gebhart/patrepeval huggingface dataset:
A localization method of lesions induced by High Intensity Focused Ultrasound based on acoustic backscatter change (2008)

High Intensity Focused Ultrasound (HIFU) has been investigated as a therapeutic modality for many medical applications. We investigated a noninvasive technique for the localization of HIFU-induced lesions based on the change in backscattered radio frequency (RF) signals. HIFU was applied to chicken breast tissue and we compared lesion locations obtained from RF data with our processing method, from the dissected tissues after exposure, and from B-mode images if exposures had resulted in hyperecho. RF amplitude of the focal spot was found to decrease, even without hyperecho in B-mode images. No significant difference was found on localization accuracy between the RF-based and the hyperecho-based method (p=0.76). In cases without hyperecho, the distance between RF-based locations and measured physical lesion locations was 3.37 +/- 1.59 mm. The axial and lateral difference was 2.00 +/- 2.31 mm and 0.85 +/- 2.15 mm, respectively, and no statistically significant difference was found between lesion coordinates in the axial (p=0.37) and lateral (p=0.15) directions. Based on the ex vivo tissue experiments, we have demonstrated the feasibility of the proposed RF-based method for the localization of the center of HIFU-induced lesions.
Fullerene‐Terminated Dendritic Multiporphyrin Arrays: “Dendrimer Effects” on Photoinduced Charge Separation (2003)

Energy funnels: A large dendritic zinc porphyrin heptamer (7PZn) in a C60-terminated electron-transfer relay system 7PZn-C60 (see picture) not only harvests visible light for the electron transfer to the C60 terminus, but also retards the back-electron-transfer process, thus resulting in a longer lifetime of the charge-separated state (7P-C). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51460_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Toxicity of metal nanoparticles with a focus on silver (2013)

Properties of nanoparticles are significantly different from their bulk counterparts, including their biological and toxic activity. The properties of silver nanoparticles governing their toxicological effects are summarized. These basic characteristics can be used as descriptors for modelling the toxic properties of nanoparticles.
Single‐Molecule Analysis Determines Isozymes of Human Alkaline Phosphatase in Serum (2020)

Alkaline phosphatase (ALP) is an important biomarker, as high levels of ALP in blood can indicate liver disease or bone disorders. However, current clinical blood tests only measure the total concentration of ALP but are unable to distinguish enzyme isotypes. Here, we demonstrate a novel and rapid approach to profile various ALP isozymes in blood via a single-molecule-analysis platform. The microarray platform provides enzyme kinetics of hundreds of individual molecules at high throughput. Using these single molecule kinetics, we characterize the different activity profiles of ALP isotypes. By analyzing both healthy and disease samples, we found the single molecule activity distribution of ALP in serum reflects the health status of patients. This result demonstrates the potential utility of the method for improving the conventional ALP test, as well as for analyzing other enzymatic biomarkers, including enzyme isotypes.
Supplementary Figure Legends from YAP Orchestrates Heterotypic Endothelial Cell Communication via HGF/c-MET Signaling in Liver Tumorigenesis (2023)

&lt;p&gt;Supplementary Figure Legends&lt;/p&gt;
Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis (2022)

Archived formalin fixed paraffin-embedded (FFPE) tissues are powerful tools in medicine, capable of harboring diagnostic and genetic answers to challenging clinical questions. Successful utilization of DNA derived from FFPE samples is dependent upon repairing DNA damage generated from the fixation process. Methods to repair FFPE DNA have been successful in human medicine for a variety of research and clinical applications, yet remain underutilized in veterinary medicine. Despite the available technology, our study is the first to evaluate the repair of FFPE derived DNA from veterinary species for single-nucleotide polymorphism (SNP) analysis using the Illumina OvineSNP50 BeadChip and Illumina FFPE QC and DNA Restore kit. To accomplish this, 48 ovine FFPE samples were run using the Illumina OvineSNP50 BeadChip with and without restoration. Compared to pre-restore data, we found increased sample call rates, SNP call frequency, and assay metrics for all samples post-restoration. Further, we utilized four sheep with available parallel fresh DNA and FFPE DNA to compare assay metrics and genotype calls between the two starting sample types. Although fresh samples generated increased call rates, we found 99% concordance in allele calls between restored FFPE and fresh DNA for all four samples. Our results indicate successful restoration and genotyping of ovine FFPE samples using this technology, with potential for utilization in other veterinary species.
Micro-Anode Guided Electroplating (MAGE) Control System (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Differential Interaction of the Staphylococcal Toxins Panton–Valentine Leukocidin and γ-Hemolysin CB with Human C5a Receptors (2015)

Staphylococcus aureus is well adapted to the human host. Evasion of the host phagocyte response is critical for successful infection. The staphylococcal bicomponent pore-forming toxins Panton-Valentine leukocidin LukSF-PV (PVL) and γ-hemolysin CB (HlgCB) target human phagocytes through interaction with the complement receptors C5aR1 and C5aR2. Currently, the apparent redundancy of both toxins cannot be adequately addressed in experimental models of infection because mice are resistant to PVL and HlgCB. The molecular basis for species specificity of the two toxins in animal models is not completely understood. We show that PVL and HlgCB feature distinct activity toward neutrophils of different mammalian species, where activity of PVL is found to be restricted to fewer species than that of HlgCB. Overexpression of various mammalian C5a receptors in HEK cells confirms that cytotoxicity toward neutrophils is driven by species-specific interactions of the toxins with C5aR1. By taking advantage of the species-specific engagement of the toxins with their receptors, we demonstrate that PVL and HlgCB differentially interact with human C5aR1 and C5aR2. In addition, binding studies illustrate that different parts of the receptor are involved in the initial binding of the toxin and the subsequent formation of lytic pores. These findings allow a better understanding of the molecular mechanism of pore formation. Finally, we show that the toxicity of PVL, but not of HlgCB, is neutralized by various C5aR1 antagonists. This study offers directions for the development of improved preclinical models for infection, as well as for the design of drugs antagonizing leukocidin toxicity.
Successful Pelvic Resection for Acetabular Hydatidosis (2017)

In a young patient, hydatidosis of the pelvic bone can be treated with satisfying results through wide resection of the hip coupled with an antiparasitic treatment administered before and after the surgery. Prosthetic reconstruction, similar to what is done in cancer surgery, restores good functions.
Supplementary Figures S1-S9 from Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell–like Program Conserved in HPV-Positive Cancers (2023)

&lt;p&gt;Supplementary data depicted in Supplementary Figures S1-S9&lt;/p&gt;
Synthesis of 4‐Aryl‐butylamine Fluorescent Probes. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Synthese von (+)‐Abscisinsäure (1989)

Synthesis of (+)‐Abscisic Acid . Starting from (4 S )‐4‐hydroxy‐2,6,6‐trimethylcyclohex‐2‐enone ( 2 ), a short synthesis of the natural (+)‐abscisic acid ((+)‐ 1 ) has been accomplished.
Scalable Topologies for Time-Optimal Authentication of UAV Swarms (2022)

Swarm-based Unmanned Aerial Vehicle (UAV) applications require a large number of UAVs to be deployed across a region to work cooperatively. To operate a large number of unattended UAVs in hostile environments, it is critical to secure UAV-BS (base station) communications. UAV authentication based on Physical Unclonable Functions (PUFs) has recently emerged as a potential solution for overcoming adversarial attacks. The performance of PUF-based authentication protocols is strongly influenced by various factors, including the time required to generate the topology, the number of bottleneck connections, and the network's traffic load. This article investigates how the authentication time for a UAV swarm is affected by various factors such as the type of topology, number of UAVs in the swarm and the number of parallel connections.
Polymer Nuclear Magnetic Resonance Spectroscopy. XX. Helix-Coil Transitions in Poly(γ-benzyl D,L-glutamates) (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer Nuclear Magnetic Resonance Spectroscopy. XX. Helix-Coil Transitions in Poly(γ-benzyl D,L-glutamates)F. A. Bovey, J. J. Ryan, G. Spach, and F. HeitzCite this: Macromolecules 1971, 4, 4, 433–434Publication Date (Print):July 1, 1971Publication History Published online1 May 2002Published inissue 1 July 1971https://pubs.acs.org/doi/10.1021/ma60022a012https://doi.org/10.1021/ma60022a012research-articleACS PublicationsRequest reuse permissionsArticle Views55Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Silicon photonic-electronic neural network for fibre nonlinearity compensation (2021)

In optical communication systems, fibre nonlinearity is the major obstacle in increasing the transmission capacity. Typically, digital signal processing techniques and hardware are used to deal with optical communication signals, but increasing speed and computational complexity create challenges for such approaches. Highly parallel, ultrafast neural networks using photonic devices have the potential to ease the requirements placed on the digital signal processing circuits by processing the optical signals in the analogue domain. Here we report a silicon photonice-lectronic neural network for solving fibre nonlinearity compensation of submarine optical fibre transmission systems. Our approach uses a photonic neural network based on wavelength-division multiplexing built on a CMOS-compatible silicon photonic platform. We show that the platform can be used to compensate optical fibre nonlinearities and improve the signal quality (Q)-factor in a 10,080 km submarine fibre communication system. The Q-factor improvement is comparable to that of a software-based neural network implemented on a 32-bit graphic processing unit-assisted workstation. Our reconfigurable photonic-electronic integrated neural network promises to address pressing challenges in high-speed intelligent signal processing.
First clinical validation of whole genome screening on standard trophectoderm biopsies of preimplantation embryos (2022)

Abstract Whole Genome Sequencing (WGS) is used in healthcare and in the clinic, with the notable exception of preimplantation genetic testing (PGT). In PGT, only a few cells are available for sequencing, requiring DNA amplification which reduces data quality, sequence fidelity and sharply limits subsequent clinical impact. Here we demonstrate the first clinical validation of WGS on embryo biopsies using our lab development protocol, opening the door to broad use of WGS in fertility. We find that amplified DNA with comparable sensitivity and specificity to genomic DNA when performing whole genome sequencing assays. DNA amplification on cell lines and donated human embryos had an amplification success rate of &gt;99.9% and 98.2% respectively and accuracy on both was &gt;99.9% on aneuploidy status. GIAB samples (Genome in the Bottle reference NA12878) showed that our amplified DNA was broadly comparable to genomic DNA (99.99% accuracy, 99.99% specificity, 98.0% sensitivity and 98.1% precision). Using our assay, we were able to call variants, detect mitochondrial heteroplasmy, perform high precision screening without access to parental genomes, detect compound heterozygous variants, and score microdups/dels and uniparental disomies (to reduce risk of diseases such as DiGeorge syndrome and Prader-Willi syndrome). Our clinical study suggests that the full spectrum of traditional clinical genome bioinformatics, so far reserved to large samples, can now be performed on embryos before implantation.
Maximizing the Signal in Nonlinear Beam-Deflection (2023)

We calculate how the Beam-Deflection signal for determining nonlinear refraction is maximized at a specific spatial displacement between probe and excitation beams while varying their spot size ratio.
Polymerization Stereochemistry with Ziegler−Natta Catalysts Containing Dialkylpropane Diethers:  A Tool for Understanding Internal/External Donor Relationships (1996)

A study on a new generation of MgCl2-supported Ziegler−Natta catalysts, which contain dialkylpropane diethers as internal donors and have the property of producing highly active and stereospecific catalysts without any external donor, has been performed. The behavior of three different diethers (2,2-diisobutyl-1,3-dimethoxypropane, 2,2-dicyclopentyl-1,3-dimethoxypropane, and 2-ethyl-2-butyl-1,3-dimethoxypropane) as internal donors is compared with the behavior of the same diethers when they are used as external donors with a catalyst containing diisobutyl phthalate as internal donor. The results obtained show that the same isospecific centers are produced when the same diether donor is present as an internal donor or replaces diisobutyl phthalate during polymerization when it is added as an external donor. The sum of the present results and of the previously obtained findings on traditional supported Ziegler−Natta catalysts has enabled us to reach some conclusions on the role and reciprocal behavior of internal and external donors.
γ-Secretase Modulators as Potential Disease Modifying Anti-Alzheimer’s Drugs (2010)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTγ-Secretase Modulators as Potential Disease Modifying Anti-Alzheimer's DrugsDaniel Oehlrich*, Didier J.-C. Berthelot, and Harrie J. M. Gijsen*View Author Information Medicinal Chemistry, Janssen Research and Development, a Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium*To whom correspondence should be addressed. For D.O.: phone, +32 (0)14 60 3100; fax, +32 (0) 14 60 5344; e-mail, [email protected]. For H.J.M.G.: phone, +32 (0)14 60 6830; fax, +32 (0) 14 60 5344; e-mail, [email protected]Cite this: J. Med. Chem. 2011, 54, 3, 669–698Publication Date (Web):December 9, 2010Publication History Received8 September 2010Published online9 December 2010Published inissue 10 February 2011https://pubs.acs.org/doi/10.1021/jm101168rhttps://doi.org/10.1021/jm101168rreview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views5718Altmetric-Citations139LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Central nervous system,Peptides and proteins,Redox reactions,Rodent models Get e-Alerts
Super-resolution Fluorescence Quenching Microscopy of Graphene (2012)

Lately, fluorescence quenching microscopy (FQM) has been introduced as a new tool to visualize graphene-based sheets. Even though quenching of the emission from a dye molecule by fluorescence resonance energy transfer (FRET) to graphene happens on the nanometer scale, the resolution of FQM so far is still limited to several hundreds of nanometers due to the Abbe limit restricting the resolution of conventional light microscopy. In this work, we demonstrate an advancement of FQM by using a super-resolution imaging technique for detecting fluorescence of color centers used in FQM. The technique is similar to stimulated emission depletion microscopy (STED). The combined "FRET+STED" technique introduced here for the first time represents a substantial improvement to FQM since it exhibits in principle unlimited resolution while still using light in the visible spectral range. In the present case we demonstrate all-optical imaging of graphene with resolution below 30 nm. The performance of the technique in terms of imaging resolution and contrast is well described by a theoretical model taking into account the general distance dependence of the FRET process and the distance distribution of donor centers with respect to the flake. In addition, the change in lifetime for partially quenched emitters allows extracting the quenching distance from experimental data for the first time.
Designing cable-driven actuation networks for kinematic chains and trees (2017)

In this paper we present an optimization-based approach for the design of cable-driven kinematic chains and trees. Our system takes as input a hierarchical assembly consisting of rigid links jointed together with hinges. The user also specifies a set of target poses or keyframes using inverse kinematics. Our approach places torsional springs at the joints and computes a cable network that allows us to reproduce the specified target poses. We start with a large set of cables that have randomly chosen routing points and we gradually remove the redundancy. Then we refine the routing points taking into account the path between poses or keyframes in order to further reduce the number of cables and minimize required control forces. We propose a reduced coordinate formulation that links control forces to joint angles and routing points, enabling the co-optimization of a cable network together with the required actuation forces. We demonstrate the efficacy of our technique by designing and fabricating a cable-driven, animated character, an animatronic hand, and a specialized gripper.
Creating non-volatile electronics by spintronics technology (2009)

To realize this dream of normally-off electronic equipment requires development of non-volatile electronics technology for the main memory (DRAM and SRAM) and for the logic unit of computers. As the first stage of research and development aiming at normally-off electronics, AIST is doing R & D to achieve the first of those two requirements, a large-capacity, high-speed and highly-reliable non-volatile computer memory. Here, high reliability mainly refers to rewrite durability. To replace the DRAM and SRAM that serve as the main memory of computers, it is necessary to attain the practically limitless write endurance of 10 15 rewrite cycles without failure. Incidentally, the write endurance of the flash memory used in current external storage devices is only 10 4 to 10 6 rewrite cycles, and so is not usable as main memory. The ferro-electric memory devices (FeRAM), typical non-volatile memory devices that are already on the market, have a write endurance of 10 8 rewrite cycles, still inadequate to serve as computer main memory. The phase change memory (called PRAM or PCRAM) devices currently under development as non-volatile memory also have limited rewrite times. Spintronics technology (explained below), on the other hand, enables the development of nonvolatile memory that has unlimited rewrite times.
An advanced boundary element method (BEM) implementation for the forward problem of electromagnetic source imaging (2004)

The forward problem of electromagnetic source imaging has two components: a numerical model to solve the related integral equations and a model of the head geometry. This study is on the boundary element method (BEM) implementation for numerical solutions and realistic head modelling. The use of second-order (quadratic) isoparametric elements and the recursive integration technique increase the accuracy in the solutions. Two new formulations are developed for the calculation of the transfer matrices to obtain the potential and magnetic field patterns using realistic head models. The formulations incorporate the use of the isolated problem approach for increased accuracy in solutions. If a personal computer is used for computations, each transfer matrix is calculated in 2.2 h. After this pre-computation period, solutions for arbitrary source configurations can be obtained in milliseconds for a realistic head model. A hybrid algorithm that uses snakes, morphological operations, region growing and thresholding is used for segmentation. The scalp, skull, grey matter, white matter and eyes are segmented from the multimodal magnetic resonance images and meshes for the corresponding surfaces are created. A mesh generation algorithm is developed for modelling the intersecting tissue compartments, such as eyes. To obtain more accurate results quadratic elements are used in the realistic meshes. The resultant BEM implementation provides more accurate forward problem solutions and more efficient calculations. Thus it can be the firm basis of the future inverse problem solutions.