gebhart/patrepeval huggingface dataset:
Toolbox of Post‐Synthetic Mordenite Modification Strategies: Impact on Textural, Acidic and Catalytic Properties (2019)

Abstract Which post‐synthetic modification strategy is the best suited for the generation of particular textural or chemical features in mordenite for a desired catalytic application? The aim of this contribution is to shed light on the effective quality of zeolite hierarchization through the rational study of structure/catalytic property dependency. Our study focused on mordenite, as this zeolite is of particular importance due to its strong acidity and monodimensional channel system, which explains why mordenite is industrially extensively employed. A toolbox of post‐synthetic hierarchization strategies on aluminum rich and poor mordenites has been developed based on basic treatments assisted by CTAB and pyridine at various temperatures (in conventional and microwave heating) and acid HF etching in aqueous and organic medium. A systematic study of over 30 post‐synthetically modified mordenites was conducted, which allowed us to assess the impact of each hierarchization strategy on textural, morphological, chemical and catalytic properties. Major correlations between structural features and catalytic activity, selectivity and stability in both the monomolecular n ‐hexane cracking and the bimolecular toluene disproportionation were deduced.
Healing of knit lines in injection-molded liquid crystalline polymers (2007)

Randomization and healing of oriented layers and knit line regions in injection-molded samples of thermotropic Vectra A950 [poly(4-hydroxy benzoic acid-co-2-hydroxy-6-naphthoic acid)] have been studied by thermal optical analysis (TOA), thermal mechanical analysis (TMA), differential scanning calorimetry (DSC), wide-angle x-ray scattering (WAXS), and tensile testing. Annealing below the crystal melting temperature range resulted in no healing effects, whereas the knit line strength increased progressively with increasing annealing temperature within the melting range 275–293°C. TOA, TMA, WAXS, and DSC on oriented samples taken from the surface layer showed that oriented films undergo a randomization process when annealed in the melting temperature range. The macroscopic chain orientation decreased suddenly on heating in this temperature range and appeared also to be constant under isothermal conditions. It is proposed that the melting of small crystallites is a prerequisite for this randomization. Isothermal annealing of the fully nematic melt caused a very slow randomization of the oriented structure.
Comparison of Congestion-Control Feedback Approaches for Heterogeneous and Dynamically Changing Networks (2004)

Abstract—In the current Internet, TCP’s congestion control is performed end-to-end, possibly assisted by simple and limited congestion feedback mechanisms in routers such as Explicit Congestion Notification (ECN) or Random Early Detection (RED). In order to control network traffic more accurately by reducing or even preventing congestion in (parts of) the network, and to improve the overall performance of TCP flows, a number of more complex and powerful feedback mechanisms for use in routers have been proposed. This paper describes the main ideas behind some of the most important of such router congestion feedback (RCF) approaches based on network-information sharing (NIS). In addition, the properties, functionalities, and expected performance gain of these RCF approaches are compared and their applicability in the current Internet environment is investigated. The aim of this paper is to find potential RCF candidates that can be used to improve congestion control in the current Internet as well as in future IPbased networks where diverse wired and wireless access technologies are used in parallel.
In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates (2019)

Listeriosis is an important food-borne disease responsible for high rates of morbidity and mortality. L. monocytogenes has been the cause of several foodborne outbreaks and its ability to adapt and survive in a wide range of environmental conditions makes eradication difficult. Many L. monocytogenes strains are avirulent but have the ability to increase their virulence if exposed to environmental stresses. The aim of this study was to explain the observed increase in virulence of outbreak L. monocytogenes isolates by using phenotypic assays and whole genome sequencing. Four L. monocytogenes isolates from sweetcorn and one isolate from a raw milk (control) were sequenced and characterised using a range of phenotypic assays. The four L. monocytogenes sweetcorn isolates displayed a significant increase for in vitro adhesion and invasion of epithelial cells compared to the control isolate. They also showed a higher level of colonisation of the liver and spleen in vivo. In addition, the four L. monocytogenes isolates displayed an increased ability to form biofilms, resist heat stress and resist a combination of antimicrobials. Investigation of the genomes of the four L. monocytogenes sweet corn isolates identified Single Nucleotide Polymorphisms (SNPs) in genes, which may have a role in the observed phenotypes characteristic of these strains, particularly in response to survival properties within the environment or in terms of virulence. We highlight the importance of combining whole genomic sequencing with phenotypic characterisation as a key element in the investigation of outbreaks of foodborne pathogens.
Virological profile of hepatitis B infection in Black African HBsAg chronic carriers (2013)

Aims: 1) Describe virological profile of patients followed-up for chronic Hepatitis B virus (HBV); 2) Search for a correlation between cirrhosis and virological profile of patients. Patients and Methods: Retrospective study about 75 HBsAg positive patients followed-up for at least one year in two medical structures of Abidjan. Studied parameters: clinical signs, biological check-up (serum transaminases every 3 months for at least one year, platelets count and prothrombin rate), abdominal echography, virological check-up (HBsAg, HBeAg, anti-HBe, total anti-HBc, anti-VHC and anti- HIV Ab, HBV DNA biannual quantification during at least one year). Histological or biochemical evaluation of hepatic activity and fibrosis were realized in case of transaminases elevation or HBV DNA > 2000 IU/ml. Results: The mean age of our 75 patients (54 men) was 42.1 ± 11.54 years. HBV was fortuitously discovered in most of our patients (74.7% of the cases). The HBV inactive chronic carriage was 50.7%; HBeAg-positive and HBeAg-negative chronic hepatitis represented respectively 9.3% and 40% of the cases. Mean B viral load was 327.5 IU/ml in HBV inactive chronic carriers, 44,047,663 IU/ml in HBeAg-positive chronic HBV and 20,231,822 IU/ml in HBeAg-negative chronic HBV. Cirrhosis prevalence was significantly high- er in positive or negative HBeAg chronic HBV than in HBV inactive chronic carriers (32.4% vs. 5.3%, p = 0.008; OR = 8.6). Conclusion: Our patients’ virological profile was dominated by HBeAg-negative chronic HBV and HBV inactive chronic carriage. The risk of having cirrhosis was multiplied by 8.6 in case of active chronic hepatitis compared with HBV inactive chronic carriage.
Cathodic reduction of CO2 to formic acid: Effect of the nature of the cathode for pressurized systems (2023)

Electrochemical conversion of CO2 into formic acid (FA) in an aqueous electrolyte is considered a promising strategy to valorise waste-CO2. Some studies, mainly performed using Sn cathodes, have shown that the performance of the process can be strongly improved using pressurized systems. On the other hand, other studies, usually carried out in non-pressurized systems, have indicated that the nature of the cathode can strongly affect the process. Hence, in this work, we have investigated the coupled effect of nature of the cathode and CO2 pressure (PCO2) on the electrochemical conversion of CO2 to FA. Four electrodes (Sn, Sn/C-NP, Bi, Bi/C-NP) have been used as model cathodes. The results obtained have shown that the increase of PCO2 enhances the production of FA and the faradic efficiency of the process (FEFA) for all tested cathodes. Moreover, it has been observed that nanoparticle-based cathodes provided better results for electrolyses carried out at 1 bar and high current density. Conversely, at relatively high PCO2, the effect of the nature of the cathode becomes less important and bulk Sn and Bi electrodes display very interesting results in terms of production of FA, FEFA and stability.
A Template‐Assembled Synthetic Protein Surface Mimetic of the von Willebrand Factor A1 domain Inhibits Botrocetin‐Induced Platelet Aggregation (2004)

Platelet adhesion, the initial step of platelet activation, is mediated by the interaction of von Willebrand factor (VWF) with its platelet receptor, the GPIb-IX complex. The binding of VWF to GPIb-IX is induced either by increased shear stress or by exogenous modulators, such as botrocetin. At a molecular level, this interaction takes place between the A1 domain of VWF and the GPIb alpha chain of the GPIb-IX complex. We report here the design and functional characteristics of a VWF template-assembled synthetic protein (TASP), a chimeric four-helix-bundle TASP scaffold mimicking the surface of the A1 domain. Twelve residues located on helices alpha 3 and alpha 4 in the native A1 domain were grafted onto a surface formed by two neighboring helices of the TASP. VWF TASP was found to inhibit specifically botrocetin-induced platelet aggregation and to bind both botrocetin and GPIb alpha. However, in contrast to the native A1 domain, VWF TASP did not bind simultaneously to both ligands. Modeling studies revealed that the relative orientation of the alpha helices in VWF TASP led to a clash of bound botrocetin and GPIb alpha. These results demonstrate that a chimeric four-helix-bundle TASP as a scaffold offers a suitable surface for presenting crucial residues of the VWF A1 domain; the potential of the TASP approach for de novo protein design and mimicry is thereby illustrated.
Continuous size fractionation of magnetic nanoparticles by using simulated moving bed chromatography (2021)

Abstract The size fractionation of magnetic nanoparticles is a technical problem, which until today can only be solved with great effort. Nevertheless, there is an important demand for nanoparticles with sharp size distributions, for example for medical technology or sensor technology. Using magnetic chromatography, we show a promising method for fractionation of magnetic nanoparticles with respect to their size and/or magnetic properties. This was achieved by passing magnetic nanoparticles through a packed bed of fine steel spheres with which they interact magnetically because single domain ferro-/ferrimagnetic nanoparticles show a spontaneous magnetization. Since the strength of this interaction is related to particle size, the principle is suitable for size fractionation. This concept was transferred into a continuous process in this work using a so-called simulated moving bed chromatography. Applying a suspension of magnetic nanoparticles within a size range from 20 to 120 nm, the process showed a separation sharpness of up to 0.52 with recovery rates of 100%. The continuous feed stream of magnetic nanoparticles could be fractionated with a space-time-yield of up to 5 mg/(L∙min). Due to the easy scalability of continuous chromatography, the process is a promising approach for the efficient fractionation of industrially relevant amounts of magnetic nanoparticles.
The in vitro ejection of zinc from human immunodeficiency virus (HIV) type 1 nucleocapsid protein by disulfide benzamides with cellular anti-HIV activity. (1996)

Several disulfide benzamides have been shown to possess wide-spectrum antiretroviral activity in cell culture at low micromolar to submicromolar concentrations, inhibiting human immunodeficiency virus (HIV) type 1 (HIV-1) clinical and drug-resistant strains along with HIV-2 and simian immunodeficiency virus [Rice, W. G., Supko, J. G., Malspeis, L., Buckheit, R. W., Jr., Clanton, D., Bu, M., Graham, L., Schaeffer, C. A., Turpin, J. A., Domagala, J., Gogliotti, R., Bader, J. P., Halliday, S. M., Coren, L., Sowder, R. C., II, Arthur, L. O. & Henderson, L. E. (1995) Science 270, 1194-1197]. Rice and coworkers have proposed that the compounds act by "attacking" the two zinc fingers of HIV nucleocapsid protein. Shown here is evidence that low micromolar concentrations of the anti-HIV disulfide benzamides eject zinc from HIV nucleocapsid protein (NCp7) in vitro, as monitored by the zinc-specific fluorescent probe N-(6-methoxy-8-quinoyl)-p-toluenesulfonamide (TSQ). Structurally similar disulfide benzamides that do not inhibit HIV-1 in culture do not eject zinc, nor do analogs of the antiviral compounds with the disulfide replaced with a methylene sulfide. The kinetics of NCp7 zinc ejection by disulfide benzamides were found to be nonsaturable and biexponential, with the rate of ejection from the C-terminal zinc finger 7-fold faster than that from the N-terminal. The antiviral compounds were found to inhibit the zinc-dependent binding of NCp7 to HIV psi RNA, as studied by gel-shift assays, and the data correlated well with the zinc ejection data. Anti-HIV disulfide benzamides specifically eject NCp7 zinc and abolish the protein's ability to bind psi RNA in vitro, providing evidence for a possible antiretroviral mechanism of action of these compounds. Congeners of this class are under advanced preclinical evaluation as a potential chemotherapy for acquired immunodeficiency syndrome.
Vertical motion microactuator based on the concept of ECLIA (Electrostatic Controlled Linear Inchworm Actuator) (2003)

A vertical motion microactuator is proposed, which moves in a vertical direction from the substrate. The microactuator is designed based on the concept of ECLIA (Electrostatic Controlled Linear Inchworm Actuator), so that it can provide the following features in vertical motion: stepwise linear motion, high accuracy, large stroke, large force, and parallel motion of arrayed actuators. A large number of sliders utilize an upward and downward motion of the driving energy source and move in a vertical direction independently. The vertical motion microactuator has been designed, fabricated and operated.
Robust servo-control for underwater robots using banks of visual filters (2009)

We present an application of machine learning to the semi-automatic synthesis of robust servo-trackers for underwater robotics. In particular, we investigate an approach based on the use of Boosting for robust visual tracking of color objects in an underwater environment. To this end, we use AdaBoost, the most common variant of the Boosting algorithm, to select a number of low-complexity but moderately accurate color feature trackers and we combine their outputs. The novelty of our approach lies in the design of this family of weak trackers, which enhances a straightforward color segmentation tracker in multiple ways. From a large and diverse family of possible filters, we select a small subset that optimizes the performance of our trackers. The tracking process applies these trackers on the input video frames, and the final tracker output is chosen based on the weights of the final array of trackers. By using computationally inexpensive, but somewhat accurate trackers as members of the ensemble, the system is able to run at quasi real-time, and thus, is deployable on-board our underwater robot. We present quantitative cross-validation results of our spatio-chromatic visual tracker, and conclude by pointing out some difficulties faced and subsequent shortcomings in the experiments we performed, along with directions of future research in the area of ensemble tracking in real-time.
Synaptic depression related to presynaptic axon conduction block. (1976)

1. The depression of synaptic transmission, which occurs during prolonged repetitive activation, was examined in the opener muscle of the crayfish walking leg. 2. Excitatory post-synaptic potentials (e.p.s.p.s) initially facilitated but then declined to low amplitudes after about 4000 stimulus pulses had been delivered; this depression is presynaptic in origin; 3. Axon conduction blocks occured at points of bifurcation along the entire length of the presynaptic nerve. This resulted in failure of the nerve impulse to invade some branches of the terminal arborization. 4. Nerve terminal invasion failure caused either intermittent or complete inactiviation of some synaptic release sites; this was associated with depression of the post-synaptic response. 5. The statistics of transmitter release during prolonged repetitive stimulation were examined by focal extracellular recording methods. Transmitter release could be described by binomial statistics, and depression involved a drop in m, n and p. 6. The rate of spontaneous quantal release did not decrease, however, arguing against transmitter depletion. 7. It is concluded that repetitive stimulation eventually leads to depolarization of the axon membrane. This causes impulse propagation failure which reduces the number of synaptic release sites that are activated and mimics a drop in the effective stimulation rate; both effects cause synaptic depression.
Differential Oxidation of Protein-tyrosine Phosphatases (2004)

Oxidation is emerging as an important regulatory mechanism of protein-tyrosine phosphatases (PTPs). Here we report that PTPs are differentially oxidized, and we provide evidence for the underlying mechanism. The membrane-proximal RPTPalpha-D1 was catalytically active but not readily oxidized as assessed by immunoprobing with an antibody that recognized oxidized catalytic site cysteines in PTPs (oxPTPs). In contrast, the membrane-distal RPTPalpha-D2, a poor PTP, was readily oxidized. Oxidized catalytic site cysteines in PTP immunoprobing and mass spectrometry demonstrated that mutation of two residues in the Tyr(P) loop and the WPD loop that reverse catalytic activity of RPTPalpha-D1 and RPTPalpha-D2 also reversed oxidizability, suggesting that oxidizability and catalytic activity are coupled. However, catalytically active PTP1B and LAR-D1 were readily oxidized. Oxidizability was strongly dependent on pH, indicating that the microenvironment of the catalytic cysteine has an important role. Crystal structures of PTP domains demonstrated that the orientation of the absolutely conserved PTP loop arginine correlates with oxidizability of PTPs, and consistently, RPTPmu-D1, with a similar conformation as RPTPalpha-D1, was not readily oxidized. In conclusion, PTPs are differentially oxidized at physiological pH and H(2)O(2) concentrations, and the PTP loop arginine is an important determinant for susceptibility to oxidation.
Characterization of mutants of influenza A virus selected with the neuraminidase inhibitor 4-guanidino-Neu5Ac2en (1996)

The development of viral resistance to the neuraminidase (NA) inhibitor, 4-guanidino-Neu5Ac2en, of influenza viruses was studied by serial passage of A/Turkey/Minnesota/833/80 (H4N2) in Madin-Darby canine kidney cells in the presence of increasing concentrations of inhibitor. Resistant mutants selected after eight passages, had a 10,000-fold reduction in sensitivity to the inhibitor in plaque assays, but their affinity (1/Kd) to the inhibitor was similar to that of the parental virus. Electron microscopic analysis revealed aggregation of the mutant virus at the cell surface in the presence of the inhibitor. Sequence analysis established that a substitution had occurred in the NA (Arg-249 to Lys) and in the HA2 subunit of the hemagglutinin (Gly-75 to Glu), in the vicinity of the proposed second sialic acid binding site. The change of residue 249 appears to be a chance mutation, for we were unable to reisolate this mutant, whereas subsequent experiments indicate changes in the hemagglutinin. After 13 passages of the parental virus, mutants that were resistant to the high concentrations of inhibitor tested were obtained. These viruses retained their drug-resistant phenotype even after five passages without the inhibitor. Electron microscopic analysis revealed no aggregation of virus on the surface of infected cells in the presence of the inhibitor. Sequence analysis of the NA gene from these drug-resistant mutants revealed an additional substitution of Glu to Ala at the conserved amino acid residue 119. This substitution is responsible for reducing the affinity of the inhibitor to the NA. Our findings suggest that the emergence of mutants resistant to 4-guanidine-Neu5Ac2en is a multistep process requiring prolonged exposure to the inhibitor.
Affine Beilinson-Bernstein localization at the critical level (2022)

We prove the Frenkel-Gaitsgory localization conjecture describing regular Kac-Moody representations at critical level via eigensheaves on the affine Grassmannian using categorical Moy-Prasad theory. This extends previous work of the authors.
On–Off Porosity Switching in a Molecular Organic Solid (2010)

Plötzliche Kehrtwende: Ein kristalliner molekularer organischer Festkörper bestehend aus Käfigmolekülen wird vorgestellt, dessen Mikroporosität an- und ausgeschaltet werden kann (siehe Schema). Das Schalten wird durch die konformative Flexibilität des „weichen“ organischen Kristalls erleichtert. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Assessing Predicted HIV-1 Replicative Capacity in a Clinical Setting (2011)

HIV-1 replicative capacity (RC) provides a measure of within-host fitness and is determined in the context of phenotypic drug resistance testing. However it is unclear how these in-vitro measurements relate to in-vivo processes. Here we assess RCs in a clinical setting by combining a previously published machine-learning tool, which predicts RC values from partial pol sequences with genotypic and clinical data from the Swiss HIV Cohort Study. The machine-learning tool is based on a training set consisting of 65000 RC measurements paired with their corresponding partial pol sequences. We find that predicted RC values (pRCs) correlate significantly with the virus load measured in 2073 infected but drug naïve individuals. Furthermore, we find that, for 53 pairs of sequences, each pair sampled in the same infected individual, the pRC was significantly higher for the sequence sampled later in the infection and that the increase in pRC was also significantly correlated with the increase in plasma viral load and with the length of the time-interval between the sampling points. These findings indicate that selection within a patient favors the evolution of higher replicative capacities and that these in-vitro fitness measures are indicative of in-vivo HIV virus load.