scholarly journals Insight into the Fluid-Phase Miscibility of Ester and Ether Phospholipids through Analysis of Nearest-Neighbor RecognitionJ.Am.Chem.Soc.1996,118, 7069−7074

1996 ◽  
Vol 118 (37) ◽  
pp. 8985-8986
Author(s):  
Takehisa Dewa ◽  
Steven L. Regen
Keyword(s):  
Nearest Neighbor ◽  
Fluid Phase ◽  
Ether Phospholipids ◽  
Insight Into

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

scholarly journals Discrimination between Alternative Herbal Medicines from Different Categories with the Electronic Nose

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 2936 ◽  
Author(s):  
Xianghao Zhan ◽  
Xiaoqing Guan ◽  
Rumeng Wu ◽  
Zhan Wang ◽  
You Wang ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Electronic Nose ◽  
Nearest Neighbor ◽  
Herbal Medicines ◽  
Principal Component ◽  
Support Vector ◽  
Linear Discriminant ◽  
Convenient Means ◽  
Electronic Nose System ◽  
Insight Into

As alternative herbal medicine gains soar in popularity around the world, it is necessary to apply a fast and convenient means for classifying and evaluating herbal medicines. In this work, an electronic nose system with seven classification algorithms is used to discriminate between 12 categories of herbal medicines. The results show that these herbal medicines can be successfully classified, with support vector machine (SVM) and linear discriminant analysis (LDA) outperforming other algorithms in terms of accuracy. When principal component analysis (PCA) is used to lower the number of dimensions, the time cost for classification can be reduced while the data is visualized. Afterwards, conformal predictions based on 1NN (1-Nearest Neighbor) and 3NN (3-Nearest Neighbor) (CP-1NN and CP-3NN) are introduced. CP-1NN and CP-3NN provide additional, yet significant and reliable, information by giving the confidence and credibility associated with each prediction without sacrificing of accuracy. This research provides insight into the construction of a herbal medicine flavor library and gives methods and reference for future works.

New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers

2016 ◽  
Vol 18 (35) ◽  
pp. 24185-24197 ◽  
Author(s):  
Moirangthem Kiran Singh ◽  
Him Shweta ◽  
Mohammad Firoz Khan ◽  
Sobhan Sen
Keyword(s):  
Lipid Bilayers ◽  
Fluid Phase ◽  
Probe Location ◽  
Fluorescent Molecules ◽  
Insight Into ◽  
Fluid Phases

Location dependent polarity and hydration probed by a new series of 4-aminophthalimide-based fluorescent molecules (4AP-Cn;n= 2–10, 12) show different behaviour at gel- and fluid-phase lipid/water interfaces.

scholarly journals Formation Conditions and 40Ar/39Ar Age of the Gem-Bearing Boqueirão Granitic Pegmatite, Parelhas, Rio Grande do Norte, Brazil

Minerals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 233 ◽  
Author(s):  
Strmić Palinkaš ◽  
Palinkaš ◽  
Neubauer ◽  
Scholz ◽  
Šoštarić ◽  
...  
Keyword(s):  
Fluid Inclusion ◽  
Melt Inclusions ◽  
Fluid Phase ◽  
Granitic Pegmatite ◽  
Northeast Brazil ◽  
High Quality ◽  
Late Cambrian ◽  
Formation Conditions ◽  
Zone Ii ◽  
Insight Into

The Boqueirão granitic pegmatite, alias Alto da Cabeça pegmatite, is situated in Borborema Pegmatitic Province (BPP) in Northeast Brazil. This pegmatitic province hosts globally important reserves of tantalum and beryllium, as well as significant quantities of gemstones, including aquamarine, morganite, and the high-quality turquoise-blue “Paraíba Elbaite”. The studied lithium-cesium-tantalum Boqueirão granitic pegmatite intruded meta-conglomerates of the Equador Formation during the late Cambrian (502.1 ± 5.8 Ma; 40Ar/39Ar plateau age of muscovite). The pegmatite exhibits a typical zonal mineral pattern with four defined zones (Zone I: muscovite, tourmaline, albite, and quartz; Zone II: K-feldspar (microcline), quartz, and albite; Zone III: perthite crystals (blocky feldspar zone); Zone IV: massive quartz). Huge individual beryl, spodumene, tantalite, and cassiterite crystals are common as well. Microscopic examinations revealed that melt inclusions were entrapped simultaneously with fluid inclusions, suggesting the magmatic–hydrothermal transition. The magmatic–hydrothermal transition affected the evolution of the pegmatite, segregating volatile compounds (H2O, CO2, N2) and elements that preferentially partition into a fluid phase from the viscous silicate melt. Fluid inclusion studies on microcline and associated quartz combined with microthermometry and Raman spectroscopy gave an insight into the P-T-X characteristics of entrapped fluids. The presence of spodumene without other LiAl(SiO3)2 polymorphs and constructed fluid inclusion isochores limited the magmatic–hydrothermal transition at the gem-bearing Boqueirão granitic pegmatite to the temperature range between 300 and 415 °C at a pressure from 1.8 to 3 kbar.

Uniform Sampling of Subshifts of Finite Type on Grids and Trees

2017 ◽  
Vol 28 (03) ◽  
pp. 263-287 ◽  
Author(s):  
Jean Mairesse ◽  
Irène Marcovici
Keyword(s):  
Finite Type ◽  
Nearest Neighbor ◽  
Sampling Methods ◽  
Probability Measures ◽  
Probabilistic Cellular Automata ◽  
Subshift Of Finite Type ◽  
Uniform Sampling ◽  
Subshifts Of Finite Type ◽  
Uniform Random Sampling ◽  
Insight Into

Let us color the vertices of the grid ℤd or the infinite regular tree 𝕋d, using a finite number of colors, with the constraint that some predefined pairs of colors are not allowed for adjacent vertices. The set of admissible colorings is called a nearest-neighbor subshift of finite type (SFT). We study “uniform” probability measures on SFT, with the motivation of having an insight into “typical” admissible configurations. We recall the known results on uniform measures on SFT on grids and we complete the picture by presenting some contributions to the description of uniform measures on SFT on 𝕋d. Then we focus on the problem of uniform random sampling of configurations of SFT. We propose a first method based on probabilistic cellular automata, which is valid under some restrictive conditions. Then we concentrate on the case of SFT on ℤ for which we propose several alternative sampling methods.

scholarly journals Behavior of prey links midwater and demersal piscivorous reef fishes

2009 ◽  
Vol 7 (1) ◽  
pp. 109-112 ◽  
Author(s):  
Peter J. Auster ◽  
Jeff Godfrey ◽  
Anya Watson ◽  
Amy Paquette ◽  
Greg McFall
Keyword(s):  
Growth Rates ◽  
Nearest Neighbor ◽  
Prey Species ◽  
Reef Fishes ◽  
Predatory Behavior ◽  
Physical Processes ◽  
Predator Prey ◽  
Nearest Neighbor Distances ◽  
Insight Into ◽  
Demersal Fishes

Pelagic and demersal guilds of piscivorous fishes are linked by a variety of biological and physical processes that mediate interactions with common prey species. Understanding the behaviors of predators and prey can provide insight into the conditions that make such linkages possible. Here we report on the behaviors of mid-water piscivorous fishes and the responses of prey that produce feeding opportunities for demersal piscivorous fishes associated with "live bottom" ledge habitats off the coast of Georgia (northwest Atlantic Ocean). Prey taxa reduced nearest neighbor distances and retreated towards the seafloor during predatory attacks by mid-water fishes. Demersal fishes subsequently attacked and consumed prey in these ephemeral high density patches. No predation by demersal fishes was observed when prey species were at background densities. If the predator-prey interactions of demersal piscivorous fishes are commonly mediated by the predatory behavior of midwater piscivorous fishes and their prey, such indirect facilitative behaviors may be important in terms of the population processes (e.g., prey consumption and growth rates) of these demersal fishes.

INSIGHT INTO THE STRUCTURAL REQUIREMENTS OF SULFONYL DERIVATIVES BASED ON TWO AND THREE-DIMENSIONAL DESCRIPTORS: QSAR STUDIES

INDIAN DRUGS ◽  
2019 ◽  
Vol 56 (01) ◽  
pp. 81-86
Author(s):  
M. C Sharma ◽  
Keyword(s):  
Nearest Neighbor ◽  
Three Dimensional ◽  
Structural Features ◽  
At1 Receptor ◽  
Field Analysis ◽  
K Nearest Neighbor ◽  
Qsar Studies ◽  
Contour Plots ◽  
The Relationship ◽  
Insight Into

The present work provides the rationale to the changes in the structure to have more potent analogs sulfonyl derivatives were reported to possess potent activity for the angiotensin AT1 receptor. We report here 2D QSAR and k-nearest neighbor molecular field analysis based model for sulfonylureas compounds as AT1 receptor. The here k-nearest neighbor contour plots provided further understanding of the relationship between structural features of substituted sulfonyl derivatives and their activities which should be applicable to design newer potential AT1 receptor.

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Alice Capecchi ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Jean-Louis Reymond
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

Influence of Head Group Mismatch on the Miscibility of Phospholipids in the Physiologically-Relevant Fluid Phase:  A Nearest-Neighbor Recognition Analysis

1997 ◽  
Vol 119 (16) ◽  
pp. 3797-3801 ◽  
Author(s):  
Maki Uragami ◽  
Takehisa Dewa ◽  
Minoru Inagaki ◽  
Robert A. Hendel ◽  
Steven L. Regen
Keyword(s):  
Nearest Neighbor ◽  
Fluid Phase ◽  
Head Group ◽  
Neighbor Recognition
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