gebhart/patrepeval huggingface dataset:
Cloning of a serotype-specific antigen from Pasteurella haemolytica A1 (1986)

Recombinant plasmids coding for a soluble (or surface) antigen of Pasteurella haemolytica A1 were identified. Two plasmids, both containing the same 5.4 kilobase pairs of insert DNA, were recovered independently by screening a clone band of P. haemolytica A1 genomic DNA in Escherichia coli for the expression of P. haemolytica A1 soluble antigens (R. Y. C. Lo and L.A. Cameron, Can. J. Biochem. Cell Biol. 64:73-76, 1986). E. coli cells carrying the plasmids were found to be agglutinated by an antiserum raised against the P. haemolytica A1 soluble antigens. Analysis of the E. coli clones by electron microscopy revealed patches of amorphous material on the surface of the cells which were not present on the controls. Further characterization with protein A-colloidal gold labeled both these patches and the outer membranes of these cloned cells pretreated with the specific antiserum. These results indicated that the cloned antigen was expressed on the surface of the E. coli cells. The cloned antigen was found to be specific for serotype 1 when tested by slide agglutination against a collection of P. haemolytica typing antisera. Southern blot hybridization, using the cloned DNA as a probe, labeled the genomic DNA from P. haemolytica serotype 1 as well as the cross-agglutinating serotypes 2 and 7, but not DNA from the non-cross-agglutinating serotypes 3 and 4 and Pasteurella multocida. These results demonstrated that serotype specificity could be attributed to the particular antigenic determinants in the genome of the organism.
Measuring vehicle speed at a license plate using a pair of linescan cameras (2006)

Abstract An automatic vehicle speed measurement system is presented that can reliably associate the vehicle ID with the retrieved vehicle speed. The system captures images of vehicles passing between two points on the ground that are in the same vicinity, using a pair of linescan cameras installed in a parallel configuration, and measures the speed of passing vehicles by measuring the time taken for the vehicle license plate to move between the two points. In the proposed method, a pair of linescan cameras arranged in parallel is first used to detect passing vehicles and retrieve images of the front sections of the vehicles by capturing images of the vehicles from an angle diagonal to the direction of motion. High‐resolution images of the front section of the vehicles are obtained by image capture at a diagonal to the direction of the vehicles in order to obtain high spatial and temporal resolution images of the objects passing in front of the linescan cameras without the images being overly large. However, the license plate in the retrieved images is distorted depending on the position of the plate and the vehicle speed, and this distortion is corrected by performing a geometrical transformation on the images, based on the position at which the license plate passes the cameras and the time the vehicle takes to pass, as determined by finding corresponding blocks. After this, license plate recognition is used to determine the vehicle speed at the position of the license plate. A 24‐hour vehicle speed measurement experiment that used an infrared LED for illumination only during the nighttime achieved an 85.1% success rate in measuring the speeds of vehicles at the position of the license plates, thus verifying the validity of the proposed method. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 89(10): 33–45, 2006; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjc.20274
Isozymic changes in myosin of human atrial myocardium induced by overload. Immunohistochemical study using monoclonal antibodies. (1984)

An immunohistochemical study using monoclonal antibodies specific for the heavy chains of either human atrial (HC alpha) or ventricular (HC beta) myosin was performed to clarify the distribution of each isozyme in normal as well as pressure-overloaded human hearts. In normal human ventricles, all muscle fibers were stained by a monoclonal antibody (HMC14) specific for HC beta, whereas a small number of fibers reacted with a monoclonal antibody (CMA19) specific for HC alpha. In contrast, in normal human atria, almost all muscle fibers were stained by CMA19, and a relatively larger number of muscle fibers also reacted with HMC14. Furthermore, in pressure-overloaded atria, muscle fibers reactive with HMC14 were strikingly increased while those reactive with CMA19 showed a corresponding decrease. The extent of this isozymic redistribution was in good correlation with atrial pressure. These results not only confirmed the existence of isoforms of myosin heavy chain in human hearts, but also demonstrated that redistribution of iso-myosins could occur as an adaptation to pressure overload.
Independently Addressable Silicon Microcavity Plasma Arrays (2007)

Summary form only given. Addressable microcavity plasma devices with three electrode, dielectric barrier designs have been fabricated in 20 times 20 or 50 times 50 device arrays in Si and characterized in Ne, Ne/Xe, and Ar/D <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas mixtures. Each device comprises two metal electrode layers, a dielectric stack, and an inverted square pyramid microcavity having an emitting aperture of 50 times 50 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> 100 times 100 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . In this device structure, Si microcavity serves as the mold or backbone for subsequent processing. Arrays with filling factors of 11% and 25% (for (100 mum) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and (50 mum) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> device arrays, respectively) and a crossed electrode geometry exhibit operating voltages in Ne of ~220-300 V (RMS) when driven by a 20 kHz sinusoidal driving voltage. Displacement currents are ~50% of those for previous Si microplasma device arrays and, when exciting the array with 100-140 V pulses, the risetime of the wavelength-integrated fluorescence is observed to be <600 ns for pure Ne or Ne/5%Xe gas mixtures at a pressure of 700 Torr. A full address and sustain pulse sequence has also been demonstrated with the three electrode device structure. The voltage margin and discharge delay were measured with several different device geometries and discharge properties of an addressed microcavity will be discussed.
Induced Helical Backbone Conformations of Self-Organizable Dendronized Polymers (2008)

Control of function through the primary structure of a molecule presents a significant challenge with valuable rewards for nanoscience. Dendritic building blocks encoded with information that defines their three-dimensional shape (e.g., flat-tapered or conical) and how they associate with each other are referred to as self-assembling dendrons. Self-organizable dendronized polymers possess a flat-tapered or conical self-assembling dendritic side chain on each repeat unit of a linear polymer backbone. When appended to a covalent polymer, the self-assembling dendrons direct a folding process (i.e., intramolecular self-assembly). Alternatively, intermolecular self-assembly of dendrons mediated by noncovalent interactions between apex groups can generate a supramolecular polymer backbone. Self-organization, as we refer to it, is the spontaneous formation of periodic and quasiperiodic arrays from supramolecular elements. Covalent and supramolecular polymers jacketed with self-assembling dendrons self-organize. The arrays are most often comprised of cylindrical or spherical objects. The shape of the object is determined by the primary structure of the dendronized polymer: the structure of the self-assembling dendron and the length of the polymer backbone. It is therefore possible to predictably generate building blocks for single-molecule nanotechnologies or arrays of supramolecules for bottom-up self-assembly. We exploit the self-organization of polymers jacketed with self-assembling dendrons to elucidate how primary structure determines the adopted conformation and fold (i.e., secondary and tertiary structure), how the supramolecules associate (i.e., quaternary structure), and their resulting functions. A combination of experimental techniques is employed to interrogate the primary, secondary, tertiary, and quaternary structure of the self-organizable dendronized polymers. We refer to the process by which we interpolate between the various levels of structural information to rationalize function as retrostructural analysis. Retrostructural analysis validates our hypothesis that the self-assembling dendrons induce a helical backbone conformation in cylindrical self-organizable dendronized polymers. This helical conformation mediates unprecedented functions. Self-organizable dendronized polymers have emerged as powerful building blocks for nanoscience by virtue of their dimensions and ability to self-organize. Discrete cylindrical and spherical structures with well-defined dimensions can be visualized and manipulated individually. More importantly, they provide a robust framework for elucidating functions available only at the nanoscale. This Account will highlight structures and functions generated from self-organizable dendronized polymers that enable integration of the nanoworld with its macroscopic universe. Emphasis is placed on those structures and functions derived from the induced helical backbone conformation of cylindrical self-organizable dendronized polymers.
Recent Developments in 5&#x2018;-Terminal Cap Analogs: Synthesis and Biological Ramifications. (2008)

The 5‘-terminus of eukaryotic messenger RNA (mRNA) molecules contains a unique ‘cap’ structure: 7- methylguanosine (m7G) linked by a 5‘-5‘-triphosphate bridge to the first nucleoside in the standard polymer chain. This 5‘- cap is recognized by numerous enzymes involved in the transport and translation of mRNA, as well as its processing, both in terms of generating mature mRNA from the initial transcript and its natural degradation. In vitro generation of capped RNAs uses a cap analog in which two nucleosides are joined in a 5‘-5‘ triphosphate linkage, allowing incorporation of the cap along with the first nucleotide in the polymer chain. The conventional cap analog, m7G[5‘]ppp[5‘]G, has a 3‘-OH on both nucleoside moieties, resulting in the incorporation of the dinucleotide in either orientation. This results in one-third to one-half of the mRNAs containing a non-methylated cap and a methylated initial nucleotide. These ‘reverse cap’ structures bind poorly to elF4E and other cap binding proteins, greatly reducing the overall translational efficiency in vitro and biological activity in vivo. This drawback of the conventional cap analog has been addressed by creating an “anti-reverse cap analog” (ARCA), m2 7, 3-OG[5‘]ppp[5‘]G, in which the 3‘-OH of the ribose connected to the m7Guo moiety is replaced with a 3‘-O-methyl group, allowing incorporation only in the forward orientation due to the presence of the single extendable 3‘-OH group. In addition to the chemical modification at the 3‘-OH group of the ribose connected to the m7G moiety, modifications at the 2‘-OH group also preclude attachment of a second nucleotide by polymerase, again forcing the forward orientation. This mini-review focuses on recent developments in the synthesis of novel cap analogs, highlighting modifications at several positions including; the heterocyclic bases, the sugars, and the α-, β-, and γ-phosphates in the triphosphate chain, and assessing their impact on biological activity.
Condenser optics, partial coherence, and imaging for soft x ray projection lithography (1992)

A condenser system couples the radiation source to an imaging system, controlling the uniformity and partial coherence at the object, which ultimately affects the characteristics of the aerial image. A soft-x-ray projection lithography system based on a ring-field imaging system and a laser-produced plasma x-ray source places considerable constraints on the design of a condenser system. Two designs are proposed, critical illumination and Kohler illumination, each of which requires three mirrors and scanning for covering the entire ring field with the required uniformity and partial coherence. Images based on Hopkins' formulation of partially coherent imaging are simulated.
High-speed Fourier ptychographic microscopy based on programmable annular illuminations (2018)

High-throughput quantitative phase imaging (QPI) is essential to cellular phenotypes characterization as it allows high-content cell analysis and avoids adverse effects of staining reagents on cellular viability and cell signaling. Among different approaches, Fourier ptychographic microscopy (FPM) is probably the most promising technique to realize high-throughput QPI by synthesizing a wide-field, high-resolution complex image from multiple angle-variably illuminated, low-resolution images. However, the large dataset requirement in conventional FPM significantly limits its imaging speed, resulting in low temporal throughput. Moreover, the underlying theoretical mechanism as well as optimum illumination scheme for high-accuracy phase imaging in FPM remains unclear. Herein, we report a high-speed FPM technique based on programmable annular illuminations (AIFPM). The optical-transfer-function (OTF) analysis of FPM reveals that the low-frequency phase information can only be correctly recovered if the LEDs are precisely located at the edge of the objective numerical aperture (NA) in the frequency space. By using only 4 low-resolution images corresponding to 4 tilted illuminations matching a 10×, 0.4 NA objective, we present the high-speed imaging results of in vitro Hela cells mitosis and apoptosis at a frame rate of 25 Hz with a full-pitch resolution of 655 nm at a wavelength of 525 nm (effective NA = 0.8) across a wide field-of-view (FOV) of 1.77 mm<sup>2</sup>, corresponding to a space-bandwidth-time product of 411 megapixels per second. Our work reveals an important capability of FPM towards high-speed high-throughput imaging of in vitro live cells, achieving video-rate QPI performance across a wide range of scales, both spatial and temporal.
Graphene Magnetic Field Sensors (2010)

Graphene extraordinary magnetoresistance (EMR) devices have been fabricated and characterized in varying magnetic fields at room temperature. The atomic thickness, high carrier mobility and high current carrying capabilities of graphene are ideally suited for the detection of nanoscale sized magnetic domains. The device sensitivity can reach 10 mV/Oe, larger than state of the art InAs 2DEG devices of comparable size and can be tuned by the electric field effect via a back gate or by imposing a biasing magnetic field.
SPACE: Secure Protocol for Address Book based Connection Establishment. (2006)

We present SPACE an application-level protocol for secure automatic ad-hoc connection-establishment between two devices based on their address book entries. Our protocol is based on the simple premise that if two people have each others contact details in their address books, they probably know and trust each other in some limited way and this can form a basis for a trust relationship between their devices, without additional user intervention. We show how our protocol is resistant to specific security attacks and can accommodate for privacy concerns. Existing connectionestablishment protocols for Bluetooth and IEEE 802.11 have known security flaws, and can be compromised using wellknown techniques and off-the-shelf hardware. In addition, these protocols require explicit user intervention, like entering a passkey. We believe that these factors have directly impacted the widespread application of ad-hoc networking in the context of mobile phones and other consumer devices. 1
Benign prostatic hyperplasia‐associated prostate‐specific antigen (BPSA) shows unique immunoreactivity with anti‐PSA monoclonal antibodies (2000)

We previously identified a modified molecular form of prostate-specific antigen that is significantly elevated in the nodular transition zone tissue of prostates with benign prostatic hyperplasia. This prostate-specific antigen form, designated BPSA, is inactive and contains clipped polypeptide bonds at amino-acid residues Lys145-146 and Lys182-183. BPSA is not elevated in prostate cancer tissues and may therefore be a prostate-specific antigen marker to better discriminate benign prostatic hyperplasia from early prostate cancer. In this work we characterize the immunoreactivity of BPSA in competition assays with prostate-specific antigen using anti-prostate-specific antigen mAb recognizing six different epitopes on the prostate-specific antigen molecule. One mAb showed > 50% loss of immunoreactivtiy with BPSA compared with prostate-specific antigen, while the binding of two mAbs was largely unaffected and three mAbs had intermediate reactivity. BPSA purified from prostate tissue and seminal plasma, as well as BPSA generated in vitro by mild trypsin-treatment were found to have a similar pattern of reactivity to the six mAbs. However, other forms of inactive seminal plasma prostate-specific antigen, either intact or clipped at Lys145 only, had immunoreactivity similar to total prostate-specific antigen. These results demonstrate that BPSA has unique immunological properties from other forms of prostate-specific antigen, which should allow the development of BPSA-specific mAbs for the study of benign prostatic hyperplasia. Measurement of BPSA levels in the serum may help discriminate benign prostatic hyperplasia from early prostate cancer.
A novel soft-switching power factor correction AC/DC converter (2002)

In this paper, a novel efficiency improved single stage soft switching AC/DC converter is presented. The converter utilizes the leakage inductance of the output transformer and the capacitance of the switches to provide zero voltage switching (ZVS) condition for the main switch. Based on a specific design example for a 100 W converter at 28 V DC and 500 kHz, a prototype has been built to experimentally verify the theoretical analysis. It is shown that with the additional voltage clamped auxiliary switch, the converter can operate in ZVS condition with keeping near unity power factor.
Polarization-independent actively tunable colour generation on imprinted plasmonic surfaces (2015)

Structural colour arising from nanostructured metallic surfaces offers many benefits compared to conventional pigmentation based display technologies, such as increased resolution and scalability of their optical response with structure dimensions. However, once these structures are fabricated their optical characteristics remain static, limiting their potential application. Here, by using a specially designed nanostructured plasmonic surface in conjunction with high birefringence liquid crystals, we demonstrate a tunable polarization-independent reflective surface where the colour of the surface is changed as a function of applied voltage. A large range of colour tunability is achieved over previous reports by utilizing an engineered surface which allows full liquid crystal reorientation while maximizing the overlap between plasmonic fields and liquid crystal. In combination with imprinted structures of varying periods, a full range of colours spanning the entire visible spectrum is achieved, paving the way towards dynamic pixels for reflective displays.
Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein–Protein Interaction (2021)

Inhibition of murine double minute 2 (MDM2)-p53 protein-protein interaction with small molecules has been shown to reactivate p53 and inhibit tumor growth. Here, we describe rational, structure-guided, design of novel isoindolinone-based MDM2 inhibitors. MDM2 X-ray crystallography, quantum mechanics ligand-based design, and metabolite identification all contributed toward the discovery of potent <i>in vitro</i> and <i>in vivo</i> inhibitors of the MDM2-p53 interaction with representative compounds inducing cytostasis in an SJSA-1 osteosarcoma xenograft model following once-daily oral administration.
Overcoming Metastable CO<sub>2</sub> Adsorption in a Bulky Diamine-Appended Metal–Organic Framework (2021)

Carbon capture at fossil fuel-fired power plants is a critical strategy to mitigate anthropogenic contributions to global warming, but widespread deployment of this technology is hindered by a lack of energy-efficient materials that can be optimized for CO<sub>2</sub> capture from a specific flue gas. As a result of their tunable, step-shaped CO<sub>2</sub> adsorption profiles, diamine-functionalized metal-organic frameworks (MOFs) of the form diamine-Mg<sub>2</sub>(dobpdc) (dobpdc<sup>4-</sup> = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate) are among the most promising materials for carbon capture applications. Here, we present a detailed investigation of dmen-Mg<sub>2</sub>(dobpdc) (dmen = 1,2-diamino-2-methylpropane), one of only two MOFs with an adsorption step near the optimal pressure for CO<sub>2</sub> capture from coal flue gas. While prior characterization suggested that this material only adsorbs CO<sub>2</sub> to half capacity (0.5 CO<sub>2</sub> per diamine) at 1 bar, we show that the half-capacity state is actually a metastable intermediate. Under appropriate conditions, the MOF adsorbs CO<sub>2</sub> to full capacity, but conversion from the half-capacity structure happens on a very slow time scale, rendering it inaccessible in traditional adsorption measurements. Data from solid-state magic angle spinning nuclear magnetic resonance spectroscopy, coupled with van der Waals-corrected density functional theory, indicate that ammonium carbamate chains formed at half capacity and full capacity adopt opposing configurations, and the need to convert between these states likely dictates the sluggish post-half-capacity uptake. By use of the more symmetric parent framework Mg<sub>2</sub>(pc-dobpdc) (pc-dobpdc<sup>4-</sup> = 3,3'-dioxidobiphenyl-4,4'-dicarboxylate), the metastable trap can be avoided and the full CO<sub>2</sub> capacity of dmen-Mg<sub>2</sub>(pc-dobpdc) accessed under conditions relevant for carbon capture from coal-fired power plants.
Integrated sensing and actuation of muscle-like actuators (2009)

The excellent overall performance and compliant nature of Dielectric Elastomer Actuators (DEAs) make them ideal candidates for artificial muscles. Natural muscle however is much more than just an actuator, it provides position feedback to the brain that is essential for the body to maintain balance and correct posture. If DEAs are to truly earn the moniker of "artificial muscles" they need to be able to reproduce, if not improve on, this functionality. Self-sensing DEAs are the ideal solution to this problem. This paper presents a system by which the capacitance of a DEA can be sensed while it is being actuated and used for feedback control. This system has been strongly influenced by the desire for portability i.e. designed for use in a battery operated microcontroller based system. It is capable of controlling multiple independent DEAs using a single high voltage power supply. These features are important developments for artificial muscle devices where accuracy and low mass are important e.g. a prosthetic hand or force-feedback surgical tools. A numerical model of the electrical behaviour of the DEA that incorporates arbitrary leakage currents and the impact of arbitrary variable capacitance has been created to model a DEA system. A robust capacitive self-sensing method that uses a slew-rate controlled Pulse Width Modulation (PWM) signal and compensates for the effects of leakage current and variable capacitance is presented. The numerical model is then used to compare the performance of this new method with an earlier method previously published by the authors.