cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10071575
title: MOESM6 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 6. A domain sequences used for phylogenetic analysis.
DOI: 10.6084/m9.figshare.10071575.v1
title: MOESM6 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 6. A domain sequences used for phylogenetic analysis.
DOI: 10.6084/m9.figshare.10071581
title: MOESM7 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 7. KS domain sequences used for phylogenetic analysis.
DOI: 10.6084/m9.figshare.10071581.v1
title: MOESM7 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 7. KS domain sequences used for phylogenetic analysis.
DOI: 10.6084/m9.figshare.10071584
title: MOESM8 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 8. Sanger sequencing results of the PCR products of the 22 genes chosen for PCR validation of in silico gene prediction result of S. brachiariae. (TXT 20 kb)
DOI: 10.6084/m9.figshare.10071584.v1
title: MOESM8 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 8. Sanger sequencing results of the PCR products of the 22 genes chosen for PCR validation of in silico gene prediction result of S. brachiariae. (TXT 20 kb)
DOI: 10.6084/m9.figshare.7974449.v1
title: Differential expression of microRNA-411 and 376c is associated with hypertension in pregnancy

description: Preeclampsia is a major reason of morbidity and mortality in pregnant women and perinatal fetus. Hence, it is of prime importance that diagnostic markers are defined to predict chances of preeclampsia in pregnant women. It has been previously shown that microRNA (miRNA)-376c expression is decreased in the placenta of preeclampsia patients at term. Even though this decrease was not mimicked in the placenta at the pre-term stage, miR-376c expression was decreased in the plasma of these patients as early as the second trimester. Plasma and placenta specimens were obtained from pregnant women having unifetal gestation undergoing perinatal care between January 2014 and December 2016 (n=49). Early trimester placentas were collected from patients undergoing terminated pregnancies through dilation and curettage procedure. Our results showed that in addition to miR-376c, miR-441 levels were decreased in the placenta of preeclampsia patients, and this decrease occurred both at pre-term and at term. This decrease is also mimicked in the plasma levels at both early and late weeks of pregnancy, highlighting that miR-441 levels can serve as a diagnostic marker of risk of preeclampsia in pregnant women. Overexpression of the miR-441, as well as miR-376c, promoted cell viability, migration, and invasion in the human immortalized cytotrophoblast cell line HTR8/SVneo, indicating that their decrease in pregnant women would result in anomalous apoptosis and functional imbalance resulting in premature abortion and other complications. MiR-441 level can thus potentially serve as diagnostic marker of preeclampsia in pregnant women.
DOI: 10.6084/m9.figshare.6401651.v1
title: Additional file 6: of RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum

description: Table S8 GO analysis of the genes with altered m6A levels between wild-type and Alkbh5-deficient mice exposed to hypobaric hypoxia. (XLSX 83Â kb)
DOI: 10.6084/m9.figshare.25195553
title: Supplementary Material for: Capsular Block Syndrome After an Intravitreal Injection of Ranibizumab: A Case Report

description: Introduction: We present a case of capsular block syndrome that occurred after intravitreal injection of ranibizumab in a patient with age-related macular degeneration, which has not been reported in the literature. 
Case Presentation: A 78-year-old male presented with decreased visual acuity in the right eye. Slit-lamp examination findings were unremarkable; however, AMD was diagnosed based on fundus examination, fluorescein angiography, and optical coherence tomography (OCT). Subsequently, the patient was administered an intravitreal injection of ranibizumab. A slit-lamp examination revealed residual cortical material, numerous inflammatory cells, and posterior capsular distension one week after the injection. OCT showed an adhesion of the intraocular lens to the continuous curvilinear capsulorhexis site. The patient's vision improved following Nd:YAG laser posterior capsulotomy. 
Conclusion: Meticulous cortical removal is crucial during phacoemulsification to prevent capsular block syndrome. In patients with a history of cataract surgery, verifying the absence of residual cortical material before administering an intravitreal injection of ranibizumab is important.
DOI: 10.6084/m9.figshare.25195553.v1
title: Supplementary Material for: Capsular Block Syndrome After an Intravitreal Injection of Ranibizumab: A Case Report

description: Introduction: We present a case of capsular block syndrome that occurred after intravitreal injection of ranibizumab in a patient with age-related macular degeneration, which has not been reported in the literature. 
Case Presentation: A 78-year-old male presented with decreased visual acuity in the right eye. Slit-lamp examination findings were unremarkable; however, AMD was diagnosed based on fundus examination, fluorescein angiography, and optical coherence tomography (OCT). Subsequently, the patient was administered an intravitreal injection of ranibizumab. A slit-lamp examination revealed residual cortical material, numerous inflammatory cells, and posterior capsular distension one week after the injection. OCT showed an adhesion of the intraocular lens to the continuous curvilinear capsulorhexis site. The patient's vision improved following Nd:YAG laser posterior capsulotomy. 
Conclusion: Meticulous cortical removal is crucial during phacoemulsification to prevent capsular block syndrome. In patients with a history of cataract surgery, verifying the absence of residual cortical material before administering an intravitreal injection of ranibizumab is important.
DOI: 10.25549/usctheses-c89-355627
title: etd-DankwaLind-8852-c
DOI: 10.5519/qd.4k7wjeoh
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (10372 records)
DOI: 10.6084/m9.figshare.24751940
title: Associations between extreme temperature exposure and hypertensive disorders in pregnancy: a systematic review and meta-analysis

description: Background: Hypertensive disorders in pregnancy (HDP) are a major cause of maternal mortality and morbidity. Recent studies indicated that pregnant women are the most vulnerable populations to ambient temperature influences, but it affected HDP with inconsistent conclusions. Our objective is to systematically review whether extreme temperature exposure is associated with a changed risk for HDP. Method: We searched PubMed, EMBASE, Web of Science and Cochrane Library databases. We included cohort or case control studies examining the association between extreme temperature exposure before or during pregnancy and HDP. Heat sources such as saunas and hot baths were excluded. We pooled the odds ratio (OR) to assess the association between extreme temperature exposure and preeclampsia or eclampsia. Results: Fifteen studies involving 4,481,888 patients were included. Five studies were included in the meta-analysis. The overall result demonstrated that in the first half of pregnancy, heat exposure increases the risk of developing preeclampsia or eclampsia and gestational hypertension, and cold exposure decreases the risk. The meta-analysis revealed that during the first half of pregnancy, heat exposure increased the risk of preeclampsia or eclampsia (OR 1.54, 95% confidence interval (CI): 1.10, 2.15), whereas cold exposure decreased the risk (OR 0.90, 95% CI: 0.84, 0.97). Conclusion: The ambient temperature is an important determinant for the development of HDP, especially for preeclampsia or eclampsia. The effects of extreme temperatures may be bidirectional during the different trimesters of pregnancy, which should be evaluated by future studies. This review provided hints of temperature regulation in HDP administration.
DOI: 10.6084/m9.figshare.24751940.v1
title: Associations between extreme temperature exposure and hypertensive disorders in pregnancy: a systematic review and meta-analysis

description: Background: Hypertensive disorders in pregnancy (HDP) are a major cause of maternal mortality and morbidity. Recent studies indicated that pregnant women are the most vulnerable populations to ambient temperature influences, but it affected HDP with inconsistent conclusions. Our objective is to systematically review whether extreme temperature exposure is associated with a changed risk for HDP. Method: We searched PubMed, EMBASE, Web of Science and Cochrane Library databases. We included cohort or case control studies examining the association between extreme temperature exposure before or during pregnancy and HDP. Heat sources such as saunas and hot baths were excluded. We pooled the odds ratio (OR) to assess the association between extreme temperature exposure and preeclampsia or eclampsia. Results: Fifteen studies involving 4,481,888 patients were included. Five studies were included in the meta-analysis. The overall result demonstrated that in the first half of pregnancy, heat exposure increases the risk of developing preeclampsia or eclampsia and gestational hypertension, and cold exposure decreases the risk. The meta-analysis revealed that during the first half of pregnancy, heat exposure increased the risk of preeclampsia or eclampsia (OR 1.54, 95% confidence interval (CI): 1.10, 2.15), whereas cold exposure decreased the risk (OR 0.90, 95% CI: 0.84, 0.97). Conclusion: The ambient temperature is an important determinant for the development of HDP, especially for preeclampsia or eclampsia. The effects of extreme temperatures may be bidirectional during the different trimesters of pregnancy, which should be evaluated by future studies. This review provided hints of temperature regulation in HDP administration.
DOI: 10.6084/m9.figshare.10071980
title: MOESM2 of Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid

description: Additional file 2: Table S1. Phosphopeptides and their phosphorylation sites (marked by lowercase letters of the amino acid residue) identified by NanoLC-MS/MS analysis.
DOI: 10.6084/m9.figshare.10071980.v1
title: MOESM2 of Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid

description: Additional file 2: Table S1. Phosphopeptides and their phosphorylation sites (marked by lowercase letters of the amino acid residue) identified by NanoLC-MS/MS analysis.
DOI: 10.6084/m9.figshare.10071992
title: MOESM3 of Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid

description: Additional file 3: Table S2. Rice phosphoproteins identified by NanoLC-MS/MS analysis.
DOI: 10.6084/m9.figshare.10071992.v1
title: MOESM3 of Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid

description: Additional file 3: Table S2. Rice phosphoproteins identified by NanoLC-MS/MS analysis.
DOI: 10.6084/m9.figshare.23700654
title: Additional file 3 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 3:ELISA kits information.
DOI: 10.6084/m9.figshare.23700654.v1
title: Additional file 3 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 3:ELISA kits information.
DOI: 10.6084/m9.figshare.23700657
title: Additional file 4 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 4:Antibodies information of Immunofluorescence.
DOI: 10.6084/m9.figshare.23700666
title: Additional file 7 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 7: (A) VCAN expression is significantly higher in BLCA tissues than in adjacent normal tissues. (B) Immunofluorescence shows that the fluorescence intensity of VCAN in CAFs is notably brighter than in NFs, and in OEFAP-HFFs it is notably brighter than in NCFAP-HFFs.
DOI: 10.6084/m9.figshare.23700651.v1
title: Additional file 2 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 2: Antibodies information of Western blotting.
DOI: 10.6084/m9.figshare.13212452
title: Additional file 3 of Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells

description: Additional file 3: Table S1. GO terms of genes dynamically changed along hematopoietic lineage differentiation.
DOI: 10.6084/m9.figshare.23700675
title: Additional file 10 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 10: (A) BLCA with lymphovascular invasion expressed more FAP and VCAN than without lymphovascular invasion. In OS (B) and DSS (C) events, FAP, VCAN, N-cadherin, and Vimentin expression in the deceased group is higher than in the alive group. (D) In PFI events, VCAN and N-cadherin are more highly expressed in the deceased group. Immunohistochemistry (E) and dot blot (F) shows that the expression of TGF-β1, FAP, VCAN, N-cadherin, and Vimentin in BLCA tissues is significantly higher than in adjacent normal tissues, while the expression of E-cadherin in BLCA tissues is lower than in adjacent normal tissues. (G) TGF-β1 dominates stromal fibroblast-mediated EMT of bladder cancer cells via the FAP/VCAN axis to promote the invasion and metastasis of BLCA.
DOI: 10.6084/m9.figshare.23700648
title: Additional file 1 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 1: Primer sequences of quantitative real-time.
DOI: 10.6084/m9.figshare.23700669.v1
title: Additional file 8 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 8: (A) Immunofluorescence shows that the fluorescence intensity of VCAN in HFFs is markedly enhanced under the induction of TGF-β1; TGF-β1 neutralizing antibody significantly reduces this enhanced fluorescence intensity. (B) qRT-PCR verifies that the expression of VCAN in OEVCAN-HFFs is significantly higher than in NCVCAN-HFFs and T24 cells. (C) Immunofluorescence reveals that the VCAN fluorescence intensity in OEVCAN-HFFs is notably brighter than in NCVCAN-HFFs and T24 cells. (D) ELISA shows that the concentration of VCAN in the OEVCAN-HFF supernatant is significantly higher than in NCVCAN-HFF and T24 cell supernatant. (E) WB show that OEVCAN-HFF-CM can downregulate E-cadherin as well as upregulate N-cadherin and Vimentin.
DOI: 10.6084/m9.figshare.23700675.v1
title: Additional file 10 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 10: (A) BLCA with lymphovascular invasion expressed more FAP and VCAN than without lymphovascular invasion. In OS (B) and DSS (C) events, FAP, VCAN, N-cadherin, and Vimentin expression in the deceased group is higher than in the alive group. (D) In PFI events, VCAN and N-cadherin are more highly expressed in the deceased group. Immunohistochemistry (E) and dot blot (F) shows that the expression of TGF-β1, FAP, VCAN, N-cadherin, and Vimentin in BLCA tissues is significantly higher than in adjacent normal tissues, while the expression of E-cadherin in BLCA tissues is lower than in adjacent normal tissues. (G) TGF-β1 dominates stromal fibroblast-mediated EMT of bladder cancer cells via the FAP/VCAN axis to promote the invasion and metastasis of BLCA.
DOI: 10.6084/m9.figshare.23700672
title: Additional file 9 of TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells

description: Additional file 9: qRT-PCR (A, B), WB(C, D), and immunohistochemistry (E, F) showed that TGF-β1/FAP/VCAN axis regulates bladder cancer EMT in vivo. CAF has a stronger EMT-inducing effect than NF. Overexpression of FAP enhanced the EMT-inducing effects of stromal fibroblasts, while knockdown of FAP weakened those effects.
DOI: 10.6084/m9.figshare.22655089
title: Propulsive cell entry diverts pathogens from immune degradation by remodeling phagocytic synapse

description: Phagocytosis is a critical immune function for infection control and tissue homeostasis. This process is typically described as pathogens being internalized passively and degraded in phagolysosomes. For pathogens that evade immune degradation, the prevailing view is that virulence factors that biochemically disrupt the biogenesis of phagoslysosomes are required. In contrast, here we report that physical forces exerted by pathogens during cell entry divert them away from the canonical phagolysosomal degradation pathway, and this altered intracellular fate was determined at the time of phagocytic synapse formation. To differentiate the effect of physical forces from the that of virulence factors in phagocytosis, we developed a strategy that used magnetic forces to induce propulsive entry of inactivated parasite <em>Toxoplasma gondii </em>into macrophage cells. Experiments and computer simulations collectively reveal that large propulsive forces suppress productive activation of receptors by hindering their spatial segregation from phosphatases at the phagocytic synapse. Consequently, the inactivated parasites, instead of being degraded in phagoslysosomes, are engulfed into vacuoles that fail to mature into degradative units, following an intracellular pathway strikingly similar to that of the live motile parasite. These results reveal previously unknown aspects of immune evasion by demonstrating how physical forces, independent of virulence factors, can help pathogens circumvent phagolysosomal degradation.
DOI: 10.5281/zenodo.10638566
title: Origin and evolution of pentanucleotide repeat expansions at the familial cortical myoclonic tremor with epilepsy type1 - SAMD12 locus

description: Our investigation focused on the origin and evolution of pure (TTTTA)exp and (TTTTA)exp(TTTCA)exp at this locus. This database includes targeted third-generation sequencing of 10 pure TTTTAexp carriers,  and the haplotype data from all families in the article.
DOI: 10.5281/zenodo.10638567
title: Origin and evolution of pentanucleotide repeat expansions at the familial cortical myoclonic tremor with epilepsy type1 - SAMD12 locus

description: Our investigation focused on the origin and evolution of pure (TTTTA)exp and (TTTTA)exp(TTTCA)exp at this locus. This database includes targeted third-generation sequencing of 10 pure TTTTAexp carriers,  and the haplotype data from all families in the article.
DOI: 10.6084/m9.figshare.23700599.v1
title: Additional file 1 of Duck plague virus tegument protein vp22 plays a key role in the secondary envelopment and cell-to-cell spread

description: Additional file 1. Sequences and primer pair characteristics.
DOI: 10.6084/m9.figshare.5353759
title: Modeling <i>in vivo</i> relative biological effectiveness in particle therapy for clinically relevant endpoints

description: <b>Background:</b> The relative biological effectiveness (RBE) of particle therapy compared to photon radiotherapy is known to be variable but the exact dependencies are still subject to debate. <i>In vitro</i> data suggested that RBE is to a large extend independent of ion type if parametrized by the beam quality Q. This study analyzed the RBE dependence of pre-clinical data on late toxicity with an emphasis on the beam quality. <b>Material and methods:</b> Published pre-clinical RBE dose-response data of the spinal cord following one and two fractions of photon and carbon ion irradiation were compiled. The beam quality for each treatment condition was obtained from Monte Carlo simulations. The <i>α<sub>p</sub></i> and <i>β<sub>p</sub></i> parameters of the linear-quadratic (LQ) model for particle irradiation were determined from the pre-clinical data and was provided as a function of <i>Q</i>. An introduced model proposed <i>α<sub>p</sub></i> to increase linearly with <i>Q</i> and <i>β<sub>p</sub></i> to remain constant. RBE values predicted by the model were compared to the published data. <b>Results:</b> The α<sub>p</sub> parameter was highly correlated with <i>Q (R<sup>2</sup></i> = 0.96) with a linear slope of 0.019 Gy<sup>−1</sup>. No significant variation of <i>β<sub>p</sub></i> with <i>Q</i> was found. RBE and <i>Q</i> were also highly correlated (<i>R</i><sup>2</sup> = 0.98) for one and two fractions. The (extrapolated) RBE at <i>Q</i> = 0 (theoretical photon limit) for one and two fractions was 1.22 and significantly larger than 1 (<i>p</i> = .004). The model reproduced the dependence of RBE on fractionation well. <b>Conclusions</b>: Fraction dose and beam quality <i>Q</i> were sufficient to describe the RBE variability for a late toxicity model within a carbon ion treatment field. Assuming the independence of the identified RBE parameters on the ion type might suggest the translation of variable (pre-) clinical RBE data from carbon ion to proton therapy.
DOI: 10.6084/m9.figshare.5353759.v1
title: Modeling <i>in vivo</i> relative biological effectiveness in particle therapy for clinically relevant endpoints

description: <b>Background:</b> The relative biological effectiveness (RBE) of particle therapy compared to photon radiotherapy is known to be variable but the exact dependencies are still subject to debate. <i>In vitro</i> data suggested that RBE is to a large extend independent of ion type if parametrized by the beam quality Q. This study analyzed the RBE dependence of pre-clinical data on late toxicity with an emphasis on the beam quality. <b>Material and methods:</b> Published pre-clinical RBE dose-response data of the spinal cord following one and two fractions of photon and carbon ion irradiation were compiled. The beam quality for each treatment condition was obtained from Monte Carlo simulations. The <i>α<sub>p</sub></i> and <i>β<sub>p</sub></i> parameters of the linear-quadratic (LQ) model for particle irradiation were determined from the pre-clinical data and was provided as a function of <i>Q</i>. An introduced model proposed <i>α<sub>p</sub></i> to increase linearly with <i>Q</i> and <i>β<sub>p</sub></i> to remain constant. RBE values predicted by the model were compared to the published data. <b>Results:</b> The α<sub>p</sub> parameter was highly correlated with <i>Q (R<sup>2</sup></i> = 0.96) with a linear slope of 0.019 Gy<sup>−1</sup>. No significant variation of <i>β<sub>p</sub></i> with <i>Q</i> was found. RBE and <i>Q</i> were also highly correlated (<i>R</i><sup>2</sup> = 0.98) for one and two fractions. The (extrapolated) RBE at <i>Q</i> = 0 (theoretical photon limit) for one and two fractions was 1.22 and significantly larger than 1 (<i>p</i> = .004). The model reproduced the dependence of RBE on fractionation well. <b>Conclusions</b>: Fraction dose and beam quality <i>Q</i> were sufficient to describe the RBE variability for a late toxicity model within a carbon ion treatment field. Assuming the independence of the identified RBE parameters on the ion type might suggest the translation of variable (pre-) clinical RBE data from carbon ion to proton therapy.