Execution Steps Research Articles

ICOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input and outputs insightful statistics. Our iCOMIC toolkit pipeline featuring many independent workflows is embedded in the popular Snakemake workflow management system. It can analyze whole-genome and transcriptome data and is characterized by a user-friendly GUI that offers several advantages, including minimal execution steps and eliminating the need for complex command-line arguments. Notably, we have integrated algorithms developed in-house to predict pathogenicity among cancer-causing mutations and differentiate between tumor suppressor genes and oncogenes from somatic mutation data. We benchmarked our tool against Genome In A Bottle benchmark dataset (NA12878) and got the highest F1 score of 0.971 and 0.988 for indels and SNPs, respectively, using the BWA MEM—GATK HC DNA-Seq pipeline. Similarly, we achieved a correlation coefficient of r = 0.85 using the HISAT2-StringTie-ballgown and STAR-StringTie-ballgown RNA-Seq pipelines on the human monocyte dataset (SRP082682). Overall, our tool enables easy analyses of omics datasets, significantly ameliorating complex data analysis pipelines.

Augmented Reality for Automatically Generating Robust Manufacturing and Maintenance Logs

Logs describing the execution of procedural steps during manufacturing and maintenance tasks are important for quality control and configuration management. Such logs are currently hand-written or typed during a procedure, which requires engineers to frequently step away from their work and results in difficulties for searching and optimizing logs. In this paper, we propose to automatically generate standardized, searchable logs, by visually perceiving and monitoring the progress of the procedure in real-time, and comparing this to the expected procedure. Unlike related work, we propose an approach which does not restrict the engineers to rigid, sequential sequences and instead allows them to execute procedures in a variety of different sequences where possible. The proposed framework is experimentally validated on the task of (dis)assembling a Duplo block model and operates properly when occlusions are absent.

Distributed Adaptive Mittag–Leffler Formation Control for Second-Order Fractional Multi-Agent Systems via Event-Triggered Control Strategy

This brief investigates the Mittag–Leffler formation bounded control problem for second-order fractional multi-agent systems (FMASs), where the dynamical nodes of followers are modeled to satisfy quadratic (QUAD) condition. Firstly, under the undirected communication topology, for the considered second-order nonlinear FMASs, a distributed event-triggered control scheme (ETCS) is designed to realize the global Mittag–Leffler bounded formation control goal. Secondly, by introducing adaptive weights into triggering condition and control protocol, an adaptive event-triggered formation protocol is presented to achieve the global Mittag–Leffler bounded formation. Thirdly, a five-step algorithm is provided to describe protocol execution steps. Finally, two simulation examples are given to verify the effectiveness of the proposed schemes.

System Integrity Protection Schemes: Naming Conventions and the Need for Standardization

The energy transition is placing increased strain on power systems and making it challenging for Transmission System Operators (TSOs) to securely operate power systems. System Integrity Protection Schemes (SIPSs) are one of the solutions to address these challenges. SIPSs are a type of over-arching power system control; their goals are to increase the secure utilization of power system assets and to limit the impact of large disturbances on the system. Due to societal developments, the interest in utilizing SIPSs is increasing internationally, highlighting the importance of the standardization of terms and definitions to support collaboration between internationally interconnected power systems. This paper addresses the issue of increasing SIPS literature and the efficient exchange of knowledge about SIPSs by providing a new, up-to-date literature review and proposal for the standardization of SIPS terminology. The need for standardized terminology is highlighted by gathering various terms used to describe SIPSs and proposing a standardization of definitions, terms, and SIPS operational execution steps. The goal of the proposed standardization is to provide clarity and to decrease the sources of misinterpretation in an international collaborative environment. The analyzed literature is further classified according to the SIPS features it addresses, and conclusions about well-established and interesting future research areas are drawn. For example, it has been observed that the most commonly considered SIPS action is load shedding, while more sophisticated actions, e.g., using HVDC (High Voltage Direct Current) and FACTS (Flexible AC Transmission System) installations, controlled together with var rescheduling, are more in the realm of future research that may provide additional benefits to TSOs.

Adequacy of Serial Self-performed SARS-CoV-2 Rapid Antigen Detection Testing for Longitudinal Mass Screening in the Workplace

Longitudinal mass testing using rapid antigen detection tests (RADT) for serial screening of asymptomatic persons has been proposed for preventing SARS-CoV-2 community transmission. The feasibility of this strategy relies on accurate self-testing. To quantify the adequacy of serial self-performed SARS-CoV-2 RADT testing in the workplace, in terms of the frequency of correct execution of procedural steps and accurate interpretation of the range of possible RADT results. This prospective repeated cross-sectional study was performed from July to October 2021 at businesses with at least 2 active cases of SARS-CoV-2 infection in Montreal, Canada. Participants included untrained persons in their workplace, not meeting Public Health quarantine criteria (ie, required quarantine for 10 days after a moderate-risk contact with someone infected with SARS-CoV-2). Interpretation and performance were compared between participants who received instructions provided by the manufacturer vs those who received modified instructions that were informed by the most frequent or most critical errors we observed. Data were analyzed from October to November 2021. RADT testing using a modified quick reference guide compared with the original manufacturer's instructions. The main outcome was the difference in correctly interpreted RADT results. Secondary outcomes included difference in proportions of correctly performed procedural steps. Additional analyses, assessed among participants with 2 self-testing visits, compared the second self-test visit with the first self-test visit using the same measures. Overall, 1892 tests were performed among 647 participants, of whom 278 participants (median [IQR] age, 43 [31-55] years; 156 [56.1%] men) had at least 1 self-testing visit. For self-test visit 1, significantly better accuracy in test interpretation was observed among participants using the modified quick reference guide than those using the manufacturer's instructions for reading results that were weak positive (64 of 115 participants [55.6%] vs 20 of 163 participants [12.3%]; difference, 43.3 [95% CI, 33.0-53.8] percentage points), positive (103 of 115 participants [89.6%] vs 84 of 163 participants [51.5%]; difference, 38.1 [95% CI, 28.5-47.5] percentage points), strong positive (219 of 229 participants [95.6%] vs 274 of 326 participants [84.0%]; difference, 11.6 [95% CI, 6.8-16.3] percentage points), and invalid (200 of 229 participants [87.3%] vs 252 of 326 participants [77.3%]; difference, 10.0 [95% CI, 3.8-16.3] percentage points). Use of the modified guide was associated with improvements on self-test visit 2 for results that were weak positive (difference, 15.4 [95% CI, 0.7-30.1] percentage points), positive (difference, 19.0 [95% CI, 7.2-30.9] percentage points), and invalid (difference, 8.0 [95% CI, 0.8-15.4] percentage points). For procedural steps identified as critical for test validity, adherence to procedural testing steps did not differ meaningfully according to instructions provided or reader experience. In this cross-sectional study of self-performed SARS-CoV-2 RADT in an intended-use setting, a modified quick reference guide was associated with significantly improved accuracy in RADT interpretations.

Preclinical Validation of a Semi-Autonomous Robot for Transperineal Prostate Biopsy

Prostate biopsy is a manual procedure carried out mostly under ultrasound (US) guidance to confirm the presence of cancer. The standard biopsy is random and includes at least 12 insertions; targeted biopsy makes use of dedicated hardware and software, but is still performed manually. We present here the pre-clinical validation of PROST, a robot primarily designed to automate targeted transperineal biopsy. The overall validation of the system was performed on cadavers, while some features, such as image segmentation, were tested on human tissue. PROST is designed to minimize human error by introducing some autonomy in the execution of key steps of the procedure, i.e., target selection, image fusion and needle positioning. The protocol was approved by the ethics committee; 10 cadavers were included in the study. We envision that PROST has the potential to increase the detection of clinically significant prostate cancer, to simplify the procedure, to reduce human errors and to shorten training time. The use of a robot for the biopsy of the prostate will create the possibility to include also a treatment, such as focal ablation, to be delivered through the same system.

In-Memory Computing Architecture for a Convolutional Neural Network Based on Spin Orbit Torque MRAM

Recently, numerous studies have investigated computing in-memory (CIM) architectures for neural networks to overcome memory bottlenecks. Because of its low delay, high energy efficiency, and low volatility, spin-orbit torque magnetic random access memory (SOT-MRAM) has received substantial attention. However, previous studies used calculation circuits to support complex calculations, leading to substantial energy consumption. Therefore, our research proposes a new CIM architecture with small peripheral circuits; this architecture achieved higher performance relative to other CIM architectures when processing convolution neural networks (CNNs). We included a distributed arithmetic (DA) algorithm to improve the efficiency of the CIM calculation method by reducing the excessive read/write times and execution steps of CIM-based CNN calculation circuits. Furthermore, our method also uses SOT-MRAM to increase the calculation speed and reduce power consumption. Compared with CIM-based CNN arithmetic circuits in previous studies, our method can achieve shorter clock periods and reduce read times by up to 43.3% without the need for additional circuits.

DeepNet-Based 3D Visual Servoing Robotic Manipulation

The fourth industrial revolution (industry 4.0) demands high-autonomy and intelligence robotic manipulators. The goal is to accomplish autonomous manipulation tasks without human interventions. However, visual pose estimation of target object in 3D space is one of the critical challenges for robot-object interaction. Incorporating the estimated pose into an autonomous manipulation control scheme is another challenge. In this paper, a deep-ConvNet algorithm is developed for object pose estimation. Then, it is integrated into a 3D visual servoing to achieve a long-range mobile manipulation task using a single camera setup. The proposed system integrates (1) deep-ConvNet training using only synthetic single images, (2) 6DOF object pose estimation as sensing feedback, and (3) autonomous long-range mobile manipulation control. The developed system consists of two main steps. First, a perception network trains on synthetic datasets and then efficiently generalizes to real-life environment without postrefinements. Second, the execution step takes the estimated pose to generate continuous translational and orientational joint velocities. The proposed system has been experimentally verified and discussed using the Husky mobile base and 6DOF UR5 manipulator. Experimental findings from simulations and real-world settings showed the efficiency of using synthetic datasets in mobile manipulation task.

Hermeneutic phenomenology for spatial analysis

PurposeFrom scholars' view, there are various research approaches to investigate the city and its spaces. However, there is a need to examine the city and its spaces from the residents' perspective. Hermeneutic phenomenology might be applicable and valuable. Also, communication is a requirement for successful participatory planning and spatial analysis. Architects, urban designers and landscape architects must possess intersubjective competencies to communicate and engage with the public. Hermeneutic knowledge is the source for developing these intersubjective capabilities essential for communication. All design preparation and execution steps require distorted-free communication, starting with defining a problem and ending with implementation, monitoring and evaluation.Design/methodology/approachThe paper aims to test the applicability of hermeneutic phenomenology in urban studies. The author examines the right to the city and producing space in Cairo, Egypt. Besides web pages, documents and social networks, data sources vary, including proverbs and poems. Semiotics is the qualitative research technique used to interrogate the collected material using qualitative data analysis software.FindingsCairo's growth is the outcome of the division of labor, administration and power dynamics. Egyptians' right to take part in Cairo's planning and management is the issue. Hermeneutic phenomenology is an approach to perform spatial environmental investigations. It could inform decision-making, ensure the planning process's validity and guarantee people's ownership of planned projects.Originality/valuePhenomenology allows for inside and outside the understanding of a spatial phenomenon. The current focus of architectural and planning schools' curricula is on technical actions. These schools consider increasing the dose of social sciences in their curricula. Educators could teach students how to use hermeneutic phenomenological research methodologies. Using hermeneutic knowledge in communication encourages public engagement in formulating and implementing projects, thus ensuring their long-term viability.

An execution time optimized state of charge estimation method for lithium-ion battery

State of charge (SOC) estimation is one of the most important outputs of the battery management system (BMS). There are several algorithms for SOC estimation. Each method has advantages like self-correction ability and disadvantages like computational complexity for an embedded system. In the first part of this article, different estimation techniques are reviewed and compared. Particular emphasis was placed on two methods: Coulomb Counting (CC) and Sigma Point Kalman Filter (SPKF). These two methods are analyzed in terms of several aspects such as tolerance to noisy signal, recovery ability from an intentional SOC distortion as well as estimation accuracy comparison. Also, an embedded development kit is used to analyze execution time of each method. The results show that using SPKF alone is a computationally expensive method especially for a battery pack with a high number of cells in series. On the other hand, using CC alone could be vulnerable to SOC distortion and noisy measurement signals and this may lead to inaccurate predictions. Based on these facts, a hybrid approach has been proposed to take advantage of each method’s superiority. The emphasis in this paper is on execution step time analyses under different conditions and drive cycles. On top of this article, further studies may pave the way for more cost effective solutions like downsizing of the processor.

Dynamics of cortical and corticomuscular connectivity during planning and execution of visually guided steps in humans.

The cortical mechanisms underlying the act of taking a step-including planning, execution, and modification-are not well understood. We hypothesized that oscillatory communication in a parieto-frontal and corticomuscular network is involved in the neural control of visually guided steps. We addressed this hypothesis using source reconstruction and lagged coherence analysis of electroencephalographic and electromyographic recordings during visually guided stepping and 2 control tasks that aimed to investigate processes involved in (i) preparing and taking a step and (ii) adjusting a step based on visual information. Steps were divided into planning, initiation, and execution phases. Taking a step was characterized by an upregulation of beta/gamma coherence within the parieto-frontal network during planning followed by a downregulation of alpha and beta/gamma coherence during initiation and execution. Step modification was characterized by bidirectional modulations of alpha and beta/gamma coherence in the parieto-frontal network during the phases leading up to step execution. Corticomuscular coherence did not exhibit task-related effects. We suggest that these task-related modulations indicate that the brain makes use of communication through coherence in the context of large-scale, whole-body movements, reflecting a process of flexibly fine-tuning inter-regional communication to achieve precision control during human stepping.

Electronic Decision Support in the Delivery Room Using Augmented Reality to Improve Newborn Life Support Guideline Adherence: A Randomized Controlled Pilot Study.

IntroductionThe Newborn Life Support (NLS) guideline aims to provide healthcare professionals a consistent approach during neonatal resuscitation. Adherence to this and analogous guidelines has repetitively been proven to be difficult.This study evaluates adherence to guideline using a novel augmented reality (Microsoft HoloLens) electronic decision support tool during standardized simulated neonatal resuscitation compared with subjects working from memory alone.MethodsIn this randomized controlled pilot study, 18 professionals responsible for neonatal resuscitation were randomized to the intervention group and 11 to the control group. Demographic characteristics were similar between both groups. A standardized neonatal resuscitation scenario was performed, which was recorded and later assessed for adherence to the NLS algorithm by 2 independent reviewers. Secondary outcomes were error classification in case of algorithm deviation and time to the execution or completion of critical steps in the algorithm to determine delay.ResultsMedian (interquartile range) scores of a theoretical maximum of 40 in the intervention group were 34 (32.5–35.5) versus 29 (27–33) in the control group (P = 0.004). Errors of commission were committed less frequently with the electronic decision support tool 2 (1–2.5) compared with 4 (2–4) in the control group (P = 0.029). Analysis of time to initiation or completion of key steps in the NLS algorithm showed no significant differences between both groups.ConclusionsHealthcare professionals using an electronic decision support tool showed improved adherence to the NLS guideline during simulated neonatal resuscitation.

FACIAL EMOTION DETECTION USING OPEN CV

Automatic Face Detection innovations have made numerous upgrades in evolving world. Brilliant ATTENDANCE SYSTEM utilizing ongoing face acknowledgment is a genuine world arrangement which accompanies everyday exercises of taking care of understudies participation. The administration of participation framework can be an extraordinary weight on educators in case it is finished by hands.To determine this issue we utilize auto and brilliant participation framework which is by and large executed with the assistance of biometric called Face Detection. The primary execution steps utilized in this kind of framework are face location and perceiving the identified countenances. Face Detection is an interaction where the framework will actually want to recognize the human faces which will be caught by the camera. Here , we execute a computerized participation the board framework for understudies of the class by utilizing face acknowledgment method..

Non-canonical role of the ATR pathway in axon regeneration as a mechanosensitive brake.

Non-canonical role of the ATR pathway in axon regeneration as a mechanosensitive brake.

Analysis of the influence of the type of curing on the axial compressive strength of concrete

The curing process is one of the most important steps in the concrete execution, providing the complete hydration of the Portland cement compounds, avoiding the shrinkage phenomenon and ensuring the strength of the structure. This paper intends to understand the influence of immersed in water and lime curing, chemical curing, with the use of plastic film, and open air curing on concretes with axial compressive strength fck 30 Mpa. The specimens were analyzed for 63 days, at 4 ages of rupture. The concretes, when submitted to immersed curing in water and lime, had a significant difference when compared to the other methods. The concretes that were submitted to the other cures had a lower mechanical resistance, sometimes significative, sometimes not significant when compared among themselves.

Design and implementation of an ASIP for SHA-3 hash algorithm

In recent years, application specific instruction set processor (ASIP) has attracted many researchers attention. These processors resemble application specific integrated circuits (ASICs) and digital signal processors (DSPs) from the performance and flexibility point of view, respectively. In other words, ASIP makes compromise between performance and flexibility criteria. The SHA-3 hashing algorithm has been introduced as the safest and the newest algorithm in 2015 as a global standard. In this paper, a processor with specific instruction set is designed and implemented with regard to variant execution steps of this algorithm. In order to do the modelling and simulation of the processor, we have used the VHDL hardware description language and the ModelSim SE 6.1 tool. Moreover, in order to implement it on a field programmable gate array (FPGA) platform we have used the Xilinx ISE 10.1 tool. The implemented processor has 213.356 MHz operating frequency and 3.004 Mbps throughput.

Measurement of the runoff coefficient of extensive greenroof

Describes the procedure of experimental measurement of the runoff coefficient C, both of individual layers and the entire composition extensive green roofs. Experimental measurements make it possible to determine the reference behaviour of runoff characteristics, namely runoff coefficient C, with emphasis on the simulation of the real behaviour of extensive green roofs. The aim is an elementary description of the structural and physical behaviour of extensive green roofs. For the needs of experimental measurement, the dimensional and shape limits of test specimens are described, the conditions for conditioning of individual specimens, the boundary conditions of execution and individual steps of the experiment. Then is specified the method of evaluation and subsequent verification of measured data. The result of the experimental measurement is the amount of drained water from the tested specimens of the extensive green roof at time t, which shows a nonlinear behaviour. From the set of measured data, it is then possible to predict the behaviour of extensive green roofs in real conditions and to determine the runoff coefficient C of the tested specimens. These data represent reference values for the subsequent design of sub-elements and structures of buildings.

Getting started for migration: A focus on EMT cellular dynamics and mechanics in developmental models.

The conversion of epithelial cells into mesenchymal ones, through a process known as epithelial-mesenchymal transition (or EMT) is a reversible process involved in critical steps of animal development as early as gastrulation and throughout organogenesis. In pathological conditions such as aggressive cancers, EMT is often associated with increased drug resistance, motility and invasiveness. The characterisation of the upstream signals and main decision takers, such as the EMT-transcription factors, has led to the identification of a core molecular machinery controlling the specification towards EMT. However, the cellular execution steps of this fundamental shift are poorly described, especially in cancerous cells. Here we review our current knowledge regarding the stepwise nature of EMT in model organisms as diverse as sea urchin, Drosophila, zebrafish, mouse or chicken. We focus on the cellular dynamics and mechanics of the transitional stages by which epithelial cells progressively become mesenchymal and leave the epithelium. We gather the currently available pieces of the puzzle, including the overlooked property of EMT cells to produce mechanical forces along their apico-basal axis before detaching from their neighbours. We discuss the interplay between EMT and the surrounding tissue. Finally, we propose a conceptual framework of EMT cell dynamics from the very first hint of epithelial cell reorganisation to the successful exit from the epithelial sheet.

Bcl-xL and IP3R interaction: Intimate relationship with an uncertain outcome

Bcl-2 family proteins are major apoptosis regulators. They control a key step in apoptosis execution referred to as the mitochondrial outer membrane permeabilization. Several Bcl-2 homologs were also reported to act at the level of the endoplasmic reticulum (ER) where they control intracellular Ca2+ trafficking. There is an increasing body of evidence that, in addition to their conventional role as MOMP regulators, several Bcl-2 family members, including Bcl-xL, are linked to Ca2+ -dependent processes, independent of cell death. Among them Bcl-xL has been proposed to promote IP3R1 channel opening and sustain mitochondrial bioenergetics. A recent article by Rosa and colleagues in Cell Death & Differentiation challenges this model and support the notion that Bcl-xL acts more as a repressor than as a sensitizer of IP3R1 opening. They suggest the existence of intrafamilial competition among the Bcl-2 family of protein with respect to their effect on IP3R Ca2+ permeability, which might be important regarding their respective non-canonical functions. In this regard, the results by Rosa and colleagues open exciting avenues regarding the biological process by which Bcl-xL affects Ca2+ trafficking through IP 3 R channels.

Bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses.

bollito is an automated, flexible and parallelizable computational pipeline for the comprehensive analysis of single-cell RNA-seq data. Starting from FASTQ files or preprocessed expression matrices, bollito performs both basic and advanced tasks in single-cell analysis integrating >30 state-of-the-art tools. This includes quality control, read alignment, dimensionality reduction, clustering, cell-marker detection, differential expression, functional analysis, trajectory inference and RNA velocity. bollito is built using the Snakemake workflow management system, which easily connects each execution step and facilitates the reproducibility of results. bollito's modular design makes it easy to incorporate other packages into the pipeline enabling its expansion with new functionalities. Source code is freely available at https://gitlab.com/bu_cnio/bollito under the MIT license. Supplementary data are available at Bioinformatics online.