ARTICLE | doi:10.20944/preprints202301.0039.v1
Subject: Biology, Other Keywords: somatic point mutations; non-coding RNA; biomarker discovery; driver genes; non-coding RNAs prioritization; health data analytics
Online: 4 January 2023 (02:22:00 CET)
Previous studies demonstrate the critical importance of non-coding RNAs interfacing with chromatin-modifying machinery resulting in promoter-enhancer-based gene regulation and raise the possibility that many other enhancer-like RNAs may operate via similar mechanisms. Critically, more than 80% of the disease-linked variations identified in genome-wide studies are located in the non-coding regions of genomes, especially non-coding RNA, suggesting non-coding RNAs are relevant to disease. Thus, a critical path forward for understanding non-coding RNAs' role, especially long non-coding RNAs, is to understand the genomic regions' transcriptional regulation, especially non-coding regions. Here, we developed a user-friendly R package called SomaGene for studying and identifying enhancer-like non-coding RNAs with enriched somatic mutations in the cancer genome. SomaGene accepts different genomic variants (whole genome/exome somatic point mutations, structural variations, copy number variations) to identify those RNAs that significantly mutated in diseases (e.g., cancer). It then uses multiple publicly available genomics and epigenetics datasets including ENCODE epigenomics annotations, FANTOM5 tissue-specific expression profiles, disease-associated genome-wide association SNPs, and tissue-specific eQTL pairs to identify those RNAs with potentially enhancer function. SomaGene, as a powerful R package, can provide the opportunity to cancer scientists to study the roles of non-coding RNAs in different cancer genomes.
ARTICLE | doi:10.20944/preprints202108.0216.v1
Online: 10 August 2021 (09:02:30 CEST)
Current adaptive cruise control (ACC) systems adopt fixed desired time headway, which leads to an abrupt speed reduction after being cut-in by a lane changer in front or when changing lanes too close to the new leader. In contrast, human drivers behave differently and feature a variable spacing within 20 or 30 seconds right after a cut-in or lane change. Motivated by the smooth transition found in driver relaxation, the paper aims to incorporate relaxation into ACC systems. Based on the open-source ACC platform, Openpilot, Comma.ai, the paper proposes a feasible relaxation model compatible with current factory ACCs, which has also been tested using a market car with stock ACC hardware. The study further investigates the impact of relaxation ACC on traffic operation. Numerical simulation suggests that incorporating relaxation into ACC can help: i) reduce the magnitude of speed perturbations in both cut-in vehicles and followers; ii) stabilize the lane-changing traffic by reducing the speed variance and prevent the lateral propagation of congestion, and iii) increase the average vehicle speed and capacity in merging traffic.
ARTICLE | doi:10.20944/preprints202110.0356.v1
Subject: Engineering, Automotive Engineering Keywords: Deep learning; HVAC; Cabin air temperature; Driver behvaiour; NARX
Online: 25 October 2021 (13:29:38 CEST)
The vehicular technology has integrated many features in the system, which enhances the safety and comfort of the user. Among these features, heating, ventilation, and air conditioning (HVAC) is the only feature that maintains the set cabin air temperature (CAT). The user’s command drives the set CAT, and the thermostat provides feedback to the HVAC to maintain the set CAT. The CAT is increased by extracting the heat from the engine surface produced by the fuel combustion, whereas the CAT is reduced by the known processes of the air conditioning system (ACS). Therefore, the CAT driven by the user’s command may not be optimal, and estimating the optimal CAT is still unsolved. In this work, the user was allowed to input a range for CAT instead of a single value. Optimal HVAC criteria were defined, and the CAT was estimated by performing iterative analysis in the user-selected range satisfying the criteria. The HVAC criteria were defined based on two measurable parameters: air conditioning refrigerant fluid pressure (ACRFP) and engine surface temperature (EST) empirically defined as the vector CATOP. In this article, a NARX DL model by mapping the vehicle-level vectors (VLV) to predict the CATOP in real-time using field data obtained from a 2020 Cadillac CT5 test vehicle. Utilising the DL model, CATOP for future time steps were predicted by varying the CAT in the definite range and applying HVAC criteria. Thus, an optimal set CAT was estimated, corresponding to the optimal CATOP defined by the HVAC criteria. We performed the validation of the DL model for multiple datasets using traditional statistical techniques, namely, signal-to-noise ratio (SNR) values, first-order derivatives (FOD), and root-mean-square error (RMSE).
COMMUNICATION | doi:10.20944/preprints202011.0629.v1
Subject: Behavioral Sciences, Applied Psychology Keywords: road safety; advanced driver assistance; safe system approach; LMIC
Online: 25 November 2020 (10:06:33 CET)
Abstract: Traffic collisions cause a huge problem of public health in low and middle income countries.. The safe system approach is generally considered as the leading concept on the way to road safety. Based on the fundamental premise that humans make mistakes, the overall traffic system should be ‘forgiving’. Sustainable safe road design is one of the key elements of the safe system approach. However, the road design principles behind the safe system approach are certainly not leading in today’s infrastructure developments in most LMICs. Cities are getting larger and road networks are expanding. In many cases, existing through-roads in local communities are up-graded, resulting in heavy traffic loads and high speeds on places, that are absolutely not suited for this kind of through-traffic. Furthermore a safe system would require that functional design properties of cars and roads would be conceptually integrated, which is not the case at all. Although advanced driver assistance systems are on their way of development for quite a long period, their potential role in the safe system concept is mostly unclear and at least strongly underexposed. The vision on future cars is dominated by the concept of automation. This paper argues that the way to self-driving cars, should take a route via the concept of guidance, i.e. vehicles that guide drivers, both on self-explaining roads and on more or less unsafe roads. Such an in-vehicle support system may help drivers to choose transport mode, route and speed, based on criteria related to safety and sustainability. It is suggested to develop a driver assistance system using relatively simple and cheap technologies, particularly for the purpose of use in LMICs. Such a GUIDE (Generic User Interface for Driving Evolution) may make roads self-explaining - not only by their physical design characteristics - but also by providing in-car guidance for drivers. In future the functional characteristics of both cars and roads should be conceptualized into one integrated safe system, in which the user plays the central role. As such GUIDE may serve as the conceptual bridge between vehicle and roadway characteristics. It is argued that GUIDE is necessary to bring a breakthrough in road safety developments in LMICs and also give an acceleration towards zero fatalities in HICs.
ARTICLE | doi:10.20944/preprints202106.0446.v1
Subject: Social Sciences, Education Studies Keywords: digital divide, e-learning, covid-19, driver of digital divide
Online: 16 June 2021 (12:48:11 CEST)
The devastating COVID-19 pandemic forced academia to go virtual. Educational institutions around the world have stressed online learning programs in the aftermath of the pandemic. However, because of insufficient access to ICT, a substantial number of students failed to harness the opportunity of online learning. This study explores the latent digital divide exhibited during the COVID-19 pandemic while online learning activities are emphasized among Bangladeshi students. It also explores the digital divide exposure and the significant underlying drivers of the divide. A cross-sectional survey was employed to collect quantitative data mixed with open-ended questions to collect qualitative information from the student community. The findings revealed that despite the majority of students have physical access to ICT but only 32.5% of students could attend online classes seamlessly, 34.1% of the students reported the data prices as the critical barrier, and 39.8% of students identified the poor network infrastructure is the significant barrier for them to participate in online learning activities. This paper aimed to explore the underlying issues of the digital divide among Bangladeshi students to assist relevant stakeholders (e.g., the Bangladesh government, Educational Institutions, Researchers) in providing the necessary insights to arrange for students to undertake online learning activities successfully.
ARTICLE | doi:10.20944/preprints202212.0111.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: effective number of bits ADC; ADC driver; operational amplifier; maximum output voltage slew rate; signal delay in ADC driver; linear and nonlinear operational amplifier modes
Online: 7 December 2022 (02:26:54 CET)
The influence of linear and nonlinear modes of ADC driver on the operational amplifier (Op-Amp), which has different values of maximum output voltage slew rate, on the effective number of bits of ADC is considered. It is shown that the effective number of bits of ADC when op-amps on bipolar transistors with input signal amplitudes exceeding 50-100 mV is determined by the nonlinear modes of its input differential stage.
ARTICLE | doi:10.20944/preprints202110.0249.v1
Subject: Engineering, Automotive Engineering Keywords: Adaptive Cruise Control; Driver behvaiour; Deep learning; Engine Operating Point; NARX
Online: 18 October 2021 (14:48:11 CEST)
The ACC feature when activated augments the engine performance in real-time. This article presents a novel methodology to predict the optimal adaptive cruise control set speed profile (ACCSSP) by considering all the effecting parameters. This paper investigates engine operating conditions (EOC) criteria to develop a predictive model of ACCSSP in real-time. We developed a deep learning (DL) model using the NARX method to predict engine operating point (EOP) mapping the vehicle-level vectors (VLV). We used real-world field data obtained from Cadillac test vehicles driven by activating the ACC feature for developing the DL model. We used a realistic set of assumptions to estimate the VLV for the future time steps for the range of allowable speed values and applied them at the input of the developed DL model to generate multiple sets of EOP’s. We imposed the defined EOC criteria on these EOPs, and the top three modes of speeds satisfying all the requirements are derived for each second. Thus three eligible speed values are estimated for each second, and an additional criterion is defined to generate a unique ACCSSP for future time steps. Performance comparison between predicted and constant ACCSSPs indicates that the predictive model outperforms constant ACCSSP.
ARTICLE | doi:10.20944/preprints202101.0330.v1
Subject: Medicine & Pharmacology, Allergology Keywords: germline; rare variant; cancer; lymphoid; B-cell; lymphomal; CLL; driver; prognosis
Online: 18 January 2021 (12:14:32 CET)
Growing evidence has revealed the implication of germline variation in cancer predisposition and prognostication. Here, we describe an analysis of putatively disruptive rare variants across the genomes of 726 patients with B-cell lymphoid neoplasms. We discovered a significant enrichment of 26 genes in germline protein truncating variants (PTVs), affecting cell signaling (MET, JAK2, ANGPT2), energy metabolism (ACO1) and nucleic acid metabolism and repair pathways (NT5E, DCK). Interestingly, some of these variants were restricted to either chronic lymphocytic leukemia (CLL) (i.e., ANGPT2 and AKR1C3) or B-cell lymphoma cases (PNMT, TPT1 and IGHMBP2). Additionally, we detected 1,675 likely disrupting variants in genes associated with cancer, of which 44.75% were novel events and 7.88% were PTVs. Among these, the most frequently affected genes were ATM, BIRC6, CLTCL1A and TSC2. Homozygous or compound heterozygous variants were detected in 28 cases; and coexisting somatic events were observed in 17 patients, some of which affected key lymphoma drivers such as ATM, KMT2D and MYC. Finally, we observed that variants in the helicase gene WRN were independently associated with shorter survival in CLL. Our study results support an important role for rare germline variation in the pathogenesis, clinical presentation and disease outcome of B-cell lymphoid neoplasms.
ARTICLE | doi:10.20944/preprints201711.0037.v1
Subject: Behavioral Sciences, Other Keywords: social learning; self-efficacy; subjective norm; betel nut chewing; taxi driver
Online: 6 November 2017 (07:27:59 CET)
The betel nut chewing habit of taxi drivers has shown that can promote companionship, relaxation, and emotional stability at work. 19.3% of betel nut behaviors are instigated by an invitation among drivers to engage in the habit. The objective of this study was to explore the impact of social learning, subjective norm, and self-efficacy on betel nut chewing in taxi drivers in Taiwan. We conducted a cross-sectional study on taxis’ driver of betel nut behaviour and measured their evaluations of its consequences using a self-report questionnaire. Other variables include socio-demographic characteristics and chewing-related experience. The overall variance is 44.5% in socio-demographic variable, social learning, self-efficacy, and subjective norm. Results show that the variables of affected betel nut chewing behavior, driving years has the strongest influence, followed by learning about betel nut from the media, relatives, and friends, and education level, which positively affect betel nut chewing behavior. Findings indicated that education related to quitting betel nut chewing, significant others, and rules of the taxi fleet are adopted to design a plan for quitting betel chewing to reduce the positive expectations of taxi drivers for betel nut chewing and decrease their betel nut chewing behavior.
ARTICLE | doi:10.20944/preprints202111.0230.v1
Subject: Engineering, Automotive Engineering Keywords: Convolutional neural network; Driver drowsiness; ECG signal; Heart rate variability; Wavelet scalogram
Online: 12 November 2021 (15:01:50 CET)
Driver drowsiness is one of the leading causes of traffic accidents. This paper proposes a new method for classifying driver drowsiness using deep convolution neural networks trained by wavelet scalogram images of electrocardiogram (ECG) signals. Three different classes were de-fined for drowsiness based on video observation of driving tests performed in a simulator for manual and automated modes. The Bayesian optimization method is employed to optimize the hyperparameters of the designed neural networks, such as the learning rate and the number of neurons in every layer. To assess the results of the deep network method, Heart Rate Variability (HRV) data is derived from the ECG signals, some features are extracted from this data, and finally, random forest and k-nearest neighbors (KNN) classifiers are used as two traditional methods to classify the drowsiness levels. Results show that the trained deep network achieves balanced accuracies of about 77% and 79% in the manual and automated modes, respectively. However, the best obtained balanced accuracies using traditional methods are about 62% and 64%. We conclude that designed deep networks working with wavelet scalogram images of ECG signals significantly outperform KNN and random forest classifiers which are trained on HRV-based features.
REVIEW | doi:10.20944/preprints202111.0194.v1
Subject: Biology, Other Keywords: Complexity; Evolution; Major transitions; Multicellularity; Selective driver; Environment; Size; Division of labor
Online: 10 November 2021 (08:39:39 CET)
In order to understand the evolution of multicellularity, we must understand how and why selection favors the first steps in this process: the evolution of simple multicellular groups. Multicellularity has evolved many times in independent lineages with fundamentally different ecologies, yet no work has yet systematically examined these diverse selective drivers. Here we review recent developments in systematics, comparative biology, paleontology, synthetic biology, theory, and experimental evolution, highlighting ten selective drivers of simple multicellularity. Our survey highlights the many ecological opportunities available for simple multicellularity, and stresses the need for additional work examining how these first steps impact the subsequent evolution of complex multicellularity.
REVIEW | doi:10.20944/preprints202207.0321.v1
Subject: Biology, Other Keywords: Somatic evolution; driver gene; clone selection; healthy tissues; cancer initiation; cancer early detection
Online: 21 July 2022 (10:43:07 CEST)
Seemingly normal tissues progressively become populated by mutant clones over time. Most of these clones bear mutations in well-known cancer genes but only rarely do they transform into cancer. This poses questions on what triggers cancer initiation and what implications somatic variation has for cancer early detection. We analysed recent mutational screens of healthy and cancer-free diseased tissues to compare somatic drivers and the causes of somatic variation across tissues. We then reviewed the mechanisms of clonal expansion and their relationships with age and diseases other than cancer. We finally discussed the relevance of somatic variation for cancer initiation and how it can help or hinder cancer detection and prevention. The extent of somatic variation is highly variable across tissues and depends on intrinsic features, such as tissue architecture and turnover, as well as the exposure to endogenous and exogenous insults. Most somatic mutations driving clone expansion are tissue-specific and inactivate tumour suppressor genes involved in chromatin modification and cell growth signalling. Some of these genes are more frequently mutated in normal tissues than cancer, indicating a context-dependent cancer promoting or protective role. Mutant clones can persist over a long time or disappear rapidly, suggesting that their fitness depends on the dynamic equilibrium with the environment. The disruption of this equilibrium is likely responsible for their transformation into malignant clones and knowing what triggers this process is key for cancer prevention and early detection. Somatic variation should be considered in liquid biopsy, where it may contribute cancer-independent mutations, and in the identification of cancer drivers, since not all mutated genes favouring clonal expansion also drive tumourigenesis. Somatic variation and the factors governing homeostasis of normal tissues should be taken into account when devising strategies for cancer prevention and early detection.
ARTICLE | doi:10.20944/preprints202106.0459.v1
Subject: Engineering, Automotive Engineering Keywords: Autonomous Driving System; In-Car Gaming; Driver Behavior; Driving Related Tasks; 3D-VR/AR
Online: 17 June 2021 (12:29:00 CEST)
As Automated Driving Systems (ADS) technology gets assimilated into the market, the driver’s obligation will be changed to a supervisory role. A key point to consider is the driver’s engagement in the secondary task to maintain the driver/user in the control loop. The paper’s objective is to monitor driver engagement with a game and identify any impacts the task has on hazard recognition. We designed a driving simulation using Unity3D and incorporated three tasks: No-task, AR-Video, and AR-Game tasks. The driver engaged in an AR object interception game while monitoring the road for threatening road scenarios. From the results, there was less than 1 second difference between the means of gaming task (mean = 2.55s, std = 0.1002s) to no-task (mean = 2.55s, std = 0.1002s). Game scoring followed three profiles/phases: learning, saturation, and decline profile. From the profiles, it is possible to quantify/infer drivers’ engagement with the game task. The paper proposes alternative monitoring that has utility, i.e., entertaining the user. Further experiments AR-Game focusing on real-world car environment will be performed to confirm the performance following the recommendations derived from the current test.
ARTICLE | doi:10.20944/preprints202012.0096.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: AHB LED constant-current driver; Digital Current-programmed control; discrete-time modeling; Modulation effect
Online: 4 December 2020 (10:09:24 CET)
The high-power Asymmetric half-bridge Converter (AHBC) LED constant current driver controlled by digital current mode is a fourth-order system. Static operating point, parasitic resistance, load characteristics, sampling effect, modulation mode and loop delay will have great influence on its dynamic performance. In this paper, the small-signal pulse transfer function of the driver is established by the discrete-time modeling method for the two operating points corresponding to the three modulation modes of the trailing edge, leading edge and double edge. And, the effects of parasitic parameters, delay effect, sampling effect and load effect are fully considered in modeling. For a large number of complex exponential matrix operations, the first order Taylor formula is used for approximate calculation after the coefficient matrix is obtained by substituting the data. Then, Matlab software is used to compare and analyze the discrete-time model and the discrete-average model. The results show that the proposed discrete-time model can more accurately characterize the resonant peak and high-frequency dynamic characteristics, and is very suitable for the design of high frequency digital controller.
ARTICLE | doi:10.20944/preprints202108.0285.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: Eddy current driver–pickup sensor; surface crack; depth measurement; thin-skin regime; non-destructive testing.
Online: 13 August 2021 (08:27:46 CEST)
Electromagnetic eddy current sensors are commonly used to identify and quantify the surface notches of metals. However, the unintentional tilt of eddy current sensors affects results of size profiling, particularly for the depth profiling. In this paper, based on the eddy current thin-skin regime, a revised algorithm has been proposed for the analytical voltage or impedance of a tilted driver–pickup eddy current sensor scanning across a long ideal notch. Considering the resolution of the measurement, the bespoke driver–pickup, also termed as transmitter-receiver (T-R) sensor is designed with a small mean radius of 1 mm. Besides, the T-R sensor is connected to the electromagnetic instrument and controlled by a scanning stage with high spatial travel resolution , with a limit of 0.2 μm and selected as 0.25 mm. Experiments have been out on the voltage imaging of an aluminium sheet with 7 machined long notches of different depths using T-R sensor under different tilt angles. By fitting the measured voltage (both real and imaginary part) with proposed analytical algorithms, the depth profiling of notches is less affected by the tilt angle of sensors. From the results, the depth of notches can be retrieved within a deviation of 10 % for tilt angles up to 60 degrees.
ARTICLE | doi:10.20944/preprints201704.0128.v3
Subject: Engineering, Automotive Engineering Keywords: driver assistance systems; autonomous and cooperative driving; driving schools; driving simulators; multiple head-mounted displays; shared virtual environments
Online: 16 October 2017 (13:27:33 CEST)
Automotive manufacturers and suppliers develop new vehicle systems, such as Advanced Driver Assistance Systems (ADAS), to increase traffic safety and driving comfort. ADAS are technologies that provide drivers with essential information or take over demanding driving tasks. More complex and intelligent vehicle systems are being developed toward fully autonomous and cooperative driving. Apart from the technical development challenges, training of drivers with these complex vehicle systems represents an important concern for automotive manufacturers. This paper highlights the new evolving requirements concerning the training of drivers with future complex vehicle systems. In accordance with these requirements, a new training concept is introduced, and a prototype of a training platform is implemented for utilization in future driving schools. The developed training platform has a scalable and modular architecture so that more than one driving simulator can be networked to a common driving instructor unit. The participating driving simulators provide fully immersive visualization to the drivers by utilizing head-mounted displays instead of conventional display screens and projectors. The driving instructor unit consists of a computer with a developed software tool for training session control, monitoring, and evaluation. Moreover, the driving instructor can use a head-mounted display to participate interactively within the same virtual environment of any selected driver. A simulation model of an autonomous driving system was implemented and integrated in the participating driving simulators. Using this simulation model, training sessions were conducted with the help of a group of test drivers and professional driving instructors to prove the validity of the developed concept and show the usability of the implemented training platform.
ARTICLE | doi:10.20944/preprints202111.0266.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: Pan-Cancer; somatic point mutations; cancer subtyping; biomarker discovery; driver genes; per-sonalized medicine; health data analytics
Online: 15 November 2021 (13:51:33 CET)
The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, resulting in identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence there is no “silver bullet” for the treatment of a cancer type. This reveals the importance of developing a pipeline to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific treatment types. In this study, we propose a new machine learning pipeline to identify protein-coding genes mutated in a significant portion of samples to identify cancer subtypes. We applied our pipeline to 12270 samples collected from the International Cancer Genome Consortium (ICGC), covering 19 cancer types. Here we identified 17 different cancer subtypes. Comprehensive phenotypic and genotypic analysis indicates distinguishable properties, including unique cancer-related signaling pathways, in which, for most of them, targeted treatment options are currently available. This new subtyping approach offers a novel opportunity for cancer drug development based on the mutational profile of patients. We also comprehensive study the causes of mutations among samples in each subtype by mining the mutational signatures, which provides important insight into their active molecular mechanisms. Some of the pathways we identified in most subtypes, including the cell cycle and the Axon guidance pathways, are frequently observed in cancer disease. Interestingly, we also identified several mutated genes and different rates of mutation in multiple cancer subtypes. In addition, our study on “gene-motif” suggests the importance of considering both the context of the mutations and mutational processes in identifying cancer-associated genes. The source codes for our proposed clustering pipeline and analysis are publicly available at: https://github.com/bcb-sut/Pan-Cancer.