gebhart/patrepeval huggingface dataset:
Dynamic development of the protein corona on silica nanoparticles: composition and role in toxicity (2013)

The formation and composition of the protein corona on silica (SiO2) nanoparticles (NP) with different surface chemistries was evaluated over time. Native SiO2, amine (-NH2) and carboxy (-COO(-)) modified NP were examined following incubation in mammalian growth media containing fetal bovine serum (FBS) for 1, 4, 24 and 48 hours. The protein corona transition from its early dynamic state to the later more stable corona was evaluated using mass spectrometry. The NP diameter was 22.4 ± 2.2 nm measured by scanning transmission electron microscopy (STEM). Changes in hydrodynamic diameter and agglomeration kinetics were studied using dynamic light scattering (DLS). The initial surface chemistry of the NP played an important role in the development and final composition of the protein corona, impacting agglomeration kinetics and NP toxicity. Particle toxicity, indicated by changes in membrane integrity and mitochondrial activity, was measured by lactate dehydrogenase (LDH) release and tetrazolium reduction (MTT), respectively, in mouse alveolar macrophages (RAW264.7) and mouse lung epithelial cells (C10). SiO2-COO(-) NP had a slower agglomeration rate, formed smaller aggregates, and exhibited lower cytotoxicity compared to SiO2 and SiO2-NH2. Composition of the protein corona for each of the three NP was unique, indicating a strong dependence of corona development on NP surface chemistry. This work underscores the need to understand all aspects of NP toxicity, particularly the influence of agglomeration on effective dose and particle size. Furthermore, the interplay between materials and local biological environment is emphasized and highlights the need to conduct toxicity profiling under physiologically relevant conditions that provide an appropriate estimation of material modifications that occur during exposure in natural environments.
β-Glycosphingolipids improve glucose intolerance and hepatic steatosis of the Cohen diabetic rat (2008)

A link between altered levels of various gangliosides and the development of insulin resistance was described in transgenic mice. Naturally occurring glycosphingolipids were shown to exert immunomodulatory effects in a natural killer T (NKT) cell-dependent manner. This study examined whether glycosphingolipid-induced modulation of the immune system may reduce pancreatic and liver steatosis and stimulate insulin secretion in the Cohen diabetes-sensitive (CDS) rat, a lean model of non-insulin-resistant, nutritionally induced diabetes. Four groups of CDS rats fed a diabetogenic diet were treated with daily intraperitoneal injections of glycosphingolipids beta-glucosylceramide, beta-lactosylceramide, a combination of both (IGL), or vehicle (PBS) for up to 45 days. Immune modulation was assessed by fluorescence-activated cell sorting analysis of intrahepatic and intrasplenic lymphocytes. Steatosis was assessed by MRI imaging and histological examination of liver and pancreas, Blood glucose and plasma insulin concentrations were assessed during an oral glucose tolerance test. Administration of glycosphingolipids, particularly IGL, increased intrahepatic trapping of CD8 T and NKT lymphocytes. Pancreatic and liver histology were markedly improved and steatosis was reduced in all treated groups compared with vehicle-treated rats. Insulin secretion was restored after glycosphingolipid treatment, resulting in improved glucose tolerance. The immunomodulatory effect of beta-glycosphingolipids improved the beta-cell function of the hyperglycemic CDS rat. Thus our results suggest a role for the immune system in the pathogenesis of diabetes in this model.
Three-dimensional structure of thaumatin I, an intensely sweet protein. (1985)

Thaumatin and monellin are the two sweetest compounds known to man--about 100,000 times sweeter than sugar on a molar basis and 3000 times on a weight basis. These proteins represent a unique class of proteins that are taste-active. We report the three-dimensional structure of thaumatin I at 3.1 A resolution.
An heregulin-EGFR-HER3 autocrine signaling axis can mediate acquired lapatinib resistance in HER2+ breast cancer models (2013)

Molecular analysis of acquired therapeutic resistance to lapatinib identified a new resistance mechanism based on incomplete and "leaky" inhibition of EGFR by lapatinib. The selective pressure applied by incomplete inhibition of the EGFR drug target resulted in selection of ligand-driven feedback that sustained EGFR activation in the face of constant exposure to the drug. Inadequate target inhibition driven by a ligand-mediated autocrine feedback loop may represent a broader mechanism of therapeutic resistance to HER TKIs and suggests adopting a different strategy for selecting more effective TKIs to advance into the clinic.
Casting Methods and Plantar Pressure (2006)

Foot orthoses are widely used to treat various foot problems. A literature search revealed no publications on differences in plantar pressure distribution resulting from casting methods for foot orthoses. Four casting methods were used for construction of orthoses. Two foam box techniques were used: accommodative full weightbearing method (A) and functional semiweightbearing method (B). Also, two suspension plaster casting techniques were used: accommodative casting (C) and functional subtalar joint neutral position (Root) method (D). Their effects on contact area, plantar pressure, and walking convenience were evaluated. All orthoses increased the total contact area (mean, 17.4%) compared with shoes without orthoses. Differences in contact areas between orthoses for total plantar surface were statistically significant. Peak pressures for the total plantar surface were lower with orthoses than without orthoses (mean, 22.8%). Among orthoses, only the difference between orthoses A and B was statistically significant. Differences between orthoses for the forefoot were small and not statistically significant. The gait lines of the shoe without an insole and of the accommodative orthoses are more medially located than those of functional orthoses. Walking convenience in the shoe was better rated than that with orthoses. There were no differences in perception of walking convenience between orthoses A, B, and C. Orthosis D had the lowest convenience rating. The four casting methods resulted in differences between orthoses with respect to contact areas and walking convenience but only slight differences in peak pressures.
A heterogeneous set of FMR1 proteins is widely distributed in mouse tissues and is modulated in cell culture (1995)

The fragile X syndrome is an X-linked inherited disease and is the result of transcriptional inactivation of the FMR1 gene and the absence of its encoded FMR protein (FMRP). Using a specific monoclonal antibody directed against human FMRP, we have studied the steady-state levels of its murine homolog in several tissues and organs of adult and young mice. In immunoblot analyses, the antibody recognizes a heterogeneous subset of proteins with apparent molecular weights ranging from 80 to 70 kDa. These proteins are detected in all the 27 tissues tested; however, the relative proportion of each polypeptide recognized varies between tissues, and a significantly higher expression is observed in young animals. Northern blot analysis of RNA extracted from selected tissues from adult mouse shows that these tissues express the major 4.8 kb mRNA, although at different levels, and contain several additional shorter transcripts, particularly in muscular tissues. We also report that expression of the FMR1 gene is modulated in proliferating and quiescent primary mouse kidney cell cultures with an inverse relationship between levels of FMR1 mRNA and of its encoded proteins. This suggests that FMRPs are highly stable in quiescent cells and that FMR1 expression is likely post-transcriptionally controlled. Our results document the widespread expression of the FMR1 gene, and suggest that it is controlled by different mechanisms implicated in cell growth and differentiation.
Metabolism of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) by human cytochrome P4501B1 (1997)

Cytochrome P4501B1 (CYP1B1) is the most recently identified member of the dioxin-inducible CYP1 family. CYP1B1 is constitutively expressed in most human tissues, including colon and breast, and can activate numerous chemically diverse carcinogens. We evaluated the metabolism of the dietary heterocyclic amine carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) by microsomes from yeast expressing the human CYP1B1 protein. PhIP metabolites were analysed by HPLC with fluorescence and absorbance detection. We found that human CYP1B1 metabolizes PhIP to three products: N2-OH-PhIP, a mutagenic activation product; 4'-OH-PhIP, a detoxification product; and 2-OH-PhIP, the mutagenic potential of which is unknown. Metabolite identity was confirmed by co-elution with authentic standards and synchronous fluorescence spectroscopy. The identity of the 2-OH-PhIP standard was additionally confirmed by mass spectrometry. Kinetic studies of the formation of N2-OH-PhIP, 4'-OH-PhIP and 2-OH-PhIP by CYP1B1 indicated apparent Km values of 5.7 +/- 1.3, 2.2 +/- 0.5 and 1.3 +/- 0.2 microM, respectively. Apparent turnover rates were 0.40 +/- 0.03, 0.93 +/- 0.02 and 0.04 +/- 0.00 nmol product/min nmol P450, respectively. At saturating levels of substrate, CYP1B1-mediated formation of the non-mutagenic metabolite 4'-OH-PhIP was favored two-fold over that of the mutagenic metabolite, N2-OH-PhIP and >10-fold over that of 2-OH-PhIP. The formation of N2-OH-PhIP, a potent mutagen implicated in the etiology of human colon and breast cancer, indicates that CYP1B1 may play an important role in PhIP-mediated carcinogenesis.
Baseband filters for IS-95 CDMA receiver applications featuring digital automatic frequency tuning (2002)

This paper presents fully-integrated dual (I and Q) low-pass seventh-order Chebychev continuous-time filters for IS-95 CDMA channel selection applications. The capabilities of digital signal processors, available in almost all modern transceivers, are exploited to adapt the filter bandwidth to the desired frequency with minimum additional hardware. To fulfill the requirement of handling signals with a wide dynamic range, an active RC filter topology is adopted. Digital tunability is provided by constructing each integrating capacitor with an array of binary-weighted capacitors. The capacitors are switched in or out under the control of the DSP. The ratio of the fixed capacitor to the total variable capacitors is chosen based on the expected RC time-constants variations.
A study on the condition for differential electrophoretic transport at a channel entrance (2007)

Electrophoretic differential transport of ionic species in a solution moving from a large reservoir into a small channel is investigated numerically. The system setup is similar to the experiments of Polson, Savin, and Hayes (J. Microcol. Sep. 2000, 12, 98), where the bulk flow into a fused-silica capillary was driven by a pressure differential. A critical condition for achieving the defined differential transport near the channel entrance is found and this condition is solely determined by a dimensionless parameter when the geometry of the system is prescribed. This dimensionless parameter is the ratio between the electrophoretic migration velocity of the species based on the apparent electric intensity and the centerline fluid velocity of the fully developed channel flow. Species concentration distributions are also computed for various conditions. A separation technique can be derived from the experimental condition where a targeted division of species can be created at the channel entrance.
Cellular Uptake and Infection by Canine Parvovirus Involves Rapid Dynamin-Regulated Clathrin-Mediated Endocytosis, Followed by Slower Intracellular Trafficking (2000)

Canine parvovirus (CPV) is a small, nonenveloped virus that is a host range variant of a virus which infected cats and changes in the capsid protein control the ability of the virus to infect canine cells. We used a variety of approaches to define the early stages of cell entry by CPV. Electron microscopy showed that virus particles concentrated within clathrin-coated pits and vesicles early in the uptake process and that the infecting particles were rapidly removed from the cell surface. Overexpression of a dominant interfering mutant of dynamin in the cells altered the trafficking of capsid-containing vesicles. There was a 40% decrease in the number of CPV-infected cells in mutant dynamin-expressing cells, as well as a approximately 40% decrease in the number of cells in S phase of the cell cycle, which is required for virus replication. However, there was also up to 10-fold more binding of CPV to the surface of mutant dynamin-expressing cells than there was to uninduced cells, suggesting an increased receptor retention on the cell surface. In contrast, there was little difference in virus binding, virus infection rate, or cell cycle distribution between induced and uninduced cells expressing wild-type dynamin. CPV particles colocalized with transferrin in perinuclear endosomes but not with fluorescein isothiocyanate-dextran, a marker for fluid-phase endocytosis. Cells treated with nanomolar concentrations of bafilomycin A1 were largely resistant to infection when the drug was added either 30 min before or 90 min after inoculation, suggesting that there was a lag between virus entering the cell by clathrin-mediated endocytosis and escape of the virus from the endosome. High concentrations of CPV particles did not permeabilize canine A72 or mink lung cells to alpha-sarcin, but canine adenovirus type 1 particles permeabilized both cell lines. These data suggest that the CPV entry and infection pathway is complex and involves multiple vesicular components.
DNA-mediated electrostatic assembly of gold nanoparticles into linear arrays by a simple drop-coating procedure (2001)

The assembly of nanoparticles in topologically predefined superstructures is an important problem in the area of nanoscale architecture. In this letter, we demonstrate the electrostatic assembly of lysine-capped colloidal gold particles on drop-coated DNA films. Electrostatic interaction between the positive charges on the gold nanoparticles and the negative charges on the phosphate groups of the DNA template molecules leads to the assembly of the gold nanoparticles in linear superstructures. The use of DNA as templates for the assembly of nanoparticles shows promise for extension to more complex geometries through rational design of the DNA base sequences as well as in the realization of nanowires by stringing together metal nanoparticles.
Polymorphisms in Nucleotide Excision Repair Genes and Endometrial Cancer Risk (2011)

Because of multiple redundancies in DNA repair pathways (and therefore a low prior probability) and the large number of associations examined, false-positive findings are likely. Further characterization of the relation between variation in NER genes and endometrial cancer risk is warranted.
An algorithm for three‐dimensional visualization of radiation therapy beams (1988)

A computer algorithm to display radiation beams superimposed on three-dimensional (3-D) views of patient anatomy has been developed. It may be implemented as a postprocessing step to existing software for 3-D presentation and display. The algorithm takes as input a shaded 3-D view (reconstructed, for example, from computed tomography scans), together with the associated depth map, and generates as output an enhanced 3-D view highlighting in color the visible points which lie within the projected beam outlines. The algorithm is independent of the method used to generate the 3-D view (surface or volume rendering techniques may be used) and is independent of beam shape (beams may be modified with shielding blocks). It is not restricted to external surfaces and will correctly show radiation beams projected onto cut-away views of internal organs. The method is illustrated by application to a tangential pair for breast malignancy, using 3-D views generated with volume rendering software.
ColorSync: synchronizing the color behavior of your devices (2002)

In this paper we probe into some of the difficulties involved in obtaining consistent color reproduction, and review the concept of device-independent color matching. We then discuss how ColorSync 2.0 provides an operating-system level solution with its open architecture and cross-platform device profile description, as well as presenting some performance data.
Default Risk of Government Guarantees in Croatia (2011)

The Annex to the semi-annual report on the execution of the 2011 state budget, submitted by the Government for parliamentary debate and adoption contains a Report on Issued Guarantees1 . This Report shows that Croatia is still exposed to default risk in respect of issued guarantees, which might easily be converted into the general government debt. Particularly disturbing is the increase in outstanding guarantees from 0.7 % of GDP in 1996 to a high of 16.6 % in 2011.
Reactions between calcium oxide and flue gas containing sulfur dioxide at lower temperatures (1993)

Abstract An experimental study has been performed of the reactions occurring when the reactive particles of calcium oxide are exposed to sulfur dioxide bearing flue gas. Using a differential, fixed‐bed reactor, kinetic measurements have been made in the temperature range of 170 and 580°C. A relatively simple correlation based on the amassed data has been proposed. This correlation allows the estimation of the reaction rate as a function of temperature, conversion of the solids and concentration of sulfur dioxide in the gas phase. The proposed rate law equation makes it possible to predict in a straightforward manner the rate of sorption which would be required to design the performance of a desulfurization unit.
Fluorescent HPLC assay for 20-HETE and otherP-450 metabolites of arachidonic acid (2000)

This study describes a fluorescent HPLC assay for measuring 20-hydroxyeicosatetraenoic acid (20-HETE) and other cytochrome P-450 metabolites of arachidonic acid in urine, tissue, and interstitial fluid. An internal standard, 20-hydroxyeicosa-6(Z),15(Z)-dienoic acid, was added to samples, and the lipids were extracted and labeled with 2-(2,3-naphthalimino)ethyl trifluoromethanesulfonate. P-450 metabolites were separated on a C18 reverse-phase HPLC column. Coelution and gas chromatography-mass spectrometry studies confirmed the identity of the 20-HETE peak. The 20-HETE peak can be separated from those for dihydroxyeicosatrienoic acids, other HETEs, and epoxyeicosatrienoic acids. Known amounts of 20-HETE were used to generate a standard curve (range 1-10 ng, r(2) = 0.98). Recovery of 20-HETE from urine averaged 95%, and the intra-assay variation was <5%. Levels of 20-HETE were measured in 100 microliter of urine and renal interstitial fluid or 0.1 mg of renal tissue. The assay was evaluated by studying the effects of 1-aminobenzotriazole (ABT) on the excretion of 20-HETE in rats. ABT reduced excretion of 20-HETE by >65% and inhibited the formation of 20-HETE by renal microsomes. The availability of this assay should facilitate work in this field.
Analysis and application of miniature 3D inductor (2003)

The structure of the miniature 3D inductors is presented in this paper. The proposed miniature 3D inductors have been fabricated in a standard 0.35-/spl mu/m one-poly-four-metal (1P4M) CMOS process. According to the measurement results, the self-resonance frequency (f/sub SR/) of the proposed miniature 3D inductor is at least 34% higher than the conventional stacked inductor. Moreover, the proposed miniature 3D inductor occupies only 16% area of the conventional planar spiral inductor with the same inductance. The analytical equations are derived and the capacitances distribution model is proposed to elucidate why the miniature 3D inductor has the higher self-resonance frequency. A CMOS voltage controlled oscillator (VCO), which utilized the proposed miniature 3D inductors, has also been demonstrated.
Fabrication of 70 nm channel length polymer organic thin-film transistors using nanoimprint lithography (2002)

We report on the fabrication of short-channel polymer organic thin-film transistors (OTFTs) using nanoimprint lithography. Currently, there is significant interest in OTFTs due to their potential application in inexpensive, large-area electronics. However, polymer carrier mobilities are typically poor, and thus to increase the OTFT drive current per unit area, there is a need for short-channel devices. We have fabricated working devices with channel lengths from 1 μm down to 70 nm with high yields. The performance of these devices was studied as the channel length was reduced. We find that drive current density increases as expected, while the on/off current ratio remains 104. However, at short-channel lengths, OTFTs no longer saturate due to space charge limiting current effects.
Does Baum-Welch re-estimation help taggers? (1994)

In part of speech tagging by Hidden Markov Model, a statistical model is used to assign grammatical categories to words in a text. Early work in the field relied on a corpus which had been tagged by a human annotator to train the model. More recently, Cutting et al. (1992) suggest that training can be achieved with a minimal lexicon and a limited amount of a priori information about probabilities, by using an Baum-Welch re-estimation to automatically refine the model. In this paper, I report two experiments designed to determine how much manual training information is needed. The first experiment suggests that initial biasing of either lexical or transition probabilities is essential to achieve a good accuracy. The second experiment reveals that there are three distinct patterns of Baum-Welch reestimation. In two of the patterns, the re-estimation ultimately reduces the accuracy of the tagging rather than improving it. The pattern which is applicable can be predicted from the quality of the initial model and the similarity between the tagged training corpus (if any) and the corpus to be tagged. Heuristics for deciding how to use re-estimation in an effective manner are given. The conclusions are broadly in agreement with those of Merialdo (1994), but give greater detail about the contributions of different parts of the model.
Expression of the myc gene family in different stages of human colorectal cancer. (1989)

Colorectal carcinoma serves as a model system for the study of changes in gene expression and structure relating to tumorigenesis. In this study, the levels of c-myc, N-myc and L-myc mRNAs were assessed in normal human colonic mucosa in 33 cases representing different stages of adenocarcinoma and in 36 adenomatous polyps, the presumed premalignant stage. Consistent with the findings of Erisman et al. (1985), we found that the c-myc gene was overexpressed (3-24-fold) in approximately two-thirds of the tumors examined. Amplification of the gene (3-4-fold) was observed in 2 of 12 tumors examined and did not correlate with the level of expression. Greater amounts of c-myc-specific mRNA than occur in normal tissue was also found in about two-thirds of the polyps examined demonstrating that premalignant lesions also overexpress the gene. N-myc and L-myc specific transcripts can be detected at low abundance in normal colonic mucosa. These genes were found to be frequently overexpressed in tumors and polyps, but in most cases the level of overexpression was modest. A single case of adenocarcinoma showed an approximately 30-fold increase in the level of N-myc mRNA without gene amplification. Adenomatous polyps more frequently overexpressed the L-myc gene than tumors.