gebhart/patrepeval huggingface dataset:
Quantitative exploration of the REF52 protein database: Cluster analysis reveals the major protein expression profiles in responses to growth regulation, serum stimulation, and viral transformation (1990)

Quantitative protein databases reveal the response of cells to experimental variables, such as exposure to growth factors or transfection with a transforming gene. The nature of the response depends on the type of cell and its internal state at the time of the stimulus. By constructing a protein database to study a given cell line, we can better understand the differentiated state of the cell, the growth regulatory mechanisms it employs, the particular mechanisms it uses to cope with its environment, and the ways these mechanisms may have been compromised through mutation or transformation. The REF52 database is a quantitative database designed to study growth control and transformation in a well-defined family of normal and transformed rat cell lines. The database, which has been described and analyzed elsewhere (J. I. Garrels and B. R. Franza, J. Biol. Chem. 1989, 264, 5283-5298 and J. I. Garrels and B. R. Franza, J. Biol. Chem. 1989, 264, 5299-5312) is further explored here using cluster analysis. This method reveals the most common protein expression profiles for each series of two-dimensional gels without requiring any prior hypothesis or queries on the part of the investigator. This study reveals, for each experiment, large and small clusters of protein expression profiles, most of which have readily apparent biological meaning. For example, large clusters of proteins induced or repressed during growth to confluence have been revealed, and several clusters of transformation-sensitive proteins reveal differential effects of transformation by DNA- and RNA-tumor viruses. This analysis extends our earlier quantitative explorations of the REF52 protein database and helps to show how such a database can be used to provide context and guidance for molecular studies of regulation in a given cell system.
Expression of the genes encoding bovine LH in a line of Chinese hamster ovary cells. (1987)

Synthesis of biologically active LH is complex, due in part to its heterodimeric subunit structure and to the numerous post-translation modifications of each subunit. Through the use of mammalian expression vectors we have been able to introduce the bovine alpha subunit and LH-beta genes into a Chinese hamster ovary cell line deficient in dihydrofolate reductase. The bovine genes are actively expressed and the Chinese hamster ovary cells secrete biologically active LH. The expression vector containing the bovine alpha subunit gene also contains a modified mouse gene encoding dihydrofolate reductase, permitting the use of methotrexate to amplify selectively the bovine alpha subunit gene after its integration into the genome of the Chinese hamster cells. This provides a novel means for assessing the importance of alpha subunit concentration with respect to assembly of the heterodimer. In addition, methotrexate selection leads to the over-production of LH (10 micrograms/10(6) cells/24 h). Finally, because the bovine LH produced in the Chinese hamster ovary cells is glycosylated, this transfection system can be used in conjunction with in-vitro mutagenesis to determine whether site-specific changes in glycosylation have an effect on subunit assembly and biological activity. This transfection approach therefore offers multiple avenues to explore further the molecular mechanisms underlying the complex biosynthetic pathway of bovine LH.
The intracellular distribution of the ES cell totipotent markers OCT4 and Sox2 in adult stem cells differs dramatically according to commercial antibody used (2009)

To characterize ES cells, researchers have at their disposal a list of pluripotent markers, such as OCT4. In their quest to determine if adult stem cell populations, such as MSCs and ASCs, are pluripotent, several groups have begun to report the expression of these markers in these cells. Consistent with this, human ASCs (hASCs) are shown in this study to express a plethora of ES pluripotent markers at the gene and protein level, including OCT4, Sox2, and Nanog. When intracellular distribution is examined in hASCs, both OCT4 and Sox2 are expressed within the nuclei of hASCs, consistent with their expression patterns in ES cells. However, a significant amount of expression can be noted within the hASC cytoplasm and a complete absence of nuclear expression is observed for Nanog. Recent descriptions of OCT4 transcript variants may explain the cytoplasmic expression of OCT4 in hASCs and consistent with this, hASCs do express both the OCT4A and 4B transcript variants at the gene level. However, discrepancies arise when these three pluripotent markers are studied at the protein level. Specifically, distinct differences in intracellular expression patterns were noted for OCT4, Sox2, and Nanog from commercial antibody to commercial antibody. These antibody discrepancies persisted when hMSCs and rat ASCs and MSCs were examined. Therefore, confirming the expression of OCT4, Sox2, and Nanog in adult stem cells with today's commercial antibodies must be carefully considered before the designation of pluripotent can be granted.
Common and Dissociable Mechanisms of Executive System Dysfunction Across Psychiatric Disorders in Youth (2016)

These findings provide novel evidence that common and dissociable deficits within the brain's executive system are present in association with dimensions of psychopathology in youth.
Permissive Hypotension Strategies for the Far-Forward Fluid Resuscitation of Significant Hemorrhage (2004)

Acute hemorrhage accounts for about 50% of the deaths on the battlefield in conventional warfare. In addition, hemorrhage is the primary cause of death in 30% of injured soldiers who die from wounds. With future combat strategies focused around the Objective Force Warrior, greater dispersal of troops and fighting in urban settings and on non-linear battlefields, the likelihood of longer evacuation times for combat casualties is suggested. As a consequence of these conditions and the logistic limitations of weight and cube, fluid resuscitation research within the Army's Combat Casualty Care Research Program is focused to investigate limited- or small-volume fluid resuscitation strategies, including permissive hypotension, in far forward areas for the treatment of severe hemorrhage. The goals are to improve battlefield survival and to reduce or prevent early and late deleterious sequelae. Utilizing both anesthetized and conscious large (swine) and small (rodent) animal models, current efforts are focused on evaluating available crystalloid and colloid fluids such as lactated Ringer s, Hespan and Hextend. In addition, other studies are evaluating hemoglobin therapeutics as well as hypertonic/hyperoncotic fluids. Preliminary data suggest that colloid containing fluids offer volume sparing effects over standard isotonic crystalloids, but under these animal model conditions, no obvious advantage of an oxygen-carrying fluid has been observed. Studies to evaluate limitations of hypertonic fluids under these conditions are currently in progress. As there are little data available on the consequences of permissive hypotension coupled with longer evacuation times for the military, these studies have important implications towards the development of optimal fluid resuscitation strategies for stabilization of the combat casualty.
Identification and transcriptional analysis of the Escherichia coli htrE operon which is homologous to pap and related pilin operons (1993)

We have characterized a new Escherichia coli operon consisting of two genes, ecpD and htrE. The ecpD gene encodes a 27-kDa protein which is 40% identical at the amino acid level to the pilin chaperone PapD family of proteins. Immediately downstream of the ecpD gene is the htrE gene. The htrE gene encodes a polypeptide of 95 kDa which is processed to a 92-kDa mature species. The HtrE protein is 38% identical to the type II pilin porin protein PapC. The ecpD htrE operon is located at 3.3 min on the genetic map, corresponding to the region from kbp 153 to 157 of the E. coli physical map. The htrE gene was identified on the basis of a Tn5 insertion mutation which resulted in a temperature-sensitive growth phenotype above 43.5 degrees C. The transcription of this operon is induced with a temperature shift from 22 to 37 or 42 degrees C but not to higher temperatures, e.g., 50 degrees C. Consistent with this result, the temperature-induced transcription was shown to be independent of the rpoH gene product (sigma 32). The transcription of this operon was further shown to require functional integration host factor protein, since himA or himD mutant bacteria possessed lower levels of ecpD htrE transcripts. Among the three transcriptional start sites discovered, one, defined by the P2 promoter, was found to be under the positive regulation of the katF (rpoS) gene, which encodes a putative sigma factor required for the transcription of many growth phase-regulated genes.
Mesenchymal Stem Cell Conditioned Medium Promotes Proliferation and Migration of Alveolar Epithelial Cells under Septic Conditions In Vitro via the JNK-P38 Signaling Pathway (2015)

Our data suggest MSC promote epithelial cell repair through releasing a repertoire of paracrine factors via activation of JNK and P38 MAPK.
The Case Against Credit Card Interest Rate Regulation (1986)

This article analyzes recent proposals to regulate credit card interest rates on a national scale. The proposals are a modern chapter in a very old story. Usury laws-laws forbidding or limiting payment for money loans-are among the most ancient forms of price control. Like previous economic studies of usury controls, this one concludes that they are unjustified because the supply of credit is highly competitive, and would be harmful because they would cause an artificial contraction in the supply of credit and other economic inefficiencies.
Surface modification by continuous graft copolymerization. III. Photoinitiated graft copolymerization onto poly(ethylene terephthalate) fiber surface (1990)

Abstract Photoinitiated grafting is an excellent method to modify the surface properties of a polymer. The presoaking photografting method applied to poly(ethylene terephthalate) (PET) with acrylic acid or acrylamide as monomer using benzophenone as photoinitiator has been investigated. The photografting proceeds under nitrogen atmosphere in a continuous process. The relative intensity of the ESCA lines of nitrogen over carbon of the fiber grafted with acrylamide increased from 3–4% (background) to 8% for 20‐s irradiation time. Measured by titration, the amount of grafted poly(acrylic acid) is 0.821 and 1.528 mg/m 2 with 0.5 M and 2.0 M acrylic acid concentration, respectively, in the presoaking solution at 10‐s irradiation time. The dyeability of the fiber, measured by UV absorption, improved. The concentration of initiator and monomer and the solvent used affected the grafting yield. Appropriate conditions promoted photografting of the poly(ethylene terephthalate) fiber. Acetone was a somewhat better solvent than methylethylketone and methylpropylketone.
Role of endopeptidase‐24.11 in the inactivation of atrial natriuretic peptide (1988)

The circulating form of atrial natriuretic factor is a 28-residue peptide containing a 17-residue disulphide-linked ring. It has important actions on the kidney, largely on its haemodynamics, and at other sites including the adrenal cortex and CNS. It has a short half-life in vivo and is rapidly inactivated when incubated with kidney microvillar membranes. Of the battery of peptidases present in that membrane, only one, endopeptidase-24.11, is responsible for initiating the attack, and this commences with hydrolysis of the Cys7-Phe8 bond within the ring. Hydrolysis at this and other points has been shown to inactivate the peptide and this information has pointed the way to the synthesis of resistant analogues.
Hammerhead ribozyme-mediated destruction of nuclear foci in myotonic dystrophy myoblasts (2003)

Myotonic dystrophy type 1 (DM1) is caused by an unstable CTG expansion in the 3' untranslated region (3'UTR) of the myotonic dystrophy protein kinase gene (DMPK). Transcripts from this altered gene harbor large CUG expansions that are retained in the nucleus of DM1 cells and form foci. It is believed that the formation of these foci is closely linked to DM1 muscle pathogenesis. Here we investigated the possibility of using a nuclear-retained hammerhead ribozyme expressed from a modified tRNAmeti promoter to target and cleave mutant transcripts of DMPK. Accessible ribozyme target sites were identified in the 3'UTR of the DMPK mRNA and a hammerhead ribozyme was designed to cut the most accessible site. Utilizing this system, we have achieved 50 and 63% reductions, respectively, of the normal and CUG expanded repeat-containing transcripts. We also observed a significant reduction in the number of DMPK mRNA-containing nuclear foci in human DM1 myoblasts. Reduction of mutant DMPK mRNA and nuclear foci also corroborates with partial restoration of insulin receptor isoform B expression in DM1 myoblasts. These studies demonstrate for the first time intracellular ribozyme-mediated cleavage of nuclear-retained mutant DMPK mRNAs, providing a potential gene therapy agent for the treatment of myotonic dystrophy.
PHASE, a portable host access system environment (2003)

The portable host access system environment (PHASE) allows portable PCs to change their point of connection to the internet and continue to be accessible by a fully specified internet domain name. The author offers a solution to the problem of maintaining a proper mapping of internet protocol (IP) addresses to portable machines that have the ability to assume different IP addresses. The portable host access component (PHAC) of the PHASE provides a temporary IP address to each PC that connects to it. A modified internet domain name server, called the dynamic domain name server (DDNS), automatically manages the temporary IP addresses of PCs and provides a mechanism for other hosts to connect to the portable PC. The pros and cons of different methods used to ensure the integrity of the DDNS database are discussed. As a result of this technology, internet hosts can now initiate connections to portable hosts. This gives PCs connected to the PHAC the ability to run server protocols. An example military application of a mobile communications environment involving a portable PC connected to the PHAC, running an SMTP (simple mail transfer protocol) server protocol is portrayed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cloning, sequence, and expression of bovine interferon-gamma. (1986)

Bovine interferon-gamma (IFN-gamma) sequences have been isolated by screening a cDNA library with a human IFN-gamma cDNA probe. The cDNA library was constructed from RNA isolated from concanavalin A-stimulated bovine lymph node cells. The open reading frame predicts that the bovine IFN-gamma precursor is composed of 166 amino acids with a predicted m.w. of 19,393. Alignment of the amino acid sequence with human IFN-gamma indicates that mature bovine IFN-gamma is composed of 143 amino acids with a predicted m.w. of 16,858. It has an amino acid homology of 63% with human IFN-gamma, and 47% with murine IFN-gamma. Biologically active bovine IFN-gamma was synthesized in an Escherichia coli expression system.
The Structure-Function Dilemma of the Hammerhead Ribozyme (2005)

A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
Secure communication over CANBus (2017)

In this paper, we propose hardware based secure and trusted communication over CAN bus in the intra vehicle network connecting electronic Control Units (ECUs). CAN bus is an insecure communication channel, connecting resource constraint devices that have limited resources to devote for data security and real-time requirements to meet the safety critical design specifications. We propose a hardware based secure and trusted framework that implements lightweight PUF based mutual authentication and secure encryption over the insecure communication channel. The paper discusses the framework design and implementation details along with the resource utilization and performance analysis of the proposed system.
Elevated levels of Rad51 recombination protein in tumor cells. (2002)

Rad51 is the key enzyme for homologous recombination, an evolutionarily conserved mechanism for the repair of DNA damage and the generation of genetic diversity. Given the observation that many tumors become resistant to radiation therapy and DNA-damaging chemotherapeutics and also that tumor cell populations can acquire a high number of genetic alterations and then expand clonally, dysfunction of the mammalian Rad51 recombinase could play a major role in the multistep process of tumorigenesis. The data we present provide further strong support for this hypothesis. Using anti-Rad51 immunofluorescence staining, widely different tumor cell lines displayed increased numbers of nuclei with focally concentrated Rad51 protein compared with nonmalignant control cell lines. These nuclear foci are thought to represent a repairosome-type assembly of Rad51 and other proteins required for recombinational DNA repair. By Western blot analyses, the net amount of Rad51 protein was increased 2-7-fold in all tested tumor cell lines. Inhibition of de novo protein synthesis by cycloheximide treatment showed a similar half-life of Rad51 protein in normal and tumor cells. Fluorescence in situ hybridization experiments did not detect Rad51 gene amplifications in tumors. Because Northern blot analysis demonstrated highly elevated Rad51 mRNA levels, we conclude that the increases in Rad51 protein and nuclear foci formation in tumor cells are the result of transcriptional up-regulation.
Palladium-Mediated Direct Synthesis of N-Substituted 4-Methyl- and 4-Ethylisoquinolone Derivatives (2008)

N-Substituted 4-methyl- and 4-ethylisoquinolone derivatives are prepared from different N-allylbenzamide derivatives in a single step through a ligand-free palladium-mediated intramolecular Heck cyclization.
Photon-blockade-induced Mott transitions andXYspin models in coupled cavity arrays (2007)

We propose a physical system where photons could exhibit strongly correlated effects. We demonstrate how a Mott-insulator phase of atom-photon excitations (polaritons) can arise in an array of individually addressable coupled electromagnetic cavities when each of these cavities is coupled resonantly to a single two-level system (atom, quantum dot, or Cooper pair). This Mott phase is characterized by the same integral number of net polaritonic excitations with photon blockade providing the required repulsion between the excitations in each site. Detuning the atomic and photonic frequencies suppresses this effect and induces a transition to a photonic superfluid. Finally, on resonance the system can straightforwardly simulate the dynamics of many-body spin systems.
Genotyping on a Thermal Gradient DNA Chip (2003)

Silicon-based chips with discrete, independently temperature-controlled islands have been developed for use in DNA microarray hybridization studies. Each island, containing a heater made of a diffusion layer and a temperature sensor based on a p-n junction, is created on a silicon dioxide/nitride surface by anisotropic etching. Different reactive groups are subsequently added to the surface of the islands, and allele-specific oligonucleotide probes are attached to discrete spots on the chip. Hybridization is performed with Cy5-tagged single-stranded targets derived by PCR from genomic DNA. Results are assessed by measuring fluorescence of bound dye-tagged targets after hybridization and washing. Temperatures at each island can be set at different values to obtain optimal distinction between perfect matches and mismatches. This approach facilitates definition of optimal temperatures for probe/target annealing and for distinction between perfectly matched versus mismatched solution-phase targets. The thermal gradient DNA chips were then tested for genotyping, and the results for four different loci in two genes are presented. Unambiguous typing was achieved for clinically relevant loci within the factor VII and hemochromatosis genes.
The collection of the motile population of cells from a living tumor. (2000)

In this study, we report that needles containing chemoattractants can be used to collect the subpopulation of motile and chemotactic tumor cells from a primary tumor in a live rat as a pure population suitable for further analysis. The most efficient cell collection requires the presence of chemotactic cytokines, such as epidermal growth factor and serum components, and occurs with 15-fold higher efficiency in metastatic tumors compared with nonmetastatic tumors. Although tumor cells of the nonmetastatic tumors show a motility response to serum, they were not collected with high efficiency into needles in vivo in response to serum, indicating that additional factors besides motility are required to explain differences in cell collection efficiencies between metastatic and nonmetastatic tumors. The results reported here indicate that needles filled with growth factors and matrigel, when inserted into the primary tumor, can faithfully mimic the environment that supports invasion and intravasation in vivo. Furthermore, the results indicate that the same cell behaviors that contribute to chemotaxis in vitro also contribute to invasion in vivo.
A Blockchain-Based Architecture for Integrated Smart Parking Systems (2019)

In this paper, we introduce an integrated smart parking system. The proposed integrated smart parking system brings multiple parking service providers together under a unified platform aiming to provide one-stop parking information services to the commuters in a smart city. However, the adaptation of such a system is prone to tempering while a massive amount of data is shared among different parties which raise concerns related to trust and performance. To address this challenge, we propose a blockchain-based architecture specific to the integrated smart parking systems. Finally, we present a set of design principles which shows the applicability of our proposed blockchain-based integrated parking system.