8,802 results on '"symbols"'
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2. War Through Other Means: Examining the Role of Symbols in Bosnia and Herzegovina
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Pauker, Iva, Simić, Olivera, editor, Volčič, Zala, editor, and Philpot, Catherine R., editor
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- 2012
- Full Text
- View/download PDF
3. A novel protein truncating mutation in L2HGDH causes L-2-hydroxyglutaric aciduria in a consanguineous Pakistani family
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Christian Enzinger, Jasmin Blatterer, Christian Windpassinger, Saadullah Khan, Klaus Wagner, Safeer Ahmad, Muhammad Zeeshan Ali, Muzammil Ahmad Khan, Erwin Petek, Syed Khizar Shah, Sundas Taj, Beatrice A. Brugger, and Muhammad Muzammal
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Male ,Intellectual disability ,Biochemistry ,Frameshift mutation ,Cellular and Molecular Neuroscience ,symbols.namesake ,Consanguinity ,medicine ,Humans ,Pakistan ,L2HGDH ,Exome ,Exome sequencing ,Genetics ,Sanger sequencing ,Cerebellar ataxia ,business.industry ,Macrocephaly ,Whole exome sequencing ,Leukoaraiosis ,N-terminal frameshift mutation ,Brain Diseases, Metabolic, Inborn ,Disease gene identification ,Alcohol Oxidoreductases ,L-2-hydroxyglutaric aciduria ,Mutation ,symbols ,Original Article ,Neurology (clinical) ,medicine.symptom ,business - Abstract
Background L-2-hydroxyglutaric aciduria (L2HGA) is a rare neurometabolic disorder that occurs due to accumulation of L-2-hydroxyglutaric acid in the cerebrospinal fluid (CSF), plasma and urine. The clinical manifestation of L2HGA includes intellectual disability, cerebellar ataxia, epilepsy, speech problems and macrocephaly. Methods In the present study, we ascertained a multigenerational consanguineous Pakistani family with 5 affected individuals. Clinical studies were performed through biochemical tests and brain CT scan. Locus mapping was carried out through genome-wide SNP genotyping, whole exome sequencing and Sanger sequencing. For in silico studies protein structural modeling and docking was done using I-TASSER, Cluspro and AutoDock VINA tools. Results Affected individuals presented with cognitive impairment, gait disturbance, speech difficulties and psychomotor delay. Radiologic analysis of a male patient revealed leukoaraiosis with hypoattenuation of cerebral white matter, suggestive of hypomyelination. Homozygosity mapping in this family revealed a linkage region on chromosome 14 between markers rs2039791 and rs781354. Subsequent whole exome analysis identified a novel frameshift mutation NM_024884.3:c.180delG, p.(Ala62Profs*24) in the second exon of L2HGDH. Sanger sequencing confirmed segregation of this mutation with the disease phenotype. The identification of the most N-terminal loss of function mutation published thus far further expands the mutational spectrum of L2HGDH.
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- 2021
4. Design and Evaluation of Multiplex One-Step Reverse Transcription PCR–Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens
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Peifeng Ke, Xiangsheng Yang, Hui Xiao, Ning Xu, Li Luo, Sheng Qin, Qiong Li, Qiang Luo, Zheng Shuilan, Zhenjie Liu, Qianming Chen, and Xianzhang Huang
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Sanger sequencing ,Mycoplasma pneumoniae ,Chromatography ,Respiratory tract infections ,SARS-CoV-2 ,COVID-19 ,General Medicine ,Dipstick ,Reverse Transcription ,Biology ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Microbiology ,Sensitivity and Specificity ,Article ,Reverse transcription polymerase chain reaction ,symbols.namesake ,Chlamydophila pneumoniae ,Multiplex polymerase chain reaction ,medicine ,symbols ,Humans ,Multiplex ,Multiplex Polymerase Chain Reaction - Abstract
Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens. Supplementary Information The online version contains supplementary material available at 10.1007/s00284-021-02621-7.
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- 2021
5. The mediating effect of literacy of LMS between self-evaluation online teaching effectiveness and self-directed learning readiness
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Sumi Han and Jeongchul Heo
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Self-Evaluation Online Teaching Effectiveness (SEOTE) ,media_common.quotation_subject ,Bivariate analysis ,Library and Information Sciences ,Literacy ,Article ,Education ,Developmental psychology ,symbols.namesake ,0502 economics and business ,Linear regression ,Self-directed Learning Readiness (SDLR) ,media_common ,Literacy of Learning Manage System (LLMS) ,05 social sciences ,Educational technology ,050301 education ,Regression analysis ,Variance (accounting) ,Pearson product-moment correlation coefficient ,Online Education ,Autodidacticism ,symbols ,050211 marketing ,Psychology ,0503 education - Abstract
The aim of this study was to analyze whether the self-evaluation online teaching effectiveness (SEOTE) and literacy of learning manage system (LLMS) did significantly have effect on the level of self-directed learning readiness (SDLR). Furthermore, it was another purpose to examine whether the LLMS was a significant mediating effect between SEOTE and SDLR. Pearson correlation, multiple linear regression, and mediated regression analysis were conducted for this study. This study included 210 online college students in Korea who responded to three web-survey questionnaires (SEOTE, LLMS, and SDLR). The bivariate (Pearson) correlation analysis showed that SEOTE significantly influenced on SDLR (r=524, p
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- 2021
6. Violating the normality assumption may be the lesser of two evils
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Ulrich Knief and Wolfgang Forstmeier
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Mixed model ,0106 biological sciences ,Heteroscedasticity ,Randomization ,Computer science ,media_common.quotation_subject ,Gaussian ,Linear model ,Monte Carlo method ,Extrapolation ,Normal Distribution ,Experimental and Cognitive Psychology ,010603 evolutionary biology ,01 natural sciences ,Article ,03 medical and health sciences ,symbols.namesake ,Arts and Humanities (miscellaneous) ,Overdispersion ,Developmental and Educational Psychology ,Econometrics ,Humans ,General Psychology ,Normality ,030304 developmental biology ,Statistical hypothesis testing ,media_common ,0303 health sciences ,Estimation theory ,Reproducibility of Results ,Random effects model ,Regression ,Hypothesis testing ,Data Interpretation, Statistical ,Sample Size ,Outlier ,symbols ,Analysis of variance ,Psychology (miscellaneous) ,Monte Carlo Method ,Type I and type II errors ,Count data - Abstract
When data are not normally distributed (e.g. skewed, zero-inflated, binomial, or count data) researchers are often uncertain whether it may be legitimate to use tests that assume Gaussian errors (e.g. regression, t-test, ANOVA, Gaussian mixed models), or whether one has to either model a more specific error structure or use randomization techniques.Here we use Monte Carlo simulations to explore the pros and cons of fitting Gaussian models to non-normal data in terms of risk of type I error, power and utility for parameter estimation.We find that Gaussian models are remarkably robust to non-normality over a wide range of conditions, meaning that P-values remain fairly reliable except for data with influential outliers judged at strict alpha levels. Gaussian models also perform well in terms of power and they can be useful for parameter estimation but usually not for extrapolation. Transformation of data before analysis is often advisable and visual inspection for outliers and heteroscedasticity is important for assessment. In strong contrast, some non-Gaussian models and randomization techniques bear a range of risks that are often insufficiently known. High rates of false-positive conclusions can arise for instance when overdispersion in count data is not controlled appropriately or when randomization procedures ignore existing non-independencies in the data.Overall, we argue that violating the normality assumption bears risks that are limited and manageable, while several more sophisticated approaches are relatively error prone and difficult to check during peer review. Hence, as long as scientists and reviewers are not fully aware of the risks, science might benefit from preferentially trusting Gaussian mixed models in which random effects account for non-independencies in the data in a transparent way.Tweetable abstractGaussian models are remarkably robust to even dramatic violations of the normality assumption.
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- 2021
7. Genetic Mosaicism as a Cause of Inborn Errors of Immunity
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Jahnavi Aluri and Megan A. Cooper
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0301 basic medicine ,Immunology ,Computational biology ,Biology ,primary immunodeficiency ,Genetic analysis ,Genome ,DNA sequencing ,Germline ,Diagnosis, Differential ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Germline mutation ,CME Review ,medicine ,Immunology and Allergy ,Humans ,somatic mutation ,Genetic Predisposition to Disease ,Exome ,Alleles ,Genetic Association Studies ,Germ-Line Mutation ,Genetic testing ,Sanger sequencing ,medicine.diagnostic_test ,Mosaicism ,Genetic Diseases, Inborn ,Immunity ,Inborn errors of immunity ,030104 developmental biology ,Phenotype ,Immune System Diseases ,Mutation ,symbols ,030215 immunology - Abstract
Inborn errors of immunity (IEIs) are a heterogeneous group of disorders due to genetic defects in the immune response that have a broad clinical spectrum. Diagnosis of the precise genetic cause of IEI has led to improved care and treatment of patients; however, genetic diagnosis using standard approaches is only successful in ~40% of patients and is particularly challenging in “sporadic” cases without a family history. Standard genetic testing for IEI evaluates for germline changes in genes encoding proteins important for the immune response. It is now clear that IEI can also arise from de novo mutations leading to genetic variants present in germ cells and/or somatic cells. In particular, somatic mosaicism, i.e., post-zygotic genetic changes in DNA sequence, is emerging as a significant contributor to IEI. Testing for somatic mosaicism can be challenging, and both older sequencing techniques such as Sanger sequencing and newer next-generation sequencing may not be sensitive enough to detect variants depending on the platform and analysis tools used. Investigation of multiple tissue samples and specifically targeting sequence technologies to detect low frequency variants is important for detection of variants. This review examines the role and functional consequences of genetic mosaicism in IEI. We emphasize the need to refine the current exome and genome analysis pipeline to efficiently identify mosaic variants and recommend considering somatic mosaicism in disease discovery and in the first-tier of genetic analysis.
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- 2021
8. Estimating duration distribution aided by auxiliary longitudinal measures in presence of missing time origin
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Yi Xiong, X. Joan Hu, and W. John Braun
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Mixed model ,Mixed effects model ,Interval censoring ,Canada ,Computer science ,Wiener process with random drift ,01 natural sciences ,Article ,First-hitting-time model ,010104 statistics & probability ,03 medical and health sciences ,symbols.namesake ,Wiener process ,Statistics ,Humans ,Computer Simulation ,0101 mathematics ,Joint modelling ,030304 developmental biology ,Event (probability theory) ,0303 health sciences ,Likelihood Functions ,Weak convergence ,Applied Mathematics ,Estimator ,General Medicine ,Empirical distribution function ,symbols ,Smoothing ,Algorithms - Abstract
Understanding the distribution of an event duration time is essential in many studies. The exact time to the event is often unavailable, and thus so is the full event duration. By linking relevant longitudinal measures to the event duration, we propose to estimate the duration distribution via the first-hitting-time model (e.g. Lee and Whitmore in Stat Sci 21(4):501–513, 2006). The longitudinal measures are assumed to follow a Wiener process with random drift. We apply a variant of the MCEM algorithm to compute likelihood-based estimators of the parameters in the longitudinal process model. This allows us to adapt the well-known empirical distribution function to estimate the duration distribution in the presence of missing time origin. Estimators with smooth realizations can then be obtained by conventional smoothing techniques. We establish the consistency and weak convergence of the proposed distribution estimator and present its variance estimation. We use a collection of wildland fire records from Alberta, Canada to motivate and illustrate the proposed approach. The finite-sample performance of the proposed estimator is examined by simulation. Viewing the available data as interval-censored times, we show that the proposed estimator can be more efficient than the well-established Turnbull estimator, an alternative that is often applied in such situations. Supplementary Information The online version contains supplementary material available at 10.1007/s10985-021-09520-w.
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- 2021
9. Maillard reaction in vivo and its relevance to diseases: editorial and dedication
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Motoko Takahashi and Naoyuki Taniguchi
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Maillard reaction ,symbols.namesake ,Editorial ,Chemistry ,In vivo ,symbols ,Relevance (information retrieval) ,Cell Biology ,Bioinformatics ,Molecular Biology ,Biochemistry - Published
- 2021
10. Reconstruction scheme for excitatory and inhibitory dynamics with quenched disorder: application to zebrafish imaging
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Francesco Vanzi, Gloria Cecchini, Ludovico Silvestri, Duccio Fanelli, Giuseppe de Vito, Lapo Turrini, Ihusan Adam, Roberto Livi, Francesco S. Pavone, and Lorenzo Chicchi
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0301 basic medicine ,Current (mathematics) ,Zebrafish larva ,Cognitive Neuroscience ,disorder, zebrafish, light-sheet, two-photon ,Models, Neurological ,FOS: Physical sciences ,Inverse ,Inhibitory postsynaptic potential ,Synthetic data ,Article ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,symbols.namesake ,0302 clinical medicine ,Animals ,Pareto distribution ,Zebrafish ,Physics ,Neurons ,Network reconstruction ,Quantitative Biology::Neurons and Cognition ,Heterogeneous mean field approximation ,Reconstruction algorithm ,Disordered Systems and Neural Networks (cond-mat.dis-nn) ,Leak integrate and fire ,Condensed Matter - Disordered Systems and Neural Networks ,Sensory Systems ,030104 developmental biology ,Distribution (mathematics) ,Quantitative Biology - Neurons and Cognition ,FOS: Biological sciences ,Excitatory postsynaptic potential ,symbols ,Neurons and Cognition (q-bio.NC) ,Biological system ,030217 neurology & neurosurgery ,Algorithms ,Neuroscience - Abstract
An inverse procedure is developed and tested to recover functional and structural information from global signals of brains activity. The method assumes a leaky-integrate and fire model with excitatory and inhibitory neurons, coupled via a directed network. Neurons are endowed with a heterogenous current value, which sets their associated dynamical regime. By making use of a heterogenous mean-field approximation, the method seeks to reconstructing from global activity patterns the distribution of in-coming degrees, for both excitatory and inhibitory neurons, as well as the distribution of the assigned currents. The proposed inverse scheme is first validated against synthetic data. Then, time-lapse acquisitions of a zebrafish larva recorded with a two-photon light sheet microscope are used as an input to the reconstruction algorithm. A power law distribution of the in-coming connectivity of the excitatory neurons is found. Local degree distributions are also computed by segmenting the whole brain in sub-regions traced from annotated atlas.
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- 2021
11. Stieltjes constants of L-functions in the extended Selberg class
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Sumaia Saad Eddin, Ade Irma Suriajaya, and Shōta Inoue
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Algebra and Number Theory ,L-function ,Laurent series ,010102 general mathematics ,Stieltjes constants ,010103 numerical & computational mathematics ,01 natural sciences ,Upper and lower bounds ,Article ,Combinatorics ,symbols.namesake ,11N37 ,Number theory ,Laurent–Stieltjes constant ,11Y60 ,Extended Selberg class ,symbols ,Arithmetic function ,0101 mathematics ,Selberg class ,Dirichlet series ,Upper bound ,Mathematics - Abstract
Let f be an arithmetic function and let $${\mathcal {S}}^\#$$ S # denote the extended Selberg class. We denote by $${\mathcal {L}}(s) = \sum _{n = 1}^{\infty }\frac{f(n)}{n^s}$$ L ( s ) = ∑ n = 1 ∞ f ( n ) n s the Dirichlet series attached to f. The Laurent–Stieltjes constants of $${\mathcal {L}}(s)$$ L ( s ) , which belongs to $${\mathcal {S}}^\#$$ S # , are the coefficients of the Laurent expansion of $${\mathcal {L}}$$ L at its pole $$s=1$$ s = 1 . In this paper, we give an upper bound of these constants, which is a generalization of many known results.
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- 2021
12. On Regularization Based Twin Support Vector Regression with Huber Loss
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Deepak Gupta and Umesh Gupta
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0209 industrial biotechnology ,Computer Networks and Communications ,Computer science ,Gaussian ,02 engineering and technology ,Laplacian noise ,Regularization (mathematics) ,Gaussian noise ,Article ,symbols.namesake ,020901 industrial engineering & automation ,Singularity ,Huber loss ,Artificial Intelligence ,0202 electrical engineering, electronic engineering, information engineering ,Twin support vector regression ,General Neuroscience ,Support vector machine ,Noise ,Support vector regression ,Outlier ,symbols ,020201 artificial intelligence & image processing ,Algorithm ,Software - Abstract
Twin support vector regression (TSVR) is generally employed with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \varepsilon $$\end{document}ε-insensitive loss function which is not well capable to handle the noises and outliers. According to the definition, Huber loss function performs as quadratic for small errors and linear for others and shows better performance in comparison to Gaussian loss hence it restrains easily for a different type of noises and outliers. Recently, TSVR with Huber loss (HN-TSVR) has been suggested to handle the noise and outliers. Like TSVR, it is also having the singularity problem which degrades the performance of the model. In this paper, regularized version of HN-TSVR is proposed as regularization based twin support vector regression (RHN-TSVR) to avoid the singularity problem of HN-TSVR by applying the structured risk minimization principle that leads to our model convex and well-posed. This proposed RHN-TSVR model is well capable to handle the noise as well as outliers and avoids the singularity issue. To show the validity and applicability of proposed RHN-TSVR, various experiments perform on several artificial generated datasets having uniform, Gaussian and Laplacian noise as well as on benchmark different real-world datasets and compare with support vector regression, TSVR, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \varepsilon $$\end{document}ε-asymmetric Huber SVR, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \varepsilon $$\end{document}ε-support vector quantile regression and HN-TSVR. Here, all benchmark real-world datasets are embedded with a different significant level of noise 0%, 5% and 10% on different reported algorithms with the proposed approach. The proposed algorithm RHN-TSVR is showing better prediction ability on artificial datasets as well as real-world datasets with a different significant level of noise compared to other reported models.
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- 2021
13. Stimulated Low-Frequency Raman Scattering in Brome Mosaic Virus
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T. V. Mironova, M. V. Arkhipenko, N. V. Tcherniega, S. F. Umanskaya, Sergey M. Pershin, Anna D. Kudryavtseva, V. I. Savichev, Maxim Karpov, Olga Karpova, and M. A. Shevchenko
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Materials science ,02 engineering and technology ,Low frequency ,01 natural sciences ,Molecular physics ,Article ,010309 optics ,symbols.namesake ,020210 optoelectronics & photonics ,Brome mosaic virus ,brome mosaic virus ,0103 physical sciences ,0202 electrical engineering, electronic engineering, information engineering ,viruses ,Suspension (vehicle) ,acoustics ,Engineering (miscellaneous) ,eigenfrequency ,biology ,stimulated low-frequency Raman scattering ,Phosphate buffered saline ,Energy conversion efficiency ,biology.organism_classification ,Atomic and Molecular Physics, and Optics ,resonance impact ,Quadrupole ,symbols ,Raman scattering - Abstract
We experimentally register stimulated low-frequency Raman scattering (SLFRS) in the suspension of brome mosaic virus (BMV) in phosphate buffer with very high conversion efficiency. We identify two components of the SLFRS spectrum as the breathing and quadrupole modes of BMV and determine damping characteristics and gain factors for these modes. We show that, using the core–shell model for BMV and taking into account the influence of the environment, the acoustic properties of individual components of such a composite nanosystem can be determined. Thus, we define the sound velocity in the RNA core of BMV, in view of spectral characteristics of SLFRS.
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- 2021
14. The use of segmented regression for evaluation of an interrupted time series study involving complex intervention: the CaPSAI project experience
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James Kiarie, My Huong Nguyen, Soe Soe Thwin, Victoria Boydell, Joanna Paula Cordero, Donat Shamba, Dela Nai, Petrus S. Steyn, and Ndema Habib
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Computer science ,Quasi-experiment ,Interrupted time series ,Poisson distribution ,01 natural sciences ,Gee ,Article ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Complex intervention ,Intervention (counseling) ,Statistics ,030212 general & internal medicine ,Poisson regression ,0101 mathematics ,Segmented regression ,Modern contraception uptake ,Generalized estimating equation ,Health Policy ,010102 general mathematics ,Community-driven intervention ,Public Health, Environmental and Occupational Health ,Regression ,symbols - Abstract
An interrupted time series with a parallel control group (ITS-CG) design is a powerful quasi-experimental design commonly used to evaluate the effectiveness of an intervention, on accelerating uptake of useful public health products, and can be used in the presence of regularly collected data. This paper illustrates how a segmented Poisson model that utilizes general estimating equations (GEE) can be used for the ITS-CG study design to evaluate the effectiveness of a complex social accountability intervention on the level and rate of uptake of modern contraception. The intervention was gradually rolled-out over time to targeted intervention communities in Ghana and Tanzania, with control communities receiving standard of care, as per national guidelines. Two ITS GEE segmented regression models are proposed for evaluating of the uptake. The first, a two-segmented model, fits the data collected during pre-intervention and post-intervention excluding that collected during intervention roll-out. The second, a three-segmented model, fits all data including that collected during the roll-out. A much simpler difference-in-difference (DID) GEE Poisson regression model is also illustrated. Mathematical formulation of both ITS-segmented Poisson models and that of the DID Poisson model, interpretation and significance of resulting regression parameters, and accounting for different sources of variation and lags in intervention effect are respectively discussed. Strengths and limitations of these models are highlighted. Segmented ITS modelling remains valuable for studying the effect of intervention interruptions whether gradual changes, over time, in the level or trend in uptake of public health practices are attributed by the introduced intervention.Trial Registration: The Australian New Zealand Clinical Trials registry.Trial registration number: ACTRN12619000378123.Trial Registration date: 11-March-2019.
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- 2020
15. Feasibility, Acceptance, and Safety of Metacognitive Training for Problem and Pathological Gamblers (Gambling-MCT): A Pilot Study
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Steffen Moritz, Josefine Gehlenborg, Mira Berthold, Franziska Miegel, and Lara Bücker
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Adult ,Male ,Sociology and Political Science ,Psychological intervention ,030508 substance abuse ,Metacognition ,Pilot Projects ,law.invention ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Randomized controlled trial ,law ,Interim ,Intervention (counseling) ,Humans ,General Psychology ,Protocol (science) ,Original Paper ,Cognitive Behavioral Therapy ,Cognition ,Feasibility ,Middle Aged ,Patient Acceptance of Health Care ,Self Concept ,030227 psychiatry ,Treatment ,Acceptance ,Bonferroni correction ,Treatment Outcome ,Gambling ,symbols ,Feasibility Studies ,Female ,Safety ,0305 other medical science ,Psychology ,Clinical psychology - Abstract
Approximately 90% of problem and pathological gamblers remain untreated. This treatment gap may be diminished by the implementation of low-threshold treatment programs. As cognitive distortions play a crucial role in the development and maintenance of gambling problems, interventions targeting gambling-related biases may be particularly effective. The aim of the present study was to examine the feasibility, acceptance, and safety of a novel metacognitive training for individuals with gambling problems (Gambling-MCT). Twenty-five participants were included in an uncontrolled pilot trial with two assessment points (intervention). The intervention comprised eight training modules targeting gambling-specific cognitive distortions. At baseline and post assessment, symptom severity, as measured with the PG-YBOCS, and gambling-related cognitive distortions, as measured with the GABS, were assessed. In addition, interim assessments measuring session-specific changes were conducted. Subjective appraisal was examined after each module and also post treatment. On average, participants took part in 4.16 (SD = 2.84) training sessions. Both intent-to-treat and per protocol analyses showed significant improvements on the PG-YBOCS and the GABS (dz = 0.37–1.37). After Bonferroni correction for multiple testing, linear mixed models for the analysis of session-specific changes showed no deterioration in participants’ mental state after any of the modules. Subjective appraisal of Gambling-MCT was good. The present pilot study provides first evidence for the feasibility, acceptance, and safety of Gambling-MCT. Recruitment of participants remains challenging, emphasizing the importance of overcoming patient-related treatment barriers. Future studies need to investigate the efficacy of Gambling-MCT in randomized controlled trials. Electronic supplementary material The online version of this article (10.1007/s10899-020-09975-w) contains supplementary material, which is available to authorized users.
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- 2020
16. Expand or Oversize? Planning Internet Access Network in a Demand Growth Scenario
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Thiago Melo Machado-Coelho, Gustavo Luís Soares, Matheus Pereira Libório, Renata de Mello Lyrio, Petr Iakovlevitch Ekel, and Patrícia Campos Bernardes
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business.product_category ,Operations research ,Computer Networks and Communications ,Computer science ,business.industry ,Geoprocessing ,Strategy and Management ,Optimization algorithms ,Decision problem ,Demand forecasting ,Investment (macroeconomics) ,Passive optical network ,Steiner tree problem ,Article ,Network planning strategies ,symbols.namesake ,Hardware and Architecture ,Network service ,Internet access ,symbols ,The Internet ,business ,Internet forecast model ,Information Systems ,Decision-making - Abstract
Internet network design specialists are looking for technologies and strategies to deliver network service under increased demand conditions. The choice of strategies is based on applying optimization and decision-making methods to select the most appropriate cable network design considering criteria established by the problem definition. However, this definition is itself a decision problem that has not received analysis in the literature. In particular, one of the most important questions is the necessity to define an expansion strategy. The first alternative (expansion) is to design a network to serve consumers with Internet demand equal to or greater than the predefined one to expand the network annually to serve consumers that reach the predefined Internet speed. The second alternative (oversizing) is to design a network to serve consumers with future Internet demand (after 5 years) at or above that the predefined one. Considering this, the objective of this research is to define the most advantageous strategy of expansion planning to attend a 5 years forecasted Internet demand, considering: (1) the possibility of utilizing a Gigabit-capable Passive Optical Network technology; (2) the application of the minimal Steiner tree and Dijkstra algorithms in planning procedures; (3) the influence of economic and technological factors on the demand forecast; (4) the aggressive, moderate, and conservative scenarios in decision-making. The results show that the over-dimensioning strategy reduces network investment by between 30 and 41%, but that this reduction does not always lead to a market investment ratio higher than that observed in the expansion strategy.
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- 2020
17. Global Dynamics of a Susceptible-Infectious-Recovered Epidemic Model with a Generalized Nonmonotone Incidence Rate
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Shigui Ruan, Min Lu, Pei Yu, and Jicai Huang
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Hopf bifurcation ,Cusp (singularity) ,010102 general mathematics ,Degenerate energy levels ,Multiplicity (mathematics) ,Saddle-node bifurcation ,Codimension ,Degenerate Hopf bifurcation of codimension three ,01 natural sciences ,Article ,010101 applied mathematics ,Combinatorics ,symbols.namesake ,Nilpotent ,symbols ,Quantitative Biology::Populations and Evolution ,Generalized nonmonotone incidence rate ,Backward bifurcation ,Bogdanov–Takens bifurcation of codimension three ,0101 mathematics ,Analysis ,Bifurcation ,Mathematics ,SIRS epidemic model - Abstract
A susceptible-infectious-recovered (SIRS) epidemic model with a generalized nonmonotone incidence rate \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\frac{kIS}{1+\beta I+\alpha I^2}$$\end{document}kIS1+βI+αI2 (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta >-2 \sqrt{\alpha }$$\end{document}β>-2α such that \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1+\beta I+\alpha I^{2}>0$$\end{document}1+βI+αI2>0 for all \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$I\ge 0$$\end{document}I≥0) is considered in this paper. It is shown that the basic reproduction number \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R_0$$\end{document}R0 does not act as a threshold value for the disease spread anymore, and there exists a sub-threshold value \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R_*(
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- 2020
18. Probes for Fluorescent Visualization of Specific Cellular Organelles
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Timothy P. Foster
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Chemistry ,Endoplasmic reticulum ,Mitochondrion ,Golgi apparatus ,Fluorescence ,Cell biology ,Visualization ,symbols.namesake ,medicine.anatomical_structure ,Lysosome ,Organelle ,symbols ,medicine ,Actin - Abstract
The defining characteristic of eukaryotic cells is the segregation of critical cellular functions within various membrane bound cellular organelles, including the nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, and mitochondria. Cell biologists therefore have extensively utilized organelle specific counterstains to help identify the localization of specific proteins or other targets of interest in order to garner an understanding of either their potential functions or their effects on the cell. There currently is a wide array of fluorescent dyes and reagents that can be utilized in live and fixed cells to identify organelles, thereby creating challenges in both choosing between the plethora of options and optimizing their use. Here we present a discussion of commonly utilized commercially available organelle dyes and summarize the factors that influence selection of the various dyes for: a given organelle; live versus fixed cellular conditions; adaptation to a specific protocol; spectral multiplexing; or matching excitation/emission spectra to available imaging equipment. Also presented are recommended protocols for a typical example reagent that can be reliably utilized to visualize its target cellular organelle.
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- 2021
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- View/download PDF
19. Clinical Translation of Stimulated Raman Histology
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Todd C. Hollon, Cordelia Orillac, and Daniel A. Orringer
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Microscope ,Materials science ,Histology ,Laser ,Signal ,law.invention ,symbols.namesake ,law ,Microscopy ,symbols ,Raman spectroscopy ,Raman scattering ,Biomedical engineering ,Macromolecule - Abstract
Stimulated Raman histology (SRH) images are created by the label-free, nondestructive imaging of tissue using stimulated Raman scattering (SRS) microscopy. In a matter of seconds, these images provide real-time histologic information on biopsied tissue in the operating room. SRS microscopy uses two lasers (pump beam and Stokes beam) to amplify the Raman signal of specific chemical bonds found in macromolecules (lipids, proteins, and nucleic acids) in these tissues. The concentrations of these macromolecules are used to produce image contrast. These images are acquired and displayed using an imaging system with five main components: (1) fiber coupled microscope, (2) dual-wavelength fiber-laser module, (3) laser control module, (4) microscope control module, and (5) a computer. This manuscript details how to assemble the dual-wavelength fiber-laser module and how to generate an SRH image.
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- 2021
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20. Validation of Circular RNAs by PCR
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Debojyoti Das, Aniruddha Das, and Amaresh C. Panda
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Large class ,Exonuclease ,Sanger sequencing ,biology ,Chemistry ,RNA ,Molecular biology ,Reverse transcriptase ,law.invention ,symbols.namesake ,Rolling circle replication ,law ,biology.protein ,symbols ,Northern blot ,Polymerase chain reaction - Abstract
High-throughput RNA-sequencing (RNA-seq) technologies combined with novel bioinformatic algorithms discovered a large class of covalently closed single-stranded RNA molecules called circular RNAs (circRNAs ). Although RNA-seq has identified more than a million circRNAs, only a handful of them is validated with other techniques, including northern blotting, gel-trap electrophoresis, exonuclease treatment assays, and polymerase chain reaction (PCR). Reverse transcription (RT) of total RNA followed by PCR amplification is the most widely used technique for validating circRNAs identified in RNA-seq. RT-PCR is a highly reproducible, sensitive, and quantitative method for the detection and quantitation of circRNAs. This chapter details the basic guidelines for designing suitable primers for PCR amplification and validation of circRNAs .
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- 2021
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21. Metabolic Labeling of Proteoglycans and Analysis of Their Synthesis and Sorting in Filter-Grown and Polarized Epithelial Cells
- Author
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Ravi Adusumalli and Kristian Prydz
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Chemistry ,Endocytic cycle ,Golgi apparatus ,Epithelium ,Cell biology ,Glycosaminoglycan ,symbols.namesake ,medicine.anatomical_structure ,symbols ,medicine ,Secretion ,Intracellular ,Epithelial polarity ,Lumen (unit) - Abstract
Studies of synthesis, turnover, and secretion of macromolecules in cell culture are carried out to address mechanisms of cellular and physiological importance. Culture systems have been developed to mimic the in vivo situation as much as possible. In line with this aim, epithelial and endothelial cells have been grown on filters for more than three decades. Growing such cells on permeable support allows for nutrient uptake via the basolateral membrane of tight epithelial monolayers, from a medium reservoir underneath the filter. While this basolateral medium reservoir resembles the blood supply, the apical medium reservoir resembles the organ lumen. Growing the cells in a polarized manner allows for studies of differential transport and localization of apical and basolateral proteins and of endocytic and secretory transport at both sides of the epithelium. Here we describe how metabolic labeling of proteoglycans (PGs) with 35S-labeled sulfate enables analysis of synthesis of different types of PGs, with respect to size, glycosaminoglycan (GAG) chain length, and charge. We also describe protocols for studies of intracellular PG sorting, in the apical and basolateral direction in polarized epithelial cells, in the absence and presence of inhibitors of synthesis and transport.
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- 2021
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22. Analysis of 3′-Phosphoadenosine 5′-Phosphosulfate Transporters: Transporter Activity Assay, Real-Time Reverse Transcription Polymerase Chain Reaction, and Immunohistochemistry
- Author
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Shoko Nishihara and Hideo Egawa
- Subjects
Reverse transcription polymerase chain reaction ,chemistry.chemical_compound ,symbols.namesake ,3'-Phosphoadenosine-5'-phosphosulfate ,Cytosol ,Sulfation ,chemistry ,Biochemistry ,symbols ,Transporter ,Sulfuryl ,Golgi apparatus ,Yeast - Abstract
3'-Phosphoadenosine 5'-phosphosulfate transporters (PAPSTs) play an important role in transporting 3'-phosphoadenosine 5'-phosphosulfate (PAPS), the universal sulfuryl donor for sulfation, from the cytosol into the lumen of the Golgi apparatus. Here, we describe three methods for the analysis of PAPST; a transporter activity assay with yeast or mammalian cell fraction, real-time reverse transcription polymerase chain reaction on tissue samples, and immunohistochemistry on brain sections.
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- 2021
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23. One-Pot Enzymatic Synthesis of Heparin from N-Sulfoheparosan
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Robert J. Linhardt and Li Fu
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chemistry.chemical_classification ,Anticoagulant drug ,Chemistry ,Heparin ,Heparan sulfate ,Golgi apparatus ,medicine.disease_cause ,law.invention ,Glycosaminoglycan ,symbols.namesake ,chemistry.chemical_compound ,Enzyme ,Biochemistry ,law ,medicine ,symbols ,Recombinant DNA ,Escherichia coli ,medicine.drug - Abstract
Heparin, a glycosaminoglycan-based anticoagulant drug, is prepared as an extract of animal tissues. Heparosan, an Escherichia coli (E. coli) K5 capsular polysaccharide with the structure →4)-β-D-glucuronic acid (1 → 4)-β-D-N-acetylglucosamine (1→, corresponds to the precursor backbone in the Golgi-based biosynthesis of heparin. Anticoagulant heparin is prepared in a one-pot synthesis using a chemically prepared derivative of heparosan called N-sulfoheparosan (NSH), recombinant Golgi enzymes expressed in E. coli, and the 3-phosphoadenosine-5-phosphosulfate (PAPS) cofactor.
- Published
- 2021
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24. Computational Modeling of Glycan Processing in the Golgi for Investigating Changes in the Arrangements of Biosynthetic Enzymes
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A. Jamie Wood, Daniel Ungar, and Ben West
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Glycan biosynthesis ,Glycan ,Glycosylation ,biology ,Computer science ,Computational biology ,Golgi apparatus ,Biosynthetic enzyme ,carbohydrates (lipids) ,chemistry.chemical_compound ,symbols.namesake ,chemistry ,Proof of concept ,Stochastic simulation ,biology.protein ,symbols ,Approximate Bayesian computation - Abstract
Modeling glycan biosynthesis is becoming increasingly important due to the far-reaching implications that glycosylation can exhibit, from pathologies to biopharmaceutical manufacturing. Here we describe a stochastic simulation approach, to overcome the deterministic nature of previous models, that aims to simulate the action of glycan modifying enzymes to produce a glycan profile. This is then coupled with an approximate Bayesian computation methodology to systematically fit to empirical data in order to determine which set of parameters adequately describes the organization of enzymes within the Golgi. The model is described in detail along with a proof of concept and therapeutic applications.
- Published
- 2021
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25. Recent Advances Toward Engineering Glycoproteins Using Modified Yeast Display Platforms
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Anjali Shenoy and Adam W. Barb
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chemistry.chemical_classification ,Glycan ,Glycosylation ,biology ,Computational biology ,Protein engineering ,Golgi apparatus ,Yeast display ,Yeast ,symbols.namesake ,chemistry.chemical_compound ,chemistry ,biology.protein ,symbols ,Glycoprotein ,Function (biology) - Abstract
Yeast are capable recombinant protein expression hosts that provide eukaryotic posttranslational modifications such as disulfide bond formation and N-glycosylation. This property has been used to create surface display libraries for protein engineering; however, yeast surface display (YSD) with common laboratory strains has limitations in terms of diversifying glycoproteins due to the incorporation of high levels of mannose residues which often obscure important epitopes and are immunogenic in humans. Developing new strains for efficient and appropriate display will require combining existing technologies to permit efficient glycoprotein engineering. Foundational efforts generating knockout strains lacking characteristic hypermannosylation reactions exhibited morphological defects and poor growth. Later strains with "humanized" N-glycosylation machinery surmounted these limitations by targeting a small suite of glycosylhydrolase and glycosyltransferase enzymes from other taxa to the endoplasmic reticulum and Golgi. Advanced yeast strains also provide key modifications at the glycan termini that are essential for the full function of many glycoproteins. Here we review progress toward glycoprotein engineering when glycosylation is required for full function using advanced yeast expression platforms and the suitability of each for YSD of glycoproteins.
- Published
- 2021
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26. Quantification of Mitochondrial RNA Editing Efficiency Using Sanger Sequencing Data
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Mizuki Takenaka
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chemistry.chemical_classification ,Sanger sequencing ,Computational biology ,Mitochondrion ,Biology ,ENCODE ,Amino acid ,symbols.namesake ,Real-time polymerase chain reaction ,chemistry ,RNA editing ,Organelle ,symbols ,Plastid - Abstract
C-to-U RNA editing in mitochondria and plastids is widespread in almost all terrestrial plants, where it mainly changes codons to encode conserved amino acids in organelle mRNAs. In flowering plants, the number of RNA editing sites reaches 400-600 in mitochondria and about 40 in plastids, respectively. To date, more than 100 factors involved in RNA editing have been identified. Since target cytidines of each factor are often distributed across multiple transcripts, comprehensive monitoring of all RNA editing sites is necessary for their characterization. Comparing the signals of C and T in the Sanger sequencing chromatogram of RT-PCR products is the most frequently employed method for quantification of RNA editing efficiency, although several methods based on next-generation sequencing have been developed. I here describe a quick and easy method for quantification of RNA editing efficiency at several hundred sites using the Sanger sequencing chromatogram data.
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- 2021
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27. Anytime parallel tempering
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Sumeetpal S. Singh, Lawrence Murray, Alix Marie d’Avigneau, Marie d’Avigneau, Alix [0000-0001-8229-6850], Apollo - University of Cambridge Repository, and Marie d’Avigneau, A [0000-0001-8229-6850]
- Subjects
FOS: Computer and information sciences ,Statistics and Probability ,Computer science ,Monte Carlo method ,Bayesian inference ,Inference ,Cloud computing ,Parallel computing ,Statistics - Computation ,Article ,Theoretical Computer Science ,symbols.namesake ,State space ,62-08, 62F15 ,Computation (stat.CO) ,business.industry ,Markov chain Monte Carlo ,Anytime Monte Carlo ,Markov chain Monte Carlo (MCMC ) ,Parallel tempering ,Task (computing) ,Approximate Bayesian computation (ABC ) ,Computational Theory and Mathematics ,symbols ,Likelihood-free inference ,Statistics, Probability and Uncertainty ,business - Abstract
Developing efficient MCMC algorithms is indispensable in Bayesian inference. In parallel tempering, multiple interacting MCMC chains run to more efficiently explore the state space and improve performance. The multiple chains advance independently through local moves, and the performance enhancement steps are exchange moves, where the chains pause to exchange their current sample amongst each other. To accelerate the independent local moves, they may be performed simultaneously on multiple processors. Another problem is then encountered: depending on the MCMC implementation and inference problem, local moves can take a varying and random amount of time to complete. There may also be infrastructure-induced variations, such as competing jobs on the same processors, which arises in cloud computing. Before exchanges can occur, all chains must complete the local moves they are engaged in to avoid introducing a potentially substantial bias (Proposition 2.1). To solve this issue of randomly varying local move completion times in multi-processor parallel tempering, we adopt the Anytime Monte Carlo framework of Murray et al. (2016): we impose real-time deadlines on the parallel local moves and perform exchanges at these deadlines without any processor idling. We show our methodology for exchanges at real-time deadlines does not introduce a bias and leads to significant performance enhancements over the na\"ive approach of idling until every processor's local moves complete. The methodology is then applied in an ABC setting, where an Anytime ABC parallel tempering algorithm is derived for the difficult task of estimating the parameters of a Lotka-Volterra predator-prey model, and similar efficiency enhancements are observed., Comment: 34 Pages, 10 Figures
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- 2021
28. Tipping Cascades in a Multi-patch System with Noise and Spatial Coupling
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Alan Hastings and Abhishek Mallela
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Singular perturbation ,General Mathematics ,Immunology ,Population ,Population Dynamics ,Perturbations ,Models, Biological ,General Biochemistry, Genetics and Molecular Biology ,Tipping points ,symbols.namesake ,Alternative stable states ,Alternative stable state ,Quantitative Biology::Populations and Evolution ,Computer Simulation ,Statistical physics ,education ,Ecosystem ,General Environmental Science ,Mathematics ,Allee effect ,Pharmacology ,Stochasticity ,education.field_of_study ,Extinction ,Resilience ,General Neuroscience ,Allee effects ,Spectral density ,Mathematical Concepts ,Spatial heterogeneity ,Computational Theory and Mathematics ,Coupling (computer programming) ,symbols ,Original Article ,General Agricultural and Biological Sciences - Abstract
Forecasting tipping points in spatially extended systems is a key area of interest to ecologists. A slowly declining spatially distributed population is an important example of an ecological system that could exhibit a cascade of tipping points. Here, we develop a spatial two-patch model with environmental stochasticity that is slowly forced through population collapse, in the presence of changing environmental conditions. We begin with a basic spatial model, then introduce a fast–slow version of the model using geometric singular perturbation theory, followed by the inclusion of stochasticity. Using the spectral density of the fluctuating subpopulation in each patch, we derive analytic expressions for candidate indicators of population extinction and evaluate their performance through a simulation study. We find that coupling and spatial heterogeneity decrease the magnitude of the proposed indicators in coupled populations relative to isolated populations. Moreover, the degree of coupling dictates the trends in summary statistics. We conclude that this theory may be applied to other contexts, including the control of invasive species.
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- 2021
29. Carbohydrate-Based Fat Mimetics Can Affect the Levels of 3-Monochloropropane-1,2-Diol Esters and Glycidyl Esters in Shortbread Biscuits
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Anna Sadowska-Rociek and Ewa Cieślik
- Subjects
0301 basic medicine ,food.ingredient ,business.operation ,Pectin ,Diol ,Inulin ,Population ,Glycidyl esters ,Carbohydrates ,alpha-Chlorohydrin ,Shortbread ,03 medical and health sciences ,chemistry.chemical_compound ,symbols.namesake ,0404 agricultural biotechnology ,food ,3-monochloropropane-1,2-diol esters ,Bound water ,Food science ,education ,Fat Substitutes ,Fat mimetics ,education.field_of_study ,Original Paper ,030109 nutrition & dietetics ,GE ,food and beverages ,Esters ,04 agricultural and veterinary sciences ,Bread ,Carbohydrate ,040401 food science ,Dietary Fats ,3-MCPDE ,Maillard reaction ,chemistry ,Chemistry (miscellaneous) ,symbols ,Epoxy Compounds ,Pectins ,business ,Food Analysis ,Food Science - Abstract
Shortbread biscuits have become one of the most desirable snacks in all population groups but due to its high fat content it is searching for new solutions of fat reduction such as the use of carbohydrate-based fat mimetics. However, the thermal processing of food containing lipids in the presence of certain carbohydrates can contribute to the formation of toxic compounds or alter its levels. Therefore, the aim of the study was to evaluate the use of inulin and pectin gels as partial fat replacers (10–40%) in classical shortbread biscuits in a view of the changes of 3-monochloropropane-1,2-diol ester (3-MCPDE) and glycidyl ester (GE) levels after baking, and also after a two-months storage. The experiment showed that the amount of inulin gel higher than 10% promoted the endogenous formation of 3-MCPDE probably due to the higher amount of Maillard products formed in the biscuits, but after two months the levels decreased and were comparable with those transferred from shortening. Pectin did not demonstrate such phenomenon, owing to the presence of bound water in gel. Glycidyl esters were partially decomposed during baking and also during storage, particularly in the samples with the addition of pectin gel, which presumably caused by low stability of GE under acidic conditions resulting from the occurrence of galacturonic acid in pectin. Electronic supplementary material The online version of this article (10.1007/s11130-019-00723-z) contains supplementary material, which is available to authorized users.
- Published
- 2019
30. Phase Transition in the Boltzmann–Vlasov Equation
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Andrew C. Fowler and SFI
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Physics ,Phase transition ,Scale (ratio) ,Vlasov equation ,Statistical and Nonlinear Physics ,State (functional analysis) ,Stability theory ,01 natural sciences ,Boltzmann equation ,Article ,010305 fluids & plasmas ,Term (time) ,symbols.namesake ,stabiity theory ,phase transition ,0103 physical sciences ,Boltzmann constant ,symbols ,010306 general physics ,Mathematical Physics ,Mathematical physics - Abstract
In this paper we revisit the problem of explaining phase transition by a study of a form of the Boltzmann equation, where inter-molecular attraction is included by means of a Vlasov term in the evolution equation for the one particle distribution function. We are able to show that for typical gas densities, a uniform state is unstable if the inter-molecular attraction is large enough. Our analysis relies strongly on the assumption, essential to the derivation of the Boltzmann equation, that \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\nu \ll 1,$$\end{document}ν≪1, where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\nu =d/l$$\end{document}ν=d/l is the ratio of the molecular diameter to the mean inter-particle distance; in this case, for fluctuations on the scale of the molecular spacing, the collision term is small, and an explicit approximate solution is possible. We give reasons why we think the resulting approximation is valid, and in conclusion offer some possibilities for extension of the results to finite amplitude.
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- 2019
31. Thermodynamic integration via differential evolution: A method for estimating marginal likelihoods
- Author
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Jeffrey Annis, Nathan J. Evans, and Psychologische Methodenleer (Psychologie, FMG)
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Population ,Monte Carlo method ,Thermodynamic integration ,Experimental and Cognitive Psychology ,Models, Psychological ,01 natural sciences ,050105 experimental psychology ,Article ,Cognitive modeling ,010104 statistics & probability ,symbols.namesake ,Cognition ,Arts and Humanities (miscellaneous) ,Developmental and Educational Psychology ,Applied mathematics ,Humans ,0501 psychology and cognitive sciences ,Computer Simulation ,0101 mathematics ,education ,General Psychology ,education.field_of_study ,Likelihood Functions ,Models, Statistical ,05 social sciences ,Sampling (statistics) ,Markov chain Monte Carlo ,Bayes factor ,Bayes Theorem ,Marginal likelihood ,Markov Chains ,Differential evolution ,symbols ,Psychology (miscellaneous) ,Bayesian model selection ,Monte Carlo Method - Abstract
A typical goal in cognitive psychology is to select the model that provides the best explanation of the observed behavioral data. The Bayes factor provides a principled approach for making these selections, though the integral required to calculate the marginal likelihood for each model is intractable for most cognitive models. In these cases, Monte Carlo techniques must be used to approximate the marginal likelihood, such as thermodynamic integration (TI; Friel & Pettitt, Journal of the Royal Statistical Society: Series B (Statistical Methodology), 70(3), 589–607 2008; Lartillot & Philippe, Systematic Biology, 55(2), 195–207 2006), which relies on sampling from the posterior at different powers (called power posteriors). TI can become computationally expensive when using population Markov chain Monte Carlo (MCMC) approaches such as differential evolution MCMC (DE-MCMC; Turner et al., Psychological Methods, 18(3), 368 2013) that require several interacting chains per power posterior. Here, we propose a method called thermodynamic integration via differential evolution (TIDE), which aims to reduce the computational burden associated with TI by using a single chain per power posterior (R code available at https://osf.io/ntmgw/). We show that when applied to non-hierarchical models, TIDE produces an approximation of the marginal likelihood that closely matches TI. When extended to hierarchical models, we find that certain assumptions about the dependence between the individual- and group-level parameters samples (i.e., dependent/independent) have sizable effects on the TI approximated marginal likelihood. We propose two possible extensions of TIDE to hierarchical models, which closely match the marginal likelihoods obtained through TI with dependent/independent sampling in many, but not all, situations. Based on these findings, we believe that TIDE provides a promising method for estimating marginal likelihoods, though future research should focus on a detailed comparison between the methods of estimating marginal likelihoods for cognitive models.
- Published
- 2019
32. In vitro targeting and selective killing of mcf-7 and colo320dm cells by 5-fluorouracil anchored to carboxylated SWCNTs and MWCNTs
- Author
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Mangesh A. Bhutkar, Rutuja V Kamble, Shrinivas K Mohite, Somnath D. Bhinge, and Dheeraj S. Randive
- Subjects
Materials science ,Biomedical Engineering ,Biophysics ,Bioengineering ,Apoptosis ,02 engineering and technology ,In Vitro Techniques ,010402 general chemistry ,Spectrum Analysis, Raman ,01 natural sciences ,Nitric Acid ,Biomaterials ,symbols.namesake ,Drug Delivery Systems ,X-Ray Diffraction ,Cell Line, Tumor ,Spectroscopy, Fourier Transform Infrared ,Cytotoxic T cell ,Humans ,Fourier transform infrared spectroscopy ,Calorimetry, Differential Scanning ,Nanotubes, Carbon ,Sulfuric Acids ,021001 nanoscience & nanotechnology ,In vitro ,Chromatin ,0104 chemical sciences ,Delivery Systems ,Drug Liberation ,MCF-7 ,Cell culture ,Thermogravimetry ,symbols ,MCF-7 Cells ,Microscopy, Electron, Scanning ,Surface modification ,Fluorouracil ,0210 nano-technology ,Raman spectroscopy ,Nuclear chemistry - Abstract
The intention of the present work was to synthesize the f-MWCNT and f-SWCNT terminated with proper functional group, loading of 5-Flurouracil and to perform cytotoxic activity. Functionalization of MWCNTs and SWCNTs was achieved through the acid treatment (H2SO4 + HNO3). 5-flurouracil was loaded into the prepared functionalized CNTs, thereafter; in vitro drug loading capacity and % drug release were calculated. Also the prepared f-CNTs, 5-flurouracil loaded CNTs were distinguished by using SEM, TGA, DSC, X-ray diffraction, Raman and FTIR spectroscopy. MCF-7 and COLO320DM cells were treated with selected concentrations of 5-FU loaded f-MWCNTs and f-SWCNTs to estimate the cytotoxic activity. It was observed that 5-FU loaded f-SWCNTs showed good activity against selected cell lines than others. Moreover, apoptosis percentage was reported to be 84.46 ± 4.3515 and 92.78 ± 2.6549 for 5-FU loaded f-SWCNTs against MCF-7 and COLO320DM cells respectively. It is evident from the results that the prepared drug loaded CNTs have comparable antitumor activity in cancer cell lines.
- Published
- 2021
33. A homozygous truncating variant in GDF9 in siblings with primary ovarian insufficiency
- Author
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Alison H. Trainer, James Wolfe, Frida Djukiadmodjo, Bryony A. Thompson, Sarah A Price, and Kunal P Verma
- Subjects
0301 basic medicine ,Adult ,Candidate gene ,medicine.medical_specialty ,endocrine system ,Adolescent ,Granulosa cell ,Primary ovarian insufficiency ,Reproductive medicine ,Growth Differentiation Factor 9 ,Primary Ovarian Insufficiency ,Bioinformatics ,03 medical and health sciences ,symbols.namesake ,Young Adult ,0302 clinical medicine ,Ovarian Follicle ,Transforming Growth Factor beta ,Follicular phase ,medicine ,Genetics ,Morphogenesis ,Humans ,In patient ,Genetic Predisposition to Disease ,Genetics (clinical) ,030219 obstetrics & reproductive medicine ,Granulosa Cells ,business.industry ,Siblings ,Obstetrics and Gynecology ,General Medicine ,Human genetics ,030104 developmental biology ,Reproductive Medicine ,Mendelian inheritance ,symbols ,Oocytes ,Female ,business ,Developmental Biology - Abstract
Premature or primary ovarian insufficiency (POI) affects approximately 1% of women and can be due to a variety of causes. Genetic causes include syndromic and non-syndromic POI. There are several promising candidate genes for whom a clear Mendelian association with non-syndromic POI has not yet been conclusively established, including GDF9. GDF9 is an oocyte-secreted factor and is part of the TGF-beta superfamily of morphogens. It has an important role in follicular development and granulosa cell maturation. We report the case of two siblings with primary ovarian insufficiency (POI) and a homozygous truncating variant in GDF9 (c.604C>T; p.(Gln202*). This report helps establish a clear gene-disease association between GDF9 and POI and argues for routine evaluation for GDF9 variants in patients undergoing genomic investigation for POI.
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- 2021
34. An in silico model using prognostic genetic factors for ovarian response in controlled ovarian stimulation: A systematic review
- Author
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J.S. Cunha-Filho, B S Eisele, Rafaela Donato, Vanessa Krebs Genro, G C Villalba Silva, and Camila Karsburg Bessow
- Subjects
0301 basic medicine ,In silico ,Gene regulatory network ,Computational biology ,Fertilization in Vitro ,Biology ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Betweenness centrality ,Ovulation Induction ,Interaction network ,Genetics ,Humans ,Computer Simulation ,Gene Regulatory Networks ,Protein Interaction Maps ,Gene ,Genetics (clinical) ,030219 obstetrics & reproductive medicine ,Ovary ,Obstetrics and Gynecology ,Computational Biology ,General Medicine ,Prognosis ,Human genetics ,030104 developmental biology ,Bonferroni correction ,Reproductive Medicine ,Genetic marker ,symbols ,Female ,Developmental Biology - Abstract
PURPOSE: To study the use of in silica model to better understand and propose new markers of ovarian response to controlled ovarian stimulation before IVF. METHODS: A systematic review and in silica model using bioinformatics. After the selection of 103 papers from a systematic review process, we performed a GRADE qualification of all included papers for evidence-based quality evaluation. We included 57 genes in the silica model using a functional protein network interaction. Moreover, the construction of protein-protein interaction network was done importing these results to Cytoscape. Therefore, a cluster analysis using MCODE was done, which was exported to a plugin BINGO to determine Gene Ontology. A p value of < 0.05 was considered significant, using a Bonferroni correction test. RESULTS: In silica model was robust, presenting an ovulation-related gene network with 87 nodes (genes) and 348 edges (interactions between the genes). Related to the network centralities, the network has a betweenness mean value = 102.54; closeness mean = 0.007; and degree mean = 8.0. Moreover, the gene with a higher betweenness was PTPN1. Genes with the higher closeness were SRD5A1 and HSD17B3, and the gene with the lowest closeness was GDF9. Finally, the gene with a higher degree value was UBB; this gene participates in the regulation of TP53 activity pathway. CONCLUSIONS: This systematic review demonstrated that we cannot use any genetic marker before controlled ovarian stimulation for IVF. Moreover, in silica model is a useful tool for understanding and finding new markers for an IVF individualization. PROSPERO: CRD42020197185 SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10815-021-02141-0.
- Published
- 2021
35. A Contextual Planck Parameter and the Classical Limit in Quantum Cosmology
- Author
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João Magueijo, John D. Barrow, Magueijo, João [0000-0003-1408-3313], and Apollo - University of Cambridge Repository
- Subjects
4902 Mathematical Physics ,Cosmology and Nongalactic Astrophysics (astro-ph.CO) ,Uncertainty principle ,FOS: Physical sciences ,General Physics and Astronomy ,General Relativity and Quantum Cosmology (gr-qc) ,Cosmological constant ,01 natural sciences ,General Relativity and Quantum Cosmology ,Classical limit ,Article ,symbols.namesake ,Theoretical physics ,Quantum cosmology ,0103 physical sciences ,Planck ,010306 general physics ,Quantum ,Physics ,Quantum Physics ,010308 nuclear & particles physics ,symbols ,49 Mathematical Sciences ,Quantum Physics (quant-ph) ,51 Physical Sciences ,5107 Particle and High Energy Physics ,Astrophysics - Cosmology and Nongalactic Astrophysics ,Hubble's law ,Planck length - Abstract
Funder: Science and Technology Facilities Council; doi: http://dx.doi.org/10.13039/501100000271, We propose that whatever quantity controls the Heisenberg uncertainty relations (for a given complementary pair of observables) it should be identified with an effective Planck parameter. With this definition it is not difficult to find examples where the Planck parameter depends on the region under study, varies in time, and even depends on which pair of observables one focuses on. In quantum cosmology the effective Planck parameter depends on the size of the comoving region under study, and so depends on that chosen region and on time. With this criterion, the classical limit is expected, not for regions larger than the Planck length, $$l_{P}$$ l P , but for those larger than $$l_{Q}=(l_{P}^{2}H^{-1})^{1/3}$$ l Q = ( l P 2 H - 1 ) 1 / 3 , where H is the Hubble parameter. In theories where the cosmological constant is dynamical, it is possible for the latter to remain quantum even in contexts where everything else is deemed classical. These results are derived from standard quantization methods, but we also include more speculative cases where ad hoc Planck parameters scale differently with the length scale under observation. Even more speculatively, we examine the possibility that similar complementary concepts affect thermodynamical variables, such as the temperature and the entropy of a black hole.
- Published
- 2021
36. Multiplexed Raman Imaging in Tissues and Living Organisms
- Author
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Travis M. Shaffer and Sanjiv S. Gambhir
- Subjects
inorganic chemicals ,Materials science ,technology, industry, and agriculture ,Raman imaging ,Nanoparticle ,Nanotechnology ,Molecular Fingerprint ,Multiplexing ,symbols.namesake ,In vivo ,symbols ,Raman spectroscopy ,Preclinical imaging ,Raman scattering - Abstract
Surface-enhanced Raman scattering (SERS) nanoparticles (NPs) are ideal multiplexing probes for in vivo imaging and tissue staining. Their remarkable sensitivity and unique Raman molecular fingerprint results in minimal background compared to other optical modalities. These characteristics also allow multiplexing down to the attomolar concentration. Here we describe the synthesis and in vivo multiplexing application of a SERS NP library.
- Published
- 2021
- Full Text
- View/download PDF
37. Using FTIR Imaging to Investigate Silk Fibroin-Based Materials
- Author
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Xiaojie Zhou, Chao Ye, Yuzhao Tang, Jiajia Zhong, and Wenjie Yu
- Subjects
Materials science ,fungi ,technology, industry, and agriculture ,Fibroin ,Nanotechnology ,macromolecular substances ,Characterization (materials science) ,symbols.namesake ,SILK ,Fourier transform ,symbols ,Sample preparation ,Fourier transform infrared spectroscopy ,Raman spectroscopy ,Protein secondary structure - Abstract
The secondary structures of silk fibroin (SF) are critical in the determination of the mechanical properties of the animal silks. Different characterization techniques, such as X-ray diffraction, nuclear magnetic resonance, Raman spectroscopy, and Fourier transform infrared (FTIR) technique, have been applied to study the secondary structure of animal silks. Among these techniques, FTIR is most widely used as it is sensitive to all secondary structures of proteins. Especially with the development of FTIR imaging, it is now possible to image the secondary structures of proteins at the micrometer scale, so as to understand the spatial distribution of proteins and the interaction of proteins with other materials at specific locations of interest. In this chapter, we present the methods and protocols of FTIR imaging to silk protein-based materials. We primarily introduce how to set up the instruments and accessories, as well as how to choose the appropriate imaging methods and sample preparation methods according to sample morphologies. The critical protocols for data analysis are also introduced in the last section.
- Published
- 2021
- Full Text
- View/download PDF
38. Atomic Force Microscopy for Live-Cell and Hydrogel Measurement
- Author
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Natalie J. Kirkland, Alexander J. Whitehead, and Adam J. Engler
- Subjects
0301 basic medicine ,Materials science ,Atomic force microscopy ,Stiffness ,020101 civil engineering ,Young's modulus ,02 engineering and technology ,Fibroblasts ,Microscopy, Atomic Force ,Article ,0201 civil engineering ,03 medical and health sciences ,symbols.namesake ,030104 developmental biology ,Elastic Modulus ,Cell Transdifferentiation ,Self-healing hydrogels ,symbols ,medicine ,Animals ,Humans ,medicine.symptom ,Myofibroblasts ,Cells, Cultured ,Biomedical engineering - Abstract
Atomic force microscopy (AFM) has emerged as a popular method for determining the mechanical properties of cells, their components, and biomaterials. Here, we describe AFM setup and application to obtain stiffness measurements from single indentations for hydrogels and myofibroblasts.
- Published
- 2021
- Full Text
- View/download PDF
39. ITC for Characterization of Self-Assembly Process of Cationic Dendrons for siRNA Delivery
- Author
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Maurizio Fermeglia, Natasa Skoko, Domenico Marson, Suzana Aulic, Erik Laurini, Sabrina Pricl, Laurini, E., Aulic, S., Skoko, N., Marson, D., Fermeglia, M., and Pricl, S.
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siRNA delivery ,02 engineering and technology ,Micelle ,03 medical and health sciences ,symbols.namesake ,Amphiphilic cationic dendrons ,Critical micelle concentration ,Isothermal titration calorimetry ,Micelles ,Self-assembly ,Amphiphile ,030304 developmental biology ,0303 health sciences ,Aggregation number ,Chemistry ,Cationic polymerization ,021001 nanoscience & nanotechnology ,Combinatorial chemistry ,Gibbs free energy ,Amphiphilic cationic dendron ,symbols ,0210 nano-technology - Abstract
siRNAs are emerging as promising therapeutic agents due to their ability to inhibit specific genes in many diseases. However, these tools require specific vehicles in order to be safely delivered to the targeted site. Among different siRNA delivery systems, self-assembled nanomicelles based on amphiphilic cationic dendrons (ACDs) have recently outperformed nanovectors based on covalent carriers. This chapter describes how isothermal titration calorimetry (ITC) can be exploited as one of the best techniques to investigate the self-assembly process of ACDs. Specifically, ITC can provide, as such or via specific analysis methods, a full thermodynamic characterization of these nanomicelles, including their critical micellar concentration, micelle aggregation number, degree of counterion binding, Gibbs free energy of micellization, and its enthalpic and entropic components.
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- 2021
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40. Molecularly Imprinted Polymers Coupled with Surface-Enhanced Raman Spectroscopy to Detect Chemical Hazards in Foods
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Marti Z. Hua, Xiaonan Lu, and Shaolong Feng
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symbols.namesake ,Materials science ,Chromatography ,Molecularly imprinted polymer ,symbols ,Substrate (chemistry) ,Molecule ,Sample preparation ,Surface-enhanced Raman spectroscopy ,Raman spectroscopy - Abstract
Preparation of molecularly imprinted polymers coupled with surface-enhanced Raman spectroscopy (MIP-SERS) sensor and its application in detecting chemical hazards in food matrices are described. Sample cleaning is achieved by molecularly imprinted solid-phase extraction (MISPE), and target molecules are detected by SERS. Procedures of MIP synthesis, MISPE preparation, SERS substrate preparation, spectral collection, data analysis, and food analysis application are described.
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- 2021
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41. Fourier Multiplexed Fluorescence Lifetime Imaging
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Leilei Peng
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Fluorescence-lifetime imaging microscopy ,Materials science ,business.industry ,Confocal ,Laser ,Multiplexing ,Fluorescence ,law.invention ,symbols.namesake ,Förster resonance energy transfer ,Fourier transform ,law ,symbols ,Optoelectronics ,Tomography ,business - Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a widely used functional imaging method in bioscience. Fourier multiplexed FLIM (FmFLIM), a frequency-domain lifetime measurement method, explores the principle of Fourier (frequency) multiplexing to achieve parallel lifetime detection on multiple fluorescence labels. Combining FmFLIM with a confocal scanning microscope allows multiplexed 3D lifetime imaging of cells and tissues. FmFLIM can also be integrated with the scanning laser tomography imaging method to perform 3D multiplex lifetime imaging of whole embryos and thick tissues.
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- 2021
- Full Text
- View/download PDF
42. Giardia duodenalis: Detection by Quantitative Real-Time PCR and Molecular Diversity
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Pamela C. Köster, David Carmena, and Alejandro Dashti
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Sanger sequencing ,symbols.namesake ,Quantitative Real Time PCR ,Genetic marker ,Giardia duodenalis ,Small subunit ,symbols ,Computational biology ,Biology ,Ribosomal RNA ,Genotyping ,Triosephosphate isomerase - Abstract
Conventional microscopy is being progressively replaced by molecular (PCR and Sanger sequencing) methods for the first-line detection, identification, and genotyping of diarrhea-causing enteric parasites in modern clinical and research laboratories. These technologies allow increased sample testing, improved throughput, and optimized laboratory workflow in a cost-effective manner. Here, we describe the methodological algorithm used in a national reference center for the diagnosis and molecular characterization of Giardia duodenalis, a major contributor to the enormous burden of diarrheal disease globally. Initial detection of the parasite is conducted by a sensitive real-time PCR to amplify the small subunit of the ribosomal RNA of G. duodenalis, whereas a multilocus sequence genotyping scheme based on three constitutive genetic markers (glutamate dehydrogenase, β-giardin, and triose phosphate isomerase) is used for genotyping and sub-genotyping purposes. The advantages and disadvantages of these PCR-based methods are commented.
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- 2021
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43. Split Green Fluorescent Protein–Based Contact Site Sensor (SPLICS) for Heterotypic Organelle Juxtaposition as Applied to ER–Mitochondria Proximities
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Marisa Brini and Tito Calì
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0301 basic medicine ,Cell physiology ,Endosome ,Chemistry ,Split GFP ,Endoplasmic reticulum ,ER–Mitochondria tethering ,Mitochondria ,Organelle contact sites ,SPLICS ,Cellular homeostasis ,Golgi apparatus ,Peroxisome ,Cell biology ,03 medical and health sciences ,symbols.namesake ,030104 developmental biology ,0302 clinical medicine ,Lipid droplet ,Organelle ,symbols ,030217 neurology & neurosurgery - Abstract
In the last decades, membrane contact sites (MCSs) have been the object of intense investigation in different fields of cell physiology and pathology and their importance for the correct functioning of the cell is now widely recognized. MCS between any known intercellular organelles, including endoplasmic reticulum (ER), mitochondria, Golgi, endosomes, peroxisomes, lysosomes, lipid droplets, and the plasma membrane (PM), have been largely documented and in some cases the molecules responsible for the tethering also identified. They represent specific membrane hubs where a tightly coordinated exchange of ions, lipids, nutrients, and factors required to maintain proper cellular homeostasis takes place. Their delicate, dynamic, and sometimes elusive nature prevented and/or delayed the development of tools to easily image interorganelle proximity under physiological conditions and in living organisms. Nowadays, this aspect received great momentum due to the finding that MCSs' dysregulation is involved in several pathological conditions. We have recently developed modular, split-GFP-based contact site sensors (SPLICS) engineered to fluoresce when homo- and heterotypic juxtapositions between ER and mitochondria occur over a range of specific distances. Here we describe in detail, by highlighting strengths and weaknesses, the use and the application of these novel genetically encoded SPLICS sensors and how to properly quantify short- and long-range ER-mitochondria interactions.
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- 2021
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44. Applications of Constrained Optimization
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Wu-Sheng Lu and Andreas Antoniou
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Optimal design ,Hessian matrix ,Mathematical optimization ,Computer science ,Multivariable calculus ,Constrained optimization ,ComputerApplications_COMPUTERSINOTHERSYSTEMS ,Measure (mathematics) ,Nonlinear system ,symbols.namesake ,Quadratic equation ,symbols ,Differentiable function ,Computer Science::Databases - Abstract
Constrained optimization provides a general framework in which a variety of design criteria and specifications can be readily imposed on the required solution. Usually, a multivariable objective function that quantifies a performance measure of a design can be identified. This objective function may be linear, quadratic, or highly nonlinear, and usually it is differentiable so that its gradient and sometimes Hessian can be evaluated. In a real-life design problem, the design is carried out under certain physical limitations with limited resources. If these limitations can be quantified as equality or inequality constraints on the design variables, then a constrained optimization problem can be formulated whose solution leads to an optimal design that satisfies the limitations imposed.
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- 2021
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45. The Riemann Mapping Theorem
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Robert B. Burckel
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Riemann Xi function ,symbols.namesake ,Pure mathematics ,Geometric function theory ,Fundamental theorem of calculus ,Riemann surface ,Mathematical analysis ,Uniformization theorem ,Riemann mapping theorem ,symbols ,Open mapping theorem (complex analysis) ,Brouwer fixed-point theorem ,Mathematics - Abstract
In his Gottingen dissertation of 1851 Bernard Riemann enunciated (p. 40 of his Werke) and attempted to prove the famous theorem that now bears his name: Theorem 9.1 Every simply-connected region other than ℂ itself is conformal to an open disk.
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- 2021
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46. Method of Using Raman Spectroscopy to Understand the Conformation of Fibrous Proteins
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Liang Zhou, Wenli Gao, Shengjie Ling, Hongchong Guo, Ting Shu, and Qiang Liu
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Quantitative Biology::Biomolecules ,Crystallography ,symbols.namesake ,Aqueous solution ,Materials science ,Chemical bond ,Moisture ,symbols ,Chemical modification ,Orientation (graph theory) ,Raman spectroscopy - Abstract
Raman spectroscopy has been widely used in the research of fibrous proteins because of the insensitivity to moisture, less amount of sample, and better signal-to-noise ratio. In recent years, Raman spectroscopy is adopted to investigate the secondary structures of solid or aqueous protein, the conformation transition under different conditions (concentration, temperature, pressure, pH, chemical modification, external force, etc.), the orientation of the molecular chains, and some important chemical bonds. Here, we will introduce the methods for using Raman spectroscopy to analyze the conformation and orientation of samples, which would be an efficient method to get the "structure-property" relationship.
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- 2021
- Full Text
- View/download PDF
47. Analysing Microbial Biofilm Formation at a Molecular Level: Role of Fourier Transform Infrared and Raman Spectroscopy
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Abarna Chatterjee, Dibyajit Lahiri, Anushka Ghosh, Moupriya Nag, Prateek Banerjee, Ritwik Banerjee, and Rina Rani Ray
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symbols.namesake ,Molecular level ,Fourier transform ,Materials science ,Infrared ,Biofilm ,symbols ,Photochemistry ,Raman spectroscopy - Published
- 2021
- Full Text
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48. Multiplexed Fourier Transform Infrared and Raman Imaging
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Guillermo Quintás, Hugh J. Byrne, Bayden R. Wood, and David Perez-Guaita
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Multimodal imaging ,symbols.namesake ,Materials science ,Fourier transform ,Infrared ,business.industry ,symbols ,Raman imaging ,Optoelectronics ,business ,Raman spectroscopy ,Sample (graphics) ,Multiplexing - Abstract
Infrared (IR) and Raman spectroscopies are being increasingly employed for the label-free analysis of biochemical samples. Both are vibrational imaging techniques, but they provide complementary information about the chemical composition of the sample, and thus the integration of Raman and IR images leads to a comprehensive understanding of the samples. Here, we summarize the steps needed for performing multiplexed infrared and Raman imaging, identifying and overcoming the two main challenges: first, the technical difficulties caused by the incompatibilities of the techniques and, second, the necessity to extract the information from the large number of vibrational variables found in both IR and Raman spectra.
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- 2021
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49. Measuring Mechanical and Adhesive Properties of Single Cells Using an Atomic Force Microscope
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Faramarz Dehghani and Tim Hohmann
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0301 basic medicine ,Cantilever ,Materials science ,Atomic force microscopy ,Modulus ,Young's modulus ,Adhesion ,Elasticity (physics) ,03 medical and health sciences ,symbols.namesake ,030104 developmental biology ,0302 clinical medicine ,030220 oncology & carcinogenesis ,symbols ,Adhesive ,Composite material - Abstract
Atomic force microscopy allows the determination of both mechanical and adhesive properties of living single cells and generation of high-resolution surface images. Here, we describe a method to determine the Young's modulus of a cell and adhesion between a coated cantilever and a cell, as well as an overview of the analysis of the data obtained. Additionally, we point out typical and important pitfalls during the measurement and analysis.
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- 2021
- Full Text
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50. Synthesis and Characterization of Mitochondria-Targeted Triphenylphosphonium Bolaamphiphiles
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Cecilia Bombelli, Giovanna Mancini, Raffaele Proroga, Alessia Ciogli, Simona Sennato, Stefano Casciardi, Francesca Ceccacci, Edoardo Rossi, Federico Bordi, Valentina Mussi, Marco Diociaiuti, and Stefano Sarti
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Kinetic traps ,Equilibrium systems ,Pyridones ,Triphenylphosphonium bolaamphiphiles ,02 engineering and technology ,Conductivity ,010402 general chemistry ,Electron ,U-shaped/extended conformation ,01 natural sciences ,Krafft temperature ,symbols.namesake ,chemistry.chemical_compound ,Organophosphorus Compounds ,Transmission ,Methylene ,Furans ,Raman ,Microscopy ,Aqueous solution ,Molecular Structure ,Chemistry ,Spectrum Analysis ,Water ,Thermomorphic electrolytic solution ,Kolbe electrolysis ,021001 nanoscience & nanotechnology ,Combinatorial chemistry ,Dynamic Light Scattering ,Mitochondria ,0104 chemical sciences ,Characterization (materials science) ,Microscopy, Electron, Transmission ,Spectrum Analysis, Raman ,Transmission electron microscopy ,symbols ,0210 nano-technology ,Raman spectroscopy ,Mitochondria targeted - Abstract
In this chapter we describe: (1) the procedure for the synthesis of four single chain bolaamphiphiles, displaying chains of 12, 16, 20 and 30 methylene units and triphenylphosphonium moieties as headgroups (TPP1-TPP4); (2) the methods used to characterize TPP1-TPP4 spontaneous aggregation in aqueous solution. We illustrate the determination of Krafft point and cac by conductivity measurements and the procedures used to investigate dimensions, morphology, and stability by dynamic and dielectrophoretic laser light scattering, dialysis, transmission electron microscopy, and Raman spectroscopy measurements.
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- 2021
- Full Text
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