gebhart/patrepeval huggingface dataset:
Potential of monoclonal antibodies to improve therapeutic monitoring of cyclosporine. (1987)

We show that monitoring of cyclosporine by immunoassay could be improved by using monoclonal antibodies (MAbs) of restricted specificity instead of polyclonal antisera that recognize both unmodified cyclosporine and its metabolites. MAbs with high affinity for cyclosporine have been prepared and characterized. We tested their ability to discriminate between native cyclosporine and its metabolites in indirect solid-phase enzyme immunoassay with a set of cyclosporine metabolites modified at residues 1, 4, 6, and 9 (corresponding to the six known sites of metabolism of cyclosporine). All the metabolites tested were detected by MAb1 at least 15- to 1000-fold less well than unmodified cyclosporine. A second MAb recognized unmodified cyclosporine and most of its metabolites equally well. Both MAbs retained their activity when coupled to alkaline phosphatase and could therefore be used in a direct solid-phase enzyme immunoassay.
HDAC Inhibition in Lupus Models (2011)

Systemic lupus erythematosus (SLE) is a prototypic autoimmune inflammatory disease characterized by the production of autoantibodies directed against nuclear antigens such as nucleosomes, DNA and histone proteins found within the body’s cells and plasma. Autoantibodies may induce disease by forming immune complexes that lodge in target organs or by crossreacting with targeted antigens and damaging tissue. In addition to autoantibody production, apoptotic defects and impaired removal of apoptotic cells contribute to an overload of autoantigens that initiate an autoimmune response. Besides the well-recognized genetic susceptibility to SLE, environmental and epigenetic factors play a crucial role in disease pathogenesis as evidenced by monozygotic twins typically being discordant for disease. Changes in DNA methylation and histone acetylation alter gene expression and are thought to contribute to the epigenetic deregulation in disease. In SLE, global and gene-specific DNA methylation changes have been demonstrated to occur. Additionally, aberrant histone acetylation is evident in individuals with SLE. Moreover, histone deacetylase inhibitors (HDACi) have been shown to reverse the skewed expression of multiple genes involved in SLE. In this review, we discuss the implications of epigenetic alterations in the development and progression of SLE, and how therapeutics designed to alter histone acetylation status may constitute a promising avenue to target disease.
Fast temperature programmed sensing for micro-hotplate gas sensors (1995)

We describe an operating mode of a gas sensor that greatly enhances the capability of the device to determine the composition of a sensed gas. The device consists of a micromachined hotplate with integrated heater, heat distribution plate, electrical contact pads, and sensing film. The temperature programmed sensing (TPS) technique uses millisecond timescale temperature changes to modify the rates for adsorption, desorption, and reaction of gases on the sensing surface during sensor operation. A repetitive train of temperature pulses produces a patterned conductance response that depends on the gas composition, as well as the temperature pulse width, amplitude, and specific sequence of pulses. Results are shown for the vapors of water, ethanol, methanol, formaldehyde, and acetone.
Design and characterisation of a novel interleukin-15 receptor alpha fusion protein and analysis of interleukin-15 complexation (2019)

Interleukin-15 (IL15) is one of the most important cytokines currently being considered for cancer therapy applications. It is thought that by administering IL15 in complex with its cognate receptor alpha chain (IL15Rα) its biological activity could be increased manifold. We produced a fusion protein of mouse IL15Rα and the F8 antibody, that targets the alternatively-spliced extra-domain A (EDA) of fibronectin, which is overexpressed in many types of cancer. The fusion protein F8IL15Rα was cloned, expressed and characterized in vitro and its ability to bind to mouse IL15 was assessed with both size exclusion chromatography (SEC) and surface plasmon resonance (SPR) experiments. Furthermore, mouse and human IL15 and their corresponding Fc fused IL15Rα subunits were purchased, characterized and used to compare the capacity of F8IL15Rα to generate complexes. Surprisingly, none of the IL15Rα fusion proteins showed IL15 complexation on SEC. However, on SPR, F8IL15Rα displayed the ability to bind IL15. In a cell-based activity assay none of the IL15Rα fusions were able to increase cellular proliferation in combination with IL15 compared to IL15 alone. A better understanding of the molecular requirements for effective IL15 signalling are likely to be important for the development of IL15-based biopharmaceuticals.
Cysteine pairing in the glycoprotien IIbIIIa antagonist kistrin using NMR, chemical analysis, and structure calculations (1993)

The pairing of the cysteines in disulfide bonds was investigated for the 68-residue RGD-containing protein kistrin, a potent antagonist of the integrin GP IIbIIIa and an inhibitor of platelet aggregation. Kistrin belongs to a family of homologous proteins found in snake venoms termed disintegrins, all of which have a cysteine content. The disulfide pairing of the 12 cysteines was investigated by chemical analysis, NMR spectroscopy, and distance geometry calculations. The data show that the disulfide pairs are 4-19, 6-14, 13-36, 27-33, 32-57, and 45-64. The various means for assigning the disulfide bonds are described, and the results are compared with the cysteine pairings reported for other disintegrin proteins.
Vasculogenesis (1995)

Induction by fibroblast growth factors of mesoderm during gastrulation leads to blood-forming tissue, including angioblasts and hemopoietic cells, that together constitute the blood islands of the yolk sac. The differentiation of angioblasts from mesoderm and the formation of primitive blood vessels from angioblasts at or near the site of their origin are the two distinct steps during the onset of vascularization that are defined as vasculogenesis. Vascular endothelial growth factor and its high-affinity receptor tyrosine kinase flk-1 represent a paracrine signaling system crucial for the differentiation of endothelial cells and the development of the vascular system. Specific cell adhesion molecules such as VE-cadherin and PECAM-1 (CD-31), and transcription factors such as ets-1, as well as mechanical forces and vascular regression and remodeling are involved in the subsequent events of endothelial cell differentiation, apoptosis, and angiogenesis.
THE USE OF2H,13C,15N MULTIDIMENSIONAL NMR GTO STUDY THE STRUCTURE AND DYNAMICS OF PROTEINS (1998)

During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.
Interferon gamma is involved in the recovery of athymic nude mice from recombinant vaccinia virus/interleukin 2 infection. (1990)

Athymic nude mice recover from an infection with recombinant vaccinia virus (VV) encoding murine interleukin 2 (IL-2), but treatment with a mAb to IL-2 accentuated infection. Administration of a mAb against interferon gamma (IFN-gamma) to mice infected with the IL-2-encoding virus completely prevented the IL-2-induced mechanisms of recovery. Both asialo-GM1+ (NK) and asialo-GM1- (non-NK) cells were participants in the IFN-gamma-mediated recovery of nude mice from infection with the IL-2-encoding VV recombinant. Depletion of asialo-GM1+ cells exacerbated infection, though not as much as anti-IFN-gamma mAb. In vitro, both asialo-GM1+ and asialo-GM1- nude mouse splenocytes produced IFN-gamma in response to IL-2.
Synthesis and Activity of a New Generation of Ruthenium-Based Olefin Metathesis Catalysts Coordinated with 1,3-Dimesityl-4,5-dihydroimidazol-2-ylidene Ligands (1999)

[formula: see text] A new family of 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene-substituted ruthenium-based complexes 9a-c has been prepared starting from RuCl2(=CHPh)(PCy3)2 2. These air- and water-tolerant complexes were shown to exhibit an increased ring-closing metathesis activity at elevated temperature when compared to that of the parent complex 2 and the previously developed complex 3. In many instances the activity of these complexes also rivaled or exceeded that of the alkoxy-imido molybdenum complex 1. Catalyst loadings of as low as 0.05 mol% could be used.
A super-regenerative ASK receiver with ΔΣ pulse-width digitizer and SAR-based fast frequency calibration for MICS applications (2009)

This paper presents a 400MHz super-regenerative receiver (SR-RX) with a proposed ΔΣpulse-width digitizer (ΔΣ-PWD) and a SAR-based fast frequency calibration (SAR-FFC). The ΔΣ-PWD can be considered as a PW-domain counterpart of a conventional ΔΣ modulator. It achieves high-resolution PW-to-digital conversion. The SAR-FFC enables rapid setting of the oscillator frequency to the MICS band. Fabricated in a 0.18µm CMOS process, this RX draws 700µA from a 1.3V supply. With a 156kbps data rate, the RX achieves an energy efficiency of 5.8nJ/bit and −80dBm sensitivity. The measured frequency calibration time is around 1.5µs.
ACOUSTIC DEWATERING AND DRYING (LOW AND HIGH FREQUENCY): STATE OF THE ART REVIEW (1985)

ABSTRACT The potential of ultrasonic energy to dry heat-sensitive materials was proven by studies conducted a number of years ago. Ultrasonic irradiation improved the rates of drying and the temperatures seldom exceeded 1 C above ambient. Recent developments in energy related areas of technology have caused a new search for more economical methods of drying. This paper reviews both past and present literature on acoustic dewatering and drying and discusses the current state of the technology. The studies reviewed represent a broad spectrum including effects at very low sonic to ultrasonic frequencies. The fundamental aspects and applications of the technique to a variety of materials are presented.
New Aircraft II (2012)

The McDonnell Douglas (now Boeing) F/A-18 Hornet is a twin-engine supersonic, all-weather carrier-capable multirole fighter jet, designed to dogfight and attack ground targets (F/A for Fighter/Attack). The Lockheed AC-130 gunship is a heavily-armed ground-attack aircraft variant of the C-130 Hercules transport plane. The Bell AH-1 SuperCobra is a twin-engine attack helicopter based on the US Army's AH-1 Cobra. The Boeing AH-64 Apache is a four-blade, twin-engine attack helicopter with a tailwheel-type landing gear arrangement, and a tandem cockpit for a two-man crew. The Northrop T-38 Talon is a twin-engine supersonic jet trainer. The McDonnell Douglas (now Boeing) AV-8B Harrier II is a second-generation vertical/short takeoff and landing (V/STOL) ground-attack aircraft. The Rockwell (now part of Boeing) B-1 Lancer is a four-engine variable-sweep wing strategic bomber used by the United States Air Force (USAF). The Northrop Grumman B-2 Spirit (also known as the Stealth Bomber) is an American strategic bomber, featuring low observable stealth technology designed for penetrating dense anti-aircraft defenses; it is able to deploy both conventional and nuclear weapons.
A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection (2003)

With recent advances in mass spectrometry techniques, it is now possible to investigate proteins over a wide range of molecular weights in small biological specimens. This advance has generated data-analytic challenges in proteomics, similar to those created by microarray technologies in genetics, namely, discovery of 'signature' protein profiles specific to each pathologic state (e.g. normal vs. cancer) or differential profiles between experimental conditions (e.g. treated by a drug of interest vs. untreated) from high-dimensional data. We propose a data-analytic strategy for discovering protein biomarkers based on such high-dimensional mass spectrometry data. A real biomarker-discovery project on prostate cancer is taken as a concrete example throughout the paper: the project aims to identify proteins in serum that distinguish cancer, benign hyperplasia, and normal states of prostate using the Surface Enhanced Laser Desorption/Ionization (SELDI) technology, a recently developed mass spectrometry technique. Our data-analytic strategy takes properties of the SELDI mass spectrometer into account: the SELDI output of a specimen contains about 48,000 (x, y) points where x is the protein mass divided by the number of charges introduced by ionization and y is the protein intensity of the corresponding mass per charge value, x, in that specimen. Given high coefficients of variation and other characteristics of protein intensity measures (y values), we reduce the measures of protein intensities to a set of binary variables that indicate peaks in the y-axis direction in the nearest neighborhoods of each mass per charge point in the x-axis direction. We then account for a shifting (measurement error) problem of the x-axis in SELDI output. After this pre-analysis processing of data, we combine the binary predictors to generate classification rules for cancer, benign hyperplasia, and normal states of prostate. Our approach is to apply the boosting algorithm to select binary predictors and construct a summary classifier. We empirically evaluate sensitivity and specificity of the resulting summary classifiers with a test dataset that is independent from the training dataset used to construct the summary classifiers. The proposed method performed nearly perfectly in distinguishing cancer and benign hyperplasia from normal. In the classification of cancer vs. benign hyperplasia, however, an appreciable proportion of the benign specimens were classified incorrectly as cancer. We discuss practical issues associated with our proposed approach to the analysis of SELDI output and its application in cancer biomarker discovery.
Intrastriatal grafts derived from fetal striatal primordia. I. Phenotypy and modular organization (1989)

Fetal striatal grafts display a striking modularity of composition. With acetylcholinesterase (AChE) histochemistry, the tissue of such grafts can be divided into regions with strong AChE staining of the neuropil and regions in which AChE staining of the neuropil is weak. In the experiments reported here, we reexamined the nature of this modularity. Striatal grafts were made by injecting dissociated cells of E15 ganglionic eminence into the striatum of adult rats, which 7 days before had recived intrastriatal deposits of ibotenic acid. Some donors had been exposed to 3H-thymidine at E11-E15. After 9-17 month survivals, the anatomical organization of the grafts was studied by histochemistry, immunohistochemistry, and autoradiography. In every graft, the AChE-rich regions formed patches (P regions) in a larger AChE-poor surround (NP regions). Neurons labeled with 3H-thymidine appeared in both P and NP regions, suggesting that donor cells were distributed in each type of region and that neither type of tissue, P or NP, was composed exclusively of host tissue. In the AChE-rich P regions, markers characteristic of normal perinatal and mature rat striatum were expressed by medium-sized cells: calcium-binding protein (calbindin D28k) immunostaining, metenkephalin (mENK) immunostaining, and, more rarely, somatostatin (SOM) immunostaining. In the NP regions, however, medium-sized cells expressing calbindin and mENK immunostaining were very rare, and there was an abundance of neuronal types not found in normal mature striatal tissue. These included (1) large, multipolar, calbindin-positive neurons with well-ramified, densely stained dendrites, (2) large, SOM-positive neurons with prominent dendritic trees, and (3) mENK-positive cells smaller than typical striatal, medium-sized, mENK-immunoreactive neurons. In Nissl stains, the AChE-rich P regions resembled the normal striatum of mature animals, whereas the AChE-poor NP regions did not. These findings suggest that the P regions of fetal striatal grafts achieve a phenotypy similar to that of normal striatum at maturity and during much of postnatal development. The dominant expression of perikaryal calbindin-like immunoreactivity in the P regions further suggests that these zones have a high proportion of tissue resembling striatal matrix. By contrast, expression of marker antigens in the NP zones of the grafts suggests that these zones are predominantly composed of nonstriatal tissue or that they have the phenotypy of immature striatum intermixed with some nonstriatal cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Structural Deep Network Embedding (2016)

Network embedding is an important method to learn low-dimensional representations of vertexes in networks, aiming to capture and preserve the network structure. Almost all the existing network embedding methods adopt shallow models. However, since the underlying network structure is complex, shallow models cannot capture the highly non-linear network structure, resulting in sub-optimal network representations. Therefore, how to find a method that is able to effectively capture the highly non-linear network structure and preserve the global and local structure is an open yet important problem. To solve this problem, in this paper we propose a Structural Deep Network Embedding method, namely SDNE. More specifically, we first propose a semi-supervised deep model, which has multiple layers of non-linear functions, thereby being able to capture the highly non-linear network structure. Then we propose to exploit the first-order and second-order proximity jointly to preserve the network structure. The second-order proximity is used by the unsupervised component to capture the global network structure. While the first-order proximity is used as the supervised information in the supervised component to preserve the local network structure. By jointly optimizing them in the semi-supervised deep model, our method can preserve both the local and global network structure and is robust to sparse networks. Empirically, we conduct the experiments on five real-world networks, including a language network, a citation network and three social networks. The results show that compared to the baselines, our method can reconstruct the original network significantly better and achieves substantial gains in three applications, i.e. multi-label classification, link prediction and visualization.
Viscoelastic properties and gelation of an elastin-like polypeptide (2009)

Tropoelastin, the native monomeric form of elastin, and elastin-like polypeptides undergo a process of temperature-induced phase separation (coacervation) resulting in self-organization of a polymeric network that can subsequently be cross-linked into an elastomeric polymer. In this study, the rheological properties of a recombinantly produced polypeptide mimicking the sequences and domain arrangements of tropoelastin were investigated to understand post-coacervation changes in structure and assembly. This polypeptide, designated EP20-24-24, consisted of three hydrophobic domains of native human tropoelastin flanking two cross-linking domains. Temperature-induced formation of coacervate droplets resulted in a small increase in viscosity. A higher temperature produced a second temperature-dependent transition (Tv) to a gel state characterized by a much higher viscosity, strong shear thinning, and a high ratio of storage to loss moduli. This gel state was fully reversible if the temperature was immediately lowered. However, incubation above Tv for 60 min resulted in a further transformation of the network, limiting thermal reversibility of the gelation process. These results demonstrate that for elastin-like polypeptides mimicking the sequence and domain arrangements of tropoelastin, temperature-induced coacervation and transition of the coacervate to a gel-like state are distinguishable events with separate transition temperatures. Moreover, gels formed by these elastin-like polypeptides undergo a process of maturation, reducing the reversibility of the gel state.
Dynamics of a Bonding Front (2005)

A description of the bonding front propagation between two adhesive plates is proposed. The model relates the velocity of a bonding front to the adhesion energy, with application to wafer direct bonding. Its derivation is based on a competition between the bonding energy and the viscous drag of the air flow in the gap between the two wafers. The model describes well the experimental data, including the wafer deformation profile during bonding or the dependence of the velocity on the gas viscosity, pressure, and wafer thickness.
Real-time vision-based surgical tool segmentation with robot kinematics prior (2018)

Robot-assisted minimally invasive surgery combines the skills and techniques of highly-trained surgeons with the robustness and precision of machines. Several advantages include precision beyond human dexterity alone, greater kinematic degrees of freedom at the surgical tool tip, and possibilities in remote surgical practices through teleoperation. Nevertheless, obtaining accurate force feedback during surgical operations remains a challenging hurdle. Though direct force sensing using tool tip mounted sensors is theoretically possible, it is not amenable to required sterilization procedures. Vision-based force estimation according to real-time analysis of tissue deformation serves as a promising alternative. In this application, along with numerous related research in robotassisted minimally invasive surgery, segmentation of surgical instruments in endoscopic images is a prerequisite. Thus, a surgical tool segmentation algorithm robust to partial occlusion is proposed using DFT shape matching of robot kinematics shape prior (u) fused with log likelihood mask (Q) in the Opponent color space to generate final mask (U). Implemented on the Raven II surgical robot system, a real-time performance robust to tool tip orientation and up to 6 fps without GPU acceleration is achieved.
Spreadsheet data manipulation using examples (2012)

Millions of computer end users need to perform tasks over large spreadsheet data, yet lack the programming knowledge to do such tasks automatically. We present a programming by example methodology that allows end users to automate such repetitive tasks. Our methodology involves designing a domain-specific language and developing a synthesis algorithm that can learn programs in that language from user-provided examples. We present instantiations of this methodology for particular domains of tasks: (a) syntactic transformations of strings using restricted forms of regular expressions, conditionals, and loops, (b) semantic transformations of strings involving lookup in relational tables, and (c) layout transformations on spreadsheet tables. We have implemented this technology as an add-in for the Microsoft Excel Spreadsheet system and have evaluated it successfully over several benchmarks picked from various Excel help forums.