Analysis Of Multiple Specimens Research Articles

Optimized Analysis Method for Evaluating the Shear Strength Parameters of Rock Joint Surfaces

The results obtained from the mechanical test of rock samples inevitably suffer dispersion owing to discrepancies between test specimens. In view of these deficiencies, the present study proposes a method based on the empirical equation of shear strength developed by Barton to determine the shear strength parameters of joint surfaces using a single test specimen. This approach is then applied to optimize the analysis of multiple specimens. An analysis of experimental results verifies that the shear strength parameters of joint surfaces obtained by the proposed method can more accurately reflect the shear mechanics of multiple specimens than conventional multiple sample analyses; meanwhile, the results are reasonable and reliable. More importantly, the optimized method ensures the shear strength parameters are no longer affected by the sequence of specimens employed during shear test. The optimized analysis method eliminates the effect of differences between specimens and the influence of subjective factors on test results and therefore provides more realistic evaluations of shear strength parameters.

Abstract 3576: Accurate identification of somatic mutations in cancer patient specimens in the lack of normal tissue by targeted high-throughput sequencing

Abstract Tumor molecular profiling is rapidly becoming the standard clinical test for selecting targeted therapies in refractory cancer patients. DNA extracted from patient samples is enriched for cancer genes and sequenced to identify actionable somatic mutations therein. A major challenge arises when tumor-derived data is analyzed in the absence of normal tissue data, as it is common in clinical scenarios. The distinction between somatic and germline variants become difficult, leaving clinicians to resort to crude heuristic filtering. We present here a variant calling software, developed under quality system regulation protocols, capable of accurately identifying somatic mutations from targeted next-generation sequencing data. A novel Bayesian Network approach models the distribution of reads harboring germline and somatic mutations, estimates the contamination from normal tissue in the sample, scores somatic mutations, and imputes germline variants, without matching normal tissue data. This approach also allows joint analysis of multiple specimens from the same patient (e.g. FFPE and ctDNA), when available, improving the limit of detection. To improve specificity, our caller can also utilize prior information from different databases including somatic mutations, germline variation, and healthy controls data, in a principled fashion. We validated our method by analyzing data from the TOMA OS-Seq 131 cancer gene panel using the Illumina platform. Sample inputs ranging from 2-600ng of DNA were sequenced to a depth of >1000X, achieving on target rates ≤73% and uniformity ≥ 3.2 fold 80 penalty. Through adaptors with molecular barcodes we measured a median duplicate rate <2. We analyzed somatic mutations simulated at various variant allele fractions on a background of data from reference samples from the Genome-in-a-Bottle consortium, data on a dilution series from two reference samples, and several commercial control and clinical samples, including matched FFPE, PBMC, and ctDNA specimens. In the absence of normal tissue, our method scores each variant with respect to their likelihood of being somatic or germline. We show that, as compared to other commonly used methods, our algorithm can achieve a higher true positive rate whilst controlling a false discovery rate of 1%. We also show that jointly analyzing serial samples (e.g. ctDNA), we can improve sensitivity of shared variants. In conclusion, in contrast to currently used academic software developed for research projects, we observe that our caller outperforms these software and is particularly well suited for the clinical use cases. Note: This abstract was not presented at the meeting. Citation Format: Francisco M. De La Vega, Sean Irvine, David Ware, Kurt Gaastra, Yannick Pouiliot, Len Trigg. Accurate identification of somatic mutations in cancer patient specimens in the lack of normal tissue by targeted high-throughput sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3576. doi:10.1158/1538-7445.AM2017-3576

Development of 4-hydroxyproline analysis kit and its application to collagen quantification

4-Hydroxyproline (4-Hyp) is a specific amino acid of collagen and widely used as a factor to estimate the collagen content in biological specimens. The authors have developed an analysis kit with the ability to detect collagen on microwells. The method includes chromophore formation without solvent transfers, that allows the analysis of multiple specimens with excellent sensitivity, high specificity at low cost with shorter analysis time. The calibration curve of 4-HYP kit exhibiting a high positive relationship ( R 2 = 0.999) while showing a very low detection limit of (1.0 μg/ml). Specificity of 4-HYP kit was decreased with increasing hydrolysed non-collagenous biomolecules (HNCB), however this was negligible since only a few collagen specimens have a high amount of HNCB. The 4-HYP kit was successfully applied to commercial collagen quantification, measuring the collagen content of connective tissue and collagen synthesis of fibroblast with high satisfactory results; therefore, this is a more suitable alternative to previous analysis methods.

Validation of a New Endoscopic Technique to Assess Acid Output in Zollinger–Ellison Syndrome

To safely manage the hypersecretory state in patients with Zollinger-Ellison syndrome, both upper endoscopy and gastric analysis are required to titrate optimal medical therapy. Conventional gastric analysis requires more than 1 hour to perform and results in significant patient dissatisfaction. In this study, we have validated endoscopic gastric analysis as a novel technique that can effectively replace conventional gastric analysis. In a prospective, cross-over study, 12 patients with Zollinger-Ellison syndrome underwent gastric analysis, first by the conventional method and then by an endoscopic technique performed on the same day. Acid concentration was determined by titration, volume output was recorded, and acid output was calculated using standard methodologies and formulas. Agreement was assessed following the Bland-Altman method. To assess repeatability, both techniques were repeated on the same day in a subset of patients. Excellent agreement was reported between acid output (95% limits of agreement, -1.27 to 1.61 mEq/h) and acid concentration (95% limits of agreement, -0.01 to 0.01 mEq/mL), although poor agreement was observed between volume output measured. Endoscopic gastric analysis showed greater reproducibility regarding acid and volume output measured. We introduce a new, rapid, reproducible, and accurate endoscopic technique to measure acid output in patients with Zollinger-Ellison syndrome who require both annual endoscopy and gastric analysis. The data presented here suggest that endoscopic gastric analysis would be equally effective in determining acid output in other hypersecretory states. Additional analysis of cost effectiveness is needed to evaluate its use as a screening tool in select populations.

A time series study of the carbon isotopic composition of deep-sea benthic foraminifera

[1] Variation of the δ13C of living (Rose Bengal stained) deep-sea benthic foraminifera is documented from two deep-water sites (∼2430 and ∼3010 m) from a northwest Atlantic Ocean study area 275 km south of Nantucket Island. The carbon isotopic data of Hoeglundina elegans and Uvigerina peregrina from five sets of Multicorer and Soutar Box Core samples taken over a 10-month interval (March, May, July, and October 1996 and January 1997) are compared with an 11.5 month time series of organic carbon flux to assess the effect of organic carbon flux on the carbon isotopic composition of dominant taxa. Carbon isotopic data of Hoeglundina elegans at 3010 m show 0.3‰ lower mean values following an organic carbon flux maximum resulting from a spring phytoplankton bloom. This δ13C change following the spring bloom is suggested to be due to the presence of a phytodetritus layer on the seafloor and the subsequent depletion of δ13C in the pore waters within the phytodetritus and overlying the sediment surface. Carbon isotopic data of H. elegans from the 2430 m site show an opposite pattern to that found at 3010 m with a δ13C enrichment following the spring bloom. This different pattern may be due to spatial variation in phytodetritus deposition and resuspension or to a limited number of specimens recovered from the March 1996 cruise. The δ13C of Uvigerina peregrina at 2430 m shows variation over the 10 month interval, but an analysis of variance shows that the variability is more consistent with core and subcore variability than with seasonal changes. The isotopic analyses are grouped into 100 μm size classes on the basis of length measurements of individual specimens to evaluate δ13C ontogenetic changes of each species. The data show no consistent patterns between size classes in the δ13C of either H. elegans or U. peregrina. These results suggest that variation in organic carbon flux does not preferentially affect particular size classes, nor do δ13C ontogenetic changes exist within the >250 to >750 μm size range for these species at this locality. On the basis of the lack of ontogenetic changes a range of sizes of specimens from a sample can be used to reconstruct δ13C in paleoceanographic studies. The prediction standard deviation, which is composed of cruise, core, subcore, and residual (replicate) variability, provides an estimate of the magnitude of variability in fossil δ13C data; it is 0.27‰ for H. elegans at 3010 m and 0.4‰ for U. peregrina at the 2430 m site. Since these standard deviations are based on living specimens, they should be regarded as minimum estimates of variability for fossil data based on single specimen analyses. Most paleoceanographic reconstructions are based on the analysis of multiple specimens, and as a result, the standard error would be expected to be reduced for any particular sample. The reduced standard error resulting from the analysis of multiple specimens would result in the seasonal and spatial variability observed in this study having little impact on carbon isotopic records.

Detection and typing of human papillomavirus DNA from cervical biopsies by the slot-blot hybridization method

Cervical biopsies collected from 105 consecutive patients participating in a prospective follow-up study for cervical human papillomavirus (HPV) infections were tested for the presence of HPV 6, 11, 16 and 18 DNA by the slot-blot hybridization method. Detectable HPV types 6 and 11 could be distinguished in high stringency hybridization assay. The overall HPV-DNA detection rate was 35.2% in our group of patients. The slot-blot technique is more rapid than Southern-blotting procedure and well suited for analysis of multiple specimens.

Alteration of the complement system in children with acquired thyroid disease

The complement system was studied in detail in 23 children with acquired thyroid disease of various etiologies. Seventeen patients had elevated titers of antithyroglobulin and/or antimicrosomal antibodies; 16 had complement abnormalities. Five of 6 patients with thyromegaly, but without circulating antibodies, also had alterations in serum complement. Of the 21 children with complement abnormalities, 13 had alterations in the classical pathway consisting of decreased serum levels of C4 or C2. Serum levels of C1 and the ability of these sera to lyse an antibody-coated target cell or consume C3–C9 with a preformed immune precipitate were normal. Alternative pathway abnormalities were also present in 8 of these 13 patients while isolated alternative pathway changes were found in another eight patients. Alternative pathway abnormalities were varied and consisted of depressed serum levels of factor B, properdin, and/or properdin convertase. In addition, various sera failed to support the lysis of rabbit erythrocytes or C3–C9 consumption with zymosan and/or cobra venom factor. Analysis of multiple specimens from 10 patients over a period of one year revealed the persistence of the original complement abnormalities. Complement changes were independent of the diagnostic classification of the thyroid disease, the presence or type of antithyroid antibody, abnormalities in thyroid function, or the response to therapy. These data indicate a diffuse alteration of the complement system in most children with acquired thyroid disease. Whether this alteration reflects the involvement of complement in the pathogenesis of these disorders remains unclear.