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https://www.readbyqxmd.com/read/28752757/a-detailed-investigation-and-comparison-of-the-xcms-and-mzmine-2-chromatogram-construction-and-chromatographic-peak-detection-methods-for-preprocessing-mass-spectrometry-metabolomics-data
#1
Owen D Myers, Susan J Sumner, Shuzhao Li, Stephen Barnes, Xiuxia Du
XCMS and MZmine 2 are two widely used software packages for preprocessing untargeted LC/MS metabolomics data. Both construct extracted ion chromatograms (EICs) and detect peaks from the EICs, the first two steps in the data preprocessing workflow. While both packages have performed admirably in peak picking, they also detect a problematic number of false positive EIC peaks and can also fail to detect real EIC peaks. The former and latter translate downstream into spurious and missing compounds, and present significant limitations with most existing software packages that preprocess untargeted mass spectrometry metabolomics data...
July 28, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28752754/one-step-forward-for-reducing-false-positive-and-false-negative-compound-identifications-from-mass-spectrometry-metabolomics-data-new-algorithms-for-constructing-extracted-ion-chromatograms-and-detecting-chromatographic-peaks
#2
Owen D Myers, Susan J Sumner, Shuzhao Li, Stephen Barnes, Xiuxia Du
False positive and false negative peaks detected from extracted ion chromatograms (EIC) are an urgent problem with existing software packages that preprocess untargeted liquid or gas chromatography-mass spectrometry metabolomics data because they can translate downstream into spurious or missing compound identifications. We have developed new algorithms that carry out the sequential construction of EICs and detection of EIC peaks. We compare the new algorithms to two popular software packages XCMS and MZmine 2, and present evidence that these new algorithms detect significantly fewer false positives...
July 28, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28696781/early-intervention-of-cystic-fibrosis-pulmonary-exacerbations-based-on-home-monitoring-eice-through-the-looking-glass
#3
Scott C Bell
No abstract text is available yet for this article.
July 11, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28621737/comprehensive-identification-of-guan-xin-shu-tong-capsule-via-a-mass-defect-and-fragment-filtering-approach-by-high-resolution-mass-spectrometry-in-vitro-and-in-vivo-study
#4
Xun Gao, Jingqing Mu, Qing Li, Shaoyi Guan, Ran Liu, Yiyang Du, Huifen Zhang, Kaishun Bi
The Guan-Xin-Shu-Tong capsule (GXSTC) is a well-known traditional Chinese medicine that is used for the treatment of coronary heart disease. Despite its common use in China, basic pharmacological research on its active components is limited. A comprehensive analytical method using quadrupole-time-of-flight mass spectrometry (Q-TOF/MS), specifically with the Triple TOF 5600 platform, was developed to characterize the compounds in the GXSTC powder itself (in vitro) as well as the active components in healthy and heart disease model rats after its oral administration (in vivo)...
June 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28608719/home-monitoring-in-cf-to-identify-and-treat-acute-pulmonary-exacerbations-eice-study-results
#5
Noah Lechtzin, Nicole Mayer-Hamblett, Natalie E West, Sarah Allgood, Ellen Wilhelm, Umer Khan, Moira L Aitken, Bonnie W Ramsey, Michael P Boyle, Peter J Mogayzel, Ronald L Gibson, David Orenstein, Carlos Milla, John P Clancy, Veena Antony, Christopher H Goss
RATIONALE: Individuals with cystic fibrosis (CF) suffer frequent acute pulmonary exacerbations, which lead to decreased lung function and reduced quality of life. OBJECTIVES: The goal of this study was to determine if an intervention directed toward early detection of pulmonary exacerbations using home spirometry and symptom monitoring would result in slower decline in lung function compared to controls. METHODS: A multicenter randomized trial at 14 CF centers in subjects ≥14 years...
June 13, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28561755/rapid-screening-and-identification-of-diterpenoids-in-tinospora-sinensis-based-on-high-performance-liquid-chromatography-coupled-with-linear-ion-trap-orbitrap-mass-spectrometry
#6
Lu-Lu Xu, Feng-Xia Guo, Sen-Sen Chi, Zi-Jian Wang, Yan-Yan Jiang, Bin Liu, Jia-Yu Zhang
Diterpenoids are considered the major active compounds in Tinospora sinensis in virtue of their special structures and activities. Herein, an analytical method was developed for rapid screening and identification of diterpenoids in T. sinensis using high-performmance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry (HPLC-LTQ-Orbitrap) in negative ion mode. Two diterpenoid reference standards were first analyzed to obtain their characteristic ESI-MS/MS fragmentation patterns. Then, based on the extracted ion chromatogram (EIC) data-mining method and characteristic fragmentation pathways analysis, diterpenoids in T...
May 31, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28436401/effects-of-amplitude-and-phase-duration-modification-on-electrically-induced-contraction-force-and-discomfort
#7
Shmuel Springer, Maxim Shapiro
BACKGROUND: Neuromuscular electrical stimulation (NMES) is commonly used in rehabilitation. However, the optimal combination of phase-duration and amplitude for enhancing motor output is not yet resolved. OBJECTIVE: To test the effects of increasing phase-duration and amplitude on isometric knee extension force and discomfort, while controlling the effects of electrode-skin resistance and body mass index (BMI). METHODS: Twenty-one healthy volunteers participated in the study...
April 14, 2017: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/28385557/changes-in-hormonal-levels-associated-with-enforced-interval-copulation-and-anxiety-in-sexually-inexperienced-and-experienced-male-rats
#8
Tzintli Meraz-Medina, Marisela Hernández-González, Herlinda Bonilla-Jaime, Miguel Angel Guevara, Leopoldo Flores-Mancilla, Rosa María Vigueras-Villaseñor, Marcela Arteaga-Silva
This study evaluated the effect of sexual experience on anxiety and hormonal levels associated with the performance of sexual behavior. Two groups of male rats, one with, the second without, sexual experience, were exposed to four different copulatory conditions: ad libitum copulation until ejaculation (ADC-E); enforced interval copulation until ejaculation (EIC-E); ad libitum copulation up to 3 intromissions (ADC-3I); and enforced interval copulation up to 3 intromissions (EIC-E3I). At the end of each condition the animals were subjected to an open-field test to measure anxiety, before being sacrificed to measure corticosterone (CORT) and testosterone (T) levels...
April 4, 2017: Physiology & Behavior
https://www.readbyqxmd.com/read/28383950/multilevel-factorial-designs-with-experiment-induced-clustering
#9
Inbal Nahum-Shani, John J Dziak, Linda M Collins
Factorial experimental designs have many applications in the behavioral sciences. In the context of intervention development, factorial experiments play a critical role in building and optimizing high-quality, multicomponent behavioral interventions. One challenge in implementing factorial experiments in the behavioral sciences is that individuals are often clustered in social or administrative units and may be more similar to each other than to individuals in other clusters. This means that data are dependent within clusters...
April 6, 2017: Psychological Methods
https://www.readbyqxmd.com/read/28277460/aspects-ct-in-acute-ischemia-review-of-current-data
#10
Supada Prakkamakul, Albert J Yoo
The Alberta Stroke Program Early CT score (ASPECTS) is a 10-point semiquantitative topographic scoring system developed for the assessment of early ischemic changes (EICs) on noncontrast-enhanced computed tomography (NCCT) in patients with acute ischemic stroke involving the middle cerebral artery (MCA) territory. One point is subtracted from a total score of 10, if an EIC is present in any part of each of the ASPECTS regions. Higher ASPECTS has been associated with better outcomes and a lower risk of symptomatic intracerebral hemorrhage...
June 2017: Topics in Magnetic Resonance Imaging: TMRI
https://www.readbyqxmd.com/read/28168039/dnm1-mutation-status-sex-and-sterilization-status-of-a-cohort-of-labrador-retrievers-with-and-without-cranial-cruciate-ligament-rupture
#11
Kari J Ekenstedt, Katie M Minor, Aaron K Rendahl, Michael G Conzemius
BACKGROUND: Exercise-induced collapse (EIC) due to DNM1 mutation and rupture of the cranial cruciate ligament are both common syndromes in the Labrador retriever breed. A cohort of 313 Labradors was recruited based on their CCLR status and were subsequently genetically tested for EIC. Epidemiological aspects of the cohort were also described, including sex, sterilization status, and age at sterilization. RESULTS: No sex difference was observed in dogs susceptible to EIC (homozygous for the mutant genotype) compared to dogs not susceptible to EIC (heterozygotes and dogs homozygous for the normal genotype)...
2017: Canine Genetics and Epidemiology
https://www.readbyqxmd.com/read/28113005/understanding-the-influence-of-stigma-and-medical-mistrust-on-engagement-in-routine-healthcare-among-black-women-who-have-sex-with-women
#12
Alaina Brenick, Kelly Romano, Christopher Kegler, Lisa A Eaton
PURPOSE: For Black women who have sex with women (BWSW), obtaining routine healthcare can be obstructed by a number of psychosocial barriers, including experiences of stigma, related to both sexual orientation and race, and medical mistrust, both race-based and global. Previous research demonstrates that sexual orientation and race-based stigma, as well as global and race-based medical mistrust, each have a negative impact on health outcomes and engagement in care (EIC) independently...
February 2017: LGBT Health
https://www.readbyqxmd.com/read/28093342/march-2017-editor-in-chief-letter
#13
EDITORIAL
Ed Benzel
No abstract text is available yet for this article.
March 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28046369/su-g-201-05-comparison-of-different-methods-for-output-verification-of-eleckta-nucletron-s-valencia-skin-applicators
#14
J Barrett, M Yudelev
PURPOSE: The provided output factors for Elekta Nucletron's skin applicators are based on Monte Carlo simulations. These outputs have not been independently verified, and there is no recognized method for output verification of the vendor's applicators. The purpose of this work is to validate the outputs provided by the vendor experimentally. METHODS: Using a Flexitron Ir-192 HDR unit, three experimental methods were employed to determine dose with the 30 mm diameter Valencia applicator: first a gradient method using extrapolation ionization chamber (Far West Technology, EIC-1) measurements in solid water phantom at 3 mm SCD was used...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/27906789/radon-and-thoron-in-air-occupational-exposure-study-within-selected-wine-cellars-of-the-western-cape-south-africa-and-associated-annual-effective-doses
#15
MULTICENTER STUDY
R Botha, R T Newman, R Lindsay, P P Maleka
This is the first known study of exposure of Rn (radon) and secondarily Rn (thoron) in-air activity concentrations assessed within nine selected wine cellars in four wine districts of the Western Cape (South Africa) and the associated annual occupational effective doses. E-PERM electret ion chambers (EIC) and RAD-7 α-detectors were used to perform these measurements. The radon in-air levels ranged from 12 ± 4 Bq m to 770 ± 40 Bq m within the nine selected wine cellars. Eight of the nine wine cellars (excluding results from cellar w-6) had a median radon in-air activity concentration of 48 ± 8 Bq m...
January 2017: Health Physics
https://www.readbyqxmd.com/read/27855523/immunomodulatory-and-cellular-anti-oxidant-activities-of-caffeic-ferulic-and-p-coumaric-phenolic-acids-a-structure-activity-relationship-study
#16
Soumaya Kilani-Jaziri, Imen Mokdad-Bzeouich, Mounira Krifa, Nouha Nasr, Kamel Ghedira, Leila Chekir-Ghedira
Many studies have been performed to assess the potential utility of natural products as immunomodulatory agents to enhance host responses and to reduce damage to the human body. To determine whether phenolic compounds (caffeic, ferulic, and p-coumaric acids) have immunomodulatory effects and clarify which types of immune effector cells are stimulated in vitro, we evaluated their effect on splenocyte proliferation and lysosomal enzyme activity. We also investigated the activity of natural killer (NK) cells and cytotoxic T lymphocytes (CTL)...
November 18, 2016: Drug and Chemical Toxicology
https://www.readbyqxmd.com/read/27818924/identification-and-differentiation-of-panax-ginseng-panax-quinquefolium-and-panax-notoginseng-by-monitoring-multiple-diagnostic-chemical-markers
#17
Wenzhi Yang, Xue Qiao, Kai Li, Jingran Fan, Tao Bo, De-An Guo, Min Ye
To differentiate traditional Chinese medicines (TCM) derived from congeneric species in TCM compound preparations is usually challenging. The roots of Panax ginseng (PG), Panax quinquefolium (PQ) and Panax notoginseng (PN) are used as popular TCM. They contain similar triterpenoid saponins (ginsenosides) as the major bioactive constituents. Thus far, only a few chemical markers have been discovered to differentiate these three species. Herein we present a multiple marker detection approach to effectively differentiate the three Panax species, and to identify them in compound preparations...
November 2016: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/27810455/january-2017-editor-s-letter
#18
EDITORIAL
Ed Benzel
No abstract text is available yet for this article.
January 2017: World Neurosurgery
https://www.readbyqxmd.com/read/27796460/active-fragments-guided-drug-discovery-and-design-of-selective-tropane-alkaloids-using-ultra-high-performance-liquid-chromatography-quadrupole-time-of-flight-tandem-mass-spectrometry-coupled-with-virtual-calculation-and-biological-evaluation
#19
Mengge Zhou, Xiaoyao Ma, Jixue Sun, Guoyu Ding, Qingxin Cui, Yan Miao, Yuanyuan Hou, Min Jiang, Gang Bai
Tropane alkaloids (TAs), rich in the plant of Physochlaina infundibularis Kuang, which is named Huashanshen (HSS) in China, showed good effects on types of spasms. However, no data were collected to explore the relationship between the specificity for muscarinic receptor subtypes and the structures of these TAs. To address this issue, an extracted ion chromatogram (EIC) strategy using ultra-high performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-Q/TOF-MS) based on the fragmentation behavior of the TA standards was established to rapidly capture the varied TAs from HSS...
October 29, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27796459/quantitation-of-human-milk-proteins-and-their-glycoforms-using-multiple-reaction-monitoring-mrm
#20
Jincui Huang, Muchena J Kailemia, Elisha Goonatilleke, Evan A Parker, Qiuting Hong, Rocchina Sabia, Jennifer T Smilowitz, J Bruce German, Carlito B Lebrilla
Human milk plays a substantial role in the child growth, development and determines their nutritional and health status. Despite the importance of the proteins and glycoproteins in human milk, very little quantitative information especially on their site-specific glycosylation is known. As more functions of milk proteins and other components continue to emerge, their fine-detailed quantitative information is becoming a key factor in milk research efforts. The present work utilizes a sensitive label-free MRM method to quantify seven milk proteins (α-lactalbumin, lactoferrin, secretory immunoglobulin A, immunoglobulin G, immunoglobulin M, α1-antitrypsin, and lysozyme) using their unique peptides while at the same time, quantifying their site-specific N-glycosylation relative to the protein abundance...
January 2017: Analytical and Bioanalytical Chemistry
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