cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6hdr7sr4d
title: Data from: The impact of land surface properties on haboobs and dust lofting

description: Haboobs are dust storms formed by strong surface winds in convective storm
 outflow boundaries, or cold pools, which can loft large quantities of
 mineral dust as they propagate. Both cold pools and the dust they loft are
 impacted by land surface properties resulting in complex surface
 interactions on haboobs. As a result of these additional complexities
 brought about by surface interactions, it is unclear which surface
 parameters and physical processes are important for predicting haboob
 intensity and dust concentrations. Here we applied the Morris
 one-at-a-time (MOAT) global sensitivity statistical method to an ensemble
 of 120 idealized simulations of daytime and nighttime haboobs to
 investigate the land surface properties that affect both dust mobilization
 and cold pool dynamics. MOAT identifies and ranks the importance of
 different input factors, which for the prediction of haboob strength and
 dust concentrations are 1) initial cold pool temperature, 2) surface type
 (vegetation), 3) soil type (clay content), and 4) soil moisture. The
 underlying physical mechanisms driving these feedbacks were then analyzed
 using a traditional one-at-a-time factor analysis. Time of day is
 significant for determining boundary layer height and dissipation via
 surface fluxes, leading to shallower, more intense cold pools/haboobs at
 night. Most of the land parameters modify the cold pool through impacts on
 surface fluxes, while surface type is dominated by roughness length
 effects. By ranking the importance of these surface factors, we have
 identified which variables are most sensitive and must be constrained via
 observations and data assimilation in numerical dust prediction models.
description: Methods for processing the data: Initial conditions for the input
 factors were selected with the Morris-one-at-a-Time (MOAT), or Elementary
 Effects, statistical method with the Sensitivity Analysis For Everybody
 (SAFE) Toolbox for MATLAB. There is a random component to the generation
 of MOAT initial conditions, thus they cannot be recreated exactly as they
 appear in the Simulation Guide.
description: File formats and the software required to open them:
 README_Source_Code.txt – Text file
 ERA5_Initial_Conditions.xlsx – Microsoft Excel Workbook
 Simulation_Guide.xlsx – Microsoft Excel Workbook
 rdint.f90 – Fortran90 code in text file
 aero_sources.f90 – Fortran90 code in text file
 Namelists – Fortran90 code in text files
DOI: 10.5061/dryad.kd51c5b97
title: Data from: Gardner-like crossover from variable to persistent force contacts in granular crystals

description: We report experimental evidence of a Gardner-like crossover from variable
 to persistent force contacts in a two-dimensional, bidisperse granular
 crystal by analyzing the variability of both particle positions and force
 networks formed under uniaxial compression. Starting
 from densities just above the freezing transition, and for variable
 amounts of additional compression, we compare configurations to both their
 own initial state, and to an ensemble of equivalent, reinitialized states.
 This protocol shows that force contacts are largely undetermined
 when the density is below a Gardner-like crossover, after which
 they gradually transition to being persistent, being fully so only above
 the jamming point. We associate the disorder that underlies this effect to
 the size of the microscopic asperities of the photoelastic disks used, by
 analogy to other mechanisms that have been previously predicted
 theoretically.
description: This dataset originated as digital images taken using both a
 polariscope (for photoelasticity) and unpolarized light. The data was
 processed using custom Matlab scripts to identify all particle locations
 in each image and to measure the similarity in photoelastic
 images. 
description: The files are saved as Matlab  .mat files, which can also be
 opened by Octave or Python, both of which are open-source, as well as raw
 data in .jpg image format.
DOI: 10.5061/dryad.12jm63z24
title: Data from: Honey bees are the most abundant visitors to Australian watermelon but native stingless bees are equally effective as pollinators

description: Despite the benefits of a diverse approach to crop pollination, global
 food production remains reliant on a low diversity of managed pollinators,
 especially the European honey bee (Apis mellifera). To facilitate more
 robust pollinator management and improve the resilience of the production
 system, it is necessary to understand regional variation in the
 pollination ecology of global food crops. Watermelon (Citrullus lanatus
 (Thunb.) Matsum. & Nakai) is a highly insect pollinator-dependent
 crop and even though it is grown globally across many different climate
 zones, little is known about its pollination ecology across the diverse
 growing regions of Australia, spanning from the tropics to the arid zone.
 We compared the species composition, visitation rates, and effectiveness
 of the dominant floral visitors on 15 farms across five major
 watermelon-growing regions of Australia. We found that insect species
 composition differed significantly among regions, but honey bees were the
 dominant watermelon flower visitor, with relative abundance varying from
 73 - 94%. However, native bees (including stingless bees Tetragonula sp.,
 and bees from Families Megachilidae, and Halictidae such as Lasioglossum,
 Homalictus, Lipotriches), and flies (particularly Syrphidae sp.) also
 visited and transferred pollen onto watermelon flowers. In particular,
 native stingless bees were common visitors in several growing regions and
 deposited similar amounts of pollen to honey bees. Our findings indicate
 that the Australian watermelon industry utilizes honey bees, but the
 diverse assemblage of available native pollinating taxa provides an
 additional opportunity for growers in specific growing regions. These
 native taxa may be encouraged in the production system by deploying
 managed populations (e.g. native stingless bee colonies), employing
 pollinator-safe land management practices, as well as exploring methods
 for increasing the efficiency of managed honey bee colonies.
DOI: 10.5061/dryad.kd51c5b98
title: Data from: ETIB-T: An aquilibrium theory of island biogeography for plant traits

description: This dataset holds information on community mean seed mass, plant height
 and leaf area of 156 species and their occurrences on 15 islands ranging
 in size from 164 m2 - 19 km2. The islands are located in Western Australia
 off Perth. Further, the dataset provides information on island
 coordinates, size, isolation and elevation. The islands were sampled four
 times within four decades. The data can be used to investigate spatial and
 temporal turnover dynamics on islands.
DOI: 10.5061/dryad.t1g1jwt5r
title: Glacier Bay National Park mammal and plant community data

description: 1. Disturbance is a key driver of community assembly and patterns of
 diversity. Whereas successional changes in vegetation have been well
 studied, post-disturbance successional patterns of wildlife communities
 remain poorly understood. 2. Here, we investigated the roles of site age
 and habitat in shaping community assembly and the diversity of terrestrial
 mammals in Glacier Bay National Park, Alaska (GBNP), which has undergone
 the most rapid and extensive deglaciation in the world since the Little
 Ice Age. Deglaciation has extensively altered the landscape, opening up
 new habitat for recolonization by plants and animals.  3. We used
 camera traps, small mammal trapping and vegetation surveys to investigate
 the patterns of mammalian succession and beta diversity following
 deglaciation, using a space-for-time substitution across 10 sites during
 summers 2017 and 2018. Site age and habitat characteristics were not
 strongly correlated (r &lt; 0.46), allowing the influences of time
 since disturbance and habitat changes to be distinguished. 4. PERMANOVA
 analyses indicated that mammal community assembly was more strongly
 influenced by site age than habitat, whereas habitat and age had similar
 effects on beta (between site) diversity. Beta diversity was higher for
 smaller, less mobile mammals than larger, more mobile mammals and was
 primarily driven by species turnover among sites, whereas relative
 turnover was much lower for larger mammals. A comprehensive review of
 historic distributions of mammals in GBNP supported our findings that
 species turnover is a driving influence of community assembly for smaller
 mammals.  5. Our results indicate that body size of mammals may
 play an important role in shaping colonization patterns post-disturbance,
 likely via size-related differences in mobility. Patterns of wildlife
 community assembly may therefore not track vegetation succession following
 disturbances if there are barriers to movement or if dispersal ability is
 limited, highlighting the importance of incorporating landscape
 connectivity and species traits into wildlife conservation efforts
 following disturbances. This knowledge may improve predictions of
 mammalian community assembly following major disturbance events.
DOI: 10.5061/dryad.31zcrjdq7
title: Atmospheric river variability over the last millennium driven by annular modes: Part 1 (AR tags for LME Members #2–7)

description: Atmospheric rivers (ARs) are filamentary structures of intense water vapor
 transport commonly found in the extratropical atmosphere. ARs are a
 crucial component of the Earth’s general circulation: ARs account for up
 to 90% of poleward moisture transport and are a reliable (and sometimes
 extreme) source of precipitation for midlatitude coastal regions around
 the world. Although ARs operate primarily in the extratropics, how ARs
 respond to extratropical climate variability remains poorly understood. In
 this study, we use millennium-long climate model simulations to examine
 how annular modes of climate variability—the dominant mode of climate
 variability in the extratropics in both the Northern and Southern
 Hemispheres—affect ARs. We find that phases of the annular modes induce
 strong north–south displacements in AR activity, with up to ~20–25
 mm/month associated changes in precipitation. These AR changes are also
 found in the observational record, indicating that our model results are
 representative of real-world influences. Our results provide a robust
 baseline of natural AR variability from which to contextualize projected
 21st-century AR intensification. This is one part of a three-part dataset
 and contains AR tags for LME Members #2–7.
DOI: 10.5061/dryad.3n5tb2rmh
title: Atmospheric river variability over the last millennium driven by annular modes: Part 2 (AR tags for LME Members #8–13)

description: Atmospheric rivers (ARs) are filamentary structures of intense water vapor
 transport commonly found in the extratropical atmosphere. ARs are a
 crucial component of the Earth’s general circulation: ARs account for up
 to 90% of poleward moisture transport and are a reliable (and sometimes
 extreme) source of precipitation for midlatitude coastal regions around
 the world. Although ARs operate primarily in the extratropics, how ARs
 respond to extratropical climate variability remains poorly understood. In
 this study, we use millennium-long climate model simulations to examine
 how annular modes of climate variability—the dominant mode of climate
 variability in the extratropics in both the Northern and Southern
 Hemispheres—affect ARs. We find that phases of the annular modes induce
 strong north–south displacements in AR activity, with up to ~20–25
 mm/month associated changes in precipitation. These AR changes are also
 found in the observational record, indicating that our model results are
 representative of real-world influences. Our results provide a robust
 baseline of natural AR variability from which to contextualize projected
 21st-century AR intensification. This is one part of a three-part dataset
 and contains AR tags for LME Members #8–13.
DOI: 10.5281/zenodo.17976864
title: Resource data for: Composite SMG5-SMG6 PIN domain formation is essential for NMD

description: Resource data for the publication: Composite SMG5-SMG6 PIN domain formation is essential for NMD

The RawData.zip file is organized by Figures and Panels and contains the quantifications from qPCR, as well as raw image files e.g. from RT-PCR gels and Western blots used in the study. For RT-PCR images, TIF (.tif) and raw Bio-Rad Image Lab Image Document (.scn) files are provided. For Western blots, multi-page TIFs (pages: 1. overlay, 2. raw chemiluminescence, 3. marker image, 4. final) are provided. The metadata and processed results of RNA-seq analyses (differential gene expression via DESeq2 & differential transcript expression via edgeR) are included as well.

Also provided are the outputs of AlphaFold-Multimer and AlphaFold3 in separate folders.
DOI: 10.5281/zenodo.18401619
title: Resource data for: Composite SMG5-SMG6 PIN domain formation is essential for NMD

description: Resource data for the publication: Composite SMG5-SMG6 PIN domain formation is essential for NMD

The RawData.zip file is organized by Figures and Panels and contains the quantifications from qPCR, as well as raw image files e.g. from RT-PCR gels and Western blots used in the study. For RT-PCR images, TIF (.tif) and raw Bio-Rad Image Lab Image Document (.scn) files are provided. For Western blots, multi-page TIFs (pages: 1. overlay, 2. raw chemiluminescence, 3. marker image, 4. final) are provided. The metadata and processed results of RNA-seq analyses (differential gene expression via DESeq2 & differential transcript expression via edgeR) are included as well.

Also provided are the outputs of AlphaFold-Multimer and AlphaFold3 in separate folders.
DOI: 10.5061/dryad.hdr7sqvmr
title: Data for: A hierarchical framework for unpacking the nitrogen challenge

description: To feed the world population while mitigating pressing nitrogen (N)
 pollution problems, tremendous efforts have been devoted to developing and
 implementing N-efficient technologies in food production, but limited
 progress has been made. The N management improvement on a farm does not
 necessarily translate to N pollution reduction on a broader scale due to
 complex responses of natural and human systems and lack of coordination
 among stakeholders. Consequently, it is imperative to develop an N
 management framework that encompasses the complex N dynamics across
 systems and spatial scales, yet simple enough to guide policies and
 actions of various stakeholders. Here, we propose a new framework, CAFE,
 that defines four N management systems (Cropping, Animal-crop, Food, and
 Ecosystem) in a hierarchical manner, and apply it to 13 representative
 countries to partition N surpluses across systems in a simple and
 consistent manner, thereby facilitating the identification and
 prioritization of systems-based intervention strategies. Surprisingly, the
 Cropping system contributes less than half of the total N surplus within
 its Ecosystem for most countries, highlighting the importance of N
 management beyond croplands. As N surplus increases along the CAFE
 hierarchy, systems-based intervention strategies are revealed: coupling
 chemical fertilizers with other N sources by maintaining half of the N
 from manure and N bio-fixation; coupling animal-crop production by
 reducing animal density to lower than 1.2 livestock units, and increasing
 self-sufficiency of animal feed to above 50%; coupling food trade with
 domestic demand and production; and coupling population needs for economic
 opportunities with environmental capacity of the region.
description: Data of nitrogen contents and the classification of different
 crop and animal products were provided in Supplementary Data “SI_DataS1”,
 data of nitrogen budgets across CAFE system during the defined periods for
 the selected countries can be access from Supplementary Data
 “SI_DataS2”.
DOI: 10.5061/dryad.1jwstqjzh
title: Age-specific effects of deletions: Implications for ageing theories

description: Evolution of ageing requires mutations with late-life deleterious effects.
 Classic theories assume these mutations either have neutral (Mutation
 Accumulation) or beneficial (Antagonistic Pleiotropy) effects early in
 life, but it is also possible that they start out as mildly harmful and
 gradually become more deleterious with age. Despite a wealth of studies on
 the genetics of ageing, we still have a poor understanding of how common
 mutations with age-specific effects are and what ageing theory they
 support. To advance our knowledge on this topic we measure a set of
 genomic deletions for their heterozygous effects on juvenile performance,
 fecundity at three ages, and adult survival. Most deletions have
 age-specific effects, and these are commonly harmful late in life. Many of
 the deletions assayed here would thus contribute to ageing if present in a
 population. Taking only age-specific fecundity into account, some
 deletions support Antagonistic Pleiotropy, but the majority of them better
 fit a scenario where their negative effects on fecundity become
 progressively worse with age. Most deletions have a negative effect on
 juvenile performance, a fact which strengthens the conclusion that
 deletions primarily contribute to ageing through negative effects that
 amplify with age.
DOI: 10.5061/dryad.95x69p8pb
title: Data from: Role of backbone fault system on earthquake spawning and geohazards in the Seoul metropolitan area

description: Major earthquakes in continental regions may cause significant damages.
 Preexisting fault system across megacity receives high attention for
 possible seismic damages. Earthquake occurrence mechanism is important to
 assess the geohazard potentials. Continental-scale Quaternary fault system
 is developed across the Seoul metropolitan area where the population is
 the largest in the Korean Peninsula. Historical seismic-damage records
 suggest potential seismic hazards in the Seoul metropolitan area. We
 investigate the fault motions and spatial distribution of earthquakes in
 the Seoul metropolitan area using a matched-filter technique that is based
 on stacked waveform crosscorrelation functions among densely-deployed
 seismic stations. The analysis detects 1,103 earthquakes that include 360
 events with magnitudes (ML) of -0.6 to 2.0 around the Chugaryeong fault
 and 34 events with magnitudes of -0.5 to 2.7 around Wangsukcheon, Pocheon,
 and Yeseonggang faults. The seismicity suggests a set of near-vertical
 subparallel (or orthogonal) faults that develop from the major faults. The
 Major fault system behaves as a backbone structure that makes branch
 faults develop, producing seismicity including major earthquakes. The
 backbone structure may control the fault development that conforms to the
 ambient stress field. The backbone faults may play a role in increasing
 geohazard potentials.
description: This data set is concerned with the article "Role of
 backbone fault system on earthquake spawning and geohazards in the Seoul
 metropolitan area" submitted to Earth and Space Science by Seongjun
 Park, Tae-Kyung Hong, Byeongwoo Kim, and Junhyung Lee in 2022. We provide
 the event lists analyzed in the article. All data files are given in ASCII
 format. Please see the detailed information in the file
 "README".
DOI: 10.5061/dryad.fn2z34tz7
title: Data from: Augmin prevents merotelic attachments by promoting proper arrangement of bridging and kinetochore fibers

description: The human mitotic spindle is made of microtubules nucleated at
 centrosomes, at kinetochores, and from pre-existing microtubules by the
 augmin complex. However, it is unknown how the augmin-mediated nucleation
 affects distinct microtubule classes and thereby mitotic fidelity. Here we
 use superresolution microscopy to analyze the previously indistinguishable
 microtubule arrangements within the crowded metaphase plate area and
 demonstrate that augmin is vital for the formation of uniformly arranged
 parallel units consisting of sister kinetochore fibers connected by a
 bridging fiber. This ordered geometry helps both prevent and resolve
 merotelic attachments. Whereas augmin-nucleated bridging fibers prevent
 merotelic attachments by creating a nearly parallel and highly bundled
 microtubule arrangement unfavorable for creating additional attachments,
 augmin-nucleated k-fibers produce robust force required to resolve errors
 during anaphase. STED microscopy revealed that bridging fibers were
 impaired twice as much as k-fibers following augmin depletion. The
 complete absence of bridging fibers from a significant portion of
 kinetochore pairs, especially in the inner part of the spindle, resulted
 in the specific reduction of the interkinetochore distance. Taken
 together, we propose a model where augmin promotes mitotic fidelity by
 generating assemblies consisting of bridging and kinetochore fibers that
 align sister kinetochores to face opposite poles, thereby preventing
 erroneous attachments.
DOI: 10.5061/dryad.k0p2ngfc0
title: Data from: Theta-phase-specific modulation of dentate gyrus memory neurons

description: The theta rhythm, a quasi-periodic 4-10 Hz oscillation, is observed during
 memory processing in the hippocampus, with different phases of theta
 hypothesized to separate independent streams of information related to the
 encoding and recall of memories. At the cellular level, the discovery of
 hippocampal memory cells (engram neurons), as well as the modulation of
 memory recall through optogenetic activation of these cells, has provided
 evidence that certain memories are stored, in part, in a sparse ensemble
 of neurons in the hippocampus. In previous research, however, engram
 reactivation has been carried out using open loop stimulation at fixed
 frequencies; the relationship between engram neuron reactivation and
 ongoing network oscillations has not been taken into consideration. To
 address this concern, we implemented a closed-loop reactivation of engram
 neurons that enabled phase-specific stimulation relative to theta
 oscillations in the local field potential. Using this real-time approach,
 we tested the impact of activating engram neurons during the peak
 (encoding phase) and trough (recall phase) of theta oscillations.
 Consistent with previously hypothesized functions of theta oscillations in
 memory function, we show that stimulating engram neurons at the trough of
 theta is more effective in eliciting behavioral recall than either fixed
 frequency stimulation or stimulation at the peak of theta. Moreover,
 phase-specific trough stimulation is accompanied by an increase in the
 coupling between gamma and theta oscillations in CA1 hippocampus. Oure
 results provide a causal link between phasespecific activation of engram
 cells and the behavioral expression of memory.
description: This dataset is composed of both freezing and LFP data from mice
 undergoing optogentic stimulation. The mice had bilateral fiber optics
 implanted over DG as well as a recording electrode in CA1. The files have
 the motion of the animal, the stimulation times, and the raw LFP
 values.
description: The files are .csv, so almost any software can open the data
 files.