scholarly journals Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference

2021 ◽  
Author(s):  
Yan-Ting Jin ◽  
Cong Ma ◽  
Xin Wang ◽  
Shu-Xuan Wang ◽  
Kai-Yue Zhang ◽  
...  
Keyword(s):  
Protein Function ◽  
Codon Position ◽  
Systematic Investigation ◽  
Functional Category ◽  
Gene Clustering ◽  
Base Frequency ◽  
Significant Difference ◽  
Prokaryotic Genomes ◽  
Functional Classes ◽  
Clustering Pattern

AbstractIn 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2–T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence. Graphical abstract

Determination of Sample Size and Influencing Factors to Characterize Faulting in Jointed Concrete Pavements

2021 ◽  
pp. 036119812199670
Author(s):  
Ruohan Li ◽  
Jorge A. Prozzi
Keyword(s):  
Sample Size ◽  
Plain Concrete ◽  
Concrete Pavements ◽  
Portland Cement Concrete ◽  
Federal Highway ◽  
Significant Difference ◽  
Jointed Concrete Pavement ◽  
Functional Classes ◽  
High Precipitation ◽  
Departments Of Transportation

The objective of this study is to evaluate the field variability of jointed concrete pavement (JCP) faulting and its effects on pavement performance. The standard deviation of faulting along both the longitudinal and transverse directions are calculated. Based on these, the overall variability is determined, and the required sample sizes needed for a given precision at a certain confidence level are calculated and presented. This calculation is very important as state departments of transportation are required to report faulting every 0.1 mi to the Federal Highway Administration as required by the 2015 FAST Act. On average, twice the number of measurements are needed on jointed reinforced concrete pavements (JRCP) to achieve the same confidence and precision as on jointed plain concrete pavements (JPCP). For example, a sample size of 13 is needed to achieve a 95% confidence interval with a precision of 1.0 mm for average faulting of JPCP, while 26 measurements are required for JRCP ones. Average faulting was found to correlate with several climatic, structural, and traffic variables, while no significant difference was found between edge and outer wheelpath measurements. The application of Portland cement concrete overlay and the use of dowel bars (rather than aggregate interlock) are found to significantly reduce faulting. Older sections located on higher functional classes, and in regions of high precipitation or where the daily temperature change is larger, tend to have higher faulting, and might require larger samples sizes as compared with the rest when faulting surveys are to be conducted.

scholarly journals CORRELATION BETWEEN VAS OPRESSIN CONCENTRATION AND CHRONIC HEART FAILURE SEVE RITY: CHARAC TERISTICS OF PA TIENTS WITH TERMINAL AND DECOMPE NSA TED HEART FAILURE

The Clinician ◽  
2018 ◽  
Vol 12 (1) ◽  
pp. 36-42
Author(s):  
E. S. Trofimov ◽  
A. S. Poskrebysheva ◽  
N. А. Shostak
Keyword(s):  
Heart Failure ◽  
Chronic Heart Failure ◽  
Clinical Symptoms ◽  
Left Ventricular ◽  
Stage Iii ◽  
Left Ventricular Ejection ◽  
Control Group ◽  
Ventricular Ejection Fraction ◽  
Significant Difference ◽  
Functional Classes

Objective: to evaluate vasopressin (VP) concentration in patients with varying severity of chronic heart failure (CHF), intensity of clinical symptoms, and decreased level of left ventricular ejection fraction (LVEF). Materials and methods. In total, 120 patients (44 males, 76 females) with CHF of varying genesis (mean age 72.12 ± 10.18 years) and 30 clinically healthy individuals (18 males, 12 females) as a control group (mean age 33.4 ± 6.23 years) were examined. All patients underwent comprehensive clinical and instrumental examination in accordance with the standards for patients with CHF. The VP level was determined using ELISA. Statistical analysis was performed using the IBM SPSS Statistics v. 23 software.Results. The patients with CHF had significantly higher blood VP levels compared to the control group (72.91 ± 53.9 pg/ml versus 6.6 ± 3.2 pg/ml respectively; p <0.01). At the same time, patients with stage III CHF had significantly lower VP levels than patients with stages IIВ and IIА (35.61 ± 21.53 pg/ml versus 71.67 ± 48.31 pg/ml and 86.73 ± 59.78 pg/ml respectively; p<0.01). A similar picture was observed for the functional classes (FC). For instance, for CHF FC II and III, the VP level was 91.93 ± 67.13 pg/ml and 77.95 ± 54.01 pg/ml respectively, while for FC IV it decreased to 50.49 ± 28.18 pg/ml (p <0.01). The VP concentration in patients who subsequently perished was significantly lower than in patients who survived (48.79 ± 26.30 pg/ml versus 79.72 ± 57.73 pg/ml; p = 0.012). Moreover, in patients with LVEF <50 %, the VP level was significantly lower than in patients with LVEF >50 % (59.43 ± 42.51 pg/ml versus 86.43 ± 62.46 pg/ml respectively; p <0.05).Conclusion. The observed significant differences in VP in patients with stage III and IV CFH can indicate depletion of neurohumoral mediators in this patient category. However, a correlation between the VP level and the level of LVEF decrease can indicate a significant difference in the role of VP in CHF pathogenesis in patients with preserved and decreased LVEF. This observation requires further research.

scholarly journals Hierarchical Ensemble Methods for Protein Function Prediction

2014 ◽  
Vol 2014 ◽  
pp. 1-34 ◽  
Author(s):  
Giorgio Valentini
Keyword(s):  
Protein Function ◽  
Protein Function Prediction ◽  
Ensemble Methods ◽  
Function Prediction ◽  
Future Research ◽  
Prediction Methods ◽  
Multiple Sources ◽  
Open Problems ◽  
Functional Classes ◽  
Hierarchical Relationships

Protein function prediction is a complex multiclass multilabel classification problem, characterized by multiple issues such as the incompleteness of the available annotations, the integration of multiple sources of high dimensional biomolecular data, the unbalance of several functional classes, and the difficulty of univocally determining negative examples. Moreover, the hierarchical relationships between functional classes that characterize both the Gene Ontology and FunCat taxonomies motivate the development of hierarchy-aware prediction methods that showed significantly better performances than hierarchical-unaware “flat” prediction methods. In this paper, we provide a comprehensive review of hierarchical methods for protein function prediction based on ensembles of learning machines. According to this general approach, a separate learning machine is trained to learn a specific functional term and then the resulting predictions are assembled in a “consensus” ensemble decision, taking into account the hierarchical relationships between classes. The main hierarchical ensemble methods proposed in the literature are discussed in the context of existing computational methods for protein function prediction, highlighting their characteristics, advantages, and limitations. Open problems of this exciting research area of computational biology are finally considered, outlining novel perspectives for future research.

scholarly journals Preparation and bioactivity of anti-Newcastle disease virus-phosphoprotein cytoplasmic transduction peptide antibody

2020 ◽  
Author(s):  
Benqiang Li ◽  
Man Wang ◽  
Jianguo Zhu
Keyword(s):  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Newcastle Disease ◽  
Protein Function ◽  
Cell Protection ◽  
Test Analysis ◽  
Hiv Tat ◽  
Significant Difference ◽  
Macromolecular Protein ◽  
And Control

Abstract On the basis of cell-penetrating peptide’s character that it can penetrate cytomembrane and transfer macromolecular protein to cytoplasm so to play biological function, we took the experiments. The fuse penetrating peptide our experiment adoptted is HIV-TAT derived fragment-CTP512, with good transmember effect and distinct cytoplasm-position. In this chapter, the research of transmembrane character was processed first. According to the tests on trans- member protein with different concentrations, the best trans-member concentration is 3µM. Afterwards, we found that the location of trans-member antibody is overlapping with phosphoprotein using indirect immunofluorescence test analysis. According to MTT test, there is no significant difference between CTP fusion protein and control on cell proliferation and viability. TCID50 test was used to detect the protective effect of trans-member antibody on cell. Result showed that trans- member antibody has significant cell protection effect compared to the control in the order: ZL.103>ZL.17>Control. Fluorogenic quantitative PCR result showed that trans- member antibody can disturb the duplication and transcription of Newcastle disease virus. This results not only paved a good way to research the transport of disease related protein, but also provide a splendid tool on protein function research.

scholarly journals Investigating the Influence of Bridge Officer Experience on Ice Management Effectiveness Using a Marine Simulator Experiment

2019 ◽  
Vol 141 (4) ◽  
Author(s):  
Erik Veitch ◽  
David Molyneux ◽  
Jennifer Smith ◽  
Brian Veitch
Keyword(s):  
Systematic Investigation ◽  
Relative Importance ◽  
Management Effectiveness ◽  
Offshore Structure ◽  
Experience Levels ◽  
Pack Ice ◽  
Significant Difference ◽  
Ice Concentration ◽  
Ice Conditions ◽  
Insight Into

The research investigates the influence of human expertise on the effectiveness of ice management operations. The key contribution is an experimental method for investigating human factor issues in an operational setting. Ice management is defined as a systematic operation that enables a marine operation to proceed safely in the presence of sea ice. In this study, the effectiveness of ice management operations was assessed in terms of ability to modify the presence of pack ice around an offshore structure. This was accomplished in a full-mission marine simulator as the venue for a systematic investigation. In the simulator, volunteer participants from a range of seafaring experience levels were tasked with individually completing ice management tasks. Recorded from 36 individuals' simulations, we compared ice management effectiveness metrics against two independent variables: (i) experience level of the participant, categorized as either cadet or seafarer and (ii) ice severity, measured in ice concentration. The results showed a significant difference in ice management effectiveness between experience categories. We examined what the seafarers did that made them more effective and characterized their operational tactics. The research provides insight into the relative importance of vessel operator skills in contributing to effective ice management, as well as how this relative importance changes as ice conditions vary from mild to severe. This may have implications for training in the nautical sciences and could help to inform good practices in ice management.

The receptive field of the primate P retinal ganglion cell, I: Linear dynamics

1997 ◽  
Vol 14 (1) ◽  
pp. 169-185 ◽  
Author(s):  
Ethan A. Benardete ◽  
Ehud Kaplan
Keyword(s):  
Transfer Function ◽  
Receptive Field ◽  
Ganglion Cells ◽  
Cell Dynamics ◽  
Early Form ◽  
Filter Model ◽  
First Order ◽  
Significant Difference ◽  
Functional Classes ◽  
Spatial Transfer Function

AbstractThe ganglion cells of the primate retina include two major anatomical and functional classes: P cells which project to the four parvocellular layers of the lateral geniculate nucleus (LGN), and M cells which project to the two magnocellular layers. The characteristics of the P-cell receptive field are central to understanding early form and color vision processing (Kaplan et al., 1990; Schiller & Logothetis, 1990). In this and in the following paper, P-cell dynamics are systematically analyzed in terms of linear and nonlinear response properties. Stimuli that favor either the center or the surround of the receptive field were produced on a CRT and modulated with a broadband signal composed of multiple m-sequences (Benardete et al., 1992b; Benardete & Victor, 1994). The first-order responses were calculated and analyzed in this paper (part I). The findings are: (1) The first-order responses of the center and surround depend linearly on contrast. (2) The dynamics of the center and surround are well described by a bandpass filter model. The most significant difference between center and surround dynamics is a delay of approximately 8 ms in the surround response. (3) In the LGN, these responses are attenuated and delayed by an additional 1–5 ms. (4) The spatial transfer function of the P cell in response to drifting sine gratings at three temporal frequencies was measured. This independent method confirmed the delay between the (first-order) responses of the center and surround. This delay accounts for the dependence of the spatial transfer function on the frequency of stimulation.

scholarly journals Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

2020 ◽  
Author(s):  
Rafael Pinilla-Redondo ◽  
Saadlee Shehreen ◽  
Nicole D. Marino ◽  
Robert D. Fagerlund ◽  
Chris M. Brown ◽  
...  
Keyword(s):  
Mobile Genetic Elements ◽  
Gene Clustering ◽  
Type I ◽  
Defense Gene ◽  
Genetic Elements ◽  
Defense Systems ◽  
Prokaryotic Genomes ◽  
New Type ◽  
Genomic Regions ◽  
Potential Exploitation

AbstractMany prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have evolved Anti-CRISPR (Acr) proteins to bypass this immunity, yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we uncover 11 new type I anti-CRISPR genes encoded on numerous chromosomal and extrachromosomal mobile genetic elements within Enterobacteriaceae and Pseudomonas. Candidate genes were identified adjacent to anti-CRISPR associated gene 5 (aca5) and assayed against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas), revealing the type I-F and/or I-E acr genes and a new aca (aca9). We find that acr genes not only associate with other acr genes, but also with inhibitors of distinct bacterial defense systems. These genomic regions appear to be “anti-defense islands”, reminiscent of the clustered arrangement of “defense islands” in prokaryotic genomes. Our findings expand on the diversity of CRISPR-Cas inhibitors and reveal the potential exploitation of acr loci neighborhoods for identifying new anti-defense systems.

scholarly journals Comparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2‡

2021 ◽  
Vol 12 ◽  
Author(s):  
Xingxing Xu ◽  
Qiao Bian ◽  
Yun Luo ◽  
Xiaojun Song ◽  
Shan Lin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Antibiotic Resistance ◽  
Sequence Type ◽  
Gene Clustering ◽  
Whole Genome ◽  
Toxin B ◽  
Clostridioides Difficile ◽  
Significant Difference ◽  
Sporulation Capacity

Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ2 = 0.024–2.667, P &gt; 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b. Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ2 = 12.30, P &lt; 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection.

Investigating the Influence of Bridge Officer Experience on Ice Management Effectiveness Using a Marine Simulator Experiment

2018 ◽  
Author(s):  
Erik Veitch ◽  
David Molyneux ◽  
Jennifer Smith ◽  
Brian Veitch
Keyword(s):  
Systematic Investigation ◽  
Average Concentration ◽  
Relative Importance ◽  
Management Effectiveness ◽  
Offshore Structure ◽  
Experience Levels ◽  
Pack Ice ◽  
Significant Difference ◽  
Ice Concentration ◽  
Ice Conditions

The research investigates the influence of human expertise on the effectiveness of ice management operations. Ice management is defined as a systematic operation that enables a marine operation to proceed safely in the presence of sea ice. In this study, a method has been applied for assessing the effectiveness of ice management operations in terms of ability to modify the presence of pack ice around an offshore structure. This was accomplished in a real-time marine simulator environment as the venue for a systematic investigation. In the simulator, volunteer participants from a range of seafaring experience levels were tasked with individually completing ice management tasks. Recorded from 36 individuals’ simulations was the extent to which the ice in a defined area was impacted, measured in terms of tenths ice concentration. These responses were then compared to two independent variables: 1) experience level of the participant, categorized as either cadet or seafarer, and 2) ice severity, measured in ice concentration. The results showed a significant difference in ice management effectiveness between experience categories, where effectiveness was defined as the average drop in ice concentration during simulation. Results also showed that the human factor of experience and the environmental factor of ice concentration both had significant effects on average concentration drop. The research provides insight into the relative importance of vessel operator skills in contributing to effective ice management, as well as how this relative importance changes as ice conditions vary from mild to severe. This may have implications for training in the nautical sciences and could help to inform good practices in ice management.

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