gebhart/patrepeval huggingface dataset:
Method for noninvasive measurement of central aortic systolic pressure (1987)

A method for noninvasive generation of central aortic systolic pressure curves is presented. The method is based on plotting the occlusive pressure values applied at the brachial artery level against the time intervals needed for the aortic pressure wave to equalize and break through the occlusive pressure at the brachial artery level. These time intervals were obtained by measuring the time from the beginning of depolarization (the QRS complex) to the detection of the pressure wave at the temporarily occluded brachial artery. The validity of the method was documented by 3 different approaches. The pressure values measured by a device developed by us were superimposed on the simultaneously measured central intra-aortic pressure waves and all values were within one standard deviation from the central aortic recordings in 8 of the 10 patients studied. At the same time, the noninvasively recorded pressure waves were completely different from the peripheral artery pressure recorded simultaneously at the femoral artery site. The DP/DT values derived from the central aortic recordings and the noninvasive device correlated (r = 0.83). These results indicate that the noninvasive device measures the central aortic pressure or a close approximation of it. By combining noninvasive pressure measurements with volume measurements obtained by radionuclide angiography, noninvasive pressure-volume curves were generated in 10 subjects. Possible clinical application of the systolic noninvasive pressure-volume curves is suggested.
Complete, gene-specific siRNA libraries: Production and expression in mammalian cells (2005)

Short interfering RNAs (siRNAs) are widely used to silence the expression of specific genes. Current practice for designing effective siRNAs is to use algorithms based on sequence-efficacy correlations; however, there are many highly effective sequences that these algorithms do not anticipate. To ensure that the best siRNAs are identified, all possible gene-specific siRNA sequences of appropriate lengths should be screened in cell culture. Synthesizing and testing all such sequences individually is costly. A potentially much easier alternative is to prepare a mixture of all these sequences (a gene-specific library), express them in cells, select cells having the desired phenotype, and identify the siRNA contained within the selected cells. Here we describe two new methods for preparing and expressing such libraries. The first uses cloned Dicer or RNase III to digest gene-specific RNA duplexes to siRNAs, which are then converted to the corresponding DNA sequences by attaching RNA primers and performing reverse transcription-PCR. The second method involves partial DNase I digestion of gene-specific DNA, purification of a 20-30-bp fraction, and amplification by attaching DNA adapters followed by PCR. DNA libraries specific for TNF-alpha, DsRed, and part of the hepatitis C virus genome, generated by methods, were inserted into siRNA expression vectors between convergent human U6 and H1 promoters. Randomly selected clones from each library together with vectors expressing the corresponding target genes were cotransfected into 293FT cells and assayed for target gene inhibition. About 10%-20% of siRNAs represented in these libraries show significant inhibition of their target genes. Most of these inhibitory sequences are not predicted by existing algorithms.
Gas Sensing Interactions at Hydrogenated Diamond Surfaces (2007)

Hydrogenated diamond (HD) samples exhibit a p-type surface conductivity (SC) which is caused by transfer doping to an adsorbed liquid electrolyte layer. We report on gas sensing experiments showing that such samples selectively respond to NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> gases at room temperature. Successive substitution of H-terminated surface sites by O-termination ones causes an increase in both the sensor baseline resistance and the gas-induced resistance changes. Thermal desorption of the surface electrolyte layer, on the other hand, causes the sensor baseline resistance to increase and the gas sensing effect to disappear. Readsorption of the surface electrolyte reestablishes both the sensor baseline resistance and the gas sensing effect. Our results indicate that the gas sensing effect is caused by local pH-changes due to acid/base reactions of the adsorbed gas molecules in the surface electrolyte layer. It is argued that this dissociative gas sensing mechanism represents a valuable complement with regard to the established surface combustion mechanism that is operative on heated metal oxide surfaces.
Development of Protein Degradation Inducers of Androgen Receptor by Conjugation of Androgen Receptor Ligands and Inhibitor of Apoptosis Protein Ligands (2017)

Targeted protein degradation using small molecules is a novel strategy for drug development. We have developed hybrid molecules named specific and nongenetic inhibitor of apoptosis protein [IAP]-dependent protein erasers (SNIPERs) that recruit IAP ubiquitin ligases to degrade target proteins. Here, we show novel SNIPERs capable of inducing proteasomal degradation of the androgen receptor (AR). Through derivatization of the SNIPER(AR) molecule at the AR ligand and IAP ligand and linker, we developed 42a (SNIPER(AR)-51), which shows effective protein knockdown activity against AR. Consistent with the degradation of the AR protein, 42a inhibits AR-mediated gene expression and proliferation of androgen-dependent prostate cancer cells. In addition, 42a efficiently induces caspase activation and apoptosis in prostate cancer cells, which was not observed in the cells treated with AR antagonists. These results suggest that SNIPER(AR)s could be leads for an anticancer drug against prostate cancers that exhibit AR-dependent proliferation.
Reducing Maternal Mortality: An Ultrasound System for Village Midwives (2011)

On average a woman dies in childbirth approximately every 90 seconds, and the majority of these deaths take place in Africa and Asia [1]. While ultrasound imaging is an effective tool for identifying maternal mortality risk factors, it is nearly absent in many rural healthcare facilities in developing regions due to the high costs of both equipment and required training. To leverage existing healthcare systems commonly found in these contexts, we have focused on increasing the diagnostic capabilities of village midwives -- often central medical figures in rural and low-income communities. We have developed a low-cost, portable, easy-to-use ultrasound system designed specifically to enable local midwives to identify high-risk conditions for referral to a well-equipped health care facility. Our focus has been on designing an appropriate system for our context. Specifically, we had to: simplify our user interface, support a solitary work environment, balance cost and features, and create an integrated teaching help system. This paper describes technical, socio-technical, and socio-cultural factors, drawn from our collaboration with the University of Washington Department of Radiology and our field experiences with midwives in Uganda, that have influenced our design.
DNA-protein interactions at theS.cerevisiaeα2 operatorin vivo (1993)

Two homodimeric proteins, alpha 2 and MCM1, are required to repress transcription of a-cell type specific genes in haploid yeast alpha-cells. In vitro studies by others of the interactions of these proteins with operator DNA have suggested that MCM1 binds to the middle and alpha 2 to the ends of the 31 bp operator. We have previously shown that alpha 2 organizes chromatin structure adjacent to the operator; in the presence of alpha 2 repressor, a precisely positioned nucleosome abuts the operator in both minichromosomes and the genome. We present in vivo footprinting evidence consistent with occupancy of the operator by MCM1 in both a- and alpha-cells and by alpha 2 repressor in alpha-cells. Interestingly, our in vivo results differ from previous in vitro work in detail. In contrast to the broad block of reagent accessibility to DNA by the factors seen in vitro, we find a pattern of strand-specific protection or augmented reactivity in vivo. The in vivo results are consistent with genetic data concerning transcriptional regulation of a-cell specific genes and corroborate the crystallographic data of others.
Proteomics in plant biotechnology and secondary metabolism research (2000)

Proteomics, the systematic analysis of (differentially) expressed proteins, is a tool for the identification of proteins involved in cellular processes. Proteomics has already been used for many different applications in plant sciences, including the study of proteins of biosynthetic pathways leading to secondary metabolites. In secondary metabolism, many enzymes are involved, often working in close collaboration to catalyse cascades of reactions. Besides the enzymes, transport and regulatory proteins are also involved, which makes the proteome an essential topic for studying metabolic pathways. Proteomics technology is based on high-throughput techniques for the separation and identification of proteins, allowing an integral study of many proteins at the same time. For the separation of protein mixtures the most powerful technique available is two-dimensional polyacrylamide gel electrophoresis: after separation, proteins can be subsequently identified by mass spectrometry (MS). The increasing amount of genome sequence data has to be followed by deciphering the function of the genes and proteins. Studying differential expression by proteomics is a complementary tool for functional analysis. In this review practical aspects and applications of proteomics in plant sciences, with particular emphasis on secondary metabolism, are discussed. Copyright © 2000 John Wiley & Sons, Ltd.
A high performance 90 nm logic technology with a 37 nm gate length, dual plasma nitrided gate dielectric and differential offset spacer (2003)

A 90 nm logic technology is presented featuring an aggressively scaled 37 nm gate length, 1.3 nm EOT plasma nitrided gate dielectric with differential offset spacer and leading edge CV/I performance. NMOS and PMOS transistors have been optimized with different extension offsets for NMDD and PMDD implants, which enables independent optimization of short channel effects, parasitic capacitance and drive current. The gate dielectric meets reliability requirements at 1.2 V operation. The technology includes a standard Vt (SVt) transistor, low Vt (LVt) transistor and 1.5 V IO transistor with l00 nm gate length and dual plasma nitrided gate dielectric.
Early Growth and Development of Pawpaw [Asimina triloba (L.) Dunal] Seedlings in the Greenhouse as Influenced by Shade and Root-zone Modification (1997)

This experiment was designed to determine the optimal light level for growing pawpaw seedlings in the greenhouse. In addition, we wanted to determine if modifying the root-zone would positively impact pawpaw seedling growth and development. Experimental treatments were imposed from seed sowing until the plants were destructively harvested. The experimental design was a split-plot, where blocking was done by position in the greenhouse. The main plot of the experiment was shade. This was accomplished by growing seedlings under a wooden frame covered with shadecloth to reduce incident light intensity received by the plant by 30%, 55%, 80%, or 95%. The control treatment was 0% shade or ambient greenhouse light level. The split-plot was root-zone modification. Half of all growing containers were untreated (control) while the other half were painted with SpinOut™, a commercially available product used to reduce root spiraling in nursery containers. There were 40 replicate seedlings per experimental treatment combination per block. Seedling shoot length and unfolded leaf number was recorded twice a week from seedling emergence until destructive harvest. Whole-plant leaf area was also determined. Leaves, stems, and tap and lateral roots were separated and dried to determine biomass partitioned to the respective organs. Up to 55% shade did not significantly reduce whole-plant biomass, while plants at 80% and 95% shade were stunted. Shade in the greenhouse is not required as was previously thought. Specific leaf mass and lateral root mass decreased as shade increased. Neither tap or lateral root dry weights were significantly affected by root-zone modification. New recommendations for container production of pawpaws in the greenhouse will be discussed.
Determination of Cytotoxic Trichothecenes in Corn by Cell Culture Toxicity Assay (1987)

The great sensitivity of some cell species to toxins has been adapted to a direct biological determination of trichothecene contamination of food and feeds. The murine spleen lymphocyte stimulated by PHA (Phaseolus vulgaris phytohaemagglutinin) appeared to be the most convenient cells because of their particular sensitivity to cytotoxic trichothecenes and the opportunity to translate this cytotoxicity to immunosuppressive hazard, one of the most important concerns for trichothecenes. In this paper, the use of cell cultures was adapted for a survey of corn. The toxins were extracted by aqueous methanol, and the extract was defatted with hexane and purified on a silica gel/Florisil column. This extract was then used for a gas chromatographic (GC) determination and the biological test. The growth of cells was measured by the incorporation of tritiated thymidine (3H Tdr), and the inhibition was expressed by the IC50: concentration of corn extract inhibiting by half the 3H Tdr incorporation. We have tested pure toxins, control corn, corn spiked with T-2 toxin, corn experimentally inoculated with toxigenic Fusarium strains, and naturally contaminated corn. A good correlation exists between IC50 and the T-2 toxin concentration as determined by GC analysis. The response is not affected by the presence of zearalenone or by small amounts of deoxynivalenol. A quantitative evaluation of cytotoxic trichothecenes in corn is valuable in the range of 100 ppb to 10 ppm, expressed as T-2 toxin equivalents. The result is obtained in 48 h.
Amplified spontaneous emission in active channel waveguides produced by electron-beam lithography in LiF crystals (2001)

In this letter we report the observation of amplified spontaneous emission of the red light from LiF:F2 centers in active channel waveguides realized by electron-beam lithography in lithium fluoride crystals. Low pumping power densities have been used in quasi-continuous-wave regime at room temperature; the appreciable values of the gain coefficients, 4.67 cm−1 with an exciting power density of 0.31 W/cm2 at 458 nm, make this material a good candidate for the realization of active integrated optical devices.
An adaptive hybrid time‐stepping scheme for highly non‐linear strongly coupled problems (2005)

Abstract This paper deals with the design and implementation of an adaptive hybrid scheme for the solution of highly non‐linear, strongly coupled problems. The term ‘hybrid’ refers to a composite time stepping scheme where a controller decides whether a monolithic scheme or a fractional step (splitting) scheme is appropriate for a given time step. The criteria are based on accuracy and efficiency. The key contribution of this paper is the development of a framework for incorporating error criteria for stepsize selection and a mechanism for choosing from splitting or monolithic possibilities. The resulting framework is applied to silylation, a highly non‐linear, strongly coupled problem of solvent diffusion and reaction in deforming polymers. Numerical examples show the efficacy of our new hybrid scheme on both two‐ and three‐dimensional silylation simulations in the context of microlithography. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Investigation of a rotating biological contactor (RBC) for treatment of industrial wastewaters (1980)

An investigation of a rotating biological contactor (RBC) for treatment of industrial wastewaters from an explosives formulation and blending plant with associated nitric acid and acetic anhydride production and acetic acid dehydration facilities, was made by analyzing the influent and effluent for pH, alkalinity, dissolved oxygen, ammonia, nitrate/nitrite, BOD, COD, and formaldehyde, and confirmed that the wastewaters from this facility could be degraded biologically in RBC's. BOD and COD reductions of >95% and 85%, respectively, were achieved consistently. A maximum BOD loading of 2.5 lb of soluble BOD/1000 sq ft of disk per day was achieved. The RBC was manufactured by George A. Hormel and Co. The wastewater treatment facility studied should produce water of sufficient quality to meet EPA guidelines.
Production and Potential of Bioactive Glass Nanofibers as a Next‐Generation Biomaterial (2006)

Abstract Over the past decades, bioactive glass has played a central role in the bone regeneration field, due to its excellent bioactivity, osteoconductivity, and even osteoinductivity. Herein, exploitation of bioactive glass as a one‐dimensional nanoscale fiber by employing an electrospinning process based on a sol–gel precursor is reported for the first time. Under controlled processing conditions, continuous nanofibers have been generated successfully with variable diameters. The excellent bioactivity of the nanofiber is confirmed in vitro within a simulated body fluid by the rapid induction of bonelike minerals onto the nanofiber surface. The bone‐marrow‐derived cells are observed to attach and proliferate actively on the nanofiber mesh, and differentiate into osteoblastic cells with excellent osteogenic potential. The bioactive nanofibers have been further exploited in various forms, such as bundled filament, nanofibrous membrane, 3D macroporous scaffold, and nanocomposite with biopolymer, suggesting their versatility and potential applications in bone‐tissue engineering. Based on this study, the bioactive nanofibrous matrix is regarded as a promising next‐generation biomaterial in the bone‐regeneration field.
Load Limiting Behavior in CRS Tether Anchors as a Method to Mitigate Head and Neck Injuries Sustained by Children in Frontal Crash (2008)

Implementation of load-limiting behavior in the upper tether and lower LATCH anchors of the child restraint system effectively reduces the head and neck injuries sustained by toddlers in a frontal vehicle crash while controlling forward head excursion within the limits as defined by NHTSA.
3D image reconstruction using complete data in pinhole SPECT (2003)

Inhomogeneous spatial resolution or axial blurring is a major problem in conventional pinhole SPECT, which is largely attributed to the incompleteness of the acquired projection data sets. In this study we have developed new system that provides 3D images without the axial blurring. The complete projection data sets were acquired using a pinhole collimator fitted to a conventional gamma camera with different two circular orbits (i.e. the 90 degrees and 45 degrees tilted angles to axis of rotation). Data sets from these orbits satisfied the Tuy's condition (Tuy, 1983), to which the 3D-OSEM algorithm was applied. The present system was first evaluated by a cylindrical phantom that had several disk areas of 0.5 mm thickness filled with Tc-99m solution separated by a 10 mm gap. The reconstructed imaged with two orbital data sets demonstrated no axial blurring and better image quality than the image reconstructed with only one orbit. This study suggested that accurate reconstruction without axial blurring could be obtained by acquiring complete data set in pinhole SPECT. This system will be useful for quantitative analysis of bio-physiological functions in small animals.
Untethered Magnetic Micromanipulation (2015)

This chapter discusses the methods and state of the art in microscale manipulation in remote environments using untethered microrobotic devices. It focuses on manipulation at the size scale of tens to hundreds of microns, where small size leads to a dominance of microscale physical effects and challenges in fabrication and actuation. To motivate the challenges of operating at this size scale, the chapter includes coverage of the physical forces relevant to microrobot motion and manipulation below the millimeter-size scale. It then introduces the actuation methods commonly used in untethered manipulation schemes, with particular focus on magnetic actuation due to its wide use in the field. The chapter divides these manipulation techniques into two types: contact manipulation, which relies on direct pushing or grasping of objects for motion, and noncontact manipulation, which relies indirectly on induced fluid flow from the microrobot motion to move objects without any direct contact.
Abstract 424: Vascular Smooth Muscle Cell Expression of S100a12 in Vivo Induces Enhanced Oxidative Stress & Vascular Remodeling (2008)

S100A12 is a small calcium binding protein that is a signal transduction ligand of the receptor for advance glycation endproducts (RAGE). S100A12, like RAGE, is expressed in the vessel wall of atherosclerotic vasculature, particularly in smooth muscle cells (SMC). While RAGE has been extensively implicated in inflammatory states such as atherosclerosis, the role of S100A12 is less clear. We tested the hypothesis that expression of human S100A12 directly exacerbates vascular inflammation. Several lines of Bl6/J transgenic mice (tg) expressing human S100A12 in SMC under control of the SM22a promoter were generated. Primary aortic SMC from tg and wild type (wt) littermates were isolated and analyzed for (i) proliferation using MTS/Formazan Assay and BrdU incorporation, (ii) oxidative stress using using flow cytometry with MitoSOX antibody, oxidative DNA damage using immunofluorescence microscopy with anti-8-oxo-dG antibody, and NF-kB activation measured by EMSA and (iii) cytokine expression measured by IL-6 ELISA. Furthermore, the aortas from tg and wt mice were examined. Results: Tg but not wt SMC expressed S100A12 protein. Tg SMC had a significant 1.9 to 2.7 fold increase in conversion of MTS into Formazan at 24–96 hours likely reflective of increased metabolic activity since BrdU incorporation into DNA was less in tg compared to wt SMC (4% vs 21% positive BrdU nuclei, p &lt;0.05). Tg SMC showed significantly higher levels of mitochondrial generated ROS, nuclear staining for oxidative DNA damage which was not detected in the nuclei of wt SMC’s, and a 2.5 fold increase in NFkB activity. IL-6 production at baseline was higher in tg SMC’s (615 vs 213 pg/ml, p&lt; 0.05) and increased dramatically after LPS treatment (10 ng/ml) in tg SMC’s (2130 vs 415 pg/ml). Histologic examination of the thoracic aorta at 10 weeks of age revealed increased collagen deposition in the aortic media with fragmentation and disarray of elastic fibers. In vivo ultrasound revealed a progressive dilation of the aortic arch from age 10 weeks to 16 weeks of age (1.27 to 1.60 mm, p&lt;0.05) in tg but not in wt littermate mice (1.30 to 1.33 mm, p=0.1). These data reveal the novel finding that targeted expression of human S100A12 in SMC modulates oxidative stress, inflammation and vascular remodeling.