gebhart/patrepeval huggingface dataset:
Abstract 1241: Targeting the IL-13 receptor alpha 2 with novel antibody-drug conjugates for the treatment of cancer. (2013)

Abstract The IL-13 receptor alpha 2 (IL-13Rα2) is a transmembrane protein that is highly expressed on several cancers including glioblastoma, ovarian, pancreatic cancers. It can internalize after binding to its ligand IL-13 or in response to ligation with an antibody. In addition, we have discovered that IL-13Rα2 is up-regulated in tumor cell lines that are resistant to chemotherapeutic drugs. These properties make IL-13Rα2 an attractive target for antibody-drug conjugate (ADC), an emerging modality of molecularly targeted cancer therapies. A humanized monoclonal antibody, hAB08 with an affinity of 0.17 nM to the soluble recombined hIL-13Rα2, was conjugated with two novel microtubule inhibitors (MTIs), MTI1 and MTI2, developed by Pfizer. In vitro cytotoxicity of the conjugates was tested against IL-13Rα2 positive and negative cell lines. These conjugates were effective against the IL-13Rα2 positive cell lines (PC3MM2 and A375), having an IC50 ranging from 1.1 to 3.8 ng Ab/mL. However, both of the ADCs were not active against the IL-13Rα2 negative H460 cell line. When treating mice with established human PC3MM2 and A375 tumors, these conjugates were efficacious at 3 mg/kg in reducing tumor growth. In the PC3MM2 model, treatment with hAB08-MTI1 and hAB08-MTI2 resulted in 5 out of 8 or 3 out of 8 animals without measurable tumors at Day 76, respectively. In contrast, the vehicle control group and control ADC (hIgG8.8-MTI1 and hIgG8.8-MTI2) groups were terminated at Day 15, 15, 19 due to the large size of tumors, respectively. These in vitro and in vivo results demonstrate potent antitumor activities of hAB08-MTI1 and hAB08-MTI2 against IL-13Rα2 positive tumors. The findings support the development of novel hAB08-MTI1 or hAB08-MTI2 ADCs as a molecularly targeted therapy for cancer patients that are resistant to standard chemotherapy. Citation Format: Dangshe Ma, Haige Zhang, Fang Jin, Manoj Charati, Kiran Khandke, Judy Lucas, Max Follettie, L. Nathan Tumey, Hans-Peter Gerber, Lioudmila Tchistiakova, Puja Sapra. Targeting the IL-13 receptor alpha 2 with novel antibody-drug conjugates for the treatment of cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1241. doi:10.1158/1538-7445.AM2013-1241
In situ methane enrichment in anaerobic digestion (1990)

A major cost consideration in the use of anaerobic digestion to convert biomass and waste to utility-grade gas is the expense of separating CO(2) from the product gas. Anaerobic digestion has a number of inherent properties that can be exploited to increase the methane content of the gas directly produced by the digester, the most important of which is the high solubility of CO(2)(40-60 times that of methane) in water under digestion conditions. The methane enrichment concept examined in this study involved the recirculation of a liquid stream from the digester through a CO(2) desorption process and the return of the liquid stream back to the digester for absorption of additional CO(2) produced by the conversion of organic materials. A steady-state equilibrium model predicted that a digester gas methane content exceeding 94% could be achieved with this scheme using modest recirculation rates provided a desorption process could be designed to achieve a 60+% CO(2) removal efficiency in the degassing of the liquid recycle stream. Using fixed-film laboratory digesters operated on synthetic feedstocks, the technique of methane enrichment was tested under pressurized and unpressurized conditions. A 93 + 2% methane gas stream was produced from a volatile-acid-fed bench-scale digester simulating the methanogenic stage of two-phase digestion under conditions of (1) a pH swing achieved without caustic addition that allowed digestion at pH 7. 5 and air stripping at pH 6. 5-7. 0, (2) digester pressurization to 30 psig, and (3) a recycle rate of 0. 33 L/L reactor/day. Significant but lower levels of methane enrichment were achieved with the single-stage digester at the low experimental recycle rate. However, the narrow range among all experiments of CO(2) desorption efficiencies achieved in air stripping the recycle stream (35-60% CO(2) removal) suggests that comparable methane enrichment-may be achieved with unpressurized single-stage digestion using greater recycle rates. A materials balance analysis of data from an unpressurized, single-stage digester employing no chemical addition and using laboratory degassing efficiencies indicated that 94% methane could be produced at recycle rates of less than 1. 4 L/L reactor/day with a methane loss of less than 2%.
Collagen fiber orientation disorder from H&E images is prognostic for early stage breast cancer: clinical trial validation (2021)

Collagen fiber organization has been found to be implicated in breast cancer prognosis. In this study, we evaluated whether computerized features of Collagen Fiber Orientation Disorder in Tumor-associated Stroma (CFOD-TS) on Hematoxylin & Eosin (H&E) slide images were prognostic of Disease Free Survival (DFS) in early stage Estrogen Receptor Positive (ER+) Invasive Breast Cancers (IBC). A Cox regression model named M<sub>CFOD-TS</sub>, was constructed using cohort S<sub>t</sub> (N = 78) to predict DFS based on CFOD-TS features. The prognostic performance of M<sub>CFOD-TS</sub> was validated on cohort S<sub>v</sub> (N = 219), a prospective clinical trial dataset (ECOG 2197). M<sub>CFOD-TS</sub> was prognostic of DFS in both S<sub>t</sub> and S<sub>v</sub>, independent of clinicopathological variables. Additionally, the molecular pathways regarding cell cycle regulation were identified as being significantly associated with M<sub>CFOD-TS</sub> derived risk scores. Our results also found that collagen fiber organization was more ordered in patients with short DFS. Our study provided a H&E image-based pipeline to derive a potential prognostic biomarker for early stage ER+ IBC without the need of special collagen staining or advanced microscopy techniques.
Biocatalytic Synthesis of <scp>d</scp>-Amino Acids (2006)

A biocatalytic asymmetric approach to unnatural α-amino acids has been described. Directed evolution using both rational and random mutagenesis and screening from wild-type enzyme meso-diaminopimelate d-dehydrogenase (DAPDH) has provided d-amino acid dehydrogenase BC621 (1). This mutant mediates the reductive amination of 2-keto acids 2 with ammonia and NADPH as cofactor to give d-amino acids 3 in excellent enantioselectivities. Linear and branched alkyl substrates, as well as aryl precursors can be used.
Theory and Analysis of GaAs MESFET Mixers (Short Papers) (1984)

A generalized analysis of the GaAs MESFET mixer is presented. Its advantage is that many of the simplifying assumptions in previous approaches have been substantially eliminated. Using this approach, the nonlinearities of any number of elements in the FET equivalent circuit may be included, any number of Iocal oscillator (LO) harmonics and mixing products may he considered, unusual mixers such as subharmonic mixers, upconverters, and mixers with high IF frequencies can be analyzed. The theory has been verified experimentally. Two mixers are described: one exhibits 11.5-dB conversion gain with + 9-dBm LO power, 5.6-dB minimum noise figure and + 15-dBm third-order intermodulation intercept, and another which exhibits 500-MHz bandwidth, 6-dB minimum gain, 5.5-dB maximum noise figure, and + 12-dBm third-order intercept at + 6-dBm LO power.
Transfer of Microparticles across Laminar Streams from Non-Newtonian to Newtonian Fluid (2016)

Engineering inertial lift forces and elastic lift forces is explored to transfer microparticles across laminar streams from non-Newtonian to Newtonian fluid. A co-stream of non-Newtonian flow loaded with microparticles (9.9 and 2.0 μm in diameter) and a Newtonian carrier medium flow in a straight rectangular conduit is devised. The elastic lift forces present in the non-Newtonian fluid, undeterred by particle-particle interaction, successfully pass most of the larger (9.9 μm) particles over to the Newtonian fluid. The Newtonian fluid takes over the larger particles and focus them on the equilibrium position, separating the larger particles from the smaller particles. This mechanism enabled processing of densely suspended particle samples. The method offers dilution-free (for number densities up to 10,000 μL(-1)), high throughput (6700 beads/s), and highly efficient (>99% recovery rate, >97% purity) particle separation operated over a wide range of flow rate (2 orders of magnitude).
Design of an Atraumatic Compliant Surgical Grasper (2012)

Frontiers Abstracts Design of an Atraumatic Compliant Surgical Grasper Alan Goyzueta, Alan Goyzueta Search for other works by this author on: This Site PubMed Google Scholar Carl A. Nelson Carl A. Nelson Dept. of Mechanical & Materials Engineering;University of Nebraska–Lincoln Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information Carl A. Nelson Dept. of Mechanical & Materials Engineering;University of Nebraska–Lincoln J. Med. Devices. Mar 2012, 6(1): 017544 (1 pages) https://doi.org/10.1115/1.4026722 Published Online: March 12, 2012 Article history Received: May 27, 2011 Revision Received: November 7, 2011
Evolution of the Architecture and Technology of Data Centers towards Exascale and Beyond (2013)

The continual growth of data centers cannot be maintained through incremental advances in today’s technologies and architectures. An alternative architecture based on reconfigurable WDM optical networking technology is presented for realizing future, exascale, elastic data centers.
Synergistic Neutralization of HIV-1 by Human Monoclonal Antibodies Against the V3 Loop and the CD4-Binding Site of gp120 (1992)

Two distinct regions or epitope clusters of human immunodeficiency virus type 1 (HIV-1) gp120 have been shown to elicit neutralizing antibodies: the V3 loop and the CD4-binding site. We have isolated neutralizing human monoclonal antibodies (HuMAbs) against conserved epitopes in both of these regions. In this study, we demonstrate that an equimolar mixture of two of these HuMAbs, one directed against the V3 loop and the other against the CD4-binding site, neutralizes HIV-1 at much lower concentrations than does either of the individual HuMAbs. Mathematical analysis of this effect suggests cooperative neutralization of HIV-1 by the two HuMAbs and demonstrates a high level of synergy, with combination indices (CIs) of 0.07 and 0.16 for 90% neutralization of the MN and SF-2 strains, respectively. The dose reduction indices (DRIs) for each of the two HuMAbs at 99% neutralization range approximately from 10 to 150. A possible mechanism for this synergism is suggested by binding studies with recombinant gp160 of the MN strain; these show enhanced binding of the anti-CD4 binding site HuMAb in the presence of the anti-V3 loop HuMAb. These results demonstrate the advantage of including both V3 loop and CD4-binding site epitopes in a vaccine against HIV-1 and indicate that combinations of HuMAbs against these two sites may be particularly effective in passive immunotherapy against the virus.
Clickable Nucleic Acids: Sequence‐Controlled Periodic Copolymer/Oligomer Synthesis by Orthogonal Thiol‐X Reactions (2015)

Synthetic polymer approaches generally lack the ability to control the primary sequence, with sequence control referred to as the holy grail. Two click chemistry reactions were now combined to form nucleobase-containing sequence-controlled polymers in simple polymerization reactions. Two distinct approaches are used to form these click nucleic acid (CNA) polymers. These approaches employ thiol-ene and thiol-Michael reactions to form homopolymers of a single nucleobase (e.g., poly(A)n ) or homopolymers of specific repeating nucleobase sequences (e.g., poly(ATC)n). Furthermore, the incorporation of monofunctional thiol-terminated polymers into the polymerization system enables the preparation of multiblock copolymers in a single reaction vessel; the length of the diblock copolymer can be tuned by the stoichiometric ratio and/or the monomer functionality. These polymers are also used for organogel formation where complementary CNA-based polymers form reversible crosslinks.
Polynomial approach to optimal one-wafer cyclic scheduling of treelike hybrid multi-cluster tools via Petri nets (2017)

A treelike hybrid multi-cluster tool is composed of both single-arm and dual-arm cluster tools with a treelike topology. Scheduling such a tool is challenging. For a hybrid treelike multi-cluster tool whose bottleneck individual tool is process-bound, this work aims at finding its optimal one-wafer cyclic schedule. It is modeled with Petri nets such that a onewafer cyclic schedule is parameterized as its robots' waiting time. Based on the model, this work proves the existence of its onewafer cyclic schedule that features with the ease of industrial implementation. Then, computationally efficient algorithms are proposed to find the minimal cycle time and optimal onewafer cyclic schedule. Multi-cluster tool examples are given to illustrate the proposed approach. The use of the found schedules enables industrial multi-cluster tools to operate with their highest productivity.
Stability analysis of a Scanning Tunneling Microscope control system (2017)

Control system of a Scanning Tunneling Microscope is analyzed. For the aim of model-based control system analysis and design, open-loop model of the plant is obtained based on the closed-loop system identification tests. We conduct identification tests in the frequency-domain, derive transfer function models of the open-loop system, and discuss the main sources that lead to model uncertainties. We define appropriate closed-loop stability and performance measures, and evaluate performance of a conventional PI controller in the framework of the defined criteria. We show that uncertainties arising from a quantum mechanical property of the tunneling junction, known as the Work Function, can have a destabilizing effect on the control system. This increases the risk of tip-sample crash which is a prevalent operational problem in STM. We experimentally evaluate the presented analysis, and suggest guidelines for PI gain tuning.
Introducing Real-Time On-Board SAR Image Generation using an Optronic SAR Processor (2010)

This paper introduces a compact optronic processor prototype that has the capability to instantaneously generate SAR images. This real-time processor is light weight, low power consuming and small in size, the design being specifically targeted for on-board SAR image processing. SAR images are typically processed electronically applying dedicated Fourier transformations. This may be performed optically at the speed of light, however. The optronic processor architecture provides inherent parallel computing capabilities for fast SAR processing. Indeed, SAR images have been generated from ENVISAT / ASAR raw data. A review of the design of the optronic processor prototype and an analysis of the SAR images it produces are presented.
Response to Comment on "All-optical machine learning using diffractive deep neural networks" (2018)

In their Comment, Wei et al. (arXiv:1809.08360v1 [cs.LG]) claim that our original interpretation of Diffractive Deep Neural Networks (D2NN) represent a mischaracterization of the system due to linearity and passivity. In this Response, we detail how this mischaracterization claim is unwarranted and oblivious to several sections detailed in our original manuscript (Science, DOI: 10.1126/science.aat8084) that specifically introduced and discussed optical nonlinearities and reconfigurability of D2NNs, as part of our proposed framework to enhance its performance. To further refute the mischaracterization claim of Wei et al., we, once again, demonstrate the depth feature of optical D2NNs by showing that multiple diffractive layers operating collectively within a D2NN present additional degrees-of-freedom compared to a single diffractive layer to achieve better classification accuracy, as well as improved output signal contrast and diffraction efficiency as the number of diffractive layers increase, showing the deepness of a D2NN, and its inherent depth advantage for improved performance. In summary, the Comment by Wei et al. does not provide an amendment to the original teachings of our original manuscript, and all of our results, core conclusions and methodology of research reported in Science (DOI: 10.1126/science.aat8084) remain entirely valid.
Stacked frequency reconfigurable Yagi‐like MIMO antenna system (2020)

In this work, a 2‐layer frequency reconfigurable Yagi‐like multiple‐input–multiple‐output (MIMO) antenna system is proposed based on a closed pentagonal slot‐loop excitation. The MIMO system consists of 4 identical active antenna elements reactively loaded with varactor diodes to achieve frequency reconfigurability over a band from 1.5 to 2.1 GHz. The distinguishing feature of the proposed work is achieving Yagi‐like directional characteristics over a very wide frequency band. The conventional omni‐directional pattern of a slot antenna is made directional by using a parasitic metallic reflector layer below the substrate. By using the reflector element, the back‐lobe radiation is highly suppressed and a front‐to‐back ratio of 5–13 dB is achieved within the entire frequency band of operation. The proposed design is compact with an overall size of , and a reflector size of . A single element has a maximum peak gain of 4 dBi and total measured radiation efficiency of 76%. The antenna system also shows good MIMO performance with high port isolation of 11.3 dB and very low envelope correlation coefficient values within the operational band.
Toward Incremental FIB Aggregation with Quick Selections (FAQS) (2018)

Several approaches to mitigating the Forwarding Information Base (FIB) overflow problem were developed and software solutions using FIB aggregation are of particular interest. One of the greatest concerns to deploy these algorithms to real networks is their high running time and heavy computational overhead to handle thousands of FIB updates every second. In this work, we manage to use a single tree traversal to implement faster aggregation and update handling algorithm with much lower memory footprint than other existing work. We utilize 6-year realistic IPv4 and IPv6 routing tables from 2011 to 2016 to evaluate the performance of our algorithm with various metrics. To the best of our knowledge, it is the first time that IPv6 FIB aggregation has been performed. Our new solution is 2.53 and 1.75 times as fast as the-state-of-the-art FIB aggregation algorithm for IPv4 and IPv6 FIBs, respectively, while achieving a near-optimal FIB aggregation ratio.
Exploiting Idle Resources in a High-Radix Switch for Supplemental Storage (2018)

A general-purpose switch for a high-performance network is usually designed with symmetric ports providing credit-based flow control and error recovery via link-level re-transmission. Because port buffers must be sized for the longest links and modern asymmetric network topologies have a wide range of link lengths, we observe that there can be a significant amount of unused buffer memory, particularly in edge switches. We also observe that the tiled architecture used in many high-radix switches contains an abundance of internal bandwidth. We combine these observations to create a new switch architecture that allows ports to stash packets in unused buffers on other ports, accessible via excess internal bandwidth in the tiled switch. We explore this architecture through two use cases: end-to-end resilience and congestion mitigation. We find that stashing is highly effective and does not degrade network performance.
Acoustic tomography at basin scales and clock errors (1997)

A basin scale underwater acoustic tomography simulation is carried out for the northeast Pacific Ocean to determine the accuracy with which time must be kept at the sources when clocks at the receivers are accurate. A sequential Kalman filter is used to estimate sound-speed perturbation and clock errors. Using an acoustic array of 4 fixed sources and 20 drifting receivers, it is found that the percentage of the modeled ocean’s sound-speed variance accounted for with tomography is 92% at 400-km resolution, practically regardless of the accuracy of the clocks. Clocks which drift up to hundreds of seconds of error (or even more) for a year do not degrade tomographic reconstruction of the model ocean. It is shown that tomographic reconstructions of the sound-speed field are insensitive to clock errors primarily because of a wide variety of distances between the receivers and each particular source. Every receiver ‘‘sees’’ the same clock error from the source, regardless of section length, but changes of travel time associated with the sound-speed perturbation depend on the section length. The Kalman filter is thus able to reconstruct clock error and to map the sound-speed field accurately. [Work supported by ARPA, ♯MDA972-931-0004.]
Approximate data structures with applications (1994)

In this paper we introduce the notion of approximate da2a siruclures, in which a small amount of error is tolerated in the output. Approximate data structures trade error of approximation for faster operation, leading to theoretical and practical speedups for a wide variety of algorithms. We give approximate variants of the van Emde Boas data structure, which support the same dynamic operations as the standard van Emde Boas data structure [28, 201, except that answers to queries are approximate. The variants support all operations in constant time provided the error of approximation is l/polylog(n), and in O(loglog n) time provided the error is l/polynomial(n), for n elements in the data structure. We consider the tolerance of prototypical algorithms to approximate data structures. We study in particular Prim’s minimumspanning tree algorithm, Dijkstra’s single-source shortest paths algorithm, and an on-line variant of Graham’s convex hull algorithm. To obtain output which approximates the desired output with the error of approximation tending to zero, Prim’s algorithm requires only linear time, Dijkstra’s algorithm requires O(mloglogn) time, and the on-line variant of Graham’s algorithm requires constant amortized time per operation.
Structural Basis for Differential Neutralization of Ebolaviruses (2012)

There are five antigenically distinct ebolaviruses that cause hemorrhagic fever in humans or non-human primates (Ebola virus, Sudan virus, Reston virus, Taï Forest virus, and Bundibugyo virus). The small handful of antibodies known to neutralize the ebolaviruses bind to the surface glycoprotein termed GP₁,₂. Curiously, some antibodies against them are known to neutralize in vitro but not protect in vivo, whereas other antibodies are known to protect animal models in vivo, but not neutralize in vitro. A detailed understanding of what constitutes a neutralizing and/or protective antibody response is critical for development of novel therapeutic strategies. Here, we show that paradoxically, a lower affinity antibody with restricted access to its epitope confers better neutralization than a higher affinity antibody against a similar epitope, suggesting that either subtle differences in epitope, or different characteristics of the GP₁,₂ molecules themselves, confer differential neutralization susceptibility. Here, we also report the crystal structure of trimeric, prefusion GP₁,₂ from the original 1976 Boniface variant of Sudan virus complexed with 16F6, the first antibody known to neutralize Sudan virus, and compare the structure to that of Sudan virus, variant Gulu. We discuss new structural details of the GP₁-GP₂ clamp, thermal motion of various regions in GP₁,₂ across the two viruses visualized, details of differential interaction of the crystallized neutralizing antibodies, and their relevance for virus neutralization.