Specimen Collection Research Articles

A-085 Comparing CO2 stability in patient samples and proficiency testing material

Abstract Background Total carbon dioxide (tCO2) measurements are important in the assessment of acid-base disorders. The collection and storage conditions of specimens are important preanalytical factors that can influence the accuracy of tCO2 measurements. Proficiency testing (PT) materials are used to assess the accuracy and reliability of a laboratory’s test performance. Unsuccessful performance on PT challenges can be an indicator of procedural issues. However, the stability of tCO2 in PT material compared to physiologic specimens is unknown and no guidance is provided to laboratories on how to handle PT samples for tCO2 measurement. This study aims to compare tCO2 stability in PT material with that of plasma samples when exposed to ambient air at room temperature. Methods Using enzymatic endpoint measurement on Vitros 4600 Chemistry System, tCO2 was measured in PT material (n = 5) and patient samples (n = 6) at baseline and after exposure to air for 15, 30, 60, 90, and 120 minutes. 500μL of each sample was aliquoted into EZ-nest tube adapters and baseline measurements were immediately analyzed. Average percent difference from baseline was calculated and >-10% bias was considered acceptable. Results The average percent difference from baseline in PT samples exceeded -10% as early as 30 minutes; whereas -3% bias was observed in patient samples at 60 minutes. Results are summarized in the table below. Conclusions The assessment of tCO2 stability ensures the reliability of laboratory measurements. Our results indicate tCO2 in PT material is not stable when exposed to air beyond 15 minutes, however tCO2 in most patient samples remained stable beyond 120 minutes. Understanding the stability limits of tCO2 in PT material allows us to devise workflows that prevent sample degradation during PT events. By establishing best practices for maintaining tCO2 integrity in PT material, laboratories can enhance the accuracy of proficiency testing results.

A-145 Are EDTA and Citrate Collection Devices Interchangeable for Estimating Blood Platelets Values using Sysmex XN™Analyzers ?

Abstract Background In the Sentara Healthcare System patient blood platelets are estimated using Sysmex XN™ analyzers. The blood specimens are collected in devices with EDTA anticoagulant. In the Emergency Departments, upon the first assessment of a patient a number of collection devices, including one with Na citrate anticoagulant, are obtained in case repeated testing is required. To prevent the collection of an additional EDTA device we investigated whether devices with Na citrate anticoagulant could be used interchangeably with EDTA devices for platelets values estimation. Methods Instruments: Sixteen Sysmex XN analyzers (Siemens) located in several institutions. Specimens: Seven-hundred nighty-eight patient blood specimens were obtained with both EDTA and citrate BD™ collection devices. The specimens, platelets numbers between 5000 and 800,000 platelets/mcL, were assayed in parallel within two minutes, after receipt in the laboratory, and then at intervals to reach 20 hours. The data were transferred electronically to Minitab® (version 21, Minitab Inc) statistical software. The paired data were analyzed with orthogonal, ordinary least squares (OLS), weighted polynomial ordinary least squares (WPOLS) and locally weighted scatterplot smoother (lowess) regression models and their graphic representations. The CLIA’s total error criterion (target value ± 25%) was used for evaluating acceptable variability. Results The parallel box plot of the differences between specimens as obtained with EDTA and those as obtained with Na citrate, showed that the distribution of the differences was similar between instruments and within the allowable total error of ± 25%. The orthogonal and the OLS models showed similar regression lines (Orthogonal: Y=3.3+0.94X: OLS: Y=-1+0.93X) and increase in variance for increasing platelets values. Consequently, a WPOLS model was employed for additional analyses. The ANOVA table of the WPOLS showed that there were no probabilistically significant differences between regression lines for either platelet’s values (P = 0.5) or specimen age (P = 0.1). Tridimensional surface plots clearly illustrated that the differences were distributed within -12.5% and the zero lines. The aptness of the WPOLS model was demonstrated by the standardized residual (std. res.) analysis showing quasi-normal distribution, with a few outliers (std. res. > |3|) and two influential observations for (Hi > 0.5) which were for platelets values less than 10,000 platelets/mcL. Conclusions The differences between EDTA and citrated specimens were within zero and -12.5%, this represented half of the CLIA’s criterion. The weighted polynomial regression model was employed due to the heteroscedasticity of the variance, The simultaneous evaluation by platelets values and the age of the specimen did not detect probabilistically significant differences by either platelets values or age of the specimen. This limited study suggested that EDTA and citrate anticoagulated specimens may be used interchangeably for patient care for specimens with platelets values between 10,000 and 800,000/mcL and within twenty hours from collection. However, the limited number of patients precluded to evaluate whether the detected outliers represented group(s) of patients with a particular medical condition and or pharmacotherapeutic treatment. Finally, the electronic collection and transfer of specimens to statistical software, such as Minitab, was crucial for performing this study.

B-013 Improving the Workflow of Blood and Coagulation Tests in clinical laboratory through the Utilization of Laboratory Automation Track Systems

Abstract Background The Laboratory Automation Track System (TLA) is an automated system designed for executing highly repetitive tasks within a laboratory, commonly applied in biochemical and immunological testing systems. It aims to reduce human errors in specimen handling, enhance the overall process quality, and provide better Turnaround Time (TAT) from specimen collection to result reporting. For the first time in our laboratory, we have integrated the blood and coagulation systems with TLA. Consequently, we seek to evaluate the differences in the testing workflow and reporting efficiency of the blood and coagulation systems after being connected to TLA. Methods Abbott GLP systems Track was the TLA system for connecting with blood and coagulation systems. Two Sysmex XN-9100 fully automatic hematology systems and two Sysmex CS-5100 fully automatic coagulation analyzers were developed for blood and coagulation system, respectively. TUNYEN Laboratory Information System was established for Laboratory information system (LIS). Results Through the analysis of quality indicators and integration with intelligent information systems, improvements have been made, including the reduction of blood collection tube usage, efficient manpower utilization management, tracking of specimen progress and achievement of timely reporting rates.(1)Approximately 2,915 blood collection test tubes are saved every month, with a converted cost of 0.15 USD per tube, and a total saving of 437 USD. And reduce the carbon emissions of 32 kgCO2e, comply with the spirit of ESG sustainable development.(2)The TLA no longer requires staff to collect and deliver specimens as in the past,reducing staff and enhancing work efficiency.One of manpower was saved and new inspection items were developed.(3)Tracking of specimen progress:The laboratory has set up a specimen tracking system to monitor the specimen delivery location and provide timely response to the clinical status.The one-hour TAT for blood and coagulation increased from 82.0% and 76.9% before improvement to 91.8% and 93.3% after improvement respectively. Conclusions The implementation of Laboratory Automation Track Systems (TLA) leads to a reduction in medical errors and specimen sample volume, while also enhancing accuracy and precision, thereby improving the safety of laboratory staff. Although the introduction of TLA may require an initial investment, it brings the benefits of automation, offering ease and efficiency to laboratory processes.

A-324 Performance and Turnaround Time of Plasma Lactate Assay on POCT, Blood Gas Instrument, and Chemistry Analyzer

Abstract Background Time is a critical factor of plasma lactate testing in the management of patients with sepsis. To best serve these patients, we must optimize testing methods to provide a turnaround time (TAT) that guides efficient patient care. Point of care tests (POCTs) provide rapid results for emergency department and medical intensive care unit but are not feasible for all hospital settings. Laboratory testing methods on an automation line provide greater efficiency but result slowly due to need of specimen preparation and longer analytical time. The goal of this study is to provide detailed TATs of plasma lactate testing among the methods of POCT, chemistry analyzer in an automation line, and blood gas analyzer. Methods Plasma lactate testing was performed by three methods, GEM Premier ChemSTAT (POCT in ER only), Beckman AU5800 (chemistry analyzer), and Radiometer ABL800 (blood gas instrument). The TAT of lactate for each method was measured and include the time from specimen collection to laboratory receipt (except for POCT method), and time from specimen receipt to resulting (including specimen preparation for Beckman AU5800). Results The average TATs of lactate testing for each method in all hospital sites are detailed with respect to each event and subcategorized (Table 1). The average TAT of 12.0 min on Radiometer ABL800 is higher than the TAT of 2.5 on GEM Premier ChemSTAT method but is greatly reduced compared to the TAT of 35.4 min on Beckman AU5800. Conclusions Radiometer ABL800 method could be the optimal laboratory method for plasma lactate testing fulfilling the TAT (average 12 min), with less test cancellation due to specimen stability issue, and combines testing with blood gases. Using three Radiometer ABL800 instruments, we manage the performance of around 70 plasma lactate tests daily.

A-317 Development of a patient-focused volumetric absorptive microsampling strategy to assess urinary amino acid excretion

Abstract Background Biochemical determinations of urinary amino acid excretion patterns can diagnose specific inborn errors of metabolism (IEM). Clinical management of these genetic metabolic patients may require frequent urine amino acid tests. A simplified process for transporting home collected urine specimens would benefit the IEM community. Volumetric absorptive microsampling (VAMS) is an emergent alternative sampling technique for the collection of dried biological specimens. We describe the development and preliminary validation results of a VAMS strategy for the analysis of creatinine and amino acids (N=22) from microsampled dried urine. Methods Urine creatinine and amino acids were respectively measured in a clinical laboratory setting using established assays on a CobasPro (Roche) and a MassTrak ultra-performance liquid chromatography (UPLC) amino acid analysis (AAA) solution (Waters). Two 30 µL VAMS tips from a Mitra device (Neoteryx) were used to sample each random urine specimen. An ultrasonication-based solvent extraction procedure was optimized to extract the amino acids and creatinine from the VAMS tips. Solvent extracts were subsequently dried by centrifugal evaporation. Extract from one tip was re-dissolved in water and tested for creatinine using an enzymatic method. The other extract was re-dissolved in 0.02 N sodium hydroxide and tested according to the MassTrak AAA procedure, which deploys pre-column AccQTag derivatization with reversed-phase UPLC on a C18 column (2.1 × 150 mm; 1.7 µm) and UV detection at 260 nm. Accuracy, within-batch precision and short-term stability of the optimized VAMS protocol were determined. Results Extraction solvent with a 60:40 (v/v) water:methanol mixture provided the highest average amino acid recovery. This extraction solvent produced higher average amino acid recoveries at pH 11 (89±13%), than pH 3 (82±10%) or pH 7 (72±11%). Creatinine measured from the VAMS tips (N=44) had a consistent negative bias of 20% relative to neat urine (R=0.9905, slope=0.802, intercept=0.02). The creatinine corrected urine amino acid results from the Mitra device were corrected for this observed concentration bias. The accuracy of the amino acid results derived from the VAMS tip vs neat urine was 104 ± 14%. The average within-batch precision (CV%) of the amino acids was 9.8% (range=6.7% (cystine) to 17.6% (arginine)) and 6.2% for creatinine. The average 1 week storage stability at ambient temperature was 91% (range=73% (ornithine) to 107% (glycine)) for the amino acids and 107% for creatinine. The devised VAMS strategy was applied to the analysis of microsampled dried urine from a patient with cystinuria (OMIM no. 220100). Marked elevations in arginine, cystine, lysine and ornithine were respectively observed and are consistent with the biochemical diagnosis of the patient. Conclusions Creatinine corrected amino acid results from the devised VAMS strategy exhibit good precision and accuracy when compared to tradition analyses of neat urine. The potential use of microsampled dried urine for the diagnosis and monitoring of selected IEM has been demonstrated. The analytical and clinical performance of this VAMS protocol must be further validated, including the use of microsampled dried urine from home specimen collections.

The utility of disc space and vertebral body specimens cell count differential for the diagnosis of native vertebral osteomyelitis: a prospective cohort study.

Diagnostic methods for native vertebral osteomyelitis (NVO) often yield inconclusive results. Image-guided spine biopsies for culture are specific but diagnose NVO in only 50% of cases. Pre-exposure to antimicrobials further reduces diagnostic yield. Our study assesses the value of neutrophil percentage in disc space fluid and vertebral body (DS/VB) samples for diagnosing NVO. Adults referred for spine biopsy at Mayo Clinic from August 2022 to September 2023 were consented and enrolled at the time of biopsy. Following routine specimen collection, the biopsy needle was rinsed in saline into an EDTA tube for cell analysis. NVO diagnosis required organism identification in spine tissue or blood and/or positive histopathology, and consistent symptoms and imaging. Sixty-eight patients were prospectively enrolled, comprising 14 with NVO and 54 with alternative diagnoses. The median biopsy sample polymorphonuclear (PMN) percentage for NVO patients was 80.5% (IQR 72.5-85.2), compared to 64.5% (IQR 54.0-69.0) for those without NVO (p < 0.001). Nine (64.3%) NVO patients received antibiotics within 10 days prior to spine biopsy. As a continuous measure, PMN differential showed a moderately strong ability in classifying NVO status with an area under ROC curve of 0.795; an optimal point on the curve of 71.5% corresponded to a sensitivity of 78.6%, specificity of 79.6%, negative predictive value of 93.5% and positive predictive value of 50.0%. PMN differential in DS/VB biopsies may serve as an effective diagnostic tool in the evaluation of patients with NVO particularly in ambiguous cases with an initially negative spine biopsy. Future efforts will aim to implement these findings within routine clinical practice.

Ticks and tick-borne pathogens in ruminant farms of Peninsular Malaysia: First molecular evidence of Borrelia theileri in Rhipicephalus microplus (Acari: Ixodidae).

To shed light on the importance of tick-borne diseases, especially in farm animals that often contact with farm workers, this study aimed to identify ticks and tick-borne pathogens in ruminants in Malaysia. Accordingly, specimen collection was conducted across Peninsular Malaysia yielded a total of 1241 ticks collected from 674 farm ruminants. Among these, four tick species were identified, with Rhipicephalus microplus being the most prevalent, constituting 99.03 % of the total tick population. Analysis of 130 tick pools revealed three positives for Borrelia. BLAST analyses of the flaB and 16S rRNA genes revealed high similarities to Borrelia theileri, ranging from 98.78 to 100 % for flaB and 99.23–99.45 % for 16S rRNA. These results align with the phylogenetic trees, where sequences from both genes clustered together with B. theileri, further supporting this identification. No Rickettsia and Bartonella bacteria were detected. This study represents the first occurrence of B. theileri in R. microplus in Malaysia.

Improving the OncotypeDX ordering process in patients with ER+ HER2- early-stage breast cancer: A longitudinal QI project.

292 Background: Use of the 21-gene recurrence score assay, OncotypeDX, is an NCCN category 1 recommendation to define adjuvant treatment planning for patients with hormone receptor positive (HR+), HER2 negative (HER2-) early-stage breast cancer. The assay is a key part of the decision-making process to define who may benefit from adjuvant chemotherapy with delays in testing that may impact patient care and loss of trust between oncologists and patients. Methods: We first created a comprehensive process map of the system in place to order OncotypeDX and met with an interdisciplinary team to determine the best area of intervention. A nurse coordinator from medical oncology took over OncotypeDX ordering in September 2023. To determine impact, we obtained data on OncotypeDX orders (N=473) sent by medical oncologists at Washington University in St. Louis between 9/2022 and 4/2024. We determined the delay between specimen collection and OncotypeDX order and the time from order to delivery of the report in the electronic medical record system. We then assessed our outcome measure, the date of the first office visit after surgery and whether patients had an OncotypeDX test result at that visit for 270 consecutive orders spanning pre- and post-intervention (6/2023 – 4/2024). Results: We used a p-chart to assess our outcome measure of OncotypeDX availability at the time of office visit with medical oncology, a key metric for both treatment planning and patient trust. We observed a positive trend of seven data points in the most recent data when mapping the 270 patients by consecutive groups of 10. In our most recent data pull from April 2024, 85% (22/26) of patients who required an OncotypeDX had one completed at the time of office visit, in comparison to 50% (20/40) in August 2023, the month prior to the intervention. We used XmR and S charts to determine impact on delay from specimen collection to OncotypeDX order, which showed increased precision and a trend of decreased delay after implementing the nurse coordinator. The overall delay decreased from an average of 28 days pre-intervention (9/2022-9/2023) to 24 days in the most recent post-intervention data (3/2024). Average time between order and delivery, our balancing measure, decreased during these time periods from 16 days to 13 days. Conclusions: Implementing a nurse coordinator improved delays in specimen collection to order and order to receipt. This intervention increased the percentage of patients who had an OncotypeDX result at the time of office visit with medical oncology after surgery.

Acute Hematogenous Osteomyelitis in Pediatric Patients.

This article focuses on the advancements made in diagnostic techniques and drug interventions of acute hematogenous osteomyelitis. A diagnosis necessitates a combination of factors, including inflammatory markers and imaging findings, as well as the collection of specimens for culture when feasible. Subsequently, treatment should be based on epidemiology, mechanisms of resistance, and susceptibility findings. A brief course of intravenous (IV) antibiotics, followed by oral antibiotics, may be employed for uncomplicated infections if there is improvement in the clinical condition and a decline in C-reactive protein levels. However, for complex infections caused by methicillin-resistant Staphylococcus aureus, prolonged administration of IV antibiotics is recommended, along with surgical intervention if necessary. [Pediatr Ann. 2024;53(10):e392-e395.].

Prevalence of anal high-risk human papillomavirus (HR-HPV) types in people living with HIV and a history of cancer.

Referral tertiary care hospital for adult patients with cancer. We reviewed data of patients from the AIDS Cancer Clinic on antiretroviral therapy in chronic control who were consecutively referred for high-resolution anoscopy (HRA), where they underwent anal evaluation, collection of specimens for anal cytology and anal human papillomavirus (HPV) followed by HRA with directed biopsy if needed. A total of 155 patients were included; 149 (96.1%) were men, all of them men who have sex with men (MSM); the median age was 39 (IQR 32-47) years; 105 (67.7%) with Kaposi sarcoma, 40 (25.8%) with non-Hodgkin lymphoma and 10 (6.4%) with other neoplasms; only 7 (4.5%) had active cancer. The prevalence of HR-HPV infection was 89% (n=138) (95% CI 83-93) with at least one HR-HPV infection, and 62% (96) had coinfection with at least two types; the median HR-HPV types of coinfection were 3 (IQR 2-4). The number of patients infected with HPV 16 was 64 (41.3%, 95% CI 33.8-49.3), HPV 18 was 74 (47.7%, 95% CI 39.9-55.7) and with both 35 (22.6%). Some 59 patients (38%) had high-grade squamous intraepithelial lesions (HSIL) and 49 (31.6%) had low-grade squamous intraepithelial lesions (LSIL). The prevalence of HR-HPV and HSIL among patients aged ≤35 and >35 years was the same. In this cohort of PLWHIV with a history of malignancy we found a high prevalence of HR-HPV 16 and 18 and anal HSIL, even in persons aged ≤35 years. These data highlight the importance of anal cancer screening in PLWHIV and history of malignancy.

Tools, techniques, and challenges in preparing cytology specimens for ancillary studies: results of the ASC Optimizing Cytology and Small Biopsy Specimen Processing for Ancillary Studies Task Force survey

IntroductionAncillary testing on cytopathology and other small biopsy specimens is crucial for diagnosis and provides critical information to clinicians. Testing is dependent on pre-analytic factors and would benefit from standardization of specimen collection protocols across laboratories. To assess institutional practices and areas of need for evidence-based standards, we surveyed current practices across cytopathology laboratories. Materials and MethodsA twelve-question electronic survey was distributed to American Society of Cytopathology (ASC) members through email, social media, and the ASC from January 8th to March 1, 2024. Survey responses were tabulated. ResultsOf 294 respondents, 257 (87%) completed at least 10/12 questions. Formalin-fixed, paraffin-embedded cell blocks (CB) are utilized for immunohistochemistry, molecular testing, and in situ hybridization by 89%, 84%, and 71% of respondents, respectively. For fine needle aspirations, no collection medium is utilized by a majority of respondents. In contrast, 61% utilize no collection medium for fluids; 64% predominantly utilize liquid-based preservatives for other exfoliative specimens. For CB preparation, 58% of respondents use coagulating agent; 67% use no fixative before formalin. The two most significant factors limiting clinical utility of ancillary testing in cytology specimens are low cellularity and lack of validation (49% and 23% of respondents, respectively). ConclusionsThere is wide variation in current practices among laboratories, reflecting lack of consensus. Although laboratories utilize different collection media for different specimen types, for CB utilization, current survey results are similar to those reported previously. ASC has convened a task force to facilitate specimen standardization and minimize variability among pre-analytic factors.

Leveraging social media and community science data for environmental niche models: A case study with native Australian bees

Museum occurrence records are popular sources of information for creating Environmental Niche Models (ENMs), which allow the mapping of the potential niche ranges of species. Occurrence data is often downloaded en masse from established databases. However, the use of non-traditional data sources, such as occurrence records from community/citizen science outreach and social media, is increasing in use and abundance. Data from non-traditional data sources are potentially valuable records of information, particularly for species where museum occurrence records may be comparatively scarce. In the current study, we aimed to determine the impact of adding occurrence data from non-traditional databases to ENMs that were originally created using traditional databases with a group of comparatively understudied species, native Australian bees. We used the Maxent algorithm to model the potential environmental niches of eight species. We created three models for each species: 1) one consisting of only location data from museum specimen collection records from the Atlas of Living Australia (ALA) (a traditional database), 2) one combining ALA and geo-tagged social media (Flickr) data, and 3) a model combining ALA and geo-tagged community science data from iNaturalist. This resulted in 24 different models. By comparing the models produced from each of the augmented data sets with the traditional species data set (ALA vs. ALA & Flickr; ALA vs. ALA & iNaturalist) we showed that there were significant differences, not only in predicted ranges, but also in the weighting of environmental variables used by the models to predict the environmental niche. Differences were more greatly influenced by the geographic location of the extra occurrences rather than the number of additional occurrence points. We demonstrate the potential value and risks of including social media and community science geo-tagged image data in supplementing knowledge of species distributions, particularly for relatively under-sampled species such as native bees.

The 2030 Declaration on Scientific Plant and Fungal Collecting

Societal Impact StatementBiological samples and their associated information are an essential resource used by scientists, governments, policymakers, practitioners and communities to ensure that biodiversity can be appropriately protected and sustainably used. Yet, considering the enormous task of documenting the vast numbers of as‐yet‐unknown plant and fungal species, greater international coordination for biological collecting and recording is necessary, built on equitable collecting practices and standards. Here, we propose five commitments to accelerate and enhance scientific knowledge of plant and fungal diversity, while increasing collaboration, benefit sharing and efficiency.SummaryAlmost all life depends on plants and fungi, making knowledge of their diversity and distribution—primarily derived from biological collections—fundamental to national and international conservation, restoration and sustainable use commitments. However, it is estimated that some 15% of all plant species and over 90% of all fungal species have not yet been scientifically described, hampering our ability to assess and demonstrate the impact of efforts to halt biodiversity loss. In addition, organisations and researchers around the world lack a concerted strategy for increasing complementarity and avoiding overlap in botanical and mycological research, particularly in relation to the collection of specimens. We here present the 2030 Declaration on Scientific Plant and Fungal Collecting, summarising a commitment towards such a necessary strategy. Its components were identified from discussions during and after a series of four workshops and plenary discussions at the 2023 State of the World's Plants and Fungi symposium convened by the Royal Botanic Gardens, Kew, and were then consolidated into the present form by the authors. The Declaration was subsequently opened up for endorsement by signatories. Collectively, we agree on a set of five commitments for cataloguing the world's flora and funga, designed to maximise efficiency, facilitate knowledge exchange and promote equitable collaborations: (1) use evidence‐based collection strategies; (2) strengthen local capacity; (3) collaborate across taxa and disciplines; (4) collect for the future; and (5) share the benefits. This Declaration is a first step towards increased global and regional coordination of scientific collecting efforts.

Biobanking, digital health and privacy: the choices of 1410 volunteers and neurological patients regarding limitations on use of data and biological samples, return of results and sharing

BackgroundThe growing diffusion of artificial intelligence, data science and digital health has highlighted the role of collection of data and biological samples, thus raising legal and ethical concerns regarding its use and dissemination. Further, the expansion of biobanking, from the basic collection of frozen specimens to the virtual biobanks of specimens and associated data that exist today, has given a revolutionary potential on healthcare systems, particularly in the field of neurological diseases, due to the inaccessibility of central nervous system and the need of non-invasive investigation approaches. Informed Consent (IC) is considered mandatory in all research studies and specimen collections, and must specifically take into account the ethical respect to the individuals to whom the used biological material and data belong.MethodsWe evaluated the attitudes of patients with neurological diseases (NP) and healthy volunteers (HV) towards the donation of biological samples to a biobank for future research studies on neurological diseases, and limitations on the use of data, related to the requirements set by the General Data Protection Regulation (GDPR). The study involved a total of 1454 subjects, including 502 HVs and 952 NPs, recruited at Santa Lucia Foundation IRCCS, Rome, from 2020 to 2024.ResultsWe found that (i) almost all subjects agreed with the participation in biobanking (ii) and authorization to genetic studies (HV = 99.1%; NP = 98.3%); Regarding the return of results, (iii) we found a statistically significant difference between NP and HV, the latter preferring not to be informed of potential results (HV = 43%; NP = 11.3%; p < 0.0001); (iv) a small number limited the sharing inside European Union (EU) (HV = 4.6%; NP = 6.6%), whereas patients were more likely to refuse transfer outside EU (HV = 7.4%; NP = 10.7% p = 0.05); (v) nearly all patients agreed with the use of additional health data from EMR for research purposes (98.9%).ConclusionsConsent for the donation of material for research purposes is crucial for biobanking and biomedical research studies that use biological material of human origin. Here, we have shown that choices regarding participation in a neurological biobank can be different between HVs and NPs, even if the benefit for research and scientific progress is recognized. NP have a strong interest in being informed of possible results but limit sharing of samples, highlighting a perception of greater individual or relative benefit, while HV prefer a wide dissemination and sharing of data but not to have the return of the results, favoring a possible benefit for society and knowledge. The results underline the need to carefully manage biological material and data collected in biobanks, in compliance with the GDPR and the specific requests of donors.

Manually operated microtube automatic capper/decapper system for clinical laboratory and biological laboratory personnel

Polymerase chain reaction (PCR) is an effective method for diagnosing infectious diseases and has been the primary method throughout the novel coronavirus disease (COVID-19) pandemic. PCR tests (from specimen collection to result acquisition) involve sample pretreatment, nucleic acid extraction, and PCR procedure. Automating the pretreatment process is crucial to mitigate the risk of infection for workers and to reduce the likelihood of sample contamination-triggered misdiagnosis, particularly when handling centrifuge tubes, cryopreservation tubes, and microtubes. Robotic systems have been engineered to automate cell culture and PCR-based diagnosis, predominantly designed for use with screw-capped containers. However, this leaves a notable gap in automation solutions for microtubes equipped with press-type caps. To address this gap, we developed a versatile microtube capper/decapper system. On the other hand, many tasks of manual operation using microtubes, which are routinely conducted in clinical tests and biological experiments, are performed. Compared to screw-type caps for centrifuge and cryopreservation tubes, press-type caps for microtubes present a considerably higher risk of the worker's fingers contacting the inside of the cap and/or generating airborne droplets. Despite the risks of contamination and infection derived from the manual handling of microtube caps, which can compromise diagnosis/experiment accuracy and worker safety, devices for manually opening and closing microtube caps without direct contact remain lacking. Therefore, leveraging the technology from the developed versatile microtube capper/decapper system for laboratory automation, we created a manually operated microtube equipped with an automatic capper/decapper system tailored for personnel in clinical and biological laboratories.In this study, we first examined the required specifications and prerequisites for a manual microtube capper/decapper and clarified the operating methods, operating procedures, operation environment, device size, accompanying functions, etc. Based on the required specifications and preconditions, we proceeded with the mechanical and control design of the conceptual model, manufactured a prototype, and confirmed its basic functions and performance. The compliant to the required specifications and preconditions and the usefulness of the proposed manual microtube capper/decapper were validated through various experiments and demonstrations. Using the proposed microtube capper/decapper, even small-scale operations, which are challenging to streamline, can be performed nearly as efficiently as full manual operations. Although operation time was not reduced, the ability to open and close microtubes without manual contact is crucial for improving diagnostic and experimental accuracy and for reducing the burden on and enhancing the safety of laboratory personnel. Because microtubes are used in various clinical tests and biological experiments, we believe that the proposed system can markedly reduce the workload for personnel across numerous clinical and biological laboratories.

The Future of Referencing Specimens Is Near: Cite the Digital Specimen DOI

Specimens are often mentioned in scholarly publications or data infrastructures by referencing the local identifiers attached to the objects held in specimen collections. However, these are often only unique to the issuing institution and not resolvable. Transforming these into globally unique identifiers, such as the 'Darwin Core Triplet' constructed from codes that specify the institution, the collection and the accession or catalog number, is an imperfect solution. These cannot be unambiguously validated nor be dereferenced (Guralnick et al. 2015, Groom et al. 2019), are vulnerable to human error, and rely on accession numbers that sometimes change over time. Earlier approaches to give specimens globally unique and resolvable identifiers had limited success (Page 2009). Attaching labels with new identifiers is too costly and time consuming, apart from digital infrastructure challenges. The Digital Extended Specimen is a new object on the internet, containing all known information about the specimen, thus acting as a surrogate for the physical object. To distinguish it from its physical counterpart, it needs a new identifier, which also provides a solution to unambiguously and persistently refer to specimens. Digital specimens get Digital Object Identifiers (DOIs) and Persistent Identifiers, in the infrastructure developed in the BiCIKL project (see deliverable D7.1 and this blog post). Ties to these accession or catalog numbers of physical specimens, allow these local identifiers to change over time, while still persistently resolving to the digital object. DOIs guarantee global uniqueness, persistence and reliable resolution through the oversight of the DOI Foundation and its registration agencies (RAs). DiSSCo, Distributed System of Scientific Collections, is creating a partnership with DataCite RA, where both partners invest to provide Digital Specimen DOIs and enhance their findability, leveraging from their metadata services. This aids the potential of Digital Specimen DOIs to reliably create links with data in other infrastructures, cite individual specimens, and improve the FAIR-ness (Findable, Accessible, Interoperable, Reusable) of specimen data worldwide. We will present how to use these new DOIs in practice. The use of Digital Specimen DOIs in a publication to reference a specimen is already piloted (Deeleman-Reinhold et al. 2024). All specimen records cited in the publication have been assigned a DOI that points to a digital representation of the specimen, the Digital Specimen, which can evolve over time to become a digital extended specimen by digitally linking it to relevant ecological, environmental, and related data such as the publication itself. The DOIs redirect both to a machine readable and a human readable version and include metadata in the DOI record for machine actionability that is also findable in DataCite Commons. The Crosscite citation formatter offers guidance to users how to cite a Digital Specimen DOI, similar to DOIs that refer to other works.

Reevaluation of pollen differentiation in Altingiaceae: Challenges in distinguishing deciduous (Liquidambar) and evergreen (Altingia) types using multivariate statistics and machine learning

Altingiaceae, a family of woody plants, comprising evergreen Altingia and deciduous Liquidambar groups, exhibits distinct leaf morphology, yet both groups overlap in geographical range and climatic conditions. While some tropical Altingia species are confined to Myanmar, Thailand, Cambodia and India without Liquidambar, and some temperate Liquidambar species to northern China without Altingia. Their fossil pollen have significant implications in reconstructing palaeoclimate and historical biogeography, based on classification of Altingia-type and Liquidambar-type. However, the results of previous studies to differentiate pollen types of evergreen Altingia and deciduous Liquidambar were based on limited pollen specimens. Therefore pollen morphology of Altingiaceae and differentiation of above mentioned types needs reevaluation using more specimens from wider geographical range.In this study, we present new findings on Altingiaceae pollen morphology from extensive collection of specimens and reassess the diagnostic features to distinguish evergreen and deciduous types. To improve the credibility of palaeoecological and palaeoclimatic interpretations, we applied multivariate statistical analyses to pollen size, number of pores, pollen wall thickness, and size and density of ornamental elements from light microscopy (LM) and Scanning Electronic Microscope (SEM) images. Additionally, random forest classification models were applied to test the accuracy of differentiating Altingiaceae pollen types. Our results reveal significant morphological overlap between the pollen of evergreen Altingia and deciduous Liquidambar, with classification models showing limited accuracy and explainability. Thus, fossil pollen of Altingiaceae cannot be confidently classified into evergreen or deciduous types, highlighting challenges in using their pollen morphology for taxonomic classification in palaeoecological research.

Beyond 4 × 4: Paramotoring a novel approach to accelerate plant exploration in challenging environments

Societal Impact StatementAddressing the burning environmental crisis, we explore how the ‘extreme sport’ of paramotoring can enhance and accelerate scientific exploration with minimal environmental impact compared to off‐road vehicles. Our study demonstrates the scientific potential of paramotoring to access fragile desert ecosystems and investigate unrecorded habitats and species. Comparisons with 4 × 4s showed significant reductions in CO2‐eq emissions for longer missions and ninefold faster travel times. Unlike off‐road vehicles, which can damage the equivalent of over one football pitch in area per linear kilometre driven, paramotors cause minimal damage. Integrating extreme sports and science can accelerate data and specimen collection for more effective habitat conservation. This has the potential to spark discoveries and engagement across diverse communities.Summary In the face of an urgent climate and environmental crisis, we explore the potential of paramotoring to expand scientific reach and collection capability without the environmental harm associated with off‐road vehicles. In Peru's fog oasis desert, we brought together paramotor experts and scientists to conduct missions involving monitoring, plant sampling, surveying, sensor placement and transportation. We compared the environmental impact and time taken by paramotoring with surveys conducted using off‐road vehicles and walking. Shorter paramotor missions showed small differences in CO2 equivalents and time efficiency compared to off‐road vehicles. However, longer missions (28 km from base camp) revealed up to nine times faster travel and two thirds less CO2 equivalent emissions. Notably, off‐road vehicles left a substantial environmental footprint (700 to 8000 m2 per km), whilst paramotors had a minimal impact, with a tiny surface ‘footprint’ of just a few square metres, representing orders of magnitude (1000 to 10,000) less environmental impact. With basic training in identification and sampling, paramotorists collected plant specimens that are invaluable for ongoing and future scientific study. Whilst logistical and safety challenges in transporting scientists via paramotors need further investigation, the benefits, especially compared to surface travel, are evident. Integrating extreme sports into scientific endeavour promises wider and more comprehensive exploration, new discoveries and increased engagement across diverse communities—and in summary—offers significant potential to address urgent environmental challenges.

Abstract C172: Diversifying translational research models to address outcomes disparities in lung cancer

Abstract Introduction: Racial disparities in lung cancer remains a persistent and challenging problem, with African Americans experiencing the highest mortality of any race or ethnic group. Emerging evidence suggests that multiple biological factors affect the development and progression of lung cancer. Three-dimensional organoid culture models have become important instruments to use for biomarker analysis and drug sensitivity screening. Despite this strong rationale and potential, there is a lack of representative preclinical models from African American patients with lung cancer. Furthermore, there are no studies evaluating the ability to create organoids successfully using samples from different races. As such, our goal was to establish a diverse biobank of organoid models and determine the rate of successful development based on race and other factors. Methods: Patients with lung cancer from a large urban medical center were recruited to participate in the study from 2021 to 2024. Specimens were collected from surgical pulmonary resection or endobronchial biopsy. Each tissue specimen was divided into 3 pieces and allocated for genomic, transcriptomic and organoid development. Once collected, specimens allocated for organoid development were processed within 8 hours. Cells were isolated from tissues by mechanical and enzymatic dissociation and plated in Matrigel drops overlayed with optimized organoid media. Patient demographics, tumor characteristics and method of specimen collection were recorded. Results: A total of 29 patients consented to the study and had evaluable specimens collected. Mean age was 67 years. Fifty-five percent of patients (16/29) were female. White patients were 55 percent of cohort (16/29), while Black patients made up 45% (13/29). Approximately 62 (18/29) percent of patients were diagnosed with adenocarcinoma, followed by squamous cell carcinoma in 28 percent (8/29) of patients. Tumor stage was 55%, 28%, 3% and 14% for stages I, II, III and IV respectively. Overall, there was a successful organoid development rate of 69 percent (20/29). There was a strong trend toward higher success rates in Black patients compared to White patients (85% vs. 56%, p = 0.10). There were no significant differences in successful organoid development based on gender (p = 0.43), histology (p = 0.18) or tumor stage (p = 0.84). Conclusions: Establishment of a racially diverse set of organoid models will be an invaluable tool for biomarker discovery and for screening novel therapeutic agents. Black patients appear to have similar to improved propensity for successful organoid development. Future efforts should be focused on creating diverse biobanks to strengthen precision oncology efforts for Black patients, collectively helping to reduce racial outcomes disparities in patients with lung cancer. Citation Format: Amanda Pilling, Hollis Hutchings, Avi Cohen, Shirish Gadgeel, Ikenna Okereke. Diversifying translational research models to address outcomes disparities in lung cancer [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C172.

Preanalytical Errors in Hematology: Insights From a Tertiary Care Hospital.

Introduction Errors occur in the laboratory at any level of the testing process. Recognizing these errors may cause patient distress by delaying diagnosis and management until results are released. This study aims to assess preanalytical errors in the laboratory and suggests methods to prevent them to improve accuracy and efficiency in the hematology department of a tertiary care hospital. The background emphasizes the critical role of preanalytical procedures in ensuring accurate hematological diagnoses and highlights the frequent mistakes that occur during specimen collection, handling, and transportation. Staff training, process standardization, using suitable collecting and transport equipment, putting quality control measures in place, and using automation technologies are some strategies for reducing errors and speeding up turnaround times. To increase diagnostic accuracy, patient care outcomes, and laboratory efficiency, hematology laboratories should address preanalytical mistakes and employ fostering methods. Aims and objectives The objective of this research is to evaluate the frequency and characteristics of preanalytical errors within the hematology laboratory of a tertiary care hospital. The study seeks to gauge the scope of the problem, identify key factors contributing to these errors, such as issues in specimen collection, handling, and transportation, and highlight areas where improvements can be made. Also, it intends to assess how preanalytical errors affect hematological accuracy and turnaround times, with a focus on patient care outcomes, and recommend techniques to reduce preanalytical errors and improve the accuracy of hematological results. Materials and methods This study was conducted at the hematology laboratory of our hospital from January 2023 to June 2024 after getting proper approval from the Institutional Review Board (IRB approval number 294/08/2024/PG/SRB/SMCH). It is a retrospective analytical study, and the study population comprised samples of patients from the emergency, inpatient, and outpatient departments, which included 51,155 complete blood count (CBC) and 5,449 peripheral smear(PS) samples. The study included only test samples sent specifically for hematological analysis, while those sent for cytological, biochemical, or microbiological testing were excluded. The distribution frequency of the samples and the number of rejected samples were analyzed, and the results were then compared and correlated. Results During the study period, a total of 56,604 samples were processed in the hematology laboratory. Of these, 886 samples (1.3%) were rejected due to preanalytical errors. The most frequent error was submitting an insufficient sample (54.17%), while the least frequent was the use of an empty or defective tube (0.4%). In the emergency department, the primary issues were insufficient and clotted samples, while in pediatric cases, errors were mainly due to inadequate or diluted samples. Conclusion Preanalytical errors in hematology laboratories, though often overlooked, can significantly impact diagnostic accuracy and patient care. Our study highlights that a substantial portion of errors arise from inadequate sample collection and handling, particularly in emergency and pediatric cases. Adherence to standard laboratory techniques can dramatically reduce preanalytical errors.