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BMC Bioinformatics Jun 2024Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic...
BACKGROUND
Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps.
RESULTS
Here, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage's utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage's capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results.
CONCLUSIONS
Entourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license.
Topics: Software; Genome, Viral; Humans; High-Throughput Nucleotide Sequencing; SARS-CoV-2; Metagenomics; Viruses; COVID-19; Virome; HeLa Cells
PubMed: 38914932
DOI: 10.1186/s12859-024-05846-y -
Psychological Research Jun 2024The presentation of one task increases the reaction time on a subsequent task, if stimulus onset asynchrony (SOA) between tasks is short. This psychological refractory...
The presentation of one task increases the reaction time on a subsequent task, if stimulus onset asynchrony (SOA) between tasks is short. This psychological refractory period (PRP) effect is typically leveling off as SOA approaches 1 s, which has been documented both in classical laboratory paradigms and in simulated car driving. Here we report a more persistent effect on the subsequent task that goes well beyond the typical duration of the PRP effect. In a driving simulator, 120 healthy older participants followed a lead car that mostly drove at a constant speed. They had to maintain a regular distance from the lead car and had to brake when the lead car braked. Participants also engaged in several additional tasks during driving (two types of tasks: typing three-digit numbers, stating arguments on public issues). SOA between the braking task and the last preceding additional task was 11.49 s ± 1.99 (mean and standard deviation). In a control condition, the braking task was administered without additional tasks. Main performance outcome was Braking Reaction Time (RT, in s), as the interval between onset of brake lights of the lead car and the moment participants released the gas pedal. Additionally, foot movement time (MT, in s), i.e., the difference between gas pedal release and brake pedal onset, was considered for possible compensation behavior. Inter-vehicle distance to the lead car (in m) was taken into account as a moderator. We found that RT averaged 0.77 s without additional tasks, but averaged 1.45 s with additional tasks. This RT difference was less pronounced at smaller inter-vehicle distances, and was not compensated for by faster MT from the gas pedal to the brake pedal. We conclude that detrimental effects of additional tasks on subsequent braking responses can be more persistent than suggested by the PRP effect, possibly because of maintaining multiple task sets, requiring increased executive control. We further conclude that potential detrimental effects can be ameliorated at small inter-vehicle distances by mobilizing extra cognitive resources when response urgency is higher. As a practical implication of our study, distracting stimuli can have persisting detrimental effects on traffic safety.
PubMed: 38914809
DOI: 10.1007/s00426-024-01988-z -
Multiple Sclerosis (Houndmills,... Jun 2024The Konectom™ smartphone-based cognitive processing speed (CPS) test is designed to assess processing speed and account for impact of visuomotor function on performance.
Konectom™ cognitive processing speed test enables reliable remote, unsupervised cognitive assessment in people with multiple sclerosis: Exploring the use of substitution time as a novel digital outcome measure.
BACKGROUND
The Konectom™ smartphone-based cognitive processing speed (CPS) test is designed to assess processing speed and account for impact of visuomotor function on performance.
OBJECTIVE
Evaluate reliability and validity of Konectom CPS Test, performed in clinic and remotely.
METHODS
Data were collected from people with multiple sclerosis (PwMS) aged 18-64 years and healthy control participants (HC) matched for age, sex, and education. Remote test-retest reliability (intraclass correlation coefficients, ICC); correlation with established clinical measures (Spearman correlation coefficients); group analyses between cognitively impaired/unimpaired PwMS; and influence of age, sex, education, and upper limb motor function on CPS Test measures were assessed.
RESULTS
Eighty PwMS and 66 HC participated. CPS Test measures from remote tests had good test-retest reliability (ICC of 0.67-0.87) and correlated with symbol digit modalities test (highest |ρ| = 0.80, < 0.0001). Remote measures were stable (change from baseline < 5%) and correlated with MS disability (highest |ρ| = 0.39, = 0.0004) measured by Expanded Disability Status Scale. CPS Test measures displayed sensitivity to cognitive impairment (highest = 1.47). Demographics and motor function had the lowest impact on CPS Test substitution time, a measure accounting for visuomotor function.
CONCLUSION
Konectom CPS Test measures provide valid, reliable remote measurements of cognitive processing speed in PwMS.
PubMed: 38912764
DOI: 10.1177/13524585241259650 -
The Indian Journal of Radiology &... Jul 2024Macrodystrophia lipomatosa (MDL) is a rare congenital, nonhereditary anomaly characterized by overgrowth of all the mesenchymal elements, predominantly the fibroadipose...
Macrodystrophia lipomatosa (MDL) is a rare congenital, nonhereditary anomaly characterized by overgrowth of all the mesenchymal elements, predominantly the fibroadipose tissue in a sclerotomal distribution commonly involving the median nerve territory in the upper extremity and plantar nerve territory in the lower extremity. It can be either static or progressive, with the former being the more common. MDL is usually present since birth and the affected digit/region increases in length and girth, and growth ceases after puberty. We discuss a rare case of ulnar nerve territory involvement that progressed to grow even after puberty.
PubMed: 38912255
DOI: 10.1055/s-0043-1777745 -
Journal of Alzheimer's Disease Reports 2024The evidence supporting the effectiveness of combined interventions in Alzheimer's disease (AD) patients remains inconclusive.
BACKGROUND
The evidence supporting the effectiveness of combined interventions in Alzheimer's disease (AD) patients remains inconclusive.
OBJECTIVE
The aim of this study was to evaluate the mid- and long-term effectiveness of physical training, alone or combined with cognitive games, on cognitive performance in patients with moderate AD.
METHODS
Seventy-nine AD patients (≈73% females, age of ≈70±1 years) were randomly divided into three groups: aerobic-based training (AT-group, = 27), aerobic-based training plus cognitive games (ACT-group, = 25), and a control group engaged in reading (CG, = 26), two sessions per week. Cognitive performance was evaluated at the start, 4th week (W4), end of the 8th week (W8), and after a 4-week detraining period (W12), using problem-solving (Tower-of-Hanoi), selective attention (Stroop-test), and working memory (Digit-Span-test) assessments. Stress levels and quality of life were also evaluated. Aerobic and combined training induced a positive effect on all cognitive functions tested at W4 (except problem-solving) and W8 (all < 0.001) with greater improvements in working-memory and problem-solving in ACT-group ( < 0.05). Depression levels also decreased significantly, and quality of life improved at W8 ( < 0.001) in both groups. After 4 weeks of detraining, the beneficial effect of AT and ACT was still observed. The CG did not show any significant improvements at all time points. Physical and cognitive interventions appear effective for improving cognitive-functions, quality-of-life, and reducing depression in AD patients. Combined training emerges as a more effective strategy to mitigate AD progression. Further research is necessary to validate these results and explore their potential for preventing early cognitive decline.
PubMed: 38910946
DOI: 10.3233/ADR-249003 -
Cureus May 2024Atlantoaxial dislocations (AAD) are a diverse set of C1-C2 rotatory subluxations that include the inferior and superior axial facet articulations. C1-C2 segments are...
Atlantoaxial dislocations (AAD) are a diverse set of C1-C2 rotatory subluxations that include the inferior and superior axial facet articulations. C1-C2 segments are both covered by cranial-cervical ligaments, indicating that AAD would damage both joints. Whenever the posterior elements are missing or impaired, lateral mass screw fixation has replaced alternative posterior cervical fixation procedures as the preferred treatment for securing the sub-axial cervical spine. An increase in muscle tone, hyperreflexia, pathological reflexes, digit/hand clumsiness, and gait deviations caused by spinal cord compression at the cervical level are the most common clinical features. A 23-year-old female patient came with the chief complaint of weakness, tingling sensation, and numbness in both upper and lower limbs along with imbalance while walking. She had a history of falls which was managed conservatively. As the symptoms progressed, an MRI, a CT scan, and an X-ray of the neck were done to rule out the level of injury which revealed AAD, and the patient was operated on for C1-C2 lateral mass fixation. Post-operatively, the patient was referred to the physiotherapy department for further management. The patient's quality of life and daily functioning were positively affected after undergoing early intervention as measured by the Functional Independence Measure, Neck Disability Index, Berg Balance Scale, and Dynamic Gait Index.
PubMed: 38910634
DOI: 10.7759/cureus.60913 -
Hand (New York, N.Y.) Jun 2024Periosteal sleeve fractures, or avulsions of cartilage and/or periosteum with or without an osseous fragment in skeletally immature individuals, are notoriously easy to...
Periosteal sleeve fractures, or avulsions of cartilage and/or periosteum with or without an osseous fragment in skeletally immature individuals, are notoriously easy to miss and a high index of suspicion is necessary for accurate diagnosis and treatment. While periosteal sleeve avulsion fractures are classically reported in the patella, they have also been reported in the shoulder, clavicle, and elsewhere in the knee. However, no published reports exist for a periosteal sleeve avulsion fracture in the hand. This case details the first reported instance of such an injury involving a thumb metacarpal in a 3-year-old boy, treated with open reduction and percutaneous pinning of the thumb metacarpal.
PubMed: 38910454
DOI: 10.1177/15589447241260074 -
Journal of Neurology Jun 2024Robust predictive models of clinical impairment and worsening in multiple sclerosis (MS) are needed to identify patients at risk and optimize treatment strategies.
BACKGROUND
Robust predictive models of clinical impairment and worsening in multiple sclerosis (MS) are needed to identify patients at risk and optimize treatment strategies.
OBJECTIVE
To evaluate whether machine learning (ML) methods can classify clinical impairment and predict worsening in people with MS (pwMS) and, if so, which combination of clinical and magnetic resonance imaging (MRI) features and ML algorithm is optimal.
METHODS
We used baseline clinical and structural MRI data from two MS cohorts (Berlin: n = 125, Amsterdam: n = 330) to evaluate the capability of five ML models in classifying clinical impairment at baseline and predicting future clinical worsening over a follow-up of 2 and 5 years. Clinical worsening was defined by increases in the Expanded Disability Status Scale (EDSS), Timed 25-Foot Walk Test (T25FW), 9-Hole Peg Test (9HPT), or Symbol Digit Modalities Test (SDMT). Different combinations of clinical and volumetric MRI measures were systematically assessed in predicting clinical outcomes. ML models were evaluated using Monte Carlo cross-validation, area under the curve (AUC), and permutation testing to assess significance.
RESULTS
The ML models significantly determined clinical impairment at baseline for the Amsterdam cohort, but did not reach significance for predicting clinical worsening over a follow-up of 2 and 5 years. High disability (EDSS ≥ 4) was best determined by a support vector machine (SVM) classifier using clinical and global MRI volumes (AUC = 0.83 ± 0.07, p = 0.015). Impaired cognition (SDMT Z-score ≤ -1.5) was best determined by a SVM using regional MRI volumes (thalamus, ventricles, lesions, and hippocampus), reaching an AUC of 0.73 ± 0.04 (p = 0.008).
CONCLUSION
ML models could aid in classifying pwMS with clinical impairment and identify relevant biomarkers, but prediction of clinical worsening is an unmet need.
PubMed: 38909341
DOI: 10.1007/s00415-024-12507-w -
Scientific Reports Jun 2024Vehicle identification systems are vital components that enable many aspects of contemporary life, such as safety, trade, transit, and law enforcement. They improve...
Vehicle identification systems are vital components that enable many aspects of contemporary life, such as safety, trade, transit, and law enforcement. They improve community and individual well-being by increasing vehicle management, security, and transparency. These tasks entail locating and extracting license plates from images or video frames using computer vision and machine learning techniques, followed by recognizing the letters or digits on the plates. This paper proposes a new license plate detection and recognition method based on the deep learning YOLO v8 method, image processing techniques, and the OCR technique for text recognition. For this, the first step was the dataset creation, when gathering 270 images from the internet. Afterward, CVAT (Computer Vision Annotation Tool) was used to annotate the dataset, which is an open-source software platform made to make computer vision tasks easier to annotate and label images and videos. Subsequently, the newly released Yolo version, the Yolo v8, has been employed to detect the number plate area in the input image. Subsequently, after extracting the plate the k-means clustering algorithm, the thresholding techniques, and the opening morphological operation were used to enhance the image and make the characters in the license plate clearer before using OCR. The next step in this process is using the OCR technique to extract the characters. Eventually, a text file containing only the character reflecting the vehicle's country is generated. To ameliorate the efficiency of the proposed approach, several metrics were employed, namely precision, recall, F1-Score, and CLA. In addition, a comparison of the proposed method with existing techniques in the literature has been given. The suggested method obtained convincing results in both detection as well as recognition by obtaining an accuracy of 99% in detection and 98% in character recognition.
PubMed: 38909147
DOI: 10.1038/s41598-024-65272-1 -
NPJ Digital Medicine Jun 2024
PubMed: 38909083
DOI: 10.1038/s41746-024-01168-8