cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b5mkkwhdp
title: Functional groups in piscivorous fishes

description: Piscivory is a key ecological function in aquatic ecosystems, mediating
 energy flow within trophic networks. However, our understanding of the
 nature of piscivory is limited; we currently lack an empirical assessment
 of the dynamics of prey capture, and how this differs between piscivores.
 We therefore conducted aquarium-based performance experiments, to test the
 feeding abilities of 19 piscivorous fish species. We quantified their
 feeding morphology, striking, capturing, and processing behaviour. We
 identify two major functional groups: grabbers and engulfers. Grabbers are
 characterised by horizontal, long-distance strikes, capturing their prey
 tail first, and subsequently processing their prey using their oral jaw
 teeth. Engulfers strike from short distances, from high angles above or
 below their prey, engulfing their prey, and swallowing their prey whole.
 Based on a meta-analysis of 2,209 published in situ predator-prey
 relationships in marine and freshwater aquatic environments, we show
 resource partitioning between grabbers and engulfers, with grabbers
 feeding on relatively larger prey than engulfers. Our results provide a
 functional classification for piscivorous fishes, delineating patterns
 which transcend habitats, that may help explain size structures in fish
 communities.
description: 'morphology data' folder has the morphological
 variables of the predators used in the study.
 'behaviour' folders are the data of the behaviours
 quantified from the experiments (videos). behaviour 1:
 Angle refers to the strike angle, Strike_D is the strike distance
 (mm). 'behaivour 2' is the capture behaviour.
 1=grab, 0=engulf.
DOI: 10.5061/dryad.bk3j9kdcn
title: Data from: Uncovering key metabolic determinants of the drug interactions between trimethoprim and erythromycin in Escherichia coli

description: Understanding interactions between antibiotics used in combination is an
 important theme in microbiology. Using the interactions between the
 antifolate drug trimethoprim and the ribosome-targeting antibiotic
 erythromycin in Escherichia coli as a model, we applied a transcriptomic
 approach for dissecting interactions between two antibiotics with
 different modes of action. When trimethoprim and erythromycin were
 combined, the transcriptional response of genes from the sulfate reduction
 pathway deviated from the dominant effect of trimethoprim on the
 transcriptome. We successfully altered the drug interaction from
 additivity to suppression by increasing the sulfate level in the growth
 environment and identified sulfate reduction as an important metabolic
 determinant that shapes the interaction between the two drugs. Our work
 highlights the potential of using prioritization of gene expression
 patterns as a tool for identifying key metabolic determinants that shape
 drug-drug interactions. We further demonstrated that the sigma
 factor-binding protein gene crl shapes the interactions between the two
 antibiotics, which provides a rare example of how naturally occurring
 variations between strains of the same bacterial species can sometimes
 generate very different drug interactions.
description: FASTQ files from HiSeq 2500 V4 paired-end 125 bp sequencing were
 trimmed to remove Illumina adaptors. The reads were then quality filtered
 and mapped to the <i>E.
 coli</i> MG1655 reference genome with gene annotations retrieved
 from Ensembl Bacteria (genome assembly:
 ASM584v2): MG1655.fa:
 Reference genome FASTA file MG1655.genome: Gene
 annotation file   BAM files were
 generated using Samtools commands for viewing, indexing and
 sorting: 1-1_s.bam: <em>E. coli</em> MG1655
 treated with trimethoprim (IC<sub>50</sub>); biological
 replicate 1 2-1_s.bam: <em>E. coli</em>
 MG1655 treated with trimethoprim (IC<sub>50</sub>); biological
 replicate 2 1-6_s.bam: <em>E. coli</em>
 MG1655 treated with erythromycin (IC<sub>50</sub>); biological
 replicate 1 2-6_s.bam: <em>E. coli</em>
 MG1655 treated with erythromycin (IC<sub>50</sub>); biological
 replicate 2 1-7_s.bam: <em>E. coli</em>
 MG1655 treated with trimethoprim (IC<sub>50</sub>)
 + erythromycin (IC<sub>50</sub>); biological replicate
 1 2-7_s.bam: <em>E. coli</em> MG1655
 treated with trimethoprim (IC<sub>50</sub>) + erythromycin
 (IC<sub>50</sub>); biological replicate 2
 1-8_s.bam: <em>E. coli</em> MG1655 no-drug control;
 biological replicate 1 2-8_s.bam: <em>E.
 coli</em> MG1655 no-drug control; biological replicate 2
 *.bam.bai files are accompanying BAM index files.
description: Gene counts were extracted from
 the sorted and indexed BAM files using the Python script
 <em>HTSeq</em>. Subsequent
 differential gene expression analysis was performed using the <em>DESeq2</em>
 Bioconductor package as described in the Materials and Methods section of
 the manuscript.
DOI: 10.5061/dryad.crjdfn34g
title: The relationship between umbilical–portal–systemic venous shunt and outcome in 11 fetuses

description: Objective: To investigate the relationship between congenital
 umbilical–portal–systemic venous shunt (UPSVs) and fetal outcome. Methods:
 The ultrasonographic and genetic characteristics of 11 cases of UPSVS were
 retrospectively analyzed and followed up to postnatal. Results: Four cases
 of ductus venosus -- systemic shunt (DVSS), one case of extrahepatic
 portal -- systemic shunt (EHPSS), and one case of umbilical systemic shunt
 (USS) combined with intrahepatic portal-systemic shunt (IHPSS), six cases
 of intrahepatic portal-systemic shunt (IHPSS) were observed. chromosomal
 abnormalities were observed in 9.1% (1/11), other ultrasonic abnormalities
 in 54.5% (6/11), cardiothoracic ratio increase in 45.5% (5/11), fetal
 growth restriction in 36.4% (4/11), edema was in 9.1% (1/11) and live
 birth was in 72.7% (8/11). Conclusion: The incidence of IHPSS is the
 highest and the outcome is the best. Shunt of DVSS and IHPSS can be closed
 spontaneously after birth. When the prenatal diagnosis is congenital
 UPSVs, chromosomal abnormalities and other ultrasonic abnormalities should
 be required further examination, and the growth and development of the
 fetus should be closely monitored.
description: Retrospective analysis was performed on 11
 cases of UPSVSs admitted to the prenatal diagnosis center of our hospital
 l from December 1, 2019, to December 1, 2020. According to the UPSVS
 classification criteria, four cases were DVSS, and six cases were IHPSS,
 including one case of USS combined with IHPSS and one case of EHPSS. All
 patients signed an informed consent form, performed routine ultrasound
 examinations of the fetus, placenta and amniotic fluid, and then performed
 detailed examinations and records of each fetus’s heart, celiac vessel and
 middle cerebral artery, focusing on observation of the umbilical vein and
 ductus venosus , main portal vein, left and right branch morphology,
 internal echo and surrounding structures, observed whether there are
 abnormal ducts between the umbilical vein, ductus venosus, portal vein,
 hepatic vein and other systemic veins, and follow up until the shunt is
 closed after birth. The karyotype and low-coverage massively parallel copy
 number variation sequencing (CNV-seq) of the fetus were further examined
 by amniocentesis. Statistical methods: Descriptive statistics were used to
 retrospectively analyze the clinical features and pregnancy outcomes of 11
 cases. SPSS20.0 software was used for statistical analysis of data.
 Measurement data was expressed as mean(±SD), and the Bonferroni adjustment
 method in ANOVA was used for pairwise comparison. p&lt;0.05 indicates
 that the difference is statistically significant. Counting data are
 expressed as percentages.
DOI: 10.5061/dryad.2280gb5sm
title: Data from: Opposing effects of competition and selection on macroevolutionary dynamics

description: The diversity of species and traits is the outcome of multiple
 evolutionary processes operating over millions of years. These processes
 affect rates of trait evolution, speciation, and extinction. A key problem
 is identifying the relative importance of distinct processes in driving
 observed patterns in species traits and phylogenetic trees. Here, we show
 how two processes, competition and stabilising selection, can act
 opposingly but still leave identifiable traces in macroevolutionary data.
 Building on previous simulation studies, we model the joint influence of
 competition and stabilising selection on rates of trait evolution,
 speciation completion, and extinction. We find that opposing effects
 result in nuanced patterns of trait evolution and diversification dynamics
 that, when considered in isolation, could easily lead to
 misinterpretation. In particular, while the best fitting likelihood model
 of trait evolution is typically Brownian motion when competition and
 stabilising selection act simultaneously, we find stronger phylogenetic
 signal than expected under BM and trait distributions that are distinctly
 platykurtic. Taken together, we suggest that by considering multiple
 simple metrics measuring trait evolution and diversification dynamics it
 may be possible, though challenging, to identify the relative contribution
 of these two processes operating together in macroevolutionary data.
description: The attached data includes the output
 from all simulations described in the manuscript, and empirical datasets
 used for analyses.
description: The zipped files contains the outputs of simulations run under
 the CAMPSITE model. The sims.zip file contains
 simulations run under different combinations of pre-determined parameters.
 The simulations are stored as .rds files - each .rds file is a list of 100
 simulations run under different parameter values - the titles of the
 different .rds files reflect the different parameters used.
 Each simulation (out of 100) is an output of the CAMPSITE model,
 and thus is a list containing the following three lists:
 1. all: containing tree (the full phylogeny), tips (a vector of
 trait values at the tips), trait_mat (a list of vectors, each one the
 trait values of the lineage in each time step. NA if lineage did not exist
 at that time step), lin_mat (matrix of data on each lineage, including
 speciation and extinction times).<br>2. gsp_fossil: containing tree
 (the phylogeny with extant and extinct good species), tips (a vector of
 trait values at the tips).<br>3. gsp_extant: containing tree (the
 phylogeny with extant only good species), tips (a vector of trait values
 at the tips).<br> <br>The empirical.zip zipped file contains
 .csv files with trait data (in the data folder) and .tre files with
 associated phylogenies (in the trees folder). The file metdata.csv
 contains descriptions of the data and sources.
DOI: 10.5061/dryad.cnp5hqc56
title: Data from: Predicting range shifts of Davidia involucrata Ball. under future climate change

description: Understanding and predicting how species will respond to climate
 change is crucial for biodiversity conservation.
 Here, we assessed future climate change impacts
 on the distribution of a rare and endangered plant
 species, Davidia involucrate in China, using
 the most recent global circulation models developed in the sixth
 Assessment Report of the Intergovernmental Panel on Climate Change
 (IPCC6). We assessed the potential range shifts in this species
 by using an ensemble of species distribution models (SDMs). The ensemble
 SDMs exhibited high predictive ability and suggested that
 the temperature annual range, annual mean temperature, and
 precipitation of the driest month are the most influential
 predictors in shaping distribution patterns of this species. The
 projections of the ensemble SDMs also suggested that D.
 involucrate is very vulnerable to future climate change,
 with at least one-third of its suitable range expected to be lost in all
 future climate change scenarios and will shift to the northward of
 high-latitude regions. Similarly, at least
 one-fifthof the overlap area of
 the current nature
 reserve networks and projected suitable
 habitat is also expected to be lost. These findings
 suggest that it is of
 great importance to ensure
 that adaptive conservation management
 strategies are in place to mitigate the impacts of
 climate change on D. involucrate.
DOI: 10.5061/dryad.b5mkkwhdq
title: The dose makes the poison: feeding of antibiotic-treated winter honey bees, Apis mellifera, with probiotics and b-vitamins

description: Honey stores of Apis mellifera colonies are replaced with sugar water by
 beekeepers, which may result in malnutrition. Nutritional supplements have
 been developed, but the importance of bacterial probiotics and vitamins is
 poorly understood. Given that supplementary feeding with vitamins and
 probiotics enhances worker weight and longevity, this would suggest a
 feasible approach to mitigate winter colony losses. Here, we conducted a
 laboratory hoarding cage study with freshly emerged winter bees, which
 were treated with the antibiotic tetracycline to reduce gut bacteria and
 subsequently assigned to feeding regimes: sucrose only, sucrose + pollen,
 probiotics (low and high dosage), probiotics + pollen (low and high
 dosage), or b-vitamins (low and high dosage), (N=8 treatments, 29
 workers/cage x8 replicates). In parallel, controls remained on their frame
 (=Frame) to establish their gut microbiota and were subsequently fed with
 sucrose only or sucrose + pollen (N=2 treatments, 29 workers/cage x4
 replicates). Higher body weights were found in workers fed pollen, and in
 notably the Frame Sucrose + Pollen group, confirming a role of gut
 bacteria in protein digestion. Furthermore, both Frame groups and the
 antibiotic-treated workers fed with probiotic low + pollen survived longer
 than all other groups, highlighting an inherent host-microbial
 relationship. In contrast, high dosages of both probiotic and b-vitamins
 significantly reduced life span compared to their low concentration
 counterparts, probably due to dysbiosis and toxicity, suggesting that the
 outcome was dose-dependent. These results highlight that bacterial
 supplementation can alter longevity with advisable caution since harmful
 concentrations appear to exist.
DOI: 10.5061/dryad.547d7wm8g
title: Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species

description: 1. Despite worldwide reports of high tree mortality, growing evidence
 indicates that many tree species are well adapted to survive repeated dry
 spells. The drought resilience of trees is related to their phenotypic
 plasticity and ecotypic differentiation. Whether these two mechanisms act
 at the same organisational level of a tree and involve similar plant
 traits is still unknown. 2. We assessed phenotypic plasticity and ecotypic
 differentiation across four populations of Pinus sylvestris and Pinus
 nigra seedlings grown for three years under a recurrent summer drought
 treatment or well-watered control conditions in a common garden. We
 measured the response to the summer drought treatment of a total of 26
 traits including shoot and needle morphology, needle anatomy, and foliar
 macronutrients, and related the traits to the growing season water deficit
 (GSWD) at the location of the seed origin. 3. Foliar phenotypic plasticity
 in response to recurrent summer drought was surprisingly low, with the
 needle length and the fraction of mesophyll and phloem tissue adjusting to
 some extent. In comparison, shoot morphological traits were much more
 plastic in both species with predominant responses to the summer drought
 stress including shorter and less numerous apical and lateral shoots.
 These three traits were also correlated with GSWD at the seed origin,
 indicating local adaptation. In contrast, between-population variation of
 foliar morphological and anatomical traits, and macronutrients were mostly
 unrelated to the GSWD at the seed origin. 4. Consequently, phenotypic
 plasticity and ecotypic differentiation occurred at the same level of
 organisation and in the same plant traits, i.e. shoot morphology. This
 combination of plasticity and ecotypic differentiation allowed P.
 sylvestris and P. nigra seedlings to rapidly acclimate to recurrent and
 long-lasting dry-spells. 5. Synthesis: P. sylvestris and P. nigra
 seedlings showed considerable ecotypic differentiation and phenotypic
 plasticity of shoot morphological traits, and not foliar traits.
 Acclimation to recurrent severe summer drought was achieved by reducing
 shoot growth.
DOI: 10.5061/dryad.4tmpg4fb3
title: Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles

description: We aimed to simplify our fetal RHD genotyping protocol by changing the
 method to attach Illumina’s sequencing adaptors to PCR products from the
 ligation-based method to a PCR-based method, and to improve its
 quantitative accuracy by introducing unique molecular indexes, which allow
 us to count the numbers of DNA fragments used as PCR templates and to
 minimize the effects of PCR and sequencing errors. Both of the newly
 established protocols reduced time and cost compared with our conventional
 protocol. Removal of PCR duplicates using UMIs reduced the frequencies of
 erroneously mapped sequences reads likely generated by PCR and sequencing
 errors. The modified protocols will help us facilitate implementing fetal
 RHD genotyping for East Asian populations into clinical practice.
description: Amplicon sequencing libraries for <i>Rhesus box
 </i>regions<i> </i>and for <i>RHD/RHCE</i>
 exon 9 regions were prepared for twelve combinations of genomic DNA
 mixtures of two individuals (A and B) at a 10:1 ratio, which served as
 approximation models of cfDNA from RhD-negative pregnant women. The
 libraries were subjected to paired-end sequencing (151 bp × 2) on a MiSeq
 system (Illumina) using MiSeq Reagent Kit v2 Nano. Fastq flies (.fastq.gz)
 for Read 1 and Read 2 were generated for each of the libararies using the
 Generate FASTQ workflow of the MiSeq Reporter v2 software (Illumina). Each
 of four zip files (TableS2_Rh_box.zip, TableS2_exon9.zip,
 TableS3_Rh_box.zip, TableS3_exon9.zip) contains twelve pairs of fastq
 files corresponding to the twelve combinations of genmic DNA mixtures.
 TableS2 and TableS3 filesets correspond to the libraries prepared by the
 one-step PCR whiout UMI and those prepared by the linear and PCR
 amplification protocol with UMI.
DOI: 10.5061/dryad.fn2z34tv2
title: Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

description: Sugarcane (Saccharum spp.) is an important economic crop for both sugar
 and biomass, the yields of which are negatively affected by flowering. The
 molecular mechanisms controlling flowering in sugarcane are nevertheless
 poorly understood. RNA-seq data analysis and database searches have
 enabled a comprehensive description of the PEBP gene family in sugarcane.
 It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes,
 two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER
 (TFL)-like genes. As expected, these genes all show very high homology to
 their corresponding genes in Sorghum, and also to FT-like, MFT-like, and
 TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in
 Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late
 flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot.
 High expression levels of ScFT3 in leaves of short day-induced sugarcane
 plants coincided with initial stages of floral induction in the shoot
 apical meristem as shown by histological analysis of meristem dissections.
 This suggests that ScFT3 is likely to play a role in floral induction in
 sugarcane; however, other sugarcane FT-like genes may also be involved in
 the flowering process.
description: Sugarcane reference transcriptome
 Sugarcane genotypes SP91-1049 and SP83-2847 were cultivated in
 the field for 9 months. Samples of +1 leaf were collected at three
 different times (7 am, noon and 5 pm) and RNA was extracted using the
 RNeasy Plant Kit (Qiagen). The RNA quality was checked by 2100 Bioanalyzer
 (Agilent) and single-end libraries were made using a mRNA-Seq Sample
 Preparation kit following the manufacturer's instructions (Illumina
 Inc., San Diego, CA, USA). RNA sequencing was performed on an Illumina
 Hi-Seq 2,500 platform. All reads were submitted to quality checking using
 the FASTX-Toolkit and the read-end bases without desirable quality (q20)
 were trimmed. Reads that gave a Blast alignment match against yeast,
 bacteria or ribosomal sequences were also excluded. In the end, a total of
 630,770,178 reads were selected. The Trinity assembly pipeline was applied
 to create a non-redundant dataset of 44,558,361 reads (Grabherr <i>et al</i>. 2011. Nature Biotechnology <b>29</b>, 644–652.). These reads were assembled in different steps using the Velvet and Oases algorithms (Zerbino and Birney, 2008. Genome Research <b>18</b>, 821–829; Schulz et al., 2012. Bioinformatics <b>28</b>, 1086–1092). The assembly procedure was based on the concept that different sensitivities can be assessed using different k-mers. We started with k-mer 55 followed by re-assembling the transcripts using smaller k-mers (47, 39 and 31) in consecutive independent steps. The input for each step were the transcripts assembled and unused sequences from the last assembly. This approach resulted in 191,871 sugarcane transcript sequences.
DOI: 10.5061/dryad.sxksn033q
title: Sound improves neuronal encoding of visual stimuli in mouse primary visual cortex

description: In everyday life, we integrate visual and auditory information in routine
 tasks such as navigation and communication. While concurrent sound can
 improve visual perception, the neuronal correlates of audiovisual
 integration are not fully understood. Specifically, it remains unclear
 whether neuronal firing patters in the primary visual cortex (V1) of awake
 animals demonstrate similar sound-induced improvement in visual
 discriminability. Furthermore, presentation of sound is associated with
 movement in the subjects, but little is understood about whether and how
 sound-associated movement affects audiovisual integration in V1. Here, we
 investigated how sound and movement interact to modulate V1 visual
 responses in awake, head-fixed mice and whether this interaction improves
 neuronal encoding of the visual stimulus. We presented visual drifting
 gratings with and without simultaneous auditory white noise to awake mice
 while recording mouse movement and V1 neuronal activity. Sound modulated
 activity of 80% of light-responsive neurons, with 95% of neurons
 increasing activity when the auditory stimulus was present. A generalized
 linear model revealed that sound and movement had distinct and
 complementary effects of the neuronal visual responses. Furthermore,
 decoding of the visual stimulus from the neuronal activity was improved
 with sound, an effect that persisted even when controlling for movement.
 These results demonstrate that sound and movement modulate visual
 responses in complementary ways, improving neuronal representation of the
 visual stimulus. This study clarifies the role of movement as a potential
 confound in neuronal audiovisual responses and expands our knowledge of
 how multimodal processing is mediated at a neuronal level in the awake
 brain.
description: The electrophysiological recordings were collected in awake,
 head-fixed mice in response to audio-visual stimuli as described in the
 manuscript.
DOI: 10.6084/m9.figshare.31166749
title: <b>Transient Thermal Behaviour in Brake Linings and Rotors</b>

description: This is the dataset used for generating the graphs in the manuscript.
DOI: 10.6084/m9.figshare.31166749.v1
title: <b>Transient Thermal Behaviour in Brake Linings and Rotors</b>

description: This is the dataset used for generating the graphs in the manuscript.