gebhart/patrepeval huggingface dataset:
DNA‐crosslinker cisplatin eradicates bacterial persister cells (2016)

For all bacteria, nearly every antimicrobial fails since a subpopulation of the bacteria enter a dormant state known as persistence, in which the antimicrobials are rendered ineffective due to the lack of metabolism. This tolerance to antibiotics makes microbial infections the leading cause of death worldwide and makes treating chronic infections, including those of wounds problematic. Here, we show that the FDA-approved anti-cancer drug cisplatin [cis-diamminodichloroplatinum(II)], which mainly forms intra-strand DNA crosslinks, eradicates Escherichia coli K-12 persister cells through a growth-independent mechanism. Additionally, cisplatin is more effective at killing Pseudomonas aeruginosa persister cells than mitomycin C, which forms inter-strand DNA crosslinks, and cisplatin eradicates the persister cells of several pathogens including enterohemorrhagic E. coli, Staphylococcus aureus, and P. aeruginosa. Cisplatin was also highly effective against clinical isolates of S. aureus and P. aeruginosa. Therefore, cisplatin has broad spectrum activity against persister cells. Biotechnol. Bioeng. 2016;113: 1984-1992. © 2016 Wiley Periodicals, Inc.
Improving the Safety of Fresh Fruit and Vegetables (2005)

Fresh fruit and vegetables have been identified as a significant source of pathogens and chemical contaminants. As a result, there has been a wealth of research on identifying and controlling hazards at all stages in the supply chain. Improving the safety of fresh fruit and vegetables reviews this research and its implications for food processors.
Marine Natural Products with P-Glycoprotein Inhibitor Properties (2014)

P-glycoprotein (P-gp) is a protein belonging to the ATP-binding cassette (ABC) transporters superfamily that has clinical relevance due to its role in drug metabolism and multi-drug resistance (MDR) in several human pathogens and diseases. P-gp is a major cause of drug resistance in cancer, parasitic diseases, epilepsy and other disorders. This review article aims to summarize the research findings on the marine natural products with P-glycoprotein inhibitor properties. Natural compounds that modulate P-gp offer great possibilities for semi-synthetic modification to create new drugs and are valuable research tools to understand the function of complex ABC transporters.
Combining multiple depth cameras and projectors for interactions on, above and between surfaces (2010)

Instrumented with multiple depth cameras and projectors, LightSpace is a small room installation designed to explore a variety of interactions and computational strategies related to interactive displays and the space that they inhabit. LightSpace cameras and projectors are calibrated to 3D real world coordinates, allowing for projection of graphics correctly onto any surface visible by both camera and projector. Selective projection of the depth camera data enables emulation of interactive displays on un-instrumented surfaces (such as a standard table or office desk), as well as facilitates mid-air interactions between and around these displays. For example, after performing multi-touch interactions on a virtual object on the tabletop, the user may transfer the object to another display by simultaneously touching the object and the destination display. Or the user may "pick up" the object by sweeping it into their hand, see it sitting in their hand as they walk over to an interactive wall display, and "drop" the object onto the wall by touching it with their other hand. We detail the interactions and algorithms unique to LightSpace, discuss some initial observations of use and suggest future directions.
Differential expression of genes in milk of dairy cattle during lactation (2015)

The milk fat globule (MFG) is one of the most representative of mammary gland tissues and can be utilized to study gene expression of lactating cows during lactation. In this study, RNA-seq technology was employed to detect differential expression of genes in MFGs at day 10 and day 70 after calving between two groups of cows with extremely high (H group) and low (L group) 305-day milk yield, milk fat yield and milk protein yield. In total, 1232, 81, 429 and 178 significantly differentially expressed genes (false discovery rate q < 0.05) were detected between H10 and L10, H70 and L70, H10 and H70, and L10 and L70 respectively. Gene Ontology enrichment and pathway analysis revealed that these differentially expressed genes were enriched in biological processes involved in mammary gland development, protein and lipid metabolism process, signal transduction, cellular process, differentiation and immune function. Among these differentially expressed genes, 178 (H10 vs. L10), 4 (H70 vs. L70), 68 (H10 vs. H70) and 22 (L10 vs. L70) were found to be located within previously reported QTL regions for milk production traits. Based on these results, some promising candidate genes for milk production traits in dairy cattle were suggested.
Increased CD40 Expression on Muscle Cells of Polymyositis and Dermatomyositis: Role of CD40-CD40 Ligand Interaction in IL-6, IL-8, IL-15, and Monocyte Chemoattractant Protein-1 Production (2000)

In polymyositis (PM)/dermatomyositis (DM), T cells infiltrate the muscle tissues and interact with muscle cells via cell surface molecules. Recently, myoblasts have been reported to express CD40, but little is known about the role of CD40 in myoblasts. In the present study we examined the expression and involvement of CD40 and CD40 ligand (CD40L) in the interaction between muscle cells and T cells in PM/DM. Immunohistochemical staining revealed that CD40 was expressed on muscle cells in five of five PM and four of five DM patients, and that infiltrating mononuclear cells (MNCs) expressed CD40L in all cases of PM/DM. These CD40L-expressing MNCs were primarily CD4+ T cells. IFN-gamma, which is known to induce CD40 expression on various types of cells, was also expressed on the MNCs in four of the PM and four of the DM patients. Although cultured human myoblasts (SkMC 2859) did not express CD40 constitutively, IFN-gamma induced CD40 expression in a dose-dependent manner. To clarify the functional roles of CD40-mediated signals, the effects of a trimeric form of recombinant human CD40L on cytokine production were studied in SkMC 2859 that were prestimulated with IFN-gamma to express CD40. Recombinant human CD40L markedly increased the production of IL-6, IL-8, IL-15, and monocyte chemoattractant protein-1 of SkMC 2859. The expression of these humoral factors in muscle cells of PM and DM was demonstrated by immunohistochemistry. These results suggest that interaction between T cells and muscle cells via the CD40-CD40L system contributes to the immunopathogenesis of PM/DM by augmenting inflammation via cytokine production by the muscle cells.
Deliberate reduction of hemagglutinin and neuraminidase expression of influenza virus leads to an ultraprotective live vaccine in mice (2013)

A long-held dogma posits that strong presentation to the immune system of the dominant influenza virus glycoprotein antigens neuraminidase (NA) and hemagglutinin (HA) is paramount for inducing protective immunity against influenza virus infection. We have deliberately violated this dogma by constructing a recombinant influenza virus strain of A/PR8/34 (H1N1) in which expression of NA and HA genes was suppressed. We down-regulated NA and HA expression by recoding the respective genes with suboptimal codon pair bias, thereby introducing hundreds of nucleotide changes while preserving their codon use and protein sequence. The variants PR8-NA(Min), PR8-HA(Min), and PR8-(NA+HA)(Min) (Min, minimal expression) were used to assess the contribution of reduced glycoprotein expression to growth in tissue culture and pathogenesis in BALB/c mice. All three variants proliferated in Madin-Darby canine kidney cells to nearly the degree as WT PR8. In mice, however, they expressed explicit attenuation phenotypes, as revealed by their LD50 values: PR8, 32 plaque-forming units (PFU); HA(Min), 1.7 × 10(3) PFU; NA(Min), 2.4 × 10(5) PFU; (NA+HA)(Min), ≥3.16 × 10(6) PFU. Remarkably, (NA+HA)(Min) was attenuated >100,000-fold, with NA(Min) the major contributor to attenuation. In vaccinated mice (NA+HA)(Min) was highly effective in providing long-lasting protective immunity against lethal WT challenge at a median protective dose (PD50) of 2.4 PFU. Moreover, at a PD50 of only 147 or 237, (NA+HA)(Min) conferred protection against heterologous lethal challenges with two mouse-adapted H3N2 viruses. We conclude that the suppression of HA and NA is a unique strategy in live vaccine development.
Antitumor activity, mitogenicity, and lethal toxicity of chemically synthesized monosaccharide analogs of lipid A. (1988)

Antitumor activity of three derivatives of chemically synthesized diacyloxyacylglucosamine-4-phosphate (acyl-GlcN-4P) linked 3-deoxy-D-manno-2-octulosonic acid (KDO) and 12 derivatives of acyl-GlcN-4P or acyloxyacylglucosamine-6-phosphate (acyl-GlcN-6P) with chiral acyloxyacyl groups at the C-2 and C-3 positions was examined. Ehrlich carcinoma cells (1 x 10(4] were inoculated i.p. into ddY mice on day 0, and these compounds (100 micrograms/d/mouse) were administered i.p. on days -5, -2, +1, +3, and +5. Although the antitumor activity of the acyl-GlcN-4P linked KDO was weaker than that of the natural lipopolysaccharide, groups of mice administered A-301 with di-3-hexadecanoyloxytetradecanoyl [(R)C14-O-C16] at C-2, -3, and A-303 with di-3-tetradecanoyloxytetradecanoyl [(R)C14-O-C14] showed longer mean survival times than the control group. However, KDO-attachment appeared not to enhance the antitumor activity of acyl-GlcN-4P. The group of mice administered acyl-GlcN-4P (A-145) or acyl-GlcN-6P (A-144 and A-146), which have an acyloxyacyl group at C-2, -3, showed prolonged survival times when compared to the control group, but the differences were not significant. On the other hand, when compound A-107 with [(S)C14-O-C14] at the C-2 position and 6-phosphate was administered to 5 mice, 3 mice survived for 25 d. Furthermore, mitogenicity for splenocytes of C57BL/6 mice and lethal toxicity in C57BL/6 mice sensitized with D-galactosamine were observed with the acyl-GlcN-4P or -6P derivatives with (R) or (S) isomers of fatty acid.(ABSTRACT TRUNCATED AT 250 WORDS)
Inhibition of the Growth of Patient-Derived Pancreatic Cancer Xenografts with the MEK Inhibitor Trametinib Is Augmented by Combined Treatment with the Epidermal Growth Factor Receptor/HER2 Inhibitor Lapatinib (2013)

Mutations of the oncogene KRAS are important drivers of pancreatic cancer progression. Activation of epidermal growth factor receptor (EGFR) and human EGFR2 (HER2) is observed frequent in pancreatic adenocarcinomas. Because of co-activation of these two signaling pathways, we assessed the efficacy of inhibition of EGFR/HER2 receptors and the downstream KRAS effector, mitogen-activated protein kinase/extracellular-signal regulated kinase (ERK) kinase 1 and 2 (MEK1/2), on pancreatic cancer proliferation in vitro and in a murine orthotopic xenograft model. Treatment of established and patient-derived pancreatic cancer cell lines with the MEK1/2 inhibitor trametinib (GSK1120212) inhibited proliferation, and addition of the EGFR/HER2 inhibitor lapatinib enhanced the inhibition elicited by trametinib in three of eight cell lines. Importantly, in the orthotopic xenograft model, treatment with lapatinib and trametinib resulted in significantly enhanced inhibition of tumor growth relative to trametinib treatment alone in four of five patient-derived tumors tested and was, in all cases, significantly more effective in reducing the size of established tumors than treatment with lapatinib or trametinib alone. Acute treatment of established tumors with trametinib resulted in an increase in AKT2 phosphorylation that was blunted in mice treated with both trametinib and lapatinib. These data indicate that inhibition of the EGFR family receptor signaling may contribute to the effectiveness of MEK1/2 inhibition of tumor growth possibly through the inhibition of feedback activation of receptor tyrosine kinases in response to inhibition of the RAS-RAF-MEK-ERK pathway. These studies provide a rationale for assessing the co-inhibition of these pathways in the treatment of pancreatic cancer patients.
Neuropathic Pain Develops Normally in Mice Lacking both Nav1.7 and Nav1.8 (2005)

Two voltage gated sodium channel alpha-subunits, Nav1.7 and Nav1.8, are expressed at high levels in nociceptor terminals and have been implicated in the development of inflammatory pain. Mis-expression of voltage-gated sodium channels by damaged sensory neurons has also been implicated in the development of neuropathic pain, but the role of Nav1.7 and Nav1.8 is uncertain. Here we show that deleting Nav1.7 has no effect on the development of neuropathic pain. Double knockouts of both Nav1.7 and Nav1.8 also develop normal levels of neuropathic pain, despite a lack of inflammatory pain symptoms and altered mechanical and thermal acute pain thresholds. These studies demonstrate that, in contrast to the highly significant role for Nav1.7 in determining inflammatory pain thresholds, the development of neuropathic pain does not require the presence of either Nav1.7 or Nav1.8 alone or in combination.
Modulation of Th1/Th2 subsets by granulocyte-colony stimulating factor (2001)

The recent article published in Blood by Sloand et al[1][1] suggests that pharmacologic doses of granulocyte-colony stimulating factor (G-CSF) affect cytokine production by lymphocytes in vitro and in vivo. Sloand et al demonstrated that G-CSF decreases interferon (IFN)-γ and increases interleukin-
Manufacturable plastic microfluidic valves using thermal actuation (2009)

A low-cost, manufacturable, thermally actuated, plastic microfluidic valve has been developed. The valve contains an encapsulated, temperature-sensitive fluid, which expands, deflecting a thin elastomeric film into a fluidic channel to control fluid flow. The power input for thermal expansion of each microfluidic valve can be controlled using a printed circuit board (PCB)-based controller, which is suitable for mass production and large-scale integration. A plastic microfluidic device with such valves was fabricated using compression molding and thermal lamination. The operation of the valves was investigated by measuring a change in the microchannel's ionic conduction current mediated by the resistance variation corresponding to the deflection of the microvalve. Valve closing was also confirmed by the disappearance of fluorescence when a fluorescent solution was displaced in the valve region. Valve operation was characterized for heater power ranging from 36 mW to 80 mW. When the valve was actuating, the local channel temperature was 10 to 19 degrees C above the ambient temperature depending on the heater power used. Repetitive valve operations (up to 50 times) have been demonstrated with a flow resulting from a hydrostatic head. Valve operation was tested for a flow rate of 0.33-4.7 microL/min.
Double Emulsion Templated Monodisperse Phospholipid Vesicles (2008)

We present a novel approach for fabricating monodisperse phospholipid vesicles with high encapsulation efficiency using controlled double emulsions as templates. Glass-capillary microfluidics is used to generate monodisperse double emulsion templates. We show that the high uniformity in size and shape of the templates are maintained in the final phospholipid vesicles after a solvent removal step. Our simple and versatile technique is applicable to a wide range of phospholipids.
Recognition of mycobacterial antigens by sera from patients with leprosy (1988)

Mycobacterium leprae sonic extracts prepared from armadillo-derived bacteria were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting (immunoblotting) procedures and probed with serum or plasma samples from 20 patients with lepromatous leprosy and 14 healthy endemic controls. Five proteins of 33, 25, 18, 15, and 12 kilodaltons (kDa) were frequently recognized; the 33- and 15-kDa proteins were, respectively, recognized with high intensity by 16 and 13 of the 20 samples from patients with leprosy, whereas only one healthy donor had antibodies that recognized the 15-kDa protein. By the use of M. leprae-specific murine monoclonal antibodies it was demonstrated that the 33-, 25-, and 15-kDa antigens were different from those bound by the available murine monoclonal antibodies. The 18- and 12-kDa proteins detected had molecular masses similar to those detected by the corresponding murine monoclonal antibodies. The serum and plasma samples from patients with leprosy were also used to probe Western blots of a soluble extract of M. tuberculosis. They recognized, among others, antigens with molecular weights similar to those detected in the M. leprae antigenic preparations, although with less intensity and at a lower frequency.
Recent advances in the understanding of the biochemistry and clinical pharmacology of interleukin-2. (1987)

This review covers significant developments in the understanding of the biochemistry and clinical pharmacology of Interleukin-2 (IL-2) that were achieved from 1984 through September 1986. These include developments in the molecular biology of IL-2 and its receptors. Human IL-2 was cloned and sequenced by Taniguchi et al. in 1983. The gene for human IL-2 is located on the long arm of chromosome 4. The secondary structure of the gene is predominantly alpha helix. The mature gene product is a 133 amino acid glycoprotein with a molecular weight of 15,420 Daltons. The IL-2 receptor was revealed to be a glycoprotein of 272 amino acids. The mature receptor has a molecular weight of 55,000 Daltons. A more precise understanding of the mechanism of action IL-2, in particular its role in the induction of the IL-2 receptor, and aspects of the control of IL-2 production was also achieved. Metabolic and morphologic studies have revealed that activation of the T-cell antigen receptor renders the cells responsive to IL-2, but does not move them through the cell cycle. Rather, it appears that IL-2 stimulates G1 progression to S phase ie. blastic transformation. During this progression the cellular proto-oncogene c-myb is induced transiently to 6 to 7 times basal levels. The role of IL-2 as a growth factor for several subsets of T cells has been confirmed, and a new role as a growth factor for B cells was defined. Most importantly, IL-2 was shown to be directly mitogenic for and to expand subpopulations of peripheral blood cells, termed lymphokine-activated killer (LAK) cells and tumor-infiltrating lymphocytes (TIL). A number of pathologies of IL-2 production or activity have been defined, including Hodgkin's disease, graft versus host disease, systemic lupus erythematosus, lepromatous leprosy, acquired immune deficiency syndrome, and adult T cell leukemia. Murine and human in vivo studies reviewed here have revealed significant parameters of the therapeutic potential as well as the toxicity of this growth factor. Finally, the modulation of IL-2 receptors on human PBL's by thymosin fraction 5 and thymosin alpha 1 suggests that it might be possible to up-regulate IL-2 receptor expression in certain disease states and thus increase the efficacy of IL-2.
Longitudinal Surface Plasmon Resonance Based Gold Nanorod Biosensors for Mass Spectrometry (2010)

A "strategy" for analyte capture/ionization based on chemical derivatization of gold nanorods and infrared laser desorption ionization (IR-LDI) is described. This is the first example of laser desorption/ionization of biomolecules using gold nanorods irradiated with an IR laser. LDI is performed at wavelengths (1064 nm) that overlap with the longitudinal surface plasmon resonance (LSPR) mode of gold nanorods. The absorbed energy from the laser facilitates desorption and ionization of the analyte. The wavelength of the LSPR band can be tuned by controlling the aspect ratio (length-to-diameter) of the nanorod. For example, the SPR band for Au nanorods having an aspect ratio of 5:1 is centered at approximately 840 nm, and this band overlaps with the 1064 nm output of a Nd:YAG laser. We show that a variety of biomolecules can be efficiently desorbed and ionized by 1064 nm irradiation of nanorods. We also show that analyte capture can be controlled by surface chemistry of the nanorods. The results of these studies are important for designing nanomaterial-based capture assays for mass spectrometry and interfacing nanomaterials with imaging/spatial profiling mass spectrometry experiments.
Effect of Chinese and Western Antimicrobial Agents on Selected Oral Bacteria (1982)

The susceptibility of selected oral bacteria, including suspected periodontopathogens, to a commonly employed Chinese herbal medicine Huang-chin (HC, Scutellaria baicalensis) was tested in vitro. The minimum inhibitory concentration (MIC) and minimum bactericidal concentrations (MBC) were determined. HC was also compared with tetracycline, alexidine, and stannous fluoride. HC decoction, at a concentration of 2%, was bacteriostatic in eight of 11 bacteria tested, but a concentration of 3.13% or greater was required for bactericidal effect. Among the tested bacteria, Bacteroides melaninogenicus ss intermedius was the most sensitive (MIC = 1.57%, MBC = 2%); Actinomyces viscosus was the least sensitive (MIC = 6.25%, MBC = 12.5%). Tetracycline, alexidine, and SnF2 were bactericidal in vitro in all bacteria tested at concentrations lower than those used clinically.
Instrumentation for Multi-modal Spectroscopic Diagnosis of Epithelial Dysplasia (2003)

Reflectance and fluorescence spectroscopies have shown great promise for early detection of epithelial dysplasia. We have developed a clinical reflectance spectrofluorimeter for multimodal spectroscopic diagnosis of epithelial dysplasia. This clinical instrument, the FastEEM, collects white light reflectance and fluorescence excitation-emission matrices (EEM's) within a fraction of a second. In this paper we describe the FastEEM instrumentation, designed for collection of multi-modal spectroscopic data. We illustrate its performance using tissue phantoms with well defined optical properties and biochemicals of known fluorescence properties. In addition, we discuss our plans to develop a system that combines a multi-spectral imaging device for wide area surveillance with this contact probe device.
NS-187, a potent and selective dual Bcr-Abl/Lyn tyrosine kinase inhibitor, is a novel agent for imatinib-resistant leukemia (2005)

Although the Abelson (Abl) tyrosine kinase inhibitor imatinib mesylate has improved the treatment of breakpoint cluster region-Abl (Bcr-Abl)-positive leukemia, resistance is often reported in patients with advanced-stage disease. Although several Src inhibitors are more effective than imatinib and simultaneously inhibit Lyn, whose overexpression is associated with imatinib resistance, these inhibitors are less specific than imatinib. We have identified a specific dual Abl-Lyn inhibitor, NS-187 (elsewhere described as CNS-9), which is 25 to 55 times more potent than imatinib in vitro. NS-187 is also at least 10 times as effective as imatinib in suppressing the growth of Bcr-Abl-bearing tumors and markedly extends the survival of mice bearing such tumors. The inhibitory effect of NS-187 extends to 12 of 13 Bcr-Abl proteins with mutations in their kinase domain but not to T315I. NS-187 also inhibits Lyn without affecting the phosphorylation of Src, Blk, or Yes. These results suggest that NS-187 may be a potentially valuable novel agent to combat imatinib-resistant Philadelphia-positive (Ph+) leukemia.
Multi-target-Directed Ligands To Combat Neurodegenerative Diseases (2008)

A review. The authors review the investigations reported in the past decade that illustrate the ability of medicinal chemists to design multi-target-directed ligands (MTDLs) to confront neurodegenerative diseases. The authors briefly illustrate the multifactorial nature of these diseases before discussing the possible development of MTDLs in light of the known mol. bases of the main neurodegenerative pathologies.