gebhart/patrepeval huggingface dataset:
In vitro models of TGF-β-induced fibrosis suitable for high-throughput screening of antifibrotic agents (2007)

Progressive fibrosis is a cause of progressive organ dysfunction. Lack of quantitative in vitro models of fibrosis accounts, at least partially, for the slow progress in developing effective antifibrotic drugs. Here, we report two complementary in vitro models of fibrosis suitable for high-throughput screening. We found that, in mesangial cells and renal fibroblasts grown in eight-well chamber slides, transforming growth factor-beta1 (TGF-beta1) disrupted the cell monolayer and induced cell migration into nodules in a dose-, time- and Smad3-dependent manner. The nodules contained increased interstitial collagens and showed an increased collagen I:IV ratio. Nodules are likely a biological consequence of TGF-beta1-induced matrix overexpression since they were mimicked by addition of collagen I to the cell culture medium. TGF-beta1-induced nodule formation was inhibited by vacuum ionized gas treatment of the plate surface. This blockage was further enhanced by precoating plates with matrix proteins but was prevented, at least in part, by poly-l-lysine (PLL). We have established two cell-based models of TGF-beta-induced fibrogenesis, using mesangial cells or fibroblasts cultured in matrix protein or PLL-coated 96-well plates, on which TGF-beta1-induced two-dimensional matrix accumulation, three-dimensional nodule formation, and monolayer disruption can be quantitated either spectrophotometrically or by using a colony counter, respectively. As a proof of principle, chemical inhibitors of Alk5 and the antifibrotic compound tranilast were shown to have inhibitory activities in both assays.
The niche of stellate cells within rat liver # (2009)

The space of Disse shows analogies to typical stem cell niches comprising of basal lamina components, sympathetic innervation, and adjacent cells that constitute a milieu by paracrine factors and direct physical interactions to retain HSCs at this site and to influence their cellular fate. The space of Disse serves as a niche of stellate cells, which is a novel function of this unique organ structure.
Polyoxomolybdate Promoted Hydrolysis of a DNA-Model Phosphoester Studied by NMR and EXAFS Spectroscopy (2011)

Hydrolysis of (p-nitrophenyl)phosphate (NPP), a commonly used phosphatase model substrate, was examined in molybdate solutions by means of (1)H, (31)P, and (95)Mo NMR spectroscopy and Mo K-edge Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. At 50 °C and pD 5.1 the cleavage of the phosphoester bond in NPP proceeds with a rate constant of 2.73 × 10(-5) s(-1) representing an acceleration of nearly 3 orders of magnitude as compared to the hydrolysis measured in the absence of molybdate. The pD dependence of k(obs) exhibits a bell-shaped profile, with the fastest cleavage observed in solutions where [Mo(7)O(24)](6-) is the major species in solution. Mixing of NPP and [Mo(7)O(24)](6-) resulted in formation of these two intermediate complexes that were detected by (31)P NMR spectroscopy. Complex A was characterized by a (31)P NMR resonance at -4.27 ppm and complex B was characterized by a (31)P NMR resonance at -7.42 ppm. On the basis of the previous results from diffusion ordered NMR spectroscopy, performed with the hydrolytically inactive substrate phenylphosphonate (PhP), the structure of these two complexes was deduced to be (NPP)(2)Mo(5)O(21)(4-) (complex A) and (NPP)(2)Mo(12)O(36)(H(2)O)(6)(4-) (complex B). The pH studies point out that both complexes are hydrolytically active and lead to the hydrolysis of phosphoester bond in NPP. The NMR spectra did not show evidence of any paramagnetic species, excluding the possibility of Mo(VI) reduction to Mo(V), and indicating that the cleavage of the phosphomonoester bond is purely hydrolytic. The Mo K-edge XANES region also did not show any sign of Mo(VI) to Mo(V) reduction during the hydrolytic reaction. (95)Mo NMR and Mo K-edge EXAFS spectra measured during different stages of the hydrolytic reaction showed a gradual disappearance of [Mo(7)O(24)](6-) during the hydrolytic reaction and appearance of [P(2)Mo(5)O(23)](6-), which was the final complex observed at the end of hydrolytic reaction.
Tuning electronic transport via hepta-alanine peptides junction by tryptophan doping (2016)

Charge migration for electron transfer via the polypeptide matrix of proteins is a key process in biological energy conversion and signaling systems. It is sensitive to the sequence of amino acids composing the protein and, therefore, offers a tool for chemical control of charge transport across biomaterial-based devices. We designed a series of linear oligoalanine peptides with a single tryptophan substitution that acts as a "dopant," introducing an energy level closer to the electrodes' Fermi level than that of the alanine homopeptide. We investigated the solid-state electron transport (ETp) across a self-assembled monolayer of these peptides between gold contacts. The single tryptophan "doping" markedly increased the conductance of the peptide chain, especially when its location in the sequence is close to the electrodes. Combining inelastic tunneling spectroscopy, UV photoelectron spectroscopy, electronic structure calculations by advanced density-functional theory, and dc current-voltage analysis, the role of tryptophan in ETp is rationalized by charge tunneling across a heterogeneous energy barrier, via electronic states of alanine and tryptophan, and by relatively efficient direct coupling of tryptophan to a Au electrode. These results reveal a controlled way of modulating the electrical properties of molecular junctions by tailor-made "building block" peptides.
Using Datacube Technology for In-Situ-Enhanced Precision Farming (2018)

Goal of the BigPicture project is to enhance satellite-based information with empirical in-situ ground-truthing. In this approach, the symptoms detected from remote sensing data are a mere starting point where additional data -- like long-term time series, location of unusually growing areas, and weather conditions -- get mixed in to ultimately obtain recommendations on soil treatments and applications of seeds, fertilizers and plant protection products.
Sensitivity and Clinical Use of<i>Phytophthora</i>-Specific Immunoassay Kits (1992)

The sensitivity of a Phytophthora-specific immunoassay kit was tested on 17 species of Phytophthora collected throughout the world, including 18 isolates each of P. cinnamomi and P. cactorum. Kits were also used in the diagnosis of plant specimens with symptoms characteristic of Phytophthora infection, which were sent to Oregon State University's Plant Disease Clinic. All Phytophthora isolates tested produced a positive reaction with the immunoassay kit. The lowest absorbencies relative to other species were obtained from P. cinnamomi and P. megasperma (originally isolated from cherry) (.)
Additional toxins for feral pig (Sus scrofa) control: identifying and testing Achilles’ heels (2008)

A literature review was conducted in order to identify unique weaknesses in the physiology or metabolism of pigs that could be targeted with specific chemicals (i.e. an ‘Achilles’ heel’ search). A promising weakness identified was the species’ susceptibility to methaemoglobin-forming compounds, most likely related to their uniquely low levels of methaemoglobin reductase. Further examination revealed that sodium nitrite is a cost-effective, readily available methaemoglobin-forming compound that is highly toxic to domestic pigs, which has caused numerous accidental poisonings. Pen trials on pigs showed that sodium nitrite delivered by gavage (&gt;90 mg kg-1) and freely consumed in bait (&gt;400 mg kg-1) caused rapid and lethal rises in methaemoglobin. Sodium nitrite appeared to be more humane than currently used toxins, with deaths following bait consumption being considerably quicker and with fewer symptoms (within 80 min of clinical signs beginning; clinical signs including infrequent vomiting, lethargy, ataxia and dyspnoea). The review also identified a second deficiency in the metabolism of pigs, namely high sensitivity to selective inhibition of cytochrome P450 liver enzymes. This leads to potentially lethal interactions between various drugs, such as two antibiotics, monensin and tiamulin. A pen trial confirmed that the antibiotic combination in a single gavage dose was reliably and rapidly lethal to pigs. However, its utility as a pig toxin is low, because it was unpalatable to pigs when delivered in bait and appeared to cause pain and suffering (leading to the early termination of pen trials). The findings presented here demonstrate the potential of sodium nitrite as an additional feral pig toxin.
Kit method of preparation of 4-lodoantipyrine (I-123) from Na123I: concise communication. (1976)

4-Iodoantipyrine (4-IAP), containing 123I, has been suggested as a radio-pharmaceutical for direct imaging of regional cerebral perfusion. In routine clinical use, a reliable source of the labeled compound is required. The 4-IAP (I-123) can be prepared by exchange between Na123I and 4-bromoantipyrine (4-BrAP) or 4-IAP with heating in aqueous acidic solution. Using an H3PO4 buffer system at pH 2.5 during labeling, with addition of NaOH for subsequent buffering at pH 7.0, a convenient reliable kit for routine preparation of 4-IAP (I-123) from commercially available Na123I has been developed.
Increased Interferon Production in Human Cells Irradiated with Ultraviolet Light (1974)

Polyinosinate-polycytidylate [poly(I).poly(C)]-induced interferon production in cultures of human foreskin fibroblast strains was increased by ultraviolet irradiation of cells at the time of exposure to inducer or at 2 h after induction. Incubation of cells with interferon prior to induction (priming) and ultraviolet irradiation exerted a cooperative enhancing effect on interferon production. The resulting interferon yields were generally somewhat higher than the yields from cultures subjected to sequential treatment with cycloheximide and actinomycin D.
Organization of rRNA structural genes in the archaebacterium<i>Thermoplasma acidophilum</i> (1982)

In the archaebacterium Thermoplasma acidophilum, each of the structural genes for 5S, 16S and 23S rRNA occur once per genome. In contrast to those of eubacteria and eukaryotes, they appear unlinked. The distance between the 16S and the 23S rDNA is at least 7.5 Kb, that between 23S and 5S rDNA at least 6 Kb and that between 16S and 5S rDNA at least 1.5 Kb. No linkage between those genes has been found by the analysis of recombinant plasmids carrying Bam HI and Hind III rDNA fragments as by hybridizing those plasmids to fragments of Thermoplasma DNA generated by 6 individual restriction endonucleases, recognizing hexanucleotide sequences.
Fatty acid synthase-catalyzed de novo fatty acid biosynthesis: from anabolic-energy-storage pathway in normal tissues to jack-of-all-trades in cancer cells. (2005)

In 1994, Kuhajda and colleagues unambiguously identified the oncogenic antigen-519, a prognostic molecule found in breast cancer patients with markedly worsened prognosis, as fatty acid synthase (FAS),the key enzyme for the de novo fatty acid biosynthesis. It now appears that human carcinomas and their pre-neoplastic lesions constitutively over express FAS and undergo significant endogenous fatty acid biosynthesis. Moreover, FAS blockade specifically induces apoptotic cancer cell death and prolongs survival of cancer xenograft hosts. Therefore, FAS signaling seems to play a central role in the maintenance of the malignant phenotype by enhancing cancer cell survival and proliferation. This review documents the rapidly changing perspectives on the function of FAS in cancer biology. First, we describe molecular mechanism by which aberrant transduction cascades driven by oncogenic changes subvert the down-regulatory effects of dietary fatty acids, resulting in tumor-associated FAS insensitivity to nutritional signals. Second, we speculate von the putative function that hypoxia can play as the epigenetic factor that triggers and maintains FAS overexpression in cancer cells by inducing changes in gene expression and in metabolism for survival. Third, we explore the role that FAS exhibits in cancer evolution by specifically regulating cancer-related proteins such as Her-2/neu oncogene and estrogen receptor. Finally, we reveal previously unrecognized functions of FAS on the response of cancer cells to chemo-,endocrine-,and immuno therapies. These findings, all together, should ultimately enhance our understanding of how FAS-dependent endogenous fatty acid metabolism, once considered a minor anabolic-energy-storage pathway in normal cells, has become a jack-of-all-trades in cancer cells.
Vertical two‐phase flow part I. Flow pattern correlations (1974)

Abstract Two‐phase gas‐liquid flow has been investigated in a 1‐inch internal diameter vertical tube coil containing two risers and a downcomer all connected by “U” bends. Flow pattern data were obtained in the three vertical tubes, each 17.30 ft. long, for five different air‐liquid systems at about 25 psia over flow ranges of 0–700 lb m air/min‐ft 2 and 140–25300 lb m liquid/min‐ft 2 . Liquid phase viscosities ranged from 1 to 12 cp. A flow pattern classification with six regimes including coring‐bubble, bubbly‐slug, falling film, falling bubbly‐film, froth and annular flow regimes was established for downflow. Flow patterns in the bends were also classified. Data from the present investigation were used to formulate an empirical flow pattern graphical correlation for both upflow and downflow which is based upon the coordinates (R v ) 1/2 and Fr TP /A, where R v is the delivered gas‐to‐liquid volume ratio, Fr TP is the mixture Froude number, and A = μ s /(S L σ s 3 ) 1/4 in which μ s , S L , σ s are specific viscosity, specific density and specific surface tension respectively of the liquid with reference to water. The correlation was satisfactorily tested with independent literature data for upflow systems, including air‐water, steam‐water at various pressures, nitrogen‐mercury and air‐heptane, and data from flowing gas‐oil wells. No independent literature data appear to be available for testing the correlation for downflow systems, but it is anticipated that the correlation will prove to be generally applicable. The coring phenomenon in downward bubble flow was examined by means of high speed motion photography and is explained by the development of a lift force on a bubble.
Neuroprotection in Glaucoma: Drug-Based Approaches (2008)

In recent years the focus of glaucoma research has shifted toward neuroprotection, as the traditional strategies of lowering intraocular pressure have been shown to be unable to prevent progressive vision loss in some glaucoma patients. As a result various neuroprotective drug-based approaches have been shown capable of reducing the death of retinal ganglion cells, which is the hallmark of glaucomatous optic neuropathy. There has been increasing evidence that glaucomatous neurodegeneration is analogous to other neurodegenerative diseases in the central nervous system, with recent work from our group elucidating a strong link between basic cellular processes in glaucoma and Alzheimer's disease. Additionally, there is a growing trend for using existing neuroprotective strategies in central nervous system diseases for the treatment of glaucoma. In fact, a trial treating patients with primary open-angle glaucoma with memantine, a drug approved for the treatment of Alzheimer's disease, has recently been completed. Results of this trial are not yet available. In this review, we will examine currently advocated neuroprotective drug-based strategies in the potential management of glaucoma.
Sugarcane genome architecture decrypted with chromosome‐specific oligo probes (2020)

Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n = 100-120) are highly polyploids and aneuploids derived from interspecific hybridization between Saccharum officinarum (2n = 80) and Saccharum spontaneum (2n = 40-128). Chromosome-specific oligonucleotide probes were used in combination with genomic in situ hybridization to analyze the genome architecture of modern cultivars and representatives of their parental species. The results validated a basic chromosome number of x = 10 for S. officinarum. In S. spontaneum, rearrangements occurred from a basic chromosome of x = 10, probably in the Northern part of India, in two steps leading to x = 9 and then x = 8. Each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical extension of clones with x = 8. We showed that the S. spontaneum contribution to modern cultivars originated from cytotypes with x = 8 and varied in proportion between cultivars (13-20%). Modern cultivars had mainly 12 copies for each of the first four basic chromosomes, and a more variable number for those basic chromosomes whose structure differs between the two parental species. One-four of these copies corresponded to entire S. spontaneum chromosomes or interspecific recombinant chromosomes. In addition, a few inter-chromosome translocations were revealed. The new information and cytogenetic tools described in this study substantially improve our understanding of the extreme level of complexity of modern sugarcane cultivar genomes.
Polymer waveguide couplers based on metal nanoparticle–polymer nanocomposites (2015)

In this work Au nanoparticles (AuNPs) are incorporated into poly(methyl methacrylate) (PMMA) waveguides to develop optical couplers that are compatible with planar organic polymer photonics. A method for growing AuNPs (of 10 to 100 nm in size) inside the commercially available Novolak resist is proposed with the intention of tuning the plasmon resonance and the absorption/scattering efficiencies inside the patterned structures. The refractive index of the MNP-Novolak nanocomposite (MNPs: noble metal nanoparticles) is carefully analysed both experimentally and numerically in order to find the appropriate fabrication conditions (filling factor and growth time) to optimize the scattering cross section at a desired wavelength. Then the nanocomposite is patterned inside a PMMA waveguide to exploit its scattering properties to couple and guide a normal incident laser light beam along the polymer. In this way, light coupling is experimentally demonstrated in a broad wavelength range (404-780 nm). Due to the elliptical shape of the MNPs the nanocomposite demonstrates a birefringence, which enhances the coupling to the TE mode up to efficiencies of around 1%.
Review of Lithium Production and Recovery from Minerals, Brines, and Lithium-Ion Batteries (2019)

Rechargeable lithium-ion batteries (LIBs) are widely employed in portable electric devices, electric vehicles (EVs), and hybrid electric vehicles (HEVs), indicating a potential increasing demand for LIBs over the next decade. Lithium, a critical element in LIBs, might encounter a potential supply crisis in the future. The irregular distribution of lithium mineral resources in countries and the unequal concentration in brine reserves also causes lithium extraction to be of critical importance. Today lithium is mainly recovered from minerals (especially spodumene) by acid, alkaline, and chlorination processes, and from brines by crystallization, solvent extraction, and ion-exchange processes. Regarding the secondary resources, i.e., recycling the spent LIBs, the recycling process consists of dismantling the LIBs, in some cases the separation of the cathode and anode materials, leaching of shredded material, and separation and recovery of metals. Nonetheless, the industry standard for recycling of LIBs currently is the pyrometallurgy processes, mostly are focused on the base metals recovery, such as cobalt and nickel, rather than lithium. Varying compositions of batteries for different applications require the development of a suitable and sustainable recycling process to recover metals from all types of LIBs. This paper provides a comprehensive review of lithium recovery processes that have already been studied and are currently in industrial practice, in the hope of providing some inspirations to explore new technologies for sustainable recovery of lithium from minerals, brines and LIBs.
Enlarged Peroxisomes Are Present in Oleic Acid–grown <i>Yarrowia lipolytica</i> Overexpressing the <i>PEX16</i> Gene Encoding an Intraperoxisomal Peripheral Membrane Peroxin (1997)

Pex mutants of the yeast Yarrowia lipolytica are defective in peroxisome assembly. The mutant strain pex16-1 lacks morphologically recognizable peroxisomes. Most peroxisomal proteins are mislocalized to a subcellular fraction enriched for cytosol in pex16 strains, but a subset of peroxisomal proteins is localized at, or near, wild-type levels to a fraction typically enriched for peroxisomes. The PEX16 gene was isolated by functional complementation of the pex16-1 strain and encodes a protein, Pex16p, of 391 amino acids (44,479 D). Pex16p has no known homologues. Pex16p is a peripheral protein located at the matrix face of the peroxisomal membrane. Substitution of the carboxylterminal tripeptide Ser-Thr-Leu, which is similar to the consensus sequence of peroxisomal targeting signal 1, does not affect targeting of Pex16p to peroxisomes. Pex16p is synthesized in wild-type cells grown in glucose-containing media, and its levels are modestly increased by growth of cells in oleic acid-containing medium. Overexpression of the PEX16 gene in oleic acid- grown Y. lipolytica leads to the appearance of a small number of enlarged peroxisomes, which contain the normal complement of peroxisomal proteins at levels approaching those of wild-type peroxisomes.
Sparse code multiple access: An energy efficient uplink approach for 5G wireless systems (2014)

The rapid traffic growth and ubiquitous access requirements make it essential to explore the next generation (5G) wireless communication networks. In the current 5G research area, non-orthogonal multiple access has been proposed as a paradigm shift of physical layer technologies. Among all the existing non-orthogonal technologies, the recently proposed sparse code multiple access (SCMA) scheme is shown to achieve a better link level performance. In this paper, we extend the study by proposing an unified framework to analyze the energy efficiency of SCMA scheme and a low complexity decoding algorithm which is critical for prototyping. We show through simulation and prototype measurement results that SCMA scheme provides extra multiple access capability with reasonable complexity and energy consumption, and hence, can be regarded as an energy efficient approach for 5G wireless communication systems.
A Pseudorigid-Body 3R Model for Determining Large Deflection of Cantilever Beams Subject to Tip Loads (2009)

In this paper, a pseudorigid-body (PRB) 3R model, which consists of four rigid links joined by three revolute joints and three torsion springs, is proposed for approximating the deflection of a cantilever beam subject to a general tip load. The large deflection beam equations are solved through numerical integration. A comprehensive atlas of the tip deflection for various load modes is obtained. A three-dimensional search routine has been developed to find the optimal set of characteristic radius factors and spring stiffness of the PRB 3R model. Detailed error analysis has been done by comparing with the precomputed tip deflection atlas. Our results show that the approximation error is much less than that of the conventional PBR 1R model. To demonstrate the use of the PRB 3R model, a compliant four-bar linkage is studied and verified by a numerical example. The result shows a maximum tip deflection error of 1.2% compared with the finite element analysis model. The benefits of the PRB 3R model include that (a) the model parameters are independent of external loads, (b) the approximation error is relatively small for even large deflection beams, and (c) the derived kinematic and static constraint equations are simpler to solve compared with the finite element model.