cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21629995.v2
title: Decreased echinocandin susceptibility in <i>Candida parapsilosis</i> causing candidemia and emergence of a pan-echinocandin resistant case in China

description: <i>Candida parapsilosis</i> is becoming a predominant non-<i>albicans</i> cause of invasive candidiasis (IC). Echinocandins are the preferred choice for IC treatment and prophylaxis. Resistance to echinocandins in <i>C. parapsilosis</i> has emerged in several countries, but little is known about the susceptibility profile in China or about mechanisms of resistance. Here, we investigated the echinocandin susceptibilities of 2523 <i>C. parapsilosis</i> isolates collected from China and further explored the resistance mechanism among echinocandin-resistant isolates. Anidulafungin exhibited the highest MICs (MIC<sub>50/90</sub>, 1 and 2 µg/mL; GM, 0.948 µg/mL), while caspofungin showed better activity (0.5 and 1 µg/mL; 0.498 µg/mL). Significantly higher echinocandin MICs were observed among blood-derived isolates compared to others, especially for caspofungin (GM, 1.348 µg/mL vs 0.478 µg/mL). Isolates from ICU and surgical wards also showed higher MICs. Twenty isolates showed intermediate phenotypes for at least one echinocandin. One was resistant to all three echinocandins, fluconazole and voriconazole, which caused breakthrough IC during long-term exposure to micafungin. WGS revealed this isolate carried a mutation S656P in hotspot1 region of Fks1. Bioinformatics analyses suggested that this mutation might lead to an altered protein conformation. CRISPR Cas9-mediated introduction of this mutation into a susceptible reference <i>C. parapsilosis</i> strain increased MICs of all echinocandins 64-fold, with similar results found in the subspecies, <i>C. orthopsilosis</i> and <i>C. metapsilosis</i>. This is the first report of a multi-azole resistant and pan-echinocandin resistant <i>C. parapsilosis</i> isolate, and the identification of a <i>FKS1</i><sup>S656P</sup> conferring pan-echinocandin resistance. Our study underscores the necessity of rigorous management of antifungal use and of monitoring for antifungal susceptibility.
DOI: 10.6084/m9.figshare.30837407
title: Distinct inflammation-related proteins associated with T cell immune recovery during chronic HIV-1 infection

description: Chronic inflammation and T cell dysregulation persist in individuals infected with human immunodeficiency virus type 1 (HIV-1), even after successful antiretroviral treatment. The mechanism involved is not fully understood. Here, we used Olink proteomics to comprehensively analyze the aberrant inflammation-related proteins (IRPs) in chronic HIV-1-infected individuals, including in 24 treatment-naïve individuals, 33 immunological responders, and 38 immunological non-responders. T cell dysfunction was evaluated as T cell exhaustion, activation, and differentiation using flow cytometry. We identified a cluster of IRPs (cluster 7), including CXCL11, CXCL9, TNF, CXCL10, and IL18, which was closely associated with T cell dysregulation during chronic HIV-1 infection. Interestingly, IRPs in cluster 5, including ST1A1, CASP8, SIRT2, AXIN1, STAMBP, CD40, and IL7, were negatively correlated with the HIV-1 reservoir size. We also identified a combination of CDCP1, CXCL11, CST5, SLAMF1, TRANCE, and CD5, which may be useful for distinguishing immunological responders and immunological non-responders. In conclusion, the distinct inflammatory milieu is closely associated with immune restoration of T cells, and our results provide insight into immune dysregulation during chronic HIV-1 infection.
DOI: 10.6084/m9.figshare.30837407.v1
title: Distinct inflammation-related proteins associated with T cell immune recovery during chronic HIV-1 infection

description: Chronic inflammation and T cell dysregulation persist in individuals infected with human immunodeficiency virus type 1 (HIV-1), even after successful antiretroviral treatment. The mechanism involved is not fully understood. Here, we used Olink proteomics to comprehensively analyze the aberrant inflammation-related proteins (IRPs) in chronic HIV-1-infected individuals, including in 24 treatment-naïve individuals, 33 immunological responders, and 38 immunological non-responders. T cell dysfunction was evaluated as T cell exhaustion, activation, and differentiation using flow cytometry. We identified a cluster of IRPs (cluster 7), including CXCL11, CXCL9, TNF, CXCL10, and IL18, which was closely associated with T cell dysregulation during chronic HIV-1 infection. Interestingly, IRPs in cluster 5, including ST1A1, CASP8, SIRT2, AXIN1, STAMBP, CD40, and IL7, were negatively correlated with the HIV-1 reservoir size. We also identified a combination of CDCP1, CXCL11, CST5, SLAMF1, TRANCE, and CD5, which may be useful for distinguishing immunological responders and immunological non-responders. In conclusion, the distinct inflammatory milieu is closely associated with immune restoration of T cells, and our results provide insight into immune dysregulation during chronic HIV-1 infection.
DOI: 10.5061/dryad.522
title: Data from: Primates and their pinworm parasites: the Cameron hypothesis revisited

description: A morphologically based cladistic analysis of the Enterobiinae, which
 includes most of the Oxyuridae parasitic in Primates, allows a
 reevaluation of the Cameron's hypothesis of close coevolution with
 cospeciation between hosts and parasites. Each of the three genera
 separated in the Enterobiinae fits with one of the suborders defined in
 Primates: Lemuricola with the Strepsirhini, Trypanoxyuris with the
 Platyrrhini, and Enterobius with the Catarrhini. Inside each of the three
 main groups, the subdivisions observed in the parasite tree also fit with
 many of the subdivisions generally accepted within the Primate order.
 These results confirm the subgroups previously described in the subfamily
 and support Cameron's hypothesis in its aspect of association by
 descent. Although the classification of the Enterobiinae generally closely
 underlines the classification of Primates, several discordances also are
 observed. These are discussed case by case, with use of computed
 reconstruction scenarios. Given that the occurrences of the same pinworm
 species as a parasite for several congeneric host species is not the
 generalized pattern, and given that several occurrences also are observed
 in which the speciations of the parasites describe a more complex network,
 Cameron's hypothesis of a slower rhythm of speciation in the
 parasites can be considered partly refuted. The presence of two genera
 parasitic on squirrels in a family that contains primarily primate
 parasites also is discussed. The cladistic analysis does not support close
 relationships between the squirrel parasites and suggests an early
 separation from the Enterobiinae for the first (Xeroxyuris), and a tardy
 host-switching from the Platyrrhini to the squirrels for the second
 (Rodentoxyuris).
description: Hugot Data
 SetHugot.htm
DOI: 10.6084/m9.figshare.21655846
title: A rabies virus-vectored vaccine expressing two copies of the Marburg virus glycoprotein gene induced neutralizing antibodies against Marburg virus in humanized mice

description: Marburg virus disease (MVD) is a lethal viral haemorrhagic fever caused by Marburg virus (MARV) with a case fatality rate as high as 88%. There is currently no vaccine or antiviral therapy approved for MVD. Due to high variation among MARV isolates, vaccines developed against one strain fail to protect against other strains. Here we report that three recombinant rabies virus (RABV) vector vaccines encoding two copies of GPs covering both MARV lineages induced pseudovirus neutralizing antibodies in BALB/c mice. Furthermore, high-affinity human neutralizing antibodies were isolated from a humanized mouse model. The three vaccines produced a Th1-biased serological response similar to that of human patients. Adequate sequential immunization enhanced the production of neutralizing antibodies. Virtual docking suggested that neutralizing antibodies induced by the Angola strain seemed to be able to hydrogen bond to the receptor-binding site (RBS) in the GP of the Ravn strain through hypervariable regions 2 (CDR2) and CDR3 of the VH region. These findings demonstrate that three inactivated vaccines are promising candidates against different strains of MARV, and a novel fully humanized neutralizing antibody against MARV was isolated.
DOI: 10.6084/m9.figshare.21655846.v2
title: A rabies virus-vectored vaccine expressing two copies of the Marburg virus glycoprotein gene induced neutralizing antibodies against Marburg virus in humanized mice

description: Marburg virus disease (MVD) is a lethal viral haemorrhagic fever caused by Marburg virus (MARV) with a case fatality rate as high as 88%. There is currently no vaccine or antiviral therapy approved for MVD. Due to high variation among MARV isolates, vaccines developed against one strain fail to protect against other strains. Here we report that three recombinant rabies virus (RABV) vector vaccines encoding two copies of GPs covering both MARV lineages induced pseudovirus neutralizing antibodies in BALB/c mice. Furthermore, high-affinity human neutralizing antibodies were isolated from a humanized mouse model. The three vaccines produced a Th1-biased serological response similar to that of human patients. Adequate sequential immunization enhanced the production of neutralizing antibodies. Virtual docking suggested that neutralizing antibodies induced by the Angola strain seemed to be able to hydrogen bond to the receptor-binding site (RBS) in the GP of the Ravn strain through hypervariable regions 2 (CDR2) and CDR3 of the VH region. These findings demonstrate that three inactivated vaccines are promising candidates against different strains of MARV, and a novel fully humanized neutralizing antibody against MARV was isolated.
DOI: 10.5061/dryad.21533
title: Data from: Extraction and separation of active ingredients in Schisandra chinensis (Turcz.) Baill and the study of their antifungal effects

description: Schisandra chinensis extracts (SEs) have traditionally been used as an
 oriental medicine for the treatment of various human diseases, however,
 their further application in the biocontrol of plant disease remains
 poorly understood. This study was conducted to develop eco-friendly
 botanical pesticides from extracts of S. chinensis and assess whether they
 could play a key role in plant disease defense. Concentrated active
 fractions (SE-I, SE-II, and SE-III) were obtained from S. chinensis via
 specific extraction and separation. Then, lignan-like substances, such as
 Schisanhenol B, were detected via High-Performance Liquid
 Chromatography-ElectroSpray Ionization-Mass Spectrometry (HPLC-ESI-MS)
 analyses of the active fractions. Moreover, the results from biological
 tests on colony growth inhibition and spore germination indicated that
 SE-I, SE-II, and SE-III could inhibit hyphal growth and spore generation
 of three important plant pathogenic fungi (Monilinia fructicola, Fusarium
 oxysporum, and Botryosphaeria dothidea). The study of the mechanisms of
 resistant fungi revealed that the oxidation resistance system, including
 reactive oxygen species (ROS), malondialdehyde (MDA), catalase (CAT), and
 superoxide dismutase (SOD), was activated. The expression of genes related
 to defense, such as pathogenesis-related protein (PR4), α-farnesene
 synthase (AFS), polyphenol oxidase (PPO), and phenylalanine ammonia lyase
 (PAL) were shown to be up-regulated after treatment with SEs, which
 suggested an increase in apple immunity and that fruits were induced to
 effectively defend against the infection of pathogenic fungi (B.
 dothidea). This study revealed that SEs and their lignans represent
 promising resources for the development of safe, effective, and
 multi-targeted agents against pathogenic fungi.
description: Original Data for this
 experimentOriginal
 Data.xlsx
DOI: 10.5061/dryad.kq30q
title: Data from: Plant ants use resistance-related plant odours to assess host quality before colony founding

description: 1. Establishing a horizontally transmitted mutualism is a critical step
 for many organisms, particularly when an individual can engage with only
 one partner over its lifetime. Ant foundresses shed their wings before
 they start to lay eggs, which makes host choice particularly critical for
 plant-ants that exclusively colonize myrmecophytes. 2. Volatile organic
 compounds (VOCs) can indicate the identity and physiological condition of
 an individual and frequently serve as signals or cues that facilitate
 partner choice. Thus, we hypothesised that obligate plant-ants use VOCs to
 determine the quality of potential host plants. 3. Indeed, winged females
 of the plant-ant, Pseudomyrmex ferrugineus, used plant odours to identify
 high-quality acacia hosts among different species and among individuals of
 the same species. The VOC blend of a branch was related to reward
 production and, interestingly, the least attractive blend contained the
 highest number of compounds. 4. Whereas only seven different VOCs could be
 detected in the blend of the high-reward host species, the low-reward host
 emitted 13 different compounds, among which (S)-(-)-limonene and
 β-linalool were the dominant ones. Complementing the odour of the
 high-reward host with (S)-(-)-limonene, β-linalool or α-terpinene reduced
 its attractiveness. Strikingly, these compounds inhibited bacterial
 pathogens of the host plant. 5. Synthesis. Plant-ants can utilise host
 plant odours that contain resistance-related VOCs to judge on host
 quality, likely because of negative crosstalk between direct resistance to
 disease and investment in ant-mediated defence. VOCs can serve as cues
 that provide reliable information for partner choice, particularly when
 their emission results from a physiological process that causally relates
 to the quality of an individual as a mutualist.
description: RazoBelmanetal_(2017)
 Journal of Ecology 2017-0005All data on volatile
 organic compounds (VOCs) emitted from Acacia branches (sheet 1),
 extrafloral nectar (EFN) secretion (sheet 2), data on EFN secretion and
 VOC emission from the same branches that were used in Fig. 3 (sheet 3),
 results of the behavioural assays of ant queens in the cage (sheet 4) and
 in the olfactometer (sheet 5) and data of the inhibition assays using
 natural bacterial pathogens (sheet 6).
DOI: 10.5281/zenodo.18367272
title: Tympaki LL_ Meteorological forcing dataset

description: This dataset containts:



ERA5-derived, bias-adjusted (using in-situ data) areal-averaged monthly PET (Hargreaves: Temperature-based formula) over the 3 sub-basins, as well as the whole area, of Tympaki basin, Crete, Greece (for the period 1950-2022).

ERA5-derived, bias-adjusted (using in-situ data) areal-averaged monhtly Precipitation over the 3 sub-basins, as well as the whole area, of Tympaki basin, Crete, Greece (for the period 1950-2022).

Stochastically-generated drought scenario (composed by 5 consecutive years with precipitation below annual average) of areal-averaged monthly Precipitation and PET (Hargreaves: Temperature-based formula) over the 3 sub-basins of Tympaki basin, Crete, Greece, as well as stochastically-generated, and cross-correlated, monthly Runoff at Geropotamos gauging station (for the period 1980-2022).

Stochastically-generated drought scenario (composed by 7 consecutive years with precipitation below annual average) of areal-averaged monthly Precipitation and PET (Hargreaves: Temperature-based formula) over the 3 sub-basins of Tympaki basin, Crete, Greece, as well as stochastically-generated, and cross-correlated, monthly Runoff at Geropotamos gauging station (for the period 1980-2022).
DOI: 10.5281/zenodo.18367273
title: Tympaki LL_ Meteorological forcing dataset

description: This dataset containts:



ERA5-derived, bias-adjusted (using in-situ data) areal-averaged monthly PET (Hargreaves: Temperature-based formula) over the 3 sub-basins, as well as the whole area, of Tympaki basin, Crete, Greece (for the period 1950-2022).

ERA5-derived, bias-adjusted (using in-situ data) areal-averaged monhtly Precipitation over the 3 sub-basins, as well as the whole area, of Tympaki basin, Crete, Greece (for the period 1950-2022).

Stochastically-generated drought scenario (composed by 5 consecutive years with precipitation below annual average) of areal-averaged monthly Precipitation and PET (Hargreaves: Temperature-based formula) over the 3 sub-basins of Tympaki basin, Crete, Greece, as well as stochastically-generated, and cross-correlated, monthly Runoff at Geropotamos gauging station (for the period 1980-2022).

Stochastically-generated drought scenario (composed by 7 consecutive years with precipitation below annual average) of areal-averaged monthly Precipitation and PET (Hargreaves: Temperature-based formula) over the 3 sub-basins of Tympaki basin, Crete, Greece, as well as stochastically-generated, and cross-correlated, monthly Runoff at Geropotamos gauging station (for the period 1980-2022).
DOI: 10.5061/dryad.3dr96
title: Data from: Parentage analysis of Ansell's mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal

description: To better understand evolutionary pathways leading to eusociality,
 interspecific comparisons are needed, which would use a common axis, such
 as that of reproductive skew, to array species. African mole-rats
 (Bathyergidae, Rodentia) provide an outstanding model of social evolution
 because of a wide range of social organizations within a single family;
 however, their reproductive skew is difficult to estimate, due to their
 cryptic lifestyle. A maximum skew could theoretically be reached in groups
 where reproduction is monopolized by a stable breeding pair, but the value
 could be decreased by breeding-male and breeding-female turnover, shared
 reproduction and extra-group mating. The frequency of such events should
 be higher in species or populations inhabiting mesic environments with
 relaxed ecological constraints on dispersal. To test this prediction, we
 studied patterns of parentage and relatedness within 16 groups of
 Ansell's mole-rat (Fukomys anselli) in mesic miombo woodland.
 Contrary to expectation, there was no shared reproduction (more than one
 breeder of a particular sex) within the studied groups, and proportion of
 immigrants and offspring not assigned to current breeding males was low.
 The within-group parentage and relatedness patterns observed resemble arid
 populations of ‘eusocial’ Fukomys damarensis, rather than a mesic
 population of ‘social’ Cryptomys hottentotus. As a possible explanation,
 we propose that the extent ecological conditions affect reproductive skew
 may be markedly affected by life history and natural history traits of the
 particular species and genera.
description: Fukomys_anselli_genotypesThe genotypes of nine microsatellite loci obtained using the fragment analysis (ABI PRISM 3130) and scored using th GeneMapper 3.7. For each individual, its ID, sex, reproductive status, weight and group membership is shown.
DOI: 10.5061/dryad.2m5c4
title: Data from: Chemical ecology of fruit defense: synergistic and antagonistic interactions among amides from Piper

description: 1. Although ripe, fleshy fruits function primarily to attract seed
 dispersers, they must also be defended against diverse communities of seed
 predators and pathogens. For some plants, the concentration and diversity
 of secondary metabolites in fruits can exceed that of leaves and other
 plant parts, but little is known about the functional significance of the
 suites of compounds found in fruits. Fruit secondary metabolites may
 function in defense, or they may play a variety of other roles in seed
 development and dispersal. 2. In this study, we conducted a series of
 experiments to test the effects of amides, a highly diverse class of
 secondary metabolites found in Piper fruits, on a variety of antagonistic
 fruit pests, including an insect seed predator (Sibaria englemani,
 Pentatomidae) and three unidentified species of fungi isolated from ripe
 Piper reticulatum (Piperaceae) fruits. We tested the effects of amide-rich
 extracts from unripe and ripe fruits of Piper reticulatum and the effects
 of two pure compounds, piperine and piplartine, presented alone and in
 combination. 3. Amide-rich extracts from unripe and ripe fruits had no
 effect on insect feeding preferences, but strong negative effects on
 fungal growth rates. A comparison of the relative bioactivity of unripe
 and ripe fruit extracts, controlling for concentration, showed that the
 specific composition of compounds in unripe fruits provides a more
 effective defense than that of ripe fruits against two of the three fungal
 species tested. 4. Pure amides had variable effects on insect feeding
 preferences and strong negative effects on fungal growth rates. Tests of
 the bioactivity of two pure amides, presented alone and in combination,
 showed that the same two compounds can interact either synergistically or
 antagonistically in mixtures depending on the particular consumer
 involved. 5. Together, these results suggest that the secondary
 metabolites in fruits may be a key characteristic contributing to fruit
 defense and plant reproductive success. Specifically, our results
 emphasize: 1) the potential for slight changes in the composition of
 mixtures to alter the efficacy of defense, and 2) the potential for
 complex interactions among compounds in mixtures that can alter the
 bioactivity of secondary metabolites differentially among different
 consumers.
description: Effects of amides on
 insect feeding choice and fungal growthDryad
 Data.zip
DOI: 10.5061/dryad.83ft4
title: Data from: Altitudinal flower size variation correlates with local pollinator size in a bumblebee-pollinated herb, Prunella vulgaris L. (Lamiaceae)

description: The influence of locally different species interactions on trait evolution
 is a focus of recent evolutionary studies. However, few studies have
 demonstrated that geographically different pollinator-mediated selection
 influence geographic variation in floral traits, especially across a
 narrow geographic range. Here, we hypothesized that floral size variation
 in the Japanese herb Prunella vulgaris L. (Lamiaceae) is affected by
 geographically different pollinator sizes reflecting different pollinator
 assemblages. To evaluate this hypothesis, we posed two questions. 1) Is
 there a positive correlation between floral length and the proboscis
 length of pollinators (bumblebees) across altitude in a mountain range? 2)
 Does the flower–pollinator size match influence female and male plant
 fitness? We found geographic variation in the assemblage of pollinators of
 P. vulgaris along an altitudinal gradient, and, as a consequence, the mean
 pollinator proboscis length also changed altitudinally. The floral corolla
 length of P. vulgaris also varied along an altitudinal gradient, and this
 variation strongly correlated with the local pollinator size but did not
 correlate with altitude itself. Furthermore, we found that the size match
 between the floral corolla length and bee proboscis length affected female
 and male plant fitness and the optimal size match (associated with peak
 fitness) was similar for the female and male fitness. Collectively, these
 results suggest that pollinator-mediated selection influences spatial
 variation in the size of P. vulgaris flowers at a fine spatial scale.
description: Kuriya et al. data
 setsKuriya
 data sets.xlsx