gebhart/patrepeval huggingface dataset:
Activation of Natural Killer Cell Migration by Leukocyte Integrin-binding Peptide from Intracellular Adhesion Molecule-2 (ICAM-2) (1995)

Intracellular adhesion molecule-2 (ICAM-2), one of the ligands of CD11a/CD18 (LFA-1), is mainly expressed on endothelial and hematopoietic cells. The biological significance of ICAM-2 has remained unclear. Previous findings have shown that a peptide from ICAM-2, spanning residues 21-42 from the first immunoglobulin domain, enhances natural killer (NK) cell cytotoxicity and induces T cell aggregation. We have now studied the effect of the same ICAM-2 peptide on NK cell migration in the Boyden chamber assay. The peptide significantly increased NK cell migration up to 215 +/- 21%, as compared to migration of control cells (100%), and the induction was inhibited by anti-CD11a monoclonal antibodies. The ICAM-2 peptide also induced polymerization of F-actin at the leading edge of migratory NK cells. Cross-linking of CD11a/CD18 receptors with anti-CD11a or anti-CD18 monoclonal antibodies and secondary antibodies resulted in receptor recycling, increased migration, and actin polymerization, but led to slight inhibition of cytotoxicity. The ICAM-2 peptide did not induce such a receptor recycling. Phosphotyrosine immunoblotting experiments showed that the ICAM-2 peptide increased the phosphorylation of 150- and 35-kDa proteins. During cross-linking with antibodies, only the 150-kDa protein showed increased phosphorylation. The results show that depending on the type of CD11a/CD18 receptor ligation different kinds of signals are transduced in NK cells. These signals may either trigger only locomotion, or both locomotion and cytotoxicity. Based on these findings, a major function for ICAM-2 on endothelium may be triggering of migration of adhering leukocytes.
An Integrated Microfluidics-Tandem Mass Spectrometry System for Automated Protein Analysis (1998)

We describe an integrated analytical system consisting of a microfluidics device micromachined using photolithography/etching technology, a panel of computer-controlled high-voltage relays, and an electrospray ionization tandem mass spectrometer. Movement of solvents and samples on the device and off the device to the mass spectrometer was achieved by directed electroosmotic pumping induced by the activation of a suitable constellation of high-voltage relays. The system was used for the sequential automated analysis of protein digests. We demonstrate low femtomole per microliter sensitivity of detection and compatibility of the system with the automated analysis of proteins separated by two-dimensional gel electrophoresis.
Supercontinuum generation in planar rib waveguides enabled by anomalous dispersion (2006)

We predict and numerically study supercontinuum generation extending over almost two octaves in planar rib waveguides, with anomalous dispersion at the input wavelength provided by the waveguide contribution. Such planar nonlinear waveguides generating broadband coherent radiation can be intergrated with other components to constitute a building block in intergrated optical circuits.
Neural induction and early patterning in vertebrates (2012)

In vertebrates, the development of the nervous system is triggered by signals from a powerful 'organizing' region of the early embryo during gastrulation. This phenomenon--neural induction--was originally discovered and given conceptual definition by experimental embryologists working with amphibian embryos. Work on the molecular circuitry underlying neural induction, also in the same model system, demonstrated that elimination of ongoing transforming growth factor-β (TGFβ) signaling in the ectoderm is the hallmark of anterior neural-fate acquisition. This observation is the basis of the 'default' model of neural induction. Endogenous neural inducers are secreted proteins that act to inhibit TGFβ ligands in the dorsal ectoderm. In the ventral ectoderm, where the signaling ligands escape the inhibitors, a non-neural fate is induced. Inhibition of the TGFβ pathway has now been demonstrated to be sufficient to directly induce neural fate in mammalian embryos as well as pluripotent mouse and human embryonic stem cells. Hence the molecular process that delineates neural from non-neural ectoderm is conserved across a broad range of organisms in the evolutionary tree. The availability of embryonic stem cells from mouse, primates, and humans will facilitate further understanding of the role of signaling pathways and their downstream mediators in neural induction in vertebrate embryos.
Naphthalene biodegradation in environmental microcosms: estimates of degradation rates and characterization of metabolites (1987)

Naphthalene biodegradation was investigated in microcosms containing sediment and water collected from three ecosystems which varied in past exposure to anthropogenic and petrogenic chemicals. Mineralization half-lives for naphthalene in microcosms ranged from 2.4 weeks in sediment chronically exposed to petroleum hydrocarbons to 4.4 weeks in sediment from a pristine environment. Microbiological analysis of sediments indicated that hydrocarbon-utilizing microbial populations also varied among ecosystems and were 5 to 12 times greater in sediment after chronic petrogenic chemical exposure than in sediment from an uncontaminated ecosystem. Sediment from an ecosystem exposed to agricultural chemicals had a mineralization half-life of 3.2 weeks for naphthalene and showed about a 30-fold increase in heterotrophic bacterial populations in comparison to uncontaminated sediments, but only a 2- to 3-fold increase in hydrocarbon-degrading bacteria. Analysis of organic solvent-extractable residues from the microcosms by high-pressure liquid chromatography detected polar metabolites which accounted for 1 to 3% of the total radioactivity. Purification of these residues by thin-layer chromatography and further analysis by gas chromatography-mass spectrometry indicated that cis-1,2-dihydroxy-1,2-dihydronaphthalene, 1-naphthol, salicylic acid, and catechol were metabolites of naphthalene. These results provide useful estimates for the rates of naphthalene mineralization in different natural ecosystems and on the degradative pathway for microbial metabolism of naphthalene in freshwater and estuarine environments.
Genetic analysis of indefinite division in human cells: evidence for a cell senescence-related gene(s) on human chromosome 4. (1991)

Earlier studies had demonstrated that fusion of normal with immortal human cells yielded hybrids having limited division potential. This indicated that the phenotype of limited proliferation (cellular senescence) is dominant and that immortal cells result from recessive changes in normal growth-regulatory genes. In additional studies, we exploited the fact that the immortal phenotype is recessive and, by fusing various immortal human cell lines with each other, identified four complementation groups for indefinite division. Assignment of cell lines to specific groups allowed us to take a focused approach to identify the chromosomes and genes involved in growth regulation that have been modified in immortal cells. We report here that introduction of a normal human chromosome 4 into three immortal cell lines (HeLa, J82, T98G) assigned to complementation group B resulted in loss of proliferation and reversal of the immortal phenotype. No effect on the proliferation potential of cell lines representative of the other complementation groups was observed. This result suggests that a gene(s) involved in cellular senescence and normal growth regulation resides on chromosome 4.
Frameshift Mutations and the Genetic Code (1966)

The genetic message is translated sequentially, three bases at a time, starting from a defined point at the beginning of a cistron (Crick et al., 1961; Terzaghi et al., 1966). The message can thus be separated into groups of three bases (codons) by a "reading frame" which is set in register at the beginning of the message (Crick et al., 1961). Deletions or insertions of a base (or bases) into the genome cause a shift in the reading frame and are thus called frameshift mutations; they result in a grossly different translation of the message beyond the site of the mutation. If the deletion of a base is followed by the insertion of a base, the reading frame, and the amino acid sequence of the protein product, might be altered only in the region between the mutations. Such double mutant strains may produce active protein and thus be pseudowild.
ChemInform Abstract: Enantioselective Syntheses of Isotopically Labeled α‐Amino Acids. Preparation of (ε‐13C)‐L‐α‐Aminoadipic Acid and Five Isotopomers of L‐Lysine with 13C, 15N and 2H in the δ‐ and ε‐Positions. (1990)

Abstract The asymmetric synthesis of (ε‐13C)‐L‐α‐aminoadipic acid (VI) and various isotopomers (VII) and (VIIIa)‐(VIIId) of L‐lysine is described as shown for (VI) and (VII).
<title>Patterned alignment liquid crystal diffractive spatial light modulators and devices</title> (1998)

Recent advances in diffractive liquid crystal (LC) modulation structures for projection display service have generated diffractive spatial light modulator (SLM) devices capable of high performance in transmission and/or reflection. Patterning of the LC domain alignments has resulted in the generation of near perfect phase diffraction grating structures in the lC material, which can be controlled by a single electrode or by an array of segmented electrodes, such as an array of pixels. Consequently, diffractive artifacts from inter-electrode gaps can be eliminated and/or suppressed in a wider spectrum of applications with enhanced performance relative to previous structures. Transmissive diffractive LC modulators suitable for display or switch applications with modulation efficiencies in excess of 90 percent and contrast ratios of greater than 1500:1 in un-polarized light have been demonstrated. Operation of this type of modulator in reflection has also been verified and demonstrated. Comparison of patterned alignment, LC device performance with MEMS and other diffractive structures will be given. Extensions of these techniques to devices which include beam scanners and controllable diffractive optics will be proposed.
On the fidelity of DNA replication: manganese mutagenesis in vitro (1985)

Manganese is mutagenic in vivo and in vitro in studies with a variety of enzymes and templates. Using Escherichia coli DNA polymerase I with poly[d(A-T)] and phi X174 DNA templates, we analyzed the mechanism of manganese mutagenesis by determining the dependence of error rate on free Mn2+ concentration and comparing this to measured dissociation constants of Mn2+ from enzyme, template, and deoxynucleoside triphosphate substrates. This comparison suggests several conclusions: (1) At very low Mn2+ concentrations, the enzyme is activated at high fidelity. Thus, it is unlikely that activation with manganese per se significantly alters the conformation of the enzyme so as to affect nucleotide selection. (2) At low free Mn2+ concentrations (less than 100 microM), manganese causes errors in incorporation via its interaction with the DNA template. The concentration dependence of mutagenesis is determined by the strength of binding Mn2+ to the particular DNA template used. The data do not allow one to rule out the possibility that Mn2+-deoxynucleoside triphosphate interactions contribute to mutagenesis in selected situations. This range of free Mn2+ concentrations is the one of greatest relevance for in vivo mutagenesis. (3) At higher concentrations (between 500 microM and 1.5 mM), further mutagenesis by Mn2+ occurs. This mutagenesis probably is due either to binding of manganese to single-stranded regions within the DNA or to weak accessory sites on the enzyme.
Gradient and curvature from the photometric-stereo method, including local confidence estimation (1994)

The photometric-stereo method is one technique for three-dimensional shape determination that has been implemented in a variety of experimental settings and that has produced consistently good results. The idea is to use intensity values recorded from multiple images obtained from the same viewpoint but under different conditions of illumination. The resulting radiometric constraint makes it possible to obtain local estimates of both surface orientation and surface curvature without requiring either global smoothness assumptions or prior image segmentation. Photometric stereo is moved one step closer to practical possibility by a description of an experimental setting in which surface gradient estimation is achieved on full-frame video data at near-video-frame rates (i.e., 15 Hz). The implementation uses commercially available hardware. Reflectance is modeled empirically with measurements obtained from a calibration sphere. Estimation of the gradient (p, q) requires only simple table lookup. Curvature estimation additionally uses the reflectance map R(p, q). The required lookup table and reflectance maps are derived during calibration. Because reflectance is modeled empirically, no prior physical model of the reflectance characteristics of the objects to be analyzed is assumed. At the same time, if a good physical model is available, it can be retrofitted to the method for implementation purposes. Photometric stereo is subject to error in the presence of cast shadows and interreflection. No purely local technique can succeed because these phenomena are inherently nonlocal. Nevertheless, it is demonstrated that one can exploit the redundancy in three-light-source photometric stereo to detect locally, in most cases, the presence of cast shadows and interreflection. Detection is facilitated by the explicit inclusion of a local confidence estimate in the lookup table used for gradient estimation.
Rapid fabrication of microfluidic devices in poly(dimethylsiloxane) by photocopying (2001)

A very simple and fast method for the fabrication of poly(dimethylsiloxane) (PDMS) microfluidic devices is introduced. By using a photocopying machine to make a master on transparency instead of using lithographic equipment and photoresist, the fabrication process is greatly simplified and speeded up, requiring less than 1.5 h from design to device. Through SEM characterization, any micro-channel network with a width greater than 50 microm and a depth in the range of 8-14 microm can be made by this method. After sealing to a Pyrex glass plate with micromachined platinum electrodes, a microfluidic device was made and the device was tested in FIA mode with on-chip conductometric detection without using either high voltage or other pumping methods.
On the transmission of information by orthogonal time functions (1960)

In a digital communication system each digit of a character may be represented by one function of an orthogonal set of functions. This function is multiplied by + 1 or - 1 if binary digits are being used. All functions of the character are added and transmitted in parallel. This sum of functions is correlated in the receiver with each function of the orthogonal set and voltages of amplitude + 1 or - 1 are obtained. No interference between the digits of a character occurs if the signal is not band limited. The crosstalk between the digits because of band limitation is computed for a system of orthogonal sine and cosine functions. The results show that a binary Teletype system transmitting 60 words per minute can be operated with about 25 cps (cycles per second) bandwidth. This figure decreases to the theoretical minimum of 15 cps per channel for a multichannel system. Tests of experimental equipment have shown very good agreement with the theory.
A Transposable Partitioning Locus Used To Stabilize Plasmid-Borne Hydrogen Oxidation and Trifolitoxin Production Genes in a Sinorhizobium Strain (1998)

Improved nitrogen-fixing inoculum strains for leguminous crops must be able to effectively compete with indigenous strains for nodulation, enhance legume productivity compared to the productivity obtained with indigenous strains, and maintain stable expression of any added genes in the absence of selection pressure. We constructed a transposable element containing the tfx region for expression of increased nodulation competitiveness and the par locus for plasmid stability. The transposon was inserted into tetA of pHU52, a broad-host-range plasmid conferring the H2 uptake phenotype. The resulting plasmid, pHUTFXPAR, conferred the plasmid stability, trifolitoxin production, and H2 uptake phenotypes in the broad-host-range organism Sinorhizobium sp. strain ANU280. The broad applications of a transposon conferring plasmid stability are discussed.
Weight Control and Risk Factor Reduction in Obese Subjects Treated for 2 Years With Orlistat (1999)

Two-year treatment with orlistat plus diet significantly promotes weight loss, lessens weight regain, and improves some obesity-related disease risk factors.
Ongoing normal pregnancy after transfer of zona-free blastocysts: implications for embryo transfer in the human (1997)

Recent reports suggest that transfer of day 5 blastocysts improves implantation rates in in-vitro fertilization programmes. This paper reports a successful ongoing pregnancy after the transfer of zona-free day 6 expanded and hatching blastocysts. The patient was 37 years old and had undergone six stimulated and two thaw cycles previously, all of which had failed. Stimulation was by down-regulation and oocytes recovered transvaginally by ultrasound guidance. Two pronuclear embryos were co-cultured on Vero cells to day 6. The zonae of two hatching and two fully expanded blastocysts were removed using 0.5% pronase, and the zona-free blastocysts were then transferred. Pregnancy was confirmed on day 18 with a positive human chorionic gonadotrophin (HCG) and ultrasound at 6 weeks showed a single healthy fetal heart inside a clear sac. At 14 weeks a triple test (oestriol, J-HCG and alpha-fetoprotein) was normal and at 22 weeks a detailed ultrasound scan showed no congenital anomalies. This is the first report in the human of a normal ongoing pregnancy after the transfer of zona-free day 6 embryos.
Mitotic block induced in HeLa cells by low concentrations of paclitaxel (Taxol) results in abnormal mitotic exit and apoptotic cell death. (1996)

Paclitaxel at low concentrations (10 nM for 20 h) induces approximately 90% mitotic block at the metaphase/anaphase transition in HeLa cells, apparently by suppressing dynamics of spindle microtubules (M. A. Jordan et al., Proc. Natl. Acad. Sci. USA, 90: 9552-9556, 1993). It is not known, however, whether inhibition of mitosis by such low paclitaxel concentrations results in cell death. In the present work, we found that after removal of paclitaxel (10 nM-1 microM), blocked cells did not resume proliferation. Instead, cells exited mitosis abnormally within 24 h. They did not progress through anaphase or cytokinesis but entered an interphase-like state (chromatin decondensed, and an interphase-like microtubule array and nuclear membranes reformed). Many cells (> or = 55%) contained multiple nuclei. Additional DNA synthesis and polyploidy did not occur. DNA degradation into nucleosome-sized fragments characteristic of apoptosis began during drug incubation and increased after drug removal. Cells died within 48-72 h. Incubation with paclitaxel (10 nM for 20 h) resulted in high intracellular drug accumulation (8.3 microM) and little efflux after paclitaxel removal; intracellular retention of paclitaxel may contribute to its efficacy. The results support the hypothesis that the most potent chemotherapeutic mechanism of paclitaxel is kinetic stabilization of spindle microtubule dynamics.
Regeneration of nigrostriatal dopaminergic axons by degradation of chondroitin sulfate is accompanied by elimination of the fibrotic scar and glia limitans in the lesion site (2006)

Chondroitin sulfate increases around a lesion site after central nervous system injury and is believed to be an impediment to axonal regeneration, because administration of chondroitinase ABC, a chondroitin sulfate-degrading enzyme, promotes axonal regeneration of central neurons. To examine the physiological role of chondroitin sulfate up-regulation after injury, the nigrostriatal dopaminergic axons were unilaterally transected in mice, and chondroitinase ABC was then injected into the lesion site. In mice transected only, tyrosine hydroxylase-immunoreactive axons did not extend across the lesion at 1 or 2 weeks after the transection. Immunoreactivities of chondroitin sulfate side chains and core protein of NG2 proteoglycan increased in and around the lesion site, and a fibrotic scar containing type IV collagen deposits developed in the lesion center. In contrast, in mice transected and treated with chondroitinase ABC, numerous tyrosine hydroxylase-immunoreactive axons were regenerated across the lesion at 1 and 2 weeks after the transection. In these animals, chondroitin sulfate immunoreactivity remarkably decreased, and immunoreactivity of 2B6 antibody, which recognizes the stub of degraded chondroitin sulfate side chains, was enhanced. Furthermore, the formation of a fibrotic scar and a glia limitans that surrounds the former was completely prevented, although type IV collagen immunoreactivity remained in newly formed blood capillaries around the lesion site. We discuss the question of whether the chondroitin sulfate is acting as a direct inhibitor of axonal regeneration or whether the observed changes are due to a prevention of the fibrotic scar formation and a rearrangement of astrocytic membranes.
The Cause and Pathogenesis of the Eosinophilia-Myalgia Syndrome (1992)

Current evidence suggests that the epidemic of the eosinophilia-myalgia syndrome was caused by contaminated L-tryptophan preparations originating from a single manufacturer. Peak E or other, as yet unidentified, contaminants may trigger activation of eosinophils and inflammatory cells and increase biosynthesis of connective tissue components, resulting in the clinical and pathologic manifestations of the eosinophilia-myalgia syndrome. Further studies of the interaction of eosinophils, inflammatory cells, and fibroblasts may increase the understanding of the pathogenesis of the eosinophilia-myalgia syndrome. The insights gained from the epidemic may be applicable to more common idiopathic diseases associated with eosinophilia and fibrosis.
Excretion of the egl gene product of Pseudomonas solanacearum (1989)

Pseudomonas solanacearum is an important phytopathogen which excretes a variety of extracellular enzymes. Pulse-chase experiments showed that one of these enzymes, a beta-1,4-endoglucanase (EGL) encoded by the egl gene, is synthesized as a higher-molecular-weight precursor polypeptide (pEGL) which is subsequently excreted into the extracellular medium as a 43-kilodalton mature protein. S1 nuclease transcript mapping and DNA sequence analysis were used to identify the transcription start site and the possible translation start site of egl. Pulse-chase experiments and comparison of the putative NH2-terminal amino acid sequence of pEGL with the actual NH2-terminal amino acid sequence of mature excreted EGL suggested that pEGL has a 45-residue leader sequence preceding the N terminus of EGL which is proteolytically cleaved during export to the extracellular environment. The first 20 residues of the leader sequence resembled a typical lipoprotein signal peptide. The excretion of EGL by P. solanacearum apparently requires a membrane potential since it was blocked by carbonyl cyanide m-chlorophenyl hydrazone.