Poor Quality Samples Research Articles

Establishment and characterization of a novel kidney cell line derived from the common bottlenose dolphin.

Common bottlenose dolphin (Tursiops truncatus) is a well-known cetacean species that inhabits temperate and tropical seas worldwide. Limited supply and poor quality of samples hinder the investigation of the effects of various pathogens and environmental pollutants on this cetacean species. Cultured cells are useful for experimental studies; however, no cell lines derived from cetaceans are generally available. Therefore, in this study, we established a novel kidney cell line, TK-ST, derived from T. truncatus. Primary cells exhibited the morphological characteristics of epithelial and fibroblast cells, but their immortalization and passaging resulted in a predominantly epithelial cell morphology. TK-ST was immortalized using the large T SV40 antigen and human telomerase reverse transcriptase and exhibited long-term stable cell growth. TK-ST cells are generally cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum at 37°C and 5% CO2 but can also be cultured in 5-20% fetal bovine serum and several other classical media commonly used for common animal cell culture. TK-ST cells were found to be susceptible to several viruses, including the dolphin morbillivirus (most important virus in cetaceans), and exhibited cytopathic effects, facilitating the replication of the dolphin morbillivirus. Furthermore, mRNA expression levels of cytokine genes were increased in TK-ST cells after stimulation with lipopolysaccharides and poly(I:C). Therefore, the novel TK-ST cell line derived in this study can potentially be used for further in vitro studies on cetaceans.

Formalin-Fixed, Paraffin-Embedded–Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Chromosomal rearrangements are important drivers in cancer and their robust detection is essential for diagnosis, prognosis and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based NGS method 'FFPE-TLC' has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. Here, the utility of FFPE-TLC in bone and soft tissue tumor diagnostics was evaluated. FFPE-TLC sequencing was successfully applied on non- and decalcified FFPE samples (n=44) and control samples (n=19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples and none in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed either due to detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.

Assessment of inconclusive biopsies at a tertiary care dental hospital

Background: Biopsy has crucial role in definitive diagnosis of lesions followed by appropriate treatment of the same. There are situations to clinicians when the report from the oral pathologists comes as “inconclusive biopsy”, instead of a definitive diagnosis. Objectives: To determine the frequency and reasons for inconclusive biopsy as the final diagnosis, in biopsy samples obtained for histopathological evaluation. Methods: This retrospective chart review was conducted in a total of 982 biopsy reports from the archive of the Department of Oral Pathology of Kantipur Dental College. Reports from 2016 to 2021 A.D were assessed after institutional ethical approval utilising convenience sampling. Clinical details were assessed from the patient's biopsy requisition form. Inconclusive diagnosis as the final sign-outs were evaluated, to analyse the reasons for such reports according to the standard criteria. For analysis, SPSS v.20 software was used. Results: Out of 982 biopsy reports, 140 (14.2%) inconclusive biopsy reports were recovered. The reasons for inconclusive biopsy in descending order was 129 (92.1%) poor quality of sample, five (3.6%) insufficient biopsy, three (2.1%) inappropriate fixative, two (1.4%) both insufficient and poor-quality sample and one (0.7%) lack of clinical or radiographic details. Comparison between central and peripheral inconclusive reports was not statistically significant (p >0.05). Conclusion: This study indicates that careful surgical approach is a must along with proper transportation of the biopsy sample and a detailed clinical and radiographic information to avoid inconclusive biopsy reports.

AI-based radiodiagnosis using chest X-rays: A review.

Chest Radiograph or Chest X-ray (CXR) is a common, fast, non-invasive, relatively cheap radiological examination method in medical sciences. CXRs can aid in diagnosing many lung ailments such as Pneumonia, Tuberculosis, Pneumoconiosis, COVID-19, and lung cancer. Apart from other radiological examinations, every year, 2 billion CXRs are performed worldwide. However, the availability of the workforce to handle this amount of workload in hospitals is cumbersome, particularly in developing and low-income nations. Recent advances in AI, particularly in computer vision, have drawn attention to solving challenging medical image analysis problems. Healthcare is one of the areas where AI/ML-based assistive screening/diagnostic aid can play a crucial part in social welfare. However, it faces multiple challenges, such as small sample space, data privacy, poor quality samples, adversarial attacks and most importantly, the model interpretability for reliability on machine intelligence. This paper provides a structured review of the CXR-based analysis for different tasks, lung diseases and, in particular, the challenges faced by AI/ML-based systems for diagnosis. Further, we provide an overview of existing datasets, evaluation metrics for different[][15mm][0mm]Q5 tasks and patents issued. We also present key challenges and open problems in this research domain.

Correction to: Myocardial Cytoskeletal Adaptations in Advanced Kidney Disease.

HomeJournal of the American Heart AssociationVol. 12, No. 6Correction to: Myocardial Cytoskeletal Adaptations in Advanced Kidney Disease Open AccessCorrectionPDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citations ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toOpen AccessCorrectionPDF/EPUBCorrection to: Myocardial Cytoskeletal Adaptations in Advanced Kidney Disease Originally published9 Mar 2023https://doi.org/10.1161/JAHA.121.027645Journal of the American Heart Association. 2023;12:e027645This article corrects the followingMyocardial Cytoskeletal Adaptations in Advanced Kidney DiseaseOther version(s) of this articleYou are viewing the most recent version of this article. Previous versions: March 9, 2023: Ahead of Print In the article by Arvin Halim et al, “Myocardial Cytoskeletal Adaptations in Advanced Kidney Disease” which published online February 18, 2022 (J Am Heart Assoc. 2022;11:e022991. DOI: 10.1161/JAHA.121.022991) and was included in the March 1, 2022 issue of the journal, corrections were needed.Figure 1 indicated that samples in all 3 cohorts (50 total) underwent RNA sequencing. The figure has been revised to show that that only a subset of samples from 2 cohorts underwent the final transcriptomic analysis.On page 3 of the Methods section, in the first paragraph under the heading Next Generation RNA Sequencing, the following sentence described the removal of samples from the final analysis: “Samples with low total reads (<1×106) were removed from further analyses.”This sentence has been revised to clarify the number of samples that were removed from the final analysis and the reasons for their removal: “Several samples were removed from the final analysis because of poor sample quality (ie, low total reads of <1×106) and technical batch effect that could not be corrected. The final analysis includes 13 hemodialysis and 5 healthy control hearts.”On page 4 of the Methods section, in the last paragraph under the heading Next Generation RNA Sequencing, the authors stated, “All RNA‐seq data have been deposited into the NCBI Gene Expression Omnibus (GEO) repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE160145).”The following text has been added to provide additional detail about the samples deposited and to indicate which samples were included in the final transcriptomic analyses: “Ex vivo human heart samples are designated as N (Control), CAD (HTN), RF (HD), and PD (peritoneal dialysis group) followed by sample number. Heart samples that were included in the final RNA‐seq analysis were: N10, N12, N13, N14, N15, RF2, RF3, RF4, RF8, RF9, RF11, RF12, RF13, RF15_2, RF16, RF17, RF18, and RF19. In vitro human cell samples are designated as A (atrial fibroblasts), V (ventricular fibroblasts), M (mixed atrial and ventricular fibroblasts), ‐N (Control), ‐P (elevated phosphate treatment), ‐C (elevated calcium treatment), and ‐PC (combined elevated phosphate and elevated calcium treatment) followed by technical repeat number (1‐3). Cell samples that were included in the supplemental final RNA‐seq analysis were: VN1, VN2, VN3, VPC1_2, VPC2, and VPC3.”On page 5 of the Results section, in the first paragraph under the heading Transcriptomic Profiling of Human Hearts, the RNA sequencing analysis was described as follows: “Among the top 1000 differentially expressed genes between hemodialysis and healthy control hearts, 5 were significantly upregulated and 21 were significantly downregulated in hearts from the hemodialysis group compared with control (P<0.05) (Figure 3A).”This sentence has been revised to provide additional information about the samples included in the analysis: “Among the top 1000 differentially expressed genes between hemodialysis (n=13) and healthy control (n=5) hearts, 5 were significantly upregulated and 21 were significantly downregulated in hearts from the hemodialysis group compared with control (P<0.05) (Figure 3A).”The authors regret the errors.The online version of the article has been updated and is available here: https://www.ahajournals.org/doi/10.1161/JAHA.121.022991. Previous Back to top Next FiguresReferencesRelatedDetailsRelated articlesMyocardial Cytoskeletal Adaptations in Advanced Kidney DiseaseKenneth Lim, et al. Journal of the American Heart Association. 2022;11 March 21, 2023Vol 12, Issue 6Article InformationMetrics Copyright © 2023 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley BlackwellThis is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.https://doi.org/10.1161/JAHA.121.027645PMID: 36892070 Originally publishedMarch 9, 2023 PDF download

Flow cell sorting followed by PCR-based clonality testing may assist in questionable diagnosis and monitoring of acute lymphoblastic leukemia.

Multicolor flow cytometry (MFC) has highly reliable and flexible algorithms for diagnosis and monitoring of acute lymphoblastic leukemia (ALL). However, MFC analysis can be affected by poor sample quality or novel therapeutic options (e.g., targeted therapies and immunotherapy). Therefore, an additional confirmation of MFC data may be needed. We propose a simple approach for validation of MFC findings in ALL by sorting questionable cells and analyzing immunoglobulin/T-cell receptor (IG/TR) gene rearrangements via EuroClonality-based multiplex PCR. We obtained questionable MFC results for 38 biological samples from 37 patients. In total, 42 cell populations were isolated by flow cell sorting for downstream multiplex PCR. Most of the patients (n=29) had B-cell precursor ALL and were investigated for measurable residual disease (MRD); 79% of them received CD19-directed therapy (blinatumomab or CAR-T). We established the clonal nature of 40 cell populations (95.2%). By using this technique, we confirmed very low MRD levels (<0.01% MFC-MRD). We also applied it to several ambiguous findings for diagnostic samples, including those with mixed-phenotype acute leukemia, and the results obtained impacted the final diagnosis. We have demonstrated possibilities of a combined approach (cell sorting and PCR-based clonality assessment) to validate MFC findings in ALL. The technique is easy to implement in diagnostic and monitoring workflows, as it does not require isolation of a large number of cells and knowledge of individual clonal rearrangements. We believe it provides important information for further treatment.

High-quality thin film growth of the weak topological insulator BiSe on Si (111) substrates via pulsed laser deposition

In this work, we report the growth of high-quality BiSe thin films deposited on Si (111) substrates at different temperatures via pulsed laser deposition. We observe poor sample quality at a low substrate temperature (Tsub=175°C), and as the substrate temperature increases, the crystallinity of the samples increases. At a substrate temperature, Tsub=250°C, BiSe Raman modes (modes centered around 97.6 and 112.9 cm−1) start to emerge with less intensity and evolve with the increase in the substrate temperature and at Tsub=325°C closely match with that of single crystals. These modes correspond to the vibrations of Se-atoms from the Bi2Se3 quintuple layers and Bi-atoms from the Bi-bilayer. By carefully investigating the structural properties and the Raman modes of BiSe thin films at each substrate temperature, we provide an optimal condition to grow high-quality thin films of BiSe by pulsed laser deposition.

Primary inflammatory myofibroblastic tumour of the liver: aclinicopathological and genetic study including a subset with ETV6::NTRK3 fusion.

Inflammatory myofibroblastic tumour (IMT) is an intermediate neoplasm and rarely occurs in the liver. The aim of this study was to analyse the clinicopathological and genetic features of the largest primary hepatic IMT. A total of 10 cases were identified (four males and six females aged 1-48 years, median= 35 years) from 2011 to 2021, which accounted for 2.5% of IMTs occurring in all organ systems. Histological findings revealed that myofibroblastic/fibroblastic cells with inflammatory infiltration and focal hypocellularity were observed in three children. Immunostaining showed ALK-diffuse cytoplasmic positive in six cases (six of 10; 60%) and pan-TRK nuclear positive in three cases (three of 10; 30%). Hypercellular pattern was detected in ALK-positive IMTs and obvious collagenous/myxoid matrix was observed in the pan-TRK-positive subgroup. ALK rearrangement was demonstrated in three of five interpretable ALK-positive IMTs by fluorescence in-situ hybridisation (FISH), and one case failed due to poor sample quality. Next-generation sequencing indicated an IMT with TFG::ALK and FCHSD2::ALK fusion and TP53 mutation. ETV6::NTRK3 fusion was confirmed by RT-PCR, but FISH-negative results were found in two of three cases with pan-TRK-positive IMTs. No genetic alteration was detected in one tumour. One patient died 1 year after biopsy, while nine patients survived without evidence of disease in the follow-up surveillance (17-119months). This article describes the first example of primary paediatric hepatic IMTs with ETV6::NTRK3 fusion. Besides the common ALK-positive subgroup, the proportion of NTRK3 fusion is high. Recognising the association between clinicopathological and molecular alterations is critical to accurate diagnosis of hepatic IMTs.

Management of Intermittent Hemodialysis in the Critically Ill Patient.

Intermittent hemodialysis remains a cornerstone of extracorporeal KRT in the intensive care unit, either as a first-line therapy for AKI or a second-line therapy when patients transition from a continuous or prolonged intermittent therapy. Intermittent hemodialysis is usually provided 3 days per week in this setting on the basis that no clinical benefits have been demonstrated with more frequent hemodialysis. This should not detract from the importance of continually assessing and refining the hemodialysis prescription (including the need for extra treatments) according to dynamic changes in extracellular volume and other parameters, and ensuring that an adequate dose of hemodialysis is being delivered to the patient. Compared with other KRT modalities, the cardinal challenge encountered during intermittent hemodialysis is hemodynamic instability. This phenomenon occurs when reductions in intravascular volume, as a consequence of ultrafiltration and/or osmotic shifts, outpace compensatory plasma refilling from the extravascular space. Myocardial stunning, triggered by intermittent hemodialysis, and independent of ultrafiltration, may also contribute. The hemodynamic effect of intermittent hemodialysis is likely magnified in patients who are critically ill due to an inability to mount sufficient compensatory physiologic responses in the context of multiorgan dysfunction. Of the many interventions that have undergone testing to mitigate hemodynamic instability related to KRT, the best evidence exists for cooling the dialysate and raising the dialysate sodium concentration. Unfortunately, the evidence supporting routine use of these and other interventions is weak owing to poor study quality and limited sample sizes. Intermittent hemodialysis will continue to be an important and commonly used KRT modality for AKI in patients with critical illness, especially in jurisdictions where resources are limited. There is an urgent need to harmonize the definition of hemodynamic instability related to KRT in clinical trials and robustly test strategies to combat it in this vulnerable patient population.

A New Image Simulation Technique for Deep-Learning-Based Radar Target Recognition

Radar target recognition via deep learning has been an active research area recently. However, this family of methods depends on the quality of radar images and the number of training samples. Given limited training samples of poor quality, these methods will cause severe overfitting. To solve this problem, this paper proposes a new method combining the physical model and deep learning. A new radar measurement simulation technique is presented. The radar measurements are first modeled by the attributed scattering center model. The target is reconstructed by the estimated model parameters. The corresponding residual is formed simultaneously. The reconstructed target and the residual are then frozen. A mask with random shape is imposed on the frequency data. The masked components are reset accordingly. The resulting data are combined and transformed from the frequency domain into the image domain. The new radar measurement can be then generated via the re-imaging process of target. We aim to simulate the unforeseen disturbances during data collection. The simulated radar measurements are used to improve the learning efficiency of deep models under limited sample environments. Multiple comparative studies are performed to demonstrate the advantages of the proposed method.

VITALITY AND BACTERIOLOGICAL PROFILE OF LIPTOV BOLD-SPOTTED RABBIT SEMEN

Since semen quality is important for the successful artificial insemination (AI) or cryopreservation, we focused on the evaluation of Slovak national rabbit breeds, New Zealand rabbit and Liptov Bold-Spotted rabbit semen as a possible source of gene reserve. Besides standard sperm traits such as motility, viability, acrosome integrity, and oxidative damage (ROS), bacterial profiles were also assessed in semen samples of New Zealand rabbit (control; n=2; N1 and N2) and Liptov Bold-Spotted rabbit (experimental; n=2; L2 and L4). After initial analysis, samples were divided into good (&gt;70%) and poor (&lt;70%) quality samples according to motility and viability. The results showed significantly higher (P&lt;0.05) totally motile spermatozoa in N1, N2 (76.53±1.22%; 77.30±1.22%) compared to L2 (35.86±5.39%) as well as higher progressively motile spermatozoa in N1 (60.53±1.35%) and N2 (68.13±4.14%) compared to L2 (24.16±1.95%). However, no significant differences in L4 (45.11±4.05%) compared to other groups were recorded. The proportion of dead/live, apoptotic, acrosome damaged, mitochondrial active and ROS produced rabbit sperm was assessed via flow cytometry using fluorescent dyes: DRAQ7, SYBR-14, Yo-Pro-1, PNA, MitoTracker and CellROX, respectively. Significant (p&lt;0.05) decrease of live sperm was observed in L4 (42.73±6.89%) compared to N1 (75.22±5.75%) sample. In adittion, significant (p&lt;0.05) increased presence of dead sperm was in L4 (41.20±10.16%) group compared to N2 (11.16±3.01%). The activity of rabbit sperm mitochondria assessed via mitochondrial membrane potential was significantly (p&lt;0.05) higher in N1 (93.37±1.46%) and N2 (94.35±0.74%) compared to L4 (57.34±1.92). The results from the bacteriological analysis showed that the sperm in good quality (N1 and N2) contained mainly microbial genus such as Brevundimonas, Brevibacterium, Bacillus or Achromobacter. Other samples with poor quality (L2, L4) contained different kind of bacterial genus such as Pseudomonas, Delftia, Acidovorax, Acinetobacter or Staphylococcus. Although the microorganism profile appeared different, obligate pathogenic species were not present. Therefore, further analyses are needed to find out the reason of poor semen quality.

Seven years of SNPs: An assessment of methods utilized for generating profiles for forensic genetic genealogy

Over the past seven years, hundreds of cases have been processed with the goal of phenotyping, biogeographical ancestry, and/or forensic genetic genealogy (FGG) research. However, not all profiles developed were suitable for upload to public databases or for phenotype and ancestry estimations, while some poor-quality samples surprisingly were. The capabilities for FGG testing have grown in the past year and are still improving. This summary will serve to compare the results that can be expected from three very different DNA profiling systems; single nucleotide polymorphism (SNP) array, whole genome sequencing (WGS), and targeted SNP testing via next generation sequencing (NGS). The ability of these testing methods to handle varying sample types, degradation, inhibition, the presence of non-human DNA, and low quantities of DNA will be examined. The information gained over the past seven years and hundreds of samples later can inform the decision-making processes moving forward as the field of FGG continues to grow. This summary will conclude by highlighting a successful case with a challenged sample processed with the intention of forensic genetic genealogy research.

A Global Multi-Scale Channel Adaptation Network for Pine Wilt Disease Tree Detection on UAV Imagery by Circle Sampling

Pine wilt disease is extremely ruinous to forests. It is an important to hold back the transmission of the disease in order to detect diseased trees on UAV imagery, by using a detection algorithm. However, most of the existing detection algorithms for diseased trees ignore the interference of complex backgrounds to the diseased tree feature extraction in drone images. Moreover, the sampling range of the positive sample does not match the circular shape of the diseased tree in the existing sampling methods, resulting in a poor-quality positive sample of the sampled diseased tree. This paper proposes a Global Multi-Scale Channel Adaptation Network to solve these problems. Specifically, a global multi-scale channel attention module is developed, which alleviates the negative impact of background regions on the model. In addition, a center circle sampling method is proposed to make the sampling range of the positive sample fit the shape of a circular disease tree target, enhancing the positive sample’s sampling quality significantly. The experimental results show that our algorithm exceeds the seven mainstream algorithms on the diseased tree dataset, and achieves the best detection effect. The average precision (AP) and the recall are 79.8% and 86.6%, respectively.

Dissolved Heavy Metal Pollution and Assessment of a Karst Basin around a Mine, Southwest China.

Karst water quality is one of the most important environmental issues in karst areas. The study's purpose was to investigate dissolved heavy metal pollution and health risk assessment in karst water basins around mines. River water and groundwater samples were analyzed by principal component analysis, correlation analysis, water quality index, hazard quotient, and hazard index. Median concentrations of dissolved heavy metals in the Sidi River were similar to the world average with a slightly alkaline characteristic. The concentrations of most dissolved heavy metals in river water were higher than those in groundwater. The concentrations of Zn, Pb, and Cd around the mine exceeded the limits of drinking water indicators. The poor water quality samples with high water quality index values were distributed around the mine. Lead (Pb), Zn, As, Cd, and Cr were potentially threatening metals in the study area. The pollution level of dissolved heavy metals in the Sidi River was at a medium level compared with other rivers worldwide. Principal component analysis and correlation analysis showed that Cu, Pb, Zn, Cd, Mn, Fe, As, and Sr mainly came from mine drainage; Ca2+, Mg2+, and Cr mainly came from the contribution of carbonate rocks; Na+ and K+ were related to local human agricultural activities. The concentrations of dissolved heavy metals in groundwater were affected by karst aquifers. The results of this study can provide a data reference for water resources prevention and human health protection in the Sidi River's karst basin and similar karst basins.

Characterization of the nasopharyngeal microbiome in patients with Kawasaki disease

IntroductionThe aetiology of Kawasaki disease (KD) remains unknown. Several studies have linked the human microbiome with some diseases. However, there are limited studies on the role of the respiratory microbiome in KD. The aim of our study was to make a more thorough analysis of the causes and processes that increase the susceptibility to KD. MethodsCase-control study comparing the respiratory microbiome of KD patients with that of healthy children. The V3–V4 region of the 16S rRNA bacterial gene and 16 respiratory viruses were analysed by real-time polimerase-chain reaction. We used the Ribosomal Database Project (RDP) version 11.5 (taxonomic assignment). ResultsThe initial sample included 11 cases and 11 controls matched for age, sex and seasonality. One of the cases was excluded to poor sample quality. The final analysis included 10 cases and 10 controls. In the case group, the analysis detected Haemophilus, Moraxella, Streptococcus and Corynebacterium species (27.62%, 19.71%, 25.28%, 11.86%, respectively). In the control group, it found Haemophilus, Streptococcus, Moraxella, and Dolosigranulum species (38.59%, 23.71%, 16.08, 8.93%, respectively). We found a higher relative abundance of Corynebacterium in patients with KD (11.86% vs. 1.55%; P = 0.004). ConclusionsTo our knowledge, this is the first study that has found differences in the composition of the respiratory microbiome between patients with KD and healthy controls. The relative abundance of Corynebacterium spp. was greater in the KD group. This study shows differences in the microbiome between cases and controls, which suggests that the microbiome may play a role in facilitating the development of KD.

RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.

Reverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, 'noise', that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting. The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE). Supplementary data are available at Bioinformatics online.

The Conditions and Quality of Postmortem Hair Sampling May Have a Subsequent Impact on the Interpretation of Toxicological Results in Hair.

In “postmortem” cases of high-energy trauma or extensively decomposed bodies, typical samples used for toxicological investigation (i.e., blood or urine) may not be available. In this context, alternative matrices (i.e., nails and hair) have proven to be valuable substitutes (1). Hair grows at around 1 cm per month (0.9–1.2 cm owing to inter- and intra-individual variations, nutrition, hormone status, etc. (2)). Consequently, segmental hair analysis provides a useful tool to determine drug exposure history. Analysis of fingernails and toenails can also be performed in “postmortem” cases alternatively and/or complementary to hair testing (3). Given the rate of nail growth speed (∼3 and 1.1 mm per month for fingernails and toenails, respectively (4)) and the incorporation of drugs along the entire length of the nails, it is routinely accepted that the windows of drug detection are 3–6 and 8–16 months in fingernail and toenail clippings, respectively (5). Nevertheless, segmental analyses cannot be performed on nails, and available data for the interpretation of nail results remain sparser than those for hair. The interpretation of results from nail or hair analyses can be complicated in cases of high-energy traumas or advanced stages of putrefaction owing to several pitfalls (e.g., external contamination by body fluids at the time of the death or by putrefaction fluids). In addition, sampling conditions can be challenging in such situations giving rise to poor-quality biological samples. The following case is intended to illustrate how a degraded quality of “postmortem” hair samples (performed by non-professionals, under poor conditions, i.e., not in an autopsy room) can have an impact on the interpretation of “postmortem” toxicological results in hair.

Rapid Assessment of Lipidomics Sample Purity and Quantity Using Fourier-Transform Infrared Spectroscopy.

Despite the increasing popularity of liquid chromatography–mass spectrometry (LC-MS)-based lipidomics, there is a lack of accepted and validated methods for lipid extract quality and quantity assessment prior to LC-MS. Fourier-Transform Infrared Spectroscopy (FTIR) has been reported for quantification of pure lipids. However, the impact of complex lipid sample complexity and purity on total lipid quantification accuracy has not been investigated. Here, we report comprehensive assessment of the sample matrix on the accuracy of lipid quantification using Attenuated Total Reflectance (ATR)-FTIR and establish a simple workflow for lipidomics sample quantification. We show that both pure and complex lipids show characteristic FTIR vibrations of CH- and C=O-stretching vibrations, with a quantitative range of 40–3000 ng and a limit of detection of 12 ng, but sample extraction method and local baseline subtraction during FTIR spectral processing significantly impact lipid quantification via CH stretching. To facilitate sample quality screening, we developed the Lipid Quality (LiQ) score from a spectral library of common contaminants, using a ratio of peak heights between CH stretching vibrations maxima and the collective vibrations from amide/amine, CH-stretching minima and sugar moieties. Taking all tested parameters together, we propose a rapid FTIR workflow for routine lipidomics sample quality and quantity assessment and tested this workflow by comparing to the total LC-MS intensity of targeted lipidomics of 107 human plasma lipid extracts. Exclusion of poor-quality samples based on LiQ score improved the correlation between FTIR and LC-MS quantification. The uncertainty of absolute quantification by FTIR was estimated using a 795 ng SPLASH LipidoMix standard to be <10%. With low sample requirement, we anticipate this simple and rapid method will enhance lipidomics workflow by enabling accurate total lipid quantification and normalization of lipid quantity for MS analysis.

Post-Mortem Analysis of Heroin Biomarkers, Morphine and Codeine in Stomach Wall Tissue in Heroin-Related Deaths.

Toxicological analysis of some cases can be complicated by poor sample quality caused by decomposition. Although heroin-related deaths have been researched extensively, the interpretation of toxicology findings in these cases is challenging, especially in instances where blood samples are unavailable. Thus, it is important to develop analytical methods for different sample types. In this study. a method for the quantification of 6-monoacetylmorphine, 6-acetylcodeine, morphine, and codeine in postmortem stomach wall tissue using liquid chromatography coupled with tandem mass spectrometry was developed and validated. All calibration curves prepared with the stomach wall tissue were linear and ranged from 0.5–1000 ng/g with determination coefficients of >0.99 and a lower limit of quantification of 1.0 ng/g. The coefficients of variation for within-run precision and between-run precision were <9%. Matrix effects of stomach wall tissues and their extraction recoveries were investigated and ranged from −19% to +17% and 76% to 80%, respectively. Among the 16 analyzed heroin-related death cases, 6-monoacetylmorphine, 6-acetylcodeine, morphine, and codeine were detected in 75%, 31%, 100%, and 94% of all stomach wall tissues with median concentrations of 90 ng/g, 20 ng/g, 140 ng/g, and 30 ng/g, respectively. This study provides new data on the distribution of 6-monoacetylmorphine, 6-Acetylcodeine, morphine, and codeine in postmortem stomach wall tissue and suggests the usefulness of alternative matrices for investigating heroin-related fatalities when blood samples are unavailable. In addition, the prevalence of 6-monoacetylmorphine in the stomach wall tissue was higher than that in the liver and kidney tissues.

Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges.

Simple SummaryThe use of liquid biopsy for tumor genomic profiling to identify genomic biomarkers for targeted therapies has revolutionized the clinical practice in oncology management. In this review, we have summarized the recent advancements of liquid biopsy-based genomic profiling that have led to their approval for treatment selection in advanced cancer patients and highlighted the major factors that should be considered to choose the most appropriate genomic profiling assay for different patients under different clinical conditions.Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a ‘plasma first’ or ‘tissue first’ approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the ‘right assay for the right patient at the right time’.