gebhart/patrepeval huggingface dataset:
Four degree of freedom liquid dispenser for direct write capillary self-assembly with sub-nanoliter precision (2012)

Capillary forces provide a ubiquitous means of organizing micro- and nanoscale structures on substrates. In order to investigate the mechanism of capillary self-assembly and to fabricate complex ordered structures, precise control of the meniscus shape is needed. We present a precision instrument that enables deposition of liquid droplets spanning from 2 nl to 300 μl, in concert with mechanical manipulation of the liquid-substrate interface with four degrees of freedom. The substrate has sub-100 nm positioning resolution in three axes of translation, and its temperature is controlled using thermoelectric modules. The capillary tip can rotate about the vertical axis while simultaneously dispensing liquid onto the substrate. Liquid is displaced using a custom bidirectional diaphragm pump, in which an elastic membrane is hydraulically actuated by a stainless steel syringe. The syringe is driven by a piezoelectric actuator, enabling nanoliter volume and rate control. A quantitative model of the liquid dispenser is verified experimentally, and suggests that compressibility in the hydraulic line deamplifies the syringe stroke, enabling sub-nanoliter resolution control of liquid displacement at the capillary tip. We use this system to contact-print water and oil droplets by mechanical manipulation of a liquid bridge between the capillary and the substrate. Finally, we study the effect of droplet volume and substrate temperature on the evaporative self-assembly of monodisperse polymer microspheres from sessile droplets, and demonstrate the formation of 3D chiral assemblies of micro-rods by rotation of the capillary tip during evaporative assembly.
198-nm cw laser source for lithographic applications (2003)

As integrated circuitry becomes increasingly complex, the semiconductor industry continues to be driven towards the use of ever shorter exposure and inspection wavelengths to enable smaller feature sizes via optical lithography. This ongoing trend in turn provides an incentive for the development of new laser light sources to generate the required short optical wavelengths. A continuous-wave laser system capable of delivering more than 100 milliwatts of near-diffraction-limited output at a nominal wavelength of 198 nm has been developed by Coherent Laser Group with the support of International SeMaTech. The desired ultraviolet (uv) wavelength is obtained by sum-frequency mixing several hundred milliwatts of 244-nm pump light provided by either a frequency-doubled argon-ion laser or the equivalent output from a novel all-solid-state laser system (based upon optically pumped semiconductor technology) with several hundred watts of 1064-nm light circulating within a high-Q diode-pumped Nd:vanadate laser resonator. The overall laser system performance and operating characteristics will be described. In addition, ongoing observations of photo-induced damage in several materials commonly employed for uv-wavelength optical components will also be reviewed.
Composition and structure of boron nitride films deposited by chemical vapor deposition from borazine (1990)

The composition and structure of boron nitride films prepared by thermal and plasma enhanced chemical vapor deposition (CVD) using borazine as a precursor have been studied. Thermal CVD at temperatures between 475 and 550 °C using either a hot-wall or cold-wall reactor results in amorphous boron-rich films of approximate composition BN0.67. Plasma enhanced CVD consistently gives films of 1:1 boron to nitrogen stoichiometry, but the hydrogen content of films deposited below 300 °C is so high that the films react with atmospheric moisture. Optimum conditions for the growth of stoichiometric BN with relatively low hydrogen content were found to be low plasma power, hydrogen–borazine gas mixtures, and a substrate temperature of 550 °C. Films deposited under these conditions are mixtures of poorly crystalline hexagonal and cubic boron nitride.
A new technique for characterization of digital-to-analog converters in high-speed systems (2007)

In this paper, a new technique for characterization of digital-to-analog converters (DAC) used in wideband applications is described. Unlike the standard narrowband approach, this technique employs Least Square Estimation to characterize the DAC from dc to any target frequency. Characterization is performed using a random sequence with certain temporal and probabilistic characteristics suitable for intended operating conditions. The technique provides a linear estimation of the system and decomposes nonlinearity into higher-order harmonics and deterministic periodic noise. The technique can also be used to derive the impulse response of the converter, predict its operating bandwidth, and provide far more insight into its sources of distortion.
Evasion of the Mucosal Innate Immune System by Herpes Simplex Virus Type 2 (2009)

Understanding the mechanisms by which herpes simplex virus (HSV) evades host immune defenses is critical to defining new approaches for therapy and prevention. We performed transcriptional analyses and immunocytochemistry on sequential biopsy specimens of lesional tissue from the acute through the posthealing phases of recurrent mucocutaneous HSV-2 infection. Histological analysis of these biopsy specimens during the acute stage revealed a massive infiltration of T cells, as well as monocytes/macrophages, a large amount of myeloid, and a small number of plasmacytoid dendritic cells, in the dermis of these lesional biopsy specimens. Type I interferon (IFN-beta and IFN-alpha) was poorly expressed and gamma IFN (IFN-gamma) potently induced during time periods in which we detected abundant amounts of HSV-2 antigens and HSV-2 RNA. IFN-stimulated genes were also markedly upregulated, with expression patterns that more closely matched those in primary human fibroblasts treated by IFN-gamma than those in fibroblasts treated by IFN-beta. Transcriptional arrays of the same lesional biopsy sites during healing and at 2 and 4 weeks posthealing revealed no HSV nucleic acids or antigen; however, there was persistent expression of IFN-gamma, with very low levels of IFN-beta and IFN-alpha. The findings of extremely low levels of IFN-alpha and IFN-beta, despite the presence of a large number of cells capable of synthesizing these substances, suggest a potent alteration in host defense during HSV-2 infection in vivo. HSV-2's blockade of the innate immune system's production of type I IFN may be a major factor in allowing the virus to break through host mucosal defenses.
Combined simulator statistics and block code sampling to study performance enhancement of microarchitecture (2005)

This paper presents a simple approach combining the statistics of simulation and block code sampling to study the performance enhancement of the microarchitecture with duplicated pipelines (enhanced microarchitectures). We collect the statistics from the simulation of EEMBC benchmark code on a TriCore/spl trade/ 2.0 implementation and use them to sample blocks of code and simulate different enhanced microarchitectures. The new simulation results are used to analyse the performance benefits of each microarchitecture enhancement, which can narrow down the design space exploration.
Durham Microreactors for Direct Fluorination (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
High emission current of 1000 μA at 4 × 10−10 Pa from W⟨310⟩ cold field emitter in electron gun (2016)

Total cold field emission (CFE) current has generally been limited to 30 μA because a higher current may initiate a vacuum arc that destroys the emitter. However, high emission current is needed to reduce the operation time in analytical electron microscopy and to further enhance the brightness of CFE. The authors achieved a total emission current of 1000 μA by reducing the pressure around the electron gun to 4 × 10−10 Pa. This high emission current was achieved without initiating a vacuum arc apparently because the number of ions striking the emitter surface was reduced. While a high angular current density of 1670 μA/sr was obtained at 1000 μA, current fluctuation occurred during the initial “plateau region” period of the probe current, and this needs to be investigated. This fluctuation is attributed to surface adsorption of gases emitted by electron stimulated desorption (ESD). Evaluation of the effect of introducing dominant ESD gases, namely, H2 or CO, on the current fluctuation revealed that the adsorption of H2 maintained the plateau region while the adsorption of CO caused current fluctuation in the plateau region.
ECATS - Mission of Association for an environmentally compatible air transport system (2010)

After 5 years of operation and collaboration the ECATS Network of Excellence (NoE) will now transform itself into a registered Association of European Research Establishments and Universities leading in the field of aeronautics and the environment. The transition from NoE to the Association will take place during 2010 and 2011. This future ECATS Association has the vision to support endeavours to make aviation more sustainable focussing on scientific expertise and exchange of information. ECATS' Virtual Fuel Centre focusses on alternative fuel characterisation allowing operating a premix burner, measuring flame velocities, expanding kinetic schemes and spray characterisation. ECATS' Airport Air Quality (AAQ) focus area povides an assessment of this highly interdisciplinary research field, and develops improved characterisation and approximation specifications for aviation particulate matter emissions. ECATS' third focus area is dealing with global impact of aviation and green flight. Close collaboration is exploited in order to provide updated estimates and synergies with other programmes established. The future ECATS Association provides an efficient framework for collaboration between universities and research establishments and helps making aviation more sustainable.
Complications in reverse shoulder arthroplasty (2016)

The reported rate of complications of reverse shoulder arthroplasty (RSA) seems to be higher than the complication rate of anatomical total shoulder arthroplasty.The reported overall complication rate of primary RSA is approximately 15%; when RSA is used in the revision setting, the complication rate may approach 40%.The most common complications of RSA include instability, infection, notching, loosening, nerve injury, acromial and scapular spine fractures, intra-operative fractures and component disengagement.Careful attention to implant design and surgical technique, including implantation of components in the correct version and height, selection of the best glenosphere-humeral bearing match, avoidance of impingement, and adequate management of the soft tissues will hopefully translate in a decreasing number of complications in the future. Cite this article: Barco R, Savvidou OD, Sperling JW, Sanchez-Sotelo J, Cofield RH. Complications in reverse shoulder arthroplasty. <i>EFORT Open Rev</i> 2016;1:72-80. DOI: 10.1302/2058-5241.1.160003.
Comparison of the methods for profiling glycoprotein glycans—HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study (2007)

Mass spectrometry (MS) of glycoproteins is an emerging field in proteomics, poised to meet the technical demand for elucidation of the structural complexity and functions of the oligosaccharide components of molecules. Considering the divergence of the mass spectrometric methods employed for oligosaccharide analysis in recent publications, it is necessary to establish technical standards and demonstrate capabilities. In the present study of the Human Proteome Organisation (HUPO) Human Disease Glycomics/Proteome Initiative (HGPI), the same samples of transferrin and immunoglobulin-G were analyzed for N-linked oligosaccharides and their relative abundances in 20 laboratories, and the chromatographic and mass spectrometric analysis results were evaluated. In general, matrix-assisted laser desorption/ionization (MALDI) time-of-flight MS of permethylated oligosaccharide mixtures carried out in six laboratories yielded good quantitation, and the results can be correlated to those of chromatography of reductive amination derivatives. For underivatized oligosaccharide alditols, graphitized carbon-liquid chromatography (LC)/electrospray ionization (ESI) MS detecting deprotonated molecules in the negative ion mode provided acceptable quantitation. The variance of the results among these three methods was small. Detailed analyses of tryptic glycopeptides employing either nano LC/ESI MS/MS or MALDI MS demonstrated excellent capability to determine site-specific or subclass-specific glycan profiles in these samples. Taking into account the variety of MS technologies and options for distinct protocols used in this study, the results of this multi-institutional study indicate that MS-based analysis appears as the efficient method for identification and quantitation of oligosaccharides in glycomic studies and endorse the power of MS for glycopeptide characterization with high sensitivity in proteomic programs.
Quantification and Characterization of Mucosa-Associated and Intracellular Escherichia coli in Inflammatory Bowel Disease (2013)

Intracellular E. coli are more common in CD than in UC and not identified in HC. Most intracellular E. coli did not have characterizing pathogenic features, suggesting a significant role for defects in mucosal immunity or barrier dysfunction in their ability to gain intracellular access.
Induction of gastrin releasing peptide by all-trans retinoic acid in small cell lung cancer cells. (1998)

All-trans retinoic acid (RA) has been shown to inhibit cell proliferation while increasing neuroendocrine differentiation in small cell lung cancer (SCLC) cells. RA and related compounds are rapidly becoming integrated into clinical trials to prevent lung cancers and other aerodigestive neoplasms. We found that expression of gastrin releasing peptide (GRP), which can promote lung tumorigenesis in model systems, was increased by RA in SCLC cells which have functional retinoid signaling. In SCLC cells that possess functional GRP receptors, ectopic expression of RARc increased GRP expression and augmented cloning efficiency, demonstrating that these maneuvers result in biologically active GRP. SCLC cells with defects in RA pathway signaling did not efficiently induce GRP upon RA exposure. In these cells, transfection of RARs rendered the cells competent to induce GRP upon RA exposure. These data show that activation of intact retinoid signaling by RA can induce GRP, a growth factor that can act as a tumor promoter. Our findings suggest the possibility that retinoids may increase, rather than decrease, lung cancer risks in some individuals.
HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells (2017)

The HIV-1 frameshift-stimulating (FSS) RNA, a regulatory RNA of critical importance in the virus' life cycle, has been posited as a novel target for anti-HIV drug development. We report the synthesis and evaluation of triazole-containing compounds able to bind the FSS with high affinity and selectivity. Readily accessible synthetically, these compounds are less toxic than previously reported olefin congeners. We show for the first time that FSS-targeting compounds have antiviral activity against replication-competent HIV in human cells, including a highly cytopathic, multidrug-resistant strain. These results support the viability of the HIV-1 FSS RNA as a therapeutic target and more generally highlight opportunities for synthetic molecule-mediated interference with protein recoding in a wide range of organisms.
Properties of protein kinase and adenylate cyclase‐deficient variants of a macrophage‐like cell line (1979)

Stable variants of the macrophage-like cell line J774.2, defective in adenylate cyclase and protein kinase activities, were selected by cloning cells resistant to the growth-inhibitory effect of cholera toxin and 8-bromo-adenosine 3':5' cyclic monophosphoric acid (8 Br-cAMP), respectively. These variants were analyzed for their ability to respond to cyclic AMP-mediated enhancement of phagocytosis and cyclic AMP-mediated inhibition of plasminogen activator secretion and growtn. The adenylate cyclase variants were unaffected by cholera toxin but were sensitive to 8 Br-cAMP-mediated inhibition of plasminogen activator secretion and growth. One of these variants exhibited a defect in phagocytosis that could be corrected by 8 Br-cAMP. The protein kinase variants exhibited normal basal phagocytosis that could not be stimulated by either 8 Br-cAMP or cholera toxin; they were also insensitive to cyclic AMP-mediated inhibition of plasminogen activator secretion and growth. The studies demonstrate that the three effects of cyclic AMP in J774.2--inhibition of growth and plasminogen activator secretion, and enhancement of basal Fc-mediated phagocytosis--are mediated by a cyclic AMP-dependent portein kinase. The results support the usefulness of variants in cyclic nucleotide metabolism in understanding the regulation of differentiated cell function by cyclic AMP.
Abstract 5325: Inhibition of CD4+CD25+ regulatory T cell suppression to anti-tumor responses by OK-432 (lyophilized Streptococcus pyogenes) (2010)

Abstract It is important to control the suppressive activity to anti-tumor immune responses mediated by CD4+CD25+ regulatory T cell (Treg) for effective immunological cancer treatment. Recently, a number of studies have shed new light on recognition of pathogen-associated molecular patterns through toll like receptors (TLRs) to break the suppressive environment present at the tumor local site. TLR signals are not only able to block the suppressive activity of CD4+CD25+ Tregs but can also break CD8+ tolerance even in the presence of CD4+CD25+ Tregs. Recently, we reported that while high-avidity NY-ESO-1-specific CD4+ T cell precursors are indeed present in naïve T cell populations, their activation following peptide vaccination is kept under the strict control of Tregs, resulting in a selective activation/expansion of low-avidity NY-ESO-1 peptide-specific CD4+ T cells. Additionally, following DNA vaccination, high-avidity NY-ESO-1-specific CD4+ T cells can only be observed transiently and become rapidly suppressed by Tregs. Here, we focused on OK-432 (lyophilized preparation of Streptococcus pyogenes) that can stimulate TLRs and explored 1) whether OK-432 administrated into tumor-associated exudate fluids (chest or abdominal cavity) inhibits local Treg function and accumulation, and 2) whether OK-432 used as an adjuvant of cancer vaccine can break Treg suppression and induce the activation of high-avidity tumor antigen-specific T cell precursors. Levels of Tregs in cells collected from pleural effusion or ascites of cancer patients treated with OK-432 were assessed by staining with antibodies for CD4, CD25 and Foxp3. The frequency of Foxp3+ Tregs significantly decreased after OK-432 administration. Furthermore, suppressive function of Tregs from patients also decreased after OK-432 treatment. PBMCs were collected from patients receiving vaccination with tumor antigens (HER2 and NY-ESO-1), formulated in choresteryl hydrophobized pullulan (CHP) together with OK-432 and the presence of high-avidity NY-ESO-1-specific CD4+ T cells in effector/memory (CD25-CD45RO+) T cell population was examined. NY-ESO-1-specific CD4+ T cells were detected within CD45RO+ memory T cell population after vaccination. In contast to peptide vaccination, CD4+ T cell clones induced from these NY-ESO-1-protein vaccinated patients in the presence of OK-432 had high-affinity T cell receptors and recognized naturally-processed NY-ESO-1 protein presented by dendritic cells. Taken together, OK-432 appears to inhibit Treg function and contribute to the durable differentiation of high-avidity tumor antigen-specific naive T cell precursors into effector/memory T cells with relative resistance to Tregs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5325.
Hemoglobin conformation couples erythrocyte S -nitrosothiol content to O 2 gradients (2005)

It is proposed that the bond between nitric oxide (NO) and the Hb thiol Cys-beta(93) (SNOHb) is favored when hemoglobin (Hb) is in the relaxed (R, oxygenated) conformation, and that deoxygenation to tense (T) state destabilizes the SNOHb bond, allowing transfer of NO from Hb to form other (vasoactive) S-nitrosothiols (SNOs). However, it has not previously been possible to measure SNOHb without extensive Hb preparation, altering its allostery and SNO distribution. Here, we have validated an assay for SNOHb that uses carbon monoxide (CO) and cuprous chloride (CuCl)-saturated Cys. This assay is specific for SNOs and sensitive to 2-5 pmol. Uniquely, it measures the total SNO content of unmodified erythrocytes (RBCs) (SNO(RBC)), preserving Hb allostery. In room air, the ratio of SNO(RBC) to Hb in intact RBCs is stable over time, but there is a logarithmic loss of SNO(RBC) with oxyHb desaturation (slope, 0.043). This decay is accelerated by extraerythrocytic thiol (slope, 0.089; P < 0.001). SNO(RBC) stability is uncoupled from O(2) tension when Hb is locked in the R state by CO pretreatment. Also, SNO(RBC) is increased approximately 20-fold in human septic shock (P = 0.002) and the O(2)-dependent vasoactivity of RBCs is affected profoundly by SNO content in a murine lung bioassay. These data demonstrate that SNO content and O(2) saturation are tightly coupled in intact RBCs and that this coupling is likely to be of pathophysiological significance.
Lubrication in a corner (2005)

A mathematical model for the evolution of a thin film in an interior corner region is presented. The model is based on the idea that the film can be considered thin everywhere in the $\eta$ -direction if viewed in the new coordinate system $\xi\,{=}\,x^2\,{-}\,y^2$ , $\eta\,{=}\,2xy$ . Lubrication theory is applied to the governing equations written in this coordinate system. The exact integration of the mass conservation equation for a no-slip boundary condition yields a single evolution equation, which is integrated numerically. The evolution of a thin film driven by surface tension and gravity is predicted as a function of the Bond number and successfully compared to laboratory experiments.
Cryptosporidiosis in Children in Sub‐Saharan Africa: A Lingering Challenge (2008)

Hospital- and community-based studies in sub-Saharan Africa document a high prevalence of cryptosporidiosis in children aged 6-36 months, particularly among those who are malnourished or positive for human immunodeficiency virus (HIV) infection and during rainy seasons. This is despite advances in developed countries that have curbed the incidence of cryptosporidiosis in the general and HIV-positive populations. Transmission in sub-Saharan Africa appears to occur predominantly through an anthroponotic cycle. The preponderance of Cryptosporidium hominis, given its limited host range, and the dominance of the more ubiquitous Cryptosporidium parvum after coexposure to both species, however, suggest that the current knowledge of transmission is incomplete. Given the poor sanitation and hygiene, limited availability of antiretrovirals, and the high prevalence of cryptosporidiosis in children-independent of HIV infection-in this region, effective control measures for cryptosporidiosis are desperately needed. Molecular targets from the recently sequenced parasite genome should be exploited to develop an effective and safe treatment for children.