Multi-strategy improved parallel antlion algorithm and applied to feature selection

Antlion Optimization Algorithm (ALO) is a promising bionic swarm intelligence algorithm, which has good robustness and convergence, but there are still many areas to be improved and modified. Aiming at the fact that the ALO algorithm is more likely to fall into the local optimum, proposes three strategies to improve the classic ALO algorithm in this paper. First of all, we adopt a parallel idea in the algorithm, through the communication strategy between groups based on Quantum-Behaved to enhance the diversity of the population. Secondly, we adopted two strategies, Opposition Learning, and Gaussian Mutation, to balance the performance of exploration and exploitation during the execution of the algorithm, further formed the MSALO algorithm. The CEC2013 Benchmark function is selected as the standard, and MSALO is compared with other intelligent optimization algorithms. The experimental results show that MSALO has stronger optimization performance compared with other intelligent algorithms. Besides, we applied MSALO to the practical scenarios of feature selection, and use SVM classifiers as training evaluators to improve the accuracy of feature extraction from high-dimensional data.

[The value of CXorf67 and H3K27me3 for diagnosing germ cell tumors in central nervous system]

Objective: To investigate immunohistochemical patterns of CXorf67 and H3K27me3 proteins in central nervous system germ cell tumors (GCTs) and to assess their values in both diagnosis and differential diagnosis. Methods: A total of 370 cases of central nervous system GCTs were collected from 2013 to 2020 at Huashan Hospital of Fudan University, Shanghai, China. The expression of CXorf67, H3K27me3 and commonly-used GCT markers including OCT4, PLAP, CD117, D2-40, and CD30 by immunohistochemistry (EnVision method) was examined in different subtypes of central nervous system GCTs. The sensitivity and specificity of each marker were compared by contingency table and area under receiver operating characteristic (ROC) curve. Results: Of the 370 cases there were 282 males and 88 females with a mean age of 19 years and a median age of 17 years (range, 2-57 years). Among the GCTs with germinoma, the proportions of male patients and the patients with GCT located in sellar region were both higher than those of GCTs without germinoma (P<0.05), respectively. CXorf67 was present in the nuclei of germinoma and normal germ cells, but not in other subtypes of GCT. H3K27me3 was negative in germinoma, but positive in the nuclei of surrounding normal cells and GCTs other than germinoma. In the 283 GCTs with germinoma components, the expression rate of CXorf67 was 90.5% (256/283), but no cases were positive for H3K27me3. There was also an inverse correlation between them (r²=-0.831, P<0.01). The expression rates of PLAP, OCT4, CD117 and D2-40 were 81.2% (231/283), 89.4% (253/283), 73.9% (209/283) and 88.3% (250/283), respectively. In 63 mixed GCTs with germinoma components, the expression rate of CXorf67 was 84.1% (53/63), while all cases were negative for H3K27me3. The expression rates of PLAP, OCT4, CD117 and D2-40 were 79.4% (50/63), 79.4% (50/63), 66.7% (42/63) and 87.3% (55/63), respectively. The 6 markers with largest area under ROC curve in ranking order were H3K27me3, CXorf67, D2-40, OCT4, PLAP and CD117 (P<0.05). Conclusions: CXorf67 and H3K27me3 have high sensitivity and high specificity in diagnosing germinoma. There is a significant inverse correlation between them. Therefore, they can both be used as new specific immunohistochemical markers for the diagnosis of GCTs.

[Association of CYP19A1 gene rs7176005 single nucleotide polymorphism with breast cancer risk and clinicopathologic features of tumor]

Objective: The aim of this study was to investigate the association of the CYP19A1 rs7176005 single nucleotide polymorphism (SNP) with breast cancer risk and with clinicopathologic features of tumors. Methods: This study was conducted by including 138 patients with breast cancer (cancer group), those who diagnosed as primary breast cancer after operation by pathology. There were 293 cases in the group of benign breast disease which was presented as a solid mass by the color ultrasound and pathologically diagnosed as "fibroadenoma or adenosis" (benign breast disease group), the cases were paired with breast cancer patients by age±5 in the same period, and there were 259 cases in the group of healthy control who received routine physical examination during the same period and were paired with breast cancer patients by age±5 without any detection of breast related diseases (healthy control group) at West China hospital between September 2012 and November 2016. The CYP19A1 rs7176005 SNP was detected by a direct sequencing method. Hardy-Weinberg test was used to analyze the genetic balance of the 3 groups. Chi square test was used to compare the distribution of rs7176005 genotypes between the 3 groups, and the differences of clinicopathological features in breast cancer patients carrying different genotypes. Results: The ages of the breast cancer cases, the benign breast disease group and the healthy control group were (44.69±8.09), (42.33±11.44) and (41.92±9.61) years old, respectively. Hardy-Weinberg equilibrium test identified that the composition ratios of alleles C and T in breast cancer group, benign breast disease group and healthy group were not statistically significant (χ(2) values were 0.83, 0.34 and 0.04, respectively, P values were 0.363, 0.561, and 0.852, respectively). All the three groups met the genetic balance, had consistency and could represent the population. Among the 138 cases of breast cancer, the CYP19A1 rs7176005 SNP was significantly associated with the diameter of the tumor (P=0.031). The majority of tumor size was <2 cm in patients who carrying TT and CT genotypes, and the proportion was 75% (12/16) and 58% (40/69), respectively. While those patients with TT genotype were mainly >2 cm and ≤5 cm, and the proportion was 51% (27/53). The distribution of TNM stage among patients with different genotypes was also statistically significant (χ(2)=11.19, P=0.025). The most common stage was Ⅱ in Patients who carrying CC and CT genotypes, and the proportion was 45.3% (24/53) and 52.2% (36/69), respectively. While those patients with TT genotype was mainly in stage Ⅰ and the proportion was 56.3% (9/16). Conclusion: Though the CYP19A1 rs7176005 SNP is not associated with breast cancer development, breast cancer patients with the C allele exhibit a high tumor growth rate and large diameters.

[Relief effect of CT-guided (125)I seed implantation on patients with spinal and paraspinal osteolytic metastatic tumors]

Objective: To evaluate the clinical value of computed tomography (CT)-guided (125)I seed implantation in the treatment of patients with spinal and/or paraspinal osteolytic metastatic tumors. Methods: The radiation dose distribution was planned for 27 patients with 35 spinal and paraspinal osteolytic metastatic tumors by a treatment planning system (TPS). CT-guided (125)I seed implantation was carried out in the patients, and the quality of treatment was evaluated based on CT-imaging follow-up. Results: All the 27 patients underwent CT-guided (125)I seed implantation successfully. 12 to 50 (125)I seeds were injected into each spinal or paraspinal metastatic tumor, 39.15 on average, and the specific radioactive activity of the particles ranged from 0.60 to 0.80 mCi, 0.73 mCi on average. The minimal percentage of the dose received by 90% of the target volume (D(90)) of the spinal and paraspinal metastatic tumors ranged from 90 to 165 Gy, 115.03 Gy on average. Among the 27 patients, 21 (77.8%) had partial remission (PR) and 6(22.2%)had stable disease (SD). The Numerical Rating Scale (NRS) scores before implantation and at postoperative 3 and 6 months were 7.81±0.74, 2.04±1.10 and 1.81±0.79, respectively, (P<0.05). The assessment of pain intensity before (125)I seed implantation and at 3 postoperative months showed obvious improvements in the patients evaluated according to the American Spinal Injury Association (ASIA) impairment scale: 12 (44.4%) patients with ASIA grade C were changed to grade D, 3 (11.1%) from grade C to grade E, 8 (29.6%) from grade D to grade E, 3 (11.1%) with a stable grade D, and 1 (3.7%)with a stablegrade C. The Karnovsky performance scale (KPS) scores before treatment and at 3 months and 6 months postoperatively were 66.30±6.88, 85.93±9.31 and 87.91±8.56, respectively (P<0.05). Their local control rate (LCR) at 3 months, 6 months and 1 year postoperatively were 100%, 92.6% and 51.9%, respectively, and the overall survival rates(OSR) were 100%, 92.6% and 55.6%, respectively. Conclusions: CT-guided (125)I seed implantation can significantly relieve local pain, has advantages of less complications and higher local control rate. Therefore, it is a safe, effective and feasible treatment option for patients with spinal and paraspinal osteolytic metastatic tumors.

Note: Pre-pulse characterization of femtosecond laser pulse by filamentation in transparent media

A new method and associating system has been presented to characterize pre-pulses of femtosecond laser using laser filamentation in transparent media. Pre-pluses of the laser system has been measured experimentally and it is in good agreement with the results obtained by third order cross-correlator. This method can be used for fast detection of temporal laser intensity relatively in order to avoid formation of pre-plasmas before laser matter interaction experiments.

First Report of Sweet potato leaf curl Georgia virus Infecting Tall Morning Glory (Ipomoea purpurea) in China

In September 2013, tall morning glory (Ipomoea purpurea) plants showing vein yellowing and leaf curl symptoms typical of a begomovirus infection were observed in Jingzhou, Hubei Province, China. Total nucleic acids were extracted from a symptomatic plant using cetyltrimethylammonium bromide (CTAB). Rolling circle amplification (RCA) was conducted using TempliPhi kit (GE Healthcare) to recover the genome of a putative begomovirus. Digestion of the RCA product with PstI yielded a ~2.8 kbp DNA fragment suggestive of a monomerized begomoviral genome. The fragment was cloned and sequenced and the sequence was deposited in GenBank under accession no. KF769447. SDTv1.0 (species demarcation tool) analysis revealed that the putative begomovirus showed 98.5 and 92.0% nucleotide sequence identity with Sweet potato leaf curl Georgia virus (SPLCGV)-[China:Hebei:2011] (GenBank Accession No. JX448368) and SPLCGV-[US:Geo:16] (AF326775), respectively. The virus contained six ORFs, which encoded proteins showing 96.5 to 100% and 90.6 to 95.6% amino acid sequence identity with their counterparts of SPLCGV-[China:Hebei:2011] and SPLCGV-[US:Geo:16], respectively. Thus, the virus should be considered as an isolate of SPLCGV-[China:Hebei:2011]. Tall glory morning in a nearby field (which covers an area of 3 square kilometers) was surveyed and 70 to 100% of plants were found showing symptoms reminiscent of begomoviral infection. Total nucleic acid was extracted from 13 randomly selected (10 symptomatic and 3 healthy) plants and used as templates for PCR with a pair of specific primers (5'-CGCAGCCTTTCCACACTATC-3'/5'-AAAACAGTTTGGGCTCGGTC-3') designed according to the sequence described above. Positive results were obtained for all of the symptomatic, but none of the healthy-looking tall morning glory plants. SPLCGV (genus Begomovirus, family Geminiviridae) was reported to infect sweet potato (I. batatas) in the United States (4), India (2), and China (3). To our knowledge, this is the first report of SPLCGV infecting tall morning glory in China. Also, it is the first report of a geminivirus in Hubei, a province of central China. Whereas the finding of SPLCGV in sweet potato (3) may be a result of vegetative propagation of this crop, the detection of SPLCGV in tall morning glory, an annual plant, raises the possibility that this virus is transmissible and is spreading in China. References: (1) B. Muhire et al. Arch. Virol. 158:1411, 2013. (2) G. Prasanth and V. Hegde. Plant Dis. 92:311, 2008. (3) Y. Qin et al. Plant Dis. 97:1388, 2013. (4) R. A. Valverde and D. L. Gutierrez. Rev. Mex. Fitopatol. 21:128, 2003.

First Report of Wild tomato mosaic virus Infecting Tobacco (Nicotiana tabacum) in China

Wild tomato mosaic virus (WTMV), a potyvirus, has been reported in Laichau, Vietnam, infecting Solanum torvum (wild tomato) in 2008 (3), and Kanchanaburi, Thailand, infecting Capsicum spp. in 2013 (KF250353). In mid-May 2013, Nicotiana tabacum showing yellowing, mosaic, and/or ringspot symptoms were found in natural tobacco fields of Nanxiong, Guangdong Province, China. Total RNA was extracted from symptomatic leaves and reverse transcribed with M4T (5'-GTTTTCCCAGTCACGAC (T)₁₅-3') as the 3' anchoring primer (1). The cDNA was used as template in a PCR assay using primers M4: 5'-GTTTTCCCAGTCACGAC-3' and Sprimer: 5'-GGXAAYAAYAGYGGXCAZCC-3', which amplifies a region comprising part of the NIb protein gene, the entire coat protein (CP) gene and the 3' nontranslated region (UTR) of a potyvirus (1). A ~1,700-bp product was amplified from the cDNA derived from three of the five diseased plants. The product (KF639967) showed 87% and 84% nucleotide sequence identities with those of WTMV isolates KAN and Laichau, respectively. The CP deduced from the sequence of the product shared 87% and 86% nucleotide and 94% and 93% amino acid sequence identities with those of WTMV isolates KAN and Laichau, respectively. The 3'-UTR of the putative virus shared 93% and 92% nucleotide sequence identities to those of WTMV isolates KAN and Laichau, respectively. Thus, according to the molecular criteria for potyvirus species demarcation (2), the virus we identified should be an isolate of WTMV (isolate GD1). One of the diseased samples was homogenized in 0.1 mol/liter phosphate buffer (pH 7.0) and used to inoculate the potyvirus to healthy, two to four leaf-stage Capsicum annuum L., N. tabacum, and N. benthamiana. The inoculated, as well as mock-treated plants, which were inoculated only with phosphate buffer, were grown in soil under 12 h day/12 h night at 25°C. All inoculated N. tabacum and N. benthamiana plants developed yellowing and mosaic symptoms by 14 days post inoculation (dpi). For N. benthamiana, the symptom became very severe by 21 dpi and some diseased plants died prematurely. About 10% of inoculated C. annuum L. developed very mild veinal chlorosis 18 dpi. Cloning and sequencing experiments showed that all the symptomatic plants tested were WTMV positive, but Cucumber mosaic virus, Tobacco mosaic virus, and Tobacco etch virus negative. To our knowledge, this is the first report of WTMV in China. Also, it is the first report that WTMV infects Nicotiana spp. Although further experiments are needed to definitively attribute the disease observed in the field to WTMV, our results indicate that WTMV, which forms a monophyletic clade with a number of other potyviruses infecting Solanaceae species in phylogenetic analysis, is widely distributed, or is spreading in Southeast Asia. It may pose a threat to Solanaceae species cultivation in this region. References: (1) Chen et al. Arch. Virol. 146:757, 2001. (2) Adams et al. Arch. Virol. 150:459, 2005. (3) Ha et al. Arch. Virol. 153:25, 2008.

Identification and molecular characterization of two begomoviruses from Pouzolzia zeylanica (L.) Benn. exhibiting yellow mosaic symptoms in adjacent regions of China and Vietnam

Two monopartite begomoviruses were isolated from Pouzolzia zeylanica (L.) Benn. plants showing yellow mosaic symptoms in Gaoyao, Guangdong Province, China (GD1) and in Phu Tho, Vietnam (VN), respectively. A comparison of the complete genome sequence of GD1 (2,739 nucleotides [nt]) with VN (2,741 nt) indicated that they shared 86.2 % nt sequence identity. GD1 and VN shared the highest nucleotide sequence identity at 86.7 % and 91.4 % respectively, with isolate TY01 of pouzolzia golden mosaic virus (PGMV-TY01), another begomovirus isolated from P. zeylanica. Phylogenetic analysis revealed that GD1, VN, and PGMV-TY01 were members of a distinct begomovirus clade. Based on the ICTV guidelines for begomoviral species demarcation, GD1 belongs to a new begomovirus species, for which the name Pouzolzia yellow mosaic virus is proposed. Likewise, VN represents a previously unreported strain of PGMV. Recombination analysis predicted that VN was a recombinant between PGMV-TY01 and ageratum yellow vein China virus isolate G13 (AYVCNV-G13), and that PGMV-TY01 and VN were likely the parents of GD1 through recombination with allamanda leaf curl virus isolate G10 (AlLCV-G10), a begomovirus endemic to Guangdong Province of China.

First Report of Tomato yellow leaf curl Kanchanaburi virus Infecting Eggplant in Laos

Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) is a bipartite begomovirus (genus Begomovirus, family Geminiviridae) reported to infect tomato and eggplant in Thailand and Vietnam (1,2). In April 2013, eggplant (Solanum melongena L.) plants exhibiting yellow mosaic symptoms were found in a suburb of Vientiane, Laos. Three symptomatic samples were collected. Total DNA was extracted from leaves by the CTAB method, and used as template for PCR using the degenerate primer pair AV494/CoPR (3). The PCR results suggested that the plants were infected by a begomovirus. The begomoviral genome was amplified by rolling circle amplification (RCA) with TempliPhi kit (GE Healthcare) following the manufacturer's protocol. RCA product was digested with the endonucleases BamH I, EcoR I, Hind III, Kpn I, Pst I, and Xba I, respectively. The fragments about 2.1 kbp (with Pst I digestion) and 1.5 kbp (with Xba I digestion) in size were cloned and sequenced. The sequence of the 2.1-kbp fragment showed similarity with begomovirus DNA-A component. A pair of primers for amplification of the full-length DNA-A, AF (5'-CTTCATCGTTTCTCAGCATCAT-3') and AR (5'-CACTTGCACACGATCTCTAAGA-3') were designed from the 2.1-kbp sequence. The full-length DNA-A was 2,752 nucleotides and encoded six putative ORFs (GenBank Accession No. KF218820). The sequence of the 1.5-kbp fragment shared similarity with begomoviruses DNA-B. The begomoviral circular DNA-B was amplified using the pair of primers BF (5'-GTAACAGCCGAAGTGCACG-3') and BR (5'-AATGGAGAGACACCAGTCTGCC-3') designed from the 1.5-kbp sequence. PCR yielded a product of expected size (~1.4 kbp). The full-length DNA-B sequence was obtained by assembling the two sequences. The DNA-B was 2,734 nucleotides and encoded two putative ORFs (GenBank Accession No. KF218821). The sequences of DNA-A and DNA-B of isolate Laos shared the highest nucleotide sequences identities at 99.0% and 98.0% with those of TYLCKaV-[TH:Kan 1:01] (AF511529), and [TH:Kan 2:Egg:01] (AF511527), respectively. The results indicated that the virus associated with eggplant yellow mosaic disease was an isolate of TYLCKaV. To our knowledge, this is the first report of this begomovirus in Laos. Our results indicate that this virus may be spreading in Southeast Asia and scientists there should be aware of this virus when developing begomovirus-resistant varieties of tomato or eggplant. References: (1) S. K. Green et al. Plant Dis. 87:446, 2003. (2) C. Ha et al. J. Gen. Virol. 89:312, 2008.(3) Z. F. He et al. Arch. Virol. 154:1199, 2009.

First Report of Potato Blackleg Disease Caused by Pectobacterium atrosepticum in Guangdong China

Potato (Solanum tuberosum L.) is an important crop in China. In 2013, diseased potatoes exhibiting blackleg and soft rot symptoms were found in the winter potato growing areas of Huizhou city, Guangdong Province, China, with an incidence of approximately 20%. Initially, the stem bases of infected plants blackened and this symptom spread upward. Later, foliage of the diseased plants became yellow and the stem rotted with vascular discoloration. Twenty diseased plants with typical black leg symptoms were collected from a 10-ha potato field with approximately 60,000 potato plants per hectare. A bacterium with small, irregular, round, fluidal, white colonies was isolated from the vascular tissue of all diseased plants on nutrient agar at 26°C for 2 days. Ten strains were randomly selected for pathogenicity assays. Potato plants (cv. Favorita) at the five- to six-leaf stage were inoculated by injecting their stems with 1 ml of each strain in a bacterial suspension (3 × 10⁸ CFU/ml). The inoculated potato plants were incubated at 16 to 21°C and 65 to 85% humidity, and exhibited the same symptoms as the diseased potato plants in the field by 3 to 5 days post inoculation (dpi). The bacterium was reisolated from the diseased tissue (stem) of the inoculated potato plants and produced characteristic pits on crystal violet pectate medium (1). The bacterium utilized a-methyl glucoside, glucose, lactose, maltose, cellobiose, raffinose, melibiose, and citrate, but not d-arabitol, sorbitol, or malonate. The bacteria also gave a positive reaction for catalase and production of reducing substances from sucrose, but gave a negative reaction for oxidase, production of phosphatase, and indole. Using the universal bacterial 16S rDNA primer set, 27f/1541R (4), 1,400-bp fragments were amplified from the 10 strains. The sequences of the 10 fragments (GenBank Accessions KC695819 to KC695828) were identical and had 100% sequence identity with 16S rDNA of Pectobacterium atrosepticum CFBP 1526 (JN600332). Further, the 438-bp and 690-bp fragments were respectively amplified from all 10 strains with the P. atrosepticum-specific primers Y45/Y46 (3) and ECA1f/ECA2r (2). To our knowledge, this is the first report of potato blackleg disease caused by P. atrosepticum (formerly named as Erwinia carotovora subsp. atroseptica) in Guangdong Province, China. References: (1) D. Cupples et al. Phytopathology 64:468, 1974. (2) S. H. De Boer et al. Phytopathology 85:854, 1995. (3) D. Frenchon et al. Potato Research 41:63, 1995. (4) M. Horita et al. J. Gen. Plant Pathol. 70:278, 2004.