scholarly journals First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Matti Ropo ◽  
Markus Schneider ◽  
Carsten Baldauf ◽  
Volker Blum
Keyword(s):  
Amino Acids ◽  
First Principles ◽  
Data Set

Review and Analysis of Bluff Body Flame Stabilization Data

2008 ◽  
Author(s):  
Sajjad A. Husain ◽  
Ganesh Nair ◽  
Santosh Shanbhogue ◽  
Tim C. Lieuwen
Keyword(s):  
Activation Energy ◽  
Kinetic Modeling ◽  
First Principles ◽  
Bluff Body ◽  
Large Range ◽  
Flame Stabilization ◽  
Local Extinction ◽  
Data Set ◽  
Flame Sheet ◽  
Semi Empirical

This paper compiles and analyzes bluff body stabilized flame blowoff data from the literature. Many of these studies contain semi-empirical blowoff correlations that are, in essence, Damko¨hler number correlations of their data. This paper re-analyzes these data, utilizing various Damko¨hler number correlations based upon detailed kinetic modeling for determining chemical time scales. While the results from this compilation are similar to that deduced from many earlier studies, it demonstrates that a rather comprehensive data set taken over a large range of conditions can be correlated from “first-principles” based calculations that do not rely on empirical fits or adjustable constants (e.g., global activation energy or pressure exponents). The paper then discusses the implications of these results on understanding of blowoff. Near blowoff flames experience local extinction of the flame sheet, manifested as “holes” that form and convect downstream. However, local extinction is distinct from blowoff — in fact, under certain conditions the flame can apparently persist indefinitely with certain levels of local extinction. We hypothesize that simple Damko¨hler number correlations contain the essential physics describing this first stage of blowoff; i.e., they are correlations for the conditions where local extinction on the flame begins, but do not fundamentally describe the ultimate blowoff condition itself. However, such correlations are reasonably successful in correlating blowoff limits because the ultimate blowoff event appears to be correlated to some extent to the onset of this first stage.

P–283 Combination between amino acids profile of the spent culture media and morphokinetics parameters of human embryos to determine its viability

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
N Adel ◽  
M Kadah ◽  
S Abdulghafar ◽  
M Elmahdy ◽  
D Ghareeb ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Embryo Development ◽  
Culture Medium ◽  
Essential Amino Acids ◽  
Human Embryos ◽  
Data Set ◽  
Group A ◽  
Amino Acids Profile ◽  
Group D

Abstract Study question How to determine human embryo viability noninvasively before embryo transfer? Summary answer We propose that the combination of the amino acid profile of an individual embryo with its morphokinetics will provide noninvasive tool to determine its viability. What is known already It was already known that human embryos at early cleavage require non-essential amino acids, while at the 8-cell to blastocyst stages, a mixture of non-essential and essential amino acids. Amino acids have important roles during embryo development. Acting as biosynthetic precursors,buffers of intracellular pH in the embryo, antioxidants, energy sources and regulators of metabolic function and signaling pathways. Many studies have used time-lapse to analyze human embryonic development including the process of fertilization and assessment of early events and introducednoninvasive prognostic markers which predict embryo development and correlate it to IVF treatment outcomes. Study design, size, duration This study was a prospective cohort study approved by the Clinical Trial Ethical Committee of Faculty of Medicine, Alexandria University according to ethical standards of scientific research (Serial number: 0303721).Thirty females aged 30.13 ± 4.83 years undergoing ICSI cycle in the Madina Fertility Center, during the period of March 2018 to November 2019.202 MII oocytes were incubated individually in embryoscope. Participants/materials, setting, methods Embryos (n = 161) were divided on Day 5 into two groups –developed embryos “Group D” (embryos that developed to blastocyst) and arrested embryos “Group A” (embryos remain at cleavage stage and fail to develop to blastocys).Developed embryos (Group D) included 99 embryos, and Arrested embryos (Group A) included 62 embryos. For each group, morphokinetic developmental points using embryoscope and the different amino acids concentrations in spent culture medium were analyzed using LC- mass spectro etry. Main results and the role of chance On one hand, the first appearance of pronuclei (TPNa), t2, t4 and CC2 in group D occurred significantly earlier than those of Group A.Analysis of 19 essential and non-essential amino acids in spent culture medium of each embryo in the two studied groups D and A showed a significantly higher concentration of two essential amino acids L-Valine (145.73 ± 150.96) and L-Phenylalanine (61.59 ± 55.78) in Group D than their concentration in Group A ( 104.58 ± 33.58, 44.24 ± 14.61, respectively , p ≤ 0.05).and significantly lower concentration of three non-essential amino acids L-Tyrosine (62.56 ± 41.03) , L-Cysteine (19.48 ± 11.90), and L-Alanine (136.0 ± 389.83) observed in Group D when compared to Group A (69.57 ± 20.78, 22.37 ± 8.59,145.33 ± 165.22, respectively, Limitations, reasons for caution It is important to note, that results were developed on a data set from one clinic with different stimulation protocols, a multicenter data and a correlation with the stimulation protocol used should be involved in future studies, in addition a larger sample size to avoid high standard deviation is recommended Wider implications of the findings: We can conclude that amino acid turnover is independent of the traditional morphological assessment of embryos and it may reflect its viability. The prospective combined use of amino acids profile of individual embryo and its morphokinetic parameters may contribute to introduce a new noninvasivs tool that may improve implantation rate Trial registration number 0303721

scholarly journals Comparison of Soil Properties and Organic Components in Infusions According to Different Aerial Appearances of Tea Plantations in Central Taiwan

2020 ◽  
Vol 12 (11) ◽  
pp. 4384
Author(s):  
Prapasiri Tongsiri ◽  
Wen-Yu Tseng ◽  
Yuan Shen ◽  
Hung-Yu Lai
Keyword(s):  
Amino Acids ◽  
Soil Properties ◽  
Free Amino Acids ◽  
Free Amino ◽  
Data Set ◽  
Organic Components ◽  
Chemical Soil ◽  
Tea Plantations ◽  
Central Taiwan ◽  
Physical And Chemical

The soil properties, climate, type of management, and fermentation process critically affect the productivity and quality of tea. In this study, tender tea leaves were collected from central Taiwan, and organic components in their infusions as well as physical and chemical soil properties differentiated using aerial photographs where good (G) and bad (B) growth exhibitions were determined. Eleven physical and chemical soil properties as well as five compounds in tea infusions were analyzed to determine the main factor that affects the growth of these tea trees. The Fleiss’ kappa statistic results revealed that the wet aggregate stability, pH, and exchangeable potassium content exhibit the most significant effect, with scores of 0.86, 0.64, and 0.62, respectively. Soil quality calculated using the mean weight diameter based on 11 soil properties revealed that ~67% of the total score of G is greater than that of B. Generally, contents of total polyphenols (51.67%) and catechins (51.76%) in the infusions of B were greater than those of G. In addition, significant positive correlations between the free amino acids content and soil properties, including pH and copper content, were observed. However, a negative correlation between the free amino acids and flavone contents and most of the soil properties was observed. The survey data set obtained from this study can provide useful information for the improved management of tea plantations.

scholarly journals First-Principles Calculations on the Adsorption Behavior of Amino Acids on a Titanium Carbide MXene

2020 ◽  
Vol 3 (9) ◽  
pp. 5913-5921 ◽  
Author(s):  
José D. Gouveia ◽  
Gerard Novell-Leruth ◽  
Pedro M. L. S. Reis ◽  
Francesc Viñes ◽  
Francesc Illas ◽  
...  
Keyword(s):  
Amino Acids ◽  
Titanium Carbide ◽  
First Principles ◽  
Adsorption Behavior ◽  
First Principles Calculations

scholarly journals Crystallization and preliminary X-ray diffraction studies of the C-terminal domain ofChlamydia trachomatisCdsD

2014 ◽  
Vol 70 (10) ◽  
pp. 1431-1433 ◽  
Author(s):  
Gitte Meriläinen ◽  
Rik K. Wierenga
Keyword(s):  
Amino Acids ◽  
Type Iii Secretion ◽  
Type Iii Secretion System ◽  
Secretion System ◽  
Size Exclusion ◽  
Diffusion Method ◽  
Data Set ◽  
Cell Parameters ◽  
Type Iii ◽  
Terminal Domain

The inner membrane ring of the bacterial type III secretion system (TTSS) is composed of two proteins. InChlamydia trachomatisthis ring is formed by CdsD (gene nameCT_664) and CdsJ (gene nameCTA_0609). CdsD consists of 829 amino acids. The last 400 amino acids at its C-terminal end relate it to the type III secretion system YscD/HrpQ protein family. The C-terminal domain, consisting of amino acids 558–771, ofC. trachomatisCdsD was overexpressed inEscherichia coliand purified using immobilized metal-affinity chromatography (IMAC) and size-exclusion chromatography. The protein was crystallized using the vapour-diffusion method. A data set was collected to 2.26 Å resolution. The crystals have the symmetry of space groupC2, with unit-cell parametersa= 106.60,b= 23.91,c= 118.65 Å, β = 104.95°. According to the data analysis there is expected to be one molecule in the asymmetric unit, with a Matthews coefficient of 3.0 Å3 Da−1.

scholarly journals Incorporating User Input Into Optimal Constraining Procedures for Survey Estimates

2013 ◽  
Vol 29 (3) ◽  
pp. 375-396 ◽  
Author(s):  
Matthew Williams ◽  
Emily Berg
Keyword(s):  
First Principles ◽  
Contingency Table ◽  
Nonlinear Constraints ◽  
Constrained Estimation ◽  
Data Set ◽  
User Input ◽  
Optimal Estimates ◽  
Linear And Nonlinear Constraints ◽  
Linear And Nonlinear ◽  
Survey Estimates

Abstract We examine the incorporation of analyst input into the constrained estimation process. In the calibration literature, there are numerous examples of estimators with “optimal” properties. We show that many of these can be derived from first principles. Furthermore, we provide mechanisms for injecting user input to create user-constrained optimal estimates. We include derivations for common deviance measures with linear and nonlinear constraints and we demonstrate these methods on a contingency table and a simulated survey data set. R code and examples are available at https://github.com/mwilli/Constrained-estimation.git.

scholarly journals Native like helices in a specially designed β peptide in the gas phase

2015 ◽  
Vol 17 (7) ◽  
pp. 5376-5385 ◽  
Author(s):  
Franziska Schubert ◽  
Kevin Pagel ◽  
Mariana Rossi ◽  
Stephan Warnke ◽  
Mario Salwiczek ◽  
...  
Keyword(s):  
Amino Acids ◽  
Gas Phase ◽  
First Principles ◽  
Open Chain ◽  
Gas Phase Spectroscopy

First principles simulations and gas phase spectroscopy suggest equilibrium of helices for an oligomer of open chain β amino acids.

scholarly journals Prediction of amyloidogenicity based on the n-gram analysis

2016 ◽  
Author(s):  
Michał Jan Burdukiewicz ◽  
Piotr Sobczyk ◽  
Stefan Rödiger ◽  
Anna Duda-Madej ◽  
Paweł Mackiewicz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Hot Spots ◽  
Permutation Test ◽  
Strongly Correlated ◽  
Amino Acid Residues ◽  
Data Set ◽  
Amyloid Peptides ◽  
External Data ◽  
N Gram

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers, based on data collected in the AmyLoad database. Only the most informative n-grams, selected by our Quick Permutation Test, were considered. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on more general properties of amino acids, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids, which are strongly correlated with hydrophobicity, a tendency to form ß-sheets and rigidity of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were already confirmed experimentally. AmyloGram is available as a web-server: www.smorfland.uni.wroc.pl/amylogram/. The code and results are publicly available at: www.github.com/michbur/prediction_amyloidogenicity_ngram/.

Evaluating the Efficacy of Amino Acids as CO2Capturing Agents: A First Principles Investigation

2011 ◽  
Vol 45 (19) ◽  
pp. 8582-8588 ◽  
Author(s):  
M. Althaf Hussain ◽  
Yarasi Soujanya ◽  
G. Narahari Sastry
Keyword(s):  
Amino Acids ◽  
First Principles
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