gebhart/patrepeval huggingface dataset:
Inhibition of Lassa and Marburg Virus Production by Tetherin (2008)

Recently, tetherin has been identified as an effective cellular factor that prevents the release of human immunodeficiency virus type 1. Here, we show that the production of virus-like particles induced by viral matrix proteins of Lassa virus or Marburg virus was markedly inhibited by tetherin and that N-linked glycosylation of tetherin was dispensable for this antiviral activity. Our data also suggest that viral matrix proteins or one or more components that originate from host cells are targets of tetherin but that viral surface glycoproteins are not. These results suggest that tetherin inhibits the release of a wide variety of enveloped viruses from host cells by a common mechanism.
Quantification of Indole-3-Acetic Acid in Dark-Grown Seedlings of the Diageotropica and Epinastic Mutants of Tomato (Lycopersicon esculentum Mill.) (1988)

Endogenous indoleacetic acid (IAA) levels were examined in 7-day-old, dark-grown tomato seedlings (Lycopersicon esculentum Mill. cv VFN8), and in two single-gene mutants, Epinastic and diageotropica. Gas chromatography-mass spectrometry was employed to quantify IAA using (13)C(6)-[benzene ring]indoleacetic acid as internal standard. IAA concentrations ranged from 89 to 134 nanograms per gram dry weight and were not significantly different for the three genotypes. Ethylene over-production by dark-grown Epi seedlings is not likely to result from increased IAA. Assuming similar recovery percentages for each genotype, indole-3-ethanol, a purported storage form of IAA, was identified by GC-MS and found to be more prevalent in the parent tomato, VFN8, with only trace amounts observed in Epi. No IEt was detected by high performance liquid chromatography/fluorescence in dgt (detection limit >100 picograms).
Pathogenicity of T cells responsive to diverse cryptic epitopes of myelin basic protein in the Lewis rat (1995)

The cellular immunology of experimental autoimmune encephalomyelitis, a model for multiple sclerosis, has been studied, for the most part, using T cells directed to dominant epitopes of the Ag myelin basic protein (MBP). To characterize T cells reactive to cryptic epitopes of MBP, we immunized Lewis rats with each of 17 overlapping peptides of the 18.5-kDa isoform of rat MBP. We found that, in addition to the known 71-90 epitope, six other peptides induced active encephalomyelitis in the majority the injected rats. T cell lines raised to six different MBP epitopes were encephalitogenic upon adoptive transfer to naive rats. In contrast to the T cells specific for the dominant 71-90 peptide, the T cell lines reactive to cryptic epitopes were not restricted in their TCR genes to V beta 8.2, and some of the lines caused prolonged disease. Thus, T cells of different specificities and TCR usage can be pathogenic.
Statistical Methods to Preserve Patient Privacy When Sharing and Analyzing Data (2020)

Sometimes a study can get better results using data from different sites. In these cases, researchers may want to share patient data, including personal and private information such as dates of birth and addresses. However, researchers may not want to share data across sites because of worries about patient privacy. Some statistical methods can change patients' sensitive individual data into summary data that hides individuals' personal information. These privacy-protecting methods, or PPMs, make it safe to share data across sites. But researchers don't know if PPMs produce accurate results.
60 GHz SiGe-BiCMOS Radio for OFDM Transmission (2007)

This paper reports implementation details of a 60 GHz short range communication system for data rates up to 2 Gbit/s. Based on a MATLAB model the main PHY parameters were derived, and the modules of the analog frontend were specified. For system verification, a demonstrator was developed. The analog RF and IF circuits of the demonstrator are implemented in a 0.25 μm SiGe BiCMOS technology. Measurement results of the analog modules and the complete demonstrator are given. Using OFDM modulation, the maximum data rate transmitted via airlink so far, is 960 Mbit/s.
Gallium adsorption onto (1120) gallium nitride surfaces (2004)

We report on a systematic study of transients in reflection high energy electron diffraction specular intensities due to adsorption and subsequent desorption of gallium onto (112̄0) GaN surfaces both during the gallium adsorption by itself or during the growth of GaN by plasma-assisted molecular beam epitaxy. We determined the boundaries between N-rich growth, Ga-rich growth with only a two-dimensional phase of adsorbed Ga, and Ga-rich growth with droplets of liquid Ga. The thermal dependence of the boundary between the Ga-rich regimes with and without droplets was found to be approximately 3.2 eV for both the cases of gallium adsorption and GaN growth. This temperature dependence is explained in terms of a quasiequilibrium model for the interaction between the surface phases. Evidence is presented indicating that the two-dimensional phase saturates at submonolayer coverage for temperatures below 700 °C.
The Vertical Seismic Isolator by using a link-crank mechanism (2013)

In recent years, to prevent art objects from falling by earthquake, various seismic isolators are developed. Many seismic isolators only have efficiency for horizontal direction because objects are almost fallen down by horizontal vibration. However, development of seismic isolator corresponded to vertical vibration is required, since great earthquake of vertical vibration like Niigata Prefecture Chuetsu Earthquake in 2004 occurred. As previous study of the vertical seismic isolator, we developed seismic isolator using negative stiffness mechanism to reduce natural frequency. However, to receive the weight by vertical spring, the static deflection of spring becomes bigger when natural frequency is reduced. Additionally, the height of seismic isolator increases when negative stiffness is used to reduce static deflection. In fact, it is difficult to balance reducing natural frequency and downsizing of seismic isolator. In this study, using of the fact that arbitrary design of spring characteristic from positive to negative can be achieved by link-crank mechanism, we developed vertical seismic isolator which can support load in using horizontal spring without using vertical spring. By this, we achieved vertical seismic isolator which has major stroke, lower installation height. We verified performance of this vertical seismic isolator by conducting shaking tests and math calculation.
Computer extracted nuclear features from Feulgen and H&E images to predict biochemical recurrence in prostate cancer patients following radical prostatectomy. (2016)

5067 Background: After radical prostatectomy, around 30% of prostate cancer (PCa) patients experience biochemical recurrence (BCR), for which the best predictor has been the qualitative Gleason score (GS). Computerized image analysis methods have allowed for enumeration of quantitative histomorphometric (QH) measurements from H&E images and been predictive of BCR. Additionally the Feulgen (FG) stain reflects nuclear DNA content, a feature linked to PCa presence and aggressiveness. We show that BCR can be accurately predicted by combining QH measurements of morphology and architecture from H&E and FG tissue images. Methods: We used 69 patients (20 BCR and 49 non-recurrence (NR)) with follow up to 14 years, T2 or T3 stage, and GS of 6 to 9. Each patient had 242 QH features calculated from the stained TMA core images. Feature selection chose the 10 most discriminating features of each stain which were combined via a random forest classifier to predict BCR. Kaplan-Meier analysis evaluated classifier predictions of BCR. Results: QH features extracted from FG and H&E images revealed statistically different outcomes. Combining GS, H&E and FG yielded the highest classification accuracy, the lowest p-value and a high concordance index (Table 1). GS did not show statistically significant (p > 0.05) differences in BCR-free survival via a log-rank test and had the lowest concordance index (Table 1). Conclusions: Combining nuclear morphology and DNA related features predicted BCR more accurately than GS. With validation of these findings, the combined H&E + FG classifier would allow better risk stratification and post-surgical patient management. Accuracy, concordance index, mean survival rates with 95% confidence interval, and p-value of each classifier. Accuracy Concordance Index Mean Predicted NR Survival Rate (yrs) Mean Predicted BCR Survival Rate (yrs) p-Value GS 0.69 +/- 0.03 0.75 4.8 (3.6 - 6.1) 2.2 (0.8 - 3.6) 0.199 FG 0.72 +/- 0.04 0.82 5.3 (3.7 - 7.0) 3.2 (2.1 - 4.4) 0.019 H&E 0.69 +/- 0.03 0.77 5.1 (3.7 - 6.5) 4.0 (2.4 - 5.7) 0.002 H&E + FG 0.74 +/- 0.04 0.95 5.1 (3.8 - 6.3) 3.0 (1.7 - 4.3) 9.13e-6 GS + H&E + FG 0.75 +/- 0.03 0.94 5.2 (3.9 - 6.5) 3.0 (1.7 - 4.3) 3.002 e-7
Are Phosphatidic Acids Ubiquitous in Mammalian Tissues or Overemphasized in Mass Spectrometry Imaging Applications? (2023)

Abstract Mass spectrometry imaging (MSI) is an invaluable tool for the spatial visualization of molecules in vivo. However, the question of whether observed annotations are endogenous or artificial (i. e., from in‐source fragmentation) is critical and has been largely unexplored in multimodal MSI. In matrix‐assisted laser desorption/ionization (MALDI)‐MSI datasets from researchers worldwide, PAs were found to represent up to 18 % of annotations in rat brain. Rat brain was additionally imaged here using nanospray desorption electrospray ionization (nano‐DESI), a softer ionization strategy. No PAs observed with MALDI were present in the nano‐DESI dataset. Further investigation strongly indicated lipid fragmentation to PAs for MALDI‐MSI, but not with nano‐DESI‐MSI. We finally extend this observation to the MALDI‐MSI analyses of human tissues, showing that PA annotations comprised up to 16 % of annotations. Therefore, this study shows that MSI annotations should be carefully interrogated, as in‐source fragmentation or modification of lipids may contribute substantially to false annotations and incorrect biological interpretations.
Defective Autophagy and mTORC1 Signaling in Myotubularin Null Mice (2012)

Autophagy is a vesicular trafficking pathway that regulates the degradation of aggregated proteins and damaged organelles. Initiation of autophagy requires several multiprotein signaling complexes, such as the ULK1 kinase complex and the Vps34 lipid kinase complex, which generates phosphatidylinositol 3-phosphate [PtdIns(3)P] on the forming autophagosomal membrane. Alterations in autophagy have been reported for various diseases, including myopathies. Here we show that skeletal muscle autophagy is compromised in mice deficient in the X-linked myotubular myopathy (XLMTM)-associated PtdIns(3)P phosphatase myotubularin (MTM1). Mtm1-deficient muscle displays several cellular abnormalities, including a profound increase in ubiquitin aggregates and abnormal mitochondria. Further, we show that Mtm1 deficiency is accompanied by activation of mTORC1 signaling, which persists even following starvation. In vivo pharmacological inhibition of mTOR is sufficient to normalize aberrant autophagy and improve muscle phenotypes in Mtm1 null mice. These results suggest that aberrant mTORC1 signaling and impaired autophagy are consequences of the loss of Mtm1 and may play a primary role in disease pathogenesis.
Blood-Direct InvaderPlus ® As a New Method for Genetic Testing (2012)

Blood-direct InvaderPlus allowed accurate, simple and rapid detection of genetic polymorphisms.
Study of elastic nonlinearity of soft solids with transient elastography: Landau coefficients and finite amplitude shear wave (2002)

Transient elastography allows one to accurately achieve the Youngs modulus of soft tissues from the measurement of the shear-wave velocity. The Youngs modulus is a second-order elastic moduli and describes the linear behavior of a medium. In order to achieve the third-order elastic moduli in soft tissues (which characterize the nonlinearity), we have used transient elastography in an acoustoelasticity-like experiment. It consists in measuring shear-wave velocities in a uniaxial pre-stressed medium. This technique uses an ultrafast scanner and allows one to measure thenonlinear third-order elastic Landau coefficients A, B, C in an Agar-gelatin based phantom. The several orders of magnitude found between these three constants appear to be a characteristic of soft tissues. In a second part, we present the first experimental displacements of a finite amplitude transverse wave. The results are compared to a simulation based on the modified Burgers equation. In both approaches, it appears that contrary to longitudinal wave for which even harmonics are created during the propagation, only odd harmonics are present on the displacement spectra of a finite amplitude transverse wave.
Suboptimal influenza vaccination results in higher numbers of pulmonary macrophages upon influenza challenge in mice (2016)

Abstract Macrophages are innate immune cells present in the airways and are important for the initial immune answer against invading pathogens. Alveolar macrophages (AM) are transiently lost in the mouse-influenza infection model during the first days of infection. During later stages of infection, AM recover to similar numbers as before challenge. We investigated if AM were protected during experimental sublethal influenza challenge after vaccination with an alum-adjuvanted trivalent inactivated influenza vaccine (TIV) that antigenically matches the challenge virus. TIV vaccination could not prevent morbidity, however, it correlated with lower viral lung titers and faster recovery after challlenge. AM were completely abolished at seven days post infection in negative control mice, but not in TIV-vaccinated mice. Taken together, using the mouse influenza infection model we observed that suboptimal vaccination with TIV results in higher levels of AM in lungs upon sublethal challenge with homologous virus. The possible impact of higher levels of pulmonary macrophages on antigen presentation and disease modulation are further investigated.
Anisotropic Local Motions and Location of Amide Protons in Proteins (2005)

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.
IR-GRIN optics for imaging (2016)

Infrared (IR) transmitting gradient index (GRIN) materials have been developed for broad-band IR imaging. This material is derived from the diffusion of homogeneous chalcogenide glasses has good transmission for all IR wavebands. The optical properties of the IR-GRIN materials are presented and the fabrication methodologies are discussed. Modeling and optimization of the diffusion process is exploited to minimize the deviation of the index profile from the design profile.
Interaction of the Coffee Diterpenes Cafestol and 16-O-Methyl-Cafestol Palmitates with Serum Albumins (2020)

The main coffee diterpenes cafestol, kahweol, and 16-<i>O</i>-methylcafestol, present in the bean lipid fraction, are mostly esterified with fatty acids. They are believed to induce dyslipidaemia and hypercholesterolemia when taken with certain types of coffee brews. The study of their binding to serum albumins could help explain their interactions with biologically active xenobiotics. We investigated the interactions occurring between cafestol and 16-<i>O</i>-methylcafestol palmitates with Bovine Serum Albumin (BSA), Human Serum Albumin (HSA), and Fatty Free Human Serum Albumin (ffHSA) by means of circular dichroism and fluorimetry. Circular Dichroism (CD) revealed a slight change (up to 3%) in the secondary structure of fatty-free human albumin in the presence of the diterpene esters, suggesting that the aliphatic chain of the palmitate partly occupies one of the fatty acid sites of the protein. A warfarin displacement experiment was performed to identify the binding site, which is probably close but not coincident with Sudlow site I, as the affinity for warfarin is enhanced. Fluorescence quenching titrations revealed a complex behaviour, with Stern-Volmer constants in the order of 10<sup>3</sup>-10<sup>4</sup> Lmol<sup>-1</sup>. A model of the HSA-warfarin-cafestol palmitate complex was obtained by docking, and the most favourable solution was found with the terpene palmitate chain inside the FA4 fatty acid site and the cafestol moiety fronting warfarin at the interface with site I.
Interaction of phosphatidylinositol 3-kinase-associated p85 with epidermal growth factor and platelet-derived growth factor receptors. (1992)

One of the immediate cellular responses to stimulation by various growth factors is the activation of a phosphatidylinositol (PI) 3-kinase. We recently cloned the 85-kDa subunit of PI 3-kinase (p85) from a lambda gt11 expression library, using the tyrosine-phosphorylated carboxy terminus of the epidermal growth factor (EGF) receptor as a probe (E. Y. Skolnik, B. Margolis, M. Mohammadi, E. Lowenstein, R. Fischer, A. Drepps, A. Ullrich, and J. Schlessinger, Cell 65:83-90, 1991). In this study, we have examined the association of p85 with EGF and platelet-derived growth factor (PDGF) receptors and the tyrosine phosphorylation of p85 in 3T3 (HER14) cells in response to EGF and PDGF treatment. Treatment of cells with EGF or PDGF markedly increased the amount of p85 associated with EGF and PDGF receptors. Binding assays with glutathione S-transferase (GST) fusion proteins demonstrated that either Src homology region 2 (SH2) domain of p85 is sufficient for binding to EGF and PDGF receptors and that receptor tyrosine autophosphorylation is required for binding. Binding of a GST fusion protein expressing the N-terminal SH2 domain of p85 (GST-N-SH2) to EGF and PDGF receptors was half-maximally inhibited by 2 and 24 mM phosphotyrosine (P-Tyr), respectively, suggesting that the N-SH2 domain interacts more stably with PDGF receptors than with EGF receptors. The amount of receptor-p85 complex detected in HER14 cells treated with EGF or PDGF. Growth factor treatment also increased the amount of p85 found in anti-PDGF-treated HER14 cells, suggesting that the vast majority of p85 in the anti-P-Tyr fraction is receptor associated but not phosphorylated on tyrosine residues. Only upon transient overexpression of p85 and PDGF receptor did p85 become tyrosine phosphorylated. These are consistent with the hypothesis that p85 functions as an adaptor molecule that targets PI 3-kinase to activated growth factor receptors.
Systemic medical management of diabetic retinopathy (2013)

Diabetes mellitus (DM) has assumed epidemic proportions and as a consequence, diabetic retinopathy is expected to be a major societal problem across the world. Diabetic retinopathy (DR) affects the vision by way of proliferative disease that results in vitreous hemorrhage and traction retinal detachment or by way of diabetic maculopathy (DME). The present-day management of diabetic retinopathy revolves around screening the diabetics for evidence of retinopathy and treating the retinopathy with laser photocoagulation. DME is treated with laser photocoagulation and/or intra- vitreal injection of anti-vascular endothelial growth factor (VEGF) agents or steroids. Laser remains the mainstay of treatment and is potentially destructive. Systemic management aims at preventing or delaying the onset of retinopathy; reversing the early retinopathy; or delaying the progression of established retinopathy. Evidence from multiple studies has confirmed the protective role of rigid control of blood glucose and blood pressure. The evidence for lipid control versus maculopathy was less definitive. However, the use of fenofibrates (originally used for lowering serum lipids) has shown a benefit on both proliferative disease and maculopathy outside their lipid-lowering effect. Other drugs being tried are the Protein Kinase C (PKC) inhibitors, other peroxisome proliferator-activated receptors (PPAR) agonists, Forsoklin (which binds GLUT 1 receptor), minocycline (for its anti inflammatory effect), and Celecoxib (Cox-2 inhibitor).
Synthesis and evaluation of synthetic retinoid derivatives as inducers of stem cell differentiation (2008)

All-trans-retinoic acid (ATRA) and its associated analogues are important mediators of cell differentiation and function during the development of the nervous system. It is well known that ATRA can induce the differentiation of neural tissues from human pluripotent stem cells. However, it is not always appreciated that ATRA is highly susceptible to isomerisation when in solution, which can influence the effective concentration of ATRA and subsequently its biological activity. To address this source of variability, synthetic retinoid analogues have been designed and synthesised that retain stability during use and maintain biological function in comparison to ATRA. It is also shown that subtle modifications to the structure of the synthetic retinoid compound impacts significantly on biological activity, as when exposed to cultured human pluripotent stem cells, synthetic retinoid 4-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-ylethynyl)benzoic acid, 4a (para-isomer), induces neural differentiation similarly to ATRA. In contrast, stem cells exposed to synthetic retinoid 3-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-ylethynyl)benzoic acid, 4b (meta-isomer), produce very few neurons and large numbers of epithelial-like cells. This type of structure-activity-relationship information for such synthetic retinoid compounds will further the ability to design more targeted systems capable of mediating robust and reproducible tissue differentiation.
Evidence of NK cell dysfunction in SIV‐infected rhesus monkeys: Impairment of cytokine secretion and NKG2C/C2 expression (2006)

Defects in the adaptive immune response have been extensively characterized in human immunodeficiency virus type-1 (HIV-1)-infected individuals; however, much less is known about the function of natural killer (NK) cells during the course of HIV-1 infection. In the present study, we demonstrate that the NK cells from simian immunodeficiency virus (SIV)-infected rhesus monkeys are significantly impaired in their ability to secrete IFN-gamma, TNF-alpha, and IL-2, while NK cell function in SIV-infected long-term non-progressor monkeys is similar to that of normal monkeys. These findings suggest that abnormal NK cell activity may contribute to the global immune dysfunction observed in HIV-1-infected individuals. NK cell function is modulated by several families of cell surface receptors, including the CD94/NKG2 family. We evaluated the messenger RNA levels of these inhibitory and activating NKG2 molecules in SIV-infected rhesus monkeys. These experiments demonstrate that the activating molecules NKG2C and NKG2C2 are significantly down-regulated in peripheral blood mononuclear cells of SIV-infected rhesus monkeys, suggesting that the dysregulation of these molecules may contribute to the abnormal NK cell function observed in the setting of infection.