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Fungi fibrinolytic compound 1 (FGFC1) is a rare marine-derived compound that can enhance fibrinolysis both in vitro and in vivo. The fibrinolytic activity characterization of FGFC1 mediated by plasminogen (Glu-/Lys-) and a single-chain urokinase-type plasminogen activator (pro-uPA) was further evaluated. The binding sites and mode of binding between FGFC1 and plasminogen were investigated by means of a combination of in vitro experiments and molecular docking. A 2.2-fold enhancement of fibrinolytic activity was achieved at 0.096 mM FGFC1, whereas the inhibition of fibrinolytic activity occurred when the FGFC1 concentration was above 0.24 mM. The inhibition of fibrinolytic activity of FGFC1 by 6-aminohexanoic acid (EACA) and tranexamic acid (TXA) together with the docking results revealed that the lysine-binding sites (LBSs) play a crucial role in the process of FGFC1 binding to plasminogen. The action mechanism of FGFC1 binding to plasminogen was inferred, and FGFC1 was able to induce plasminogen to exhibit an open conformation by binding through the LBSs. The molecular docking results showed that docking of ligands (EACA, FGFC1) with receptors (KR1–KR5) mainly occurred through hydrophilic and hydrophobic interactions. In addition, the binding affinity values of EACA to KR1–KR5 were −5.2, −4.3, −3.7, −4.5, and −4.3 kcal/moL, respectively, and those of FGFC1 to KR1–KR5 were −7.4, −9.0, −6.3, −8.3, and −6.7 kcal/moL, respectively. The findings demonstrate that both EACA and FGFC1 bound to KR1–KR5 with moderately high affinity. This study could provide a theoretical basis for the clinical pharmacology of FGFC1 and establish a foundation for practical applications of FGFC1. [ABSTRACT FROM AUTHOR]

Many aerial images with similar appearances have different but correlated scene labels, which causes the label ambiguity. Label distribution learning (LDL) can express label ambiguity by giving each sample a label distribution. Thus, a sample contributes to the learning of its ground-truth label as well as correlated labels, which improve data utilization. LDL has gained success in many fields, such as age estimation, in which label ambiguity can be easily modeled on the basis of the prior knowledge about local sample similarity and global label correlations. However, LDL has never been applied to scene classification, because there is no knowledge about the local similarity and label correlations and thus it is hard to model label ambiguity. In this paper, we uncover the sample neighbors that cause label ambiguity by jointly capturing the local similarity and label correlations and propose neighbor-based LDL (N-LDL) for aerial scene classification. We define a subspace learning problem, which formulates the neighboring relations as a coefficient matrix that is regularized by a sparse constraint and label correlations. The sparse constraint provides a few nearest neighbors, which captures local similarity. The label correlations are predefined according to the confusion matrices on validation sets. During subspace learning, the neighboring relations are encouraged to agree with the label correlations, which ensures that the uncovered neighbors have correlated labels. Finally, the label propagation among the neighbors forms the label distributions, which leads to label smoothing in terms of label ambiguity. The label distributions are used to train convolutional neural networks (CNNs). Experiments on the aerial image dataset (AID) and NWPU_RESISC45 (NR) datasets demonstrate that using the label distributions clearly improves the classification performance by assisting feature learning and mitigating over-fitting problems, and our method achieves state-of-the-art performance. [ABSTRACT FROM AUTHOR]

Phytic acid, a naturally occurring compound predominantly found in cereals and legumes, is the focus of this review. This review investigates its distribution across various food sources, elucidating its dual roles in foods. It also provides new insights into the change in phytic acid level during food storage and the evolving trends in phytic acid management. Although phytic acid can function as a potent color stabilizer, flavor enhancer, and preservative, its antinutritional effects in foods restrict its applications. In terms of management strategies, numerous treatments for degrading phytic acid have been reported, each with varying degradation efficacies and distinct mechanisms of action. These treatments encompass traditional methods, biological approaches, and emerging technologies. Traditional processing techniques such as soaking, milling, dehulling, heating, and germination appear to effectively reduce phytic acid levels in processed foods. Additionally, fermentation and phytase hydrolysis demonstrated significant potential for managing phytic acid in food processing. In the future, genetic modification, due to its high efficiency and minimal environmental impact, should be prioritized to downregulate the biosynthesis of phytic acid. The review also delves into the biosynthesis and metabolism of phytic acid and elaborates on the mitigation mechanism of phytic acid using biotechnology. The challenges in the application of phytic acid in the food industry were also discussed. This study contributes to a better understanding of the roles phytic acid plays in food and the sustainability and safety of the food industry., (© 2024 Institute of Food Technologists®.)

Maize (Zea mays L.) C-type cytoplasmic male sterility (CMS-C) is a highly used CMS system for maize commercial hybrid seed production. Rf4 is the major dominant restorer gene for CMS-C. Inbreds were recently discovered which contain the restoring Rf4 allele yet are unable to restore fertility due to the lack of an additional gene required for Rf4's restoration. To find this additional gene, QTL mapping and positional cloning were performed using an inbred that contained Rf4 but was incapable of restoring CMS-C. The QTL was mapped to a 738-kb interval on chromosome 2, which contains a Pentatricopeptide Repeat (PPR) gene cluster. Allele content comparisons of the inbreds identified three potential candidate genes responsible for fertility restoration in CMS-C. Complementation via transformation of these three candidate genes showed that PPR153 (Zm00001eb114660) is required for Rf4 to restore fertility to tassels. The PPR153 sequence is present in B73 genome, but it is not capable of restoring CMS-C without Rf4. Analysis using NAM lines revealed that Rf4 requires the presence of PPR153 to restore CMS-C in diverse germplasms. This research uncovers a major CMS-C genetic restoration pathway and can be used for identifying inbreds suitable for maize hybrid production with CMS-C cytoplasm., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Jaqueth et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Dietary prenylated stilbenoids, found in various food sources, offer multiple health benefits, including liver protection. However, the underlying mechanisms of hepatoprotection remain unclear. In this study, we synthesized 13 natural prenylated stilbenoids and examined their hepatoprotective activities, with silent mating type information regulation 2 homologue-1 (SIRT1) as the primary target for screening. Among all of the prenylated stilbenoids tested, 4- C -geranyl oxyresveratrol demonstrated superior performance. It activated SIRT1 activity more effectively than resveratrol, a well-known SIRT1 activator. To further investigate the mechanism of liver protection, two in vitro models were used: the palmitic acid-induced lipid accumulation model and the H 2 O 2 -induced apoptosis model. Our findings suggested that 4- C -geranyl oxyresveratrol mitigated lipid accumulation through the SIRT1-PGC1α pathway, reduced apoptosis via the SIRT1-p53-p21 pathway, and exerted antioxidant effects through the SIRT1-Nrf2 pathway. These findings provide new insights into the chemical basis of the health benefits of prenylated stilbenoids and their potential use as functional food additives.

Background: A growing body of researches indicate that the disrupted expression of long non-coding RNA (lncRNA) is linked to a range of human disorders. Therefore, the effective prediction of lncRNA-disease association (LDA) can not only suggest solutions to diagnose a condition but also save significant time and labor costs., Method: In this work, we proposed a novel LDA predicting algorithm based on graph convolutional network and transformer, named GCNFORMER. Firstly, we integrated the intraclass similarity and interclass connections between miRNAs, lncRNAs and diseases, and built a graph adjacency matrix. Secondly, to completely obtain the features between various nodes, we employed a graph convolutional network for feature extraction. Finally, to obtain the global dependencies between inputs and outputs, we used a transformer encoder with a multiheaded attention mechanism to forecast lncRNA-disease associations., Results: The results of fivefold cross-validation experiment on the public dataset revealed that the AUC and AUPR of GCNFORMER achieved 0.9739 and 0.9812, respectively. We compared GCNFORMER with six advanced LDA prediction models, and the results indicated its superiority over the other six models. Furthermore, GCNFORMER's effectiveness in predicting potential LDAs is underscored by case studies on breast cancer, colon cancer and lung cancer., Conclusions: The combination of graph convolutional network and transformer can effectively improve the performance of LDA prediction model and promote the in-depth development of this research filed., (© 2023. The Author(s).)

Goss's wilt, caused by the Gram-positive actinobacterium Clavibacter nebraskensis, is an important bacterial disease of maize. The molecular and genetic mechanisms of resistance to the bacterium, or, in general, Gram-positive bacteria causing plant diseases, remain poorly understood. Here, we examined the genetic basis of Goss's wilt through differential gene expression, standard genome-wide association mapping (GWAS), extreme phenotype (XP) GWAS using highly resistant (R) and highly susceptible (S) lines, and quantitative trait locus (QTL) mapping using 3 bi-parental populations, identifying 11 disease association loci. Three loci were validated using near-isogenic lines or recombinant inbred lines. Our analysis indicates that Goss's wilt resistance is highly complex and major resistance genes are not commonly present. RNA sequencing of samples separately pooled from R and S lines with or without bacterial inoculation was performed, enabling identification of common and differential gene responses in R and S lines. Based on expression, in both R and S lines, the photosynthesis pathway was silenced upon infection, while stress-responsive pathways and phytohormone pathways, namely, abscisic acid, auxin, ethylene, jasmonate, and gibberellin, were markedly activated. In addition, 65 genes showed differential responses (up- or down-regulated) to infection in R and S lines. Combining genetic mapping and transcriptional data, individual candidate genes conferring Goss's wilt resistance were identified. Collectively, aspects of the genetic architecture of Goss's wilt resistance were revealed, providing foundational data for mechanistic studies., Competing Interests: Conflicts of interest JJ and BL are employees of Corteva Agriscience. The authors affirm that they have no other conflicts of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Tetrahymenosis, caused by about 10 Tetrahymena species, is an emerging problem inflicting a significant economic loss on the aquaculture industry worldwide. However, in the order Tetrahymenida, there are many unresolved evolutionary relationships among taxa. Here we report 21 new sequences, including SSU-rRNA, ITS1-5.8S-ITS2 rRNA and LSU-rRNA, genes of 10 facultative parasitic Tetrahymena associated with tetrahymenosis, and conduct phylogenetic analyses based on each individual gene and a three-gene concatenated dataset. The main findings are: (1) All the parasitic and facultative parasitic species cluster in borealis group. (2) With the addition of new sequences, Tetrahymena is still divided into three groups, namely the "borealis group", the "australis group," and the " paravorax group." (3) the cluster pattern of all the newly sequenced facultative parasitic Tetrahymena species shows that members of the "borealis" group may be more susceptible to parasitism. (4) phylogeny based on concatenated genes show that T. pyriformis , T. setosa , and T. leucophrys have close relationship., Competing Interests: All authors declare that they have no conflicts of interest., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

The blood-brain barrier (BBB) is a dynamic barrier separating neurocytes and brain tissues from blood that is extremely sealed and strictly regulated by transporters such as aquaporin-4 (AQP-4), glucose transporter (GLUT), and specialized tight junctional complexes (TJCs) including tight junctions (TJs), adherens junctions (AJs), and Zonulae occludens (ZOs). With specifically selective transcellular and paracellular permeability, the BBB maintains a homeostatic microenvironment to protect the central nervous system (CNS). In recent years, increasing attention has been paied to the importance of BBB disruption and dysfunction in the pathology of neurological disorders and diseases, such as Alzheimer's diseases (AD), Parkinson diseases (PD), stroke and cerebral edema. However, the further research on how the integral structure and function of BBB are altered under the physiological or pathological conditions is still needed. Focusing on the ultrastructural features of the BBB and combining the latest research on associated proteins and transporters, physiological regulation and pathological change of the BBB were elucidated. By summarizing the protective effects of known bioactive compounds derived from marine life on the BBB, this review aims to highlight the BBB as a key to the treatment of several major neurological diseases instead of a normally described obstacle to drug absorption and transport. Overall, the BBB's morphological characteristics and physiological function and their regulation provide the theoretical basis for the study on the BBB and inspire the diagnosis of and therapy for neurological diseases.

Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, is crucial for the development of new disease-resistant varieties. We analysed the nucleotide-binding leucine-rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians. We found that NLRs in both species contain a large diversity of atypical integrated domains, including many domains that have not previously been found in the NLRs of other species. Additionally, the single Z. luxurians genome was found to have greater integrated atypical domain diversity than all 26 NAM founder lines combined, indicating that this species may represent a rich source of novel resistance genes. NLRs were also found to have very high sequence diversity and presence-absence variation among the NAM founder lines, with a large NLR cluster on Chr10 representing a diversity hotspot. Additionally, NLRs were shown to be mobile within maize genomes, with several putative interchromosomal translocations identified., (© 2023 Corteva Agriscience. Molecular Plant Pathology published by John Wiley & Sons Ltd on behalf of British Society for Plant Pathology.)

Northern corn leaf blight, caused by the fungal pathogen Exserohilum turcicum, is a major disease of maize. The first major locus conferring resistance to E. turcicum race 0, Ht1, was identified over 50 years ago, but the underlying gene has remained unknown. We employed a map-based cloning strategy to identify the Ht1 causal gene, which was found to be a coiled-coil nucleotide-binding, leucine-rich repeat (NLR) gene, which we named PH4GP-Ht1. Transgenic testing confirmed that introducing the native PH4GP-Ht1 sequence to a susceptible maize variety resulted in resistance to E. turcicum race 0. A survey of the maize nested association mapping genomes revealed that susceptible Ht1 alleles had very low to no expression of the gene. Overexpression of the susceptible B73 allele, however, did not result in resistant plants, indicating that sequence variations may underlie the difference between resistant and susceptible phenotypes. Modelling of the PH4GP-Ht1 protein indicated that it has structural homology to the Arabidopsis NLR resistance gene ZAR1, and probably forms a similar homopentamer structure following activation. RNA sequencing data from an infection time course revealed that 1 week after inoculation there was a threefold reduction in fungal biomass in the PH4GP-Ht1 transgenic plants compared to wild-type plants. Furthermore, PH4GP-Ht1 transgenics had significantly more inoculation-responsive differentially expressed genes than wild-type plants, with enrichment seen in genes associated with both defence and photosynthesis. These results demonstrate that the NLR PH4GP-Ht1 is the causal gene underlying Ht1, which represents a different mode of action compared to the previously reported wall-associated kinase northern corn leaf blight resistance gene Htn1/Ht2/Ht3., (© 2022 PIONEER HI-BRED INTERNATIONAL, INC. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.)

Southern corn leaf blight (SLB), caused by the necrotrophic pathogen Cochliobolus heterostrophus, is one of the maize foliar diseases and poses a great threat to corn production around the world. Identification of genetic variations underlying resistance to SLB is of paramount importance to maize yield and quality. Here, we used a random-open-parent association mapping population containing eight recombinant inbred line populations and one association mapping panel consisting of 513 diversity maize inbred lines with high-density genetic markers to dissect the genetic basis of SLB resistance. Overall, 109 quantitative trait loci (QTLs) with predominantly small or moderate additive effects, and little epistatic effects were identified. We found 35 (32.1%) novel loci in comparison with the reported QTLs. We revealed that resistant alleles were significantly enriched in tropical accessions and the frequency of about half of resistant alleles decreased during the adaptation process owing to the selection of agronomic traits. A large number of annotated genes located in the SLB-resistant QTLs were shown to be involved in plant defence pathways. Integrating genome-wide association study, transcriptomic profiling, resequencing and gene editing, we identified ZmFUT1 and MYBR92 as the putative genes responsible for the major QTLs for resistance to C. heterostrophus. Our results present a comprehensive insight into the genetic basis of SLB resistance and provide resistant loci or genes as direct targets for crop genetic improvement., (© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences including SSU-rRNA, ITS1-5.8S- ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU-rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two-gene concatenated dataset. For the first time, multi-genes were used to analyze phylogenetic relationships in the class Colpodea. The main findings are: (1) SSU-rRNA, ITS1-5.8S- ITS2 rRNA, and mtSSU-rRNA gene sequences of C . reniformis and C . grandis are provided for the first time, and these two species group into the clade including C . inflata , C . lucida , C . cucullus , and C . henneguyi ; (2) clustering pattern and morphological similarity indicate that Bresslauides discoideus has a close relation with Colpodidae spp.; (3) Emarginatophrya genus diagnosis is improved to be 'Hausmanniellidae with sharply shortened and isometric leftmost 1-4 ciliary rows' and Colpoda elliotti is transferred to Emarginatophrya ; (4) the genus Colpoda is still non-monophyletic with the addition of 10 populations from five Colpoda species sequences, but there are only two Colpoda groups left based on the present work: Group I comprises C . inflata , C . lucida , C . cucullus , C . henneguyi , C . reniformis , and C . grandis , Group II comprises C . maupasi and C . ecaudata , and the presence of diagonal grooves and the way the vestibular opens might be the two key features that differentiates Colpoda species groups; (5) a close molecular relationship, and highly similar merotelokinetal mode, somatic ciliary pattern, and basic organization of the oral apparatus with P . steinii suggests Bromeliothrix metopoides should be temporarily assigned to Colpodidae., Competing Interests: All authors declare that they have no conflicts of interest., (© 2022 Harbin Normal University. Ecology and Evolution published by John Wiley & Sons Ltd.)

The morphology and molecular phylogeny of three freshwater scuticociliates, Variuronema elegans gen. nov., spec. nov. (type species), V. similis spec. nov. and Uronema rigidum spec. nov., collected from Qixing River Wetland, northeastern China, were investigated using live observation and silver carbonate staining methods; the phylogenetic placements were inferred from the small subunit rRNA gene. Variuronema gen. nov., assigned to the family Uronematidae, is distinguished from the other genera mainly by its membranelles 1 and 2, each consisting of four longitudinal rows of kinetids, and the paroral membrane extending anteriorly to the front part of membranelle 3. The phylogenetic analyses indicate that: (1) Variuronema spp. form an independent, fully supported clade. However, its position among other uronematids is unresolved. (2) The family Uronematidae is not monophyletic based on the SSU rRNA gene, which is in accordance with previous studies., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

The morphology and ciliary pattern of two new heterotrich ciliates, Blepharisma orientale n. sp. and B. sinicum n. sp., collected from Sanjiang Plain Wetland, northeastern China, were investigated using living observation and protargol staining. Blepharisma orientale n. sp. is characterized by the following combination of characteristics: limnetic; body in vivo 280-380 × 120-190 μm, slender to elongate, cortical granules dark pink, ventral margin somewhat sigmoid; buccal field about 55-60% of body length; 30-39 somatic kineties; 70-76 adoral membranelles, each comprising two long rows of basal bodies; paroral membrane consists of dikinetids with the posterior third obliquely arranged, both basal bodies in each dikinetid are ciliated. Blepharisma sinicum n. sp. is recognized by the combination of the following characters: limnetic; body 190-260 × 100-170 μm in size in vivo, irregularly sigmoid and slightly bilaterally flattened, dorsal margin curved; cortical granules pale pink in color; buccal field about 60-75% of body length; 25-29 somatic kineties; 53-82 adoral membranelles; paroral membrane consisting entirely of dikinetids. Phylogenetic analyses based on small subunit rRNA (SSU rRNA) gene sequence data recovered the two new species as sister taxa, both the sister group of B. penardi., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

Broad-spectrum resistance has great values for crop breeding. However, its mechanisms are largely unknown. Here, we report the cloning of a maize NLR gene, RppK, for resistance against southern corn rust (SCR) and its cognate Avr gene, AvrRppK, from Puccinia polysora (the causal pathogen of SCR). The AvrRppK gene has no sequence variation in all examined isolates. It has high expression level during infection and can suppress pattern-triggered immunity (PTI). Further, the introgression of RppK into maize inbred lines and hybrids enhances resistance against multiple isolates of P. polysora, thereby increasing yield in the presence of SCR. Together, we show that RppK is involved in resistance against multiple P. polysora isolates and it can recognize AvrRppK, which is broadly distributed and conserved in P. polysora isolates., (© 2022. The Author(s).)

Though beneficial for encouraging the visual question answering (VQA) models to discover the underlying knowledge by exploiting the input-output correlation beyond image and text contexts, the existing knowledge VQA data sets are mostly annotated in a crowdsource way, e.g., collecting questions and external reasons from different users via the Internet. In addition to the challenge of knowledge reasoning, how to deal with the annotator bias also remains unsolved, which often leads to superficial overfitted correlations between questions and answers. To address this issue, we propose a novel data set named knowledge-routed visual question reasoning for VQA model evaluation. Considering that a desirable VQA model should correctly perceive the image context, understand the question, and incorporate its learned knowledge, our proposed data set aims to cut off the shortcut learning exploited by the current deep embedding models and push the research boundary of the knowledge-based visual question reasoning. Specifically, we generate the question-answer pair based on both the visual genome scene graph and an external knowledge base with controlled programs to disentangle the knowledge from other biases. The programs can select one or two triplets from the scene graph or knowledge base to push multistep reasoning, avoid answer ambiguity, and balance the answer distribution. In contrast to the existing VQA data sets, we further imply the following two major constraints on the programs to incorporate knowledge reasoning. First, multiple knowledge triplets can be related to the question, but only one knowledge relates to the image object. This can enforce the VQA model to correctly perceive the image instead of guessing the knowledge based on the given question solely. Second, all questions are based on different knowledge, but the candidate answers are the same for both the training and test sets. We make the testing knowledge unused during training to evaluate whether a model can understand question words and handle unseen combinations. Extensive experiments with various baselines and state-of-the-art VQA models are conducted to demonstrate that there still exists a big gap between the model with and without groundtruth supporting triplets when given the embedded knowledge base. This reveals the weakness of the current deep embedding models on the knowledge reasoning problem.

Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is a major threat to maize production worldwide. Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR. Here, we report the molecular cloning and characterization of RppC, which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus. Furthermore, we identified the corresponding avirulence effector, AvrRppC, which is secreted by P. polysora and triggers RppC-mediated resistance. Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance, indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production. Currently, RppC is the most frequently deployed SCR resistance gene in China, and a better understanding of its mode of action is critical for extending its durability., (Copyright © 2022 The Author. Published by Elsevier Inc. All rights reserved.)

Rolling bearings act as key parts in many items of mechanical equipment and any abnormality will affect the normal operation of the entire apparatus. To diagnose the faults of rolling bearings effectively, a novel fault identification method is proposed by merging variational mode decomposition (VMD), average refined composite multiscale dispersion entropy (ARCMDE) and support vector machine (SVM) optimized by multistrategy enhanced swarm optimization in this paper. Firstly, the vibration signals are decomposed into different series of intrinsic mode functions (IMFs) based on VMD with the center frequency observation method. Subsequently, the proposed ARCMDE, fusing the superiorities of DE and average refined composite multiscale procedure, is employed to enhance the ability of the multiscale fault-feature extraction from the IMFs. Afterwards, grey wolf optimization (GWO), enhanced by multistrategy including levy flight, cosine factor and polynomial mutation strategies (LCPGWO), is proposed to optimize the penalty factor C and kernel parameter g of SVM. Then, the optimized SVM model is trained to identify the fault type of samples based on features extracted by ARCMDE. Finally, the application experiment and contrastive analysis verify the effectiveness of the proposed VMD-ARCMDE-LCPGWO-SVM method.

Collaborative reasoning for understanding image-question pairs is a very critical but underexplored topic in interpretable visual question answering systems. Although very recent studies have attempted to use explicit compositional processes to assemble multiple subtasks embedded in questions, their models heavily rely on annotations or handcrafted rules to obtain valid reasoning processes, which leads to either heavy workloads or poor performance on compositional reasoning. In this paper, to better align image and language domains in diverse and unrestricted cases, we propose a novel neural network model that performs global reasoning on a dependency tree parsed from the question; thus, our model is called a parse-tree-guided reasoning network (PTGRN). This network consists of three collaborative modules: i) an attention module that exploits the local visual evidence of each word parsed from the question, ii) a gated residual composition module that composes the previously mined evidence, and iii) a parse-tree-guided propagation module that passes the mined evidence along the parse tree. Thus, PTGRN is capable of building an interpretable visual question answering (VQA) system that gradually derives image cues following question-driven parse-tree reasoning. Experiments on relational datasets demonstrate the superiority of PTGRN over current state-of-the-art VQA methods, and the visualization results highlight the explainable capability of our reasoning system.

Background: Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a major environmental threat of crop production worldwide, is of great value for drought-tolerant gene identification., Results: A total of 627 RNA-seq analyses are performed for 224 maize accessions which represent a wide genetic diversity under three water regimes; 73,573 eQTLs are detected for about 30,000 expressing genes with high-density genome-wide single nucleotide polymorphisms, reflecting a comprehensive and dynamic genetic architecture of gene expression in response to drought. The regulatory variants controlling the gene expression constitutively or drought-dynamically are unraveled. Focusing on dynamic regulatory variants resolved to genes encoding transcription factors, a drought-responsive network reflecting a hierarchy of transcription factors and their target genes is built. Moreover, 97 genes are prioritized to associate with drought tolerance due to their expression variations through the Mendelian randomization analysis. One of the candidate genes, Abscisic acid 8'-hydroxylase, is verified to play a negative role in plant drought tolerance., Conclusions: This study unravels the effects of genetic variants on gene expression dynamics in drought response which allows us to better understand the role of distal and proximal genetic effects on gene expression and phenotypic plasticity. The prioritized drought-associated genes may serve as direct targets for functional investigation or allelic mining.

Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious threat to global public health, because it exhibits resistance to existing antibiotics and therefore high rates of morbidity and mortality. In this study, twenty-one natural product-based acylphloroglucinol congeners were synthesized, which possessed different side chains. Antibacterial screening against MRSA strains revealed that acyl moiety tailoring is a prerequisite for the antibacterial activity. Moreover, the lipophilicity, rather than the magnitude of the hydrophobic acyl tail dominates variability in activity potency. Compound 11j was identified as a promising lead for the generation of new anti-MRSA drug development. It was discovered by optimization of the side chain length in light of the potency, the breadth of the antibacterial spectrum, the rate of bactericidal action, as well as the membrane selectivity. Compound 11j exerted profound in vitro antibacterial activity against the MRSA strain (JCSC 2172), and its MIC was 3-4 orders of magnitude lower than that of vancomycin. A preliminary mode of action study of compound 11j at the biophysical and morphology levels disclosed that the mechanism underlying its anti-MRSA activity included membrane depolarization and, to a lesser extent, membrane disruption and cell lysis., (Copyright © 2016 Elsevier Masson SAS. All rights reserved.)

Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

Head smut is a systemic disease in maize caused by the soil-borne fungus Sporisorium reilianum that poses a grave threat to maize production worldwide. A major head smut quantitative resistance locus, qHSR1, has been detected on maize chromosome bin2.09. Here we report the map-based cloning of qHSR1 and the molecular mechanism of qHSR1-mediated resistance. Sequential fine mapping and transgenic complementation demonstrated that ZmWAK is the gene within qHSR1 conferring quantitative resistance to maize head smut. ZmWAK spans the plasma membrane, potentially serving as a receptor-like kinase to perceive and transduce extracellular signals. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Impaired expression in the mesocotyl compromised ZmWAK-mediated resistance. Deletion of the ZmWAK locus appears to have occurred after domestication and spread among maize germplasm, and the ZmWAK kinase domain underwent functional constraints during maize evolution.

3D (three-dimensional) structured light scanning system is widely used in the field of reverse engineering, quality inspection, and so forth. Camera calibration is the key for scanning precision. Currently, 2D (two-dimensional) or 3D fine processed calibration reference object is usually applied for high calibration precision, which is difficult to operate and the cost is high. In this paper, a novel calibration method is proposed with a scale bar and some artificial coded targets placed randomly in the measuring volume. The principle of the proposed method is based on hierarchical self-calibration and bundle adjustment. We get initial intrinsic parameters from images. Initial extrinsic parameters in projective space are estimated with the method of factorization and then upgraded to Euclidean space with orthogonality of rotation matrix and rank 3 of the absolute quadric as constraint. Last, all camera parameters are refined through bundle adjustment. Real experiments show that the proposed method is robust, and has the same precision level as the result using delicate artificial reference object, but the hardware cost is very low compared with the current calibration method used in 3D structured light scanning system.

Activated sludge of wastewater treatment plants carries a diverse microflora. However, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. In this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in Shanghai, China, by a culture-independent metagenomic approach. Three sets of consensus degenerate hybrid oligonucleotide primers (CODEHOPs) targeting conserved domains of public carboxypeptidases have been designed to amplify carboxypeptidase gene sequences in the metagenomic DNA of activated sludge by PCR. The desired amplicons were evaluated by carboxypeptidase sequence clone libraries and phylogenetic analyses. We uncovered a significant diversity of carboxypeptidases present in the activated sludge. Deduced carboxypeptidase amino acid sequences (127-208 amino acids) were classified into three distinct clusters, α, β, and γ. Sequences belonging to clusters α and β shared 58-97 % identity to known carboxypeptidase sequences from diverse species, whereas sequences in the cluster γ were remarkably less related to public carboxypeptidase homologous in the GenBank database, strongly suggesting that novel carboxypeptidase families or microbial niches exist in the activated sludge. We also observed numerous carboxypeptidase sequences that were much closer to those from representative strains present in industrial and sewage treatment and bioremediation. Thermostable and halotolerant carboxypeptidase sequences were also detected in clusters α and β. Coexistence of various carboxypeptidases is evidence of a diverse microflora in the activated sludge, a feature suggesting a valuable gene resource to be further explored for biotechnology application.

A method was developed for the quantitative analysis of tetrodotoxin (TTX) in fermentation broth of distiller's yeast by ion chromatography. After extraction with acetonitrile solution (containing 0.1% phosphoric acid) and purification with an ion-exchange column, the tetrodotoxin was separated by ion chromatography and detected by a ultraviolet-visible (UV-VIS) absorbance detector. The experimental results showed that the tetrodotoxin had a good linearity (r2 = 0.997) in the range of 10 - 100 mg/L and the detection limit (3 of signal-to-noise ratio) was 1.0 mg/L. The average recoveries were between 90% - 103% with a relative standard deviation lower than 4.9%. The analysis of real samples verified the reliability of this method and demonstrated that the ion chromatography can be used for the quantification detection of the tetrodotoxin. The degradation experiment results suggested that distiller's yeast had a remarkable effect on the tetrodotoxin degradation.

The title compound, C(9)H(8)BrNO(2), which was synthesized by the condensation of 4-bromo-benzaldehyde with nitro-ethane, possesses a trans configuration. The dihedral angle between the benzene ring and the mean plane of the double bond is 7.31 (3)°. The crystal structure is stabilized by short inter-molecular Br⋯O contacts [3.168 (4) Å].

We studied the effect of photodynamic therapy with phycobiliproteins on human liver cancer cells in vitro. With 3-(4, 5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay (MTT assay), we used two phycobiliproteins, R-phycoerythrin (R-PE) and C-phycocyanin (C-PC) prepared from Porphyra yezoensis, to determine the killing rates and apoptosis rates of human liver cancer cells (SMMC-7721) mediated by laser. When the concentration of R-PE was 120 mg/L, the survival rate of human liver cancer cells was 27% after treated by Argon laser with 100 J/cm2 doses, while the survival rate in the control group (without adding R-PE) was 65%. When the C-PC concentration was 120 mg/L, the survival cell rate was 47% after treated by He-Ne laser with 35 J/cm2 dose, while the survival rate in the control group (without adding C-PC) was 70%. After handled only with these two kinds of phycobiliproteins for 72 h, the growth of cancer cells presented significant inhibition. The maximal inhibition rates reached up to 31% with R-PE (120 mg/L concentration) and 27% with C-PC (250 mg/L concentration) respectively. After irradiated by laser for 8 h, the maximal cell apoptosis rates were 31.54% with R-PE and 32.54% with C-PC, respectively. It indicated that R-PE and C-PC extracted from Porphyra yezoensis could develop to new photosensitizers for cancer photodynamic therapy.

The title compound, C(16)H(18)ClNO(3), was obtained by the organocatalytic asymmetric Michael addition of cyclo-hexa-none to 1-chloro-4-[(1E,3E)-4-nitro-buta-1,3-dien-yl]benzene. The double bond has an E configuration. The cyclo-hexa-none ring adopts a chair conformation. The conformation of the mol-ecule is stabilized by a weak intra-molecular C-H⋯O hydrogen bond.

The title compound, C(20)H(14)FNO(4)S, was synthesized from hydro-quinone, p-toluene-sulfonyl chloride and 3,4-difluoro-benzonitrile. A folded conformation is adopted by the crystal structure. Inter-molecular C-H⋯N hydrogen bonds form dimers arranged around inversion centers.

The main structural unit of the title compoud, C(21)H(18)O(6), is a fused three-ring group consisting of coumarin and tetra-hydro-pyrane ring systems. Two C atoms of the tetra-hydro-pyran ring are displaced by 0.295 (3) and -0.360 (2) Å from the mean plane of coumarin ring. The dihedral angle between the phenyl and coumarin rings is 73.94 (3)°. Inter-molecular O-H⋯O hydrogen bonds are present in the crystal structure.

The title hydro-chloride salt, C(18)H(21)N(2)O(+)·Cl(-), is an imidazolidinone catalyst, which was derived from L-phenyl-alanine through cyclization with acetophenone. The imidazolidinone compound has a five-membered heterocyclic ring including two chiral centres. The imidazolidinone ring displays an envelope conformation, with the flap protonated N atom lying 0.497 (3) Å above the mean plane of the remaining four atoms. In the crystal structure, one-dimensional supra-molecular chains parallel to the crystallographic 2(1) screw axis are formed by N-H⋯Cl hydrogen bonds involving the NH(2) (+) and Cl(-) groups. Intra-molecular N-H⋯Cl inter-actions are also present.

In the title compound, C(11)H(18)N(2)S(2+)·2Br(-), the pyrrolidine ring displays a half-chair conformation, with the flap C atom lying 0.522 (5) Å out of the plane of the other four atoms. The methyl-ene C atom, which connects the pyrrolidinium ring and the thio-ether group, is displaced from the plane of four pyrrolidinium atoms by 0.690 (6) Å in the same direction as the flap C atom. The plane of four pyrrolidinium atoms is almost perpendicular to the benzene ring [dihedral angle = 75.02 (4)°]. The crystal structure is stabilized by hydrogen bonds between the N and Br atoms.

We used whole genome scan association mapping to identify loci with major effect on oleic acid content in maize kernels. Single nucleotide polymorphism haplotypes at 8,590 loci were tested for association with oleic acid content in 553 maize inbreds. A single locus with major effect on oleic acid was mapped between 380 and 384 cM in the IBM2 neighbors genetic map on chromosome 4 and confirmed in a biparental population. A fatty acid desaturase, fad2, identified approximately 2 kb from the associated genetic marker, is the most likely candidate gene responsible for the differences in the phenotype. The fad2 alleles with high- and low-oleic acid content were sequenced and allelic differences in fad2 RNA level in developing embryos was investigated. We propose that a non-conservative amino acid polymorphism near the active site of fad2 contributes to the effect on oleic acid content. This is the first report of the use of a high resolution whole genome scan association mapping where a putative gene responsible for a quantitative trait was identified in plants.

The maize (Zea mays) floury1 (fl1) mutant was first reported almost 100 years ago, but its molecular identity has remained unknown. We report the cloning of Fl1, which encodes a novel zein protein body membrane protein with three predicted transmembrane domains and a C-terminal plant-specific domain of unknown function (DUF593). In wild-type endosperm, the FL1 protein accumulates at a high level during the period of zein synthesis and protein body development and declines to a low level at kernel maturity. Immunogold labeling showed that FL1 resides in the endoplasmic reticulum surrounding the protein body. Zein protein bodies in fl1 mutants are of normal size, shape, and abundance. However, mutant protein bodies ectopically accumulate 22-kD alpha-zeins in the gamma-zein-rich periphery and center of the core, rather than their normal discrete location in a ring at outer edge of the core. The 19-kD alpha-zein is uniformly distributed throughout the core in wild-type protein bodies, and this distribution is unaffected in fl1 mutants. Pairwise yeast two-hybrid experiments showed that FL1 DUF593 interacts with the 22-kD alpha-zein. Results of these studies suggest that FL1 participates in protein body formation by facilitating the localization of 22-kD alpha-zein and that this is essential for the formation of vitreous endosperm.

Separation of the life cycle of flowering plants into two distinct growth phases, vegetative and reproductive, is marked by the floral transition. The initial floral inductive signals are perceived in the leaves and transmitted to the shoot apex, where the vegetative shoot apical meristem is restructured into a reproductive meristem. In this study, we report cloning and characterization of the maize (Zea mays) flowering time gene delayed flowering1 (dlf1). Loss of dlf1 function results in late flowering, indicating dlf1 is required for timely promotion of the floral transition. dlf1 encodes a protein with a basic leucine zipper domain belonging to an evolutionarily conserved family. Three-dimensional protein modeling of a missense mutation within the basic domain suggests DLF1 protein functions through DNA binding. The spatial and temporal expression pattern of dlf1 indicates a threshold level of dlf1 is required in the shoot apex for proper timing of the floral transition. Double mutant analysis of dlf1 and indeterminate1 (id1), another late flowering mutation, places dlf1 downstream of id1 function and suggests dlf1 mediates floral inductive signals transmitted from leaves to the shoot apex. This study establishes an emergent framework for the genetic control of floral induction in maize and highlights the conserved topology of the floral transition network in flowering plants.

The most critical step in maize (Zea mays ssp. mays) domestication was the liberation of the kernel from the hardened, protective casing that envelops the kernel in the maize progenitor, teosinte. This evolutionary step exposed the kernel on the surface of the ear, such that it could readily be used by humans as a food source. Here we show that this key event in maize domestication is controlled by a single gene (teosinte glume architecture or tga1), belonging to the SBP-domain family of transcriptional regulators. The factor controlling the phenotypic difference between maize and teosinte maps to a 1-kilobase region, within which maize and teosinte show only seven fixed differences in their DNA sequences. One of these differences encodes a non-conservative amino acid substitution and may affect protein function, and the other six differences potentially affect gene regulation. Molecular evolution analyses show that this region was the target of selection during maize domestication. Our results demonstrate that modest genetic changes in single genes can induce dramatic changes in phenotype during domestication and evolution.

Objective: To investigate telomerase gene expression in precancerous mammary lesion, such as atypical ductal hyperplasia and breast cancer and to study the relationship between expression and malignant transformation., Methods: Expression of human telomerase genes (hTR) and human reverse transcriptase gene (hTRT) in 76 cases of mammary tissue was evaluated using in situ hybridization and included 50 cases of mammary hyperplasia, 6 of which were benign hyperplasia, 9 were mild atypical hyperplasia, 12 were moderate atypical hyperplasia, 23 were severe atypical hyperplasia and 26 were mammary cancer., Results: The expressions of hTR and hTRT mRNA were much weaker or negative in benign hyperplasia (16.6%, 0), weak to mild moderate in atypical hyperplasia (22.2%, 11.1%, 33.3%, 25.0%), strong in severe atypical hyperplasia (60.9%, 52.1%), and significantly strong in mammary cancer (88.5%, 80.8%). The difference between mild-moderate atypical hyperplasia, invasive ductal carcinoma and severe atypical hyperplasia was significant (P < 0.05) and the difference between severe atypical hyperplasia and intraductal carcinoma was not significant (P > 0.05)., Conclusion: Telomerase genes (hTR and hTRT) expressions are related to the transformation of atypical hyperplasia. Activated telomerase may play a role in mammary cancer development.

Objective: To investigate the relationship of telomerase genes and the malignant transformation of atypical mammary ductal hyperplasia., Methods: Telomerase genes hTR and hTRT in 50 cases of mammary hyperplasia (the cases included 6 benign hyperplasia, 9 mild atypical hyperplasia, 12 medium atypical hyperplasia, 23 severe atypical hyperplasia) and 26 cases of breast carcinoma were detected by in situ hybridization., Results: The expression of hTR and hTRT mRNA were weak or negative in benign hyperplasia (1/6, 0), weaker in mild-moderate atypical hyperplasia (2/9, 1/9, 4/12, and 3/12), strong in severe atypical hyperplasia (14/23, 60.9% and 12/23, 52.1%), while very strong expression (23/26, 88.5% and 21/25, 80.8%) in carcinoma of the breast. The difference between mild-moderate atypical hyperplasia, invasive ductal carcinoma and severe atypical hyperplasia was significant (P < 0.05) and the difference between severe atypital hyperplasia and intraductal carcinoma was not significant (P > 0.05)., Conclusions: Telmerase genes (hTR, hTRT) expression is closely related to the malignant transformation of atypical hyperplasia. The reactivated telomerase may play a crucial role in the development of breast cancer.