gebhart/patrepeval huggingface dataset:
Magnetic resonance (MR) safety testing of implants using numerical simulation for worst-case determination (2011)

MR safety and compatibility are important issues for all devices used within an MR environment. MR testing of medical devices is required for device approval by the regulatory agencies worldwide. Besides basic testing also computer modeling of electromagnetic fields and SAR distribution of passive devices has been established. Further methods for numerical analysis and testing are currently under development for active implantable medical devices. The methods will be published soon as an ISO Technical Specification listing such as RF- and gradient-induced voltages, heating, vibration and device malfunction by exposure to the static magnetic, switched gradient magnetic and electromagnetic field.
Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution (2012)

We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550–1720 cm−1). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.
Cumulative sum quality control for calibrated breast density measurements (2009)

The BL calibration dataset must be monitored and periodically updated, when necessary, to account for sustained system variations to maintain the calibration accuracy.
Dynamics and control of micromachined gyroscopes (1999)

We summarize principles of operation of micromachined gyroscopes, analyze dynamics of ideal and non-ideal systems, and propose an approach for formulation and solving problems of control. The suggested approach uses active nonlinear feedback control for drive and compensation of errors. Both non-adaptive and adaptive strategies are presented. These strategies can be used for a broad class of micromachined vibratory gyroscopes including those for angle and angular rate measurement.
Platelet Aggregation and Coagulation Inhibitors in Leech Saliva and Their Roles in Leech Therapy (1996)

Prolonged bleeding by the host after the leech ceases to feed and several reports that the use of leeches restores blood flow in the microcirculation after plastic surgery led us to search for inhibitors of platelet aggregation in Hirudo medicinalis saliva. Dilute leech saliva was collected by phagostimulating starved leeches with a solution of arginine in saline. The saliva is shown to inhibit human platelet aggregation induced by thrombin, collagen, adenosine diphosphate (ADP), epinephrine, platelet activating factor (1-O-alkyl-2-acetyl-sn-3-glycerophophoryl choline [PAF]), and arachidonic acid. We have isolated the PAF inhibitor and found it to be an amphipathic phosphoglyceride. We have also purified apyrase adenosine triphosphate ([ATP] diphosphohydrolase), which inhibits ADP-induced platelet aggregation, and have described collagenase. Besides well-known hirudin, Hirudo saliva contains a potent inhibitor of coagulation factor Xa. We also report antiaggregant and anticoagulant activities in the crop content of the closely related Nile leech, Limnatis nilotica. Anticoagulants of hematophagous species are surveyed. We have used medicinal leeches in plastic surgery for decompression of skin flaps and in patients with postphlebitic syndrome and peripheral arterial occlusions. Preliminary results indicate certain beneficial effects of leech therapy.
Columnstore and B+ tree - Are Hybrid Physical Designs Important? (2018)

Commercial DBMSs, such as Microsoft SQL Server, cater to diverse workloads including transaction processing, decision support, and operational analytics. They also support variety in physical design structures such as B+ tree and columnstore. The benefits of B+ tree for OLTP workloads and columnstore for decision support workloads are well-understood. However, the importance of hybrid physical designs, consisting of both columnstore and B+ tree indexes on the same database, is not well-studied --- a focus of this paper. We first quantify the trade-offs using carefully-crafted micro-benchmarks. This micro-benchmarking indicates that hybrid physical designs can result in orders of magnitude better performance depending on the workload. For complex real-world applications, choosing an appropriate combination of columnstore and B+ tree indexes for a database workload is challenging. We extend the Database Engine Tuning Advisor for Microsoft SQL Server to recommend a suitable combination of B+ tree and columnstore indexes for a given workload. Through extensive experiments using industry-standard benchmarks and several real-world customer workloads, we quantify how a physical design tool capable of recommending hybrid physical designs can result in orders of magnitude better execution costs compared to approaches that rely either on columnstore-only or B+ tree-only designs.
Light Source Spectrum Strongly Influences the <i>In Vitro</i> Estimation of Sun Protection Factor (2012)

Irradiation from an artificial solar simulator that matches the relative cumulative erythema effectiveness (RCEE) of sunlight is used for in vivo sun protection factor (SPF) testing, whereas irradiation that matches the spectrum of natural sunlight (NS) is generally used for in vitro SPF testing. This study was designed to clarify whether this difference is important. Eight sunscreens spread on artificial substrates and several optical filters as sunscreen mimics were used. Their in vitro SPF values were evaluated using RCEE-compliant and NS spectrum-matching light sources in calculation. The calculated in vitro SPF values obtained using NS light (SPF [NS]) were lower than those obtained using RCEE light (SPF [RCEE]). The in vitro SPF (RCEE) values showed a better correlation and better agreement with in vivo SPF values, as compared with the in vitro SPF (NS) values. A marked difference between in vitro SPF values obtained with the two light sources in calculation was found for sunscreens showing low transmittance in the ultraviolet B region. To obtain in vitro SPF values that correspond well to in vivo SPF values measured with currently accepted methodology, it is important to use an RCEE-compliant light source.
“Interferometric ground-roll removal: Attenuation of scattered surface waves in single-sensor data,” G <scp>EOPHYSICS</scp> , 75, no. 2, SA15–SA25. (2010)

Abstract To: “Interferometric ground-roll removal: Attenuation of scattered surface waves in single-sensor data,” David F. Halliday, Andrew Curtis, Peter Vermeer, Claudio Strobbia, Anna Glushchenko, Dirk-Jan van Manen, and Johan O. A. Robertsson, Geophysics, 75, no. 2, SA15–SA25.
Mechanism of Lethal Toxin Neutralization by a Human Monoclonal Antibody Specific for the PA20 Region of Bacillus anthracis Protective Antigen (2011)

The primary immunogenic component of the currently approved anthrax vaccine is the protective antigen (PA) unit of the binary toxin system. PA-specific antibodies neutralize anthrax toxins and protect against infection. Recent research has determined that in humans, only antibodies specific for particular determinants are capable of effecting toxin neutralization, and that the neutralizing epitopes recognized by these antibodies are distributed throughout the PA monomer. The mechanisms by which the majority of these epitopes effect neutralization remain unknown. In this report we investigate the process by which a human monoclonal antibody specific for the amino-terminal domain of PA neutralizes lethal toxin in an in vitro assay of cytotoxicity, and find that it neutralizes LT by blocking the requisite cleavage of the amino-terminal 20 kD portion of the molecule (PA(20)) from the remainder of the PA monomer. We also demonstrate that the epitope recognized by this human monoclonal does not encompass the (166)RKKR(169) furin recognition sequence in domain 1 of PA.
Towards gene therapy against HIV-1: new therapeutic target in gag RNA accessible to ribozymes and RNA interference molecules (2014)

Antisense molecules targeting HIV-1 RNA have the potential to be used as part of combination gene or drug therapy to treat HIV-1 infection to reach a functional or complete cure. Only a small number of extremely active molecules currently exist and a treatment option has not yet been identified in clinical trials. We have previously developed new hepatitis delta virus (HDV)-derived ribozymes (Rzs) called "switch on-off adaptor" (SOFA) to target HIV-1 RNA Our aim is to develop highly active RNA-based molecules with complementary mechanisms, which are able to reach a large number of HIV-1 variants.
Autotransplantation in mdx Mice of mdx Myoblasts Genetically Corrected by an HSV-1 Amplicon Vector (2002)

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder, characterized by a lack of dystrophin. To eliminate the need for immunosuppressive drugs, transplantation of genetically modified autologous myoblasts has been proposed as a possible therapy for this myopathy. An HSV-1 amplicon vector (HSVDGN), containing a 17.3-kb full-length MCK-driven mouse dystrophin cDNA, an eGFP gene, and a neomycin resistance gene driven by CMV or SV40 promoters, respectively, was constructed and used to transduce mdx primary myoblasts. The presence of the eGFP and neomycin resistance genes facilitated the evaluation of the initial transduction efficiency and the permanent transduction frequency. At low multiplicities of infection (MOI 1-5), the majority of myoblasts (60-90%) expressed GFP. The GFP-positive mdx myoblasts were sorted by FACS and selected with neomycin (300 microg/ml) for 2 weeks. Up to 2% of initially infected mdx myoblasts stably expressed the three transgenes without further selection at that time. These altered cells were grafted into the tibialis anterior muscles of 18 mdx mice. Some of the mice were immunosuppressed with FK506 due to the anticipation that eGFP and the product of neomycin resistance gene might be immunogenic. One month after transplantation, numerous muscle fibers expressing mouse dystrophin were detected by immunohistochemistry, in both immunosuppressed (10-50%) and nonimmunosuppressed (5-25%) mdx mice. Our results demonstrated the capability of permanently expressing a full-length dystrophin in dystrophic myoblasts with HSV-1 amplicon vector and raised the possibility of an eventual treatment of DMD based on the transplantation of genetically modified autologous myoblasts.
Recent advances in the synthesis of C-terminally modified peptides (2020)

C-Terminally modified peptides are important for the development and delivery of peptide-based pharmaceuticals because they impact peptide activity, stability, hydrophobicity, and membrane permeability. Additionally, the vulnerability of C-terminal esters to cleavage by endogenous esterases makes them excellent pro-drugs. Methods for post-SPPS C-terminal functionalization potentially enable access to libraries of modified peptides, facilitating tailoring of their solubility, potency, toxicity, and uptake pathway. Apparently minor structural changes can significantly impact the binding, folding, and pharmacokinetics of the peptide. This review summarizes developments in chemical methods for C-terminal modification of peptides published since the last review on this topic in 2003.
On the Use of Dynamic Time Warping for Word Spotting and Connected Word Recognition* (1981)

Several variations on algorithms for dynamic time warping for speech processing applications have been proposed. This paper compares two of these algorithms, the fixed-range method and the local minimum method. We show that, based on results from some simple word spotting and connected word recognition experiments, the local minimum method performs considerably better than the fixed-range method. We describe explanations of this behavior and techniques for optimizing the parameters of the local minimum algorithm for both word spotting and connected word recognition.
Quantum Pattern Recognition With Liquid State NMR (2008)

A novel quantum pattern recognition scheme is presented, which combines the idea of a classic Hopfield neural network with adiabatic quantum computation. Both the input and the memorized patterns are represented by means of the problem Hamiltonian. In contrast to classic neural networks, the algorithm can return a quantum superposition of multiple recognized patterns. A proof of principle for the algorithm for two qubits is provided using a liquid state NMR quantum computer.
Anti-Epstein-Barr Virus (EBV) Activity of β- <scp>l</scp> -5-Iododioxolane Uracil Is Dependent on EBV Thymidine Kinase (2000)

ABSTRACT β- l -5-Iododioxolane uracil was shown to have potent anti-Epstein-Barr virus (EBV) activity (50% effective concentration = 0.03 μM) with low cytotoxicity (50% cytotoxic concentration = 1,000 μM). It exerts its antiviral activity by suppressing replicative EBV DNA and viral protein synthesis. This compound is phosphorylated in cells where the EBV is replicating but not in cells where the EBV is latent. EBV-specific thymidine kinase could phosphorylate β- l -5-iododioxolane uracil to the monophosphate metabolite. The K m of β- l -5-iododioxolane uracil with EBV thymidine kinase was estimated to be 5.5 μM, which is similar to that obtained with thymidine but about fivefold higher than that obtained with 2′ fluoro-5-methyl-β- l -arabinofuranosyl uracil, the first l -nucleoside analogue discovered to have anti-EBV activity. The relative V max is seven times higher than that of thymidine. The anti-EBV activity of β- l -5-iododioxolane uracil and its intracellular phosphorylation could be inhibited by 5′-ethynylthymidine, a potent EBV thymidine kinase inhibitor. The present study suggests that β- l -5-iododioxolane uracil exerts its action after phosphorylation; therefore, EBV thymidine kinase is critical for the antiviral action of this drug.
Colorectal tumor identification by transferring knowledge from pan-cytokeratin to H&E (2019)

Tumor budding is a recently recognized, independent prognostic factor in colorectal cancer, but lacks a standardized assessment methodology. Although staining with pan-cytokeratin has been shown to mitigate the issue of lack of reproducible, intra-observer agreement, usage of this antibody remains expensive and is limited in clinical practice. We propose an automated image analysis framework to take advantage of the visual superiority of pan-cytokeratin and the routine use of H&E to detect and quantify tumor budding. Our framework has demonstrated promising ability to identify tumor regions of colorectal slides – 92.0% accuracy, 94.5% sensitivity, and 85% specificity – across four independent datasets.
Structure-activity relationships of nogalamycin analogs (1982)

Nogalamycin (1) has been modified by changes at C-10 and C-7 and in the dimethylamino group to prepare an extensive series of analogues. The chemistry involved in the modifications and structure--activity relationships among these nogalamycin analogues are discussed, as well as comparisons with previously reported compounds 1, 7-con-O-methylnogarol (2), and disnogamycin (11).
Metabolic Signatures of Extreme Longevity in Northern Italian Centenarians Reveal a Complex Remodeling of Lipids, Amino Acids, and Gut Microbiota Metabolism (2013)

The aging phenotype in humans has been thoroughly studied but a detailed metabolic profiling capable of shading light on the underpinning biological processes of longevity is still missing. Here using a combined metabonomics approach compromising holistic (1)H-NMR profiling and targeted MS approaches, we report for the first time the metabolic phenotype of longevity in a well characterized human aging cohort compromising mostly female centenarians, elderly, and young individuals. With increasing age, targeted MS profiling of blood serum displayed a marked decrease in tryptophan concentration, while an unique alteration of specific glycerophospholipids and sphingolipids are seen in the longevity phenotype. We hypothesized that the overall lipidome changes specific to longevity putatively reflect centenarians' unique capacity to adapt/respond to the accumulating oxidative and chronic inflammatory conditions characteristic of their extreme aging phenotype. Our data in centenarians support promotion of cellular detoxification mechanisms through specific modulation of the arachidonic acid metabolic cascade as we underpinned increased concentration of 8,9-EpETrE, suggesting enhanced cytochrome P450 (CYP) enzyme activity. Such effective mechanism might result in the activation of an anti-oxidative response, as displayed by decreased circulating levels of 9-HODE and 9-oxoODE, markers of lipid peroxidation and oxidative products of linoleic acid. Lastly, we also revealed that the longevity process deeply affects the structure and composition of the human gut microbiota as shown by the increased extrection of phenylacetylglutamine (PAG) and p-cresol sulfate (PCS) in urine of centenarians. Together, our novel approach in this representative Italian longevity cohort support the hypothesis that a complex remodeling of lipid, amino acid metabolism, and of gut microbiota functionality are key regulatory processes marking exceptional longevity in humans.
Surface Acoustic Wave Transducer Study. (1978)

Abstract : A theoretical and experimental study of surface acoustic wave transducers is carried out to improve the modeling technique and the implementation configuration. The capacity weighted transducer with the response controlled by integrated circuit capacitors has been developed. The response is improved because the SAW beam has a uniform width and the transducer taps may be adjusted over a wide range. The excitation theory of transducers has been reformulated to account for nearest neighbor interactions over a wide range of harmonics. This modeling approach significantly expands the versatility and accuracy of the model. An experimental procedure for measuring the transducer excitation function is described. (Author)
Enhancing dynamic cloud-based services using network virtualization (2009)

It is envisaged that services and applications will migrate to a cloud-computing paradigm where thin-clients on user devices access, over the network, applications hosted in data centers by application service providers. Examples are cloud based gaming applications and cloud-supported virtual desktops. For good performance and efficiency, it is critical that these services are delivered from locations that are the best for the current (dynamically changing) set of users. To achieve this, we expect that services will be hosted on virtual machines in interconnected data centers and that these virtual machines will migrate dynamically to locations best suited for the current user population. A basic network infrastructure need then is the ability to migrate virtual machines across multiple networks without losing service continuity. In this paper, we develop mechanisms to accomplish this using a network-virtualization architecture that relies on a set of distributed forwarding elements with centralized control (borrowing on several recent proposals in a similar vein). We describe a preliminary prototype system, built using Openflow components, that demonstrates the feasibility of this architecture in enabling seamless migration of virtual machines and in enhancing delivery of cloud-based services.
Antivertigo agents. II. Structure-activity relationships of 6-substituted 5,6,7,8-tetrahydro-1,6-naphthyridines. (1984)

A number of 6-substituted 5, 6, 7, 8-tetrahydro-1, 6-naphthyridines designed as cyclic homologues of betahistine, 2-(2-methylaminoethyl) pyridine, were synthesized by the reduction of the corresponding 1, 6-naphthyridinium salts. The antivertigo activity of these derivatives was evaluated in terms of their ability to inhibit spontaneous nystagmus in cats. The relationships between the molecular structures of the test compounds and their antivertigo activities were investigated by a regression analysis based on the lipophilicity (π) of the substituents at the 6-position and by a conformational analysis of the compounds of interest using the modified neglect of diatomic overlap molecular orbital method. Among these compounds, the 6-allyl-and 6-cyclopropylmethyl derivatives exhibited extremely potent activity with greatly reduced hypotensive action.
Spectral optical coherence tomography for ophthalmologic applications (2006)

The overview of the Spectral Optical Coherence Tomography an alternative method to more popular Time domain modality is given. Examples from medical practice utilizing high resolution, ultra fast SOCT device are presented.
Nanofluidic Devices for Sensing and Flow Control (2006)

Nanofluidics is concerned with fluidic channels that are typically 1–100 nm in size. We have fabricated nanofluidic devices using both 1-D silica nanotubes and 2-D nanochannels to explore transport phenomena at the nanoscale. Here we review our work on 2-D nanochannels that provide confinement in one dimension. Our work mainly deals with two aspects of nanofluidics (a) effects related to electrostatic interactions and (b) effects related to biomolecule size. Surface charge plays an important role in nanofluidic channels, when the channel size is comparable to the Debye length. Using both electrical conductance measurements and fluorescence imaging, we studied the effects of surface charge in our nanofluidic devices, and demonstrated that the environment in nanochannels is governed by surface charge. We modified the nanochannel surface and showed that these modifications can be sensed by measuring ionic conductance of the nanochannels. Further, binding reactions involving biomolecules can be sensed at both low and high ionic concentrations. Our results showed that at low concentrations, conductance is governed by biomolecule charge, while at high concentrations it is governed by biomolecule size. Based on electrostatic effects in nanochannels, we also developed a nanofluidic transistor for flow control. This metal-oxide-solution field effect transistor was fabricated by patterning a metal gate electrode over nanochannels, similar to a MOSFET. Just as the gate voltage of a MOSFET controls carrier concentration in the semiconductor, we demonstrated that the gate voltage in a nanofluidic transistor controls the concentration of ions and biomolecules in the nanochannel, and hence controls their transport. Our fabrication process uses standard lithography, and is amenable to making networks of nanochannels. It suggests that rationally designed nanofluidic networks could be developed using this process for applications in sample preparation, sensing and switching. We are currently studying flow control and switching using field-effect, as well as ionic transport using patterned surface charge in nanofluidic devices.