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https://www.readbyqxmd.com/read/29035042/nmrml-a-community-supported-open-data-standard-for-the-description-storage-and-exchange-of-nmr-data
#1
Daniel Schober, Daniel Jacob, Michael Wilson, Joseph A Cruz, Ana Marcu, Jason R Grant, Annick Moing, Catherine Deborde, Luis F de Figueiredo, Kenneth Haug, Philippe Rocca-Serra, John M Easton, Timothy M D Ebbels, Jie Hao, Christian Ludwig, Ulrich L Günther, Antonio Rosato, Matthias S Klein, Ian Lewis, Claudio Luchinat, Andrew R Jones, Arturas Grauslys, Martin Larralde, Masashi Yokochi, Naohiro Kobayashi, Andrea Porzel, Julian Griffin, Mark R Viant, David S Wishart, Christoph Steinbeck, Reza M Salek, Steffen Neumann
NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters and, where available, spectral metadata such as chemical structures associated with spectral assignments...
October 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29021156/safety-and-accuracy-of-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-to-identify-highly-pathogenic-organisms
#2
James T Rudrik, Marty K Soehnlen, Michael J Perry, Maureen Sullivan, Wanda Reiter-Kintz, Philip A Lee, Denise Pettit, Anthony Tran, Erin Swaney
Matrix-assisted laser desorption ionization -- time of flight mass spectrometry (MALDI-TOF MS) sample preparation methods including the direct, on-plate formic acid, and ethanol/formic acid tube extraction were evaluated for their ability to render highly pathogenic organisms non-viable and safe for handling in a Biosafety Level-2 laboratory. Of these, the tube extraction procedure was the most successful, with none of the tested strains surviving this sample preparation method. Tube extracts from several agents of bioterrorism and their near neighbors were analyzed in an eight laboratory study to examine the utility of the Bruker Biotyper and Vitek MS MALDI-TOF MS systems and their IVD, research use only, and Security-Relevant databases, as applicable, to accurately identify these agents...
October 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28987027/formation-of-oxidative-and-non-oxidative-dimers-in-metallothioneins-implications-for-charge-state-analysis-for-structural-determination
#3
Gordon W Irvine, Lina Heinlein, Justin B Renaud, Mark W Sumarah, Martin J Stillman
RATIONALE: Metallothioneins (MTs) are a class of dynamic proteins that have been investigated extensively using mass spectrometric methods due to their amenability to ionization. Here we detect the formation of oxidative and non-oxidative MT dimers using high resolution mass spectrometry which has previously been overlooked with lower resolution techniques. METHODS: Recombinant human MT1a and its isolated domain fragments were analyzed by high-resolution Thermo Q-Exactive and Bruker-TOF MS...
October 7, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28981189/in-vivo-assessment-of-the-placental-anatomy-and-perfusion-in-a-mouse-model-of-intrauterine-inflammation
#4
Dan Wu, Jun Lei, Bei Jia, Han Xie, Yan Zhu, Jiadi Xu, Susumu Mori, Jiangyang Zhang, Irina Burd
BACKGROUND: Magnetic resonance imaging (MRI) provides useful markers to examine placental function. MRI features of placental injury due to intrauterine inflammation-a common risk during pregnancy, are not well known. PURPOSE: To investigate the capability of structural MRI and intravoxel incoherent motion (IVIM) imaging in examining acute placental injury in a mouse model of intrauterine inflammation, as well as gestation-dependent placental changes. STUDY TYPE: Prospective study...
October 5, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28976847/effect-of-light-activation-of-pulp-capping-materials-and-resin-composite-on-dentin-deformation-and-the-pulp-temperature-change
#5
C J Soares, M S Ferreira, A A Bicalho, M de Paula Rodrigues, Ssl Braga, A Versluis
OBJECTIVES: To analyze the effect of pulp-capping materials and resin composite light activation on strain and temperature development in the pulp and on the interfacial integrity at the pulpal floor/pulp-capping materials in large molar class II cavities. METHODS: Forty extracted molars received large mesio-occlusal-distal (MOD) cavity bur preparation with 1.0 mm of dentin remaining at the pulp floor. Four pulp-capping materials (self-etching adhesive system, Clearfil SE Bond [CLE], Kuraray), two light-curing calcium hydroxide cements (BioCal [BIO], Biodinâmica, and Ultra-Blend Plus [ULT], Ultradent), and a resin-modified glass ionomer cement- (Vitrebond [VIT], 3M ESPE) were applied on the pulpal floor...
October 4, 2017: Operative Dentistry
https://www.readbyqxmd.com/read/28963643/is-bone-analysis-with-%C3%AE-ct-useful-for-short-postmortem-interval-estimation
#6
Erwan Le Garff, Vadim Mesli, Elodie Marchand, Hélène Behal, Xavier Demondion, Anne Becart, Valery Hedouin
The evaluation of the postmortem interval (PMI) is an important consideration in forensic medicine. The time between death and the discovery thereof is extremely important, not only in terms of the legal process, but also for the course of the investigation. At the time of the discovery of human bones, the evaluation of the PMI is extremely difficult. To date, there is no really effective tool for this evaluation. The objective of our study is to characterize the architectural modifications of human bones using micro-tomography (μCT) in the postmortem period...
September 30, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28932775/spectral-and-raw-quasi-in-situ-energy-dispersive-x-ray-data-captured-via-a-tem-analysis-of-an-ods-austenitic-stainless-steel-sample-under-1%C3%A2-mev-kr-2-high-temperature-irradiation
#7
Adam J Brooks, Zhongwen Yao
The data presented in this article is related to the research experiment, titled: 'Quasi in-situ energy dispersive X-ray spectroscopy observation of matrix and solute interactions on Y-Ti-O oxide particles in an austenitic stainless steel under 1 MeV Kr(2+) high temperature irradiation' (Brooks et al., 2017) [1]. Quasi in-situ analysis during 1 MeV Kr(2+) 520 °C irradiation allowed the same microstructural area to be observed using a transmission electron microscope (TEM), on an oxide dispersion strengthened (ODS) austenitic stainless steel sample...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28932564/assessment-of-pulmonary-microstructural-changes-by-hyperpolarized-129-xe-diffusion-weighted-imaging-in-an-elastase-instilled-rat-model-of-emphysema
#8
Ke Wang, Ting Pan, Hao Yang, Weiwei Ruan, Jianping Zhong, Guangyao Wu, Xin Zhou
BACKGROUND: The purpose of this study was to explore the feasibility of hyperpolarized (129)Xe diffusion-weighted imaging (DWI) for the evaluation of pulmonary microstructural changes in the presence of pancreatic porcine elastase (PPE)-induced pulmonary emphysema rat model. METHODS: Sixteen male Sprague-Dawley (SD) rats were randomly divided into two groups, the emphysema model group and control group. Experimental emphysematous models were made by instilling elastase into rat lungs of model group, the control group were instilled with isodose saline...
August 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28929959/-in-vitro-effect-of-vancomycin-and-daptomycin-on-biofilm-formation-of-coagulase-negative-staphylococci-strains
#9
Duygu Nilüfer Öcal, İştar Dolapçı, Zeynep Gençtürk, Alper Tekeli
Coagulase-negative staphylococci (CNS) are one of the primer agents of blood stream infections (BSI) and catheter-related bloodstream infections (CR-BSI) which are associated mostly with the usage of central venous catheters and, important causes of morbidity and mortality despite the usage of antibacterial and supportive treatment. It is important to determine the properties of these causative microorganisms in order to make appropriate treatment of such infections. The aims of our study were to evaluate the biofilm formation of coagulase negative staphylococci (CNS) which were causative agents of bloodstream (BSI) and catheter related bloodstream infections (CR-BSI), to determine the minimum inhibitory concentration (MIC) of planktonic forms and minimal biofilm eradication concentration (MBEC) of sessile forms for vancomycin and daptomycin and to evaluate the efficacy of these antibiotics in infections with biofilm-forming isolates in vitro...
July 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28912147/performance-of-a-pet-insert-for-high-resolution-small-animal-pet-mr-imaging-at-7t
#10
Greg Stortz, Jonathan D Thiessen, Daryl Bishop, Muhammad S Khan, Piotr Kozlowski, Fabrice Retière, Graham Schellenberg, Ehsan Shams, Xuezhu Zhang, Christopher J Thompson, Andrew Goertzen, Vesna Sossi
We present the characterization of a compact magnetic resonance (MR) compatible positron emission tomography (PET) insert for simultaneous pre-clinical PET/MR imaging. While specifically designed with the strict size constraint to fit inside the 114 mm inner diameter of the BGA-12S gradient coil used in the Bruker 70/20 and 94/20 series of small animal MR imaging (MRI) systems, the insert can be easily installed in any appropriate MRI scanner or used as a stand-alone PET system. Methods: The insert is made from a ring of 16 detector-blocks each made from depth-of-interaction capable dual-layer-offset arrays of cerium-doped lutetium-yttrium oxyorthosilicate crystals read out by silicon photomultiplier (SiPM) arrays...
September 14, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28899453/application-of-maldi-tof-ms-systems-in-the-rapid-identification-of-campylobacter-spp-of-public-health-importance
#11
Ying-Hsin Hsieh, Yun F Wang, Hercules Moura, Nancy Miranda, Steven Simpson, Ramnath Gowrishankar, John Barr, Khalil Kerdahi, Irshad M Sulaiman
Campylobacteriosis is an infectious gastrointestinal disease caused by Campylobacter spp.In most cases, it is either underdiagnosed or underreported due to poor diagnostics and limited databases. Several DNA-based molecular diagnostic techniques, including 16S ribosomal RNA (rRNA) sequence typing, have been widely used in the species identification of Campylobacter. Nevertheless, these assays are time-consuming and require a high quality of bacterial DNA. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS is an emerging diagnostic technology that can provide the rapid identification of microorganisms by using their intact cells without extraction or purification...
September 12, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28895085/use-of-an-open-port-sampling-interface-coupled-to-electrospray-ionization-for-the-on-line-analysis-of-organic-aerosol-particles
#12
Kenneth D Swanson, Anne L Worth, Gary L Glish
A simple design for an open port sampling interface coupled to electrospray ionization (OPSI-ESI) is presented for the analysis of organic aerosols. The design uses minimal modifications to a Bruker electrospray (ESI) emitter to create a continuous flow, self-aspirating open port sampling interface. Considerations are presented for introducing aerosol to the open port sampling interface including aerosol gas flow and solvent flow rates. The device has been demonstrated for use with an aerosol of nicotine as well as aerosol formed in the pyrolysis of biomass...
September 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28887770/optimization-of-1-h-decoupling-eliminates-sideband-artifacts-in-3d-trosy-based-triple-resonance-experiments
#13
Youlin Xia, Paolo Rossi, Marco Tonelli, Chengdong Huang, Charalampos G Kalodimos, Gianluigi Veglia
TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality and hamper data analysis. Specifically, these experiments produce sidebands in the (13)C(t 1) dimension with inverted phase corresponding to (1)HN resonance frequencies, with approximately 5% intensity of the parent (13)C crosspeaks...
September 8, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28877672/chronic-lower-extremity-wound-infection-due-to-kerstersia-gyiorum-in-a-patient-with-buerger-s-disease-a-case-report
#14
Irmak Baran, Arife Polat Düzgün, İpek Mumcuoğlu, Neriman Aksu
BACKGROUND: Kerstersia gyiorum is an extremely rare pathogen of human infection. It can cause chronic infection in patients with underlying conditions. It can easily be misdiagnosed if proper diagnostic methods are not used. CASE PRESENTATION: A 47-year-old male patient with a history of Buerger's Disease for 28 years presented to our hospital with an infected chronic wound on foot. The wound was debrided, and the specimen was sent to Microbiology laboratory. Gram staining of the specimen showed abundant polymorphonuclear leukocytes and gram-negative bacilli...
September 6, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28846858/effects-of-dietary-induced-alterations-in-rat-brain-docosahexaenoic-acid-accrual-on-phospholipid-metabolism-and-mitochondrial-bioenergetics-an-in%C3%A2-vivo-31-p-mrs-study
#15
Diana M Lindquist, Ruth H Asch, Jennifer D Schurdak, Robert K McNamara
Evidence from (31)P magnetic resonance spectroscopy ((31)P MRS) studies suggest that different psychiatric disorders, which typically emerge during adolescence and young adulthood, are associated with abnormalities in mitochondrial bioenergetics and membrane phospholipid metabolism. These disorders are also associated with deficits in omega-3 polyunsaturated fatty acids (n-3 PUFA), including docosahexaenoic acid (DHA) which accumulates in mitochondrial and synaptic membranes. The present study investigated the effects of dietary-induced alterations in brain DHA accrual during adolescence on phospholipid metabolism and bioenergetics in the adult rat brain using (31)P MRS...
August 24, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28840993/comparison-of-a-new-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-platform-asta-microidsys-with-bruker-biotyper-for-species-identification
#16
Yangsoon Lee, Ji Yeon Sung, Hyunsoo Kim, Dongeun Yong, Kyungwon Lee
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, with its accuracy and speed, is widely used for bacterial identification. The ASTA MicroIDSys system (ASTA, Korea) was recently developed for species identification. We compared its performance with that of Bruker Biotyper (Bruker Daltonics, Germany). Microbes were recovered from sputum, urine, and pus samples from patients admitted to a tertiary care hospital in Korea from January to April 2016. Matrix solution (α-cyano-4-hydroxycinnamic acid) was used, and the peptide profiles acquired from the Microflex LT (Bruker Daltonics) and Tinkerbell LT (ASTA) were analyzed by using their respective software...
November 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28837671/development-of-acute-hydrocephalus-does-not-change-brain-tissue-mechanical-properties-in-adult-rats-but-in-juvenile-rats
#17
Alice C Pong, Lauriane Jugé, Lynne E Bilston, Shaokoon Cheng
INTRODUCTION: Regional changes in brain stiffness were previously demonstrated in an experimental obstructive hydrocephalus juvenile rat model. The open cranial sutures in the juvenile rats have influenced brain compression and mechanical properties during hydrocephalus development and the extent by which closed cranial sutures in adult hydrocephalic rat models affect brain stiffness in-vivo remains unclear. The aims of this study were to determine changes in brain tissue mechanical properties and brain structure size during hydrocephalus development in adult rat with fixed cranial volume and how these changes were related to brain tissue deformation...
2017: PloS One
https://www.readbyqxmd.com/read/28822458/-the-research-and-application-of-pretreatment-method-for-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-identification-of-filamentous-fungi
#18
Y F Huang, Z Chang, J Bai, M Zhu, M X Zhang, M Wang, G Zhang, X Y Li, Y G Tong, J L Wang, X X Lu
Objective: To establish and evaluate the feasibility of a pretreatment method for matrix-assisted laser desorption ionization-time of flight mass spectrometry identification of filamentous fungi developed by the laboratory. Methods: Three hundred and eighty strains of filamentous fungi from January 2014 to December 2016 were recovered and cultured on sabouraud dextrose agar (SDA) plate at 28 ℃ to mature state. Meanwhile, the fungi were cultured in liquid sabouraud medium with a vertical rotation method recommended by Bruker and a horizontal vibration method developed by the laboratory until adequate amount of colonies were observed...
August 8, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28817943/-maldi-tof-ms-comparison-of-blood-culture-positive-bottle-pretreatment-kit
#19
Takenori Yamashita
Identification of bacteria of sepsis or bacteremia is a useful result for treatment policy. In recent years, bacterial identification has become possible from blood culture bottles by MALDI‒TOF, but it is not as accurate as bacterial identification from agar colonies. Blood culture pretreatment kit (MALDI Sepcityper Kit) is currently on sale from Bruker. However, the current situation has not reached good accuracy. This time, a new blood culture pretreatment kit appeared, so I studied. Up to now, the blood culture pretreatment kit was only MALDI Sepcityper Kit using enzyme digestion method...
August 15, 2017: JARMAM: Journal of the Association for Rapid Method and Automation in Microbiology
https://www.readbyqxmd.com/read/28815683/phase-imaging-quality-improvement-by-modification-of-afm-probes-cantilever
#20
J Skibinski, J Rebis, L Kaczmarek, T Wejrzanowski, T Plocinski, K Rozniatowski
Imaging of the surface of materials by atomic force microscopy under tapping and phase imaging mode, with use of modified probes is addressed. In this study, the circularly shaped holes located in varying distance from the probe base, were cut out by focused ion beam. Such modification was a consequence of the results of the previous experiments (probe tip sharpening and cantilever thinning) where significant improvement of image quality in tapping and phase imaging mode has been revealed. The solution proposed herein gives similar results, but is much simpler from the technological point of view...
August 16, 2017: Journal of Microscopy
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