gebhart/patrepeval huggingface dataset:
Synthesis and pharmacology of some 2-aminotetralins. Dopamine receptor agonists (1975)

A series of 2-amino-1,2,3,4-tetrahydronaphthalene compounds bearing substituents on the nitrogen and in the aromatic ring was synthesized from beta-tetralone intermediates. Compounds were screened in vivo for dopaminergic activity using tests in which apomorphine was especially active. It was found that apparent dopaminergic activity is inherent in 2-dialkylaminotetralins, the dipropylamine substitution being the most consistently productive amine group studies. Activity was greatly enhanced by proper substitution in the aromatic ring. The 5,6-dihydroxy group was the best potentiating group found. These data support the idea that the extended conformation for the phenylethylamine moiety of ampmorphine and dopamine is favorable for dopaminergic agonist activity. They also suggest that an unetherified catechol group may not be essential for such activity.
A six-channel wavelength multiplexer and demultiplexer for single mode systems (1985)

We have fabricated and evaluated the first single mode wavelength multiplexer based on a diffraction grating and strip waveguides. The waveguides were employed to minimize the physical spacing between inputs in order to maximize the ratio of channel width to channel separation. The center channel insertion losses for the six channel device were 6.4, 4.9, 6.0, 5.6, 6.8, and 7.8 dB at 1279, 1308, 1338, 1508, 1536, and 1566 nm, respectively. The 1-dB full channel widths averaged 6.0 nm. A matching demultiplexer with multi-mode outputs was also fabricated. The center channel insertion losses were 0.9, 1.1, 1.2, 1.7, 1.8, and 2.1 dB at 1278, 1310, 1337, 1505, 1533, and 1563 nm, respectively. Full 1-dB channel widths ranged from 15 to 11 nm. Out of band rejection exceeded 35 dB.
Epidemiology, Clinical Features, and Disease Severity in Patients With Coronavirus Disease 2019 (COVID-19) in a Children’s Hospital in New York City, New York (2020)

In this case series study of children and adolescents hospitalized with COVID-19, the disease had diverse manifestations. Infants and immunocompromised patients were not at increased risk of severe disease. Obesity was significantly associated with disease severity. Elevated inflammatory markers were seen in those with severe disease.
Sub-5 nm Domains in Ordered Poly(cyclohexylethylene)-block-poly(methyl methacrylate) Block Polymers for Lithography (2014)

A series of poly(cyclohexylethylene)-block-poly(methyl methacrylate) (PCHE–PMMA) diblock copolymers with varying molar mass (4.9 kg/mol ≤ Mn ≤ 30.6 kg/mol) and narrow molar mass distribution were synthesized through a combination of anionic and atom transfer radical polymerization (ATRP) techniques. Heterogeneous catalytic hydrogenation of α-(hydroxy)polystyrene (PS-OH) yielded α-(hydroxy)poly(cyclohexylethylene) (PCHE-OH) with little loss of hydroxyl functionality. PCHE-OH was reacted with α-bromoisobutyryl bromide (BiBB) to produce an ATRP macroinitiator used for the polymerization of methyl methacrylate. PCHE–PMMA is a glassy, thermally stable material with a large effective segment–segment interaction parameter, χeff = (144.4 ± 6.2)/T – (0.162 ± 0.013), determined by mean-field analysis of order-to-disorder transition temperatures (TODT) measured by dynamic mechanical analysis and differential scanning calorimetry. Ordered lamellar domain pitches (9 ≤ D ≤ 33 nm) were identified by small-angle X-ray scattering from neat BCPs containing 43–52 vol % PCHE (fPCHE). Atomic force microscopy was used to show ∼7.5 nm lamellar features (D = 14.8 nm) which are some of the smallest observed to date. The lowest molar mass sample (Mn = 4.9 kg/mol, fPCHE = 0.46) is characterized by TODT = 173 ± 3 °C and sub-5 nm nanodomains, which together with the sacrificial properties of PMMA and the high overall thermal stability place this material at the forefront of “high-χ” systems for advanced nanopatterning applications.
Demonstration of hemolytic and fusion activities of influenza C virus (1982)

Influenza C virus showed a marked hemolytic activity when incubated with murine erythrocytes at 37 degrees C in acidic medium. The virus-specific hemolysis was most efficient at pH 5.0. Extensive cell fusion also occurred when the erythrocytes were treated with the virus at acidic pH. When propagated in MDCK cells, the virus had an extremely low infectivity and did not display hemolytic activity in any pH range. When the inactive virus was subjected to mild trypsin treatment, hemolytic activity was drastically manifested, accompanying a drastic increase in infectivity. The glycoprotein in the inactive virus was cleaved into smaller components by trypsin treatments. These results indicated that the envelope of influenza C virus can fuse with the cellular membrane under acidic conditions and that the activation of influenza C virus by cleavage was due to the appearance of this envelope fusion activity.
Prediction of response during interferon alfa 2b therapy in chronic hepatitis C patients using viral and biochemical characteristics: A comparison (1997)

Patients with chronic hepatitis C (n = 103) were treated for 24 weeks with interferon alfa 2b and followed up for 24 weeks after cessation of therapy (week 48). When hepatitis C virus (HCV) RNA at week 48 was used to assess interferon response, 15 (14.6%) were virological complete responders, and all have remained HCV RNA negative for a mean of 3 years. At week 48, 3 of 15 virological complete responders had elevated alanine transaminase (ALT) values. When serum ALT level was used at week 48 to determine response to interferon, 20 (19.4%) were biochemical complete responders. However, 8 of the 20 patients with normal ALT levels were HCV RNA positive at week 48, and 7 of these individuals have had a recurrence of elevated ALT levels within 3 years after cessation of treatment. These findings indicate that measurement of HCV RNA was more accurate than ALT in determining true responses to interferon therapy. Identification of nonresponders early during the course of interferon treatment showed that an elevated ALT level at week 12 was 92% predictive (odds ratio 3.7) but misidentified 33% (5 of 15) of the patients who were virological complete responders at week 48. In contrast, a positive HCV RNA at week 12 of treatment was 98% predictive (odds ratio 35.5) and misidentified only 6.7% (1 of 15) of the virological complete responders. Thus, positive HCV RNA at week 12 of therapy was more accurate in identifying eventual virological nonresponders than measurement of ALT at this time. Termination of interferon therapy in patients who were HCV RNA positive at week 12 would result in a 27% reduction in the direct medical costs and keep patients from undergoing unnecessary treatment. Therefore, testing for HCV RNA at week 12 to identify nonresponders and then discontinuing their treatment is practical, cost-efficient and beneficial both to patients and to third-party payers.
Structured models for joint decoding of repeated utterances (2008)

Due to speech recognition errors, repetition can be a frequent occurrence in voice-search applications. While a proper treatment of this phenomenon requires the joint modeling of two or more utterances simultaneously, currently deployed systems typically treat the utterances independently. In this paper, we analyze the structure of repetitions and find that in at least one commercial directory assistance application, repetitions follow simple structural transformations more than 70% of the time. We present preliminary results that suggest that significant gains are possible by explicitly modeling this structure in a joint decoding process.
Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells (2004)

Real-time visualization of specific endogenous mRNA expression in vivo has the potential to revolutionize medical diagnosis, drug discovery, developmental and molecular biology. However, conventional liposome- or dendrimer-based cellular delivery of molecular probes is inefficient, slow, and often detrimental to the probes. Here we demonstrate the rapid and sensitive detection of RNA in living cells using peptide-linked molecular beacons that possess self-delivery, targeting and reporting functions. We conjugated the TAT peptide to molecular beacons using three different linkages and demonstrated that, at relatively low concentrations, these molecular beacon constructs were internalized into living cells within 30 min with nearly 100% efficiency. Further, peptide-based delivery did not interfere with either specific targeting by or hybridization-induced fluorescence of the probes. We could therefore detect human GAPDH and survivin mRNAs in living cells fluorescently, revealing intriguing intracellular localization patterns of mRNA. We clearly demonstrated that cellular delivery of molecular beacons using the peptide-based approach has far better performance compared with conventional transfection methods. The peptide-linked molecular beacons approach promises to open new and exciting opportunities in sensitive gene detection and quantification in vivo.
Study on porous silk fibroin materials. II. Preparation and characteristics of spongy porous silk fibroin materials (2001)

Porous silk fibroin materials, with average pore size 10 ∼ 300 μm, pore density 1 ∼ 2000/mm2, and porosity 35 ∼ 70%, were prepared by freeze drying aqueous solution of silk fibroin obtained by dissolving silk fibroin in ternary solvent CaCl2 · CH3CH2OH · H2O. Pore size distribution of such materials mostly accorded with logarithmic normal distribution. It is possible to control the aforementioned structural parameters and the physical properties of moisture permeability, compressibility, strength, elongation, etc., by adjusting freezing temperature and concentration of silk fibroin solution. Above glass transition zone (−34 ∼ −20°C) of silk fibroin, the freezing temperature has more significant effect on the structure and properties of porous silk fibroin materials. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 79: 2192–2199, 2001
Human iPS Cell-Derived Insulin Producing Cells Form Vascularized Organoids under the Kidney Capsules of Diabetic Mice (2015)

Type 1 diabetes (T1D) is caused by autoimmune disease that leads to the destruction of pancreatic β-cells. Transplantation of cadaveric pancreatic organs or pancreatic islets can restore normal physiology. However, there is a chronic shortage of cadaveric organs, limiting the treatment of the majority of patients on the pancreas transplantation waiting list. Here, we hypothesized that human iPS cells can be directly differentiated into insulin producing cells (IPCs) capable of secreting insulin. Using a series of pancreatic growth factors, we successfully generated iPS cells derived IPCs. Furthermore, to investigate the capability of these cells to secrete insulin in vivo, the differentiated cells were transplanted under the kidney capsules of diabetic immunodeficient mice. Serum glucose levels gradually declined to either normal or near normal levels over 150 days, suggesting that the IPCs were secreting insulin. In addition, using MRI, a 3D organoid appeared as a white patch on the transplanted kidneys but not on the control kidneys. These organoids showed neo-vascularization and stained positive for insulin and glucagon. All together, these data show that a pancreatic organ can be created in vivo providing evidence that iPS cells might be a novel option for the treatment of T1D.
Remineralization of in vitro dental caries assessed with polarization-sensitive optical coherence tomography (2006)

Polarization-sensitive optical coherence tomography (PS-OCT) is potentially useful for imaging the nonsurgical remineralization of dental enamel. This study uses an all-fiber-based PS-OCT system operating at 1310 nm to image demineralized and fluoride-enhanced remineralized artificial lesions. PS-OCT images of lesions before and after remineralization are compared with the relative mineral loss DeltaZ (%vol x microm), obtained from high resolution digital microradiography (DM), and chemical composition changes by infrared spectroscopy. Severe early artificial caries show a significant increase in perpendicular-axis integrated reflectivity after remineralization. After sectioning the samples, DM demonstrates that the lesions remineralized with new mineral and the lesion surface zone show significant restoration of mineral volume. PS-OCT and DM both do not show a major change in lesion depth. For less severe artificial caries, the perpendicular-axis image resolves the scattering and depolarization of an outer growth layer after remineralization. This outer layer has a mineral volume close to that of sound enamel, and spectroscopic analysis indicates that the layer is a highly crystalline phase of apatite, without carbonate substitutions that increase the solubility of sound enamel. This study determines that PS-OCT can image the effects of fluoride-enhanced remineralization of mild and severe early artificial in vitro caries.
A new gravity‐driven microfluidic‐based electrochemical assay coupled to magnetic beads for nucleic acid detection (2010)

In this work, the characterisation and the optimisation of hybridisation assays based on a novel, rapid and sensitive micro-analytical, gravity-driven, flow device is reported. This device combines a special chip containing eight polymer microchannels, with a portable, computer-controlled instrument. The device is used as a platform for affinity experiments using oligonucleotide-modified paramagnetic particles. In our approach, both hybridisation and labelling events are performed on streptavidin-coated paramagnetic microparticles functionalized with a biotinylated capture probe. Modified particles, introduced in the microchannel inlet of the chip, accumulate near the electrode surface by virtue of a magnetic holder. After hybridisation with the complementary sequence, the hybrid is labelled with an alkaline phosphatase conjugate. The electrochemical substrate for alkaline phosphatase revelation is p-aminophenyl phosphate. Solutions and reagents are sequentially passed through the microchannels, until enzyme substrate is added for in situ signal detection. Upon readout, the magnet array is flipped away, beads are removed by addition of regeneration buffer, and the so-regenerated chip is ready for further analysis. This protocol has been applied to the analytical detection of specific DNA sequences of Legionella pneumophila, with an RSD=8.5% and a detection limit of 0.33 nM.
Beam Control Technologies With a High-Efficiency Phased Array for Microwave Power Transmission in Japan (2013)

Beam control and/or beamforming technologies involving phased arrays can be used to enable highly efficient microwave power transmission (MPT) systems. In Japan, several field MPT experiments using a phased array have been conducted over the years. In 1992, a joint collaborative group successfully conducted a fuel-free flight experiment using phased-array technology, which was referred to as the MIcrowave Lifted Airplane eXperiment. In 2008, Kobe University (Kyoto, Japan) and a U.S. research group successfully conducted an MPT experiment using a phased array that resulted in power transmission over a distance of 150 km. Furthermore, Kyoto University proposed and demonstrated a magnetron-based phased array and conducted MPT from an airship to the ground in spring 2009. In FY2010, Kyoto University developed new highly efficient phased arrays for MPT and solar power satellites. This study provides an overview of past and present Japanese MPT experiments using phased-array technologies.
Tumor‐specific CD4+ T cells from a patient with renal cell carcinoma recognize diverse shared antigens (2005)

Murine models for immune-mediated tumor regression have defined an essential role for CD4+ T helper (Th) cells, but the contribution of these cells to antitumoral immune responses in humans remains poorly defined. Here, we investigated the Th cell response against the autologous tumor in a patient with metastasized renal cell carcinoma (RCC) exhibiting objective clinical response to immunotherapy. Peripheral blood T cells of the patient were repeatedly stimulated in vitro using either autologous IFNgamma-treated whole tumor cells or Epstein-Barr virus-immortalized B cells (EBV-B) pulsed with tumor cell lysate. CD4+ T-cell clones recognizing autologous tumor cells but not EBV-B cells were efficiently reactivated and expanded with both types of stimulator cells, establishing the latter as potentially useful for isolating CD4+ T cells reactive against MHC class II-negative tumors. Two T-cell clones from both stimulation protocol were further characterized. The restricting MHC class II molecules were defined by using allogeneic EBV-B cells pulsed with tumor lysate, and the expression pattern of the antigens was examined by analyzing lysates from normal kidney cells, allogeneic RCCs as well as tumors of different histologic origin. Furthermore, the subcellular localization of the antigens recognized by the T-cell clones was examined by fractionating the tumor lysate, and the Th phenotype was determined by assessing the cytokines released after T cell activation. These experiments show that a dual Th1/Th2, MHC class II-restricted T-helper-cell response against diverse shared tumor antigens has been elicited in this patient.
Activation of telomerase in human lymphocytes and hematopoietic progenitor cells (1995)

This is the first report describing up-regulation of telomerase activity in human normal cells. Telomerase, a ribonucleoprotein enzyme, has been thought to be involved in maintaining telomere length stability in germline and most cancer cells, but not in normal cells. However, in the present study, we demonstrate that telomerase activity is detectable at low levels in normal human T and B cells, increases by in vitro mitogenic stimulation, increases in hematopoietic progenitor cells upon their proliferation and differentiation, and decreases with aging. Understanding the regulation of telomerase activity in normal cells may provide important insights not only into the mechanisms of normal cellular senescence but also into the mechanisms of telomerase activity deregulation as part of cancer development.
The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target (2012)

DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.
Axisymmetric Adhesion Test To Examine the Interfacial Interactions between Biologically-Modified Networks and Models of the Extracellular Matrix (2002)

The adhesion between artificial extracellular matrixes (ECMs), or scaffolds, and native tissue is an often overlooked component of the tissue engineering design process. Therefore, we developed an axisymmetric adhesion test method to examine the interfacial interactions between hydrogel scaffolds and a model of the articular cartilage ECM. Semi-interpenetrating polymer networks (semi-IPNs), consisting of poly(N-isopropylacrylamide-co-acrylic acid) [P(NIPAAm-co-AAc)] hydrogels and physically entangled linear P(AAc) chains grafted with peptides that bind to hyaluronic acid (HA), were synthesized, and the adhesion between the P(NIPAAm-co-AAc)-based semi-IPNs and hemispherical glass lenses (plain or HA-grafted) was examined as a function of temperature, contact time, and semi-IPN type. The adhesion between the semi-IPNs and the lenses significantly increased with increasing contact time and significantly decreased with increasing temperature, independent of the P(NIPAAm-co-AAc)-based matrix type. Furthermore, when using a 5-min contact time at 22 °C, the peptide-modified P(NIPAAm-co-AAc)-based semi-IPNs demonstrated significantly greater adhesion to the HA-grafted lenses, compared to that exhibited between nonfunctionalized P(NIPAAm-co-AAc)-based semi-IPNs and HA-grafted lenses. The method developed is useful for examining the interfacial interactions between biologically modified polymer scaffolds and models of the native ECM and may aid in improving the integration between synthetic polymers and native tissues.
Unique Mode of GCC Box Recognition by the DNA-binding Domain of Ethylene-responsive Element-binding Factor (ERF Domain) in Plant (1998)

Ethylene-responsive element-binding proteins (EREBPs)have novel DNA-binding domains (ERF domains), which are widely conserved in plants, and interact specifically with sequences containing AGCCGCC motifs (GCC box). Deletion experiments show that some flanking region at the N terminus of the conserved 59-amino acid ERF domain is required for stable binding to the GCC box. Three ERF domain-containing fragments of EREBP2, EREBP4, and AtERF1 from tobacco and Arabidopsis, bind to the sequence containing the GCC box with a high binding affinity in the pM range. The high affinity binding is conferred by a monomeric ERF domain fragment, and DNA truncation experiments show that only 11-base pair DNA containing the GCC box is sufficient for stable ERF domain interaction. Systematic DNA mutation analyses demonstrate that the specific amino acid contacts are confined within the 6-base pair GCCGCC region of the GCC box, and the first G, the fourth G, and the sixth C exhibit highest binding specificity common in all three ERF domain-containing fragments studied. Other bases within the GCC box exhibit modulated binding specificity varying from protein to protein, implying that these positions are important for differential binding by different EREBPs. The conserved N-terminal half is likely responsible for formation of a stable complex with the GCC box and the divergent C-terminal half for modulating the specificity.
Role of platelet-derived growth factor in vascular remodeling during pulmonary hypertension in the ovine fetus (2003)

Platelet-derived growth factor (PDGF) is a potent smooth muscle cell mitogen that may contribute to smooth muscle hyperplasia during the development of chronic pulmonary hypertension (PH). We studied changes in PDGFalpha- and beta-receptor and ligand expression in lambs with chronic intrauterine PH induced by partial ligation of the ductus arteriosus (DA) at gestational age 124-128 days (term = 147 days). Western blot analysis performed on whole lung homogenates from PH animals after 8 days of DA ligation showed a twofold increase in PDGFalpha- and beta-receptor proteins compared with age-matched controls (P < 0.05). Lung PDGF-A and -B mRNA expression did not differ between PH and control animals. We treated PH animals with NX1975, an aptamer that selectively inhibits PDGF-B, by infusion into the left pulmonary artery for 7 days after DA ligation. NX1975 reduced the development of muscular thickening of small pulmonary arteries by 47% (P < 0.05) and right ventricular hypertrophy (RVH) by 66% (P < 0.02). Lung PDGFalpha- and beta-receptor expression is increased in perinatal PH, and NX1975 reduces the increase in wall thickness of small pulmonary arteries and RVH in this model. We speculate that PDGF signaling contributes to structural vascular remodeling in perinatal PH and that selective PDGF inhibition may provide a novel therapeutic strategy for the treatment of chronic PH.