Structural Classification of Complex Molecules by Artificial Intelligence Techniques

Author(s):  
Francisco Torrens ◽  
Gloria Castellano

Algorithms for classification and taxonomy bases on criteria, e.g., information entropy. The feasibility of replacing a given molecule by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using structural properties. In taxonomy the detailed comparison of the sequences of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree. The method is applied to the classifications of (1) indazolols (against Trichomonas vaginalis), (2) fullerenes and fullerite, (3) living and heat-inactivated lactic acid bacteria against cytokines, (4) phylogenesis of avian birds and 1918 influenza virus, (5) local anaesthetics, (6) transdermal-delivery percutaneous enhancers, (7) quantitative structure–activity relationship of anti-human immunodeficiency virus (HIV) compounds, (8) HIV inhibitors, e.g., thiocarbamates, N-aryloxazolidinone-5-carboxamides and styrylquinolines, (9) antimalarial aryltriazolylhydroxamates, (10) N-aryl-N-(3-aryl-1,2,4-oxadiazol-5-yl) amines against prostate cancer, antimitotic 2-phenylindole-3-carbaldehydes against breast cancer and anti-tubulin agents against gastric cancer with indole ring. The entropy contributions may be studied with the equipartition conjecture. It is not within the scope of our simulation method to replace biological tests of drugs or field data in palaeontology, but such simulation methods can be useful to assert priorities in detailed experimental research. Available experimental and field data should be examined by different classification algorithms to reveal possible features of real biological significance.

2007 ◽  
Vol 20 (3) ◽  
pp. 252 ◽  
Author(s):  
Stephen D. Hopper ◽  
Andrew P. Brown

Drakaea Lindley, 1840 is a genus of 10 species of geophytic orchids endemic to the South-west Australian Floristic Region. The genus is renowned for its morphological and chemical adaptations, achieving pollination by sexual deception of male thynnid wasps. The history of taxa in Drakaea has been one of dispute and confusion right to the present day. Here we provide a revision of the genus, the first made by using modern collections and field data, formalising names for undescribed taxa featured by Hoffman and Brown (1992, 1998), several of which are threatened with extinction. We describe six new species: D. andrewsiae, D. concolor, D. confluens, D. gracilis, D. isolata and D. micrantha. Experimental baiting of male wasps has helped show the specific status of some of these new taxa. Molecular phylogenetic research is needed to clarify relationships and patterns of speciation in the genus. Five of the 10 Drakaea species are legally protected under the Western Australian Wildlife Conservation Act and the Commonwealth Environment Protection and Biodiversity Conservation Act, signalling the ongoing need for research and management to ensure the conservation of this unique part of Australia’s orchid heritage. D. andrewsiae has been recorded only three times from the Gnowangerup–Tunney district. Urgent surveys are needed to establish its conservation status.


2001 ◽  
Vol 121 (2) ◽  
pp. 262-263 ◽  
Author(s):  
Minwon Park ◽  
Kenji Matsuura ◽  
Masakazu Michihira
Keyword(s):  

ZooKeys ◽  
2021 ◽  
Vol 1079 ◽  
pp. 1-33
Author(s):  
Jakob von Tschirnhaus ◽  
Claudio Correa

Telmatobius halli was the first representative of its genus to be described exclusively for Chile, yet for 85 years no new individuals could be located due to the vagueness with which its type locality was described. The type series was collected by one of the members of the International High Altitude Expedition to Chile (IHAEC) of 1935. Recently, three studies successively claimed to have located the type locality in different places. The third study proved, according to the chronicles of the IHAEC, that the actual locality is Miño, at the origin of the Loa River, where currently there are no published records of Telmatobius. In this study, additional documentary antecedents and graphic material are provided that corroborate that Miño is indeed the type locality of T. halli. Additionally, the recently rediscovered Telmatobius population from Miño and the environment it inhabits are described. The external characteristics of the frogs are consistent with the description of T. halli. Furthermore, molecular phylogenetic analyses were performed that showed that T. halli, T. dankoi, and T. vilamensis, all known only from their type localities in Chile, comprise a clade without internal resolution. A detailed comparison of the diagnoses of the three species revealed that the few phenotypic differences between these taxa were based on characteristics that vary widely within and between populations of the genus, hence their conspecificity is proposed. The implications of this synonymy for the taxonomy, biogeography, and conservation of the Telmatobius from the extreme south of its distribution in Chile are discussed.


Nematology ◽  
2014 ◽  
Vol 16 (6) ◽  
pp. 683-693 ◽  
Author(s):  
Natsumi Kanzaki ◽  
Natsumi Kanzaki ◽  
Robin M. Giblin-Davis ◽  
Natsumi Kanzaki ◽  
Robin M. Giblin-Davis ◽  
...  

During an experimental host-plant survey for the invasive redbay ambrosia beetle, Xyleborus glabratus, in Homestead, Florida, it and three native species of ambrosia beetle, Xyleborus affinis, X. volvulus and Xyleborinus gracilis were found to be associated with a Bursaphelenchus species. This nematode species, isolated from ambrosia beetles from the tribe Xyleborini, was cultured on Monilinia fructicola or Botryotinia fuckeliana for further study and was determined to be new to science and a putative sister species to B. kiyoharai because of two apomorphic characters in males, viz., possession of a tail spike vs the typical bursal flap, and the apparent absence of the P1 ventral single papilla, both typically plesiomorphic characters for the genus. Additionally, B. kiyoharai is associated with X. serriatus suggesting that the host and microbiome associations that are shared between these two species, both of which are carried by ambrosia beetles, may have ecological and biological significance in their evolution and lineage radiation. Molecular phylogenetic analyses of the near-full-length small subunit (SSU: 18S) and the D2/D3 expansion segments of the large subunit (LSU: 28S) confirmed that B. penai n. sp. is very closely related to B. kiyoharai which is a member of the B. fungivorus clade that includes B. thailandae and B. willibaldi. Bursaphelenchus penai n. sp. and B. kiyoharai both share very similar overall spicule morphology with the B. fungivorus clade. The new species is described and can be typologically differentiated from B. kiyoharai by the position of the hemizonid and excretory pore and its different geographical and host associations.


2002 ◽  
Vol 5 (02) ◽  
pp. 126-134 ◽  
Author(s):  
R.O. Baker ◽  
F. Kuppe ◽  
S. Chugh ◽  
R. Bora ◽  
S. Stojanovic ◽  
...  

Summary Modern streamline-based reservoir simulators are able to account for actual field conditions such as 3D multiphase flow effects, reservoir heterogeneity, gravity, and changing well conditions. A streamline simulator was used to model four field cases, with approximately 400 wells and 150,000 gridblocks. History-match run times were approximately 1 CPU hour per run, with the final history matches completed in approximately 1 month per field. In all field cases, a high percentage of wells were history matched within the first two to three runs. Streamline simulation not only enables a rapid turnaround time for studies, but it also serves as a different tool in resolving each of the studied fields' unique characteristics. The primary reasons for faster history matching of permeability fields using 3D streamline technology as compared to conventional finite-difference (FD) techniques are as follows: Streamlines clearly identify which producer-injector pairs communicate strongly (flow visualization). Streamlines allow the use of a very large number of wells, thereby substantially reducing the uncertainty associated with outer-boundary conditions. Streamline flow paths indicate that idealized drainage patterns do not exist in real fields. It is therefore unrealistic to extract symmetric elements out of a full field. The speed and efficiency of the method allows the solution of fine-scale and/or full-field models with hundreds of wells. The streamline simulator honors the historical total fluid injection and production volumes exactly because there are no drawdown constraints for incompressible problems. The technology allows for easy identification of regions that require modifications to achieve a history match. Streamlines provide new flow information (i.e., well connectivity, drainage volumes, and well allocation factors) that cannot be derived from conventional simulation methods. Introduction In the past, streamline-based flow simulation was quite limited in its application to field data. Emanuel and Milliken1 showed how hybrid streamtube models were used to history match field data rapidly to arrive at both an updated geologic model and a current oil-saturation distribution for input to FD simulations. FD simulators were then used in forecast mode. Recent advances in streamline-based flow simulators have overcome many of the limitations of previous streamline and streamtube methods.2-6 Streamline-based simulators are now fully 3D and account for multiphase gravity and fluid mobility effects as well as compressibility effects. Another key improvement is that the simulator can now account for changing well conditions due to rate changes, infill drilling, producer-injector conversions, and well abandonments. With advances in streamline methods, the technique is rapidly becoming a common tool to assist in the modeling and forecasting of field cases. As this technology has matured, it is becoming available to a larger group of engineers and is no longer confined to research centers. Published case studies using streamline simulators are now appearing from a broad distribution of sources.7–12 Because of the increasing interest in this technology, our first intent in this paper is to outline a methodology for where and how streamline-based simulation fits in the reservoir engineering toolbox. Our second objective is to provide insight into why we think the method works so well in some cases. Finally, we will demonstrate the application of the technology to everyday field situations useful to mainstream exploitation or reservoir engineers, as opposed to specialized or research applications. The Streamline Simulation Method For a more detailed mathematical description of the streamline method, please refer to the Appendix and subsequent references. In brief, the streamline simulation method solves a 3D problem by decoupling it into a series of 1D problems, each one solved along a streamline. Unlike FD simulation, streamline simulation relies on transporting fluids along a dynamically changing streamline- based flow grid, as opposed to the underlying Cartesian grid. The result is that large timestep sizes can be taken without numerical instabilities, giving the streamline method a near-linear scaling in terms of CPU efficiency vs. model size.6 For very large models, streamline-based simulators can be one to two orders of magnitude faster than FD methods. The timestep size in streamline methods is not limited by a classic grid throughput (CFL) condition but by how far fluids can be transported along the current streamline grid before the streamlines need to be updated. Factors that influence this limit include nonlinear effects like mobility, gravity, and well rate changes.5 In real field displacements, historical well effects have a far greater impact on streamline-pattern changes than do mobility and gravity. Thus, the key is determining how much historical data can be upscaled without significantly impacting simulation results. For all cases considered here, 1-year timestep sizes were more than adequate to capture changes in historical data, gravity, and mobility effects. It is worth noting that upscaling historical data also would benefit run times for FD simulations. Where possible, both SL and FD methods would then require similar simulation times. However, only for very coarse grids and specific problems is it possible to take 1-year timestep sizes with FD methods. As the grid becomes finer, CFL limitations begin to dictate the timestep size, which is much smaller than is necessary to honor nonlinearities. This is why streamline methods exhibit larger speed-up factors over FD methods as the number of grid cells increases.


2012 ◽  
Vol 482-484 ◽  
pp. 1442-1446
Author(s):  
Rui Hong Tong ◽  
Yi Lv

This paper first to roll bending forming algorithm is-implicit algorithm and genetic algorithm was carried on the detailed comparison demonstrates to the existing literature experiment for object model, based on the implicit algorithm, established for prediction of the residual stress multi-channel times roll bending forming simulation method, solve the problems of the simulation process convergence, and the influence of the cold bending forming the prediction precision steel simulation parameters were analyzed. Sure the implicit algorithm based on the roll bending forming lane simulation method, and emphasizes to discuss how to solve the resulting convergence problem.


Author(s):  
Vitthal S. Kulkarni ◽  
Wayne H. Anderson ◽  
Rhoderick E. Brown

The biological significance of the sphingomyelins (SM) and monoglycosylated sphingolipids like galactosylceramides (GalCer) are well documented Our recent investigation showed tubular bilayers in the aqueous dispersions of N-nervonoyl GalCer [N-(24:lΔ15,cls) GalCer] (a major fatty acyl moiety of natural GalCer). To determine the influence of lipid head groups on the resulting mesophasic morphology, we investigated microstructural self-assemblies of N-nervonoyl-SM [N-(24:1 Δ15,cls) SM; the second most abundant sphingomyelin in mammalian cell membranes], 1- palmitoyl-2-nervonoyl phosphatidylcholine [PNPC] (the lipid species with the same acyl chain configuration as in N-(24: 1) GalCer) and also compared it with egg-SM by freeze-fracture EM.Procedures for synthesizing and purifying N-(24:1) GalCer, N-(24:1) SM, and PNPC have been reported . Egg-SM was purchased from Avanti Polar Lipids, Alabaster AL. All lipids were >99% pure as checked by thin layer chromatography. Lipid dispersions were prepared by hydrating dry lipid with phosphate buffer (pH 6.6) at 80-90°C (3-5 min), vigorously vortexing (1 min) and repeating this procedure for three times prior to three freeze-thaw cycles.


Author(s):  
Dong Yuming ◽  
Yang Guanglin ◽  
Wu Jifeng ◽  
Chen Xiaolin

On the basis of light microscopic observation, the ultrastructural localization of CEA in gastric cancer was studied by immunoelectron microscopic technique. The distribution of CEA in gastric cancer and its biological significance and the mechanism of abnormal distribution of CEA were further discussed.Among 104 surgically resected specimens of gastric cancer with PAP method at light microscopic level, the incidence of CEA(+) was 85.58%. All of mucinous carcinoma exhibited CEA(+). In tubular adenocarcinoma the incidence of CEA(+) showed a tendency to rising with the increase of degree of differentiation. In normal epithelia and intestinal metaplasia CEA was faintly present and was found only in the luminal surface. The CEA staining patterns in cancer cells were of three types--- cytoplasmic, membranous and weak reactive type. The ultrastructural localization of CEA in 14 cases of gastric cancer was studied by immunoelectron microscopic technique.There was a little or no CEA in the microvilli of normal epithelia. In intestinal metaplasia CEA was found on the microvilli of absorptive cells and among the mucus particles of goblet cells. In gastric cancer CEA was also distributed on the lateral and basal surface or even over the entire surface of cancer cells and lost their polarity completely. Many studies had proved that the alterations in surface glycoprotein were characteristic changes of tumor cells. The antigenic determinant of CEA was glycoprotein, so the alterations of tumor-associated surface glycoprotein opened up a new way for the diagnosis of tumors.


Anaesthesia ◽  
2000 ◽  
Vol 55 (9) ◽  
pp. 938-938
Author(s):  
K. R. Milligan

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