A systematic strategy for estimating hERG block potency and its implications in a new cardiac safety paradigm.

INTRODUCTION: hERG block potency is widely used to calculate a drug's safety margin against its torsadogenic potential. Previous studies are confounded by use of different patch clamp electrophysiology protocols and a lack of statistical quantification of experimental variability. Since the new cardiac safety paradigm being discussed by the International Council for Harmonisation promotes a tighter integration of nonclinical and clinical data for torsadogenic risk assessment, a more systematic approach to estimate the hERG block potency and safety margin is needed. METHODS: A cross-industry study was performed to collect hERG data on 28 drugs with known torsadogenic risk using a standardized experimental protocol. A Bayesian hierarchical modeling (BHM) approach was used to assess the hERG block potency of these drugs by quantifying both the inter-site and intra-site variability. A modeling and simulation study was also done to evaluate protocol-dependent changes in hERG potency estimates. RESULTS: A systematic approach to estimate hERG block potency is established. The impact of choosing a safety margin threshold on torsadogenic risk evaluation is explored based on the posterior distributions of hERG potency estimated by this method. The modeling and simulation results suggest any potency estimate is specific to the protocol used. DISCUSSION: This methodology can estimate hERG block potency specific to a given voltage protocol. The relationship between safety margin thresholds and torsadogenic risk predictivity suggests the threshold should be tailored to each specific context of use, and safety margin evaluation may need to be integrated with other information to form a more comprehensive risk assessment.

Action of clathrodin and analogues on voltage-gated sodium channels.

Clathrodin is a marine alkaloid and believed to be a modulator of voltage-gated sodium (Na(V)) channels. Since there is an urgent need for small molecule Na(V) channel ligands as novel therapeutics, clathrodin could represent an interesting lead compound. Therefore, clathrodin was reinvestigated for its potency and Na(V) channel subtype selectivity. Clathrodin and its synthetic analogues were subjected to screening on a broad range of Na(V) channel isoforms, both in voltage clamp and patch clamp conditions. Even though clathrodin was not found to exert any activity, some analogues were capable of modulating the Na(V) channels, hereby validating the pyrrole-2-aminoimidazole alkaloid structure as a core structure for future small molecule-based Na(V) channel modulators.

Architecting the Finite Element Method Pipeline for the GPU.

The finite element method (FEM) is a widely employed numerical technique for approximating the solution of partial differential equations (PDEs) in various science and engineering applications. Many of these applications benefit from fast execution of the FEM pipeline. One way to accelerate the FEM pipeline is by exploiting advances in modern computational hardware, such as the many-core streaming processors like the graphical processing unit (GPU). In this paper, we present the algorithms and data-structures necessary to move the entire FEM pipeline to the GPU. First we propose an efficient GPU-based algorithm to generate local element information and to assemble the global linear system associated with the FEM discretization of an elliptic PDE. To solve the corresponding linear system efficiently on the GPU, we implement a conjugate gradient method preconditioned with a geometry-informed algebraic multi-grid (AMG) method preconditioner. We propose a new fine-grained parallelism strategy, a corresponding multigrid cycling stage and efficient data mapping to the many-core architecture of GPU. Comparison of our on-GPU assembly versus a traditional serial implementation on the CPU achieves up to an 87 × speedup. Focusing on the linear system solver alone, we achieve a speedup of up to 51 × versus use of a comparable state-of-the-art serial CPU linear system solver. Furthermore, the method compares favorably with other GPU-based, sparse, linear solvers.

Ligand- and structure-based virtual screening for clathrodin-derived human voltage-gated sodium channel modulators.

Voltage-gated sodium channels (VGSC) are attractive targets for drug discovery because of the broad therapeutic potential of their modulators. On the basis of the structure of marine alkaloid clathrodin, we have recently discovered novel subtype-selective VGSC modulators I and II that were used as starting points for two different ligand-based virtual screening approaches for discovery of novel VGSC modulators. Similarity searching in the ZINC database of drug-like compounds based on compound I resulted in five state-dependent Na(v)1.3 and Na(v)1.7 modulators with improved activity compared to I (IC50 < 20 µM). Compounds 2 and 16 that blocked sodium permeation in Na(v)1.7 with IC50 values of 7 and 9 µM, respectively, are among the most potent clathrodin analogs discovered so far. In the case of compound II, 3D similarity searching in the same database was followed by docking of an enriched compound library into our human Na(v)1.4 open-pore homology model. Although some of the selected compounds, e.g., 31 and 32 displayed 21% and 22% inactivated state I(peak) block of Na(v)1.4 at 10 µM, respectively, none showed better Na(v)1.4 modulatory activity than compound II. Taken together, virtual screening yielded compounds 2 and 16, which represent novel scaffolds for the discovery of human Na(v)1.7 modulators.

Influence of tumor histology on preoperative staging accuracy of breast metastases to the axilla.

Histologic confirmation of axillary nodal metastases preoperatively avoids a sentinel node biopsy and enables a one step surgical procedure. The aim of this study was to establish the local positive predictive value of axillary ultrasound (AUS) and guided needle core biopsy (NCB) in axillary staging of breast cancer, and to identify factors influencing yield. A prospective audit of 142 consecutive patients (screening and symptomatic) presenting from 1st December 2008-31st May 2009 with breast lesions categorized R4-R5, who underwent a preoperative AUS, and proceeded to surgery was undertaken. Ultrasound-guided NCB was performed on nodes radiologically classified R3-R5. Lymph node size, number, and morphological features were documented. Yield was correlated with tumor size, grade, and histologic type. AUS/NCB was correlated with post surgical pathologic findings to determine sensitivity, specificity, positive and negative predictive value of AUS and NCB. A total of 142 patients underwent surgery, of whom 52 (37%) had lymph node metastases on histology. All had a preoperative AUS, 51 (36%) had abnormal ultrasound findings. 46 (90%) underwent axillary node NCB of which 24 (52%) were positive. The smallest tumor size associated with positive nodes at surgery was 11.5 mm. The sensitivity of AUS was 65%. Specificity was 81%, with a positive predictive value (PPV) of 67% and negative predictive (NPV) value of 80%. Sensitivity of U/S-guided NCB was 75%, with a specificity of 100%, PPV 100% and NPV 64%. Sensitivity of AUS for lobular carcinoma was 36% versus 76% for all other histologies. Sensitivity of NCB for lobular cancer was 33% versus 79% for all other histologies. The most significant factor producing discordance between preoperative AUS and definitive histologic evidence of lymph node metastasis was tumor type. Accurate preoperative lymph node staging was prejudiced by lobular histology (p < 0.0019).

A study of different modeling choices for simulating platelets within the immersed boundary method.

The Immersed Boundary (IB) method is a widely-used numerical methodology for the simulation of fluid-structure interaction problems. The IB method utilizes an Eulerian discretization for the fluid equations of motion while maintaining a Lagrangian representation of structural objects. Operators are defined for transmitting information (forces and velocities) between these two representations. Most IB simulations represent their structures with piecewise linear approximations and utilize Hookean spring models to approximate structural forces. Our specific motivation is the modeling of platelets in hemodynamic flows. In this paper, we study two alternative representations - radial basis functions (RBFs) and Fourier-based (trigonometric polynomials and spherical harmonics) representations - for the modeling of platelets in two and three dimensions within the IB framework, and compare our results with the traditional piecewise linear approximation methodology. For different representative shapes, we examine the geometric modeling errors (position and normal vectors), force computation errors, and computational cost and provide an engineering trade-off strategy for when and why one might select to employ these different representations.

Time Is a Critical Factor When Evaluating Oligonucleotide Therapeutics in hERG Assays.

In accord with International Conference on Harmonization S7B guidelines, an in vitro human ether-a-go-go-related gene (hERG) assay is one component of an integrated risk assessment for delayed ventricular repolarization. Function of hERG could be affected by direct (acute) mechanisms, or by indirect (chronic) mechanisms. Some approved oligonucleotide therapeutics had submitted hERG data to regulatory agents, which were all collected with the same protocol used for small-molecule testing (incubation time <20 min; acute), however, oligonucleotides have unique mechanisms and time courses of action (indirect). To reframe the hERG testing strategy for silencing RNA (siRNA), an investigation was performed to assess the time course for siRNA-mediated inhibition of hERG function and gene expression. Commercially available siRNAs of hERG were evaluated in a stable hERG-expressed cell line by whole-cell voltage clamp using automated electrophysiology and polymerase chain reaction. In the acute hERG study, no effects were observed after treatment with 100 nM siRNA for 20 min. The chronic effects of 100 nM siRNAs on hERG function were evaluated and recorded over 8-48 h following transfection. At 8 h there was no significant effect, whereas 77% reduction was observed at 48 h. Measurement of hERG mRNA levels demonstrated a 79% and 93% decrease of hERG mRNA at 8 and 48 h, respectively, consistent with inhibition of hERG transcription. The results indicate that an anti-hERG siRNA requires a long exposure time (48 h) in the hERG assay to produce a maximal reduction in hERG current; short exposures (20 min-8 h) had no effect. These findings imply that off-target profiling of novel oligonucleotides could benefit from using hERG protocol with long incubation times to de-risk potential off-target (indirect) effects on the hERG channel. This hERG assay modification may be important to consider if the findings are used to support an integrated nonclinical-clinical risk assessment for QTc (the duration of the QT interval adjusted for heart rate) prolongation.

New aryl and acylsulfonamides as state-dependent inhibitors of Nav1.3 voltage-gated sodium channel.

Voltage-gated sodium channels (Navs) play an essential role in neurotransmission, and their dysfunction is often a cause of various neurological disorders. The Nav1.3 isoform is found in the CNS and upregulated after injury in the periphery, but its role in human physiology has not yet been fully elucidated. Reports suggest that selective Nav1.3 inhibitors could be used as novel therapeutics to treat pain or neurodevelopmental disorders. Few selective inhibitors of this channel are known in the literature. In this work, we report the discovery of a new series of aryl and acylsulfonamides as state-dependent inhibitors of Nav1.3 channels. Using a ligand-based 3D similarity search and subsequent hit optimization, we identified and prepared a series of 47 novel compounds and tested them on Nav1.3, Nav1.5, and a selected subset also on Nav1.7 channels in a QPatch patch-clamp electrophysiology assay. Eight compounds had an IC50 value of less than 1 µM against the Nav1.3 channel inactivated state, with one compound displaying an IC50 value of 20 nM, whereas activity against the inactivated state of the Nav1.5 channel and Nav1.7 channel was approximately 20-fold weaker. None of the compounds showed use-dependent inhibition of the cardiac isoform Nav1.5 at a concentration of 30 µM. Further selectivity testing of the most promising hits was measured using the two-electrode voltage-clamp method against the closed state of the Nav1.1-Nav1.8 channels, and compound 15b displayed small, yet selective, effects against the Nav1.3 channel, with no activity against the other isoforms. Additional selectivity testing of promising hits against the inactivated state of the Nav1.3, Nav1.7, and Nav1.8 channels revealed several compounds with robust and selective activity against the inactivated state of the Nav1.3 channel among the three isoforms tested. Moreover, the compounds were not cytotoxic at a concentration of 50 µM, as demonstrated by the assay in human HepG2 cells (hepatocellular carcinoma cells). The novel state-dependent inhibitors of Nav1.3 discovered in this work provide a valuable tool to better evaluate this channel as a potential drug target.

Multi-Omic Integration of Blood-Based Tumor-Associated Genomic and Lipidomic Profiles Using Machine Learning Models in Metastatic Prostate Cancer.

PURPOSE: To determine prognostic and predictive clinical outcomes in metastatic hormone-sensitive prostate cancer (mHSPC) and metastatic castrate-resistant prostate cancer (mCRPC) on the basis of a combination of plasma-derived genomic alterations and lipid features in a longitudinal cohort of patients with advanced prostate cancer. METHODS: A multifeature classifier was constructed to predict clinical outcomes using plasma-based genomic alterations detected in 120 genes and 772 lipidomic species as informative features in a cohort of 71 patients with mHSPC and 144 patients with mCRPC. Outcomes of interest were collected over 11 years of follow-up. These included in mHSPC state early failure of androgen-deprivation therapy (ADT) and exceptional responders to ADT; early death (poor prognosis) and long-term survivors in mCRPC state. The approach was to build binary classification models that identified discriminative candidates with optimal weights to predict outcomes. To achieve this, we built multi-omic feature-based classifiers using traditional machine learning (ML) methods, including logistic regression with sparse regularization, multi-kernel Gaussian process regression, and support vector machines. RESULTS: The levels of specific ceramides (d18:1/14:0 and d18:1/17:0), and the presence of CHEK2 mutations, AR amplification, and RB1 deletion were identified as the most crucial factors associated with clinical outcomes. Using ML models, the optimal multi-omics feature combination determined resulted in AUC scores of 0.751 for predicting mHSPC survival and 0.638 for predicting ADT failure; and in mCRPC state, 0.687 for prognostication and 0.727 for exceptional survival. The models were observed to be superior than using a limited candidate number of features for developing multi-omic prognostic and predictive signatures. CONCLUSION: Using a ML approach that incorporates multiple omic features improves the prediction accuracy for metastatic prostate cancer outcomes significantly. Validation of these models will be needed in independent data sets in future.

Square-Net Topological Semimetals: How Spectroscopy Furthers Understanding and Control.

Square-net materials are well positioned to lead optical spectroscopic explorations into the electronic structure, photoinduced dynamics, and phase transitions in topological semimetals. Hundreds of square-net topological semimetals can be prepared that have remarkably different electronic and optical properties despite having similar structures. Here we present what has been gleaned recently from these materials with the whole gamut of optical spectroscopies, ranging from steady-state reflectance and Raman investigations into topological band structures, electronic correlations, and equilibrium phase transitions to time-resolved techniques used to decipher ultrafast relaxation dynamics and nonequilibrium photoinduced phase transitions. We end with a discussion of some major remaining questions and possible future research directions.

Particle Merging-and-Splitting.

Robustly handling collisions between individual particles in a large particle-based simulation has been a challenging problem. We introduce particle merging-and-splitting, a simple scheme for robustly handling collisions between particles that prevents inter-penetrations of separate objects without introducing numerical instabilities. This scheme merges colliding particles at the beginning of the time-step and then splits them at the end of the time-step. Thus, collisions last for the duration of a time-step, allowing neighboring particles of the colliding particles to influence each other. We show that our merging-and-splitting method is effective in robustly handling collisions and avoiding penetrations in particle-based simulations. We also show how our merging-and-splitting approach can be used for coupling different simulation systems using different and otherwise incompatible integrators. We present simulation tests involving complex solid-fluid interactions, including solid fractures generated by fluid interactions.

Development of ASIC1a ligand-gated ion channel drug screening assays across multiple automated patch clamp platforms.

Human acid-sensing ion channels (ASIC) are ligand-gated ionotropic receptors expressed widely in peripheral tissues as well as sensory and central neurons and implicated in detection of inflammation, tissue injury, and hypoxia-induced acidosis. This makes ASIC channels promising targets for drug discovery in oncology, pain and ischemia, and several modulators have progressed into clinical trials. We describe the use of hASIC1a as a case study for the development and validation of low, medium and high throughput automated patch clamp (APC) assays suitable for the screening and mechanistic profiling of new ligands for this important class of ligand-gated ion channel. Initial efforts to expand on previous manual patch work describing an endogenous hASIC1a response in HEK cells were thwarted by low current expression and unusual pharmacology, so subsequent work utilized stable hASIC1a CHO cell lines. Ligand-gated application protocols and screening assays on the Patchliner, QPatch 48, and SyncroPatch 384 were optimized and validated based on pH activation and nM-µM potency of reference antagonists (e.g., Amiloride, Benzamil, Memantine, Mambalgin-3, A-317567, PcTx1). By optimizing single and stacked pipette tip applications available on each APC platform, stable pH-evoked currents during multiple ligand applications enabled cumulative EC50 and IC50 determinations with minimized receptor desensitization. Finally, we successfully demonstrated for the first time on an APC platform the ability to use current clamp to implement the historical technique of input resistance tracking to measure ligand-gated changes in membrane conductance on the Patchliner platform.

An Audit on Oncological Safety with Magseed Localised Breast Conserving Surgery.

Wire-localised wide local excision (W-WLE) has been standard of care for impalpable breast lesions. Logistics and risks of wire localisation can be challenging. Magseed-localised wide local excision (M-WLE) is an alternative to W-WLE. We compare safety parameters and length of hospital stay (LOS) in patients undergoing M-WLE to W-WLE. All M-WLEs performed at single institution over an 8-month period were included and compared to historic matched cohort of W-WLEs who would have been suitable for Magseed localisation. Data including patient demographics, successful placements, re-excision rates, tumour size, and length of stay (LOS) was analysed. Two hundred thirty-eight patients were included in the study. Cancers were safely excised in all cases. A significant difference in re-excisions rates favouring M-WLE group was seen (2.9% vs 10.4%). Median waiting time to surgery was significantly shorter in M-WLE group (4 h 15 min vs 7 h 3 min). No significant difference in median LOS between the two groups was seen. M-WLE has been shown to be oncologically safe and non-inferior to W-WLE with significantly lower re-excision rate. Reduced pre-operative waiting time in the M-WLE group will have a positive effect on patient journey. Further research should focus on potential impact on day-bed utilisation and theatre efficiency.

Vector Field Decompositions Using Multiscale Poisson Kernel.

Extraction of multiscale features using scale-space is one of the fundamental approaches to analyze scalar fields. However, similar techniques for vector fields are much less common, even though it is well known that, for example, turbulent flows contain cascades of nested vortices at different scales. The challenge is that the ideas related to scale-space are based upon iteratively smoothing the data to extract features at progressively larger scale, making it difficult to extract overlapping features. Instead, we consider spatial regions of influence in vector fields as scale, and introduce a new approach for the multiscale analysis of vector fields. Rather than smoothing the flow, we use the natural Helmholtz-Hodge decomposition to split it into small-scale and large-scale components using progressively larger neighborhoods. Our approach creates a natural separation of features by extracting local flow behavior, for example, a small vortex, from large-scale effects, for example, a background flow. We demonstrate our technique on large-scale, turbulent flows, and show multiscale features that cannot be extracted using state-of-the-art techniques.

The Effect of Data Transformations on Scalar Field Topological Analysis of High-Order FEM Solutions.

High-order finite element methods (HO-FEM) are gaining popularity in the simulation community due to their success in solving complex flow dynamics. There is an increasing need to analyze the data produced as output by these simulations. Simultaneously, topological analysis tools are emerging as powerful methods for investigating simulation data. However, most of the current approaches to topological analysis have had limited application to HO-FEM simulation data for two reasons. First, the current topological tools are designed for linear data (polynomial degree one), but the polynomial degree of the data output by these simulations is typically higher (routinely up to polynomial degree six). Second, the simulation data and derived quantities of the simulation data have discontinuities at element boundaries, and these discontinuities do not match the input requirements for the topological tools. One solution to both issues is to transform the high-order data to achieve low-order, continuous inputs for topological analysis. Nevertheless, there has been little work evaluating the possible transformation choices and their downstream effect on the topological analysis. We perform an empirical study to evaluate two commonly used data transformation methodologies along with the recently introduced L-SIAC filter for processing high-order simulation data. Our results show diverse behaviors are possible. We offer some guidance about how best to consider a pipeline of topological analysis of HO-FEM simulations with the currently available implementations of topological analysis.

Patient-reported Upper Limb Function After Sentinel Lymph Node Biopsy for Breast Cancer: A Prospective Observational Study.

INTRODUCTION: Sentinel lymph node biopsy (SLNB) is the standard procedure for axillary staging in breast cancer. There is a lack of consistency in studies reporting on upper limb morbidity after SLNB. We present a prospective study evaluating upper limb function after SLNB using the validated quickDASH questionnaire. MATERIALS AND METHODS: Consecutive patients who underwent wide local excision and SLNB were included in the study. Arm function was assessed using the quickDASH questionnaire at 3 time points - prior to surgery and 2 weeks and 3 months after SLNB. The scores obtained were labeled as A, B, and C respectively. The mean and median scores were compared using the paired t test and Wilcoxon signed rank test. RESULTS: Ninety-nine patients met all inclusion criteria and were included in the final analysis. The mean A, B, and C scores were 8.46, 16.05, and 13.36. The median A, B, and C scores were 2.27, 7.5, and 4.54. There was a statistically significant difference between mean and median A and B scores, B and C scores, and A and C scores. A similar trend was observed in patients with better preoperative upper limb function. Patients with a higher body mass index had significantly worse B and C scores. CONCLUSION: There is a significant deterioration in upper limb function following SLNB. This improves at 3 months but does not reach baseline levels. Larger studies with long-term follow-up are required to establish the extent of upper limb functional morbidity and natural course of functional recovery after SLNB.

Transient Drude Response Dominates Near-Infrared Pump-Probe Reflectivity in Nodal-Line Semimetals ZrSiS and ZrSiSe.

The ultrafast optical response of nodal-line semimetals ZrSiS and ZrSiSe was studied in the near-infrared using transient reflectivity. The materials exhibit similar responses, characterized by two features, well-resolved in time and energy; the first decays after hundreds of femtoseconds, and the second lasts for nanoseconds. Using Drude-Lorentz fits of the materials' equilibrium reflectance, we show that these are well-represented by a sudden change of the electronic properties (increase of screening or reduction of the plasma frequency) followed by an increase of the Drude scattering rate. This directly connects the transient data to a physical picture in which carriers, after excitation into the conduction band, return to the valence band by sharing excess energy with the phonon bath, resulting in a hot lattice that relaxes through slow diffusive processes. The emerging picture reveals that the sudden electronic reorganization instantaneously modifies the materials' electronic properties on a time scale not compatible with electron-phonon thermalization.

Weyl fermions, Fermi arcs, and minority-spin carriers in ferromagnetic CoS2.

Magnetic Weyl semimetals are a newly discovered class of topological materials that may serve as a platform for exotic phenomena, such as axion insulators or the quantum anomalous Hall effect. Here, we use angle-resolved photoelectron spectroscopy and ab initio calculations to discover Weyl cones in CoS2, a ferromagnet with pyrite structure that has been long studied as a candidate for half-metallicity, which makes it an attractive material for spintronic devices. We directly observe the topological Fermi arc surface states that link the Weyl nodes, which will influence the performance of CoS2 as a spin injector by modifying its spin polarization at interfaces. In addition, we directly observe a minority-spin bulk electron pocket in the corner of the Brillouin zone, which proves that CoS2 cannot be a true half-metal.

Effect of selective IK,ACh inhibition by XAF-1407 in an equine model of tachypacing-induced persistent atrial fibrillation.

BACKGROUND AND PURPOSE: Inhibition of the G-protein gated ACh-activated inward rectifier potassium current, IK,ACh may be an effective atrial selective treatment strategy for atrial fibrillation (AF). Therefore, the anti-arrhythmic and electrophysiological properties of a novel putatively potent and highly specific IK,ACh inhibitor, XAF-1407 (3-methyl-1-[5-phenyl-4-[4-(2-pyrrolidin-1-ylethoxymethyl)-1-piperidyl]thieno[2,3-d]pyrimidin-6-yl]azetidin-3-ol), were characterised for the first time in vitro and investigated in horses with persistent AF. EXPERIMENTAL APPROACH: The pharmacological ion channel profile of XAF-1407 was investigated using cell lines expressing relevant ion channels. In addition, eleven horses were implanted with implantable cardioverter defibrillators enabling atrial tachypacing into self-sustained AF. The electrophysiological effects of XAF-1407 were investigated after serial cardioversions over a period of 1 month. Cardioversion success, drug-induced changes of atrial tissue refractoriness, and ventricular electrophysiology were assessed at baseline (day 0) and days 3, 5, 11, 17, and 29 after AF induction. KEY RESULTS: XAF-1407 potently and selectively inhibited Kir 3.1/3.4 and Kir 3.4/3.4, underlying the IK,ACh current. XAF-1407 treatment in horses prolonged atrial effective refractory period as well as decreased atrial fibrillatory rate significantly (~20%) and successfully cardioverted AF, although with a decreasing efficacy over time. XAF-1407 shortened atrioventricular-nodal refractoriness, without effect on QRS duration. QTc prolongation (4%) within 15 min of drug infusion was observed, however, without any evidence of ventricular arrhythmia. CONCLUSION AND IMPLICATIONS: XAF-1407 efficiently cardioverted sustained tachypacing-induced AF of short duration in horses without notable side effects. This supports IK,ACh inhibition as a potentially safe treatment of paroxysmal AF in horses, suggesting potential clinical value for other species including humans.