cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3r2280gmt
title: Data for: Higher abundance of adult pike in Baltic Sea coastal areas adjacent to restored wetlands compared to reference bays

description: The abundance of pike, a keystone top-predator, has declined dramatically
 in the Baltic Sea since the 1990s likely owing to recruitment failure. It
 has been proposed that wetland restoration can aid the recovery of the
 pike stock by increasing the number of recruits produced by anadromous
 populations. Yet, no previous studies have addressed whether wetland
 restorations are associated with higher abundances of adult pike in the
 coastal habitat. To address this, we performed standardised rod-and-reel
 survey fishing in paired bays with and without wetlands across three
 coastal areas and three years. To estimate dispersal and the contribution
 of wetland pike to the coastal stock, we tagged captured pike with passive
 integrated responders (PIT) and employed PIT-reader stations in wetland
 inlets. The results showed that pike abundances were on average 90% higher
 in bays with an adjacent wetland although the effect varied among areas.
 Moreover, PIT-data uncovered that wetland pike constituted a high
 proportion of the pike found in adjacent coastal habitats and that some
 wetland fish dispersed up to 10 km. These results support that wetland
 restoration is a valuable tool to aid the coastal pike stock and
 ultimately restore the function and services of the coastal ecosystem.
description: Combination of standardized rod-and-reel survey fishing and
 mark-recapture.
DOI: 10.5061/dryad.msbcc2g3d
title: Trait-based and multi-scale approach provides insight on responses of freshwater mussels to environmental heterogeneity

description: Our understanding of the factors driving the distribution of
 metacommunities at different scales can be obscured by high variation in
 species composition between sites and a lack of fine-scale distribution
 data. Trait-based approaches have long been used to better identify and
 examine ecological patterns. Most recent studies of riverine
 metacommunities examining trait-based patterns have focused on
 shorter-lived organisms. Here we focused on a group of longer-lived,
 sedentary riverine organisms, unionid freshwater mussels. The objective of
 this study was to examine how (1) the distribution of mussels with
 different life history strategies (trait-based approach) and (2) the
 relative importance of environmental and spatial factors (as a proxy for
 dispersal) would differ with spatial scale and position in the river; and
 to (3) further compare this with patterns derived from a taxonomic
 approach. Fine-scale distribution data of mussels and environmental
 factors were collected every 100 m in spatially extensive surveys in an
 up- and downstream segment (200 sites/20 km-segment) of a semi-arid river,
 making them some of the most spatially intensive surveys documented to
 date. A combination of redundancy analysis, asymmetric eigenvector
 mapping, and variation partitioning analyses revealed that more variation
 was explained by environmental factors where more environmental
 differences occur between sites. Where environmental heterogeneity was
 lower the amount of variation explained by smaller-scale spatial factors
 was higher, likely mostly associated with stochastic rather than dispersal
 processes. A higher amount of unexplained variation at the taxonomic level
 suggests that stochasticity may also play an important role in determining
 species composition. In contrast, different life history groups had a
 highly predictable distribution pattern driven by environmental
 heterogeneity, especially between river segments and mesohabitat, which
 was associated with different flow conditions. The role we predict for
 environmental heterogeneity and stochasticity in shaping the distribution
 of mussels in our study river likely also applies to other taxa and
 ecosystems at a spatial scale at which neither dispersal limitation nor
 mass effects occur. Thus, understanding the magnitude and extent of
 dispersal relative to the amount of environmental heterogeneity may be key
 for predicting metacommunity structure and dynamics for different
 organisms.
DOI: 10.5061/dryad.kwh70rz8m
title: Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

description: Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and
 cell division, are known to generate β-1,4-glucan. However, whether they
 are propelled in the membrane as the glucan chains they produce assemble
 into microfibrils is unknown. To address this, we endogenously tagged all
 eight CSLDs in Physcomitrium patens and discovered that they all localize
 to the apex of tip-growing cells and to the cell plate during cytokinesis.
 Actin is required to target CSLD to cell tips concomitant with cell
 expansion, but not to cell plates, which depend on actin and CSLD for
 structural support. Like Cellulose Synthase (CESA), CSLD requires
 catalytic activity to move in the plasma membrane. We discovered that CSLD
 moves significantly faster, with shorter duration and less linear
 trajectories than CESA. In contrast to CESA, CSLD movement was insensitive
 to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and
 CESA function within different complexes possibly producing structurally
 distinct cellulose microfibrils.
description: mEGFP-CesA10 and mEGFP-CSLD6 particles were imaged with VAEM
 every 2s for 10-20 minutes. Images were processed before tracking using
 subtract background and enhance contrast in Fiji. Particle tracking was
 performed with the Fiji plugin TrackMate (Tinevez et al., 2017). For
 CesA10, stacks were reduced by 10, resulting in 20 s time intervals
 between frames. For CSLD6, stacks were reduced by 6, resulting in 12 s
 time intervals between frames. LoG detector (estimate blob diameter 0.3
 µm) and LAP tracker (frame to frame linking max distance 0.5 µm;
 Penalties: Quality=1; no gap closing allowed) were selected. The filters
 on tracks were set as follows: duration &gt;60 s; track displacement
 &gt;0.5 µm. Mean speed and the confinement ratio of tracks were
 obtained and plotted in Figure 3. The confinement ratio is a ratio of the
 straight-line distance between the start and end points of the trajectory
 divided by the actual trajectory distance. The closer the confinement
 ratio value is to one, the more linear the trajectory.
DOI: 10.5061/dryad.83bk3j9ws
title: Data from: In diverse conditions intrinsic chromatin condensate have liquid-like material properties

description: The organization of eukaryotic chromatin is important in many nuclear
 processes. Recent studies have shown that chromatin fragments can
 self-assemble by phase separation into micron-scale structures in the
 presence of salt in vitro. There are discrepancies regarding
 whether these structures generally have liquid-like or solid-like
 behaviors, an important distinction in considering how processes such as
 transcription and chromosome remodeling by loop extrusion can occur in
 cells. Here, we resolve conflicting reports by demonstrating that
 chromatin condensates have liquid-like behaviors in diverse solution
 conditions and describing aspects of sample handling that can lead to
 artifactual solid-like behaviors. Our data suggest how chromatin can be
 dynamic on short length scales but restrained on long length scales, as
 observed in cells.
DOI: 10.5061/dryad.866t1g1vv
title: Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification

description: The Neotropics contain one of the most diverse assemblages of freshwater
 fishes worldwide. Part of this diversity is shared between the Orinoco and
 Amazon basins. These basins have been separated for a long time due to the
 Vaupes Arch, rising between 10 - 11 Ma. Today, there is only one permanent
 connection between the Orinoco and Negro (Amazon) basins, known as the
 Casiquiare Canal. However, alternative corridors allowing fish dispersion
 between both basins have been proposed. The cardinal tetra (Paracheirodon
 axelrodi), the most important fish in the ornamental world market, is
 distributed in both basins. Here we investigated P. axelrodi
 phylogeography, population structure, and potential routes of migration
 and connectivity between the two basins. A total of 468 bp of the
 mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and
 8 microsatellite loci were analyzed. As a result, we found two major
 genetic clusters as the most likely scenario (K=2), but they were not
 discreetly distributed between basins. A gradient of genetic admixture was
 observed in Cucui and São Gabriel da Cachoeira, between the upper Negro
 River and the upper Orinoco. Samples from the middle-lower Negro River
 were highly structured. Cucui (Negro basin) was more similar to the
 Orinoco than to the rest of the Negro basin populations. However,
 substructure was also observed by the discriminant analysis, fixation
 indices and other hierarchichal structure analyses (K=3-6), showing three
 major geographic clusters: Orinoco, Cucui, and the remaining of the Negro
 basin. Unidirectional migration patterns were detected between basins: via
 Cucui toward Orinoco and via the remaining of the Negro basin toward
 Orinoco. Results from the Relaxed Random Walk analysis support a very
 recent origin of this species in the headwater Orinoco basin (Western
 Guiana Shield, at late Pleistocene) with a later rapid colonization of the
 remaining Orinoco basin and almost simultaneously the Negro River via
 Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and
 population genetic patterns observed here for Cardinal tetra, seem to be
 better explained by river capture, physical, or ecological barriers than
 due to the geographic distance.
description: Muscle tissue samples (one per
 individual) were collected along the Orinoco and Amazon basins on the
 distribution area for <em>P.
 axelrodi. </em>Once the fish were received, they were
 euthanized by rapid chilling (hypothermic shock) on
 ice. Then, all individuals and tissue samples
 were preserved in ethanol at 95% and stored at 4°C. Genomic DNA was
 extracted.
description: The data files included are Excel files(.xlsx)
DOI: 10.5061/dryad.j0zpc86k9
title: Data for: Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence

description: In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip
 degeneration (PTD) starts with growth arrest of the inflorescence meristem
 dome, followed basipetally by the degeneration of floral primordia and the
 central axis. Due to its quantitative nature and environmental
 sensitivity, inflorescence PTD constitutes a complex, multilayered trait
 affecting final grain number. This trait was studied by microscopic
 dissection of immature inflorescence meristems under standardized growth
 conditions. We combined spatiotemporal metabolomic, transcriptomic, and
 genetic approaches to elucidate the mechanism of barley inflorescence PTD
 in two- and six-rowed barley cultivars ‘Bowman’ and ‘Morex,’ respectively.
 Metabolome profiling includes hormones and primary metabolites such as
 sugars, TCA intermediates, and amino acids by dividing spike meristems
 into dying apical and viable central and basal parts at four developmental
 stages during the spike growth phase. Similarly, RNA sequencing was
 performed for three developmental stages in both genotypes. RNA sequencing
 data analyses were performed to identify differentially expressed and
 tissue-specific transcripts. Further, PTD-associated hub genes were
 identified by weighted gene coexpression network analysis. Based on
 transcriptome analyses, we identified an important modulator of
 inflorescence PTD and functionally validated it using Cas9-mediated
 mutagenesis and gene-based associated study using a diverse panel of
 barley accessions.
DOI: 10.5878/002467
title: The Regional Western Sweden SOM Survey 1998
title: Den västsvenska SOM-undersökningen 1998
title: Väst-SOM 1998

description: Western SOM has been conducted yearly since 1992, but was initially limited to residents of Gothenburg and its surrounding municipalities. In 1998, the survey was extended to include the entire Västra Götaland County plus the municipality of Kungsbacka. 

The purpose of the regional surveys is to enable SOM researchers to study attitudes and behaviour linked to local and regional issues. They emphasise public services and media, although many of the questions are identical with those used in National SOM in order to make the answers comparable both between the regions and with Sweden at large.

Purpose:

Study attitudes and behaviors that are linked to local and regional issues and phenomena
description: Detta är den sjunde studien i serien SOM-undersökningar genomförda i Västsverige. Undersökningen genomfördes med två olika enkätformulär: ett riktat till invånarna i Göteborg med kranskommuner och ett till dem hemmahörande i resterande delar av Västra Götaland. Enkätformulären innehåller till största delen gemensamma frågor. Några frågor är dock enbart ställda i en av de två enkäterna; framför allt handlar det om frågor enbart ställda i formuläret till invånarna i Göteborgsregionen. Båda enkäterna innehåller frågeområdena: Massmedier; Politik och samhälle; Trafik och miljö; Fritid och medieanvändning; samt Bakgrundsfrågor.

Syfte:

Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser
DOI: 10.5878/000360
title: The Regional Western Sweden SOM Survey 1998
title: Den västsvenska SOM-undersökningen 1998
title: Väst-SOM 1998

description: Western SOM has been conducted yearly since 1992, but was initially limited to residents of Gothenburg and its surrounding municipalities. In 1998, the survey was extended to include the entire Västra Götaland County plus the municipality of Kungsbacka. 

The purpose of the regional surveys is to enable SOM researchers to study attitudes and behaviour linked to local and regional issues. They emphasise public services and media, although many of the questions are identical with those used in National SOM in order to make the answers comparable both between the regions and with Sweden at large.

Purpose:

Study attitudes and behaviors that are linked to local and regional issues and phenomena
description: Detta är den sjunde studien i serien SOM-undersökningar genomförda i Västsverige. Undersökningen genomfördes med två olika enkätformulär: ett riktat till invånarna i Göteborg med kranskommuner och ett till dem hemmahörande i resterande delar av Västra Götaland. Enkätformulären innehåller till största delen gemensamma frågor. Några frågor är dock enbart ställda i en av de två enkäterna; framför allt handlar det om frågor enbart ställda i formuläret till invånarna i Göteborgsregionen. Båda enkäterna innehåller frågeområdena: Massmedier; Politik och samhälle; Trafik och miljö; Fritid och medieanvändning; samt Bakgrundsfrågor.

Syfte:

Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser
DOI: 10.5061/dryad.7d7wm380p
title: Quantum chemical investigation of the predominant conformation of the antibiotic azithromycin in water and DMSO solutions: an integrated thermodynamic and NMR analysis

description: Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and
 treat serious infections (mycobacteria or MAC) that significantly inhibit
 bacterial growth. Knowledge of the predominant conformation in solution is
 of fundamental importance for advancing our understanding of the
 intermolecular interactions of AZM with biological targets. We report an
 extensive density functional theory (DFT) study of plausible AZM
 structures in solution considering implicit and explicit solvent effects.
 The best match between the experimental and theoretical nuclear magnetic
 resonance (NMR) profiles was used to assign the preferred conformer in
 solution, which was supported by the thermodynamic analysis. Among the 15
 distinct AZM structures, conformer M14, having a short intramolecular
 C6-OH…N H-bond, is predicted to be dominant in water and DMSO solutions.
 The results indicated that the X-ray structure backbone is mostly
 conserved in solution, showing that large flexible molecules with several
 possible conformations may assume a preferential spatial orientation in
 solution, which is the molecular structure that ultimately interacts with
 biological targets.
description: This folder contains all the XYZ files of the most relevant optimized
 cartesian coordinates of azithromycin. For any further details please
 contact Dr. Wagner Batista de Almeida (wbdealmeida@gmail.com).
DOI: 10.5061/dryad.nzs7h44wm
title: Monitoring the evolution of relative product populations at early times during a photochemical reaction

description: Identifying multiple rival reaction products and transient species formed
 during ultrafast photochemical reactions and determining their
 time-evolving relative populations are key steps towards understanding and
 predicting photochemical outcomes. Yet, most contemporary ultrafast
 studies struggle with clearly identifying and quantifying competing
 molecular structures/species amongst the emerging reaction products. Here,
 we show that mega-electronvolt ultrafast electron diffraction in
 combination with ab initio molecular dynamics calculations offers a unique
 route to determine time-resolved populations of the various isomeric
 products formed after UV (266 nm) excitation of the five-membered
 heterocyclic molecule thiophenone. This strategy reveals an unexpectedly
 high (~50%) yield of an episulfide isomer containing a strained 3-membered
 ring within ~1 ps at early times and rapid interconversions between the
 rival photoproducts.   
description: UED dataset: raw data of the 15uJ experiment discussed in the
 main text. Trajectory dataset: xyz trajectories of the
 dynamics discussed in the main text. See supplementary
 material for the details of the collection.
description: Trajectory dataset: xyz files can be opened with a text editor or
 a molecular visualizer (VMD).
DOI: 10.5061/dryad.jwstqjqfj
title: Composition of non-volant small mammals inhabiting a degradation gradient in a lowland tropical forest in Uganda

description: A study aimed at assessing the structure of rodent and shrew assemblages
 inhabiting a degradation gradient while considering rainfall patterns was
 conducted in one of the few remaining lowland tropical forests in Eastern
 Africa. We collected a unique dataset of 1411 rodents and shrews,
 representing 24 species (19 rodents, 5 shrews). The most abundant species
 alternated in dominance as species abundance significantly fluctuated
 across the study period following a degradation gradient, While
 only generalist species were observed near the degraded forest edge,
 habitat specialists such as Deomys ferrugineus, Malacomys longipes and
 Scutisorex congicus, were observed in the primary forest interior
 suggesting a significant association between species and their
 associated habitats and habitat attributes. There was also an observed
 correlation between rainfall patterns and species abundance. Capturing
 more species in adjacent fallows and along the degraded forest edge
 suggests that many species are able to live in degraded habitats that
 offer a variety of food resources. The continued pressure on forest
 resources, however, may lead to changes in habitat structure. This,
 coupled with the dependence of forest ecological functions on rainfall,
 which is typically not the case, may ultimately cause the local extinction
 of highly specialized but less adaptable species.
description: Data was collected in Mabira Central Forest Reserve for 12 months
 between August 2018 and December 2019. Data were intermittently collected
 (with a one-month break after two months of data collection) along a
 gradient of habitat degradation that included a primary forest interior, a
 degraded forest edge, and fallows, gardens, sugarcane plantations,
 homesteads close to the forest, collectively referred to as adjacent
 habitats. Rodents and shrews were trapped using Sherman traps Morphometric
 measurements were taken from every captured specimen including the total
 length (TL), tail vertebrae length (TV), hind foot length (Hf), ear
 length, and weight (Wt). All measurements were recorded in millimeters and
 weight in grams. All specimens collected were kept as wet specimens in 75%
 ethanol and kept as vouchers in Makerere Zoological Museum. Collected
 specimens were identified to species using morphometric measurements cross
 references with published identification guides (Brambell 1973, Delany
 1975, Thorn & Kerbis 2009, Monadjem et al. 2015) For selected
 individuals of each morphotype, identifications were confirmed by
 sequencing of partial mitochondrial cytochrome b gene (i.e. DNA barcoding)
 from 96% ethanol-preserved samples at the Institute of Vertebrate Biology
 (IVB) of the Czech Academy of Sciences.
DOI: 10.5281/zenodo.18210247
title: A computer-assisted well-founded descent for Collatz components under dyadic leaf certificates in the 6-bit hierarchy Mt = 9 · 214+6t (shifts64 scale M1 = 9 · 220, version m = 7

description: Collatz, 3x+1, number theory, certificates, computational verification, well-founded descent
DOI: 10.5061/dryad.f1vhhmh26
title: Cell tracking data from: Automated timelapse data segmentation reveals in vivo cell state dynamics

description: Embryonic development proceeds as a series of orderly cell state
 transitions built upon noisy molecular processes. Here, we defined gene
 expression and cell motion states using single cell RNA sequencing data
 and in vivo timelapse cell tracking data of the zebrafish tailbud. We
 performed a parallel identification of these states using dimensional
 reduction methods and a change point detection algorithm. Both types of
 cell states were quantitatively mapped onto embryos, and we utilized the
 cell motion states to study the dynamics of biological state transitions
 over time. The time average pattern of cell motion states is reproducible
 among embryos. However, individual embryos exhibit transient deviations
 from the time average forming left-right asymmetries in collective cell
 motion. Thus, the reproducible pattern of cell states and bilateral
 symmetry arises from temporal averaging. In addition, collective cell
 behavior can be a source of asymmetry rather than a buffer against noisy
 individual cell behavior.
description: Zebrafish embryos were injected the mRNA encoding H2A-mRFP at the
 one-cell stage and then incubated until the 8-somite stage. They were
 mounted dorsal side up and the tailbud was imaged on a point-scanning
 confocal every three minutes for up to three hours. Cells were tracked
 using Imaris. Data was collected on wild-type embryos and those subject to
 signalling perturbations. Specifically, starting at the 6-somite stage
 embryos were incubated in 50 mM of SU5402 or 40 mM of DMH1 for two hours
 to inhibit FGF or BMP signaling, respectively. Wnt signaling was inhibited
 by injecting notum-1 mRNA at a concentration of 150 ng/mL into embryos at
 the single cell stage and then incubating them until the 10-somite stage.
 This treatment yields a phenotypic spectrum, and embryos with nascent body
 elongation defects were chosen for further experiments.