cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7900118.v1
title: Establishment of a rat model for uterine leiomyomas based on Western and traditional Chinese medicine theories

description: Uterine leiomyomas (ULs) are benign monoclonal tumors that arise from the underlying myometrial tissue in the uterus. Effective therapies are still lacking because of poor understanding of the pathophysiology and epidemiology. Hence, it is urgent to establish efficient animal models to screen novel anti-UL therapies. In this study, for the first time, traditional Chinese medicine and Western medicine were combined to establish an animal model of ULs in rats. In order to evaluate the function and value of the novel model, it was compared with other models. The long-term and short-term rat models for ULs were established using progesterone and diethylstilbestrol. Rats in Qi stagnation and blood stasis group were injected with epinephrine hydrochloride and received chronic unpredictable stress for two weeks. Rats in combining disease with syndrome group (CDWSG) received not only epinephrine hydrochloride injection and chronic unpredictable stress but also progesterone and diethylstilbestrol treatment. We analyzed differences in organ coefficient, uterus size, uterine pathology, concentrations of progesterone, estradiol, progesterone receptor, estrogen receptor, expression of desmin, α-smooth muscle actin, and vimentin among the five groups. The animal model of ULs was successfully constructed by loading the rats with estrogen and progesterone. The rat model of CDWSG was more stable than other groups and the method was the most efficient.
DOI: 10.6084/m9.figshare.14715038
title: Additional file 4 of Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

description: Additional file 4: Table S3. Microbiological cases - all other cases.
DOI: 10.6084/m9.figshare.7375538.v2
title: Table S1 from The histone deacetylase NlHDAC1 regulates both female and male fertility in the brown planthopper, <i>Nilaparvata lugens</i>.

description: Histone acetylation is a specific type of chromatin modification that serves as a key regulatory mechanism for many cellular processes in mammals. However, little is known about its biological function in invertebrates. Here, we identified 12 members of histone deacetylases (NlHDACs) in the brown planthopper (BPH), <i>Nilaparvata lugens</i>. RNAi-mediated silencing assay showed that <i>NlHdac1</i>, <i>NlHdac3</i> and <i>NlHdac4</i> played critical roles in female fertility via regulating ovary maturation or ovipositor development. Silencing of <i>NlHdac1</i> substantially increased acetylation level of histones H3 and H4 in ovaries, indicating NlHDAC1 is the main histone deacetylase in ovaries of BPH. RNA sequencing (RNA-seq) analysis showed that knockdown of <i>NlHdac1</i> impaired ovary development via multiple signalling pathways including the TOR pathway. Acoustic recording showed that males with <i>NlHdac1</i> knockdown failed to make courtship songs, and thus were unacceptable to wild-type females, resulting in unfertilized eggs. Competition mating assay showed that wild-type females overwhelmingly preferred to mate with control males over <i>NlHdac1</i>-knockdown males. These findings improve our understanding of reproductive strategies controlled by HDACs in insects and provide a potential target for pest control.
DOI: 10.5281/zenodo.10624086
title: Test Dataset
DOI: 10.5281/zenodo.10624087
title: Test Dataset
DOI: 10.6084/m9.figshare.7375553.v1
title: Table S2 from The histone deacetylase NlHDAC1 regulates both female and male fertility in the brown planthopper, <i>Nilaparvata lugens</i>

description: Histone acetylation is a specific type of chromatin modifications that serves as a key regulatory mechanism for many cellular processes in mammals. However, little is known about its biological function in invertebrates. Here, we identified 12 members of histone deacetylases (NlHDACs) in the brown planthopper (BPH), <i>Nilaparvata lugens</i>. RNAi-mediated silencing assay showed that the <i>NlHdac1</i>, <i>NlHdac3</i> and <i>NlHdac4</i> played critical roles in female fertility via regulating ovary maturation or ovipositor development. Silencing of <i>NlHdac1</i> substantially increased acetylation level of histones H3 and H4 in ovaries, indicating NlHDAC1 is the main histone deacetylase in ovaries of BPH. RNA sequencing (RNA-seq) analysis showed that knockdown of <i>NlHdac1</i> impaired ovary development via multiple signalling pathways including the TOR pathway. Acoustic recording showed that males with <i>NlHdac1</i> knockdown failed to make courtship songs, and thus were unacceptable to wild-type females, resulting in unfertilized eggs. Competition mating assay showed that wild-type females overwhelmingly preferred to mate with control males over <i>NlHdac1</i>-knockdown. These findings improve our understanding of reproductive strategies controlled by HDACs in insects and provide a potential target for pest control.
DOI: 10.6084/m9.figshare.8948855
title: tip dating p6 from Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds

description: Recently, comprehensive morphological datasets including nearly all the well-recognized Mesozoic birds became available, making it feasible for statistically rigorous methods to unveil finer evolutionary patterns during early avian evolution. Here, we exploited the advantage of Bayesian tip dating under relaxed morphological clocks to estimate both the divergence times and evolutionary rates while accounting for their uncertainties. We further subdivided the characters into six body regions (i.e. skull, axial skeleton, pectoral girdle and sternum, forelimb, pelvic girdle and hindlimb) to assess evolutionary rate heterogeneity both along the lineages and across partitions. We observed extremely high rates of morphological character changes during early avian evolution, and the clock rates are quite heterogeneous among the six regions. The branch subtending Pygostylia shows an extremely high rate in the axial skeleton, while the branches subtending Ornithothoraces and Enantiornithes show notably high rates in the pectoral girdle and sternum and moderately high rates in the forelimb. The extensive modifications in these body regions largely correspond to refinement of the flight capability. This study reveals the power and flexibility of Bayesian tip dating implemented in MrBayes to investigate evolutionary dynamics in deep time.
DOI: 10.6084/m9.figshare.12094668
title: SAD-B modulates epileptic seizure by regulating AMPA receptors in patients with temporal lobe epilepsy and in the PTZ-induced epileptic model

description: α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are the predominant mediators of glutamate-induced excitatory neurotransmission. It is widely accepted that AMPA receptors are critical for the generation and spread of epileptic seizure activity. Dysfunction of AMPA receptors as a causal factor in patients with intractable epilepsy results in neurotransmission failure. Brain-specific serine/threonine-protein kinase 1 (SAD-B), a serine-threonine kinase specifically expressed in the brain, has been shown to regulate AMPA receptor-mediated neurotransmission through a presynaptic mechanism. In cultured rat hippocampal neurons, the overexpression of SAD-B significantly increases the frequency of miniature excitatory postsynaptic currents (mEPSCs). Here, we showed that SAD-B downregulation exerted antiepileptic activity by regulating AMPA receptors in patients with temporal lobe epilepsy (TLE) and in the pentylenetetrazol (PTZ)-induced epileptic model. We first used immunoblotting and immunohistochemistry analysis to demonstrate that SAD-B expression was increased in the epileptic rat brain. Subsequently, to explore the function of SAD-B in epilepsy, we used siRNA to knock down SAD-B protein and observed behavior after PTZ-induced seizures. We found that SAD-B downregulation attenuated seizure severity and susceptibility in the PTZ-induced epileptic model. Furthermore, we showed that the antiepileptic effect of SAD-B downregulation on PTZ-induced seizure was abolished by CNQX (an AMPA receptor inhibitor), suggesting that SAD-B modulated epileptic seizure by regulating AMPA receptors in the brain. Taken together, these findings suggest that SAD-B may be a potential and novel therapeutic target to limit epileptic seizures.
DOI: 10.6084/m9.figshare.13143233.v1
title: An Extended Youden Design in Biological Assays

description: Cell-based biological assays (also called bioassays) are an essential analytical tool used for quality assessment of biologic drug substances and drug products. In particular, they are used to determine the potency compared against a standard preparation under assumptions of similarity. In the design of bioassays, orthogonality between preparations and nuisance factors is desired. Block designs are an efficient way to assay multiple preparations simultaneously and mitigate bias from multiple sources, such as plates, locations within plates, and operators. The construction of a block design of a bioassay is challenging because of the treatment/control setup and the presence of multiple block effects. In many cases, absolute orthogonality is not feasible, and consequently, we need a design that achieves “near-orthogonality.” We propose an extended Youden design with mathematical construction such that near-orthogonality can be achieved in the presence of these multiple confounding effects. We also provide an efficient algorithm implementation with R. Numerical results show that the extended Youden design is the optimal design for the given scenario when absolute orthogonality is not achievable.
DOI: 10.6084/m9.figshare.7375556.v1
title: Table S4 from The histone deacetylase NlHDAC1 regulates both female and male fertility in the brown planthopper, <i>Nilaparvata lugens</i>

description: Histone acetylation is a specific type of chromatin modifications that serves as a key regulatory mechanism for many cellular processes in mammals. However, little is known about its biological function in invertebrates. Here, we identified 12 members of histone deacetylases (NlHDACs) in the brown planthopper (BPH), <i>Nilaparvata lugens</i>. RNAi-mediated silencing assay showed that the <i>NlHdac1</i>, <i>NlHdac3</i> and <i>NlHdac4</i> played critical roles in female fertility via regulating ovary maturation or ovipositor development. Silencing of <i>NlHdac1</i> substantially increased acetylation level of histones H3 and H4 in ovaries, indicating NlHDAC1 is the main histone deacetylase in ovaries of BPH. RNA sequencing (RNA-seq) analysis showed that knockdown of <i>NlHdac1</i> impaired ovary development via multiple signalling pathways including the TOR pathway. Acoustic recording showed that males with <i>NlHdac1</i> knockdown failed to make courtship songs, and thus were unacceptable to wild-type females, resulting in unfertilized eggs. Competition mating assay showed that wild-type females overwhelmingly preferred to mate with control males over <i>NlHdac1</i>-knockdown. These findings improve our understanding of reproductive strategies controlled by HDACs in insects and provide a potential target for pest control.
DOI: 10.6084/m9.figshare.7900046
title: Exenatide ameliorates hepatic steatosis and attenuates fat mass and FTO gene expression through PI3K signaling pathway in nonalcoholic fatty liver disease

description: Non-alcoholic fatty liver disease (NAFLD) is a common disease associated with metabolic syndrome and can lead to life-threatening complications like hepatic carcinoma and cirrhosis. Exenatide, a glucagon-like peptide-1 (GLP-1) receptor agonist antidiabetic drug, has the capacity to overcome insulin resistance and attenuate hepatic steatosis but the specific underlying mechanism is unclear. This study was designed to investigate the underlying molecular mechanisms of exenatide therapy on NAFLD. We used in vivo and in vitro techniques to investigate the protective effects of exenatide on fatty liver via fat mass and obesity associated gene (FTO) in a high-fat (HF) diet-induced NAFLD animal model and related cell culture model. Exenatide significantly decreased body weight, serum glucose, insulin, insulin resistance, serum free fatty acid, triglyceride, total cholesterol, low-density lipoprotein, aspartate aminotransferase, and alanine aminotransferase levels in HF-induced obese rabbits. Histological analysis showed that exenatide significantly reversed HF-induced lipid accumulation and inflammatory changes accompanied by decreased FTO mRNA and protein expression, which were abrogated by PI3K inhibitor LY294002. This study indicated that pharmacological interventions with GLP-1 may represent a promising therapeutic strategy for NAFLD.
DOI: 10.6084/m9.figshare.7900046.v1
title: Exenatide ameliorates hepatic steatosis and attenuates fat mass and FTO gene expression through PI3K signaling pathway in nonalcoholic fatty liver disease

description: Non-alcoholic fatty liver disease (NAFLD) is a common disease associated with metabolic syndrome and can lead to life-threatening complications like hepatic carcinoma and cirrhosis. Exenatide, a glucagon-like peptide-1 (GLP-1) receptor agonist antidiabetic drug, has the capacity to overcome insulin resistance and attenuate hepatic steatosis but the specific underlying mechanism is unclear. This study was designed to investigate the underlying molecular mechanisms of exenatide therapy on NAFLD. We used in vivo and in vitro techniques to investigate the protective effects of exenatide on fatty liver via fat mass and obesity associated gene (FTO) in a high-fat (HF) diet-induced NAFLD animal model and related cell culture model. Exenatide significantly decreased body weight, serum glucose, insulin, insulin resistance, serum free fatty acid, triglyceride, total cholesterol, low-density lipoprotein, aspartate aminotransferase, and alanine aminotransferase levels in HF-induced obese rabbits. Histological analysis showed that exenatide significantly reversed HF-induced lipid accumulation and inflammatory changes accompanied by decreased FTO mRNA and protein expression, which were abrogated by PI3K inhibitor LY294002. This study indicated that pharmacological interventions with GLP-1 may represent a promising therapeutic strategy for NAFLD.
DOI: 10.6084/m9.figshare.12094761
title: Integral transform analysis of radionuclide transport in variably saturated media using a physical non-equilibrium model: application to solid waste leaching at a uranium mining installation

description: Abstract: The Generalized Integral Transform Technique (GITT) was employed to simulate transient one-dimensional flow in variably saturated porous media, as well as radioactive waste transport within different layers (a solid waste pile, nearby soil, and a granular aquifer) towards the edge of a uranium mining installation under institutional control. Computational codes, written using the Mathematica software system, were implemented and tested for solution of the coupled advection-dispersion equations for an arbitrary number of daughter products within a radioactive chain migrating in saturated and unsaturated soil layers. The computer simulations were verified in great detail against results obtained using the built-in routine NDSolve of the Mathematica platform and the HYDRUS-1D software system. The present work reports the main results for 238U chain radionuclide transport using data extracted from a safety assessment of solid waste repositories at a uranium mining and milling installation in Caetité, state of Bahia, Brazil, operated by INB (Indústrias Nucleares do Brasil). Concentration evolutions of the various radionuclides obtained with the simulations were analyzed for five different cases to explore variations in the infiltration and recharge rates, the effect of assuming physical equilibrium or non-equilibrium transport conditions, and of different initial concentrations of some of the radionuclides.
DOI: 10.6084/m9.figshare.7900121.v1
title: Imbalance of γδT17/γδTreg cells in the pathogenesis of allergic asthma induced by ovalbumin

description: We aimed to explore the imbalance between the T helper 17 γδT cells (γδT17) and the regulatory γδT cells (γδTreg) in asthmatic mice. Male Balb/c mice were randomly divided into the normal control group and the asthmatic model group. The asthmatic model group mice were intraperitoneally injected with the mixture of ovalbumin (OVA)/Al(OH)3 and then activated by exposure of the animals to OVA atomization. Airway hyperresponsiveness (AHR) was determined by a non-invasive lung function machine. Hematoxylin and eosin and Alcian blue-periodic acid Schiff staining were done for histopathological analysis. Interleukin (IL)-17 and IL-35 levels in bronchoalveolar lavage fluid were detected by ELISA. The percentage of IL-17+ γδT cells and Foxp3+ γδT cells in spleen cells suspension were detected and the transcription levels of RORγt and Foxp3 in the lung tissue were determined. Compared with the normal control, the severity of airway inflammation and AHR were higher in the asthmatic mice. Furthermore, mice in the asthmatic group displayed significant increases of IL-17+ γδT cells, expression of IL-17A, and RORγt, whereas control mice displayed marked decreases of Foxp3+ γδT cells, expression of IL-35, and transcription factor Foxp3. In addition, the mRNA expression of RORγt was positively correlated with the percentage of IL-17+γδT cells, and the mRNA level of Foxp3 was positively correlated with the percentage of Foxp3+ γδT cells. The imbalance of γδT17/γδTreg in the asthmatic mice may contribute to the pathogenesis of OVA-induced asthma.
DOI: 10.6084/m9.figshare.8948696.v1
title: Visualising confirmation of the endophytic relationship of <i>Metarhizium anisopliae</i> with maize roots using molecular tools and fluorescent labelling

description: <i>Metarhizium anisopliae</i>, an entomopathogenic fungus, is found to contribute to plant nutrient uptake and condidered as a plant endophyte. However, there is very little visual evidence that demonstratrates the endophytic relationship. Since the incidence of <i>Metarhizium</i> within host plants may be ephemeral or of limited distribution within host tissue, visualisation is reliant on both presence and the ability to detect the fungus even when present at low levels. We inoculated maize seeds with an <i>egfp</i>-labelled isolate of <i>M. anisopliae</i>, and then detected the <i>egfp</i> fragment by qualitative and quantitative PCR, and examined fluorescence of mycelia in the inoculated roots by laser scanning confocal microscopy (LSCM). The optimised PCR qualitatively identified the presence of <i>egfp</i>-labelled <i>M. anisopliae</i> at a 1:3000 <i>M. anisopliae</i>-maize DNA ratio. Root samplings of inoculated plants at intervals over 24 days were discovered <i>egfp</i>-labelled fragments with 14-d roots having the highest proportion with amplification. The <i>egfp</i>-label concentrations ranged very low in 2.976 × 10<sup>−7.42∼−7.02</sup> ng/μL, with a rise process in 4–11 days after <i>M. anisopliae</i> treatment. Under LSCM, fluorescent mycelia in roots were identified, and the clear images were captured to show hyphal development extending along a longitudinal line of root cells and even forming a hyphal mass in the intercellular space. There were many hyphae at the branch junctions of the lateral roots. The methodology used to detect the fungus will be important for exploring the multi-trophic function of <i>M. anisopliae</i> and co-evolution in plants.
DOI: 10.6084/m9.figshare.7899947.v1
title: CT-guided minimally-invasive penile fracture repair

description: ABSTRACT We present the case of a 28 year old patient with an incomplete tear of the tunica albuginea occurred after having sexual intercourse in the female superior position. The diagnostic assessment was performed first clinically, then with CT, owing to its high resolution, allowed to exactly detect the tear location leading to precise preoperative planning. After adequate diagnosis through imaging and proper planning, the patient was performed a selective minimally invasive surgical approach to repair the lesion. The patient had good erection with no angular deformity or plaque formation after a 3-month follow-up.
DOI: 10.6084/m9.figshare.7375568.v2
title: Table S5 from The histone deacetylase NlHDAC1 regulates both female and male fertility in the brown planthopper, <i>Nilaparvata lugens</i>.

description: Histone acetylation is a specific type of chromatin modification that serves as a key regulatory mechanism for many cellular processes in mammals. However, little is known about its biological function in invertebrates. Here, we identified 12 members of histone deacetylases (NlHDACs) in the brown planthopper (BPH), <i>Nilaparvata lugens</i>. RNAi-mediated silencing assay showed that <i>NlHdac1</i>, <i>NlHdac3</i> and <i>NlHdac4</i> played critical roles in female fertility via regulating ovary maturation or ovipositor development. Silencing of <i>NlHdac1</i> substantially increased acetylation level of histones H3 and H4 in ovaries, indicating NlHDAC1 is the main histone deacetylase in ovaries of BPH. RNA sequencing (RNA-seq) analysis showed that knockdown of <i>NlHdac1</i> impaired ovary development via multiple signalling pathways including the TOR pathway. Acoustic recording showed that males with <i>NlHdac1</i> knockdown failed to make courtship songs, and thus were unacceptable to wild-type females, resulting in unfertilized eggs. Competition mating assay showed that wild-type females overwhelmingly preferred to mate with control males over <i>NlHdac1</i>-knockdown males. These findings improve our understanding of reproductive strategies controlled by HDACs in insects and provide a potential target for pest control.
DOI: 10.6084/m9.figshare.7899854.v1
title: Tea polyphenols induce S phase arrest and apoptosis in gallbladder cancer cells

description: Gallbladder cancer (GBC) is the most common malignancy in the biliary tract. Without effective treatment, its prognosis is notoriously poor. Tea polyphenols (TPs) have many pharmacological and health benefits, including antioxidant, anti-inflammatory, anti-tumor, anti-thrombotic, antibacterial, and vasodilatory properties. However, the anti-cancer effect of TPs in human gallbladder cancer has not yet been determined. Cell viability and colony formation assay were used to investigate the cell growth. Cell cycle and apoptosis were evaluated by flow cytometry analysis. Western blot assay was used to detect the expression of proteins related to cell cycle and apoptosis. Human tumor xenografts were used to examine the effect of TPs on gallbladder cancer cells in vivo. TPs significantly inhibited cell growth of gallbladder cancer cell lines in a dose- and time-dependent manner. Cell cycle progression in GBC cells was blocked at the S phase by TPs. TPs also induced mitochondrial-related apoptosis in GBC cells by upregulating Bax, cleaved caspase-3, and cleaved PARP expressions and downregulating Bcl-2, cyclin A, and Cdk2 expressions. The effects of TPs on GBC were further proven in vivo in a mouse xenograft model. Our study is the first to report that TPs inhibit GBC cell growth and these compounds may have potential as novel therapeutic agents for treating gallbladder cancer.