Survival and Decision-Making in Patients Turned Down for Abdominal Aortic Aneurysm Repair: A Retrospective Study with Focus on COVID-19 Impact.

OBJECTIVES: To investigate and analyse various aspects related to patients who have been placed on a "turn-down list" for elective or emergency repair of abdominal aortic aneurysms (AAA). METHODS: This retrospective study analysed data from the Black Country Vascular Network (BCVN). Multidisciplinary team (MDT) meetings assessed AAA patients referred through National Abdominal Aortic Aneurysm Screening Programme (NAAASP)or directly to vascular surgery. Patients considered unfit for intervention were added to a prospectively kept turndown list. Survival and cause of death data were collected, along with cardiopulmonary exercise testing (CPET) results and British Aneurysm Repair (BAR) scores for some patients. The study covered a period from January 2015 to May 2023. RESULTS: After exclusions 247 (16%) patients were placed on the turndown list with a median age of 85 years (IQR 8 years). The mortality of turndown cases on medical grounds was 74.1%. Survival was significantly higher for patients who completed CPET before being turned down (p = 0.004). Gender analysis revealed a higher proportion of females being turned down compared to males (p = 0.044). COVID-19 led to a notable reduction in the number of discussed cases and interventions, while the turndown rates remained consistent. Survival at one year in turndown patients was 66%, at three it was 29%, at four years it was18% and at 7 years it was 5%. Most patients whose cause of death was known died of respiratory complications (30%) or malignancy (19%). BAR scores and aneurysm size were not significant predictors of mortality. CONCLUSION: Patients on the turndown list have a substantial mortality rate. A significant proportion of female patients were being turned down compared to men and the reasons for this are not clear. Patients who completed CPET before being turned down had a longer survival time. While COVID-19 impacted healthcare services reducing the number of interventions, it did not influence turndown decisions. The study showed that the cause of death for a significant number of patients was respiratory complications or malignancy.

Myoferlin: a potential marker of response to radiotherapy and survival in locally advanced rectal cancer.

PURPOSE: Patients with locally advanced rectal cancer often require neo-adjuvant chemoradiotherapy to downstage the disease, but the response is variable with no predictive biomarkers. We have previously revealed through proteomic profiling that myoferlin is associated with response to radiotherapy. The aims of this study were to further validate this finding and explore the potential for myoferlin to act as a prognostic and/or therapeutic target. MATERIALS AND METHODS: Immunohistochemical analysis of a tissue microarray for 111 patients was used to validate the initial proteomic findings. Manipulation of myoferlin was achieved using siRNA, a small molecular inhibitor (wj460) and a CRISPR-Cas9 knockout cell line. Radiosensitisation following treatment was assessed using 2D clonogenic assays, 3D spheroid models and patient derived organoids. Underlying mechanisms were investigated using electrophoresis, immunofluorescence and immunoblotting. RESULTS: Analysis of both the diagnostic biopsy and tumour resection samples confirmed that low myoferlin expression correlated with a good response to neoadjuvant LCRT. High myoferlin expression was associated with spread to local lymph nodes and worse 5-year survival (p = 0.01, HR 3.5, 95%CI [1.27, 10.04]). This was externally validated using the S:CORT database. Quantification of myoferlin using immunoblotting in immortalised colorectal cancer cell lines and organoids demonstrated that high myoferlin expression was associated with increased radioresistance. Biological and pharmacological manipulation of myoferlin resulted in significantly increased radiosensitivity across all cell lines in 2D and 3D models. Following irradiation, myoferlin knockdown cells had a significantly impaired ability to repair DNA double strand breaks. This appeared to be mediated via non-homologous end-joining. CONCLUSIONS: We have confirmed that high expression of myoferlin in rectal cancer is associated with poor response to neoadjuvant therapy and worse long-term survival. Furthermore, the manipulation of myoferlin led to increased radiosensitivity in vitro. This suggests that myoferlin could be targeted to enhance the sensitivity of rectal cancer patients to radiotherapy and further work is required.

Successful treatment of a large profunda femoris artery aneurysm and associated pseudoaneurysm using endovascular stenting.

Profunda femoris artery aneurysms are a rare form of peripheral arterial aneurysm. In this report, we present the case of an 83-year-old lady who was found to have a 65 mm aneurysm arising from the proximal left profunda femoris artery and associated pseudoaneurysm. Successful treatment was achieved using an endovascular approach in which two stents were deployed.

What Are the Real Issues in Providing Extracorporeal Membrane Oxygenation (ECMO) Support: A Survey.

INTRODUCTION: By using a novel survey our study aimed to assess the challenges ECMO and Critical Care (CC) teams face when initiating and managing patient's ECMO support. METHODS: A qualitative survey-based observational study was performed of members of 2 Critical Care Medicine organizations involved in decision-making around the practice of Extracorporeal Membrane Oxygenation (ECMO). The range of exploratory questions covered ethical principles of informed consent, autonomy and goals of care discussions, beneficence, non-maleficence (offering life-sustaining treatments in end-of-life care), and justice (insurance-related limitations of treatment). Questions also covered pragmatic practice and quality improvement areas, such as exploring whether palliative care or ethics teams were involved in such decision-making. RESULTS: 305 members received the survey links, and a total of 61 completed surveys were received, for an overall response rate of 20% among all eligible members. Only 70% of the participants who manage ECMO patients are involved in the ECMO initiation decision process. The majority do not involve Ethics or Palliative care at the initial ECMO initiation decision step. Of the ethical and moral dilemmas reported, the majority revolved around 1. Prognostication of patients receiving VV and VA ECMO support, 2. Lack of knowledge of patient's wishes and goals, 3. Disconnect between expectations of families and outcomes and 4. Staff moral distress around when to stop ECMO in case of futility. CONCLUSION: Our survey highlights areas of distress and dilemma which have been stressed before in the initiation, management, and outcomes of ECMO patients, however with the increasing use of this modality of cardiopulmonary mechanical support being offered, the survey results can offer a guidance using sound ethical principles.

Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels.

To address the challenge of performance portability and facilitate the implementation of electronic structure solvers, we developed the basic matrix library (BML) and Parallel, Rapid O(N), and Graph-based Recursive Electronic Structure Solver (PROGRESS) library. The BML implements linear algebra operations necessary for electronic structure kernels using a unified user interface for various matrix formats (dense and sparse) and architectures (CPUs and GPUs). Focusing on density functional theory and tight-binding models, PROGRESS implements several solvers for computing the single-particle density matrix and relies on BML. In this paper, we describe the general strategies used for these implementations on various computer architectures, using OpenMP target functionalities on GPUs, in conjunction with third-party libraries to handle performance critical numerical kernels. We demonstrate the portability of this approach and its performance in benchmark problems.

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

The impact of community teaching sessions on onward referral to specialist diabetic foot services.

INTRODUCTION: Prompt referral of patients with diabetic foot ulceration (DFU) to specialist services can lead to more timely assessment of these patients and subsequent improved rates of limb salvage and patient outcomes. In this study we wanted to determine the impact of education in the primary care setting on onward referrals to our specialist Diabetic Foot multi-disciplinary team (MDT) clinic. METHODS: As part of a Diabetic Foot Roadshow, four teaching sessions were delivered in primary care settings across Shropshire by our specialist team from 17th March to the 25th May 2022. Attendees included podiatrists, tissue viability nurses, district nurses and wound care practitioners. Hospital records were used to identify all onward referrals to our Diabetic Foot MDT clinic in the weeks before and after delivery of the roadshow education sessions. RESULTS: 184 referrals were made to the diabetic foot clinic from January to July 2022. There were 0.3 referrals per day in the months prior to the commencement of the education sessions, compared to 1.5 referrals per day following the commencement of the teaching sessions. This increase in referrals was statistically significant (p < 0.0001). CONCLUSION: Teaching sessions delivered to community specialist healthcare professionals significantly increase onward referral of patients to specialist services, facilitating more timely assessment and management of patients with DFUs.

Validation of the Iowa Head-Mounted Open-Source Perimeter.

Purpose: To assess the validity of visual field (VF) results from the Iowa Head-Mounted Display (HMD) Open-Source Perimeter and to test the hypothesis that VF defects and test-retest repeatability are similar between the HMD and Octopus 900 perimeters. Methods: We tested 20 healthy and nine glaucoma patients on the HMD and Octopus 900 perimeters using the Open Perimetry Interface platform with size V stimuli, a custom grid spanning the central 26° of the VF, and a ZEST thresholding algorithm. Historical data from the Humphrey Field Analyzer (HFA) were also analyzed. Repeatability was analyzed with the repeatability coefficient (RC), and VF defect detection was determined through side-by-side comparisons. Results: The pointwise RCs were 2.6 dB and 3.4 dB for the HMD and Octopus 900 perimeters in ocular healthy subjects, respectively. Likewise, the RCs were 4.2 dB and 3.5 dB, respectively, in glaucomatous patients. Limits of agreement between the HMD and Octopus 900 perimeters were ±4.6 dB (mean difference, 0.4 dB) for healthy patients and ±8.9 dB (mean difference, 0.1 dB) for glaucomatous patients. Retrospective analysis showed that pointwise RCs on the HFA2 perimeter were between 3.4 and 3.7 dB for healthy patients and between 3.9 and 4.7 dB for glaucoma patients. VF defects were similar between the HMD and Octopus 900 for glaucoma subjects. Conclusions: The Iowa Virtual Reality HMD Open-Source Perimeter is as repeatable as the Octopus 900 perimeter and is a more portable and less expensive alternative than traditional perimeters. Translational Relevance: This study demonstrates the validity of the visual field results from the Iowa HMD Open-Source Perimeter which may help expand perimetry access.

Molecular-dynamics simulations of macromolecular diffraction, part II: Analysis of protein crystal simulations.

Molecular-dynamics (MD) simulations have contributed substantially to our understanding of protein structure and dynamics, yielding insights into many biological processes including protein folding, drug binding, and mechanisms of protein-protein interactions. Much of what is known about protein structure comes from macromolecular crystallography (MX) experiments. MD simulations of protein crystals are useful in the study of MX because the simulations can be analyzed to calculate almost any crystallographic observable of interest, from atomic coordinates to structure factors and densities, B-factors, multiple conformations and their populations/occupancies, and diffuse scattering intensities. Computing resources and software to support crystalline MD simulations are now readily available to many researchers studying protein structure and dynamics and who may be interested in advanced interpretation of MX data, including diffuse scattering. In this work, we outline methods of analyzing MD simulations of protein crystals and provide accompanying Jupyter notebooks as practical resources for researchers wishing to perform similar analyses on their own systems of interest.

Interpreting macromolecular diffraction through simulation.

This chapter discusses the use of diffraction simulators to improve experimental outcomes in macromolecular crystallography, in particular for future experiments aimed at diffuse scattering. Consequential decisions for upcoming data collection include the selection of either a synchrotron or free electron laser X-ray source, rotation geometry or serial crystallography, and fiber-coupled area detector technology vs. pixel-array detectors. The hope is that simulators will provide insights to make these choices with greater confidence. Simulation software, especially those packages focused on physics-based calculation of the diffraction, can help to predict the location, size, shape, and profile of Bragg spots and diffuse patterns in terms of an underlying physical model, including assumptions about the crystal's mosaic structure, and therefore can point to potential issues with data analysis in the early planning stages. Also, once the data are collected, simulation may offer a pathway to improve the measurement of diffraction, especially with weak data, and might help to treat problematic cases such as overlapping patterns.

Molecular-dynamics simulations of macromolecular diffraction, part I: Preparation of protein crystal simulations.

Molecular-dynamics (MD) simulations of protein crystals enable the prediction of structural and dynamical features of both the protein and the solvent components of macromolecular crystals, which can be validated against diffraction data from X-ray crystallographic experiments. The simulations have been useful for studying and predicting both Bragg and diffuse scattering in protein crystallography; however, the preparation is not yet automated and includes choices and tradeoffs that can impact the results. Here we examine some of the intricacies and consequences of the choices involved in setting up MD simulations of protein crystals for the study of diffraction data, and provide a recipe for preparing the simulations, packaged in an accompanying Jupyter notebook. This article and the accompanying notebook are intended to serve as practical resources for researchers wishing to put these models to work.

Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.

Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and time-resolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals.

Next-generation sequencing (NGS) has been proven to address some of the limitations of the current testing methods for adventitious virus detection in biologics. The International Alliance for Biological Standardization (IABS), the U.S. Food and Drug Administration (FDA), and the European Directorate for the Quality of Medicines and Healthcare (EDQM) co-organized the "3rd Conference on Next-generation Sequencing for Adventitious Virus Detection in Biologics for Humans and Animals", which was held on September 27-28, 2022, in Rockville, Maryland, U.S.A. The meeting gathered international representatives from regulatory and public health authorities and other government agencies, industry, contract research organizations, and academia to present the current status of NGS applications and the progress on NGS standardization and validation for detection of viral adventitious agents in biologics, including human and animal vaccines, gene therapies, and biotherapeutics. Current regulatory expectations were discussed for developing a scientific consensus regarding using NGS for detection of adventitious viruses. Although there are ongoing improvements in the NGS workflow, the development of reference materials for facilitating method qualification and validation support the current use of NGS for adventitious virus detection.

A vascular multi-arm multi-stage trial to prevent groin wound surgical site infection: A feasibility survey.

Surgical site infection (SSI) is common following arterial surgery involving a groin incision. There is a lack of evidence regarding interventions to prevent groin wound SSI, therefore, a survey of vascular clinicians was undertaken to assess current opinion and practice, equipoise and feasibility of a randomised controlled trial (RCT). Participants at the Vascular Society of Great Britain and Ireland 2021 Annual Scientific Meeting were surveyed regarding three separate interventions designed to prevent SSI in the groin; impregnated incise drapes, diakylcarbomoyl chloride dressings and antibiotic impregnated collagen sponges. Results were collated via an online survey using the Research Electronic Data Capture platform. Seventy-five participants completed the questionnaire, most were consultant vascular surgeons (50/75, 66.7%). The majority agree that groin wound SSI is a major problem (73/75, 97.3%), and would be content using either of the three interventions (51/61, 83.6%) and had clinical equipoise to randomise patients to any of the three interventions versus standard of care (70/75, 93.3%). There was some reluctance to not use impregnated incise drapes as may be considered "standard of care". Groin wound SSI is perceived as major problem in vascular surgery, and a multicentre RCT of three preventative interventions appears acceptable to vascular surgeons.

Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.

Structural dynamics of water and its hydrogen-bonding networks play an important role in enzyme function via the transport of protons, ions, and substrates. To gain insights into these mechanisms in the water oxidation reaction in Photosystem II (PS II), we have performed crystalline molecular dynamics (MD) simulations of the dark-stable S1 state. Our MD model consists of a full unit cell with 8 PS II monomers in explicit solvent (861 894 atoms), enabling us to compute the simulated crystalline electron density and to compare it directly with the experimental density from serial femtosecond X-ray crystallography under physiological temperature collected at X-ray free electron lasers (XFELs). The MD density reproduced the experimental density and water positions with high fidelity. The detailed dynamics in the simulations provided insights into the mobility of water molecules in the channels beyond what can be interpreted from experimental B-factors and electron densities alone. In particular, the simulations revealed fast, coordinated exchange of waters at sites where the density is strong, and water transport across the bottleneck region of the channels where the density is weak. By computing MD hydrogen and oxygen maps separately, we developed a novel Map-based Acceptor-Donor Identification (MADI) technique that yields information which helps to infer hydrogen-bond directionality and strength. The MADI analysis revealed a series of hydrogen-bond wires emanating from the Mn cluster through the Cl1 and O4 channels; such wires might provide pathways for proton transfer during the reaction cycle of PS II. Our simulations provide an atomistic picture of the dynamics of water and hydrogen-bonding networks in PS II, with implications for the specific role of each channel in the water oxidation reaction.

Visual Field Pointwise Analysis of the Idiopathic Intracranial Hypertension Weight Trial (IIH:WT).

Purpose: This study was designed to determine if point analysis of the Humphrey visual field (HVF) is an effective outcome measure for people with idiopathic intracranial hypertension (IIH) compared with mean deviation (MD). Methods: Using the IIH Weight Trial data, we performed a pointwise analysis of the numerical retinal sensitivity. We then defined a medically treated cohort as having MDs between -2 dB and -7 dB and calculated the number of points that would have the ability to change by 7 dB. Results: The HVF 24-2 mean ± SD MD in the worse eye was -3.5 ± 1.1 dB (range, -2.0 to -6.4 dB). Total deviation demonstrated a preference for the peripheral and blind spot locations to be affected. Points between 0 dB and -10 dB demonstrated negligible ability to improve, compared with those between -10 dB and -25 dB. For the evaluation of the feasibility for a potential medical intervention trial, only 346 points were available for analysis between -10 dB and -25 dB bilaterally, compared with 4123 points in baseline sensitivities of 0 to -10 dB. Conclusions: Patients with IIH have mildly affected baseline sensitivities in the visual field based on HVF analyzer findings, and the majority of points do not show substantial change over 24 months in the setting of a randomized clinical trial. Most patients with IIH who are eligible for a medical treatment trial generally have the mildest affected baseline sensitivities. In such patients, pointwise analysis offers no advantage over MD in detection of visual field change.

Predicting Visual Field Worsening with Longitudinal OCT Data Using a Gated Transformer Network.

PURPOSE: To identify visual field (VF) worsening from longitudinal OCT data using a gated transformer network (GTN) and to examine how GTN performance varies for different definitions of VF worsening and different stages of glaucoma severity at baseline. DESIGN: Retrospective longitudinal cohort study. PARTICIPANTS: A total of 4211 eyes (2666 patients) followed up at the Johns Hopkins Wilmer Eye Institute with at least 5 reliable VF results and 1 reliable OCT scan within 1 year of each reliable VF test. METHODS: For each eye, we used 3 trend-based methods (mean deviation [MD] slope, VF index slope, and pointwise linear regression) and 3 event-based methods (Guided Progression Analysis, Collaborative Initial Glaucoma Treatment Study scoring system, and Advanced Glaucoma Intervention Study [AGIS] scoring system) to define VF worsening. Additionally, we developed a "majority of 6" algorithm (M6) that classifies an eye as worsening if 4 or more of the 6 aforementioned methods classified the eye as worsening. Using these 7 reference standards for VF worsening, we trained 7 GTNs that accept a series of at least 5 as input OCT scans and provide as output a probability of VF worsening. Gated transformer network performance was compared with non-deep learning models with the same serial OCT input from previous studies-linear mixed-effects models (MEMs) and naive Bayes classifiers (NBCs)-using the same training sets and reference standards as for the GTN. MAIN OUTCOME MEASURES: Area under the receiver operating characteristic curve (AUC). RESULTS: The M6 labeled 63 eyes (1.50%) as worsening. The GTN achieved an AUC of 0.97 (95% confidence interval, 0.88-1.00) when trained with M6. Gated transformer networks trained and optimized with the other 6 reference standards showed an AUC ranging from 0.78 (MD slope) to 0.89 (AGIS). The 7 GTNs outperformed all 7 MEMs and all 7 NBCs accordingly. Gated transformer network performance was worse for eyes with more severe glaucoma at baseline. CONCLUSIONS: Gated transformer network models trained with OCT data may be used to identify VF worsening. After further validation, implementing such models in clinical practice may allow us to track functional worsening of glaucoma with less onerous structural testing. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.

Graph-based quantum response theory and shadow Born-Oppenheimer molecular dynamics.

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born-Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. The proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

A deep learning model incorporating spatial and temporal information successfully detects visual field worsening using a consensus based approach.

Glaucoma is a leading cause of irreversible blindness, and its worsening is most often monitored with visual field (VF) testing. Deep learning models (DLM) may help identify VF worsening consistently and reproducibly. In this study, we developed and investigated the performance of a DLM on a large population of glaucoma patients. We included 5099 patients (8705 eyes) seen at one institute from June 1990 to June 2020 that had VF testing as well as clinician assessment of VF worsening. Since there is no gold standard to identify VF worsening, we used a consensus of six commonly used algorithmic methods which include global regressions as well as point-wise change in the VFs. We used the consensus decision as a reference standard to train/test the DLM and evaluate clinician performance. 80%, 10%, and 10% of patients were included in training, validation, and test sets, respectively. Of the 873 eyes in the test set, 309 [60.6%] were from females and the median age was 62.4; (IQR 54.8-68.9). The DLM achieved an AUC of 0.94 (95% CI 0.93-0.99). Even after removing the 6 most recent VFs, providing fewer data points to the model, the DLM successfully identified worsening with an AUC of 0.78 (95% CI 0.72-0.84). Clinician assessment of worsening (based on documentation from the health record at the time of the final VF in each eye) had an AUC of 0.64 (95% CI 0.63-0.66). Both the DLM and clinician performed worse when the initial disease was more severe. This data shows that a DLM trained on a consensus of methods to define worsening successfully identified VF worsening and could help guide clinicians during routine clinical care.