gebhart/patrepeval huggingface dataset:
Neutralizing Host Responses in Hepatitis C Virus Infection Target Viral Entry at Post-Binding Steps and Membrane Fusion (2008)

Hepatitis C virus (HCV) is a leading cause of chronic hepatitis worldwide. Viral attachment and entry–representing the first steps of the virus with the host cell interaction- are major targets of adaptive host cell defences. The mechanisms of antibody-mediated neutralization by the host neutralizing responses in HCV infection are only poorly understood. Retroviral HCV pseudotypes (HCVpp) have been successfully used to study viral entry and antibody-mediated neutralization. In this study, we used this model system to study the mechanism of antibody-mediated neutralization by monoclonal anti-envelope antibodies and polyclonal anti-HCV immunoglobulins purified from HCV-infected patients. Using a panel of monoclonal anti-E1 and anti-E2 antibodies, we show that anti-envelope antibodies neutralize HCV entry during various steps of HCV entry including binding and post-binding events. Interestingly, we observed that host neutralizing responses in the majority of HCV-infected individuals target HCV entry after binding of the virus to the target cell membrane. Using a kinetic assay based on HCVpp entry, we demonstrate that purified antiviral immunoglobulins derived from individual HCV infected patients appear to inhibit HCV infection at an entry step closely linked to CD81. Our results indicate that host neutralizing responses in HCV-infected patients target viral entry after HCV binding most likely related to HCV-CD81, -SR-BI or -claudin–1 interaction and membrane fusion. These findings have implications not only for the understanding of the pathogenesis of HCV infection but also for the design of novel immunotherapeutic and preventive strategies.
Heparin-Associated Thrombocytopenia (1980)

We studied the mechanism of platelet injury in 20 patients receiving heparin, three of whom became thrombocytopenic. Platelets from these three patients had increased levels of IgG and C3, which correlated with the presence of thrombocytopenia; their plasma caused the release of serotonin from normal platelets at concentrations of heparin within the usual therapeutic range. This reaction required IgG and an intact classic complement pathway. The 17 patients receiving heparin in whom thrombocytopenia did not develop had normal levels of platelet-associated IgG and C3. Plasma from 14 of these patients caused the release of serotonin, but only at heparin concentrations above the therapeutic range, in a reaction that also required IgG and complement. The addition of heparin to 15 normal plasma samples did not cause platelet injury in vitro. These studies indicate that heparin administration can be associated with complement-mediated platlet injury. The dose-dependent nature of this process may account for the occurrence of thrombocytopenia in some of these patients.
Supplementary Video 2 from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by <i>In Vivo</i> Microscopy and Single-Cell Pharmacodynamics (2023)

Supplementary Video 2 from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by &lt;i&gt;In Vivo&lt;/i&gt; Microscopy and Single-Cell Pharmacodynamics
Molecular Dynamics Simulation of Amorphous Poly(ethylene terephthalate) (1998)

A conformational energy model has been set up for poly(ethylene terephthalate) (PET) for use in molecular dynamics simulations. The molecular dimensions, as expressed by the characteristic ratio, and the dipolar correlation factor of PET are key parameters in the simulations because they depend very differently on the conformational characteristics of the individual bond types in the chain. These parameters as well as the equation of state of the melt were emphasized in testing the model, and satisfactory representation was accomplished. It was found, however, difficult to achieve the experimental glass volume in MD cooling experiments below Tg. Packing features of bulk PET are discussed in terms of radial distribution functions. Dipolar correlation was found to be largely intramolecular in nature.
A study on the digitization of audio signals for video tape recorder (2005)

The digitization of audio signals for video tape recorder has been studied, and a prototype VTR providing digital audio sounds has been developed. Depth recording technique has been adopted for digital audio recording to avoid interference between audio and video signals. Using Offset-QPSK modulation, a symbol error rate of less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> is attained at a transmission rate of 2.6 Mbps. A newly developed digital signal processing circuit has also been employed to record audio signals having asynchronous sampling frequency with video signals. With this VTR, digital dubbing from various audio sources such as the DBS system and CD player can be performed.
Adaptive Data Broadcast in Hybrid Networks (1997)

Hybrid networks combine multiple communication modes and are fast emerging as the most viable solution for the ever increasing demand for bandwidth and data services. Taking advantage of this new technology, we are proposing a hybrid scheme which effectively combines broadcast for massive data dissemination and unicast for individual data delivery. The goal is to build highly scalable systems with small response time. In this paper, we describe a technique that continuously adapts the broadcast content to match the hot-spot of the workload. We show that the hot-spot can be accurately obtained by monitoring the "broadcast misses" observed through direct requests. This is a major departure from all other broadcast optimization schemes which are handicapped by their total reliance on complete knowledge of both "hits" and "misses". We also show that the proposed adaptive scheme performs effectively even under very dynamic and rapidly changing workloads. Extensive simulation results demonstrate both the scalability and versatility of the technique. Another basic result obtained in this paper is that the overall system's throughput depends only on the size of the hot-spot and not on the volume of the workload. This has far reaching implications for very large scale and high volume wide area information systems.
Exploring agency and self-other processing: an FMRI study of dynamic cooperation using an adaptively paced finger tapping task with variable auditory feedback (2011)

Ensemble musicians must be flexible and learn to adapt their performance to that of their partners and do so appropriately based on available sensory information streams. To further describe this type of dynamic joint action, we present a functional MRI study of sensorimotor synchronization with an adaptive “virtual partner” (VP). In particular, we investigate the behavioural and neural effects of variable auditory feedback (off, different to or same as pacing tones) associated with finger tapping performance across varying degrees of VP adaptivity (α). We predict that auditory feedback will bias the system to either i) integrate or ii) segregate information regarding “self” or the VP (“other”). We acquired subjective ratings of sense of oneness (self-other merging) and influence (self-other distinction) which we expected to vary with the availability and reliability (ambiguous-same vs. distinct-different) of pertinent auditory information. Behavioural data show a significant interaction effect of auditory feedback on α and synchronization such that distinctive self-other auditory information results in improvements in synchronization, especially at higher levels of α. Furthermore, auditory feedback was seen to have a significant effect on perceived oneness. Specifically, improved synchronization correlates with both ratings of oneness and activation of the precuneus and posterior cingulate, areas thought to integrate external and self generated information. By contrast, a comparison of neural activation in different and same auditory conditions reveals SMA and cerebellum activity. Identification of these structures may be related to greater sensitivity to prediction error as well as self-other distinction necessary for agency processing.
Abnormal development of the olfactory bulb and reproductive system in mice lacking prokineticin receptor PKR2 (2006)

Prokineticins, multifunctional secreted proteins, activate two endogenous G protein-coupled receptors PKR1 and PKR2. From in situ analysis of the mouse brain, we discovered that PKR2 is predominantly expressed in the olfactory bulb (OB). To examine the role of PKR2 in the OB, we created PKR1- and PKR2-gene-disrupted mice (Pkr1(-/-) and Pkr2(-/-), respectively). Phenotypic analysis indicated that not Pkr1(-/-)but Pkr2(-/-)mice exhibited hypoplasia of the OB. This abnormality was observed in the early developmental stages of fetal OB in the Pkr2(-/-) mice. In addition, the Pkr2(-/-) mice showed severe atrophy of the reproductive system, including the testis, ovary, uterus, vagina, and mammary gland. In the Pkr2(-/-) mice, the plasma levels of testosterone and follicle-stimulating hormone were decreased, and the mRNA transcription levels of gonadotropin-releasing hormone in the hypothalamus and luteinizing hormone and follicle-stimulating hormone in the pituitary were also significantly reduced. Immunohistochemical analysis revealed that gonadotropin-releasing hormone neurons were absent in the hypothalamus in the Pkr2(-/-) mice. The phenotype of the Pkr2(-/-) mice showed similarity to the clinical features of Kallmann syndrome, a human disease characterized by association of hypogonadotropic hypogonadism and anosmia. Our current findings demonstrated that physiological activation of PKR2 is essential for normal development of the OB and sexual maturation.
CFTRmutation combinations producing frequent complex alleles with different clinical and functional outcomes (2012)

Genotype-phenotype correlations in cystic fibrosis (CF) may be difficult to establish because of phenotype variability, which is associated with certain CF transmembrane conductance regulator (CFTR) gene mutations and the existence of complex alleles. To elucidate the clinical significance of complex alleles involving p.Gly149Arg, p.Asp443Tyr, p.Gly576Ala, and p.Arg668Cys, we performed a collaborative genotype-phenotype correlation study, collected epidemiological data, and investigated structure-function relationships for single and natural complex mutants, p.[Gly576Ala;Arg668Cys], p.[Gly149Arg;Gly576Ala;Arg668Cys], and p.[Asp443Tyr;Gly576Ala;Arg668Cys]. Among 153 patients carrying at least one of these mutations, only three had classical CF and all carried p.Gly149Arg in the triple mutant. Sixty-four had isolated infertility and seven were healthy individuals with a severe mutation in trans, but none had p.Gly149Arg. Functional studies performed on all single and natural complex mutants showed that (1) p.Gly149Arg results in a severe misprocessing defect; (2) p.Asp443Tyr moderately alters CFTR maturation; and (3) p.Gly576Ala, a known splicing mutant, and p.Arg668Cys mildly alter CFTR chloride conductance. Overall, the results consistently show the contribution of p.Gly149Arg to the CF phenotype, and suggest that p.[Arg668Cys], p.[Gly576Ala;Arg668Cys], and p.[Asp443Tyr;Gly576Ala;Arg668Cys] are associated with CFTR-related disorders. The present study emphasizes the importance of comprehensive genotype-phenotype and functional studies in elucidating the impact of mutations on clinical phenotype.
Anomaly Classification in People Counting and Occupancy Sensor Systems (2020)

People counting and occupancy sensor systems are used in diverse smart building applications like lighting controls, HVAC controls and workspace management. Anomalies in people counting and occupancy sensor data can result in undesirable application behavior. We address the problem of anomaly classification of sensor data using 3-class random forest classifiers in this work. We specifically consider sensor deployment scenarios where sensor fields-of-view may overlap. Depending on the sensor type, we devise signal features in time, frequency and spatio-temporal domains. The proposed random forest classifiers are evaluated using people counting and binary occupancy sensor data in an office environment, and are shown to have higher true positive rate and a lower false positive rate in comparison to an unsupervised k -means method and a random forest classifier with a single signal energy feature.
A First-Principles Investigation of the Driving Forces Defining the Selectivity of TiO2 Atomic Layer Deposition (2023)

Area-selective deposition (ASD) is a technique to deposit material only on a defined area of a prepatterned surface, while no deposition occurs on adjacent surface areas. It is the subject of intense investigations by the scientific and engineering communities as it offers the prospect to simplify and improve patterning processes for fabrication of nanoelectronic devices as well as to reduce the manufacturing costs. Numerous efforts have been dedicated to identify process conditions for highly selective ASD processes. Still, the search for optimal conditions is often an empirical process due to the limited understanding of the mechanisms that take place at the atomic scale. Understanding the links between precursor reactivity, surface treatments, and the reactor operating conditions could greatly contribute to the development of highly selective ASD processes. In this paper, we therefore combine first-principles calculations with statistical thermodynamics to understand the role of the precursors in area-selective TiO2 atomic layer deposition (ALD). First, we investigate the selectivity loss mechanisms for TiCl4/H2O ALD on SiO2 nongrowth surfaces with different surface terminations (e.g., OH groups and trimethylsilyl groups). We link the resulting thermodynamic driving forces to experimental reports. Subsequently, we extend the investigation to a total of 26 commercially available titanium precursors and to three different oxygen sources and rank their potential for TiO2 ASD for the SiO2 surfaces with different surface terminations (OH groups and trimethylsilyl groups). We find that the combination of TiCl4 with H2O offers the best performance in terms of selectivity. The theoretical approach proposed here is expected to greatly assist and accelerate the design of precursors for different ASD approaches.
Supplementary Table 2 from Global Evaluation of Eph Receptors and Ephrins in Lung Adenocarcinomas Identifies EphA4 as an Inhibitor of Cell Migration and Invasion (2023)

&lt;p&gt;PDF file, 94K, Multicovariate analysis showing the association between ephrin receptor and ephrin gene expression and overall survival or relapse-free survival in patients resected for a lung adenocarcinoma.&lt;/p&gt;
Performance Loss of Activated Carbon Electrodes in Capacitive Deionization: Mechanisms and Material Property Predictors (2020)

Understanding the material property origins of performance decay in carbon electrodes is critical to maximizing the longevity of capacitive deionization (CDI) systems. This study investigates the cycling stability of electrodes fabricated from six commercial and two post-processed activated carbons. We find that the capacity decay rate of electrodes in half cells is positively correlated with the specific surface area and total surface acidity of the activated carbons. We also demonstrate that half-cell cycling stability is consistent with full cell desalination performance durability. Additionally, our results suggest that increase in internal resistance and physical pore blockage resulting from extensive cycling may be important mechanisms for the specific capacitance decay of activated carbon electrodes in this study. Our findings provide crucial guidelines for selecting activated carbon electrodes for stable CDI performance over long-term operation and insight into appropriate parameters for electrode performance and longevity in models assessing the techno-economic viability of CDI. Finally, our half-cell cycling protocol also offers a method for evaluating the stability of new electrode materials without preparing large, freestanding electrodes.
Molecular Modeling Studies on G-Quadruplex Complexes of Telomerase Inhibitors:  Structure−Activity Relationships (1999)

Inhibition of the ability of the enzyme telomerase to add telomeric repeats to the end of chromosomes is a novel target for potential anticancer therapy. This paper examines the hypothesis that compounds possessing a planar aromatic chromophore inhibit telomerase via stabilization of, and binding to, a folded guanine quadruplex structure. Two series of telomerase inhibitors have been designed based on the 2,6-disubstituted amidoanthracene-9,10-dione and 3,6-disubstituted acridine chromophores in order to investigate structure-activity relationships between biological activity and substituent group size. The relative binding energies between these compounds and the folded human telomere DNA quadruplex were determined using molecular simulation methods, involving explicitly solvated structures. The results obtained are in excellent agreement with the biological activity as measured in vitro using a modified TRAP assay and in general agreement with the ranking order of binding enthalpies found in isothermal titration calorimetry studies. This broad agreement provides strong support for the hypothesis that guanine quadruplexes are the primary target for telomerase inhibitors with extended planar chromophores.
Operation of a femtosecond Ti:sapphire solitary laser in the vicinity of zero group-delay dispersion (1993)

We report the operating characteristics of a self-mode-locked Ti:sapphire solitary laser at reduced group-delay dispersion. The generation of asymptotically equal to 12.3 fs near-sech(2) optical pulses at 775 nm is reported, together with experimental evidence for the dominant role of third-order dispersion (TOD) as a limiting factor to further pulse shortening in the oscillator. At reduced second-order dispersion excessive residual TOD is shown to lead to dispersive wave generation, and the position of the dispersive resonance is used to determine the ratio of the net second- and third-order intracavity dispersions. Since the magnitude of TOD rapidly decreases with increasing wavelength in prism-pair dispersion-compensated resonators, the oscillator presented has the potential for producing sub-10-fs pulses in the 800-nm wavelength region.
Recherche de nouveaux régulateurs de la phase mitochondriale de l'apoptose : approche génétique chez la levure : approche pharmacologique in cellulo (2005)

L’apoptose est un evenement clef dans le maintien de l’integrite de l’organisme et peut etre implique dans des pathologies humaines. La comprehension des mecanismes de controle et l’identification de nouveaux regulateurs peut etre essentiel au developpemment de nouvelle stategies therapeutiques. L’objectif de cette these a ete d’identifier de nouveaux regulateurs de l’etape mitochondriale de l’apoptose. Trois axes de recherche ont ete explores :(i) L’etude de la cytotoxicite de Bax chez la levure. La surexpression de la proteine pro-apoptotique Bax induit la mort des cellules et une permeabilisation de la membrane externe mitochondriale (PMM). Une approche genetique chez la levure a permis de mettre en evidence l’implication du processus de l’autophagie dans la cytotoxicite induite par Bax. (ii) L’identification de la cible cellulaire du nelfinavir (NFV). Cet inhibiteur de la protease du virus de l’immunodeficience humaine (VIH) presente egalement un effet anti-apoptotique. L’approche in cellulo et biochimique a permis d’identifier la cible du NFV comme etant le translocateur a adenine, un des constituants du pore de transition de permeabilite. (iii) L’etude de la fonction pro-poptotique de la glyceraldehyde 3 phosphate deshydrogenase (GAPDH). La GAPDH est une proteine glycolitique egalement decrite pour intervenir dans l’apoptose. Dans ce contexte, nous avons montre qu’une augmentation de la GAPDH dans les mitochondries pouvait induire une activation de la PMM en interagissant avec la porine VDAC. L’utilisation de ces differentes approches a permis de caracteriser des regulateurs exogenes et endogenes de la phase mitochondriale de l’apoptose
Strengthening magnesium by design: integrating alloying and dynamic processing (2021)

Magnesium (Mg) has the lowest density of all structural metals and has excellent potential for wide use in structural applications. While pure Mg has inferior mechanical properties; the addition of further elements at various concentrations has produced alloys with enhanced mechanical performance and corrosion resistance. An important consequence of adding such elements is that the saturated Mg matrix can locally decompose to form solute clusters and intermetallic particles, often referred to as precipitates. Controlling the shape, number density, volume fraction, and spatial distribution of solute clusters and precipitates significantly impacts the alloy's plastic response. Conversely, plastic deformation during thermomechanical processing can dramatically impact solute clustering and precipitation. In this paper, we first discuss how solute atoms, solute clusters, and precipitates can improve the mechanical properties of Mg alloys. We do so by primarily comparing three alloy systems: Mg-Al, Mg-Zn, and Mg-Y-based alloys. In the second part, we provide strategies for optimizing such microstructures by controlling nucleation and growth of solute clusters and precipitates during thermomechanical processing. In the third part, we briefly highlight how one can enable inverse design of Mg alloys by a more robust Integrated Computational Materials Design (ICMD) approach.
Stimulation of fungal spore germination and inhibition of sporulation in fungal vegetative thalli by fatty acids and their volatile peroxidation products (1980)

As little as 200 parts per billion of 2,4-hexadienal in aerial solution stimulated germination of Alternaria alternata conidiospores in soil-imposed stasis. This compound, as well as trans-2-hexene-1-ol, and palmitic acid, stimulated germination of Fusarium solani f. sp. pisi conidiospores. Other 5- to 10-carbon aldehydes, ketones, and alcohols, as well as some 16- to 18-carbon aldehydes and fatty acids, stimulated germination of these spores at 10- or 100-fold higher concentrations. Chlamydospores of F. solanif. sp. pisi were stimulated to germinate by heptanal, octanal, nonanal,trans,trans-2,4-nonadienal, decanal, and undecanal at 20 000 or 20 0000 parts per billion in air, but not by any compound at lower concentrations. Compounds similar to those stimulating germination of conidiospores or chlamydospores inhibited sporulation of vegetative A. alternata thalli at concentrations as low as 800 parts per billion.
FBG-based multi-channel low dispersion WDM filters (2002)

Multi-channel FBGs for use as low dispersion WDM filters are reported. The filters are realised in a single section of optical fibre using superposition techniques and are designed for use in high-speed networks (10–40 Gbit/s) where they may be employed in OADM applications.