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https://www.readbyqxmd.com/read/29444641/oasis-2-improved-online-analysis-of-small-rna-seq-data
#1
Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing. RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy...
February 14, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29431907/simultaneous-determination-of-29-pharmaceuticals-in-fish-muscle-and-plasma-by-ultrasonic-extraction-followed-by-spe-uhplc-ms-ms
#2
You-Yu Liu, Xia-Lin Hu, Yi-Fan Bao, Da-Qiang Yin
A confirmatory method for the simultaneous detection of 29 pharmaceuticals in fish muscle and plasma was developed by using solid-phase extraction combined with ultra high performance liquid chromatography and tandem mass spectrometry. Fish samples were extracted with methanol and enriched using Oasis HLB solid-phase extraction columns in one step. Twenty-nine target pharmaceuticals were quantified by the internal standard method and the calibration curves showed good linearity in a wide range with determination coefficients of greater than 0...
February 12, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29426215/comparison-of-the-sampling-rates-and-partitioning-behaviour-of-polar-and-non-polar-contaminants-in-the-polar-organic-chemical-integrative-sampler-and-a-monophasic-mixed-polymer-sampler-for-application-as-an-equilibrium-passive-sampler
#3
Yoonah Jeong, Andreas Schäffer, Kilian Smith
In this work, Oasis HLB® beads were embedded in a silicone matrix to make a single phase passive sampler with a higher affinity for polar and ionisable compounds than silicone alone. The applicability of this mixed polymer sampler (MPS) was investigated for 34 aquatic contaminants (log KOW -0.03 to 6.26) in batch experiments. The influence of flow was investigated by comparing uptake under static and stirred conditions. The sampler characteristics of the MPS was assessed in terms of sampling rates (RS) and sampler-water partition coefficients (KSW), and these were compared to those of the polar organic chemical integrative sampler (POCIS) as a reference kinetic passive sampler...
February 2, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29404054/application-of-an-lc-ms-ms-method-for-the-analysis-of-amlodipine-valsartan-and-hydrochlorothiazide-in-polypill-for-a-bioequivalence-study
#4
Jaivik V Shah, Jignesh M Parekh, Priyanka A Shah, Priya V Shah, Mallika Sanyal, Pranav S Shrivastav
A sensitive and selective method has been proposed for the simultaneous determination of amlodipine (AML), valsartan (VAL) and hydrochlorothiazide (HCTZ) in human plasma by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The analytes and their deuterated analogs were quantitatively extracted from 100 µL human plasma by solid phase extraction on Oasis HLB cartridges. The chromatographic separation of the analytes was achieved on a Chromolith RP18e (100 mm × 4.6 mm) analytical column within 2...
October 2017: Journal of Pharmaceutical Analysis
https://www.readbyqxmd.com/read/29404038/highly-sensitive-assay-for-the-determination-of-therapeutic-peptide-desmopressin-in-human-plasma-by-uplc-ms-ms
#5
Shiva Kumar Gudlawar, Nageswara Rao Pilli, Sridhar Siddiraju, Jaya Dwivedi
An analytical method based on ultra-performance liquid chromatography with positive ion electrospray ionization (ESI) coupled with tandem mass spectrometry detection (UPLC-MS/MS) was developed and validated for the determination of therapeutic peptide desmopressin in human plasma. A desmopressin stable labeled isotope (desmopressin d8) was used as an internal standard. Analyte and the internal standard were extracted from 200 µL of human plasma via solid-phase extraction technique using Oasis WCX cartridges...
June 2017: Journal of Pharmaceutical Analysis
https://www.readbyqxmd.com/read/29404033/fast-and-sensitive-lc-ms-ms-method-for-the-simultaneous-determination-of-lisinopril-and-hydrochlorothiazide-in-human-plasma
#6
Jaivik V Shah, Priyanka A Shah, Priya V Shah, Mallika Sanyal, Pranav S Shrivastav
A sensitive and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed for the simultaneous determination of lisinopril (LIS) and hydrochlorothiazide (HCTZ) in human plasma using their labeled internal standards (ISs). Sample pre-treatment involved solid phase extraction on Waters Oasis HLB cartridges using 100 µL of plasma, followed by liquid chromatography on Hypersil Gold C18 (50 mm×3.0 mm, 5 µm) column. The analytes were eluted within 2.0 min using acetonitrile-5...
June 2017: Journal of Pharmaceutical Analysis
https://www.readbyqxmd.com/read/29385109/development-and-validation-of-a-uplc-ms-ms-and-uplc-hr-ms-method-for-the-determination-of-fumonisin-b1-and-its-hydrolysed-metabolites-and-fumonisin-b2-in-broiler-chicken-plasma
#7
Siegrid De Baere, Siska Croubels, Barbara Novak, Gerlinde Bichl, Gunther Antonissen
A sensitive and specific method for the quantitative determination of Fumonisin B1 (FB1), its partially hydrolysed metabolites pHFB1a+b and hydrolysed metabolite HFB1, and Fumonisin B2 (FB2) in broiler chicken plasma using ultra-performance liquid chromatography combined with tandem mass spectrometry (UPLC-MS/MS) was developed. The sample preparation was rapid, straightforward and consisted of a deproteinization and phospholipid removal step using an Oasis® OstroTM 96-well plate. Chromatography was performed on an Acquity HSS-T3 column, using 0...
January 31, 2018: Toxins
https://www.readbyqxmd.com/read/29379899/fast-geodesic-regression-for-population-based-image-analysis
#8
Yi Hong, Polina Golland, Miaomiao Zhang
Geodesic regression on images enables studies of brain development and degeneration, disease progression, and tumor growth. The high-dimensional nature of image data presents significant computational challenges for the current regression approaches and prohibits large scale studies. In this paper, we present a fast geodesic regression method that dramatically decreases the computational cost of the inference procedure while maintaining prediction accuracy. We employ an efficient low dimensional representation of diffeomorphic transformations derived from the image data and characterize the regressed trajectory in the space of diffeomorphisms by its initial conditions, i...
September 2017: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/29379183/new-egyptian-sauropod-reveals-late-cretaceous-dinosaur-dispersal-between-europe-and-africa
#9
Hesham M Sallam, Eric Gorscak, Patrick M O'Connor, Iman A El-Dawoudi, Sanaa El-Sayed, Sara Saber, Mahmoud A Kora, Joseph J W Sertich, Erik R Seiffert, Matthew C Lamanna
Prominent hypotheses advanced over the past two decades have sought to characterize the Late Cretaceous continental vertebrate palaeobiogeography of Gondwanan landmasses, but have proved difficult to test because terrestrial vertebrates from the final ~30 million years of the Mesozoic are extremely rare and fragmentary on continental Africa (including the then-conjoined Arabian Peninsula but excluding the island of Madagascar). Here we describe a new titanosaurian sauropod dinosaur, Mansourasaurus shahinae gen...
January 29, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29369214/ginseng-for-improving-semen-quality-parameters-a-protocol-of-systematic-review
#10
Hye Won Lee, Ki-Jung Kil, YoungJoo Lee, Myeong Soo Lee
BACKGROUND: The aim of this systematic review is to determine whether ginseng is effective in improving sperm quality. METHODS AND ANALYSIS: Twelve databases will be searched from their inception to the present date: PubMed, EMBASE, AMED, the Cochrane Library, 5 Korean medical databases (KoreaMed, DBpia, OASIS, the Research Information Service System [RISS], and the Korean Studies Information Service System [KISS]), and 3 Chinese medical databases (China National Knowledge Infrastructure [CNKI], the Wanfang Database, and the Chinese Scientific Journals Database [VIP])...
January 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29358126/differential-mobility-spectrometry-followed-by-tandem-mass-spectrometry-with-multiple-ion-monitoring-for-bioanalysis-of-eptifibatide-in-rat-plasma
#11
Tianming Ren, Runzhi Li, Xiangjun Meng, J Paul Fawcett, Dong Sun, Jingkai Gu
Eptifibatide is a therapeutic cyclic peptide with poor collision-induced dissociation (CID) efficiency for multiple reaction monitoring (MRM), which limits the development of a traditional liquid chromatography-tandem mass spectrometry (LC-MS/MS) bioassay with MRM. In this study, a method combining differential mobility spectrometry (DMS) with liquid chromatography-multiple ion monitoring (LC-DMS-MIM) was developed for the quantitation of eptifibatide in rat plasma. After solid phase extraction (SPE) of 100 μL plasma on an Oasis® HLB cartridge, the analyte and I...
January 11, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29353810/development-and-validation-of-a-solid-phase-extraction-sample-cleanup-procedure-for-the-recovery-of-trace-levels-of-nitro-organic-explosives-in-soil
#12
Jennifer L Thomas, Christopher C Donnelly, Erin W Lloyd, Robert F Mothershead, Mark L Miller
An improved cleanup method has been developed for the recovery of trace levels of 12 nitro-organic explosives in soil, which is important not only for the forensic community, but also has environmental implications. A wide variety of explosives or explosive-related compounds were evaluated, including nitramines, nitrate esters, nitroaromatics, and a nitroalkane. Fortified soil samples were extracted with acetone, processed via solid phase extraction (SPE), and then analyzed by gas chromatography with electron capture detection...
December 19, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29324280/effective-phospholipids-removing-microelution-solid-phase-extraction-lc-ms-ms-method-for-simultaneous-plasma-quantification-of-aripiprazole-and-dehydro-aripiprazole-application-to-human-pharmacokinetic-studies
#13
Aneta Wojnicz, Carmen Belmonte, Dora Koller, Ana Ruiz-Nuño, Manuel Román, Dolores Ochoa, Francisco Abad Santos
A simple liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed and validated for simultaneous quantification of aripiprazole and its active metabolite, dehydro-aripiprazole, in human plasma. Stable isotopically labeled aripiprazole, aripiprazole-D8, has been used as the internal standard (IS) for both analytes. Only 200 μl of human plasma was needed for analyte extraction, using effective phospholipids-eliminating three-step microelution-solid-phase extraction (SPE, Oasis PRiME HLB 96-well μElution Plate)...
December 28, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29323424/in-vitro-and-in-vivo-effects-of-ophthalmic-solutions-on-silicone-hydrogel-bandage-lens-material-senofilcon-a
#14
Nejla B Erdal, Karin H Adolfsson, Sara De Lima, Minna Hakkarainen
BACKGROUND: Acuvue Oasys silicone hydrogel contact lenses (Senofilcon A) are used as bandage lenses and often combined with ophthalmic solutions in the treatment of ocular diseases. Concerns have been raised regarding the compatibility and effect of eye-drop solutions on the bandage lenses, which have led to frequent replacement of lenses causing clinical problems. Some patients experience pain or discomfort during treatments and the accumulation of drugs and preservatives in lenses has been suggested as a possible reason...
January 11, 2018: Clinical & Experimental Optometry: Journal of the Australian Optometrical Association
https://www.readbyqxmd.com/read/29318767/determination-of-synephrine-in-feeds-by-a-novel-quechers-solid-phase-extraction-method-combined-with-uhplc-ms-ms
#15
Yue Song, Tingting Chai, Shengting Lou, Yuechen Zhao, Xining Zhang, Shuming Yang, Yongzhong Qian, Jing Qiu
To detect and quantify synephrine in feed, an effective analytical method based on quick, easy, cheap, effective, rugged and safe solid-phase extraction coupled to ultra high performance liquid chromatography with tandem mass spectrometry was developed with isotopic internal standards. Pretreatment was performed using quick, easy, cheap, effective, rugged and safe solid-phase extraction with primary secondary amine (PSA) and C18 sorbent (C18) as sorbents in combination with Oasis MCX column clean-up to extract and purify feed samples...
January 10, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29306411/evaluating-solid-phase-micro-extraction-tools-to-analyze-freely-ionizable-and-permanently-charged-cationic-surfactants
#16
Niels Timmer, Peter Scherpenisse, Joop L M Hermens, Steven T J Droge
Working with and analysis of cationic surfactants can be problematic since aqueous concentrations are difficult to control, both when taking environmental aqueous samples as well as performing laboratory work with spiked concentrations. For a selection of 32 amine based cationic surfactants (including C8- to C18-alkylamines, C14-dialkyldimethylammonium, C8-tetraalkylammonium, benzalkonium and pyridinium compounds), the extraction from aqueous samples was studied in detail. Aqueous concentrations were determined using solid phase extraction (SPE; 3 mL/60 mg Oasis WCX-SPE cartridges) with recoveries of ≥80% for 30 compounds, and ≥90% for 16 compounds...
March 9, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29298307/persistent-differences-between-coastal-and-offshore-kelp-forest-communities-in-a-warming-gulf-of-maine
#17
Jon D Witman, Robert W Lamb
Kelp forests provide important ecosystem services, yet coastal kelp communities are increasingly altered by anthropogenic impacts. Kelp forests in remote, offshore locations may provide an informative contrast due to reduced impacts from local stressors. We tested the hypothesis that shallow kelp assemblages (12-15 m depth) and associated fish and benthic communities in the coastal southwest Gulf of Maine (GOM) differed significantly from sites on Cashes Ledge, 145 km offshore by sampling five coastal and three offshore sites at 43...
2018: PloS One
https://www.readbyqxmd.com/read/29274564/the-validity-and-reliability-of-screening-measures-for-depression-and-anxiety-disorders-in-multiple-sclerosis
#18
Ruth Ann Marrie, Lixia Zhang, Lisa M Lix, Lesley A Graff, John R Walker, John D Fisk, Scott B Patten, Carol A Hitchon, James M Bolton, Jitender Sareen, Renée El-Gabalawy, James J Marriott, Charles N Bernstein
OBJECTIVE: We aimed to evaluate the validity and reliability of multiple screening measures for depression and anxiety for use in the clinical care of people with multiple sclerosis (MS). METHODS: Participants with MS completed the Patient Health Questionnaire (PHQ-9), Hospital Anxiety and Depression Scale (HADS), Kessler-6 Distress Scale, PROMIS Emotional Distress Depression Short-Form 8a (PROMIS Depression) and Anxiety Short-Form 8a (PROMIS Anxiety), Generalized Anxiety Disorder 7-item Scale (GAD-7), and the Overall Anxiety and Severity Impairment Scale (OASIS)...
December 16, 2017: Multiple Sclerosis and related Disorders
https://www.readbyqxmd.com/read/29273992/multi-scale-analysis-of-the-relationship-between-landscape-patterns-and-a-water-quality-index-wqi-based-on-a-stepwise-linear-regression-slr-and-geographically-weighted-regression-gwr-in-the-ebinur-lake-oasis
#19
Xiaoping Wang, Fei Zhang
Water quality is highly dependent on landscape characteristics. This study explored the relationships between landscape patterns and water quality in the Ebinur Lake oasis in China. The water quality index (WQI) has been used to identify threats to water quality and contribute to better water resource management. This study established the WQI and analyzed the influence of landscapes on the WQI based on a stepwise linear regression (SLR) model and geographically weighted regression (GWR) models. The results showed that the WQI was between 56...
December 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29251672/the-role-of-omadacycline-in-skin-and-soft-tissue-infections
#20
Philippe Montravers, Alexy Tran Dinh, Sebastien Tanaka
PURPOSE OF REVIEW: Skin and soft tissue infections (SSTIs) are among the most frequent infections, contributing to significant morbidity and healthcare costs. Although numerous antibiotics are available for this indication, several medical needs remain unmet, especially for treating methicillin-resistant Staphylococcus aureus (MRSA) or mixed infections. This review summarizes the results achieved in the development of omadacycline, a new aminomethylcycline, which could have useful properties for the treatment of SSTIs...
December 14, 2017: Current Opinion in Infectious Diseases
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