cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq83bk3r9
title: Short-term prediction through ordinal patterns

description: Prediction in natural environments is a challenging task, and there is a
 lack of clarity around how a myopic organism can make short-term
 predictions given limited data availability and cognitive resources. In
 this context, we may ask what kind of resources are available to the
 organism to help it address the challenge of short-term prediction within
 its own cognitive limits. We point to one potentially important resource:
 ordinal patterns, which are extensively used in physics but not in the
 study of cognitive processes. We explain the potential importance of
 ordinal patterns for short-term prediction, and how natural constraints
 imposed through (1) ordinal pattern types, (2) their transition
 probabilities and (3) their irreversibility signature may support
 short-term prediction. Having tested these ideas on a massive data set of
 Bitcoin prices representing a highly fluctuating environment, we provide
 preliminary empirical support showing how organisms characterized by
 bounded rationality may generate short-term predictions by relying on
 ordinal patterns.
description: The data file holds 60000 samples of 62 minutes of trade prices
 in permutations form of the bitcoin exchange bitstamp
 The readme files contain the explanation of the code for the
 article.
description: The main function has the code for the run and only the local
 path for the files directory is needed to be changed.
 The epoch variable is the window size to use and can be up to
 60.
DOI: 10.5517/ccdc.csd.cc2pwbgd
title: CCDC 2498924: Experimental Crystal Structure Determination

description: Related Article: Horacio López Sandoval|2026|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pwbhf
title: CCDC 2498925: Experimental Crystal Structure Determination

description: Related Article: Horacio López Sandoval|2026|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.n5tb2rbtr
title: The effect of sertraline on depression and associations with persistent depression in survivors of HIV-related cryptococcal meningitis

description: Background: Depression is associated with worse outcomes in persons living
 with HIV/AIDS and has a prevalence more than three times as high as in the
 general population. Despite this, there are few randomized studies of
 antidepressants in HIV-infected Africans. Methods: We enrolled 460
 HIV-infected Africans with cryptococcal meningitis into a randomized
 clinical trial of adjunctive sertraline vs placebo (2015-2017). We
 screened for clinical depression using the Center for Epidemiologic
 Studies Depression Scale (CES-D) at one and three months after meningitis
 diagnosis and initiation of treatment. We evaluated the relationship
 between sertraline and depression, as well as associations with persistent
 depression, at three months. Results: At one- and three-months post
 meningitis diagnosis, 62% (108/174) and 44% (74/169) of all subjects had
 depression (CES&gt;15), respectively. At three months,
 sertraline-treated subjects were non-significantly more likely to be
 depressed than placebo-treated subjects (64% vs 37%, p=0.09) but were
 significantly less likely to have severe depression (CES&gt;26) (OR
 0.335; 95%CI, 0.130-0.865). Of those with depression at one month,
 sertraline-treated subjects were less likely than placebo-treated subjects
 to be depressed at three months (p=0.05). Sertraline was the only factor
 we found significant in predicting persistent depression at three months
 among those who had depression at one month. Conclusions: Depression is
 highly prevalent in HIV-infected persons who have survived cryptococcal
 meningitis. We found that sertraline is associated with a modest reduction
 in depression in those with depression at baseline and a significant
 reduction in severe depression.
description: Using DataFax SAS was used to combine CRFs
 into a unified dataset
description: 1=male ,       2=female 1=on ART,     2=not on ART 1=GCS &lt; 15, 2=GCS = 15 GCS= Glascow Coma Scale ART=Antiretroviral Therapy CSF= Cerebral Spinal Fluid LP= Lumbar Punctures CESD= Center for Epidemiological Studies Depression Scale The underscore than numbers is a time. _000 means baseline.  CSF WBCs are &lt;5 or 5+ Sterile14= sterile CSF culture at 14 weeks Sterile18= sterile CSF culture at 18 weeks CESD4 means CESD numeric score at 4 weeks post diagnosis with Cryptococcal Meningitis CESD12 is CESD score at 12 weeks vnum= visit number
DOI: 10.5517/ccdc.csd.cc2pwbjg
title: CCDC 2498926: Experimental Crystal Structure Determination

description: Related Article: Horacio López Sandoval|2026|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.q83bk3jgs
title: Data from: Development and testing of an environmental DNA (eDNA) assay for endangered Atlantic sturgeon to assess its potential as a monitoring and management tool

description: Significant declines in Atlantic sturgeon (Acipenser oxyrhynchus
 oxyrhynchus) abundances along the US east coast have spurred major
 research efforts and management actions over the last 50 years, yet
 information on spawning stock abundances and habitat use is still lacking
 for many river systems, including in the Chesapeake Bay, USA. Here, we
 developed and tested a new quantitative PCR (qPCR) assay to detect
 Atlantic sturgeon environmental DNA (eDNA) in water samples with the goal
 of providing an alternative method to monitor presence and relative
 abundance. We also examined Atlantic sturgeon eDNA shedding rates in
 laboratory experiments. A qPCR-probe assay targeting
  Cytochrome-B  was developed and showed no amplification
 of other related and co-occurring fishes. Pond trials at a density of ~0.2
 g/L sturgeon produced relatively strong eDNA detections (~1,000-25,000
 copies/L) in all seven water samples assayed. Water samples taken from two
 river systems in the Chesapeake Bay produced zero eDNA detections in the
 summer, while fall sampling during sturgeon spawning produced positive
 eDNA detections in 26% of samples, though at much lower concentrations
 (400-1,800 copies/L) compared with the pond (mesocosm) detections.
  Acoustic detections of sturgeon near river sampling sites were
 positively associated with eDNA detections. However, the eDNA assay failed
 to detect the presence of sturgeon in some samples when abundances were
 very low or when fish were in deep water. Finally, Atlantic sturgeon eDNA
 shedding rates were estimated to be on the order of estimates for other
 fish species, which suggests that relatively weak detections in the field
 are not necessarily driven by low rates of eDNA shedding. Overall, eDNA
 analysis represents a promising new monitoring tool for Atlantic sturgeon.
 Applying these methods in other rivers along the US east coast is an
 important next step in documenting Atlantic sturgeon distribution for
 management and conservation purposes.
description: Water samples were collected from two rivers in the Chesapeake
 Bay (Nanticoke River, Pamunkey River), pond mesocosms, and indoor
 mesocosms (both with Atlantic sturgeon), and processed to detect Atlantic
 sturgeon eDNA using a quantitative PCR (qPCR) assay. 
description: The ATSDecay_Feb2021_R_Final.csv dataset contains eDNA abundance
 data over time from two replicate mesocosms (tanks ATT1 and ATT2, with 2
 replicate water samples, A and B, at each time point) from the shedding
 rate experiment. The  ATS_Env_Detections_Final.fasta file contains the
 trimmed Sanger sequences produced via the re-amplification and sequencing
 of all positive eDNA detections of Atlantic sturgeon in ponds and
 environmental (river) samples.  <em>Note that
 previous versions of these files (datasets) contained errors so only the
 latest versions (February 2021) are accurate. </em>
DOI: 10.5517/ccdc.csd.cc2pwbkh
title: CCDC 2498927: Experimental Crystal Structure Determination

description: Related Article: Horacio López Sandoval|2026|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.1vhhmgqrq
title: Gaps in genetic knowledge affect conservation management of kiwi (Apteryx) species

description: Worldwide, there is growing appreciation of the importance of integrating
 genetic information into conservation management. However, there are
 commonly occurring problems which impact on doing this successfully. This
 issue is well illustrated by kiwi Apteryx species. Like
 many endangered taxa, extant kiwi populations are small, fragmented and
 isolated, raising concerns of potential inbreeding depression.
 Accordingly, kiwi conservation includes discussion of genetic management
 and translocations. To date, kiwi taxa have been the subject of 41 genetic
 studies. Here we provide the first synthesized review of these studies. We
 conclude that despite the impressive study effort, current understanding
 of kiwi genetics is insufficient to guide genetic management, predict
 translocation outcomes and manage biological diversity to achieve future
 sustainability of the species. We explain why, and outline research
 questions that can be addressed with new genome science technologies.
 Using new technologies to build on the foundation of work already
 undertaken, we see a great opportunity to address key issues for North
 Island Brown Kiwi Apteryx mantelli that are central to
 the conservation concerns for many threatened species. Specifically, we
 suggest that historical, disjunct, mainland populations combined with
 translocations of North Island Brown Kiwi to offshore islands have
 generated unique case studies to investigate the effects of fragmentation,
 cessation of gene flow, inbreeding, outbreeding and hybridization on
 biological diversity.
description: This is a compilation of all published mt DNA sequences from any
 <em>Apteryx</em> species
DOI: 10.6084/m9.figshare.31165051.v1
title: Data for: Measuring community-level functional resistance and community rescue potential under environmental stress

description: The widely used half maximal inhibitory concentration and related indices, e.g., minimum inhibitory concentration and mutant prevention concentration, are <i>in vitro</i> measures of response of biological or biochemical processes to inhibitor substances. We propose to adapt the above concepts for developing standard measures of functional resistance and rescue of ecological communities under environmental pollution. Specifically, a “half inhibitory concentration” index (IC<sub>50</sub>) is defined as the concentration at which a pollutant reduces a community-level function to 50% of the baseline state immediately after exposure. A “half community rescue prevention concentration” index (CRPC<sub>50</sub>) is the concentration at which a pollutant can prevent community-level ecological function from recovering to 50% of the baseline state after a prolonged period of recovery. CRPC<sub>50 </sub>is supposedly higher than IC<sub>50</sub>. We performed two experiments with natural aquatic microbial communities and considered respiration rate as a surrogate of whole-community function. The IC<sub>50</sub> and CRPC<sub>50</sub> of the herbicide glyphosate and the heavy metallic salt copper sulfate were estimated by dose-response curves. One specific finding is that CRPC<sub>50 </sub>values of glyphosate were typically higher than IC<sub>50</sub> by &gt; 2.4 folds, while for copper sulfate the CRPC<sub>50 </sub>values did not significantly differ from IC<sub>50</sub>. This suggested that our microbial communities showed little adaptive response to the latter pollutant agent. Standardized measures of functional resistance and community rescue potential such as those proposed in the present study would be comparable across environmental stress agents and study systems, and improve our study of short- and long-term consequences of environmental pollutants for microbial community functioning.
DOI: 10.6084/m9.figshare.31165051
title: Data for: Measuring community-level functional resistance and community rescue potential under environmental stress

description: The widely used half maximal inhibitory concentration and related indices, e.g., minimum inhibitory concentration and mutant prevention concentration, are <i>in vitro</i> measures of response of biological or biochemical processes to inhibitor substances. We propose to adapt the above concepts for developing standard measures of functional resistance and rescue of ecological communities under environmental pollution. Specifically, a “half inhibitory concentration” index (IC<sub>50</sub>) is defined as the concentration at which a pollutant reduces a community-level function to 50% of the baseline state immediately after exposure. A “half community rescue prevention concentration” index (CRPC<sub>50</sub>) is the concentration at which a pollutant can prevent community-level ecological function from recovering to 50% of the baseline state after a prolonged period of recovery. CRPC<sub>50 </sub>is supposedly higher than IC<sub>50</sub>. We performed two experiments with natural aquatic microbial communities and considered respiration rate as a surrogate of whole-community function. The IC<sub>50</sub> and CRPC<sub>50</sub> of the herbicide glyphosate and the heavy metallic salt copper sulfate were estimated by dose-response curves. One specific finding is that CRPC<sub>50 </sub>values of glyphosate were typically higher than IC<sub>50</sub> by &gt; 2.4 folds, while for copper sulfate the CRPC<sub>50 </sub>values did not significantly differ from IC<sub>50</sub>. This suggested that our microbial communities showed little adaptive response to the latter pollutant agent. Standardized measures of functional resistance and community rescue potential such as those proposed in the present study would be comparable across environmental stress agents and study systems, and improve our study of short- and long-term consequences of environmental pollutants for microbial community functioning.
DOI: 10.7280/d1v39h
title: Proposed managed aquifer recharge projects in California groundwater sustainability plans

description: This dataset contains the text description of Managed Aquifer Recharge
 (MAR) projects proposed by Groundwater Sustainability Agencies
 in California to comply with the requirements of the Sustainable
 Groundwater Management Act (SGMA). The dataset includes projects proposed
 in the Groundwater Sustainability Plans submitted in 2020 for
 critically-overdrafted basins.
description: The Groundwater Sustainability Plans were accessed from https://sgma.water.ca.gov/portal/gsp/all. From each GSP’s list of proposed “Projects and Management Actions”, we identified all projects that specifically mentioned “recharge” in the name or text description. Upon review of the full text description, projects that did not directly aim to achieve recharge (whether directly or in lieu) were dropped. The full text descriptions for all remaining projects are provided in the dataset.
DOI: 10.5061/dryad.05qfttf1q
title: Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae) confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the California big cone pines

description: We sampled 130 individuals (2 to 25 per taxon) of subsections Ponderosae
 and Sabinianae. Nucleotide sequences were obtained by targeting 703 low
 copy nuclear genes. From the unenriched portion of the short reads, we
 assembled nearly complete plastome nucleotide sequences. We used 600
 nuclear genes and the plastome sequences to create phylogenies and species
 trees that we compared to evaluate cytonuclear concordance and
 reticulation. We found that Pinus jeffreyi belongs with subsect.
 Sabinianae based on morphological synapomorphies as well as strong
 molecular phylogenetic support. Pinus ponderosa sensu lato is
 paraphyletic, and we suggest treatment as threes species: P. ponderosa
 sensu stricto (with var. ponderosa, var. benthamiana, and var.
 washoensis), P. scopulorum, and P. brachyptera. The persistence of
 lineages with the footprints of ancient nuclear introgression (labeled bpw
 in clade N4) and chloroplast capture (labeled bpw in clade P1) should
 caution species identification in the Ponderosae based on limited
 molecular data. The hybrid frequency was low based on cytonuclear
 discordance, and the persistence of an ancient P1 plastid clade is a
 better explanation than hybridization between P. ponderosa and P. jeffreyi
 for unexpected plastid associations in the western Sierra Nevada, USA. We
 identified a new potential zone of ancient admixture between P. ponderosa
 and P. scopulorum in Idaho, USA. Some populations of P. arizonica, P.
 brachyptera, P. engelmannii, and P. scopulorum in the USA are more closely
 related to taxa with distributions limited to Mexico than they are to each
 other. To integrate phylogeny and taxonomy, future work should sample
 widely in Mexico and the USA, score morphological characters (including
 seedling characters from the known seed parent), on the same individual as
 used for molecular data, and use methods that are based on individuals
 rather than population frequencies.
description: Nucleotide sequences were obtained by targeting 703 low copy
 nuclear genes. From the unenriched portion of the short reads, we
 assembled nearly complete plastome nucleotide sequences. We used 600
 nuclear genes and the plastome sequences to create phylogenies and species
 trees that we compared to evaluate cytonuclear concordance and
 reticulation.
DOI: 10.5061/dryad.gtht76hk8
title: Data for: Nest cavity reuse by the cooperatively breeding Acorn Woodpecker

description: Although primary cavity-nesting species are capable of excavating new
 cavities, they often reuse old ones. To determine potential factors
 driving such reuse, we studied nest-cavity reuse in the Acorn Woodpecker
 (Melanerpes formicivorus), a cooperative breeding species that reuses old
 cavities for 57.2% of nests at Hastings Reservation in central coastal
 California, USA. We found no evidence for significant fitness costs or
 benefits of cavity reuse compared to using newly constructed cavities. In
 contrast, several lines of evidence supported a role for constraints on
 both cavity reuse and on new cavity construction. The main constraint on
 reuse was cavities failing to survive from one year to the next, usually
 because the limb fell apart, filled with water, or was usurped by another
 species. Evidence that constraints on new cavity construction may be
 important included more frequent cavity reuse when groups renested and use
 of artificial cavities when they were experimentally provided. Nest-cavity
 reuse in this population appears to be driven primarily by constraints,
 including the energetic costs and time required to excavate a new cavity,
 rather than fitness consequences, even though Acorn Woodpeckers regularly
 excavate small holes in trees for acorn storage and the energetic costs of
 new cavity construction are apparently insufficient to significantly
 depress reproductive success. Constraints play a significant role in
 cavity reuse and may affect both the intraspecific and interspecific
 frequency of cavity reuse among facultative excavating species.
description: There are 3 datasets.  ACWOnestmain.xls has
 data for each cavity for each time it was used for nesting.
 ACWOgroupcav.xls was used to test whether reusing an old nest was
 beneficial or not the next year ACWOnestsurv.xls was
 used to conduct survival analyses on the nest cavities
description: See ReadMe.doc file
DOI: 10.5061/dryad.ngf1vhhsh
title: Data from: Belowground competition favors character convergence but not character displacement in root traits

description: 1. Character displacement can play a major role in species ecology and
 evolution, however, research testing whether character displacement can
 influence the evolution of root traits in plant systems remains scarce in
 the literature. Here we investigated the potential that character
 displacement may influence the evolution of root traits using two closely
 related morning glory species, Ipomoea purpurea and I. hederacea. 2. We
 performed a field experiment where we grew the common morning glory, I.
 purpurea, in the presence and absence of competition from I. hederacea and
 examined the potential that the process of character displacement could
 influence the evolution of root traits. 3. We found maternal line
 variation in root phenotypes and evidence that belowground competition
 acts as an agent of selection on these traits. Our test of character
 displacement, however, showed evidence of character convergence on our
 measure of root architecture rather than displacement. These results
 suggest that plants may be constrained by their local environments to
 express a phenotype that enhances fitness. Therefore, the conditions of
 the competitive environment experienced by a plant may influence the
 potential for character convergence or displacement to influence the
 evolution of root traits.