gebhart/patrepeval huggingface dataset:
Complete nucleotide sequence of the new simian T-lymphotropic virus, STLV-PH969 from a Hamadryas baboon, and unusual features of its long terminal repeat (1997)

A third type of primate T-lymphotropic virus, PTLV-L, with STLV-PH969 as a prototype, has recently been isolated from an African baboon (Papio hamadryas). Classification of this virus has been based on partial sequence analysis of cDNA from a virus-producing cell line, PH969. We obtained the complete nucleotide sequence of this virus with a proviral genome of 8,916 bp. All major genes, homologous in all human T-cell lymphotropic virus (HTLV)-related viruses, and their corresponding mRNAs, including appropriate splicing, were identified. One additional nonhomologous open reading frame in the proximal pX region is accessible for translation through alternative splicing. Sequence comparison shows that STLV-PH969 is equidistantly related to HTLV type 1 (HTLV-1) and HTLV-2. In all coding regions, the similarity tends to be the lowest between STLV-PH969 and HTLV-1. However, in the long terminal repeat (LTR) region, the lowest similarity was found between STLV-PH969 and HTLV-2. The U3-R and R-U5 boundaries of the STLV-PH969 LTR were experimentally determined at nucleotides 268 and 524, respectively. This 695-bp LTR is 60 and 73 bp shorter than the LTRs of HTLV-1 and HTLV-2, respectively, but its general organization is similar to the one found in the HTLV-bovine leukemia virus genus. In the long region between the polyadenylation signal and the poly(A) site, sequence similarity with the HTLV-1 Rex-responsive element (RexRE) core and secondary structure prediction suggest the presence of a RexRE. The presence of three 21-bp repeats is conserved within the U3 region of HTLV-1, HTLV-2, and BLV. Only two direct repeats with similarity to these Tax-responsive elements were found in the STLV-PH969 LTR, which might suggest differences in the Tax-mediated transactivation of this virus. We conclude that STLV-PH969 has all the genes and genomic regions to suggest a replication cycle comparable to that of HTLV-1 and HTLV-2.
Targeted treatment of pruritus: a look into the future (2011)

Recent advances in pruritus research have elucidated mediators and neuronal pathways involved in itch transmission, and this fast emerging knowledge may possibly be translated into new therapies in the near future. In the skin and peripheral nerves, potential mediator and receptor therapeutic targets include the H4 histamine receptor, protease-activated receptor 2, serine proteases, cathepsin S, peripheral mu- and kappa-opioid receptors, interleukin-31, transient receptor potential vanilloid 1 and 3, fatty acid amide hydrolase, nerve growth factor and its receptor, acetylcholine, and the Mas-related G protein-coupled receptors. In the spinal cord, gastrin-related peptide and its receptor, as well as substance P and its receptor neurokinin receptor-1 serve as potential therapeutic targets. In the brain, reduction of itch perception and modulation of emotions may possibly be achieved through drugs acting on the anterior cingulate cortex. Clinically, management of pruritus should be instituted early and should address the skin pathology, peripheral neuropathy, central sensitization, and the cognito-affective aspects of the disease.
Spatially Resolved Visible Luminescence of Self-Assembled Semiconductor Quantum Dots (1995)

Ensembles of defect-free InAIAs islands of ultrasmall dimensions embedded in AIGaAs have been grown by molecular beam epitaxy. Cathodoluminescence was used to directly image the spatial distribution of the quantum dots by mapping their luminescence and to spectrally resolve very sharp peaks from small groups of dots, thus providing experimental verification for the discrete density of states in a zero-dimensional quantum structure. Visible luminescence is produced by different nominal compositions of InxAI(1-x)As-AIyGa(1-y)As.
Anemia in older persons. (2010)

Anemia in older persons is commonly overlooked despite mounting evidence that low hemoglobin levels are a significant marker of physiologic decline. Using the World Health Organization definition of anemia (hemoglobin level less than 13 g per dL [130 g per L] in men and less than 12 g per dL [120 g per L] in women), more than 10 percent of persons older than 65 years are anemic. The prevalence increases with age, approaching 50 percent in chronically ill patients living in nursing homes. There is increasing evidence that even mild anemia is associated with increased morbidity and mortality. Anemia warrants evaluation in all older persons, except those at the end of life or who decline interventions. About one third of persons have anemia secondary to a nutritional deficiency, one third have anemia caused by chronic inflammation or chronic kidney disease, and one third have unexplained anemia. Nutritional anemia is effectively treated with vitamin or iron replacement. Iron deficiency anemia often is caused by gastrointestinal bleeding and requires further investigation in most patients. Anemia of chronic inflammation or chronic kidney disease may respond to treatment of the underlying disease and selective use of erythropoiesis-stimulating agents. The treatment of unexplained anemia is difficult, and there is little evidence that treatment decreases morbidity and mortality, or improves quality of life. Occasionally, anemia may be caused by less common but potentially treatable conditions, such as autoimmune hemolytic anemia, malignancy, or myelodysplastic syndrome.
Surface tension-powered self-assembly of microstructures - The state-of-the-art (2003)

Because of the low dimensional power of its force scaling law, surface tension is appropriate for carrying out reshaping and assembly in the microstructure size domain. This paper reviews work on surface tension powered self-assembly of microstructures. The existing theoretical approaches for rotational assembly are unified. The demonstrated fabrication processes are compared. Mechanisms for accurately determining the assembled shape are discussed, and the limits on accuracy and structural distortion are considered. Applications in optics, electronics and mechanics are described. More complex operations (including the combination of self-assembly and self-organization) are also reviewed.
Profile of a Serial Killer: Cellular and Molecular Approaches to Study Individual Cytotoxic T‐Cells following Therapeutic Vaccination (2010)

T-cell vaccination may prevent or treat cancer and infectious diseases, but further progress is required to increase clinical efficacy. Step-by-step improvements of T-cell vaccination in phase I/II clinical studies combined with very detailed analysis of T-cell responses at the single cell level are the strategy of choice for the identification of the most promising vaccine candidates for testing in subsequent large-scale phase III clinical trials. Major aims are to fully identify the most efficient T-cells in anticancer therapy, to characterize their TCRs, and to pinpoint the mechanisms of T-cell recruitment and function in well-defined clinical situations. Here we discuss novel strategies for the assessment of human T-cell responses, revealing in part unprecedented insight into T-cell biology and novel structural principles that govern TCR-pMHC recognition. Together, the described approaches advance our knowledge of T-cell mediated-protection from human diseases.
Coordinately Regulated Alternative Splicing of Genes Involved in Cholesterol Biosynthesis and Uptake (2011)

Genes involved in cholesterol biosynthesis and uptake are transcriptionally regulated in response to cellular sterol content in a coordinated manner. A number of these genes, including 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) and LDL receptor (LDLR), undergo alternative splicing, resulting in reductions of enzyme or protein activity. Here we demonstrate that cellular sterol depletion suppresses, and sterol loading induces, alternative splicing of multiple genes involved in the maintenance of cholesterol homeostasis including HMGCR and LDLR, the key regulators of cellular cholesterol biosynthesis and uptake, respectively. These changes were observed in both in vitro studies of the HepG2 human hepatoma derived cell line, as well as in vivo studies of St. Kitts vervets, also known as African green monkeys, a commonly used primate model for investigating cholesterol metabolism. These effects are mediated in part by sterol regulation of polypyrimidine tract binding protein 1 (PTBP1), since knock-down of PTBP1 eliminates sterol induced changes in alternative splicing of several of these genes. Single nucleotide polymorphisms (SNPs) that influence HMGCR and LDLR alternative splicing (rs3846662 and rs688, respectively), have been associated with variation in plasma LDL-cholesterol levels. Sterol-induced changes in alternative splicing are blunted in carriers of the minor alleles for each of these SNPs, indicating an interaction between genetic and non-genetic regulation of this process. Our results implicate alternative splicing as a novel mechanism of enhancing the robust transcriptional response to conditions of cellular cholesterol depletion or accumulation. Thus coordinated regulation of alternative splicing may contribute to cellular cholesterol homeostasis as well as plasma LDL levels.
Cytochrome c oxidase: Structural studies by electron microscopy of two‐dimensional crystals (1994)

Cytochrome c oxidase is a complex integral membrane protein consisting of 13 different polypeptide chains and four metal centers having a total molecular weight of approximately 200,000 daltons. It can be isolated in two 2-dimensional crystalline forms differing in aggregation state of the enzyme. One crystal form consists of cytochrome oxidase dimers (approximately 400,000 daltons) embedded unidirectionally in the lipid bilayer of a collapsed vesicle while the other form consists of crystalline sheets of cytochrome oxidase monomers. Both crystal forms have been studied by electron microscopy during the past two decades, and this paper summarizes the results of early structural studies as well as more recent results applying techniques of cryoelectron microscopy and digital image processing. The structure of frozen-hydrated cytochrome oxidase dimers at 20 A resolution is discussed as well as the packing of monomers within dimers and the site of cytochrome c binding.
Taxol increases steady-state levels of lipopolysaccharide-inducible genes and protein-tyrosine phosphorylation in murine macrophages (1992)

Taxol, a microtubule stabilizing agent, exhibits promise in the treatment of breast and ovarian tumors. Recently, this novel drug has been shown to activate murine macrophages to express TNF-alpha and to down-regulate TNF-alpha receptors, activities shared by bacterial LPS. Our study sought to determine if taxol could regulate gene expression in murine macrophages and to examine further the ability of taxol to generate an LPS-like signal. Toward this end, the ability of taxol to induce TNF-alpha mRNA and five other genes (IL-1 beta, IP-10, D3, D7, and D8) associated with LPS-activation of macrophages was examined by Northern blot analysis. Taxol alone (1-30 microM) induced murine C3H/OuJ macrophages to secrete bioactive TNF-alpha and express increased levels of each of the six genes under investigation. The magnitude and the kinetics of induction of each gene closely resembled that seen with Escherichia coli K235 LPS. Macrophages from LPS-hyporesponsive C3H/HeJ mice, however, failed to induce detectably any of the genes in response to taxol, despite being sensitive to the microtubule stabilizing effects of taxol as determined by immunofluorescence microscopy. The gene induction activity of taxol was in marked contrast to an alternative macrophage activator, heat killed Staphylococcus aureus, which induced a distinct gene profile in C3H/OuJ macrophages and which was equally active in C3H/OuJ and C3H/HeJ macrophages. These data are consistent with an ability of taxol to generate an LPS-like signal, possibly through a common signaling intermediate. As a first step toward identifying signal responses shared by taxol and LPS, we have shown that taxol, as shown previously for LPS, rapidly induces the tyrosine phosphorylation of a 41- and 42-kDa protein.
Economic Analysis of Greenhouse Lighting: Light Emitting Diodes vs. High Intensity Discharge Fixtures (2014)

Lighting technologies for plant growth are improving rapidly, providing numerous options for supplemental lighting in greenhouses. Here we report the photosynthetic (400-700 nm) photon efficiency and photon distribution pattern of two double-ended HPS fixtures, five mogul-base HPS fixtures, ten LED fixtures, three ceramic metal halide fixtures, and two fluorescent fixtures. The two most efficient LED and the two most efficient double-ended HPS fixtures had nearly identical efficiencies at 1.66 to 1.70 micromoles per joule. These four fixtures represent a dramatic improvement over the 1.02 micromoles per joule efficiency of the mogul-base HPS fixtures that are in common use. The best ceramic metal halide and fluorescent fixtures had efficiencies of 1.46 and 0.95 micromoles per joule, respectively. We also calculated the initial capital cost of fixtures per photon delivered and determined that LED fixtures cost five to ten times more than HPS fixtures. The five-year electric plus fixture cost per mole of photons is thus 2.3 times higher for LED fixtures, due to high capital costs. Compared to electric costs, our analysis indicates that the long-term maintenance costs are small for both technologies. If widely spaced benches are a necessary part of a production system, the unique ability of LED fixtures to efficiently focus photons on specific areas can be used to improve the photon capture by plant canopies. Our analysis demonstrates, however, that the cost per photon delivered is higher in these systems, regardless of fixture category. The lowest lighting system costs are realized when an efficient fixture is coupled with effective canopy photon capture.
Reduced Activation Energy for Grain Growth in Nanocrystalline Yttria-Stabilized Zirconia (2003)

Nanocrystalline (similar to15-20 nm) 3 mol % yttria-stabilized zirconia (3YSZ) powder is synthesized via sol-gel technique. A reduced activation energy value of similar to13.0 +/- 0.9 kJ/mol is observed for grain growth in nano-3YSZ powder, within the calcination temperature range of 400-1200 degreesC, which is much lower than that (580 kJ/mol) reported for submicron/micron-sized 3YSZ. This is attributed to large oxygen-ion vacancy concentration in nano-3YSZ.
Exploration of Backbone Space in Foldamers Containing α‐ and β‐Amino Acid Residues: Developing Protease‐Resistant Oligomers that Bind Tightly to the BH3‐Recognition Cleft of Bcl‐xL (2007)

Protein-protein interactions play crucial roles in cell-signaling events and are often implicated in human disease. Molecules that bind tightly to functional protein-surface sites and show high stability to degradative enzymes could be valuable pharmacological tools for dissection of cell-signaling networks and might ultimately lead to therapeutic agents. We recently described oligomers containing both alpha- and beta-amino acid residues that bind tightly to the BH3 recognition site of the anti-apoptotic protein Bcl-x(L). The oligomers with highest affinity had a nine-residue N-terminal segment with a 1:1 alpha:beta residue repeat and a six-residue C-terminal segment containing exclusively proteinogenic alpha-residues. The N-terminal portions of such (alpha/beta+alpha)-peptides are highly resistant to proteolysis, but the C-terminal alpha-segments are susceptible. This study emerged from efforts to modify the alpha-segment in an (alpha/beta+alpha)-peptide in a way that would diminish proteolytic degradation but retain high affinity for Bcl-x(L). Some of the oligomers reported here could prove useful in certain biological applications, particularly those for which extended incubation in a biological milieu is required.
Neuroleptic activity in 5-aryltetrahydro-.gamma.-carbolines (1980)

A series of 5-aryltetrahydro-gamma-carbolines was prepared by a novel N-arylation procedure and tested for neuroleptic activity in a rat antiamphetamine model. The systematic exploration of structural parameters leading to 8-fluoro-5-(4-fluorophenyl)-2-[4-hydroxy-4-(4-fluorophenyl)butyl]-2,3,5-tetrahydro-1H-pyrido[4,3-b]indole (CP-36,584, flutroline), a potent and long-acting neuroleptic compound, is described. These semirigid compounds provide a new, structurally distinct series with which to probe the conformational requirements for potent activity at the dopamine receptor.
Activating and inhibitory receptors on synovial fluid natural killer cells of arthritis patients: role of CD94/NKG2A in control of cytokine secretion (2007)

Natural killer (NK) cells are activated early during inflammatory events and contribute to the shaping of the ensuing adaptive immune response. To further understand the role for NK cells in inflammation, we investigated the phenotype and function of synovial fluid (SF) NK cells from patients with chronic joint inflammation, as well as from patients with transient inflammation of the knee following trauma. We confirm that synovial NK cells are similar to the well-characterized CD56(bright) peripheral blood (PB) NK-cell subset present in healthy individuals. However, compared to this PB subset the synovial NK cells express a higher degree of activation markers including CD69 and NKp44, the latter being up-regulated also on CD56(bright) NK cells in the PB of patients. Activated synovial NK cells produced interferon-gamma and tumour necrosis factor, and the production was further up-regulated by antibody masking of CD94/NKG2A, and down-regulated by target cells expressing human leucocyte antigen-E in complex with peptides known to engage CD94/NKG2A. We conclude that synovial NK cells have an activated phenotype and that CD94/NKG2A is a key regulator of synovial NK-cell cytokine synthesis.
Regioselective synthesis of 6-substituted 2-hydroxybenzaldehyde: efficient synthesis of the immunomodulator tucaresol and related analogues (1997)

Two new improved procedures have been developed for the preparation of the immunostimulant tucaresol 1 [4-(2-formyl-3-hydroxyphenoxymethyl)benzoic acid]. These approaches, which start from resorcinol or 2,6-dimethoxybenzaldehyde, are practical and therefore amenable to scale-up. In the case of the second approach, the multi-step synthesis reported in the literature has been reduced to three steps. Furthermore, unlike the reported method, our synthesis is versatile for the preparation of tucaresol analogues. The method is general and applicable for the preparation of 6-substituted 2-hydroxybenzaldehydes.
TRANSLATIONAL REGULATION OFGCN4AND THE GENERAL AMINO ACID CONTROL OF YEAST (2005)

Cells reprogram gene expression in response to environmental changes by mobilizing transcriptional activators. The activator protein Gcn4 of the yeast Saccharomyces cerevisiae is regulated by an intricate translational control mechanism, which is the primary focus of this review, and also by the modulation of its stability in response to nutrient availability. Translation of GCN4 mRNA is derepressed in amino acid-deprived cells, leading to transcriptional induction of nearly all genes encoding amino acid biosynthetic enzymes. The trans-acting proteins that control GCN4 translation have general functions in the initiation of protein synthesis, or regulate the activities of initiation factors, so that the molecular events that induce GCN4 translation also reduce the rate of general protein synthesis. This dual regulatory response enables cells to limit their consumption of amino acids while diverting resources into amino acid biosynthesis in nutrient-poor environments. Remarkably, mammalian cells use the same strategy to downregulate protein synthesis while inducing transcriptional activators of stress-response genes under various stressful conditions, including amino acid starvation.
Antibody-Mediated Neutralization and Simian Immunodeficiency Virus Models of HIV/AIDS (2007)

Over the last two decades, use of SIV for experimental infection of Asian macaques has provided important leads in the quest for an AIDS vaccine, served as the genesis of recombinant SIV/HIV viruses (SHIV), and perhaps most importantly, helped establish or confirm biological relevance for a variety of hypotheses related to the host immune response to infection and the corresponding viral strategies for evading that response. The env genes of HIV-1 and SIV encode proteins bearing a high degree of structural similarity and sharing an identical suite of essential functions. The Env complexes formed by these proteins are present on the surface of virus-producing cells and virions, where they are the primary targets of the host neutralizing antibody response. In this review, we briefly describe the similarities between HIV-1 infection and SIV experimental models, then focus specifically on the use of the SIV/macaque model as a tool for understanding the humoral immune response to infection and resistance to antibody-mediated neutralization in HIV infection and AIDS.
Crystal structure of Bacillus licheniformis 1,3‐1,4‐β‐d‐glucan 4‐glucanohydrolase at 1.8 Å resolution (1995)

The crystal structure of the 1,3-1,4-beta-D-glucan 4-glucanohydrolase from Bacillus licheniformis is solved at a resolution of 1.8 A and refined to R = 16.5%. The protein has a similar beta-sandwich structure as the homologous enzyme from Bacillus macerans and the hybrid H(A16-M). This demonstrates that the jellyroll fold of these proteins is remarkably rigid and only weakly influenced by crystal contacts. The crystal structure permits to extend mechanistic considerations derived for the B. licheniformis enzyme to the entire class of bacterial 1,3-1,4-beta-D-glucan 4-glucanohydrolases.
Synthesis and characterization of 5'-fluorescent-dye-labeled oligonucleotides. (1993)

Fluorescent-dye-labeled oligonucleotides are used in many procedures, including DNA sequencing, PCR, restriction mapping, the study of genetic disease, and forensics identification. In this paper, we describe detailed methods for the synthesis, purification, and quantification of 5'-fluorescent-dye-labeled oligonucleotides. The relationship of specific and nonspecific dye attachment to synthetic oligonucleotides is discussed, and the importance of primer design is considered as a way to prevent chemical problems from interfering with biological reactions.
Enhancing Incretin Action for the Treatment of Type 2 Diabetes (2003)

GLP-1R agonists and DPP-IV inhibitors have shown promising results in clinical trials for the treatment of type 2 diabetes. The need for daily injections of potentially immunogenic GLP-1-derived peptides and the potential for unanticipated side effects with chronic use of DPP-IV inhibitors will require ongoing scrutiny of the risk-benefit ratio for these new therapies as they are evaluated in the clinic.