cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12172830.v1
title: Pro-inflammatory cytokines are associated with the development of post-stroke depression in the acute stage of stroke: A meta-analysis

description: <b>Background</b>: Pro-inflammatory cytokines may be associated with post-stroke depression (PSD); however, results from different studies are inconsistent. <b>Objectives</b>: To investigate whether pro-inflammatory cytokines are associated with the development of PSD in acute stroke. <b>Methods</b>: PubMed, Embase, and Web of science were searched for relevant literature. Meta-analyzes were performed to determine whether the baseline blood concentrations of pro-inflammatory cytokines differed between acute stroke patients with and without depression. Sensitivity analyzes and regression analyzes were conducted to explore sources of heterogeneity. <b>Results</b>: We included 889 acute stroke patients from eight original studies, 312 of whom developed PSD and 577 did not. The serum concentrations of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) were higher in the PSD group, compared with the non-PSD group (IL-6: SMD = 1.26, 95% CI = [0.55, 1.97], <i>P</i> &lt; 0.001; TNF-α: SMD = 0.61, 95% CI = [0.13, 1.10], <i>P</i> = 0.010). <b>Conclusions</b>: This study indicates IL-6 and TNF-α as potential biomarkers of PSD in the acute stage of stroke and provides theoretical support for the early prevention and treatment of PSD.
DOI: 10.6084/m9.figshare.14270471
title: Flower transcriptome dynamics during nectary development in pepper (Capsicum annuum L.)

description: Abstract The measurement of gene expression can provide important information about gene function and the molecular basis for developmental processes. We analyzed the transcriptomes at three different developmental stages of pepper flower [sporogenous cell division, stage (B1); pollen mother cell meiosis, stage (B2); and open flower (B3)]. In the cDNA libraries for B1, B2, and B3: 82718, 77061, and 91491 unigenes were assembled, respectively. A total of 34,445 unigene sequences and 128 pathways were annotated by KEGG pathway analysis. Several genes associated with nectar biosynthesis and nectary development were identified, and 8,955, 12,182, and 23,667 DEGs were identified in the B2 vs B1, B3 vs B1, and B3 vs. B2 comparisons. DEGs were involved in various metabolic processes, including flower development, nectar biosynthesis, and nectary development. According to the RNA-seq data, all 13 selected DEGs showed similar expression patterns after q-PCR analysis. Sucrose-phosphatase, galactinol-sucrose galactosyltransferase, and sucrose synthase played very important roles in nectar biosynthesis, and CRABS CLAW could potentially be involved in mediating nectary development. A significant number of simple sequence repeat and single nucleotide polymorphism markers were predicted in the Capsicum annuum sequences. The new results provide valuable genetic information about flower development in pepper.
DOI: 10.6084/m9.figshare.14270420.v1
title: Geochronological systematics of the Huayna Potosí, Zongo and Taquesi plutons, Cordillera Real of Bolivia, by the K/Ar, Rb/Sr and U/Pb methods

description: Abstract The Huayna Potosi, Zongo and Taquesi are Triassic plutons located at the core of the Real Cordillera of Bolivia. In this paper, several Rb-Sr and K-Ar ages obtained in the past at the São Paulo Geochronology Laboratory, yet unpublished, will be presented, along with newer U-Pb Sensitive High-Resolution Ion Microprobe (SHRIMP) determinations made in the same laboratory, allowing us to redefine the geologic history of this part of the Central Andes. Rb/Sr analyses of some low grade metapelitic country rocks of the early Paleozoic (Amutara and Cancañiri Formations) yielded a Rb-Sr isochron age of 344 ± 38 Ma, indicating the action of an early Gondwanide regional event. A five-point Rb-Sr isochron from a granite outcrop of the Huayna Potosi pluton yielded an age of 224 ± 28 Ma. In addition, an important Ar loss in micas was detected in the Zongo granitoids and their country rocks, recording a thermal event that opened this isotopic system in the Oligocene. Newer U-Pb SHRIMP zircon ages of ca. 221 Ma were obtained in two other granitic outcrops of the Huayna Potosi granite. They confirmed its Triassic crystallization age, and a similar U-Pb SHRIMP age of 221.9 ± 1.5 Ma was obtained for one sample of the Taquesi pluton. For the Zongo pluton, many of the zircon grains obtained from one sample of its Kuticucho facies yielded extremely high uranium content, which produced reverse discordant apparent ages. However, due to the fair alignment of the analytical points in the Concordia diagram, possibly corresponding to a linear correlation, we made a regression calculation and the interception of the Concordia curve resulted in a rather imprecise age of 220 ± 20 Ma. Our conclusion was that the final magmatic crystallization and the intrusion of plutons in the central part of the Cordillera Real of Bolivia have occurred close to 221.5 ± 2.0 Ma, in late Triassic times. Finally, the U-Pb SHRIMP ages obtained in inherited zircon xenocrysts from the four available granitic rocks yielded very different ages, and many of them are related to previous magmatic episodes of the Andean Tectonic System. A few other age measurements indicated sources related to much older Proterozoic magmatic events associated with rocks from the Andean basement.
DOI: 10.6084/m9.figshare.14270471.v1
title: Flower transcriptome dynamics during nectary development in pepper (Capsicum annuum L.)

description: Abstract The measurement of gene expression can provide important information about gene function and the molecular basis for developmental processes. We analyzed the transcriptomes at three different developmental stages of pepper flower [sporogenous cell division, stage (B1); pollen mother cell meiosis, stage (B2); and open flower (B3)]. In the cDNA libraries for B1, B2, and B3: 82718, 77061, and 91491 unigenes were assembled, respectively. A total of 34,445 unigene sequences and 128 pathways were annotated by KEGG pathway analysis. Several genes associated with nectar biosynthesis and nectary development were identified, and 8,955, 12,182, and 23,667 DEGs were identified in the B2 vs B1, B3 vs B1, and B3 vs. B2 comparisons. DEGs were involved in various metabolic processes, including flower development, nectar biosynthesis, and nectary development. According to the RNA-seq data, all 13 selected DEGs showed similar expression patterns after q-PCR analysis. Sucrose-phosphatase, galactinol-sucrose galactosyltransferase, and sucrose synthase played very important roles in nectar biosynthesis, and CRABS CLAW could potentially be involved in mediating nectary development. A significant number of simple sequence repeat and single nucleotide polymorphism markers were predicted in the Capsicum annuum sequences. The new results provide valuable genetic information about flower development in pepper.
DOI: 10.6084/m9.figshare.20037471
title: Evolution of erythrocyte morphology in amphibians (Amphibia: Anura)

description: ABSTRACT We compared the morphology of the erythrocytes of five anurans, two toad species - Bufo gargarizans (Cantor, 1842) and Duttaphrynus melanostictus (Schneider, 1799) and three frog species - Fejervarya limnocharis (Gravenhorst, 1829), Microhyla ornata (Duméril & Bibron, 1841), and Rana zhenhaiensis (Ye, Fei & Matsui, 1995). We then reconstructed the ancestral state of erythrocyte size (ES) and nuclear size (NS) in amphibians based on a molecular tree. Nine morphological traits of erythrocytes were all significantly different among the five species. The results of principal component analysis showed that the first component (49.1% of variance explained) had a high positive loading for erythrocyte length, nuclear length, NS and ratio of erythrocyte length/erythrocyte width; the second axis (28.5% of variance explained) mainly represented erythrocyte width and ES. Phylogenetic generalized least squares analysis showed that the relationship between NS and ES was not affected by phylogenetic relationships although there was a significant linear relationship between these two variables. These results suggested that (1) the nine morphological traits of erythrocytes in the five anuran species were species-specific; (2) in amphibians, larger erythrocytes generally had larger nuclei.
DOI: 10.6084/m9.figshare.14270153
title: Aspiration with or without lavage in the treatment of acute suppurative thyroiditis secondary to pyriform sinus fistula

description: ABSTRACT Objective There is currently no consensus regarding the optimal management of acute suppurative thyroiditis (AST) secondary to pyriform sinus fistula (PSF). To investigate the benefits and adverse events of aspiration with or without lavage for the treatment of AST secondary to PSF. Subjects and methods This was a retrospective analysis of consecutive patients with AST secondary to PSF who were admitted at the Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University between August 2012 and December 2018. Clinical information, procedural data, and imaging data were analyzed. Results Seven patients (five women; mean age, 16.9 ± 6.3 years; range, 8-26 years) were included. The patients most presented with anterior neck pain and swelling (n = 7), fever (n = 7), or odynophagia (n = 5). Six cases of AST occurred on the left side of the thyroid and 1 on the right. All patients had thyroid abscess. AST was diagnosed by ultrasound-guided needle aspiration cytology in all cases. PSF was diagnosed during the inflammatory stage in five patients and during the quiescent stage in two. All patients were treated with empiric antibiotics. Needle aspiration without lavage was performed in three cases. Needle aspiration with lavage was performed in four cases. Repeat aspiration was performed in three cases. All patients recovered completely, with no procedure-related complications. During 18.3 ± 7.8 months of follow-up, AST recurred in one case. Excision of the PSF was performed in another case. Conclusion Ultrasound-guided aspiration with or without lavage had a good treatment effect and without adverse events for the management of AST secondary to PSF.
DOI: 10.6084/m9.figshare.19519402
title: A global dataset for prevalence of Salmonella Gallinarum between 1945 and 2021

description: Standard operating procedures were applied to remove duplicates and ensure accuracy of up-to-date results from available articles involving the prevalence of S. Gallinarum. It's the world’s largest dataset ever, including 201 independent studies between 1945 and 2021, covering 520 records of 901,491,709 million samples.<br>
DOI: 10.6084/m9.figshare.14794958.v1
title: Supplementary Table 1. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: Species surveyed in the screen of eukaryotic mitochondrial genomes.
DOI: 10.6084/m9.figshare.22134352.v1
title: Online Smooth Backfitting for Generalized Additive Models

description: We propose an online smoothing backfitting method for generalized additive models coupled with local linear estimation. The idea can be extended to general nonlinear optimization problems. The strategy is to use an appropriate-order expansion to approximate the nonlinear equations and store the coefficients as sufficient statistics which can be updated in an online manner by the dynamic candidate bandwidth method. We investigate the statistical and algorithmic convergences of the proposed method. By defining the relative statistical efficiency and computational cost, we further establish a framework to characterize the trade-off between estimation performance and computation performance. Simulations and real data examples are provided to illustrate the proposed method and algorithm.
DOI: 10.6084/m9.figshare.14270044
title: Dynamic changes of periostin and collagen I in the sclera during progressive myopia in guinea pigs

description: ABSTRACT Purpose: To investigate periostin and collagen I expression during a scleral remodeling in myopic eyes and to determine their role in collagen remodeling of the myopic sclera. Methods: Fifty one-week-old guinea pigs were divided into the control and form-deprivation myopia (FDM) groups. The eyes of animals in the form-deprivation myopia group were covered for 2, 4, and 8 weeks, or were covered for 4 weeks and then uncovered for 2 weeks. The diopters and axial lengths in the eyes in each group of guinea pigs were measured. Immunohistochemistry and reverse transcription polymerase chain reaction were used to detect the relative protein and mRNA expressions of periostin and collagen I in the scleral tissues of guinea pig. Results: Before masking, guinea pigs in the control and form-deprivation myopia groups were hypermetropic and did not differ significantly (p&gt;0.05). Hypermetropic refraction in the control group gradually decreased. In guinea pigs from the form-deprivation myopia group, the refractive power gradually changed from +2.14 ± 0.33 D to -7.22 ± 0.51 D, and the axial length gradually changed from 5.92 ± 0.37 mm to 8.05 ± 0.34 mm from before until the end of masking. Before covering, no significant difference was observed in the relative collagen I and periostin mRNA and protein expression levels in the sclera of the guinea pig control and form-deprivation myopia groups (p&gt;0.05). The relative collagen I and periostin protein and mRNA expression levels in the sclera of guinea pigs in the form-deprivation myopia group at 2, 4, and 8 weeks, and after covering the eyes for 4 weeks followed by uncovering for 2 weeks, were significantly lower than those in the control group (p&lt;0.05). The collagen I and periostin mRNA expression levels were positively correlated with protein expression levels in the sclera of guinea pigs (protein: r=0.936, p&lt;0.05; mRNA: r=0.909, p&lt;0.05). Conclusions: Periostin was expressed in the myopic sclera of guinea pigs, and changes in periostin and collagen I expression were highly consistent. Periostin and collagen I may be involved in the regulation of scleral remodeling in myopia.
DOI: 10.6084/m9.figshare.22658871.v1
title: The Leverage Effect Puzzle under Semi-nonparametric Stochastic Volatility Models

description: This paper extends the solution proposed by Aït-Sahalia, Fan, and Li (2013) for the leverage effect puzzle, which refers to a fact that empirical correlation between daily asset returns and the changes of daily volatility estimated from high frequency data is nearly zero. Complementing the analysis in Aït-Sahalia, Fan, and Li (2013) via the Heston model, we work with a generic semi-nonparametric stochastic volatility model via an operator-based expansion method. Under such a general setup, we identify a new source of bias due to the flexibility of variance dynamics, distinguishing the leverage effect parameter from the instantaneous correlation parameter. For estimating the leverage effect parameter, we show that the main results on analyzing the various sources of biases as well as the resulting statistical procedures for biases correction in Aït-Sahalia, Fan, and Li (2013) hold true and are thus indeed theoretically robust. For estimating the instantaneous correlation parameter, we developed a new nonparametric estimation method.
DOI: 10.6084/m9.figshare.22655351
title: Additional file 4 of FACI is a novel clathrin adaptor protein 2-binding protein that facilitates low-density lipoprotein endocytosis

description: Additional file 4: Table S4. Lists of 32 FACI interactors based on stringent prediction criteria and their gene ontology analysis.
DOI: 10.6084/m9.figshare.22655351.v1
title: Additional file 4 of FACI is a novel clathrin adaptor protein 2-binding protein that facilitates low-density lipoprotein endocytosis

description: Additional file 4: Table S4. Lists of 32 FACI interactors based on stringent prediction criteria and their gene ontology analysis.
DOI: 10.6084/m9.figshare.14794953.v1
title: Supplementary Dataset 1. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>Schematic visualization of the evolutionary changes on KEGG pathways analyzed in this work.</b> Each file corresponds to one pathway, where the symbols are equivalent to those listed in <b>Supplementary Figure 4.</b> The scores of each enzyme are represented by the size of the dot (see legend), and they can be interactively added/removed. Each symbol represents a gene which, upon hover with the cursor, displays an informative box. This provides many lines of evolutionary information: 1) Gene name, one of the kegg orthologs (KOs) and name of the enzyme, KO for which the mapping was established. 2) Evolutionary processes found in this gene, including duplication (duplicated_in_any), positive selection (possel), mitochondrial retargeting (mito_retargeting), loss (lost_in_any), co-loss (co-lost_in_, meaning that this gene is lost together with orthologs of the other CI loss events), orphan and the intersections between all these categories. For orphan genes, the top 5 <i>blastp</i> hits to the latest version of the <i>trembl</i> database are shown, which should help to understand if they are true orphans. 3) The codon adaptation index (CAI) of the gene and the one of the orthologs of the sister CI+ species (CI+ orthologs). 4) The results of subcellular localization prediction (performed using <i>deeploc</i>) where, for each location with a p &gt; 0.1, the probability of localization (pLoc) of the gene and the CI+ orthologs are shown. 5) The interproscan annotations of the genes, where each gene is one annotation. 6) The InterProScan annotation of all CI+ orthologs, where each line corresponds to one ortholog, and the annotations are delimited by “|”.
DOI: 10.6084/m9.figshare.14794955.v1
title: Supplementary Table 5. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>Scores of all pathways in the recent CI loss.</b> Show are the scores for all the pathways according to our pathway scoring method.
DOI: 10.6084/m9.figshare.12173169.v1
title: Revision of <i>Triplicatella</i> (Orthothecida, Hyolitha) with preserved digestive tracts from the early Cambrian Chengjiang Lagerstätte, South China

description: The cap-shaped shells of <i>Triplicatella</i> are known almost exclusively from small shelly fossil assemblages with articulated specimens showing unequivocally that they represent the operculum of a hyolith. Abundant specimens of <i>Triplicatella opimus</i> from the fine-grained shales of the Chengjiang Lagerstätte of South China with soft-part preservation are documented herein. The soft tissues, including the feeding apparatus and complex digestive system, in <i>T. opimus</i> strongly suggest that <i>Triplicatella</i> was a deposit feeder. The digestive tract of <i>T. opimus</i> consists of two limbs, a spiral loop folded into a chevron-like structure and a slightly recurved to straight anal tube, which are preserved as reddish-black traces enriched in iron. The new anatomical information obtained from <i>T. opimus</i> in the Chengjiang Biota suggests an intermediate stage in the development of the characteristic folded gut of orthothecid hyoliths. The new anatomical information reported here shows that <i>Triplicatella</i> is one of the best-preserved early members of the Orthothecida and promotes our understanding of the general anatomy and evolution of the Hyolitha.
DOI: 10.6084/m9.figshare.6406052.v1
title: Marginal Bayesian Semiparametric Modeling of Mismeasured Multivariate Interval-Censored Data

description: Motivated by data gathered in an oral health study, we propose a Bayesian nonparametric approach for population-averaged modeling of correlated time-to-event data, when the responses can only be determined to lie in an interval obtained from a sequence of examination times and the determination of the occurrence of the event is subject to misclassification. The joint model for the true, unobserved time-to-event data is defined semiparametrically; proportional hazards, proportional odds, and accelerated failure time (proportional quantiles) are all fit and compared. The baseline distribution is modeled as a flexible tailfree prior. The joint model is completed by considering a parametric copula function. A general misclassification model is discussed in detail, considering the possibility that different examiners were involved in the assessment of the occurrence of the events for a given subject across time. We provide empirical evidence that the model can be used to estimate the underlying time-to-event distribution and the misclassification parameters without any external information about the latter parameters. We also illustrate the effect on the statistical inferences of neglecting the presence of misclassification. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.14794947.v1
title: Supplementary Table 4. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>All results of the GO enrichment analysis.</b> See results.
DOI: 10.6084/m9.figshare.14794950.v1
title: Supplementary Table 3. from Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

description: <b>Annotation of all genes in any of the intersections between duplication, positive selection and/or mitochondrial retargeting.</b> See <b>Figure 2.</b>
DOI: 10.6084/m9.figshare.5357833.v1
title: Spatial-temporal relationships of late Mesozoic granitoids in Zhejiang Province, Southeast China: constraints on tectonic evolution

description: Late Mesozoic granitoids in South China are generally considered to have been generated under the Palaeo–Pacific tectonic regime, however, the precise subduction mechanism remains controversial. Detailed zircon U–Pb geochronological, major and trace element, and Sr–Nd–Hf isotopic data are used to document the spatiotemporal distribution of the granitoids in Zhejiang Province. Three periods of late Mesozoic magmatism, including stage 1 (170–145 Ma), stage 2 (145–125 Ma), and stage 3 (125–90 Ma), can be distinguished based on systematic zircon U–Pb ages that become progressively younger towards the SE. Stage 1 granitic rocks are predominantly I-type granitoids, but minor S- or A-type rocks also occur. Sr–Nd–Hf isotopic data suggest that these granitoids were generated from hybrid magmas that resulted from mixing between depleted mantle-derived and ancient crust-derived magmas that formed in an active continental margin environment related to the low-angle subduction of the Palaeo–Pacific plate beneath Southeast China mainland. Stage 2 granitic rocks along the Jiangshan–Shaoxing Fault are predominantly I- and A-type granitoids with high initial <sup>87</sup>Sr/<sup>86</sup>Sr, low <i>ε</i><sub>Nd</sub>(<i>t</i>), <i>ε</i><sub>Hf</sub>(<i>t</i>) values and Mesoproterozoic Nd–Hf model ages. These results suggest that stage 2 granitoids were derived from mixing between enriched mantle-derived mafic magmas and ancient crust-derived magmas in an extensional back-arc setting related to rollback of the Palaeo–Pacific slab. Stage 3 granitic rocks along the Lishui–Yuyao Fault comprise mainly A- and I-type granitoids with high initial <sup>87</sup>Sr/<sup>86</sup>Sr ratios, and low <i>ε</i><sub>Nd</sub>(<i>t</i>) and <i>ε</i><sub>Hf</sub>(<i>t</i>) values, again suggesting mixing of enriched mantle-derived mafic magmas with more ancient crustal magmas in an extensional back-arc setting, related in this case to the continued rollback the Palaeo–Pacific plate and the outboard retreat of its subduction zone.