cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21202183.v4
title: MERS-CoV nsp1 regulates autophagic flux via mTOR signalling and dysfunctional lysosomes

description: Autophagy, a cellular surveillance mechanism, plays an important role in combating invading pathogens. However, viruses have evolved various strategies to disrupt autophagy and even hijack it for replication and release. Here, we demonstrated that Middle East respiratory syndrome coronavirus (MERS-CoV) non-structural protein 1(nsp1) induces autophagy but inhibits autophagic activity. MERS-CoV nsp1 expression increased ROS and reduced ATP levels in cells, which activated AMPK and inhibited the mTOR signalling pathway, resulting in autophagy induction. Meanwhile, as an endonuclease, MERS-CoV nsp1 downregulated the mRNA of lysosome-related genes that were enriched in nsp1-located granules, which diminished lysosomal biogenesis and acidification, and inhibited autophagic flux. Importantly, MERS-CoV nsp1-induced autophagy can lead to cell death <i>in vitro</i> and <i>in vivo</i>. These findings clarify the mechanism by which MERS-CoV nsp1-mediated autophagy regulation, providing new insights for the prevention and treatment of the coronavirus.
DOI: 10.6084/m9.figshare.19346232
title: A nasal omicron vaccine booster elicits potent neutralizing antibody response against emerging SARS-CoV-2 variants

description: SARS-CoV-2 has caused the COVID-19 pandemic since early 2020. As of January 2022, the worldwide spreading of SARS-CoV-2 leads to approximately 0.35 billion of human infections and five millions of deaths. Current vaccination is one of the effective ways to control SARS-CoV-2 transmission and reduce the disease severity. However, the antibody level against the immunogen significantly drops several months after the standard two-dose vaccination, and hence a third or fourth dose booster (the same immunogen) has been suggested to boost the antibody response. Here, we described an ultra-effective nasal vaccine booster that potently induced the extraordinary high-level of neutralizing antibody in pre-vaccinated mice. The vaccine booster is composed of a recombinant receptor binding domain of SARS-CoV-2 spike (either wild-type or omicron) fused with a domain of SARS-CoV-2 nucleoprotein. In the absence of adjuvants, a single intranasal administration of the booster in pre-vaccinated mice significantly induced systemic and mucosal antibody responses as evidenced by the elevation of the cross-variant neutralizing antibody and induction of IgA in bronchoalveolar lavage respectively. Most importantly, the single dose nasal vaccine booster (omicron version) potently enhanced the neutralizing activity against authentic SARS-CoV-2 omicron virus infection. Taken together, the induction of respiratory mucosal immunity and the enhancement of cross-variant neutralizing activity by the nasal vaccine booster warrants further clinical trials in humans.
DOI: 10.6084/m9.figshare.19346232.v2
title: A nasal omicron vaccine booster elicits potent neutralizing antibody response against emerging SARS-CoV-2 variants

description: SARS-CoV-2 has caused the COVID-19 pandemic since early 2020. As of January 2022, the worldwide spreading of SARS-CoV-2 leads to approximately 0.35 billion of human infections and five millions of deaths. Current vaccination is one of the effective ways to control SARS-CoV-2 transmission and reduce the disease severity. However, the antibody level against the immunogen significantly drops several months after the standard two-dose vaccination, and hence a third or fourth dose booster (the same immunogen) has been suggested to boost the antibody response. Here, we described an ultra-effective nasal vaccine booster that potently induced the extraordinary high-level of neutralizing antibody in pre-vaccinated mice. The vaccine booster is composed of a recombinant receptor binding domain of SARS-CoV-2 spike (either wild-type or omicron) fused with a domain of SARS-CoV-2 nucleoprotein. In the absence of adjuvants, a single intranasal administration of the booster in pre-vaccinated mice significantly induced systemic and mucosal antibody responses as evidenced by the elevation of the cross-variant neutralizing antibody and induction of IgA in bronchoalveolar lavage respectively. Most importantly, the single dose nasal vaccine booster (omicron version) potently enhanced the neutralizing activity against authentic SARS-CoV-2 omicron virus infection. Taken together, the induction of respiratory mucosal immunity and the enhancement of cross-variant neutralizing activity by the nasal vaccine booster warrants further clinical trials in humans.
DOI: 10.6084/m9.figshare.21202183.v3
title: MERS-CoV nsp1 regulates autophagic flux via mTOR signalling and dysfunctional lysosomes

description: Autophagy, a cellular surveillance mechanism, plays an important role in combating invading pathogens. However, viruses have evolved various strategies to disrupt autophagy and even hijack it for replication and release. Here, we demonstrated that Middle East respiratory syndrome coronavirus (MERS-CoV) non-structural protein 1(nsp1) induces autophagy but inhibits autophagic activity. MERS-CoV nsp1 expression increased ROS and reduced ATP levels in cells, which activated AMPK and inhibited the mTOR signalling pathway, resulting in autophagy induction. Meanwhile, as an endonuclease, MERS-CoV nsp1 downregulated the mRNA of lysosome-related genes that were enriched in nsp1-located granules, which diminished lysosomal biogenesis and acidification, and inhibited autophagic flux. Importantly, MERS-CoV nsp1-induced autophagy can lead to cell death <i>in vitro</i> and <i>in vivo</i>. These findings clarify the mechanism by which MERS-CoV nsp1-mediated autophagy regulation, providing new insights for the prevention and treatment of the coronavirus.
DOI: 10.5061/dryad.4g313
title: Data from: Experimental inhibition of a key cellular antioxidant affects vocal communication

description: 1.There is substantial interest of evolutionary ecologists in the
 proximate mechanisms that modulate vocal communication. In recent times,
 there has been growing interest in the role of oxidative stress as a
 mediator of avian song expression. 2.Here we tested whether the
 experimental inhibition of the synthesis of a key cellular antioxidant
 (glutathione) reduces song rate metrics of male European starlings
 (Sturnus vulgaris). We measured the effect of our treatment on total song
 rate and on its two components, undirected and nest-box oriented song,
 outside the breeding season. 3.Treated males that did not own a nest-box
 (subordinate males likely to be of lower quality) suffered increased
 oxidative stress relative to untreated males, while treated males that
 owned a nest-box (dominant males likely to be of higher quality) did not.
 Treated non-owners also reduced their undirected song rate, whereas
 treated nest-box owners did not suffer any reduction in song rate. 4.Our
 results revealed that inhibition of a key cellular antioxidant results in
 decreased vocal communication in a social vertebrate, and that this effect
 is dependent on its social status (nest-box owner versus non-owner).
 5.This work provides support for the hypothesis that acoustic signals may
 honestly convey information about the individual oxidative status and
 capacity to regulate the oxidative balance. Our findings raise the
 possibility of hitherto unexplored impacts of oxidative stress on fitness
 traits in social species.
description: FunctEcol2017_TableS1This table includes data on oxidative stress markers and body mass.FunctEcol2017_TableS2This table includes data on song rate.
DOI: 10.6084/m9.figshare.19214326
title: Metformin attenuated sepsis-related liver injury by modulating gut microbiota

description: Increased evidence shows that gut microbiota acts as the primary regulator of the liver; however, its role in sepsis-related liver injury (SLI) in the elderly is unclear. This study assessed whether metformin could attenuate SLI by modulating gut microbiota in septic-aged rats. Cecal ligation and puncture (CLP) was used to induce SLI in aged rats. Fecal microbiota transplantation (FMT) was used to validate the roles of gut microbiota in these pathologies. The composition of gut microbiota was analysed by 16S rRNA sequencing. Moreover, the liver and colon tissues were analysed by histopathology, immunofluorescence, immunohistochemistry, and reverse transcription polymerase chain reaction (RT–PCR). Metformin improved liver damage, colon barrier dysfunction in aged SLI rats. Moreover, metformin improved sepsis-induced liver inflammation and damage under gut microbiota. Importantly, FMT assay showed that rats gavaged with faeces from metformin-treated SLI rats displayed less severe liver damage and colon barrier dysfunctions than those gavaged with faeces from SLI rats. The gut microbiota composition among the sham-operated, CLP-operated and metformin-treated SLI rats was different. In particular, the proportion of <i>Klebsiella</i> and <i>Escherichia_Shigella</i> was higher in SLI rats than sham-operated and metformin-treated SLI rats; while metformin could increase the proportion of <i>Bifidobacterium</i>, <i>Muribaculaceae</i>, <i>Parabacteroides_distasonis</i> and <i>Alloprevitella</i> in aged SLI rats. Additionally, <i>Klebsiella</i> and <i>Escherichia_Shigella</i> correlated positively with the inflammatory factors in the liver. Our findings suggest that metformin may improve liver injury by regulating the gut microbiota and alleviating colon barrier dysfunction in septic-aged rats, which may be an effective therapy for SLI.
DOI: 10.6084/m9.figshare.19214326.v2
title: Metformin attenuated sepsis-related liver injury by modulating gut microbiota

description: Increased evidence shows that gut microbiota acts as the primary regulator of the liver; however, its role in sepsis-related liver injury (SLI) in the elderly is unclear. This study assessed whether metformin could attenuate SLI by modulating gut microbiota in septic-aged rats. Cecal ligation and puncture (CLP) was used to induce SLI in aged rats. Fecal microbiota transplantation (FMT) was used to validate the roles of gut microbiota in these pathologies. The composition of gut microbiota was analysed by 16S rRNA sequencing. Moreover, the liver and colon tissues were analysed by histopathology, immunofluorescence, immunohistochemistry, and reverse transcription polymerase chain reaction (RT–PCR). Metformin improved liver damage, colon barrier dysfunction in aged SLI rats. Moreover, metformin improved sepsis-induced liver inflammation and damage under gut microbiota. Importantly, FMT assay showed that rats gavaged with faeces from metformin-treated SLI rats displayed less severe liver damage and colon barrier dysfunctions than those gavaged with faeces from SLI rats. The gut microbiota composition among the sham-operated, CLP-operated and metformin-treated SLI rats was different. In particular, the proportion of <i>Klebsiella</i> and <i>Escherichia_Shigella</i> was higher in SLI rats than sham-operated and metformin-treated SLI rats; while metformin could increase the proportion of <i>Bifidobacterium</i>, <i>Muribaculaceae</i>, <i>Parabacteroides_distasonis</i> and <i>Alloprevitella</i> in aged SLI rats. Additionally, <i>Klebsiella</i> and <i>Escherichia_Shigella</i> correlated positively with the inflammatory factors in the liver. Our findings suggest that metformin may improve liver injury by regulating the gut microbiota and alleviating colon barrier dysfunction in septic-aged rats, which may be an effective therapy for SLI.
DOI: 10.5061/dryad.hd7tm
title: Data from: A generalized solution procedure for in-plane free vibration of rectangular plates and annular sectorial plates

description: A generalized solution procedure is developed for in-plane free vibration
 of rectangular and annular sectorial plates with general boundary
 conditions. For the annular sectorial plate, the introduction of a
 logarithmic radial variable simplifies the basic theory and the expression
 of the total energy. The coordinates, geometric parameters and potential
 energy for the two different shapes are organized in a unified framework
 such that a generalized solving procedure becomes feasible. By using the
 improved Fourier-Ritz approach, the admissible functions are formulated in
 trigonometric form, which allows the explicit assembly of global mass and
 stiffness matrices for both rectangular and annular sectorial plates,
 thereby making the method computationally effective, especially when
 analyzing annular sectorial plates. Moreover, the improved Fourier
 expansion eliminates the potential discontinuity of the original normal
 and tangential displacement functions and their derivatives in the entire
 domain, and accelerates the convergence. The generalized Fourier-Ritz
 approach for both shapes has the characteristics of generality, accuracy
 and efficiency. These features are demonstrated via a few numerical
 examples.
description: data and program of
 normalized frequency parameter for square plates with various boundary
 conditionsNormalized frequency parameter
 for square plates .docx
DOI: 10.5061/dryad.6d5046c
title: Data from: Top carnivore decline has cascading effects on scavengers and carrion persistence

description: Top carnivores have suffered widespread global declines, with
 well-documented effects on mesopredators and herbivores. We know less
 about how carnivores affect ecosystems through scavenging. Tasmania’s top
 carnivore, the Tasmanian devil (Sarcophilus harrisii), has suffered severe
 disease-induced population declines, providing a natural experiment on the
 role of scavenging in structuring communities. Using remote cameras and
 experimentally-placed carcasses, we show that mesopredators consume more
 carrion in areas where devils have declined. Carcass consumption by the
 two native mesopredators was best predicted by exploitation competition
 for carrion, whereas consumption by the invasive mesopredator, the feral
 cat (Felis catus), was better predicted by the landscape-level abundance
 of devils, suggesting a relaxed landscape of fear where devils are
 suppressed. Reduced discovery of carcasses by devils was balanced by
 increased discovery by mesopredators. Nonetheless, carcasses persisted
 ~2.6-fold longer where devils have declined, highlighting their importance
 for rapid carrion removal. The major beneficiary of increased carrion
 availability was the forest raven (Corvus tasmanicus). Population trends
 of ravens increased 2.2-fold from 1998-2017, the period of devil decline,
 but this increase occurred Tasmania-wide, making the cause unclear. This
 case study provides a little-studied potential mechanism for mesopredator
 release, with broad relevance to the vast areas of the world that have
 suffered carnivore declines.
description: Foraging duration in a
 scavenging experimentData comes from a
 scavenging experiment conducted in Tasmania, Australia, to investigate the
 effects of Tasmanian devil population declines on community-wide carrion
 consumption. Tasmanian pademelon (Thylogale billardierii) carcasses were
 experimentally placed at 96 locations among twelve independent study
 sites. See readme file for variable descriptions.carcass_foraging_duration_conciseversion.csvCarcass persistence and discovery data from a scavenging experimentData comes from a scavenging experiment conducted in Tasmania, Australia, to investigate the effects of Tasmanian devil population declines on community-wide carrion consumption. Tasmanian pademelon (Thylogale billardierii) carcasses were experimentally placed at 96 locations among twelve independent study sites. This dataset was used for survival analysis. See the paper for detailed methodology.carcass_survival_persist_concise.csv
DOI: 10.5061/dryad.7qr3f154
title: Data from: Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.)

description: In classical weed biological control, small collections of arthropods are
 made from one or a few sites in the native range of the target plant and
 are introduced to suppress the plant where it has become invasive, often
 across a wide geographic range. Ecological mismatches in the new range are
 likely, and success using the biocontrol agent may depend on post release
 evolution of beneficial life history traits. In this study we measure
 evolution of critical day length for diapause induction, (day length at
 which 50% of the population enters dormancy), in a beetle (Diorhabda
 carinulata) introduced into North America from China to control an exotic
 shrub, Tamarix spp. Beetle populations were sampled from four sites in
 North America seven years after introduction and critical day length was
 shown to have declined, forming a cline over a latitudinal gradient At one
 field site decreased critical day length was correlated with 16 additional
 days of reproductive activity, resulting in a closer match between beetle
 life history and the phenology of Tamarix. These findings indicate an
 enhanced efficacy and an increasingly wider range for D. carinulata in
 Tamarix control.
description: Data for CDL study Bean
 et al
DOI: 10.5061/dryad.4tn86
title: Data from: Low second-to-fourth digit ratio predicts indiscriminate social suspicion, not improved trustworthiness detection

description: Testosterone administration appears to make individuals less trusting, and
 this effect has been interpreted as an adaptive adjustment of social
 suspicion, that improved the accuracy of trusting decisions. Here, we
 consider another possibility, namely that testosterone increases the
 subjective cost of being duped, decreasing the propensity to trust without
 improving the accuracy of trusting decisions. In line with this
 hypothesis, we show that second-to-fourth digit ratio (2D : 4D, a proxy
 for effects of testosterone in the foetus) correlates with the propensity
 to trust, but not with the accuracy of trusting decisions. Trust game
 players (n = 144) trusted less when they had lower 2D : 4D (high prenatal
 testosterone), but their ability to detect the strategy of other players
 was constant (and better than chance) across all levels of digit ratio.
 Our results suggest that early prenatal organizing effects of testosterone
 in the foetus might impair rather than boost economic outcomes, by
 promoting indiscriminate social suspicion.
description: Transfer rates and digit
 ratiosDataDeNeysHopfensitzBonnefon.xls
DOI: 10.5061/dryad.s926r
title: Data from: Possible influence of B chromosomes on genes included in immune response and parasite burden in Apodemus flavicollis

description: Genetic background underlying wild populations immune response to
 different parasites is still not well understood. We studied immune
 response to multiple infections and to competition between different
 parasite species at different developmental stages in population of
 yellow-necked mouse, Apodemus flavicollis. Quantitative real-time PCR was
 used to investigate associations of MHC II-DRB, IL-10 and Tgf-β genes
 expressions with presence of intestinal parasites at different
 developmental stages. Furthermore, we were interested whether the host
 related characteristics (sex, age, body condition, presence of B
 chromosomes or expression of other genes) or characteristics of present
 parasites (number of adult parasites of each identified species, egg count
 of each parasite genus, total number of nematode individuals) affect
 differential expression of the studied genes. A significant invert
 association between the expression of MHC II-DRB and Tgf-β gene was found,
 which together with absence of IL-10 association confirmed modified Th2 as
 the main type of immune response to nematode infections. Effect of
 recorded parasites and parasite life-cycle stage on expression levels of
 MHC II-DRB gene was detected only through interactions with host-related
 characteristics such as sex, age, and the presence of B chromosomes. The
 presence of B chromosomes is associated with lower expression level of
 Tgf-β gene. Although the influence of host genetic background on parasite
 infection has already been well documented, this is the first study in
 mammals that gave presence of B chromosomes on immune response full
 consideration.
description: Suplementary file for:
 Possible influence of B chromosomes on genes included in immune response
 and parasite burden in Apodemus flavicollisHost-related (sex, age,
 body condition index, presence of Bs in genotype, expression of other
 genes) and parasite-related (number of adult parasites of each identified
 species, egg count of each parasite genus, total number of nematode
 individuals) variables used in analysis.Possible influence of B
 chromosomes on genes included in immune response and parasite burden in
 Apodemus flavicollis.xls
DOI: 10.5061/dryad.129g9
title: Data from: Phosphorus amendment mitigates nitrogen addition-induced phosphorus limitation in two plant species in a desert steppe, China

description: Background and aims: The increasing deposition of atmospheric nitrogen (N)
 due to anthropogenic activities has significantly enhanced N inputs to
 ecosystems, resulting in an imbalance in the N: phosphorus (P) ratios in
 plants and soils. This study aimed to determine whether, and to what
 extent, P addition alleviates N-induced P limitation in a desert steppe
 ecosystem. Methods: We conducted a multi-level N:P supply experiment
 (i.e., constant N with varied P-addition levels) for a grass species,
 Pennisetum centrasiaticum, and a N-fixing species, Glycyrrhiza uralensis.
 Results: With increasing amounts of P addition (thereby decreasing the N:P
 ratio), green-leaf P concentrations of the two species studied tended to
 increase, while P-resorption proficiency and efficiency tended to
 decrease. There were no consistent trends in green-leaf N concentrations
 in response to P addition. However, both species exhibited high
 N-resorption proficiency, especially in G. uralensis, with high P
 addition. Generally, the carbon (C):P and N:P ratios both in soils and in
 green leaves had positive relationships with green-leaf N concentration
 and P-resorption proficiency of P. centrasiaticum as well as P-resorption
 traits of G. uralensis, but negative relationships with green-leaf P
 concentrations in both species. Conclusions: Our study indicates that P
 addition can alter P-conservation strategy and thereby releasing plant
 species from the N-induced imbalance of N:P ratios. However, large amounts
 of P addition could overcompensate and pose a risk of N limitation in
 desert steppe ecosystems.
description: nutrient resorption and
 soils indicesdata.xls
DOI: 10.5281/zenodo.18384308
title: Intelligent Extraction, Restoration, Reconstruction, and Adaptive Methods for Miao Ethnic Embroidery Patterns
title: Code, data, survey
DOI: 10.5281/zenodo.18384309
title: Intelligent Extraction, Restoration, Reconstruction, and Adaptive Methods for Miao Ethnic Embroidery Patterns
title: Code, data, survey