gebhart/patrepeval huggingface dataset:
Identification and sequence analysis of the promoter for the leukocyte integrin beta-subunit (CD18): a retinoic acid-inducible gene (1992)

Leukocyte adhesion receptors (LFA-1; Mac-1; p150,95) are a family of heterodimeric cell-surface adhesion molecules expressed exclusively in granulocytes, lymphocytes, and macrophages. Expression of these proteins is under complex regulatory control, but to date promoters for these genes have not been identified. The CD18 gene codes for the common beta-subunit of the leukocyte adhesion receptors. Transcription of CD18 is highly tissue-specific, hormonally inducible (by retinoic acid [RA]), and coordinately regulated with leukocyte integrin alpha-chains. To identify the CD18 promoter, we screened a human genomic phage library with a human CD18 cDNA probe and obtained a clone that contains an exon coding for the 5' untranslated region (UTR). Using rapid amplification of cDNA ends (RACE), RNAse protection, S1 nuclease, and primer extension assays, we demonstrated the existence of multiple transcription start sites clustered in a 45-nt region. We investigated the transcription-promoting activity of the genomic sequences 5' to the CD18 gene by performing transient expression assays with a growth hormone reporter gene in various hematopoietic cell lines. The CD18 promoter was active in Jurkat cells, a lineage that normally expresses CD18 but was considerably less active in K562, an early erythroid line that does not normally express CD18. The genomic sequences upstream of the start site cluster lack CAAT and TATA boxes, but have two Sp1 binding sites and 10 T(G/C)AC(C/A) boxes, which may represent binding sites for RA receptors (RAR). These features distinguish the CD18 promoter from the promoters of other tissue-specific, hormone-inducible genes, and may be representative of leukocyte integrin promoters in general.
On the Interactions of the Hypothalamic-Pituitary-Adrenal (HPA) Axis and Sleep: Normal HPA Axis Activity and Circadian Rhythm, Exemplary Sleep Disorders (2005)

The hypothalamic-pituitary-adrenal (HPA) axis plays important roles in maintaining alertness and modulating sleep. Dysfunction of this axis at any level (CRH receptor, glucocorticoid receptor, or mineralocorticoid receptor) can disrupt sleep. Herein, we review normal sleep, normal HPA axis physiology and circadian rhythm, the effects of the HPA axis on sleep, as well as the effects of sleep on the HPA axis. We also discuss the potential role of CRH in circadian-dependent alerting, aside from its role in the stress response. Two clinically relevant sleep disorders with likely HPA axis dysfunction, insomnia and obstructive sleep apnea, are discussed. In insomnia, we discuss how HPA axis hyperactivity may be partially causal to the clinical syndrome. In obstructive sleep apnea, we discuss how HPA axis hyperactivity may be a consequence of the disorder and contribute to secondary pathology such as insulin resistance, hypertension, depression, and insomnia. Mechanisms by which cortisol can affect slow wave sleep are discussed, as is the role the HPA axis plays in secondary effects of primary sleep disorders.
Low- and high-temperature superconducting microwave filters (1991)

Stripline and microstrip filters at X-band were designed and fabricated using low- and high-temperature superconductors in quarter-wave, parallel-coupled section configurations. Low-temperature superconducting niobium thin films, deposited on single-crystal sapphire, were used to build to six-pole stripline filters with adjacent passbands and approximately 3 dB crossovers and 1.2% bandwidth. Four- and six-pole microstrip filters were made with in situ epitaxial YBa/sub 2/Cu/sub 3/O/sub 7/ (YBCO) films on LaAlO/sub 3/ substrates. All the YBCO filters showed 77 K passbands with clean skirts and high out-of-band rejection. The six-pole filters had adjacent passbands with -28 dB crossovers and 1.5% bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Worsening of motor performance in patients with Parkinson's disease following transdermal nicotine administration (1999)

Nicotine has been reported to have positive effects on motor performance in patients with Parkinson's disease. In this study, motor performance was evaluated in 16 patients with idiopathic Parkinson's disease during a practical off-period using the motor part of the Unified Parkinson's Disease Rating Scale after 12 hours' exposure to a transdermal patch containing 35 mg nicotine or placebo. The study was performed using a double-blind crossover design. In contrast to previous reports, nicotine exposure was followed by a worsening of symptoms compared with placebo. A negative response to subthreshold dopaminergic stimulation, resulting from an inhibitory effect of low striatal dopamine concentrations acting on a subset of dopamine receptors, might possibly account for this finding.
Design and Electro-Optical Characterization of Si-Based Resonant Cavity Light Emitting Devices (2011)

The fabrication and characterization of electrically pumped silicon/silicon dioxide (Si/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) Fabry-Perot microcavities is reported. The active region of these devices consists of an Er-implanted silicon-rich oxide (SRO:Er) film placed in the center of a λ-cavity polysilicon spacer. The structures have been designed in order to enhance the electroluminescence signal at 1540 nm, which is an important wavelength for telecommunication systems, and to achieve high directionality and high-purity spectra. The active region design allows the Er-implanted SRO film to be driven electrically. These Si-based resonant cavity light emitting diodes are fabricated by chemical vapor deposition on a silicon substrate. Microcavities with a quality factor ranging from 50 to 118, depending on the number of Si/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> pairs constituting the dielectric mirrors, have been fabricated. Low operating voltages and electrical stability have been achieved. The emitted power versus current flowing in the active medium was measured for the structures with different quality factors. An enhancement of the electroluminescence signal at the selected emission wavelength was achieved with a proper design.
Combination Treatment with TRA-8 Anti–Death Receptor 5 Antibody and CPT-11 Induces Tumor Regression in an Orthotopic Model of Pancreatic Cancer (2007)

Combination TRA-8 and CPT-11 therapy produced enhanced cytotoxicity and survival in the MIA PaCa-2 orthotopic model of pancreatic cancer.
Incremental Boosting Convolutional Neural Network for Facial Action Unit Recognition (2017)

Recognizing facial action units (AUs) from spontaneous facial expressions is still a challenging problem. Most recently, CNNs have shown promise on facial AU recognition. However, the learned CNNs are often overfitted and do not generalize well to unseen subjects due to limited AU-coded training images. We proposed a novel Incremental Boosting CNN (IB-CNN) to integrate boosting into the CNN via an incremental boosting layer that selects discriminative neurons from the lower layer and is incrementally updated on successive mini-batches. In addition, a novel loss function that accounts for errors from both the incremental boosted classifier and individual weak classifiers was proposed to fine-tune the IB-CNN. Experimental results on four benchmark AU databases have demonstrated that the IB-CNN yields significant improvement over the traditional CNN and the boosting CNN without incremental learning, as well as outperforming the state-of-the-art CNN-based methods in AU recognition. The improvement is more impressive for the AUs that have the lowest frequencies in the databases.
Comparative studies on efficacy of different vaccines against fowl typhoid in chickens (1998)

Studies were conducted to compare the efficacy of live avirulent 9R vaccine, protein extracts and formalin- killed bacterin for the protection of chickens against fowl typhoid. Vaccination of birds at 9 weeks of age using strain 9R with and without Freund's complete adjuvant resulted in 95 and 100% survivors, but the challenge strain persisted in the organs of 1 bird each. The use of crude protein extract + adjuvant resulted in 100% survival rate along with total clearance of the challenge strain of Salmonella gallinarum from all the survivor birds. Addition of Freund's complete adjuvant during primary vaccination resulted in higher antibody titres and survival rate. Killed bacterin without adjuvant gave minimum protection against fowl typhoid.
Indium-induced smoothing of GaAs films during MBE growth (1996)

A new technique is reported for obtaining a smooth growth surface during molecular beam epitaxy growth of GaAs on (001) GaAs substrates. The smoothing is achieved by exposing the surface to an indium flux during growth of the GaAs buffer layer at high substrate temperature (590 °C). In situ light scattering shows a dramatic reduction in surface roughness along the [110] direction during this process, consistent with ex situ scanning force microscopy measurements on the films, which reveal atomically flat terraces oriented along the &lt;110&gt; directions. The surface reconstruction shifts from (2 × 4) to (4 × 2) under the indium flux, as revealed by reflection high-energy electron diffraction. The sticking coefficient of the indium as determined by secondary-ion mass spectroscopy is less than 10%. We attribute the observed effects to a transition from group V to group III termination, induced by surface segregation of the nonincorporated indium.
Amyloid precursors and amyloidosis in inflammatory arthritis (2001)

Recent data demonstrating the multifunctional role of serum amyloid A (SAA) in the pathogenesis of amyloidosis have yielded important insights into this potentially fatal consequence of chronic inflammation. SAA has been shown to participate in chemotaxis, cellular adhesion, cytokine production, and metalloproteinase secretion and is thus integrally involved in the disease process. In addition to its production by the liver as part of the acute phase response, SAA is also expressed by several pathologic tissues such atherosclerotic plaques, rheumatoid synovitis and in the brains of patients with Alzheimer disease. Its constitutive production in normal tissue suggests a role for SAA in host defense and tissue turnover. Many pathways are involved in the regulation of SAA, and as more becomes known about these, potential therapeutic targets may be identified. However, the prevention of secondary amyloidosis is best achieved by early and adequate treatment of patients with chronic inflammatory disorders. Suppression of the acute phase response and normalization of SAA levels are likely to significantly impact on the incidence of amyloidosis in inflammatory arthritis.
The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development (2006)

Arabidopsis (Arabidopsis thaliana) contains approximately 100 homeobox genes, many of which have been shown to play critical roles in various developmental processes. Here we characterize the zinc finger-homeodomain (ZF-HD) subfamily of homeobox genes, consisting of 14 members in Arabidopsis. We demonstrate that the HDs of the ZF-HD proteins share some similarities with other known HDs in Arabidopsis, but they contain distinct features that cluster them as a unique class of plant HD-containing proteins. We have carried out mutational analyses to show that the noncanonical residues present in the HDs of this family of proteins are important for function. Yeast (Saccharomyces cerevisiae) two-hybrid matrix analyses of the ZF-HD proteins reveal that these proteins both homo- and heterodimerize, which may contribute to greater selectivity in DNA binding. These assays also show that most of these proteins do not contain an intrinsic activation domain, suggesting that interactions with other factors are required for transcriptional activation. We also show that the family members are all expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development. Furthermore, we have identified loss-of-function mutations for six of these genes that individually show no obvious phenotype, supporting the idea that the encoded proteins have common roles in floral development. Based on these results, we propose the ZF-HD gene family encodes a group of transcriptional regulators with unique biochemical activities that play overlapping regulatory roles in Arabidopsis floral development.
Association of Small Low-Density Lipoprotein Particles With the Incidence of Coronary Artery Disease in Men and Women (1996)

LDL size was significantly smaller in CAD cases than in controls in a prospective, population-based study. These findings support other evidence of a role for small, dense LDL particles in the etiology of atherosclerosis.
Modulation of metastatic potential by cell surface urokinase of murine melanoma cells. (1988)

We have carried out enzymatic, immunofluorescence, and surface iodination studies which show that B16 melanoma cells express the single chain form of the urokinase type plasminogen activator (uPA) on their cell surface, and that these cells are capable of plasminogen-dependent fibronectin degradation. The significance of the expression of surface single-chain uPA and uPA activity to the metastatic process was examined by preincubating melanoma cells with uPA modulating agents followed by i.v. injection of the cells into mice and enumeration of pulmonary nodules 17 days later. B16 cells that had been pretreated with anti-uPA immunoglobulins that were inhibitory to uPA activity invariably showed significantly decreased numbers of metastases compared to controls. On the contrary, pretreatment with plasmin, which is not only the product of the uPA catalyzed reaction but is also able to convert single-chain uPA to uPA, significantly increased the numbers of metastases. Control treatments, which included normal rabbit and mouse immunoglobulins, monovalent noninhibitory anti-uPA Fab fragments, and various monoclonal and polyclonal antibodies directed against other B16 cell surface antigens, did not affect the metastatic potential of the cells. Divalent inhibitory anti-uPA F(ab)2 fragments, on the contrary, inhibited metastasis as efficiently as intact IgG. The results support the hypothesis that proteolysis of extracellular matrix components by cell surface-localized uPA may be a critical step during the process of tumor cell invasion and metastasis.
[Vasculitis--aspect of cellular and molecular pathogenesis]. (2001)

Vasculitis, inflammation of the vessel wall, can be observed in acute and chronic inflammatory processes, in vascular rejection of allogeneic transplants and can be encountered as primary vasculitis of arterial, arteriolar, capillary and venular vessels. Although the numerous forms of vasculitis and their associations with different diseases result in a multitude of etiologic and pathogenetic factors there are pathogenetic factors common to several vasculitides. These include innate immunity factors, transcription factors such as NFkB, endothelial cytoprotective agents such as NO and anti-neutrophilic cytoplasmic auto-antibodies (ANCA). ANCA may be directed against several antigens, in the majority of cases against proteinase 3 and myeloperoxidase. The complex of proteinase 3 and ANCA leads to an increased expression of CD18, CD14 and an elevated synthesis of cytokines and chemokines such as interleukin 1, interleukin 8 in monocytes. In granulocytes generation of reactive oxygen species is found in addition. In both cells apoptosis finally occurs. ANCA may also bind to a surface glycoprotein (gp130) expressed on glomerular and peritubular endothelia in the kidney. Thus the activation of granulocytes, monocytes and endothelial cells by ANCA may be a critical step in the initiation phases of vasculitis. NO is cytoprotective for endothelial cells in small concentrations. Our group has shown in detailed studies that inhibition of endothelial NO synthase is detrimental and enhancement of activity of endothelial NO synthase is beneficial for allogeneic solid organ transplants. The transcription factor complex NFkB is a key regulatory transcription factor for the expression of genes and proteins associated with acute inflammatory processes and endothelialitis. Inhibition of NFkB activity by a decoy-oligonucleotide prevented activation of endothelial calls in reperfusion injury and vascular rejection. The complement system probably plays an essential role in the initiation and propagation phases of vasculitis. Specifically the pneumococcal C-polysaccharide-reactive protein (CRP), synthesized after trauma and infection, can potently activate the complement cascade which leads to an activation of endothelial cells with increased expression of adhesion molecules. The 4 shortly described pathogenetic mechanisms of vasculitis seem to be important and common factors for the generation and maintenance of vascular inflammation; nevertheless these factors are only part of the spectrum of different humoral and cellular responses in vasculitis. The described experimental investigations on endothelial damage and endothelialitis may lead to new therapeutic strategies in vasculitis.
Sources of variability in nicotine and cotinine levels with use of nicotine nasal spray, transdermal nicotine, and cigarette smoking (1997)

Plasma levels of nicotine and cotinine produced by nicotine therapies are highly variable, due to both wide variability in individual pharmacokinetics and in dose delivery from the products. To compensate for individual differences in clearance, individualization of nicotine dosing based on therapeutic drug monitoring with comparison to nicotine or continine levels during cigarette smoking prior to treatment may be necessary to optimize nicotine therapy. This study also validates a recently proposed method for estimating absolute bioavailability of a drug using drug and metabolite pharmacokinetic data, and presents novel data on plasma levels of the metabolite trans-3'-hydroxycotinine in people.
Kinetic analysis of ligand binding to interleukin‐2 receptor complexes created on an optical biosensor surface (1996)

The interleukin-2 receptor (IL-2R) is composed of at least three cell surface subunits, IL-2R alpha, IL-2R beta, and IL-2R gamma c. On activated T-cells, the alpha- and beta-subunits exist as a preformed heterodimer that simultaneously captures the IL-2 ligand as the initial event in formation of the signaling complex. We used BIAcore to compare the binding of IL-2 to biosensor surfaces containing either the alpha-subunit, the beta-subunit, or both subunits together. The receptor ectodomains were immobilized in an oriented fashion on the dextran matrix through unique solvent-exposed thiols. Equilibrium analysis of the binding data established IL-2 dissociation constants for the individual alpha- and beta-subunits of 37 and 480 nM, respectively. Surfaces with both subunits immobilized, however, contained a receptor site of much higher affinity, suggesting the ligand was bound in a ternary complex with the alpha- and beta-subunits, similar to that reported for the pseudo-high-affinity receptor on cells. Because the binding responses had the additional complexity of being mass transport limited, obtaining accurate estimates for the kinetic rate constants required global fitting of the data sets from multiple surface densities of the receptors. A detailed kinetic analysis indicated that the higher-affinity binding sites detected on surfaces containing both alpha- and beta-subunits resulted from capture of IL-2 by a preformed complex of these subunits. Therefore, the biosensor analysis closely mimicked the recognition properties reported for these subunits on the cell surface, providing a convenient and powerful tool to assess the structure-function relationships of this and other multiple subunit receptor systems.
Distinct Mutations in <i>IRAK-4</i> Confer Hyporesponsiveness to Lipopolysaccharide and Interleukin-1 in a Patient with Recurrent Bacterial Infections (2003)

We identified previously a patient with recurrent bacterial infections who failed to respond to gram-negative LPS in vivo, and whose leukocytes were profoundly hyporesponsive to LPS and IL-1 in vitro. We now demonstrate that this patient also exhibits deficient responses in a skin blister model of aseptic inflammation. A lack of IL-18 responsiveness, coupled with diminished LPS and/or IL-1-induced nuclear factor-kappaB and activator protein-1 translocation, p38 phosphorylation, gene expression, and dysregulated IL-1R-associated kinase (IRAK)-1 activity in vitro support the hypothesis that the defect lies within the signaling pathway common to toll-like receptor 4, IL-1R, and IL-18R. This patient expresses a "compound heterozygous" genotype, with a point mutation (C877T in cDNA) and a two-nucleotide, AC deletion (620-621del in cDNA) encoded by distinct alleles of the IRAK-4 gene (GenBank/EMBL/DDBJ accession nos. AF445802 and AY186092). Both mutations encode proteins with an intact death domain, but a truncated kinase domain, thereby precluding expression of full-length IRAK-4 (i.e., a recessive phenotype). When overexpressed in HEK293T cells, neither truncated form augmented endogenous IRAK-1 kinase activity, and both inhibited endogenous IRAK-1 activity modestly. Thus, IRAK-4 is pivotal in the development of a normal inflammatory response initiated by bacterial or nonbacterial insults.
The Behavioral Ecology of Resource Consumption: Why “Being Green” Is So Hard (2014)

The life history and behavior of humans, like those of other species, are shaped by natural selection. Some life history traits that heighten our resource consumption arise from an unusual combination of high intelligence and extreme sociality; as humans evolved, we have become ever smarter and more efficient about obtaining resources for ourselves. We humans are doing what other species do, extracting resources from the environment to survive and reproduce—but we have become so good at it that we are having an ever-increasing impact on populations of other species. The reactions of other species depend in part on their life history, shaped by their evolutionary past: have they repeatedly confronted extremes? Changes? Or, if they have had a long history of relatively little change in important environmental variables, how can they cope? Further, their life histories and ecologies are strong determinants of the most efficient human extraction techniques. Understanding life histories, both of other species and of our own, is important for a sustainable future; in some important ways, our evolutionary past constrains our ecological future. Here I present an overview of what is known.
Joint Raman spectroscopy and HRXRD investigation of cubic gallium nitride layers grown on 3C-SiC (2016)

Abstractauthoren Cubic gallium nitride (GaN) films are analyzed with high-resolution X-ray diffraction (HRXRD) and Raman spectroscopy. Several cubic GaN layers were grown on 3C-SiC (001) substrate by radio-frequency plasma-assisted molecular beam epitaxy. The layer thickness of the cubic GaN was varied between 75 and 505 nm. The HRXRD analysis reveals a reduction of the full-width at half-maximum (FWHM) of omega scans for growing layer thicknesses, which is caused by a partial compensation of defects. The Raman characterization confirms well-formed c-GaN layers. A more detailed examination of the longitudinal optical mode hints at a correlation of the FWHM of the Raman mode with the dislocation density, which shows the possibility to determine dislocation densities by Raman spectroscopy on a micrometer scale, which is not possible by HRXRD. Furthermore, this Raman analysis shows that normalized Raman spectra present an alternative way to determine layer thicknesses of thin GaN films.