gebhart/patrepeval huggingface dataset:
Fast Implementation of KCipher-2 for Software and Hardware (2013)

KCipher-2 is a word-oriented stream cipher and an ISO/IEC 18033 standard. It is listed as a CRYPTREC cryptographic algorithm for Japanese governmental use. It consists of two feedback shift registers and a non-linear function. The size of each register in KCipher-2 is 32 bits and the non-linear function mainly applies 32-bit operations. Therefore, it can be efficiently implemented as software. SNOW-family stream ciphers are also word-oriented stream ciphers, and their high performance has already been demonstrated.We propose optimised implementations of KCipher-2 and compare their performance to that of the SNOW-family and other eSTREAM portfolios. The fastest algorithm is SNOW 2.0 and KCipher-2 is the second fastest despite the complicated irregular clocking mechanism. However, KCipher-2 is the fastest of the feasible algorithms, as SNOW 2.0 has been shown to have a security flaw. We also optimise the hardware implementation for the Virtex-5 field-programmable gate array (FPGA) and show two implementations. The first implementation is a rather straightforward optimisation and achieves 16,153 Mbps with 732 slices. In the second implementation, we duplicate the non-linear function using the structural advantage of KCipher-2 and we achieve 17,354 Mbps with 813 slices. Our implementation of KCipher-2 is around three times faster than those of the SNOW-family and efficiency, which is evaluated by “Throughput/Area (Mbps/slice)”, is 3.6-times better than that of SNOW 2.0 and 8.5-times better than that of SNOW 3G. These syntheses are performed using Xilinx ISE version 12.4.
Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches (2017)

Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic acid residues, is involved in numerous biotechnological applications in cosmetics, agriculture, pharmaceuticals, food and petroleum industries. Additionally, its oligosaccharides were shown to possess antimicrobial, antioxidant, and few other properties. Yet, despite its extensive usage, little is known about xanthan gum degradation pathways and mechanisms. <i>Thermogutta terrifontis</i>, isolated from a sample of microbial mat developed in a terrestrial hot spring of Kunashir island (Far-East of Russia), was described as the first thermophilic representative of the <i>Planctomycetes</i> phylum. It grows well on xanthan gum either at aerobic or anaerobic conditions. Genomic analysis unraveled the pathways of oligo- and polysaccharides utilization, as well as the mechanisms of aerobic and anaerobic respiration. The combination of genomic and transcriptomic approaches suggested a novel xanthan gum degradation pathway which involves novel glycosidase(s) of DUF1080 family, hydrolyzing xanthan gum backbone beta-glucosidic linkages and beta-mannosidases instead of xanthan lyases, catalyzing cleavage of terminal beta-mannosidic linkages. Surprisingly, the genes coding DUF1080 proteins were abundant in <i>T. terrifontis</i> and in many other <i>Planctomycetes</i> genomes, which, together with our observation that xanthan gum being a selective substrate for many planctomycetes, suggest crucial role of DUF1080 in xanthan gum degradation. Our findings shed light on the metabolism of the first thermophilic planctomycete, capable to degrade a number of polysaccharides, either aerobically or anaerobically, including the biotechnologically important bacterial polysaccharide xanthan gum.
New Polyhydroxylated Pyrrolidine, Piperidine, and Pyrrolizidine Alkaloids from Scilla sibirica (2002)

Chromatographic separation of an extract of the bulbs of Scilla sibirica resulted in the isolation of five pyrrolidines, two pyrrolidine glycosides, six piperidines, one piperidine glycoside, and eight pyrrolizidines. 2,5-Dideoxy-2,5-imino-glycero-d-manno-heptitol (homoDMDP, 1) is a common alkaloid in all plants of the Hyacinthaceae examined to date and was also found in S. sibirica. The structures of the new alkaloids were elucidated by spectroscopic methods as 7-deoxy-homoDMDP (4), 2,5-dideoxy-2,5-imino-glycero-d-galacto-heptitol (5), the 4-O-beta-d-mannoside (6) and the 4-O-beta-d-mannobioside (7) of 6-deoxy-homoDMDP (2), 7-deoxyhomonojirimycin (12), 7-deoxyhomomannojirimycin (13), and polyhydroxypyrrolizidines, hyacinthacines A(4) (15), A(5) (16), A(6) (17), A(7) (18), B(4) (20), B(5) (21), and B(6) (22). HomoDMDP (1) is a potent inhibitor of beta-glucosidase and beta-galactosidase, while 6-deoxy-homoDMDP (2) showed significantly less inhibition. However, 7-deoxygenation of 1, leading to 4, showed no effect on the inhibitory activity toward both enzymes. Although 2 is not an inhibitor of alpha-l-fucosidase, the monomannoside of 2 shows inhibitory activity toward alpha-l-fucosidase. Elongation of the beta-mannopyranosyl chain of 6 to give 7 enhanced the inhibitory activity.
Synthesis and Biological Evaluation of 4-Amino-1-β-D-Ribofuranosylpyrrolo[3,2-c]Pyriding (3-Deazatubercidin) (1989)

Abstract 4-Amino-1-β-D-ribofuranosylpyrrolo[3,2-c]pyridine (3-deazatubercidin) has been synthesized in four steps by glycosylation of the anion of the 4,6-dichloro-1H-pyrrolo[3,2-c]pyridine with 1-chloro-2,3-O-isopropylidene-5-O-(t-butyl)dimethylsily 1-α-D-ribofuranose. 3-Deaza-tubercidin was found devoid of antitumor activity in vitro.
Semantics and Metaphysics in Informatics: Toward an Ontology of Tasks (2011)

This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes.
Correlated compressive sensing for networked data (2014)

We consider the problem of recovering sparse correlated data on networks. To improve accu-racy and reduce costs, it is strongly desirable to take the potentially useful side-information of network structure into consideration. In this pa-per we present a novel correlated compressive sensing method called CorrCS for networked data. By naturally extending Bayesian compres-sive sensing, we extract correlations from net-work topology and encode them into a graphical model as prior. Then we derive posterior infer-ence algorithms for the recovery of jointly sparse and correlated networked data. First, we design algorithms to recover the data based on pairwise correlations between neighboring nodes in the network. Next, we generalize this model through a diffusion process to capture higher-order cor-relations. Both real-valued and binary data are considered. Our models are extensively tested on several real datasets from social and sensor networks and are shown to outperform baseline compressive sensing models in terms of recovery performance. 1
An Expeditious Synthesis of Lasofoxifene and Nafoxidine via the Novel Three-component Coupling Reaction (2006)

Abstract The simple and efficient synthesis of lasofoxifene (4), a possible candidate for alleviating osteoporosis, via the novel three-component coupling reaction among 4-pivaloyloxybenzaldehyde (5), cinnamyltrimethylsilane (6), and anisole in the presence of HfCl4 is illustrated. The successive cationic cyclization of the coupling product, olefin formation, and migration of the double-bond are performed to afford the common synthetic intermediate of lasofoxifene (4) and nafoxidine (3) via a very concise procedure.
Benchmarking Dynamic Capacitated Arc Routing Algorithms Using Real-World Traffic Simulation (2022)

The dynamic capacitated arc routing problem (DCARP) aims at re-scheduling the service plans of agents, such as vehicles in a city scenario, when dynamic events deteriorate the quality of the current schedule. Various algorithms have been proposed to solve DCARP instances in different dynamic scenarios. However, most existing work evaluated their algorithms' performance based on artificially constructed dynamic environments instead of using more realistic traffic simulations which are built on actual traffic data. In this paper, we constructed a novel DCARP benchmarking framework based on the Simulation of Urban MObility (SUMO) transportation simulation software, which allows to include real-world traffic environments for generating a set of DCARP instances from dynamic events, such as road congestion or task changes. The flexibility of the framework allows to develop DCARP optimization algorithms and evaluate their effectiveness more comprehensively. We use the benchmarking framework to generate 12 different dynamic instances using real-world traffic data of Dublin City. We then demonstrate the value of our framework by using these instances to compare our previously proposed hybrid local search algorithm (HyLS) with a state-of-the-art meta-heuristic optimization algorithm. The generated benchmark scenarios indicate that HyLS is a very effective optimizer on DCARP scenarios with real traffic data for reducing the total service cost. They also demonstrate the importance of our DCARP benchmarking framework for the development and benchmarking of optimization algorithms in more realistic scenarios.
Real-World Scenario Improvements in Serum Phosphorus Levels and Pill Burden in Peritoneal Dialysis Patients Treated with Sucroferric Oxyhydroxide (2018)

Among PD patients prescribed SO as part of routine care, improvements in serum phosphorus control and >50% reduction in PB pills/day were observed.
Single-dose activity of PSMA ADC against prostate cancer xenograft and explant tumors. (2010)

e13534 Background: Prostate-specific membrane antigen (PSMA) is an attractive target for antibody-targeted therapy of prostate cancer due to its abundant and selective expression on the surface of prostate cancer cells. We have generated a novel antibody-drug conjugate (ADC) by linking a fully human PSMA monoclonal antibody to monomethylauristatin-E (MMAE), a potent tubulin inhibitor. Here, we describe the use of PSMA ADC to treat SCID mice bearing LNCaP xenografts or LuCaP explants derived from surgical resections of prostate cancer patients. Methods: PSMA expression in LNCaP and LuCaP tumor cells was evaluated by flow cytometry. Activity of PSMA ADC, assessed by decrease in tumor volume, was evaluated in LNCaP xenograft and LuCaP explant models. SCID mice were implanted subcutaneously with cultured LNCaP tumor cells or disaggregated human LuCaP 70 or LuCaP 77 prostate tumor tissue obtained from tumor-bearing mice. When average tumor size reached ∼300mm3, animals were randomized into groups of 9–10 mice and each animal was treated with a single intravenous dose of vehicle control, a control ADC of irrelevant specificity, or PSMA ADC. Treatment effects were assessed by measuring tumor volume and overall survival for up to 41 days post-treatment. Results: Surface expression of PSMA was assessed by flow cytometry, with a rank order of expression as follows: LNCaP > LuCaP 70, LuCaP 77, LuCaP 105 > LuCaP 96.1 > LuCaP 35V, LuCaP 141. Single-dose PSMA ADC demonstrated significant activity against LNCaP xenografts at a dose of 5 mg/kg (p<0.0001 relative to either vehicle or control ADC) and against LuCaP 77 explants at a dose of 10 mg/kg (p=0.0003 relative to either vehicle or control ADC). A trend toward delayed tumor growth was observed in the LuCaP 70 tumor model. Conclusions: Single-dose PSMA ADC showed activity against LNCaP xenografts and LuCaP explants derived from surgical resections of prostate cancer patients. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration PSMA Development Company, LLC
NRAM: a disruptive carbon-nanotube resistance-change memory (2018)

Advanced memory technology based on carbon nanotubes (CNTs) (NRAM) possesses desired properties for implementation in a host of integrated systems due to demonstrated advantages of its operation including high speed (nanotubes can switch state in picoseconds), high endurance (over a trillion), and low power (with essential zero standby power). The applicable integrated systems for NRAM have markets that will see compound annual growth rates (CAGR) of over 62% between 2018 and 2023, with an embedded systems CAGR of 115% in 2018-2023 (http://bccresearch.com/pressroom/smc/bcc-research-predicts:-nram-(finally)-to-revolutionize-computer-memory). These opportunities are helping drive the realization of a shift from silicon-based to carbon-based (NRAM) memories. NRAM is a memory cell made up of an interlocking matrix of CNTs, either touching or slightly separated, leading to low or higher resistance states respectively. The small movement of atoms, as opposed to moving electrons for traditional silicon-based memories, renders NRAM with a more robust endurance and high temperature retention/operation which, along with high speed/low power, is expected to blossom in this memory technology to be a disruptive replacement for the current status quo of DRAM (dynamic RAM), SRAM (static RAM), and NAND flash memories.
Creep Behavior of Lead Free Solder Interconnects in Microelectronic Packages: Impression Creep Testing and Constitutive Modeling (2005)

The creep behavior of ball grid array (BGA) or flip-chip (FC) solder joints during thermo-mechanical cycling associated with service often limits the reliability of microelectronic packages. In addition, the fine intermetallic precipitates (Ag3Sn and/or Cu6Sn5) in the microstructures of the new lead-free solders (Sn-Ag and Sn-Ag-Cu) can undergo significant in situ strain-enhanced coarsening during TMC, resulting in in-service evolution of the creep behavior of the joints. Since there are significant microstructural/ compositional differences between bulk solder samples and tiny microelectronic solder joints, it is critical to develop accurate creep testing methodologies on tiny life-sized solder joints and microstructurally adaptive constitutive creep models for the emerging Pb-free solder alloys. In this paper, we present creep data obtained from tests conducted on individual Sn4Ag0.5Cu ball grid array (BGA) solder balls attached to a packaging substrate, using a newly developed miniaturized impression creep apparatus, which affords high test throughput with minimal sample preparation. Coarsening of intermetallic particles is demonstrated to influence creep behavior in two ways. At low stresses, the creep rate increases proportionately with precipitate size. At high stresses, precipitate coarsening influences creep response by altering the threshold stress for particle-limited creep. Based on the experimental observations, a microstructurally adaptive creep model, which accounts for the effects of coarsening on the creep response of solder joints, and is capable of adjusting itself as solder joint microstructures evolve during service, is presented, along with experimental determination of the relevant coarsening kinetics parameters.
Light Directed Electrophoretic Deposition for Additive Manufacturing: Spatially Localized Deposition Control with Photoconductive Counter Electrodes (2015)

Electrophoretic deposition (EPD) has traditionally been viewed as a thin film deposition technique for coating conductive surfaces. Recently, there have been reports of producing functional parts with EPD to near net shape, often containing gradients in material properties normal to the conductive deposition surface. By using reconfigurable electrode systems, a few researchers have gone beyond purely out-of-plane gradients and demonstrated gradients in material properties in the plane of the deposition electrode, a necessary condition for 3D additive manufacturing. In this work, we build upon a previously published technique called light directed electrophoretic deposition (LD-EPD) in which the deposition electrode is photoconductive and can be activated with light, leading to a patterned deposit. Here, we demonstrate that the LD-EPD technique can also lead to patterned deposits on any conductive surface by utilizing the photoconductive electrode as the counter electrode. This eliminates several issues with standard LD-EPD by allowing the potentially expensive photoconductive electrode to be reused, as well as mitigates post-processing material compatibility issues by allowing deposition on any conductive surface. We also detail the results of a finite element simulation of the deposition process in LD-EPD systems that captures key features seen experimentally in the final deposit.
Optical signal processing for millimeter-wave wireless systems (2012)

This presentation will discuss optical signal processing techniques for high-speed modulation of millimeter-wave, which can provide high-speed wireless transmission of 40Gb/s. Pure optical two-tone signals can be converted into millimeter-wave signals by using high-speed photodetectors.
Explaining AI (2020)

Explainable AI (XAI) has started experiencing explosive growth, echoing the explosive growth that has preceded it of AI becoming used for practical purposes that impact the general public. This spread of AI into the world outside of research labs brings with it pressures and requirements that many of us have perhaps not thought about deeply enough. In this keynote address, I will explain why I think we have a very long way to go.
Design, synthesis and applications of core–shell, hollow core, and nanorattle multifunctional nanostructures (2016)

With the evolution of nanoscience and nanotechnology, studies have been focused on manipulating nanoparticle properties through the control of their size, composition, and morphology. As nanomaterial research has progressed, the foremost focus has gradually shifted from synthesis, morphology control, and characterization of properties to the investigation of function and the utility of integrating these materials and chemical sciences with the physical, biological, and medical fields, which therefore necessitates the development of novel materials that are capable of performing multiple tasks and functions. The construction of multifunctional nanomaterials that integrate two or more functions into a single geometry has been achieved through the surface-coating technique, which created a new class of substances designated as core-shell nanoparticles. Core-shell materials have growing and expanding applications due to the multifunctionality that is achieved through the formation of multiple shells as well as the manipulation of core/shell materials. Moreover, core removal from core-shell-based structures offers excellent opportunities to construct multifunctional hollow core architectures that possess huge storage capacities, low densities, and tunable optical properties. Furthermore, the fabrication of nanomaterials that have the combined properties of a core-shell structure with that of a hollow one has resulted in the creation of a new and important class of substances, known as the rattle core-shell nanoparticles, or nanorattles. The design strategies of these new multifunctional nanostructures (core-shell, hollow core, and nanorattle) are discussed in the first part of this review. In the second part, different synthesis and fabrication approaches for multifunctional core-shell, hollow core-shell and rattle core-shell architectures are highlighted. Finally, in the last part of the article, the versatile and diverse applications of these nanoarchitectures in catalysis, energy storage, sensing, and biomedicine are presented.
Supplementary Table 3 from Robust Antitumor Immunity in a Patient with Metastatic Colorectal Cancer Treated with Cytotoxic Regimens (2023)

&lt;p&gt;Supplementary Table 3&lt;/p&gt;
Synthesis of Psymberin/Irciniastatin A (2006)

Irciniastatin A and Psymberin were isolated independently by the groups of Pettit and Crews in 2004 from the sponges Ircinia ramose and Psammocinia sp., respectively. This synthesis established the stereochemistry at C4 and C8, left unresolved at the time of isolation, and showed that Psymberin and Irciniastatin A are identical. Psymberin/Irciniastatin A is a very potent antitumor agent.
P04.52 Spontaneous intratumoral T cell responses against glioblastoma-associated antigens (2018)

Glioblastomas (GBMs) are so-called “cold tumors” with a low mutational load and low intratumoral T cell abundance. Hence, major histocompatibility class (MHC) I or II-restricted tumor-specific T cell responses are rare or not even identifiable. In our study, we aim at identifying spontaneous intratumoral tumor-associated antigen (TAA)-specific T cell responses. TAAs such as cancer/testis antigens (CTAs), are frequently overexpressed across multiple cancer entities. Previous studies have shown that certain TAAs show limited or no expression in normal brain tissue and can therefore be exploited as targets for glioblastoma immunotherapy. However, the presence and extent of spontaneous TAA-reactive T cells within the intratumoral T cell repertoire remains unclear. GBM tumor-infiltrating lymphocytes (TILs) from three patients were expanded in vitro with a combination of high dose interleukin (IL)-2 and anti-CD3 antibody. RNA-sequencing (RNA-seq) and quantitative PCR (qPCR) analyses from corresponding cryopreserved tissues were performed to evaluate individual TAA expression. Expression levels were compared to normal brain homogenates (n=50, cut-off: 1 rpkm). Patient-individual TAAs were ranked according to expression levels and in silico HLA-restricted binding predictions and compared to GBM-associated targets that were identified by RNA-seq of 144 archival GBM tissues. HLA-typing from PBMCs was performed by next generation sequencing. ELISpot peptide TIL-T cell co-culture assays were performed using expanded GBM-derived TILs and autologous dendritic cells. For HLA-A2-positive patients, K562 cells were transduced with HLA-A*02:01 and used as artificial antigen presenting cells. Four promising shared GBM-associated targets were identified by RNA-seq of 144 archival tissues and subsequently validated by Fluidigm analyses. Based on the applied selection criteria, there was no overlap between the top five ranked individual TAAs and the four identified shared GBM-associated antigens. Evaluation of intratumoral spontaneous T cell immune responses revealed reactivity in one of three evaluated patients against individual and shared overexpressed targets, respectively. For HLA-A2+ patients, artificial antigen presenting cells are reasonable off-the-shelf tools to evaluate intratumoral T cell responses. In contrast to spontaneous neoepitope-specific T cell responses, spontaneous intratumoral TAA-specific T cell responses can be identified. Thorough evaluation of expression levels, relative tumor-restriction and analyses of spontaneous intratumoral T cell responses may revive immunotherapeutic strategies targeting TAAs in the era of neo-epitopes.
Comprehensive Breast Cancer Risk Assessment for CHEK2 and ATM Pathogenic Variant Carriers Incorporating a Polygenic Risk Score and the Tyrer-Cuzick Model (2021)

In <i>CHEK2</i> and <i>ATM</i> PV carriers, risk assessment including PRS, Tyrer-Cuzick, and PV status has the potential for more precise direction of screening and prevention strategies.
Analyzing surface sampling patterns using the localized pair correlation function (2016)

Point distributions with different characteristics have a crucial influence on graphics applications. Various analysis tools have been developed in recent years, mainly for blue noise sampling in Euclidean domains. In this paper, we present a new method to analyze the properties of general sampling patterns that are distributed on mesh surfaces. The core idea is to generalize to surfaces the pair correlation function (PCF) which has successfully been employed in sampling pattern analysis and synthesis in 2D and 3D. Experimental results demonstrate that the proposed approach can reveal correlations of point sets generated by a wide range of sampling algorithms. An acceleration technique is also suggested to improve the performance of the PCF.