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Journal articles on the topic 'Ramachandran Map'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Ramakrishnan, C. "Ramachandran and his Map." Resonance 6, no. 10 (2001): 48–56. http://dx.doi.org/10.1007/bf02836967.

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2

Walther, Dirk, and Fred E. Cohen. "Conformational attractors on the Ramachandran map." Acta Crystallographica Section D Biological Crystallography 55, no. 2 (1999): 506–17. http://dx.doi.org/10.1107/s0907444998013353.

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Frequency distributions of protein backbone dihedral angles φ and ψ have been analyzed systematically for their apparent correlation with various crystallographic parameters, including the resolution at which the protein structures had been determined, the R factor and the free R factor, and the results have been displayed in novel differential Ramachandran maps. With improved sensitivity compared with conventionally derived heuristic Ramachandran maps, such differential maps automatically reveal conformational `attractors' to which φ/ψ distributions converge as the crystallographic resolution

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3

SZABADKA, ZOLTÁN, RAFAEL ÖRDÖG, and VINCE GROLMUSZ. "THE RAMACHANDRAN MAP OF MORE THAN 6,500 PERFECT POLYPEPTIDE CHAINS." Biophysical Reviews and Letters 02, no. 03n04 (2007): 267–71. http://dx.doi.org/10.1142/s1793048007000519.

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The Protein Data Bank (PDB) is the most important depository of protein structural information, containing more than 45,000 deposited entries today. Because of its inhomogeneous structure, its fully automated processing is almost impossible. In a previous work, we cleaned and re-structured the entries in the Protein Data Bank, and from the result we have built the RS-PDB database. Using the RS-PDB database, we draw a Ramachandran-plot from 6,593 "perfect" polypeptide chains found in the PDB, containing 1,192,689 residues. This is a more than tenfold increase in the size of data analyzed before

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4

Srinivasan, Narayanaswamy. "Chandrasekharan Ramakrishnan (1939–2019): The student behind the Ramachandran map." Protein Science 28, no. 11 (2019): 1920–22. http://dx.doi.org/10.1002/pro.3723.

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5

Pal, Debnath, and Pinak Chakrabarti. "On residues in the disallowed region of the Ramachandran map." Biopolymers 63, no. 3 (2002): 195–206. http://dx.doi.org/10.1002/bip.10051.

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6

Issa, Joseph B., Karsten Krogh-Jespersen, and Stephan S. Isied. "Conformational Dependence of Electronic Coupling Across Peptide Bonds: A Ramachandran Map." Journal of Physical Chemistry C 114, no. 48 (2010): 20809–12. http://dx.doi.org/10.1021/jp1071764.

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7

Malika, Bourjila, El Gridani Abderrahmane, Tijar Rachida, El Merbouh Brahim, and Drissi El Bouzaidi Rachid. "Theoretical investigation of Ramachandran plot of N-formyl-L-alanine-amide." Chemistry International 4, no. 4 (2018): 216–20. https://doi.org/10.5281/zenodo.1475389.

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The full conformational space of N-formyl-L-alanine-amide was explored by the semi-empirical method AM1 coupled to the Multi Niche Crowding (MNC) genetic algorithm implemented in a package of programs developed in our laboratory. The structural and energy analysis of the resulting conformational space E(,ψ) exhibits 5 regions or minima ɣL, ɣD, ɛL, D and αD. The technique provides better detection of local and global minima within a reasonable time.

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Siodłak, D., M. A. Broda, B. Rzeszotarska, A. E. Kozioł, and I. Dybała. "Conformational properties of N',N'-dimethylamides of N-acetyldehydroalanine and N-acetyl-(Z)-dehydrophenylalanine." Acta Biochimica Polonica 48, no. 4 (2001): 1179–83. http://dx.doi.org/10.18388/abp.2001_3888.

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Conformational preferences of Ac-deltaAla-NMe2 and Ac-(Z)-deltaPhe-NMe2 were studied and compared with those of their monomethyl counterparts as well as with those of their saturated analogues. X-Ray data and energy calculations revealed a highly conservative conformation of the dehydro dimethylamides, which is located in a high-energy region of the Ramachandran map.

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9

Mowbray, Sherry L., Charlotte Helgstrand, Jill A. Sigrell, Alexander D. Cameron, and T. Alwyn Jones. "Errors and reproducibility in electron-density map interpretation." Acta Crystallographica Section D Biological Crystallography 55, no. 7 (1999): 1309–19. http://dx.doi.org/10.1107/s0907444999005211.

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Three investigators, with varying levels of experience, independently built and refined the structure of Escherichia coli ribokinase at 2.6 Å resolution. At the end of the refinement/rebuilding processes the models had essentially converged, although each had its own particular pattern of remaining errors. The subsequent refinement of the same structure at 1.8 Å resolution allowed an overall quality check of each of the lower resolution models, and an analysis of which graphics-based tools were generally most efficient in locating these errors. Criteria which are useful in the application of R

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10

Kumar, Mayank, та R. S. Rathore. "RamPlot: a webserver to draw 2D, 3D and assorted Ramachandran (φ, ψ) maps". Journal of Applied Crystallography 58, № 2 (2025): 630–36. https://doi.org/10.1107/s1600576725001669.

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The Ramachandran steric map of torsion angles (φ, ψ) introduced in 1963 has been widely used for protein structure validation and model building. Many developments in the field have made it essential to develop a utility to plot assorted types of maps for the following specific reasons: (i) to investigate different types (Gly, Val/Ile, pre/trans/cis-Pro and general) of 2D and 3D maps, addressing the diverse steric environments and frequency distribution of conformations, (ii) to examine polypeptides containing non-standard residues, (iii) for better visualization and analysis of conformational

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11

Perczel, Aandrás, Márton Kajtar, John F. Marcoccia, and Imre G. Csizmadia. "The utility of the four-dimensional ramachandran map for the description of peptide conformations." Journal of Molecular Structure: THEOCHEM 232 (July 1991): 291–319. http://dx.doi.org/10.1016/0166-1280(91)85261-5.

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12

GÖKOĞLU, GÖKHAN, and TARIK ÇELİK. "ALPHA-HELIX FORMATION IN C-PEPTIDE RNASE-A INVESTIGATED BY PARALLEL TEMPERING SIMULATIONS." International Journal of Modern Physics C 18, no. 01 (2007): 91–98. http://dx.doi.org/10.1142/s0129183107010292.

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We have performed parallel tempering simulations of a 13-residue peptide fragment of ribonuclease-A, c-peptide, in implicit solvent with constant dielectric permittivity. This peptide has a strong tendency to form α-helical conformations in solvent as suggested by circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments. Our results demonstrate that 5th and 8–12 residues are in the α-helical region of the Ramachandran map for global minimum energy state in solvent environment. Effects of salt bridge formation on stability of α-helix structure are discussed.

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13

Roche, Julien. "Ramachandran Map Analysis of the Monomeric Aβ 1-40 and Aβ 1-42 Peptides by Solution NMR". Biophysical Journal 112, № 3 (2017): 481a. http://dx.doi.org/10.1016/j.bpj.2016.11.2605.

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14

CHEON, MOOKYUNG, MUYOUNG HEO, IKSOO CHANG, and CHOONGRAK KIM. "CLASSIFICATIONS OF AMINO ACIDS IN PROTEINS BY THE SELF-ORGANIZING MAP." International Journal of Modern Physics C 16, no. 10 (2005): 1609–16. http://dx.doi.org/10.1142/s0129183105008175.

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We present the clustering properties of amino acids, which are building blocks of proteins, according to their physico-chemical characters. To classify the 20 kinds of amino acids, we employ a Self-Organizing Map (SOM) analysis for the Miyazawa-Jernigan (MJ) pairwise-contact matrix, the Environment-dependent One-body energy Parameters (EOP) and the one-body energy parameters incorporating the Ramachandran angle information (EOPR) over the EOP in proteins. We provide the new result of the SOM clustering for amino acids based on the EOPR and compare that with those from the MJ and the EOP matrix

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15

Saad, Esmaiel I. F. "Designing an Inhibitor Molecule to Combat Cancer through the Inhibition of Mutant PI3K (P110 α) Subunit Protein". Al-Mukhtar Journal of Sciences 38, № 4 (2023): 333–41. http://dx.doi.org/10.54172/y4bfxs70.

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The PI3K pathway plays a crucial role in the development of various types of cancers. Specifically, the P110 α component is frequently modified in the formation of human cancer, leading to disruptions in cell growth regulation and the emergence of malignancies. This research paper delves into the increasing utilization of computational tools to forecast potential molecules capable of inhibiting cancer. To validate stable structures of PI3K (P110α) component protein models, the study employed Ramachandran map analysis, which revealed active regions in close proximity to the mutation site. Throu

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Roche, Julien, Yang Shen, Jung Ho Lee, Jinfa Ying та Ad Bax. "Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil". Biochemistry 55, № 5 (2016): 762–75. http://dx.doi.org/10.1021/acs.biochem.5b01259.

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17

Ramakrishnan, Chandrashekharan, Ramanathan Sowdhamini, and Padmanabhan Balaram. "Analysis of short interproton distances in proline peptides as a guide in the interpretation of nuclear Overhauser effects." Collection of Czechoslovak Chemical Communications 53, no. 11 (1988): 2801–9. http://dx.doi.org/10.1135/cccc19882801.

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The conformational dependence of interproton distances in model proline peptides has been investigated in order to facilitate interpretation of the results of Nuclear Overhauser Effect (NOE) studies on such peptides. For this purpose two model systems, namely, Ac-Pro-NHMe and Ac-Pro-X-NHMe have been chosen and used. In the former, short interproton distances detectable in NOE experiments permit a clear distinction between conformations with Pro ψ = -300 (helical region) and those in which ψ is around 1200 (polyproline region). For the latter, the variation of distances between the protons of m

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18

Baldoni, H. A., G. N. Zamarbide, R. D. Enriz, et al. "Peptide models XXIX. cis – trans Isomerism of peptide bonds: ab initio study on small peptide model compound; the 3D-Ramachandran map of formylglycinamide." Journal of Molecular Structure: THEOCHEM 500, no. 1-3 (2000): 97–111. http://dx.doi.org/10.1016/s0166-1280(00)00372-9.

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19

Rudnev, Vladimir R., Kirill S. Nikolsky, Denis V. Petrovsky та ін. "3β-Corner Stability by Comparative Molecular Dynamics Simulations". International Journal of Molecular Sciences 23, № 19 (2022): 11674. http://dx.doi.org/10.3390/ijms231911674.

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This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square

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20

Ganesan, Mahendiraprabu, and Selvarengan Paranthaman. "Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study." Journal of Theoretical and Computational Chemistry 19, no. 06 (2020): 2050014. http://dx.doi.org/10.1142/s0219633620500145.

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Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] an

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21

Klotz, Remi, Alexis Zukowski, Mohamed Kamal, Frank Attenelo, Srinivas Ramachandran, and Min Yu. "Abstract 1242: Single cell multiomic map reveals regulatory landscape of human brain metastases." Cancer Research 83, no. 7_Supplement (2023): 1242. http://dx.doi.org/10.1158/1538-7445.am2023-1242.

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Abstract Capturing comprehensive brain metastasis landscape is critical to the establishment of effective anti-tumor strategies. This study took advantage of single-cell multiomics sequencing to profile the molecular and cellular dynamics in tumor cells and associated microenvironment during brain metastasis. Among different primary cancer types, our data suggest that there are conserved yet distinct tumor cell subpopulations, governed by specific changes in gene expression, chromatin accessibility and tumor-stroma interactions. We characterized the conserved tumor subpopulations of brain meta

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22

Brereton, Andrew E., and P. Andrew Karplus. "Native proteins trap high-energy transit conformations." Science Advances 1, no. 9 (2015): e1501188. http://dx.doi.org/10.1126/sciadv.1501188.

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During protein folding and as part of some conformational changes that regulate protein function, the polypeptide chain must traverse high-energy barriers that separate the commonly adopted low-energy conformations. How distortions in peptide geometry allow these barrier-crossing transitions is a fundamental open question. One such important transition involves the movement of a non-glycine residue between the left side of the Ramachandran plot (that is, ϕ < 0°) and the right side (that is, ϕ > 0°). We report that high-energy conformations with ϕ ~ 0°, normally expected to occur only as

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23

Korobkov, A. A., A. A. Khurmuzakiy, N. G. Esipova, V. G. Tymanyan та A. A. Anashkina. "The refinement of the parameters of β-turns using neutron diffraction data". Биофизика 68, № 6 (2023): 1141–48. http://dx.doi.org/10.31857/s0006302923060054.

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Beta-bends are a difficult to interpret type of polypeptide chain backbone structure of globular proteins. Beta-bends are usually classified according to the dihedral angles φ and ψ of amino acid residues i + 1 and i + 2. Ramachandran map analysis of amino acid residues i + 1 and i + 2 indicates the resulting conformational stresses in bending. The mechanism of stabilization of their energetically disadvantageous conformations is still unclear. This kind of conformation stresses can only be compensated by additional interactions, such as additional hydrogen bonds, whose geometry and energy com

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24

Feigel, Martin, Gerhard Lugert, Javier Manero, and Matthias Bremer. "Konformation von Anthranilsäurepeptiden: Kristallstruktur von tert-Butyloxycarbonyl-Anthranilsäure-Glycinmethylester und semiempirische (AM 1) Beschreibung der Ramachandran-Hyperfläche / Conformation of Anthranilic Acid Peptides: Crystal Structure of tert-Butyloxycarbonyl-Anthranilic-Acid-Glycin-Methyl-Ester and Semi-Empirical (AM 1) Description of the Ramachandran Map." Zeitschrift für Naturforschung B 44, no. 9 (1989): 1109–16. http://dx.doi.org/10.1515/znb-1989-0919.

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Two different molecules are observed in the asymmetric unit of the crystal structure of tert-butyloxycarbonyl-anthranilic-acid-glycin-methyl-ester (1). The whole conformational area (φ and ψ) of the amino acid part of 1 was investigated with the semi-empirical quantenmechanical method AM 1. The structures of 1 in the crystal are well described by the calculations. Rules are derived for the conformational space of peptides containing esters and anthranilic acids.

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25

Bond, Paul S., Keith S. Wilson, and Kevin D. Cowtan. "Predicting protein model correctness in Coot using machine learning." Acta Crystallographica Section D Structural Biology 76, no. 8 (2020): 713–23. http://dx.doi.org/10.1107/s2059798320009080.

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Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that is produced by combining multiple sources of information using a neural network. The residues in 639 automatically built models were marked as correct or incorrect by comparing them with the coordinates deposited in the PDB. A number of features were also calculated for each residue using Coot, including map-to-model correlation, density values, B

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Nambigari, Navaneetha. "Cancer Therapeutics: Structure-Based Drug Design of Inhibitors for a Novel Angiogenic Growth Factor." Mathematical Biology and Bioinformatics 18, no. 1 (2023): 72–88. http://dx.doi.org/10.17537/2023.18.72.

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Angiogenesis, the formation of new blood vessels, is a critical and rate-limiting tumor growth step controlled by pro-angiogenic factors and specific inhibitors. Tumor angiogenesis is essential for cancer progression and metastasis. Platelet growth factors (PDGF) and their receptors (PDGFR) are associated with tumor angiogenesis through overexpression of PDGF. Inhibition of PDGF and its signaling pathway is a new approach to the discovery of anticancer therapeutic agents. The present study focuses on the PDGF-C protein in the identification of novel anti-angiogenic compounds. MODELLER 9.10 sof

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Paiz, Elisia A., Karen A. Lewis, and Steven T. Whitten. "Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins." Molecules 26, no. 3 (2021): 634. http://dx.doi.org/10.3390/molecules26030634.

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The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for t

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Guan, Tianzhu, Ning Li, Ya Gao, et al. "Interaction behavior between bisphenol AP and pepsin: Insights from density functional theory, and spectroscopic and molecular dynamic simulation." Quality Assurance and Safety of Crops & Foods 14, no. 2 (2022): 1–12. http://dx.doi.org/10.15586/qas.v14i2.1023.

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Overuse of polymer materials has caused increasing direct human exposure to bisphenol AP (BPAP). Through the contaminated environment and food chains, the adverse effects of BPAP on humans and plants induce growing concerns. In this study, the effects of BPAP on pepsin structure changes were exhaustively investigated by multi-spectral methods. Under mimic physiological conditions, BPAP caused a gradient intrinsic fluorescence quenching by inducing microenvironmental changes surrounding residues with the endogenous fluorescence in pepsin. During the ground-state complex formation, the senior st

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Endrédi, G., A. Perczel, O. Farkas, et al. "Peptide models XV. The effect of basis set size increase and electron correlation on selected minima of the ab initio 2D-Ramachandran map of For-Gly-NH2 and For-l-Ala-NH2." Journal of Molecular Structure: THEOCHEM 391, no. 1-2 (1997): 15–26. http://dx.doi.org/10.1016/s0166-1280(96)04695-7.

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Roterman, Irena, Katarzyna Stapor, and Leszek Konieczny. "Secondary Structure in Amyloids in Relation to Their Wild Type Forms." International Journal of Molecular Sciences 24, no. 1 (2022): 154. http://dx.doi.org/10.3390/ijms24010154.

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The amyloid structures and their wild type forms, available in the PDB database, provide the basis for comparative analyses. Globular proteins are characterised by a 3D spatial structure, while a chain in any amyloid fibril has a 2D structure. Another difference lies in the structuring of the hydrogen bond network. Amyloid forms theoretically engage all the NH and C=O groups of the peptide bonds in a chain with two hydrogen bonds each. In addition, the hydrogen bond network is highly ordered—as perpendicular to the plane of the chain. The β-structure segments provide the hydrogen bond system w

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Çöltekin, Arzu, Gianna Hartung, and Martina Meyer. "Deconstructing the relief inversion effect: Contributors of the problem and its solutions." Abstracts of the ICA 1 (July 15, 2019): 1–2. http://dx.doi.org/10.5194/ica-abs-1-48-2019.

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<p><strong>Abstract.</strong> <i>Terrain reversal</i> (also known as <i>relief inversion</i>) effect is a common and well-known illusion encountered in shaded relief maps and satellite imagery where the main depth cue is shading/shadows (Imhof, 1967; Bernabe-Poveda, Callejo, &amp; Ballari, 2005; Saraf, Das, Agarwal, &amp; Sundaram, 1996; Biland &amp; Çöltekin, 2016; Çöltekin, Rautenbach, Coetzee, &amp; Mokwena, 2018). This illusion interferes with our perception of <i>shape from shading</i> (e.g., see Kleffner &amp; Rama

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Josefsson, Martin. "Properties of bisect-diagonal quadrilaterals." Mathematical Gazette 101, no. 551 (2017): 214–26. http://dx.doi.org/10.1017/mag.2017.61.

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The general class of quadrilaterals where one diagonal is bisected by the other diagonal has appeared very rarely in the geometrical literature, but they have been named several times in connection with quadrilateral classifications. Günter Graumann strangely gave these objects two different names in [1, pp. 192, 194]: sloping-kite and sliding-kite. A. Ramachandran called them slant kites in [2, p. 54] and Michael de Villiers called them bisecting quadrilaterals in [3, pp. 19, 206]. The latter is a pretty good name, although a bit confusing: what exactly is bisected?We have found no papers and

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WAHL, G., P. ENYONG, A. NGOSSO, et al. "Onchocerca ochengi: epidemiological evidence of cross-protection against Onchocerca volvulus in man." Parasitology 116, no. 4 (1998): 349–62. http://dx.doi.org/10.1017/s003118209700228x.

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In North Cameroon, the vector of Onchocerca volvulus (causative agent of human onchocerciasis) also transmits 2 filariae of animals: O. ochengi from cattle and O. ramachandrini from wart hogs. In order to assess the qualitative and quantitative roles of these ‘animal filariae’ in the epidemiology of O. volvulus, the transmission of the 3 parasites was measured in 2 villages and related to the endemicity of human onchocerciasis. In Galim, a cattle-farming Guinea savanna village where wild animals are rare, the overwhelming majority of all filarial infections found in the Simulium damnosum s.l.

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Pléh, Csaba. "Until when do we still need psychology?" Magyar Pszichológiai Szemle 67, no. 2 (2012): 237–66. http://dx.doi.org/10.1556/mpszle.67.2012.2.1.

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A pszichológia a 20. század egyik diadalmas tudománya és hivatása. Mégis a kezdetetektől visszatérő hullámokban kételyek kísérik, vagy egyáltalán lehetőségét, vagy (vélt) intellektuális szárazságát, vagy gyakorlati sterilitását. Ezek a kételyek ma újra ébrednek, de ma már nem a fenyegetettség, hanem a világos szakmai identitás nevében tudjuk ironikusan visszautasítani őket. A 19. század második felében a születő pszichológiát az egyik oldalon Comte kezelte kétellyel, mint aminek tartalma megoszlik a szociológia és a neurobiológia között, a másik oldalon pedig Dilthey, Frege és Husserl tartottá

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Fortin, Jerome, Ming-Feng Chiang, Cem Meydan, et al. "Abstract A16: Multi-omic analyses in genetically engineered mice reveal distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells." Blood Cancer Discovery 4, no. 3_Supplement (2023): A16. http://dx.doi.org/10.1158/2643-3249.aml23-a16.

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Abstract Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we

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Kivi, Indrek, Priit Moeller, Jaan Aruväli, and Gunnar Nurk. "Influence of A-site Deficiency and Ni/Co Ratio in B-site on Electrochemical Performance of (La_0.25Sr_0,25Ca_0.45)_yTi_0.95Ni_0.05-xCo_xO_3- _d Anode." ECS Meeting Abstracts MA2023-01, no. 54 (2023): 80. http://dx.doi.org/10.1149/ma2023-015480mtgabs.

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La0.25Sr0.25Ca0.45TiO3 -d (LSCT) is a perovskite (ABO3) type mixed ionic-electronic conductive (MIEC) oxide and has been proposed as an electrode material for high temperature fuel cell [1]. This material owing high conductivity, robustness in hydrocarbon fuels and significant amount of attention has been paid to improve the electrochemical activity [1, 2]. Doping of B-site with some d-metal cation (Ni, Co, Mn, V, Mo) has been demonstrated to improve the catalytic activity. One of the advantages of the MIEC conducting scaffold based electrodes is that the catalyst phase on the electrode surfac

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ALAM, AHM Zahirul. "EDITORIAL." IIUM Engineering Journal 22, no. 1 (2021): i. http://dx.doi.org/10.31436/iiumej.v22i1.1719.

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CHIEF EDITOR Ahmad Faris Ismail, IIUM, Malaysia TECHNICAL EDITOR Sany Izan Ihsan, IIUM, Malaysia EXECUTIVE EDITOR AHM Zahirul Alam, IIUM, Malaysia ASSOCIATE EDITOR Nor Farahidah Za’bah, IIUM, Malaysia LANGUAGE EDITOR Lynn Mason, Malaysia COPY EDITOR Hamzah Mohd. Salleh, IIUM, Malaysia EDITORIAL BOARD MEMBERS Abdullah Al-Mamun, IIUM, Malaysia Abdumalik Rakhimov, IIUM, Malaysia Ali Sophian, IIUM, Malaysia Erwin Sulaeman, IIUM, Malaysia Hanafy Omar, Saudi Arabia Hazleen Anuar, IIUM, Malaysia Konstantin Khanin, University of Toronto, Canada Ma'an Al-Khatib, IIUM, Malaysia Md Zahangir Alam, IIUM, M

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Alam, AHM Zahirul. "Editorial." IIUM Engineering Journal 23, no. 2 (2022): i. http://dx.doi.org/10.31436/iiumej.v23i2.2460.

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CHIEF EDITOR  Ahmad Faris Ismail, IIUM, Malaysia  TECHNICAL EDITOR  Sany Izan Ihsan, IIUM, Malaysia  EXECUTIVE EDITOR  AHM Zahirul Alam, IIUM, Malaysia  ASSOCIATE EDITOR  Nor Farahidah Za’bah, IIUM, Malaysia  LANGUAGE EDITOR  Lynn Mason, Malaysia  COPY EDITOR  Hamzah Mohd. Salleh, IIUM, Malaysia  MALAY TRANSLATOR  Nurul Arfah Che Mustapha, IIUM, Malaysia   EDITORIAL BOARD MEMBERS  Abdullah Al-Mamun, IIUM, Malay

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Alam, AHM Zahirul. "Editorial." IIUM Engineering Journal 23, no. 1 (2022): i. http://dx.doi.org/10.31436/iiumej.v23i1.2246.

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CHIEF EDITOR Ahmad Faris Ismail, IIUM, Malaysia TECHNICAL EDITOR Sany Izan Ihsan, IIUM, Malaysia EXECUTIVE EDITOR AHM Zahirul Alam, IIUM, Malaysia ASSOCIATE EDITOR Nor Farahidah Za’bah, IIUM, Malaysia LANGUAGE EDITOR Lynn Mason, Malaysia COPY EDITOR Hamzah Mohd. Salleh, IIUM, Malaysia MALAY TRANSLATOR Nurul Arfah Che Mustapha, IIUM, Malaysia  EDITORIAL BOARD MEMBERS Abdullah Al-Mamun, IIUM, Malaysia Abdumalik Rakhimov, IIUM, Malaysia Ali Sophian, IIUM, Malaysia Erwin Sulaeman, IIUM

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Alam, AHM Zahirul. "Editorial." IIUM Engineering Journal 19, no. 2 (2018): i—iv. http://dx.doi.org/10.31436/iiumej.v19i2.1008.

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 (IIUMEJ)  IIUM ENGINEERING JOURNAL ISSN: 1511-788X E-ISSN: 2289-7860 Volume 19, Issue 2, December 2018 https://doi.org/10.31436/iiumej.v19i2   CHIEF EDITOR Ahmad Faris Ismail, IIUM, Malaysia TECHNICAL EDITOR Erry Yulian Triblas Adesta, IIUM, Malaysia EXECUTIVE EDITOR AHM Zahirul Alam, IIUM, Malaysia ASSOCIATE EDITOR Anis Nurashikin Nordin, IIUM, Malaysia LANGUAGE EDITOR Lynn Mason, Malaysia COPY EDITOR Hamzah Mohd. Salleh, IIUM, Malaysia  EDITORIAL BOARD MEMBERS Abdull

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Amita, O. Sankhwal, D. Shah Shruti, J. Gavali Deepa, and N. Dudani Sumesh. "Riparian Flora of Mahi River, Gujarat." Biolife 3, no. 4 (2022): 820–26. https://doi.org/10.5281/zenodo.7306479.

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<strong>ABSTRACT</strong> The rivers are important channels of materials and energy, which are constantly reeling under the impacts of human influences that often lead to problems in biodiversity conservation and ecosystem functions. The Mahi River in Gujarat is a west-flowing perennial river holding lot of ecological and religious importance. Hence, this study was carried out to document the floristic diversity in selected villages of Vadodara district falling in the riparian zone of the river. Total 328 species of flowering plants belonging to 230 genera and 73 different families was recorde

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Alam, AHM Zahirul. "Editorial." IIUM Engineering Journal 19, no. 1 (2018): i—iv. http://dx.doi.org/10.31436/iiumej.v19i1.917.

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    IIUM ENGINEERING JOURNAL    CHIEF EDITOR Ahmad Faris Ismail, IIUM, Malaysia TECHNICAL EDITOR Erry Yulian Triblas Adesta, IIUM, Malaysia EXECUTIVE EDITOR AHM Zahirul Alam, IIUM, Malaysia ASSOCIATE EDITOR Anis Nurashikin Nordin, IIUM, Malaysia LANGUAGE EDITOR Lynn Mason, Malaysia COPY EDITOR Hamzah Mohd. Salleh, IIUM, Malaysia  EDITORIAL BOARD MEMBERS Abdullah Al-Mamun, IIUM, Malaysia Abdumalik Rakhimov, IIUM, Malaysia Amir Akramin Shafie, IIUM, Malaysia Erwin S

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"UNITED NATIONS ACTIVITIES." Environmental Policy and Law 42, no. 6 (2012): 296–328. http://dx.doi.org/10.3233/epl-2012-42_6_02.

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UN / GA 67th Session - Key Sentiments in the 2nd Committee 296 UN / GA - Tackling Rio+20 Outcomes 296 CBD / COP-11 - Beginning of the Implementation Era? (Elsa Tsioumani) 298 CBD / Cartagena Protocol - COP / MOP-6 (Focus on Challenges) 304 UNFCCC - Key Regime Ingredients Yet to be Agreed (Soledad Aguilar and Eugenia Recio) 310 UNFCCC - Adaptation Policy Road Map Appraisal (A. Saleem Khan and A. Ramachandran) 312 ISA-18 - Environmental Law Highlights (Elisa Morgera) 317 FAO - Global Committees Address Food, Hunger, Agriculture and Environment 318 UNEP / ICCM-3 - The Future of the Chemicals Mana

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Chahkandi, Behzad, and Mohammad Chahkandi. "An accurate DFT study within conformational survey of the d-form serine−alanine protected dipeptide." BMC Chemistry 17, no. 1 (2023). http://dx.doi.org/10.1186/s13065-023-01051-9.

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AbstractThe conformational analysis of n-formyl-d-serine-d-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD–γL, is in the β‒turn region

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Duraisamy, Nithyadevi, Mohd Yasir Khan, Abid Ullah Shah, Reda Nacif Elalaoui, Mohammed Cherkaoui, and Maged Gomaa Hemida. "Machine learning tools used for mapping some immunogenic epitopes within the major structural proteins of the bovine coronavirus (BCoV) and for the in silico design of the multiepitope-based vaccines." Frontiers in Veterinary Science 11 (October 2, 2024). http://dx.doi.org/10.3389/fvets.2024.1468890.

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IntroductionBCoV is one of the significant causes of enteritis in young calves; it may also be responsible for many respiratory outbreaks in young calves. BCoV participates in the development of bovine respiratory disease complex in association with other bacterial pathogens. Our study aimed (1) to map the immunogenic epitopes (B and T cells) within the major BCoV structural proteins. These epitopes are believed to induce a robust immune response through the interaction with major histocompatibility complex (MHC class II) molecules (2) to design some novel BCoV multiepitope-based vaccines.Mate

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Newell, Nicholas E. "MapTurns: mapping the structure, H-bonding and contexts of beta turns in proteins." Bioinformatics, December 16, 2024. https://doi.org/10.1093/bioinformatics/btae741.

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Abstract Motivation Beta turns are the most common type of secondary structure in proteins after alpha helices and beta sheets and play many key structural and functional roles. Turn backbone (BB) geometry has been classified at multiple levels of precision, but the current picture of side chain (SC) structure and interaction in turns is incomplete, because the distribution of SC conformations associated with each sequence motif has commonly been represented only by a static image of a single, typical structure for each turn BB geometry, and only motifs which specify a single amino acid (e. g.

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Singh, Prathvi, Venkatnarayanan Ramanathan, and Ramasubbu Sankararamakrishnan. "Self‐contacting Cys, Ser, and Thr residues in high‐resolution protein crystal structures: Tertiary constraints or hydrogen bonds?" Protein Science 33, no. 12 (2024). http://dx.doi.org/10.1002/pro.5218.

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AbstractFunctional groups in the side‐chains of at least 10 amino acids are mainly involved in tertiary interactions. However, structural and functional significance of intra‐residue interactions has not been fully recognized. In this study, we have analyzed ~5800 non‐redundant high‐resolution protein structures and identified 1166 self‐contacts between the side‐chain S‐H/O‐H and backbone C=O groups in Cys, Ser, and Thr residues that satisfied the geometric criteria to form hydrogen bonds. Quantum chemical calculations using model compounds were used to evaluate single point energy for 45 repr

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Le Trang, Nguyen, Bui Thi Thu Trang, Mai Van Trinh, Nguyen Tien Sy, and Nguyen Manh Khai. "Application of DNDC Model for Mapping Greenhouse Gas Emission from Paddy Rice Cultivation in Nam Dinh Province." VNU Journal of Science: Earth and Environmental Sciences 35, no. 2 (2019). http://dx.doi.org/10.25073/2588-1094/vnuees.4373.

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Abstract: This study used the Denitrification-Decomposition (DNDC) model to calculate greenhouse gas emissions from a paddy rice cultivation in Nam Dinh province. The results show that the total CH4 emission from paddy rice field in Nam Dinh province ranges from 404 to 1146kg/ha/year. Total N2O emissions range from 0.8 to 4.2 kg/ha/year; The total amount of CO2e varies between 10,000 and 30,000 kg CO2e / ha / year. CH4 emissions on typical salinealluvial soils, light mechanics are the highest and lowest on alkaline soils. Alluvium, alkaline soils have the highest N2O emissions and the lowest

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Rajamannar, Janani, Mahesh Vakamudi, Gayathri Sakthivel, V. Rajesh Kumar Kodali, and Aruna Parameswari. "Comparative Efficacy of 20-Degree versus 30-Degree Angled Wedges on Inferior Vena Cava Diameter and Haemodynamic Stability during Spinal Anaesthesia for Caesarean Section: A Randomised Controlled Trial." JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH, July 1, 2025. https://doi.org/10.7860/jcdr/2025/79139.21218.

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Introduction: Spinal anaesthesia is the preferred method of choice for Lower Segment Caesarean Section (LSCS) and is safe for both the mother and foetus. Spinal anaesthesia also provides adequate pain relief for parturient. The most common condition that occurs during the pregnancy is supine hypotension syndrome, which gets aggravated after spinal anaesthesia. Hypotension can be prevented by fluid preloading, vasopressors, inotropes and by placing the wedge below the right gluteal region. Aim: To know the impact of different angled wedges on Inferior Vena Cava (IVC) diameter and its effect on

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Ranjit, PD Shiv, Akilan Elangovan, TV Ramakrishnan, Tamilanbu Panneerselvam, and J. Janifer Jasmine. "Comparison of qSOFA, MEDS, and APACHE II Scores in Early Identification of Sepsis for Patients with 28 days Mortality and ICU Admission: A cross-sectional Study." JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH, 2024. http://dx.doi.org/10.7860/jcdr/2024/68367.19331.

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Introduction: Sepsis is a life-threatening infection that results in organ dysfunction due to an increased pathogen load, necessitating urgent intervention. There is a gap in clinicians’ ability to identify septic patients at high-risk with poor outcomes, highlighting the need for validated predictive scores for early intervention, favourable outcomes, and prompt recovery. Aim: To validate the predictive capacity of the Sequential Organ Failure Assessment (qSOFA), Mortality in Emergency Department Sepsis (MEDS), and Acute Physiology and Chronic Health Evaluation (APACHE 2) scores in patients w

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