gebhart/patrepeval huggingface dataset:
Essential Roles for Soluble Virion-Associated Heparan Sulfonated Proteoglycans and Growth Factors in Human Papillomavirus Infections (2012)

A subset of human papillomavirus (HPV) infections is causally related to the development of human epithelial tumors and cancers. Like a number of pathogens, HPV entry into target cells is initiated by first binding to heparan sulfonated proteoglycan (HSPG) cell surface attachment factors. The virus must then move to distinct secondary receptors, which are responsible for particle internalization. Despite intensive investigation, the mechanism of HPV movement to and the nature of the secondary receptors have been unclear. We report that HPV16 particles are not liberated from bound HSPG attachment factors by dissociation, but rather are released by a process previously unreported for pathogen-host cell interactions. Virus particles reside in infectious soluble high molecular weight complexes with HSPG, including syndecan-1 and bioactive compounds, like growth factors. Matrix mellatoproteinase inhibitors that block HSPG and virus release from cells interfere with virus infection. Employing a co-culture assay, we demonstrate HPV associated with soluble HSPG-growth factor complexes can infect cells lacking HSPG. Interaction of HPV-HSPG-growth factor complexes with growth factor receptors leads to rapid activation of signaling pathways important for infection, whereas a variety of growth factor receptor inhibitors impede virus-induced signaling and infection. Depletion of syndecan-1 or epidermal growth factor and removal of serum factors reduce infection, while replenishment of growth factors restores infection. Our findings support an infection model whereby HPV usurps normal host mechanisms for presenting growth factors to cells via soluble HSPG complexes as a novel method for interacting with entry receptors independent of direct virus-cell receptor interactions.
Nonlinear reflectivity of semiconductor microcavities in the weak- and strong-coupling regimes: Experiment and theory (1996)

We use an entirely classical model to describe the nonlinear properties of semiconductor microcavities in both the weak- and strong-coupling regimes, as measured in a series of spectrally and temporally resolved pump-probe experiments. The model, which follows on from a linear dispersion model previously used to describe the linear properties, provides very good qualitative agreement between a wide range of experimental and theoretical spectra. We also find that on the time scales of our observation (tens of picoseconds), the model provides an excellent description of the complex temporal evolution of the nonlinear spectra.
PhysGNN: A Physics-Driven Graph Neural Network Based Model for\n Predicting Soft Tissue Deformation in Image-Guided Neurosurgery (2021)

Correctly capturing intraoperative brain shift in image-guided neurosurgical\nprocedures is a critical task for aligning preoperative data with\nintraoperative geometry for ensuring accurate surgical navigation. While the\nfinite element method (FEM) is a proven technique to effectively approximate\nsoft tissue deformation through biomechanical formulations, their degree of\nsuccess boils down to a trade-off between accuracy and speed. To circumvent\nthis problem, the most recent works in this domain have proposed leveraging\ndata-driven models obtained by training various machine learning algorithms --\ne.g., random forests, artificial neural networks (ANNs) -- with the results of\nfinite element analysis (FEA) to speed up tissue deformation approximations by\nprediction. These methods, however, do not account for the structure of the\nfinite element (FE) mesh during training that provides information on node\nconnectivities as well as the distance between them, which can aid with\napproximating tissue deformation based on the proximity of force load points\nwith the rest of the mesh nodes. Therefore, this work proposes a novel\nframework, PhysGNN, a data-driven model that approximates the solution of the\nFEM by leveraging graph neural networks (GNNs), which are capable of accounting\nfor the mesh structural information and inductive learning over unstructured\ngrids and complex topological structures. Empirically, we demonstrate that the\nproposed architecture, PhysGNN, promises accurate and fast soft tissue\ndeformation approximations, and is competitive with the state-of-the-art (SOTA)\nalgorithms while promising enhanced computational feasibility, therefore\nsuitable for neurosurgical settings.\n
A molecular dynamics study of catestatin docked on nicotinic acetylcholine receptors to identify amino acids potentially involved in the binding of chromogranin A fragments (2015)

Catestatin, a cationic and hydrophobic 21-amino acid fragment of chromogranin A, is known to be a non-competitive nicotinic antagonist acting through nicotinic acetylcholine receptors (nAChRs) to inhibit catecholamine release. Since this receptor is the target of several neuronal and non-neuronal disorder prophylaxes and treatments, this study aims at the elucidation of the binding of human catestatin to the entire nAChR reconstructed in lipid bilayers by means of docking followed by full atomistic molecular dynamics simulations. The obtained results show that the minimum free energy for the binding of the peptide and the receptor attains minimal values for locations at the pore site and in the outer beta subunit. This result is consistent with previous studies showing that catestatin occludes the pore opening. A new finding is an additional even stronger binding seat at the beta subunit and that membrane presence could be an important factor. Specific amino acids involved in catestatin binding have been identified, indicating targets for point mutation studies. In addition to improving the understanding of the interaction between the peptide and muscle-type and even other nAChR subtypes, the results of this study provide directions for future peptidomimetic research.
Acute mechanisms underlying antibody effects in anti–N‐methyl‐D‐aspartate receptor encephalitis (2014)

Our data support an antibody-mediated mechanism of disease pathogenesis driven by immunoglobulin-induced receptor internalization. Antibody-mediated downregulation of surface NMDARs engages homeostatic synaptic plasticity mechanisms, which may inadvertently contribute to disease progression.
Oxidative activity of cytoplasmic particles of apples: Krebs cycle oxidations, oxidative phosphorylation, & cytochromes (1961)

Previous studies of procedures for isolating apple mitochondria showed the importance of pH during homogenization of the tissues (12,13). Virtually no mitochondrial activity could be detected in particles from neutral homogenates. Highest comparative rates of reduced diphosphopyridine nucleotide (DPNH) oxidase, DPNHcytochrome c reductase, diaph-orase, and cytochrome oxidase were recorded with particles from pH 9.9 homogenates. Maximal succinoxidase and succinic-cytochrome c reductase activities were found in particles from pH 8.4 homogenates. These particles were, therefore, characterized with respect to their electron transport chain activities. The purpose of the present study is to further characterize these apple particles and establish whether or not they can be identified as mitochondria. It will be shown that Krebs cycle activity, oxidativephosphorylation, and cytochrome spectra, typical of other plant mitochondria, can be demonstrated with some of these particles. These data thus provide presumptive evidence for the presence of mitochondria in apple pulp tissue.
Sites of Labeling with N-(3-Pyrene)Maleimide on Ca2+-Transporting ATPase of the Sarcoplasmic Reticulum1 (1995)

The characteristics of the interaction between N-(3-pyrene)maleimide (PMI) and the sarcoplasmic reticulum (SR) membranes were investigated, and the sites of labeling with PMI on Ca(2+)-transporting ATPase were identified. PMI was dissolved in the membrane lipids before reacting with the ATPase protein. The measurement of resonance energy transfer from PMI to 1-(dimethylaminophenyl)-6-phenyl-1,3,5-hexatriene revealed that the pyrene moiety of PMI stayed in the lipid layer after it had been covalently attached to the ATPase molecule. PMI-labeled SR membranes at an average labeling density of 1 mol PMI/mol ATPase were digested with trypsin, and the labeled peptides were purified through a series of reversed-phase HPLC procedures on C18 and C4 columns. The amino acid analysis of the purified peptides revealed multiple cysteine residues mainly distributed over the C-terminal half of the cytoplasmic domain of the ATPase molecule as the targets of PMI. This implied that PMI molecules mediated cross-linking between the cytoplasmic domain of the ATPase molecule and the membranes. The distortion of the structure of the former due to this cross-linking may explain the uncoupling of ATP-splitting from Ca(2+)-transport caused by PMI.
[On the crystallisation of amphetaminil base into its hydrochloride salt (author's transl)]. (1975)

In an aqueous medium in the presence of hydrochloric acid, amphetaminil (AN 1¿R) directly crystallises into the needle forming hydrochloride. The hydrochloride and base of the substance AN 1 have the same degree of insolubility in water. Such a reaction is relatively seldom observed in organic substances. Correspondingly, there is no similarity between the physical and chemical reactions of AN 1 and other well-known substances. In order to attain suitable judgement on the pharmaceutical/dynamic effect of AN 1, the clinical results known to date should not be disregarded.
A compact C-band bandpass filter using one eighth substrate integrated waveguide resonator (2012)

In this paper, a triangular shaped resonator which is one eighth of a square substrate integrated waveguide (SIW) cavity is used to design a novel miniaturized C-band bandpass filter. With the proposed one eighth SIW resonator (ESIWR) and new coupling structures, a conventional SIW filter can be reduced in size by about 87.5%. A four pole ESIWR filter with a center frequency of 5.8GHz and a fractional bandwidth of 8% is implemented. Good agreement between simulated and measured results demonstrates the validity of the proposed method.
Extreme-ultraviolet high-order harmonic pulses in the microjoule range (2002)

We study high-order harmonic generation at a high pumping energy using a long focal length lens. We identify different saturation regimes of the harmonic emission, revealing the interplay between phase matching, absorption, and laser defocusing. In the optimal conditions, high conversion efficiencies are obtained, resulting in an increase of at least one order of magnitude of the harmonic energies compared to previously reported values. In xenon, microjoule energies are reached, opening new perspectives for the applications of this ultrashort coherent radiation.
Omadacycline Gut Microbiome Exposure Does Not Induce Clostridium difficile Proliferation or Toxin Production in a Model That Simulates the Proximal, Medial, and Distal Human Colon (2018)

A clinically reflective model of the human colon was used to investigate the effects of the broad-spectrum antibiotic omadacycline on the gut microbiome and the subsequent potential to induce simulated <i>Clostridium difficile</i> infection (CDI). Triple-stage chemostat gut models were inoculated with pooled human fecal slurry from healthy volunteers (age, ≥60 years). Models were challenged twice with 10<sup>7</sup> CFU <i>C. difficile</i> spores (PCR ribotype 027). Omadacycline effects were assessed in a single gut model. Observations were confirmed in a parallel study with omadacycline and moxifloxacin. Antibiotic instillation was performed once daily for 7 days. The models were observed for 3 weeks postantibiotic challenge. Gut microbiota populations and <i>C. difficile</i> total viable and spore counts were enumerated daily by culture. Cytotoxin titers and antibiotic concentrations were also measured. Gut microbiota populations were stable before antibiotic challenge. Moxifloxacin instillation caused an ∼4 log<sub>10</sub> CFU/ml decline in enterococci and <i>Bacteroides fragilis</i> group populations and an ∼3 log<sub>10</sub> CFU/ml decline in bifidobacteria and lactobacilli, followed by simulated CDI (vegetative cell proliferation and detectable toxin). In both models, omadacycline instillation decreased populations of bifidobacteria (∼8 log<sub>10</sub> CFU/ml), <i>B. fragilis</i> group populations (7 to 8 log<sub>10</sub> CFU/ml), lactobacilli (2 to 6 log<sub>10</sub> CFU/ml), and enterococci (4 to 6 log<sub>10</sub> CFU/ml). Despite these microbial shifts, there was no evidence of <i>C. difficile</i> bacteria germination or toxin production. In contrast to moxifloxacin, omadacycline exposure did not facilitate simulated CDI, suggesting this antibiotic may have a low propensity to induce CDI in the clinical setting.
The value of non-invasive measurement of cardiac output and total peripheral resistance to categorize significant changes of intradialytic blood pressure: a prospective study (2018)

This technology provides multi-dimensional insight into intradialytic hemodynamic parameters, which may be more informative than blood pressure only. Using hemodynamic parameters to describe patients' status is more specific and accurate, and could help to work out specific and effective therapeutic actions according to underlying abnormalities.
ChemInform Abstract: SYNTHESIS OF 1,4‐BENZODIOXINS (1978)

Abstract Die Bromierung der Benzodioxane (I) mit N‐Brom‐succinimid liefert in Gegenwart von radikalischen Initiatoren die Dibromverbindungen (II), die mit Nal zu (III) dehydrobromiert werden können.
A Finite State Transducer (FST) based Font Converter (2012)

This paper describes the rule based approach towards the development of an Oriya Font Converter that effectively converts the SAMBAD and AKRUTI proprietary font to standardize Unicode font. This can be very much helpful towards electronic storage of information in the native language itself, proper search and retrieval. Our approach mainly involves the Apertium machine translation tool that uses Finite State Transducers for conversion of symbolic data to standardized Unicode Oriya font. To do so it requires a map table mapping the commonly used Oriya syllables in Proprietary font to its corresponding font code and the dictionary specifying the rules for mapping the proprietary font code to Unicode font. Further some unhandled symbols that appear in the intermediate converted file are rectified by Flex scanner tool. The converted text thus obtained is in standard Unicode font and remains unchanged as Unicode font is supported by almost all the platforms.
An E-Machine workbench (1983)

The development environment for microprogramming an implementation (E-Machine) of the Burroughs stack architecture (E-Mode) is discussed with an overview of a supporting hardware organization (the Alpha machine). The set of information-sharing tools in the E-Machine workbench, especially the structured language Ohne, is described and a sample E-Mode operator is used to illustrate several of these tools.
Conversion of Amines to Imines Employing Polymer‐Supported Sulfoxide (PSS) and Polymer‐Supported Perruthenate (PSP): Synthesis of Pyrrolo[2,1‐c][1,4]benzodiazepines. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Impact of Supersaturation Ratio on the Kinetics of Gas Evolution at Elevated Pressures (2020)

The kinetics of gas evolution in supersaturated solutions is a critical uncertainty in the design and operation of gas/liquid separators. Incorrectly predicting the amount of gas that evolves in a gas/liquid separator can lead to gas carry under with the liquid, resulting in equipment damage downstream of the separator. Central to addressing this problem is the measurement of the gas evolution rate at specific levels of supersaturation. The supersaturation ratio (S) is defined as S=Pg,oPg,ss−1, where Pg,o is the pressure before depressurization and Pg,ss is the pressure after depressurization. Exxsol D-110, a model oil, was used as the liquid phase, and methane was used as the gaseous phase. The rate of gas evolution was investigated at six supersaturation ratios (0.15, 0.30, 0.70, 1.30, 2.00, and 2.83) and at three different rates of energy dissipation (mixing speeds: 100, 250, and 500 rpm). The rate of gas absorption into the oil was within 20% of the rate of gas evolution up to a supersaturation ratio of 1.30. At a supersaturation ratio of 2.83, the rate of gas evolution was higher than the rate of absorption. At a supersaturation ratio of 2.00, the rate of gas evolution was higher than the rate of absorption only at 500 rpm. Thus, the supersaturation ratio and the rate of energy dissipation (mixing speed/shear environment) are key parameters that affect the rate of gas evolution.
When Infants Wail: Frustration and Gender as Variables in Distress Disclosure (1995)

Gender and differences in self-disclosure following a frustrating event were investigated. The Emotional Self-Disclosure Scale assessed the extent to which 100 male college students and 100 female college students were willing to disclose their emotions. The frustrating stimulus presented was a tape of an infant crying, played at 85 dB for 10 min. Men exposed to the noxious stimulus were less willing to disclose than men who were not. All of the men were less willing than the women to disclose in either condition. Women in the two conditions showed no differences in disclosure. These findings are interpreted with respect to how disclosure is affected by the immediate environment and with respect to male-female differences.
Phospho-Akt Overexpression in Non–Small Cell Lung Cancer Confers Significant Stage-Independent Survival Disadvantage (2004)

Overexpression of pAkt is an independent prognostic factor. Additional studies of human NSCLCs are warranted to drive the development of targeted tumor-specific antineoplastic therapies.
How Potent are Evasion Attacks for Poisoning Federated Learning-Based Signal Classifiers? (2023)

There has been recent interest in leveraging federated learning (FL) for radio signal classification tasks. In FL, model parameters are periodically communicated from participating devices, training on their own local datasets, to a central server which aggregates them into a global model. While FL has privacy/security advantages due to raw data not leaving the devices, it is still susceptible to several adversarial attacks. In this work, we reveal the susceptibility of FL-based signal classifiers to model poisoning attacks, which compromise the training process despite not observing data transmissions. In this capacity, we develop an attack framework in which compromised FL devices perturb their local datasets using adversarial evasion attacks. As a result, the training process of the global model significantly degrades on in-distribution signals (i.e., signals received over channels with identical distributions at each edge device). We compare our work to previously proposed FL attacks and reveal that as few as one adversarial device operating with a low-powered perturbation under our attack framework can induce the potent model poisoning attack to the global classifier. Moreover, we find that more devices partaking in adversarial poisoning will proportionally degrade the classification performance.
RSBP-1 Is a Membrane-targeting Subunit Required by the Gαq-specific But Not the Gαo-specific R7 Regulator of G protein Signaling inCaenorhabditis elegans (2009)

Regulator of G protein signaling (RGS) proteins inhibit G protein signaling by activating Galpha GTPase activity, but the mechanisms that regulate RGS activity are not well understood. The mammalian R7 binding protein (R7BP) can interact with all members of the R7 family of RGS proteins, and palmitoylation of R7BP can target R7 RGS proteins to the plasma membrane in cultured cells. However, whether endogenous R7 RGS proteins in neurons require R7BP or membrane localization for function remains unclear. We have identified and knocked out the only apparent R7BP homolog in Caenorhabditis elegans, RSBP-1. Genetic studies show that loss of RSBP-1 phenocopies loss of the R7 RGS protein EAT-16, but does not disrupt function of the related R7 RGS protein EGL-10. Biochemical analyses find that EAT-16 coimmunoprecipitates with RSBP-1 and is predominantly plasma membrane-associated, whereas EGL-10 does not coimmunoprecipitate with RSBP-1 and is not predominantly membrane-associated. Mutating the conserved membrane-targeting sequence in RSBP-1 disrupts both the membrane association and function of EAT-16, demonstrating that membrane targeting by RSBP-1 is essential for EAT-16 activity. Our analysis of endogenous R7 RGS proteins in C. elegans neurons reveals key differences in the functional requirements for membrane targeting between members of this protein family.
An Attractant Trap for Autodissemination of Entomopathogenic Fungi into Populations of the Japanese Beetle Popillia japonica (Coleoptera: Scarabaeidae) (1999)

Autodissemination may be effective against the Japanese beetle, Popillia japonica Newman, in situations where habitats of its larvae are inaccessible. Trapping systems with attractants for both male and female Japanese beetles are commercially available. We fabricated an inoculation chamber which fits between the top of a standard Trece Catch CanTM Japanese beetle Trap and its holding canister. Beetles which are attracted to the trap fall through a hole in the inoculation chamber and land on a mesh screen. A partial funnel and canister attachment from a metal Ellisco Japanese Beetle Trap was secured beneath a hole in the floor at the opposite end of the chamber. A 10-cm section in the middle of the box, between the entrance hole in the roof and the exit hole in the floor, allows space for a dish containing the inoculum to be placed into the chamber through a door in the side of the unit. The trap has been tested with Metarhizium anisopliae (Metschnikoff) Sorokin as the pathogen. Beetles emerging from the device in the field were captured and returned to the laboratory where the presence of conidia and mortality to adult beetles from the fungus were confirmed. Keywords: Microbial ControlMetarhizium AnisopliaeInoculative ReleaseEntomopathogenAutodisseminationPopillia Japonica
Compiling Functional Parllelism on a Family of Distributed Memory Architectures (1994)

In an earlier work, a Threshold Scheduling Algorithm was proposed to schedule the functional parallelism in a program on distributed memory systems. In this work, we address the issue of regeneration of the schedule for a set of distributed memory architectures with different communication costs. A new concept of dominant edges of a schedule is introduced to denote those edges which dictate schedule regeneration due to the changes in their communication costs. It is shown that under certain conditions, schedule on the whole or at least part of the graph can be reused for a different architecture reducing the cost of program re-partitioning and re-scheduling. The usefulness of this method is demonstrated by incorporating it in the scheduler of the compiler backend for targeting Sisal (Streams and Iterations in a Single Assignment Language) on a family of Intel i860 architectures : Gamma, Delta and Paragon which vary in their communication costs. It is shown that almost SO to 65 % of the schedule can be reused, thereby, avoiding program re-partitioning to a large degree.