The Survey of the Code Clone Detection Techniques and Process with Types (I, II, III and IV)

In software upgradation code clones are regularly utilized. So, we can contemplate on code location strategies goes past introductory code. In condition of-craftsmanship on clone programming study, we perceived the absence of methodical overview. We clarified the earlier research-in view of deliberate and broad database find and the hole of research for additionally think about. Software support cost is more than outlining cost. Code cloning is useful in several areas like detecting library contents, understanding program, detecting malicious program, etc. and apart from pros several serious impact of code cloning on quality, reusability and continuity of software framework. In this paper, we have discussed the code clone and its evolution and classification of code clone. Code clone is classified into 4 types namely Type I, Type II, III and IV. The exact code as well as copied code is depicted in detail for each type of code clone. Several clone detection techniques such as: Text, token, metric, hybrid based techniques were studied comparatively. Comparison of detection tools such as: clone DR, covet, Duploc, CLAN, etc. based on different techniques used are highlighted and cloning process is also explained. Code clones are identical segment of source code which might be inserted intentionally or unintentionally. Reusing code snippets via copying and pasting with or without minor alterations is general task in software development. But the existence of code clones may reduce the design structure and quality of software like changeability, readability and maintainability and hence increase the continuation charges

Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils

HelD, an RNA polymerase binding protein from Bacillus subtilis, stimulates transcription and helps in timely adaptation of cells under diverse environmental conditions. At present, no structural information is available for HelD. In the current study, we performed size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS) which suggests that HelD is predominantly monomeric and globular in solution. Using combination of size exclusion chromatography and analytical ultracentrifugation, we also show that HelD has a tendency to form higher order oligomers in solution. CD experiments suggest that HelD has both α-helical (∼35%) and β sheet (∼26%) secondary structural elements. Thermal melting experiments suggest that even at 90°C, there is only about 30% loss in secondary structural contents with Tm of 44°C. However, with the increase in temperature, there was a gain in the β-sheet content and significant irreversible loss of α-helical content. Using a combination of X-ray fiber diffraction analysis, and dye based assays including Thioflavin-T based fluorescence and Congo red binding assays, we discovered that HelD forms amyloid-like fibrils at physiologically relevant conditions in vitro. Using confocal imaging, we further show that HelD forms amyloid inclusions in Escherichia coli. Bioinformatics-based sequence analysis performed using three independent web-based servers suggests that HelD has more than 20 hot-spots spread across the sequence that may aid the formation of amyloid-like fibrils. This discovery adds one more member to the growing list of amyloid or amyloid-like fibril forming cytosolic proteins in bacteria. Future studies aimed at resolving the function of amyloid-like fibrils or amyloid inclusions may help better understand their role, if any, in the bacterial physiology

Mycobacterium tuberculosis CarD, an essential global transcriptional regulator forms amyloid-like fibrils

CarD is an essential global transcription regulator from Mycobacterium tuberculosis (Mtb) that binds RNA polymerase and activates transcription by stabilizing the transcription initiation complex. Available crystal structures have captured two distinct, monomeric and domain-swapped homodimeric, oligomeric states of CarD. However, the actual oligomeric state of CarD in solution and its biological relevance has remained unclear. Here, we confirm the presence of the homodimeric state of CarD in solution by using synchrotron-based small-angle X-ray scattering. Furthermore, by using biochemical and biophysical experiments, in addition to mass-spectrometry, transmission electron microscopy, and confocal imaging, we show that CarD is the first soluble cytosolic protein in Mtb which displays the tendency to form amyloid-like fibrils both in vitro as well as in vivo. We demonstrate that the deletion of the fourteen N-terminal residues involved in domain-swapping hampers amyloid formation, thus, suggesting that domain-swapping is crucial in amyloidogenesis. The discovery of the amyloidogenic property of an essential cytosolic global transcription regulator, CarD, in a pathogenic bacteria will further open up new frontiers in research.Peer reviewe

A Comprehensive Study of Phenotypic and Genotypic Techniques to Detect Metallo-β-lactamases in Carbapenem-resistant Escherichia coli (E. coli) and Klebsiella pneumoniae (KP) Strains Derived through Numerous Clinical Specimens in Advanced Health care Facilities

In recent years, an increase in Escherichia coli and Klebsiella pneumoniae resistant to carbapenem was reported globally. Due to their high prevalence and extensive range of medical conditions, Escherichia coli and Klebsiella pneumoniae are both confirmed to be major public health concerns. Furthermore, carbapenem resistance restricts treatment options for individuals infected with these bacteria. Consequently, early detection of carbapenem resistance is essential for starting effective therapy, achieving successful management, and avoiding the infection from spreading further in the future. This study’s objective was to identify the phenotypic and genotypic identification of Metallo-β-lactamases (MBL) in carbapenem-resistant E. coli and K. pneumoniae in advanced healthcare facilities. Meropenem resistance was tested in E. coli and K. pneumoniae using the Kirby-Bauer disc diffusion technique. MBL was discovered using a combination of Disc diffusion testing and the Modified Hodge Test. The Polymerase Chain Reaction was used to determine the genotypes of the bla NDM-1 genes that express these enzymes. Out of 427 strains, including 223 E. coli and 204 K. pneumoniae, 35 (8.2%) consisted of carbapenem-resistant, and 29 (82.85%) showed phenotypically verified as metallo-beta-lactamase producers by using the Combined disc test and 20 (57.14%) using the Modified Hodge test. Polymerase Chain Reaction tests for genes detect those three different strains all showed the bla NDM-1 gene. Carbapenemase production and MBL can be recognized with the help of phenotypic combination disc and MHT tests in labs. Since both tests showed 100% concordance, laboratories may use the less expensive CDT instead of the MHT. The current study supports institutional antibiotic stewardship programmes to manage antibiotic use and prevent CRE worldwide

Effect of strain rate on pore pressure evolution and effective stress path of soft soil under different stress history conditions

Soft marine soils are highly plastic fine-grained soils and known for their high compressibility, large water content and low shear strength behaviour. The previous research on soft soils is restricted to stress–strain response under conventional loading conditions with and without its treatment. The effect of strain rate on pore pressure evolution and effective stress path of soft soil under different stress history conditions has not been explored. In the current research, an extensive experimental research has been performed on Kanjurmarg soft marine soil to evaluate its pore pressure evolution, effective stress path, obliquity and effective stress ratio at different strain rates and varying stress history conditions. A wide range of strain rate, 0.005% per min to 5% per min, was used to perform the CU triaxial tests on soft soil. Such large strain rates are used to analyse the behaviour of soil under various field conditions such as rapid excavation, rapid application of surcharge, aircraft wheel loading on runways, fast installation process of pile and projectile penetration. The effect of stress history on soft soil was also explored for OCR values of 1, 2, 5, 10 at different strain rates. The soil was also tested at different confining pressures at varying strain rates to evaluate the combined effect of strain rate and confining pressure.by Gundeep K. Sudan and Ajanta Sacha

Association of Serum Beta-Trace Protein Levels in Patients with Chronic Kidney Disease: A Case-control Study

Introduction: Chronic Kidney Disease (CKD) is common disorder showing decreased Glomerular Filtration Rate (GFR) value (<60 mL/min/1.73 m2). Because of limitations of creatinine as a biomarker of GFR, new alternative biomarkers are being investigated, such as Beta-Trace Protein (BTP) is low molecular weight proteins that are filtered by the glomeruli. Serum BTP have been shown to be more helpful for estimating GFR. Aim: To assess the role of Beta-Trace Protein (BTP) as a potential biomarker of Chronic Kidney Disease (CKD) in comparison to serum urea, serum creatinine, fasting blood sugar and Creatinine Clearance Rate (CCR). Materials and Methods: This case-control study was conducted at Government Medical College, Rajouri, Jammu and Kashmir, India, from February 2021 to December 2021. Total 50 known patients of kidney diseases and 50 healthy individuals above the age of 18 years were enrolled in the study. Blood samples were collected from all individuals and serum BTP, serum urea level, serum creatinine level, fasting blood sugar were measured. Correlation of BTP with serum urea level, serum creatinine level, Fasting Blood Glucose (FBG) level, and CCR was calculated by Pearson Correlation test. Results: In present study, 50 patients in case groups (33 male and 17 females) and 50 healthy controls (25 males and 25 females) were included. Among controls, the mean age of patients was 52.12±5.66 years and among cases 55.94±10.51 years. BTP level was increased two times (from 32.06±11.25 µg/ml to 66.36±27.80 µg/ml) in CKD patients than controls individuals. BTP level was positively correlated with serum urea level, serum creatinine level, and FBG level while negatively correlated with CCR. Conclusion: BTP may be a useful and reliable serum marker for identifying the magnitude of renal dysfunction in patients with CKD and may have its place beside serum creatinine as an alternative endogenous GFR marker

SDS-PAGE analysis of purified recombinant fusion proteins and their confirmation by immunoblotting with anti-His antibodies.

<p><b>(A)</b> SDS-PAGE analysis of purified full length recombinant AtCyp19-3, and deleted versions AtCyp19-3 _(35–176) and AtCyp19-3 _(71–176). Total proteins were isolated from recombinant <i>E</i>.<i>coli</i> BL21(DE3) before (UI) and after induction (I) with 0.5 mM IPTG, and purified by Ni-NTA affinity column. Arrows indicate the purified recombinant proteins. <b>(B)</b> Confirmation of the purified recombinant proteins (arrows) by immunoblotting with the anti-His antibodies. M: markers.</p

Redox control mechanisms in AtCyp19-3 and TaCypA-1 (A)

<p>Potential metal binding site (Site1) in TaCypA-1 comprising of Cys-122, His-99 and Cys-126 amino acids (yellow) as predicted by TEMSP. Cys-122-Cys-126 pair (3.905 <i>Å</i>) in TaCypA-1 which may be involved in Redox 2-Cys mechanism similar to SmCypA, is also shown. <b>(B)</b> Second potential metal binding site (Site 2) consisting of Cys-40, His-54 and Cys-168 (red). Disulfide bond between Cys-40 and Cys-168 (5.489 <i>Å</i>), and hydrogen bond network linking side chains of Glu-83(red) with divergent loop residues Lys-48 and Ser-49 (magenta) in TaCypA-1 are implicated in allosteric control similar to Redox 2-Cys Mechanism in CsCypA. <b>(C)</b> Cartoon showing His-54 and disulfide bridge forming pair Cys-40-Cys-168 (5.4 <i>Å</i>) in AtCyp19-3. This triad (yellow) may form a metal binding site in AtCyp19-3. <b>(D)</b> Hydrogen bond connecting side chain carboxyl group of Glu-83(red) with main chain amide group of Lys-48 (green) from the divergent loop in AtCyp19-3. Formation of Cys-40-Cys-168 disulfide bond disrupts this interaction and closes the active site. Distances have been shown as black dashed lines while hydrogen bonds as black solid lines.</p

PPIase activity of purified recombinant fusion protein AtCyp19-3

<p><b>(A)</b> Hydrolysis of N-succinyl-ala-ala-pro-phe-p-nitroanilidine (peptidyl prolyl <i>cis-trans</i> isomerase or PPIase activity) in the presence of 4.34 nM of recombinant AtCyp19-3 and 52.4 nM and 65.87 nM each of AtCyp19-3_(35–176) and AtCyp19-3_(71–176) proteins. The rate of reaction is expressed as first order rate constant (k) Bovine serum albumin (BSA) was used as a negative control. <b>(B)</b> Effect of purified AtCyp19-3 on rate constant. <b>(C)</b> Effect of cyclophilin inhibitor, cyclosporin A (CsA), and FKBP inhibitor, FK506, on the PPIase activity of AtCyp19-3 <b>(D)</b> Determination of inhibition constant (k_i) of AtCyp19-3 for CsA. Inhibition constant (k_i) for CsA was determined as gradient of the line of the best fit from a plot of [CsA]/(1-k/k_o) against k_o/k, where k is the rate constant at any given CsA concentration and k_o is the rate constant in the absence of CsA. The slope of the line represents the k_i.</p