gebhart/patrepeval huggingface dataset:
Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures ofEmiliania huxleyiStrain 1516 (2005)

The marine coccolithophorid Emiliania huxleyi is a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. The biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. Although it has been well documented that biomineralization in E. huxleyi is promoted by growth under phosphate-limited conditions, the genes and proteins that govern the processes of calcification and coccolithogenesis remain unknown. Suppressive subtractive hybridization (SSH) libraries were constructed from cultures grown in phosphate-limited and phosphate-replete media as tester and driver populations for reciprocal SSH procedures. Positive clones from each of the two libraries were randomly selected, and dot blotting was performed for the analysis of expression patterns. A total of 513 clones from the phosphate-replete library and 423 clones from the phosphate-limited library were sequenced, assembled, and compared to sequences in GenBank using BLASTX. Of the 103 differentially expressed gene fragments from the phosphate-replete library, 34% showed significant homology to other known proteins, while only 23% of the 65 differentially expressed gene fragments from the phosphate-limited library showed homology to other proteins. To further assess mRNA expression, real-time RT-PCR analysis was employed and expression profiles were generated over a 14-day time course for three clones from the phosphate-replete library and five clones from the phosphate-limited library. The fragments isolated provide the basis for future cloning of full-length genes and functional analysis.
Enantiodivergent Synthesis of (R)- and (S)-Rolipram (1998)

Both enantiomers of rolipram (1) have been prepared in large quantity from a common intermediate rac-3-(3’-cyclopentyloxy-4’-methoxy)phenyl-4-nitro butyric acid (6), which was resolved by way of the two readily separable diastereoisomeric amides obtained with (S)-(-)-phenylethylamine. Reduction of the nitro group and intramolecular transamidation gave (R)-(-)-1 and (S)-(+)-1, respectively. CD spectra of both enantiomers of rolipram are reported and discussed. Both enantiomers of rolipram presented the same potency of inhibitory activity against recombinant cyclic-AMP-selective phosphodiesterase (PDE4) subtypes.
BioLabs-On-A-Chip: Monitoring Cells using CMOS Biosensors (2006)

Cell clinics, CMOS/MEMS hybrid microsystems for capturing and in-situ investigation of living cells, aims at providing high-speed, automated, and economical cell monitoring. Integrated sensors are being developed for extracellular signal amplification, cell-substrate capacitance sensing, contact imaging, and fluorescence detection. We describe the methodology for characterizing the responses of these sensors to biological cells. We also present results obtained from the long-term monitoring of cells cultured on-chip using two of the sensors: (i) a bioamplifier, used for amplifying weak extracellular potentials from electrically active cells, and (ii) a cell-substrate capacitance sensor, used for tracking cell adhesion and assessing cell viability.
Cationic Lipid Binding to DNA:  Characterization of Complex Formation (1996)

We recently demonstrated that cationic lipids, added in monomer or micellar form, bind to DNA, resulting in the formation of a hydrophobic complex. This complex can serve as a well-defined intermediate in the preparation of DNA-lipid particles (DLPs) with many potential applications for delivery of polynucleotides in vitro and in vivo. To develop a better understanding of the factors governing complex formation, we have characterized the cationic lipid/DNA binding reaction. This was evaluated by measuring DNA and cationic lipid (DODAC) complex formation using the Bligh and Dyer extraction procedure. Efficient recovery of DNA (> 95%) in the organic phase was achieved when sufficient monocationic lipids interact with DNA phosphate groups. The rate of binding depends on the amount of DNA or cationic lipid present in the system. The time required to generate the hydrophobic complex was increased when < 10 micrograms of DNA or < 40 nmol of DODAC was present. Surprisingly, the rate of complex formation was contingent on the incubation period after partitioning the DNA/lipid mixture into organic and aqueous phases. These results suggest that the cationic lipid/DNA complex forms at the aqueous/organic interface and that DNA/lipid binding is dependent on multivalent interactions at this interface. A Scatchard analysis of DNA/DODAC binding demonstrated that the binding reaction exhibits a high degree of positive cooperativity. The apparent dissociation constant (Kn), using data obtained under conditions where DODAC binding to DNA approached saturation, indicated a high-affinity reaction (Kn > 10(-11) mol L-1). At this point, approximately 8400 mol of DODAC was bound per mole of DNA, which is equivalent to a charge ratio (+/-) of 0.585 for the 7.2 kb plasmid used and suggests that formation of the hydrophobic complex occurs at a stage prior to charge neutralization. The influence of other lipids on DNA/cationic lipid binding at the aqueous/organic interface was also studied. Cholesterol and DOPC had little effect on DNA/DODAC binding while the anionic lipids LPI, DOPS, and DMPG inhibited complex formation. The zwitterionic lipid DOPE, however, had a concentration-dependent effect on cationic lipid binding that was also dependent on the mixing order. We believe that this approach for evaluating lipid/DNA binding provides an effective procedure for assessing factors which control the dissociation of lipids from DNA and may be beneficial in the selection of lipids for effective use in gene transfection studies.
The role of the maltodextrin-binding site in determining the transport properties of the LamB protein. (1986)

We have examined by the liposome swelling technique the permeability properties of the modified LamB proteins isolated from mutants of Escherichia coli K12 with altered affinities toward starch and/or maltose (Ferenci, T., and Lee, K-S. (1982) J. Mol. Biol. 160, 431-444). The results revealed the following. A mutant strain exhibiting a markedly lowered affinity toward starch produced a LamB protein that has lost the ability to permeate longer maltodextrins. This protein retained a nonspecific pore for a wide variety of small sugars. A mutant strain with partially reduced affinity for starch produced a LamB protein which still permeated maltodextrins, maltose, and non-maltose sugars but had also gained an ability to permit the diffusion of sucrose and raffinose; in this strain sucrose and raffinose could now compete for the starch-binding site. A mutant with enhanced affinity for both maltose and starch produced a protein which exhibited elevated rates of diffusion for longer maltodextrins but still permeated other small sugars. Two other mutants with altered affinities showed relatively minor changes in the diffusion of maltose and non-maltose sugars. It could be concluded from these studies that the LamB proteins form pores allowing the diffusion of a wide variety of monosaccharides irrespective of the presence or the absence of affinity of a binding site for maltodextrins. However, the presence of a sugar-binding site is crucial in determining the rate of the diffusion of maltodextrins or other oligosaccharides.
Chaining layered integrity checks (1999)

No work the size of this dissertation is done in isolation, and I would like to thank the people who worked with and supported me over the last four years. Harold F. Bower has worked with me on numerous occasions. He found and added the entry points in the BIOS source to call AEGIS. He also served as a sounding board for me in the design of AEGIS, and the AEGIS interrupt service routine (ISR). Hal and I also worked together on a pre-cursor of AEGIS, the Security Enhanced Processor (SEP). The problems encountered with the SEP project lead to AEGIS. Hal is also responsible for RATBAG which is described in Chapter 3. Angelos Keromytis and I jointly designed the protocol used with the AEGIS network recovery and DHCP++. Angelos also served as the ideal person to discuss ideas. He is never shy about telling someone that their idea is nuts. Scott Alexander, Angelos, and I worked together on the design of SANE, Section 7.1. Scott’s contributions are “above the OS”, and mine are “below the OS”. Angelos worked with both Scott and myself, and developed the naming and threat models. Ralph Droms et. al. developed the DHCP authentication scheme described in Section 7.2. I developed the delayed aspect of the authentication mechanism along with the threat model.
Non-Destructive Method of Observing Inhomogeneities in p-n Junctions with a Chopped Photon Beam (1981)

A flying-spot scanner is constructed to obtain scanning images of p-n junctions made upon Si wafers, having diameters of 50 to 60 mm. The specimen is set upon a metal stage, and the junction surface is entirely covered with a 15-µm thick mylar sheet. A wide transparent electrode is put upon the sheet. A photon beam whose chopping frequency and diameter are 2 kHz and nearly 100 µm, respectively, irradiates the specimen through the transparent electrode and the mylar sheet. Ac photovoltages are measured. Variations of junction depths of 1.1 to 1.4 µm, and those of diffusion lengths in the substrate wafer are easily revealed with the present method.
Thrombospondin 1 Is an Autocrine Negative Regulator of Human Dendritic Cell Activation (2003)

Thrombospondin 1 (TSP) elicits potent antiinflammatory activities in vivo, as evidenced by persistent, multiorgan inflammation in TSP null mice. Herein, we report that DCs represent an abundant source of TSP at steady state and during activation. Human monocyte-derived immature dendritic cells (iDCs) spontaneously produce TSP, which is strongly enhanced by PGE2 and to a lesser extent by transforming growth factor (TGF) beta, two soluble mediators secreted by macrophages after engulfment of damaged tissues. Shortly after activation via danger signals, DCs transiently produce interleukin (IL) 12 and tumor necrosis factor (TNF) alpha, thereby eliciting protective and inflammatory immune responses. Microbial stimuli increase TSP production, which is further enhanced by IL-10 or TGF-beta. The endogenous TSP produced during early DC activation negatively regulates IL-12, TNF-alpha, and IL-10 release through its interactions with CD47 and CD36. After prolonged activation, DCs extinguish their cytokine synthesis and become refractory to subsequent stimulation, thereby favoring the return to steady state. Such "exhausted" DCs continue to release TSP but not IL-10. Disrupting TSP-CD47 interactions during their restimulation restores their cytokine production. We conclude that DC-derived TSP serves as a previously unappreciated negative regulator contributing to arrest of cytokine production, further supporting its fundamental role in vivo in the active resolution of inflammation and maintenance of steady state.
Modulation of α‐tropomyosin expression by α‐tocopherol in rat vascular smooth muscle cells (1999)

The effect of alpha-tocopherol (vitamin E) on gene expression in rat vascular smooth muscle cells was studied by the differential display technique. One gene out of about 1000 genes analyzed, identified as alpha-tropomyosin, showed an increased transcription level caused by alpha-tocopherol treatment. Northern and Western blot analysis revealed a time-dependent transient up-regulation of the amount of mRNA (peak between 2 and 3 h) and protein (peak at 5 h) in alpha-tocopherol-treated cells. No effect was observed in cells treated with beta-tocopherol.
Comparative thermodynamic analysis and integration issues of CCS steam power plants based on oxy-combustion with cryogenic or membrane based air separation (2009)

When realizing CSS steam power plants based on oxy-combustion, the energy demand for oxygen production is one of the main causes for efficiency losses. This comparative study focuses on the impact of the air separation technology - cryogenic as well as high temperature membrane based - on the efficiency of a coal-fired oxyfuel steam power plant. As a result of this study both show comparable efficiency potentials whereas the membrane based technology needs a higher degree of integration into the power cycle to compete efficiencies of the oxyfuel power plant with cryogenic ASU.
Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors (2007)

The human HDAC (histone deacetylase) family, a well-validated anticancer target, plays a key role in the control of gene expression through regulation of transcription. While HDACs can be subdivided into three main classes, the class I, class II and class III HDACs (sirtuins), it is presently unclear whether inhibiting multiple HDACs using pan-HDAC inhibitors, or targeting specific isoforms that show aberrant levels in tumours, will prove more effective as an anticancer strategy in the clinic. To address the above issues, we have tested a number of clinically relevant HDACis (HDAC inhibitors) against a panel of rhHDAC (recombinant human HDAC) isoforms. Eight rhHDACs were expressed using a baculoviral system, and a Fluor de Lystrade mark (Biomol International) HDAC assay was optimized for each purified isoform. The potency and selectivity of ten HDACs on class I isoforms (rhHDAC1, rhHDAC2, rhHDAC3 and rhHDAC8) and class II HDAC isoforms (rhHDAC4, rhHDAC6, rhHDAC7 and rhHDAC9) was determined. MS-275 was HDAC1-selective, MGCD0103 was HDAC1- and HDAC2-selective, apicidin was HDAC2- and HDAC3-selective and valproic acid was a specific inhibitor of class I HDACs. The hydroxamic acid-derived compounds (trichostatin A, NVP-LAQ824, panobinostat, ITF2357, vorinostat and belinostat) were potent pan-HDAC inhibitors. The growth-inhibitory effect of the HDACis on HeLa cells showed that both pan-HDAC and class-I-specific inhibitors inhibited cell growth. The results also showed that both pan-HDAC and class-I-specific inhibitor treatment resulted in increased acetylation of histones, but only pan-HDAC inhibitor treatment resulted in increased tubulin acetylation, which is in agreement with their activity towards the HDAC6 isoform.
Gene Targeting with Viral Vectors (2005)

Genetic manipulation of cells for scientific and therapeutic goals can be achieved by both gene-addition and gene-targeting methods. Gene targeting precisely alters a gene in its natural chromosome location, providing distinct advantages over gene-addition approaches. Classic gene-targeting delivery systems (microinjection, electroporation, or calcium phosphate transfection) have led to major scientific advances, but are too inefficient in their current state to be used for some applications, including gene therapy. This review describes the development of gene-targeting vectors based on three types of viruses (retrovirus, adenovirus, and adeno-associated virus) and discusses the design, possible mechanisms of action, and applications of gene-targeting vectors based on adeno-associated virus.
Identification of two distinct regions of the type III connecting segment of human plasma fibronectin that promote cell type-specific adhesion. (1987)

The principal region of the human plasma fibronectin molecule mediating the adhesion of melanoma cells appears to be the alternatively spliced type III connecting segment (IIICS (Humphries, M. J., Akiyama, S. K., Komoriya, A., Olden, K., and Yamada, K. M. (1986a) J. Cell Biol., in press]. A series of overlapping synthetic peptides spanning the entire IIICS (CS peptides) were examined for their effects on B16-F10 melanoma cell adhesion to the parent fibronectin molecule. Two nonadjacent CS peptides, designated CS1 and CS5, were inhibitory. In contrast, neither inhibited fibronectin-mediated spreading of fibroblastic baby hamster kidney cells. When N-terminal cysteine derivatives of the CS peptides were conjugated to IgG by covalent cross-linking with N-succinimidyl-3(2-pyridyldithio)propionate, both the CS1 and CS5 conjugates promoted B16-F10 melanoma cell spreading. All conjugates were inactive for spreading of baby hamster kidney cells, confirming the cell type specificity of the IIICS adhesion site. Determination of the amounts of CS peptide required to support melanoma cell adhesion revealed that the activity of CS1 was only 2.4-fold lower than that of the intact fibronectin molecule. CS5 was approximately 320-fold less active than fibronectin, suggesting that the CS1 region may be the major site of interaction with the melanoma cell surface. The adhesion-promoting activities of CS1-IgG and CS5-IgG were additive as were the inhibitory activities of the free peptides for B16-F10 cell spreading on fibronectin. These findings suggest that both regions of the IIICS can function separately or together in mediating the interaction of melanoma cells with fibronectin. Since CS1 and CS5 are each found in separate alternatively spliced regions of the IIICS, it is conceivable that the adhesion-promoting activity of fibronectin for different cell types may be under complex regulation.
Image registration based on boundary mapping (1996)

A new two-stage approach for nonlinear brain image registration is proposed. In the first stage, an active contour algorithm is used to establish a homothetic one-to-one map between a set of region boundaries in two images to be registered. This mapping is used in the second step: a two-dimensional transformation which is based on an elastic body deformation. This method is tested by registering magnetic resonance images to atlas images.
Evaluation of a human monocytic cell line THP-1 model for assay of the intracellular activities of antimicrobial agents against Legionella pneumophila (2000)

We examined the intracellular activities of 11 antimicrobial agents against Legionella pneumophila using a human monocyte-derived cell line, THP-1. Colony counting and microscopic examination of L. pneumophila co-incubated with THP-1 cells (5 x 105 cells/well) were performed. Both extra- and intra-cellular multiplication of L. pneumophila were observed and were dependent on the inoculum of L. pneumophila in the culture; L. pneumophila did not grow in the cell culture medium alone. Light microscopic examination confirmed that extracellular L. pneumophila originated from THP-1 cells disrupted by bacterial multiplication. L. pneumophila multiplied by 3-4 logs after 24 h incubation with THP-1 cells and their number remained stable at 106-107 cfu/mL until 72 h. The results of viability studies using four antimicrobial agents-ciprofloxacin, erythromycin, minocycline and rifampicin-demonstrated that our system was suitable for the intracellular activity assay. We used a concept of 'minimum extracellular concentration inhibiting intracellular multiplication' (MIEC) to evaluate the intracellular activity of antimicrobial agents. The MIECs of three beta-lactams were markedly higher than their conventional MICs while those of macrolides, quinolones, rifampicin and minocycline were similar to their MICs. Our results suggest that evaluation of the clinical efficacy of drugs against L. pneumophila should include determination of their intracellular activity against the bacteria, which could be measured using our assay system in THP-1 cells.
Endothelium-Dependent Effects of Statins (2003)

The vascular endothelium is a dynamic endocrine organ that regulates contractile, secretory, and mitogenic activities in the vessel wall and hemostatic processes within the vascular lumen. Risk factors for cardiovascular disease, such as cigarette smoking, hypertension, and elevated serum lipid levels, impair endothelial function and lead to the development of atherosclerotic vessels. Recent studies suggest that statins reduce cardiovascular events in part by improving endothelial function. Statins reduce plasma cholesterol levels, thereby decreasing the uptake of modified lipoproteins by vascular wall cells. There is increasing evidence, however, that statins may also exert effects beyond cholesterol lowering. Indeed, many of these cholesterol-independent or "pleiotropic" vascular effects of statins appear to involve restoring or improving endothelial function through increasing the bioavailability of nitric oxide, promoting re-endothelialization, reducing oxidative stress, and inhibiting inflammatory responses. Thus, the endothelium-dependent effects of statins are thought to contribute to many of the beneficial effects of statin therapy in cardiovascular disease.
How depolymerization can promote polymerization: the case of actin and profilin (2009)

Rapid polymerization and depolymerization of actin filaments in response to extracellular stimuli is required for normal cell motility and development. Profilin is one of the most important actin-binding proteins; it regulates actin polymerization and interacts with many cytoskeletal proteins that link actin to extracellular membrane. The molecular mechanism of profilin has been extensively considered and debated in the literature for over two decades. Here we discuss several accepted hypotheses regarding the mechanism of profilin function as well as new recently emerged possibilities. Thermal noise is routine in molecular world and unsurprisingly, nature has found a way to utilize it. An increasing amount of theoretical and experimental research suggests that fluctuation-based processes play important roles in many cell events. Here we show how a fluctuation-based process of exchange diffusion is involved in the regulation of actin polymerization.
Comparative effectiveness of light emitting diodes (LEDs) and Lasers in near infrared photoimmunotherapy (2016)

Near infrared photoimmunotherapy (NIR-PIT) is a new cancer treatment that combines the specificity of antibodies for targeting tumors with the toxicity induced by photosensitizers after exposure to near infrared (NIR) light. Herein we compare two NIR-light sources; light emitting diodes (LEDs) and Lasers, for their effectiveness in NIR-PIT. A photosensitizer, IRDye-700DX, conjugated to panitumumab (pan-IR700), was incubated with EGFR-expressing A431 and MDA-MB-468-luc cells. NIR-light was provided by LEDs or Lasers at the same light dose. Laser-light produced more cytotoxicity and greater reductions in IR700-fluorescence intensity than LED-light. Laser-light also produced more cytotoxicity in vivo in both cell lines. Assessment of super-enhanced permeability and retention (SUPR) effects were stronger with Laser than LED. These results suggest that Laser-light produced significantly more cytotoxic effects compared to LEDs. Although LED is less expensive, Laser-light produces superior results in NIR-PIT.
cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs (2016)

While there is apparently no ideal platform for all challenges of miRNome analyses, cPAS shows high technical reproducibility and supplements the hitherto available platforms.