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Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.

Epidemiological and other studies have shown that the occurrence and progression of rheumatoid arthritis (RA) are closely related to diet. To further explore the causal association between dietary habits and RA, we performed a bidirectional Mendelian randomization (MR) analysis. The dataset related to dietary habits is from genome-wide association studies, including 143 dietary habits. The dataset of RA is from the FinnGen database. Inverse variance weighted (IVW), MR-Egger, simple mode, weighted median, and weighted mode were used for the 2-sample, 2-way MR analysis. At the same time, a variety of pleiotropic and heterogeneity tests were used to ensure the accuracy of the results. IVW results show that among current drinkers (drinks usually with meals yes + it varies vs no) was positively correlated with RA (β, 0.563 [95% confidence interval [CI], 0.286–0.840]; P = 6.7 × 10−5). Spread type (low fat spread vs any other) was negatively correlated with RA (β, −2.536 [95% CI, −3.725 to −1.346]; P = 2.9 × 10−5). In addition, the reverse MR results showed that RA was positively correlated with milk type (skimmed vs any other; β, 0.006 [95% CI, 0.000–0.011]; P = 4.5 × 10−2). RA was positively correlated with spread type (tub margarine vs never; β, 0.016 [95% CI, 0.002–0.029]; P = 2.5 × 10−2). The results of pleiotropy and heterogeneity tests showed that there was no pleiotropy (P > .05) in the obtained results. The analysis results of MR-Egger, simple mode, weighted median, and weighted mode are consistent with our IVW results. This study reveals a potential association between specific dietary habits and RA. Among current drinkers (drinks usually with meals yes + it varies vs no) was positively correlated with RA. Spread type (low fat spread vs any other) was negatively correlated with RA. RA was positively correlated with milk type (skimmed vs any other) and spread type (tub margarine vs never).

Deep vein thrombosis (DVT) is one of the common complications after joint replacement, which seriously affects the quality of life of patients. We systematically searched nine databases, a total of eleven studies on prediction models to predict DVT after knee/hip arthroplasty were included, eight prediction models for DVT after knee/hip arthroplasty were chosen and compared. The results of network meta-analysis showed the XGBoost model (SUCRA 100.0%), LASSO (SUCRA 84.8%), ANN (SUCRA 72.1%), SVM (SUCRA 53.0%), ensemble model (SUCRA 40.8%), RF (SUCRA 25.6%), LR (SUCRA 21.8%), GBT (SUCRA 1.1%), and best prediction performance is XGB (SUCRA 100%). Results show that the XGBoost model has the best predictive performance. Our study provides suggestions and directions for future research on the DVT prediction model. In the future, well-designed studies are still needed to validate this model.

Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy “flowers” through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia“Chiang Mai Pink” and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifoliacontains a residual signal of whole-genome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among C. alismatifoliacultivars. In addition, we identified the key genes that produce different colored bracts in C. alismatifolia, such as F3′5'H, DFR, ANSand several transcription factors for anthocyanin synthesis, as well as chlHand CAOin the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C. alismatifoliaand related species. It is also important to understand the variation in the evolution of the Zingiberaceae family.

The ammonia consumption, respiration rates (sOURNH4), expression of functional genes (amoA and hao) and community structures of ammonia-oxidizing bacteria (AOB) under copper (Cu) shock loads were simultaneously studied. The results showed that respiratory activities and gene transcriptional responses were sensitive to Cu toxicity. Cu inhibition and nitrite accumulation stimulation co-effected the expression of amoA. A Cu loading concentration at the ppm (mg L–1) level produced an irreversible inhibition of the expression of hao. The self-repair ability of amoA was stronger than that of hao under Cu shock loadings. A principal component regression analysis model revealed that soluble Cu and intracellular Cu played important roles in the inhibitory actions of Cu shock loading on AOB. Furthermore, the linear model (R2= 0.92) adequately fitted the inhibition of soluble Cu to sOURNH4while the inhibition actions of the intracellular Cu on AOB respiration conformed to a biological receptor model (I%inhibition= 100/(1 + Ki/[M]), Ki= 7.4). An uncultured Nitrosospira sp. exhibited stronger tolerance to Cu toxicity than Nitrosomonas sp. in this study. The results and their understanding lead to a deep comprehension of Cu inhibitory mechanisms on AOB in complex activated sludge systems.

Objective This study aimed to examine the mechanism of hyperphosphatemia-induced vascular calcification (HPVC).Methods Primary human aortic smooth muscle cells and rat aortic rings were cultured in Dulbecco’s modified Eagle’s medium supplemented with 0.9 mM or 2.5 mM phosphorus concentrations. Type III sodium-dependent phosphate cotransporter-1 (Pit-1) small interfering RNA and phosphonoformic acid (PFA), a Pit-1 inhibitor, were used to investigate the effects and mechanisms of Pit-1 on HPVC. Calcium content shown by Alizarin red staining, expression levels of Pit-1, and characteristic molecules for phenotypic transition of vascular smooth muscle cells were examined.Results Hyperphosphatemia induced the upregulation of Pit-1 expression, facilitated phenotypic transition of vascular smooth muscle cells, and led to HPVC in cellular and organ models. Treatment with Pit-1 small interfering RNA or PFA significantly inhibited Pit-1 expression, suppressed phenotypic transition, and attenuated HPVC.Conclusions Our findings suggest that Pit-1 plays a pivotal role in the development of HPVC. The use of PFA as a Pit-1 inhibitor has the potential for therapeutic intervention in patients with HPVC. However, further rigorous clinical investigations are required to ensure the safety and efficacy of PFA before it can be considered for widespread implementation in clinical practice.

ABSTRACTAs the most commonly used driven data for gross primary productivity (GPP) estimation, satellite remote sensing vegetation indexes (VI), such as the leaf area index (LAI), often seriously suffer from data quality problems induced by cloud contamination and noise. Although various filtering methods are applied to reconstruct the missing data and eliminate noises in the VI time series, the impacts of these data quality problems on GPP estimation are still not clear. In this study, the accuracy differences of the GPP estimations driven by different VI series are comprehensively analyzed based on two light use efficiency (LUE) models (the big-leaf MOD17 and the two-leaf RTL-LUE). Four VI filtering methods are applied for comparison, and GPP data across 169 eddy covariance (EC) sites are used for validation. The results demonstrate that all the filtering methods can improve the GPP simulation accuracy, and the SeasonL1 filtering method exhibits the best performance both for the MOD17 model (∆R2 = 0.06) and the RTL-LUE model (∆R2 = 0.07). The reconstruction of the key change points in the temporally continuous gaps may be the primary reason for the different performance of the four methods. Moreover, the effects of filtering processes on GPP estimation vary with latitudes and seasons due to the differences in the primary data quality. More significant improvements can be observed during the growing season and in the regions near the equator, where the data quality is relatively poor with lower primary GPP estimation accuracy. This study can guide the preprocessing of the VI data before GPP estimation.

ABSTRACTOsteoblastic bone formation and osteoclastic bone resorption dynamically maintain the bone homeostasis; in the present study, we attempt to investigate the mechanism of the excessive activation of osteoclasts inducing the deregulation of bone homeostasis from the perspective of non-coding RNA regulation. Differentially expressed patterns of circRNAs were examined in non-treated and RANKL + CSF1-treated bone marrow monocyte/macrophage (BMM) cells and differentially-expressed miRNAs during osteoclast differentiation were analyzed and identified. We found that circRNA_28313 was significantly induced by RANKL + CSF1 treatment. circRNA_28313 knockdown significantly inhibited RANKL + CSF1-induced differentiation of osteoclasts within BMM cells in vitro, while suppressed ovariectomized (OVX)-induced bone resorption in mice in vivo. Via bioinformatics analyses, it has been demonstrated that miR-195a might bind to circRNA_28313 and CSF1 and together form a circRNA-miRNA-mRNA network. circRNA_28313 relieves miR-195a-mediated suppression on CSF1 via acting as a ceRNA, therefore modulating the osteoclast differentiation in BMM cells. In conclusion, circRNA_28313, miR-195a, and CSF1 form a ceRNA network to function in RANKL + CSF1-induced osteoclast differentiation, thus affecting OVX-induced bone absorption in mice.

The human leukocyte antigen (HLA) genes are the most polymorphic genes in the human genome and have great power in forensic applications, especially in relationship testing and personal identification. However, the extreme polymorphism of HLA has made unambiguous genotyping of these genes very challenging and resulted in the limited application in relationship testing. Fortunately, massively parallel sequencing (MPS) technology offers the promise of unambiguous and high-throughput HLA typing. In this study, 11 HLA genes were typed in one extended family residing in North China and encompassing six generations. Phase-resolved genotypes for HLA genes were generated and HLA haplotype structure was defined. The paternity/kinship index, or in other words, likelihood ratio (LR) was calculated. A total of 88 alleles were identified, of which eight alleles were newly discovered. The inheritance of HLA alleles followed Mendelian law. With the discovery of new HLA alleles and three recombination events, a total of eleven new HLA haplotypes were identified in this population. LR distribution showed that, when HLA alleles were applied, the Log10LR for a single locus could reach very high and the median average Log10LRs of HLA genes were much higher than that of short tandem repeat loci. The result showed that high-throughput HLA genotyping could be achieved rapidly by MPS, and the contribution of HLA genes on system performance could be high, which may be applied as a supplement in forensic genetics studies. This study was also valuable in demonstrating the genetic mechanisms governing the generation of polymorphisms of the HLA genes.

Exotic species vary in how harmful they are. The earlier we can predict the outcome of an invasion, the more time is available for management. We conducted a “marsh organ” experiment with six elevation treatments to evaluate how the exotic grass Spartina alterniflora, which has invaded almost the entire coastline of China, affects a native (Kandelia obovata) and an exotic (Sonneratia apetala) mangrove in Zhangjiang Estuary, southern China. Survival of transplants in monoculture over two growing seasons in the marsh organ was high except at extreme high and low elevations. All three plants displayed hump‐shaped patterns of biomass across elevation in monoculture, but K. obovataperformed best at slightly higher and S. alternifloraat slightly lower elevations, whereas S. apetalaperformed well across all four intermediate elevations and grew larger than the other two plants. In mixtures, S. alterniflorasuppressed growth of mangrove seedlings of both species by up to 90%. The competitive effect of S. alterniflorawas greatest at intermediate elevations where its biomass was greatest. When transplanted into adjacent stands of S. alterniflora, K. obovataremained stunted, but S. apetalagrew quickly and began to emerge from the canopy of S. alternifloraby the end of the second growing season. At this site, past and ongoing disturbances to mature stands of K. obovataare likely to allow both exotics to increase in abundance. Aggressive management intervention will be needed to prevent estuaries in southern China from transitioning to near complete dominance by the exotic mangrove S. apetala.

High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau and the development of the monsoon—provided new habitats that promoted remarkable radiation. However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation. Here we investigate the spatio-temporal divergence patterns of the Chinese flora using a dated phylogeny of 92% of the angiosperm genera for the region, a nearly complete species-level tree comprising 26,978 species and detailed spatial distribution data. We found that 66% of the angiosperm genera in China did not originate until early in the Miocene epoch (23 million years ago (Mya)). The flora of eastern China bears a signature of older divergence (mean divergence times of 22.04–25.39 Mya), phylogenetic overdispersion (spatial co-occurrence of distant relatives) and higher phylogenetic diversity. In western China, the flora shows more recent divergence (mean divergence times of 15.29–18.86 Mya), pronounced phylogenetic clustering (co-occurrence of close relatives) and lower phylogenetic diversity. Analyses of species-level phylogenetic diversity using simulated branch lengths yielded results similar to genus-level patterns. Our analyses indicate that eastern China represents a floristic museum, and western China an evolutionary cradle, for herbaceous genera; eastern China has served as both a museum and a cradle for woody genera. These results identify areas of high species richness and phylogenetic diversity, and provide a foundation on which to build conservation efforts in China.

Brain tissue is one of the softest parts of the human body, composed of white matter and grey matter. The mechanical behavior of the brain tissue plays an essential role in regulating brain morphology and brain function. Besides, traumatic brain injury (TBI) and various brain diseases are also greatly influenced by the brain's mechanical properties. Whether white matter or grey matter, brain tissue contains multiscale structures composed of neurons, glial cells, fibers, blood vessels, etc., each with different mechanical properties. As such, brain tissue exhibits complex mechanical behavior, usually with strong nonlinearity, heterogeneity, and directional dependence. Building a constitutive law for multiscale brain tissue using traditional function-based approaches can be very challenging. Instead, this paper proposes a data-driven approach to establish the desired mechanical model of brain tissue. We focus on blood vessels with internal pressure embedded in a white or grey matter matrix material to demonstrate our approach. The matrix is described by an isotropic or anisotropic nonlinear elastic model. A representative unit cell (RUC) with blood vessels is built, which is used to generate the stress-strain data under different internal blood pressure and various proportional displacement loading paths. The generated stress-strain data is then used to train a mechanical law using artificial neural networks to predict the macroscopic mechanical response of brain tissue under different internal pressures. Finally, the trained material model is implemented into finite element software to predict the mechanical behavior of a whole brain under intracranial pressure and distributed body forces. Compared with a direct numerical simulation that employs a reference material model, our proposed approach greatly reduces the computational cost and improves modeling efficiency. The predictions made by our trained model demonstrate sufficient accuracy. Specifically, we find that the level of internal blood pressure can greatly influence stress distribution and determine the possible related damage behaviors.

A hydroponics experiment was aimed at identifying the lead (Pb) tolerance and phytoremediation potential of Moso bamboo (Phyllostachys pubescens) seedlings grown under different Pb treatments. Experimental results indicated that at the highest Pb concentration (400 μmol/L), the growth of bamboo seedlings was inhibited and Pb concentrations in leaves, stems, and roots reached the maximum of 148.8, 482.2, and 4282.8 mg/kg, respectively. Scanning electron microscopy revealed that the excessive Pb caused decreased stomatal opening, formation of abundant inclusions in roots, and just a few inclusions in stems. The ultrastructural analysis using transmission electron microscopy revealed that the addition of excessive Pb caused abnormally shaped chloroplasts, disappearance of endoplasmic reticulum, shrinkage of nucleus and nucleolus, and loss of thylakoid membranes. Although ultrastructural analysis revealed some internal damage, even the plants exposed to 400 μmol/L Pb survived and no visual Pb toxicity symptoms such as necrosis and chlorosis were observed in these plants. Even at the highest Pb treatment, no significant difference was observed for the dry weight of stem compared with controls. It is suggested that use of Moso bamboo as an experimental material provides a new perspective for remediation of heavy metal contaminated soil owing to its high metal tolerance and greater biomass.

Gastric cardia cancer (GCC), which occurs at the gastric-esophageal boundary, is one of the most malignant tumors. Despite its high mortality and morbidity, the molecular mechanism of initiation and progression of this disease is largely unknown. In this study, using proteomics and metabolomics approaches, we found that the level of several enzymes and their related metabolic intermediates involved in glucose metabolism were deregulated in GCC. Among these enzymes, two subunits controlling pyruvic acid efflux, lactate dehydrogenase A (LDHA) and pyruvate dehydrogenase B (PDHB), were further analyzed in vitro. Either down-regulation of LDH subunit LDHA or overexpression of PDH subunit PDHB could force pyruvic acid into the Krebs cycle rather than the glycolysis process in AGS gastric cancer cells, which inhibited cell growth and cell migration. Our results reflect an important glucose metabolic signature, especially the dysregulation of pyruvic acid efflux in the development of GCC. Forced transition from glycolysis to the Krebs cycle had an inhibitory effect on GCC progression, providing potential therapeutic targets for this disease.

Gastric cardia cancer (GCC), which occurs at the gastric-esophageal boundary, is one of the most malignant tumors. Despite its high mortality and morbidity, the molecular mechanism of initiation and progression of this disease is largely unknown. In this study, using proteomics and metabolomics approaches, we found that the level of several enzymes and their related metabolic intermediates involved in glucose metabolism were deregulated in GCC. Among these enzymes, two subunits controlling pyruvic acid efflux, lactate dehydrogenase A (LDHA) and pyruvate dehydrogenase B (PDHB), were further analyzed in vitro. Either down-regulation of LDH subunit LDHAor overexpression of PDH subunit PDHBcould force pyruvic acid into the Krebs cycle rather than the glycolysis process in AGS gastric cancer cells, which inhibited cell growth and cell migration. Our results reflect an important glucose metabolic signature, especially the dysregulation of pyruvic acid efflux in the development of GCC. Forced transition from glycolysis to the Krebs cycle had an inhibitory effect on GCC progression, providing potential therapeutic targets for this disease.

Abstract: In this paper, we consider a class of two-dimensional (2-D) local state-space (LSS) Fornasini–Marchesini (FM) second models with delays in the states, and we study delay-independent and delay-dependent H ∞ control problems via output feedback. First, based on the definition of H ∞ disturbance attenuation γ for 2-D state-delayed systems, we propose a delay-dependent bounded real lemma. Specifically, a new Lyapunov functional candidate is introduced and free-weighting matrices are added to the difference Lyapunov functional for 2-D systems possessing two directions. Then delay-independent and delay-dependent output feedback H ∞ controllers are developed that ensure that the closed-loop system is asymptotically stable and has H ∞ performance γ in terms of linear matrix inequality (LMI) feasibility. Furthermore, the minimum H ∞ norm bound γ is obtained by solving linear objective optimization problems. Numerical examples demonstrate the effectiveness and advantages of the LMI approach to H ∞ control problems for 2-D state-delayed systems.

The separation of C2H4from C2H6/C2H4mixture is of great importance but difficult and energy intensive. Adsorptive separation provides an alternative approach to ameliorate this situation. Here, we report a microporous metal–organic framework (MOF) BUT-315-a as a C2H6-selective adsorbent for the separation of C2H6/C2H4gas mixture. BUT-315-a combines good IAST selectivity of 2.35 with high C2H6uptake of 97.5 cm3 g−1, giving superior high separation potential ΔQ (2226 mmol L−1) for equimolar C2H6/C2H4at 298 K. Impressively, such excellent performance can be preserved at higher temperatures of 313 and 323 K to accommodate industrial conditions. Efficient dynamic separation performance of BUT-315-a has been demonstrated by column breakthrough experiments under varied temperatures and gas ratios. Theoretical calculations further reveal multiple synergistic interactions between C2H6and the framework. This work highlights a new benchmark material for C2H6/C2H4separation and provides guidance for designing adsorbent for separation applications.

The neural basis of the automatic activation of words was investigated in an fMRI study. In the study, words were presented briefly (51 or 151 msec) followed by a mask. To prevent attentional processing, subjects attended to the masks and not the words, and were required to make perceptual judgment about the masks. We found that a distributed neural network (including the frontal, temporal, occipital, parietal lobes, and the cerebellum) was activated during non‐attentional processing of words in both exposure durations. A significant main effect of presentation duration was found in bilateral cerebellum and the right fusiform gyrus, suggesting their role in the later (151 msec) processing of words. In addition, a significant interaction between presentation duration and word frequency was obtained. When the presentation duration was 151 msec, no significant difference in activation was found between high‐ and low‐frequency words. Alternatively, when the presentation duration was 51 msec, high‐frequency words evoked significantly greater activation in bilateral fusiform gyri, cerebellum, right inferior parietal lobe, medial frontal gyrus (BA 45/46/9), and the right temporal‐occipital junction (BA 21/37). These results suggest that these regions are sensitive to word frequency, and are related to both the attentional and non‐attentional access of lexical representations. Hum. Brain Mapping 18:215–221, 2003. © 2003 Wiley‐Liss, Inc.

The neural basis of the automatic activation of words was investigated in an fMRI study. In the study, words were presented briefly (51 or 151 msec) followed by a mask. To prevent attentional processing, subjects attended to the masks and not the words, and were required to make perceptual judgment about the masks. We found that a distributed neural network (including the frontal, temporal, occipital, parietal lobes, and the cerebellum) was activated during non-attentional processing of words in both exposure durations. A significant main effect of presentation duration was found in bilateral cerebellum and the right fusiform gyrus, suggesting their role in the later (151 msec) processing of words. In addition, a significant interaction between presentation duration and word frequency was obtained. When the presentation duration was 151 msec, no significant difference in activation was found between high- and low-frequency words. Alternatively, when the presentation duration was 51 msec, high-frequency words evoked significantly greater activation in bilateral fusiform gyri, cerebellum, right inferior parietal lobe, medial frontal gyrus (BA 45/46/9), and the right temporal-occipital junction (BA 21/37). These results suggest that these regions are sensitive to word frequency, and are related to both the attentional and non-attentional access of lexical representations. Hum. Brain Mapping 18:215–221, 2003. © 2003 Wiley-Liss, Inc.

The rapid and accurate detection of the moisture content is of great significance to the quality evaluation and oil extraction process of walnut kernel. Near-infrared (NIR) spectroscopy is an ideal method for measuring the moisture content in walnut kernel. In this study, a regression model for moisture content in walnut kernel was developed based on NIR diffuse reflectance spectroscopy using chemometric methods. The different spectral pretreatment methods were adopted to preprocess the original spectral data. The whole spectra band was divided into 5 subbands, 10 subbands, 15 subbands, and 20 subbands to screen specific wavelengths relevant to the walnut kernel moisture content. PLS (partial least square regression), MLR (multivariate linear regression), PCR (principle component regression), and SVR (support vector regression) were used to establish the relationship model between the spectral data and measurement values of the moisture content. In comparison, the optimized modeling conditions were determined as follows: detection wavelength 1349–1490 nm, SNV-FD (standard normal variate transformation and first derivative) preprocessing method, and PLS algorithm. Under these conditions, the square correlation coefficient (R2) and root mean square error of prediction (RMSEP) of the prediction model were 0.9865 and 0.0017, respectively. The results of this study provided a feasible method for the rapid detection of moisture content in walnut kernel. To improve the performance and applicability of the model, it is necessary to continuously expand the size of the sample set.

In order to identify and monitor a large scale of indoor personnel, this paper combines network robots, RFID and ZigBee, and designs a network robot identification system. CC1110 is used to formulate RFID module, CSMA are combined with TDMA to fulfil multi-card function and overcome data collision. With the processing core S3C6410 and software technology like Linux multi-thread and H.264 decoding, the robot serves as a mobile node to identify IDs and displays guidance video according to targets priority. Gateway module is designed to collect IDs and delivery commands. PC monitoring centre based on Qt can receives IDs and displays them. Test results show that the system can identify targets accurately and provide high-priority goals with guiding service, meets the application requirement.