gebhart/patrepeval huggingface dataset:
Catalytic Conversion of Cellulosic Biomass or Algal Biomass plus Methane to Drop in Hydrocarbon Fuels and Chemicals (2018)

The goal of this Bioincubator Project was to improve the pyrolysis of biomass through the use of methane. Our initial concept was to use methane as a fluidizing gas with a hydrogen transfer catalyst. The results of the experiments did show that methane as a fluidizing gas, with a hydrogen transfer catalyst, does enhance catalytic pyrolysis over that which is achieved with an inert fluidizing gas. Using methane as a fluidizing gas, with a hydrogen transfer catalyst, consistently produced better products with lower oxygen content than the products produced when an inert gas was used. These improvements were also consistent with the results obtained through pure component testing as well. However, the improvement was too small to justify any significant expense. The addition of hydrogen with a hydrogen transfer catalyst consistently showed a much greater, more significant effect than methane. This indicates that hydropyrolysis is a more effective approach to improved catalytic pyrolysis than methane addition. During the course of this project, another way to significantly increase biogenic liquid yields from pyrolysis through the use of methane was discovered. We discovered a remarkably stable CO2/steam reforming catalyst which directly makes a 2:1 H2/CO synthesis gas from the CO, CO2, methane, ethane and propane product gas from integrated hydropyrolysis and hydroconversion (IH2®). The biogenic synthesis gas can then be converted to liquid hydrocarbons using Fischer Tropsch. The hydrogen for the IH2 unit would then be provided through the use of added methane. By utilizing the biogenic gas to make liquids, 40% more biogenic liquid hydrocarbons can be made from wood, thereby increasing liquid yields from IH2 from 86GPT to 126GPT. It also simplifies the hydrogen plant since no CO or CO2 removal is required.
Performance Improvement of Lithium Metal Batteries Enabled By LiBF3CN as a New Electrolyte Additive (2022)

A newly synthesized electrolyte additive, lithium trifluoro(cyano) borate (LiBF 3 CN), has been investigated for electrochemical performance improvement of lithium metal batteries. The LiBF 3 CN has a structure where one fluorine atom of BF 4 − is substituted with a cyano group (−CN) prepared by the reaction of boron trifluoride etherate with lithium cyanide. The electrochemical performance in symmetric Li/Li cells and NCM523/Li cells is significantly improved upon the incorporation of LiBF 3 CN as an electrolyte additive into a carbonate-based electrolyte. Extensive characterization of the deposited lithium metal reveals that a thin (≈20 nm) and robust SEI composed of LiN x O y , Li 3 N and Li 2 O is formed by the reductive decomposition of the LiBF 3 CN additive, which plays an important role in decreasing the resistance and stabilizing lithium deposition/stripping. The insight into the substitution effect of a functional group obtained from this work provides guidance for the design of new electrolyte additives.
Improving Drug Discovery by Nucleic Acid Delivery in Engineered Human Microlivers (2019)

The liver plays a central role in metabolism; however, xenobiotic metabolism variations between human hepatocytes and those in model organisms create challenges in establishing functional test beds to detect the potential drug toxicity and efficacy of candidate small molecules. In the emerging areas of RNA interference, viral gene therapy, and genome editing, more robust, long-lasting, and predictive human liver models may accelerate progress. Here, we apply a new modality to a previously established, functionally stable, multi-well bioengineered microliver-fabricated from primary human hepatocytes and supportive stromal cells-in order to advance both small molecule and nucleic acid therapeutic pipelines. Specifically, we achieve robust and durable gene silencing in vitro to tune the human metabolism of small molecules, and demonstrate its capacity to query the potential efficacy and/or toxicity of candidate therapeutics. Additionally, we apply this engineered platform to test siRNAs designed to target hepatocytes and impact human liver genetic and infectious diseases.
Determining Persistence of Bocavirus DNA in the Respiratory Tract of Children by Pyrosequencing (2016)

Children with HBoV1 infection commonly shed for a prolonged period leading to repeated viral DNA detection. Recurrence after 8-9 months suggests possible persistence and reactivation. Infections with 2 different HBoV1 subtypes within 1-year period are uncommon. Newly acquired HBoV1-URI is often complicated by AOM.
Paper 157: MIS versus Standard TKR: A Prospective Randomized Double Blinded Study Comparing Postoperative Strength and Functional Recovery (2012)

Advantages of MIS TKR include less postoperative pain and improved early range of motion. However, all studies to date are either retrospective or at best prospective comparisons with matched controls and as such fail to control for patient expectations/placebo effect and in many cases selection bias. The purpose of this study was to determine whether the MIS midvastus approach to TKR resulted in quantitative differences in quadriceps muscle strength as well as the previously cited advantages.
A unified approach for modeling complex occlusions in fluid simulations (2003)

No abstract available.
Multicasting Precoder Design for Vehicular Joint Radar-Communication Systems (2021)

We consider the problem of multicasting a single data stream to multiple vehicles in a vehicular network from a joint radar and communication (JRC) equipped vehicle that simultaneously aims to detect multiple targets and estimate their localization parameters such as ranges, Doppler shifts and angles. Assuming channel state information (CSI) is known at the JRC car, we design a precoder that exploits to maximize multicasting rate while simultaneously maximizing the radar Signal to Clutter plus Noise Ratio (SCNR) at the JRC vehicle.
Comments on ionization potentials of some N-heterocyclic compounds (1972)

(1972). Comments on ionization potentials of some N-heterocyclic compounds. Molecular Physics: Vol. 23, No. 1, pp. 185-186.
Constitutive RelB activation in v‐Src‐transformed fibroblasts: Requirement for IκB degradation (1999)

RelB, an NF-κB/Rel-related transacting factor, was initially identified as an immediate-early gene product in fibroblasts and subsequently shown to exhibit constitutive DNA binding activity in lymphoid cells. The data presented in this report show that RelB is also constitutively active, as monitored by electrophoretic mobility shift assay, in the v-Src-transformed fibroblast cell line, SR1. By contrast, nontransformed parental (3Y1) cells displayed inducible NF-κB activity; RelB activity was also observed, although to a lesser extent, in two additional v-Src-transformed fibroblast lines. RelB activation in SR1 cells did not require an increase in RelB expression or result from a decrease in the levels of IκBα or p105, proteins previously shown to bind to and inhibit the activity of the Rel proteins. Numerous studies have shown that stimulus-dependent Rel activation requires degradation of IκBα, p105 or other member of the IκB family, and that this process is precluded by agents that inhibit proteasome activity. We show that treatment of SR1 cells with proteasome inhibitors abolishes RelB activity and thus suggest that RelB in these cells is associated with IκB and that v-Src transformation activates RelB by accelerating IκB proteolysis. Additional data show that serum and tumor necrosis factor-α (TNF-α) increase RelB protein levels in 3Y1 cells and that this process is blocked by proteasome inhibitors. J. Cell. Biochem. 73:237–247, 1999. © 1999 Wiley-Liss, Inc.
Isolation and Characterization of a Monobody with a Fibronectin Domain III Scaffold That Specifically Binds EphA2 (2015)

Monobodies are binding scaffold proteins originating from a human fibronectin domain III (Fn3) scaffold that can be easily engineered with specificity and affinity. Human EphA2 (hEphA2) is an early detection marker protein for various tumors including lung, breast, and colon cancer. In this study, we isolated two hEphA2-specific monobodies (E1 and E10) by screening a yeast surface display library. They showed the same amino acid sequence except in the DE loop and had high affinity (~2 nM Kd) against hEphA2. E1 bound only hEphA2 and mEphA2, although it bound hEphA2 with an affinity 2-fold higher than that of mEphA2. However, E10 also bound the mEphA6 and mEphA8 homologs as well as hEphA2 and mEphA2. Thus, E1 but not E10 was highly specific for hEphA2. E1 specifically bound human cells and xenograft tumor tissues expressing hEphA on the cell surface. In vivo optical imaging showed strong targeting of Cy5.5-labeled E1 to mouse tumor tissue induced by PC3 cells, a human prostate cancer cell line that expresses a high level of hEphA2. In conclusion, the highly specific monobody E1 is useful as a hEphA2 probe candidate for in vivo diagnosis and therapy.
A Palladium/Chiral Amine Co‐catalyzed Enantioselective Dynamic Cascade Reaction: Synthesis of Polysubstituted Carbocycles with a Quaternary Carbon Stereocenter (2013)

Polysubstituted 5- and 6-membered carbocycles were synthesized by the title reaction. The one-pot dynamic relay process generates four new stereocenters, including a quaternary carbon center, in a highly enantioselective fashion (99.5:0.5→99:0.5 e.r.) by using a simple combination of palladium and chiral amine co-catalysts.
Functional characterization of cannabinoid receptor‐interacting protein CRIP1a (2013)

G‐protein‐coupled CB 1 cannabinoid receptors (CB 1 Rs) are highly expressed in the brain and together with the endocannabinoids, anandamide and 2‐arachidonoylglycerol (2‐AG), modulate appetite, reward, pain, memory and motor activity. Cannabinoid receptor‐interacting protein 1a (CRIP 1a ) is a novel regulatory protein that binds to the C‐terminus of CB 1 Rs but not CB 2 Rs. Studies in cell models in which CRIP 1a was co‐expressed with CB 1 Rs at a molar ratio of 5:1, respectively, showed that CRIP 1a did not alter CB 1 R expression levels but inhibited agonist‐stimulated and constitutive CB 1 R‐mediated G‐protein activation, as determined by [ 35 S]GTPγS binding. Electrophysiological studies in cultured hippocampal neurons showed that CRIP 1a over‐expression attenuated 2‐AG‐mediated inhibition of excitatory synaptic activity. These results suggest that CRIP 1a negatively regulates CB 1 R signaling. To determine effects of loss of CRIP 1a function, we generated Cnrip1 genetic null mice. Cnrip1 null mice are viable and do not express CRIP 1a protein in the brain or spinal cord, thus providing a valuable tool to assess CRIP 1a function in vivo. Supported by R21‐ DA025321 and R01‐DA030404 from NIDA and an A.D. Williams Multischool Award.
Progress towards picometer accuracy laser metrology for the space interferometry mission (2017)

The Space Interferometry Mission, scheduled for launch in 2008, is an optical stellar interferometer with a 10 meter baseline capable of micro-arcsecond accuracy astrometry. A mission-enabling technology development program is underway at JPL, including the design and test of heterodyne interferometer metrology gauges to monitor the separation of optical components of the stellar interferometer. The gauges are required to have a resolution of 15 picometers and to track the motion of mirrors over several meters. We report laboratory progress in meeting these goals.
Group IVA Oxide Surface Modification of LSCF Cathode Powders by Atomic Layer Deposition (2017)

(La0.6Sr0.4)0.95Co0.2Fe0.8O3-δ (LSCF) powder has been modified by atomic layer deposition (ALD) with Group IVA based oxides, including zirconia, hafnia, and cobalt doped compositions. Amide zirconium and hafnium and amidinate cobalt precursors were used in an ALD process to treat 0.3 mm nominal diameter LSCF powder at 240°C using water as a co-reactant. The effect of the number of ALD cycles and level of Co additions have been examined up to 15% Co. The morphology and physical properties of sintered samples were similar to untreated powders with a modest shift to lower porosity and pore volume, but well within the desired range of microstructural properties. Depending on the recipe, initial polarization of cathodes in symmetrical electrochemical cells varied slightly compared to uncoated powders. Degradation of cathodes made from treated powders was improved compared to cathodes made from untreated powders.
Supplemental Figure S3 from Loss of <i>ARID1A</i> Activates <i>ANXA1</i>, which Serves as a Predictive Biomarker for Trastuzumab Resistance (2023)

&lt;p&gt;Supplemental Figure S3: ARID1A loss correlates with ANXA1 expression in endometrial cancer&lt;/p&gt;
Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces (2020)

A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 °C) cellulose disruption occurs only above 150 °C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (R<sub>g</sub> ∼ 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent water-rich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.
Specific Inhibitors of Protein Synthesis Do Not Block RNA Synthesis or Settlement in Larvae of a Marine Gastropod Mollusk (Haliotis rufescens) (1993)

Antibiotic inhibitors of protein synthesis were tested for their effectiveness in larvae of the red abalone, Haliotis rufescens (gastropod mollusk). Emetine and anisomycin proved highly effective in this system, while cycloheximide, fusidic acid, puromycin, and tetracycline were less effective. Emetine and anisomycin specifically inhibited protein synthesis but not RNA synthesis. The contribution to protein synthesis by chloramphenicolsensitive prokaryotic contaminants was found to be undetectable, except following the onset of symptoms of toxicity resulting from prolonged exposure to emetine or anisomycin. The induction of larval settlement and plantigrade attachment by γ-aminobutyric acid (GABA), a functional analog of the natural inducer of settlement, occurred even under conditions in which most protein synthesis was inhibited, as expected for a chemosensory system response, whereas subsequent developmental metamorphosis was completely blocked. Because emetine and anisomycin block protein synthesis--including the synthesis of new transcription factors--but do not block early transcription, treatment of marine invertebrate embryos and larvae with these inhibitors can be used to obtain a selective enrichment in the mRNA population of "early gene" transcripts induced directly by GABA and other morphogenetic signals, without dilution by new mRNAs, the appearance of which is dependent on the synthesis of new protein transcription factors.
Fluid balance as a biomarker: impact of fluid overload on outcome in critically ill patients with acute kidney injury (2008)

Fluid therapy is fundamental to the acute resuscitation of critically ill patients. In general, however, early and appropriate goal-directed fluid therapy contributes to a degree of fluid overload in most if not all patients. Recent data imply that a threshold may exist beyond which, after acute resuscitation, additional fluid therapy may cause harm. In patients with acute kidney injury and/or oliguria, a positive fluid balance is almost universal. Few studies have examined the impact of fluid balance on clinical outcomes in critically ill adults with acute kidney injury. Payen and coworkers, in a secondary analysis of the SOAP (Sepsis Occurrence in Acutely Ill Patients) study, now present evidence that there is an independent association between mortality and positive fluid balance in a cohort of critically ill patients with acute kidney injury. In this commentary, we discuss these findings within the context of prior literature and propose that assessment of fluid balance should be considered as a potentially valuable biomarker of critical illness.
Synthesis and Biological Evaluation of Derivatives of Indoline as Highly Potent Antioxidant and Anti-inflammatory Agents (2018)

We describe the preparation and evaluation of novel indoline derivatives with potent antioxidant and anti-inflammatory activities for the treatment of pathological conditions associated with chronic inflammation. The indolines are substituted at position 1 with chains carrying amino, ester, amide, or alcohol groups, and some have additional substituents, Cl, MeO, Me, F, HO, or BnO, on the benzo ring. Concentrations of 1 pM to 1 nM of several compounds protected RAW264.7 macrophages against H<sub>2</sub>O<sub>2</sub> induced cytotoxicity and LPS induced elevation of NO, TNF-α, and IL-6. Several derivatives had anti-inflammatory activity at 1/100th of the concentration of unsubstituted indoline. Four compounds with ester, amine, amide, or alcohol side chains injected subcutaneously in mice at a dose of 1 μmol/kg or less, like dexamethasone (5.6 μmol/kg) prevented LPS-induced cytokine elevation in the brain and peripheral tissues. Subcutaneous injection of 100 μmol/kg of these compounds caused no noticeable adverse effects in mice during 3 days of observation.
Prostate cancer multiparametric magnetic resonance imaging visibility is a tumor-intrinsic phenomena (2022)

Multiparametric magnetic resonance imaging (mpMRI) is an emerging standard for diagnosing and prognosing prostate cancer, but ~ 20% of clinically significant tumors are invisible to mpMRI, as defined by the Prostate Imaging Reporting and Data System version 2 (PI-RADSv2) score of one or two. To understand the biological underpinnings of tumor visibility on mpMRI, we examined the proteomes of forty clinically significant tumors (i.e., International Society of Urological Pathology (ISUP) Grade Group 2)-twenty mpMRI-visible and twenty mpMRI-invisible, with matched histologically normal prostate. Normal prostate tissue was indistinguishable between patients with visible and invisible tumors, and invisible tumors closely resembled the normal prostate. These data indicate that mpMRI-visibility arises when tumor evolution leads to large-magnitude proteomic divergences from histologically normal prostate.
Quality Estimation & Interpretability for Code Translation. (2020)

Recently, the automated translation of source code from one programming language to another by using automatic approaches inspired by Neural Machine Translation (NMT) methods for natural languages has come under study. However, such approaches suffer from the same problem as previous NMT approaches on natural languages, viz. the lack of an ability to estimate and evaluate the quality of the translations; and consequently ascribe some measure of interpretability to the model's choices. In this paper, we attempt to estimate the quality of source code translations built on top of the TransCoder model. We consider the code translation task as an analog of machine translation (MT) for natural languages, with some added caveats. We present our main motivation from a user study built around code translation; and present a technique that correlates the confidences generated by that model to lint errors in the translated code. We conclude with some observations on these correlations, and some ideas for future work.
Educational Question Mining At Scale: Prediction, Analysis and Personalization (2021)

Online education platforms enable teachers to share a large number of educational resources such as questions to form exercises and quizzes for students. With large volumes of available questions, it is important to have an automated way to quantify their properties and intelligently select them for students, enabling effective and personalized learning experiences. In this work, we propose a framework for mining insights from educational questions at scale. We utilize the state-of-the-art Bayesian deep learning method, in particular partial variational auto-encoders (p-VAE), to analyze real students' answers to a large collection of questions. Based on p-VAE, we propose two novel metrics that quantify question quality and difficulty, respectively, and a personalized strategy to adaptively select questions for students. We apply our proposed framework to a real-world dataset with tens of thousands of questions and tens of millions of answers from an online education platform. Our framework not only demonstrates promising results in terms of statistical metrics but also obtains highly consistent results with domain experts' evaluation.
Preface (2007)

Dendritic cells (DCs) comprise a family of professional antigen presenting cells that are unique in their ability to activate T lymphocytes. Dendritic cells patrol all the tissues at the interface with the external world, including skin and mucosal surfaces, for the presence of invaders. The DC system is characterized by a remarkable plasticity that allows the induction both of immunity and tolerance toward the encountered antigens. This is achieved through the combination of a number of different factors, including the subsets of DCs, their activation state and environmental cells that can regulate DC function. DCs are present in the periphery in an immature form that is particularly apt at capturing antigens and at deciphering the messages associated therein. After an activation stimulus that is delivered by some antigens (including bacteria) or by inflammatory cytokines released during inflammation, activated DCs acquire a migratory phenotype and reach the draining lymph node. Here, DCs present the antigens captured in the periphery and initiate T cell adaptive immune responses.
Molecular basis for dengue virus broad cross-neutralization by humanized monoclonal antibody 513 (2018)

Dengue is a widespread viral disease with 3.6 billion people at risk worldwide. Humanized monoclonal antibody (mAb) 513, currently undergoing clinical trials in Singapore, targets an epitope on the envelope protein domain III exposed at the surface of the viral particle. This antibody potently neutralizes all four dengue virus serotypes in a humanized mouse model that recapitulates human dengue infection, without signs of antibody-mediated enhancement of the disease. The crystal structure of single-chain variable fragment (scFv) 513 bound to the envelope protein domain III from dengue virus serotype 4 was used as a template to explore the molecular origins of the broader cross-reactivity and increased in vivo potency of mAb 513, compared to the parent murine mAb 4E11, using molecular dynamics simulations and network analyses. These two methods are a powerful complement to existing structural and binding data and detail specific interactions that underpin the differential binding of the two antibodies. We found that a Glu at position H55 (GluH55) from the second Complementarity Determining Region of the Heavy chain (CDR-H2) which corresponds to Ala in 4E11, is a major contributor to the enhancement in the interactions of mAb 513 compared to 4E11. Importantly, we also validate the importance of GluH55using site-directed mutagenesis followed by isothermal titration calorimetry measurements.