gebhart/patrepeval huggingface dataset:
Fabrication of 0.2 µm Fine Patterns Using Optical Projection Lithography with an Oil Immersion Lens (1992)

Fine patterns are fabricated by using optical projection lithography with both an oil immersion lens of NA=1.25 and a conventional single-layer resist. Chlorobenzene soak is used in order to remove the immersion oil and to improve the side wall profile of the resist patterns. Some samples are lightly etched by O 2 plasmas in order to remove a residual resist at the bottom of the resist patterns. Finally, it is found that a 0.18 µm fine resist pattern with a good edge definition can be fabricated. Al line and space pattern with a width of about 0.21 µm is also fabricated by lift-off technique.
Development of a methoxyfenozide‐responsive gene switch for applications in plants (2006)

The ecdysone receptor (EcR) has been used to develop gene switches for conditional regulation of transgene expression in plants and humans. All EcR-based gene switches developed to date for use in plants are monopartate and require micromolar concentrations of ligand for activation of the transgene; this has limited the use of these gene switches. We have developed a Choristoneura fumiferana ecdysone receptor (CfEcR)-based two-hybrid gene switch that works through the formation of a functional heterodimer between EcR and the retinoid X receptor (RXR) upon application of the chemical ligand methoxyfenozide. Methoxyfenozide is already registered for field use with an excellent safety profile, and it has potential as a gene switch ligand for applications in the field. The receptor constructs were prepared by fusing DEF domains (hinge region plus ligand-binding domain) of CfEcR to the GAL4 DNA-binding domain and EF domains (ligand-binding domain) of ultraspiracle from Choristoneura fumiferana (CfUSP) or RXR from Locusta migratoria (LmRXR), Mus musculus (MmRXR) or Homo sapiens (HsRXR) to the VP16 activation domain. These receptor constructs were tested for their ability to induce expression of the luciferase gene placed under the control of 5x GAL4 response elements and -46 35S minimal promoter in tobacco, corn and soybean protoplasts and in transgenic Arabidopsis and tobacco plants. By adopting the two-hybrid format, the sensitivity of the CfEcR gene switch has been improved from micromolar to nanomolar concentrations of methoxyfenozide. The sensitivity of the CfEcR + LmRXR two-hybrid switch was 25 to 625 times greater than the monopartate gene switch, depending on the plant species tested.
Quantitative analysis of heart rate variability (1995)

In the modern industrialized countries every year several hundred thousands of people die due to sudden cardiac death. The individual risk for this sudden cardiac death cannot be defined precisely by common available, noninvasive diagnostic tools like Holter monitoring, highly amplified ECG and traditional linear analysis of heart rate variability (HRV). Therefore, we apply some rather unconventional methods of nonlinear dynamics to analyze the HRV. Especially, some complexity measures that are based on symbolic dynamics as well as a new measure, the renormalized entropy, detect some abnormalities in the HRV of several patients who have been classified in the low risk group by traditional methods. A combination of these complexity measures with the parameters in the frequency domain seems to be a promising way to get a more precise definition of the individual risk. These findings have to be validated by a representative number of patients. (c) 1995 American Institute of Physics.
Matrix Metalloprotease 2-Responsive Multifunctional Liposomal Nanocarrier for Enhanced Tumor Targeting (2012)

A novel "smart" multifunctional drug delivery system was successfully developed to respond to the up-regulated matrix metalloprotease 2 (MMP2) in the tumor microenvironment and improve cancer cell-specific delivery of loaded drugs. The system represents a surface-functionalized liposomal nanocarrier, for which two functional polyethylene glycol (PEG)-lipid conjugates were synthesized and characterized. The functionalized liposome was further modified with the tumor cell-specific antinucleosome monoclonal antibody (mAb 2C5). In the resulting system, several drug delivery strategies were combined in the same nanocarrier in a simple way and coordinated in an optimal fashion. The functions of the nanocarrier include (i) the hydrophilic and flexible long PEG chains to prevent nanocarrier nonspecific interactions and prolong its circulation time; (ii) a nanoscale size of the system that allows for its passive tumor targeting via the enhanced permeability and retention (EPR) effect; (iii) a mAb 2C5 to allow for the specific targeting of tumor cells; (iv) a matrix metalloprotease 2-sensitive bond between PEG and lipid that undergoes cleavage in the tumor by the highly expressed extracellular MMP2 for the removal of PEG chains; (v) cell-penetrating peptide (TATp) triggering of the enhanced intracellular delivery of the system after long-chain PEG removal and exposure of the previously hidden surface-attached TATp. It is shown that such a design can enhance the targetability and internalization of nanocarriers in cancer cells.
Naturally Occurring Incompatibilities between Different Culex pipiens pallens Populations as the Basis of Potential Mosquito Control Measures (2013)

Our findings indicate that naturally occurring patterns of cytoplasmic incompatibility between Cx. pipiens pallens populations can be the basis of a control strategy for this important vector species. The observed incompatibilities are caused by Wolbachia. More tests including field trials are warranted to evaluate the feasibility of this strategy as a supplement to other control measures.
Combinatorial libraries against libraries for selecting neoepitope activation-specific antibodies (2010)

A systematic approach to the discovery of conformation-specific antibodies or those that recognize activation-induced neoepitopes in signaling molecules and enzymes will be a powerful tool in developing antibodies for basic science and therapy. Here, we report the isolation of antibody antagonists that preferentially bind activated integrin Mac-1 (alpha(M)beta(2)) and are potent in blocking neutrophil adhesion and migration. A novel strategy was developed for this task, consisting of yeast surface display of Mac-1 inserted (I) domain library, directed evolution to isolate active mutants of the I domain, and screening of phage display of human antibody library against the active I domain in yeast. Enriched antibody library was then introduced into yeast surface two-hybrid system for final quantitative selection of antibodies from monomeric antigen-antibody interaction. This led to highly efficient isolation of intermediate to high affinity antibodies, which preferentially reacted with the active I domain, antagonized the I domain binding to intercellular adhesion molecule (ICAM)-1, complement C3 fragment iC3b, and fibronectin, and potently inhibited neutrophil migration on fibrinogen. The strategy demonstrated herein can be broadly applicable to developing antibodies against modular domains that switch between inactive and active conformations, particularly toward the discovery of antibody antagonists in therapeutic and diagnostic applications.
Impact of Oral Chronic Administration of Sildenafil in Children and Young Adults After the Fontan Operation (2011)

Evaluation of: Goldberg DJ, French B, McBride MG et al. Impact of oral sildenafil on exercise performance in children and young adults after the Fontan operation: a randomized, double-blind, placebo-controlled, crossover trial. Circulation 123, 1185-1193 (2011). After the Fontan operation, patients often have decreased exercise capacity as a result of an inability to increase cardiac output during exercise. Evidence exists that limitation in ventricular preload, related to pulmonary artery resistance plays an important role. A drug able to decrease pulmonary vascular resistance might increase transpulmonary flow and ventricular preload, therefore improving cardiac output and exercise performance. The article by Goldberg et al. is the first randomized, double-blind, placebo controlled, crossover trial to evaluate the impact of the phosphodiestarase-5 inhibitor sildenafil on exercise performance in patients after they have received the Fontan operation. The study included 28 patients with a mean age of 14.9 years. In this population, 6 weeks of sildenafil administration significantly improved ventilatory efficiency. The authors also noted an increase in exercise capacity during submaximal exercise, after 6 weeks of sildenafil in those patients with single left or mixed ventricular morphology and in those with more advanced heart failure (baseline serum brain natriuretic peptide level >100 pg/ml). The drug was well tolerated with no significant side effects. These findings suggest that sildenafil may play a role in improving exercise performance and exercise-induced breathlessness in children and young adults with single-ventricle physiology after the Fontan operation. Additional data on the possible benefit in terms of long-term clinical outcome and safety of sildenafil in this setting are needed.
RoadRunner: Towards Automatic Data Extraction from Large Web Sites (2001)

The paper investigates techniques for extracting data from HTML sites through the use of automatically generated wrappers. To automate the wrapper generation and the data extraction process, the paper develops a novel technique to compare HTML pages and generate a wrapper based on their similarities and differences. Experimental results on real-life data-intensive Web sites confirm the feasibility of the approach.
Mode of Action of Pituitary Growth Hormone on Target Cells (1985)

Normal postnatal somatic growth becomes progressively dependent on GH with time. In contrast to other hormones, GH is the only hormone known to produce a dose-dependent stimulation of postnatal growth. Most of the effects attributed to GH action appear to be the result of a direct effect of GH on cells in different peripheral tissues, including cartilage. In addition to the growth-stimulating effect, GH has the intrinsic properties of being able to exert both insulin-like and insulin-antagonistic effects in adipose tissue and skeletal muscle. These two apparently antagonistic effects seem to be explained by the stage of responsiveness of the target cells to GH, which is determined by the previous influence of endogenous GH. An inhibition of adenylate cyclase with a concomitant decrease in intracellular cAMP might be an important early cellular event in the course of GH action, but it is not known whether or how this change in nucleotide metabolism relates to the various expressed effects of the hormone. The recognition that GH directly interacts with chondrocytes in cartilage suggests that alterations in the concentration of circulating somatomedins cannot be the only factor regulating skeletal growth. The recent discovery by Green and coworkers (42) demonstrating that GH specifically stimulates the differentiation of cloned preadipose cells and myoblasts in tissue culture may be a major breakthrough in the understanding of the mechanism of action of the growth-promoting effect of GH. Green (42) has proposed that GH directly stimulates terminal differentiation of cells in many different tissues including epiphyseal plate cartilage. The finding that GH binds specifically to cells in the resting cell zone but not to differentiated chondrocytes in the growth plate suggests that prechondrocytes in the growth plate are the target cells for GH action. If it is correct that GH directly stimulates the differentiation of prechondrocytes, we suggest that, during the process of chondrocyte differentiation in the growth plate, the genes that code for growth factors of the somatomedin class, such as IGF-I, are expressed. As a consequence, the clonal expansion of the chondrocytes in the proliferative zone of the growth plate that occurs in vivo during the process of normal growth is the result of this local production of growth factors.
Small RNA asymmetry in RNAi: Function in RISC assembly and gene regulation (2005)

RNAi is a conserved gene-specific regulatory mechanism, which silences target gene expression transcriptionally and post-transcriptionally. The RNAi machinery converts the sequence specific information of a long double stranded RNAs (dsRNAs) into small 21-22 nt long dsRNAs (siRNAs, miRNAs) which assemble into an effector complex, the RNA induced silencing complex (RISC). RISC assembly is asymmetric; one strand of an siRNA or a miRNA preferentially incorporates into the RNA-protein complex. Here, I review the rules of the asymmetric RISC formation and discuss their possible regulatory function in several steps in RNAi.
A method for the synthesis of submicron particles (1987)

Powder synthesis by thermally induced vapor-phase reactions in aerosol reactors is described. The powders generated by this technique consist of high-purity, spherical, nonagglomerated, and uniformly sized particles&#13;\nin the 0.1-µm size range. Most of the particles are crystalline spheres. A theoretical examination based on the discrete-sectional model is presented. The comparison shows that the calculated size distribution of the final product from the aerosol reactor is fairly consistent with that observed experimentally.
Glycosaminoglycans inhibit Candida albicans adherence to extracellular matrix proteins (1992)

The ability of Candida albicans to adhere to subendothelial extracellular matrix (ECM) may be important in the pathogenesis of disseminated candidiasis. ECM proteins, such as fibronectin, laminin, and types I and IV collagen bind C. albicans avidly. These proteins all posses heparin-binding domains. The influence of the glycosaminoglycans (GAGS) including heparin, heparan sulfate and dextran sulfate on C. albicans adherence to subendothelial ECM and ECM proteins was studies. It was demonstrated that the GAGS inhibited C. albicans adherence to ECM and ECM proteins. This possibly occurred by the GAGS binding to the ECM proteins and, in so doing, masking a preferred ligand for C. albicans adherence.
Surface Roughness, Porosity, and Texture as Modifiers of Cellular Adhesion (1996)

Substrate topography in the micrometer range is reviewed as a modifier of the response of cultured cells and of biocompatibility when implanted into tissues. Characterization methods for substrate topography are discussed, including scanning electron microscopy, profilometry, laser scanning, and confocal microscopy. Because of the current technical limitations in reproducing micron-level topographic details, only one method, ion-beam etching, has been found suitable for texturing substrates on nonplanar surfaces.
Positive surgical margins and ipsilateral breast tumor recurrence predict disease‐specific survival after breast‐conserving therapy (2003)

Positive surgical margins and IBTR are predictors of systemic recurrence and disease-specific survival after BCT. Aggressive local therapy is necessary to ensure adequate surgical margins and to minimize IBTR.
Use NIR spectroscopy for on-line gasoline analysis (1992)

The traditional method of determining a gasoline's distillation range is to do simple distillation and measure the relationship between distill-off volume vs. temperature according to the strict conditions of GB255-77 (Chinese standard), and similar standards in other countries. However, this method is time consuming, requires large samples, and is not suited for rapid on-line measurement. This paper reports that with the aid of multiple linear regression analysis, a better method of determining distillation range was established by short wavelength near infrared (SW-NIR) spectra. Thus, this research offers a reliable means of analysis that is accurate, convenient, inexpensive and quick enough for on-line analysis.
Discovering patterns to extract protein–protein interactions from full texts (2004)

The program is available on request from the authors.
The Short Isoform of NF‐YA Belongs to the Embryonic Stem Cell Transcription Factor Circuitry (2012)

Totipotency of embryonic stem cells (ESCs) is controlled at the transcriptional level by a handful of transcription factors (TFs) that promote stemness and prevent differentiation. One of the most enriched DNA elements in promoters and enhancers of genes specifically active in ESCs is the CCAAT box, which is recognized by NF-Y, a trimer with histone-like subunits--NF-YB/NF--YC--and the sequence-specific NF-YA. We show that the levels of the short NF-YA isoform--NF-YAs--is high in mouse ESCs (mESCs) and drops after differentiation; a dominant negative mutant affects expression of important stem cells genes, directly and indirectly. Protein transfections of TAT-NF-YAs stimulate growth and compensate for withdrawal of leukemia inhibitory factor (LIF) in cell cultures. Bioinformatic analysis identifies NF-Y sites as highly enriched in genomic loci of stem TFs in ESCs. Specifically, 30%-50% of NANOG peaks have NF-Y sites and indeed NF-Y-binding is required for NANOG association to DNA. These data indicate that NF-Y belongs to the restricted circle of TFs that govern mESCs, and, specifically, that NF-YAs is the active isoform in these cells.
Database marketing: the ultimate marketing tool (1993)

From the Publisher:
Database marketing is the ultimate extension of direct marketing-selling to an individual rather than to groups, coming full circle to the one-on-one relationship eroded by decades of mass marketing. Other books discuss the subject in theory, but only Marketing shows how to use this revolutionary tool to sell everything from packaged goods to financial services. Marketing delivers inside guidance from the industry's acknowledged master strategist. Ed Nash reveals the wealth of database techniques he has pioneered for mega-marketers like Procter & Gamble, Chrysler, Merrill Lynch, and Mutual of Omaha. Whether you're an executive looking for bottom-line proof or a marketing manager in the trenches, you'll discover the facts you need to know, including how to calculate the economics of database marketing (and see why it's often more cost-effective than any other advertising or promotional method); mine existing sources of names; build, refine, and enhance your own custom lists; apply databases in every aspect of marketing - to introduce products, build retail traffic, cross-sell, and extend product lines; launch conquest mail against specific users of competing brands; take advantage of psychographics as well as demographic and category usage methods; solicit loyalty (because your own customers are probably your most neglected market); soothe your customers' concerns about privacy - and even use them to strengthen the sales relationship. Database marketing is the marketing battleground of the next century, which is why major corporations are already building their arsenals, says Ed Nash. Join the leaders. Marketing is your complete reference - and your indispensable guide to the most significant marketing tool since direct marketing itself.
Systematic identification in silico of covalently bound cell wall proteins and analysis of protein-polysaccharide linkages of the human pathogen Candida glabrata (2004)

Candida glabrata is an important cause of systemic candidiasis in humans. This paper reports a systematic analysis of the putative glycosylphosphatidylinositol-modified (GPI) proteins of C. glabrata, a large part of which are covalently bound to the cell wall glucan network and the remainder of which are retained in the plasma membrane, and of cell wall proteins (CWPs) which are covalently bound in a mild-alkali-sensitive manner. In silico genomic analysis revealed 106 putative GPI proteins. Fifty-one of these GPI proteins could be categorized as adhesive proteins, potentially implicated in fungus-host interactions or biofilm formation during the development of fungal infections. Eleven proteins belonged to well-known GPI protein families of glycoside hydrolases, probably involved in cell wall expansion and remodelling during growth. Other identified GPI proteins included phospholipases, aspartic proteases, homologues of ScEcm33p and ScKre1p, and structural CWPs. Interestingly, the GPI algorithm predicted three orthologues of an abundant CWP in S. cerevisiae, Cwp1p, which is absent in Candida albicans. To evaluate the in silico predictions, isolated cell walls were extracted using HF-pyridine, which specifically cleaves phosphodiester bonds, to release GPI-CWPs. Immunological analysis of the extract using one-dimensional SDS-PAGE and anti-ScCwp1p antiserum indicated the presence of a Cwp1p homologue in C. glabrata cell walls. Further analysis by two-dimensional gel electrophoresis and electrospray ionization tandem mass spectrometry (ESI-MS/MS) confirmed the presence of two of the predicted Cwp1p proteins, Cwp1.1p and Cwp1.2p. Crh1p, a putative 1,3-beta-glucan remodelling enzyme, was also identified. In silico genomic analysis further revealed five putative Pir proteins (Pir1-5p) and five members of the Bgl2 glycoside hydrolase family 17, belonging to a class of putative CWPs that can be extracted with NaOH. Immunological analysis of mild-alkali-extracted CWPs showed the presence of a ScPir2p homologue. Together, these experimental data and in silico predictions represent the first systematic analysis of the C. glabrata cell wall proteome.
Improving Physical Layer Secrecy Using Full-Duplex Jamming Receivers (2013)

This paper studies secrecy rate optimization in a wireless network with a single-antenna source, a multi-antenna destination and a multi-antenna eavesdropper. This is an unfavorable scenario for secrecy performance as the system is interference-limited. In the literature, assuming that the receiver operates in half duplex (HD) mode, the aforementioned problem has been addressed via use of cooperating nodes who act as jammers to confound the eavesdropper. This paper investigates an alternative solution, which assumes the availability of a full duplex (FD) receiver. In particular, while receiving data, the receiver transmits jamming noise to degrade the eavesdropper channel. The proposed self-protection scheme eliminates the need for external helpers and provides system robustness. For the case in which global channel state information is available, we aim to design the optimal jamming covariance matrix that maximizes the secrecy rate and mitigates loop interference associated with the FD operation. We consider both fixed and optimal linear receiver design at the destination, and show that the optimal jamming covariance matrix is rank-1, and can be found via an efficient 1-D search. For the case in which only statistical information on the eavesdropper channel is available, the optimal power allocation is studied in terms of ergodic and outage secrecy rates. Simulation results verify the analysis and demonstrate substantial performance gain over conventional HD operation at the destination.