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DR-MIL: deep represented multiple instance learning distinguishes COVID-19 from community-acquired pneumonia in CT images.

Comput Methods Programs Biomed 2021 Sep 9;211:106406. Epub 2021 Sep 9.

Department of Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China. Electronic address:

Background And Objective: Given that the novel coronavirus disease 2019 (COVID-19) has become a pandemic, a method to accurately distinguish COVID-19 from community-acquired pneumonia (CAP) is urgently needed. However, the spatial uncertainty and morphological diversity of COVID-19 lesions in the lungs, and subtle differences with respect to CAP, make differential diagnosis non-trivial.

Methods: We propose a deep represented multiple instance learning (DR-MIL) method to fulfill this task. Read More

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September 2021

Sensitivity, specificity and limitation of in vitro hippocampal slice and neuron-based assays for assessment of drug-induced seizure liability.

Toxicol Appl Pharmacol 2021 Sep 15:115725. Epub 2021 Sep 15.

Department of Gene Tox and In Vitro Cellular Toxicology, Safety Assessment & Laboratory Animal Resources (SALAR), Merck & Co., Inc., West Point, PA 19486, USA.

An effective in vitro screening assay to detect seizure liability in preclinical development can contribute to better lead molecule optimization prior to candidate selection, providing higher throughput and overcoming potential brain exposure limitations in animal studies. This study explored effects of 26 positive and 14 negative reference pharmacological agents acting through different mechanisms, including 18 reference agents acting on glutamate signaling pathways, in a brain slice assay (BSA) of adult rat to define the assay's sensitivity, specificity, and limitations. Evoked population spikes (PS) were recorded from CA1 pyramidal neurons of hippocampus (HPC) in the BSA. Read More

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September 2021

Levator-Urethra Gap: Normative Data in a Nonpregnant Nulliparous Population.

Female Pelvic Med Reconstr Surg 2021 Sep 15. Epub 2021 Sep 15.

From the Division of Urogynecology Department of Obstetrics and Gynecology, OHSU, Portland, OR.

Objective: This study aimed to establish a normative range of the levator-urethra gap (LUG) measurement in nonpregnant, nulliparous women to be used as a standard against which assessments of injury or avulsion of the levator ani could be made.

Methods: Nulliparous women in the Pacific Northwest who were planning pregnancy within the ensuing 12 months underwent high-resolution magnetic resonance imaging (MRI) and 3-dimensional transperineal ultrasonography. In the plane of minimal hiatal dimensions, the LUG was measured on both the right and left sides for 3 contiguous image slices. Read More

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September 2021

ChipQA: No-Reference Video Quality Prediction via Space-Time Chips.

IEEE Trans Image Process 2021 Sep 17;PP. Epub 2021 Sep 17.

We propose a new model for no-reference video quality assessment (VQA). Our approach uses a new idea of highly-localized space-time (ST) slices called Space-Time Chips (ST Chips). ST Chips are localized cuts of video data along directions that implicitly capture motion. Read More

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September 2021

An HDAC8-selective fluorescent probe for imaging in living tumor cell lines and tissue slices.

Org Biomol Chem 2021 Sep 16. Epub 2021 Sep 16.

School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, PR China.

Histone deacetylase 8 (HDAC8) has been used as a therapeutic target for many cancers as it is highly expressed in neuroblastoma cells and breast cancer cells. HDAC8-selective fluorescent probes need to be urgently developed. Herein, two novel fluorescent probes, namely and , based on the conjugation of 1,8-naphthalimide with a highly selective inhibitor of HDAC8 () were reported. Read More

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September 2021

First Report of Xanthomonas campestris pv. campestris Causing Marginal Leaf Necrosis of Arugula (Eruca vesicaria subsp. sativa) in Serbia.

Plant Dis 2021 Sep 15. Epub 2021 Sep 15.

University of Belgrade, Faculty of Agriculture, Institute of Phytomedicine, Plant Pathology, Nemanjina 6, Belgrade, Serbia, 11080;

Arugula (Eruca vesicaria subsp. sativa (Miller) Thell., syn. Read More

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September 2021

Precision vibratome for high-speed ultrathin biotissue cutting and organ-wide imaging.

iScience 2021 Sep 25;24(9):103016. Epub 2021 Aug 25.

Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China.

Cutting tissues into ultrathin slices is highly desired in sectioning-based organ-wide imaging. However, it is difficult to perform tissue cutting at a high speed with excellent quality. Here, we design a precision vibratome based on a paired double parallelogram flexure, which enables a vibrating blade to move strictly along a straight line. Read More

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September 2021

3D Isotropic Super-resolution Prostate MRI Using Generative Adversarial Networks and Unpaired Multiplane Slices.

J Digit Imaging 2021 Sep 10. Epub 2021 Sep 10.

Department of Radiology, Columbia University Irving Medical Center, 622 W 168 11th St, New York, NY, USA.

We developed a deep learning-based super-resolution model for prostate MRI. 2D T2-weighted turbo spin echo (T2w-TSE) images are the core anatomical sequences in a multiparametric MRI (mpMRI) protocol. These images have coarse through-plane resolution, are non-isotropic, and have long acquisition times (approximately 10-15 min). Read More

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September 2021

An [18F]FDG-PET/CT deep learning method for fully automated detection of pathological mediastinal lymph nodes in lung cancer patients.

Eur J Nucl Med Mol Imaging 2021 Sep 14. Epub 2021 Sep 14.

Laboratoire D'Imagerie Translationnelle en Oncologie, U1288 Inserm, Institut Curie, PSL, Université Paris Saclay, Paris, France.

Purpose: The identification of pathological mediastinal lymph nodes is an important step in the staging of lung cancer, with the presence of metastases significantly affecting survival rates. Nodes are currently identified by a physician, but this process is time-consuming and prone to errors. In this paper, we investigate the use of artificial intelligence-based methods to increase the accuracy and consistency of this process. Read More

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September 2021

Hybrid reflection retrieval method for terahertz dielectric imaging of human bone.

Biomed Opt Express 2021 Aug 12;12(8):4807-4820. Epub 2021 Jul 12.

School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT, UK.

Terahertz imaging is becoming a biological imaging modality in its own right, alongside the more mature infrared and X-ray techniques. Nevertheless, extraction of hyperspectral, biometric information of samples is limited by experimental challenges. Terahertz time domain spectroscopy reflection measurements demand highly precise alignment and suffer from limitations of the sample thickness. Read More

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Super-resolution reconstruction of T2-weighted thick-slice neonatal brain MRI scans.

J Neuroimaging 2021 Sep 10. Epub 2021 Sep 10.

Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland.

Background And Purpose: Super-resolutionreconstruction (SRR) can be used to reconstruct 3-dimensional (3D) high-resolution (HR) volume from several 2-dimensional (2D) low-resolution (LR) stacks of MRI slices. The purpose is to compare lengthy 2D T2-weighted HR image acquisition of neonatal subjects with 3D SRR from several LR stacks in terms of image quality for clinical and morphometric assessments.

Methods: LR brain images were acquired from neonatal subjects to reconstruct isotropic 3D HR volumes by using SRR algorithm. Read More

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September 2021

Optogenetic Activation of Astrocytes-Effects on Neuronal Network Function.

Int J Mol Sci 2021 Sep 4;22(17). Epub 2021 Sep 4.

Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, Khlopina St. 11, 194021 St. Petersburg, Russia.

Optogenetics approach is used widely in neurobiology as it allows control of cellular activity with high spatial and temporal resolution. In most studies, optogenetics is used to control neuronal activity. In the present study optogenetics was used to stimulate astrocytes with the aim to modulate neuronal activity. Read More

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September 2021

Using Optical Coherence Tomography and Intravascular Ultrasound Imaging to Quantify Coronary Plaque Cap Stress/Strain and Progression: A Follow-Up Study Using 3D Thin-Layer Models.

Front Bioeng Biotechnol 2021 23;9:713525. Epub 2021 Aug 23.

School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.

Accurate plaque cap thickness quantification and cap stress/strain calculations are of fundamental importance for vulnerable plaque research. To overcome uncertainties due to intravascular ultrasound (IVUS) resolution limitation, IVUS and optical coherence tomography (OCT) coronary plaque image data were combined together to obtain accurate and reliable cap thickness data, stress/strain calculations, and reliable plaque progression predictions. IVUS, OCT, and angiography baseline and follow-up data were collected from nine patients (mean age: 69; m: 5) at Cardiovascular Research Foundation with informed consent obtained. Read More

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First Report of Bacterial Canker on Blueberry (Vaccinium corymbosum) Caused by Pseudomonas syringae pv. syringae in Serbia.

Plant Dis 2021 Sep 7. Epub 2021 Sep 7.

Institute for Plant Protection and Environment, Plant Pathology Dept., Teodora Drajzera 9, Belgrade, Serbia, 11040;

During May 2021, necrosis of young twigs and flower buds were observed on two-year-old highbush blueberry plants (Vaccinium corymbosum) cv. Draper, in a 1 hectare orchard in the municipality of Šabac, Serbia. Disease symptoms included reddish-brown to black irregularly shaped cankers developing on the shoot tips that extended downwards along the branches. Read More

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September 2021

Hybrid Variation-aware Network for Angle-closure Assessment in AS-OCT.

IEEE Trans Med Imaging 2021 Sep 6;PP. Epub 2021 Sep 6.

Automatic angle-closure assessment in Anterior Segment OCT (AS-OCT) images is an important task for the screening and diagnosis of glaucoma, and the most recent computer-aided models focus on a binary classification of anterior chamber angles (ACA) in AS-OCT, i.e., open-angle and angle-closure. Read More

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September 2021

Differential signaling induced by α7 nicotinic acetylcholine receptors in hippocampal dentate in vitro and in vivo.

J Physiol 2021 Sep 6. Epub 2021 Sep 6.

Neurobiology Laboratory, NIEHS / NIH, 111 T.W. Alexander Dr., Durham, NC, 27709, United States.

Key Points: α7 nicotinic receptors are widely distributed throughout the central nervous system and regulate a variety of brain functions including learning and memory. Understanding the cellular signaling mechanisms of their activations among different neuronal populations is important for delineating their actions in cognitive function, and developing effective treatment strategies for cognitive deficits. We report that α7 nAChR activation leads to Ca and cAMP increases in granule cells (but not in GABAergic interneurons) in hippocampal dentate in vitro, a key region for pattern separation during learning. Read More

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September 2021

Neuroanatomy of the grey seal brain: bringing pinnipeds into the neurobiological study of vocal learning.

Philos Trans R Soc Lond B Biol Sci 2021 Oct 6;376(1836):20200252. Epub 2021 Sep 6.

Comparative Bioacoustics Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.

Comparative animal studies of complex behavioural traits, and their neurobiological underpinnings, can increase our understanding of their evolution, including in humans. Vocal learning, a potential precursor to human speech, is one such trait. Mammalian vocal learning is under-studied: most research has either focused on vocal learning in songbirds or its absence in non-human primates. Read More

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October 2021

Recent advances in human respiratory epithelium models for drug discovery.

Biotechnol Adv 2021 Sep 2:107832. Epub 2021 Sep 2.

UCL Centre for Biomaterials in Surgical Reconstruction and Regeneration, Department of Surgical Biotechnology, Division of Surgery & Interventional Science, University College London, London NW3 2PF, UK. Electronic address:

The respiratory epithelium is intimately associated with the pathophysiologies of highly infectious viral contagions and chronic illnesses such as chronic obstructive pulmonary disorder, presently the third leading cause of death worldwide with a projected economic burden of £1.7 trillion by 2030. Preclinical studies of respiratory physiology have almost exclusively utilised non-humanised animal models, alongside reductionistic cell line-based models, and primary epithelial cell models cultured at an air-liquid interface (ALI). Read More

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September 2021

3D Muscle Loss (3DML) assessment: A novel CT-based quantitative method to evaluate rotator cuff muscle fatty infiltration.

J Shoulder Elbow Surg 2021 Aug 31. Epub 2021 Aug 31.

IMT Atlantique, LaTIM INSERM U1101, Brest, France.

Introduction: Rotator cuff fatty infiltration (FI) is one of the most important parameters to predict the outcome of certain shoulder conditions. The primary objective of this study was to define a new computed tomography (CT)-based quantitative 3-dimensional (3D) measure of muscle loss (3DML) based on the rationale of the 2-dimensional (2D) qualitative Goutallier score. The secondary objective of this study was to compare this new measurement method to traditional 2D qualitative assessment of FI according to Goutallier et al and to a 3D quantitative measurement of fatty infiltration (3DFI). Read More

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In Vitro Spatio-Temporal NMR Metabolomics of Living 3D Cell Models.

Anal Chem 2021 Sep 3. Epub 2021 Sep 3.

Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany.

Three-dimensional cell cultures are of growing importance in biochemical research as they represent tissue features more accurately than standard two-dimensional systems, but to investigate these challenging new models an adaptation of established analytical techniques is required. Spatially resolved data for living organoids are needed to gain insight into transport processes and biochemical characteristics of domains with different nutrient supply and waste product removal. Within this work, we present an NMR-based approach to obtain dynamically radial metabolite profiles for cell spheroids, one of the most frequently used 3D models. Read More

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September 2021

Detecting hip osteoarthritis on clinical CT: a deep learning application based on 2-D summation images derived from CT.

Osteoporos Int 2021 Sep 2. Epub 2021 Sep 2.

Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.

We developed and compared deep learning models to detect hip osteoarthritis on clinical CT. The CT-based summation images, CT-AP, that resemble X-ray radiographs can detect radiographic hip osteoarthritis and in the absence of large training data, a reliable deep learning model can be optimized by combining CT-AP and X-ray images.

Introduction: In this study, we aimed to investigate the applicability of deep learning (DL) to assess radiographic hip osteoarthritis (rHOA) on computed tomography (CT). Read More

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September 2021

Improving Algorithm for the Alignment of Consecutive, Whole-Slide, Immunohistochemical Section Images.

J Pathol Inform 2021 3;12:29. Epub 2021 Aug 3.

Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan.

Background: Accurate and precise alignment of histopathology tissue sections is a key step for the interpretation of the proteome topology and cell level three-dimensional (3D) reconstruction of diseased tissues. However, the realization of an automated and robust method for aligning nonglobally stained immunohistochemical (IHC) sections is still challenging. In this study, we aim to assess the feasibility of multidimensional graph-based image registration on aligning serial-section and whole-slide IHC section images. Read More

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Priority of PET-CT vs CT Thorax for EBUS-TBNA 22G vs 19G: Mesothorax Lymphadenopathy.

J Cancer 2021 5;12(19):5874-5878. Epub 2021 Aug 5.

Ear, Nose and Throat (ENT) Department, Ludwig-Maximilians University of Munich, Munich, Germany.

Lung lesions and undiagnosed mesothorax lymphadenopathy is an issue that several doctors face in the everyday clinical practice. PET-CT and CT of the thorax are usually the first examinations to identify characteristics of the lesions before biopsy. We performed a retrospective study with 450 patients that had EBUS-TBNA with 22G, Upgraded 22G and 19G needles with and without PET-CT in order to identify the cost effeteness of performing EBUS-TBNA before or after PET-CT. Read More

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Effect of nonthermal atmospheric plasma on the push-out bond strength of epoxy resin-based and bioceramic root canal sealers: An study.

J Conserv Dent 2021 Jan-Feb;24(1):41-45. Epub 2021 Jul 5.

Department of Chemistry, Indian Institute of Space Science and Technology, Thiruvananthapuram, Kerala, India.

Aim: The aim of this study was to evaluate the effect of nonthermal atmospheric plasma (NTAP) on the bond strength of epoxy resin-based and bioceramic root canal sealers.

Materials And Methods: Freshly extracted forty ( = 40) single-rooted mandibular premolar teeth were divided into four groups ( = 10) based on the sealer used and NTAP application - Group 1: Epoxy resin-based sealer (AH Plus) without NTAP application, Group 2: Epoxy resin-based sealer (AH Plus) with NTAP application for 30 s, Group 3: Bioceramic sealer (BioRoot RCS) without NTAP application, and Group 4: Bioceramic sealer (BioRoot RCS) with NTAP application for 30 s. After NTAP application in Groups 2 and 4, all the samples were obturated using sealers according to their grouping protocols. Read More

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[Discussion on rationality of Yinpian commodity grades--Sophora flavescentis as an example].

Zhongguo Zhong Yao Za Zhi 2021 Aug;46(16):4040-4050

Capital Medical University Beijing 100069, China.

In recent years, the establishment of the commercial grade of Yinpian [traditional Chinese medicine(TCM) pieces for decoction] in the TCM industry has been hotly disputed. In this article, Sophorae Flavescentis Radix(SFR) was selected as a representative example to investigated. Through systematic comparison and analysis, the different grades of SFR slices were traced, verified and evaluated. Read More

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[Application of QAMS for quality evaluation and control of Chinese patent medicines:taking Bufonis Venenum-contained preparations as examples].

Zhongguo Zhong Yao Za Zhi 2021 Jun;46(12):2931-2941

National Engineering Laboratory of Quality Control Technology of Chinese Materia Medica, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China.

As a new strategy capable of uncovering the characteristics of traditional Chinese medicines, the quantitative analysis of multi-components by single-marker(QAMS) has been widely employed for the quality evaluation of Chinese medicinal materials, slices, and extracts. However, its application in the assessment of Chinese patent medicines is yet to be explored. By referring to the determination of three bufogenins in Bufonis Venenum by QAMS described in Chinese Pharmacopoeia(2020 Edition), this paper selected seven representative preparations containing Bufonis Venenum and explored whether the relative correction factors(RCFs) of cinobufagin(CB) to bufalin(BF) and resibufogenin(RB) could be directly used for the quality control of Bufonis Venenum-contained preparations. Read More

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Comparison of Thermal Neutron and Hard X-ray Dark-Field Tomography.

J Imaging 2020 Dec 23;7(1). Epub 2020 Dec 23.

Chair of Biomedical Physics, Department of Physics and Munich School of Bioengineering, Technical University of Munich, 85748 Garching, Germany.

High visibility (0.56) neutron-based multi-modal imaging with a Talbot-Lau interferometer at a wavelength of 1.6 Å is reported. Read More

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December 2020

Fully 3D Active Surface with Machine Learning for PET Image Segmentation.

Albert Comelli

J Imaging 2020 Oct 23;6(11). Epub 2020 Oct 23.

Ri.MED Foundation, 90133 Palermo, Italy.

In order to tackle three-dimensional tumor volume reconstruction from Positron Emission Tomography (PET) images, most of the existing algorithms rely on the segmentation of independent PET slices. To exploit cross-slice information, typically overlooked in these 2D implementations, I present an algorithm capable of achieving the volume reconstruction directly in 3D, by leveraging an active surface algorithm. The evolution of such surface performs the segmentation of the whole stack of slices simultaneously and can handle changes in topology. Read More

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October 2020

Two-Stage Alignment of FIB-SEM Images of Rock Samples.

J Imaging 2020 Oct 10;6(10). Epub 2020 Oct 10.

Schlumberger Moscow Research Center, 125171 Moscow, Russia.

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a comparison of two adjacent slices. Read More

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October 2020

A Plate-Based Assay for the Measurement of Endogenous Monoamine Release in Acute Brain Slices.

J Vis Exp 2021 Aug 11(174). Epub 2021 Aug 11.

Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine at City College;

Monoamine neurotransmitters are associated with numerous neurologic and psychiatric ailments. Animal models of such conditions have shown alterations in monoamine neurotransmitter release and uptake dynamics. Technically complex methods such as electrophysiology, Fast Scan Cyclic Voltammetry (FSCV), imaging, in vivo microdialysis, optogenetics, or use of radioactivity are required to study monoamine function. Read More

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