gebhart/patrepeval huggingface dataset:
The involvement of cellular ATP in receptor-mediated internalization of epidermal growth factor and hormone-induced internalization of beta-adrenergic receptors. (1986)

Beta-Adrenergic receptors and epidermal growth factor receptors are both expressed on the cell surface of human astrocytoma cells. Incubation with a catecholamine or epidermal growth factor results in rapid internalization of the respective receptor. The internalized receptors co-migrate in light fractions on sucrose gradients. Astrocytoma cells maintain a constant ATP concentration by either glycolytic or mitochondrial ATP production. When cells are incubated in a medium depleted of substrates for glycolysis and gluconeogenesis, addition of inhibitors of mitochondrial ATP synthesis causes a rapid reduction in cellular ATP content. An immediate return to control ATP levels occurs upon addition of an appropriate nutrient, such as glucose. Decreasing the cellular ATP content to less than 10% of control markedly inhibits internalization of beta-adrenergic receptors and epidermal growth factor. The inhibition of endocytosis is reversed as soon as the intracellular ATP content is restored. Previous work by others (Clarke, B.L., and Weigel, P.H. (1985) J. Biol. Chem. 260, 128-133) suggested that ATP is not required for internalization (per se) of asialoglycoprotein in hepatocytes but was required for recycling of the asialoglycoprotein receptor. In contrast, our results indicate that in astrocytoma cells the process of internalization of epidermal growth factor and beta-adrenergic receptors, per se, is highly ATP dependent.
Supplementary Figure 1 from BAG3 Regulates Motility and Adhesion of Epithelial Cancer Cells (2023)

Supplementary Figure 1 from BAG3 Regulates Motility and Adhesion of Epithelial Cancer Cells
Inversion without Explicit Jacobian Calculations in Electrical Impedance Tomography (2014)

Electrical impedance tomography (EIT) is the inverse problem of finding the internal conductivity distribution of a medium given boundary electrical measurements performed via an electrode array onto its surface. Conventional inversion schemes adopt Tikhonov regularized Newton-type methods. Following a transport back-transport approach, we develop in this work an adjoint approach which allows reducing computational burden in enabling inversion without explicit Jacobian calculation. Forward and back-projection operators are defined from potential gradients, along with their efficient implementation. These derivations allow the transparent use of inversion algorithms. We first check the implementation of operators. We then evaluate how reconstructions perform on simulated noisy data using a preconditioned conjugate gradient. We eventually practice our inversion framework on experimental data acquired in vitro from a saline phantom.
Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58 (1996)

The structure of bovine pancreatic trypsin inhibitor has been refined to a resolution of 1.1 A against data collected at 125 K. The space group of the form II crystal is P2(1)2(1)2(1) with a = 75.39(3), b = 22.581(7), c = 28.606 (9) A (cf. a = 74.1, b = 23.4, c = 28.9 A at room temperature). The structure was refined by restrained least-squares minimization of summation operator w(F (o)(2)- F (c)(2))(2) with the SHELXL93 program. As the model improved, water molecules were included and exceptionally clear electron density was found for two residues, Gly57 and Ala58, that had been largely obscured at room temperature. The side chains of residues Glu7 and Arg53 were modelled over two positions with refined occupancy factors. The final model contains 145.6 water molecules distributed over 167 sites, and a single phosphate group disordered over two sites. The root-mean-square discrepancy between Calpha atoms in residues Arg1-Gly56 at room and low temperatures is 0.4 A. A comparison of models refined with anisotropic and isotropic thermal parameters revealed that there were no significant differences in atomic positions. The final weighted R-factor on F(2) (wR(2)) for data in the range 10-1.1 A was 35.9% for the anisotropic model and 40.9% for the isotropic model. Conventional R-factors based on F for F > 4sigma(F) were 12.2 and 14.6%, respectively, corresponding to 16.1 and 18.7% on all data. These large R-factor differences were not reflected in values of R(free), which were not significantly different at 21.5(5) and 21.8(4)%, respectively. These results, along with the relatively straightforward nature of the refinement, clearly highlight the benefits of low-temperature data collection.
High-Throughput Information and In Vitro Assays for T-Cell Epitope Determination: Application to the Design of Epitope-Driven Vaccines (2004)

Induction of epitope-specific T-cell responses may provide an effective means of protecting against diseases for which no conventional vaccines exist. Unlike B cells, which only recognize epitopes directly on the surface of free antigens, T lymphocytes recognize peptide fragments bound to class I or class II molecules encoded by the major histocompatibility complex (MHC). A peptide that binds MHC and is recognized by the T-cell receptor (TCR) constitutes a T-cell epitope. In humans, MHC class I molecules include HLA-A, HLA-B, and HLA-C. The MHC class II molecules include HLA-DR, HLA-DP, and HLA-DQ.
Desloratadine prevents compound 48/80‐induced mast cell degranulation: visualization using a vital fluorescent dye technique (2004)

Desloratadine may have a mast cell stabilizing effect at low concentrations in response to repeated mast cell activation in vitro.
Explainable AI for Trees: From Local Explanations to Global Understanding (2019)

Tree-based machine learning models such as random forests, decision trees, and gradient boosted trees are the most popular non-linear predictive models used in practice today, yet comparatively little attention has been paid to explaining their predictions. Here we significantly improve the interpretability of tree-based models through three main contributions: 1) The first polynomial time algorithm to compute optimal explanations based on game theory. 2) A new type of explanation that directly measures local feature interaction effects. 3) A new set of tools for understanding global model structure based on combining many local explanations of each prediction. We apply these tools to three medical machine learning problems and show how combining many high-quality local explanations allows us to represent global structure while retaining local faithfulness to the original model. These tools enable us to i) identify high magnitude but low frequency non-linear mortality risk factors in the general US population, ii) highlight distinct population sub-groups with shared risk characteristics, iii) identify non-linear interaction effects among risk factors for chronic kidney disease, and iv) monitor a machine learning model deployed in a hospital by identifying which features are degrading the model's performance over time. Given the popularity of tree-based machine learning models, these improvements to their interpretability have implications across a broad set of domains.
Generalized Bloch model: A theory for pulsed magnetization transfer (2021)

The proposed theory unifies the original Bloch model, Henkelman's steady-state theory for MT, and the commonly assumed rotation induced by hard pulses (i.e., strong and infinitesimally short applications of RF-fields) and describes experimental data better than previous models.
Antistaphylococcal Nanocomposite Films Based on Enzyme−Nanotube Conjugates (2010)

Infection with antibiotic-resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) is one of the primary causes of hospitalizations and deaths. To address this issue, we have designed antimicrobial coatings incorporating carbon nanotube-enzyme conjugates that are highly effective against antibiotic-resistant pathogens. Specifically, we incorporated conjugates of carbon nanotubes with lysostaphin, a cell wall degrading enzyme, into films to impart bactericidal properties against Staphylococcus aureus and Staphylococcus epidermidis. We fabricated and characterized nanocomposites containing different conjugate formulations and enzyme loadings. These enzyme-based composites were highly efficient in killing MRSA (>99% within 2 h) without release of the enzyme into solution. Additionally, these films were reusable and stable under dry storage conditions for a month. Such enzyme-based film formulations may be used to prevent growth of pathogenic and antibiotic-resistant microorganisms on various common surfaces in hospital settings. Polymer and paint films containing such antimicrobial conjugates, in particular, could be advantageous to prevent risk of staphylococcal-specific infection and biofouling.
Abstract IA3: In tumor screening for novel targets in papillary serous ovarian cancer (2013)

Abstract In search of new, potential therapeutic target proteins in primary ovarian cancer cells, we have performed in-tumor shRNA screens in an established, human ovarian cancer (ov ca) cell line growing either subcutaneously or intraperitoneally in immunologically incompetent mice. Validation tests were then performed on the confirmed hits in viability/proliferation assays performed, in parallel, in at least two, cultured primary papillary serous ov ca cell strains each of which was generated by direct intraperitoneal injection of primary, patient- derived ov ca cells. The lentiviral shRNA library used contained ~8,000 hairpins, collectively directed against all known human protein kinases and a number of established human oncoproteins. Approximately 40 hits were detected and confirmed in this study, in which the screen involved deep sequencing of DNA isolated from residual tumor material growing in multiple animals. Here the search was for any hairpins that were selectively and specifically depleted from these DNA samples. Currently, we are focusing on two, new hits in this effort with special attention to their effects on primary human ov ca cell tumor formation in nude mice. Citation Format: Maria Giuseppina Baratta, Maria Giuseppina Baratta, Joyce Liu, Joyce Liu, Yaara Zwang, Yaara Zwang, Yaara Zwang, Anna Schinzel, Anna Schinzel, Ronny Drapkin, Ronny Drapkin, William Hahn, William Hahn, William Hahn, David M. Livingston, David M. Livingston. In tumor screening for novel targets in papillary serous ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA3.
Characterization of Interfacial Structure in Polymer-Fullerene Bulk Heterojunctions via C13 {H2} Rotational Echo Double Resonance NMR (2018)

We introduce a new application of solid state NMR measurements towards characterizing the donor-acceptor interfaces within bulk heterojunction (BHJ) films. Rotational echo double resonance (REDOR) is used to measure dipolar couplings between ^{13}C nuclei on the acceptor phenyl-C_{61}-butyric acid methyl ester (PCBM) fullerene cage, which is ≈18% isotopically enriched with ^{13}C, and beta hydrogens on the donor poly(3-hexyl thiophene) (P3HT) main chain, which are >95% isotopically enriched with ^{2}H. The ^{13}C-^{2}H dipolar couplings are used for constraining possible models of molecular packing in the amorphous mixed phase of a P3HT/PCBM BHJ. The films studied are highly mixed (>80%) and have a maximum length scale of composition nonuniformity of ≈6 nm in the mixed phase, as demonstrated by ^{1}H spin diffusion NMR and supported by TEM. The REDOR results show that despite the lack of phase separation at length scales greater than ≈6 nm, neat P3HT and PCBM clusters exist on ≈3 nm size scales, and, for the average PCBM molecule, the number of nearest neighbors P3HTs is two.
Control of Cellular Activity (2005)

This chapter contains sections titled: Photochemical Release of Second Messengers – Caged Cyclic Nucleotides Introduction Overview of Phototriggers for cNMPs ortho-Nitrobenzyl Derivatives (Coumarin-4-yl)methyl Derivatives Others Selection of the Most Useful Phototriggers Applications of Caged Cyclic Nucleotides Cyclic Nucleotide-Gated (CNG) Channels HCN Channels Dorsal Root Ganglion Cells cGMP-Signaling Pathway in Sperm Miscellaneous Systems Photochemical Release of Second Messengers – Caged Nitric Oxide Introduction Photosensitive Precursors to Nitric Oxide Endogenous Photosensitive Precursors to Nitric Oxide Inorganic Photosensitive Precursors to Nitric Oxide Organic Photosensitive Precursors to Nitric Oxide Conclusions Photochemical Release of Neurotransmitters – Transient Kinetic Investigations of Membrane-bound Receptors on the Surface of Cells in the Microsecond-to-Millisecond Time Region Introduction Cell Flow Technique Photochemical Properties of Caged Neurotransmitters Laser Pulse Photolysis Technique Determination of the Rate and Equilibrium Constants of the Channel-Opening Mechanism Comparison of the Values Obtained for the Rate and Equilibrium Constants of the Channel-Opening Process Using Independent Techniques Summary Caged Neurotransmitters for Probing Neuronal Circuits, Neuronal Integration, and Synaptic Plasticity Introduction Functional Mapping of Neuronal Connections Example: Uncaging Glutamate to Map Local Connections in the Mammalian Cortex Example: Use of Caged Glutamate for Probing Refinement of Neuronal Connectivity Conclusions and Future Challenges Probing Neuronal Integration Examples Conclusions and Future Challenges Investigating Synaptic Plasticity Conclusions and Future Challenges
A high visibility Talbot-Lau neutron grating interferometer to investigate stress-induced magnetic degradation in electrical steel (2020)

Neutron grating interferometry (nGI) is a unique technique allowing to probe magnetic and nuclear properties of materials not accessible in standard neutron imaging. The signal-to-noise ratio of an nGI setup is strongly dependent on the achievable visibility. Hence, for analysis of weak signals or short measurement times a high visibility is desired. We developed a new Talbot-Lau interferometer using the third Talbot order with an unprecedented visibility (0.74) over a large field of view. Using the third Talbot order and the resulting decreased asymmetry allows to access a wide correlation length range. Moreover, we have used a novel technique for the production of the absorption gratings which provides nearly binary gratings even for thermal neutrons. The performance of the new interferometer is demonstrated by visualizing the local magnetic domain wall density in electrical steel sheets when influenced by residual stress induced by embossing. We demonstrate that it is possible to affect the density of the magnetic domain walls by embossing and therefore to engineer the guiding of magnetic fields in electrical steel sheets. The excellent performance of our new setup will also facilitate future studies of dynamic effects in electric steels and other systems.
Angular Sampling, Test Signal, and Near-Field Aspects for Over-The-Air Total Radiated Power Assessment in Anechoic Chambers (2018)

5th-generation mobile network systems operating in millimeter-wave bands will employ base stations with integrated active antenna systems. Such systems are capable of beam-tracking using narrow beams obtained from antenna arrays. Regulatory limits for unwanted radio frequency and Over-The-Air methods for TRP of unwanted emissions are needed. The method investigated here uses power density measurements on a spherical surface in an anechoic chamber. Two major challenges with such a method are: need for a large number of angular points and search for a worst case antenna configuration per frequency for electrically large devices at high frequencies. These challenges are addressed by investigating sparse sampling and use of beam sweeping. Finally, it is investigated how and in which spatial regions near-field tangential electric field measurements can be used to assess TRP.
Nitric oxide dosed in short bursts at high concentrations may protect against Covid 19 (2020)

It has long been suggested that NO may inhibit an early stage in viral replication. Furthermore, in vitro tests have shown that NO inhibits the replication cycle of severe acute respiratory syndrome coronavirus. Despite smoking being listed as a risk factor to contract Covid-19, only a low proportion of the smokers suffered from SARS-corona infection in China 2003, and from Covid-19 in China, Europe and the US. We hypothesize, that the intermittent bursts of high NO concentration in cigarette smoke may be a mechanism in protecting against the virus. Mainstream smoke from cigarettes contains NO at peak concentrations of between about 250 ppm and 1350 ppm in each puff as compared to medicinal use of no more than 80 to a maximum of 160 ppm. The diffusion of NO through the cell wall to reach the virus should be significantly more effective at the very high NO concentration in the smoke, according to classic laws of physics. The only oxide of nitrogen in the mainstream smoke is NO, and the NO2 concentration that is inhaled is very low or undetectable, and methemoglobin levels are lower in smokers than non-smokers, reasonably explained by the breaths of air in between the puffs that wash out the NO. Specialized iNO machines can now be developed to provide the drug intermittently in short bursts at high concentration dose, which would then provide both a preventative drug for those at high risk, as well as an effective treatment, without the health hazards associated with smoking.
Two versions of the gene encoding the 41-kilodalton subunit of the telomere binding protein of Oxytricha nova. (1990)

Macronuclear chromosomes of the ciliated protozoan Oxytricha nova terminate with a single-stranded (T4G4)2 overhang. The (T4G4)2 telomeric overhang is tenaciously bound by a protein heterodimer. We have cloned and sequenced the gene encoding the 41-kDa subunit of this telomere binding protein. The predicted amino acid sequence comprises two distinct regions, a carboxyl-terminal two-thirds that is 23% lysine and bears similarity to histone H1 and an amino-terminal one-third containing a hydrophobic stretch of about 15 amino acids. Two macronuclear versions of the gene differ in nucleotide sequence at several positions, but the derived polypeptides differ only at a single position, Ser-110 or Ala-110. Both versions harbor a small intron. The existence of this intron demonstrates that, despite the elimination of 95% of the micronuclear genome from the developing macronucleus, at least some noncoding DNA is retained during macronuclear development of hypotrichous ciliates.
A two-step chemical and circular dichroic method for assigning the absolute configurations of sphingosines (1995)

Breakdown products of sphingolipids are involved in cell regulaion and exhibit a wide variety of activities related to signal transduction. The backbone of sphingolipids are the sphingosines which have two stereogenic centers. A general, rapid, chemical/chiroptical micromethod based on the bichromophoric CD exciton chirality principle was developed to distinguish all four possible stereoisomers nonambiguously at a level of ca. 1 microgram.
KAPLAN: A 3D Point Descriptor for Shape Completion (2020)

We present a novel 3D shape completion method that operates directly on unstructured point clouds, thus avoiding resource-intensive data structures like voxel grids. To this end, we introduce KAPLAN, a 3D point descriptor that aggregates local shape information via a series of 2D convolutions. The key idea is to project the points in a local neighborhood onto multiple planes with different orientations. In each of those planes, point properties like normals or point-to-plane distances are aggregated into a 2D grid and abstracted into a feature representation with an efficient 2D convolutional encoder. Since all planes are encoded jointly, the resulting representation nevertheless can capture their correlations and retains knowledge about the underlying 3D shape, without expensive 3D convolutions. Experiments on public datasets show that KAPLAN achieves state-of-the-art performance for 3D shape completion.
Biofiltration of Volatile Pollutants: Solubility Effects (2001)

This project investigates and collects fundamental partitioning data for a variety of sparingly soluble subsurface contaminants (e.g., TCE, etc.) between vapor, aqueous phase, and matrices containing substantial quantities of biomass and biomass components. Due to the difficulty of obtaining these measurements, environmental models have generally used solubility constants of chemicals in pure water or, in a few rare cases, simple linear models. Our prior EMSP work has shown that the presence of biological material can increase effective solubilities by an order of magnitude for sparingly soluble organics; therefore, the previous simple approaches are not valid and are extremely poor predictors of actual bio-influenced partitioning. It is likely that environmental contaminants will partition in a similar manner into high-biomass phases (e.g. biobarriers and plants) or humic soils. Biological material in the subsurface can include lipids, fatty acids, humic materials, as well a s the lumped and difficult to estimate 'biomass'. Our measurements include partition into these biological materials to allow better estimation. Fundamental data collected will be used in mathematical models predicting transport and sorption in subsurface environments, with the impacts on bioremediation being evaluated based on this new information. Our 2-D Win95/98 software program, Biofilter 1.0, developed as a part of our prior EMSP efforts for describing biofiltration processes with consideration given to both kinetic and mass transfer factors, will be extended to incorporate and use this information.
Convolutions for Spatial Interaction Modeling (2022)

In many different fields interactions between objects play a critical role in determining their behavior. Graph neural networks (GNNs) have emerged as a powerful tool for modeling interactions, although often at the cost of adding considerable complexity and latency. In this paper, we consider the problem of spatial interaction modeling in the context of predicting the motion of actors around autonomous vehicles, and investigate alternatives to GNNs. We revisit 2D convolutions and show that they can demonstrate comparable performance to graph networks in modeling spatial interactions with lower latency, thus providing an effective and efficient alternative in time-critical systems. Moreover, we propose a novel interaction loss to further improve the interaction modeling of the considered methods.