gebhart/patrepeval huggingface dataset:
Microfluidic arenas for war games between neutrophils and microbes (2019)

Measurements of neutrophil activities such as cell migration and phagocytosis are generally performed using low-content bulk assays, which provide little detail activity at the single cell level, or flow cytometry methods, which have the single cell resolution but lack perspective on the kinetics of the process. Here, we present a microfluidic assay for measuring the essential functions that contribute to the antimicrobial activity of neutrophils: migration towards the target, and killing of microbes. The assay interrogates the interactions between isolated human neutrophils and populations of live, proliferating microbes. The outcome is measured in a binary mode that is reflective of in vivo infections, which are either cleared or endure the host response. The outcome of the interactions is also characterized at single cell resolution for both the neutrophils and the microbes. We applied the assay to test the response of neutrophils from intensive care patients to live Staphylococcus aureus, and observed alterations of antimicrobial neutrophil activity in patients, including those with sepsis. By directly measuring neutrophil activity against live targets at high spatial and temporal resolution, this assay provides unique insights into the life-or-death contest shaping the outcome of interactions between populations of neutrophils and microbes.
Biobased mineral‐oil barrier‐coated food‐packaging films (2016)

ABSTRACT Toxic mineral oils can migrate into foods from cardboard boxes made of recycled fibers. This is an emerging issue for the whole dry‐food‐packaging industry. Breakfast cereals, for example, are typically packaged in boxes with or without inner bags and consumed without further processing. Currently, fossil‐based high‐density polyethylene (HDPE) films are used as a major raw material for such inner bags. However, HDPE is a very poor barrier against mineral‐oil migration. Biobased coatings from cellulose nanofibrils (CNFs), hydroxypropylated xylan, and hydroxypropylated cellulose were applied onto biobased high‐density polyethylene (bio‐HDPE) films, and the mineral‐oil barrier properties were evaluated. All of the coated films significantly decreased the migration of n ‐decane, isobutylbenzene, 1‐cyclohexylbutane, 1‐cyclohexylheptane, and 1‐cyclohexyldecane. Biobased barrier bags prepared from (2,2,6,6‐tetramethylpiperidin‐1‐yl)oxy oxidized CNF coated bio‐HDPE film protected the content to a great extent from mineral‐oil migration compared to noncoated bio‐HDPE and other commercial breakfast cereal‐bag films. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134 , 44586.
Fiber optic cone penetrometer raman probe for in situ chemical characterization of the Hanford underground waste tanks (1997)

A field hardened fiber optic Raman probe has been developed for cone penetrometer deployment in the Hanford underground chemical waste storage tanks. The corrosive chemical environment of the tanks, as well as Hanford specific deployment parameters, provide unique challenges for the design of an optical probe.
Antibody gene transfer with adeno‐associated viral vectors as a method for <scp>HIV</scp> prevention (2017)

Broadly neutralizing antibodies (bNAbs) against human immunodeficiency virus (HIV) show great promise in HIV prevention as they are capable of potently neutralizing a considerable breadth of genetically diverse strains. Passive transfer of monoclonal bNAb proteins can confer protection in animal models of HIV infection at modest concentrations, inspiring efforts to develop an HIV vaccine capable of eliciting bNAb responses. However, these antibodies demonstrate high degrees of somatic mutation and other unique characteristics that may hinder the ability of conventional approaches to consistently and effectively produce bNAb analogs. As an alternative strategy, we and others have proposed vector-mediated gene transfer to generate long-term, systemic production of bNAbs in the absence of immunization. Herein, we review the use of adeno-associated virus (AAV) vectors for delivery of HIV bNAbs and antibody-like proteins and summarize both the advantages and disadvantages of this strategy as a method for HIV prevention.
Opportunities and Challenges for Organic Electrodes in Electrochemical Energy Storage (2020)

As the world moves toward electromobility and a concomitant decarbonization of its electrical supply, modern society is also entering a so-called fourth industrial revolution marked by a boom of electronic devices and digital technologies. Consequently, battery demand has exploded along with the need for ores and metals to fabricate them. Starting from such a critical analysis and integrating robust structural data, this review aims at pointing out there is room to promote organic-based electrochemical energy storage. Combined with recycling solutions, redox-active organic species could decrease the pressure on inorganic compounds and offer valid options in terms of environmental footprint and possible disruptive chemistries to meet the energy storage needs of both today and tomorrow. We review state-of-the-art developments in organic batteries, current challenges, and prospects, and we discuss the fundamental principles that govern the reversible chemistry of organic structures. We provide a comprehensive overview of all reported cell configurations that involve electroactive organic compounds working either in the solid state or in solution for aqueous or nonaqueous electrolytes. These configurations include alkali (Li/Na/K) and multivalent (Mg, Zn)-based electrolytes for conventional "sealed" batteries and redox-flow systems. We also highlight the most promising systems based on such various chemistries relying on appropriate metrics such as operation voltage, specific capacity, specific energy, or cycle life to assess the performances of electrodes.
Poor Video Streaming Performance Explained (and Fixed) (2018)

HTTP-based video streaming is a key application on the Internet today, comprising the majority of Internet traffic today. Yet customers remain dissatisfied with video quality, resulting in lost revenue for content providers. Recent studies have blamed this on the adaptive bitrate selection (ABR) algorithm used by client players, claiming it interacts poorly with TCP when the video buffer is full, which causes it to underestimate available network bandwidth. We show that the root cause of the problem lies in the data plane, and that even a perfect control plane (ABR) algorithm is not enough to guarantee video flows their fair share of network bandwidth. Namely, it is the sequential download of (small) video segments that is at fault, as they disrupt the normal interaction between TCP congestion control and router queue occupancy. We analytically derive the throughput of a video flow as a function of download size and network conditions, and use this to develop an adaptive algorithm for selecting the download size. Combined with pipelining, our approach achieves near-optimal throughput and fast bitrate adaptation, regardless of the control plane algorithm. We implement our approach as a DASH video player called Sprint, and evaluate it against state-of-the-art proposals from the literature as well as deployed players from Netflix, Youtube, Hulu, and Amazon. Sprint consistently achieves above 90% of its fair-share throughput, while the previous state-of-the-art exhibits high variability (e.g., from 31% to close to fair share depending on the network conditions). Industry players often achieve below 50% of their fair share.
Novel Helix-Constrained Nociceptin Derivatives Are Potent Agonists and Antagonists of ERK Phosphorylation and Thermal Analgesia in Mice (2010)

The nociceptin opioid peptide receptor (NOP, NOR, ORL-1) is a GPCR that recognizes nociceptin, a 17-residue peptide hormone. Nociceptin regulates pain transmission, learning, memory, anxiety, locomotion, cardiovascular and respiratory stress, food intake, and immunity. Nociceptin was constrained using an optimized helix-inducing cyclization strategy to produce the most potent NOP agonist (EC50 = 40 pM) and antagonist (IC50 = 7.5 nM) known. Alpha helical structures were measured in water by CD and 2D (1)H NMR spectroscopy. Agonist and antagonist potencies, evaluated by ERK phosphorylation in mouse neuroblastoma cells natively expressing NOR, increased 20-fold and 5-fold, respectively, over nociceptin. Helix-constrained peptides with key amino acid substitutions had much higher in vitro activity, serum stability, and thermal analgesic activity in mice, without cytotoxicity. The most potent agonist increased hot plate contact time from seconds up to 60 min; the antagonist prevented this effect. Such helix-constrained peptides may be valuable physiological probes and therapeutics for treating some forms of pain.
Hardware synthesis from guarded atomic actions with performance specifications (2005)

We present a new hardware synthesis methodology for guarded atomic actions (or rules), which satisfies performance-related scheduling specifications provided by the designer. The methodology is based on rule composition, and relies on the fact that a rule derived by the composition of two rules behaves as if the two rules were scheduled simultaneously. Rule composition is a well understood transformation in the TRS theoretical framework; however, previous rule composition approaches resulted in an explosion of the number of rules during synthesis, making them impractical for realistic designs. We avoid this problem through composition of conditional actions which generates one rule instead of 2/sup n/ rules when we combine n rules. We then show how this conditional composition of rules can be compiled into an efficient hardware structure which introduces new but derived interfaces in modules. We demonstrate the approach via a small circuit example (GCD) and then show its impact on the methodology to implement pipelined processors in Bluespec. Many ways of dealing with branches in pipelined processors or bypassing values can be expressed simply as different schedules. The results show improvements in performance over previous rule-based synthesis approaches as well as the ease of performance-related architectural exploration. In a somewhat surprising result, we show that simply by specifying a different schedule, one can automatically transform a single-issue processor pipeline into a superscalar pipeline.
Monoclonal Antibodies Against the Staphylococcus aureus Bicomponent Leukotoxin AB Isolated Following Invasive Human Infection Reveal Diverse Binding and Modes of Action (2017)

The 2-component leukotoxin LukAB is critical for Staphylococcus aureus targeting and killing of human neutrophils ex vivo and is produced in the setting of human infection. We report 3 LukAB-specific human monoclonal antibodies (mAbs) with distinct mechanisms of toxin neutralization and in vivo efficacy. Three hybridomas secreting mAbs with anti-LukAB activity (designated SA-13, -15, and -17) were generated from B cells obtained from a 12-year-old boy with S. aureus osteomyelitis. Each of the 3 mAbs neutralized LukAB-mediated neutrophil toxicity, exhibited differing levels of potency, recognized different antigenic sites on the toxin, and displayed at least 2 distinct mechanisms for cytotoxic inhibition. SA-15 bound exclusively to the dimeric form of the toxin, suggesting that human B cells recognize epitopes on the dimerized form of LukAB during natural infection. Both SA-13 and SA-17 bound the LukA monomer and the LukAB dimer. Although all 3 mAbs potently neutralized cytotoxicity, only SA-15 and SA-17 significantly inhibited toxin association with the cell surface. Treatment with a 1:1 mixture of mAbs SA-15 and SA-17 resulted in significantly lower bacterial colony counts in heart, liver, and kidneys in a murine model of S. aureus sepsis. These data describe the isolation of diverse and efficacious antitoxin mAbs.
Optimization of the Refractive Index of a Gap Material Used for the 4-layer DOI Detector (2014)

We have developed a 4-layer depth-of-interaction (DOI) detector which consists of four layers of scintillation crystal arrays and a position sensitive photomultiplier tube (PS-PMT). To control the behavior of scintillation light in each DOI crystal array, some reflectors between crystals are removed so that all crystal responses in the four layers are expressed in one two-dimensional (2D) position histogram by implementing an Anger-type calculation of the PS-PMT signals. Since the method utilizes spread of scintillation light through the boundary of the crystals with no reflectors, positioning performance in the 2D position histogram depends on the crystal dimensions, the crystal surface finish, and gap materials. In this work, we propose an adjustment method for crystal identification performance of the 4-layer DOI detector by selecting the optimal refractive index for the gap materials between the crystals in which the reflectors are removed. We fabricated single-layer detectors and 4-layer detectors using LYSO scintillators and evaluated the crystal identification performance, while varying the refractive index of the gap materials (by using different optical cements). As a result, we found the 2D position histogram changes as a function of the refractive index of the optical cement between crystals and the optimal refractive indices can be determined for the detector using the LYSO crystals. We concluded that the crystal response of the 2D position histograms can be adjusted and crystal identification performance can be optimized by changing the refractive index of the gap materials.
Fire‐resistant polyimides and copolyimides based on 1‐[(dialkoxyphosphinyl)methyl]‐2,4‐ and ‐2,6‐diaminobenzenes (1984)

Abstract Various phosphorus‐containing polyimides were prepared by the reaction of 1‐[(dialkoxyphosphinyl)methyl]‐2,4‐ and ‐2,6‐diaminobenzenes (1) with a tetracarboxylic dianhydride like pyromellitic dianhydride (PMDA) and benzophenone tetracarboxylic dianhydride (BTDA). In addition, copolyimides that contained approximately 3% phosphorus were prepared by the reaction of 1 and m ‐phenylenediamine (MPD) with the aforementioned tetracarboxylic dianhydrides. Elemental analysis, inherent viscosity, infrared (IR) spectroscopy, differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA) studies were performed to characterize the polymers. Their thermal properties were compared with those of the corresponding common polyimides. It was shown that the molecular weight and thermal stability of the polymers were reduced as the concentration of the phosphorus moieties increased. The fire‐resistance of the copolyimides was evaluated by determining their limiting oxygen index (LOI) value. Copolyimides that contained about 3% phosphorus showed an LOI value approximately 30% higher, than the value of the corresponding common polyimides. In addition, a model diamic acid and diimide was synthesized by the reaction of 1‐[di(2‐chloroethoxyphosphinyl)methyl]‐2,4‐ and ‐ 2,6‐diaminobenzene (DCEPD) with phthalic anhydride and characterized by elemental analysis, IR, proton nuclear magnetic ( 1 H‐NMR) spectroscopy, DSC, and TGA. The pyrolysis behavior of the model compounds was investigated by gas chromatography‐mass spectrometry (GC‐MS). A direct cleavage of the PC bond and a possible rearrangement to diisocyanates occurred during their pyrolysis.
System and method for reducing combustion dynamics and NO.sub.x in a combustor (2015)

A system for reducing combustion dynamics and NO.sub.x in a combustor includes a tube bundle that extends radially across at least a portion of the combustor, wherein the tube bundle comprises an upstream surface axially separated from a downstream surface. A shroud circumferentially surrounds the upstream and downstream surfaces. A plurality of tubes extends through the tube bundle from the upstream surface through the downstream surface, wherein the downstream surface is stepped to produce tubes having different lengths through the tube bundle. A method for reducing combustion dynamics and NO.sub.x in a combustor includes flowing a working fluid through a plurality of tubes radially arranged between an upstream surface and a downstream surface of an end cap that extends radially across at least a portion of the combustor, wherein the downstream surface is stepped.
Terahertz-wave radars based on resonant-tunneling-diode oscillators (2019)

Several terahertz-wave radar techniques based on a resonant-tunneling-diode (RTD) oscillator are under investigation. First, an amplitude-modulated continuous-wave (AMCW) radar able to measure the absolute distance was achieved by demodulating the wave returning from the target and measuring its phase, either by determining the time delay with an oscilloscope, or by using an IQ demodulator to determine the sine and cosine of the phase. Our current record with this type of radar is a ranging error of 0.063 mm; however, it can only measure the distance up to a single reflecting surface. Second, a subcarrier frequency-modulated continuous-wave (FMCW) radar has been demonstrated to work and is expected to allow the simultaneous ranging of several targets. The ranging error for this radar was found to be 0.73 mm. Additionally, a radar technique based on the swept source optical coherence tomography (SS-OCT) principle is proposed. Terahertz-wave 2D imaging can be combined with these radar techniques to obtain a 3D imaging system.
Lifetime control in silicon through impact sound stressing (1977)

ISS is applied a) to produce damage on silicon surfaces in a controlled manner and b) to achieve “damage gettering” in Si. ISS damage introduced on the wafer backside is used to monitor generation-lifetime of electrical carriers during semiconductor processing. This is shown for silicon substrates, for epitaxial silicon films, and for epitaxial silicon films grown on ion-implanted surfaces. ISS improves lifetime in silicon by several orders of magnitude. Such lifetime improvements on ISS' ed silicon wafers are correlated with a reduction of crystallographic defects. ISS wird benutzt, um a) Damage auf Siliziumoberflächen in kontrollierter Weise herzustellen und b) um „Damage-Getterung”︁ in Si zu erhalten. ISS-Damage auf der Rückseite des Wafer wird benutzt, um die Generationslebensdauer der elektrischen Ladungsträger während der Halbleiterbehandlung zu verfolgen. Dies wird für Siliziumsubstrate, für Silizium-Epitaxieschichten sowie für Silizium-Epitaxieschichten gezeigt, die auf ionenimplantierten Oberflächen wachsen. ISS verbessert die Lebensdauer in Silizium um mehrere Größenordnungen. Derartige Lebensdauerverbesserungen der ISS-behandelten Silizium-Wafer sind korreliert mit einer Verringerung der kristallographischen Defekte.
Targeting T cells against brain tumors with a bispecific ligand-antibody conjugate (1998)

High-affinity receptors expressed on the surface of some tumors can be exploited by chemically conjugating the ligand for the receptor and an antibody against immune effector cells, thus redirecting their cytolytic potential against the tumor. Ovarian carcinomas and some brain tumors express the high-affinity folate receptor (FR). In this report, a transgenic mouse model that generates endogenously arising choroid plexus tumors was used to show that folate/anti-T-cell receptor antibody conjugates can direct infiltration of T cells into solid brain tumor masses. An engineered single-chain Fv form of the anti-T-cell receptor antibody KJ16 was conjugated with folate, to produce a bispecific agent that was substantially smaller than most previously characterized bispecific antibodies. Folate conjugation to the antibody increased T-cell infiltration into the tumors by 10- to 20-fold, and significantly prolonged survival of the mice.
Comparative Analysis of Single-Box and Two-Box RF Power Amplifiers’ Behavioral Models Sensitivity to Delay Misliagnment (2018)

This paper examines the sensitivity of power amplifiers behavioral models to time-delay misalignment. Memory polynomial and twin-nonlinear two-box models are derived, from measured data, to model the behavior of a GaN based Doherty power amplifier under various time misalignment conditions. The results show that the memory polynomial model is much less sensitive to delay misalignment than twin-nonlinear two-box models. In particular, the memory polynomial model accuracy is not altered by a delay underestimation up to one sample, and is only degraded when the delay is overestimated. Conversely, twin-nonlinear two-box models performances are degraded whether the delay is underestimated or overestimated. Hence, the identification of twin-nonlinear two-box models unavoidably requires accurate delay alignment with a sub-sample resolution while the memory polynomial model can be derived from low complexity coarse delay alignment. Thus, in comparison with the two-box models, the complexity of the memory polynomial model identification can be offset by the use of low-complexity coarse time-delay alignment algorithms.
Control of engines with fully variable valvetrains (2005)

To improve performance, fuel economy, and emissions of automotive engines, automakers have introduced a number of devices intended to vary a previously fixed engine parameter with operating condition. Such devices include variable cam timing and valve lift, variable compression ratio, intake manifold tuning, etc. Combining these devices in an engine promises improved fuel economy, but raises the issue of scheduling and coordination to achieve the benefit and prevent undesirable failure modes. This paper introduces the problem of controlling a fully variable valvetrain configuration, and shows an algorithm for synchronizing variables that have different rates of response with the goal of preventing potential piston-valve interference in mechanically unprotected engines.
S3-R1 (2004)

One of the key components of tele-presence systems is automatic awareness of the remote environment. This very same capability of automatic situation awareness is currently being developed and deployed in the context of the next generation smart surveillance systems. Smart surveillance systems use a number of automatic video analysis techniques like object detection, tracking and classification in conjunction with database and web application servers to provide users with the capability of distributed smart surveillance. The IBM smart surveillance system is one of the few advanced surveillance systems which provides not only the capability to automatically monitor a scene but also the capability to manage the surveillance data, perform event based retrieval, receive real time event alerts thru standard web infrastructure and extract long term statistical patterns of activity.
Anhydrolide Macrolides. 1. Synthesis and Antibacterial Activity of 2,3-Anhydro-6-<i>O</i>-methyl 11,12-Carbamate Erythromycin A Analogues (1998)

A series of 3-descladinosyl-2,3-anhydro-6-O-methylerythromycin A 11, 12-carbamate analogues have been synthesized and evaluated for antibacterial activity. These compounds were found to be potent antibacterial agents against Gram-positive organisms in vitro, many having MIC values below 1 microg/mL for the macrolide-susceptible Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae, as well as improved activity compared to erythromycin A against the inducibly MLS (macrolide, lincosamide, and streptogramin B)-resistant organisms. Structure-activity studies revealed that arylalkyl carbamates with two and four carbon atoms between the aromatic moiety and carbamate nitrogen have the best in vitro activity. All of the C-10 epi analogues evaluated were found to have substantially less activity than the corresponding natural C-10 isomer. Several analogues demonstrated moderate antibacterial activity against the constitutively resistant S.aureus A-5278, S. pneumoniae5979, and S.pyogenes 930. However, despite potent in vitro activity, these analogues showed only moderate in vivo activity in mouse protection studies.