Improved standardization of transcribed digital specimen data

There are more than 1.2 billion biological specimens in the world's museums and herbaria. These objects are particularly important forms of biological sample and observation. They underpin biological taxonomy but the data they contain have many other uses in the biological and environmental sciences. Nevertheless, from their conception they are almost entirely documented on paper, either as labels attached to the specimens or in catalogues linked with catalogue numbers. In order to make the best use of these data and to improve the findability of these specimens, these data must be transcribed digitally and made to conform to standards, so that these data are also interoperable and reusable. Through various digitization projects, the authors have experimented with transcription by volunteers, expert technicians, scientists, commercial transcription services and automated systems. We have also been consumers of specimen data for taxonomical, biogeographical and ecological research. In this paper, we draw from our experiences to make specific recommendations to improve transcription data. The paper is split into two sections. We first address issues related to database implementation with relevance to data transcription, namely versioning, annotation, unknown and incomplete data and issues related to language. We then focus on particular data types that are relevant to biological collection specimens, namely nomenclature, dates, geography, collector numbers and uniquely identifying people. We make recommendations to standards organizations, software developers, data scientists and transcribers to improve these data with the specific aim of improving interoperability between collection datasets.Peer reviewe

Butterflies in bags: permanent storage of Lepidoptera in glassine envelopes

In terms of amateurs and professionals studying and collecting insects, Lepidoptera represent one of the most popular groups. It is this popularity, in combination with wings being routinely spread during mounting, which results in Lepidoptera often taking up the largest number of drawers and space in entomological collections. As resources grow increasingly scarce in natural history museums, any process that results in more efficient use of resources is a welcome addition to collection management practices. Therefore, we propose an alternative method to process papered Lepidoptera: a workflow to digitize (imaging and data registration) papered specimens and to store them (semi)permanently, still unmounted, in glassine envelopes. The mounting of specimens will be limited to those for which it is considered essential. The entire workflow of digitization and repacking can be carried out by non-expert volunteers. By releasing data and images on the internet, taxonomic experts worldwide can assist with identifications. This method was tested for Papilionidae. Results suggest that the workflow and permanent storage in glassine envelopes described here can be applied to most groups of Lepidoptera

A Proof of Concept Study on Real-Pime LiMAx CYP1A2 Liver Function Assessment of Donor Grafts During Normothermic Machine Perfusion

No single reliable parameter exists to assess liver graft function of extended criteria donors during ex-vivo normothermic machine perfusion (NMP). The liver maximum capacity (LiMAx) test is a clinically validated cytochromal breath test, measuring liver function based on 13CO2 production. As an innovative concept, we aimed to integrate the LiMAx breath test with NMP to assess organ function. Eleven human livers were perfused using NMP. After one hour of stabilization, LiMAx testing was performed. Injury markers (ALT, AST, miR-122, FMN, and Suzuki-score) and lactate clearance were measured and related to LiMAx values. LiMAx values ranged between 111 and 1838 µg/kg/h, and performing consecutive LiMAx tests during longer NMP was feasible. No correlation was found between LiMAx value and miR-122 and FMN levels in the perfusate. However, a significant inverse correlation was found between LiMAx value and histological injury (Suzuki-score, R = − 0.874, P < 0.001), AST (R = − 0.812, P = 0.004) and ALT (R = − 0.687, P = 0.028). Furthermore, a significant correlation was found with lactate clearance (R = 0.683, P = 0.043). We demonstrate, as proof of principle, that liver function during NMP can be quantified using the LiMAx test, illustrating a positive correlation with traditional injury markers. This new breath-test application separates livers with adequate cytochromal liver function from inadequate ones and may support decision-making in the safe utilization of extended criteria donor grafts

A benchmark dataset of herbarium specimen images with label data

More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Different methods, such as crowdsourcing and artificial intelligence, are being developed to optimise transcription, but herbarium specimens pose difficulties in data extraction for many reasons. To provide developers of transcription methods with a means of optimisation, we have compiled a benchmark dataset of 1,800 herbarium specimen images with corresponding transcribed data. These images originate from nine different collections and include specimens that reflect the multiple potential obstacles that transcription methods may encounter, such as differences in language, text format (printed or handwritten), specimen age and nomenclatural type status. We are making these specimens available with a Creative Commons Zero licence waiver and with permanent online storage of the data. By doing this, we are minimising the obstacles to the use of these images for transcription training. This benchmark dataset of images may also be used where a defined and documented set of herbarium specimens is needed, such as for the extraction of morphological traits, handwriting recognition and colour analysis of specimens

Fast, robust and effective decellularization of whole human livers using mild detergents and pressure controlled perfusion

Human whole-liver perfusion-decellularization is an emerging technique for producing bio-scaffolds for tissue engineering purposes. The native liver extracellular matrix (ECM) provides a superior microenvironment for hepatic cells in terms of adhesion, survival and function. However, current decellularization protocols show a high degree of variation in duration. More robust and effective protocols are required, before human decellularized liver ECM can be considered for tissue engineering applications. The aim of this study is to apply pressure-controlled perfusion and test the efficacy of two different detergents in porcine and human livers. To test this, porcine livers were decellularized using two different protocols; a triton-x-100 (Tx100)-only protocol (N = 3) and a protocol in which Tx100 was combined with SDS (N = 3) while maintaining constant pressure of 120 mm Hg. Human livers (N = 3) with different characteristics (age, weight and fat content) discarded for transplantation were decellularized using an adapted version of the Tx-100-only protocol. Decellularization efficacy was determined by histology and analysis of DNA and RNA content. Furthermore, the preservation of ECM components was assessed. After completing the perfusion cycles with detergents the porcine li

Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1

DiSSCo, the Distributed System of Scientific Collections, is a pan-European Research Infrastructure (RI) mobilising, unifying bio- and geo-diversity information connected to the specimens held in natural science collections and delivering it to scientific communities and beyond. Bringing together 120 institutions across 21 countries and combining earlier investments in data interoperability practices with technological advancements in digitisation, cloud services and semantic linking, DiSSCo makes the data from natural science collections available as one virtual data cloud, connected with data emerging from new techniques and not already linked to specimens. These new data include DNA barcodes, whole genome sequences, proteomics and metabolomics data, chemical data, trait data, and imaging data (Computer-assisted Tomography (CT), Synchrotron, etc.), to name but a few; and will lead to a wide range of end-user services that begins with finding, accessing, using and improving data. DiSSCo will deliver the diagnostic information required for novel approaches and new services that will transform the landscape of what is possible in ways that are hard to imagine today. With approximately 1.5 billion objects to be digitised, bringing natural science collections to the information age is expected to result in many tens of petabytes of new data over the next decades, used on average by 5,000 – 15,000 unique users every day. This requires new skills, clear policies and robust procedures and new technologies to create, work with and manage large digital datasets over their entire research data lifecycle, including their long-term storage and preservation and open access. Such processes and procedures must match and be derived from the latest thinking in open science and data management, realising the core principles of 'findable, accessible, interoperable and reusable' (FAIR). Synthesised from results of the ICEDIG project ('Innovation and Consolidation for Large Scale Digitisation of Natural Heritage', EU Horizon 2020 grant agreement No. 777483) the DiSSCo Conceptual Design Blueprint covers the organisational arrangements, processes and practices, the architecture, tools and technologies, culture, skills and capacity building and governance and business model proposals for constructing the digitisation infrastructure of DiSSCo. In this context, the digitisation infrastructure of DiSSCo must be interpreted as that infrastructure (machinery, processing, procedures, personnel, organisation) offering Europe-wide capabilities for mass digitisation and digitisation-on-demand, and for the subsequent management (i.e., curation, publication, processing) and use of the resulting data. The blueprint constitutes the essential background needed to continue work to raise the overall maturity of the DiSSCo Programme across multiple dimensions (organisational, technical, scientific, data, financial) to achieve readiness to begin construction. Today, collection digitisation efforts have reached most collection-holding institutions across Europe. Much of the leadership and many of the people involved in digitisation and working with digital collections wish to take steps forward and expand the efforts to benefit further from the already noticeable positive effects. The collective results of examining technical, financial, policy and governance aspects show the way forward to operating a large distributed initiative i.e., the Distributed System of Scientific Collections (DiSSCo) for natural science collections across Europe. Ample examples, opportunities and need for innovation and consolidation for large scale digitisation of natural heritage have been described. The blueprint makes one hundred and four (104) recommendations to be considered by other elements of the DiSSCo Programme of linked projects (i.e., SYNTHESYS+, COST MOBILISE, DiSSCo Prepare, and others to follow) and the DiSSCo Programme leadership as the journey towards organisational, technical, scientific, data and financial readiness continues. Nevertheless, significant obstacles must be overcome as a matter of priority if DiSSCo is to move beyond its Design and Preparatory Phases during 2024. Specifically, these include: Organisational: Strengthen common purpose by adopting a common framework for policy harmonisation and capacity enhancement across broad areas, especially in respect of digitisation strategy and prioritisation, digitisation processes and techniques, data and digital media publication and open access, protection of and access to sensitive data, and administration of access and benefit sharing. Pursue the joint ventures and other relationships necessary to the successful delivery of the DiSSCo mission, especially ventures with GBIF and other international and regional digitisation and data aggregation organisations, in the context of infrastructure policy frameworks, such as EOSC. Proceed with the explicit aim of avoiding divergences of approach in global natural science collections data management and research. Technical: Adopt and enhance the DiSSCo Digital Specimen Architecture and, specifically as a matter of urgency, establish the persistent identifier scheme to be used by DiSSCo and (ideally) other comparable regional initiatives. Establish (software) engineering development and (infrastructure) operations team and direction essential to the delivery of services and functionalities expected from DiSSCo such that earnest engineering can lead to an early start of DiSSCo operations. Scientific: Establish a common digital research agenda leveraging Digital (extended) Specimens as anchoring points for all specimen-associated and -derived information, demonstrating to research institutions and policy/decision-makers the new possibilities, opportunities and value of participating in the DiSSCo research infrastructure. Data: Adopt the FAIR Digital Object Framework and the International Image Interoperability Framework as the low entropy means to achieving uniform access to rich data (image and non-image) that is findable, accessible, interoperable and reusable (FAIR). Develop and promote best practice approaches towards achieving the best digitisation results in terms of quality (best, according to agreed minimum information and other specifications), time (highest throughput, fast), and cost (lowest, minimal per specimen). Financial Broaden attractiveness (i.e., improve bankability) of DiSSCo as an infrastructure to invest in. Plan for finding ways to bridge the funding gap to avoid disruptions in the critical funding path that risks interrupting core operations; especially when the gap opens between the end of preparations and beginning of implementation due to unsolved political difficulties. Strategically, it is vital to balance the multiple factors addressed by the blueprint against one another to achieve the desired goals of the DiSSCo programme. Decisions cannot be taken on one aspect alone without considering other aspects, and here the various governance structures of DiSSCo (General Assembly, advisory boards, and stakeholder forums) play a critical role over the coming years

Chlamydiatrachomatis and placental inflammation in early preterm delivery

Chlamydiatrachomatis may infect the placenta and subsequently lead to preterm delivery. Our aim was to evaluate the relationship between the presence of Chlamydiatrachomatis and signs of placental inflammation in women who delivered at 32 weeks gestation or less. Setting: placental histology and clinical data were prospectively obtained from 304 women and newborns at the Erasmus MC-Sophia, Rotterdam, the Netherlands. C.trachomatis testing of placentas was done retrospectively using PCR. C.trachomatis was detected in 76 (25%) placentas. Histological evidence of placental inflammation was present in 123 (40%) placentas: in 41/76 (54%) placentas with C.trachomatis versus 82/228 (36%) placentas without C.trachomatis infection (OR 2.1, 95% CI 1.2–3.5). C.trachomatis infection correlated with the progression (P = 0.009) and intensity (P = 0.007) of materno-fetal placental inflammation. C.trachomatis DNA was frequently detected in the placenta of women with early preterm delivery, and was associated with histopathological signs of placental inflammation

The IDENTIFY study: the investigation and detection of urological neoplasia in patients referred with suspected urinary tract cancer - a multicentre observational study

Objective To evaluate the contemporary prevalence of urinary tract cancer (bladder cancer, upper tract urothelial cancer [UTUC] and renal cancer) in patients referred to secondary care with haematuria, adjusted for established patient risk markers and geographical variation. Patients and Methods This was an international multicentre prospective observational study. We included patients aged ≥16 years, referred to secondary care with suspected urinary tract cancer. Patients with a known or previous urological malignancy were excluded. We estimated the prevalence of bladder cancer, UTUC, renal cancer and prostate cancer; stratified by age, type of haematuria, sex, and smoking. We used a multivariable mixed-effects logistic regression to adjust cancer prevalence for age, type of haematuria, sex, smoking, hospitals, and countries. Results Of the 11 059 patients assessed for eligibility, 10 896 were included from 110 hospitals across 26 countries. The overall adjusted cancer prevalence (n = 2257) was 28.2% (95% confidence interval [CI] 22.3–34.1), bladder cancer (n = 1951) 24.7% (95% CI 19.1–30.2), UTUC (n = 128) 1.14% (95% CI 0.77–1.52), renal cancer (n = 107) 1.05% (95% CI 0.80–1.29), and prostate cancer (n = 124) 1.75% (95% CI 1.32–2.18). The odds ratios for patient risk markers in the model for all cancers were: age 1.04 (95% CI 1.03–1.05; P < 0.001), visible haematuria 3.47 (95% CI 2.90–4.15; P < 0.001), male sex 1.30 (95% CI 1.14–1.50; P < 0.001), and smoking 2.70 (95% CI 2.30–3.18; P < 0.001). Conclusions A better understanding of cancer prevalence across an international population is required to inform clinical guidelines. We are the first to report urinary tract cancer prevalence across an international population in patients referred to secondary care, adjusted for patient risk markers and geographical variation. Bladder cancer was the most prevalent disease. Visible haematuria was the strongest predictor for urinary tract cancer

Naturalis Biodiversity Center (NL) - Orthopteroidea

Database contains specimen records from the Orthopteroidea collection of the Naturalis Biodiversity Center (Leiden, Netherlands). These specimens originate from the collections of the National Museum of Natural History (RMNH; Rijksmuseum voor Natuurlijke Historie), later National Museum of Natural History, Naturalis in Leiden and of the former Zoological Museum Amsterdam (ZMA). On request more information or pictures (if available) can be provided