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BioRxiv : the Preprint Server For... Jun 2024The mouse digit tip regenerates following amputation, a process mediated by a cellularly heterogeneous blastema. We previously found the gene Mest to be highly expressed...
The mouse digit tip regenerates following amputation, a process mediated by a cellularly heterogeneous blastema. We previously found the gene Mest to be highly expressed in mesenchymal cells of the blastema and a strong candidate pro-regenerative gene. We now show Mest digit expression is regeneration-specific and not upregulated in post-amputation fibrosing proximal digits. Mest homozygous knockout mice exhibit delayed bone regeneration though no phenotype is found in paternal knockout mice, inconsistent with the defined maternal genomic imprinting of Mest. We demonstrate that promoter switching, not loss of imprinting, regulates biallelic Mest expression in the blastema and does not occur during embryogenesis, indicating a regeneration-specific mechanism. Requirement for Mest expression is tied to modulating neutrophil response, as revealed by scRNAseq and FACS comparing wildtype and knockout blastemas. Collectively, the imprinted gene Mest is required for proper digit tip regeneration and its blastema expression is facilitated by promoter switching for biallelic expression.
PubMed: 38915675
DOI: 10.1101/2024.06.12.598713 -
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 -
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 -
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 -
Journal of Dairy Science Jun 2024Poor limb conformation in cattle is believed to be closely associated with claw and limb disorders. Limb conformation is part of genetic evaluation and is assessed...
Poor limb conformation in cattle is believed to be closely associated with claw and limb disorders. Limb conformation is part of genetic evaluation and is assessed visually. In this descriptive study, the assessment of conformation in calves was evaluated objectively using joint angle measurements. A total of 100, 30- to 90-d-old, heifer calves of the Brown Swiss (n = 50) and Holstein (n = 50) breeds were photographed from both sides and the front and rear. Carpal, tarsal, autopodium and fetlock joint angles of the fore- or hind limbs were measured on the images using anatomic reference points and the ImageJ/Fiji® program. Each angle was measured 3 times, and the mean was used for analysis. Values from both sides were pooled. Deviations from defined standard angles were classified as slight or moderate. The positions of the front and hind feet were measured and scored. On average, the calves had moderate "knock-kneed" carpal conformation, and the autopodium of the front limb had a slight lateral deviation. In the rear view, the calves had slight, but close to moderate, "cow-hocked" tarsal conformation, and the autopodium of the hind limbs was parallel, but close to slightly deviated. Holstein calves were moderately, and Brown Swiss calves were slightly "cow-hocked". A moderate lateral deviation occurred in the metacarpal-digit angle in the front view and a slight lateral deviation occurred in the metatarsal-digit angle in the rear view. The front feet position score was >17° in 69% of the calves, and the hind feet position score was <17° in 90% of the calves. In the side views, the calves were slightly "over at the carpus" and slightly "straight-hocked" and had average fetlock conformation. In the mean values, most measured joint angles did not correspond to the straight or parallel classifications in our calves; moderate "knock-kneed" and slight "cow-hocked", and "toed-out" classifications were most common. The limb angles measured were based on anatomical features and therefore are unlikely to change substantially with increasing age. These aspects should be considered when assessing linear traits and investigating the relationship between limb conformation and claw diseases.
PubMed: 38908704
DOI: 10.3168/jds.2024-24765 -
NPJ Digital Medicine Jun 2024Tremor is one of the most common neurological symptoms. Its clinical and neurobiological complexity necessitates novel approaches for granular phenotyping. Instrumented...
Tremor is one of the most common neurological symptoms. Its clinical and neurobiological complexity necessitates novel approaches for granular phenotyping. Instrumented neurophysiological analyses have proven useful, but are highly resource-intensive and lack broad accessibility. In contrast, bedside scores are simple to administer, but lack the granularity to capture subtle but relevant tremor features. We utilise the open-source computer vision pose tracking algorithm Mediapipe to track hands in clinical video recordings and use the resulting time series to compute canonical tremor features. This approach is compared to marker-based 3D motion capture, wrist-worn accelerometry, clinical scoring and a second, specifically trained tremor-specific algorithm in two independent clinical cohorts. These cohorts consisted of 66 patients diagnosed with essential tremor, assessed in different task conditions and states of deep brain stimulation therapy. We find that Mediapipe-derived tremor metrics exhibit high convergent clinical validity to scores (Spearman's ρ = 0.55-0.86, p≤ .01) as well as an accuracy of up to 2.60 mm (95% CI [-3.13, 8.23]) and ≤0.21 Hz (95% CI [-0.05, 0.46]) for tremor amplitude and frequency measurements, matching gold-standard equipment. Mediapipe, but not the disease-specific algorithm, was capable of analysing videos involving complex configurational changes of the hands. Moreover, it enabled the extraction of tremor features with diagnostic and prognostic relevance, a dimension which conventional tremor scores were unable to provide. Collectively, this demonstrates that current computer vision algorithms can be transformed into an accurate and highly accessible tool for video-based tremor analysis, yielding comparable results to gold standard tremor recordings.
PubMed: 38906946
DOI: 10.1038/s41746-024-01153-1 -
Cognition Jun 2024It is often claimed that probabilistic expectations affect visual perception directly, without mediation by selective attention. However, these claims have been...
It is often claimed that probabilistic expectations affect visual perception directly, without mediation by selective attention. However, these claims have been disputed, as effects of expectation and attention are notoriously hard to dissociate experimentally. In this study, we used a new approach to separate expectations from attention. In four experiments (N = 60), participants searched for a target in a rapid serial visual presentation (RSVP) stream and had to identify a digit or a letter defined by a low-level cue (colour or shape). Expectations about the target's alphanumeric category were probabilistically manipulated. Since category membership is a high-level feature and since the target was embedded among many distractors that shared its category, targets from the expected category should not attract attention more than targets from the unexpected category. In the first experiment, these targets were more likely to be identified relative to targets from the unexpected category. Importantly, in the following experiments, we also included behavioural and electrophysiological indices of attentional guidance and engagement. This allowed us to examine whether expectations also modulated these or earlier attentional processes. Results showed that category-based expectations had no modulatory effects on attention, and only affected processing at later encoding-related stages. Alternative interpretation of expectation effects in terms of repetition priming or response bias were also ruled out. These observations provide new evidence for direct attention-independent expectation effects on perception. We suggest that expectations can adjust the threshold required for encoding expectations-congruent information, thereby affecting the speed with which target objects are encoded in working memory.
PubMed: 38906015
DOI: 10.1016/j.cognition.2024.105864