Development of a multi-color gas puff imaging diagnostic on HL-2A tokamak

A Multi-Color (MC) gas puff imaging diagnostic has been developed on HL-2A tokamak. This diagnostic can simultaneously measure two-dimensional (2D, radial, and poloidal) electron density and temperature distributions with a good spatial resolution of 2.5 × 2.5 mm² and a temporal resolution of about 100 µs at best in edge plasmas. The 2D electron density and temperature distributions are inferred from the ratios of intensities of three different neutral helium emission lines; therefore, it is also referred to as helium beam probe or beam emission spectroscopy on thermal helium. A compact light splitter is used to split the inlet visible emission beam into four channels, and the specific neutral helium lines of the wavelengths λ₁ = 587.6 nm, λ₂ = 667.8 nm, λ₃ = 706.5 nm, and λ₄ = 728.1 nm are measured, respectively. This MC diagnostic has been experimentally tested and calibrated on a linear magnetic confinement device Peking University Plasma Test device, and the measured 2D electron density and temperature distributions are compared with the Langmuir probe measurements.

Blood test shows high accuracy in detecting stage I non-small cell lung cancer

Background

In a previous study (Goebel et. al, Cancer Genomics Proteomics 16:229-244, 2019), we identified 33 biomarkers for an early stage (I-II) Non-Small Cell Lung Cancer (NSCLC) test with 90% accuracy, 80.3% sensitivity, and 95.4% specificity. For the current study, we used a narrowed ensemble of 21 biomarkers while retaining similar accuracy in detecting early stage lung cancer.

Methods

A multiplex platform, 486 human plasma samples, and 21 biomarkers were used to develop and validate our algorithm which detects early stage NSCLC. The training set consisted of 258 human plasma with 79 Stage I-II NSCLC samples. The 21 biomarkers with the statistical model (Lung Cancer Detector Test 1, LCDT1) was then validated using 228 novel samples which included 55 Stage I NSCLC.

Results

The LCDT1 exhibited 95.6% accuracy, 89.1% sensitivity, and 97.7% specificity in detecting Stage I NSCLC on the blind set. When only NSCLC cancers were analyzed, the specificity increased to 99.1%.

Conclusions

Compared to current approved clinical methods for diagnosing NSCLC, the LCDT1 greatly improves accuracy while being non-invasive; a simple, cost-effective, early diagnostic blood test should result in expanding access and increase survival rate.

Diagnosis of Non-small Cell Lung Cancer for Early Stage Asymptomatic Patients

BACKGROUND/AIM

In 2016 in the United States, 7 of 10 patients were estimated to die following lung cancer diagnosis. This is due to a lack of a reliable screening method that detects early-stage lung cancer. Our aim is to accurately detect early stage lung cancer using algorithms and protein biomarkers.

PATIENTS AND METHODS

A total of 1,479 human plasma samples were processed using a multiplex immunoassay platform. 82 biomarkers and 6 algorithms were explored. There were 351 NSCLC samples (90.3% Stage I, 2.3% Stage II, and 7.4% Stage III/IV).

RESULTS

We identified 33 protein biomarkers and developed a classifier using Random Forest. Our test detected early-stage Non-Small Cell Lung Cancer (NSCLC) with a 90% accuracy, 80% sensitivity, and 95% specificity in the validation set using the 33 markers.

CONCLUSION

A specific, non-invasive, early-detection test, in combination with low-dose computed tomography, could increase survival rates and reduce false positives from screenings.

The Vaginal Microbiome of Transgender Men

BACKGROUND

Hormonal changes influence the composition of vaginal flora, which is directly related to the health of an individual. Transgender men prescribed testosterone experience a vaginal hormone composition that differs from cisgender women. To the author's knowledge, there are no clinical studies evaluating the influence that testosterone administration has on the vaginal microbiome.

METHODS

Vaginal swabs were self-collected by a cohort of self-identified healthy transgender men prescribed testosterone for at least 1 year (n = 28) and from cisgender women who were used as the comparator (n = 8). Participants completed a questionnaire to indicate the mode and dose of testosterone administration, sexual history, and vaginal health. Serum was collected for hormone analysis. Bacterial community profiles were assessed with broad-range PCR primers targeting the V3-V4 hypervariable region of the 16S bacterial rRNA, next-generation sequencing, and analysis by phylogenetic placement.

RESULTS

Compared to cisgender women, the vaginal floras of transgender men were less likely to have Lactobacillus as their primary genus. Intravaginal estrogen administration was positively associated with the presence of Lactobacillus in transgender men (P = 0.045). Transgender men had a significantly increased relative abundance of >30 species and a significantly higher α diversity (P = 0.0003). The presence of Lactobacillus was significantly associated with a lower α diversity index (P = 0.017).

CONCLUSIONS

The vaginal microbiome of transgender men who were assigned a female sex at birth and use testosterone may differ from that of cisgender women. Intravaginal estrogen administration may reduce these differences by promoting colonization with Lactobacillus species and decreasing α diversity.

Discontinuous spread of millet agriculture in eastern Asia and prehistoric population dynamics

Although broomcorn and foxtail millet are among the earliest staple crop domesticates, their spread and impacts on demography remain controversial, mainly because of the use of indirect evidence. Bayesian modeling applied to a dataset of new and published radiocarbon dates derived from domesticated millet grains suggests that after their initial cultivation in the crescent around the Bohai Sea ca. 5800 BCE, the crops spread discontinuously across eastern Asia. Our findings on the spread of millet that intensified during the fourth millennium BCE coincide with published dates of the expansion of the Sino-Tibetan languages from the Yellow River basin. In northern China, the spread of millet-based agriculture supported a quasi-exponential population growth from 6000 to 2000 BCE. While growth continued in northeastern China after 2000 BCE, the Upper/Middle Yellow River experienced decline. We propose that this pattern of regional divergence is mainly the result of internal and external anthropogenic factors.

Clinical diagnostic significance of prealbumin, cholinesterase and retinol binding protein in liver cirrhosis combined with encephalopathy

OBJECTIVE

Hepatic encephalopathy is a common consequence of liver cirrhosis, but diagnosis can be difficult as it is based on clinical criteria alone. We hypothesised that serum prealbumin, cholinesterase and retinol binding protein (RBP) can help support the diagnosis of hepatic encephalopathy.

METHODS

We enrolled 306 cirrhotic patients (110 with encephalopathy), 100 chronic hepatitis B patients and 50 healthy controls, measuring routine liver function tests (ALT, AST, GGT, ALP, and bilirubin), albumin, prothrombin time, prealbumin, cholinesterase and RBP by routine methods. Logistic regression analysis and areas under the receiver operating characteristic curves (AUCs) were used to find predictive factors for hepatic encephalopathy.

RESULTS

There were differences in all laboratory indices between the three groups (all p < 0.001). In univariate analysis, albumin, prothrombin time, prealbumin, cholinesterase and RBP were significantly altered in those with encephalopathy (p < 0.01), but only prealbumin, cholinesterase and RBP levels were significant predictors in multivariate analysis, and each was linked to the severity of liver fibrosis defined by the Child-Pugh score (all p < 0.001). The AUCs (95% CI) of prealbumin, cholinesterase and RBP for diagnosing liver cirrhosis with hepatic encephalopathy were comparable at 0.85 (81-90), 0.81 (0.76-0.85) and 0.81 (0.76-0.86), respectively (all p < 0.01).

CONCLUSIONS

Serum prealbumin, cholinesterase and RBP levels are of potential clinical value in diagnosis of liver cirrhosis complicated by encephalopathy.

SPIDR: small-molecule peptide-influenced drug repurposing

Background

Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which compounds that have already gone through some level of clinical testing are examined for efficacy against diseases divergent than their original application. Repurposing of existing drugs circumvents the time and considerable cost of early stages of drug development, and can be accelerated by using software to screen existing chemical databases to identify suitable drug candidates.

Results

Small-molecule Peptide-Influenced Drug Repurposing (SPIDR) was developed to identify small molecule drugs that target a specific receptor by exploring the conformational binding space of peptide ligands. SPIDR was tested using the potent and selective 16-amino acid peptide α-conotoxin MII ligand and the α₃β₂-nicotinic acetylcholine receptor (nAChR) isoform. SPIDR incorporates a genetic algorithm-based, heuristic search procedure, which was used to explore the ligand binding domain of the α₃β₂-nAChR isoform using a library consisting of 640,000 α-conotoxin MII peptide analogs. The peptides that exhibited the highest affinity for α₃β₂-nAChR were used as models for a small-molecule structure similarity search of the PubChem Compound database. SPIDR incorporates the SimSearcher utility, which generates shape distribution signatures of molecules and employs multi-level K-means clustering to insure fast database queries. SPIDR identified non-peptide drugs with estimated binding affinities nearly double that of the native α-conotoxin MII peptide.

Conclusions

SPIDR has been generalized and integrated into DockoMatic v 2.1. This software contains an intuitive graphical interface for peptide mutant screening workflow and facilitates mapping, clustering, and searching of local molecular databases, making DockoMatic a valuable tool for researchers in drug design and repurposing.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2153-y) contains supplementary material, which is available to authorized users.

Concordance study of PD-L1 expression in primary and metastatic bladder carcinomas: comparison of four commonly used antibodies and RNA expression

Therapy with anti-PD-L1 immune check-point inhibitors is approved for several cancers, including advanced urothelial carcinomas. PD-L1 prevalence estimates vary widely in bladder cancer, and lack of correlation between expression and clinical outcomes and immunotherapy response may be attributed to methodological differences of the immunohistochemical reagents and procedures. We characterized PD-L1 expression in 235 urothelial carcinomas including 79 matched pairs of primary and metastatic cancers using a panel of four PD-L1 immunoassays in comparison with RNAscope assay using PD-L1-specific probe (CD274). The antibody panel included three FDA-approved clones (22C3 for pembrolizumab, 28.8 for nivolumab, SP142 for atezolizumab), and a commonly used clone E1L3N. Manual scoring of tissue microarrays was performed in each of 235 tumors (624 tissue cores) and compared to an automated image analysis. Expression of PD-L1 in tumor cells by ≥1 marker was detected in 41/142 (28.9%) primary tumors, 13/77 (16.9%) lymph nodes, and 2/16 (12.5%) distant metastases. In positive cases, high PD-L1 expression (>50% cells) was detected in 34.1% primary and 46.7% metastases. Concordant PD-L1 expression status was present in 71/79 (89.9%) cases of matched primary and metastatic urothelial carcinomas. PD-L1 sensitivity ranked from highest to lowest as follows: RNAscope, clone 28.8, 22C3, E1L3N, and SP142. Pairwise concordance correlation coefficients between the four antibodies in 624 tissue cores ranged from 0.76 to 0.9 for tumor cells and from 0.30 to 0.85 for immune cells. RNA and protein expression levels showed moderate to high agreement (0.72-0.87). Intra-tumor expression heterogeneity was low for both protein and RNA assays (interclass correlation coefficients: 0.86-0.94). Manual scores were highly concordant with automated Aperio scores (0.94-0.97). A significant subset of 56/235 (23.8%) urothelial carcinomas stained positive for PD-L1 with high concordance between all four antibodies and RNA ISH assay. Despite some heterogeneity in staining, the overall results are highly concordant suggesting diagnostic equivalence of tested assays.

Prevalence of Obesity, Prediabetes, and Diabetes in Sexual Minority Men: Results From the 2014 Behavioral Risk Factor Surveillance System

Purpose The purpose of this study is to assess the prevalence and related odds ratios for obesity, prediabetes, and diabetes in sexual minority men (SMM) in relation to straight men. Methods A secondary analysis of 2014 Behavioral Risk Factor Surveillance System data from 19 states (n = 53 542) was conducted. Weighted means and standard errors were computed to estimate prevalence rates of obesity, prediabetes, and diabetes across male sexual orientation groups, respectively. Unadjusted and adjusted (demographics, depression, and health care access factors) weighted logistic regression models were developed. Results Obesity prevalence was lower in gay men relative to straight men with logistic regression modeling indicating gay men were significantly less likely to be obese, relative to their straight counterparts, in the unadjusted and adjusted models. In terms of prediabetes, rates were low across all sexual orientation groups with no significant differences observed. Yet bisexual men, relative to straight men, had higher rates of diabetes with significantly increased odds for the disease in both the unadjusted and adjusted models. Conclusion Findings indicate gay men have reduced risk for obesity while bisexual men may have increased diabetes burden. Across all male sexual orientation groups, prediabetes prevalence was low, suggesting the need for more aggressive prediabetes screening. Additional research is necessary to confirm the findings.

Temperature and Driving Cycle Significantly Affect Carbonaceous Gas and Particle Matter Emissions from Diesel Trucks

The present study examines the effects of fuel [an ultralow sulfur diesel (ULSD) versus a 20% v/v soy-based biodiesel-80% v/v petroleum blend (B20)], temperature, load, vehicle, driving cycle, and active regeneration technology on gas- and particle-phase carbon emissions from light and medium heavy-duty diesel vehicles (L/MHDDV). The study is performed using chassis dynamometer facilities that support low-temperature operation (-6.7 °C versus 21.7 °C) and heavy loads up to 12 000 kg. Organic and elemental carbon (OC-EC) composition of aerosol particles is determined using a thermal-optical technique. Gas- and particle-phase semivolatile organic compound (SVOC) emissions collected using traditional filter and polyurethane foam sampling media are analyzed using advanced gas chromatograpy/mass spectrometry methods. Study-wide OC and EC emissions are 0.735 and 0.733 mg/km, on average. The emissions factors for diesel vehicles vary widely, and use of a catalyzed diesel particle filter (CDPF) device generally mutes the carbon particle emissions in the exhaust, which contains ~90% w/w gas-phase matter. Interestingly, replacing ULSD with B20 did not significantly influence SVOC emissions, for which sums range from 0.030 to 9.4 mg/km for the L/MHDDVs. However, both low temperature and vehicle cold-starts significantly increase SVOCs in the exhaust. Real-time particle measurements indicate vehicle regeneration technology did influence emissions, although regeneration effects went unresolved using bulk chemistry techniques. A multistudy comparison of the toxic particle-phase polycyclic aromatic hydrocarbons (PAHs; molecular weight (MW) ≥ 252 amu) in diesel exhaust indicates emission factors that span up to 8 orders of magnitude over the past several decades. This study observes conditions under which PAH compounds with MW ≥ 252 amu appear in diesel particles downstream of the CDPF and can even reach low-end concentrations reported earlier for much larger HDDVs with poorly controlled exhaust streams. This rare observation suggests that analysis of PAHs in particles emitted from modern L/MHDDVs may be more complex than recognized previously.

Comparison of Estrogen and Progesterone Receptor Antibody Reagents Using Proficiency Testing Data

CONTEXT

- Immunohistochemical analysis of estrogen receptor (ER) and progesterone receptor (PgR) expression in breast cancer is the current standard of care and directly determines therapy. In 2010 the American Society of Clinical Oncology and the College of American Pathologists (ASCO/CAP) published guidelines for ER and PgR predictive testing, encompassing preanalytic, analytic, postanalytic factors; antibody validation; and proficiency testing.

OBJECTIVE

- To compare the performance of different antibody reagents for ER and PgR immunohistochemical analysis by using CAP proficiency testing data.

DESIGN

- The CAP PM2 survey uses tissue microarrays of ten 2-mm cores per slide. We analyzed survey data from 80 ER and 80 PgR cores by antibody clone from more than 1200 laboratories.

RESULTS

- Laboratories used the ER antibodies SP1 (72%), 6F11 (17%), 1D5 (3%), and the PgR antibodies 1E2 (61%), 16 (12%), PgR-636 (13%), PgR-1294 (8%) in 2015. While 63 of 80 ER cores (79%) were scored similarly using each of the 3 antibodies, there were significant differences for others, with SP1 yielding more positive interpretations. Four cores were scored as ER negative by more than half of the laboratories using 1D5 or 6F11, while SP1 produced positive results in more than 70% of laboratories using that antibody. Despite the greater variety of PgR antibody reagents and greater PgR tumor heterogeneity, 61 of 80 cores (76%) were scored similarly across the 4 PgR antibodies.

CONCLUSIONS

- Accurate ER and PgR testing in breast cancer is crucial for appropriate treatment. The CAP proficiency testing data demonstrate differences in staining results by ER clone, with SP1 yielding more positive results.

CAP/ACMG proficiency testing for biochemical genetics laboratories: a summary of performance

Purpose

Testing for inborn errors of metabolism is performed by clinical laboratories worldwide, each utilizing laboratory-developed procedures. We sought to summarize performance in the College of American Pathologists’ (CAP) proficiency testing (PT) program and identify opportunities for improving laboratory quality. When evaluating PT data, we focused on a subset of laboratories that have participated in at least one survey since 2010.

Methods

An analysis of laboratory performance (2004 to 2014) on the Biochemical Genetics PT Surveys, a program administered by CAP and the American College of Medical Genetics and Genomics. Analytical and interpretive performance was evaluated for four tests: amino acids, organic acids, acylcarnitines, and mucopolysaccharides.

Results

Since 2010, 150 laboratories have participated in at least one of four PT surveys. Analytic sensitivities ranged from 88.2 to 93.4%, while clinical sensitivities ranged from 82.4 to 91.0%. Performance was higher for US participants and for more recent challenges. Performance was lower for challenges with subtle findings or complex analytical patterns.

Conclusion

US clinical biochemical genetics laboratory proficiency is satisfactory, with a minority of laboratories accounting for the majority of errors. Our findings underscore the complex nature of clinical biochemical genetics testing and highlight the necessity of continuous quality management.

Genetic Algorithm Managed Peptide Mutant Screening: Optimizing Peptide Ligands for Targeted Receptor Binding

This study demonstrates the utility of genetic algorithms to search exceptionally large and otherwise intractable mutant libraries for sequences with optimal binding affinities for target receptors. The Genetic Algorithm Managed Peptide Mutant Screening (GAMPMS) program was used to search an α-conotoxin (α-CTx) MII mutant library of approximately 41 billion possible peptide sequences for those exhibiting the greatest binding affinity for the α₃β₂-nicotinic acetylcholine receptor (nAChR) isoform. A series of top resulting peptide ligands with high sequence homology was obtained, with each mutant having an estimated ΔG_bind approximately double that of the potent native α-CTx MII ligand. A consensus sequence from the top GAMPMS results was subjected to more rigorous binding free energy calculations by molecular dynamics and compared to α-CTx MII and other related variants for binding with α₃β₂-nAChR. In this study, the efficiency of GAMPMS to substantially reduce the sample population size through evolutionary selection criteria to produce ligands with higher predicted binding affinity is demonstrated.

Impact of Uniform Methods on Interlaboratory Antibody Titration Variability: Antibody Titration and Uniform Methods

Context.—Substantial variability between different antibody titration methods prompted development and introduction of uniform methods in 2008.

Objective.—To determine whether uniform methods consistently decrease interlaboratory variation in proficiency testing.

Design.—Proficiency testing data for antibody titration between 2009 and 2013 were obtained from the College of American Pathologists. Each laboratory was supplied plasma and red cells to determine anti-A and anti-D antibody titers by their standard method: gel or tube by uniform or other methods at different testing phases (immediate spin and/or room temperature [anti-A], and/or anti-human globulin [AHG: anti-A and anti-D]) with different additives. Interlaboratory variations were compared by analyzing the distribution of titer results by method and phase.

Results.—A median of 574 and 1100 responses were reported for anti-A and anti-D antibody titers, respectively, during a 5-year period. The 3 most frequent (median) methods performed for anti-A antibody were uniform tube room temperature (147.5; range, 119–159), uniform tube AHG (143.5; range, 134–150), and other tube AHG (97; range, 82–116); for anti-D antibody, the methods were other tube (451; range, 431–465), uniform tube (404; range, 382–462), and uniform gel (137; range, 121–153). Of the larger reported methods, uniform gel AHG phase for anti-A and anti-D antibodies had the most participants with the same result (mode). For anti-A antibody, 0 of 8 (uniform versus other tube room temperature) and 1 of 8 (uniform versus other tube AHG), and for anti-D antibody, 0 of 8 (uniform versus other tube) and 0 of 8 (uniform versus other gel) proficiency tests showed significant titer variability reduction.

Conclusion.—Uniform methods harmonize laboratory techniques but rarely reduce interlaboratory titer variance in comparison with other methods.

Alternative splicing directs two IL-20R2 isoforms and is responsible for the incomplete gene knockout via the exon I ablation

Two heterodimeric receptors consisting of interleukin (IL)-20R2 are shared by three of the IL-20 family of cytokines, IL-19, IL-20 and IL-24. Along with IL-22, these cytokines are downstream effectors of IL-23 and have been implicated in keratinocyte functions and the pathogenesis of psoriasis. Surprisingly, whereas knocking out either the IL-23 or IL-22 gene abolished imiquimod-induced psoriatic phenotypes in mice, similar attempt for IL-20R2 had little effect. Here, we report that the apparent disparity may result from a new IL-20R2 isoform encoded by an alternatively spliced transcript which survived the previous attempt for IL-20R2 gene knockout via the exon I deletion.