gebhart/patrepeval huggingface dataset:
Monitoring the Conformational Fluctuations of DNA Hairpins Using Single-Pair Fluorescence Resonance Energy Transfer (2001)

We present single-pair fluorescence resonance energy transfer (spFRET) observations of individual opening and closing events of surface-immobilized DNA hairpins. Two glass-surface immobilization strategies employing the biotin-streptavidin interaction and a third covalent immobilization strategy involving formation of a disulfide bond to a thiol-derivatized glass surface are described and evaluated. Results from image and time-trace data from surface-immobilized molecules are compared with those from freely diffusing molecules, which are unperturbed by surface interactions. Using a simple two-state model to analyze the open and closed time distributions for immobilized hairpins, we calculate the lifetimes of the two states. For hairpins with a loop size of 40 adenosines and a stem size of either seven or nine bases, the respective closed-state lifetimes are 45 +/- 2.4 and 103 +/- 6.0 ms, while the respective open-state lifetimes are 133 +/- 5.5 and 142 +/- 22 ms. These results show that the open state of the hairpin is favored over the closed state of the hairpin under these conditions, consistent with previous diffusion fluorescence correlation spectroscopy (FCS) experiments on poly(A)-loop hairpins. The measured open-state lifetime is about 30 times longer than the calculated 3 ms open-state lifetime for both hairpins based on a closing rate scaling factor derived from a previous FCS study for hairpins in diffusion with 12-30 thymidines in their loops. As predicted, the closed-state lifetime is dependent on the stem length and is independent of the loop characteristics. Our findings indicate that current models should consider sequence dependence in calculating ssDNA thermostability. The surface immobilization chemistries and other experimental techniques described here should prove useful for studies of single-molecule populations and dynamics.
Physiological Association between Limb Ballistocardiogram and Arterial Blood Pressure Waveforms: A Mathematical Model-Based Analysis (2019)

By virtue of its direct association with the cardiovascular (CV) functions and compatibility to unobtrusive measurement during daily activities, the limb ballistocardiogram (BCG) is receiving an increasing interest as a viable means for ultra-convenient CV health and disease monitoring. However, limited insights on its physical implications have hampered disciplined interpretation of the BCG and systematic development of the BCG-based approaches for CV health monitoring. In this study, a mathematical model that can predict the limb BCG in responses to the arterial blood pressure (BP) waves in the aorta was developed and experimentally validated. The validated mathematical model suggests that (i) the limb BCG waveform reveals the timings and amplitudes associated with the aortic BP waves; (ii) mechanical filtering exerted by the musculoskeletal properties of the body can obscure the manifestation of the arterial BP waves in the limb BCG; and (iii) the limb BCG exhibits meaningful morphological changes in response to the alterations in the CV risk predictors. The physical insights garnered by the analysis of the mathematical model may open up new opportunities toward next generation of the BCG-based CV healthcare techniques embedded with transparency, interpretability, and robustness against the external variability.
5. Fazit und Ausblick (2019)

Mit Musik gemeinsam gegen das Trauma: Rhythmisches Musizieren in der Gruppe zielt als nonverbale traumapädagogische Intervention auf die Förderung und Steigerung der (Selbst-)Heilungsressourcen gewalterfahrener und traumatisierter Jugendlicher in der stationären Kinder- und Jugendhilfe.
Ventricular asystole in the presence of a biventricular device (2020)

In pacemaker-dependent patients with a newly implanted cardiac device, acute lead dislodgement constitutes one of the most common causes of loss of capture and ventricular asystole. In a biventricular system, it would be expected that such a potentially catastrophic event would be prevented with back-up right ventricular pacing unless both leads dislodge.
Colloidal Polymers: Synthesis and Characterization (2007)

Free-Radical Emulsion Polymerization and Aqueous Polymer Dispersions: A Long History with More Challenges To Meet in the Future Jean-Claude Daniel Controlled Free-Radical Polymerization: A Way To Design Polymer Architecture and Surface Properties of Latex Particles Celine Farcet, Carine Burguiere, and Bernadette Charleux Preparation of Microlatexes Using Polymeric Surfactants or Mixed Surfactants Peihong Ni and Shoukuan Fu Catalytic Polymerization of Olefins in Emulsion: A Breakthrough in Polymer Colloids Remi Soula, Jerome Claverie, Roger Spitz, and Alain Guyot Functionalization of Colloidal Particles Changchun Wang, Wuli Yang, and Shoukuan Fu Poly(N-isopropylacrylamide) Based Particles: Preparation and Colloidal Characterization Francoise Meunier and Abdelhamid Elaissari Microemulsion Polymerization: A Way To Synthesize Well-Defined Highly Functionalized Nanoparticles Chantal Larpent Hollow Particles: Synthetic Pathways and Potential Applications Elodie Bourgeat-Lami Preparation of Polymer and Hybrid Colloids by Miniemulsion for Biomedical Applications Katharuna Landfester Synthesis, Characterization, and Biomedical Application of Conducting Polymer Particles Mohamed Chehimi, Ammar Azioune, Smain Bousalem, Amel Ben Slimane, and Abderrahim Yassar Preparation of Magnetic Latexes Abdelhamid Elaissari, Florence Sauzedde, Franck Montagne, and Christian Pichot Polymer Beads in Biomedical Chromatography: Preparation and Characterization Ali Tuncel, E. Unsal, and S. Senel Assembling of Polymer Particles onto Solid Supports for Medical Applications Jean-Paul Chapel and Tatsuo Taniguchi The Necessary in Colloidal Characterization of Colloid Polymer Olivier Mondain Monval and Abdelhamid Elaissari Electrokinetic and Small-Angle Neutron Scattering Studies of Thermally Sensitive Polymer Colloids Brian R. Saunders Index
Protein biomarkers for motor neuron disease (2010)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease of motor neurons located in the motor cortex, brainstem and spinal cord. There currently are no diagnostic tests for ALS, and a rapid diagnostic test would assist clinicians to initiate treatments and/or enroll subjects into clinical trials at early disease stages. We used mass spectrometry based proteomics to discover candidate biomarkers for ALS. Our current study uses separate training and test sets to verify and validation protein biomarkers for ALS. Cerebrospinal fluid (CSF) from 105 patients with ALS, and 60 control subjects (including healthy controls, ALS disease mimics, and other neurologic disease controls) were used for further mass spectrometry and enzyme‐linked immunosorbent assay (ELISA) studies. We validated our prior mass spectrometry results, demonstrating that cystatin C and transthyretin are contained in a predictive biomarker panel for ALS. ELISA studies were performed for a number of candidate biomarkers and we determined that a combination of phosphorylated neurofilament protein and complement c3 provided an overall sensitivity of 87% and specificity of 94% for ALS. These results indicate that an ELISA based assay may provide a predictive assay for ALS. Funding support to RB by NIH grants ES013469 and NS061867.
A rapid one‐step radiosynthesis of the β‐amyloid imaging radiotracer N‐methyl‐[11C]2‐(4′‐methylaminophenyl)‐6‐hydroxybenzothiazole ([11C]‐6‐OH‐BTA‐1) (2004)

Abstract The promising β ‐amyloid PET imaging agent, [ 11 C]‐6‐OH‐BTA‐1, has been radiolabelled in one step using [ 11 C]‐methyl triflate. No protection of the 6‐hydroxy group is required, greatly simplifying the synthetic method. The reaction may be carried out in solution or by the captive solvent ‘loop’ method. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Search for Hidden-Sector Bosons in B[superscript 0] → K[superscript *0]μ[superscript +]μ[superscript −] Decays (2015)

A search is presented for hidden-sector bosons, χ, produced in the decay B[superscript 0] → K[superscript *](892)[superscript 0]χ, with K[superscript *](892)[superscript 0] → K[superscript +]π[superscript -] and χ → μ[superscript +]μ[superscript -]. The search is performed using pp-collision data corresponding to 3.0 fb[superscript -1] collected with the LHCb detector. No significant signal is observed in the accessible mass range 214 ≤ m(χ) ≤ 4350 MeV, and upper limits are placed on the branching fraction product B(B[superscript 0] → K[superscript *](892)[superscript 0]χ) × B(χ → μ[superscript +]μ[superscript -]) as a function of the mass and lifetime of the χ boson. These limits are of the order of 10[superscript -9] for χ lifetimes less than 100 ps over most of the m(χ) range, and place the most stringent constraints to date on many theories that predict the existence of additional low-mass bosons.
QuickSuggest (2010)

As traditional media and information devices integrate with the web, they must suddenly support a vastly larger database of relevant items. Many devices use remote controls with on-screen keyboards which are not well suited for text entry but are difficult to displace. We introduce a text entry method which significantly improves text entry speed for on-screen keyboards using the same simple Up/Down/Left/Right/Enter interface common to remote controls and gaming devices used to enter text. The paper describes QuickSuggest's novel adaptive user interface, demonstrates quantitative improvements from simulation results on millions of user queries and shows ease of use and efficiency with no learning curve in user experiments.
Modeling Higher-Order Correlations within Cortical Microcolumns (2014)

We statistically characterize the population spiking activity obtained from simultaneous recordings of neurons across all layers of a cortical microcolumn. Three types of models are compared: an Ising model which captures pairwise correlations between units, a Restricted Boltzmann Machine (RBM) which allows for modeling of higher-order correlations, and a semi-Restricted Boltzmann Machine which is a combination of Ising and RBM models. Model parameters were estimated in a fast and efficient manner using minimum probability flow, and log likelihoods were compared using annealed importance sampling. The higher-order models reveal localized activity patterns which reflect the laminar organization of neurons within a cortical column. The higher-order models also outperformed the Ising model in log-likelihood: On populations of 20 cells, the RBM had 10% higher log-likelihood (relative to an independent model) than a pairwise model, increasing to 45% gain in a larger network with 100 spatiotemporal elements, consisting of 10 neurons over 10 time steps. We further removed the need to model stimulus-induced correlations by incorporating a peri-stimulus time histogram term, in which case the higher order models continued to perform best. These results demonstrate the importance of higher-order interactions to describe the structure of correlated activity in cortical networks. Boltzmann Machines with hidden units provide a succinct and effective way to capture these dependencies without increasing the difficulty of model estimation and evaluation.
Cardioprotective Effects of Erythropoietin in Rats Subjected to Ischemia–Reperfusion Injury: Assessment of Infarct Size with99mTc-Annexin V (2008)

This study demonstrated that a single treatment with EPO immediately after release of coronary ligation suppressed cardiac remodeling and functional deterioration. (99m)Tc-annexin V autoradiographs and TUNEL staining confirm that this change is due to a decrease in the extent of myocardial apoptosis in the ischemic/reperfused region.
ChemInform Abstract: Electromechanical Computing at 500 °C with Silicon Carbide. (2010)

Abstract A microfabricated electromechanical inverter with SiC nanoelectromechanical system switches is developed that is capable of operating at 500 °C with ultralow leakage current achieving virtually zero off‐state current, microwave operating frequencies, and radiation hardness.
Exciton Formation Dynamics and Band‐Like Free Charge‐Carrier Transport in 2D Metal Halide Perovskite Semiconductors (2023)

Abstract Metal halide perovskite (MHP) semiconductors have driven a revolution in optoelectronic technologies over the last decade, in particular for high‐efficiency photovoltaic applications. Low‐dimensional MHPs presenting electronic confinement have promising additional prospects in light emission and quantum technologies. However, the optimisation of such applications requires a comprehensive understanding of the nature of charge carriers and their transport mechanisms. This study employs a combination of ultrafast optical and terahertz spectroscopy to investigate phonon energies, charge‐carrier mobilities, and exciton formation in 2D (PEA) 2 PbI 4 and (BA) 2 PbI 4 (where PEA is phenylethylammonium and BA is butylammonium). Temperature‐dependent measurements of free charge‐carrier mobilities reveal band transport in these strongly confined semiconductors, with surprisingly high in‐plane mobilities. Enhanced charge‐phonon coupling is shown to reduce charge‐carrier mobilities in (BA) 2 PbI 4 with respect to (PEA) 2 PbI 4 . Exciton and free charge‐carrier dynamics are disentangled by simultaneous monitoring of transient absorption and THz photoconductivity. A sustained free charge‐carrier population is observed, surpassing the Saha equation predictions even at low temperature. These findings provide new insights into the temperature‐dependent interplay of exciton and free‐carrier populations in 2D MHPs. Furthermore, such sustained free charge‐carrier population and high mobilities demonstrate the potential of these semiconductors for applications such as solar cells, transistors, and electrically driven light sources.
Carbonylation of Dimethyl Ether to Methyl Acetate over SSZ-13 (2019)

The small-pore zeolite with the chabazite framework topology, SSZ-13, is found to be an active catalyst in the carbonylation of dimethyl ether to methyl acetate (MA). The production of MA over SSZ-13 after 24 h on stream at 165 °C and 1 bar approaches that obtained from mordenite and is significantly higher than from ferrierite at comparable Si/Al of ca. 10. To understand the origin of the activity, SSZ-13 materials are synthesized with variable Si/Al, characterized via several techniques including multinuclear magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, and evaluated for their carbonylation activity. While MA production rates increase with decreasing Si/Al, the correlation is nonlinear due to the effect of Si/Al on the acid site distribution within different confining environments, and the associated impact of the latter on the rate-determining transition state barrier. Enhanced MA production rates trend with acid sites located at the eight-membered ring (8MR) that are increasingly populated as framework Al content increases. Density functional theory analyses of transition state energies as a function of active site location support the experimental findings, where the lowest apparent barriers are associated with the methoxy groups that orient within the plane of the 8MR window. This is due to an optimal charge stabilization of the cationic transition states with the negatively charged oxygens within the 8MR window. The effects of catalyst chemical composition, separate from framework topology, are also investigated using SAPO-34 (the silicoaluminophosphate analog of SSZ-13). Analyses of the 1H MAS NMR signals and carbonylation activity suggest that the higher acid site strength of SSZ-13 compared to that of the SAPO material is required for effective Brønsted acid catalysis of Koch-type carbonylation pathways.
A Method for Constructing the C44−C51 Side Chain of Altohyrtin C (1999)

[formula: see text] A method to construct the C44-C51 side chain of altohyrtin C has been developed and applied to a model aldehyde derived from D-glucose. The approach relies on a Wittig reaction to couple the side chain to an aldehyde and utilizes an allylic diazene rearrangement to place the C45 double bond in the correct position.
The Effect of PACAP38 on MyD88-Mediated Signal Transduction in Ischemia-/Hypoxia-Induced Acute Kidney Injury (2010)

our data reveal that the TLR4-mediated cytokine responses to hypoxia are primarily dependent on MyD88 signaling and highlight the pivotal role of MyD88-dependent mechanisms in the coordination of the innate immune responses to ischemic/hypoxic acute renal tubular injury. The renoprotective effect of PACAP in AKI involves both MyD88-dependent and -independent pathways.
Calculation of elongated carbon structures with Density Functional Theory and fast Poisson solver (2015)

The solution of the Poisson equation is an essential stage in the calculation of quantum properties of materials as it appears both in the electrostatic Hartree term and in the Fock exchange operator. We discuss here an integral method for the calculation of Poisson potential and demonstrate its integration with a Density Functional Theory (DFT) code. We show some results on elongated carbon chains.
Ce que les réformes font aux institutions (2011)

La place des acteurs dans le changement est évoquée tout au long du texte, même si les auteurs se gardent de donner une importance trop importante à l’intention de ces derniers (illusion héroïque de Dobry). Ils analysent donc les acteurs pris dans des contraintes d’institutions (routine, valeurs..) et les replacent dans une condition de négociation pour aboutir à des changements.
Biosynthesis-Guided Discovery of Enteropeptins, Unusual Sactipeptides Containing an N-Methylornithine (2021)

The combination of next-generation DNA sequencing technologies and bioinformatics have revitalized natural product discovery. Using a new bioinformatic search strategy, we recently identified ~600 gene clusters in animal microbiomes that code for ribosomal peptide natural products synthesized by radical S-adenosylmethionine enzymes. These grouped into 16 subfamilies and pointed to an unexplored microbiome biosynthetic landscape. Herein, we report the structure, biosynthesis, and function of one of these natural product groups, that we term enteropeptins, from the gut microbe Enterococcus cecorum. We elucidate three novel reactions, each catalyzed by a different family of metalloenzymes, in the biosynthesis of enteropeptins. Among these, we characterize the founding member of a widespread superfamily of Fe-S-containing methyltransferases, which, together with a di-Mn-dependent arginase, installs an N-methylornithine in the peptide sequence. Biological assays with the mature product revealed bacteriostatic activity only against the producing strain, extending an emerging theme of fratricidal or self-inhibitory metabolites in microbiome firmicutes.
Porphyrin Network Polymers Prepared via a Click Reaction and Facilitated Oxygen Permeation Through Their Membranes (2014)

Network polymers of cobaltporphyrin derivatives are prepared by a facile click reaction via the Michael addition of acetoacetate-substituted tetraphenyl cobaltporphyrin and tri- or tetra-acrylates. The conversion is saturated for 1 h in the presence of a catalyst, which almost reaches the same gelation point of the formed network polymers. Deeply and homogeneously red-colored membranes with a sub-micrometer thickness are yielded on a porous supporting membrane. They are still tough even with a very high content of the rigid porphyrin residue. The oxygen permeability is high, at 10-100 Barrer, and the oxygen/nitrogen permselectivity (PO2/PN2) is significantly enhanced with the porphyrin content reaching 30, for the membranes with ca. 70 wt% porphyrin content.
Glucocorticoid-Induced Protection in Circulatory Shock: Role of Reticuloendothelial System Function (1975)

Experiments with rats indicate that: (i) hydrocortisone sodium succinate (HC) and methylprednisolone sodium succine (MP) enhance survival after hemorrhage; (ii) MP is approximately 10-times more potent than HC; (iii) both HC and MP are more efficacious if administered prior to hemorrhage; (iv) efficacy of postshock therapy with both steroids is not only time- but dose-dependent; and (v) HC and MP can ameliorate or completely prevent the early RES phagocytic depression observed in circulatory shock. Overall, these data could be used to suggest that: (i) the RES may play a pivotal role in the beneficial actions of synthetic adrenocorticosteroids in circulatory shock, and (ii) numerical RES phagocytic indices may be diagnostic and prognostic parameters in circulatory shock therapy.
Sintering of Particulate Composites under a Uniaxial Stress (1990)

The sintering of particulate composites consisting of a finegrained zinc oxide matrix and &lt;10 vol% of coarse silicon carbide inclusions was investigated at 725°C under a uniaxial stress of ⋍250 kPa. Data for the densification and creep rates of the composite were compared with those for the unreinforced matrix. The inclusions cause a drastic reduction in the measured densification and creep rates. They have a greater effect on the densification process, however; the ratio of the densification rate to the creep rate of the composite is approximately half that of the unreinforced compact. The factors that cause the reduction in this ratio are present from the very early stage of sintering.
High Temperature Potting Materials for Wire Bond Encapsulation (2016)

Abstract Test results for a range of potting materials for encapsulation of wire bonds for a high temperature multi-chip module is presented. The potting materials include gels and more rigid epoxies, silicone, and silicone-ceramic materials. The materials were initially screened based on ease of processing, cracking, and weight loss at 200, 225, and 250°C. Materials that performed well after this initial screening were tested for insulation resistance at 200, 225, and 250°C and wire bonds were encapsulated for thermal cycled at −55 to 200°C and −55 to 250°C.
The characterization of intima development in left ventricular assist device (LVAD) and total artificial heart (TAH). (1976)

1. The study of PNI development provides useful information in the design and improvement of the prosthetic devices. 2. Improved gelatin aldehyde impregnation on the dacron covered diaphragm of cardiac prostheses resulted in a reduced PNI thickness and minimized interfacial degeneration of PNI. 3. The PNI on the diaphragm's surface started with a platelet rich interface and ended with a striated fibrin and platelet matrix at the blood interface. 4. The PNI in the TAH's had a higher involvement of polymorphonuclear leukocytic cells at the PNI-housing or diaphragm interface than the LVAD's. 5. The aldehyde treated pericardial surface of cardiac prostheses generated a thin PNI that was fibrin-rich, a viable cell infiltration, no interfacial degeneration, and endothelial-like cells on its surface.
Towards an Accessible Interface for Story World Building (2015)

In order to use computational intelligence for automated narrative synthesis, domain knowledge of the story world must be defined, a task which is currently confined to experts. This paper discusses the benefits and tradeoffs between agent-centric and event-centric approaches towards authoring the domain knowledge of story worlds. In an effort to democratize story world creation, we present an accessible graphical platform for content creators and even end users to create their own story worlds, populate it with smart characters and objects, and define narrative events that can be used by existing tools for automated narrative synthesis. We demonstrate the potential of our system by authoring a simple bank robbery story world, and integrate it with existing solutions for event-centric planning to synthesize example digital stories.