scholarly journals Identification and Analysis of Activity Cliffs Using 3D Similarity Techniques

Author(s):  
Mark Mackey ◽  
Timothy J. Cheeseright ◽  
Paolo Tosco

<p>The analysis of activity landscapes and activity cliffs is a widely used method to locate critical regions of SAR. Knowledge of what changes in a series of molecules caused unexpectedly large changes in affinity allows the chemist to focus on the molecular features which are crucial for activity. We examine the usefulness of activity cliff analysis with a metric based on 3D shape and electrostatic similarity, utilizing a ligand-based alignment method. We demonstrate that 3D activity cliff analysis is complementary to the more usual 2D fingerprint-based methods, in that each finds cliffs that the other misses. Moreover, we show that analysis of the activity landscape in the context of a consensus 3D alignment allows the source of the activity cliff to be investigated in terms of the effect that a structural change has on the steric and electrostatic properties of a molecule. The technique is illustrated with two set of compounds with activity against acetylcholinesterase and dipeptidyl peptidase.</p>

2020 ◽  
Author(s):  
Mark Mackey ◽  
Timothy J. Cheeseright ◽  
Paolo Tosco

<p>The analysis of activity landscapes and activity cliffs is a widely used method to locate critical regions of SAR. Knowledge of what changes in a series of molecules caused unexpectedly large changes in affinity allows the chemist to focus on the molecular features which are crucial for activity. We examine the usefulness of activity cliff analysis with a metric based on 3D shape and electrostatic similarity, utilizing a ligand-based alignment method. We demonstrate that 3D activity cliff analysis is complementary to the more usual 2D fingerprint-based methods, in that each finds cliffs that the other misses. Moreover, we show that analysis of the activity landscape in the context of a consensus 3D alignment allows the source of the activity cliff to be investigated in terms of the effect that a structural change has on the steric and electrostatic properties of a molecule. The technique is illustrated with two set of compounds with activity against acetylcholinesterase and dipeptidyl peptidase.</p>


1992 ◽  
Vol 5 (1) ◽  
pp. 53-67
Author(s):  
D.S. Nava

The EEC Treaty contains no specific provisions for the control of concentrations. Only the competition rules. Articles 85 and 86 EEC, could be considered as possible legal instruments for regulating concentrations. The Commission has had to examine whether and to what extent these provisions could be used to this end.The Commission's view has been that Article 85 does not apply to operations resulting in structural change, as is the case of concentrations and concentrative joint ventures. Cooperative operations, such as cooperative joint ventures, on the other hand fall to be assessed under Article 85. The Philip Morris case has made this position uncertain. According to the extensive interpretation of this judgement Article 85 is now applicable to certain concentrations and thus to concentrative joint ventures.There is no such uncertainty regarding the role of Article 86 in controlling concentrative joint ventures, for the Court has established in the Continental Can case that concentrations can be caught by Article 86.With the adoption in 1989 of the Regulation on concentration control the Commission finally has a legal instrument specifically designed to regulate concentrations. However, only concentrations and concentrative joint ventures which comply with certain turnover thresholds (the so-called concentrations or concentrative joint ventures with a Community dimension) can be assessed by the Commission under the Regulation. This means that the provisions of the Regulation can not be applied to concentrative joint ventures beneath the threshold.Because of the difficulty in distinguishing concentrative operations from cooperative ones, the Commission published the Notice regarding the concentrative and cooperative operations under the Regulation on the control of concentrations.


Author(s):  
Anastasius Moumtzoglou

People-centered health care represents a structural change in thinking, which encapsulates before anything else the consideration of the patient. The development of people-centered care might include a partnership approach based on equal footing, capacity-building and the expansion of organizational care. Its central values encompass empowerment, participation, family, community, and the abolition of any kind of discrimination. As a result, they bestow people on shared decision-making not exclusively on issues of treatment but also for health care organization. On the other hand, a global e-health agreement is beginning to take shape on the engagement of stakeholders, the interoperability, and standards. Consequently, e-health can have a significant impact on people-centered care, despite the challenges of implementation and adoption.


Biometrika ◽  
2020 ◽  
Author(s):  
Yining Chen

Summary We consider the problem of segmented linear regression with a single breakpoint, with the focus on estimating the location of the breakpoint. If $n$ is the sample size, we show that the global minimax convergence rate for this problem in terms of the mean absolute error is $O(n^{-1/3})$. On the other hand, we demonstrate the construction of a super-efficient estimator that achieves the pointwise convergence rate of either $O(n^{-1})$ or $O(n^{-1/2})$ for every fixed parameter value, depending on whether the structural change is a jump or a kink. The implications of this example and a potential remedy are discussed.


1994 ◽  
Vol 40 (9) ◽  
pp. 1686-1691 ◽  
Author(s):  
M Maes ◽  
S Scharpé ◽  
I De Meester ◽  
P Goossens ◽  
A Wauters ◽  
...  

Abstract We investigated the components of biological variation in plasma prolyl endopeptidase (PEP; EC 3.4.21.26) and dipeptidyl-peptidase IV (DPP IV; EC 3.4..14.5) activity in healthy individuals. We took monthly blood samples from 26 healthy volunteers for determination of plasma PEP and DPP IV activity during one calendar year. The estimated CVs for PEP activity were: total (CVt) = 25.0%, interindividual (CVg) = 13.9%, and intraindividual (CVi) = 16.8%. There was a statistically significant (P &lt; 0.0001) seasonal pattern in plasma PEP activity, with significantly higher values in the fall than in the other seasons. The peak-trough difference in the yearly variation in PEP activity, expressed as a percentage of the mean, was as high as 56.8%. The estimated CVs for DPP IV activity were: CVt = 17.1%, CVg = 14.5%, and CVi = 8.2%. DPP IV activity was significantly (P &lt; 0.0001) higher in summer than in the other seasons but the amplitude of the yearly variation was small.


2003 ◽  
Vol 77 (14) ◽  
pp. 8127-8140 ◽  
Author(s):  
Sarah A. Connolly ◽  
Daniel J. Landsburg ◽  
Andrea Carfi ◽  
Don C. Wiley ◽  
Gary H. Cohen ◽  
...  

ABSTRACT Herpes simplex virus (HSV) entry into cells requires the binding of glycoprotein D (gD) to one of several cell surface receptors. The crystal structure of gD bound to one of these receptors, HveA/HVEM, reveals that the core of gD comprises an immunoglobulin fold flanked by a long C-terminal extension and an N-terminal hairpin loop. HveA is a member of the tumor necrosis factor receptor family and contains four cysteine-rich domains (CRDs) characteristic of this family. Fourteen amino acids within the gD N-terminal loop comprise the entire binding site for HveA. To determine the contribution of each gD contact residue to virus entry, we constructed gD molecules mutated in these amino acids. We determined the abilities of the gD mutants to bind receptors, facilitate virus entry, and mediate cell-cell fusion. Seven of the gD mutants exhibited wild-type levels of receptor binding and gD function. Results from the other seven gD mutants revealed three critical regions at the gD-HveA interface. (i) Several gD residues that participate in an intermolecular β-sheet with HveA were found to be crucial for HveA binding and entry into HveA-expressing cells. (ii) Two gD residues that contact HveA-Y23 contributed to HveA binding but were not required for mediating entry into cells. HveA-Y23 fits into a crevice on the surface of gD and was previously shown to be essential for gD binding. (iii) CRD2 was previously shown to contribute to gD binding, and this study shows that one gD residue that contacts CRD2 contributes to HveA binding. None of the gD mutations prevented interaction with nectin-1, another gD receptor. However, when cotransfected with the other glycoproteins required for fusion, two gD mutants gained the ability to mediate fusion of cells expressing nectin-2, a gD receptor that interacts with several laboratory-derived gD mutants but not with wild-type gD. Thus, results from this panel of gD mutants as well as those of previous studies (A. Carfi, S. H. Willis, J. C. Whitbeck, C. Krummenacher, G. H. Cohen, R. J. Eisenberg, and D. C. Wiley, Mol. Cell 8:169-179, 2001, and S. A. Connolly, D. J. Landsburg, A. Carfi, D. C. Wiley, R. J. Eisenberg, and G. H. Cohen, J. Virol. 76:10894-10904, 2002) provide a detailed picture of the gD-HveA interface and the contacts required for functional interaction. The results demonstrate that of the 35 gD and HveA contact residues that comprise the gD-HveA interface, only a handful are critical for complex formation.


2017 ◽  
Vol 3 (1) ◽  
pp. 13
Author(s):  
Tajerin Tajerin

Kajian ini bertujuan menganalisis perubahan struktur keterkaitan sektor perikanan dalam perekonomian Indonesia. Data yang digunakan merupakan data sekunder yang diperoleh dari buku Tabel Input Output (I-O) Tahun 1990, 1995 dan 2000 untuk transaksi domestik dan transaksi total atas dasar harga produsen. Analisis data dilakukan dengan pendekatan model I-O melalui perolehan nilai Multiplier Product Matrix (MPM) dari hasil perhitungan menggunakan Soni's Technique. Hasil analisis menujukkan bahwa berdasarkan kecenderungan rata-rata ketinggian nilai MPM sektor perikanan pada ”economic landscape” transaksi domestik yang meningkat selama periode analisis (1990-2000), diperoleh indikasi secara struktural keterkaitan sektor perikanan mengalami perubahan yang meningkat dengan sektor-sektor lainnya dalam perekonomian Indonesia. Namun sebagaimana ditunjukkan oleh adanya perbedaan ratarata ketinggian MPM yang semakin besar antara transaksi domestik dengan transaksi total, perubahan struktur keterkiatan sektor perikanan tersebut ternyata belum dapat berubah meningkat tanpa menghilangkan ketergantungannya terhadap penggunaan input faktor yang berasal dari luar negeri dalam proses produksinya. Kedua temuan tersebut memberikan implikasi pentingnya mempertimbangkan kembali penerapan kebijakan dan strategi substitusi impor bagi pengembangan sektor perikanan Indonesia ke depan. Tittle: Structural Change of Fisheries Sectors Linkage in The Indonesian Economy:An Analysis of the Multiplier Product Matrix (MPM) Using Soni's Technique.This study was aimed to analyzing the structural change of fisheries sectors linkage in the Indonesian Economy. Secondary data used in this research were obtained from Input Output Table of 1990, 1995 and 2000 for domestic transactions and total transactions based on Producer's Prices. Data analysis was done using I-O approach through Multiplier Product Matrix (MPM) with Soni’s Technique. Results showed that during the analysis period (1990 – 2000), the fisheries sectors MPM of the domestic transactions economic landscapee with the other sectors are rising. However, the analysis also showed that there was a gap of average MPM value between domestic and total transactions by which tend to rise during the analized period. This indicates that the structural change fisheries sector is still heavily depended on import of inputs from abroad. The implication of those two findings was imperative to consider re-applying the old, abandoned import substitution policy and strategy for future fisheries sectors development.


2021 ◽  
Author(s):  
Yongliang Hu ◽  
Yuqin Chen ◽  
Xiaoxia Su ◽  
Jiawei Huang ◽  
Hongxing Yin ◽  
...  

Abstract The present study reports observation of a field chilli pepper disease consisting of a co-infection with two potyviruses: Wild tomato mosaic virus Dehong isolate (WTMV-Dh) and Chili veinal mottle virus Dehong isolate (ChiVMV-Dh). We obtained the complete genome sequences of these two viruses by NGS sequencing. The WTMV-Dh is 9,598 nucleotides (nt) in length and encodes a complete polyprotein of 3,075 amino acids (aa). The polyprotein of WTMV-Dh shares 76.1–82.6% nt and 85.3–89.5% aa identities with the other three WTMV isolates reported previously. The ChiVMV-Dh is 9688 nt in length and encodes a complete polyprotein with 3, 089 aa. The polyprotein of ChiVMV-Dh shares 80.8–92.2% nt and 85.3–95.6% aa identities with the other ChiVMV isolates reported previously. Following phylogenetic analysis based on the polyprotein sequences of other potyviruses, WTMV-Dh clustered with the Vietnam strain WTMV-Laichau while ChiVMV-Dh clustered with several ChiVMV Sichuan isolates. Evaluation of the recombination events within the WTMV and ChiVMV subgroups indicated that some putative recombination events occurred in critical regions. These regions include the N-terminal of HC-Pro and P1 region of WTMV-Dh, CP and the P3 to CI region of ChiVMV-Dh, which may be new evidence of adaptive evolution of potyviruses.


2017 ◽  
Vol 50 (4) ◽  
pp. 319-330 ◽  
Author(s):  
Natalija Bogdanov ◽  
Vesna Rodić ◽  
Matteo Vittuari

The economic and political crisis Serbia had to face during the nineties affected the competitive advantages its agricultural sector had in comparison with the other countries of the region. Despite a number of differences related to the specific economic, political and social settings and developments, the reform path Serbia started in 2000 showed a number of similarities, but also some differences in comparison with most of the Central and Eastern European Countries. In this paper the main features of structural changes in the Serbian agricultural sector are analyzed, also in comparison with other countries in the region, the basic factors that contributed to these changes are identified and explained, and the key consequences and implications of this process are examined.


2017 ◽  
Vol 46 (1) ◽  
Author(s):  
Marco Brusotti

AbstractAfter discovering the short cosmological treatise L’éternité par les astres at the end of 1937, Benjamin ‘constellates’ the author, Louis-Auguste Blanqui, with Baudelaire and Nietzsche under the sign of eternal recurrence. From then on, eternal recurrence is given a central place in Benjamin’s analysis of modernity. Under many aspects his thoughts are rooted in the dramatic years in which they were developed: a conception of myth problematic in itself is misapplied to Nietzsche, the analogy with Blanqui’s cosmology leads to misunderstandings, and Benjamin does not grasp the connection between a task relevant for himself, the redemption of the past, and Zarathustra’s thought of eternal recurrence. Nevertheless, this constellation charged with tension is theoretically productive. Benjamin interprets the two faces of Nietzsche’s eternal recurrence in the context of his own theory of the structural change of experience in modernity. On the one hand, eternal recurrence is linked in multiple ways to the new forms of technical reproduction and compulsory repetition arising in the nineteenth century. On the other hand, it is assigned the task of compensating for an irretrievable loss. Is this compensation thoroughly illusory? Or does it contain a ‘motive of salvation’? Guided by these questions, the paper investigates the ‘polyphony’ of Benjamin’s remarks on Nietzsche’s thought of eternal recurrence and their heuristic potential.


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