Evolution of self-compatibility by a mutant Sm-RNase in citrus

Self-incompatibility (SI) is an important mechanism that prevents self-fertilization and inbreeding in flowering plants. The most widespread SI system utilizes S ribonucleases (S-RNases) and S-locus F-boxes (SLFs) as S determinants. In citrus, SI is ancestral, and Citrus maxima (pummelo) is self-incompatible, while Citrus reticulata (mandarin) and its hybrids are self-compatible (SC). Here, we identify nine highly polymorphic pistil-specific, developmentally expressed S-RNases from pummelo that segregate with S haplotypes in a gametophytic manner and cluster with authentic S-RNases. We provide evidence that these S-RNases function as the female S determinants in citrus. Moreover, we show that each S-RNase is linked to approximately nine SLFs. In an analysis of 117 citrus SLF and SFL-like (SLFL) genes, we reveal that they cluster into 12 types and that the S-RNases and intra-haplotypic SLF and SLFL genes co-evolved. Our data support the notion that citrus have a S locus comprising a S-RNase and several SLFs that fit the non-self-recognition model. We identify a predominant single nucleotide mutation, S_m-RNase, in SC citrus, which provides a 'natural' loss of function. We show that SI-SC transitions due to the S_m-RNase initially arose in mandarin, spreading to its hybrids and became fixed. Identification of an evolutionarily distant new genus utilizing the S-RNase-based SI system, >100 million years separated from the nearest S-RNase family, is a milestone for evolutionary comparative studies.

Revealing dynamic impacts of socioeconomic factors on air pollution changes in Guangdong Province, China

The rapid development of cities leads to the frequent occurrence of air pollution incidents, which seriously hinders urban sustainability. This study develops a dynamic regional air pollution analysis (DRA) model to explore the mechanism of air pollutant emission changes. Specifically, the emissions differences among various sectors are distinguished by multi-angle accounting (MAA) method, and sectors' evolutionary trajectories are described by sector evolution analysis (SEA). Through combining emission deconstruction analysis (EDA) and structural decomposition analysis (SDA), key emission patterns and decisive socioeconomic factors are identified. The empirical results indicate that different sectors play different roles in the urban emission system and differentiated regulation policies should be formulated according to their characteristics. Changes of demand and supply patterns can result in the fluctuation in regional air pollutant emissions. Exports and worker's reward are the most significant contributors to air pollution on demand and supply sides, accounting for more than 54.3% and 44.0% of total emissions, respectively. The final demand level and the primary input level are the two biggest drivers of the emission increase, while emission intensity is the most crucial factor that offsets the emission growth. Also, there are significant differences in demand and supply structure. The contribution of primary input structure to emission reduction was more significant than that of final demand structure, which contributed 14.6% in 2015. The findings in this study will provide reliable information for developing more comprehensive and effective mitigation policies.

[Diagnostic performance of pathology, culture and ROSE of lung biopsy for suspected pulmonary infectious diseases]

Objective: To explore the diagnostic performance of CT guided percutaneous lung biopsy (PTLB) with pathology, culture and rapid on-site evaluation (ROSE) in patients with pulmonary infectious diseases. Methods: From January 2016 to June 2018, a retrospective study was implemented in the Department of Pulmonary and Critical Care Medicine of the First Affiliated Hospital of Wenzhou Medical University. Patients who received PTLB, suspected with lung infection were included. The basic information, clinical symptoms, imaging findings, diagnostic methods, complications, and changes in treatment of cases were collected. The diagnostic sensitivity of histopathology, microbial culture, and ROSE were evaluated at the same time. Results: A total of 529 cases were enrolled, including 354 males and 175 females, (59±14) years old in average. Tuberculosis was identified in 197 cases, non-tuberculosis mycobacteria (NTM) pulmonary disease in 8, cryptococcosis in 95, pulmonary aspergillosis in 27, filamentous fungal pneumonia in 3, talaromyces marneffei pulmonary infection in 3 and pulmonary candidiasis in 1, bacterial pneumonia in 39, and pathogen were unknown in 156 cases. A total of 417 cases were submitted for histopathology and microbial culture at the same time, the diagnostic value of pathology and microbial culture were 35.0% (146/417) and 45.6% (190/417), respectively. Combined pathology with microbial culture, the diagnostic value increased to 62.8% (262/417). The diagnostic accuracy of ROSE was 51.8% (71/137). The most common complication of PTLB was pneumothorax 26.1% (138/529). 56.1% (297/529) of the patients received targeted treatment after the diagnosis was confirmed, and 43.9% (232/529) maintained the original treatment. Conclusion: The pathology, microbial culture, and ROSE of PTLB have relative high diagnostic value for pulmonary infectious diseases.

Identification of two additional plasmodesmata localization domains in the tobacco mosaic virus cell-to-cell-movement protein

Despite decades of intensive studies, the failure to identify plasmodesmata (PD) localization sequences has constrained our understanding of Tobacco mosaic virus (TMV) movement. Recently, we identified the first PD localization signal (major PLS) in the TMV movement protein (MP), which encompasses the first 50 amino acid residues of the MP. Although the major PLS is sufficient for PD targeting, the efficiency is lower than the full-length TMV MP. To address this efficiency gap, we identified two additional PLS domains encompassing amino acid residues 61 to 80, and 147 to 170 of the MP and showed that these two domains target to PD, but do not transit to adjacent cells. We also demonstrated that the MP^61-80 fragment interacts with Arabidopsis synaptotagmin A, which was also shown to interact with the major TMV MP PLS. Therefore, our findings have provided new insights to more fully understand the mechanism underlying plasmodesmal targeting of TMV MP.

Conserved and novel roles of miR164-CUC2 regulatory module in specifying leaf and floral organ morphology in strawberry

MicroRNAs (miRNAs) are a kind of short noncoding RNA (20-24 nt), playing versatile roles in plant growth and development. Strawberry generates leaves and flowers with unique features. However, few miRNAs have been functionally characterised in strawberry, especially for their developmental regulation. Here, we identified one ethyl methanesulfonate (EMS) mutant, deeply serrated (des), in the woodland strawberry Fragaria vesca that has wrinkled leaves with deeper serrations, serrated petals and deformed carpels. The causative mutation occurs in the 19^th nucleotide of the FvemiR164a mature sequence. Overexpressing FveMIR164A rescued the phenotypes of des/fvemir164a except the petal serrations. Furthermore, we identified two allelic mutants of FveCUC2a, one target of FvemiR164a, which developed leaves with smooth margins and fused leaflets. Phenotypes of the double mutant fvemir164a fvecuc2a indicated that the two genes act linearly in leaf and carpel development, but synergistically in the development of other floral organs and inflorescence architecture. This work demonstrates the conserved and novel roles of the miR164-CUC2 module in leaf and flower development in different plant species, and reveals that the 19^th nucleotide of FvemiR164a is important for its processing.

An ultrasensitive Fano resonance biosensor using two dimensional hexagonal boron nitride nanosheets: theoretical analysis

This study proposed a novel Fano resonance (FR) biosensor with ultrahigh detection sensitivity by integrating two dimensional (2D) hexagonal boron nitride (h-BN) nanosheets with a plasmonic silver film–silicon hybrid nanostructure. Owing to its ultralow-loss in surface plasmon polaritons (SPPs), 2D h-BN nanosheets can act as a planar photon waveguide (PWG) for generating energy level splitting. Notably, both asymmetric FR sharp lines and plasmon induced transparency (PIT) can be produced by modulating the coupling strength between the planar PWG mode provided by h-BN nanosheets and the surface plasmon polariton (SPP) mode in the silver film–silicon hybrid nanostructure. Compared with conventional phase-modulation SPR biosensors, our proposed configuration based on Fano resonance can produce ultrahigh reflectivity of 0.934 and overcome the limitation of quasi-darkness reflectivity which is difficult for further phase extraction. More importantly, our proposed FR configuration can provide a promising phase detection sensitivity as high as 3.13 × 10⁶ degree per RIU (refractive index unit, RIU), which is enhanced by almost 100 times compared with conventional phase-modulation SPR biosensors. In addition, our proposed configuration has also shown the characteristics of multiple-order Fano resonances, largely depending on the partial coupling between the SPP mode and the different-order PWG mode. Our proposed FR biosensor can provide a highly promising candidate for designing a multiple-order FR platform for performing ultrasensitive detection.

This paper proposed an ultrasensitive FR biosensor with multiple-order characteristics using two dimensional hexagonal boron nitride nanosheets in the visible region.

Ethylene response factor NtERF91 positively regulates alkaloid accumulations in tobacco (Nicotiana tabacum L.)

Tobacco alkaloid metabolism is regulated by various transcription factors (TFs). Here, we have characterized a non-NIC2 locus gene, Ethylene Response Factor 91 (ERF91), function in regulation of alkaloid accumulation in tobacco. NtERF91 was preferentially expressed in roots and induced by jasmonic acid. Additionally, NtERF91 was able to in vitro bind to the NtPMT2 and NtQPT2 promoters via directly targeting the GCC-box elements and transactivate NtQPT2 gene expression. Ectopic overexpression of NtERF91 not only increased the expression of most nicotine biosynthetic genes, but also altered alkaloid accumulation profile, resulting in dramatically anatabine accumulation. We conclude that NtERF91 plays an overlapped but distinct role in regulating tobacco alkaloid accumulations.

[Effects of low temperature on trehalose and trehalase contents in Culex pipiens pallens]

OBJECTIVE

To examine the effect of low temperature on trehalose and trehalase levels in Culex pipiens pallens.

METHODS

The fourth instar larvae and female adult mosquitoes of Cx. pipiens pallens were exposed at 4 ℃ for 0, 1, 3, 6, 12, 18, 24 h and 0, 1, 3, 6, 12, 18, 24, 36, 48, 72 h, respectively. Then, the trehalose and trehalase contents were detected by enzyme-linked immunosorbent assay (ELISA) in mosquitoes.

RESULTS

The contents of trehalose and trehalase significantly increased in the larval and female adult mosquitoes post-exposure to low temperature. The changing trend of trehalose levels was consistent in the larval and female adult mosquitoes, and the highest levels were (2.458 8 ± 0.379 2) mg/g and (2.825 7 ± 0.211 1) mg/g 3 h post-exposure to low temperature, respectively. The trehalose and trehalase levels fluctuated greatly within the first 6 h post-exposure to low temperature. Following adaptation for a period of time, the trehalose and trehalase levels remained at a relatively high level.

CONCLUSIONS

Low temperature may induce the production of trehalose and trehalase in Cx. pipiens pallens, and the trehalose and trehalase may play an important role in the improvement of the cold resistance.

[Piperine inhibits the transformation of endothelial cells into fibroblasts]

Objective: To investigate the role of piperine on the transformation of endothelial cells into fibroblasts. Methods: Cultured human umbilical vein endothelial cells (HUVECs, 4-6 passage) were used for the main experiments. The transformation models of endothelial cells into fibroblasts were induced by transforming growth factor β (TGF-β) stimulation. HUVECs were divided into 6 groups: control group, TGF-β group and 4 groups treated with various concentrations of piperine (1, 5, 10, 20 μmol/L). CKK-8 was used to detect cell proliferation. The CD31/α-smooth muscle actin (α-SMA) expression level was detected by fluorescent staining. The vascular endothelial cadherin (VE-cadherin)/vimentin expression was detected by immunofluorescence staining. RT-PCR was used detect the mRNA expressions of transformation markers. Western blot was used to detect the protein expression of snail and twist. Results: TGF-β increased HUVECs proliferation (P<0.05), which could be significantly inhibited by 10 and 20 μmol/L of piperine, but not by 1 and 5 μmol/L of piperine. Immunofluorescence results demonstrated that TGF-β increased HUVECs transformation to fibroblasts as shown by downregulated expression of endothelial markers CD31, VE-cadherin, and upregulated expression of α-SMA and vimentin, again, these effects could be attenuated by 10 and 20 μmol/L piperine. The expression levels of collagen type Ⅰ and type Ⅲ were significantly higher in TGF-β group than in control group (P<0.05), significantly lower in TGF-β+10 μmol/L piperine group and TGF-β+20 μmol/L piperine group than in TGF-β group (P<0.05).In addition, RT-PCR results showed that TGF-β increased mRNA expression of transformation markers (snail1, snail2, twist1, twist2), while 10 and 20 μmol/L of piperine could significantly downregulated the mRNA expressions of these markers. The protein expression levels of snail and twist were significantly higher in TGF-β group than in control group (both P<0.05), which was significantly lower in TGF-β+20 μmol/L piperine group than in TGF-β group (both P<0.05). Conclusions: Piperine can inhibit the transformation of endothelial cells into fibroblasts. This effect might be viewed as one of the potential mechanisms of reduced myocardial fibrosis post piperine treatment.

[Preliminary clinical outcomes of patients with acute myocardial infarction complicated with cardiogenic shock treated with PIE-2R model]

Objective: To investigate the clinical experience of application of PIE-2R model to treat patients with acute myocardial infarction (AMI) complicated with cardiogenic shock (CS). Methods: A total of 129 patients with AMI complicated with CS treated with PIE-2R model, featuring in respiratory management, pacemaker, mechanical circulatory support (MCS) and timely myocardial revascularization, admitted in Beijing Anzhen Hospital, Capital Medical University between January 2013 and December 2018, were consecutively enrolled. Patient's baseline characteristics, implementation of each component of PIE-2R model, and in-hospital mortality were analyzed. Results: Participants' average age was 60 years, and male patients accounted for 78%. In all enrolled patients, 61% were implanted with temporary pacemaker due to severe bradyarrhythmia, 73% were treated with mechanical ventilation because of acute respiratory failure or pulmonary edema, and all patients were treated with percutaneous coronary intervention (PCI) supported by MCS (85% of cases with intra-aortic balloon pump and 15% of cases with veno-arterial extracorporeal membrane oxygenation or Impella), with an average first medical contact to MCS time of 87 minutes, and 79% were treated with second-generation drug-eluting stent. Eventually, after emergency treatment using PIE-2R model, 69 patients survived and in-hospital mortality was 46.5%. Conclusion: The application of PIE-2R model in patients with acute myocardial infarction complicated with cardiogenic shock is feasible, with a lower in-hospital mortality.

Genome-wide identification and characterization of ABA receptor PYL/RCAR gene family reveals evolution and roles in drought stress in Nicotiana tabacum

BACKGROUND

Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component of ABA Receptor (RCAR) (hereafter referred to as PYLs) has been identified as the ABA receptors. The PYL family members have been well studied in many plants. However, the members of PYL family have not been systematically identified at genome level in cultivated tobacco (Nicotiana tabacum) and its two ancestors. In this study, the phylogenic relationships, chromosomal distribution, gene structures, conserved motifs/regions, and expression profiles of NtPYLs were analyzed.

RESULTS

We identified 29, 11, 16 PYLs in the genomes of allotetraploid N. tabacum, and its two diploid ancestors N. tomentosiformis and N. sylvestris, respectively. The phylogenetic analysis revealed that NtPYLs can be divided into three subfamilies, and each NtPYL has one counterpart in N. sylvestris or N. tomentosiformis. Based on microarray analysis of NtPYL transcripts, four NtPYLs (from subfamily II, III), and five NtPYLs (from subfamily I) are highlighted as potential candidates for further functional characterization in N. tabacum seed development, response to ABA, and germination, and resistance to abiotic stresses, respectively. Interestingly, the expression profiles of members in the same NtPYL subfamily showed somehow similar patterns in tissues at different developmental stages and in leaves of seedlings under drought stress, suggesting particular NtPYLs might have multiple functions in both plant development and drought stress response.

CONCLUSIONS

NtPYLs are highlighted for important functions in seed development, germination and response to ABA, and particular in drought tolerance. This work will not only shed light on the PYL family in tobacco, but also provides some valuable information for functional characterization of ABA receptors in N. tabacum.

Erratum: Author Correction: Updated annotation of the wild strawberry Fragaria vesca V4 genome

[This corrects the article DOI: 10.1038/s41438-019-0142-6.].

miR-195 contributes to human osteoarthritis via targeting PTHrP

The dysregulated expression of the osteoarthritis (OA)-related genes in cartilage, such as matrix metalloproteinase 13 (MMP-13) and type X collagen (Col X), facilitates the onset and progression of OA. Reduced parathyroid hormone-related protein (PTHrP) may also accelerate this progression. Furthermore, miRNAs, endogenous regulators of mRNAs, are thought to play key roles in the pathogenesis of OA. In this study, we found that miR-195 levels were significantly upregulated in OA tissue, while PTHrP mRNA/protein expression was substantially downregulated, and there was a negative correlation between miR-195 and PTHrP. Upregulated miR-195 strongly inhibited Aggrecan, type II collagen (Col II) mRNA/protein expression, while it enhanced the expression of MMP-13 and Col X at mRNA/protein level; conversely, downregulated miR-195 significantly increased Col II mRNA/protein expression, while it decreased the expression of MMP-13 and Col X mRNA/protein. Moreover, our study demonstrated that PTHrP is a novel target of miR-195 using dual luciferase reporter assay. Finally, miR-195-mediated changes of Col II and OA-related genes were substantially attenuated by siRNA_PTHrP treatment. These results suggested that miR-195 is involved in the pathogenesis of OA via PTHrP.

[Knapp procedure and modified Knapp procedure with Foster suture for the treatment of double elevator palsy]

Objective: To investigate the efficacy of Knapp procedure and modified Knapp procedure with Foster suture in the treatment of double elevator palsy(DEP). Methods: Retrospective study. Twenty-two patients with congenital DEP were underwent Knapp procedure (n=15) and modified Knapp procedure(n=7). The clinical data were retrospectively analyzed, including the preoperative and postoperative vertical deviation in the primary position, ocular motility, and binocular vision. Results: The average vertical deviation in the primary position was (34.7±8.6) prism diopters(PD) before surgery and (6.5±6.5) PD after surgery (t=30.41, P=0.00) in the group underwent Knapp procedure. The mean preoperative and postoperative deviations of the group underwent modified procedure were respectively (38.6±14.6) PD and (5.7±9.3)PD (t=15.33, P=0.00). The mean corrected vertical deviation of the latter (32.8±5.7) PD was greater than that of the former (28.1±3.6) PD(t=-2.39, P=0.03). The mean improved upgaze in the modified group (2.6±0.5) was more obvious than that in the Knapp group (1.9±0.6) (t=2.41, P=0.02). There is no significant difference in the surgical effect on downgaze between two groups (U=43.00, P=0.54). Seven patients having binocular vision with abnormal head posture (AHP) before surgery obtained binocular single vision in the primary position and reading position after operations. AHP disappeared or reduced to less than 5°. The surgical outcomes were satisfied in 72.7% patients. But the patients with ≥40 PD preoperative vertical deviation were under-corrected and needed the further operations. Conclusions: Knapp procedure and modified Knapp procedure with Foster suture were the efficient procedures for treatment of DEP without restriction of ipsilateral inferior rectus. Both procedures can obviously correct the vertical deviation and improve upgaze without remarkable limitation of downgaze, which is good to obtain the binocular single vision in the primary and reading position. The modified procedure has more powerful effect on the corrected vertical deviation and improved upgaze. (Chin J Ophthalmol, 2017, 53: 903-907).

Urban agglomeration (Guangzhou-Foshan-Zhaoqing) ecosystem management under uncertainty: A factorial fuzzy chance-constrained programming method

In this study, a factorial fuzzy chance-constrained programming (FFCP) method is developed for planning urban agglomeration ecosystem under uncertainty. FFCP cannot only address uncertainties presented as possibility distributions and random variables, but also quantitatively evaluate the individual and the interactive effects of multiple eco-environmental factors on urban agglomeration ecosystem. The FFCP method is applied to planning the Guangzhou-Foshan-Zhaoqing (GFZ) urban agglomeration, one of the most important economic circles of the Pearl River Delta region. With rapid industrialization, urbanization and population growth, a number of eco-environmental issues (e.g., water contamination, air pollution, and ecological deterioration) are becoming more and more serious. Results reveal that (i) the main environmental problem of Guangzhou is water pollution due to excessive chemical oxygen demand (COD) discharge (with a contribution of 53.1%), (ii) Foshan would suffer air pollution due to sulfur dioxide (SO₂) emitted from industrial processing and production, and (iii) solid waste disposal would continue to be challenge faced by Zhaoqing. Results also disclose that multiple uncertainties in system components have sound effects on the urban agglomeration ecosystem management as well as eco-environmental constraints have individual and/or joint effects on the system benefit. Different probability levels would lead to changed land-use patterns. Decisions at a lower violation level would lead to an increased reliability in fulfilling ecosystem requirement but with a lower system benefit. The findings can help decision makers to gain insights into tradeoff between economic development and eco-environmental protection as well as generate synergetic development strategies of urban agglomeration in an economic-effective and ecological-harmonious way.

Genome-wide analysis of the HAK potassium transporter gene family reveals asymmetrical evolution in tobacco (Nicotiana tabacum)

Being an essential mineral nutrient, potassium (K+) plays numerous important roles in plant growth and development and determines the yield and quality of crop products. The cellular level of K+ is controlled to a large extent by the K+ transporter, which belongs to the KT/HAK/KUP (HAK) family. However, little is known about these genes in tobacco. In this study, we surveyed the tobacco genome and identified 41 putative NtHAK genes (NtHAKS1-NtHAKS21 and NtHAKT1-NtHAKT20). Investigation of the cis-elements in upstream regions of these NtHAK genes suggests that members of this family respond to environmental cues and phytohormones. Expression data mining reveals that NtHAK genes showed clear sub-genome dominance. In all, these results will provide molecular insights into K+ transporter research in tobacco.

Effects of euphorbia kansui on the serum levels of IL-6, TNF-α, NF-κB, sTNFR and IL-8 in patients with severe acute pancreatitis

In this study, effects of euphorbia kansui on serum levels of inflammatory factors in patients with severe acute pancreatitis were investigated, and the mechanisms underlying the role of Euphorbia kansui in the treatment of severe acute pancreatitis were discussed. 36 patients hospitalized in the Third Affiliated Hospital of Wenzhou Medical University from March 2017 to May 2018 due to severe acute pancreatitis were selected and divided into two groups using a randomized grouping method. ELISA (enzyme-linked immunosorbent assay) was used to detect expressions of various inflammatory cytokines, such as tumor necrosis factor α (TNF-α), soluble TNF receptors (sTNFR), nuclear factor-κB (NF-κB), interleukin-6 (IL-6), and interleukin-8 (IL-8), in the serum of patients at different time points. The results showed no significant difference between the two groups in terms of age, gender, predisposing factors, Balthaza CT scores, and APACHEII (Acute Physiology and Chronic Health Evaluation) scores. According to the experimental results, euphorbia kansui effectively reduced the expression of inflammation related cytokines, such as NF-κB, TNF-α, sTNFR, IL-6, and IL-8, in the serum of patients with severe acute pancreatitis. It was also proposed that euphorbia kansui hindered the release of inflammatory factors and treated SAP by inhibiting the activation of the NF-κB signaling pathway.

[Plasma relative abundance of epidermal growth factor receptor mutations predicts clinical response to epidermal growth factor receptor-tyrosine kinase inhibitors in patients with advanced lung adenocarcinoma]

Objective: To determine whether relative abundance of epidermal growth factor receptor (EGFR) mutations in plasma predicts clinical response to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) in patients with advanced lung adenocarcinoma. Methods: In this prospective study, adult patients with advanced lung adenocarcinoma were enrolled in our hospital from 1 April 2016 to 1 January 2017. EGFR mutations in tumor tissues were detected by ADx-amplification refractory mutation system (ADx-ARMS). EGFR mutations of plasma free tumor DNA were detected by ADx-ARMS and ADx-super amplification refractory mutation system (ADx-SuperARMS) at the same time. Patients with EGFR-mutant in tumor tissues and receiving EGFR-TKIs were finally enrolled. Plasma mutation-positive patients with both methods were high abundance group.Patients with positive mutations by ADx-SuperARMS but negative by ADx-ARMS were medium abundance group. Mutation-negative patients with both methods were recognized as low abundance group. The correlation between EGFR mutation abundance and clinical response to EGFR-TKIs were analyzed. Results: Among 71 patients enrolled, 42 harbored EGFR mutations in plasma were detected by ADx-ARMS, while 53 were found by ADx-SuperARMS.There were 42 patients in high abundance group, 11 in medium group while the other 18 in low group. The objective response rates (ORRs) were 69.0%, 7/11 and 10/18 in high, medium and low groups, respectively. The difference was significant between high and low abundances groups (P=0.006). Median progression-free survival (PFS) in high, medium and low groups were 11.0, 8.5 and 9.0 monthes, respectively (P<0.001). In patients with tumor 19-Del, the ORRs were 70.4%, 5/7 and 6/11 in high, medium and low abundance groups, respectively. The median PFS of high abundance group was significantly longer than the other two groups (12.0 monthes vs 9.0, 9.0 monthes). As to subjects with L858R mutation, the ORRs were 10/15, 2/4 and 3/6, respectively, with median PFS 9.6, 5.5 and 9.5 monthes. Conclusions: The relative abundance of EGFR mutations in plasma predicts clinical response to EGFR-TKIs in patients with advanced lung adenocarcinoma. The higher the mutation abundance is, the better the efficacy of EGFR-TKIs is.

The entropy solution of a reaction-diffusion equation on an unbounded domain

The degenerate parabolic equations from the reaction-diffusion problems are considered on an unbounded domain Ω ⊂ R N . It is expected that only a partial boundary should be imposed the homogeneous boundary value, but how to give the analytic expression of this partial boundary seems very difficult. A new method, which is called the general characteristic function method, is introduced in this paper. By this new method, a reasonable analytic expression of the partial boundary value condition is found. Moreover, the stability of the entropy solutions is established based on this partial boundary value condition.

Updated annotation of the wild strawberry Fragaria vesca V4 genome

The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry (Fragaria × ananassa, 8x) and the Rosaceae family. The F. vesca genome was initially published in 2011 using older technologies. Recently, a new and greatly improved F. vesca genome, designated V4, was published. However, the number of annotated genes is remarkably reduced in V4 (28,588 genes) compared to the prior annotations (32,831 to 33,673 genes). Additionally, the annotation of V4 (v4.0.a1) implements a new nomenclature for gene IDs (FvH4_XgXXXXX), rather than the previous nomenclature (geneXXXXX). Hence, further improvement of the V4 genome annotation and assigning gene expression levels under the new gene IDs with existing transcriptome data are necessary to facilitate the utility of this high-quality F. vesca genome V4. Here, we built a new and improved annotation, v4.0.a2, for F. vesca genome V4. The new annotation has a total of 34,007 gene models with 98.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCOs). In this v4.0.a2 annotation, gene models of 8,342 existing genes are modified, 9,029 new genes are added, and 10,176 genes possess alternatively spliced isoforms with an average of 1.90 transcripts per locus. Transcription factors/regulators and protein kinases are globally identified. Interestingly, the transcription factor family FAr-red-impaired Response 1 (FAR1) contains 82 genes in v4.0.a2 but only two members in v4.0.a1. Additionally, the expression levels of all genes in the new annotation across a total of 46 different tissues and stages are provided. Finally, miRNAs and their targets are reanalyzed and presented. Altogether, this work provides an updated genome annotation of the F. vesca V4 genome as well as a comprehensive gene expression atlas with the new gene ID nomenclature, which will greatly facilitate gene functional studies in strawberry and other evolutionarily related plant species.

Effluent trading planning and its application in water quality management: A factor-interaction perspective

In this study, a Bayesian risk-induced interval stochastic modeling framework (BRISF) is proposed for planning effluent trading program among point and nonpoint sources as well as identifying interactions of important trading factors under system risk. BRISF incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian inference with random walk Metropolis algorithm (RWM), and constraint-violation risk-based two-stage stochastic programming (CRTSP) within a general framework. Bayesian inference is employed for uncertainty analysis of SWAT model parameters and uncertain prediction of nutrient loadings; this process provides the random inputs for optimization process. CRTSP is capable of dealing with multiple uncertainties in modeling effluent trading program as well as system risk of environmental allowance violation. BRISF is applied to a real case of Xiangxihe watershed in China for water quality management. Solutions for optimal trading scheme corresponding to different risk levels are generated. Thousands of scenarios are examined to analyze the individual and interactive effects of trading ratios and treatment rates on trading system. Comparison between cross-industry and intra-industry effluent trading scheme is also conducted. It is proved that cross-industry trading would bring about higher benefit with reduced pollution loading; cross-industry effluent trading scheme would be recommended to achieve optimal water quality management and system benefit.

Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca

Fragaria vesca, a wild diploid strawberry, has recently emerged as a model for the cultivated strawberry and other members of the Rosaceae. Differentiation and maintenance of meristems largely determines plant architecture, flower development and ultimately fruit yield. However, in strawberry, our knowledge of molecular regulation of meristems in different developmental context is limited. In this study, we hand dissected three types of tissues than contain meristematic tissues corresponding to shoot apical meristem (SAM), flower meristem (FM), and receptacle meristem (REM), in F. vesca for RNA-seq analyses. A total of 3,009 differentially expressed genes (DEGs) were identified through pairwise comparisons. These DEGs were grouped into nine clusters with dynamic and distinct expression patterns. In these nine clusters, 336 transcription factor genes belong to 46 families were identified; some of which were significantly enriched in FM and REM such as the MADS-box family or in REM such as the B3 family. We found conserved and distinctive expression patterns of totally 149 genes whose homologs regulate flowering time or SAM, leaf, and flower development in other plant species. In addition to the ABCE genes in flower development, new MADS box genes were identified to exhibit differential expression in these different tissues. Additionally, the cytokinin and auxin pathway genes also exhibited distinct expression patterns. The Arabidopsis homeobox gene WUSCHEL (WUS), essential for stem cell maintenance, is expressed in organizing center of meristems. The F. vesca homolog FvWUS1 exhibited a broader expression domain in young strawberry flowers than its Arabidopsis counterpart. Altogether, this work provides a valuable data resource for dissecting gene regulatory networks operating in different meristematic tissues in strawberry.

An air quality index-based multistage type-2-fuzzy interval-stochastic programming model for energy and environmental systems management under multiple uncertainties

In this study, a multistage type-2-fuzzy interval-stochastic programming (MTIP) method is developed, which extends upon the existing multistage stochastic programming (MSP) by allowing uncertainties expressed as probabilistic distributions, interval values and type-2 fuzzy sets to be effectively incorporated within the optimization framework. Through coupling air quality index (AQI) with MTIP, an AQI-MTIP model is formulated for energy and environmental systems (EES) management of Tianjin. A number of scenarios based on changed AQIs are examined to analyze the impacts of environmental requirements on the city's energy system. Results indicate that (i) with the improvement of environmental requirement, utilization of clean energies (especially natural gas) is provoked markedly; (ii) PM_2.5 is the primary pollutant, 64.50% of which should be reduced each period to maintain the city's air quality at a health-safe level. These findings can help decision makers adjust energy structure, make effective mitigation strategy, and gain deep insight into the relationship between energy consumption and environmental requirement.

Analyzing urban ecosystem variation in the City of Dongguan: A stepwise cluster modeling approach

In this study, a stepwise cluster modeling approach (SCMA) is developed for analyzing urban ecosystem variation via Normalized Difference Vegetation Index (NDVI). NDVI is an indicator of vegetation growth and coverage and useful in reflecting urban ecosystem. SCMA is established on a cluster tree that can characterize the complex relationship between independent and dependent variables. SCMA is applied to the City of Dongguan for simulating the urban NDVI and identifying associated drivers of human activity, topography and meteorology without specific functions. Results show that SCMA performances better than conventional statistical methods, illustrating the ability of SCMA in capturing the complex and nonlinear features of urban ecosystem. Results disclose that human activities play negative effects on NDVI due to the destruction of green space for pursuing more space for buildings. NDVI reduces gradually from the south part to the north part of Dongguan due to increased gross domestic product and population density, indicating that the ecosystem in Dongguan is better in the south part. NDVI in the northeast part (dominated by agriculture) is sensitive to the growth of economy and population. More attention should be paid to this part for sustainable development, such as increasing afforestation, planting grass and constructing parks. Precipitation has a positive effect on NDVI due to the promotion of soil moisture that is beneficial to plants' growth. Awareness of these complexities is helpful for sustainable development of urban ecosystem.