Suitable Reference Research Articles

Evaluation and Validation of Reliable Reference Genes for Quantitative Real-Time PCR Analysis of the Gene Expression in Macadamia integrifolia

Macadamia is an economically significant crop, with its kernel oil being abundant in monounsaturated fatty acids (MUFA). Analyzing the expression of genes related to MUFA biosynthesis is essential for understanding the complex regulatory networks in Macadamia. However, there are few reports on the identification of suitable reference genes for use as internal controls in this species. Consequently, selecting a reliable reference gene for gene expression studies under various conditions is critical. In this study, we evaluated the expression stability of 11 traditional housekeeping genes: α-tubulin (TUBa), β-tubulin (TUBb), malate dehydrogenase (MDH), 18S ribosomal RNA (18S), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-elongation factor 1 (EF1a), β-elongation factor 1 (EF1b), ubiquitin (UBQ), ubiquitin-conjugating enzyme (UBC), cyclophilin (CYP), and actin (ACT) under abiotic stresses, hormonal treatments and in variety of plant tissues using the online tool RefFinder, which integrates four commonly used software programs: ΔCt, geNorm (version 3.4), NormFinder (version 0953), and BestKeeper (version 1.0). A comprehensive expression stability ranking was established by integrating results from these four methods based on the geometric mean. The findings indicated that ACT was the most stable gene across all samples, including those subjected to cold stress, NaCl stress, PEG stress, ABA treatment, MeJA treatment, and both stem and leaf tissues. EF1b was identified as the most stable gene in GA treatment and heat stress samples, while UBC and CYP were ranked highest in ethrel treatment and root tissue samples, respectively. Finally, the reliability of these findings was further validated using the target gene SAD through qRT-PCR. In summary, this study evaluated and validated appropriate reference genes for qRT-PCR, which will facilitate future investigations into the molecular mechanisms in Macadamia.

Selection and validation of reference genes for quantitative expression analysis of regeneration-related genes in Cheilomenes sexmaculata by real-time qRT-PCR.

Regeneration is a fascinating phenomenon that has intrigued scientists for a long time. Cheilomenes sexmaculata (Fabricius), a zig-zag ladybird beetle, possesses a high capacity for limb regeneration. The molecular mechanics of the zig-zag ladybird beetle are under-explored. Current research trends are focused on uncovering functional genes associated with limb regeneration. Most of these investigations involve quantitative real-time PCR (qRT-PCR) for their rapid and accurate analysis of gene expression levels. Hence, a stable and suitable reference gene is required to normalize the gene expression data. In this study, five housekeeping genes were selected from the transcriptomics data (in-house unpublished data) of C. sexmaculata (Fabricius). The expression stabilities of the selected genes were evaluated under different time intervals post-amputation using geNorm, normFinder, and refFinder software. Actin was revealed to be the most stable housekeeping gene, along with elongation factor 2 and glyceraldehyde-3-phosphate dehydrogenase. A target gene named engrailed (an important segment-forming gene) was used to validate the selected reference genes. The expression levels were found to be consistent with the transcriptomics results. According to our study, actin, along with elongation factor 2 and glyceraldehyde-3-phosphate dehydrogenase, serve as the most stable reference genes and are suitable for regeneration-related research. This study is a groundbreaking effort to identify the most stable reference gene for limb regeneration in C. sexmaculata (Fabricius), and the findings can be applied to other related insect species.

Identification of stable housekeeping genes in mouse liver for studying carbon tetrachloride-induced injury and cellular senescence

Acute liver injury (ALI) presents a challenging problem worldwide, prompting extensive research efforts. Cellular senescence has been found to be induced following ALI, and targeting cellular senescence has shown therapeutic potential. Therefore, understanding the expression of senescence-related genes in ALI can help to explore pathogenesis and treatment of this common disease. Carbon tetrachloride (CCl4) is commonly used to study ALI. Although polymerase chain reaction (PCR) is a convenient and economical molecular biology technique widely used in basic medicine, research on selecting suitable reference genes to obtain objective and reproducible PCR data is scarce. Moreover, evidence supporting the choice of reference genes for experimental studies of CCl4-induced ALI and hepatic senescence in mice is limited. In this study, we obtained murine livers at four time points (0, 12, 24, and 48 h) following CCl4 treatment. We used five algorithms (geNorm, BestKeeper, NormFinder, delta Ct, and RefFinder) to rank 12 candidate genes in real-time reverse-transcription quantitative PCR (RT-qPCR) experiments. Focusing on cellular senescence in this model, we adopted four senescence-associated secretory phenotype (SASP) genes (Il6, Il1b, Ccl2, and Ccl5) as target genes. Our results confirmed Gapdh and Tbp as suitable reference genes in murine CCl4-induced ALI models. Furthermore, we provide a table of published studies recommending reference genes for various liver disease models. This study provides a valuable reference for enhancing the reliability and reproducibility of ALI molecular findings.

Identification of Reliable Reference Genes for Use in Gene Expression Studies in Rat Febrile Seizure Model.

The study of the pathogenesis of febrile seizures and their consequences frequently necessitates gene expression analysis. The primary methodology employed for such analysis is reverse transcription with quantitative polymerase chain reaction (RT-qPCR). To ensure the accuracy of data obtained by RT-qPCR, it is crucial to utilize stably expressed reference genes. The objective of this study was to identify the most suitable reference genes for use in the analysis of mRNA production in various brain regions of rats following prolonged neonatal febrile seizures. The expression stability of eight housekeeping genes was evaluated using the online tool RefFinder in the dorsal and ventral hippocampal regions and in the temporal and medial prefrontal cortex of the brain. The Ppia gene exhibited the greatest stability of expression. Conversely, the genes with the least stable expression levels were Actb and Ywhaz; thus, it is not recommended to use them for normalization in a febrile seizure model. Additionally, the majority of housekeeping genes demonstrate age-related, region-specific fluctuations. Therefore, it is crucial to employ the appropriate housekeeping genes for each brain structure under investigation when examining the expression dynamics of genes of interest in a febrile seizure model.

Color restoration of mural images based on a reversible neural network: leveraging reversible residual networks for structure and texture preservation

AbstractThe Mogao Grottoes in Dunhuang, a treasure of China's and the world's cultural heritage, contains rich historical and cultural deposits and has left precious relics of the history of human art. Over centuries, the Mogao Caves have been affected by natural and human factors, resulting in irreversible fading and discoloration of many murals. In recent years, deep learning technology has shown great potential in the field of virtual mural color restoration. Therefore, this paper proposes a mural image color restoration method based on a reversible neural network. The method first employs an automatic reference selection module based on structural and texture similarity to choose suitable reference mural images for the faded murals. Then, it utilizes a reversible residual network to extract deep features of the mural images without information loss. Next, a channel refinement module is used to eliminate redundant information in the network channels. Finally, an unbiased color transfer module restores the color of the faded mural images. Compared to other image color restoration methods, the proposed method achieves superior color restoration effects while effectively preserving the original structure and texture details of the mural images. Compared to baseline methods, the Structural Similarity Index (SSIM), Feature Similarity Index (FSIM), and Perception-based Image Quality Evaluator (PIQE) values are improved by 7.97%, 3.46%, and 13.98%, respectively. The color restoration of the Dunhuang Mural holds significant historical, artistic, cultural, and economic values, and plays a positive role in the preservation and inheritance of Chinese culture, as well as in the promotion of cultural exchange and mutual understanding.

DAANISH: A mnemonic to aid in memorizing and recalling important strategies contributing to the prevention of perioperative stroke.

Perioperative stroke, defined as a stroke occurring within 30 days post-surgery, typically emerges within the first week. The incidence of perioperative stroke among adults undergoing non-cardiac and non-neurological surgeries ranges from 0.1% to 1% after a surgical intervention. Mortality rates following perioperative stroke surge, reaching up to eight times higher than controls, with approximately one in four cases resulting in death. Fortunately, various strategies are available to potentially prevent perioperative strokes. However, the vast amount of data poses challenges for physicians in memorization and recall for clinical use. This study aims to summarize essential perioperative stroke prevention strategies and determine an effective mnemonic for their memorization and recall. The initial search in PubMed focused solely on review articles published within the last 10 years. It utilized the keywords "perioperative stroke" and "prevention." An initial search found 39 articles, with two suitable for review. Using data from selected review articles, further searches were conducted on Google Scholar and PubMed for articles from 2000 to 2024, identifying 30 additional suitable references. From these 32 articles, the author developed a mnemonic, "DAANISH," to aid in remembering strategies for preventing perioperative stroke. Implementing this mnemonic may help reduce the risk of perioperative stroke and improve patient outcomes. Future research is needed to confirm its effectiveness.

A systematic review on the selection of reference genes for gene expression studies in rodents: are the classics the best choice?

Rodents are commonly used as animal models in studies investigating various experimental conditions, often requiring gene expression analysis. Quantitative real-time reverse transcription PCR (RT-qPCR) is the most widely used tool to quantify target gene expression levels under different experimental conditions in various biological samples. Relative normalization with reference genes is a crucial step in RT-qPCR to obtain reliable quantification results. In this work, the main reference genes used in gene expression studies among the three rodents commonly employed in scientific research-hamster, rat, and mouse-are analyzed and described. An individual literature search for each rodent was conducted using specific search terms in three databases: PubMed, Scopus, and Web of Science. A total of 157 articles were selected (rats = 73, mice = 79, and hamsters = 5), identifying various reference genes. The most commonly used reference genes were analyzed according to each rodent, sample type, and experimental condition evaluated, revealing a great variability in the stability of each gene across different samples and conditions. Classic genes, which are expected to be stably expressed in both samples and conditions analyzed, demonstrated greater variability, corroborating existing concerns about the use of these genes. Therefore, this review provides important insights for researchers seeking to identify suitable reference genes for their validation studies in rodents.

A method for the quantitative analysis of Lycium barbarum polysaccharides (LBPs) using Fourier-transform infrared spectroscopy (FTIR): From theoretical computation to experimental application

Lycium barbarum polysaccharides (LBPs) is one of the most important active substances in Lycium barbarum (LB). It is a challenge to quantitatively determine the content due to their complex structures and lack of suitable reference standard in practice. In this study, a quantitative analysis method of LBPs in LB was established based on Fourier-transform infrared spectroscopy (FTIR). The stretching vibration of CO on the pyranose ring of saccharide at 921 cm−1 was selected as the characteristic absorption band by theoretical calculation, which can’t be impacted by the preparation methods and interfered by the component monosaccharides. The molecular weight CRM of dextran (Mw 63.3 kDa) served as the reference standard. The introducing internal standard (KSCN) can obtain a good precision (RSD = 1.10 %) and effectively compensate for the analysis errors caused by the environment, quality loss and uneven distribution during the tablet pressing processes. The methodological verification suggested that the method had good accuracy according to the recovery rate (96.61 %–105.45 %) and the blank recovery (92.39 %–99.37 %), respectively. The LOD and LOQ of CRMD were 0.10 mg and 0.32 mg, respectively. The polysaccharide content of LB from 24 different regions (0.50–2.54 %) and 10 batches of LB extracts (7.09–10.56 %) determined by the developed method less than the ones using phenol–sulfuric acid assay (1.95 %–4.83 % for LB and 9.83–15.53 % for extracts, respectively). The established method based on FTIR could be served as a supplement to phenol–sulfuric acid assay and a rapid quantitative assay for polysaccharides products. In additional, this study provided a new idea for the quantitative analysis of plant polysaccharides.

Inter-laboratory variation for urine albumin among laboratories in a Swedish external quality assessment scheme 2005–2023

IntroductionIncreased albuminuria is associated with elevated mortality. Urine albumin (U-ALB) above 20 mg/L or albumin-to-creatinine ratio (U-ACR) of 3 g/mol are indicative of moderately increased albuminuria. Due to limited standardization among U-ALB methods, diagnosis of increased albuminuria might prove difficult. Materials and methodsData from Equalis’s external quality assessment scheme for low U-ALB levels during 2005–2023 were categorized according to manufacturer and divided into central laboratory (CLAB) and point-of-care testing (POCT) methods. Manufacturer median values were compared to total group mean consensus values and manufacturer CV% was compared at different U-ALB levels. ResultsCLAB was generally closer to consensus values and had lower CV% than POCT at U-ALB levels around 20 mg/L. For CLAB, Roche methods were approximately equal to consensus U-ALB, Abbott 4 % above, and Siemens 5 % below. For POCT, HemoCue was 1 % below, Siemens 7 % above, and Abbott 8 % below. For U-Creatinine, all manufacturers generally had a good agreement differing on average by 1–4 % from consensus. ConclusionsAlthough U-ALB methods generally meet The National Kidney Disease Education Program (NKDEP) recommendations of method bias less than 13 % and imprecision less than 30 %, differences among manufacturers have increased over the last years, with 2023 showing the largest differences between methods. This highlights the need for guidelines for albuminuria and ACR to take method differences into consideration, but also for implementation of suitable urine reference materials.

Exergy analysis of hybrid air-conditioning systems with different evaporative-cooling condensers under hot-humid climates

Evaporative cooling (EC) technology can effectively improve the energy efficiency of the mechanical vapor compression (MVC) system by enhancing the heat exchange capacity of its condenser. However, the current evaporative-cooling condenser system is usually only equipped with a single-stage evaporative cooler as the precooling unit, and these designs are mainly suitable for hot-dry conditions. In this study, three hybrid air-conditioning systems with different two-stage evaporative-cooling condenser configurations were proposed, one is single-condenser type and the other two are dual-condenser type, which are used to improve the exergy performance and adaptability of the evaporative condenser system under hot-humid climates. Then, the all systems were modeled via the distributed parametric method and analyzed comparatively based on the exergy method. A suitable exergy reference temperature at air saturation was discussed. Finally, the effect of four key parameters (ambient temperature and relative humidity, outdoor airflow rate and room heat load) was studied. The results showed that under the high temperature, relative humidity or room heat load conditions, the hybrid systems have a low exergy efficiency ratio (EXR) and high exergy efficiency (ηx,OEC). Among them, the newly countercurrent dual-condenser configuration (MVC-TSEC(C)) exhibits the best exergy performance under most hot-humid conditions. Compared to the conventional MVC system, the EXR and ηx,OEC of MVC-TSEC(C) increased by at most 35.0 % and 78.2 %, respectively. Moreover, its components like compressor, condenser and expansion valve have the maximum reduction rates of exergy destruction of 43.5 %, 17.2 % and 55.3 %, respectively.

Comprehensive Screening and Validation of Stable Internal Reference Genes for Accurate qRT-PCR Analysis in Holotrichia parallela under Diverse Biological Conditions and Environmental Stresses.

Holotrichia parallela is among the world's most destructive pests. For accurate qPCR and gene expression studies, the selection of stable and appropriate reference genes is crucial. However, a thorough evaluation of potential reference genes for use in H. parallela research is lacking. In this study, 11 reference genes (GAPDH, RPL32, RPL7A, RPS18, RPL13a, RPL18, Actin, RPS7, RPS3, VATB,and EF1A) were evaluated under different biological conditions and environmental stresses. The stability of 11 potential reference gene transcripts was evaluated through various computational tools, including geNorm, BestKeeper, NormFinder, theΔCt method, and the RefFinder program. Under various developmental stages and RNAi conditions, RPL18 and RPL13a exhibited the greatest stability. RPL13a, RPL18, and RPL32 were the most stable genes in both male and female adults. Under differing tissue conditions, RPL13a and RPS3 stood out as the most reliable. Moreover, under varying photoperiod conditions, RPL13a, RPS3 and RPL32 were the most stable genes. Lastly, Actin and RPL13a were the most stable genes across different temperatures. These findings offer essential criteria for selecting suitable reference genes across diverse experimental settings, thereby establishing a solid basis for accurate gene expression studies in H. parallela using RT-qPCR.

Potassium Alloy Reference Electrodes for Potassium-Ion Batteries: The K-In and K-Bi Systems.

Potassium-ion batteries (KIBs) are a promising alternative to conventional lithium-ion batteries with reduced critical mineral dependency but accurate three-electrode characterization is hindered by the lack of a suitable reference electrode. Potassium metal is frequently used as a reference electrode out of necessity, but its high reactivity and unstable potential limit its reliability. Here we investigate the K-In and K-Bi alloy systems, synthesize two-phase In-In4K and Bi-Bi2K alloys, and identify Bi-Bi2K as a promising material owing to its stable potential of 1.07 V vs K+/K. We prove the use of Bi-Bi2K as a reference electrode by cycling graphite in three-electrode cells and demonstrate that it results in significantly less electrolyte reduction than potassium metal, facilitating the accurate electrochemical characterization necessary to accelerate KIB development.

Evaluation of suitable reference genes for qPCR normalisation of gene expression in a Achilles tendon injury model.

Tendons are one of the major load-bearing tissues in the body; subjected to enormous peak stresses, and thus vulnerable to injury. Cellular responses to tendon injury are complex, involving inflammatory and repair components, with the latter employing both resident and recruited exogenous cell populations. Gene expression analyses are valuable tools for investigating tendon injury, allowing assessment of repair processes and pathological responses such as fibrosis, and permitting evaluation of therapeutic pharmacological interventions. Quantitative polymerase chain reaction (qPCR) is a commonly used approach for such studies, but data obtained by this method must be normalised to reference genes: genes known to be stably expressed between the experimental conditions investigated. Establishing suitable tendon injury reference genes is thus essential. Accordingly we investigated mRNA expression stability in a rat model of tendon injury, comparing both injured and uninjured tendons, and the effects of rapamycin treatment, at 1 and 3 weeks post injury. We used 11 candidate genes (18S, ACTB, AP3D1, B2M, CSNK2A2, GAPDH, HPRT1, PAK1IP1, RPL13a, SDHA, UBC) and assessed stability via four complementary algorithms (Bestkeeper, deltaCt, geNorm, Normfinder). Our results suggests that ACTB, CSNK2A2, HPRT1 and PAK1IP1 are all stably expressed in tendon, regardless of injury or drug treatment: any three of these would serve as universally suitable reference gene panel for normalizing qPCR expression data in the rat tendon injury model. We also reveal 18S, UBC, GAPDH, and SDHA as consistently poor scoring candidates (with the latter two exhibiting rapamycin- and injury-associated changes, respectively): these genes should be avoided.

Beyond Keywords: Effective Strategies for Building Consistent Reference Lists in Scientific Research

Critical to navigating research literature is ensuring the inclusion of relevant sources while filtering out irrelevant ones. Selecting suitable references demands careful attention and methodological rigor. This review article presents a systematic approach consisting of 11 sequential steps for constructing a reference list, ranging from broad initial searches to excluding irrelevant references. It emphasizes refining methodologies to develop a coherent list of references aligned with the study’s scope, bolstering the knowledge base, and facilitating subsequent analyses. Urban planners and designers can apply these steps in database searches to create robust reference lists, thereby enhancing the quality and reliability of their research and ensuring future adaptability.

Identification and validation of reference genes for RT-qPCR analysis in Iris domestica under Cd stress

Iris domestica is a widely used ornamental garden and important medicinal plant. Our previous studies have shown that it exhibits significant uptake and translocation capacity under Cd stress compared to other Iris species. Gene expression is studied using RT-qPCR; however, there are no reference genes have been found for I. domestica under Cd stress. In this investigation, thirteen possible reference genes from previous studies and our transcriptome were screened using RT-qPCR in the leaves and roots of Cd-stressed plants. The findings revealed that UBC9 and ACT were the best reference genes for roots with and without Cd stress, whereas YLS8 and ACT7 were the best reference genes for leaves. Among the different tissues without Cd stress, UBC9 and UBC28 exhibited the best results, whereas PP2C06 and UBC9 exhibited the best results under Cd stress. The most stable reference genes in the leaves and roots were UBC9 and UBC28, respectively, under and without Cd stress, and GADPH was the most unstable. Finally, three metal ion response genes, NRAMP2, YSL9 and CYP81Q32 were detected using RT-qPCR and compared with the transcriptome data to further confirm the reliability of the chosen genes. This study identified suitable reference genes for I. domestica under Cd-stress conditions.

The Alzheimer's Association Global Biomarker Standardization Consortium (GBSC) plasma phospho-tau Round Robin study.

Phosphorylated tau (p-tau) is a specific blood biomarker for Alzheimer's disease (AD) pathology. Multiple p-tau biomarkers on several analytical platforms are poised for clinical use. The Alzheimer's Association Global Biomarker Standardisation Consortium plasma phospho-tau Round Robin study engaged assay developers in a blinded case-control study on plasma p-tau, aiming to learn which assays provide the largest fold-changes in AD compared to non-AD, have the strongest relationship between plasma and cerebrospinal fluid (CSF), and show the most consistent relationships between methods (commutability) in measuring both patient samples and candidate reference materials (CRM). Thirty-three different p-tau biomarker assays, built on eight different analytical platforms, were used to quantify paired plasma and CSF samples from 40 participants. AD biomarker status was categorised as "AD pathology" (n=25) and "non-AD pathology" (n=15) by CSF Aβ42/Aβ40 (US-FDA; CE-IVDR) and p-tau181 (CE-IVDR) methods. The commutability of four CRM, at three concentrations, was assessed across assays. Plasma p-tau217 consistently demonstrated higher fold-changes between AD and non-AD pathology groups, compared to other p-tau epitopes. Fujirebio LUMIPULSE G, UGOT IPMS, and Lilly MSD p-tau217 assays provided the highest median fold-changes. In CSF, p-tau217 assays also performed best, and exhibited substantially larger fold-changes than their plasma counterparts, despite similar diagnostic performance. P-tau217 showed the strongest correlations between plasma assays (rho=0.81 to 0.97). Plasma p-tau levels were weakly-to-moderately correlated with CSF p-tau, and correlations were non-significant within the AD group alone. The evaluated CRM were not commutable across assays. Plasma p-tau217 measures had larger fold-changes and discriminative accuracies for detecting AD pathology, and better agreement across platforms than other plasma p-tau variants. Plasma and CSF markers of p-tau, measured by immunoassays, are not substantially correlated, questioning the interchangeability of their continuous relationship. Further work is warranted to understand the pathophysiology underlying this dissociation, and to develop suitable reference materials facilitating cross-assay standardisation. Alzheimer's Association (#ADSF-24-1284328-C).

Robust and fast emulation of PV panels using FSL algorithm and nonlinear power stage controller

The effective implementation of Photovoltaic (PV) systems relies heavily on controlled testing using Photovoltaic Emulator (PVE). This paper presents a novel PVE for rapid and robust testing of PV systems. A fifteen segments linearization (FSL) methodology is put-forward to resolve the nonlinear current-voltage (I-V) equations of PV modules. The I-V curve is precisely segmented into 15 linear elements, whose coordinates are used to construct a suitable reference voltage for the PVE. To ensure a robust and fast emulation of the solar panel, a nonlinear power stage controller (NPSC) is designed to maximize the Buck converter-power stage of the PVE. Several experiments have been performed under diverse environmental and load testing profiles, revealing a mean error and maximum error of less than 0.2 %, and less than 0.6 % respectively for three classes of commercial PV modules (multicrystal KC200GT, poly-crystalline MSX-60, and mono-crystalline CS6K-280 M). The high computation accuracy of the FSL position the proposed PVE as a simple but powerful emulation tool for PV systems. By evaluating its performance and comparing it to the state-of-the-art emulators, this paper aims to demonstrate the effectiveness and superiority of the FSL-NPSC-PVE in achieving rapid and robust emulation of different commercial solar panels.

Minimum entropy constrained cooperative inversion of electrical resistivity, seismic and magnetic data

Geophysical methods are widely used to gather information about the subsurface as they are non-intrusive and comparably cheap. However, the solution to the geophysical inverse problem is inherently non-unique, which introduces considerable uncertainties. As a partial remedy to this problem, independently acquired geophysical data sets can be jointly inverted to reduce ambiguities in the resulting multi-physical subsurface images. A novel cooperative inversion approach with joint minimum entropy constraints is used to create more consistent multi-physical images with sharper boundaries with respect to the single-method inversions. Here, this approach is implemented in an open-source software and its applicability on electrical resistivity tomography (ERT), seismic refraction tomography (SRT), and magnetic data is investigated. A synthetic 2D ERT and SRT data study is used to demonstrate the approach and to investigate the influence of the governing parameters. The findings showcase the advantage of the joint minimum entropy (JME) stabilizer over separate, conventional smoothness-constrained inversions. The method is then used to analyze field data from Rockeskyller Kopf, Germany. 3D ERT and magnetic data are combined and the results confirm the expected volcanic diatreme structure with improved details. The multi-physical images of both methods are consistent in some regions, as similar boundaries are produced in the resulting models. Because of its sensitivity to hydrologic conditions in the subsurface, observations suggest that the ERT method senses different structures than the magnetic method. These structures in the ERT result do not seem to be enforced on the magnetic susceptibility distribution, showcasing the flexibility of the approach. Both investigations outline the importance of a suitable parameter and reference model selection for the performance of the approach and suggest careful parameter tests prior to the joint inversion. With proper settings, the JME inversion is a promising tool for geophysical imaging, however, this work also identifies some objectives for future studies and additional research to explore and optimize the method.

Disentangling cobionts and contamination in long-read genomic data using sequence composition.

The recent acceleration in genome sequencing targeting previously unexplored parts of the tree of life presents computational challenges. Samples collected from the wild often contain sequences from several organisms, including the target, its cobionts, and contaminants. Effective methods are therefore needed to separate sequences. Though advances in sequencing technology make this task easier, it remains difficult to taxonomically assign sequences from eukaryotic taxa that are not well represented in databases. Therefore, reference-based methods alone are insufficient. Here, I examine how we can take advantage of differences in sequence composition between organisms to identify symbionts, parasites, and contaminants in samples, with minimal reliance on reference data. To this end, I explore data from the Darwin Tree of Life project, including hundreds of high-quality HiFi read sets from insects. Visualizing two-dimensional representations of read tetranucleotide composition learned by a variational autoencoder can reveal distinct components of a sample. Annotating the embeddings with additional information, such as coding density, estimated coverage, or taxonomic labels allows rapid assessment of the contents of a dataset. The approach scales to millions of sequences, making it possible to explore unassembled read sets, even for large genomes. Combined with interactive visualization tools, it allows a large fraction of cobionts reported by reference-based screening to be identified. Crucially, it also facilitates retrieving genomes for which suitable reference data are absent.

Evaluation of reference genes suitable for studying mRNAs and microRNAs expression in thyroid neoplasms

Analysis of gene expression is a pivotal method at the core of biomarkers studies and cancer research. Currently, RT-qPCR is the most commonly used technique to investigate the expression of certain genes. The accurate and reliable result relies on an effective normalization step using suitable reference genes. The present study was designed to evaluate the eligibility of a set of candidate mRNAs and snoRNA as reference genes in the most common human thyroid neoplasms. We tested the expression levels of eleven mRNA and small RNA housekeeping genes in thyroid samples. The stability of the candidate genes was examined in different thyroid lesions and under different experimental conditions. Results were compared to the reported data in the TCGA database. Our results suggested HPRT1 and ACTB as the best mRNA reference genes, SNORD96A, and SNORD95 as the best miRNA reference genes in thyroid tissues. These genes showed the most stable expression pattern among different thyroid lesions as well as different experimental conditions. The findings in this study highlight the effect of reference genes selection on data interpretation and emphasize the importance of testing for suitable reference genes to be used in specific types of cells and experimental conditions to ensure the validity and accuracy of results.