Conventional Screening Methods Research Articles

PP148 Liquid Biopsy For The Detection Of Ovarian Or Endometrial Cancer In Samples Taken From The Pap Smear: PapSEEK

IntroductionThe PapSEEK test is an emerging minimally invasive technique in which samples are collected from the endocervical or intrauterine cavity with the Papanicolaou (Pap) brush or the Tao brush to detect somatic mutations or aneuploidies indicating the presence of endometrial or ovarian cancer.MethodsWe systematically searched for articles published up to October 2020 in the following electronic databases: Medline, Embase, the Cochrane Library, and the Centre for Reviews and Dissemination. We included experimental studies, observational primary studies, and cost-effectiveness studies evaluating the safety, effectiveness, and cost effectiveness of the PapSEEK test for the early detection of ovarian or endometrial cancer. Relevant outcomes included sensitivity, specificity, the coefficient of variation, re-test rates, the incremental cost-effectiveness ratio, the incremental cost-utility ratio, and the cost of each alternative.ResultsA single relevant retrospective study was identified. In this study, samples from women with endometrial cancer (n = 656) and ovarian cancer (n = 254) were collected with the Pap brush and Tao brush and compared with samples from healthy women (n = 1,002). The diagnostic validity for somatic mutation or aneuploidies obtained with a Pap brush had a sensitivity of 81% for endometrial cancer and 33% for ovarian cancer, and a specificity of 99% for both conditions. When samples were collected from the intrauterine cavity with a Tao brush, the sensitivity increased to 93% for endometrial cancer and to 45% for ovarian cancer. The sensitivity of the PapSEEK test increased only for ovarian cancer when plasma samples to detect circulating tumor DNA were collected in addition to Pap smear samples. This strategy provided a diagnostic validity of 43%, which was higher in late-stage ovarian cancer (56% versus 35%), and a specificity of 100%.ConclusionsProspectively designed studies are required to assess the safety and effectiveness of the PapSEEK test in screening settings, as well as studies comparing the technology with conventional screening methods. No cost-effectiveness studies have been conducted for the PapSEEK test.

Improved phenotyping procedure for evaluating resistance in rice against gall midge (Orseolia oryzae, Wood-Mason)

BackgroundThe rice gall midge (RGM, Orseolia oryzae, Wood-Mason), an important stem-feeding pest worldwide, has caused serious production losses over the past decades. Rice production practices indicate that the most reliable method for managing RGM is the deployment of cultivars that incorporate host resistance. However, the conventional phenotypic screening method of rice resistance to RGM suggested by the International Rice Research Institute (IRRI) has been used for approximately 30 years, and only 12 rice varieties/lines (including controls) can be evaluated in one tray. It is not suitable for high-throughput phenotyping of rice germplasm. Moreover, a suitable method to prepare samples for molecular biological studies of rice resistance against RGM is imperative with the rapid development of modern molecular techniques.ResultsThe proper density of seedlings/RGM was determined for four seeding arrangements. A high-throughput phenotyping method (HTPM) for 60 lines/varieties infested with 36 female RGM adults in one tray, as described by method 4–3 (seeded 60 lines/varieties), was developed and verified using mutant screening. Furthermore, one RGM resistance gene flanked by markers 12RM28346 and 12RM28739 on chromosome 12 was simultaneously detected using method 2–2 (seeded 30 lines/varieties in one tray) treated with 24 RGM and analyzed using conventional and simplified grading systems. Genetic analysis of the RGM resistance gene was confirmed using a method identical to that suggested by IRRI. Finally, one bucket with 24 seedlings treated with at least five female RGM adults was efficacious and could offer adequate samples for insect development observation or molecular biological studies.ConclusionA highly efficient and reliable procedure for evaluation of resistance in rice to RGM was developed and improved, and was verified through mutant screening, gene mapping, genetic analysis, and insect growth and development observations.

Comparison of Time Taken to Assess Cognitive Function Using a Fully Immersive and Automated Virtual Reality System vs. the Montreal Cognitive Assessment.

Introduction: Dementia is increasingly prevalent globally. Existing questionnaire-based cognitive assessment tools may not comprehensively assess cognitive function and real-time task-performance across all cognitive domains. CAVIRE (Cognitive Assessment by VIrtual REality), a fully immersive virtual reality system incorporating automated audio-visual instructions and a scoring matrix was developed to assess the six cognitive domains, with potential to maintain consistency in execution of the testing environment and possibly time-saving in busy primary care practice.Aims: This is a feasibility study to compare the completion times of the questionnaire-based Montreal Cognitive Assessment (MoCA) and the CAVIRE in cognitively-healthy Asian adults aged between 35 and 74 years, overall, and in and across each 10-year age group (35–44; 45–54; 55–64; 65–74).Methods: A total of 100 participants with a MoCA score of 26 or more were recruited equally into the four 10-year age groups at a primary care clinic in Singapore. Completion time for the MoCA assessment for each participant was recorded. They were assessed using the CAVIRE, comprising 13 segments featuring common everyday activities assessing all six cognitive domains, and the completion time was also recorded through the embedded automated scoring and timing framework.Results: Completion time for CAVIRE as compared to MoCA was significantly (p < 0.01) shorter, overall (mean difference: 74.9 (SD) seconds) and in each age group. Younger, vs. older, participants completed both the MoCA and CAVIRE tasks in a shorter time. There was a greater variability in the completion time for the MoCA, most markedly in the oldest group, whereas completion time was less variable for the CAVIRE tasks in all age groups, with most consistency in the 45–54 year-age group.Conclusion: We demonstrate almost equivalent completion times for a VR and a questionnaire-based cognition assessment, with inter-age group variation in VR completion time synonymous to that in conventional screening methods. The CAVIRE has the potential to be an alternative screening modality for cognition in the primary care setting.

A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by Alcaligenes faecalis Soil Isolate MZ921504.

The continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated with several species that are antibiotic producers. In this study, combination of conventional screening methods with Liquid chromatography- Mass spectroscopy (LC/MS) and metagenomic nanopore sequence analysis have been conducted for the deciphering the active metabolites produced by soil isolate(s). Preliminary soil screening resulted in a Gram-negative isolate identified via 16S ribosomal RNA as Alcaligenes faecalis isolate MZ921504 with promising antimicrobial activities against wide range of MDR gram-positive and gram-negative pathogens. The LC/MS analysis of the metabolites of A. faecalis isolate MZ921504 confirmed the presence of ectoine, bacillibactin, quinolobactin and burkholderic acid. Metagenomics sequence analysis of the soil sample (NCBI GenBank accession PRJNA771993) revealed the presence of conserved biosynthetic gene clusters of ectoine, bacteriocin, bacillibactin, quinolobactin, terpene and burkholderic acid of A. faecalis. In conclusion, A. faecalis isolate MZ921504 is a promising source for antimicrobial metabolites. LC/MS spectral analysis and third generation sequencing tools followed by secondary metabolite gene clusters analysis are useful methods to predict the nature of the antimicrobial metabolites.

Anti-Cancer Drug Screening with Microfluidic Technology

The up-and-coming microfluidic technology is the most promising platform for designing anti-cancer drugs and new point-of-care diagnostics. Compared to conventional drug screening methods based on Petri dishes and animal studies, drug delivery in microfluidic systems has many advantages. For instance, these platforms offer high-throughput drug screening, require a small number of samples, provide an in vivo-like microenvironment for cells, and eliminate ethical issues associated with animal studies. Multiple cell cultures in microfluidic chips could better mimic the 3D tumor environment using low reagents consumption. The clinical experiments have shown that combinatorial drug treatments have a better therapeutic effect than monodrug therapy. Many attempts have been made in this field in the last decade. This review highlights the applications of microfluidic chips in anti-cancer drug screening and systematically categorizes these systems as a function of sample size and combination of drug screening. Finally, it provides a perspective on the future of the clinical applications of microfluidic systems for anti-cancer drug development.

Promising Epigenetic Biomarkers for the Early Detection of Colorectal Cancer: A Systematic Review.

Simple SummaryHigh-performance, non-invasive screening is a requirement in colorectal cancer (CRC) as early detection is a key in reducing disease-related mortality in CRC patients. However, colonoscopy, the actual gold standard in CRC screening, is invasive and often avoided by patients. Conventional screening methods encounter several limitations; therefore, new testing strategies have been considered. DNA methylation is the most prevalent epigenetic alteration that occurs in all stages of carcinogenesis. Our research focused on identifying potential DNA methylation single biomarkers or panels as promising tools in the early detection of CRC; it evaluated methylated genes currently targeted by already approved diagnostic kits. A panel of five CTCF methylated binding sites holds the promise for early-stage specific detection of CRC. CRC screening compliance and accuracy can be enhanced by employing a stool mt-DNA methylation test.In CRC, screening compliance is decreased due to the experienced discomfort associated with colonoscopy, although this method is the gold standard in terms of sensitivity and specificity. Promoter DNA methylation (hypomethylation or hypermethylation) has been linked to all CRC stages. Study objectives: to systematically review the current knowledge on approved biomarkers, reveal new potential ones, and inspect tactics that can improve performance. This research was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines; the risk of bias was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies criteria (QUADAS-2). The Web of Science® Core Collection, MEDLINE® and Scopus® databases were searched for original articles published in peer-reviewed journals with the specific keywords “colorectal cancer”, “early detection”, “early-stage colorectal cancer”, “epigenetics”, “biomarkers”, “DNA methylation biomarkers”, “stool or blood or tissue or biopsy”, “NDRG4”, “BMP3”, “SEPT9”, and “SDC2”. Based on eligibility criteria, 74 articles were accepted for analysis. mSDC2 and mSEPT9 were frequently assessed in studies, alone or together as part of the ColoDefense panel test—the latter with the greatest performance. mBMP3 may not be an appropriate marker for detecting CRC. A panel of five methylated binding sites of the CTCF gene holds the promise for early-stage specific detection of CRC. CRC screening compliance and accuracy can be enhanced by employing a stool mt-DNA methylation test.

Characterization and application of dried neem leaf powder as a bio-additive for salt less animal skin preservation for tanneries.

Sodium chloride (NaCl) is commonly used as a curing/preservative agent for raw hides and skins in tanneries and is removed through a soaking process with total dissolved solids (TDS) and other organic pollutants in effluent, causing significant pollution load to the environment. Hence, the present study evaluated to apply dried neem leaf powder (DNL) as an additive to reduce the usage of salt in skin processing and preservation. To make certain of DNL antimicrobial properties, solvent extracts were performed against proteolytic bacteria isolated from raw skins. Initial characterization of DNL revealed the presence of bioactive compounds nimbolide and dehydro salannol and acetone extract with 16.9-mm, 10-mm and 8-mm zone of inhibition against Salmonella sp., E. coli sp. and Bacillus sp. identified using phenotypic conventional biochemical screening method. Further, skin curing experiments were carried out using four different treatments of DNL (10% 15%, 20% and 25% w/w) along with 15% w/w of conventional salt to obtain an optimum concentration for pilot-scale studies. Thus, the application of optimal DNL (15%) and salt (15%) resulted in no physical changes such as smell and hair slip and was taken for further studies for hydroxyproline activity, pollution load and organoleptic properties along compared with control 40% salt. DNL-aided salt less preservation of freshly flayed goat skins at ambient condition showed no hair slip or putrefaction during the preservation period with significant reduction of TDS (86%) and chloride (71%) in soak liquors compared to conventional salt preservation and enhanced organic load requiring additional treatment. However, the application of the organoleptic, physical and hydrothermal properties of resulting leathers produced from the DNL applied skins was on par with results of leather obtained from conventional salt. Thus, our results demonstrate DNL-aided salt less preservation method is able to reduce the amount of salt for preservation of goat skins significantly, leading to reduced salinity issues during leather processing.

Protecting Consumer Health by Developing an Electrochemical Immunosensor for the Detection of Banned Antibiotic Residues in Honey

IntroductionChemical (eg pesticides, veterinary drugs, etc.) and bacteriological contaminants (eg. foodborne pathogens) could contaminate animal and plant derived food products for human consumption. Some antibiotic residues (eg. chloramphenicol, nitrofuran metabolites, dyes) are banned in foodstuffs of animal origin (eg. milk, meat, eggs, etc.) in European Union because of toxicological risks for the consumer. The European Regulation has set Minimum Required Performance Limits (MRPL) [1] or Reference Point for Action (RPA) for banned substances [2]. Food containing residues of substances at or above the MRPL or RPA are declared non-compliant and consignments are rejected from the consumer's market.Screening methods are the first stage of food control and so are essential for food safety monitoring. Conventional screening methods are microbiological methods (eg. plate tests, tube tests), immunological methods (eg. ELISA, radioimmunoassays) or physico-chemical methods (Thin Layer Chromatography, High Performance Liquid Chromatography (HPLC), liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)). These methods sometimes lack of sensitivity or specificity; they also could be time and money consuming. There is thus a need to develop novel screening methods for antibiotic residues detection, preferably with the potential for the field-testing (eg. farm control, self-control). Electrochemical biosensors make it possible to develop a promising and economically interesting approach.Electrochemical immunosensorAn innovative electrochemical method based on disposable Screen Printed Carbon Electrodes (SPCE), coupled to magnetic beads (MB), allowing the simultaneous detection of 3 families of antibiotics in milk, was published by a Spanish academic team [3]. This technique presents major advantages: low cost (eg. disposable electrodes, potentiostat), promising detection limits, portability, and possible automatisation. Our laboratory has evaluated the transferability of the method. An electrochemical immunosensor has been developed for the detection of chloramphenicol residues in honey as a proof of concept. Honey composition and colour varies considerably depending on the botanical origin. Moreover some honey ingredients can interfere with the electrochemical detection, especially substances with antioxidant activities (eg. polyphenols). Therefore a lot of work had to be done to improve sample extraction to reduce matrix effects.The objective is to develop an electrochemical bead-based immunosensor for the multiplex detection of banned antibiotics (eg. chloramphenicol, nitrofuran metabolites, dyes) in bovine milk.MethodAntibodies (Abs) against antibiotics are grafted on the surface of magnetic beads (MBs). Milk samples and antibiotic conjugated with Horseradish peroxidase (HRP) are mixed with MBs-Abs. A competition occurs between the HRP conjugates and the antibiotic residues if present in the sample, for the binding to the antibody. The MBs are washed to remove free antibiotics and conjugates. Then, a Screen Printed Carbon Electrode (SPCE) with MBs on its surface (maintained by a magnet) is soaked into a buffer solution containing hydroquinone; when adding hydrogen peroxide (H2O2) to the solution, an electrochemical signal is produced, due to the enzymatic activity of HRP and measured. The electrochemical signal is inversely proportional to the antibiotic concentration in the sample.Results and ConclusionsScreening methods for the detection of veterinary drugs in food products have to be validated according to the European regulation [1] and to the European guideline for the validation of screening methods [4]. After the development and the optimization of the analytical parameters (eg. sample preparation, HRP concentration, incubation time, applied potential, etc), the methods developed for single compounds will be evaluated and validated according to the European regulations. Then the single compound methods will be merged into one multiplex method if possible. The results will be presented to the conference, discussing the advantages and drawbacks of electrochemical biosensors for the screening of antibiotic residues in food products.

Optimal Screening of Populations with Heterogeneous Risk Profiles Under the Availability of Multiple Tests

We study the design of large-scale group testing schemes under a heterogeneous population (i.e., subjects with potentially different risk) and with the availability of multiple tests. The objective is to classify the population as positive or negative for a given binary characteristic (e.g., the presence of an infectious disease) as efficiently and accurately as possible. Our approach examines components often neglected in the literature, such as the dependence of testing cost on the group size and the possibility of no testing, which are especially relevant within a heterogeneous setting. By developing key structural properties of the resulting optimization problem, we are able to reduce it to a network flow problem under a specific, yet not too restrictive, objective function. We then provide results that facilitate the construction of the resulting graph and finally provide a polynomial time algorithm. Our case study, on the screening of HIV in the United States, demonstrates the substantial benefits of the proposed approach over conventional screening methods. Summary of Contribution: This paper studies the problem of testing heterogeneous populations in groups in order to reduce costs and hence allow for the use of more efficient tests for high-risk groups. The resulting problem is a difficult combinatorial optimization problem that is NP-complete under a general objective. Using structural properties specific to our objective function, we show that the problem can be cast as a network flow problem and provide a polynomial time algorithm.

Rapid optimization of processes for the integrated purification of biopharmaceuticals.

Straight‐through chromatography, wherein the eluate from one column passes directly onto another column without adjustment, is one strategy to integrate and intensify manufacturing processes for biologics. Development and optimization of such straight‐through chromatographic processes is a challenge, however. Conventional high‐throughput screening methods optimize each chromatographic step independently, with limited consideration for the connectivity of steps. Here, we demonstrate a method for the development and optimization of fully integrated, multi‐column processes for straight‐through purification. Selection of resins was performed using an in silico tool for the prediction of processes for straight‐through purification based on a one‐time characterization of host‐cell proteins combined with the chromatographic behavior of the product. A two‐step optimization was then conducted to determine the buffer conditions that maximized yield while minimizing process‐ and product‐related impurities. This optimization of buffer conditions included a series of range‐finding experiments on each individual column, similar to conventional screening, followed by the development of a statistical model for the fully integrated, multi‐column process using design of experiments. We used this methodology to develop and optimize integrated purification processes for a single‐domain antibody and a cytokine, obtaining yields of 88% and 86%, respectively, with process‐ and product‐related variants reduced to phase‐appropriate levels for nonclinical material.

A fast wavelet-based functional association analysis replicates several susceptibility loci for birth weight in a Norwegian population

BackgroundBirth weight (BW) is one of the most widely studied anthropometric traits in humans because of its role in various adult-onset diseases. The number of loci associated with BW has increased dramatically since the advent of whole-genome screening approaches such as genome-wide association studies (GWASes) and meta-analyses of GWASes (GWAMAs). To further contribute to elucidating the genetic architecture of BW, we analyzed a genotyped Norwegian dataset with information on child’s BW (N=9,063) using a slightly modified version of a wavelet-based method by Shim and Stephens (2015) called WaveQTL.ResultsWaveQTL uses wavelet regression for regional testing and offers a more flexible functional modeling framework compared to conventional GWAS methods. To further improve WaveQTL, we added a novel feature termed “zooming strategy” to enhance the detection of associations in typically small regions. The modified WaveQTL replicated five out of the 133 loci previously identified by the largest GWAMA of BW to date by Warrington et al. (2019), even though our sample size was 26 times smaller than that study and 18 times smaller than the second largest GWAMA of BW by Horikoshi et al. (2016). In addition, the modified WaveQTL performed better in regions of high LD between SNPs.ConclusionsThis study is the first adaptation of the original WaveQTL method to the analysis of genome-wide genotypic data. Our results highlight the utility of the modified WaveQTL as a complementary tool for identifying loci that might escape detection by conventional genome-wide screening methods due to power issues. An attractive application of the modified WaveQTL would be to select traits from various public GWAS repositories to investigate whether they might benefit from a second analysis.

Development of a novel biomarker for the early detection of colorectal cancer

Colorectal cancer (CRC) is one of the most common cancer and a leading cause of cancer related deaths both in men and in women worldwide including US. A positive family history is strongly correlated with an increased risk of CRC diagnosis during lifetime. However, CRC is an indolent disease in its early stages and usually becomes symptomatic when it progresses to more advanced stages. Conventional screening methods have several limitations and currently, there is no screening procedure available to detect CRC at a very early stage. Under normal physiological condition, the epithelial lining of the gut gets breached by various factors including food, that creates local wound. The surviving epithelial cells around the wound lose their differentiated structure and undergoes epithelial mesenchymal transition (EMT) and migrate and proliferate to cover the injured area. Once the wound is covered, the cells start differentiating back into their normal cell type and become a part of the epithelium. If the cells fail to stop proliferating following wound closure by overriding the switch to differentiating that can lead to colonic polyp, or tumor, and if not detected in a timely manner than, it leads ultimately to CRC development. Previously, we reported that β-catenin; an adherence junction protein gets phosphorylated by Janus kinase 3 (Jak3), a non-receptor tyrosine kinase, where Jak3 directly phosphorylates three tyrosine residues, viz. Tyr30, Tyr64, and Tyr86 in the N-terminal domain (NTD) of β-catenin. Now, our data show that human biopsies from colonic polyps not only associate with EMT, but also with only those mutation in β-catenin where Jak3, fail to phosphorylate β-catenin thereby making the cells override the switch and undergo uncontrolled proliferation and polyp formation. Based on this mechanistic understanding, the present study demonstrates the development of probe that detects the transition of colonic cells from proliferative stage to a differentiated (non-proliferative) stage that can diagnose CRC at the pre-polyp stage. The probe can not only play an important role in the early detection and/or treatment of patients with colorectal cancer but also increase life expectancy post detection. For this study, we collectedde-identified and discarded specimen from normal and/or polyps (n=40 cases; 20 normal and 20 polyps) through our collaboration with clinicians from local hospitals. Briefly, snap-frozen tissues were used to isolate DNA with the QIAamp DNA mini kit (Qiagen) as reported before by our group. All DNA samples were quantified using UV spectrophotometer and analyzed through agarose gel electrophoresis. The DNA sample was used as template in PCR reactions using the β-catenin-probes to amplify the regions encompassing Y30, Y64, and Y86 followed by sequencing of PCR samples. This was followed by histological analysis of colonic polyp sections from each patient stained with H&E and images were taken with phase contrast microscope. Our results show strongly correlation between mutations and histological analysis indicating the aforementioned detection of intactness of EMT switch as potential novel biomarker for the early detection of colorectal cancer.

Economic Impact of Coverage Expansion for Non-invasive Prenatal Testing Through a Performance-Based Risk-Sharing Agreement.

BackgroundHarvard Pilgrim Health Care expanded coverage for non-invasive prenatal testing (NIPT) to include all pregnant, single-gestation women aged < 35 years, through a performance-based risk-sharing (PBRS) agreement with Illumina to offset costs from coverage expansion. NIPT analyzes cell-free DNA fragments from a maternal blood sample to screen for fetal aneuploidies and is considered a more accurate screening method than conventional serum biochemical screening and nuchal translucency ultrasound-based approaches.ObjectiveThis study assessed the impact of NIPT coverage expansion on prenatal screening strategies and payer expenditures.MethodsThis was a real-world comparison of utilization and expenditures of prenatal screening and diagnostic testing in pregnant women aged < 35 years pre- (1 March 2016–28 February 2018) and post- (1 March 2018–30 September 2019) coverage expansion. Incidence rate ratios (IRRs) with 95% confidence intervals (CIs) were estimated to compare changes in utilization of conventional and NIPT-based prenatal screening methods. Change in per member per month (PMPM) expenditures in $US year 2020 were assessed post-coverage expansion using a budget impact model.ResultsA total of 5041 and 4109 distinct pregnancies were identified in pre- and post-coverage expansion periods, respectively. Mean ± standard deviation maternal age was consistent between pre- and post-coverage expansion periods (30.35 ± 3.35 and 30.33 ± 3.28, respectively). Screening orders for conventional methods decreased, with an adjusted IRR in the post-expansion period of 0.87 (95% CI 0.85–0.90) times the rate in the pre-expansion period; orders for NIPT increased, with an adjusted IRR in the post-expansion period of 1.41 (95% CI 1.32–1.51) times the rate in the pre-expansion period. Invasive diagnostic testing was low at baseline (1.0%) and did not change post-coverage expansion. The change in PMPM is estimated at $US0.026 post-coverage expansion.ConclusionThe PBRS agreement to expand NIPT coverage for women aged < 35 years was associated with an increase in NIPT utilization, decreases in conventional screening methods, and a modest increase in PMPM expenditures.Supplementary InformationThe online version contains supplementary material available at 10.1007/s41669-021-00261-y.

Rare chromosomal abnormalities: Can they be identified using conventional first trimester combined screening methods?

ObjectiveTo evaluate the performance of first trimester combined screening for the detection of rare chromosomal abnormalities, other than Trisomies 21, 18 or 13 or 45 × .Study designA database containing 36,254 pregnancies was analyzed. These patients were recruited at 15 US centers and included singleton pregnancies from 10 3/7–13 6/7 weeks. All patients had a nuchal translucency (NT) scan and those without a cystic hygroma (N = 36,120) underwent a combined first trimester screening test ('FTS' - NT, PAPP-A and fbHCG). A risk cut-off of 1:300, which was used for defining high risk for Trisomy 21, was also used to evaluate the detection rate for rare chromosomal abnormalities using the combined FTS test.Results36,120 patients underwent combined FTS. Of these, 123 were found to have one of the following chromosomal abnormalities: Trisomy 21, Trisomy 18, Trisomy 13 or Turner syndrome. This study focuses on 40 additional patients who were found to have ‘other’ rare chromosomal abnormalities such as triploidy, structural chromosomal abnormalities, sex chromosome abnormalities or unusual chromosomal abnormalities (e.g. 47XX + 16), giving an incidence of 1.1 in 1000 for these rare chromosomal abnormalities. Of these 40 pregnancies, only 2 (5%) had an NT measurement of ≥3 mm. The detection rate for combined FTS, using a risk cut-off of ≥1:300, was 35 % (14 of 40 cases). Therefore, 65 % of cases of rarer fetal chromosomal abnormalities had a ‘normal’ combined FTS risk (<1:300) and 95 % had a ‘normal’ NT (<3 mm).ConclusionTraditional FTS methods are unable to identify the vast majority of rare chromosomal abnormalities. Our data do not support the potential detection of rare fetal chromosomal abnormalities as a reason to favour nuchal translucency-based first trimester screening over NIPT.

Druggable Transient Pockets in Protein Kinases

Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity, adverse off-target effects and inevitable failures in clinical trials. Conventional chemical screening methods may miss potent small molecules because of their use of simple but outdated kits composed of recombinant enzyme proteins. Non-canonical inhibitors targeting a hidden pocket in a protein have received considerable research attention. Kii and colleagues identified an inhibitor targeting a transient pocket in the kinase DYRK1A during its folding process and termed it FINDY. FINDY exhibits a unique inhibitory profile; that is, FINDY does not inhibit the fully folded form of DYRK1A, indicating that the FINDY-binding pocket is hidden in the folded form. This intriguing pocket opens during the folding process and then closes upon completion of folding. In this review, we discuss previously established kinase inhibitors and their inhibitory mechanisms in comparison with FINDY. We also compare the inhibitory mechanisms with the growing concept of “cryptic inhibitor-binding sites.” These sites are buried on the inhibitor-unbound surface but become apparent when the inhibitor is bound. In addition, an alternative method based on cell-free protein synthesis of protein kinases may allow the discovery of small molecules that occupy these mysterious binding sites. Transitional folding intermediates would become alternative targets in drug discovery, enabling the efficient development of potent kinase inhibitors.

An evaluation of Cochrane Crowd found that crowdsourcing produced accurate results in identifying randomized trials

Background and ObjectivesFiltering the deluge of new research to facilitate evidence synthesis has proven to be unmanageable using current paradigms of search and retrieval. Crowdsourcing, a way of harnessing the collective effort of a “crowd” of people, has the potential to support evidence synthesis by addressing this information overload created by the exponential growth in primary research outputs. Cochrane Crowd, Cochrane's citizen science platform, offers a range of tasks aimed at identifying studies related to health care. Accompanying each task are brief, interactive training modules, and agreement algorithms that help ensure accurate collective decision-making.The aims of the study were to evaluate the performance of Cochrane Crowd in terms of its accuracy, capacity, and autonomy and to examine contributor engagement across three tasks aimed at identifying randomized trials. Study Design and SettingCrowd accuracy was evaluated by measuring the sensitivity and specificity of crowd screening decisions on a sample of titles and abstracts, compared with “quasi gold-standard” decisions about the same records using the conventional methods of dual screening. Crowd capacity, in the form of output volume, was evaluated by measuring the number of records processed by the crowd, compared with baseline. Crowd autonomy, the capability of the crowd to produce accurate collectively derived decisions without the need for expert resolution, was measured by the proportion of records that needed resolving by an expert. ResultsThe Cochrane Crowd community currently has 18,897 contributors from 163 countries. Collectively, the Crowd has processed 1,021,227 records, helping to identify 178,437 reports of randomized controlled trials (RCTs) for Cochrane's Central Register of Controlled Trials. The sensitivity for each task was 99.1% for the RCT identification task (RCT ID), 99.7% for the RCT identification task of trials from ClinicalTrials.gov (CT ID), and 97.7% for the identification of RCTs from the International Clinical Trials Registry Platform (ICTRP ID). The specificity for each task was 99% for RCT ID, 98.6% for CT ID, and 99.1% for CT ICTRP ID. The capacity of the combined Crowd and machine learning workflow has increased fivefold in 6 years, compared with baseline. The proportion of records requiring expert resolution across the tasks ranged from 16.6% to 19.7%. ConclusionCochrane Crowd is sufficiently accurate and scalable to keep pace with the current rate of publication (and registration) of new primary studies. It has also proved to be a popular, efficient, and accurate way for a large number of people to play an important voluntary role in health evidence production. Cochrane Crowd is now an established part of Cochrane's effort to manage the deluge of primary research being produced.

Development and Application of Image-Based High-Throughput Phenotyping Methodology for Salt Tolerance in Lentils

Soil salinity is a major abiotic stress in Australian lentil-producing areas. It is therefore imperative to identify genetic variation for salt tolerance in order to develop lentil varieties suitable for saline soils. Conventional screening methods include the manual assessment of stress symptoms, which can be very laborious, time-consuming, and error-prone. Recent advances in image-based high-throughput phenotyping (HTP) technologies have provided unparalleled opportunities to screen plants for a range of stresses, such as salt toxicity. The current study describes the development and application of an HTP method for salt toxicity screening in lentils. In a pilot study, six lentil genotypes were evaluated to determine the optimal salt level and the growth stage for distinguishing lentil genotypes using red–green–blue (RGB) images on a LemnaTec Scanalyzer 3D phenomics platform. The optimized protocol was then applied to screen 276 accessions that were also assessed earlier in a conventional phenotypic screen. Detailed phenotypic trait assessments, including plant growth and green/non-green color pixels, were made and correlated to the conventional screen (r = 0.55; p &lt; 0.0001). These findings demonstrated the improved efficacy of an image-based phenotyping approach that is high-throughput, efficient, and better suited to modern breeding programs.

Altered retinal oxygen metabolism in patients with combined ocular and central nervous system sarcoidosis.

To evaluate retinal oxygen metabolism by retinal oximetry for ocular and CNS diseases in a cross-sectional study of sarcoidosis. Overall 201 eyes from 103 biopsy-verified sarcoidosis patients were included and divided into four groups depending on the organ affection: (i) sarcoidosis without ocular or CNS affection, (ii) ocular sarcoidosis, (iii) CNS sarcoidosis, and (iv) combined ocular and CNS sarcoidosis. Retinal oximetry was obtained and analysed, with the mean retinal arteriolar and venular saturation as well as arteriovenous difference as principal outcomes. Comparison between groups was done in a multi linear regression model adjusted for age, sex, duration of sarcoidosis, best corrected visual acuity and retinal oximetry quality. Mean (s.d.) age was 50.5 (13.4) (95% CI: 47.9, 53.1) years and 52.2% were males. Eyes of the combined Ocular/CNS group had a higher retinal arteriovenous difference than eyes of the Non-ocular/no-CNS group (42.1% vs 37.7%, P = 0.012) but did not differ between other groups. Eyes in the four groups (Non-ocular/no-CNS, Ocular, CNS and Ocular/CNS) did not differ according to retinal arterial (94.5%, 93.5%, 93.5% and 94.5%, respectively) or venular (57.5%, 56.4%, 55.0% and 52.5%, respectively) oxygen saturation. The results of this study suggest that eyes of sarcoidosis patients with combined ocular and CNS affection have an altered oxygen metabolism indicating a subclinical eye affection that is not recognized by conventional screening methods.

Selection and evaluation of quality control markers in propolis based on its hyperlipidemia therapy via regulating PXR/CYP3A4 expression

BackgroundPropolis and its preparations are components of TCM and functional food sources for antihyperlipidemia therapy. However, due to the metabolic properties of propolis, its individual components remain ambiguous, especially those that are therapeutically active. PurposeThe study presented here identified the primary target (PXR/CYP3A4) of propolis activity against hyperlipidemia and evaluated individual compounds of propolis to select a quality control marker based on this activity. MethodsMice fed a high-fat diet were used to study the efficacy of propolis, followed by identification of substantially influenced glycolipid regulatory target(s) by propolis. Since propolis had the strongest effect on PXR expression, we took advantage of its downstream target CYP3A4, the drug metabolism activity of such enzyme is affected by alterations in PXR expression. Thus, we used the production of 1’-hydroxy-midazolam as an indicator. Compounds found by UHPLC-TOF-MS were added to a HepG2 cell solution (transfected by PXR mRNA and the CYP3A4 plasmid to simulate drug metabolism in the body) in the form of a monomer, followed by the addition of midazolam. Changes in the amount of “indicator” were used to investigate each compound's qualitative (promote or suppress) and quantitative activity. Compounds with obvious effects were quantified in propolis extract, as confirmed via Western Blot analysis regarding their PXR regulatory activity, and subjected to pharmacokinetic analysis to biter understand their metabolism in the body. Finally, components passing these screens could be regarded as quality control markers capable of indicating the efficacy of antihyperlipidemic activity via PXR/CYP3A4 regulation. ResultsThe use of propolis was effective in lowering TG and TC levels in mice, as well as in repairing their injured livers; its activity was comparable to the chemical and TCM positive controls. Propolis mainly suppressed PXR expression compared with other regulatory targets that were tested. Most of the individual compounds from propolis (13 out of 15) showed obvious regulatory activity of PXR/CYP3A4; however, content quantification and pharmacokinetic analyses narrowed the selection to 2 compounds, kaempferol and chrysin, as the main active components responsible for the antihyperlipidemic effect of propolis. In other words, this study suggested that propolis mainly acts on the PXR/CYP3A4 pathway to regulate glycolipid metabolism, and the 2 compounds mentioned above can be used as quality control markers (QM) to evaluate the efficacy of this activity. ConclusionPropolis's antihyperlipidemic effect relies on its regulation of PXR/CYP3A4 expression. Kaempferol and chrysin can be regarded as QMs. In addition, the metabolite-based method for evaluating regulatory activity is much faster, more effective, and more reliable than the conventional screening method, paving the way for its future applications.

CBIO-23. PROXIMITY-DEPENDENT BIOTIN IDENTIFICATION (BIOID2) INDICATES MEMBRANE TRAFFICKING AND VESICLE TRANSPORT AS A POTENTIAL NOVEL FUNCTION OF EXTRACELLULAR SIGNAL-REGULATED KINASE 5 (ERK5)

Abstract INTRODUCTION Pediatric High-Grade Gliomas (PHGG), which include Diffuse Midline Gliomas (DMG), are a leading cause of brain tumor death in children. Our recent work has identified extracellular signal-regulated kinase 5 (ERK5) as a critical mediator of cell survival in DMG, as ERK5 knockdown decreases cell proliferation and extends survival time in orthotopic xenograft mice. Further investigation into the structure of ERK5 shows that it has a kinase domain and, unlike other ERKs, a transactivation domain, and both are important for promoting cell proliferation. HYPOTHESIS AND METHODS We hypothesize that identifying interactors and substrates of ERK5 could identify clinically actionable proteins and provide a more mechanistic insight into ERK5 in the progression of PHGGS. To determine protein–protein associations (PPAs), we employed the proximity-dependent biotin identification (BioID2) method and generated inducible ERK5-BioID2 and ERK2-BioID2 constructs to overcome barriers of conventional screening methods for PPAs. ERK2, similar in structure but much more studied than ERK5, was used as a comparison. Using DIPG lines as proof of principle, we performed streptavidin pull down assays for putative biotinylated ERK PPA and followed with mass spectrometry to identify the ERK2 and ERK5 interactomes. RESULTS Using data-dependent acquisition (DDA), we identified several unique and common interactors of ERK5 compared to ERK2. Through STRING network and pathway analysis, we identified a novel function of ERK5 with respect to membrane trafficking and vesicle transport. Identification of interactors with ERK5 may lead to effective therapeutic combinations. Our current work is focused on validating these interactions and the function of ERK5 in these biological processes. CONCLUSIONS Currently, ERK5 is not as understood as ERK1 or ERK2. Identification of interactors and substrates of ERK5 will further our understanding of PHGG biology, and may lead to identifying druggable targets and pathways.