scholarly journals Tautomeric Conflicts in Forty Small-Molecule Databases

2021 ◽  
Author(s):  
Devendra Kumar Dhaked ◽  
Marc Nicklaus
Keyword(s):  
Small Molecule ◽  
Data Set ◽  
Almost All ◽  
Small Molecule Databases

We have analyzed forty different databases ranging in size from a few thousand to nearly 100 million molecules, comprising a total of over 200 million structures, for their tautomeric conflicts. A tautomeric conflict is defined as an occurrence of two or more structures within a data set identified by the tautomeric rules applied as being tautomers of each other. We tested a total of 119 detailed tautomeric transform rules expressed as SMIRKS, out of which 79 yielded at least one conflict. The databases analyzed spanned a wide variety of types including large aggregating databases, drug collections, and experimentally based structure collections. Almost all databases analyzed showed intra-database tautomeric conflicts. The conflict rates as percentage of the database were typically in the few tenths of a percent range, which for the largest databases amounts to more than 100,000 cases per database.

scholarly journals Tautomeric Conflicts in Forty Small-Molecule Databases

2021 ◽  
Author(s):  
Devendra Kumar Dhaked ◽  
Marc Nicklaus
Keyword(s):  
Small Molecule ◽  
Data Set ◽  
Almost All ◽  
Small Molecule Databases

We have analyzed forty different databases ranging in size from a few thousand to nearly 100 million molecules, comprising a total of over 200 million structures, for their tautomeric conflicts. A tautomeric conflict is defined as an occurrence of two or more structures within a data set identified by the tautomeric rules applied as being tautomers of each other. We tested a total of 119 detailed tautomeric transform rules expressed as SMIRKS, out of which 79 yielded at least one conflict. The databases analyzed spanned a wide variety of types including large aggregating databases, drug collections, and experimentally based structure collections. Almost all databases analyzed showed intra-database tautomeric conflicts. The conflict rates as percentage of the database were typically in the few tenths of a percent range, which for the largest databases amounts to more than 100,000 cases per database.

Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2

2019 ◽  
Author(s):  
Devendra K. Dhaked ◽  
Wolf Ihlenfeldt ◽  
Hitesh Patel ◽  
Marc Nicklaus
Keyword(s):  
Small Molecule ◽  
Comprehensive Treatment ◽  
Experimental Literature ◽  
Web Tool ◽  
Valence Tautomerism ◽  
Standard Version ◽  
Small Molecule Databases

<p>We have collected 86 different transforms of tautomeric interconversions. Out of those, 54 are for prototropic (non-ring-chain) tautomerism; 21 for ring-chain tautomerism; and 11 for valence tautomerism. The majority of these rules have been extracted from experimental literature. Twenty rules – covering the most well-known types of tautomerism such as keto-enol tautomerism – were taken from the default handling of tautomerism by the chemoinformatics toolkit CACTVS. The rules were analyzed against nine differerent databases totaling over 400 million (non-unique) structures as to their occurrence rates, mutual overlap in coverage, and recapitulation of the rules’ enumerated tautomer sets by InChI V.1.05, both in InChI’s Standard and a Non-Standard version with the increased tautomer-handling options 15T and KET turned on. These results and the background of this study are discussed in the context of the IUPAC InChI Project tasked with the redesign of handling of tautomerism for an InChI version 2. Applying the rules presented in this paper would approximately triple the number of compounds in typical small-molecule databases that would be affected by tautomeric interconversion by InChI V2. A web tool has been created to test these rules at https://cactus.nci.nih.gov/tautomerizer.</p>

In vitro effectiveness of biapenem against IMP-producing Enterobacteriaceae

2021 ◽  
Vol 70 (10) ◽  
Author(s):  
Kazuyoshi Gotoh ◽  
Makoto Miyoshi ◽  
I Putu Bayu Mayura ◽  
Koji Iio ◽  
Osamu Matsushita ◽  
...  
Keyword(s):  
Therapeutic Option ◽  
Small Data ◽  
Limited Data ◽  
Data Set ◽  
Content Type ◽  
Link Type ◽  
Almost All ◽  
New Treatments ◽  
Time Kill

The options available for treating infections with carbapenemase-producing Enterobacteriaceae (CPE) are limited; with the increasing threat of these infections, new treatments are urgently needed. Biapenem (BIPM) is a carbapenem, and limited data confirming its in vitro killing effect against CPE are available. In this study, we examined the minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of BIPM for 14 IMP-1-producing Enterobacteriaceae strains isolated from the Okayama region in Japan. The MICs against almost all the isolates were lower than 0.5 µg ml−1, indicating susceptibility to BIPM, while approximately half of the isolates were confirmed to be bacteriostatic to BIPM. However, initial killing to a 99.9 % reduction was observed in seven out of eight strains in a time–kill assay. Despite the small data set, we concluded that the in vitro efficacy of BIPM suggests that the drug could be a new therapeutic option against infection with IMP-producing CPE.

scholarly journals Volcanic impact on the climate – the stratospheric aerosol load in the period 2006–2015

2018 ◽  
Vol 18 (15) ◽  
pp. 11149-11169 ◽  
Author(s):  
Johan Friberg ◽  
Bengt G. Martinsson ◽  
Sandra M. Andersson ◽  
Oscar S. Sandvik
Keyword(s):  
Radiative Forcing ◽  
Volcanic Eruptions ◽  
Stratospheric Aerosol ◽  
Temperature Threshold ◽  
Data Set ◽  
Volcanic Impact ◽  
Almost All ◽  
Stratospheric Clouds ◽  
Correct Data

Abstract. We present a study on the stratospheric aerosol load during 2006–2015, discuss the influence from volcanism and other sources, and reconstruct an aerosol optical depth (AOD) data set in a resolution of 1∘ latitudinally and 8 days timewise. The purpose is to include the “entire” stratosphere, from the tropopause to the almost particle-free altitudes of the midstratosphere. A dynamic tropopause of 1.5 PVU was used, since it enclosed almost all of the volcanic signals in the CALIOP data set. The data were successfully cleaned from polar stratospheric clouds using a temperature threshold of 195 K. Furthermore, a method was developed to correct data when the CALIOP laser beam was strongly attenuated by volcanic aerosol, preventing a negative bias in the AOD data set. Tropospheric influence, likely from upwelling dust, was found in the extratropical transition layer in spring. Eruptions of both extratropical and tropical volcanoes that injected aerosol into the stratosphere impacted the stratospheric aerosol load for up to a year if their clouds reached lower than 20 km altitude. Deeper-reaching tropical injections rose in the tropical pipe and impacted it for several years. Our AODs mostly compare well to other long-term studies of the stratospheric AOD. Over the years 2006–2015, volcanic eruptions increased the stratospheric AOD on average by ∼40 %. In absolute numbers the stratospheric AOD and radiative forcing amounted to 0.008 and −0.2 W m−2, respectively.

Intermittency and related issues in 16O-Ag/Br collision at 200A GeV/c

2010 ◽  
Vol 88 (8) ◽  
pp. 575-584 ◽  
Author(s):  
M. K. Ghosh ◽  
P. K. Haldar ◽  
S. K. Manna ◽  
A. Mukhopadhyay ◽  
G. Singh
Keyword(s):  
Particle Density ◽  
Simulated Data ◽  
Space Distribution ◽  
Monte Carlo Code ◽  
Final State ◽  
Data Set ◽  
Fractal Properties ◽  
Self Similar ◽  
Singly Charged ◽  
Almost All

In this paper we present some results on the nonstatistical fluctuation in the 1-dimensional (1-d) density distribution of singly charged produced particles in the framework of the intermittency phenomenon. A set of nuclear emulsion data on 16O-Ag/Br interactions at an incident momentum of 200A GeV/c, was analyzed in terms of different statistical methods that are related to the self-similar fractal properties of the particle density function. A comparison of the present experiment with a similar experiment induced by the 32S nuclei and also with a set of results simulated by the Lund Monte Carlo code FRITIOF is presented. A similar comparison between this experiment and a pseudo-random number generated simulated data set is also made. The analysis reveals the presence of a weak intermittency in the 1-d phase space distribution of the produced particles. The results also indicate the occurrence of a nonthermal phase transition during emission of final-state hadrons. Our results on factorial correlators suggests that short-range correlations are present in the angular distribution of charged hadrons, whereas those on oscillatory moments show that such correlations are not restricted only to a few particles. In almost all cases, the simulated results fail to replicate their experimental counterparts.

scholarly journals A unified haplotype-based method for accurate and comprehensive variant calling

2018 ◽  
Author(s):  
Daniel P Cooke ◽  
David C Wedge ◽  
Gerton Lunter
Keyword(s):  
De Novo ◽  
Variant Calling ◽  
Normal Sample ◽  
Sequencing Data ◽  
Somatic Variation ◽  
Data Set ◽  
Small Complex ◽  
Physical Linkage ◽  
Germline Variation ◽  
Almost All

Haplotype-based variant callers, which consider physical linkage between variant sites, are currently among the best tools for germline variation discovery and genotyping from short-read sequencing data. However, almost all such tools were designed specifically for detecting common germline variation in diploid populations, and give sub-optimal results in other scenarios. Here we present Octopus, a versatile haplotype-based variant caller that uses a polymorphic Bayesian genotyping model capable of modeling sequencing data from a range of experimental designs within a unified haplotype-aware framework. We show that Octopus accurately calls de novo mutations in parent-offspring trios and germline variants in individuals, including SNVs, indels, and small complex replacements such as microinversions. In addition, using a carefully designed synthetic-tumour data set derived from clean sequencing data from a sample with known germline haplotypes, and observed mutations in large cohort of tumour samples, we show that Octopus accurately characterizes germline and somatic variation in tumours, both with and without a paired normal sample. Sequencing reads and prior information are combined to phase called genotypes of arbitrary ploidy, including those with somatic mutations. Octopus also outputs realigned evidence BAMs to aid validation and interpretation.

Analyzing Growth Trends of Reusable Software Components

2013 ◽  
pp. 40-54 ◽  
Author(s):  
Kuljit Kaur
Keyword(s):  
Software Evolution ◽  
Point Of View ◽  
Software Components ◽  
Data Set ◽  
Reusable Components ◽  
Reusable Software ◽  
Evolution Analysis ◽  
Software Modules ◽  
Almost All ◽  
Monitoring Software

Reusable software components are the software modules that can be (re)used across a number of applications in a particular domain. Component users prefer to use those components which can be adapted easily for their changing requirements. So components have to evolve continuously in order to attract users. This chapter focuses on the evolutionary aspects of software components. It mentions various techniques for monitoring software evolution. It uses metrics based analysis as the technique to show software evolution of 15 reusable components from the point of view of their size, complexity, and functionality. The evolution analysis is motivated by laws of software evolution which suggest that as software ages, it increases in size and complexity (unless it is managed) and it has to offer increased functionality to please its users. The findings of the study indicate that the size of the software components (in this data set) grows at a linear rate, and complexity is well managed. However, increase in functionality is sub linear for almost all the components. It remains almost constant for some of them.

scholarly journals A Novel Method for the Deblurring of Photogrammetric Images Using Conditional Generative Adversarial Networks

2020 ◽  
Vol 12 (16) ◽  
pp. 2586 ◽  
Author(s):  
Pawel Burdziakowski
Keyword(s):  
Point Clouds ◽  
Aerial Images ◽  
Generative Adversarial Networks ◽  
Camera Motion ◽  
Data Set ◽  
Adversarial Networks ◽  
Blur Kernel ◽  
Almost All ◽  
Blurred Images

The visual data acquisition from small unmanned aerial vehicles (UAVs) may encounter a situation in which blur appears on the images. Image blurring caused by camera motion during exposure significantly impacts the images interpretation quality and consequently the quality of photogrammetric products. On blurred images, it is difficult to visually locate ground control points, and the number of identified feature points decreases rapidly together with an increasing blur kernel. The nature of blur can be non-uniform, which makes it hard to forecast for traditional deblurring methods. Due to the above, the author of this publication concluded that the neural methods developed in recent years were able to eliminate blur on UAV images with an unpredictable or highly variable blur nature. In this research, a new, rapid method based on generative adversarial networks (GANs) was applied for deblurring. A data set for neural network training was developed based on real aerial images collected over the last few years. More than 20 full sets of photogrammetric products were developed, including point clouds, orthoimages and digital surface models. The sets were generated from both blurred and deblurred images using the presented method. The results presented in the publication show that the method for improving blurred photo quality significantly contributed to an improvement in the general quality of typical photogrammetric products. The geometric accuracy of the products generated from deblurred photos was maintained despite the rising blur kernel. The quality of textures and input photos was increased. This research proves that the developed method based on neural networks can be used for deblur, even in highly blurred images, and it significantly increases the final geometric quality of the photogrammetric products. In practical cases, it will be possible to implement an additional feature in the photogrammetric software, which will eliminate unwanted blur and allow one to use almost all blurred images in the modelling process.

scholarly journals Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

2007 ◽  
Vol 89 (2) ◽  
pp. 93-106 ◽  
Author(s):  
NOELLE A. BARKLEY ◽  
ROB E. DEAN ◽  
ROY N. PITTMAN ◽  
MING L. WANG ◽  
CORLEY C. HOLBROOK ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Data Set ◽  
Mini Core Collection ◽  
Genomic Ssr ◽  
Cultivated Peanut ◽  
The Mean ◽  
Wild Accessions ◽  
Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

scholarly journals Ozone and temperature decadal solar-cycle responses, and their relation to diurnal variations in the stratosphere, mesosphere, and lower thermosphere, based on measurements from SABER on TIMED

2019 ◽  
Vol 37 (4) ◽  
pp. 471-485 ◽  
Author(s):  
Frank T. Huang ◽  
Hans G. Mayr
Keyword(s):  
Solar Cycle ◽  
Local Time ◽  
Satellite Data ◽  
Diurnal Cycle ◽  
Lower Thermosphere ◽  
Diurnal Variations ◽  
Local Times ◽  
Data Set ◽  
Orbital Drift ◽  
Almost All

Abstract. There is evidence that the ozone and temperature responses to the solar cycle of ∼11 years depend on the local times of measurements. Here we present relevant results based on SABER data over a full diurnal cycle, which were not previously available. In this area, almost all satellite data used are measured at only one or two fixed local times, which can differ among various satellites. Consequently, estimates of responses can be different depending on the specific data set. Furthermore, over years, due to orbital drift, the local times of the measurements of some satellites have also drifted. In contrast, SABER makes measurements at various local times, providing the opportunity to estimate diurnal variations over 24 h. We can then also estimate responses to the solar cycle over both a diurnal cycle and at the fixed local times of specific satellite data for comparison. Responses derived in this study, based on zonal means of SABER measurements, agree favorably with previous studies based on data from the HALOE instrument, which only measured data at sunrise and sunset, thereby supporting the analysis of both studies. We find that for ozone above ∼40 km, zonal means reflecting specific local times (e.g., 6, 12, 18, 24 LST – local solar time) lead to different values of responses, and to different responses based on zonal means that are also averages over the 24 h local time period, as in 3-D models. For temperature, the effects of diurnal variations on the responses are not negligible even at ∼30 km and above. We also considered the consequences of local time variations due to orbital drifts of certain operational satellites, and, for both ozone and temperature, their effects can be significant above ∼30 km. Previous studies based on other satellite data do not describe the treatment, if any, of local times. Some studies also analyzed data merged from different sources, with measurements made at different local times. Generally, the results of these studies do not agree very well among themselves. Although responses are a function of diurnal variations, this is not to say that they are the major reason for the differences, as there are likely other data-related issues. The effects due to satellite orbital drift may explain some unexpected variations in the responses, especially above 40 km.

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