cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24262354
title: Joint Network Reconstruction and Community Detection from Rich but Noisy Data

description: Most empirical studies of complex networks return rich but noisy data, as they measure the network structure repeatedly but with substantial errors due to indirect measurements. In this article, we propose a novel framework, called the group-based binary mixture (GBM) modeling approach, to simultaneously conduct network reconstruction and community detection from such rich but noisy data. A generalized expectation-maximization (EM) algorithm is developed for computing the maximum likelihood estimates, and an information criterion is introduced to consistently select the number of communities. The strong consistency properties of the network reconstruction and community detection are established under some assumption on the Kullback-Leibler (KL) divergence, and in particular, we do not impose assumptions on the true network structure. It is shown that joint reconstruction with community detection has a synergistic effect, whereby actually detecting communities can improve the accuracy of the reconstruction. Finally, we illustrate the performance of the approach with numerical simulations and two real examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12197124.v1
title: Additional file 1 of The effects of different doses of dexmedetomidine on the requirements for propofol for loss of consciousness in patients monitored via the bispectral index: a double-blind, placebo-controlled trial

description: Additional file 1. Raw data on oxygen saturation (SpO2), mean arterial pressure (MAP) and heart rate (HR).
DOI: 10.6084/m9.figshare.24262354.v1
title: Joint Network Reconstruction and Community Detection from Rich but Noisy Data

description: Most empirical studies of complex networks return rich but noisy data, as they measure the network structure repeatedly but with substantial errors due to indirect measurements. In this article, we propose a novel framework, called the group-based binary mixture (GBM) modeling approach, to simultaneously conduct network reconstruction and community detection from such rich but noisy data. A generalized expectation-maximization (EM) algorithm is developed for computing the maximum likelihood estimates, and an information criterion is introduced to consistently select the number of communities. The strong consistency properties of the network reconstruction and community detection are established under some assumption on the Kullback-Leibler (KL) divergence, and in particular, we do not impose assumptions on the true network structure. It is shown that joint reconstruction with community detection has a synergistic effect, whereby actually detecting communities can improve the accuracy of the reconstruction. Finally, we illustrate the performance of the approach with numerical simulations and two real examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.24262363
title: Varying Coefficient Model via Adaptive Spline Fitting

description: The varying coefficient model is a potent dimension reduction tool for nonparametric modeling and has received extensive attention from researchers. Most existing methods for fitting this model use polynomial splines with equidistant knots and treat the number of knots as a hyperparameter. However, imposing equidistant knots tends to be overly rigid, and systematically determining the optimal number of knots is also challenging. In this article, we address these challenges by employing polynomial splines with adaptively selected and predictor-specific knots to fit the varying coefficients in the model. We propose an efficient dynamic programming algorithm to find the optimal solution. Numerical results demonstrate that our new method achieves significantly smaller mean squared errors for coefficient estimations compared to the equidistant spline fitting method. An implementation of our method in R is available at https://github.com/wangxf0106/vcmasf. Proofs of the theorems are provided in the online supplementary materials.
DOI: 10.6084/m9.figshare.24262363.v1
title: Varying Coefficient Model via Adaptive Spline Fitting

description: The varying coefficient model is a potent dimension reduction tool for nonparametric modeling and has received extensive attention from researchers. Most existing methods for fitting this model use polynomial splines with equidistant knots and treat the number of knots as a hyperparameter. However, imposing equidistant knots tends to be overly rigid, and systematically determining the optimal number of knots is also challenging. In this article, we address these challenges by employing polynomial splines with adaptively selected and predictor-specific knots to fit the varying coefficients in the model. We propose an efficient dynamic programming algorithm to find the optimal solution. Numerical results demonstrate that our new method achieves significantly smaller mean squared errors for coefficient estimations compared to the equidistant spline fitting method. An implementation of our method in R is available at https://github.com/wangxf0106/vcmasf. Proofs of the theorems are provided in the online supplementary materials.
DOI: 10.6084/m9.figshare.21111210.v1
title: Rapid and sensitive detection of flubendiamide in grapes and tomatoes using a colloidal gold immunochromatography assay

description: In this study, we developed a monoclonal antibody (mAb)-based colloidal gold immunochromatography assay (CG-ICA) strip for the rapid and sensitive detection of flubendiamide (FBD) in food samples. Our anti-FBD mAb 2B1 was highly specific and had a half-maximal inhibitory concentration (IC<sub>50</sub>) of 1.55 ng/mL under optimal conditions. It belongs to the IgG2a isotype and has a K<sub>aff</sub> value of 1.52 × 10<sup>9</sup> mol/L. The strip provided a visual detection limit of 50 ng/g for both grapes and tomatoes, with a cut-off value of 1,000 ng/g and these qualitative results were observed within 15 min. For quantitative analysis, the calculated detection limits were 6 ng/g and 5 ng/g in grapes and tomatoes, respectively. The average recoveries of FBD ranged from 88.8% to 111.8% in grapes and 94.5% to 110.6% in tomatoes. The proposed strip assay is highly practical for screening FDB in food samples.
DOI: 10.6084/m9.figshare.13246934
title: MoSec61β, the beta subunit of Sec61, is involved in fungal development and pathogenicity, plant immunity, and ER-phagy in <i>Magnaporthe oryzae</i>

description: The process of protein translocation into the endoplasmic reticulum (ER) is the initial and decisive step in the biosynthesis of all secretory proteins and many soluble organelle proteins. In this process, the Sec61 complex is the protein-conducting channel for transport. In this study, we identified and characterized the β subunit of the Sec61 complex in <i>Magnaporthe oryzae</i> (MoSec61β). Compared with the wild-type strain Guy11, the Δ<i>Mosec61β</i> mutant exhibited highly branched mycelial morphology, reduced conidiation, high sensitivity to cell wall integrity stress, severely reduced virulence to rice and barley, and restricted biotrophic invasion. The turgor pressure of Δ<i>Mosec61β</i> was notably reduced, which affected the function of appressoria. Moreover, Δ<i>Mosec61β</i> was also sensitive to oxidative stress and exhibited a reduced ability to overcome plant immunity. Further examination demonstrated that MoSec61β affected the normal secretion of the apoplastic effectors Bas4 and Slp1. In addition, Δ<i>Mosec61β</i> upregulated the level of ER-phagy. In conclusion, our results demonstrate the importance of the roles played by MoSec61β in the fungal development and pathogenesis of <i>M. oryzae</i>.
DOI: 10.25794/reference/amqk_3k3
title: Xancac-8004
DOI: 10.6084/m9.figshare.16922605
title: distance_deviation

description: In the environment with and without obstacles, the
distance deviation to the target and the
distance deviation to the two nearest neighbors obtained after 30 simulations of 500 steps
each time by ADM, LCPSO, SMCH, ADM_VFH, LCPSO_VFH, SMCH_MWF, ADM_VFH_CDTA, ADM_VFH_GDTA, LCPSO_VFH_CDTA, LCPSO_VFH_GDTA, and SMCH_MWF_MSTA algorithm.
DOI: 10.25794/reference/njj4vhix
title: Xancac-CN05

description: EGN-PP reannotation using Xanthomix Project RNASeq data
DOI: 10.25794/reference/spkuzl91
title: Xancac-CN14

description: EGN-PP reannotation using Xanthomix Project RNASeq data
DOI: 10.25794/reference/axfxrd9l
title: Xancar-CFBP5828R

description: EGN-PP reannotation using Xanthomix Project RNASeq data
DOI: 10.6084/m9.figshare.16922819
title: Contrasting Early Palaeozoic provenance of the Yemaquan and Harlik arcs in the SW Altaids (NW China): identification of cryptic sutures in accretionary orogens

description: The means and timing of amalgamation of the Harlik arc to the Yemaquan arc remain controversial. To address these polemic relations, we report new field data and zircon U-Pb analyses of early Palaeozoic strata in the Harlik Mountains. Field investigations reveal that the Huangcaopo Group in northern Harlik are composed mainly of clastic rocks, while their counterparts in central Harlik (Harlik arc) are dominantly volcanic and pyroclastic rocks. Weighted mean ages of the youngest group of samples from northern Harlik are 455 ± 9 Ma and 456 ± 7 Ma, whereas their counterparts in central Harlik have a weighted mean age of 446 ± 4 Ma, indicating that parts of the Huangcaopo Group in central Harlik should be re-defined as the early Silurian Hongliuxia Formation. The youngest grain from the Dananhu Formation in central Harlik is 421 ± 3 Ma, the time of deposition in early Devonian. Age spectra of the Huangcaopo Group in northern Harlik have only two peaks at 488 Ma and 923 Ma, demonstrating affinity with the Tuva-Mongolian microcontinent, a correlation supported by the occurrence of Silurian Tuvaella brachiopod fauna in those strata. In contrast, multiple peaks at 494 Ma, 813 Ma, 1485 Ma, 1872 Ma and 2469 Ma in the Hongliuxia and Dananhu Formations in central Harlik have neither an affinity with the Tuva-Mongolian nor with the Central Tianshan microcontinent, which suggests that the Harlik arc probably evolved independently as a Japan-type arc in the early Palaeozoic. The above disparate relations, combined with the fact that the Silurian Tuvaella brachiopod fauna occurs throughout the Kelameili ophiolite belt but not in the Harlik arc, provide robust evidence that the contrasting provenance of the Yemaquan and Harlik arcs is an expression of a cryptic suture in northern Harlik rather than along the Kelameili ophiolite belt to the north.
DOI: 10.6084/m9.figshare.24787216
title: Investigation of Mitochondrial Homeostasis Changes in Lens Epithelium of High-Myopic Cataract

description: High myopia is demonstrated as a pathogenic factor for nuclear cataract. The main mechanism of high-myopia cataracts (HMC) is oxidative damage, which causes mitochondrial homeostasis imbalance. This study aimed to explore the mitochondrial homeostasis alterations in lens epithelial cells (LECs) of HMC. The lens epithelium tissues of 20 patients with HMC and 20 control subjects with age-related cataracts (ARC) were collected. The real-time quantitative PCR and western blot assays were performed for gene expressions. Immunofluorescence (IF) assays were performed for mitochondrial marker TOM20, DNA damage marker 15A3, and autophagosome marker LC3. Transmission electron microscopy (TEM) was used to observe the changes in mitochondria morphology. Mitochondrial ROS, and mitochondrial membrane potential were detected by MitoSOX fluorescence, and JC-1 MitoMP staining, respectively. Rat lenses cultured <i>in vitro</i> were pretreated with CCCP and H<sub>2</sub>O<sub>2</sub> (10 and 400 µM) for 24 h. The copy number of mtDNA was decreased in HMC patients compared to the ARC patients. Increased mitochondrial-oriented oxidative stress response was detected in LECs of HMC compared to that of ARC. Altered expressions of mitochondrial homeostasis and mitophagy markers, including TFAM, PGC1α, MFN1, MFN2, Drp1, PINK1, Parkin and LC3, were found in HMC patients. Reciprocally, no significant differences in the expression of BNIP3 and FUNDC1 were found between HMC and ARC patients. Importantly, TEM revealed that the obvious mitochondrial fission and mitophagy phenomena occur in the LECs of HMC patients compared to the ARC patients. Moreover, CCCP aggreated the mitoROS production and depolarized mitochondrial membrane potential in the H<sub>2</sub>O<sub>2</sub>-treated human lens epithelial cells line (SRA01/04); Most important, rat lens organ culture experiments indicated a significant increase <i>in</i> H<sub>2</sub>O<sub>2</sub>-induced <i>lens</i> opacity following mitochondrial uncoupling CCCP treatment. This study has identified for the first time the abnormal mitochondrial homeostasis in HMC, and provide a new perspective on the potential mechanisms of HMC, which occurs earlier and at a higher incidence rate than ARC.
DOI: 10.6084/m9.figshare.24787216.v1
title: Investigation of Mitochondrial Homeostasis Changes in Lens Epithelium of High-Myopic Cataract

description: High myopia is demonstrated as a pathogenic factor for nuclear cataract. The main mechanism of high-myopia cataracts (HMC) is oxidative damage, which causes mitochondrial homeostasis imbalance. This study aimed to explore the mitochondrial homeostasis alterations in lens epithelial cells (LECs) of HMC. The lens epithelium tissues of 20 patients with HMC and 20 control subjects with age-related cataracts (ARC) were collected. The real-time quantitative PCR and western blot assays were performed for gene expressions. Immunofluorescence (IF) assays were performed for mitochondrial marker TOM20, DNA damage marker 15A3, and autophagosome marker LC3. Transmission electron microscopy (TEM) was used to observe the changes in mitochondria morphology. Mitochondrial ROS, and mitochondrial membrane potential were detected by MitoSOX fluorescence, and JC-1 MitoMP staining, respectively. Rat lenses cultured <i>in vitro</i> were pretreated with CCCP and H<sub>2</sub>O<sub>2</sub> (10 and 400 µM) for 24 h. The copy number of mtDNA was decreased in HMC patients compared to the ARC patients. Increased mitochondrial-oriented oxidative stress response was detected in LECs of HMC compared to that of ARC. Altered expressions of mitochondrial homeostasis and mitophagy markers, including TFAM, PGC1α, MFN1, MFN2, Drp1, PINK1, Parkin and LC3, were found in HMC patients. Reciprocally, no significant differences in the expression of BNIP3 and FUNDC1 were found between HMC and ARC patients. Importantly, TEM revealed that the obvious mitochondrial fission and mitophagy phenomena occur in the LECs of HMC patients compared to the ARC patients. Moreover, CCCP aggreated the mitoROS production and depolarized mitochondrial membrane potential in the H<sub>2</sub>O<sub>2</sub>-treated human lens epithelial cells line (SRA01/04); Most important, rat lens organ culture experiments indicated a significant increase <i>in</i> H<sub>2</sub>O<sub>2</sub>-induced <i>lens</i> opacity following mitochondrial uncoupling CCCP treatment. This study has identified for the first time the abnormal mitochondrial homeostasis in HMC, and provide a new perspective on the potential mechanisms of HMC, which occurs earlier and at a higher incidence rate than ARC.
DOI: 10.25387/g3.14301467
title: Supplemental Material for Hu et al., 2021

description: The fat content of other zinc related
transporter mutants in supplementary zinc had no changed compare to wild type N2 worms.<i>cdf-1 </i>or <i>sur-7</i>
mutants could restore the zinc level of depletion of SCD, <i>fat-6</i>RNAi
worms, they could not restore the <i>fat-6</i>RNAi
lipid droplets back to wild type.
DOI: 10.25387/g3.14301467.v1
title: Supplemental Material for Hu et al., 2021

description: The fat content of other zinc related
transporter mutants in supplementary zinc had no changed compare to wild type N2 worms.<i>cdf-1 </i>or <i>sur-7</i>
mutants could restore the zinc level of depletion of SCD, <i>fat-6</i>RNAi
worms, they could not restore the <i>fat-6</i>RNAi
lipid droplets back to wild type.
DOI: 10.6084/m9.figshare.16916731
title: Additional file 1 of Posterior-only debridement, internal fixation, and interbody fusion using titanium mesh in the surgical treatment of thoracolumbar tuberculosis with spinal epidural abscess: a minimum 5-year follow-up

description: Additional file 1.
DOI: 10.6084/m9.figshare.16916731.v1
title: Additional file 1 of Posterior-only debridement, internal fixation, and interbody fusion using titanium mesh in the surgical treatment of thoracolumbar tuberculosis with spinal epidural abscess: a minimum 5-year follow-up

description: Additional file 1.
DOI: 10.6084/m9.figshare.12198651
title: Additional file 3 of LBX2-AS1 up-regulated by NFIC boosts cell proliferation, migration and invasion in gastric cancer through targeting miR-491-5p/ZNF703

description: Additional file 3: Table S1 List of LBX2-AS1-bond miRNAs predicted by starBase.
DOI: 10.6084/m9.figshare.16916617
title: Additional file 2 of Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline

description: Additional file 2. The index information of each secondary pool.
DOI: 10.6084/m9.figshare.16916617.v1
title: Additional file 2 of Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline

description: Additional file 2. The index information of each secondary pool.
DOI: 10.6084/m9.figshare.12198660
title: Additional file 5 of LBX2-AS1 up-regulated by NFIC boosts cell proliferation, migration and invasion in gastric cancer through targeting miR-491-5p/ZNF703

description: Additional file 5: Table 2 List of miR-491-5p-targeted mRNAs predicted by starBase.
DOI: 10.5281/zenodo.10649440
title: THE SOCIO-ECONOMIC IMPORTANCE OF ENTREPRENEURSHIP
DOI: 10.5281/zenodo.10649441
title: THE SOCIO-ECONOMIC IMPORTANCE OF ENTREPRENEURSHIP
DOI: 10.6084/m9.figshare.12198588
title: Lateral mechanical impedance rather than frontal promotes cortical expansion of roots

description: It has long been considered that mechanical impedance on root will restrict root elongation and consequently promote radial growth. When seedlings grew in sands, we did observe radial expansion of roots and it, however, arose before elongation restriction. Mechanical impedance of sands can be classified into frontal- and lateral-type based on the interaction site of root. Therefore, we suspected that radial expansion might be mainly stimulated by lateral- rather than frontal-impedance. To verify our speculation, roots were exposed to frontal- and lateral-impedance separately. Small plastic caps were used to provide pure frontal impedance on root tips and cylindrical plastic containers were used to provide pure lateral impedance. Root elongation was remarkably suppressed under the frontal impedance of plastic caps, and more than that in sand-condition. However, the radial expansion of the plastic-cap-fitted roots was far inferior to that of the sand-cultured roots. Microstructural analysis revealed that sand-condition thickened root largely dependents on cortical expansion, whereas plastic cap did it mainly by thickening stele. In cylindrical plastic containers, mechanical impedance came only from the lateral direction and promoted the expansion of cortex like sand-condition. Thus, we proposed that the expansion of cortex and the consequent radial growth of roots were mainly due to lateral impedance when seedlings grew in sands.
DOI: 10.6084/m9.figshare.23733130
title: Additional file 1 of LncRNA SOX21-AS1 accelerates endometrial carcinoma progression through the miR-7-5p/RAF1 pathway

description: Additional file 1. F.rar and D.rar.
DOI: 10.6084/m9.figshare.23733130.v1
title: Additional file 1 of LncRNA SOX21-AS1 accelerates endometrial carcinoma progression through the miR-7-5p/RAF1 pathway

description: Additional file 1. F.rar and D.rar.
DOI: 10.6084/m9.figshare.12198651.v1
title: Additional file 3 of LBX2-AS1 up-regulated by NFIC boosts cell proliferation, migration and invasion in gastric cancer through targeting miR-491-5p/ZNF703

description: Additional file 3: Table S1 List of LBX2-AS1-bond miRNAs predicted by starBase.
DOI: 10.6084/m9.figshare.12197124
title: Additional file 1 of The effects of different doses of dexmedetomidine on the requirements for propofol for loss of consciousness in patients monitored via the bispectral index: a double-blind, placebo-controlled trial

description: Additional file 1. Raw data on oxygen saturation (SpO2), mean arterial pressure (MAP) and heart rate (HR).
DOI: 10.6084/m9.figshare.14095582
title: c-Fos is upregulated in the genital tubercle of DEHP-induced hypospadiac rats and the prepuce of patients with hypospadias

description: This study aimed to investigate the expression of Fos proto-oncogene, AP-1 transcription factor subunit (c-Fos) in the genital tubercle (GT) of rats with di(2-ethylhexyl) phthalate (DEHP)-induced hypospadias and in the prepuce of patients with hypospadias compared with unaffected controls. Pregnant rats were given 750 mg/kg/day DEHP orally from gestational days 12–19. Western blotting showed that c-Fos expression was increased in DEHP-induced hypospadiac male offspring. In addition, 30 prepuce tissue specimens obtained during hypospadias repair surgery were divided into 2 groups: the mild hypospadias group (n = 15) and the severe hypospadias group (n = 15). Fifteen normal prepuce tissue specimens were harvested during elective circumcision as normal controls. Real-time quantitative polymerase chain reaction, western blotting and immunohistochemistry analyses were used to assess c-Fos expression. c-Fos protein levels were higher in the GT of DEHP-induced rats than in that of control rats. c-Fos mRNA and protein levels were also higher in the hypospadias groups than in the control group (<i>p</i> &lt; 0.05, <i>p</i> &lt; 0.001), and c-Fos protein levels were significantly higher in the severe hypospadias group than in the mild hypospadias group (<i>p</i> &lt; 0.01). The expression of c-Fos was increased in both the GT of DEHP-induced hypospadiac rats and the prepuce of hypospadias patients. Thus, c-Fos overexpression might contribute to hypospadias. <b>Abbreviations:</b> DEHP: di(2-ethylhexyl) phthalate; c-Fos: Fos proto-oncogene, AP-1 transcription factor subunit; Mafb: the masculinization-regulatory gene v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B; GT: genital tubercle; ED: embryonic day; AGD: anogenital distance; AGI: anogenital distance index; ED: embryonic day.