scholarly journals Improved Label-Free LC-MS Analysis by Wavelet-Based Noise Rejection

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Salvatore Cappadona ◽  
Paolo Nanni ◽  
Marco Benevento ◽  
Fredrik Levander ◽  
Piera Versura ◽  
...  
Keyword(s):  
Protein Identification ◽  
Label Free ◽  
Computational Framework ◽  
Noise Rejection ◽  
Software Packages ◽  
Ms Analysis ◽  
More Care ◽  
Multiple Samples ◽  
Common Laboratory

Label-free LC-MS analysis allows determining the differential expression level of proteins in multiple samples, without the use of stable isotopes. This technique is based on the direct comparison of multiple runs, obtained by continuous detection in MS mode. Only differentially expressed peptides are selected for further fragmentation, thus avoiding the bias toward abundant peptides typical of data-dependent tandem MS. The computational framework includes detection, alignment, normalization and matching of peaks across multiple sets, and several software packages are available to address these processing steps. Yet, more care should be taken to improve the quality of the LC-MS maps entering the pipeline, as this parameter severely affects the results of all downstream analyses. In this paper we show how the inclusion of a preprocessing step of background subtraction in a common laboratory pipeline can lead to an enhanced inclusion list of peptides selected for fragmentation and consequently to better protein identification.

scholarly journals Optical Monitoring of the Production Quality of Si-Nanoribbon Chips Intended for the Detection of ASD-Associated Oligonucleotides

Micromachines ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 147
Author(s):  
Kristina A. Malsagova ◽  
Tatyana O. Pleshakova ◽  
Vladimir P. Popov ◽  
Igor N. Kupriyanov ◽  
Rafael A. Galiullin ◽  
...  
Keyword(s):  
Production Quality ◽  
Autism Spectrum ◽  
Covalent Immobilization ◽  
Biological Macromolecules ◽  
Label Free ◽  
Raman Scattering Spectroscopy ◽  
Dna Oligonucleotides ◽  
Highly Sensitive ◽  
Highly Sensitive Detection

Gas-phase etching and optical lithography were employed for the fabrication of a silicon nanoribbon chip (Si-NR chip). The quality of the so-fabricated silicon nanoribbons (Si-NRs) was monitored by optical Raman scattering spectroscopy. It was demonstrated that the structures of the Si-NRs were virtually defect-free, meaning they could be used for highly sensitive detection of biological macromolecules. The Si-NR chips were then used for the highly sensitive nanoelectronics detection of DNA oligonucleotides (oDNAs), which represent synthetic analogs of 106a-5p microRNA (miR-106a-5p), associated with the development of autism spectrum disorders in children. The specificity of the analysis was attained by the sensitization of the Si-NR chip sur-face by covalent immobilization of oDNA probes, whose nucleotide sequence was complementary to the known sequence of miR-106a-5p. The use of the Si-NR chip was demonstrated to al-low for the rapid label-free real-time detection of oDNA at ultra-low (~10−17 M) concentrations.

scholarly journals Female aging

2015 ◽  
Vol 61 (6) ◽  
pp. 553-556 ◽  
Author(s):  
Isabel Cristina Esposito Sorpreso ◽  
José Maria Soares Júnior ◽  
Angela Maggio da Fonseca ◽  
Edmund Chada Baracat
Keyword(s):  
Quality Of Life ◽  
Life Cycle ◽  
Functional Capacity ◽  
Overweight And Obesity ◽  
Natural Process ◽  
More Care ◽  
Female Aging ◽  
The Individual ◽  
Harmful Effects

SUMMARY Female aging is a process that involves hypoestrogenism time, the individual impact on each woman, and what we can do as experts to reduce morbidity and provide quality of life. This natural process in the female life cycle has been of concern to women after menopause. Changes in different biophysical and psychosocial aspects, and their individual experiences, have repercussions on the lives of patients seeking specialized and multidisciplinary support to reduce the harmful effects of prolonged hypoestrogenism. Overweight and obesity, inadequate living habits and the presence of multi-morbidities cause damage to the quality of life and impact the functional capacity. Behavioral prescription and hormone therapy are among the treatments given to ease symptoms and reduce morbidity. A better understanding of these factors can help identify groups that require more care after menopause.

The application of the MPEG-4 standard to telepathology images for electronic patient records

2003 ◽  
Vol 9 (1_suppl) ◽  
pp. 19-21 ◽  
Author(s):  
Georg A Brox ◽  
Janis L Huston
Keyword(s):  
Image Quality ◽  
Patient Records ◽  
Electronic Patient Records ◽  
Diagnostic Image ◽  
Diagnostic Quality ◽  
Compressed Images ◽  
Software Packages ◽  
Mapping Software ◽  
Pixel Mapping

summary We conducted a pilot study to compare the diagnostic quality of digital telepathology images compressed using two software packages, each of which incorporated the MPEG-4 standard. Both software packages produced lossy (rather than lossless) compressed images. Lossy images can be less reliable for diagnostic purposes and the aim of the study was to examine how the MPEG-4 standard affects image quality. The results showed that manipulation of the images by the software did not dramatically alter the image quality but they highlighted the need to develop both pixel-mapping software and associated standards. Standards will help to determine which bits of a diagnostic image can be safely removed during compression while ensuring the integrity and reliability of images for diagnostic purposes.

scholarly journals When good ligands go bad

2014 ◽  
Vol 70 (a1) ◽  
pp. C1269-C1269
Author(s):  
Ethan Merritt
Keyword(s):  
Task Force ◽  
Structure Refinement ◽  
Binding Pocket ◽  
Software Packages ◽  
Protein Model ◽  
Protein Components ◽  
First Time ◽  
Standard Software ◽  
New Protein

"Tools for validating structural models of proteins are relatively mature and widely implemented. New protein crystallographers are introduced early on to the importance of monitoring conformance with expected φ/ψ values, favored rotamers, and local stereochemistry. The protein model is validated by the PDB at the time of deposition using criteria that are also available in the standard software packages used to refine the model being deposited. By contrast, crystallographers are typically much less familiar with procedures to validate key non-protein components of the model – cofactors, substrates, inhibitors, etc. It has been estimated that as many as a third of all ligands in the PDB exhibit preventable errors of some sort, ranging from minor deviations in expected bond angles to wholly implausible placement in the binding pocket. Following recommendations from the wwPDB Validation Task Force, the PDB recently began validating ligand geometry as an integral part of deposition processing. This means that many crystallographers will soon receive for the first time a ""grade"" on the quality of ligands in the structure they have just deposited. Some will be surprised, as I was following my first PDB deposition of 2014, at how easily bad ligand geometry can slip through the cracks in supposedly robust structure refinement protocols that their lab has used for many years. I will illustrate use of current tools for generating ligand restraints to guide model refinement. One is the jligand+coot+cprodrg pipeline integrated into the CCP4 suite. Another is the Grade web server provided as a community resource by Global Phasing Ltd. Furthermore I will show examples from recent in-house refinements of how things can still go wrong even if you do use these tools, and how we recovered. The new PDB deposition checks may expose errors in your ligand descriptions after the fact. This presentation may help you avoid introducing those errors in the first place."

Despeckling Algorithms for Optical Coherence Tomography Images

2019 ◽  
pp. 286-310
Author(s):  
Anoop B. N. ◽  
G. N. Girish ◽  
Sudeep P. V. ◽  
Jeny Rajan
Keyword(s):  
Optical Coherence Tomography ◽  
Noise Suppression ◽  
Imaging Technique ◽  
Visual Quality ◽  
Optical Coherence ◽  
Non Invasive ◽  
Computerized Analysis ◽  
Feature Preservation ◽  
Software Packages

Optical coherence tomography (OCT) is a non-invasive imaging technique widely used in ophthalmology. The presence of speckle affects the quality of OCT images. Despeckling is necessary to improve its visual quality, and it is an integral part of software packages used for the computerized analysis of OCT. Even though a few methods for despeckling OCT are available in the literature, a cross-comparison of their performance is not known to be available. In this chapter, the techniques available in the literature for despeckling the OCT images have been identified. The results of the despeckling algorithms are compared both qualitatively and quantitatively by concerning the noise suppression capability and feature preservation. Among the available techniques, iterative adaptive unbiased (IAUB) filter is found to be superior as far as its performance regarding despeckling on retinal OCT images.

Amyloidosis: diagnosis and new therapies for a misunderstood and misdiagnosed disease

2019 ◽  
Vol 9 (6) ◽  
Author(s):  
Victoria E Thomas ◽  
Justin Smith ◽  
Merrill D Benson ◽  
Noel R Dasgupta
Keyword(s):  
Quality Of Life ◽  
Light Chain ◽  
Protein Identification ◽  
Amyloid Fibril ◽  
Immunoglobulin Light Chain ◽  
Transthyretin Amyloidosis ◽  
Identification Methods ◽  
Novel Treatments ◽  
Noninvasive Cardiac Imaging

Amyloidosis is a group of diseases characterized by extracellular deposition of amyloid fibril complexes. Fibril deposition results in organ dysfunction and possible failure. Amyloidosis is regarded as a rare disease, but in general is underdiagnosed. The two main types of systemic amyloidosis are immunoglobulin light chain and transthyretin amyloidosis. The increased availability of noninvasive cardiac imaging, genetic testing and improved laboratory assays and protein identification methods have led to increased diagnosis. However, in many cases, the diagnosis is not made until the patient develops organ impairment. Earlier diagnosis is required to prevent irreversible organ failure. Novel treatments for immunoglobulin light chain and transthyretin amyloidosis that halt disease progression, prolong and increase quality of life have recently become available.

scholarly journals Chromatographic Profiling of Rose Petals in Unani Formulations (Gulkand, Arq-e-Gulab, and Rose Sharbat) Using HPTLC and GC–MS

2020 ◽  
Vol 103 (3) ◽  
pp. 684-691
Author(s):  
Rabea Parveen ◽  
Sultan Zahiruddin ◽  
Akshay Charegaonkar ◽  
Abhijeet Khale ◽  
Saikat Mallick
Keyword(s):  
Traditional Medicine ◽  
Chromatographic Analysis ◽  
Herbal Products ◽  
Unani Medicine ◽  
Ms Analysis ◽  
Rose Petals ◽  
The Rose ◽  
Hptlc Method ◽  
Chromatographic Profiling

Abstract Background: One of the most precious systems of traditional medicine is the Unani system of medicine. A wide variety of formulations indigenous to the Unani medicine have been preserved over the years. These formulations are potent and effective even after ages of postformulation. Rose petals are an example of such an herb, which is extensively and popularly used in Unani formulations for edible and cosmetic purposes. Rose petals are rich in terpenes, glycosides, flavonoids, and anthocyanins. Objective: The aim of this study was to characterize the phytochemical profiling of different rose varieties and their marketed formulations. Method: HPTLC method was developed for detecting overall profile and assessing variations among the rose varieties available in market along with the popular formulations of rose such as gulkand (Brand A and Brand B), Arq-e-gulab or Gulab Jal (Brand C), and sharbat (Brand D). GC–MS analysis was also carried out for fingerprinting of rose varieties and formulations. Results: HPTLC and GC–MS fingerprinting showed some common peaks in rose samples as well as in the formulation samples. The methods also gave different peaks for the adulterant that might be used in place of rose. Conclusions: Both the methods could be used for standardization of herbal products containing rose as one of the ingredients and also used to check for the adulteration. Highlights: The current advanced chromatographic analysis is a valuable tool to determine the quality of the formulation.

Mediating Effects of Social Support on Caregiver Burden and Quality of Life for Compound and Noncompound Caregivers

2020 ◽  
pp. 104438942094722
Author(s):  
Christina N. Marsack-Topolewski
Keyword(s):  
Quality Of Life ◽  
Social Support ◽  
Caregiver Burden ◽  
Adult Child ◽  
Autism Spectrum ◽  
Mediating Effect ◽  
Informal Social Support ◽  
More Care ◽  
The Relationship

This study sought to explore the mediating effect of informal social support on the relationship between caregiver burden and quality of life among compound and noncompound caregivers. Parents ( N = 320) completed a web-based survey aimed to examine effects of caring for an adult child with autism spectrum disorder. Results of the mediation analysis suggested that informal social support partially mediated the relationship between caregiver burden and quality of life for both groups. Informal social support appears to be more impactful for noncompound caregivers compared with compound caregivers based on a greater reduction in explained variance. These results highlight the importance of informal social support as caregivers juggle ongoing challenges to provide care to one or more care recipients.

scholarly journals Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools

2019 ◽  
Vol 2 (1) ◽  
pp. 8 ◽  
Author(s):  
Jesse Meyer
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Gene Knockout ◽  
Tandem Mass ◽  
Label Free ◽  
Software Packages ◽  
Complex Process ◽  
Data Files ◽  
Using Data ◽  
Free Quantification

The identification of nearly all proteins in a biological system using data-dependent acquisition (DDA) tandem mass spectrometry has become routine for organisms with relatively small genomes such as bacteria and yeast. Still, the quantification of the identified proteins may be a complex process and often requires multiple different software packages. In this protocol, I describe a flexible strategy for the identification and label-free quantification of proteins from bottom-up proteomics experiments. This method can be used to quantify all the detectable proteins in any DDA dataset collected with high-resolution precursor scans and may be used to quantify proteome remodeling in response to drug treatment or a gene knockout. Notably, the method is statistically rigorous, uses the latest and fastest freely-available software, and the entire protocol can be completed in a few hours with a small number of data files from the analysis of yeast.

scholarly journals Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

2020 ◽  
pp. mcp.R120.002095 ◽  
Author(s):  
Daniel G Delafield ◽  
Lingjun Li
Keyword(s):  
Mass Difference ◽  
Label Free ◽  
Mass Defect ◽  
Chemical Labeling ◽  
The Past ◽  
Software Packages ◽  
Recent Advances ◽  
Analytical Approaches ◽  
Free Quantification ◽  
Identification And Characterization

Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.

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