gebhart/patrepeval huggingface dataset:
Anti-metastatic Inhibitors of Lysyl Oxidase (LOX): Design and Structure–Activity Relationships (2019)

Lysyl oxidase (LOX) is a secreted copper-dependent amine oxidase that cross-links collagens and elastin in the extracellular matrix and is a critical mediator of tumor growth and metastatic spread. LOX is a target for cancer therapy, and thus the search for therapeutic agents against LOX has been widely sought. We report herein the medicinal chemistry discovery of a series of LOX inhibitors bearing an aminomethylenethiophene (AMT) scaffold. High-throughput screening provided the initial hits. Structure-activity relationship (SAR) studies led to the discovery of AMT inhibitors with sub-micromolar half-maximal inhibitory concentrations (IC<sub>50</sub>) in a LOX enzyme activity assay. Further SAR optimization yielded the orally bioavailable LOX inhibitor CCT365623 with good anti-LOX potency, selectivity, pharmacokinetic properties, as well as anti-metastatic efficacy.
Evaluation of a thoracic elastic registration method using anatomical constraints in oncology (2002)

The aim of our work is to improve data analysis in thoracic oncology applications by means of non-rigid registration of CT and PET images. A mutual information-driven transformation using B-spline free-form deformations performs the alignment of the image volumes. Special constraints relying on hierarchically identifying corresponding structures in both modalities have been added to guarantee the convergence towards an optimal registration.
Estimation of algae concentration in water solutions using spectrophotometry measurements and absorbance first derivative (2016)

The monitoring and detection of algae in wastewater and surface solutions is important in controlling the quality of surface water and wastewater, yet there is currently no quick and simple method to achieve this. The present work illustrates a new method to determine the concentration of algae in different water samples using spectrophotometric measurements and the absorbance first derivative. The relationship between algal concentration and absorbance for three types of water solution (distilled, surface, and wastewater) was established in the 200-800 nm wavelength range, and the effect of using the absorbance first derivative on improving algal concentration detection limit was estimated. In the distilled water samples, the lowest detection limits, using absorbance measurement and the absorbance first derivative, were 0.53 mg TVS/L and 0.47 mg TVS/L, respectively. In samples collected from surface water and wastewater treatment plants, the detection limits varied between 0.56 to 3.84 mg TVS/L depending on the NOM in the water sample. Higher detection limits were possible with the chlorophyll extraction methods.
A Study of the Mechanism of Inhibition of Fibrinolysis by Activated Thrombin-activable Fibrinolysis Inhibitor (1998)

TAFI (thrombin-activable fibrinolysis inhibitor) is a recently described plasma zymogen that, when exposed to the thrombin-thrombomodulin complex, is converted by proteolysis at Arg92 to a basic carboxypeptidase that inhibits fibrinolysis (TAFIa). The studies described here were undertaken to elucidate the molecular basis for the inhibition of fibrinolysis. When TAFIa is included in a clot undergoing fibrinolysis induced by tissue plasminogen activator and plasminogen, the time to achieve lysis is prolonged, and free arginine and lysine are released over time. In addition, TAFIa prevents a 2.5-fold increase in the rate constant for plasminogen activation which occurs when fibrin is modified by plasmin in the early course of fibrin degradation. The effect is specific for the Glu- form of plasminogen. TAFIa prevents or at least attenuates positive feedback expressed through Lys-plasminogen formation during the process of fibrinolysis initiated by tissue plasminogen activator and plasminogen. TAFIa also inhibits plasmin activity in a clot and prolongs fibrinolysis initiated with plasmin. We conclude that TAFIa suppresses fibrinolysis by removing COOH-terminal lysine and arginine residues from fibrin, thereby reducing its cofactor functions in both plasminogen activation and the positive feedback conversion of Glu-plasminogen to Lys-plasminogen. At relatively elevated concentrations, it also directly inhibits plasmin.
New water disinfection system using UVA light-emitting diodes (2007)

We newly developed UVA irradiation system and found that UVA alone was able to disinfect the water efficiently. This will become a useful disinfection system.
Abstract LB-198: Discovery of a novel anti-CD47 antibody with anti-cancer therapeutic potential and minimal RBC binding (2019)

Abstract CD47 is a widely expressed cell surface protein that functions as a checkpoint in the immune system. When overexpressed on tumor cells, CD47 can bind SIRPα on myeloid cells, leading to suppression of tumor cell phagocytosis and other innate immune functions. Thus, targeting CD47 is becoming a hot spot of cancer immunotherapy. However, its ubiquitous expression on circulating cells, especially RBCs and hepatocyte, poses a safety concern in CD47 targeted therapy.In this study, we discovered a novel anti-CD47 antibody, GenSci-059. GenSci-059 exhibited equivalent anticancer effects with Hu5F9-G4, a humanized anti-CD47 antibody in clinical trial, evidenced by inducing significant phagocytosis of tumor cells in vitro and prolonging the survival of xenografted mice. Especially for non-Hodgkin’s lymphoma (NHL), GenSci-059 showed almost 100% tumor growth inhibition with 100% response rate in the patient-derived xenograft (PDX) NHL models tested. Remarkably, GenSci-059 did not bind to human RBCs and induced minimal RBC phagocytosis by in vitro assay. In cynomolgus monkeys, GenSci-059 was well tolerated at doses up to 300 mg/kg, and did not produce adverse effects including anemia and hepatic dysfunction, which are common side effects of other anti-CD47 therapies. Overall, GenSci-059 is a promising candidate with great potential and safety profile for cancer immunotherapy. Citation Format: Xiao Feng, Dawei Sun, Suofu Qin, Lei Jin, Tao Wang, Hongbo Yan. Discovery of a novel anti-CD47 antibody with anti-cancer therapeutic potential and minimal RBC binding [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-198.
Reorientable Spin Direction for Spin Current Produced by the Anomalous Hall Effect (2017)

We show experimentally that the spin direction of the spin current generated by spin-orbit interactions within a ferromagnetic layer can be reoriented by turning the magnetization direction of this layer. We do this by measuring the field-like component of spin-orbit torque generated by an exchange-biased FeGd thin film and acting on a nearby CoFeB layer. The relative angle of the CoFeB and FeGd magnetic moments is varied by applying an external magnetic field. We find that the resulting torque is in good agreement with predictions that the spin current generated by the anomalous Hall effect from the FeGd layer depends on the FeGd magnetization direction $\hat{m}_{FeGd}$ according to $\vecσ\propto\left ( \hat{y}\cdot \hat{m}_{FeGd} \right )\hat{m}_{FeGd}$, where $\hat{y}$ is the in-plane direction perpendicular to the applied charge current. Because of this angular dependence, the spin-orbit torque arising from the anomalous Hall effect can be non-zero in a sample geometry for which the spin Hall torque generated by non-magnetic materials is identically zero.
Design and fabrication of radially symmetric computer generated holograms (1991)

High efficiency radially symmetric computer generated holograms have been designed and fabricated using an iterative encoding method. This method, termed radially symmetric iterative discrete on-axis (RSIDO), is similar to the previously reported IDO encoding method. 1 The RSIDO method was developed for on-axis systems and takes into account the discrete phase levels and phase transitions introduced by fabrication. Computation time is reduced by taking advantage of radial symmetry. This method has been used to achieve diffraction efficiencies of >80% for low f /No. elements. It has also been used to produce holographic optical elements with minimal chromatic aberrations for spectral bandwidths as large as 30 nm. An eight-phase level F /1 holographic lens was fabricated and tested.
Restoration of Controllable Hysteresis in Partially Depleted SOI CMOS Schmitt Trigger Circuits (2004)

This paper presents a new circuit technique to alleviate the uncontrollable floating-body-induced hysteretic component present in the transfer characteristics of voltage-mode CMOS Schmitt trigger circuits in a partially depleted silicon-on-insulator technology. This technique integrates a successive switching threshold shift mechanism with the systematic body contact scheme, resulting in improved noise immunity and well-defined hysteresis behavior for the Schmitt trigger circuit that is suitable for use as a low-noise receiver, level shifter, waveform-reshaping circuit, and delay element in very large-scale integrated applications.
Bringing mobile into meetings (2016)

Most teleconferencing tools treat users in distributed meetings monolithically: all participants are meant to be interconnected in more-or-less the same manner. In practice, people connect to meetings in different contexts, sometimes sitting in front of a laptop or tablet giving their full attention, but at other times mobile and concurrently involved in other tasks or as a liminal participant in a larger group meeting. In this paper, we present the design and evaluation of two applications, MixMeetWear and MixMeetMate, to help users in non-standard contexts flexibly participate in meetings.
Automatic linearity and frequency response tests with built-in pattern generator and analyzer (2006)

We present a built-in self-test (BIST) approach based on a direct digital synthesizer (DDS) for functionality testing of analog circuitry in mixed-signal systems. A main contribution of this paper is the BIST-based hardware implementation and measurement of amplifier linearity (IP3) and frequency response, including both phase and gain. The approach has been implemented in Verilog and synthesized into a field-programmable gate array (FPGA), where it was used for functional testing of an actual device under test (DUT) and compared to simulation results.
Reduced narrow-width effects in a scaled local oxidation of silicon process (1985)

The reduction of narrow-width effects in VLSI transistors is of great importance if small-geometry devices are to be of real use in advanced circuits. These effects are caused by boron encroaching into the transistor channel from underneath the field isolation oxide. In this paper we describe the results of experiments to reduce this encroachment by the use of high-pressure oxidation. We show that the substitution of this process into a VLSI process flow, for the field oxidation step, allows the channel-stop implant dose to be significantly reduced (50%) without degradation of interdevice isolation.
Potential new photosensitizers for photodynamic therapy (1990)

In continuation of the effort to search for an ideal photosensitizer, two groups of potential new photosensitizers were synthesized and investigated for their photodynamic actions against tumors in mice. These were derivatives of methyl pheophorbide-a and of silicon naphthalocyanine. Of the former group, the 2 (1-0--hexyl) ethyl-desvinyl--methyl pheophorbide-a, or }IEDP, was the most active sensitizer. HEDP could be readily produced in large quantities and showed an optimum photodynamic action at 665 mu where it absorbs strongly. Also HEDP was cleared from the mouse skin within 4 days after administration, thus possibly alleviating the long-term phototoxic side-effects observed in Photofrin-based therapy. Of the second group of photosensitizers, the bis (dimethyl hydroxypropylsiloxy) silicon naphthalocyanine (HPSiNc) , and the corresponding acetoxy derivative (APSiNc) were of particular interest. At a drug-light dose of 1.0 mg/kg-135 J/cm2 (delivered by a laser at 772 nm), they showed antitumor activities comparable to that of PhotofrinTM. Further studies on these photosensitizers are warranted.
The ORF3 Protein of Porcine Circovirus Type 2 Interacts with Porcine Ubiquitin E3 Ligase Pirh2 and Facilitates p53 Expression in Viral Infection (2007)

Porcine circovirus type 2 (PCV2) is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome. We previously showed that a newly identified protein, ORF3, plays a major role in virus-induced apoptosis and is involved in viral pathogenesis in vitro and in vivo. To characterize the role of the ORF3 protein in modulation of cellular function, a yeast two-hybrid system was used to screen a porcine cDNA library to find its interacting partner. We have isolated and characterized pPirh2 (for "porcine p53-induced RING-H2"), an E3 ubiquitin ligase, which specifically interacts with the ORF3 protein of PCV2. This interaction was further confirmed when the ORF3 protein coimmunoprecipitated with and colocalized to pPirh2 in PK15 cells. The ORF3 protein has been found to interact with the p53 binding domain of pPirh2 in yeast cells. Expression of the protein results in less pPirh2 expression in PCV2-infected cells. Furthermore, increases in p53 expression were observed in PCV2-infected and ORF3 (alone)-transfected cells. Phosphorylation of p53 at Ser-46, which is related to p53-induced apoptosis, was also time-dependently activated in PCV-infected and ORF3-transfected cells. Taken together, our results show that the PCV2 ORF3 protein specifically interacts with pPirh2 and inhibits its stabilization; this may lead to increasing p53 expression, resulting in apoptosis.
Characterization of Prostate Microstructure Using Water Diffusion and NMR Relaxation (2018)

For many pathologies, early structural tissue changes occur at the cellular level, on the scale of micrometers or tens of micrometers. Magnetic resonance imaging (MRI) is a powerful non-invasive imaging tool used for medical diagnosis, but its clinical hardware is incapable of reaching the cellular length scale directly. In spite of this limitation, microscopic tissue changes in pathology can potentially be captured indirectly, from macroscopic imaging characteristics, by studying water diffusion. Here we focus on water diffusion and NMR relaxation in the human prostate, a highly heterogeneous organ at the cellular level. We present a physical picture of water diffusion and NMR relaxation in the prostate tissue, that is comprised of a densely-packed cellular compartment (composed of stroma and epithelium), and a luminal compartment with almost unrestricted water diffusion. Transverse NMR relaxation is used to identify fast and slow <i>T</i> <sub><i>2</i></sub> components, corresponding to these tissue compartments, and to disentangle the luminal and cellular compartment contributions to the temporal evolution of the overall water diffusion coefficient. Diffusion in the luminal compartment falls into the short-time surface-to-volume (<i>S/V</i>) limit, indicating that only a small fraction of water molecules has time to encounter the luminal walls of healthy tissue; from the <i>S/V</i> ratio, the average lumen diameter averaged over three young healthy subjects is measured to be 217.7±188.7 μm. Conversely, the diffusion in the cellular compartment is highly restricted and anisotropic, consistent with the fibrous character of the stromal tissue. Diffusion transverse to these fibers is well described by the random permeable barrier model (RPBM), as confirmed by the dynamical exponent <i>ϑ</i> = 1/2 for approaching the long-time limit of diffusion, and the corresponding structural exponent <i>p</i> = -1 in histology. The RPBM-derived fiber diameter and membrane permeability were 19.8±8.1 μm and 0.044±0.045 μm/ms, respectively, in agreement with known values from tissue histology and membrane biophysics. Lastly, we revisited 38 prostate cancer cases from a recently published study, and found the same dynamical exponent <i>ϑ</i> = 1/2 of diffusion in tumors and benign regions. Our results suggest that a multi-parametric MRI acquisition combined with biophysical modeling may be a powerful non-invasive complement to prostate cancer grading, potentially foregoing biopsies.
Microbial battery for efficient energy recovery (2013)

By harnessing the oxidative power of microorganisms, energy can be recovered from reservoirs of less-concentrated organic matter, such as marine sediment, wastewater, and waste biomass. Left unmanaged, these reservoirs can become eutrophic dead zones and sites of greenhouse gas generation. Here, we introduce a unique means of energy recovery from these reservoirs-a microbial battery (MB) consisting of an anode colonized by microorganisms and a reoxidizable solid-state cathode. The MB has a single-chamber configuration and does not contain ion-exchange membranes. Bench-scale MB prototypes were constructed from commercially available materials using glucose or domestic wastewater as electron donor and silver oxide as a coupled solid-state oxidant electrode. The MB achieved an efficiency of electrical energy conversion of 49% based on the combustion enthalpy of the organic matter consumed or 44% based on the organic matter added. Electrochemical reoxidation of the solid-state electrode decreased net efficiency to about 30%. This net efficiency of energy recovery (unoptimized) is comparable to methane fermentation with combined heat and power.
Synthesis of Difluorocatharanthine and Investigation of its Biomimetic Coupling with Vindoline (2012)

International audience
Oscillation regimes of a solid-state ring laser with active beat-note stabilization: From a chaotic device to a ring-laser gyroscope (2007)

We report an experimental and theoretical study of a rotating diode-pumped Nd-YAG ring laser with active beat-note stabilization. Our experimental setup is described in the usual Maxwell-Bloch formalism. We analytically derive a stability condition and some frequency response characteristics for the solid-state ring-laser gyroscope, illustrating the important role of mode coupling effects on the dynamics of such a device. Experimental data are presented and compared with the theory on the basis of realistic laser parameters, showing very good agreement. Our results illustrate the duality between the very rich nonlinear dynamics of the diode-pumped solid-state ring laser (including chaotic behavior) and the possibility to obtain a very stable beat note, resulting in a potentially new kind of rotation sensor.
Heterogeneously integrated silicon lasers for optical interconnects (2015)

Aurrion heterogeneous platform combines best-in-class active III-V materials for lasers, modulators and photodetectors with advanced passive components on a single chip. By leveraging existing silicon industry infrastructure for manufacturing and packaging, low-cost photonics can be closely integrated with electronics in system-in-package solutions. Such solutions are well suited to meet the demands of next generation optical interconnects.
Improved Oxidative Stability of Biodiesel Fuels: Antioxidant Research and Development (2011)

Biodiesel is a domestic, renewable fuel that is gaining wide acceptance, especially in Europe. When blended with conventional petroleum diesel, biodiesel reduces hydrocarbon, particulate and carbon monoxide emissions, while having minimal to no effect on NOx. It also improves lubricity, lowers sulfur, and has a high cetane number. The promise of biodiesel is tremendous, but some significant obstacles remain to its complete acceptance by diesel engine manufacturers, most significantly with respect to oxidative stability. This proposed project will investigate the factors associated with biodiesel oxidative stability, including natural and synthetic antioxidants, storage and processing conditions. Results of this project will provide much needed guidelines to industry with regards to storage conditions and antioxidant additive levels. Additionally, biodiesel production changes will be recommended which will optimize the preservation of natural antioxidant levels in the fuel. Finally, factors required for the development of a user-level sensor for biodiesel oxidative stability will be quantified.
Computer control of gas metal arc welding (1988)

The state of an arc weld is determined by the composition of the weld and base metal and its thermomechanical history. The composition of the deposited weld metal depends primarily on the amount of filler metal dilution which occurs. The heat input to the weld, comprising pre-heat and process heat, is the controlling factor in the thermal cycle to which the material responds metallurgically, to produce a specific set of weld properties. Thus, control of the arc welding process should focus on rational specification and real-time control of the heat and mass input to the weld. A process control model has been developed for the gas metal arc welding (GMAW) process using the state variables, time-domain method. The governing equations have been solved for the process parameters as functions of the desired heat input (in terms of heat per unit length) and mass input (in terms of transverse reinforcement area) to the weld. The resulting nonlinear model has been used with a simple proportional controller with deadband and variable coefficients to control the weld heat input and reinforcement area independently. A welding machine has been developed for this work, consisting of a computer-controlled welding head, positioning table, and operator panel,more » which is the front end for a conventional 300 A constant voltage power supply. Software for the system is written in the HPL language. System components communicate over an IEEE-488 bus. 9 refs., 6 figs.« less
cw midinfrared “W” diode and interband cascade lasers (2006)

We studied the I-V characteristics, lasing thresholds, and wall plug efficiencies of type-II “W” mid-IR diode lasers from 16 different wafers. At T=90K, the wall plug efficiency for a 1-mm-long gain-guided device was &gt;10% and the slope efficiency was 142mW∕A (38% external quantum efficiency). When a 22-μm-wide ridge was lithographically defined on a five-period W with ap-GaSb etch stop layer, the maximum cw operating temperature increased to 230K. We also investigated ten-stage interband cascade lasers containing W active quantum wells. While the low-temperature threshold current densities were somewhat higher than in the W diodes, at higher temperatures the pulsed thresholds were slightly lower. The threshold voltage was only ≈0.1V larger than the photon energy multiplied by the number of stages, corresponding to a voltage efficiency of &gt;96%, while the differential series resistance-area product above threshold was as low as 0.21mΩcm2 at 100K. At T=78K, the cw slope efficiency was 0.48mW∕A (126% external quantum efficiency), and a maximum cw power of 514mW was produced by an epi-side-up-mounted 2-mm-long laser cavity with uncoated facets.