scholarly journals FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics

2019 ◽  
Author(s):  
Kyowon Jeong ◽  
Jihyung Kim ◽  
Manasi Gaikwad ◽  
Siti Nurul Hidayah ◽  
Laura Heikaus ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Top Down ◽  
High Quality ◽  
Simple Transformation ◽  
Execution Speed ◽  
Quality Issues

AbstractFeature deconvolution, the determination of intact proteoform masses, is crucial for top-down proteomics, but currently suffers from long runtimes and quality issues. We present FLASHDeconv, an algorithm based on a simple transformation of mass spectra, which turns deconvolution into the search for constant patterns thus greatly accelerating the process. We show higher deconvolution quality and two to three orders of magnitude faster execution speed than existing approaches.

Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra

2019 ◽  
Vol 35 (18) ◽  
pp. 3489-3490 ◽  
Author(s):  
Diogo B Lima ◽  
André R F Silva ◽  
Mathieu Dupré ◽  
Marlon D M Santos ◽  
Milan A Clasen ◽  
...  
Keyword(s):  
Quality Control ◽  
Mass Spectra ◽  
Rate Increase ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Top Down ◽  
High Quality ◽  
Garbage Collector ◽  
E Coli ◽  
Spectral Libraries

Abstract Motivation We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates. Results We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable. Availability and implementation http://patternlabforproteomics.org/tdgc, freely available for academic use. Supplementary information Supplementary data are available at Bioinformatics online.

Disability as a social phenomenon

2020 ◽  
pp. 22-38
Author(s):  
Natalia Guseva ◽  
Vitaliy Berdutin
Keyword(s):  
Social Protection ◽  
Russian Society ◽  
Stage Model ◽  
High Quality ◽  
Rehabilitation Programs ◽  
Current State ◽  
The Social ◽  
Consistent Solution ◽  
First Time

At present, the problem of establishing disability is a point at issue in Russia. Despite the fact that medical criteria for disability are being developed very actively, high-quality methods for assessing social hallmarks are still lacking. Since disability is a phenomenon inherent in any society, each state forms a social and economic policy for people with disabilities in accordance with its level of development, priorities and opportunities. We have proposed a three-stage model, which includes a system for the consistent solution of the main tasks aimed at studying the causes and consequences of the problems encountered today in the social protection of citizens with health problems. The article shows why the existing approaches to the determination of disability and rehabilitation programs do not correspond to the current state of Russian society and why a decrease in the rate of persons recognized as disabled for the first time does not indicate an improvement in the health of the population. The authors proposed a number of measures with a view to correcting the situation according to the results of the study.

scholarly journals Development of new total RNA isolation method for tissues with rich phenolic compounds

2020 ◽  
Vol 45 (4) ◽  
pp. 343-350
Author(s):  
Zafer Seçgin ◽  
Gökhan Gökdemir ◽  
Elif Seda Atabay ◽  
Aslıhan Kurt Kızıldoğan ◽  
Musa Kavas
Keyword(s):  
Phenolic Compounds ◽  
Rna Sequencing ◽  
Rna Isolation ◽  
Wall Structure ◽  
Isolation Method ◽  
High Quality ◽  
Ctab Method ◽  
Total Rna Isolation

AbstractBackgroundRNAs to be used in transcriptome analysis must be of high quality and pure in order to ensure maximum representation of the expressed genes. RNA isolation is difficult in hazelnut tissues containing large amounts of secondary metabolite, phenolic compounds and the cell wall structure. Commonly used protocols for RNA isolation are those that require a lot of labor and time and also do not allow sufficient RNA isolation when applied to tissues rich in phenolic compounds. This study was aimed to develop an efficient method for isolation of total RNAs from bud of hazelnut to be used in RNA sequencing.Materials and methodsAn optimized new method was successfully applied on three different hazelnuts genotypes (Çakıldak, Palaz, Tombul) and about 25 times higher amount of total RNAs per mg fresh tissues were obtained compared to classical CTAB method. Different methods have been tried for the isolation of RNA from hazelnut tissues and the determination of the quality of the obtained RNAs.ResultsThe quality and quantity of isolalated total RNAs were determined by spectrophotometer, electrophoresis and PCR. This success has been caught without any compromise of purity since A260/A280 ratios ranged from 1.90 to 2.04 and A260/A230 ratios were >2.0 in all purified RNAs.ConclusionThe total RNAs isolated with new protocol was found to be suitable for RNA sequencing and other molecular applications.

Femtosecond ultrafast pulse generation with high-quality 2H-TaS2 nanosheets via top-down empirical approach

Nanoscale ◽  
2021 ◽  
Author(s):  
Qiang Yu ◽  
Shun Wang ◽  
Yan Zhang ◽  
Zhuo Dong ◽  
Haiqin Deng ◽  
...  
Keyword(s):  
Transition Metal ◽  
Phase Diagrams ◽  
Carrier Concentration ◽  
Layered Structure ◽  
Pulse Generation ◽  
Transition Metal Dichalcogenide ◽  
Top Down ◽  
High Quality ◽  
Rich Phase ◽  
Ultrafast Pulse Generation

Tantalum disulfide (TaS2), an emerging group VB transition metal dichalcogenide, with unique layered structure, rich phase diagrams, semimetallic behavior, higher carrier concentration and mobility is emerging as a prototype for...

scholarly journals Unraveling the long-pursued Au144 structure by x-ray crystallography

2018 ◽  
Vol 4 (10) ◽  
pp. eaat7259 ◽  
Author(s):  
Nan Yan ◽  
Nan Xia ◽  
Lingwen Liao ◽  
Min Zhu ◽  
Fengming Jin ◽  
...  
Keyword(s):  
Metal Nanoparticles ◽  
Weak Interactions ◽  
Gold Nanoclusters ◽  
Atomic Level ◽  
High Quality ◽  
X Ray ◽  
X Ray Crystallography ◽  
Quantum Size ◽  
First Time

The transition from nanocluster to nanocrystal is a central issue in nanoscience. The atomic structure determination of metal nanoparticles in the transition size range is challenging and particularly important in understanding the quantum size effect at the atomic level. On the basis of the rationale that the intra- and interparticle weak interactions play critical roles in growing high-quality single crystals of metal nanoparticles, we have reproducibly obtained ideal crystals of Au144(SR)60 and successfully solved its structure by x-ray crystallography (XRC); this structure was theoretically predicted a decade ago and has long been pursued experimentally but without success until now. Here, XRC reveals an interesting Au12 hollow icosahedron in thiolated gold nanoclusters for the first time. The Au–Au bond length, close to that of bulk gold, shows better thermal extensibility than the other Au–Au bond lengths in Au144(SR)60, providing an atomic-level perspective because metal generally shows better thermal extensibility than nonmetal materials. Thus, our work not only reveals the mysterious, long experimentally pursued structure of a transition-sized nanoparticle but also has important implications for the growth of high-quality, single-crystal nanoparticles, as well as for the understanding of the thermal extensibility of metals from the perspective of chemical bonding.

Electric and thermoelectric properties of CdTe/PbTe epitaxial nanocomposite

2014 ◽  
Vol 07 (06) ◽  
pp. 1440007
Author(s):  
Michal Szot ◽  
Krzysztof Dybko ◽  
Piotr Dziawa ◽  
Leszek Kowalczyk ◽  
Viktor Domukhovski ◽  
...  
Keyword(s):  
Thermoelectric Properties ◽  
Carrier Mobility ◽  
Room Temperature ◽  
Molecular Beam ◽  
High Quality ◽  
Polycrystalline Solid ◽  
Hall Effect Measurements ◽  
Shubnikov De Haas Oscillations

The electric and thermoelectric properties of novel, CdTe / PbTe layered nanocomposite material are investigated. The molecular beam epitaxy (MBE) method was used for preparation of samples with well controlled distances (from 20 to 70 nm) between the layers of CdTe nanograins embedded in PbTe thermoelectric matrix as well as with number of these layers from 2 to 10. The Hall effect measurements performed in temperature range from 4–300 K revealed that carrier mobility is strongly affected by scattering on CdTe grain boundaries. The observation of Shubnikov-de Haas oscillations confirms high quality of the samples and allows determination of effective mass of conducting electrons m* = 0.04m0. The measurements of the room temperature Seebeck coefficient together with electrical conductivity lead to the power factors which are comparable to those reported in PbTe / CdTe polycrystalline solid solutions.

scholarly journals Determination of Main Spectral and Luminescent Characteristics of Winter Wheat Seeds Infected with Pathogenic Microflora

Photonics ◽  
2021 ◽  
Vol 8 (11) ◽  
pp. 494
Author(s):  
Alexey M. Bashilov ◽  
Igor Yu. Efremenkov ◽  
Mikhail V. Belyakov ◽  
Alexander V. Lavrov ◽  
Anatoly A. Gulyaev ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Physical Properties ◽  
Agricultural Products ◽  
High Quality ◽  
Crop Losses ◽  
Software Complex ◽  
Fusarium Infection ◽  
Constant Growth ◽  
Wheat Seeds

In connection with the constant growth of demand for high-quality food products, there is a need to develop effective methods for storing agricultural products, and the registration and predicting infection in the early stages. The studying of the physical properties of infected plants and seeds has fundamental importance for determining crop losses, conducting a survey of diseases, and assessing the effectiveness of their control (assessment of the resistance of crops and varieties, the effect of fungicides, etc.). Presently, photoluminescent methods for diagnosing seeds in the ultraviolet and visible ranges have not been studied. For research, seeds of winter wheat were selected, and were infected with one of the most common and dangerous diseases for plants—fusarium. The research of luminescence was carried out based on a hardware–software complex consisting of a multifunctional spectrofluorometer “Fluorat-02-Panorama”, a computer with software “Panorama Pro” installed, and an external camera for the samples under study. Spectra were obtained with a diagnostic range of winter wheat seeds of 220–400 nm. Based on the results obtained for winter wheat seeds, it is possible to further develop a method for determining the degree of fusarium infection.

scholarly journals Determination of the Anatomical Features of the Temporal Bones at the Stage of Planning Extraoral Implantation in Ectoprosthetics of the Auricle

2021 ◽  
pp. 12-24
Author(s):  
D. A. Lezhnev ◽  
S. D. Arutyunov ◽  
E. Yu. Lazarenko ◽  
M. V. Magomedbekova
Keyword(s):  
Surgical Intervention ◽  
Maxillofacial Surgery ◽  
Present Stage ◽  
High Quality ◽  
Anatomical Features ◽  
Prosthetic Reconstruction ◽  
Intervention Planning ◽  
Temporal Bones ◽  
Fixation System

At the present stage of the development of maxillofacial surgery, the treatment of patients with defects in the auricles is one of the most difficult. Defects of the auricles, characterized by its absence, are divided according to the etiological factor into two main groups: congenital (microtia) and acquired (as a result of injuries of various origins). Microtia (including anotia the complete absence of the auricle) is a malformation of the auricle and the external auditory canal caused by anomalies of the first and second zygomatic arch and the first sulcus.Congenital malformations of the auricle occur in 1 out of 700–15 000 newborns and more often have a right-sided localization. In 15 % of cases, they are hereditary, and in 85 % they are sporadic, in boys they are detected on average 2–2,5 times more often than in girls.Currently, much attention is paid to the prosthetic reconstruction of the auricle with fixation by means of cranial intraosseous implants. At the same time precise diagnostics of the state of the temporal bones in the area of the proposed implantation and the correct positioning of the intraosseous supports are the basis of an effective fixation system. Among the methods of radiological diagnostics used for planning ectoprosthetics of the auricles, radiography has long been preferred. However, the introduction of computed tomography into clinical practice has provided a high-quality assessment of the temporal bones state, which has increased the efficiency of surgical intervention planning and treatment.

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