gebhart/patrepeval huggingface dataset:
Pharmacokinetics and biodistribution of genetically-engineered antibodies. (1998)

Monoclonal antibodies (MAbs), because of their inherent specificity, are ideal targeting agents. They can be used to deliver radionuclides, toxins or cytotoxic drugs to a specific tissue or malignant cell populations. Intact immunoglobulin (IgG) molecules have several practical limitations of their pharmacology; their relatively large size of approximately 150,000 daltons leads to a slow clearance from the blood pool and the body resulting in significant exposure to normal organs with limited quantities delivered to tumors. The IgG molecule shows a relatively poor diffusion from the vasculature into and through the tumor. Attempts to modify the pharmacology of the Ig molecule have classically involved the use of proteases to generate F(ab')2 and Fab' fragments with molecular weights of approximately 100,000 and 50,000 daltons, respectively. Fv fragments of IgG are one of the smallest size functional modules of antibodies that retain high affinity binding of an antigen. Their smaller size, approximately 25,000 daltons, enables better tumor penetration and makes them potentially more useful than a whole antibody molecule for clinical applications. Molecular cloning and expression of the variable region genes of IgG has greatly facilitated the generation of engineered antibodies. A single-chain Fv (scFv) recombinant protein, prepared by connecting genes encoding for heavy-chain and light-chain variable regions at the DNA level by an appropriate oligonucleotide linker, clears from the blood at much faster rate than intact IgG. The scFv fragment can retain an antigen-binding affinity similar to that of a monovalent Fab' fragment; this however, represents a relative decrease in binding affinity when compared to intact antibodies. The scFv with its faster clearance and lower affinity results in a lower percent-injected dose localizing in tumors when compared to the divalent IgG molecule. This may be adequate for imaging but probably not for therapy. The valency of the MAb fragment is critical for the functional affinity of an antibody to a cell surface or a polymeric antigen. In attempts to generate multivalent forms of scFv molecules, non-covalently linked scFv dimeric and trimeric molecules, disulfide linked dimeric scFvs, as well as covalently linked chimeric scFvs have been studied. These multivalent scFvs generally have a higher functional affinity than the monovalent form resulting in better in vivo targeting. Another way to alter the pharmacology of the scFvs is to modify its net charge. Charge-modified scFvs with desired isoelectric points (pI), have been prepared by inserting negatively charged amino acids on the template of the variable region genes. This can help to overcome undesirable elevations in renal uptake seen with most antibody fragments. In conclusion, genetic manipulations of the immunoglobulin molecules are effective means of altering stability, functional affinity, pharmacokinetics, and biodistribution of the antibodies required for the generation of the "magic bullet".
Transactivated and chemically inducible gene expression in plants (2006)

Several vector systems are available for tissue-specific transactivation or chemical induction of transgene expression in plants. The choice facing researchers is which promoter system to commit to as this determines the range and characteristics of the expression resources available. The decision will not be the same for all species or applications. We present some general discussion on the use of these technologies and review in detail the properties in various (mainly angiosperm) species of the most promising: mGal4:VP16/UAS and pOp/LhG4 for transactivation, and the alc-switch, GVE/VGE, GVG, pOp6/LhGR, and XVE systems for chemical induction.
Polymerization of acetylenes and cyclic olefins induced by metal carbynes (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymerization of acetylenes and cyclic olefins induced by metal carbynesThomas J. Katz, Thoi Huu Ho, Neng Yang Shih, Yuan Chi Ying, and Van I. W. StuartCite this: J. Am. Chem. Soc. 1984, 106, 9, 2659–2668Publication Date (Print):May 1, 1984Publication History Published online1 May 2002Published inissue 1 May 1984https://pubs.acs.org/doi/10.1021/ja00321a029https://doi.org/10.1021/ja00321a029research-articleACS PublicationsRequest reuse permissionsArticle Views561Altmetric-Citations100LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A Novel .eta.7 Coordination Mode of a Benzyl Ligand in a Cationic Zirconium Complex (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Novel .eta.7 Coordination Mode of a Benzyl Ligand in a Cationic Zirconium ComplexClaudio Pellecchia, Attilio Immirzi, Daniela Pappalardo, and Andrea PelusoCite this: Organometallics 1994, 13, 10, 3773–3775Publication Date (Print):October 1, 1994Publication History Published online1 May 2002Published inissue 1 October 1994https://pubs.acs.org/doi/10.1021/om00022a009https://doi.org/10.1021/om00022a009research-articleACS PublicationsRequest reuse permissionsArticle Views230Altmetric-Citations56LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Induction of Chemoresistance by All-Trans Retinoic Acid via a Noncanonical Signaling in Multiple Myeloma Cells (2014)

Despite the successful application of all-trans retinoic acid (ATRA) in multiple myeloma treatment, ATRA-induced chemoresistance in the myeloma patients is very common in clinic. In this study, we evaluated the effect of ATRA on the expression of apurinic endonuclease/redox factor-1 (Ape/Ref-1) in the U266 and RPMI-8226 myeloma cells to explore the chemoresistance mechanism involved. ATRA treatment induced upregulation of Ape/Ref-1 via a noncanonical signaling pathway, leading to enhanced pro-survival activity counteracting melphalan (an alkylating agent). ATRA rapidly activated p38-MSK (mitogen- and stress activated protein kinase) cascade to phosphorylate cAMP response element-binding protein (CREB). Phosphorylated CREB was recruited to the Ape/Ref-1 promoter to evoke the gene expression. The stimulation of ATRA on Ape/Ref-1 expression was attenuated by either p38-MSK inhibitors or overexpression of dominant-negative MSK1 mutants. Moreover, ATRA-mediated Ape/Ref-1 upregulation was correlated with histone modification and activation of CBP/p300, an important cofactors for CREB transcriptional activity. C646, a competitive CBP/p300 inhibitor, abolished the upregulation of Ape/Ref-1 induced by ATRA. Intriguingly, CBP rather than p300 played a dominant role in the expression of Ape/Ref-1. Hence, our study suggests the existence of a noncanonical mechanism involving p38-MSK-CREB cascade and CBP induction to mediate ATRA-induced Ape/Ref-1 expression and acquired chemoresistance in myeloma cells.
Coronary Angiography Using Noninvasive Imaging Techniques of Cardiac CT and MRI (2008)

Noninvasive coronary angiography has become an important imaging tool in the evaluation of patients with and at risk for coronary artery disease (CAD). Multidetector computed tomographic (MDCT) angiography offers excellent negative predictive value (>/=95%) for the absence of coronary artery disease and has shown promising results in evaluating allograft vasculopathy, bypass grafts, and degenerative aortic valve disease. A single MDCT scan in the emergency department is valuable in ruling out both cardiac and noncardiac causes of acute chest pain. Cardiac magnetic resonance (MR) currently lacks the spatial resolution of MDCT limiting its assessment of the coronary vasculature, but the proximal coronary arteries can be evaluated along with myocardial function and viability without exposure to contrast dye or ionizing radiation. In addition, MR imaging also has great potential for characterizing coronary plaques, as well as following their progression and regression.
Electrocatalytic Reduction of CO2to Small Organic Molecule Fuels on Metal Catalysts (2010)

The electrocatalytic reduction of carbon dioxide (CO2) to liquid fuels has tremendous positive impacts on atomospheric carbon balance and help to reduce global warming issues. This paper reviewed current knowledge of electrochemical CO2 reduction to small organic molecule fuels on metal catalysts and gas-phase CO2 reduction techniques based on gas diffusion electrode and solid polymer electrolyte. Future research and development needs in this area were also discussed.
MEKK1 suppresses oxidative stress-induced apoptosis of embryonic stem cell-derived cardiac myocytes (1999)

A combination of in vitro embryonic stem (ES) cell differentiation and targeted gene disruption has defined complex regulatory events underlying oxidative stress-induced cardiac apoptosis, a model of postischemic reperfusion injury of myocardium. ES cell-derived cardiac myocytes (ESCM) having targeted disruption of the MEKK1 gene were extremely sensitive, relative to wild-type ESCM, to hydrogen peroxide-induced apoptosis. In response to oxidative stress, MEKK1-/- ESCM failed to activate c-Jun kinase (JNK) but did activate p38 kinase similar to that observed in wild-type ESCM. The increased apoptosis was mediated through enhanced tumor necrosis factor alpha production, a response that was positively and negatively regulated by p38 and the MEKK1-JNK pathway, respectively. Thus, MEKK1 functions in the survival of cardiac myocytes by inhibiting the production of a proapoptotic cytokine. MEKK1 regulation of the JNK pathway is a critical response for the protection against oxidative stress-induced apoptosis in cardiac myocytes.
APSS (2005)

APSS, a proactive secret sharing (PSS) protocol for asynchronous systems, is explained and proved correct. The protocol enables a set of secret shares to be periodically refreshed with a new, independent set, thereby thwarting mobile-adversary attacks. Protocols for asynchronous systems are inherently less vulnerable to denial-of-service attacks, which slow processor execution or delay message delivery. So APSS tolerates certain attacks that PSS protocols for synchronous systems cannot.
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers (2011)

The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.
Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli (1990)

The most important function of carotenoid pigments, especially beta-carotene in higher plants, is to protect organisms against photooxidative damage (G. Britton, in T. W. Goodwin, ed., Plant Pigments--1988, 1988; N. I. Krinsky, in O. Isler, H. Gutmann, and U. Solms, ed., Carotenoids--1971, 1971). beta-Carotene also functions as a precursor of vitamin A in mammals (G. A. J. Pitt, in I. Osler, H. Gutmann, and U. Solms, ed., Carotenoids--1971, 1971). The enzymes and genes which mediate the biosynthesis of cyclic carotenoids such as beta-carotene are virtually unknown. We have elucidated for the first time the pathway for biosynthesis of these carotenoids at the level of enzyme-catalyzed reactions, using bacterial carotenoid biosynthesis genes. These genes were cloned from a phytopathogenic bacterium, Erwinia uredovora 20D3 (ATCC 19321), in Escherichia coli and located on a 6,918-bp fragment whose nucleotide sequence was determined. Six open reading frames were found and designated the crtE, crtX, crtY, crtI, crtB, and crtZ genes in reference to the carotenoid biosynthesis genes of a photosynthetic bacterium, Rhodobacter capsulatus; only crtZ had the opposite orientation from the others. The carotenoid biosynthetic pathway in Erwinia uredovora was clarified by analyzing carotenoids accumulated in E. coli transformants in which some of these six genes were expressed, as follows: geranylgeranyl PPiCrtB----prephytoene PPiCrtE----phytoeneCrtI---- lycopeneCrtY----beta-caroteneCrtZ----zeaxanthinCrtX--- -zeaxanthin-beta- diglucoside. The carotenoids in this pathway appear to be close to those in higher plants rather than to those in bacteria. Also significant is that only one gene product (CrtI) for the conversion of phytoene to lycopene is required, a conversion in which four sequential desaturations should occur via the intermediates phytofluene, zeta-carotene, and neurosporene.
Differential killer sensitivity as a tool for fingerprinting wine-yeast strains ofSaccharomyces cerevisiae (1996)

The extreme variability of the killer phenomenon in nature, expressed differently in different strains of the same yeast species, embodies an exceptional potential for the discrimination of yeasts at the strain level. Killer-sensitive relationships between a killer reference panel of 24 yeasts belonging to 13 species of six genera, and different industrial wine-starters of Saccharomyces cerevisiae can be used profitably for a rapid and simple fingerprinting procedure.
Organ Bioengineering and Regeneration as the New Holy Grail for Organ Transplantation (2013)

Organ transplantation is a victim of its own success. In view of the excellent results achieved to date, the demand for organs is escalating whereas the supply has reached a plateau. Consequently, waiting times and mortality on the waiting list are increasing dramatically. Recent achievements in organ bioengineering and regeneration have provided proof of principle that the application of organ bioengineering and regeneration technologies to manufacture organs for transplant purposes may offer the quickest route to clinical application. As investigators are focusing their interest on the utilization and manipulation of autologous cells, ideally the end product will be the equivalent of an autograft such that the recipient will not require any antirejection medication. Achievement of an immunosuppression-free state has been pursued but has proven to be a difficult odyssey since the early days of the transplant era, yet an immediate, stable, durable, and reproducible immunosuppression-free state remains an unfulfilled quest. As organ bioengineering and regeneration has shown the potential to meet both the needs for a new source of organs that may eclipse the increasing organ demand and an immunosuppression-free state, advances in this field could become the new Holy Grail for transplant sciences.
Efficient Private Information Retrieval for Geographical Aggregation (2014)

Abstract Knowledge of patients’ location information (postal/zip codes) is critical in public health research. However, the inclusion of location information makes it easier to determine the identity of the individuals in the data sets. An efficient way to anonymize location information is through aggregation. In order to aggregate the locations efficiently, the data holder needs to know the locations’ adjacency information. A location adjacency matrix is big, and requires constant updates, thus it cannot be stored at the data holder's end. A possible solution would be to have the adjacency matrix stored on a cloud server, the data holder can then query the required adjacency records. However, queries reveal information on patients’ locations, thus, we need to privately query the cloud server's database. Existing private information retrieval protocols are inefficient for our context, therefore, in this paper, we present an efficient protocol to privately query the server's database for adjacency information and thus preserving patients’ privacy.
An analysis of the mechanism by which cetiedil inhibits the gardos phenomenon (1984)

Energy depletion in the human erythrocyte causes a rise in intracellular calcium. This in turn accelerates the transmembrane movement of potassium and chloride, resulting in cell dehydration. This process, known as the Gardos phenomenon, is inhibited by cetiedil. The present study examines the mechanism by which cetiedil inhibits the Gardos phenomenon. The ability of cetiedil to retard the initial step in the Gardos phenomenon, a rise in intracellular calcium, was first tested. Cetiedil did not prevent calcium accumulation. Cetiedil's ability to inhibit anion movement was next evaluated, as cetiedil could appear to be blocking K movement when in fact it was preventing the movement of its accompanying anion. No inhibitory effect on anion movement was seen. Since cetiedil prevented neither calcium accumulation nor anion movement, it must inhibit the Gardos phenomenon by preventing the opening of the K-specific gate in the erythrocyte membrane. The fact that cetiedil's effect on the Gardos phenomenon could not be removed with repeated cell washing indicates that this effect is irreversible.
Human Endothelial Progenitor Cells (2011)

Human endothelial progenitor cells (EPCs) have been generally defined as circulating cells that express a variety of cell surface markers similar to those expressed by vascular endothelial cells, adhere to endothelium at sites of hypoxia/ischemia, and participate in new vessel formation. Although no specific marker for an EPC has been identified, a panel of markers has been consistently used as a surrogate marker for cells displaying the vascular regenerative properties of the putative EPC. However, it is now clear that a host of hematopoietic and vascular endothelial subsets display the same panel of antigens and can only be discriminated by an extensive gene expression analysis or use of a variety of functional assays that are not often applied. This article reviews our current understanding of the many cell subsets that constitute the term EPC and provides a concluding perspective as to the various roles played by these circulating or resident cells in vessel repair and regeneration in human subjects.
Interaction of dihydrofolate reductase with methotrexate: Ensemble and single-molecule kinetics (2002)

The thermodynamics and kinetics of the interaction of dihydrofolate reductase (DHFR) with methotrexate have been studied by using fluorescence, stopped-flow, and single-molecule methods. DHFR was modified to permit the covalent addition of a fluorescent molecule, Alexa 488, and a biotin at the N terminus of the molecule. The fluorescent molecule was placed on a protein loop that closes over methotrexate when binding occurs, thus causing a quenching of the fluorescence. The biotin was used to attach the enzyme in an active form to a glass surface for single-molecule studies. The equilibrium dissociation constant for the binding of methotrexate to the enzyme is 9.5 nM. The stopped-flow studies revealed that methotrexate binds to two different conformations of the enzyme, and the association and dissociation rate constants were determined. The single-molecule investigation revealed a conformational change in the enzyme-methotrexate complex that was not observed in the stopped-flow studies. The ensemble averaged rate constants for this conformation change in both directions is about 2-4 s(-1) and is attributed to the opening and closing of the enzyme loop over the bound methotrexate. Thus the mechanism of methotrexate binding to DHFR involves multiple steps and protein conformational changes.
Tn 7 inserts in both orientations at a single chromosomal location and apparently forms cointegrates in Pasteurella multocida (1990)

Pasteurella multocida transconjugants isolated after mating with Escherichia coli strains that carry one or the other of two Tn7-containing suicide plasmids, pRKTV5 and pUW964 (pRKTV5::Tn5), were analysed. These plasmids have the ColE1 replication origin and were thus expected to deliver transposons but not be maintained as free replicons in Pasteurella. Five out of six transconjugants selected for acquisition of Tn7 from E. coli (pRKTV5) had simple insertions of the transposon, in either orientation, at a single chromosomal location, while the sixth had pRKTV5 integrated at the same location. By contrast, all of 27 transconjugants selected for acquisition of either Tn7 or Tn5 from E. coli (pUW964) maintained pUW964. Of seven subsequently examined at the molecular level, all had pUW964 (in one case, a deletion derivative) integrated at the same location as the Tn7 insertions obtained with pRKTV5. A copy of Tn7 was present at each boundary between the integrated plasmids (pRKTV5 or pUW964) and the chromosome in each strain. The two copies of Tn7 at either end of an integrated plasmid were either in the same (six cases) or in opposite (two cases) orientations with respect to each other. These seem to be products of replicative transposition by Tn7 but can also derive from conservative mechanisms.
2-micrometers DNA-like plasmids in the osmophilic haploid yeast Saccharomyces rouxii (1982)

DNA plasmids were detected in two independent strains of Saccharomyces rouxii among 100 yeast strains other than Saccharomyces cerevisiae tested. The plasmids, pSR1 and pSR2, had almost the same mass (approximately 4 X 10(6) daltons) as 2-micrometers DNA of S. cerevisiae. pSR1 and pSR2 gave identical restriction maps with restriction endonucleases BamHI, EcoRI, HincII, HindIII, and XhoI, and both lacked restriction sites for PstI, SalI, and SmaI. These maps, however, differed significantly from that of S. cerevisiae 2-micrometers DNA. Restriction analysis also revealed two isomeric forms of each plasmid and suggested the presence of a pair of inverted repeat sequences in the molecules where intramolecular recombination took place. DNA-DNA hybridization between the pSR1 and pSR2 DNAs indicated significant homology between their base sequences, whereas no homology was detected between pSR1 and pJDB219, a chimeric plasmid constructed from a whole molecule of 2-micrometers DNA, plasmid pMB9, and a 1.2-kilobase DNA fragment of S. cerevisiae bearing the LEU2 gene. A chimeric plasmid constructed with pSR1 and YIp1, the larger EcoRI-SalI fragment of pBR322 ligated with a 6.1-kilobase DNA fragment of S. cerevisiae bearing the HIS3 gene, could replicate autonomously in an S. cerevisiae host and produced isomers, presumably by intramolecular recombination at the inverted repeats.