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Modeling Bacterial Species: Using Sequence Similarity with Clustering Techniques

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Computers, Materials & Continua 2021年第8期68卷 1661-1672页

作者： miguel-angel sicilia Elena García-Barriocanal Marçal Mora-Cantallops Salvador Sánchez-Alonso Lino González University of Alcalá Alcaláde Henares(Madrid)28871Spain Camilo JoséCela University Madrid28007Spain

Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine potential bacterial clusters that are not identified by species naming.This paper describes the use of sequence data obtained from MLST databases as input for a k-means algorithm extended to deal with housekeeping gene sequences as a metric of similarity for the clustering process.An implementation of the k-means algorithm has been developed based on an existing source code implementation,and it has been evaluated against MLST data.Results point out to potential bacterial clusters that are close to more than one different named species and thus may become candidates for alternative classifications accounting for genotypic information.The use of hierarchical clustering with sequence comparison as similarity metric has the potential to find clusters different from named species by using a more informed cluster formation strategy than a conventional nominal variant of the algorithm.

关键词： Clustering bacterial species k-means sequence alignment

Software Project Effort Estimation Based on Multiple Parametric Models Generated Through Data Clustering

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Journal of Computer Science & Technology 2007年第3期22卷 371-378页

作者： Juan J.Cuadrado Gallego Daniel Rodríguez miguel angel sicilia miguel Garre Rubio angel García Crespo Department of Computer Science The University of Alcalá AlcaláSpain Department of Computer Science Carlos Ⅲ University.Madrid Spain

Parametric software effort estimation models usually consists of only a single mathematical relationship. With the advent of software repositories containing data from heterogeneous projects, these types of models suffer from poor adjustment and predictive accuracy. One possible way to alleviate this problem is the use of a set of mathematical equations obtained through dividing of the historical project datasets according to different parameters into subdatasets called partitions. In turn, partitions are divided into clusters that serve as a tool for more accurate models. In this paper, we describe the process, tool and results of such approach through a case study using a publicly available repository, ISBSG. Results suggest the adequacy of the technique as an extension of existing single-expression models without making the estimation process much more complex that uses a single estimation model. A tool to support the process is also presented. Keywords software engineering, software measurement, effort estimation, clustering

关键词： software engineering software measurement effort estimation clustering

Inflammatory bowel diseases: A disease (s) of modern times? Is incidence still increasing?

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World Journal of Gastroenterology 2008年第36期14卷 5491-5498页

作者： Cristina Saro Gismera Beatriz sicilia Aladrén Service of Digestive Diseases Hospital de Cabuees Gijón Spain Service of Digestive Diseases Alcaiz Hospital Spain

Inflammatory bowel diseases (IBD) are a heterogeneous group of diseases, not always easy to diagnose, even more difficult to classify, and diagnostic criteria are not always uniform. Well done population-based studies are not abundant, and so comparisons among different geographical areas or populations are not always very reliable. In this article, we have reviewed epidemiological studies available on the world’s population while making a critical review of published data.

关键词：肠炎流行病学诊断标准胃肠疾病

Use of agents stimulating erythropoiesis in digestive diseases

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World Journal of Gastroenterology 2009年第37期15卷 4675-4685页

作者： Rosario Moreno López Beatriz sicilia Aladrén Fernando Gomollón García Department of Nephrology San Juan de Dios Hospital Paseo Colón 14 50006 Zaragoza Spain Department of Medicine Universidad de Zaragoza 50009 Zaragoza Spain Department of Medicine (Gastroenterology) Alcaiz Hospital 44600 Alcaiz (Teruel) Spain Department of Gastroenterology Clinical University Hospital "Lozano Blesa" Department of Medicine University of Zaragoza IACS CIBEREHD 50009 Zaragoza Spain

Anemia is the most common complication of inflammatory bowel disease (IBD). Control and inadequate treatment leads to a worse quality of life and increased morbidity and hospitalization. Blood loss, and to a lesser extent, malabsorption of iron are the main causes of iron def iciency in IBD. There is also a variable component of anemia related to chronic inflammation. The anemia of chronic renal failure has been treated for many years with recombinant human erythropoietin (rHuEPO), which significantly improves quality of life and survival. Subsequently, rHuEPO has been used progressively in other conditions that occur with anemia of chronic processes such as cancer, rheumatoid arthritis or IBD, and anemia associated with the treatment of hepatitis C virus. Erythropoietic agents complete the range of available therapeutic options for treatment of anemia associated with IBD, which begins by treating the basis of the inflammatory disease, along with intravenous iron therapy as f irst choice. In cases of resistance to treatment with iron, combined therapy with erythropoietic agents aims to achieve near-normal levels of hemoglobin/hematocrit (11-12 g/dL). New formulations of intravenous iron (iron carboxymaltose) and the new generation of erythropoietic agents (darbepoetin and continuous erythropoietin receptor activator) will allow better dosing with the same eff icacy and safety.

关键词：人红细胞生成素消化系统疾病慢性肾功能衰竭传染性法氏囊病红细胞生成素受体综合治疗类风湿关节炎丙型肝炎病毒

基于高频超声评价不同针刺深度治疗膝骨关节炎的临床研究

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基于高频超声评价不同针刺深度治疗膝骨关节炎的临床研究

作者：琪丽妲（Kasandra sicilia Muntianu Fajardo）北京中医药大学

学位级别：硕士

目的:观察不同针刺深度治疗膝骨关节炎的疗效评价及对超声成像下积液、软骨厚度与滑膜的变化影响。方法:将90例膝骨关节炎患者,随机分为常规针刺组,口服西药组与浅刺组。常规针刺组与浅刺组取穴相同,均选取血海穴,梁丘穴,膝阳关穴,阳陵... 详细信息

目的:观察不同针刺深度治疗膝骨关节炎的疗效评价及对超声成像下积液、软骨厚度与滑膜的变化影响。方法:将90例膝骨关节炎患者,随机分为常规针刺组,口服西药组与浅刺组。常规针刺组与浅刺组取穴相同,均选取血海穴,梁丘穴,膝阳关穴,阳陵泉穴,阴陵泉穴,足三里穴,犊鼻穴,内膝眼穴,鹤顶穴,阿是穴。常规针刺组针刺深度为15-30mm,进针后,捻转片刻,以有酸麻胀触电感为佳。浅刺组直刺2mm,进针后,不进行任何手法操作。以上两组均留针20分钟,每周治疗3次。口服西药组给予硫酸氨基葡萄糖胶囊,一次2粒,每日3次。治疗时间持续8周。分别在治疗前、治疗4周后、治疗8周后,采用WOMAC膝关节功能评分量表和VAS疼痛量表评价其临床疗效。治疗前、治疗8周后通过膝关节超声观察膝关节软骨、滑膜和关节积液的变化,以评价临床疗效。结果:1、三组患者治疗前及治疗8周后高频超声进行组内比较:软骨内外侧厚度方面,三组组内治疗8周后较治疗前差异均无统计学意义（P＞0.05）;滑膜厚度方面,常规针刺组和浅刺组组内治疗8周后较治疗前差异有统计学意义（P＜0.05）,口服西药组差异无统计学意义（P＞0.05）,说明治疗8周后常规针刺和浅刺法明显减少膝关节滑膜厚度病变;关节积液方面,三组组内治疗8周后较治疗前差异均有统计学意义（P＜0.05）,说明治疗8周后三种方法明显减少治疗膝关节积液深度。2、三组患者治疗前及治疗8周后高频超声进行组间比较:软骨厚度、滑膜厚度及关节积液方面,三个组间差异均无统计学意义（P＞0.05）。治疗8周后关节积液方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异无统计学意义（P＞0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。治疗8周后滑膜厚度方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异有统计学意义（P＜0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。治疗8周后软骨厚度外内侧方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异无统计学意义（P＞0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。说明滑膜厚度方面常规针刺组比口服西药组的组间差异明显,常规针刺组的改善滑膜厚度效果最明显。3、三组患者治疗前、治疗4周及治疗8周后WOMAC评分进行组内比较:疼痛、僵硬和关节功能评分方面,三组组内治疗4周及治疗8周后较治疗前差异均有统计学意义（P＜0.05）,说明治疗4周及治疗8周后三种方法明显减轻膝关节疼痛、僵硬和关节功能的评分。4、三组患者治疗前、治疗4周及治疗8周后WOMAC评分进行组间比较:治疗4周后疼痛、僵硬、关节功能评分方面,三个组间差异均无统计学意义（P＞0.05）。治疗4周后疼痛方面,常规针刺组与浅刺组组间差异有统计学意义（P＜0.05）;常规针刺组与口服西药组组间差异有统计学意义（P＜0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。治疗4周后关节僵硬方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异无统计学意义（P＞0.05）;口服西药组与浅刺组组间差异有统计学意义（P＜0.05）。治疗4周后关节功能方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异无统计学意义（P＞0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。说明疼痛方面常规针刺组比另外两个组的组间差异最明显;僵硬方面浅刺组比口服西药组的组间差异明显。常规针刺组的缓解疼痛效果最明显。5、治疗8周后僵硬评分方面,三个组间差异均无统计学意义（P＞0.05）;治疗8周后疼痛和关节功能评分方面,三个组间差异均有统计学意义（P＜0.05）。治疗8周后疼痛方面,常规针刺组与浅刺组组间差异有统计学意义（P＜0.05）;常规针刺组与口服西药组组间差异有统计学意义（P＜0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。治疗8周后关节僵硬方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异有统计学意义（P=0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。治疗8周后关节功能方面,常规针刺组与浅刺组组间差异无统计学意义（P＞0.05）;常规针刺组与口服西药组组间差异有统计学意义（P＜0.05）;口服西药组与浅刺组组间差异无统计学意义（P＞0.05）。说明疼痛方面常规针刺组比另外两个组的组间差异最明显;僵硬和关节功能方面常规针刺组比口服西药组的组间差异明显。常规针刺组的缓解疼痛、僵硬和关节功能效果最明显。6、三组患者治疗前、治疗4周及治疗8周后VAS评分进行组内比较:三组组内治疗4周及治疗8周后较治疗前差异均有统计学意义（P＜

关键词：超声评价膝骨关节炎针刺深度针刺疗效

Systematic Approach for Web Protection Runtime Tools’Effectiveness Analysis

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Computer Modeling in Engineering & Sciences 2022年第12期133卷 579-599页

作者： Tomás Sureda Riera Juan Ramón Bermejo Higuera Javier Bermejo Higuera Juan Antonio sicilia Montalvo José Javier Martínez Herráiz Computer Science Department University of AlcaláMadrid28801Spain Escuela Superior de Ingeniería y Tecnología Universidad Internacional de La RiojaLogrono26006Spain

Web applications represent one of the principal vehicles by which attackers gain access to an organization’s network or resources.Thus,different approaches to protect web applications have been proposed to date.Of them,the two major approaches are Web Application Firewalls(WAF)and Runtime Application Self Protection(RASP).It is,thus,essential to understand the differences and relative effectiveness of both these approaches for effective decisionmaking regarding the security of web applications.Here we present a comparative study between WAF and RASP simulated settings,with the aim to compare their effectiveness and efficiency against different categories of attacks.For this,we used computation of different metrics and sorted their results using F-Score index.We found that RASP tools scored better than WAF tools.In this study,we also developed a new experimental methodology for the objective evaluation ofweb protection tools since,to the best of our knowledge,nomethod specifically evaluates web protection tools.

关键词： Web Application Firewall(WAF) Runtime Application Self Protection(RASP) F-Score web attacks experimental methodology

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贾斯汀和英勇骑士(3D)

读写算(科技知识动漫) 2013年第11期 38-39页

作者： Manuel sicilia Matthew Jacobs

导演:Manuel sicilia编剧:Manuel sicilia/Matthew Jacobs主演:西尔莎·罗南/马克·斯特朗/安东尼奥·班德拉斯类型:动画/冒险制片国家/地区:西班牙观赏指数:★★★★★★剧情介绍热血少年经过历练成长为英雄的故事,大银幕上从不鲜见。... 详细信息

导演:Manuel sicilia编剧:Manuel sicilia/Matthew Jacobs主演:西尔莎·罗南/马克·斯特朗/安东尼奥·班德拉斯类型:动画/冒险制片国家/地区:西班牙观赏指数:★★★★★★剧情介绍热血少年经过历练成长为英雄的故事,大银幕上从不鲜见。最近,一部此类题材的动画电影己在英国上映。这部电影的名字叫《贾斯汀和英勇骑士》(又译《天平与剑》)。贾斯汀一直希望能成为像他祖父一样优秀的骑士,但是他的父亲却想要让他成为一名律师。在贾斯汀与祖母的一次见面后,他终于

关键词：贾斯汀

Combinatorial Method with Static Analysis for Source Code Security in Web Applications

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Computer Modeling in Engineering & Sciences 2021年第11期129卷 541-565页

作者： Juan Ramon Bermejo Higuera Javier Bermejo Higuera Juan Antonio sicilia Montalvo Tomas Sureda Riera Christopher I.Argyros A.Alberto Magrenan Escuela Superior de Ingenierıa y Tecnologıa Universidad Internacional de La RiojaLogronoLa Rioja26006Spain Computer Science Department University of AlcalaMadrid28801Spain Department of Computing and Technology Cameron UniversityLawton73505OklahomaUSA Universidad de la Rioja LogronoLa Rioja26006Spain

Security weaknesses in web applications deployed in cloud architectures can seriously affect its data confidentiality and integrity.The construction of the procedure utilized in the static analysis tools of source code security differs and therefore each tool finds a different number of each weakness type for which it is designed.To utilize the possible synergies different static analysis tools may process,this work uses a new method to combine several source codes aiming to investigate how to increase the performance of security weakness detection while reducing the number of false positives.Specifically,five static analysis tools will be combined with the designed method to study their behavior using an updated benchmark for OWASP Top Ten Security Weaknesses(OWASP TTSW).The method selects specific metrics to rank the tools for different criticality levels of web applications considering different weights in the ratios.The findings show that simply including more tools in a combination is not synonymous with better results;it depends on the specific tools included in the combination due to their different designs and techniques.

关键词： Weakness benchmark security testing analysis comparative methodology tools combination web application

Benchmarking Approach to Compare Web Applications Static Analysis Tools Detecting OWASP Top Ten Security Vulnerabilities

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Computers, Materials & Continua 2020年第9期64卷 1555-1577页

作者： Juan R.Bermejo Higuera Javier Bermejo Higuera Juan A.sicilia Montalvo Javier Cubo Villalba Juan JoséNombela Pérez Escuela Superior de Ingeniería y Tecnología Universidad Internacional de La RiojaLa Rioja26006Spain

To detect security vulnerabilities in a web application,the security analyst must choose the best performance Security Analysis Static Tool(SAST)in terms of discovering the greatest number of security vulnerabilities as possible.To compare static analysis tools for web applications,an adapted benchmark to the vulnerability categories included in the known standard Open Web Application Security Project(OWASP)Top Ten project is required.The information of the security effectiveness of a commercial static analysis tool is not usually a publicly accessible research and the state of the art on static security tool analyzers shows that the different design and implementation of those tools has different effectiveness rates in terms of security performance.Given the significant cost of commercial tools,this paper studies the performance of seven static tools using a new methodology proposal and a new benchmark designed for vulnerability categories included in the known standard OWASP Top Ten project.Thus,the practitioners will have more precise information to select the best tool using a benchmark adapted to the last versions of OWASP Top Ten project.The results of this work have been obtaining using widely acceptable metrics to classify them according to three different degree of web application criticality.

关键词： Web application benchmark security vulnerability Security Analysis Static Tools assessment methodology false positive false negative precision f-measure