gebhart/patrepeval huggingface dataset:
Zena Werb, Ph.D, “Queen of the Matrix”: In Memoriam (1945–2020) (2020)

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To understand Zena's beginnings is to understand the essence of who Zena was as a person, mentor, matriarch, and as a world-class scientist. We are fortunate to have crossed paths with her.

Zena's achievements are remarkable, considering the hardships she faced as she
Bacteriophage T7 deoxyribonucleic acid replication invitro. Bacteriophage T7 DNA polymerase: an an emzyme composed of phage- and host-specific subunits. (1975)

The DNA polymerase induced after infection of Escherichia coli by phage T7 has been purified 500-fold to near homogeneity as judged by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The purified enzyme complements extracts of cells infected with a T7 gene 5 mutant to permit cell-free replication of duplex T7 DNA. In contrast, purified T4 DNA polymerase or E. coli DNA polymerase I is unable to do so, thus suggesting a specific requirement for the T7 enzyme in the replication of the viral DNA. E. coli TsnC protein is present in purified T7 DNA polymerase in one-to-one stoichiometry with T7 gene 5 protein, and can be isolated in homogeneous form from heat-denatured enzyme by chromatography on DEAE-cellulose. The inactive form of T7 gene 5 protein that accumulates in tsnC hosts has been partially purified. When partially purified gene 5 protein is mixed with purified TsnC protein, DNA polymerase activity is restored, and formation of a one-to-one complex between the two proteins occurs. These results indicate that the functional form ofT7 DNA polymerase is a complex composed of phage- and host-specified subunits.
Formation of distorted rutile-type NbO2, MoO2, and WO2 films by reactive sputtering (2019)

We report the film growth of distorted rutile-type NbO2 (4d1 system), MoO2 (4d2), and WO2 (5d2) by radio-frequency (RF) magnetron reactive sputtering. Through optimization of growth conditions for the three oxides on Al2O3(0001), we found that the increase/decrease in the RF power had an equivalent role to that of the decrease/increase in the oxygen ratio in the Ar–O2 sputtering gas. X-ray photoelectron spectroscopy supported the d1 electronic configuration of NbO2 and d2 electronic configurations of MoO2 and WO2. An electrical transport measurement confirmed that NbO2 was insulating, while MoO2 and WO2 were metallic, consistent with the d-electron filling in the molecular orbital bonding band. The growth scheme presented in this study will be useful for valence control in various oxide thin films with a simple sputtering technique.
Reductions In Tolerance To Central Hypovolemia During Passive Heat Stress Are Accurately Tracked By The Compensatory Reserve Index. (2015)

BACKGROUND: The Compensatory Reserve Index (CRI) quantifies, on a scale of 0 (imminent cardiovascular instability/decompensation) to 1 (maximum ability to compensate), the body’s physiological reserve to compensate for progressive reductions in central blood volume. Passive heat stress reduces tolerance to central hypovolemia, yet it is unknown if this is accurately reflected by the CRI. PURPOSE: We tested the hypothesis that passive heat stress reduces CRI independently, and that the CRI tracks further reductions in central blood volume during combined heat stress and progressive lower body negative pressure (LBNP). METHODS: On separate and randomized days, tolerance to central hypovolemia was evaluated in 12 healthy male subjects (32 ± 6 y, 182 ± cm, 84 ± 12 kg) following whole-body passive heat stress or a normothermic time control period. Tolerance to central hypovolemia was quantified as the time to pre-syncope during progressive LBNP. The CRI was derived from a machine learning algorithm designed to extract and assess features of the arterial pressure waveform that were obtained from continuous photoplethysmography via finger pulse oximetry. RESULTS: Pre heat stress CRI was similar between conditions (0.91 ± 0.04 vs. 0.91 ± 0.05, p=0.92). Prior to LBNP, intestinal temperature was greater (38.2 ± 0.2 vs. 37.1 ± 0.2°C, p<0.01) and CRI was lower (0.57 ± 0.26 vs. 0.86 ± 0.04, p<0.01) with heat stress compared to the normothermic condition. Tolerance to central hypovolemia was reduced by 46 ± 32% with heat stress (482 ± 242 vs. 1015 ± 434 sec, p<0.01). The reduction in CRI during progressive LBNP significantly differed between conditions (time × condition, p<0.01). CRI was lower during heat stress at 20% (0.54 ± 0.26 vs. 0.75 ± 0.16), 40% (0.39 ± 0.27 vs. 0.65 ± 0.18) and 60% (0.30 ± 0.25 vs. 0.46 ± 0.19) of total LBNP time (all p<0.01). In contrast, CRI values at pre-syncope were similar between conditions (0.16 ± 0.11 vs. 0.25 ± 0.18, p=0.16). CONCLUSIONS: These data show that the CRI accurately tracks the compromised physiological capacity to compensate for progressive reductions in central blood volume during whole-body passive heat stress. Funding support: Department of Defense Grant #110475007.
The Mechanism of Mucus Production in Bronchial Asthma (2009)

Mucus production is a cardinal feature of bronchial asthma, contributing to morbidity and mortality in the disease. Goblet cells are major mucus-producing cells, and goblet cell hyperplasia (GCH) is one feature of airway remodeling, defined as structural changes occurring in the airway. A number of studies have demonstrated that Th2-type cells play critical roles in this process and that particularly interleukin-13 (IL-13), among Th2-type cytokines, is a central mediator for GCH. However, the mechanism underlying how Th2 cytokines induce mucus production or GCH is poorly understood. Mouse calcium-activated chloride channel-3 (mCLCA-3; gob-5)/human CLCA-1 acts as a downstream molecule of Th2 cytokines, IL-4/IL-9/IL-13 signals, playing an important role in mucus production. Moreover, we have recently found that pendrin, an anion transporter, is induced by IL-13 and causes mucus production in airway epithelial cells. It is hoped that if we can clarify how mucus is produced, this will lead to development of novel therapeutic reagents to suppress mucus production in bronchial asthma.
Supplementary Figure 2 from Pacritinib Combined with Sirolimus and Low-Dose Tacrolimus for GVHD Prevention after Allogeneic Hematopoietic Cell Transplantation: Preclinical and Phase I Trial Results (2023)

&lt;p&gt;Safety measures monitored on trial including (A) QTcF, (B) cardiac ejection fraction, (C) prothrombin time, (D) partial thromboplastin time, (E) and thrombin time&lt;/p&gt;
Adaptive Distortion Compensation With Integrated Optical Finite Impulse Response Filters in High Bitrate Optical Communication Systems (2004)

In high-bit-rate optical transmission systems, distortions due to dynamic chromatic dispersion, polarization mode dispersion, and power changes are larger than the distortion tolerances of the system. To meet the tolerances and the desired quality of service, an adaptive equalizer is necessary. We demonstrate the capabilities of planar lightwave circuit integrated optical finite impulse response filters for mitigating distortions of the transmission channel, and we investigate two adaptive equalization approaches. The first approach uses an adaptive feedback generated from electrical spectrum monitoring; the second one uses intersymbol interference minimization with a least mean square error algorithm. We successfully demonstrated adaptive equalization of chromatic dispersion, self-phase modulation, and polarization mode dispersion, as well as combinations of these distortions.
Pt/C Decorated with N-Doped Carbon Layers as a Highly Durable Electrocatalyst for the Oxygen Reduction Reaction (2021)

Exploiting advanced electrocatalysts for the sluggish oxygen reduction reaction (ORR) of the cathode is greatly crucial for proton-exchange membrane fuel cell (PEMFC) commercial application but still exhibit a significant challenge, especially the stability issues that have drawn attractive attention. Therefore, we introduced a nitrogen-doped carbon layer into the Pt/C surface, which not only prevents aggregation of Pt nanoparticles but also endows the electrocatalyst with enhanced performance without hiding the internal Pt active sites. The accelerated durability tests show an ignorable ORR activity loss (10 mV) in the as-prepared Pt/C@NC-0.06 sample compared to the pristine Pt/C catalyst (37 mV) after 5000 cyclic voltammetry cycles. Furthermore, in comparison to the pristine Pt/C catalyst (0.28 mA cm–2), the as-obtained Pt/C@NC-0.06 sample exhibits 2.32-fold improvement for the specific activity. The enhanced ORR properties of the Pt/C@NC-X catalyst in this work supplies a promising way to facilitate the electrocatalytic performance of catalysts in PEMFCs.
Measurements ofϕmeson production in relativistic heavy-ion collisions at the BNL Relativistic Heavy Ion Collider (RHIC) (2009)

We present results for the measurement of ϕ meson production via its charged kaon decay channel ϕ→K[superscript +]K[superscript -] in Au+Au collisions at √(s[subscript NN])=62.4,130, and 200 GeV, and in p+p and d+Au collisions at √(s[subscript NN])=200 from the STAR experiment at the BNL Relativistic Heavy Ion Collider (RHIC). The midrapidity (|y|&lt;0.5) ϕ meson transverse momentum (p[subscript T]) spectra in central Au+Au collisions are found to be well described by a single exponential distribution. On the other hand, the p[subscript T] spectra from p+p, d+Au, and peripheral Au+Au collisions show power-law tails at intermediate and high p[subscript T] and are described better by Levy distributions. The constant ϕ/K[superscript -] yield ratio vs beam species, collision centrality, and colliding energy is in contradiction with expectations from models having kaon coalescence as the dominant mechanism for ϕ production at RHIC. The Ω/ϕ yield ratio as a function of p[subscript T] is consistent with a model based on the recombination of thermal s quarks up to p[subscript T]~4 GeV/c, but disagrees at higher transverse momenta. The measured nuclear modification factor, RdAu, for the ϕ meson increases above unity at intermediate p[subscript T], similar to that for pions and protons, while R[subscript AA] is suppressed due to the energy loss effect in central Au+Au collisions. Number of constituent quark scaling of both R[subscript cp] and v[subscript 2] for the ϕ meson with respect to other hadrons in Au+Au collisions at √(sNN)=200 GeV at intermediate p[subscript T] is observed. These observations support quark coalescence as being the dominant mechanism of hadronization in the intermediate p[subscript T] region at RHIC.
Evaluation of the First Cytostatically Active 1-Aza-9-oxafluorenes as Novel Selective CDK1 Inhibitors with P-Glycoprotein Modulating Properties (2003)

The first series of synthetic 1-aza-9-oxafluorenes with cytostatic activities in the micromolar range was evaluated as cyclin-dependent kinase (CDK1) inhibitors. Activity was found to be selective in comparison to the inhibition of other kinases within the CDK family. Compounds were shown to inhibit the membrane-efflux pump P-glycoprotein responsible for multidrug resistance in cancer cells. First structure-activity relationships are discussed.
Pion femtoscopy inp + pcollisions ats=200GeV (2011)

Made available in DSpace on 2015-06-30T20:40:12Z (GMT). No. of bitstreams: 1 2-s2.0-79961105929.pdf: 1050256 bytes, checksum: aff184aa5443e25762d99b40d9fbc0cd (MD5) Previous issue date: 2011
ALL-associated JAK1 mutations confer hypersensitivity to the antiproliferative effect of type I interferon (2010)

Activating mutations in JAK1 have been reported in acute lymphoblastic leukemias (ALLs). In this study, we found a type I interferon (IFN) transcriptional signature in JAK1 mutation-positive human ALL samples. This signature was recapitulated in vitro by the expression of JAK1 mutants in BW5147 and BaF3 hematopoietic cell lines. Binding of JAK1 to the IFN receptor was essential because mutations in the FERM domain abrogated this effect. Beside the constitutive activation of the type I IFN signaling cascade, JAK1 mutations also strongly potentiated the response to IFN in vitro. Typically, the proliferation of cell lines expressing JAK1(A634D) was abrogated by type I IFNs. Interestingly, we found that different JAK1 mutations differentially potentiate responses to type I IFNs or to interleukin-9, another cytokine using JAK1 to mediate its effects. This suggests that the type of mutation influences the specificity of the effect on distinct cytokine receptor signaling. Finally, we also showed in an in vivo leukemia model that cells expressing JAK1(A634D) are hypersensitive to the antiproliferative and antitumorigenic effect of type I IFN, suggesting that type I IFNs should be considered as a potential therapy for ALL with JAK1-activating mutations.
Adaptive Routing in InfiniBand Hardware (2022)

Interconnection networks are the communication backbone of modern high-performance computing systems and an optimised interconnection network is crucial for the performance and utilisation of the system as a whole. One element of the interconnection network is the routing algorithm, which directly influences how we are able to utilise the physical network topology. InfiniBand is one of the most common network architectures used in high-performance computing and traditionally it only supported static routing. For multi-path networks such as Fat-trees, static routing is inefficient because it cannot balance traffic in real-time nor utilise multiple paths efficiently under adversarial traffic. This again potentially leads to unnecessary contention and an underutilised network, which has led to numerous proposals on how to avoid this by using adaptive routing. Adaptive routing has recently been introduced in InfiniBand and in this paper we evaluate to what extent the expected benefits of adaptive routing is true for InfiniBand. Through a set of experiments on HDR InfiniBand equipment we describe the basic behaviour of adaptive routing in InfiniBand, its benefits in Fat tree topologies and the unfortunate side effects related to unfairness that adaptive routing in general might introduce, including such phenomena as the reverse parking lot problem and congestion spreading.
Using reference trajectories to predicted uncertain systems: exemplified on a power plant (2007)

This paper presents a method for prediction of uncertain closed loop systems, where the uncertainties are depending on operating points. Such model uncertainties are often present when complicated non-linear systems are predicted. The method uses precomputed mean and variances of the prediction error depending on the operation point given by references and disturbances. These uncertainty models are stored in a model bank, linear interpolation is applied to the elements of the model bank in order to predict uncertainty bounds on the predictions using the statistics of the past prediction uncertainties. It is as well proposed to update the uncertainty prediction models on-line. The potential of the method is illustrated by an example from a coal-fired power plant. This example shows prediction of the uncertainties as a bounded region in which the given system variable can be assumed to be contained in. In the example these successfully bound the system variables while in comparison applying a simple prediction diverges from the system.
Preview Control for Vehicle Lateral Guidance in Highway Automation (1993)

The continuous time deterministic optimal preview control algorithm is applied to the lateral guidance of a vehicle for an automated highway. In the lateral guidance problem, the front wheel steering angle of the vehicle is controlled so that the vehicle follows the center for a lane with small tracking error and maintains good ride quality simultaneously. A preview control algorithm is obtained by minimizing a quadratic performance index which includes terms representing the passenger ride quality as well as the lateral tracking error, each of these terms is multiplied by a frequency dependent weight. This design method is known as a frequency shaped linear quadratic (FSLQ) optimal control approach. It permits incorporating frequency domain design specifications such as high frequency robustness and ride quality in the optimal controller design. It is shown that the optimal preview control law consists of a feedback control term and two feedforward control terms. The feedback term is exactly the same as that of traditional LQ control algorithm. The feedforward preview control action significantly improves the tracking performance and ride quality. Frequency-domain analyses, as well as numerical simulation results, show the improvements achieved by using the preview control algorithm in both the frequency and time domains.
Magnetoelastic Torquemeter System for LCAC Hovercraft Turboshaft Engine Monitoring and Control (2012)

This paper presents the development of a magnetoelastic torque-meter for use on the Landing Craft Air Cushion (LCAC) hovercraft’s high speed gas turbine engines. As the gas turbine can produce in excess of the nominal torque limit of the right angle gearbox, torque limiting is required. Limiting torque based on torque tables (as is done currently) penalizes the overall performance of the majority of the fleet due to a significant variance in engine output horsepower. This sub-optimal operation of the craft could be overcome by measuring actual torque produced by each engine with a torque-meter; however conventional torque-meter designs were deemed impractical to retrofit due to the design requirements, and issues with integration and reliability / maintainability. An in-depth search by the US Navy identified a torque-meter concept utilizing magnetoelastic polarized band technology. The aim of this paper is to: (i) outline the general architecture of the system, (ii) highlight the performance of the torque-meter developed for the LCAC, (iii) describe the efforts that helped to mature this technology to Technology Readiness Level 8 and to transition it from motorsport applications to use on the LCAC, and (iv) summarize the initial results of the torque-meter system validation obtained through dynamometer tests on the engine and craft tests on the LCAC.
Low-temperature thin film nitride transformation reactions (2012)

This study illustrates a novel method of transforming between two refractory nitride thin films at temperatures well below their respective melting points. Silicon nitride (Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) is an excellent thermal and electronic insulator, with applications in the microelectronic, automotive and technical ceramic industries. Thermodynamically, there is a significant decrease in the Gibb's Free Energy inherent in the transformation between Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> and a number of refractory metal nitrides if they are in contact at high temperature; however, these transformation reactions are limited in the pure state by a kinetic barrier at any temperature appreciably lower than the melting point of Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> (-2173 K). Previous results presented at this conference illustrated the successful conversion of powdered amorphous Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> to TiN. The transformation is made possible by a liquid phase present in a number of Ti-based alloys at temperatures in the vicinity of 800 °C. Current results indicate the full conversion of SiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> nitride thin films into conducting TiN. Such transformations provide a novel pathway for metallization with a variety of electronic applications.
In Vivo Interrogation of Spinal Mechanosensory Circuits (2016)

Spinal dorsal horn circuits receive, process, and transmit somatosensory information. To understand how specific components of these circuits contribute to behavior, it is critical to be able to directly modulate their activity in unanesthetized in vivo conditions. Here, we develop experimental tools that enable optogenetic control of spinal circuitry in freely moving mice using commonly available materials. We use these tools to examine mechanosensory processing in the spinal cord and observe that optogenetic activation of somatostatin-positive interneurons facilitates both mechanosensory and itch-related behavior, while reversible chemogenetic inhibition of these neurons suppresses mechanosensation. These results extend recent findings regarding the processing of mechanosensory information in the spinal cord and indicate the potential for activity-induced release of the somatostatin neuropeptide to affect processing of itch. The spinal implant approach we describe here is likely to enable a wide range of studies to elucidate spinal circuits underlying pain, touch, itch, and movement.
Analysis of volatile organic compounds in crumb and crust of different baked and toasted gluten‐free breads by direct PTR‐ToF‐MS and fast‐GC‐PTR‐ToF‐MS (2018)

Abstract Proton transfer reaction (PTR)‐time of fight (ToF)‐mass spectrometry (MS) has been recently employed as a quick, easy, and sensitive alternative to gas chromatography MS for the analysis of volatile compounds in food. In the present work, PTR‐ToF‐MS was applied to the characterization of the volatile profiles of the baked and toasted crumbs and crusts of 5 gluten‐free breads elaborated with quinoa, teff, and rice flours as well as corn and wheat starches and wheat bread as a control samples. Two hundred fifty‐nine peaks ( m / z ) were detected, 86 peaks were tentatively identified, and 56 volatile compounds were selected as important contributors to bread aroma. Fast gas chromatography PTR‐ToF‐MS analyses were performed with 42 standards to identify them in the baked crumbs and crusts, 18 of them being present in all the samples. From the baked samples, it was concluded that quinoa crust was the 1 with higher volatile compound in high abundance, characterized by volatile compounds from fermentation, lipid oxidation, 2‐acetyl‐1‐pyrroline, and diethyl‐pyrazines, while wheat crust was characterized by the highest content in furan derivatives. The toasting time led to crust samples with an increased content in all the volatile compounds: Quinoa crust was now characterized by the highest content in all the pyrazines and furan derivatives, while starches were distinguished by the highest abundance in 2‐acetyl‐1‐pyrroline and diethyl‐pyrazines. Neither the baked crumbs nor the toasted crumbs presented the highest content in none of the volatile compounds. Therefore, it was concluded that quinoa flour can be a suitable alternative for the elaboration of baked and toasted breads due to the high content of pleasant volatile compounds from fermentation, the key volatile in crust 2‐acetyl‐1‐pyrroline (baked sample), as well as pleasant pyrazines and toasted‐like furan derivatives (baked and toasted samples); however, the off‐flavor volatile compounds from lipid oxidation as well as the bitter saponins present in quinoa bread should be taken into account.
Cell-Death-Associated Molecular Patterns As Determinants of Cancer Immunogenicity (2013)

We discuss here how such CDAMP could serve as predictive biomarkers that could discriminate immunogenic from nonimmunogenic anti-cancer compounds, and, in case of deficiency, could be compensated by surrogate products to ameliorate the success rate of conventional anticancer treatment modalities.