gebhart/patrepeval huggingface dataset:
Chemical and immunochemical studies on the receptor binding domain of cholera toxin B subunit. (1985)

The contributions of various amino acids to the structure and function of cholera toxin B subunit were assessed with quantifiable, chemically conservative, reversible derivatizations, and sensitive assays of activity. A panel of monoclonal antibodies was employed to monitor the conformational integrity of modified protein and help distinguish the direct from indirect effects of chemical derivatization. We describe a novel monoclonal antibody, which competes with the receptor GM1 for binding to cholera toxin B subunit, and use this reagent to help identify critically located residues. Our data support the hypothesis that tryptophan participates directly in binding GM1. In addition, we propose a dual role for lysine: first, these basic residues maintain an electrostatic attraction vital to receptor recognition; second, at least 1 lysine resides near the receptor binding domain and may interact with GM1. The influence of arginyl and tyrosyl residues upon activity is re-examined. Finally, we present data which suggest, in variance with previous studies, that the intramolecular disulfide bond is vital to the structure and function of cholera toxin B subunit.
Finite rate of innovation sampling (2014)

In previous chapters we have seen that the UoS model can pave the way to sub-Nyquist sampling of certain categories of structured analog signals. In this chapter we consider an alternative model that relies on parametric representations: finite rate of innovation (FRI) signals [105]. This class corresponds to families of functions defined by a finite number of parameters per unit time, a quantity referred to as the rate of innovation. More specifically, a FRI signal x(t) is characterized by the fact that any finite duration segment of length r is completely determined by no more than k parameters. In this case, the function x(t) is said to have a local rate of innovation equal to k/r. The FRI viewpoint complements the UoS framework: a signal may lie in a UoS and have FRI; however, not all FRI signals can be described by a UoS model and vice versa, as we will show in examples below.
O4‐04‐02: Identification of proteins that form complexes with tau in mouse brain (2010)

Microtubule-associated protein tau (MAPT) assembles into neurofibrillary tangles (NFT) in a variety of neurodegenerative tauopathies, a group of disorders that includes Alzheimer's disease and frontotemporal dementias. The tau mediated neurodegeneration that is observed in these tauopathies may result from toxic gain-of-function, derived from the (pre-)aggregates and/or loss-of-function of tau. However the potential physiological functions of protein tau, besides promoting the stabilization of microtubules, and the pathogenic pathways that result in protein tau mediated disease are today not well understood. To increase our knowledge on the biology of protein tau we initiated the identification of (sets of) proteins that interact with protein Tau and form physiologically relevant, functional interdependent protein-complexes. Tau complexes were isolated from normal mouse brains using a panel of anti-Tau antibodies. Tau candidate interactors were identified following precise Mass Spectrometry quantification using iTRAQ (isobaric tag for relative and absolute quantification) labeling, comparing protein levels from anti-Tau and control antibody precipitates. Analysis of the tau protein complexes derived from mouse brain resulted in the identification of many specific Tau interacting proteins. Among those, a significant number have previously been reported to interact with tau and thus confirm the validity of the methodology used. Examples are Tubulin subtypes (TUBA1, TUBA4, TUBB2C, TUBB2B, TUBB5), Dynactin complex (DCTN2, DCTN3, DCTN4, ACTR1A, ACTR1b, DCTN1, CAPZB, CAPZA2), PP2A complex (PPP2R1A, PPP2CB, PPP2R2A), PP2B complex (PPP3CA, PPP3R1), 14-3-3 proteins (Ywhaq, Ywhaz, Ywhae, Ywhag, Ywhah, Ywhab), aminopeptidase NPEPPS and Triose-phosphate isomerase (TPI). Besides these a series of unknown potential tau interacting proteins were identified. Some of these can be catalogued as microtubule associated proteins, molecular chaperones, ubiquitin proteases, oxidative stress related proteins and synaptic function related proteins. Further validation of the interaction and the potential role of the interacting proteins in tau biology, is currently under evaluation using biochemical and phenotypic readouts in a variety of cellular and animal models. The combination of high quality anti-Tau antibodies with state-of-the-art quantitative Mass Spectrometry let to the identification of many potential new Tau interactors.
Inhibition of HIV infection by CXCR4 and CCR5 chemokine receptor antagonists. (2001)

The chemokine receptors CXCR4 and CCR5 are used as co-receptors by the T cell-tropic (X4) and macrophage-tropic (R5) HIV-1 strains, respectively, for entering their host cells. Viral entry can be inhibited by the natural ligands for CXCR4, the CXC chemokine SDF-1 and CCR5, the CC chemokines RANTES, MIP-1alpha and MIP-1beta. Several peptidic compounds, T22 (an 18-mer), T134 (a 14-mer), ALX40-4C (a 9-mer) and CGP 64222 (also a 9-mer), have been identified as CXCR4 antagonists and show anti-HIV activity. Also, the HIV-1 tat protein has been described as a 'natural' CXCR4 antagonist with anti-HIV-1 activity. The most potent and specific CXCR4 antagonists are the bicyclam derivatives, which also potently block X4 HIV replication. AMD3100 has proved to be a highly specific CXCR4 antagonist, which consistently blocks the outgrowth of all X4 HIV and dual-tropic (R5/X4) variants that use CXCR4 for entering the cells (cell lines, CXCR4-transfected cell lines, lymphocytes or monocytes/ macrophages). From the bicyclam analogues, AMD3100 was selected as the clinical drug candidate, which, after initial Phase I (safety) studies, has proceeded to Phase II (efficacy) trials. The first non-peptidic compound that interacts with CCR5, and not with CXCR4, is a quaternary ammonium derivative, called TAK-779, which also has potent but variable anti-HIV activity. We believe that HIV entry/fusion inhibitors will become important new antiviral agents to combat AIDS. However, like the current clinically approved agents, they will need to be used in combinations consisting of antivirals that target other aspects of the HIV replication cycle, such as reverse transcriptase and protease, to obtain optimum therapeutic effects.
Quality assurance of Mo-99/Tc-99m radionuclide generators (2018)

Abstract Gamma-ray spectrometry analyses of the radionuclide content of eluate from two Mo-99/Tc-99m radionuclide generators POLTECHNET have been performed. The relative activities of 99 Mo 103 Ru and 131 I radioisotopes with respect to the activity of 99m Tc at different time intervals after the primary pertechnetate elution of the generators have been analyzed. The relative activities of the isotopes were determined and compared to the radionuclidic purity requirements for 99m Tc.
Characterization of device parameters in high-temperature metal-oxide-semiconductor field-effect transistors in β-SiC thin films (1988)

Both inversion- and depletion-mode n-channel metal-oxide-semiconductor field-effect transistors (MOSFETs) have been fabricated on β-SiC thin films grown by chemical-vapor deposition. The inversion-mode devices were made on in situ doped (Al) p-type β-SiC(100) thin films grown on Si(100) substrates. The depletion-mode MOSFETs were made on n-type β-SiC(111) thin films grown on the Si(0001) face of a 6H α-SiC substrates. Stable saturation and low subthreshold currents were achieved at drain-source voltages exceeding 5 and 25 V for the inversion-mode and depletion-mode devices, respectively. The transconductance increased with temperature up to 673 K for the short-gate-length devices, of either mode, and then decreased with further increases in temperature. It is proposed that the transconductances and threshold voltages for the inversion-mode devices are greatly affected by minority-carrier injection from the source. Stable transistor action was observed for both types of devices at temperatures up to 823 K, with the depletion-mode devices operating very well up to 923 K.
SnAs with the NaCl-type Structure: Type-I Superconductivity and Single Valence State of Sn (2014)

We examined the superconductivity of SnAs and the valence state of Sn in its lattice with an expectation that SnAs and related compounds with the NaCl-type structure might exhibit superconductivity at a high critical temperature (Tc), as (Ba1–xKx)BiO3 (BKBO) does, owing to the similar crystallographic and chemical environments of Sn in SnAs and Bi in BKBO. Although SnAs had low Tc, 3.58 K, we clarified two important characteristics: First, SnAs exhibits weakly coupled type-I superconductivity. Second, Sn has a single valence state, like Sn3+(5s1), originating from there being only one crystallographically independent site in its NaCl-type structure. This unconventional single chemical state of Sn in SnAs would explain the superconductivity of SnAs with a three-dimensional NaCl-type structure, rather than a two-dimensional layered structure.
Surface-Normal Ge/SiGe Asymmetric Fabry–Perot Optical Modulators Fabricated on Silicon Substrates (2013)

We demonstrate the first vertical-incidence Ge/SiGe quantum well reflection modulators fabricated entirely on standard silicon substrates. These modulators could help enable massively parallel, free-space optical interconnects to silicon chips. An asymmetric Fabry-Perot resonant cavity is formed around the quantum well region by alkaline etching the backside of the Si substrate to leave suspended SiGe membranes, upon which high-index-contrast Bragg mirrors are deposited. Electroabsorption and electrorefraction both contribute to the reflectance modulation. The devices exhibit greater than 10 dB extinction ratio with low insertion loss of 1.3 dB. High-speed modulation with a 3 dB bandwidth of 4 GHz is demonstrated. The moderate-Q cavity (Q ~ 600) yields an operating bandwidth of more than 1 nm and permits operation without active thermal stabilization.
Manipulation with Shared Grasping (2020)

A shared grasp is a grasp formed by contacts between the manipulated object and both the robot hand and the environment. By trading off hand contacts for environmental contacts, a shared grasp requires fewer contacts with the hand, and enables manipulation even when a full grasp is not possible. Previous research has used shared grasps for non-prehensile manipulation such as pivoting and tumbling. This paper treats the problem more generally, with methods to select the best shared grasp and robot actions for a desired object motion. The central issue is to evaluate the feasible contact modes: for each contact, whether that contact will remain active, and whether slip will occur. Robustness is important. When a contact mode fails, e.g., when a contact is lost, or when unintentional slip occurs, the operation will fail, and in some cases damage may occur. In this work, we enumerate all feasible contact modes, calculate corresponding controls, and select the most robust candidate. We can also optimize the contact geometry for robustness. This paper employs quasi-static analysis of planar rigid bodies with Coulomb friction to derive the algorithms and controls. Finally, we demonstrate the robustness of shared grasping and the use of our methods in representative experiments and examples. The video can be found at https://youtu.be/tyNhJvRYZNk
Partial matching of interpose 3D facial data for face recognition (2009)

Three-dimensional face recognition has lately received much attention due to its robustness in the presence of lighting and pose variations. However, certain pose variations often result in missing facial data. This is common in realistic scenarios, such as uncontrolled environments and uncooperative subjects. Most previous 3D face recognition methods do not handle extensive missing data as they rely on frontal scans. Currently, there is no method to perform recognition across scans of different poses. A unified method that addresses the partial matching problem is proposed. Both frontal and side (left or right) facial scans are handled in a way that allows interpose retrieval operations. The main contributions of this paper include a novel 3D landmark detector and a deformable model framework that supports symmetric fitting. The landmark detector is utilized to detect the pose of the facial scan. This information is used to mark areas of missing data and to roughly register the facial scan with an Annotated Face Model (AFM). The AFM is fitted using a deformable model framework that introduces the method of exploiting facial symmetry where data are missing. Subsequently, a geometry image is extracted from the fitted AFM that is independent of the original pose of the facial scan. Retrieval operations, such as face identification, are then performed on a wavelet domain representation of the geometry image. Thorough testing was performed by combining the largest publicly available databases. To the best of our knowledge, this is the first method that handles side scans with extensive missing data (e.g., up to half of the face missing).
Optimization of a vector quantization codebook for objective evaluation of surgical skill. (2004)

Surgical robotic systems and virtual reality simulators have introduced an unprecedented precision of measurement for both tool-tissue and tool-surgeon interaction; thus holding promise for more objective analyses of surgical skill. Integrative or averaged metrics such as path length, time-to-task, success/failure percentages, etc., have often been employed towards this end but these fail to address the processes associated with a surgical task as a dynamic phenomena. Stochastic tools such as Markov modeling using a 'white-box' approach have proven amenable to this type of analysis. While such an approach reveals the internal structure of the of the surgical task as a process, it requires a task decomposition based on expert knowledge, which may result in a relatively large/complex model. In this work, a 'black box' approach is developed with generalized cross-procedural applications., the model is characterized by a compact topology, abstract state definitions, and optimized codebook size. Data sets of isolated tasks were extracted from the Blue DRAGON database consisting of 30 surgical subjects stratified into six training levels. Vector quantization (VQ) was employed on the entire database, thus synthesizing a lexicon of discrete, task-independent surgical tool/tissue interactions. VQ has successfully established a dictionary of 63 surgical code words and displayed non-temporal skill discrimination. VQ allows for a more cross-procedural analysis without relying on a thorough study of the procedure, links the results of the black-box approach to observable phenomena, and reduces the computational cost of the analysis by discretizing a complex, continuous data space.
Role of Coronary Myogenic Response in Pressure-Flow Autoregulation in Swine: A Meta-Analysis With Coronary Flow Modeling (2018)

Myogenic responses (pressure-dependent contractions) of coronary arterioles play a role in autoregulation (relatively constant flow vs. pressure). Publications on myogenic reactivity in swine coronaries vary in caliber, analysis, and degree of responsiveness. Further, data on myogenic responses and autoregulation in swine have not been completely compiled, compared, and modeled. Thus, it has been difficult to understand these physiological phenomena. Our purpose was to: (a) analyze myogenic data with standard criteria; (b) assign results to diameter categories defined by morphometry; and (c) use our novel multiscale flow model to determine the extent to which <i>ex vivo</i> myogenic reactivity can explain autoregulation <i>in vivo</i>. When myogenic responses from the literature are an input for our model, the predicted coronary autoregulation approaches <i>in vivo</i> observations. More complete and appropriate data are now available to investigate the regulation of coronary blood flow in swine, a highly relevant model for human physiology and disease.
Abstract 3204: Novel, rapid and sensitive technology to analyze gene expression directly from archived FFPE clinical oncology specimens without sample preparation (2012)

Abstract Formalin-Fixed Paraffin Embedded (FFPE) tissue samples are the standard for clinical oncology tissue sample archiving worldwide. It is estimated that there are approximately a billion FFPE tissue cancer samples archived in hospitals and tissue banks around the world, and many of these samples have full clinical annotation including long term follow-up data. Current methods of analyzing gene expression in these samples involve laborious and expensive sample preparation protocols and long turnaround times (2 days or longer). We have developed a novel, rapid (3 hours), sample-to-answer technology to analyze gene expression from clinical FFPE tissues without the need for RNA extraction. The technique is highly sensitive and requires only 2 mm x 5 mm x 10 microns of FFPE material scraped from a pathology slide. The gene expression data obtained directly from FFPE without sample preparation correlates highly with data obtained on RNA extracted from the same FFPE sample using conventional methods. Importantly, the gene expression data obtained from prostate and breast FFPE samples correlate highly with microarray data, and with data from matching mirrored FF (Fresh Frozen) samples. The assay can be developed for detection using Luminex instrument or Capillary Electrophoresis instrument (Caliper GX or ABI 3500). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3204. doi:1538-7445.AM2012-3204
H7N9 influenza viruses interact preferentially with α2,3-linked sialic acids and bind weakly to α2,6-linked sialic acids (2013)

The recent human outbreak of H7N9 avian influenza A virus has caused worldwide concerns. Receptor binding specificity is critical for viral pathogenicity, and still not thoroughly studied for this emerging virus. Here, we evaluated the receptor specificity of the haemagglutinin (HA) of two human H7N9 isolates (A/Shanghai/1/13 and A/Anhui/1/13) through a solid-phase binding assay and a flow cytometry-based assay. In addition, we compared it with those from several HAs from human and avian influenza viruses. We observed that the HAs from the novel H7 isolates strongly interacted with α2,3-linked sialic acids. Importantly, they also showed low levels of binding to α2,6-linked sialic acids, but significantly higher than other avian H7s.
Multicenter Evaluation of a 0-Hour/1-Hour Algorithm in the Diagnosis of Myocardial Infarction With High-Sensitivity Cardiac Troponin T (2016)

The hs-cTnT 0-hour/1-hour algorithm performs well for early rule-out and rule-in of acute myocardial infarction.
Low‐Temperature Chemical Approaches for Synthesizing Sulfides and Nitrides of Reactive Transition Metals (1997)

The advent of the sol–gel technique over the past several decades and the recognition of its excellent flexibility for synthesizing a large variety of oxide ceramics and glasses in both bulk and thin-film forms has generated considerable interest in using solution-based processes to prepare ceramic materials. Because of the success of the sol–gel technique, a number of other chemical processes have been developed utilizing metalorganic/organometallic starting materials to create molecularly architectured precursors, which have proven effective in synthesizing both oxide and non-oxide materials. In the present study, two different chemical approaches have been implemented to synthesize non-oxides (sulfides and nitrides) of reactive transition-metal elements. Accordingly, a novel thio-sol–gel process for preparing TiS2 and NbS2 powders has been studied. In the case of TiS2 synthesis, the chemical reaction has been examined in detail using Fourier-transform infrared spectroscopy (FTIR) and gas chromatography (GC). The effects of modification of the titanium precursor on the morphology of the final sulfide have also been investigated and are discussed. A second, more generalized process has been developed for synthesizing homogeneous precursors in multicomponent systems. Its utilization in preparing ternary nitrides has been demonstrated, and is also presented. © 1997 by John Wiley & Sons, Ltd.
ChemInform Abstract: CHEMISTRY IN HYDROGEN FLUORIDE. 6. OXIDATIVE FLUORINATION OF AROMATIC COMPOUNDS (1979)

Abstract Die beiden p‐substituierten Toluole (I) reagieren mit verschiedenen Oxidationsmitteln wie Bleidioxid, Nickeldioxid, Co(III)‐acetat, Co(III)‐fluorid, Silber(II)‐ fluorid oder Silber(II)‐oxid in f1.
The Frontal Aslant Tract and Supplementary Motor Area Syndrome: Moving towards a Connectomic Initiation Axis (2021)

Connectomics is the use of big data to map the brain's neural infrastructure; employing such technology to improve surgical planning may improve neuro-oncological outcomes. Supplementary motor area (SMA) syndrome is a well-known complication of medial frontal lobe surgery. The 'localizationist' view posits that damage to the posteromedial bank of the superior frontal gyrus (SFG) is the basis of SMA syndrome. However, surgical experience within the frontal lobe suggests that this is not entirely true. In a study on <i>n</i> = 45 patients undergoing frontal lobe glioma surgery, we sought to determine if a 'connectomic' or network-based approach can decrease the likelihood of SMA syndrome. The control group (<i>n</i> = 23) underwent surgery avoiding the posterior bank of the SFG while the treatment group (<i>n</i> = 22) underwent mapping of the SMA network and Frontal Aslant Tract (FAT) using network analysis and DTI tractography. Patient outcomes were assessed post operatively and in subsequent follow-ups. Fewer patients (8.3%) in the treatment group experienced transient SMA syndrome compared to the control group (47%) (<i>p</i> = 0.003). There was no statistically significant difference found between the occurrence of permanent SMA syndrome between control and treatment groups. We demonstrate how utilizing tractography and a network-based approach decreases the likelihood of transient SMA syndrome during medial frontal glioma surgery. We found that not transecting the FAT and the SMA system improved outcomes which may be important for functional outcomes and patient quality of life.
Achromatization of conical diffraction: application to the generation of a polychromatic optical vortex (2016)

Vortex beams are plagued by the intrinsic chromaticity of the physical phenomenon used to generate them. To the authors' best knowledge, attempts to generate them in a broad spectral range remain quite scarce and limited in their results. Crystal optics and especially conical diffraction (CD) (or refraction) intrinsically create achromatic vortices. The vortex is created by a wavelength-independent topological charge, embedded directly in the Fresnel equations. However, for biaxial crystals of low crystallographic symmetry, which includes all crystals used practically for CD, the dispersion of the binormal axis creates a chromaticity effect. In this Letter, we propose a new way to compensate this dispersion of the binormal axis of a biaxial crystal in order to generate white-light vortex beams by CD in a 250 nm spectral range, covering almost all the visible range. The advantages of the ability to use CD in a wide spectral range vastly exceed the sole generation of vortex beams.