gebhart/patrepeval huggingface dataset:
Abstract A63: MM-398/PEP02, a novel liposomal formulation of irinotecan, demonstrates stromal-modifying anticancer properties. (2012)

MM-398 is a stable nanotherapeutic encapsulation of the prodrug irinotecan (CPT-11) with longer plasma half-life and higher tumor deposition due to an enhanced permeability and retention effect. Pancreatic cancer has responded poorly to many therapeutics, largely because of inadequate drug penetration due to poor vascularization and the highly aggressive, hypoxic nature of the disease. We sought to better understand how MM-398, a relatively large (100nm) liposomal nanotherapeutic, could be used treat pancreatic cancer. We have tested MM-398 in several pancreatic xenograft models: BxPC3 (KRAS wild type), AsPC-1(KRAS G12D) , Panc-1 (KRAS G12D) and MiaPaCa (KRAS G12C). All models demonstrated complete tumor regression at 20 mg/kg or a human equivalent dose of 60-120 mg/m2. At this same dose, MM-398 suppresses tumor growth in a gemcitabine insensitive AsPC-1 xenograft. MM-398 functionally blocked AsPC-1 tumor cell proliferation as measured by ki-67 staining; however, gemcitabine administered at its maximum tolerated dose did not impact proliferation. MM-398 is currently in multiple clinical trials, including a phase 3 trial for patients with advanced gemcitabine-resistant pancreatic cancer (NAPOLI-1). In order to further understand mechanisms driving response to MM-398, we screened and ranked several cell lines for their ability to convert irinotecan into the active metabolite, SN38. BxPC3 and HT-29 tumors ranked highest in ability to convert irinotecan to SN-38, as measured by HPLC. In a BxPC3 pancreatic orthotopic model which spontaneously metastasizes, 10 mg/kg MM-398 significantly reduced both primary and metastatic tumor load as measured by ex vivo biophotonic imaging of BxPC3luc cells to spleen, lung, liver, diaphragm and GI associated lymph nodes (p In summary, MM-398 induces tumor regression in multiple mouse models of pancreatic cancer, including an orthotopic metastatic model. MM-398 activity may be driven in part by the ability to modify tumor microenvironment parameters, such as hypoxia and vascularization, both of which limit efficacy of chemotherapeutic agents in the treatment of pancreatic cancer. These data support the continued investigation of MM-398 in pancreatic cancer. Citation Format: Nancy Paz, Peter Laivins, Clet Niyikiza, Ulrik Nielsen, Jonathan Fitzgerald, Ashish Kalra, Milind Chalishazar, Stephan Klinz, Jaeyeon Kim, Daryl Drummond, Dmitri Kirpotin, Victor Moyo, Eliel Bayever. MM-398/PEP02, a novel liposomal formulation of irinotecan, demonstrates stromal-modifying anticancer properties. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Progress and Challenges; Jun 18-21, 2012; Lake Tahoe, NV. Philadelphia (PA): AACR; Cancer Res 2012;72(12 Suppl):Abstract nr A63.
Amide bond formation: beyond the myth of coupling reagents (2008)

Amide bond formation is a fundamentally important reaction in organic synthesis, and is typically mediated by one of a myriad of so-called coupling reagents. This critical review is focussed on the most recently developed coupling reagents with particular attention paid to the pros and cons of the plethora of "acronym" based reagents. It aims to demystify the process allowing the chemist to make a sensible and educated choice when carrying out an amide coupling reaction (179 references).
A Role for NKG2D in NK Cell–Mediated Resistance to Poxvirus Disease (2008)

Ectromelia virus (ECTV) is an orthopoxvirus (OPV) that causes mousepox, the murine equivalent of human smallpox. C57BL/6 (B6) mice are naturally resistant to mousepox due to the concerted action of innate and adaptive immune responses. Previous studies have shown that natural killer (NK) cells are a component of innate immunity that is essential for the B6 mice resistance to mousepox. However, the mechanism of NK cell-mediated resistance to OPV disease remains undefined. Here we show that B6 mice resistance to mousepox requires the direct cytolytic function of NK cells, as well as their ability to boost the T cell response. Furthermore, we show that the activating receptor NKG2D is required for optimal NK cell-mediated resistance to disease and lethality. Together, our results have important implication towards the understanding of natural resistance to pathogenic viral infections.
The effect of chromium picolinate on serum cholesterol and apolipoprotein fractions in human subjects. (1990)

Chromium has been implicated as a cofactor in the maintenance of normal lipid and carbohydrate metabolism. A deficiency of chromium results from diets low in biologically available chromium. Picolinic acid, a metabolite of tryptophan, forms stable complexes with transitional metal ions, which results in an improved bioavailability of the metal ion chromium. To determine whether or not chromium picolinate is effective in humans, 28 volunteer subjects were given either chromium tripicolinate (3.8 micromol [200 micrograms] chromium) or a placebo daily for 42 days in a double-blind crossover study. A 14-day period off capsules was used between treatments. Levels of total cholesterol, low-density lipoprotein (LDL) cholesterol, and apolipoprotein B, the principal protein of the LDL fraction, decreased significantly while the subjects were ingesting chromium picolinate. The concentration of apolipoprotein A-I, the principal protein of the high-density lipoprotein (HDL) fraction, increased substantially during treatment with chromium picolinate. The HDL-cholesterol level was elevated slightly but not significantly during ingestion of chromium picolinate. Only apolipoprotein B, of the variables measured, was altered significantly during supplementation with the placebo. These observations show that chromium picolinate is efficacious in lowering blood lipids in humans.
New Class of Amphiphiles Designed for Use in Water-in-Supercritical CO2 Microemulsions (2016)

Water-in-supercritical CO<sub>2</sub> microemulsions formed using the hybrid F-H surfactant sodium 1-oxo-1-[4-(perfluorohexyl)phenyl]hexane-2-sulfonate, FC6-HC4, have recently been shown to have the highest water-solubilizing power ever reported. FC6-HC4 demonstrated the ability to outperform not only other surfactants but also other FCm-HCn analogues containing different fluorocarbon and hydrocarbon chain lengths (Sagisaka, M. et al. Langmuir 2015, 31, 7479-7487). With the aim of clarifying the key structural features of this surfactant, this study examined the phase behavior and water/supercritical CO<sub>2</sub> aggregate formation of 1-oxo-1-[4-(perfluorohexyl)phenyl]hexane (Nohead FC6-HC4), which is an FC6-HC4 analogue but now, interestingly, without the sulfonate headgroup. Surprisingly, Nohead FC6-HC4, which would not normally be identified as a classic surfactant, yielded transparent single-phase W/CO<sub>2</sub> microemulsions with polar cores able to solubilize a water-soluble dye, even at pressures and temperatures so low as to approach the critical point of CO<sub>2</sub> (e.g., ∼100 bar at 35 °C). High-pressure small-angle scattering (SANS) measurements revealed the transparent phases to consist of ellipsoidal nanodroplets of water. The morphology of these droplets was shown to be dependent on the pressure, Nohead FC6-HC4 concentration, and water-to-surfactant molar ratio. Despite having almost the same structure as Nohead FC6-HC4, analogues containing both shorter and longer hydrocarbons were unable to form W/CO<sub>2</sub> microemulsion droplets. This shows the importance of the role of the hydrocarbon chain in the stabilization of W/CO<sub>2</sub> microemulsions. A detailed examination of the mechanism of Nohead FC6-HC4 adsorption onto the water surface suggests that the hexanoyl group protrudes into the aqueous core, allowing for association between the carbonyl group and water.
Proteomic Molecular Portrait of Interface Zone in Breast Cancer (2010)

Surgical tumor margins are intended to encompass residual tumor cells but may not always accurately delineate the boundary between tumor and normal tissue. Efforts to define tumor margins based on molecular analysis have achieved limited success. Furthermore, no clinical trials have addressed the scope of the tumor microenvironment. Here, we considered the tumor cell population and surrounding microenvironment in delineating tumor margins, classifying breast cancer into tumor and normal zones, and introducing the concept of an interface zone, the region between the invading tumor front and normal tissue, which develops during tumor invasion and metastasis through remodeling of the tumor microenvironment. Pathological signatures of invasion markers in tumor tissues are most dynamic within the invading tumor front. We compared protein profiles of tumor, normal, and interface zones using MALDI-MS. Proteins upregulated in the interface zone were identified by peptide mass fingerprinting and confirmed by database searching with chemically assisted MALDI-PSD spectra. Upregulation was confirmed for RhoGDIα, CAPG, WDR1, and CK8 by Western and immunohistochemical analyses. Our results demonstrate that the molecular profile of the interface zone is unique and suggest that upregulation of proteins here may be related to progression and metastasis of breast carcinomas.
Problems and challenges in the cellulose to cellulase fermentation (1978)

In recent years there has been a marked interest in enzymatic saccharification of cellulose, particularly due to the availability of active cellulase from Trichoderma capable of extensive hydrolysis of insoluble cellulose. Several recent symposia have evaluated the process and examined the severe technical and economic constraints on it, including limited availability of suitable substrates, necessity of costly pretreatments, and high costs of the enzyme. Interest and research have, however, continued because cellulose is the only renewable resource available in large quantities. In this paper the authors discuss some of the constraints and problem areas of producing cellulase in quantity.
“Pop-off” Technic. The Ultrastructure of Paraffinembedded Sections (1981)

Stained paraffin embedded sections sometimes contain a precise area that warrants further investigation at an ultrastructural level. A technic is described whereby an area in question may be reembedded into plastic and sectioned for examination under the electron microscope. The decoverslipped paraffin section is "popped-off" into an inverted BEEM capsule. Suspected viral inclusions in sections may be identified or ruled out with this technic. Special stains, especially heavy metal applications, not able to be utilized in conventional plastic embedding may be reembedded into plastic. The metallic granules may be visualized ultrastructurally without further grid staining. This method is especially helpful for cell smears and cell monolayers since they may be the only material available for study. Although ultrastructural detail is often poor, one does have the ability to study the identical section under both the light and the electron microscopes.
Aluminum-induced crystallization of amorphous silicon on glass substrates above and below the eutectic temperature (1998)

The achievement of high-quality continuous polycrystalline silicon (poly-Si) layers onto glass substrates by using aluminum-induced crystallization is reported. The crystallization behavior of dc sputtered amorphous silicon on glass induced by an Al interface layer has been investigated above and below the eutectic temperature of 577 °C. Secondary electron micrographs in combination with energy-dispersive x-ray microanalysis show that annealing below this temperature leads to the juxtaposed Al and Si layers exchanging places. The newly formed poly-Si layer is fully crystallized and of good crystalline quality, according to Raman spectroscopy and transmission electron microscopy investigations. At 500 °C, the time needed to crystallize a 500-nm-thick Si layer is as short as 30 min. By annealing above the eutectic temperatures, layer exchange is not as pronounced and the newly formed Al layer is found to contain a network of crystallized Si.
Cerebral arteriolar dilations by KATP channel activators needl-lysine orl-arginine (1998)

We investigated the effects of various amino acids on responses to ATP-sensitive potassium (KATP) channel openers in anesthetized cats equipped with cranial windows. The application of pinacidil by superfusion caused transient vasodilation, whereas there was sustained vasodilation from the application of stationary solution of pinacidil. In the presence of L-arginine or L-lysine, pinacidil by superfusion led to sustained vasodilation, suggesting that the rapid flow of fluid displaced these amino acids from binding on the channel and that such binding was essential for opening the channel. NG-nitro-L-arginine blocked responses to pinacidil, and this blockade was reversed by L-lysine or L-arginine but not by D-arginine, D-lysine, methyl-L-arginine, glycine, L-histidine, dimethylarginine, dimethyl-L-arginine, or hydroxylysine. The blockade of responses to pinacidil induced by glyburide was also reversed completely by L-arginine or L-lysine but not by D-arginine, suggesting that these amino acids act on the sulfonylurea receptor. Hydroxylysine but not methyl-L-lysine, dimethylarginine, or dimethyl-L-arginine blocked responses to pinacidil. The findings show that KATP channels in cerebral arterioles need L-lysine or L-arginine to open in response to agonists.
Electrical Conductivity of Lumbar Anulus Fibrosis: Effects of Porosity and Fixed Charge Density (2002)

Measured electrical conductivity was sensitive to tissue porosity, but not to fixed charged density for anulus fibrosis specimens in phosphate-buffered saline.
The Mitochondrial Targeting function of Randomly Generated Peptide Sequences Correlates with Predicted Helical Amphiphilicity (1989)

A pool of oligonucleotides encoding a start methionine and nine random amino acids was inserted at the 5'-end of the gene for the yeast cytochrome oxidase subunit IV lacking its own mitochondrial targeting sequence. Approximately one-quarter of the randomly generated sequences targeted subunit IV to its correct intramitochondrial location in vivo. Sequence analysis of 89 randomly generated sequences showed that their efficiencies as mitochondrial targeting signals correlated with the potential to fold into an amphiphilic alpha-helix. Functional targeting sequences were enriched in arginine and isoleucine residues but contained few aspartate, glutamate, and proline residues. Nonfunctional sequences predicted to have significant helical amphiphilicity often had at least one acidic or multiple helix-breaking residues that would be expected to interfere with targeting functioning. These results support the hypothesis that the signal for targeting a protein into the mitochondrial matrix is usually a positively charged amphiphilic helix.
Tuning of Vertically-Aligned Carbon Nanotube Diameter and Areal Density through Catalyst Pre-Treatment (2008)

By controlling the timing and duration of hydrogen exposure in a fixed thermal process, we tuned the diameters of carbon nanotubes (CNTs) within a vertically aligned film by a factor of 2, and tuned the areal densities by an order of magnitude. The CNT structure is correlated with the catalyst morphology, suggesting that while chemical reduction of the catalyst layer is required for growth, prolonged H2 exposure not only reduces the iron oxide and enables agglomeration of the Fe film, but also leads to catalyst coarsening. Control of this coarsening process allows tuning of CNT characteristics.
Bone Morphogenetic Protein Receptor Complexes on the Surface of Live Cells: A New Oligomerization Mode for Serine/Threonine Kinase Receptors (2000)

The bone morphogenetic proteins (BMPs) play important roles in embryogenesis and normal cell growth. The BMP receptors belong to the family of serine/threonine kinase receptors, whose activation has been investigated intensively for the transforming growth factor-beta (TGF-beta) receptor subfamily. However, the interactions between the BMP receptors, the composition of the active receptor complex, and the role of the ligand in its formation have not yet been investigated and were usually assumed to follow the same pattern as the TGF-beta receptors. Here we demonstrate that the oligomerization pattern of the BMP receptors is different and is more flexible and susceptible to modulation by ligand. Using several complementary approaches, we investigated the formation of homomeric and heteromeric complexes between the two known BMP type I receptors (BR-Ia and BR-Ib) and the BMP type II receptor (BR-II). Coimmunoprecipitation studies detected the formation of heteromeric and homomeric complexes among all the BMP receptor types even in the absence of ligand. These complexes were also detected at the cell surface after BMP-2 binding and cross-linking. Using antibody-mediated immunofluorescence copatching of epitope-tagged receptors, we provide evidence in live cells for preexisting heteromeric (BR-II/BR-Ia and BR-II/BR-Ib) and homomeric (BR-II/BR-II, BR-Ia/ BR-Ia, BR-Ib/ BR-Ib, and also BR-Ia/ BR-Ib) oligomers in the absence of ligand. BMP-2 binding significantly increased hetero- and homo-oligomerization (except for the BR-II homo-oligomer, which binds ligand poorly in the absence of BR-I). In contrast to previous observations on TGF-beta receptors, which were found to be fully homodimeric in the absence of ligand, the BMP receptors show a much more flexible oligomerization pattern. This novel feature in the oligomerization mode of the BMP receptors allows higher variety and flexibility in their responses to various ligands as compared with the TGF-beta receptors.
Droplet Dynamics and Ionization Mechanisms in Desorption Electrospray Ionization Mass Spectrometry (2006)

A droplet pickup and other mechanisms have been suggested for the ionization of biomolecules like peptides and proteins by desorption electrospray ionization. To verify this hypothesis phase Doppler particle analysis was used to study the sizes and velocities of droplets involved in DESI. It was found that impacting droplets typically have velocities of 120 m/s and average diameters of 2-4 microm. Small differences in sprayer construction influence the operating conditions at which droplets of these dimensions are produced. Under these conditions, the kinetic energy per impacting water molecule is less than 0.6 meV and sputtering through momentum transfer during collisions or ionization by other electronic processes is unlikely. Droplets arrive at the surface with velocities well below the speed of sound in common materials, thereby excluding the possibility of ionization by shockwave formation. Some droplets appear to roll along the surface, increasing contact time and presumably the amount of material that is taken up into droplets during conditions typical of the DESI experiment.
Synthesis of Cyclic Carbonates from Atmospheric Pressure Carbon Dioxide Using Exceptionally Active Aluminium(salen) Complexes as Catalysts (2007)

Abstract Dimetallic aluminium(salen) complexes show exceptionally high catalytic activity for the synthesis of cyclic carbonates from terminal epoxides at ambient temperature and pressure. The process has the potential to contribute towards decreasing atmospheric carbon dioxide emissions from the burning of fossil fuels. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits (2017)

MADS-box transcription factors are key elements of the genetic networks controlling flower and fruit development. Among these, the class D clade gathers AGAMOUS-like genes which are involved in seed, ovule, and funiculus development. The tomato genome comprises two class D genes, Sl-AGL11 and Sl-MBP3, both displaying high expression levels in seeds and in central tissues of young fruits. The potential effects of Sl-AGL11 on fruit development were addressed through RNAi silencing and ectopic expression strategies. Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation, and an extreme softening that occurs well before the onset of ripening. RNA-Seq transcriptomic profiling highlighted substantial metabolic reprogramming occurring in sepals and fruits, with major impacts on cell wall-related genes. While several Sl-AGL11-related phenotypes are reminiscent of class C MADS-box genes (TAG1 and TAGL1), the modifications observed on the placenta and cell wall and the Sl-AGL11 expression pattern suggest an action of this class D MADS-box factor on early fleshy fruit development.
Complications of Baerveldt Glaucoma Drainage Implants (1998)

A lower incidence of serious postoperative complications was observed in Baerveldt implantations in this study when compared with a recent report. Risk factors for serious complications were similar to trabeculectomy.
Effects of AAV-mediated knockdown of nNOS and GPx-1 gene expression in rat hippocampus after traumatic brain injury (2017)

Virally mediated RNA interference (RNAi) to knock down injury-induced genes could improve functional outcome after traumatic brain injury (TBI); however, little is known about the consequences of gene knockdown on downstream cell signaling pathways and how RNAi influences neurodegeneration and behavior. Here, we assessed the effects of adeno-associated virus (AAV) siRNA vectors that target two genes with opposing roles in TBI pathogenesis: the allegedly detrimental neuronal nitric oxide synthase (nNOS) and the potentially protective glutathione peroxidase 1 (GPx-1). In rat hippocampal progenitor cells, three siRNAs that target different regions of each gene (nNOS, GPx-1) effectively knocked down gene expression. However, in vivo, in our rat model of fluid percussion brain injury, the consequences of AAV-siRNA were variable. One nNOS siRNA vector significantly reduced the number of degenerating hippocampal neurons and showed a tendency to improve working memory. GPx-1 siRNA treatment did not alter TBI-induced neurodegeneration or working memory deficits. Nevertheless, microarray analysis of laser captured, virus-infected neurons showed that knockdown of nNOS or GPx-1 was specific and had broad effects on downstream genes. Since nNOS knockdown only modestly ameliorated TBI-induced working memory deficits, despite widespread genomic changes, manipulating expression levels of single genes may not be sufficient to alter functional outcome after TBI.
Electromechanical response of cellular electret films (1999)

Charged polypropylene films with a cellular structure show pseudopiezoelectric properties. Measurements of the direct and inverse electromechanical transducer constants of such films, relating to the operation as sensors and as actuators, respectively, yield values of ≈200 pC/N. These values can be explained with a theoretical model by assuming reasonable charge distributions and charge densities. The experimental and the theoretical results show the reciprocity of the transducer constants.