bluuebunny/crossref_metadata_2025 huggingface dataset:
Preanalytical considerations in testing thyroid function
Authors: Keffer J H
Published: January 2020

Remarkable technical advances have permitted analytical measurement of thyrotropin (TSH) and estimates of free thyroxine (FT4) with precision, accuracy, and favorable economics. Combined with an increased appreciation of the key insights into the pituitary-thyroid relation, preanalytical considerations infrequently introduce confounding variables. In reviewing thyroid data, preanalytical considerations include physiological and specimen-based issues. Central to the improvement in thyroid assessment is the recognition that physiological individuals maintain their FT4 within narrow limits. When this deviates, there is a logarithmic response of the TSH concentration to the arithmetic shift in FT4. In effect, the TSH deviation magnifies the subtle shift in FT4. Artifact and other nonthyroid-related preanalytical considerations are infrequently the cause of nonconcordance when discrepancy occurs between the reported values for FT4 and TSH. When abnormalities of TSH and FT4 are encountered, the probability strongly favors a disease state rather than a preanalytical variable. Infrequent but real extrathyroidal pathophysiological states are increasingly recognized as a result of the reliable assessment of the pituitary-thyroid relation.
Chemiluminescent hybridization-ligation assays for delta F508 and delta I507 cystic fibrosis mutations
Authors: Martinelli R A , Arruda J C , Dwivedi P
Published: January 2020

Chemiluminescent hybridization-ligation assays were devised to detect the delta F508 and delta I507 cystic fibrosis mutations in samples of human DNA that had been amplified by PCR. Two synthetic DNA oligomers were used in each assay. One of the oligomers was labeled with an acridinium ester and the other was immobilized on paramagnetic particles. The oligomers were hybridized to the samples and the target sequences discriminated by ligation with T4 or a thermostable DNA ligase. The performance of the assay was evaluated in a blind study of 30 samples. There was complete correspondence between the assignments based on the chemiluminescent assay and those made previously by gel electrophoresis, with one exception. The assignment of this discrepant sample by the chemiluminescent assay as a delta I507/normal heterozygote rather than a delta F508/normal heterozygote was confirmed by sequencing. The chemiluminescent hybridization-ligation assay provides a rapid and convenient means of discriminating DNA sequences differing by a single nucleotide.
Strand displacement amplification (SDA) and transient-state fluorescence polarization detection of Mycobacterium tuberculosis DNA
Authors: Walker G T , Nadeau J G , Linn C P , Devlin R F , Dandliker W B
Published: January 2020

Strand displacement amplification (SDA) is an isothermal, in vitro method of amplifying a DNA sequence for diagnostic purposes. We have combined SDA with fluorescence polarization detection in a closed, homogeneous format. A fluorescently labeled oligodeoxynucleotide detector probe hybridizes to the amplification product that increases in concentration during SDA. The single- to double-stranded conversion of the probe is accompanied by an increase in fluorescence polarization values, which can be measured in real-time without physical manipulation of the sample. The probe was labeled with the near-infrared dye La Jolla Blue, and fluorescence polarization was measured on a transient-state fluorometer. We have applied this homogeneous SDA/detection system to a target DNA sequence specific for Mycobacterium tuberculosis DNA.
Fluorometric determination of total mRNA with oligo(dT) immobilized on microtiter plates
Authors: Miura Y , Ichikawa Y , Ishikawa T , Ogura M , de Fries R , Shimada H , Mitsuhashi M
Published: January 2020

We have developed a rapid and nonradioactive method of quantifying cytosolic mRNA from crude cell lysates by using plastic plates to which oligonucleotides containing poly(dT) sequences were previously immobilized. Captured mRNA on the plate was mixed with Yoyo-1 fluorescent indicator dye, and the resulting Yoyo-1 fluorescence of the mRNA-Yoyo-1 complex was measured in a fluorometer. Because Yoyo-1 signals were linearly increased in proportion to the amount of applied mRNA in the range 10-250 ng, the amount of mRNA in test samples can be determined by comparing their Yoyo-1 fluorescence with that of known concentrations of calibrator mRNA. Using this system, we found that the amount of cytosolic mRNA in undifferentiated U937 and HL-60 cells was 268.6 +/- 13.1 and 282.0 +/- 7.8 ng/10(6) cells, respectively, significantly (P < 0.01) more than that of phorbol ester-induced differentiated U937 and HL-60 cells (145.3 +/- 13.9 and 164.7 +/- 11.6), respectively. Therefore, the present system may be applicable to both medical molecular biology research and diagnostics.
Microassay of amiodarone and desethylamiodarone in serum by capillary electrophoresis with head-column field-amplified sample stacking
Authors: Zhang C X , Aebi Y , Thormann W
Published: January 2020

Binary-system capillary electrophoresis (CE) with head-column field-amplified sample stacking permits determination of amiodarone and desethylamiodarone in 20-microL serum samples. The assay is characterized by a detection limit for both compounds of 80 nmol/L and by excellent linear response over the recommended therapeutic range for amiodarone (1.5-4 mumol/L). Intra- and interday reproducibilities (CVs) between 3% and 6% and run times of approximately 10 min are comparable with those for conventional HPLC. Besides excellent sensitivity, attractive features of the assay include low operating costs, high separation efficiency, rapid drug extraction, consumption of almost negligible amounts of organic solvents, and simple operation. If appropriate microvessels and liquid-handling facilities are available, the same assay can be performed with 2 microL of serum, and if the serum is not diluted but rather is concentrated during extraction, < 1 nmol/L of amiodarone can be detected.
Ascitic pseudouridine discriminates between hepatocarcinoma-derived ascites and cirrhotic ascites
Authors: Castaldo G , Intrieri M , Calcagno G , Cimino L , Budillon G , Sacchetti L , Salvatore F
Published: January 2020

Various biochemical indexes discriminate neoplastic from nonneoplastic ascites. However, within the latter group, the distinction between cirrhotic ascites and ascites caused by hepatocarcinoma (HC) is usually based on liver biopsy or cytology. HC-derived ascites is included in the group of nonneoplastic ascites because it is not associated with peritoneal spreading of neoplastic cells. In 54 cases of cirrhotic ascites and 17 cases of HC ascites, all histologically diagnosed, ascitic pseudouridine concentrations discriminated cirrhotic from HC ascites. For example, using the cutoff value of 4.25 mumol/L (obtained by ROC curve analysis) resulted in a diagnostic sensitivity of 88.2% and a diagnostic specificity of 90.8%. Moreover, in cirrhosis, the ascitic concentrations of pseudouridine were lower than serum concentrations, and the two sets of values were correlated; in HC, however, ascitic pseudouridine concentrations were higher than serum concentrations, and the two were unrelated. These findings strongly suggest that in cirrhotic patients ascitic pseudouridine derives from serum by diffusion, whereas in HC patients the mechanism appears to be more complex.
Analytical and clinical evaluation of refractive index-matched anomalous diffraction (RIMAD) for assessment of fetal lung maturation
Authors: Rohlfs E M , Chaing S H , Chapman J F
Published: January 2020

We have evaluated refractive index-matched anomalous defraction (RIMAD) (Dubin SB, Clin Chem 1988;34:938-43) as a potential method for assessment of fetal lung maturity (FLM). This method determines the total light scattered by the surfactant-containing lamellar bodies by subtraction of the A650 from amniotic fluid diluted in glycerol from that of amniotic fluid diluted in distilled water. It is not significantly affected by such contaminating chromogens as hemoglobin and bilirubin up to 2.0 g/L and 11.0 mg/L, respectively. However, the addition of as little as 2.5 microL of erythrocytes as whole blood resulted in significant interference. RIMADs for normal respiratory outcomes (n = 78) ranged from 0.018 to 0.471. RIMADs for respiratory distress syndrome (RDS) outcomes (n = 8) ranged from 0.004 to 0.036. Use of a RIMAD referent value of > 0.040 to indicate maturity yielded sensitivity, specificity, predictive value (PV)RDS, and PVmaturity of 100%, 96.2%, 72.2%, and 100%, respectively. The areas under the receiver-operating characteristic curves were 0.997 for the RIMAD assay, 0.993 (P = 0.3) for the TDx-FLM assay, 0.89 (P = 0.017) for the lecithin/sphingomyelin ratio, and 0.87 (P = 0.023) for the foam stability index.
Quantitative RT-PCR combined with time-resolved fluorometry for determination of BCR-ABL mRNA
Authors: Bortolin S , Christopoulos T K
Published: January 2020

A microtiter well-based quantitative reverse transcriptase-PCR assay for determination of BCR-ABL mRNA, which relies on coamplification of the target with an RNA internal standard (IS), was developed. The hapten digoxigenin (Dig) is incorporated during PCR. Target RNA and IS contain identical primer recognition sites and generate same-sized amplification products distinguishable by hybridization with probes specific to the molecules' central part. The hybrids are determined with an anti-Dig-alkaline phosphatase conjugate with fluorosalicylphosphate as substrate. Fluorescent complexes of fluorosalicylate-Tb(III)-EDTA are measured by time-resolved fluorometry. The ratio of fluorescence values for target and IS is linearly related to initial target RNA in the range of 1000 to 200000 molecules. Samples containing K562 total RNA amidst 1 microgram of RNA from normal cells give fluorescence ratios that are linearly related to 30-10000 K562 cells. CVs for 30, 200, and 900 K562 cells are approximately 11%.
Immunoadsorption assay for bone alkaline phosphatase compared with wheat germ agglutinin precipitation assay in serum from (pre)pubertal girls
Authors: Bouman A A , de Ridder C M , Nijhof J H , Netelenbos J C , Delemarre-vd Waal H A
Published: January 2020

The performance characteristics of two bone alkaline phosphatase (ALP; EC 3.1.3.1) assays, a wheat germ agglutinin (WGA) precipitation assay and a new immunoadsorption assay (IAA), were compared. The within- and between-run imprecision of the IAA (3.6-4.2% and 3.6-7.7%) was comparable with that of the WGA assay. The mean cross-reactivity with liver ALP appeared to be 4% in the WGA assay and 11% in the IAA. The reference ranges in a group of 155 healthy Caucasian (pre)pubertal schoolgirls were: 149-401 U/L (total ALP, 30 degrees C), 105-349 U/L (bone ALP, 30 degrees C, WGA assay), and 58-205 U/L (bone ALP, 25 degrees C, IAA). Comparison of the WGA assay (x) with the IAA (y) demonstrated a correlation coefficient of 0.95 [Deming regression equation: y = (0.56 +/- 0.01)x + (2.0 +/- 1.5); Sy[symbol: see text]x = 5.3 U/L]. Correlation studies of the WGA assay and the IAA results with total ALP demonstrated r = 0.98 and 0.96, respectively.
Multienzyme control serum (Seraclear-HE) containing human enzymes from established cell lines and other sources. 3: Evaluation as candidate working enzyme reference material for gamma-glutamyltransferase
Authors: Eto A , Oishi T , Nakano N I , Chikaura Y
Published: January 2020

Seraclear-HE, containing gamma-glutamyltransferase (GGT, EC 2.3.2.2) derived from the cell culture of a human macrophage cell line, was evaluated as a candidate enzyme reference material (ERM) to calibrate routine methods in terms of a Reference Method for GGT. We have compared this preparation with commercially available materials, including Certified Reference Material 319, at 30 degrees C and 37 degrees C with respect to kinetic properties and with respect to commutability between the Reference Method and each of 15 analytical procedures involving five structurally different donor substrates. GGTs of human origin are far more commutable with reagents of varied types than are GGTs derived from animals. Calibration of 44 patients' sera with Seraclear-HE decreased average intermethod variation from 20% to approximately 4%, whereas GGTs of animal origin showed intermethod variations of approximately 30% with no benefit from calibration. Seraclear-HE is promising as a secondary or working ERM to be used as an intermethod calibrator.
Effect of renal function on serum nitrogen oxide concentrations
Authors: Mackenzie I M , Ekangaki A , Young J D , Garrard C S
Published: January 2020

Nitric oxide is too short-lived to measure in vivo, but its production can be estimated by measuring its stable oxidation products, nitrites and nitrates, in serum. Renal elimination of these ions has been demonstrated, but the effect of renal function on their concentrations in serum is currently unknown. We evaluated serum and urine nitrates + nitrites as serum nitrogen oxides (sNOx), nitrogen oxide (NOx) clearance, and creatinine clearance in 71 patients on the Intensive Therapy Unit. The correlation between sNOx and plasma creatinine was strong and highly significant (P <0.001). These results suggest that renal function has a significant effect on sNOx concentrations. Studies in which the sNOx concentration is used as an index of nitric oxide production can therefore be interpreted only if renal function has been taken into account.
Plasma phospholipid fatty acids in X-linked adrenoleukodystrophy
Authors: Aveldaño M I , Donnari D
Published: January 2020

Blood cell and plasma lipid classes and their fatty acids were analyzed in a child with X-linked adrenoleukodystrophy. The increase in saturated fatty acids with very long chains typical of this disease occurred almost exclusively in sphingomyelin. In this lipid, the proportion of lignoceric (24:0) and hexacosanoic (26:0) acids increased while that of 18:0, 20:0, and 24:1 decreased. In the rest of the lipid classes, but especially in cholesteryl esters and triacylglycerols, the proportion of linoleate (18:2) decreased while that of oleate (18:1) increased. In glycerophospholipids, polyunsaturated fatty acids such as 20:4n-6, 22:5n-6, and 22:6n-3 were reduced while their immediate precursors, 20:3n-6, 22:4n-6, and 22:5n-3, respectively, were relatively increased, suggesting a defect in fatty acid desaturation mechanisms. Although less pronounced, a similar trend of changes was seen in the patient's mother; in both, all alterations were more marked in serum than in blood cells.
Physical activity releases prostate-specific antigen (PSA) from the prostate gland into blood and increases serum PSA concentrations
Authors: Oremek G M , Seiffert U B
Published: January 2020

Determination of prostate-specific antigen (PSA) is an established tool in detecting prostate cancer. However, the effect of physical activity on the PSA concentration in serum is controversial. We measured serum concentrations of PSA and prostatic acid phosphatase (PAP) in 301 healthy outpatients before and after they performed standardized exercise. Immediately after 15 min of exercise on a bicycle ergometer, their serum PSA concentrations increased by as much as threefold. The increase was age dependent and correlated to the PSA concentration before exercise. This increase was evident in both the free and complexed fractions of PSA. The amount of PSA secreted into blood depends on the volume of the prostate, whereas productivity of the prostate epithelium remains constant or increases slightly with age. We present cutoff values for clinical use. PAP was also increased, but to a lesser extent. The PSA and PAP secretion mechanisms differ. Our data suggest that extensive physical activity should be avoided before blood sampling for diagnostic purposes and, in case of an increase, the PSA concentration should be controlled after an exercise test.
Two-stage procedure for evaluating interassay carryover on random-access instruments
Authors: Schlain B , Frush H , Pennington C , Osikowicz G , Ford K
Published: January 2020

A two-stage statistical procedure based on Dunnett's multiple comparison procedures with a control has been developed for detecting interassay carryover biases on the Abbott AxSYM(TM) System, a random- and continuous-access immunoanalyzer. With this procedure, every potential source of interassay carryover can be tested and estimated. In minimizing required sample sizes, the first stage is used primarily to detect and eliminate from further testing the assay reagent sources that do not cause carryover biases and the assay sources that cause very large carryover biases. Retested more extensively in the second testing stage are the cases where the data from the first testing stage are insufficient for judgment. An example data set from the Abbott AxSYM Free T4 assay is used to illustrate the methodology.
Serum total testosterone: immunoassay compared with negative chemical ionization gas chromatography-mass spectrometry
Authors: Fitzgerald R L , Herold D A
Published: January 2020

We have developed an electron capture negative chemical ionization gas chromatography-mass spectrometry (GC-MS) procedure to quantify serum testosterone in the clinically relevant range 0.69-69.3 nmol/L and used this procedure to assess Ciba Corning Diagnostics ACS:180 testosterone immunoassay. The GC-MS method involves liquid-liquid extraction of serum samples and synthesis of a pentafluorobenzyloxime/silyl ether derivative of testosterone with excellent chromatographic and electron capturing properties. The ACS testosterone assay is the first fully automated nonradioactive testosterone immunoassay approved by the US Food and Drug Administration. Patients' specimens (101, 57 males, 44 females) were analyzed by both techniques. A plot of the GC-MS (x) vs ACS (y) testosterone concentrations for men was linear (y = 1.07x + 0.19 nmol/L), showing excellent correlation (r2 = 0.98) between the two assays. Agreement of the two assays for female specimens was poor (y = 0.72x + 1.2 nmol/L), with a poor correlation (r2 = 0.31).
Internet: road to heaven or hell for the clinical laboratory?
Authors: Chou D
Published: January 2020

The Internet started as a research project by the Department of Defense Advanced Research Projects Agency for networking computers. Ironically, the networking project now predominantly supports human rather than computer communications. The Internet's growth, estimated at 20% per month, has been fueled by commercial and public perception that it will become an important medium for merchandising, marketing, and advertising. For the clinical laboratory, the Internet provides high-speed communications through e-mail and allows the retrieval of important information held in repositories. All this capability comes at a price, including the need to manage a complex technology and the risk of instrusions on patient privacy.
Defining the smallest analyte concentration an immunoassay can measure
Authors: Brown E N , McDermott T J , Bloch K J , McCollom A D
Published: January 2020

An immunoassay's minimal detectable concentration (MDC), the smallest analyte concentration the assay can reliably measure, is one of its most important properties. Bayes' theorem is used to unify the five current mathematical MDC definitions. The unified definition has significant implications for defining positive results for screening and diagnostic tests, setting criteria for immunoassay quality control and optimal design, reliably measuring biological substances at low concentrations, and, in general, measuring small analyte concentrations with calibrated analytic methods. As an illustration, we apply the unified definition to the microparticle capture enzyme immunoassay for prostate-specific antigen (PSA) developed for the Abbott IMx automated immunoassay system. The MDC of this assay as estimated by our unifying approach is shown to be 4.1-7.1 times greater than currently reported. As a consequence, the ability of the assay to measure reliably small concentrations of PSA to detect early recurrences of prostate cancer is probably overstated.
Immunoassay for intact amino-terminal propeptide of human type I procollagen
Authors: Melkko J , Kauppila S , Niemi S , Risteli L , Haukipuro K , Jukkola A , Risteli J
Published: January 2020

We have developed quantitative immunoassays for the intact, trimeric amino-terminal propeptide of human type I procollagen (PINP) and its Col1 domain. Intact PINP was isolated from the pleural fluids of cancer patients by a combination of ion-exchange, gel-filtration, and reversed-phase chromatographies. The amino-terminal Col1 domain of PINP was isolated after bacterial collagenase treatment of the heat-denatured trimeric propeptide. For the intact PINP assay we used a polyclonal antibody with only 1.2% cross-reaction with the monomeric Col1 domain. In human serum, this assay detects only one peak of PINP antigenicity that has the size of known intact PINP. Under similar conditions, an assay for the Coll domain of PINP recognized two circulating antigens. The biological relevance was further verified in wound fluid. Interassay and intraassay CVs were 3.1-9.3% for values within the reference intervals (mean +/- 2SD) for intact PINP in serum, which were 19-84 microg/L for women and 20-76 microg/L for men.
Analytical performance and clinical utility of a direct LDL-cholesterol assay in a hyperlipidemic pediatric population
Authors: Harris N , Neufeld E J , Newburger J W , Ticho B , Baker A , Ginsburg G S , Rimm E , Rifai N
Published: January 2020

This study compares a new latex immunoseparation method for the direct determination of plasma low-density lipoprotein cholesterol (LDL-C) with the reference procedure for LDL-C (beta-quantification) in a pediatric hyperlipidemic population. The direct LDL-C assay has a mean bias of -98 mg/L in a fasting group (n = 96) of patients (mean triglycerides 1057 +/- 720 mg/L) and a bias of +177 mg/L in a nonfasting group (n = 42, mean triglycerides 4854 +/- 5457 mg/L). The mean total analytical error calculated from our data is 13.8%. The direct LDL-C assay and the commonly used Friedewald calculation respectively classified 81% and 84% of fasting patients correctly, according to the cutoffs of 1100 and 1300 mg/L for LDL-C set by the National Cholesterol Education Program for pediatric patients. Of combined fasting and nonfasting patients, 80% were correctly classified by the direct LDL-C assay. Therefore, despite several analytical shortcomings, the direct LDL-C assay may be useful in managing hyperlipidemic children without the need for a fasting specimen.
Accumulation of arsenic species in serum of patients with chronic renal disease
Authors: Zhang X , Cornelis R , De Kimpe J , Mees L , Vanderbiesen V , De Cubber A , Vanholder R
Published: January 2020

Speciation of arsenic was determined in serum of 19 non-hemodialysis (non-HD) and 18 HD patients. The respective mean values of serum creatinine in these groups were 410 +/- 250 and 914 +/- 173 mumol/L (reference range for healthy subjects: females 50-80; males 57-93 mumol/L). The mean total arsenic concentrations were 5.12 +/-5.58 and 6.47 +/- 4.28 micrograms/L, respectively (reference value: 0.958 +/-1.52 micrograms/L). Dimethylarsinic acid (DMA) and arsenobetaine (AsB) were the major As species in serum of the non-HD and HD patients, with mean values of 0.82 +/- 1.05 and 1.93 +/- 1.51 micrograms/L for DMA and 3.55 +/- 4.58 and 3.47 +/- 2.89 micrograms/L for AsB, respectively. Serum concentrations of inorganic As and monomethylarsonic acid in both groups were below the detection limits for these compounds. Measurement of As concentration before vs after 4 h of HD treatment indicated that 68% of total As in serum was removed, as was 16% of the total As in packed cells. The efficiency of DMA and AsB removal during dialysis corresponded to that of total As.
Determination of dexamethasone in saliva
Authors: Thijssen J H , Gispen-de Wied C C , van Heeswijk G M , Veeman W
Published: January 2020

We conducted experiments to demonstrate that the determination of dexamethasone in saliva is a valuable tool to assess dexamethasone concentrations in the body after administration of this synthetic corticosteroid. After extraction of saliva, a RIA involving highly specific commercially available antibodies was established and evaluated. This RIA was easy to conduct, reliable, and sensitive enough to measure dexamethasone until approximately 24 h after oral administration of 1 mg per 70 kg of body weight. On the morning after the administration, the mean concentration in saliva was 540 pmol/L. Over a large range (10(3)-10(6) pmol/L), plasma concentrations correlated very well with salivary concentrations; plasma contained six times more dexamethasone than saliva.
DNA-based carrier screening in primary healthcare: screening for aspartylglucosaminuria mutations in maternity health offices
Authors: Hietala M , Aula P , Syvänen A C , Isoniemi A , Peltonen L , Palotie A
Published: January 2020

Large-scale genetic screening programs are complex enterprises in which ethical, technical, medical, and socioeconomic aspects have to be handled with professional expertise. Establishment of automated, relatively robust, and inexpensive laboratory techniques is one step of this path. Here a pilot carrier-screening program for the mutations causing aspartylglucosaminuria was carried out for pregnant women in primary care maternity health offices. Women (1975) were tested before their 12th week of pregnancy, and 31 heterozygotes were detected. The sampling was based on dried blood strips, facilitating convenient handling and inexpensive mailing to the laboratory. The mutation detection technique, solid-phase mini-sequencing simplified by the use of scintillation microplates and automated equipment, proved to be rapid, simple, inexpensive, and reliable, with a low repeat rate (2.5%). In conclusion, we found that good collaboration between the primary healthcare unit, the laboratory, and counseling experts, combined with modern laboratory technology, facilitate reliable low-cost genetic testing.
Validation of an enzymatic total magnesium determination based on activation of modified isocitrate dehydrogenase
Authors: Stone M J , Chowdrey P E , Miall P , Price C P
Published: January 2020

We have evaluated an enzymatic assay for the determination of Mg in serum, based on the activation of a chemically modified form of isocitrate dehydrogenase by Mg2+. In the presence of potassium isocitrate and NADP+, NADPH, which absorbs light at 340 nm, is produced, and its increase is proportional to Mg2+ in the sample. We have shown linearity to at least 5 mmol/L Mg and good precision by within-run CVs between 1.4% and 3.5% and day to day CVs between 3.2% and 5.4%. The method (y) is accurate, comparing well with the xylidyl blue method (x), with a Deming regression of y = 0.930x - 0.063 (r = 0.98, S(y/x) = 0.019), and with atomic absorption spectrophotometry (x), with a Deming regression of y = 0.932x - 0.016 (r = 0.97, S(y/x) = 0.023), and shows no interference from common endogenous compounds in blood and various metal ions except for visibly hemolyzed samples. A rapid assay, with reagents that are stable for at least 30 days at 4 degrees C and requiring no prior preparation, it is simple to use and suitable for adaptation onto automated chemistry analyzers.
High-Accuracy Determination of Microsatellite Instability Compatible with Liquid Biopsies
Authors: Silveira Amanda Bortolini , Bidard François-Clément , Kasperek Amélie , Melaabi Samia , Tanguy Marie-Laure , Rodrigues Manuel , Bataillon Guillaume , Cabel Luc , Buecher Bruno , Pierga Jean-Yves , Proudhon Charlotte , Stern Marc-Henri
Published: January 2020

Background

Microsatellite instability (MSI) has recently emerged as a predictive pan-tumor biomarker of immunotherapy efficacy, stimulating the development of diagnostic tools compatible with large-scale screening of patients. In this context, noninvasive detection of MSI from circulating tumor DNA stands as a promising diagnostic and posttreatment monitoring tool.

Methods

We developed drop-off droplet-digital PCR (ddPCR) assays targeting BAT-26, activin A receptor type 2A (ACVR2A), and defensin beta 105A/B (DEFB105A/B) microsatellite markers. Performances of the assays were measured on reconstitution experiments of various mutant allelic fractions, on 185 tumor samples with known MSI status, and on 72 blood samples collected from 42 patients with advanced colorectal or endometrial cancers before and/or during therapy.

Results

The 3 ddPCR assays reached analytical sensitivity <0.1% variant allelic frequency and could reliably detect and quantify MSI in both tumor and body fluid samples. High concordance between MSI status determination by the three-marker ddPCR test and the reference pentaplex method were observed (100% for colorectal tumors and 93% for other tumor types). Moreover, the 3 assays showed correlations with r ≥ 0.99 with other circulating tumor DNA markers and their dynamic during treatment correlated well with clinical response.

Conclusions

This innovative approach for MSI detection provides a noninvasive, cost-effective, and fast diagnostic tool, well suited for large-scale screening of patients that may benefit from immunotherapy agents, as well as for monitoring treatment responses.
Bayesian-Based Spectrum Sensing and Optimal Channel Estimation for MAC Layer Protocol in Cognitive Radio Sensor Networks
Authors: Maisuria Jemish V , Mehta Saurabh N
Published: January 2020

Cognitive radio (CR) is an intelligent and adaptive radio technology that automatically detects the available channels in the wireless spectrum and sometimes changes the transmission parameters to enable effective communication. Spectrum sensing in CR prevents harmful interference with the licensed users and maximizes the spectrum utilization. Thus, this paper proposes a technique for optimal channel estimation and spectrum sensing for MAC layer protocol in CR networks such that the scheduling issues are addressed. Initially, in the CR networks, spectrum sensing is done using the proposed optimal naive Bayes classifier (ONBC) based on the signal statistics, such as energy and likelihood ratio. The ONBC is developed by integrating the bat–bird swarm algorithm (BBSA) with the naive Bayes classifier, which works based on the Bayesian concept. The BBSA is newly developed by integrating the bird swarm algorithm (BSA) and bat algorithm. Finally, the channel estimation is done using the pilot-based sequential procedure and least square estimation (LSE). The analysis of the proposed method is done in the Rayleigh and Rician environments using 256 and 512 sub-carriers. From the results, it is exposed that the proposed BBSA + LSE pilot-based sequential method obtains the bit error rate, normalized energy and Probability detection (PD) of is 0.0126, 0.8446 and 0.9355, respectively.
Predicting responsiveness to information: consumer acceptance of biotechnology in animal products
Authors: Ortega David L , Lusk Jayson L , Lin Wen , Caputo Vincenzina
Published: January 2020

We propose a novel framework using individual choice data and Bayesian updating to predict which consumers are most responsive to information—namely those consumers whose pre-information choices reveal a high level of uncertainty surrounding their preferences. We apply our method to the study of consumer acceptance of genetically modified animal products, which prior research has revealed is a particularly polarising subject. Utilising conditional willingness-to-pay estimates from mixed logit models, we find that individuals with higher preference uncertainty prior to receiving information are most responsive. Implications of our results are discussed in the context of recent breakthroughs in biotechnology.
Impact of myocardial fibrosis on left ventricular remodelling, recovery, and outcome after transcatheter aortic valve implantation in different haemodynamic subtypes of severe aortic stenosis
Authors: Puls Miriam , Beuthner Bo Eric , Topci Rodi , Vogelgesang Anja , Bleckmann Annalen , Sitte Maren , Lange Torben , Backhaus Sören Jan , Schuster Andreas , Seidler Tim , Kutschka Ingo , Toischer Karl , Zeisberg Elisabeth Maria , Jacobshagen Claudius , Hasenfuß Gerd
Published: January 2020

Aims 

Myocardial fibrosis (MF) might represent a key player in pathophysiology of heart failure in aortic stenosis (AS). We aimed to assess its impact on left ventricular (LV) remodelling, recovery, and mortality after transcatheter aortic valve implantation (TAVI) in different AS subtypes.

Methods and results 

One hundred patients with severe AS were prospectively characterized clinically and echocardiographically at baseline (BL), 6 months, 1 year, and 2 years following TAVI. Left ventricular biopsies were harvested after valve deployment. Myocardial fibrosis was assessed after Masson’s trichrome staining, and fibrotic area was calculated as percentage of total tissue area. Patients were stratified according to MF above (MF+) or below (MF−) median percentage MF (≥11% or <11%). Myocardial fibrosis burden differed significantly between AS subtypes, with highest levels in low ejection fraction (EF), low-gradient AS and lowest levels in normal EF, high-gradient AS (29.5 ± 26.4% vs. 13.5 ± 16.1%, P = 0.003). In the entire cohort, MF+ was significantly associated with poorer LV function, higher extent of pathological LV remodelling, and more pronounced clinical heart failure at BL. After TAVI, MF+ was associated with a delay in normalization of LV geometry and function but not per se with absence of reverse remodelling and clinical improvement. However, 22 patients died during follow-up (mean, 11 months), and 14 deaths were classified as cardiovascular (CV) (n = 9 arrhythmia-associated). Importantly, 13 of 14 CV deaths occurred in MF+ patients (CV mortality 26.5% in MF+ vs. 2% in MF− patients, P = 0.0003). Multivariate analysis identified MF+ as independent predictor of CV mortality [hazard ratio (HR) 27.4 (2.0–369), P = 0.01].

Conclusion 

Histological MF is associated with AS-related pathological LV remodelling and independently predicts CV mortality after TAVI.
Allotype-specific processing of the CD16a N45-glycan from primary human natural killer cells and monocytes
Authors: Patel Kashyap R , Roberts Jacob T , Barb Adam W
Published: January 2020

Fc γ receptor IIIa/CD16a is an activating cell surface receptor with a well-defined role in natural killer (NK) cell and monocyte effector function. The extracellular domain is decorated with five asparagine (N)-linked glycans; N-glycans at N162 and N45 directly contribute to high-affinity antibody binding and protein stability. N-glycan structures at N162 showed significant donor-dependent variation in a recent study of CD16a isolated from primary human NK cells, but structures at N45 were relatively homogeneous. In this study, we identified variations in N45 glycan structures associated with a polymorphism coding for histidine instead of leucine at position 48 of CD16a from two heterozygous donors. It is known that H48 homozygous individuals suffer from immunodeficiency and recurrent viral infections. A mass spectrometry analysis of protein isolated from the primary natural killer cells of individuals expressing both CD16a L48 and H48 variants demonstrated clear processing differences at N45. CD16a H48 displayed a greater proportion of complex-type N45 glycans compared to the more common L48 allotype with predominantly hybrid N45-glycoforms. Structures at the four other N-glycosylation sites showed minimal differences from data collected on donors expressing only the predominant L48 variant. CD16a H48 purified from a pool of monocytes similarly displayed increased processing at N45. Here, we provide evidence that CD16a processing is affected by the H48 residue in primary NK cells and monocytes from healthy human donors.
Early life factors for endometriosis: a systematic review
Authors: Olšarová Karolína , Mishra Gita D
Published: January 2020

BACKGROUND

Despite its high prevalence and health burden, many aspects of endometriosis remain unclear, including risk factors and the underlying biological mechanisms. Exposures during early life, including in utero, are thought to play an important role in the subsequent onset of the condition. To date, however, much of the evidence from studies on early life exposures and diagnosed endometriosis appears mixed and difficult to assess.

OBJECTIVE AND RATIONALE

This study aims to provide a systematic review of the epidemiologic evidence on early life factors associated with the subsequent diagnosis of endometriosis. In utero and early life exposures have previously been linked to a range of adult health outcomes, including infertility.

SEARCH METHODS

A systematic review of case–control, cross-sectional and cohort studies was conducted using the search terms ‘endometriosis’[MeSH] AND (‘risk factors’[MeSH] OR ‘protective factors’[MeSH]) AND (‘in utero’, ‘fetal’, ‘neonatal, ‘perinatal’, ‘developmental origins’, ‘early life’, ‘childhood’ OR ‘life course’) in Embase, PubMed and Scopus databases. The review included articles published in English until 10 June 2018 with original data from studies with diagnosed endometriosis. The quality of primary studies was evaluated using the Newcastle–Ottawa Scale by both authors independently. Due to the degree of inconsistency in the measurements and study methods, a qualitative assessment of findings was undertaken rather than meta-analysis.

OUTCOMES

The search retrieved 70 records without duplicates that contained 20 records on human case–control, cross-sectional or cohort studies, from which 11 papers/studies were selected based on their assessment score. The majority of studies found that women born with low birthweight (<2.5 kg or <5.5 lb) were more likely to be diagnosed with endometriosis. For other early life factors, the evidence is mixed or limited, with further research needed on the association of endometriosis with preterm birth, in utero exposure to diethylstilbestrol and to maternal smoking, passive smoking in early life, and infant formula feeding (compared with breastfeeding).

WIDER IMPLICATIONS

While the weight of evidence points to low birthweight as a risk factor for diagnosis of endometriosis, future research is warranted on this and other key early life exposures where the findings are mixed to provide more robust evidence and for insights on potential causal pathways. Such research, however, needs to address current methodological issues, such as the use of prospective data from large population-based studies, better diagnostic methods to confirm disease free status, more consistent definitions of variables and consideration of potential biological mechanisms to guide the analyses. The improvements will advance the future synthesis of evidence to support clinically relevant risk assessment for a more timely diagnosis and treatment of endometriosis.
The Economic Strategies of U.S. Nonproliferation Policy during the Nixon-Ford Years
Authors: Sarkar Jayita
Published: January 2020

Much of international relations scholarship attributes the United States’ commitment to prevent the global spread of nuclear weapons as the outcome of US national security interests. Yet, US nonproliferation policy comprises a compelling set of economic goals and strategies, beyond economic sanctions. Without incorporating economic factors and actors, and their convergence with the Cold War US national security state, the understanding of US nonproliferation policy remains incomplete. The 1970s challenged US postwar economic preeminence through the “Nixon shock,” the end of dollar convertibility to gold of the Bretton Woods system, and the 1973 oil price shock. Concurrently, the United States’ market share in terms of global nuclear reactor sales declined while those of West European suppliers like France and West Germany increased. This essay argues that US nonproliferation efforts, which in the Nixon-Ford era took the form of the Nuclear Suppliers Group (NSG) after India's 1974 nuclear explosion, were guided as much by security concerns about proliferation as by Washington's aim to reclaim its market share to protect US nuclear industry against West European competition.
Asteroid triple-system 2001 SN263: surface characteristics and dynamical environment
Authors: Winter O C , Valvano G , Moura T S , Borderes-Motta G , Amarante A , Sfair R
Published: January 2020

The (153591) 2001 SN263 asteroid system, a target of the first Brazilian interplanetary space mission, is one of the known three triple systems within the population of near-Earth asteroids. One of the mission objectives is to collect data about the formation of this system. The analysis of these data will help in the investigation of the physical and dynamical structures of the components (Alpha, Beta, and Gamma) of this system, in order to find vestiges related to its origin. In this work, we assume the irregular shape of the 2001 SN263 system components as uniform-density polyhedra and computationally investigate the gravitational field generated by these bodies. The goal is to explore the dynamical characteristics of the surface and environment around each component. Then, taking into account the rotational speed, we analyse their topographic features through the quantities geometric altitude, tilt, geopotential, slope, and surface accelerations among others. Additionally, the investigation of the environment around the bodies made it possible to construct zero-velocity curves, which delimit the location of equilibrium points. The Alpha component has a peculiar number of 12 equilibrium points, all of them located very close to its surface. In the cases of Beta and Gamma, we found four equilibrium points not so close to their surfaces. Then, performing numerical experiments around their equilibrium points, we identified the location and size of just one stable region, which is associated with an equilibrium point around Beta. Finally, we integrated a spherical cloud of particles around Alpha and identified the location on the surface of Alpha where the particles have fallen.
The UTMOST survey for magnetars, intermittent pulsars, RRATs, and FRBs – I. System description and overview
Authors: Venkatraman Krishnan V , Flynn C , Farah W , Jameson A , Bailes M , Osłowski S , Bateman T , Gupta V , van Straten W , Keane E F , Barr E D , Bhandari S , Caleb M , Campbell-Wilson D , Day C K , Deller A , Green A J , Hunstead R , Jankowski F , Lower M E , Parthasarathy A , Plant K , Price D C , Rosado P A , Temby D
Published: January 2020

We describe the ongoing ‘survey for magnetars, intermittent pulsars, rotating radio transients, and fast radio bursts’ (SMIRF), performed using the newly refurbished UTMOST telescope. SMIRF repeatedly sweeps the southern Galactic plane performing real-time periodicity and single pulse searches, and is the first survey of its kind carried out with an interferometer. SMIRF is facilitated by a robotic scheduler which is capable of fully autonomous commensal operations. We report on the SMIRF observational parameters, the data analysis methods, the survey’s sensitivity to pulsars, techniques to mitigate radio frequency interference, and present some early survey results. UTMOST’s wide field of view permits a full sweep of the Galactic plane to be performed every fortnight, two orders of magnitude faster than previous surveys. In six months of operations from 2018 January to June, we have performed ∼10 sweeps of the Galactic plane with SMIRF. Notable blind redetections include the magnetar PSR J1622−4950, the RRAT PSR J0941−3942 and the eclipsing pulsar PSR J1748−2446A. We also report the discovery of a new pulsar, PSR J1659−54. Our follow-up of this pulsar at an average flux limit of ≤20 mJy, categorizes this as an intermittent pulsar with a high nulling fraction of <0.002.
circSamd4 represses myogenic transcriptional activity of PUR proteins
Authors: Pandey Poonam R , Yang Jen-Hao , Tsitsipatis Dimitrios , Panda Amaresh C , Noh Ji Heon , Kim Kyoung Mi , Munk Rachel , Nicholson Thomas , Hanniford Douglas , Argibay Diana , Yang Xiaoling , Martindale Jennifer L , Chang Ming-Wen , Jones Simon W , Hernando Eva , Sen Payel , De Supriyo , Abdelmohsen Kotb , Gorospe Myriam
Published: January 2020

By interacting with proteins and nucleic acids, the vast family of mammalian circRNAs is proposed to influence many biological processes. Here, RNA sequencing analysis of circRNAs differentially expressed during myogenesis revealed that circSamd4 expression increased robustly in mouse C2C12 myoblasts differentiating into myotubes. Moreover, silencing circSamd4, which is conserved between human and mouse, delayed myogenesis and lowered the expression of myogenic markers in cultured myoblasts from both species. Affinity pulldown followed by mass spectrometry revealed that circSamd4 associated with PURA and PURB, two repressors of myogenesis that inhibit transcription of the myosin heavy chain (MHC) protein family. Supporting the hypothesis that circSamd4 might complex with PUR proteins and thereby prevent their interaction with DNA, silencing circSamd4 enhanced the association of PUR proteins with the Mhc promoter, while overexpressing circSamd4 interfered with the binding of PUR proteins to the Mhc promoter. These effects were abrogated when using a mutant circSamd4 lacking the PUR binding site. Our results indicate that the association of PUR proteins with circSamd4 enhances myogenesis by contributing to the derepression of MHC transcription.
Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types
Authors: Wang Zishan , Yin Jiaqi , Zhou Weiwei , Bai Jing , Xie Yunjin , Xu Kang , Zheng Xiangyi , Xiao Jun , Zhou Li , Qi Xiaolin , Li Yongsheng , Li Xia , Xu Juan
Published: January 2020

Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcriptional dysregulation (DMTD) across cancers has not been portrayed. Here, we systematically identified DMTD by integrative analysis of transcriptome, methylome and regulatome across 22 human cancer types. Our results revealed that transcriptional regulation was affected by DNA methylation, involving hundreds of methylation-sensitive TFs (MethTFs). In addition, pan-cancer MethTFs, the regulatory activity of which is generally affected by DNA methylation across cancers, exhibit dominant functional characteristics and regulate several cancer hallmarks. Moreover, pan-cancer MethTFs were found to be affected by DNA methylation in a complex pattern. Finally, we investigated the cooperation among MethTFs and identified a network module that consisted of 43 MethTFs with prognostic potential. In summary, we systematically dissected the transcriptional dysregulation mediated by DNA methylation across cancer types, and our results provide a valuable resource for both epigenetic and transcriptional regulation communities.