gebhart/patrepeval huggingface dataset:
Electron Transfer and Ligand Binding to Cytochrome c‘ Immobilized on Self-Assembled Monolayers (2006)

We have successfully immobilized Allochromatium vinosum cytochrome c' on carboxylic acid-terminated thiol monolayers on gold and have investigated its electron-transfer and ligand binding properties. Immobilization could only be achieved for pH's ranging from 3.5 to 5.5, reflecting the fact that the protein is only sufficiently positively charged below pH 5.5 (pI = 4.9). Upon immobilization, the protein retains a near-native conformation, as is suggested by the observed potential of 85 mV vs SHE for the heme FeIII/FeII transition, which is close to the value of 60 mV reported in solution. The electron-transfer rate to the immobilized protein depends on the length of the thiol spacer, displaying distance-dependent electron tunneling for long thiols and distance-independent protein reorganization for short thiols. The unique CO-induced dimer-to-monomer transition observed for cytochrome c' in solution also seems to occur for immobilized cytochrome c'. Upon saturation with CO, a new anodic peak corresponding to the oxidation of an FeII-CO adduct is observed. CO binding is accompanied by a significant decrease in protein coverage, which could be due to weaker electrostatic interactions between the self-assembled monolayer and cytochrome c' in its monomeric form as compared to those in its dimeric form. The observed CO binding rate of 24 M-1 s-1 is slightly slower than the binding rate in solution (48 M-1 s-1), which could be due to electrostatic protein-electrode interactions or could be the result of protein crowding on the surface. This study shows that the use of carboxyl acid-terminated thiol monolayers as a protein friendly method to immobilize redox proteins on gold electrodes is not restricted to cytochrome c, but can also be used for other proteins such as cytochrome c'.
Design of a plate type multi-DOF ultrasonic motor and its driving characteristics (2004)

Multi-DOF actuators have become more useful in the field of robotics, thanks to the increasing number of DOFs of systems. General features of ultrasonic motor are suitable for constructing a direct-drive multi-DOF actuator. However, those previously developed do not have advantages in volume and weight against the multi-DOF motion unit composed of several electromagnetic motors. In the present study authors develop a novel multi-DOF ultrasonic motor with a plate stator and a spherical rotor. First, a new driving principle of the motor is proposed. Next, the stator geometry is designed in detail using finite element method, and the prototype of the multi-DOF ultrasonic motor with plate stator is produced. The stator is relatively compact against the rotor. Then, vibration characteristics of the stator and driving characteristics of the motor have been measured, respectively. The result confirms that the motor successfully provides the multi-DOF motion of rotor around orthogonal axes by single plate stator. Finally, self-oscillation driving circuit for the motor is proposed.
Functional mechanical behavior of the murine pulmonary heart valve (2023)

Genetically modified mouse models provide a versatile and efficient platform to extend our understanding of the underlying disease processes and evaluate potential treatments for congenital heart valve diseases. However, applications have been limited to the gene and molecular levels due to the small size of murine heart valves, which prohibits the use of standard mechanical evaluation and in vivo imaging methods. We have developed an integrated imaging/computational mechanics approach to evaluate, for the first time, the functional mechanical behavior of the murine pulmonary heart valve (mPV). We utilized extant mPV high resolution µCT images of 1-year-old healthy C57BL/6J mice, with mPVs loaded to 0, 10, 20 or 30 mmHg then chemically fixed to preserve their shape. Individual mPV leaflets and annular boundaries were segmented and key geometric quantities of interest defined and quantified. The resulting observed inter-valve variations were small and consistent at each TVP level. This allowed us to develop a high fidelity NURBS-based geometric model. From the resultant individual mPV geometries, we developed a mPV shape-evolving geometric model (SEGM) that accurately represented mPV shape changes as a continuous function of transvalvular pressure. The SEGM was then integrated into an isogeometric finite element based inverse model that estimated the individual leaflet and regional mPV mechanical behaviors. We demonstrated that the mPV leaflet mechanical behaviors were highly anisotropic and nonlinear, with substantial leaflet and regional variations. We also observed the presence of strong axial mechanical coupling, suggesting the important role of the underlying collagen fiber architecture in the mPV. When compared to larger mammalian species, the mPV exhibited substantially different mechanical behaviors. Thus, while qualitatively similar, the mPV exhibited important functional differences that will need to accounted for in murine heart valve studies. The results of this novel study will allow detailed murine tissue and organ level investigations of semi-lunar heart valve diseases.
p53-abhängige und -unabhängige Apoptose als molekulare Mechanismen des Amanitin-induzierten Leberversagens (2006)

Einleitung: 95% aller tödlich verlaufenden Pilzvergiftungen sind die Folge des Verzehrs von Knollenblätterpilzen. Die typische Symptomatik lässt sich hauptsächlich auf die Wirkung von Amanitinen zurückführen. Amanitine führen zum Absterben von Zellen mit raschem Proteinumsatz wie Hepatozyten. Nach bisherigem Kenntnisstand ist die Wirkung der Amanitine hauptsächlich auf eine Hemmung der RNA-Polimerase II zurückzuführen. Wir konnten zeigen, dass die lebertoxische Wirkung von Amanitin auf der Induktion von Apoptose beruht. Wir haben die durch Amanitin in Hepatozyten aktivierten Apoptose-Signalwege weiter charakterisiert.
Muscarinic, Ca++ antagonist and specific butyrylcholinesterase inhibitory activity of dried ginger extract might explain its use in dementia (2008)

Abstract Ginger rhizome (Zingiber officinale) has been used for centuries to treat dementia in South Asia. This study was undertaken to possibly justify its use. A 70% aqueous/methanolic extract of dried ginger (Zo.Cr) was used. Zo.Cr tested positive for the presence of terpenoids, flavonoids, secondary amines, phenols, alkaloids and saponins. When tested on isolated rat stomach fundus, Zo.Cr showed a spasmogenic effect (0.03–5.00 mg mL−1); it relaxed the tissue at concentrations ≥5 mg mL−1. The stimulant effect was resistant to blockade by hexamethonium and methysergide, but sensitive to atropine, indicating activity via muscarinic receptors. In atropinized (0.1 μM) preparations, Zo.Cr (0.3–3.0 mg mL−1) relaxed high K+ (80 mm)-induced contractions, indicating Ca++ antagonism in addition to the muscarinic effect. This possible Ca++ antagonist activity was investigated in Ca++-free conditions, with the inhibitory effect of the extract tested against contractions induced by externally administered Ca++. Zo.Cr (0.1–0.3 mg mL−1), similar to verapamil (0.03–0.10 μm), shifted the contractions induced by externally administered Ca++ to the right, thus suggesting an inhibitory interaction between Zo.Cr and voltage-operated Ca++ channels. Zo.Cr (0.1–3.0 μg mL−1) also potentiated acetylcholine peak responses in stomach fundus, similar to physostigmine, a cholinesterase inhibitor. Zo.Cr, in an in-vitro assay, showed specific inhibition of butyrylcholinesterase (BuChE) rather than acetylcholinesterase enzyme. Different pure compounds of ginger also showed spasmolytic activity in stomach fundus, with 6-gingerol being the most potent. 6-Gingerol also showed a specific anti-BuChE effect. This study shows a unique combination of muscarinic, possible Ca++ antagonist and BuChE inhibitory activities of dried ginger, indicating its benefit in dementia, including Alzheimer's disease.
Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system (2004)

Shiga toxin (Stx) genes in Stx producing Escherichia coli (STEC) are encoded in prophages of the lambda family, such as H-19B. The subpopulation of STEC lysogens with induced prophages has been postulated to contribute significantly to Stx production and release. To study induced STEC, we developed a selectable in vivo expression technology, SIVET, a reporter system adapted from the RIVET system. The SIVET lysogen has a defective H-19B prophage encoding the TnpR resolvase gene downstream of the phage PR promoter and a cat gene with an inserted tet gene flanked by targets for the TnpR resolvase. Expression of resolvase results in excision of tet, restoring a functional cat gene; induced lysogens survive and are chloramphenicol resistant. Using SIVET we show that: (i) approximately 0.005% of the H-19B lysogens are spontaneously induced per generation during growth in LB. (ii) Variations in cellular physiology (e.g. RecA protein) rather than in levels of expressed repressor explain why members of a lysogen population are spontaneously induced. (iii) A greater fraction of lysogens with stx encoding prophages are induced compared to lysogens with non-Stx encoding prophages, suggesting increased sensitivity to inducing signal(s) has been selected in Stx encoding prophages. (iv) Only a small fraction of the lysogens in a culture spontaneously induce and when the lysogen carries two lambdoid prophages with different repressor/operators, 933W and H-19B, usually both prophages in the same cell are induced.
Safety and Efficacy of Activated Transfected Killer Cells for Neutropenic Fungal Infections (2010)

These results lay the groundwork for continued translational development of this promising, novel technology for the treatment of refractory infections in neutropenic hosts.
Ultrasound Contrast Agents For Ultrasound Molecular Imaging (2014)

Ultrasound is a real-time imaging technique which is widely used in many clinical applications for its capacity to provide anatomic information with high spatial and temporal resolution. The advent of ultrasound contrast agents in combination with contrast-specific imaging modes has given access to perfusion assessments at an organ level, leading to an improved diagnostic accuracy. More recently, the development of biologically-targeted ultrasound contrast agents has expanded the role of ultrasound even further into molecular imaging applications. Ultrasound molecular imaging can be used to visualize the expression of intravascular markers, and to assess their local presence over time and/or during therapeutic treatment. Major applications are in the field of inflammation and neoangiogenesis due to the strictly intravascular presence of microbubbles. Various technologies have been investigated for attaching the targeting moiety to the shell from simple biotin-avidin constructs to more elaborated insertion within the shell through attachment to PEG residues. This important improvement has allowed a clinical translation of initial pre-clinical investigations, opening the way for an early detection and an accurate characterization of lesions in patients. The combination of anatomic, functional and molecular information/data provided by contrast ultrasound is a powerful tool which is still in its infancy due to the lack of agents suitable for clinical use. The advantages of ultrasound techniques combined with the molecular signature of lesions will represent a significant advance in imaging in the field of personalized medicine.
Variation in serum prostate‐specific antigen levels in men with prostate cancer managed with active surveillance (2015)

We observed a high probability of variability in PSA levels for patients on AS. The probability of changes in PSA, defined by an increase to the specified thresholds or a rise >1 ng/mL within 6 months and subsequent decrease of equal or greater value on a subsequent measurement, increases over time; therefore, a single change in PSA level is not a reliable endpoint for patients on AS.
Transfection of Fibroblasts by Cloned Abelson Murine Leukemia Virus DNA and Recovery of Transmissible Virus by Recombination with Helper Virus (1982)

A cloned, permuted DNA copy of the Abelson murine leukemia virus (A-MuLV) genome was capable of eliciting the morphological transformation of NIH/3T3 fibroblasts when applied to cells in a calcium phosphate precipitate. The efficiency of the process was extremely low, yielding approximately one transformant per microgram of DNA under conditions which give 10(4) transfectants per microgram of other DNAs (e.g., Moloney sarcoma virus proviral DNA). The DNA was able to induce foci, even though the 3' end of the genome was not present. The transforming gene was thus localized to the 5' portion of the genome. The transformed cells all produced viral RNA and the virus-specific P90 protein. Transmissible virus could be rescued from these cells at very low frequencies by superinfection with helper virus; the rescued A-MuLV virus had variable 3' ends apparently derived by recombination with the helper. Dimerization of the permuted A-MuLV cloned genome to reconstruct a complete provirus did not improve transformation efficiency. Virus could be rescued from these transformants, however, at a high efficiency. Cotransfection of the permuted A-MuLV DNA with proviral M-MuLV DNA yielded a significant increase in the efficiency of transformation and cotransfection of dimeric A-MuLV and proviral M-MuLV resulted in a high-efficiency transformation yielding several thousand more transformants per microgram than A-MuLV DNA alone. We propose that helper virus efficiently rescues A-MuLV from transiently transfected cells which would not otherwise have grown into foci. We hypothesize that multiple copies of A-MuLV DNA introduced into cells by transfection are toxic to cells. In support of this hypothesis, we have shown that A-MuLV DNA sequences can inhibit the stable transformation of cells by other selectable DNAs.
Phage-Displayed Mimotopes Recognizing a Biologically Active Anti–HIV-1 gp120 Murine Monoclonal Antibody (2002)

Antibody-dependent cellular cytotoxicity (ADCC) is a host defense mechanism in which Fc receptor-bearing effector cells in combination with antigen-specific antibodies recognize and kill antigen-expressing target cells. The authors previously described a murine monoclonal antibody (MAb-ID6) that mediated ADCC activity against HIV-infected cells. It was demonstrated that the specificity of MAb-ID6 maps to the first 204 amino acids of gp120; however, the exact epitope was not identified. In the present work, by screening phage display libraries with MAb-ID6, the authors have mapped the corresponding epitope to amino acids 86-100 (HIV-1 gp120 sequence). This epitope lies within the C1 region of gp120 and is highly conserved among all subtypes and circulating recombinant forms of HIV-1. Thus, these phage mimotopes of C1 may serve as components of a vaccine for the induction of gp120-specific antibodies mimicking MAb-ID6.
21st Century Locomotive Technology: Quarterly Technical Status Report 6 DOE/AL68284-TSR06 (2004)

Experimental work to map the performance of the High Pressure Common Rail (HPCR) system on a locomotive is in progress. The experimental trends agree with KIVA modeling predictions. Injection optimization is in progress. Electrically-assisted turbocharger modeling was used to study passenger locomotive performance improvements. Energy storage cycling life testing began, and an improved battery state algorithm was determined. The hybrid locomotive energy storage was prepared for energy management system algorithm testing. Progress in reliable methods for computing optimal driving plans, and methods to reduce the complexity of the necessary optimization are reported.
Supramolecular Loop Stitches of Discrete Block Molecules on Graphite: Tunable Hydrophobicity by Naphthalenediimide End-Capped Oligodimethylsiloxane (2018)

The noncovalent functionalization of surfaces has gained widespread interest in the scientific community, and it is progressively becoming an extremely productive research field offering brand new directions for both supramolecular and materials chemistry. As the end-groups often play a dominant role in the surface properties obtained, creating loops with end-groups only at the surface will lead to unexpected architectures and hence properties. Here we report the self-assembly of discrete block molecules-structures in-between block copolymers and liquid crystals-featuring oligodimethylsiloxanes (ODMS) end-capped with naphthalenediimides (NDIs) at the 1-phenyloctane/highly oriented pyrolytic graphite (1-PO/HOPG) interface. These structures produce unprecedented vertically nanophase-separated monolayers featuring NDI moieties that regularly arrange on the HOPG surface, while the highly dynamic ODMS segments form loops above them. Such arrangement is preserved upon drying and generates hydrophobic HOPG substrates in which the ODMS block length tunes the hydrophobicity. Thus, the exact structural fidelity of the discrete macromolecules allows for the correlation of nanoscopic organization with macroscopic properties of the self-assembled materials. We present a general strategy for tunable hydrophobic coatings on graphite based on molecularly combining crystalline aromatic moieties and immiscible oligodimethylsiloxanes.
<title>Born type iterative method for imaging of heterogeneous scattering media and its application to simulated breast tissue</title> (1997)

In this paper, we present a Born-Type iterative algorithm for reconstruction of absorption and diffusion coefficient distributions of a heterogeneous scattering medium. This method is derived based on the integral form of the diffusion equation for the photon flux. It takes into account the nonlinear nature of the problem by using an iterative perturbation approach. Within each iteration, the forward problem (update of the total field and Green's function) is solved by the finite element method (FEM), and the inverse problem (update of the medium properties) is obtained by a regularized least squares method. This method has been used to reconstruct 'pathologies' embedded in an inhomogeneous test medium simulating a normal female breast from frequency domain data. The test medium is constructed by assigning optical coefficients according to an MR derived anatomical map. Our simulation results show that the algorithm is computationally practical and can yield qualitatively and quantitatively correct absorption and scattering distributions of embedded objects from simulated data with up to 5% additive noise in the simulated measurement data.
Multiple correlations and high-transverse-momentum jets in 147-GeV/cπ−pinteractions (1981)

We examine multiparticle correlations in a ${\ensuremath{\pi}}^{\ensuremath{-}}p$ experiment at 147 GeV/c performed by the Proportional Hybrid System Consortium. The major aim of this paper is to demonstrate the existence of clusters in our data. We use different statistical algorithms to assemble into clusters the particles in each event which are associated by virtue of small relative angles. We find that these clusters are stable against different choices of metric and/or algorithm, and reproduce the effects previously observed in the data corresponding to clusters. Some of these clusters have properties similar to high-${p}_{T}$ jets. A detailed study of these jetlike clusters is described, and comparisons with some counter experiments are discussed.
TRPV4 and Drug Discovery (2012)

Transient receptor potential vanilloid 4 (TRPV4) was first identified in 2000 as an osmolarity sensor. Further investigations rapidly revealed this ion channel to be a polymodal receptor with additional activating or modulating stimuli including warm temperatures, endogenous lipids, and phosphorylation. The broad tissue and cell type distribution of TRPV4, coupled with its varied activation profile, lead to a wide variety of physiological roles. These include sheer stress detection in blood vessels, osteoclast differentiation control in bone, along with temperature monitoring in skin keratinocytes and osmolarity sensing in kidneys. Recent work has also implicated TRPV4 mutations in multiple genetic disorders such as brachyolmia and Charcot–Marie–Tooth disease 2C. Characterization of its roles in disease states naturally led to a rising interest in the modulation of TRPV4 for therapeutic purposes. Therapeutic areas of interest are diverse and include several with significant unmet medical needs such as inflammatory and neuropathic pain, bladder dysfunctions, as well as mechanical lung injury. Herein we review the roles of TRPV4 in pathologies and summarize the progress made in identifying small molecule modulators of its activity for target validation and therapeutic purposes.
In Situ Real-Time Monitoring of ITO Film under a Chemical Etching Process Using Fourier Transform Electrochemical Impedance Spectroscopy (2020)

As a novel approach to the in situ real-time investigation of an ITO electrode during the wet etching process, step-excitation Fourier-transform electrochemical impedance spectroscopy (FT-EIS) was implemented. The equivalent circuit parameters (e.g., <i>R</i><sub>ct</sub>, <i>C</i><sub>dl</sub>) continuously obtained by the FT-EIS measurements during the entire etching process showed an electrode activation at the initial period as well as the completion of etching. The FT-EIS results were further validated by cyclic voltammograms and impedance measurements of partially etched ITO films using ferri- and ferrocyanide solution in combination with FESEM imaging, EDS, XRD analyses, and COMSOL simulation. We also demonstrated that this technique can be further utilized to obtain intact interdigitated array (IDA) electrodes in a reproducible manner, which is generally considered to be quite tricky due to delicacy of the pattern. Given that the FT-EIS allows for instantaneous snapshots of the electrode at every moment, this work may hold promise for in situ real-time examination of structural, electrokinetic, or mass transfer-related information on electrochemical systems undergoing constantly changing, transient processes including etching, which would be impossible with conventional electroanalytical techniques.
Applicability of the Alkylation Chemistry for Chemical C-Terminal Protein Sequence Analysis (2000)

We have evaluated the alkylation chemistry first described some years ago by Boyd et al. which is now routinely applied in a commercial instrument. We have found that the low repetitive yields observed during these analyses are due to the formation of a major side product when alkylating the C-terminal thiohydantoin. This side product, resistant to the chemical cleavage methods currently used, was characterized by NMR experiments in solution. We further demonstrate that chemical C-terminal sequence analysis of proteins using the alkylation chemistry is feasable with low picomole amounts of material. High-sensitivity C-terminal sequencing allows a complementary approach by which a protein is first subjected to N-terminal Edman degradation followed by C-terminal sequence analysis, limiting the amount of material necessary for the characterization of the protein under study. This limited C-terminal sequence information is often sufficient to solve problems that cannot be solved by applying any other analytical method commonly used today.
Synthesis ofO-AlkylD-Xylitols with Potential Luquid-Crystalline Properties1 (1997)

Abstract A general synthetic approach to enantiomerically pure x-O-alkyl-D-xylitols has been developed from D-xylose. These products provide access to new thermotropic liquid crystals. 1. Presented at the XVIIIth International Carbohydrate Symposium, Milan, Italy, July 21-26 (1996). Notes 1. Presented at the XVIIIth International Carbohydrate Symposium, Milan, Italy, July 21-26 (1996).