gebhart/patrepeval huggingface dataset:
Alteration of connexin expression is an early signal for chronic kidney disease (2011)

Chronic kidney disease is promoted by a variety of factors that induce chronic inflammation and fibrosis. Inflammation and excessive scaring have been recently associated with disruptions of the gap junction-mediated intercellular communication. Nevertheless, little is known about alterations of the expression of gap junction proteins such as connexin (Cx) 43 and 37 in chronic renal disease. In this study, we investigated the expression of these two Cxs in the hypertensive RenTg mice, the anti-glomerular basement membrane glomerulonephritis, and the unilateral ureteral obstruction models, all leading to the development of chronic kidney disease in mice. Expression of Cx43 was almost negligible in the renal cortex of control mice. In contrast, Cx43 was markedly increased in the endothelium of peritubular and glomerular capillaries of the 3-mo-old RenTg mice, in the glomeruli of mice suffering from glomerulonephritis, and in the tubules after obstructive nephropathy. The Cx43 expression pattern was paralleled closely by that of the adhesion markers such as vascular cell adhesion molecule-1 and intercellular adhesion molecule-1 as well as the inflammatory biomarker monocyte chemoattractant protein-1. In contrast, Cx37 that was abundantly expressed in the renal cortex of healthy mice was markedly decreased in the three experimental models. Interestingly, Cx43+/- mice showed restricted expression of VCAM-1 after 2 wk of obstructive nephropathy. These findings suggest the importance of Cxs as markers of chronic renal disease and indicate that these proteins may participate in the inflammatory process during the development of this pathology.
Genomics and array technology (1999)

Genome projects are providing vast amounts of sequence data. This raw material makes possible a completely new era of experimental approaches. Among these, DNA array technology, which allows one to assay thousands of unique nucleic acid samples simultaneously, will be important in genomic research, and the results of this research are likely to affect virtually every field of biology. DNA array technology is still in its infancy, but many have demonstrated its power by using it for such diverse applications as global monitoring of gene expression, mutation detection, and genetic mapping.
Killing the Killer: PARC/CUL9 Promotes Cell Survival by Destroying Cytochrome c (2014)

Balanced amounts of apoptotic cell death are essential for health; its deregulation plays key roles in neurodegeneration, autoimmunity, and cancer. Mitochondria orchestrate apoptosis through a process called mitochondrial outer-membrane permeabilization (MOMP). After MOMP, mitochondrial cytochrome c is released into the cytoplasm, where it binds the adaptor molecule APAF1, triggering caspase protease activation and cell death. In this issue of Science Signaling, Deshmukh and colleagues define a new survival mechanism downstream of mitochondrial permeabilization. Specifically, they identify proteasomal degradation of cytochrome c as a major determinant of cell survival. In an unbiased approach, PARC (also known as CUL9) was found to be the ubiquitin ligase responsible for the ubiquitination and proteasomal degradation of cytochrome c. The consequences of this survival process may be double-edged because both cancer cells and postmitotic cells use PARC/CUL9-mediated cytochrome c degradation to ensure cell survival. Ultimately, differential targeting of this process may promote survival of postmitotic tissue or enhance tumor-specific killing.
Recording media that exhibit high dynamic range for digital holographic data storage (1999)

A general strategy for fabricating thick, optically flat photopolymer recording media with high dynamic range (M/#) that exhibit low levels of recording-induced Bragg detuning for holographic data storage is presented. In particular, media with M/# values as high as 42 in 1-mm-thick formats are obtained. We believe that these results are the first demonstration of a holographic storage medium with a dynamic range of this magnitude. In addition, we report the holographic recording and recovery of high-capacity (480-kbit) digital data pages in these media, further illustrating their data-storage capabilities.
WNT5A enhances resistance of melanoma cells to targeted BRAF inhibitors (2014)

About half of all melanomas harbor a mutation that results in a constitutively active BRAF kinase mutant (BRAF(V600E/K)) that can be selectively inhibited by targeted BRAF inhibitors (BRAFis). While patients treated with BRAFis initially exhibit measurable clinical improvement, the majority of patients eventually develop drug resistance and relapse. Here, we observed marked elevation of WNT5A in a subset of tumors from patients exhibiting disease progression on BRAFi therapy. WNT5A transcript and protein were also elevated in BRAFi-resistant melanoma cell lines generated by long-term in vitro treatment with BRAFi. RNAi-mediated reduction of endogenous WNT5A in melanoma decreased cell growth, increased apoptosis in response to BRAFi challenge, and decreased the activity of prosurvival AKT signaling. Conversely, overexpression of WNT5A promoted melanoma growth, tumorigenesis, and activation of AKT signaling. Similarly to WNT5A knockdown, knockdown of the WNT receptors FZD7 and RYK inhibited growth, sensitized melanoma cells to BRAFi, and reduced AKT activation. Together, these findings suggest that chronic BRAF inhibition elevates WNT5A expression, which promotes AKT signaling through FZD7 and RYK, leading to increased growth and therapeutic resistance. Furthermore, increased WNT5A expression in BRAFi-resistant melanomas correlates with a specific transcriptional signature, which identifies potential therapeutic targets to reduce clinical BRAFi resistance.
An OSI-based interoperability architecture for managing hybrid networks (1990)

The management of hybrid corporate networks comprising a wide variety of equipment and services offered by different vendors and service providers is addressed. The public carrier environment in which such networks must operate is described. Five categories of system management functional areas set forth in the ISO/IEC Open Systems Interconnection (OSI) standards are defined. They are fault management, accounting management, configuration management, performance management, and security management. The interoperability architecture provided by the standards is examined, and two example applications are given: a corporate banking voice network, and OSI-based configuration management applied to automatic call distribution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vestibular dysgenesis in mice lacking Abr and Bcr Cdc42/RacGAPs (2002)

The inner ear develops from a simple epithelium (otic placode) into the complex structures specialized for balance (vestibule) and sound (cochlea) detection. Abnormal vestibular and cochlear development is associated with many birth defects. During recent years, considerable progress has been made in understanding the molecular bases of these conditions. To determine the biological function of two closely related GTPase activating proteins for the Cdc42/Rac GTPases, Abr and Bcr, we generated a mouse strain deficient in both of these proteins. Double null mutant mice exhibit hyperactivity, persistent circling, and are unable to swim. These phenotypes are typically found in mice with vestibular defects. Indeed, adult double null mutants display abnormal dysmorphic structures of both the saccule and utricle. Moreover, a total loss of otoconia can be seen in the utricle, whereas in the saccule, otoconia are either missing or their number is drastically decreased and they are abnormally large. Interestingly, both the cochlea and semicircular canals are normal and the double null mutant mice are not deaf. These data demonstrate that Abr and Bcr play important complementary roles during vestibular morphogenesis and that a function of Cdc42/RacGAPs and, therefore, that of the small Rho-related GTPases is critically important for balance and motor coordination.
Serum Levels, Absorption Efficiency, Faecal Elimination and Synthesis of Cholesterol during Increasing Doses of Dietary Sitostanol Esters in Hypercholesterolaemic Subjects (1994)

1. Serum cholesterol reduction and changes in cholesterol metabolism were studied during rapeseed oil feeding without and with increasing amounts of sitostanol trans-esterified with rapeseed oil fatty acids and dissolved in rapeseed oil mayonnaise. Fifteen mildly hypercholesterolaemic subjects replaced 50 g of their usual dietary fat by 50 g of rapeseed oil fat mayonnaise for 6 weeks followed by randomization so that eight subjects continued on rapeseed oil mayonnaise alone (control group) for 15 weeks and seven on rapeseed oil mayonnaise with a small dose of sitostanol ester (800 mg/day of sitostanol) for 9 weeks followed by 6 weeks with higher dose of sitostanol ester (2000 mg/day of sitostanol). 2. During the rapeseed oil period the reduction in serum low-density lipoprotein cholesterol was 14% from the home diet. The control-adjusted reduction by the low sitostanol ester dose was 7.4% (not significant) and by the higher dose it was 15.7%. 3. The low dose of sitostanol ester had no consistent effect on cholesterol precursors or cholestanol in serum, reduced serum levels of campesterol and sitosterol by 28.2% and 23.6%, respectively, and reduced cholesterol absorption efficiency significantly from 28.7% to 23.4%. In accordance, faecal excretion of neutral and particularly endogenous neutral sterols increased (16.7% and 19.7%, respectively), but faecal cholesterol elimination and cholesterol synthesis were only insignificantly increased. 4. During the high dose of sitostanol ester the high-density lipoprotein-to low-density lipoprotein-cholesterol ratio increased.(ABSTRACT TRUNCATED AT 250 WORDS)
Spatio-temporal shadow segmentation and tracking (2003)

Shadow segmentation is a critical issue for systems aiming at extracting, tracking or recognizing objects in a given scene. Shadows can in fact modify the shape and colour of objects and therefore affect scene analysis and interpretation systems in many applications, such as video database search and retrieval, as well as video analysis in applications such as video surveillance. We present a shadow segmentation algorithm which includes two stages. The first stage extracts moving cast shadows in each frame of the sequence. The second stage tracks the extracted shadows in the subsequent frames. Tentative moving shadow regions are first identified based on spectral and geometrical properties of shadows. In order to confirm this tentative identification, shadow regions are then tracked over time. This second stage aims at exploiting the prior knowledge of a shadow detected in previous frames by evaluating its temporal behaviour. Shadow tracking is a difficult task, since colour, texture, and motion features in shadow regions cannot be used for solving the correspondence problem. Colour and texture change according to changes in the background's characteristics. The measurement of motion cannot be reliably computed for shadows. Therefore shadows may be described only by a limited amount of information. The proposed tracking algorithm makes use of this information and provides a reliability estimation of shadow recognition results of the first stage over time. This temporal analysis eliminates the possible ambiguities of the first stage and improves the efficiency of the overall shadow detection algorithm. The benefit of the proposed shadow segmentation and tracking algorithm is evaluated on both indoor and outdoor scenes. The obtained results are validated based on subjective as well as objective comparisons.
Studies on nutrient digestibilities (pre‐caecal and total) in pancreatic duct‐ligated pigs and the effects of enzyme substitution (1999)

Introduction Exocrine pancreatic insufficiency causes digestive disturbances in humans and animals. However, although clinical symptoms of pancreatic insufficiency, e.g. steatorrhoea, only occurs after loss of 80–90% normal pancreatic secretory capacity (D i M agno et al. 1973), pancreatic enzyme supplementation does not always result in normalization of digestion (especially of fat), even with high doses of enzymes (L&amp; ouml ; ser and F&amp; ouml ; lsch 1995). In order to better understand the physiological and the pathological consequences of exocrine pancreatic insufficiency in humans as well as its therapy with enzyme substitution, studies have been made using an animal model of induced pancreatic exocrine insufficiency. Hither to, studies concerning pancreatic duct ligation and/or the influence of enzyme substitution have mainly been focused on estimation of enzyme activities in chyme (e.g. A bello et al. 1989) and/or on faecal analyses of total digestibility (e.g. I mmondi et al. 1972). To get more information on effects of enzymes (natural or substituted) it seems necessary to investigate the site and extent of digestion more intensively (S udendey 1995). Therefore a pig model of induced pancreatic exocrine insufficiency, via pancreatic duct ligation, was chosen and pre‐caecal digestibility was measured by means of an ileo‐caecal re‐entrant fistula. Studies on the digestibility of a high fat diet were made, since cystic fibrosis patients with exocrine pancreatic insufficiency are recommended to take in high amounts of energy to avoid catabolic metabolism and nowadays these high energy diets comprise increasing proportions of fat (D urie and P encharz 1989; S hepherd et al. 1991). The following aspects were investigated in controls and pancreatic duct‐ligated pigs that were fed a high fat diet: changes in the composition of ileal chyme and faeces; effects on nutrient digestibility (pre‐caecal and total); efficacy of enzyme substitution in total exocrine pancreatic insufficiency.
Structure-based Inhibitor Design for an Enzyme That Binds Different Steroids (2006)

Human type 5 17beta-hydroxysteroid dehydrogenase plays a crucial role in local androgen formation in prostate tissue. Several chemicals were synthesized and tested for their ability to inhibit this enzyme, and a series of estradiol derivatives bearing a lactone on the D-ring were found to inhibit its activity efficiently. The crystal structure of the type 5 enzyme in complex with NADP and such a novel inhibitor, EM1404, was determined to a resolution of 1.30 A. Significantly more hydrogen bonding and hydrophobic interactions were defined between EM1404 and the enzyme than in the substrate ternary complex. The lactone ring of EM1404 accounts for important interactions with the enzyme, whereas the amide group at the opposite end of the inhibitor contributes to the stability of three protein loops involved in the construction of the substrate binding site. EM1404 has a strong competitive inhibition, with a Ki of 6.9+/-1.4 nM, demonstrating 40 times higher affinity than that of the best inhibitor previously reported. This is observed despite the fact that the inhibitor occupies only part of the binding cavity. Attempts to soak the inhibitor into crystals of the binary complex with NADP were unsuccessful, yielding a structure with a polyethylene glycol fragment occupying the substrate binding site. The relative crystal packing is discussed. Combined studies of small molecule inhibitor synthesis, x-ray crystallography, enzyme inhibition, and molecular modeling make it possible to analyze the plasticity of the substrate binding site of the enzyme, which is essential for developing more potent and specific inhibitors for hormone-dependent cancer therapy.
Solution rheology of hydrophobically modified associative polymers: Solvent quality and hydrophobic interactions (2003)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Ahmed A. Abdala, Keith Olesen, Saad A. Khan; Solution rheology of hydrophobically modified associative polymers: Solvent quality and hydrophobic interactions. J. Rheol. 1 March 2003; 47 (2): 497–511. https://doi.org/10.1122/1.1545076 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Society of RheologyJournal of Rheology Search Advanced Search |Citation Search
Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean (2002)

Soybean mosaic virus (SMV) and peanut mottle virus (PMV) are two potyviruses that cause yield losses and reduce seed quality in infested soybean (Glycine max (L.) Merr.) fields throughout the world. Rsv1 and Rpv1 are genes that provide soybean with resistance to SMV and PMV, respectively. Isolating and characterizing Rsv1 and Rpv1 are instrumental in providing insight into the molecular mechanism of potyvirus recognition in soybean. A population of 1056 F2 individuals from a cross between SMV- and PMV-resistant line PI 96983 (Rsv1 and Rpv1) and the susceptible cultivar 'Lee 68' (rsv1 and rpv1) was used in this study. Disease reaction and molecular-marker data were collected to determine the linkage relationship between Rsv1, Rpv1, and markers that target candidate disease-resistance genes. F2 lines showing a recombination between two of three Rsv1-flanking microsatellite markers were selected for fine mapping. Over 20 RFLP, RAPD, and microsatellite markers were used to map 38 loci at high-resolution to a 6.8-cM region around Rsv1 and Rpv1. This study demonstrates that Rsv1 and Rpv1 are tightly linked at a distance of 1.1 cM. In addition, resistance-gene candidate sequences were mapped to positions flanking and cosegregating with these resistance loci. Based on comparisons of genetic markers and disease reactions, it appears likely that several tightly linked genes are conditioning a resistance response to SMV. We discuss the specifics of these findings and investigate the utility of two disease resistance related probes for the screening of SMV or PMV resistance in soybean.
Cell-Based Immunotherapy with Suppressor CD8+ T Cells in Rheumatoid Arthritis (2005)

The chronic persistence of rheumatoid synovitis, an inflammation driven by activated T cells, macrophages, and fibroblasts causing irreversible joint damage, suggests a failure in physiologic mechanisms that down-regulate and terminate chronic immune responses. In vitro CD8(+)CD28(-)CD56(+) T cells tolerize APCs, prevent the priming of naive CD4(+) T cells, and suppress memory CD4(+) T cell responses. Therefore, we generated CD8(+)CD28(-)CD56(+) T cell clones from synovial tissues, expanded them in vitro, and adoptively transferred them into NOD-SCID mice engrafted with synovial tissues from patients with rheumatoid arthritis. Adoptively transferred CD8(+)CD28(-)CD56(+) T cells displayed strong anti-inflammatory activity. They inhibited production of IFN-gamma, TNF-alpha, and chemokines in autologous and HLA class I-matched heterologous synovitis. Down-regulation of costimulatory ligands CD80 and CD86 on synovial fibroblasts was identified as one mechanism of immunosuppression. We propose that rheumatoid synovitis can be suppressed by cell-based immunotherapy with immunoregulatory CD8(+) T cells.
Design of Small Molecules That Recognize RNA: Development of Aminoglycosides as Potential Antitumor Agents That Target Oncogenic RNA Sequences (2000)

Functional single-stranded oncogenic mRNAs such as the breakpoints of the PAX3 – FKHR and Bcr – Abl oncogenes bind selectively and with high affinity to naturally occurring, as well as synthetic, aminoglycosides. The latter, neamine-derived compounds were designed to mimic their natural counterparts in recognizing RNA (the proposed mode of binding to a phosphodiester is shown) and were obtained by parallel synthesis.
Triangular color codes on trivalent graphs with flag qubits (2019)

The color code is a topological quantum error-correcting code supporting a variety of valuable fault-tolerant logical gates. Its two-dimensional version, the triangular color code, may soon be realized with currently available superconducting hardware despite constrained qubit connectivity. To guide this experimental effort, we study the storage threshold of the triangular color code against circuit-level depolarizing noise. First, we adapt the Restriction Decoder to the setting of the triangular color code and to phenomenological noise. Then, we propose a fault-tolerant implementation of the stabilizer measurement circuits, which incorporates flag qubits. We show how information from flag qubits can be used with the Restriction Decoder to maintain the effective distance of the code. We numerically estimate the threshold of the triangular color code to be 0.2%, which is competitive with the thresholds of other topological quantum codes. We also prove that 1-flag stabilizer measurement circuits are sufficient to preserve the full code distance, which may be used to find simpler syndrome extraction circuits of the color code.
The role of vitronectin in the attachment and spatial distribution of bone-derived cells on materials with patterned surface chemistry (1997)

In recent years a central objective of tissue engineering has been understanding the interaction of cells with biomaterial surfaces. In this study we examined the protein adsorption events necessary to control the attachment and the subsequent spatial distribution of bone-derived cells exposed to chemically modified surfaces. Silane chemistry and photolithography techniques were used to create substrates with alternating regions of an aminosilane, N-(2-aminoethyl)-3-aminopropyl-trimethoxysilane (EDS), along side an alkylsilane, dimethyldichlorosilane (DMS), on quartz surfaces. Sera depleted of fibronectin (Fn), vitronectin (Vn), or both were used to determine if these proteins were necessary for the initial attachment and spatial distribution of bone-derived cells exposed to modified surfaces in vitro. The kinetics and mechanisms of the spatial distribution of cells were examined using light microscopy and digital image acquisition and subsequently were analyzed. Compared to complete serum, the use of serum depleted of fibronectin with vitronectin included had minimal effect on the cell attachment, spreading, and spatial distribution on the EDS regions of the surface. However, the use of serum depleted of vitronectin with or without fibronectin included resulted in greatly reduced cell attachment and spreading. Thus the presence of vitronectin was required for the attachment, spreading, and spatial distribution of bone-derived cells exposed to EDS/DMS-patterned surfaces.