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Proton (1H) Magnetic Resonance Spectroscopy (MRS) is a non-invasive tool capable of quantifying brain metabolite concentrations in vivo. Prioritization of standardization and accessibility in the field has led to the development of universal pulse sequences, methodological consensus recommendations, and the development of open-source analysis software packages. One on-going challenge is methodological validation with ground-truth data. As ground-truths are rarely available for in vivo measurements, data simulations have become an important tool. The diverse literature of metabolite measurements has made it challenging to define ranges to be used within simulations. Especially for the development of deep learning and machine learning algorithms, simulations must be able to produce accurate spectra capturing all the nuances of in vivo data. Therefore, we sought to determine the physiological ranges and relaxation rates of brain metabolites which can be used both in data simulations and as reference estimates. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, we've identified relevant MRS research articles and created an open-source database containing methods, results, and other article information as a resource. Using this database, expectation values and ranges for metabolite concentrations and T2 relaxation times are established based upon a meta-analyses of healthy and diseased brains.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Indirect standardization, and its associated parameter the standardized incidence ratio, is a commonly-used tool in hospital profiling for comparing the incidence of negative outcomes between an index hospital and a larger population of reference hospitals, while adjusting for confounding covariates. In statistical inference of the standardized incidence ratio, traditional methods often assume the covariate distribution of the index hospital to be known. This assumption severely compromises one's ability to compute required sample sizes for high-powered indirect standardization, as in contexts where sample size calculation is desired, there are usually no means of knowing this distribution. This paper presents novel statistical methodology to perform sample size calculation for the standardized incidence ratio without knowing the covariate distribution of the index hospital and without collecting information from the index hospital to estimate this covariate distribution. We apply our methods to simulation studies and to real hospitals, to assess both its capabilities in a vacuum and in comparison to traditional assumptions of indirect standardization.

The Indian Public Health Standards (IPHS) were initially developed in 2007 to provide an effective and optimal level of quality health care in our country. IPHS was later revised in 2012, and more recently, in 2022. IPHS revised guidelines for 2022 take into account several new initiatives and programs, including Ayushman Bharat Health and Wellness Centers, the introduction of the National Urban Health Mission and Urban Primary Health Centers (polyclinics) in urban areas. These revised guidelines also make provision for the delivery of oral health services at each facility level. This review highlights the oral health-care services and delivery mechanisms mentioned in all the four volumes of IPHS revised guidelines 2022 under the headings of infrastructure, human resource, service provisions and essential drugs, diagnostics, and equipment required at all the levels of health care.

Scientific relevance. The biological activity of medicinal products may vary depending on the method of production (i.e. biological or recombinant products). The widening variety of gonadotrophin preparations, the diversity of their production methods, and the irreplaceability of biological activity bioassays with physicochemical tests require improvement of animal testing conditions.Aim. This study aimed to determine the biological activity of follicle-stimulating hormone (FSH) in several rat lines, analyse the findings, and select the most optimal testing conditions.Materials and methods. The biological activity was determined using in vivo methods. The comparative analysis used test results obtained over several years in inbred and outbred rats treated with FSH. In all cases, the authors used a three-dose randomised method based on the determination of the biological activity of test samples by comparison with that of the WHO international standard (IS) containing 183 IU of FSH bioactivity and 177 IU of LH bioactivity per ampoule (NIBSC code: 10/286). The study included immature female rats, inbred (Wistar-Kyoto or Sprague Dawley) and outbred. Testing conditions depended on the selected rat line, with the main variables being the test dose and the number of animals per group.Results. The authors compared responses of inbred and outbred rats to various doses of the FSH IS and test samples. Given the narrow range of the analytical procedure, Wistar-Kyoto rats showed a relatively weak dose–response relationship. The study demonstrated that the doses and testing duration depended on the sensitivity of the animals. Test results were less variable in inbred rats than in outbred ones. The statistical analysis of the results of FSH bioactivity testing in inbred and outbred rats showed that, with inbred rats, the number of animals could be halved without compromising the validity of the test.Conclusions. The approach proposed in this study provides for testing the biological activity of FSH with fewer experimental animals, improved cost-effectiveness, and the same reliability of results.

Non-targeted analysis (NTA) using high-resolution mass spectrometry allows scientists to detect and identify a broad range of compounds in diverse matrices for monitoring exposure and toxicological evaluation without a priori chemical knowledge. NTA methods present an opportunity to describe the constituents of a sample across a multidimensional swath of chemical properties, referred to as "chemical space." Understanding and communicating which region of chemical space is extractable and detectable by an NTA workflow, however, remains challenging and non-standardized. For example, many sample processing and data analysis steps influence the types of chemicals that can be detected and identified. Accordingly, it is challenging to assess whether analyte non-detection in an NTA study indicates true absence in a sample (above a detection limit) or is a false negative driven by workflow limitations. Here, we describe the need for accessible approaches that enable chemical space mapping in NTA studies, propose a tool to address this need, and highlight the different ways in which it could be implemented in NTA workflows. We identify a suite of existing predictive and analytical tools that can be used in combination to generate scores that describe the likelihood a compound will be detected and identified by a given NTA workflow based on the predicted chemical space of that workflow. Higher scores correspond to a higher likelihood of compound detection and identification in a given workflow (based on sample extraction, data acquisition, and data analysis parameters). Lower scores indicate a lower probability of detection, even if the compound is truly present in the samples of interest. Understanding the constraints of NTA workflows can be useful for stakeholders when results from NTA studies are used in real-world applications and for NTA researchers working to improve their workflow performance. The hypothetical ChemSpaceTool suggested herein could be used in both a prospective and retrospective sense. Prospectively, the tool can be used to further curate screening libraries and set identification thresholds. Retrospectively, false detections can be filtered by the plausibility of the compound identification by the selected NTA method, increasing the confidence of unknown identifications. Lastly, this work highlights the chemometric needs to make such a tool robust and usable across a wide range of NTA disciplines and invites others who are working on various models to participate in the development of the ChemSpaceTool. Ultimately, the development of a chemical space mapping tool strives to enable further standardization of NTA by improving method transparency and communication around false detection rates, thus allowing for more direct method comparisons between studies and improved reproducibility. This, in turn, is expected to promote further widespread applications of NTA beyond research-oriented settings.

Preclinical imaging is a critical component in translational research with significant complexities in workflow and site differences in deployment. Importantly, the National Cancer Institute's (NCI) precision medicine initiative emphasizes the use of translational co-clinical oncology models to address the biological and molecular bases of cancer prevention and treatment. The use of oncology models, such as patient-derived tumor xenografts (PDX) and genetically engineered mouse models (GEMMs), has ushered in an era of co-clinical trials by which preclinical studies can inform clinical trials and protocols, thus bridging the translational divide in cancer research. Similarly, preclinical imaging fills a translational gap as an enabling technology for translational imaging research. Unlike clinical imaging, where equipment manufacturers strive to meet standards in practice at clinical sites, standards are neither fully developed nor implemented in preclinical imaging. This fundamentally limits the collection and reporting of metadata to qualify preclinical imaging studies, thereby hindering open science and impacting the reproducibility of co-clinical imaging research. To begin to address these issues, the NCI co-clinical imaging research program (CIRP) conducted a survey to identify metadata requirements for reproducible quantitative co-clinical imaging. The enclosed consensus-based report summarizes co-clinical imaging metadata information (CIMI) to support quantitative co-clinical imaging research with broad implications for capturing co-clinical data, enabling interoperability and data sharing, as well as potentially leading to updates to the preclinical Digital Imaging and Communications in Medicine (DICOM) standard.

Background: Basic non-military flight nurse training is essential for enhancing nurses’ competency in conducting aeromedical evacuations. Trained nurses possessing flight nurse proficiency are indispensable for ensuring stable patient conditions amidst the unique physical, physiological, and psychological challenges encountered during flights. Objective: This study aimed to describe the experiences and perceptions of nurses and air ambulance service providers regarding aeromedical evacuations. Methods: This study employed a qualitative descriptive design. Data were gathered from February to July 2023 through semi-structured online interviews with seven nurses and air ambulance service providers engaged in aeromedical evacuation. Content analysis was utilized to interpret the interview data. Results: Seven themes were generated: 1) Experiences in aeromedical evacuation experiences, 2) Challenges faced by nurses and air ambulance service providers during aeromedical evacuations, 3) Essential knowledge for nurses involved in aeromedical evacuations, 4) Efforts to improve nurses’ knowledge and skills, 5) Leveling of flight nurse training, 6) Flight nurse training methods, and 7) Flight nurse training evaluation strategies. Conclusion: Nurses and air ambulance service providers acknowledge the significant influence of the flight environment on changes in patient conditions during aeromedical evacuations. To effectively manage alterations in patient conditions during flights, healthcare workers equipped with aviation health competency are imperative. One approach to enhancing the competency of healthcare workers is through flight nurse training. The findings from this study serve as a valuable resource for policymakers and health-related institutions endeavoring to formulate aeromedical evacuation strategies.

Background Guidelines for sepsis recommend treating those at highest risk within 1 hour. The emergency care system can only achieve this if sepsis is recognised and prioritised. Ambulance services can use prehospital early warning scores alongside paramedic diagnostic impression to prioritise patients for treatment or early assessment in the emergency department. Objectives To determine the accuracy, impact and cost-effectiveness of using early warning scores alongside paramedic diagnostic impression to identify sepsis requiring urgent treatment. Design Retrospective diagnostic cohort study and decision-analytic modelling of operational consequences and cost-effectiveness. Setting Two ambulance services and four acute hospitals in England. Participants Adults transported to hospital by emergency ambulance, excluding episodes with injury, mental health problems, cardiac arrest, direct transfer to specialist services, or no vital signs recorded. Interventions Twenty-one early warning scores used alongside paramedic diagnostic impression, categorised as sepsis, infection, non-specific presentation, or other specific presentation. Main outcome measures Proportion of cases prioritised at the four hospitals; diagnostic accuracy for the sepsis-3 definition of sepsis and receiving urgent treatment (primary reference standard); daily number of cases with and without sepsis prioritised at a large and a small hospital; the minimum treatment effect associated with prioritisation at which each strategy would be cost-effective, compared to no prioritisation, assuming willingness to pay £20,000 per quality-adjusted life-year gained. Results Data from 95,022 episodes involving 71,204 patients across four hospitals showed that most early warning scores operating at their pre-specified thresholds would prioritise more than 10% of cases when applied to non-specific attendances or all attendances. Data from 12,870 episodes at one hospital identified 348 (2.7%) with the primary reference standard. The National Early Warning Score, version 2 (NEWS2), had the highest area under the receiver operating characteristic curve when applied only to patients with a paramedic diagnostic impression of sepsis or infection (0.756, 95% confidence interval 0.729 to 0.783) or sepsis alone (0.655, 95% confidence interval 0.63 to 0.68). None of the strategies provided high sensitivity (> 0.8) with acceptable positive predictive value (> 0.15). NEWS2 provided combinations of sensitivity and specificity that were similar or superior to all other early warning scores. Applying NEWS2 to paramedic diagnostic impression of sepsis or infection with thresholds of > 4, > 6 and > 8 respectively provided sensitivities and positive predictive values (95% confidence interval) of 0.522 (0.469 to 0.574) and 0.216 (0.189 to 0.245), 0.447 (0.395 to 0.499) and 0.274 (0.239 to 0.313), and 0.314 (0.268 to 0.365) and 0.333 (confidence interval 0.284 to 0.386). The mortality relative risk reduction from prioritisation at which each strategy would be cost-effective exceeded 0.975 for all strategies analysed. Limitations We estimated accuracy using a sample of older patients at one hospital. Reliable evidence was not available to estimate the effectiveness of prioritisation in the decision-analytic modelling. Conclusions No strategy is ideal but using NEWS2, in patients with a paramedic diagnostic impression of infection or sepsis could identify one-third to half of sepsis cases without prioritising unmanageable numbers. No other score provided clearly superior accuracy to NEWS2. Research is needed to develop better definition, diagnosis and treatments for sepsis. Study registration This study is registered as Research Registry (reference: researchregistry5268). Funding This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 17/136/10) and is published in full in Health Technology Assessment; Vol. 28, No. 16. See the NIHR Funding and Awards website for further award information. Plain language summary Sepsis is a life-threatening condition in which an abnormal response to infection causes heart, lung or kidney failure. People with sepsis need urgent treatment. They need to be prioritised at the emergency department rather than waiting in the queue. Paramedics attempt to identify people with possible sepsis using an early warning score (based on simple measurements, such as blood pressure and heart rate) alongside their impression of the patient’s diagnosis. They can then alert the hospital to assess the patient quickly. However, an inaccurate early warning score might miss cases of sepsis or unnecessarily prioritise people without sepsis. We aimed to measure how accurately early warning scores identified people with sepsis when used alongside paramedic diagnostic impression. We collected data from 71,204 people that two ambulance services transported to four different hospitals in 2019. We recorded paramedic diagnostic impressions and calculated early warning scores for each patient. At one hospital, we linked ambulance records to hospital records and identified who had sepsis. We then calculated the accuracy of using the scores alongside diagnostic impression to diagnose sepsis. Finally, we used modelling to predict how many patients (with and without sepsis) paramedics would prioritise using different strategies based on early warning scores and diagnostic impression. We found that none of the currently available early warning scores were ideal. When they were applied to all patients, they prioritised too many people. When they were only applied to patients whom the paramedics thought had infection, they missed many cases of sepsis. The NEWS2, score, which ambulance services already use, was as good as or better than all the other scores we studied. We found that using the NEWS2, score in people with a paramedic impression of infection could achieve a reasonable balance between prioritising too many patients and avoiding missing patients with sepsis. Scientific summary Background Sepsis is a life-threatening reaction to an infection in which the immune system overreacts to infection and causes organ damage. Early recognition and treatment of sepsis has the potential to reduce mortality. Guidelines for sepsis highlight the importance of early recognition and treatment, with treatment recommended within 1 hour of presentation for those at highest risk. The emergency care system can only achieve this if sepsis is recognised and prioritised. Ambulance services can use prehospital early warning scores to identify people with a high risk of sepsis and then pre-alert the emergency department (ED) or provide the patient with prehospital treatment. However, they need to determine which score to use, the threshold of positivity for the score, and whether to apply the early warning score to all medical cases or just those where the paramedic diagnostic impression suggests sepsis, infection or a non-specific presentation. This requires estimates of the diagnostic accuracy of early warning scores and consideration of the balance between sensitivity (avoiding missing sepsis) and specificity (prioritising too many patients who do not have sepsis). Objectives We aimed to determine the accuracy, impact and cost-effectiveness of prehospital early warning scores for adults with suspected sepsis. Our specific objectives were: to estimate the accuracy of prehospital early warning scores for identifying sepsis requiring time-critical treatment in adults with possible sepsis who are attended by emergency ambulance to estimate the impact of using prehospital early warning scores to guide key prehospital decisions, in terms of the operational consequences, and the cost-effectiveness of alternative strategies. Methods We undertook (1) a retrospective cohort study to estimate the accuracy of prehospital early warning scores alongside paramedic diagnostic impression and (2) decision-analytic modelling of the operational consequences and cost-effectiveness of using prioritisation strategies based on early warning score and diagnostic impression. Retrospective cohort study We used a literature review and expert opinion to identify 21 early warning scores for evaluation. We used routine ambulance service data to identify all episodes in 2019 in which two ambulance services (Yorkshire and West Midlands) transported patients with medical presentations to four acute hospitals (Sheffield Northern General Hospital, Doncaster Royal Infirmary, Rotherham General Hospital, University Hospitals Coventry and Warwickshire). We excluded episodes with injury, mental health problems, cardiac arrest or direct transfer to specialist services, and cases with no vital signs recorded. We calculated early warning scores from the first recorded vital signs on the ambulance service electronic patient-report form and categorised the paramedic diagnostic impression as sepsis, infection, non-specific presentation or other specific presentation. We then determined the number of cases that ambulance services would prioritise at each hospital using each early warning score alongside the categorised paramedic diagnostic impression. We planned to use the National Health Service (NHS) Digital Data Access Request Service to link ambulance service to hospital data but NHS Digital were unable to provide this service. We therefore instituted a rescue plan to link ambulance service to hospital data at one participating hospital (Sheffield) to determine whether patients had a reference standard diagnosis of sepsis, adjudicated by two independent clinicians following hospital record review. The primary reference standard consisted of meeting the sepsis-3 definition [evidence of infection with a change of two or more points in the Sequential (sepsis-related) Organ Failure Assessment (SOFA) score] and receiving treatment for sepsis. The secondary reference standard consisted of meeting the sepsis-3 definition alone. We analysed the ambulance service data descriptively to report the mean daily number of cases that the ambulance service would pre-alert to each hospital for each combination of early warning score and diagnostic impression. For the accuracy analysis, we constructed receiver operating characteristic (ROC) curves to evaluate sensitivity and specificity over the range of each score. We calculated the area under the ROC curve, sensitivities, specificities, and positive and negative predictive values at key cut-points, each with a 95% confidence interval (CI). Reporting of the results highlights sensitivity and positive predictive value as these best indicate under-triage (sensitivity, the proportion of sepsis cases prioritised) and overtriage (positive predictive value, the proportion of prioritised cases with sepsis). To select strategies for the decision-analytic modelling, we calculated the proportion of mean daily ambulance arrivals that would be prioritised at each hospital and excluded strategies that would prioritise a potentially unmanageable proportion (> 10%). We then compared the accuracy of strategies and excluded those with sensitivity and specificity both inferior to another strategy. We also excluded strategies that were not clearly superior to a comparable strategy involving the National Early Warning Score, version 2 (NEWS2) on the basis that NEWS2 is already widely used by NHS ambulance services, whereas other strategies would require additional training and support to implement. Decision-analytic modelling We developed a decision-analytic model to evaluate the consequences to healthcare providers and the cost-effectives for the health services of using 23 different strategies to prioritise patients transported to hospital with possible sepsis. Due to the paucity of data associated with the benefit of early treatment for sepsis and conflicting results from studies where data existed, threshold analyses were independently undertaken to estimate the reduction in mortality, the reduction in general ward length of stay (LoS) and the reduction in intensive care unit LoS that would be required by each strategy in order to be cost-effective compared with a strategy of no prioritisation of patients. We additionally present the number of prehospital alerts associated with each strategy, the number of patients with sepsis who have been correctly prioritised and the number of patients with sepsis who are not prioritised. Results Retrospective cohort study We collected data from 95,022 ambulance episodes involving 71,204 patients with median age 66 years, and included 37,588 (53.0%) women, and 40,045 (94.9%) with white ethnicity. The mean (standard deviation) number of daily attendances meeting the study inclusion criteria was 93.5 (14.7) at Sheffield Northern General Hospital, 59.5 (10.8) at Doncaster Royal Infirmary, 51.3 (8.9) at Rotherham General Hospital and 74 (11) at University Hospitals Coventry and Warwickshire. Most early warning scores operating at their pre-specified thresholds would prioritise fewer than 10% of attendances when applied only to those with a diagnostic impression of sepsis or infection, but would prioritise more than 10% when applied to non-specific attendances or all attendances. The exceptions were qSOFA (threshold > 1), the Screening to Enhance PrehoSpital Identification of Sepsis (SEPSIS) score, the Critical Illness Score (CIS; threshold > 4), the Paramedic Initiated Treatment of Sepsis Targeting Out-of-hospital Patients clinical trial rule, the PRESS score and the sepsis alert criteria. Yorkshire Ambulance Service recorded only one diagnostic impression, whereas West Midlands Ambulance Service recorded multiple unranked impressions, so strategies prioritised a greater proportion of patients transported to University Hospitals Coventry and Warwickshire. Consequently, in the West Midlands most strategies prioritised more than 10% of cases when applied to those with a diagnostic impression of infection or sepsis. We linked 12,870 out of 24,955 (51.6%) cases to the Sheffield Northern General Hospital records at Sheffield and identified 348 (2.7%) with the primary reference standard. The sensitivity and positive predictive value of paramedic diagnostic impression were 0.328 (95% CI 0.28 to 0.379) and 0.285 (95% CI 0.243 to 0.331) for sepsis, 0.572 (95% CI 0.519 to 0.623) and 0.156 (95% CI 0.137 to 0.176) for infection or sepsis, and 0.897 (95% CI 0.86 to 0.924) and 0.053 (95% CI 0.048 to 0.059) for non-specific presentation, infection or sepsis. The early warning scores had a greater area under the ROC curve when applied to all cases rather than alongside diagnostic impression, but the low prevalence of the reference standard meant that thresholds with sensitivity above 0.7 generally had positive predictive value below 0.15, which would prioritise an unmanageable number of cases. When higher thresholds were used to provide acceptable positive predictive value and a manageable number of cases, strategies that applied the early warning score only to those with a diagnostic impression of sepsis or infection tended to have better overall accuracy. NEWS2 had the highest area under the ROC curve when applied only to those with a paramedic diagnostic impression of sepsis or infection (0.756, 95% CI 0.729 to 0.783) or sepsis alone (0.655, 95% CI 0.63 to 0.68). Only the SEPSIS score had a higher area under the ROC curve than NEWS2 when applied to non-specific presentation, infection or sepsis (0.862 vs. 0.858) and all cases (0.882 vs. 0.877). None of the strategies provided high sensitivity (e.g. > 0.8) with acceptable positive predictive value (e.g. > 0.15). NEWS2, using varying thresholds and combinations with diagnostic impression, provided combinations of sensitivity and specificity that were similar or superior to all other early warning scores. We identified strategies reflecting published recommendations for prioritisation that could offer options with varying trade-offs between sensitivity and positive predictive value. Applying NEWS2 only to those with a paramedic diagnostic impression of sepsis or infection respectively provided sensitivities and positive predictive values of 0.522 (95% CI 0.469 to 0.574) and 0.216 (95% CI 0.189 to 0.245) with a threshold > 4, 0.447 (95% CI 0.395 to 0.499) and 0.274 (95% CI 0.239 to 0.313) with a threshold > 6, and 0.314 (95% CI 0.268 to 0.365) and 0.333 (95% CI 0.284 to 0.386) with a threshold > 8. Applying qSOFA > 1 only to those with a paramedic diagnostic impression of sepsis or infection provided sensitivity of 0.305 (95% CI 0.259 to 0.355) and positive predictive value of 0.356 (95% CI 0.304 to 0.412). Decision-analytic modelling The modelling provided estimates for a range of strategies with varying sensitivity and specificity of the number of cases (overall and with sepsis) that would be prioritised in a large and a small hospital. At a large hospital receiving 93.5 eligible cases per day, applying NEWS2 > 4 only to those with a diagnostic impression of infection or sepsis would prioritise 6.10 cases per day, including 1.32 with sepsis, while failing to prioritise 1.21 with sepsis. The corresponding numbers using NEWS2 > 6 were 4.11, 1.13 and 1.40, using NEWS2 > 8 were 2.38, 0.79 and 1.73, and using qSOFA > 1 were 2.17, 0.77 and 1.76. At a small hospital receiving 53.1 eligible cases per day, applying NEWS2 > 4 only to those with a diagnostic impression of infection or sepsis would prioritise 3.35 cases per day, including 0.72 with sepsis, while failing to prioritise 0.66 with sepsis. The corresponding numbers using NEWS2 > 6 were 2.26, 0.62 and 0.77, using NEWS2 > 8 were 1.31, 0.44 and 0.95, and using qSOFA > 1 were 1.19, 0.42 and 0.96. The threshold analysis showed that the relative risk of mortality associated with prioritisation at which each strategy would be cost-effective compared to no prioritisation [assuming willingness to pay £20,000 per quality-adjusted life-year (QALY) gained] ranged from 0.977 applying NEWS2 > 0 only to those with a diagnostic impression of infection or sepsis, to 0.996 applying NEWS2 > 11 only to those with a diagnostic impression of sepsis. The comparable ranges for other measures of effectiveness for these two strategies were: increase in QALYs 0.00056–0.00002; reduction in length of ward stay 3.8–0.7 days; reduction in intensive care LoS 1.2–0.2 days. Conclusions We were unable to identify a strategy that would prioritise a substantial majority of patients with sepsis without prioritising a potentially unmanageable number of patients for the ED. Most early warning scores, used at a recommended threshold, are likely to prioritise an unmanageable number of cases unless they are only used to prioritise cases with a paramedic diagnostic impression of infection or sepsis. However, paramedic diagnostic impression of infection or sepsis only identified 57% of cases with a reference standard diagnosis of sepsis requiring urgent treatment. The NEWS2 provides sensitivity and specificity for identifying sepsis that is generally similar or superior to other scores operating at a comparable threshold. We therefore found no evidence to justify the support and training required to implement an alternative strategy to NEWS2, which is already widely used in NHS ambulance services. National Early Warning Score, version 2, could be used at thresholds of > 4 or > 6 in presentations with a diagnostic impression of infection or sepsis, reflecting the Academy of Medical Royal Colleges clinical decision support framework, or > 8 to provide similar sensitivity and specificity to the use of qSOFA > 1 recommended in the sepsis-3 guidelines. These strategies provide a range of options that ambulance services and hospitals could use, depending upon capacity to manage prioritised cases and what prioritisation involves. Health economic modelling suggests that sensitive strategies for identifying patients with possible sepsis for prioritisation could be cost-effective, if we are convinced that reducing treatment delay reduces mortality and the emergency care system has the capacity to deliver meaningful prioritisation to substantial numbers of cases. Limitations Inability of NHS Digital to link ambulance service to hospital data meant that we were only able to estimate the accuracy of early warning scores at one hospital using data from 51.6% of the eligible population for whom the ambulance service had NHS numbers. The included patients were markedly older than the excluded patients. We were unable to identify reliable evidence to estimate the effectiveness of early treatment for sepsis, so were unable to identify the most cost-effective strategy. Future research Research into prehospital early warning scores for sepsis is limited by our current inability to clinically measure the dysregulated host response that characterises sepsis and uncertain estimates of the benefits of early treatment. We therefore need to prioritise research to develop better ways of defining and diagnosing sepsis, and to develop and evaluate effective early treatment for sepsis. Future research involving routine ambulance service and hospital data requires a system for NHS data management that supports health data science. Study registration This study is registered as Research Registry (reference: researchregistry5268). Funding This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: 17/136/10) and is published in full in Health Technology Assessment; Vol. 28, No. 16. See the NIHR Funding and Awards website for further award information.

Levothyroxine tablets, although highly prescribed in the United States, have been one of the most frequently recalled products. Because of the importance of the medication, several efforts have been put in place by the United States Food and Drug Administration (US FDA) to control the quality of levothyroxine tablets available to patients using the drug. The choice of excipients used in the formulation has been shown to impact the hygroscopicity and microenvironment, and ultimately the stability of the levothyroxine tablets formulations. Based on information generated from the US FDA Enforcement Report database, one of the main reasons for recalls is the low potency of different batches of the product. The yearly product recall trends for levothyroxine formulations were determined using the FDA Enforcement Report database. Three brands of levothyroxine tablets were selected with excipient lists similar to those products that have been historically recalled. The samples were placed at ambient (~23 °C), accelerated stability (40 °C/75% RH), and stress (50 °C/75% RH) conditions for up to 6 months. Sample potencies were determined at 0, 1.5, 3, and 6 months using the methods for assay and impurities in the United States Pharmacopeia (USP) monograph for levothyroxine tablets. Additional sample monitoring was conducted by overlaying the initial powder X-ray diffractograms (PXRD) of the samples from 0 months with the patterns generated thereafter. There has been a decline in the number of levothyroxine tablets recalled over the years. The highest numbers of recalls were recorded in the years 2013 [33] and 2020 [23]; no recalls occurred in the years 2019 and 2022. All of the brands evaluated met the USP 95.0–105.0% assay requirements at 1.5 months under accelerated conditions; only one of the brands complied at 3 months. Under ambient conditions, two brands were stable at 6 months, with borderline assay results. For stability, levothyroxine was found in microgram quantities in the formulations and PXRD could not detect changes at these low levels. However, we found some distinguishing data for samples under stress conditions. [ABSTRACT FROM AUTHOR]

Nine models were evaluated as candidate glomerular filtration rate (GFR) reference standards in three datasets using [51Cr(EDTA)]– or [169Yb(DTPA)]2− anions in 98 studies. Noncompartmental methods formed an upper limit for estimating mass excreted and voluntary urine collection formed a lower limit. For current models and methods, reduced GFR in adults resulted in inflated clearance estimates. Two different logarithmic models with exponential tails were created and may have underestimated reduced clearance. The logarithmic formulae can be used with only two plasma samples, and fit 13 multiple time-samples from 5 min to 24 h with an 8% standard deviation of residuals compared to 20% error for monoexponentials. For shorter times (4 or 5 h) the fit errors decreased but the ratio of errors remained at circa 2.5 times lesser for the logarithmic versus monoexponential models. Adaptively regularised gamma variate, Tk-GV, models that are well documented, but not in common use, were largely contained within the reference extreme values, were unbiased for different levels of clearance and were the only models to be uncorrelated to volume of distribution from mean residence time divided by weight. Using Tk-GV as a candidate reference standard, potentially better methods for routine clinical usage were discussed. Prospective clinical testing, and metabolic scaling of decreased renal function is advised for potential changes to patient triage. [ABSTRACT FROM AUTHOR]

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Cerebral small vessel disease (CSVD) is a research hotspot in recent 20 years. In order to standardize the name and definition of the imaging features of CSVD, the STandards for ReportIng Vascular changes on nEuroimaging (STRIVE) recommended the imaging diagnostic criteria for CSVD in 2013, namely STRIVE⁃1. In 2023, this standard updated according to the research achievement in recent 10 years. This paper aims to introduce STRIVE⁃2, especially focus on explaining the differences between these two standards in order to help clinicians and researchers understand the changes.

The most important component of national health policy is the assurance of quality, efficacy, and safety of medicines entering the pharmaceutical market in the Russian Federation. In this interview, we have discussed the quality control of medicines; its interconnections with various branches of science, in particular, with analytical chemistry; and the matters of material and equipment supply with Elena L. Kovaleva (Doctor of Pharmaceutical Sciences, Deputy Director of the Centre for Medicinal Products Evaluation and Control of the Scientific Centre for Expert Evaluation of Medicinal Products of the Ministry of Health of the Russian Federation), Yuri A. Zolotov (Academician of the Russian Academy of Sciences, Full Professor, Doctor of Chemical Sciences), and Dmitry V. Somov (Candidate of Pharmaceutical Sciences, Acting Director General of the Information and Methodological Center for Expertise, Accounting, and Analysis of the Circulation of Medicinal Products of the Federal Service for Surveillance in Healthcare).

Scientific relevance. Deuterated analogues of test substances, when used as internal standards, enable analysts to determine traces of residual pesticides in a medicinal plant raw material by gas or liquid chromatography coupled with mass spectrometry. This prompts the search for an undemanding method for the synthesis of deuterated reference standards, with the ultimate goal of expanding the range of reference standards produced in Russia.Aim. The study aimed to synthesise deuterated reference standards (malathion-D6, chlorophos-D6, dichlorophos-D6, and their precursors) and determine their spectral characteristics using 1Н, 2Н, 13С and 31Р nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry.Materials and methods. The study involved methanol-D4, phosphorus pentasulfide, phosphorus trichloride, maleic acid diethyl ether, triethylamine, hydroquinone, and chloral hydrate. The authors recorded 1H, 2H, 13C, and 31P NMR spectra using a QONE AS400 NMR spectrometer operating at a temperature of 298 °K and respective frequencies of 399.83, 61.38, 100.55, and 161.85 MHz. Mass spectra were obtained using an analytical system comprising an Agilent Infinity 1260 liquid chromatograph equipped with an automatic sample injector and coupled with a Thermo Scientific Orbitrap Fusion Lumos high-resolution mass-selective tandem spectrometer operating in electrospray ionisation mode.Results. The authors used existing methods for the synthesis of organophosphate pesticides as a basis and developed synthesis routes to produce the deuterated analogues malathion-D6, chlorophos-D6, and dichlorophos-D6. The synthesised compounds were identified by NMR spectroscopy and high-resolution mass spectrometry.Conclusions. The synthesised compounds are highly pure and suitable for use as internal standards in the determination of organophosphate pesticides in medicinal plant raw materials. The synthesis methods developed by the authors can be used to produce reference standards in Russia.

Measurement of oxygen consumption is a powerful and uniquely informative experimental technique. It can help identify mitochondrial mechanisms of action following pharmacologic and genetic interventions, and characterize energy metabolism in physiology and disease. The conceptual and practical benefits of respirometry have made it a frontline technique to understand how mitochondrial function can interface with-and in some cases control-cell physiology. Nonetheless, an appreciation of the complexity and challenges involved with such measurements is required to avoid common experimental and analytical pitfalls. Here we provide a practical guide to oxygen consumption measurements covering the selection of experimental models and instrumentation, as well as recommendations for the collection, interpretation and normalization of data. These guidelines are provided with the intention of aiding experimental design and enhancing the overall reputability, transparency and reliability of oxygen consumption measurements.

In efforts to increase rigor and reproducibility, the USA National Primate Research Centers (NPRCs) have focused on qualification of reagents, cross-laboratory validations, and proficiency testing for methods to detect infectious agents and accompanying immune responses in nonhuman primates. The pathogen detection working group, comprised of laboratory scientists, colony managers, and leaders from the NPRCs, has championed the effort to produce testing that is reliable and consistent across laboratories. Through multi-year efforts with shared proficiency samples, testing percent agreement has increased from as low as 67.1% for SRV testing in 2010 to 92.1% in 2019. The 2019 average agreement for the four basic SPF agents improved to >96% (86.5% BV, 98.9 SIV, 92.1 SRV, and 97.0 STLV). As new pathogens such as SARS coronavirus type 2 emerge, these steps can now be quickly replicated to develop and implement new assays that ensure rigor, reproducibly, and quality for NHP pathogen detection.

To address limitations that exist with existing definitions of menstrual bleeding changes that occur with contraceptive methods, we assembled a panel to develop new recommendations for standardization of bleeding data analyses associated with contraceptive use to better inform users, clinicians, investigators, pharmaceutical companies, and regulatory agencies. We propose three criteria for assessing bleeding outcomes: pattern, flow, and duration. The descriptors within each criterion depend on whether the contraceptive is designed to result in a predictable or unpredictable bleeding pattern. Predictable pattern outcomes quantify days of scheduled, unscheduled and no bleeding, while unpredictable pattern outcomes assess frequency. Flow is quantified based on patient comparisons to their typical flow when not using contraception, with spotting representing no menstrual products use. Duration of a prolonged bleeding and/or spotting episode is more than 7 days. Studies should assess bleeding characteristics for a minimum of 12 months for 21/7, 24/4, extended cycle or continuous regimens, two years for injectables, and the full duration of use for long-acting contraceptives. Describing pattern, flow and duration as independent categories allows a fuller understanding of the bleeding outcomes and better future assessments of acceptability and continuation. Standardization of outcomes permits better comparison between studies and data synthesis; standardization will also improve the ability of clinicians and patients to understand differences between products.

Background MRI-derived proton density fat fraction (PDFF) is an accurate, reliable, and safe biologic marker for use in the noninvasive diagnosis of hepatic steatosis in patients with nonalcoholic fatty liver disease (NAFLD). Because of the cost and limited availability of MRI, it is necessary to develop an accurate method to diagnose NAFLD with potential point-of-care access. Purpose To compare the diagnostic accuracy of the quantitative US (QUS) fat fraction (FF) estimator with that of the controlled attenuation parameter (CAP) in the diagnosis of NAFLD using contemporaneous MRI-derived PDFF as the reference standard. Materials and Methods Participants with or suspected of having NAFLD were prospectively recruited at the NAFLD Research Center between July 2015 and July 2019. All participants underwent MRI-derived PDFF measurement, transient elastography with CAP measurement, and QUS. QUS FF was derived using computed QUS parameters from the acquired radiofrequency US data using a calibrated reference phantom. The area under the receiver operating characteristic curve (AUC) was calculated to assess the accuracy of QUS FF and CAP in the diagnosis of hepatic steatosis (defined as MRI-derived PDFF ≥ 5%). AUCs were compared using the DeLong test. Results A total of 123 participants were included (mean age, 52 years ± 13 [SD]; 67 [54%] women). Of these participants, 100 (81%) had MRI-derived PDFF of 5% or more. QUS FF had a significantly higher AUC for diagnosis of NAFLD than did CAP (0.92 [95% CI: 0.87, 0.98] vs 0.79 [95% CI: 0.67, 0.90], P = .03). QUS FF had a sensitivity of 98% (98 of 100) and a specificity of 48% (11 of 23). CAP had a sensitivity of 87% (87 of 100) and a specificity of 57% (13 of 23). Conclusion The quantitative US fat fraction estimator is more accurate than the controlled attenuation parameter in the diagnosis of hepatic steatosis in patients with or suspected of having nonalcoholic fatty liver disease. © RSNA, 2022 Online supplemental material is available for this article. See also the editorial by Ito in this issue.

ObjectivesThe lack of standardized X-ray imaging remains a challenge for comparative studies on spatial scans acquired from different clinic-specific X-ray scanners. The central objectives of this study are: 1) to delineate mineral density (MD) values, and 2) generate spatial MD maps of various physiologic and pathologic biominerals, and 3) propose a standardization protocol within the safe-operating zone of a CT scanner that underpins normalization of absorbed dose to shape and density of tissues.MethodsA systematic approach to propose a standardization protocol for CT imaging in vivo included: 1) estimation of pathologic MD ranges by performing a comparative meta-analysis on 2009-2019 data from the PubMed database; 2) calibration of cone-beam CT (CBCT) and micro-CT scanners with phantoms of known mineral densities (0, 250, 500, 750 and 3000 mg/cc) and shapes (cylinders and polyhedrons); 3) scanning craniofacial bones (N = 5) and dental tissues (N = 5), and ectopic minerals from humans (N = 3 each, pulp, salivary gland, kidney and prostrate stones, and penile and vascular plaques); 4) underscoring the effect of shape-factor (surface area-to-volume ratio) on MD of biominerals.ResultsHigher MDs of physiologic and pathologic cortical bones (504-1009 mg/cc) compared to trabecular bone (82-212 mg/cc) were observed. An increase in shape-factor increased the CBCT error in MD measurement and revealed that the scanner resolution is dependent on the absorbed dose and shape-factor of detectable features.SignificanceCT scanners should be calibrated with phantoms containing segments of known shape-factors and mineral densities to identify safe-operating zones. The calibrated approach will narrow the gap between length-scale dependent measurements, and will permit spatiotemporal quantitative and reliable detection of pathologies.

BACKGROUND: Optimal drug dosing is important to ensure adequate response to treatment, prevent development of drug resistance and reduce drug toxicity. The aim of these clinical standards is to provide guidance on 'best practice´ for dosing and management of TB drugs.METHODS: A panel of 57 global experts in the fields of microbiology, pharmacology and TB care were identified; 51 participated in a Delphi process. A 5-point Likert scale was used to score draft standards. The final document represents the broad consensus and was approved by all participants.RESULTS: Six clinical standards were defined: Standard 1, defining the most appropriate initial dose for TB treatment; Standard 2, identifying patients who may be at risk of sub-optimal drug exposure; Standard 3, identifying patients at risk of developing drug-related toxicity and how best to manage this risk; Standard 4, identifying patients who can benefit from therapeutic drug monitoring (TDM); Standard 5, highlighting education and counselling that should be provided to people initiating TB treatment; and Standard 6, providing essential education for healthcare professionals. In addition, consensus research priorities were identified.CONCLUSION: This is the first consensus-based Clinical Standards for the dosing and management of TB drugs to guide clinicians and programme managers in planning and implementation of locally appropriate measures for optimal person-centred treatment to improve patient care.

BackgroundThere is an increasing consensus on the relevance of musculoskeletal fitness for health throughout the life cycle, requiring evaluation approaches and description of results capable of characterizing different age groups and body sizes. This study aimed to describe the musculoskeletal fitness of young Portuguese people aged 10–18 through handgrip strength (HGS) and vertical jump power (VJP) and investigate differences between the sexes.MethodsThe sample included 736 participants (359 girls recruited from schools. HGS (kg) was assessed using a handheld dynamometer, and VJP (W) was assessed using a force platform; both measurements were standardized for body mass.ResultsHigher HGS and VJP were observed in boys than in girls from 13 years old (13 years: p ≤ 0.05; 14–18 years: p ≤ 0.001), with no significant differences before this age. The percentile distributions of HGS and VJP are described for each sex using the lambda, mu, sigma (LMS) method. The pattern of development of these variables as a function of age is presented.ConclusionsHandgrip strength and vertical jump power show differences between the sexes from 13 years of age and similar trajectories to populations in other countries in the same age group.

India has a sparkling pharmaceutical sector that holds a distinguished place by producing and supplying high-quality and affordable medicines across the globe. Ensuring the quality and safety of the marketed medicinal products is one of the most important components of the drug regulatory framework and assessment of the quality of medicines is usually achieved by referring to the public standards of the official Pharmacopoeia. In India, the Indian Pharmacopoeia (IP) is published at regular intervals to fulfill the requirements of the Drugs and Cosmetics Act, 1940 to ensure the quality of medicines being manufactured and/or marketed in India. The present article aims to provide an overview of the history of the IP, its standards-setting process, and the current status of monographs in the 9th edition of the IP 2022. Special focus is placed on the newly added and upgraded general chapters and monographs within the IP 2022. There are a total of 223 general chapters and 3152 drug monographs available under various categories in the IP 2022. This study also highlights a total of 92 new drug monograph additions and 412 monograph revisions in the IP 2022. It is anticipated that the standards laid down in the IP 2022 will play an imperative role in delivering quality medicines to patients within and outside India.

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.

Essential oils are a common group of bioactive compounds, yet their standardisation remains relevant.The aim of the study was to compare pharmacopoeial approaches to the standardisation of herbal drugs and herbal drug preparations containing essential oils using the examples of the State Pharmacopoeia of the Russian Federation (14th edition) and the European Pharmacopoeia (10th edition).The advantages of Russian pharmacopoeial approaches include testing for additional groups of bioactive compounds that contribute significantly to the pharmacotherapeutic effect of extractive preparations. The main compendial method for the component analysis of essential oils is gas chromatography with a flame ionisation detector; its limitations include the need for a considerable number of reference standards. The essential oil content limits established by the two pharmacopoeias for the same types of herbal drugs are not the same. The differences may be associated with differences in sample preparation conditions and analytical procedures for the determination of essential oil content, as well as with growth conditions of plants used to obtain data sets for the standardisation of this quality attribute. As a particular medicinal plant may have several chemotypes differing in the essential oil composition, it seems relevant to consider this composition in the studies of pharmacological activity of herbal drugs associated with essential oils.

The edge of a micro-/nanoscale line pattern fabricated by lithography is not a straight line as in the design but has a roughness. This is called the line edge roughness (LER) and is important dimensional information related to the device performance, and reference standards containing known LER values are needed for fundamental research on lithography-related technology. We propose a novel framework for developing LER reference standards that contain the necessary characteristics. The proposed framework has three main features: (i) a self-affine fractal roughness model for the development of next-generation devices; (ii) a reliable evaluation method based on LER reference metrology using SI-traceable atomic force microscopy (AFM); and (iii) a versatile evaluation method using scanning electron microscopy-based LER metrology verified by the previous AFM-based LER reference metrology. In an experiment to verify the proposed framework, we fabricated an LER reference standard by using electron-beam lithography. The results show that the proposed framework can be used to develop LER reference standards for next-generation functional micro-/nanostructures. • Developmental framework of line edge roughness reference standards. • Precise control and measurement of roughness profile based on a self-affine fractal. • This framework allows the evaluation of fabrication fidelity of the developed sample. [ABSTRACT FROM AUTHOR]

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Large single-cell atlases are now routinely generated to serve as references for analysis of smaller-scale studies. Yet learning from reference data is complicated by batch effects between datasets, limited availability of computational resources and sharing restrictions on raw data. Here we introduce a deep learning strategy for mapping query datasets on top of a reference called single-cell architectural surgery (scArches). scArches uses transfer learning and parameter optimization to enable efficient, decentralized, iterative reference building and contextualization of new datasets with existing references without sharing raw data. Using examples from mouse brain, pancreas, immune and whole-organism atlases, we show that scArches preserves biological state information while removing batch effects, despite using four orders of magnitude fewer parameters than de novo integration. scArches generalizes to multimodal reference mapping, allowing imputation of missing modalities. Finally, scArches retains coronavirus disease 2019 (COVID-19) disease variation when mapping to a healthy reference, enabling the discovery of disease-specific cell states. scArches will facilitate collaborative projects by enabling iterative construction, updating, sharing and efficient use of reference atlases.

BackgroundReliable and field-applicable diagnosis of schistosome infections in non-human animals is important for surveillance, control, and verification of interruption of human schistosomiasis transmission. This study aimed to summarize uses of available diagnostic techniques through a systematic review and meta-analysis.Methodology and principal findingsWe systematically searched the literature and reports comparing two or more diagnostic tests in non-human animals for schistosome infection. Out of 4,909 articles and reports screened, 19 met our inclusion criteria, four of which were considered in the meta-analysis. A total of 14 techniques (parasitologic, immunologic, and molecular) and nine types of non-human animals were involved in the studies. Notably, four studies compared parasitologic tests (miracidium hatching test (MHT), Kato-Katz (KK), the Danish Bilharziasis Laboratory technique (DBL), and formalin-ethyl acetate sedimentation-digestion (FEA-SD)) with quantitative polymerase chain reaction (qPCR), and sensitivity estimates (using qPCR as the reference) were extracted and included in the meta-analyses, showing significant heterogeneity across studies and animal hosts. The pooled estimate of sensitivity was 0.21 (95% confidence interval (CI): 0.03-0.48) with FEA-SD showing highest sensitivity (0.89, 95% CI: 0.65-1.00).Conclusions/significanceOur findings suggest that the parasitologic technique FEA-SD and the molecular technique qPCR are the most promising techniques for schistosome diagnosis in non-human animal hosts. Future studies are needed for validation and standardization of the techniques for real-world field applications.

Concerns regarding both the limited generalizability and the slow pace of traditional randomized trials have led to calls for greater use of real-world evidence in the evaluation of new treatments or products. Real-world clinical trials or pragmatic trials often differ from traditional clinical trials in the use of open-label or nonblinded treatments delivered by real-world clinicians in community practice settings. Blinding and standardization of treatment may sometimes be necessary for internal validity, but they may also obscure or distort meaningful differences between treatments. When investigators consider whether blinding of clinicians, patients, or assessors is necessary, we suggest they consider several specific questions: Will clinicians, patients, and assessors have expectations or preferences regarding benefits or adverse effects? How might those expectations affect treatment uptake, treatment adherence, or assessment of outcomes? Will expectations differ in the settings where trial results will be applied? How would blinding of treatment reduce biases? How would blinding obscure true differences between treatments? How would procedures necessary for blinding reduce acceptability or increase risk of trial participation? When investigators consider how strictly treatments should be standardized, we suggest they consider several specific questions: How would treatment effectiveness or safety vary according to clinician experience or expertise? What level of experience or expertise is available in potential trial settings and settings where trial results would be applied? Is some level of standardization necessary for valid inference? Considering any special vulnerabilities of the study population, is some level of standardization necessary to assure participant safety?

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Copyright of FACSalud is the property of Revista FACSalud and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Aim: There is a critical need to validate biofluid-based biomarkers as diagnostic and drug development tools for traumatic brain injury (TBI). As part of the TBI Endpoints Development Initiative, we identified four potentially predictive and pharmacodynamic biomarkers for TBI: astroglial markers GFAP and S100B and the neuronal markers UCH-L1 and Tau. Materials & methods: Several commonly used platforms for these four biomarkers were identified and compared on analytic performance and ability to detect gold standard recombinant protein antigens and to pool control versus TBI cerebrospinal fluid (CSF). Results: For each marker, only some assay formats could differentiate TBI CSF from the control CSF. Also, different assays for the same biomarker reported divergent biomarker values for the same biosamples. Conclusion: Due to the variability of TBI marker assay in performance and reported values, standardization strategies are recommended when comparing reported biomarker levels across assay platforms.

It is widely appreciated that the spectrum of traumatic brain injury (TBI), mild through severe, contains distinct clinical presentations, variably referred to as subtypes, phenotypes, and/or clinical profiles. As part of the Brain Trauma Blueprint TBI State of the Science, we review the current literature on TBI phenotyping with an emphasis on unsupervised methodological approaches, and describe five phenotypes that appear similar across reports. However, we also find the literature contains divergent analysis strategies, inclusion criteria, findings, and use of terms. Further, whereas some studies delineate phenotypes within a specific severity of TBI, others derive phenotypes across the full spectrum of severity. Together, these facts confound direct synthesis of the findings. To overcome this, we introduce PhenoBench, a freely available code repository for the standardization and evaluation of raw phenotyping data. With this review and toolset, we provide a pathway toward robust, data-driven phenotypes that can capture the heterogeneity of TBI, enabling reproducible insights and targeted care.

Due to COVID-19 travel disruptions, the International Association of Breath Research hosted the planned 2021 Breath Summit virtually as a symposium with oral and poster presentations. The event was comprised of a week-long social media asynchronous online event for sharing research abstracts, posters and discussions. Subsequently, there were two days of real-time webinar platform interactions each featuring three technical presentations, open forum questions, answers, and commentary. The symposium was well attended and well received. It allowed the breath community to share new research and to reconnect with colleagues and friends. This report presents an overview of the topics presented and various salient discussion points.

BackgroundPhyllodes tumors are rare fibroepithelial neoplasms that are classified by tiered histopathologic features. While there are protocols for the reporting of cancer specimens, no standardized reporting protocol exists for phyllodes.MethodsWe performed an 11-institution contemporary review of phyllodes tumors. Granular histopathologic details were recorded, including the features specifically considered for phyllodes grade classification.ResultsOf 550 patients, median tumor size was 3.0 cm, 68.9% (n = 379) of tumors were benign, 19.6% (n = 108) were borderline, and 10.5% (n = 58) were malignant. All cases reported the final tumor size and grade classification. Complete pathologic reporting of all histopathologic features was present in 15.3% (n = 84) of cases, while an additional 35.6% (n = 196) were missing only one or two features in the report. Individual details regarding the degree of stromal cellularity was not reported in 53.5% (n = 294) of cases, degree of stromal atypia in 58.0% (n = 319) of cases, presence of stromal overgrowth in 56.2% (n = 309) of cases, stromal cell mitoses in 37.5% (n = 206) of cases, and tumor border in 54.2% (n = 298) of cases. The final margin status (negative vs. positive) was omitted in only 0.9% of cases, and the final negative margin width was specifically reported in 73.8% of cases. Reporting of details was similar across all sites.ConclusionIn this academic cohort of phyllodes tumors, one or more histopathologic features were frequently omitted from the pathology report. While all features were considered by the pathologist for grading, this limited reporting reflects a lack of reporting consensus. We recommend that standardized reporting in the form of a synoptic-style cancer protocol be implemented for phyllodes tumors, similar to other rare tumors.

Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.

Recent biomarker innovations hold potential for transforming diagnosis, prognostic modeling, and precision therapeutic targeting of traumatic brain injury (TBI). However, many biomarkers, including brain imaging, genomics, and proteomics, involve vast quantities of high-throughput and high-content data. Management, curation, analysis, and evidence synthesis of these data are not trivial tasks. In this review, we discuss data management concepts and statistical and data sharing strategies when dealing with biomarker data in the context of TBI research. We propose that application of biomarkers involves three distinct steps-discovery, evaluation, and evidence synthesis. First, complex/big data has to be reduced to useful data elements at the stage of biomarker discovery. Second, inferential statistical approaches must be applied to these biomarker data elements for assessment of biomarker clinical utility and validity. Last, synthesis of relevant research is required to support practice guidelines and enable health decisions informed by the highest quality, up-to-date evidence available. We focus our discussion around recent experiences from the International Traumatic Brain Injury Research (InTBIR) initiative, with a specific focus on four major clinical projects (Transforming Research and Clinical Knowledge in TBI, Collaborative European NeuroTrauma Effectiveness Research in TBI, Collaborative Research on Acute Traumatic Brain Injury in Intensive Care Medicine in Europe, and Approaches and Decisions in Acute Pediatric TBI Trial), which are currently enrolling subjects in North America and Europe. We discuss common data elements, data collection efforts, data-sharing opportunities, and challenges, as well as examine the statistical techniques required to realize successful adoption and use of biomarkers in the clinic as a foundation for precision medicine in TBI.

Abstract Objectives To investigate whether making the Standards for Reporting Diagnostic Accuracy (STARD) mandatory by the leading journal ‘Radiology’ in 2016 improved the quality of reporting of diagnostic accuracy studies. Methods A validated search term was used to identify diagnostic accuracy studies published in Radiology in 2015 and 2019. STARD adherence was assessed by two independent reviewers. Each item was scored as yes (1 point) if adequately reported or as no (0 points) if not. The total STARD score per article was calculated. Wilcoxon–Mann–Whitney tests were used to evaluate differences of the total STARD scores between 2015 and 2019. In addition, the total STARD score was compared between studies stratified by study design, citation rate, and data collection. Results The median number of reported STARD items for the total of 66 diagnostic accuracy studies from 2015 to 2019 was 18.5 (interquartile range [IQR] 17.5–20.0) of 29. Adherence to the STARD checklist significantly improved the STARD score from a median of 18.0 (IQR 15.5–19.5) in 2015 to a median of 19.5 (IQR 18.5–21.5) in 2019 (p

Pathology is practiced by visual inspection of histochemically stained tissue slides. While the hematoxylin and eosin (H&E) stain is most commonly used, special stains can provide additional contrast to different tissue components. Here, we demonstrate the utility of supervised learning-based computational stain transformation from H&E to special stains (Masson's Trichrome, periodic acid-Schiff and Jones silver stain) using kidney needle core biopsy tissue sections. Based on the evaluation by three renal pathologists, followed by adjudication by a fourth pathologist, we show that the generation of virtual special stains from existing H&E images improves the diagnosis of several non-neoplastic kidney diseases, sampled from 58 unique subjects (P = 0.0095). A second study found that the quality of the computationally generated special stains was statistically equivalent to those which were histochemically stained. This stain-to-stain transformation framework can improve preliminary diagnoses when additional special stains are needed, also providing significant savings in time and cost.

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

BackgroundMicrobiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome.ResultsIn this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions.ConclusionsStandardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

BackgroundThe 2017 Alzheimer's disease (AD) Strategic Biomarker Roadmap (SBR) structured the validation of AD diagnostic biomarkers into 5 phases, systematically assessing analytical validity (Phases 1-2), clinical validity (Phases 3-4), and clinical utility (Phase 5) through primary and secondary Aims. This framework allows to map knowledge gaps and research priorities, accelerating the route towards clinical implementation. Within an initiative aimed to assess the development of biomarkers of tau pathology, we revised this methodology consistently with progress in AD research.MethodsWe critically appraised the adequacy of the 2017 Biomarker Roadmap within current diagnostic frameworks, discussed updates at a workshop convening the Alzheimer's Association and 8 leading AD biomarker research groups, and detailed the methods to allow consistent assessment of aims achievement for tau and other AD diagnostic biomarkers.ResultsThe 2020 update applies to all AD diagnostic biomarkers. In Phases 2-3, we admitted a greater variety of study designs (e.g., cross-sectional in addition to longitudinal) and reference standards (e.g., biomarker confirmation in addition to clinical progression) based on construct (in addition to criterion) validity. We structured a systematic data extraction to enable transparent and formal evidence assessment procedures. Finally, we have clarified issues that need to be addressed to generate data eligible to evidence-to-decision procedures.DiscussionThis revision allows for more versatile and precise assessment of existing evidence, keeps up with theoretical developments, and helps clinical researchers in producing evidence suitable for evidence-to-decision procedures. Compliance with this methodology is essential to implement AD biomarkers efficiently in clinical research and diagnostics.

Background and aimsElectronic health record (EHR)-based research allows the capture of large amounts of data, which is necessary in NAFLD, where the risk of clinical liver outcomes is generally low. The lack of consensus on which International Classification of Diseases (ICD) codes should be used as exposures and outcomes limits comparability and generalizability of results across studies. We aimed to establish consensus among a panel of experts on ICD codes that could become the reference standard and provide guidance around common methodological issues.Approach and resultsResearchers with an interest in EHR-based NAFLD research were invited to collectively define which administrative codes are most appropriate for documenting exposures and outcomes. We used a modified Delphi approach to reach consensus on several commonly encountered methodological challenges in the field. After two rounds of revision, a high level of agreement (>67%) was reached on all items considered. Full consensus was achieved on a comprehensive list of administrative codes to be considered for inclusion and exclusion criteria in defining exposures and outcomes in EHR-based NAFLD research. We also provide suggestions on how to approach commonly encountered methodological issues and identify areas for future research.ConclusionsThis expert panel consensus statement can help harmonize and improve generalizability of EHR-based NAFLD research.

BackgroundControlled attenuation parameter (CAP) is an ultrasound-based point-of-care method to quantify liver fat; however, the optimal threshold for CAP to detect pathologic liver fat among persons living with human immunodeficiency virus (HIV; PLWH) is unknown. Therefore, we aimed to identify the diagnostic accuracy and optimal threshold of CAP for the detection of liver-fat among PLWH with magnetic resonance imaging proton-density fat fraction (MRI-PDFF) as the reference standard.MethodsPatients from a prospective single-center cohort of PLWH at risk for HIV-associated nonalcoholic fatty liver disease (NAFLD) who underwent contemporaneous MRI-PDFF and CAP assessment were included. Subjects with other forms of liver disease including viral hepatitis and excessive alcohol intake were excluded. Receiver operatic characteristic (ROC) curve analysis were performed to identify the optimal threshold for the detection of HIV-associated NAFLD (liver fat ≥ 5%).ResultsSeventy PLWH (90% men) at risk for NAFLD were included. The mean (± standard deviation) age and body mass index were 48.6 (±10.2) years and 30 (± 5.3) kg/m2, respectively. The prevalence of HIV-associated NAFLD (MRI-PDFF ≥ 5%) was 80%. The M and XL probes were used for 56% and 44% of patients, respectively. The area under the ROC curve of CAP for the detection of MRI-PDFF ≥ 5% was 0.82 (0.69-0.95) at the cut-point of 285 dB/m. The positive predictive value of CAP ≥ 285 dB/m was 93.2% in this cohort with sensitivity of 73% and specificity of 78.6%.ConclusionsThe optimal cut-point of CAP to correctly identify HIV-associated NAFLD was 285 dB/m, is similar to previously published cut-point for primary NAFLD and may be incorporated into routine care to identify patients at risk of HIV-associated NAFLD.

BackgroundDiagnostic terms used in histopathology reports of cutaneous melanocytic lesions are not standardized. We describe dermatopathologists' views regarding diverse diagnostic terminology and the utility of the Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis (MPATH-Dx) for categorizing melanocytic lesions.MethodsJuly 2018-2019 survey of board-certified and/or fellowship-trained dermatopathologists with experience interpreting melanocytic lesions.ResultsAmong 160 participants, 99% reported witnessing different terminology being used for the same melanocytic lesion. Most viewed diverse terminology as confusing to primary care physicians (98%), frustrating to pathologists (83%), requiring more of their time as a consultant (64%), and providing necessary clinical information (52%). Most perceived that adoption of the MPATH-Dx would: improve communication with other pathologists and treating physicians (87%), generally be a change for the better (80%), improve patient care (79%), be acceptable to clinical colleagues (68%), save time in pathology report documentation (53%), and protect from malpractice (51%).ConclusionsMost dermatopathologists view diverse terminology as contributing to miscommunication with clinicians and patients, adversely impacting patient care. They view the MPATH-Dx as a promising tool to standardize terminology and improve communication. The MPATH-Dx may be a useful supplement to conventional pathology reports. Further revision and refinement are necessary for widespread clinical use.