gebhart/patrepeval huggingface dataset:
Epigenomic Consequences of Immortalized Plant Cell Suspension Culture (2008)

Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture.
Study of the design model of a liquid metal induction pump (1998)

The design of an electromagnetic pump for liquid metal is optimized. The model includes both electrodynamics and fluid-dynamics of the liquid metal. End effects are included in the model, in order to take into account the finite length of the pump and consequently the decrease of efficiency. For the Electrodynamic model, the permeability of the ferromagnetic core is assumed to be infinite. A finite slot configuration of the primary windings is assumed. In the design problem considered, the optimization regards the electrical supply system, the pump dimensions and the slot configuration.
10-Gbps duobinary-4-PAM for High-Performance Access Networks (2014)

This paper reports on an experimental demonstration of a seven level duobinary-4-PAM signal operating at 10.16 Gbps, implemented analogically and featuring direct detection at the receiver side.
Synthesis of a [2.2.2] Cryptand Containing Reactive Functional Groups (2009)

The functional group-containing potassium ionophore 19(5),24(5)-dibromo-4,7,13,16,20,23-hexaoxa-1,10-diaza-19(1,2),24(1,2)-dibenzabicyclo[8.8.6]tetracosaphane has been synthesized.
Patterns of Chromosomal Alterations in Breast Ductal Carcinoma <b> <i>In situ</i> </b> (2004)

Abstract Purpose: Ductal carcinoma in situ (DCIS) is thought to be a nonobligate precursor of invasive cancer. Genomic changes specific to pure DCIS versus invasive cancer, as well as alterations unique to individual DCIS subtypes, have not been fully defined. Experimental Design: Chromosomal copy number alterations were examined by comparative genomic hybridization in 34 cases of pure DCIS and compared with 12 cases of paired synchronous DCIS and invasive ductal cancer, as well as to 146 additional cases of invasive breast cancer of ductal or lobular histology. Genomic differences between high-grade and low/intermediate-grade DCIS, as well as between pure DCIS and invasive cancer, were identified. Results: Pure DCIS showed almost the same degree of chromosomal instability as invasive ductal cancers. A higher proportion of low/intermediate-grade versus high-grade DCIS had loss of 16q (65 versus 12%, respectively; P = 0.002). When compared with lower grade DCIS, high-grade DCIS exhibited more frequent gain of 17q (65 versus 41%; P = 0.15) and higher frequency loss of 8p (77 versus 41%; P = 0.04). Chromosomal alterations in those cases with synchronous DCIS and invasive ductal cancer showed a high degree of shared changes within the two components. Conclusions: DCIS is genetically advanced, showing a similar degree of chromosomal alterations as invasive ductal cancer. The pattern of alterations differed between high- and low/intermediate-grade DCIS, supporting a model in which different histological grades of DCIS are associated with distinct genomic changes. These regions of chromosomal alterations may be potential targets for treatment and/or markers of prognosis.
Lightweight and Confidential Data Discovery and Dissemination for Wireless Body Area Networks (2014)

As a special sensor network, a wireless body area network (WBAN) provides an economical solution to real-time monitoring and reporting of patients' physiological data. After a WBAN is deployed, it is sometimes necessary to disseminate data into the network through wireless links to adjust configuration parameters of body sensors or distribute management commands and queries to sensors. A number of such protocols have been proposed recently, but they all focus on how to ensure reliability and overlook security vulnerabilities. Taking into account the unique features and application requirements of a WBAN, this paper presents the design, implementation, and evaluation of a secure, lightweight, confidential, and denial-of-service-resistant data discovery and dissemination protocol for WBANs to ensure the data items disseminated are not altered or tampered. Based on multiple one-way key hash chains, our protocol provides instantaneous authentication and can tolerate node compromise. Besides the theoretical analysis that demonstrates the security and performance of the proposed protocol, this paper also reports the experimental evaluation of our protocol in a network of resource-limited sensor nodes, which shows its efficiency in practice. In particular, extensive security analysis shows that our protocol is provably secure.
A<sub>1</sub>adenosine receptor-mediated Ins(1,4,5)<i>P</i><sub>3</sub>generation in allergic rabbit airway smooth muscle (1998)

The signal transduction pathway for A1 adenosine receptor in airway smooth muscle from allergic rabbits was studied by investigating the effect of the selective A1 adenosine-receptor agonist N6-cyclopentyladenosine (CPA) on tissue levels of inositol 1,4, 5-trisphosphate [Ins(1,4,5)P3] measured by protein binding assay. CPA caused a rapid, transient, and concentration-dependent elevation of Ins(1,4,5)P3 in airways from allergic rabbits. The agonist also produced a concentration-dependent contraction of the airway preparations from these animals. Both the Ins(1,4,5)P3 and contractile responses generated by CPA were attenuated by the phospholipase C (PLC) inhibitor U-73122, indicating the coupling of these responses to PLC. The CPA-induced Ins(1,4,5)P3 production observed in the allergic rabbit tissues was also inhibited by the adenosine-receptor antagonist 8-( p-sulfophenyl)-theophylline, suggesting that the effect was mediated by A1 adenosine receptors. On the other hand, the A2 adenosine-receptor agonist CGS-21680 was ineffective in altering the tissue concentration of Ins(1,4,5)P3, indicating that A2 adenosine receptors may not be involved in the activation of PLC in the allergic rabbit airway smooth muscle. In this preparation, the Gi-Go inhibitor pertussis toxin (PTX) attenuated the CPA-induced Ins(1,4,5)P3 accumulation, providing evidence that the generation of Ins(1,4,5)P3 by A1 adenosine-receptor stimulation is coupled to a PTX-sensitive G protein(s). The results suggest that activation of A1 adenosine receptors in allergic rabbit airway smooth muscle causes the production of Ins(1,4,5)P3 via a PTX-sensitive G protein-coupled PLC, and this signaling mechanism may be involved, at least in part, in the generation of contractile responses. It is hypothesized that this process may contribute to adenosine-induced bronchoconstriction in allergic asthma.
Comparison of 3M™ Petrifilm™ Environmental <i>Listeria</i> Plates against Standard Enrichment Methods for the Detection of <i>Listeria monocytogenes</i> of Epidemiological Significance from Environmental Surfaces (2007)

Environmental monitoring using sensitive methods for detection and elimination of harborage sites of Listeria monocytogenes is key to the control of this organism. The 3M Petrifilm Environmental Listeria (EL) Plate-a no enrichment method-was compared with the USDA/FSIS, modified USDA/FSIS (mUSDA), and ISO methods for detection/recovery of L. monocytogenes on 4 environmental surfaces (brick, dairy board, stainless steel, and epoxy resin). The efficacy of 3 sampling devices including the Microbial-Vac system((R)), environmental sponge, and 3M Quick swab in recovering epidemiologically significant strains of uninjured and sublethally injured L. monocytogenes from environmental surfaces was evaluated. Environmental surfaces were inoculated with Listeria to obtain final cell densities of approximately 10 to 100 CFU/100 cm(2). The surfaces were then sampled and processed. For all methods, percent recovery (% samples where Listeria was detected) was significantly higher (P < 0.05) for uninjured cells (75% to 100%) compared to injured cells (58.9% to 81.1%). The Petrifilm EL Plate method efficiently recovered both low level and injured Listeria populations from environmental test surfaces when used in conjunction with environmental sponge and the 3M Quick swab sampling. The mUSDA method was superior to all other methods for recovering both uninjured (100% recovery) and injured L. monocytogenes (80.8% to 81.1% recovery). Sponges and swabs were equally effective in recovering uninjured and injured Listeria and were significantly different (P < 0.05) from the Microbial-Vac system. The findings indicate that both mUSDA and Petrifilm EL Plate methods can be used for the detection of potentially injured Listeria on food processing environmental surfaces.
Synthesis of Cu2O from CuO thin films: Optical and electrical properties (2015)

Hole conducting, optically transparent Cu2O thin films on glass substrates have been synthesized by vacuum annealing (5×10−6 mbar at 700 K for 1 hour) of magnetron sputtered (at 300 K) CuO thin films. The Cu2O thin films are p-type and show enhanced properties: grain size (54.7 nm), optical transmission 72% (at 600 nm) and Hall mobility 51 cm2/Vs. The bulk and surface Valence band spectra of Cu2O and CuO thin films are studied by temperature dependent Hall effect and Ultra violet photo electron Spectroscopy (UPS). CuO thin films show a significant band bending downwards (due to higher hole concentration) than Cu2O thin films.
The Mirage of Impairing Drug Concentration Thresholds: A Rationale for Zero Tolerance Per Se Driving under the Influence of Drugs Laws (2012)

Motor vehicle crashes are a leading cause of morbidity and mortality in the United States. Drivers with measurable quantities of potentially impairing illicit or prescription drugs in their body fluids are multiple times more likely to be involved in motor vehicle crashes than those without such drugs in their bodies. Drug-related impairment, however, cannot be inferred solely on the basis of the presence of drugs in biological fluids. Thus, for more than a quarter century, there has been a search for drug blood concentrations that are the equivalent of the 0.08 g/dL threshold for alcohol-impaired driving in the United States. We suggest that such equivalents are a mirage, and cannot be determined due to variable drug tolerance, lack of consistent relationships between drug blood concentrations and impairment, innumerable drug combinations and multiple other factors. Thus, while the idea of determining impairing drug concentrations is attractive, it is ultimately unattainable, and withholding drugged driving legislation pending the acquisition of such data is tantamount to a plan for inaction with regard to an important and growing public health and safety problem. We propose specific legislation to address alcohol- and drug-impaired driving in the United States.
Taxonomies in operation, design, and meta-design (2005)

Taxonomies are a well-established instrument fororganizing and accessing resources in Information,Content and Knowledge Management (ICKM) systems.Furthermore, they contribute to a common understandingand an improved communication in the user community byfostering the development and usage of a sharedvocabulary.In addition to these operational usage scenarios, weargue in this paper that a taxonomy is also a valuablemedium in system design. We present a meta-designframework for systematically supporting the user in thesetup, customization and evolution of Web-based ICKMsystem instances, which is based on a model-based domainconstruction approach. Taxonomies are exploited both asthe fundamental basis for the construction process itselfand as the principal support for context-driven access the common metamodel in this framework implementingthe ontological commitment underlying the completeframework.These manifold forms of taxonomy exploitation aresupported by a flexible taxonomy component that enablesmultiple classifications of arbitrary resources, effectivetaxonomy management, and context-adaptive taxonomyreduction in our ICKM meta-design framework.
Extracting Troubles from Daily Reports based on Syntactic Pieces (2008)

PACLIC / The University of the Philippines Visayas Cebu College Cebu City, Philippines / November 20-22, 2008
Magnetic properties and microstructure of isolated Fe-Pt nanoparticle-monolayer assembly by protective coating (2005)

In order to diminish coalescence and interparticle sintering during high-temperature annealing of Fe-Pt nanoparticle films above 700 K, carbon or hafnium oxide overcoats are deposited on the nanoparticle-monolayer films. TEM observations reveal that grains in the Fe-Pt nanoparticle-monolayers are kept to be 4 nm in size even after annealing at 873 K; the particle size is close to the crystallite size estimated using Scherrer's formula as 4 nm from x-ray diffraction. In-plane coercivity of the monolayer films at room temperature is 4 kOe and much higher than that without any overcoats. Furthermore, the hafnium-oxide coated monolayer-film shows a high magnetocrystalline anisotropy (K/sub u/=4/spl times/10/sup 7/ erg/cm/sup 3/) and a high K/sub u/ V/kT value of 39.2 at 300 K, indicating the Fe-Pt nanoparticle-monolayers have high thermal stability as magnetic recording media.
ChemInform Abstract: PHOTOCHEMICAL RING‐OPENING REACTIONS OF SUBSTITUTED CHROMENES AND ISOCHROMENES (1975)

Abstract 2,2‐Dimethyl‐chromen (I) wird in Methanol photolytisch zu (II) und (III) gespalten; in Gegenwart von Corexfilter erhält man (III) sowie (IV)‐(VI).
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2 (2021)

Even in a homogeneous environment, macrophage proteomes are heterogeneous. This heterogeneity correlates to the inflammatory axis of classically and alternatively activated macrophages. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass spectrometry and demonstrates the potential for inferring transcriptional and post-transcriptional regulation from variability across single cells.
Monoclonal antibodies specific for Ia glycoproteins raised by immunization with activated T cells: possible role of T cellbound Ia antigens as targets of immunoregulatory T cells. (1984)

Two monoclonal antibodies, Y-3P and Y-8P, specific for conventional mouse Ia glycoprotein antigens are described. Both were raised by repeated immunization of primed mice with activated T cells over a period of 1 yr, and both detect a new and broad public Ia specificity. Both of the antibodies react with I-A subregion-controlled A alpha:A beta complexes of all mouse strains apart from the responder strain (H-2d), as well as the equivalent of A alpha:A beta complexes in rats carrying seven independent haplotypes. These antibodies have great utility as almost universal Ia reagents. On the basis of these results, we propose that Ia antigens presented to the immune system bound to activated T cells are immunogenic, and may induce the production of Ia antibodies of novel and broad specificity. In addition, we propose that such bound Ia glycoproteins could be a target for immunoregulatory T cells, and could account for the specificity of suppression of graft-vs-host reactions and Ia-restricted helper T cells observed by others in F1 animals injected with parental T cells.
Large-Scale Generation of Natural Killer Lymphocytes for Clinical Application (2002)

Natural killer (NK) lymphocytes can be used for adoptive immunotherapeutic strategies. Alternatively, they may be employed as adjuvants for stem cell/bone marrow transplantation, either to re-induce remission, or to purge autografts of contaminating malignant cells. We developed a new protocol that enables the generation of NK cells on a clinical scale in a closed system that enables good manufacturing practice (GMP) conformity. Aside from the initial NK cell inoculum, our protocol includes activated feeder cells [irradiated peripheral blood mononuclear cells (PBMC) and no transformed blasts], cytokines [interleukin-2 (IL-2) and IL-15], human serum, and a complex basic media formulation. During the whole expansion period of approximately 14 days, the cells were handled in PTFE (Teflon) bags, whereby fresh medium was added without opening the system. The use of immortalized or virus-transformed feeder cells, as used in many other current research protocols, was completely avoided. A precise controlling of a number of environmental factors was necessary to achieve reproducible results. Increases in NK cell number ranged between 80- and 200-fold. The resulting NK cells were CD56(+), CD3(-), and CD16(+) (75%). They were highly cytotoxic against different malignant target cells and did not produce significant levels of interferon-gamma. Therefore, they belonged to the cytotoxic rather than the immunoregulatory NK subpopulation. No non-specific activation against normal allogenous lymphocytes occurred. This work might permit the realization of future protocols for evaluating the clinical effect of NK lymphocytes in human disease.
A new endogenous natriuretic factor: LLU-alpha. (1996)

For over three decades, renal physiology has sought a putative natriuretic hormone (third factor) that might control the body's pool of extracellular fluid, an important determinant in hypertension, congestive heart failure, and cirrhosis. In our search for this hormone, we have isolated several pure natriuretic factors from human uremic urine that would appear, alone or in combination, to mark a cluster of phenomena previously presumed to be that of a single "natriuretic hormone." This paper reports the purification, chemical structure, and total synthesis of the first of these compounds, LLU-alpha, which proved to be 2,7,8-trimethyl-2-(beta-carboxyethyl)-6-hydroxychroman, presumably a metabolite of gamma-tocopherol. Both natural LLU-alpha and synthetic material are identical (except for optical activity) with respect to structure and biological activity. It appears that the natriuretic activity of LLU-alpha is mediated by inhibition of the 70 pS K+ channel in the apical membrane of the thick ascending limb of the kidney.
Proliferative activity in invasive breast carcinoma. (1996)

Start, Cross linking basic pathological science with applied clinical situations. Such interactions are enhanced by the use of photography or still video imaging.
Translational block to expression of the Escherichia coli Tn9-derived chloramphenicol-resistance gene in Bacillus subtilis. (1982)

The Gram-negative product-encoding Tn9-derived chloramphenicol-resistance (Cmr) gene can be cloned but not phenotypically expressed in Bacillus subtilis. We show that, even when transcribed from B. subtilis promoters, the ribosomal binding site for the Cmr gene does not function well in B. subtilis. The Cmr gene product, chloramphenicol acetyltransferase (CmAcTase; acetyl-CoA:chloramphenicol 3-O-acetyltransferase, EC 2.3.1.28), is detected in B. subtilis when the promoters, ribosomal binding sites, and initiation codons of B. subtilis genes are fused to the Cmr gene. These gene fusions lead to the in vivo production of mRNAs containing B. subtilis translation start signals followed in an open reading frame by the translation start site normally used by Escherichia coli to initiate translation of Cmr mRNA. Both fusion and native CmAcTase proteins are produced in E. coli, but only fusion CmAcTase is produced in B. subtilis. We conclude that the absence of native CmAcTase in B. subtilis is due to inability of the E. coli ribosomal binding site to function well in B. subtilis. Since fusion CmAcTase polypeptides are produced in E. coli, we conclude that these particular B. subtilis regulatory elements function heterologously in E. coli. The absence of a suitable binding site on the Cmr gene for B. subtilis ribosomes is consistent with reports that many E. coli genes are not expressed in B. subtilis and that E. coli mRNA functions poorly in B. subtilis in vitro translation systems. The functioning of B. subtilis regulatory sequences in E. coli is consistent with in vivo and in vitro data showing the expression of B. subtilis genes in E. coli. To confirm the hypothesis that the large CmAcTase proteins are NH2-terminal fusions of native CmAcTase we partially determined the sequence of one CmAcTase fusion protein.
Double Layer of a Gold Electrode Probed by AFM Force Measurements (2003)

Colloidal probe atomic force microscopy was used to determine the electric double layer interactions between a gold electrode and a spherical silica probe. The double layer properties of the gold/solution interface were varied through the pH and salt concentration of the electrolyte, as well as by externally applying an electric potential. The double layer potentials ψ(d) of the gold surface were obtained by fitting the force-distance curves according to the DLVO (Derjaguin-Landau-Verwey-Overbeek) theory, using earlier obtained values for the double layer potential of the silica probe as input parameter. It was found that the gold electrode combines the features of reversible and polarizable interfaces; i.e., its charge and potential are determined by both the solution pH and the external potential. The pH dependence is attributed to proton adsorption and desorption from oxidic groups on the gold surface. In the potential range studied, ψ(d) varies linearly with the applied potential; the variation in ψ(d) is roughly 10% of that in the applied potential. The potential of zero force (the external potential at which ψ(d) = 0) varies with pH. The various features of the gold/electrolyte interface are described well by an amphifunctional double layer model. The results of this study form the basis of the interpretation of adsorption studies on gold as a function of pH and externally applied potential.
Photo Wake-Up: 3D Character Animation From a Single Photo (2019)

We present a method and application for animating a human subject from a single photo. E.g., the character can walk out, run, sit, or jump in 3D. The key contributions of this paper are: 1) an application of viewing and animating humans in single photos in 3D, 2) a novel 2D warping method to deform a posable template body model to fit the person's complex silhouette to create an animatable mesh, and 3) a method for handling partial self occlusions. We compare to state-of-the-art related methods and evaluate results with human studies. Further, we present an interactive interface that allows re-posing the person in 3D, and an augmented reality setup where the animated 3D person can emerge from the photo into the real world. We demonstrate the method on photos, posters, and art. The project page is at https://grail.cs.washington.edu/projects/wakeup/.