gebhart/patrepeval huggingface dataset:
Regulation of rat brain natriuretic peptide transcription. A potential role for GATA-related transcription factors in myocardial cell gene expression. (1994)

GATA-binding proteins are transcription factors that regulate the stage- and tissue-specific expression of globin genes in cells of the erythroid lineage. Recently, a cardiac GATA-binding protein was found to be the earliest gene expressed during cardiogenesis; however, the target genes of this transcription factor in the heart are unknown. Since brain natriuretic peptide (BNP) is activated early in cardiac growth and development, we evaluated whether it could serve as a target gene for GATA-binding protein-mediated induction. Upon isolating and sequencing 2.5 kilobases of the rat BNP 5'-flanking sequence (FS), a variety of putative transcriptional enhancer sites were identified, including several GATA consensus sequences (WGATAR), one of which apparently serves as the major promoter site. Primary myocardial cells were transfected with BNP/luciferase fusion genes; reporter expression was strongly induced by typical growth factors such as phorbol esters, serum, or alpha 1-adrenergic agonists, as well as by GATA-4 overexpression. Truncation analyses showed that inducibility mapped primarily to the proximal -116 base pair of the rat BNP 5'-FS, where there are two consensus GATA sites in addition to the GATA sequence at the TATA box. Point mutation analyses showed that at least one of the GATA sites was required to confer full GATA-4-inducible transcription. These results demonstrate that a proximal region of the rat BNP 5'-FS is required for growth factor- and GATA-inducible transcription, supporting the view that the BNP gene could serve as a target for GATA-binding proteins during early cardiac development.
Molecular biological methods (DGGE) as a tool to investigate nitrification inhibition in wastewater treatment (2003)

Incomplete nitrification at an activated sludge plant for biological pre-treatment of rendering plant effluents led to a detailed investigation on the origin and solution of this problem. Preliminary studies revealed that an inhibition of ammonia oxidising microorganisms (AOM) by process waters of the rendering plant was responsible for the situation. We were able to show a correlation between the existence of specific AOM and nitrification capacity expressed as oxygen uptake rate for maximal nitrification (OURNmax). Only Nitrosospira sp. was found in the activated sludge of the rendering plant and another industrial wastewater treatment plant with problems in nitrification, while reference plants without nitrification problems showed Nitrosomonas spp. as the predominant ammonia oxidising bacteria. By accompanying engineering investigations and experiments (cross-feeding experiments, operation of a two-stage laboratory plant) with molecular biological methods (DGGE--Denaturing Gradient Gel Electrophoresis) we were able to elaborate an applicable solution for the rendering plant. Laboratory experiments with a two-stage process layout finally provided complete nitrification overcoming the inhibiting nature of process waters from the rendering plant. DGGE analysis of the second stage activated sludge from the laboratory plant showed a shift in population structure from Nitrosospira sp. towards Nitrosomonas spp. simultaneous to the increase of nitrification capacity. Nitrification capacities comparable to full-scale municipal wastewater treatment plants could be maintained for more than two months. As the design of wastewater treatment plants for nitrification is linked to the growth characteristics of Nitrosomonas spp., established criteria can be applied for the redesign of the full-scale plant.
FAIRVIS: Visual Analytics for Discovering Intersectional Bias in Machine Learning (2019)

The growing capability and accessibility of machine learning has led to its application to many real-world domains and data about people. Despite the benefits algorithmic systems may bring, models can reflect, inject, or exacerbate implicit and explicit societal biases into their outputs, disadvantaging certain demographic subgroups. Discovering which biases a machine learning model has introduced is a great challenge, due to the numerous definitions of fairness and the large number of potentially impacted subgroups. We present FAIRVIS, a mixed-initiative visual analytics system that integrates a novel subgroup discovery technique for users to audit the fairness of machine learning models. Through FAIRVIS, users can apply domain knowledge to generate and investigate known subgroups, and explore suggested and similar subgroups. FAIRVIS's coordinated views enable users to explore a high-level overview of subgroup performance and subsequently drill down into detailed investigation of specific subgroups. We show how FAIRVIS helps to discover biases in two real datasets used in predicting income and recidivism. As a visual analytics system devoted to discovering bias in machine learning, FAIRVIS demonstrates how interactive visualization may help data scientists and the general public understand and create more equitable algorithmic systems.
Integration of passive components in thin film multilayer MCM-D technology for wireless front-end applications (2002)

In the current trend towards portable applications, the integration of passive components has become very important. This paper introduces high quality integrated passive components in thin film multilayer MCM-D technology. The main characteristics and modeling issues for use at RF and microwave frequencies are discussed. Also, a number of circuits applicable in wireless front-ends using the integrated passives are presented. These show that MCM-D may be used for the integration of miniature systems for wireless applications.
Development of a 1×2 piezoelectric optical fiber switch (2007)

This paper presents the design, fabrication and performance of a 1×2 piezoelectric optical switch. The optical switch is developed based on the concept that the input fiber is directly moved by the deflection of a piezoelectric tube actuator. The piezoelectric tube actuator used in this switch is manufactured through an electrophoretic deposition process. The tube is inexpensive to produce and compact in size with high mechanical performance. It has a maximum deflection of 30μm which is capable to actuate the input fiber for switching. The multimode fiber optical switch has been successfully assembled. To reduce the misalignment loss between the fibers, the output fibers are precisely aligned in silicon vgrooves. Different components are bonded with low shrinkage adhesive in order to minimize their position inaccuracy. The performance characteristics of the optical switch have been measured, with an insertion loss of 1dB, crosstalk of -45dB and switching speed from 5 to 10ms. The switch also shows good reliability and requires small driving power. The development of multimode optical switch prototypes proves that the idea of piezoelectric switching is feasible. Further developments include the improvement of switching performance, reduction of the prototype size and the fabrication of multiple output prototypes.
Novel Fixation of Plant Tissue, Staining through Paraffin with Alcian Blue and Hematoxylin, and Improved Slide Preparation (1995)

Onion (Allium cepa) root tips were fixed in a proprietary solution without aldehyde, toxic metals or acetic acid. Fixed specimens were embedded in paraffin, sectioned on a rotary microtome and mounted on detergent-washed slides without adhesive. Slides with ribbon segments affixed were immersed in 0.2% aqueous alcian blue 8GX in screw-capped Coplin jars in a water bath at 50 C for 1 hr. Excess alcian blue was rinsed off under cold running tap water and the slides were immersed in quick-mixed hematoxylin at room temperature for 15 min. Stained slides were deparaffinized, rinsed with isopropanol, air dried, and coverslips were affixed with resin. Thus, the traditional paraffin microtechnique has been modified at all steps from fixation to finishing slides with coverslips.
Preparation of CaCO3-TiO2 Composite Particles and Their Pigment Properties (2018)

CaCO₃-TiO₂ composite particles were prepared with calcium carbonate (CaCO₃) and TiO₂ in stirred mill according the wet grinding method. The pigment properties, morphology, and structure of CaCO₃-TiO₂ composite particles and the interaction behaviors between CaCO₃ and TiO₂ particles were explored. In the CaCO₃-TiO₂ composite particles, TiO₂ is uniformly coated on the surface of CaCO₃ and the firm combination between CaCO₃ and TiO₂ particles is induced by the dehydration reaction of surface hydroxyl groups. CaCO₃-TiO₂ composite particles have similar pigment properties to pure TiO₂. The hiding power, oil absorption, whiteness and ultraviolet light absorption of composite particles are close to those of pure TiO₂. The application performance of CaCO₃-TiO₂ composite particles in the paint is consonant with their pigment properties. The contrast ratio of the exterior paint containing CaCO₃-TiO₂ composite particles is equivalent to that of the paint containing the same proportion of pure TiO₂.
The tensor t‐function: A definition for functions of third‐order tensors (2020)

Summary A definition for functions of multidimensional arrays is presented. The definition is valid for third‐order tensors in the tensor t‐product formalism, which regards third‐order tensors as block circulant matrices. The tensor function definition is shown to have similar properties as standard matrix function definitions in fundamental scenarios. To demonstrate the definition's potential in applications, the notion of network communicability is generalized to third‐order tensors and computed for a small‐scale example via block Krylov subspace methods for matrix functions. A complexity analysis for these methods in the context of tensors is also provided.
Oxygenation of biological membranes by the pure reticulocyte lipoxygenase. (1990)

We find that the reticulocyte lipoxygenase can oxygenate rat liver mitochondrial membranes, beef heart submitochondrial particles, rat liver endoplasmic membranes, and erythrocyte plasma membranes (inside-out and right side-out ghosts) without prior action of a phospholipase. After alkaline hydrolysis of the ester lipids, the main products were identified as 15S-hydro(pero)xy-5Z,8Z,11Z,13E-eicosatetr aenoic acid, 17S-hydro(pero)xy-4Z,7Z,10Z,13Z,15E, 19Z,-docosahexaenoic acid, 13S-hydro(pero)xy-9Z,11E-octadecadienoic acid, 9(S/R)-hydro(pero)xy-10E,12Z-octadecadienoic acid as well as the two all-E hydro(pero)xy octadecadienoic acid isomers. At low membrane concentrations (1 mg of protein/ml), the enzyme maintains a high stereospecificity for the S-configuration, but at higher concentrations (20 mg/ml), the products were virtually racemic. Addition of the antioxidant 2,6-ditert-butyl-p-cresol counteracted this tendency to lose stereospecificity. During these enzyme-catalyzed reactions, substantially more oxygen is consumed than can be accounted for as the hydro(pero)xy products. This discrepancy is due to secondary reactions which lead to the decomposition of the primary oxygenation products, the hydroperoxy lipids, and to oxidative modifications of membrane proteins. These data indicate that the reticulocyte lipoxygenase can oxygenate polyenoic fatty acids in various types of biological membrane and that the oxidative modifications are not restricted to the membrane lipids. The results are discussed in terms of the proposed role of the enzyme in the breakdown of mitochondria and other intracellular organelles during the maturation of red blood cells.
Nucleation and Growth Synthesis of Siloxane Gels to Form Functional, Monodisperse, and Acoustically Programmable Particles (2014)

Nucleation and growth methods offer scalable means of synthesizing colloidal particles with precisely specified size for applications in chemical research, industry, and medicine. These methods have been used to prepare a class of silicone gel particles that display a range of programmable properties and narrow size distributions. The acoustic contrast factor of these particles in water is estimated and can be tuned such that the particles undergo acoustophoresis to either the pressure nodes or antinodes of acoustic standing waves. These particles can be synthesized to display surface functional groups that can be covalently modified for a range of bioanalytical and acoustophoretic sorting applications.
Short Time Dialysis with Continuous Blood Volume Control (1990)

Continuous measurement of haemoglobin concentration is used to control changes of blood volume during haemodialysis. Ultrafiltration is either kept constant throughout the session or after starting with a rate (1.5 to 2 l/h), is manually controlled in order to limit blood volume reduction to a pre-set percentage. Ultrafiltration is step-wise decreased (a) or switched on and off (b) accordingly. Blood volume decrease with constant ultrafiltration is compared with method (a) and (b) in 4 stable haemodialysis patients. Constant ultrafiltration rate and the same total amount of ultrafiltrate causes a nearly 3% (mean) greater volume reduction as compared with method (a) and (b). No difference was observed in blood pressure and heart rate. We conclude that ultrafiltration in stable haemodialysis patients can be completed in short time without consequences for cardiovascular stability.
Acrolein contributes strongly to antimicrobial and heterocyclic amine transformation activities of reuterin (2016)

Glycerol/diol dehydratases catalyze the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA), the basis of a multi-component system called reuterin. Reuterin has antimicrobial properties and undergoes chemical conjugation with dietary heterocyclic amines (HCAs). In aqueous solution reuterin is in dynamic equilibrium with the toxicant acrolein. It was the aim of this study to investigate the extent of acrolein formation at various physiological conditions and to determine its role in biological and chemical activities. The application of a combined novel analytical approach including IC-PAD, LC-MS and NMR together with specific acrolein scavengers suggested for the first time that acrolein, and not 3-HPA, is the active compound responsible for HCA conjugation and antimicrobial activity attributed to reuterin. As formation of the HCA conjugate was observed in vivo, our results imply that acrolein is formed in the human gut with implications on detoxification of HCAs. We propose to re-define the term reuterin to include acrolein.
Reflections on the Spread of Metastasis to Cancer Prevention (2011)

Most patients with a lethal cancer die of metastasis, the control of which deserves to be one of the most urgent missions of cancer treatment. For some subsets of colorectal cancer, metastasis is stimulated by chemokines or Notch signaling at early stages that coincide with the inflammatory phase of postoperative wound healing. This temporary phase may provide a unique opportunity for "metastasis prevention," because some novel agents have been developed that target such chemokine receptors or Notch signaling.
A Novel 3-D Predict Hexagon Search Algorithm for Fast Block Motion Estimation on H.264 Video Coding (2006)

In the upcoming video coding standard MPEG-4 AVC/JVT/H.264, motion estimation is allowed to use multiple references and multiple block sizes to improve the rate-distortion performance. However, full exhaustive search of all block sizes is computational intensive with complexity increasing linearly to the number of allowed reference frames and block sizes. In block motion estimation, a search pattern with a different shape or size has a very important impact on search speed and distortion performance. Based on an in-depth examination for the influence of search pattern on speed performance, a novel search algorithm, three-dimensional predict hexagon search (3DPHS), is proposed in this paper. The 3DPHS depends on the characteristics of motion vector distribution; it can predict the object movement in horizontal and vertical direction with a novel search pattern. The proposed algorithm also considers the characteristics of multiple reference frames and multiple block sizes in H.264. The analysis results show that the speed improvement of 3DPHS over some popular fast search algorithms is about 25%-75%. The compression quality is almost the same compared with Full Search
Overlay performance in advanced processes (2000)

To guarantee less than 45 nm product overlay required for the 130 nm IC technology node a key in lithographic tools is a sophisticated wafer alignment sensor that is able to deal with the influences of new, advanced IC processing. To prove that product overlay performance in this range is achievable, overlay results are presented that confirm the operational concept of the new ATHENA alignment sensor on various advanced processes in both front-end as well as back-end-of-line. In particular, the influences related to Chemical Mechanical Polishing (CMP) have been studied. The robustness of the system to large variations of W-CMP process parameters is highlighted. It is argued that full exploitation of the flexibility of the sensor will allow further optimization of its operation in actual production environments and that a product overlay of 35 nm is feasible.
Overexpression of Aldehyde Dehydrogenase-2 (ALDH2) Transgene Prevents Acetaldehyde-induced Cell Injury in Human Umbilical Vein Endothelial Cells (2004)

Acetaldehyde, the major ethanol metabolite that is far more toxic and reactive than ethanol, has been postulated to be responsible for alcohol-induced tissue and cell injury. This study was to examine whether facilitated acetaldehyde metabolism affects acetaldehyde-induced oxidative stress and apoptosis. Transgene-encoding human aldehyde dehydrogenase-2 (ALDH2), which converts acetaldehyde into acetate, was constructed under chicken beta-actin promoter and transfected into human umbilical vein endothelial cells (HUVECs). Efficacy of ALDH2 transfection was verified using green fluorescent protein and ALDH2 enzymatic assay. Generation of reactive oxygen species (ROS) was measured using chloromethyl-2',7'-dichlorodihydrofluorescein diacetate. Apoptosis was evaluated by 4',6'-diamidino-2'-phenylindoladihydrochloride fluorescence microscopy, quantitative DNA fragmentation, and caspase-3 assay. Acetaldehyde (0-200 microm) elicited ROS generation and apoptosis in HUVECs in a time- and concentration-dependent manner, associated with activation of the stress signal molecules ERK1/2 and p38 mitogen-activated protein (MAP) kinase. A close liner correlation was observed between the acetaldehyde-induced ROS generation and apoptosis. Interestingly, the acetaldehyde-induced ROS generation, apoptosis, activation of ERK1/2, and p38 MAP kinase were prevented by the ALDH2 transgene or antioxidant alpha-tocopherol. The involvement of ERK1/2 and p38 MAP kinase in acetaldehyde-induced apoptosis was confirmed by selective kinase inhibitors U0126, SB203580, and SB202190. Collectively, our data revealed that facilitation of acetaldehyde metabolism by ALDH2 transgene overexpression may prevent acetaldehyde-induced cell injury and activation of stress signals. These results indicated therapeutic potential of ALDH2 enzyme in the prevention and detoxification of acetaldehyde or alcohol-induced cell injury.
Synthesis of LacdiNAc-terminated glycoconjugates by mutant galactosyltransferase - A way to new glycodrugs and materials (2009)

Human placental beta1,4-galactosyltransferase-I (EC 2.4.1.38) transfers the galactosyl moiety from UDP-Gal to various GlcNAc or Glc acceptors in vivo. Here, we describe the construction of its Y284L mutant as a His(6)propeptide-catbeta4GalT1 construct, in which the Gal-transferase activity was totally abolished in favor of its GalNAc-transferase activity. We used this mutant in the synthesis of three mono- and bivalent LacdiNAc glycomimetics with good yields. These compounds proved to be powerful ligands of two activation receptors of natural killer cells, NKR-P1 and CD69. A synthetic bivalent tethered di-LacdiNAc is the best currently known precipitation agent for both of these receptors and has promising potential for the development of immunoactive glycodrugs.
2004 Drag reduction in turbulent flow of polymer solutions (2013)

Progress in understanding turbulent drag reduction by polymer additives has recently been made on several fronts. The near-wall dynamics of Newtonian turbulence is becoming better understood. Detailed computations of complex flows of model polymer solutions are now possible. Insights into the effects of viscoelasticity have been gained from a number of important model flows, and the understanding of the dynamics of dilute polymer solutions, as well as the ability to perform detailed simulations of them, is maturing. We review the advances in these fronts and illustrate their contributions to the understanding of both turbulence and drag reduction. Finally, we highlight open questions and propose a general conceptual framework that would, if validated, unify observations of drag reduction from turbulence onset to the maximum drag reduction asymptote.
p53 mutations in human lung tumors. (1992)

Mutation of one p53 allele and loss of the normal p53 allele [loss of heterozygosity (LOH)] occur in many tumors including lung cancers. These alterations apparently contribute to development of cancer by interfering with the tumor suppressor activity of p53. We directly sequenced amplified DNA in the mutational hot spots (exons 4-8) of p53 in DNA samples from 40 lung cancers. Most (31 of 40) samples were preselected for LOH in the region of p53. We detected 23 p53 mutations within these exons in 22 lung cancers; no p53 mutations were found in normal tissue of the patients. One-half of the mutations were G to T transversions on the nontranscribed strand, consistent with mutagenesis by tobacco smoke. Mutations of C to A on the nontranscribed strand, which would result from G to T mutations on the transcribed strand, were detected only in one sample. Three of 23 mutations were nonsense mutations; to date, nonsense mutations of p53 have not been reported in lung cancer. Mutation of this p53-coding region was detected in 20 of 27 small cell lung cancer samples, representing a 70% occurrence. Mutation of the p53 gene is apparently very frequent in small cell lung cancers. When LOH in the p53 region could be determined, complete concordance occurred between a sample having both a p53 mutation and LOH in the region of p53 (18 of 18 samples). Twelve samples of lung cancer had LOH in the region of p53, but the samples had no detectable p53 mutations, suggesting either alterations outside the known mutational hot spots of p53 or alterations of another unidentified tumor suppressor gene in the region of p53.