.15454/qstxwf/4ghoyw
title: Gel_consumption.mp4

description: Video of kits consuming gels
DOI: 10.15454/qstxwf/5wsuec
title: Gel_consumption_access.mp4

description: Video of kits consuming gels with competition
DOI: 10.15454/qstxwf/rfyx9v
title: Host_data.csv

description: All the phenotypic data collected on the rabbits sampled (n=150) together with blood and caecal parameters evaluated with biochemcial measurements
DOI: 10.15454/qstxwf/wb3kgz
title: readme.txt
DOI: 10.15454/qstxwf/xvffxg
title: Path_abun_unstrat_transpo.csv

description: Metacyc pathways obtained by PICRUST2 with the OTU table for the analysis of potential functional capacities of the caecal microbiota
DOI: 10.15454/qstxwf/03nmfz
title: Rabbits_weight-1.tab

description: Weights of all the rabbit litters before weaning and all the individuals raised after weaning
DOI: 10.15454/qstxwf/9tljg5
title: J1_1802_114.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/a0flmh
title: J1_1802_126.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/epzlgi
title: Within_distance_wunifrac.csv

description: Wunifrac phylogenetic distances sorted to obtain the distances within individuals between their caecum and their appendix microbiomes
DOI: 10.15454/qstxwf/k7rtym
title: caecal_appendix_microbiome_rabbit_newSILVAdatabase.rdata

description: Gut microbiota data (based on 16S rDNA amplicons sequencing of caecal and appendix luminal content) together with samples information, after processing the sequences with FROGS pipeline. n=296 samples from 2 gut locations (caecum and appendix) collected on150 animals. Taxonomic affiliations were obtained using the SILVA138 database
DOI: 10.15454/qstxwf/yflmzr
title: OTU_abundances.tab

description: :unav
DOI: 10.15454/qstxwf/aq4lad
title: J1_1802_314.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/ba7xg4
title: J1_1802_304.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/dxnud3
title: J1_1802_319.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/r3ztd7
title: J1_1802_301.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/rvnubi
title: J1_1802_129.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/2bsk2f
title: J1_1802_307.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/anibix
title: J1_1802_128.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/fqy1n5
title: J1_1802_305.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/nictzs
title: J1_1802_310.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/xgsini
title: J1_1802_316.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/1hgmnu
title: J1_1802_306mort.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/4wtwlo
title: J1_1802_218.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/dy5zln
title: J1_1802_228.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/libiah
title: J1_1802_227.jpg

description: :unav
DOI: 10.15454/qstxwf/qslg9q
title: J1_1802_327.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/ueohao
title: J1_1802_210.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/5oiys8
title: J1_1802_206.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/eio7tq
title: J1_1802_109.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/hskurw
title: J1_1802_101.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/yrp5t4
title: J1_1802_329.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/yvtsea
title: J1_1802_323.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/7vklib
title: J1_1802_220.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/cvxjgq
title: J1_1802_320.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/gw4dya
title: J1_1802_303.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/jggkv1
title: J1_1802_214.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/yr61xg
title: J1_1802_219.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/6snhun
title: J1_1802_107.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/aksqj0
title: J1_1802_309.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/c8dccy
title: J1_1802_103.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/lzoo8i
title: J1_1802_313.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/nszzyz
title: J1_1802_208mort.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/zshnun
title: J1_1802_226.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/2megzg
title: J1_1802_215.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/9bpgsy
title: J1_1802_311.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/bhbioj
title: J1_1802_216.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/mdmbov
title: J1_1802_207.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/oyqsl9
title: J1_1802_130.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/58ovsk
title: J1_1802_217.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/mq9hx4
title: J1_1802_211.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/oxwbre
title: J1_1802_113.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/q0jtmo
title: J1_1802_202.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/yy8gde
title: J1_1802_221.jpg

description: :unav
DOI: 10.15454/qstxwf/2ou7td
title: J1_1802_111.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/ctekqw
title: J1_1802_118.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/n11vno
title: J1_1802_116.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/riml79
title: J1_1802_229.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/sgxmlc
title: J1_1802_222.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/djvtjr
title: J1_1802_201.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/ltqhko
title: J1_1802_102.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/oijop8
title: J1_1802_318.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/rtzihv
title: J1_1802_127.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/uwqkhb
title: J1_1802_223.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/6wzamz
title: J1_1802_321.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/7yvktu
title: J1_1802_302.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/k20xap
title: J1_1802_225.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/nb7b7y
title: J1_1802_124.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/pegxei
title: J1_1802_312.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/c5qbnz
title: Milk_consumption.txt

description: Milk consumption by suckling rabbits from 3 to 21 days of age in controlled nursing conditions (suckling once a day)
DOI: 10.15454/qstxwf/k7vtsz
title: Table_primer.txt

description: Primer sequences for qPCR gene expression measurments in rabbit caecal mucosa
DOI: 10.15454/qstxwf/lboumc
title: J1_1802_315.jpg

description: Thermal photograph of the nest of the young rabbits 1 day after birth
DOI: 10.15454/qstxwf/shnkek
title: Metabolites_caecum.txt

description: Metabolites present in the caecal luminal milieu of rabbit from 18 to 58 days of age quantified with H1 NMR spectra
DOI: 10.15454/qstxwf/xqaueq
title: Host_data.txt

description: All the phenotypic data collected on the rabbits sampled (n=150) together with blood and caecal parameters evaluated with biochemcial measurements
DOI: 10.15454/qstxwf/ybq0ci
title: Gel_consumption.txt

description: Consumption of gel foods (starter food made from pellets mash mixed with water and gelling agent) by suckling rabbits (in addition with the doe's milk) from 7 to 17 days of age after correction for water loss by evaporation
DOI: 10.15454/qstxwf/7kecqh
title: RNA_ileon.txt

description: provide qPCR normalize data regarding gene expression in the ileal mucosa
DOI: 10.15454/qstxwf/a7kgzk
title: RNA_caecum.txt

description: provide qPCR normalize data regarding gene expression in the caecal mucosa
DOI: 10.15454/qstxwf/kkzxw3
title: Pellet_consumption.txt

description: Consumption of pellets per rabbits before weaning (from d15 to d36)
DOI: 10.15454/qstxwf/qyigjs
title: Within_distance_wunifrac.txt

description: Wunifrac phylogenetic distances sorted to obtain the distances within individuals between their caecum and their appendix microbiomes
DOI: 10.15454/qstxwf/unf7xs
title: Path_abun_unstrat_transpo.txt

description: Metacyc pathways obtained by PICRUST2 with the OTU table for the analysis of potential functional capacities of the caecal microbiota
DOI: 10.57745/qtzdlg
title: CP1802_CPMG.zip

description: Raw data 1H NMR spectrum (CPMG 600 MHz D2O)
DOI: 10.6084/m9.figshare.25024463
title: gDNA barcode sequencing for proving memory of resistance - processed data

description: Processed (repo/analyzed) fastqs of barcode sequencing. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.6084/m9.figshare.25024463.v1
title: gDNA barcode sequencing for proving memory of resistance - processed data

description: Processed (repo/analyzed) fastqs of barcode sequencing. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.3886/icpsr38898.v1
title: Inequality, Social Capital, and Health in Bolivia, 2008-2009
title: Version 1

description: This randomized controlled trial examined the independent effect of village income inequality and individual income on individual health. Specifically, the study assessed how these two variables interacted with social capital to affect individual health. For the trial, 40 villages were selected for two experimental treatments.
In the first treatment, 13 villages were picked at random to receive 782kg of edible rice as in-kind income. The 782kg of rice was split equally between all households in the village. For the second treatment, another 13 villages were picked at random. Each village in the second treatment received the same amount of rice as the villages in the first treatment (782kg), but all of the rice went to the poorest 20 percent of households in the village, with each household getting the same amount of rice. All households in the remaining 14 villages and all households in the top 80 percent of the village income distribution of the second treatment acted as controls, and received 6kg of high-yielding, improved rice seeds.
The baseline survey was administered between February and May 2008, households received the rice between October 2008 and January 2009, and the end-line survey was administered between February and May 2009. Outcomes included anthropometric indicators of nutritional status, perceived health, and blood pressure.
description: The main aim of this randomized controlled trial was to assess the independent effect of village income inequality and individual income on individual health.
description: All Tsimane' living in 40 villages during the baseline survey (2008) were included in this study.
description: Datasets: 
DS1: Inequality, Social Capital, and Health in Bolivia, 2008-2009
description: Tsimane' living in 40 villages in Bolivia in 2008. Smallest Geographic Unit: Village
description: face-to-face interview; paper and pencil interview (PAPI)
DOI: 10.5063/f14j0ccp
title: List of Useful Plant species according to the State of the World's Plants report (RBG Kew, 2016)

description: The Royal Botanic Gardens, Kew (RBG Kew) published in 2016 the first State of the World's Plant report, with key statistics on plants. One of the highlights was the indication of at least 31,128 flowering plant species with a documented use. We provide here this list, including family, genus, full species name (with authors) and the level 1 of use, according to a simplified version of the economic botany data standards.Suggested citation:Diazgranados M., Allkin B., Black N., Canteiro C., Eastwood R., Hargreaves S., Hudson A., Milliken W., Nesbitt M., Willis K. & Ulian T. 2018. List of Useful Plant species according to the State of the World`s Plants report (RBG Kew, 2016). Knowledge Network for Biocomplexity.
DOI: 10.6084/m9.figshare.25029338
title: gDNA barcode sequencing for proving memory of resistance - raw data

description: Raw (2021_05_24_DLS005_DLS004_RAR_BC_gDNA) fastqs of barcode sequencing for proving memory of resistance. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.6084/m9.figshare.25029338.v1
title: gDNA barcode sequencing for proving memory of resistance - raw data

description: Raw (2021_05_24_DLS005_DLS004_RAR_BC_gDNA) fastqs of barcode sequencing for proving memory of resistance. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.5281/zenodo.6377140
title: Transmission electron microscopy (TEM) image datasets of peptide / protein nanowire morphologies

description: TEM image dataset containing four nanowire morphologies of bio-derived protein nanowires and synthetic peptide nanowires.

The peptide / protein nanowires used in this study were synthesized and imaged by Brian Montz in Prof. Todd Emrick's research group at the Department of Polymer Science and Engineering Department, University of Massachusetts Amherst. 

We acknowledge financial support from the U.S. National Science Foundation, Grant NSF DMREF #1921839 and DMREF #1921871.

Nanowires were classified into either of the four morphologies: bundle, singular, dispersed or network. Each morphology contains 100 images (jpg files).

For the dispersed and network morphologies, because these two morphologies are harder to visually distinguish, we have created manual segmentation labels of the nanowires (included in these two morphology folders as png files). Percolation analysis was done on these manually segmented nanowires to provide quantitative metric on whether the nanowires form a network in the image. 

seg_mask_5_resolutions.zip contains ground truth 2D binary encoding of segmented nanowires at 5 resolutions.

encoders_trained_with_optimized_hyperparameter.zip contains 4 sets of encoders trained with either SimCLR or Barlow-Twins self-supervised methods on either generic TEM images, or generic everyday photographic images (each with 5 replicates with different random seed) with optimized hyperparameters.

Open-access datasets that have been used during self-supervised training.



2021-CEM500K.zip contains 10,000 images that was used as "generic TEM images" to train the encoders with self-supervised methods, these are a random selection from the CEM500k open-access dataset. DOI: 10.7554/eLife.65894

2022-1000-ImageNet.zip contains 1,000 images from the ImageNet1k dataset, each come from a different category. DOI: 10.1007/s11263-015-0816-y


Open-access datasets that our machine learning workflow have been applied to:



2022-AutoDetect-mNP-morphology.zip contains a selected TEM images of nanoparticles categorized in 3 morphologies from the AutoDetect-mNP datasets: DOI: 10.6078/D1WT44 and DOI: 10.6078/D1S12H

2021-TEM virus.zip contains TEM images of 9 types of viruses from the TEM virus dataset. Matuszewski, Damian; Sintorn, Ida-Maria (2021), “TEM virus dataset”, Mendeley Data, V3, DOI: 10.17632/x4dwwfwtw3.3


The official github page of the implementation of the machine learning models is semi-supervised_learning_microscopy_images.

If you use the dataset or the codes in the repository linked above, please cite the following manuscript:

S. Lu, B. Montz, T. Emrick and A. Jayaraman, Digital Discovery, 2022, 1, 816-833 , DOI: 10.1039/D2DD00066K
DOI: 10.5281/zenodo.6377141
title: Transmission electron microscopy (TEM) image datasets of peptide / protein nanowire morphologies

description: TEM image dataset containing four nanowire morphologies of bio-derived protein nanowires and synthetic peptide nanowires. The peptide / protein nanowires used in this study were synthesized and imaged by Brian Montz in Prof. Todd Emrick's research group at the Department of Polymer Science and Engineering Department, University of Massachusetts Amherst. We acknowledge financial support from the U.S. National Science Foundation, Grant NSF DMREF #1921839 and DMREF #1921871. Nanowires were classified into either of the four morphologies: bundle, singular, dispersed or network. Each morphology contains 100 images (jpg files). For the dispersed and network morphologies, because these two morphologies are harder to visually distinguish, we have created manual segmentation labels of the nanowires (included in these two morphology folders as png files). Percolation analysis was done on these manually segmented nanowires to provide quantitative metric on whether the nanowires form a network in the image. seg_mask_5_resolutions.zip contains ground truth 2D binary encoding of segmented nanowires at 5 resolutions. encoders_trained_with_optimized_hyperparameter.zip contains 4 sets of encoders trained with either SimCLR or Barlow-Twins self-supervised methods on either generic TEM images, or generic everyday photographic images (each with 5 replicates with different random seed) with optimized hyperparameters. The official github page of the implementation of the machine learning models is self-supervised_learning_microscopy_images. If you use the dataset or the codes in the repository linked above, please cite the following manuscript: <pre><code>@misc{lu2022selfsupervised, title={Self-supervised machine learning model for analysis of nanowire morphologies from transmission electron microscopy images}, author={Shizhao Lu and Brian Montz and Todd Emrick and Arthi Jayaraman}, year={2022}, eprint={2203.13875}, archivePrefix={arXiv}, primaryClass={cond-mat.mtrl-sci} }</code></pre>