Computational methods for the discovery and analysis of genes and other functional DNA sequences

The need for automating genome analysis is a result of the tremendous amount of genomic data. As of today, a high-throughput DNA sequencing machine can run millions of sequencing reactions in parallel, and it is becoming faster and cheaper to sequence the entire genome of an organism. Public databases containing genomic data are growing exponentially, and hence the rise in demand for intuitive automated methods of DNA analysis and subsequent gene identification. However, the complexity of gene organization makes automation a challenging task, and smart algorithm design and parallelization are necessary to perform accurate analyses in reasonable amounts of time. This work describes two such automated methods for the identification of novel genes within given DNA sequences. The first method utilizes negative selection patterns as an evolutionary rationale for the identification of additional members of a gene family. As input it requires a known protein coding gene in that family. The second method is a massively parallel data mining algorithm that searches a whole genome for inverted repeats (palindromic sequences) and identifies potential precursors of non-coding RNA genes. Both methods were validated successfully on the fully sequenced and well studied plant species, Arabidopsis thaliana --Abstract, page iv

A quantitative study of gene identification techniques based on evolutionary rationales

Current gene identification (GI) techniques typically rely on matching biological or chemical properties of specific genes, specific species, specific ecotypes, etc...In this thesis, a new automated GI technique is proposed, and compared against another computer-based technique proposed earlier. Both methods utilize EST data available from NCBI databases to discover previously unknown genes. The newly proposed method identifies one gene family at a time and is based on a distinctive negative selection pattern (NSP) of differences, which is seen between the coding regions of gene family members. The other technique, called ESTminer, attempts genome-wide gene family identification for any organism, by detecting single nucleotide polymorphisms between potential family members. In this thesis, a complete automated analysis of both techniques is presented --Abstract, page iii

Fractals and music

Many natural phenomena we find in our surroundings, are fractals.  Studying and learning about fractals in classrooms is always a challenge for both teachers and students. We here show that the sound of musical instruments can be used as a good resource in the laboratory to study fractals. Measurement of fractal dimension which indicates how much fractal content is there, is always uncomfortable, because of the size of the objects like coastlines and mountains. A simple fractal source is always desirable in laboratories. Music serves to be a very simple and effective source for fractal dimension measurement. In this paper, we are suggesting that music which has an inherent fractal nature can be used as an object in classrooms to measure fractal dimensions. To find the fractal dimension we used the box-counting method. We studied the sound produced by different stringed instruments and some common noises. For good musical sound, the fractal dimension obtained is around 1.6882

Defining 'energy' in micro canonical ensemble

The micro canonical ensemble (MCE) represents an isolated system having fixed energy. The nature of energy in MCE is always a subject of discussion. In this paper we are distinguishing the energy possessed by the system and the energy offered by the system for measurement in MCE. This we hope will help the learners of statistical mechanics to have a more understanding of MCE

A Study on the Cavity Problems in Patients Who Have Undergone Functional Endoscopic Sinus Surgery

Background and Objectives: Studies on the postoperative problems of endoscopic sinus surgery are rare in literature. The objective is to study the postoperative symptoms of patients and findings on nasal endoscopy after functional endoscopic sinus surgery (FESS). Adequate postoperative care necessary after FESS and ways to reduce the cavity problems to be studied. Methods:113 patients who underwent FESS for various pathologies were followed up at regular intervals with nasal endoscopy. Postoperative  symptoms of patients were documented, nasal endoscopy done and findings noted. Necessary interventions performed according to the problems visualized. Results were analysed at 1 month and 3 monthspost surgery and as required thereafter.Results: Postoperative review at 1 month showed symptoms of smell disturbances(24 cases), nasal obstruction(16 cases), headache(4) and nasal discharge(2). Nasal endoscopy revealed synechiae in 16 patients, significant crusting and fungal debris in 11 patients each. AFRS (17 out of 25 cases) and ethmoidal polyps (19 out of 52 cases) had maximum problem rate. Procedure wise, revision FESS and cases with septal correction showed maximum problems. Necessary intervention performed. Review at 3 months showed persistent smell disturbances in 6 ethmoidal polyp cases and persistent fungal debris in 5 of the AFRS cases. Rest of the cases improved. Outside this review, 1 case of antrochoanal polyp and 9 cases of ethmoidal polyps showed recurrence later on which was treated endoscopically.Interpretation and Conclusion: AFRS and ethmoidal polyps require rigorous postoperative care with nasal endoscopy and appropriate intervention as they are prone for recurrence and postoperative problems. Revision FESS need extensive preoperative assessment to reduce problem rate. Duration of follow up necessary for each case need more extensive long term studies. Keywords: Functional Endoscopic Sinus Surgery, Post operative, Cavity Problem

Marketing de Recrutamento - Uma Análise Bibliométrica

Purpose: The purpose of the study is to conduct a Bibliometric analysis of Recruitment Marketing.   Theoretical framework: Recruitment Marketing is a technique that has evolved recently to nurture candidates before they apply for a job. Understanding and applying recruitment marketing techniques is essential to retain a talent pool. Since Recruitment Marketing is a new strategy, there is still much to research and discover.   Design/methodology/approach: The current scenario of publications from 2000-2020 on Recruitment Marketing listed in the Clarivate Web of Science database was explored in this bibliometric study. To build a bibliometric map, descriptive and inferential statistical methods were utilized. Bibliometric analysis was performed using R-based software Biblioshiny.   Findings: The findings revealed that the topic is not well established in the literature but has scope for growth in the coming future. The results reported that only very few studies were undertaken in the area of recruitment marketing globally. USA and Australia are the countries which contributed articles in this area when compared to other countries. The most commonly used words are 'loyalty,' 'attraction,' and 'conceptual-model'. New developments in recruitment marketing have not been sufficiently studied and understood logically and concisely. This study utilized a conceptual framework to organize and analyze the field's various research streams and themes. These themes and subthemes have suggested research recommendations and crucial research areas.   Research, Practical & Social implications: Authors recommend in-depth study for the future and identify the areas that need more exploration. The current study can help researchers and recruiters to analyze the upcoming recruiting trends and strategies.   Originality/value: The study is found to be primary and original research that contributes to the bibliometric representation of recruitment marketing.Propósito: El propósito del estudio es realizar un análisis Bibliométrico sobre “Marketing de Reclutamiento”. Marco teórico: El marketing de reclutamiento es una técnica que ha evolucionado recientemente para nutrir a los candidatos antes de que realmente soliciten un trabajo. Comprender y aplicar técnicas de marketing de reclutamiento es muy esencial para retener un grupo de talentos. Dado que el Marketing de Reclutamiento es una estrategia nueva, aún queda mucho por investigar y descubrir al respecto. Diseño/metodología/enfoque: En este estudio bibliométrico se exploró el escenario actual de publicaciones de 2000-2020 sobre “Recruitment Marketing” que figuran en la base de datos Clarivate Web of Science. Para construir un mapa bibliométrico se utilizaron métodos de estadística descriptiva e inferencial. El análisis bibliométrico se realizó utilizando un software basado en R. Hallazgos: Los hallazgos revelaron que el tema no está bien establecido en la literatura, pero tiene posibilidades de crecimiento en el futuro próximo. Los resultados informaron que solo hay muy pocos estudios realizados en el área de marketing de reclutamiento en todo el mundo. EE. UU. y Australia son los países que contribuyeron con artículos en esta área en comparación con otros países. Las palabras más utilizadas son 'lealtad', 'atracción' y 'modelo conceptual'. Los nuevos desarrollos en marketing de reclutamiento no han sido suficientemente estudiados y entendidos de una manera lógica y concisa. Este estudio utilizó un marco conceptual para organizar y analizar las diversas corrientes de investigación y temas en el campo. Estos temas y subtemas han sugerido recomendaciones de investigación y áreas de investigación cruciales. Implicaciones de investigación, prácticas y sociales: los autores recomiendan un estudio en profundidad para el futuro e identifican las áreas que necesitan más exploración. El estudio actual puede ayudar tanto a los investigadores como a los reclutadores a analizar. Originalidad/valor: se considera que el estudio es una investigación primaria y original que contribuye a la representación bibliométrica del marketing de reclutamiento. Palabras clave: análisis bibliométrico; Estructura conceptual; software R; Comercialización de Reclutamiento; Web de la CienciaObjetivo: O objetivo do estudo é realizar uma análise Bibliométrica sobre “Marketing de Recrutamento”. Quadro teórico: O Marketing de Recrutamento é uma técnica que evoluiu recentemente para nutrir os candidatos antes que eles realmente se candidatem a um emprego. Compreender e aplicar técnicas de marketing de recrutamento é muito essencial para reter um pool de talentos. Como o Marketing de Recrutamento é uma estratégia nova, ainda há muito o que pesquisar e descobrir sobre ele. Design/metodologia/abordagem: O cenário atual de publicações de 2000-2020 sobre “Recruitment Marketing” listados na base de dados Clarivate Web of Science foi explorado neste estudo bibliométrico. Para a construção do mapa bibliométrico, foram utilizados métodos de estatística descritiva e inferencial. A análise bibliométrica foi realizada usando um software baseado em R. Resultados: Os resultados revelaram que o tema não está bem estabelecido na literatura, mas tem espaço para crescimento no futuro próximo. Os resultados relataram que há muito poucos estudos realizados na área de marketing de recrutamento em todo o mundo. EUA e Austrália são os países que mais contribuíram com artigos nesta área quando comparados a outros países. As palavras mais usadas são “lealdade”, “atração” e “modelo conceitual”. Novos desenvolvimentos no marketing de recrutamento não foram suficientemente estudados e compreendidos de forma lógica e concisa. Este estudo utilizou uma estrutura conceitual para organizar e analisar as várias linhas e temas de pesquisa no campo. Recomendações de pesquisa e áreas de pesquisa cruciais foram sugeridas por esses temas e subtemas. Pesquisa, implicações práticas e sociais: os autores recomendam um estudo aprofundado para o futuro e identificam as áreas que precisam de mais exploração. O estudo atual pode ajudar tanto os pesquisadores quanto os recrutadores a analisar o aspecto do marketing de recrutamento. Originalidade/valor: O estudo é considerado uma pesquisa primária e original que contribui para a representação bibliométrica do marketing de recrutamento. Palavras-chave:  Análise bibliométrica; Estrutura conceitual;software R; Marketing de Recrutamento; Web da Ciênci

An Analytical study Correlating the Significance of Serum Lipids in the Development of Clinically Significant Macular Edema in Patients with Diabetic Retinopathy

INTRODUCTION: The ETDRS (Early Treatment Diabetic Retinopathy Study) has classified Diabetic Retinopathy into NPDR(Non Proliferative Diabetic Retinopathy) and PDR(Proliferative Diabetic Retinopathy. This classification is based on the findings in the clinical examination and comparing it with the standard photographs. Very mild NPDR, mild NPDR, moderate NPDR, severe and very severe NPDR forms the further classification of NPDR. Mild-moderate, High risk PDR and (ADED) Advanced Diabetic Eye Disease forms the sub classification of PDR. Chronically elevated blood glycemic levels is the most important factor leading to the development of diabetic retinopathy and its various complications. AIM OF THE STUDY: To correlate the levels of serum lipid and presence of clinically significant macular oedema in diabetic retinopathy patients. OBJECTIVES: To compare the serum lipid profile of patients with and without clinically significant macular oedema and to emphasize the importance of doing serum lipid profile as a routine investigation in patients with diabetic retinopathy and to initiate treatment for those appropriate. MATERIALS AND METHODS: 200 patients with diabetic retinopathy were selected for the study and divided equally into 2 groups containing 100 patients each. RESULTS: Total cholesterol levels in patients of Group A ranged from 140–518 mg/dl with a mean of 318.69 mg / dl and Group B from 112– 412 mg / dl with a mean of 199.57 mg / dl. Total cholesterol level was found to be statistically significant with a ‘p’ value of 0.0000. Patients without CSME had a mean triglyceride levels of 164.89 mg/dl whereas patients with CSME had a higher triglyceride levels with a mean of 257.07 mg / dl with the ‘p’ value of 0.0000. Patients with CSME had mean HDL-C levels of 35.49 mg/dl and those who did not have CSME had a mean of 49.13 mg / dl. Patients with CSME had higher serum LDL-C levels with a mean of 195.48 mg / dl compared to patients without CSME who had 107.73 mg% (p=0.0000). Blood urea and serum Creatinine had no significance in the development of CSME (p=0.1197 and 0.2470, respectively). Patients in both the groups had a mean SBP and DBP higher than normal values and showed statistical significance (P=0.0003 and P=0.0058 respectively). OBSERVATIONS: Increased total cholesterol, triglyceride, LDL cholesterol and decreased levels of HDL cholesterol were found to be significant in the development of CSME. Those with increased duration of diabetes had severe stages of DR and had CSME. Duration of insulin usage was also found to be a significant causative factor in the development of CSME. There was no correlation seen with blood urea, serum creatinine. Both systolic and diastolic BP were observed to be significant. CONCLUSION: Serum lipid profile and blood pressure must be part of the routine investigation in diabetic retinopathy patients in order to prevent vision threatening complications like clinically significant macular oedema

Protein Secondary Structure Prediction using Parallelized Rule Induction from Coverings

Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm\u27s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2]