gebhart/patrepeval huggingface dataset:
Retinoid‐responsive transcriptional changes in epidermal keratinocytes (2009)

Retinoids (RA) have been used as therapeutic agents for numerous skin diseases, from psoriasis to acne and wrinkles. While RA is known to inhibit keratinocyte differentiation, the molecular effects of RA in epidermis have not been comprehensively defined. To identify the transcriptional targets of RA in primary human epidermal keratinocytes, we compared the transcriptional profiles of cells grown in the presence or absence of all-trans retinoic acid for 1, 4, 24, 48, and 72 h, using large DNA microarrays. As expected, RA suppresses the protein markers of cornification; however the genes responsible for biosynthesis of epidermal lipids, long-chain fatty acids, cholesterol, and sphingolipids, are also suppressed. Importantly, the pathways of RA synthesis, esterification and metabolism are activated by RA; therefore, RA regulates its own bioavailability. Unexpectedly, RA regulates many genes associated with the cell cycle and programmed cell death. This led us to reveal novel effects of RA on keratinocyte proliferation and apoptosis. The response to RA is very fast: 315 genes were regulated already after 1 h. More than one-third of RA-regulated genes function in signal transduction and regulation of transcription. Using in silico analysis, we identified a set of over-represented transcription factor binding sites in the RA-regulated genes. Many psoriasis-related genes are regulated by RA, some induced, others suppressed. These results comprehensively document the transcriptional changes caused by RA in keratinocytes, add new insights into the molecular mechanism influenced by RA in the epidermis and demonstrate the hypothesis-generating power of DNA microarray analysis.
How to very efficiently functionalize gold nanoparticles by “click” chemistry (2008)

Difficulties previously encountered in the very useful "click" functionalization of gold nanoparticles (AuNPs) resulting in low yields are now overcome by using specific conditions: 1:1 water-THF medium, stoichiometric CuSO(4) and sodium ascorbate, inert atmosphere at 20 degrees C that provide quantitative "click" reactions between azidoalkylthiolate-AuNPs with various hydrophilic (PEG-containing) and hydrophobic (organic and organometallic) alkynes.
A globally convergent adaptive pole placement algorithm without a persistency of excitation requirement (1984)

This paper presents an indirect adaptive control scheme for deterministic plants which are not necessarily minimum phase. Global convergence is established for the scheme in the sense that the closed loop poles are asymptotically assigned and the system input and output remain bounded for all time. A key feature of the scheme is that no persistency of excitation condition is required. The algorithm has been designed with time-varying problems in mind and uses recursive least squares with variable forgetting factor, normalized regression vectors, and a matrix gain with constant trace.
Maturation-Dependent Acquired Coronary Structural Alterations and Atherogenesis in the Dahl Sodium-Sensitive Hypertensive Rat (2002)

The maturation-dependent high-fat conditioning of these postweanling rats correlated with an accelerated rate of atherogenesis on the initiation of the high-sodium/high-fat diet, possibly as a direct result of an alteration in arterial elasticity.
Long–Term Effect of VVI Pacing on Atrial and Ventricular Function in Patients with Sick Sinus Syndrome (1998)

We conducted a prospective, 6-month echocardiographic study on the effect of VVI pacing on left atrial and ventricular function and dimensions in patients with sick sinus syndrome. Thirty-nine patients (23 women and 16 men, aged 71 +/- 9.2 years; 30 in sinus rhythm and 9 in atrial fibrillation) who had a VVI pacemaker implanted because of sick sinus syndrome were recruited in the study. In 26 patients who presented with and remained in sinus rhythm, paced left ventricular ejection fraction and stroke volume were significantly decreased (71.4% +/- 11.8% to 67.0% +/- 13.6%, and 73.9 +/- 29.0 cm3 to 66.3 +/- 21.1 cm3, respectively, P < 0.001 for both), whereas the paced diastolic dimension of the left atrium was significantly increased (3.2 +/- 0.7 cm to 3.7 +/- 0.9 cm, P < 0.001) at 6 months as compared with preimplantation. In nine patients with atrial fibrillation at implantation paced left ventricular ejection fraction at follow-up was significantly decreased (67.7% +/- 10.1% to 64.2% +/- 10.6%, P =0.003), but paced stroke volume and left atrial diastolic dimension were not significantly changed (75.1 +/- 25.6 cm3 to 79.0 +/- 22.7 cm3, and 4.3 +/- 1.2 cm to 4.6 +/- 1.5 cm, P = NS for both) at follow-up. Cessation of pacing and restoration of sinus rhythm in 21 patients at follow-up did not result in any significant change of ejection fraction (67.5% +/- 10.2% ti 67.6% +/- 9.7%, P = NS) whereas stroke volume was increased (59.1 +/- 19.6 cm3 to 69.1 +/- 22.3 cm3, P < 0.0001) in comparison with paced values. However, compared with preimplantation values, ejection fraction was significantly decreased (70.4% +/- 10.0% to 67.6% +/- 9.7%, P = 0.001), whereas stroke volume was not significantly changed (68.4 +/- 22.3 cm3 to 69.1 +/- 22.3 cm3, P = NS) during sinus rhythm at follow-up. In 14 of those patients, discontinuation of pacing resulted in a significant increase of left atrial fractional shortening (8.1% +/- 1.7% to 20.1% +/- 4.3%, P < 0.001) and significant increase of left atrial diastolic dimension compared with paced and preimplantation levels (3.8 +/- 0.7 cm vs 3.6 +/- 0.7 cm and 3.0 +/- 0.5 cm, respectively, P < 0.001). Long-term VVI pacing in patients with sick sinus syndrome results in increase of the left ventricular end-systolic dimension and permanent reduction of the left ventricular ejection fraction. In the left atrium, VVI pacing causes an immediate reduction of the fractional shortening as well as long-term increase of the diastolic dimension.
Two cylindrical obstacles in a rectangular waveguide-resonances and filter applications (1989)

Two metallic or lossy dielectric cylinders placed in one cross section of a rectangular waveguide are investigated by the orthogonal expansion method. Resonances are shown by frequency responses of the transmission coefficient. They are discussed by patterns of the magnetic field and diagrams of the Poynting vector. Physical explanations of the resonances are given. The structure may be used as a filter element. With two small dielectric posts, a frequency characteristic with two stopbands can be obtained. Center frequencies are tunable by moving the posts. Using one large metallic and one small dielectric post, a tunable passband characteristic can be realized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cloning, Sequencing, and Expression of the Gene Coding for the Human Platelet α <sub>2</sub> -Adrenergic Receptor (1987)

The gene for the human platelet alpha 2-adrenergic receptor has been cloned with oligonucleotides corresponding to the partial amino acid sequence of the purified receptor. The identity of this gene has been confirmed by the binding of alpha 2-adrenergic ligands to the cloned receptor expressed in Xenopus laevis oocytes. The deduced amino acid sequence is most similar to the recently cloned human beta 2- and beta 1-adrenergic receptors; however, similarities to the muscarinic cholinergic receptors are also evident. Two related genes have been identified by low stringency Southern blot analysis. These genes may represent additional alpha 2-adrenergic receptor subtypes.
Computer Vision, Statistics in (2005)

Abstract Computer Vision (CV) broadly refers to the discipline where extraction of useful 2D and/or 3D information from one or more images is of interest. Useful information could consist of features such as edges, lines, curves and textures, or information about depth, motion, object descriptions, etc. CV problems are usually ill‐posed inverse problems. Since the image data is usually obtained from sensors such as video cameras, infrared, radar, etc., the information extraction processes often have to deal with data that is corrupted by noise from the sensors and the environment. Statistics can help in obtaining robust and accurate solutions to these inverse problems by modeling the noise processes. We present here a broad overview of the applications of statistics to different computer vision problems and explain in detail two particular applications, tracking and motion analysis, where statistical approaches have been used very successfully.
Microstructural Properties of Combustion‐Synthesized and Dynamically Consolidated Titanium Boride and Titanium Carbide (1990)

Full‐density TiB 2 and TiC have been fabricated by combustion synthesis reactions followed by dynamic compaction of the still hot, porous ceramic body. The relationship between the morphologies and purities of the precursor powders used and the ceramic product structures is presented. Intergrain bonding and residual porosity of the dynamically consolidated products are found to depend strongly on the impurity levels of the precursor powders. Analysis of the TiC indicates that density and microhardness increase as a function of the C/Ti ratio, with maximum values at the ratio of 1.0.
A comprehensive SoC design methodology for nanometer design challenges (2006)

Summary form only for tutorial. SoC design methodologies are under constant revision due to adoption of fast shrinking process technologies at nanometer levels. Nanometer process geometries exhibit new complex design challenges in silicon which were not seen in higher geometries. This tutorial highlights nanometer chip design challenges and recommends a tool independent design flow which meets the current trends. Covered are ASIC synthesis concepts along with integrated design for testability flow. The focus here is on different approaches to address the convergence challenges during synthesis along with some of the key design optimizations and transformations which would directly impact quality of results (QoR) post P&R. Verification methodology is also discussed. New verification languages and structural tools for linting and code coverage, latest trends in functional verification from the methodology and technology perspective are covered. Also new verification methodology that identifies and provides definition of metrics for functional coverage is reviewed.
VIROLOGIC STUDIES OF ACUTE RESPIRATORY DISEASE IN YOUNG ADULTS (1972)

Hamre, D. and M. Beem (DepL Pediatrics, Univ. of Chicago, Chicago, III. 60637). Virologic studies of acute respiratory disease in young adults. V. Coronavirus 229E infections during six years of surveillance. Am J Epidemiol 96: 94–106, 1972.—In a surveillance study of acute respiratory disease in medical students that spanned six consecutive seasons between 1961 and 1968 and encompassed 937 student years of observation, infection with coronavirus 229E was identified by virus isolation and serologic studies. Virus isolation identified 12 infections, 8 in one season, 4 in another. Complement fixing (CF) antibody titer rises identified 133 infections that occurred in all six seasons of surveillance, involving from 15 to 35% of students in three seasons of “high” prevalence, and 1 to 5% in intervening seasons of “low” prevalence. Infection occurred in a winter-spring seasonal pattern and was associated with acute respiratory illness that was not clinically distinctive. Neutralizing antibody to 229E was commonly present in the sera of the students. The level of this did not appear to influence the occurrence of, or likelihood of illness with, reinfection as judged by CF seroconversion; however, the frequency of significant rise in neutralizing antibody titer with reinfection was inversely related to pre-infection levels of this antibody. Infection with other common respiratory viruses did not stimulate significant CF or neutralizing antibody titer rises to 229E.
Enhancing cofactor recycling in the bioconversion of racemic alcohols to chiral amines with alcohol dehydrogenase and amine dehydrogenase by coupling cells and cell‐free system (2018)

Alcohol dehydrogenase (ADH) and amine dehydrogenase (AmDH)-catalyzed one-pot cascade conversion of an alcohol to an amine provides a simple preparation of chiral amines. To enhance the cofactor recycling in this reaction, we report a new concept of coupling whole-cells with the cell-free system to enable separated intracellular and extracellular cofactor regeneration and recycling. This was demonstrated by the respective biotransformation of racemic 4-phenyl-2-butanol 1a and 1-phenyl-2-propanol 1b to (R)-4-phenylbutan-2-amine 3a and (R)-1-phenylpropan-2-amine 3b. Escherichia coli cells expressing S-enantioselective CpsADH, R-enantioselective PfODH, and NADH oxidase (NOX) was developed to oxidize racemic alcohols 1a-b to ketones 2a-b with full conversion via intracellular NAD<sup>+</sup> recycling. AmDH and glucose dehydrogenase (GDH) were used to convert ketones 2a-b to amines (R)-3a-b with 89-94% conversion and 891-943 times recycling of NADH. Combining the cells and enzymes for the cascade transformation of racemic alcohols 1a-b gave 70% and 48% conversion to the amines (R)-3a and (R)-3b in 99% ee, with a total turnover number (TTN) of 350 and 240 for NADH recycling, respectively. Improved results were obtained by using the E. coli cells with immobilized AmDH and GDH: (R)-3a was produced in 99% ee with 71-84% conversion and a TTN of 1410-1260 for NADH recycling, the highest value so far for the ADH-AmDH-catalyzed cascade conversion of alcohols to amines. The concept might be generally applicable to this type of reactions.
Physical characteristics of protein-deficient particles derived from the 50S ribosomal subunit (1976)

Sedimentation coefficients, diffusion coefficients, density increments, extinction coefficients, and molecular weights were determined for selected core particles from the 50S Escherichia coli ribosomal subunits. These core particles were found to be loosened structures containing less than half the protein present on the intact 50S subunits and totally lacking peptidyl transferase and polyphenylalanine synthesis activity unless reconstituted. The results of this study confirm that a loosening of the subunit takes place upon the removal of protein, but this loosening is not necessarily due to the loss of the protein.
Graph Theory and Its Applications (2005)

Already an international bestseller, with the release of this greatly enhanced second edition, Graph Theory and Its Applications is now an even better choice as a textbook for a variety of courses -- a textbook that will continue to serve your students as a reference for years to come.The superior explanations, broad coverage, and abundance
Synergistic and strain-specific effects of bovine spongiform encephalopathy and scrapie prions in the cell-free conversion of recombinant prion protein (2006)

This study describes the conversion of murine PrP(C) by PrP(Sc) from three different mouse scrapie strains (ME7, 87V and 22A) and from a mouse-passaged bovine spongiform encephalopathy (BSE) strain (BSE/Bl6). This was demonstrated by a modified, non-radioactive, cell-free conversion assay using bacterial prion protein, which was converted into a proteinase K (PK)-resistant fragment designated PrP(res). Using this assay, newly formed PrP(res) could be detected by an antibody that discriminated de novo PrP(res) and the original PrP(Sc) seed. The results suggested that PrP(res) formation occurs in three phases: the first 48 h when PrP(res) formation is delayed, followed by a period of substantially accelerated PrP(res) formation and a plateau phase when a maximum concentration of PrP(res) is reached after 72 h. The conversion of prokaryotically expressed PrP(C) by ME7 and BSE prions led to unglycosylated, PK-digested, abnormal PrP(res) fragments, which differed in molecular mass by 1 kDa. Therefore, prion strain phenotypes were retained in the cell-free conversion, even when recombinant PrP(C) was used as the substrate. Moreover, co-incubation of ME7 and BSE prions resulted in equal amounts of both ME7- and BSE-derived PrP(res) fragments (as distinguished by their different molecular sizes) and also in a significantly increased total amount of de novo-generated PrP(res). This was found to be more than twice the amount of either strain when incubated separately. This result indicates a synergistic effect of both strains during cell-free conversion. It is not yet known whether such a cooperative action between BSE and scrapie prions also occurs in vivo.
Experimental demonstration of replicated multimode interferometer power splitter in Zr-doped sol-gel (2006)

A single-mode waveguide and a 1 /spl times/ 3 multimode interference (MMI) power splitter are fabricated in hybrid zirconium (Zr)-doped sol-gel material by a microreplication technology with a polydimethylsiloxane (PDMS) replica. The power splitter, as optimized using a finite-difference beam-propagation method (FD-BPM) simulation with self-imaging effects, represents one of the first experimental demonstrations of a high-tolerance manufactured device using replication methods. The fabrication of the microreplicated power splitter demonstrates high-quality optical and geometrical properties. The local uniformity in thickness of the multimode waveguide is less than 1.0%, and the average surface roughness is about 5.35 nm. The measured splitting loss is less than 0.6 dB for both transverse polarizations at the 1550-nm wavelength. Experimental achievements indicate that the soft lithography technology allows for the performance of applications in integrated optical devices in Zr-doped sol-gel materials with high standards.
Purification and characterization of a 32-kDa laccase-like stilbene oxidase produced by Botrytis cinerea Pers.:Fr. (1998)

A 32-kDa laccase-like stilbene oxidase was purified to homogeneity (one single band on SDS-PAGE) from Botrytis cinerea liquid culture medium enriched with pectin. Two major isoforms with pI 4.35 and 4.3 were revealed by isoelectric focusing (IEF). This enzyme oxidizes the grape stilbenic phytoalexins, resveratrol and pterostilbene. Syringaldazine is poorly oxidized by this stilbene oxidase as compared to the rate of stilbene oxidation. This enzyme catalyses the oxidation of resveratrol to ?-viniferin.
Dynamic Network Embedding : An Extended Approach for Skip-gram based Network Embedding (2018)

Network embedding, as an approach to learn low-dimensional representations of vertices, has been proved extremely useful in many applications. Lots of state-of-the-art network embedding methods based on Skip-gram framework are efficient and effective. However, these methods mainly focus on the static network embedding and cannot naturally generalize to the dynamic environment. In this paper, we propose a stable dynamic embedding framework with high efficiency. It is an extension for the Skip-gram based network embedding methods, which can keep the optimality of the objective in the Skip-gram based methods in theory. Our model can not only generalize to the new vertex representation, but also update the most affected original vertex representations during the evolvement of the network. Multi-class classification on three real-world networks demonstrates that, our model can update the vertex representations efficiently and achieve the performance of retraining simultaneously. Besides, the visualization experimental result illustrates that, our model is capable of avoiding the embedding space drifting.
Development of a Sensitive Detection Method for Stressed <i>E</i>. <i>coli</i> O157:H7 in Source and Finished Drinking Water by Culture-qPCR (2011)

A sensitive and specific method that also demonstrates viability is of interest for detection of E. coli O157:H7 in drinking water. A combination of culture and qPCR was investigated. Two triplex qPCRs, one from a commercial source and another designed for this study were optimized from 5 different assays to be run on a single qPCR plate. The qPCR assays were specific for 33 E. coli O157:H7 strains tested and detected 500 cells spiked in a background of 10(8) nontarget bacterial cells. The qPCR detection was combined with an enrichment process using Presence Absence (P/A) broth to detect chlorine and starvation stressed cells. qPCR analysis performed post-enrichment allowed the detection of 3-4 cells/L as indicated by a sharp increase in fluorescence (lowering of Ct values) from pre-enrichment levels, demonstrating a 5-6 log increase in the number of cells. When six vulnerable untreated surface water samples were examined, only one was positive for viable E. coli O157:H7 cells. These results suggest that the culture-PCR procedure can be used for rapid detection of E. coli O157:H7 in drinking water.
Topology-Preserving Off-screen Visualization: Effects of Projection Strategy and Intrusion Adaption (2017)

With the increasing amount of data being visualized in large information spaces, methods providing data-driven context have become indispensable. Off-screen visualization techniques, therefore, have been extensively researched for their ability to overcome the inherent trade-off between overview and detail. The general idea is to project off-screen located objects back to the available screen real estate. Detached visual cues, such as halos or arrows, encode information on position and distance, but fall short showing the topology of off-screen objects. For that reason, state of the art techniques integrate visual cues into a dedicated border region. As yet, the dimensions of the navigated space are not reflected properly, which is why we propose to adapt the intrusion of the border pursuant to the position in space. Moreover, off-screen objects are projected to the border region using one out of two projection methods: Radial or Orthographic. We describe a controlled experiment to investigate the effect of the adaptive border intrusion to the topology as well as the users' intuition regarding the projection strategy. The results of our experiment suggest to use the orthographic projection strategy for unconnected point data in an adaptive border design. We further discuss the results including the given informal feedback of participants.
Modeling, Simulation, and Control Implementation for a Split-Torque, Geared Neutral, Infinitely Variable Transmission (1991)

<div class="htmlview paragraph">Split-torque, geared-neutral transmissions have been shown to improve vehicle performance over a conventional continuously variable transmission. Although control of these transmissions has presented significant problems in the past, we have been able to achieve good driveability and fuel economy through the use of an integrated engine/transmission control philosophy.</div> <div class="htmlview paragraph">Development of the transmission/engine control strategies are based on detailed dynamic models and computer simulations of the driveline. In developing the control laws, specific attention has been given to providing characteristics similar to that of a conventional automatic transmission, such as creep and hill-holding capabilities.</div> <div class="htmlview paragraph">Test results show adequate transmission response with high initial jerk if demanded, excellent stability at the geared-neutral point, and smooth transitions through the synchronous point as well as in all other driving conditions.</div>