gebhart/patrepeval huggingface dataset:
Use of Polymerase Chain Reaction for the Rapid Construction of Synthetic Genes (2003)

Although the polymerase chain reaction (PCR) (1,2) is invaluable for the cloning and manipulation of existing DNA sequences, PCR also makes it possible to create new DNA fragments consisting of a nucleic acid sequence that is specified entirely by the investigator. In this chapter we describe a simple two-step PCR method for the rapid construction of synthetic genes (3). This method is based on early observations by Mullis et al. (4) in which multiple overlapping oligonucleotides could be used to generate synthetic DNA through several sequential rounds of Klenow-based PCR amplification. The method described in this chapter utilizes the thermostabile Taq polymerase and allows for the generation of synthetic genes in as little as 1 d. This method has proven useful in studies in which synthetic genes were constructed for the HIV-2 Rev protein (3,5) and the Wilms' tumor locus zinc finger protein (6). Furthermore, this method has been successfully employed in extensive mutagenesis of the HIV-1 rev response element (7).
Identification of a glycine-rich sequence as an NAD(P)H-binding site and tyrosine 128 as a dicumarol-binding site in rat liver NAD(P)H:quinone oxidoreductase by site-directed mutagenesis. (1992)

Site-directed mutagenesis was utilized to identify binding sites for NAD(P)H and dicumarol in rat liver NAD(P)H:quinone oxidoreductase (NQOR, EC 1.6.99.2). The mutant cDNA clones were generated by a procedure based on the polymerase chain reaction and were expressed in Escherichia coli. The mutant enzymes were purified to apparent homogeneity as judged by SDS-polyacrylamide gel electrophoresis and were found to contain 2 FADs/enzyme molecule identical with that of the wild-type NQOR. Purified mutant enzymes Y128D, G150F, G150V, S151F, and Y155D showed dramatic decreases in activities in the reduction of dichlorophenolindophenol in comparison with the activities of the wild-type enzyme, whereas the activities of F124L, T127V, T127E, Y128V, Y128F, S151A, and Y155V were similar to those of NQOR. Enzyme kinetic analysis revealed that the Km values of T127E, Y128D, G150F, G150V, S151F, and Y155D were, respectively, 4-, 2-, 13-, 5-, 26-, and 19-fold higher than the Km of NQOR for NADPH, and were, respectively, 2-, 3-, 7-, 3-, 20-, and 11-fold higher than that of NQOR for NADH. The kcat values of Y128D, G150F, and G150V were also much lower than those of NQOR, but the kcat values of other mutants were similar to those of the wild-type enzyme. The Km values of the mutants for dichlorophenolindophenol were the same or slightly higher than that of NQOR. The apparent inhibition constants (Ki) for dicumarol on Y128V and F124L were elevated 12 and 8 times, respectively. Similar, but smaller, changes on Ki for 4-hydroxycoumarin were also observed. This study demonstrated that residues Gly150, Ser151, and Tyr155 in the glycine-rich region of NQOR are essential for NADPH and NADH binding and Tyr128 is important for dicumarol binding. Based on the results of the study, it is proposed that the glycine-rich region of the enzyme, along with other residues around the region, forms a beta sheet-turn-alpha helix structure important for the binding of the pyrophosphate group of NADPH and NADH.
Controlled ring‐opening polymerization of propylene oxide catalyzed by double metal‐cyanide complex (2002)

Abstract A double metal‐cyanide catalyst based on Zn 3 [Co(CN) 6 ] 2 was prepared. This catalyst is very effective for the ring‐opening polymerization of propylene oxide. Polyether polyols of moderate molecular weight having low unsaturation (&lt;0.015 meq/g) can be prepared under mild conditions. The molecular weight of polymer is entirely controlled by a reacted monomer‐to‐initiator ratio. The polymers prepared with stepwise addition of monomer exhibit a narrower molecular weight distribution as compared with those prepared with one‐step addition of monomer. Various compounds containing active hydrogen, except basic compounds and low‐carbon carboxylic acid, may be used as initiators. The reaction rate increases with increasing catalyst amount and decreases with rising initiator concentration. Polymerization involves a rapid exchange reaction between the active species and the dormant species. It was also proven that, to a certain extent, the chain termination of this catalytic system is reversible or temporary. 13 C NMR analysis showed that the polymer has a random distribution of the configurational sequences and head‐to‐tail regiosequence. It is assumed that the polymerization proceeds via a cationic coordination mechanism. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1142–1150, 2002
Discovery of Efficacious Pseudomonas aeruginosa-Targeted Siderophore-Conjugated Monocarbams by Application of a Semi-mechanistic Pharmacokinetic/Pharmacodynamic Model (2015)

To identify new agents for the treatment of multi-drug-resistant Pseudomonas aeruginosa, we focused on siderophore-conjugated monocarbams. This class of monocyclic β-lactams are stable to metallo-β-lactamases and have excellent P. aeruginosa activities due to their ability to exploit the iron uptake machinery of Gram-negative bacteria. Our medicinal chemistry plan focused on identifying a molecule with optimal potency and physical properties and activity for in vivo efficacy. Modifications to the monocarbam linker, siderophore, and oxime portion of the molecules were examined. Through these efforts, a series of pyrrolidinone-based monocarbams with good P. aeruginosa cellular activity (P. aeruginosa MIC90 = 2 μg/mL), free fraction levels (>20% free), and hydrolytic stability (t1/2 ≥ 100 h) were identified. To differentiate the lead compounds and enable prioritization for in vivo studies, we applied a semi-mechanistic pharmacokinetic/pharmacodynamic model to enable prediction of in vivo efficacy from in vitro data.
A system architecture for context-aware mobile computing (1995)

Computer applications traditionally expect a static execution environment. However, this precondition is generally not possible for mobile systems, where the world around an application is constantly changing. This thesis explores how to support and also exploit the dynamic configurations and social settings characteristic of mobile systems. More specifically, it advances the following goals: (1) enabling seamless interaction across devices; (2) creating physical spaces that are responsive to users; and (3) and building applications that are aware of the context of their use. Examples of these goals are: continuing in your office a program started at home; using a PDA to control someone else&amp;apos;s windowing UI; automatically canceling phone forwarding upon return to your office; having an airport overheaddisplay highlight the flight information viewers are likely to be interested in; easily locating and using the nearest printer or fax machine; and automatically turning off a PDA&amp;apos;s audible e-mail notification when in a meeting.
Lack of correlation between N-myc and MAX expression in neuroblastoma tumors and in cell lines: implication for N-myc-MAX complex formation. (1994)

Detectable levels of MAX messenger RNA were found in a set of human neuroblastoma tumors and established cell lines. MAX mRNA levels were independent of tumor stage and N-myc genomic amplification. By contrast, N-myc mRNA transcripts were detectable only in tumors with amplification of N-myc gene and in cell lines. Analysis by reverse transcriptase polymerase chain reaction and hybridization to specific oligodeoxynucleotide probes revealed approximately equal amounts of two MAX transcripts in all cases analyzed. Immunoprecipitations with a specific antibody to MAX detected two proteins of M(r) 21,000 and 22,000 in approximately equal amounts in all neuroblastoma lines regardless of N-myc amplification and/or expression. On the other hand, protein binding to the myc DNA consensus sequence correlated with N-myc expression in neuroblastoma cells. Thus, N-myc expression might be a limiting factor in the formation of the N-myc-MAX heterodimer in neuroblastomas.
Dual-Modality Image-Guided Surgery of Prostate Cancer with a Radiolabeled Fluorescent Anti-PSMA Monoclonal Antibody (2014)

Dual-labeled (111)In-DTPA-D2B-IRDye800CW enables specific and sensitive detection of prostate cancer lesions in vivo with micro-SPECT/CT and NIRF imaging. In addition to preoperative micro-SPECT/CT imaging to detect tumors, NIRF imaging enables image-guided surgical resection. These preclinical findings warrant clinical studies with (111)In-DTPA-D2B-IRDye800CW to improve tumor detection and resection in prostate cancer patients.
Metallocenes : synthesis, reactivity, applications (1998)

Part 1 Synthesis and reactivity: main group metallocenes lanthanocenes roup 3 metallocenes titanocenes zirconocenes group 5 and 6 metallocenes half-sandwich complexes as metallocene analogs synthesis of chiral titanocene and zirconocene dichlorides. Part 2 applications: metallocene catalysts for olefin polymerization chiral titanocenes and zirconocenes in synthesis new chiral ferrocenyl ligands for asymmetric catalysis metallocene-based polymers.
Targeting HSP70 induced thermotolerance for design of thermal sensitizers (2002)

Thermal therapy has been shown to be an extremely powerful anti-cancer agent and a potent radiation sensitizer. However, the full potential of thermal therapy is hindered by a number of considerations including highly conserved heat resistance pathways in tumour cells and inhomogeneous heating of deep-seated tumours due to energy deposition and perfusion issues. This report reviews recent progress in the development of hyperthermia sensitizing drugs designed to specifically amplify the effects of hyperthermia. Such agents might be particularly useful in situations where heating is not adequate for the full biological effect or is not homogeneously delivered to tumours. The particular pathway concentrated on is thermotolerance, a complex, inducible cellular response that leads to heat resistance. This paper will concentrate on the molecular pathways of thermotolerance induction for designing inhibitors of heat resistance/thermal sensitizers, which may allow the full potential of thermal therapy to be utilized.
Reduction in BACE1 decreases body weight, protects against diet-induced obesity and enhances insulin sensitivity in mice (2011)

Insulin resistance and impaired glucose homoeostasis are important indicators of Type 2 diabetes and are early risk factors of AD (Alzheimer's disease). An essential feature of AD pathology is the presence of BACE1 (β-site amyloid precursor protein-cleaving enzyme 1), which regulates production of toxic amyloid peptides. However, whether BACE1 also plays a role in glucose homoeostasis is presently unknown. We have used transgenic mice to analyse the effects of loss of BACE1 on body weight, and lipid and glucose homoeostasis. BACE1-/- mice are lean, with decreased adiposity, higher energy expenditure, and improved glucose disposal and peripheral insulin sensitivity than wild-type littermates. BACE1-/- mice are also protected from diet-induced obesity. BACE1-deficient skeletal muscle and liver exhibit improved insulin sensitivity. In a skeletal muscle cell line, BACE1 inhibition increased glucose uptake and enhanced insulin sensitivity. The loss of BACE1 is associated with increased levels of UCP1 (uncoupling protein 1) in BAT (brown adipose tissue) and UCP2 and UCP3 mRNA in skeletal muscle, indicative of increased uncoupled respiration and metabolic inefficiency. Thus BACE1 levels may play a critical role in glucose and lipid homoeostasis in conditions of chronic nutrient excess. Therefore strategies that ameliorate BACE1 activity may be important novel approaches for the treatment of diabetes.
Molecular cloning, sequencing, and identification of a metalloprotease gene from Listeria monocytogenes that is species specific and physically linked to the listeriolysin gene (1991)

The entire nucleotide sequence of an open reading frame located immediately downstream of the listeriolysin gene from a virulent Listeria monocytogenes serotype 1/2a strain was determined. The product of the open reading frame was 510 amino acids with a predicted molecular weight of 57,400. The deduced amino acid sequence of this open reading frame is highly similar to that of a family of secreted metalloproteases produced by various members of the genus Bacillus, of which thermolysin is the prototype. Immunoblots performed with specific antisera raised against thermolysin from Bacillus stearothermophilus allowed the detection of a 60-kDa polypeptide, corresponding to the pro-form of the protease, in culture supernatants of L. monocytogenes strains. In maxicell experiments, Escherichia coli recombinants harboring this open reading frame also specifically directed production of a 60-kDa protein. Protease activity was low to undetectable in both Listeria strains and E. coli recombinants. This is due to lack of processing of the inactive pro-form of the protease to its mature active form in both species. We have designated this gene mpl for metalloprotease of L. monocytogenes. The gene was present only in pathogenic L. monocytogenes strains, in which it was physically linked to the listeriolysin gene.
CD4+ Peptide Epitopes from the WT1 Oncoprotein Stimulate CD4+ and CD8+ T Cells That Recognize and Kill Leukemia and Solid Tumor Cells. (2006)

Abstract Wilms tumor protein 1 (WT1) is a transcription factor over-expressed in several types of leukemias and solid tumors, making it an ideal target for immunotherapy. A number of class I binding WT1 peptides have been identified and shown to stimulate CD8+ T cells. These peptides are being tested as potential cancer vaccine candidates in a variety of clinical trials. However, the induction and maintenance of a robust memory CD8+ cytotoxic T cell response requires CD4+ T cell help. Herein we report the identification of three HLA Class II peptide epitopes of WT1 using the SYFPEITHI and RANKPEP predictive algorithms. Peptides 328–349 and 423–441 are able to stimulate a peptide specific CD4+ response that can recognize WT1 positive tumor cells in multiple HLA-DRB*1 settings, as determined by IFN-gamma ELISPOT assays. Due to the highly polymorphic nature of the HLA class II alleles, such broad reactivity is critical in the development of a universal therapeutic. In addition, we identified a WT1 CD4+ peptide epitope (122–140) that lies within close proximity to a previously identified CD8+ peptide epitope (126–134). Residue 126 was mutated from an Arginine (R) to a Tyrosine (Y) thereby embedding a synthetic immunogenic analog CD8+ peptide that was previously designed to improve immunogenicity and induce a potent CD8+ response. Mutated peptide 122–140 is able to induce a CD4+ and cytotoxic CD8+ WT1 specific T cell response that can recognize the native WT1 epitopes on the surface of human CML and solid tumor cells. Cross-priming experiments demonstrated that APCs pulsed with either CML or mesothelioma tumor lysates can process and present each of the CD4+ peptides identified. These studies provide the rationale for using the three WT1 CD4+ peptides in conjunction with CD8+ peptide epitopes to vaccinate patients with WT1 expressing cancers.
Prohibitin in breast cancer cell lines: loss of antiproliferative activity is linked to 3' untranslated region mutations. (1996)

The evolutionarily conserved prohibitin gene is located on human chromosome 17q21, and two alleles have been identified. Our previous studies characterizing prohibitin in immortalized cells, classified into four complementation groups (A-D) based on the ability of whole-cell hybrids to become senescent, have suggested that it has tumor suppressor activity in group B cells. Only the cell lines assigned to group B are sensitive to the antiproliferative activity of prohibitin, and all are homozygous for an allele designated B because of its exclusive association with this group. Prohibitin genotyping of 22 breast cancer cell lines identified 17 homozygous for the B allele, 5 homozygous for the non-B allele, and no heterozygotes. Four of these cell lines were chosen for further characterization of prohibitin. In cell proliferation assays, the homozygous B breast cancer cell lines (BT-20, SK-BR-3, and MCF7) are all inhibited from traversing the cell cycle following the introduction of wild-type prohibitin transcripts. The cell line homozygous for the alternative non-B allele (BT-549) is not inhibited by transcripts. All of the breast cancer cell lines overexpress the longer form of the prohibitin mRNA (1.9 kb) and the protein. Mutational analysis of the protein-coding region detected no mutations in any of the lines. However, BT-20, SK-BR-3, and MCF7 cells are all mutated in the final 200 bases of the 3' untranslated region (3'UTR) exclusive to the 1.9-kb transcript, but BT-549 cells had no alterations in this region of the 3'UTR. Functional mapping experiments performed in the mutated SK-BR-3 line showed that the wild-type 3'UTR alone is sufficient to inhibit cell cycle progression, indicating that the antiproliferative activity of the prohibitin transcript is localized to this region. Overall, our results show that most (80%) of the cell lines derived from breast tumors have a common prohibitin genotype, suggesting that they belong to the same group of immortalized cells, group B. The results also show that the prohibitin 3'UTR exhibits the characteristics of a trans-acting regulatory RNA (riboregulator), the tumor suppressor activity of which is inactivated by mutation in group B immortalized cells.
Class Construction in C and C++: Object-Oriented Programming Fundamentals (1992)

A knowledge of C++ is often highly desirable and, in many cases, an essential skill in today's job market. In this book, specifically designed for C programmers interested in learning about C++, Sessions gives an introduction to the paradigm of object-oriented programming and the concept of developing classes. Developing classes in C++, developing them well, and learning to use them as building blocks for complex applications is the focus of this book. Sessions teaches object-oriented programming before C++, discusses the object-oriented subset of C++ (OOS/C++) and looks at this subset in detail.
Lipopolysaccharide-Binding Protein for Monitoring of Postoperative Sepsis: Complemental to C-Reactive Protein or Redundant? (2011)

During the first 14 days of postoperative sepsis, LBP plasma concentrations showed a time course that was very similar to CRP with a high concordance in the pattern of day-to-day changes. Furthermore, like CRP, LBP does not provide a reliable clue for outcome in this setting.
Eukaryotic Initiation Factor 4G-Poly(A) Binding Protein Interaction Is Required for Poly(A) Tail-Mediated Stimulation of Picornavirus Internal Ribosome Entry Segment-Driven Translation but Not for X-Mediated Stimulation of Hepatitis C Virus Translation (2001)

Efficient translation of most eukaryotic mRNAs results from synergistic cooperation between the 5' m(7)GpppN cap and the 3' poly(A) tail. In contrast to such mRNAs, the polyadenylated genomic RNAs of picornaviruses are not capped, and translation is initiated internally, driven by an extensive sequence termed IRES (for internal ribosome entry segment). Here we have used our recently described poly(A)-dependent rabbit reticulocyte lysate cell-free translation system to study the role of mRNA polyadenylation in IRES-driven translation. Polyadenylation significantly stimulated translation driven by representatives of each of the three types of picornaviral IRES (poliovirus, encephalomyocarditis virus, and hepatitis A virus, respectively). This did not result from a poly(A)-dependent alteration of mRNA stability in our in vitro translation system but was very sensitive to salt concentration. Disruption of the eukaryotic initiation factor 4G-poly(A) binding protein (eIF4G-PABP) interaction or cleavage of eIF4G abolished or severely reduced poly(A) tail-mediated stimulation of picornavirus IRES-driven translation. In contrast, translation driven by the flaviviral hepatitis C virus (HCV) IRES was not stimulated by polyadenylation but rather by the authentic viral RNA 3' end: the highly structured X region. X region-mediated stimulation of HCV IRES activity was not affected by disruption of the eIF4G-PABP interaction. These data demonstrate that the protein-protein interactions required for synergistic cooperativity on capped and polyadenylated cellular mRNAs mediate 3'-end stimulation of picornaviral IRES activity but not HCV IRES activity. Their implications for the picornavirus infectious cycle and for the increasing number of identified cellular IRES-carrying mRNAs are discussed.
Induced Pluripotent Reprogramming from Promiscuous Human Stemness‐Related Factors (2009)

Ectopic expression of pluripotency gene sets provokes nuclear reprogramming in permissive somatic tissue environments generating induced pluripotent stem (iPS) cells. The evolutionary conserved function of stemness orthologs was here tested through interspecies transduction. A spectrum of HIV-based lentiviral vectors was designed, and point mutations in the HIV-1 capsid region identified for efficient infectivity and expanded trans-species tropism. Human pluripotent gene sequences, OCT3/4, SOX2, KLF4 and c-MYC, packaged into engineered lentiviral expression vectors achieved consistent expression in non-human fibroblasts. Despite variation in primary amino-acid sequence between species, introduction of human pluripotent genes produced cell lines with embryonic stem cell-like morphology. Transduced fibroblasts differentiated in vitro into all three germ layers according to gastrulation gene expression profiles, and formed in vivo teratoma with multi-lineage potential. Reprogrammed progeny incorporated into non-human morula to produce blastomeres capable of developing into chimeric embryos with competent organogenesis. This model system establishes a prototypic approach to examine consequences of human stemness factors induced reprogramming in the context of normal embryonic development, exploiting non-human early stage embryos. Thus, ectopic xeno-transduction across species unmasks the promiscuous nature of stemness induction, suggesting evolutionary selection of core processes for somatic tissue reprogramming.
Self-assembled bionanostructures: proteins following the lead of DNA nanostructures (2014)

Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction.