gebhart/patrepeval huggingface dataset:
Abstract 631: Monovalency unleashes the full therapeutic potential of the DN-30 anti-Met antibody (2011)

Abstract Met, the high affinity receptor for Hepatocyte Growth Factor (HGF), is one of the most frequently activated tyrosine kinases in human cancer and a validated target for cancer therapy. We previously developed a mouse monoclonal antibody directed against the extracellular portion of Met (DN-30) that induces Met proteolytic cleavage (receptor ‘shedding’) followed by proteasome-mediated receptor degradation, leading to inhibition of HGF/Met-mediated biological activities. However, DN-30 binding to Met also results in partial activation of the Met kinase due to antibody-mediated receptor dimerization. To safely harness the therapeutic potential of DN-30, its shedding activity must be disassociated from its agonistic activity. We have generated a DN-30 Fab fragment that maintains high affinity Met binding, elicits efficient receptor shedding and down-regulation, and does not promote kinase activation. In Met-addicted tumor cell lines, DN-30 Fab displays potent cytostatic and cytotoxic activity in a dose-dependent fashion. DN-30 Fab also inhibits anchorage-independent growth of several tumor cell lines. In mouse tumorigenesis assays using Met-addicted carcinoma cells, intra-tumor administration of DN-30 Fab or systemic delivery of a chemically stabilized form of the same molecule results in reduction of Met phosphorylation and inhibition of tumor growth. These data provide proof-of-concept that monovalency unleashes the full therapeutic potential of the DN-30 antibody and point at DN-30 Fab as a promising tool for Met-targeted therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 631. doi:10.1158/1538-7445.AM2011-631
New oleandomycin 9-oximes. Synthesis, characterization and biological activity. (1994)

A series of the novel oleandomycin 9-oximes has been prepared and characterized by spectroscopic data and X-ray analysis. The antibacterial in vitro activities of the oximes (6-10) were compared with that of oleandomycin (1). Among the novel derivatives the most active compound was 8(R)-methyloleandomycin-9-oxime (9) in contrast ot its 8(S)-isomer (10) which possessed only low potency. Some preliminary pharmacokinetic data of 9 confirmed its activity. Compound 9 has been advanced to further biological study.
Shared Low Frequency Vibroseis Acquisition (2016)

Summary The most efficient way of generating seismic waves whose wavelengths are much bigger than the distance between two or more sources is by emitting them in phase. This simple idea is exploited in the proposed vibroseis acquisition and processing method here referred to as shared low frequency vibroseis. I formulate the theory and I present the promising results obtained using onshore seismic data.
A Chemical Stain for Identifying Arsenic‐Treated Wood Products (2007)

Abstract Convenient and rapid detection of arsenic in treated wood products is necessary when evaluating possible exposure risks from the product during in‐service use and disposal. For this study, a modified stannous chloride stain capable of specifically identifying arsenic in preservative‐treated wood was developed by causing the over‐reduction of molybdenum with stannous chloride prior to sample addition. This reduced the stain's sensitivity to the background phosphate levels in the wood and permitted the detection of elevated arsenate concentrations. The modified stain was confirmed through field testing with weathered wood samples. Alternative application techniques, such as wipes, were further explored.
Protease-Deficient<i>Saccharomyces</i><i>cerevisiae</i>Strains for the Synthesis of Human-Compatible Glycoproteins (2013)

Saccharomyces cerevisiae strains engineered previously to produce proteins with mammalian high mannose structures showed severe growth defects and decreased protein productivity. In strain YAB101, derived from one of these strains by a mutagenesis technique based on the disparity theory of evolution, these undesirable phenotypes were alleviated. Here we describe further engineering of YAB101 with the aim of synthesizing heterologous glycoproteins with Man5GlcNAc2, an intermediate for the mammalian hybrid and complex type oligosaccharides. About 60% conversion of Man8GlcNAc2 to Man5GlcNAc2 was observed after integration of Aspergillus saitoi α-1,2-mannosidase fused to the transmembrane domain of S. cerevisiae Och1. To obtain a higher yield of the target protein, a protease-deficient version of this strain was generated by disruption of PEP4 and PRB1, resulting in YAB101-4. Inactivation of these vacuolar proteases enhanced the secretion of human interferon-β by approximately 10-fold.
Cooperative Modulation Classification of multiple signals in Cognitive Radio Networks (2014)

Automatic Modulation Classification (AMC) is an important component in Cognitive Radio (CR) Networks. Multiuser AMC classifies the modulation schemes of simultaneous multiple unknown transmitters. In addition, cooperation among multiple CR receivers for modulation classification offers significant improvements in classification performance and overcomes the detrimental channel effects that degrades the single CR classifier performance. In this paper, a novel centralized soft-combining data fusion algorithm based on the joint probability distribution of fourth order cumulants is presented for cooperative modulation classification. Fourth order cumulants of the received signals are calculated as discriminating features for different modulation schemes at each CR node and sent to a centralized data Fusion Center (FC). The FC chooses the modulation scheme that maximizes the joint probability of the estimated cumulants. As compared to independent receiver classification, cooperative classification results are significantly improved under the same multi-path environment.
Fast formation cycling for lithium ion batteries (2017)

The formation process for lithium ion batteries typically takes several days or more, and it is necessary for providing a stable solid electrolyte interphase on the anode (at low potentials vs. Li/Li+) for preventing irreversible consumption of electrolyte and lithium ions. An analogous layer known as the cathode electrolyte interphase layer forms at the cathode at high potentials vs. Li/Li+. However, several days, or even up to a week, of these processes result in either lower LIB production rates or a prohibitively large size of charging-discharging equipment and space (i.e. excessive capital cost). In this study, a fast and effective electrolyte interphase formation protocol is proposed and compared with an Oak Ridge National Laboratory baseline protocol. Graphite, NMC 532, and 1.2 M LiPF6 in ethylene carbonate: diethyl carbonate were used as anodes, cathodes, and electrolytes, respectively. Finally, results from electrochemical impedance spectroscopy show the new protocol reduced surface film (electrolyte interphase) resistances, and 1300 aging cycles show an improvement in capacity retention.
Intelligent Tuning of a Kalman Filter for INS/GPS Navigation Applications (2007)

The demand for low-cost portable civil navigation systems has been growing over the last several years. The Global Positioning System has been the backbone of most current navigation systems, but its usefulness in harsh environments, such as downtown urban areas or under heavily treed terrain is limited due to signal blockages. To help bridge these signal gaps inertial navigation systems have been commonly used. An integrated INS/GPS system can provide a continuous navigation solution regardless of the environment. For civil applications the use of MEMS sensors are needed due to cost, size and regulatory restrictions of higher grade inertial units. The Kalman Filter has traditionally been used to optimally weight the GPS and INS measurements, but when using MEMS grade sensors the a priori tuning parameters given by the designer or manufacturer are not always optimal. In these cases, the position errors during loss of the GPS signals accumulate faster than the ideally tuned case. To aid in the on-line tuning process, a reinforcement learning algorithm was used to tune the Kalman filter parameters as navigation data was collected. Tuning any Kalman filter is a difficult task and is often done before navigation with the aid of the filter designer. This process often entails much iteration using human expertise and is in no way guaranteed to result in optimal parameters. Reinforcement learning is an intelligent and adaptable solution to this problem which uses a combination of dynamic programming and trial and error exploration to develop a set of parameters that improve as navigation data is collected by the user. In comparison to a manual tuning approach it was found that using reinforcement learning led to similar estimates of the tuning parameter values for a single integrated system. This is encouraging since the reinforcement learning was done online without any need of intervention by the designer. Furthermore, when the results of tuning one sensor were applied to a second integrated sensor, the tuning converged almost immediately and improved the positioning accuracy of the system by several meters in comparison to using the values generated from tuning the first sensor.
A Phase 2 Clinical Trial of SGN-40 Monotherapy in Relapsed Diffuse Large B-Cell Lymphoma. (2008)

Abstract BACKGROUND: SGN-40 is a humanized monoclonal antibody that targets CD40. Upon binding to CD40, SGN-40 triggers pro-apoptotic signal transduction pathways and mediates effector cell functions (ADCC and ADCP). SGN-40 demonstrated preliminary anti-tumor activity in a phase 1 study of non-Hodgkin lymphoma, including diffuse large B-cell lymphoma (DLBCL) patients (ASH 2006, Abstract 695). METHODS: We conducted a multicenter, phase 2, open-label study to determine the overall response rate and toxicity profile of SGN-40 in patients with relapsed DLBCL. Tumor samples were assessed by a central lab for pathology confirmation and CD40 expression. Eligible patients had de novo or transformed DLBCL at diagnosis and were excluded if previously treated for indolent lymphoma. Required prior therapy consisted of combination chemotherapy with rituximab and, if eligible, autologous stem cell transplantation. Patients received 6 intravenous infusions of SGN-40 over 5 weeks (Cycle 1) with intra-patient dose loading (1 mg/kg on Day 1; 2 mg/kg on Day 4; 4 mg/kg on Day 8) and 8 mg/kg/wk thereafter. Responding patients and those with stable disease were eligible to continue therapy until disease progression or a maximum of 12 cycles. RESULTS: Forty-six patients (28 M, 18 F), with a median age of 72 years (range 17–85), were enrolled at 10 centers in the US. Patients were heavily pre-treated, with a median of 4 prior systemic chemotherapy regimens (range 1–10). Immunohistochemistry analysis of patient tumor samples demonstrated high expression of CD40 in all patients with the exception of 1 patient who was negative. Thirty-eight of the 46 patients met predefined criteria for evaluation (completed dose loading and had no major protocol violations). Best responses seen were CR (n=2, 5%) and PR (n=2, 5%), yielding an ORR of 10%. Furthermore, 9 (24%) patients had SD as best response. Reductions in tumor size were seen in approximately one-third of patients. Twenty (53%) patients had PD and 5 (13%) patients have yet to be assessed. Treatment with SGN-40 was generally well tolerated. Grade 3/4 events that occurred in more than 1 patient in the intent-to-treat population (N=46), regardless of drug attribution were thrombocytopenia (n=5); neutropenia (n=4); and anemia, fatigue, pneumonia, hyponatremia, DVT, and disease progression (n=2 pts each). Of these events, only fatigue (n=2) and neutropenia (n=2) were considered drug related by the investigator. CONCLUSION: Monotherapy with SGN-40 in DLBCL patients is well tolerated and resulted in objective responses consistent with the previous phase 1 experience. These data support further evaluation of SGN-40 in combination with chemotherapy in non-Hodgkin lymphoma; 3 combination clinical trials are ongoing. Retrospective correlation of clinical outcome and a gene signature that includes baseline CD40 activation status are planned.
Simulation of Quantum Circuits via Stabilizer Frames (2014)

Generic quantum-circuit simulation appears intractable for conventional computers and may be unnecessary because useful quantum circuits exhibit significant structure that can be exploited during simulation. For example, Gottesman and Knill identified an important subclass, called stabilizer circuits, which can be simulated efficiently using group-theory techniques and insights from quantum physics. Realistic circuits enriched with quantum error-correcting codes and fault-tolerant procedures are dominated by stabilizer subcircuits and contain a relatively small number of non-Clifford components. Therefore, we develop new data structures and algorithms that facilitate parallel simulation of such circuits. Stabilizer frames offer more compact storage than previous approaches but require more sophisticated bookkeeping. Our implementation, called Quipu, simulates certain quantum arithmetic circuits (e.g., reversible ripple-carry adders) in polynomial time and space for equal superpositions of n-qubits. On such instances, known linear-algebraic simulation techniques, such as the (state-of-the-art) BDD-based simulator QuIDDPro, take exponential time. We simulate quantum Fourier transform and quantum fault-tolerant circuits using Quipu, and the results demonstrate that our stabilizer-based technique empirically outperforms QuIDDPro in all cases. While previous high-performance, structure-aware simulations of quantum circuits were difficult to parallellize, we demonstrate that Quipu can be parallelized with a nontrivial computational speedup.
A watermark embedding and extracting method for printed documents (2005)

Abstract In this paper, we propose a new method of embedding watermarks into printed documents as well as extracting the watermarks from the printed documents. In the embedding process, unique mesh patterns in which microdots are assigned with equal spaces between them are inserted. We then assign 0 or 1 symbols to them, and generate and print a document image in which information is embedded by superimposing these mesh patterns as a document background. The extraction method involves filtering a scanned image of a watermarked printed document. We use a symbol assigned dot pattern as a 2D waveform, and a Gabor filter as a watermark detection filter. In this way, we implemented watermark detection resistant to various kinds of noise such as printing and scanning, or daily usage. We also provide results of basic performance evaluations, as well as test system evaluations for embedding and extracting watermarks in a practical environment. © 2005 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 88(7): 43–51, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjc.20142
Deep Learning to Generate <i>in Silico</i> Chemical Property Libraries and Candidate Molecules for Small Molecule Identification in Complex Samples (2019)

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g., mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e., without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (<i>m</i>/<i>z</i>, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large data set of structures with <i>m</i>/<i>z</i> labels. Next, <i>in silico</i> property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller data sets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.
Influence of UV illumination on the cold temperature operation of a LiNbO_3 Q-switched Nd:YAG laser (2010)

UV illumination of a lithium niobate Q-switch was demonstrated as an effective means to eliminate a loss in hold-off and associated prelasing that occurs under cold temperature operation of Q-switched lasers. This degradation occurs due to the pyroelectric effect, where an accumulation of charge on crystal faces results in a reduction in the Q-switch hold-off and a spatially variable loss of the Q-switch in its high-transmission state, both resulting in lowering of the maximum Q-switched pulse energy. With UV illumination, the resulting creation of photo-generated carriers was shown to be effective in eliminating both of these effects. A Q-switched Nd:YAG laser utilizing UV-illuminated LiNbO(3) was shown to operate under cold temperatures without prelasing or spatially variable loss.
Juggling the Effects of Latency (2015)

Projector-camera (pro-cam) systems afford a wide range of interactive possibilities, combining both natural and mixed-reality 3D interaction. However, the latency inherent within these systems can cause the projection to ?slip? from any moving target, so pro-cam systems have typically shied away from truly dynamic scenarios. We explore software-only techniques to reduce latency; considering the best achievable results with widely adopted commodity devices (e.g. 30Hz depth cameras and 60Hz projectors). We achieve 50% projection alignment on objects in free flight (a 34% improvement) and 69% alignment on dynamic human movement (a 40% improvement).
Tests of regional elemental tracers of pollution aerosols. 1. Distinctness of regional signatures, stability during transport, and empirical validation (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTests of regional elemental tracers of pollution aerosols. 1. Distinctness of regional signatures, stability during transport, and empirical validationDouglas H. Lowenthal, Kenneth R. Wunschel, and Kenneth A. RahnCite this: Environ. Sci. Technol. 1988, 22, 4, 413–420Publication Date (Print):April 1, 1988Publication History Published online1 May 2002Published inissue 1 April 1988https://doi.org/10.1021/es00169a008RIGHTS & PERMISSIONSArticle Views43Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
System for loading slab-gel holders for electrophoresis separation. [DOE patent] (1979)

A slab-gel loading system includes a prismatic chamber for filling a plurality of slab-gel holders simultaneously. Each slab-gel holder comprises a pair of spaced apart plates defining an intermediate volume for gel containment. The holders are vertically positioned in the chamber with their major surfaces parallel to the chamber end walls. A liquid inlet is provided at the corner between the bottom and a side wall of the chamber for distributing a polymerizable monomer solution or a coagulable colloidal solution into each of the holders. The chamber is rotatably supported so that filling can begin with the corner having the liquid inlet directed downwardly such that the solution is gently funneled upwardly, without mixing, along the diverging side and bottom surfaces. As filling proceeds, the chamber is gradually rotated to position the bottom wall in a horizontal mode. The liquid filling means includes a plastic envelope with a septum dividing it into two compartments for intermixing two solutions of different density and thereby providing a liquid flow having a density gradient. The resulting gels have a density gradient between opposite edges for subsequent use in electrophoresis separations.
Development of a high-explosive driven crowbar switch (1973)

A compact explosively-driven, metal-to-metal contact, solid dielectric switch was developed for use as a low-resistance, <10- mu OMEGA , low- inductance, < 10-nH, crowbar switch. A l00-milligram high-explosive charge is used to extrude a 0.090-in. plate through 0.040-in. polyethylene and achieve a hard current contact with a 0.625-in.-diameter die plate. The closure time, from the signal, which initiates the charge, to beginning of current rise in the switch, is 11.0 mu sec plus or minus 0.3 mu sec. In crowbar application the switch has carried 180 to 330 kA, which decays with a 1/e time of approximately 1.2 msec. (auth)