gebhart/patrepeval huggingface dataset:
Suppression of T-cell proliferation by Mycobacterium leprae and its products: the role of lipopolysaccharide. (1990)

Addition of soluble molecules obtained from sonicated Mycobacterium leprae markedly suppressed the proliferative response to the mitogen anti-CD3 of peripheral blood mononuclear cells and isolated T cells. Suppression was nonspecific and occurred with cells from lepromatous and tuberculoid leprosy patients as well as control donors. The purified lipoarabinomannans from M. leprae and Mycobacterium tuberculosis had a similar spectrum of inhibition whereas their deacylated derivatives were without effect. All mycobacterial preparations of either a crude or purified state, which suppressed cellular responses, contained appreciable quantities of bacterial lipopolysaccharide by the Limulus amebocyte assay. Contamination with lipopolysaccharide could account for the extent and nonselectivity of the T-cell suppression. Suppression was also monocyte-dependent and in part due to the release of arachidonate metabolites of the cyclooxygenase pathway.
The Impact of Carrier Transport Confinement on the Energy Transfer Between InGaN/GaN Quantum‐Well Nanorods and Colloidal Nanocrystals (2012)

Abstract The energy transfer (ET) between InGaN/GaN multiple‐quantum‐well (MQW) nanorods (NRs) and semiconductor nanocrystals (NCs) for efficient color conversion is studied. An exceptional contribution of carrier transport confinement to the ET mechanisms is observed in the proximal side‐wall coupling system, which consists of InGaN/GaN NRs and CdSe NCs. Under relatively low or high excitation, the ET rate shows different carrier‐density dependence, resulting from different electron‐hole configurations, i.e., bound excitons and free carriers. In the localized exciton regime, the ET rate decreases when increasing temperature from 20 K to 200 K. However, in the free‐carrier regime, the ET rate varies insignificantly in the same temperature range. The temperature dependence in this NR‐NC coupling system is different from that in the previously studied planar MQW‐NC coupling system. It is suggested that the carrier transport confinement in NRs is a major factor for these divergences. The highly efficient ET with efficiency up to 80% shows a promising potential of using such NR‐NC coupled structures for ET‐pumped, NC‐based, light‐emitting devices.
Photoreceptor Cells With Profound Structural Deficits Can Support Useful Vision in Mice (2014)

Photoreceptors that lack fully formed outer segments can support useful vision. This challenges the idea that normal cellular structure needs to be completely reproduced for transplanted cells to contribute to useful vision.
TGF-ß PLAYS A CRITICAL ROLE IN PROMOTING CHIMERISM AND TOLERANCE (2010)

1University Of Louisville, Institure for Cellular Therapeutics, 40202/UNITED STATES OF AMERICA, 2Plastic Surgery/surgery, University of Pittsburgh, Pittsburgh/PA/UNITED STATES OF AMERICA, 3University Of Louisville, Institute for Cellular Therapeutics, Louisville/KY/UNITED STATES OF AMERICA, 4Plastic Surgery/surgery, University of Pittsburgh, Pittsburgh/UNITED STATES OF AMERICA
A Nonlinear Observer-Based Strategy for Aircraft Oscillatory Failure Detection: A380 Case Study (2011)

Robust and early detection of oscillatory failures in the electrical flight control system of an aircraft is a crucial issue. Oscillatory failures, if not detected and passivated in time, can lead to strong interactions with loads and aeroelasticity and may potentially lead to structural damages. A nonlinear observer-based solution to detect such failures with small amplitude at a very early stage is presented. The stability and convergence proofs are given and experimental results with real A380 flight data are presented.
Genome Sequence and Assessment of Safety and Potential Probiotic Traits of Lactobacillus johnsonii CNCM I-4884 (2022)

The probiotic strain <i>Lactobacillus johnsonii</i> CNCM I-4884 exhibits anti-<i>Giardia</i> activity in vitro and in vivo in a murine model of giardiasis. The aim of this study was the identification and characterization of the probiotic potential of <i>L. johnsonii</i> CNCM I-4884, as well as its safety assessment. This strain was originally classified as <i>Lactobacillus gasseri</i> based on 16S gene sequence analysis. Whole genome sequencing led to a reclassification as <i>L. johnsonii</i>. A genome-wide search for biosynthetic pathways revealed a high degree of auxotrophy, balanced by large transport and catabolic systems. The strain also exhibits tolerance to low pH and bile salts and shows strong bile salt hydrolase (BSH) activity. Sequencing results revealed the absence of antimicrobial resistance genes and other virulence factors. Phenotypic tests confirm that the strain is susceptible to a panel of 8 antibiotics of both human and animal relevance. Altogether, the in silico and in vitro results confirm that <i>L. johnsonii</i> CNCM I-4884 is well adapted to the gastrointestinal environment and could be safely used in probiotic formulations.
Expeditious entry to C-alkyl and C-aryl pyranoid glycals: reaction of anomeric glycosyl chlorides with organolithiums (1996)

A. M. Gómez, M. Casillas, S. Valverde and J. C. López, Chem. Commun., 1996, 2357 DOI: 10.1039/CC9960002357
Association of Baseline Visual Acuity and Retinal Thickness With 1-Year Efficacy of Aflibercept, Bevacizumab, and Ranibizumab for Diabetic Macular Edema (2015)

clinicaltrials.gov Identifier: NCT01627249.
Formation of Al Nanostructures on Alq3: An in Situ Grazing Incidence Small Angle X-ray Scattering Study during Radio Frequency Sputter Deposition (2013)

The formation of metal/organic interfaces is a complicated process involving chemical interaction, physical nucleation and diffusion, and thin film growth. It is closely related to the performance of organic electronic devices. To understand this process, we investigate the system of aluminum (Al) and tris(8-hydroxyquinolinato)aluminum (Alq3) as a model, owing to the well-known strong chemical interaction between both and their close technological relevance to organic light emitting devices. By using grazing small angle incidence X-ray scattering (GISAXS), we follow the Al thin film development on top of Alq3 during radio frequency (rf) sputter deposition in real-time and without interrupting the growth process. Three growth stages have been clearly distinguished: Al diffusion into Alq3, Al/Alq3 complex agglomeration and self-assembled Al pillar nanostructure thin film development. Thus in situ GISAXS yields the fundamental insights into the formation of the metal/organic interface for small organic semiconductor devices, prepared via vacuum based deposition techniques.
An angle-dependent estimation of CT x-ray spectrum from rotational transmission measurements (2014)

An angle-dependent estimation technique of CT x-ray spectra from rotational transmission measurements was proposed. Compared with the conventional technique, the proposed method simplifies the measurement procedures and enables incident spectral estimation for a wide range of angular trajectories. The proposed technique is suitable for rigorous research objectives as well as routine clinical quality control procedures.
Non-hydrolytic metal oxide films for perovskite halide overcoating and stabilization (2023)

A method of protecting a perovskite halide film from moisture and temperature includes positioning the perovskite halide film in a chamber. The chamber is maintained at a temperature of less than 200 degrees Celsius. An organo-metal compound is inserted into the chamber. A non-hydrolytic oxygen source is subsequently inserted into the chamber. The inserting of the organo-metal compound and subsequent inserting of the non-hydrolytic oxygen source into the chamber is repeated for a predetermined number of cycles. The non-hydrolytic oxygen source and the organo-metal compound interact in the chamber to deposit a non-hydrolytic metal oxide film on perovskite halide film. The non-hydrolytic metal oxide film protects the perovskite halide film from relative humidity of greater than 35% and a temperature of greater than 150 degrees Celsius, respectively.
Effect of Substrate Size on the Electrochemical Properties of Boron-doped Diamond Powders for Screen-printed Diamond Electrode (2018)

Boron-doped diamond powder (BDDP) was prepared using various sizes of diamond powder (DP) core (300–2600 nm), and the electrochemical properties of a screen-printed electrode obtained using the BDD...
Circuit implementation of synchronized chaos with applications to communications (1993)

An analog circuit implementation of the chaotic Lorenz system is described and used to demonstrate two possible approaches to private communications based on synchronized chaotic systems.Received 21 January 1993DOI:https://doi.org/10.1103/PhysRevLett.71.65©1993 American Physical Society
UrbanRama: Navigating Cities in Virtual Reality (2021)

Exploring large virtual environments, such as cities, is a central task in several domains, such as gaming and urban planning. VR systems can greatly help this task by providing an immersive experience; however, a common issue with viewing and navigating a city in the traditional sense is that users can either obtain a local or a global view, but not both at the same time, requiring them to continuously switch between perspectives, losing context and distracting them from their analysis. In this article, our goal is to allow users to navigate to points of interest without changing perspectives. To accomplish this, we design an intuitive navigation interface that takes advantage of the strong sense of spatial presence provided by VR. We supplement this interface with a perspective that warps the environment, called UrbanRama, based on a cylindrical projection, providing a mix of local and global views. The design of this interface was performed as an iterative process in collaboration with architects and urban planners. We conducted a qualitative and a quantitative pilot user study to evaluate UrbanRama and the results indicate the effectiveness of our system in reducing perspective changes, while ensuring that the warping doesn't affect distance and orientation perception.
Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry for Top-Down Characterization of the Mycobacterium marinum Secretome (2014)

Capillary zone electrophoresis (CZE) with an electrokinetically pumped sheath-flow nanospray interface was coupled with a high-resolution Q-Exactive mass spectrometer for the analysis of culture filtrates from Mycobacterium marinum. We confidently identified 22 gene products from the wildtype M. marinum secretome in a single CZE-tandem mass spectrometry (MS/MS) run. A total of 58 proteoforms were observed with post-translational modifications including signal peptide removal, N-terminal methionine excision, and acetylation. The conductivities of aqueous acetic acid and formic acid solutions were measured from 0.1% to 100% concentration (v/v). Acetic acid (70%) provided lower conductivity than 0.25% formic acid and was evaluated as low ionic-strength and a CZE-MS compatible sample buffer with good protein solubility.
Quantitative Gait Evaluation of Coxarthrosis Using Gait Analysis (2005)

In this report, gait analysis was performed on 176 patients (mean age 61.1 years) who underwent total hip arthroplasty from March 2003 to June 2004. All patients were tested during "free" walking along an 5-m walkway in which a ground reaction force plate (gait scan 8000; Nitta, Inc.) was installed. Clinical evaluation was carried out on age, sex, Japanese Orthopaedic Association (JOA) score, OA stage, and limb length discrepancy.Multivariate analysis showed that clinical data associated with single support duration were JOA pain score (p<0.001), JOA gait score (p<0.001), and JOA ROM score (p<0.05). Clinical data associated with double support duration were JOA pain score (p<0.001) and JOA gait score (p<0.001). The results of gait analysis can be used as objective index of hip pain and gait ability.
Role of CD4+ and CD8+ T cells in the rejection of concordant pancreas xenografts1 (2002)

The current results show that CD4 T cells are necessary and sufficient for mediating the rejection of Lewis rat pancreas xenografts in STZ-induced diabetic mice. However, CD8 cells, when activated, can also induce acute rejection of concordant pancreas xenografts.
Molecular characterization of the diabetes-associated mouse MHC class II protein, I-Ag7 (1997)

The MHC class II molecule of the non-obese diabetic (NOD) mice, I-Ag7, is associated with susceptibility to autoimmune diabetes. To try to understand the molecular basis of this association, we analyzed the peptide binding properties and intracellular behavior of I-Ag7 in comparison with other I-A haplotypes. We found that I-Ag7 molecules manifested normal intracellular trafficking and lifespan, and a small but clearly detectable fraction of I-Ag7 in the cells formed SDS-resistant compact dimers. The binding of an antigenic reference peptide to I-Ag7 was stable and was accompanied by compact dimer formation. Our analysis of the binding specificity of I-Ag7 revealed a peptide binding motif of nine amino acids with a degenerate position at P1 and three conserved anchor positions: P4, P6 and P9. An allele-specific preference for negatively charged residues was found at P9, apparently due to the presence of the rare Ser residue at position 57 of the I-Ag7 beta chain. These findings could have implications for the mechanisms of MHC-mediated susceptibility to autoimmune diabetes in the NOD mice.
Active Velocity Estimation using Light Curtains via Self-Supervised Multi-Armed Bandits (2023)

To navigate in an environment safely and autonomously, robots must accurately estimate where obstacles are and how they move. Instead of using expensive traditional 3D sensors, we explore the use of a much cheaper, faster, and higher resolution alternative: programmable light curtains. Light curtains are a controllable depth sensor that sense only along a surface that the user selects. We adapt a probabilistic method based on particle filters and occupancy grids to explicitly estimate the position and velocity of 3D points in the scene using partial measurements made by light curtains. The central challenge is to decide where to place the light curtain to accurately perform this task. We propose multiple curtain placement strategies guided by maximizing information gain and verifying predicted object locations. Then, we combine these strategies using an online learning framework. We propose a novel self-supervised reward function that evaluates the accuracy of current velocity estimates using future light curtain placements. We use a multi-armed bandit framework to intelligently switch between placement policies in real time, outperforming fixed policies. We develop a full-stack navigation system that uses position and velocity estimates from light curtains for downstream tasks such as localization, mapping, path-planning, and obstacle avoidance. This work paves the way for controllable light curtains to accurately, efficiently, and purposefully perceive and navigate complex and dynamic environments. Project website: https://siddancha.github.io/projects/active-velocity-estimation/
Liprin β1 is highly expressed in lymphatic vasculature and is important for lymphatic vessel integrity (2009)

The lymphatic vasculature is important for the regulation of tissue fluid homeostasis, immune response, and lipid absorption, and the development of in vitro models should allow for a better understanding of the mechanisms regulating lymphatic vascular growth, repair, and function. Here we report isolation and characterization of lymphatic endothelial cells from human intestine and show that intestinal lymphatic endothelial cells have a related but distinct gene expression profile from human dermal lymphatic endothelial cells. Furthermore, we identify liprin beta1, a member of the family of LAR transmembrane tyrosine phosphatase-interacting proteins, as highly expressed in intestinal lymphatic endothelial cells in vitro and lymphatic vasculature in vivo, and show that it plays an important role in the maintenance of lymphatic vessel integrity in Xenopus tadpoles.
An infrared study of the effects of hydration on cation-loaded nafion thin films (2000)

We explore the effects of hydration on the vibrational spectra of cation-exchanged Nafion thin films. In addition to the initial H+ form of the membrane, the cations selected for study include: Na+, NH, tetramethylammonium, tetrabutylammonium, hexadecyltrimethylammonium, and tris(2,2′-bipyridine)osmium(II). A flow cell is used to follow the changes occurring in a 1000-Å film in response to variations in the humidity of a nitrogen purge gas flowing through the cell. The structural changes occurring due to the binding of water to these cation-exchanged membranes is followed across a broad range of water contents with IR difference spectroscopy. Our results demonstrate a complex role for water in mediating the polyanion–cation interactions. Side-chain reconstructions may play an important role in the ion-binding and transport properties of the ionomer domains. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1512–1520, 2000
Born Normalization for Fluorescence Optical Projection Tomography for Whole Heart Imaging (2009)

Optical projection tomography is a three-dimensional imaging technique that has been recently introduced as an imaging tool primarily in developmental biology and gene expression studies. The technique renders biological sample optically transparent by first dehydrating them and then placing in a mixture of benzyl alcohol and benzyl benzoate in a 2:1 ratio (BABB or Murray s Clear solution). The technique renders biological samples optically transparent by first dehydrating them in graded ethanol solutions then placing them in a mixture of benzyl alcohol and benzyl benzoate in a 2:1 ratio (BABB or Murray s Clear solution) to clear. After the clearing process the scattering contribution in the sample can be greatly reduced and made almost negligible while the absorption contribution cannot be eliminated completely. When trying to reconstruct the fluorescence distribution within the sample under investigation, this contribution affects the reconstructions and leads, inevitably, to image artifacts and quantification errors.. While absorption could be reduced further with a permanence of weeks or months in the clearing media, this will lead to progressive loss of fluorescence and to an unrealistically long sample processing time. This is true when reconstructing both exogenous contrast agents (molecular contrast agents) as well as endogenous contrast (e.g. reconstructions of genetically expressed fluorescent proteins).
Combination of 3D Printing and ALD for Dentin Fabrication from Dental Pulp Stem Cell Culture (2021)

A combination of fused deposition modeling printing with atomic layer deposition (ALD) of titania was designed to achieve templated biomineralization and terminal odontogenic differentiation of dental pulp stem cells on three-dimensional (3D) printed polylactic acid (PLA) scaffolds. In the absence of the ALD-deposited titania coating, we had previously shown that both plating efficiency and differentiation are adversely impacted when scaffolds are produced by 3D printing rather than traditional polymer molding. These differences were removed when both printed and molded structures were coated with ALD of titania, which improved the outcomes regardless of the manufacturing method. In this case, on all titania-coated substrates, the plating efficiency increased, copious mineral deposition was observed, and RT-PCR indicated a significant upregulation of osteocalcin, a gene associated with mineral deposition. The influence of additional coatings of collagen, gelatin, or fibronectin on the ALD titania-coated and uncoated PLA-printed and molded scaffolds was also investigated. Upregulation of the odontogenic late-stage differentiation sibling protein, dentin sialoprotein, was observed on the collagen ALD-titania-coated scaffolds and to a lesser extent on the gelatin ALD-titania-coated scaffolds.
ChemInform Abstract: Trofimov Pyrrole Synthesis (2012)

Abstract Review: 18 refs.
Structure/function studies and protein engineering of ATP‐dependent peptide ligases (2007)

Glutathione is found in mammals, plants, and bacteria and is synthesized by glutathione synthetase (GS). Some plants synthesize glutathione analogs in which ?‐alanine replaces glycine. The chemical diversity of these molecules suggests that the substrate specificity of the GS‐like peptide ligases differs from GS, but the molecular basis for this variety remains unclear. To better understand the reaction mechanism of Arabidopsis GS (AtGS) site‐directed mutagenesis was performed. Residues interacting with bound magnesium ions (E148, N150, E371, and E429) were essential for activity. K313 and K367 were important for ATP binding. Kinetic analysis suggests that R132 provides a key catalytic role. To define the determinants of substrate specificity, we compared AtGS (glycine specific) with Glycine max (soybean) homo‐glutathione synthetase (GmhGS; ?‐alanine specific). Sequence alignments suggest that two active site residues (AtGS: A466 and A467; GmhGS: L466 and P467) modulate substrate preference between glycine and ?‐alanine. The interconversion of AtGS to GmhGS and vice versa is described. GmhGS displays a 700‐fold preference for ?‐alanine, whereas, the double mutant accepts either substrate with equal efficiency. This suggests that differences outside the active site further define substrate specificity in this family of enzymes, and emphasize the need for crystallographic studies.
Optical and structural studies of compositional inhomogeneity in strain-relaxed indium gallium nitride films (2002)

The structural and optical properties of indium gallium nitride (In/sub x/Ga/sub 1-x/N) films with 0.04<x<0.47, grown by metal-organic chemical vapor deposition, were examined by X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS), optical transmittance, and cathodoluminescence (CL) spectroscopies. The average indium fraction (x/sub avg/) was measured by wavelength-dispersive X-ray spectroscopy in an electron-probe microanalyzer (WDS/EPMA). Pure GaN and InN films were also characterized. Comparison of the 0006 XRD data with the WDS data shows that the lattice constant c is a linear function of x/sub avg/. A small amount of a high-indium (x/spl ap/0.99) phase was observed in films with x/sub avg//spl ges/0.44. From EXAFS, the composition of the indium second-neighbor shell is equal (within the 2/spl sigma/ measurement uncertainty) to x/sub avg/. These results are consistent with a random-alloy structure. The optical band gap, determined from the position of the absorption edge in the transmittance spectrum, and also from the highest-energy CL peak, is described well by a quadratic function of x/sub avg/ with a second-order (bowing) parameter of (-4.57/spl plusmn/0.75) eV. The magnitude of the composition fluctuations in the alloy films, denoted /spl Delta/x, was estimated by analyzing the full widths at half maximum (FWHMs) of the XRD peaks and also the band-edge CL peaks. The two calculations of /spl Delta/x give similar results.