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Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy.

ACS Nano 2021 Apr 9. Epub 2021 Apr 9.

Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany.

Graphene exhibits outstanding fluorescence quenching properties that can become useful for biophysics and biosensing applications, but it remains challenging to harness these advantages due to the complex transfer procedure of chemical vapor deposition-grown graphene to glass coverslips and the low yield of usable samples. Here, we screen 10 graphene-on-glass preparation methods and present an optimized protocol. To obtain the required quality for single-molecule and super-resolution imaging on graphene, we introduce a graphene screening method that avoids consuming the investigated sample. Read More

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An experimental system to evaluate impact shear failure of rock discontinuities.

Rev Sci Instrum 2021 Mar;92(3):034501

School of Geosciences, University of Edinburgh, Edinburgh EH9 3FE, United Kingdom.

Conventionally, the evaluation of shear failure of discontinuities in rocks and other geomaterials has been conducted under static shear loading. In such methods, the shear failure behaviors of rock discontinuities are significantly influenced by loading velocities. To evaluate the shear failure process under dynamic loading, in this paper, we propose a new experimental methodology by taking advantages of recently available high-speed optical and mechanical measurement techniques. Read More

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Application of Seq2Seq Models on Code Correction.

Front Artif Intell 2021 19;4:590215. Epub 2021 Mar 19.

Department of Computer Science, Boston University, Boston, MA, United States.

We apply various seq2seq models on programming language correction tasks on Juliet Test Suite for C/C++ and Java of Software Assurance Reference Datasets and achieve 75% (for C/C++) and 56% (for Java) repair rates on these tasks. We introduce pyramid encoder in these seq2seq models, which significantly increases the computational efficiency and memory efficiency, while achieving similar repair rate to their nonpyramid counterparts. We successfully carry out error type classification task on ITC benchmark examples (with only 685 code instances) using transfer learning with models pretrained on Juliet Test Suite, pointing out a novel way of processing small programming language datasets. Read More

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Addressing the Frenkel and charge transfer character of exciton states with a model Hamiltonian based on dimer calculations: Application to large aggregates of perylene bisimide.

J Chem Phys 2021 Mar;154(12):124101

Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy.

To understand the influence of interchromophoric arrangements on photo-induced processes and optical properties of aggregates, it is fundamental to assess the contribution of local excitations [charge transfer (CT) and Frenkel (FE)] to exciton states. Here, we apply a general procedure to analyze the adiabatic exciton states derived from time-dependent density functional theory calculations, in terms of diabatic states chosen to coincide with local excitations within a restricted orbital space. In parallel, motivated by the need of cost-effective approaches to afford the study of larger aggregates, we propose to build a model Hamiltonian based on calculations carried out on dimers composing the aggregate. Read More

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A Transfer Learning Approach on the Optimization of Edge Detectors for Medical Images Using Particle Swarm Optimization.

Entropy (Basel) 2021 Mar 31;23(4). Epub 2021 Mar 31.

IMOGEN Research Institute, County Clinical Emergency Hospital, 400006 Cluj-Napoca, Romania.

Edge detection is a fundamental image analysis task, as it provides insight on the content of an image. There are weaknesses in some of the edge detectors developed until now, such as disconnected edges, the impossibility to detect branching edges, or the need for a ground truth that is not always accessible. Therefore, a specialized detector that is optimized for the image particularities can help improve edge detection performance. Read More

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Realizing Innate Potential: CAR-NK Cell Therapies for Acute Myeloid Leukemia.

Cancers (Basel) 2021 Mar 29;13(7). Epub 2021 Mar 29.

Apoptosis Research Center, National University of Ireland Galway, H91 TK33 Galway, Ireland.

Next-generation cellular immunotherapies seek to improve the safety and efficacy of approved CD19 chimeric antigen receptor (CAR) T-cell products or apply their principles across a growing list of targets and diseases. Supported by promising early clinical experiences, CAR modified natural killer (CAR-NK) cell therapies represent a complementary and potentially off-the-shelf, allogeneic solution. While acute myeloid leukemia (AML) represents an intuitive disease in which to investigate CAR based immunotherapies, key biological differences to B-cell malignancies have complicated progress to date. Read More

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Measuring Online Teaching Service Quality in Higher Education in the COVID-19 Environment.

Int J Environ Res Public Health 2021 03 1;18(5). Epub 2021 Mar 1.

Department of Applied Economics II, Faculty of Economics and Business, University of Seville, Avenida Ramón y Cajal, 1, 41018 Seville, Spain.

The use of the Internet to develop new technologies has generated a considerable change in teaching and student learning in higher education. The pandemic caused by COVID-19 has forced universities to switch from face-to-face to online instruction. Furthermore, this transfer process was planned and executed quickly, with urgent redesigns of courses originally conceived for live teaching. Read More

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Deep Learning Driven Noise Reduction for Reduced Flux Computed Tomography.

Sensors (Basel) 2021 Mar 9;21(5). Epub 2021 Mar 9.

College of Petroleum Engineering and Geosciences (CPG), King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.

Deep neural networks have received considerable attention in clinical imaging, particularly with respect to the reduction of radiation risk. Lowering the radiation dose by reducing the photon flux inevitably results in the degradation of the scanned image quality. Thus, researchers have sought to exploit deep convolutional neural networks (DCNNs) to map low-quality, low-dose images to higher-dose, higher-quality images, thereby minimizing the associated radiation hazard. Read More

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Bulb Cannula Safety for Breast Fat Grafting.

Aesthet Surg J Open Forum 2020 Jun 13;2(2):ojaa014. Epub 2020 Apr 13.

Medical Affairs Coordinator at Establishment Labs, Alajuela, Costa Rica.

Autologous fat transfer is a common technique to refine the contour of the breast after prosthetic augmentation or reconstruction, correcting remaining asymmetries by injecting previously harvested fat tissue with a cannula. Current procedures are often performed without visualization of the cannula at the delivery site and may require subsequent verification of the implant's integrity. The present paper aims to evaluate the safety of a new bulb tip cannula to be used during breast implant procedures for injecting fat adjacent to a breast implant that reduce the risk of damaging the implant. Read More

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Simultaneous readout of multiple FRET pairs using photochromism.

Nat Commun 2021 03 31;12(1):2005. Epub 2021 Mar 31.

Department of Chemistry, KU Leuven, Leuven, Belgium.

Förster resonant energy transfer (FRET) is a powerful mechanism to probe associations in situ. Simultaneously performing more than one FRET measurement can be challenging due to the spectral bandwidth required for the donor and acceptor fluorophores. We present an approach to distinguish overlapping FRET pairs based on the photochromism of the donor fluorophores, even if the involved fluorophores display essentially identical absorption and emission spectra. Read More

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Applying the 3Rs to non-human primate research: Barriers and solutions.

Drug Discov Today Dis Models 2017 21;23:51-56. Epub 2017 Nov 21.

NC3Rs Board, Gibbs Building, 2I5 Euston Road, London NWI 2BE, UK.

Progress is being made in the development and application of methods to replace, reduce and refine the use of non-human primates (NHPs) in biomedical research and testing of products and devices. However, there remain considerable cultural and practical barriers to widespread uptake of available 3Rs techniques and to further advancement of the 3Rs in NHP research, over and above scientific obstacles. While most of these barriers apply also to the use of other vertebrate species, there is arguably a greater imperative to overcome them in the case of the NHPs, given their high sentience and the degree of societal concern about their use. Read More

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November 2017

Multidimensional Face Representation in a Deep Convolutional Neural Network Reveals the Mechanism Underlying AI Racism.

Front Comput Neurosci 2021 10;15:620281. Epub 2021 Mar 10.

Department of Psychology & Tsinghua Laboratory of Brain and Intelligence, Tsinghua University, Beijing, China.

The increasingly popular application of AI runs the risk of amplifying social bias, such as classifying non-white faces as animals. Recent research has largely attributed this bias to the training data implemented. However, the underlying mechanism is poorly understood; therefore, strategies to rectify the bias are unresolved. Read More

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Measuring the impact of productive failure on nursing students' learning in healthcare simulation: A quasi-experimental study.

Nurse Educ Today 2021 Mar 17;101:104871. Epub 2021 Mar 17.

Faculty of Information Technologies, Monash University, Victoria, Australia.

Background: Previous research suggests that making errors in a non-threatening simulated environment can facilitate learning. Productive failure, which combines problem-solving tasks followed by instruction, enables students to learn from making mistakes. This teaching approach has demonstrated improved learning outcomes such as explanatory knowledge and transfer of knowledge compared to a direct instruction approach where students receive instruction prior to problem-solving tasks. Read More

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Peptide substrate screening for the diagnosis of SARS-CoV-2 using fluorescence resonance energy transfer (FRET) assay.

Mikrochim Acta 2021 03 25;188(4):137. Epub 2021 Mar 25.

Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia.

The novel corona (SARS-CoV-2) virus causes a global pandemic, which motivates researchers to develop reliable and effective methods for screening and detection of SARS-CoV-2. Though there are several methods available for the diagnosis of SARS-CoV-2 such as RT-PCR and ELSIA, nevertheless, these methods are time-consuming and may not apply at the point of care. In this study, we have developed a specific, sensitive, quantitative and fast detection method for SARS-CoV-2 by fluorescence resonance energy transfer (FRET) assay. Read More

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Modeling Radiation-Induced Neoplastic Cell Transformation In Vitro and Tumor Induction In Vivo with the Local Effect Model.

Radiat Res 2021 Mar 24. Epub 2021 Mar 24.

GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany.

Ionizing radiation induces DNA damage to cycling cells which, if left unrepaired or misrepaired, can cause cell inactivation or heritable, viable mutations. The latter can lead to cell transformation, which is thought to be an initial step of cancer formation. Consequently, the study of radiation-induced cell transformation promises to offer insights into the general properties of radiation carcinogenesis. Read More

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Dynamics of the price-volume information flow based on surrogate time series.

Chun-Xiao Nie

Chaos 2021 Jan;31(1):013106

School of Statistics and Mathematics, Zhejiang Gongshang University, Hangzhou 310018, China.

This paper uses transfer entropy and surrogates to analyze the information flow between price and transaction volume. We use random surrogates to construct local random permutation (LRP) surrogates that can analyze the local information flow in detail. The analysis based on the toy models verifies the effectiveness of the LRP method. Read More

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January 2021

Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals.

Sci Rep 2021 Mar 22;11(1):6491. Epub 2021 Mar 22.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.

Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. Read More

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Clinical application of sequencing-based methods for parallel preimplantation genetic testing for mitochondrial DNA disease and aneuploidy.

Fertil Steril 2021 Mar 18. Epub 2021 Mar 18.

Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom; Juno Genetics, Oxford, United Kingdom.

Objective: To validate and apply a strategy permitting parallel preimplantation genetic testing (PGT) for mitochondrial DNA (mtDNA) disease and aneuploidy (PGT-A).

Design: Preclinical test validation and case reports.

Setting: Fertility centers. Read More

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Cell-permeable transgelin-2 as a potent therapeutic for dendritic cell-based cancer immunotherapy.

J Hematol Oncol 2021 Mar 17;14(1):43. Epub 2021 Mar 17.

School of Life Sciences, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Gwangju, 61005, Korea.

Background: Transgelin-2 is a 22 kDa actin-binding protein that has been proposed to act as an oncogenic factor, capable of contributing to tumorigenesis in a wide range of human malignancies. However, little is known whether this tiny protein also plays an important role in immunity, thereby keeping body from the cancer development and metastasis. Here, we investigated the functions of transgelin-2 in dendritic cell (DC) immunity. Read More

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Light-triggered elimination of CO and absorption of O (artificial breathing reaction) in photolysis of 2-(4-nitrophenyl)-1H-indole derivatives.

Photochem Photobiol Sci 2021 Mar 26;20(3):421-434. Epub 2021 Feb 26.

Department of Chemistry, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, 739-8526, Japan.

A new chromophore, 2-(4-nitrophenyl)-1H-indole (NPI), was synthesized as a potential photolabile protecting group. Caged benzoic acids featuring the NPI chromophore were synthesized as model compounds. Benzoic acid was released in moderate yields (~ 40-60%) upon photolysis of the caged benzoic acids without any additional chemical reagents. Read More

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Why is Anatomy Difficult to Learn? The Implications for Undergraduate Medical Curricula.

Anat Sci Educ 2021 Mar 15. Epub 2021 Mar 15.

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong.

The impact of the medical curricular reform on anatomy education has been inconclusive. A pervasive perception is that graduates do not possess a sufficient level of anatomical knowledge for safe medical practice; however, the reason is less well-studied. This qualitative study investigated the perceived challenges in learning anatomy, possible explanations, and ways to overcome these challenges. Read More

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Therapeutic applications of the cancer immunoediting hypothesis.

Semin Cancer Biol 2021 Mar 9. Epub 2021 Mar 9.

Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA. Electronic address:

Since the late 19th century, the immune system has increasingly garnered interest as a novel avenue for cancer therapy, particularly given scientific breakthroughs in recent decades delineating the fundamental role of the immune system in tumorigenesis. The immunoediting hypothesis has articulated this role, describing three phases of the tumor-immune system interaction: Elimination, Equilibrium, and Escape wherein tumors progress from active immunologic surveillance and destruction through dynamic immunologic stasis to unfettered growth. The primary goals of immunotherapy are to restrict and revert progression through these phases, thereby improving the immune system's ability to control tumor growth. Read More

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In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy.

Sci Rep 2021 Mar 11;11(1):5756. Epub 2021 Mar 11.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic information rely on selection of suitable residue pairs for chemical modification. Selection of pairs of amino acids, that show sufficient distance changes upon activity of the protein, can be a tedious process. Read More

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Biodynamic digital holographic speckle microscopy for oocyte and embryo metabolic evaluation.

Appl Opt 2021 Feb;60(4):A222-A233

Assisted reproductive technologies seek to improve the success rate of pregnancies. Morphology scoring is a common approach to evaluate oocyte and embryo viability prior to embryo transfer in utero, but the efficacy of the method is low. We apply biodynamic imaging, based on dynamic light scattering and low-coherence digital holography, to assess the metabolic activity of oocytes and embryos. Read More

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February 2021

Digital holographic imaging and classification of microplastics using deep transfer learning.

Appl Opt 2021 Feb;60(4):A38-A47

We devise an inline digital holographic imaging system equipped with a lightweight deep learning network, termed CompNet, and develop the transfer learning for classification and analysis. It has a compression block consisting of a concatenated rectified linear unit (CReLU) activation to reduce the channels, and a class-balanced cross-entropy loss for training. The method is particularly suitable for small and imbalanced datasets, and we apply it to the detection and classification of microplastics. Read More

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February 2021

Single-molecule FRET imaging of GPCR dimers in living cells.

Nat Methods 2021 Apr 8;18(4):397-405. Epub 2021 Mar 8.

Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.

Class C G protein-coupled receptors (GPCRs) are known to form stable homodimers or heterodimers critical for function, but the oligomeric status of class A and B receptors, which constitute >90% of all GPCRs, remains hotly debated. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful approach with the potential to reveal valuable insights into GPCR organization but has rarely been used in living cells to study protein systems. Here, we report generally applicable methods for using smFRET to detect and track transmembrane proteins diffusing within the plasma membrane of mammalian cells. Read More

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Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging.

NPJ Digit Med 2021 Mar 8;4(1):44. Epub 2021 Mar 8.

Department of Computer Science, University of California, Los Angeles, CA, USA.

One of the core challenges in applying machine learning and artificial intelligence to medicine is the limited availability of annotated medical data. Unlike in other applications of machine learning, where an abundance of labeled data is available, the labeling and annotation of medical data and images require a major effort of manual work by expert clinicians who do not have the time to annotate manually. In this work, we propose a new deep learning technique (SLIVER-net), to predict clinical features from 3-dimensional volumes using a limited number of manually annotated examples. Read More

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Photochromic holo-cellulose wood-based aerogel grafted azobenzene derivative by SI-ATRP.

Ming Li Shiyu Fu

Carbohydr Polym 2021 May 3;259:117736. Epub 2021 Feb 3.

State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, PR China. Electronic address:

Wood is actually a natural polymers composite that is easy to process, mainly constituted of cellulose, hemicellulose and lignin. However, most wood-based functional materials are prepared by physical methods, which undoubtedly limit the application of wood-based materials. Herein, the wood aerogel (WA) was obtained from wood by delignification and freezing dried. Read More

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Green Picosecond Laser Machining of Thermoset and Thermoplastic Carbon Fiber Reinforced Polymers.

Micromachines (Basel) 2021 Feb 17;12(2). Epub 2021 Feb 17.

Laser Industrial Technology Research Group, Korea Institute of Machinery and Materials (KIMM), 48, Mieumsandan 5-ro 41beon-gil, Busan 46744, Korea.

There has been an increase in demand for the development of lightweight and high-strength materials for applications in the transportation industry. Carbon fiber reinforced polymer (CFRP) is known as one of the most promising materials owing to its high strength-to-weight ratio. To apply CFRP in the automotive industry, various machining technologies have been reported because it is difficult to machine. Read More

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February 2021

Numerical Analysis of a Continuous Vulcanization Line to Enhance CH Reduction in XLPE-Insulated Cables.

Materials (Basel) 2021 Feb 21;14(4). Epub 2021 Feb 21.

Computational Transport Phenomena Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.

Herein, we apply a computational diffusion model based on Fick's law to study the manner in which a cable production line and its operating conditions can be enhanced to effectively reduce the CH4 concentration in cables insulated with cross-linked polyethylene (XLPE). Thus, we quantitatively analyze the effect of the conductor temperature, curing tube temperature distribution, transition zone length, and online relaxation on CH4 generation and transport during the production of 132 kV cables with an insulation thickness of 16.3 mm. Read More

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February 2021