gebhart/patrepeval huggingface dataset:
Characterization of Human Tumor-Infiltrating Lymphocytes Expanded in Hollow-Fiber Bioreactors for Immunotherapy of Cancer (2001)

We attempted to grow tumor-infiltrating lymphocytes (TIL) from 34 fresh tumors of eight different histologies using flasks for the initiation phase and hollow fiber bioreactors to expand TIL to therapeutic numbers. Overall success rate was 76% (26/34) including melanoma (9/14, 64%) and renal cell carcinoma (11/11, 100%). The mean number of days required to reach successful initiation (1 x 10(9) TIL) for all tumor types was 29 +/- 16 days (mean +/- S.D.). Therapeutic doses of TIL required an average of 88 +/- 23 days (initiation plus expansion) with an average TIL number of 3.2 x 10(10) +/- 2.8 x 10(10). TIL phenotype was predominantly CD4+ in 53% (16/30) and CD8+ in 47% (14/30), renal cell carcinoma samples accounted for 12/14 of the predominantly CD8+ TIL. Cells bearing the natural killer (NK) phenotype represented only 0-7% of TIL while LAK phenotype represented 0-68% (mean 11 +/- 15%); LAK was the predominant phenotype in one patient with kidney cancer. Cytotoxicity tests showed consistent NK and LAK activity in addition to cytolysis of autologous tumor. Autologous tumor cell restricted cytolysis was noted for three TIL cultures. The overall success rate and characteristics of TIL were similar to our results with TIL expanded in semi-permeable plastic bags. This work confirms that hollow-fiber bioreactors are a suitable alternative to semi-permeable bags and roller bottle systems for the expansion of human TIL for therapeutic use in cancer patients.
Role of N-glycosylation in the synthesis, dimerization and secretion of human interferon-γ (1994)

Human interferon-gamma (IFN-gamma) is a secretory glycoprotein, which has two potential N-linked glycosylation sites at positions Asn-25 and Asn-97 of its 143 amino acid long mature polypeptide chain. In order to understand the role of glycan residues in the synthesis and secretion of human IFN-gamma, both or either one of the potential N-linked glycosylation sites were mutated to Gln. The mutant and the wild-type (Wt) polypeptides were expressed in insect cells using a baculovirus vector. Elimination of the N-glycosylation site at position Asn-97 (N97Q) resulted in secreted protein yields of 70-90% as compared with the Wt production, whereas only 10-25% (N25Q) and 1-10% (N25Q,N97Q) levels of protein production was observed when the first or both sites were mutated, respectively. Although there was a difference between extracellular levels of produced protein, the kinetics of secretion was similar for all different IFN-gamma molecules. The Wt and the N-glycosylation site mutants were all secreted as dimers. The formation of biologically active dimers was more efficient for IFN-gamma polypeptides that had the intact glycosylation site at Asn-25 as compared with the other two mutant forms of IFN-gamma. The extent of dimerization correlated well with the observed secretion. The specific antiviral activity was of the same order (1 x 10(7) i.u./mg of protein) for the glycosylated IFN-gamma molecules, whereas it was slightly lower (0.5 x 10(7) i.u./mg of protein) for the unglycosylated mutant form.
Interleukin‐31: Its Role in Canine Pruritus and Naturally Occurring Canine Atopic Dermatitis (2013)

This chapter contains sections titled: Introduction Materials and methods Results Discussion Acknowledgements Supporting Information
Nanoporous Gold Leaf: “Ancient Technology”/Advanced Material (2004)

A free-standing nanoporous gold (NPG) membrane is made by dealloying commercially available white-gold leaf in nitric acid (see Figure). This porous material has an unusual combination of characteristics in that it is metallic with a continuous crystal lattice throughout the porous network, and has a pore size that is adjustable via simple room-temperature post-processing. This ultra-high-surface-area material is potentially very useful for applications such as electrocatalysis and sensing.
Nasba Technology: Isothermal RNA Amplification in Qualitative and Quantitative Diagnostics (1997)

Nucleic acid amplification technologies allow for the development of highly sensitive and specific diagnostic assays. The capacity to amplify and detect analyte targets, which may be present in a clinical sample as a single copy; is characteristic of many of these amplification technologies. NASBA is an isothermal method of nucleic acid amplification with such capability, and is particularly well suited for the amplification of RNA analytes. NASBA utilizes the coordinated activities of three enzymes (AMV-RT, RNase H, T7 RNA polymerase), and two oligonucleotide primers which are specific for the analyte target. The amplification process is part of a total system which includes a versatile nucleic acid isolation procedure, and powerful detection methodology. In this report, the development of NASBA technology for the detection of human Retrovirus RNA will be discussed. Specifically, a qualitative NASBA assay for the RNA of HTLV I, and a quantitative NASBA assay for HIV-1 will be described.
Cone beam tomography with circular, elliptical and spiral orbits (1992)

A general formula for image reconstruction from cone beam data is described. Applying this formula to various cone beam geometries results in a class of filtered backprojection algorithms. This formula is known to lead to exact reconstructions in cases in which the cone vertices form certain unbounded curves. An example of such a curve is an infinite straight line. In the case where the curve is a circle, this formula leads to the well-known Feldkamp algorithm, for which the reconstructions are only approximations to the true image. The authors apply this general formula to the cases where the curve is an ellipse and a sprial, and new algorithms are derived. The properties of these algorithms are investigated through studies of the point spread function and reconstructions of computer generated phantom data.
Characterization of Cadmium Uptake in Lactobacillus plantarum and Isolation of Cadmium and Manganese Uptake Mutants (1999)

Two different Cd(2+) uptake systems were identified in Lactobacillus plantarum. One is a high-affinity, high-velocity Mn(2+) uptake system which also takes up Cd(2+) and is induced by Mn(2+) starvation. The calculated K(m) and V(max) are 0.26 microM and 3.6 micromol g of dry cell(-1) min(-1), respectively. Unlike Mn(2+) uptake, which is facilitated by citrate and related tricarboxylic acids, Cd(2+) uptake is weakly inhibited by citrate. Cd(2+) and Mn(2+) are competitive inhibitors of each other, and the affinity of the system for Cd(2+) is higher than that for Mn(2+). The other Cd(2+) uptake system is expressed in Mn(2+)-sufficient cells, and no K(m) can be calculated for it because uptake is nonsaturable. Mn(2+) does not compete for transport through this system, nor does any other tested cation, i.e., Zn(2+), Cu(2+), Co(2+), Mg(2+), Ca(2+), Fe(2+), or Ni(2+). Both systems require energy, since uncouplers completely inhibit their activities. Two Mn(2+)-dependent L. plantarum mutants were isolated by chemical mutagenesis and ampicillin enrichment. They required more than 5,000 times as much Mn(2+) for growth as the parental strain. Mn(2+) starvation-induced Cd(2+) uptake in both mutants was less than 5% the wild-type rate. The low level of long-term Mn(2+) or Cd(2+) accumulation by the mutant strains also shows that the mutations eliminate the high-affinity Mn(2+) and Cd(2+) uptake system.
Direct imaging of photonic nanojets (2008)

We report the direct experimental observation of photonic nanojets created by single latex microspheres illuminated by a plane wave at a wavelength of 520 nm. Measurements are performed with a fast scanning confocal microscope in detection mode, where the detection pinhole defines a diffraction-limited observation volume that is scanned in three dimensions over the microsphere vicinity. From the collected stack of images, we reconstruct the full 3 dimensional photonic nanojet beam. Observations are conducted for polystyrene spheres of 1, 3 and 5 microm diameter deposited on a glass substrate, the upper medium being air or water. Experimental results are compared to calculations performed using the Mie theory. We measure nanojet sizes as small as 270 nm FWHM for a 3 microm sphere at a wavelength lambda of 520 nm. The beam keeps a subwavelength FWHM over a propagation distance of more than 3 lambda, displaying all the specificities of a photonic nanojet.
Site-specific cleavage of duplex DNA by a semisynthetic nuclease via triple-helix formation. (1990)

A Lys-84----Cys mutant staphylococcal nuclease was selectively linked to the 5' and/or 3' terminus of a thiol-containing polypyrimidine oligonucleotide via a disulfide bond. The oligonucleotide-staphylococcal nuclease adduct is capable of binding to a homopurine-homopyrimidine region of Watson-Crick duplex DNA by the formation of a triple-helical structure. Upon the addition of Ca2+, the nuclease cleaves DNA at sites adjacent to the homopurine tract. Specific double-strand cleavage occurred predominantly at A + T-rich sites to the 5' side of the homopurine tract for both the 5'-derivatized and the 5',3'-diderivatized nucleases; the 3'-derivatized nuclease gave no cleavage. The cleavage pattern is asymmetric and consists of multiple cleavage sites shifted to the 5' side on each strand, centered at the terminal base pair of the binding site. Microgram amounts of plasmid pDP20 DNA (4433 base pairs) containing a homopurine-homopyrimidine tract were selectively cleaved by a semisynthetic nuclease with greater than 75% efficiency at room temperature within 1 hr. Cleavage reaction conditions were optimized with respect to pH, temperature, reaction times, and reaction components. Semisynthetic nucleases of this type should provide a powerful tool in chromosomal DNA manipulations.
Amplification of dopaminergic signaling by a positive feedback loop (2000)

Dopamine and cAMP-regulated phosphoprotein of M(r) 32,000 (DARPP-32) plays an obligatory role in most of the actions of dopamine. In resting neostriatal slices, cyclin-dependent kinase 5 (Cdk5) phosphorylates DARPP-32 at Thr-75, thereby reducing the efficacy of dopaminergic signaling. We report here that dopamine, in slices, and acute cocaine, in whole animals, decreases the state of phosphorylation of striatal DARPP-32 at Thr-75 and thereby removes this inhibitory constraint. This effect of dopamine is achieved through dopamine D1 receptor-mediated activation of cAMP-dependent protein kinase (PKA). The activated PKA, by decreasing the state of phosphorylation of DARPP-32-Thr-75, de-inhibits itself. Dopamine D2 receptor stimulation has the opposite effect. The ability of activated PKA to reduce the state of phosphorylation of DARPP-32-Thr-75 is apparently attributable to increased protein phosphatase-2A activity, with Cdk5 being unaffected. Together, these results indicate that via positive feedback mechanisms, Cdk5 signaling and PKA signaling are mutually antagonistic.
Characterization of X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis subsp. lactis (1991)

A dipeptidyl aminopeptidase catalysing hydrolysis of X-prolyl amidomethylcoumarin (AMC) substrates has been purified from Lactococcus lactis subsp. lactis H1. The active enzyme has a molecular mass of approximately 150 kDa, a subunit molecular mass of 82 to 83 kDa and is inhibited by the serine protease inhibitor phenylmethylsulphonyl fluoride. The K m and k cat values for five different dipeptidyl AMC substrates (Gly-Pro-; Leu-Pro-; Lys-Pro-; Phe-Pro- and Glu-Pro-AMC) are similar except for the K m value for Glu-Pro-AMC, which is about threefold higher than that for the other substrates. The enzyme also catalyses hydrolysis of X-Ala-AMC substrates but with much lower k cat and higher K m values than the corresponding X-Pro-AMC substrates. The β -casein-derived heptapeptides Lys-Ala-Val-Pro-Tyr-Pro-Gln and Tyr-Pro-Phe-Pro-Gly-Pro-Ile were hydrolysed, but bradykinins with N-terminal sequences Arg-Pro-Pro- and Lys-Pro-Pro-were not. Dipeptidyl aminopeptidase specific activity is the same in a plasmid-free strain of L . lactis subsp. lactis H1 and in the wild-type, indicating that the enzyme is chromosomally encoded.
Insulin Activates Ras in the PC12 Cell Line (1997)

To address whether Ras can be activated by insulin in the PC12 cell line, proteins interacting with insulin receptor and IRS-1 molecules and their tyrosine phosphorylation were analyzed by immunoblotting following immunoprecipitation with antibodies. Tyrosine phosphorylation of the insulin receptor and IRS-1 was increased by insulin. Grb2 and Ras-GAP appeared in the immunoprecipitates by anti-insulin receptor and anti-IRS-1 from insulin-treated cells. In addition, PI 3-kinase was activated by insulin treatment in this cell line and Grb2, Ras-GAP, and MAP kinase were coprecipitated with Ras from both insulin-treated and NGF-treated cells. Analysis of MAP kinases from insulin-treated cells revealed that insulin, like NGF, increased tyrosine phosphorylation. However, activation of the MAP kinase by NGF lasted longer than activation by insulin. These results indicate that Ras can be activated by insulin in the PC12 cell line and that Ras activation is neither an accurate nor a plausible method of discriminating signals between proliferation and differentiation.
Human defensins and LL-37 in mucosal immunity (2009)

Defensins are widespread in nature and have activity against a broad range of pathogens. Defensins have direct antimicrobial effects and also modulate innate and adaptive immune responses. We consider the role of human defensins and the cathelicidin LL-37 in defense of respiratory, gastrointestinal, and genitourinary tracts and the oral cavity, skin, and eye. Human beta-defensins (hBDs) and human defensins 5 and 6 (HD5 and -6) are involved most obviously in mucosal responses, as they are produced principally by epithelial cells. Human alpha-defensins 1-4 (or HNPs 1-4) are produced principally by neutrophils recruited to the mucosa. Understanding the biology of defensins and LL-37 is the beginning to clarify the pathophysiology of mucosal inflammatory and infectious diseases (e.g., Crohn's disease, atopic dermatitis, lung or urinary infections). Challenges for these studies are the redundancy of innate defense mechanisms and the presence and interactions of many innate defense proteins in mucosal secretions.
Adaptive network/service fault detection in transaction-oriented wide area networks (2003)

Algorithms and online software for automated and adaptive detection of network/service anomalies have been developed and field-tested for transaction-oriented wide area networks (WAN). These transaction networks are integral parts of electronic commerce infrastructures. Our adaptive network/service anomaly detection algorithms are demonstrated in a commercially important production WAN, currently monitored by our recently implemented real-time software system, TRISTAN (transaction instantaneous anomaly notification). TRISTAN adaptively and proactively detects network/service performance degradations and failures in multiple service-class transaction-oriented networks, where performances of service classes are mutually dependent and correlated, and where external or environmental factors can strongly impact network and service performances. In this paper, we present the architecture, summarize the implemented algorithms, and describe the operation of TRISTAN as deployed in the AT&T transaction access services (TAS) network. TAS is a commercially important, high volume, multiple service classes, hybrid telecommunication and data WAN that services transaction traffic in the USA and neighboring countries. It is demonstrated that TRISTAN detects network/service anomalies in TAS effectively. TRISTAN can automatically and dynamically detect network/service faults, which can easily elude detection by the traditional alarm-based network monitoring systems.
Rationale for a Queueable Object Distributed Interprocess Communication System (1982)

We consider the problem of designing an interprocess communication system usable as a base for writing real-time operating and applications systems in a distributed environment where processes may be connected by anything from shared virtual memory to radios. By requiring an interface that minimizes the code an application program must devote to communications, a facility of substantially higher level than basic message passing becomes necessary. This is largely a consequence of four major performance problems with interprocess communication in a distributed environment: system reliability, server congestion, throughput, and response time. We summarize these problems, and introduce an interprocess communication system based on two mechanisms: queueable objects and connectable objects. We briefly review our experience with a limited implementation of queueable objects.
High-confinement SiGe low-loss waveguides for Si-based optoelectronics (1999)

The realization of two-dimensional SiGe/Si strained-layer low-loss waveguide (1.7 db/cm) is reported. The waveguide geometry is grown by selective epitaxy. It ensures loosened cutoff and critical thickness conditions. This geometry could be applied for waveguide active devices like light emitting diodes, photodetectors, or modulators. Because of the high cross section of the guided mode, these devices could be easily interfaced with optical fibers.
A Convenient New Route to Tetradentate and Pentadentate Macrocyclic Tetraamide Ligands (1999)

A crucial diamide diamine intermediate in the synthesis of tetradentate macrocyclic tetraamide ligands protected against oxidative decomposition has been synthesized without the use of potentially hazardous organic azide intermediates. This intermediate has also been used to synthesize a new class of pentadentate macrocyclic tetraamide ligands.
Exploiting GAN-Based SAR to Optical Image Transcoding for Improved Classification via Deep Learning (2018)

Learning the proxy task of transcoding SAR images into optical images forces an employed conditional generative adversarial network (GAN) to distinguish between different land surfaces. Such a network can then be used to build a classifier with significantly fewer free parameters that generalizes well even when trained on a very small amount of labeled data. We train such a GAN on aligned Sentinel-1 and Sentinel-2 image pairs. We then show that a pre-trained classifier using these features learned from transcoding outperforms classifiers that are trained from scratch when only a very limited amount of labeled pixels are available for training.
Measurement of optical properties of biological tissues by low-coherence reflectometry (1993)

We show that optical properties of dense biological tissues can be determined from backscattered power curves measured by a low-coherence reflectometer. Our measurement approach is based on a first-order scattering theory that relates the backscattered power to the total and backscattering cross sections of scatterers in a turbid medium. As a validation of the technique, measurements were made with a commercially available reflectometer on suspensions of polystyrene microspheres having known optical properties. With this reflectometer, which employs a 1300-nm LED source that emits less than 20 µW, we found that skin tissues could be probed to a depth of nearly 1 mm. Estimates of optical coefficients of human dermis and of a variety of excised animal tissues are given.
Laser Welding in Urethral Surgery: Improved Results with a Protein Solder (1988)

Reconstruction of the rat urethra using the CO2 laser and a protein solder has dramatically decreased the postoperative fistula rate and decreased surgical time over conventional microsurgical reconstruction. Using the rat as a model, a partial transection of the ventral urethra was repaired in one of three ways in 39 animals: conventional microsuture repair, laser assisted microsuture repair and laser assisted microsuture repair with a protein solder. The success rate in each group was 50%, 58% and 90% respectively. Therefore, the laser repair is an efficacious as conventional microsuture repair. More importantly, laser with solder is significantly better than either the conventional method or laser alone.
Structural organization of mouse peroxisome proliferator-activated receptor gamma (mPPAR gamma) gene: alternative promoter use and different splicing yield two mPPAR gamma isoforms. (1995)

To gain insight into the regulation of expression of peroxisome proliferator-activated receptor (PPAR) isoforms, we have determined the structural organization of the mouse PPAR gamma (mPPAR gamma) gene. This gene extends > 105 kb and gives rise to two mRNAs (mPPAR gamma 1 and mPPAR gamma 2) that differ at their 5' ends. The mPPAR gamma 2 cDNA encodes an additional 30 amino acids N-terminal to the first ATG codon of mPPAR gamma 1 and reveals a different 5' untranslated sequence. We show that mPPAR gamma 1 mRNA is encoded by eight exons, whereas the mPPAR gamma 2 mRNA is encoded by seven exons. Most of the 5' untranslated sequence of mPPAR gamma 1 mRNA is encoded by two exons, whereas the 5' untranslated sequence and the extra 30 N-terminal amino acids of mPPAR gamma 2 are encoded by one exon, which is located between the second and third exons coding for mPPAR gamma 1. The last six exons of mPPAR gamma gene code for identical sequences in mPPAR gamma 1 and mPPAR gamma 2 isoforms. The mPPAR gamma 1 and mPPAR gamma 2 isoforms are transcribed from different promoters. The mPPAR gamma gene has been mapped to chromosome 6 E3-F1 by in situ hybridization using a biotin-labeled probe. These results establish that at least one of the PPAR genes yields more than one protein product, similar to that encountered with retinoid X receptor and retinoic acid receptor genes. The existence of multiple PPAR isoforms transcribed from different promoters could increase the diversity of ligand and tissue-specific transcriptional responses.
ChemInform Abstract: A STUDY OF 3‐HYDROXY‐1,2,3‐BENZOTRIAZIN‐4‐ONE AND ITS O‐METHYL AND O‐ACYL DERIVATIVES (1977)

Abstract Die aus der Hydroxamsäure (I) erhältliche Titelverbindung (II) wird durch Methylierung bzw. Acylierung in die Derivate (III) bzw. (IV) übergeführt.
Flexible Porous Metal-Organic Frameworks for a Controlled Drug Delivery (2008)

Flexible nanoporous chromium or iron terephtalates (BDC) MIL-53(Cr, Fe) or M(OH)[BDC] have been used as matrices for the adsorption and in vitro drug delivery of Ibuprofen (or alpha- p-isobutylphenylpropionic acid). Both MIL-53(Cr) and MIL-53(Fe) solids adsorb around 20 wt % of Ibuprofen (Ibuprofen/dehydrated MIL-53 molar ratio = 0.22(1)), indicating that the amount of inserted drug does not depend on the metal (Cr, Fe) constitutive of the hybrid framework. Structural and spectroscopic characterizations are provided for the solid filled with Ibuprofen. In each case, the very slow and complete delivery of Ibuprofen was achieved under physiological conditions after 3 weeks with a predictable zero-order kinetics, which highlights the unique properties of flexible hybrid solids for adapting their pore opening to optimize the drug-matrix interactions.
One-Dimensional Zigzag Chain Structures with Intermolecular C–H···π and C–H···O Interactions Consisted of Phthalic Acid and Pyridine Derivatives (2001)

Abstract Crystal structures of co-crystals of phthalic acid with 4,4′-bipyridine or 4,4′-dipyridylacetylene contain one-dimensional zigzag chains connected by intermolecular O–H···N hydrogen bonds and edge-to-face packing of phthalic acid and pyridine rings stabilized by intermolecular C–H···π and C–H···O interactions.