cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6xk8cq9
title: Automatic Labeling of Special Diagnostic Mammography Views from Images and DICOM Headers

description: Applying state-of-the-art machine learning techniques to medical images
 requires a thorough selection and normalization of input data. One of such
 steps in digital mammography screening for breast cancer is the labeling
 and removal of special diagnostic views, in which diagnostic tools or
 magnification are applied to assist in assessment of suspicious initial
 findings. As a common task in medical informatics is prediction of disease
 and its stage, these special diagnostic views, which are only enriched
 among the cohort of diseased cases, will bias machine learning disease
 predictions. In order to automate this process, here, we develop a machine
 learning pipeline that utilizes both DICOM headers and images to predict
 such views in an automatic manner, allowing for their removal and the
 generation of unbiased datasets. We achieve AUC of 99.72% in predicting
 special mammogram views when combining both types of models. Finally, we
 apply these models to clean up a dataset of about 772,000 images with
 expected sensitivity of 99.0%. The pipeline presented in this paper can be
 applied to other datasets to obtain high-quality image sets suitable to
 train algorithms for disease detection.
description: Data represents model weights as described on the Github
 page https://github.com/DSLituiev/mammoviews <pre> e5ce2d69b035975cb5336cec0da9a32a -- general image model (99 x 99 pixels) e8e71fc090141d7c6fb334359152d295 -- wire localization model (399 x 399 pixels)</pre>    
description: See https://github.com/DSLituiev/mammoviews
DOI: 10.7272/q6st7n00
title: Biphasic response of Protein Kinase A to cyclic adenosine monophosphate triggers distinct epithelial phenotypes

description: Protein Kinase A (PKA) is an important cellular signaling hub whose
 activity has long been assumed to monotonically depend on the level of
 cyclic adenosine monophosphate (cAMP). Using an optogenetic tool that can
 inject precise amounts of cAMP, we characterize instead a biphasic
 response of PKA activity to cAMP concentration in MDCKI cells in which PKA
 activity increases and then decreases as a function of cAMP. We reveal
 that this behavior results from the integration of many cellular signals
 by PKA. In addition to the direct activation of PKA, cAMP also modulates
 the activity of p38 and ERK MAPK, which then converge on PKA to inhibit
 it. These interactions and their ensuing biphasic PKA profile have
 important physiological repercussions, triggering two distinct
 transcriptional programs elicited by low and high cAMP doses. These
 transcriptional responses in turn influence the ability of MDCKI cells to
 proliferate and form acini. Our data, supported by computational analyses,
 synthesize a set of network interconnections involving PKA and other
 important signaling pathways into a model that demonstrates how cells can
 capitalize on signal integration to create a diverse set of responses to
 cAMP concentration and produce complex input-output relationships.
DOI: 10.7280/d1vh4r
title: Crystal Cove Marine Conservation Area Science Monitoring

description: Crystal Cove Conservancy operates the Crystal Cove Marine Protected Area
 Science Cruise in partnership with Newport Landing Sportfishing. 
 Under the supervision of trained Crystal Cove Conservancy staff, junior
 high school and high school students collect data on fish and plankton
 biodiversity and nearshore water quality in the Crystal Cove Marine
 Conservation Area, following protocols designed in partnership with UCI
 and other researchers. See README file for more detailed information.
 “Data made available in the OC Data Portal in partnership with UCI
 Libraries”
description: Contact Crystal Cove
 Conservancy for detailed protocols. Fish biodiversity: Used an
 underwater camera to perform a vertical transect within the kelp forest or
 rocky reef to look for presence or absence of 6 key fish species. Videos
 available upon request. Plankton biodiversity: Used 3
 plankton nets to perform a surface horizontal tow and identified presence
 or absence of 9 key species using a microscope. Water
 Quality: Used Van Dorn bottles to collect water from the surface to 14
 meters in two meter intervals. Tested for temperature, salinity and
 pH.
DOI: 10.7280/d1th5t
title: Toward low-cloud-permitting cloud superparameterization with explicit boundary layer turbulence -- simulation data

description: This data set contains the simulation outputs used in the study summarized
 below:   Systematic biases in the representation of boundary
 layer (BL) clouds are a leading source of uncertainty in climate
 projections. A variation on superparameterization (SP) called
 ‘‘ultraparameterization’’ (UP) is developed, in which the grid spacing of
 the cloud-resolving models (CRMs) is fine enough (250x20 m) to explicitly
 capture the BL turbulence, associated clouds, and entrainment in a global
 climate model capable of multiyear simulations. UP is implemented within
 the Community Atmosphere Model using 2-degree resolution (14,000 embedded
 CRMs) with one-moment microphysics. By using a small domain and mean-state
 acceleration, UP is computationally feasible today and promising for
 exascale computers. Short-duration global UP hindcasts are compared with
 SP and satellite observations of top-of-atmosphere radiation and cloud
 vertical structure. The most encouraging improvement is a deeper BL and
 more realistic vertical structure of subtropical stratocumulus (Sc)
 clouds, due to stronger vertical eddy motions that promote entrainment.
 Results from 90 day integrations show climatological errors that are
 competitive with SP, with a significant improvement in the diurnal cycle
 of offshore Sc liquid water. Ongoing concerns with the current UP
 implementation include a dim bias for near-coastal Sc that also occurs
 less prominently in SP and a bright bias over tropical continental deep
 convection zones. Nevertheless, UP makes global eddy-permitting simulation
 a feasible and interesting alternative to conventionally parameterized
 GCMs or SP-GCMs with turbulence parameterizations for studying BL
 cloud-climate and cloud-aerosol feedback.
description: All instructions and information are provided in the attached
 Readme.txt file. Please download the latest version for the full data
 set.
DOI: 10.5061/dryad.36cq8k2
title: Evaluating the performance of probabilistic algorithms for phylogenetic analysis of big morphological datasets: a simulation study

description: Reconstructing the tree of life is an essential task in evolutionary
 biology. It demands accurate phylogenetic inference for both extant and
 extinct organisms, the latter being almost entirely dependent on
 morphological data. While parsimony methods have traditionally dominated
 the field of morphological phylogenetics, a rapidly growing number of
 studies are now employing probabilistic methods (maximum likelihood and
 Bayesian inference). The present-day toolkit of probabilistic methods
 offers varied software with distinct algorithms and assumptions for
 reaching global optimality. However, benchmark performance assessments of
 different software packages for the analyses of morphological data,
 particularly in the era of big data, are still lacking. Here, we test the
 performance of four major probabilistic software under variable taxonomic
 sampling and missing data conditions: the Bayesian inference-based
 programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE
 and RAxML. We evaluated software performance by calculating the distance
 between inferred and true trees using a variety of metrics, including
 Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF)
 distances. Our results show that increased taxonomic sampling improves
 accuracy, precision, and resolution of reconstructed topologies across all
 tested probabilistic software applications and all levels of missing data.
 Under the RF metric, Bayesian inference applications were the most
 consistent, accurate, and robust to variation in taxonomic sampling in all
 tested conditions, especially at high levels of missing data, with little
 difference in performance between the two tested programs. The MS metric
 favored more resolved topologies that were generally produced by IQ-TREE.
 Adding more taxa dramatically reduced performance disparities between
 programs. Importantly, our results suggest that the RF metric penalizes
 incorrectly resolved nodes (false positives) more severely than the MS
 metric, which instead tends to penalize polytomies. If false positives are
 to be avoided in systematics, Bayesian inference should be preferred over
 maximum likelihood for the analysis of morphological data.
description: Supplementary_DataSupplementary figures and tablesSim_dataSimulated data sets used in the studyTrue_treesTrees used to generate data matricesR_scriptsR scripts used to generate trees and data sets for the study
DOI: 10.5061/dryad.sk244r4
title: Estimating phylogenies from shape and similar multidimensional data: why it is not reliable

description: In recent years, there has been controversy whether multidimensional data
 such as geometric morphometric data or information on gene expression can
 be used for estimating phylogenies. This study uses simulations of
 evolution in multidimensional phenotype spaces to address this question
 and to identify specific factors that are important for answering it. Most
 of the simulations use phylogenies with four taxa, so that there are just
 three possible unrooted trees and the effect of different combinations of
 branch lengths can be studied systematically. In a comparison of methods,
 squared-change parsimony performed similarly well as maximum likelihood,
 and both methods outperformed Wagner and Euclidean parsimony,
 neighbor-joining and UPGMA. Under an evolutionary model of isotropic
 Brownian motion, phylogeny can be estimated reliably if dimensionality is
 high, even with relatively unfavorable combinations of branch lengths. By
 contrast, if there is phenotypic integration such that most variation is
 concentrated in one or a few dimensions, the reliability of phylogenetic
 estimates is severely reduced. Evolutionary models with stabilizing
 selection also produce highly unreliable estimates, which are little
 better than picking a phylogenetic tree at random. To examine how these
 results apply to phylogenies with more than four taxa, we conducted
 further simulations with up to eight taxa, which indicated that the
 effects of dimensionality and phenotypic integration extend to more than
 four taxa, and that convergence among internal nodes may produce
 additional complications specifically for greater numbers of taxa.
 Overall, the simulations suggest that multidimensional data, under
 evolutionary models that are plausible for biological data, do not produce
 reliable estimates of phylogeny.
description: Zip file with
 Supplementary materialX Online Appendix 1 -
 Mahalanobis distances.pdf Brief description of the methods and results for
 the simulations run using Mahalanobis distances. X Online Appendix 2 -
 Tree topologies Brief description of the methods and results for the
 simulations using more than four taxa and different topologies. X R
 Scripts R Scripts used in this paper. Within that folder you can find
 another README file with a brief description of each script. X
 Supplementary Figure S1.pdf Results from the simulations exploring the
 effect of number of taxa on tree distances by using quartet distances. X
 Tables S1, S2 and S3 Results for the comparison among phylogenetic
 methods.Online
 material.zip
description: The paper contains simulations, for which R scripts are avaiable
 here.
DOI: 10.5061/dryad.1555n1k
title: Data from: Staying ahead of the game –plasticity in chorusing behavior allows males to remain attractive in different social environments

description: The dynamic nature of many breeding aggregations, where the composition
 and attractiveness of a male’s competitors is ever changing, places
 extreme pressure on advertising males to remain competitive. In response
 to this challenge, males may adjust the properties of their calls, or
 change when they signal relative to their nearest neighbors, which are
 likely their strongest competitors. We used two playback experiments - one
 simulating a conspecific environment and the other simulating a
 mixed-species environment - to test the hypothesis that males use social
 plasticity in signal features, signal timing, or both, to remain
 attractive. Further, we examined whether this plasticity is mediated by
 selective attention, through which males change calling behavior in
 response to the most relevant competitors, while disregarding less
 relevant rivals. We find that males change some temporal call features,
 but rely strongly on signal timing to remain attractive relative to
 rivals. Simultaneous assessment of both types of calling plasticity
 allowed us to makes sense of counterintuitive responses of male calling
 behavior that would otherwise appear non-adaptive. We further show that
 this plasticity is most pronounced in response to attractive/conspecific
 males. We discuss how sexual selection by female choice may influence the
 trade-off between call feature and call timing plasticity, as well as how
 competitive interactions on a local scale may affect the overall acoustic
 environment in the chorus.
description: Data for Staying ahead
 of the game -plasticity in chorusing behavior allows males to remain
 attractive in different social environmentsIncluded are 4 excel
 data sheets containing the data for the Interspecific and Intraspecific
 Male Call Plasticity and Interspecific and Intraspecific Signal Timing
 Experiments in Hyla cinerea.Data for Staying Ahead of the
 Game .xlsx
DOI: 10.5061/dryad.kb56cd1
title: Data from: Whistling shares a common tongue with speech: bioacoustics from real-time MRI of the human vocal tract

description: Most human communication is carried by modulations of the voice. However,
 a wide range of cultures has developed alternate forms of communication
 that make use of a whistled sound source. For example, whistling is used
 as a highly salient signal for capturing attention, can have iconic
 cultural meanings such as the cat-call, enact a formal code as in
 boatswain’s calls, or stand as a proxy for speech in whistled languages.
 We used real-time magnetic resonance imaging to examine the muscular
 control of whistling to describe a strong association between the shape of
 the tongue and the whistled frequency. This bioacoustic profile parallels
 the use of the tongue in vowel production. This is consistent with the
 role of whistled languages as proxies for spoken languages, in which one
 of the acoustical features of speech sounds are substituted with a
 frequency modulated whistle. Furthermore, previous evidence that non-human
 apes may be capable of learning to whistle from humans suggests that these
 animals may have similar sensorimotor abilities to those that are used to
 support speech in humans.
description: Tongue traces and
 whistled frequency dataContains subdirected for
 each of the three whistled conditions. Each subdirectory contains a
 separate comma separate files for 1) F0 sampled from the audio,
 synchronized to MR data collection and downsampled to the same resolution
 so that each row corresponds to an MR image. Frames at which f0 could not
 be determined are marked --undefined-- and should be removed from both
 audio and MR data. 2) A vector Y coordinates beginning at the tongue root,
 3) A vector a Z coordinates beginning at the tongue
 root.extracted_data.zipRaw rtMRI dataDicom format t1-weighted MRI images. Each .dcm file contains a single sagittal image that coresponds to one frame of MRI videography. Frames should be played a at a rate of 16.67Hz. Image headers were anonimised using MATLAB's dicomanaon function.raw_dicom.zipraw_dicom.zipPreprocessed audio.wav files cut to the length of each MRI scanning run. Files have been preprocessed to remove MRI noise artefacts. MB examined the files for remaining artefacts, clipping or breathy sections where f0 tracking was unreliable and forced the waveform to zero for such segments. For this analysis pipeline the effect is to remove MRI frames for that time period from further analysis.filtered_audio.zipvideoVideos of MRI data synchronized to preprocessed audio. Includes python code for constructing these videos from .dcm and .wav files.Belyk_whistle_fda_code1) Praat script for audio measurement. 2_Matlab script for tracing tongue masks. See github reference for previously release Matlab script for the creation of tongue masks. 3) R script for analysis pipeline including data import & wrangling, functional data analysis, and inference from linear mixed models.code.zip
DOI: 10.5061/dryad.r24352h
title: Data from: Telomere length is repeatable, shortens with age and reproductive success, and predicts remaining lifespan in a long-lived seabird

description: Telomeres are protective caps at the end of chromosomes, and their length
 is positively correlated with individual health and lifespan across taxa.
 Longitudinal studies have provided mixed results regarding the
 within-individual repeatability of telomere length. While some studies
 suggest telomere length to be highly dynamic and sensitive to
 resource-demanding or stressful conditions, others suggest that
 between-individual differences are mostly present from birth and
 relatively little affected by the later environment. This dichotomy could
 arise from differences between species, but also from methodological
 issues. In our study, we used the highly reliable Terminal Restriction
 Fragment analysis method to measure telomeres over a 10-year period in
 adults of a long-lived seabird, the common tern (Sterna hirundo).
 Telomeres shortened with age within individuals. The individual
 repeatability of age-dependent telomere length was high (&gt; 0.53),
 and independent of the measurement interval (i.e. 1 vs. 6 years). A small
 (R2 = 0.01), but significant part of the between-individual variation in
 telomere length was, however, explained by the number of fledglings
 produced in the previous year, while reproduction in years prior to the
 previous year had no effect. We confirmed that age-dependent telomere
 length predicted an individual’s remaining lifespan. Overall, our study
 suggests that the majority of between-individual variation in adult
 telomere length is consistent across adult life, and that a smaller part
 of the variation can be explained by dynamic factors, such as
 reproduction.
DOI: 10.5517/ccdc.csd.cc259b94
title: CCDC 2004965: Experimental Crystal Structure Determination

description: Related Article: Yuan Yang, Zhiyang Lu|2025|CSD Communication|||
description: Related Article: Yuan Yang, Zhiyang Lu|2021|Mol.Cryst.Liq.Cryst.|722|47|doi:10.1080/15421406.2020.1856616
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc259bb5
title: CCDC 2004966: Experimental Crystal Structure Determination

description: Related Article: Yuan Yang, Zhiyang Lu|2021|Mol.Cryst.Liq.Cryst.|722|47|doi:10.1080/15421406.2020.1856616
description: Related Article: Yuan Yang, Zhiyang Lu|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ghxzw
title: CCDC 2279429: Experimental Crystal Structure Determination

description: Related Article: Geethanjali N Karthammaiah |2025|CSD Communication|||
description: Related Article: Geethanjali N. Karthammaiah ,  N.S. Venkataramanan ,  K. Anand Solomon|2025|J.Mol.Struct.|1336|142056|doi:10.1016/j.molstruc.2025.142056
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.1c35112
title: Data from: Primate hippocampus size and organization are predicted by sociality but not diet

description: The hippocampus is well known for its roles in spatial navigation and
 memory, but it is organized into regions that have different connections
 and functional specializations. Notably, the region CA2 has a role in
 social cognition, and not spatial cognition as is the case for the regions
 CA1 and CA3 that surround it. Here we investigated the evolution of the
 hippocampus in terms of its size and its organization into regions in
 relation to the evolution of social and ecological variables in primates,
 namely home range, diet and different measures of group size. We found
 that the volumes within the whole cornu ammonis coevolve with group size,
 while only the volume of CA1 and subiculum can be predicted by home range
 size. On the other hand, diet, expressed as a shift from folivory toward
 frugivory, was shown to not be related to hippocampal volume.
 Interestingly, CA2 was shown to exhibit phylogenetic signal (Pagel’s λ)
 only against certain measures of group size but not with ecological
 factors. We also found that in primates sex differences in the hippocampus
 are related to body size sex dimorphism. This is in line with reports of
 sex differences in hippocampal volume in non-primates that are related to
 social structure and sex differences in behaviour.
description: Supplementary
 filesFolder data -
 phylogenetic trees and all data used, Folder PGLS results - full results
 from PGLS and ANOVA tables, dredging.txt has all models dredged with
 weights above 0.05, full model.txt includes a full model with hippocampus
 as dependent variable. Additionally included are the R code and summary
 table of the missing data.Supplementary.zip
DOI: 10.5517/ccdc.csd.cc2hc6vy
title: CCDC 2304690: Experimental Crystal Structure Determination

description: Related Article: Takahide Shimada, Takashi Kaneko, Yusuke Notsuka, Jinseok Kim, Shigeki Mori, Soji Shimizu, Jiwon Kim, Kenji Kamada, Dongho Kim, Yoshihisa Yamaoka, Hiroyuki Furuta, Masatoshi Ishida|2024|ACS Appl. Opt. Mater.|2|211|doi:10.1021/acsaom.3c00400
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hc6wz
title: CCDC 2304691: Experimental Crystal Structure Determination

description: Related Article: Takahide Shimada, Takashi Kaneko, Yusuke Notsuka, Jinseok Kim, Shigeki Mori, Soji Shimizu, Jiwon Kim, Kenji Kamada, Dongho Kim, Yoshihisa Yamaoka, Hiroyuki Furuta, Masatoshi Ishida|2024|ACS Appl. Opt. Mater.|2|211|doi:10.1021/acsaom.3c00400
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.