Complex structural variants(CSVs)are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.How-ever,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 com-pared with simple structural variants.Here,we systematically analyzed the multi-breakpoint con-nection 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.

We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical diagnosis.JAX-CNV is thus developed for CNV detection from WGS data.The perfor-mance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and com-pared to the 112 CNVs reported by clinically validated CMAs for these 31 samples.The result showed that JAX-CNV recalled 100％of these CNVs.Besides,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated CMAs.Experimental validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17％.A robustness test on lower-coverage data revealed a 100％sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×coverage.For CNVs larger than 50 kb,sensi-tivities were 100％for coverages deeper than 20×,97％for 15×,and 95％for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100％with about a FDR of 4％.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS.JAX-CNV is available at https://github.com/The J acksonLaboratory/JAX-CNV.

Objective This exploratory study aimed to assess effectiveness with ethylene oxide treatment for removing DNA contamination. Methods 98 different spiked samples such as saliva, dander, skin cell, hair, blood and cartilage were conducted with ethylene oxide treatment. After extraction of samples, the dna was amplified and then the STR analysis was performed with 3130xl or 3500xl. Results A 6h EO treatment results showed that two saliva stains of 44 samples STR profile were detected; Just one hair of 54 samples treated with ethylene oxide was detected contaminating DNA with EO treatment for 8 hours. Conclusion This work suggested that it was more successful to reduce DNA contamination by using ethylene oxide treatment.

Objective This study aimed to assess the efficiency and purification of the Trace DNA extraction with a quantified method for the magnetic bead-based DNA extraction as performed on the Tecan Automated systems with TE-MAGS magnetic separator. Methods Serial dilutions of standard commercial DNA 9947A were used with the total DNA contents, 0.1ng, 0.2ng,0.3ng, 0.4ng,0.5ng, 0.6ng, 0.7ng, 0.8ng, 0.9ng,1ng,diluted progressively and a 1ng DNA (standard commercial DNA 9947A) admixed with 6 common DNA-PCR inhibitors were extracted on the Automated systems and then performed via Fluorogenic probe quantitative PCR and STR genotype for the quantification analysis of recovery and purification. Results The recovery rate of standard 9947A DNA diluted with 0.1~1ng was 38.92~60.01%, and 0.3ng and more DNA could observed the full STR profiles. For the different PCR inhibitors, above 94.5% of bile acid, collagen and urea were efficient removal during the purification process, and the hemoglobin, melanin and humic acid removal efficiency were about 97.5%, 97.85%, 82.14%, respectively.Conclusion Our results suggested that The TE-MAGS magnetic bead-based DNA extraction was suitable for the extraction of trace DNA with high recovery efficiency and purification ability.

Latent reservoir (LR) of HIV is the cells (such as CD4(+)T cell) where HIV is able to hide. These cellular reservoirs are located throughout the body, including the spleen, lymph nodes, gastrointestinal lymphoid tissues, and become the major obstacle to cure HIV infection. To truly cure patients, a new strategy "shock and kill" was put forward by scientists, which is to shock HIV-infected cells out of hidden reservoirs in the body and then kill them. Quantitatively evaluating the size of long-lived LR is essential to this strategy. This paper reviews assays that measure the magnitude of the latent HIV reservoir, including Alu-gag PCR, quantitative viral outgrowth assay (Q-VOA) and tat/rev induced limiting dilution assay(TILDA). Alu-gag PCR can differentiate the integrated and un-integrated HIV DNA, however, it cannot distinguish defective virus from competent virus, leading to overestimate the real size of LR. Q-VOA is based on cell culture, and is the golden standard for measuring the LR since it provides a definitive minimal estimate of reservoir size. Its disadvantages are being more costly, large amount of blood sample required, and underestimating the true size, which was resulted from particles being not released after one round of stimulation. TILDA measures cells with inducible msRNA as these transcripts are absent in latently infected cells but induced upon viral reactivation. It requires small blood sample size, does not need extraction of viral nucleic acids, can be completed in 2 d and covers a wide dynamic range of reservoir sizes, but has the disadvantage of overestimating the true size of LR.

OBJECTIVE:To study the chemical constituents of the flower of Zang Epipremnum aureum. METHODS:The con-stituents of ethyl acetate extract of the flower of E. aureum were separated and purified with varied chromatographic techniques, and the structures were identified based on spectral data and chemical properties. RESULTS:Ten compounds were isolated from eth-yl acetate extract of the flower of E. aureum,they were identified as rutamontine(1),edgeworoside C(2),edgeworin(3),tiliro-side (4),helichrysoside (5),kaempferol (6),2,4-dihydroxypheny-2-hydroxy-4-metho-xybenzyl-ketone (7),ethyl caffeate (8), phthalic acid bis-(2-ethyl-hexyl) ester (9) and noreugenin (10). CONCLUSIONS:Compound 7 is firstly isolated from natural source,compounds 5,8 and 9 is firstly isolated from the family Thymelaeaceae,compound 6 is firstly isolated from Edgeworthia and compound 2 and 10 are firstly isolated from the flowers of E. aureum. The study lays certain foundation for the quality evalua-tion of E. aureum.

Objective To investigate the value of flexi-rigid thoracoscopy in pleural effusion of unknown causes and the correlation with CEA, TK1 and ADA. Methods The clinical data and results of CEA, TK1 and ADA of 25 patients were retrospective analyzed in our department from 2015 January to November 2015. These patients accepted the examination of flexi-rigid thoracoscopy with pleural effusion of unknown causes. Results In the 25 patients with pleural effusion of unknown causes, definite diagnosis was made in 22 cases (88.00 %), of which 9 cases were malignant pleural effusion (36.00 %), 11 cases were tuberculous pleural effusion (44.00 %), 2 cases were inflammatory pleural effusion (8.00 %), 3 cases were undetermined (12.00 %). The positive rate of TK1 and CEA in malignant group was significantly higher than that in the tuberculosis group and inflammatory group, the positive rate of ADA in the tuberculosis group was significantly higher than that in the malignant group and inflammatory group. Conclusion Flexi-rigid medical thoracoscopy examination is an effective and safe method for diagnosis of unexplained pleural effusion with high exact diagnosis rate, less trauma and less complication. Combination with CEA, TK1 and ADA are helpful to improve diagnostic rate of pleural effusion of unknown causes.

Objective To investigate the expression of AIF, CYT C, PAF-1, caspase-3, and XIAP in Sprague-Dawley rats with spontaneous mammary neoplasms.Methods One-hundred and thirty 3-4-week old SPF Spargue-Dawley rats (♀∶♂=1∶1) were fed in a specific pathogen free (SPF) breeding barrier for 60 weeks.The occurrence of spontane-ous breast tumors was recorded and histopathology was performed to identify the types of tumors.The rats were divided into 3 groups:rats with normal breast tissue ( group I) , with benign tumors ( group II) and with malignant tumors ( group III) . The expression of AIF, CYT C, APAF-1, caspase-3 and XIAP proteins and mRNAs were detected by immunhistochemistry ( IHC) and RT-PCR assay.Results Among these 130 SD rats, 14 rats were observed having spontaneous mammary neo-plasms with the incidence rate of 10.77%(14/130).In these neoplasm cases, 7 cases were mammary fibroadenomas, 7 cases of breast carcinoma, both with an incidence rate of 5.38%.Immunohistochemistry showed that, compared with the group I, the positive expressions of AIF, APAF-1, caspase-3 were decreased significantly (P<0.01), and the CYT C and XIAP expressions were significantly increased in the group II.The positive expression of all genes except XIAP was de-creased in the group III(P<0.01).Compared with the group II, APAF-1 and XIAP were significantly higher in the group III (P<0.01), and the positive expression of AIF, Cyt C, and caspases-3 were significantly decreased (P<0.01).In the results of RT-PCR assay, except APAF-1 which showed significant correlation with the results of immunohistochemistry ( P<0.05 ) , all the others showed an extremely significant correlation with immunohistochemical results ( P <0.01 ) . Conclusions Mammary tumors are most common spontaneous neoplasms in SD rats.Abnormal expression of mitochondrial apoptotic pathway-related factors AIF, CytC, APAF-1, caspase-3, and XIAP are correlated with the carcinogenesis and de-velopment of breast tumors.

Objective To observe the effects of a motor relearning programme (MRP) combined with different early acupuncture interventions on muscle tension and motor function recovery after cerebral infarction.MethodsA total of 90 patients with cerebral infarction who met the inclusion criteria were divided into three groups at random:a YANGMING meridian acupuncture and MRP group ( group A),an anti-spasm acupuncture and MRP group ( group B),and an MRP group ( group C ).All of the patients in all three groups were treated with routine medication.The National Institute of Health stroke scale (NIHSS),the composite spasticity scale (CSS),Fugl-Meyer assessment (FMA),the Fugl-Meyer balance scale (FM-B) and the modified Barthel index (MBI) were used to measure performance before treatment and after 4 weeks of treatment.Another comparison was intra-group between before and after treatment. ResultsThere were significant differences in the assessment results in all of the groups after treatment compared with those before treatment.After treatment,group B was superior to group C only in terms of NIHSS scores.There was no significant NIHSS score difference between groups A and C.The FMA,CSS and MBI results revealed significant differences among all three groups,with the scores of group A consistently the highest.The average FMA score in group B was significantly higher than in group C but there was no statistically significant difference in FM-B scores among the three groups. ConclusionMRP therapy combined with early acupuncture intervention can improve motor function and muscular tension after cerebral infarction.Anti-spasm acupuncture can improve motor function and control muscular tension effectively at the same time,making it beneficial for MRP training.

In this study, apoptosis was induced by new type gosling viral enteritis virus (NGVEV) in experimentally infected goslings is reported in detail for the first time. After 3-day-old goslings were orally inoculated with a NGVEV-CN strain suspension, the time course of NGVEV effects on apoptotic morphological changes of the internal tissues was evaluated. These changes were observed by histological analysis with light microscopy and ultrastructural analysis with transmission electron microscopy. DNA fragmentation was assessed with a terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and DNA ladder analysis. A series of characteristic apoptotic morphological changes including chromatin condensation and margination, cytoplasmic shrinkage, plasma membrane blebbing, and formation of apoptotic bodies were noted. Apoptosis was readily observed in the lymphoid and gastrointestinal organs, and sporadically occurred in other organs after 3 days post-infection (PI). The presence and quantity of TUNEL-positive cells increased with infection time until 9 days PI. DNA extracted from the NGVEV-infected gosling cells displayed characteristic 180~200 bp ladders. Apoptotic cells were ubiquitously distributed, especially among lymphocytes, macrophages, monocytes, and epithelial and intestinal cells. Necrosis was subsequently detected during the late NGVEV-infection phase, which was characterized by cell swelling, plasma membrane collapse, and rapidly lysis. Our results suggested that apoptosis may play an important role in the pathogenesis of NGVE disease.
*Adenoviridae/classification/pathogenicity ; Adenoviridae Infections/pathology/*veterinary/virology ; Animals ; *Anseriformes ; *Apoptosis ; Bird Diseases/*virology ; DNA Fragmentation ; Enteritis/*veterinary/virology ; Epithelial Cells/cytology/virology ; In Situ Nick-End Labeling ; Intestines/cytology/virology ; Leukocytes/cytology/virology ; Lymphoid Tissue/cytology/virology ; Macrophages ; Microscopy, Electron, Transmission