cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80gb5mksp
title: Telecentric bright-field transmitted light microscopic dataset

description: Living cell segmentation from bright-field light microscopic images is
 challenging due to the image complexity and temporal changes in the living
 cells. Recently developed deep learning (DL)-based methods became popular
 in medical and microscopic image segmentation tasks due to their success
 and promising outcomes. The main objective of this paper is to develop a
 deep learning, UNet-based method to segment the living cells of the HeLa
 line in bright-field transmitted light microscopy. To find the most
 suitable architecture for our datasets, we have proposed a residual
 attention U-Net and compared it with an attention and a simple U-Net
 architecture. The attention mechanism highlights the remarkable features
 and suppresses activations in the irrelevant image regions. The residual
 mechanism overcomes with vanishing gradient problem. The Mean-IoU score
 for our datasets reaches 0.9505, 0.9524, and 0.9530 for the simple,
 attention, and residual attention U-Net, respectively. We achieved the
 most accurate semantic segmentation results in the Mean-IoU and Dice
 metrics by applying the residual and attention mechanisms together. The
 watershed method applied to this best – Residual Attention – semantic
 segmentation result gave the segmentation with the specific information
 for each cell.
description: Human HeLa cell line was growing to low optical density overnight
 at 37◦ C,  5% CO2, and 90% RH. The nutrient solution consisted of DMEM
 (87.7%) with high glucose (&gt;1 g L−1 ), fetal bovine serum (10%),
 antibiotics and antimycotics  (1%), L-glutamine (1%), and gentamicin
 (0.3%; all purchased from Biowest, Nu aille, France). The HeLa cells were
 maintained in a Petri dish with a cover glass bottom and lid at room
 temperature of 37◦ C when we were running experiments during data
 collection phase in different time laps experiments. We captured
 time-lapse image series of living human HeLa cells using a high resolved
 bright-field light microscope for observation of sub-microscopic objects
 and cells. This microscope was designed by the Institute of Complex System
 (ICS, Nov´e Hrady, Czech Republic) and built by Optax (Prague, Czech
 Republic) and ImageCode (Brloh, Czech Republic) in 2021. The microscope
 has a simple construction of the optical path. The light from two
 light-emitting diods CL-41 (Optika Microscopes, Ponteranica, Italy) was
 passing through a sample to reach a telecentric measurement objective
 TO4.5/43.4-48-F-WN (Vision & Control GmbH, Shul, Germany) and an
 Arducam AR1820HS 1/2.3-inch 10-bit RGB camera with a chip of 4912×3684
 pixel resolution. The images were captured as a primary (raw) signal with
 theoretical pixel size (size of the object projected onto the camera
 pixel) of 113 nm. The software (developed by the ICS) controls to capture
 the primary signal with the camera exposure of 2.75 ms. All the
 experiments we performed in time-lapse to observe cells’ behaviour over
 time.
DOI: 10.5061/dryad.fxpnvx0tt
title: Exposure to lysed bacteria can promote or inhibit growth of neighboring live bacteria depending on local abiotic conditions

description: Abstract Microbial death is extremely common in nature, yet the ecological
 role of dead bacteria is unclear. Dead cells are assumed to provide
 nutrients to surrounding microbes, but may also affect them in other ways.
 We found that adding lysate prepared from dead bacteria to cultures of
 Escherichia coli in nutrient-rich conditions suppressed their final
 population density. This is in stark contrast with the notion that the
 primary role of dead cells is nutritional, although we also observed this
 type of effect when we added dead bacteria to cultures that were not
 supplied with other nutrients. We only observed the growth-suppressive
 effect of our dead-bacteria treatment after they had undergone significant
 lysis, suggesting a key role for cellular contents released during lysis.
 Transcriptomic analysis indicated changes in gene expression in response
 to dead cells in growing populations, particularly in genes involved in
 motility. This was supported by experiments with genetic knockouts and
 copy-number manipulation. Because lysis is commonplace in natural and
 clinical settings, the growth-suppressive effect of dead cells we describe
 here may be a widespread and previously unrecognized constraint on
 bacterial population growth.
DOI: 10.5061/dryad.8931zcrsm
title: The timing of spring warming shapes reproductive effort in a warm-water fish: the role of mismatches between hepatic and gonadal processes

description: Spring-spawning fishes native to northern environments rely on both
 increasing temperature and lengthening photoperiod to cue reproduction and
 may thus be particularly sensitive to rapid warming earlier in the year
 while day lengths remain short. We investigated the reproductive response
 of pumpkinseed sunfish Lepomis gibbosus to spring warming commencing at a
 range of day lengths (9 – 15 hours), corresponding to various calendar
 days (January 10 – May 22). In both the laboratory and field, both male
 and female fish that experienced early warming while day lengths were
 &lt;11 hours: 1) failed to initiate reproductive preparation in the
 liver before gonad development began, and 2) had reduced reproductive
 allocation. Analysis of published data on temperate fishes suggested that
 liver development prior to gonad development is widespread across warm-,
 cool-, and cold-water thermal guilds, though the precise phenology of
 liver relative to gonad development appears to vary widely among species.
 Together, our results point toward dampened reproductive preparation as a
 novel mechanism mediating reduced reproductive output in both warm- and
 cool-water fish following earlier spring warming.
description: Data were collected from lethal samples of pumpkinseed either
 from laboratory experiments or field collections. All measurements were
 collected within 4 hours of fish euthanization. All euthanized fish were
 kept on ice and collected with appropriate animal care protocol approvals
 and animal collections permits (see manuscript for more information). The
 attached data file includes unprocessed raw data (organ and fish masses).
 Indices followed by a "1" (GSI1 = GSI; LSI1 = HSI) were
 calculated as indicated in the manuscript. Indices without a "1"
 were calculated without removing the mass of the indexed organ from fish
 wet weight (e.g., LSI = HSI = WETLIVWT / WETBODWT*100).
description: Organ masses (WETGONWT: gonad; WETLIVWT: liver) were recorded in
 milligrams and whole fish body masses are in grams. Male fish are coded as
 "1" and females are coded as "2." Fish length was
 recorded as fork length in millimetres. Ash weight and water content were
 inconsistently recorded so there are missing values throughout these
 columns. EXPTCD 11-17 contain data for experimental spring warming
 treatments, and EXPTCD 92-93 contain data for field collections. Other
 EXPTCD's were used to generate the figures in the Appendix and Figure
 S2 in the Supplementary Material, including data from fish held in large
 tanks over the course of the project (see README_DataDictionary). Please
 do not hesitate to reach out to the corresponding author if you have any
 questions!
DOI: 10.5061/dryad.prr4xgxp4
title: Data from: A peirosaurid mandible from the Albian (Lower Cretaceous) of Algeria and the taxonomic content of Hamadasuchus (Crocodylomorpha, Peirosauridae)

description: Peirosaurids form an extinct clade of terrestrial crocodylomorphs known
 from the Cretaceous of Africa and South America. Here, we describe a new
 mandibular ramus attributable to Hamadasuchus cf. rebouli from the
 Albian/Cenomanian of La Gara Samani (Algeria). We propose an emended
 diagnosis for this taxon, originally described from a left dentary
 fragment from the Kem Kem beds of Morocco and discuss the assignation of
 the specimens currently referred to it. Using ontogenetic series of extant
 crocodylians, we show that several mandibular characters commonly used to
 differentiate between close taxa instead record intraspecific or
 ontogenetic variability. On the other hand, reliable mandibular characters
 allow us to propose that the current taxonomic content of Hamadasuchus
 rebouli should be reduced to three specimens, pending future description
 of relatable cranial remains that will confirm or not this hypothesis.
 Finally, we demonstrate the importance of mandibular characters in
 phylogenies, by recovering the new specimen from La Gara Samani as closely
 related to North African peirosaurids on the basis of a data matrix
 designed solely on mandibular characters.
DOI: 10.17026/ar/vxnlgs
title: Inventariserend veldonderzoek - verkennende fase Meirseweg 10-B te Zundert, gemeente Zundert (NB) Inventariserend veldonderzoek - verkennende fase Meirseweg 10-B te Zundert, gemeente Zundert (NB)

description: &lt;p&gt;Laagland Archeologie heeft in januari 2025 een Inventariserend veldonderzoek - verkennende fase uitgevoerd aan de Meirseweg 10-B te Zundert. Het onderzoek vond plaats in verband met de ruimtelijke procedure rondom de nieuwbouw van een woning.&lt;br&gt;Het onderzoek is uitgevoerd conform de protocollen SIKB KNA 4003.&lt;br&gt;Het bureauonderzoek had tot doel een archeologisch verwachtingsmodel op te stellen.&lt;br&gt;Centraal staat daarbij de vraag of en zo ja welke archeologische resten (complextype, datering, diepteligging en gaafheid) in het plangebied kunnen worden verwacht. Hiertoe zijn landschappelijke, archeologische en historische bronnen geraadpleegd.&lt;br&gt;Op basis van het bureauonderzoek geldt voor het plangebied een hoge archeologische verwachting voor resten uit de periode Laat-Paleolithicum-Vroege Middeleeuwen en een hoge archeologische waarde voor resten uit de periode Late Middeleeuwen-Nieuwe Tijd.&lt;br&gt;Het plangebied ligt in vergelijking met het beekdal van de Aa of Weerijs circa 200 m ten westen hoger in het landschap op waarschijnlijk een terrasafzettingswelving. De relatief hoge ligging van het gebied nabij open water heeft waarschijnlijk voor gunstige bewoningsomstandigheden gezorgd vanaf het Laat-Paleolithicum.&lt;br&gt;Het uitgevoerde verkennende booronderzoek heeft tot doel het verwachtingsmodel te toetsen en zo nodig aan te vullen. Hiertoe zijn verspreid over het toegankelijke deel van het plangebied verkennende boringen gezet. In dit stadium is verkennend booronderzoek de meest efficiënte onderzoekswijze om de archeologische potentie van het plangebied in kaart te brengen.&lt;br&gt;Op basis van het uitgevoerde booronderzoek is de kans klein dat het plangebied archeologische sporen bevat. Zowel de (grotendeels verstoorde) humeuze bovengrond en (niet verstoorde ondergrond) zijn nat (de humeuze bovengrond onderin) en roesthoudend. De ondiepe ondergrond is lemig en veroorzaakt waterstagnatie. Verder was zover bekend er geen bebouwing aanwezig voor 1969. Voor de bouw van het huis in 1969 toen het terrein heel waarschijnlijk is opgehoogd om het terrein geschikt te maken, was het plangebied waarschijnlijk niet favoriet als plek voor bewoning.&lt;br&gt;Om deze reden adviseren we geen vervolgonderzoek uit te voeren en het plangebied vrij te geven.&lt;br&gt;De implementatie van dit advies is in handen van de gemeente Zundert, hierin vertegenwoordigd door de archeologisch adviseur van de gemeente, de Regioarcheologen Regio West-Brabant.&lt;br&gt;Mochten bij graafwerkzaamheden onverhoopt toch archeologische resten worden aangetroffen, dan geldt conform de Erfgoedwet (art. 5.10) een meldingsplicht. Dit kan bij Rijksdienst voor het Cultureel Erfgoed (033 421 74 56) of via de website: www.cultureelerfgoed.nl/contact.&lt;/p&gt;
DOI: 10.5061/dryad.573n5tb9c
title: The knock-down of the chloroquine resistance transporter PfCRT is linked to oligopeptide handling in Plasmodium falciparum

description: The chloroquine resistance transporter, PfCRT, is an essential factor
 during intraerythrocytic development of the human malaria parasite
 Plasmodium falciparum. PfCRT resides at the digestive vacuole of the
 parasite, where hemoglobin taken up by the parasite from its host cell is
 degraded. PfCRT can acquire several mutations that render PfCRT a drug
 transporting system expelling compounds targeting hemoglobin degradation
 from the digestive vacuole. The non-drug related function of PfCRT is less
 clear, although a recent study has suggested a role in oligopeptide
 transport based on studies conducted in a heterologous expression system.
 The uncertainty about the natural function of PfCRT is partly due to a
 lack of a null mutant and a dearth of functional assays in the parasite.
 Here, we report on the generation of a conditional PfCRT knock-down mutant
 in P. falciparum. The mutant accumulated oligopeptides 2 to at least 8
 residues in length under knock-down conditions, as shown by comparative
 global metabolomics. The accumulated oligopeptides were structurally
 diverse, had an isoelectric point between 4.0 and 5.4 and were
 electrically neutral or carried a single charge at the digestive vacuolar
 pH of 5.2. Fluorescently-labeled dipeptides and live cell imaging
 identified the digestive vacuole as the compartment where oligopeptides
 accumulated. Our findings suggest a function of PfCRT in oligopeptide
 transport across the digestive vacuolar membrane in P. falciparum and
 associated with it a role in nutrient acquisition and the maintenance of
 the colloid osmotic balance.
description: This file contains the data underpining the article by Sanchez et
 al. 2022 (Microbiology Spectrum).
DOI: 10.5061/dryad.8w9ghx3pf
title: A mechanistic model of functional response provides new insights into indirect interactions among arctic tundra prey

description: Prey handling processes are considered a dominant mechanism leading to
 short-term positive indirect effects between prey that share a predator.
 However, a growing body of research indicates that predators are not
 necessarily limited by such processes in the wild. Density-dependent
 changes in predator foraging behavior can also generate positive indirect
 effects but they are rarely included as explicit functions of prey
 densities in functional response models. With the aim of untangling
 proximate mechanisms of species interactions in natural communities and
 improving our ability to quantify interaction strength, we extended the
 multi-prey version of the Holling disk equation by including
 density-dependent changes in predator foraging behavior. Our model, based
 on species traits and behavior, was inspired by the vertebrate community
 of the arctic tundra, where the main predator (the arctic fox) is an
 active forager feeding primarily on cyclic small rodent (lemming) and eggs
 of various tundra-nesting bird species. Short-term positive indirect
 effects of lemmings on birds have been documented over the circumpolar
 Arctic but the underlying mechanisms remain poorly understood. We used a
 unique data set, containing high-frequency GPS tracking, accelerometer,
 behavioral, and experimental data to parameterize the multi-prey model,
 and a 15-year time series of prey densities and bird nesting success to
 evaluate interaction strength between species. We found that: (i) prey
 handling processes play a minor role in our system and (ii) changes in
 arctic fox daily activity budget and distance traveled can partly explain
 the predation release on birds observed during lemming peaks. These
 adjustments in predator foraging behavior with respect to the main prey
 density thus appear as the dominant mechanism leading to positive indirect
 effects commonly reported among arctic tundra prey. Density-dependent
 changes in functional response components have been little studied in
 natural vertebrate communities and deserve more attention to improve our
 ability to quantify the strength of species interactions.
description: The datasets (fox_daily_activity and
 LPS_Densities_NestingSuccess) provided here contain raw data used in the
 models presented in the article "A mechanistic model of functional
 response provides new insights into indirect interactions among arctic
 tundra prey". Refer to the article for more details on each analysis.
 Arctic fox GPS data are available through the Movebank Data Repository at
 Berteaux, D. 2020, Arctic fox Bylot-GPS tracking, Movebank Study ID
 1241071371.
description: The README
 file contains column descriptions. General information for the analyses is
 presented in the article as well as equations and parameter
 values.
DOI: 10.5061/dryad.xgxd254jc
title: Genetic diversity and lifespan of transplanted colonies

description: Selection may favour traits throughout an individuals lifetime or at a
 particular life stage. In many species of social insects, established
 colonies that are more genetically diverse outperform less diverse
 colonies with respect to a variety of traits that contribute to fitness,
 but whether selection favours high diversity in small colonies is unknown.
 We tested the hypothesis that selection favours genetically diverse
 colonies during the juvenile period using a multi-year field experiment
 with the harvester ant, Pogonomyrmex occidentalis. We used controlled
 matings to generate colonies that varied in genetic diversity and
 transplanted them into the field. We monitored their survival for seven
 (the 2015 cohort, N = 149) and six (the 2016 cohort, N = 157) years.
 Genetically more diverse colonies had greater survival, resulting in
 significant viability selection. However, in both cohorts survival was not
 influenced by genetic diversity until colonies were three years old. We
 suggest that changes in their internal organization enabled colonies to
 use the benefits of multiple genotypes, and discuss possible mechanisms
 that can generate this pattern. The accompanying data give the number of
 patrilines, the date of transplant and the number of years that the colony
 survived.  
description: Colonies were constructed using directed matings and transplanted
 over two years (2015-2016).  We monitored colonies for survival to
 establish longevity.  Colonies could survive for a maximum or 7 years (the
 2015 cohort) or 6 years (the 2016 transplant cohort).  A sample of 24
 workers was genotyped to establish the number of times that the queen
 mated.  
description: There is a README file for the dataset.
DOI: 10.5281/zenodo.18399936
title: Dataset 2 for paper "First-principles guidelines to select promising van der Waals materials for hybrid photovoltaic-triboelectric nanogenerators" (https://doi.org/10.1039/D4NR02217C)
DOI: 10.5281/zenodo.18399937
title: Dataset 2 for paper "First-principles guidelines to select promising van der Waals materials for hybrid photovoltaic-triboelectric nanogenerators" (https://doi.org/10.1039/D4NR02217C)
DOI: 10.5061/dryad.sj3tx966v
title: Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris Sea Urchins

description: Changes in developmental gene regulatory networks (dGRNs) underlie much of
 the diversity of life, but the evolutionary mechanisms that operate on
 interactions with these networks remain poorly understood. Closely related
 species with extreme phenotypic divergence provide a valuable window into
 the genetic and molecular basis for changes in dGRNs and their
 relationship to adaptive changes in organismal traits. Here we analyze
 genomes, epigenomes, and transcriptomes during early development in two
 sea urchin species in the genus Heliocidaris that exhibit highly divergent
 life histories and in an outgroup species. Signatures of positive
 selection and changes in chromatin status within putative gene regulatory
 elements are both enriched on the branch leading to the derived life
 history, and particularly so near core dGRN genes; in contrast, positive
 selection within protein-coding regions have at most a modest enrichment
 in branch and function. Single-cell transcriptomes reveal a dramatic delay
 in cell fate specification in the derived state, which also has far fewer
 open chromatin regions, especially near dGRN genes with conserved roles in
 cell fate specification. Experimentally perturbing the function of three
 key transcription factors reveals profound evolutionary changes in the
 earliest events that pattern the embryo, disrupting regulatory
 interactions previously conserved for ~225 million years. Together, these
 results demonstrate that natural selection can rapidly reshape
 developmental gene expression on a broad scale when selective regimes
 abruptly change and that even highly conserved dGRNs and patterning
 mechanisms in the early embryo remain evolvable under appropriate
 ecological circumstances.
DOI: 10.5061/dryad.9cnp5hqkv
title: Greenhouse plant-soil feedback experiment at Cedar Creek Ecosystem Science Reserve

description: We conducted a reciprocal greenhouse experiment to examine how the growth
 of prairie grass species depended on the soil communities conditioned by
 conspecific or heterospecific plant species in the field. The source soil
 came from monocultures in a long-term competition experiment (LTCE, Cedar
 Creek Ecosystem Science Reserve, MN, USA). Within the LTCE, six species of
 perennial prairie grasses were grown in monocultures or in eight pairwise
 competition plots for 12 years under conditions of low and high soil
 nitrogen availability. In six cases, one species clearly excluded the
 other; in two cases, the pair appeared to coexist. In year 12, we gathered
 soil from all 12 soil types (monocultures of six species by two nitrogen
 levels) and grew seedlings of all six species in each soil type for seven
 weeks.
DOI: 10.5061/dryad.k0p2ngfb1
title: Data from: Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma)

description: The history of riverine fish diversification is largely a product of
 geographic isolation. Physical barriers that reduce or eliminate gene flow
 between populations facilitate divergence via genetic drift and natural
 selection, eventually leading to speciation. For freshwater organisms,
 diversification is often the product of drainage basin rearrangements. In
 young clades where the history of isolation is the most recent,
 evolutionary relationships can resemble a tangled web. One especially
 recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma
 nigrum) species complex, where traditional taxonomy and molecular
 phylogenetics indicate a history of gene flow and conflicting inferences
 of species diversity. Here we assemble a genomic dataset using double
 digest restriction site associated DNA (ddRAD) sequencing and use
 phylogenomic and population genetic approaches to investigate the
 evolutionary history of the complex of species that includes E. nigrum, E.
 olmstedi, E. perlongum, and E. susanae. We reveal and validate several
 evolutionary lineages that we delimit as species, highlighting the need
 for additional work to formally describe the diversity of the Etheostoma
 nigrum complex. Our analyses also identify gene flow among recently
 diverged lineages, including one instance involving E. susanae, a
 localized and endangered species. Phylogeographic structure within the
 Etheostoma nigrum species complex coincides with major geologic events,
 such as parallel divergence in river basins during Pliocene inundation of
 the Atlantic coastal plain and multiple northward post-glacial
 colonization routes tracking river basin rearrangements. Our study serves
 as a nuanced example of how low dispersal rates coupled with geographic
 isolation among disconnected river systems in eastern North America have
 produced one of the world’s freshwater biodiversity hotspots.