cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bh7mc
title: Data from: Physconia labrata, a new species from western North America and Asia

description: A new species belonging to the lichen genus Physconia is described from
 Alaska and the Canadian and American Rocky Mountains and adjacent forested
 regions. It is also reported from China, Nepal, India and Siberia. The new
 species, Physconia labrata, is superficially similar to P. perisidiosa,
 but can be distinguished by having a blackened, corticate lower surface
 and a paraplectenchymatous upper cortex.
description: PhysconiaLabrataAlignmentForDryadAlignment trimmed to nearly equal length sequences, including all of ITS1 and 2.
DOI: 10.5061/dryad.kb699
title: Data from: Response of moose hunters to predation following wolf return in Sweden

description: Background: Predation and hunter harvest constitute the main mortality
 factors affecting the size and dynamics of many exploited populations. The
 re-colonization by wolves (Canis lupus) of the Scandinavian Peninsula may
 therefore substantially reduce hunter harvest of moose (Alces alces), the
 main prey of wolves. Methodology/Principal findings: We examined possible
 effects of wolf presence on hunter harvest in areas where we had data
 before and after wolf establishment (n = 25), and in additional areas that
 had been continuously exposed to wolf predation during at least ten years
 (n = 43). There was a general reduction in the total number of moose
 harvested (n = 31,827) during the ten year study period in all areas
 irrespective of presence of wolves or not. However, the reduction in
 hunter harvest was stronger within wolf territories compared to control
 areas without wolves. The reduction in harvest was larger in small
 (500-800 km2) compared to large (1,200-1,800 km2) wolf territories. In
 areas with newly established wolf territories moose management appeared to
 be adaptive with regard to both managers (hunting quotas) and to hunters
 (actual harvest). In these areas an instant reduction in moose harvest
 over-compensated the estimated number of moose killed annually by wolves
 and the composition of the hunted animals changed towards a lower
 proportion of adult females. Conclusions/Significance: We show that the
 re-colonization of wolves may result in an almost instant functional
 response by another large predator—humans—that reduced the potential for a
 direct numerical effect on the density of wolves’ main prey, the moose.
 Because most of the worlds’ habitat that will be available for future
 colonization by large predators are likely to be strongly influenced by
 humans, human behavioural responses may constitute a key trait that govern
 the impact of large predators on their prey.
description: harvest_and_quotasIncludes data of harvest quotas and number of harvested moose.
DOI: 10.5061/dryad.k669c
title: Data from: Secondary compounds from exotic tree plantations change female mating preferences in the palmate newt (Lissotriton helveticus)

description: Selection can favor phenotypic plasticity in mate choice in response to
 environmental factors that alter the costs and benefits of being choosy,
 or of choosing specific mates. Human-induced environmental change could
 alter sexual selection by affecting the costs of mate choice, or by
 impairing the ability of individuals to identify preferred mates. For
 example, variation in mate choice could be driven by environmentally
 induced differences in body condition (e.g. health) that change the cost
 of choosiness, or by environmental effects on the ability to detect or
 discriminate sexual signals. We teased apart these possibilities
 experimentally, by comparing female mate choice in the palmate newt
 Lissotriton helveticus between environments that mimic water from either
 native oak forests or exotic eucalypt plantations. In laboratory
 two-choice mate trials in clean water, females with prolonged exposure (21
 days) to waterborne chemicals leached from eucalypt leaves did not
 preferentially associate with the male with a stronger immune response,
 but females exposed to water with chemicals from oak leaves did. In
 contrast, female choice was unaffected by the immediate presence or
 absence of eucalypt leachates during mate choice (using only females
 previously held in oak-treated water). The habitat-related change in
 female choice we observed is likely to be driven by effects of eucalypt
 leachates on female physiology, rather than immediate inhibition of
 pheromone transmission or blocking of pheromone reception.
description: Data for Experiment
 1This
 is the data for the Experiment 1 for the manuscript “Secondary compounds
 from exotic tree plantations change female mating preferences in the
 palmate newt (Lissotriton helveticus)”. Data was collected by MIC and CC.
 All methods are described in the associated manuscript. Column headings
 are described in the excel spreadsheet.Experiment
 1.xlsxData for Experiment
 2This
 is the data for the Experiment 2 for the manuscript “Secondary compounds
 from exotic tree plantations change female mating preferences in the
 palmate newt (Lissotriton helveticus)”. Data was collected by MIC and CC.
 All methods are described in the associated manuscript. Column headings
 are described in the excel spreadsheet.Experiment
 2.xlsx
DOI: 10.5061/dryad.2dn09
title: Data from: The mutational structure of metabolism in Caenorhabditis elegans

description: A properly functioning organism must maintain metabolic homeostasis.
 Deleterious mutations degrade organismal function, presumably at least in
 part via effects on metabolic function. Here we present an initial
 investigation into the mutational structure of the Caenorhabditis elegans
 metabolome by means of a mutation accumulation experiment. We find that
 pool sizes of 29 metabolites vary greatly in their vulnerability to
 mutation, both in terms of the rate of accumulation of genetic variance
 (the mutational variance, VM) and the rate of change of the trait mean
 (the mutational bias, ΔM). Strikingly, some metabolites are much more
 vulnerable to mutation than any other trait previously studied in the same
 way. Although we cannot statistically assess the strength of mutational
 correlations between individual metabolites, principal component analysis
 provides strong evidence that some metabolite pools are genetically
 correlated, but also that there is substantial scope for independent
 evolution of different groups of metabolites. Averaged over mutation
 accumulation lines, PC3 is positively correlated with relative fitness,
 but a model in which metabolites are uncorrelated with fitness is nearly
 as good by Akaike's Information Criterion.
description: Normalized metabolite
 dataColumn A
 ("Line") is the number of the MA line or the common ancestor of
 the MA lines. Column B ("Treatment") is the treatment, MA (G250)
 or Ancestor (G0). Column C ("Rep") is the replicate number.
 Columns D-AF are the normalized relative concentrations of the metabolite
 named in the column header. See Methods in the main text for details of
 the normalization.Data for
 Dryad.csv
DOI: 10.5061/dryad.qs626
title: Data from: Mechanical conflict system: a novel operant method for the assessment of nociceptive behavior

description: A new operant test for preclinical pain research, termed the Mechanical
 Conflict System (MCS), is presented. Rats were given a choice either to
 remain in a brightly lit compartment or to escape to a dark compartment by
 crossing an array of height-adjustable nociceptive probes. Latency to
 escape the light compartment was evaluated with varying probe heights (0,
 .5, 1, 2, 3, and 4 mm above compartment floor) in rats with neuropathic
 pain induced by constriction nerve injury (CCI) and in naive control rats.
 Escape responses in CCI rats were assessed following intraperitoneal
 administration of pregabalin (10 and 30 mg/kg), morphine (2.5 and 5
 mg/kg), and the tachykinin NK1 receptor antagonist, RP 67580 (1 and 10
 mg/kg). Results indicate that escape latency increased as a function of
 probe height in both naive and CCI rats. Pregabalin (10 and 30 mg/kg) and
 morphine (5 mg/kg), but not RP 67580, decreased latency to escape in CCI
 rats suggesting an antinociceptive effect. In contrast, morphine (10
 mg/kg) but not pregabalin (30 mg/kg) increased escape latency in naive
 rats suggesting a possible anxiolytic action of morphine in response to
 light-induced fear. No order effects following multiple test sessions were
 observed. We conclude that the MCS is a valid method to assess behavioral
 signs of affective pain in rodents.
description: PONE-D-14-48547R2_DATAExcel workbook containing reported data for naive and chronic constriction injury (CCI) experimental groups. Data are organized into 6 worksheets that correspond to manuscript Figures 2-5, S1, and S2.PONE-D-14-48547R2_RAW DATA.xlsx
DOI: 10.6084/m9.figshare.19096217
title: A network pharmacology approach to predict potential targets and mechanisms of “<i>Ramulus Cinnamomi (cassiae) – Paeonia lactiflora</i>” herb pair in the treatment of chronic pain with comorbid anxiety and depression

description: Traditional Chinese medicine (TCM) prescriptions have multiple bioactive properties. “Gui Zhi–Shao Yao” herb pair is widely used to treat chronic pain (CP), as well as anxiety and depression. However, its related targets and underlying mechanisms have not been deciphered. In this study, the network pharmacology method was used to explore the bioactive components and targets of “Gui Zhi–Shao Yao” herb pair and further elucidate its potential biological mechanisms of action in the treatment of CP with comorbid anxiety disorder (AD) and mental depression (MD). Following a series of analyses, we identified 15 active compounds, hitting 130 potential targets. After the intersections the targets of this herb pair and CP, AD and MD – sorted by the value of degree – nine targets were identified as the vital ones: Akt1, IL6, TNF, PTGS2, JUN, CASP3, MAPK8, PPARγ and NOS3. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results demonstrated 11 pathways, such as AGE-RAGE signalling pathway, IL-17 signalling pathway, TNF signalling pathway, which primarily participate in the pathological processes. This study preliminarily predicted and verified the pharmacological and molecular mechanisms of “Gui Zhi–Shao Yao” herb pair for treating CP with comorbid AD and MD from a holistic perspective. <i>In vivo</i> and <i>in vitro</i> experiments will be required to further investigate the mechanisms.KEY MESSAGEA network pharmacology approach was applied to identify key targets and molecular mechanisms.Nine targets were regarded as the vital targets for chronic pain with comorbid anxiety and depression.Predicted 11 pathways were the potential therapy targets and pharmacological mechanism of “Gui Zhi–Shao Yao” herb pair. A network pharmacology approach was applied to identify key targets and molecular mechanisms. Nine targets were regarded as the vital targets for chronic pain with comorbid anxiety and depression. Predicted 11 pathways were the potential therapy targets and pharmacological mechanism of “Gui Zhi–Shao Yao” herb pair.
DOI: 10.6084/m9.figshare.19096217.v1
title: A network pharmacology approach to predict potential targets and mechanisms of “<i>Ramulus Cinnamomi (cassiae) – Paeonia lactiflora</i>” herb pair in the treatment of chronic pain with comorbid anxiety and depression

description: Traditional Chinese medicine (TCM) prescriptions have multiple bioactive properties. “Gui Zhi–Shao Yao” herb pair is widely used to treat chronic pain (CP), as well as anxiety and depression. However, its related targets and underlying mechanisms have not been deciphered. In this study, the network pharmacology method was used to explore the bioactive components and targets of “Gui Zhi–Shao Yao” herb pair and further elucidate its potential biological mechanisms of action in the treatment of CP with comorbid anxiety disorder (AD) and mental depression (MD). Following a series of analyses, we identified 15 active compounds, hitting 130 potential targets. After the intersections the targets of this herb pair and CP, AD and MD – sorted by the value of degree – nine targets were identified as the vital ones: Akt1, IL6, TNF, PTGS2, JUN, CASP3, MAPK8, PPARγ and NOS3. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results demonstrated 11 pathways, such as AGE-RAGE signalling pathway, IL-17 signalling pathway, TNF signalling pathway, which primarily participate in the pathological processes. This study preliminarily predicted and verified the pharmacological and molecular mechanisms of “Gui Zhi–Shao Yao” herb pair for treating CP with comorbid AD and MD from a holistic perspective. <i>In vivo</i> and <i>in vitro</i> experiments will be required to further investigate the mechanisms.KEY MESSAGEA network pharmacology approach was applied to identify key targets and molecular mechanisms.Nine targets were regarded as the vital targets for chronic pain with comorbid anxiety and depression.Predicted 11 pathways were the potential therapy targets and pharmacological mechanism of “Gui Zhi–Shao Yao” herb pair. A network pharmacology approach was applied to identify key targets and molecular mechanisms. Nine targets were regarded as the vital targets for chronic pain with comorbid anxiety and depression. Predicted 11 pathways were the potential therapy targets and pharmacological mechanism of “Gui Zhi–Shao Yao” herb pair.
DOI: 10.5061/dryad.kb1fh
title: Data from: Silk wrapping of nuptial gifts aids cheating behaviour in male spiders

description: Sexual traits, such as nuptial gifts, are costly and often
 condition-dependent. Males should be under selection to reduce these costs
 without impairing their reproductive success. Spider gifts consist of
 silk-wrapped food, but may also consist of worthless (non-nutritive)
 donations that successfully lead to mating, despite yielding shorter
 copulations. Worthless gifts may either represent a cheaper cheating
 strategy or the inability to produce genuine gifts due to resource
 limitations (i.e. poor body condition). Unless energetic constraints limit
 expenditure in silk, males should apply more silk to worthless gifts to
 compensate for their lower reproductive value. We ask whether in Pisaura
 mirabilis 1) worthless gifts are condition-dependent and 2) males
 strategically use silk based on gift type (genuine vs worthless). We
 tested whether male body condition explains the gift-giving strategy and
 compared silk amounts covering each gift type, in gifts collected from the
 field and produced in the laboratory by males given different feeding
 regimes. Our findings show that worthless gifts are not promoted by poor
 body condition or limited resources. They rather result from a cheating
 strategy evolved to opportunistically reduce the costs of genuine gifts
 while ensuring nutritional advantages, with cheaters gaining body mass.
 Males applied more silk to worthless gifts regardless of their body
 condition or feeding state, suggesting they can strategically adjust silk
 expenditure despite its costs. By masking gift contents and prolonging
 female feeding, silk is crucial for the maintenance of cheating, likely
 resulting from an evolutionary arms race between male deception and female
 assessment.
description: Experiment 1_Field
 studyBEHECO-2016-0378.R1.EXP1_Field
 gifts.xlsxExperiment 2_Lab
 studyBEHECO-2016-0378.R1.EXP2_Lab
 gifts.xlsx
DOI: 10.6084/m9.figshare.21436089
title: Profiling non-coding RNA expression in cerebrospinal fluid of amyotrophic lateral sclerosis patients

description: Objective biomarkers for the fatal neurodegenerative disease amyotrophic lateral sclerosis or motor neuron disease (ALS/MND) are critical for diagnosis, drug development, clinical trials, and insight into disease pathology. Key candidates for biomarkers present in biofluids include non-coding RNA (ncRNA) transcripts including microRNA, piwi-interacting RNA and transfer RNA. To determine if the central nervous system was the source of the dysregulated ncRNA biomarkers we previously observed in serum, we sought to identify dysregulated ncRNA candidates in cerebrospinal fluid (CSF) which may provide new insight into the disease pathology. Small RNA sequencing (RNA-seq) was undertaken on CSF samples from healthy controls (<i>n</i> = 18), disease mimics (<i>n</i> = 8), and ALS patients (<i>n</i> = 40) in our Oxford Study for Biomarkers of ALS cohort, with RT-qPCR used to confirm their dysregulation. We found a range of ncRNA that were dysregulated in the RNA-seq screen, but these failed to be validated or detected in some cases using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Additionally, our previously identified serum ncRNA biomarker showed no change in CSF or correlation to serum. This study suggests the CSF may not be the source of dysregulated ncRNA in the serum and highlights the difficulty in identifying ncRNA in CSF as biomarkers for ALS.KEY MESSAGESIn this current study, we investigated the expression of non-coding RNA transcripts in the cerebrospinal fluid of ALS patients compared to healthy controls.RNA-seq identified dysregulated non-coding RNA transcripts, but these were not validated with RT-qPCR.We conclude that cerebrospinal fluid is not a suitable source of diagnostic biomarkers. In this current study, we investigated the expression of non-coding RNA transcripts in the cerebrospinal fluid of ALS patients compared to healthy controls. RNA-seq identified dysregulated non-coding RNA transcripts, but these were not validated with RT-qPCR. We conclude that cerebrospinal fluid is not a suitable source of diagnostic biomarkers.
DOI: 10.6084/m9.figshare.21436089.v1
title: Profiling non-coding RNA expression in cerebrospinal fluid of amyotrophic lateral sclerosis patients

description: Objective biomarkers for the fatal neurodegenerative disease amyotrophic lateral sclerosis or motor neuron disease (ALS/MND) are critical for diagnosis, drug development, clinical trials, and insight into disease pathology. Key candidates for biomarkers present in biofluids include non-coding RNA (ncRNA) transcripts including microRNA, piwi-interacting RNA and transfer RNA. To determine if the central nervous system was the source of the dysregulated ncRNA biomarkers we previously observed in serum, we sought to identify dysregulated ncRNA candidates in cerebrospinal fluid (CSF) which may provide new insight into the disease pathology. Small RNA sequencing (RNA-seq) was undertaken on CSF samples from healthy controls (<i>n</i> = 18), disease mimics (<i>n</i> = 8), and ALS patients (<i>n</i> = 40) in our Oxford Study for Biomarkers of ALS cohort, with RT-qPCR used to confirm their dysregulation. We found a range of ncRNA that were dysregulated in the RNA-seq screen, but these failed to be validated or detected in some cases using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Additionally, our previously identified serum ncRNA biomarker showed no change in CSF or correlation to serum. This study suggests the CSF may not be the source of dysregulated ncRNA in the serum and highlights the difficulty in identifying ncRNA in CSF as biomarkers for ALS.KEY MESSAGESIn this current study, we investigated the expression of non-coding RNA transcripts in the cerebrospinal fluid of ALS patients compared to healthy controls.RNA-seq identified dysregulated non-coding RNA transcripts, but these were not validated with RT-qPCR.We conclude that cerebrospinal fluid is not a suitable source of diagnostic biomarkers. In this current study, we investigated the expression of non-coding RNA transcripts in the cerebrospinal fluid of ALS patients compared to healthy controls. RNA-seq identified dysregulated non-coding RNA transcripts, but these were not validated with RT-qPCR. We conclude that cerebrospinal fluid is not a suitable source of diagnostic biomarkers.
DOI: 10.6084/m9.figshare.19096208
title: A MALDI-TOF mass spectrometry-based haemoglobin chain quantification method for rapid screen of thalassaemia

description: Thalassaemia is one of the most common inherited monogenic diseases worldwide with a heavy global health burden. Considering its high prevalence in low and middle-income countries, a cheap, accurate and high-throughput screening test of thalassaemia prior to a more expensive confirmatory diagnostic test is urgently needed. In this study, we constructed a machine learning model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains in blood, and for the first time, evaluated its diagnostic efficacy in 674 thalassaemia (including both asymptomatic carriers and symptomatic patients) and control samples collected in three hospitals. Parameters related to haemoglobin imbalance (α-globin, β-globin, γ-globin, α/β and α-β) were used for feature selection before classification model construction with 8 machine learning methods in cohort 1 and further model efficiency validation in cohort 2. The logistic regression model with 5 haemoglobin peak features achieved good classification performance in validation cohort 2 (AUC 0.99, 95% CI 0.98–1, sensitivity 98.7%, specificity 95.5%). Furthermore, the logistic regression model with 6 haemoglobin peak features was also constructed to specifically identify β-thalassaemia (AUC 0.94, 95% CI 0.91–0.97, sensitivity 96.5%, specificity 87.8% in validation cohort 2). For the first time, we constructed an inexpensive, accurate and high-throughput classification model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains and demonstrated its great potential in rapid screening of thalassaemia in large populations.Key messagesThalassaemia is one of the most common inherited monogenic diseases worldwide with a heavy global health burden.We constructed a machine learning model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains to screen for thalassaemia. Thalassaemia is one of the most common inherited monogenic diseases worldwide with a heavy global health burden. We constructed a machine learning model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains to screen for thalassaemia.