gebhart/patrepeval huggingface dataset:
Human prostate cancer model: Roles of growth factors and extracellular matrices (1992)

A human prostate cancer model was established by inoculating a prostate specific antigen (PSA)-producing LNCaP cell line with either prostate or bone fibroblasts. Alternatively, this human prostate cancer model can also be established by inoculating LNCaP cells with growth factor(s) (GFs) and extracellular matrix (ECM) immobilized on Gelfoam. The resulting LNCaP tumors were used to evaluate PSA production and excretion in athymic hosts. This model was also employed to examine the biochemical nature of mesenchymal cell-derived growth-promoting protein(s) and to assess the efficacy of potential chemotherapeutic agents. Because of the propensity of human prostate cancer to metastasize to the bone, this study defined a 1.0 M NaCl-eluted fraction, MS1, from the conditioned medium of a bone stromal cell line (MS) by heparin-affinity column chromatography. The growth-promoting activity was assayed both in vivo (e.g., tumor formation) and in vitro (e.g., soft agar colony formation). We found that the growth-promoting activity was trypsin- and heat-sensitive, and partially degraded by acid and dithiothreitol. Immunochemical studies indicated that the polyclonal antibody raised against MS1 blocked the growth-promoting effect elicited by the bone-conditioned media. This growth-promoting factor was found to be immunochemically dissimilar to KGF, HGF, and bFGF. However, addition of bFGF, HGF and NGF, but not aFGF, TGF beta, IGF1, IGF2, PDGF, EGF, TGF alpha and KGF, stimulated anchorage-independent growth of prostate cells, a condition closely parallel to tumor formation in vivo. We found that the MS1 fraction also contained fibronectin and tenascin but not laminin or collagen IV.(ABSTRACT TRUNCATED AT 250 WORDS)
Countercurrent Chromatography of an Anti-trypanosomal Factor from <i>Pseudomonas Fluorescens</i> (1988)

Abstract Countercurrent chromatography (CCC) employing the Ito multilayer coiled column was an effective procedure for the purification of an anti-trypanosomal factor (ATF-II) from Pseudomonas fluorescens. Two types of anti-trypanosomal activity were observed, i.e., lysis, and paralysis and killing of the parasites without lysis. High performance liquid chromatography (HPLC) was very useful for the differentiation and further purification of these fractions, and bioassays performed with Trypanosoma equiperdum, indicated the characteristic pathologic changes produced by these components. The lipopolysaccharide content of the purified fractions was markedly reduced and indicated an additional advantage of CCC in future studies with experimental infections with T. cruzi.
NVP-DPP728 (1-[[[2-[(5-Cyanopyridin-2-yl)amino]ethyl]amino]acetyl]-2-cyano-(<i>S</i>)-pyrrolidine), a Slow-Binding Inhibitor of Dipeptidyl Peptidase IV (1999)

Inhibition of dipeptidyl peptidase IV (DPP-IV) has been proposed recently as a therapeutic approach to the treatment of type 2 diabetes. N-Substituted-glycyl-2-cyanopyrrolidide compounds, typified by NVP-DPP728 (1-[[[2-[(5-cyanopyridin-2-yl)amino]ethyl]amino]acetyl]-2-cyano-(S )-p yrrolidine), inhibit degradation of glucagon-like peptide-1 (GLP-1) and thereby potentiate insulin release in response to glucose-containing meals. In the present study NVP-DPP728 was found to inhibit human DPP-IV amidolytic activity with a K(i) of 11 nM, a k(on) value of 1.3 x 10(5) M(-)(1) s(-)(1), and a k(off) of 1.3 x 10(-)(3) s(-)(1). Purified bovine kidney DPP-IV bound 1 mol/mol [(14)C]-NVP-DPP728 with high affinity (12 nM K(d)). The dissociation constant, k(off), was 1.0 x 10(-)(3) and 1.6 x 10(-)(3) s(-)(1) in the presence of 0 and 200 microM H-Gly-Pro-AMC, respectively (dissociation t(1/2) approximately 10 min). Through kinetic evaluation of DPP-IV inhibition by the D-antipode, des-cyano, and amide analogues of NVP-DPP728, it was determined that the nitrile functionality at the 2-pyrrolidine position is required, in the L-configuration, for maximal activity (K(i) of 11 nM vs K(i) values of 5.6 to >300 microM for the other analogues tested). Surprisingly, it was found that the D-antipode, despite being approximately 500-fold less potent than NVP-DPP728, displayed identical dissociation kinetics (k(off) of 1.5 x 10(-)(3) s(-)(1)). NVP-DPP728 inhibited DPP-IV in a manner consistent with a two-step inhibition mechanism. Taken together, these data suggest that NVP-DPP728 inhibits DPP-IV through formation of a novel, reversible, nitrile-dependent complex with transition state characteristics.
Characterization of Inhibitory Anti-Duffy Binding Protein II Immunity: Approach to Plasmodium vivax Vaccine Development in Thailand (2012)

Plasmodium vivax Duffy binding protein region II (DBPII) is an important vaccine candidate for antibody-mediated immunity against vivax malaria. A significant challenge for vaccine development of DBPII is its highly polymorphic nature that alters sensitivity to neutralizing antibody responses. Here, we aim to characterize naturally-acquired neutralizing antibodies against DBPII in individual Thai residents to give insight into P. vivax vaccine development in Thailand. Anti-DBPII IgG significantly increased in acute vivax infections compared to uninfected residents and naive controls. Antibody titers and functional anti-DBPII inhibition varied widely and there was no association between titer and inhibition activity. Most high titer plasmas had only a moderate to no functional inhibitory effect on DBP binding to erythrocytes, indicating the protective immunity against DBPII binding is strain specific. Only 5 of 54 samples were highly inhibitory against DBP erythrocyte-binding function. Previously identified target epitopes of inhibitory anti-DBPPII IgG (H1, H2 and H3) were localized to the dimer interface that forms the DARC binding pocket. Amino acid polymorphisms (monomorphic or dimorphic) in H1 and H3 protective epitopes change sensitivity of immune inhibition by alteration of neutralizing antibody recognition. The present study indicates Thai variant H1.T1 (R308S), H3.T1 (D384G) and H3.T3 (K386N) are the most important variants for a DBPII candidate vaccine needed to protect P. vivax in Thai residents.
User-initialized active contour segmentation and golden-angle real-time cardiovascular magnetic resonance enable accurate assessment of LV function in patients with sinus rhythm and arrhythmias (2015)

User-initialized active contours and golden-angle real-time radial CMR can be used to determine time-varying LV function in patients. These methods will be very useful for the assessment of LV function in patients with frequent arrhythmias.
Sulfide glass solid-state electrolyte separators for Li metal batteries: using an interlayer to increase rate performance and reduce stack pressure (2022)

A range of sulfide glass electrolyte compositions were found to be insoluble in ether-based solvents. A critical current density of 3 mA cm −2 was achieved with a 0.1 MPa stack pressure and a thin ether-based liquid electrolyte interlayer.
Evolution of a Practical Total Synthesis of Ciguatoxin CTX3C (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
The Stability and Complexity of Antibody Responses to the Major Surface Antigen of Plasmodium falciparum Are Associated with Age in a Malaria Endemic Area (2011)

Individuals that are exposed to malaria eventually develop immunity to the disease with one possible mechanism being the gradual acquisition of antibodies to the range of parasite variant surface antigens in their local area. Major antibody targets include the large and highly polymorphic Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family of proteins. Here, we use a protein microarray containing 123 recombinant PfEMP1-DBLα domains (VAR) from Papua New Guinea to seroprofile 38 nonimmune children (<4 years) and 29 hyperimmune adults (≥15 years) from the same local area. The overall magnitude, prevalence and breadth of antibody response to VAR was limited at <2 years and 2-2.9 years, peaked at 3-4 years and decreased for adults compared with the oldest children. An increasing proportion of individuals recognized large numbers of VAR proteins (>20) with age, consistent with the breadth of response stabilizing with age. In addition, the antibody response was limited in uninfected children compared with infected children but was similar in adults irrespective of infection status. Analysis of the variant-specific response confirmed that the antibody signature expands with age and infection. This also revealed that the antibody signatures of the youngest children overlapped substantially, suggesting that they are exposed to the same subset of PfEMP1 variants. VAR proteins were either seroprevalent from early in life, (<3 years), from later in childhood (≥3 years) or rarely recognized. Group 2 VAR proteins (Cys2/MFK-REY+) were serodominant in infants (<1-year-old) and all other sequence subgroups became more seroprevalent with age. The results confirm that the anti-PfEMP1-DBLα antibody responses increase in magnitude and prevalence with age and further demonstrate that they increase in stability and complexity. The protein microarray approach provides a unique platform to rapidly profile variant-specific antibodies to malaria and suggests novel insights into the acquisition of immunity to malaria.
Crystal structure of two new bifunctional nonsubstrate type thrombin inhibitors complexed with human α‐thrombin (1996)

The crystal structures of two new thrombin inhibitors, P498 and P500, complexed with human alpha-thrombin have been determined at 2.0 A resolution and refined to crystallographic R-factors of 0.170 and 0.169, respectively. These compounds, with picomolar binding constants, belong to a family of potent bifunctional inhibitors that bind thrombin at two remote sites: the active site and the fibrinogen recognition exosite (FRE). The inhibitors incorporate a nonsubstrate type active site binding fragment: Dansyl-Arg-(D)Pipecolic acid (Dns-Arg-(D)Pip), reminiscent of the active-site directed inhibitors MD-805 and MQPA, rendering them resistant to thrombin-induced hydrolysis. The FRE binding fragment of these inhibitors corresponds to the hirudin55-65 sequence. They differ in the chemical nature of the nonpeptidyl linker bridging these two functional activities. In both cases, the active site binding fragment is well defined in the electron density. The DnsH1, ArgH2, and (D)PipH3 groups occupy the S3, S1, and S2 subsites of thrombin, respectively, in a way similar to that observed in the thrombin-MQPA complexes. Binding in the active site of thrombin is characterized by numerous van der Waals contacts and ring-ring system interactions. Unlike in the substrate-like inhibitors, ArgH2 enters the S1 specificity pocket from the P2 position and adopts a bent conformation to make an hydrogen bond to the carboxylate of Asp189. In this noncanonical position, its carbonyl points away from the oxyanion hole, which is now occupied by well-ordered solvent molecules. The linkers fit in the groove extending from the active site to the FRE. The C-terminal fragments of both inhibitors bind in the same way as analogous FRE binding elements in previously described complexes.
A MACH Filter-Based Reconstruction-Free Target Detector and Tracker for Compressive Sensing Cameras (2020)

Compressive sensing cameras hold the promise of cost-effective hardware, lower data rates, and improved video quality, particularly outside the visible spectrum. However, these improvements involve significant computational cost, as sensor output must be reconstructed in order to form an image viewable by a human. This paper describes a prototype automated detection and tracking system using a compressive sensing camera that does not rely on computationally costly image reconstructions. It operates on raw sensor data for an approximately ten-fold improvement in computation time over a comparable reconstruct-then-track algorithm. The detector is successful at a sensing rate of 0.3, comparable to that required for high-quality image reconstructions. If initialized with the location of a target, the tracker holds the target at a sensing rate of 0.005, below the boundary where reconstruction breaks down. These results show not only that direct tracking from compressive cameras is possible, but also give support to the pursuit of direct inference from compressive sensors of all types.
Graphene-Like-Graphite as Fast-Chargeable and High-Capacity Anode Materials for Lithium Ion Batteries (2017)

Here we propose the use of a carbon material called graphene-like-graphite (GLG) as anode material of lithium ion batteries that delivers a high capacity of 608 mAh/g and provides superior rate capability. The morphology and crystal structure of GLG are quite similar to those of graphite, which is currently used as the anode material of lithium ion batteries. Therefore, it is expected to be used in the same manner of conventional graphite materials to fabricate the cells. Based on the data obtained from various spectroscopic techniques, we propose a structural GLG model in which nanopores and pairs of C-O-C units are introduced within the carbon layers stacked with three-dimensional regularity. Three types of highly ionic lithium ions are found in fully charged GLG and stored between its layers. The oxygen atoms introduced within the carbon layers seem to play an important role in accommodating a large amount of lithium ions in GLG. Moreover, the large increase in the interlayer spacing observed for fully charged GLG is ascribed to the migration of oxygen atoms within the carbon layer introduced in the state of C-O-C to the interlayer space maintaining one of the C-O bonds.
Magneto-electric magnetic tunnel junction logic devices (2015)

Magneto-electrics (MEs) are rapidly emerging as a key technology for applications in various beyond-CMOS spin based device technologies [1]. As the focus on ME materials has sharpened in recent years, there has been growing interest in implementing different spintronic devices that can take advantage of the full promise of these materials. The magneto-electric magnetic tunnel junction (ME-MTJ) is a device based on MEs that shows great promise for future memory and logic applications. In this device, switching is achieved by reversing the magnetization of the so-called “free” Ferromagnet (FM) of a magnetic tunnel junction. Specifically, the magnetization reversal is induced by means of the voltage-control of magnetism provided by a proximal magneto-electric (ME) layer [2]. Voltage control minimizes power consumption by making use of exchange biasing between the antiferromagnetic magneto-electric (ME-AFM) layer and the free FM. This makes the ME-MTJ an extremely low power device. It is expected to operate with a supply of +/− 0.1–0.2 V. The voltage-driven switching scheme of figure 1 introduces three-terminal transistor functionality to the MTJ, a device that has traditionally been restricted to two-terminal operation. The innovative feature of this device therefore derives from the control of the magnetic state of the free electrode by means of the exchange bias produced by the ME's boundary magnetization. Boundary magnetization at the ME-AFM layer interface has the inherent property of non-volatility [3]. This makes ME-MTJs attractive for memory applications.
Isolating and understanding concurrency errors using reconstructed execution fragments (2011)

In this paper we propose Recon, a new general approach to concurrency debugging. Recon goes beyond just detecting bugs, it also presents to the programmer short fragments of buggy execution schedules that illustrate how and why bugs happened. These fragments, called reconstructions , are inferred from inter-thread communication surrounding the root cause of a bug and significantly simplify the process of understanding bugs. The key idea in Recon is to monitor executions and build graphs that encode inter-thread communication with enough context information to build reconstructions. Recon leverages reconstructions built from multiple application executions and uses machine learning to identify which ones illustrate the root cause of a bug. Recon's approach is general because it does not rely on heuristics specific to any type of bug, application, or programming model. Therefore, it is able to deal with single- and multiple-variable concurrency bugs regardless of their type ( e.g. , atomicity violation, ordering, etc). To make graph collection efficient, Recon employs selective monitoring and allows metadata information to be imprecise without compromising accuracy. With these optimizations, Recon's graph collection imposes overheads typically between 5x and 20x for both C/C++ and Java programs, with overheads as low as 13% in our experiments. We evaluate Recon with buggy applications, and show it produces reconstructions that include all code points involved in bugs' causes, and presents them in an accurate order. We include a case study of understanding and fixing a previously unresolved bug to showcase Recon's effectiveness.
Intelligent Modeling Approach to Predict Effluent Quality of Wastewater Treatment Process (2018)

Monitoring of effluent quality remains a challenge to the wastewater treatment process (WWTP). In order to provide a reliable tool for the online monitoring of effluent quality, an intelligent modeling approach, which consists of online sensors and an effluent quality predicting plant, is developed to predict effluent quality in this chapter. The intelligent modeling approach, based on a self-organizing fuzzy neural network (SOFNN), is able to enhance the modeling performance by organizing the structure and adjusting the parameters simultaneously. The experimental studies of intelligent modeling approach have been performed on several systems to verify the effectiveness. The comparison with other existing methods has been made and demonstrated that the intelligent modeling approach is of better performance.
New One-Dimensional Implicit Numerical Dynamic Sewer and Storm Model (2002)

A one-dimensional hydrodynamic numerical model has been developed and implemented into Haestad Methods' hydraulics software for modeling of unsteady flows in sewer and storm water urban drainage system. The new numerical model uses an implicit four-point, finite-difference solution technique to solve the one-dimensional Saint-Venant equations and the scheme was initially developed by the National Weather Service for open channel flow routing and river flood forecasting. Advanced numerical techniques, such as Local Partial Inertial modification (LPI) for subcritical, supercritical, and transitional flows, and relaxation for pipe/channel networks, are used to achieve computational performance and robustness as required for practical use in a water resources engineering commercial software package.
Computerized Macular Pathology Diagnosis in Spectral Domain Optical Coherence Tomography Scans Based on Multiscale Texture and Shape Features (2011)

To develop an automated method to identify the normal macula and three macular pathologies (macular hole [MH], macular edema [ME], and age-related macular degeneration [AMD]) from the fovea-centered cross sections in threedimensional (3D) spectral-domain optical coherence tomography (SD-OCT) images.
Macrotetrolide biosynthesis: A novel type II polyketide synthase (2002)

Polyketide biosynthesis is catalyzed by polyketide synthase (PKS) and three types of bacterial PKS are known to date. Feeding experiments with isotope-labeled precursors established the polyketide origin of the macrotetrolides, but the labeling pattern cannot be rationalized according to the established PKS paradigm. Genetic analysis of the macrotetrolide biosynthesis unveiled an unprecedented organization for a polyketide gene cluster that features five genes encoding discrete ketoacyl synthase (KS) and four genes encoding discrete ketoreductase (KR) but lacking an acyl carrier protein (ACP). Macrotetrolide biosynthesis is proposed to involve a novel type II PKS that acts directly on acyl CoA substrates, functions noniteratively, and catalyzes both C-C and C-O bond formation. These findings demonstrate once again Nature's versatility in making complex molecules and suggests new strategies for PKS engineering to further expand the scope and diversity of polyketide library. They also should serve as an inspiration in searching for PKS with novel chemistry for combinatorial biosynthesis.
Real-time multistage IR image-based tracker (1999)

In this paper we describe a real time algorithm for a missile-based IR tracking system. A correlation-based tracker is considered to be the primary tracker, while a feature-based is chosen to provide support on a secondary level. A prescreener runs concurrently with the trackers to provide a list of probable target centroids. This information is used to provide a level a confidence to the tracker. The tracker subfunctions are implemented in both programmable logic hardware and software operating on digital signal processors. The maximum sustained pixel data rate that can be processed is 10 MHz, which will provide a 60 Hz tracker with a 256 X 256 input image and a 30 Hz tracker for a 512 X 512 input image. The prescreener functions is implemented in reprogrammable hardware subfunctions that operate up to the full 10 MHz pixel rate producing target centroids.
Hybrid Wireless-Wired Optical Sensor for Extreme Temperature Measurement in Next Generation Energy Efficient Gas Turbines (2010)

Accuracy, reliability, and long lifetimes are critical parameters for sensors measuring temperature in gas turbines of clean coal-fired power plants. Greener high efficiency next generation power plants need gas turbines operating at extremely high temperatures of 1500°C, where present thermocouple temperature probe technology fails to operate with reliable and accurate readings over long lifetimes. To solve this pressing problem, we have proposed the concept of a new hybrid class of all-silicon carbide (SiC) optical sensor, where a single crystal SiC optical chip is embedded in a sintered SiC tube assembly, forming a coefficient of thermal expansion (CTE) matched all-SiC front-end probe. Because chip and host material are CTE matched, optimal handling of extreme thermal ramps and temperatures is possible. In this article, we demonstrate the first successful industrial combustor rig test of this hybrid all-SiC temperature sensor front-end probe indicating demonstrated probe structural robustness to 1600°C and rig test data to ∼1200°C. The design of the rig test sensor system is presented and data are analyzed.
A novel spot size convertor for hybrid integrated light sources on photonics-electronics convergence system (2012)

We have developed a spot size converter (SSC) with a trident silicon (Si) waveguide for the hybrid integrated light source in a photonics-electronics convergence system. Low loss coupling was achieved with just the simple planar form of a Si waveguide with no use of complicated structures such as vertical tapers or extra dielectric core overlaid on the waveguide. The coupling loss was 2.3 dB and the tolerance of misalignment up to a 1-dB loss increase was about ± 0.9 μm. We also confirmed that the coupling efficiency was quite robust against manufacturing fluctuations of the waveguide width compared with a conventional SSC with an inverse taper waveguide. We were able to fabricate a 52-channel light source with highly uniform output power by using the proposed trident SSC.