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1.
Value Health ; 2024 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-38977194

RESUMO

OBJECTIVES: To use the EQ-5D questionnaire with bolt-on dimensions in economic evaluation studies, new value sets are needed. In this study, we explored the feasibility of a new approach called the scaling factor model, which estimates bolt-on value sets using estimated EQ-5D dimensional weights. METHODS: We designed a 2-arm study, inviting university students to value health states with and without bolt-on items using the composite time trade-off method. We selected 25 health states from an orthogonal array and added the 5 mildest EQ-5D states in the design. In arm 1, EQ-5D without self-care and standard EQ-5D states were valued, and in arm 2, standard EQ-5D states and EQ-5D with vision were valued. By arm, we compared the mean observed values of health states with and without bolt-on item. Next, by arm, we estimated value sets for the EQ-5D with bolt-on states using both standard model and scaling factor model. Model performances were compared in terms of prediction accuracy and correlation with likelihood-based mean values. RESULTS: Adding a five-level bolt-on to EQ-5D resulted in statistically lower values. This effect was consistent across 2 arms and bolt-on items. The scaling factor models outperformed the standard models in all statistics. CONCLUSIONS: The scaling factor model offers a methodologically viable and low-cost option for producing value sets for EQ-5D supplemented with bolt-on items. Future studies should further test this method using other bolt-on items and more relevant study populations.

2.
Calcif Tissue Int ; 113(1): 110-125, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37147466

RESUMO

The skeleton is a secretory organ, and the goal of some osteoporosis therapies is to maximize bone matrix output. Nmp4 encodes a novel transcription factor that regulates bone cell secretion as part of its functional repertoire. Loss of Nmp4 enhances bone response to osteoanabolic therapy, in part, by increasing the production and delivery of bone matrix. Nmp4 shares traits with scaling factors, which are transcription factors that influence the expression of hundreds of genes to govern proteome allocation for establishing secretory cell infrastructure and capacity. Nmp4 is expressed in all tissues and while global loss of this gene leads to no overt baseline phenotype, deletion of Nmp4 has broad tissue effects in mice challenged with certain stressors. In addition to an enhanced response to osteoporosis therapies, Nmp4-deficient mice are less sensitive to high fat diet-induced weight gain and insulin resistance, exhibit a reduced disease severity in response to influenza A virus (IAV) infection, and resist the development of some forms of rheumatoid arthritis. In this review, we present the current understanding of the mechanisms underlying Nmp4 regulation of the skeletal response to osteoanabolics, and we discuss how this unique gene contributes to the diverse phenotypes among different tissues and stresses. An emerging theme is that Nmp4 is important for the infrastructure and capacity of secretory cells that are critical for health and disease.


Assuntos
Osteoporose , Hormônio Paratireóideo , Camundongos , Animais , Hormônio Paratireóideo/metabolismo , Camundongos Knockout , Fatores de Transcrição/genética , Regulação da Expressão Gênica , Osteoporose/tratamento farmacológico , Osteoporose/genética
3.
Sensors (Basel) ; 22(19)2022 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-36236587

RESUMO

Smart grids are being expanded in scale with the increasing complexity of the equipment. Edge computing is gradually replacing conventional cloud computing due to its low latency, low power consumption, and high reliability. The CORDIC algorithm has the characteristics of high-speed real-time processing and is very suitable for hardware accelerators in edge computing devices. The iterative calculation method of the CORDIC algorithm yet leads to problems such as complex structure and high consumption of hardware resource. In this paper, we propose an RDP-CORDIC algorithm which pre-computes all micro-rotation directions and transforms the conventional single-stage iterative structure into a three-stage and multi-stage combined iterative structure, thereby enabling it to solve the problems of the conventional CORDIC algorithm with many iterations and high consumption. An accuracy compensation algorithm for the direction prediction constant is also proposed to solve the problem of high ROM consumption in the high precision implementation of the RDP-CORDIC algorithm. The experimental results showed that the RDP-CORDIC algorithm had faster computation speed and lower resource consumption with higher guaranteed accuracy than other CORDIC algorithms. Therefore, the RDP-CORDIC algorithm proposed in this paper may effectively increase computation performance while reducing the power and resource consumption of edge computing devices in smart grid systems.

4.
Arch Toxicol ; 95(1): 91-102, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33159584

RESUMO

The aim of the present study was to develop a generic rat physiologically based kinetic (PBK) model that includes a novel testing strategy where active biliary excretion is incorporated using estradiol-17ß glucuronide (E217ßG) as the model substance. A major challenge was the definition of the scaling factor for the in vitro to in vivo conversion of the PBK-model parameter Vmax. In vitro values for the Vmax and Km for transport of E217ßG were found in the literature in four different studies based on experiments with primary rat hepatocytes. The required scaling factor was defined based on fitting the PBK model-based predicted values to reported experimental data on E217ßG blood levels and cumulative biliary E217ßG excretion. This resulted in a scaling factor of 129 mg protein/g liver. With this scaling factor the PBK model predicted the in vivo data for blood and cumulative biliary E217ßG levels with on average of less than 1.8-fold deviation. The study provides a proof of principle on how biliary excretion can be included in a generic PBK model using primary hepatocytes to define the kinetic parameters that describe the biliary excretion.


Assuntos
Bile/metabolismo , Estradiol/análogos & derivados , Hepatócitos/metabolismo , Modelos Biológicos , Administração Intravenosa , Animais , Estradiol/administração & dosagem , Estradiol/sangue , Estradiol/farmacocinética , Eliminação Hepatobiliar , Estudo de Prova de Conceito , Ratos Sprague-Dawley
5.
Entropy (Basel) ; 23(12)2021 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-34945956

RESUMO

In the past decade, rapid development in digital communication has led to prevalent use of digital images. More importantly, confidentiality issues have also come up recently due to the increase in digital image transmission across the Internet. Therefore, it is necessary to provide high imperceptibility and security to digitally transmitted images. In this paper, a novel blind digital image watermarking scheme is introduced tackling secured transmission of digital images, which provides a higher quality regarding both imperceptibility and robustness parameters. A block based hybrid IWT- SVD transform is implemented for robust transmission of digital images. To ensure high watermark security, the watermark is encrypted using a Pseudo random key which is generated adaptively from cover and watermark images. An encrypted watermark is embedded in randomly selected low entropy blocks to increase the security as well as imperceptibility. Embedding positions within the block are identified adaptively using a Blum-Blum-Shub Pseudo random generator. To ensure higher visual quality, Initial Scaling Factor (ISF) is chosen adaptively from a cover image using image range characteristics. ISF can be optimized using Nature Inspired Optimization (NIO) techniques for higher imperceptibility and robustness. Specifically, the ISF parameter is optimized by using three well-known and novel NIO-based algorithms such as Genetic Algorithms (GA), Artificial Bee Colony (ABC), and Firefly Optimization algorithm. Experiments were conducted for the proposed scheme in terms of imperceptibility, robustness, security, embedding rate, and computational time. Experimental results support higher effectiveness of the proposed scheme. Furthermore, performance comparison has been done with some of the existing state-of-the-art schemes which substantiates the improved performance of the proposed scheme.

6.
Xenobiotica ; 50(9): 1064-1075, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32125203

RESUMO

In vitro-in vivo extrapolation (IVIVE) using human liver microsomes has been widely used to predict metabolic clearance, but some of the factors used in the process of prediction show variability for the same compound: notably, microsomal intrinsic clearance values corrected by the unbound fraction (CLint, u), physiological parameters used for scale-up, and the source of in vivo clearance data.The purpose of this study was to assess the correlation between in vitro and in vivo CLint with a focus on factors showing variability using four cytochrome P450 (CYP)3A substrates.We surveyed in vivo clearance values in literature and also determined the microsomal CLint, u values. A scaling factor (SFdirect) was defined as in vivo CLint divided by the microsomal CLint, u, which ranged from 1190 to 2310 (mg protein per kg body weight). The application of a mean SFdirect of 1600 (mg protein per kg body weight) and further normalization by the microsomal CLint, u values of midazolam, the most commonly used substrate, resulted in improved prediction accuracy for CLint, u values from various microsomal batches.The results suggest the normalization of variability might be useful for predicting the in vivo CLint.


Assuntos
Taxa de Depuração Metabólica , Microssomos Hepáticos/fisiologia , Citocromo P-450 CYP3A , Hepatócitos , Humanos , Cinética , Fígado , Midazolam/metabolismo
7.
Xenobiotica ; 49(4): 404-414, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29619871

RESUMO

In this study, total body clearance (CLt), volume of distribution at steady state (Vss) and plasma concentration-time profiles in humans of model compounds were predicted using chimeric mice with humanized livers. On the basis of assumption that unbound intrinsic clearance (CLUint) per liver weight in chimeric mice was equal to those in humans, CLt were predicted by substituting human liver blood flow and liver weights in well-stirred model. Vss were predicted by Rodgers equation using scaling factors of tissue-plasma concentration ratios (SFKp) in chimeric mice estimated from a difference between the observed and predicted Vss. These physiological approaches showed high prediction accuracy for CLt and Vss values in humans. We compared the predictability of CLt and Vss determined by the physiologically based predictive approach using chimeric mice with those from predictive methods reported by Pharmaceutical Research Manufacturers of America. The physiological approach using chimeric mice indicated the best prediction accuracy in each predictive method. Simulation of human plasma concentration-time profiles were generally successful with physiologically based pharmacokinetic (PBPK) model incorporating CLUint and SFKp obtained from chimeric mice. Combined application of chimeric mice and PBPK modeling is effective for prediction of human PK in various compounds.


Assuntos
Quimera/fisiologia , Fígado/fisiologia , Farmacocinética , Animais , Simulação por Computador , Humanos , Camundongos , Fatores de Tempo
8.
Mol Pharm ; 15(10): 4677-4688, 2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-29996058

RESUMO

The use of in vitro data for the quantitative prediction of transporter-mediated clearance is critical. Central to this evaluation is the use of hepatocytes, since they contain the full complement of transporters and metabolic enzymes. In general, uptake clearance (CLuptake) is evaluated by measuring the appearance of compound in the cell. Passive clearance (CLpd) is often determined by conducting parallel studies at 4 °C or by attempting to saturate uptake pathways. Both approaches have their limitations. Recent studies have proposed the use of Rifamycin-SV (RFV) as a pan-inhibitor of hepatic uptake pathways. In our studies, we confirm that transport activity of all major hepatic uptake transporters is inhibited significantly by RFV at 1 mM (OATP1B1, 1B3, and 2B1 = NTCP (80%), OCT1 (65%), OAT2 (60%)). Under these incubation conditions, we found that the free intracellular concentration of RFV is ∼175 µM and that several major CYPs and UGTs can be reversibly inhibited. Using this approach, we also determined CLuptake and CLpd of nine known OATP substrates across three different lots of human hepatocytes. The scaling factors generated for these compounds at 37 °C with RFV and 4 °C were found to be similar. The CLpd of passively permeable compounds like metoprolol and semagacestat were found to be higher at 37 °C compared to 4 °C, indicating a temperature effect on these compounds. In addition, our data also suggests that incorporation of medium concentrations into CLuptake and CLpd calculations may be critical for highly protein bound and highly lipophilic drugs. Overall, our data indicate that RFV, instead of 4 °C, can be reliably used to measure CLuptake and CLpd of drugs.


Assuntos
Hepatócitos/metabolismo , Fígado/metabolismo , Rifamicinas/metabolismo , Alanina/análogos & derivados , Alanina/metabolismo , Azepinas/metabolismo , Transporte Biológico , Humanos , Cinética , Metoprolol/metabolismo
9.
Doc Ophthalmol ; 137(1): 63-70, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30030672

RESUMO

PURPOSE: Many mfERG displays show normal responses that are larger at the center than peripherally, and the typical linear display of signals is inaccurate with respect to the retinal location of the signals. Printouts do not always indicate retinal or field view, they sometimes emphasize 3-D topographic plots which are not always representative of physiologic signals, and they show ring response densities which are different in every ring and hard to interpret without norms. These problems limit the clinical usefulness of the mfERG and limit communication in the literature. We share our Stanford Display to illustrate possible solutions to these problems. METHODS: We have changed the scaling factor for our mfERG unit to produce a trace array with near equal signals everywhere. We display responses is a spatially scaled array, in a retinal view, so that signals appear in their correct anatomic locations relative to a fundus image. The 3-D display is minimized on the page of signal analysis, and we emphasize ring response averages rather than ring response densities. RESULTS: The new scaling and trace array display greatly facilitate the analysis of retinal disease. Regions of loss are easily recognized in their fundus location. Ring ratios based upon response amplitudes all have a normal value of 1.0 which simplifies analysis. A case of early hydroxychloroquine retinopathy demonstrates the use of this Stanford display. CONCLUSIONS: Recognition of these recording and display options may help mfERG users to maximize the value of the test. Proper scaling of the mfERG stimulus array facilitates localization of retinal disease and simplifies ring response analysis. Different laboratories will have different priorities for signal analysis, but mfERG displays should always indicate the eccentricity of responses, and the use of a retina or field view.


Assuntos
Antirreumáticos/toxicidade , Apresentação de Dados , Eletrorretinografia/efeitos dos fármacos , Hidroxicloroquina/toxicidade , Retina/fisiopatologia , Doenças Retinianas/fisiopatologia , Eletrorretinografia/métodos , Feminino , Fundo de Olho , Humanos , Pessoa de Meia-Idade , Valores de Referência , Retina/efeitos dos fármacos , Doenças Retinianas/induzido quimicamente
10.
Am J Physiol Gastrointest Liver Physiol ; 311(2): G267-75, 2016 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-27340127

RESUMO

We have previously shown that the sequential transcription factors Xbp1→Mist1 (Bhlha15) govern the ultrastructural maturation of the secretory apparatus in enzyme-secreting zymogenic chief cells (ZCs) in the gastric unit. Here we sought to identify transcriptional regulators upstream of X-box binding protein 1 (XBP1) and MIST1. We used immunohistochemistry to characterize Hnf4α(flox/flox) adult mouse stomachs after tamoxifen-induced deletion of Hnf4α We used qRT-PCR, Western blotting, and chromatin immunoprecipitation to define the molecular interaction between hepatocyte nuclear factor 4 alpha (HNF4α) and Xbp1 in mouse stomach and human gastric cells. We show that HNF4α protein is expressed in pit (foveolar) cells, mucous neck cells, and zymogenic chief cells (ZCs) of the corpus gastric unit. Loss of HNF4α in adult mouse stomach led to reduced ZC size and ER content, phenocopying previously characterized effects of Xbp1 deletion. However, HNF4α(Δ/Δ) stomachs also exhibited additional phenotypes including increased proliferation in the isthmal stem cell zone and altered mucous neck cell migration, indicating a role of HNF4α in progenitor cells as well as in ZCs. HNF4α directly occupies the Xbp1 promoter locus in mouse stomach, and forced HNF4α expression increased abundance of XBP1 mRNA in human gastric cancer cells. Finally, as expected, loss of HNF4α caused decreased Xbp1 and Mist1 expression in mouse stomachs. We show that HNF4α regulates homeostatic proliferation in the gastric epithelium and is both necessary and sufficient for the upstream regulation of the Xbp1→Mist1 axis in maintenance of ZC secretory architecture.


Assuntos
Diferenciação Celular , Proliferação de Células , Células Epiteliais/metabolismo , Mucosa Gástrica/metabolismo , Fator 4 Nuclear de Hepatócito/metabolismo , Animais , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Sítios de Ligação , Linhagem Celular , Células Epiteliais/patologia , Mucosa Gástrica/patologia , Regulação da Expressão Gênica , Genótipo , Fator 4 Nuclear de Hepatócito/deficiência , Fator 4 Nuclear de Hepatócito/genética , Homeostase , Humanos , Camundongos Knockout , Fenótipo , Regiões Promotoras Genéticas , Transdução de Sinais , Transfecção , Proteína 1 de Ligação a X-Box/genética , Proteína 1 de Ligação a X-Box/metabolismo
11.
Med Vet Entomol ; 30(1): 39-52, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26685926

RESUMO

The avian zoonotic agent for West Nile virus (WNV) can cause neuroinvasive disease in horses and humans and is expanding its range in Europe. Analyses of the risk for transmission to these hosts in non-endemic areas are necessary. Host preferences of mosquitoes (Diptera: Culicidae), the main vectors of WNV, were determined in Switzerland using animal-baited trap (horse, chickens) experiments at a natural and a periurban site. This was undertaken on four occasions during May-September 2014. In addition, the hosts of 505 blood-fed mosquitoes collected in a zoo and in the field were determined. Mosquito data obtained in the animal bait experiments were corrected for host weight and body surface area and by Kleiber's scaling factor. Collections of 11-14 different mosquito species were achieved with these approaches. Statistically significant host preferences were identified in three species in both approaches. The other species showed opportunistic feeding behaviours to varying extents. Specifically, the invasive species Hulecoeteomyia japonica (= Aedes japonicus) was identified for the first time as feeding on avians in nature. Abundance data, spatiotemporal activity and laboratory vector competence for WNV suggested that, in addition to the main WNV vector Culex pipiens, H. japonica and Aedimorphus vexans (= Aedes vexans) are the most likely candidate bridge vectors for WNV transmission in Switzerland.


Assuntos
Galinhas , Culicidae/fisiologia , Cadeia Alimentar , Cavalos , Interações Hospedeiro-Parasita , Insetos Vetores/fisiologia , Animais , Cidades , Comportamento Alimentar , Feminino , Humanos , Masculino , Parques Recreativos , Suíça , Febre do Nilo Ocidental/transmissão , Febre do Nilo Ocidental/virologia , Vírus do Nilo Ocidental/fisiologia , Áreas Alagadas
12.
Sensors (Basel) ; 16(12)2016 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-27941635

RESUMO

Existing vision-based displacement sensors (VDSs) extract displacement data through changes in the movement of a target that is identified within the image using natural or artificial structure markers. A target-less vision-based displacement sensor (hereafter called "TVDS") is proposed. It can extract displacement data without targets, which then serve as feature points in the image of the structure. The TVDS can extract and track the feature points without the target in the image through image convex hull optimization, which is done to adjust the threshold values and to optimize them so that they can have the same convex hull in every image frame and so that the center of the convex hull is the feature point. In addition, the pixel coordinates of the feature point can be converted to physical coordinates through a scaling factor map calculated based on the distance, angle, and focal length between the camera and target. The accuracy of the proposed scaling factor map was verified through an experiment in which the diameter of a circular marker was estimated. A white-noise excitation test was conducted, and the reliability of the displacement data obtained from the TVDS was analyzed by comparing the displacement data of the structure measured with a laser displacement sensor (LDS). The dynamic characteristics of the structure, such as the mode shape and natural frequency, were extracted using the obtained displacement data, and were compared with the numerical analysis results. TVDS yielded highly reliable displacement data and highly accurate dynamic characteristics, such as the natural frequency and mode shape of the structure. As the proposed TVDS can easily extract the displacement data even without artificial or natural markers, it has the advantage of extracting displacement data from any portion of the structure in the image.

13.
Biopharm Drug Dispos ; 36(8): 491-506, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26037524

RESUMO

Physiological based pharmacokinetic (PBPK) modeling is now commonly used in drug development to integrate human or animal physiological data in order to predict pharmacokinetic profiles. The aim of this work was to construct and refine a PBPK model of irbesartan taking into account its active uptake via OATP1B1/B3 in order to predict more accurately its pharmacokinetic profile using Simcyp(®). The activity and expression of the human hepatocyte transporters OATP1B1 and OATP1B3 were studied. The relative activity factors (RAFs) for OATP1B1 and OATP1B3 transporters were calculated from intrinsic clearances obtained by concentration dependent uptake experiments in human hepatocytes and HEK overexpressing cells: RAF1B1 using estrone-3-sulfate and pitavastatine clearances, and RAF1B3 using cholecystokinine octapeptide (CCK-8) clearances. The relative expression factor (REF) was calculated by comparing immunoblotting of hepatocytes (REFHH ) or tissues (REFtissue) with those of overexpressing HEK cells for each transporter. These scaling factors were applied in a PBPK model of irbesartan using the Simcyp® simulator. Pharmacokinetic simulation using REFHH (1.82 for OATP1B1, 8.03 for OATP1B3) as an extrapolation factor was the closest to the human clinical pharmacokinetic profile of irbesartan. These investigations show the importance of integrating the contribution of the active uptake of a drug in the liver to improve PBPK modeling.


Assuntos
Bloqueadores do Receptor Tipo 1 de Angiotensina II/farmacocinética , Compostos de Bifenilo/farmacocinética , Hepatócitos/metabolismo , Fígado/metabolismo , Modelos Biológicos , Tetrazóis/farmacocinética , Adulto , Western Blotting , Células Cultivadas , Cromatografia Líquida , Simulação por Computador , Glicosilação , Células HEK293 , Humanos , Irbesartana , Cinética , Transportador 1 de Ânion Orgânico Específico do Fígado , Transportadores de Ânions Orgânicos/genética , Transportadores de Ânions Orgânicos/metabolismo , Transportadores de Ânions Orgânicos Sódio-Independentes/genética , Transportadores de Ânions Orgânicos Sódio-Independentes/metabolismo , Cultura Primária de Células , Membro 1B3 da Família de Transportadores de Ânion Orgânico Carreador de Soluto , Espectrometria de Massas em Tandem , Transfecção
14.
Muscle Nerve ; 50(6): 932-8, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24585686

RESUMO

INTRODUCTION: The aim of this study was to evaluate test feasibility, validity, and reproducibility of the rate of force development scaling factor (RFD-SF) for the hip muscles. METHODS: Feasibility was assessed as the testing compliance, validity as the ability to compute the RFD-SF from a linear regression, and reproducibility with a test-retest design in 20 healthy subjects. Reliability and agreement (reproducibility) were evaluated using intraclass correlation coefficient (ICC3,1) and percent standard error of measurement (SEM), respectively. RESULTS: The RFD-SF testing protocol was completed successfully by all subjects, although the analysis had to be modified for hip rotators. Reliability was high (ICC3,1 > 0.70) for all muscles except hip abductors (ICC3,1 = 0.69) and internal rotators (ICC3,1 = 0.58). Agreement was high for all muscles (SEM < 10%). CONCLUSIONS: Hip adductor, flexor, and external rotator RFD-SF can be evaluated with confidence, provided the analysis is modified for external rotators, whereas hip abductor and internal rotator RFD-SF assessment is not recommended.


Assuntos
Articulação do Quadril/fisiologia , Contração Muscular/fisiologia , Força Muscular/fisiologia , Músculo Esquelético/fisiologia , Fisiologia/métodos , Adulto , Estudos de Viabilidade , Feminino , Humanos , Modelos Lineares , Masculino , Junção Neuromuscular/fisiologia , Amplitude de Movimento Articular/fisiologia , Reprodutibilidade dos Testes , Rotação
15.
bioRxiv ; 2024 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-37693542

RESUMO

Recent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profiling of targeted genes and their locations in fixed tissues. Normalization of gene expression data is often needed to account for technical factors that may confound underlying biological signals. Here, we investigate the potential impact of different gene count normalization methods with different targeted gene panels in the analysis and interpretation of im-SRT data. Using different simulated gene panels that overrepresent genes expressed in specific tissue regions or cell types, we demonstrate how normalization methods based on detected gene counts per cell differentially impact normalized gene expression magnitudes in a region- or cell type-specific manner. We show that these normalization-induced effects may reduce the reliability of downstream analyses including differential gene expression, gene fold change, and spatially variable gene analysis, introducing false positive and false negative results when compared to results obtained from gene panels that are more representative of the gene expression of the tissue's component cell types. These effects are not observed with normalization approaches that do not use detected gene counts for gene expression magnitude adjustment, such as with cell volume or cell area normalization. We recommend using non-gene count-based normalization approaches when feasible and evaluating gene panel representativeness before using gene count-based normalization methods if necessary. Overall, we caution that the choice of normalization method and gene panel may impact the biological interpretation of the im-SRT data.

16.
Genome Biol ; 25(1): 153, 2024 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-38867267

RESUMO

BACKGROUND: Recent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profiling of targeted genes and their locations in fixed tissues. Normalization of gene expression data is often needed to account for technical factors that may confound underlying biological signals. RESULTS: Here, we investigate the potential impact of different gene count normalization methods with different targeted gene panels in the analysis and interpretation of im-SRT data. Using different simulated gene panels that overrepresent genes expressed in specific tissue regions or cell types, we demonstrate how normalization methods based on detected gene counts per cell differentially impact normalized gene expression magnitudes in a region- or cell type-specific manner. We show that these normalization-induced effects may reduce the reliability of downstream analyses including differential gene expression, gene fold change, and spatially variable gene analysis, introducing false positive and false negative results when compared to results obtained from gene panels that are more representative of the gene expression of the tissue's component cell types. These effects are not observed with normalization approaches that do not use detected gene counts for gene expression magnitude adjustment, such as with cell volume or cell area normalization. CONCLUSIONS: We recommend using non-gene count-based normalization approaches when feasible and evaluating gene panel representativeness before using gene count-based normalization methods if necessary. Overall, we caution that the choice of normalization method and gene panel may impact the biological interpretation of the im-SRT data.


Assuntos
Perfilação da Expressão Gênica , Análise de Célula Única , Análise de Célula Única/métodos , Perfilação da Expressão Gênica/métodos , Transcriptoma , Humanos , Animais
17.
J Magn Reson ; 358: 107611, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38104491

RESUMO

Accurate assignment of 19F NMR has long been a challenge, and quantum chemical methods are possible solutions. Herein we reported a scaling method for the prediction of 19F NMR chemical shift with freely available ORCA program package. Performance of 31 DFT functionals coupled with 11 basis sets were evaluated and influence of geometry optimization was also studied with five functionals coupled with three basis sets. The significance of geometry was further examined through the execution of relaxed surface scans of seven flexible compounds, and averaged shieldings of obtained conformers yielded notable improvement of the correlation between calculated isotropic shielidings and experimental chemical shifts. Utilization of the best scaling factor obtained successfully assigned of fluorine atoms in multifluorinated molecules with different conformations. The method reported here was computationally inexpensive, easily available with acceptable accuracy.

18.
Phys Eng Sci Med ; 46(1): 185-195, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36593380

RESUMO

Ionometric electron dosimetry inside water-equivalent plastic phantoms demands special considerations including determination of depth scaling and fluence scaling factors (cpl and hpl) to shift from in-phantom measurements to those relevant to water. This study evaluates these scaling factors for RW3 slab phantom and also introduces a new coefficient, k(RW3), for direct conversion from RW3 measurements to water without involving scaling factors. The RW3 solid phantom developed by the PTW Company was used and the corresponding scaling factors including cpl, hpl, and k(RW3) were measured for conventional electron energies of 4, 6, 9, 12, and 16 MeV. Separate measurements were performed in water and the RW3 slab phantom using the Advanced Markus chamber. The validity of the reported scaling factors was confirmed by comparing the direct and indirect percentage depth dose (PDD) measurements in water and in the RW3 phantom. The cpl values for the RW3 phantom were respectively equal to 0.915, 0.927, 0.934, 0.937, and 0.937 for 4, 6, 9, 12, and 16 MeV electron energies. The hpl and k(RW3) values were dependent on the depth of investigation and electron energy. Application of the cpl-hpl factors and k(RW3) coefficients to measured data inside the RW3 can reliably reproduce the measured PDD curves in water. The mean difference between the PDDs measured directly and indirectly in water and in the RW3 phantom was less than 1.2% in both approaches for PDD conversion (cpl-hpl coupling and the use of k(RW3)). The measured scaling factors and k(RW3) coefficients are sufficiently relevant to mimic water-based dosimetry results through indirect measurements inside the RW3 slab phantom. Nevertheless, employing k(RW3) is more straightforward than the cpl-hpl approach because it does not involve scaling and it is also less time-consuming.


Assuntos
Elétrons , Plásticos , Radiometria , Dosagem Radioterapêutica , Água
19.
AAPS J ; 25(3): 40, 2023 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-37052732

RESUMO

In vitro-in vivo extrapolation ((IVIVE) and empirical scaling factors (SF) of human intrinsic clearance (CLint) were developed using one of the largest dataset of 455 compounds with data from human liver microsomes (HLM) and human hepatocytes (HHEP). For extended clearance classification system (ECCS) class 2/4 compounds, linear SFs (SFlin) are approximately 1, suggesting enzyme activities in HLM and HHEP are similar to those in vivo under physiological conditions. For ECCS class 1A/1B compounds, a unified set of SFs was developed for CLint. These SFs contain both SFlin and an exponential SF (SFß) of fraction unbound in plasma (fu,p). The unified SFs for class 1A/1B eliminate the need to identify the transporters involved prior to clearance prediction. The underlying mechanisms of these SFs are not entirely clear at this point, but they serve practical purposes to reduce biases and increase prediction accuracy. Similar SFs have also been developed for preclinical species. For HLM-HHEP disconnect (HLM > HHEP) ECCS class 2/4 compounds that are mainly metabolized by cytochrome P450s/FMO, HLM significantly overpredicted in vivo CLint, while HHEP slightly underpredicted and geometric mean of HLM and HHEP slightly overpredicted in vivo CLint. This observation is different than in rats, where rat liver microsomal CLint correlates well with in vivo CLint for compounds demonstrating permeability-limited metabolism. The good CLint IVIVE developed using HLM and HHEP helps build confidence for prospective predictions of human clearance and supports the continued utilization of these assays to guide structure-activity relationships to improve metabolic stability.


Assuntos
Fígado , Microssomos Hepáticos , Humanos , Ratos , Animais , Microssomos Hepáticos/metabolismo , Fígado/metabolismo , Estudos Prospectivos , Taxa de Depuração Metabólica/fisiologia , Hepatócitos/metabolismo , Modelos Biológicos
20.
Toxicol Lett ; 388: 30-39, 2023 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-37806368

RESUMO

Including active renal excretion in physiologically based kinetic (PBK) models can improve their use in quantitative in vitro- in vivo extrapolation (QIVIVE) as a new approach methodology (NAM) for predicting the acute toxicity of organic cation transporter 2 (OCT2) substrates like paraquat (PQ). To realise this NAM, kinetic parameters Vmax and Km for in vitro OCT2 transport of PQ were obtained from the literature. Appropriate scaling factors were applied to translate the in vitro Vmax to an in vivo Vmax. in vitro cytotoxicity data were defined in the rat RLE-6TN and L2 cell lines and the human A549 cell line. The developed PQ PBK model was used to apply reverse dosimetry for QIVIVE translating the in vitro cytotoxicity concentration-response curves to predicted in vivo toxicity dose-response curves after which the lower and upper bound benchmark dose (BMD) for 50% lethality (BMDL50 and BMDU50) were derived by applying BMD analysis. Comparing the predictions to the in vivo reported LD50 values resulted in a conservative prediction for rat and a comparable prediction for human showing proof of principle on the inclusion of active renal excretion and prediction of PQ acute toxicity for the developed NAM.


Assuntos
Modelos Biológicos , Paraquat , Ratos , Humanos , Animais , Paraquat/toxicidade , Transportador 2 de Cátion Orgânico , Eliminação Renal , Linhagem Celular
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