gebhart/patrepeval huggingface dataset:
Emerging roles of proteasomes in ischemia-reperfusion injury of organs. (2004)

Proteasomes are the main non-lysosomal, multicatalytic proteinase complexes involved in the degradation of most intracellular proteins and in numerous cell processes. Studies from isolated cell models indicate that agents that induce oxidative stress may also damage proteasomes. Similarly, continuous oxidative stress during cell aging may impair proteasome activity. In ischemia-reperfusion models of organ injury, proteasomes may be involved in several ways. First, proteasomes were found to be targets of ischemia-reperfusion injury of the brain and heart. Second, proteasome activity increased in liver models of ischemia-reperfusion. Third, proteasome inhibition prevented ischemia-reperfusion injury of the brain, heart and kidney. A major mechanism by which proteasome inhibitors may confer tissue protection is inactivation of transcription activator nuclear factor-kappaB resulting in a block of expression of cytokines and cell adhesion molecules during the reperfusion phase. Thus, proteasome inhibition represents a novel strategy for the treatment of pathologies such as stroke, infarction, and kidney failure.
Mammalian Cell Culture (2003)

As discussed in the previous chapters of this book, mammalian cell-culture technology facilitates the production of complex therapeutic proteins (biopharmaceutical drugs). The mammalian cell-culture process is performed with a host cell line that has been transfected with DNA plasmids encoding for the protein of interest. The host cell line is selected based on the post-translational modifications necessary for protein efficacy. The most common production host-cell lines reported are Chinese hamster ovary (CHO) cell lines or murine myeloma lines (SP2/0, NSO). The site and number of plasmids inserted into the host cell line during transfection is somewhat of a random event and generates multiple variations in the initial population pool. Single-cell clones are isolated from the initial population pool of transfected cells. A single-cell clone for production is then selected based on performance in screening studies, and is expanded, dispensed into 1–2-mL vials, and then stored in a quiescent state (generally frozen or freeze dried). These vials are the master cell bank (MCB) that supplies the cells necessary to produce the development, clinical, launch, and commercial supplies.
Nitric oxide is a mediator of apoptosis in the rheumatoid joint (2000)

This study indicates that NO acts as a mediator of apoptosis in RA and suggests that NOS inhibitors reverse this process.
Decreased transcription-coupled nucleotide excision repair capacity is associated with increased p53- and MLH1-independent apoptosis in response to cisplatin (2010)

The present work indicates that CSB and TC-NER play a prominent role in determining the sensitivity of tumour cells to cisplatin even in the absence of p53 and DNA mismatch repair. These results further suggest that CSB represents a potential target for cancer therapy that may be important to overcome resistance to cisplatin in the clinic.
Experiments on Raman versus primary light scattering fluxes from pressed discs (1979)

Abstract Relative fluxes of transmitted and backscattered Raman (inelastic) and also Rayleigh plus macroscopically (elastic) scattered radiation from powdered samples pressed to discs have been measured as a function of the thickness of the discs. Specular reflection is the biggest source of error and must be avoided in such measurements. The resulting curves are in qualitative accordance with calculations by other authors.
Intelligent Material Systems Using Epoxy Particles to Repair Microcracks and Delamination Damage in GFRP (1999)

The objective of this study is to propose an intelligent material system that can perform a self-repairing operation against initial damage that might occur in GFRP laminates. Specifically, we highlight the development of a novel actuator to be used in such self-repairing operations. There has been much research on sensor systems to detect damage and some actuators to control the shape of the structure or to control the vibration. However, no literature can be found on the actuator aiming at the self-repair of damage. For this purpose, a small grain particle-type adhesive is embedded in a glass/epoxy composite (GFRP) laminate. The diameter of the particle is approximately 50 gim. Hence, in the developed intelligent material system, coldsetting epoxy resin is used as the matrix, uni-directionally arranged glass fiber is used as the reinforcement, and a thermosetting epoxy particle is used as a repairing actuator. The volume fraction of the particles in the matrix was approximately 40%. The embedded particles can repair the damage, when melted by heat. Basic characteristics of the particles were investigated first, and we confirmed that the embedded particles in the matrix can melt by heat and flow to repair the crack. We also confirmed that the embedded particles do not deteriorate the stiffness of the GFRP laminate. Then we investigated the efficiency of the repairing operation against initial damage such as microscopic matrix cracks and delamination, by conducting two typical tests, i.e., static three-point bending of [0/90] laminate and tensile fatigue of [O/90], laminate. Damage was observed by CCD camera. As a result, the decrease in the stiffness due to initial damage has been recovered and consequently increased the residual fatigue life.
Acoustic properties of carbon nanotube electrodes in BAW resonators (2013)

In this paper the acoustic characterization of a layer of carbon nanotubes (CNT) deposited on AlN solidly mounted resonators is described. The structure of the CNT layer is analyzed by scanning electron microscopy and Raman spectroscopy. The electrical sheet resistance is derived from 4 point probe measurements and from the fitting of the electrical response of the resonators. Values of sheet resistance around 100 Ω/□ are measured. The longitudinal acoustic velocity is derived from the fitting of the electrical response of the resonators using Mason's model, by adjusting the overtones produced in the CNT layer. A mean value of 62000 m·s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> is obtained, although some devices show values around 90000 m·s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> , close to the theoretical value of 100000 m·s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> . Some results on the deposition of CNT layers on metallic top electrodes and their influence on the performance of the resonator are also presented.
Sabbath Day Home Automation: "It's Like Mixing Technology and Religion" (2007)

We present a qualitative study of 20 American Orthodox Jewish families' use of home automation for religious purposes. These lead users offer insight into real-life, long-term experience with home automation technologies. We discuss how automation was seen by participants to contribute to spiritual experience and how participants oriented to the use of automation as a religious custom. We also discuss the relationship of home automation to family life. We draw design implications for the broader population, including surrender of control as a design resource, home technologies that support long-term goals and lifestyle choices, and respite from technology.
A fast box counting algorithm for determining the fractal dimension of sampled continuous functions (2003)

An adaptation of the box counting algorithm to samples of a continuous signal is given. An iterative scheme is combined with an exploitation of continuity to yield a fast method. This reduces the algorithm's complexity from quadratic to linear. The method is applied to speech segments; in this context it is faster than morphological filtering and Hurst analysis, and has comparable performance. The new algorithm is also suitable to be parallelized. It is applied to calculation of the dimension of fricative phonemes and automatic segmentation of speech into periodic/noiselike segments. This dimension value may be used instead of zero crossing rate in some applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Archiving technology for plant inspection images captured by mobile active cameras "4D visible memory" (2005)

The storage and later retrieval of observed data is an essential part of any support system aiding the safe operation and maintenance of a nuclear power plant. Archiving such data, however, which is broadly spread over space and time, is challenging: problems include how to reduce the amount of data, how to maintain relationships between data, how to normalize the data and so on. We propose a new concept, 4D Visible Memory, whose basic idea is to store the data in a virtual space extended in the time dimension, as a solution. In this paper, a specific system which embodies the concept in the special case of archiving the image data gathered by mobile robots is introduced. Some experimental results show the actual usefulness of the concept.
Cadherin-catenin complex: Protein interactions and their implications for cadherin function (1996)

Cadherins comprise a family of calcium-dependent glycoproteins that function in mediating cell-cell adhesion in virtually all solid tissues of multicellular organisms. In epithelial cells, E-cadherin represents a key molecule in the establishment and stabilization of cellular junctions. On the cellular level, E-cadherin is concentrated at the adherens junction and interacts homophilically with E-cadherin molecules of adjacent cells. Significant progress has been made in understanding the extra- and intracellular interactions of E-cadherin. Recent success in solving the three-dimensional structure of an extracellular cadherin domain provides a structural basis for understanding the homophilic interaction mechanism and the calcium requirement of cadherins. According to the crystal structure, individual cadherin molecules cooperate to form a linear cell adhesion zipper. The intracellular anchorage of cadherins is regulated by the dynamic association with cytoplasmic proteins, termed catenins. The cytoplasmic domain of E-cadherin is complexed with either beta-catenin or plakoglobin (gamma-catenin). Beta-catenin and plakoglobin bind directly to alpha-catenin, giving rise to two distinct cadherin-catenin complexes (CCC). Alpha-catenin is thought to link both CCC's to actin filaments. The anchorage of cadherins to the cytoskeleton appears to be regulated by tyrosine phosphorylation. Phosphorylation-induced junctional disassembly targets the catenins, indicating that catenins are components of signal transduction pathways. The unexpected association of catenins with the product of the tumor suppressor gene APC has led to the discovery of a second, cadherin-independent catenin complex. Two separate catenin complexes are therefore involved in the cross-talk between cell adhesion and signal transduction. In this review we focus on protein interactions regulating the molecular architecture and function of the CCC. In the light of a fundamental role of the CCC during mammalian development and tissue morphogenesis, we also discuss the phenotypes of embryos lacking E-cadherin or beta-catenin.
Interview with the retinoblastoma family members: Do they help each other? (2002)

The ultimate destiny of a cell to undergo division, differentiation, survival, and death results from an intricate balance between multiple regulators including oncogenes, tumor suppressor genes, and cell cycle associated proteins. Deregulation of the cell cycle machinery switches the phenotype from a normal cell to a cancerous cell. Fundamental alterations of tumor suppressor genes may result in an unregulated cell cycle with the accumulation of mutations and eventual neoplastic transformation. As such, one may define cancer as a genetic disease of the cell cycle. In this review, we will emphasize our current understanding of how the cell cycle machinery maintains cellular homeostasis by studying the consequences of its deregulation.
Assessing aneuploidy with repetitive element sequencing (2019)

Abstract We report a sensitive PCR-based assay that can detect aneuploidy in samples containing as little as 3 picograms of DNA. Using a single primer pair, we amplified ∼750,000 amplicons distributed throughout the genome Aneuploidy was detected in 49% of liquid biopsies from a total of 883 non-metastatic cancers of eight different types. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% at 99% specificity.
Automatic Computation of the Screw Parameters of Rigid-Body Motions. Part I: Finitely-Separated Positions (1986)

Introduced in this paper is a novel approach that leads to efficient algorithms for computing the screw parameters of rigid-body motions. This is based on invariants associated with the said motions. Finitely-separated positions are treated in this paper, infinitesimally-separated positions being the subject of an accompanying paper. The algorithms presented in both papers are meant for the real-time computation of the aforementioned parameters.
FOXO1 Represses Peroxisome Proliferator-activated Receptor-γ1 and -γ2 Gene Promoters in Primary Adipocytes (2006)

FOXO1 and peroxisome proliferator-activated receptor-gamma (PPARgamma) are crucial transcription factors that regulate glucose metabolism and insulin responsiveness in insulin target tissues. We have shown that, in primary rat adipocytes, both factors regulate transcription of the insulin-responsive GLUT4 gene and that PPARgamma2 detachment from the GLUT4 promoter upon thiazolidinedione binding up-regulates GLUT4 gene expression, thus increasing insulin sensitivity (Armoni, M., Kritz, N., Harel, C., Bar-Yoseph, F., Chen, H., Quon, M. J., and Karnieli, E. (2003) J. Biol. Chem. 278, 30614-30623). However, the mechanisms regulating PPARgamma gene transcription are largely unknown. We studied the effects of FOXO1 on human PPARgamma gene expression in primary rat adipocytes and found that both genes are endogenously expressed. FOXO1 coexpression dose-dependently repressed transcription from either the PPARgamma 1 or PPARgamma2 promoter reporter by 65%, whereas insulin (100 nm, 20-24 h) either partially or completely reversed this effect. Phosphorylation-defective FOXO1 mutants T24A, S256A, S319A, and T24A/S256A/S319A still repressed the PPARgamma1 promoter and partially lost their effects on the PPARgamma2 promoter in either basal or insulin-stimulated cells. Use of DNA binding-defective FOXO1 (H215R) indicated that this domain is crucial for FOXO1 repression of the PPARgamma2 (but not PPARgamma1) promoter. Progressive 5'-deletion and gel retardation analyses revealed that this repression involves direct and specific binding of FOXO1 to the PPARgamma2 promoter; chromatin immunoprecipitation analysis confirmed that this binding occurs in cellulo. We suggest a novel paradigm to increase insulin sensitivity in adipocytes in which FOXO1 repression of PPARgamma, the latter being a repressor of the GLUT4 promoter, consequently leads to GLUT4 derepression/up-regulation, thus enhancing cellular insulin sensitivity. The newly identified FOXO1-binding site on the PPARgamma2 promoter may serve as a therapeutic target for type 2 diabetes.
Enzyme-Mediated Methodology for the Site-Specific Radiolabeling of Antibodies Based on Catalyst-Free Click Chemistry (2013)

An enzyme- and click chemistry-mediated methodology for the site-selective radiolabeling of antibodies on the heavy chain glycans has been developed and validated. To this end, a model system based on the prostate specific membrane antigen-targeting antibody J591, the positron-emitting radiometal (89)Zr, and the chelator desferrioxamine has been employed. The methodology consists of four steps: (1) the removal of sugars on the heavy chain region of the antibody to expose terminal N-acetylglucosamine residues; (2) the incorporation of azide-modified N-acetylgalactosamine monosaccharides into the glycans of the antibody; (3) the catalyst-free click conjugation of desferrioxamine-modified dibenzocyclooctynes to the azide-bearing sugars; and (4) the radiolabeling of the chelator-modified antibody with (89)Zr. The site-selective labeling methodology has proven facile, reproducible, and robust, producing (89)Zr-labeled radioimmunoconjguates that display high stability and immunoreactivity in vitro (>95%) in addition to highly selective tumor uptake (67.5 ± 5.0%ID/g) and tumor-to-background contrast in athymic nude mice bearing PSMA-expressing subcutaneous LNCaP xenografts. Ultimately, this strategy could play a critical role in the development of novel well-defined and highly immunoreactive radioimmunoconjugates for both the laboratory and clinic.
Interactions of 2‘-modified azido- and haloanalogs of deoxycytidine 5‘-triphosphate with the anaerobic ribonucleotide reductase of Escherichia coli (1994)

The anaerobic Escherichia coli ribonucleotide reductase (class III reductase) responsible for the synthesis of the deoxyribonucleotides required for anaerobic DNA replication contains an oxygen-sensitive glycyl radical (Gly-681) suggesting involvement of radical chemistry in catalysis. The amino acid sequence of this enzyme completely differs from that of earlier described aerobic class I (prototype, aerobic E. coli) and class II (prototype, Lactobacillus leichmanii) reductases that use radical chemistry but employ other means for radical generation. Here, we study the interaction between the anaerobic E. coli reductase with the 5'-triphosphates of 2'-chloro-2'-deoxycytidine, 2'-fluoro-2'-deoxycytidine, and 2'-azido-2'-deoxycytidine (N3CTP), which are mechanism-based inhibitors of class I and II reductases and, on interaction with these enzymes, decompose to base, inorganic di(tri)phosphate and 2'-methylene-3(2H)-furanone. Also, with the anaerobic E. coli reductase, the 2'-substituted nucleotides act as mechanism-based inhibitors and decompose. N3CTP scavenges the glycyl radical of the enzyme similar to the interaction of N3CDP with the tyrosyl radical of class I enzymes. However, we found no evidence for a new transient radical species as is the case with class I enzymes. Our results suggest that the chemistry at the nucleotide level for the reduction of ribose by class III enzymes is similar to the chemistry employed by class I and II enzymes.
Regulation of Plant Arginase by Wounding, Jasmonate, and the Phytotoxin Coronatine (2004)

In mammalian cells, induced expression of arginase in response to wound trauma and pathogen infection plays an important role in regulating the metabolism of L-arginine to either polyamines or nitric oxide (NO). In higher plants, which also utilize arginine for the production of polyamines and NO, the potential role of arginase as a control point for arginine homeostasis has not been investigated. Here, we report the characterization of two genes (LeARG1 and LeARG2) from Lycopersicon esculentum (tomato) that encode arginase. Phylogenic analysis showed that LeARG1 and -2, like all other plant arginases, are more similar to agmatinase than to arginases from vertebrates, fungi, and bacteria. Nevertheless, recombinant LeARG1 and -2 exhibited specificity for L-arginine over agmatine and related guanidino substrates. The plant enzymes, like mammalian arginases, were inhibited (K(i) approximately 14 microM) by the NO precursor N(G)-hydroxy-L-arginine. These results indicate that plant arginases define a distinct group of ureohydrolases that function as authentic L-arginases. LeARG1 and LeARG2 transcripts accumulated to their highest levels in reproductive tissues. In leaves, LeARG2 expression and arginase activity were induced in response to wounding and treatment with jasmonic acid (JA), a potent signal for plant defense responses. Wound- and JA-induced expression of LeARG2 was not observed in the tomato jasmonic acid-insensitive1 mutant, indicating that this response is strictly dependent on an intact JA signal transduction pathway. Infection of wild-type plants with a virulent strain of Pseudomonas syringae pv. tomato also up-regulated LeARG2 expression and arginase activity. This response was mediated by the bacterial phytotoxin coronatine, which exerts its virulence effects by co-opting the host JA signaling pathway. These results highlight striking similarities in the regulation of arginase in plants and animals and suggest that stress-induced arginase may perform similar roles in diverse biological systems.
Laser Drilling: Determination of Energy Required to Remove Rock (2001)

Abstract Samples of sandstone, limestone, and shale were prepared for laser beam interaction with a 1.6 kW pulsed Nd:YAG laser beam to determine how the beam's size, power, repetition rate, pulse width, exposure time and energy can affect the amount of energy transferred to the rock for the purposes of spallation, melting and vaporization. The purpose of the laser rock interaction experiment was to determine the threshold parameters required to remove a maximum rock volume from the samples while minimizing energy input. Absorption of radiant energy from the laser beam gives rise to the thermal energy transfer required for the destruction and removal of the rock matrix. Results from the tests indicate that each rock type has a set of optimal laser parameters to minimize specific energy values as observed in a set of linear track and spot tests. In addition, it was observed that the rates of heat diffusion in rocks are easily and quickly overrun by absorbed energy transfer rates from the laser beam to the rock. As absorbed energy outpaces heat diffusion by the rock matrix, local temperatures rise to the minerals’ melting points and quickly increase SE values. The lowest specific energy values are obtained in the spalling zone just prior to the onset of melting.
A beetle-inspired solution for underwater adhesion (2007)

Glue-free reversible adhesion was achieved underwater using a beetle-inspired mushroom-shaped fibrillar microstructure. Structured surfaces reveal a 25% increase in pull-off force when immersed in water and their underwater attachment is 20 times more effective than that of flat surfaces. The van der Waals interaction that underlies the adhesion of the mushroom-shaped fibrillar microstructure is significantly enhanced by a suction effect when underwater. This results in a higher adhesive capability of the material, with potential in medicine, bio- and marine technologies and a range of applications in liquid-dominated environments.