Pindel-TD:A Tandem Duplication Detector Based on A Pattern Growth Approach

Tandem duplication(TD)is a major type of structural variations(SVs)that plays an important role in novel gene formation and human diseases.However,TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational signals.Herein,we developed a TD detection module for the Pindel tool,referred to as Pindel-TD,based on a TD-specific pattern growth approach.Pindel-TD is capable of detecting TDs with a wide size range at single nucleotide resolution.Using simulated and real read data from HG002,we demonstrated that Pindel-TD outperforms other leading methods in terms of precision,recall,F1-score,and robustness.Furthermore,by applying Pindel-TD to data generated from the K562 cancer cell line,we identified a TD located at the seventh exon of SAGE1,providing an explanation for its high expression.Pindel-TD is available for non-commercial use at https://github.com/xjtu-omics/pindel.

Quantifying the natural growth rate of hepatocellular carcinoma:A real-world retrospective study in southwestern China

BACKGROUND In recent years,approximately half of the newly diagnosed cases and mortalities attributed to hepatocellular carcinoma(HCC)have been reported in China.Despite the high incidence of HCC,there remains a paucity of data regarding the natural growth pattern and the determination of optimal surveillance intervals specific to the Chinese population.AIM To quantify the natural tumor growth pattern of HCC in regional China.METHODS A retrospective analysis was performed on patients from a single institution in Southwest China who had undergone two or more serial dynamic computed tomography or magnetic resonance imaging scans between 2014 and 2020,without having received any anti-cancer therapy.Tumor growth was assessed using tumor volume doubling time(TVDT)and tumor growth rate(TGR),with volumes measured manually by experienced radiologists.Simple univariate linear regression and descriptive analysis were applied to explore associations between growth rates and clinical factors.RESULTS This study identifies the median TVDT for HCC as 163.4 d,interquartile range(IQR)72.1 to 302.3 d,with a daily TGR of 0.42%(IQR 0.206%-0.97%).HCC growth patterns reveal that about one-third of tumors grow indolently with TVDT exceeding 270 d,another one-third of tumors exhibit rapid growth with TVDT under 90 d,and the remaining tumors show intermediate growth rates,with TVDT ranging between 3 to 9 months.CONCLUSION The identified TGRs support biannual surveillance and follow-up for HCC patients in certain regions of China.Given the observed heterogeneity in HCC growth,further investigation is warranted.

基于FP-Growth算法的运毒嫌疑车辆智能推荐研究

毒品运输是毒品犯罪的重要环节,虽然毒品运输的手段越来越多样化,但公路运输仍然是主要的运输方式之一,而运毒人员有着各自经典的运毒模式。文中对运毒模式进行特征挖掘,发现存在前后车伴随的规律,根据实际业务中前后车行为以半小时为时间间隔导向,建模时选择PostgreSQL数据库。在数据库中建立过往车辆前半小时中间表、后半小时中间表、中间跨度表,运用人工智能数据挖掘技术实现从大量的通行车辆中抽取车辆伴随信息,采用FP-Growth算法挖掘频繁项集,查找高频出现车牌号,通过设定阈值并找到对应的关联规则,经过缉毒民警提供的黑名单进行过滤并排序,最后进行车辆嫌疑度的推荐,为民警拦截嫌疑车辆提供支持,能够在一定程度上提高对嫌疑车辆排查的针对性、准确性和有效性。

Mako:A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.However,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy.As a result,there has been limited progress for CSV discovery compared with simple structural variants.Here,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read sequencing.Specifically,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined models.Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms.Notably,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,respectively.Moreover,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed duplication.Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs.Mako is publicly available at https://github.com/xjtu-omics/Mako.

Hybrid Reliability Parameter Selection Method Based on Text Mining, Frequent Pattern Growth Algorithm and Fuzzy Bayesian Network

Reliability parameter selection is very important in the period of equipment project design and demonstration. In this paper, the problem in selecting the reliability parameters and their number is proposed. In order to solve this problem, the thought of text mining is used to extract the feature and curtail feature sets from text data firstly, and frequent pattern tree （FPT） of the text data is constructed to reason frequent item-set between the key factors by frequent patter growth （FPC） algorithm. Then on the basis of fuzzy Bayesian network （FBN） and sample distribution, this paper fuzzifies the key attributes, which forms associated relationship in frequent item-sets and their main parameters, eliminates the subjective influence factors and obtains condition mutual information and maximum weight directed tree among all the attribute variables. Furthermore, the hybrid model is established by reason fuzzy prior probability and contingent probability and concluding parameter learning method. Finally, the example indicates the model is believable and effective.

Spatial patterns of urban land use growth in Beijing

By using digitized land use maps of Beijing in 1982, 1992 and 1997 and employing GIS spatial analysis techniques, this paper conducts an empirical study on the spatial differentiation and spatial patterns of urban land use growth in Beijing in the period of 1982–1997. It is observed that urban land use growth in Beijing went beyond the control of urban planning, in terms of the extraordinary high growth rate and undesired spatial pattern. The rate of urban expansion after 1982, which was predominated by growth of industrial land, was extraordinary high compared to its historical period. While its growth centers have been actively shifting toward the northern part, rather than toward the southern and eastern parts as designated by the latest General Plan (1991–2010) of Beijing, its spatial pattern of urban land use growth in general was in distinct concentric sprawl, which seriously violated the General Plan of Beijing.

Study on Clonal Growth Pattern of Sabina vulgaris in Mu Us Sandland

The clonal growth pattern of Sabina vulgaris, a coniferous clonal plant in Mu Us sandland, Inner Mongolia Autonomous Region was surveyed. The results showed that with the stolon extending, internode length and branching angle decreased, the branching intensity increased gradually within the 3 m range from the edge of the shrub to its center along the stolon. Internode length, branching intensity and branching angle were 5.9 cm, 4.4 and 55.3°in the shrub, and 1.6 cm, 13.7 and 38.3°at the edge of the shrub, respectively. The clonal architecture exhibited plasticity. The internode length, branching intensity and ramet length changed with an exponential model with extention of the stolon. The stolon of S. vulgaris was monopodial branching, and each ramet should possess more than 3 adventitious roots. Ramets could take on the phenomenon of 搒elf-thinning?with clonal growth. There was a prior grade in allocation of the nutrients gained from heterogeneous space. The clonal architecture of S. vulgaris was the 搈ixed?type.

Growth Pattern and Its Indication of Spheroidal Nano-Micro Crystal Aggregates of Pyrite in the Baiyunpu Pb-Zn Polymetallic Deposit, Central Hunan

The Baiyunpu deposit lies in the southwest plunging Dachengshan anticline in central Hunan, which is a large Pb-Zn polymetallic deposit. The orebodies were surrounded by the Qiziqiao Formation limestone in the Middle Devonian, and its geological occurrence is consistent with the wall rocks. A large number of spheroidal pyrite aggregates are found unevenly distributed in the ores. The spheroidal aggregates are made up of kernels and concentric rings. The kernels are composed of approximately epigranular pyrite nanocrystals, while the rings are composed of accumulated pyrite microcrystals growing along the radial direction. The spheroidal pyrite aggregate and its outer zones can be divided into five areas（A–E）. The results of electron probe micro analysis（EPMA） show that from the zone A1 to B, Co/Ni 〈1, the sum of Co and Ni is 0.08%–0.26%, S/Fe increases from 2.06 to 2.15. While from the zone C to E, Ni cannot be detected and S/Fe decreases from 2.22 to 2.08. Powder X-ray diffraction（XRD） analysis in the micro zone shows obvious crystalline characteristics in the aggregates. Moving from the inside outwards, the maximum diffraction peak intensity of the（111） and（220） crystal planes of pyrite increases, and the crystallinity improves. The degree of change in the（111） plane is the most prominent. Considering the theory of crystal growth along with the geologic features of the depositional environment where the spheroidal pyrite aggregates developed, we confirm that the spheroidal aggregates are the result of nano-micro crystalline gathering and growth occurring by the following sequence of processes：nano-crystalline nucleation and growth, gathering into a ball, oriented growth of microcrystals, continuous accumulation, and adjustment of grain boundaries. The formation of the spheroidal pyrite aggregates in the late Qiziqiao Formation of the Middle Devonian occurred in a neutral to weak alkaline and reductive sedimentary environment in the normal oxygen-rich shallowwater carbonate platform edge. The variations in the S/Fe ratio and crystallisation characteristics indicate that during pyrite crystal growth, the sulphur fugacity was high locally and rose constantly, the degree of supersaturation decreased locally and the growth environment was stable relatively.

Growth pattern of reed in Caogang Lake,Huanghuaihai Plain,China

The researches about reed growth were mainly concentrated on seasonal dynamics, investigation of reed resource, and comparison of different ecotypes of reed. By means of fractal geometric theory of non linear science, the fractal character of growth pattern of reed, for the purpose of quantitatively exploring the mechanism of reed growth was studied. The way to calculate fractal dimension of reed growth is box dimension (BD) and information dimension (ID). The results showed that the difference between two samplings in May and those among three samplings in June and later were not remarkable for both BD or ID. It was noted that the difference between samplings in and after May is significant. It was demonstrated that the fractal dimension of size distribution of reed ranged from 0 6235 to 0 8761 The distribution pattern could be statistically divided as two significant periods: the size of reed is quite well distributed at the beginning of reed growth (fractal dimension>0 8), but is irregular in the middle and later growth season (fractal dimension<0 7). These results are benefit to reach the goal of rational use of reed resources and to protect the biodiversity in wetland ecosystem.

Clinical implications and mechanism of histopathological growth pattern in colorectal cancer liver metastases

Liver is the most common site of metastases of colorectal cancer,and liver metastases present with distinct histopathological growth patterns(HGPs),including desmoplastic,pushing and replacement HGPs and two rare HGPs.HGP is a miniature of tumor-host reaction and reflects tumor biology and pathological features as well as host immune dynamics.Many studies have revealed the association of HGPs with carcinogenesis,angiogenesis,and clinical outcomes and indicates HGP functions as bond between microscopic characteristics and clinical implications.These findings make HGP a candidate marker in risk stratification and guiding treatment decision-making,and a target of imaging observation for patient screening.Of note,it is crucial to determine the underlying mechanism shaping HGP,for instance,immune infiltration and extracellular matrix remodeling in desmoplastic HGP,and aggressive characteristics and special vascularization in replacement HGP(rHGP).We highlight the importance of aggressive features,vascularization,host immune and organ structure in formation of HGP,hence propose a novel"advance under camouflage"hypothesis to explain the formation of rHGP.

Histologic features and genomic alterations of primary colorectal adenocarcinoma predict growth patterns of liver metastasis

BACKGROUND Different histological growth patterns(HGPs)of colorectal carcinoma(CRC)liver metastasis are associated with patients’prognosis and response to antiangiogenic therapy.However,the relationship between HGPs of liver metastasis and clinicopathological and genomic characteristics of primary cancer has not been well established.AIM To assess whether certain clinicopathological and genomic features of primary CRC could predict the HGPs of liver metastasis.METHODS A total of 29 patients with paired resections of both primary CRC and liver metastasis were divided into two groups:A(15 cases with desmoplastic liver metastasis)and B(14 cases with replacement liver metastasis).Clinical information was obtained from patients’charts.Mismatch repair proteins,BRAFV600E,and PD-L1 were evaluated by immunohistochemistry.Five cases were selected randomly from each group for whole exome sequencing(WES)analysis.RESULTS In the primary tumor,expanding growth pattern,low tumor budding score(TBS),and Crohn’s disease-like response(CDR)were associated with desmoplastic liver metastasis and better overall survival,whereas infiltrating growth pattern alone of primary carcinoma could predict the replacement liver metastasis and worse overall survival(P<0.05).On WES analysis,primary carcinoma with desmoplastic liver metastasis showed mutations in APC(4/5);TP53(3/5);KRAS,PIK3CA,and FAT4(2/5);BRCA-1,BRCA2,BRAF,and DNAH5(1/5),whereas primary carcinoma with replacement liver metastasis showed mutations in APC and TP53(3/5);KRAS,FAT4,DNH5,SMAD,ERBB2,ERBB3,LRP1,and SDK1(1/5).CONCLUSION The HGPs,TBS,and CDR of primary CRC as well as the presence of specific genetic mutations such as those in PIK3CA could be used to predict the HGPs of liver metastasis,response to therapy,and patients’prognosis.

Can Emerging Economies Catch-up Sustainably？-An Analysis of BRICS＇ Economic Growth Pattern

The BRICS （Brazil, Russia, India, China and South Africa） and other emerging economies have become a driving global force for the past twenty years. However, their growth patterns are obsolete, impeding the quality and competitiveness of their economic growth, while simultaneously threatening the sustainability of their economic convergence with developed nations. Transforming the domestic growth pattern-the solution to the middle-income trap-has therefore become a key priority for each of these economies. This paper presents a comparative analysis of how to transform the pattern of economic growth in BRICS and achieve sustainable economic convergence with a comparative analysis of the pattern of economic growth and problems among BRICS countries.

Age, growth, reproductive biology, color pattern, and ontogenetic divergence of two closely related rock?shes (Sebastes koreanus and S. nudus) off the coasts of the Shandong Peninsula, China

The live-bearing genus Sebastes is renowned for its outstanding species richness and color diversity,and its speciation has been a point of interest.This study investigated the age,growth,reproductive biology,color pattern and ontogenetic divergence of a pair of closely related rockfishes from the coasts of the Shandong Peninsula,namely,Sebastes koreanus(n=879)and S.nudus(n=257).Marginal increment analysis of sectioned otoliths showed that annulus formation occurred once a year between June and July in both species.The sex-pooled growth curves of S.nudus and 3 populations of S.koreanus differed significantly from each other.No apparent latitudinal cline in growth parameters was found in S.koreanus.For both species,the peak parturition periods were from April to May,and the peak copulation periods were from November to December.S.nudus has a highly variable and conspicuous color pattern while S.koreanus has a stable and dull color pattem.This difference,together with the overlapping distribution and the close relationship,make S.koreanus and S.nudus an ideal model to investigate the color-driven speciation of the Sebastes.We confirmed that S.nudus changes its body color with age and season and fully expresses the carotenoid-based nuptial coloration when the fish reaches first maturity.Moreover,our comparisons of morphological traits that are likely related to survival and quality of these fishes suggested that S.nudus may suffer higher predation risk and foraging difficulty beginning at age 3.In light of the ontogenetic development of the color pattern in S.nudus,we suggested that the full expression of nuptial coloration most likely triggers the strong selective pressure to enhance swimming performance,anti-predator defense and foraging capacity of S.nudus through predator-prey interactions.By understanding all these details,we further inferred a hypothesis that both color pattem and bathymetric segregation play key roles in facilitating the speciation of demersal rockfishes.

Growth Pattern in Children with Juvenile Idiopathic Arthritis: A Retrospective Study

Aim of this study is to assess growth pattern in children with juvenile idiopathic arthritis (JIA) and factors associated with growth retardation. Methods: A retrospective chart review of all cases of JIA following up at Pediatric Department of King Abdulaziz University Hospital, between July 2000 to July 2016. Demographic, clinical and biological data were collected and analyzed as risk factor for growth retardation. These included age, gender, age at diagnosis, disease duration, type of JIA, the presence of uveitis, rheumatoid factor (RF) positivity, antinuclear antibody (ANA) titer and treatment. Growth pattern was assessed as the percentile for height-for-age, weight-for-age and weight-for-height in reference to the Growth Chart for Saudi Children and Adolescents. Change in percentile rank was divided into 3 categories: regression (a drop of ≥1 percentile);stable (uphold of the same percentile);and progression (change for a superior percentile). Results: A total 78 children were eligible, 52.6% females, mean ± SD age = 9.94 ± 4.92 years, and age at diagnosis = 7.44 ± 4.52 years, mean ± SD [range] disease duration = 2.93 ± 2.70 [6 months;15 years]. The most frequent types of JIA were systemic (33.3%), oligoarticular (30.8%) and polyarticular negative RF (26.9%). Other parameters included positive ANA in 41.0%, positive RF in 7.7% and uveitis in 9.0%. The most frequent treatment was methotrexate (59.0%), followed by biological therapy (47.4%), non-steroid anti-inflammatory drugs (43.6%) and prednisolone (33.3%). Growth data were available for 67 (85.9%) children, and assessments showed 36% cases of break of the growth curve in both height-for-age and weight-for-age percentiles and 31% in weight-for-height percentiles. In all three parameters, there were shifts towards lower percentiles from time of diagnosis to last follow-up, in both males and females. Correlation and regression analysis showed low age at diagnosis and disease duration to be significant predictors for growth retardation severity. Conclusion: One in three children with JIA has growth retardation, the severity of which is predicted by low age at disease onset and long disease duration.

The Growth Pattern of <i>Chamaecyparis obtuse</i>Stand along Longevity in Gyeongnam Province, South Korea

Tree growth is affected by environmental factors, climate condition and tree age. The objective of this study was to evaluate the growth patterns of Chamaecyparis obtusa (C. obtusa) stand in the Gyeongnam province. Data was collected from two cities and one county by using sample quadrats of 20 * 20 m. A total of 11 quadrats were used to collect tree height, diameter at the breast height (DBH), annual growth rings and soil data. The data analysis of soil moisture content, pH, organic matter (%), EC (cmol + /kg of soil), and available phosphorous was conducted. Growth ring was analyzed by using computer based software and the ages of the trees were identified. Average growth of height and DBH was computed from the surveyed data and annual growth of each tree was assessed by computer based reading of annual growth rings. The results of the study revealed that tree growth showed a reducing trend along the longevity. It was identified that soil pH, age, variation in annual average temperature, and altitude were the main factors related with growth of C. obtusa trees along the life of the stand.

The evaluation of the growth pattern of coal-production in Jiangsu Province and suggestions for its sound development

Using Cobb-Douglas production function and Solow Residual, this study establishes a discriminant index to measure the intensive index of coal-production at the section-level, so as to analyze the transfer trend of the growth pattern of Jiangsu＇s coal-production since 1990s. The research shows that the transition of coal production in Jiangsu Province has mainly experienced three phases, which are the quick transition phase from extensive growth to intensive growth （from 1990 to 1994）, the fluctuation phase （from 1995 to 1999）, and the transition back phase from intensive growth to extensive growth （from 2000 to 2003）. On the whole, the coal production in Jiangsu Province nowadays is still featured by extensive growth pattern and largely dependent upon capital inputs. Finally, from the aspect of the technology progress, improving the qualities of labor, changing product structures and improving enterprise management, this study puts forward suggestions on how to transfer the growth pattern of Jiangsu＇s coal-production into intensive type.

Three-dimensional interfacial wave theory of dendritic growth: (Ⅱ). non-axi-symmetric global wave modes and selection criterion of pattern formation

This paper is ttie continuation of part （Ⅰ）, which completes the derivations of the 3D global wave modes solutions, yields the stability criterion and, on the basis of the results obtained, demonstrates the selection criterion of pattern formation.

AGE STRUCTURE AND SPATIAL PATTERN OF OLD-GROWTH KOREAN PINE FOREST IN XIAOXING'ANLING MOUNTAIN

Spatial pattern of trees, basal stem increment and height were examined in a 5.0 ha mixed deciduous/ Pinus koraiensis forest from October in 1984 to May in 1987. Conclusions arc as following: 1. Analysis of the age-structure of the korcan pine forest shows that it is different from general steady-state forest type. The lack of saplings and individuals in small-diameter class clearly indicates that regeneration is not continuous. Continuous regeneration depends on thinning of the canopy to form a gap. Similar-aged korcan pine seedings grow in these gaps. 2. The horizontal structure of the korcan pine is a mosaic of more or less even-aged groups of trees. The mosaic is a result of korcan pine by regeneration strategy. The aggregations of korcan pine of different ages overlaps to form a continuous population generation. As a results, the population is maintained in steady state.

Resource constraint,sustainable economic growth pattern and transformation of economic system in China

Over the past 20 years, China has made spectacular achievements in economic growth as well as in thetransformation of economic growth pattern. Industrial structure is being updated, and technology is playing a more andmore important role in economic development. The energy and resource consumption in many industries and enterprisesare reducing. However, we should realize that there are still many problems in changing the economic growth pattern,such as high input, high consumption, high discharge, inharmony, recycling difficulty, and low efficiency, which havegreatly impaired and restrict Chinese economic development. Therefore, the fundamental change of the economic growthpattern is inevitable. Based on the analysis on the status quo and the exploit of resources, this paper suggests that thetransformation from unsustainable to sustainable growth is the only choice in changing the economic growth pattern. Inaddition, the transformation should not completely rely on the fundamental effects of market mechanism. We should makefull use of the power of governments to speed up the transformation of economic system.

A numerical study on pattern selection in crystal growth by using anisotropic lattice Boltzmann-phase field method

Pattern selection during crystal growth is studied by using the anisotropic lattice Boltzmann-phase field model.In the model,the phase transition,melt flows,and heat transfer are coupled and mathematically described by using the lattice Boltzmann(LB)scheme.The anisotropic streaming-relaxation operation fitting into the LB framework is implemented to model interface advancing with various preferred orientations.Crystal pattern evolutions are then numerically investigated in the conditions of with and without melt flows.It is found that melt flows can significantly influence heat transfer,crystal growth behavior,and phase distributions.The crystal morphological transition from dendrite,seaweed to cauliflower-like patterns occurs with the increase of undercoolings.The interface normal angles and curvature distributions are proposed to quantitatively characterize crystal patterns.The results demonstrate that the distributions are corresponding to crystal morphological features,and they can be therefore used to describe the evolution of crystal patterns in a quantitative way.