gebhart/patrepeval huggingface dataset:
A multi-component spatially-distributed model of two-phase flow for estimation and control of fuel cell water dynamics (2007)

The critical task of controlling the water distribution within the gas diffusion layer of a fuel cell suggests a partial differential equation (PDE) approach. Starting from first principles, the model of a fuel cell is represented as a boundary value problem for a set of three coupled, nonlinear, second-order PDEs. These three PDEs are approximated, with justification rooted in linear systems theory and a time-scale decomposition approach, by a single nonlinear PDE. A hybrid set of numerical transient, analytic transient, and analytic steady-state solutions for both the original and single PDE- based model are presented, and a more accurate estimate of the liquid water distribution is obtained using the single PDE-based model. The single PDE derived represents our main contribution on which future development of control, estimation, and diagnostics algorithms can be based.
Microbial Reduction of Metal-Organic Frameworks Enables Synergistic Chromium Removal (2018)

Abstract Microbe-material redox interactions underpin many emerging technologies, including bioelectrochemical cells and bioremediation. However, commonly utilized material substrates, such as metal oxides, suffer from a lack of tunability and can be challenging to characterize. In contrast, metal-organic frameworks, a class of porous materials, exhibit well-defined structures, high crystallinity, large surface areas, and extensive chemical tunability. Here, we report that metal-organic frameworks can support the growth of the electroactive bacterium Shewanella oneidensis. Specifically, we demonstrate that Fe(III)-containing frameworks, MIL-100 and Fe-BTC, can be reduced by the bacterium via its extracellular electron transfer pathways and that reduction rate/extent is tied to framework structure, surface area, and particle morphology. In a practical application, we show that cultures containing S. oneidensis and reduced frameworks can remediate lethal concentrations of Cr(VI), and that pollutant removal exceeds the performance of either component in isolation or bioreduced iron oxides. Repeated cycles of Cr(VI) dosing had little effect on bacterial viability or Cr(VI) adsorption capacity, demonstrating that the framework confers protection to the bacteria and that no regenerative step is needed for continued bioremediation. In sum, our results show that metal-organic frameworks can serve as microbial respiratory substrates and suggest that they may offer a promising alternative to metal oxides in applications seeking to combine the advantages of bacterial metabolism and synthetic materials.
The Gadolinium(III)−Water Hydrogen Distance in MRI Contrast Agents (2003)

The ion-nuclear distance of Gd(III) to a coordinated water proton, r(Gd)(-)(H), is central to the understanding of the efficacy of gadolinium-based MRI contrast agents. The dipolar relaxation mechanism operative for contrast agents has a 1/r(6) dependence. Estimates in the literature for this distance span 0.8 A (2.5-3.3 A). This study describes a direct determination of r(Gd)(-)(H) using the anisotropic hyperfine constant T( perpendicular ) determined from pulsed ENDOR spectra. Five Gd(III) complexes were examined: [Gd(H(2)O)(8)](3+), [Gd(DTPA)(H(2)O)](2)(-), [Gd(BOPTA)(H(2)O)](2)(-), MS-325, and [Gd(HP-DO3A)(H(2)O)]. The distance, r(Gd)(-)(H), was the same within error for all five complexes: 3.1 +/- 0.1 A. These distance estimates should aid in the design of new contrast agents, and in the interpretation of other molecular factors influencing relaxivity.
Faculty Opinions recommendation of In cis inhibition of antigen processing by the latency-associated nuclear antigen I of Kaposi sarcoma herpes virus. (2006)

Kaposi sarcoma Herpes virus (KSHV), also known as human Herpes virus 8 (HHV8), can persist as episome in target cells. The latency-associated nuclear antigen 1 (LANA-1) is a key component of the latency process, and may be a functional equivalent of the EBNA-1 protein of Epstein-Barr virus. EBNA-1 can subdue immune recognition by virtue of a long glycine and alanine-rich repeat, which interferes with the proteasomal degradation of EBNA-1 and in this way averts the presentation of antigenic peptides derived from it. LANA-1 contains a strongly acidic-repeat region of approximately 580 amino acids, which consists almost exclusively of aspartic acid, glutamine, and glutamic acid residues. The LANA-1 repeat is not similar to the EBNA-1 Gly-Ala-rich repeat. We demonstrate that this acidic region could inhibit antigen processing in cis. Upon transfection of expression vectors containing LANA-1-eGFP fusion genes the cells did not present an ovalbumin-derived H2K(b)-restricted CTL epitope inserted at the carboxyl terminus of the GFP reporter. Deletion of the central acidic-repeat region of LANA-1 abolished the capacity of LANA-1 to block antigen presentation. Similar to the EBNA-1-derived Gly-Ala-rich repeat, the LANA-1 repeat does not inhibit presentation in trans: co-transfection of LANA-1 expression vectors does not inhibit presentation of the ova epitope from the GFP(Ova) fusion protein. These data demonstrate for the first time that the acidic-repeat region of LANA-1 could function as an in cis acting inhibitor of antigen presentation. This may contribute to the immune evasion of cells latently infected by KSHV. PMID: 16828498
An intrusion detection system for wireless process control systems (2008)

A recent trend in the process control system (PCS) is to deploy sensor networks in hard-to-reach areas. Using wireless sensors greatly decreases the wiring costs and increases the volume of data gathered for plant monitoring. However, ensuring the security of the deployed sensor network, which is part of the overall security of PCS, is of crucial importance. In this paper, we design a model-based intrusion detection system (IDS) for sensor networks used for PCS. Given that PCS tends to have regular traffic patterns and a well-defined request-response communication, we can design an IDS that models normal behavior of the entities and detects attacks when there is a deviation from this model. Model-based IDS can prove useful in detecting unknown attacks.
Evolution of curvature and anisotropy near a nonsingular bounce (2011)

We consider bouncing cosmologies in which an ekpyrotic contraction phase with $w\ensuremath{\gg}1$ is followed by a bouncing phase with $w&lt;\ensuremath{-}1$ that violates the null energy condition. The bouncing phase, induced by ghost condensation, is designed to produce a classically nonsingular bounce at a finite value of the scale factor. We show that the initial curvature and anisotropy, though diluted during the ekpyrotic phase, grow back exponentially during the bouncing phase. Moreover, curvature perturbations and anisotropy are generated by quantum fluctuations during the ekpyrotic phase. In the bouncing phase, however, an adiabatic curvature perturbation grows to dominate and contributes a blue spectrum that spoils the scale invariance. Meanwhile, a scalar shear perturbation grows nonlinear and creates an overwhelming anisotropy that disrupts the nonsingular bounce altogether.
Isolation and Properties of an Angiotensin II-Cleaving Peptidase from Mesquite Pollen (1995)

Biochemical studies of pollen proteins have been focused, primarily, in investigating their roles as allergens. These molecules, some of which have enzymatic activity, act as antigens and initiate the production of IgE antibodies, leading to allergic and/or asthmatic responses. Included in this mixture of proteins are proteinases which, although they may or may not be allergenic, could still be involved in airway dysfunction. We have isolated an arginine-specific endopeptidase to homogeneity from mesquite (Prosopis velutina) pollen, a known wind-borne allergen, which has a molecular mass near 84 kDa by NaDodSO4-gel electrophoresis, a pH optimum in the neutral to alkaline range, and a requirement for Ca2+ for stabilization. The enzyme is inhibited by diisopropyl fluorophosphate (DFP) and N-p-tosyl-L-lysine chloromethylketone but not by N-p-tosyl-L-phenylalanine chloromethylketone, EDTA, or iodoacetamide. It was also not inhibited by human plasma proteinase inhibitors nor several other naturally occurring plant and animal inhibitors. Cleavage by the endopeptidase was primarily on the carboxy-terminal side of arginine residues in peptides, whereas proteins such as kallikrein and prothrombin were only activated and/or degraded extremely slowly. Several bioactive peptides that may be involved in maintaining normal lung function were readily fragmented, including angiotensin II, a vasoconstrictor, and atrial natriuretic peptide, a modulator of vascular permeability, both of which were rapidly cleaved at low enzyme:substrate molar ratios. Thus, the pollen endopeptidase could be involved in exacerbating the development of asthma by inactivating bioactive peptides that have ameliorating effects in maintaining lung airway homeostasis.
CD45 cross-linking regulates phospholipase C activation and tyrosine phosphorylation of specific substrates in CD3/Ti-stimulated T cells (1991)

In lymphocytes, CD45 regulates the increase in cytoplasmic calcium concentration that occurs after receptor cross-linking. Here we show that T cell receptor complex (CD3/Ti)-mediated inositol phosphate production was inhibited by CD45 ligation in Jurkat cells. CD3/Ti signaling in normal T cells was also inhibited by CD45 ligation, but coupling of CD4 with CD3/Ti gave augmented calcium signals that were entirely resistant to the inhibitory effect of CD45. In contrast, CD3-induced T cell proliferation was suppressed by immobilized CD45 mAb even in the presence of CD4 mAb. The effect of CD45 and CD4 ligation on tyrosine phosphorylation during T cell activation was directly examined by immunoblotting with anti-phosphotyrosine. Using immobilized mAb, CD45 ligation suppressed the tyrosine phosphorylation of specific substrates induced by CD3/Ti stimulation, including almost complete suppression of 150-, 36-, and 35-kDa proteins and partial suppression of 76- and 80-kDa proteins. Other tyrosine-phosphorylated proteins induced by CD3/Ti stimulation, including 135- and 21-kDa proteins, were not suppressed by simultaneous ligation of CD3/Ti and CD45. Simultaneous ligation of CD3 and CD4 enhanced tyrosine phosphorylation of all substrates, but did not overcome the CD45-mediated suppression of tyrosine phosphorylation of the 35- and 36-kDa proteins. The CD45-mediated suppression of phospholipase C activation is therefore modulated by association with CD4 without altering the specific inhibition of tyrosine phosphorylation and T cell proliferation after co-ligation of CD45 and CD3/Ti.
A serum proteomic study of two case-control cohorts identifies novel biomarkers for bipolar disorder (2022)

We set out to identify novel protein associations with potential as clinically viable biomarkers for bipolar disorder. To this end, we used proximity extension assay to analyze 201 unique proteins in blood serum from two independent cohorts comprising patients with bipolar disorder and healthy controls (total n = 493). We identified 32 proteins significantly associated with bipolar disorder in both case-control cohorts after adjusting for relevant covariates. Twenty-two findings are novel to bipolar disorder, but 10 proteins have previously been associated with bipolar disorder: chitinase-3-like protein 1, C-C motif chemokine 3 (CCL3), CCL4, CCL20, CCL25, interleukin 10, growth/differentiation factor-15, matrilysin (MMP-7), pro-adrenomedullin, and TNF-R1. Next, we estimated the variance in serum protein concentrations explained by psychiatric drugs and found that some case-control associations may have been driven by psychiatric drugs. The highest variance explained was observed between lithium use and MMP-7, and in post-hoc analyses and found that the serum concentration of MMP-7 was positively associated with serum lithium concentration, duration of lithium therapy, and inversely associated with estimated glomerular filtration rate in an interaction with lithium. This is noteworthy given that MMP-7 has been suggested as a mediator of renal tubulointerstitial fibrosis, which is characteristic of lithium-induced nephropathy. Finally, we used machine learning to evaluate the classification performance of the studied biomarkers but the average performance in unseen data was fair to moderate (area under the receiver operating curve = 0.72). Taken together, our serum biomarker findings provide novel insight to the etiopathology of bipolar disorder, and we present a suggestive biomarker for lithium-induced nephropathy.
Target TMPRSS6 for the Treatment of Hereditary Hemochromatosis (2011)

Abstract Abstract 1047 Hereditary hemochromatosis (HH) is a genetic disorder in which hyperabsorption of dietary iron leads to accumulation of iron in multiple tissues including liver and heart. A common clinical manifestation in HH patients is cirrhosis and hepatocellular carcinoma as a result of iron-mediated injury in liver. The most prevalent genetic defect for HH is the failure to up-regulate hepcidin, a peptide hormone that inhibits the absorption of iron in duodenum and the release of iron from intracellular iron storage such as macrophages. Mutations in a number of genes have been identified as the cause for HH, including hepcidin itself. However, the most common mutation is C282Y mutation in HFE, which is a positive regulator for hepcidin expression. C282Y mutation represents about 85% of the HH population. HFE C282Y HH is an autosomal recessive disease with a ∼50% penetrance. Currently, the only treatment available for iron overload is phlebotomy which will continue throughout the patient's life. Hepcidin is mainly expressed and secreted by the liver and its expression is regulated predominantly at the transcription level. TMPRSS6, a transmembrane serine protease mutated in iron-refractory, iron-deficient anemia, is a major suppressor for hepcidin expression. It's been demonstrated that hepcidin expression is significantly elevated in Tmprss6−/− mice and reduction of TMPRSS6 in Hfe−/− mice could ameliorate the iron overload phenotype (Du et al. Science 2008; Folgueras et al. Blood 2008; Finberg KE et al., Blood, 2011). Using second generation antisense technology, we identified antisense oligonucleotides (ASOs) targeting mouse TMPRSS6 for the treatment of HH. These compounds were first identified through in vitro screens in mouse primary hepatocytes. After 4 weeks of treatment in C57BL/6 mice on normal chow, we observed an 80% to 90% reduction of liver TMPRSS6 mRNA with a subsequent 2–3 fold induction of liver hepcidin mRNA. Serum iron and transferrin saturation levels were reduced by ∼50%. These ASOs are currently being evaluated in a diet-induced iron overload model and an Hfe−/− iron overload model. Our preliminary results demonstrate that targeting TMPRSS6 is a viable approach for the treatment of hereditary hemochromatosis and possibly other iron-loading diseases associated with suppressed hepcidin levels. Disclosures: Booten: Isis Pharmaceuticals: Employment. Knox:Isis Pharmaceuticals: Summer Intern. Alvarado:Isis Pharmaceuticals: Employment. Guo:Isis Pharmaceuticals: Employment. Monia:Isis Pharmaceuticals: Employment.
Modular Synthesis of Cyclopropane‐Fused N‐Heterocycles Enabled by Underexplored Diazo Reagents (2022)

Abstract Cyclopropane‐fused N ‐heterocycles are featured in various biologically active compounds and represent attractive scaffolds in medicinal chemistry. However, synthesis routes to access structurally and functionally diverse cyclopropane‐fused N ‐heterocycles remain underexplored. Leveraging novel α‐diazo acylating agents, we report a general approach for the direct and modular synthesis of cyclopropane‐fused lactams from unsaturated amines. The operationally simple transformation, which proceeds through successive acylation, (3+2) cycloaddition and fragmentation, tolerates a broad range of functional groups and yields a wide spectrum of complex molecular scaffolds, including fused, bridged and spiro ring systems. We demonstrate the utility of this transformation in the concise syntheses of therapeutic agents milnaciprane and amitifadine.
CSI-Based Localization with CNNs Exploiting Phase Information (2021)

In this paper we study the use of the Channel State Information (CSI) as fingerprint inputs of a Convolutional Neural Network (CNN) for localization. We examine whether the CSI can be used as a distinct fingerprint corresponding to a single position by considering the inconsistencies with its raw phase that cause the CSI to be unreliable. We propose two methods to produce reliable fingerprints including the phase information. Furthermore, we examine the structure of the CNN and more specifically the impact of pooling on the positioning performance, and show that pooling over the subcarriers can be more beneficial than over the antennas.
Pancreatic Pseudocyst Rupture into the Renal Collecting System (1989)

Pseudocyst formation is a well-recognized complication of pancreatitis. Involvement of a pseudocyst with the kidney is rare. We report an unusual case of a pancreatic pseudocyst with rupture into the renal collecting system. The surgical management of this problem is described and the world-wide experience is reviewed briefly.
Quantitative assessment of the central versus peripheral effect of intravenous clonidine using baroreflex equilibrium diagrams (2021)

Clonidine is a first-generation central antihypertensive that reduces sympathetic nerve activity (SNA). Although clonidine also exerts peripheral vasoconstriction, the extent to which this vasoconstriction offsets the centrally mediated arterial pressure (AP)-lowering effect remains unknown. In anesthetized rats (n = 8), we examined SNA and AP responses to stepwise changes in carotid sinus pressure under control conditions and after intravenous low-dose (2 μg/kg) and high-dose clonidine (5 μg/kg). In the baroreflex equilibrium diagram analysis, the operating-point AP under the control condition was 115.2 (108.5-127.7) mmHg [median (25th-75th percentile range)]. While the operating-point AP after low-dose clonidine was not significantly different with or without the peripheral effect, the operating-point AP after high-dose clonidine was higher with the peripheral effect than without [81.3 (76.2-98.2) mmHg vs. 70.7 (57.7-96.9), P < 0.05]. The vasoconstrictive effect of clonidine partly offset the centrally mediated AP-lowering effect after high-dose administration.
Optical Control of Phosphoinositide Binding: Rapid Activation of Subcellular Protein Translocation and Cell Signaling (2021)

Cells utilize protein translocation to specific compartments for spatial and temporal regulation of protein activity, in particular in the context of signaling processes. Protein recognition and binding to various subcellular membranes is mediated by a network of phosphatidylinositol phosphate (PIP) species bearing one or multiple phosphate moieties on the polar inositol head. Here, we report a new, highly efficient method for optical control of protein localization through the site-specific incorporation of a photocaged amino acid for steric and electrostatic disruption of inositol phosphate recognition and binding. We demonstrate general applicability of the approach by photocaging two unrelated proteins, sorting nexin 3 (SNX3) and the pleckstrin homology (PH) domain of phospholipase C delta 1 (PLCδ1), with two distinct PIP binding domains and distinct subcellular localizations. We have established the applicability of this methodology through its application to Son of Sevenless 2 (SOS2), a signaling protein involved in the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) cascade. Upon fusing the photocaged plasma membrane-targeted construct PH-enhanced green fluorescent protein (EGFP), to the catalytic domain of SOS2, we demonstrated light-induced membrane localization of the construct resulting in fast and extensive activation of the ERK signaling pathway in NIH 3T3 cells. This approach can be readily extended to other proteins, with minimal protein engineering, and provides a method for acute optical control of protein translocation with rapid and complete activation.
UV Irradiation of Polycyclic Aromatic Hydrocarbons in Ices: Production of Alcohols, Quinones, and Ethers (1999)

Polycyclic aromatic hydrocarbons (PAHs) in water ice were exposed to ultraviolet (UV) radiation under astrophysical conditions, and the products were analyzed by infrared spectroscopy and mass spectrometry. Peripheral carbon atoms were oxidized, producing aromatic alcohols, ketones, and ethers, and reduced, producing partially hydrogenated aromatic hydrocarbons, molecules that account for the interstellar 3.4-micrometer emission feature. These classes of compounds are all present in carbonaceous meteorites. Hydrogen and deuterium atoms exchange readily between the PAHs and the ice, which may explain the deuterium enrichments found in certain meteoritic molecules. This work has important implications for extraterrestrial organics in biogenesis.
Flow control of thermotropic lipid monolayers (2011)

There is an increasing interest in using liquid crystalline media as mobile phases in two-dimensional nanofluidic systems. Their small-scale, reduced dimensionality, and plentiful opportunities for functionalisation render such phases advantageous. However, flow control has been difficult to achieve, as the wetting processes which drive area expansion are not dynamically controllable. Here, we report on temperature-controlled monolayer spreading of 1,2-dielaidoyl-sn-glycero-3-phosphoethanolamine (DEPE) on the hydrophobic substrates SU-8, and Teflon AF (amorphous fluoropolymer). The gel/liquid phase transition of DEPE at Tc ∼ 38 °C is exploited to toggle spreading of a molecular lipid film on SU-8. We observed that on Teflon AF, DEPE monolayer spreading occurs even below Tc, and exhibits strongly accelerated spreading above the phase transition temperature. Our results demonstrate that switching DEPE monolayer spreading on and off, or, alternatively, switching between fast and slow area expansion, is a feasible approach towards establishing control over lipid film flow in two-dimensional fluidic systems. We also present a chip-based device integrating a patterned surface for 2D-microfluidics and on-chip heating.
A Real-Time Range Indicator for EVs Using Web-Based Environmental Data and Sensorless Estimation of Regenerative Braking Power (2018)

Most of the commercially available range indicator systems for electric vehicles (EVs) do not provide a sufficiently accurate range to destination, as the environmental factors and driver's behavior are generally not taken into account. In this paper, a real-time range indicator system is developed and implemented using online environmental data from various internet resources to estimate accurately the real-time state of charge and the remaining range for the EV while it is on the road. The estimation considers 1) the dynamic wind speed and wind direction with respect to vehicle position, 2) the probability of rain and ambient temperature, 3) the dynamic effective rolling resistance and terrain adhesion coefficient (based on the condition of the road surface), 4) the time-domain efficiency analysis of the propulsion system, 5) the online traffic conditions and auxiliary loads, and 6) the braking force distribution used in commercially available EVs. The real-time range indicator system is validated using measured data from a 2012 Nissan Leaf driven along a selected route in Australia with the maximum error of 8% for the entire route and less than 1% error at the destination.