gebhart/patrepeval huggingface dataset:
Nonequilibrium viscosity of glass (2009)

Since glass is a nonequilibrium material, its properties depend on both composition and thermal history. While most prior studies have focused on equilibrium liquid viscosity, an accurate description of nonequilibrium viscosity is essential for understanding the low temperature dynamics of glass. Departure from equilibrium occurs as a glass-forming system is cooled through the glass transition range. The glass transition involves a continuous breakdown of ergodicity as the system gradually becomes trapped in a subset of the available configurational phase space. At very low temperatures a glass is perfectly nonergodic (or ``isostructural''), and the viscosity is described well by an Arrhenius form. However, the behavior of viscosity during the glass transition range itself is not yet understood. In this paper, we address the problem of glass viscosity using the enthalpy landscape model of Mauro and Loucks [Phys. Rev. B 76, 174202 (2007)] for selenium, an elemental glass former. To study a wide range of thermal histories, we compute nonequilibrium viscosity with cooling rates from ${10}^{\ensuremath{-}12}$ to ${10}^{12}\text{ }\text{K}/\text{s}$. Based on these detailed landscape calculations, we propose a simplified phenomenological model capturing the essential physics of glass viscosity. The phenomenological model incorporates an ergodicity parameter that accounts for the continuous breakdown of ergodicity at the glass transition. We show a direct relationship between the nonequilibrium viscosity parameters and the fragility of the supercooled liquid. The nonequilibrium viscosity model is validated against experimental measurements of Corning EAGLE XG™ glass. The measurements are performed using a specially designed beam-bending apparatus capable of accurate nonequilibrium viscosity measurements up to ${10}^{16}\text{ }\text{Pa}\text{ }\text{s}$. Using a common set of parameters, the phenomenological model provides an accurate description of EAGLE XG™ viscosity over the full range of measured temperatures and fictive temperatures.
The Science Behind Erosion Qualification Testing of Frac Pack Tools (2010)

Abstract Frac packing tool erosion is a growing concern as more high-profile deepwater wells are completed using this technique. Today many deepwater wells require frac pack pump rates of at least 40 barrels per minute (bbl/min) with proppant loads reaching 300,000 lbm. As zone lengths are increased and multizone operations are performed, jobs requiring 60 bbl/min pump rates with proppant loads reaching 1,500,000 lbm are becoming more typical. The current frac packing tool designs must be optimized to accommodate the higher pump rates and proppant volumes required to complete these deepwater wells. Extensive research and development, including computational fluid dynamics analysis and scale-model erosion testing, have led to the development of a new series of sand control tools that have been optimized for ultra-high-rate frac packing applications. Analyzing various patterns such as velocity, fluid path, erosion, and sand concentration at high rates helps identify critical areas within the system that require design optimization. Results from full-scale erosion qualification testing of this new series of sand control tools are discussed. The qualification tests are designed to simulate extreme applications for tools in terms of pump rate, treatment volumes, and proppant properties, while testing conditions remain consistent with actual job specifications. The qualification test parameters were chosen to emulate and, in some cases, exceed the parameters of frac pack treatments currently being planned for the deepwater Gulf of Mexico. Erosion properties of the crossover, extension, and casing will be discussed, and depicted.
Prediction of Virological Response and Assessment of Resistance Emergence to the HIV-1 Attachment Inhibitor BMS-626529 During 8-Day Monotherapy With Its Prodrug BMS-663068 (2013)

Nonresponse to BMS-663068 was associated with low baseline susceptibility to BMS-626529 and the presence of M426L. In this short-term trial, there was minimal evidence of selection for BMS-626529 high-level resistance over 8 days of monotherapy with BMS-663068 by population-based approaches.
A Framework for Mitigating Attacks Against Measurement-Based Adaptation Mechanisms in Unstructured Multicast Overlay Networks (2008)

Many multicast overlay networks maintain application-specific performance goals by dynamically adapting the overlay structure when the monitored performance becomes inadequate. This adaptation results in an unstructured overlay where no neighbor selection constraints are imposed. Although such networks provide resilience to benign failures, they are susceptible to attacks conducted by adversaries that compromise overlay nodes. Previous defense solutions proposed to address attacks against overlay networks rely on strong organizational constraints and are not effective for unstructured overlays. In this work, we identify, demonstrate and mitigate insider attacks against measurement-based adaptation mechanisms in unstructured multicast overlay networks. We propose techniques to decrease the number of incorrect adaptations by using outlier detection and limit the impact of malicious nodes by aggregating local information to derive global reputation for each node. We demonstrate the attacks and mitigation techniques through real-life deployments of a mature overlay multicast system.
Small directional microelectromechanical systems (MEMS) microphone arrays (2013)

Directional microphone arrays that are physically small compared to the acoustic wavelength are of great interest for hand-held communication devices. Spatially directive microphones can reduce the impact of background acoustic noise without adding distortion to the signal. This talk will present some design topologies and requirements as well as a new physical design for a MEMS velocity sensing microphone that could enable directional microphone responses while being small in size.
Comparison of Packed Beds and Qiagen Columns for Recovering Trace Amounts of B. anthracis DNA from Liquid Suspensions (2006)

The goal of this work was to optimize and evaluate LLNL's in-bed amplification technology to improve the level of detection for suspensions containing trace amounts of anthracis DNA. The binding/cleaning performance of the packed bed is compared to the conventional commercial approach; Qiagen column cleanup and elution, followed by detection through an ex-situ amplification process. Five liquid suspensions were spiked with B.anthracis DNA in concentration series. These suspensions were: (1) water, (2) water with EDTA, (3) dirty water from carpet extraction, (4) dirty carpet extraction with phosphate buffered saline (PBS) plus 0.1% Tween 20 plus 0.1% gelatin, and (5) a subway aerosol collected in water. Each suspension matrix was spiked with DNA and injected (in replicate) into either Qiagen Microcolumns (using the kit processing instructions) or LLNL's packed bed (using the LLNL in-bed purification and amplification protocol). The process output was assayed by quantitative polymerase chain reaction (QPCR). Table ES-1 shows the level of DNA (pg per 100 uL of input suspension) that resulted in successful amplification for all reactions (X=Y), and the level for which at least one of the reactions was successful (X>0). For each suspension and DNA concentration, there were Y QPCR assays of which X showed successful amplification. LLNL's packed bed technology outperformed Qiagen Microcolumns for all five suspensions, typically by one order of magnitude in both the limit of assured detection (all reactions positive), and the lower limit of detection (some reactions positive).
Long-term ciprofloxacin treatment for the prevention of biliary stent blockage: a prospective randomized study (1999)

Long-term use of ciprofloxacin does not prevent blockage of polyethylene biliary stents.
Treatment with mRNA coding for the necroptosis mediator MLKL induces antitumor immunity directed against neo-epitopes (2018)

Cancer immunotherapy can induce durable antitumor responses. However, many patients poorly respond to such therapies. Here we describe a generic antitumor therapy that is based on the intratumor delivery of mRNA that codes for the necroptosis executioner mixed lineage kinase domain-like (MLKL) protein. This intervention stalls primary tumor growth and protects against distal and disseminated tumor formation in syngeneic mouse melanoma and colon carcinoma models. Moreover, MLKL-mRNA treatment combined with immune checkpoint blockade further improves the antitumor activity. MLKL-mRNA treatment rapidly induces T cell responses directed against tumor neo-antigens and requires CD4<sup>+</sup> and CD8<sup>+</sup> T cells to prevent tumor growth. Type I interferon signaling and Batf3-dependent dendritic cells are essential for this mRNA treatment to elicit tumor antigen-specific T cell responses. Moreover, MLKL-mRNA treatment blunts the growth of human lymphoma in mice with a reconstituted human adaptive immune system. MLKL-based treatment can thus be exploited as an effective antitumor immunotherapy.
Mortality in Mexican Patients with Chronic Pigeon Breeder's Lung Compared with Those with Usual Interstitial Pneumonia (1993)

The clinical course of chronic pigeon breeder's lung (CPBL) is unknown, especially in comparison with usual interstitial pneumonia (UIP). We studied a cohort of 125 consecutive patients with interstitial lung diseases, including 78 patients with CPBL (74 biopsied) and 47 patients with UIP in the lung biopsy. Patients with UIP were divided into 17 without bird exposure (UIP) and 30 with bird exposure (UIP + BE). All patients were treated with corticosteroids and followed for 33 +/- 23 months. The best predictors of mortality (Cox proportional hazards model) were age > 44 yr, with a relative risk (RR) of 2.5 and 95% confidence interval (CI) of 1.4 to 4.7, masculine gender (RR 4.0, CI 2.1 to 7.6), x-ray honeycombing (RR 7.0, CI 3.8 to 12.7), and severity of fibrosis in the lung biopsy (RR 4.8, CI 2.3 to 9.7). Survival in CPBL 5 yr after diagnosis was 0.71 (SEM 0.08) and in UIP was 0.23 (SEM 0.08), with no statistical difference between UIP + BE and UIP. After adjusting for severity of fibrosis and honeycombing, however, the correlation of diagnosis with survival disappeared. In conclusion, mortality in CPBL is considerable, but lower than in UIP. Lung fibrosis and honeycombing seem to be a final common pathway for the ILD. Adjusting for them, the effect of diagnosis in survival is not significant.
Results of Topical Myeloperoxidase/Glucose Oxidase/Glucose in the Walker-Mason Burn Model (2005)

One area of research at tile ISR is soft tissue trauma encompassing infection control and wound healing. Treatments are evaluated in vivo using the Walker-Mason model which is a fall thickness thermal injury and infection model. We have identified a novel proprietary topical antimicrobial which may be amenable to treating a variety of wounds. The system consists of an enzyme, myeloperoxidase (MPO) and the requisite substrates which have been optimized for the production of bactericidal reactive oxygen species. Sepsis data is gathered for 21 days and end survivorship of the test article groups are compared to the survivorship of tile untreated group. The survival data is supplemented by monitoring the bacterial infection via bioluminescent imaging by using genetically engineered P. aeruginosa (ATCC 59-1244). The survivorship data is conclusive in stating tile Topical Myeloperoxidase antimicrobial was unsuccessful in recovering an animal from septic infection. The imaging data shows tile movement of bacteria from tile dorsum to the internal cavity and infection of internal organs.
Supramolecular PEGylation of biopharmaceuticals (2016)

The covalent modification of therapeutic biomolecules has been broadly explored, leading to a number of clinically approved modified protein drugs. These modifications are typically intended to address challenges arising in biopharmaceutical practice by promoting improved stability and shelf life of therapeutic proteins in formulation, or modifying pharmacokinetics in the body. Toward these objectives, covalent modification with poly(ethylene glycol) (PEG) has been a common direction. Here, a platform approach to biopharmaceutical modification is described that relies on noncovalent, supramolecular host-guest interactions to endow proteins with prosthetic functionality. Specifically, a series of cucurbit[7]uril (CB[7])-PEG conjugates are shown to substantially increase the stability of three distinct protein drugs in formulation. Leveraging the known and high-affinity interaction between CB[7] and an N-terminal aromatic residue on one specific protein drug, insulin, further results in altering of its pharmacological properties in vivo by extending activity in a manner dependent on molecular weight of the attached PEG chain. Supramolecular modification of therapeutic proteins affords a noncovalent route to modify its properties, improving protein stability and activity as a formulation excipient. Furthermore, this offers a modular approach to append functionality to biopharmaceuticals by noncovalent modification with other molecules or polymers, for applications in formulation or therapy.
A Novel Reconfigurable Sensing Scheme for Variable Level Storage in Phase Change Memory (2011)

This paper presents a novel reconfigurable sensing scheme with the flexibility to change reading precision of analog resistance levels for MLC PCM. A 2Mcell PCM chip was fabricated in 90nm CMOS technology and was tested. Operating at 8-bits precision (adequate for 7b/cell PCM i.e., 128 resistance levels), read access latency is 5μs (measured at 50MHz clock), compared to 35-50μs in state-of-art 2b/cell NAND Flash.
Synthesis and properties of semiconducting aromatic polyquinonediimines (1986)

Abstract A new class of poly‐conjugated polymers has been obtained by condensation of anthraquinones with aromatic diamines in polyphosphoric acid. The polymers are black, intractable powders. Toward obtaining tractable materials, the effect of monomer structure on polymer tractability has been studied. Copolymerizations were also carried out to “soften” these materials. Electrical conductivities in the semiconducting range, 10 −4 ‐ 10 −8 (ohm cm) −1 were observed. Doping with iodine showed small increases.
Transgenic Loblolly Pine Trees from Diverse Elite Families (2003)

Loblolly pine (Pinus taeda L.) has been the focus of genetic improvement for nearly 100 years because of the value of this species to the forestry industry. The application of gene transfer technology to loblolly pine improvement has been limited by the regeneration of transgenic tissue into plants. We have developed gene transfer systems that allow the regeneration of trees after the transformation of embryogenic cultures from a large number of genetically diverse families. Genetic transformation was achieved by biolistic and Agrobacterium-mediated techniques. Biolistic transformation efficiency was increased by identifying the optimal target using secondary somatic embryogenesis and by determining the long-term effects of tissue culture manipulations. Improvements to selection and the tissue culture system facilitated the production of stable transformants from 72% of the cell lines attempted from 15 elite families, with an escape rate of less than 1%. Molecular analysis of transgenic trees produced from biolistic transformation found that 36% of the trees had three inserts or less. Transgenic trees produced by biolistics have exhibited normal morphology for up to five growing seasons, to date. An Agrobacterium-mediated transformation system was developed for loblolly pine using tissue culture and selection procedures of the biolistic system. Agrobacterium tumefaciens has been used to produce transgenic trees of clones from elite loblolly families, as well as clones of P. radiata and P. taeda x rigida. Genomic blot analysis of Agrobacterium-transformed somatic embryos is ongoing. Field tests with Agrobacterium-transformed loblolly and the hybrid loblolly have been established each year since 2001. The efficiency of the Agrobacterium transformation system has made it possible for ArborGen to scale-up for high-throughput gene testing in a conifer. Transgenic trees have been produced with genes for lignin modification, accelerated growth, and flowering control.
Pd-Catalyzed Synthesis of Ar-SCF3 Compounds under Mild Conditions (2011)

Good to excellent yields of aryl trifluoromethyl sulfides, which are an important class of compounds in both the pharmaceutical and agrochemical areas, can be achieved under mild conditions by the Pd-catalyzed reaction of aryl bromides with a trifluoromethylthiolate nucleophile (see scheme).
Machine Teaching: A New Paradigm for Building Machine Learning Systems (2017)

The current processes for building machine learning systems require practitioners with deep knowledge of machine learning. This significantly limits the number of machine learning systems that can be created and has led to a mismatch between the demand for machine learning systems and the ability for organizations to build them. We believe that in order to meet this growing demand for machine learning systems we must significantly increase the number of individuals that can teach machines. We postulate that we can achieve this goal by making the process of teaching machines easy, fast and above all, universally accessible. While machine learning focuses on creating new algorithms and improving the accuracy of "learners", the machine teaching discipline focuses on the efficacy of the "teachers". Machine teaching as a discipline is a paradigm shift that follows and extends principles of software engineering and programming languages. We put a strong emphasis on the teacher and the teacher's interaction with data, as well as crucial components such as techniques and design principles of interaction and visualization. In this paper, we present our position regarding the discipline of machine teaching and articulate fundamental machine teaching principles. We also describe how, by decoupling knowledge about machine learning algorithms from the process of teaching, we can accelerate innovation and empower millions of new uses for machine learning models.
Bandwidth, Power and Carrier Configuration Resilient Neural Networks Digital Predistorter (2023)

This paper proposes a neural networks predistorter based on the bidirectional long-short-term memory (BiLSTM) structure. The proposed predistorter was trained while ensuring that it captures the full intrinsic behavior of the device under test including its memory effects and nonlinear distortions. For this purpose, the device under test was characterized while operating at peak power level with a test signal that emulates strong memory effects. Extensive experimental validation carried on a commercial Gallium Nitride power amplifier prototype demonstrated the ability of the proposed predistorter to maintain standard compliant adjacent channel leakage ratio over a wide range of operating conditions including operating average power, signal bandwidth, and carriers’ configurations. It has been shown that a digital predistorter (DPD) derived from one single training condition was able to linearize the device under test for 72 different test conditions with signal bandwidths between 10MHz and 40MHz, and an operating power range of 5dB. Furthermore, benchmarking results showed that the BiLSTM DPD is unable to maintain satisfactory performance when trained with a sub-optimal signal which does not emulate the full behavior of the device under test. Moreover, it has been shown that the use of the optimal characterization signal along with a generalized memory polynomial predistorter does not lead to satisfactory performance. Hence, the resilience of the predistorter is obtained by combining the suitable model structure along with the appropriate training approach. Such resilient DPD presents a paradigm shift in predistortion techniques which significantly minimizes the need for update. It is anticipated that this work will pave the road for a new generation of DPDs resilient to a wide range of operating conditions.
Elastic parameter estimation for sweet spot identification in unconventional shale plays, Vaca Muerta Formation, Neuquén Basin, Argentina (2019)

Analyzing elastic rock properties helps in the identification of sweet spots in unconventional plays like the Vaca Muerta Formation. The vertical and lateral heterogeneity of total organic carbon (TOC) and carbonate content are two critical factors that partly control the geomechanical response of the rock. These types of unconventional reservoirs have low permeability, making necessary to define brittle zones to stimulate the rock and induce fractures to produce. This leads to the definition of mineralogy ranges, based on rock properties and related to geomechanical parameters, to identify zones with hydrocarbon presence and brittle rock that could show good response to hydraulic stimulation for production purposes. Presentation Date: Monday, September 16, 2019 Session Start Time: 1:50 PM Presentation Start Time: 3:30 PM Location: 304B Presentation Type: Oral
Succinylated Chitosan Derivative Has Local Protective Effects on Intestinal Inflammation (2017)

We have previously reported on the anti-inflammatory effects of a water-soluble chitosan derivative, zwitterionic chitosan (ZWC). In the present study, we hypothesized that orally-administered ZWC would provide local anti-inflammatory effects in the intestinal lumen. ZWC indeed showed anti-inflammatory effects in various <i>in-vitro</i> models including peritoneal macrophages, engineered THP1 monocytes, and Caco-2 cells. In Caco-2 cells, ZWC applied before the lipopolysaccharide (LPS) challenge was more effective than when it was applied after it in preventing LPS-induced cell damage. When administered to mice via drinking water as a prophylactic measure, ZWC protected the animals from 2,4,6-trinitrobenzene sulphonic acid (TNBS)-induced colitis, helping them to recover the body weight, restore the gross and histological appearance of the colon, and generate FoxP3<sup>+</sup> T cells. In contrast, orally-administered ZWC did not protect the animals from LPS-induced systemic inflammation. These results indicate that orally-administered ZWC reaches the colon with minimal absorption through the upper gastrointestinal tract and provides a local anti-inflammatory effect.
Synthesis, molecular modeling, and biology of the 1-benzyl derivative of APDC-an apparent mGluR6 selective ligand (1997)

The synthesis of the 1-benzyl derivative of (2R,4R)-4-aminopyrrolidine-2,4-dicarboxylic acid (1-benzyl-APDC) starting from cis-4-hydroxy-D-proline is disclosed together with a study of the activity of this compound at metabotropic glutamate receptors (mGluRs). The compound was found to display good mGluR6 selectivity, and may thus be a useful pharmacological research tool.
A population of CD4hiCD38hi T cells correlates with disease severity in patients with acute malaria (2020)

In naturally infected adults with acute malaria, a prominent population of type 1 regulatory T cells arises that can be defined by high co-expression of CD4 and CD38 (CD4<sup>hi</sup>CD38<sup>hi</sup>) and that correlates with disease severity in patients with falciparum malaria. This study provides fundamental insights into T-cell biology, including the first evidence that CD4 expression is modulated at the mRNA level. These findings have important implications for understanding the balance between immunity and immunopathology during malaria.