Abnormal morphology biases hematocrit distribution in tumor vasculature and contributes to heterogeneity in tissue oxygenation.

Oxygen heterogeneity in solid tumors is recognized as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal vascular structure of the tumor, but the precise mechanisms linking abnormal structure and compromised oxygen transport are only partially understood. In this paper, we investigate the role that red blood cell (RBC) transport plays in establishing oxygen heterogeneity in tumor tissue. We focus on heterogeneity driven by network effects, which are challenging to observe experimentally due to the reduced fields of view typically considered. Motivated by our findings of abnormal vascular patterns linked to deviations from current RBC transport theory, we calculated average vessel lengths [Formula: see text] and diameters [Formula: see text] from tumor allografts of three cancer cell lines and observed a substantial reduction in the ratio [Formula: see text] compared to physiological conditions. Mathematical modeling reveals that small values of the ratio λ (i.e., [Formula: see text]) can bias hematocrit distribution in tumor vascular networks and drive heterogeneous oxygenation of tumor tissue. Finally, we show an increase in the value of λ in tumor vascular networks following treatment with the antiangiogenic cancer agent DC101. Based on our findings, we propose λ as an effective way of monitoring the efficacy of antiangiogenic agents and as a proxy measure of perfusion and oxygenation in tumor tissue undergoing antiangiogenic treatment.

Physician-reported Clinical Unmet Needs, Burden and Treatment Patterns of Paediatric Psoriasis Patients: A US and EU Real-world Evidence Study.

This study is a retrospective analysis using data collected from the Adelphi Paediatric Psoriasis Disease-Specific Programme cross-sectional survey. Despite being treated for their psoriasis, a substantial proportion of paediatric patients presented with moderate (18.3%) or severe (1.3%) disease at sampling; 42.9% and 92.0% had a body surface area (BSA) of >10%, and 38.8% and 100.0% had a Psoriasis Area Severity Index (PASI) score >10, respectively. Overall, 69.9% of patients had only ever been treated with a topical therapy for their psoriasis. For patients with moderate or severe disease at sampling, 16.3% and 14.4% were currently receiving conventional systemics or biologic therapy, respectively. There is a clinical unmet need in this paediatric population; a considerable percentage of patients still experienced moderate or severe disease and persistent psoriasis symptoms, with numerous body areas affected. A significant proportion of patients were undertreated, which may explain the high burden of disease observed.

Descriptors of Sepsis Using the Sepsis-3 Criteria: A Cohort Study in Critical Care Units Within the U.K. National Institute for Health Research Critical Care Health Informatics Collaborative.

OBJECTIVES: To describe the epidemiology of sepsis in critical care by applying the Sepsis-3 criteria to electronic health records. DESIGN: Retrospective cohort study using electronic health records. SETTING: Ten ICUs from four U.K. National Health Service hospital trusts contributing to the National Institute for Health Research Critical Care Health Informatics Collaborative. PATIENTS: A total of 28,456 critical care admissions (14,332 emergency medical, 4,585 emergency surgical, and 9,539 elective surgical). MEASUREMENTS AND MAIN RESULTS: Twenty-nine thousand three hundred forty-three episodes of clinical deterioration were identified with a rise in Sequential Organ Failure Assessment score of at least 2 points, of which 14,869 (50.7%) were associated with antibiotic escalation and thereby met the Sepsis-3 criteria for sepsis. A total of 4,100 episodes of sepsis (27.6%) were associated with vasopressor use and lactate greater than 2.0 mmol/L, and therefore met the Sepsis-3 criteria for septic shock. ICU mortality by source of sepsis was highest for ICU-acquired sepsis (23.7%; 95% CI, 21.9-25.6%), followed by hospital-acquired sepsis (18.6%; 95% CI, 17.5-19.9%), and community-acquired sepsis (12.9%; 95% CI, 12.1-13.6%) (p for comparison less than 0.0001). CONCLUSIONS: We successfully operationalized the Sepsis-3 criteria to an electronic health record dataset to describe the characteristics of critical care patients with sepsis. This may facilitate sepsis research using electronic health record data at scale without relying on human coding.

A Caching Scheme To Accelerate Kinetic Monte Carlo Simulations of Catalytic Reactions.

Kinetic Monte Carlo (KMC) simulations have been instrumental in advancing our fundamental understanding of heterogeneously catalyzed reactions, with particular emphasis on structure sensitivity, ensemble effects, and the interplay between adlayer structure and adsorbate-adsorbate lateral interactions in shaping the observed kinetics. Yet, the computational cost of KMC remains high, thereby motivating the development of acceleration schemes that would improve the simulation efficiency. We present an exact such scheme, which implements a caching algorithm along with shared-memory parallelization to improve the computational performance of simulations incorporating long-range adsorbate-adsorbate lateral interactions. This scheme is based on caching information about the energetic interaction patterns associated with the products of each possible lattice process (adsorption, desorption, reaction etc.). Thus, every time a reaction occurs ("ongoing reaction"), it enables fast updates of the rate constants of "affected reactions", i.e., possible reactions in the region of influence of the "ongoing reaction". Benchmarks on KMC simulations of NOx oxidation/reduction, yielded acceleration factors of up to 20, when comparing single-thread runs without caching to runs on 16 threads with caching, for simulations with a cluster expansion Hamiltonian that incorporates up to 8th-nearest-neighbor interactions.

Real-world outcomes in patients with chronic spontaneous urticaria receiving omalizumab: insights from a clinical practice survey.

OBJECTIVE: Chronic spontaneous urticaria (CSU) is a debilitating inflammatory skin condition, often impacting quality of life. International guidelines recommend omalizumab, an anti-immunoglobulin E antibody, for second-line treatment. Our objective was to understand patient characteristics associated with prescription of omalizumab, and assess real-world outcomes in patients with CSU treated with omalizumab. METHODS: We analyzed data from the Adelphi Real World CSU Disease Specific Programme, a cross-sectional survey with retrospective data collection (December 2020-October 2021) from physicians and patients with CSU in the United States. RESULTS: Data from allergists (n = 45), dermatologists (n = 51), and primary care physicians (PCPs; n = 20) were included. At the time of data collection, one-third of patients were receiving omalizumab (n = 220) and 67% were eligible for but not receiving omalizumab (n = 455). Using logistic regression, the odds of receiving omalizumab were higher in patients whose entire bodies were affected by hives [odds ratio (OR) = 2.551; 95% confidence interval (CI) 1.502-4.333; p < 0.001] or with deteriorating/unstable prognoses at treatment initiation [OR = 2.219; 95% CI 1.031-4.777; p = 0.042], and lower in patients managed by PCPs [OR = 0.276; 95% CI 0.130-0.584; p < 0.001]. Estimates from an inverse probability weighted regression adjustment model indicated that patients receiving omalizumab had higher treatment satisfaction, improvements in itching, hives, angioedema, insomnia, and anxiety, and lower impact on work productivity, compared with patients not receiving omalizumab. CONCLUSION: Around two-thirds of patients with CSU considered eligible for omalizumab were not receiving the guideline-recommended therapy. Patients receiving omalizumab had better real-world outcomes compared with patients not receiving omalizumab. Ensuring patients receive the most appropriate treatment could benefit patients with CSU.

People with a skin rash known as chronic spontaneous urticaria (also called long-lasting hives) have itchy spots that last longer than 6 weeks. People with long-lasting hives may be treated with a medicine called omalizumab to help their itching. We asked doctors why they gave some people omalizumab. We found that only one out of every three people with long-lasting hives were given omalizumab. Doctors gave some people omalizumab because they had long-lasting hives on their whole body or their hives were getting worse. Other people received omalizumab because they were seeing a specialist doctor (allergist) instead of a primary care physician (also called a general practitioner). When compared with people who received other medicines, people being treated with omalizumab had reduced itching, less anxiety, and better well-being. These findings could help doctors choose the right medicine for people with long-lasting hives.

Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions.

Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.

Real-world health outcomes in US adult patients with mild to moderate plaque psoriasis taking topical therapy.

BACKGROUND: Limited health outcomes information exists for patients with mild to moderate plaque psoriasis (hereafter, referred to as psoriasis) prescribed topical treatment(s). AIM: We evaluated clinical characteristics of patients with systemic-naïve mild to moderate psoriasis after topical use in the United States. METHODS: Data were drawn from 2017 to 2018 Adelphi Psoriasis Disease Specific Programme™, a point-in-time survey of physicians and adult psoriasis patients, capturing data on topical treatment at time of consultation prescribed to systemic-naïve patients with mild to moderate psoriasis (i.e. body surface area [BSA] ≤ 10%) at current treatment initiation. Patient clinical characteristics before/after topical use were evaluated descriptively. RESULTS: Among 304 patients (median age 43.0 years; 53.6% female), mean time since diagnosis was 60.9 months. After a mean 6.9 months on their current topical, 14.5% of patients achieved ≥75% BSA reduction, 38.9% ≥50% BSA reduction, and 50.2% no BSA reduction. Residual psoriasis symptoms included scaling (76.5%), inflamed skin (65.9%), and itching (60.4%). Most patients (71.2%) had residual psoriasis in special body areas: nails (92.3%), palmoplantar (78.9%), scalp (75.9%), and face (65.8%). CONCLUSION: We found unmet need in topical treatment effectiveness in mild to moderate psoriasis patients, in terms of BSA reduction, symptoms, and special body areas affected.

Bayesian imputation of COVID-19 positive test counts for nowcasting under reporting lag.

Obtaining up to date information on the number of UK COVID-19 regional infections is hampered by the reporting lag in positive test results for people with COVID-19 symptoms. In the UK, for 'Pillar 2' swab tests for those showing symptoms, it can take up to five days for results to be collated. We make use of the stability of the under reporting process over time to motivate a statistical temporal model that infers the final total count given the partial count information as it arrives. We adopt a Bayesian approach that provides for subjective priors on parameters and a hierarchical structure for an underlying latent intensity process for the infection counts. This results in a smoothed time-series representation nowcasting the expected number of daily counts of positive tests with uncertainty bands that can be used to aid decision making. Inference is performed using sequential Monte Carlo.

CMakeCatchTemplate: A C++ template project.

CMakeCatchTemplate (https://github.com/MattClarkson/CMakeCatchTemplate) is a project to provide a starting structure for C++ projects configured with CMake, that can be customised to work in a variety of scenarios, allowing developers to deploy new algorithms to users in a shorter timeframe. Main features include a SuperBuild to build optional dependencies; unit tests using Catch; support for CUDA, OpenMP and MPI; examples of command line and GUI applications; Doxygen integration; Continuous Integration templates and support for building/deploying Python modules.

Full, Partial, and Modified Permutations of the Mayo Score: Characterizing Clinical and Patient-Reported Outcomes in Ulcerative Colitis Patients.

Background: Understanding ulcerative colitis disease activity assessed via the full, modified, or partial Mayo Score may help clinicians apply results from clinical trials to practice and facilitate interpretation of recent and older studies. Methods: Mayo Score variables were assessed in a cross-sectional study of 2608 ulcerative colitis patients. Results: Permutations of Mayo Scores were highly correlated, and models predicting the omitted variable from each permutation demonstrated significant agreement between predicted and observed values. Conclusions: Partial/modified Mayo Scores may be used to predict endoscopic and Physician's Global Assessment scores, and serve as proxies for the full Mayo Score in clinical practice/trials.

abYsis: Integrated Antibody Sequence and Structure-Management, Analysis, and Prediction.

abYsis is a web-based antibody research system that includes an integrated database of antibody sequence and structure data. The system can be interrogated in numerous ways-from simple text and sequence searches to sophisticated queries that apply 3D structural constraints. The publicly available version includes pre-analyzed sequence data from the European Molecular Biology Laboratory European Nucleotide Archive (EMBL-ENA) and Kabat as well as structure data from the Protein Data Bank. A researcher's own sequences can also be analyzed through the web interface. A defining characteristic of abYsis is that the sequences are automatically numbered with a series of popular schemes such as Kabat and Chothia and then annotated with key information such as complementarity-determining regions and potential post-translational modifications. A unique aspect of abYsis is a set of residue frequency tables for each position in an antibody, allowing "unusual residues" (those rarely seen at a particular position) to be highlighted and decisions to be made on which mutations may be acceptable. This is especially useful when comparing antibodies from different species. abYsis is useful for any researcher specializing in antibody engineering, especially those developing antibodies as drugs. abYsis is available at www.abysis.org.

Simplification and its consequences in biological modelling: conclusions from a study of calcium oscillations in hepatocytes.

Systems Biology requires that biological modelling is scaled up from small components to system level. This can produce exceedingly complex models, which obscure understanding rather than facilitate it. The successful use of highly simplified models would resolve many of the current problems faced in Systems Biology. This paper questions whether the conclusions of simple mathematical models of biological systems are trustworthy. The simplification of a specific model of calcium oscillations in hepatocytes is examined in detail, and the conclusions drawn from this scrutiny generalized. We formalize our choice of simplification approach through the use of functional 'building blocks'. A collection of models is constructed, each a progressively more simplified version of a well-understood model. The limiting model is a piecewise linear model that can be solved analytically. We find that, as expected, in many cases the simpler models produce incorrect results. However, when we make a sensitivity analysis, examining which aspects of the behaviour of the system are controlled by which parameters, the conclusions of the simple model often agree with those of the richer model. The hypothesis that the simplified model retains no information about the real sensitivities of the unsimplified model can be very strongly ruled out by treating the simplification process as a pseudo-random perturbation on the true sensitivity data. We conclude that sensitivity analysis is, therefore, of great importance to the analysis of simple mathematical models in biology. Our comparisons reveal which results of the sensitivity analysis regarding calcium oscillations in hepatocytes are robust to the simplifications necessarily involved in mathematical modelling. For example, we find that if a treatment is observed to strongly decrease the period of the oscillations while increasing the proportion of the cycle during which cellular calcium concentrations are rising, without affecting the inter-spike or maximum calcium concentrations, then it is likely that the treatment is acting on the plasma membrane calcium pump.

Choice of boundary condition for lattice-Boltzmann simulation of moderate-Reynolds-number flow in complex domains.

Modeling blood flow in larger vessels using lattice-Boltzmann methods comes with a challenging set of constraints: a complex geometry with walls and inlets and outlets at arbitrary orientations with respect to the lattice, intermediate Reynolds (Re) number, and unsteady flow. Simple bounce-back is one of the most commonly used, simplest, and most computationally efficient boundary conditions, but many others have been proposed. We implement three other methods applicable to complex geometries [Guo, Zheng, and Shi, Phys. Fluids 14, 2007 (2002); Bouzidi, Firdaouss, and Lallemand, Phys. Fluids 13, 3452 (2001); Junk and Yang, Phys. Rev. E 72, 066701 (2005)] in our open-source application hemelb. We use these to simulate Poiseuille and Womersley flows in a cylindrical pipe with an arbitrary orientation at physiologically relevant Re number (1-300) and Womersley (4-12) numbers and steady flow in a curved pipe at relevant Dean number (100-200) and compare the accuracy to analytical solutions. We find that both the Bouzidi-Firdaouss-Lallemand (BFL) and Guo-Zheng-Shi (GZS) methods give second-order convergence in space while simple bounce-back degrades to first order. The BFL method appears to perform better than GZS in unsteady flows and is significantly less computationally expensive. The Junk-Yang method shows poor stability at larger Re number and so cannot be recommended here. The choice of collision operator (lattice Bhatnagar-Gross-Krook vs multiple relaxation time) and velocity set (D3Q15 vs D3Q19 vs D3Q27) does not significantly affect the accuracy in the problems studied.

Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis.

There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In this paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurring in areas where wall shear stress (WSS) gradients exist. We propose two possible mechanisms to account for the observed increase in velocity and WSS between P5 and P6: (i) the measured reduction in typical vessel diameter between both time points and (ii) the reduction in network density triggered by the pruning process. The methodology developed herein is applicable to other biomedical domains where microvasculature can be imaged but experimental flow measurements are unavailable or difficult to obtain.

Impact of blood rheology on wall shear stress in a model of the middle cerebral artery.

Perturbations to the homeostatic distribution of mechanical forces exerted by blood on the endothelial layer have been correlated with vascular pathologies, including intracranial aneurysms and atherosclerosis. Recent computational work suggests that, in order to correctly characterize such forces, the shear-thinning properties of blood must be taken into account. To the best of our knowledge, these findings have never been compared against experimentally observed pathological thresholds. In this work, we apply the three-band diagram (TBD) analysis due to Gizzi et al. (Gizzi et al. 2011 Three-band decomposition analysis of wall shear stress in pulsatile flows. Phys. Rev. E 83, 031902. (doi:10.1103/PhysRevE.83.031902)) to assess the impact of the choice of blood rheology model on a computational model of the right middle cerebral artery. Our results show that, in the model under study, the differences between the wall shear stress predicted by a Newtonian model and the well-known Carreau-Yasuda generalized Newtonian model are only significant if the vascular pathology under study is associated with a pathological threshold in the range 0.94-1.56 Pa, where the results of the TBD analysis of the rheology models considered differs. Otherwise, we observe no significant differences.