Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments

© 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.The binarization of consensus partition matrices (Bi-CoPaM) method has, among its unique features, the ability to perform ensemble clustering over the same set of genes from multiple microarray datasets by using various clustering methods in order to generate tunable tight clusters. Therefore, we have used the Bi-CoPaM method to the most synchronized 500 cell-cycle-regulated yeast genes from different microarray datasets to produce four tight, specific and exclusive clusters of co-expressed genes. We found 19 genes formed the tightest of the four clusters and this included the gene CMR1/YDL156W, which was an uncharacterized gene at the time of our investigations. Two very recent proteomic and biochemical studies have independently revealed many facets of CMR1 protein, although the precise functions of the protein remain to be elucidated. Our computational results complement these biological results and add more evidence to their recent findings of CMR1 as potentially participating in many of the DNA-metabolism processes such as replication, repair and transcription. Interestingly, our results demonstrate the close co-expressions of CMR1 and the replication protein A (RPA), the cohesion complex and the DNA polymerases α, δ and ɛ, as well as suggest functional relationships between CMR1 and the respective proteins. In addition, the analysis provides further substantial evidence that the expression of the CMR1 gene could be regulated by the MBF complex. In summary, the application of a novel analytic technique in large biological datasets has provided supporting evidence for a gene of previously unknown function, further hypotheses to test, and a more general demonstration of the value of sophisticated methods to explore new large datasets now so readily generated in biological experiments.National Institute for Health Researc

Collective analysis of multiple high-throughput gene expression datasets

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonModern technologies have resulted in the production of numerous high-throughput biological datasets. However, the pace of development of capable computational methods does not cope with the pace of generation of new high-throughput datasets. Amongst the most popular biological high-throughput datasets are gene expression datasets (e.g. microarray datasets). This work targets this aspect by proposing a suite of computational methods which can analyse multiple gene expression datasets collectively. The focal method in this suite is the unification of clustering results from multiple datasets using external specifications (UNCLES). This method applies clustering to multiple heterogeneous datasets which measure the expression of the same set of genes separately and then combines the resulting partitions in accordance to one of two types of external specifications; type A identifies the subsets of genes that are consistently co-expressed in all of the given datasets while type B identifies the subsets of genes that are consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets. This contributes to the types of questions which can addressed by computational methods because existing clustering, consensus clustering, and biclustering methods are inapplicable to address the aforementioned objectives. Moreover, in order to assist in setting some of the parameters required by UNCLES, the M-N scatter plots technique is proposed. These methods, and less mature versions of them, have been validated and applied to numerous real datasets from the biological contexts of budding yeast, bacteria, human red blood cells, and malaria. While collaborating with biologists, these applications have led to various biological insights. In yeast, the role of the poorly-understood gene CMR1 in the yeast cell-cycle has been further elucidated. Also, a novel subset of poorly understood yeast genes has been discovered with an expression profile consistently negatively correlated with the well-known ribosome biogenesis genes. Bacterial data analysis has identified two clusters of negatively correlated genes. Analysis of data from human red blood cells has produced some hypotheses regarding the regulation of the pathways producing such cells. On the other hand, malarial data analysis is still at a preliminary stage. Taken together, this thesis provides an original integrative suite of computational methods which scrutinise multiple gene expression datasets collectively to address previously unresolved questions, and provides the results and findings of many applications of these methods to real biological datasets from multiple contexts.National Institute for Health Research (NIHR) and the Brunel College of Engineering, Design and Physical Science

Climate change and agricultural water demand: Impacts and adaptations

Global climate change related to natural and anthropogenic processes has been the topic of concern and interest world - wide. One of the most significant impacts of the ‘greenhouse effect’ is anticipated to be on water resources. Thus, the impact of climate change appears to be an additional component on top of the large number of existing water-related problems. The objective of the present paper is to analyze the climate change impacts on crop and irrigation water requirements, applying the CROPWAT model to several incremental climatic change scenarios for the West Bank governorate of Jericho and Al-Aghwar as a case study. The results clearly show that the greatest threat occurs if a temperature rise of 3°C is accompanied by 20% decrease in precipitation levels. For that scenario, there is a need to increase the amount of water for irrigation by 2.9 MCM/Y. A number of possible adaptation measures (at both sector/policy level and farm level) were evaluated. The evaluation was based on analysis of the relevant literature and stakeholder participation with respect to the following issues: adaptive capacity, technical feasibility and potential costs of implementation

Pregnant Women’s Satisfaction about Antenatal Care Services in Umbada Hospital for Maternal and Child Health Care Sudan, 2020

يعتبر مستوى رضا النساء الحوامل مؤشر مهم لتقييم خدمات رعاية الام الحامل المقدمة للزبائن القادمين في المراكز الصحية لتلقي العلاج او الوقاية، الحصول على اعلى مسويات الرضى لدى النساء الحوامل يقلل معدل وفيات الأمهات والامراضية وكذلك تخفيض معدل وفيات الاجنة وحديثي الولادة وتمنع ولادة الاطفال ناقصي الوزن. الهدف: دراسة مستوى رضا النساء الحوامل عن خدمات رعاية الام الحامل بمستشفى امبدة لصحة الام والطفل، نوع الدراسة والطريقة: أُجريت دراسة وصفية مقطعية في المستشقى،مجتمع الدراسة هو كل النساء الحوامل المترددات بوحدة متابعة الحمل بالمستشفى وتم اختيار التغطية الشاملة للنساء المترددات بالمركز لمدة شهر (1-30/12/ 2020م، فترة الدراسة) وشملت العدد الكلي 188امرأة. تم استخدام الاستبيان وعمل ثلاث مجموعات النقاش لعدد 22امرأة من الستهدفين واجراء المقابلة الشخصية مع المدير الطبي لجمع البيانات ومعلومات بالدراسة، النتائــج والخاتمــة: من ابرز النتائج التي توصلت اليها هذه الدراسة هي ان مستوى الرضا العام للنساء الحوامل المترددات بالمركز تجاه خدمات رعاية الحوامل هو 78.22%، مقسمة الى 39.2% منهن راضيات جدا، 28.42%منهن راضيات الى حد معقول، 10.6% منهن راضيات الى حد قليل، بينما 21.7% منهن غير راضيات بالخدمات المقدمة اليهن، وايضا وجد ان متوسط مستوى الرضا العام هو 51.9 ±52.9 اوضحت الدراسة ان هنالك فجوات كبيرة في خدمات رعاية الام الحامل المقدمة بالمركز وتتمثل في عدم الاهتمام بعلاج حالات الامراض المعدية الاخرى وغياب قسم امراض النساء في سن الانجاب وغياب خدمات الصحة النفسية والاراشاد النفسي للنساء المترددات بالمركز نسبة لعدم وجود الطبيب النفسي او الباحث الاجتماعي بالمركز واطالة زمن الانتظار لتلقي الخدمة الصحية (يستغرق اكثر من 60دقيقة). كما ان الاغلبية العظمى منهن (90%) لم تتلق اي مواد النظافة الشخصية ومواد غسل اليدين،وكذلك حوالي اكثر من ثلثين (65%) منهن لم يجدن اي خدمات التوعية الصحية عن صحتهن اثناء الحمل، اضافة الى ان ( 88%) منهن لم يتم اخبارهن عن اي ارشادات و طرق الوقاية من عدوى الامراض المنقولة جنسيا كالايدز وطرق الكشف المبكر عن سرطان الثدي وسرطان عنق الرحم. وايضا توصلت الدراسة من خلال المقابلة الشخصية مع المدير الطبي ونتائج مجموعات النقاش الثلاثة الى ان من المعوقات او الصعوبات التي تعيق تلقي خدمات رعاية الام الحامل هي: نقص أدوية الرعاية الصحية الاساسية، عدم وجود قسم التحصين ضد التيتانوس بداخل مركز متابعة الحمل وقلة الوعي لديهن تجاه اهمية التطعيم ضد التيتانوس، عدم الاهتمام بعلاج الامراض المعدية والمزمنة، صعوبة المواصلات، اثار انتشار جائحة الكرونا، تكاليف العميات القيصرية وبعض الادوية ، ضعف التزام بعض الاطباء لتقديم الخدمة الصحية للنساء الحوامل في الزمن المحدد مما تسبب ذلك في اطالة زمن الانتظار. على الرغم من ذلك وجد ان 16(74%) من النساء في مجموعات النقاش راضيات بالخدمة المقدمة اليهن. ختامــــاً، على الرغم من ان ارتفاع مستوى الرضا العام الى (78.22%) نجد ان كل نقاط القصور في خدمات رعاية الام الحامل المذكورة سابقاً تشير بشكل واضح الى ضعف جودة خدمات الرعاية الصحية للحوامل بهذا المستشفى، وخلصت الدراسـة الى التوصيات الاتية لإدارة المستشفى ووزارة الصحة الولائية: توفير ادوية الرعاية الصحية الاساسية في المستشفى وتوزيعها بشكل مستمر، انشاء قسم خاص بتدريب مقدمي الخدمة الصحية على كيفية التعرف وعلاج الامراض المعدية الاخري والاهتمام بالصحة النفسية والارشاد النفسي للنساء الحوامل، زيادة عدد اطباء قسم متابعة الحوامل وتنظيم العمل لتغطية الخدمة في وقت وجيز ولتفادي مشقة الانتظار الطويل والازدحام و كذلك ارجاع قسم التحصين/التطعيم الخاص بالحوامل من االخارج الى قسم متابعة الحوامل وان تكون خدمات رعاية الام ومتابعة الحمل مجانية بالمركز مع توفير برنامج التأمين ال

Dihedral codes with prescribed minimum distance

Dihedral codes, particular cases of quasi-cyclic codes, have a nice algebraic structure which allows to store them efficiently. In this paper, we investigate it and prove some lower bounds on their dimension and minimum distance, in analogy with the theory of BCH codes. This allows us to construct dihedral codes with prescribed minimum distance. In the binary case, we present some examples of optimal dihedral codes obtained by this construction.Comment: 13 page

Cloud ConsultingCrowdsourcing-Based Framework for ERP Consulting

Information Technology (IT) altered the way of running businesses in all fields. The installation and integration of an Enterprise Resource Planning (ERP) system is a critical process. With the emergence of Web 2.0, many businesses were created or reengineered to gain an advantage from this technology. This offers an enormous network of users with different interests and skills, and support knowledge transfer. Our expectation is that ERP consulting business will be the next to be changed. In this work, a cloud consulting framework will be provided to enhance the services offered based on crowdsourcing. After examining literature on crowdsourcing and ERP consulting, the following research question was stated: “How can cloud consulting employ crowdsourcing to improve ERP consultancy?” Thus, the research objective is to develop a cloud consulting framework for ERP consulting based on crowdsourcing

Charles Malamoud, La Danse des pierres. Études sur la scène sacrificielle dans l’Inde ancienne

Le recueil d’articles qui constituent cet ouvrage vient à la suite de deux autres publiés successivement en 2002 et 2005, Le Jumeau solaire qui traite de la mort et La Féminité de la parole qui au contraire met l’accent sur la vie. Ici le sacrifice védique est considéré sous l’angle de la méthode d’approche du rituel dont le sous-titre constitue une des clés. Les articles des trois livres ont d’abord été publiés dans des revues et datent à peu près de la même période. Cela signifie que Charle..

Clustering consistency in neuroimaging data analysis

Clustering techniques have been applied to neuroscience data analysis for decades. New algorithms keep being developed and applied to address different problems. However, when it comes to the applications of clustering, it is often hard to select the appropriate algorithm and evaluate the quality of clustering results due to the unknown ground truth. It is also the case that conclusions might be biased based on only one specific algorithm because each algorithm has its own assumption of the structure of the data, which might not be the same as the real data. In this paper, we explore the benefits of integrating the clustering results from multiple clustering algorithms by a tunable consensus clustering strategy and demonstrate the importance and necessity of consistency in neuroimaging data analysis