scholarly journals CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

2007 ◽  
Vol 36 (Supplement_1) ◽  
pp. D504-D511 ◽  
Author(s):  
Yi Huang ◽  
Susanna K. P. Lau ◽  
Patrick C. Y. Woo ◽  
Kwok-yung Yuen
Keyword(s):  
Comparative Analysis ◽  
Comparative Sequence Analysis ◽  
Nomenclature System ◽  
Comprehensive Database ◽  
Representative Sequence ◽  
Phylogenetic Studies ◽  
Complete Genomes ◽  
Downstream Analysis ◽  
Bat Coronavirus ◽  
Group 1

Abstract The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.

scholarly journals Comparative analysis of physical development parameters of children with stages 1 to 3 of chronic kidney disease

2017 ◽  
Vol 98 (1) ◽  
pp. 5-9
Author(s):  
T L Nastausheva ◽  
O A Zhdanova ◽  
N S Nastausheva ◽  
L I Stahurlova ◽  
I V Grebennikova
Keyword(s):  
Chronic Kidney Disease ◽  
Comparative Analysis ◽  
Kidney Disease ◽  
Physical Development ◽  
Average Height ◽  
Time Period ◽  
Ckd Stage ◽  
Group 2 ◽  
Stage 1 ◽  
Group 1

Aim. To conduct comparative analysis of height, weight and body mass index in children with stages 1 to 3 of chronic kidney disease (CKD) caused by recurrent urinary tract infection due to congenital anomalies of kidney and urinary tract.Methods. The study was performed on 210 children: 110 patients examined in 2001-2002 (group 1) and 100 children examined in 2011-2012 (group 2). Stage 1 of CKD was observed in 94 (85.4%) children in group 1 and in 93 (93%) in group 2, stage 2 - in 16 (14.6%) and 7 (7%) patients, respectively. From both groups patients matched by sex, age, diagnosis and social status were selected: 20 patients with stage 1, 19 children with stage 2; in addition, 6 children with stage 3 were examined.Results. Nowadays children with CKD stage 1 are taller compared to patients of the beginning of the XXI century (Z-score: -0.14±1.43 and 0.20±0.98 respectively, p=0.01). Significant differences in weight were found in children with stage 1 in 2011-2012 compared to the patients in 2001-2002 (0.18±0.46 and 0.78±1.19 for groups 1 and 2, respectively, р=0.026). A tendency towards decrease of average height in children with stage 3 is observed compared to patients with stage 1, i.e. due to the progression of the disease.Conclusion. The data obtained reflect modern tendencies towards increase of children height and weight. No significant differences were found in physical development parameters of children with stages of chronic kidney disease 1 and 2 examined at the same time period but a tendency towards children’s height decrease from stages 1 to 3 of CKD of non-glomerular etiology was revealed.

Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis

Genome ◽  
2020 ◽  
Vol 63 (7) ◽  
pp. 337-348
Author(s):  
Guanglong Hu ◽  
Lili Cheng ◽  
Wugang Huang ◽  
Qingchang Cao ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Information ◽  
Molecular Breeding ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Identification Of Species

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159–160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

Survival Trends in Adult T-Acute Lymphoblastic Leukemia / Lymphoma (ALL), a Comparative Analysis of 92 Patients By Year of Diagnosis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2490-2490
Author(s):  
Hassan B Alkhateeb ◽  
Tasha Lin ◽  
Moussab Damlaj ◽  
Aref Al-Kali ◽  
Naseema Gangat ◽  
...  
Keyword(s):  
Overall Survival ◽  
Comparative Analysis ◽  
Acute Lymphoblastic Leukemia ◽  
Research Funding ◽  
Lymphoblastic Leukemia ◽  
Autologous Transplantation ◽  
Cell Transplant ◽  
Patient Groups ◽  
Group 2 ◽  
Group 1

Abstract Background: Adult T-cell acute lymphoblastic leukemia / lymphoma (T-ALL) is an rare and aggressive hematological malignancy with overall survival (OS) according to the UKALL XII/E2993 of 48% at 5 years (Marks et al, Blood 2009). Over the last decade, the incorporation of L-asparaginase, dose intensification (similar to pediatric protocols), availability of newer agents such as clofarabine (Dec 2004) and nelarabine (Oct 2005) have been shown to improve outcomes. We carried out this study to see if the above mentioned changes in treatment have translated to an OS benefit. Methods: After due IRB approval, adults diagnosed with T-ALL from 1990-2014 at Mayo Clinic were identified. All clinical and pathologic data was retrospectively reviewed Comparative analysis was performed based on year of diagnosis before and after 2005 (Group 1, diagnosis prior to 2005, and Group 2, diagnosis post 2005). Survival was estimated using the Kaplan-Meier Method and log-rank test. Chi-square test was used to compare variables. Results: A. Patient Characteristics: Between 1990 and 2014, a total of 92 consecutive patients (pts) with T-ALL were identified. Median age at diagnosis was 33 years (range; 18-88 years) with 72% males. Distribution of pts by year of diagnosis was as follows: Group 1(n= 47) (51%), and Group 2 (n=45) (49%). Median overall survival was 97.2 months. Median follow up for Group 1 was 50 months, during which time 23 (39%) deaths were documented, and 22.8 months (0.9 - 115.4) for Group 2 at which time19 deaths (42%) were documented (p= 0.04). Pts in Group 2 were older than Group1 (median age 41 vs 27 years (p= 0.004). Apart from age, the two groups were similar in other characteristics (Table 1). B. Therapy received by patient groups: We observed a high use of L-asparaginase containing regimens in Group 1 vs Group 2 [35(74%) pts vs 19 (42%), p=0.0013]. In contrast there was an increase in use of Hyper-CVAD in Group 2; 23(51%) vs. 3 (6%) (p<0.0001). There was no difference in the use of intensive pediatric protocols (p=0.11). There was a trend of increased use of nelarabine in Group 2, however clofarabine usage was not different (p=0.09, and p=0.6 respectively) (Table1). Allogenic stem cell transplant was offered more in Group 2 compared to Group 1, 16 (36%) patients vs. 10 (21%) patients (p=0.0009). In contrast, 7 (19%) patients underwent autologous transplantation in group 1 vs. none in group 2 (p=0.0009). C. Overall outcome by patient groups: We did not observe any difference in CR, or relapse rates among the two groups. The median OS and time to relapse were also not statistically different among Group 1 and 2 [102.6 vs 61.8 months Figure A, and 7.1 vs 14.1 months respectively]. Furthermore, age adjusted survival analysis was also not statistically significant. Conclusion: In this large cohort of adult T-ALL patients, in spite of significant advances in treatment strategies over the last two decades, we observed no difference in overall and relapse free survival prior to and after 2005. Figure 1. Figure 1. Figure 2. Figure 2. Disclosures Al-Kali: Celgene: Research Funding. Thompson:Kite Pharma: Research Funding. Witzig:Spectrum: Research Funding; Novartis: Research Funding; Celgene: Research Funding; Amgen: Honoraria; Valeant Pharma: Equity Ownership.

scholarly journals The Comparative Analysis of the Influence of Traditional Education and Distance Learning by the Results of the Discipline “Internal Medicine” in Graduate Students

2020 ◽  
Vol 5 (6) ◽  
pp. 323-328
Author(s):  
H. Taktashov ◽  
◽  
N. Hrona ◽  
Ya. Voloshyn ◽  
O. Homozova ◽  
...  
Keyword(s):  
Internal Medicine ◽  
Academic Performance ◽  
Distance Learning ◽  
Comparative Analysis ◽  
Graduate Students ◽  
Traditional Education ◽  
Group 2 ◽  
Academic Year ◽  
Group 1

The introduction of distance learning was the feature of teaching students during the last third of 2019-2020 academic year in the conditions of quarantine measures for SARS-COV-2. Partly traditional and partly distance learning fragmentariness of this academic year of different students’ groups allows substantiating the possibility and necessity of the comparative assessment and comparison of the results of these teaching approaches. The purpose of the study was to assess the features of the influence of traditional education and distance learning on the graduate students’ performance in “Internal Medicine” based on the results of the state exam. Materials and methods. The study of the results of the final exam of the 6th year students of the Medical University of the IV level of accreditation was carried out. The examination for distance students was held using “Standardized patient” model which was in the form of the situational task based on a real clinical case with laboratory instrumental data in the subdisciplines of Internal Medicine (“cardiology”, “pulmonology”, “gastroenterology”, “endocrinology”, “nephrology”, “rheumatology”, “hematology”). We identified 2 main groups for the comparative analysis. Group I consisted of 110 students who studied during the autumn and early spring terms in the context of traditional education with practical training of full value. Group II included 55 students who were taught in the form of distance learning using such educational platform and resources as Google Classroom, Google Meet during the spring term. Statistical processing of obtained results was carried out using the Statistica-Stat-Soft, USA and Microsoft Excel software package. Results and discussion. The analysis revealed the small differences in the levels of current academic performance in the subject of Internal Medicine in the context of distance learning in relation to the traditional one. When comparing the results of the two training forms we noted prevailing results of qualitative progress with the most pronounced differences in the subdisciplines “cardiology”, “gastroenterology”, in Group 1 and they reliably depended on the academic ranking in the discipline. The nature of the decline in the levels of general and high-quality academic performance based on the exam results with the most pronounced differences in the subdisciplines “rheumatology” and “gastroenterology” did not correlate with the academic ranking indicators of the current training in Group 2. When analyzing the structure of standardized exam questions, the highest efficiency of the answers was demonstrated basing on the skills of “Diagnosis of the leading syndrome”, and “Determination of a preliminary clinical diagnosis”, “Determination of the plan of examination, prognosis and prevention” in the general discipline and, especially, in such subdisciplines as “cardiology”, “gastroenterology”, “nephrology” in both groups, and, with Group 1 predominating. The lowest rates of the answers of Group 2 were recorded for the skills “Treatment, management tactics”, “Evaluation of laboratory and instrumental methods of examination” in the discipline in general and to a greater extent in the subdisciplines “gastroenterology”, “endocrinology”, “rheumatology”. Conclusion. The study showed a negative tendency of the peculiarities of the influence of the distance learning form on the current and final academic performance in the absence of the possibility of mastering theoretical material during direct work with the patient. The use of distance learning is possible as an addition to the traditional one in the blended learning and is promising in the implementation of high-tech informative methods to improve the quality of self-preparation of students for classroom studies

scholarly journals In silico comparative analysis of crispr-cas system structures of Yersinia pseudotuberculosis causing different clinical manifestations of pseudotuberculosis

2019 ◽  
Vol 11 (2) ◽  
pp. 80-87
Author(s):  
N. P. Peretolchina ◽  
Yu. P. Dzhioev ◽  
A. Yu. Borisenko ◽  
L. A. Stepanenko ◽  
E. A. Voskresenskaya ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Yersinia Pseudotuberculosis ◽  
Protein Structures ◽  
Clinical Manifestations ◽  
Systemic Infection ◽  
Complete Genomes ◽  
Nucleotide Database ◽  
Cas Genes ◽  
Species Variability ◽  
Cas Proteins

The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTarget.Results. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953: array YP1 located near cas-genes, arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers.Conclusion. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific molecular marks of analyzed strains during the study of intra-species variability and evolution of Y. pseudotuberculosis.

scholarly journals Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250092
Author(s):  
Bruce Parrello ◽  
Rory Butler ◽  
Philippe Chlenski ◽  
Gordon D. Pusch ◽  
Ross Overbeek
Keyword(s):  
Draft Genome ◽  
Single Copy ◽  
Metagenomic Data ◽  
Use Case ◽  
High Quality ◽  
Complete Genomes ◽  
Downstream Analysis ◽  
Low Coverage ◽  
Derived Data ◽  
Reference Genomes

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

scholarly journals INFLUENCE OF THE LEVEL MILK PRODUCTIVITY OF MOTHER COWS ON THE GROWTH AND DEVELOPMENT OF HOLSTEIN HEIFERS

2020 ◽  
pp. 165-172
Author(s):  
G.G. Karlikova ◽  
◽  
A.F. Conte ◽  
Keyword(s):  
Comparative Analysis ◽  
Milk Fat ◽  
Growth And Development ◽  
Milk Protein ◽  
Milk Productivity ◽  
Daily Growth ◽  
Group 3 ◽  
Group 2 ◽  
Different Levels ◽  
Group 1

The experiment is carried out on 3 groups of cows (1 - with productivity up to 7500 kg, 2 – from 7500 to 9000 kg and the 3rd group-9000 and above kg of milk for the previous lactation). Milk yield for 305 days of lactation of cows of group 3 averaged 9068 kg (P≤ 0,01), group 2-8682 (P≤ 0,05) and group 1 – 7940 kg of milk. Milk fat production in cows of group 3 - 369 kg (P≤ 0,05), group 2-351 and group 1 – 326 kg. The yield of milk protein from cows of group 3 is 285 kg (P≤ 0,01), group 2-270 (P≤ 0,05) and group 1-248 kg. A comparative analysis of the growth and development of heifers with mothers with different levels of productivity was carried out. At the 2nd month of growing, the weight of heifers of the 3rd group is 76 kg (P≤0,10), the 2nd - 72 kg (P≤0,10). The average daily growth of group 3 heifers at 6 months was 1244 g (P≤0,10), group 2 - 1127 and group 1-617 g.Group 3 Heifers at 9 months weighed 301,2 kg (P≤0,05), group 2 – 299,3 kg (P≤0,05). Heifers of group 3 at 12 months reached 380,6 kg (P≤0,05), group 2–378,5 (P≤0,05) and group 1 – 353,7 kg. The growth of experimental heifers of group 2 was 887,6 g (P≤0,05), group 3–829,6 and group 1 – 710 g per day. Monitoring of growth and development of heifers continues.

Comparative analysis of human papillomavirus type 6 complete genomes originated from head and neck and anogenital disorders

2019 ◽  
Vol 71 ◽  
pp. 140-150
Author(s):  
Mihály Szinai ◽  
Zsófia Nagy ◽  
Petra Máté ◽  
Dávid Kovács ◽  
Levente Laczkó ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Comparative Analysis ◽  
Head And Neck ◽  
Complete Genomes
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