cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rv15dv4bv
title: Late gene therapy limits the restoration of retinal function in a mouse model of retinitis pigmentosa

description: Retinitis pigmentosa is an inherited photoreceptor degeneration that
 begins with rod loss followed by cone loss. This cell loss greatly
 diminishes vision, with most patients becoming legally blind. Gene
 therapies are being developed, but it is unknown how retinal function
 depends on the time of intervention. To uncover this dependence, we
 utilize a mouse model of retinitis pigmentosa capable of artificial
 genetic rescue. This model enables a benchmark of best-case gene therapy
 by removing variables that complicate the ability to answer this vital
 question. Complete genetic rescue was performed at 25%, 50%, and 70% rod
 loss (early, mid, and late, respectively). Here we show early- and
 mid-treatment restores retinal function to near wild-type levels,
 specifically the sensitivity and signal fidelity of retinal ganglion
 cells, the output neurons of the retina. However, some anatomical defects
 persist. Late treatment retinas exhibit continued, albeit slowed, loss of
 sensitivity and signal fidelity among retinal ganglion cells, as well as
 persistent gliosis. We conclude that gene replacement therapies delivered
 after 50% rod loss are unlikely to restore visual function to normal. This
 is critical information for administering gene therapies to rescue vision.
description: Raw, unprocessed microscopy images used to generate Figures
 1-3. 
description: Files can be opened using the open source software
 ImageJ/FIJI.
DOI: 10.5061/dryad.z08kprrhm
title: Dataset about sharks in French Polynesia extracted from the ORP citizen science network

description: Observers of the Polynesian Shark Observatory (ORP), a citizen science
 network organized mainly through the Polynesian dive centers, collected an
 unprecedented amount of data in 43% of the islands of French Polynesia
 between July 8, 2011, and April 11, 2018, during 13,916 dives. The
 objective of such a data collection, not accessible to standard research
 resources, was to provide a unique dataset, offering the opportunity to
 explore the specific diversity, distribution, seasonality and abundance of
 many elasmobranch species spread out throughout the overall French
 Polynesia territory. Indeed, since the data are based on random citizen
 observation, the spatial distribution was biased toward the most
 frequented sites and islands where the scuba diving activity is mostly
 developed. Overall, the increase in observed abundance of rays and sharks
 observed in French Polynesia and the three most sampled islands, as well
 as the high specific diversity recorded for the region, provide the first
 evidence of the effectiveness of the Shark Sanctuary established in 2006.
 These data, collected randomly by the volunteers, also give insights about
 potential movement patterns and site fidelity of some species more often
 seen. While not leading to final conclusion, the network of volunteers
 filling with information to the Polynesian Shark Observatory is essential
 in giving preliminary results and research perspectives and directions for
 future projects on sharks and rays in French Polynesia.
DOI: 10.17632/jtsx83g88h
title: On the Unified Field Theory and the Structure of Space-Time

description: This paper proposes a geometric Unified Field Theory where all fundamental interactions, mediator
particles, and vacuum fluctuations are treated as manifestations of space-time curvature. We establish a
direct link between the Ricci scalar curvature (R) and the nature of forces, and introduce a quantized
space-time structure that selectively filters particles based on their volumetric oscillation amplitudes.
DOI: 10.17632/jtsx83g88h.1
title: On the Unified Field Theory and the Structure of Space-Time

description: This paper proposes a geometric Unified Field Theory where all fundamental interactions, mediator
particles, and vacuum fluctuations are treated as manifestations of space-time curvature. We establish a
direct link between the Ricci scalar curvature (R) and the nature of forces, and introduce a quantized
space-time structure that selectively filters particles based on their volumetric oscillation amplitudes.
DOI: 10.5061/dryad.2z34tmpqx
title: Data from: Standing decomposition of dead leaves in winter and its legacy effects should not be ignored in subtropical forests

description: Background and Aims Dead leaves may remain standing all winter before
 entering the soil as litter in subtropical forests. However, little is
 known about the standing decomposition of dead leaves and how this might
 influence subsequent litter decomposition in the soil. Methods We
 conducted an investigation of the standing decomposition of dead leaves in
 winter in a subtropical forest. In the following summer, we conducted a
 decomposition experiment of pre-standing litter (dead leaves picked
 immediately after leaf death) and post-standing litter (dead
 leaves picked after winter) in the soil using the litterbag method,
 further exploring the influences of the standing process on subsequent
 litter decomposition in the soil. Results After 159 days of standing
 decomposition, up to 43% of leaf mass was lost, with lignin and cellulose
 degraded by 30% and 35%, respectively. After 163 days of decomposition in
 the soil, the mass losses of pre-standing and post-standing litter were
 31% and 52%, respectively. The decomposition rate (k) of post-standing
 litter was 2 times that of pre-standing litter. Restrained by the low
 photodegradability of litter in the later stage of decomposition, standing
 decomposition still conformed to the exponential decomposition model.
 Conclusion The standing decomposition of dead leaves in winter is driven
 predominantly by the abiotic process of photodegradation with leaching,
 resulting in substantial carbon loss in the standing phase and a doubling
 of the subsequent litter decomposition rate in soil, thus profoundly
 influencing the carbon process of subtropical forest ecosystems.
DOI: 10.5061/dryad.vt4b8gtwz
title: Datasets from: Local- and landscape-scale drivers of terrestrial herbaceous plant diversity along a tropical rainfall gradient in Western Ghats, India

description: This data set contains information on local- and landscape-level
 terrestrial herbaceous plant diversity and critical abiotic factors along
 a 36-km East-West transect in Mudumalai Tiger Reserve, Tamil Nadu India.
 Understory angiosperms with no above-ground wood (secondary cambial
 growth) were considered as herbaceous plants.
description: We collected this data through field
 surveys of understory plants for three seasons (onset of drought/dry
 season, end of drought, and rainy season) during December 2018 to November
 2019 in the Mudumalai National Park and Tiger Reserve in Tamil Nadu,
 India. The surveys were done in 13 one-ha forest-monitoring plots
 established during 1988–94 Indian Institute of Science, Bengaluru
 (IISc.). Rainfall (mean annual precipitation) data
 was obtained by kriging data from 16 rain gauges along the landscape. Soil
 moisture (percentage soil water) was estimated using gravimetry. Gap
 Fraction (or canopy gap proportion, as a proxy to understory light
 availability) was estimated by analyzing canopy photographs taken using a
 fisheye lens fitted onto a cellphone. Soil samples were analyzed in Kerala
 Agricultural University (India) to estimate plot-level soil
 physico-chemical properties used in principal component analysis (PCA),
 the results of which (PCA axes) is provided in the second datasheet.
 Fire-frequency data (1990–2019) was
 recorded by IISc., since the establishment of the
 plots. There
 are three worksheets: (1) “Herb_Species_Mudumalai (2018-19).csv” contains
 the list of all herbaceous plants, their families, and orders in 13 one-ha
 plots (627 subplots of dimensions 1m x 1m); (2) “Landscape (Plot-level)
 herb data_Mudumalai 2018-19.csv” contains landscape-level (13 one-ha
 plots) data of herbaceous diversity, rainfall, soil moisture, understory
 light (gap fraction), soil factors, fire frequency, and ground cover of
 all understory plants (annual and for three seasons: drought onset,
 drought end, and rainy); (3) “Local (Subplot-level) herb data_Mudumalai
 2018-19.csv” contains local-level (600 subplots) data of herbaceous
 diversity, soil moisture, understory light, and ground cover of all
 understory plants (annual and for three seasons).
description: We used the software R (version 4.1.2)
 to open the data files.
DOI: 10.5061/dryad.kwh70rz7t
title: Supplementary material for: Increased morbidity in gynecomastia: A nationwide register-based cohort study

description: Context: Evidence on the long-term and general health of males with
 gynecomastia is entirely lacking. Objectives: To assess health prior to
 and following a diagnosis of gynecomastia. Methods: A register-based
 cohort study of 140,574 males, of which 23,429 males were diagnosed with
 incident gynecomastia and age- and calendar-matched (1:5) to 117,145 males
 without gynecomastia from the background population. Males with
 gynecomastia were stratified into males without (idiopathic) or with a
 known pre-existing risk factor (disease/medication). Cox and logistic
 regression models investigated associations of disease risk according to
 ICD-10 chapters following and prior to gynecomastia diagnosis. Results: A
 total of 16,253 (69.4%) males in the cohort were identified with
 idiopathic gynecomastia. These males had a statistically significant
 higher risk of future disease across all included disease chapters (HR
 range: 1.19 to 1.89), with endocrine diseases representing the greatest
 disease risk (HR 1.89, 95% CI: 1.76 to 2.03). The highest sub-chapter
 disease risk was observed for disorders of endocrine glands (OR 7.27, 95%
 CI: 6.19 to 8.54). Similarly, the odds ratios of comorbidities were higher
 across all included disease chapters (OR range 1.05 to 1.51), except for
 psychiatric disease (OR 0.72, 95% CI: 0.68 to 0.78), with the highest
 association with musculoskeletal/connective tissue (OR 1.51, 95% CI: 1.46
 to 1.57) and circulatory (OR 1.36, 95% CI: 1.29 to 1.43) diseases.
 Conclusions: The presence of idiopathic gynecomastia is an important first
 clinical symptom of an underlying disease and a significant predictor of
 future disease risk. These findings should stimulate more awareness among
 healthcare providers to increase identification of gynecomastia and its
 causes in males.
DOI: 10.5061/dryad.vq83bk3xr
title: Fungal community composition and genetic potential regulate fine root decay in northern temperate forests

description: Understanding how genetic differences among soil microorganisms regulate
 spatial patterns in litter decay remains a persistent challenge in
 ecology. Despite fine root litter accounting for ~50% of total litter
 production in forest ecosystems, far less is known about the microbial
 decay of fine roots relative to aboveground litter. Here, we evaluated
 whether fine root decay occurred more rapidly where fungal communities
 have a greater genetic potential for litter decay. Additionally, we tested
 if linkages between decay and fungal genes can be adequately captured by
 delineating saprotrophic and ectomycorrhizal fungal functional groups
 based on whether they have genes encoding certain ligninolytic class II
 peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To
 address these ideas, we used a litterbag study paired with fungal DNA
 barcoding to characterize fine root decay rates and fungal community
 composition at the landscape scale in northern temperate forests, and we
 estimated the genetic potential of fungal communities for litter decay
 using publicly available genomes. Fine root decay occurred more rapidly
 where fungal communities had a greater genetic potential for decay,
 especially of cellulose and hemicellulose. Fine root decay was positively
 correlated with ligninolytic saprotrophic fungi and negatively correlated
 with ECM fungi with ligninolytic peroxidases, likely because these
 saprotrophic and ectomycorrhizal functional groups had the highest and
 lowest genetic potentials for plant cell wall degradation, respectively.
 These fungal variables overwhelmed direct environmental controls,
 suggesting fungal community composition and genetic variation are primary
 controls over fine root decay in temperate forests at regional scales.
DOI: 10.5061/dryad.59zw3r2c8
title: Range expansions of sexual versus asexual organisms: Effects of reproductive assurance and migration load

description: It is generally considered that sexual organisms show faster evolutionary
 adaptation than asexual organisms because sexuals can accumulate adaptive
 mutations through recombination. Yet empirical evidence often shows that
 the geographic range size of sexual species is narrower than that of
 closely-related asexual species, which may seem as if asexuals can adapt
 to more varied environments. Two potential explanations for this apparent
 contradiction considered by existing theory are reproduction assurance and
 migration load. Here, we consider both reproductive assurance and
 migration load within a single model to comparatively examine their
 effects on range expansions of sexuals and asexuals across an
 environmental gradient. The model shows that higher dispersal propensity
 decreases sexuals’ disadvantage in reproductive assurance while increasing
 their disadvantage in migration load. Moreover, lower mutation rate
 constrains adaptation more strongly in asexuals than in sexuals. Thus,
 high dispersal propensity and high mutation rates promote that asexuals
 have wider range sizes than sexuals. Intriguingly, our model reveals that
 sexuals can have wider geographic range sizes than asexuals under low
 dispersal propensity and low mutation rates, a pattern consistent with a
 few exceptional empirical cases. Combining reproductive assurance and
 migration load provides a useful perspective to better understand the
 relationships between species’ mating systems and their geographic ranges.
description: We develop this computer simulation model.
description: JDK 1.8
DOI: 10.5061/dryad.41ns1rnjh
title: Cations make a difference: Soil nutrient patches and fine-scale root abundance of individual species in a mountain grassland

description: 1. Root densities in the field vary at the centimetre scale, but we have
 no information on whether this variation is linked to variation in
 nutrient concentrations and availability. Roots of many species are able
 to proliferate in nutrient-rich patches in controlled conditions in
 culture, but because data on nutrient concentrations and, in particular,
 on their temporal stability in the field are scarce, we do not know to
 what extent root distribution in the soil bears traces of such a response.
 2. Here, we linked centimetre-scale measurements of soil nutrient
 concentrations over a period of 6 weeks with estimation of root biomass
 and its species composition at the same points to determine whether there
 is any association between the two. In addition to phosphorus, nitrate and
 ammonium, we determined the concentrations of metal cations (magnesium,
 calcium and potassium). We used qPCR to determine the quantities of
 individual species in the root biomass samples. 3. We found that calcium
 and magnesium (and to a lesser degree phosphorus and potassium) showed
 fine-scale patchiness that was stable over the duration of the study (6
 weeks) and was consistent over all these elements. Nutrient patches were
 associated with high root biomass and the occurrence of roots of several
 species. Such patches are formed primarily by elements with known low
 mobility in soil (cations, phosphorus). In contrast, nitrogen ions showed
 overwhelmingly high temporal variation with no relationship between root
 density and nitrogen concentration. 4. Soil nutrient concentrations thus
 constitute a multidimensional signal. Some elements strongly vary in time,
 while some are much more stable and thus form stable patches that permit
 root response over periods of weeks or months. Among them, calcium and
 magnesium play an important role in forming soil heterogeneity at a scale
 comparable to the scale at which fine root densities also vary. As these
 cations affect a number of plant functions, their association with higher
 root densities confirms their role in growth dynamics of terrestrial
 ecosystems.
DOI: 10.17632/fvyxx8mfsv
title: Suplementary data_Utilization of Bacterial Ghosts as innovative transport vehicles for platinum-based anticancer drugs

description: Element Mapping and Distribution of non-loaded EcN bacterial ghost cells (BGs) and EcN BGs loaded with the anticancer metal complex oxalipaltin OXA. Table S1. shows energy-dispersive X-ray (EDX) weight ratios and element distributions in a selected OXA-loaded BGs sample.
DOI: 10.5061/dryad.rfj6q57fp
title: Global warming leads to habitat loss and genetic erosion of alpine biodiversity

description: Aim: Species living on steep environmental gradients are expected to be
 especially sensitive to global climate change. Here, we combined genetic,
 ecological niche modelling and climatic niche comparisons to investigate
 the influence of climate on the biogeography of three alpine species with
 overlapping ranges. Location: Te Waipounamu (South Island) Aotearoa–New
 Zealand. Taxon: Endemic alpine-adapted Cataontopinae grasshoppers.
 Methods: We used niche modelling to estimate and project the potential
 niche of three focal species under past and future climate scenarios.
 Vulnerability assessments were performed using niche factor analyses.
 Demographic trends and phylogeographic structure were investigated using
 samples from 15 mountain tops to generate mitochondrial DNA haplotype
 networks and population genetic statistics. Results: Niche models and
 genetic data suggest suitable habitat for all three alpine species was
 more widespread and contiguous in the past than today. Demographic
 analyses indicate in situ survival rather than post-Pleistocene
 colonisation of current habitat. Population structuring and genetic
 divergence suggest that mountain uplift during the Pliocene and
 environmental barriers during Pleistocene glacial and interglacial stages
 shaped contemporary population structure of each species. Though
 geographically overlapping, niche analyses suggest these alpine species
 are not ecologically identical, and each shows similar but distinct
 responses to environmental change, but all will lose intraspecific
 diversity through population extinction. Main conclusions: Climatic,
 biological and geophysical factors controlled population structuring of
 three cold-adapted species during the Pleistocene with a legacy of
 spatially separate intraspecific lineages. Ecological niche models for
 each species emphasise distinct combinations of environmental proxies, but
 all are expected to experience severe habitat reduction during climate
 warming. Increased global temperatures drive available habitat to higher
 elevation resulting in population contractions, range shifts, habitat
 fragmentation, local extinctions, and genetic impoverishment. Despite
 alpine species not being ecologically identical, we predict all mountain
 biota will lose significant genetic diversity due to global warming.
DOI: 10.17632/fvyxx8mfsv.1
title: Suplementary data_Utilization of Bacterial Ghosts as innovative transport vehicles for platinum-based anticancer drugs

description: Element Mapping and Distribution of non-loaded EcN bacterial ghost cells (BGs) and EcN BGs loaded with the anticancer metal complex oxalipaltin OXA. Table S1. shows energy-dispersive X-ray (EDX) weight ratios and element distributions in a selected OXA-loaded BGs sample.
DOI: 10.5061/dryad.c2fqz61d1
title: Escaping ESKAPE resistance: In vitro and in silico studies of multifunctional carbamimidoyl-tethered indoles against antibiotic-resistant bacteria

description: Combining the hybridization and repurposing strategies, six compounds from
 our in-house library with a designed hybrid structure of MBX-1162,
 pentamidine and MMV688271 were repurposed as potential antibacterial
 agents. Amongst them, compounds 1a and 1d elicited potential sub-µg/mL
 activity against the high-priority antibiotic-resistant Gram-positive
 members of ESKAPE bacteria as well as antibiotic-susceptible Gram-positive
 bacteria. Furthermore, they showed potential low µg/mL activity against
 the explored critical priority antibiotic-resistant Gram-negative members
 of ESKAPE bacteria. In time-kill assay, compound 1a has effective 0.5 and
 0.25 µg/mL antibacterial lethal concentrations against MRSA in the
 exponential growth phase. In silico investigations predicted compounds 1a
 and 1d as inhibitors of the open conformation of undecaprenyl diphosphate
 synthase involved in bacterial isoprenoid synthesis. In addition,
 compounds 1a and 1d were predicted as inhibitors of the NADPH-free but not
 the NADPH-bound form of ketol-acid reductoisomerase and may also serve as
 potential B-DNA minor groove binders with possible differences in the
 molecular sequence recognition. Overall, compounds 1a and 1d are presented
 as multifunctional potential antibacterial agents for further development
 against high and critical-priority Gram-positive and Gram-negative
 antibiotic-resistant ESKAPE bacterial pathogens as well as
 antibiotic-susceptible Gram-positive bacterial pathogens.
DOI: 10.17632/ddr5h589xt
title: Brief Report: A pharmacokinetic study of single-dose periungual methotrexate injections that induced multi month remission of Nail Psoriasis in five patients.

description: This dataset contains supplementary methods and results for the article "Brief Report: A pharmacokinetic study of single-dose periungual methotrexate injections that induced multi month remission of Nail Psoriasis in five patients.", published to Journal of American Academy of Dermatology .
DOI: 10.7272/q6h70d20
title: Mapping between Human Phenotype Ontology and phecode terminologies

description: This biomedical data repository contains a mapping between the Human
 Phenotype Ontology (HPO) and phecodes which are curated groupings of
 International Classification of Diseases (ICD) codes. These data
 correspond to the mappings published and evaluated in the JAMIA Open
 manuscript, "Linking rare and common disease vocabularies by mapping
 between the Human Phenotype Ontology and phecodes." This mapping was
 created using a variety of data sources and methods, including text
 matching, the National Library of Medicine's Unified Medical Language
 System, Wikipedia, SORTA, and PheMap. The mapping includes 38,950 links,
 and the files allow users to tailor the HPO-phecode links via a variety of
 filters for diverse applications across the spectrum of monogenic to
 polygenic diseases. Other intermediate files and the most up-to-date
 mappings can be found at the "phecode-HPO-map" GitHub repository
 (https://github.com/emcarthur/phecode-HPO-map/).
description: The map between phecodes and HPO terms is constructed using
 multiple types of evidence including string or sub-string match, UMLS,
 SORTA, WikiMedMap and PheMap. The HPO terms used are from the 2022-04-14
 release and phecodes are from version 1.2 available in the PheWAS catalog
 (https://phewascatalog.org/). Mappings are also replicated with Phecode X, which has increased granularity and coverage of terms related to pregnancy, congenital anomalies, and neonatology. Further technical details of the integration process can be found in the manuscript methods. The code used the process, plot, and create the data are in the "phecode-HPO-map" github repository (https://github.com/emcarthur/phecode-HPO-map/).
description: Files are tab-delimited text files that can be opened in any text
 editor or spreadsheet software. Use examples with dataframes in python
 along with a flowchart to recommend mappings for specific needs are
 available in the "phecode-HPO-map" github repository (https://github.com/emcarthur/phecode-HPO-map/).