cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p8cz8w9qv
title: Data from: Disturbance alters the forest soil microbiome

description: Billions of microorganisms perform critical below-ground functions in all
 terrestrial ecosystems. While largely invisible to the naked eye, they
 support all higher lifeforms, form symbiotic relationships with ~90% of
 terrestrial plant species, stabilize soils, and facilitate biogeochemical
 cycles. Global increases in the frequency of disturbances are driving
 major changes in the structure and function of forests. However, despite
 their functional significance, the disturbance responses of forest
 microbial communities are poorly understood. Here we explore the influence
 of disturbance on the soil microbiome (archaea, fungi and bacteria) of
 some of the world’s tallest and most carbon-dense forests, the Mountain
 Ash forests of southeastern Australia. From 80 sites, we identified 23,277
 and 19,056 microbial operational taxonomic units from the 0-10 cm and
 20-30 cm depths of soil respectively. From this extensive dataset, we
 found the diversity and composition of these often-cryptic communities has
 been altered by human and natural disturbance events. For instance, the
 diversity of ectomycorrhizal fungi declined with clearcut logging, the
 diversity of archaea declined with salvage logging, and bacterial
 diversity and overall microbial diversity declined with the number of
 fires. Moreover, we identified key associations between edaphic (soil
 properties), environmental (slope, elevation) and spatial variables and
 the composition of all microbial communities. Specifically, we found that
 soil pH, manganese, magnesium, phosphorus, iron and nitrate were
 associated with the composition of all microbial communities. In a period
 of widespread degradation of global forest ecosystems, our findings
 provide an important and timely insight into the disturbance responses of
 soil microbial communities, which may influence key ecological functions.
description: Please see manuscript for detailed methods.
description: <strong>Dryad_Microbial_OTU_Tables_10</strong> - OTU tables of fungi, archaea and bacteria in the 0-10 cm depth of soil w/ taxonomy.<br> *Cols "39198-39376" are unique site IDs<br> <br> <strong>Dryad_Microbial_OTU_Tables_20</strong> - OTU tables of fungi, archaea and bacteria in the 20-30 cm depth of soil w/ taxonomy.<br> *Cols "39197-39375" are unique site IDs <strong>Dryad_Microbial_enviro_table</strong> - Site data: soils, soil fertility, microbial diversity, disturbance.<br> *Cols: "CLF" & "clearcut"= clearcut logging; "Salv_log" & "Salvage"=salvage logging; "TSD"= time since last disurbance;<br> "Fungi_020cm"= fungal diversity 20-30 cm soil; "Bacteria_020cm"= bacteria diversity 20-30 cm soil; "Archaea_020cm"​​​​​​​= archaea diversity 20-30 cm soil. <br> "Fungi_010cm"​​​​​​​= fungal diversity 0-10 cm soil; ​​​​​​​"Bacteria_010cm"​​​​​​​= bacteria diversity 0-10 cm soil; "Archaea_010cm"​​​​​​​= archaea diversity 0-10 cm soil.
DOI: 10.5061/dryad.qrfj6q5g7
title: A morphometrics analysis of the widespread Triplaris americana (Polygonaceae)

description: Triplaris (Polygonaceae) is a genus of 18 species of fast-growing
 dioecious trees. Triplaris is widely distributed in the Neotropics, with a
 center of diversity in the western portion of the Amazon basin. The most
 recent revision of the genus was one of consolidation, lumping a large
 number of names into a small number of species concepts. One species in
 particular, T. americana, is presently an amalgamation of 15 historical
 taxonomic concepts. Moreover, as currently circumscribed, T. americana is
 morphologically variable and ranges over the whole of the Neotropics,
 despite the fact that most species in the genus have restricted geographic
 ranges. Given the recent taxonomic history of Triplaris, the infraspecific
 variation observed in T. americana, and the narrow endemism observed in
 most species of Triplaris, it is reasonable to question whether T.
 americana, as it is currently circumscribed, in fact constitutes a single
 species. This study examined the circumscription of T. americana using a
 morphological species concept, morphometrics, and hierarchical clustering.
 Hierarchical clustering revealed that the morphological variation present
 in 136 specimens of T. americana could be explained by dividing those
 specimens into two groups of plants. These groups however, could not be
 reliably distinguished morphologically. The distribution of values and
 morphologies among the various groups always overlapped. As a result, this
 work supports retaining T. americana as a single, widespread, and
 morphologically variable species.
description: To generate the plots, users must have R and RStudio
 installed.
DOI: 10.5061/dryad.pc866t1p2
title: Gene expression profiles compared in environmental and malnutrition enteropathy in Zambian children and adults

description: Background: Environmental enteropathy (EE) contributes to growth
 failure in millions of children worldwide, but its relationship to
 clinical malnutrition has not been elucidated. We used RNA sequencing to
 compare duodenal biopsies from adults and children with EE, and from
 children with severe acute malnutrition (SAM), to define key features of
 these malnutrition-related enteropathies. Methods: RNA was
 extracted and sequenced from biopsies of children with SAM in hospital
 (n=27), children with non-responsive stunting in the community (n=30), and
 adults living in the same community (n=37) using an identical sequencing
 and analysis pipeline. Two biopsies each were profiled and differentially
 expressed genes (DEGs) were computed from the comparisons of the three
 groups. DEG lists from these comparisons were then subjected to analysis
 with CompBio software to assemble a holistic view of the biological
 landscape and IPA software to interrogate canonical pathways.
 Findings: Dysregulation was identified in goblet cell/mucin
 production and xenobiotic metabolism/detoxification for both cohorts of
 children, versus adults. Within the SAM cohort, substantially
 greater induction of immune response and barrier function,
 including NADPH oxidases was noted, concordant with broadly reduced
 expression of genes associated with the brush border and intestinal
 structure/transport/absorption. Interestingly, down regulation of
 genes associated with the hypothalamic-pituitary-adrenal axis was
 selectively observed within the cohort of children with stunting.
 Interpretation: Gene expression profiles in environmental
 enteropathy and severe acute malnutrition have similarities, but SAM has
 several distinct transcriptional features. The intestinal capacity to
 metabolise drugs and toxins in malnourished children requires further
 study.
description: RNA sequencing was performed on biopsies of small intestinal
 mucosa in three groups of individuals in Lusaka, Zambia: adults with
 environmental enteropathy, children with stunting living in the same
 community as the adults, and children in hospital with severe acute
 malnutrition (SAM) and persistent diarrhoea. Data are FPKM values for
 individual transcripts obtained using RSEM software.
description: Please refer to README file for usage notes.
DOI: 10.5061/dryad.wdbrv15pg
title: Staying close to home: Ecological constraints on space use and range fidelity of a mountain ungulate

description: Understanding patterns of animal space use
 and range fidelity has important
 implications for species and habitat conservation. For
 species that live in highly seasonal environments, such as mountain goats
 (Oreamnos americanus), spatial use patterns are expected to vary in
 relation to seasonal changes in environmental conditions and sex‐ or
 age-specific selection pressures. To address hypotheses
 about sex, age, and
 seasonality influence on space use ecology, we
 collected GPS location data from 263 radio‐collared mountain goats (males,
 n = 140; females, n =123) in coastal Alaska during 2005 – 2016. Location
 data were analyzed to derive seasonal and sex‐specific
 fixed-kernel home range estimates, and to quantify the
 degree of seasonal range and utilization distribution
 overlap. Overall, we determined that home range size
 was  smallest during winter, expanded coincident with
 the onset of green-up and parturition, and were largest
 during summer. Home range size of
 males and females did not differ significantly during winter, but females
 had larger home ranges than males during summer; a relationship
 that was switched during the mating season. Pairwise
 comparisons involving individual females across subsequent years
 indicated home ranges were significantly
 smaller during years when they gave birth to offspring. Mountain
 goats exhibited a strong degree of range fidelity,
 and  99% (n =138) of individual
 animals returned to their previous year’s
 seasonal range with an average
 annual Bhattacharyya’s Affinity utilization
 distribution overlap index of
 68%. Similarity of seasonal home
 range utilization distributions varied in relation to
 sex and season in some respects. Home
 range overlap was highest during the
 summer vegetation growing season, particularly among
 females. These findings advance our understanding about how environmental
 variation and sex- and age-related reproductive constraints influence
 space use and range fidelity among alpine
 ungulates. Documentation of the high degree
 of range fidelity among mountain goats has
 important conservation implications in landscapes increasingly altered by
 anthropogenic activities.
DOI: 10.5061/dryad.b8gtht7cv
title: Materials characterization and adsorption isotherm data

description: Nano-zirconia (ZO) was synthesized using a microwave assisted one pot
 precipitation route. Two biopolymers, chitosan (CTS) and carboxymethyl
 cellulose (CMC), were then combined with zirconia at different w/w ratios
 in order to identify the system with the most improved sorption properties
 towards Pb(II), Cd(II), As(V) and F-. The formulation with 30% w/w
 chitosan (ZO-CTS) was found to give enhanced uptake of F- and As(V).
 Improved sorption properties could not be observed for Pb(II) and Cd(II)
 in any of the ZO-polymer blends, with ZO being the most potent sorbent
 here. ZO and the lead system ZO-CTS were characterized in detail using
 Fourier transform infra-red spectroscopy, scanning electron microscopy,
 X-ray diffraction and X-ray photoelectron spectroscopy (XPS). These
 confirmed the formation of a composite system comprising nanoparticles
 with 50 nm in size in which ZO was present in the amorphous form.
 Interactions between Zr and the amide and hydroxide groups of chitosan
 were suggested from XPS. Batch adsorption studies were carried out and
 equilibrium adsorption data were fitted to a series of isotherm models. It
 was observed that the combination of ZO with CTS improved the F- and As(V)
 adsorption capacity most notably at pH 5.2. Fluoride adsorption by ZO-CTS
 followed the Freundlich isotherm model, with an adsorption capacity of 120
 mg/g. Adsorption of As(V) by ZO-CTS could be fitted with both the Langmuir
 and Freundlich isotherm models, and was found to have a capacity of 14.8
 mg/g. Gravity filtration studies were also carried out at two different pH
 levels to test the feasibility of ZO-CTS in real-world applications. These
 indicated that the sorbent could be used to filter a significant volume of
 water and ensure that pollutant levels remained below acceptable values.
DOI: 10.5061/dryad.2v6wwpznk
title: Host identity matters – up to a point: the community context of Batrachochytrium dendrobatidis transmission

description: The level of detail on host communities needed to understand multi-host
 parasite invasions is an unresolved issue in disease ecology. Coarse
 community metrics that ignore functional differences between hosts, like
 host species richness, can be good predictors of invasion outcomes. Yet,
 if host species vary in the extent to which they maintain and transmit
 infections, then explicitly accounting for those differences may be
 important. Through controlled mesocosm experiments and modelling, we show
 that interspecific differences between host species are important for
 community-wide infection dynamics of the multi-host fungal parasite of
 amphibians, Batrachochytrium dendrobatidis (Bd), but only up to a point.
 The most abundant host species in our system, fire salamander larvae
 (Salamandra salamandra), did not maintain or transmit infections. Rather,
 two less abundant ‘auxiliary’ host species, Iberian tree frog (Hyla
 molleri) and spiny toad (Bufo spinosus) larvae, maintained and transmitted
 Bd. Frogs had the highest mean rates of Bd shedding, giving them the
 highest contributions to R0. Toad contributions to R0 were substantial
 however, and when examining community-level patterns of infection and
 transmission, the effects of frogs and toads were similar. Specifying more
 than just host species richness to distinguish salamanders from auxiliary
 host species was critical for predicting community-level Bd prevalence and
 transmission. Distinguishing frogs from toads, however, did not improve
 predictions. These findings demonstrate limitations to the importance of
 host species identities in multi-host infection dynamics. Host species
 that exhibit different functional traits, like susceptibility and
 infectiousness, may play similar epidemiological roles in the broader
 community.
DOI: 10.5061/dryad.905qfttm2
title: A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long-distance dispersal

description: Aim: Digitization of herbarium specimens and DNA sequencing
 efforts in the past decade have enabled integrative analyses of patterns
 of diversity and endemism in a phylogenetic context. Here, we compare the
 best available floristic databases to a comprehensive specimen database to
 examine spatial patterns of moss phylogenetic assembly. We test the
 hypotheses that 1) mosses exhibit phylogenetic regionalization, 2) islands
 contain significantly high phylogenetic diversity, and 3) that moss
 phylogenetic endemism is low on a global scale. Location: Global
 Taxon: Mosses Methods: We developed a phylogeny of 3,654
 moss species using 25 markers and compiled a global specimen database from
 online repositories. We calculated floristic and phylogenetic measures of
 diversity and endemism and performed randomizations to test for
 significant deviations from expectations. We use rarefaction and
 extrapolation to alleviate substantial differences in sampling effort
 across the globe. We used both phylogenetic and floristic methods to test
 for spatial regionalization. We compare our specimen-based results to
 those obtained using a floristic dataset. 
 Results: Phylogenetic diversity is more robust to missing data
 than species richness. Mean phylogenetic distance was significantly higher
 than expected in areas with high species richness, indicating that
 reported richness in these areas is likely a product of repeated
 colonization. Phylogenetic endemism is low globally. Phylogenetic
 regionalizations cluster into a Holarctic/Holantarctic temperate region, a
 pantropical region, and a region composed of Australia, New Zealand, and
 South Africa. Main Conclusions: Future efforts for collecting,
 sequencing, and databasing moss species should focus on the tropics,
 particularly Africa and Southeast Asia. We provide further evidence to
 support several important theories developed in moss biogeography,
 including the role of long-distance dispersal in shaping floristic
 patterns, the dominance of anagenesis in driving patterns of island
 diversity, and the role of climatic instability in driving patterns of
 assembly in the Holarctic.
DOI: 10.5061/dryad.9w0vt4bg3
title: Health care-related economic burden of polycystic ovary syndrome in the United States: Pregnancy-related and long-term health consequences - supplemental data

description: Context: Polycystic ovary syndrome (PCOS) is the most common
 endocrine disorder of reproductive-aged women, affecting approximately
 5-20% of women of reproductive age. A previous estimate noted that the
 economic burden of PCOS approximates $3.7 billion annually in 2020 USD
 when considering only the costs of the initial diagnosis and of
 reproductive endocrine morbidities, not considering the costs of
 pregnancy-related and long-term morbidities. Objective: To
 estimate the excess prevalence and economic burden of pregnancy-related
 and long-term health morbidities attributable to PCOS. Data
 Sources: PubMed, EmBase and Cochrane Library. Study
 Selection: Studies in which the diagnosis of PCOS was consistent
 with the Rotterdam, National Institutes of Health (NIH), or Androgen
 Excess & PCOS (AE-PCOS) Society criteria, or that used electronic
 medical record diagnosis codes, or diagnosis based on histopathologic
 sampling were eligible for inclusion. Studies that included an outcome of
 interest and a control group of non-PCOS patients who were
 matched or controlled for body mass index (BMI) were
 included.   Data Extraction: Two investigators
 working independently extracted data on study characteristics and
 outcomes.  Data Synthesis: Data was pooled using
 random-effects meta-analysis. The I 2 statistic was used
 to assess inter-study heterogeneity. The quality of selected
 studies was assessed using the Newcastle-Ottawa Scale.
 Results: The additional total healthcare-related economic burden
 due to pregnancy-related and long-term morbidities associated with PCOS in
 the United States is estimated to be $4.3 billion annually in 2020 USD.
description: PubMed, EmBase, and the Cochrane Library were searched to
 identify English-language articles with no date restriction.
 Observational, controlled studies that examined the risk of adverse
 pregnancy outcomes (GDM, gHTN, and preeclampsia), or long-term health
 outcomes (T2DM, MI, or stroke) in women with PCOS compared with a control
 group were eligible for inclusion. Studies without a control group, or
 that did not match or control for body mass index (BMI) were excluded.
 Studies that reported relative risks, odds ratios, or incidence data were
 eligible for inclusion, while those reporting hazard ratios were
 excluded.  Search strategy and study identification was
 performed by one investigator (C.R.) using a standardized approach.
 Articles selected for inclusion were then screened by a second author
 (A.Z.). Two investigators worked in duplicate to independently extract
 data on study characteristics
DOI: 10.5061/dryad.8kprr4xp1
title: Smoking data of hospitalized Covid-19 patients

description: Data related to 1040 patients with Covid-19 admitted to hospitals in Iran
 have been collected. These patients were randomly selected from patients
 admitted to hospitals in Rasht, Tehran, and Bojnord. Of these 1040
 patients, 375 of them are female, and 665 of them are male. Also, the age
 of these people is between 14 and 91 years, and the average age is about
 54 years.
DOI: 10.5061/dryad.6wwpzgn00
title: Agricultural intensification erodes taxonomic and functional diversity in Mediterranean olive groves by filtering out rare species

description: 1. Agri-Environmental Schemes (AES) have been proposed to mitigate the
 impact of agriculture on both taxonomic and functional biodiversity.
 However, a better knowledge of the mechanisms involved in the loss of
 agrobiodiversity is needed to implement efficient AES. An unbalanced
 effort on research towards arable lands compared to permanent crops, and
 on fauna relative to plants, is patent, which limits the generalization of
 AES effectiveness. 2. We evaluated the effects of agricultural
 management and landscape simplification on taxonomic and functional
 diversity of the ground herb cover of 40 olive groves. We use a recently
 developed approach based on Hill numbers (rare, common and dominant
 species based) to analyze taxonomic and functional dissimilarity between
 farms with contrasting agricultural practices, and its potential
 attenuation by landscape complexity. We further explore the filtering
 effect of agricultural intensification on functional traits, and the
 relationship between functional and species richness across landscapes. 3.
 We found that taxonomic and functional dissimilarity of herb assemblages
 between intensively and low-intensively managed fields was mainly due to
 rare species. Dissimilarity decreased as landscape complexity increased,
 evidencing that complex landscapes attenuate the impact of agriculture
 intensification on herb assemblage composition. Agricultural
 intensification favoured more functionally homogeneous assemblages and
 disfavoured the herbs pollinated by insects, while it did not seem to
 affect wind-pollinated species. 4. Overall, functional richness increased
 exponentially with species richness across landscapes, but the latter was
 insufficient to drive any clear enhancement in functional richness in
 simple landscapes. In contrast, high species richness accelerated the
 enhancement in functional richness in intermediate and complex landscapes.
 These results highlight the functional filtering that intensive
 agriculture has generated for decades in homogeneous olive-dominated
 landscapes. 5. Herb cover is essential to support the fauna of permanent
 croplands and their sustainable production. Hence, AES in these croplands
 should promote management practices favouring the diversity and
 functionality of herb assemblages. Such AES should be particularly
 prioritized in homogeneous landscapes, where ground herb cover composition
 and function has long been homogenized to a great extent.
description: All the methods are described in detail in the scientific paper
 associated.