Using a manifold-based approach to extract clinical codes associated with winter respiratory viruses at an emergency department

Every winter, respiratory viruses put most Emergency Departments (ED) around the world under intense pressure. To reduce the consequent stress for hospitals, anticipation of the massive increase of intakes for illness-based symptoms is essential. As the Covid-19 2020 pandemic clearly illustrates, patients are not systematically tested. The ED staff therefore has no real-time knowledge of the presence of the virus in the patients flow. To address this issue, we propose here to use the hospital's laboratory-confirmed database as an attractor for the manifold-based approach for clustering the clinical codes associated with respiratory viruses. We propose a new framework based on the embedding of time series onto the Stiefel manifold, coupled with a density-based clustering algorithm (HDBSCAN) enhanced by a reduction of dimension (UMAP) for the clustering on that manifold. In particular, we show, based on real data sets of two academic hospitals in France, the significant benefits of using geometrical approaches for time series clustering as compared to traditional methods.

Fraud Detection Model Using Semi-supervised Learning

Everything is moving to online platforms in this digital age. The frauds connected to this are likewise rising quickly. After COVID, the amount of fraudulent transactions increased, making this a very essential area of research. This study intends to develop a fraud detection model using machine learning's semi-supervised approach. It combines supervised and unsupervised learning methods and is far more practical than the other two. A bank fraud detection model utilizing the Laplacian model of semi-supervised learning is created. To determine the optimal model, the parameters were adjusted over a wide range of values. This model's strength is that it can handle a big volume of unlabeled data with ease. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

Comprehensive analysis of the novel omicron receptor AXL in cancers.

The SARS-CoV-2 is constantly mutating, and the new coronavirus such as Omicron has spread to many countries around the world. Anexelekto (AXL) is a transmembrane protein with biological functions such as promoting cell growth, migration, aggregation, metastasis and adhesion, and plays an important role in cancers and coronavirus disease 2019 (COVID-19). Unlike angiotensin-converting enzyme 2 (ACE2), AXL was highly expressed in respiratory system cells. In this study, we verified the AXL expression in cancer and normal tissues and found AXL expression was strongly correlated with cancer prognosis, tumor mutation burden (TMB), the microsatellite instability (MSI) in most tumor types. Immune infiltration analysis also demonstrated that there was an inextricable link between AXL expression and immune scores in cancer patients, especially in BLCA, BRCA and CESC. The NK-cells, plasmacytoid dendritic cells, myeloid dendritic cells, as one of the important components of the tumor microenvironment, were highly expressed AXL. In addition, AXL-related tumor neoantigens were identified and might provide the novel potential targets for tumor vaccines or SARS-Cov-2 vaccines research in cancer patients.

THE THRESHOLD VALUE OF THE NUMBER OF HOSPITAL BEDS IN A SEIHR EPIDEMIC MODEL

To investigate the impact of the number of hospital beds on the control of infectious diseases and help allocate the limited medical resources in a region, a SEIHR epidemic model including exposed and hospitalized classes is established. Different from available models, the hospitalization rate is expressed as a function of the number of empty beds. The existence and stability of the equilibria are analyzed, and it is proved that the system undergoes backward bifurcation, Hopf bifurcation, and Bogdanov-Takens bifurcation of codimension 2 under certain conditions by using the center manifold theory and normal form theory. In particular, our results show that there is a threshold value for the capacity of hospital beds in a region. If the capacity of hospital beds is lower than this threshold value, there will be a backward bifurcation, which means that even if the basic reproduction number, R0, is less than unity, it is not enough to prevent the outbreaks. Before taking disease control measures, one should compare the number of beds with the threshold value to avoid misjudgment and try to increase the capacity of hospital beds above this threshold value. The method to estimate the threshold value is also given. In addition, the impacts of the duration of the exposed period on the basic reproduction number and disease transmission are investigated. © 2023 American Institute of Mathematical Sciences. All rights reserved.

A predicament of oxygen supply system at an Indian hospital during COVID-19

Research methodology: This case is based on a project carried out in a tertiary care hospital of the Northeastern region of India for a period of eight months and is written by Dr Ankit Singh, Dr Meenal Kulkarni and Mr Avinash Poojari. The case was developed with the help of the hospital's management team, disguised on request as Mr Raghugopal Ramalinga (Chief Hospital Administrator), Mr Suresh Kumar (Chief Engineer), Ms Linney Krubah (Chief Nursing Superintendent), Dr Premanand Ale (Chief Medical Superintendent) and Mr Srikrishna Shukla (Chief Finance Officer). Case overview/synopsis: This case is about Trident Hospital, which faces issues pertaining to oxygen supply. Oxygen supply at Trident Hospitals is through three options as highlighted in the case, but due to the lack of preventive maintenance and no risk assessment done for the crucial medical oxygen, interruptions and additional work for the staff became a common phenomenon. The existing situation can lead to patient harm or death and can attract medico-negligence suit against the hospital, threatening the overall existence of the hospital. The hospital administrator is currently viewing the problem from only the cost perspective, which is a high-risk and a short-term approach. Complexity academic level: Students pursuing full time/part time/diploma programme in health-care management, hospital administration/hospital operations;and undergraduate and post-graduate level students. © 2022, Emerald Publishing Limited.

Classification of audio signals using spectrogram surfaces and extrinsic distortion measures.

Representation of one-dimensional (1D) signals as surfaces and higher-dimensional manifolds reveals geometric structures that can enhance assessment of signal similarity and classification of large sets of signals. Motivated by this observation, we propose a novel robust algorithm for extraction of geometric features, by mapping the obtained geometric objects into a reference domain. This yields a set of highly descriptive features that are instrumental in feature engineering and in analysis of 1D signals. Two examples illustrate applications of our approach to well-structured audio signals: Lung sounds were chosen because of the interest in respiratory pathologies caused by the coronavirus and environmental conditions; accent detection was selected as a challenging speech analysis problem. Our approach outperformed baseline models under all measured metrics. It can be further extended by considering higher-dimensional distortion measures. We provide access to the code for those who are interested in other applications and different setups (Code: https://github.com/jeremy-levy/Classification-of-audio-signals-using-spectrogram-surfaces-and-extrinsic-distortion-measures). Supplementary Information: The online version contains supplementary material available at 10.1186/s13634-022-00933-9.

THE THRESHOLD VALUE OF THE NUMBER OF HOSPITAL BEDS IN A SEIHR EPIDEMIC MODEL

To investigate the impact of the number of hospital beds on the control of infectious diseases and help allocate the limited medical resources in a region, a SEIHR epidemic model including exposed and hospitalized classes is established. Different from available models, the hospitalization rate is expressed as a function of the number of empty beds. The existence and stability of the equilibria are analyzed, and it is proved that the system undergoes backward bifurcation, Hopf bifurcation, and Bogdanov-Takens bifurcation of codimension 2 under certain conditions by using the center manifold theory and normal form theory. In particular, our results show that there is a threshold value for the capacity of hospital beds in a region. If the capacity of hospital beds is lower than this threshold value, there will be a backward bifurcation, which means that even if the basic reproduction number, R0, is less than unity, it is not enough to prevent the outbreaks. Before taking disease control measures, one should compare the number of beds with the threshold value to avoid misjudgment and try to increase the capacity of hospital beds above this threshold value. The method to estimate the threshold value is also given. In addition, the impacts of the duration of the exposed period on the basic reproduction number and disease transmission are investigated.

Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity.

Cryo-electron microscopy (cryo-EM) has produced a number of structural models of the SARS-CoV-2 spike, already prompting biomedical outcomes. However, these reported models and their associated electrostatic potential maps represent an unknown admixture of conformations stemming from the underlying energy landscape of the spike protein. As with any protein, some of the spike's conformational motions are expected to be biophysically relevant, but cannot be interpreted only by static models. Using experimental cryo-EM images, we present the energy landscape of the glycosylated spike protein, and identify the diversity of low-energy conformations in the vicinity of its open (so called 1RBD-up) state. The resulting atomic refinement reveal global and local molecular rearrangements that cannot be inferred from an average 1RBD-up cryo-EM model. Here we report varied degrees of "openness" in global conformations of the 1RBD-up state, not revealed in the single-model interpretations of the density maps, together with conformations that overlap with the reported models. We discover how the glycan shield contributes to the stability of these low-energy conformations. Five out of six binding sites we analyzed, including those for engaging ACE2, therapeutic mini-proteins, linoleic acid, two different kinds of antibodies, switch conformations between their known apo- and holo-conformations, even when the global spike conformation is 1RBD-up. This apo-to-holo switching is reminiscent of a conformational preequilibrium. We found only one binding site, namely that of AB-C135 remains in apo state within all the sampled free energy-minimizing models, suggesting an induced fit mechanism for the docking of this antibody to the spike.

Expansion of plasmablasts and loss of memory B cells in peripheral blood from COVID-19 patients with pneumonia.

Studies on the interactions between SARS-CoV-2 and humoral immunity are fundamental to elaborate effective therapies including vaccines. We used polychromatic flow cytometry, coupled with unsupervised data analysis and principal component analysis (PCA), to interrogate B cells in untreated patients with COVID-19 pneumonia. COVID-19 patients displayed normal plasma levels of the main immunoglobulin classes, of antibodies against common antigens or against antigens present in common vaccines. However, we found a decreased number of total and naïve B cells, along with decreased percentages and numbers of memory switched and unswitched B cells. On the contrary, IgM+ and IgM- plasmablasts were significantly increased. In vitro cell activation revealed that B lymphocytes showed a normal proliferation index and number of dividing cells per cycle. PCA indicated that B-cell number, naive and memory B cells but not plasmablasts clustered with patients who were discharged, while plasma IgM level, C-reactive protein, D-dimer, and SOFA score with those who died. In patients with pneumonia, the derangement of the B-cell compartment could be one of the causes of the immunological failure to control SARS-Cov2, have a relevant influence on several pathways, organs and systems, and must be considered to develop vaccine strategies.