gebhart/patrepeval huggingface dataset:
Improved Squalene Production via Modulation of the Methylerythritol 4-Phosphate Pathway and Heterologous Expression of Genes from Streptomyces peucetius ATCC 27952 in Escherichia coli (2009)

Putative hopanoid genes from Streptomyces peucetius were introduced into Escherichia coli to improve the production of squalene, an industrially important compound. High expression of hopA and hopB (encoding squalene/phytoene synthases) together with hopD (encoding farnesyl diphosphate synthase) yielded 4.1 mg/liter of squalene. This level was elevated to 11.8 mg/liter when there was also increased expression of dxs and idi, E. coli genes encoding 1-deoxy-d-xylulose 5-phosphate synthase and isopentenyl diphosphate isomerase.
A Novel Peptide Isolated from a Phage Display Library Inhibits Tumor Growth and Metastasis by Blocking the Binding of Vascular Endothelial Growth Factor to Its Kinase Domain Receptor (2002)

Vascular endothelial growth factor (VEGF), one of the most important angiogenic factors, plays an essential role in both physiological and pathological angiogenesis. The VEGF receptor KDR/Flk-1 (a kinase domain receptor) mediates various biological activities of VEGF related to proliferation, differentiation, and migration of endothelial cells. Here we present a novel peptide designated K237-(HTMYYHHYQHHL), which was isolated from a phage-displayed peptide library, binding to KDR with high affinity and specificity. By interfering with the VEGF-KDR interaction, the peptide K237 inhibited proliferation of cultured primary human umbilical vein endothelial cells induced by recombinant human VEGF(165) in a dose-dependent and cell type-specific manner. The peptide also exerted an anti-angiogenesis activity in vivo as revealed using the chick embryo chorioallantoic membrane angiogenesis assay. Moreover, the peptide K237 significantly inhibited the growth of solid tumors implanted beneath the breasts and their metastases to lungs in severe combined immunodeficient mice. Taken together, these findings suggest that the peptide K237 can functionally disrupt the interaction between VEGF and the KDR receptor and cause potent biological effects that include the inhibition of angiogenesis and tumor growth. As a consequence, this peptide (and its future derivatives) may have use as a potential cancer therapy.
Phylogenetic Analysis of Enteroaggregative and Diffusely Adherent Escherichia coli (1999)

The phylogenetics of the various pathotypes of diarrheagenic Escherichia coli are not completely understood. In this study, we identified several plasmid and chromosomal genes in the pathogenic enteroaggregative E. coli (EAEC) prototype strain 042 and determined the prevalence of these loci among EAEC and diffusely adherent E. coli strains. The distribution of these genes is analyzed within an evolutionary framework provided by the characterization of allelic variation in housekeeping genes via multilocus enzyme electrophoresis. Our data reveal that EAEC strains are heterogeneous with respect to chromosomal and plasmid-borne genes but that the majority harbor a member of a conserved family of virulence plasmids. Comparison of plasmid and chromosomal relatedness of strains suggests clonality of chromosomal markers and a limited transfer model of plasmid distribution.
Comparison study of semi-crystalline and highly crystalline multiwalled carbon nanotubes (2001)

Very different types of straight and long multiwalled carbon nanotubes, ranging from semi-crystalline to highly crystalline, are obtained using a floating reactant method, by merely changing the flow rate of the carrier gas. Graphitization behaviors of these nanotubes are studied comparatively in terms of their microstructure and morphology, showing a large change in structure for the semi-crystalline nanotubes, but little change in the highly crystalline nanotubes with heat treatment.
Evaluating the Effect of Force Feedback in Cell Injection (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Conventional methods of manipulating individual biological cells have been prevalent in the field of molecular biology. These methods do not have the ability to provide force feedback to an operator. Poor control of cell injection force is one of the primary reasons for low success rates in cell injection and transgenesis in particular. Therefore, there exists a need to incorporate force feedback into a cell injection system. We have developed a force feedback interface, which has the capability of measuring forces in the range of <formula formulatype="inline"><tex>$\mu{\rm N}$</tex></formula> and provide a haptic display of the cell injection forces in real time. Using this force feedback interface, we performed several human factors studies to evaluate the effect of force feedback on cell injection outcomes. We tested our system with 40 human subjects and our experimental results indicate that the subjects were able to feel the cell injection force and confirmed our research hypothesis that the use of combined vision and force feedback leads to a higher success rate in cell injection task compared to using vision feedback alone. </para>
Application of self-assembled ultra-thin film coatings to stabilize macromolecule encapsulation in alginate microspheres (2005)

Alginate-based hydrogels have several unique properties that have enabled them to be used as a matrix for the entrapment of a variety of enzymes, proteins and cells for applications in bioprocessing, drug delivery and chemical sensing. However, control over release rates or, in some cases, stable encapsulation remains a difficult goal, especially for small particles with high surface-area-to-volume ratios. In this work, the potential to limit diffusion of macromolecules embedded in alginate spheres with nanofilm coatings was assessed. Alginate microspheres were fabricated using an emulsification process with high surfactant concentration to form beads in the size range of 2-10 microm. Using calcium chloride for ionotropic gelation, dextran was encapsulated in the gel phase by mixing with the alginate in solution. The exterior surface was then modified with polyelectrolyte coatings using the layer-by-layer self assembly technique. Leaching studies to assess retention of dextran with varying molecular weights confirmed that the application of multi-layer thin films to the alginate microspheres was effective in reducing leaching rate and total loss of the encapsulated material from the microspheres. For the best case, the rate of release for dextran of 2,000,000 Dalton molecular weight decreased from 1% h(-1) in bare microspheres to 0.1% h(-1) in polyelectrolyte-coated microspheres. The effectiveness of nanofilms reducing loss of the encapsulated macromolecules was found to vary between different polycation materials used. These studies support the feasibility of using these microsystems for development of long-term stable encapsulated systems, such as implantable biosensors.
Partial SOI LDMOSFETs for high-side switching (2003)

This paper describes the switching characteristics of Partial SOI LDMOSFET's in high-side configuration based on the results of numerical simulations. The effects of the substrate bias on the on-state and output capacitances of a device on a Partial SOI substrate are discussed and compared to a conventional SOI substrate. It is shown that having the Partial SOI LDMOSFETs operating in source-high conditions will help to achieve a faster turn-off due to reduced parasitic capacitances. In addition, it is shown that the turn-off speed of Partial SOI LDMOSFETs is at least 3 times higher than of conventional SOI LDMOSFETs.
mRNA stability in mammalian cells (1995)

This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end.
Influence of age on wound healing and fibrosis (2012)

The incidence and severity of fibrotic lung diseases increase with age, but very little is known about how age-related changes affect the mechanisms that underlie disease emergence and progression. Normal ageing includes accumulation of DNA mutations, oxidative and cell stresses, mitochondria dysfunction, increased susceptibility to apoptosis, telomere length dysfunction and differential gene expression as a consequence of epigenetic changes and miR regulation. These inevitable ageing-related phenomena may cause dysfunction and impaired repair capacity of lung epithelial cells, fibroblasts and MSCs. As a consequence, the composition of the extracellular matrix changes and the dynamic interaction between cells and their environment is damaged, resulting ultimately in predisposition for several diseases. This review summarizes what is known about age-related molecular changes that are implicated in the pathobiology of lung fibrosis in lung tissue.
Molecular considerations for development of phage antibody libraries (2011)

Nowadays, phage display libraries are used as robust tools for discovery and evolution of peptide/protein based drugs as well as targeting molecules, in particular monoclonal antibodies (mAbs) and its fragments (i.e., scFvs, Fabs, or bivalent F(ab')₂). Phage display technology, as a molecular diversity approach, enables selection of antibody fragments (e.g., scFv/Fab) with high affinity, specificity and effector functions against various targets. However, such selection process itself is largely dependent upon various molecular factors such as methods for construction of phage library, phage/phagemid vectors, helper phage, host cells and biopanning processes. The current review article provides important molecular considerations for successful development of phage antibody libraries that may be used as a platform for translation of antibody fragments into viable diagnostic/therapeutic reagents.
Synthesis of N-(3-Fluoro-2-phosphonomethoxypropyl) (FPMP) Derivatives of Heterocyclic Bases (1993)

A new group of compounds has been prepared: N -(3-fluoro-2-phosphonomethoxypropyl) (FPMP) derivatives of purine and pyrimidine bases which exhibit a significant selective activity against a broad spectrum of retroviruses. Racemic N -(3-fluoro-2-phosphonomethoxypropyl) derivatives of adenin ( V ), guanine ( IX ), cytosine ( XIII ), 2,6-diaminopurine ( XXI ), 3-deazaadenin e( XVII ), xanthine ( X ) and hypoxanthin ( VI ) were prepared from the corresponding N -(3-fluoro-2-hydroxypropyl) derivatives after protection of amino group at the heterocyclic ring by selective benzoylation, reaction with diisopropyl p -toluenesulfonyloxymethylphosphonate ( II ), and subsequent removal of the protecting groups. Chiral FPMP derivatives were prepared by reaction of heterocyclic base with the corresponding chiral synthon ( XXX, XXXVII ) followed by deprotection. The required chiral synthons were obtained from enantiomeric 3-fluoro-1,2-propanediols by two methods. In the first, the primary hydroxyl group was tritylated, the obtained derivative was reacted with compound II , the trityl group was removed and the product was mesylated to give synthon XXXVII . The second pathway consisted in selective tosylation of the primary hydroxyl group and conversion of the secondary hydroxyl into the acetoxymethyl ether via the methoxymethyl ether; treatment of the acetoxy compound with bromotrimethylsilane and triisopropyl phosphite afforded the desired synthon XXX .
The genus Cladosporium (2012)

Cladosporium allicinum (Fr.: Fr.) Bensch, U. Braun & Crous, comb. nov., C. astroideum var. catalinense U. Braun, var. nov., Fusicladium tectonicola (Yong H. He & Z.Y. Zhang) U. Braun & Bensch, comb. nov., Septoidium uleanum (Henn.) U. Braun, comb. nov., Zasmidium adeniae (Hansf.) U. Braun, comb. nov., Zasmidium dianellae (Sawada & Katsuki) U. Braun, comb. nov., Zasmidium lythri (Westend.) U. Braun & H.D. Shin, comb. nov., Zasmidium wikstroemiae (Petch) U. Braun, comb. nov.
Identification of Yeast Cofilin Residues Specific for Actin Monomer and PIP2 Binding (2001)

Cofilin/ADF is a ubiquitous actin-binding protein that is important for rapid actin dynamics in vivo. The long alpha-helix (helix 3 in yeast cofilin) forms the most highly conserved region in cofilin/ADF proteins, and residues in the NH2-terminal half of this alpha-helix have been shown to be essential for actin binding in cofilin/ADF. Recent studies also suggested that the basic residues in the COOH-terminal half of this alpha-helix would play an important role in F-actin binding. In contrast to these studies, we show here that the charged residues in the COOH-terminal half of helix 3 are not important for actin filament binding in yeast cofilin. Mutations in these residues, however, result in a small defect in actin monomer interactions. We also show that yeast cofilin can differentiate between various phosphatidylinositides, and mapped the PI(4,5)P2 binding site by using a collection of cofilin mutants. The PI(4,5)P2 binding site of yeast cofilin is a large positively charged surface that consists of residues in helix 3 as well as residues in other parts of the cofilin molecule. This suggests that cofilin/ADF proteins probably interact simultaneously with more than one PI(4,5)P2 molecule. The PI(4,5)P2-binding site overlaps with areas that are important for F-actin binding, explaining why the actin-related activities of cofilin/ADF are inhibited by PI(4,5)P2. The biological roles of actin and PI(4,5)P2 interactions of cofilin are discussed in light of phenotypes of specific yeast strains carrying mutations in residues that are important for actin and PI(4,5)P2 binding.
Chalcone carboxylic acids. Potent differentiation inducers of human promyelocytic cells HL-60. (1985)

Alkyl-substituted chalcone-4'-carboxylic acids are very potent inducers of differentiation of human promyelocytic cells HL-60. The differentiated cells are morphologically and functionally granulocytes.
Interactive ray tracing for isosurface rendering (1998)

We show that it is feasible to perform interactive isosurfacing of very large rectilinear datasets with brute-force ray tracing on a conventional (distributed) shared-memory multiprocessor machine. Rather than generate geometry representing the isosurface and render with a z-buffer, for each pixel we trace a ray through a volume and do an analytic isosurface intersection computation. Although this method has a high intrinsic computational cost, its simplicity and scalability make it ideal for large datasets on current high-end systems. Incorporating simple optimizations, such as volume bricking and a shallow hierarchy, enables interactive rendering (i.e. 10 frames per second) of the 1 GByte full resolution Visible Woman dataset on an SGI Reality Monster. The graphics capabilities of the Reality Monster are used only for display of the final color image.
Molecular indexing of human genomic DNA (2001)

Molecular indexing sorts DNA fragments into subsets for inter-sample comparisons. Type IIS or interrupted palindrome restriction endonucleases, which result in single-stranded ends not including the original recognition sequence of the enzyme, are used to produce the fragments. The ends can then be any sequence but will always be specific for a given fragment. Fragments with particular ends are selected by ligation to a corresponding indexing adapter. We describe iterative indexing, a new process that after an initial round of indexing uses a Type IIS restriction endonuclease to expose additional sequence for further indexing. New plasmids, pINDnn, were produced for novel use as indexing adapters. Together, the plasmids index all 16 possible dinucleotides. Their large size can be increased by dimerisation in vitro and allows the isolation of indexed material by size separation. Fragments produced from human genomic DNA by Type II restriction endonucleases were sorted using six bases in total to a possible enrichment of 1920-fold. By comparison with the public human sequence databases, fidelity of indexing was shown to be high and was tolerant of repetitive sequences. Genome-wide comparisons on a candidate or non-candidate basis are made possible by this approach.
Improved Methodology for the Preparation of Water-Soluble Maleimide-Functionalized Small Gold Nanoparticles (2012)

Improved methodology to prepare maleimide-functionalized, water-soluble, small (<3 nm) gold nanoparticles using a retro-Diels-Alder strategy that we developed for similar organic-soluble AuNP's is described. Importantly, our results suggest that a recent paper by Zhu, Waengler, Lennox, and Schirrmacher describing a similar strategy gave results inconsistent with the formation of the titled maleimide-modified AuNP (Zhu, J.; Waengler, C.; Lennox, R. B.; Schirrmacher, R. Langmuir2012, 28, 5508) as the major product, but consistent with the major product being an adduct derived from the hydrolysis of maleimide formed under the conditions used for the required deprotection of the maleimide. Our methodology provides an efficient and accessible route to pure maleimide-modified small AuNP's that circumvents the formation of the hydrolysis product. The maleimide-modified small AuNP's are versatile because they are soluble in water and in a wide range of organic solvents and their reactivity can now be properly exploited as a reactive moiety in Michael addition for bioconjugation studies in aqueous solution.
Indoleamine 2,3-dioxygenase-expressing dendritic cells are involved in the generation of CD4+CD25+regulatory T cells in Peyer's patches in an orally tolerized, collagen-induced arthritis mouse model (2008)

Our data suggest that tolerogenic CD11c+ DCs are closely linked with the induction of oral tolerance through an IDO-dependent mechanism and that this pathway may provide a new therapeutic modality to treat autoimmune arthritis.
Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains (2002)

RNA ligases participate in repair, splicing, and editing pathways that either reseal broken RNAs or alter their primary structure. Bacteriophage T4 RNA ligase (gp63) is the best-studied member of this class of enzymes, which includes yeast tRNA ligase and trypanosome RNA-editing ligases. Here, we identified another RNA ligase from the bacterial domain--a second RNA ligase (Rnl2) encoded by phage T4. Purified Rnl2 (gp24.1) catalyzes intramolecular and intermolecular RNA strand joining through ligase-adenylate and RNA-adenylate intermediates. Mutational analysis identifies amino acids required for the ligase-adenylation or phosphodiester synthesis steps of the ligation reaction. The catalytic residues of Rnl2 are located within nucleotidyl transferase motifs I, IV, and V that are conserved in DNA ligases and RNA capping enzymes. Rnl2 has scant amino acid similarity to T4 gp63. Rather, Rnl2 exemplifies a distinct ligase family, defined by variant motifs, that includes the trypanosome-editing ligases and a group of putative RNA ligases encoded by eukaryotic viruses (baculoviruses and an entomopoxvirus) and many species of archaea. These findings have implications for the evolution of covalent nucleotidyl transferases and virus-host dynamics based on RNA restriction and repair.
The CCR5 and CXCR4 Coreceptors—Central to Understanding the Transmission and Pathogenesis of Human Immunodeficiency Virus Type 1 Infection (2004)

In this review, we will discuss what is known, what is suspected, and what still remains obscure about the central role played by coreceptor expression and usage in the transmission and pathogenic consequences of human immunodeficiency virus type 1 (HIV-1) infection. An emphasis will be on the HIV-1 phenotypic variants that are defined by their usage of the CCR5 or CXCR4 coreceptors, and how the different cellular tropism of these variants influences how and where HIV-1 replicates in vivo. We will also review what might happen when coreceptor antagonists are used clinically to treat HIV-1 infection.
Cervical Pedicle Screws (2000)

The use of a computer-assisted image guidance system did not enhance safety or accuracy in placing pedicle screws compared with Abumi's technique. Both techniques have a noteworthy risk of injuring a critical structure if inserted into the pedicles with a diameter of less than 4.5 mm. Under laboratory conditions, pedicles with a diameter of more than 4.5 mm have a significantly greater likelihood of being safely instrumented by either technique. These data indicate that cervical pedicle screw placement is feasible, but it should be reserved for selected circumstances with clear indications and in the presence of suitable pedicle morphology.
Importance of Nitric Oxide Synthase in the Control of Infection by Bacillus anthracis (2006)

The spore-forming, gram-positive bacterium Bacillus anthracis, the causative agent of anthrax, has achieved notoriety due to its use as a bioterror agent. In the environment, B. anthracis exists as a dormant endospore. Upon infection, germination of endospores occurs during their internalization within the phagocyte, and the ability to survive exposure to antibacterial killing mechanisms, such as O2*-, NO*, and H2O2, is a key initial event in the infective process. Macrophages generate NO* from the oxidative metabolism of L-arginine, using an isoform of nitric oxide synthase (NOS 2). Exposure of murine macrophages (RAW264.7 cells) to B. anthracis endospores up-regulated the expression of NOS 2 12 h after exposure, and production of NO* was comparable to that achieved following other bacterial infections. Spore-killing assays demonstrated a NO*-dependent bactericidal response that was significantly decreased in the presence of the NOS 2 inhibitor L-N6-(1-iminoethyl)lysine and in L-arginine-depleted media. Interestingly, we also found that B. anthracis bacilli and endospores exhibited arginase activity, possibly competing with host NOS 2 for its substrate, L-arginine. As macrophage-generated NO* is an important pathway in microbial killing, the ability of endospores of B. anthracis to regulate production of this free radical has important implications in the control of B. anthracis-mediated infection.