Deep Learning of Rhabdomyosarcoma Pathology Images for Classification and Survival Outcome Prediction.

Rhabdomyosarcoma (RMS), the most common malignant soft tissue tumor in children, has several histologic subtypes that influence treatment and predict patient outcomes. Assistance with histologic classification for pathologists as well as discovery of optimized predictive biomarkers is needed. A convolutional neural network for RMS histology subtype classification was developed using digitized pathology images from 80 patients collected at time of diagnosis. A subsequent embryonal rhabdomyosarcoma (eRMS) prognostic model was also developed in a cohort of 60 eRMS patients. The RMS classification model reached a performance of an area under the receiver operating curve of 0.94 for alveolar rhabdomyosarcoma and an area under the receiver operating curve of 0.92 for eRMS at slide level in the test data set (n = 192). The eRMS prognosis model separated the patients into predicted high- and low-risk groups with significantly different event-free survival outcome (likelihood ratio test; P = 0.02) in the test data set (n = 136). The predicted risk group is significantly associated with patient event-free survival outcome after adjusting for patient age and sex (predicted high- versus low-risk group hazard ratio, 4.64; 95% CI, 1.05-20.57; P = 0.04). This is the first comprehensive study to develop computational algorithms for subtype classification and prognosis prediction for RMS histopathology images. Such models can aid pathology evaluation and provide additional parameters for risk stratification.

Perinuclear mitochondrial clustering, increased ROS levels, and HIF1 are required for the activation of HSF1 by heat stress.

The heat shock response (HSR) is a conserved cellular defensive response against stresses such as temperature, oxidative stress and heavy metals. A significant group of players in the HSR is the set of molecular chaperones known as heat shock proteins (HSPs), which assist in the refolding of unfolded proteins and prevent the accumulation of damaged proteins. HSP genes are activated by the HSF1 transcription factor, a master regulator of the HSR pathway. A variety of stressors activate HSF1, but the key molecular players and the processes that directly contribute to HSF1 activation remain unclear. In this study, we show that heat shock induces perinuclear clustering of mitochondria in mammalian cells, and this clustering is essential for activation of the HSR. We also show that this perinuclear clustering of mitochondria results in increased levels of reactive oxygen species in the nucleus, leading to the activation of hypoxia-inducible factor-1α (HIF-1α). To conclude, we provide evidence to suggest that HIF-1α is one of the crucial regulators of HSF1 and that HIF-1α is essential for activation of the HSR during heat shock.

Inhibiting Erastin-Induced Ferroptotic Cell Death by Purine-Based Chelators.

Ferroptosis is a cell death event caused by increased lipid peroxidation leading to iron-dependent oxidative stress and is associated with a wide variety of diseases. In recent years, ferroptosis inhibition has emerged as a novel strategy to target different pathologies. Here, we report the synthesis of two purine derivatives, 1 and 2, for iron chelation strategy and evaluate their potency to inhibit erastin-induced ferroptosis. Both compounds showed efficient iron chelation in solution as well as in cellular environment. The crystal structure of the purine derivatives with iron demonstrated a 2 : 1 (ligand to metal center) stoichiometry for iron and purine derivative complexation. The synthesized compounds also decrease the reactive oxygen species concentration in cell cultures. Compound 2 showed better potency towards the prevention of ferroptotic cell death as compared to commercially available iron chelator in the erastin-induced ferroptosis cell culture model. Such purine analogues are potential functional scaffolds for the development of target molecules for ferroptosis inhibition.

Lateral flow-based nucleic acid detection of SARS-CoV-2 using enzymatic incorporation of biotin-labeled dUTP for POCT use.

The degree of detrimental effects inflicted on mankind by the COVID-19 pandemic increased the need to develop ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable) POCT (point of care testing) to overcome the current and any future pandemics. Much effort in research and development is currently advancing the progress to overcome the diagnostic pressure built up by emerging new pathogens. LAMP (loop-mediated isothermal amplification) is a well-researched isothermal technique for specific nucleic acid amplification which can be combined with a highly sensitive immunochromatographic readout via lateral flow assays (LFA). Here we discuss LAMP-LFA robustness, sensitivity, and specificity for SARS-CoV-2 N-gene detection in cDNA and clinical swab-extracted RNA samples. The LFA readout is designed to produce highly specific results by incorporation of biotin and FITC labels to 11-dUTP and LF (loop forming forward) primer, respectively. The LAMP-LFA assay was established using cDNA for N-gene with an accuracy of 95.65%. To validate the study, 82 SARS-CoV-2-positive RNA samples were tested. Reverse transcriptase (RT)-LAMP-LFA was positive for the RNA samples with an accuracy of 81.66%; SARS-CoV-2 viral RNA was detected by RT-LAMP-LFA for as low as CT-33. Our method reduced the detection time to 15 min and indicates therefore that RT-LAMP in combination with LFA represents a promising nucleic acid biosensing POCT platform that combines with smartphone based semi-quantitative data analysis.

A Role for Artificial Intelligence in the Classification of Craniofacial Anomalies.

ABSTRACT: Development of an objective algorithm to diagnose and assess craniofacial conditions has the potential to facilitate early diagnosis, especially for care providers with limited craniofacial expertise. Deep learning, a branch of artificial intelligence, can automatically analyze and categorize disease without human assistance. Convolutional neural networks (CNN) have excelled in utilizing medical images to automatically classify disease. In this study, the authors developed CNN models to detect and classify non-syndromic craniosynostosis (CS) using 2D images. The authors created an annotated data set of labeled CS (normal, metopic, sagittal, and unicoronal) conditions using standard clinical photography from the image repository at our center. The authors extended this dataset set by adding photographic images of children with craniofacial conditions from the internet. A total of 1076 images were used in this study. The authors developed a CNN model using a pre-trained ResNet-50 model to classify the data as metopic, sagittal, and unicoronal. The testing accuracy for the CS ResNet50 model achieved an overall testing accuracy of 90.6%. The sensitivity and precision were: 100% and 100% for metopic, 93.3% and 100% for sagittal, and 66.7% and 100% for unicoronal, respectively. The CNN model performed with promising accuracy. These results support the idea that deep learning has a role in diagnosis of craniofacial conditions. Using standard 2D clinical photography, such systems can provide automated screening and detection of these conditions. In the future, ML may be applied to prediction and assessment of surgical outcomes, or as an open-source remote diagnostic resource.

Comparison of Preterm and Term Wharton's Jelly-Derived Mesenchymal Stem Cell Properties in Different Oxygen Tensions.

Mesenchymal stem cells (MSCs) have shown promise as therapeutic agents in treating morbidities associated with premature birth. MSCs derived from the human umbilical cord are easy to isolate and have low immunogenicity and a robust ability to secrete paracrine factors. To date, there are no studies evaluating preterm versus term umbilical cord tissue-derived MSCs. Therefore, our aim was twofold: (1) to compare stem cell properties in preterm versus term MSCs and (2) to examine the impact of oxygen tension on stem cell behavior. Umbilical cord tissue was obtained from 5 preterm and 5 term neonates. The cells were isolated and characterized as MSCs in accordance with the International Society for Cellular Therapy. We exposed MSCs to different oxygen tensions to examine the impact of environmental factors on cell performance. We studied the following stem cell properties: (i) motility, (ii) proliferation, (iii) senescence, (iv) cell viability, (v) colony-forming unit efficiency, and (vi) inflammatory cytokine expression. Under normoxia (21% O2), cells from preterm and term infants had similar properties. Under hypoxic conditions (1% O2), term MSCs had better cell proliferation; however, cells exposed to hyperoxia (90% O2) had the slowest motility and lowest cell viability (p < 0.05). There was no difference in the expression of senescence or cytokine expression between the groups. The term cells demonstrated more colony-forming efficiency than the preterm cells. In sum, our preliminary findings suggest that MSCs derived from term and preterm umbilical cords have similar characteristics, offering the potential of future autologous/allogeneic MSC transplants in neonates.

Loss of laforin or malin results in increased Drp1 level and concomitant mitochondrial fragmentation in Lafora disease mouse models.

Lafora disease (LD) is an autosomal recessive form of a fatal disorder characterized by the myoclonus epilepsy, ataxia, psychosis, dementia, and dysarthria. A hallmark of LD is the presence of abnormal glycogen inclusions called Lafora bodies in the affected tissues including the neurons. LD can be caused by defects either in the laforin phosphatase coded by the EPM2A gene or in the malin E3 ubiquitin ligase coded by the NHLRC1 gene. The mouse models of LD, created by the targeted disruption of the LD genes, display several neurodegenerative changes. Prominent among them are the autophagic defects, abnormally large lysosomes, neurofibrillary tangles, amyloid beta deposits, and abnormal mitochondria. However, whether or not such neurodegenerative changes are a direct effect of the loss of laforin/malin was not unequivocally established. Here, we show that laforin- or malin-deficient neurons and fibroblasts display a significantly higher number of fragmented mitochondria. Loss of laforin or malin resulted in increased levels of the mitochondrial fission GTPase Drp1, its enhanced mitochondrial targeting, and increased intracellular calcium levels. Intriguingly, laforin and malin display opposite effects on the cellular level of parkin, an ubiquitin ligase of Drp1; loss of laforin led to reduced levels of parkin while the loss of malin resulted in increased parkin levels. Laforin and malin, however, interact with and positively regulate the activity of parkin, thus explaining the molecular basis of increased Drp1 levels in LD tissues. Our results suggest that laforin and malin are novel regulators of mitochondrial quality control pathway and that the mitochondrial dysfunction resulting from the increased Drp1 levels could underlie neuropathology in LD.

A comparative evaluation of concordance and speed between smartphone app-based and artificial intelligence web-based cephalometric tracing software with the manual tracing method: A cross-sectional study.

Background: This study compared the accuracy and speed of cephalometric analysis using an artificial intelligence web-based method and a smartphone app-based system with manual cephalometric analysis as the reference standard. Material and Methods: In this cross-sectional study, the lateral cephalograms were analysed using four methods: manual tracing, smartphone app tracing, artificial intelligence web-based automated tracing without manual landmark identification correction and artificial intelligence web-based automated tracing with manual landmark identification correction. The principal investigator obtained linear and angular cephalometric measurements to compare the accuracies of the four methods being assessed. Additionally, the duration required for landmark identification and subsequent analysis was recorded. Results: The analyses included 40 lateral cephalograms that were selected based on the inclusion and exclusion criteria. Very good to excellent agreement was observed in the accuracies of the artificial intelligence web-based and smartphone app-based systems compared with manual tracing (interclass correlation coefficient values ranging from 0.707 to 0.9, p< 0.001). Of the artificial intelligence web-based systems, the method without correction of automated landmark detection showed less reliable measurements than the other methods. Cephalometric analysis using artificial intelligence web-based and smartphone app-based systems consumed less time than manual tracing (p< 0.001). Conclusions: Artificial intelligence web-based automated tracing with manual landmark identification correction and smartphone-based app provide results that are comparable to those from the manual tracing method. However, artificial intelligence web-based systems require improvements in terms of automated landmark identification to obtain results that are similar to those from the other methods being assessed. Key words:Artificial Intelligence, Cephalometry, Computer software, Mobile application.

Iron limitation indirectly reduces the Escherichia coli torCAD operon expression by a reduction of molybdenum cofactor availability.

The expression of most molybdoenzymes in Escherichia coli has so far been revealed to be regulated by anaerobiosis and requires the presence of iron, based on the necessity of the transcription factor FNR to bind one [4Fe-4S] cluster. One exception is trimethylamine-N-oxide reductase encoded by the torCAD operon, which has been described to be expressed independently from FNR. In contrast to other alternative anaerobic respiratory systems, the expression of the torCAD operon was shown not to be completely repressed by the presence of dioxygen. To date, the basis for the O2-dependent expression of the torCAD operon has been related to the abundance of the transcriptional regulator IscR, which represses the transcription of torS and torT, and is more abundant under aerobic conditions than under anaerobic conditions. In this study, we reinvestigated the regulation of the torCAD operon and its dependence on the presence of iron and identified a novel regulation that depends on the presence of the bis-molybdopterin guanine dinucleotide (bis-MGD) molybdenum cofactor . We confirmed that the torCAD operon is directly regulated by the heme-containing protein TorC and is indirectly regulated by ArcA and by the availability of iron via active FNR and Fur, both regulatory proteins that influence the synthesis of the molybdenum cofactor. Furthermore, we identified a novel regulation mode of torCAD expression that is dependent on cellular levels of bis-MGD and is not used by other bis-MGD-containing enzymes like nitrate reductase.IMPORTANCEIn bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. FNR is a very important transcription factor that represents the master switch for the expression of target genes in response to anaerobiosis. Only Escherichia coli trimethylamine-N-oxide (TMAO) reductase escapes this regulation by FNR. We identified that the expression of TMAO reductase is regulated by the amount of bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor synthesized by the cell itself, representing a novel regulation pathway for the expression of an operon coding for a molybdoenzyme. Furthermore, TMAO reductase gene expression is indirectly regulated by the presence of iron, which is required for the production of the bis-MGD cofactor in the cell.

Detection of Reverse Transcriptase LAMP-Amplified Nucleic Acid from Oropharyngeal Viral Swab Samples Using Biotinylated DNA Probes through a Lateral Flow Assay.

This study focuses on three key aspects: (a) crude throat swab samples in a viral transport medium (VTM) as templates for RT-LAMP reactions; (b) a biotinylated DNA probe with enhanced specificity for LFA readouts; and (c) a digital semi-quantification of LFA readouts. Throat swab samples from SARS-CoV-2 positive and negative patients were used in their crude (no cleaning or pre-treatment) forms for the RT-LAMP reaction. The samples were heat-inactivated but not treated for any kind of nucleic acid extraction or purification. The RT-LAMP (20 min processing time) product was read out by an LFA approach using two labels: FITC and biotin. FITC was enzymatically incorporated into the RT-LAMP amplicon with the LF-LAMP primer, and biotin was introduced using biotinylated DNA probes, specifically for the amplicon region after RT-LAMP amplification. This assay setup with biotinylated DNA probe-based LFA readouts of the RT-LAMP amplicon was 98.11% sensitive and 96.15% specific. The LFA result was further analysed by a smartphone-based IVD device, wherein the T-line intensity was recorded. The LFA T-line intensity was then correlated with the qRT-PCR Ct value of the positive swab samples. A digital semi-quantification of RT-LAMP-LFA was reported with a correlation coefficient of R2 = 0.702. The overall RT-LAMP-LFA assay time was recorded to be 35 min with a LoD of three RNA copies/µL (Ct-33). With these three advancements, the nucleic acid testing-point of care technique (NAT-POCT) is exemplified as a versatile biosensor platform with great potential and applicability for the detection of pathogens without the need for sample storage, transportation, or pre-processing.

Post Covid-19 Sinonasal Candidiasis: A Crisis Within the Pandemic.

The aim of this study was to find out the association of sinonasal candidiasis and Covid-19 infection. A prospective observational study was conducted at a tertiary care centre from April to September 2021, involving all patients with invasive candidiasis of the paranasal sinuses having a history of Covid-19 infection. A total of 18 patients of covid associated sinonasal candidiasis among the 475 cases of fungal rhinosinusitis were studied. All patients had involvement of nose and sinuses and 2 patients had orbital involvement with no loss of vision, while 3 had intracranial extensions and 1 had pulmonary involvement. Mandible was involved in 1 patient alone, while the maxilla and palate were involved in 5 patients. 15 patients were hypertensive, 12 diabetics and 1 had aplastic anaemia. Cultures showed that 8 patients had C. parapsilosis, 5 had C. albicans, 3 had C. tropicalis and 2 had mixed fungal infections. All patients underwent surgical debridement and antifungal administration. They were followed up for a minimum of 3 months. There was only one mortality (with aplastic anaemia), rest 17 were disease free at the time of writing this article. This is perhaps the first case series of post covid sinonasal candidiasis in the world. Invasive sinonasal candidiasis is a newer sequela of COVID-19 infection. Uncontrolled diabetes and over-zealous use of steroids at the time of Covid-19 are few of the known risk factors. Early surgical intervention and anti-fungal treatment should be sought for management.

Ironing the mitochondria: Relevance to its dynamics.

The mitochondrion is "jack of many trades and master of one". Despite being a master in energy generation, it plays a significant role in other cellular processes, including calcium homeostasis, cell death, and iron metabolism. Since mitochondria employ the majority of cellular iron, it plays a central role in the iron homeostasis. Iron could be a major regulator of mitochondrial dynamics as the excess of iron leads to oxidative stress, which causes a disturbance in mitochondrial dynamics. Remarkably, abnormal iron accumulation has been observed in the brain regions of the neurodegenerative disorders patients. These neurodegenerative disorders are also often associated with the abnormal mitochondrial dynamics. Here in this article, we will mainly discuss the studies focused on unravelling the role of iron in mitochondrial dynamics.