基于Scopus的植物表型组学研究进展分析

Bibliometric analyses are capable of demonstrating the history and the tendency of scientific and technological development. This article aims to use big scientific data to explore the present status of plant phenomics, based on which sound recommendations could be provided for the development of this emerging research domain. [Methods] Based on academic outputs such as research publications, citations, collaborations, research areas, academic organizations, and authors retrieved from the Scopus database between 2013 and September 2018, statistical analysis tools such as SciVal and CiteSpace 5.0 were applied to quantitatively visualize the development and tendency of plant phenotyping, plant phenomics, and related research areas. [Results] This Scopus-based research has retrieved 20 953 articles that are related to plant phenotyping, plant phenomics, and related applications in plant research, with a total citation of 217 105 and 2.0% of them are TOP1% highly cited papers. According to total citations, the TOP10 countries are the United States, China, Germany, the United Kingdom, France, Japan, Australia, Spain, Canada, and the Netherlands. The TOP10 research organizations based on total citations are Chinese Academy of Sciences (CAS), Institut National de la Recherche Agronomique (INRA), the US Department of Agriculture, Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Agricultural Sciences, Cornell University, Spanish National Research Council, University of California at Davis, Universite Paris-Sacly, and Wageningen University & Research. The scholar with the most academic outputs is Alisdair Robert Fernie at the Koch Planck Institute of Molecular Plant Physiology, Germany. He has published 58 papers using plant cellular phenotypes and was cited 1 246 times. At present, plant phenomics research has focused on a number of plant species, including Arabidopsis, rice, wheat, corn, tomato and soybean. [Conclusion] As an emerging research domain, plant phenomics requires interdisciplinary efforts to integrate agriculture, cultivation, breeding, and other plant biological research with computing sciences. In particular, high-throughput image analysis and related data analysis has become an important research theme at the present stage, with the topical saliency index reaches 98.8%, a very high relevance score

Evolution of the strange-metal scattering in momentum space of electron-doped La2−xCexCuO4{\rm La}_{2-x}{\rm Ce}_x{\rm CuO}_4

The linear-in-temperature resistivity is one of the important mysteries in the strange metal state of high-temperature cuprate superconductors. To uncover this anomalous property, the energy-momentum-dependent imaginary part of the self-energy Im ${\rm \Sigma}(k, \omega)$ holds the key information. Here we perform systematic doping, momentum, and temperature-dependent angle-resolved photoemission spectroscopy measurements of electron-doped cuprate ${\rm La}_{2-x}{\rm Ce}_x{\rm CuO}_4$ and extract the evolution of the strange metal scattering in momentum space. At low doping levels and low temperatures, Im ${\rm\Sigma} \propto \omega$ dependence dominates the whole momentum space. For high doping levels and high temperatures, Im ${\rm\Sigma} \propto \omega^2$ shows up, starting from the antinodal region. By comparing with the hole-doped cuprates ${\rm La}_{2-x}{\rm Sr}_x{\rm CuO}_4$ and ${\rm Bi}_2{\rm Sr}_2{\rm CaCu}_2{\rm O}_8$, we find a dichotomy of the scattering rate exists along the nodal and antinodal direction, which is ubiquitous in the cuprate family. Our work provides new insight into the strange metal state in cuprates

Exploring a novel seven-gene marker and mitochondrial gene TMEM38A for predicting cervical cancer radiotherapy sensitivity using machine learning algorithms

BackgroundRadiotherapy plays a crucial role in the management of Cervical cancer (CC), as the development of resistance by cancer cells to radiotherapeutic interventions is a significant factor contributing to treatment failure in patients. However, the specific mechanisms that contribute to this resistance remain unclear. Currently, molecular targeted therapy, including mitochondrial genes, has emerged as a new approach in treating different types of cancers, gaining significant attention as an area of research in addressing the challenge of radiotherapy resistance in cancer.MethodsThe present study employed a rigorous screening methodology within the TCGA database to identify a cohort of patients diagnosed with CC who had received radiotherapy treatment. The control group consisted of individuals who demonstrated disease stability or progression after undergoing radiotherapy. In contrast, the treatment group consisted of patients who experienced complete or partial remission following radiotherapy. Following this, we identified and examined the differentially expressed genes (DEGs) in the two cohorts. Subsequently, we conducted additional analyses to refine the set of excluded DEGs by employing the least absolute shrinkage and selection operator regression and random forest techniques. Additionally, a comprehensive analysis was conducted in order to evaluate the potential correlation between the expression of core genes and the extent of immune cell infiltration in patients diagnosed with CC. The mitochondrial-associated genes were obtained from the MITOCARTA 3.0. Finally, the verification of increased expression of the mitochondrial gene TMEM38A in individuals with CC exhibiting sensitivity to radiotherapy was conducted using reverse transcription quantitative polymerase chain reaction and immunohistochemistry assays.ResultsThis process ultimately led to the identification of 7 crucial genes, viz., GJA3, TMEM38A, ID4, CDHR1, SLC10A4, KCNG1, and HMGCS2, which were strongly associated with radiotherapy sensitivity. The enrichment analysis has unveiled a significant association between these 7 crucial genes and prominent signaling pathways, such as the p53 signaling pathway, KRAS signaling pathway, and PI3K/AKT/MTOR pathway. By utilizing these 7 core genes, an unsupervised clustering analysis was conducted on patients with CC, resulting in the categorization of patients into three distinct molecular subtypes. In addition, a predictive model for the sensitivity of CC radiotherapy was developed using a neural network approach, utilizing the expression levels of these 7 core genes. Moreover, the CellMiner database was utilized to predict drugs that are closely linked to these 7 core genes, which could potentially act as crucial agents in overcoming radiotherapy resistance in CC.ConclusionTo summarize, the genes GJA3, TMEM38A, ID4, CDHR1, SLC10A4, KCNG1, and HMGCS2 were found to be closely correlated with the sensitivity of CC to radiotherapy. Notably, TMEM38A, a mitochondrial gene, exhibited the highest degree of correlation, indicating its potential as a crucial biomarker for the modulation of radiotherapy sensitivity in CC

A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.

Substantial progress has been made in identification of type 2 diabetes (T2D) risk loci in the past few years, but our understanding of the genetic basis of T2D in ethnically diverse populations remains limited. We performed a genome-wide association study and a replication study in Chinese Hans comprising 8,569 T2D case subjects and 8,923 control subjects in total, from which 10 single nucleotide polymorphisms were selected for further follow-up in a de novo replication sample of 3,410 T2D case and 3,412 control subjects and an in silico replication sample of 6,952 T2D case and 11,865 control subjects. Besides confirming seven established T2D loci (CDKAL1, CDKN2A/B, KCNQ1, CDC123, GLIS3, HNF1B, and DUSP9) at genome-wide significance, we identified two novel T2D loci, including G-protein-coupled receptor kinase 5 (GRK5) (rs10886471: P = 7.1 × 10(-9)) and RASGRP1 (rs7403531: P = 3.9 × 10(-9)), of which the association signal at GRK5 seems to be specific to East Asians. In nondiabetic individuals, the T2D risk-increasing allele of RASGRP1-rs7403531 was also associated with higher HbA(1c) and lower homeostasis model assessment of β-cell function (P = 0.03 and 0.0209, respectively), whereas the T2D risk-increasing allele of GRK5-rs10886471 was also associated with higher fasting insulin (P = 0.0169) but not with fasting glucose. Our findings not only provide new insights into the pathophysiology of T2D, but may also shed light on the ethnic differences in T2D susceptibility

Potential candidates for liver resection in liver-confined advanced HCC: a Chinese multicenter observational study

BackgroundAdvanced hepatocellular carcinoma (HCC) is characterized as symptomatic tumors [performance status (PS) score of 1-2], vascular invasion and extrahepatic spread, but patients with PS1 alone may be eliminated from this stage. Although liver resection is used for liver-confined HCC, its role in patients with PS1 alone remains controversial. Therefore, we aimed to explore its application in such patients and identify potential candidates.MethodsEligible liver-confined HCC patients undergoing liver resection were retrospectively screened in 15 Chinese tertiary hospitals, with limited tumor burden, liver function and PS scores. Cox-regression survival analysis was used to investigate the prognostic factors and develop a risk-scoring system, according to which patients were substratified using fitting curves and the predictive values of PS were explored in each stratification.ResultsFrom January 2010 to October 2021, 1535 consecutive patients were selected. In the whole cohort, PS, AFP, tumor size and albumin were correlated with survival (adjusted P<0.05), based on which risk scores of every patient were calculated and ranged from 0 to 18. Fitting curve analysis demonstrated that the prognostic abilities of PS varied with risk scores and that the patients should be divided into three risk stratifications. Importantly, in the low-risk stratification, PS lost its prognostic value, and patients with PS1 alone achieved a satisfactory 5-year survival rate of 78.0%, which was comparable with that PS0 patients (84.6%).ConclusionSelected patients with PS1 alone and an ideal baseline condition may benefit from liver resection and may migrate forward to BCLC stage A

Identify optimal HAP series scores for unresectable HCC patients undergoing TACE plus sorafenib: A Chinese multicenter observational study

BackgroundHepatoma arterial-embolization prognostic (HAP) series scores have been proposed for prognostic prediction in patients with unresectable hepatocellular carcinoma (uHCC) undergoing transarterial chemoembolization (TACE). However, their prognostic value in TACE plus sorafenib (TACE-S) remains unknown. Here, we aim to evaluate their prognostic performance in such conditions and identify the best model for this combination therapy.MethodsBetween January 2012 and December 2018, consecutive patients with uHCC receiving TACE-S were recruited from 15 tertiary hospitals in China. Cox regression analyses were used to investigate the prognostic values of baseline factors and every scoring system. Their prognostic performance and discriminatory performance were evaluated and confirmed in subgroup analyses.ResultsA total of 404 patients were enrolled. In the whole cohort, the median follow-up period was 44.2 (interquartile range (IQR), 33.2–60.7) months, the median overall survival (OS) time was 13.2 months, and 336 (83.2%) patients died at the end of the follow-up period. According to multivariate analyses, HAP series scores were independent prognostic indicators of OS. In addition, the C-index, Akaike information criterion (AIC) values, and time-dependent area under the receiver operating characteristic (ROC) curve (AUC) indicated that modified HAP (mHAP)-III had the best predictive performance. Furthermore, the results remained consistent in most subsets of patients.ConclusionHAP series scores exhibited good predictive ability in uHCC patients accepting TACE-S, and the mHAP-III score was found to be superior to the other HAP series scores in predicting OS. Future prospective high-quality studies should be conducted to confirm our results and help with treatment decision-making

Correcting a major error in assessing organic carbon pollution in natural waters

Microbial degradation of dissolved organic carbon (DOC) in aquatic environments can cause oxygen depletion, water acidification, and CO2 emissions. These problems are caused by labile DOC (LDOC) and not refractory DOC (RDOC) that resists degradation and is thus a carbon sink. For nearly a century, chemical oxygen demand (COD) has been widely used for assessment of organic pollution in aquatic systems. Here, we show through a multicountry survey and experimental studies that COD is not an appropriate proxy of microbial degradability of organic matter because it oxidizes both LDOC and RDOC, and the latter contributes up to 90% of DOC in high-latitude forested areas. Hence, COD measurements do not provide appropriate scientific information on organic pollution in natural waters and can mislead environmental policies. We propose the replacement of the COD method with an optode-based biological oxygen demand method to accurately and efficiently assess organic pollution in natural aquatic environments