gebhart/patrepeval huggingface dataset:
Anodic bonding of imperfect surfaces (1983)

The intimate surface contact necessary for anodic bonding of a metal to a glass is examined in terms of the electrostatic forces which promote this contact and surface imperfections which prevent this contact. Surface imperfections that are considered include foreign particles, isolated hillocks, and periodic curved and angular surfaces. With curved and angular surfaces, a critical voltage exists that causes spontaneous mating of the surfaces by elastic or plastic deformation. Below this voltage, intimate surface contact is achieved by viscous flow. For isolated hillocks and foreign particles, surface conformation generally occurs by viscous flow because of large stress concentrations at these imperfections. The resulting time required for intimate surface contact is a very sensitive function of the imperfection size.
Farnesyltransferase inhibitors: mechanism and applications (2001)

Farnesyltransferase (FT) inhibitors (FTIs) are among the first wave of signal transduction inhibitors to be clinically tested for antitumour properties. FTIs were designed to attack Ras oncoproteins, the function of which depends upon post-translational modification by farnesyl isoprenoid. Extensive preclinical studies have demonstrated that FTIs compromise neoplastic transformation and tumour growth. In preclinical models, FTIs display limited effects on normal cell physiology and in Phase I human trials FTIs have been largely well tolerated. Exactly how FTIs selectively target cancer cells has emerged as an important question, one which has become more pressing with the somewhat disappointing results from initial Phase II efficacy trials. Although FTI development was predicated on Ras inhibition, it has become clear that the drugs' antineoplastic properties are based to a large degree on altering the prenylation and function of proteins other than Ras. One key candidate that has emerged is RhoB, an endosomal protein that has been implicated in selective growth inhibition and apoptosis in neoplastic cells. On the basis of mechanistic studies and other recent developments, we propose that FTIs may be useful to treat a unique spectrum of diseases including not only inflammatory breast cancer and melanoma but also non-neoplastic diseases such as diabetic retinopathy and macular degeneration.
Avian blood parasite infection during the non-breeding season: an overlooked issue in declining populations? (2013)

Q5.
The Human Xist Gene Promoter Prevents Silencing of an Integrated Reporter Gene. (2004)

Abstract Epigenetic silencing and position dependent expression are long-standing problems which continue to limit the development of gene replacement therapy. As a strategy to overcome this problem we have tested the ability of the human XIST (X inactivation-specific transcript) gene promoter to overcome epigenetic silencing. The XIST gene is one of a relatively small number of genes which are expressed from the inactive X chromosome. The product of this gene is an untranslated structural RNA which coats the X chromosome destined for inactivation prior to H3 Lys 9 hypoacetylation, H3 Lys 9 methylation, CpG island methylation and the subsequent silencing of most of the genes on the chromosome. Continued expression of the XIST gene in this highly repressive environment is required to maintain the chromosome in an inactive state. The region of the proximal promoter of the XIST gene on the inactive X chromosome has been shown to retain an active chromatin structure. Based on these findings we hypothesized that the XIST gene promoter would be able to resist the epigenetic changes which lead to transgene silencing. To test this idea, we subcloned a minimal XIST promoter upstream of an enhanced GFP reporter gene in a pUC-based plasmid which also contained a neomycin resistance gene. The same plasmid, with a CMV promoter, served as a control vector. The plasmids were electroporated into mouse erythroleukemia (MEL) cells and then grown in media containing G418. The MEL cell line was chosen because genes transferred into these cells are frequently silenced and because it is often used as a first screen for vectors with potential for use in therapeutic gene transfer to erythroid cells. Individual colonies were selected and G418 removed. After expansion of the clones, flow cytometry was used to determine the percentage of cells in each clonal population which were expressing GFP as determined by comparison to the untransduced MEL cell line. Silencing typically involves a gradual decrease in the proportion of cells expressing the integrated transgene. Statistical analyses of results were performed using the t-test. 16 XIST and 13 CMV clones were available for analysis at the start of the experiment (time 0). 11/13 CMV clones and 12/16 XIST clones initially expressed GFP. Of the clones which were expressing GFP, the average percentages of positive cells were higher for those with the XIST promoter (63% vs. 41%, p= 0.015). Expression was reanalyzed after 6 weeks of culture in the absence of G418 selection. At this time point, the average percentage of GFP expressing cells was much higher for the XIST clones (57% vs. 19%, p=0.00008) and when analyzed for silencing, XIST clones were expressing at an average of 90% of their time 0 levels vs. 46% for the CMV clones (p=.0008). These results indicate that the XIST promoter is resistant to silencing in our model system and is a candidate for further development and mechanistic studies.
Epidemiology of Alcohol-Related Liver and Pancreatic Disease in the United States (2008)

In the United States, AP is the most common discharge diagnosis among alcohol-related liver or pancreas complications, while CH has the highest case fatality rate and male to female ratio. Blacks have the highest frequency of alcohol-related pancreatic disease.
MicroRNA-mediated regulation of gene expression is affected by disease-associated SNPs within the 3′-UTR via altered RNA structure (2012)

Single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) or their target sites (miR-SNPs) within the 3'-UTR of mRNAs are increasingly thought to play a major role in pathological dysregulation of gene expression. Here, we studied the functional role of miR-SNPs on miRNA-mediated post-transcriptional regulation of gene expression. First, analyses were performed on a SNP located in the miR-155 target site within the 3'-UTR of the Angiotensin II type 1 receptor (AGTR1; rs5186, A > C) mRNA. Second, a SNP in the 3'-UTR of the muscle RAS oncogene homolog (MRAS; rs9818870, C > T) mRNA was studied which is located outside of binding sites of miR-195 and miR-135. Using these SNPs we investigated their effects on local RNA structure, on local structural accessibility and on functional miRNA binding, respectively. Systematic computational RNA folding analyses of the allelic mRNAs in either case predicted significant changes of local RNA structure in the vicinity of the cognate miRNA binding sites. Consistently, experimental in vitro probing of RNA showing differential cleavage patterns and reporter gene-based assays indicated functional differences of miRNA-mediated regulation of the two AGTR1 and MRAS alleles. In conclusion, we describe a novel model explaining the functional influence of 3'-UTR-located SNPs on miRNA-mediated control of gene expression via SNP-related changes of local RNA structure in non-coding regions of mRNA. This concept substantially extends the meaning of disease-related SNPs identified in non protein-coding transcribed sequences within or close to miRNA binding sites.
A simple physical model for scaling in protein-protein interaction networks (2005)

It has recently been demonstrated that many biological networks exhibit a "scale-free" topology, for which the probability of observing a node with a certain number of edges (k) follows a power law: i.e., p(k) approximately k(-gamma). This observation has been reproduced by evolutionary models. Here we consider the network of protein-protein interactions (PPIs) and demonstrate that two published independent measurements of these interactions produce graphs that are only weakly correlated with one another despite their strikingly similar topology. We then propose a physical model based on the fundamental principle that (de)solvation is a major physical factor in PPIs. This model reproduces not only the scale-free nature of such graphs but also a number of higher-order correlations in these networks. A key support of the model is provided by the discovery of a significant correlation between the number of interactions made by a protein and the fraction of hydrophobic residues on its surface. The model presented in this paper represents a physical model for experimentally determined PPIs that comprehensively reproduces the topological features of interaction networks. These results have profound implications for understanding not only PPIs but also other types of scale-free networks.
A comparison of methods for determining dimensionality in Rasch measurement (1996)

Abstract This study compares the Rasch item fit approach for detecting multidimensionality in response data with principal component analysis without rotation using simulated data. The data in this study were simulated to represent varying degrees of multidimensionality and varying proportions of items representing each dimension. Because the requirement of unidimensionality is necessary to preserve the desirable measurement properties of Rasch models, useful ways of testing this requirement must be developed. The results of the analyses indicate that both the principal component approach and the Rasch item fit approach work in a variety of multidimensional data structures. However, each technique is unable to detect multidimensionality in certain combinations of the level of correlation between the two variables and the proportion of items loading on the two factors. In cases where the intention is to create a unidimensional structure, one would expect few items to load on the second factor and the correlation between the factors to be high. The Rasch item fit approach detects dimensionality more accurately in these situations.
Electronic Structure of Bis(<i>o</i>-iminobenzosemiquinonato)metal Complexes (Cu, Ni, Pd). The Art of Establishing Physical Oxidation States in Transition-Metal Complexes Containing Radical Ligands (2001)

The ligand 2-anilino-4,6-di-tert-butylphenol and its 2-(3,5-dichloroanilino)-4,6-di-tert-butylphenol analogue react in CH(3)CN or CH(3)OH solutions with divalent transition metal ions in the presence of air and triethylamine. Depending on the metal:ligand ratio (1:1, 1:2, or 1:3) and the presence (or absence) of the cyclic amine 1,4-dimethyl-1,4,7-triazacyclononane (dmtacn), the following complexes have been isolated as crystalline solids: [Co(III)(L(ISQ))(3)] (1); [Cu(II)(dmtacn)(L(ISQ))]PF(6) (2); [Cu(II)(L(ISQ))(2)] (3); [Ni(II)(L(ISQ))(2)] (4a); [Ni(II)((Cl)L(ISQ))(2)] (4b); [Pd(II)(L(ISQ))(2)] (5). (L(ISQ))(-) represents the monoanionic o-iminobenzosemiquinonate radical (S(rad) = (1)/(2)). Compounds 1-5 have been characterized by single-crystal X-ray crystallography at 100(2) K. For all complexes it is unambiguously established that the O,N-coordinated o-iminobenzosemiquinonato(1-) ligand is present. Complexes 3, 4b, and 5 are square planar molecules which possess an S(t) = (1)/(2), 0, and 0 ground state, respectively, as was established by (1)H NMR and EPR spectroscopies and variable-temperature magnetic susceptibility measurements. Complex 2 possesses an S(t) = 1 ground state which is attained via strong intramolecular ferromagnetic coupling (J = +195 cm(-1)) between the d(x)2-(y)2 magnetic orbital of the Cu(II) ion and the pi-orbital of the ligand radical. Complex 1 contains three mutually orthogonal (L(ISQ))(-*) ligands and has an S(t) = (3)/(2) ground state. It is shown that the electronic structure of 4a and 5 is adequately described as singlet diradical containing a divalent, diamagnetic d(8) configurated central metal ion and two strongly antiferromagnetically coupled (L(ISQ))(-) radical ligands. It is concluded that the same electronic structure prevails in the classic bis(o-diiminobenzosemiquinonato)- and bis(o-benzosemiquinonato)metal complexes of Ni(II), Pd(II), and Pt(II). The electrochemistry of all complexes has been investigated in detail. For 3, 4a, and 5 a series of reversible one-electron-transfer waves leads to the formation of the anions and cations [M(L)(2)](2-),(1-),(1+),(2+) which have been characterized spectroelectrochemically. All redox processes are shown to be ligand-based.
Direct Thiazolidinedione Action on Isolated Rat Skeletal Muscle Fuel Handling Is Independent of Peroxisome Proliferator–Activated Receptor-γ−Mediated Changes in Gene Expression (2001)

Thiazolidinediones (TZDs) are believed to induce insulin sensitization by modulating gene expression via agonistic stimulation of the nuclear peroxisome proliferator-activated receptor-gamma (PPAR-gamma). We have shown earlier that the TZD troglitazone inhibits mitochondrial fuel oxidation in isolated rat skeletal muscle. In the present study, rat soleus muscle strips were exposed to TZDs to examine whether the inhibition of fuel oxidation is mediated by PPAR-gamma activation. Our findings consistently indicated direct, acute, and PPAR-gamma-independent TZD action on skeletal muscle fuel metabolism. Rapid stimulation of lactate release by 20 micromol/l troglitazone within 30 min suggested that direct TZD action on skeletal muscle in vitro does not rely on changes in gene expression rates (12.6 +/- 0.6 [control] vs. 16.0 +/- 0.8 micromol. g(-1). h(-1) [troglitazone]; P < 0.01). This conclusion was supported by the failure of actinomycin D and cycloheximide to block the effects of troglitazone. Mitochondrial fuel oxidation was consistently inhibited by six different TZDs (percent inhibition of CO(2) production from palmitate after 25 h: troglitazone, -61 +/- 2%; pioglitazone, -43 +/- 7%; rosiglitazone, -22 +/- 6%; BM13.1258, -47 +/- 9%; BM15.2054, -51 +/- 4%; and T-174, -59 +/- 4% [P < 0.005 each]), but not by PPAR-gamma agonistic compounds not belonging to the TZD class (JTT-501, -5 +/- 7% [NS]; prostaglandin J(2), 17 +/- 7% [P < 0.05]), which further argues against dependence on PPAR-gamma activation. In summary, our findings provided good evidence that direct inhibition of mitochondrial fuel oxidation in isolated skeletal muscle is a group-specific effect of TZDs and is independent of PPAR-gamma-mediated gene expression.
Searching images using Ultimedia Manager (1995)

IBM's Ultimedia Manager is a software product for management and retrieval of image data. The product includes both traditional database search and content based search. Traditional database search allows images to be retrieved by text descriptors or business data such as price, date, and catalog number. Content based search allows retrieval by similarity to a specified color, texture, shape, position or any combination of these. The two can be combined, as in 'retrieve all images with the text `beach' in their description, and sort them in order by how much blue they contain.' Functions are also available for fast browning, and for database navigation. The two main components of Ultimedia Manger are a database population tool to prepare images for query by identifying areas of interest and computing their features, and the query tool for doing retrievals. Application areas include stock photography, electronic libraries, retail, cataloging, and business graphics.
CapProbe: A Simple and Accurate Technique to Measure Path Capacity (2004)

Abstract: Measuring the capacity of the narrow link in an Internet path in an unobtrusive and end-to-end manner is a fundamental issue and has received a lot of attention in previous literature. Most attempts have been based on packet dispersion measurements, but they have been so far not very accurate. Both ‘Packet Pairs ’ and ‘Packet Trains ’ have been shown to be inadequate. In this work, we extend the packet dispersion paradigm as a result of a fundamental queuing delay observation. Our technique, called CapProbe, makes use of not only the dispersion between packets of the Packet Pair, but also the actual delays of the packets. Using various simulation experiments, we show that our technique works across a very broad range of cross-traffic scenarios. In fact, the only case where our technique does not work is when the cross-traffic is predominantly non-reactive (like UDP). Even in this case, the scheme fails only when the UDP traffic saturates the bottleneck link, a very unlikely event in the current Internet dominated by TCP applications.
NO inhibits signal transduction pathway for ATP release from erythrocytes via its action on heterotrimeric G protein G<sub>i</sub> (2004)

The release of ATP from erythrocytes involves a signal transduction pathway of which cystic fibrosis transmembrane conductance regulator, PKA, adenylyl cyclase, and the heterotrimeric G proteins G(s) and G(i) are components. In the pulmonary circulation, ATP released from the erythrocyte stimulates nitric oxide (NO) synthesis, thereby regulating vascular resistance. We reported that NO liberated from an NO donor inhibited ATP release from erythrocytes in response to decreased Po(2) or mechanical deformation. Here, we investigated the hypothesis that NO inhibits ATP release from erythrocytes via inactivation of G(i). Washed rabbit erythrocytes were incubated in the presence or absence of the NO donor N-(2-aminoethyl)-N-(2-hydroxy-2-nitrosohydrazino)-1,2-ethylenediamine (spermine NONOate; 100 nM, 20 min), followed by treatment with agents that activate specific components of the signal transduction pathway promoting ATP release. Neither ATP release nor cAMP accumulation induced by either forskolin (100 microM, n = 7) or iloprost (100 nM, n = 6) was inhibited by spermine NONOate. These experiments suggest that the inhibitory action of NO is not the result of inactivation of adenylyl cyclase or G(s), respectively. However, spermine NONOate completely inhibited ATP release in response to mastoparan (10 microm, P < 0.05, n = 5), a specific activator of G(i). Spermine (100 nM, 20 min), the polyamine remaining after liberation of NO from spermine NONOate, had no affect on mastoparan-induced ATP release (n = 4). These results support the hypothesis that NO inhibits ATP release from erythrocytes via inactivation of the heterotrimeric G protein G(i).
WLC22-3: New Distributed QoS Control Scheme for IEEE 802.16 Wireless Access Networks (2006)

The IEEE 802.16 WirelessMAN standard provides a comprehensive quality-of-service (QoS) control structure to enable flow Isolation and service differentiation over the common wireless network Interface. By specifying a particular set of service parameters, the media access control (MAC) mechanisms defined in the standard are capable of offering service guarantees on the connection basis. However, the design of efficient, flexible and yet bandwidth-saving scheduling algorithms for such QoS provisioning still remains an open topic. This paper proposes a new distributed QoS control scheme that guarantees particular service parameter settings for both uplink and downlink connections. Detailed simulation experiments are presented to study the performance and to validate the effectiveness of the proposed algorithm.
Tumor development is retarded in mice lacking the gene for urokinase-type plasminogen activator or its inhibitor, plasminogen activator inhibitor-1. (2000)

In vivo tumor progression in mice with targeted deficiencies in urokinase-type plasminogen activator (UPA-/-) and its inhibitor, plasminogen activator inhibitor-1 (PAI-1-/-), was studied using a fibrosarcoma tumor model. Murine T241 fibrosarcoma cells were s.c. implanted into three groups of mice with the following genotypes, wild-type (WT), UPA-/-, and PAI-1-/-. A significantly diminished primary tumor growth in UPA-/- and PAI-1-/- mice occurred, relative to WT mice. Tumors in UPA-/- and PAI-1-/- mice displayed lower proliferative and higher apoptotic indices and displayed a different neovascular morphology, as compared with WT mice. These results are consistent with the decreased growth rates of this tumor in these gene-deleted mice. Immunohistochemical analyses of the tumors revealed a decrease in vascularity and vascular endothelial growth factor expression only in tumors in PAI-1-/- mice. Analyses of the relative extents of corneal angiogenesis in these same animals, induced by basic fibroblast growth factor, corroborated the resistance of PAI-1-/- mice to neovascularization. The results obtained suggest that the host fibrinolytic system plays an important role in tumor growth in this model. Alterations in host expression of components of this system may alter tumor growth and dissemination by affecting the balance between tumor cell death and proliferation, as well as extracellular matrix changes needed for invasiveness and angiogenesis.
Multi-method modeling (2013)

Frequently, the problem cannot completely conform to one of the three existing modeling paradigms (discrete event, system dynamics, or agent based modeling). Thinking in terms of a single-method modeling language, the modeler inevitably either starts using workarounds (unnatural and cumbersome constructs), or just leaves part of the problem outside the scope of the model (treats it as exogenous). If our goal is to capture business, economic, and social systems in their interaction, this becomes a serious limitation. In this paper we offer an overview of most used multi-method (or multi-paradigm) model architectures, discuss the technical aspects of linking different methods within one model, and consider examples of multi-method models. The modeling language of AnyLogic is used throughout the paper.
Surface morphology analysis in correlation with crystallinity of CeO2(110) layers on Si(100) substrates (2000)

CeO 2 layers having various crystallinity are prepared in the vicinity of the critical condition for epitaxial growth, using conventional evaporation and electron beam assisted evaporation. Surface morphology of CeO2 layers is studied using atomic force microscopy in correlation with crystallinity of the layer determined by reflection high energy electron diffraction. It is clearly observed that surface morphology changes with crystallinity of the CeO2 layers. Single crystal CeO2(110) layers have a nanometer-scale-periodically corrugated surface structure, which consists of (111) facets. As the crystalline quality of samples becomes worse, the number of irregular shaped hillocks and tetrahedral hillocks increases, which correspond to distorted (110) grains and (111)-oriented polycrystalline grains, respectively. It is found that crystalline quality is not uniform but various crystallinity regions are distributed from place to place and their population ratio changes according to the degree of crystalline quality. The surface of polycrystalline layers with a tendency of (111) orientation consists of tetrahedral hillocks with irregular in-plane rotational orientations within the horizontal plane. These features are discussed in terms of the surface properties of the substrates at the early stage of growth.
Time-decorrelated multifocal array for multiphoton microscopy and micromachining (2000)

We demonstrate a temporally decorrelated, multifocal multiphoton microscope. Using an etalon, we split the 800-nm light from either an ultrashort-pulsed Ti:Al (2)O (3) oscillator or a Ti:Al (2)O (3) regenerative amplifier into an array of beamlets that are delayed with respect to one another in time. The collimated beams overlap at slightly different input angles at the entrance pupil of a 1.25-numerical aperture oil-immersion objective to produce an array of foci that are temporally decorrelated at the focal plane of the objective. The temporal decorrelation eliminates any interference among the foci and permits multifocal multiphoton imaging with the resolution of single-point illumination.