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Investigation of Single and Multiple Mutations Prediction Using Binary Classification Approach

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Intelligent Automation & Soft Computing 2023年第4期36卷 1189-1203页

作者： T.Edwin Ponraj j.charles Department of Computer Applications Noorul Islam Centre for Higher EducationKumaracoil629180India Department of Software Engineering Noorul Islam Centre for Higher EducationKumaracoil629180India

The mutation is a critical element in determining the proteins’stability,becoming a core element in portraying the effects of a drug in the pharmaceutical *** wet laboratory tests to provide a better perspective on protein mutations is expensive and time-intensive since there are so many potential muta-tions,computational approaches that can reliably anticipate the consequences of amino acid mutations are *** work presents a robust methodology to analyze and identify the effects of mutation on a single protein ***,the context in a collection of words is determined using a knowledge graph for feature selection *** proposed prediction is based on an easier and sim-pler logistic regression inferred binary classiﬁcation *** approach can able to obtain a classiﬁcation accuracy(AUC)Area Under the Curve of 87%when randomly validated against experimental energy ***,for each cross-fold validation,the precision,recall,and F-Score are *** results support the validity of our strategy since it performs the vast majority of prior studies in this domain.

关键词： Proteins data science mutation analysis random forest neighbor proteins single and double mutations

Endoscopic therapies of gastroesophageal reflux disease

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World journal of Gastroenterology 2006年第17期12卷 2641-2655页

作者： Atif Iqbal Vanessa Salinas charles j Filipi Department of Surgery University of Missouri Columbia One Hospital DriveColumbiaMO 65211United States Department of Surgery Creighton University 601 N 30th StreetOmaha NE 68131United States

The high prevalence of gastroesophageal reflux disease （GERD） in Western societies has accelerated the need for new modalities of treatment. Currently, medical and surgical therapies are widely accepted among patients and physicians. New potent antisecretory drugs and the development of minimally invasive surgery for the management of GERD are at present the pivotal and largely accepted approaches to treatment. The minimally invasive treatment revolution, however, has stimulated several new endoscopic techniques for GERD. Up to now, the data is limited and further studies are necessary to compare the advantages and disadvantages of the various endoscopic techniques to medical and laparoscopic management of GERD. New journal articles and abstracts are continuously being published. The Food and Drug Administration has approved 3 modalities, thus gastroenterologists and surgeons are beginning to apply these techniques. Further trials and device refinements will assist clinicians. This article will present an overview of the various techniques that are currently on study. This review will report the efficacy and durability of various endoscopic therapies for gastroesophageal reflux disease （GERD）. The potential for widespread use of these techniques will also be discussed. Articles and abstracts published in English on this topic were retrieved from Pubmed. Due to limited number of studies and remarkable differences between various trials, strict criteria were not used for the pooled data presented, however, an effort was made to avoid bias by including only studies that used off-PPI scoring as baseline and intent to treat.

关键词： Endoscopic Treatment Gastroesophageal reflux disease

Roles of the main olfactory and vomeronasal systems in the detection of androstenone in inbred strains of mice

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Current Zoology 2010年第6期56卷 813-818页

作者： Vera V. VOZNESSENSKAYA Maria A. KLYUCHNIKOVA charles j. WYSOCKI A.N. Severtzov Institute of Ecology & Evolution RAS Monell Chemical Senses Center

We investigated the role of the main olfactory and accessory olfactory systems （MOS and AOS respectively） in the detection of androstenone. We used the following experimental approaches： behavioral, surgical removal of the vomeronasal organ （VNX） followed by histochemical verification and Fos immunohistochemistry. Using a Y-maze paradigm we estimated sensitivity of NZB/B1Nj and CBA/j mice to androstenone. CBA mice were 2,000-fold more sensitive to androstenone than NZB mice. VNX caused a 4-tol6-fold decrease in sensitivity to androstenone in highly-sensitive CBA mice, but did not affect thresholds in NZB mice. Results indicate the involvement of the MOS and AOS in the detection of androstenone. We observed a specific pattern of Fos-positive cells in the main olfactory bulb of CBA mice but not in NZB mice subsequent to exposure of mice to androstenone; the compound activated cells in the accessory olfactory bulb in both strains of mice, indicating the involvement of the vomeronasal organ. Patterns of Fos-positive cells in the vomeronasal organ were recorded subsequent to exposure to androstenone. Fos-positive receptor cells in the vomeronasal organ of CBA and NZB mice were different, in CBA mice Fos-positive cells were noted in both the basal and apical zones, however, in NZB mice activation was observed only in the apical zone [Current Zoology 56 （6）： 813-818, 2010].

关键词： Olfaction Vomeronasal organ Chemosensory receptors Olfactory behavior Immunohistochemistry

Isotretinoin for the treatment of nonobstructive azoospermia: a pilot study

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Asian journal of Andrology 2021年第5期23卷 537-540页

作者： john K Amory charles H Muller Thomas j Walsh Department of Medicine University of WashingtonSeattleWA 98195USA Department of Urology University of WashingtonSeattleWA 98195USA

The treatment of men with infertility from azoospermia is *** some men with severe oligozoospermia improve sperm output during treatment with isotretinoin,we treated nine men with azoospermia with isotretinoin to determine if azoospermic men would also respond to isotretinoin *** of these men who had a previous negative testicular sperm extraction(TESE)was found to have an area of sperm production on a postisotretinoin testicular *** man achieved a pregnancy and a live birth of a healthy,term daughter after in vitro fertilization coupled with intracytoplasmic sperm injection(IVF/ICSI).A second subject had a positive TESE after treatment as *** study of isotretinoin therapy in men with azoospermia undergoing testicular sperm harvesting procedures is warranted.

关键词： treatment injection pregnancy

Balancing Frequencies and Fault Detection in the In-Parameter-Order Algorithm

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journal of Computer Science & Technology 2015年第5期30卷 957-968页

作者：高世伟吕江花杜冰磊 charles j. Colbourn 马世龙 State Key Laboratory of Software Development Environment Beihang University Beijing 100191 China School of Computing Informaties and Decision Systems Engineering Arizona State University Tempe AZ 85287-8809 U.S.A.

The In-Parameter-Order （IPO） algorithm is a widely used strategy for the construction of software test suites for combinatorial testing （CT） whose goal is to reveal faults triggered by interactions among parameters. Variants of IPO have been shown to produce test suites within reasonable amounts of time that are often not much larger than the smallest test suites known. When an entire test suite is executed, all faults that arise from t-way interactions for some fixed t are surely found. However, when tests are executed one at a time, it is desirable to detect a fault as early as possible so that it can be repaired. The basic IPO strategies of horizontal and vertical growth address test suite size, but not the early detection of faults. In this paper, the growth strategies in IPO are modified to attempt to evenly distribute the values of each parameter across the tests. Together with a reordering strategy that we add, this modification to IPO improves the rate of fault detection dramatically （improved by 31% on average）. Moreover, our modifications always reduce generation time （2 times faster on average） and in some eases also reduce test suite size.

关键词： combinatorial testing IPO test suite generation expected time to fault detection software under test

Cross-specific amplification of microsatellite DNA markers in Shorea platyclados

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journal of Forestry Research 2016年第1期27卷 27-32页

作者： Asif j.Muhammad charles H.Cannon Wickneswari Ratnam Department of Biological Sciences Texas Tech University Faculty of Science and Technology School of Environmental and Natural Resource SciencesUniversiti Kebangsaan Malaysia

In the megadiverse forests of Southeast Asia, hundreds of timber species are economically important but the population genetics of only a few taxa are known. Cross-specific amplification of microsatellite loci among closely related taxa could enhance our ability to study and manage previously unstudied species. We successfully utilized STMS markers in Shorea platyclados, originally developed for Shorea curtisii. The six primer pairs we tried successfully produced PCR products of expected sizes. The number of alleles observed ranged from 10 to 14 and an average of 12 alleles were detected per locus. A high expected and observed heterozygosity was observed and it ranges from 0.718 to 0.827 among all populations across all six loci tested. Microsatellite DNA markers are highly polymorphic, co-dominant, reproducible, and amenable to high throughput genetic analyses. Overall, the cross- specific amplification of microsatellite loci appears to be complicated by numerous factors. While the approach may be effective for local management and conservation ofpoorly known species, the results must be carefully interpreted.

关键词： Genetic marker systems Populationgenetics SSR Selective logging Tropical timber Capillary electrophoresis

CLUSTERING PATENTS USING NON-EXHAUSTIVE OVERLAPS

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journal of Systems Science and Systems Engineering 2010年第2期19卷 162-181页

作者： charles V. TRAPPEY Amy j.C. TRAPPEY Chun-Yi WU Department of Management Science National Chiao Tung University Taiwan China Department of Industrial Engineering & Management National Taipei University of Technology Taiwan China Department of lndustrial Engineering & Engineering Management National Tsing Hua University Taiwan China

Patent documents are unique external sources of information that reveal the core technology underlying new inventions. Patents also serve as a strategic data source that can be mined to discover state-of-the-art technical development and subsequently help guide R＆D investments. This research incorporates an ontology schema to extract and represent patent concepts. A clustering algorithm with non-exhaustive overlaps is proposed to overcome deficiencies with exhaustive clustering methods used in patent mining and technology discovery. The non-exhaustive clustering approach allows for the clustering of patent documents with overlapping technical findings and claims, a feature that enables the grouping of patents that define related key innovations. Legal advisors can use this approach to study potential cases of patent infringement or devise strategies to avoid litigation. The case study demonstrates the use of non-exhaustive overlaps algorithm by clustering US and japan radio frequency identification （RFID） patents and by analyzing the legal implications of automated discovery of patent infringement.

关键词： Data mining patent analysis patent infringement non-exhaustive overlap clustering ontology schema

Palatability and profitability of co-occurring seeds alter indirect interactions among rodent-dispersed trees

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Integrative Zoology 2022年第2期17卷 206-216页

作者： Zhishu XIAO Marcel HOLYOAK charles j.KREBS Xiaoqun HUANG State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture Institute of ZoologyChinese Academy of SciencesChina University of Chinese Academy of Sciences BeijingChina Department of Environmental Science and Policy University of CaliforniaDavisUSA Department of Zoology University of British ColumbiaVancouverCanada

Beyond direct species interactions,seed dispersal is potentially affected by indirect seed–seed interactions among co-occurring nut-bearing trees which are mediated by scatter-hoarding animals as shared seed dispersers.A relevant question in such systems is to what extent different functional traits related to food palatability and profitability affect the kinds of indirect interactions that occur among co-occurring seeds,and the consequences for seed *** used field experiments to track seed dispersal with individually tagged seeds in both monospecific and mixed seed *** measured indirect effects based on 3 seed–seed species pairs from the family Fagaceae with contrasting seed size,tannin level,and dormancy in a subtropical forest in Southwest *** all else was equal,the presence of adjacently placed seeds with contrasting seed traits created different indirect effects measured through a variety of dispersal-related *** mutualism was reciprocal due to increasing seed dispersal in mixed seed patches with mixed differences in seed tannins and ***,differences in either seed size or dormancy in co-occurring adjacently placed seeds caused apparent competition with reduced seed removal or seed dispersal(distance)in at least one *** study supports the hypothesis that different functional traits related to food palatability and profitability in co-occurring seeds modify foraging decisions of scatter-hoarding animals,and subsequently cause indirect effects on seed dispersal among rodent-dispersed *** conclude that such indirect effects mediated by shared seed dispersers may act as an important determinant of seed dispersal for co-fruiting animal-dispersed trees in many natural forests.

关键词： dispersal distance functional trait scatter-hoarding rodents seed dispersal trait-mediated indirect interactions

Machine learning-guided accelerated discovery of structure-property correlations in lean magnesium alloys for biomedical applications

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journal of Magnesium and Alloys 2024年第6期12卷 2267-2283页

作者： Sreenivas Raguraman Maitreyee Sharma Priyadarshini Tram Nguyen Ryan McGovern Andrew Kim Adam j.Griebel Paulette Clancy Timothy P.Weihs Department of Materials Science and Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Hopkins Extreme Materials Institute Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Department of Chemical and Biomolecular Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Translational Tissue Engineering Center Johns Hopkins School of Medicine400 N BroadwayBaltimore21231MDU.S.A Department of Biomedical Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A Research and Development Fort Wayne Metals Research ProductsLLC9609 Ardmore AveFort Wayne46809INU.S.A Department of Mechanical Engineering Johns Hopkins University3400 N Charles StBaltimore21218MDU.S.A

Magnesium alloys are emerging as promising alternatives to traditional orthopedic implant materials thanks to their biodegradability,biocompatibility,and impressive mechanical ***,their rapid in-vivo degradation presents challenges,notably in upholding mechanical integrity over *** study investigates the impact of high-temperature thermal processing on the mechanical and degradation attributes of a lean Mg-Zn-Ca-Mn alloy,*** rapid,cost-efficient characterization methods like X-ray diffraction and optical microscopy,we swiftly examine microstructural changes post-thermal *** Pearson correlation coefficient analysis,we unveil the relationship between microstructural properties and critical targets(properties):hardness and corrosion ***,leveraging the least absolute shrinkage and selection operator(LASSO),we pinpoint the dominant microstructural factors among closely correlated *** findings underscore the significant role of grain size refinement in strengthening and the predominance of the ternary Ca_(2)Mg_(6)Zn_(3)phase in corrosion *** suggests that achieving an optimal blend of strength and corrosion resistance is attainable through fine grains and reduced concentration of ternary *** thorough investigation furnishes valuable insights into the intricate interplay of processing,structure,and properties in magnesium alloys,thereby advancing the development of superior biodegradable implant materials.

关键词： Magnesium alloys Machine learning Corrosion Mechanical properties Rapid characterization