gebhart/patrepeval huggingface dataset:
ASYMMETRIC DYES (1923)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTASYMMETRIC DYESC. W. Porter and Harry K. IhrigCite this: J. Am. Chem. Soc. 1923, 45, 8, 1990–1993Publication Date (Print):August 1, 1923Publication History Published online1 May 2002Published inissue 1 August 1923https://pubs.acs.org/doi/10.1021/ja01661a020https://doi.org/10.1021/ja01661a020research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Origin of Atomic Clusters during Ion Sputtering (2001)

Previous studies have shown that the size distributions of small clusters ( n < or = 40; n = number of atoms/cluster) generated by sputtering obey an inverse power law with an exponent between -8 and -4. Here we report electron microscopy studies of the size distributions of larger clusters ( n > or = 500) sputtered by high-energy ion impacts. These new measurements also yield an inverse power law, but one with an exponent of -2 and one independent of sputtering yield, indicating that the large clusters are produced when shock waves, generated by subsurface displacement cascades, ablate the surface.
Perforin-Mediated Cytotoxicity Is Critical for Surveillance of Spontaneous Lymphoma (2000)

Immune surveillance by cytotoxic lymphocytes against cancer has been postulated for decades, but direct evidence for the role of cytotoxic lymphocytes in protecting against spontaneous malignancy has been lacking. As the rejection of many experimental cancers by cytotoxic T lymphocytes and natural killer cells is dependent on the pore-forming protein perforin (pfp), we examined pfp-deficient mice for increased cancer susceptibility. Here we show that pfp-deficient mice have a high incidence of malignancy in distinct lymphoid cell lineages (T, B, NKT), indicating a specific requirement for pfp in protection against lymphomagenesis. The susceptibility to lymphoma was accentuated by simultaneous lack of expression of the p53 gene, mutations in which also commonly predispose to human malignancies, including lymphoma. In contrast, the incidence and age of onset of sarcoma was unaffected in p53-deficient mice. Pfp-deficient mice were at least 1,000-fold more susceptible to these lymphomas when transplanted, compared with immunocompetent mice in which tumor rejection was controlled by CD8(+) T lymphocytes. This study is the first that implicates direct cytotoxicity by lymphocytes in regulating lymphomagenesis.
Neosaxitoxin as a Local Anesthetic (2007)

Neosaxitoxin showed an effective local anesthetic effect when injected in the subcutaneous plane. The efficacy of a 50-microg dose of neosaxitoxin was shown. This is the first report of neosaxitoxin as a local anesthetic in a human trial.
Purification and characterization of native type XIV collagen. (1992)

A new molecule, type XIV collagen, with domains homologous to type IX and XII collagens has been recently discovered in pepsin extracts of fetal bovine tissues (Dublet, B., and van der Rest, M. (1991) J. Biol. Chem. 266, 6853-6858). In the present study, we describe the purification and the characterization of the intact native form of this newly discovered collagen. By using only two chromatographic steps we were able to obtain pure type XIV collagen. Furthermore, minor modifications of the protocol allowed us to perform the simultaneous large scale purification of type XII and type XIV collagens from the same tissue. Intact type XIV collagen migrates on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) as two bands of 220 and 290 kDa (reducing conditions). After collagenase treatment, a single band of 190 kDa is observed, which represents the large non-collagenous domain of the molecule (NC3). Rotary shadowing electron micrographs of intact type XIV collagen show a cross-shaped structure formed by a thin tail attached through a central globule to three identical "fingers." These properties are similar to those previously described for intact chicken type XII collagen (Dublet, B., Oh, S., Sugrue, S. P., Gordon, M. K., Gerecke, D. R., Olsen, B. R., and van der Rest, M. (1989) J. Biol. Chem. 264, 13150-13156), but the two molecules are different gene products and have charge and glycosylation differences. Finally, we show that the three chains of purified type XIV collagen have an apparent molecular mass of approximately 220 kDa and are not cross-linked to each other by bonds other than disulfide bridges. The same observation was made for type XII collagen. In both cases, the 290-kDa migrating band in SDS-PAGE is due to incomplete denaturation in electrophoresis sample buffer in the absence of urea.
THE EVOLUTION OF RESTRICTED RECOMBINATION AND THE ACCUMULATION OF REPEATED DNA SEQUENCES (1986)

We suggest hypotheses to account for two major features of chromosomal organization in higher eukaryotes. The first of these is the general restriction of crossing over in the neighborhood of centromeres and telomeres. We propose that this is a consequence of selection for reduced rates of unequal exchange between repeated DNA sequences for which the copy number is subject to stabilizing selection: microtubule binding sites, in the case of centromeres, and the short repeated sequences needed for terminal replication of a linear DNA molecule, in the case of telomeres. An association between proximal crossing over and nondisjunction would also favor the restriction of crossing over near the centromere. The second feature is the association between highly repeated DNA sequences of no obvious functional significance and regions of restricted crossing over. We show that highly repeated sequences are likely to persist longest (over evolutionary time) when crossing over is infrequent. This is because unequal exchange among repeated sequences generates single copy sequences, and a population that becomes fixed for a single copy sequence by drift remains in this state indefinitely (in the absence of gene amplification processes). Increased rates of exchange thus speed up the process of stochastic loss of repeated sequences.
Brain-implantable biomimetic electronics as the next era in neural prosthetics (2001)

An interdisciplinary multilaboratory effort to develop an implantable neural prosthetic that can coexist and bidirectionally communicate with living brain tissue is described. Although the final achievement of such such a goal is many years in the future, it is proposed that the path to an implantable prosthetic is now definable, allowing the problem to be solved in a rational, incremental manner. Outlined in this report is our collective progress in developing the underlying science and technology that will enable the functions of specific brain damaged regions to be replaced by multichip modules consisting of novel hybrid analog/digital microchips. The component microchips are "neurocomputational" incorporating experimentally based mathematical models of the nonlinear dynamic and adaptive properties of biological neurons and neural networks. The hardware developed to date, although limited in capacity, can perform computations supporting cognitive functions such as pattern recognition, but more generally will support any brain function for which there is sufficient experimental information. To allow the "neurocomputational" multichip module to communicate with existing brain tissue, another novel microcircuitry element has been developed-silicon-based multielectrode arrays that are "neuromorphic," i.e., designed to conform to the region-specific cytoarchitecture of the brain, When the "neurocomputational" and "neuromorphic" components are fully integrated, our vision is that the resulting prosthetic, after intracranial implantation, will receive electrical impulses from targeted subregions of the the brain, process the information using the hardware model of that brain region, and communicate back to the functioning brain. The proposed prosthetic microchips also have been designed with parameters that can be optimized after implantation, allowing each prosthetic to adapt to a particular user/patient.
Sync: a Java framework for mobile collaborative applications (1997)

Introducing the factors of wireless mobile systems into the development of collaborative applications complicates developers' lives significantly. Application frameworks targeted for coordinating wireless mobile applications simplify development. The authors describe Sync, a development framework that provides high-level primitives that enable programmers to create arbitrarily complex, synchronized, replicated data objects. Designed for wireless networks, Sync enables applications to share changes at a granularity as small as updates to basic types and so enables better performance on low-bandwidth connections.
Rational Design of a Humanized Glucagon‐Like Peptide‐1 Receptor Agonist Antibody (2014)

Bovine antibody BLV1H12 possesses a unique "stalk-knob" architecture in its ultralong heavy chain CDR3, allowing substitutions of the "knob" domain with protein agonists to generate functional antibody chimeras. We have generated a humanized glucagon-like peptide-1 (GLP-1) receptor agonist antibody by first introducing a coiled-coil "stalk" into CDR3H of the antibody herceptin. Exendin-4 (Ex-4), a GLP-1 receptor agonist, was then fused to the engineered stalk with flexible linkers, and a Factor Xa cleavage site was inserted immediately in front of Ex-4 to allow release of the N-terminus of the fused peptide. The resulting clipped herceptin-Ex-4 fusion protein is more potent in vitro in activating GLP-1 receptors than the Ex-4 peptide. The clipped herceptin-Ex-4 has an extended plasma half-life of approximately four days and sustained control of blood glucose levels for more than a week in mice. This work provides a novel approach to the development of human or humanized agonist antibodies as therapeutics.
Iterative hard-decision decoding of braided BCH codes for high-speed optical communication (2013)

Designing error-correcting codes for optical communication is challenging mainly because of the high data rates (e.g., 100 Gbps) required and the expectation of low latency, low overhead (e.g., 7% redundancy), and large coding gain (e.g., >9dB). Although soft-decision decoding (SDD) of low-density parity-check (LDPC) codes is an active area of research, the mainstay of optical transport systems is still the iterative hard-decision decoding (HDD) of generalized product codes with algebraic syndrome decoding of the component codes. This is because iterative HDD allows many simplifications and SDD of LDPC codes results in much higher implementation complexity. In this paper, we use analysis and simulation to evaluate tightly-braided block codes with BCH component codes for high-speed optical communication. Simulation of the iterative HDD shows that these codes are competitive with the best schemes based on HDD. Finally, we suggest a specific design that is compatible with the G.709 framing structure and exhibits a coding gain of >9.35 dB at 7% redundancy under iterative HDD with a latency of approximately 1 million bits.
Expression Cloning of a Rat Hypothalamic Galanin Receptor Coupled to Phosphoinositide Turnover (1997)

The neuropeptide galanin is widely distributed throughout the central and peripheral nervous systems and participates in the regulation of processes such as nociception, cognition, feeding behavior, and insulin secretion. Multiple galanin receptors are predicted to underlie its physiological effects. We now report the isolation by expression cloning of a rat galanin receptor cDNA distinct from GALR1. The receptor, termed GALR2, was isolated from a rat hypothalamus cDNA library using a 125I-porcine galanin (125I-pGAL) binding assay. The GALR2 cDNA encoded a protein of 372 amino acids exhibiting 38% amino acid identity with rat GALR1. Binding of 125I-pGAL to transiently expressed GALR2 receptors was saturable (KD = 0.15 nM) and displaceable by galanin peptides and analogues in rank order: porcine galanin approximately M32 approximately M35 approximately M40 >/= galanin-(1-16) approximately M15 approximately [D-Trp2]galanin-(1-29) > C7 >> galanin-(3-29). This profile resembles that of the rat GALR1 receptor with the notable exception that [D-Trp2]galanin exhibited significant selectivity for GALR2 over GALR1. Activation of GALR2 receptors with porcine galanin and other galanin analogues increased inositol phospholipid turnover and intracellular calcium levels in stably transfected Chinese hamster ovary cells and generated calcium-activated chloride currents in Xenopus oocytes, suggesting that the rat GALR2 receptor is primarily coupled to the activation of phospholipase C.
Internal vs Fishhook Hairpin DNA: Unzipping Locations and Mechanisms in the α-Hemolysin Nanopore (2014)

Studies on the interaction of hairpin DNA with the α-hemolysin (α-HL) nanopore have determined hairpin unzipping kinetics, thermodynamics, and sequence-dependent DNA/protein interactions. Missing from these results is a systematic study comparing the unzipping process for fishhook (one-tail) vs internal (two-tail) hairpins when they are electrophoretically driven from the cis to the trans side of α-HL via a 30-mer single-stranded tail. In the current studies, fishhook hairpins showed long unzipping times with one deep blockage current level. In contrast, the internal hairpins demonstrated relatively fast unzipping and a characteristic pulse-like current pattern. These differences were further explored with respect to stem length and sequence context. Further, a series of internal hairpins with asymmetric tails were studied, for which it was determined that a second tail longer than 12 nucleotides results in internal hairpin unzipping behavior, while tail lengths of 6 nucleotides behaved like fishhook hairpins. Interestingly, these studies were able to resolve a current difference of ~6% between hairpin DNA immobilized in the nanopore waiting to unzip vs the translocating unzipped DNA, with the latter showing a deeper current blockage level. This demonstration of different currents for immobilized and translocating DNA has not been described previously. These results were interpreted as fishhook hairpins unzipping inside the vestibule, while the internal hairpins unzip outside the vestibule of α-HL. Lastly, we used this knowledge to study the unzipping of a long double-stranded DNA (>50 base pairs) outside the vestibule of α-HL. The conclusions drawn from these studies are anticipated to be beneficial in future application of nanopore analysis of nucleic acids.
Compatibility of Primary Hepatocytes with Oxidized Nanoporous Silicon (2001)

Porous silicon is a substrate highly compatible with living cells!Particularly after treatment of the surface with adhesive serum proteins, primary rat hepatocytes are easily attached while staying viable (shown by fluorescence microscopy with a vital dye—see Figure). Cells thus immobilized remain active even over a two week period, as their unchanged albumin and urea production reveals.
Experimental results on optical proximity correction with variable-threshold resist model (1997)

In previous work we combined fast aerial image simulation with a closed-loop Optical Proximity Correction (OPC) control system to generate pre-compensated mask geometries which account for pattern transfer distortion effects at small feature sizes. We also presented the variable- threshold resist (VTR) model in which an image-dependent threshold is used to calculate linewidths directly from the image intensity. The model parameters can be determined by `tuning' the model with linewidth measurements from chosen sample sites on the wafer. In this paper, we present verify our OPC approach experimentally by showing after etch SEM wafers of corrected and uncorrected designs. In doing so, we show that (1) OPC can eliminate bridging effects in uncorrected designs, (2) VTR model is fairly insensitive to process variations and (3) mask writing effects are important and cannot be ignored.
Identification of functional regions on the tail of Acanthamoeba myosin-II using recombinant fusion proteins. I. High resolution epitope mapping and characterization of monoclonal antibody binding sites. (1990)

We used a series of COOH-terminally deleted recombinant myosin molecules to map precisely the binding sites of 22 monoclonal antibodies along the tail of Acanthamoeba myosin-II. These antibodies bind to 14 distinguishable epitopes, some separated by less than 10 amino acids. The positions of the binding sites visualized by electron microscopy agree only approximately with the physical positions of these sites on the alpha-helical coiled-coil tail. On the other hand, the epitope map agrees precisely with competitive binding studies: all antibodies that share an epitope compete with each other for binding to myosin. Antibodies with adjacent epitopes can compete with each other at linear distances up to 5 or 6 nm, and many antibodies that bind 3-7-nm apart can enhance the binding of each other to myosin. Most of the antibodies that bind to the distal 37 nm of the tail disrupt assembly of octameric minifilaments and, depending upon the exact location of the binding site, stop assembly at specific steps yielding, for example, monomers, antiparallel dimers, parallel dimers or antiparallel tetramers. The effects of these antibodies on assembly identify sites on the tail that are required for individual steps in minifilament assembly. Experiments on the assembly of truncated myosin-II tails have revealed a complementary group of sites that participate in the assembly reactions (Sinard, J.H., D.L. Rimm, and T.D. Pollard. 1990. J. Cell Biol. 111:2417-2426). Antibodies that bind to the distal tail but do not affect assembly appear to have a low affinity for myosin-II. Antibodies that bind to the proximal 50 nm of the tail do not inhibit the assembly of minifilaments. Many antibodies that bind to the tail of myosin-II, even some that have no obvious effect on minifilament assembly, can inhibit the actomyosin ATPase activity and the contraction of an actin gel formed in crude extracts. An antibody that binds between amino acids 1447 and 1467 inhibits the phosphorylation of serine residues distal to residue 1483.
Tumor-specific idiotype vaccines. I. Generation and characterization of internal image tumor antigen. (1986)

The concept of idiotype vaccines against tumor-associated antigens (TAA) was tested in the DBA/2 L1210 lymphoma subline, L1210/GZL. Monoclonal antibodies against a TAA that cross-reacts with the envelope glycoprotein gp52 of the mammary tumor virus were used to make hybridoma anti-idiotype antibodies (Ab2). In this report we describe the characterization of monoclonal anti-idiotypic antibodies against the combining site of 11C1 (Ab1), which recognizes a shared determinant of gp52 of mouse mammary tumor virus (MMTV) and the TAA of L1210/GZL. Hybridomas expressing the internal image of gp52 were screened by an idiotype inhibition assay. Mice sensitized with radiated L1210/GZL cells produced specific delayed type hypersensitivity (DTH) against the Ab2 hybridoma. Five Ab2 hybridomas were selected and were used to immunize DBA/2 mice. Such immunized animals showed specific DTH reaction against a challenge with the L1210/GZL tumor cells. Similar results were obtained in mice immunized with purified Ab2. Fluorescence-activated cell sorter analysis demonstrated that fluorescence staining of L1210/GZL cells by 11C1 can be completely inhibited with preabsorption on Ab2 hybridoma cells. Mice immunized with 2F10 and 3A4 coupled to keyhole limpet hemocyanin (KLH) contained antibodies binding to MMTV. But only in mice immunized with 2F10-KLH was significant inhibition of L1210/GZL tumor growth observed. Collectively, these results indicate that certain anti-idiotypic antibodies can mimic the MMTV gp52 antigen, as well as the gp52-like epitope expressed on the L1210/GZL tumor cells. These properties of anti-idiotypic antibodies mimicking TAA could be exploited for making idiotype vaccines against tumors.
Loss of stromal caveolin-1 leads to oxidative stress, mimics hypoxia and drives inflammation in the tumor microenvironment, conferring the “reverse Warburg effect”: A transcriptional informatics analysis with validation (2010)

Cav-1 (-/-) deficient stromal cells are a new genetic model for myofibroblasts and cancer-associated fibroblasts. Using an unbiased informatics analysis of the transcriptional profile of Cav-1 (-/-) deficient mesenchymal stromal cells, we have now identified many of the major signaling pathways that are activated by a loss of Cav-1, under conditions of metabolic restriction (with low glucose media). Our informatics analysis suggests that a loss of Cav-1 induces oxidative stress, which mimics a constitutive pseudo-hypoxic state, leading to (1) aerobic glycolysis and (2) inflammation in the tumor stromal microenvironment. This occurs via the activation of two major transcription factors, namely HIF (aerobic glycolysis) and NFκB (inflammation) in Cav-1 (-/-) stromal fibroblastic cells. Experimentally, we show that Cav-1 deficient stromal cells may possess defective mitochondria, due to the over-production of nitric oxide (NO), resulting in the tyrosine nitration of the mitochondrial respiratory chain components (such as complex I). Elevated levels of nitro-tyrosine were observed both in Cav-1 (-/-) stromal cells, and via acute knock-down with siRNA targeting Cav-1. Finally, metabolic restriction with mitochondrial (complex I) and glycolysis inhibitors was synthetically lethal with a Cav-1 (-/-) deficiency in mice. As such, Cav-1 deficient mice show a dramatically reduced mitochondrial reserve capacity. Thus, a mitochondrial defect in Cav-1 deficient stromal cells could drive oxidative stress, leading to aerobic glycolysis, and inflammation, in the tumor microenvironment. These stromal alterations may underlie the molecular basis of the "reverse Warburg effect", and could provide the key to targeted anti-cancer therapies using metabolic inhibitors. In direct support of these findings, the transcriptional profile of Cav-1 (-/-) stromal cells overlaps significantly with Alzheimer disease, which is characterized by oxidative stress, NO over-production (peroxynitrite formation), inflammation, hypoxia and mitochondrial dysfunction. We conclude that Cav-1 (-/-) deficient mice are a new whole-body animal model for an activated lethal tumor microenvironment, i.e., "tumor stroma" without the tumor. Since Cav-1 (-/-) mice are also an established animal model for profibrotic disease, our current results may have implications for understanding the pathogenesis of scleroderma (systemic sclerosis) and pulmonary fibrosis, which are also related to abnormal mesenchymal stem cell function.