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Ong, Oselyne T. W., Lauren J. Young, and Julie M. Old. "Evaluation of reference genes for gene expression in red-tailed phascogale (Phascogale calura) liver, lung, small intestine and spleen." PeerJ 4 (October 13, 2016): e2552. http://dx.doi.org/10.7717/peerj.2552.
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BackgroundReference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune tissues is yet to be tested. Therefore, an assessment of reference genes is needed for the selection of stable, expressed genes across different marsupial tissues.MethodsThe study was conducted on red-tailed phascogales (Phascogale calura) using five juvenile and five adult males. The stability of five reference genes (glyceraldehyde-3-phosphate dehydrogenase,GAPDH;β-actin,ACTB;18SrRNA,18S; 28SrRNA, 28S;and ribosomal protein L13A,RPL13A) was investigated using SYBR Green and analysed with the geNorm application available in qBasePLUSsoftware.ResultsGene stability for juvenile and adult tissue samples combined show thatGAPDHwas most stable in liver and lung tissue, and18Sin small intestine and spleen. While all reference genes were suitable for small intestine and spleen tissues, all reference genes except28Swere stable for lung and only18Sand28Swere stable for liver tissue. Separating the two age groups, we found that two different reference genes were considered stable in juveniles (ACTBandGAPDH) and adults (18Sand28S), andRPL13Awas not stable for juvenile small intestine tissue. Except for28S, all reference genes were stable in juvenile and adult lungs, and all five reference genes were stable in spleen tissue.DiscussionBased on expression stability,ACTBandGAPDHare suitable for all tissues when studying the expression of marsupials in two age groups, except for adult liver tissues. The expression stability between juvenile and adult liver tissue was most unstable, as the stable reference genes for juveniles and adults were different. Juvenile and adult lung, small intestine and spleen share similar stable reference genes, except for small intestine tissues where all reference genes were stable in adults butRPL13Awas not suitable in juveniles.
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Zheng, Yangyi, Yao Ma, Jianning Luo, et al. "Identification and Analysis of Reference and Tissue-Specific Genes in Bitter Gourd Based on Transcriptome Data." Horticulturae 9, no. 12 (2023): 1262. http://dx.doi.org/10.3390/horticulturae9121262.
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Accurate and standardized quantification of reverse transcription PCR (qRT-PCR) results relies on the use of a dependable reference gene. The precise control of transgene expression in terms of both spatial and temporal aspects necessitates the utilization of tissue-specific gene promoters. However, the identification of stable reference genes across various tissues, particularly in fruits at different ripening stages, as well as tissue-specific genes in bitter gourds, remains largely unexplored. In this study, we employed RNA-Seq-based transcriptome datasets obtained from nine tissues to comprehensively screen for new reference genes (NRGs) and tissue-specific genes. Through the utilization of five algorithms in conjunction with qRT-PCR analysis, we successfully identified two highly stable reference genes, namely HMG1/2 and PHOS32, from a pool of 11 NRGs and five traditional reference genes (TRGs). To validate their reliability, we performed expression pattern analysis of two genes associated with fruit ripening (McACO1 and McACO2) using HMG1/2 and PHOS32, as well as an unstable reference gene, HSCP2. Furthermore, we conducted qRT-PCR validation of 12 tissue-specific genes using HMG1/2 as the reference gene. This study not only contributes to the precise normalization of target genes in bitter gourd but also provides a solid foundation for regulating transgenes through the utilization of suitable tissue-specific promoters.
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Zuba, Iga, and Halina Polkowska-Motrenko. "Ratio primary reference measurement procedure (RPRMP) for the certification of chromium content in biological reference materials." Radiochimica Acta 107, no. 2 (2019): 141–47. http://dx.doi.org/10.1515/ract-2018-2993.
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Abstract Primary reference measurement procedure for Cr determination in biological samples by radiochemical neutron activation analysis (RNAA) has been elaborated. The procedure is based on quantitative and selective separation of chromium from neutron irradiated sample by column chromatography using MnO2-Resin and determination of 51Cr by γ-ray spectrometry. Quality components have been incorporated into the RNAA method which makes it possible to meet the requirements of the definition of ratio primary reference measurement procedure. The usefulness of the elaborated procedure to assign the certified values for Cr in new certified reference material (CRMs) based on animal tissues is demonstrated. The tentative certified values for Cr have been proposed for: MODAS M-4 Cormorant Tissue and M-5 Cod Tissue CRMs.
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Yaqub, Maqsood, Berckel Bart NM van, Alie Schuitemakers, et al. "Optimization of supervised cluster analysis for extracting reference tissue input curves in (R)-[(11)C]PK11195 brain PET studies." Journal of Cerebral Blood Flow & Metabolism 32, no. 8 (2012): 1600–8. https://doi.org/10.1038/jcbfm.2012.59.
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Performance of two supervised cluster analysis (SVCA) algorithms for extracting reference tissue curves was evaluated to improve quantification of dynamic (R)-[(11)C]PK11195 brain positron emission tomography (PET) studies. Reference tissues were extracted from images using both a manually defined cerebellum and SVCA algorithms based on either four (SVCA4) or six (SVCA6) kinetic classes. Data from controls, mild cognitive impairment patients, and patients with Alzheimer's disease were analyzed using various kinetic models including plasma input, the simplified reference tissue model (RPM) and RPM with vascular correction (RPMV(b)). In all subject groups, SVCA-based reference tissue curves showed lower blood volume fractions (V(b)) and volume of distributions than those based on cerebellum time-activity curve. Probably resulting from the presence of specific signal from the vessel walls that contains in normal condition a significant concentration of the 18 kDa translocation protein. Best contrast between subject groups was seen using SVCA4-based reference tissues as the result of a lower number of kinetic classes and the prior removal of extracerebral tissues. In addition, incorporation of V(b) in RPM improved both parametric images and binding potential contrast between groups. Incorporation of V(b) within RPM, together with SVCA4, appears to be the method of choice for analyzing cerebral (R)-[(11)C]PK11195 neurodegeneration studies.
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Xue, Miaomiao, Haibo Wen, Pao Xu, et al. "Validation and Functional Analysis of Reference and Tissue-Specific Genes in Adipose Tissue of Freshwater Drum, Aplodinotus grunniens, under Starvation and Hypothermia Stress." Cells 12, no. 9 (2023): 1328. http://dx.doi.org/10.3390/cells12091328.
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Adipose tissue is critical to the growth, development, and physiological health of animals. Reference genes play an essential role in normalizing the expression of mRNAs. Tissue-specific genes are preferred for their function and expression in specific tissues or cell types. Identification of these genes contributes to understanding the tissue–gene relationship and the etiology and discovery of new tissue-specific targets. Therefore, reference genes and tissue-specific genes in the adipose tissue of Aplodinotus grunniens were identified to explore their function under exogenous starvation (1 d, 2 w, 6 w) and hypothermic stress (18 °C and 10 °C for 2 d and 8 d) in this study. Results suggest that 60SRP was the most stable reference gene in adipose tissue. Meanwhile, eight genes were validated as tissue-specific candidates from the high-throughput sequencing database, while seven of them (ADM2, β2GP1, CAMK1G, CIDE3, FAM213A, HSL, KRT222, and NCEH1) were confirmed in adipose tissue. Additionally, these seven tissue-specific genes were active in response to starvation and hypothermic stress in a time- or temperature-dependent manner. These results demonstrate that adipose-specific genes can be identified using stable internal reference genes, thereby identifying specific important functions under starvation and hypothermic stress, which provides tissue-specific targets for adipose regulation in A. grunniens.
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Chen, Xiatian, Yujie Yu, Tao Gao, Zhifei Liu, Shuaiyu Chen, and Yudong Jia. "Determination of Stable Reference Genes for Gene Expression Analysis in Black Rockfish (Sebastes schlegeli) Under Hypoxia Stress." Genes 16, no. 1 (2024): 9. https://doi.org/10.3390/genes16010009.
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Background: Hypoxia triggers stress, leading to significant alterations in gene expression patterns, which in turn affect fish’s growth and development. Real-time quantitative PCR (RT-qPCR) is a pivotal technique for assessing changes in gene expression. However, its accuracy is highly contingent upon the stable expression of reference genes. Ribosomal RNA (18s), β-actin (actb), elongation factor 1-α (ef1a), α tubulin (tuba), and ribosomal protein L17 (rpl17) are the widely used reference genes, but their expression stability in the tissues of black rockfish under hypoxic conditions remains unclear. Methods: The expression of genes was detected by RT-qPCR and the stability was assessed by Delta Ct, geNorm, NormFinder, and BestKeeper algorithms. Results: Results showed that tuba exhibited stable expression in liver, heart, gill tissues under normoxic conditions, and in the liver and head kidney under hypoxic conditions. Ef1a was identified as the most stably expressed gene in gill tissue under hypoxia. For hypoxic heart studies, rpl17 and tuba were recommended as reference genes. 18s showed high stability in spleen tissue under hypoxic conditions. Actb was the most stably expressed gene in spleen and head kidney tissues under normoxic conditions. Conclusions: The identified reference genes exhibited tissue-specific stability, and it was necessary to select appropriate reference genes based on the specific tissue type for gene expression studies under hypoxic conditions. These findings help in enhancing the accuracy of gene expression analysis in the mechanism of hypoxia for black rockfish.
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Okamoto, Kensaku, and Keiichiro Fuwa. "Mussel tissue powder, a certified reference material." Analyst 110, no. 7 (1985): 785. http://dx.doi.org/10.1039/an9851000785.
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Paredes, L., J. Azorín, M. Balcázar, and J. L. François. "Neutron kerma coefficient: Reference tissue for tumours." Radiation Measurements 45, no. 10 (2010): 1445–48. http://dx.doi.org/10.1016/j.radmeas.2010.05.024.
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Yaqub, Maqsood, Bart NM van Berckel, Alie Schuitemaker, et al. "Optimization of Supervised Cluster Analysis for Extracting Reference Tissue Input Curves in (R)-[11C]PK11195 Brain PET Studies." Journal of Cerebral Blood Flow & Metabolism 32, no. 8 (2012): 1600–1608. http://dx.doi.org/10.1038/jcbfm.2012.59.
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Performance of two supervised cluster analysis (SVCA) algorithms for extracting reference tissue curves was evaluated to improve quantification of dynamic (R)-[11C]PK11195 brain positron emission tomography (PET) studies. Reference tissues were extracted from images using both a manually defined cerebellum and SVCA algorithms based on either four (SVCA4) or six (SVCA6) kinetic classes. Data from controls, mild cognitive impairment patients, and patients with Alzheimer's disease were analyzed using various kinetic models including plasma input, the simplified reference tissue model (RPM) and RPM with vascular correction (RPM V b). In all subject groups, SVCA-based reference tissue curves showed lower blood volume fractions ( V b) and volume of distributions than those based on cerebellum time-activity curve. Probably resulting from the presence of specific signal from the vessel walls that contains in normal condition a significant concentration of the 18 kDa translocation protein. Best contrast between subject groups was seen using SVCA4-based reference tissues as the result of a lower number of kinetic classes and the prior removal of extracerebral tissues. In addition, incorporation of V b in RPM improved both parametric images and binding potential contrast between groups. Incorporation of V b within RPM, together with SVCA4, appears to be the method of choice for analyzing cerebral (R)-[11C]PK11195 neurodegeneration studies.
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Ma, Long, Ting Jiang, Xiangya Liu, Haijun Xiao, Yingchuan Peng, and Wanna Zhang. "Evaluation of candidate reference genes for gene expression analysis in the brassica leaf beetle, Phaedon brassicae (Coleoptera: Chrysomelidae)." PLOS ONE 16, no. 6 (2021): e0251920. http://dx.doi.org/10.1371/journal.pone.0251920.
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The brassica leaf beetle Phaedon brassicae is a notorious defoliator of cruciferous vegetables. However, few molecular studies of this pest have been conducted due to limited sequence data. Recently, RNA sequencing has offered a powerful platform to generate numerous transcriptomic data, which require RT-qPCR to validate target gene expression. The selection of reliable reference genes to normalize RT-qPCR data is a prerequisite for gene expression analysis. In the present study, the expression stabilities of eight candidate reference genes under biotic conditions (development stages and various tissues) and abiotic perturbations (thermal stress and pesticide exposure) were evaluated using four different statistical algorithms. The optimal suites of reference genes were recommended for the respective experimental conditions. For tissue expression analysis, RPL32 and EF-1α were recommended as the suitable reference genes. RPL19 and TBP were the optimal reference genes across different developmental stages. RPL32 and TBP were identified as the most suitable references for thermal stress. Furthermore, RPL32 and RPL19 were ranked as the best references for insecticide exposure. This work provides a systematic exploration of the optimal reference genes for the respective experimental conditions, and our findings would facilitate molecular studies of P. brassicae.
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Young, Alexander P., Carmen F. Landry, Daniel J. Jackson, and Russell C. Wyeth. "Tissue-specific evaluation of suitable reference genes for RT-qPCR in the pond snail, Lymnaea stagnalis." PeerJ 7 (October 15, 2019): e7888. http://dx.doi.org/10.7717/peerj.7888.
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Reverse transcription quantitative PCR (RT-qPCR) is a robust technique for the quantification and comparison of gene expression. To obtain reliable results with this method, one or more reference genes must be employed to normalize expression measurements among treatments or tissue samples. Candidate reference genes must be validated to ensure that they are stable prior to use in qPCR experiments. The pond snail (Lymnaea stagnalis) is a common research organism, particularly in the areas of learning and memory, and is an emerging model for the study of biological asymmetry, biomineralization, and evolution and development. However, no systematic assessment of qPCR reference genes has been performed in this animal. Therefore, the aim of our research was to identify stable reference genes to normalize gene expression data from several commonly studied tissues in L. stagnalis as well as across the entire body. We evaluated a panel of seven reference genes across six different tissues in L. stagnalis with RT-qPCR. The genes included: elongation factor 1-alpha, glyceraldehyde-3-phosphate dehydrogenase, beta-actin, beta-tubulin, ubiquitin, prenylated rab acceptor protein 1, and a voltage gated potassium channel. These genes exhibited a wide range of expression levels among tissues. The tissue-specific stability of each of the genes was consistent when measured by the standard stability assessment algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. Our data indicate that the most stable reference genes vary among the tissues that we examined (central nervous system, tentacles, lips, penis, foot, mantle). Our results were generally congruent with those obtained from similar studies in other molluscs. Given that a minimum of two reference genes are recommended for data normalization, we provide suggestions for strong pairs of reference genes for single- and multi-tissue analyses of RT-qPCR data in L. stagnalis.
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Eleveld, Nick, Diana C. Esquivel-Franco, Gea Drost, et al. "The Influence of Extracerebral Tissue on Continuous Wave Near-Infrared Spectroscopy in Adults: A Systematic Review of In Vivo Studies." Journal of Clinical Medicine 12, no. 8 (2023): 2776. http://dx.doi.org/10.3390/jcm12082776.
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Near-infrared spectroscopy (NIRS) is a non-invasive technique for measuring regional tissue haemoglobin (Hb) concentrations and oxygen saturation (rSO2). It may be used to monitor cerebral perfusion and oxygenation in patients at risk of cerebral ischemia or hypoxia, for example, during cardiothoracic or carotid surgery. However, extracerebral tissue (mainly scalp and skull tissue) influences NIRS measurements, and the extent of this influence is not clear. Thus, before more widespread use of NIRS as an intraoperative monitoring modality is warranted, this issue needs to be better understood. We therefore conducted a systematic review of published in vivo studies of the influence of extracerebral tissue on NIRS measurements in the adult population. Studies that used reference techniques for the perfusion of the intra- and extracerebral tissues or that selectively altered the intra- or extracerebral perfusion were included. Thirty-four articles met the inclusion criteria and were of sufficient quality. In 14 articles, Hb concentrations were compared directly with measurements from reference techniques, using correlation coefficients. When the intracerebral perfusion was altered, the correlations between Hb concentrations and intracerebral reference technique measurements ranged between |r| = 0.45–0.88. When the extracerebral perfusion was altered, correlations between Hb concentrations and extracerebral reference technique measurements ranged between |r| = 0.22–0.93. In studies without selective perfusion modification, correlations of Hb with intra- and extracerebral reference technique measurements were generally lower (|r| < 0.52). Five articles studied rSO2. There were varying correlations of rSO2 with both intra- and extracerebral reference technique measurements (intracerebral: |r| = 0.18–0.77, extracerebral: |r| = 0.13–0.81). Regarding study quality, details on the domains, participant selection and flow and timing were often unclear. We conclude that extracerebral tissue indeed influences NIRS measurements, although the evidence (i.e., correlation) for this influence varies considerably across the assessed studies. These results are strongly affected by the study protocols and analysis techniques used. Studies employing multiple protocols and reference techniques for both intra- and extracerebral tissues are therefore needed. To quantitatively compare NIRS with intra- and extracerebral reference techniques, we recommend applying a complete regression analysis. The current uncertainty regarding the influence of extracerebral tissue remains a hurdle in the clinical implementation of NIRS for intraoperative monitoring. The protocol was pre-registered in PROSPERO (CRD42020199053).
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Brumbaugh, William G., and Michael J. Walther. "Improved Selenium Recovery from Tissue with Modified Sample Decomposition." Journal of AOAC INTERNATIONAL 74, no. 3 (1991): 570–71. http://dx.doi.org/10.1093/jaoac/74.3.570.
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Abstract The present paper describes a simple modification of a recently reported decomposition method for determination of selenium In biological tissue by hydride generation atomic absorption. The modified method yielded slightly higher selenium recoveries (3-4%) for selected reference tissues and fish tissue spiked with selenomethionine. Radiotracer experiments indicated that the addition of a small volume of hydrochloric acid to the wet digestate mixture reduced slight losses of selenium as the sample initially went to dryness before ashing. With the modified method, selenium spiked as selenomethionine behaved more like the selenium in reference tissues than did the inorganic spike forms when this digestion modification was used
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Guo, Chaohui, Zihao Zhang, Meina Zhang, et al. "Screening and Stability Analysis of Reference Genes for Gene Expression Normalization in Hybrid Yellow Catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) Fed Diets Containing Different Soybean Meal Levels." Aquaculture Nutrition 2023 (September 22, 2023): 1–17. http://dx.doi.org/10.1155/2023/1232518.
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In this study, we screened the expression stability of six reference genes (18S rRNA, β-actin, GAPDH, EF1a, B2M, and HPRT1) in hybrid yellow catfish (n = 6), considering the SBM levels, sampling time points, and different tissues. Four different statistical programs, BestKeeper, NormFinder, Genorm, and Delta Ct, combined with a method that comprehensively considered all results, were used to evaluate the expression stability of these reference genes systematically. The results showed that SBM levels significantly impacted the expression stability of most of the reference genes studied and that this impact was time-, dose-, and tissue-dependent. The expression stability of these six reference genes varied depending on tissue, sampling time point, and SBM dosage. Additionally, more variations were found among different tissues than among different SBM levels or sampling time points. Due to its high expression, 18S rRNA was excluded from the list of candidate reference genes. β-actin and GAPDH in the liver and β-actin, HPRT1 and EF1a in the intestine were the most stable reference genes when SBM levels were considered. HPRT1, and EF1a in tissues sampled at 2 W and EF1a and β-actin in tissues sampled at 4 and 6 W were proposed as two stable reference genes when different tissues were considered. When the sampling time points were considered, β-actin, EF1a, and HPRT1 were the top three stable reference genes in the intestine. In contrast, β-actin and B2M are the most stable reference genes in the liver. In summary, β-actin, EF1a, and HPRT1 were the more stable reference genes in this study. The stability of reference genes depends on the tissues, sampling time points, and SBM diet levels in hybrid yellow catfish. Therefore, attention should be paid to these factors before selecting suitable reference genes for normalizing the target genes.
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Bhattacharya, Arjun, Alina M. Hamilton, Melissa A. Troester, and Michael I. Love. "DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing." Nucleic Acids Research 49, no. 8 (2021): e48-e48. http://dx.doi.org/10.1093/nar/gkab031.
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Abstract Targeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we present DeCompress, a semi-reference-free deconvolution method for targeted panels. DeCompress leverages a reference RNA-seq or microarray dataset from similar tissue to expand the feature space of targeted panels using compressed sensing. Ensemble reference-free deconvolution is performed on this artificially expanded dataset to estimate cell-type proportions and gene signatures. In simulated mixtures, four public cell line mixtures, and a targeted panel (1199 samples; 406 genes) from the Carolina Breast Cancer Study, DeCompress recapitulates cell-type proportions with less error than reference-free methods and finds biologically relevant compartments. We integrate compartment estimates into cis-eQTL mapping in breast cancer, identifying a tumor-specific cis-eQTL for CCR3 (C–C Motif Chemokine Receptor 3) at a risk locus. DeCompress improves upon reference-free methods without requiring expression profiles from pure cell populations, with applications in genomic analyses and clinical settings.
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Brito, A. B., J. S. Lima, D. C. Brito, et al. "Validation of reference genes for ovarian tissue from capuchin monkeys (Cebus apella)." Zygote 21, no. 2 (2012): 167–71. http://dx.doi.org/10.1017/s0967199411000748.
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SummaryThere is no tradition in studies reporting the effect of exposure to cryoprotectants or simply hypoxia and hypothermia on gene expression in the ovarian tissue and there has been only one study on reference or target genes quantification, and comparisons of normoxic with hypoxic, hypothermic and toxic conditions. Our aim in the present study was to investigate the stability of three reference genes in the ovarian tissue of capuchin monkeys (Cebus apella). To this end, fresh and cryoprotectant-exposed ovarian biopsies were used. Both fresh and exposed ovarian tissues were subjected to total RNA extraction and synthesis of cDNA. cDNA was amplified by real-time polymerase chain reaction (PCR), and GeNorm, BestKeeper and NormFinder software were used to evaluate the stability of glyceraldehyde-2-phosphate dehydrogenase (GAPDH), hypoxanthine phosphoribosyltransferase 1 (HPRT1) and TATA-binding protein (TBP). Results demonstrated that, in the ovarian tissue from capuchin monkeys, HPRT1 and TBP were the most suitable reference genes and thus could be used as parameters to normalize data in future studies. In contrast, GAPDH appeared as the least stable gene among the tested reference genes. In conclusion, HPRT1 and TBP were the most stable reference genes in fresh and cryoprotectant-exposed ovarian tissue from capuchin monkeys.
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Nesvadbová, M., and A. Knoll. "Evaluation of reference genes for gene expression studies in pig muscle tissue by real-time PCR." Czech Journal of Animal Science 56, No. 5 (2011): 213–16. http://dx.doi.org/10.17221/1428-cjas.
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The selection of reference genes is essential for gene expression studies when using a real-time quantitative polymerase chain reaction (PCR). Reference gene selection should be performed for each experiment because the gene expression level may be changed in different experimental conditions. In this study, the stability of mRNA expression was determined for seven genes: HPRT1, RPS18, NACA, TBP, TAF4B, RPL32 and OAZ1. The stability of these reference genes was investigated in the skeletal muscle tissue of pig foetuses, piglets and adult pigs using real-time quantitative PCR and SYBR green chemistry. The expression of stability of the used reference genes was calculated using the geNorm application. Different gene expression profiles among the age categories of pigs were found out. RPS18 has been identified as the gene with the most stable expression in the muscle tissue of all pig age categories. HPRT1 and RPL32 were found to have the highest stability in piglets and adult pigs, and in foetuses and adults pigs, respectively. The newly used reference gene, TAF4B, reached the highest expression stability in piglets.
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Wang, Linjie, Xingyue Chen, Tianzeng Song, et al. "Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats." Animals 10, no. 9 (2020): 1626. http://dx.doi.org/10.3390/ani10091626.
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Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white adipose tissue (WAT), it is necessary to utilize Quantitative PCR (qPCR) to study gene expression profiling. In this study, we identified reference genes that were consistently expressed during the transformation from goat BAT to WAT using RNA-seq data. Then, twelve genes were evaluated as candidate reference genes for qPCR in goat perirenal adipose tissue using three tools (geNorm, Normfinder, and BestKeeper). In addition, the selected reference genes were used to normalize the gene expression of PGC-1α and GPAT4. It was found that traditional reference genes, such as GAPDH, RPLP0, HPRT1, and PPIA were not suitable for target gene normalization. In contrast, CTNNB, PFDN5, and EIF3M, selected from RNA sequencing data, showed the least variation and were recommended as the best reference genes during the transformation from BAT to WAT.
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Crooks, S. R. H., W. J. Mccaughey, C. T. Elliott, J. D. Mcevoy, and S. A. Hewitt. "The production of pig tissue sulphadimidine reference material." Food Additives and Contaminants 13, no. 2 (1996): 211–19. http://dx.doi.org/10.1080/02652039609374399.
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Lammertsma, Adriaan A., and Susan P. Hume. "Simplified Reference Tissue Model for PET Receptor Studies." NeuroImage 4, no. 3 (1996): 153–58. http://dx.doi.org/10.1006/nimg.1996.0066.
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Hurschler, Christof, Paolo P. Provenzano, and Ray Vanderby,. "Application of a Probabilistic Microstructural Model to Determine Reference Length and Toe-to-Linear Region Transition in Fibrous Connective Tissue." Journal of Biomechanical Engineering 125, no. 3 (2003): 415–22. http://dx.doi.org/10.1115/1.1579046.
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This study shows how a probabilistic microstructural model for fibrous connective tissue behavior can be used to objectively describe soft tissue low-load behavior. More specifically, methods to determine tissue reference length and the transition from the strain-stiffening “toe-region” to the more linear region of the stress-strain curve of fibrous connective tissues are presented. According to a microstructural model for uniaxially loaded collagenous tissues, increasingly more fibers are recruited and bear load with increased tissue elongation. Fiber recruitment is represented statistically according to a Weibull probability density function (PDF). The Weibull PDF location parameter in this formulation corresponds to the stretch at which the first fibers begin to bear load and provides a convenient method of determining reference length. The toe-to-linear region transition is defined by utilizing the Weibull cumulative distribution function (CDF) which relates the fraction of loaded fibers to the tissue elongation. These techniques are illustrated using representative tendon and ligament data from the literature, and are shown to be applicable retrospectively to data from specimens that are not heavily preloaded. The reference length resulting from this technique provides an objective datum from which to calculate stretch, strain, and tangent modulus, while the Weibull CDF provides an objective parameter with which to characterize the limits of low-load behavior.
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Liu, Xin, Yingbo Gao, Xinyi Zhao, et al. "Validation of Novel Reference Genes in Different Rice Plant Tissues through Mining RNA-Seq Datasets." Plants 12, no. 23 (2023): 3946. http://dx.doi.org/10.3390/plants12233946.
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Reverse transcription quantitative real-time PCR (RT-qPCR) is arguably the most prevalent and accurate quantitative gene expression analysis. However, selection of reliable reference genes for RT-qPCR in rice (Oryza sativa) is still limited, especially for a specific tissue type or growth condition. In this study, we took the advantage of our RNA-seq datasets encompassing data from five rice varieties with diverse treatment conditions, identified 12 novel candidate reference genes, and conducted rigorous evaluations of their suitability across typical rice tissues. Comprehensive analysis of the leaves, shoots, and roots of two rice seedlings subjected to salt (30 mmol/L NaCl) and drought (air-dry) stresses have revealed that OsMED7, OsACT1, and OsOS-9 were the robust reference genes for leaf samples, while OsACT1, OsZOS3-23, and OsGDCP were recommended for shoots and OsMED7, OsOS-9, and OsGDCP were the most reliable reference genes for roots. Comparison results produced by different sets of reference genes revealed that all these newly recommended reference genes displayed less variation than previous commonly used references genes under the experiment conditions. Thus, selecting appropriate reference genes from RNA-seq datasets leads to identification of reference genes suitable for respective rice tissues under drought and salt stress. The findings offer valuable insights for refining the screening of candidate reference genes under diverse conditions through the RNA-seq database. This refinement serves to improve the accuracy of gene expression in rice under similar conditions.
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Zhang, X. D., Y. Zhang, X. Liu, et al. "132 REFERENCE GENE SCREENING FOR ANALYZING GENE EXPRESSION ACROSS FEMALE GOAT TISSUE." Reproduction, Fertility and Development 26, no. 1 (2014): 179. http://dx.doi.org/10.1071/rdv26n1ab132.
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Quantitative RT-PCR (RT-qPCR) is an important method for investigating changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of RT-qPCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We applied absolute quantification using the standard curve method to the detection of the expression levels of 8 reference gene candidates (18S, TBP, YWHAZ, HMBS, ACTB, HPRT1, GAPDH, and EEF1A2) in 10 different tissue types (heart, liver, spleen, lung, kidney, stomach, uterus, ovary, small intestine, and muscle) sourced from a 5-month-old female Boer goat. All the experiments were performed using 3 biological replicates and technical triplicates of each cDNA sample. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder, and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in gene expression stability. When all tissues were considered, 18S, TBP, and HMBS with the smallest paired variation coefficient is the optimal reference combination for calibrating RT-qPCR analysis of gene expression from goat tissues. The stability of each gene was evaluated, taking into account all of the data. The stability values (M) for these genes were 0.643/0.634/0.799, 0.156/0.467/0.584, and 0.396/0.445/0.566 by geNorm, NormFinder, and Bestkeeper, respectively. Dividing the dataset by different tissues, ACTB was the most stable in stomach, small intestine, and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney, and GAPDH in muscle. Overall, this study provided valuable information about the female goat reference genes that can be used in order to perform a proper normalisation when relative quantification by RT-qPCR studies is undertaken. This work was supported by National ‘863’ Program (2011AA100307-4), the Technology Innovation Project – Special Program and the Science and Technology Program of Anhui Province (11Z0101095 and 11010302108).
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Klumpers, Ursula MH, Dick J. Veltman, Ronald Boellaard, et al. "Comparison of Plasma Input and Reference Tissue Models for Analysing [11C]flumazenil Studies." Journal of Cerebral Blood Flow & Metabolism 28, no. 3 (2007): 579–87. http://dx.doi.org/10.1038/sj.jcbfm.9600554.
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A single-tissue compartment model with plasma input is the established method for analysing [11C]flumazenil ([11C]FMZ) studies. However, arterial cannulation and measurement of metabolites are time-consuming. Therefore, a reference tissue approach is appealing, but this approach has not been fully validated for [11C]FMZ. Dynamic [11C]FMZ positron emission tomography scans with arterial blood sampling were performed in nine drug-free depressive patients and eight healthy subjects. Regions of interest were defined on co-registered magnetic resonance imaging scans and projected onto dynamic [11C]FMZ images. Using a Hill-type metabolite function, single (1T) and reversible two-tissue (2T) compartmental models were compared. Simplified reference tissue model (SRTM) and full reference tissue model (FRTM) were investigated using both pons and (centrum semiovale) white matter as reference tissue. The 2T model provided the best fit in 59% of cases. Two-tissue VT values were on average 1.6% higher than 1T VT values. Owing to the higher rejection rate of 2T fits (7.3%), the 1T model was selected as plasma input method of choice. SRTM was superior to FRTM, irrespective whether pons or white matter was used as reference tissue. BPND values obtained with SRTM correlated strongly with 1T VT ( r = 0.998 and 0.995 for pons and white matter, respectively). Use of white matter as reference tissue resulted in 5.5% rejected fits, primarily in areas with intermediate receptor density. No fits were rejected using pons as reference tissue. Pons produced 23% higher BPND values than white matter. In conclusion, for most clinical studies, SRTM with pons as reference tissue can be used for quantifying [11C]FMZ binding.
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Tang, Jing, Enjiao Li, Jiexia Liu, et al. "Selection of Reliable Reference Genes for Gene Expression Normalization in Sagittaria trifolia." Genes 14, no. 7 (2023): 1321. http://dx.doi.org/10.3390/genes14071321.
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Real-time quantitative PCR (RT-qPCR) is a method with high sensitivity and convenience that has been extensively used to analyze the expression level of target genes. A reference gene with a highly stable expression is required to ensure the accuracy of experimental results. However, the report on appropriate reference genes in arrowheads (Sagittaria trifolia) is still limited. In this study, eight candidate reference genes (ACT5, UBQ, GAPDH, CYP, NAC, IDH, SLEEPER and PLA) were selected. The candidate genes were employed in a RT-qPCR assay in different tissues at different developmental stages of the same tissue (including corm, leaf and leafstalk) in arrowheads. Five statistical algorithms, GeNorm, NormFinder, BestKeeper, delta cycle threshold (ΔCt) and RefFinder, were used to evaluate the stability of these genes’ expressions in order to identify the appropriate reference genes. The results showed that UBQ was the optimum reference gene in leaf, leafstalk, root, stolon and corm, IDH exhibited the most stable expression during the expansion of corm, UBQ and PLA were the most stable reference genes in developmental stages of leaf and leafstalk, respectively. Finally, the reliability of reference genes was further confirmed by the normalization of PDS and EXP1 genes under different arrowhead tissues and developmental stages of corm, respectively. This study constitutes important guidance for the selection of reliable reference genes for analyzing the tissue- and developmental-stage-specific expression of genes in arrowheads.
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Pei, Guangsheng, Yulin Dai, Zhongming Zhao, and Peilin Jia. "deTS: tissue-specific enrichment analysis to decode tissue specificity." Bioinformatics 35, no. 19 (2019): 3842–45. http://dx.doi.org/10.1093/bioinformatics/btz138.
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Abstract Motivation Diseases and traits are under dynamic tissue-specific regulation. However, heterogeneous tissues are often collected in biomedical studies, which reduce the power in the identification of disease-associated variants and gene expression profiles. Results We present deTS, an R package, to conduct tissue-specific enrichment analysis with two built-in reference panels. Statistical methods are developed and implemented for detecting tissue-specific genes and for enrichment test of different forms of query data. Our applications using multi-trait genome-wide association studies data and cancer expression data showed that deTS could effectively identify the most relevant tissues for each query trait or sample, providing insights for future studies. Availability and implementation https://github.com/bsml320/deTS and CRAN https://cran.r-project.org/web/packages/deTS/ Supplementary information Supplementary data are available at Bioinformatics online.
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Troeltzsch, Daniel, Stefan Markus Niehues, Tabea Fluegge, et al. "The diagnostic performance of perfusion CT in the detection of local tumor recurrence in head and neck cancer." Clinical Hemorheology and Microcirculation 76, no. 2 (2020): 171–77. http://dx.doi.org/10.3233/ch-209209.
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BACKGROUND: Detecting local tumor recurrence from post-treatment changes in head and neck cancer (HNC) remains a challenge. Based on the hypothesis that post-therapeutically altered tissue is bradytroph, lower perfusion values are expected in perfusion CT (PCT) while higher perfusion values are expected in recurrent malignant tissue. OBJECTIVES: This prospective study investigates PCT for post-treatment recurrent HNC detection with a maximum slope algorithm. METHODS: A total of 80 patients who received PCT of the head and neck for post-therapy follow-up, of which 63 had no tumor recurrence and 17 presented a histopathologically confirmed recurrence were examined. Regions of interest were placed in the location of the initial tumor, in reference ipsilateral nuchal muscle tissue and the corresponding internal carotid artery. Perfusion was calculated using a single-input maximum slope algorithm. RESULTS: With PCT, recurrent HNC can be differentiated from post-treatment tissue (p < 0.05). It further allows delineating recurrent tumor tissue from benign nuchal tissue of reference (p < 0.05). PCT data of patients with and without recurrent HNC are comparable as perfusion values of reference tissues in patients with and without HNC do not differ (p > 0.05). CONCLUSIONS: PCT in combination with a commercially available maximum slope algorithm offers radiologists a reliable imaging tool to detect recurrent head and neck cancer within post-therapeutically altered tissue.
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Lee, Sang-Yun, Yong-Ho Choe, Jang-Ho Han, et al. "HPRT1 Most Suitable Reference Gene for Accurate Normalization of mRNA Expression in Canine Dermal Tissues with Radiation Therapy." Genes 13, no. 11 (2022): 1928. http://dx.doi.org/10.3390/genes13111928.
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Reference genes are crucial in molecular biological studies as an internal control for gene re-search as they exhibit consistent expression patterns across many tissue types. In canines, radiation therapy is the most important therapeutic tool to cure various diseases like cancer. However, when using radiation for therapeutic strategy, radiation exposure to healthy tissues leads to some possible side effects such as acute radiation-induced skin injury and alters gene expression. Therefore, the analysis of a change in reference gene expression during the skin recovery process after radiation therapy is essential in healthy canine tissue. In the present study, we analyzed eight reference genes (ACTB, GAPDH, YWHAZ, GUSB, HPRT1, RPL4, RPS5, and TBP) in canine dermal tissues at 0, 1, 2, 3, 4, 5, 7, and 9 weeks of radiation exposure that affected the skin condition of canines. The stability of reference genes is determined by evaluating radiation therapy’s effect on healthy canine dermal tissue. Epidermal marker, Keratin 10 expression varies each week after irradiation, and HPRT1 is found to be the most suitable for normalization of mRNA expression in radiation-exposed canine dermal tissues. Changes in the gene expression level were evaluated by using a reliable tool such as quantitative real-time polymerase chain reaction (qRT-PCR). In order to achieve a valid qRT-PCR result, the most stable reference genes used for normalization after the radiation exposure process are important. Therefore, the current study was designed to evaluate the most stable reference gene for the post-irradiation canine tissues. After radiation exposure, the alternation of reference gene expression was estimated by three algorithms (geNorm, Normfinder, and Bestkeeper). The RG validation programs (GeNorm and NormFinder) suggested that HPRT1, RPL4, and TBP were suitable for normalization in qRT-PCR. Furthermore, three algorithms suggested that HPRT1 was the most stable reference gene for normalization with qRT-PCR results, regardless of before and after radiation exposure. Whereas GAPDH was found to be the most unstable reference gene. In addition, the use of stable or unstable reference genes for the normalization of Keratin 10 expression showed statistical differences. Therefore, we observed that, to obtain accurate and suitable PCR results of the canine tissues with and without radiation exposure, the HPRT1 reference gene is recommended for normalization with its high stability. Additionally, the use of RGs such as HPRT1, RPL4, and TBP for normalization in qRT-PCR experiments is recommended for post-radiation canine tissues to generate more accurate and reliable data. These results will provide fundamental information regarding internal controls for gene expression studies and can be used for the analysis of gene patterns in regenerative medicine.
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Too, Issac H. K., and Maurice H. T. Ling. "Signal Peptidase Complex Subunit 1 and Hydroxyacyl-CoA Dehydrogenase Beta Subunit Are Suitable Reference Genes in Human Lungs." ISRN Bioinformatics 2012 (December 28, 2012): 1–7. http://dx.doi.org/10.5402/2012/790452.
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Lung cancer is a common cancer, and expression profiling can provide an accurate indication to advance the medical intervention. However, this requires the availability of stably expressed genes as reference. Recent studies had shown that genes that are stably expressed in a tissue may not be stably expressed in other tissues suggesting the need to identify stably expressed genes in each tissue for use as reference genes. DNA microarray analysis has been used to identify those reference genes with low fluctuation. Fourteen datasets with different lung conditions were employed in our study. Coefficient of variance, followed by NormFinder, was used to identify stably expressed genes. Our results showed that classical reference genes such as GAPDH and HPRT1 were highly variable; thus, they are unsuitable as reference genes. Signal peptidase complex subunit 1 (SPCS1) and hydroxyacyl-CoA dehydrogenase beta subunit (HADHB), which are involved in fundamental biochemical processes, demonstrated high expression stability suggesting their suitability in human lung cell profiling.
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Yokoi, Kakeru, Takuya Tsubota, Akiya Jouraku, Hideki Sezutsu, and Hidemasa Bono. "Reference Transcriptome Data in Silkworm Bombyx mori." Insects 12, no. 6 (2021): 519. http://dx.doi.org/10.3390/insects12060519.
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Herein, we performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. The sequences were mapped onto the reference genome assembly and the reference transcriptome data were successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly improved the gene model for other genes. The transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified. We successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research as well as the practical use of these insects.
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Li, Ziyi, Zhenxing Guo, Ying Cheng, Peng Jin, and Hao Wu. "Robust partial reference-free cell composition estimation from tissue expression." Bioinformatics 36, no. 11 (2020): 3431–38. http://dx.doi.org/10.1093/bioinformatics/btaa184.
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Abstract Motivation In the analysis of high-throughput omics data from tissue samples, estimating and accounting for cell composition have been recognized as important steps. High cost, intensive labor requirements and technical limitations hinder the cell composition quantification using cell-sorting or single-cell technologies. Computational methods for cell composition estimation are available, but they are either limited by the availability of a reference panel or suffer from low accuracy. Results We introduce TOols for the Analysis of heterogeneouS Tissues TOAST/-P and TOAST/+P, two partial reference-free algorithms for estimating cell composition of heterogeneous tissues based on their gene expression profiles. TOAST/-P and TOAST/+P incorporate additional biological information, including cell-type-specific markers and prior knowledge of compositions, in the estimation procedure. Extensive simulation studies and real data analyses demonstrate that the proposed methods provide more accurate and robust cell composition estimation than existing methods. Availability and implementation The proposed methods TOAST/-P and TOAST/+P are implemented as part of the R/Bioconductor package TOAST at https://bioconductor.org/packages/TOAST. Contact ziyi.li@emory.edu or hao.wu@emory.edu Supplementary information Supplementary data are available at Bioinformatics online.
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Nasar, Mustafa, Donald J. Ferguson, Johnny Joung-Lin Liaw, Laith Makki, and Nikhilesh R. Vaid. "What is the best soft-tissue reference plane to quantify lip change in bimaxillary protrusion cases? A retrospective cohort study." APOS Trends in Orthodontics 10 (September 18, 2020): 178–84. http://dx.doi.org/10.25259/apos_136_2020.
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Objectives: The objective of the study was to evaluate the validity of five soft-tissue profile planes to actual horizontal lower lip changes following treatment of severe bimaxillary protrusion patients with vertical maxillary excess using extra-alveolar miniscrews. The null hypothesis was no differences in the incremental changes of horizontal lower lip changes from pre-treatment to post-treatment of the five methods compared to actual changes. Materials and Methods: Seventy adults were treated orthodontically with extractions for bimaxillary protrusion and “gummy” smile using extra-alveolar miniscrews. Lower lip horizontal position was assessed with pre- and post-treatment lateral cephalograms and five commonly used soft-tissue reference lines were used to measure horizontal lower lip treatment change. Results: Compared to actual therapeutic lower lip horizontal retraction (4.38 mm), soft-tissue references Ricketts’ E-line (3.89 mm) and Steiner’s S-line (3.88 mm) demonstrated no statistical difference (P > 0.05) from actual change. The five profile plane measures showed moderately high to high intercorrelations among themselves, but none of them were related to the actual amount of anteroposterior lip change that occurred. None of the five soft-tissue measurements showed a statistically significant difference (P > 0.05) between subgroups with least and greatest lower lip retraction. Conclusion: Under conditions of maximum lower lip retraction, Rickett’s E-line and Steiner’s S-line were fair measures of horizontal lower lip change. Although actual lower lip change and soft-tissue reference plane changes were correlated poorly, intercorrelations among the five soft-tissue references planes were moderately high. None of the five soft-tissue measurements was able to discriminate (P > 0.05) between treatments with least and greatest lower lip retraction. It may be concluded that Rickett’s E-line and Steiner’s S-line soft-tissue profile references are valid when there is considerable therapeutic retraction (4+ mm) of the lower lip.
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Rodríguez-Parra, Alba, Jesús Picazo-Aragonés, and Francisco Balao. "Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR." Plants 11, no. 4 (2022): 518. http://dx.doi.org/10.3390/plants11040518.
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Dianthus broteri is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation. In these cases, real-time polymerase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.
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Song, Chen, Evan Janzen, Tessa Devoe, et al. "Abstract 7045: RNA sequencing approaches enable tissue specific B and T cell gene expression and immune repertoire profiling." Cancer Research 84, no. 6_Supplement (2024): 7045. http://dx.doi.org/10.1158/1538-7445.am2024-7045.
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Abstract The adaptive immune system defends the human body from pathogens through the recognition ability of antigen receptors from B and T cells. Different organs play various immune function roles, and therefore present varied B and T cell gene expression and immune repertoire profiles. Abnormality of these profiles may reflect immunological disorder, presence of neoplastic tissue, or response to infectious agent. High-throughput sequencing technology has facilitated the understanding of gene expression and related cell functions, but in-depth understanding of B and T cell phenotype and clonotype profiling is an emerging application that has yet to take full advantage of sequencing technology for diagnosis and prognosis of disease. Here, we share results of RNA sequencing of immune system tissues; including B cell and T cell specific gene expression and full-length immune repertoire profiling. Total RNA was extracted from various tissue samples including healthy donor peripheral blood mononuclear cells (PBMC), lymph nodes, bone marrow, spleen, thyroid, thymus and colon, as well as diseased PBMC and colon samples. RNA-seq and Immune-seq libraries were made from these samples and sequenced on Illumina NextSeq2000. Gene expression analysis and immune repertoire profiling from RNA-seq data were performed using edgeR and TRUST4. Immune repertoire sequencing data was processed using pRESTO and IgBlast. We correlated RNA-seq with Immune-seq results for B-cell receptor and T-cell receptor clonotypes. Differential expression and clonotype profiling comparisons were also performed between normal and diseased RNA samples. The effect of reference on immune repertoire detection sensitivity and accuracy was further investigated by comparing IMGT reference and AIRR-C Human IG Reference Sets. This study has identified tissue specific B/T cell phenotype and clonality patterns that relate to tissue functions and disease progression. RNA-seq enables highly multiplex immunophenotyping which is traditionally performed by flow cytometry. RNA-seq can detect high-abundant clones that correlate with Immune-seq, with the latter targeted approach providing more in depth clonality signatures. References comparison results show the importance of continued community effort to develop more representative and accurate immunorepertoire germ line references for clonotype annotation in diverse populations. Integrating both RNA sequencing and immune repertoire sequencing approaches allows accurate phenotype and clonotype determination for immune landscape in various tissues. Citation Format: Chen Song, Evan Janzen, Tessa Devoe, Ariel Erijman, Gautam Naishadham, Li Song, Bradley W. Langhorst. RNA sequencing approaches enable tissue specific B and T cell gene expression and immune repertoire profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7045.
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Kasprzyk, Paula, Paweł M. Wróbel, Joanna Dudała, et al. "Elemental Composition of Skeletal Muscle Fibres Studied with Synchrotron Radiation X-ray Fluorescence (SR-XRF)." International Journal of Molecular Sciences 23, no. 14 (2022): 7931. http://dx.doi.org/10.3390/ijms23147931.
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Diseases of the muscle tissue, particularly those disorders which result from the pathology of individual muscle cells, are often called myopathies. The diversity of the content of individual cells is of interest with regard to their role in both biochemical mechanisms and the structure of muscle tissue itself. These studies focus on the preliminary analysis of the differences that may occur between diseased tissues and tissues that have been recognised as a reference group. To do so, 13 samples of biopsied human muscle tissues were studied: 3 diagnosed as dystrophies, 6 as (non-dystrophic) myopathy and 4 regarded as references. From these sets of muscle biopsies, 135 completely measured muscle fibres were separated altogether, which were subjected to investigations using synchrotron radiation X-ray fluorescence (SR-XRF). Muscle fibres were analysed in terms of the composition of elements such as Br, Ca, Cl, Cr, Cu, Fe, K, Mn, P, S and Zn. The performed statistical tests indicate that all three groups (dystrophies—D; myopathies—M; references—R) show statistically significant differences in their elemental compositions, and the greatest impact, according to the multivariate discriminate analysis (MDA), comes from elements such as Ca, Cu, K, Cl and S.
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Stewart, Calum, Timothy A. Liddle, and Tyler J. Stevenson. "Abundance, efficiency, and stability of reference transcript expression in a seasonal rodent: The Siberian hamster." PLOS ONE 17, no. 10 (2022): e0275263. http://dx.doi.org/10.1371/journal.pone.0275263.
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Quantitative PCR (qPCR) is a common molecular tool to analyse the expression of transcripts in non-traditional animal models. Most animals experience tissue-specific seasonal changes in cell structure, growth, and cellular function. As a consequence, the choice of reference or ‘house-keeping’ genes is essential to standardize expression levels of target transcripts of interest for qPCR analyses. This study aimed to determine the abundance, efficiency and stability of several reference genes commonly used for normalisation of qPCR analyses in a model of seasonal biology: the Siberian hamster (Phodopus sungorus). Liver, brown-adipose tissue (BAT), white adipose tissue (WAT), testes, spleen, kidney, the hypothalamic arcuate nucleus, and the pituitary gland from either long or short photoperiod Siberian hamsters were dissected to test tissue-specific and photoperiod effects on reference transcripts. qPCR was conducted for common reference genes including 18s ribosomal RNA (18s), glyceraldehyde 3-phosphate dehydrogenase (Gapdh), hypoxanthine-guanine phosphoribosyltransferase (Hprt), and actin-β (Act). Cycling time (Ct), efficiency (E) and replicate variation of Ct and E measured by percent coefficient of variance (CV%) was determined using PCR miner. Measures of stability were assessed using a combined approach of NormFinder and BestKeeper. 18s and Act did not vary in Ct across photoperiod conditions. Splenic, WAT and BAT Gapdh Ct was higher in long compared to short photoperiod. Splenic Hprt Ct was higher in long photoperiods. There was no significant effect of photoperiod, tissue or interaction on measures of efficiency, Ct CV%, or efficiency CV%. NormFinder and BestKeeper confirmed that 18s, Gapdh and Hprt were highly stable, while Act showed low stability. These findings suggest that 18s and Hprt show the most reliable stability, efficiency, and abundance across the tissues. Overall, the study provides a comprehensive and standardised approach to assess multiple reference genes in the Siberian hamster and help to inform molecular assays used in studies of photoperiodism.
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Fairhead, Andrew C. "ICRU Report 61: Providing reference data for tissue properties." Journal of the Acoustical Society of America 105, no. 2 (1999): 1324. http://dx.doi.org/10.1121/1.426203.
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Gunn, Roger N., Sylvain Houle, and Adriaan A. Lammertsma. "Investigation of Irreversible Reference Tissue Models for Parametric Imaging." NeuroImage 7, no. 4 (1998): A24. http://dx.doi.org/10.1016/s1053-8119(18)31893-7.
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Hill, Kate, Aswegen Sunet Van, M. Corrie Schoeman, et al. "Foraging at wastewater treatment works affects brown adipose tissue fatty acid profiles in banana bats." Biology Open 5, no. 2 (2016): 92–99. https://doi.org/10.5281/zenodo.13453020.
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(Uploaded by Plazi for the Bat Literature Project) In this study we tested the hypothesis that the decrease in habitat quality at wastewater treatment works (WWTW), such as limited prey diversity and exposure to the toxic cocktail of pollutants, affect fatty acid profiles of interscapular brown adipose tissue (iBrAT) in bats. Further, the antioxidant capacity of oxidative tissues such as pectoral and cardiac muscle may not be adequate to protect those tissues against reactive molecules resulting from polyunsaturated fatty acid auto-oxidation in the WWTW bats. Bats were sampled at two urban WWTW, and two unpolluted reference sites in KwaZulu-Natal, South Africa. Brown adipose tissue (BrAT) mass was lower in WWTW bats than in reference site bats. We found lower levels of saturated phospholipid fatty acids and higher levels of mono- and polyunsaturated fatty acids in WWTW bats than in reference site bats, while C18 desaturation and n-6 to n-3 ratios were higher in the WWTW bats. This was not associated with high lipid peroxidation levels in pectoral and cardiac muscle. Combined, these results indicate that WWTW bats rely on iBrAT as an energy source, and opportunistic foraging on abundant, pollutant-tolerant prey may change fatty acid profiles in their tissue, with possible effects on mitochondrial functioning, torpor and energy usage.
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Hill, Kate, Aswegen Sunet Van, M. Corrie Schoeman, et al. "Foraging at wastewater treatment works affects brown adipose tissue fatty acid profiles in banana bats." Biology Open 5, no. 2 (2016): 92–99. https://doi.org/10.5281/zenodo.13453020.
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(Uploaded by Plazi for the Bat Literature Project) In this study we tested the hypothesis that the decrease in habitat quality at wastewater treatment works (WWTW), such as limited prey diversity and exposure to the toxic cocktail of pollutants, affect fatty acid profiles of interscapular brown adipose tissue (iBrAT) in bats. Further, the antioxidant capacity of oxidative tissues such as pectoral and cardiac muscle may not be adequate to protect those tissues against reactive molecules resulting from polyunsaturated fatty acid auto-oxidation in the WWTW bats. Bats were sampled at two urban WWTW, and two unpolluted reference sites in KwaZulu-Natal, South Africa. Brown adipose tissue (BrAT) mass was lower in WWTW bats than in reference site bats. We found lower levels of saturated phospholipid fatty acids and higher levels of mono- and polyunsaturated fatty acids in WWTW bats than in reference site bats, while C18 desaturation and n-6 to n-3 ratios were higher in the WWTW bats. This was not associated with high lipid peroxidation levels in pectoral and cardiac muscle. Combined, these results indicate that WWTW bats rely on iBrAT as an energy source, and opportunistic foraging on abundant, pollutant-tolerant prey may change fatty acid profiles in their tissue, with possible effects on mitochondrial functioning, torpor and energy usage.
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Kidd, Mark, Boaz Nadler, Shrikant Mane, et al. "GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR." Physiological Genomics 30, no. 3 (2007): 363–70. http://dx.doi.org/10.1152/physiolgenomics.00251.2006.
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Accurate quantitation of target genes depends on correct normalization. Use of genes with variable tissue transcription ( GAPDH) is problematic, particularly in clinical samples, which are derived from different tissue sources. Using a large-scale gene database (Affymetrix U133A) data set of 36 gastrointestinal (GI) tumors and normal tissues, we identified 8 candidate reference genes and established expression levels by real-time RT-PCR in an independent data set ( n = 42). A geometric averaging method (geNorm) identified ALG9, TFCP2, and ZNF410 as the most robustly expressed control genes. Examination of raw CT values demonstrated that these genes were tightly correlated between themselves ( R2 > 0.86, P < 0.0001), with low variability [coefficient of variation (CV) <12.7%] and high interassay reproducibility ( r = 0.93, P = 0.001). In comparison, the alternative control gene, GAPDH, exhibited the highest variability (CV = 18.1%), was significantly differently expressed between tissue types ( P = 0.05), was poorly correlated with the three reference genes ( R2 < 0.4), and was considered the least stable gene. To illustrate the importance of correct normalization, the target gene, MTA1, was significantly overexpressed ( P = 0.0006) in primary GI neuroendocrine tumor (NET) samples (vs. normal GI samples) when normalized by geNormATZ but not when normalized using GAPDH. The geNormATZ approach was, in addition, applicable to adenocarcinomas; MTA1 was overexpressed ( P < 0.04) in malignant colon, pancreas, and breast tumors compared with normal tissues. We provide a robust basis for the establishment of a reference gene set using GeneChip data and provide evidence for the utility of normalizing a malignancy-associated gene ( MTA1) using novel reference genes and the geNorm approach in GI NETs as well as in adenocarcinomas and breast tumors.
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V. V., KRISHTAL. "THE CONCEPT OF HUMAN ORGANS AND TISSUES WITH REFERENCE TO TRANSPLANTATION: LESSONS FROM INTERNATIONAL LAW." Journal of the Belarusian State University. International relations, no. 1 (June 17, 2022): 57–65. http://dx.doi.org/10.33581/2521-6848-2022-1-57-65.
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The definition of the term “human organs and tissues” is considered with reference to the transplantation of organs and tissues. We review the doctrinal approaches, provisions of international legal acts, international instruments, and national legal frameworks related to the transplantation of human organs and tissues. We conclude by proposing a definition of the terms “human organ” and “human tissue” with emphasis on the substantive aspects inherent in them.
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Viñas, Ramon, Chaitanya K. Joshi, Dobrik Georgiev, et al. "Hypergraph factorization for multi-tissue gene expression imputation." Nature Machine Intelligence 5, no. 7 (2023): 739–53. http://dx.doi.org/10.1038/s42256-023-00684-8.
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AbstractIntegrating gene expression across tissues and cell types is crucial for understanding the coordinated biological mechanisms that drive disease and characterize homoeostasis. However, traditional multi-tissue integration methods either cannot handle uncollected tissues or rely on genotype information, which is often unavailable and subject to privacy concerns. Here we present HYFA (hypergraph factorization), a parameter-efficient graph representation learning approach for joint imputation of multi-tissue and cell-type gene expression. HYFA is genotype agnostic, supports a variable number of collected tissues per individual, and imposes strong inductive biases to leverage the shared regulatory architecture of tissues and genes. In performance comparison on Genotype–Tissue Expression project data, HYFA achieves superior performance over existing methods, especially when multiple reference tissues are available. The HYFA-imputed dataset can be used to identify replicable regulatory genetic variations (expression quantitative trait loci), with substantial gains over the original incomplete dataset. HYFA can accelerate the effective and scalable integration of tissue and cell-type transcriptome biorepositories.
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Larjava, H., L. Koivisto, L. Häkkinen, and J. Heino. "Epithelial Integrins with Special Reference to Oral Epithelia." Journal of Dental Research 90, no. 12 (2011): 1367–76. http://dx.doi.org/10.1177/0022034511402207.
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Adhesion of epithelium to the extracellular matrix is crucial for the maintenance of systemic and oral health. In the oral cavity, teeth or artificial dental implants penetrate the soft tissue of the gingiva. In this interface, gingival soft tissue needs to be well attached via the epithelial seal to the tooth or implant surface to maintain health. After injury or wounding, epithelial tissue rapidly migrates to form the initial epithelial cover to restore the barrier against infection. These events are crucially dependent on deposition of extracellular matrix and proper activation and function of integrin receptors in the epithelial cells. Recent experimental evidence suggests that epithelial integrins also participate in the regulation of periodontal inflammation. In this review, we will discuss the structure and function of epithelial integrins and their extracellular ligands and elaborate on their potential role in disease and repair processes in the oral cavity.
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Steinacher, Claudia, Dietmar Rieder, Jasmin E. Turner, et al. "Validation of RNA Extraction Methods and Suitable Reference Genes for Gene Expression Studies in Developing Fetal Human Inner Ear Tissue." International Journal of Molecular Sciences 25, no. 5 (2024): 2907. http://dx.doi.org/10.3390/ijms25052907.
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A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods and evaluated different reference genes for gene expression studies in the fetal human inner ear. We compared the RNA extracted from formalin-fixed paraffin-embedded tissue with fresh tissue stored at −80 °C in RNAlater solution and validated the expression stability of 12 reference genes (from gestational week 11 to 19). The RNA from fresh tissue in RNAlater resulted in higher amounts and a better quality of RNA than that from the paraffin-embedded tissue. The reference gene evaluation exhibited four stably expressed reference genes (B2M, HPRT1, GAPDH and GUSB). The selected reference genes were then used to examine the effect on the expression outcome of target genes (OTOF and TECTA), which are known to be regulated during inner ear development. The selected reference genes displayed no differences in the expression profile of OTOF and TECTA, which was confirmed by immunostaining. The results underline the importance of the choice of the RNA extraction method and reference genes used in gene expression studies.
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HSIAO, LI-LI, FERNANDO DANGOND, TAKUMI YOSHIDA, et al. "A compendium of gene expression in normal human tissues." Physiological Genomics 7, no. 2 (2001): 97–104. http://dx.doi.org/10.1152/physiolgenomics.00040.2001.
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This study creates a compendium of gene expression in normal human tissues suitable as a reference for defining basic organ systems biology. Using oligonucleotide microarrays, we analyze 59 samples representing 19 distinct tissue types. Of ∼7,000 genes analyzed, 451 genes are expressed in all tissue types and designated as housekeeping genes. These genes display significant variation in expression levels among tissues and are sufficient for discerning tissue-specific expression signatures, indicative of fundamental differences in biochemical processes. In addition, subsets of tissue-selective genes are identified that define key biological processes characterizing each organ. This compendium highlights similarities and differences among organ systems and different individuals and also provides a publicly available resource (Human Gene Expression Index, the HuGE Index, http://www.hugeindex.org ) for future studies of pathophysiology.
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Figueira da Costa, Tatienne Neder, Sandra Andreotti, Talita da Silva Mendes de Farias, Fábio Bessa Lima, and Paula Bargi-Souza. "The Influence of Melatonin on the Daily 24-h Rhythm of Putative Reference Gene Expression in White Adipose Tissues." Journal of Biological Rhythms 35, no. 6 (2020): 530–41. http://dx.doi.org/10.1177/0748730420949337.
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In adipose tissue, the expression of hundreds of genes exhibits circadian oscillation, which may or may not be affected by circulating melatonin levels. Using control and pinealectomized rats, we investigated the daily expression profile of Actb, Hprt-1, B2m, and Rpl37a, genes that are commonly used as reference genes for reverse transcription quantitative polymerase chain reaction (RT-qPCR), in epididymal (EP), retroperitoneal (RP), and subcutaneous (SC) adipose tissues. In control rats, Actb expression presented a daily oscillation in all adipose tissues investigated, Hprt-1 showed 24-h fluctuations in only RP and SC depots, B2m was stable over 24 h for EP and RP but oscillated over 24 h in SC adipose tissue, and Rpl37a presented a daily oscillation in only RP fat. In the absence of melatonin, the rhythmicity of Actb in all adipose depots was abolished, the daily rhythmicity of Hprt-1 and B2m was disrupted in SC fat, the peak expression of Rpl37a and Hprt-1 was delayed, and the amplitude of Rpl37a was reduced in RP adipose tissue. Collectively, our results demonstrate that the expression of putative reference genes displays a daily rhythm influenced by melatonin levels in a manner specific to the adipose depot. Thus, the proper standardization and daily profile expression of reference genes should be performed carefully in temporal studies using RT-qPCR analysis.
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Nakaki, Tetsuro, Kuniko Nakakura-Ohshima, Eizo Nakagawa, et al. "Donor–host tissue interaction in allogenic transplanted tooth germ with special reference to periodontal tissue." Journal of Oral Biosciences 60, no. 1 (2018): 21–30. http://dx.doi.org/10.1016/j.job.2018.02.002.
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Tavane, Pradeep N., Sathish Abraham, Anand U. Madihalli, Naveen S. Yadav, P. Manoranjan Reddy, and G. Baiju. "A Comparative Study of Impression Procedures for Distal Extension Removable Partial Dentures." Journal of Contemporary Dental Practice 12, no. 5 (2011): 333–38. http://dx.doi.org/10.5005/jp-journals-10024-1055.
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ABSTRACT Aim This study was carried out with the purpose of comparing three impression methods as to which of them placed tissues most favorably. Methods The methods used were Hindels method, selective tissue placement method and functional reline method. The measurements obtained were analyzed to determine which of the three impression methods placed the mucosal tissues maximally. To compare and measure tissue placements, autopolymerizing acrylic resin platforms were constructed to the height of the occlusal surfaces of the remaining teeth. 15 orthodontic buccal tubes were placed on each side of the platform. They were arranged in three sets of five and attached to the platform over selected reference regions by means of autopolymerizing resin. The selected reference areas were in anterior, middle and posterior areas of the ridge on either side. Results No significant difference was seen in tissue placement in the anterior middle and posterior regions in each of the three methods when each method was assessed separately. Selective tissue placement method placed the tissues maximally (7.547 mm) followed by Hindels method (7.2110 mm) and the least placement was by functional reline method (5.856 mm). Tissue placement was significantly higher in Hindels method as compared to functional reline method (p < 0.001). Conclusion Tissue placement was maximum in the posterior region, followed by the middle region and least in the anterior region of the mandibular ridge for all three methods. Selective tissue placement method showed the maximum overall tissue placement followed by the Hindels method and minimum placement was by functional reline method. Clinical significance Selective tissue placement method provided maximum overall tissue placement and can be a preferred technique for impression making for bilateral distal extension removable partial denture fabrication. How to cite this article Madihalli AU, Tavane PN, Yadav NS, Abraham S, Reddy PM, Baiju G. A Comparative Study of Impression Procedures for Distal Extension Removable Partial Dentures. J Contemp Dent Pract 2011;12(5):333-338.
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FULLER, N. J., C. R. HARDINGHAM, M. GRAVES, et al. "Predicting composition of leg sections with anthropometry and bioelectrical impedance analysis, using magnetic resonance imaging as reference." Clinical Science 96, no. 6 (1999): 647–57. http://dx.doi.org/10.1042/cs0960647.
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Magnetic resonance imaging (MRI) was used to evaluate and compare with anthropometry a fundamental bioelectrical impedance analysis (BIA) method for predicting muscle and adipose tissue composition in the lower limb. Healthy volunteers (eight men and eight women), aged 41 to 62 years, with mean (S.D.) body mass indices of 28.6 (5.4) kg/m2 and 25.1 (5.4) kg/m2 respectively, were subjected to MRI leg scans, from which 20-cm sections of thigh and 10-cm sections of lower leg (calf) were analysed for muscle and adipose tissue content, using specifically developed software. Muscle and adipose tissue were also predicted from anthropometric measurements of circumferences and skinfold thicknesses, and by use of fundamental BIA equations involving section impedance at 50 kHz and tissue-specific resistivities. Anthropometric assessments of circumferences, cross-sectional areas and volumes for total constituent tissues matched closely MRI estimates. Muscle volume was substantially overestimated (bias: thigh, -40%; calf, -18%) and adipose tissue underestimated (bias: thigh, 43%; calf, 8%) by anthropometry, in contrast to generally better predictions by the fundamental BIA approach for muscle (bias: thigh, -12%; calf, 5%) and adipose tissue (bias: thigh, 17%; calf, -28%). However, both methods demonstrated considerable individual variability (95% limits of agreement 20–77%). In general, there was similar reproducibility for anthropometric and fundamental BIA methods in the thigh (inter-observer residual coefficient of variation for muscle 3.5% versus 3.8%), but the latter was better in the calf (inter-observer residual coefficient of variation for muscle 8.2% versus 4.5%). This study suggests that the fundamental BIA method has advantages over anthropometry for measuring lower limb tissue composition in healthy individuals.