gebhart/patrepeval huggingface dataset:
New mechanisms of pulmonary arterial hypertension: role of Ca<sup>2+</sup>signaling (2012)

Pulmonary arterial hypertension (PAH) is a severe and progressive disease that usually culminates in right heart failure and death if left untreated. Although there have been substantial improvements in our understanding and significant advances in the management of this disease, there is a grim prognosis for patients in the advanced stages of PAH. A major cause of PAH is increased pulmonary vascular resistance, which results from sustained vasoconstriction, excessive pulmonary vascular remodeling, in situ thrombosis, and increased pulmonary vascular stiffness. In addition to other signal transduction pathways, Ca(2+) signaling in pulmonary artery smooth muscle cells (PASMCs) plays a central role in the development and progression of PAH because of its involvement in both vasoconstriction, through its pivotal effect of PASMC contraction, and vascular remodeling, through its stimulatory effect on PASMC proliferation. Altered expression, function, and regulation of ion channels and transporters in PASMCs contribute to an increased cytosolic Ca(2+) concentration and enhanced Ca(2+) signaling in patients with PAH. This review will focus on the potential pathogenic role of Ca(2+) mobilization, regulation, and signaling in the development and progression of PAH.
Defining the relevant combinatorial space of the PKC/CARD-CC signal transduction nodes (2017)

Abstract Biological signal transduction typically display a so-called bow-tie or hour glass topology: Multiple receptors lead to multiple cellular responses but the signals all pass through a narrow waist of central signaling nodes. One such critical signaling node for several inflammatory and oncogenic signaling pathways in humans are the CARD-CC / Bcl10 / MALT1 (CBM) complexes, which get activated by upstream protein kinase C (PKC). In humans, there are four phylogenetically distinct CARD-CC family (CARD9, −10, −11 and −14) proteins and 9 true PKC isozymes (α to ι). At this moment, less than a handful of PKC/CARD-CC relationships are known from experimental evidence. In order to explore the biologically relevant combinatorial space out of all 36 potential permutations in this two-component signaling event, we made use of CRISPR/Cas9 genome-edited HEK293T cells to mutate CARD10 for subsequent pairwise cotransfections of all CARD-CC family members and activated mutants of all true PKCs. By quantitative reporter gene expression readout, we could define specific strong and weak PKC/CARD-CC relationships. Surprisingly as many as 21 PKC/CARD-CC combinations were found to have synergistic effects. We also discovered heterodimerization between different CARD-CC proteins, and that this can influence their PKC response profile. This information will be valuable for future studies of novel signaling pathways dependent on the CBM complex signaling nodes.
A Consensus Approach for Targeted Muscle Reinnervation in Amputees (2023)

Amputations have been performed with few modifications since the dawn of surgery. Blood vessels are ligated, bones are shortened, and nerves are cut. In a percentage of people, this can result in severe neuropathic, residual limb, and phantom limb pain. Targeted muscle reinnervation is a surgical procedure initially conceived to optimize function for myoelectric prostheses in amputees. Recently, it has been adopted more widely by surgeons for the prevention and treatment of neuropathic pain. Perhaps as a function of its relatively recent development, many authors perform this operation differently, and there has been no overall agreement regarding the principles, indications, technical specifics, and postoperative management guidelines. This article is written as a consensus statement by surgeons focused on the treatment of neuropathic pain and those with extensive experience performing targeted muscle reinnervation. It is designed to serve as a roadmap and template for extremity surgeons to consider when performing targeted muscle reinnervation.
Extensile to contractile transition in active microtubule–actin composites generates layered asters with programmable lifetimes (2022)

We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing the concentration of filamentous actin controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. These self-regulating structures undergo internal reorganization, which appears to minimize the surface area and maintain the ordered layering, even when undergoing aster merging events. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. These results challenge the current models of active matter. They demonstrate self-organized dynamical states and patterns evocative of those observed in the cytoskeleton do not require precise biochemical regulation, but can arise from purely mechanical interactions of actively driven filamentous materials.
Injection seeding and modelocking of metal-metal Terahertz quantum cascade lasers (2015)

Injection seeding of terahertz quantum-cascade-lasers with metal-metal waveguides is demonstrated at liquid nitrogen temperatures through injection of phase-locked terahertz pulses. Coherent detection and modelocking of the QCL are demonstrated with the generation of 11ps pulses.
Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome (2019)

The Chip/LIM-domain binding protein (LDB)-single-stranded DNA-binding protein (SSDP) (ChiLS) complex controls numerous cell-fate decisions in animal cells, by mediating transcription of developmental control genes via remote enhancers. ChiLS is recruited to these enhancers by lineage-specific LIM-domain proteins that bind to its Chip/LDB subunit. ChiLS recently emerged as the core module of the Wnt enhanceosome, a multiprotein complex that primes developmental control genes for timely Wnt responses. ChiLS binds to NPFxD motifs within Pygopus (Pygo) and the Osa/ARID1A subunit of the BAF chromatin remodeling complex, which could synergize with LIM proteins in tethering ChiLS to enhancers. Chip/LDB and SSDP both contain N-terminal dimerization domains that constitute the bulk of their structured cores. Here, we report the crystal structures of these dimerization domains, in part aided by DARPin chaperones. We conducted systematic surface scanning by structure-designed mutations, followed by in vitro and in vivo binding assays, to determine conserved surface residues required for binding between Chip/LDB, SSDP, and Pygo-NPFxD. Based on this, and on the 4:2 (SSDP-Chip/LDB) stoichiometry of ChiLS, we derive a highly constrained structural model for this complex, which adopts a rotationally symmetrical SSDP<sub>2</sub>-LDB<sub>2</sub>-SSDP<sub>2</sub> architecture. Integrity of ChiLS is essential for Pygo binding, and our mutational analysis places the NPFxD pockets on either side of the Chip/LDB dimer, each flanked by an SSDP dimer. The symmetry and multivalency of ChiLS underpin its function as an enhancer module integrating Wnt signals with lineage-specific factors to operate context-dependent transcriptional switches that are pivotal for normal development and cancer.
Electro-oxidation of Ethanol at Gas Diffusion Electrodes A DEMS Study (2007)

The ethanol electro-oxidation at gas diffusion electrodes made of different catalysts, PtC, PtRu(1:1)/C, and PtSn(7:3)/C, were studied by on-line differential electrochemical mass spectrometry in a wide temperature range (30-90°C) as a function of the anode potential, the fuel concentration, and catalyst loading. The C O2 current efficiency (CCE) of the ethanol oxidation reaction (EOR) exhibits a maximum at about 0.6 V and decreases rapidly with further increasing potentials. The CCE for the EOR goes down with the increase in concentration of ethanol. CCE for ethanol oxidation reaction shows a strong increase with increasing catalyst loading. The CCE increases with increasing temperature, exceeding 75% at 90°C, 0.1 M ethanol, and 5 mg cm2 Pt catalyst loading. PtSnC shows high CCE, like PtC. But PtRuC exhibits very small CCE. Of the intermediates, acetaldehyde is quite active for further oxidation. But acetic acid is fairly resistant against further oxidation. Our result s indicate that the C-C bond scission observed for the EOR with CCE in excess of 50% has to proceed in parallel with ethanol oxidation to either acetaldehyde or acetic acid, and not sequentially from acetic acid further on, as acetic acid cannot be oxidized any further.
Local Dynamics of Stereoregular PMMAs Using Molecular Simulation (2001)

The physical origin of the large differences between the glass transition temperatures (Tg) exhibited by various stereoregular PMMA is not yet fully understood. Currently available theories on the glass transition phenomena are not able to predict the observed behavior. In this paper, results obtained from molecular dynamics (MD) simulations are presented. Actually, MD is a very powerful tool to investigate and differentiate the local dynamics of molecular groups embedded in either the backbone or the side chain. From the calculated WLF parameters it is found that the dynamics of the backbone is independent of the PMMA tacticity whereas the dynamics of the side chain strongly depends on the PMMA stereoregularity. However, since the frequency of side-chain rotations is more important in isotactic PMMA compared to syndiotactic, the overall mobility of the isotactic chains becomes higher. Consequently, according to the free volume concept, the Tg of isotactic PMMA is lower than the Tg of the syndiotactic isomer.
ChemInform Abstract: Incorporation of 2′‐Deoxysangivamycin in DNA Duplexes: The Conversion of a Pyrrolo[2,3‐d]pyrimidine Nitrile to a Carboxamide upon Oligonucleotide Deprotection. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Resonance Frequency Measurement Method of PICCs and the Environmental Influence (2007)

Abstract – A chipcard- or RFID-system operating at 13.56 MHz normally consists of three main components: A Proximity Coupling Device (PCD), a Proximity Integrated Circuit Card (PICC) and a host computer. The PICC consists mainly of a loop antenna which provides the magnetic coupling with the PCD and the IC which is needed for the communication between PCD / PICC and digital data processing. The loop antenna and the input circuitry of the IC together form a resonance circuit whose resonance frequency has a great impact on the efficiency of the magnetic coupling and is therefore an important parameter to characterize the PICC. In this paper the resonance frequency of a PICC is defined and derived by using the circuit analysis. Then a resonance frequency measurement method is investigated and its performance is analyzed theoretically. The influence of the environment on the accuracy of the method is analyzed by simulation and reference measurements. Finally, a setup for the practical implementation of the measurement is presented. I.
Characterization of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoprotein Conformational States on Infectious Virus Particles (2022)

ABSTRACT Human immunodeficiency virus (HIV-1) entry into cells involves triggering of the viral envelope glycoprotein (Env) trimer ((gp120/gp41) 3 ) by the primary receptor, CD4, and coreceptors, CCR5 or CXCR4. The pretriggered (State-1) conformation of the mature (cleaved) Env is targeted by broadly neutralizing antibodies (bNAbs), which are inefficiently elicited compared with poorly neutralizing antibodies (pNAbs). Here we characterize variants of the moderately triggerable HIV-1 AD8 Env on virions produced by an infectious molecular proviral clone; such virions contain more cleaved Env than pseudotyped viruses. We identified three types of cleaved wild-type AD8 Env trimers on virions: 1) State-1-like trimers preferentially recognized by bNAbs and exhibiting strong subunit association; 2) trimers recognized by pNAbs directed against the gp120 coreceptor-binding region and exhibiting weak, detergent-sensitive subunit association; and 3) a minor gp41-only population. The first Env population was enriched and the other Env populations reduced by introducing State-1-stabilizing changes in the AD8 Env or by treatment of the virions with crosslinker or the State-1-preferring entry inhibitor, BMS-806. These stabilized AD8 Envs were also more resistant to gp120 shedding induced by a CD4-mimetic compound or by incubation on ice. Conversely, a State-1-destabilized, CD4-independent AD8 Env variant exhibited weaker bNAb recognition and stronger pNAb recognition. Similar relationships between Env triggerability and antigenicity/shedding propensity on virions were observed for other HIV-1 strains. Our results show that State-1 Envs on virions can be significantly enriched by optimizing Env cleavage; stabilizing the pretriggered conformation by Env modification, crosslinking or BMS-806 treatment; strengthening Env subunit interactions; and using CD4-negative producer cells. IMPORTANCE Efforts to develop an effective HIV-1 vaccine have been frustrated by the inability to elicit broad neutralizing antibodies that recognize multiple virus strains. Such antibodies are able to bind a particular shape of the HIV-1 envelope glycoprotein trimer, as it exists on a viral membrane but before engaging receptors on the host cell. Here, we establish simple yet powerful assays to characterize the envelope glycoproteins in a natural context on virus particles. We find that, depending on the HIV-1 strain, some envelope glycoproteins change shape and fall apart, creating decoys that can potentially divert the host immune response. We identify requirements to keep the relevant envelope glycoprotein target for broad neutralizing antibodies intact on virus-like particles. These studies suggest strategies that should facilitate efforts to produce and use virus-like particles as vaccine immunogens.
Gas Permeation of Sulfur Thin-Films and Potential as a Barrier Material (2019)

Elemental sulfur was formed into poly(ether sulfone)-supported thin-films (ca. 10 µm) via a melt-casting process. Observed permeabilities of C<sub>2</sub>H<sub>4</sub>, CO<sub>2</sub>, H<sub>2</sub>, He, and N<sub>2</sub> through the sulphur thin-films were <1 barrer. The sulfur thin-films were observed to age over a period of ca. 15 days, related to the reversion of polymerized sulfur to the S<sub>8</sub> allotrope. This structural conversion was observed to correlate with an increase in the permeability of all gases.
Production of Antibodies and Development of an Immunoassay for the Anticoagulant, Diphacinone (1988)

Diphacinone, a commonly used anticoagulant rodenticide, was coupled to protein via an (O-carboxymethyl) oxime bridge. Immunization in rabbits produced antibodies with good ability to recognize the hapten as demonstrated by indirect EIA and affinity column adsorption. A competitive EIA was developed which clearly measured 10 micrograms/L diphacinone concentrations showing the sensitivity of the assay. Cross-reactivity study with chlorophacinone showed that the antisera possessed a high degree of diphacinone specificity.
Sur la division euclidienne d'un nombre premier par son rang (1998)

International audience
Simultaneous reflection - refraction acquisition (1987)

The deeper geological targets of exploration projects are not always detected by seismic reflection. This may be due to weak or progressive impedance contrast or multiple reflections from the overburden. In some cases, seismic refraction can provide deeper information and complement reflection results. When a vibrating source is used, refraction data can be obtained together with conventional reflection data by using simultaneous vibrating techniques. Similar techniques were described by Garotta (1983) for simultaneous recording of several reflection lines, which is especially attractive for 3D acquisition, and by Garotta (1985) for simultaneous recording of conventional and shallow reflection data. Simultaneous recording of several offset VSPs was also described by Naville (1984). In simultaneous reflection and refraction profiling, refraction data acquisition must not in any respect adversely affect the quality of the reflection data, and the production of the conventional reflection crew must not be reduced by more than a few percent. The reflection recording spread can be used for refraction as: 1. 8 to 10 Hz geophones have low enough responses to record refracted energy; 2. refraction events from deeper strata usually have wavelengths of several hundred metres, and thus are not affected by the most comonly used geophane patterns, of some tens of metres; 3. modern reflection spreads are most of ten 4-6 km long, which is a reasonabIe length for a refraction spread; 4. although the usual reflection trace spacing is shorter than for refraction recording, this is not really a drawback.
Effects of Hemoadsorption with a Novel Adsorbent on Sepsis: In vivo and in vitro Study (2015)

CTR appeared to have a favorable effect on kidney function despite no immediate effects on cytokine removal. However, CTR2 beads did result in a late decrease of cytokines.
Author response: Characterization and functional analysis of cathelicidin-MH, a novel frog-derived peptide with anti-septicemic properties (2021)

The novel cathelicidin cathelicidin-MH was identified from the skin of M. heymonsivogt frog, which protects against lipopolysaccharide- and cecal ligation and puncture-induced sepsis, effectively ameliorates multi-organ pathology, especially in lung.
B-3-31 On R&D Plan of Application of Vision Metrology to Large Reflector of Mobile Communication Satellite (2015)

In the experiment with Engineering Testing Satellite VIII with thirteen meters aperture reflector, pointing offset and change of antenna pattern likely due to deformation of reflector was reported1. A dynamic beam control technique to compensate a beam change due to deformation of reflector is required for next generation mobile satellite service. NICT have started the contracted research project by R&D on dynamic beam control technique for next generation mobile communication satellite”. Application of vision metrology to large aperture reflector on satellite will enable us to evaluate shape of deformed large aperture reflector in high precision. High precision measurement of shape of large aperture reflector give us a possibility of modification antenna pattern deteriorated by reflector shape deformation. Application of vision metrology to measure the shape of reflector in high precision in orbit is considered and the prototyping simulator to derived the expected precision by bundle adjustment for vision metrology or photogrammetry. By measurement experiment of configured model by using prototyping simulator, preliminary results shows that the expected precision for twenty meters reflector is two or three millimeters.
Realistic Evaluation of Transductive Few-Shot Learning (2022)

Transductive inference is widely used in few-shot learning, as it leverages the statistics of the unlabeled query set of a few-shot task, typically yielding substantially better performances than its inductive counterpart. The current few-shot benchmarks use perfectly class-balanced tasks at inference. We argue that such an artificial regularity is unrealistic, as it assumes that the marginal label probability of the testing samples is known and fixed to the uniform distribution. In fact, in realistic scenarios, the unlabeled query sets come with arbitrary and unknown label marginals. We introduce and study the effect of arbitrary class distributions within the query sets of few-shot tasks at inference, removing the class-balance artefact. Specifically, we model the marginal probabilities of the classes as Dirichlet-distributed random variables, which yields a principled and realistic sampling within the simplex. This leverages the current few-shot benchmarks, building testing tasks with arbitrary class distributions. We evaluate experimentally state-of-the-art transductive methods over 3 widely used data sets, and observe, surprisingly, substantial performance drops, even below inductive methods in some cases. Furthermore, we propose a generalization of the mutual-information loss, based on $α$-divergences, which can handle effectively class-distribution variations. Empirically, we show that our transductive $α$-divergence optimization outperforms state-of-the-art methods across several data sets, models and few-shot settings. Our code is publicly available at https://github.com/oveilleux/Realistic_Transductive_Few_Shot.
Size matters: Improved color‐difference estimation for small visual targets (2009)

Abstract— A long‐standing problem in color science is the accurate estimation of color differences for visual targets of small angular subtense. For instance, “What is the magnitude of a 0.5° color difference that will be as discriminable as a given 2° color difference?” Or, “What is the reduced angular subtense (or increased distance) at which two visual fields of given colors will become appreciably less discriminable than they were at larger subtense (or smaller distance)?” Past attempts at solving this problem have been specific to a particular color‐difference equation and, as such, the work lost relevance as improved color‐difference formulae were developed. This article proposes a structural model based upon the response of retinal cone cells to small‐subtense symbol images scattered by the ocular media. The method is demonstrated to be applicable without alteration to very different contemporary color‐difference equations, to be practical with a wide range of surround intensities, and to have high correlation with human search performance involving small color symbols on an electronic information display.
Nonimmunogenic Hydrogel-Mediated Delivery of Antibiotics Outperforms Clinically Used Formulations in Mitigating Wound Infections (2021)

Treatment of chronic wound infections caused by Gram-positive bacteria such as <i>Staphylococcus aureus</i> is highly challenging due to the low efficacy of existing formulations, thereby leading to drug resistance. Herein, we present the synthesis of a nonimmunogenic cholic acid-glycine-glycine conjugate (<b>A6</b>) that self-assembles into a supramolecular viscoelastic hydrogel (<b>A6</b> gel) suitable for topical applications. The <b>A6</b> hydrogel can entrap different antibiotics with high efficacy without compromising its viscoelastic behavior. Activities against different bacterial species using a disc diffusion assay demonstrated the antimicrobial effect of the ciprofloxacin-loaded <b>A6</b> hydrogel (CPF-Gel). Immune profiling and gene expression studies after the application of the <b>A6</b> gel to mice confirmed its nonimmunogenic nature to host tissues. We further demonstrated that topical application of CPF-Gel clears <i>S. aureus</i>-mediated wound infections more effectively than clinically used formulations. Therefore, cholic acid-derived hydrogels are an efficacious matrix for topical delivery of antibiotics and should be explored further.