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Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces of RUNX1 and quantify their effect on activities of downstream cellular programs. We evaluate single-cell RNA profiles of 115 mutations in myelogenous leukemia cells and categorize them into three functionally distinct groups, wild-type (WT)-like, loss-of-function (LoF)-like, and hypomorphic, that we validate in orthogonal assays. LoF-like variants dominate the DNA-binding site and are recurrent in cancer; however, recurrence alone does not predict functional impact. Hypomorphic variants share characteristics with LoF-like but favor protein interactions, promoting gene expression indicative of nerve growth factor (NGF) response and cytokine recruitment of neutrophils. Accessible DNA near differentially expressed genes frequently contains RUNX1-binding motifs. Finally, we reclassify 16 variants of uncertain significance and train a classifier to predict 103 more. Our work demonstrates the potential of targeting protein interactions to better define the landscape of phenotypes reachable by missense mutations.

Abstract The accurate extraction of surgical data from electronic health records (EHRs), particularly operative notes through manual chart review (MCR), is complex, crucial, and time-intensive, limited by human error due to fatigue and the level of training. This study aimed to develop and validate a novel Natural Language Processing (NLP) algorithm integrated with a Large Language Model (LLM; GPT4-Turbo) to automate the extraction of spinal surgery data from EHRs. The algorithm employed a two-stage approach. Initially, a rule-based NLP framework reviewed and classified candidate segments from the text, preserving their reference segments. These segments were then verified in the second stage through the LLM. The primary outcomes of this study were the accurate extraction of surgical data, including the type of surgery, levels operated, number of disks removed, and presence of intraoperative incidental durotomies. Secondary objectives explored time efficiency, tokenization lengths, and costs. The performance of the algorithm was assessed across two validation databases, analyzing metrics such as accuracy, sensitivity, discrimination, F1-score, and precision, with 95% confidence intervals calculated using percentile-based bootstrapping. The NLP + LLM algorithm markedly outperformed all performance metrics, demonstrating significant improvements in time and cost efficiency. These results suggest the potential for widespread adoption of this technology.

BackgroundThe Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.ResultsPerformance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.ConclusionsResults show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Deregulation of neuroblastoma-derived myc (N-myc) is a leading cause of malignant brain tumors in children. To target N-myc-driven medulloblastoma, most research has focused on identifying genomic alterations or on the analysis of the medulloblastoma transcriptome. Here, we have broadly characterized the translatome of medulloblastoma and shown that N-myc unexpectedly drives selective translation of transcripts that promote protein homeostasis. Cancer cells are constantly exposed to proteotoxic stress associated with alterations in protein production or folding. It remains poorly understood how cancers cope with proteotoxic stress to promote their growth. Here, our data revealed that N-myc regulates the expression of specific components (∼5%) of the protein folding machinery at the translational level through the major cap binding protein, eukaryotic initiation factor eIF4E. Reducing eIF4E levels in mouse models of medulloblastoma blocked tumorigenesis. Importantly, targeting Hsp70, a protein folding chaperone translationally regulated by N-myc, suppressed tumor growth in mouse and human medulloblastoma xenograft models. These findings reveal a previously hidden molecular program that promotes medulloblastoma formation and identify new therapies that may have impact in the clinic.SignificanceTranslatome analysis in medulloblastoma shows that N-myc drives selective translation of transcripts that promote protein homeostasis and that represent new therapeutic vulnerabilities.

Altered amygdala development is implicated in the neurobiology of autism, but little is known about the coordinated development of the brain regions directly connected with the amygdala. Here we investigated the volumetric development of an amygdala-connected network, defined as the set of brain regions with monosynaptic connections with the amygdala, in autism from early to middle childhood. A total of 950 longitudinal structural MRI scans were acquired from 282 children (93 female) with autism and 128 children with typical development (61 female) at up to four time points (mean ages: 39, 52, 64, and 137 months, respectively). Volumes from 32 amygdala-connected brain regions were examined using mixed effects multivariate distance matrix regression. The Social Responsiveness Scale-2 was administered to assess degree of autistic traits and social impairments. The amygdala-connected network exhibited persistent diagnostic differences (p values ≤ 0.03) that increased over time (p values ≤ 0.02). These differences were most prominent in autistics with more impacted social functioning at baseline. This pattern was not observed across regions without monosynaptic amygdala connection. We observed qualitative sex differences. In males, the bilateral subgenual anterior cingulate cortices were most affected, while in females the left fusiform and superior temporal gyri were most affected. In conclusion, (1) autism is associated with widespread alterations to the development of brain regions connected with the amygdala, which were associated with autistic social behaviors; and (2) autistic males and females exhibited different patterns of alterations, adding to a growing body of evidence of sex differences in the neurobiology of autism.SIGNIFICANCE STATEMENT Global patterns of development across brain regions with monosynaptic connection to the amygdala differentiate autism from typical development, and are modulated by social functioning in early childhood. Alterations to brain regions within the amygdala-connected network differed in males and females with autism. Results also indicate larger volumetric differences in regions having monosynaptic connection with the amygdala than in regions without monosynaptic connection.

Variant interpretation remains a central challenge for precision medicine. Missense variants are particularly difficult to understand as they change only a single amino acid in a protein sequence yet can have large and varied effects on protein activity. Numerous tools have been developed to identify missense variants with putative disease consequences from protein sequence and structure. However, biological function arises through higher order interactions among proteins and molecules within cells. We therefore sought to capture information about the potential of missense mutations to perturb protein interaction networks by integrating protein structure and interaction data. We developed 16 network-based annotations for missense mutations that provide orthogonal information to features classically used to prioritize variants. We then evaluated them in the context of a proven machine-learning framework for variant effect prediction across multiple benchmark datasets to demonstrate their potential to improve variant classification. Interestingly, network features resulted in larger performance gains for classifying somatic mutations than for germline variants, possibly due to different constraints on what mutations are tolerated at the cellular versus organismal level. Our results suggest that modeling variant potential to perturb context-specific interactome networks is a fruitful strategy to advance in silico variant effect prediction.

Here, we describe a protocol combining functional metrics with genomic data to elucidate drivers of within-cell-type heterogeneity via the phenotype-to-genotype link. This technique involves using fluorescence tagging to label and isolate cells grown in 3D culture, enabling high-throughput enrichment of phenotypically defined cell subpopulations by fluorescence-activated cell sorting. We then perform a validated phenotypically supervised single-cell analysis pipeline to reveal unique functional cell states, including genes and pathways that contribute to cellular heterogeneity and were undetectable by unsupervised analysis. For complete details on the use and execution of this protocol, please refer to Chen et al. (2020).

The major cap-binding protein eukaryotic translation initiation factor 4E (eIF4E), an ancient protein required for translation of all eukaryotic genomes, is a surprising yet potent oncogenic driver. The genetic interactions that maintain the oncogenic activity of this key translation factor remain unknown. In this study, we carry out a genome-wide CRISPRi screen wherein we identify more than 600 genetic interactions that sustain eIF4E oncogenic activity. Our data show that eIF4E controls the translation of Tfeb, a key executer of the autophagy response. This autophagy survival response is triggered by mitochondrial proteotoxic stress, which allows cancer cell survival. Our screen also reveals a functional interaction between eIF4E and a single anti-apoptotic factor, Bcl-xL, in tumor growth. Furthermore, we show that eIF4E and the exon-junction complex (EJC), which is involved in many steps of RNA metabolism, interact to control the migratory properties of cancer cells. Overall, we uncover several cancer-specific vulnerabilities that provide further resolution of the cancer translatome.

SARS-CoV-2 antibodies develop within two weeks of infection, but wane relatively rapidly post-infection, raising concerns about whether antibody responses will provide protection upon re-exposure. Here we revisit T-B cooperation as a prerequisite for effective and durable neutralizing antibody responses centered on a mutationally constrained RBM B cell epitope. T-B cooperation requires co-processing of B and T cell epitopes by the same B cell and is subject to MHC-II restriction. We evaluated MHC-II constraints relevant to the neutralizing antibody response to a mutationally-constrained B cell epitope in the receptor binding motif (RBM) of the spike protein. Examining common MHC-II alleles, we found that peptides surrounding this key B cell epitope are predicted to bind poorly, suggesting a lack MHC-II support in T-B cooperation, impacting generation of high-potency neutralizing antibodies in the general population. Additionally, we found that multiple microbial peptides had potential for RBM cross-reactivity, supporting previous exposures as a possible source of T cell memory.

Neuroinflammation is associated with Alzheimer's disease, but the application of cerebrospinal fluid measures of inflammatory proteins may be limited by overlapping pathways and relationships between them. In this work, we measure 15 cerebrospinal proteins related to microglial and T-cell functions, and show them to reproducibly form functionally-related groups within and across diagnostic categories in 382 participants from the Alzheimer's Disease Neuro-imaging Initiative as well participants from two independent cohorts. We further show higher levels of proteins related to soluble tumor necrosis factor receptor 1 are associated with reduced risk of conversion to dementia in the multi-centered (p = 0.027) and independent (p = 0.038) cohorts of people with mild cognitive impairment due to predicted Alzheimer's disease, while higher soluble TREM2 levels associated with slower decline in the dementia stage of Alzheimer's disease. These inflammatory proteins thus provide prognostic information independent of established Alzheimer's markers.

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.

Liver fibrosis is a histological hallmark of most chronic liver diseases, which can progress to cirrhosis and liver failure, and predisposes to hepatocellular carcinoma. Accurate diagnosis of liver fibrosis is necessary for prognosis, risk stratification, and treatment decision-making. Liver biopsy, the reference standard for assessing liver fibrosis, is invasive, costly, and impractical for surveillance and treatment response monitoring. Elastography offers a noninvasive, objective, and quantitative alternative to liver biopsy. This article discusses the need for noninvasive assessment of liver fibrosis and reviews the comparative advantages and limitations of ultrasound and magnetic resonance elastography techniques with respect to their basic concepts, acquisition, processing, and diagnostic performance. Variations in clinical contexts of use and common pitfalls associated with each technique are considered. In addition, current challenges and future directions to improve the diagnostic accuracy and clinical utility of elastography techniques are discussed. Level of Evidence: 5 Technical Efficacy Stage: 2 J. Magn. Reson. Imaging 2020;51:25-42.

PurposeAmplifications of receptor tyrosine kinases (RTKS) are therapeutic targets in multiple tumor types (e.g. HER2 in breast cancer), and amplification of the chromosome 4 segment harboring the three RTKs KIT, PDGFRA, and KDR (4q12amp) may be similarly targetable. The presence of 4q12amp has been sporadically reported in small tumor specific series but a large-scale analysis is lacking. We assess the pan-cancer landscape of 4q12amp and provide early clinical support for the feasibility of targeting this amplicon.Experimental designTumor specimens from 132,872 patients with advanced cancer were assayed with hybrid capture based comprehensive genomic profiling which assays 186-315 genes for all classes of genomic alterations, including amplifications. Baseline demographic data were abstracted, and presence of 4q12amp was defined as 6 or more copies of KIT/KDR/PDGFRA. Concurrent alterations and treatment outcomes with matched therapies were explored in a subset of cases.ResultsOverall 0.65% of cases harbored 4q12amp at a median copy number of 10 (range 6-344). Among cancers with >100 cases in this series, glioblastomas, angiosarcomas, and osteosarcomas were enriched for 4q12amp at 4.7%, 4.8%, and 6.4%, respectively (all p < 0.001), giving an overall sarcoma (n = 6,885) incidence of 1.9%. Among 99 pulmonary adenocarcinoma cases harboring 4q12amp, 50 (50%) lacked any other known driver of NSLCC. Four index cases plus a previously reported case on treatment with empirical TKIs monotherapy had stable disease on average exceeding 20 months.ConclusionWe define 4q12amp as a significant event across the pan-cancer landscape, comparable to known pan-cancer targets such as NTRK and microsatellite instability, with notable enrichment in several cancers such as osteosarcoma where standard treatment is limited. The responses to available TKIs observed in index cases strongly suggest 4q12amp is a druggable oncogenic target across cancers that warrants a focused drug development strategy.Implications for practiceCoamplification of the receptor tyrosine kinases (rtks) KIT/KDR/PDGFRA (4q12amp) is present broadly across cancers (0.65%), with enrichment in osteosarcoma and gliomas. Evidence for this amplicon having an oncogenic role is the mutual exclusivity of 4q12amp to other known drivers in 50% of pulmonary adenocarcinoma cases. Furthermore, preliminary clinical evidence for driver status comes from four index cases of patients empirically treated with commercially available tyrosine kinase inhibitors with activity against KIT/KDR/PDGFRA who had stable disease for 20 months on average. The sum of these lines of evidence suggests further clinical and preclinical investigation of 4q12amp is warranted as the possible basis for a pan-cancer drug development strategy.

The CAGI-5 pericentriolar material 1 (PCM1) challenge aimed to predict the effect of 38 transgenic human missense mutations in the PCM1 protein implicated in schizophrenia. Participants were provided with 16 benign variants (negative controls), 10 hypomorphic, and 12 loss of function variants. Six groups participated and were asked to predict the probability of effect and standard deviation associated to each mutation. Here, we present the challenge assessment. Prediction performance was evaluated using different measures to conclude in a final ranking which highlights the strengths and weaknesses of each group. The results show a great variety of predictions where some methods performed significantly better than others. Benign variants played an important role as negative controls, highlighting predictors biased to identify disease phenotypes. The best predictor, Bromberg lab, used a neural-network-based method able to discriminate between neutral and non-neutral single nucleotide polymorphisms. The CAGI-5 PCM1 challenge allowed us to evaluate the state of the art techniques for interpreting the effect of novel variants for a difficult target protein.

BackgroundThe major histocompatibility complex class I (MHC-I) molecule is a protein complex that displays intracellular peptides to T cells, allowing the immune system to recognize and destroy infected or cancerous cells. MHC-I is composed of a highly polymorphic HLA-encoded alpha chain that binds the peptide and a Beta-2-microglobulin (B2M) protein that acts as a stabilizing scaffold. HLA mutations have been implicated as a mechanism of immune evasion during tumorigenesis, and B2M is considered a tumor suppressor gene. However, the implications of somatic HLA and B2M mutations have not been fully explored in the context of antigen presentation via the MHC-I molecule during tumor development. To understand the effect that B2M and HLA MHC-I molecule mutations have on mutagenesis, we analyzed the accumulation of mutations in patients from The Cancer Genome Atlas according to their MHC-I molecule mutation status.ResultsSomatic B2M and HLA mutations in microsatellite stable tumors were associated with higher overall mutation burden and a larger fraction of HLA-binding neoantigens when compared to B2M and HLA wild type tumors. B2M and HLA mutations were highly enriched in patients with microsatellite instability. B2M mutations tended to occur relatively early during patients' respective tumor development, whereas HLA mutations were either early or late events. In addition, B2M and HLA mutated patients had higher levels of immune infiltration by natural killer and CD8+ T cells and higher levels of cytotoxicity.ConclusionsOur findings add to a growing body of evidence that somatic B2M and HLA mutations are a mechanism of immune evasion by demonstrating that such mutations are associated with a higher load of neoantigens that should be presented via MHC-I.

HIV-associated neurocognitive disorder (HAND) is a common condition in both developed and developing nations, but its cause is largely unknown. Previous research has inconsistently linked Alzheimer's disease (AD), viral burden, and inflammation to the onset of HAND in HIV-infected individuals. Here we simultaneously measured cerebrospinal fluid (CSF) levels of established amyloid and tau biomarkers for AD, viral copy numbers, and six key cytokines in 41 HIV-infected individuals off combination anti-retroviral therapy (14 with HAND) who underwent detailed clinical and neuropsychological characterization, and compared their CSF patterns with those from young healthy subjects, older healthy subjects with normal cognition, and older people with AD. HAND was associated with the lowest CSF levels of phosphorylated tau (p-Tau181) after accounting for age and race. We also found very high CSF levels of the pro-inflammatory interferon gamma-induced protein 10 (IP-10/CXCL10) in HIV regardless of cognition, but elevated CSF interleukin 8 (IL-8/CXCL8) only in HIV-NC but not HAND. Eleven HIV-infected subjects underwent repeat CSF collection six months later and showed strongly correlated longitudinal changes in p-Tau181 and IL-8 levels (R = 0.841). These data suggest reduced IL-8 relative to IP-10 and reduced p-Tau181 to characterize HAND.

More reliable and cheaper sequencing technologies have revealed the vast mutational landscapes characteristic of many phenotypes. The analysis of such genetic variants has led to successful identification of altered proteins underlying many Mendelian disorders. Nevertheless the simple one-variant one-phenotype model valid for many monogenic diseases does not capture the complexity of polygenic traits and disorders. Although experimental and computational approaches have improved detection of functionally deleterious variants and important interactions between gene products, the development of comprehensive models relating genotype and phenotypes remains a challenge in the field of genomic medicine. In this context, a new view of the pathologic state as significant perturbation of the network of interactions between biomolecules is crucial for the identification of biochemical pathways associated with complex phenotypes. Seminal studies in systems biology combined the analysis of genetic variation with protein-protein interaction networks to demonstrate that even as biological systems evolve to be robust to genetic variation, their topologies create disease vulnerabilities. More recent analyses model the impact of genetic variants as changes to the "wiring" of the interactome to better capture heterogeneity in genotype-phenotype relationships. These studies lay the foundation for using networks to predict variant effects at scale using machine-learning or algorithmic approaches. A wealth of databases and resources for the annotation of genotype-phenotype relationships have been developed to support developments in this area. This overview describes how study of the molecular interactome has generated insights linking the organization of biological systems to disease mechanism, and how this information can enable precision medicine. This article is categorized under: Translational, Genomic, and Systems Medicine > Translational Medicine Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models Analytical and Computational Methods > Computational Methods.

Biological networks can substantially boost power to identify disease genes in genome-wide association studies. To explore different network GWAS methods, we challenged students of a UC San Diego graduate level bioinformatics course, Network Biology and Biomedicine, to explore and improve such algorithms during a four-week-long classroom competition. Here, we report the many creative solutions and share our experiences in conducting classroom crowd science as both a research and pedagogical tool.

Precision cancer medicine promises to tailor clinical decisions to patients using genomic information. Indeed, successes of drugs targeting genetic alterations in tumors, such as imatinib that targets BCR-ABL in chronic myelogenous leukemia, have demonstrated the power of this approach. However, biological systems are complex, and patients may differ not only by the specific genetic alterations in their tumor, but also by more subtle interactions among such alterations. Systems biology and more specifically, network analysis, provides a framework for advancing precision medicine beyond clinical actionability of individual mutations. Here we discuss applications of network analysis to study tumor biology, early methods for N-of-1 tumor genome analysis, and the path for such tools to the clinic.

Introduction:Converging evidence suggests that hippocampal subregions subserve different functions, and are differentially affected by psychosis illness progression. Despite this fact, studies have not often studied subregions cross-sectionally across the psychosis spectrum. Furthermore, little is known about associations between subregion volumes and hippocampus-mediated cognition. Methods:A total of 222 participants (61 ultra high risk [UHR], 91 schizophrenia [SCZ], and 70 healthy volunteers) underwent a 3T MRI scan, as well as structured clinical interviews and a cognitive battery. Hippocampal subfield analysis was conducted with Freesurfer. We compared subregion volumes across groups, controlling for age, gender, and intracranial volume. We also examined associations in the UHR and SCZ groups between hippocampal subregion volumes and verbal learning, visual learning, and working memory. Results:We found a dose-dependent relationship such that the SCZ group showed significantly greater subfield volume reductions than the UHR group, which in turn showed significantly greater subfield volume reductions than the healthy volunteer group. We also found associations between subregion volume and cognitive performance in the visual memory, verbal memory, and working memory domains. Discussion:Our study examined hippocampal subregion volumes cross-sectionally in a large sample across the psychosis spectrum, as well as links with hippocampus-mediated cognitive function. Our findings suggest that hippocampal abnormalities emerge before first psychosis episode onset, and may be etiologically informative.

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Abstract The standard treatment of transposition of the great arteries is the arterial switch operation (ASO). Despite successful surgical correction, patients cannot tolerate extubation after the operation. Major aortopulmonary collaterals (MAPCAs) are one of the rare causes of prolonged mechanical ventilation due to significant hemodynamic effects. We report a 28-day-old newborn with transposition of the great arteries and a ventricular septal defect (VSD) who underwent ASO and VSD closure. After postoperative extubation failed twice, four large MAPCAs were revealed during heart catheterization. After transcatheter closure of these four MAPCAs, the patient was extubated and discharged 27 days after the procedure.

ObjectiveClinical management is hypothesized to be critical for hospital management and hospital performance. The aims of this study were to develop and validate professional involvement scales for measuring the level of clinical management by physicians and nurses in European hospitals.DesignTesting of validity and reliability of scales derived from a questionnaire of 21 items was developed on the basis of a previous study and expert opinion and administered in a cross-sectional seven-country research project 'Deepening our Understanding of Quality improvement in Europe' (DUQuE).Setting and participantsA sample of 3386 leading physicians and nurses working in 188 hospitals located in Czech Republic, France, Germany, Poland, Portugal, Spain and Turkey.Main outcome measuresValidity and reliability of professional involvement scales and subscales.ResultsPsychometric analysis yielded four subscales for leading physicians: (i) Administration and budgeting, (ii) Managing medical practice, (iii) Strategic management and (iv) Managing nursing practice. Only the first three factors applied well to the nurses. Cronbach's alpha for internal consistency ranged from 0.74 to 0.86 for the physicians, and from 0.61 to 0.81 for the nurses. Except for the 0.74 correlation between 'Administration and budgeting' and 'Managing medical practice' among physicians, all inter-scale correlations were

ObjectiveTo explore how European hospitals have implemented patient safety strategies (PSS) and evidence-based organization of care pathway (EBOP) recommendations and examine the extent to which implementation varies between countries and hospitals.DesignMixed-method multilevel cross-sectional design in seven countries as part of the European Union-funded project 'Deepening our Understanding of Quality improvement in Europe' (DUQuE).Setting and participantsSeventy-four acute care hospitals with 292 departments managing acute myocardial infarction (AMI), hip fracture, stroke, and obstetric deliveries. Main outcome measure Five multi-item composite measures-one generic measure for PSS and four pathway-specific measures for EBOP.ResultsPotassium chloride had only been removed from general medication stocks in 9.4-30.5% of different pathways wards and patients were adequately identified with wristband in 43.0-59.7%. Although 86.3% of areas treating AMI patients had immediate access to a specialist physician, only 56.0% had arrangements for patients to receive thrombolysis within 30 min of arrival at the hospital. A substantial amount of the total variance observed was due to between-hospital differences in the same country for PSS (65.9%). In EBOP, between-country differences play also an important role (10.1% in AMI to 57.1% in hip fracture).ConclusionsThere were substantial gaps between evidence and practice of PSS and EBOP in a sample of European hospitals and variations due to country differences are more important in EBOP than in PSS, but less important than within-country variations. Agencies supporting the implementation of PSS and EBOP should closely re-examine the effectiveness of their current strategies.

ObjectiveTo assess whether there is a relationship between having quality as an item on the board's agenda, perceived external pressure (PEP) and the implementation of quality management in European hospitals.DesignA quantitative, mixed method, cross-sectional study in seven European countries in 2011 surveying CEOs and quality managers and data from onsite audits.ParticipantsOne hundred and fifty-five CEOs and 155 quality managers.SettingOne hundred and fifty-five randomly selected acute care hospitals in seven European countries (Czech Republic, France, Germany, Poland, Portugal, Spain and Turkey). Main outcome measure(s) Three constructs reflecting quality management based on questionnaire and audit data: (i) Quality Management System Index, (ii) Quality Management Compliance Index and (iii) Clinical Quality Implementation Index. The main predictor was whether quality performance was on the executive board's agenda.ResultsDiscussing quality performance at executive board meetings more often was associated with a higher quality management system score (regression coefficient b = 2.53; SE = 1.16; P = 0.030). We found a trend in the associations of discussing quality performance with quality compliance and clinical quality implementation. PEP did not modify these relationships.ConclusionsHaving quality as an item on the executive board's agenda allows them to review and discuss quality performance more often in order to improve their hospital's quality management. Generally, and as this study found, having quality on the executive board's agenda matters.

ObjectiveTo describe hospitals' organizational arrangements relevant to the abstraction of administrative data, to report on the completeness of administrative data collected and to assess associations between organizational arrangements and completeness of data submission.DesignA cross-sectionalStudy designutilizing administrative data.Setting and participantsRandomly selected hospitals from seven European countries (The Czech Republic, France, Germany, Poland, Portugal, Spain, and Turkey).Main outcome measuresCompleteness of data submission for four quality indicators: mortality after acute myocardial infarction, stroke and hip fractures and complications after normal delivery.ResultsIn general, hospitals were able to produce data on the four indicators required for this research study. A substantial proportion had missing data on one or more data items. The proportion of hospitals that was able to produce more detailed indicators of relevance for quality monitoring and improvement was low and ranged from 40.1% for thrombolysis performed on patients with acute ischemic stroke to 63.8% for hip-fracture operations performed within 48 h after admission for patients aged 65 or older. National factors were strong predictors of data completeness on the studied indicators.ConclusionsAt present, hospital administrative databases do not seem to be an appropriate source of information for comparison of hospital performance across the countries of the EU. However, given that this is a dynamic field, changes to administrative databases may make this possible in the near future. Such changes could be accelerated by an in-depth comparative analysis of the issues of using administrative data for comparisons of hospital performances in EU countries.

ObjectiveTo define a checklist that can be used to assess the performance of a department and evaluate the implementation of quality management (QM) activities across departments or pathways in acute care hospitals.DesignWe developed and tested a checklist for the assessment of QM activities at department level in a cross-sectional study using on-site visits by trained external auditors.Setting and participantsA sample of 292 hospital departments of 74 acute care hospitals across seven European countries. In every hospital, four departments for the conditions: acute myocardial infarction (AMI), stroke, hip fracture and deliveries participated.Main outcome measuresFour measures of QM activities were evaluated at care pathway level focusing on specialized expertise and responsibility (SER), evidence-based organization of pathways (EBOP), patient safety strategies and clinical review (CR).ResultsParticipating departments attained mean values on the various scales between 1.2 and 3.7. The theoretical range was 0-4. Three of the four QM measures are identical for the four conditions, whereas one scale (EBOP) has condition-specific items. Correlations showed that every factor was related, but also distinct, and added to the overall picture of QM at pathway level.ConclusionThe newly developed checklist can be used across various types of departments and pathways in acute care hospitals like AMI, deliveries, stroke and hip fracture. The anticipated users of the checklist are internal (e.g. peers within the hospital and hospital executive board) and external auditors (e.g. healthcare inspectorate, professional or patient organizations).

ObjectiveThe aim of this study was to develop and validate an index to assess the implementation of quality management systems (QMSs) in European countries.DesignQuestionnaire development was facilitated through expert opinion, literature review and earlier empirical research. A cross-sectional online survey utilizing the questionnaire was undertaken between May 2011 and February 2012. We used psychometric methods to explore the factor structure, reliability and validity of the instrument.Setting and participantsAs part of the Deepening our Understanding of Quality improvement in Europe (DUQuE) project, we invited a random sample of 188 hospitals in 7 countries. The quality managers of these hospitals were the main respondents.Main outcome measureThe extent of implementation of QMSs.ResultsFactor analysis yielded nine scales, which were combined to build the Quality Management Systems Index. Cronbach's reliability coefficients were satisfactory (ranging from 0.72 to 0.82) for eight scales and low for one scale (0.48). Corrected item-total correlations provided adequate evidence of factor homogeneity. Inter-scale correlations showed that every factor was related, but also distinct, and added to the index. Construct validity testing showed that the index was related to recent measures of quality. Participating hospitals attained a mean value of 19.7 (standard deviation of 4.7) on the index that theoretically ranged from 0 to 27.ConclusionAssessing QMSs across Europe has the potential to help policy-makers and other stakeholders to compare hospitals and focus on the most important areas for improvement.

ObjectiveTo investigate the relationship between ISO 9001 certification, healthcare accreditation and quality management in European hospitals.DesignA mixed method multi-level cross-sectional design in seven countries. External teams assessed clinical services on the use of quality management systems, illustrated by four clinical pathways.Setting and participantsSeventy-three acute care hospitals with a total of 291 services managing acute myocardial infarction (AMI), hip fracture, stroke and obstetric deliveries, in Czech Republic, France, Germany, Poland, Portugal, Spain and Turkey.Main outcome measureFour composite measures of quality and safety [specialized expertise and responsibility (SER), evidence-based organization of pathways (EBOP), patient safety strategies (PSS) and clinical review (CR)] applied to four pathways.ResultsAccreditation in isolation showed benefits in AMI and stroke more than in deliveries and hip fracture; the greatest significant association was with CR in stroke. Certification in isolation showed little benefit in AMI but had more positive association with the other conditions; greatest significant association was in PSS with stroke. The combination of accreditation and certification showed least benefit in EBOP, but significant benefits in SER (AMI), in PSS (AMI, hip fracture and stroke) and in CR (AMI and stroke).ConclusionsAccreditation and certification are positively associated with clinical leadership, systems for patient safety and clinical review, but not with clinical practice. Both systems promote structures and processes, which support patient safety and clinical organization but have limited effect on the delivery of evidence-based patient care. Further analysis of DUQuE data will explore the association of certification and accreditation with clinical outcomes.

ObjectiveThe objective of this study was to describe the involvement of patients or their representatives in quality management (QM) functions and to assess associations between levels of involvement and the implementation of patient-centred care strategies.DesignA cross-sectional, multilevelStudy designthat surveyed quality managers and department heads and data from an organizational audit.SettingRandomly selected hospitals (n = 74) from seven European countries (The Czech Republic, France, Germany, Poland, Portugal, Spain and Turkey).ParticipantsHospital quality managers (n = 74) and heads of clinical departments (n = 262) in charge of four patient pathways (acute myocardial infarction, stroke, hip fracture and deliveries) participated in the data collection between May 2011 and February 2012.Main outcome measuresFour items reflecting essential patient-centred care strategies based on an on-site hospital visit: (1) formal survey seeking views of patients and carers, (2) written policies on patients' rights, (3) patient information literature including guidelines and (4) fact sheets for post-discharge care. The main predictors were patient involvement in QM at the (i) hospital level and (ii) pathway level.ResultsCurrent levels of involving patients and their representatives in QM functions in European hospitals are low at hospital level (mean score 1.6 on a scale of 0 to 5, SD 0.7), but even lower at departmental level (mean 0.6, SD 0.7). We did not detect associations between levels of involving patients and their representatives in QM functions and the implementation of patient-centred care strategies; however, the smallest hospitals were more likely to have implemented patient-centred care strategies.ConclusionsThere is insufficient evidence that involving patients and their representatives in QM leads to establishing or implementing strategies and procedures that facilitate patient-centred care; however, lack of evidence should not be interpreted as evidence of no effect.

Study Design: : Retrospective Chart Review. Objectives: Incidental durotomies (IDs) are common spine surgery complications. In this study, we present a review on the most commonly utilized management strategies, report our institutional experience with case examples, and describe a stepwise management algorithm. Methods: A retrospective review was performed of the electronic medical records of all patients who underwent a thoracolumbar or lumbar spine surgery between March 2017 and September 2019. Additionally, a literature review of the current management approaches to treat IDs and persistent postoperative CSF leaks following lumbar spine surgeries was performed. Results: We looked at 1133 patients that underwent posterior thoracolumbar spine surgery. There was intraoperative evidence of ID in 116 cases. Based on our cohort and the current literature, we developed a progressive treatment algorithm for IDs that begins with a primary repair, which can be bolstered by dural sealants or a muscle patch. If this fails, the primary repair can be followed by a paraspinal muscle flap, as well as a lumbar drain. If the patient cannot be weaned from temporary CSF diversion, the final step in controlling postoperative leak is longterm CSF diversion via a lumboperitoneal shunt. In our experience, these shunts can be weaned once the patient has no further clinical or radiographic signs of CSF leak. Conclusions: There is no standardized management approach of IDs and CSF leaks in the literature. This article intends to provide a progressive treatment algorithm and contribute to the development process of a treatment consensus. [ABSTRACT FROM AUTHOR]

The purpose of this study was to implement a new lactate-edited 3D 1H magnetic resonance spectroscopic imaging (MRSI) sequence at 3 T and demonstrate the feasibility of using this sequence for measuring lactate in patients with gliomas. A 3D PRESS MRSI sequence incorporating shortened, high bandwidth 180° pulses, new dual BASING lactate-editing pulses, high bandwidth very selective suppression (VSS) pulses and a flyback echo-planar readout was implemented at 3 T. Over-prescription factor of PRESS voxels was optimized using phantom to minimize chemical shift artifacts. The lactate-edited flyback sequence was compared with lactate-edited MRSI using conventional elliptical k-space sampling in a phantom and volunteers, and then applied to patients with gliomas. The results demonstrated the feasibility of detecting lactate within a short scan time of 9.5 min in both phantoms and patients. Over-prescription of voxels gave less chemical shift artifacts allowing detection of lactate on the majority of the selected volume. The normalized SNR of brain metabolites using the flyback encoding were comparable to the SNR of brain metabolites using conventional phase encoding MRSI. The specialized lactate-edited 3D MRSI sequence was able to detect lactate in brain tumor patients at 3 T. The implementation of this technique means that brain lactate can be evaluated in a routine clinical setting to study its potential as a marker for prognosis and response to therapy.