Predicting EGFR mutational status from pathology images using a real-world dataset.

Treatment of non-small cell lung cancer is increasingly biomarker driven with multiple genomic alterations, including those in the epidermal growth factor receptor (EGFR) gene, that benefit from targeted therapies. We developed a set of algorithms to assess EGFR status and morphology using a real-world advanced lung adenocarcinoma cohort of 2099 patients with hematoxylin and eosin (H&E) images exhibiting high morphological diversity and low tumor content relative to public datasets. The best performing EGFR algorithm was attention-based and achieved an area under the curve (AUC) of 0.870, a negative predictive value (NPV) of 0.954 and a positive predictive value (PPV) of 0.410 in a validation cohort reflecting the 15% prevalence of EGFR mutations in lung adenocarcinoma. The attention model outperformed a heuristic-based model focused exclusively on tumor regions, and we show that although the attention model also extracts signal primarily from tumor morphology, it extracts additional signal from non-tumor tissue regions. Further analysis of high-attention regions by pathologists showed associations of predicted EGFR negativity with solid growth patterns and higher peritumoral immune presence. This algorithm highlights the potential of deep learning tools to provide instantaneous rule-out screening for biomarker alterations and may help prioritize the use of scarce tissue for biomarker testing.

Implementing E-MOTIVE for detection and treatment of postpartum haemorrhage in South Africa.

Postpartum haemorrhage is the leading cause of preventable maternal mortality in South Africa. In a significant breakthrough in the management of PPH, the E-MOTIVE trial found that a multifaceted health service intervention reduced severe PPH after vaginal delivery by 60% in 78 hospitals in Nigeria, Kenya, Tanzania and SA. The E-MOTIVE approach comprises objective blood loss measurement monitored every 15 minutes during the first hour after delivery to detect PPH early and trigger a bundle of first-line treatments, including massaging the uterus, oxytocin infusion, tranexamic acid infusion, intravenous crystalloid fluids, examination for the cause, emptying the bladder and, if necessary, escalation of care. E-MOTIVE was integrated into the existing Essential Steps in Managing Obstetric Emergencies algorithm. Certain research-related elements of the trial setting cannot be replicated in routine practice. Therefore, we need to develop local strategies to ensure the essential clinical elements of the intervention are implemented. Potential strategies include incorporating the E-MOTIVE principles into national guidelines, ongoing training strategies and ensuring all facilities are equipped with necessary medication, equipment and delegations. This breakthrough intervention provides hope for women in SA, and requires a purposeful, co-ordinated implementation strategy on a national scale to reach all levels of the health service.

Persistent maternal tachycardia: A clinical alert for healthcare professionals providing maternity care in South Africa.

Cardiac disease is one of the commonest causes of indirect maternal deaths globally. This brief report is a reminder that isolated maternal tachycardia at rest is a clinical alert and warrants a detailed history in relation to cardiac disorders, thorough clinical examination of all organ systems, relevant investigations such as imaging, and expert advice to avoid serious adverse events. We reflect on a belatedly investigated persistent maternal tachycardia resulting in a fatal postpartum collapse due to mitral stenosis. The lost window of opportunity for appropriate investigation and management of the tachycardia provides an insight into many similar maternal deaths in South Africa. Key clinical messages regarding persistent maternal tachycardia are presented for midwives and doctors caring for pregnant women.

The Data Use Ontology to streamline responsible access to human biomedical datasets.

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Empirical validation of an automated approach to data use oversight.

The current paradigm for data use oversight of biomedical datasets is onerous, extending the timescale and resources needed to obtain access for secondary analyses, thus hindering scientific discovery. For a researcher to utilize a controlled-access dataset, a data access committee must review her research plans to determine whether they are consistent with the data use limitations (DULs) specified by the informed consent form. The newly created GA4GH data use ontology (DUO) holds the potential to streamline this process by making data use oversight computable. Here, we describe an open-source software platform, the Data Use Oversight System (DUOS), that connects with DUO terminology to enable automated data use oversight. We analyze dbGaP data acquired since 2006, finding an exponential increase in data access requests, which will not be sustainable with current manual oversight review. We perform an empirical evaluation of DUOS and DUO on selected datasets from the Broad Institute's data repository. We were able to structure 118/123 of the evaluated DULs (96%) and 52/52 (100%) of research proposals using DUO terminology, and we find that DUOS' automated data access adjudication in all cases agreed with the DAC manual review. This first empirical evaluation of the feasibility of automated data use oversight demonstrates comparable accuracy to human-based data access oversight in real-world data governance.

Relationship between 'on-treatment platelet reactivity', shear stress, and micro-embolic signals in asymptomatic and symptomatic carotid stenosis.

BACKGROUND: Assessment of 'high on-treatment platelet reactivity (HTPR)' could enhance understanding of the pathophysiology of first or recurrent vascular events in carotid stenosis patients on antiplatelet therapy. METHODS: This prospective, multi-centre study assessed antiplatelet-HTPR status and its relationship with micro-emboli signals (MES) in asymptomatic vs. symptomatic ≥ 50-99% carotid stenosis. Platelet function/reactivity was assessed under 'moderately high shear stress' with the PFA-100® and 'low shear stress' with VerifyNow® and Multiplate® analysers. Bilateral 1-h transcranial Doppler ultrasound of the middle cerebral arteries classified patients as MES + ve or MES - ve. RESULTS: Data from 34 asymptomatic patients were compared with 43 symptomatic patients in the 'early phase' (≤ 4 weeks) and 37 patients in the 'late phase' (≥ 3 months) after TIA/ischaemic stroke. Median daily aspirin doses were higher in early symptomatic (225 mg; P < 0.001), but not late symptomatic (75 mg; P = 0.62) vs. asymptomatic patients (75 mg). There was a lower prevalence of aspirin-HTPR in early (28.6%; P = 0.028), but not late symptomatic (38.9%; P = 0.22) compared with asymptomatic patients (56.7%) on the PFA-100®, but not on the VerifyNow® or Multiplate® (P ≤ 0.53). Early symptomatic patients had a higher prevalence of aspirin-HTPR on the PFA-100® (28.6%) vs. VerifyNow® (9.5%; P = 0.049), but not Multiplate® assays (11.9%, P = 0.10). There was no difference in aspirin-HTPR prevalence between any symptomatic vs. asymptomatic MES + ve or MES - ve subgroup. DISCUSSION: Recently symptomatic moderate-severe carotid stenosis patients had a lower prevalence of aspirin-HTPR than their asymptomatic counterparts on the PFA-100®, likely related to higher aspirin doses. The prevalence of antiplatelet-HTPR was positively influenced by higher shear stress levels, but not MES status.

Responsible sharing of biomedical data and biospecimens via the "Automatable Discovery and Access Matrix" (ADA-M).

Given the data-rich nature of modern biomedical research, there is a pressing need for a systematic, structured, computer-readable way to capture, communicate, and manage sharing rules that apply to biomedical resources. This is essential for responsible recording, versioning, communication, querying, and actioning of resource sharing plans. However, lack of a common "information model" for rules and conditions that govern the sharing of materials, methods, software, data, and knowledge creates a fundamental barrier. Without this, it can be virtually impossible for Research Ethics Committees (RECs), Institutional Review Boards (IRBs), Data Access Committees (DACs), biobanks, and end users to confidently track, manage, and interpret applicable legal and ethical requirements. This raises costs and burdens of data stewardship and decreases efficient and responsible access to data, biospecimens, and other resources. To address this, the GA4GH and IRDiRC organizations sponsored the creation of the Automatable Discovery and Access Matrix (ADA-M, read simply as "Adam"). ADA-M is a comprehensive information model that provides the basis for producing structured metadata "Profiles" of regulatory conditions, thereby enabling efficient application of those conditions across regulatory spheres. Widespread use of ADA-M will aid researchers in globally searching and prescreening potential data and/or biospecimen resources for compatibility with their research plans in a responsible and efficient manner, increasing likelihood of timely DAC approvals while also significantly reducing time and effort DACs, RECs, and IRBs spend evaluating resource requests and research proposals. Extensive online documentation, software support, video guides, and an Application Programming Interface (API) for ADA-M have been made available.

Altered stimulus representation in rat auditory cortex is not causal for loss of consciousness under general anaesthesia.

BACKGROUND: Current concepts suggest that impaired representation of information in cortical networks contributes to loss of consciousness under anaesthesia. We tested this idea in rat auditory cortex using information theory analysis of multiunit responses recorded under three anaesthetic agents with different molecular targets: isoflurane, propofol, and dexmedetomidine. We reasoned that if changes in the representation of sensory stimuli are causal for loss of consciousness, they should occur regardless of the specific anaesthetic agent. METHODS: Spiking responses were recorded with chronically implanted microwire arrays in response to acoustic stimuli incorporating varied temporal and spectral dynamics. Experiments consisted of four drug conditions: awake (pre-drug), sedation (i.e. intact righting reflex), loss of consciousness (a dose just sufficient to cause loss of righting reflex), and recovery. Measures of firing rate, spike timing, and mutual information were analysed as a function of drug condition. RESULTS: All three drugs decreased spontaneous and evoked spiking activity and modulated spike timing. However, changes in mutual information were inconsistent with altered stimulus representation being causal for loss of consciousness. First, direction of change in mutual information was agent-specific, increasing under dexmedetomidine and decreasing under isoflurane and propofol. Second, mutual information did not decrease at the transition between sedation and LOC for any agent. Changes in mutual information under anaesthesia correlated strongly with changes in precision and reliability of spike timing, consistent with the importance of temporal stimulus features in driving auditory cortical activity. CONCLUSIONS: The primary sensory cortex is not the locus for changes in representation of information causal for loss of consciousness under anaesthesia.

Registered access: authorizing data access.

The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.

Simplifying research access to genomics and health data with Library Cards.

The volume of genomics and health data is growing rapidly, driven by sequencing for both research and clinical use. However, under current practices, the data is fragmented into many distinct datasets, and researchers must go through a separate application process for each dataset. This is time-consuming both for the researchers and the data stewards, and it reduces the velocity of research and new discoveries that could improve human health. We propose to simplify this process, by introducing a standard Library Card that identifies and authenticates researchers across all participating datasets. Each researcher would only need to apply once to establish their bona fides as a qualified researcher, and could then use the Library Card to access a wide range of datasets that use a compatible data access policy and authentication protocol.

Failure to perform assisted deliveries is resulting in an increased neonatal and maternal morbidity and mortality: An expert opinion.

The need to perform assisted vaginal delivery (AVD) has been regarded as self-evident. In high-income countries, rates of AVD range between 5% and 20% of all births. In South Africa, the rate of AVD is only 1%. This has resulted in increased neonatal morbidity and mortality due to intrapartum asphyxia, and increased maternal morbidity and mortality due to a rise in second-stage caesarean deliveries. In this article, we address the possible causes leading to a decrease in AVD and propose measures to be taken to increase the rates of AVD and subsequently reduce morbidity and mortality.

High-throughput identification of RNA nuclear enrichment sequences.

In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality. We applied MPRNA to identify RNA-based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine-rich motif. These nuclear enrichment sequences are highly conserved and over-represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single-molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA-based functionalities.

Dogs on livestock farms: A cross-sectional study investigating potential roles in zoonotic pathogen transmission.

Dogs are often present on livestock farms, where they serve important management and companion roles, yet may be involved in zoonotic pathogen transmission. Numerous factors can potentially alter the risk of exposure to zoonotic pathogens, such as the dog's access to livestock, close dog-human contact and an increasing immunocompromised human population. The objective of this study was to quantify and qualify dog ownership among livestock owners, their dog husbandry and biosecurity practices, the dogs' access to livestock and potential risks for zoonotic pathogen transmission. A questionnaire was developed and mailed to 2,000 presumed Ohio livestock owners. Data were collected on demographics, dog husbandry practices, attitudes surrounding zoonotic diseases and attachment to and preventive veterinary care for the dogs. There were 446 responders who met the study inclusion criteria as an Ohio livestock farm owner, with 297 (67%) also owning dogs. Approximately 52% of dog-owning households included at least one individual at higher disease risk (i.e., <5 years, ≥65 years, diagnosed with an immunocompromising condition). Most respondents had little/no concern for disease transmission from livestock to dogs (90%), from dogs to livestock (87%) and from dogs to people (94%). Dogs were allowed access to livestock by 70% of respondents and nearly all (96%; 198) indicated at least one higher risk dog-livestock management practice. In addition, many reported never leashing or fencing their dog (61%) and rarely to never picking up dog faeces (76%). Households with higher risk members reported similar husbandry, biosecurity and concern levels as households without those members (all p > .05). Numerous opportunities for zoonotic pathogen transmission and low level of zoonotic disease concern suggest a need for improved education and outreach for the livestock dog-owning community, particularly for higher risk households.

Review article: acute severe ulcerative colitis - evidence-based consensus statements.

BACKGROUND: Acute severe ulcerative colitis (ASUC) is a potentially life-threatening complication of ulcerative colitis. AIM: To develop consensus statements based on a systematic review of the literature of the management of ASUC to improve patient outcome. METHODS: Following a literature review, the Delphi method was used to develop the consensus statements. A steering committee, based in Australia, generated the statements of interest. Three rounds of anonymous voting were carried out to achieve the final results. Acceptance of statements was pre-determined by ≥80% votes in 'complete agreement' or 'agreement with minor reservation'. RESULTS: Key recommendations include that patients with ASUC should be: hospitalised, undergo unprepared flexible sigmoidoscopy to assess severity and to exclude cytomegalovirus colitis, and be provided with venous thromboembolism prophylaxis and intravenous hydrocortisone 100 mg three or four times daily with close monitoring by a multidisciplinary team. Rescue therapy such as infliximab or ciclosporin should be started if insufficient response by day 3, and colectomy considered if no response to 7 days of rescue therapy or earlier if deterioration. With such an approach, it is expected that colectomy rate during admission will be below 30% and mortality less than 1% in specialist centres. CONCLUSION: These evidenced-based consensus statements on acute severe ulcerative colitis, developed by a multidisciplinary group, provide up-to-date best practice recommendations that improve and harmonise management as well as provide auditable quality assessments.

Maternal deaths from bleeding associated with caesarean delivery: A national emergency.

Maternal deaths associated with caesarean deliveries (CDs) have been increasing in South Africa over the past decade. The objective of this report is to bring national attention to this increasing epidemic of maternal deaths due to bleeding associated with CD in the majority of provinces of the country. Individual chart reviews of women who died from bleeding at or after CD show that 71% had avoidable factors. Among the steps we can take are to improve surgical skills and experience, especially in rural hospitals, to improve clinical observations in the immediate postoperative period and in the postnatal wards, and to ensure that appropriate oxytocic agents are given to prevent postpartum haemorrhage. CEOs and medical managers of health facilities, district clinical specialists, heads of obstetrics and gynaecology, and midwifery training institutions must show leadership and accountability in providing an appropriate environment to ensure that women who require CD receive the procedure for the correct indications and in a safe manner to minimise risks.

A chondrocyte infiltrated collagen type I/III membrane (MACI® implant) improves cartilage healing in the equine patellofemoral joint model.

UNLABELLED: Autologous chondrocyte implantation (ACI) has improved outcome in long-term studies of joint repair in man. However, ACI requires sutured periosteal flaps to secure the cells, which precludes minimally-invasive implantation, and introduces complications with arthrofibrosis and graft hypertrophy. This study evaluated ACI on a collagen type I/III scaffold (matrix-induced autologous chondrocyte implantation; MACI(®)) in critical sized defects in the equine model. METHODS: Chondrocytes were isolated from horses, expanded and seeded onto a collagen I/III membrane (ACI-Maix™) and implanted into one of two 15-mm defects in the femoral trochlear ridge of six horses. Control defects remained empty as ungrafted debrided defects. The animals were examined daily, scored by second look arthroscopy at 12 weeks, and necropsy examination 6 months after implantation. Reaction to the implant was determined by lameness, and synovial fluid constituents and synovial membrane histology. Cartilage healing was assessed by arthroscopic scores, gross assessment, repair tissue histology and immunohistochemistry, cartilage glycosaminoglycan (GAG) and DNA assay, and mechanical testing. RESULTS: MACI(®) implanted defects had improved arthroscopic second-look, gross healing, and composite histologic scores, compared to spontaneously healing empty defects. Cartilage GAG and DNA content in the defects repaired by MACI implant were significantly improved compared to controls. Mechanical properties were improved but remained inferior to normal cartilage. There was minimal evidence of reaction to the implant in the synovial fluid, synovial membrane, subchondral bone, or cartilage. CONCLUSIONS: The MACI(®) implant appeared to improve cartilage healing in a critical sized defect in the equine model evaluated over 6 months.

Visualization of lncRNA by single-molecule fluorescence in situ hybridization.

Single-molecule RNA fluorescence in situ hybridization is a technique that holds great potential for the study of long noncoding RNA. It enables quantification and spatial resolution of single RNA molecules within cells via hybridization of multiple, labeled nucleic acid probes to a target RNA. It has recently become apparent that single-molecule RNA FISH probes targeting noncoding RNA are more prone to off-target binding yielding spurious results than when targeting mRNA. Here we present a protocol for the application of single-molecule RNA FISH to the study of noncoding RNA as well as an experimental procedure for validating legitimate signals.

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.

BACKGROUND: Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visualization of lncRNAs in single cells at single-molecule resolution. RESULTS: We use single-molecule RNA-FISH to systematically quantify and categorize the subcellular localization patterns of a representative set of 61 lncRNAs in three different cell types. Our survey yields high-resolution quantification and stringent validation of the number and spatial positions of these lncRNA, with an mRNA set for comparison. Using this highly quantitative image-based dataset, we observe a variety of subcellular localization patterns, ranging from bright sub-nuclear foci to almost exclusively cytoplasmic localization. We also find that the low abundance of lncRNAs observed from cell population measurements cannot be explained by high expression in a small subset of 'jackpot' cells. Additionally, nuclear lncRNA foci dissolve during mitosis and become widely dispersed, suggesting these lncRNAs are not mitotic bookmarking factors. Moreover, we see that divergently transcribed lncRNAs do not always correlate with their cognate mRNA, nor do they have a characteristic localization pattern. CONCLUSIONS: Our systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs.

Increased thrombin generation potential in symptomatic versus asymptomatic moderate or severe carotid stenosis and relationship with cerebral microemboli.

INTRODUCTION: The importance of thrombin generation in the pathogenesis of TIA or stroke and its relationship with cerebral microembolic signals (MES) in asymptomatic and symptomatic carotid stenosis has not been comprehensively assessed. METHODS: Plasma thrombin generation parameters from patients with moderate or severe (≥ 50%) asymptomatic carotid stenosis were compared with those from patients with symptomatic carotid stenosis in the early (≤ 4 weeks) and late phases (≥ 3 months) after TIA or stroke in this prospective, pilot observational study. Thrombin generation profile was longitudinally assessed in symptomatic patients with data at each time point. Bilateral transcranial Doppler ultrasound monitoring of the middle cerebral arteries was performed whenever possible to classify patients as MES-positive or MES-negative. RESULTS: Data from 31 asymptomatic, 46 'early symptomatic' and 35 'late symptomatic' patients were analysed. Peak thrombin (344.2 nM vs 305.3 nM; p = 0.01) and endogenous thrombin potential (1772.4 vs 1589.7; p = 0.047) were higher in early symptomatic than asymptomatic patients. Peak thrombin production decreased in symptomatic patients followed up from the early to late phase after TIA or stroke (339.7 nM vs 308.6 nM; p = 0.02). Transcranial Doppler ultrasound data were available in 25 asymptomatic, 31 early symptomatic and 27 late symptomatic patients. Early symptomatic MES-positive patients had a shorter 'time-to-peak thrombin' than asymptomatic MES-positive patients (p=0.04), suggesting a more procoagulant state in this early symptomatic subgroup. DISCUSSION: Thrombin generation potential is greater in patients with recently symptomatic than asymptomatic carotid stenosis, and decreases over time following TIA or stroke associated with carotid stenosis. These data improve our understanding of the haemostatic/thrombotic biomarker profile in moderate-severe carotid stenosis.