gebhart/patrepeval huggingface dataset:
Cytochrome P450-Dependent Arachidonate Metabolites Affect Renal Transport in the Rabbit (1993)

Arachidonic acid (AA) inhibited 86Rb uptake in a dose-dependent manner in rabbit medullary tubules representing the thick ascending limb of the loop of Henle (mTALH). We have shown that CoCl2 treatment of rabbits reduced renal AA metabolism by cytochrome P450-dependent enzymes (P450). After CoCl2 treatment, AA was without effect on 86Rb uptake in mTALH cells. However, the two principal P450-AA metabolites produced by the mTALH, 20-HETE and 20-COOH-AA, inhibited 86Rb uptake in a dose-dependent manner in mTALH cells whether obtained from control or CoCl2-treated rabbits. These data support our hypothesis that CoCl2 treatment impairs ion transport function of mTALH cells by blocking cytochrome P450-AA metabolism, a blockade circumvented by the relevant P450-AA metabolites.
Development of Sulfur-Tolerant Components For the Molten Carbonate Fuel Cell (1981)

The sulfur tolerance of candidate anode and anode current collector materials for the molten carbonate fuel cell were evaluated in an electrochemical half-cell using both steady-state and transient potentiostatic techniques. H2S was introduced into the fuel at concentrations of 50 and 1000 ppm. At the higher sulfur concentration using low-Btu fuel, both nickel and cobalt were observed to undergo a negative shift in their open-circuit potentials, and high anodic and cathodic currents were observed compared with clean fuels. Kinetic currents measured using the transient potentiostatic technique were not greatly affected by 50 ppm H2S introduced into the fuel. However at higher sulfur concentrations, higher kinetic currents were observed, indicating a probable sulfidation reaction. Of the new anode materials evaluated Mg0.05La0.95CrO3 and TiC showed good stability in the anodic region. With the former material, exchange current densities in low-Btu fuel were calculated to be ≃ 11 mA/cm2 at 650° C, lower values than found for either nickel or cobalt anodes under similar conditions.
Experimental and Analytical Study of Micro-Serrations on Surgical Blades (2015)

This paper reports on a study and application of laser ablation for machining of micro-serrations on surgical blades. The proposed concept is inspired by nature and mimics a mosquito’s maxilla, which is characterized by a number of serrations along its edge in order to painlessly penetrate human skin and tissue. The focus of this study is to investigate the maxilla’s penetration mechanisms and its application to commercial surgical blades. The fundamental objective is to understand the friction and cutting behavior between a serrated hard surface and soft materials, as well as to identify serration patterns that would minimize the cutting force and the friction of the blade during tissue cutting. Micro-serrations characterized by different patterns and sizes ranging from 200 μm to 400 μm were designed and manufactured on surgical blades. As supported by finite element methods (FEM), a reduction of 20∼30% in the force during blade cutting has been achieved, which encourages further studies and their applications to biomedical devices.
Quasiplanar Chiral Nanostructures: Circular Dichroism in Higher‐Order Diffraction Beams from Chiral Quasiplanar Nanostructures (Advanced Optical Materials 11/2018) (2018)

Ventsislav K. Valev and co-workers (article number 1800098) report strong circular dichroism in the third-order diffracted beams from chiral nanoarrays, made of gold. Numerical data support the experiments, further validated by using Babinet's principle. This work opens up unexplored directions in the optical properties of chiral nanoarrays. The cover art image is a photograph of the experimental setup, where the nanoarrays burst into colorful lines of research.
Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis (2019)

Abstract Signal transduction deregulation is a hallmark of many complex diseases, including Multiple Sclerosis (MS). Here, we performed ex vivo multiplexed phosphoproteomic assays in PBMCs from 180 MS patients either untreated or treated with fingolimod, natalizumab, interferon-beta, glatiramer acetate or the experimental therapy epigallocatechin gallate (EGCG), and from 60 matched healthy controls. Fitting a bespoke literature-derived network of MS-related pathways using logic modeling yielded a signaling network specific for each patient. Patient models were merged to characterize healthy-, disease- and drug-specific signaling networks. We defined a co-druggability score based on the topology for each drug’s network. We used this score to identify kinase interactions whose activity could be reverted to a "healthy-like" status by combination therapy. We predicted several combinations with approved MS drugs. Specifically, TAK1 kinase, involved in TGF-B, toll-like receptor, B-cell receptor and response to inflammation pathways was found to be highly deregulated and co-druggable with four MS drugs. One of these predicted combinations, Fingolimod with a TAK1 inhibitor, was validated in an animal model of MS. Our approach based on patient-specific signaling networks enables prediction of targets for combination therapy for MS and other complex diseases. One sentence summary A new approach to predict combination therapies based on modeling signaling architecture using phosphoproteomics from patients with Multiple Sclerosis characterizes deregulated signaling pathways and reveals new therapeutic targets and drug combinations.
Insulin Resistance in Heart Failure: Differences Between Patients with Reduced and Preserved Left Ventricular Ejection Fraction (2015)

IR is present in non-diabetic patients with HFpEF and HFrEF. However, distinct differences in the insulin sensitivity characteristics in HFpEF and HFrEF become apparent by more advanced testing. Patients with HFrEF showed more severe IR.
Confining Free Radicals in Close Vicinity to Contaminants Enables Ultrafast Fenton‐like Processes in the Interspacing of MoS<sub>2</sub> Membranes (2019)

Abstract Heterogenous Fenton‐like reactions are frequently proposed for treating persistent pollutants through the generation of reactive radicals. Despite great efforts to optimize catalyst activity, their broad application in practical settings has been restricted by the low efficiency of hydrogen peroxide or persulfate decomposition as well as ultrafast self‐quenching of the activated radicals. Theoretical calculations predicted that two‐dimensional (2D) metallic 1T phase MoS 2 materials with exposed (001) surfaces and (100) edges should have remarkable affinity towards crucial intermediates in the peroxymonosulfate (PMS) activation process. X‐ray photoelectron spectroscopy and in situ Raman spectroscopy were used to show that the exposed metallic Mo sites accelerate the rate‐limiting step of electron transfer. A lamellar membrane made from a stack of 2D MoS 2 with tunable interspacing was then designed as the catalyst. The non‐linear transport between the MoS 2 nanolayers leads to high water diffusivity so that the short‐lived reactive radicals efficiently oxidize contaminants.
High-LET Patterns of DSBs in DNA Loops, the HPRT Gene and Phosphorylation Foci (2007)

We present new results obtained with our model based on the track structure and chromatin geometry that predicts the DSB spatial and genomic distributions in a cell nucleus with the full genome represented. The model generates stochastic patterns of DSBs in the physical space of the nucleus filled with the realistic configuration of human chromosomes. The model was re-used to find the distribution of DSBs in a physical volume corresponding to a visible phosphorylation focus believed to be associated with a DSB. The data shows whether there must more than one DSB per foci due to finite size of the visible focus, even if a single DSB is radiochemically responsible for the phosphorylation of DNA in its vicinity. The same model can predict patterns of closely located DSBs in a given gene, or in a DNA loop, one of the large-scale chromatin structures. We demonstrated for the example of the HPRT gene, how different sorts of radiation lead to proximity effect in DSB locations, which is important for modeling gene deletions. The spectrum of intron deletions and total gene deletions was simulated for the HPRT gene. The same proximity effect of DSBs in a loop can hinder DSB restitutions, as parts of the loop between DSBs is deleted with a higher likelihood. The distributions of DSBs and deletions of DNA in a loop are presented.
DNP-Enhanced MAS NMR of Bovine Serum Albumin Sediments and Solutions (2014)

Protein sedimentation sans cryoprotection is a new approach to magic angle spinning (MAS) and dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) spectroscopy of proteins. It increases the sensitivity of the experiments by a factor of ∼4.5 in comparison to the conventional DNP sample preparation and circumvents intense background signals from the cryoprotectant. In this paper, we investigate sedimented samples and concentrated frozen solutions of natural abundance bovine serum albumin (BSA) in the absence of a glycerol-based cryoprotectant. We observe DNP signal enhancements of ε ∼ 66 at 140 GHz in a BSA pellet sedimented from an aqueous solution containing the biradical polarizing agent TOTAPOL and compare this with samples prepared using the conventional protocol (i.e., dissolution of BSA in a glycerol/water cryoprotecting mixture). The dependence of DNP parameters on the radical concentration points to the presence of an interaction between TOTAPOL and BSA, so much so that a frozen solution sans cryoprotectant still gives ε ∼ 50. We have studied the interaction of BSA with another biradical, SPIROPOL, that is more rigid than TOTAPOL and has been reported to give higher enhancements. SPIROPOL was also found to interact with BSA, and to give ε ∼ 26 close to its maximum achievable concentration. Under the same conditions, TOTAPOL gives ε ∼ 31, suggesting a lesser affinity of BSA for SPIROPOL with respect to TOTAPOL. Altogether, these results demonstrate that DNP is feasible in self-cryoprotecting samples.
The Unfolded Protein Response and Integrated Stress Response to Anoxia (2007)

The lack of oxygen delivery to tumor cells has profound consequences for tumor growth and correlates with poor prognosis. Some tumors contain regions of very severe hypoxia called anoxia, which constitutes a functionally different state to hypoxia. In response to anoxia, mammalian cells induce coordinated cytoprotective programs that are critical for tumor survival: the unfolded protein response and integrated stress response. Therefore, targeting additional components of anoxic pathways, besides the hypoxia-inducible response, may be effective for future anticancer therapies.
Supplementary Figure Legends from Depletion of Dendritic Cells Delays Ovarian Cancer Progression by Boosting Antitumor Immunity (2023)

Supplementary Figure Legends from Depletion of Dendritic Cells Delays Ovarian Cancer Progression by Boosting Antitumor Immunity
Computational Insights Into Avidity of Polymeric Multivalent Binders (2019)

Abstract Multivalent binding interactions are commonly found throughout biology to enhance weak monovalent binding such as between glycoligands and protein receptors. Designing multivalent polymers to bind to viruses and toxic proteins is a promising avenue for inhibiting their attachment and subsequent infection of cells. Several studies have focused on oligomeric multivalent inhibitors and how changing parameters such as ligand shape and size, and linker length and flexibility affect binding. However, experimental studies of how larger structural parameters of multivalent polymers such as degree of polymerization affect binding avidity to targets have mixed results with some finding an improvement with longer polymers and some finding no effect. Here, we use Brownian dynamics simulations to provide a theoretical understanding of how degree of polymerization affects the binding avidity of multivalent polymers. We show that longer polymers increase binding avidity to multivalent targets, but reach a limit in binding avidity at high degrees of polymerization. We also show that when interacting with multiple targets simultaneously, longer polymers are able to use inter-target interactions to promote clustering and improve binding efficiency. We expect our results to narrow the design space for optimizing the structure and effectiveness of multivalent inhibitors, as well as be useful to understand biological design strategies for multivalent binding.
Non-rigid point set registration: Coherent Point Drift (2007)

We introduce Coherent Point Drift (CPD), a novel probabilistic method for nonrigid registration of point sets. The registration is treated as a Maximum Likelihood (ML) estimation problem with motion coherence constraint over the velocity field such that one point set moves coherently to align with the second set. We formulate the motion coherence constraint and derive a solution of regularized ML estimation through the variational approach, which leads to an elegant kernel form. We also derive the EM algorithm for the penalized ML optimization with deterministic annealing. The CPD method simultaneously finds both the non-rigid transformation and the correspondence between two point sets without making any prior assumption of the transformation model except that of motion coherence. This method can estimate complex non-linear non-rigid transformations, and is shown to be accurate on 2D and 3D examples and robust in the presence of outliers and missing points.
Ag/FeCo/Ag Core/Shell/Shell Magnetic Nanoparticles with Plasmonic Imaging Capability (2015)

Magnetic nanoparticles (NPs) have been used to separate various species such as bacteria, cells, and proteins. In this study, we synthesized Ag/FeCo/Ag core/shell/shell NPs designed for magnetic separation of subcellular components like intracellular vesicles. A benefit of these NPs is that their silver metal content allows plasmon scattering to be used as a tool to observe detection by the NPs easily and semipermanently. Therefore, these NPs are considered a potential alternative to existing fluorescent probes like dye molecules and colloidal quantum dots. In addition, the Ag core inside the NPs suppresses the oxidation of FeCo because of electron transfer from the Ag core to the FeCo shell, even though FeCo is typically susceptible to oxidation. The surfaces of the Ag/FeCo/Ag NPs were functionalized with ε-poly-L-lysine-based hydrophilic polymers to make them water-soluble and biocompatible. The imaging capability of the polymer-functionalized NPs induced by plasmon scattering from the Ag core was investigated. The response of the NPs to a magnetic field using liposomes as platforms and applying a magnetic field during observation by confocal laser scanning microscopy was assessed. The results of the magnetophoresis experiments of liposomes allowed us to calculate the magnetic force to which each liposome was subjected.
What does it take to generate natural textures (2017)

Natural image generation is currently one of the most actively explored fields in Deep Learning. Many approaches, e.g. for state-of-the-art artistic style transfer or natural texture synthesis, rely on the statistics of hierarchical representations in supervisedly trained deep neural networks. It is, however, unclear what aspects of this feature representation are crucial for natural image generation: is it the depth, the pooling or the training of the features on natural images? We here address this question for the task of natural texture synthesis and show that none of the above aspects are indispensable. Instead, we demonstrate that natural textures of high perceptual quality can be generated from networks with only a single layer, no pooling and random filters.
Quels programmes d'amélioration génétique des animaux pour des systèmes d'élevage agro-écologiques ? (2017)

L’agro-écologie utilise les processus naturels et les ressources locales plutôt que des intrants chimiques pour assurer la production tout en limitant l’impact environnemental de l’agriculture. A cette fin, des innovations en génétique sont nécessaires pour disposer d’animaux productifs et adaptés à des contextes locaux variés. Pour toute filière d’élevage, réorienter les programmes de sélection actuels semble plus utile que développer des programmes spécifiques qui peineront à être efficaces en termes de coûts et de progrès génétiques attendus. Améliorer la robustesse des animaux vise à promouvoir leurs capacités d’adaptation en intégrant de nombreux\ncritères de sélection, en particulier de reproduction, santé, et d’adaptation à des ressources alimentaires peu digestibles et au changement climatique. Cela amène à considérer les interactions génotype-environnement dans la prédiction des valeurs génétiques et à évaluer les performances des animaux dans des systèmes à bas intrants pour sélectionner ceux qui sont adaptés à des conditions limitantes. La standardisation tant des animaux que des conditions d’élevage paraît antinomique avec les principes de l’agro-écologie prônant une adaptation des animaux aux ressources et contraintes locales dans des systèmes peu artificialisés et très liés à leur environnement physique. Il n’y a donc pas UN animal type agro-écologique, mais DES animaux aux profils variés permettant de répondre aux attentes de l’agro-écologie. Face à la diversité des milieux et des systèmes d’élevage, il faut conserver une diversité génétique importante intra-race, mais aussi préserver la diversité génétique entre races. Cela nécessite une caractérisation phénotypique et génétique des races locales. Enfin, il s’agit de favoriser l'appropriation par les éleveurs et les techniciens d’élevage des outils et des ressources génétiques disponibles pour répondre à leurs besoins.
Conductive Atomic Force Microscopy of Small Magnetic Tunnel Junctions With Interface Anisotropy (2015)

Magnetization reversal in CoFeB/MgO/CoFeB magnetic tunnel junctions with perpendicular magnetic anisotropy was studied as a function of both diameter (from 87 to 500 nm) and voltage (from -900 to 900 mV) using a conducting atomic force microscope. We found that the tunneling magnetoresistance near zero voltage was ~100% for all device sizes. The coercivity of the top CoFeB layer was identical within experimental error for the sizes between 158 and 500 nm but was smaller for 87 nm devices. This suggests a transition from domain-wall-nucleation-driven magnetization reversal to coherent rotation between 87 and 158 nm.
An efficient model for near-ground wave propagation in the presence of building walls/indoor obstacles (2009)

A semi-analytic model for near-earth wave propagation in the presence of building walls or similar obstacles is devised. The method is based on physical optics type approximations used in conjunction with the volume equivalence principle. Norton surface waves that are typically neglected in more common indoor propagation techniques such as ray tracing are included in this method as they prove to be vital for the accurate prediction of fields especially for sources close to ground. Simulation results have shown that, this method gives much more accurate results than ray tracing and proves to be computationally better than a numerical method and hence could be used to analyze field propagation in indoor structures that are large in terms of wavelength.
(±)-4-Oxo-9-deoxy-9-azaprostaglandin I<sub>2</sub> derivatives. Very stable prostacyclin analogs (1987)

The synthesis of 4-oxo-9-deoxy-9-azaprostaglandin I 2 (23a) and two ω-chain analogues thereof (23c and 23e) is described. The most salient features of the synthetic process used were (a) introduction of the nitrogen functionality at C-9 by [3,3] sigmatropic rearrangement of the trichloroacetamidate 5b to the trichloroacetamide 6, (b) transformation of 6 into the bicyclic lactam 7 with sodium borohydride, (c) stereospecific introduction of the 11α-hydroxyl group via the bromohydrin 8a, and (d) attachment of the α chain by extrusion of sulfur from the thioimidates 20 by the Eschenmoser sulfide contraction process.
Exercise Capacity Recovers Slowly But Fully in Patients With a Left Ventricular Assist Device (1996)

Left ventricular assist devices (LVAD) are used increasingly as bridges to cardiac transplantation. The typical LVAD candidate is a bedridden, critically ill, New York Heart Association (NYHA) Class IV patient with congestive heart failure (CHF) who is dependent upon intravenous, inotropic, and, in many cases, intra-aortic balloon support. The LVAD provides the potential for pre transplant rehabilitation by allowing the patient to become ambulatory, and by improving muscle tone, muscle mass, and nutritional status before transplantation. However, whether the abnormal exercise capacity of these patients improves after implantation has not been elucidated. The purpose of the present study was to evaluate the exercise capacity of patients with CHF after LVAD implantation (n = 10) using peak oxygen consumption during maximal exercise (MVO2), and comparing the results with those of a group of NYHA Class III patients with CHF (n = 14). After 2 months of implantation, MVO2 of the patients with LVAD was 12.8 +/- 0.3 ml/kg/min, which was comparable to that of the NYHA Class III patients with CHF (12.5 +/- 0.5 ml/kg/min). Four of 10 patients with LVAD were monitored for more than 5 months when MVO2 rose to 15.4 +/- 1.0 ml/kg/min (p < 0.05 vs NYHA Class III). In conclusion, the exercise capacity of patients with LVAD recovers slowly but significantly after 5 months of implantation, promising the potential for complete recovery from heart failure in patients supported with an LVAD.
Symmetrical Monopole Three-Wire HVDC Transmission System based on Hybrid Modular Multilevel and Alternate Arm Converters (2022)

Conversion of existing alternating current (ac) systems into direct current (dc) is a possible option to avoid wholescale construction of new corridors for future medium-voltage (MV) and high-voltage (HV) projects. This paper explores a symmetrical monopole three-wire HVDC transmission system based on an modular multilevel converter (MMC) and an alternate arm converter (AAC). It is shown that the power carrying capability can be further enhanced by 11% with the proposed novel method that two sets of resistors are inserted in positive and negative poles. However, technical complexities and financial feasibility of such implementations should be further overcome for practical project execution.