Parallel Patch Research Articles

PAC-UNet: Parallel Dual Self-Attention with Convolution for Meniscal MRI Image Segmentation

Meniscal tears are common sports-injury disorders, and thus accurate segmentation of the meniscus is a worthwhile means of medical diagnosis. However, due to the limited research on image segmentation of the meniscus, most previous works have poor segmentation effects on the meniscus, which affects the adoption of assisted medical diagnosis of meniscus. To address this issue, we propose an improved neural network model, termed as the PAC-UNet model, which introduces a parallel dual self-attention with depth-wise convolution for the meniscus image segmentation. Firstly, in the encoder stage, the parallel block is used to eliminate the negative impact of weak modeling ability caused by weight sharing on shared dimensions, so as to better learn the semantic information. Then, in the decoder stage, the parallel block and patch expansion are used to restore the predicted results of meniscus segmentation by performing self-attention and up-sampling on the features. By analyzing the outcomes of experiments on the meniscus dataset, which were collected from the hospital, it is found that the proposed network performed better than other medical image segmentation networks, where the average Dice Similarity Coefficient (DSC), Intersection Over Union (IOU), precision, and Hausdorff_95 of the medial meniscus and lateral meniscus are up to 89.01%, 80.81%, 90.5%, and 2.43, respectively.

Development of automated patch clamp assays to overcome the burden of variants of uncertain significance in inheritable arrhythmia syndromes.

Advances in next-generation sequencing have been exceptionally valuable for identifying variants in medically actionable genes. However, for most missense variants there is insufficient evidence to permit definitive classification of variants as benign or pathogenic. To overcome the deluge of Variants of Uncertain Significance, there is an urgent need for high throughput functional assays to assist with the classification of variants. Advances in parallel planar patch clamp technologies has enabled the development of automated high throughput platforms capable of increasing throughput 10- to 100-fold compared to manual patch clamp methods. Automated patch clamp electrophysiology is poised to revolutionize the field of functional genomics for inheritable cardiac ion channelopathies. In this review, we outline i) the evolution of patch clamping, ii) the development of high-throughput automated patch clamp assays to assess cardiac ion channel variants, iii) clinical application of these assays and iv) where the field is heading.

Improving povidone-iodine and iodine preparations for patch testing.

Allergy evaluation by patch testing with povidone-iodine (PVP-I) or iodine remains challenging, because current patch test preparations frequently lead to false-positive or irritant skin reactions. To investigate different preparations for iodine patch tests and to assess their clinical relevance with repeated open application tests (ROATs). We monocentrically analyzed 95 patients with suspected allergy to disinfectants in retrospect who underwent parallel iodine patch testing with four preparations: PVP-I 2% aq., 5% aq., 10% aq., and iodine 0.5% pet. In 27 of 95 patients (28.4%), we found positive reactions to one of the four test preparations. After ROATs in 22 of these 27 positively tested individuals, only one patient was diagnosed with iodine allergy. In contrast, 31 of 95 patients (32.6%) showed irritant or questionable patch test reactions on day 2 (D2) and/or D3 and/or D7 to one or more test preparations. Testing with PVP-I 2% aq. resulted in the lowest number of doubtful skin reactions while detecting the single allergic patient. PVP-I 2% aq. was found to be the optimal patch test preparation. In general, iodine allergy appears to be substantially overestimated, and positive patch test responses to iodine should prompt an urgent ROAT for confirmation before diagnosing iodine allergy.

Evaluating the usage of fault localization in automated program repair: an empirical study

Fault localization techniques are originally proposed to assist in manual debugging by generally producing a rank list of suspicious locations. With the increasing popularity of automated program repair, the fault localization techniques have been introduced to effectively reduce the search space of automated program repair. Unlike developers who mainly focus on the rank information, current automated program repair has two strategies to use the fault localization information: suspiciousness-first algorithm (SFA) based on the suspiciousness accuracy and rank-first algorithm (RFA) relying on the rank accuracy. However, despite the fact that the two different usages are widely adopted by current automated program repair and may result in different repair results, little is known about the impacts of the two strategies on automated program repair. In this paper we empirically compare the performance of SFA and RFA in the context of automated program repair. Specifically, we implement the two strategies and six well-studied fault localization techniques into four state-of-the-art automated program repair tools, and then use these tools to perform repair experiments on 60 real-world bugs from Defects4J. Our study presents a number of interesting findings: RFA outperforms SFA in 70.02% of cases when measured by the number of candidate patches generated before a valid patch is found (NCP), while SFA performs better in parallel repair and patch diversity; the performance of SFA can be improved by increasing the suspiciousness accuracy of fault localization techniques; finally, we use SimFix that deploys SFA to successfully repair four extra Defects4J bugs which cannot be repaired by SimFix originally using RFA. These observations provide a new perspective for future research on the usage and improvement of fault localization in automated program repair.

Millimeter-Wave TE20-Mode SIW Dual-Slot-Fed Patch Antenna Array With a Compact Differential Feeding Network

A millimeter-wave series–parallel patch antenna array is presented, in which the dual-slot feeding structure is handily implemented using the intrinsic field distribution of TE20 mode in substrate-integrated waveguide (SIW). One 28 GHz patch antenna element fed by the TE20-mode SIW is first designed, achieving a 10 dB impedance bandwidth of 10.2% and a simulated peak gain of 6.48 dBi. Based on the antenna element, a $4 \times 4$ array with a compact series–parallel differential feeding network is developed accordingly. Due to the novel compact SIW-based series–parallel feeding network, the antenna array can achieve superior radiation performances, which is the highlight of this communication. The simulation and measurement results of the proposed antenna array are in good agreement, demonstrating a performance of 8.5% impedance bandwidth, 19.1 dBi peak gain, symmetrical radiation patterns, and low cross-polarization levels (−30 dB in E-plane and −25 dB in H-plane) in the operating frequency band of 26.65–29.14 GHz.

A compact circularly‐polarized GPS antenna using LTCC technology

ABSTRACTA circularly‐polarized GPS antenna for L1 (1575 MHz) is designed and fabricated using low temperature cofired ceramic (LTCC) technology. A parallel patch and high dielectric constant composite ceramic with LTCC fabrication method are employed to design a compact structure. The electrical connected parallel patch interval and size are the main parameters for achieving resonance frequency at L1‐band to support modern GPS coding schemes. The proposed electrically connected upper and lower patches are connected together with vertical via pins and therefore did not have any connection with the ground plane. By embedding a truncated corner patch and rectangular slots to this design, the right‐hand circularly‐polarized (RHCP) field property is achieved. By using these features, a compact simple CP‐GPS antenna with 2.32 dBic gain at 1575 MHz is designed and fabricated. The proposed antenna has a total compact size of 15 × 15× 4 mm3and operates over the frequency band from 1570 to 1585 MHz for VSWR < 2. © 2016 Wiley Periodicals, Inc. Microwave Opt Technol Lett 58:2926–2930, 2016

Comprehensive Cardiac Safety Screening: Pharmacology of Stem Cell-Derived Cardiomyocytes using High-Throughput Automated Patch Clamp

Drug discovery is challenged by poor predictability of proarrhythmic effects of present safety screening approaches. The Comprehensive in Vitro Proarrhythmia Assay (CiPA), an FDA-directed initiative, is specifically focused on improved preclinical assessment of torsade de pointes (TdP) risk, striving to optimize the drug discovery process.In recent years, human stem cell-derived cardiomyocytes have proven to recapitulate key features of human cardiac electrophysiology in vitro. Furthermore, it has become apparent that the intact ensemble of cardiac ion channels is necessary to determine proarrhythmic effects reliably. Hence, due to their relatively easy availability, stem cell-derived cardiomyocytes have become the preferred choice of cardiac cells.We present chip-based approaches allowing parallel patch clamp recordings without compromising data quality or technical sophistication. Culture and harvesting protocols have been optimized on cardiomyocytes for success rate but also the number of cells used.We show patch clamp data from two automated patch clamp platforms (medium throughput - Patchliner and high throughput - SyncroPatch 384/768PE). The Patchliner and the SyncroPatch 384/768PE both boast temperature control to enable recordings at physiological temperature - an important feature since drug efficacies may vary with temperature. Here, we present pharmacological data on voltage-dependent channels of the CiPA panel at different temperatures.The effect of drugs on action potentials is important for assessing the interaction of the cardiac ion channel ensemble. Both patch clamp platforms have amplifiers capable of current clamp. Compound effects on action potentials will also be presented.Patchliner and SyncroPatch 384/768PE are both planar patch-clamp platforms combining all the necessary features for successful drug discovery (well-suited for stem cell-derived cardiomyocytes, temperature control, and current clamp mode).

Multiple patch–based broadband piezoelectric energy harvesting on plate-based structures

Several engineering systems, such as aircraft structures, are composed of load-bearing thin plates that undergo vibrations and employ wireless health, usage, and condition monitoring components, which can be made self-powered using vibrational energy harvesting technologies. Integrated piezoelectric patches can be implemented for enabling self-powered sensors in the neighborhood of plate-based structures. In this work, coupled electroelastic modeling and experimental validations of broadband energy harvesting from structurally integrated piezoelectric patches on a rectangular thin plate are presented. A distributed-parameter electroelastic model for multiple patch–based energy harvesters attached on a thin plate is developed. Closed-form structural and electrical response expressions are derived for multiple vibration modes of a fully clamped thin plate for the series and parallel connection configurations of multiple patch–based energy harvesters. Experimental and analytical case studies are then compared for validating the analytical models of structurally integrated multiple patch–based energy harvesters. It is shown that analytical electroelastic frequency response functions exhibit very good agreement with the experimental frequency response function measurements for the series and parallel connection cases. In addition to offering an effective interface for energy harvesting from two-dimensional thin structures, series and parallel multiple patch–based energy harvester configurations yield effective broadband energy harvesting by combining the electrical outputs of harvester patches for multiple vibration modes.

Compact ultra‐wideband antenna with band‐notched based on defected ground structure

A simple and very compact planar monopole ultra-wideband antenna with a 3.5 GHz band rejection is proposed in this Letter. The compact antenna is etched on an FR4 substrate with the size of 14 × 16 × 1 mm3, consists of a tree-shaped radiation patch with modified ground structure. To reject certain frequency band, a pair of parallel strip patch, acting as a parasitic element is used. Prototype of the proposed antenna was constructed and measured. The measured impedance bandwidth of the realised antenna with optimal parameters is from 2.6 to 12 GHz (128%) for voltage standing wave ratio <2 with an unwanted band notched from 3.3 to 4 GHz. Moreover, the antenna has good omnidirectional radiation patterns in the H-plane.

Automated Patch Clamping of 384 Cells at Once for Massively Parallel Ion Channel Screening

Automated patch clamping is well established within academic research and drug discovery efforts. Still, there is a longstanding desire to have gold standard electrophysiology compatible with primary ion channel drug screening requirements. We here present a chip-based approach for massively parallel patch clamp recordings. Using microstructured glass bottom microtitre plates, recordings from 384 cells are performed in an automated fashion. The recording system contains 384 patch clamp amplifiers and is integrated into a liquid handling robot with 384 channel pipettor, so all experiments are done completely in parallel. Success rates achieved are routinely over 85%. A full run of 384 cells for dose response analysis takes less than 15 minutes, delivering several thousand data points per hour.The figure below shows a screenshot of an experiment on 384 CHO cells expressing Kv1.3 channels. (Raw current responses to a voltage step protocol). In this presentation, recordings from various ligand- and voltage-gated ion channels on the 384 channel platform will be shown.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Monitoring contact sensitization top-phenylenediamine (PPD) by patch testing with PPD 0.3% in petrolatum

Being a contact allergen of general relevance, p-phenylenediamine (PPD) is patch tested in the baseline series. However, PPD 1% in petrolatum may actively sensitize. Patch testing with PPD at 0.35% pet. proved to be safe, as far as active sensitization is concerned. To determine whether PPD 0.3% pet. reliably detects PPD sensitization. Patch testing with PPD 0.3% pet. and 1% pet. synchronously was performed in consecutive patients in a multicentre study within the Information Network of Departments of Dermatology. Altogether, 2042 patients were patch tested. PPD 1% pet. yielded 6.0% positive reactions (n = 123), and PPD 0.3% pet. yielded 4.7% (n = 95). The synchronous reproducibility of PPD reactions was similar as known from parallel patch tests with identical PPD concentrations. The diagnostic properties of PPD 0.3% pet. expressed as reaction index and positivity ratio were good. Of the 123 patients reacting to PPD 1% pet., 32 (26%) had no positive reaction to PPD 0.3% pet. In 22 of these 32 patients (69%), no clinical relevance could be found. As patch testing with PPD 0.3% pet. is reliable according to our results, we recommend replacing PPD 1% pet. in the baseline series with PPD 0.3% pet.

A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order in a 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can creatennumber of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.

Episodic tremors and deep slow-slip events in Central California

Observations of episodic tremor and slip (ETS) events have given insight into the seismic hazards along subduction zones by demonstrating that strain release was possible from slow-slip events (SSEs). Here, we show evidences that recurring episodes of nonvolcanic tremors (NVT) along the San Andreas Fault (SAF) in the Parkfield, California area, are reminiscent of seismic events associated with ETS and SSEs observed in subduction zones. Nonetheless, the Parkfield episodes are not uniformly periodic through time but exhibit systematic differences between aperiodic and periodic recurrences that are related to the 2004 M6.0 Parkfield earthquake and the long-term SAF slip rate. By constraining the locations of the NVT episodes, their duration, and the correlated response between episodes and repeating earthquake activity along the SAF, we propose a simple SSE model for the 52 Parkfield episodes observed in ∼9.7 yr. Our findings suggest that ∼10-day period slow-slips corresponding to maximum slips of ∼7.8mm occur on a SAF parallel patch that is ∼25km long and 15km wide centered at ∼25km depth. SSE moment magnitudes range between 5.0 and 5.4 and imply a stress drop of ∼10kPa. We also show that seismicity patterns above the SSE zone show correspondence with the SSE timing, and this emphasizes the importance of NVT episodes as in situ measurements to inferred fault slip transients below the seismogenic zone. Finally, we compare the source parameters of the SAF SSEs with SSEs of other regions and we show that they follow similar scalings.

Decrease in phosphatidylinositol 4,5‐bisphosphate levels mediates desensitization of the cold sensor TRPM8 channels

The activity of the cold- and menthol-activated transient receptor potential melastatin 8 (TRPM8) channels diminishes over time in the presence of extracellular Ca(2+), a phenomenon referred to as desensitization or adaptation. Here we show that activation of TRPM8 by cold or menthol evokes a decrease in cellular phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] levels. The decrease in PtdIns(4,5)P(2) levels was accompanied by increased inositol 1,4,5 trisphosphate (InsP(3)) production, and was inhibited by loading the cells with the Ca(2+) chelator BAPTA-AM, showing that it was the consequence of the activation of phospholipase C (PLC) by increased intracellular Ca(2+) concentrations. PtdIns(4,5)P(2) hydrolysis showed excellent temporal correlation with current desensitization in simultaneous patch clamp and fluorescence-based PtdIns(4,5)P(2) level measurements. Intracellular dialysis of PtdIns(4,5)P(2) inhibited desensitization both in native neuronal and recombinant TRPM8 channels. PtdIns(4)P, the precursor of PtdIns(4,5)P(2), did not inhibit desensitization, consistent with its minimal effect in excised patches. Omission of MgATP from the intracellular solution accelerated desensitization, and MgATP reactivated TRPM8 channels in excised patches in a phosphatidylinositol 4-kinase (PI4K)-dependent manner. PLC-independent depletion of PtdIns(4,5)P(2) using a voltage-sensitive phosphatase (ci-VSP) inhibited TRPM8 currents, and omission of ATP from the intracellular solution inhibited recovery from this inhibition. Inhibitors of PKC had no effect on the kinetics of desensitization. We conclude that Ca(2+) influx through TRPM8 activates a Ca(2+)-sensitive PLC isoform, and the resulting depletion of PtdIns(4,5)P(2) plays a major role in desensitization of both cold and menthol responses.

Highly Parallel Planar Patch Clamp for Ion Channel Screening

To meet the ever increasing demand for higher throughput in ion channel screening and safety testing, new platforms are being introduced allowing for yet more throughput whilst retaining data quality. A new platform recording from 96 cells at a time with giga-seals, with continuous recording during compound application and addition of multiple compounds to each of the 96 cells being recorded will be described. This new platform vastly increases throughput, while reducing the cost per data point. Borosilicate glass substrates containing microstructured apertures are used for parallel patch clamp experiments. In the figure below, a screenshot of an experiment on 96 cells in a parallel is displayed. Shown are raw current responses of CaV3.2 channels expressed in HEK293 cells to a current voltage relationship step protocol.Recordings from various ligand- and voltage-gated ion channels on this platform will be shown.View Large Image | View Hi-Res Image | Download PowerPoint Slide

96 Parallel Gigaseal Patch Clamp Recordings

Over the last several years ion channels have received more and more interest as potential drug targets, because of their known involvement in chronic and acute disease. Patch clamp is the gold standard for obtaining highly relevant information about ion channels and their effectors but it is a notoriously laborious technique. To meet the ever increasing demand for higher throughput in ion channel screening and safety testing we have developed a highly parallel patch clamp platform, the SyncroPatch 96. The platform supports giga-seal recordings, continuous recording during compound application and addition of multiple compounds at each of the 96 cells recorded from at a time.View Large Image | View Hi-Res Image | Download PowerPoint SlideThe figure shows 96 individually recorded IV's of the sodium channel hNav1.5 expressed in HEK 293 cells.Here we present high quality data of voltage gated and ligand gated channels expressed in various cell lines. Whole cell access was achieved using either pore forming agents such as Nystatin, or by short applications of suction pulses.The SyncroPatch 96 offers high throughput without compromising data quality.

Effect of compound plate composition on measurement of hERG current IC 50 using PatchXpress

Inhibition of the human ether-a-go-go-related gene (hERG) potassium channel by pharmaceutical agents can lead to acquired long QT syndrome and the generation of potentially lethal arrhythmias. Higher throughput automated patch clamp systems, such as PatchXpress ®, can greatly increase the speed and capacity of evaluation of pharmaceutical compounds for hERG blocking activity. A factor that may affect the IC 50 value of a compound measured in this system is the composition of the multi-well compound plate. Hydrophobic compounds may adsorb to the surfaces of multi-well plates resulting in a reduction in the effective concentration of the compound delivered to the cell and altered IC 50 values. In the present study, we investigated the effects of four different compound plates – glass vials, non-binding polystyrene, hydrophilic polystyrene, and polystyrene – on determination of IC 50s for four compounds – sotalol, dofetilide, cisapride, and bepridil – which ranged in hydrophobicity. In addition, we investigated the effects of incubation time in the compound plate on determination of IC 50s. hERG currents were measured using the PatchXpress 7000A Automated Parallel Patch Clamp System (Molecular Devices Corporation; Sunnyvale, CA) and hERG channels stably expressed in HEK293 cells. The results suggest that more hydrophobic compounds may adsorb to non-binding polystyrene, hydrophilic, and polystyrene compound plates versus glass plates, especially with increasing time on the plates, resulting in altered IC 50 values.

Highly Parallel Automated Patch Clamp Platform For High Quality Recordings From Up To 96 Cells At A Time

Ion channels have for several years now, received more and more interest as drug targets, because of their known involvement in chronic and acute disease. The frequently cited fact that 15% of the 100 top selling drugs target ion channels, motivates the pharmaceutical industry to search for techniques that accurately can determine ion channel function, associated with an acceptable data throughput and reasonable cost per data point. Patch clamp is the gold standard for obtaining highly relevant information about ion channels and their effectors, but is an extremely laborious technique. This has spurred the development of automated patch clamps that are capable of high quality recordings, at a much higher throughput. Up to now, several automated patch clamp platforms are commercially available which allow for high quality recordings. None of these meet the throughput requirements given by high throughput screening in drug discovery.To meet the ever increasing demand for higher throughput in ion channel screening and safety testing we have developed a highly parallel patch clamp platform. The platform supports giga-seal recordings, continuous recording during compound application and addition of multiple compounds at each of the 96 cells recorded from at a time. The platform allows recordings in the whole-cell configuration with high success rates. Due to the open structure of the patch clamp substrate, dose-responses can be obtained, thus cutting the costs per data point to be compatible to industrial requirements. Data from different cell types and ion channels will be presented.

Characterization of compounds on nicotinic acetylcholine receptor alpha7 channels using higher throughput electrophysiology

Alpha7 nicotinic acetylcholine receptor channels are important ligand-gated ion channels that are fast desensitizing, cation selective and have been implicated in the pathophysiology of schizophrenia and Alzheimer's disease. We report here high quality α7 parallel patch clamp recordings using the QPatch automated patch clamp system. The QPatch patch clamps up to 48 cells in parallel with the same high fidelity as conventional patch clamp. EC 50 and IC 50 values were comparable to values obtained with conventional patch clamp. The EC 50 value for acetylcholine (ACh) on the QPatch with area under the curve (AUC) analysis was 26 μM compared to a value of 29 μM determined from conventional patch clamp experiments. Sequential additions of ACh can be made with minimal decay of the peak amplitude. The competitive α7 antagonist methyllycaconitine (MLA) blocked currents with an IC 50 value of 0.25 nM which is similar to published IC 50 values for MLA. Finally, two different classes of positive allosteric modulators represented by PNU-120596 and NS-1738 elicited characteristic responses, thus allowing accurate characterization of modulation and measurements of potency. These results demonstrate that α7 nicotinic acetylcholine receptor channels can be studied reliably in a higher throughput, parallel manner with the QPatch automated patch clamp system.

Assessing hERG Channel Inhibition Using PatchXpress

PatchXpress, an automated 16-channel parallel patch clamp system, was used to determine inhibition of human ether-a-go-go related gene (hERG) potassium channels by known blockers. A monoclonal cell line stably expressing hERG potassium channels was generated in CHO-K1 cells. Results were compared to conventional patch clamp experiments using similar voltage protocols and solutions. Success rates were evaluated for cell recordings under a variety of conditions, including Accumax versus trypsin treatment to harvest cells, single versus double compound additions, and polystyrene versus glass-coated compound plates. Finally, polystyrene versus glass-coated compound plates were evaluated, and the authors found that for some compounds (but not all), preparation of compound samples in glass-coated plates resulted in inhibition that more closely matched data obtained by conventional experiments.