gebhart/patrepeval huggingface dataset:
Use Of Low Light Image Microscopy To Monitor Genetically Engineered Bacterial Luciferase Gene Expression In Living Cells And Gene Activation Throughout The Development Of A Transgenic Organism (1989)

Procaryotic and eucaryotic expression vectors which contain a marker gene for selection of transformants linked to genes encoding bacterial luciferase for detection of promoter activated gene expression in vivo were used to transform the appropriate host organisms and drug resistant colonies, cells, or calli were obtained. Bacterial luciferase expression was measured by a luminescence assay for quantitative determination of promoter activation. The cellular localization of bacteria inside the host plant cell cytoplasm was achieved in a single infected plant cell based on the light emitting ability of the genetically engineered bacteria. In addition, the bacterial luciferase marker gene fusions were used to monitor cell type, tissue, and organ specific gene expression in transgenic plants in vivo. To monitor physiological changes during ontogeny of a transformed plant, low light video microscopy, aided by real time image processing techniques developed specifically to enhance extreme low light images, was successfully applied.
ChemInform Abstract: Total Synthesis of (S)‐Espicufolin and Absolute Structure Determination of Espicufolin. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Drug Stability Analysis by Raman Spectroscopy (2014)

Pharmaceutical drugs are available to astronauts to help them overcome the deleterious effects of weightlessness, sickness and injuries. Unfortunately, recent studies have shown that some of the drugs currently used may degrade more rapidly in space, losing their potency before their expiration dates. To complicate matters, the degradation products of some drugs can be toxic. Here, we present a preliminary investigation of the ability of Raman spectroscopy to quantify mixtures of four drugs; acetaminophen, azithromycin, epinephrine, and lidocaine, with their primary degradation products. The Raman spectra for the mixtures were replicated by adding the pure spectra of the drug and its degradant to determine the relative percent contributions using classical least squares. This multivariate approach allowed determining concentrations in ~10 min with a limit of detection of ~4% of the degradant. These results suggest that a Raman analyzer could be used to assess drug potency, nondestructively, at the time of use to ensure crewmember safety.
Ti underlayer effect on the ordering of CoPt in (Co/Pt)4 multilayer thin films on Si/SiO2 substrates (2020)

Abstract L 1 2 -ordered CoPt 3 and L 1 0 -ordered CoPt are formed in electron-beam-deposited (Co/Pt) 4 multilayer thin films with and without a Ti underlayer, respectively, on Si/SiO 2 substrates by rapid thermal annealing. The crystal structures, magnetic properties, and surface morphologies of the films are investigated by grazing incidence X-ray diffraction (GI-XRD), vibrating sample magnetometer (VSM), and scanning electron microscope (SEM), respectively. In the film without a Ti underlayer, L 1 0 -ordered CoPt with an isolated round grain structure is confirmed, showing an in-plane coercivity of 2.7 kOe. In contrast, in the film with a Ti underlayer, L 1 2 -ordered CoPt 3 is confirmed together with Co-rich A 1-disordered CoPt, showing an in-plane coercivity of 500 Oe, which exhibits an angular-outlined continuous film structure. The three sets of experimental results from GI-XRD, VSM, and SEM coincide well with each other.
Structural and kinetic mapping of side-chain exposure onto the protein energy landscape (2011)

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.
The effect of three human recombinant hematopoietic growth factors (granulocyte-macrophage colony-stimulating factor, granulocyte colony- stimulating factor, and interleukin-3) on phagocyte oxidative activity (1993)

Hematopoietic growth factors not only modulate blood progenitor cell activity but also alter the function of mature phagocytes. Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF; 1 ng/mL for 60 min) did not stimulate luminol-enhanced chemiluminescence of polymorphonuclear leukocytes (PMNs) in suspension but primed PMN for as much as a 15-fold increase in chemiluminescence in response to f-met- leu-phe (fMLP). Mixed mononuclear leukocytes (monocytes [approximately 20%] and lymphocytes [approximately 80%]; MNL) chemiluminescence was very low even after rhGM-CSF priming, but MNLs added to the PMNs (PMN- MNL) resulted in near doubling of rhGM-CSF-primed PMN fMLP-stimulated chemiluminescence. The enhancing factor(s) from MNLs were inherent rather than induced by the GM-CSF, and purified lymphocytes increased GM-CSF-primed PMN chemiluminescence equal to mixed MNLs. We could not detect cell-free “enhancing factor(s),” but cell-to-cell contact further enhanced rhGM-CSF-primed fMLP-stimulated PMN-MNL oxidative activity by 40%. Polyclonal rabbit anti-tumor necrosis factor (TNF) (but not preimmune serum) decreased both fMLP-stimulated rhGM-CSF- primed PMNs and PMN-MNL chemiluminescence, suggesting that TNF on the PMN surface is enhancing GM-CSF-primed chemiluminescence. GM-CSF priming markedly increased PMN superoxide release (sevenfold), but PMN superoxide release was not further enhanced by the presence of MNLs. Recombinant human granulocyte colony-stimulating factor (rhG-CSF) and interleukin-3 (rhIL-3) displayed much smaller effects on pure PMNs and mixed PMN-MNL chemiluminescence and superoxide release than rhGM-CSF. rhGM-CSF primes PMNs for increased oxidative activity more than rhG-CSF and rhIL-3. Maximal oxidative activity was observed when mixed PMN-MNL were primed with GM-CSF in a cell pellet-promoting cell-to-cell contact. This enhanced activity can be attributed, in part, to both inherent enhancing factor(s) on lymphocytes and PMN-associated TNF induced by GM-CSF.
Abstract 24: Two Locus Inheritance of Non-Syndromic Midline Craniosynostosis Via Rare SMAD6 and Common BMP2 Alleles (2017)

PURPOSE: Non-syndromic sagittal and/or metopic craniosynostosis, occurring once in every 4,000 live births, accounts for half of all craniosynostosis cases. Despite success in identifying the genes underlying rare syndromic craniosynostoses, mutations in these genes are very rarely found in their non-syndromic counterparts. We considered that the often sporadic occurrence of non-syndromic craniosynostosis might frequently be attributable to de novo mutation or incomplete penetrance of rare transmitted variants. METHODS: To identify mutations contributing to common non-syndromic midline (sagittal and metopic) craniosynostosis, we performed exome sequencing of 132 parent-offspring trios and 59 additional probands. RESULTS: Thirteen probands (7%) had damaging de novo or rare transmitted mutations in SMAD6, an inhibitor of BMP - induced osteoblast differentiation (p<10–20). SMAD6 mutations nonetheless showed striking incomplete penetrance (<60%). Genotypes of a common variant near BMP2 that is strongly associated with midline craniosynostosis explained nearly all the phenotypic variation in these kindreds, with highly significant evidence of genetic interaction between these loci via both association and analysis of linkage. A de novo mutation in SMURF1, a SMAD6 binding partner, was also identified. CONCLUSION: This epistatic interaction of rare and common variants defines the most frequent cause of midline craniosynostosis and has implications for the genetic basis of other diseases.
Femtosecond dynamics of the laser-induced solid-to-liquid phase transition in aluminum (2007)

We present femtosecond time-resolved measurements of the reflectivity of aluminum during the laser-induced solid-to-liquid phase transition over the $1.7--3.5\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ spectral range. Previous optical and electron-diffraction studies have shown discrepancies on the order of picoseconds in the time scale of the solid-to-liquid phase change. As a result, it is not clear if the transition mechanism is thermal or nonthermal. Our experiments conclusively show that this transition is a thermal process mediated through the transfer of heat from the photoexcited electronic population to the lattice. Our findings agree with the results of the electron-diffraction study and rule out the nonthermal mechanism proposed by the optical study.
Ultrasonic determination of the properties of food dispersions. (1999)

Ultrasound has many advantages for the determination of the properties of foods. It can be non-invasive and even non-intrusive. It is safe, economic and penetrates many optically opaque materials. It normally gives a bulk average reading over the volume of the ultrasonic beam and may be used in both transmission and reflection modes. Recent advances in the understanding of the interaction between ultrasound and dispersions, together with newly available apparatus, have greatly expanded the available range of ultrasound techniques. Here the basic theory and techniques for the determination of the properties of food dispersions are reviewed.
Automated Noninvasive Clinical Dehydration Detection Device (2009)

Dehydration is a common problem in healthy individuals as well as the elderly and chronically ill. People are often poorly attuned to hydration, and despite widespread awareness of the problem, fatal and near-fatal episodes occur frequently. Typical indicators of hydration status include changes in body weight, urine specific gravity, blood plasma levels, and bioelectrical impedance. Challenges to estimating hydration status from these indicators include the invasive nature of some methods as well as the cost and time required. We have developed a noninvasive device for monitoring hydration status. Our design is inspired by the traditional clinical protocol that approximates fluid loss on the order of 1-2% dehydration by assessing radial pulse before and after a supine to standing transition. The prototype comprises an inertial measurement unit (Xsens MTi) and a wearable heart rate monitor (Polar S810i). In order to compare heart rate behavior under normal and low hydration levels, fluid loss equivalent to 1-4% of the baseline body weight was induced by exercise in three healthy subjects during two data collection sessions. In the first (control) session, subjects replaced fluids every 15 minutes during exercise to maintain their body weight within 0.2% of their baseline value. Fluids were not replaced during the second (test) session, and subjects lost an average of 1.2% of their body weight. Heart rate and body position measurements were recorded before and after exercise while subjects performed repeated supine-to-standing movements and knee-to-chest stretching exercises (supine position only). All post-processing was performed using MATLAB (The MathWorks). Average heart rate was calculated over a 10 second period. Pilot data demonstrates the device's ability to detect hydration changes on the order of 1% in one-third the time required by the traditional clinical protocol (30 seconds compared to 90 seconds). The average rise time from baseline to maximum heart rate and the maximum heart rate following supine-to-standing transitions were significantly longer and greater, respectively, in the dehydrated subjects. Although not statistically significant, the average heart rate during knee-to-chest stretching exercises was elevated in the dehydrated state.
Tailored Protocol Development Using ESTEREL (1994)

Syntax Notation One (ASN 1)&amp;quot;, Geneva, July 1987. [Madeleine 89] E. Madelaine and D. Vergamini. Auto}: A Verification Tool for Distributed Systems Using Reduction of Finite Automata Networks&amp;quot;. Proc. FORTE&amp;apos;89 Conference. Vancouver. 1989. [Merlin 76] P. M. Merlin. A Methodology for the Design and Implementation of Communication Protocols. IEEE Transactions on Communications. Vol. COM-24, No. 6. June 1976. [Partridge 92] C. Partridge and S. Pink ; &amp;quot;An Implementation of the Revised Internet Stream Protocol (ST II). Internetworking : Research and Experience ; Vol. 3, pp. 27-54, 1992. [Roy 90] V. Roy and R. de Simone. &amp;quot;Auto and Autograph&amp;quot;. Proceedings of CAV &amp;apos; 90. R. Kurshan Editor. June 1990. [Smith 83] F. D. Smith, C. H. West. Technologies for Network Architecture and Implementation. IBM Journal on R&amp;amp;D. Vol. 27, No. 1. January 1983. [Touati 93] H. Touati and G. Berry. &amp;quot; Optimized Controller Synthesis Using Esterel &amp;quot;. Proceedings of the International Workshop on Logic Synthesis IWLS &amp;apos;9...
Polymerase Activity Induced by Metal Ions and Its Use for Logic Gate Operations (2010)

We have developed a new strategy in which a polymerase enzyme is controlled to accomplish an unnatural extension reaction even at the mismatched site of a primer with template DNA. The validity of this novel concept was systematically demonstrated by using Hg2+ and Ag+ ions to intentionally trigger an unusual illusionary polymerase activity at respective T-T and C-C mismatched primers on the basis of their specific interactions with the respective mismatched base pairs T-T and C-C. By utilizing this new concept, a molecular scale logic gate system has been successfully constructed by rationally designing primers and selecting the type of DNA polymerase employed. The most notable feature of the logic gates devised herein is their simplicity and cost-effective design since the only requirement for construction of the new logic gates is the incorporation of a single mismatched base (T and C) at the 3’ end of the primer and the application of metal ions (Hg2+ and Ag+). Moreover, this novel concept that the unnatural polymerase activity could be triggered by metal ions could be utilized to develop new strategies for the detection of metal ions (Hg2+ and Ag+).
Sequential involvement of CCR2 and CCR6 ligands for immature dendritic cell recruitment: possible role at inflamed epithelial surfaces (2002)

To reach the site of antigen deposition at epithelial surfaces, dendritic cells (DC) have to traverse the endothelial barrier, progress through the tissue (i.e., dermis) and cross the dermo-epithelial junction (basal membrane). In the present study, we demonstrate that (1) circulating blood DC and monocytes express high levels of CCR2 and primarily respond to monocyte chemotactic protein (MCP) and not to macrophage inflammatory protein (MIP)-3alpha/CCL20; (2) while the CD34(+) hematopoietic progenitor cells (HPC)-derived CD1a(+) precursors committed to Langerhans cell differentiation primarily respond to MIP-3alpha/CCL20, the HPC-derived CD14(+) precursors respond to both MCP and MIP-3alpha/CCL20; (3) in concordance with the sequential expression of CCR2 and CCR6, the HPC-derived CD14(+) precursors initially acquire the ability to migrate in response to MCP-4/CCL13 and subsequently in response to MIP-3alpha/CCL20; and (4) in vivo, in inflamed epithelium, MCP-4/CCL13 and MIP-3alpha/CCL20 form complementary gradients, with MCP-4/CCL13 expressed in basal epithelial cells at the contact of blood vessels, while MIP-3alpha/CCL20 expression is restricted to epithelial cells bordering the external milieu. These observations suggest that the recruitment of DC to the site of infection is controlled by the sequential action of different chemokines: (i) CCR2(+) circulating DC or DC precursors are mobilized into the tissue via the expression of MCP by cells lining blood vessels, and (ii) these cells traffic from the tissue to the site of pathogen invasion via the production of MIP-3alpha/CL20 by epithelial cells and the up-regulation of CCR6 in response to the tissue environment.
GITR contributes to the systemic adjuvanticity of the Escherichia coli heat‐labile enterotoxin (2009)

The Escherichia coli heat-labile enterotoxin (LT) possesses a powerful mucosal and systemic adjuvant effect. However, little is known about the cellular and molecular basis of the immunostimulatory activity of LT at the mucosal level, and even less information is available on the mechanisms underlying its systemic adjuvant activity. In this study, we show that distinct mechanisms are responsible for the parenteral and mucosal adjuvanticity of LT. Indeed, the systemic administration of LT upregulates the expression of glucocorticoid-induced TNFR-related protein (GITR), but not other activation markers, in naive T cells. Using WT and GITR-deficient mice and LT and its enzymatically inactive mutant LTK63 as adjuvants, we show that the induction of GITR expression in T cells accounts for the systemic immunostimulatory capacity of LT, which requires an intact enzymatic activity. In contrast, the mucosal administration of LT does not induce GITR expression on Peyer's patche T cells and accordingly no differences are observed in the mucosal adjuvanticity of LT between WT and GITR-deficient mice. Altogether, our results demonstrate the distinct effect of LT after parenteral administration when compared with the mucosal delivery, and describe a new mechanism of LT adjuvanticity related to its ability to induce the expression of GITR in CD4(+) T cells.
Manifestation of aberrations in full-field optical coherence tomography (2021)

We report on a theoretical model for image formation in full-field optical coherence tomography (FFOCT). Because the spatial incoherence of the illumination acts as a virtual confocal pinhole in FFOCT, its imaging performance is equivalent to a scanning time-gated coherent confocal microscope. In agreement with optical experiments enabling a precise control of aberrations, FFOCT is shown to have nearly twice the resolution of standard imaging at moderate aberration level. Beyond a rigorous study on the sensitivity of FFOCT with respect to aberrations, this theoretical model paves the way towards an optimized design of adaptive optics and computational tools for high-resolution and deep imaging of biological tissues.
Determination of time-varying pressure field from phase contrast MRI data (2012)

Methods We propose a numerical framework for determining pressure field in large arteries, the main components of which are: axi-symmetric 1-D unsteady wave-propagation model with elastic walls and an optimization framework for model personalization via parameter estimation from measured flow and anatomical data (Fig 1). 4D PC MRI data was acquired using a multi-slice phase contrast FLASH cine sequence with 3d velocity encoding (Siemens Magnetom Verio, temporal resolution 52 ms, matrix 100x192, FOV 319x219 mm, slice thickness 5 mm) in a sagittal to coronal slice orientation. Siemens 4D Flow WIP software was used for background phase, motion and venc anti-aliasing corrections, extracting vessel models including centerline trees and lumen boundary, and for automated extraction of flow profiles and cross-sectional areas. We use a linear elastic model for the vessel wall, with an axially varying stiffness. The parameters of the material model are estimated by a numerical optimization procedure, wherein the simulated deformation is fitted to the observed deformation of the vessel wall extracted from the MR data. Unsteady flow rate at the aortic inlet is extracted from PC-MRI data and used as the inlet boundary condition. To obtain physiologically valid mean and pulse pressure values and the wave propagation effects, we use a structured tree outflow boundary condition, wherein a morphological or fractal vessel tree is introduced to model the downstream behavior at the outlets of the vessel tree. The parameters for the outlet boundary condition are then independently perturbed at each individual outlet in order to match the measured unsteady outflow rate from PC-MRI data. This is achieved by adapting the final radius at which the asymmetric binary tree is terminated. The hyperbolic PDEs are solved using finite differences based on 2nd-order Lax-Wendroff method. Simulations converge after 3 cycles, with a maximum relative difference of 1% in pressure and flow between 2 consecutive cycles.
Quantitative description of macrocycle-mediated cation separations in liquid membranes and on silica gel as a function of system parameters (1988)

Abstract
ChemInform Abstract: Total Synthesis of the Incorrectly Proposed Quaterpyridine Isolated from the Hoplonemertine Sea Worm. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Box Shaped Monopole Antenna for RF Excitation at 9.4T MRI (2014)

It is a big challenge to produce as homogeneous as possible B1+ field with single channel antenna in traveling wave configuration. For that purpose, we proposed a new and very simple antenna concept. Antenna is entirely made of copper and without any lumped elements. By small changes in geometry different RF excitation patterns can be produced. We presented design that produced as homogeneous as possible B1+ field in sagittal, coronal and transversal planes. The second proposed design produced B1+field pattern in lower brain and neck region.
Analytic performance models for bounded queueing systems (2008)

Pipelined computing applications often have their performance modeled using queueing techniques. While networks with infinite capacity queues have well understood properties, networks with finite capacity queues and blocking between servers have resisted closed-form solutions and are typically analyzed with approximate solutions. It is this latter case that more closely represents the circumstances present for pipelined computation. In this paper, we extend an existing approximate solution technique and, more importantly, provide guidance as to when the approximate solutions work well and when they fail.