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Evaluation of massively parallel sequencing for forensic DNA methylation profiling

Published: Jun 5, 2018

Author(s): Rebecca Richards, Jayshree Patel, Kate Stevenson, SallyAnn Harbison

Journal: ELECTROPHORESIS

Abstract Epigenetics is an emerging area of interest in forensic science. DNA methylation, a type of epigenetic modification, can be applied to chronological age estimation, identical twin differentiation and body fluid identification. However, there is not yet an agreed, established methodology for targeted detection and analysis of DNA methylation markers in forensic research. Recently, a massively parallel sequencing‐based...

Read More thumbnail image: Evaluation of massively parallel sequencing for forensic DNA methylation profiling

Cancer in the crosshairs: targeting cancer metabolism with hyperpolarized carbon‐13 MRI technology

Published: Jun 5, 2018

Author(s): Cornelius Morze, Matthew E. Merritt

Journal: NMR in Biomedicine

Magnetic resonance (MR)‐based hyperpolarized (HP) 13C metabolic imaging is under active pursuit as a new clinical diagnostic method for cancer detection, grading, and monitoring of therapeutic response. Following the tremendous success of metabolic imaging by positron emission tomography, which already plays major roles in clinical oncology, the added value of HP 13C MRI is emerging. Aberrant glycolysis and central carbon metabolism is a hallmark of...

Read More thumbnail image: Cancer in the crosshairs targeting cancer metabolism with hyperpolarized carbon13 MRI technology

Complementary middle‐down and intact monoclonal antibody proteoform characterization by capillary zone electrophoresis – mass spectrometry

Published: Jun 5, 2018

Author(s): Arseniy M. Belov, Li Zang, Roberto Sebastiano, Marcia R. Santos, David R. Bush, Barry L. Karger, Alexander R. Ivanov

Journal: ELECTROPHORESIS

Abstract High‐resolution capillary zone electrophoresis – mass spectrometry (CZE‐MS) has been of increasing interest for the analysis of biopharmaceuticals. In this work, a combination of middle‐down and intact CZE‐MS analyses has been implemented for the characterization of a biotherapeutic monoclonal antibody (mAb) with a variety of post‐translational modifications (PTMs) and glycosylation structures. Middle‐down and intact CZE...

Read More thumbnail image: Complementary middledown and intact monoclonal antibody proteoform characterization by capillary zone electrophoresis  mass spectrometry

Enhanced oil recovery assignment using a new strategy for clustering oil reservoirs: Application of fuzzy logics

Published: Jun 5, 2018

Author(s): Mohsen Khojastehmehr, Abbas Naderifar, Babak Aminshahidy

Journal: Journal of Chemometrics

Abstract Enhanced Oil Recovery (EOR) aims at producing more oil from low productive reservoirs. EOR is a costly process due to the time and expenses required to allocate a suitable EOR method to an oil reservoir. For this purpose, this work presents a systematic approach to incorporate past experiences into a compact system to assign the EOR process to oil reservoirs. Because the number of clusters within the reservoirs data is not...

Read More thumbnail image: Enhanced oil recovery assignment using a new strategy for clustering oil reservoirs Application of fuzzy logics

Multimode complex process monitoring using double‐level local information based local outlier factor method

Published: Jun 5, 2018

Author(s): Lei Wang, Xiaogang Deng, Yuping Cao

Journal: Journal of Chemometrics

Abstract Industrial processes typically have multiple operating modes with complex data distribution and locality faults, which challenges the traditional multivariate statistical process monitoring methods. To address this problem, a double‐level local information‐based local outlier factor (LOF) method is proposed in this work for multimode complex process monitoring. First, to handle the multimodality, the local neighborhood...

Read More thumbnail image: Multimode complex process monitoring using doublelevel local information based local outlier factor method

Ex vivo diffusion MRI of the human brain: Technical challenges and recent advances

Published: Jun 4, 2018

Author(s): Alard Roebroeck, Karla L. Miller, Manisha Aggarwal

Journal: NMR in Biomedicine

This review discusses ex vivo diffusion magnetic resonance imaging (dMRI) as an important research tool for neuroanatomical investigations and the validation of in vivo dMRI techniques, with a focus on the human brain. We review the challenges posed by the properties of post‐mortem tissue, and discuss state‐of‐the‐art tissue preparation methods and recent advances in pulse sequences and acquisition techniques to tackle these. We then...

Read More thumbnail image: Ex vivo diffusion MRI of the human brain Technical challenges and recent advances

An adaptive denoising method for Raman spectroscopy based on lifting wavelet transform

Published: Jun 4, 2018

Author(s): Hao Chen, Weiliang Xu, Neil Broderick, Jianda Han

Journal: Journal of Raman Spectroscopy

Abstract Noise, especially high‐level noise, is a severe problem in Raman spectral analysis. It smears informative Raman peaks, distorts spectral features, and therefore affects final analytical results, particularly in multivariate analysis, which is frequently used in Raman spectroscopy. This becomes even worse when it comes to optical Raman probe‐based biological applications due to limited acquisition time, laser power, and...

Read More thumbnail image: An adaptive denoising method for Raman spectroscopy based on lifting wavelet transform

A review of orthogonal projections for calibration

Published: Jun 4, 2018

Author(s): Jean‐Michel Roger, Jean‐Claude Boulet

Journal: Journal of Chemometrics

Abstract Effective methods often rely on simple mathematical operators. Among these operators, orthogonal projections have been widely used because of their simplicity in compensating for detrimental factors. This efficiency depends largely on the way these tools are prepared. This article links the mathematical basics of orthogonal projections to the notion of vectoral subspaces, highlighting which information should be removed in...

Read More thumbnail image: A review of orthogonal projections for calibration

Preparation, intercalation, and characterization of nanostructured (Zn, Al) layered double hydroxides (LDHs)

Published: Jun 1, 2018

Author(s): M. Richetta, A. Varone, A. Mattoccia, P.G. Medaglia, S. Kaciulis, A. Mezzi, P. Soltani, R. Pizzoferrato

Journal: Surface and Interface Analysis

The term layered double hydroxides (LDHs) is used to define synthetic or natural lamellar hydroxides with 2 or more kinds of metallic cations in the main layers, and hydrated interlayer domains, containing anionic species. Layered double hydroxides, also known as hydrotalcite materials, have attracted considerable interest from both industry and academia. They are interesting for their intercalation properties as they are capable of...

Read More thumbnail image: Preparation intercalation and characterization of nanostructured Zn Al layered double hydroxides LDHs

Microchip electrophoresis separation of a panel of preterm birth biomarkers

Published: Jun 1, 2018

Author(s): Anna V. Nielsen, Jacob B. Nielsen, Mukul Sonker, Radim Knob, Vishal Sahore, Adam T. Woolley

Journal: ELECTROPHORESIS

Abstract Preterm birth (PTB) is responsible for over one million infant deaths annually worldwide. Often, the first and only indication of PTB risk is the onset of early labor. Thus, there is an urgent need for an early PTB risk diagnostic that is inexpensive, reliable, and robust. Here, we describe the development of a microchip electrophoresis (μCE) method for separating a mixture of six PTB protein and peptide biomarkers present...

Read More thumbnail image: Microchip electrophoresis separation of a panel of preterm birth biomarkers

Sequence‐based US population data for the SE33 locus

Published: Jun 1, 2018

Author(s): Lisa A. Borsuk, Katherine B. Gettings, Carolyn R. Steffen, Kevin M. Kiesler, Peter M. Vallone

Journal: ELECTROPHORESIS

Abstract A set of 1036 U.S. Population Samples were sequenced using the Illumina ForenSeq DNA Signature Prep Kit. This sample set has been highly characterized using a variety of marker systems for human identification. The FASTQ files obtained from a ForenSeq DNA Signature Prep Kit experiment include several STR loci that are not reported in the associated software. These include SE33, DXS8377, DXS10148, DYS456, and DYS461. The...

Read More thumbnail image: Sequencebased US population data for the SE33 locus

Preparative isolation of ganoderic acid S, ganoderic acid T and ganoderol B from Ganoderma lucidum mycelia by high‐speed counter‐current chromatography

Published: May 31, 2018

Author(s): Na Feng, Yutian Wei, Jie Feng, Qingjiu Tang, Zhong Zhang, Jingsong Zhang, Wei Han

Journal: Biomedical Chromatography

Abstract Ganoderic acid S, ganoderic acid T and ganoderal B are the main bioactive triterpenes of Ganoderma lucidum. In this study, mycelia of G. lucidum were obtained by two‐stage fermentation and then extracted by ethanol and petroleum ether sequentially to obtain crude triterpenes. The crude sample was further purified by recycling high‐speed counter‐current chromatography with n‐hexane–ethyl acetate–methanol–water (7:12:11:5, v/v/v/v) as the optimized...

Read More thumbnail image: Preparative isolation of ganoderic acid S ganoderic acid T and ganoderol B from Ganoderma lucidum mycelia by highspeed countercurrent chromatography

The expanding role of mass spectrometry in the field of vaccine development

Published: May 31, 2018

Author(s): Vaneet Kumar Sharma, Ity Sharma, James Glick

Journal: Mass Spectrometry Reviews

Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry‐based techniques are also routinely used to assess glycosylation and other post‐translational...

Read More thumbnail image: The expanding role of mass spectrometry in the field of vaccine development

Breast magnetic resonance elastography: a review of clinical work and future perspectives

Published: May 30, 2018

Author(s): A.E. Bohte, J.L. Nelissen, J.H. Runge, O. Holub, S.A. Lambert, L. Graaf, S. Kolkman, S. Meij, J. Stoker, G.J. Strijkers, A.J. Nederveen, R. Sinkus

Journal: NMR in Biomedicine

This review on magnetic resonance elastography (MRE) of the breast provides an overview of available literature and describes current developments in the field of breast MRE, including new transducer technology for data acquisition and multi‐frequency‐derived power‐law behaviour of tissue. Moreover, we discuss the future potential of breast MRE, which goes beyond its original application as an additional tool in differentiating benign...

Read More thumbnail image: Breast magnetic resonance elastography a review of clinical work and future perspectives

The effect of athletes` hyperhydration on the urinary ‘steroid profile’ markers in doping control analysis

Published: May 30, 2018

Author(s): I. Athanasiadou, S. Kraiem, S. Al‐Sowaidi, H. Al‐Mohammed, N. Dbes, S. Al‐Yazedi, W. Samsam, V. Mohamed‐Ali, A. Dokoumetzidis, M. Alsayrafi, G. Valsami, C. Georgakopoulos

Journal: Drug Testing and Analysis

Abstract The urinary ‘steroid profile’ in doping control analysis is a powerful tool aimed at detecting intra‐individual deviations related to the abuse of endogenous steroids. Factors altering the steroid profile include, among others, the excessive fluid intake leading to low endogenous steroids concentrations compared to an individual's normal values. Cases report the use of hyperhydration by athletes as a masking method during...

Read More thumbnail image: The effect of athletes hyperhydration on the urinary steroid profile markers in doping control analysis

Dr. Yves Bonnaire

Published: May 29, 2018

Author(s): Ludovic Bailly‐Chouriberry

Journal: Drug Testing and Analysis

Read More thumbnail image: Dr_ Yves Bonnaire

Sensitive quantification of the somatostatin analog AP102 in plasma by ultra‐high pressure liquid chromatography–tandem mass spectrometry and application to a pharmacokinetic study in rats

Published: May 29, 2018

Author(s): Philippe J. Eugster, Christina N. Boyle, Sylvain Prod'hom, Erika Tarasco, Thierry Buclin, Thomas A. Lutz, Alan G. Harris, Eric Grouzmann

Journal: Drug Testing and Analysis

Abstract AP102 is a di‐iodinated octapeptide somatostatin agonist (SSA) designed to treat acromegaly and neuroendocrine tumors. A sensitive and selective method was validated for the quantification of AP102 in plasma following the European Medicines Agency (EMA) and Food and Drug Administration (FDA) guidelines. Sample preparation was performed using solid‐phase extraction microplates. Chromatographic separation was achieved on an...

Read More thumbnail image: Sensitive quantification of the somatostatin analog AP102 in plasma by ultrahigh pressure liquid chromatographytandem mass spectrometry and application to a pharmacokinetic study in rats

Roles of iron and lithium in silicate glasses by Raman spectroscopy

Published: May 29, 2018

Author(s): Manjunath T. Nayak, J.A. Erwin Desa

Journal: Journal of Raman Spectroscopy

Abstract Raman spectroscopy has been used in a qualitative analysis of iron containing lithium silicate glasses. The iron was kept fixed at 8 mol% for all the iron containing samples with varying concentrations of Li2O and SiO2, as this resulted in samples that were fully vitreous in nature. The method of deconvolution of peaks in these data has been employed to understand the relative numbers of Q0, Q1, Q2, Q3, and Q4 silicate structural...

Read More thumbnail image: Roles of iron and lithium in silicate glasses by Raman spectroscopy

Encoding and readout strategies in magnetic resonance elastography

Published: May 28, 2018

Author(s): Christian Guenthner, Sebastian Kozerke

Journal: NMR in Biomedicine

Magnetic resonance elastography (MRE) has evolved significantly since its inception. Advances in motion‐encoding gradient design and readout strategies have led to improved encoding and signal‐to‐noise ratio (SNR) efficiencies, which in turn allow for higher spatial resolution, increased coverage, and/or shorter scan times. The purpose of this review is to summarize MRE wave‐encoding and readout approaches in a unified mathematical...

Read More thumbnail image: Encoding and readout strategies in magnetic resonance elastography

Defining Cell Identity with Single‐Cell Omics

Published: May 28, 2018

Author(s): Laura Mincarelli, Ashleigh Lister, James Lipscombe, Iain C. Macaulay

Journal: PROTEOMICS

Abstract Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display...

Read More thumbnail image: Defining Cell Identity with SingleCell Omics
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