gebhart/patrepeval huggingface dataset:
Effects of Seeding Layer on Perovskite Transformation, Microstructure and Transmittance of Sol-Gel-Processed Lanthanum-Modified Lead Zirconate Titanate Films (1994)

A series of sol-gel-processed lanthanum-modified lead zirconate titanate (PLZT) thin films with La/Zr/Ti ratios of 8.5/65/35, 9/65/35, 9.5/65/35, 15.5/40/60 and 18/30/70 were prepared on indium tin oxide (ITO)-coated Corning 7059 glass substrates and heat-treated at different temperatures from 475° C to 685° C. The X-ray diffraction, microstructure, optical transmittance spectra and the polarization vs electric field curves were investigated. The P(L)ZT thin films of higher Ti/Zr ratio show lower transformation (from pyrochlore to perovskite) temperature. The PLZT(8.5–9.5/65/35) thin film with the seeding layer shows improved phase content, high optical transmittance and enhanced perovskite transformation kinetics. The grain sizes are reduced (from 5–6 µ m to 0.1–0.2 µ m) and uniform. The fracture surfaces of the films with a seeding layer consist of columnar structure of which the grains grew from the seeding layer. The optical transmittance is enhanced, and the polarization value at 400 KV/cm increases for the film with the seeding layer.
Step-by-Step Seeding Procedure for Preparing HKUST-1 Membrane on Porous α-Alumina Support (2011)

Metal-organic framework (MOF) membranes have attracted considerable attention because of their striking advantages in small-molecule separation. The preparation of an integrated MOF membrane is still a major challenge. Depositing a uniform seed layer on a support for secondary growth is a main route to obtaining an integrated MOF membrane. A novel seeding method to prepare HKUST-1 (known as Cu(3)(btc)(2)) membranes on porous α-alumina supports is reported. The in situ production of the seed layer was realized in step-by-step fashion via the coordination of H(3)btc and Cu(2+) on an α-alumina support. The formation process of the seed layer was observed by ultraviolet-visible absorption spectroscopy and atomic force microscopy. An integrated HKUST-1 membrane could be synthesized by the secondary hydrothermal growth on the seeded support. The gas permeation performance of the membrane was evaluated.
Insulin enhanced thrombin-activable fibrinolysis inhibitor expression through PI3 kinase/Akt pathway (2005)

Thrombin-activable fibrinolysis inhibitor (TAFI) is a key modulator of fibrinolysis. We have reported the elevated levels of plasma TAFI and their correlation with visceral fat area and insulin resistance in the patients with type 2 diabetes. Furthermore, the expression of TAFI was demonstrated in adipose tissues. Thus, we hypothesized that TAFI secreted from adipose tissues might be an important causative factor of hypofibrinolysis in patients with insulin resistance and that insulin was a modulator of the gene expression of TAFI. To evaluate this hypothesis, we examined the regulation of TAFI expression by insulin in adipocytes. TAFI mRNA was induced dose-dependently by insulin in 3T3-L1 adipocytes. PI3 kinase inhibitor wortmannin inhibited insulin-induced expression, but MEK1 inhibitor PD98059 had no effects. These data suggested that the gene expression of TAFI was regulated by PI3 kinase signaling pathway. Moreover, activated Akt induced the expression of TAFI mRNA to a similar extent by insulin in 3T3-L1 adipocytes expressing tamoxifen-regulatable Akt. In conclusion, TAFI was induced by insulin through PI3 kinase/Akt pathway in adipocytes. It is supposed that plasma TAFI levels are regulated at least in part by transcription levels in adipose tissues of patients with insulin resistance.
Organization and structure of the mouse interleukin-2 gene (1984)

We have cloned a chromosomal DNA segment which covers the entire sequence for the murine interleukin-2 gene and analysed the structure of the gene. The coding regions are separated into four blocks by three introns each of which is located similarly to the corresponding human gene. The exon sequences can be aligned perfectly with the previously cloned cDNA sequence. Of particular interests is the presence of sequences within the 5'-flanking region which are highly conserved between mouse and man. The conserved region which spans more than 400 base pairs may play a role in the regulation of IL-2 gene expression.
Human small cell lung cancer cell lines express functional atrial natriuretic peptide receptors. (1993)

Small cell lung cancer cell (SCLC) lines, NCI-H82, NCI-H660, and NCI-H1284, and HeLa cells were analyzed for the presence of atrial natriuretic peptide (ANP) receptors. In these SCLC cell lines and HeLa cells, ANP A receptor mRNA was identified by Southern blot analyses of polymerase chain reaction products and RNase protection assays using poly(A)(+)-selected RNA. Saturable binding assays revealed that HeLa cells had 2000 to 5000 high affinity atrial natriuretic peptide receptors per cell with a dissociation constant of 140 pM. In the SCLC cell lines, the binding was saturable but too low to accurately estimate the number of binding sites. After addition of human ANP, radioimmunoassays revealed accumulation of cyclic GMP in SCLC cells as well as HeLa cells in a dose-dependent fashion. The half-maximal stimulation concentration of cyclic GMP accumulation in HeLa and these SCLC cell lines was approximately 2 nM. Tetrazolyl blue assays and tritiated thymidine incorporation did not show any remarkable growth inhibition or growth stimulation of SCLC cell lines after addition of human ANP up to 3.3 microM, more than 1000-fold greater than the half-maximal stimulation concentration of cyclic GMP accumulation. Our results indicate that human SCLC cells express functional ANP receptors but ANP addition produced no detectable change in their growth pattern.
ABCA1-mediated Cholesterol Efflux Is Defective in Free Cholesterol-loaded Macrophages (2002)

In advanced atherosclerosis, macrophage foam cells progressively accumulate large amounts of unesterified or "free" cholesterol (FC), a process that is thought to contribute to foam cell death and lesional necrosis. The cellular consequences of early FC accumulation, including those that lead to further FC accumulation, are poorly understood. In this context, we show that cholesterol and phospholipid efflux mediated by ABCA1, which is initially induced in the cholesterol-loaded macrophage, was inhibited by approximately 80% in pre-toxic FC-loaded macrophages. Cholesterol efflux to HDL(2), which is mediated by a non-ABCA1 pathway, was inhibited by only approximately 20% in FC-loaded macrophages. FC loading led to decreased levels of ABCA1 protein via increased degradation of ABCA1, and not by decreased transcription or translation of AbcA1 mRNA. The decrease in ABCA1 protein occurred relatively early and was not prevented by caspase inhibitors, indicating that it was not a consequence of FC-induced apoptosis. However, inhibition of proteasomal function by lactacystin largely prevented the degradation of ABCA1. Importantly, the FC-induced decrease in ABCA1 function and protein was almost entirely prevented in macrophages that had partial deficiency of npc1 or were exposed to nanomolar concentrations of U18666A, both of which lead to defective cholesterol trafficking to the endoplasmic reticulum, but leave trafficking to the plasma membrane largely intact. Thus, a relatively early event during FC loading of macrophages is increased degradation of ABCA1, which appears to require trafficking of cholesterol to a peripheral cellular site, but not bulk trafficking of excess cholesterol to the plasma membrane. These findings provide new insight into the post-translational regulation of ABCA1 and the pathobiology of the FC-loaded macrophage.
Underground structure monitoring with wireless sensor networks (2007)

Environment monitoring in coal mines is an important application of wireless sensor networks (WSNs) that has commercial potential. We discuss the design of a Structure-Aware Self-Adaptive WSN system, SASA. By regulating the mesh sensor network deployment and formulating a collaborative mechanism based on a regular beacon strategy, SASA is able to rapidly detect structure variations caused by underground collapses. A prototype is deployed with 27 Mica2 motes. We present our implementation experiences as well as the experimental results. To better evaluate the scalability and reliability of SASA, we also conduct a large-scale trace-driven simulation based on real data collected from the experiments.
DNIC-mediated analgesia produced by a supramaximal electrical or a high-dose formalin conditioning stimulus: roles of opioid and α2-adrenergic receptors (2010)

It is demonstrated that DNIC produced by different types of conditioning stimuli can be mediated by different descending inhibitory controls, indicating the organization within the central nervous circuit is complex and possibly exhibits particular clinical manifestations.
Escherichia coli Secretion of an Active Chimeric Antibody Fragment (1988)

A chimeric mouse-human Fab protein that binds specifically to the human carcinoma cell line C3347 has been expressed and secreted from Escherichia coli. This molecule, which contains functionally assembled kappa and Fd proteins, binds as effectively to sites on the surface of C3347 cells as Fab fragments prepared proteolytically from whole chimeric or mouse antibody. The production in Escherichia coli of foreign heterodimeric protein reagents, such as Fab, should prove useful in the management of human disease.
Developing a clinical translational neuroscience taxonomy for anxiety and mood disorder: protocol for the baseline-follow up Research domain criteria Anxiety and Depression (“RAD”) project (2016)

ClinicalTrials.gov Identifier: NCT02220309 . Registered: August 13, 2014.
Phage-Display Libraries of Murine and Human Antibody Fab Fragments (2003)

We provide efficient and detailed procedures for construction, expression, and screening of comprehensive libraries of murine or human antibody Fab fragments displayed on the surface of filamentous phage. In addition, protocols for producing and using ultra-electrocompetent cells, for producing Fab phages from libraries, and for selecting antigen binders by panning are presented. The latter protocol includes a procedure for trypsin elution of bound phage.
Cobalt Oxide Nanomaterials by Vapor-Phase Synthesis for Fast and Reversible Lithium Storage (2010)

The design and assembly of suitable nanosystems are key issues in the development of smaller and more efficient lithium batteries. To this regard, cobalt oxides possess very favorable properties for use as negative electrode materials. In this work, we describe a convenient synthesis route to cobalt oxide nanomaterials (both single- and mixed-phase CoO and Co3O4) supported on Ti. The systems are grown by chemical vapor deposition starting from an innovative second-generation molecular source, Co(hfa)2·TMEDA (hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate, TMEDA = N,N,N′,N′-tetramethylethylenediamine). Controlled variations of the substrate temperature and O2 pressure in the reaction atmosphere enabled tailoring both the phase composition and the system morphology. The electrochemical properties of the obtained nanosystems were evaluated by galvanostatic measurements and impedance spectroscopy. The results showed excellent cycling performances and very high specific capacity values, offering attractive perspectives for the use of the present systems as advanced anode materials in Li-ion batteries.
Surface Enhanced Raman Spectroscopy of Individual Rhodamine 6G Molecules on Large Ag Nanocrystals (1999)

To explore the relationship between local electromagnetic field enhancement and the large SERS (surface enhanced Raman scattering) enhancement that enables the observation of single molecule Raman spectra, we measure both resonant Rayleigh scattering spectra and rhodamine 6G Raman spectra from single Ag particles. Our apparatus combines the techniques of dark-field optical microscopy for resonant Rayleigh measurements, and grazing incidence Raman spectroscopy. The Rayleigh spectra show that the citrate-reduced Ag colloid is extremely heterogeneous. Only the larger particles, in part created by salt induced aggregation, show a large SERS effect. In agreement with the work of Nie and Emory, we find that a few nanocrystals show huge single molecule R6G SERS intensities. While all SERS active particles have some resonant Rayleigh scattering at the 514.5 nm laser wavelength, there is no correlation between the resonant Rayleigh spectra and the SERS intensity. We discuss a model in which huge SERS intensities result from single chemisorbed molecules interacting with ballistic electrons in optically excited large Ag particles. This model is a natural consequence of the standard local electromagnetic field model for SERS and the high surface sensitivity of plasmon dephasing in the noble metals.
Comprehensive Proteomic Analysis of Human Par Protein Complexes Reveals an Interconnected Protein Network (2004)

The polarization of eukaryotic cells is controlled by the concerted activities of asymmetrically localized proteins. The PAR proteins, first identified in Caenorhabditis elegans, are common regulators of cell polarity conserved from nematode and flies to man. However, little is known about the molecular mechanisms by which these proteins and protein complexes establish cell polarity in mammals. We have mapped multiprotein complexes formed around the putative human Par orthologs MARK4 (microtubule-associated protein/microtubule affinity-regulating kinase 4) (Par-1), Par-3, LKB1 (Par-4), 14-3-3zeta and eta (Par-5), Par-6a, -b, -c, and PKClambda (PKC3). We employed a proteomic approach comprising tandem affinity purification (TAP) of protein complexes from cultured cells and protein sequencing by tandem mass spectrometry. From these data we constructed a highly interconnected protein network consisting of three core complex "modules" formed around MARK4 (Par-1), Par-3.Par-6, and LKB1 (Par-4). The network confirms most previously reported interactions. In addition we identified more than 50 novel interactors, some of which, like the 14-3-3 phospho-protein scaffolds, occur in more than one distinct complex. We demonstrate that the complex formation between LKB1.Par-4, PAPK, and Mo25 results in the translocation of LKB1 from the nucleus to the cytoplasm and to tight junctions and show that the LKB1 complex may activate MARKs, which are known to introduce 14-3-3 binding sites into several substrates. Our findings suggest co-regulation and/or signaling events between the distinct Par complexes and provide a basis for further elucidation of the molecular mechanisms that govern cell polarity.
Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family (2014)

Our understanding of fungal cellulose degradation has shifted dramatically in the past few years with the characterization of a new class of secreted enzymes, the lytic polysaccharide monooxygenases (LPMO). After a period of intense research covering structural, biochemical, theoretical and evolutionary aspects, we have a picture of them as wedge-like copper-dependent metalloenzymes that on reduction generate a radical copper-oxyl species, which cleaves mainly crystalline cellulose. The main biological function lies in the synergism of fungal LPMOs with canonical hydrolytic cellulases in achieving efficient cellulose degradation. Their important role in cellulose degradation is highlighted by the wide distribution and often numerous occurrences in the genomes of almost all plant cell-wall degrading fungi. In this review, we provide an overview of the latest achievements in LPMO research and consider the open questions and challenges that undoubtedly will continue to stimulate interest in this new and exciting group of enzymes.
The CIMT-monitoring panel: a two-step approach to harmonize the enumeration of antigen-specific CD8+ T lymphocytes by structural and functional assays (2007)

The interpretation of the results obtained from immunomonitoring of clinical trials is a difficult task due to the variety of methods and protocols available to detect vaccine-specific T-cell responses. This heterogeneity as well as the lack of standards has led to significant scepticism towards published results. In February 2005, a working group was therefore founded under the aegis of the Association for Immunotherapy of Cancer ("CIMT") in order to compare techniques and protocols applied for the enumeration of antigen-specific T-cell responses. Here we present the results from two consecutive phases of an international inter-laboratory testing project referred to as the "CIMT monitoring panel". A total of 13 centers from six European countries participated in the study in which pre-tested PBMC samples, synthetic peptides and PE-conjugated HLA-tetramers were prepared centrally and distributed to participants. All were asked to determine the number of antigen-specific T-cells in each sample using tetramer staining and one functional assay. The results of the first testing round revealed that the total number of cells analyzed was the most important determinant for the sensitive detection of antigen-specific CD8(+) T-cells by tetramer staining. Analysis by ELISPOT was influenced by a combination of cell number and a resting phase after thawing of peripheral blood mononuclear cells. Therefore, the experiments were repeated in a second phase but now the participants were asked to change their protocols according to the new guidelines distilled from the results of the first phase. The recommendations improved the number of antigen-specific T-cell responses that were detected and decreased the variability between the laboratories. We conclude that a two-step approach in inter-laboratory testing allows the identification of distinct variables that influence the sensitivity of different T-cell assays and to formally show that a defined correction to the protocols successfully increases the sensitivity and reduces the inter-center variability. Such "two-step" inter-laboratory projects could define rational bases for accepted international guidelines and thereby lead to the harmonization of the techniques used for immune monitoring.
PIK3CA Gene Mutations in Pediatric and Adult Glioblastoma Multiforme (2006)

The phosphatidylinositol 3-kinases (PI3K) are a family of enzymes that relay important cellular growth control signals. Recently, a large-scale mutational analysis of eight PI3K and eight PI3K-like genes revealed somatic mutations in PIK3CA, which encodes the p110alpha catalytic subunit of class IA PI3K, in several types of cancer, including glioblastoma multiforme. In that report, 4 of 15 (27%) glioblastomas contained potentially oncogenic PIK3CA mutations. Subsequent studies, however, showed a significantly lower mutation rate ranging from 0% to 7%. Given this disparity and to address the relation of patient age to mutation frequency, we examined 10 exons of PIK3CA in 73 glioblastoma samples by PCR amplification followed by direct DNA sequencing. Overall, PIK3CA mutations were found in 11 (15%) samples, including several novel mutations. PIK3CA mutations were distributed in all sample types, with 18%, 9%, and 13% of primary tumors, xenografts, and cell lines containing mutations, respectively. Of the primary tumors, PIK3CA mutations were identified in 21% and 17% of pediatric and adult samples, respectively. No evidence of PIK3CA gene amplification was detected by quantitative real-time PCR in any of the samples. This study confirms that PIK3CA mutations occur in a significant number of human glioblastomas, further indicating that therapeutic targeting of this pathway in glioblastomas is of value. Moreover, this is the first study showing PIK3CA mutations in pediatric glioblastomas, thus providing a molecular target in this important pediatric malignancy.
Humoral Immune Responses of Dengue Fever Patients Using Epitope-Specific Serotype-2 Virus-Like Particle Antigens (2009)

Dengue virus (DENV) is a serious mosquito-borne pathogen causing significant global disease burden, either as classic dengue fever (DF) or in its most severe manifestation dengue hemorrhagic fever (DHF). Nearly half of the world's population is at risk of dengue disease and there are estimated to be millions of infections annually; a situation which will continue to worsen with increasing expansion of the mosquito vectors and epidemic DF/DHF. Currently there are no available licensed vaccines or antivirals for dengue, although significant effort has been directed toward the development of safe and efficacious dengue vaccines for over 30 years. Promising vaccine candidates are in development and testing phases, but a better understanding of immune responses to DENV infection and vaccination is needed. Humoral immune responses to DENV infection are complex and may exacerbate pathogenicity, yet are essential for immune protection. In this report, we develop DENV-2 envelope (E) protein epitope-specific antigens and measure immunoglobulin responses to three distinct epitopes in DENV-2 infected human serum samples. Immunoglobulin responses to DENV-2 infection exhibited significant levels of individual variation. Antibody populations targeting broadly cross-reactive epitopes centered on the fusion peptide in structural domain II were large, highly variable, and greater in primary than in secondary DENV-2 infected sera. E protein domain III cross-reactive immunoglobulin populations were similarly variable and much larger in IgM than in IgG. DENV-2 specific domain III IgG formed a very small proportion of the antibody response yet was significantly correlated with DENV-2 neutralization, suggesting that the highly protective IgG recognizing this epitope in murine studies plays a role in humans as well. This report begins to tease apart complex humoral immune responses to DENV infection and is thus important for improving our understanding of dengue disease and immunological correlates of protection, relevant to DENV vaccine development and testing.
Chemokine expression in rat stab wound brain injury (1996)

A traumatic injury to the adult mammalian central nervous system (CNS) results in reactive astrogliosis and the migration of hematogenous cells into the damaged neural tissue. Chemokines, a novel class of chemoattractant cytokines, are now being recognized as mediators of the inflammatory changes that occur following injury. The expression of MCP-1 (macrophage chemotactic peptide-1), a member of the beta family of chemokines, has recently been demonstrated in trauma in the rat brain (Berman et al.: J Immunol 156:3017-3023, 1996). Using a stab wound model for mechanical injury, we studied the expression of two other beta chemokines: RANTES (Regulated on Activation, Normal T cell Expressed and Secreted) and MIP-1 beta (macrophage inflammatory protein-1 beta) in the rat brain. The stab wound injury was characterized by widespread gliosis and infiltration of hematogenous cells. Immunohistochemical staining revealed the presence of RANTES and MIP-1 beta in the injured brain. RANTES and MIP-1 beta were both diffusely expressed in the necrotic tissue and were detected as early as 1 day post-injury (dpi). Double-labeling studies showed that MIP-1 beta, but not RANTES, was expressed by reactive astrocytes near the lesion site. In addition, MIP-1 beta staining was also detected on macrophages at the site of injury. The initial expression of the chemokines closely correlated with the appearance of inflammatory cells in the injured CNS, suggesting that RANTES and MIP-1 beta may play a role in the inflammatory events of traumatic brain injury. This study also demonstrates for the first time MIP-1 beta expression in reactive astrocytes following trauma to the rat CNS.