gebhart/patrepeval huggingface dataset:
Supplementary material, methods and data from Dose and Schedule Determine Distinct Molecular Mechanisms Underlying the Efficacy of the p53–MDM2 Inhibitor HDM201 (2023)

<p>Supplementary material and methods include the description for the bioanalytical method for HDM201 detection in plasma and tumor, the human and mouse gene expression analysis in vitro and in vivo, the live-cell quantification of cleaved-caspase activation, the western blot analysis, the immunohistochemistry, the splinkerette PCR for the amplification of transposon integration sites and the tumor sequencing, mapping of insertion sequences to the mouse genome and identification of common integration site, additional information on the shRNA screen and the tumor models and supplementary references. Supplementary figures include: Ã¢â‚¬Â¢ Fig S1: the SJSA-1 inhibition growth curves when treated with HDM201 at different doses and for different times and the data for MOLM-3. Ã¢â‚¬Â¢ Fig S2: the cumulative percentage of cleaved-caspase-3/7 positive cells over the time, the GI50 of HDM201, CGM097 or nutlin-3a on SJSA-1 cells and the cellular apoptosis, as judged by AUC of cleaved-caspase-3/7 positive cells, induced by these compounds. Ã¢â‚¬Â¢ Fig S3: the PK profile in plasma and tumor of HDM201 in SJSA-1 tumors-bearing rat after p.o. and i.v. treatment, the Bcl-xl mRNA levels in tumors after HDM201 treatment, representative images of SJSA-1 tumors stained with p53 and cleaved-caspase 3 antibodies after HDM201 treatment and the individual data for the efficacy experiment in SJSA-1 tumor-bearing rats. Ã¢â‚¬Â¢ Fig S4: the PD of HDM201 in PB tumor bearing nude mice after single dose administration. Supplementary tables include: Ã¢â‚¬Â¢ Table S1: Biochemical profile of HDM201. Ã¢â‚¬Â¢ Table S2: List of cell lines tested for their sensitivity to HDM201 (n=291) Ã¢â‚¬Â¢ Table S3: Contingency table indicating association between sensitivity to HDM201 and TP53 wild-type status. Ã¢â‚¬Â¢ Table S4: List of cell lines tested for their sensitivity to both MDM2 knock-down by shRNA and HDM201 (n=261) Ã¢â‚¬Â¢ Table S5: Contingency table indicating association between sensitivity to HDM201 and sensitivity to MDM2 shRNA. Ã¢â‚¬Â¢ Table S6: List of significant rescuer and sensitizer genes following both HDM201 treatment types Ã¢â‚¬Â¢ Table S7: Pharmacokinetic parameters for HDM201 after p.o. and i.v. dosing in rat. Ã¢â‚¬Â¢ Table S8: Summary of primary PK parameters for HDM201 daily regimen after single dose (Day 1) in patients. Ã¢â‚¬Â¢ Table S9: Summary of primary PK parameters for HDM201 daily regimen on Day 14 in patients. Ã¢â‚¬Â¢ Table S10: Summary of primary PK parameters for HDM201 q3w regimen after single dose in patients.</p>
Patterned Protein Microarrays for Bacterial Detection (2002)

Patterned microarrays of antibodies were fabricated and tested for their ability to bind targeted bacteria. These arrays were used in a series of bacterial immunoassays to detect E. coli 0157:H7 and Renibacterium salmoninarum (RS). Microarrays were fabricated using microcontact printing (μCP) and characterized using scanning probe microscopy (SPM). The high-resolution SPM imaging showed that targeted bacteria had a higher binding selectivity to complementary antibody patterns than to unfunctionalized regions of the substrate. Additional studies indicated a significant reduction in binding of bacteria when the microarrays were exposed to nonspecific bacteria. These studies demonstrate how protein microarrays could be developed into useful platforms for sensing microorganisms.
High Stability Gain Structure and Filter Realization with less than 50 ppm/° C Temperature Variation with Ultra-low Power Consumption using Switched-capacitor and Sub-threshold Biasing (2018)

This paper presents the design of an ultra-low power subthreshold Gm stage where transconductance is very stable with process, temperature, and voltage variations. This technique is used to design a differential amplifier with constant gain and a second order biquad filter with constant cut off frequency. The amplifier gain achieves a small temperature coefficient of 48.6 ppm/°C and exhibits small sigma of 75 mdB with process. The second order biquad achieves temperature stability of 69 ppm/°C and a voltage coefficient of only 49 ppm/mV.
Upregulation of plasma C9 protein in gastric cancer patients (2010)

Gastric cancer is one of the leading causes of cancer-related deaths worldwide. Current biomarkers used in the clinic do not have sufficient sensitivity for gastric cancer detection. To discover new and better biomarkers, protein profiling on plasma samples from 25 normal, 15 early-stage and 21 late-stage cancer was performed using an iTRAQ-LC-MS/MS approach. The level of C9 protein was found to be significantly higher in gastric cancer compared with normal subjects. Immunoblotting data revealed a congruent trend with iTRAQ results. The discriminatory power of C9 between normal and cancer states was not due to inter-patient variations and was independent from gastritis and Helicobacter pylori status of the patients. C9 overexpression could also be detected in a panel of gastric cancer cell lines and their conditioned media compared with normal cells, implying that higher C9 levels in plasma of cancer patients could be attributed to the presence of gastric tumor. A subsequent blind test study on a total of 119 plasma samples showed that the sensitivity of C9 could be as high as 90% at a specificity of 74%. Hence, C9 is a potentially useful biomarker for gastric cancer detection.
Controlled Detritylation of Antisense Oligonucleotides (2003)

The last chemical step in standard oligonucleotide synthesis, the acid-catalyzed removal of 4,4‘-dimethoxytrityl (DMTr) protecting groups from the 5‘-terminus of oligonucleotides is accompanied by hydrolysis of purine nucleoside glycosidic linkages (depurination). A mild procedure for controlled DMTr removal using NaOAc (10 mM, pH 3.0) under a fixed set of conditions has been developed. The calculation of the reaction time is based on a t1/2 versus pH profile, specifically determined for each individual oligonucleotide sequence. The effect of various solvent components on the reaction kinetics has been evaluated. As a result, oligonucleotides with improved impurity profile are obtained consistently from laboratory scale to production scale.
<title>Eye-safe laser illuminators as less-than-lethal weapons</title> (1997)

Law enforcement and military forces are often faced with situations requiring less-than-lethal response options. Low- power, eye-safe laser illuminators have been shown to be effective, non-lethal weapons for a variety of law enforcement and other-than-war military applications. Through the effects of illumination, glare, and psychological impact; lasers can provide unequivocal warning, threat assessment based on reaction to the warning, hesitation, distraction, and reductions in combat and functional effectiveness. This paper discusses ongoing research and development by Science and Engineering Associates into laser illuminator concepts for civilian and military use. Topics include fundamental design and safety issues, laser diode requirements, and laser illuminator concepts, including a grenade shell laser system that converts a standard 40-mm grenade launcher into a laser illuminator.
Diagnostic test generation for small delay defect diagnosis (2010)

Small delay defect is becoming an important defect mechanism that leads to yield loss and performance hit in high performance VLSI designs. Small delay defects usually cause a small number of failures in production test patterns, and hence provide little evidence for logic fault diagnosis to isolate a defect. In this paper, we present a diagnostic test generation technique that targets creating more tester failures for a small delay defect in order to improve the diagnostic resolution. Experimental results show the effectiveness of the proposed technique.
Subcarrier multiplexing system with built-in dispersion reduction (1995)

Dispersion is effectively reduced in a 1550-nm subcarrier-multiplexed fiber link by using optical pre-filtering at the receiver. Recent experimental results demonstrate transmission of two 2.5 Gbit/s data channels over 220 km of ordinary single-mode fiber.
Recombinant alpha 1-antitrypsin Pittsburgh (Met 358----Arg) is a potent inhibitor of plasma kallikrein and activated factor XII fragment. (1986)

In normal plasma, the serine protease inhibitor alpha 1-antitrypsin (alpha 1-AT) plays little or no role in the control of plasma kallikrein or activated Factor XII fragment (Factor XIIf), this function being performed by Cl-inhibitor. Recently, an alpha 1-AT variant was described with a Met----Arg mutation at the reactive center P1 residue (position 358) which altered the specificity of inhibition from the Met- or Val-specific protease neutrophil elastase to thrombin, an Arg-specific protease. We have now examined the inhibition of plasma kallikrein and Factor XIIf, both Arg-specific enzymes, with recombinant alpha 1-AT(Met358----Arg) produced by an Escherichia coli strain carrying a mutated human alpha 1-AT gene. The engineered protein was a very efficient inhibitor of both enzymes. It was more effective than Cl-inhibitor by a factor of 4.1 for kallikrein and 11.5 for Factor XIIf. These results suggest that recombinant alpha 1-AT(Met358----Arg) has therapeutic potential for disease states where activation of the plasma kinin-forming system is observed, for example in hereditary angioedema or septic shock.
Cellular neural networks: applications (1988)

The theory of a novel class of information-processing systems, called cellular neural networks, which are capable of high-speed parallel signal processing, was presented in a previous paper (see ibid., vol.35, no.10, p.1257-72, 1988). A dynamic route approach for analyzing the local dynamics of this class of neural circuits is used to steer the system trajectories into various stable equilibrium configurations which map onto binary patterns to be recognized. Some applications of cellular neural networks to such areas as image processing and pattern recognition are demonstrated, albeit with only a crude circuit. In particular, examples of cellular neural networks which can be designed to recognize the key features of Chinese characters are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Broadband circularly polarized antennas for UHF SATCOM (2011)

Novel circularly polarized (CP) antenna configurations derived from Moxon type antenna (bent dipole element over a ground plane) for broadband UHF SATCOM applications. A sequence of topologies starting from a single vertical element to two vertical elements of the Moxon arms, then widened strip arm elements were studied. Further, arms were widened to bowtie structures with bents at 90°. for achieving broadband operation. Bowtie elements were further split and optimized at a certain angle to achieve wider bandwidth. The logic in this evolution was to obtain highest possible gain based on Fano-Chu limits, which suggests that higher gain can be achieved in an electrically small antenna with maximized metallization in the structure that fill the volume. Circular polarization is obtained by two Moxon based cross elements that are fed through a hybrid 90° quadrature coupler. For the antennas that are prototyped, return loss S11 measurements were performed, and gains are simulated using HFSS. For the band of 225-400 MHz, antenna gain varies between 8-12 dB, and S11 is measured to be below 10 dB. Fabricated antennas coupled to a hybrid coupler yielded excellent bandwidths, low cross-polarization and low back lobes on the finite ground planes.
3-Amino-3-demethoxyfortimicin A and the c-2 epimeric-2-amino-3-o-demethyl-2-deoxyfortimicins A. (1983)

Selective reactions of 3-O-demethyl-3-O-methanesulfonyl-4-N, 5-O-methylenefortimicin derivatives have been used as the key steps in the syntheses of 3-amino-3-demethoxyfortimicin A and the C-2 epimeric 2-amino-3-O-demethyl-2-deoxyfortimicins A. In vitro antibacterial activities of the new fortimicin derivatives are reported.
Toward a cure for chronic lymphocytic leukemia: an attack on multiple fronts (2013)

Recent developments in molecular therapeutics have armed us with powerful tools to mount a multifaceted offensive against CLL, of which BCL2-targeting agents are a critical element. A strategy consisting of initial debulking of leukemia cells in the periphery (chemoimmunotherapy), fostering exit of neoplastic B cells from the protective environment (B-cell receptor-targeting agents) and killing cells in the protective niche (drug combinations) is poised to dramatically reduce residual disease, prolong progression-free survival, increase overall survival and ultimately improve the lives of millions of CLL patients. We believe it is time to start using all these drugs in rationally designed combination trials.
Design and Performance Evaluation of an Implantable Ultrasonic Networking Platform for the Internet of Medical Things (2020)

Wireless networks of electronically controlled implantable medical sensors and actuators will be the basis of many innovative and potentially revolutionary therapies. The biggest obstacle in realizing this vision of networked implants is posed by the dielectric nature of the human body, which strongly attenuates radio-frequency (RF) electromagnetic waves. In this paper we present the first hardware and software architecture of an Internet of Medical Things (IoMT) platform with ultrasonic connectivity for intra-body communications. This platform can be used as a basis for building future IoT-ready medical implants and wearable devices. We demonstrate that ultrasonic waves can be efficiently generated and received with low-power mm-sized components, and that despite the conversion loss introduced by ultrasonic transducers, the attenuation of 2.4 GHz RF is substantially greater than ultrasound, e.g., ultrasound attenuates 70 dB less than RF at distances over 10 cm. We show that the proposed IoMT platform requires significantly less transmission power than 2.4 GHz RF with equal reliability, e.g., 35 dBm less at distances over 12 cm with 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> Bit Error Rate (BER) thus enabling a lower energy per bit and a longer device lifetime. Finally, we experimentally establish 2.4 GHz RF links do not function at distances greater than 12 cm, while ultrasonic links achieve a reliability of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> BER up to a distance of 20 cm with less than 0 dBm transmission power.
Angular Dependence of Reversible Transverse Susceptibility in Magnetic Nanoparticles (2006)

We present angular dependence measurements of reversible transverse susceptibility for two different single magnetic domain nanoparticle systems. A modified alternating gradient magnetometer was used for the measurements. This study supplements previous reversible transverse susceptibility measurements, usually performed at a limited number of angles by inductive techniques. The angular dependence measurements reveal several features in reversible transverse susceptibility of oriented magnetic nanoparticles that have previously gone undetected. The theoretically predicted peaks at the coercive magnetic field, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$H_C$</tex> , appear only at certain narrow, primarily nonorthogonal angular orientations. In addition, we find that the magnitude of the reversible transverse susceptibility has a maximum at angles different from both the easy and hard nanoparticle axes, which might have important consequences for use of such nanoparticles in enhancement of magnetic resonance signals.
Image segmentation using joint spatial-intensity-shape features: application to CT lung nodule segmentation (2009)

Automatic segmentation of medical images is a challenging problem due to the complexity and variability of human anatomy, poor contrast of the object being segmented, and noise resulting from the image acquisition process. This paper presents a novel feature-guided method for the segmentation of 3D medical lesions. The proposed algorithm combines 1) a volumetric shape feature (shape index) based on high-order partial derivatives; 2) mean shift clustering in a joint spatial-intensity-shape (JSIS) feature space; and 3) a modified expectation-maximization (MEM) algorithm on the mean shift mode map to merge the neighboring regions (modes). In such a scenario, the volumetric shape feature is integrated into the process of the segmentation algorithm. The joint spatial-intensity-shape features provide rich information for the segmentation of the anatomic structures or lesions (tumors). The proposed method has been evaluated on a clinical dataset of thoracic CT scans that contains 68 nodules. A volume overlap ratio between each segmented nodule and the ground truth annotation is calculated. Using the proposed method, the mean overlap ratio over all the nodules is 0.80. On visual inspection and using a quantitative evaluation, the experimental results demonstrate the potential of the proposed method. It can properly segment a variety of nodules including juxta-vascular and juxta-pleural nodules, which are challenging for conventional methods due to the high similarity of intensities between the nodules and their adjacent tissues. This approach could also be applied to lesion segmentation in other anatomies, such as polyps in the colon.
Hybrid Power Management (HPM) Program Resulted in Several New Applications (2003)

Hybrid Power Management (HPM) is the innovative integration of diverse, state-of-the-art power devices in an optimal configuration for space and terrestrial applications. The appropriate application and control of the various power devices significantly improves overall system performance and efficiency. The advanced power devices include ultracapacitors, fuel cells, and photovoltaics. HPM has extremely wide potential with applications from nanowatts to megawatts. Applications include power generation, transportation systems, biotechnology systems, and space power systems. HPM has the potential to significantly alleviate global energy concerns, improve the environment, and stimulate the economy.
.beta.-glucosidase 5 (BGL5) compositions (2010)

The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.
Plasma and Recombinant Thrombin-activable Fibrinolysis Inhibitor (TAFI) and Activated TAFI Compared with Respect to Glycosylation, Thrombin/Thrombomodulin-dependent Activation, Thermal Stability, and Enzymatic Properties (1998)

Thrombin-activable fibrinolysis inhibitor (TAFI) is a human plasma zymogen similar to pancreatic pro-carboxypeptidase B. Cleavage of the zymogen by thrombin/thrombomodulin generates the enzyme, activated TAFI (TAFIa), which retards fibrin clot lysis in vitro and likely modulates fibrinolysis in vivo. In the present work we stably expressed recombinant TAFI in baby hamster kidney cells, purified it to homogeneity from conditioned serum-free medium, and compared it to plasma TAFI (pTAFI) with respect to glycosylation and kinetics of activation by thrombin/thrombomodulin. Although rTAFI is glycosylated somewhat differently than pTAFI, cleavage products with thrombin/thrombomodulin are indistinguishable, and parameters of activation kinetics are very similar with kcat = 0.55 s-1, K(m) = 0.54 microM, and Kd = 6.0 nM for rTAFI and kcat = 0.61 s-1, K(m) = 0.55 microM, and Kd = 6.6 nM for pTAFI. The respective TAFIa species also were prepared and compared with respect to thermal stability and enzymatic properties, including inhibition of fibrinolysis. The half-life of both enzymes at 37 degrees C is about 10 min, and the decay of enzymatic activity is associated with a quenching (to approximately 62% of the initial value at 60 min) of the intrinsic fluorescence of the enzyme. Stability was highly temperature-dependent, which, according to transition state theory, indicates both high enthalpy and entropy changes associated with inactivation (delta Ho++ approximately equal to 45 kcal/mol and delta So++ approximately equal to 80 cal/mol/K). Both species of TAFIa are stabilized by the competitive inhibitors 2-guanidinoethylmercaptosuccinic acid and epsilon-aminocaproic acid. rTAFIa and pTAFIa are very similar with respect to kinetics of cleavage of small substrates, susceptibility to inhibitors, and ability to retard both tPA-induced and plasmin-mediated fibrinolysis. These studies provide new insights into the thermal instability of TAFIa, a property which could be a significant regulator of its activity in vivo; in addition, they show that rTAFI and rTAFIa are excellent surrogates for the natural plasma-derived species, a necessary prerequisite for future studies of structure and function by site-specific mutagenesis.
Ternary pseudorandom encoding of Fourier transform holograms (1999)

Pseudorandom encoding is a statistical method for designing Fourier transform holograms by mapping ideal complex-valued modulations onto spatial light modulators that are not fully complex. These algorithms are notable because their computational overhead is low and because the space-bandwidth product of the encoded signal is identical to the number of modulator pixels. All previous pseudorandom-encoding algorithms were developed for analog modulators. A less restrictive algorithm for quantized modulators is derived that permits fully complex ranges to be encoded with as few as three noncollinear modulation values that are separated by more than 180 degrees on the complex plane.
Stator design of a 2DOF traveling-wave rotary piezoelectric motor (2009)

A two degree-of-freedom motor system constructed with two sets of piezoelectric actuators mutually perpendicular around a spherical surface is designed. Each set is employed with a series of piezoelectric actuators driven by voltage with appropriate phase difference on the neighboring actuators so that traveling wave is generated. Such a system can be used for robot (eyes or joints), flight guide control system (seeker), and medical measurement for endoscope and magnetic resonance imaging (MRI), etc. Curved piezoelectric actuator and spherical stator design, etc. are the focus in this article. Via ANSYS and analytical computation, resolution and angular velocity are estimated for the present stator structure.