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gFACs:Gene Filtering,Analysis,and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 305-310页

作者： madison Caballero Jill Wegrzyn department of Ecology and Evolutionary Biology University of Connecticut

Published genomes frequently contain erroneous gene models that represent issues associated with identification of open reading frames,start sites,splice sites,and related structural *** source of these inconsistencies is often traced back to integration across text file formats designed to describe long read alignments and predicted gene *** addition,the majority of gene prediction frameworks do not provide robust downstream filtering to remove problematic gene annotations,nor do they represent these annotations in a format consistent with current file *** frameworks also lack consideration for functional attributes,such as the presence or absence of protein domains that can be used for gene model *** provide oversight to the increasing number of published genome annotations,we present a software package,the Gene Filtering,Analysis,and Conversion(gFACs),to filter,analyze,and convert predicted gene models and *** software operates across a wide range of alignment,analysis,and gene prediction files with a flexible framework for defining gene models with reliable structural and functional *** supports common downstream applications,including genome browsers,and generates extensive details on the filtering process,including distributions that can be visualized to further assess the proposed gene *** is freely available and implemented in Perl with support from BioPerl libraries at https://***/PlantGenomicsLab/gFACs.

关键词： Genome annotation Bioinformatics Protein annotation Gene prediction Alignment

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南海北部海面高度季节变化的机制

海洋学报 2002年第S1期24卷 134-141页

作者：刘秦玉贾英来杨海军刘征青岛海洋大学物理海洋教育部重点实验室山东青岛266003 university of wisconsin madison

利用POM模式对南海环流进行了数值模拟和数值试验 ,结果表明 :南海北部SSH的变化主要应归于南海局地的动力、热力强迫和黑潮的影响 ;黑潮对南海北部SSH平均态的影响要大于对SSH异常场的影响 ;对于南海北部深水区冬季局地风应力与浮力通... 详细信息

利用POM模式对南海环流进行了数值模拟和数值试验 ,结果表明 :南海北部SSH的变化主要应归于南海局地的动力、热力强迫和黑潮的影响 ;黑潮对南海北部SSH平均态的影响要大于对SSH异常场的影响 ;对于南海北部深水区冬季局地风应力与浮力通量的作用相反量级相同 ,黑潮对南海北部SSH的控制作用在冬季显得最重要 ,约占 50 %～ 80 % ;春季 ,夏季和秋季 ,局地风应力、浮力通量和黑潮三者都使深水区SSH上升 ,局地风应力使深水海盆SSH上升的作用约占 4 0 %～ 6 0 % ,浮力通量的作用约占 2 0 % ,黑潮的影响约占 2 0 %～ 30 % .在夏季 ,尽管南海北部深水海盆SSH达到全年最高 ,但黑潮对南海北部深水海盆SSH的贡献最小 .在广东沿岸陆架海域 ,SSH季节变化的机制与深水海盆SSH季节变化的机制不同 :春、夏季 ,局地风应力使SSH上升的作用几乎与浮力通量使SSH下降的作用相当 ;秋、冬季 ,东北季风使SSH上升的作用大于浮力通量和黑潮使SSH下降的作用 ,陆架区SSH为正。

关键词：南海海面高度季节变化数值模拟动力机制

Biosynthesis of the thiopeptide antibiotic thiostrepton from Streptomyces laurentii

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Biosynthesis of the thiopeptide antibiotic thiostrepton from...

The 3～(rd) International Conference on Natural Products :Natural Products -a Must for Human Survival ABSTRACTS

作者： Haibin Deng, Ben Shen, Gongli Tang, and Wen Liu Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China School of Pharmacy, university of wisconsin-madison, madison, wi, 53705

Thiostrepton is a member of the family of sulfur-rich peptide natural products known as the thiopeptide antibiotics, many of which exhibit broad spectra of antimicrobial activities and are clinically used as veterinary drugs. Recently, studies have been shown that thiostrepton inhibits protein synthesis in the blood stage of the malaria parasite at low concentrations. Although thiopeptide antibiotics may share the same mechanism of formation based on their high degree of sequence identity and structural similarity, the mode of biosynthesis of the thiopeptide antibiotics has not been clearly elucidated for any of the member of the family. Studying the unprecedented mechanism of thiostrepton will not only provide the biosynthetic platform to generate the structural diversity for drug discovery and development, but also contribute to the fundamental mechanisms of non-ribosome peptide synthase (NRPS) chemistry and enzyme catalysis, and eventually enrich the toolbox of combinatorial biosynthesis.

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THE WEIGHTED HERZ-TYPE HARDY SPACES hK_q^(α,p)(ω_1,ω_2)

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Analysis in Theory and Applications 1997年第4期13卷 19-41页

作者： Fan Dashan and Yang Dachun (university of wi~Milwaukee, U. S. A. and Beijing Normal university, China) 1. department of Mathematical Sciences University of Wisconsin-Milwaukee P.O. Box 413 53201 Milwaukee WI U.S.A. 2. department of mathematics Beijing Normal University 100875 Beijing The People's Republic of China

Let (.the Muckenhoupt class). In this paper, the author introduce the weighted Herz-type Hardy spaces (w2) and present their atomic decomposition. Using the atomic decomposition, the author find out their dual spaces, establish the boundedness on these spaces of the pseudo-differential operators of order zero and show that , the class of C(Rn)-functions with compactly support, is dense in and there is a subsequence, which converges in distrbutional sense to some distribution of , of any bounded sequence in In addition, the author also set up the boundedness of some non-linear quantities in compensated compactness.

关键词： THE WEIGHTED HERZ-TYPE HARDY SPACES hK_q III Math

Study on Soil and Pine-Seedling Zn and Mn and Predicting-Model Design

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Pedosphere 1992年第2期2卷 153-160页

作者： ZHANGJI－ZHEN J.G.JYER AnhuiAgriculturalCollege Hefei230036（China） departmentofScience UniversityofWisconsin－Madison53706（U

Soils were collected from 2-year (2-y) and 3-year (3-y) old red-pine seedling plots in two tree nurseries, Hayward in the north and wilson in the southwestern part of wisconsin State respectively, and equilibrated with 0.01 M Ca(NO3)2 for soil solution Zn and Mn (solu-Zn and Mn), and with 0.01 M Ca(NO3)2+0.005 M EDTA for soil adsorbed Zn and Mn (ad-Zn and Mn). Buffering capacity of soil Zn and Mn (b-Zn and Mn) was obtained from the ratio of ad-Zn and Mn to the solu-Zn and Mn. The concerned traces in pine seedling needles (ndls), stems(sts) and roots (rts) were simultaneously measured. The results obtained show that:About 60% of solu- and ad- Zn ranged from 0.2 to 0.4 and from 1 to 2μ/g soil respectively. About 70% of b-Zn was within) *** highest content of solu-Zn compared with the lowest showed a discrepancy of more than 10-fold. The two forms of soil Zn were commonly higher in wilson than in Hayward *** 80% of solu-, ad- and b-Mn were within 3-10, 5-5.8 μg/ g soil and 1-2 respectively. Influence of low buffering capacity on solu-Zn and Mn was about 20 times stronger than that of the *** E-value, a ratio of accumulated Zn and Mn in needles to those in the soil solution, is proved to be: E-Zn > E-Mn;E-sts> E-ndls or E-rts; and E-2y > *** and/ or linear correlations between soil solu-, ad- and b-Zn and Mn and ndls-, sts-, rts-Zn and Mn were at very significant or significant *** predicting ndls-Zn and Mn, two realizable and simple models from two regression equations were established through the selection of related parameters and dependent variables. Binary regression analysis basically eliminated the influence of soil pH on the prediction of Zn and Mn in needles. Soil pH was thus thought to be excluded from the model.

关键词： manganese predicting model red-pine seedling zinc

Effects of Swimming on Rat’s Pain Tolerance Threshold and Hypothalamic Beta-endorphin and Neuropeptide Y

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Effects of Swimming on Rat’s Pain Tolerance Threshold and H...

2011年心理学与社会和谐学术会议

作者： Bo XU1,2,Feng YU2,Chenghui SONG3,Liu JI1,2 1 Key Laboratory of Adolescent Health Assessment and Exercise Intervention,Ministry of Education,Shanghai,China, 200241 2 College of Physical Education and Health,East China Normal university,Shanghai,China,200241 3 department of Psychology,university of wisconsin,P.O.Box 413,Milwaukee,wi 53201,usa

To explore whether swimming would increase the concentration of BE、NPY,and change the pain tolerance threshold.28 SD rats were divided into four groups:control group（CG）,acute exercise group（EG）, training control group（TCG）,and training acute exercise group（TEG）.The CG rats had never swim from beginning to end of the experiment,the EG rats had only swim once（60 minutes）in the ninth week before *** TCG and TEG rats,an 8-week no-load swimming session（1 hour×4times/week）was *** of the rats were tested their pain tolerance threshold on the 8th ***（RIA） was used to measure hypothalamic BE and *** results by labyrinth experiment showed that the time to reach security area for TCG and TEG rats is significantly lower than the CG and EG *** with CG, hypothalamic BE and NPY concentration in EG increased *** with CG and TCG,hypothalamic BE concentration in TEG increased *** results indicate that swimming was associated with increasing of the concentration of BE、NPY in Hypothalamic and lowers pain tolerance threshold.

关键词： swimming beta-endorphin neuropeptide Y pain tolerance threshold

QUANTIFICATION OF DETAIL SPATIAL GRADATION OF TERRAIN POSITION USING FUZZY LOGIC AND GIS TECHNIQUES

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QUANTIFICATION OF DETAIL SPATIAL GRADATION OF TERRAIN POSITI...

第11届国际模糊系统协会世界大会

作者： A-Xing Zhu Xun Shi State Key Lab of Resources and Environmental Information System Institute of Geographical Sciences and NaturalResources Research Chinese Academy of Sciences No. 11 Datun Road An Wai Beijing 100101 China email:department of Geography university of wisconsin 550 North Park Street madison wisconsin 53706 U.S.A.Email:department of Geography 014 Fairchild Dartmouth College Hanover NH 03755 U.S.A.

＜正＞ This paper presents a fuzzy logic-based method for quantifying the spatial gradation of terrain features. The method computes the fuzzy membership value （similarity value） between a local location in the landscape and the typical locations of a geomorphic feature in two general steps: locating typical locations and evaluating the similarity between a given location and the typical locations. The similarity evaluation contains three steps: calculating the similarities based on individual terrain attributes for the given location and one typical location;integrating the similarities values on individual attributes to obtain an overall similarity value for the given location and the typical location;and integrating the similarity values on multiple typical locations to get the final fuzzy membership value of the given location for the terrain position. Ridge and valley are used as examples to illustrate the process. A case study using soil samples from wisconsin shows that the fuzzy representation of terrain position derived in this way is useful in characterizing the spatial variation in soil property values.

关键词： Fuzzy logic Digital Soil Mapping Terrain Position GIS

Live-Cell Imaging of Dual-Labeled Golgi Stacks in Tobacco BY-2 Cells Reveals Similar Behaviors for Different Cisternae during Movement and Brefeldin A Treatment

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Molecular Plant 2011年第5期4卷 896-908页

作者： Stephanie L. madison Andreas Nebenfuhr department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996-0840 USA

In plant cells, the Golgi apparatus consists of numerous stacks that, in turn, are composed of several flattened cisternae with a clear cis-to-trans polarity. During normal functioning within living cells, this unusual organelle displays a wide range of dynamic behaviors such as whole stack motility, constant membrane flux through the cisternae, and Golgi enzyme recycling through the ER. In order to further investigate various aspects of Golgi stack dynamics and integrity, we co-expressed pairs of established Golgi markers in tobacco BY-2 cells to distinguish sub-compartments of the Golgi during monensin treatments, movement, and brefeldin A （BFA）-induced disassembly. A combination of cis and trans markers revealed that Golgi stacks remain intact as they move through the cytoplasm. The Golgi stack orientation during these movements showed a slight preference for the cis side moving ahead, but trans cisternae were also found at the leading edge. During BFA treatments, the different sub-compartments of about half of the observed stacks fused with the ER sequentially; however, no consistent order could be detected. In contrast, the ionophore monensin resulted in swelling of trans cisternae while medial and particularly cis cisternae were mostly unaffected. Our results thus demonstrate a re- markable equivalence of the different cisternae with respect to movement and BFA-induced fusion with the ER. In addi- tion, we propose that a combination of dual-label fluorescence microscopy and drug treatments can provide a simple alternative approach to the determination of protein localization to specific Golgi sub-compartments.

关键词： Golgi apparatus Golgi stack integrity brefeldin A monensin tobacco BY-2 cells live-cell imaging.

Generalization of Some Attacks on RSA with Small Prime Combination and Small Private Exponent

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Generalization of Some Attacks on RSA with Small Prime Combi...

2009 Asia-Pacific Conference on Information Processing

作者： Lidong Han Guangwu Xu Key Lab of Cryptographic Technology and Information Security Ministry of Education Shandong university Jinan 250100 China department of Electrical Engineering and Computer Science university of wisconsin-Milwaukee Milwaukee 53201-0784 usa

In 2002,de Weger proposed an attack on small RSA secret decryption exponent with small prime difference |p q|,which improved the insecure private key bound of wiener and Boneh-Durfee ***,Maitra and Sarkar found new weak keys in another case when 2q p is *** this paper,several results on attacking RSA with small prime differences q p,2p q and small private exponent are *** observation is that when |ip jq| is small for some integers i,j,we can explore new insecure keys in *** of our results also makes some statement in literature more accurate.

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