gebhart/patrepeval huggingface dataset:
Regulation of B‐cell activation and differentiation by the phosphatidylinositol 3‐kinase and phospholipase Cγ pathways (2000)

Signal transduction through the B-cell antigen receptor (BCR) determines the fate of B lymphocytes during their development and during immune responses. A multitude of signal transduction events are known to be activated by ligation of the BCR; however, the critical parameters determining the biological outcome of the signal transduction cascade are only just beginning to be understood. Two enzymes which act on plasma membrane phospholipids, phosphatidylinositol 3-kinase (PI3K) and phospholipase Cgamma (PLCgamma), have been implicated as critical mediators of B-cell activation and differentiation signals. Activation of these ubiquitous enzymes is regulated by B-lymphocyte-specific signal transduction proteins, such as CD 19 and B-cell linker protein. These enzymes function by generating both membrane-anchored and soluble second messenger molecules which regulate the activity of downstream signal transduction proteins. Active PI3K produces phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) and phosphatidylinositol-3,4-trisphosphate (PI(3,4,5)P3) which can bind to signaling proteins such as Btk or Akt via their pleckstrin homology domains, resulting in their membrane recruitment and activation. The lipid phosphatases SHIP and PTEN negatively regulate production of PI(3,4)P2 and PI(3,4,S)P3 and therefore function to put a "brake" on the PI3K pathway. Active PLCgamma produces inositol-1,4,5-trisphosphate, which regulates Ca2+ mobilization, and diacylglycerol, which binds to a subset of protein kinase C enzymes leading to their membrane localization and activation. Recent evidence has indicated that PLCgamma activation is partially dependent on the PI(3,4,5)P3 production by activated PI3K. Since PI3K and PLCgamma also share common downstream targets such as the NF-AT and NF-kappaB transcription factors, it is becoming clear that these two pathways are interconnected at several levels. Studies of mice deficient in components of the PI3K and PLCgamma pathways demonstrate that these pathways play critical roles in both pre-BCR and BCR-dependent selection events during B-cell differentiation. Taken together, the present data clearly indicate that PI3K and PLCgamma play critical and indispensable roles in the signal transduction cascades leading to multiple biological responses downstream of the BCR.
Measuring propagation delays of critical paths using time-resolved LADA (2014)

Laser-assisted device alteration is an established technique used to identify critical speed paths in integrated circuits. By using a synchronized pulsed laser, logic transition waveforms have been acquired that can be used to measure propagation delays of the critical path signals. A method for determining the polarity of the transitions is presented for LADA sites on bulk 28nm CMOS technology. The time-resolved LADA logic waveforms are compared to, and are in close agreement with, laser voltage probe waveforms acquired from the same device.
Measurement and Interpretation of Hailstone Density and Terminal Velocity (1983)

The mass, density, fall velocity and internal structure have been determined for low-density hailstones from an truly spring storm in Boulder, Colorado, and drag coefficients were calculated. The density of the permeable hail is determined from a new method of volume measurement. The results are compared to those of particles grown in a one-dimensional parcel model using the appropriate sounding. The implications of the results are discussed with reference to hail growth in convective storms.
Targeting FAK in human cancer: from finding to first clinical trials (2014)

It is twenty years since Focal Adhesion Kinase (FAK) was found to be overexpressed in many types of human cancer. FAK plays an important role in adhesion, spreading, motility, invasion, metastasis, survival, angiogenesis, and recently has been found to play an important role as well in epithelial to mesenchymal transition (EMT), cancer stem cells and tumor microenvironment. FAK has kinase-dependent and kinase independent scaffolding, cytoplasmic and nuclear functions. Several years ago FAK was proposed as a potential therapeutic target; the first clinical trials were just reported, and they supported further studies of FAK as a promising therapeutic target. This review discusses the main functions of FAK in cancer, and specifically focuses on recent novel findings on the role of FAK in cancer stem cells, microenvironment, epithelial-to-mesenchymal transition, invasion, metastasis, and also highlight new approaches of targeting FAK and critically discuss challenges that lie ahead for its targeted therapeutics. The review provides a summary of translational approaches of FAK-targeted and combination therapies and outline perspectives and future directions of FAK research.
Synthesis and physico-chemical characterization of a polysialate-hydroxyapatite composite for potential biomedical application (2002)

New composite materials based on aluminosilicate materials were developed to be used in orthopaedic or maxillo-facial surgery. They are called geopolymers or polysialate-siloxo (PSS) and were studied alone or mixed with hydroxyapatite (HAP). The properties of these materials were investigated for potential use in biological or surgery applications. In this work, the chemistry involved in materials preparation was described. Samples were characterized by some physico-chemical methods like X-ray diffraction (XRD), infrared spectrometry (IR) and electron dispersion X-ray spectrometry (EDX). Results indicate that the mixing hydroxyapatite-geopolymer (PSS) leads to a neutral porous composite material with interesting physico-chemical properties. A preliminary evaluation of its cytotoxicity reveals an harmlessness towards fibroblasts. These properties allow to envisage this association as a potential biomaterial.
Performance comparison between total variation (TV)-based compressed sensing and statistical iterative reconstruction algorithms (2009)

Of all available reconstruction methods, statistical iterative reconstruction algorithms appear particularly promising since they enable accurate physical noise modeling. The newly developed compressive sampling/compressed sensing (CS) algorithm has shown the potential to accurately reconstruct images from highly undersampled data. The CS algorithm can be implemented in the statistical reconstruction framework as well. In this study, we compared the performance of two standard statistical reconstruction algorithms (penalized weighted least squares and q-GGMRF) to the CS algorithm. In assessing the image quality using these iterative reconstructions, it is critical to utilize realistic background anatomy as the reconstruction results are object dependent. A cadaver head was scanned on a Varian Trilogy system at different dose levels. Several figures of merit including the relative root mean square error and a quality factor which accounts for the noise performance and the spatial resolution were introduced to objectively evaluate reconstruction performance. A comparison is presented between the three algorithms for a constant undersampling factor comparing different algorithms at several dose levels. To facilitate this comparison, the original CS method was formulated in the framework of the statistical image reconstruction algorithms. Important conclusions of the measurements from our studies are that (1) for realistic neuro-anatomy, over 100 projections are required to avoid streak artifacts in the reconstructed images even with CS reconstruction, (2) regardless of the algorithm employed, it is beneficial to distribute the total dose to more views as long as each view remains quantum noise limited and (3) the total variation-based CS method is not appropriate for very low dose levels because while it can mitigate streaking artifacts, the images exhibit patchy behavior, which is potentially harmful for medical diagnosis.
Chemically modified heparins as inhibitors of heparan sulfate specific endo-.beta.-glucuronidase (heparanase) of metastatic melanoma cells (1986)

To determine the significance of the heparan sulfate (HS) degradative endo-beta-glucuronidase (heparanase) in tumor invasion and metastasis and to develop possible antimetastatic agents, we synthesized specific inhibitors of this enzyme. We previously found that heparanase activity correlates with the lung colonization abilities of murine B16 melanoma cells and is inhibited by heparin [Nakajima, M., Irimura, T., Di Ferrante, N., & Nicolson, G. L. (1984) J. Biol. Chem. 259, 2283-2290]. In this study, heparin was chemically modified in order to determine which portions of its structure are responsible for heparanase inhibitory activity and to obtain heparanase inhibitors that have minimal additional biological effects, such as anticoagulation. N-Sulfate groups and O-sulfate in heparin were removed separately, and the resultant free amino groups were acetylated or resulfated. Heparin was also reduced at the carboxyl groups of uronic acid. The heparanase inhibitory activities of these heparin derivatives were examined by high-speed gel-permeation chromatography and by the use of radioactive HS immobilized on agarose beads. The results indicated that although N-sulfate and O-sulfate groups on glucosamine residues, and carboxyl groups on uronic acid residues, are important for heparanase inhibition, they are not essential for full activity. When highly metastatic B16-BL6 melanoma cells were incubated with N-acetylated N-desulfated heparin, N-resulfated N- and O-desulfated heparin, or carboxyl-reduced heparin and injected intravenously to syngenic C57BL/6 mice, significant reductions in the numbers of experimental melanoma lung metastases occurred.
Determinanten und Dimensionen der Entwicklung der untersuchten Industrie- und Handelskammern (2000)

Die im vorangegangenen Kapitel vorgestellte Komplexität des Forschungsgegenstandes — Industrie- und Handelskammern als intermediäre Regulierungsinstitutionen -, verknüpft mit einer mehrschichtigen Problemstellung und multiperspektivischen Betrachtung, nämlich den Funktionen und Wirkungen der Kammern zu unterschiedlichen Zeitpunkten in einem doppelten Handlungs- und Beziehungsnetzwerk, sowie deren Abhängigkeit von den spezifischen Strukturen des Handlungsraumes, der jeweiligen Kammerregion, macht es u. E. erforderlich, zunächst komprimiert darzustellen, welche Gestalt und Ausprägung die grundlegenden Determinanten und Dimensionen der Entwicklung der untersuchten IHKn hatten. Deshalb werden zunächst (Kapitel 2.1.) die ausgewählten Kammerregionen mit ihren wesentlichen Merkmalen als ein gewichtiger Teil der Handlungsbasis der Kammern vorgestellt. Sodann (Kapitel 2.2.) werden die grundlegenden Gemeinsamkeiten und Unterschiede der Ausdifferenzierung der IHKn selbst in ihren zentralen Momenten herausgearbeitet, um für die spätere ausführliche Analyse der Wiedereinrichtung der Kammern wie ihrer aktuellen Strukturen und Leistungen angesichts der überaus komplexen Materie übergeordnete Bezüge für die Offenlegung von Zusammenhängen und Differenzen zu erhalten.
Regulation of Adipose Cell Number in Man (1997)

1. Adipose tissue mass is dependent on both the average volume and the number of its constituent adipocytes. Significant alteration in body mass involves alteration in both adipocyte volume and number. 2. Increases in adipocyte number occur via replication and differentiation of preadipocytes, a process which occurs throughout life. Decreases in adipocyte number occur via preadipocyte and adipocyte apoptosis, and possibly adipocyte dedifferentiation. 3. Overall regulation of adipose mass involves endocrine, paracrine and possibly autocrine systems. Hypothalamic centres appear to control appetite, metabolic rate and activity levels in a co-ordinated manner. Within the hypothalamus, known weight regulatory molecules include glucagon-like peptide-1, neuropeptide Y and leptin. Leptin is a major afferent signal from adipose tissue to the hypothalamus, providing information on overall adipose tissue mass. However, the precise means by which the hypothalamus signals to adipose tissue is less well understood. 4. In adipose tissue, known molecular regulators of adipose cell number include insulin, ligands for the peroxisome proliferator activated receptor-gamma, retinoids, corticosteroids and tumour necrosis factor-alpha. The net effect of these and other regulators is to effect a concerted alteration in adipocyte volume and number. This review largely focuses on the control of fat cell acquisition and loss and the influence of these processes on adipose tissue mass and regional distribution.
Gα14 and Gαq Mediate the Response to Trypsin in Xenopus Oocytes (1998)

Xenopus oocytes respond to trypsin with a characteristic chloride current, virtually indistinguishable from responses mediated by a large number of native and expressed G protein-coupled receptors. We studied the involvement of G proteins of the Galphaq family as possible mediators of this and other G protein-coupled receptor-mediated responses in Xenopus oocytes. We have cloned the third member of the Galphaq family, Xenopus Galpha14, in addition to the previously cloned Xenopus Galphaq and Galpha11 (Shapira, H., Way, J., Lipinsky, D., Oron, Y., and Battey, J. F. (1994) FEBS Lett. 348, 89-92). Amphibian Galpha14 is 354 amino acids long and is 93% identical to its mammalian counterpart. Based on the Galpha14 cDNA sequence, we designed a specific antisense DNA oligonucleotide (antiGalpha14) that, together with antiGalphaq and antiGalpha11, was used in antisense depletion experiments. 24 h after injection into oocytes, either antiGalphaq or antiGalpha14 reduced the response to 1 microg/ml trypsin by 70%, whereas antiGalpha11 had no effect. A mixture of antiGalphaq and antiGalpha14 virtually abolished the response. These data strongly suggest that Galphaq and Galpha14 are the exclusive mediators of the trypsin-evoked response in Xenopus oocytes. Similar experiments with the expressed gastrin-releasing peptide receptor and muscarinic m1 receptor revealed the coupling of Galphaq and Galpha11, but not Galpha14, to these receptors in oocytes. These results confirm the hypothesis that endogenous members of the Galphaq family discriminate among different native receptors in vivo.
Characterization of the DNF15S2 locus on human chromosome 3: identification of a gene coding for four Kringle domains with homology to hepatocyte growth factor (1991)

A human genomic DNA library was screened by using conditions of reduced stringency with a bovine cDNA probe coding for the kringle domains in prothrombin in order to isolate the human prothrombin gene. Twelve positives were identified, three of which coded for prothrombin (Degen & Davie, 1987). Phage L5 was characterized in more detail because of its strong hybridization to the cDNA probe and its unique restriction map compared to the gene coding for human prothrombin. The gene in L5 was sequenced and found to code for a kringle-containing protein. A human liver cDNA library was screened by using a genomic probe from the gene in L5. cDNAs were isolated that contained sequence identical with regions in the gene in L5. Comparison of the cDNA with the gene indicated that the gene in L5 was composed of 18 exons separated by 17 intervening sequences and is 4690 bp in length. Exons ranged in size from 36 to 242 bp in length while intervening sequences ranged from 77 to 697 bp in length. The putative protein encoded by the gene in L5 contains four kringle domains followed by a serine protease-like domain. This domain structure is identical with that found in hepatocyte growth factor (HGF), although the two proteins are only about 50% identical. On the basis of the similarity of the protein encoded by L5 and HGF, we propose that the putative L5 protein be tentatively called HGF-like protein until a function is identified. The DNA sequence of the gene and cDNA and its translated amino acid sequence were compared against GenBank and NBRF databases. Sequences homologous to DNF15S1 and DNF15S2, human DNF15S2 lung mRNA, and rat acyl-peptide hydrolase were identified in exon 17 to the 3' end of the characterized sequence for the gene. From our results, it is apparent that the gene coding for human HGF-like protein is located at the DNF15S2 locus on human chromosome 3 (3p21). The gene for acyl-peptide hydrolase is 444 bp downstream of the gene coding for HGF-like protein, but on the complementary strand. The DNF15S2 locus has been proposed to code for one or more tumor suppressor genes since this locus is deleted in DNA from small cell lung carcinoma, other lung cancers, renal cell carcinoma, and von Hippel-Lindau syndrome.
Identification and molecular weight characterization of antigens from Candida albicans that are recognized by human sera (1984)

Antigenic components in the cytoplasmic extract of Candida albicans were examined after fractionation by concanavalin A-Sepharose and DEAE-Sephacel ion-exchange chromatography. Fractions from the DEAE column were tested by fused rocket immunoelectrophoresis for their reactivity with antibodies in the sera of 20 patients with disseminated candidiasis. Three groups of fractions (regions A, B, and C) from the DEAE column were defined by their reactivity with these sera. Immunoblot analysis with 20 human sera identified 18 antigenic components in regions A, B, and C. Region A contained nine antigens, region B contained four antigens, and region C contained five antigens. Region A contained an antigen with an apparent molecular weight of 48,000 that was recognized by 7 of 10 sera from patients with disseminated candidiasis. Immunoprecipitation experiments with labeled proteins from region A and 51 human sera also demonstrated the presence of a major antigen whose apparent molecular weight is 48,000 to 52,000. The 48- to 52-kilodalton protein is an abundant protein in region A and is the most frequently recognized protein by antibodies in the sera of patients with disseminated candidiasis. Patients with disseminated candidiasis had significantly higher levels of antibody (immunoglobulin G) (P less than 0.001) directed against the 48- to 52-kilodalton protein than did patients with noninvasive forms of candidiasis, patients with other fungal infections, or normal, healthy persons.
Physical properties of parabens and their mixtures: Solubility in water, thermal behavior, and crystal structures (1999)

The peculiar solubility behavior of propylparaben (propyl ester of 4-hydroxybenzoic acid) in aqueous solution, when tested separately and together with methyl-, ethyl-, and butyl-parabens, has been investigated in detail. The results clearly indicate that the decrease in solubility (approximately 50% compared to the solubility value of propylparaben alone) is typical of those mixtures containing also ethylparaben, as demonstrated by solubility experiments on binary, ternary, and quaternary mixtures of the parabens. Phase diagrams of all the six binaries show that propylparaben and ethylparaben are the only pair that form almost ideal solid solutions near the melting temperatures. Moreover, phase-solubility analysis shows that propylparaben and ethylparaben, at room temperature, can also form solid solutions whose solubility is related to the composition of the solid phase at equilibrium. To achieve an independent confirmation of the possible solid solution formation that supports the above interpretation of the solubility behavior, the crystal structures of the four parabens have been examined and isostructurality has been found to exist only between ethylparaben and propylparaben. Powder X-ray diffraction has also been performed on ethylparaben, propylparaben, and their solid solutions obtained by recrystallization from water. The progressive shift of distinctive diffraction peaks with phase composition clearly indicates that propylparaben and ethylparaben form substitutional solid solutions. The small value (<1) of the disruption index provides thermodynamic support for substitutional solid solutions based on isostructural crystals.
The GAN Landscape: Losses, Architectures, Regularization, and Normalization (2018)

Generative adversarial networks (GANs) are a class of deep generative models which aim to learn a target distribution in an unsupervised fashion. While they were successfully applied to many problems, training a GAN is a notoriously challenging task and requires a significant amount of hyperparameter tuning, neural architecture engineering, and a non-trivial amount of tricks. The success in many practical applications coupled with the lack of a measure to quantify the failure modes of GANs resulted in a plethora of proposed losses, regularization and normalization schemes, and neural architectures. In this work we take a sober view of the current state of GANs from a practical perspective. We reproduce the current state of the art and go beyond fairly exploring the GAN landscape. We discuss common pitfalls and reproducibility issues, open-source our code on Github, and provide pre-trained models on TensorFlow Hub.
Real-Time Observation of Tubule Formation from Amorphous Carbon Nanowires under High-Bias Joule Heating (2006)

The tubule formation process from amorphous carbon nanowires under high-bias-caused Joule heating was observed in real time in a high-resolution transmission electron microscope. The crystallization of the amorphous carbon nanowires occurred in two distinct ways: the formation of tubular graphitic basal planes parallel to the nanowire axis on the surface and the formation of nano-onions in the interior of the nanowire. The tubule formation mechanism is a process of solid-state atom diffusion at high temperatures. Energetically, the tubule formation is caused by the exceptionally low surface energy of the (0002) plane of graphite. Higher input power to the amorphous nanowires generally leads to improved graphitization and, in turn, to increased conductance. The results suggest that nanotube formation in the arc-discharge growth process may involve the formation and crystallization of amorphous carbon.
Proliferative activity in peripheral and coronary atherosclerotic plaque among patients undergoing percutaneous revascularization. (1993)

We evaluated the proliferative activity of human atherosclerotic lesions associated with active symptoms of ischemia, by assessing the expression of the proliferating cell nuclear antigen (PCNA). We confirmed in vitro that PCNA, an essential component of the DNA synthesis machinery, is selectively expressed in proliferating human vascular smooth muscle cells. 37 atherosclerotic lesions (18 primary and 19 restenotic) retrieved by directional atherectomy from either coronary or peripheral arteries were then studied for the expression of PCNA, using in situ hybridization or immunohistochemistry. Among plaques studied by in situ hybridization, 7 out of 11 primary and 11 out of 11 restenotic lesions contained PCNA-positive cells. The mean rate of proliferation (percent of PCNA-positive cells) was 7.2 +/- 10.8% in primary lesions and 20.6 +/- 18.2% in restenotic lesions (P < 0.05). Among specimens studied by immunohistochemistry, five out of seven primary and eight out of eight restenotic lesions contained proliferating cells. The mean rate of proliferation was again higher in the restenotic (15.2 +/- 13.6%) than primary (3.6 +/- 3.5%) lesions (P < 0.05). Proliferating cells were detected as late as 1 yr after angioplasty. We conclude that cellular proliferation is a feature of atherosclerotic lesions which are associated with symptoms of ischemia, but that it is more prominent in restenosis compared to primary lesions. These findings have implications for therapies aimed at limiting lesion growth, particularly after percutaneous revascularization.