scholarly journals Search for SINE repeats in the rice genome using correlation-based position weight matrices

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yulia M. Suvorova ◽  
Anastasia M. Kamionskaya ◽  
Eugene V. Korotkov
Keyword(s):  
Position Weight Matrix ◽  
Statistical Significance ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Search Method ◽  
Nucleotide Substitutions ◽  
Combined Application ◽  
Mammalian Genomes ◽  
High Level ◽  
Eukaryotic Genomes

Abstract Background Transposable elements (TEs) constitute a significant part of eukaryotic genomes. Short interspersed nuclear elements (SINEs) are non-autonomous TEs, which are widely represented in mammalian genomes and also found in plants. After insertion in a new position in the genome, TEs quickly accumulate mutations, which complicate their identification and annotation by modern bioinformatics methods. In this study, we searched for highly divergent SINE copies in the genome of rice (Oryza sativa subsp. japonica) using the Highly Divergent Repeat Search Method (HDRSM). Results The HDRSM considers correlations of neighboring symbols to construct position weight matrix (PWM) for a SINE family, which is then used to perform a search for new copies. In order to evaluate the accuracy of the method and compare it with the RepeatMasker program, we generated a set of SINE copies containing nucleotide substitutions and indels and inserted them into an artificial chromosome for analysis. The HDRSM showed better results both in terms of the number of identified inserted repeats and the accuracy of determining their boundaries. A search for the copies of 39 SINE families in the rice genome produced 14,030 hits; among them, 5704 were not detected by RepeatMasker. Conclusions The HDRSM could find divergent SINE copies, correctly determine their boundaries, and offer a high level of statistical significance. We also found that RepeatMasker is able to find relatively short copies of the SINE families with a higher level of similarity, while HDRSM is able to find more diverged copies. To obtain a comprehensive profile of SINE distribution in the genome, combined application of the HDRSM and RepeatMasker is recommended.

Subjective factors affecting gun shooting accuracy among employees of internal affairs agencies in process of learning

2020 ◽  
Vol 2020 (4) ◽  
pp. 198-206
Author(s):  
Anton Rozhkov ◽  
Anton Popov ◽  
Vitaliy Balahonskiy
Keyword(s):  
Subjective Experience ◽  
Statistical Significance ◽  
Self Regulation ◽  
Sensorimotor Coordination ◽  
Factors Affecting ◽  
Intelligent Behavior ◽  
Experience Of Stress ◽  
Firing Line ◽  
High Level ◽  
In Fire

The article is devoted to the study of subjective factors affecting shooting accuracy of law enforcement officers. The empirical study identified some subjective factors reducing gun shooting accuracy and effectiveness among law enforcers. These characteristics include sensorimotor coordination and subjective experience of stress during the shooting process. Scientific analysis made it possible to determine statistical significance of the influence of these factors on the accuracy of shooting. To increase the effectiveness of shooting among officers with a low index of sensorimotor coordination, the authors suggest using exercises aimed at cultivating sensorimotor coordination in fire training classes. While working with employees being under a high level of subjectively experienced stress, more attention should be paid to training techniques to overcome stress and form intelligent behavior in extreme situations. The authors also draw readers’ attention to factors increasing the effectiveness of shooting: officers’ ability to determine the subjective level of stress, their knowledge of emotional self-regulation techniques, knowledge of the sequence of their actions in the firing line.

OPERATIONS FOR ANEURISM OF THE ABDOMINAL AORTIC DEPARTMENT - RESECTION WITH THE FOLLOWING PROSTHETICS AND ENDOPROSTHETICS: A COMPARATIVE ANALYSIS OF COMPLICATIONS

2020 ◽  
pp. 43-49
Author(s):  
Андрей Анатольевич Иванов ◽  
Александр Иванович Жданов ◽  
Максим Сергеевич Шевелин ◽  
Александр Сергеевич Брежнев
Keyword(s):  
Comparative Analysis ◽  
Postoperative Complications ◽  
Statistical Significance ◽  
Aortic Aneurysms ◽  
Surgical Interventions ◽  
Vein Thrombosis ◽  
Scientific Hypothesis ◽  
Abdominal Aortic ◽  
Life Threatening ◽  
High Level

В статье представлены данные оригинального исследования по улучшению хирургического лечения аневризм брюшного отдела аорты. С этой целью произведен сравнительный анализ двух альтернативных друг другу операций: 1) резекции аневризмы с последующим протезированием аорты; 2) эндопротезирования аорты. Сформулировано научное предположение о том, что замена «классических» операций резекции аневризмы на «альтернативные» операции эндопротезирования приведет к принципиальному снижению уровня послеоперационных осложнений. В независимых группах пациентов с использованием сравниваемых хирургических вмешательств произведена точная качественная и количественная оценка послеоперационных осложнений: нетромботических - кардиальных, пульмональных, ренальных и тромботических - тромбозов глубоких вен и тромбозов браншей протеза. После реализации исследования было установлено, что замена «классических» операций на «альтернативные» достоверно приводит к принципиальному снижению уровня наиболее жизнеопасных осложнений - кардиальных (острых форм ишемической болезни сердца, нарушений сердечного ритма), пульмональных (пневмоний, тромбоэмболии легочной артерии, респираторного дистресс-синдрома взрослых) и ренальных (острой почечной недостаточности). Некоторое исключение составили менее жизнеопасные тромботические осложнения. Полученные результаты имеют высокий уровень статистической значимости, что позволяет рекомендовать их к рассмотрению к использованию в практике сосудистой хирургии The article presents data from an original study to improve the surgical treatment of abdominal aortic aneurysms. For this purpose, a comparative analysis of two alternate operations was performed: 1) aneurysm resection followed by aortic prosthetics; 2) aortic endoprosthetics. The scientific hypothesis is formulated that the replacement of the «classical» operations of resection of the aneurysm with «alternative» operations of endoprosthetics will lead to a fundamental decrease in the level of postoperative complications. In independent groups of patients using the compared surgical interventions, an accurate qualitative and quantitative assessment of postoperative complications was made: non-thrombotic - cardiac, pulmonary, renal and thrombotic - deep vein thrombosis and prosthetic jaw thrombosis. After the study was completed, it was found that the fundamental replacement of «classical» operations with «alternative» reliably leads to a fundamental decrease in the level of the most life-threatening complications - cardiac (acute forms of coronary heart disease, cardiac arrhythmias), pulmonary (pneumonia, pulmonary thromboembolism, respiratory distress syndrome of adults) and renal (acute renal failure). Some exceptions were less life-threatening thrombotic complications. The results obtained have a high level of statistical significance, which allows us to recommend them for consideration in the practice of vascular surgery

Comparing Midterm Outcomes of High-Level Athletes Versus Nonathletes Undergoing Primary Hip Arthroscopy: A Propensity-Matched Comparison With Minimum 5-Year Follow-up

2021 ◽  
pp. 036354652110417
Author(s):  
Andrew E. Jimenez ◽  
Peter F. Monahan ◽  
David R. Maldonado ◽  
Benjamin R. Saks ◽  
Hari K. Ankem ◽  
...  
Keyword(s):  
Hip Arthroscopy ◽  
Statistical Significance ◽  
Arthroscopic Surgery ◽  
Harris Hip Score ◽  
Control Group ◽  
Level Of Evidence ◽  
Femoroacetabular Impingement Syndrome ◽  
Patient Reported ◽  
High Level

Background: High-level athletes (HLAs) have been shown to have better short-term outcomes than nonathletes (NAs) after hip arthroscopy. Purpose: (1) To report midterm outcomes of HLAs after primary hip arthroscopy and (2) to compare their results with a propensity-matched cohort of NA patients. Study Design: Cohort study; Level of evidence, 3. Methods: Data were prospectively collected and retrospectively reviewed between February 2008 and November 2015 for HLAs (professional, college, or high school) who underwent primary hip arthroscopy in the setting of femoroacetabular impingement syndrome (FAIS). HLAs were included if they had preoperative, minimum 2-year, and minimum 5-year follow-up data for the modified Harris Hip Score (mHHS), Non-Arthritic Hip Score (NAHS), and Hip Outcome Score Sports-Specific Subscale (HOS-SSS). Radiographic and intraoperative findings, surgical procedures, patient-reported outcomes (PROs), patient acceptable symptomatic state (PASS), minimal clinically important difference (MCID), and return to sport were reported. The HLA study group was propensity-matched to a control group of NA patients for comparison. Results: A total 65 HLA patients (67 hips) were included in the final analysis with mean follow-up time of 74.6 ± 16.7 months. HLAs showed significant improvement in all PROs recorded, achieved high rates of MCID and PASS for mHHS (74.6% and 79.4%, respectively) and HOS-SSS (67.7% and 66.1%, respectively), and returned to sport at high rates (80.4%). When compared with the propensity-matched NA control group, HLAs reported higher baseline but comparable postoperative scores for the mHHS and NAHS. HLA patients achieved MCID and PASS for mHHS at similar rates as NA patients, but the HLA patients achieved PASS for HOS-SSS at higher rates that trended toward statistical significance (66.1% vs 48.4%; P = .07). NA patients underwent revision arthroscopic surgery at similar rates as HLA patients (14.9% vs 9.0%, respectively; P = .424). Conclusion: Primary hip arthroscopy results in favorable midterm outcomes in HLAs. When compared with a propensity-matched NA control group, HLAs demonstrated a tendency toward higher rates of achieving PASS for HOS-SSS but similar arthroscopic revision rates at minimum 5-year follow-up.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

THE ELABORATION OF A THERAPEUTIC COMPLEX FOR UNSTABLE STENOCARDIA WITH THE TYPE II DIABETES MELLITUS BACKGROUND WITH ACCOMPANYING HYPERVENTILATIVE SYNDROME: ANALYSIS OF CLINIC-CARDIOLOGY AND RESPIRATORY-METABOLICPARAMETERS

2021 ◽  
pp. 38-46
Author(s):  
Никита Игоревич Воронин ◽  
Дмитрий Сергеевич Кузнецов
Keyword(s):  
Diabetes Mellitus ◽  
Traditional Approach ◽  
Statistical Significance ◽  
Type Ii Diabetes Mellitus ◽  
Original Research ◽  
Hyperventilation Syndrome ◽  
Practical Development ◽  
Concomitant Condition ◽  
High Level ◽  
New Generation

В статье представлены данные оригинального исследования по созданию терапевтического комплекса, направленного на улучшение интенсивного лечения нозологической ассоциации «нестабильная стенокардия (в качестве основного заболевания) + сахарный диабет второго типа (в качестве фоновой патологии) + гипервентиляционный синдром (в качестве сопутствующего состояния)». Разработанный комплекс основан на контролируемом изменении вспомогательной респираторной оксигенации «в сторону уменьшения» при условии обязательного дополнения базисной фармакотерапии сбалансированной комбинацией препаратов антигипоксического действия и дезагрегантом нового поколения. Проведено сравнительное исследование двух групп тематических пациентов - с применением разработанного комплекса и с использованием «традиционного подхода». Изучены ключевые параметры клинического кардиологического и респираторно-метаболического статуса пациентов. При использовании разработанного терапевтического комплекса по сравнению с «традиционным подходом» установлено принципиальное улучшение параметров клинико-кардиологического статуса при сохранении параметров респираторно-метаболического статуса в пределах адаптивных и безопасных значений. Полученные результаты имеют высокий уровень статистической значимости. Это доказало достаточную обоснованность авторской научно-практической разработки. Представленные в статье данные отличает новизна и практическая применимость, что позволяет рекомендовать их к дальнейшему использованию в практике специалистов клиники внутренних болезней The article presents the data of the original research on the creation of a therapeutic complex aimed at improving the intensive treatment of the nosological association «unstable angina pectoris (as the main disease) + type 2 diabetes mellitus (as a background pathology) + hyperventilation syndrome (as a concomitant condition)». The developed complex is based on a controlled change in auxiliary respiratory oxygenation «downward», provided that basic pharmacotherapy must be supplemented with a balanced combination of antihypoxic drugs and a new generation of antiaggregants. A comparative study of two groups of thematic patients was carried out - using the developed complex and using the «traditional approach». The key parameters of the clinical cardiological and respiratorymetabolic status of patients were studied. When using the developed therapeutic complex in comparison with the «traditional approach», a fundamental improvement in the parameters of the clinical and cardiological status was established while maintaining the parameters of the respiratory and metabolic status within the adaptive and safe values. The results obtained have a high level of statistical significance. This proved the sufficient validity of the author's scientific and practical development. The data presented in the article are distinguished by novelty and practical applicability, which makes it possible to recommend them for further use in the practice of specialists in the clinic of internal diseases

Implications of Activity Classification Aggregation in Urban Freight Trip Generation Linear Models

2019 ◽  
pp. 22-37 ◽  
Author(s):  
Ivan D. Sanchez-Diaz ◽  
Jesus Gonzalez-Feliu
Keyword(s):  
Data Collection ◽  
Linear Models ◽  
Statistical Significance ◽  
Detailed Data ◽  
Trip Generation ◽  
Commercial Activity ◽  
Urban Freight ◽  
Levels Of Detail ◽  
High Level

This chapter studies the implication of aggregating establishments by categories with different levels of detail for modeling FTG. To this effect, the chapter conducts an assessment of freight trip generation (FTG) patterns homogeneity inside activity-based grouping. The method implemented is econometric in nature, which allows the assessment of the statistical significance of variables representing commercial activity sectors and sub-sectors. The results show that for some sectors the traditional high-level aggregation includes sub-sectors with homogenous FTG patterns and thus produces appropriate models; in some other cases (e.g., retail, manufacturing), the sub-sectors have different FTG patterns and thus more detailed data is needed to calibrate accurate models. This research can be used to enhance the efficiency of data collection, as it identifies some sub-sectors that need larger efforts for data collection, and some other categories where FTG homogeneity allows for less detailed data collection without hampering the quality of the models.

scholarly journals Prevalence and Predictors of Stress among Bankers in Enugu State South-East Nigeria

2020 ◽  
Vol 32 (2) ◽  
pp. 68-79
Author(s):  
T.J. Okwor ◽  
A.C. Ndu ◽  
S.U. Arinze-Onyia ◽  
I.J. Ogugua ◽  
I.M. Obionu ◽  
...  
Keyword(s):  
Sampling Method ◽  
Statistical Significance ◽  
Cross Sectional Study ◽  
Cross Sectional ◽  
Eastern State ◽  
Management Standards ◽  
The Mean ◽  
Enugu State ◽  
Multistage Sampling ◽  
High Level

Background: The work environment is rapidly changing and in recent times, occupational stress poses a threat to the health, morale and productivity of workers and the organization. This study sought to determine the prevalence and predictors of stress among bankers in a south-eastern state of Nigeria. Methods: A descriptive cross-sectional study was carried out among 370 bankers in Enugu State, Nigeria using the Health, Safety, Executive (HSE) management standards indicator tool. Multistage sampling method was used to select participants. Statistical analysis was done using SPSS 22.0. Level of statistical significance was set at p< 0.05.Results: The mean age of the participants was 34.54±6.3 years while the mean years of work was 6.01±4.7years. One hundred and seventy-four (47%) reported high level of stress due to relationship at work while 318 (85.9%) reported low level of stress due to roles. Being 35 years or less was found to a predictor of high (AOR 0.55, CI 0.30-1.02) level of stress due to control.Work experience of 5 years or less was found to be a predictor of both high (AOR 0.74, CI 0.40--1.37) and low (AOR 0.99, CI 0.40-1.37) levels of stress due to control.Conclusion: This study has shown that the prevalence of stress was high among bankers in Enugu State, South-East Nigeria. There is, therefore, the need for routine stress assessment and interventions in the banking industry especially for those at high risk. Keywords: Bankers; HSE Stress Questionnaire; Stress; Workplace; Southeast Nigeria

scholarly journals Population Genetics of the Highly Polymorphic RPP8 Gene Family

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 691 ◽  
Author(s):  
Alice MacQueen ◽  
Dacheng Tian ◽  
Wenhan Chang ◽  
Eric Holub ◽  
Martin Kreitman ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Direct Repeat ◽  
Single Copy ◽  
Arabidopsis Lyrata ◽  
Histocompatibility Complex ◽  
Locus System ◽  
High Level ◽  
Eukaryotic Genomes ◽  
Shared Polymorphism ◽  
Selfing Species

Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.

scholarly journals Genomic and Proteomic Study of the Inflammatory Pathway in Patients With Atrial Fibrillation and Cardiometabolic Syndrome

2020 ◽  
Vol 7 ◽  
Author(s):  
Hana A. Itani ◽  
Miran A. Jaffa ◽  
Joseph Elias ◽  
Mohammad Sabra ◽  
Patrick Zakka ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Inflammatory Cytokines ◽  
Statistical Significance ◽  
Serum Levels ◽  
Tissue Growth ◽  
Cardiometabolic Syndrome ◽  
Proteomic Study ◽  
Obesity Hypertension ◽  
High Level ◽  
And Control

Atrial fibrillation (AF) and cardiometabolic syndrome (CMS) have been linked to inflammation and fibrosis. However, it is still unknown which inflammatory cytokines contribute to the pathogenesis of AF. Furthermore, cardiometabolic syndrome (CMS) risk factors such as obesity, hypertension, insulin resistance/glucose intolerance are also associated with inflammation and increased level of cytokines and adipokines. We hypothesized that the inflammatory immune response is exacerbated in patients with both AF and CMS compared to either AF or CMS alone. We investigated inflammatory cytokines and fibrotic markers as well as cytokine genetic profiles in patients with lone AF and CMS. CMS, lone AF patients, patients with both lone AF and CMS, and control patients were recruited. Genetic polymorphisms in inflammatory and fibrotic markers were assessed. Serum levels of connective tissue growth factor (CTGF) were tested along with other inflammatory markers including platelet-to-lymphocyte ratio (PLR), monocyte-to-HDL ratio (MHR) in three groups of AF+CMS, AF, and CMS patients. There was a trend in the CTGF levels for statistical significance between the AF and AF+CMS group (P = 0.084). Genotyping showed high percentages of patients in all groups with high secretor genotypes of Interleukin-6 (IL-6) (P = 0.037). Genotyping of IFN-γ and IL-10 at high level showed an increase in expression in the AF + CMS group compared to AF and CMS alone suggesting an imbalance between the inflammatory and anti-inflammatory cytokines which is exacerbated by AF. Serum cytokine inflammatory cytokine levels showed that IL-4, IL-5, IL-10, IL-17F, and IL-22 were significant between the AF, AF+CMS, and CMS patients. Combination of both CMS and AF may be associated with a higher degree of inflammation than what is seen in either CMS or AF alone. Thus, the identification of a biomarker capable of identifying metabolic syndrome associated with disease will help in identification of a therapeutic target in treating this devastating disease.

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