gebhart/patrepeval huggingface dataset:
Structural and Immunochemical Characterization of the Lipooligosaccharides Expressed byNeisseria subflava44 (2001)

Neisserial lipooligosaccharides (LOSs) are a family of complex cell surface glycolipids. We used mass spectrometry techniques (electrospray ionization, collision-induced dissociation, and multiple step), combined with fluorophore-assisted carbohydrate electrophoresis monosaccharide composition analysis, to determine the structure of the two low-molecular-mass LOS molecules (LOSI and LOSII) expressed by Neisseria subflava 44. We determined that LOSI contains one glucose on both the alpha and beta chains. LOSII is structurally related to LOSI and differs from it by the addition of a hexose (either glucose or galactose) on the alpha chain. LOSI and LOSII were able to bind monoclonal antibody (MAb) 25-1-LC1 when analyzed by Western blotting experiments. We used a set of genetically defined Neisseria gonorrhoeae mutants that expressed single defined LOS epitopes and a group of Neisseria meningitidis strains that expresses chemically defined LOS components to determine the structures recognized by MAb 25-1-LC1. We found that extensions onto the beta-chain glucose of LOSI block the recognition by this MAb, as does further elongation from the LOSII alpha chain. The LOSI structure was determined to be the minimum structure that is recognized by MAb 25-1-LC1.
Inkorporation von Membranproteinen in festkörperunterstützte planare Lipidfilme (1995)

Durch Fusion mit ATPase‐haltigen Liposomen bilden monomolekulare Lipidfilme mit Peptidspacergruppen, die in situ auf Goldsubstraten präpariert wurden, spontan definierte Lipiddoppelschichten. Oberflächenplasmonenresonanzmessungen und elektrochemische Messungen weisen darauf hin, daß die Lipidschichten das Enzym inkorporiert enthalten können (schematische Darstellung rechts). Die Aktivität des Enzyms, d.h. die Protonentranslokation durch die Lipidschicht, bleibt erhalten, wie elektrochemische Messungen der Protonenentladung an der Goldelektrode zeigen. magnified image
Synthesis of High-Silica Erionite Driven by Computational Screening of Hypothetical Zeolites (2019)

A hypothetical zeolite framework was selected from a database of hypothetical structures and adapted based on the structural features relevant for deNOx and MTO catalysis. To attempt the realization of this structure, a computational energy-based approach was applied to select relevant organic structure directing agent (OSDA) molecules with large OSDA–zeolite stabilization energies, leading to the selection of three OSDAs (OSDA1, OSDA2, and OSDA3) as potential candidates for the synthesis of the hypothetical zeolite (Hypo#1). Instead of Hypo#1, erionite (ERI) was found to dominate the experimental product outcome when potassium was used as a mineralizing agent. In the case of OSDA3, a novel high-silica ERI was found. The different ERI products were characterized, intergrowth structures ruled out, and special attention was paid to the compositional and morphological features arising from the use of the different OSDAs. In the specific high-Si product obtained using OSDA3, a distinct tubular to prismatic crystal morphology could be seen. Theoretical stabilization energies calculated for potentially competing phases (Hypo#1, ERI, offretite (OFF), and chabazite (CHA) among others) could be used to rationalize the experimental outcome to a certain extent, but our results also show that only considering zeolite−OSDA interaction is probably not sufficient to realize hypothetical frameworks, especially for Al-containing zeolites where alkali ions play an important role during crystallization.
P2 Receptor Modeling and Identification of Ligand Binding Sites (1998)

As of now, seven subtypes of P2X receptors and four subtypes of P2Y receptors have been cloned and functionally identified. Analysis of the predicted amino acid sequences of these structurally diverse subtypes of nucleotide receptors has allowed construction of models that have aided in two- and three-dimensional visualization of P2X and P2Y receptors, respectively. Based on these models and on site-directed mutagenesis studies primarily with P2Y receptors, the ligand binding site of P2 receptors is being delineated. In this chapter, we present the current information on P2X and P2Y receptor structures and discuss the potential for amino acids in these receptors to interact with the nucleotide ligands.
An Accurately Steerable, Compact Phased Array System for Narrowbeam Ultrasound Transmission (2022)

For over more than a decade, ultrasound phased arrays have been playing a leading role in domains such as noninvasive diagnostic examination, nondestructive testing and sonar, and will continue to be indispensable in a wide range of new applications. Unlike the aforementioned traditional scanning systems, many new applications require a transmit-only configuration and work in the low ultrasound frequency range, consequently posing new challenges in low-cost phased array design. However, two sought-after features are still missing in current low-cost ultrasound phased array systems, namely broadband transmission and wide angular beam steering. In this work, a low-cost ultrasound phased array system is presented that enables the transmission of both narrowband and broadband signals. Accurate beam steering is achieved through the concept of Direct Digital Synthesis (DDS). The design features small, wide bandwidth MEMS transducers enabling grating lobe free beam patterns at high frequency and a broad angular beam steering range. The presented prototype supports 64 speaker elements and allows very fine amplitude and phase control over each transducer stage with respectively 10-bit and 12-bit resolution. The beam steering performance is validated for a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${1}\times {10}$ </tex-math></inline-formula> calibrated uniform linear array design. In these measurements, an accuracy in the order of just a few degrees was observed, even at a steering angle of 70° off-axis.
Thiocarbazate building blocks enable the construction of azapeptides for rapid development of therapeutic candidates (2022)

Peptides, polymers of amino acids, comprise a vital and expanding therapeutic approach. Their rapid degradation by proteases, however, represents a major limitation to their therapeutic utility and chemical modifications to native peptides have been employed to mitigate this weakness. Herein, we describe functionalized thiocarbazate scaffolds as precursors of aza-amino acids, that, upon activation, can be integrated in a peptide sequence to generate azapeptides using conventional peptide synthetic methods. This methodology facilitates peptide editing-replacing targeted amino acid(s) with aza-amino acid(s) within a peptide-to form azapeptides with preferred therapeutic characteristics (extending half-life/bioavailability, while at the same time typically preserving structural features and biological activities). We demonstrate the convenience of this azapeptide synthesis platform in two well-studied peptides with short half-lives: FSSE/P5779, a tetrapeptide inhibitor of HMGB1/MD-2/TLR4 complex formation, and bradykinin, a nine-residue vasoactive peptide. This bench-stable thiocarbazate platform offers a robust and universal approach to optimize peptide-based therapeutics.
A novel method to predict the pull-in voltage in a closed form for micro-plates actuated by a distributed electrostatic force (2006)

This study is devoted to finding the precise pull-in voltage/position of a micro-device formed by two parallel charged plates. Pull-in is a phenomenon where the electrostatic force induced by the applied voltage across two plates of the device exceeds the elastic, restoring force exerted by the deformed plates, leading to a contact between the two plates. To offer a precise prediction of the pull-in, a dynamic model in the form of a partial differential equation (PDE) is established based on the equilibrium among plate flexibility, residual stress and distributed electrostatic forces. The Galerkin method is employed to decompose the established PDE into discrete modal equations. By considering lower order modes and solving them, one arrives at a prediction of plate deflection in terms of the applied bias voltage. Approximating the solved deflection by a fifth-order series and full-order numerical integration, the pull-in position and voltage are successfully approximated. The pull-in position in terms of center deflection of the deformed plate is found to be 48% of the air gap between the plates, which presents a better estimation than the commonly used one-third of the gap derived by all past studies based on a less realistic one-dimensional lump model. A closed form of the pull-in voltage is derived to offer design guidelines for the device prior to production. The aforementioned theoretical findings are finally validated by finite element and experimental studies on a MEMS device of parallel charged micro-plates designed and fabricated in the laboratory.
Immunopathological aspects of Plasmodium berghei infection in five strains of mice. II. Immunopathology of cerebral and other tissue lesions during the infection. (1980)

Histological changes during the course of P. berghei infection were investigated in A/J, BALB/c, OF1, CBA and C57B1 mice. The findings were studied in relation to serological aspects (Contreras et al., 1980). High mortality and acute deaths occurred in A/J, BALB/c and OF1 mice and marked cerebral lesions were found in these strains from day 15, including congestion of meningeal and cerebral veins and capillaries, blocking of these vessels by heavily parasitized RBC, cerebral oedema and haemorrhages. Such lesions were minimal in CBA and C57B1 mice, and absent in mice examined 21 and 24 days after infection. Small deposits of IgG and traces of C3 were detected by immunofluorescence in the choroid plexus of most mice from day 9. Renal lesions included congestion, plugging of veins and capillaries, low-grade mononuclear infiltration and mesangial thickening; these changes were most marked in CBA, C57B1 and A/J mice. Glomerular deposits of IgM were present in all strains in the first week of infection. IgG and C3 were detected in the second week, but only traces were found in CBA mice. The livers showed congestion, accumulation of pigment in swollen Kupffer cells and mononuclear portal infiltration; these were most pronounced in A/J mice. In the spleen, there was a great increase in the reticuloendothelial cell population, white pulp proliferation, congestion and accumulation of pigment and plasma cell reaction; the pattern of white pulp expansion varied in the different strains. The results suggest that cerebral lesions play a significant role in the aetiology of acute deaths in this malaria model.
Flexible Nanoparticles Reach Sterically Obscured Endothelial Targets Inaccessible to Rigid Nanoparticles (2018)

Molecular targeting of nanoparticle drug carriers promises maximized therapeutic impact to sites of disease or injury with minimized systemic effects. Precise targeting demands addressing to subcellular features. Caveolae, invaginations in cell membranes implicated in transcytosis and inflammatory signaling, are appealing subcellular targets. Caveolar geometry has been reported to impose a ≈50 nm size cutoff on nanocarrier access to plasmalemma vesicle associated protein (PLVAP), a marker found in caveolae in the lungs. The use of deformable nanocarriers to overcome that size cutoff is explored in this study. Lysozyme-dextran nanogels (NGs) are synthesized with ≈150 or ≈300 nm mean diameter. Atomic force microscopy indicates the NGs deform on complementary surfaces. Quartz crystal microbalance data indicate that NGs form softer monolayers (≈60 kPa) than polystyrene particles (≈8 MPa). NGs deform during flow through microfluidic channels, and modeling of NG extrusion through porous filters yields sieving diameters less than 25 nm for NGs with 150 and 300 nm hydrodynamic diameters. NGs of 150 and 300 nm diameter target PLVAP in mouse lungs while counterpart rigid polystyrene particles do not. The data in this study indicate a role for mechanical deformability in targeting large high-payload drug-delivery vehicles to sterically obscured targets like PLVAP.
Sampling and Recovery of Pulse Streams (2011)

Compressive sensing (CS) is a new technique for the efficient acquisition of signals, images and other data that have a sparse representation in some basis, frame, or dictionary. By sparse we mean that the N-dimensional basis representation has just K <;<; N significant coefficients; in this case, the CS theory maintains that just M = O( K log N) random linear signal measurements will both preserve all of the signal information and enable robust signal reconstruction in polynomial time. In this paper, we extend the CS theory to pulse stream data, which correspond to S -sparse signals/images that are convolved with an unknown F-sparse pulse shape. Ignoring their convolutional structure, a pulse stream signal is K = SF sparse. Such signals figure prominently in a number of applications, from neuroscience to astronomy. Our specific contributions are threefold. First, we propose a pulse stream signal model and show that it is equivalent to an infinite union of subspaces. Second, we derive a lower bound on the number of measurements M required to preserve the essential information present in pulse streams. The bound is linear in the total number of degrees of freedom S + F, which is significantly smaller than the naïve bound based on the total signal sparsity K = SF. Third, we develop an efficient signal recovery algorithm that infers both the shape of the impulse response as well as the locations and amplitudes of the pulses. The algorithm alternatively estimates the pulse locations and the pulse shape in a manner reminiscent of classical deconvolution algorithms. Numerical experiments on synthetic and real data demonstrate the advantages of our approach over standard CS.
Microsystems for cell-based electrophysiology (2013)

Among the electrophysiology techniques, the voltage clamp and its subsequent scaling to smaller mammalian cells, the so-called patch clamp, led to fundamental discoveries in the last century, revealing the ionic mechanisms and the role of single-ion channels in the generation and propagation of action potentials through excitable membranes (e.g. nerves and muscles). Since then, these techniques have gained a reputation as the gold standard of studying cellular ion channels owing to their high accuracy and rich information content via direct measurements under a controlled membrane potential. However, their delicate and skill-laden procedure has put a serious constrain on the throughput and their immediate utilization in the discovery of new cures targeting ion channels until researchers discovered 'lab-on-a-chip' as a viable platform for the automation of these techniques into a reliable high-throughput screening functional assay on ion channels. This review examines the innovative 'lab-on-a-chip' microtechnologies demonstrated towards this target over a period of slightly more than a decade. The technologies are categorically reviewed according to their considerations for design, fabrication, as well as microfluidic integration from a performance perspective with reference to their ability to secure G Ω seals (gigaseals) on cells, the norm broadly accepted among electrophysiologists for quality recordings that reflect ion-channel activity with high fidelity.
A modified ZVS half-bridge DC-DC converter (2004)

A modified DCS half-bridge DC-DC converter is proposed to achieve soft switching of all switches and to reduce the leakage-inductance-related power losses. The theoretical analysis and experimental results show that the proposed topology achieves high efficiency at high switching frequencies.
Nitric Oxide Synthase in Rat Brain: Age Comparisons Quantitated with NADPH-Diaphorase Histochemistry (1997)

We examined age-related differences in nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) containing neurons and neuropil in the striatum and hippocampus of male Fischer 344 rats at 6, 12, and 26 mo of age. NADPH-d staining is considered to be a marker for neurons and neuronal processes containing nitric oxide synthase. Rat brains were processed for NADPH-d histochemistry and analyzed morphometrically using computerized image analysis. The following NADPH-d histochemical parameters were examined: neuronal density, neuronal size, and neuropil staining optical density of selected regions. In the striatum, significant age-related declines were observed in NADPH-d-positive neuronal density and in neuropil staining, while neuronal size increased between 6 and 12 mo and then declined between 12 and 26 mo. In the hippocampus no significant age-related changes were noted in NADPH-d-positive neuronal density or size, or in the optical density of the molecular layer of the hippocampal dentate gyrus. Thus, age differences in NADPH-d histochemistry appear to be regionally specific in the Fischer 344 rat.
Bases scientifiques du traitement physique de la gonarthrose (2000)

peer reviewed
Morphometry and strain distribution of the C57BL/6 mouse aorta (2002)

The goal of the present study was to obtain a systematic set of data along the length of the mouse aorta to study variations of morphometry (diameter, wall thickness, and curvature), strain, and stress of the mouse aorta. Five mice were imaged with a 13-MHz ultrasound probe to determine the in vivo diameter along the aorta. A cast was made of these aortas to validate the ultrasonic diameter measurements. The root mean squared and systematic errors for these measurements were 12.6% and 6.4% of the mean ultrasound diameter, respectively. The longitudinal variations of geometry, stress, and strain from the aortic valve to the common iliac bifurcation were documented. Our results show that the residual circumferential strain leads to a uniformity of transmural strain of the aorta in the loaded state along the entire length of the aorta. Furthermore, we validated the incompressibility condition along the length of the aorta. These data of normal mice will serve as a reference state for the study of disease in future knockout models.
Synchrotron Radiation Study of the Relation between Structure and Strain in Polyurethane Elastomers (1997)

This paper describes a system for the study of the relation between structure and applied strain in thermoplastic polyurethane elastomers using the Australian National Beamline Facility at the Photon Factory, KEK, Tsukuba, Japan. The system uses the sagittal focusing monochromator at beamline 20B to provide a high-intensity focused beam which then falls on the specimen mounted in a miniature tensometer mounted in the unique vacuum diffractometer (BIGDIFF). Imaging plates were used to record simultaneously SAXS and WAXS patterns from the specimen at a particular strain. The change in SAXS and WAXS patterns with loading and unloading was recorded using a ten-plate imaging-plate changer.
FXYD3 Expression in Gliomas and its Clinicopathological Significance (2009)

FXYD3, interacting with Na+/K+-ATPase, is considered a cell surface regulator modulating the function of ion pumps and ion channels. The FXYD3 gene was originally cloned from murine mammary tumors and then from human breast tumors. However, no study of FXYD3 has been carried out in gliomas; therefore, we examined FXYD3 expression in gliomas and its clinicopathological significance. FXYD3 expression was immunohistochemically examined in 71 primary gliomas, along with 37 matched adjacent normal brain samples and 8 recurred gliomas. The frequency of strong FXYD3 expression was higher in the primary tumors in either unmatched (p = 0.046) or matched cases (p = 0.02), compared to normal brain tissue. FXYD3 expression was significantly more increased in females than males (p = 0.01), and in multiple site gliomas than single sites (p = 0.02). There was no difference of FXYD3 expression regarding age, tumor location, size, histological type, and tumor grade (p > 0.05). The results suggest that FXYD3 expression may be involved in glioma development, especially in multiple gliomas and female patients.
Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs (2005)

Direct site-specific biotinylation of RNA molecules was achieved by specific transcription mediated by unnatural base pairs. Unnatural base pairs between 2-amino-6-(2-thienyl)purine (denoted by s) and 2-oxo(1H)pyridine (denoted by y), or 2-amino-6-(2-thiazolyl)purine (denoted as v) and y specifically function in T7 transcription. Using these unnatural base pairs, the substrate of biotinylated-y (Bio-yTP) was selectively incorporated into RNA, opposite s or v in the DNA templates, by T7 RNA polymerase. This method was applied to the immobilization of an RNA aptamer on sensor chips, and the aptamer accurately recognized its target protein. This direct site-specific biotinylation will provide a tool for RNA-based biotechnologies.
Reply: (2017)

We thank Dr Colby for his interest in our article “Computer-Extracted Texture Features to Distinguish Cerebral Radionecrosis from Recurrent Brain Tumors on Multiparametric MRI: A Feasibility Study.” We are replying to Dr Colby's specific comment, “Therefore, while it may seem impressive that
The preparation of a series of nitrostilbene ester compounds using micro reactor technology (2001)

The synthesis of stilbene esters using Wittig chemistry has been used to illustrate the generic diversity micro reactors offer in terms of chemical control and rapid method development. The micro reactor consisted of a 'T' design based on channel geometries 200 microns wide and 100 microns deep, etched into borosilicate glass and sealed with a borosilicate top plate using a thermal bonding technique. The movement of the reagent and products was achieved using electroosmotic flow (EOF), assisted by the incorporation of micro porous silica frits within the micro-channels to allow accurate solution control. To optimise the operating conditions methyl 4-formylbenzoate, premixed with sodium methoxide, was reacted with 2-nitrobenzyl-triphenylphosphonium bromide in dry degassed MeOH using flow conditions for both reagents of 0.40 microL min-1 for 20 min. A product yield of 70% (2:1 reaction stoichiometry with the aldehyde in excess) was obtained representing a 10% increase compared with the traditional batch synthesis. To demonstrate the capability of micro reactors to perform atom efficient synthesis a series of experiments based on an injection methodology (optimised to 30 s) were performed in the micro reactor at 1:1 stoichiometry resulting in a yield of 59%. Finally, the capability of micro reactors to perform a series of analogue reactions was investigated. The yields for a further three aldehydes indicated that the technology will be suitable for the development of automated device to support the generation of combinatorial libraries and rapid high throughput synthetic methods.
Teaching AI to Explain its Decisions Using Embeddings and Multi-Task Learning (2019)

Using machine learning in high-stakes applications often requires predictions to be accompanied by explanations comprehensible to the domain user, who has ultimate responsibility for decisions and outcomes. Recently, a new framework for providing explanations, called TED, has been proposed to provide meaningful explanations for predictions. This framework augments training data to include explanations elicited from domain users, in addition to features and labels. This approach ensures that explanations for predictions are tailored to the complexity expectations and domain knowledge of the consumer. In this paper, we build on this foundational work, by exploring more sophisticated instantiations of the TED framework and empirically evaluate their effectiveness in two diverse domains, chemical odor and skin cancer prediction. Results demonstrate that meaningful explanations can be reliably taught to machine learning algorithms, and in some cases, improving modeling accuracy.