Deep learning aided determination of the optimal number of detectors for photoacoustic tomography.

Photoacoustic tomography (PAT) is a non-destructive, non-ionizing, and rapidly expanding hybrid biomedical imaging technique, yet it faces challenges in obtaining clear images due to limited data from detectors or angles. As a result, the methodology suffers from significant streak artifacts and low-quality images. The integration of deep learning (DL), specifically convolutional neural networks (CNNs), has recently demonstrated powerful performance in various fields of PAT.

Self-Trained Convolutional Neural Network (CNN) for Tuberculosis Diagnosis in Medical Imaging.

Background Tuberculosis (TB) is a serious infectious disease that primarily affects the lungs. Despite advancements in the medical industry, TB remains a significant global health challenge. Early and accurate detection of TB is crucial for effective treatment and reducing transmission.

A novel hybridization capture method for direct whole genome sequencing of clinical specimens to inform Legionnaires' disease investigations.

The unprecedented precision and resolution of whole genome sequencing (WGS) can provide definitive identification of infectious agents for epidemiological outbreak tracking. WGS approaches, however, are frequently impeded by low pathogen DNA recovery from available primary specimens or unculturable samples. A cost-effective hybrid capture assay for WGS analysis directly on primary specimens was developed.

Posterior Gastric Perforation with an Opening in Transverse Mesocolon: A Rare Case Report.

Posterior gastric perforation is a very rare finding, difficult to diagnose due to the insidious onset of upper abdominal symptoms, and no air under the diaphragm on X-ray. Posterior gastric perforation which opens into transverse mesocolon is even rarer. This is a case report done to entail such a rare case, with only two cases reported in the past.

Deep learning on photoacoustic tomography to remove image distortion due to inaccurate measurement of the scanning radius.

Photoacoustic tomography (PAT) is a non-invasive, non-ionizing hybrid imaging modality that holds great potential for various biomedical applications and the incorporation with deep learning (DL) methods has experienced notable advancements in recent times. In a typical 2D PAT setup, a single-element ultrasound detector (USD) is used to collect the PA signals by making a 360° full scan of the imaging region. The traditional backprojection (BP) algorithm has been widely used to reconstruct the PAT images from the acquired signals.

Whole genome sequencing of human Borrelia burgdorferi isolates reveals linked blocks of accessory genome elements located on plasmids and associated with human dissemination.

Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting Borrelia burgdorferi spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of 299 B.

Genomic Analysis of Vancomycin-Resistant Staphylococcus aureus Isolates from the 3rd Case Identified in the United States Reveals Chromosomal Integration of the Locus.

Vancomycin-resistant Staphylococcus aureus (VRSA) is a human pathogen of significant public health concern. Although the genome sequences of individual VRSA isolates have been published over the years, very little is known about the genetic changes of VRSA within a patient over time. A total of 11 VRSA, 3 vancomycin-resistant enterococci (VRE), and 4 methicillin-resistant S.

Whole genome sequencing of isolates reveals linked clusters of plasmid-borne accessory genome elements associated with virulence.

Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of 299 patient-derived sensu stricto ( ) isolates from patients in the Eastern and Midwestern US and Central Europe.

Improved Residual Network based on norm-preservation for visual recognition.

Residual Network (ResNet) achieves deeper and wider networks with high-performance gains, representing a powerful convolutional neural network architecture. In this paper, we propose architectural refinements to ResNet that address the information flow through several layers of the network, including the input stem, downsampling block, projection shortcut, and identity blocks. We will show that our collective refinements facilitate stable backpropagation by preserving the norm of the error gradient within the residual blocks, which can reduce the optimization difficulties of training very deep networks.

Comparative analysis of multiplexed PCR and short- and long-read whole genome sequencing to investigate a large Klebsiella pneumoniae outbreak in New York State.

In 2017, the New York State Department of Health investigated a large Klebsiella pneumoniae outbreak in a health care facility. A retrospective analysis was conducted to compare the use of multiple molecular typing methods for characterizing the outbreak. Forty-four isolates were characterized using the rapid real-time PCR OpGen Acuitas® AMR Gene Panel.

Depletion of the Microbiota Has a Modest but Important Impact on the Fungal Burden of the Heart and Lungs during Early Systemic Infection in Neutropenic Mice.

The progression and systemic pathobiology of in the absence of a microbiota have not been described. Here, we describe the influence of the microbiota during the first 5 days of infection in germ-free or antibiotic-depleted mice. Depletion of the bacterial microbiota in both germ-free and antibiotic-depleted models results in a modest but important increase in the early stages of infection.

ATD: Augmenting CP Tensor Decomposition by Self Supervision.

Tensor decompositions are powerful tools for dimensionality reduction and feature interpretation of multidimensional data such as signals. Existing tensor decomposition objectives (e.g.

The role of chemical shift magnetic resonance imaging in differentiating osteoporotic benign and malignant vertebral marrow lesions.

Purpose: To evaluate the usefulness of chemical shift imaging (CSI) in differentiating benign osteoporotic and malignant vertebral marrow lesions.

Material And Methods: Patients undergoing spinal magnetic resonance imaging (MRI) for back pain, which showed altered marrow signal intensity on conventional MRI sequences, were included in the study. Patients with acute traumatic vertebral fractures, infective spondylodiscitis, paravertebral collections, etc.

Whole-Genome Sequencing of SARS-CoV-2: Assessment of the Ion Torrent AmpliSeq Panel and Comparison with the Illumina MiSeq ARTIC Protocol.

Fast and effective methods are needed for sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to track genetic mutations and to identify new and emerging variants during the ongoing pandemic. The objectives were to assess the performance of the SARS-CoV-2 AmpliSeq research panel and S5 plug-in analysis tools for whole-genome sequencing analysis of SARS-CoV-2 and to compare the results with those obtained with the MiSeq-based ARTIC analysis pipeline, using metrics such as depth, coverage, and concordance of single-nucleotide variant (SNV) calls. A total of 191 clinical specimens and a single cultured isolate were extracted and sequenced with AmpliSeq technology and analysis tools.

Regulatory roles of 5' UTR and ORF-internal RNAs detected by 3' end mapping.

Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium . Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination.

RecipeDB: a resource for exploring recipes.

Cooking is the act of turning nature into the culture, which has enabled the advent of the omnivorous human diet. The cultural wisdom of processing raw ingredients into delicious dishes is embodied in their cuisines. Recipes thus are the cultural capsules that encode elaborate cooking protocols for evoking sensory satiation as well as providing nourishment.

Nanopore MinION Sequencing Reveals Possible Transfer of Plasmid Across Bacterial Species in Two Healthcare Facilities.

Carbapenemase-producing are a major threat to global public health. carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities.

Origin of 3 Rabid Terrestrial Animals in Raccoon Rabies Virus-Free Zone, Long Island, New York, USA, 2016-2017.

During 2016-2017, three rabid terrestrial animals were discovered in the raccoon rabies virus-free zone of Long Island, New York, USA. Whole-genome sequencing and phylogenetic analyses revealed the likely origins of the viruses, enabling the rabies outbreak response (often costly and time-consuming) to be done less expensively and more efficiently.

May-Thurner syndrome: an uncommon and incidental finding in a postpartum female.

May-Thurner syndrome or Cockett syndrome is a pathological condition that arises due to extrinsic compression on iliocaval venous territory, leading to venous outflow obstruction. Here, author presents an incidental finding of left common iliac vein extrinsic compression by right common iliac artery with collateral vessels in the pelvis in a postpartum female.

Impact of Candida auris Infection in a Neutropenic Murine Model.

has become a global public health threat due to its multidrug resistance and persistence. Currently, there are limited murine models to study infection. Those models use a combination of cyclophosphamide and cortisone acetate, suppressing both innate and adaptive immunity.

Effects of Thermal Annealing Duration on the Film Morphology of Methylamine Lead Triiodide (MAPbI₃) Perovskite Thin Films in Ambient Air.

In the present communication we have studied the effect of thermal annealing duration on morphology of methylamine lead triiodide (MAPbI₃) perovskite (prepared using single step method) semiconductor that changes into lead iodide (PbI₂). Furthermore, the effect of annealing duration on thin films is investigated and correlated with its potential photovoltaic application. Thin films characteristics study by X-ray diffraction and scanning electron microscopy results indicate MAPbI₃ degraded strongly by annealing duration.

Laparoscopic Versus Open Sigmoid Loop Colostomy: A Comparative Study from a Cohort of 62 Patients Requiring Temporary Faecal Diversion at a Tertiary Care Center in North India.

Background: Over decades, colostomies have been done through open method, but laparoscopic creation of an intestinal stoma is safe, feasible and has distinct advantages over conventional techniques in specific procedures. The aim of this study compares operative and short-term outcomes of laparoscopic and open sigmoid loop colostomy formation for temporary fecal diversion.

Subjects And Methods: A single institution, comparative study conducted in the department of surgery for patients who underwent either laparoscopic or open sigmoid loop colostomy.