gebhart/patrepeval huggingface dataset:
Use of Lambda Phage DNA as a Hybrid Internal Control in a PCR-Enzyme Immunoassay To Detect <i>Chlamydia pneumoniae</i> (1998)

An inherent problem in the diagnostic PCR assay is the presence of ill-defined inhibitors of amplification which may cause false-negative results. Addition of an amplifiable fragment of foreign DNA in the PCR to serve as a hybrid internal control (HIC) would allow for a simple way to identify specimens containing inhibitors. Two oligonucleotide hybrid primers were synthesized to contain nucleic acid sequences of the Chlamydia pneumoniae 16S rRNA primers in a position flanking two primers that target the sequences of a 650-bp lambda phage DNA segment. By using the hybrid primers, hybrid DNA comprising a large sequence of lambda phage DNA flanked by short pieces of chlamydia DNA was subsequently generated by PCR, cloned into a plasmid vector, and purified. Plasmids containing the hybrid DNA were diluted and used as a HIC by adding them to each C. pneumoniae PCR test. Consequently, C. pneumoniae primers were able to amplify both chlamydia DNA and the HIC DNA. The production of a 689-bp HIC DNA band on an acrylamide gel indicated that the specimen contained no inhibitors and that internal conditions were compatible with PCR. Subsequently, a biotinylated RNA probe for the HIC was transcribed from a nested sequence of the HIC and was used for its hybridization. Detection of the HIC DNA-RNA hybrid was achieved by enzyme immunoassay (EIA). This PCR-EIA system with a HIC was initially tested with 12 previously PCR-positive and 14 previously PCR-negative specimens. Of the 12 PCR-positive specimens, 11 were reconfirmed as positive; 1 had a negative HIC value, indicating inhibition. Of the 14 previously PCR-negative specimens, 13 were confirmed as true negative; 1 had a negative HIC value, indicating inhibition. The assay was then used with 237 nasopharyngeal specimens from patients with pneumonia. Twenty-one of 237 (8.9%) were positive for C. pneumoniae, and 42 (17.7%) were found to inhibit the PCR. Specimens showing inhibitory activity were diluted 1:10 and were retested. Ten specimens were still inhibitory to the PCR and required further DNA purification. No additional positive samples were detected and 3 nasopharyngeal specimens remained inhibitory to PCR. Coamplification of a HIC DNA can help confirm true-negative PCR results by ruling out the presence of inhibitors of DNA amplification.
Monolithic integration of a spot size transformer with a planar buried heterostructure InGaAsP/InP-laser using the shadow masked growth technique (1994)

We present a vertically tapered InGaAsP/InP planar buried heterostructure (PBB) laser for low loss coupling to single-mode fibers. To achieve the vertical tapering we make use of the shadow masked growth technique. Tapered lasers with beam divergences of 15/spl deg/ in both lateral and transverse directions were realized. In comparison with untapered lasers, the coupling losses to cleaved single-mode fibers could be reduced by 4.8 dB down to 5.8 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Thermal Coefficient of Refractive Index of Optical Glasses* (1969)

The thermal coefficients of refractive index have been determined for 23 commercial glasses. The interferometric procedure consisted of determining both the change of optical path of each glass with a change of temperature at a given wavelength and set coefficient of linear thermal expansion of the glass for the same temperature range. A relationship for the dispersion of the thermal coefficient of the refractive index has been found. It has also been possible to relate the chemical composition of glass with the thermal coefficient of the refractive index.
Polarization pattern of vector vortex beams generated by q-plates with different topological charges (2012)

We describe the polarization topology of the vector beams emerging from a patterned birefringent liquid crystal plate with a topological charge q at its center (q-plate). The polarization topological structures for different q-plates and different input polarization states have been studied experimentally by measuring the Stokes parameters point-by-point in the beam transverse plane. Furthermore, we used a tuned q=1/2-plate to generate cylindrical vector beams with radial or azimuthal polarizations, with the possibility of switching dynamically between these two cases by simply changing the linear polarization of the input beam.
Over-expression of inducible HSP70 chaperone suppresses neuropathology and improves motor function in SCA1 mice (2001)

Many neurodegenerative diseases are caused by gain-of-function mechanisms in which the disease-causing protein is altered, becomes toxic to the cell, and aggregates. Among these 'proteinopathies' are Alzheimer's and Parkinson's disease, prion disorders and polyglutamine diseases. Members of this latter group, also known as triplet repeat diseases, are caused by the expansion of unstable CAG repeats coding for glutamine within the respective proteins. Spinocerebellar ataxia type 1 (SCA1) is one such disease, characterized by loss of motor coordination due to the degeneration of cerebellar Purkinje cells and brain stem neurons. In SCA1 and several other polyglutamine diseases, the expanded protein aggregates into nuclear inclusions (NIs). Because these NIs accumulate molecular chaperones, ubiquitin and proteasomal subunits--all components of the cellular protein re-folding and degradation machinery--we hypothesized that protein misfolding and impaired protein clearance might underlie the pathogenesis of polyglutamine diseases. Over-expressing specific chaperones reduces protein aggregation in transfected cells and suppresses neurodegeneration in invertebrate animal models of polyglutamine disorders. To determine whether enhancing chaperone activity could mitigate the phenotype in a mammalian model, we crossbred SCA1 mice with mice over-expressing a molecular chaperone (inducible HSP70 or iHSP70). We found that high levels of HSP70 did indeed afford protection against neurodegeneration.
Gas6 induces proliferation in prostate carcinoma cell lines expressing the Axl receptor (2004)

Axl is a tyrosine kinase receptor and although it is expressed in malignancy such as leukemia, colon cancer, melanoma, endometrial, prostate and thyroid cancers, its role has not been completely elucidated yet and appears to be complex. The ligand of Axl, Gas6, is a 75 KDa multimodular protein with an N-terminal gamma-carboxy-glutamic acid that is essential for binding. Gas6 has a mitogenic effect on several normal cell lines. The receptor Axl is expressed in primary prostate carcinoma and in prostate cancer cell lines as such as PC-3 and DU 145. We demonstrated a mitogenic activity determined by Gas6/Axl interaction in these undifferentiated metastatic human prostatic cancer cell lines. This effect is proportional to Axl expression, not due to inhibition of apoptosis, and induces AKT and MAPK phosphorylation. However, only MEK phosphorylation seems to be essential for growth signaling. Our results suggest that Axl overexpression and activation by Gas6 could be involved in progression of prostate neoplastic disease.
Effects of segregation and selection on instability of plasmid pACYC184 in Escherichia coli B (1987)

We use a mathematical model to analyze the dynamics of loss of nonconjugative pACYC184 from populations of Escherichia coli B in glucose-limited continuous culture. This model incorporates both plasmid segregation and selection against plasmid carriage. It is concluded that there is intense selection against plasmid carriage (s = 0.3 per culture generation), which amplifies the frequency of segregants arising de novo.
Characterization of biodegradable polyurethane microfibers for tissue engineering (2007)

A polyurethane designed to be biodegradable via hydrolysis and enzyme-mediated chain cleavage, has been investigated for its use as a temporary scaffold in tissue-engineering applications. The phase-segregated nature of the polyurethane imparts elastomeric properties that are attractive for soft tissue engineering. This polyurethane has been electrospun in order to create scaffolds that incorporate several biomimetic features including small fiber diameter, large void volume, and an interconnected porous network. Material properties were evaluated via gel-permeation chromatography, differential scanning calorimetry and Raman spectroscopy before and after processing. Analysis by gel-permeation chromatography showed that the molecular weights were similar, indicating that the bulk of the polymer chains were not degraded during processing. Thermal analysis revealed that the glass transition temperature did not shift and Raman spectra of the bulk polyurethane film compared to the electrospun mat were identical, confirming that the conformation of the polymer was unaffected by the shear and electric field used in the electrospinning process. In addition, field emission scanning electron microscopy revealed that the morphology of the electrospun mats had a broad fiber diameter distribution, and mechanical analysis showed that the mats had an ultimate tensile stress of 1.33 MPa and ultimate tensile strain of 78.6%. The degradation profile was investigated in the presence of chymotrypsin. These results were compared to a previous study of thin films of this polyurethane, and it was found that the increase of surface area aided the surface-mediated erosion of the material. It is believed that an electrospun matrix of this biodegradable polyurethane shows promise for use in soft tissue engineering and regenerative medicine applications.
Single Image Based Illumination Estimation for Lighting Virtual Object in Real Scene (2011)

Rendering virtual objects into real scenes with real illumination can greatly increase the realism of virtual objects and the consistency between the virtual and the real. The main challenge lies in illumination estimation from a single image. This article proposes a novel method of single image based illumination estimation for lighting virtual object in real scene. Only a single image, without any knowledge of the 3D geometry or reflectance, is needed, which greatly increases the applicability of the method. We first estimate coarse scene geometry and intrinsic components including shading image and reflectance image. Then the sparse radiance map of the scene is inferred based on the scene geometry and intrinsic components. Finally, the virtual objects are illuminated by the estimated sparse radiance map. Some experimental results show that this method can convincingly light virtual objects into a single real image, without any pre-recorded 3D geometry and reflectance, illumination acquisition equipments or imaging information of the image.
A Single Adenosine with a Neutral p <i>K</i> <sub>a</sub> in the Ribosomal Peptidyl Transferase Center (2000)

Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pKa (where Ka is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pKa of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.
In-frame deletion in a novel centrosomal/ciliary protein CEP290/NPHP6 perturbs its interaction with RPGR and results in early-onset retinal degeneration in the rd16 mouse (2006)

Centrosome- and cilia-associated proteins play crucial roles in establishing polarity and regulating intracellular transport in post-mitotic cells. Using genetic mapping and positional candidate strategy, we have identified an in-frame deletion in a novel centrosomal protein CEP290 (also called NPHP6), leading to early-onset retinal degeneration in a newly identified mouse mutant, rd16. We demonstrate that CEP290 localizes primarily to centrosomes of dividing cells and to the connecting cilium of retinal photoreceptors. We show that, in the retina, CEP290 associates with several microtubule-based transport proteins including RPGR, which is mutated in approximately 15% of patients with retinitis pigmentosa. A truncated CEP290 protein (DeltaCEP290) is detected in the rd16 retina, but in considerably reduced amounts; however, the mutant protein exhibits stronger association with specific RPGR isoform(s). Immunogold labeling studies demonstrate the redistribution of RPGR and of phototransduction proteins in the photoreceptors of rd16 retina. Our findings suggest a critical function for CEP290 in ciliary transport and provide insights into the mechanism of early-onset photoreceptor degeneration.
The atomic pair distribution function: past and present (2004)

Abstract The history of the PDF method is briefly reviewed. Recent results, principally from the Billinge group, are also reviewed.
STUDIES ON ARTHROPOD CUTICLE. II. ELECTRON MICROSCOPE STUDIES OF EXTRACTED CUTICLE,, (1948)

1. Chitin purifications alter the structure of cuticular membranes of insects more or less extensively. 2. Our data agree with the x-ray diffraction studies of Fraenkel and Rudall in showing: (a) The cuticle cannot be viewed as a rigid chitin framework iii the interstices of which other components are deposited. (b) Protein extraction methods have no value for localization of membrane components. (c) Purified chitinous membranes have no significance for studies on the permeability of arthropod cuticle. 3. Several but not all types of membranes after purification yielded microfibers of chitin which after drying have diameters of < 100 to 300 Å< 0.01 to 0.03 µ). It is suggested that these values may represent chitin micelle diameters. 4. Unexpected diversity in chitin patterns was obtained. Possible interpretations are discussed, and it is suggested that chitin cross-linkages vary considerably from one type of membrane to another type. 5. Chloroform and acetone remove the lipid epicuticle without affecting the structure of the underlying protein epicuticle and endocuticle. Detergents disrupt both the lipid epicuticle and underlying protein layers. 6. The effects of water and salt solutions on the structure of isolated cuticular membranes depend on temperature, the salt used and its concentration and the type of membrane. There is good correlation between weight losses recorded at various temperatures by Fraenkel and Rudall and structural changes found in our work. It is concluded that isolated cuticular membranes thatare free from gross discontinuities can be used to a certain extent in permeability studies employing methods of physical chemistry but only when parallel tests show thatthe particular membranes remain reasonably near their original structure and composition.
Synthesis and Structures of Novel Luminescent Bent Acenedithiophenes (2007)

1,4-dithienyl-2,5-divinylbenzenes are readily available compounds that undergo oxidative photocyclization to afford bent anthradithiophenes (BADTs). The new parent and didodecyl-functionalized derivatives have been structurally characterized, and their absorption and emission spectra are reported.
Tele-nanorobotics using atomic force microscope (2002)

A tele-nanorobotics system using an atomic force microscope (AFM) as the nanorobot has been proposed. Modeling and control of the AFM cantilever, and modeling of nanometer scale forces have been realized for telemanipulation applications. Besides 3-D virtual reality visual feedback in the user interface, a 1 DOF haptic device has been constructed for nano scale haptic sensing. For feeling the nano forces, a bilateral teleoperation control system with virtual impedance approach has been introduced. Initial experiments and simulations on the AFM and teleoperation system show that the system can be utilized for different tele-nanomanipulation applications such as 2-D nano particle assembly or biological object manipulation.
Experimental and theoretical studies on a distributed temperature sensor based on Brillouin scattering (1995)

Results are reported from recent research on the use of the Brillouin gain/loss mechanism for distributed sensing. A theoretical model of the interaction of the pulsed and CW beams is described and compared with experiments. Results from a system with a 51 km sensing length are presented. We finally investigate issues related to the variation within the sensing fiber of the polarizations of the two beams.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrolytic Synthesis and Characterization of Silver Nanopowder (2012)

This work reports a simple, novel, cost effective and eco-friendly electrolytic synthesis of silver nanoparticles using AgNO 3 as metal precursor. The synthesis rate is much faster than other methods and this approach is suitable for large scale production. They are characterized by XRD, SEM and FT-IR techniques to analyze size, morphology and functional groups. XRD studies reveal a high degree of crystallinity and monophasic Ag nanoparticles.
Temperature‐programmed surface reaction study on C <sub>2</sub> ‐oxygenate synthesis over SiO <sub>2</sub> and nanoporous zeolitic material supported Rh–Mn catalysts (2001)

Abstract Temperature‐programmed surface reaction (TPSR), temperature‐programmed reaction (TPR) and temperature‐programmed desorption (TPD) were used to study the synthesis of C 2 ‐oxygenates from syngas over Rh–Mn‐based catalysts supported on amorphous silica and mesoporous MCM‐41 supports. Both TPD and TPSR reveal the existence of several different kinds of CO species on the catalyst surface in the course of the catalytic reaction (linear, geminal, bridged and tilt‐adsorbed CO species) but only the bridged form and tilt‐adsorbed CO species are the precursors for CO dissociation and the formation of C 2 ‐oxygenates. The formation temperature of acetaldehyde is higher than that of ethanol, which suggests that they may be formed via different mechanisms. The ethanol formation activity over the Rh–Mn/MCM‐41 catalyst is lower than that over the Rh–Mn/SiO 2 , which suggests that the number of active sites for ethanol formation are fewer on the surface of Rh–Mn/MCM‐41. However, the acetaldehyde formation activities are almost identical for the Rh–Mn catalysts supported on amorphous SiO 2 and MCM‐41, meaning that acetaldehyde and ethanol might be formed on different active sites. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Accelerated Nerve Regeneration in Mice by upregulated expression of interleukin (IL) 6 and IL-6 receptor after trauma. (1996)

In this study we aimed to examine a role for interleukin 6 (IL-6) and its receptor (IL-6R) in peripheral nerve regeneration in vivo. We first observed that cultured mouse embryonic dorsal root ganglia exhibited dramatic neurite extension by simultaneous addition of IL-6 and soluble IL-6R (sIL-6R), a complex that is known to interact with and activate a signal transducing receptor component, gp130. After injury in the hypoglossal nerve in adult mice by ligation, immunoreactivity to IL-6 was upregulated in Schwann cells at the lesional site as well as in the cell bodies of hypoglossal neurons in the brain stem. In the latter, upregulation of the immunoreactivity to IL-6R was also observed. Regeneration of axotomized hypoglossal nerve in vivo was significantly retarded by the administration of anti-IL-6R antibody. Surprisingly, accelerated regeneration of the axotomized nerve was achieved in transgenic mice constitutively expressing both IL-6 and IL-6R, as compared with nontransgenic controls. These results suggest that the IL-6 signal may play an important role in nerve regeneration after trauma in vivo.
Tissue Accretion and Milk Content of Docosahexaenoic Acid in Female Rats after Supplementation with Different Docosahexaenoic Acid Sources (2005)

We conclude that PL and MG supplementation provides higher tissue DHA accretion and higher milk DHA content than TG and EE supplementation. However, we were not able to visualize the comparative advantages derived from PL vs. MG supplementation.
Endotoxemia produces coma and brain swelling in bile duct ligated rats (2007)

Injection of LPS into cirrhotic rats induces pre-coma and exacerbates cytotoxic edema because of the synergistic effect of hyperammonemia and the induced inflammatory response. Although the exact mechanism of how hyperammonemia and LPS facilitate cytotoxic edema and pre-coma in cirrhosis is not clear, our data support an important role for the nitrosation of brain proteins.
Blue Light Sensitive Dyes for Various Photopolymerization Reactions: Naphthalimide and Naphthalic Anhydride Derivatives. (2014)

Novel naphthalimide derivatives (or naphthalic anhydride derivatives) have been prepared and combined with an iodonium salt, N-vinylcarbazole, amines or 2,4,6-tris(trichloromethyl)-1,3,5-triazine to produce radicals and cations upon exposure to low intensity blue lights (e.g., a household blue LED bulb). The photochemical mechanisms are studied by electron spin resonance spin trapping, fluorescence, cyclic voltammetry, laser flash photolysis, and steady state photolysis techniques. The naphthalimide derivatives (ND4) or the naphthalic anhydride derivative (ND10) based photoinitiating systems are particularly efficient for cationic, radical and thiol–ene photopolymerizations; the synthesis of interpenetrated polymer networks IPNs can also be easily carried out. Compared to camphorquinone/amine or camphorquinone/iodonium salt, the new proposed combinations appear as highly versatile and high performance visible light photoinitiating systems. Some of these photoinitiating systems can also be used for UV LED irradiations (e.g., 365, 385, or 395 nm).
Multipotent CNS Stem Cells Are Present in the Adult Mammalian Spinal Cord and Ventricular Neuroaxis (1996)

Neural stem cells in the lateral ventricles of the adult mouse CNS participate in repopulation of forebrain structures in vivo and are amenable to in vitro expansion by epidermal growth factor (EGF). There have been no reports of stem cells in more caudal brain regions or in the spinal cord of adult mammals. In this study we found that although ineffective alone, EGF and basic fibroblast growth factor (bFGF) cooperated to induce the proliferation, self-renewal, and expansion of neural stem cells isolated from the adult mouse thoracic spinal cord. The proliferating stem cells, in both primary culture and secondary expanded clones, formed spheres of undifferentiated cells that were induced to differentiate into neurons, astrocytes, and oligodendrocytes. Neural stem cells, whose proliferation was dependent on EGF+bFGF, were also isolated from the lumbar/sacral segment of the spinal cord as well as the third and fourth ventricles (but not adjacent brain parenchyma). Although all of the stem cells examined were similarly multipotent and expandable, quantitative analyses demonstrated that the lateral ventricles (EGF-dependent) and lumbar/sacral spinal cord (EGF+bFGF-dependent) yielded the greatest number of these cells. Thus, the spinal cord and the entire ventricular neuroaxis of the adult mammalian CNS contain multipotent stem cells, present at variable frequency and with unique in vitro activation requirements.