cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tx95x6b3h
title: U.S. cereal rye winter cover crop growth database

description: Winter cover crop performance metrics (i.e., vegetative biomass quantity
 and quality) affect ecosystem services provisions but vary widely due to
 differences in agronomic practices, soil properties, and climate. Cereal
 rye (Secale cereale) is the most common winter cover crop in the United
 States due to its winter hardiness, low seed cost, and high biomass
 production. We compiled data on cereal rye winter cover crop performance
 metrics, agronomic practices, and soil properties across the eastern half
 of the United States. The dataset includes a total of 5,695 cereal rye
 biomass observations across 208 site-years between 2001–2022 and
 encompasses a wide range of agronomic, soil, and climate conditions.
 Cereal rye biomass values had a mean of 3,428 kg ha−1, a median of 2,458
 kg ha−1, and a standard deviation of 3,163 kg ha−1. The data can be used
 for empirical analyses, to calibrate, validate, and evaluate process-based
 models, and to develop decision support tools for management and policy
 decisions.
description: # U.S. cereal rye winter cover crop growth database We compiled data on
 cereal rye winter cover crop performance metrics, agronomic practices, and
 soil properties across the eastern half of the United States. The dataset
 includes a total of 5,695 cereal rye biomass observations across 208 site
 years between 2001-2022 and encompasses a wide range of agronomic, soil,
 and climate conditions. ## Description of the data and file structure Data
 files are numbered and described in the 1_data_dictionary.csv file, and an
 R script to reproduce the figures is provided. 1_data_dictionary.csv
 provides a definition of variables for the following files.
 2_study_metadata.csv provides detailed site location, study design
 information, the DOI for any published data, and methods information for
 any unpublished data. 3_rye_data.csv provides cereal rye-related data
 associated with biomass observations. 4_agronomic_data.csv provides
 agronomic management data general to each study. 5_soil_data.csv provides
 oil sample data and/or general site soil data. Empty cells or cells
 containing NA indicate that no data were available.  ## Code/Software The
 R script provided was run using the "here" package v1.0.1, the
 "tidyverse" package v1.3.2, and the "lubridate"
 package v1.8.0. The figures were producing using R v4.1.3. \#Disclaimer
 This code is provided on an "as is" basis and the user assumes
 responsibility for its use. The authors have relinquished control of the
 information and no longer has responsibility to protect the integrity,
 confidentiality, or availability of the information.
DOI: 10.5061/dryad.18931zd2s
title: BLM overexpression as a predictive biomarker for CHK1 inhibitor response in PARP inhibitor–resistant BRCA-mutant ovarian cancer

description: PARP inhibitors (PARPis) have changed the treatment paradigm in
 BRCA-mutant high-grade serous ovarian carcinoma (HGSC). However, most
 patients eventually develop resistance to PARPis, highlighting an unmet
 need for novel therapeutic strategies. Using high-throughput drug screens,
 we identified ATR/CHK1 pathway inhibitors as cytotoxic, and further
 validated monotherapy activity of the CHK1 inhibitor (CHK1i), prexasertib,
 in PARPi-resistant BRCA-mutant HGSC cells and animal models. As a
 proof-of-concept trial, we conducted a phase II study of prexasertib in
 BRCA-mutant HGSC patients. The treatment was well-tolerated but yielded an
 objective response rate of 6% (1/17; 1 PR) in patients with prior PARPi
 treatment. Exploratory biomarker analyses revealed that replication stress
 and fork stabilization were associated with clinical benefit to CHK1i. In
 particular, overexpression of BLM, and CCNE1 overexpression or copy number
 gain/amplification were seen in patients deriving durable benefit from
 CHK1i. Our findings suggest replication fork–related biomarkers should be
 further evaluated for CHK1i sensitivity in HGSC.
description: RNA-seq was performed using a HiSeq3000 sequencing system
 (Illumina) at the NCI CCR Sequencing Facility, Frederick National
 Laboratory for Cancer Research. Total RNA was isolated from pretreatment
 fresh-frozen core biopsies using the RNeasy microkit (Qiagen). RNA quality
 was evaluated using the Agilent Bioanalyzer 2100 and RNA integrity number
 (RIN) values were ensured to be &gt; 8.0. For total RNA-seq, each
 sample (20 to 100 ng) was preprocessed with NEBnext rDNA depletion kit
 (New England Biolabs) to remove ribosomal RNA, then barcoded and pooled to
 ensure at least 100 million reads per sample on a HiSeq3000 sequencing
 system (Illumina). The human reference genome hg38 and Gencode V30 were
 used to align reads, and gene expression data were generated as counts per
 million mapped reads (CPM) values. Quality check of sample and sequencing
 outputs were performed by the CCR sequencing facility and CCR
 Collaborative Bioinformatics Resource at NCI.
DOI: 10.5061/dryad.qnk98sfnd
title: Interactive effects of immediate and ancestral salt stress on fitness in duckweed

description: Premise of Research Organisms that reproduce asexually must respond to
 abiotic stresses in their environment while contending with the potential
 disadvantage of the reduced ability for genetic variation through
 recombination. Common duckweed (Lemna minor) is an aquatic plant that
 reproduces predominantly asexually through the budding of ramets. As a
 freshwater plant, duckweed experiences stress from salt (e.g., NaCl),
 which detrimentally affects growth, photosynthesis, and cellular
 processes. We took a demographic approach to examine whether ancestral
 exposure to salt stress affects the ability of duckweed offspring to
 tolerate immediate exposure to the same stress. Methodology We placed
 three consecutive clonal generations of duckweed in an environment with 2
 g L-1 NaCl (non-lethal salt stress) or 0 g L-1 NaCl (control), followed by
 an additional 0-3 generations in the control environment to vary the
 presence and schedule of ancestral stress. After these treatments, we used
 the offspring produced as focal plants for the experiment. Half were
 placed into the salt-stress environment, and half were placed in control
 conditions, and focal plants were tracked longitudinally. Pivotal Results
 Immediate stress decreased fitness, due to a slowing of reproduction,
 suggesting a cost of stress tolerance. The effects of ancestral stress,
 and the interaction of immediate and ancestral stress, were more complex.
 Specifically, recent ancestral stress induced plants to produce offspring
 more quickly, but with the potential cost of lowered offspring quality.
 Conclusions Our results amplify findings that responses to, and fitness
 consequences of, current stressors can be contingent on past exposure.
description: R software is required to run the script.
DOI: 10.5061/dryad.g4f4qrfvm
title: Take me for a ride: herbivores can facilitate plant re-invasions

description: Herbivores shape plant invasions through impacts on demography and
 dispersal, yet only demographic mechanisms are well understood. Although
 herbivores negatively impact demography by definition, they can affect
 dispersal either negatively (e.g. seed consumption), or positively (e.g.
 caching). Exploring the nuances of how herbivores influence spatial spread
 will improve forecasting of plant movement on the landscape. Here, we aim
 to understand how herbivores impact how fast plant populations spread
 through varying impacts on plant demography and dispersal. We strive to
 determine if, and under what conditions, we see net positive effects of
 herbivores, in order to find scenarios where herbivores can help promote
 spread. We draw on classic invasion theory to develop a stage-structured
 integrodifference equation model that incorporates herbivore impacts on
 plant demography and dispersal. We simulate seven herbivore
 `syndromes' (combinations of demographic and/or dispersal effects)
 drawn from the literature to understand how increasing herbivore pressure
 alters plant spreading speed. We find that herbivores with solely negative
 effects on plant demography or dispersal always slow plant spreading
 speed, and that the speed slows monotonically as herbivore pressure
 increases. However, we also find that plant spreading speed can be
 hump-shaped with respect to herbivore pressure: plants spread faster in
 the presence of herbivores (for low herbivore pressure) and then slower
 (for high herbivore pressure). This result is robust, occurring across all
 syndromes where herbivores have a positive effect on plant dispersal, and
 is a sign that the positive effects of herbivores on dispersal can
 outweigh their negative effects on demography. For all syndromes we find
 that sufficiently high herbivore pressure results in population collapse.
 Thus, our findings show that herbivores can speed up or slow down plant
 spread. These insights allow for greater understanding of how to slow
 invasions, facilitate native species recolonization, and shape range
 shifts with global change. 
description: This is a theoretical datset created in MATLAB based on
 equations.  We have processed that data in MATLAB as well.
DOI: 10.5061/dryad.rr4xgxddm
title: Estimating animal location from non-overhead camera views

description: Tracking an animal's location from video has many applications, from
 providing information on health and welfare to validating sensor-based
 technologies. Typically, accurate location estimation from video is
 achieved using cameras with overhead (top-down) views, but structural and
 financial limitations may require mounting cameras at other angles. We
 describe a user-friendly solution to manually extract an animal's
 location from non-overhead video. Our method uses QGIS, an open-source
 geographic information system, to: (1) assign facility-based coordinates
 to pixel coordinates in non-overhead frames; 2) use the referenced
 coordinates to transform the non-overhead frames to an overhead view; and
 3) determine facility-based x, y coordinates of animals from the
 transformed frames. Using this method, we could determine an object's
 facility-based x, y coordinates with an accuracy of 0.13 ± 0.09 m (mean ±
 SD; range: 0.01–0.47 m) when compared to the ground truth (coordinates
 manually recorded with a laser tape measurer). We demonstrate how this
 method can be used to answer research questions about space-use behaviors
 in captive animals, using 6 ewe-lamb pairs housed in a group pen. As
 predicted, we found that lambs maintained closer proximity to their dam
 compared to other ewes in the group and lamb-dam range sizes were strongly
 correlated. However, the distance traveled by lambs and their dams did not
 correlate, suggesting that activity levels differed within the pair. This
 method demonstrates how user-friendly, open-source GIS tools can be used
 to accurately estimate animal location and derive space-use behaviors from
 non-overhead video frames. This method will expand capacity to obtain
 spatial data from animals in facilities where it is not possible to mount
 cameras overhead.
description: Please see the description in the associated research
 publication.
description: Please see the included README file.
DOI: 10.5061/dryad.qz612jmmj
title: Going, going, gone: evidence for loss of an endemic species pair of threespine sticklebacks (Gasterosteus aculeatus) with implications for protection under species-at-risk legislation

description: Genomic extinction occurs when the unique combination of genetic traits
 that characterize distinct phenotypes is eliminated by introgressive
 hybridization even if population size is greater than zero. Benthic and
 limnetic threespine sticklebacks (Gasterosteus aculeatus) constitute
 reproductively isolated undescribed biological species that have evolved
 independently in several lakes in southwestern British Columbia, Canada
 (known as “species pairs” in each lake). Here we investigated whether the
 two species that comprise the pair from Enos Lake, southeastern Vancouver
 Island, remain as two distinct gene pools. Multi-season samples
 (&gt;1200 fish) obtained over two years from throughout the
 lake and assayed for variation in morphological traits characteristic of
 the two species (i.e., body depth, dorsal spine count, gill raker counts)
 and at 12 microsatellite DNA loci consistently indicated the existence of
 only a single group of sticklebacks. There was no consistent evidence of
 two groups in any morphological trait, and mean gill raker counts were
 consistently intermediate (20–21) to those of known benthics (~18) and
 limnetics (~24) which together comprised strikingly bimodal distributions
 in historical samples. Genetic analyses employing model-based clustering
 also consistently indicated the presence of only a single genetic group of
 sticklebacks. Compared to historical samples and to benthics and limnetics
 from other lakes, no Enos Lake fish could be identified confidently as a
 pure benthic or limnetic. Our results provide the strongest evidence yet
 that the Enos Lake sticklebacks now consist of a single morphological and
 genetic population of sticklebacks, that the unique combination of genetic
 and morphological traits that characterized benthic and limnetic
 sticklebacks no longer exist, and that their current status under Canada’s
 Species-at Risk Act as Endangered should be re-evaluated.
DOI: 10.5061/dryad.31zcrjdrf
title: Data of the tympanum and auditory sensitivity in two torrent frogs

description: Tympanic middle ears are important for anuran hearing on land; however,
 many species are observed to lose part or all of the tympanic apparatus.
 Some researchers have compared eared anurans' hearing sensitivity
 with earless species that produce calls and communicate with acoustic
 signals. Some anurans, however, lack both calling behaviour and
 well-developed tympanic membranes, and it is unclear whether they have
 fewer hearing perception-based selection pressures and how their hearing
 differs from closely related species with a developed acoustic
 communication system. Here, we compared the tympanic membranes of two
 sympatric sibling species living in noisy streams and showed that Hainan
 torrent frogs (Amolops hainanensis) were not only “dumb” but also had a
 vestigial eardrum that was smaller than that of little torrent frogs
 (Amolops torrentis) possessing a developed acoustic communication system.
 Then, we measured their auditory brainstem responses (ABRs) and compared
 the differences in ABR thresholds and latencies. Our results suggested
 that the two species exhibited significant differences in hearing
 sensitivity. A. hainanensis had higher thresholds and longer initial
 response times than A. torrentis at lower frequencies. The mechanical
 foundation and mechanism of such hearing changes require further study.
description: # Data of the tympanum and auditory sensitivity in two torrent frogs ##
 Description of the data and file structure Our data consists of three
 files. The first one (1\_morphological\_data) is the morphological traits
 of two torrent frogs, while another two (2\_ABR\_threshold;
 3\_ABR\_latency) are their hearing thresholds and hearing latencies from
 different frequencies. NA means data are not available.
DOI: 10.5061/dryad.dbrv15f67
title: CRISPR-Cas9 screen upon Olaparib+CldU treatment

description: DNA single-strand breaks (SSBs) disrupt DNA replication and induce
 chromosome breakage. However, whether SSBs induce chromosome breakage when
 present in nascent strands behind replication forks or template strands
 ahead of replication forks is unclear. To address this question, we
 exploited an exquisite sensitivity of SSB repair-defective human cells
 lacking PARP activity or XRCC1 to the thymidine analog
 5-chloro-2'-deoxyuridine (CldU). We show that incubation with CldU in
 these cells results in chromosome breakage, sister chromatid exchange, and
 cytotoxicity by a mechanism that depends on the S phase activity of uracil
 DNA glycosylase (UNG). Importantly, we show that CldU incorporation in one
 cell cycle is cytotoxic only during the following cell cycle when it is
 present in template DNA. In agreement with this, while UNG induces SSBs
 both in nascent strands behind replication forks and in template strands
 ahead of replication forks, only the latter triggers fork collapse and
 chromosome breakage. Finally, we show that BRCA-defective cells are
 hypersensitive to CldU, either alone and/or in combination with PARP
 inhibitor, suggesting that CldU may have clinical utility.
description: Two independent clones of P53-deficient RPE-1 cells expressing
 Cas9 nuclease were infected with the Brunello library containing gRNAs
 targeting the whole genome (coverage 500x). After selection for infected
 cells and population sampling 9 days after infection (samples
 "T6clon4" or "T6clon7"), the starting cell populations
 were divided into three groups. One group was an untreated control (sample
 name from the end of treatment: "T21clon4UN" or
 "T21clon7UN"), a second group was treated continuously with a
 sub-lethal concentration of olaparib (500 nM) (sample name from the end of
 the treatment: "T21clon4OLA" or "T21clon7OLA"), and a
 third population was continuously treated with both 500 nM olaparib and
 0.2 uM CldU; a combination that kills ~20% of cells (IC20) (samples name
 from the end of the treatment: "T21clon4OLACldU20" or
 "T21clon7OLACldU20"). Infected cell populations were sampled
 every 3 days from days 9-24, genomic DNA was isolated, and integrated gRNA
 abundances were measured relative to those in the “pre-treated” cell
 population at day 9 by deep sequencing.
description: # CRISPR-Cas9 screen upon Olaparib+CldU treatment ## Description of the
 data and file structure TSV files from the raw counts of sequencing. ##
 Sharing/Access information These data are discussed in Serrano-Benitez et
 al. 2023, if you require more data from the sequencing please email:
 [Steve.Jackson@cruk.cam.ac.uk](mailto:Steve.Jackson@cruk.cam.ac.uk)
DOI: 10.5061/dryad.547d7wmdn
title: Data for: Correlated biodiversity change between plant and insect assemblages resurveyed after 80 years across a dynamic habitat mosaic

description: Historical data on co-occurring taxa are extremely rare. As such, the
 extent to which distinct co-occurring taxa experience similar long-term
 patterns in species richness and compositional change (e.g., when exposed
 to a changing environment) is not clear. Using data from a diverse
 ecological community surveyed in the 1930s and the 2010s, we investigated
 whether local plant and insect assemblages displayed cross-taxon
 congruence – i.e., correlated patterns of species richness and
 compositional change – across six co-occurring taxa: vascular plants,
 non-vascular plants, grasshoppers and crickets (Orthoptera), ants
 (Hymenoptera: Formicinae), hoverflies (Diptera: Syrphidae), and
 dragonflies and damselflies (Odonata). All taxa exhibited high levels of
 turnover across the ca. 80-year time-period. Despite minimal observed
 changes at the level of the whole study-system, species richness displayed
 widespread cross-taxon congruence (i.e., correlated temporal change)
 across local assemblages within the study system. Hierarchical logistic
 regression models suggest a role for shared responses to environmental
 change underlying cross-taxon correlations and highlight stronger
 correlations between vascular plants and their direct consumers,
 suggesting a possible role for biotic interactions between these groups.
 These results provide an illustration of cross-taxon congruence in
 biodiversity change using data unique in its combination of temporal and
 taxonomic scope and highlight the potential for cascading and comparable
 effects of environmental change (abiotic and biotic) on co-occurring plant
 and insect communities. However, analyses of historical resurveys based on
 currently available data come with inherent uncertainties. As such, this
 study highlights a need for well-designed experiments, and monitoring
 programs incorporating co-occurring taxa, to determine the underlying
 mechanisms and prevalence of congruent biodiversity change as
 anthropogenic environmental change accelerates apace.
DOI: 10.5061/dryad.r2280gbhw
title: A Great Escape: resource availability and density-dependence shape population dynamics along trailing range edges

description: Populations along geographical range limits are often exposed to
 unsuitable climate and low resource availability relative to core
 populations. As such, there has been a renewed focus on understanding the
 factors that determine range limits to better predict how species will
 respond to global change. Using recent theory on range limits and
 classical understanding of density dependence, we evaluated the influence
 of resource availability on the snowshoe hare Lepus americanus along its
 trailing range edge. We estimated variation in population density, habitat
 use, survival, and parasite loads to test the Great Escape Hypothesis
 (GEH), i.e. that density dependence determines, in part, a species’
 persistence along trailing edges. We found that variability in resource
 availability affected density and population fluctuations and led to
 trade-offs in survival for snowshoe hare populations in the northeastern
 USA. Hares living in resource-limited environments had lower and less
 variable population density, yet higher survival and lower parasitism
 compared to populations living in resource-rich environments. We suggest
 that density-dependent dynamics, elicited by resource availability,
 provide hares a unique survival advantage and partly explain persistence
 along their trailing edge. We hypothesize that this low-density escape
 from predation and parasitism occurs for other prey species along trailing
 edges, but the extent to which it occurs is likely conditional on the
 quality of matrix habitat. Our work indicates that biotic factors play an
 important role in shaping species’ trailing edges and more detailed
 examination of non-climatic factors is warranted to better inform
 conservation and management decisions.
description: See methods in provided in the published paper.
description: The open source software program R were used for all statistical
 analyses. All R packages used are listed in the manuscript or in the R
 files associated with the Dryad submission for this paper.
 <strong>We politely request to be contacted by parties interested in
 data reuse to discuss collaboration</strong>.
DOI: 10.5061/dryad.8pk0p2nt4
title: Scholarly publishing in a developing nation

description: The scholarly literature from the developing world is low, and the
 scientific impact in some countries, including Libya, is much lower
 compared with their peers. This study explores the editorial
 practices and editors’ perspectives to gain insight into the standard of
 scholarly publishing in Libya.
description: Between
 January 21<sup>th</sup> 2022 and February
 12<sup>th</sup> 2022, the editors-in-chief (EC) of Libyan
 academic journals were identified and invited to participate in this
 study, with a self-administered questionnaire that includes questions on
 the editorial practices, the degree of satisfaction with the submitted and
 published manuscripts, the review process, and the journal's
 performance, as well as the challenges facing the journals. The websites
 of the journals were also examined for journal quality and indexation
 coverage and citations were assessed. Moreover, we examined the number of
 citations in Google Scholar for all articles published in 2019 in each
 journal. Descriptive statistics were used to quantitatively summarize the
 data and thematic analysis were used for the narrative text. 
description: Microsoft Excel