gebhart/patrepeval huggingface dataset:
In Situ Monitoring of Backbone Thioester Exchange by 19F NMR (2009)

19F NMR to monitor BTE: A new strategy for assessing polypeptide tertiary structural stability by using thiol–thioester exchange is described. The backbone thioester exchange (BTE) method has previously been used to evaluate fold stability with HPLC measurements. Here we show that BTE can be followed by 19F NMR, which offers technical advantages. This technique was used for rapid identification of the most stable antiparallel coiled coil in a small library of new sequences.
Priority-enabled Load Balancing for Dispersed Computing (2021)

Opportunistic managed access to local in-network compute resources can improve the performance of distributed applications and reduce the dependence on shared network resources. Instead of backhauling application data to a centralized cloud data center for processing, networked services may be adaptively and continuously dispersed into shared compute resources that are closer to the source of need. While this approach has several benefits, support for mission-aware access to computation is often an afterthought, and is implemented as a brittle extension over traditional load-balancer solutions.In this work, we investigate the design of two priority-aware resource allocation strategies and two load-balancing dispatching strategies as first class citizens in an open-source dispersed computing middleware. We present a control theoretic analysis of these load-balancing primitives to identify weaknesses and strengths in our design, and recommend future directions. In parallel, we prototype two priority-aware allocation algorithms to validate our priority predictions. In initial experiments our prototype shows substantial gains in processing prioritized load. Finally, we make our source-code and experimental configurations open source.
Data from Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor–Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;Adoptive cellular therapy (ACT) targeting neoantigens can achieve durable clinical responses in patients with cancer. Most neoantigens arise from patient-specific mutations, requiring highly individualized treatments. To broaden the applicability of ACT targeting neoantigens, we focused on &lt;i&gt;TP53&lt;/i&gt; mutations commonly shared across different cancer types. We performed whole-exome sequencing on 163 patients with metastatic solid cancers, identified 78 who had &lt;i&gt;TP53&lt;/i&gt; missense mutations, and through immunologic screening, identified 21 unique T-cell reactivities. Here, we report a library of 39 T-cell receptors (TCR) targeting &lt;i&gt;TP53&lt;/i&gt; mutations shared among 7.3% of patients with solid tumors. These TCRs recognized tumor cells in a &lt;i&gt;TP53&lt;/i&gt; mutation- and human leucocyte antigen (HLA)-specific manner &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. Twelve patients with chemorefractory epithelial cancers were treated with &lt;i&gt;ex vivo&lt;/i&gt;–expanded autologous tumor-infiltrating lymphocytes (TIL) that were naturally reactive against &lt;i&gt;TP53&lt;/i&gt; mutations. However, limited clinical responses (2 partial responses among 12 patients) were seen. These infusions contained low frequencies of mutant p53–reactive TILs that had exhausted phenotypes and showed poor persistence. We also treated one patient who had chemorefractory breast cancer with ACT comprising autologous peripheral blood lymphocytes transduced with an allogeneic HLA-A*02–restricted TCR specific for p53&lt;sup&gt;R175H&lt;/sup&gt;. The infused cells exhibited an improved immunophenotype and prolonged persistence compared with TIL ACT and the patient experienced an objective tumor regression (-55%) that lasted 6 months. Collectively, these proof-of-concept data suggest that the library of TCRs targeting shared p53 neoantigens should be further evaluated for the treatment of patients with advanced human cancers.&lt;/p&gt;&lt;p&gt;&lt;a href="https://aacrjournals.org/cancerimmunolres/article/doi/10.1158/2326-6066.CIR-22-0386" target="_blank"&gt;&lt;i&gt;See related Spotlight by Klebanoff, p. 919&lt;/i&gt;&lt;/a&gt;&lt;/p&gt;&lt;/div&gt;
Extra-intestinal Pathogenic Escherichia coli (ExPEC): Characteristics, Virulence Genes, Detection, and Control (2017)

Renowned international authors provide timely and up-to-date reviews of current cutting-edge E. coli omics, molecular- and cellular-biology research. Topics range from E. coli genome plasticity and evolution to the application of omics technologies for in silico modeling to understand stress-triggered physiological responses. Essential reading.
Pulsed ESR at 140 GHz (1992)

Abstract We report pulsed electron spin resonance (ESR) experiments at a static magnetic field (B 0 ) of 5.0T, corresponding to a microwave frequency of ˜140 GHz for g = 2 electrons. The experiments were performed with a transmission spectrometer, utilizing a 300 watt extended interaction klystron (EIK) operating in pulsed mode, together with a crossed waveguide Fabry‐Perot resonator which provided 30–40 dB of receiver isolation. Signal averaging was accomplished by mixing the pulse from the EIK with a 139.95 GHz reference oscillator, which was subsequently mixed with a local oscillator to generate a trigger signal for a digital oscilloscope. Concurrently, the ESR signal was mixed to an intermediate frequency using a second low frequency oscillator which was phase‐locked to the same source as the trigger oscillator and detected with a transient digitizer. In this configuration we achieved π/2 pulses of −14 ns, and the isolation of the Fabry‐Perot provided short spectrometer dead times (20–50 ns, including the pulse) for subsequent detection of the free induction decays. The performance of the spectrometer is demonstrated with spectra obtained from crystals of fluoranthenyl hexafluorophosphate.
REVEALED PREFERENCE AND ACTIVITY RULES IN DYNAMIC AUCTIONS (2020)

Abstract Activity rules—constraints that limit bidding in future rounds based on past bids—are intended to limit strategic bidding delays in high‐stakes auctions. This article provides a general treatment of activity rules. Traditional point‐based rules are effective for homogeneous goods and reasonably suited for substitute goods. However, they are simultaneously too strong and too weak for general environments; they allow parking, while sometimes preventing straightforward bidding. We prove that the activity rule operationalizing the generalized axiom of revealed preference (GARP) is essentially the unique rule that enforces the Law of Demand while enabling straightforward bidding and never producing “dead ends.”
On the applicability of the Fujisaki–Okamoto transformation to the BIKE KEM (2021)

The QC-MDPC code-based KEM BIKE is one of the Round-3 candidates of the NIST PQC standardization project. Its Round-2 specification document described variants claiming to have IND-CCA security. The security proof used the Fujisaki–Okamoto transformation and a decoder targeting a Decoding Failure Rate (DFR) of (Formula presented.) (for Level-1 security). However, several aspects needed to be amended in order for the IND-CCA proof to hold. The main issue is that using a decoder with DFR of (Formula presented.) does not necessarily imply that the underlying PKE is δ-correct with (Formula presented.), as required. In this paper, we handle the necessary aspects to ensure the security claim is correct. In particular, we close the gap in the proof by defining the notion of message-agnostic PKE. We show that the PKEs underlying the BIKE versions are message-agnostic. This implies that BIKE with a decoder that has a sufficiently low DFR is also an IND-CCA KEM.
Implementing fair bandwidth allocation schemes in hose-modelled VPN (2004)

The virtual private network (VPN) provides customers with predictable and secure network connections over a shared network infrastructure. The recently proposed hose model for VPNs has desirable properties in terms of greater flexibility and better multiplexing gain. However, the ‘classic’ fair bandwidth allocation scheme introduces the issue of low overall utilisation in this model; furthermore, when the VPN links are established, the VPN customers cannot manage their VPN resources by themselves dynamically. The authors propose a fluid hose-modelled VPN, and based on this model they develop an idealised fluid fair bandwidth allocation scheme to improve the performance of the VPN. With the proposed scheme, they achieve two goals: maximising the overall throughput of the VPN; and providing a mechanism that enables the VPN customers to allocate the bandwidth according to their own requirements, thus achieving the predictable QoS performance. Based on deficit round robin (DRR), a transmission scheduling scheme for output buffer switches, a novel scheme, two-dimensional deficit round robin (2-D DRR), is developed to approximate/realise the idealised fluid fair bandwidth allocation scheme for the hose-modelled VPN. The simulation results also show that the 2-D DRR can improve the overall throughput without compromising fairness and implementation complexity.
Chronic Pancreatitis: Evaluation of Pancreatic Exocrine Function with MR Pancreatography after Secretin Stimulation (2000)

Duodenal filling grade determined at MR pancreatography after secretin stimulation allows specific estimation of pancreatic exocrine function.
Measurements of top-quark pair differential and double-differential cross-sections in the $$\ell $$+jets channel with pp collisions at $$\sqrt{s}=13$$ TeV using the ATLAS detector (2019)

Abstract Single- and double-differential cross-section measurements are presented for the production of top-quark pairs, in the lepton + jets channel at particle and parton level. Two topologies, resolved and boosted, are considered and the results are presented as a function of several kinematic variables characterising the top and $$t\bar{t}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>t</mml:mi> <mml:mover> <mml:mrow> <mml:mi>t</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>¯</mml:mo> </mml:mrow> </mml:mover> </mml:mrow> </mml:math> system and jet multiplicities. The study was performed using data from pp collisions at centre-of-mass energy of 13 TeV collected in 2015 and 2016 by the ATLAS detector at the CERN Large Hadron Collider (LHC), corresponding to an integrated luminosity of $$36~\mathrm {fb}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mn>36</mml:mn> <mml:mspace/> <mml:msup> <mml:mrow> <mml:mi>fb</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:mrow> </mml:math> . Due to the large $$t\bar{t}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>t</mml:mi> <mml:mover> <mml:mrow> <mml:mi>t</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>¯</mml:mo> </mml:mrow> </mml:mover> </mml:mrow> </mml:math> cross-section at the LHC, such measurements allow a detailed study of the properties of top-quark production and decay, enabling precision tests of several Monte Carlo generators and fixed-order Standard Model predictions. Overall, there is good agreement between the theoretical predictions and the data.
Off label uses of pamidronate in rare pediatric bone diseases (Jansen's Metaphyseal Chondrodysplasia and Generalized Arterial Calcification of Infancy): A four year perspective (2019)

Searchable abstracts of presentations at key conferences on calcified tissues ISSN 2052-1219 (online)
Off-axis sparse aperture imaging using phase optimization techniques for application in wide-area imaging systems (2009)

Sparse apertures find imaging applications in diverse fields such as astronomy and medicine. We are motivated by the design of a wide-area imaging system where sparse apertures can be used to construct novel and efficient optical designs. Specifically, we investigate the use of sparse apertures for off-axis imaging at infrared wavelengths while combating the effects of chromaticity to preserve resolution. In principle, several such sparse apertures can be interleaved within a common aperture to simultaneously image in multiple directions. This can ultimately lead to the design of wide-area imaging systems that require considerably less optical and electronic hardware. The resolution achievable using a sparse aperture is the same as that of a fully open aperture. In the case of off-axis imaging, however, the point spread function (PSF) introduces a blur due to chromaticity that degrades the resolution of the system. Of course, the blur can be eliminated by imaging at a single wavelength. However the signal-to-noise ratio (SNR) is poor, which ultimately degrades image quality. To improve SNR, it is necessary to widen the band of wavelengths, which of course degrades resolution due to chromaticity. Hence there is a fundamental trade between the SNR and the resolution as a function of bandwidth. We show that by using a combination of microprisms and phase optimized micropistons it is possible to reduce the chromatic blur over a band of wavelengths and improve the PSF considerably to restore the resolution of the image. The concepts are validated by means of simulations and verified with experimental data to demonstrate the advantages of phase optimized micropistons in off-axis sparse aperture imaging systems.
A Highly Efficient Electrochemical Biosensing Platform by Employing Conductive Nanocomposite Entrapping Magnetic Nanoparticles and Oxidase in Mesoporous Carbon Foam (2011)

Abstract A conductive multi‐catalyst system consisting of Fe 3 O 4 magnetic nanoparticles (MNPs) and oxidative enzymes co‐entrapped in the pores of mesoporous carbon is developed as an efficient and robust electrochemical biosensing platform. The construction of the nanocomposite begins with the incorporation of MNPs by impregnating Fe(NO 3 ) 3 on a wall of mesoporous carbon followed by heat treatment under an Ar/H 2 atmosphere, which results in the formation of magnetic mesoporous carbon (MMC). Glucose oxidase (GOx) is subsequently immobilized in the remaining pore spaces of the MMC by using glutaraldehyde crosslinking to prevent enzyme leaching from the matrix. H 2 O 2 generated by the catalytic action of GOx in proportion to the amount of target glucose is subsequently reduced into H 2 O by the peroxidase mimetic activity of MNPs generating cathodic current, which can be detected through the conductive carbon matrix. To develop a robust and easy‐to‐use electrocatalytic biosensing platform, a carbon paste electrode is prepared by mechanically mixing the nanocomposite or MMCs and mineral oil. Using this strategy, H 2 O 2 and several phenolic compounds are amperometrically determined employing MMCs as peroxidase mimetics, and target glucose was successfully detected over a wide range of 0.5 × 10 −3 to 10 × 10 −3 M , which covers the actual range of glucose concentration in human blood, with excellent storage stability of over two months at room temperature. Sensitivities of the biosensor (19 to 36 nA m M −1 ) are about 7–14 times higher than that of the biosensor using immobilized GOx in mesoporous carbon without MNPs under optimized condition. The biosensor is of considerable interest because of its potential for expansion to any oxidases, which will be beneficial for use in practical applications by replacing unstable organic peroxidase with immobilized MNPs in a conductive carbon matrix.
[Research and development for next generation PET instrumentations]. (2012)

Positron emission tomography (PET) plays important roles in cancer diagnosis and molecular imaging research; but potential points remain for which big improvements could be made, including resolution, sensitivity and costs. For example, the sensitivity of present PET scanners does not exceed 10%. This means that more than 90% of the gamma-rays emitted from a subject are not utilized for imaging. Therefore, research on next generation PET technologies remains a hot topic worldwide. In this paper, we introduce some research trends by describing PET physics research in the National Institute of Radiological Sciences (NIRS). A depth-of-interaction (DOI) detector, for which various methods have been studied, will be a key device to get any significant improvement in sensitivity while maintaining high spatial resolution. DOI measurement also has a potential to expand PET application fields because it allows for more flexible detector arrangement. As an example, we are developing the world's first, open-type PET geometry "OpenPET", which is expected to lead to PET imaging during treatment. The DOI detector itself continues to evolve with the help of recently developed semiconductor photodetectors, often referred to as silicon photomultipliers (SiPMs). We are developing a SiPM-based DOI detector to achieve sub-mm spatial resolution, which is reaching the theoretical limitation of PET imaging.
Endotoxins induce and interferon‐α suppresses vascular endothelial growth factor (VEGF) production in human peripheral blood mononuclear cells (2001)

ABSTRACT Endotoxins, classical activators of innate immune cells, induce systemic inflammation designated by increased microvascular permeability, and, not so infrequently, circulatory shock, organ dysfunction, and death. Vascular endothelial growth factor (VEGF), besides being an endothelial‐cell mitogen, is a strong vascular permeability factor. This study demonstrates that peripheral blood mononuclear cells (PBMNCs) from healthy volunteers cultured in serum‐free medium in the absence of any stimulus release VEGF continuously into culture media. Physiological endotoxin concentrations stimulate this VEGF secretion in a dose‐dependent manner, representing an induction of de novo VEGF production, as an induction of the expression of the major 3.7‐kb VEGF mRNA transcripts was observed, and the release of VEGF was blocked by cycloheximide. Reverse transcription‐polymerase chain reaction also verified the expression of the four VEGF transcripts. Interferon‐α, a modulator of the immune system and an inhibitor of angiogenesis, inhibited VEGF release dose dependently. We conclude that endotoxin promotes VEGF production in PBMNCs. Circulating and emigrating VEGF‐producing PBMNCs may enhance the shift to angiogenic phenotype in a variety of infectious and inflammatory disorders as well as in cancer. VEGF‐producing PBMNCs may be a novel mechanism of tissue edema in systemic inflammation. Inhibition of VEGF production in PBMNCs may be one of the mechanisms of interferon‐α action.
Terrestrial Neutron-Induced Failures in Silicon Carbide Power MOSFETs and Diodes (2018)

Investigations of terrestrial neutron radiation-induced failures in silicon carbide power MOSFETs and diodes indicate that the failures are related to a hole-initiated impact ionization process followed by a thermal transient resulting in the loss of device voltage blocking ability due to the damage of lattice along a filament within the device volume. Irrespective of device type, MOSFET or diode, the start of these failures exhibits the same characteristics, and can be mitigated by decrease in field in device OFF state. These failures with origins in impact ionization and fast thermal transients are fundamentally different from those of bipolar burn-out events, observed in silicon power devices. In addition, once a failure event starts, the failure ends with all terminals shorting.
RAD-Sim: Rapid Architecture Exploration for Novel Reconfigurable Acceleration Devices (2023)

With the continued growth in field-programmable gate array (FPGA) capacity and their incorporation into new environments such as datacenters, we have witnessed the introduction of a new class of reconfigurable acceleration devices (RADs) that go beyond conventional FPGA architectures. These devices combine a reconfigurable fabric with coarse-grained domain-specialized accelerator blocks all connected via a high-performance packet-switched network-on-chip (NoC) for efficient system-wide communication. However, we lack the tools necessary to efficiently explore the huge design space for RADs, study the complex interactions between their different components and evaluate various combinations of design choices. In this work, we develop RAD-Sim, a cycle-level architecture simulator that allows rapid application-driven exploration of the design space of novel RADs. To showcase the capabilities of RADSim, we map and simulate a state-of-the-art deep learning (DL) inference overlay on a RAD instance incorporating an FPGA fabric and a complex of hard matrix-vector multiplication engines, communicating over a system-wide NoC. Through this example, we show how RAD-Sim can help architects quantify the effect of changing specific architecture parameters on end-to-end application performance.
COMPARISON OF REMIFENTANIL, ALFENTANIL AND FENTANYL DURING CRANIOTOMY (1998)

Leary, T. S.; Gupta, A. K.; Doyle, P. W.; Byrne, A.; Matta, B.; Menon, D. K. Author Information
Comparative effects of proteases on performance, carcass traits and gut structure of broilers fed diets reduced in protein and amino acids (2023)

This study aimed to evaluate the effect of supplementing different protease enzymes on growth performance, intestinal morphology, and selected carcass traits in broilers fed diets reduced 3.5% in crude protein (CP) and amino acids (AA). One thousand one-day-old Ross 308 broilers (41 g) were assigned to five dietary treatments with ten replicates of 20 birds each: a positive control (PC) diet formulated to meet Ross 308 AA requirements, a negative control (NC) diet reformulated to provide 3.5% lower CP and AA compared to PC, NC supplemented with a multi-protease (PR1) solution, containing 3 different coated proteases produced from <i>Aspergillus niger</i>, <i>Bacillus subtilis</i> and <i>Bacillus licheniformis</i>, NC supplemented with a serine protease (PR2) produced from <i>Bacillus licheniformis</i>, and NC supplemented with an alkaline protease (PR3) produced from <i>Bacillus licheniformis</i>. At slaughter, 40 birds per treatment were used to assess the effect of the different treatments on carcass traits. At 32 days, samples of the duodenum, jejunum, and ileum of 10 birds per treatment were collected for intestinal morphology evaluation. Birds fed PC and NC supplemented with multi-protease exhibited better (<i>p</i> < 0.05) feed efficiency compared to NC and NC supplemented with all the other protease enzymes. Multi-protease supplementation was linked to the highest (<i>p</i> < 0.05) carcass weight and yield. There were significant differences (<i>p</i> < 0.05) between treatments in all gut segments, with PC, PR1, PR2, and PR3 exhibiting longer villi height (VH) compared to NC. This study demonstrates that 3.5% reduction of CP and AA negatively affected for the overall period feed efficiency, carcass yield, and intestinal morphology. The supplementation of the multi-protease restored feed efficiency and improved carcass yield.
Modélisations numérique et expérimentale des écoulements sanguins dans une fistule artério veineuse (2007)

International audience
Failure Mechanism of Large Scale Field Emission Array (2021)

A 1000×1000 Si FEA went through reliability test. Under fixed gate-voltage, the emission current stays stable at ~3mA over 3 days, but suddenly dropped 92% within one second, while the gate leakage current drops simultaneously. Post-testing physical characterization reveals majority of the emitters within the array keeps their structure integrity. The sudden emission current drop is due to a small amount of shorted/damaged emitters on the edge of the array.