Collaborative Laboratory Research Articles

Detection of SARS-CoV-2 in Nigeria: laboratory preparedness and report of index case

INTRODUCTION: Heightened surveillance of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 2019 outbreak in Wuhan, China activated several collaborative laboratory drills on its detection by health institutions in Nigeria. We hereby detail the laboratory detection and confirmation of the novel SARS-CoV-2 virus of the index case imported into Nigeria. METHODS: viral RNA from sputum sample of the index case was tested for SARS-CoV-2 envelope (E) and RNA dependent RNA polymerase (RdRp) genes using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Genetic analysis using a partial sequence of RdRp gene was used for laboratory confirmation, evolutionary inferences, and relatedness to previous strains of betacoronaviruses in Nigeria. RESULTS: both qRT-PCR for the E and RdRp genes indicated the presence of the SARS-CoV-2 RNA by showing cycle threshold (ct) values of 20.27 and 25.26 respectively. On successful completion of the sequencing run, data aligned with >98% similarity of the 2019 circulating strain of Coronavirus SARS-CoV-2. Evolutionary algorithms revealed that the sequence (RdRp gene) of the outbreak circulating strains were more conserved unlike previous coronavirus outbreaks. Data showed that some coronaviruses belonging to the BetaCoV genus had earlier been reported in bats and camels in Nigeria indicating the possibility of sero-protection in exposed populations. CONCLUSIONS: pre-laboratory drills prompted early diagnosis and confirmation of SARS-CoV-2 index case in Nigeria initiating rapid case-definition, contact tracing, and successful epidemiological management of the outbreak. Rapid sequencing of the viral genome during strategic points of the outbreak curve and making libraries of new variants for improved vaccine development are recommended.

Implementing an Iterative and Collaborative Approach to Inclusive First-Semester General Chemistry Laboratory Redesign

General chemistry laboratory curriculum reform is underway at a midsized state university through a collaborative, inclusive, and iterative approach. Using a backward design approach, faculty collaborated to actualize a shared vision, define laboratory learning objectives, and outline considerations for inclusivity during summer workshops that guided the process of curriculum design. With support from an instructional designer from the Center for Innovative Teaching and Learning, as well as faculty development support through an HHMI Inclusive Excellence grant, the faculty have designed and implemented the new curriculum, assessed the implementation, and continue to make iterative change based on student data and reflection. The goal of this report is not to provide a new set of chemistry laboratories, rather, we share our framework to provide an example of how to implement a collaborative and inclusive laboratory redesign.

Balance-Of-Plant Computerized Operator Support System Implementation

A Computerized Operator Support System (COSS) is an operator assistive technology suite that aids operators in monitoring processes to detect off-normal conditions, diagnose plant faults, predict future plant states, recommend mitigation alternatives, and select appropriate mitigative actions. A COSS human-machine interface (HMI) was developed at Idaho National Laboratory (INL) in collaboration with an advanced prognostics engine called PRO-AID, developed at Argonne National Laboratory (ANL). The front-end HMI coupled with the back-end prognostics provide fault prediction to inform operators of plant faults before they occur. Historically, COSS has been focused within the control room, representing systems that are monitored and controlled solely from a centralized location. This project, however, is focused on applying the principles of previous COSS efforts to a system outside the control room, namely the boric acid concentrator and liquid radwaste (BAC/LRW) system. This effort demonstrates the applicability and usability of a COSS system in a balance-of-plant environment, and offers next steps in the development of operator support and advanced overview interfaces in existing nuclear power-generating stations, and the future advanced reactor systems.

In Memoriam

In Memoriam

Developing high-performance DIRC detector for the future Electron Ion Collider experiment

The Electron-Ion Collider (EIC) will be the next frontier project of nuclear physics in the United States. It is planned to be built in the Brookhaven National Laboratory (BNL) in close collaboration with Jefferson Lab. One of the key requirement for the EIC central detector is excellent particle identification (PID). A detector using the Detection of Internally Reflected Cherenkov light (DIRC) principle, with a radial size of only 7–8 cm, is a very attractive solution for identification of the hadrons in the final state. The R&D program performed by the EIC PID collaboration (eRD14) is focused on designing a high-performance DIRC (hpDIRC) detector that would extend the momentum coverage well beyond the state-of-the-art 3 standard deviations or more separation of π/K up to 6 GeV/c, e/π up to 1.8 GeV/c, and p/K up to 10 GeV/c. Key components of the hpDIRC detector are a 3-layer compound lens and small pixel-size photo-sensors. This article describes the status of the high-performance DIRC R&D for the EIC detector, with a focus on efforts towards developing and validating the radiation hard 3-layer lens.

The Impact of Post-Analytical Tools on New York Screening for Krabbe Disease and Pompe Disease.

New York uses a two-tier assay to screen newborns for Krabbe disease and Pompe disease. Individual enzyme activities are measured in the first-tier, and specimens from newborns with low activity are reflexed to second tier Sanger sequencing of the associated gene. Using only this two-tiered approach, the screen positive and false positive rates were high. In this study, we added an additional step that examines the activity of four additional lysosomal enzymes. Results for all enzymes are integrated using the multivariate pattern recognition software called Collaborative Laboratory Integrated Reports (CLIR) to assess the risk for disease. Results after one year of screening using the new algorithm are compared to the prior year of screening without consideration of the additional enzymes and use of CLIR. With CLIR the number of babies referred for Krabbe disease was reduced by almost 80% (from 48 to 10) and the number of babies referred for Pompe disease was reduced by almost 32% (22 to 15).

The Clinical Impact of CLIR Tools toward Rapid Resolution of Post-Newborn Screening Confirmatory Testing for X-Linked Adrenoleukodystrophy in California.

Since the start of X-linked adrenoleukodystrophy (ALD) newborn screening in California, more than half of the diagnosed cases were found to have an ATP binding cassette subfamily D member 1 (ABCD1) gene variant of uncertain significance (VUS). To determine retrospectively the likelihood that these were true positive cases, we used a web-based post-analytical tool in Collaborative Laboratory Integrated Reports (CLIR). Confirmatory plasma very long-chain fatty-acids (VLCFA) profiles for ALD screen positive infant boys were run through the CLIR ALD tool. We compared the distribution by ABCD1 variant classification (pathogenic, likely pathogenic, VUS, and no variant) with the CLIR tool score interpretation (non-informative, possibly ALD, likely ALD, and very likely ALD) and the current case diagnosis. The study showed that CLIR tool positive interpretations were consistent with 100% of the pathogenic and likely pathogenic variants on the ABCD1 gene if a more conservative guideline was used. The tool interpretations were also consistent with screened cases that were determined to not have disease (our no-disorder group). The CLIR tool identified 19 diagnosed ALD cases with VUS to be potential false positives, representing a 40% reduction among all diagnosed ALD cases with VUS. The reduction could be extended to 65% if a more aggressive threshold was used. Identifying such preventable false positives could alleviate the follow-up burden for patients, their families, and California Special Care Centers.

ManitobaSat-1: A Novel Approach for Technology Advancement

ManitobaSat-1 is a 3U CubeSat program that is determined to advance the edges of space technology by performing things differently from traditional design strategies (see Fig.1). This will enhance access to space through novel technology development and verification and enable smaller companies to benefit from satellite services. ManitobaSat-1 is being developed at the University of Manitoba by the Space Technologies and Advanced Research Laboratory (STARLab) in collaboration with the Center for Terrestrial and Planetary Exploration at the University of Winnipeg, York University, the Interlake School Division, and Magellan Aerospace, our industrial partner.

Performance of Expanded Newborn Screening in Norway Supported by Post-Analytical Bioinformatics Tools and Rapid Second-Tier DNA Analyses.

In 2012, the Norwegian newborn screening program (NBS) was expanded (eNBS) from screening for two diseases to that for 23 diseases (20 inborn errors of metabolism, IEMs) and again in 2018, to include a total of 25 conditions (21 IEMs). Between 1 March 2012 and 29 February 2020, 461,369 newborns were screened for 20 IEMs in addition to phenylketonuria (PKU). Excluding PKU, there were 75 true-positive (TP) (1:6151) and 107 (1:4311) false-positive IEM cases. Twenty-one percent of the TP cases were symptomatic at the time of the NBS results, but in two-thirds, the screening result directed the exact diagnosis. Eighty-two percent of the TP cases had good health outcomes, evaluated in 2020. The yearly positive predictive value was increased from 26% to 54% by the use of the Region 4 Stork post-analytical interpretive tool (R4S)/Collaborative Laboratory Integrated Reports 2.0 (CLIR), second-tier biochemical testing and genetic confirmation using DNA extracted from the original dried blood spots. The incidence of IEMs increased by 46% after eNBS was introduced, predominantly due to the finding of attenuated phenotypes. The next step is defining which newborns would truly benefit from screening at the milder end of the disease spectrum. This will require coordinated international collaboration, including proper case definitions and outcome studies.

Hiroshima University: KOBELCO Construction Machinery Dream-Driven Co-Creation Research Center

On April 1, 2018, Hiroshima University instituted the “Joint Research with External Organizations (Private Sector, etc.).” The first project was the “KOBELCO Construction Machinery Dream-Driven Co-Creation Research Center (DDCC Research Center).” This research center has three collaborative research laboratories, and eight joint-research studies are in progress. With the aim of developing a hydraulic excavator that is human-friendly and human-nurturing, the research and development focuses on controls that (i) work as the operator expects and (ii) create value that facilitates growth of the operator. This article gives an overview of how the research center was established and what the research center studies and develops.

SCULPTURE3D, du projet de laboratoire à l’exposition numérique

The SCULPTURE3D research project is a collaborative and multidisciplinary laboratory experiment financed by the Centre-Val de Loire region between 2014 and 2018, which aims to explore what 3D brings to the study of sculpture and to interpret the region’s heritage of sculptures from the Renaissance Era. It is an association between researchers from the University of Tours, working with the Centre d’etudes superieures de la Renaissance (CESR) and with the Fundamental and Applied Computer Science of Tours (LIFAT), and various heritage institutions (DRAC Centre, Museum of Fine Arts of Tours, CMN, Château de Blois…) as well as a team of experts on innovative softwares (CETU ILIAD3), and the new small business Kulturae’com, two innovative entities who got their start through that project. The thirty digital objects created with the help of a 3D optical scanner is the first key part of a virtual museum of 3D sculptures from the Renaissance Era in the Val de Loire, intended both for researchers and the general public. Similarly, the Sculpturoscope, la Vierge a l’Enfant du reel au virtuel meta-exposition (at the Museum of Fine Arts of Tours, from May 25th to September 10th 2018) made the results of scientific research available to the general public by using digital medias as both a tool of investigation and mediation.

Assessment of Iodine Status in Iranian Students Aged 8-10 Years: Monitoring the National Program for the Prevention and Control of Iodine Deficiency Disorders in 2016

Iodine is a key element in the synthesis of thyroid hormones. The deficiency of the secretion of them will Reduce IQ, disturbance in the psychomotor growth and shortened height. Urinary iodine is a good indicator of iodine intake status. Urinary iodine status in at-risk groups is one of the most important indicators of community status. All 56 universities/medical faculties in Iran should determine and report median urinary iodine and its relative distribution in school children aged 8 to 10 yr, to determine the status of urine output. The sample size in each university/college is 240 students and the cluster sampling method (48 clusters in each area in 2016) and based on probability Measurement. The amount of urinary iodine was measured quantitatively by acid digestion. The mean urinary iodine excretion was estimated at 18.61 μg/dl. The median urinary iodine concentration in 52 universities was sufficient, and the national mean of urinary iodine excretion rate was 19.3 μg/dl. The iodine status was estimated in the optimal range in 65.6% of the students and in only 4.7% in the range of moderate and severe deficits, based on the urinary iodine index. Iodine is sufficient in most parts of the country. The implementation of the country's national program for the prevention and control of iodine deficiency disorders has made more important the quality control of the collaborative laboratories of this program than before. Moreover, it is absolutely essential to avoid excessive iodine in order to prevent possible side effects.

Collaborative AI and Laboratory Medicine integration in precision cardiovascular medicine

Artificial Intelligence (AI) is a broad term that combines computation with sophisticated mathematical models and in turn allows the development of complex algorithms which are capable to simulate human intelligence such as problem solving and learning. It is devised to promote a significant paradigm shift in the most diverse areas of medical knowledge. On the other hand, Cardiology is a vast field dealing with diseases relating to the heart, the circulatory system, and includes coronary heart disease, cerebrovascular disease, rheumatic heart disease and other conditions. AI has emerged as a promising tool in cardiovascular medicine which is aimed in augmenting the effectiveness of the cardiologist and to extend better quality to patients. It has the ability to support decision‑making and improve diagnostic and prognostic performance. Attempt has also been made to explore novel genotypes and phenotypes in existing cardiovascular diseases, improve the quality of patient care, to enablecost-effectiveness with reducereadmissionand mortality rates. Our review addresses the integration of AI and laboratory medicine as an accelerator of personalization care associated with the precision and the need of value creation services in cardiovascular medicine.

A Comparative Effectiveness Study of Newborn Screening Methods for Four Lysosomal Storage Disorders.

Newborn screening for one or more lysosomal disorders has been implemented in several US states, Japan and Taiwan by multiplexed enzyme assays using either tandem mass spectrometry or digital microfluidics. Another multiplex assay making use of immunocapture technology has also been proposed. To investigate the potential variability in performance of these analytical approaches, we implemented three high-throughput screening assays for the simultaneous screening for four lysosomal disorders: Fabry disease, Gaucher disease, mucopolysaccharidosis type I, and Pompe disease. These assays were tested in a prospective comparative effectiveness study using nearly 100,000 residual newborn dried blood spot specimens. In addition, 2nd tier enzyme assays and confirmatory molecular genetic testing were employed. Post-analytical interpretive tools were created using the software Collaborative Laboratory Integrated Reports (CLIR) to determine its ability to improve the performance of each assay vs. the traditional result interpretation based on analyte-specific reference ranges and cutoffs. This study showed that all three platforms have high sensitivity, and the application of CLIR tools markedly improves the performance of each platform while reducing the need for 2nd tier testing by 66% to 95%. Moreover, the addition of disease-specific biochemical 2nd tier tests ensures the lowest false positive rates and the highest positive predictive values for any platform.

Expanded Screening of One Million Swedish Babies with R4S and CLIR for Post-Analytical Evaluation of Data.

Sweden has one neonatal screening laboratory, receiving 115 to 120 thousand samples per year. Among the one million babies screened by tandem mass spectrometry from November 2010 until July 2019, a total of 665 babies were recalled and 311 verified as having one of the diseases screened for with this methodology, giving a positive predictive value (PPV) of 47% and an incidence of 1:3200. The PPV was high (41%) already in the first year after start of screening, thanks to the availability of the collaborative project Region 4 Stork database. The PPV is presently 58%. This improvement was achieved by the implementation of second-tier analyses in the screening for methylmalonic aciduria, propionic aciduria, isovaleric aciduria, and homocystinuria, and the employment of various post analytical tools of the Region 4 Stork, and its successor the collaborative laboratory integrated reports.

Trauma Teams That Train as One Work as One: Invasive Procedure Training in Residency Education

Invasive surgical procedures occur infrequently in an emergency department setting; however, procedural competence is expected from trauma residents. Emergent procedures are challenging to train in a formal manner because of the urgent nature when they present. To supplement education, new and creative teaching tools such as simulation and multidisciplinary training are being used. Our study organized a multidisciplinary simulated learning workshop with surgery and emergency medicine residents for invasive, emergent procedures. In total, 14 surgical and 36 emergency medicine residents at our institution participated in a simulated learning experience. Ten workshops were organized, with six to seven residents participating in each session. Using a human cadaveric model, all residents were taught by senior-level residents and attendings from both specialties on how to perform uncommonly or anatomically challenging emergent invasive procedures. A pre- and post-laboratory survey was completed by all the residents to assess confidence in performing each of the 13 procedures. All residents (N = 50), who participated in the study, completed pre- and post-laboratory surveys. Comparison of the pre- and post-laboratory confidence levels indicated significant increases in confidence in performing all procedures. Residents stated that this multidisciplinary approach to education in a controlled setting was helpful and fostered a collaborative relationship between both specialties. Although some surgical procedures remain uncommon in the emergency department, competency is nevertheless expected for appropriate patient care. Using a collaborative simulation-based cadaver laboratory to teach emergent procedures significantly improved residents' confidence while concurrently fostering professional relationships.

Evaluation of 11 years of newborn screening for maple syrup urine disease in the Netherlands and a systematic review of the literature: Strategies for optimization.

Maple syrup urine disease (MSUD) leads to severe neurological deterioration unless diagnosed early and treated immediately. We have evaluated the effectiveness of 11 years of MSUD newborn screening (NBS) in the Netherlands (screening >72 hours, referral if both total leucine (Xle) and valine ≥400 μmol/L blood) and have explored possibilities for improvement by combining our data with a systematic literature review and data from Collaborative Laboratory Integrated Reports (CLIR). Dutch MSUD NBS characteristics and accuracy were determined. The hypothetical referral numbers in the Dutch population of additional screening markers suggested by CLIR were calculated. In a systematic review, articles reporting NBS leucine concentrations of confirmed patients were included. Our data showed that NBS of 1 963 465 newborns identified 4 MSUD patients and led to 118 false‐positive referrals (PPV 3.28%; incidence 1:491 000 newborns). In literature, leucine is the preferred NBS parameter. Total leucine (Xle) concentrations (mass‐spectrometry) of 53 detected and 8 false‐negative patients (sampling age within 25 hours in 3 patients) reported in literature ranged from 288 to 3376 (median 900) and 42 to 325 (median 209) μmol/L blood respectively. CLIR showed increasing Xle concentrations with sampling age and early NBS sampling and milder variant MSUD phenotypes with (nearly) normal biochemical profiles are causes of false‐negative NBS results. We evaluated the effect of additional screening markers and established the Xle/phenylalanine ratio as a promising additional marker ratio for increasing the PPV, while maintaining high sensitivity in the Dutch MSUD NBS.

Efficient Photonic Beamforming System Incorporating a Unique Featured Tunable Chirped Fiber Bragg Grating for Application Extended to the Ku-Band

This article demonstrates a photonic-based wideband true-time delay (TTD) beamforming network employing a raised cosine apodized linearly chirped fiber Bragg grating (FBG) of varying lengths, such as $50\,\,{\times \,\,10^{-3}}$ m, $45\,\,{\times \,\,10^{-3}}$ m, $40\,\,{\times \,\,10^{-3}}$ m, and $35\,\,{\times \,\, 10^{-3}}$ m, and different chirp parameters $25\,\,{\times \,\, 10^{-9}}$ m, $35\,\,{\times \,\, 10^{-9}}$ m, $6\,\,{\times \,\, 10^{-8}}$ m, and $8{\,\,\times \,\,10^{-8}}$ m. The proposed scheme can be used as variable TTD lines having a much lower ripple factor compared with the previously studied apodized linearly CFBG for controlling the radiation angle of phased-array antenna (PAA), i.e., the main lobe radiated by the PAA can be steered squint-free from 0° to ±36.8° suitable for continuous beam forming at microwave frequencies 8–12 GHz extended up to Ku-band. To the best of our knowledge, this is the first experimental demonstration that shows the impact of tuning wavelength on delay change due to raised cosine apodized CFBG in the RF signal fed to the respective element of the antenna array. Four sets of $1\times4$ PAAs have been fabricated with the required electrical parameters, such as reflection coefficient ( $S_{11}$ ), voltage standing wave ratio, gain, far-field radiation pattern, and so on, to show the photonic feed idea. In addition, FBG’s having raised cosine apodization function is fabricated in our collaborative laboratory.

Dramatizing Ethnographic Fieldwork. Collaborative Laboratory and the Act of Intervening

What does it mean when an ethnographer intervenes in the public sphere or when a dramaturgist or theatre director conducts ethnographic research? What are the possibilities and values of such collaboration, and how it might be turned into engaged activities? In the following article, we attempt to answer these questions drawing from our pedagogical experience resulted from a joint effort of running and supervising a collaborative laboratory. For a year, groups of students (anthropologists, dramaturgists and theatre directors) jointly conceptualised, problematised and worked on the project about different masculinities. Throughout the project, all of us have been discussing, negotiating and exchanging our research methods, strategies and ways of exploring social practices by combining ethnography and performative. The outcome included thirteen interventions, understood as immediate social actions performed in the public space. The article aim is to engage with our teaching experiences and collaborative research efforts critically, as well as to problematise the real potential of the drama-based approach to ethnographic research. We argue that the form of collaboration between ethnography and performative arts opens not only new possibilities in methodological and pedagogical approach but also has transformative potential. The interventions performed in the public sphere might be understood as new modalities for disseminating research findings, which distort rather static and normative protocols of academic research presentations in Poland. They also allow reaching broader audiences and enabling more critical, intimate and involved understanding of different social and cultural practices.

Using NMR Spectroscopy and Chemical Synthesis to Establish Diastereoselectivity of NaBH4 and Meerwein–Ponndorf–Verley (MPV) Reduction of (±)-Benzoin Isopropyl Ether: A Collaborative Discovery-Based Laboratory Experiment

A discovery-based undergraduate organic chemistry lab experiment has been developed in which students establish the diastereoselectivity of hydride reduction of the α-chiral ketone (±)-benzoin isop...