gebhart/patrepeval huggingface dataset:
Conjugation of protein to immunostimulatory DNA results in a rapid, long‐lasting and potent induction of cell‐mediated and humoral immunity (2000)

Immunostimulatory DNA sequences (ISS) are a potent Th1 adjuvant. We hypothesized that conjugation of ISS to protein antigens would strongly enhance their immunogenicity because both antigen and adjuvant (ISS) would be delivered to the same locale/antigen-presenting cell. To test this hypothesis, we conjugated a 22-mer immunostimulatory oligodeoxynucleotide (ISS-ODN) to two test antigens of differing intrinsic immunogenicity, namely Escherichia coli beta-galactosidase and the HIV-1 envelope glycoprotein gp120. We show that the antigen-ISS conjugates rapidly induce Th1 cells secreting high levels of IFN-gamma, strong CTL activity, and high titer IgG2a and HIV-neutralizing antibodies, exceeding gene and protein vaccination alone or immunization with mixtures of antigen and ISS-ODN. The data suggest that this procedure generates a novel and unique vaccine that rapidly triggers strong humoral and cell-mediated immunity.
Mechanically tissue-like elastomeric polymers and their potential as a vehicle to deliver functional cardiomyocytes (2013)

One of the major challenges in the field of biomaterials engineering is the replication of the non-linear elasticity observed in soft tissues. In the present study, non-linearly elastic biomaterials were successfully fabricated from a chemically cross-linked elastomeric poly(glycerol sebacate) (PGS) and thermoplastic poly(L-lactic acid) (PLLA) using the core/shell electrospinning technique. The spun fibrous materials, containing a PGS core and PLLA shell, demonstrated J-shaped stress-strain curves, and having ultimate tensile strength, rupture elongation, and stiffness constants respectively comparable to muscle tissue properties. In vitro evaluations also showed that PGS/PLLA fibrous biomaterials possess excellent biocompatibility, capable of supporting human stem-cell-derived cardiomyocytes over several weeks in culture. Therefore, the core/shell electrospun elastomeric materials provide a new potential scaffold to support cells in the therapy of a wide range of soft tissues exposed to cyclic deformation, such as tendon, ligament, cardiac or smooth muscle and lung epithelium.
Specific Protein Detection Using Thermally Reduced Graphene Oxide Sheet Decorated with Gold Nanoparticle‐Antibody Conjugates (2010)

A highly sensitive and selective field-effect transistor biosensor using thermally reduced graphene oxide (TRGO) sheet decorated with gold nanoparticle-antibody conjugates is demonstrated. Probe antibody (anti-Immunoglobulin G) is labeled on the surface of the TRGO sheet through gold nanoparticles and electrical detection of the protein binding (Immunoglobulin G and anti-Immunoglobulin G) is accomplished by FET and dc measurements.
Compressed Manifold Modes for Mesh Processing (2014)

Abstract This paper introduces compressed eigenfunctions of the Laplace‐Beltrami operator on 3D manifold surfaces. They constitute a novel functional basis, called the compressed manifold basis , where each function has local support. We derive an algorithm, based on the alternating direction method of multipliers (ADMM), to compute this basis on a given triangulated mesh. We show that compressed manifold modes identify key shape features, yielding an intuitive understanding of the basis for a human observer, where a shape can be processed as a collection of parts. We evaluate compressed manifold modes for potential applications in shape matching and mesh abstraction. Our results show that this basis has distinct advantages over existing alternatives, indicating high potential for a wide range of use‐cases in mesh processing.
Effect of Partially Protected Sodium Butyrate on Performance, Digestive Organs, Intestinal Villi and E. coli Development in Broilers Chickens (2014)

The aim of this study was to evaluate the effect of partially protected sodium butyrate (PSB) on performance, digestive organs, intestinal villi and E. coli development in broilers chickens. Nine hundred twenty four one-day-old mixed Cobb chicks were divided in 3 treatments with 7 replicates each in a ® randomized block design. Treatment T1 was a control diet without any growth promoter, treatment T2 was the control diet plus colistin at 100,000 IU/kgBW and treatment T3 was the control diet with PSB at 700 ppm. Chicks were fed in mash form for 3 phases: starter (1-14 days), grower (15-28 days) and finisher (29-42 days). There were no significant differences on performance among all treatments in starter phase. Chicks fed PSB in grower and finisher phases had the highest weight gain and the best feed conversion ratio. Relative digestive organs weights were not affected by treatment in any phase. Jejunum and small intestine relative lengths of birds fed PSB and colistin at 14 days were longer than those of birds fed control diet. Jejunal villi of birds fed PSB and colistin at 42 days were higher than those in birds fed the control diet. Colistin produced the deepest crypts and the lowest villi height/crypt depth ratios in all intestinal segments at 14 days. Intestinal E. coli growth was not affected by any treatment. These data indicate that partially protected sodium butyrate and colistin improves performance, colistin as an antibiotic growth promoter and PSB by improving intestinal villi development in broilers chickens.
Fluorine enhanced oxidation of silicon at low temperatures (1994)

We report the oxidation of silicon at and below 550 °C in a mixture of oxygen and fluorine. Introduction of small concentrations of fluorine (&amp;lt;0.1%) in the oxygen ambient increases the oxide growth sharply to rates in excess of 8 Å/min where the average fluorine concentration in the oxide can exceed 6 at. %. For each oxidation temperature there was a unique fluorine concentration at which the oxidation rate was at its highest. Fluorine depth profiles in the film were determined by high depth resolution nuclear reaction analysis, and high interface concentrations of fluorine were observed.
Palmitic Acid Analogs Exhibit Nanomolar Binding Affinity for the HIV-1 CD4 Receptor and Nanomolar Inhibition of gp120-to-CD4 Fusion (2010)

Considering observed differences between K(i) and K(d) values indicates clear and rational direction for improving inhibition efficacy to HIV-1 entry and infection. Taken together this report introduces a novel class of natural small molecules fusion inhibitors with nanomolar efficacy of CD4 receptor binding and inhibition of HIV-1 entry.
The Role of Protein Structure in Chromatographic Behavior (1987)

Chromatographic retention is determined by a relatively small number of amino acids located in a chromatographic contact region on the surface of a polypeptide. This region is determined by the mode of separation and the amino acid distribution within the polypeptide. The contact area may be as small as a few hundred square angstroms in bioaffinity chromatography. In contrast, the contact region in ion exchange, reversed phase, hydrophobic interaction and the other nonbioaffinity separation modes is much broader, ranging from one side to the whole external surface of a polypeptide. Furthermore, structural changes that alter the chromatographic contact region will alter chromatographic properties. Thus, although immunosorbents can be very useful in purifying proteins of similar primary structure, they will be ineffective in discriminating between small, random variations within a structure. Nonbioaffinity columns complement affinity columns in probing a much larger portion of solute surface and being able to discriminate between protein variants.
Recommendations for Treating Leishmaniasis with Sodium Stibogluconate (Pentostam) and Review of Pertinent Clinical Studies (1992)

Pentavalent antimonial compounds have been the mainstay of the treatment of visceral, cutaneous, and mucosal leishmaniasis for approximately half a century. Pentostam (sodium stibogluconate) is the pentavalent antimonial compound available in the United States (through the Centers for Disease Control). As dosage regimens for treating leishmaniasis have evolved, the daily dose of antimony and the duration of therapy have been progressively increased to combat unresponsiveness to therapy. In the 1980s, the use of 20 mg/kg/day (instead of 10 mg/kg/day) of antimony was recommended, but only to a maximum daily dose of 850 mg. The authors have concluded on the basis of recent efficacy and toxicity data that this 850-mg restriction should be removed; the evidence to date, which is summarized here, suggests that a regimen of 20 mg/kg/day of pentavalent antimony, without an upper limit on the daily dose, is more efficacious and is not substantially more toxic than regimens with lower daily doses. We recommend treating all forms of leishmaniasis with a full 20 mg/kg/day of pentavalent antimony. We treat cutaneous leishmaniasis for 20 days and visceral and mucosal leishmaniasis for 28 days. Our judgment of cure is based on clinical criteria.
PRAD1, a candidate BCL1 oncogene: mapping and expression in centrocytic lymphoma. (1991)

Rearrangement of the BCL1 (B-cell lymphoma 1) region on chromosome 11q13 appears to be highly characteristic of centrocytic lymphoma and also is found infrequently in other B-cell neoplasms. Rearrangement is thought to deregulate a nearby protooncogene, but transcribed sequences in the immediate vicinity of BCL1 breakpoints had not been identified. PRAD1, previously designated D11S287E, was identified on 11q13 as a chromosomal breakpoint region rearranged with the parathyroid hormone gene in a subset of parathyroid adenomas; this highly conserved putative oncogene, which encodes a novel cyclin, has been linked to BCL1 and implicated also in subsets of breast and squamous cell neoplasms with 11q13 amplification. We report pulsed-field gel electrophoresis data showing BCL1 and PRAD1 to be no more than 130 kilobases apart. PRAD1 mRNA is abundantly expressed in seven of seven centrocytic lymphomas (Kiel classification), in contrast to 13 closely related but noncentrocytic lymphomas. Three of the seven centrocytic lymphomas had detectable BCL1 DNA rearrangement. Also, two unusual cases of CLL with BCL1 rearrangement overexpressed PRAD1, in contrast to five CLL controls. Thus, PRAD1 is an excellent candidate "BCL1 oncogene." Its overexpression may be a key consequence of rearrangement of the BCL1 vicinity in B-cell neoplasms and a unifying pathogenetic feature in centrocytic lymphoma.
Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two‐dimensional NMR spectroscopy (1992)

The solution structure of the phosphocarrier protein, HPr, from Bacillus subtilis has been determined by analysis of two-dimensional (2D) NMR spectra acquired for the unphosphorylated form of the protein. Inverse-detected 2D (1H-15N) heteronuclear multiple quantum correlation nuclear Overhauser effect (HMQC NOESY) and homonuclear Hartmann-Hahn (HOHAHA) spectra utilizing 15N assignments (reported here) as well as previously published 1H assignments were used to identify cross-peaks that are not resolved in 2D homonuclear 1H spectra. Distance constraints derived from NOESY cross-peaks, hydrogen-bonding patterns derived from 1H-2H exchange experiments, and dihedral angle constraints derived from analysis of coupling constants were used for structure calculations using the variable target function algorithm, DIANA. The calculated models were refined by dynamical simulated annealing using the program X-PLOR. The resulting family of structures has a mean backbone rmsd of 0.63 A (N, C alpha, C', O atoms), excluding the segments containing residues 45-59 and 84-88. The structure is comprised of a four-stranded antiparallel beta-sheet with two antiparallel alpha-helices on one side of the sheet. The active-site His 15 residue serves as the N-cap of alpha-helix A, with its N delta 1 atom pointed toward the solvent to accept the phosphoryl group during the phosphotransfer reaction with enzyme I. The existence of a hydrogen bond between the side-chain oxygen atom of Tyr 37 and the amide proton of Ala 56 is suggested, which may account for the observed stabilization of the region that includes the beta-turn comprised of residues 37-40. If the beta alpha beta beta alpha beta (alpha) folding topology of HPr is considered with the peptide chain polarity reversed, the protein fold is identical to that described for another group of beta alpha beta beta alpha beta proteins that include acylphosphatase and the RNA-binding domains of the U1 snRNP A and hnRNP C proteins.
The comparison of steam injected gas turbine system with combined one in co-generation (2002)

This paper describes a comparison of steam injected gas turbine system with gas turbine combined system in co-generation. The comparison is based on the actual gas turbine KAWASAKI M7A-02 data and specifications. A brief financial portrait of the system is also shown. The result shows that (1) a suitable system which gives minimum years for payback of equity is determined in terms of the site heat demand and electric demand (2) steam injected gas turbine co-generation system gives shorter years for payback of equity when the ratio of heat demand/electric demand is greater than 0.3 (3) CCPP co-generation system gives shorter years for payback of equity when the ratio of heat demand/electric demand is 0&acd;0.3.
Combination IL-2 and IL-4 reduces glucocorticoid receptor-binding affinity and T cell response to glucocorticoids. (1993)

The mechanisms contributing to persistent T cell activation and poor response to glucocorticoids in chronic inflammatory illnesses such as steroid resistant (SR) asthma are poorly defined. We examined the possibility that certain cytokines, specifically IL-2 and IL-4, could affect T cell response to glucocorticoids. A [3H]dexamethasone radioligand-binding assay was used to measure the number of glucocorticoid receptors (GR) and dissociation constant (Kd) in PBMC from normal donors and patients with SR asthma, cultured in the absence and presence of these cytokines. PBMC from normal donors incubated for 48 h in the presence of combination IL-2 + IL-4 had nuclear GR with significantly reduced binding affinity (GR Kd = 36.1 +/- 1.63 nM, mean +/- SEM; p = 0.0001) as compared with PBMC incubated with medium alone (GR Kd = 6.74 +/- 0.46 nM). The cytosolic GR Kd remained unchanged. However, when PBMC were incubated with IL-2 alone or IL-4 alone, no change in GR-binding affinity was observed. Furthermore, when T cells and non-T cells were individually stimulated with combination IL-2 + IL-4, a significant reduction in GR-binding affinity was observed only in the T cell population (p = 0.0001). The IL-2 + IL-4-induced alteration in PBMC GR Kd was associated with an increase in GR number (8348 +/- 964 vs 1710 +/- 228 sites/cell; p = 0.0003). More importantly, the alteration in PBMC GR-binding affinity with IL-2 + IL-4 was associated with a functional change in T cell response to methylprednisolone MPN, i.e., a reduced inhibitory effect of MPN on PMA/ionomycin-induced T cell proliferation. These effects of IL-2 + IL-4 on PBMC GR affinity and response to MPN were blocked by co-incubation with IFN-gamma. Freshly isolated PBMC from four patients with SR asthma had a significantly reduced GR-binding affinity (Kd = 40.0 +/- 2.68 nM; p = 0.0001) when compared with seven normal subjects (7.15 +/- 0.41 nM). The altered PBMC GR binding from patients with SR asthma reversed to normal when incubated with medium alone, but was sustained with IL-2 + IL-4. These observations suggest that with persistent inflammation certain cytokines may contribute to an impaired response to glucocorticoids. Furthermore, the effects of IL-2 and IL-4 were blocked by IFN-gamma.
Restoration of the cAMP second messenger pathway enhances cardiac preservation for transplantation in a heterotopic rat model. (1993)

Current organ preservation strategies subject graft vasculature to severe hypoxia (PO2 approximately 20 Torr), potentially compromising vascular function and limiting successful transplantation. Previous work has shown that cAMP modulates endothelial cell (EC) antithrombogenicity, barrier function, and leukocyte/EC interactions, and that hypoxia suppresses EC cAMP levels. To explore the possible benefits of cAMP analogs/agonists in organ preservation, we used a rat heterotopic cardiac transplant model; dibutyryl cAMP added to preservation solutions was associated with a time- and dose-dependent increase in the duration of cold storage associated with successful graft function. Preservation was also enhanced by 8-bromo-cAMP, the Sp isomer of adenosine 3',5'monophosphorothioate, and types III (indolidan) and IV (rolipram) phosphodiesterase inhibitors. Neither butyrate alone nor 8-bromoadenosine were effective, and the cAMP-dependent protein kinase antagonist Rp isomer of adenosine 3',5'monophosphorothioate prevented preservation enhancement induced by 8-bromo-cAMP. Grafts stored with dibutyryl cAMP demonstrated a 5.5-fold increase in blood flow and a 3.2-fold decreased neutrophil infiltration after transplantation. To explore the role of cAMP in another cell type critical for vascular homeostasis, vascular smooth muscle cells were subjected to hypoxia, causing a time-dependent decline in cAMP levels. Although adenylate cyclase activity was unchanged, diminished oxygen tensions were associated with enhanced phosphodiesterase activity (59 and 30% increase in soluble types III and IV activity, respectively). These data suggest that hypoxia or graft ischemia disrupt vascular homeostasis, at least in part, by perturbing the cAMP second messenger pathway. Supplementation of this pathway provides a new approach for enhancing cardiac preservation, promoting myocardial function, and maintaining vascular homeostatic properties.
Dual device user interface design (1996)

Article Dual device user interface design: PDAs and interactive television Share on Authors: Scott Robertson Applied Research, US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, CO Applied Research, US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, COView Profile , Cathleen Wharton Applied Research US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, CO Applied Research US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, COView Profile , Catherine Ashworth Applied Research US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, CO Applied Research US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, COView Profile , Marita Franzke Applied Research US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, CO Applied Research US WEST, Advanced Technologies, 4001 Discovery, Dr.Boulder, COView Profile Authors Info & Claims CHI '96: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsApril 1996 Pages 79–86https://doi.org/10.1145/238386.238408Online:13 April 1996Publication History 75citation2,454DownloadsMetricsTotal Citations75Total Downloads2,454Last 12 Months34Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Reflection intensity optical fiber sensors for the mid-infrared (1997)

Two kinds of reflection intensity sensor made of chalcogenide glass fiber for the mid-IR region are demonstrated. One is a double-fiber reflection sensor based on two tied fibers with a gold-coated hollow metal waveguide connected to the far end of the fibers. The other is a single-fiber reflection sensor based on contact couplers. These reflectance sensors were coupled to a Fourier-transform IR spectrometer by a unique accessory based on nonimaging concentrators. This setup was built to measure absorption spectra of a polymer coating of an aluminum can and a sheet of drafting paper. A theoretical model treating the ratio between the signal from the target and the background is introduced. This model was helpful in deriving the sensitivity characteristics of the sensors from experimental absorption peak heights. Hence, the absorption peaks heights that we obtained using a single-fiber reflection sensor with a symmetric coupler were nearly 50% relative to those obtained with a double-fiber reflection sensor.
Common mental disorder and obesity: insight from four repeat measures over 19 years: prospective Whitehall II cohort study (2009)

These findings suggest that in British adults the direction of association between common mental disorders and obesity is from common mental disorder to increased future risk of obesity. This association is cumulative such that people with chronic or repeat episodes of common mental disorder are particularly at risk of weight gain.
A novel method for multiple alignment of sequences with repeated and shuffled elements (2004)

We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an alignment as a directed graph, possibly containing cycles. This representation provides more flexibility than does a traditional alignment matrix or the recently introduced partial order alignment (POA) graph by allowing a larger class of evolutionary relationships between the aligned sequences. Our graph representation is particularly well-suited to the alignment of protein sequences with shuffled and/or repeated domain structure, and allows one to construct multiple alignments of proteins containing (1) domains that are not present in all proteins, (2) domains that are present in different orders in different proteins, and (3) domains that are present in multiple copies in some proteins. In addition, ABA is useful in the alignment of genomic sequences that contain duplications and inversions. We provide several examples illustrating the applications of ABA.
The Genetic Basis of Preference for Sweet Substances Among Inbred Strains of Mice: Preference Ratio Phenotypes and the Alleles of the Sac and dpa Loci (1995)

Five inbred strains (129/J, BALB/cByJ, C3HeB/FeJ, C57BI/6J and DBA/2J) were examined with two-bottle (48 h) preference ratio testing across concentrations of sodium saccharin (3 x 10(-4) M, 10(-3) M, 3 x 10(-3) M and 10(-2) M), d-phenylalanine (10(-3) M, 10(-2) M and 10(-1) M), and l-glutamine (10(-2) M, 3 x 10(-2) M, 10(-1) M and 3 x 10(-1) M). Three consistent groupings of strains were observed across substances and concentrations: (1) C57BI/6J (preference at low and high concentrations); (2) BALB/cByJ and C3HeB/FeJ (preference at high concentrations); (3) 129/J and DBA/2J (preference at high concentration for sodium saccharin and indifference to d-phenylalanine and l-glutamine). If a single locus (presumably dpa or Sac) determines these phenotypes, there are likely to be three alleles. If two independent loci (presumably dpa and Sac) determine these phenotypes, an allelic assignment of Sacb/dpa+s for the C57BI/6J strain, Sacb/dpa-s for the BALB/cByJ and C3HeB/FeJ strains, and either Sacd/dpa+s or Sacd/dpa-s for the 129/J and DBA/2J strains is suggested.
Realization of Atomically Controlled Dopant Devices in Silicon (2007)

Molecular beam epitaxy and scanning tunneling microscopy (STM) patterning are combined to form highly doped, planar devices in silicon at the atomic level. The absolute device location is registered to microscopic markers (see image; scale bar: 50 μm) for the alignment of surface contacts, enabling the correlation of the electrical properties of atomically controlled devices such as nanowires, tunnel junctions, and nanodots to the dopant location, monitored using high-resolution STM techniques.