scholarly journals HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1241
Author(s):  
Louisa A. Carlisle ◽  
Teja Turk ◽  
Karin J. Metzner ◽  
Herbert A. Mbunkah ◽  
Cyril Shah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mean Absolute Error ◽  
Area Under The Curve ◽  
Absolute Error ◽  
Entire Genome ◽  
Reading Frame ◽  
Codon Positions ◽  
Characteristic Area ◽  
Improved Accuracy ◽  
Hiv 1

HIV-1 genetic diversity can be used to infer time since infection (TSI) and infection recency. We adapted this approach for HCV and identified genomic regions with informative diversity. We included 72 HCV/HIV-1 coinfected participants of the Swiss HIV Cohort Study, for whom reliable estimates of infection date and viral sequences were available. Average pairwise diversity (APD) was calculated over each codon position for the entire open reading frame of HCV. Utilizing cross validation, we evaluated the correlation of APD with TSI, and its ability to infer TSI via a linear model. We additionally studied the ability of diversity to classify infections as recent (infected for <1 year) or chronic, using receiver-operator-characteristic area under the curve (ROC-AUC) in 50 patients whose infection could be unambiguously classified as either recent or chronic. Measuring HCV diversity over third or all codon positions gave similar performances, and notable improvement over first or second codon positions. APD calculated over the entire genome enabled classification of infection recency (ROC-AUC = 0.76). Additionally, APD correlated with TSI (R2 = 0.33) and could predict TSI (mean absolute error = 1.67 years). Restricting the region over which APD was calculated to E2-NS2 further improved accuracy (ROC-AUC = 0.85, R2 = 0.54, mean absolute error = 1.38 years). Genetic diversity in HCV correlates with TSI and is a proxy for infection recency and TSI, even several years post-infection.

scholarly journals Automated Aircraft Dent Inspection via a Modified Fourier Transform Profilometry Algorithm

Sensors ◽  
2022 ◽  
Vol 22 (2) ◽  
pp. 433
Author(s):  
Pasquale Lafiosca ◽  
Ip-Shing Fan ◽  
Nicolas P. Avdelidis
Keyword(s):  
Fourier Transform ◽  
Mean Absolute Error ◽  
User Interaction ◽  
Reconstruction Algorithm ◽  
Absolute Error ◽  
Reference Plane ◽  
Pass Band ◽  
Single Shot ◽  
Original Algorithm ◽  
Improved Accuracy

The search for dents is a consistent part of the aircraft inspection workload. The engineer is required to find, measure, and report each dent over the aircraft skin. This process is not only hazardous, but also extremely subject to human factors and environmental conditions. This study discusses the feasibility of automated dent scanning via a single-shot triangular stereo Fourier transform algorithm, designed to be compatible with the use of an unmanned aerial vehicle. The original algorithm is modified introducing two main contributions. First, the automatic estimation of the pass-band filter removes the user interaction in the phase filtering process. Secondly, the employment of a virtual reference plane reduces unwrapping errors, leading to improved accuracy independently of the chosen unwrapping algorithm. Static experiments reached a mean absolute error of ∼0.1 mm at a distance of 60 cm, while dynamic experiments showed ∼0.3 mm at a distance of 120 cm. On average, the mean absolute error decreased by ∼34%, proving the validity of the proposed single-shot 3D reconstruction algorithm and suggesting its applicability for future automated dent inspections.

Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

2020 ◽  
Vol 18 (3) ◽  
pp. 210-218
Author(s):  
Guolong Yu ◽  
Yan Li ◽  
Xuhe Huang ◽  
Pingping Zhou ◽  
Jin Yan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Phylogenetic Analyses ◽  
Resistance Mutations ◽  
Protease Inhibition ◽  
Subtype B ◽  
Primary Drug Resistance ◽  
Hiv 1 ◽  
Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

Contactless Core-Temperature Monitoring by Infrared Thermal Sensor using Mean Absolute Error Analysis

2020 ◽  
Vol 15 ◽  
Author(s):  
Fahad Layth Malallah ◽  
Baraa T. Shareef ◽  
Mustafah Ghanem Saeed ◽  
Khaled N. Yasen
Keyword(s):  
Body Temperature ◽  
Embedded System ◽  
Core Temperature ◽  
Integrated Circuit ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Thermal Sensor ◽  
Human Face ◽  
Body Contact ◽  
Arduino Microcontroller

Aims: Normally, the temperature increase of individuals leads to the possibility of getting a type of disease, which might be risky to other people such as coronavirus. Traditional techniques for tracking core-temperature require body contact either by oral, rectum, axillary, or tympanic, which are unfortunately considered intrusive in nature as well as causes of contagion. Therefore, sensing human core-temperature non-intrusively and remotely is the objective of this research. Background: Nowadays, increasing level of medical sectors is a necessary targets for the research operations, especially with the development of the integrated circuit, sensors and cameras that made the normal life easier. Methods: The solution is by proposing an embedded system consisting of the Arduino microcontroller, which is trained with a model of Mean Absolute Error (MAE) analysis for predicting Contactless Core-Temperature (CCT), which is the real body temperature. Results: The Arduino is connected to an Infrared-Thermal sensor named MLX90614 as input signal, and connected to the LCD to display the CCT. To evaluate the proposed system, experiments are conducted by participating 31-subject sensing contactless temperature from the three face sub-regions: forehead, nose, and cheek. Conclusion: Experimental results approved that CCT can be measured remotely depending on the human face, in which the forehead region is better to be dependent, rather than nose and cheek regions for CCT measurement due to the smallest

scholarly journals Towards Tracking of Deep Brain Stimulation Electrodes Using an Integrated Magnetometer

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2670
Author(s):  
Thomas Quirin ◽  
Corentin Féry ◽  
Dorian Vogel ◽  
Céline Vergne ◽  
Mathieu Sarracanie ◽  
...  
Keyword(s):  
Deep Brain Stimulation ◽  
Brain Stimulation ◽  
Mean Absolute Error ◽  
Tracking System ◽  
Three Dimensional ◽  
Absolute Error ◽  
Magnetic Tracking ◽  
Magnetic Camera ◽  
Magnetic Resonance Imaging Mri ◽  
Deep Brain

This paper presents a tracking system using magnetometers, possibly integrable in a deep brain stimulation (DBS) electrode. DBS is a treatment for movement disorders where the position of the implant is of prime importance. Positioning challenges during the surgery could be addressed thanks to a magnetic tracking. The system proposed in this paper, complementary to existing procedures, has been designed to bridge preoperative clinical imaging with DBS surgery, allowing the surgeon to increase his/her control on the implantation trajectory. Here the magnetic source required for tracking consists of three coils, and is experimentally mapped. This mapping has been performed with an in-house three-dimensional magnetic camera. The system demonstrates how magnetometers integrated directly at the tip of a DBS electrode, might improve treatment by monitoring the position during and after the surgery. The three-dimensional operation without line of sight has been demonstrated using a reference obtained with magnetic resonance imaging (MRI) of a simplified brain model. We observed experimentally a mean absolute error of 1.35 mm and an Euclidean error of 3.07 mm. Several areas of improvement to target errors below 1 mm are also discussed.

scholarly journals A Review of Deep Learning-Based Contactless Heart Rate Measurement Methods

Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3719
Author(s):  
Aoxin Ni ◽  
Arian Azarang ◽  
Nasser Kehtarnavaz
Keyword(s):  
Heart Rate ◽  
Deep Learning ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Video Camera ◽  
Measurement Methods ◽  
Rate Measurement ◽  
Learning Methods ◽  
The Public ◽  
Heart Rate Measurement

The interest in contactless or remote heart rate measurement has been steadily growing in healthcare and sports applications. Contactless methods involve the utilization of a video camera and image processing algorithms. Recently, deep learning methods have been used to improve the performance of conventional contactless methods for heart rate measurement. After providing a review of the related literature, a comparison of the deep learning methods whose codes are publicly available is conducted in this paper. The public domain UBFC dataset is used to compare the performance of these deep learning methods for heart rate measurement. The results obtained show that the deep learning method PhysNet generates the best heart rate measurement outcome among these methods, with a mean absolute error value of 2.57 beats per minute and a mean square error value of 7.56 beats per minute.

scholarly journals A MYC-Driven Plasma Polyamine Signature for Early Detection of Ovarian Cancer

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 913
Author(s):  
Johannes Fahrmann ◽  
Ehsan Irajizad ◽  
Makoto Kobayashi ◽  
Jody Vykoukal ◽  
Jennifer Dennison ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Early Stage ◽  
Area Under The Curve ◽  
Polyamine Metabolism ◽  
Healthy Controls ◽  
Test Set ◽  
Exact Test ◽  
Oncogenic Driver ◽  
Characteristic Area ◽  
Validation Set

MYC is an oncogenic driver in the pathogenesis of ovarian cancer. We previously demonstrated that MYC regulates polyamine metabolism in triple-negative breast cancer (TNBC) and that a plasma polyamine signature is associated with TNBC development and progression. We hypothesized that a similar plasma polyamine signature may associate with ovarian cancer (OvCa) development. Using mass spectrometry, four polyamines were quantified in plasma from 116 OvCa cases and 143 controls (71 healthy controls + 72 subjects with benign pelvic masses) (Test Set). Findings were validated in an independent plasma set from 61 early-stage OvCa cases and 71 healthy controls (Validation Set). Complementarity of polyamines with CA125 was also evaluated. Receiver operating characteristic area under the curve (AUC) of individual polyamines for distinguishing cases from healthy controls ranged from 0.74–0.88. A polyamine signature consisting of diacetylspermine + N-(3-acetamidopropyl)pyrrolidin-2-one in combination with CA125 developed in the Test Set yielded improvement in sensitivity at >99% specificity relative to CA125 alone (73.7% vs 62.2%; McNemar exact test 2-sided P: 0.019) in the validation set and captured 30.4% of cases that were missed with CA125 alone. Our findings reveal a MYC-driven plasma polyamine signature associated with OvCa that complemented CA125 in detecting early-stage ovarian cancer.

scholarly journals Detection and Severity Evaluation of Combined Rail Defects Using Deep Learning

Vibration ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 341-356
Author(s):  
Jessada Sresakoolchai ◽  
Sakdirat Kaewunruen
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Machine Learning Techniques ◽  
Rolling Stock ◽  
Raw Data ◽  
Learning Techniques ◽  
Combined Defects

Various techniques have been developed to detect railway defects. One of the popular techniques is machine learning. This unprecedented study applies deep learning, which is a branch of machine learning techniques, to detect and evaluate the severity of rail combined defects. The combined defects in the study are settlement and dipped joint. Features used to detect and evaluate the severity of combined defects are axle box accelerations simulated using a verified rolling stock dynamic behavior simulation called D-Track. A total of 1650 simulations are run to generate numerical data. Deep learning techniques used in the study are deep neural network (DNN), convolutional neural network (CNN), and recurrent neural network (RNN). Simulated data are used in two ways: simplified data and raw data. Simplified data are used to develop the DNN model, while raw data are used to develop the CNN and RNN model. For simplified data, features are extracted from raw data, which are the weight of rolling stock, the speed of rolling stock, and three peak and bottom accelerations from two wheels of rolling stock. In total, there are 14 features used as simplified data for developing the DNN model. For raw data, time-domain accelerations are used directly to develop the CNN and RNN models without processing and data extraction. Hyperparameter tuning is performed to ensure that the performance of each model is optimized. Grid search is used for performing hyperparameter tuning. To detect the combined defects, the study proposes two approaches. The first approach uses one model to detect settlement and dipped joint, and the second approach uses two models to detect settlement and dipped joint separately. The results show that the CNN models of both approaches provide the same accuracy of 99%, so one model is good enough to detect settlement and dipped joint. To evaluate the severity of the combined defects, the study applies classification and regression concepts. Classification is used to evaluate the severity by categorizing defects into light, medium, and severe classes, and regression is used to estimate the size of defects. From the study, the CNN model is suitable for evaluating dipped joint severity with an accuracy of 84% and mean absolute error (MAE) of 1.25 mm, and the RNN model is suitable for evaluating settlement severity with an accuracy of 99% and mean absolute error (MAE) of 1.58 mm.

Trust and fuzzy inference based cross domain serendipitous item recommendations (TFCDSRS)

2021 ◽  
pp. 1-13
Author(s):  
Richa ◽  
Punam Bedi
Keyword(s):  
Fuzzy Inference ◽  
Mean Absolute Error ◽  
Information Filtering ◽  
Absolute Error ◽  
User Acceptance ◽  
Decision Making Process ◽  
End User ◽  
Cross Domain ◽  
F Measure ◽  
Filtering Approach

Recommender System (RS) is an information filtering approach that helps the overburdened user with information in his decision making process and suggests items which might be interesting to him. While presenting recommendation to the user, accuracy of the presented list is always a concern for the researchers. However, in recent years, the focus has now shifted to include the unexpectedness and novel items in the list along with accuracy of the recommended items. To increase the user acceptance, it is important to provide potentially interesting items which are not so obvious and different from the items that the end user has rated. In this work, we have proposed a model that generates serendipitous item recommendation and also takes care of accuracy as well as the sparsity issues. Literature suggests that there are various components that help to achieve the objective of serendipitous recommendations. In this paper, fuzzy inference based approach is used for the serendipity computation because the definitions of the components overlap. Moreover, to improve the accuracy and sparsity issues in the recommendation process, cross domain and trust based approaches are incorporated. A prototype of the system is developed for the tourism domain and the performance is measured using mean absolute error (MAE), root mean square error (RMSE), unexpectedness, precision, recall and F-measure.

scholarly journals Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: “The Tortoise and the Hare”

2021 ◽  
Vol 9 (1) ◽  
pp. 147
Author(s):  
Ana Santos-Pereira ◽  
Carlos Magalhães ◽  
Pedro M. M. Araújo ◽  
Nuno S. Osório
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Evolutionary Dynamics ◽  
Evolutionary Genetics ◽  
Host Cells ◽  
Whole Genome Sequencing Data ◽  
Host Immune System ◽  
Viral Mutant ◽  
Hiv 1

The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral “mutant cloud” is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.

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