gebhart/patrepeval huggingface dataset:
Abstract B14: Neoantigen burden associates with chemoresponse in muscle-invasive bladder cancer patients receiving neoadjuvant chemotherapy (2017)

Abstract Background: The basis of response to chemotherapy is incompletely characterized. The immune system is increasingly recognized as both a key player in cancer control and as druggable target. We hypothesized that the immune system impacts pathologic response in patients undergoing cisplatin-based neoadjuvant chemotherapy (NAC) for muscle-invasive (≥pT2) bladder cancer though neoantigens present in tumors. Methods: Whole exome sequencing (WES) was performed on tumor DNA from patients in two independent cohorts who underwent cisplatin-based NAC. Pathologic response was defined in the cystectomy specimen. The Memorial Sloan Kettering/Dana Farber Cancer institute (MSKCC/DFCI) cohort (n=50; 25 ≤ pTis responders) and Philadelphia cohorts (n=48; 20 ≤ pTis responders) were treated with gemcitabine/ cisplatin or methotrexate/ vinblastine/ doxorubicin/ cisplatin. Mutation analysis was performed using standard analytical pipelines. Macrohistocompatibility complex (MHC)-restricted neoantigens were identified with netMHCpan and PolySolver. Wilcoxon rank sum test was used to test for significance and all tests were two-sided. Results: In both cohorts, mutation rate associated with pathologic response (p&amp;lt;0.01 and p&amp;lt;0.001 in Philadelphia and MSKCC/DFCI cohorts, respectively). In the MSKCC/DFCI cohort, the median predicted high affinity (Kd&amp;lt;500 nM) neoantigen count was 311 versus 154 for responding and nonresponding tumors, respectively (p=0.002). For the Philadelphia cohort, the median neoantigen count was 439 versus 218 for responding and nonresponding tumors, respectively (p=8.2 x 10-7). The relationship between neoantigen density and response maintained significance independent of the definition of response (pT0, ≤ pTis, ≤ pT1) and independent of the neoantigen Kd (500 nM, 100 nM, 50 nM) in both cohorts and when cohorts were combined. Conclusions: Mutational load and neoantigen burden correlate strongly with pathologic response to NAC. Chemotherapy may therefore exert tumor cell autonomous effects through apoptotic mechanisms and a tumor cell extrinsic effect by alerting the immune system via neoantigen presentation on dying cells. Mutation rate is likely directly correlated to neoantigen burden and both may impact patient selection for chemotherapy alone or in combination with immunotherapy agents, and development of antitumor vaccines. Experiments are underway to more directly characterize the impact of the immune system in the response to chemotherapy. Citation Format: Philip H. Abbosh, David Liu, Michael H. Johnson, Wafik S. El-Deiry, Elizabeth R. Plimack, Jonathan E. Rosenberg, Eliezer M. Van Allen. Neoantigen burden associates with chemoresponse in muscle-invasive bladder cancer patients receiving neoadjuvant chemotherapy. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr B14.
Spontaneous room temperature exchange bias formation in polycrystalline IrMn based spin valves (2016)

Trabajo presentado en la 61st Annual Conference on Magnetism and Magnetic Materials, celebrada en New Orleans (Lousiana, EE.UU), del 31 de octubre al 4 de noviembre de 2016
In Situ Monitoring of Photo-Cross-Linking Reaction of Anthracene Chromophores in Polymer Langmuir−Blodgett Films by an Integrated Optical Waveguide Technique (2001)

This paper focuses on waveguide technique versatility for direct observation of photochemical reactions in polymer ultrathin films. Monolayers from the copolymer of 9-anthrylmethyl methacrylate (AMMA) with neopentyl methacrylamide (nPMA) were deposited on a tapered quartz waveguide by the Langmuir−Blodgett (LB) technique, and spectroscopic properties of the copolymer (p(nPMA-AMMA)) monolayer were precisely monitored by an integrated optical waveguide technique. Magnitude of absorbance increased by a factor of 200, compared with transmission UV−vis spectroscopy. Consequently, a photo-cross-linking reaction of p(nPMA-AMMA) LB films was characterized easily and very accurately as a function of irradiation time.
Policy Allocation for Transmission of Embedded Bit Streams over Noisy Channels with Feedback (2009)

An efficient policy allocation algorithm for the transmission of embedded bit streams over noisy channels with feedback is proposed. The transmission is based on the type-II Hybrid ARQ/FEC protocol and uses a nested sequence C of channel codes to protect the packets. There are also constraints on the total bit budget and on the allowed number of retransmissions per packet. The allocation algorithm assigns different protection policies, each policy being a subset of C, to different packets to maximize the average number of correctly received source bits. We study the performance and the complexity of the proposed scheme through the transmission of images encoded by JPEG2000 over mobile channels with correlated Rayleigh fading. We demonstrate by simulations that the proposed multiple-policy scheme provides significant improvements over a purely FEC scheme with no feedback and also the existing fixed-policy (equal error protection) schemes. Our results show that feedback is particularly helpful for poor channel conditions and that the proposed scheme is very robust against changes in the channel signal-to-noise ratio (SNR) and the mobile speed.
Characteristics of pandemic influenza A (H1N1) infection in patients presenting to a university hospital in Riyadh, Saudi Arabia. (2011)

These findings indicate indigenous influenza A (H1N1) transmission, and confirm the urgent need for prevention strategies which specifically target children and young adults, who appear to have a higher risk of infection and hospitalization. Such measures include immunization, improved personal hygiene, and increased ventilation in habitations.
Fast method for noise level estimation and integrated noise reduction (2005)

This paper describes a fast method for noise level estimation and denoising. Specifically, we address the problem of estimating the standard deviation of additive white Gaussian noise in digital images; the computed value is used to reduce Gaussian noise and eliminate defective pixels in a raw digital image. The method is particularly suitable for implementation in low power mobile devices with imaging capabilities such as camera phones, as well as digital still cameras (DSC).
Photoinduced transient symmetry breaking in plasmonic structures for ultrafast nanophotonics (2022)

We study the spatio-temporal evolution of hot electrons generated in plasmonic nanostructures under resonant excitation with fs-laser pulses. A spatially inhomogeneous version of the Three-Temperature Model for hot-electrons dynamics, coupled to semiclassical calculations of third-order optical nonlinearity in gold, enabled us to engineer a transient symmetry breaking of the optical properties at the nanoscale. This effect is exploited to achieve all-optical control of light with unprecedented speed. For instance, a photoinduced broadband dichroism, fully reversible and transiently vanishing in less than 1 picoseconds (overcoming the speed bottleneck caused by slower, electron-phonon and phonon-phonon relaxation processes), has been experimentally demonstrated in plasmonic metasurfaces with nanocross metaatoms. Also, we designed a nonlinear plasmonic metagrating (based on cross-polarized gold nanostrip dimer metaatoms), where the nanoscale symmetry breaking enables ultrafast reconfiguration of diffraction orders via control laser pulses. The photoinduced power imbalance between symmetrical diffraction orders is calculated to exceed 20% under moderate (∼2 mJ/cm<sup>2</sup>) laser fluence, and returns to the balanced diffraction in about 2 ps. Our design has been developed for gold nanomaterials, but the concept of ultrafast all-optical symmetry breaking can be exploited beyond plasmonics (e.g. in semiconductor nanostructures), with potential impact on a broad range of applications in nanophotonics.
Antioxidant and Antithrombus Activities of Enzyme-Treated <i>Salicornia herbacea </i>Extracts (2007)

This study was attempted to investigate antioxidant and antithrombus activities of water and methanol extracts of enzyme-treated Salicornia herbacea (SH)by in vitro assays observing the inhibitory activity of a rat liver microsomal lipid peroxidation, DPPH radical scavenging activity, activated partial thromboplastin times (APTT) and thromboplastin times (TT). The water and methanol extracts from enzyme-treated SH inhibited the lipid peroxidation in a dose-dependent manner over a concentration range of 0.1-1.0 mg/ml. The activity of enzyme-treated water and methanol extracts was stronger than that of non-enzyme-treated water and methanol extracts. The inhibitory activity of the water extract was higher at a concentration of 1.0 mg/ml than that of the methanol extract. The activity was the highest in the enzyme-treated water extract, and was approximately 1.08 times higher than alpha-tocopherol, a natural antioxidant. The DPPH radical scavenging activities of the SH extracts were similar to their lipid peroxidation inhibitory activity. The APTT of the water and methanol extracts was delayed at a concentration range of 0.25-2.0 mg/ml in a dose-dependent manner. The APTT of the methanol extract was longer at a concentration of 1.0 mg/ml than that of the water extracts. The enzyme-treated methanol extract exhibited the longest APTT even at a concentration of 0.50 mg/ml. The TT activities of the SH extracts were also similar to their APTT activities. These results suggest that water and methanol extracts of the enzyme-treated SH may be useful as potential antioxidant and antithrombus sources, respectively.
Near-Field Light Design with Colloidal Quantum Dots for Photonics and Plasmonics (2014)

Colloidal quantum-dots are bright, tunable emitters that are ideal for studying near-field quantum-optical interactions. However, their colloidal nature has hindered their facile and precise placement at desired near-field positions, particularly on the structured substrates prevalent in plasmonics. Here, we use high-resolution electro-hydrodynamic printing (<100 nm feature size) to deposit countable numbers of quantum dots on both flat and structured substrates with a few nanometer precision. We also demonstrate that the autofocusing capability of the printing method enables placement of quantum dots preferentially at plasmonic hot spots. We exploit this control and design diffraction-limited photonic and plasmonic sources with arbitrary wavelength, shape, and intensity. We show that simple far-field illumination can excite these near-field sources and generate fundamental plasmonic wave-patterns (plane and spherical waves). The ability to tailor subdiffraction sources of plasmons with quantum dots provides a complementary technique to traditional scattering approaches, offering new capabilities for nanophotonics.
WOUND HEALING IN SEPSIS AND TRAUMA (1997)

Wound healing represents a dynamic and immediate response of the body to tissue injury with the purpose of restoring anatomical continuity, structure and function. Success or failure of this complex cascade of events is determined largely by competence of the host's immune system. Sepsis represents one of the most formidable threats to successful wound healing. It can present as a local bacterial colonization of the injury site with minimal systemic reaction or the “systemic inflammatory response syndrome,” a primary cause of mortality among critically ill patients. Trauma also predisposes patients to wound complications especially as a result of post-traumatic immunosuppression. This phenomenon exposes the patient to the risk of microbial infection and ultimately the sepsis syndrome. The immune system, therefore, represents a vulnerable gateway through which trauma and sepsis exert their deleterious effect on the wound healing process resulting in increased morbidity and mortality for the surgical patient.
WIDEBAND LOW-OUTPUT-IMPEDANCE RF SYSTEM FOR THE SECOND HARMONIC CAVITY IN THE ISIS SYNCHROTRON (2006)

A wideband low-output-impedance RF system for the second harmonic cavity in the ISIS synchrotron has been developed by the collaboration between Argonne National Laboratory (US), KEK (Japan) and Rutherford Appleton Laboratory (UK). The system has less than 30 Ω over the frequency range of 2.7 - 6.2 MHz. High power test was performed with a ferrite-loaded second harmonic cavity at 50 Hz repetition rate. The maximum voltage of 12.6 kV peak per accelerating gap was obtained stably at earlier period of an operation cycle. A beam test with this system is planned at the ISIS synchrotron.
An Experimental Study of TLS Forward Secrecy Deployments (2014)

Many Transport Layer Security (TLS) servers use the ephemeral Diffie-Hellman (DHE) key exchange to support forward secrecy. However, in a survey of 473,802 TLS servers, the authors found that 82.9 percent of the DHE-enabled servers use weak DH parameters, resulting in a false sense of security. They compared the server throughput of various TLS setups, and measured real-world client-side latencies using an advertisement network. Their results indicate that using forward secrecy is no harder, and can even be faster using elliptic curve cryptography (ECC), than no forward secrecy.
An Ontological Approach for Run-Time Safety Management in Smart Work Environments (2016)

International audience
Interactive navigation of multiple convex patches (2021)

Abstract Among the approaches to multi‐criteria decision making, Pareto navigation is a powerful, interactive tool that has been successfully applied to a variety of real‐world problems with continuous decision variables, including chemical process design, drug manufacturing, logistical vehicle routing problems, and radiotherapy treatment planning. However, many real‐life problems are formulated using both continuous and binary decision variables. In this work, we introduce patch navigation as an algorithmic concept that extends Pareto navigation to this type of problem where the number of binary variables is relatively small. The underlying idea is the navigation across a finite set of individual, convex fronts each associated with a specific configuration of the binary variables ( patches ). We show how the user interactions employed in current Pareto front navigation, namely selection and restriction, can be adopted to handle multiple patches. These routines enable the decision maker (DM) to change the solution in small increments while controlling the related trade‐offs. We also describe additional, patch‐specific routines that enable the DM to consider only an individually chosen subset of patches in the navigation. To illustrate patch navigation, and to demonstrate its usefulness for real‐life problems, we present numerical examples of patch navigation along with an application motivated by radiotherapy planning.
P05.10 Prospective evaluation of cerebrospinal fluid circulating tumor cells (CSF CTC) in patients with HER2 positive cancers and leptomeningeal metastases receiving treatment with intrathecal trastuzumab (2018)

The validated CellSearch system (Janssen Diagnostics, LLC), utilizing an immunomagnetic CTC selection method based on EPCAM antibody conjugated ferroparticles, is an FDA-approved methodology for enumerating CTC from blood in pts with breast, prostate and colon cancers. The CellSearch system has been used to evaluate CSF CTC of pts with leptomeningeal metastasis (LM) and has demonstrated potential as a diagnostic marker and response to cancer treatment. We explored the use of CSF CTC enumeration in the follow-up of pts with LM from HER2+ cancers receiving intrathecal (IT) therapy, aimed at characterizing changes over time as a potential biomarker of treatment response. CSF from pts participating in an IRB-approved phase I/II dose escalation trial of IT trastuzumab for LM in HER2+ cancer (NCT01325207) was evaluated by CellSearch system. 3 ml CSF from a ventricular reservoir was collected for CSF CTC enumeration at pre-treatment Day 1 of each cycle and correlated with CSF cytology from the same sample, and with clinical and radiographic response. LM progression was defined as clinical or radiographic worsening. Fifteen patients with HER2+ LM (14 breast, 1 colon) were enrolled; 14 were women. Six patients had baseline positive CSF cytology; the remaining were diagnosed by MRI. Of the 15 patients, 10 had greater than 1 cycle of treatment to be evaluable; 5 patients progressed during cycle 1. Median CSF CTC at baseline was 22 per 3ml (range 0–200); 2 patients had no detectable CSF CTCs. A decrease in CSF CTC was observed in 5 patients after cycle 1 and remained low (mean =9.5, range 0–92) in 2 patients while disease was stable. 3 patients had a rise in CSF CTCs roughly 1 month prior to progression. In the 10 patients with HER2 analysis, number of CTCs correlated with HER 2 expression. CSF CTC HER2 expression provided further affirmation that CTCs are malignant. Changes in CSF CTC enumeration allow quantitative surveillance of treatment response and should be further investigated.
Nucleofection Mediates High-Efficiency Stable Gene Knockdown and Transgene Expression in Human Embryonic Stem Cells (2008)

High-efficiency genetic modification of human embryonic stem (hES) cells would enable manipulation of gene activity, routine gene targeting, and development of new human disease models and treatments. Chemical transfection, nucleofection, and electroporation of hES cells result in low transfection efficiencies. Viral transduction is efficient but has significant drawbacks. Here we describe techniques to transiently and stably express transgenes in hES cells with high efficiency using a widely available vector system. The technique combines nucleofection of single hES cells with improved methods to select hES cells at clonal density. As validation, we reduced Oct4 and Nanog expression using siRNAs and shRNA vectors in hES cells. Furthermore, we derived many hES cell clones with either stably reduced alkaline phosphatase activity or stably overexpressed green fluorescent protein. These clones retained stem cell characteristics (normal karyotype, stem cell marker expression, self-renewal, and pluripotency). These studies will accelerate efforts to interrogate gene function and define the parameters that control growth and differentiation of hES cells. Disclosure of potential conflicts of interest is found at the end of this article.
Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level (2012)

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.
ChemInform Abstract: Synthesis of N‐(9‐Oxo‐7‐phenyl‐9H‐pyrano(2,3‐g)benzothiazol‐2‐yl) benzamides from 6‐Aminoflavone. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Optimal periodic locomotion for a two piece worm with an asymmetric dry\n friction model (2017)

This paper solves the optimization problem for a simplified one-dimensional\nworm model when the friction force depends on the direction of the motion. The\nmotion of the worm is controlled by the actuator force $f(t)$ which is assumed\nto be piecewise continuous and always generates the same force in the opposite\ndirections. The paper derives the necessary condition for the force which\nmaximizes the average velocity or minimizes the power over a unit distance. The\nmaximum excursion of the worm body and the force are bounded. A simulation is\ngiven at the end of the paper.\n
To destroy them or to live there (2004)

When the Florentine colonist Piero Vaglienti, a few days before the entry of the French into Pisa in November 1494, approached the Florentine commissioner with a proposal for having one hundred fifty or two hundred leading Pisan citizens deported to Florence as a precautionary measure, he was received with a mixture of indifference and complacent arrogance. Since the commissioner found it inconceivable that the Pisans, who had been under Florentine rule for almost a century, would be able to recall the city's past liberty any more, he saw no reason to doubt their loyalty. Of course, he was spectacularly wrong. The night after the French had entered Pisa, the streets of the city resounded to the ancient cry “libertà! libertà!” The marzocchi, the Florentine lions and the very emblem of Florentine rule, on the bridges over the Arno were destroyed and thrown into the river. Over night, lifelong friendships between Pisans and Florentines turned into animosity, as Florentine citizens were attacked and their houses sacked. Around this time, a Pisan notary wrote in his Ricordi: “The Pisans have always been a free and generous people. The wars they have fought against the Ligurians and the Genoese since the commencement of the Pisan name have demonstrated their worth … Liberty has always been dear to our people, because it was given to us by our ancestors and betters.”
GaN Takes the Lead (2012)

Gallium nitride (GaN) technology is transforming RF monolithic microwave integrated circuits (MMICs) for power amplifiers (PAs), switches, low noise amplifiers, and more. Vendors are now producing GaN MMICs in volume and achieving outstanding performance. GaNs characteristics enable PA MMICs with 35 times the output power of GaAs alternatives or much smaller die sizes from L-band through Ka-band. High-power switches with low insertion loss up through 18 GHz have been developed. Low-noise amplifiers have been demonstrated with noise figures equivalent to gallium arsenide (GaAs) but with much higher input power survivability. The market for GaN RF MMICs spans commercial and military applications, including base station, cable television infrastructure, communications, radar and electronic warfare (EW), among others.
Application of Queuing Systems with Ultimate Reliability to Optimize the Operation of Drones (2017)

Multi-criteria problem of optimization of maintenance rate for drones is set and solved. Analytical characteristics of a single-server queueing system with ultimate reliability and imitation models are applied. The analysis of economical and reliability characteristics dependence on some parameters is made.