gebhart/patrepeval huggingface dataset:
Markers of macrophage differentiation in experimental silicosis (2004)

Macrophages are characterized by a marked phenotypic heterogeneity depending on their microenvironmental stimulation. Beside classical activation (M1), it has been shown that macrophages could follow a different activation pathway after stimulation with interleukin (IL)-4 or IL-13 (M2). Recently, it has been postulated that those "alternatively activated" macrophages may be critical in the control of fibrogenesis. In an experimental model of silicosis, where pulmonary macrophages play a central role, we addressed the question of whether lung fibrosis development would be associated with alternative macrophage activation. As available markers for alternative macrophage activation, type-1 arginase (Arg-1), Fizz1, Ym1/2, and mannose receptor expression were evaluated at the mRNA and/or protein levels at different stages of the disease. Nitric oxide synthase-2 (NOS-2) expression was also examined to investigate the classical counterpart. We found that the expression of Arg-1, Fizz1, and NOS-2 in adherent bronchoalveolar lavage cells was highly up-regulated 3 days after silica administration but returned to control levels during the fibrotic stage of the disease (60 days). By comparing the early response to silica in C57BL/6 and BALB/c mice, we observed that the amplitude of Arg-1 mRNA up-regulation was not associated with the severity of lung fibrosis. Using a model of manganese dioxide particles (resolutive alveolitis), we showed that this early Arg-1 mRNA was not specific to a fibrogenic lung response. Our data indicate that the modifications of M1/M2 marker expression are limited to the early inflammatory stage of silicosis and that the establishment of a fibrotic process is not necessarily associated with M2 polarization.
Stearylated Arginine-Rich Peptides:  A New Class of Transfection Systems (2001)

Membrane-permeable arginine-rich peptides, such as HIV-1 Tat-(48-60), HIV-1 Rev-(34-50), and flock house virus (FHV) coat-(35-49), have been shown to possess the ability to transfect COS-7 cells with luciferase-coding plasmid as efficiently as polyarginine (MW 5000-15 000) and polylysine (MW 9800). Not only these virus-derived cationic peptides but also oligoarginines of 4-16 residues were found to be able to transfect cells. In the case of the Tat, FHV, and octaarginine peptides, N-terminal stearylation of the peptides increases the transfection efficiency by approximately 100 times to reach the same order of magnitude as that of LipofectAMINE, one of the most efficient commercially available transfection agents. Also, a certain correlation was observed between the transfection efficiency of stearyl-(Arg)n peptides (stearyl-Rn: n = 4, 8, 12, 16) and the membrane permeability of the corresponding (Arg)n peptides (Rn).
A 6 GHz Highly Stabilized GaAs FET Oscillator Using a Dielectric Resonator (2005)

A 6 GHz GaAs FET feedback oscillator stabilized by a dielectric resonator with a new frequency tuning mechanism has been developed. The oscillator has a frequency tuning range of 50 MHz with a frequency stability of about t 10 PPM (0/spl deg/C-50/spl deg/C).
The History of Recovered People as Wounded Healers (2000)

Abstract Part I of this article traced the history of recovered alcoholics as wounded healers from their roles in late 18th century Native American cultural revitalization movements and the American temperance movement through their work as lay therapists and counselors within outpatient counseling clinics, Minnesota Model inpatient programs, industrial alcoholism programs and halfway houses. This article will focus on how the roles of the “paraprofessional” recovered alcoholic and ex-addict evolved into the professionalized role of the modem addiction counselor.
Hysteresis Caused by Water Molecules in Carbon Nanotube Field-Effect Transistors (2003)

Carbon nanotube field-effect transistors commonly comprise nanotubes lying on SiO2 surfaces exposed to the ambient environment. It is shown here that the transistors exhibit hysteresis in their electrical characteristics because of charge trapping by water molecules around the nanotubes, including SiO2 surface-bound water proximal to the nanotubes. Hysteresis persists for the transistors in vacuum since the SiO2-bound water does not completely desorb in vacuum at room temperature, a known phenomenon in SiO2 surface chemistry. Heating under dry conditions significantly removes water and reduces hysteresis in the transistors. Nearly hysteresis-free transistors are obtainable by passivating the devices with polymers that hydrogen bond with silanol groups on SiO2 (e.g., with poly(methyl methacrylate) (PMMA)). However, nanotube humidity sensors could be explored with suitable water-sensitive coatings. The results may have implications to field-effect transistors made from other chemically derived materials.
T cell activation and anti-tumor efficacy of anti-LAG-3 antibodies is independent of LAG-3 – MHCII blocking capacity (2015)

Meeting abstracts LAG-3 has been shown to act as an inhibitory molecule involved in the regulation of T cell activation, proliferation and homeostasis. Exhausted T cell populations that evolve in the tumor microenvironment or during chronic viral infections show coordinated expression of LAG-3 and
PATH at 20 -- History and Major Milestones (2006)

The California PATH Program was founded in 1986, as the first research program in North America focused on the subject now known as intelligent transportation systems (ITS). This paper reviews the history of the founding of PATH and of the national ITS program in the U.S., providing perspective on the changes that have occurred during the past twenty years
Myeloid progenitor cells transformed by the myeloproliferative leukemia virus proliferate and differentiate in vitro without the addition of growth factors. (1989)

The myeloproliferative leukemia virus (MPLV) is an acute leukemogenic, nonsarcomatogenic replication-defective murine retrovirus which carries a novel oncogene, termed mpl. We recently reported that both late and early erythroid progenitors from MPLV-infected mice acquire erythropoietin and growth factor independence. In the present study, we show that MPLV-infected pluripotent, granulomacrophage and megakaryocyte progenitor cells proliferated and differentiated in semisolid cultures in the absence of the exogenous growth factors which are absolutely required for colony formation of normal hematopoietic progenitor cells. These factor-independent colonies were morphologically and cytologically similar to normal colonies and did not show any sign of impaired differentiation. Factor-independent colony formation was not influenced by the seeding density. MPLV-infected cells were unable to stimulate colony development of uninfected progenitors in coculture assays, and retransplanted clusters continued to grow in the absence of accessory cells. These data suggest that spontaneous colony formation does not result from a paracrine secretion of growth factors and indicate that MPLV is unique among naturally occurring murine retrovirus for its ability to abrogate the growth factor requirements of a broad spectrum of hematopoietic progenitor cells.
The effect of training set size for the performance of neural networks of classification (2010)

Even though multilayer perceptrons and radial basis function networks belong to the class of artificial neural networks and they are used for similar tasks, they have very different structures and training mechanisms. So, some researchers showed better performance with radial basis function networks, while others showed some different results with multilayer perceptrons. This paper compares the classification accuracy of the two neural networks with respect to training data set size, and shows the performance of the two neural networks can be differently dependent on training data set size. Experiments show the tendency that multilayer perceptrons have better performance in relatively larger training data sets for some data sets, even though radial basis function networks have better performance in relatively smaller training set size for the same data sets. The experiment was done with four real world data sets.
Magnetic resonance imaging of dense and light non‐aqueous phase liquid in a rock fracture (2003)

Magnetic resonance (MR) imaging was used to observe the flow of dense (FC‐75) and light (dodecane) non‐aqueous phase liquids (NAPLs) through a water saturated dolomite fracture. Dynamic two‐phase behavior was influenced by (1) buoyancy of the NAPL relative to the aqueous phase, (2) fracture aperture distribution, and (3) alteration of wettability by long‐term presence of NAPL phase. MR imaging was capable of characterizing the fracture geometry and the fluid flow, but was limited by outlet flow conditions in the sample and acquisition times. This method permits observation of two‐phase flow under natural wettability and matrix porosity, providing significant advantages over plastic or glass replicas.
The Role of Heat Shock Transcription Factor 1 in the Genome-wide Regulation of the Mammalian Heat Shock Response (2003)

Previous work has implicated heat shock transcription factor 1 (HSF1) as the primary transcription factor responsible for the transcriptional response to heat stress in mammalian cells. We characterized the heat shock response of mammalian cells by measuring changes in transcript levels and assaying binding of HSF1 to promoter regions for candidate heat shock genes chosen by a combination of genome-wide computational and experimental methods. We found that many heat-inducible genes have HSF1 binding sites (heat shock elements, HSEs) in their promoters that are bound by HSF1. Surprisingly, for 24 heat-inducible genes, we detected no HSEs and no HSF1 binding. Furthermore, of 182 promoters with likely HSE sequences, we detected HSF1 binding at only 94 of these promoters. Also unexpectedly, we found 48 genes with HSEs in their promoters that are bound by HSF1 but that nevertheless did not show induction after heat shock in the cell types we examined. We also studied the transcriptional response to heat shock in fibroblasts from mice lacking the HSF1 gene. We found 36 genes in these cells that are induced by heat as well as they are in wild-type cells. These results provide evidence that HSF1 does not regulate the induction of every transcript that accumulates after heat shock, and our results suggest that an independent posttranscriptional mechanism regulates the accumulation of a significant number of transcripts.
Phenotype and Function of T Cells Infiltrating Visceral Metastases from Gastrointestinal Cancers and Melanoma: Implications for Adoptive Cell Transfer Therapy (2013)

Abstract Adoptive cell transfer of tumor-infiltrating lymphocytes (TILs) can mediate cancer regression in patients with metastatic melanoma, but whether this approach can be applied to common epithelial malignancies remains unclear. In this study, we compared the phenotype and function of TILs derived from liver and lung metastases from patients with gastrointestinal (GI) cancers (n = 14) or melanoma (n = 42). Fewer CD3+ T cells were found to infiltrate GI compared with melanoma metastases, but the proportions of CD8+ cells, T cell differentiation stage, and expression of costimulatory molecules were similar for both tumor types. Clinical-scale expansion up to ∼50 × 109 T cells on average was obtained for all patients with GI cancer and melanoma. From GI tumors, however, TIL outgrowth in high-dose IL-2 yielded 22 ± 1.4% CD3+CD8+ cells compared with 63 ± 2.4% from melanoma (p &amp;lt; 0.001). IFN-γ ELISA demonstrated MHC class I–mediated reactivity of TIL against autologous tumor in 5 of 7 GI cancer patients tested (9% of 188 distinct TIL cultures) and in 9 of 10 melanoma patients (43% of 246 distinct TIL cultures). In these assays, MHC class I–mediated up-regulation of CD137 (4-1BB) expression on CD8+ cells suggested that 0–3% of TILs expanded from GI cancer metastases were tumor-reactive. This study implies that the main challenge to the development of TIL adoptive cell transfer for metastatic GI cancers may not be the in vitro expansion of bulk TILs, but the ability to select and enrich for tumor-reactive T cells.
Geometric GAN (2017)

Generative Adversarial Nets (GANs) represent an important milestone for effective generative models, which has inspired numerous variants seemingly different from each other. One of the main contributions of this paper is to reveal a unified geometric structure in GAN and its variants. Specifically, we show that the adversarial generative model training can be decomposed into three geometric steps: separating hyperplane search, discriminator parameter update away from the separating hyperplane, and the generator update along the normal vector direction of the separating hyperplane. This geometric intuition reveals the limitations of the existing approaches and leads us to propose a new formulation called geometric GAN using SVM separating hyperplane that maximizes the margin. Our theoretical analysis shows that the geometric GAN converges to a Nash equilibrium between the discriminator and generator. In addition, extensive numerical results show that the superior performance of geometric GAN.
Noninvasive, optical detection of diabetes: model studies with porcine skin (2004)

An in vitro study was performed to evaluate noninvasive spectroscopic measurement of advanced glycation endproducts (AGEs) in skin collagen. A porcine dermis preparation was incubated in solutions simulating normal and hyperglycemic conditions. The AGEs kinetics of increase were determined by HPLC and GC/MS assays, and compared to near-infrared (NIR) and ultraviolet/visible fluorescence skin spectra. Multivariate analysis indicated that, although NIR did not discriminate between collagen samples exposed to different glucose concentrations, fluorescence changes were readily detected and correlated strongly with skin concentration of AGEs. These results suggest that measurement of skin AGEs by fluorescence spectroscopy may be useful for detection and diagnosis of type II diabetes.
Rapid detection of type A influenza viruses with monoclonal antibodies to the M protein (M1) by enzyme-linked immunosorbent assay and time-resolved fluoroimmunoassay (1991)

Monoclonal antibodies (MAbs) to the M protein (M1) were used in the development of direct detection systems for type A influenza viruses in clinical specimens. Optimal detection by an enzyme-linked immunosorbent assay was achieved when MAbs were used as capture antibodies and rabbit polyclonal antibodies were used as sandwich antibodies. Detection by the enzyme-linked immunosorbent assay required amplification of the virus. direct detection in clinical specimens (nasopharyngeal aspirates) was accomplished when MAbs recognizing two distinct antigenic sites of M1 were used in a time-resolved fluoroimmunoassay. Type A influenza viruses could be detected equally well in specimens obtained during epidemics of both H3N2 and H1N1 influenza viruses.
Identification of Structural Elements in Nox1 and Nox4 Controlling Localization and Activity (2008)

Nox NADPH oxidases differ in their mode of activation, subcellular localization, and physiological function. Nox1 releases superoxide anions (O(2)(-)) and depends on cytosolic activator proteins, whereas Nox4 extracellularly releases hydrogen peroxide (H(2)O(2)), and its activity does not require cotransfection of additional proteins. We constructed chimeric proteins consisting of Nox1 and Nox4 expressed in HEK293 cells. When the cytosolic tail of Nox4 was fused with the transmembrane part of Nox1, Nox1 became constitutively active. The reciprocal construct was inactive, suggesting that cytosolic subunit-dependent activation requires elements in the transmembrane loops. By TIRF-microscopy, Nox1 was observed in the plasma membrane, whereas Nox4 colocalized with proteins of the endoplasmic reticulum. Fusion proteins of Myc and Nox revealed that the N-terminal part of Nox1 but not Nox4 is cleaved. When the potential signal peptide of Nox4 was inserted into Nox1, plasma-membrane localization was lost, and the protein was retained in vesicle-like structures below the plasma membrane. The potential signal peptide of Nox1 failed to translocate Nox4 to the plasma membrane but switched the extracellularly detectable ROS from H(2)O(2) to O(2)(-). Thus, the very N-terminal part of Nox proteins determines subcellular localization and the ROS type released, whereas the cytosolic tail regulates activity.
Scaling law between corner frequency and seismic moment of microearthquakes: Is the breakdown of the cube law a nature of earthquakes? (2002)

The corner frequency, f C , and the seismic moment, M 0 , of microearthquakes (local magnitude from −1.3 to 1.3) are estimated from the records of sensors located at an 1800‐m‐deep borehole at the Nojima fault, central Japan. The digital waveforms of each event are recorded with two different sampling rates, 10 kHz and 100 Hz. The source parameters estimated from high‐sampling data satisfy a relationship of M 0 ∝ f C −3 , corresponding to a constant stress drop law, while those calculated from low‐sampling data follow a relationship of M 0 ∝ f C −4 . A lack of high frequency components in the 100 Hz sampling data seem to be obvious, indicating that the value of f C and M 0 are incorrectly estimated and the relationship of M 0 ∝ f C −4 is an artifact caused by the limited frequency band of these data. The scaling relationship of M 0 ∝ f C −3 is, thus, also valid for microearthquakes, and the breakdown of the constant stress drop law, reported in the literature, is not well founded.
Evaluation of inter-scorer and inter-laboratory reliability of the mouse epididymal sperm aneuploidy (m-ESA) assay (2001)

The mouse epididymal sperm aneuploidy (mESA) assay using 3-chromosome fluorescence in situ hybridization (FISH) was recently developed for assessing the aneugenic potential of chemicals on male germ cells. This study was designed to identify the major technical factors that affect inter-scorer and inter-laboratory variability of the mESA assay. Two laboratories participated in this study (GSF and Lawrence Livermore National Laboratory, LLNL). Mice (102/ElxC3H/El) F(1) were exposed in one laboratory (GSF) to vinblastine (VBL; single intraperitoneal injection of 0, 0.5, 1.0 or 2.0 mg/kg), one of the 10 priority compounds of the Commission of the European Communities (CEC) Aneuploidy Program. Twenty-two days later the mESA assay was applied to analyze sperm aneuploidy. In the initial evaluation, small but statistically significant differences were found between the two laboratories in baseline frequencies and there was also disagreement in the determination of a VBL aneuploid effect. Therefore, experiments were conducted to identify the sources of the inter-laboratory differences and technical factors that affected assay reliability and the VBL study was repeated. A harmonization experiment was conducted by bringing the microscope scorers from both laboratories to the same site (LLNL) for a cross-training exercise. Following this exercise, a second group of VBL-treated and control mice were evaluated, and we concluded that VBL is not a sperm aneugen. Our research has identified scoring criteria as the major source of inter-laboratory variation and emphasizes the importance of strict technical controls for the mESA assay, including controlling slide preparations for treatment-induced reductions in sperm count, coding of slides and selection of statistical tests. These considerations are particularly important for the interpretation of small effects (< or =2-fold) on sperm aneuploidy. Our findings suggest that 2-fold differences in frequencies can result from differences among scorers, samples and treatment groups, and are readily within the normal variation for the mESA assay. Such small differences should be viewed with caution until independently confirmed.
Akt phosphorylation and nuclear phosphoinositide association mediate mRNA export and cell proliferation activities by ALY (2008)

Nuclear PI3K and its downstream effectors play essential roles in a variety of cellular activities including cell proliferation, survival, differentiation, and pre-mRNA splicing. Aly is a nuclear speckle protein implicated in mRNA export. Here we show that Aly is a physiological target of nuclear PI3K signaling, which regulates its subnuclear residency, cell proliferation, and mRNA export activities through nuclear Akt phosphorylation and phosphoinositide association. Nuclear Akt phosphorylates Aly on threonine-219, which is required for its interaction with Akt. Aly binds phosphoinositides, and this action is regulated by Akt-mediated phosphorylation. Phosphoinositide binding but not Akt phosphorylation dictates Aly's nuclear speckle residency. Depletion of Aly results in cell growth suppression and mRNA export reduction. Inhibition of Aly phosphorylation substantially decreases cell proliferation and mRNA export. Furthermore, disruption of phosphoinositide association with Aly also significantly reduces these activities. Thus, nuclear PI3K signaling mediates both cell proliferation and mRNA export functions of Aly.
Preparation and characterization of coated silk fibroin films with mimicked re-self assembly type I collagen (2013)

The study aimed to investigate and compare characteristics of Bombyx mori silk film coated with mimicked re-self assembly collagen type I under various conditions concentration [0.25,0.5,1.0,2.0 mg/ml]. The thin films consist of collagen fibrils and result from the self-assembly of collagen. The morphological characteristics observed by scanning electron microscopy (SEM) showed that when increased in collagen concentration, collagen became increase the size of the fibrils. The structure and thermal behavior all kind of silk coated with collagen were determined by FT-IR and DSC instrument. FT-IR spectra showed both spectra of silk and collagens are assigned to β-sheet conformation of silk fibroin and collagen type I. The stability thermal peak shifted to slightly higher temperature by increasing collagen concentration content. Mechanical properties of silk film coated collagen demonstrated that coating collagen at concentration 1-2 mg/ml resulted in modification of mechanical features, with increased maximum load, stress, strain, and Young's modulus.
A drive test measurement approach to characterize on-vehicle 2&#x00D7;2 LTE-MIMO antennas (2014)

This paper presents the use of a commercially available radio scanner for characterizing on-vehicle 2×2 Long-Term Evolution (LTE) radio Multiple-Input Multiple-Output (MIMO) antennas. The scanner measures the LTE eNodeB, i.e. the cell base station, reference signals and each channel and determines the MIMO channel matrices from which the downlink throughput can be determined. For a given LTE radio, this measurement approach can be very useful for efficient comparison between MIMO antennas or among different antenna locations on the vehicle.
Group II Intron-Based Gene Targeting Reactions in Eukaryotes (2008)

Our results provide an experimental foundation for the development of group II intron-based gene targeting methods for higher organisms.