Implementing laboratory automation for next-generation sequencing: benefits and challenges for library preparation

In the wake of COVID-19, the importance of next-generation sequencing (NGS) for diagnostic testing and surveillance-based screening has never been more evident. Considering this, continued investment is critical to ensure more public health laboratories can adopt these advanced molecular technologies. However, many facilities may face potential barriers such as limited staff available to routinely prepare, test, and analyze samples, lack of expertise or experience in sequencing, difficulties in assay standardization, and an inability to handle throughput within expected turnaround times. Workflow automation provides an opportunity to overcome many of these challenges. By identifying these types of sustainable solutions, laboratories can begin to utilize more advanced molecular-based approaches for routine testing. Nevertheless, the introduction of automation, while valuable, does not come without its own challenges. This perspective article aims to highlight the benefits and difficulties of implementing laboratory automation used for sequencing. We discuss strategies for implementation, including things to consider when selecting instrumentation, how to approach validations, staff training, and troubleshooting.

Basics of laboratory statistics

The strict monitoring of examinations and evaluation of newer methods or instruments is a daily routine in clinical laboratory. The automated analyzers accumulate an enormous amount of data from patients' examinations and quality control procedures. This laboratory data is meaningless if it does not generate the information that we can extend to the population of our interest. In an analytical work, the most important operation is the comparison of data, to quantify accuracy and precision and to generate meaningful explanation for clinician and patients queries. Most of the information needed in the regular laboratory work can be obtained with the use of simple convenient statistical tools. This article describes the basics of laboratory statistics, the knowledge of which answers about the application of quality control in laboratory, accuracy and diagnostic power of our examinations, variability in reports, comparison of different methods and derivation of a biological reference interval for an analyte.

Application of Wireless Magnetic Sensors in the Urban Environment and Their Accuracy Verification

In a smart city, sensors are essential elements-the source of up-to-date traffic information. This article deals with magnetic sensors connected to wireless sensor networks (WSNs). They have a low investment cost, a long lifetime, and easy installation. However, it is still necessary to disturb the road surface locally during their installation. All road lanes to and from the city center of Žilina have sensors that send data at five-minute intervals. They send up-to-date information about the traffic flow's intensity, speed, and composition. The LoRa network ensures the data transmission, but in the event of failure, the 4G/LTE modem realizes the backup transmission. The disadvantage of this application of sensors is their accuracy. The research task was to compare the outputs from the WSN with a traffic survey. The appropriate method for the traffic survey on the selected road profile is a video recording and speed measurement using the Sierzega radar. The results show distorted values, mainly for short intervals. The most accurate output from magnetic sensors is the number of vehicles. On the other hand, traffic flow composition and speed measurement are relatively inaccurate because it is not easy to identify vehicles based on dynamic length. Another problem with sensors is frequent communication outages, which cause an accumulation of values after the outage ends. The secondary objective of the paper is to describe the traffic sensor network and its publicly accessible database. In the end, there are several proposals for data usage.

Analytical verification of the Dymind D7-CRP automated analyser

Introduction

The aim of this study was to perform a verification of the Dymind D7-CRP automated analyser and compare it with established analysers.

Materials and methods

Analytical verification included estimation of repeatability, between run precision, within-laboratory precision, and bias in control samples with low, normal and high levels. The acceptance criteria for analytical verification were defined using the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) 2019 Biological Variation Database. Method comparison between the Dymind D7-CRP and the Sysmex XN1000 for haematological parameters and the Dymind D7-CRP and the Beckman Coulter AU680 for CRP values was performed on 40 patient samples.

Results

Analytical verification criteria were adequately met with the exception of monocyte count for repeatability and within-laboratory precision (13.4% and 11.5%, respectively, acceptance criteria 10.1%) and measurement uncertainty (23.0, acceptance criteria 20.0%) at low level, eosinophil count for BIAS at the low level (37.7%, acceptance criteria 25.2%), basophil count (BAS) for BIAS at the high level (14.2%, acceptance criteria 10.9%), and mean platelet volume (MPV) for repeatability (4.2% and 6.8%), between run precision (2.2% and 4.7%), within-laboratory precision (4.0% and 7.3%) (acceptance criteria 1.7%), and measurement uncertainty (8.0 and 14.6%, acceptance criteria 3.4%) at both the low and high concentrations. Method comparison showed no clinically significant constant or proportional differences for all parameters except BAS and MPV.

Conclusion

The analytical verification of the Dymind D7-CRP showed adequate analytical characteristics. The Dymind D7-CRP can be used interchangeably with the Sysmex XN-1000 for all parameters tested, except BAS and MPV, and with the Beckman Coulter AU-680 for the determination of CRP.

Structured Verification of Machine Learning Models in Industrial Settings

The use of machine learning (ML) allows us to automate and scale the decision-making processes. The key to this automation is the development of ML models that generalize training data toward unseen data. Such models can become extremely versatile and powerful, which makes democratization of artificial intelligence (AI) possible, that is, providing ML to non-ML experts such as software engineers or domain experts. Typically, automated ML (AutoML) is being referred to as a key step toward it. However, from our perspective, we believe that democratization of the verification process of ML systems is a larger and even more crucial challenge to achieve the democratization of AI. Currently, the process of ensuring that an ML model works as intended is unstructured. It is largely based on experience and domain knowledge that cannot be automated. The current approaches such as cross-validation or explainable AI are not enough to overcome the real challenges and are discussed extensively in this article. Arguing toward structured verification approaches, we discuss a set of guidelines to verify models, code, and data in each step of the ML lifecycle. These guidelines can help to reliably measure and select an optimal solution, besides minimizing the risk of bugs and undesired behavior in edge-cases.

A verified and validated moving domain computational fluid dynamics solver with applications to cardiovascular flows

Computational fluid dynamics (CFD) in combination with patient-specific medical images has been used to correlate flow phenotypes with disease initiation, progression and outcome, in search of a prospective clinical tool. A large number of CFD software packages are available, but are typically based on rigid domains and low-order finite volume methods, and are often implemented in massive low-level C++ libraries. Furthermore, only a handful of solvers have been appropriately verified and validated for their intended use. Our goal was to develop, verify and validate an open-source CFD solver for moving domains, with applications to cardiovascular flows. The solver is an extension of the CFD solver Oasis, which is based on the finite element method and implemented using the FEniCS open source framework. The new solver, named OasisMove, extends Oasis by expressing the Navier-Stokes equations in the arbitrary Lagrangian-Eulerian formulation, which is suitable for handling moving domains. For code verification we used the method of manufactured solutions for a moving 2D vortex problem, and for validation we compared our results against existing high-resolution simulations and laboratory experiments for two moving domain problems of varying complexity. Verification results showed that the L 2 error followed the theoretical convergence rates. The temporal accuracy was second-order, while the spatial accuracy was second- and third-order using ℙ 1 / ℙ 1 and ℙ 2 / ℙ 1 finite elements, respectively. Validation results showed good agreement with existing benchmark results, by reproducing lift and drag coefficients with less than 1% error, and demonstrating the solver's ability to capture vortex patterns in transitional and turbulent-like flow regimes. In conclusion, we have shown that OasisMove is an open-source, accurate and reliable solver for cardiovascular flows in moving domains.

The Analytical and Clinical Validity of the pfSTEP Digital Biomarker of the Susceptibility/Risk of Declining Physical Function in Community-Dwelling Older Adults

Measures of stepping volume and rate are common outputs from wearable devices, such as accelerometers. It has been proposed that biomedical technologies, including accelerometers and their algorithms, should undergo rigorous verification as well as analytical and clinical validation to demonstrate that they are fit for purpose. The aim of this study was to use the V3 framework to assess the analytical and clinical validity of a wrist-worn measurement system of stepping volume and rate, formed by the GENEActiv accelerometer and GENEAcount step counting algorithm. The analytical validity was assessed by measuring the level of agreement between the wrist-worn system and a thigh-worn system (activPAL), the reference measure. The clinical validity was assessed by establishing the prospective association between the changes in stepping volume and rate with changes in physical function (SPPB score). The agreement of the thigh-worn reference system and the wrist-worn system was excellent for total daily steps (CCC = 0.88, 95% CI 0.83-0.91) and moderate for walking steps and faster-paced walking steps (CCC = 0.61, 95% CI 0.53-0.68 and 0.55, 95% CI 0.46-0.64, respectively). A higher number of total steps and faster paced-walking steps was consistently associated with better physical function. After 24 months, an increase of 1000 daily faster-paced walking steps was associated with a clinically meaningful increase in physical function (0.53 SPPB score, 95% CI 0.32-0.74). We have validated a digital susceptibility/risk biomarker-pfSTEP-that identifies an associated risk of low physical function in community-dwelling older adults using a wrist-worn accelerometer and its accompanying open-source step counting algorithm.

Predicting children's real-ear-to-coupler differences based on tympanometric data

OBJECTIVE

Paediatric hearing-aid verification relies on measures of output obtained from the ear canal or in a coupler with the child's real-ear-to-coupler difference (RECD). Measured RECD cannot always be completed in children, leading to fitting inaccuracies. Audiologists often have tympanometry data that characterises the child's ear-canal acoustics. The goal of this study was to determine if tympanometry can be used to improve predictions of measured RECD.

DESIGN

A retrospective analysis of RECD and admittance, tympanometric peak pressure, and equivalent ear-canal volume from 226 Hz tympanometry collected as part of a longitudinal study of children with hearing loss were modelled with Bayesian hierarchical regression.

STUDY SAMPLE

Two-hundred sixty-six children with mild-to-severe hearing loss contributed data.

RESULTS

Age-based average RECD models were within 3 dB of measured RECD values in 54% of cases with normal middle ear status and 50.6% of cases with abnormal middle ear status. Immittance-predicted RECD were within 3 dB in 69.6% of cases with normal middle ear status and 74.4% of cases with abnormal middle ear status.

CONCLUSION

Immittance-predicted RECD was more accurate than age-based average RECD, particularly in children with abnormal middle ear status. The findings suggest that 226 Hz tympanometry could be used clinically to improve predictions of measured RECD when it cannot be measured.

Verifiable biology

The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological systems. In particular, formal verification, complementary approach to standard computational techniques such as simulation, is used to validate the system correctness and obtain critical information about system behaviour. In this study, we survey the most frequently used computational modelling approaches and formal verification techniques for computational biology. We compare a number of verification tools and software suites used to analyse biological systems and biochemical networks, and to verify a wide range of biological properties. For users who have no expertise in formal verification, we present a novel methodology that allows them to easily apply formal verification techniques to analyse their biological or biochemical system of interest.

Application and Development of QKD-Based Quantum Secure Communication

Quantum key distribution (QKD) protocols have unique advantages of enabling symmetric key sharing with information-theoretic security (ITS) between remote locations, which ensure the long-term security even in the era of quantum computation. QKD-based quantum secure communication (QSC) enhancing the security of key generation and update rate of keys, which could be integrated with a variety of cryptographic applications and communication protocols, has become one of the important solutions to improve information security. In recent years, the research on QKD has been active and productive, the performance of novel protocol systems has been improved significantly, and the feasibility of satellite-based QKD has been experimentally verified. QKD network construction, application exploration, and standardization have been carried out in China as well as other countries and regions around the world. Although QKD-based QSC applications and industrialization are still in the initial stage, the research and exploration momentum is positive and more achievements could be expected in the future.

Inhibition of apoptosis through AKT-mTOR pathway in ovarian cancer and renal cancer

OBJECTIVE

Ovarian cancer and renal cancer are malignant tumors; however, the relationship between TTK Protein Kinase (TTK), AKT-mTOR pathway and ovarian cancer, renal cancer remains unclear.

METHODS

Download GSE36668 and GSE69428 from Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was performed. Created protein-protein interaction (PPI) network. Used Gene Ontology analysis (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional enrichment analysis. Gene Set Enrichment Analysis (GSEA) analysis and survival analysis were performed. Created animal model for western blot analysis. Gene Expression Profiling Interactive Analysis (GEPIA) was performed to explore the role of TTK on the overall survival of renal cancer.

RESULTS

GO showed that DEGs were enriched in anion and small molecule binding, and DNA methylation. KEGG analysis presented that they mostly enriched in cholesterol metabolism, type 1 diabetes, sphingolipid metabolism, ABC transporters, etc., TTK, mTOR, p-mTOR, AKT, p-AKT, 4EBP1, p-4EBP1 and Bcl-2 are highly expressed in ovarian cancer, Bax, Caspase3 are lowly expressed in ovarian cancer, cell apoptosis is inhibited, leading to deterioration of ovarian cancer. Furthermore, the TTK was not only the hub biomarker of ovarian cancer, but also one significant hub gene of renal cancer, and its expression was up-regulated in the renal cancer. Compared with the renal cancer patients with low expression of TTK, the patients with high expression of TTK have the poor overall survival (P = 0.0021).

CONCLUSION

TTK inhibits apoptosis through AKT-mTOR pathway, worsening ovarian cancer. And TTK was also one significant hub biomarker of renal cancer.

Phosphonylated tyrosine and lysine residues as biomarkers of local exposure of human hair to the organophosphorus nerve agents sarin and VX

We herein present for the first time a micro liquid chromatography-electrospray ionization high-resolution tandem-mass spectrometry (μLC-ESI MS/HR MS) procedure to detect phosphonylated tyrosine (Tyr) and lysine (Lys) residues obtained from human hair exposed to organophosphorus nerve agents (OPNA). In general, toxic OPNA react with endogenous blood proteins causing the formation of adducts representing well-known targets for biomedical analysis to prove exposure. In contrast, no protein-derived biomarker has been introduced so far to document local exposure of hair. Accordingly, we developed and characterized a μLC-ESI MS/HR MS method for the analysis of scalp hair exposed to OPNA in vitro. Type I and Type II keratin from hair was dissolved during lysis, precipitated and subjected to pronase-catalyzed hydrolysis yielding single adducted Lys and in a much higher amount Tyr residues. Exposure to sarin caused the adduction of an isopropyl methylphosphonic acid moiety and exposure to VX yielded adducts of ethyl methylphosphonic acid, well suited as biomarkers of exposure. These were of appropriate stability in the autosampler for 24 h. The biomarker yield obtained from hair of six individuals as well as from hair of six different parts of the body of one individual (armpit, beard, leg, arm, scalp, and pubic) differed reasonably indicating the variable individual protein composition and structure of hair. Exposed hair stored at ambient temperature for 9 weeks with contact to air and daylight showed stability of all adducts and therefore their suitability for verification of exposure.

Leveraging Multiple Distinct EEG Training Sessions for Improvement of Spectral-Based Biometric Verification Results

Most studies on EEG-based biometry recognition report results based on signal databases, with a limited number of recorded EEG sessions using the same single EEG recording for both training and testing a proposed model. However, the EEG signal is highly vulnerable to interferences, electrode placement, and temporary conditions, which can lead to overestimated assessments of the considered methods. Our study examined how different numbers of distinct recording sessions used as training sessions would affect EEG-based verification. We analyzed the original data from 29 participants with 20 distinct recorded sessions each, as well as 23 additional impostors with only one session each. We applied raw coefficients of power spectral density estimate, and the coefficients of power spectral density estimate converted to the decibel scale, as the input to a shallow neural network. Our study showed that the variance introduced by multiple recording sessions affects sensitivity. We also showed that increasing the number of sessions above eight did not improve the results under our conditions. For 15 training sessions, the achieved accuracy was 96.7 ± 4.2%, and for eight training sessions and 12 test sessions, it was 94.9 ± 4.6%. For 15 training sessions, the rate of successful impostor attacks over all attack attempts was 3.1 ± 2.2%, but this number was not significantly different from using six recording sessions for training. Our findings indicate the need to include data from multiple recording sessions in EEG-based recognition for training, and that increasing the number of test sessions did not significantly affect the obtained results. Although the presented results are for the resting-state, they may serve as a baseline for other paradigms.

Trusted Operation of Cyber-Physical Processes Based on Assessment of the System's State and Operating Mode

We consider the trusted operation of cyber-physical processes based on an assessment of the system's state and operating mode and present a method for detecting anomalies in the behavior of a cyber-physical system (CPS) based on the analysis of the data transmitted by its sensory subsystem. Probability theory and mathematical statistics are used to process and normalize the data in order to determine whether or not the system is in the correct operating mode and control process state. To describe the mode-specific control processes of a CPS, the paradigm of using cyber-physical parameters is taken as a basis, as it is the feature that most clearly reflects the system's interaction with physical processes. In this study, two metrics were taken as a sign of an anomaly: the probability of falling into the sensor values' confidence interval and parameter change monitoring. These two metrics, as well as the current mode evaluation, produce a final probability function for our trust in the CPS's currently executing control process, which is, in turn, determined by the operating mode of the system. Based on the results of this trust assessment, it is possible to draw a conclusion about the processing state in which the system is operating. If the score is higher than 0.6, it means the system is in a trusted state. If the score is equal to 0.6, it means the system is in an uncertain state. If the trust score tends towards zero, then the system can be interpreted as unstable or under stress due to a system failure or deliberate attack. Through a case study using cyber-attack data for an unmanned aerial vehicle (UAV), it was found that the method works well. When we were evaluating the normal flight mode, there were no false positive anomaly estimates. When we were evaluating the UAV's state during an attack, a deviation and an untrusted state were detected. This method can be used to implement software solutions aimed at detecting system faults and cyber-attacks, and thus make decisions about the presence of malfunctions in the operation of a CPS, thereby minimizing the amount of knowledge and initial data about the system.

A clinical study comparing polymer and gold fiducials for prostate cancer radiotherapy

Introduction

Image guidance with gold fiducials improves outcomes of prostate radiotherapy. However, gold produces artefact on CT imaging, interfering with contouring and verification. The purpose of this study was to compare polymer to standard gold fiducials using radiotherapy imaging modalities to assess the visibility and artefact.

Methods

Twenty eight patients with locally advanced prostate cancer were enrolled, half had three polymer fiducials implanted into the prostate and half underwent insertion of gold fiducials. Patients were imaged with CT, T2 weighted MRI, cone-beam CT (CBCT) and planar KV images. Fiducials were scored for visibility and assessed for CT artefact in surrounding prostate tissue. The artefact was quantified from Hounsfield number histograms and separated into percentile ranges and proportion of voxels in HU normal tissue range of a 2cm sphere surrounding the fiducial.

Results

Gold and polymer fiducials were sufficiently visible for CT and CBCT verification. The gold fiducials could be visualized well on KV planar imaging; however, the polymer markers were obscured by pelvic bones. Neither polymer nor gold fiducials could be visualized on MRI. The polymer fiducial produced less artefact than gold on CT, having less voxel spread for the HU percentile ranges and a greater proportion of voxels in the normal tissue range.

Conclusions

Polymer fiducials are a more suitable fiducial than gold for CT/CBCT in prostate cancer radiotherapy, demonstrating minimal artefact and good visibility on CT. However, they were not well seen on MRI or KV imaging and thus not suitable for co-registration or planar KV verification.

Pediatric reference interval verification for 17 specialized immunoassays and cancer markers on the Abbott Alinity i system in the CALIPER cohort of healthy children and adolescents

OBJECTIVES

Clinical laboratory investigation of autoimmune, metabolic, and oncologic disorders in children and adolescents relies on appropriateness of reference intervals (RIs). The Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) previously established comprehensive pediatric RIs for specialized immunoassays on the Abbott ARCHITECT system. Herein, we aim to verify performance on new Alinity i assays by evaluating sera collected from healthy children as per Clinical and Laboratory Standards Institute (CLSI) EP-28A3C guidelines.

METHODS

Precision, linearity, and method comparison experiments were completed for 17 specialized Alinity immunoassays, including cancer antigens, autoimmune peptides, and hormones. Sera collected from healthy children and adolescents (birth-18 years, n=100) were evaluated. CLSI-based verification was completed using previously established CALIPER RIs for ARCHITECT assays as the reference.

RESULTS

Of 17 specialized immunoassays assays, only anti-cyclic citrullinated peptides (anti-CCP) did not meet acceptable verification criterion (i.e., ≥90% of results within ARCHITECT reference CI). Anti-thyroglobulin, anti-thyroid peroxidase, and carcinoembryonic antigen did not require age-specific consideration beyond one year of age, with 63, 91, and 80% of samples equalling the limit of detection, respectively. Estimates were separated by sex for relevant assays (e.g., sex hormone binding globulin, total and free prostate specific antigen).

CONCLUSIONS

Findings support transferability of pediatric RIs on ARCHITECT system to the Alinity system for 16 specialized immunoassays in the CALIPER cohort and will be a useful resource for pediatric clinical laboratories using Alinity assays. Further work is needed to establish evidence-based interpretative recommendations for anti-CCP and continue to evaluate pediatric RI acceptability for newly available assay technologies.

Verification, Evaluation, and Validation: Which, How & Why, in Medical Augmented Reality System Design

This paper presents a discussion about the fundamental principles of Analysis of Augmented and Virtual Reality (AR/VR) Systems for Medical Imaging and Computer-Assisted Interventions. The three key concepts of Analysis (Verification, Evaluation, and Validation) are introduced, illustrated with examples of systems using AR/VR, and defined. The concepts of system specifications, measurement accuracy, uncertainty, and observer variability are defined and related to the analysis principles. The concepts are illustrated with examples of AR/VR working systems.

Listening Preferences of New Adult Hearing Aid Users: A Registered, Double-Blind, Randomized, Mixed-Methods Clinical Trial of Initial Versus Real-Ear Fit

Hearing aid verification with real-ear measurement (REM) is recommended in clinical practice. Improvements, over time, in accuracy of manufacturers' initial fit mean the benefit of routine REM for new adult users is unclear. This registered, double-blinded, randomized, mixed-methods clinical trial aimed to (i) determine whether new adult hearing aid users prefer initial or real-ear fit and (ii) investigate the reasons for preferences. New adult hearing aid users (n = 45) were each fitted with two programs: the initial fit and real-ear fit, both with adjustments based on immediate feedback from the patient. Participants were asked to complete daily paired-comparisons of the two programs with a magnitude estimation of the preference, one for each of clarity/comfort in quiet/noise as well as overall preference. The results revealed gain adjustment requests were low in number and small in magnitude. Deviation from NAL-NL2 targets (after adjustment for a 65 dB SPL input) was close to zero, except at high frequencies where real-ear fits were around 3 dB closer to target. There was no difference in clarity ratings between programs, but comfort ratings favored initial fit. Overall, 10 participants (22%) expressed a preference for real-ear fit. Reasons for preference were primarily based on comfort with the initial fit and clarity with real-ear fit. It may be acceptable to fit new adult users with mild-to-moderate hearing loss without the need for REMs, if the primary outcome of interest is user preference. It remains to be seen if the findings generalize to other fitting software, other outcome measures and more severe hearing loss.

Design of a temperature-feedback controlled automated magnetic hyperthermia therapy device

Introduction

Magnetic hyperthermia therapy (MHT) is a minimally invasive adjuvant therapy capable of damaging tumors using magnetic nanoparticles exposed radiofrequency alternating magnetic fields. One of the challenges of MHT is thermal dose control and excessive heating in superficial tissues from off target eddy current heating.

Methods

We report the development of a control system to maintain target temperature during MHT with an automatic safety shutoff feature in adherence to FDA Design Control Guidance. A proportional-integral-derivative (PID) control algorithm was designed and implemented in NI LabVIEW^®. A standard reference material copper wire was used as the heat source to verify the controller performance in gel phantom experiments. Coupled electromagnetic thermal finite element analysis simulations were used to identify the initial controller gains.

Results

Results showed that the PID controller successfully achieved the target temperature control despite significant perturbations.

Discussion and Conclusion

Feasibility of PID control algorithm to improve efficacy and safety of MHT was demonstrated.

Awareness and attitude toward oocyte cryopreservation for non-medical reasons: a study on women candidates for social egg freezing

PURPOSE

The present study was to investigate awareness and attitudes toward female fertility and aging, desire for a child and motherhood, and oocyte freezing for non-medical reasons among women candidates for Social Egg Freezing (SEF).

MATERIALS AND METHODS

This was a cross-sectional study on all 216 women who sought oocyte cryopreservation for nonmedical reasons at Royan Institute. A 24-item self-administered questionnaire measured knowledge and attitudes to SEF. Responses were as yes/no or a 4-point Likert scale.

RESULTS

Only 40% of participants accurately indicated that having a sexual partner does not help to preserve their fertility. A quarter of women correctly recalled chance of pregnancy with unprotected intercourse during a period of a year, for women 20 to 40 years old. Only one-third of respondents accurately identified the age-related fertility decline at 35-39 years. Only 6.9% correctly mentioned the low chance of pregnancy after egg freezing at 35 years old. Almost a third of women knew that the age range of 31-35 years is the right age to freeze an egg with the highest chance of pregnancy. Aging and health of offspring were most influential in women's decisions on SEF.

CONCLUSION

In conclusion, there was significant gaps in knowledge about age-related fertility decline, and egg cryopreservation conditions and its complications. It is crucial to impart to these women a better knowledge about fertility and a realistic picture about SEF, especially on the number of high-quality retrieved mature oocytes and live birth rates depend on women's age.

Method evaluation in the clinical laboratory

Method evaluation is one of the critical components of the quality system that ensures the ongoing quality of a clinical laboratory. As part of implementing new methods or reviewing best practices, the peer-reviewed published literature is often searched for guidance. From the outset, Clinical Chemistry and Laboratory Medicine (CCLM) has a rich history of publishing methods relevant to clinical laboratory medicine. An insight into submissions, from editors' and reviewers' experiences, shows that authors still struggle with method evaluation, particularly the appropriate requirements for validation in clinical laboratory medicine. Here, we consider through a series of discussion points an overview of the status, challenges, and needs of method evaluation from the perspective of clinical laboratory medicine. We identify six key high-level aspects of clinical laboratory method evaluation that potentially lead to inconsistency. 1. Standardisation of terminology, 2. Selection of analytical performance specifications, 3. Experimental design of method evaluation, 4. Sample requirements of method evaluation, 5. Statistical assessment and interpretation of method evaluation data, and 6. Reporting of method evaluation data. Each of these areas requires considerable work to harmonise the practice of method evaluation in laboratory medicine, including more empirical studies to be incorporated into guidance documents that are relevant to clinical laboratories and are freely and widely available. To further close the loop, educational activities and fostering professional collaborations are essential to promote and improve the practice of method evaluation procedures.

Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER

Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.

Accommodating population differences when validating risk prediction models

Validation of risk prediction models in independent data provides a more rigorous assessment of model performance than internal assessment, for example, done by cross-validation in the data used for model development. However, several differences between the populations that gave rise to the training and the validation data can lead to seemingly poor performance of a risk model. In this paper we formalize the notions of "similarity" or "relatedness" of the training and validation data, and define reproducibility and transportability. We address the impact of different distributions of model predictors and differences in verifying the disease status or outcome on measures of calibration, accuracy and discrimination of a model. When individual level information from both the training and validation data sets is available, we propose and study weighted versions of the validation metrics that adjust for differences in the risk factor distributions and in outcome verification between the training and validation data to provide a more comprehensive assessment of model performance. We provide conditions on the risk model and the populations that gave rise to the training and validation data that ensure a model's reproducibility or transportability, and show how to check these conditions using weighted and unweighted performance measures. We illustrate the method by developing and validating a model that predicts the risk of developing prostate cancer using data from two large prostate cancer screening trials.

Two triphosphate tunnel metalloenzymes from apple exhibit adenylyl cyclase activity

Adenylyl cyclase (AC) is the key catalytic enzyme for the synthesis of 3',5'-cyclic adenosine monophosphate. Various ACs have been identified in microorganisms and mammals, but studies on plant ACs are still limited. No AC in woody plants has been reported until now. Based on the information on HpAC1, three enzymes were screened out from the woody fruit tree apple, and two of them (MdTTM1 and MdTTM2) were verified and confirmed to display AC activity. Interestingly, in the apple genome, these two genes were annotated as triphosphate tunnel metalloenzymes (TTMs) which were widely found in three superkingdoms of life with multiple substrate specificities and enzymatic activities, especially triphosphate hydrolase. In addition, the predicted structures of these two proteins were parallel, especially of the catalytic tunnel, including conserved domains, motifs, and folded structures. Their tertiary structures exhibited classic TTM properties, like the characteristic EXEXK motif and β-stranded anti-parallel tunnel capable of coordinating divalent cations. Moreover, MdTTM2 and HpAC1 displayed powerful hydrolase activity to triphosphate and restricted AC activity. All of these findings showed that MdTTMs had hydrolysis and AC activity, which could provide new solid evidence for AC distribution in woody plants as well as insights into the relationship between ACs and TTMs.

Observational Verification of the Cumulative Resilience Screening Index (CRSI) Using Hurricanes, Inland Floods, and Wildfires From 2016 to 2019

Users can apply three processes to develop confidence in decision-making tools like models and indices-validation, verification, and observation. The utility of the Cumulative Resilience Screening Index (CRSI) was demonstrated by combining the processes of verification and observation using real-world natural hazard events (i.e., hurricanes, inland flooding, and wildfires). The ability of CRSI to determine the counties most vulnerable to hazards and least likely to recover quickly from natural hazards is demonstrated using these natural hazard events from outside the original index construction data set. Using Hurricane Harvey and Hurricane Michael, the counties in Texas and Florida/Georgia, respectively, experiencing the most damage and the most extended recovery intervals were determined accurately. Similarly, the most vulnerable and least recoverable counties were correctly identified as those associated with the Great Louisiana Flood of 2016. Finally, three different types of wildfires in California were examined to determine the likelihood of recovery and the strength of pre-event planning. All models and indices developed for use by decision-makers should consider undertaking this verification or a similar validation operation to enhance user confidence.