cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.326fv
title: Data from: Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for paleoproteomics

description: Vertebrate fossils have been collected for hundreds years and are stored
 in museum collections around the world. These remains provide a readily
 available resource to search for preserved proteins; however, the vast
 majority of paleoproteomic studies have focused on relatively recently
 collected bones with a well-known handling history. Here, we characterize
 proteins from the nasal turbinates of the first Castoroides ohioensis
 skull ever discovered. Collected in 1845, this is the oldest museum
 curated specimen characterized using paleoproteomic tools. Our mass
 spectrometry analysis detected many collagen I peptides, a peptide from
 hemoglobin beta, and in vivo and diagenetic post-translational
 modifications. Additionally, the identified collagen I sequences provide
 enough resolution to place C. ohioensis within Rodentia. This study
 illustrates the utility of archived museum specimens for both the recovery
 of preserved proteins and phylogenetic analyses.
description: Sample 2 - Injection 1
 Orbitrap-Ion TrapSample 2 - Injection
 10225014_GB_Bone-2-1_2-12.rawSample 2 - Injection 2 Orbitrap-Ion TrapSample 2 - Injection 20225014_GB_Bone-2-2_2-12.rawSample 1 - Injection 1 Orbitrap-Ion TrapSample 1 - Injection 20225014_GB_Bone-1-1_2-12.rawSample 1 - Injection 2 Orbitrap-Ion TrapSample 1 - Injection 20225014_GB_Bone-1-2_2-12.rawBuffer control 2 - Injection 1 Orbitrap Ion TrapBuffer control 2 - Injection 10225014_GB_Buff-2-1_2-12_150225122053.rawBuffer control 2 - Injection 2 Orbitrap Ion TrapBuffer control 2 - Injection 20225014_GB_Buff-2-2_2-12.rawBuffer control 1 - Injection 1 Orbitrap Ion TrapBuffer control 1 - Injection 10225014_GB_Buff-1-1_2-12.rawBuffer control 1 - Injection 2 Orbitrap Ion TrapBuffer control 1 - Injection 20225014_GB_Buff-1-2_2-12.rawPEAKS exports - Sample 1, Sample 2, Buffer control 1, Buffer control 2CSV exports (peptide lists, protein lists, etc.) from PEAKS searching.PEAKS exports.zipFasta of Castoroides ohioensis collagenAligned fasta file of Castoroides ohioensis collagen I alpha 1 and alpha 2castoroides collagen I.fasta
DOI: 10.5061/dryad.j4f19
title: Data from: Using decision trees to understand structure in missing data

description: Objectives: Demonstrate the application of decision trees—classification
 and regression trees (CARTs), and their cousins, boosted regression trees
 (BRTs)—to understand structure in missing data. Setting: Data taken from
 employees at 3 different industrial sites in Australia. Participants: 7915
 observations were included. Materials and methods: The approach was
 evaluated using an occupational health data set comprising results of
 questionnaires, medical tests and environmental monitoring. Statistical
 methods included standard statistical tests and the ‘rpart’ and ‘gbm’
 packages for CART and BRT analyses, respectively, from the statistical
 software ‘R’. A simulation study was conducted to explore the capability
 of decision tree models in describing data with missingness artificially
 introduced. Results: CART and BRT models were effective in highlighting a
 missingness structure in the data, related to the type of data (medical or
 environmental), the site in which it was collected, the number of visits,
 and the presence of extreme values. The simulation study revealed that
 CART models were able to identify variables and values responsible for
 inducing missingness. There was greater variation in variable importance
 for unstructured as compared to structured missingness. Discussion: Both
 CART and BRT models were effective in describing structural missingness in
 data. CART models may be preferred over BRT models for exploratory
 analysis of missing data, and selecting variables important for predicting
 missingness. BRT models can show how values of other variables influence
 missingness, which may prove useful for researchers. Conclusions:
 Researchers are encouraged to use CART and BRT models to explore and
 understand missing data.
description: Repository for Using
 Decision Trees to Understand Structure in Missing DataIn this datafile we have
 a compressed file that contains almost everything you need to entirely
 recreate the figure. For instructions as to how to do this, please see the
 README.Understanding_Missing_Data_Decision_Trees.zip
DOI: 10.5061/dryad.51s8h
title: Data from: Diffusion tensor imaging of dolphin brains reveals direct auditory pathway to temporal lobe

description: The brains of odontocetes (toothed whales) look grossly different from
 their terrestrial relatives. Because of their adaptation to the aquatic
 environment and their reliance on echolocation, the odontocetes'
 auditory system is both unique and crucial to their survival. Yet, scant
 data exist about the functional organization of the cetacean auditory
 system. A predominant hypothesis is that the primary auditory cortex lies
 in the suprasylvian gyrus along the vertex of the hemispheres, with this
 position induced by expansion of ‘associative′ regions in lateral and
 caudal directions. However, the precise location of the auditory cortex
 and its connections are still unknown. Here, we used a novel diffusion
 tensor imaging (DTI) sequence in archival post-mortem brains of a common
 dolphin (Delphinus delphis) and a pantropical dolphin (Stenella attenuata)
 to map their sensory and motor systems. Using thalamic parcellation based
 on traditionally defined regions for the primary visual (V1) and auditory
 cortex (A1), we found distinct regions of the thalamus connected to V1 and
 A1. But in addition to suprasylvian-A1, we report here, for the first
 time, the auditory cortex also exists in the temporal lobe, in a region
 near cetacean-A2 and possibly analogous to the primary auditory cortex in
 related terrestrial mammals (Artiodactyla). Using probabilistic tract
 tracing, we found a direct pathway from the inferior colliculus to the
 medial geniculate nucleus to the temporal lobe near the sylvian fissure.
 Our results demonstrate the feasibility of post-mortem DTI in archival
 specimens to answer basic questions in comparative neurobiology in a way
 that has not previously been possible and shows a link between the
 cetacean auditory system and those of terrestrial mammals. Given that
 fresh cetacean specimens are relatively rare, the ability to measure
 connectivity in archival specimens opens up a plethora of possibilities
 for investigating neuroanatomy in cetaceans and other species.
description: DelphinusDiffusion files output from FSL bedpostX necessary for tractography. Also includes average structural image (trufi...) and B0 image as well as transform from B0 space to structural space.StenellaDiffusion files output from FSL bedpostX necessary for tractography. Also includes structural image (trufi...) and B0 image.
DOI: 10.5061/dryad.4g1h2
title: Data from: Multi-scale quantification of tissue behavior during amniote embryo axis elongation

description: Embryonic axis elongation is a complex multi-tissue morphogenetic process
 responsible for the formation of the posterior part of the amniote body.
 How movements and growth are coordinated between the different posterior
 tissues (e.g. neural tube, axial and paraxial mesoderm, lateral plate,
 ectoderm, endoderm) to drive axis morphogenesis remain largely unknown.
 Here, we use quail embryos to quantify cell behavior and tissue movements
 during elongation. We quantify the tissue-specific contribution to axis
 elongation by using 3D volumetric techniques, then quantify
 tissue-specific parameters such as cell density and proliferation. To
 study cell behavior at a multi-tissue scale we used high-resolution 4D
 imaging of transgenic quail embryos expressing fluorescent proteins. We
 developed specific tracking and image analysis techniques to analyze cell
 motion and compute tissue deformations in 4D. This analysis reveals
 extensive sliding between tissues during axis extension. Further
 quantification of tissue tectonics showed patterns of rotations,
 contractions and expansions, which are coherent with the multi-tissue
 behavior observed previously. Our approach defines a quantitative and
 multiscale method to analyze the coordination between tissue behaviors
 during early vertebrate embryo morphogenetic events.
description: HH10 PGK1:H2B-chFP Tiled
 Z Stack 20x.lsm. time lapse ventral viewtime lapse of a stage
 HH10 PGK1:H2B-chFP embryo ventral view 20x objective on a Zeiss 780
 confocal microscope and Zen 2011 black edition 64 bit software.Fig 5 and
 Fig 6stage
 10 ventral view.lsmHH10 PGK1:H2B-chFP Tiled
 Z Stack 20x.lsm. time lapse dorsal viewtime lapse Dorsal view
 of a HH11PGK1:H2B-chFP embryo using a 20x objective on a Zeiss 780
 confocal microscope and Zen 2011 black edition 64 bit software.Fig 5 and
 Fig 6stage
 10 dorsal view.lsm
DOI: 10.5061/dryad.8171kv1
title: Data from: Microbial-tubeworm associations in a 440 million year old hydrothermal vent community

description: Microorganisms are the chief primary producers within present-day deep-sea
 hydrothermal vent ecosystems, and play a fundamental role in shaping the
 ecology of these environments. However, very little is known about the
 microbes that occurred within, and structured ancient vent communities.
 The evolutionary history, diversity, and the nature of interactions
 between ancient vent microorganisms and hydrothermal vent animals are
 largely undetermined. The oldest known hydrothermal vent community that
 includes metazoans is preserved within the Ordovician-early Silurian Yaman
 Kasy massive sulphide deposit, Ural Mountains, Russia. This deposit
 contains two types of tube fossil attributed to annelid worms. A
 re-examination of these fossils using a range of microscopy, chemical
 analysis and nano-tomography techniques reveals the preservation of
 filamentous microorganisms intimately associated with the tubes. The
 microfossils bear a strong resemblance to modern hydrothermal vent
 microbial filaments, including those preserved within the mineralised
 tubes of the extant vent polychaete genus Alvinella. The Yaman Kasy fossil
 filaments represent the oldest animal-microbial associations preserved
 within an ancient hydrothermal vent environment. They allude to a diverse
 microbial community, and also demonstrate that remarkable fine-scale
 microbial preservation can also be observed in ancient vent deposits,
 suggesting the possible existence of similar exceptionally-preserved
 microfossils in even older vent environments.
description: FIB-SEM image stack of
 microfossils associated with fossil Yamankasia rifeia tubes, part
 120180519_fib_data_part1_aligned.tifFIB-SEM image stack of microfossils associated with fossil Yamankasia rifeia tubes, part 220180519_fib_data_part2_aligned.tifFIB-SEM image stack of microfossils associated with mineralized Alvinella spp. tubes20171214_fib_data_aligned.tif
DOI: 10.5061/dryad.k5r31
title: Data from: How obstacles perturb population fronts and alter their genetic structure

description: As populations spread into new territory, environmental heterogeneities
 can shape the population front and genetic composition. We focus here on
 the effects of an important building block of heterogeneous environments,
 isolated obstacles. With a combination of experiments, theory, and
 simulation, we show how isolated obstacles both create long-lived
 distortions of the front shape and amplify the effect of genetic drift. A
 system of bacteriophage T7 spreading on a spatially heterogeneous
 Escherichia coli lawn serves as an experimental model system to study
 population expansions. Using an inkjet printer, we create well-defined
 replicates of the lawn and quantitatively study the population expansion
 of phage T7. The transient perturbations of the population front found in
 the experiments are well described by a model in which the front moves
 with constant speed. Independent of the precise details of the expansion,
 we show that obstacles create a kink in the front that persists over large
 distances and is insensitive to the details of the obstacle’s shape. The
 small deviations between experimental findings and the predictions of the
 constant speed model can be understood with a more general
 reaction-diffusion model, which reduces to the constant speed model when
 the obstacle size is large compared to the front width. Using this
 framework, we demonstrate that frontier genotypes just grazing the side of
 an isolated obstacle increase in abundance, a phenomenon we call
 ‘geometry-enhanced genetic drift’, complementary to the founder effect
 associated with spatial bottlenecks. Bacterial range expansions around
 nutrient-poor barriers and stochastic simulations confirm this prediction.
 The effect of the obstacle on the genealogy of individuals at the front is
 characterized by simulations and rationalized using the constant speed
 model. Lastly, we consider the effect of two obstacles on front shape and
 genetic composition of the population illuminating the effects expected
 from complex environments with many obstacles.
description: raw data: plaque growth
 around obstacles of defined size and shapesee ReadMe
 filePlaqueGrowthObstaclesDefinedSizeShape.zipraw data: plaque growth in randomly structured heterogeneous environmentssee ReadMe filePlaqueGrowthRandomlyStructuredEnvironment.zipraw data: spatial expansion of E. coli around regions with poor nutrient conditionssee ReadMe fileSpatialExpansionEcoli.zip
DOI: 10.5061/dryad.7jn61
title: Data from: Distinct copulation positions in Drosophila pachea males with symmetric or asymmetric external genitalia

description: Left-right asymmetric genitalia have appeared multiple times independently
 in insects and have been associated with changes in mating positions.
 However, there is little experimental data on how the evolution of genital
 asymmetries may have affected the evolution of mating positions or vice
 versa. As opposed to its closely-related species, Drosophila pachea has a
 conspicuous asymmetry in its male genitalia external lobes, with the left
 lobe being 1.49 ± 0.08 (SD) times longer and thinner than the right lobe.
 In a laboratory stock, we found that 20% of the males possess fully
 symmetric lobes. To better understand how asymmetric genitalia may affect
 mating, we compared D. pachea copulation behaviour between these mutant
 males and wild-type males. We found that D. pachea wild-type males adopt a
 one-sided mating posture with the male always one-sided 8.55° ± 1.79° (SD)
 towards the female’s right side. Within 45-min recordings, all wild-type
 males did mate whereas 39% of symmetric mutants failed to form a stable
 mating complex and did not mate. In successful copulations, symmetric
 mutants also adopted a right-sided mating posture but the angle between
 male and female bodies was significantly more variable compared to
 wild-type males. Our results suggest that lobe size asymmetry is required
 for the formation of a stable mating complex and for the positioning of
 the male according to a precise angle on the female. However, lobe size
 asymmetry is not required for D. pachea right-sided mating posture.
description: Movies and Genitalia
 imagesThese are movies of
 Drosophila pachea copulations and images of the male genital arch of each
 male presented in the article. In addition, a spreadsheet is provided to
 summarize each mating experiment and the sizes of the epandrial lobes. The
 md5sum of CTOZ-data.tar.gz is:
 85125a8fb835c2b7fc4a714f249f077fCTOZ-data.tar.gz
DOI: 10.5281/zenodo.18385916
title: EMSP - Efekt Mikro-Sprzężenia Pionowego: Mechanizm mikroekstremów w atmosferze

description: Efekt Mikro - Sprzężenia Pionowego (EMSP) opisuje mechanizm, w którym minimalne bodźce pionowe w górnej atmosferze - takie jak jonizacja, pionowe fale grawitacyjne i impulsy elektromagnetyczne - mogą zostać wzmocnione przez lokalne warunki w dolnej atmosferze (wilgotność, aerozole, mikroklimaty) i prowadzić do powstania mikroekstremów pogodowych.

Mechanizm EMSP tłumaczy nagłe, lokalne zmiany wyżów i niżów, które nie są przewidywalne przy użyciu standardowych modeli meteorologicznych. Dzięki zastosowaniu EMSP w obserwacjach i modelowaniu można w przyszłości uzyskać:

możliwość wcześniejszego wykrycia potencjalnych mikroekstremów,

oszacowanie prawdopodobieństwa wzmocnienia intensywności ekstremu pogodowego (np. wstępne szacowanie: 80%),

lepszą interpretację danych pionowych i lokalnych, pozwalającą zidentyfikować sytuacje, w których nagłe zmiany pogodowe są możliwe.

Koszty badań i weryfikacji efektu EMSP są relatywnie niskie w porównaniu z potencjalnymi stratami wynikającymi z nagłych i nieprzewidywalnych mikroekstremów pogodowych, które mogą wpływać na lokalne niższe i wyższe układy atmosferyczne. Dzięki wczesnej detekcji i zrozumieniu EMSP możliwe jest przewidywanie wzmocnienia ekstremalnych zjawisk pogodowych, co pozwala ograniczyć ryzyko i straty ekonomiczne, społeczne oraz środowiskowe.
DOI: 10.5281/zenodo.18385917
title: EMSP - Efekt Mikro-Sprzężenia Pionowego: Mechanizm mikroekstremów w atmosferze

description: Efekt Mikro - Sprzężenia Pionowego (EMSP) opisuje mechanizm, w którym minimalne bodźce pionowe w górnej atmosferze - takie jak jonizacja, pionowe fale grawitacyjne i impulsy elektromagnetyczne - mogą zostać wzmocnione przez lokalne warunki w dolnej atmosferze (wilgotność, aerozole, mikroklimaty) i prowadzić do powstania mikroekstremów pogodowych.

Mechanizm EMSP tłumaczy nagłe, lokalne zmiany wyżów i niżów, które nie są przewidywalne przy użyciu standardowych modeli meteorologicznych. Dzięki zastosowaniu EMSP w obserwacjach i modelowaniu można w przyszłości uzyskać:

możliwość wcześniejszego wykrycia potencjalnych mikroekstremów,

oszacowanie prawdopodobieństwa wzmocnienia intensywności ekstremu pogodowego (np. wstępne szacowanie: 80%),

lepszą interpretację danych pionowych i lokalnych, pozwalającą zidentyfikować sytuacje, w których nagłe zmiany pogodowe są możliwe.

Koszty badań i weryfikacji efektu EMSP są relatywnie niskie w porównaniu z potencjalnymi stratami wynikającymi z nagłych i nieprzewidywalnych mikroekstremów pogodowych, które mogą wpływać na lokalne niższe i wyższe układy atmosferyczne. Dzięki wczesnej detekcji i zrozumieniu EMSP możliwe jest przewidywanie wzmocnienia ekstremalnych zjawisk pogodowych, co pozwala ograniczyć ryzyko i straty ekonomiczne, społeczne oraz środowiskowe.
DOI: 10.5061/dryad.9ng87
title: Data from: Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

description: The functional basis for species sorting theory remains elusive,
 especially for microbial community assembly in deep-sea environments.
 Using artificial surface-based biofilm models, our recent work revealed
 taxonomic succession during biofilm development in a newly defined cold
 seep system, the Thuwal cold seeps II, which comprises a brine pool and
 the adjacent normal bottom water (NBW) to form a metacommunity via the
 potential immigration of organisms from one patch to another. Here, we
 designed an experiment to investigate the effects of environmental
 switching between the brine pool and the NBW on biofilm assembly, which
 could reflect environmental filtering effects during bacterial immigration
 to new environments. Analyses of 16S rRNA genes of 71 biofilm samples
 suggested that the microbial composition of biofilms established in new
 environments was determined by both the source community and the
 incubation conditions. Moreover, a comparison of 18 metagenomes provided
 evidence for biofilm community assembly that was based primarily on
 functional features rather than taxonomic identities; metal ion resistance
 and amino acid metabolism were the major species sorting determinants for
 the succession of biofilm communities. Genome binning and pathway
 reconstruction of two bacterial species (Marinobacter sp. and Oleispira
 sp.) further demonstrated metal ion resistance and amino acid metabolism
 as functional traits conferring the survival of habitat generalists in
 both the brine pool and NBW. The results of this study shed new light on
 microbial community assembly in special habitats and bridge a gap in
 species sorting theory.
description: assemblymetagenome assemblyCOG annotationCOG annotationCOGannotation.txtMarinobacter_spgenome binOleispira_spgenome binRESULTS&DATA16s simper data and results, comparative metagenome data and results, cell density, rt-pcr resultsseqs_otus16s OTU tableseqs_rep_set_alignedseqs_switch16s 454 datatreetree_alignS-brine-Al_1.fqS-brine-Al_2.fqS-brine-PVC_1.fqS-brine-PVC_2.fqS-brine-T_1.fqS-brine-T_2.fqSNBW-Al_1.fqSNBWAL_2.fqSNBW-T_SZAIPI032904-22_1.fqSNBW-T_SZAIPI032904-22_2.fq
DOI: 10.5061/dryad.mn0tv
title: Data from: Identifying consistent allele frequency differences in studies of stratified populations

description: 1. With increasing application of pooled-sequencing approaches to
 population genomics robust methods are needed to accurately quantify
 allele frequency differences between populations. Identifying consistent
 differences across stratified populations can allow us to detect genomic
 regions under selection and that differ between populations with different
 histories or attributes. Current popular statistical tests are easily
 implemented in widely available software tools which make them simple for
 researchers to apply. However, there are potential problems with the way
 such tests are used ,which means that underlying assumptions about the
 data are frequently violated. 2. These problems are highlighted by
 simulation of simple but realistic population genetic models of neutral
 evolution and the performance of different tests are assessed. We present
 alternative tests (including GLMs with quasibinomial error structure) with
 attractive properties for the analysis of allele frequency differences and
 re-analyse a published dataset. 3. The simulations show that common
 statistical tests for consistent allele frequency differences perform
 poorly, with high false positive rates. Applying tests that do not
 confound heterogeneity and main effects significantly improves inference.
 Variation in sequencing coverage likely produces many false positives and
 re-scaling allele frequencies to counts out of a common value or an
 effective sample size reduces this effect. 4. Many researchers are
 interested in identifying allele frequencies that vary consistently across
 replicates to identify loci underlying phenotypic responses to selection
 or natural variation in phenotypes. Popular methods that have been
 suggested for this task perform poorly in simulations. Overall,
 quasibinomial GLMs perform better and also have the attractive feature of
 allowing correction for multiple testing by standard procedures and are
 easily extended to other designs.
description: Summary
 DataThis archive contains
 summarised tables of data from simulation output.summary_data.tar.gzRaw data 1This archive contains raw simulation data.rawdata_fst0.1.tar.gzRaw data 2This archive contains raw simulation datarawdata_fst0.2.tar.gzRaw data 3This archive contains raw simulation datarawdata_fst0.3.tar.gz