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Journal articles on the topic 'Four variants were tested'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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1

Chanumolu, Sree K., and Matthew L. Spangler. "80 Implementation of deep learning for prediction of variation in the bovine genome." Journal of Animal Science 103, Supplement_1 (2025): 20–21. https://doi.org/10.1093/jas/skaf102.022.

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Abstract To identify highly informative features among ~60 million imputed sequence variants in Bos Taurus a deep learning model based on the attention mechanism, that can learn the contextual association between the tokens (nucleotides) from a given input sequence, was developed. Training occurred with multiple 9 nucleotide fragments of Bos Taurus from non-variant regions. The same size fragments with an observed variant at the center were used to test the model to calculate the probability of occurrence of the reported nucleotide at the center. Those variants that were predicted with the low

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Secondino, Angela, Flavio Starnone, Iolanda Veneruso, et al. "Evaluation of a Four-Gene Panel for Hereditary Cancer Risk Assessment." Genes 13, no. 4 (2022): 682. http://dx.doi.org/10.3390/genes13040682.

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BRCA1/2 are tumor suppressor genes involved in DNA double-strand break repair. They are the most penetrant genes for hereditary breast and ovarian cancers, but pathogenic variants in these two genes can be identified only in a fraction of hereditary cases. Following the diffusion of BRCA molecular testing and the availability of specific therapeutic strategies for the management of pathogenic variant carriers, the demand for the analysis of additional predisposing genetic factors has increased. Indeed, there is accumulating evidence regarding the role of other genes, including CHEK2 and PALB2.

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Carroll, Magdalen RR, Cerin John, Debbie Mantio, Natasha K. Djedovic, and Sally C. Benton. "An assessment of the effect of haemoglobin variants on detection by faecal immunochemical tests." Annals of Clinical Biochemistry: International Journal of Laboratory Medicine 55, no. 6 (2018): 706–9. http://dx.doi.org/10.1177/0004563218778716.

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Background Faecal immunochemical tests (FIT) for haemoglobin (Hb) are being used in the investigation of colorectal cancer. These tests use antibodies raised to the globin moiety of human Hb. Where the globin structure is abnormal or reduced, it is possible that antibody binding, and thus Hb-detection may be affected. Methods Lysates prepared from whole blood samples of patients with known variants were diluted in manufacturer-specific buffer to 10, 100 and 500 μg Hb/g faeces. These samples were analysed on four FIT analysers and the results compared with samples with no known variant present

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Salaš, P. "New technologies and improvement of nursery stock quality." Horticultural Science 29, No. 4 (2012): 153–60. http://dx.doi.org/10.17221/4479-hortsci.

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This four years experimentation work was aimed at research on using various waste organic materials and especially timber bark in cultivation substrates as a substitute of peat. Sixty-four special isolated cultivation beds were established for this purpose, each of 4.8 m<sup>3</sup> volume, in which 11 variants of substrates consisting of different proportions of different components in several replications were tested. Standard substrates Horticultural substrate B and RKS I. were used as controls. Another variant was used as a control for growing tests of plants in containers. All

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Lunenburg, Carin A. T. C., Linda M. Henricks, André B. P. van Kuilenburg, et al. "Diagnostic and Therapeutic Strategies for Fluoropyrimidine Treatment of Patients Carrying Multiple DPYD Variants." Genes 9, no. 12 (2018): 585. http://dx.doi.org/10.3390/genes9120585.

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DPYD genotyping prior to fluoropyrimidine treatment is increasingly implemented in clinical care. Without phasing information (i.e., allelic location of variants), current genotype-based dosing guidelines cannot be applied to patients carrying multiple DPYD variants. The primary aim of this study is to examine diagnostic and therapeutic strategies for fluoropyrimidine treatment of patients carrying multiple DPYD variants. A case series of patients carrying multiple DPYD variants is presented. Different genotyping techniques were used to determine phasing information. Phenotyping was performed

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Kusuma, Caroline M., and John F. Kokai-Kun. "Comparison of Four Methods for Determining Lysostaphin Susceptibility of Various Strains of Staphylococcus aureus." Antimicrobial Agents and Chemotherapy 49, no. 8 (2005): 3256–63. http://dx.doi.org/10.1128/aac.49.8.3256-3263.2005.

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ABSTRACT Lysostaphin is an endopeptidase that cleaves the pentaglycine cross-bridges of the staphylococcal cell wall rapidly lysing the bacteria. Recently, lysostaphin has been examined for its potential to treat infections and to clear Staphylococcus aureus nasal colonization, requiring a reliable method for determining the lysostaphin susceptibility of strains of S. aureus. We compared four methods for determining the lysostaphin susceptibility of 57 strains of methicillin-sensitive S. aureus, methicillin-resistant S. aureus, vancomycin intermediately susceptible S. aureus (VISA), mupirocin-

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Tangwangvivat, Ratanaporn, Supaporn Wacharapluesadee, Papassorn Pinyopornpanish, et al. "SARS-CoV-2 Variants Detection Strategies in Wastewater Samples Collected in the Bangkok Metropolitan Region." Viruses 15, no. 4 (2023): 876. http://dx.doi.org/10.3390/v15040876.

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Wastewater surveillance is considered a promising approach for COVID-19 surveillance in communities. In this study, we collected wastewater samples between November 2020 and February 2022 from twenty-three sites in the Bangkok Metropolitan Region to detect the presence of SARS-CoV-2 and its variants for comparison to standard clinical sampling. A total of 215 wastewater samples were collected and tested for SARS-CoV-2 RNA by real-time PCR with three targeted genes (N, E, and ORF1ab); 102 samples were positive (42.5%). The SARS-CoV-2 variants were determined by a multiplex PCR MassARRAY assay t

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Jaafar, Rita, Celine Boschi, Sarah Aherfi, et al. "High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2." Viruses 13, no. 11 (2021): 2177. http://dx.doi.org/10.3390/v13112177.

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Background: Since the beginning of the COVID-19 pandemic, several SARS-CoV-2 variants have sequentially emerged. In France, most cases were due to spike D641G-harbouring viruses that descended initially from the Wuhan strain, then by the variant of B.1.160 lineage we called Marseille-4 since the summer of 2020, which was followed by the Alpha and Beta variants in early 2021, then the Delta variant currently. Methods: We determined the neutralising antibody (nAb) titres in sera from convalescent individuals previously infected by these four major local variants and from vaccine recipients to th

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Ni, Haolin, Kate D. Ryman, Heiman Wang, et al. "Interaction of Yellow Fever Virus French Neurotropic Vaccine Strain with Monkey Brain: Characterization of Monkey Brain Membrane Receptor Escape Variants." Journal of Virology 74, no. 6 (2000): 2903–6. http://dx.doi.org/10.1128/jvi.74.6.2903-2906.2000.

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ABSTRACT Binding of yellow fever virus wild-type strains Asibi and French viscerotropic virus and vaccine strains 17D and FNV to monkey brain and monkey liver cell membrane receptor preparations (MRPs) was investigated. Only FNV bound to monkey brain MRPs, while French viscerotropic virus, Asibi, and FNV all bound to monkey liver MRPs. Four monkey brain and two mouse brain MRP escape (MRPR) variants of FNV were selected at pH 7.6 and 6.0. Three monkey brain MRPR variants selected at pH 7.6 each had only one amino acid substitution in the envelope (E) protein in domain II (E-237, E-260, or E274

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Stern-Perry, Michal, Amit Gefen, Nogah Shabshin, and Yoram Epstein. "Experimentally tested computer modeling of stress fractures in rats." Journal of Applied Physiology 110, no. 4 (2011): 909–16. http://dx.doi.org/10.1152/japplphysiol.01468.2010.

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The objective of this study was to develop a finite-element (FE) modeling methodology for studying the etiology of a stress fracture (SF). Several variants of three-dimensional FE models of a rat hindlimb, which differed in length or stiffness of tissues, enabling the analyses of mechanical strains and stress in the tibia, were created. We compared the occurrence of SFs in an animal model to validate locations of peak strains/stresses in the FE models. Four Sprague-Dawley male rats, age ∼7 wk, were subjected to mechanical cyclic loads of 1.2 Hz and ∼6 N, which were delivered to their hindlimb

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Buśko, Maciej, Anna Gracka, Henryk Jeleń, et al. "The Effect of Organic and Conventional Cultivation Systems on the Profile of Volatile Organic Compounds in Winter Wheat Grain, Including Susceptibility to Fusarium Head Blight." Metabolites 13, no. 10 (2023): 1045. http://dx.doi.org/10.3390/metabo13101045.

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The grain of 30 winter wheat cultivars differing in terms of their resistance to FHB (Fusarium head blight) was tested. The cultivars were grown in four variants of field trials established in a split-plot design: control without fungicides, chemical control of FHB with fungicides after Fusarium inoculation, Fusarium head inoculation, and organic cultivation. The profile of volatile compounds in grain samples was determined by mean headspace–solid phase microextraction and analyzed by gas chromatography time-of-flight mass spectroscopy. The identified volatile profile comprised 146 compounds b

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Babić, Violeta, Vera Rajičić, Dragan Terzić, Marijana Dugalić, Nenad Đurić, and Marija Vučić. "THE INFLUENCE OF CALCIFICATION AND NPK FERTILIZERS ON THE ECONOMICS OF TRITICALE PRODUCTION." Ekonomika poljoprivrede 70, no. 1 (2023): 201–16. http://dx.doi.org/10.59267/ekopolj2301201b.

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The tests were performed on the property of the Agricultural and Chemical School “Doctor Djordje Radic” in Kraljevo, on pseudogley soil, during a two-year period (2015/16 and 2016/17). Based on the analysis of production value and total variable costs, a production calculation was made. Elements of economic efficiency (productivity, economy and profitability) were calculated for all four variants of fertilization. The tests showed a significant variation in grain yield in the tested fertilization variants. During the two-year research, the T2 variant fertilized with mineral nutrients with incr

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Song, Xu-Ting, Jia-Nan Zhang, Duo-Wei Zhao, et al. "Molecular cloning, expression, and functional features of IGF1 splice variants in sheep." Endocrine Connections 10, no. 9 (2021): 980–94. http://dx.doi.org/10.1530/ec-21-0181.

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Insulin-like growth factor 1 (IGF1), also known as somatomedin C, is essential for the regulation of animal growth and development. In many species, the IGF1 gene can be alternatively spliced into multiple transcripts, encoding different pre-pro-IGF1 proteins. However, the exact alternative splicing patterns of IGF1 and the sequence information of different splice variants in sheep are still unclear. In this study, four splice variants (class 1-Ea, class 1-Eb, class 2-Ea, and class 2-Eb) were obtained, but no IGF1 Ec, similar to that found in other species, was discovered. Bioinformatics analy

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Reurink, Janine, Jaap Oostrik, Marco Aben, et al. "Minigene-Based Splice Assays Reveal the Effect of Non-Canonical Splice Site Variants in USH2A." International Journal of Molecular Sciences 23, no. 21 (2022): 13343. http://dx.doi.org/10.3390/ijms232113343.

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Non-canonical splice site variants are increasingly recognized as a relevant cause of the USH2A-associated diseases, non-syndromic autosomal recessive retinitis pigmentosa and Usher syndrome type 2. Many non-canonical splice site variants have been reported in public databases, but an effect on pre-mRNA splicing has only been functionally verified for a subset of these variants. In this study, we aimed to extend the knowledge regarding splicing events by assessing a selected set of USH2A non-canonical splice site variants and to study their potential pathogenicity. Eleven non-canonical splice

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Sutriah, Komar, Zainal Alim Mas’ud, Tun Tedja Irawadi, and Mohammad Khotib. "Performance of Zinc-Difattyalkyldithyocarbamate as Anti-Friction/Anti-Wear Lubricant Additives." Indonesian Journal of Chemistry 14, no. 1 (2014): 78–84. http://dx.doi.org/10.22146/ijc.21271.

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Dithyocarbamate is an organosulphur compound that has long been known and widely applied in various fields, including in agriculture and industry. Several variants of synthesized vegetable oil-based Zinc-difattyalkyldithyocarbamate were tested its anti-friction/anti-wear performance on four ball machine using the method of ASTM-D2783. Anti-friction/anti-wear test to six of additive variants of Zinc-difattyalkyldithyocarbamate at doses of 1.2% indicated that all variants of the product has welding point value higher than the lube base oil lubricant HVI 60, and from US Steel 136 standard for Hyd

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Yuan, Lisi, Harshita Mehrotra, Xin He, and David Bosler. "MET Exon 14 Variants in Non-Small Cell Lung Carcinoma: Prevalence, Clinicopathologic and Molecular Features." Journal of Molecular Pathology 4, no. 1 (2023): 46–56. http://dx.doi.org/10.3390/jmp4010006.

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Somatic MET exon 14 skipping mutations (MET ex14) are targetable driver mutations for non-small cell lung cancer (NSCLC), responsive to MET inhibitors. Objective: This study seeks to further characterize the clinicopathologic features and mutational profile of MET ex14 variant NSCLC. Design: Retrospective review of all MET ex14 tested NSCLC. Testing for selected BRAF, EGFR, HER2, KRAS, and MET mutations was performed using a clinically validated NGS assay, followed by MiSeq sequencing. Variants were classified as significant (Tier1/2) or variants of uncertain significance (VUS) per 2017 AMP/AS

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Wu, Yuxin, Isabelle V. von Hauff, Niels Jensen, Moritz J. Rossner та Michael C. Wehr. "Improved Split TEV GPCR β-arrestin-2 Recruitment Assays via Systematic Analysis of Signal Peptide and β-arrestin Binding Motif Variants". Biosensors 13, № 1 (2022): 48. http://dx.doi.org/10.3390/bios13010048.

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G protein-coupled receptors (GPCRs) are major disease-relevant drug targets; robust monitoring of their activities upon drug treatment is key to drug discovery. The split TEV cell-based assay technique monitors the interaction of an activated GPCR with β-arrestin-2 through TEV protein fragment complementation using a luminescent signal as the readout. In this work, split TEV GPCR β-arrestin-2 recruitment assays were optimized to monitor the endogenous ligand-induced activities of six GPCRs (DRD1, DRD2, HTR2A, GCGR, AVPR2, and GLP1R). Each GPCR was tested in four forms; i.e., its wildtype form,

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Żyluk, A., T. Dębniak, and P. Puchalski. "Common variants of the ALDH2 and DHDH genes and the risk of Dupuytren’s disease." Journal of Hand Surgery (European Volume) 38, no. 4 (2013): 430–34. http://dx.doi.org/10.1177/1753193412471502.

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The object of this study was the investigation of four common variants of single nucleotide polymorphisms of the aldehyde dehydrogenase H2 gene and dihydrodiol dehydrogenase gene and their association with the occurrence of Dupuytren’s disease. DNA samples were obtained from the peripheral blood of 300 consecutive patients. The control group comprised 300 healthy adults who were age matched with the Dupuytren’s patients. All four common variants were analysed using TaqMan® genotyping assays and sequencing. The differences in the frequencies of variants of single nucleotide polymorphisms in pat

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Doubrava, Karel, and Ctirad Novotný. "Sandwich Roof of the Bus – Fatigue and Strength Tests." Applied Mechanics and Materials 827 (February 2016): 3–6. http://dx.doi.org/10.4028/www.scientific.net/amm.827.3.

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Lightweight and safe roof of the bus was solved within the MIT CR: FR-TI4/349 project. Several variants of sandwich roof were tested on samples in a prior period. Several errors of adhesive joints occurred during the production of the bus roof. Methyl methacrylate adhesive was tested with respect to the declared adhesive ability for arbitrary surfaces. Standardised shear test of the adhesive joints were made for tuning of the numerical model. The obtained parameters are used forthe numerical model of sandwich roof segment. Roof segments were loaded by four points bending and experimentally obt

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Friedrich, Robert, Wehnert-Kohlenbrenner Michael, and Marco Schneider. "Natural and insecticide-free methods for protecting wood piles from bark beetles - using the example of the ash bark beetle (Hylesinus fraxini [Panzer, 1779]) on Common Ash (Fraxinus excelsior [L.])." Journal of Forest and Landscape Research 5, no. 1 (2020): 1–13. http://dx.doi.org/10.13141/jflr.v5i1.30.

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This paper is investigating the insecticide-free protection of ash wood piles through the use of semiochemical dispensers with allochthonous kairomones to control ash bark beetle populations. For this purpose, borehole counts and brood gallery analyses were carried out on log piles of ash wood stored in the forest. Studies have shown that Hylesinus fraxini is repelled by the attractant dispenser with the substance mixture Sexowit, which was actually developed to catch Ips sexdentatus. In addition, the substance mixture has an aggregating effect on various bark beetle antagonists. This causalit

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Ganguly, Agnish, Samudra Pal, Srilagna Chatterjee, Madhusudan Das, Sumantra Sarkar, and Sujay Ghosh. "Rare and novel variant load threshold for KIF7, GJA1 and PDE1C genes elevates the risk of severity of congenital heart defects in Down syndrome." PLOS One 20, no. 6 (2025): e0326566. https://doi.org/10.1371/journal.pone.0326566.

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Individuals with Down syndrome (DS) exhibit a higher incidence of congenital heart defects (CHD). The objective of the present study was to investigate ethnicity-specific genetic variants that increase the risk of CHD in children with DS from the Indian Bengali population. We conducted whole exome sequencing of the genomes of Down syndrome children with and without CHD and subsequently tested the identified variants in a larger cohort (N = 1798). Our findings revealed two rare variants, KIF7 rs138354681 and GJA1 rs778110855, as well as one novel variant, PDE1C PP785745, present in children wit

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Kreston, Sarah, Claire Gould, Kylie Blair, Leisa Jackson, Janice Riley, and Gary A. Pestano. "Abstract 5547: Evaluation of two clinically focused targeted NGS systems for liquid biopsy testing shows a high level of concordance in resulting actionable mutations." Cancer Research 83, no. 7_Supplement (2023): 5547. http://dx.doi.org/10.1158/1538-7445.am2023-5547.

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Abstract Introduction: The use of blood-based molecular diagnostics is increasingly becoming routine in clinical oncology practice. The purpose of this study was to evaluate variant resulting concordance for the four major somatic variant classes using two clinical next-generation sequencing (NGS) systems for conducting highly sensitive blood-based analyses. All donor specimens were de-identified remnants from patients previously diagnosed with advanced NSCLC. We utilized two independent panels, systems and bioinformatic pipelines that are focused on clinical testing for key actionable variant

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Nenova, L., M. Benkova, Ts Simeonova, and I. Atanassova. "Relationship between mineral fertilization, plant macro- and microelement contents and yield of wheat (Triticum aestivum L.)." Agricultural Science and Technology 16, no. 1 (2024): 94–103. http://dx.doi.org/10.15547/ast.2024.01.011.

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Abstract. The effectiveness of mineral fertilization on wheat productivity was determined in a field experiment on Alluvial-meadow soil (Fluvisol, FAO 2015) at the experimental field of Tsalapitsa village, Plovdiv region, during 2019-2020. Four increasing rates of nitrogen fertilization along with a constant background of phosphorus fertilization were tested in the following variants: N40P100; N80P100; N120P100; N160P100, and N0P0 (control) – without any fertilization. The influence of these variants on yield and the content of basic macro- and microelements in wheat’s dry biomass were assesse

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Guomei, Cao, Zhang Luyan, Dai Lingling, Huang Chunhong, and Chen Shan. "Concurrent Hearing and Genetic Screening among Newborns in Ningbo, China." Computational and Mathematical Methods in Medicine 2022 (January 10, 2022): 1–8. http://dx.doi.org/10.1155/2022/1713337.

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Objective. To detect the carrier rates of deafness gene variants in populations in Ningbo and analyze the risk of hereditary hearing loss through concurrent hearing and genetic screening tests. Methods. Two thousand one hundred and seventy-four newborns were enrolled from November 2018 to August 2019. All subjects underwent hearing screening and newborn deafness genetic screening with 15 variants in 4 genes, and the positive sites were simultaneously verified by sequencing. Results. The total carrier rate of genetic variants in Ningbo reached 4.32%, when GJB2 c.235delC was the variant with the

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Allali-Hassani, Abdellah, Gregory A. Wasney, Irene Chau, et al. "A survey of proteins encoded by non-synonymous single nucleotide polymorphisms reveals a significant fraction with altered stability and activity." Biochemical Journal 424, no. 1 (2009): 15–26. http://dx.doi.org/10.1042/bj20090723.

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On average, each human gene has approximately four SNPs (single nucleotide polymorphisms) in the coding region, half of which are nsSNPs (non-synonymous SNPs) or missense SNPs. Current attention is focused on those that are known to perturb function and are strongly linked to disease. However, the vast majority of SNPs have not been investigated for the possibility of causing disease. We set out to assess the fraction of nsSNPs that encode proteins that have altered stability and activity, for this class of variants would be candidates to perturb cellular function. We tested the thermostabilit

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Nemes-Nagy, Enikő, Zita Fazakas, Victor Balogh-Sămărghițan, et al. "Comparison of four chromatographic methods used for measurement of glycated hemoglobin." Revista Romana de Medicina de Laborator 24, no. 4 (2016): 431–39. http://dx.doi.org/10.1515/rrlm-2016-0039.

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Abstract This parameter’s results accuracy has a special importance in the management of diabetic patients since targets for optimal glycemic control are established using HbA1c values. Several error sources can influence the obtained value, some of them can be counteracted (ex. pipetting errors, storage), and others should be taken into consideration at the interpretation of the result (ex. presence of hemoglobin variants). The aim of this study was to compare four chromatographic methods regarding the costs and the influence of certain error sources on the accuracy of the result. Materials a

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Staff, Editorial. "Rapid & Low-Cost DPYD Genotyping to Guide Fluoropyrimidine Treatment in Cancer Patients." Precision Medicine Communications 3, no. 2 (2023): 83–86. https://doi.org/10.55627/pmc.003.02.0485.

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DPYD (dihydropyrimidine dehydrogenase) genotyping is relevant in the context of cancer treatment, particularly with fluoropyrimidine-based chemotherapy drugs such as 5-fluorouracil (5-FU) and capecitabine. Dihydropyrimidine dehydrogenase is an enzyme involved in the metabolism of these drugs, and certain genetic variants in the DPYD gene can lead to reduced enzyme activity, potentially causing severe and life-threatening toxicities. The implementation of upfront DPYD genotyping involves testing patients for specific DPYD variants before starting fluoropyrimidine-based chemotherapy. Pinheiro an

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Bartosiewicz, Michał, and Adam Cwudziński. "Intensification of liquid steel active flow volume in one-strand tundish using a modified ladle shroud." Metallurgical and Materials Engineering 26, no. 1 (2020): 1–14. http://dx.doi.org/10.30544/458.

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This work presents the numerical and physical simulation results of the liquid steel flow in the one-strand tundish. The results obtained during the numerical simulations and the water modeling results were compared to each other. Six types of turbulence models were tested. Among tested turbulence models the BSL k-ω was turned out the best correlating with the results from the laboratory experiments. Besides, the ladle shroud modification was proposed by the authors and the influence of the modified ladle shroud immersion depth in the liquid steel on the hydrodynamic structure in the tundish w

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Serra, Stefano, Jose-Mario Capo-Chichi, Aoife J. McCarthy, Peter Sabatini, and Runjan Chetty. "Unique MLH1 mutations in colonic adenomas in an obligate germline Lynch syndrome carrier." Journal of Clinical Pathology 73, no. 5 (2019): 291–95. http://dx.doi.org/10.1136/jclinpath-2019-206234.

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BackgroundAn obligate germline Lynch syndrome carrier had four colonic adenomas removed.Materials and methodsThe adenomas were evaluated for grade of dysplasia, MLH1, PMS2, MSH2 and MSH6 protein expression, microsatellite instability (MSI), BRAF, methylation status and a next-generation sequencing (NGS) panel of 52 cancer genes.ResultsThere were four tubular or tubulovillous adenomas from the hepatic flexure, rectosigmoid and rectum; one with low-grade and high-grade dysplasia, one with high-grade dysplasia only and two with low-grade dysplasia. All four adenomas showed retention of MLH1, MHS2

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Abtew, Mulat Alubel, Francois Boussu, Pascal Bruniaux, and Yan Hong. "Dynamic Impact Surface Damage Analysis of 3D Woven Para-Aramid Armour Panels Using NDI Technique." Polymers 13, no. 6 (2021): 877. http://dx.doi.org/10.3390/polym13060877.

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The effects of the yarn composition system inside 3D woven high-performance textiles are not well investigated and understood against their final ballistic impact behaviour. The current study aims to examine the ballistic impact performances of armour panels made of different 3D woven fabric variants through postmortem observations. Four high-performance five-layer 3D woven fabric variants were engineered based on their different warp yarn compositions but similar area density. A 50 × 50 cm2 armour system of each variant, which comprises eight nonbonded but aligned panels, namely, 3D-40-8/0 (o

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Joutovsky, Alla, Joan Hadzi-Nesic, and Michael A. Nardi. "HPLC Retention Time as a Diagnostic Tool for Hemoglobin Variants and Hemoglobinopathies: A Study of 60000 Samples in a Clinical Diagnostic Laboratory." Clinical Chemistry 50, no. 10 (2004): 1736–47. http://dx.doi.org/10.1373/clinchem.2004.034991.

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Abstract Background: Previous evaluations of HPLC as a tool for detection of hemoglobin variants have done so within newborn-screening programs and/or by use of stored samples. We describe a 32-month prospective study in a clinical diagnostic laboratory in which we evaluated the imprecision of HPLC retention times and determined the retention times for hemoglobin variants seen in a multiethnic setting. Methods: We analyzed all samples on the Bio-Rad Variant II HPLC system. For normal hemoglobin fractions and hemoglobin variants, we recorded and analyzed their retention times, their proportion

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Kien, Nguyen Trung, Tran Tin Nghia, Nguyen Minh Hoang, et al. "Prevalent Variants in the LDLR Gene Impair Responsiveness to Rosuvastatin among Family Members of Patients with Premature Myocardial Infarction." Journal of Personalized Medicine 13, no. 12 (2023): 1725. http://dx.doi.org/10.3390/jpm13121725.

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Background: Familial hypercholesterolemia (FH) is an inherited metabolic disorder characterized by high levels of low-density lipoprotein cholesterol (LDL-c) from birth. About 85% of all FH cases are caused by pathogenic variants in the LDLR gene. Individuals with FH have increased cardiovascular risk, including a high risk of premature myocardial infarction (PMI). Methods: We conducted an opportunistic exome screening to identify variants in the LDLR gene among Vietnamese patients with PMI treated at a general hospital in southern Vietnam. A cascade testing for LDLR variants was conducted in

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Chittiboina, Prashant, Denise M. Kay, James L. Mills, et al. "RF01 | PMON167 Isolated Cushing's Disease Associated With Rare Germline SDHx Variants." Journal of the Endocrine Society 6, Supplement_1 (2022): A575—A576. http://dx.doi.org/10.1210/jendso/bvac150.1194.

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Abstract Introduction Loss-of-function (LOF) germline variants in the SDHx genes (SDHA, SDHB, SDHC, and SDHD), encoding the succinate dehydrogenase subunits, are a rare cause for pituitary tumors in the setting of various familial tumor syndromes. Occasional case reports have highlighted SDHx mutations in isolated pituitary tumors (including one case of Cushing's disease, CD). The actual frequency of SDHx variants as genetic drivers of pituitary tumors, however, remains elusive. Aim We sought to determine the frequency of germline SDHx variants in a large cohort of CD patients. Methods Of the

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Bueno-Martínez, Elena, Lara Sanoguera-Miralles, Alberto Valenzuela-Palomo, et al. "RAD51D Aberrant Splicing in Breast Cancer: Identification of Splicing Regulatory Elements and Minigene-Based Evaluation of 53 DNA Variants." Cancers 13, no. 11 (2021): 2845. http://dx.doi.org/10.3390/cancers13112845.

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RAD51D loss-of-function variants increase lifetime risk of breast and ovarian cancer. Splicing disruption is a frequent pathogenic mechanism associated with variants in susceptibility genes. Herein, we have assessed the splicing and clinical impact of splice-site and exonic splicing enhancer (ESE) variants identified through the study of ~113,000 women of the BRIDGES cohort. A RAD51D minigene with exons 2–9 was constructed in splicing vector pSAD. Eleven BRIDGES splice-site variants (selected by MaxEntScan) were introduced into the minigene by site-directed mutagenesis and tested in MCF-7 cell

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BECHERESCU, Alexandra, Gheorghita HOZA, and Florin SALA. "GARDEN PEAS PRODUCTION VARIATION IN RELATION TO SOME BIOSTIMULATING SUBSTANCES." AgroLife Scientific Journal 12, no. 2 (2023): 25–34. http://dx.doi.org/10.17930/agl202324.

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The study evaluated the production of pods and green grains in garden peas in relation to some biostimulating substances. The experiment was organized in the area of Aldesti locality, Arad County, Romania. Four pea varieties were cultivated: Vidra 187 (a1), Udina (a2), Ișalnița (a3), and Marifon (a4). Three biostimulators were used: Fabo (b2), Bionat (b3), Lithovit (b4), tested together with a control variant (b1). From the combination of the two factors, 16 experimental variants resulted. A logical scheme was designed for the experimental flow. According to PCA, correlation, in relation to Pg

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De Sousa, Sunita M. C., Mark J. McCabe, Kathy Wu, et al. "Germline variants in familial pituitary tumour syndrome genes are common in young patients and families with additional endocrine tumours." European Journal of Endocrinology 176, no. 5 (2017): 635–44. http://dx.doi.org/10.1530/eje-16-0944.

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Objective Familial pituitary tumour syndromes (FPTS) account for 5% of pituitary adenomas. Multi-gene analysis via next-generation sequencing (NGS) may unveil greater prevalence and inform clinical care. We aimed to identify germline variants in selected patients with pituitary adenomas using a targeted NGS panel. Design We undertook a nationwide cross-sectional study of patients with pituitary adenomas with onset ≤40 years of age and/or other personal/family history of endocrine neoplasia. A custom NGS panel was performed on germline DNA to interrogate eight FPTS genes. Genome data were analy

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Skrahin, Aliaksandr, Huma Arshad Cheema, Maqbool Hussain, et al. "Secondary findings in a large Pakistani cohort tested with whole genome sequencing." Life Science Alliance 6, no. 3 (2023): e202201673. http://dx.doi.org/10.26508/lsa.202201673.

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Studies on genomic secondary findings (SFs) are diverse in participants’ characteristics, sequencing methods, and versions of the ACMG SF list. Based on whole genome sequencing and the version 3.1 of the ACMG SF list, we studied SFs in 863 individuals from five different regions in Pakistan. We identified 24 ACMG SFs in 23 (2.7%) of 863 individuals: 18 of 24 were related to cardiovascular disease and four to cancer syndromes. In addition to ACMG SFs, we identified 16 (1.9%) participants with pathogenic and likely pathogenic variants in genes that were not related to the participants’ clinical

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Wang, Hua, Nicholas P. Hays, Swapan K. Das, et al. "Phenotypic and Molecular Evaluation of a Chromosome 1q Region with Linkage and Association to Type 2 Diabetes in Humans." Journal of Clinical Endocrinology & Metabolism 94, no. 4 (2009): 1401–8. http://dx.doi.org/10.1210/jc.2008-2132.

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Abstract Objective: Linkage to type 2 diabetes (T2D) is well replicated on chromosome 1q21-q23. Within this region, T2D was associated with common single nucleotide polymorphisms that marked an extended linkage disequilibrium block, including the liver pyruvate kinase gene (PKLR), in several European-derived populations. In this study we sought to determine the molecular basis for the association and the phenotypic consequences of the risk haplotype. Research Design and Methods: Genes surrounding PKLR were resequenced in European-American and African-American cases and controls, and associatio

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Salakhov, Ramil R., Maria V. Golubenko, Nail R. Valiakhmetov, et al. "Application of Long-Read Nanopore Sequencing to the Search for Mutations in Hypertrophic Cardiomyopathy." International Journal of Molecular Sciences 23, no. 24 (2022): 15845. http://dx.doi.org/10.3390/ijms232415845.

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Increasing evidence suggests that both coding and non-coding regions of sarcomeric protein genes can contribute to hypertrophic cardiomyopathy (HCM). Here, we introduce an experimental workflow (tested on four patients) for complete sequencing of the most common HCM genes (MYBPC3, MYH7, TPM1, TNNT2, and TNNI3) via long-range PCR, Oxford Nanopore Technology (ONT) sequencing, and bioinformatic analysis. We applied Illumina and Sanger sequencing to validate the results, FastQC, Qualimap, and MultiQC for quality evaluations, MiniMap2 to align data, Clair3 to call and phase variants, and Annovar’s

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Wu, Shijie, Jiaojiao Zhou, and Yiding Chen. "Functional analysis of patient-derived PALB2 missense variants of uncertain significance." Journal of Clinical Oncology 38, no. 15_suppl (2020): 1531. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.1531.

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1531 Background: Inherited PALB2 pathogenic variants are associated with an increased lifetime risk for breast cancer development. However, the interpretation of numerous PALB2 missense variants of uncertain significance (VUS) identified in germline genetic testing remains a challenge. Here, we assessed the impact of breast cancer patient-derived VUS on PALB2 function and identified pathogenic PALB2 missense variants that may increase cancer risk. Methods: A total of seven potentially pathogenic PALB2 VUS identified in 2,279 breast cancer patients were selected for functional analysis. All the

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YUNG, V., M. FAVI, and J. FERNANDEZ. "Typing of the rabies virus in Chile, 2002–2008." Epidemiology and Infection 140, no. 12 (2012): 2157–62. http://dx.doi.org/10.1017/s0950268812000520.

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SUMMARYIn Chile, dog rabies has been controlled and insectivorous bats have been identified as the main rabies reservoir. This study aimed to determine the rabies virus (RABV) variants circulating in the country between 2002 and 2008. A total of 612 RABV isolates were tested using a panel with eight monoclonal antibodies against the viral nucleoprotein (N-mAbs) for antigenic typing, and a product of 320-bp of the nucleoprotein gene was sequenced from 99 isolates. Typing of the isolates revealed six different antigenic variants but phylogenetic analysis identified four clusters associated with

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Hollocher, Hope, and Allen R. Place. "Partial Correction of Structural Defects in Alcohol Dehydrogenase Through Interallelic Complementation in Drosophila melanogaster." Genetics 116, no. 2 (1987): 265–74. http://dx.doi.org/10.1093/genetics/116.2.265.

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ABSTRACT Alcohol dehydrogenases (ADH) from the F1 progeny of all pairwise crosses between 12 null-activity mutants and crosses between these mutants and four active variants, ADHn5 ADHF, ADHD and ADHS, were analyzed for the presence of active or inactive heterodimers. Gels were stained for ADH enzyme activity, and protein blots of duplicate gels were probed with ADH-specific antibody to detect cross-reacting material. Crosses between the three major electrophoretic variants. ADHF, ADHS and ADHD, all produced active heterodimers. Four mutant proteins (ADHn2, ADHn4, ADHn10 and ADHn13) did not fo

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Maegawa, Tatsuya, Hiroyuki Akagawa, Hideaki Onda, and Hidetoshi Kasuya. "Whole-exome sequencing in a Japanese multiplex family identifies new susceptibility genes for intracranial aneurysms." PLOS ONE 17, no. 3 (2022): e0265359. http://dx.doi.org/10.1371/journal.pone.0265359.

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Background Intracranial aneurysms (IAs) cause subarachnoid hemorrhage, which has high rates of mortality and morbidity when ruptured. Recently, the role of rare variants in the genetic background of complex diseases has been increasingly recognized. The aim of this study was to identify rare variants for susceptibility to IA. Methods Whole-exome sequencing was performed on seven members of a Japanese pedigree with highly aggregated IA. Candidate genes harboring co-segregating rare variants with IA were re-sequenced and tested for association with IA using additional 500 probands and 323 non-IA

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Rymarczyk, Tomasz, Grzegorz Kłosowski, Anna Hoła, et al. "Historical Buildings Dampness Analysis Using Electrical Tomography and Machine Learning Algorithms." Energies 14, no. 5 (2021): 1307. http://dx.doi.org/10.3390/en14051307.

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The article deals with the problem of detecting moisture in the walls of historical buildings. As part of the presented research, the following four methods based on mathematical modeling and machine learning were compared: total variation, least-angle regression, elastic net, and artificial neural networks. Based on the simulation data, the systems for the reconstruction of “pixel by pixel” tomographic images were trained. In order to test the reconstructive algorithms obtained during the research, images were generated based on real measurements and simulation cases. The method comparison wa

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Lynn, T., A. Campbell, and Y. Ding. "Utility of Next Generation Sequencing in the Workup and Diagnosis of Myeloproliferative neoplasm in the Peripheral Blood: A single institution experience." American Journal of Clinical Pathology 156, Supplement_1 (2021): S136. http://dx.doi.org/10.1093/ajcp/aqab191.290.

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Abstract Introduction/Objective In patients with suspicion of Myeloproliferative neoplasm (MPN) and negative for BCR-ABL1, NCCN guideline currently recommends two molecular workup pathways in peripheral blood: 1) a multi-step reflex mutation testing algorithm including JAK2 V617F, CALR, MPL, JAK2 exon12 or 2) a multigene Next Generation Sequencing (NGS) panel that includes at least JAK2, CALR and MPL genes. Here we report the clinical utilization and impact of a NGS based MPN diagnosis assay. Methods/Case Report Total of 690 consecutive cases at Geisinger between 2019 and 2021 were included in

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Su, Jiyong, and Karl Forchhammer. "The Role of Arg13 in Protein Phosphatase M tPphA from Thermosynechococcus elongatus." Enzyme Research 2012 (June 6, 2012): 1–7. http://dx.doi.org/10.1155/2012/272706.

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A highly conserved arginine residue is close to the catalytic center of PPM/PP2C-type protein phosphatases. Different crystal structures of PPM/PP2C homologues revealed that the guanidinium side chain of this arginine residue can adopt variable conformations and may bind ligands, suggesting an important role of this residue during catalysis. In this paper, we randomly mutated Arginine 13 of tPphA, a PPM/PP2C-type phosphatase from Thermosynechococcus elongatus, and obtained 18 different amino acid variants. The generated variants were tested towards p-nitrophenyl phosphate and various phosphope

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Mura-Escorche, Glorián, Ana Perdomo-Ramírez, Elena Ramos-Trujillo, Carmen Jane Trujillo-Frías, and Félix Claverie-Martín. "Characterization of pre-mRNA Splicing Defects Caused by CLCN5 and OCRL Mutations and Identification of Novel Variants Associated with Dent Disease." Biomedicines 11, no. 11 (2023): 3082. http://dx.doi.org/10.3390/biomedicines11113082.

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Dent disease (DD) is an X-linked renal tubulopathy characterized by low-molecular-weight proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis and progressive renal failure. Two-thirds of cases are associated with inactivating variants in the CLCN5 gene (Dent disease 1, DD1) and a few present variants in the OCRL gene (Dent disease 2, DD2). The aim of the present study was to test the effect on the pre-mRNA splicing process of DD variants, described here or in the literature, and describe the clinical and genotypic features of thirteen unrelated patients with suspected DD. All patient

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Ordóñez, Rosa M., Ana María Espinosa, Dolores Javier Sánchez-González, Juan Armendáriz-Borunda, and Jaime Berumen. "Enhanced oncogenicity of Asian-American human papillomavirus 16 is associated with impaired E2 repression of E6/E7 oncogene transcription." Journal of General Virology 85, no. 6 (2004): 1433–44. http://dx.doi.org/10.1099/vir.0.19317-0.

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Asian-American (AA) variants of human papillomavirus 16 (HPV-16) are linked to a high incidence of cervical cancer in Mexico, with some evidence strongly suggesting that they are more oncogenic than European (E) variants, including their association with younger women and their higher associated risk of cervical cancer. Differences in the regulation of viral E6/E7 oncogene transcription by the E2 protein may be involved in the higher oncogenicity of AA variants. In E variants, E6/E7 oncogene transcription is repressed by the E2 protein and is frequently up-regulated by the destruction of the E

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Tessier, L., E. Fortin, A. Michaud-Herbst, and K. Tremblay. "A170 DISTRIBUTION OF PHARMACOGENETIC VARIANTS IN PEOPLE SUFFERING FROM ULCERATIVE COLITIS TREATED WITH TARGETED MOLECULAR THERAPIES IN QUEBEC." Journal of the Canadian Association of Gastroenterology 8, Supplement_1 (2025): i69. https://doi.org/10.1093/jcag/gwae059.170.

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Abstract Background Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by continuous colonic inflammation. In Canada, ~160,000 people suffer from its symptoms, such as diarrhea, blood in the stool and abdominal pain, which can highly impact their quality of life. For moderate to severe forms of the disease, molecular targeted therapies (MTT) are used to control symptoms and achieve remission. There is a large variability in treatment response to MTT. Indeed, ~20-50% MTT users don’t improve following drug initiation and 50-90% suffer from adverse events. Multiple fact

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Cole, Laurence A., Jaime M. Sutton, Trefor N. Higgins, and George S. Cembrowski. "Between-Method Variation in Human Chorionic Gonadotropin Test Results." Clinical Chemistry 50, no. 5 (2004): 874–82. http://dx.doi.org/10.1373/clinchem.2003.026989.

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Abstract Background: Results on sera and calibrators vary 1.4- to 2.3-fold among commercial human chorionic gonadotropin (hCG) assays. The relative contributions of calibrators, standards, hCG charge isoforms, and major structural variants to this variation have not been quantified. Methods: Purified hCG was separated by isoelectric focusing into four fractions with pI ranges of 3–4, 4–5, 5–6, and 6–7. These four fractions together with pure hCG, hyperglycosylated hCG, hCG β-subunit (hCGb), nicked hCG, and hCGb core fragment (hCGbcf) were tested in nine commonly used commercial serum assays fo

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