gebhart/patrepeval huggingface dataset:
Molecular phenotyping of single pancreatic islet leader beta cells by “Flash-Seq” (2022)

Abstract Aims Spatially-organised increases in cytosolic Ca 2+ within pancreatic beta cells in the pancreatic islet underlie the stimulation of insulin secretion by high glucose. Recent data have revealed the existence of subpopulations of beta cells including “leaders” which initiate Ca 2+ waves. Whether leader cells possess unique molecular features, or localisation, is unknown. Main methods High speed confocal Ca 2+ imaging was used to identify leader cells and connectivity analysis, running under MATLAB and Python, to identify highly connected “hub” cells. To explore transcriptomic differences between beta cell sub-groups, individual leaders or followers were labelled by photo-activation of the cryptic fluorescent protein PA-mCherry and subjected to single cell RNA sequencing (“Flash-Seq”). Key findings Distinct Ca 2+ wave types were identified in individual islets, with leader cells present in 73 % (28 of 38 islets imaged). Scale-free, power law-adherent behaviour was also observed in 29% of islets, though “hub” cells in these islets did not overlap with leaders. Transcripts differentially expressed (295; padj&lt;0.05) between leader and follower cells included genes involved in cilium biogenesis and transcriptional regulation. Functionally validating these findings, cilia number and length tended to be lower in leader vs follower cells. Leader cells were also located significantly closer to delta cells in Euclidian space than were follower cells. Significance The existence of both a discrete transcriptome and unique localisation implies a role for these features in defining the specialized function of leaders. Specifically, these data raise the possibility of altered signalling from delta cells towards somatostatin receptors present on leader cell cilia.
Adipokines and Metabolic Regulators in Human and Experimental Pulmonary Arterial Hypertension (2021)

Pulmonary hypertension (PH) is associated with meta-inflammation related to obesity but the role of adipose tissue in PH pathogenesis is unknown. We hypothesized that adipose tissue-derived metabolic regulators are altered in human and experimental PH. We measured circulating levels of fatty acid binding protein 4 (FABP-4), fibroblast growth factor -21 (FGF-21), adiponectin, and the mRNA levels of FABP-4, FGF-21, and peroxisome proliferator-activated receptor γ (PPARγ) in lung tissue of patients with idiopathic PH and healthy controls. We also evaluated lung and adipose tissue expression of these mediators in the three most commonly used experimental rodent models of pulmonary hypertension. Circulating levels of FABP-4, FGF-21, and adiponectin were significantly elevated in PH patients compared to controls and the mRNA levels of these regulators and PPARγ were also significantly increased in human PH lungs and in the lungs of rats with experimental PH compared to controls. These findings were coupled with increased levels of adipose tissue mRNA of genes related to glucose uptake, glycolysis, tricarboxylic acid cycle, and fatty acid oxidation in experimental PH. Our results support that metabolic alterations in human PH are recapitulated in rodent models of the disease and suggest that adipose tissue may contribute to PH pathogenesis.
Binding of lysozyme to common pili of Escherichia coli (1979)

Common pili from Escherichia coli were found to bind hen egg white lysozyme. The binding was highly dependent on ionic strength, and the maximum binding occurred near an ionic strength of 0.02. The pili were aggregated by lysozyme, and this process could be followed by optical turbidity, electron microscopy, and coprecipitation. Near the maximum saturation of binding, one lysozyme molecule was bound by two pilus protein subunits. Electron micrographs of this aggregate indicated that they were paracrystalline structures. Piliated bacteria were more readily agglutinated by lysozyme than were nonpiliated bacteria. Since lysozyme is considered to be an antibacterial humoral factor and since pili are considered to be a colonization factor, the binding of lysozyme may represent an important bacterium-host interaction
Abstract 18024: Physiologic and Molecular Characterization of a Murine Model of Pulmonary Insufficiency (2010)

Introduction: Pulmonary insufficiency (PI) is a common long-term outcome after repair of tetralogy of Fallot, causing progressive right ventricular (RV) dilation and eventual RV failure. We charact...
Mapping Charge Recombination and the Effect of Point-Defect Insertion in GaAs Nanowire Heterojunctions (2021)

Electronic devices are extremely sensitive to defects in their constituent semiconductors, but locating electronic point defects in bulk semiconductors has previously been impossible. Here we apply scanning transmission electron microscopy (STEM) electron-beam-induced current (EBIC) imaging to map electronic defects in a $\mathrm{GaAs}$ nanowire Schottky diode. Imaging with a nondamaging 80 or 200 kV STEM acceleration potential reveals a minority-carrier diffusion length that decreases near the surface of the hexagonal nanowire, thereby demonstrating that the device's charge collection efficiency (CCE) is limited by surface defects. Imaging with a 300 keV STEM beam introduces vacancy-interstitial (or Frenkel) defects in the $\mathrm{GaAs}$ that increase carrier recombination and reduce the CCE of the diode. We create, locate, and characterize a single insertion event, determining that a defect inserted 7 nm from the Schottky interface broadly reduces the CCE by $10\mathrm{%}$ across the entire nanowire device. Variable-energy STEM EBIC imaging thus allows both benign mapping and pinpoint modification of a device's electron-hole-recombination landscape, enabling controlled experiments that illuminate the impact of both extended (one- and two-dimensional) and point (zero-dimensional) defects on semiconductor device performance.
Application of Contrast Enhancement Bilateral Closing Top-hat Otsu Thresholding (CEBICTOT) technique on crack images (2008)

This paper introduces the contrast enhancement bilateral closing top-hat Otsu thresholding (CEBITOT) technique to perform crack detection. This technique is based on the mathematical morphology and image filtering technique to extract the crack like patterns. Mathematical morphology highlights the cracks clearly while bilateral filtering filters out the noise from the image efficiently and preserving the edges. The performance of the proposed estimator is compared with two existing methods: Otsu method, Iyer* and Sinha method over several images. The performance of the CEBITOT is significantly greater than that of the two methods.
Vulnerability and Protocol Association of Device Firmware in Power Grid (2018)

The intelligent power grid is composed of a large number of industrial control equipment, and most of the industrial control equipment has security holes, which are vulnerable to malicious attacks and affect the normal operation of the power grid. By analyzing the security vulnerability of the firmware of industrial control equipment, the vulnerability can be detected in advance and the power grid's ability to resist attack can be improved. In this paper, a kind of industrial control device firmware protocol vulnerabilities associated technology, through the technology of information extraction from the mass grid device firmware device attributes and extract the industrial control system, the characteristics of the construction of industrial control system device firmware and published vulnerability information correlation, faster in the industrial control equipment safety inspection found vulnerabilities.
Laser modulation photothermal radiometer—a new method for measuring weak absorption in bulk materials and coatings (1985)

A new method was developed for measuring weak absorption in bulk materials and coatings. It is based on recording a change in the integrated thermal radiation flux from the surfaces of samples heated by periodic laser radiation pulses. The possibility is discussed of making absolute measurements by simulation of surface heat sources in the materials investigated, and also by comparing them with standard samples. The sensitivity of the method is estimated and the results of absorption measurements on a number of materials are presented. Consideration is given to limitations imposed on the operating range of laser pulse repetition frequencies by the thickness of the layer of the substance emitting the thermal flux and by the increase in the transverse dimensions of the illuminated area arising on account of thermal diffusion.
Distinct Roles of the First Introns on the Expression of Arabidopsis Profilin Gene Family Members (2005)

Profilin is a small actin-binding protein that regulates cellular dynamics of the actin cytoskeleton. In Arabidopsis (Arabidopsis thaliana), five profilins were identified. The vegetative class profilins, PRF1, PRF2, and PRF3, are expressed in vegetative organs. The reproductive class profilins, PRF4 and PRF5, are mainly expressed in pollen. In this study, we examined the role of the first intron in the expression of the Arabidopsis profilin gene family using transgenic plants and a transient expression system. In transgenic plants, we examined PRF2 and PRF5, which represent vegetative and reproductive profilins. The expression of the PRF2 promoter fused with the beta-glucuronidase (GUS) gene was observed in the vascular bundles, but transgenic plants carrying the PRF2 promoter-GUS with its first intron showed constitutive expression throughout the vegetative tissues. However, the first intron of PRF5 had little effect on the reporter gene expression pattern. Transgenic plants containing PRF5 promoter-GUS fusion with or without its first intron showed reproductive tissue-specific expression. To further investigate the different roles of the first two introns on gene expression, the first introns were exchanged between PRF2 and PRF5. The first intron of PRF5 had no apparent effect on the expression pattern of the PRF2 promoter. But, unlike the intron of PRF5, the first intron of PRF2 greatly affected the reproductive tissue-specific expression of the PRF5 promoter, confirming a different role for these introns. The results of a transient expression assay indicated that the first intron of PRF1 and PRF2 enhances gene expression, whereas PRF4 and PRF5 do not. These results suggest that the first introns of profilin genes are functionally distinctive and the first introns are required for the strong and constitutive gene expression of PRF1 and PRF2 in vegetative tissues.
Antitumor Vaccines Based on Dendritic Cells: From Experiments using Animal Tumor Models to Clinical Trials (2017)

The routine methods used to treat oncological diseases have a number of drawbacks, including non-specific action and severe side effects for patients. Furthermore, tumor diseases are associated with a suppression of the immune system that often leads to the inefficiency of standard treatment methods. The development of novel immunotherapeutic approaches having specific antitumor action and that activate the immune system is of crucial importance. Vaccines based on dendritic cells (DCs) loaded with tumor antigens <i>ex vivo</i> that can activate antitumor cytotoxic T-cell responses stand out among different antitumor immunotherapeutic approaches. This review is focused on analyzing different methods of DC-based vaccine preparation and current research in antitumor DC-based vaccines using animal tumor models and in clinical trials.
NMR excitation of quadrupolar order using adiabatic demagnetization in the rotating frame (1998)

Adiabatic demagnetization and remagnetization in the rotating frame (ADRF and ARRF) are shown to be practical and efficient techniques for exciting and observing quadrupolar order, T2,0, in NMR of quadrupolar nuclei such as H2 or Na23. A detailed theoretical description of ADRF and ARRF of spin I=1 and 3/2 nuclei, based on the well-known vector model of NMR, is presented and used to derive analytically a variety of pulse shapes for ADRF and ARRF. This theory is also used to calculate the state of the spin I=1 and 3/2 density operators following an ADRF or ARRF pulse and it is shown that the desired coherence transfer processes have the maximum amplitudes allowed by the well-known “universal bound” theorem. In principle, therefore, ADRF is shown to be superior as a method of exciting quadrupolar order to the Jeener-Broekaert experiment since the latter fails to excite the maximum T2,0 amplitude for spin I=3/2 nuclei. The performance of ADRF is investigated using computer calculations and simulations and the conditions under which it yields broadband (i.e., non-oscillatory) excitation of quadrupolar order are derived. Using both H2 (I=1) and Na23 (I=3/2) NMR of liquid crystalline and biological samples, ADRF and ARRF are demonstrated experimentally. The predicted broadband excitation behavior is observed for both ADRF and ARRF, whereas both the Jeener-Broekaert and double-quantum filtration experiments show excitation profiles that oscillate sinusoidally as a function of either the quadrupolar splitting parameter, ωQ, or the duration of the pulse sequence, τ. Finally, a more general discussion of ADRF and ARRF of quadrupolar nuclei is presented and it is shown that the maximum coherence transfer amplitudes are achieved for nuclei of any spin quantum number I.
Laparoscopic reversal of Hartmann procedure (2006)

Laparoscopic reversal of Hartmann is technically safe and feasible.
Green tea epigallocatechin-3-gallate inhibits platelet signalling pathways triggered by both proteolytic and non-proteolytic agonists (2003)

Epigallocatechin-3-gallate (EGCG), a component of green tea, inhibits human platelet aggregation and cytosolic [Ca(2+)](c) increases more strongly when these processes are induced by thrombin than by the non-proteolytic thrombin receptor activating peptide (TRAP), thromboxane mimetic U46619, or fluoroaluminate. In line with the previously demonstrated EGCG anti-proteolytic activity, a marked inhibition on aggregation is obtained by pre-incubation of thrombin with EGCG prior to addition to cellular suspension. The catechin also reduces cellular Ca(2+) influx following thapsigargin-induced calcium emptying of endoplasmic reticulum, and the agonist-promoted cellular protein tyrosine phosphorylation. Both tyrosine kinases Syk and Lyn, immuno-precipitated from stimulated platelets, are greatly inhibited upon cellular pre-incubation with EGCG, which also inhibits the in vitro auto-phosphorylation and exogenous activity of these two enzymes purified from rat spleen. Both thrombin-induced aggregation and [Ca(2+)](c) increase are reduced in platelets from rats that drank green tea solutions. It is concluded that EGCG inhibits platelet activation, by hindering the thrombin proteolytic activity, and by reducing the agonist-induced [Ca(2+)](c) increase through inhibition of Syk and Lyn activities.
Modeling and experimental verification of a variable-stiffness isolation system using a leverage mechanism (2011)

Recent studies have discovered that conventional isolation systems may incur excessive isolator displacement in a near-fault earthquake with strong long-period wave components. To overcome this problem without jeopardizing isolation efficiency, a novel semi-active isolation system called a Leverage-type Variable Stiffness Isolation System (LVSIS) is realized in this study. By utilizing a simple leverage mechanism, the isolation stiffness of the LVSIS can be easily controlled by adjusting the position of the pivot point on the leverage arm. For accurate analysis, the dynamic equation based on a mathematical model that considers the actual situation of all friction forces within the LVSIS is derived in the study. The mathematical model is then verified experimentally by using a prototype LVSIS tested dynamically on a shaking table. Furthermore, to determine the on-line pivot position of the LVSIS, this study also proposes a semi-active control law whose feedback gain is decided by utilizing a linear active control algorithm, such as the LQR or modal control. By comparing the isolation performance of its uncontrolled passive counterpart, the test results also demonstrate that the LVSIS with the proposed control law is especially effective in suppressing the excessive base displacement induced by a near-fault earthquake.
One-Pot Iodination of Hydroxypyridines (2009)

A one-pot, high-yielding iodination of hydroxypyridines and hydroxyquinolines is described. The iodination proceeds under mild conditions, and the products are obtained in high yield without the need for chromatographic purification. In addition, the iodination works on both 2- and 4-hydroxypyridines and -hydroxyquinolines.
Image quality evaluation using generalized natural image (2007)

Most image quality metrics are derived from feature values of specified test charts. However, such test charts can explain only a small portion of the comprehensive performances on image quality of imaging systems. Thus, designers of imaging systems need to check every possible type of natural image to verify the performance even if they check every image quality factor by test charts. But it is not clear how many and what types of images should be used to verify the performances. Meanwhile a number of studies have shown that the amplitude spectrum of natural images falls inversely with spatial frequency. This paper proposes a new image quality evaluation methodology using a quasi-random noise image that has 1/f spectrum property as a generalized natural image. After being processed by image processing operations, the power spectra of the image show reasonable responses to the operations and their parameters. In addition, a metric derived from this image can predict the subjective judgments on the spatial reproducibility of imaging systems with a high correlation coefficient. The results suggest that this image can be used for the purpose of evaluation of the comprehensive performance on image quality of imaging systems.
Test Results for Sawtooth-Pattern Damper Seals: Leakage and Rotordynamic Coefficients (1987)

Test results consisting of direct and transverse force coefficients are presented for eleven, sawtooth-pattern, damper-seal configurations. The designation “damper” seal refers to a seal which uses a deliberately roughened stator and smooth rotor, as suggested by von Pragenau [1], to increase the net seal damping force. The designation “sawtooth-pattern” refers to a stator-roughness pattern whose cross section normal to the axis of the seal resembles saw teeth with the teeth direction opposing fluid motion in the direction of shaft rotation. The sawtooth pattern yields axial grooves in the stator which are interrupted by spacer elements which act as flow constrictions or “dams.” Sawtooth-pattern seals had more damping than smooth seals but less than the round-hole-pattern seals tested previously. Stiffness of sawtooth and round-hole-pattern seals were comparable. Leakage of maximum-damping configurations was greater for sawtooth-pattern than for round-hole-pattern seals; both types of seals leaked substantially less than did smooth seals. If damping is sacrificed, sawtooth-pattern seals can be designed to leak less than round-hole-pattern seals.
Isolation of the yeast histone octamer. (1994)

Procedures for the extraction and purification of the yeast histone octamer are described. Either mechanical disruption, yielding chromatin fragments, or spheroplast formation with subsequent nuclear isolation was employed. A hexahistidine tag was inserted in the N-terminal region of histone H2B, permitting resolution of the histone octamer from high-salt extracts of nuclei or chromatin to near homogeneity. The histone octamer purified in this way was fully active in reconstitution of nucleosomes.
Radiation drive in laser-heated hohlraums (1996)

Nearly 10 years of Nova [E. M. Campbell, Laser Part. Beams 9, 209 (1991)] experiments and analysis have lead to a relatively detailed quantitative and qualitative understanding of radiation drive in laser-heated hohlraums. Our most successful quantitative modeling tool is two-dimensional (2-D) LASNEX numerical simulations [G. B. Zimmerman and W. L. Kruer, Comments Plasma Phys. Controlled Fusion 2, 51 (1975)]. Analysis of the simulations provides us with insight into the physics of hohlraum drive. In particular we find hohlraum radiation conversion efficiency becomes quite high with longer pulses as the accumulated, high-Z blow-off plasma begins to radiate. Extensive Nova experiments corroborate our quantitative and qualitative understanding.
Spectrum Sensing enhancement using Principal Component Analysis (2016)

In this paper, Principal Component Analysis (PCA) techniques are introduced in the context of Cognitive Radio to enhance the Spectrum Sensing performance. PCA step increases the SNR of the Primary User's signal and, consequently, enhances the Spectrum Sensing performance. We applied PCA as a combination scheme of a multi-antenna Cognitive Radio system. Analytic results will be presented to show the effectiveness of this technique by deriving the new SNR obtained after applying PCA, which can be considered a pre-processing step for a classical Spectrum Sensing algorithm. The effect of PCA is examined with well known detectors in Spectrum Sensing, where the proposed technique shows its efficiency. The performance of the proposed technique is corroborated through many simulations.
Evidence-Based Approach for Interpretation of Epstein-Barr Virus Serological Patterns (2009)

Diagnosis of Epstein-Barr virus (EBV) infection is based on clinical symptoms and serological markers, including the following: immunoglobulin G (IgG) and IgM antibodies to the viral capsid antigen (VCA), heterophile antibodies, and IgG antibodies to the EBV early antigen-diffuse (EA-D) and nuclear antigen (EBNA-1). The use of all five markers results in 32 possible serological patterns. As a result, interpretation of EBV serologies remains a challenge. The purpose of this study was to use a large population of patients to develop evidence-based tools for interpreting EBV results. This study utilized 1,846 serum specimens sent to the laboratory for physician-ordered EBV testing. Chart review was performed for more than 800 patients, and diagnoses were assigned based on physician-ordered testing, clinical presentation, and patient history. Testing for all five EBV antibodies was performed separately on all serum samples using the Bio-Rad BioPlex 2200 system. Presumed EBV diagnosis (based on previous publications) was compared to EBV diagnosis based on a medical record review for each serological pattern. Interestingly, of the 32 possible serological patterns, only 12 occurred in > or = 10 patients. The remaining 20 patterns were uninterpretable because they occurred with such infrequency. Two easy-to-use tables were created to interpret EBV serological patterns based on whether three (EBV VCA IgG, IgM, and heterophile) or five markers are utilized. The use of these two tables allows for interpretation of >95% of BioPlex serological results. This is the first evidence-based study of its kind for EBV serology.
In siturheo-x-ray investigation of flow-induced orientation in layered silicate–syndiotactic polypropylene nanocomposite melt (2002)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Ashish Lele, Malcolm Mackley, Girish Galgali, C. Ramesh; In situ rheo-x-ray investigation of flow-induced orientation in layered silicate–syndiotactic polypropylene nanocomposite melt. Journal of Rheology 1 September 2002; 46 (5): 1091–1110. https://doi.org/10.1122/1.1498284 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Society of RheologyJournal of Rheology Search Advanced Search |Citation Search