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Algorithmic approaches to clonal reconstruction in heterogeneous cell populations

Quantitative Biology 2019年第4期7卷 255-265页

作者： Wazim mohammed ismail Etienne Nzabarushimana Haixu Tang School of Informatics Computing and EngineeringIndiana UniversityBloomingtonIN 47405-7000USA

Background:The reconstruction of clonal haplotypes and their evolutionary history in evolving populations is a common problem in both microbial evolutionary biology and cancer *** clonal theory of evolution provides a theoretical framework for modeling the evolution of ***:In this paper,we review the theoretical framework and assumptions over which the clonal reconstruction problem is *** formally define the problem and then discuss the complexity and solution space of the *** methods have been proposed to find the phylogeny that best explains the observed *** categorize these methods based on the type of input data that they use(space-resolved or time-resolved),and also based on their computational formulation as either combinatorial or *** is crucial to understand the different types of input data because each provides essential but distinct information for drastically reducing the solution space of the clonal reconstruction *** information provided by single cell sequencing or from whole genome sequencing of randomly isolated clones can also improve the accuracy of clonal *** briefly review the existing algorithms and their *** we summarize the tools that are developed for either directly solving the clonal reconstruction problem or a related computational ***:In this review,we discuss the various formulations of the problem of inferring the clonal evolutionary history from allele frequeny data,review existing algorithms and catergorize them according to their problem formulation and solution *** note that most of the available clonal inference algorithms were developed for elucidating tumor evolution whereas clonal reconstruction for unicellular genomes are less *** conclude the review by discussing more open problems such as the lack of benchmark datasets and comparison of performance between available tools.

关键词： clonal theory infinite sites assumption clonal reconstruction problem bacteria evolution tumor evolution combinatorial algorithm probabilistic algorithm

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Low-velocity simultaneous bilateral femoral neck fracture following long-term antiepileptic therapy:A case report

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World Journal of Orthopedics 2019年第10期10卷 371-377页

作者： mohammed Sadiq Vikrant Kulkarni Syed Azher Hussain mohammed ismail Mayur Nayak Department of Orthopaedics ESIC Medical College

BACKGROUND Simultaneous bilateral femoral neck fractures are relatively rare *** are usually associated with underlying metabolic bone disorders or systemic ***-term use of narcotics and bisphosphonates can also result in similar fracture patterns;however,association of this fracture type with longterm use of antiepileptic drugs is not very *** one such case has been reported in the *** article describes the *** REPORT We report a case of simultaneous displaced bilateral femoral neck fractures in a 50-year-old epileptic patient,who had taken phenytoin for the past 3 *** fractures were a result of low-velocity injury following a fall from the *** fractures were managed with a bilateral hemi-replacement *** bisphosphonates were given to improve the bone quality in the post-operative *** patient had a good post-operative outcome,that was sustained throughout the entire follow-up period of 1 *** Antiepileptic drugs should be supplemented with bisphosphonates and vitamin D to improve bone quality and prevent fractures in epileptic patients.

关键词： Case report Bilateral femoral neck fracture Antiepileptic drug therapy Druginduced osteopenia Bisphosphonates Vitamin D

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Study on Rotation-Invariant in Aerial Object Detection using Rotatable Bounding Boxes

Study on Rotation-Invariant in Aerial Object Detection using...

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作者： AL-SOSWA,mohammed ismail AHMED 南京理工大学

学位级别：硕士

目前,神经网络和深度学习的理论与方法广泛应用于计算机视觉和目标检测的研究,其研究成果已广泛用于自动驾驶、航空出行、安防等领域。传统的目标检测方法依靠绘制在目标上的矩形,通过水平和垂直边界框来确定目标位置。航空图像中的物... 详细信息

目前,神经网络和深度学习的理论与方法广泛应用于计算机视觉和目标检测的研究,其研究成果已广泛用于自动驾驶、航空出行、安防等领域。传统的目标检测方法依靠绘制在目标上的矩形,通过水平和垂直边界框来确定目标位置。航空图像中的物体方向随机,密集且周围复杂,因此对传统的物体检测模型构成了挑战。传统的矩形框会忽略物体的方向,从而导致物体定位减少,并且在目标密集情况下重叠的框会限制进一步的处理,例如目标的理解和检测。为了克服这些局限性,本文对目标检测方法进行改进,实现更高效,更精确的检测。首先,修改目标检测边界框的定义,包括旋转,高度,宽度和框的中心点,有效的定位目标并减少背景像素的干扰;其次,应用金字塔特征网络学习多层特征生以检测小面积目标;然后,对边界框的常规编码方案进行了修改以适合提出的可旋转边界框,以便更好地估计目标的方向和位置;最后,为了克服负样本和正样本之间的不平衡问题,将难负样挖掘（Hard Negative Mining,HNM）和焦点损失（focal loss,FL）结合起来使用,从而解决正负样本不平衡的问题。通过分析模型在四个数据集上的目标检测结果,并与（Single Shot Detector,SSD）和Faster R-CNN进行比较,表明本文提出的模型超越了传统的边界框模型,尤其是旋转和密集目标。

关键词：旋转不变性卷积神经网络特征金字塔网络焦点损失可旋转边框目标检测

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An unusual cause of simultaneous bilateral spontaneous pneumothorax

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World Journal of Emergency Medicine 2017年第1期8卷 74-76页

作者： mohammed ismail Nizami Narendra Kumar Narahari Goganti Kruparao Paramjyothi Ashima Sharma Department of Emergency Medicine Nizam's Institute of Medical Sciences Hyderabad 500082 Telangana India Department of Respiratory Medicine Nizam's Institute of Medical Sciences Hyderabad 500082 Telangana India

INTRODUCTIONScrub typhus, a tropical febrile vector borne disease also known as ＂Tsutsugamushi disease＂, is caused by Orientia tsutsugamushi, a gram negative obligate intracellular slow growing bacteria. The infecti... 详细信息

关键词： simultaneous bilateral spontaneous pneumothorax

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Falafel: A Meal with Full Nutrition

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Food and Nutrition Sciences 2017年第11期8卷 1022-1027页

作者： mohammed ismail Erdogan Kucukoner Department of Food Engineering Engineering Faculty Suleyman Demirel University Isparta Turkey

There are a lot of fried food recipes that contain vegetables as a main ingredient. One of the most famous fried vegetables in the Middle East is Falafel. Falafel is a traditional Egyptian and Middle Eastern food with deferent names from country to another, for examples it is called Falafel in Iraq and Levant, and it is called Ta’amiya in Egypt. Falafel is a vegetarian recipe which reflects its nutritious value. In this article, we are going to refer to the definition of Falafel and its origin to show that Falafel is a global dish. In addition, the ingredients of Falafel are going to be mentioned. Finally, the benefits of Falafel are going to be explained to show how Falafel is considered as a nutritious meal. This study has discovered that Falafel is one of the healthy vegetarian meals due to its ingredients which are full of vitamins and also considered as a very rich source of dietary fiber.

关键词： Falafel Ta’amiya Nutrition Vegetarian Deep-Fried Ball

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Isolation and characterization of marine-derived actinomycetes with cytotoxic activity from the Red Sea coast

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Asian Pacific Journal of Tropical Biomedicine 2016年第8期6卷 651-657页

作者： Mohamed Saleh Abdelfattah mohammed ismail Youssef Elmallah Usama Wahid Hawas Lamia Taha Abou El-Kassema Mennat Allah Gamal Eid Marine Natural Products Research Unit Faculty of Science Helwan University Marine Chemistry Department Faculty of Marine Sciences King Abdulaziz University Pharmacognosy Department National Research Centre

Objective: To isolate and evaluate the cytotoxic activity of different actinomycetes species isolated from the Red Sea coast in Sharm el-Sheikh, ***: Forty actinomycetes strains were isolated from different sediments and seawater samples collected from the Red Sea coast in Egypt. Actinomycetes were recognized by morphological and microscopic examinations. Cell viability and cytotoxicity induced by the crude extracts on breast cancer cell lines MDA-MB-231 were assessed using methylene blue assay. The strains with promising cytotoxic activity were identified by sequencing and amplifying the 16 S r RNA genes. The antibacterial activities of the crude extracts were performed using Kirby–Bauer disc diffusion ***: The results indicated that five ethyl acetate extracts exhibited cytotoxicity towards breast cancer cell lines MDA-MB-231. The highest cytotoxic activity was found for the ethyl acetate extracts of EGY2 and EGY39. The isolate EGY3 was identified as a new Streptomyces species, while the actinomycete EGY22 was found to be a member of the genus Nocardiopsis sp. The crude extract of the isolate EGY8 showed slightly high antimicrobial activity against different test ***: The results of the present study reveal that marine sediments of the Red Sea are a potent source of novel species of actinomycetes. The isolates may be useful in discovery of novel bioactive compounds and an important step in the development of microbial natural product research.

关键词： Red Sea Breast cancer Actinomycetes 16S rRNA Cytotoxicity

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青黛及其有效成分抗溃疡性结肠炎药理作用及机制的研究进展

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药物评价研究 2022年第5期45卷 997-1002页

作者：张曦徐小婷 mohammed ismail 肖莉孙丽新张陆勇中国药科大学新药筛选中心江苏南京210009 湖州大学生命科学学院浙江湖州313000 广东药科大学新药研发中心广东广州510006

青黛(Indigo Naturalis)是传统中药,临床上已经用于治疗银屑病、急性早幼粒细胞白血病和溃疡性结肠炎。溃疡性结肠炎是一种慢性非特异性的炎症性肠病,近年来发病率逐渐上升。青黛及其效成分靛蓝和靛玉红治疗溃疡性结肠炎时取得显著疗效... 详细信息

青黛(Indigo Naturalis)是传统中药,临床上已经用于治疗银屑病、急性早幼粒细胞白血病和溃疡性结肠炎。溃疡性结肠炎是一种慢性非特异性的炎症性肠病,近年来发病率逐渐上升。青黛及其效成分靛蓝和靛玉红治疗溃疡性结肠炎时取得显著疗效,其药理作用机制涉及抗炎、促黏膜愈合、维护肠道免疫稳态和调节肠道菌群等多个方面。对近年来青黛及其有效成分靛蓝和靛玉红抗溃疡性结肠炎的药理作用及其机制进行总结,以期为临床合理用药及抗溃疡性结肠炎新药研发提供依据。

关键词：青黛靛蓝靛玉红抗炎黏膜愈合免疫调节

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色氨酸微生物吲哚代谢途径在IBD治疗及新药研发中的作用

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中国免疫学杂志 2022年第12期38卷 1509-1515页

作者：张倩文张曦徐小婷 mohammed ismail 江振洲焦春花(指导) 孙丽新(指导) 中国药科大学江苏省药效研究与评价服务中心南京210009 南京医科大学第一附属医院消化内科南京210000

炎症性肠病(IBD)是一种慢性非特异性肠道炎症,复发性较高。我国IBD发病逐年升高,但发病机制仍不明确,且无根治性药物。近年肠道微生物产生的小分子代谢物逐渐被重视,对调节宿主病理生理状态具有重要作用,其中色氨酸经肠道微生物群代谢... 详细信息

炎症性肠病(IBD)是一种慢性非特异性肠道炎症,复发性较高。我国IBD发病逐年升高,但发病机制仍不明确,且无根治性药物。近年肠道微生物产生的小分子代谢物逐渐被重视,对调节宿主病理生理状态具有重要作用,其中色氨酸经肠道微生物群代谢产生的吲哚类物质与IBD关系密切。本文就吲哚类物质在IBD中的变化特点、生理功能及药物对吲哚类物质代谢通路的影响进行综述,以便深入了解肠道微生物产生的吲哚类代谢物与IBD的关系,为IBD治疗和新药研发提供新的方向和突破点。

关键词：炎症性肠病色氨酸微生物代谢途径吲哚代谢物

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LncRNA调控肝脏疾病中信号转导通路的研究进展

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中国药科大学学报 2020年第3期51卷 277-286页

作者：刘丽张倩文农程张曦徐小婷 mohammed ismail 肖莉江振洲张陆勇孙丽新中国药科大学江苏省新药筛选重点实验室南京210009 湖州师范学院生命科学学院湖州313000 中国药科大学江苏省药物动力学研究与评价中心南京210009 广东药科大学药学院新药筛选与药效学评价中心广州510006

肝脏疾病的发病率逐年上升,由于肝脏疾病发病诱因复杂和发病机制尚未阐明,治愈率不够理想,迫切需要明确其作用机制以找到更有效的治疗靶点与药物。长链非编码RNA(long non-coding RNA,lncRNA)作为一种长度超过200 nt的非编码RNA,是近年... 详细信息

肝脏疾病的发病率逐年上升,由于肝脏疾病发病诱因复杂和发病机制尚未阐明,治愈率不够理想,迫切需要明确其作用机制以找到更有效的治疗靶点与药物。长链非编码RNA(long non-coding RNA,lncRNA)作为一种长度超过200 nt的非编码RNA,是近年来肝脏疾病的研究热点。本文以肝脏疾病中主要的信号转导通路为主线,对近年来lncRNA调控肝脏疾病相关信号通路的最新研究进展进行归纳总结,详细阐述lncRNA通过调节肝脏疾病中关键的信号通路,参与细胞增殖、凋亡、侵袭、迁移等多种生理过程,从而促进肝脏疾病的发生发展,为肝脏疾病的机制研究提供新的思路,为寻找治疗肝脏疾病的新靶点及生物标志物提供新的研究方向。

关键词：长链非编码RNA 肝脏疾病信号转导通路进展

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Frequency of Hypocalcaemia after Thyroid Surgery in the Omdurman Military Hospital in 2018

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Surgical Science 2023年第2期14卷 111-121页

作者： Ali Hassan Ali Ahmed Adeel Reham Abd Alhalem Hijo Khaleel Sirag Abdelazim Sirag Elnor Elwasila mohammed Gibriel Badawi ismail College of Medicine Karary University Omdurman Sudan University of Bahri Bahri Sudan

Background: Hypocalcaemia is a serious complication that may follows thyroid surgeries. So, the purpose of this study was to determine the frequency of postoperative hypocalcaemia after thyroid surgery in Omdurman military hospital (Jan.-July 2018). Materials & Methods: In this retrospective facility based cross sectional study, 124 files were reviewed, the recorded data were age, sex, residence, diagnosis, type of surgery & postoperative calcium level, data were collected by a designed pretested checklist, data were analyzed by SPSS version 20 by using frequencies & cross tabulations, for postoperative hypocalcaemia. Results: Majority of the patients were between 21 - 41 years 49.2%, majority of them were females 83.9%. 97.6% of them underwent total thyroidectomy, 25% of the patients developed postoperative hypocalcaemia, also we found that there was no relation between sex, type of thyroid surgery & development of postoperative hypocalcaemia (P > 0.001). Conclusion: Our research showed that 25% of the patients who underwent thyroid surgery developed postoperative hypocalcaemia.

关键词： Thyroid Diseases Hypocalcaemia Thyroidectomy

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