Poor Quality Samples Research Articles

New strategy for evaluating pancreatic tissue specimens from endoscopic ultrasound-guided fine needle aspiration and surgery.

Background and AimPreoperative histological evaluation of pancreatic neoplasms is important for guiding the resection strategy and preventing postoperative adverse events. However, conventional endoscopic methods have technical limitations that reduce the accuracy of the histopathological examination. Probe electrospray ionization mass spectrometry (PESI‐MS) may be a useful technique for rapidly evaluating small specimens.MethodsThis single‐center prospective study included patients with pancreatic neoplasms between October 2018 and December 2019. Pancreatic ductal adenocarcinoma (PDAC) specimens were obtained via endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA) and non‐neoplastic tissue was obtained via surgery. Specimens were subjected to PESI‐MS and the mass spectra were analyzed using partial least squares regression‐discriminant analysis.ResultsThe study included 40 patients with 20 nonneoplastic specimens and 19 PDAC specimens (1 case of neuroendocrine carcinoma was omitted). All nonneoplastic specimens were sufficient for PESI‐MS analysis, although only 7 of 19 PDAC specimens were sufficient for PESI‐MS analysis because of poor sample quality or insufficient quantity (<1 mg). Among the 27 analyzed cases, the mass spectra clearly differentiated between the PDAC and nonneoplastic specimens.ConclusionsThis study revealed that PESI‐MS could differentiate between PDAC and nonneoplastic specimens, even in cases where EUS‐FNA produced very small specimens.

Safety and quality aspects of whole and skimmed milk powders.

Nowadays, dried milk products are highly traded and consumed all over the world, so we aimed in this study to evaluate to what extent whole and skim milk powders are safe and comply with Egyptian standards. Eighty samples of dried milk (50 whole milk powder and 30 skim milk powder) were gathered from several retailers and supermarkets for evaluation of their differing quality and safety parameters. The most frequent off-flavors recovered from whole milk powder samples were cooked ones and, in the case of skim milk powder samples, flat ones. Five samples of whole milk powder were of fair quality and three samples of poor quality, according to the sensory evaluation. The compositional parameters, moisture, %, fat, %, protein, %, and acidity, %, were measured as mean values of 3.90 ±0.15, 26.90 ±0.19, 25.53 ±0.27, and 0.99 ±0.03% in the examined whole milk powder samples and 3.77 ±0.08, 1.11 ±0.05, 34.62 ±0.29, and 1.22 ±0.03% in the examined skimmed milk powder samples, respectively. These results were within the range of component requirements set by the Egyptian Standard (2014; ES: 1780/2014) for dried milk products. Also, the microbiological safety of the milk powder samples was analyzed by assessment of the total viable count, total yeast and mold count, Coliforms count, Enterobacteriaceae, E. coli, C. sakazakii, Staphylococcus aureus, Salmonella, and Listeria monocytogenes. Staphylococcus aureus was the most prevalent isolate (36.00% and 6.67%) followed by Enterobacteriaceae (20.00% and 3.33%), of whole and skim milk powder, respectively. Enterobacteriaceae isolates included Enterobacter cloacae ssp. Cloacae, and Pantoea spp., which were specified by traditional biochemical tests and Vitek2 system. All Enterobacteriaceae isolated spp. were resistant to cephalothin, neomycin, tobramycin and colistin sulphate, and sensitive to chloramphenicol, gentamycin and nalidixic acid. E. coli, C. sakazakii, Salmonella, and Listeria monocytogenes couldn't be isolated from all the tested samples. By using Inductive Coupled Plasma - Mass Spectrometer (ICP-MS), we could measure lead and mercury as mean values of 0.243 ±0.069 and 0.261 ±0.052 mg/kg for whole milk powder samples at a percentage of 68.00 and 34.00%, while for the skim milk powder samples they were 0.150 ±0.037, and 0.347 ±0.110 mg/kg at a percentage of 66.67 and 40.00%, respectively. Finally, thirty-four whole milk powder and twelve skimmed milk powder samples didn't comply with Egyptian standards, so it is necessary for authorities to put more attention on this and regular monitor it.

Assessment of the water quality of groundwater in Bohai Rim and the controlling factors—a case study of northern Shandong Peninsula, north China

This study collected 184 groundwater (GW) samples from 92 wells during the dry and wet seasons, respectively to understand the hydrochemical characteristics, water quality, and risk of GW nitrate (NO3−) to human health in northern Shandong Peninsula (NSP), China. The results showed that GW in the NSP is weakly alkaline and classified as hard fresh water. The mean concentration of NO3− in GW exceeded 100 mg·L−1, total hardness exceeded 450 mg·L−1, and total dissolved solids (TDS) was less than 1000 mg·L−1. A Piper diagram showed that the water chemistry of GW in the NSP was mainly of the SO4·Cl-Ca·Mg type. A Gibbs diagram and ion ratio analysis indicated that the weathering of silicate rocks and agricultural production were the dominant factors affecting the hydrochemical characteristics of GW in the NSP, with cation exchange, dissolution of salt rock, and weathering of carbonate rock also making contributions. Na+ and Cl− in GW are significantly affected by seawater aerosols in coastal areas. During the wet season, the hydrodynamic conditions of the aquifer are improved, agricultural activities are strengthened, and GW becomes generally homogenized. The water quality index classified the GW quality of the NSP as mainly of medium quality. There was a relatively consistent spatial distribution of water quality during different periods. Water samples of poor water quality were mainly distributed in the lower reaches of the Huangshui River. In addition, total hardness and NO3− concentrations were the main variables affecting the quality of GW in the NSP. The assessment of the risk NO3− in GW in the NSP to human health through the ingestion of drinking water demonstrated a significant risk (infants > children > adults). These results indicate the need for local management measures to reduce the potential health risks of GW quality in the NSP.

The Hidden Cost of Hemolyzed Blood Samples in the Emergency Department.

On average, patients with hemolyzed potassium samples spend about 1 h longer in the emergency department (ED), regardless of acuity level or disposition. We aimed to quantify the direct expenses associated with poor-quality preanalytic blood samples collected in the ED. We created a simple table with a range of direct expenses (i.e., costs) and rates of hemolyzed sample draws, allowing for identification of potential high-level cost-of-care impact analysis. We included a range of costs informed by review of literature on the topic. Those costs range from $600 to $3000 per bed-hour. This amount was inflation adjusted from 1996 to 2020 (1.68 × [direct cost per visit] × [100000 visits per year/365 days/24 h]). We provided a range of hemolysis incidence based on previously reported data. We showed that for an ED with 100000 annual visits, a 40% draw rate for routine chemistries (including potassium), and a 10% hemolysis incidence, the direct cost impact of hemolysis waste is approximately $4 million/year as a result of the 1 h of added length of stay on average for a patient with a hemolyzed blood sample. This amount represents an annualized estimated cost of caring for a patient in the ED with an avoidable extended length of stay. The financial burden of poor-quality blood samples can be estimated using cost per bed-hour and rate of sample failure. Similar methodology may identify additional QC issues with previously invisible financial implications.

Relationship between sleep quality and pain intensity in patients with chronic low back pain

ObjectiveThe general objective of this study was to determine the relationship between sleep quality and pain intensity in chronic low back pain patients. MethodCross-sectional analytic study with consecutive sampling. Chronic patients who met the inclusion criteria at clinic neurology Wahidin Sudirohusodo Makassar. Independent variable: sleep quality, measured by the Pittsburgh Sleep Quality Index (PSQI)score. Dependent variable: pain intensity, measured by the Visual Analog Scale (VAS)score. Data analysis using a Chi-Square test. ResultA total of 29 samples met our inclusion criteria and divided into two groups, 23 samples of poor sleep quality, and six samples of good sleep quality. Within the poor sleep quality group, five patients (21.7%) had mild pain intensity, 11 patients (47.8%) had moderate pain intensity, and seven patients (30.4%) had severe pain intensity. In good sleep quality, five patients (83.3%) had mild pain intensity, one patient (16.7%) had moderate pain intensity, and no samples with severe pain intensity. A significant relationship found between sleep quality and pain intensity (p=0.017). ConclusionThere is a relationship between sleep quality and pain intensity. Poor sleep quality is associated with increased pain intensity in patients with chronic low back pain.

A novel approach for lavender essential oil authentication and quality assessment

Currently, the quality of lavender (Lavandula angustifolia Mill.) essential oil (LEO) is defined and regulated based on standards and methods established by regulatory authorities. Unfortunately, these existing standards and methods are not sufficient for LEO quality evaluation due to the complexity of LEO and adulteration encouraged by a burgeoning market. This study provides an efficient and reliable method for LEO quality assessment and adulteration detection. After a comprehensive investigation, involving a large set of LEO samples (n = 72) analyzed by multiple techniques (GC/MS, GC/Q-ToF, NMR, and chemometric analysis), a new approach named Q-Index was proposed. Fourteen marker compounds, along with trans-furano-linalool oxide acetate (an indicator of synthetic compound adulteration in LEO), were identified. These marker compounds played significant roles in discriminating the adulterated samples from the authentic LEOs. Calculation of the Q-Index value using the identified marker compounds permitted the detection of fraudulent samples. As demonstrated, all the authentic LEOs exhibited high Q-Index values (>100), whereas the adulterated or poor-quality samples displayed low Q-Index values (<100). The NMR-based chemometric analysis, which served as an independent and complementary approach to the GC/MS and Q-Index methods, was applied in order to assess the validity of the Q-Index method. Overall, the results obtained from different methods were in good agreement. Moreover, compared to the NMR method, the Q-Index approach possessed greater sensitivity in detecting LEO adulteration associated with the addition of synthetic compounds. Results of this study demonstrated that the Q-Index method could be successfully applied for LEO quality assessment and adulteration detection. This approach may have a significant potential to improve quality control for the LEO industry.

ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects.

R Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for storing one or more matrix-like assays along with associated row and column data. These objects have been used to facilitate the storage and analysis of high-throughput genomic data generated from technologies such as single-cell RNA sequencing. One common computational task in many genomics analysis workflows is to perform subsetting of the data matrix before applying down-stream analytical methods. For example, one may need to subset the columns of the assay matrix to exclude poor-quality samples or subset the rows of the matrix to select the most variable features. Traditionally, a second object is created that contains the desired subset of assay from the original object. However, this approach is inefficient as it requires the creation of an additional object containing a copy of the original assay and leads to challenges with data provenance. To overcome these challenges, we developed an R package called ExperimentSubset, which is a data container that implements classes for efficient storage and streamlined retrieval of assays that have been subsetted by rows and/or columns. These classes are able to inherently provide data provenance by maintaining the relationship between the subsetted and parent assays. We demonstrate the utility of this package on a single-cell RNA-seq dataset by storing and retrieving subsets at different stages of the analysis while maintaining a lower memory footprint. Overall, the ExperimentSubset is a flexible container for the efficient management of subsets. ExperimentSubset package is available at Bioconductor: https://bioconductor.org/packages/ExperimentSubset/ and Github: https://github.com/campbio/ExperimentSubset. Supplementary data are available at Bioinformatics online.

Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples.

Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N=271 samples) in addition to mitochondrial (mtDNA) sequence data (N=413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation-by-distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST =0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor-quality samples.

Tuberculosis care cascade for the indigenous population in Colombia: an operational research study.

ABSTRACTObjective.Construct and evaluate the care cascade for pulmonary tuberculosis in the indigenous population of the department of Cauca (Colombia) and identify existing gaps.Methods.Mixed-methods sequential explanatory design. In the first phase, the pulmonary tuberculosis care cascade for the indigenous population of Cauca was evaluated. Data were obtained from secondary sources and all cases diagnosed from 1 January 2016 to 31 December 2017 were included. In the second phase, semi-structured interviews were done with nine program coordinators and 11 nursing auxiliaries to explain identified gaps. Absolute and percentage values were estimated for each of the steps and gaps in the care cascade. Quantitative and qualitative results were triangulated.Results.In 2016 and 2017, an estimated 202 patients with respiratory symptoms were expected to be positive and 106 cases of pulmonary tuberculosis were reported among the indigenous population of the department of Cauca. A gap of 47.5% was found for diagnosis, since only 52.5% of subjects were diagnosed in health services. This gap was explained by poor quality of samples and flawed smear techniques; flaws in correct identification of patients with respiratory symptoms; limited access to diagnostic methods, such as culture and molecular tests; and limited training and high turnover of personnel in health service provider institutions.Conclusions.The tuberculosis control program should focus actions on bridging the gap in case detection in the indigenous population.

Evaluation of errors during different phases of coronavirus disease 2019 TrueNat testing in a tertiary care hospital

Background: Although diagnostic errors have always significantly attributed to clinical and economical losses, now in the ongoing coronavirus disease 2019 (COVID-19) pandemic, the impact of these errors has unquestionably increased multifold. In the present scenario, reporting of false-negative or false-positive test results may adversely affect the public health measures and government restrictive policies, established for the containment of COVID-19 in addition to enhancing the individual suffering and economic burden. The only way to reduce errors in various phases of COVID-19 testing is to evaluate them thoroughly and subsequently follow them up with effective corrective actions. Materials and Methods: The present study was conducted at a tertiary care center, approved by Indian Council of Medical Research for COVID-19 TrueNat testing. Information regarding errors and subsequent corrective actions in preanalytical, analytical, and post-analytical phases of TrueNat testing for COVID-19 were collected. Results: A total of 112 testing errors were observed in the TrueNat testing of 1108 samples during the study duration. Around 58.93% errors occurred in the preanalytical phase of TrueNat testing, followed by 39.29% and 1.79% errors in the analytical phase and post-analytical phases, respectively. Poor quality samples constituted the predominant cause of error in the preanalytical phase. Conclusion: Delivery of accurate results is of paramount importance in this COVID-19 pandemic. A thorough analysis of the various phases of COVID-19 testing will help identify and understand the errors and implement effective corrective actions.

Proteomic profile of bone "collagen" extracted for stable isotopes: Implications for bulk and single amino acid analyses.

Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed. Protein samples that had been previously analyzed for stable isotopes, including those with marginal and poor sample quality, were characterized by liquid chromatography/mass spectrometry using an LTQ Orbitrap Velos mass spectrometer after separation on a Dionex Ultimate 3000 LC system. Data were analyzed using MetaMorpheus and custom R scripts. We found a variety of proteins in addition to collagen, although collagen I was found in the majority of the samples (most samples >80%). We also found a positive correlation between total deamidation and wt% N, suggesting that deamidation may impact the overall nitrogen signal in bulk analyses. The amino acid profiles of samples, including those of marginal or poor stable isotope quality, reflect the expected collagen I percentages, allowing their use in single amino acid stable isotope analyses. All the samples regardless of quality were found to have high concentrations of collagen I, making interpretations of dietary routing based on collagen I reasonably valid. The amino acid profiles on the marginal and poor samples reflect an expected collagen I profile and allow these samples to be recovered for single amino acid analyses.

Resilience and Depressive Symptoms in Adults With Cardiac Disease: A Systematic Review.

Depressive symptoms predict hospitalization and mortality in adults with cardiac disease. Resilience, defined as a dynamic process of positively responding to adversity, could protect against depressive symptoms in cardiac disease. No systematic review has been conducted on the relationship between these variables in this population. The aim of this review was to explore the association between psychological resilience and depressive symptoms in adults with cardiac disease. Seven databases (PubMed, EMBASE, CINAHL, PsycInfo, Web of Science, SCOPUS, and Cochrane) were searched from inception to December 2019 using the search terms "cardiac disease," "depressive symptoms," "depression," and "resilience." Inclusion criteria dictated that studies reported original research on the association between resilience and depressive symptoms in adults with a cardiac disease broadly defined. Quality ratings were performed by 2 independent raters. We identified 13 studies for final review. Study sample sizes ranged from 30 to 1022 participants, average age ranged from 52 to 72 years, and all studies had majority male participants (64%-100%). Resilience and depressive symptoms were inversely related in 10 of 13 studies. The 3 studies with poor-quality sampling techniques or significant loss to follow-up found no relationship. Resilience seems to protect against depression in adults with cardiac disease. Gaps in the literature include poor understanding of the direction of causality. Methods of promoting resilience need to be identified and studied.

Association of Psychological Resilience and Depressive Symptoms in Adults With Cardiac Disease

Depressive symptoms predict hospitalization and mortality in adults with cardiac disease. Psychological resilience may protect against depressive symptoms, but benefits are not yet conclusive. We conducted a systematic review to examine the association between resilience and depressive symptoms in adults with cardiac disease. Seven databases were searched from inception to December 2019 using the search terms “cardiac disease,” “depressive symptoms,” “depression,” and “resilience.” The 623 articles identified were narrowed through title, abstract and full-text review leaving 13 studies for final analysis. Resilience and depressive symptoms were inversely related in 10 of 13 studies. The three studies with poor quality sampling techniques or significant loss to follow-up found null results. The major gap identified in the literature was poor understanding of the longitudinal pattern between resilience and depressive symptoms. If the direction of causality functions as expected in longitudinal research, optimizing resilience could help attenuate depressive symptoms.

The effects of sample handling on proteomics assessed by reverse phase protein arrays (RPPA): Functional proteomic profiling in leukemia

Reverse phase protein arrays (RPPA) can assess protein expression and activation states in large numbers of samples (n > 1000) and evidence suggests feasibility in the setting of multi-institution clinical trials. Despite evidence in solid tumors, little is known about protein stability in leukemia. Proteins collected from leukemia cells in blood and bone marrow biopsies must be sufficiently stable for analysis. Using 58 leukemia samples, we initially assessed protein/phospho-protein integrity for the following preanalytical variables: 1) shipping vs local processing, 2) temperature (4 °C vs ambient temperature), 3) collection tube type (heparin vs Cell Save (CS) preservation tubes), 4) treatment effect (pre- vs post-chemotherapy) and 5) transit time. Next, we assessed 1515 samples from the Children's Oncology Group Phase 3 AML clinical trial (AAML1031, NCT01371981) for the effects of transit time and tube type. Protein expression from shipped blood samples was stable if processed in ≤72 h. While protein expression in pre-chemotherapy samples was stable in both heparin and CS tubes, post-chemotherapy samples were stable in only CS tubes. RPPA protein extremes is a successful quality control measure to identify and exclude poor quality samples. These data demonstrate that a majority of shipped proteins can be accurately assessed using RPPA. SignificanceRPPA can assess protein abundance and activation states in large numbers of samples using small amounts of material, making this method ideal for use in multi-institution clinical trials. However, there is little known about the effect of preanalytical handling variables on protein stability and the integrity of protein concentrations after sample collection and shipping. In this study, we used RPPA to assess preanalytical variables that could potentially affect protein concentrations. We found that the preanalytical variables of shipping, transit time, and temperature had minimal effects on RPPA protein concentration distributions in peripheral blood and bone marrow, demonstrating that these preanalytical variables could be successfully managed in a multi-site clinical trial setting.

A genotyping method combining primer competition PCR with HRM analysis to identify point mutations in Duchenne animal models

Dystrophin-null sapje zebrafish is an excellent model for better understanding the pathological mechanisms underlying Duchenne muscular dystrophy, and it has recently arisen as a powerful tool for high-throughput screening of therapeutic candidates for this disease. While dystrophic phenotype in sapje larvae can be easily detected by birefringence, zebrafish genotyping is necessary for drug screening experiments, where the potential rescue of larvae phenotype is the primary outcome. Genotyping is also desirable during colony husbandry since heterozygous progenitors need to be selected. Currently, sapje zebrafish are genotyped through techniques involving sequencing or multi-step PCR, which are often costly, tedious, or require special equipment. Here we report a simple, precise, cost-effective, and versatile PCR genotyping method based on primer competition. Genotypes can be resolved by standard agarose gel electrophoresis and high-resolution melt assay, the latter being especially useful for genotyping a large number of samples. Our approach has shown high sensitivity, specificity, and reproducibility in detecting the A/T point mutation in sapje zebrafish and the C/T mutation in the mdx mouse model of Duchenne. Hence, this method can be applied to other single nucleotide substitutions and may be further optimized to detect small insertions and deletions. Given its robust performance with crude DNA extracts, our strategy may be particularly well-suited for detecting single nucleotide variants in poor-quality samples such as ancient DNA or DNA from formalin-fixed, paraffin-embedded material.

Framework for quality assessment of whole genome cancer sequences

Bringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole genomes sequenced over several years in different sequencing centres requires a framework to compare the quality of these sequences. We used the Pan-Cancer Analysis of Whole Genomes cohort as a test case to construct such a framework. This cohort contains whole cancer genomes of 2832 donors from 18 sequencing centres. We developed a non-redundant set of five quality control (QC) measurements to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses and allow for exclusion of samples of poor quality. We have found that this is an effective framework of quality measures. The implementation of the framework is available at: https://dockstore.org/containers/quay.io/jwerner_dkfz/pancanqc:1.2.2.

Improved Sample Quality and Decreased Turnaround Time When Using Plasma Blood Collection Tubes with a Mechanical Separator in a Large University Hospital.

Serum is commonly used for clinical chemistry testing but many conditions can affect the clotting process, leading to poor sample quality and impaired workflow. With serum gel tubes, we found a high proportion of sample probe aspiration errors on our Beckman AU5800 analyzers. We decided to implement the BD Barricor™ plasma tubes, and we validated an off-specification centrifugation scheme and verified that results obtained for 65 chemistry and immunochemistry tests were comparable to those obtained in serum gel tubes. Finally, we evaluated the impact of this new tube on sample error rate and laboratory turnaround time. To validate centrifugation settings, 50 paired samples were collected in Barricor tubes and centrifuged at 1912 × g for 10 min or 5 min (off-specification). To compare serum gel tubes with Barricor plasma tubes, 119 paired samples were collected from volunteers and results were analyzed using weighed Deming regression. Finally, the proportion of aspiration errors and laboratory TAT for potassium were measured before and after implementing Barricor tubes. Barricor tubes showed clinically acceptable equivalence to serum gel tubes for the studied analytes, and the off-specification centrifugation scheme did not affect the results. Implementing Barricor tubes improved the laboratory workflow by decreasing the aspiration error rates (2.01% to 0.77%, P < 0.001) and lowering hemolysis (P < 0.001). The laboratory TAT for potassium were also significantly lowered (P < 0.001). Use of Barricor tubes instead of serum gel tubes leads to better sample quality, shorter more reproducible laboratory TAT, and decreases costs associated with error management.

Exploring study on the cutoff of vitamin D deficiency in Chinese adults

To study the relationship between 25-hydroxyvitamin D [25(OH)D] concentration and intact parathyroid hormone(iPTH) concentration in the Chinese non-clinical population aged 18-44 y, and to explore the threshold value of determining the appropriate nutritional status of vitamin D. A total of 650 plasma samples of adults aged 18-44 years old were selected from the established biological samples&apos; bank of Chinese Chronic Diseases and Nutrition Survey(CCDNS, 2015-2018). Basic information(including age, gender, region type, season, etc. ) was collected by questionnaires, and the waist circumference, height and weight of the subjects were determined unified. North and South area was divided by Qinling Mountains and Huaihe River. The serum 25(OH)D concentration was determined by high performance liquid chromatography tandem mass spectrometer, and the iPTH was determined by electronic chemiluminescence method. The relationship of 25(OH)D and iPTH were analyzed by partial correlation analysis, and the threshold of 25(OH)D was analyzed by locally weighted scatter plot smoothing method after adjusting the iPTH by age, season of blood draw, BMI, waist, sex and latitude. A total of 623 serum samples(293 male, 330 female) of 25(OH)D concentration and iPTH concentration were analyzed after excluding samples with poor blood sample quality. Significant higher 25(OH)D concentration was found in male than female(P&lt;0. 0001). And the samples from the southern China had higher 25(OH)D concentration than those from the northern China(P&lt;0. 0001). Samples from autumn had higher 25(OH)D concentration than those from spring and winter(P&lt;0. 0001). The 25(OH)D concentration of samples from cities was lower than that of rural areas(P=0. 018). The inversely relationship between 25(OH)D concentration and iPTH concentration was observed when the 25(OH)D was below 17. 6 ng/mL for both sexes. The threshold of 25(OH)D for male was 16. 2 ng/mL and it was 25. 6 ng/mL for female. The threshold and the relationship between 25(OH)D and iPTH differs by sex among Chinese adults aged 18-44 y. Further study is needed to evaluate the sex-specific ranges of optimal vitamin D.

Abstract 1335: Analytical evaluation of a targeted solid tumor next-generation sequencing assay

Abstract With the growing interest in personalized medicine for cancer patients, next generation sequencing (NGS) variant screening assays are becoming a powerful clinical tool for tumor classification. The AmpliSeqTM for Illumina Focus Panel is a targeted sequencing approach that interrogate 52 of the most common solid tumor genes for single nucleotide variants (SNVs), insertion/deletions (indels), and copy number variants (CNVs) in DNA and gene fusions in RNA concurrently. To evaluate the performance of the Focus assay, an analytical performance study was conducted. Using an automated workflow with high quality DNA reference samples, both intra-assay and inter-assay experiments resulted in high reproducibility (R2 &amp;gt;0.95) for detecting expected variants at various frequencies. Similarly, using high quality RNA reference samples, 100% of all expected fusions were detected in all experiments, demonstrating accuracy and precision of the Focus panel assay with high quality samples. To evaluate assay sensitivity, limit of detection (LOD) studies were carried out by titrating the nucleic acid input into the assay. Using a 5% variant allele frequency threshold (empirically established in the analysis pipeline), the assay detected all expected SNVs and indels across sample across sample input amounts. Using extracted DNA from a human cell line model (HL-60) with a confirmed MYC gene gain, results showed reliable MYC gain detection down to 4 copies in a diploid background. Similarly, extracted RNA from a confirmed EML4-ALK fusion positive cell line (H2228) diluted into background RNA showed 100% positive fusion calling down to 250pg or 133 copies. Finally, to understand the assay performance on clinically-relevant FFPE samples, somatic variant detection in 8 human cell lines and 68 total FFPE samples was evaluated. For FFPE DNA samples, the libraries averaged &amp;gt;90% on-target alignment and coverage uniformity with &amp;gt;3000x mean coverage across all samples. While FFPE RNA showed lower alignment for poor quality samples, the assay showed overall high positive and negative predictive value for variant and fusion calling. In summary, the AmpliSeqTM for Illumina Focus panel is an automation-compatible small panel NGS assay with robust performance to assess somatic variants in solid tumors. Citation Format: Jeff H. Tsai, Valerie Montel, Nathalie Mouttham. Analytical evaluation of a targeted solid tumor next-generation sequencing assay [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1335.

An Asphalt Damage Dataset and Detection System Based on RetinaNet for Road Conditions Assessment

The analysis and follow up of asphalt infrastructure using image processing techniques has received increased attention recently. However, the vast majority of developments have focused only on determining the presence or absence of road damages, forgoing other more pressing concerns. Nonetheless, in order to be useful to road managers and governmental agencies, the information gathered during an inspection procedure must provide actionable insights that go beyond punctual and isolated measurements: the characteristics, type, and extent of the road damages must be effectively and automatically extracted and digitally stored, preferably using inexpensive mobile equipment. In recent years, computer vision acquisition systems have emerged as a promising solution for road damage automated inspection systems when integrated into georeferenced mobile computing devices such as smartphones. However, the artificial intelligence algorithms that power these computer vision acquisition systems have been rather limited owing to the scarcity of large and homogenized road damage datasets. In this work, we aim to contribute in bridging this gap using two strategies. First, we introduce a new and very large asphalt dataset, which incorporates a set of damages not present in previous studies, making it more robust and representative of certain damages such as potholes. This dataset is composed of 18,345 road damage images captured by a mobile phone mounted on a car, with 45,435 instances of road surface damages (linear, lateral, and alligator cracks; potholes; and various types of painting blurs). In order to generate this dataset, we obtained images from several public datasets and augmented it with crowdsourced images, which where manually annotated for further processing. The images were captured under a variety of weather and illumination conditions and a quality-aware data augmentation strategy was employed to filter out samples of poor quality, which helped in improving the performance metrics over the baseline. Second, we trained different object detection models amenable for mobile implementation with an acceptable performance for many applications. We performed an ablation study to assess the effectiveness of the quality-aware data augmentation strategy and compared our results with other recent works, achieving better accuracies (mAP) for all classes and lower inference times (3× faster).