keyword
MENU ▼
Read by QxMD icon Read
search

design of experiments

keyword
https://www.readbyqxmd.com/read/28103438/acylguanidine-beta-secretase-1-inhibitors-a-combined-experimental-and-free-energy-perturbation-study
#1
Henrik Keränen, Laura Pérez-Benito, Myriam Ciordia, Francisca Delgado, Thomas B Steinbrecher, Daniel Oehlrich, Herman W T Van Vlijmen, Andrés A Trabanco, Gary Tresadern
A series of acylguanidine beta secretase 1 (BACE1) inhibitors with modified scaffold and P3 pocket substituent was synthesized and studied with Free Energy Perturbation (FEP) calculations. The resulting molecules showed potencies in enzymatic BACE1 inhibition assays up to 1 nM. The correlation between the predicted activity from the FEP calculations and the experimental activity was good for the P3 pocket substituents. The average mean unsigned error (MUE) between prediction and experiment was 0.68 ± 0.17 kcal/mol for the default 5 ns lambda window simulation time improving to 0...
January 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28103321/derivative-of-extremophilic-50s-ribosomal-protein-l35ae-as-an-alternative-protein-scaffold
#2
Anna V Lomonosova, Andrei B Ulitin, Alexei S Kazakov, Tajib A Mirzabekov, Eugene A Permyakov, Sergei E Permyakov
Small antibody mimetics, or alternative binding proteins (ABPs), extend and complement antibody functionality with numerous applications in research, diagnostics and therapeutics. Given the superiority of ABPs, the last two decades have witnessed development of dozens of alternative protein scaffolds (APSs) for the design of ABPs. Proteins from extremophiles with their high structural stability are especially favorable for APS design. Here, a 10X mutant of the 50S ribosomal protein L35Ae from hyperthermophilic archaea Pyrococcus horikoshii has been probed as an APS...
2017: PloS One
https://www.readbyqxmd.com/read/28103312/increased-cardiovascular-events-and-subclinical-atherosclerosis-in-rheumatoid-arthritis-patients-1-year-prospective-single-centre-study
#3
Piero Ruscitti, Paola Cipriani, Francesco Masedu, Silvio Romano, Onorina Berardicurti, Vasiliki Liakouli, Francesco Carubbi, Paola Di Benedetto, Saverio Alvaro, Maria Penco, Marco Valenti, Roberto Giacomelli
OBJECTIVES: Several studies showed the close relationship between Rheumatoid Arthritis (RA) and cerebro-cardiovascular events (CVEs) and subclinical atherosclerosis. In this study, we investigated the occurrence of CVEs and subclinical atherosclerosis during the course of RA and we evaluated the possible role of both traditional cardiovascular (CV) and disease related risk factors to predict the occurrence of new CVEs and the onset of subclinical atherosclerosis. METHODS: We designed a single centre, bias-adjusted, prospective, observational study to investigate, in a homogeneous subset of RA patients, the occurrence of new onset of CVEs and subclinical atherosclerosis...
2017: PloS One
https://www.readbyqxmd.com/read/28103283/orthogonal-procrustes-analysis-for-dictionary-learning-in-sparse-linear-representation
#4
Giuliano Grossi, Raffaella Lanzarotti, Jianyi Lin
In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error...
2017: PloS One
https://www.readbyqxmd.com/read/28103187/convexity-shape-prior-for-binary-segmentation
#5
Lena Gorelick, Olga Veksler, Yuri Boykov, Claudia Nieuwenhuis
Convexity is a known important cue in human vision. We propose shape convexity as a new high-order regularization constraint for binary image segmentation. In the context of discrete optimization, object convexity is represented as a sum of three-clique potentials penalizing any 1- 0- 1 configuration on all straight lines. We show that these non-submodular potentials can be efficiently optimized using an iterative trust region approach. At each iteration the energy is linearly approximated and globally optimized within a small trust region around the current solution...
February 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28102868/control-and-automation-of-multilayered-integrated-microfluidic-device-fabrication
#6
Sarit Kipper, Ludmila Frolov, Ortal Guy, Michal Pellach, Yair Glick, Asaf Malichi, Binyamin A Knisbacher, Efrat Barbiro-Michaely, Dorit Avrahami, Yehuda Yavets-Chen, Erez Y Levanon, Doron Gerber
Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications...
January 19, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28102825/versatile-modular-three-dimensional-microelectrode-arrays-for-neuronal-ensemble-recordings-from-design-to-fabrication-assembly-and-functional-validation-in-non-human-primates
#7
Falk Barz, Alessandro Livi, Marco Lanzilotto, Monica Maranesi, Luca Bonini, Oliver Paul, Patrick Ruther
<i>Objective. </i>Application-specific designs of electrode arrays offer an improved effectiveness for providing access to targeted brain regions in neuroscientific research and brain machine interfaces. The simultaneous and stable recording of neuronal ensembles is the main goal in the design of advanced neural interfaces. Here, we describe the development and assembly of highly customizable three-dimensional microelectrode arrays and demonstrate their recording performance in chronic applications in non-human primates...
January 19, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28102797/why-undertake-a-pilot-in-a-qualitative-phd-study-lessons-learned-to-promote-success
#8
Jane Wray, Uduak Archibong, Sean Walton
Background Pilot studies can play an important role in qualitative studies. Methodological and practical issues can be shaped and refined by undertaking pilots. Personal development and researchers' competence are enhanced and lessons learned can inform the development and quality of the main study. However, pilot studies are rarely published, despite their potential to improve knowledge and understanding of the research. Aim To present the main lessons learned from undertaking a pilot in a qualitative PhD study...
January 23, 2017: Nurse Researcher
https://www.readbyqxmd.com/read/28102792/a-study-exploring-the-protean-responses-of-nurses-transitioning-to-primary-healthcare
#9
Christine Ashley, Elizabeth Halcomb, Angela Brown
Background Healthcare systems are faced with changing community health profiles and ageing populations. Together with economic considerations, these factors have influenced the increase in provision of care in primary rather than other healthcare settings. Many nurses are electing to move from acute care to meet demands for a skilled primary healthcare workforce. However, little is reported about these nurses' experiences of transition. Aim To describe how role theory provides a theoretical framework to inform the design of a mixed-methods study exploring the transition of acute care nurses to roles in primary health care...
January 23, 2017: Nurse Researcher
https://www.readbyqxmd.com/read/28102768/an-experimental-strategy-validated-to-design-cost-effective-culture-media-based-on-response-surface-methodology
#10
J L Navarrete-Bolaños, G P Téllez-Martínez, R Miranda-López, H Jiménez-Islas
For any fermentation process, the production cost depends on several factors, such as the genetics of the microorganism, the process condition and the culture medium composition. In this work, a guideline for the design of cost-efficient culture media using a sequential approach based on response surface methodology is described. The procedure was applied to analyze and optimize a culture medium of registered trademark and a base culture medium obtained as a results of the screening analysis from different culture media used to grow the same strain according to the literature...
January 19, 2017: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/28102738/optimization-and-partial-characterization-of-intracellular-anticandidal-protein-from-aspergillus-giganteus-mtcc-8408-using-taguchi-doe
#11
Debashis Dutta, Mira Debnath Das
A new intracellular antifungal protein (afp) production with average molecular weight 24.3 kDa and yield of 0.65 ± 0.1 mg/gram dry cell weight (gdcw) of mycelia in submerged fermentation of Aspergillus giganteus MTCC 8408 was optimized. Taguchi's DOE (design of experiment) L27 orthogonal array (OA) was constructed using Qualitek-4 software with 8 most influensive factors namely, culture pH, temperature, slant age, inoculum volume, agitation and KH2PO4. Scanning electron microscopy (SEM) was used to correlate the effect of selected factors on fungal cell morphology and afp production...
January 19, 2017: Bioengineered
https://www.readbyqxmd.com/read/28102675/mechanistic-elucidation-of-zirconium-catalyzed-direct-amidation
#12
Helena Lundberg, Fredrik Tinnis, Jiji Zhang, Andrés G Algarra, Fahmi Himo, Hans Adolfsson
The mechanism of the zirconium-catalyzed condensation of carboxylic acids and amines for direct formation of amides was studied using kinetics, NMR-spectroscopy and DFT-calculations. The reaction is found to be first order with respect to catalyst and has a positive rate dependence on amine concentration and a negative rate dependence on carboxylic acid concentration. Kinetic experiments using Reaction Progress Kinetic Analysis (RPKA) protocols demonstrate that inhibition of the catalyst by the amide product can be avoided using a high amine concentration...
January 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28101704/molecular-cloning-and-gene-protein-expression-of-fat-cd36-from-grass-carp-ctenopharyngodon-idella-and-the-regulation-of-its-expression-by-dietary-energy
#13
Juan Tian, Wei Liu, Weihua Gao, Fan Wu, Lijuan Yu, Xing Lu, Chang-Geng Yang, Ming Jiang, Hua Wen
Fatty acid translocase/cluster of differentiation 36 (FAT/CD36) functions as a membrane long-chain fatty acid transporter in various tissues in land animals. Not much is known about the CD36 molecule in teleost fish. Therefore, we studied CD36 in grass carp (Ctenopharyngodon idella, ciCD36). The full-length complementary DNA sequence of ciCD36 was 1976 bp, with an ORF of 468 amino acids, which had high sequence similarity to the CD36 of common carp. The messenger RNA (mRNA) expression of ciCD36 was high in the intestine, heart, liver, visceral tissue, and brain, but absent in the kidney...
January 18, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/28101273/who-scared-the-cat-a-molecular-crime-scene-investigation-laboratory-exercise
#14
Laura E Ott, Susan D Carson
This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101272/isolation-and-characterization-of-agrobacterium-strains-from-soil-a-laboratory-capstone-experience
#15
Kim R Finer, Lee Fox, John J Finer
In this investigation, the students' goal was to isolate and characterize Agrobacterium strains from soil. Following selection and enrichment on 1A-t medium, putative Agrobacterium isolates were characterized by Gram stain reaction and biochemical tests. Isolates were further evaluated using polymerase chain reaction (PCR) with different primer sets designed to amplify specific regions of bacterial deoxyribonucleic acid (DNA). Primer sets included AGRH to identify isolates that were members of the Rhizobiaceae, BIOVAR1 primers to identify members of Agrobacterium biovar group I, and a third set, VIRG, to determine presence of virG (only present in pathogenic Agrobacterium strains)...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101271/the-impact-of-an-interactive-statistics-module-on-novices-development-of-scientific-process-skills-and-attitudes-in-a-first-semester-research-foundations-course
#16
Lynnsay A Marsan, Christina E D'Arcy, Jeffrey T Olimpo
Evidence suggests that incorporating quantitative reasoning exercises into existent curricular frameworks within the science, technology, engineering, and mathematics (STEM) disciplines is essential for novices' development of conceptual understanding and process skills in these domains. Despite this being the case, such studies acknowledge that students often experience difficulty in applying mathematics in the context of scientific problems. To address this concern, the present study sought to explore the impact of active demonstrations and critical reading exercises on novices' comprehension of basic statistical concepts, including hypothesis testing, experimental design, and interpretation of research findings...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101175/effect-of-mir-146a-and-mir-155-on-cardiac-xenotransplantation
#17
Zhicheng Zhao, Feng Qi, Tong Liu, Weihua Fu
The aim of the present study was to investigate the expression levels of miR-146a and miR-155 in a cardiac xenograft model treated with the immunosuppressant FK506, and to construct lentiviral vectors to further study the roles of miR-146a and miR-155 in cardiac xenotransplantation. Expression levels of miR-146a and miR-155 were examined by quantitative polymerase chain reaction analysis and protein expression of RelA, which is a member of the nuclear factor-κB family, was examined by western blot analysis...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28101134/single-cell-isolation-process-with-laser-induced-forward-transfer
#18
Yu Deng, Philippe Renaud, Zhongning Guo, Zhigang Huang, Ying Chen
BACKGROUND: A viable single cell is crucial for studies of single cell biology. In this paper, laser-induced forward transfer (LIFT) was used to isolate individual cell with a closed chamber designed to avoid contamination and maintain humidity. Hela cells were used to study the impact of laser pulse energy, laser spot size, sacrificed layer thickness and working distance. The size distribution, number and proliferation ratio of separated cells were statistically evaluated. Glycerol was used to increase the viscosity of the medium and alginate were introduced to soften the landing process...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28100829/a-mathematical-model-of-tumour-angiogenesis-growth-regression-and-regrowth
#19
Guillermo Vilanova, Ignasi Colominas, Hector Gomez
Cancerous tumours have the ability to recruit new blood vessels through a process called angiogenesis. By stimulating vascular growth, tumours get connected to the circulatory system, receive nutrients and open a way to colonize distant organs. Tumour-induced vascular networks become unstable in the absence of tumour angiogenic factors (TAFs). They may undergo alternating stages of growth, regression and regrowth. Following a phase-field methodology, we propose a model of tumour angiogenesis that reproduces the aforementioned features and highlights the importance of vascular regression and regrowth...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100559/what-is-involved-in-medicines-management-across-care-boundaries-a-qualitative-study-of-healthcare-practitioners-experiences-in-the-case-of-acute-kidney-injury
#20
Denham L Phipps, Rebecca L Morris, Tom Blakeman, Darren M Ashcroft
OBJECTIVES: To examine the role of individual and collective cognitive work in managing medicines for acute kidney injury (AKI), this being an example of a clinical scenario that crosses the boundaries of care organisations and specialties. DESIGN: Qualitative design, informed by a realist perspective and using semistructured interviews as the data source. The data were analysed using template analysis. SETTING: Primary, secondary and intermediate care in England...
January 18, 2017: BMJ Open
keyword
keyword
86599
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"