gebhart/patrepeval huggingface dataset:
Angiotensin-converting enzyme: zinc- and inhibitor-binding stoichiometries of the somatic and testis isozymes (1991)

The blood pressure regulating somatic isozyme of angiotensin-converting enzyme (ACE) consists of two homologous, tandem domains each containing a putative metal-binding motif (HEXXH), while the testis isozyme consists of just a single domain that is identical with the C-terminal half of somatic ACE. Previous metal analyses of somatic ACE have indicated a zinc stoichiometry of 1 mol of Zn2+/mol of ACE and inhibitor-binding studies have found 1 mol of inhibitor bound/mol of enzyme. These and other data have indicated that only one of the two domains of somatic ACE is catalytically active. We have repeated the metal and inhibitor-binding analyses of ACE from various sources and have determined protein concentration by quantitative amino acid analysis on the basis of accurate polypeptide molecular weights that are now available. We find that the somatic isozyme in fact contains 2 mol of Zn2+ and binds 2 mol of lisinopril (an ACE inhibitor) per mol of enzyme, whereas the testis isozyme contains 1 mol of Zn2+ and binds 1 mol of lisinopril. In the case of somatic ACE, the second equivalent of inhibitor binds to a second zinc-containing site as evidenced by the ability of a moderate excess of inhibitor to protect both zinc ions against dissociation. However, active site titration with lisinopril assayed by hydrolysis of furanacryloyl-Phe-Gly-Gly revealed that 1 mol of inhibitor/mol of enzyme abolished the activity of either isozyme, indicating that the principal angiotensin-converting site likely resides in the C-terminal (testicular) domain of somatic ACE and that binding of inhibitor to this site is stronger than to the second site.(ABSTRACT TRUNCATED AT 250 WORDS)
RNase-assisted RNA chromatography (2010)

RNA chromatography combined with mass spectrometry represents a widely used experimental approach to identify RNA-binding proteins that recognize specific RNA targets. An important drawback of most of these protocols is the high background due to direct or indirect nonspecific binding of cellular proteins to the beads. In many cases this can hamper the detection of individual proteins due to their low levels and/or comigration with contaminating proteins. Increasing the salt concentration during washing steps can reduce background, but at the cost of using less physiological salt concentrations and the likely loss of important RNA-binding proteins that are less stringently bound to a given RNA, as well as the disassembly of protein or ribonucleoprotein complexes. Here, we describe an improved RNA chromatography method that relies on the use of a cocktail of RNases in the elution step. This results in the release of proteins specifically associated with the RNA ligand and almost complete elimination of background noise, allowing a more sensitive and thorough detection of RNA-binding proteins recognizing a specific RNA transcript.
Myeloblastic leukemia cells conditionally blocked by myc-estrogen receptor chimeric transgenes for terminal differentiation coupled to growth arrest and apoptosis (1993)

Conditional mutants of the myeloblastic leukemic M1 cell line, expressing the chimeric mycer transgene, have been established. It is shown that M1 mycer cells, like M1, undergo terminal differentiation coupled to growth arrest and programmed cell death (apoptosis) after treatment with the physiologic differentiation inducer interleukin-6. However, when beta-estradiol is included in the culture medium, M1 mycer cells respond to differentiation inducers like M1 myc cell lines, where the differentiation program is blocked at an intermediate stage. By manipulating the function of the mycer transgene product, it is shown that there is a 10-hour window during myeloid differentiation, from 30 to 40 hours after the addition of the differentiation inducer, when the terminal differentiation program switches from being dependent on c-myc suppression to becoming c-myc suppression independent, where activation of c-myc has no apparent effect on mature macrophages. M1 mycer cell lines provide a powerful tool to increase our understanding of the role of c-myc in normal myelopoiesis and in leukemogenesis, also providing a strategy to clone c-myc target genes.
Broadband directional coupling in aluminum nitride nanophotonic circuits (2013)

Aluminum nitride (AlN)-on-insulator has emerged as a promising platform for the realization of linear and non-linear integrated photonic circuits. In order to efficiently route optical signals on-chip, precise control over the interaction and polarization of evanescently coupled waveguide modes is required. Here we employ nanophotonic AlN waveguides to realize directional couplers with a broad coupling bandwidth and low insertion loss. We achieve uniform splitting of incoming modes, confirmed by high extinction-ratio exceeding 33dB in integrated Mach-Zehnder Interferometers. Optimized three-waveguide couplers furthermore allow for extending the coupling bandwidth over traditional side-coupled devices by almost an order of magnitude, with variable splitting ratio. Our work illustrates the potential of AlN circuits for coupled waveguide optics, DWDM applications and integrated polarization diversity schemes.
Untersuchungen zum frühen Hydratationsverhalten von Portland- und Portlandkompositzementen (2011)

Die Untersuchung von frühen Hydratationsvorgängen beim Abbinden von Zementen bringt analytische Herausforderungen mit sich. Zur Klärung offener Fragestellungen bei der Zementhydratation ist es notwendig moderne Untersuchungsmethoden zweckmäßig einzusetzen und zu kombinieren sowie Präparationstechniken weiterzuentwickeln. Im Rahmen dieser Arbeit fand die Kryo-Rasterelektronenmikroskopie umfangreiche Anwendung zur Untersuchung der Gefügeentwicklung, der Morphologie der Hydratationsprodukte und zur chemischen Analyse der Bestandteile (EDX). Daneben wurde die in-situ Röntgendiffraktometrie und die isotherme Wärmeflusskalorimetrie zur Untersuchung der frühen Zementhydratation bis zu 3 d Reaktionszeit eingesetzt. Durch die Kombination von optischen, strukturellen und kinetischen Informationen wurden grundlegende Erkenntnisse zu den Hydratationsvorgängen in Portlandzementen erzielt. Schwerpunkte der Untersuchungen lagen auf der Beschreibung der ersten Reaktionsvorgänge nach Wasserkontakt, der morphologischen Entwicklung von Ettringit und C-S-H-Phasen und der Identifizierung von AFm-Phasen.
Simultaneous, accurate measurement of the 3D position and orientation of single molecules (2012)

Recently, single molecule-based superresolution fluorescence microscopy has surpassed the diffraction limit to improve resolution to the order of 20 nm or better. These methods typically use image fitting that assumes an isotropic emission pattern from the single emitters as well as control of the emitter concentration. However, anisotropic single-molecule emission patterns arise from the transition dipole when it is rotationally immobile, depending highly on the molecule's 3D orientation and z position. Failure to account for this fact can lead to significant lateral (x, y) mislocalizations (up to ∼50-200 nm). This systematic error can cause distortions in the reconstructed images, which can translate into degraded resolution. Using parameters uniquely inherent in the double-lobed nature of the Double-Helix Point Spread Function, we account for such mislocalizations and simultaneously measure 3D molecular orientation and 3D position. Mislocalizations during an axial scan of a single molecule manifest themselves as an apparent lateral shift in its position, which causes the standard deviation (SD) of its lateral position to appear larger than the SD expected from photon shot noise. By correcting each localization based on an estimated orientation, we are able to improve SDs in lateral localization from ∼2× worse than photon-limited precision (48 vs. 25 nm) to within 5 nm of photon-limited precision. Furthermore, by averaging many estimations of orientation over different depths, we are able to improve from a lateral SD of 116 (∼4× worse than the photon-limited precision; 28 nm) to 34 nm (within 6 nm of the photon limit).
Metabotropic Glutamate Receptors and Epileptogenesis (2002)

Activation of metabotropic glutamate receptors (mGluRs) often produces long-lasting effects on the excitability of cortical neurons. For example, mGluR stimulation induces long-term potentiation or depression of excitatory synaptic transmission in the hippocampus. Similarly, the effects of mGluRs on cortical epileptiform activities also are enduring. A transient application of group I mGluR agonists to hippocampal slices produces ictal-like discharges that persist for hours after the removal of the applied agonist. This action of group I mGluRs-transforming "normal" hippocampal slice into an "epileptic-like" one-may represent a form of epileptogenesis. The advent of such a model, in which epileptogenesis can be reliably induced in an in vitro preparation and the process is complete within hours, may facilitate the exploration of cellular mechanisms underlying epileptogenesis.
A convenient microtitre tray procedure for yeast identification (1990)

Media for yeast identification tests were incorporated into the wells of a microtitre tray. The tests included fermentation and assimilation of carbohydrates, assimilation of nitrogen compounds, growth in vitamin-free medium, resistance to cycloheximide, and observations for cell morphology and sporulation. Results of tests conducted in the trays showed very good agreement with those obtained by conventional methods. Eighteen reference yeasts were correctly identified from tests conducted in the trays. The trays of media could be stored, and provided a convenient system for yeast identification.
Bioengineered factor Xa as a potential new strategy for hemophilia therapy (2012)

Vascular damage triggers the hemostatic process producing a localized clot to prevent significant loss of blood. A failure of the system to respond appropriately leads to bleeding complications. Th...
Bayesian approach to time-resolved tomography (2015)

Conventional X-ray micro-computed tomography (μCT) is unable to meet the need for real-time, high-resolution, time-resolved imaging of multi-phase fluid flow. High signal-to-noise-ratio (SNR) data acquisition is too slow and results in motion artefacts in the images, while fast acquisition is too noisy and results in poor image contrast. We present a Bayesian framework for time-resolved tomography that uses priors to drastically reduce the required amount of experiment data. This enables high-quality time-resolved imaging through a data acquisition protocol that is both rapid and high SNR. Here we show that the framework: (i) encompasses our previous, algorithms for imaging two-phase flow as limiting cases; (ii) produces more accurate results from imperfect (i.e. real) data, where it can be compared to our previous work; and (iii) is generalisable to previously intractable systems, such as three-phase flow.
A haplotype map of the human genome (2005)

Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
HMOX1 and NQO1 Genes are Upregulated in Response to Contact Sensitizers in Dendritic Cells and THP-1 Cell Line: Role of the Keap1/Nrf2 Pathway (2008)

Electrophilicity is one of the most common features of skin contact sensitizers and is necessary for protein haptenation. The Keap1 (Kelch-like ECH-associated protein 1)/Nrf2 -signaling pathway is dedicated to the detection of electrophilic stress in cells leading to the upregulation of genes involved in protection or neutralization of chemical reactive species. Signals provided by chemical stress could play an important role in dendritic cell activation and the aim of this work was to test whether contact sensitizers were specific activators of the Keap1/Nrf2 pathway. CD34-derived dendritic cells (CD34-DC) and the THP-1 myeloid cell line were treated by a panel of sensitizers (Ni, 1-chloro 2,4-dinitrobenzene, cinnamaldehyde, 7-hydroxycitronellal, 1,4-dihydroquinone, alpha-methyl-trans-cinnamaldehyde, 2-4-tert-(butylbenzyl)propionaldehyde or Lilial, and 1,4-phenylenediamine), irritants (sodium dodecyl sulfate, benzalkonium chloride), and a nonsensitizer molecule (chlorobenzene). Three well-known Nrf2 activators (tert-butylhydroquinone, lipoic acid, sulforaphane) were also tested. Expression of hmox1 and nqo1 was measured using real-time PCR and cellular accumulation of Nrf2 was assessed by Western blot. Our results showed an increased expression at early time points of hmox1 and nqo1 mRNAs in response to sensitizers but not to irritants. Accumulation of the Nrf2 protein was also observed only with chemical sensitizers. A significant inhibition of the expression of hmox1 and nqo1 mRNAs and CD86 expression was found in 1-chloro 2,4-dinitrobenzene-treated THP-1 cells preincubated with N-acetyl cysteine, a glutathione precursor. Altogether, these data suggested that the Keap1/Nrf2-signaling pathway was activated by electrophilic molecules including sensitizers in dendritic cells and in the THP-1 cell line. Monitoring of this pathway may provide new biomarkers (e.g., Nrf2, hmox1) for the detection of the sensitization potential of chemicals.
Revealing a core signaling regulatory mechanism for pluripotent stem cell survival and self-renewal by small molecules (2010)

Using a high-throughput chemical screen, we identified two small molecules that enhance the survival of human embryonic stem cells (hESCs). By characterizing their mechanisms of action, we discovered an essential role of E-cadherin signaling for ESC survival. Specifically, we showed that the primary cause of hESC death following enzymatic dissociation comes from an irreparable disruption of E-cadherin signaling, which then leads to a fatal perturbation of integrin signaling. Furthermore, we found that stability of E-cadherin and the resulting survival of ESCs were controlled by specific growth factor signaling. Finally, we generated mESC-like hESCs by culturing them in mESC conditions. And these converted hESCs rely more on E-cadherin signaling and significantly less on integrin signaling. Our data suggest that differential usage of cell adhesion systems by ESCs to maintain self-renewal may explain their profound differences in terms of morphology, growth factor requirement, and sensitivity to enzymatic cell dissociation.
Connective tissue attachment formation following exclusion of gingival connective tissue and epithelium during healing (1985)

The present investigation was designed to evaluate the potential for reformation of connective tissue attachment on exposed and planed root surfaces by preventing the dentogingival epithelium and the gingival connective tissue from interfering with healing following periodontal surgery. Following the elevation of soft tissue flaps, the buccal and proximal alveolar bone of 24 teeth (48 roots) was removed to mid‐root level in 6 monkeys and the exposed root surfaces were carefully planed in order to remove the root cementum. Before the flaps were repositioned and sutured, a membrane (Millipore® filter) was placed over the denuded part of the root surfaces of 16 teeth (test teeth) in order to prevent the epithelium and the gingival connective tissue from interfering with healing. The membrane was adjusted to cover the tooth surfaces from midcrown level to approximately l mm apical to the bone crest. No membranes were placed around the remaining 8 teeth (control teeth) before flap repositioning. The animals were sacrificed 6 months after surgery. The jaws were removed and histological sections of test and control teeth including their buccal periodontal tissues were produced. Nine of the test teeth had to be excluded from examination due to technical failures in the surgical procedure or tissue preparation. New cementum with inserting collagen fibers was observed on all remaining 14 test roots. The length of this newly formed fibrous attachment corresponded to approximately 50% of the distance from the apical extension of root planing to the cemento‐enamel junction. In the majority of the control teeth no new attachment had formed but a “long” junctional epithelium was lining the root surfaces to the apical extension of root planing. In 3 control roots a small amount of new cementum with inserting collagen fibers was found in the most apical area of root planing. The results showed that the reformation of a connective tissue attachment was considerably favored by the placement of membranes which prevented the dentogingival epithelium and the gingival connective tissue from interfering with healing.
Experiences using a hands-free interface (2008)

Hands-free interfaces could be the best choice for Human-Computer Interaction (HCI) for people with physical disabilities that are not capable of using traditional input devices. Once a first prototype is developed in the laboratory taking into account design and usability requirements, real users is what finally categorize an interface as useful or not. Therefore, an evaluation of our interface with users with cerebral palsy and multiple sclerosis has been carried out during a project of 9 months long. This paper presents a vision-based user interface designed to achieve computer accessibility together with the validation and evaluation of its human computer interaction issues such as usability and accessibility.
One-Pot Synthesis of Protein-Embedded Metal–Organic Frameworks with Enhanced Biological Activities (2014)

Protein molecules were directly embedded in metal-organic frameworks (MOFs) by a coprecipitation method. The protein molecules majorly embedded on the surface region of MOFs display high biological activities. As a demonstration of the power of such materials, the resulting Cyt c embedded in ZIF-8 showed a 10-fold increase in peroxidase activity compared to free Cyt c in solution and thus gave convenient, fast, and highly sensitive detection of trace amounts of explosive organic peroxides in solution.
Statistical Methods in Medical Research (2002)

Statistical methods in medical research , Statistical methods in medical research , کتابخانه دیجیتال جندی شاپور اهواز
Implications of the p53 tumor-suppressor gene in clinical oncology. (1995)

Current evidence suggests that abrogation of normal p53 pathway is a common feature in human cancers, and it appears to be a critical step in the pathogenesis and progression of tumors. Analysis of p53 function and mutations in human cancers may lead to identification of the precise nature of the carcinogenic damage in human tissues. These laboratory investigations and biologic findings have raised the possibility to screen patients at increased risk for cancer, aid the diagnosis made by traditional methods, assess the prognosis of individual cancer patient, design treatment protocols, and test the response to therapeutic agents.
Rpi-vnt1.1, a Tm-22 Homolog from Solanum venturii, Confers Resistance to Potato Late Blight (2009)

Despite the efforts of breeders and the extensive use of fungicide control measures, late blight still remains a major threat to potato cultivation worldwide. The introduction of genetic resistance into cultivated potato is considered a valuable method to achieve durable resistance to late blight. Here, we report the identification and cloning of Rpi-vnt1.1, a previously uncharacterized late-blight resistance gene from Solanum venturii. The gene was identified by a classical genetic and physical mapping approach and encodes a coiled-coil nucleotide-binding leucine-rich repeat protein with high similarity to Tm-2(2) from S. lycopersicum which confers resistance against Tomato mosaic virus. Transgenic potato and tomato plants carrying Rpi-vnt1.1 were shown to be resistant to Phytophthora infestans. Of 11 P. infestans isolates tested, only isolate EC1 from Ecuador was able to overcome Rpi-vnt1.1 and cause disease on the inoculated plants. Alleles of Rpi-vnt1.1 (Rpi-vnt1.2 and Rpi-vnt1.3) that differed by only a few nucleotides were found in other late-blight-resistant accessions of S. venturii. The late blight resistance gene Rpi-phu1 from S. phureja is shown here to be identical to Rpi-vnt1.1, suggesting either that this strong resistance gene has been maintained since a common ancestor, due to selection pressure for blight resistance, or that genetic exchange between S. venturii and S. phureja has occurred at some time.
Inhibition of binding of fibronectin to matrix assembly sites by anti-integrin (alpha 5 beta 1) antibodies. (1990)

Fibroblasts have cell surface sites that mediate assembly of plasma and cellular fibronectin into the extracellular matrix. Cell adhesion to fibronectin can be mediated by the interaction of an integrin (alpha 5 beta 1) with the Arg-Gly-Asp-Ser (RGDS)-containing cell adhesion region of fibronectin. We have attempted to elucidate the role of the alpha 5 beta 1 fibronectin receptor in assembly of fibronectin in matrices. Rat monoclonal antibody mAb 13, which recognizes the integrin beta 1 subunit, completely blocked binding and matrix assembly of 125I-fibronectin as well as binding of the 125I-70-kD amino-terminal fragment of fibronectin (70 kD) to fibroblast cell layers. Fab fragments of the anti-beta 1 antibody were also inhibitory. Antibody mAb 16, which recognizes the integrin alpha 5 subunit, partially blocked binding of 125I-fibronectin and 125I-70-kD. When cell layers were coincubated with fluoresceinated fibronectin and either anti-beta 1 or anti-alpha 5, anti-beta 1 was a more effective inhibitor than anti-alpha 5 of binding of labeled fibronectin to the cell layer. Inhibition of 125I-fibronectin binding by anti-beta 1 IgG occurred within 20 min. Inhibition of 125I-fibronectin binding by anti-beta 1 Fab fragments or IgG could not be overcome with increasing concentrations of fibronectin, suggesting that anti-beta 1 and exogenous fibronectin may not compete for the same binding site. No beta 1-containing integrin bound to immobilized 70 kD. These data indicate that the beta 1 subunit plays an important role in binding and assembly of exogenous fibronectin, perhaps by participation in the organization, regeneration, or cycling of the assembly site rather than by a direct interaction with fibronectin.
Pathway choice in DNA double strand break repair: observations of a balancing act (2012)

Proper repair of DNA double strand breaks (DSBs) is vital for the preservation of genomic integrity. There are two main pathways that repair DSBs, Homologous recombination (HR) and Non-homologous end-joining (NHEJ). HR is restricted to the S and G2 phases of the cell cycle due to the requirement for the sister chromatid as a template, while NHEJ is active throughout the cell cycle and does not rely on a template. The balance between both pathways is essential for genome stability and numerous assays have been developed to measure the efficiency of the two pathways. Several proteins are known to affect the balance between HR and NHEJ and the complexity of the break also plays a role. In this review we describe several repair assays to determine the efficiencies of both pathways. We discuss how disturbance of the balance between HR and NHEJ can lead to disease, but also how it can be exploited for cancer treatment.