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Geological hazards are widely distributed, cause huge losses, and have always been the focus of attention for engineering and environmental geologists. Geological hazard evaluation is the basis of research and has important theoretical significance for preventing and controlling geological hazards. Therefore, geological hazard evaluation has become the focus of engineering and environmental geology. The question of how to build a universal index system model of geological hazard evaluation is an urgent problem that needs to be solved in geological hazard evaluation. Based on a large amount of previous research data, this paper takes landslide hazard as an example and systematically expounds the main problems that need to be solved in the current geological hazard evaluation from five aspects: basic concept, evaluation scope and accuracy, evaluation index system and evaluation criteria, evaluation method, and applicability of evaluation results. A landslide hazard assessment index system model is proposed, which applies to all regions, including all of the factors that may affect the formation of landslides. It is also hoped that this will be used as an example to establish various types of disaster evaluation and assessment systems. If the parameter has no value in the assessment process, it can be processed as 0. On this basis, further research is suggested from the perspectives of the geological hazard evaluation level, geological hazard evaluation theory, and method. To provide thoughts on and suggestions for geological hazard risk assessment method research, standard revision, investigation and evaluation, and risk management and control need to be considered. [ABSTRACT FROM AUTHOR]

Coverage quantification is required in many sequencing datasets within the field of genomics research. However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research. [ABSTRACT FROM AUTHOR]

Summary: Self‐incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S‐RNase‐based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm‐RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self‐compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786‐bp miniature inverted‐repeat transposable element (MITE) insertion in the promoter region of the FhiS2‐RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm‐RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S‐RNase; moreover, transgenic experiments show that deletion of this 786‐bp MITE insertion recovers the expression of FhiS2‐RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S‐locus affecting the SI phenotype. A family‐wide survey of the S‐locus revealed that MITE insertions occur frequently adjacent to S‐RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S‐RNase system. [ABSTRACT FROM AUTHOR]

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers. [ABSTRACT FROM AUTHOR]

SUMMARY: Chromoplasts act as a metabolic sink for carotenoids, in which plastoglobules serve as versatile lipoprotein particles. PGs in chloroplasts have been characterized. However, the features of PGs from non‐photosynthetic plastids are poorly understood. We found that the development of chromoplast plastoglobules (CPGs) in globular and crystalloid chromoplasts of citrus is associated with alterations in carotenoid storage. Using Nycodenz density gradient ultracentrifugation, an efficient protocol for isolating highly purified CPGs from sweet orange (Citrus sinensis) pulp was established. Forty‐four proteins were defined as likely comprise the core proteome of CPGs using comparative proteomics analysis. Lipidome analysis of different chromoplast microcompartments revealed that the nonpolar microenvironment within CPGs was modified by 35 triacylglycerides, two sitosterol esters, and one stigmasterol ester. Manipulation of the CPG‐localized gene CsELT1 (esterase/lipase/thioesterase) in citrus calli resulted in increased lipids and carotenoids, which is further evidence that the nonpolar microenvironment of CPGs contributes to carotenoid accumulation and storage in the chromoplasts. This multi‐feature analysis of CPGs sheds new light on the role of chromoplasts in carotenoid metabolism, paving the way for manipulating carotenoid content in citrus fruit and other crops. [ABSTRACT FROM AUTHOR]

Background: Dysbacteriosis of intestinal tract may cause systemic inflammation, making distant anatomical locations more susceptible to illness. Recent research has demonstrated that the microbiome can affect both prostatitis and the inflammation of the prostate that is linked to prostate cancer. It is still unclear, though, whether this relationship indicates causation. We conducted a Mendelian randomization investigation on two samples to fully uncover gut microbiota's potential genetic causal role in prostatitis. Method: Prostatitis (1859 prostatitis cases and 72,799 controls) was utilized as the outcome, while SNPs highly linked with 196 microbial taxa (18 340 people) were chosen as instrumental factors. Random effects, inverse variance weighting, weighted medians, and MR-Egger were used to analyze causal effects. The Cochran's Q test, funnel plot, leave-one-out analysis, and MR-Egger intercept test were all used in the sensitivity analysis. Results: A causal effect in lowering the incidence of prostatitis is anticipated for five gut microorganisms (Methanobacteria, Methanobacteriaceae, Erysipelatoclostridium, Parasutterella, and Slackia; P < 0.05). Four gut bacteria, including Faecalibacterium, LachnospiraceaeUCG004, Sutterella, and Gastranaerophilales, are predicted to play a causal role in increasing the risk of prostatitis (P < 0.05). There were no discernible estimates of pleiotropy or heterogeneity. Conclusion: Our investigation established the genetic links between nine gut microorganisms and prostatitis, which may offer fresh perspectives and a theoretical framework for the future prevention and management of prostatitis. [ABSTRACT FROM AUTHOR]

Program online judge (POJ) systems allow students to view questions, submit solution code, and receive scores automatically via the web. Most POJs use test cases for scoring. When a POJ is scored by test case pass rate or a problem that has only one test case, students can usually score by providing the direct output of the test cases (direct output cheating). Currently, there is only one work on detecting such cheating. However, its precision is very low. To solve this problem, three novel approaches are proposed to detect direct output cheating: (i) Line Statistics, which computes the proportion of output calls against other statements; (ii) the control flow graph (CFG) Search computes the maximum similarity between the CFG of a program and that of known samples; (iii) abstract syntax tree (AST) Search identifies cheating by matching rules that are summarized from ASTs of previously detected cheating attempts. A student's code is marked as cheating if the similarity exceeds a predefined threshold; and a program is detected as cheating if the proportion exceeds a predefined threshold. The proposed approaches and three well-known code plagiarism detection tools (JPlag, Sherlock, and SIM) were evaluated using 100,000 submissions for 1153 problems from a POJ based on the C programming language. The F1 scores of these approaches were determined as 0.9752 (AST Search), 0.9440 (CFG Search), 0.7405 (Line Statistics), 0.6446 (JPlag), 0.1587 (Sherlock), and 0.0076 (SIM), respectively. The result indicates that (i) AST Search is most suitable for the detection of direct output cheating; (ii) traditional code search or plagiarism detection methods based on similarity calculations are not effective for complex cheat detection because these cheats are highly similar to normal code. [ABSTRACT FROM AUTHOR]

The development of facial recognition technology has become an increasingly powerful tool in wild animal individual recognition. In this paper, we develop an automatic detection and recognition method with the combinations of body features of big cats based on the deep convolutional neural network (CNN). We collected dataset including 12 244 images from 47 individual Amur tigers (Panthera tigris altaica) at the Siberian Tiger Park by mobile phones and digital camera and 1940 images and videos of 12 individual wild Amur leopard (Panthera pardus orientalis) by infrared cameras. First, the single shot multibox detector algorithm is used to perform the automatic detection process of feature regions in each image. For the different feature regions of the image, like face stripe or spots, CNNs and multi‐layer perceptron models were applied to automatically identify tiger and leopard individuals, independently. Our results show that the identification accuracy of Amur tiger can reach up to 93.27% for face front, 93.33% for right body stripe, and 93.46% for left body stripe. Furthermore, the combination of right face, left body stripe, and right body stripe achieves the highest accuracy rate, up to 95.55%. Consequently, the combination of different body parts can improve the individual identification accuracy. However, it is not the higher the number of body parts, the higher the accuracy rate. The combination model with 3 body parts has the highest accuracy. The identification accuracy of Amur leopard can reach up to 86.90% for face front, 89.13% for left body spots, and 88.33% for right body spots. The accuracy of different body parts combination is lower than the independent part. For wild Amur leopard, the combination of face with body spot part is not helpful for the improvement of identification accuracy. The most effective identification part is still the independent left or right body spot part. It can be applied in long‐term monitoring of big cats, including big data analysis for animal behavior, and be helpful for the individual identification of other wildlife species. [ABSTRACT FROM AUTHOR]

So far, there has been no safe and convenient method to weigh the large fierce animals, like Amur tigers. To address this problem, we built models to predict the body weight of Amur tigers based on the fact that body weight is proportional to body measurements or age. Using the method of body measurements, we extracted the body measurements from 4 different kinds of the lateral body image of tigers, that is, total lateral image, central lateral image, ellipse fitting image, and rectangle fitting image, and then we respectively used artificial neural network (ANN) and power regression model to analyze the predictive relationships between body weight and body measurements. Our results demonstrated that, among all ANN models, the model built with rectangle fitting image had the smallest mean square error. Comparatively, we screened power regression models which had the smallest Akakai information criteria (AIC). In addition, using the method of age, we fitted nonlinear regression models for the relationship between body weight and age and found that, for male tigers, logistic model had the smallest AIC. For female tigers, Gompertz model had the smallest AIC. Consequently, this study could be applied to estimate body weight of captive, or even wild, Amur tigers safely and conveniently, helping to monitor individual health and growth of the Amur tiger populations. [ABSTRACT FROM AUTHOR]

Key message: The causal gene, CaHY5 of a chemical induced green-hypocotyl mutant was identified by molecular mapping. CaHY5 regulates anthocyanin accumulation by directly binding to the promoter of genes in anthocyanin pathway. Morphological markers at seedling stage are useful indicators for F1 hybrid seeds screening. Pepper is a worldwide vegetable with diverse uses, and F1 hybrids are popular in the pepper industry. Hypocotyl color is a useful marker to identify F1 hybrid seeds. However, most pepper accessions have purple hypocotyl caused by anthocyanin accumulation, while green hypocotyl pepper accessions are rare. In this study, we identified a green hypocotyl mutant (e1898) from a pepper ethylmethanesulfonate (EMS) mutant library. By combining bulked segregant RNA-seq (BSR), genome resequencing and recombinant analysis, it was found that CaHY5 is the causal gene of this mutant. Virus-induced gene silencing (VIGS) of CaHY5 resulted in the decrease of anthocyanin accumulation in pepper hypocotyls. RNA-seq data showed that many genes related to anthocyanin biosynthesis and transport decreased significantly in the mutant. Yeast one-hybrid (Y1H) assays showed that CaHY5 can bind to the promoter of CaF3H, CaF3′5'H, CaDFR, CaANS and CaGST, which are important genes in anthocyanin biosynthesis or transport. Our results indicate that CaHY5 directly regulates anthocyanin biosynthesis and transport, thus governing anthocyanin accumulation in pepper hypocotyl. The mutant and gene identified in this work shall be valuable in the purity control of hybrid pepper seeds. [ABSTRACT FROM AUTHOR]

Roses are among the most economically important ornamental plants worldwide. But prickles on the stem and leaves cause difficulties for cultivation or inconveniences during harvest and transportation, thus are an undesirable horticultural character. However, little is known about the molecular mechanisms of prickle development. In this study, we sought to develop Rosa multiflora (in the family Rosaceae) as a model plant to study prickle formation. The morphology, structure, and ontogeny of prickles were characterized, and transcriptome analysis of prickly and prickleless R. multiflora genotypes was performed. Morphological observation and microscopic analyses revealed that prickles of R. multiflora were non‐glandular prickles (NGPs) and their maturation went through five developmental stages, which was accompanied by the accumulation of secondary metabolites such as lignin and anthocyanins. Comparative transcriptome analysis identified key pathways and hub genes potentially involved in prickle formation. Interestingly, among the differentially expressed genes (DEGs), several notable development and secondary metabolism‐related transcription factors (TFs) including NAC, TCP, MYB, homeobox, and WRKY were up‐regulated in prickly internodes. KEGG enrichment analysis indicated that DEGs were enriched in the pathways related to biosynthesis of secondary metabolites, flavonoids, and phenylpropanoids in the prickly R. multiflora. Our study provides novel insights into the molecular network underlying the regulation of prickle morphogenesis in R. multiflora, and the identified candidates might be applied to the genetic improvement of roses. [ABSTRACT FROM AUTHOR]

Mitochondria are crucial for the production of primary and secondary metabolites, which largely determine the quality of fruit. However, a method for isolating high-quality mitochondria is currently not available in citrus fruit, preventing high-throughput characterization of mitochondrial functions. Here, based on differential and discontinuous Percoll density gradient centrifugation, we devised a universal protocol for isolating mitochondria from the pulp of four major citrus species, including satsuma mandarin, ponkan mandarin, sweet orange, and pummelo. Western blot analysis and microscopy confirmed the high purity and intactness of the isolated mitochondria. By using this protocol coupled with a label-free proteomic approach, a total of 3353 nonredundant proteins were identified. Comparison of the four mitochondrial proteomes revealed that the proteins commonly detected in all proteomes participate in several typical metabolic pathways (such as tricarboxylic acid cycle, pyruvate metabolism, and oxidative phosphorylation) and pathways closely related to fruit quality (such as γ-aminobutyric acid (GABA) shunt, ascorbate metabolism, and biosynthesis of secondary metabolites). In addition, differentially abundant proteins (DAPs) between different types of species were also identified; these were found to be mainly involved in fatty acid and amino acid metabolism and were further confirmed to be localized to the mitochondria by subcellular localization analysis. In summary, the proposed protocol for the isolation of highly pure mitochondria from different citrus fruits may be used to obtain high-coverage mitochondrial proteomes, which can help to establish the association between mitochondrial metabolism and fruit storability or quality characteristics of different species and lay the foundation for discovering novel functions of mitochondria in plants. [ABSTRACT FROM AUTHOR]

In order to explore the diagnostic value of prostate targeted puncture guided by MRI combined with ultrasound fusion imaging (MR-TRUS) in patients with prostate cancer of PI-RADS score ≥ 3 points, 100 patients who sought medical care in our hospital were enrolled. All of them were performed targeted biopsy via both MR-TRUS guided puncture and traditional puncture. And all the patients were tested the level of prostate specific antigen (PSA). According to 4 < PSA ≤ 10 µ g /L, 10 < PSA ≤ 20 µ g /L, 20 < PSA ≤ 50 µ g/L, and PSA > 50 µ g /L, the MR-TRUS guided puncture group (group A) and the traditional puncture group (group B) were both divided into 4 subgroups. The sensitivity, specificity and accuracy of different puncture methods for the diagnosis of prostate cancer were compared according to the postoperative pathological results. The results showed that the diagnostic rates of each subgroup in the group A were 28.57%, 66.67%, 70% and 91.67%, while the diagnostic rates of each subgroup in the group B were 9.52%, 25.00%, 60.00% and 86.11%, respectively. Compared with the traditional puncture method, MR-TRUS guided puncture significantly improved the diagnostic rate in patients of PSA ≤ 10 µ g/L and 10 < PSA ≤ 20 µ g/h (P<0.05). The diagnostic rate of the two puncture methods was not significantly different in patients of 20 < PSA ≤ 50 µ g/L and PSA > 50 µ g/L (P > 0.05). Compared with the traditional puncture method, the sensitivity and accuracy of MR-TRUS guided puncture were significantly improved (P < 0.05). In summary, patients of PSA ≤ 10 µ g/L and 10 PSA ≤ 20 µ g/L should undergo targeted puncture guided by MRI and ultrasound fusion, which can significantly improve the diagnosis rate of prostate cancer. [ABSTRACT FROM AUTHOR]

Soil salinization is a major threat to global food security and the biodiversity of natural ecosystems. To adapt to salt stress, plants rely on ROS‐mediated signalling networks that operate upstream of a broad array of physiological and genetic processes. A key player in ROS signalling is NADPH oxidase, a plasma‐membrane‐bound enzyme encoded by RBOH genes. In this study, we have conducted a comprehensive bioinformatic analysis of over 50 halophytic and glycophytic species to link the difference in the kinetics of ROS signalling between contrasting species with the abundance and/or structure of NADPH oxidases. The RBOH proteins were predicted in all the tested plant lineages except some algae species from the Rhodophyta, Chlorophyta and Streptophyta. Within the glycophytic group, the number of RBOH copies correlated negatively with salinity stress tolerance, suggesting that a reduction in the number of RBOH isoforms may be potentially related to the evolution of plant salinity tolerance. While halophytes did not develop unique protein families during evolution, they evolved additional phosphorylation target sites at the N‐termini of NADPH oxidases, potentially modulating enzyme activity and allowing more control over their function, resulting in more efficient ROS signalling and adaptation to saline conditions. Halophytes evolved additional phosphorylation target sites at N‐terminus of NADPH oxidase, potentially modulating enzyme activity and allowing more control over its function needed for more efficient ROS signalling and adaptation to conditions of high salinity. [ABSTRACT FROM AUTHOR]

The automatic individual identification of Amur tigers (Panthera tigris altaica) is important for population monitoring and making effective conservation strategies. Most existing research primarily relies on manual identification, which does not scale well to large datasets. In this paper, the deep convolution neural networks algorithm is constructed to implement the automatic individual identification for large numbers of Amur tiger images. The experimental data were obtained from 40 Amur tigers in Tieling Guaipo Tiger Park, China. The number of images collected from each tiger was approximately 200, and a total of 8277 images were obtained. The experiments were carried out on both the left and right side of body. Our results suggested that the recognition accuracy rate of left and right sides are 90.48% and 93.5%, respectively. The accuracy of our network has achieved the similar level compared to other state of the art networks like LeNet, ResNet34, and ZF_Net. The running time is much shorter than that of other networks. Consequently, this study can provide a new approach on automatic individual identification technology in the case of the Amur tiger. [ABSTRACT FROM AUTHOR]

Featured Application: The proposed method is applied to spacing allocation of the vehicles in platoon. Recently, spacing policies of the vehicular platoon have been widely developed to enhance safety, traffic efficiency, and fuel consumption. However, the integrated spacing policies aim to maximum overall benefit, and the distributed spacing policies intense to get optimal monomer benefit. Ignoring the fairness of the benefit allocation of each vehicle will reduce the motivation to constitute the platoon. To fill this critical gap, this study proposes a spacing allocation method by treating spacing decisions as cooperative games. A flock's model which is used to be the payoff function is introduced based on bionic motion principles. We present a characteristic function of the platoon for the cooperative game model considering the specific structure of the platoon. The τ value, Shapley value, and average lexicographic value are introduced and applied to allocate the spacing fairly. Proposed methods are compared with constant distance policy in some typical situations. The simulation results demonstrate that the spacing policy based on cooperative game theory improved the stable time for consistency control and the convergence of longitudinal following error. [ABSTRACT FROM AUTHOR]

Background: Human epidermal growth factor receptor 2 (ERBB2, HER-2) exon 20 insertion (ERBB2ex20ins) remains a refractory oncogenic driver in lung cancer. So far there is limited data showing the co-occurring mutation background of ERBB2ex20ins in Chinese lung cancer and its relationship with response to afatinib. Patients and Methods: A total of 112 Chinese patients with ERBB2ex20ins identified by next-generation sequencing from 17 hospitals were enrolled. The clinical outcomes of 18 patients receiving afatinib treatment were collected. Results: Among the 112 patients, insertion-site subtypes comprised of A775ins (71%; 79/112), G776indel (17%; 19/112), and P780ins (12%; 14/112). There were 66.1% (74/112) of patients carrying TP53 co-mutation and FOXA1 was the most prevalent co-amplified gene (5.5%, 3/55). The co-occurring genomic feature was similar among three insertional-site subtypes and had an overall strong concordance with the western population from the MSKCC cohort (R 2 = 0.74, P < 0.01). For the prognosis, patients with co-occurring mutation in cell-cycle pathway especially TP53 showed shorter OS than patients without [median OS: 14.5 m (95% CI:12.7–16.3 m) vs. 30.3 m (95% CI: not reached), p = 0.04], while the OS was comparable among three subtypes. For the response to afatinib, ERBB2ex20ins as a subclonal variant was an independent factor relating to shorter PFS [median PFS: 1.2 m (95% CI: 0.8–1.6 m) vs. 4.3 m (95% CI: 3.3–5.3 m), p < 0.05]. Conclusion: Our data revealed co-occurring TP53 represent an unfavorable prognosis of patients with ERBB2ex20ins, emphasizing the more valuable role of the co-mutation patterns than insertion-site subtypes in predicting prognosis of this group of patients. Moreover, the clonality status of ERBB2ex20ins was identified as a potential indicator for response to afatinib. [ABSTRACT FROM AUTHOR]

Introduction: The peritoneum is the most common metastatic site of gastric cancer and is associated with a dismal prognosis. However, there is no reliable biomarker for predicting peritoneal metastasis (PM). Materials and Methods: Whole-exome sequencing (WES) was performed on formalin-fixed, paraffin-embedded (FFPE) samples from 63 patients with stage I–III gastric cancer and circulating tumor DNA (ctDNA) samples from 10 patients with stage IV gastric cancer. Differentially expressed genes (DEGs) were identified between the PM and non-PM groups and analyzed by multiple bioinformatics analyses. Univariate and multivariate Cox regression analyses were used to identify the risk factors for PM and a risk score model was developed. Results: The number of mutant genes and the tumor mutation burden (TMB) in the PM group were higher than those in the non-PM group (p < 0.05). There was a significant positive correlation between the number of mutant genes and the TMB (R2 = 0.9997). The risk of PM was significantly higher in the high TMB group than in the low TMB group (p = 0.045). Forty-nine DEGs were identified as associated with PM in gastric cancer. CDC27 mutations were associated with a higher risk for PM and poor survival. The CDC27 mutations were located in the Apc3 region, the TPR region, and the phosphorylation region, and new mutation sites were not included in the TCGA database. Multivariable Cox regression analysis demonstrated that pathological T stage, poor tumor differentiation, Borrmann type, and CDC27 mutations were independent predictive factors of PM. A risk score model was constructed that demonstrated good performance. Conclusion: Through WES, we identified 49 DEGs relevant to PM in gastric cancer. CDC27 mutations were independently associated with PM by statistical and bioinformatics analyses. A risk score model was built and was demonstrated to effectively discriminate gastric cancer patients with and without PM. [ABSTRACT FROM AUTHOR]

Immunotherapy directed against cancer-specific neoantigens derived from non-silent mutants is a promising individualized strategy for cancer treatment. Neoantigens shared across patients could be used as a public resource for developing T cell-based therapy. To identify potential public neoantigens for therapy in gastric cancer (GC), 74 GC patients were enrolled in this study. Combined with the TCGA cohort and other published studies, whole exome sequencing data from 942 GC patients were used to detect somatic mutations and predict neoantigens shared by GC patients. The mutations pattern between our study and the TCGA cohort is comparable, and C > T is the most common substitution. The number of neoantigens was significantly higher in older patients (age ≥60) compared to younger patients (age <60), both in this study and the TCGA cohort. Recurrent neoantigens were found in eight genes (TP53, PIK3CA, PGM5, ERBB3, C6, TRIM49C, OR4C16, and KRAS) in this study. The neoantigen-associated mutations PIK3CA (p.H1047R) and TP53 (p.R175H) are common across several cancer types, indicating their potential usage. Overall, our study illustrates a comprehensive genomic landscape of GC and provides the recurrent neoantigens to facilitate further immunotherapy. [ABSTRACT FROM AUTHOR]

The present study aimed to investigate the significance of the neutrophil to lymphocyte ratio (NLR) in peripheral blood of patients with small cell lung cancer (SCLC) when selecting a first-line treatment. A total of 73 patients with SCLC who had complete clinical data and sought treatment at Fujian Medical University Union Hospital between January 2014 and May 2016 were included. Data were retrospectively analyzed, utilizing a receiver operating characteristic curve to determine the NLR cut-off value. Out of the 73 patients, 39 were classified as high-NLR (NLR ≥3.80) and 34 as low-NLR (NLR <3.80). Compared with the high-NLR group, patients in the low-NLR group had a longer progression free survival (PFS); however, there was no statistically significant difference in overall survival (OS) time. Patients with a high NLR had a significantly longer PFS (P=0.021) and OS time (P=0.042) when treated with a etoposide/cisplatin (EP) therapy regimen, compared with those treated with etoposide/carboplatin (EC). PFS was the longest in the high-NLR patients with limited stage (LS; P=0.002). Among the patients receiving the EC regimen, the PFS of the low-NLR group was significantly longer compared with the high-NLR group (P=0.003). Patients in the low-NLR group who received thoracic radiotherapy had a longer PFS (P=0.011), when comparing patients in the low-NLR group who did not receive thoracic radiotherapy, and within this group the therapeutic effect of radiation was the greatest in LS patients. Compared with the high-NLR group, the low-NLR group patients who received cranial radiotherapy had a significantly longer PFS (P=0.039). For the initial evaluation of patients with SCLC, pre-treatment NLR may be of significance for selecting first-line chemotherapy agents. As the present study was retrospective and investigated a limited number of patients, further research and prospective studies are warranted. [ABSTRACT FROM AUTHOR]

Key message: A total of 43 phyla (395 genera) of bacteria and 11 phyla (309 genera) of fungi were identified from normal sapwood (SW), wetwood (WW) and their transition zone wood (TW) in living poplar trees, with bacteria showing significantly higher diversity than fungi. Highly variable community diversities and compositions were found for bacteria but not for fungi among WW, TW and SW. Overall, 22 phyla (95 genera) bacteria and three phyla (11 genera) fungi were significantly different in relative abundance between WW and SW. Nine wood chemical properties were significantly correlated with the relative abundance of top 15 bacterial and fungal genera in all samples. Wetwood represents an abnormal condition of heartwood in living poplar trees. The cause of wetwood formation is still poorly understood, but it is generally considered to involve microbial activities. To facilitate a better understanding of wetwood formation, we sequenced the 16S rRNA and ITS (Internal Transcribed Spacer) genes of distinct regions (16S V4, ITS1) to precisely identify the microbial communities in normal sapwood (SW), wetwood (WW) and their transition zone wood (TW). Nine chemical properties of the wood samples were further determined to elucidate the correlations between the microbial communities and wood characteristics. The total sequences of 16S V4 and ITS1 from WW, TW and SW were assigned to 43 bacterial phyla (395 genera) and 11 fungal phyla (309 genera), indicating a significantly higher diversity of bacteria than fungi. Among SW, TW and WW, significant variations in community diversity and composition were found for bacteria but not for fungi. WW had the highest bacterial and lowest fungal diversities, while SW exhibited the highest fungal diversity. TW generally exhibited intermediate levels between WW and SW. Between WW and SW, 22 bacterial phyla (95 genera) were significantly different in relative abundance. Nine wood chemical properties were significantly correlated with the relative abundance of top 15 bacterial and fungal genera in all wood samples. [ABSTRACT FROM AUTHOR]

The purposes of this study are to investigate the prevalence of nonresponsive feeding practice (NRFP) and child's eating behavior (CEB) and to explore the hypothetical association between child's weight status, NRFP and CEB for 1- to 6-year-old children. In this study, 2423 caregivers of 1- to 6-year-old children are from the Nanjing Maternal and Child Health Hospital who completed the self-report questionnaires about their NRFP and CEB as well as their children's sociodemographic data. Chi-square test and multiple regression analyses were used to examine the correlation between child's weight status and NRFP and CEB. The total prevalence of overweight and obesity was 15.2 and 7.3%, respectively. High prevalence of CEB problems and NRFP was detected at 2- and 5-year-old children. Moreover, maternal NRFP was significantly positively associated with CEB. The regression and correlation analysis revealed CEB and maternal NRFP are closely associated with BMI. For instance, refusing new food (OR = 3.57, 95%CI, 1.37-9.33, 1.5-year-old) and restriction (OR = 3.01, 95%CI, 1.34-6.76) are likely to be associated with underweight. Preferring junk food (OR = 4.892, 95%CI, 1.71-14.01, 1-year-old) and inattention (OR = 2.24, 95%CI, 1.16-4.35, 1-year-old) are prone to be overweight and obese, and pressure (OR = 0.23, 95%CI, 0.06-0.91, 1-year-old) is less likely to be associated with underweight.Conclusion: The findings provide strong evidence for the correlation between NRFR and CEB, and this indicates that prevention and intervention of unhealthy weight should start in early life. However, further research is necessary to gain an understanding of the impact of NRFP on CEB and weight. What is known: • Responsive feeding practice is crucial to the formation of eating behavior, and poor practice is associated with the current epidemics of childhood obesity and underweight. What is new: • The findings provide a strong evidence for the correlation between NRFR and CEB. • This finding indicates that NRFR and CEB are associated with child's unhealthy weight. [ABSTRACT FROM AUTHOR]

Particle probability hypothesis density filtering has become a promising approach for multi-target tracking due to its capability of handling an unknown and time-varying number of targets in a nonlinear, non-Gaussian system. However, its computational complexity linearly increases with the number of obtained observations and the number of particles, which can be very time consuming, particularly when numerous targets and clutter exist in the surveillance region. To address this issue, we present a distributed computation particle probability hypothesis density(PHD) filter for target tracking. It runs several local decomposed particle PHD filters in parallel while processing elements. Each processing element takes responsibility for a portion of particles but all measurements and provides local estimates. A central unit controls particle exchange among the processing elements and specifies a fusion rule to match and fuse the estimates from different local filters. The proposed framework is suitable for parallel implementation. Simulations verify that the proposed method can significantly accelerate and maintain a comparative accuracy compared to the standard particle PHD filter. [ABSTRACT FROM AUTHOR]

Tracking micro-objects in the noisy microscopy image sequences is important for the analysis of dynamic processes in biological objects. In this paper, an automated tracking framework is proposed to extract the trajectories of micro-objects. This framework uses a probability hypothesis density particle filtering (PF-PHD) tracker to implement a recursive state estimation and trajectories association. In order to increase the efficiency of this approach, an elliptical target model is presented to describe the micro-objects using shape parameters instead of point-like targets which may cause inaccurate tracking. A novel likelihood function, not only covering the spatiotemporal distance but also dealing with geometric shape function based on the Mahalanobis norm, is proposed to improve the accuracy of particle weight in the update process of the PF-PHD tracker. Using this framework, a larger number of tracks are obtained. The experiments are performed on simulated data of microtubule movements and real mouse stem cells. We compare the PF-PHD tracker with the nearest neighbor method and the multiple hypothesis tracking method. Our PF-PHD tracker can simultaneously track hundreds of micro-objects in the microscopy image sequence. [ABSTRACT FROM AUTHOR]

The Developmental Eye Movement (DEM) test is commonly used as a clinical visual-verbal ocular motor assessment tool to screen and diagnose reading problems at the onset. No established norm exists for using the DEM test with Mandarin Chinese-speaking Chinese children. This study aims to establish the normative values of the DEM test for the Mandarin Chinese-speaking population in China; it also aims to compare the values with three other published norms for English-, Spanish-, and Cantonese-speaking Chinese children. A random stratified sampling method was used to recruit children from eight kindergartens and eight primary schools in the main urban and suburban areas of Nanjing. A total of 1,425 Mandarin Chinese-speaking children aged 5 to 12 years took the DEM test in Mandarin Chinese. A digital recorder was used to record the process. All of the subjects completed a symptomatology survey, and their DEM scores were determined by a trained tester. The scores were computed using the formula in the DEM manual, except that the “vertical scores” were adjusted by taking the vertical errors into consideration. The results were compared with the three other published norms. In our subjects, a general decrease with age was observed for the four eye movement indexes: vertical score, adjusted horizontal score, ratio, and total error. For both the vertical and adjusted horizontal scores, the Mandarin Chinese-speaking children completed the tests much more quickly than the norms for English- and Spanish-speaking children. However, the same group completed the test slightly more slowly than the norms for Cantonese-speaking children. The differences in the means were significant (P<0.001) in all age groups. For several ages, the scores obtained in this study were significantly different from the reported scores of Cantonese-speaking Chinese children (P<0.005). Compared with English-speaking children, only the vertical score of the 6-year-old group, the vertical-horizontal time ratio of the 8-year-old group and the errors of 9-year-old group had no significant difference (P>0.05); compared with Spanish-speaking children, the scores were statistically significant (P<0.001) for the total error scores of the age groups, except the 6-, 9-, 10-, and 11-year-old age groups (P>0.05). DEM norms may be affected by differences in language, cultural, and educational systems among various ethnicities. The norms of the DEM test are proposed for use with Mandarin Chinese-speaking children in Nanjing and will be proposed for children throughout China. [ABSTRACT FROM AUTHOR]

Purpose: This retrospective study was designed to evaluate the efficacy and safety of Paclitaxel (PTX) combined with Oxaliplatin (OXA) as first-line chemotherapy for locally advanced or metastatic gastric cancer (AGC). Methods: Untreated patients with histologically confirmed AGC who received PTX at 135 mg/m2 and OXA at 85 mg/m2 every 2 weeks were studied. Antitumor activity was assessed by imaging and toxicities were evaluated. Results: Thirty-nine (39) patients were enrolled. With 9.83 months median time of follow-up, 1 year OS rate was 42.0%. Complete response, partial response, stable disease and progressive disease was 2.6, 66.7, 17.9 and 12.0% respectively, the overall response rate was 69.2%. The mPFS was 8.5 months and the mOS 14.4 months. Grade 3/4 of toxicities included neutropenia (38.5%), febrile neutropenia (20.5%), vomiting (7.7%) and hypertransaminasemia (7.7%). Grade 2 peripheral neuropathy occurred in 33.3% patients. Conclusions: The combination of PTX combined with OXA is an active and safe regime for AGC and has a high overall response rate. [ABSTRACT FROM AUTHOR]

Long non-coding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. It can serve as key co-activators of proteins involved in transcriptional regulation. Studies have found that white and brown adipocytes both originate from the mesoderm. However, it remains unclear whether lncRNAs function during adipogenesis or in energy metabolism in brown adipose tissue (BAT) and white adipose tissue (WAT). In this study, we used lncRNA microarray technology to evaluate differences in the lncRNA expression profiles of WAT and BAT. We observed 735 up-regulated and 877 down-regulated lncRNAs (fold change >4.0). To reveal the potential functions of these lncRNAs, we applied GO and pathway analyses to study the differentially expressed lncRNAs. We found that AK142386 and AK133540 may affect adipogenesis and metabolism. Our data indicate that AK142386 and AK133540 may be involved in BAT and WAT development through their target genes Hoxa3 and Acad10. Together, we have identified numerous lncRNAs and these lncRNAs can potentially serve as a required component for proper adipogenesis. [ABSTRACT FROM AUTHOR]

Nanorod-like CuS and Cu2S have been fabricated by a hydrothermal approach without using any surfactant and template. The electrochemical behavior of CuS and Cu2S nanorod anodes for lithium-ion batteries reveal that they exhibit stable lithium-ion insertion/extraction reversibility and outstanding rate capability. Both of the electrodes exhibit excellent capacity retentions irrespective of the rate used, even at a high current density of 3200 mA g−1. More than 370 mAh g−1 can be retained for the CuS electrode and 260 mAh g−1 for the Cu2S electrode at the high current rate. After 100 cycles at 100 mA g−1, the obtained CuS and Cu2S electrodes show discharge capacities of 472 and 313 mAh g−1 with retentions of 92 % and 96 %, respectively. Together with the simplicity of fabrication and good electrochemical properties, CuS and Cu2S nanorods are promising anode materials for practical use the next-generation lithium-ion batteries. [ABSTRACT FROM AUTHOR]

We previously showed that the Arf1-mediated lipolysis pathway sustains stem cells and cancer stem cells (CSCs); its ablation resulted in necrosis of stem cells and CSCs, which further triggers a systemic antitumor immune response. Here we show that knocking down Arf1 in intestinal stem cells (ISCs) causes metabolic stress, which promotes the expression and translocation of ISC-produced damage-associated molecular patterns (DAMPs; Pretaporter [Prtp] and calreticulin [Calr]). DAMPs regulate macroglobulin complement-related (Mcr) expression and secretion. The secreted Mcr influences the expression and localization of enterocyte (EC)-produced Draper (Drpr) and LRP1 receptors (pattern recognition receptors [PRRs]) to activate autophagy in ECs for ATP production. The secreted ATP possibly feeds back to kill ISCs by activating inflammasome-like pyroptosis. We identify an evolutionarily conserved pathway that sustains stem cells and CSCs, and its ablation results in an immunogenic cascade that promotes death of stem cells and CSCs as well as antitumor immunity. [Display omitted] • Knocking down Arf1 results in stem cell death through a sterile immunity-like pathway • Knocking down Arf1 in intestinal stem cells induces expression of Prtp and Calr • Prtp and Calr induce expression of Drpr and LRP1 in ECs via Mcr to produce ATP • ATP kills ISCs by activating inflammasome-like pyroptosis Aggarwal et al. show that disruption of Arf1-mediated lipolysis results in stem cell death through a sterile immunity-like pathway in adult Drosophila. They identify an evolutionarily conserved pathway that specifically sustains stem cells and cancer stem cells (CSCs), and its ablation results in an immunogenic cascade that promotes death of stem cells and CSCs as well as antitumor immunity. [ABSTRACT FROM AUTHOR]

Obesity is associated with a low-grade inflammation of white adipose tissue, which can subsequently lead to insulin resistance, impaired glucose tolerance, and even diabetes. MicroRNAs (miRNAs) have been implicated as negative regulators controlling diverse biological processes at the level of post-transcriptional repression. miR-146b is an intergenic miRNA that can regulate the inflammatory process by attenuating cytokine signaling via the nuclear factor-κB pathway. In this study, we focused on investigating the expression of miR-146b in mature human adipocytes and their response to proinflammatory cytokines. Our results showed that miR-146b was highly expressed in the mature adipocytes. The mature human adipocytes responded to proinflammatory cytokines ( TNF-α and IL-6) by highly increasing the expression of miR-146b. We cloned and identified a potential promoter of the transcriptional regulation of miR-146b. Interestingly, a fragment about 950-bp length upstream sequences of miR-146b had apparent transcription activity. In addition, the increase in miR-146b promoter activity by TNF-α and IL-6 was also effectively elevated. Our results indicated that a novel role for miR-146b in adipose tissue inflammation and miR-146b may be an important mediator in the process of obesity complications via its own transcription mechanism. [ABSTRACT FROM AUTHOR]

Fatty acid-binding protein 3 (FABP3) is a low molecular weight protein with distinct tissue distribution, which may play an important role in fatty acid transport, cell growth, cellular signaling, and gene transcription. We have previously shown FABP3 was more highly expressed in myocardium with ventricular septal defects than in normal myocardium and furthermore, that overexpression of FABP3 causes mitochondrial dysfunction and induces apoptosis in the P19 mouse teratocarcinoma cell line (P19), which is a suitable model for the investigation of cardiac differentiation at the molecular and functional levels. α-Lipoic acid (α-LA), a natural dithiol compound with antioxidant properties, has been reported to protect mitochondrial function in cells. In this study, we established an FABP3-overexpressing P19 cell line for the investigation of the impact of α-LA on mitochondrial impairment and apoptosis in these cells. Mitochondrial morphology was evaluated by transmission electron microscopy, while the effects of α-LA on reactive oxygen species (ROS) production, mitochondrial membrane potential (MMP), intracellular ATP content and the amount of mitochondrial DNA were analyzed by flow cytometry, a commercially available assay and quantitative real-time PCR, respectively. The results revealed that α-LA ameliorated mitochondrial deformation and decreased intracellular ROS production. Furthermore, the MMP, intracellular ATP synthesis and the amount of mitochondrial DNA were also increased. Most significantly, α-LA was shown to reverse apoptosis. Collectively, our results indicate that abnormalities in FABP3 expression contribute to mitochondrial dysfunction and apoptosis, and that α-LA represents a suitable candidate for development as a treatment for apoptosis-related congenital cardiac malformations. [ABSTRACT FROM AUTHOR]

Accumulating evidence suggests that microRNAs (miRNAs) play an important role in regulating the pathways in adipose tissue that control processes such as adipogenesis, insulin resistance, and inflammation. MiR-143 is a well-characterized miRNA involved in adipogenesis and may be involved in regulating insulin resistance. Free fatty acids (FFAs) and adipokines, such as tumor necrosis factor-α (TNF-α), leptin, resistin, and interleukin-6 (IL-6), have already been identified as main regulators of obesity and insulin sensitivity. Therefore, we studied the effects of these inflammatory cytokines on the expression of miR-143. FFAs, resistin, and leptin downregulated miR-143 expression in human adipocytes, whereas TNF-α and IL-6 had little effect on miR-143 expression. These results suggest that the expression of miR-143 is affected by a variety of factors that are related to insulin sensitivity. Therefore, miR-143 may be an important mediator in the development of obesity-related insulin resistance. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are short non-coding RNAs that are involved in post-transcriptional regulation of gene expression. Hsa-miR-26b is an intronic miRNA located in the intron of CTDSP1 (carboxy-terminal domain, RNA polymerase II, polypeptide A, small phosphatase 1). In the present study, the expression of hsa-miR-26b was examined during human preadipocyte differentiation. 15 days after induction of differentiation, mature human adipocytes were treated with adipokines. Hsa-miR-26b was differentially expressed during human preadipocyte differentiation. Tumor necrosis factor-α (TNF-α), leptin and resistin, but not interleukin-6, caused downregulation of hsa-miR-26b expression in adipocytes. These results suggest that the expression of hsa-miR-26b is affected by TNF-α, leptin and resistin and that hsa-miR-26b may be an important mediator in regulating the obesity-related insulin sensitivity and inflammatory responses. [ABSTRACT FROM AUTHOR]

Objective: This study evaluated the efficacy and safety of adjuvant intraperitoneal perfusion chemotherapy (IPC) in resectable gastric cancer through retrospective analysis. Methods: Three hundred and sixty T2-4bN0-3M0 resectable gastric cancer patients were included in this study. One hundred and eighty-four patients used systemic chemotherapy combined with IPC (IP+ group) and 176 systemic chemotherapy only (IP- group). Results: With a median of 49.9 months of follow-up, the 5-year overall survival in IP+ patients was significantly better than in IP- patients (60.4 vs. 42.9%; p = 0.001), and the average progression-free survival in IP+ patients was significantly longer than in IP- patients (60.5 vs. 46.2 months; p = 0.001). Relapse rates of peritoneal carcinomatosis, celiac lymph node and hepatic metastasis in the IP+ patients were significantly lower than in the IP- patients. Patients with curative resection, a histological type other than mucinous adenocarcinoma and signet ring cell carcinoma, low and undifferentiated tumor grade, lymph node metastasis, and T3 and T4a benefited from adjuvant IPC. The toxicities were the same except for more patients with leukopenia in the IP+ group (p = 0.001). The number of cycles of IPC and the time of IPC start after surgery had an impact on overall and disease-free survival. Conclusion: Adjuvant IPC for resectable gastric cancer gave encouraging results and large multicenter prospective randomized controlled studies are warranted. Copyright © 2011 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Wizened buds are frequently observed in pear (Pyrus spp.) trees, which greatly reduces the yield. However, little is known about the mechanism of wizened bud formation. Here, we analyzed physiological and transcriptomic differences between normal buds and wizened buds of '710' pear trees. The results indicated that the sorbitol and boron (B) contents, during bud differentiation, were significantly reduced in wizened buds. The microscopic observation and transcriptome analysis revealed that the collapse of the organ structure and cell wall loosening process may have a close relation with wizened bud formation. Moreover, reduced transcript levels of PpyMYB39.1 and its downstream genes (PpyHT1, PpyHT2, PpyPMEI1 and PpyPMEI2) were found in wizened buds. However, the transcript levels of pentose and glucuronate interconversion pathway genes (PpyPME3, PpyPL18.1, PpyPL18.2, PpyPG1 and PpyPG2) and the concentration of pectin-degradation-related enzymes were increased in wizened buds. Correspondingly, the pectin concentration was significantly reduced in wizened buds. Taken together, PpyMYB39.1 may promote pectin degradation and decrease carbohydrate transport by regulating its downstream genes and is supposed to play a vital role in the wizened bud formation resulting from the cell wall loosening process. Our study provides fundamental insights into wizened bud formation and strategies to reduce the wizened bud occurrence in pear trees. [ABSTRACT FROM AUTHOR]

The goal of this work was to investigate the molecular profiles and metastasis markers in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. PTPRT is significantly associated with metastasis of GC, suggesting its predictive role in metastasis of GC. Patients carrying BRCA2 mutations tend not to metastasize, which may be related to their sensitivity to chemotherapy. Mutations in MACF1, CDC27, HMCN1, CDH1 and PDZD2 were moderately enriched in peritoneal metastasis (PM) samples. Furthermore, we found two genomic regions (1p36.21 and Xq26.3) were associated with PM of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (P = 0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies. [ABSTRACT FROM AUTHOR]

Obesity results from numerous, interacting genetic, behavioral, and physiological factors. Adipogenesis is partially regulated by several adipocyte-selective microRNAs (miRNAs) and transcription factors that regulate proliferation and differentiation of human adipose-derived mesenchymal stem cells (hMSCs-Ad). In this study, we examined the roles of adipocyte-selective miRNAs in the differentiation of hMSCs-Ad to adipocytes. Results showed that the levels of miR-148a, miR-26b, miR-30, and miR-199a increased in differentiating hMSCs-Ad. Among these miRNAs, miR-148a exhibited significant effects on increasing PPRE luciferase activity (it represents PPAR-dependent transcription, a major factor in adipogenesis) than others. Furthermore, miR-148a expression levels increased in adipose tissues from obese people and mice fed high-fat diet. miR-148a acted by suppressing its target gene, Wnt1, an endogenous inhibitor of adipogenesis. Ectopic expression of miR-148a accelerated differentiation and partially rescued Wnt1-mediated inhibition of adipogenesis. Knockdown of miR-148a also inhibited adipogenesis. Analysis of the upstream region of miR-148a locus identified a 3 kb region containing a functional cAMP-response element-binding protein (CREB) required for miR-148a expression in hMSCs-Ad. The results suggest that miR-148a is a biomarker of obesity in human subjects and mouse model, which represents a CREB-modulated miRNA that acts to repress Wnt1, thereby promoting adipocyte differentiation. [ABSTRACT FROM AUTHOR]