gebhart/patrepeval huggingface dataset:
Human Osteoblasts Express a Repertoire of Cadherins, Which Are Critical for BMP-2–Induced Osteogenic Differentiation (1998)

Direct cell-cell interactions are fundamental for tissue development and differentiation. We have studied the expression and function of cadherins in human osteoblasts during in vitro differentiation. Using reverse transcription-polymerase chain reaction and mRNA hybridization, we found that human trabecular bone osteoblasts (HOBs), osteoprogenitor marrow stromal cells (BMCs), and the osteogenic sarcoma lines, SaOS-2 and MG-63, expressed mRNA for cadherin-11 (C11) and N-cadherin (N-cad). HOBs and BMCs also expressed low levels of cadherin-4 (C4) mRNA. C11 was the most abundant cadherin protein present in human osteoblasts, and its expression was unaffected by bone morphogenetic protein-2 (BMP-2) treatment of either BMCs or HOBs. Likewise, N-cad mRNA did not change during BMP-2 incubation. Conversely, C4 protein, undetectable in transformed cell lines, was down-regulated by BMP-2 treatment of normal cells. Both C11 and C4 were localized to sites of cell-cell contact in both HOBs and BMCs, colocalized with beta-catenin, and bands corresponding to cadherins were coimmunoprecipitated by a beta-catenin antibody, findings indicative of functional cadherins. A decapeptide containing the HAV motif of human N-cad partially inhibited Ca2+-dependent cell-cell adhesion and completely prevented BMP-2-induced stimulation of alkaline phosphatase activity by BMCs. Thus, human osteoblasts and their progenitor cells express a repertoire of multiple cadherins. Cadherin-mediated cell-to-cell adhesion is critical for normal human osteoblast differentiation.
Group-transfer polymerization on a polymeric support (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGroup-transfer polymerization on a polymeric supportW. R. Hertler, D. Y. Sogah, and F. P. BoettcherCite this: Macromolecules 1990, 23, 5, 1264–1268Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://doi.org/10.1021/ma00207a007Request reuse permissionsArticle Views172Altmetric-Citations32LEARN 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 InReddit PDF (683 KB) Get e-Alertsclose Get e-Alerts
Energy Migration in a Poly(phenylene ethynylene):  Determination of Interpolymer Transport in Anisotropic Langmuir−Blodgett Films (1999)

The photophysical and energy transport properties of a poly(p-ethynylene), 1, were investigated in thin films. Highly aligned films of a precise thickness, prepared by sequential monolayer deposition using the Langmuir−Blodgett technique, were surface modified with luminescent traps (acridine orange, AO) for energy transfer studies. The degree of energy transfer to the traps was investigated as a function of the AO concentration and the number of polymer layers. An increased efficiency of energy transfer to the traps was observed with increasing numbers of layers until an approximate thickness of 16 layers. This behavior is consistent with a transition to a three-dimensional energy migration topology. A phenomenological model for the transport was proposed, and solutions were obtained by numerical methods. The model yields a fast (>6 × 1011 s-1) rate of energy transfer between polymer layers and a diffusion length of more than 100 Å in the Z direction (normal to the film surface).
A polyarylmethyl carbotetraanion (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA polyarylmethyl carbotetraanionAndrzej RajcaCite this: J. Am. Chem. Soc. 1990, 112, 15, 5889–5890Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/ja00171a044https://doi.org/10.1021/ja00171a044research-articleACS PublicationsRequest reuse permissionsArticle Views174Altmetric-Citations16LEARN 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
Modulation of DNA supercoiling activity of Escherichia coli DNA gyrase by F plasmid proteins. Antagonistic actions of LetA (CcdA) and LetD (CcdB) proteins. (1992)

The letA (ccdA) and letD (ccdB) genes of F plasmid contribute to stable maintenance of the plasmid in Escherichia coli cells; a product of the latter has a lethal effect on the host cell and that of the former neutralizes functions of the letD. In cells that overproduce the LetD (CcdB) protein, the plasmid DNA is extensively relaxed. Correspondingly, DNA supercoiling activity in a cell-free extract of the overproducing strain decreases to a level of less than 1% of that seen in normal cells. However, the extract does not inhibit DNA gyrase reconstituted from purified subunits, thereby indicating that the intrinsic DNA gyrase is inactivated in the overproducing strain. Upon addition of purified LetA (CcdA) protein to the extract of LetD overproducing cells, the DNA supercoiling activity was fully restored. Using this rejuvenation as an assay, we purified the "inactivated gyrase" and obtained evidence that the LetD protein formed an isolable complex with the A subunit of DNA gyrase. Thus, the LetD and the LetA proteins constitute an opposing pair in modulating the DNA supercoiling activity of gyrase, probably by direct interaction.
In Situ Observation of Antifreeze Glycoprotein Kinetics at the Ice Interface Reveals a Two-Step Reversible Adsorption Mechanism (2008)

Antifreeze glycoproteins (AFGPs) are a necessary tool for the survival of fish that live in subfreezing environments [Yeh, Y.; Feeney, R. E. Antifreeze proteins—Structures and mechanisms of function. Chem. Rev. 1996, 96 (2), 601−617]. Although scientists agree that these proteins arrest ice crystal growth by a surface adsorption mechanism, the exact nature of the interaction remains an open question. Here, we study the adsorption kinetics of AFGPs during solution ice crystal growth using confocal fluorescence microscopy within and just below the freezing−melting temperature hysteresis region. The AFGP kinetics at the ice surface reveal a two-step inhibition process: (i) incomplete adsorption or a weak interaction that modifies the surface for (ii) a stronger interaction to achieve the complete adsorption necessary to halt growth. The growth is modified from a rough interface to a faceted one, and growth is halted at supercoolings less than 0.05 °C. However, growth resumes, and the proteins desorb, return to the solution phase, and are not incorporated into the ice crystal as previously proposed. Our findings are contrary to an AFGP mechanism described by the Gibbs−Thomson model. We argue that an alternative explanation must include a solvated protein interacting with a solvated ice surface. While thermodynamics considerably alter the interfacial region, antifreeze action is a purely kinetic phenomenon.
Ligand-Specific Dynamics of the Progesterone Receptor in Living Cells and during Chromatin Remodeling In Vitro (2005)

Progesterone receptor (PR), a member of the nuclear receptor superfamily, is a key regulator of several processes in reproductive function. We have studied the dynamics of the interaction of PR with a natural target promoter in living cells through the use of fluorescence recovery after photobleaching (FRAP) analysis and also have characterized the dynamics of the interaction of PR with the mouse mammary tumor virus (MMTV) promoter reconstituted into chromatin in vitro. In photobleaching experiments, PR in the presence of the agonist R5020 exhibits rapid exchange with the MMTV promoter in living cells. Two PR antagonists, RU486 and ZK98299, have opposite effects on receptor dynamics in vivo. In the presence of RU486, PR binds to the promoter and is exchanged more slowly than the agonist-activated receptor. In contrast, PR bound to ZK98299 is not localized to the promoter and exhibits higher mobility in the nucleoplasm than the agonist-bound receptor. Significantly, PR bound to R5020 or RU486 can recruit the SWI/SNF chromatin remodeling complex to the promoter, but PR activated with ZK98299 cannot. Furthermore, we found ligand-specific active displacement of PR from the MMTV promoter during chromatin remodeling in vitro and conclude that the interaction of PR with chromatin is highly dynamic both in vivo and in vitro. We propose that factor displacement during chromatin remodeling is an important component of receptor mobility and that ligand-specific interactions with remodeling complexes can strongly influence receptor nuclear dynamics and rates of exchange with chromatin in living cells.
A retinitis pigmentosa GTPase regulator (RPGR)- deficient mouse model for X-linked retinitis pigmentosa (RP3) (2000)

The X-linked RP3 locus codes for retinitis pigmentosa GTPase regulator (RPGR), a protein of unknown function with sequence homology to the guanine nucleotide exchange factor for Ran GTPase. We created an RPGR-deficient murine model by gene knockout. In the mutant mice, cone photoreceptors exhibit ectopic localization of cone opsins in the cell body and synapses and rod photoreceptors have a reduced level of rhodopsin. Subsequently, both cone and rod photoreceptors degenerate. RPGR was found normally localized to the connecting cilia of rod and cone photoreceptors. These data point to a role for RPGR in maintaining the polarized protein distribution across the connecting cilium by facilitating directional transport or restricting redistribution. The function of RPGR is essential for the long-term maintenance of photoreceptor viability.
Site and sequence specificity of the daunomycin-DNA interaction (1987)

The site and sequence specificity of the daunomycin-DNA interaction was examined by equilibrium binding methods, by deoxyribonuclease I footprinting studies, and by examination of the effect of the antibiotic on the cleavage of linearized pBR322 DNA by restriction endonucleases PvuI and EcoRI. These three experimental approaches provide mutually consistent results showing that daunomycin indeed recognizes specific sites along the DNA lattice. The affinity of daunomycin toward natural DNA increases with increasing GC content. The quantitative results are most readily explained by binding models in which daunomycin interacts with sites containing two adjacent GC base pairs, possibly occurring as part of a triplet recognition sequence. Deoxyribonuclease I footprinting studies utilizing the 160 base pair (bp) tyrT DNA fragment and 61 and 53 bp restriction fragments isolated from pBR322 DNA further define the sequence specificity of daunomycin binding. Specific, reproducible protection patterns were obtained for each DNA fragment at 4 degrees C. Seven protected sequences, ranging in size from 4 to 14 bp, were identified within the tyrT fragment. Relative to the overall tyrT sequence, these protected sequences were GC rich and contained a more limited and distinct distribution of di- and trinucleotides. Within all of the protected sequences, a triplet containing adjacent GC base pairs flanked by an AT base pair could be found in one or more copies. Nowhere in the tyrT fragment did that triplet occur outside a protected sequence. The same triplet occurred within seven out of nine protected sequences observed in the fragments isolated from pBR322 DNA. In the two remaining cases, three contiguous GC base pairs were found. We conclude that the preferred daunomycin triplet binding site contains adjacent GC base pairs, of variable sequence, flanked by an AT base pair. This conclusion is consistent with the results of a recent theoretical study of daunomycin sequence specificity [Chen, K.-X., Gresh, N., & Pullman, B. (1985) J. Biomol. Struct. Dyn. 3, 445-466]. Adriamycin and the beta-anomer of adriamycin produce the same qualitative pattern of protection as daunomycin with the tyrT fragment. Daunomycin inhibits the rate of digestion of pBR322 DNA by PvuI (recognition sequence 5'-CGATCG-3') to a greater extent than it does EcoRI (recognition sequence 5'-GAATTC-3'), a finding consistent with the conclusions derived from our footprinting studies. Our results, as a whole, are the clearest indication to date that daunomycin recognizes a specific DNA sequence as a preferred binding site.
Simple cDNA normalization using kamchatka crab duplex-specific nuclease (2004)

We developed a novel simple cDNA normalization method [termed duplex-specific nuclease (DSN) normalization] that may be effectively used for samples enriched with full-length cDNA sequences. DSN normalization involves the denaturation-reassociation of cDNA, degradation of the double-stranded (ds) fraction formed by abundant transcripts and PCR amplification of the equalized single-stranded (ss) DNA fraction. The key element of this method is the degradation of the ds fraction formed during reassociation of cDNA using the kamchatka crab DSN, as described recently. This thermostable enzyme displays a strong preference for cleaving ds DNA and DNA in DNA-RNA hybrid duplexes compared with ss DNA and RNA, irrespective of sequence length. We developed normalization protocols for both first-strand cDNA [when poly(A)+ RNA is available] and amplified cDNA (when only total RNA can be obtained). Both protocols were evaluated in model experiments using human skeletal muscle cDNA. We also employed DSN normalization to normalize cDNA from nervous tissues of the marine mollusc Aplysia californica (a popular model organism in neuroscience) to illustrate further the efficiency of the normalization technique.
Molecular Electronic Devices Based on Single-Walled Carbon Nanotube Electrodes (2008)

As the top-down fabrication techniques for silicon-based electronic materials have reached the scale of molecular lengths, researchers have been investigating nanostructured materials to build electronics from individual molecules. Researchers have directed extensive experimental and theoretical efforts toward building functional optoelectronic devices using individual organic molecules and fabricating metal-molecule junctions. Although this method has many advantages, its limitations lead to large disagreement between experimental and theoretical results. This Account describes a new method to create molecular electronic devices, covalently bridging a gap in a single-walled carbon nanotube (SWNT) with an electrically functional molecule. First, we introduce a molecular-scale gap into a nanotube by precise oxidative cutting through a lithographic mask. Now functionalized with carboxylic acids, the ends of the cleaved carbon nanotubes are reconnected with conjugated diamines to give robust diamides. The molecular electronic devices prepared in this fashion can withstand and respond to large environmental changes based on the functional groups in the molecules. For example, with oligoanilines as the molecular bridge, the conductance of the device is sensitive to pH. Similarly, using diarylethylenes as the bridge provides devices that can reversibly switch between conjugated and nonconjugated states. The molecular bridge can perform the dual task of carrying electrical current and sensing/recognition through biological events such as protein/substrate binding and DNA hybridization. The devices based on DNA can measure the difference in electrical properties of complementary and mismatched strands. A well-matched duplex DNA 15-mer in the gap exhibits a 300-fold lower resistance than a duplex with a GT or CA mismatch. This system provides an ultrasensitive way to detect single-nucleotide polymorphisms at the individual molecule level. Restriction enzymes can cleave certain cDNA strands assembled between the SWNT electrodes; therefore, these strands maintain their native conformation when bridging the ends of the SWNTs. This methodology for creating novel molecular circuits forges both literal and figurative connections between chemistry, physics, materials science, and biology and promises a new generation of integrated multifunctional sensors and devices.
Advances in neural network hardware (2003)

After discussing possible applications of neural networks, the authors examine hardware implementation including emulators, analog microelectronic implementations, and the synaptic interconnections. Examples of neural network chips are considered. The circuits have programmable interconnections, but the weight values have to be computed externally and are then loaded onto the chip. The designs are all fabricated in standard CMOS technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Layered Higher Order N-grams for Hardening Payload Based Anomaly Intrusion Detection (2010)

Application based intrusion detection involves analysis of network packet payload data. Recently statistical methods for analyzing the payload are being used. Since behavior of every application is not same a different model is necessary for each application. Studies have revealed that higher order n-grams are good for capturing the network profile. In this paper we introduce a concept of layered version of n-gram for payload based anomaly network intrusion detection. Each layer works as an independent anomaly detection system. A packet is declared as normal after passing through all the layers. A packet is declared as anomalous if at any layer it is declared as anomalous and we stop further processing the packet. We create a set of bins and equally distribute the distinct n-grams to each bin. Each such n-gram is a 2 tulle where the first element is byte values of the n-gram and second is the frequency of gram in the entire training data. We assign an anomaly score to each bin based on the frequency of the individual gram in the bin and is termed as coverage of the bin.We evaluate the proposed scheme on normal traffic of DARLA 99 dataset mixed with a set of attacks. Experimental results shows the efficacy of the method with a false alarm rate as low as 0.001\%.
Nanometer-scale pattern formation of GaAs by in situ electron-beam lithography using surface oxide layer as a resist film (1995)

We have studied the effects of the microscopic roughness of a GaAs epitaxial surface on the oxide layer, which is used as a resist-mask material in in situ electron-beam lithography. When electron beam patterning, followed by Cl2 gas etching, was carried out for an oxide-mask layer formed on a rough surface, an indented pattern edge elongated along the [11̄0] direction, typically having a size of several tens of nm, was formed. On the other hand, when we used a misoriented substrate in order to obtain a smooth epitaxial surface by introducing the so-called step-flow growth mode, the resulting pattern exhibited a sufficiently sharp edge. Based on this improvement, together with the optimized electron-beam patterning system, we successfully fabricated an ultrafine trench structure with a width as small as 20 nm.
Liposomal cisplatin combined with gemcitabine in pretreated advanced pancreatic cancer patients: A phase I-II study (2006)

The present trial is a phase I-II study based on a new liposomal cisplatin (lipoplatin). Previous preclinical and clinical data (phase I pharmacokinetics) led to the investigation of a combined treatment modality involving lipoplatin and gemcitabine. The gemcitabine dose was kept standard at 1000 mg/m2 and the lipoplatin dose was escalated from 25 mg/m2 to 125 mg/m2. The treatment was administered to advanced pretreated pancreatic cancer patients who were refractory to previous chemotherapy which included gemcitabine. Lipoplatin at 125 mg/m2 was defined as dose limiting toxicity (DLT) and 100 mg/m2 as the maximum tolerated dose (MTD) in combination with 1000 mg/m2 of gemcitabine. Preliminary objective response rate data showed a partial response in 2/24 patients (8.3%), disease stability in 14 patients (58.3%) for a median duration of 3 months (range 2-7 months) and clinical benefit in 8 patients (33.3%). Liposomal cisplatin is a non-toxic alternative agent to bare cisplatin. In combination with gemcitabine, it has an MTD of 100 mg/m2 and shows promising efficacy in refractory pancreatic cancer.
Knock-out and Knock-in Mice to Investigate the Role of Nicotinic Receptors in the Central Nervous System (2002)

Pharmacological manipulations of nicotinic transmission have long been the only way to investigate the role of nicotinic acetylcholine receptors (nAChRs) in the brain. More recently, however, the use of genetically engineered knock-out (Ko) and knock-in (Kin) mice has provided a powerful alternative to the classical pharmacological approach. These animal models are not only useful in order to re-examine and refine the results derived from pharmacological studies, but they also provide a unique opportunity to determine the subunit composition of native receptors involved in various aspects of nicotinic transmission. Ultimately, this knowledge will be extremely valuable in the process of designing new drugs that can mimic the beneficial effects of nicotine for the treatment of certain neuropathologies or that may be useful in smoking cessation therapies. In this review, we present recent data obtained from studies of mutant mice that have contributed to our understanding of the role and composition of nAChRs in the central nervous system (CNS). The advantages and pitfalls of Ko models will also be discussed.
Polyphase codes with good periodic correlation properties (Corresp.) (1972)

This correspondence describes the construction of complex codes of the form exp <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i \alpha_k</tex> whose discrete circular autocorrelations are zero for all nonzero lags. There is no restriction on code lengths.