cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3ffbg79jb
title: Northward range expansion of rooting ungulates decreases detritivore and predatory mite abundances in boreal forests

description: The last decades wild boar populations have expanded northwards,
 colonizing boreal forests. The soil disturbances caused by wild boar
 rooting may have an impact on soil organisms that play a key role in
 organic matter turnover. However, the impact of wild boar colonisation on
 boreal forest ecosystems and soil organisms remains largely unknown. We
 investigated the effect of natural and simulated rooting on decomposer and
 predatory soil mites (total, adult and juvenile abundances; and proportion
 of adult-juvenile). Our simulated rooting experiment aimed to disentangle
 the effects of a) bioturbation due to soil mixing and b) removing organic
 material (wild boar food resources) on soil mites. Our results showed a
 decline in the abundance of adult soil mites in response to both natural
 and artificial rooting, while juvenile abundance and the relative
 proportion of adult-juvenile were not affected. The expansion of wild boar
 northwards and into new habitats has negative effects on soil decomposer
 abundances in boreal forests which may cascade through the soil food web
 ultimately affecting ecosystem processes. Our study also suggests that a
 combined use of natural and controlled experimental approaches is the way
 forward to reveal any subtle interaction between aboveground-belowground
 organisms and the ecosystem functions they drive.
DOI: 10.5061/dryad.jm63xsjbm
title: Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture

description: Premise: When divergent lineages come into secondary contact reproductive
 isolation may be incomplete, thus providing an opportunity to investigate
 how speciation is manifested in the genome. The Louisiana Irises (Iris,
 series Hexagonae) comprise a group of three or more ecologically and
 reproductively divergent lineages that can produce hybrids where they come
 into contact. In this study we sought to estimate standing genetic
 variation to understand the current distribution of population structure
 in the Louisiana Irises. Methods: We used genotyping-by-sequencing
 techniques to sample the genomes of Louisiana Iris species across their
 ranges. Twenty populations were sampled (total n=632) across 11,249 loci.
 Population genetic data were assessed using ENTROPY and PCA
 models.  Results: We discovered evidence for interspecific gene
 flow in parts of the range and revealed patterns of population structure
 at odds with widely accepted nominal taxonomy. Undescribed hybrid
 populations were discovered that were designated as belonging to the I.
 brevicaulis lineage. Iris nelsonii shared significant ancestry with only
 one of the purported parent species, I. fulva, evidence inconsistent with
 a hybrid origin. Conclusions: This study provides several key findings
 important to the investigation of standing genetic variation in the
 Louisiana Iris species complex. Iris brevicaulis has a large amount of
 genetic diversity within it relative to the other nominal species. In
 addition, this study has discovered a previously unknown hybrid zone
 between I. brevicaulis and I. hexagona along the Texas coast. Finally, I.
 nelsonii does not appear to have mixed ancestry from three parental taxa
 as has been the longstanding hypothesis.
DOI: 10.57841/casdc.0007112
title: 水凝胶组装构筑电磁波吸收结构材料
DOI: 10.5061/dryad.cvdncjt4t
title: The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models

description: Mathematical models of epidemics are important tools for predicting
 epidemic dynamics and evaluating interventions. Yet, because early models
 are built on limited information, it is unclear how long they will
 accurately capture epidemic dynamics. Using a stochastic SEIR model of
 COVID-19 fitted to reported deaths, we estimated transmission parameters
 at different time points during the first wave of the epidemic
 (March–June, 2020) in Santa Clara County, California. Although our
 estimated basic reproduction number (R0) remained stable from early April
 to late June (with an overall median of 3.76), our estimated effective
 reproduction number (RE) varied from 0.18 to 1.02 in April before
 stabilizing at 0.64 on 27 May. Between 22 April and 27 May, our model
 accurately predicted dynamics through June; however, the model did not
 predict rising summer cases after shelter-in-place orders were relaxed in
 June, which, in early July, was reflected in cases but not yet in deaths.
 While models are critical for informing intervention policy early in an
 epidemic, their performance will be limited as epidemic dynamics evolve.
 This paper is one of the first to evaluate the accuracy of a nearly
 epidemiological compartment model over time to understand the value and
 limitations of models during unfolding epidemics.
DOI: 10.5061/dryad.sj3tx965h
title: Larger males facilitate population expansion in Ophraella communa

description: One of the most intriguing concepts in animal ecology is the reproductive
 advantages offered by larger body size, and the females prefer to mate
 with larger males in order to gain reproductive advantage. Currently, it
 is not clear how females recognize signs of male “quality” and what
 mechanisms are involved in producing offspring with direct or indirect
 benefits. Our study aims to assess the preferences of females for males in
 Ophraella communa, determine the reproductive benefits and reveal the
 underlying mechanism behind this advantage. We demonstrate that male body
 size is an important determinant in the evolutionary process of O.
 communa, affecting female mate choice. Moreover, our study establishes
 that females prefer males with a larger body size, and this could further
 improve the developmental and reproductive fitness of their offspring.
 Finally, we focus on the seminal fluid proteins (SFPs) in O. communa,
 determine differentially expressed genes (i.e., OcACE, OcCBP and OcSFP) by
 analyzing their proteomes and transcriptomes, and define the role of these
 SFPs-related genes through RNAi. Our study proved that the reproductive
 benefit of large males may be regulated by biased expression of crucial
 SFPs genes. The present study advances our understanding of the biological
 significance of preferential mating.
DOI: 10.5061/dryad.t1g1jwt2x
title: The XRD and IR results of silicalite-1 seeds

description: The crystal size of ZSM-5 zeolites synthesized through the hydrothermal
 synthesis with commercial silica sol could be controlled by adding
 colloidal silicalite-1 seeds. Different-sized silicalite-1 crystals were
 synthesized uder different temperature and crystallization time by clear
 liquid reflux method. After centrifuging, washing and drying, the
 properties of the solid silicalite-1 crystals were characterized. The
 results of  XRD and IR indicated that both the seeds possessed
 MFI structure.  The crystallinity of the seed increased
 with the increase of crystallization temperature. The particle size of
 silicalite-1seeds depended on the synthesis temperature when other
 synthetic conditions were the same.  The ZSM-5 zeolites
 with controllable crystal size in the range of 200 nm-2200 nm could be
 obtained by adding the silicalite-1 seeds with different amounts and
 synthesis conditions. The growth of ZSM-5 crystal for the seed-induction
 synthesis process followed a seed surface crystallization mechanism.
DOI: 10.5061/dryad.0gb5mkm1v
title: Community species diversity mediates the trade-off between aboveground and belowground biomass for grasses and forbs in degraded alpine meadow, Tibetan Plateau

description: Although many empirical experiments have shown that increasing degradation
 results in lower aboveground biomass (AGB), our knowledge of the magnitude
 of belowground biomass (BGB) for individual plants is a prerequisite for
 accurately revealing the biomass trade-off in degraded grasslands. Here,
 by linking the AGB and BGB of individual plants, species in the community,
 and soil properties, we explored the biomass partitioning patterns in
 different plant functional groups (grasses of Stipa capillacea and forbs
 of Anaphalis xylorhiza). Our results indicated that 81% and 60% of the
 biomass trade-off variations could be explained by environmental factors
 affecting grasses and forbs, respectively. The change in community species
 diversity dominated the biomass trade-off via either direct or indirect
 effects on soil properties and biomass. However, the community species
 diversity imparted divergent effects on the biomass trade-off for grasses
 (scored at -0.72) and forbs (scored at 0.59). Our findings suggest that
 plant communities have evolved two contrasting strategies of biomass
 allocation patterns in degraded grasslands. These are the “conservative”
 strategy in grasses, in which plants with larger BGB trade-off depends on
 gigantic roots for soil resources, and the “opportunistic” strategy in
 forbs, in which plants can adapt to degraded lands using high variation
 and optimal biomass allocation.
DOI: 10.5061/dryad.8sf7m0cp6
title: Data from: Timing of spring departure of long distance migrants correlates with previous year's conditions at their breeding site

description: Precise timing of the migration is crucial for animals targeting seasonal
 resources at locations encountered across their annual cycle. Upon
 departure, long distance migrants need to anticipate unknown environmental
 conditions at their arrival site, and they do zkzdsxso with their internal
 annual clock. Here, we tested the hypothesis that long distance migrants
 synchronize their circannual clock according to the phenology of their
 environment during the breeding season, and therefore adjust their spring
 departure date according to the conditions encountered at their breeding
 site the year before. To this end, we used tracking data of Eurasian
 curlews from different locations and combined movement data with
 satellite-extracted green-up dates at their breeding site. Spring
 departure date was better explained by green-up date of the previous year,
 while arrival date at the breeding site was better explained by latitude
 and longitude of the breeding site, suggesting that other factors impacted
 migration timing en route. On a broader temporal scale, our results
 suggest that long distance migrants may be able to adjust their migration
 timing to advancing spring dates in the context of climate
 change. 
description: Spring migration dates of Eurasian curlews and green-up dates at
 the breeding sites
DOI: 10.5061/dryad.1g1jwstwv
title: Alfalfa genotyping-by-sequencing (GBS) data

description: Alfalfa (Medicago sativa L.) quantitative trait loci
 (QTL) mapping population (184 F1) derived from cultivars 3010
 (cold-tolerant) as female parent and CW 100 (cold-sensitive) as male
 parent were genotyped using genotyping-by-sequencing (GBS). Polymorphic
 SNPs unique to either 3010 (AB x AA) or CW 1010 (AA x AB) were identified
 as single dose allele (SDA) markers and used to generate the genetic
 linkage maps. Two sets of linkage maps, a set for each parent, were used
 to map the traits and the QTL were identified. With the genotyping and
 phenotyping informations we were able to map various alfalfa traits such
 as fall dormancy, winter-hardiness, freezing tolerance, flowering time,
 yield and leaf-rust resistance. The raw sequence data were deposited at
 NCBI SRA with the accession number SRP150116. This study identified
 several genomic regions and associated markers that can be further
 utilized in marker-assisted breeding to improve the alfalfa. 
description: This data was collected by sequencing alfalfa QTL mapping using
 genotyping-by-sequencing (GBS).
DOI: 10.5061/dryad.8gtht76q2
title: Label-free imaging of M1 and M2 macrophage phenotypes in the human dermis in vivo using two-photon excited FLIM

description: Macrophages (ΜΦs) are important immune effector cells that promote (M1
 ΜΦs) or inhibit (M2 ΜΦs) inflammation and are involved in numerous
 physiological and pathogenic immune responses. Their precise role and
 relevance, however, are not fully understood for lack of non-invasive
 quantification methods. Here, we show that two-photon excited fluorescence
 lifetime imaging (TPE-FLIM), a label-free non-invasive method, can
 visualize ΜΦs in the human dermis in vivo. We demonstrate in vitro that
 human dermal ΜΦs exhibit specific TPE-FLIM properties that distinguish
 them from the main components of the extracellular matrix and other dermal
 cells. We visualized ΜΦs, their phenotypes and phagocytosis in the skin of
 healthy individuals in vivo using TPE-FLIM. Additionally, machine learning
 identified M1 and M2 MФs with a sensitivity of 0.88±0.04 and 0.82±0.03 and
 a specificity of 0.89±0.03 and 0.90±0.03, respectively. In clinical
 research, TPE-FLIM can advance the understanding of the role of MФs in
 health and disease.
description: For imaging of human ΜΦs, a two-photon tomograph (Dermainspect,
 JenLab GmbH, Jena, Germany), equipped with a tunable femtosecond
 Ti:sapphire laser (Mai Tai XF, Spectra Physics, USA, 710–920 nm, 100 fs
 pulses at a repetition rate of 80 MHz), was used at 3–5 mW for
 measurements of cells in vitro and skin biopsy sections ex vivo, as well
 as human dermis in vivo at 40–50 mW. The excitation wavelength was set to
 760 nm, and a 410–680 nm band pass filter was used to detect two-photon
 excited autofluorescence (TPE-AF), whereas a 375–385 nm band pass filter
 was used to detect the second harmonic generation signals. The axial and
 lateral resolution was approximately 1.2–2.0 and 0.5 µm, respectively. The
 screening depth covers the entire papillary dermis and part of reticular
 dermis.
description: .sdt files are a proprietary file format that can be analyzed
 with SPCImage software (Becker&Hickl, Berlin, Germany)
 Alternatively flimview: A Lightweight python package for FLIM
 image processing can be used (https://github.com/mgckind/flimview) .ipynb is a Jupyter python script and contains the decision tree classifier README file is included.
DOI: 10.5061/dryad.ttdz08kzw
title: Contrasting selection pressure on body and weapon size in a polygynous megaherbivore

description: Sexual size dimorphism (SSD) is a common morphological trait in ungulates,
 with polygyny considered the leading driver of larger male body mass and
 weapon size. However, not all polygynous species exhibit SSD, while
 molecular evidence has revealed a more complex relationship between
 paternity and mating system than originally predicted. SSD is, therefore,
 likely to be shaped by a range of social, ecological and physiological
 factors. We present the first definitive analysis of SSD in the common
 hippopotamus (Hippopotamus amphibius ) using a unique morphological
 dataset collected from 2994 aged individuals. The results confirm that
 hippos exhibit SSD, but the mean body mass differed by only 5% between the
 sexes, which is rather limited compared with many other polygynous
 ungulates. However, jaw and canine mass are significantly greater in males
 than females (44% and 81% heavier, respectively), highlighting the
 considerable selection pressure for acquiring larger weapons. A
 predominantly aquatic lifestyle coupled with the physiological limitations
 of their foregut fermenting morphology likely restricts body size
 differences between the sexes. Indeed, hippos appear to be a rare example
 among ungulates whereby sexual selection favours increased weapon size
 over body mass, underlining the important role that species-specific
 ecology and physiology have in shaping SSD.
description: The data were collected in Queen Elizabeth National Park (QENP),
 Uganda from 1961–1966 by Dr Richard Laws (Nuffield Unit of Tropical Animal
 Ecology) and his research team. Detailed morphological measurements (i.e.
 body mass, height, length and lower jaw weight) were taken from 2994
 hippos culled in and around Lake Edward. All of the hippos were sexed and
 subsequently aged using jaw characteristics, tooth replacement and tooth
 wear as described in Laws (1968). The canine data were extracted from
 figures 12 & 13 in Laws (1968). Laws RM. 1968
 Dentition and Ageing of the Hippopotamus. <i>Afr. J. Ecol.</i>
 6, 19–52.
description: Not all body size metrics were recorded for each hippo. Missing
 values are denoted by empty cells in the spreadsheet.
DOI: 10.5061/dryad.v6wwpzgwn
title: Aligned LSU dataset and phylogenetic relationships of Tylopilus glutinosus

description: Tylopilus glutinosus from Bangladesh is described and illustrated based on
 morphology along with molecular data. This species is characterized by its
 caespitose habitat, a purple pileus that becomes very viscid when wet,
 unchanging context, an ixotrichodermial pileipellis with the outer layer
 consisting of 3–4 cylindrical cells and the inner layer composed of
 filamentous hyphae, broadly fusoid to fusoid basidiospores, and putative
 association with Shorea robusta. Morphologically, this species resembles
 T. plumbeoviolaceoides and T. plumbeoviolaceus. However, some distinctive
 macro- and microscopic features along with geographical distribution and
 host preference can be used to separate them from each other. Furthermore,
 DNA sequence of the nuclear ribosomal large subunit (nrLSU) analysis
 undoubtedly placed them in different lineages or clades within Tylopilus.
 Detailed morphological descriptions, illustrations of the new species, and
 its comparison with the related taxa of Tylopilus are also provided with
 phylogenetic placement.
DOI: 10.5061/dryad.qrfj6q5gn
title: Data from: Fusobacterium nucleatum and Bacteroides fragilis detection in colorectal tumours: optimal target site and correlation with total bacterial load

description: These data were generated to investigate detection of Fusobacterium
 nucleatum (F. nucleatum) and Bacteroides fragilis (B. fragilis) across
 different regions of human colorectal tumours. Relative abundance
 of each species in DNA extracted for clinical molecular mutation testing
 from formalin-fixed, paraffin-embedded (FFPE) tumour samples from 42
 patients was assessed using targeted real-time PCR quantitative
 (qPCR) (the screening cohort).  DNA was then freshly extracted
 from specific regions of tumours testing positive for one or both species
 (n = 20) and from 31 additional patients, and relative abundance of each
 species assessed using qPCR (site investigation cohort). Total bacterial
 load at the tumour luminal surface (where F. nucleatum and B. fragilis
 were most frequently detected) was also assessed by qPCR using primers
 targeting amplification of 16S rRNA. 16S sequencing was performed on
 tumour luminal surface DNA samples from five patients as an orthogonal
 method to confirm the ability to detect the targeted species by qPCR.
description: Bacterial detection was performed on the ViiA7 Real-time PCR
 System (Thermo Fisher Scientific) using PrimeTime® qPCR primers, probes
 and mastermix (IDT) according to the manufacturer’s instructions.
 Reactions were performed using 1X PrimeTime® Gene Expression Master Mix,
 1X PrimeTime®qPCR Assay and up to 10ng of DNA. Cycling conditions were
 95°C for 3 minutes, 60 cycles of 95°C for 5 seconds and 60°C for 30
 seconds. Amplification results were reviewed using QuantStudioTM Real-Time
 PCR Software version 1.1 (Thermo Fisher Scientific). Amplification of
 beta-actin and prostaglandin transporter (PGT) was used to determine
 relative abundance. Diversity profiling was performed
 by AGRF (Australian Genome Research Facility, Melbourne Australia).
 Samples were amplified with universal primers to the V1-V3 region of the
 bacterial 16S gene (forward AGAGTTTGATCMTGGCTCAG; reverse
 GWATTACCGCGGCKGCTG). Amplicons were indexed using the Nextera XT Index Kit
 (Illumina, San Diego, CA, USA) followed by Paired End sequencing on a
 MiSeq next generation sequencer (Illumina). Paired-end reads were
 assembled by aligning the forward and reverse reads using PEAR1 (version
 0.9.5). Primers were identified and trimmed. Trimmed sequences were
 processed using Quantitative Insights into Microbial Ecology (QIIME 1.8)
 USEARCH (version 8.0.1623) and UPARSE software. Sequences were quality
 filtered and sorted by abundance after removal of full-length duplicate
 sequences. Singletons or unique reads were discarded. Sequences were
 clustered and then chimera filtered using “rdp_gold” database as
 reference. Reads were mapped back to Operational Taxonomic Units with a
 minimum identity of 97% and taxonomy was assigned using the QIIME 1
 default classifier, pre-trained against Greengenes database5 (Version
 13_8, Aug 2013).
description: Please refer to ReadMe file.
DOI: 10.5061/dryad.rr4xgxd8t
title: Does the presence of a conspecific increase or decrease fear? Neophobia and habituation in zebra finches

description: Neophobia, defined as the fear of novelty, can be exhibited when
 individuals encounter unfamiliar stimuli in their environment. Neophobia
 has been shown to both increase and decrease when individuals are with
 conspecifics. An increase in latency to contact new objects can be
 explained by the negotiation hypothesis which proposes that individuals in
 groups will negotiate who will approach novelty first, thereby delaying
 the first contact. This negotiation process could co-occur with and mask a
 potential effect of risk dilution, where individuals in groups should
 approach novel objects faster due to lower perceived risk in a social than
 non-social context. Here, we aim to test the risk dilution hypothesis
 using an experimental set-up that precluded negotiation among group
 members by physically separating dyads during social trials. We presented
 zebra finches (Taeniopygia guttata) with different novel objects in both
 social and non-social contexts. We also repeated the presentation of each
 object to investigate, for the first time to our knowledge, the effect of
 social context on the change in neophobia over repeated encounters (i.e.,
 habituation). We found that social context increased the latency to
 approach a novel object upon first presentation of objects (i.e.,
 increased neophobia), but these latencies decreased faster over repeated
 presentations of the objects (i.e., faster habituation) compared to the
 non-social context. These results do not provide support for the risk
 dilution hypothesis regarding first encounters with objects (neophobia)
 but seem to support it over repeated object presentations (habituation).
 This suggests that the effect of social context is different on neophobia
 and habituation, possibly because they recruit different cognitive
 mechanisms. Future studies should investigate the impact of ecological and
 social conditions on decision-making upon first versus subsequent
 encounters with a novel object in social animals, as both processes can
 impact fitness costs and benefits of novelty
 responses.  
description: Please see accompanying paper "Does the presence of a
 conspecific increase or decrease fear? Neophobia and habituation in zebra
 finches", St.Lawrence et al.