gebhart/patrepeval huggingface dataset:
Decreased sulfhydryl groups of serum albumin in coronary artery disease. (1991)

We hypothesized that oxidative processes in myocardial tissues initiated by ischemia also cause the same kind of changes in blood proteins and lead to oxidation of sulfhydryl groups (SH). To test this hypothesis, the ratio (%MA) of mercaptalbumin to total albumin (= mercaptalbumin + nonmercaptalbumin) and the total SH contents of serum were measured in patients with coronary artery disease. There was a positive correlation between %MA and total SH contents and both values were reduced in proportion to the severity of the coronary artery disease. Furthermore, these values were lower early hours after the onset of acute myocardial infraction than 4 weeks later. These results support our hypothesis, and may provide a basis for the administration of agents which can counteract oxidative stress in order to protect myocardium in patients with coronary artery disease.
HSPPC-96 vaccine in metastatic melanoma patients: from the state of the art to a possible future (2009)

Heat-shock proteins are highly conserved, stress-induced proteins with chaperone function for trafficking and delivering peptides within the different compartments of the cell. Tumor-derived heat-shock protein-peptide complexes (HSPPCs) can be used for vaccination against malignancies. In particular, the HSPPC-96-based vaccine vitespen (formerly Oncophage) is the first autologous cancer vaccine made from individual patients' tumors that has shown encouraging results in clinical trials. In Phase I and II clinical trials, this vaccine has shown activity on different malignancies, such as gastric cancer, colorectal cancer, pancreatic cancer, non-Hodgkin's lymphoma and chronic myelogenous leukemia. In Phase III clinical trials in melanoma and kidney cancer, it demonstrated an excellent safety profile with almost no toxicity. Heat-shock protein-based vaccines can be considered as a novel therapeutic approach with a promising role in cancer management.
Biomechanical investigation of pedicle screw–vertebrae complex: a finite element approach using bonded and contact interface conditions (2003)

This study used finite element simulation to investigate the load transfer mechanisms within the screw/vertebra complex under different interface conditions, and under varying screw lengths. Both bonded and contact conditions were employed to demonstrate the interface between the screw and vertebra. Loadings were applied at the superior surface of the vertebra and screw unthreaded end, respectively, to represent two modes of flexion loads. The results indicated that the screw within the vertebra underwent a series of discontinuities of loading, identified by the localized high contact pressures, thus creating localized bending moments. The peak stress of screw was located at the junction of the screw's hub and thread, which is consistent with the location of screw failure observed in a clinical setting and the values of peak stress in the screw were proportional to the amount of moments generated by the two loading modes. The interface condition plays an important role in transferring the force within the screw/vertebra complex. A contact interface condition induces significantly higher stress in the screw than the bonded condition. Therefore providing a binding surface (with HA, or porosity coating on the screw surface) between the screw and the vertebra might be the most effective way to prevent screw failure. The influences of screw length on the peak stress in the screw become negligible when the screw is of sufficient length to extend fully into the vertebral body.
Peptide targeting by spontaneous isopeptide bond formation (2011)

Peptide fusion tags are fundamental for the identification, detection, and capture of proteins in biological assays. Commonly used peptide fusion tags rely on temporary non-covalent interactions for binding, which can put constraints on assay sensitivity. Here, peptide fusion tags were developed that could specifically interact with protein binding partners via spontaneous and irreversible isopeptide bond formation. To develop covalently interacting peptide-protein pairs, outer-membrane proteins from Gram-positive bacteria that form autocatalyzed intramolecular isopeptide bonds were dissected to generate a short peptide fragment and a protein binding partner. Initially, the major pilin subunit Spy0128 from Streptococcus pyogenes was split to develop the 16 residue isopeptag peptide and the 31 kDa pilin-C protein partner. The isopeptag:pilin-C pair were able to react via spontaneous isopeptide bond formation between an Asn residue in isopeptag and a Lys residue in pilin-C without the requirement for any accessory factors, and with a yield of 60% after a 72 hr reaction. Reconstitution between the isopeptag:pilin-C pair was robust and occurred under all biologically relevant conditions tested, and also in the complex environment of a bacterial cytosol and on the surface of mammalian cells. A similar approach was also used to dissect the small CnaB2 domain that is part of the large FbaB fibronectin-binding protein from S. pyogenes. This led to the development of a more efficient peptide-protein pair, which was rationally modified to generate the highly optimized SpyTag:SpyCatcher pair. SpyTag is a 13 amino acid peptide with a reactive Asp that forms a spontaneous intermolecular isopeptide bond with a Lys present in the 12 kDa SpyCatcher binding partner. In a reaction with SpyTag, over 40% of SpyCatcher was depleted after 1 min and SpyCatcher could no longer be detected after 2 hr. The SpyTag and SpyCatcher reaction did not require any accessory factors and proceeded efficiently at a range of biologically relevant temperatures, pH values, concentrations, buffer compositions, and in the presence of commonly used detergents. The SpyTag:SpyCatcher technology was also used for specific cell surface labelling on mammalian cell membranes. SpyTag and SpyCatcher are both composed of the regular 20 amino acids and can therefore be genetically encoded as fusion constructs for a variety of in vitro and in vivo applications. Potential applications of the SpyTag:SpyCatcher technology include specific cell surface labelling, the development of novel protein architectures, and the covalent and irreversible capture of target proteins in biological assays.
Purification and properties of a protein that binds to the C-terminal coding region of human c-myc mRNA. (1994)

The short half-life of c-myc mRNA is influenced by sequences in the 3'-untranslated region and the C-terminal part of the coding region. In cell-free extracts, a polysomal protein binds to RNA corresponding to the coding region stability determinant. This and other observations suggest that the protein is bound to polysome-associated c-myc mRNA and protects the mRNA from a ribosome-associated endoribonuclease (Bernstein, P.L., Herrick, D.J., Prokipcak, R.D., and Ross, J. (1992) Genes & Dev. 6, 642-654). Here, we describe a four-step purification of the binding protein: solubilization from ribosomes, ammonium sulfate precipitation, RNA affinity chromatography, and reverse-phase high performance liquid chromatography. The 70-kDa protein can be renatured from solutions containing sodium dodecyl sulfate or organic solvents, greatly facilitating its purification. Protein binding to c-myc coding region RNA is blocked by diamide and N-ethylmaleimide, indicating a requirement for sulfhydryl groups. The protein also binds to N-myc coding region RNA but with approximately 5-fold lower affinity than to the comparable c-myc region. Excess c-myc competitor RNA induces 8-fold destabilization of c-myc mRNA in cell-free mRNA decay extracts. In contrast, N-myc coding region competitor RNA has no effect on c-myc mRNA half-life. Therefore, the protein we have purified probably affects c-myc mRNA metabolism with high specificity.
The endoribonuclease activity of mammalian IRE1 autoregulates its mRNA and is required for the unfolded protein response (2000)

The unfolded protein response (UPR) is a signal transduction pathway that is activated by the accumulation of unfolded proteins in the endoplasmic reticulum (ER). In Saccharomyces cerevisiae the ER transmembrane receptor, Ire1p, transmits the signal to the nucleus culminating in the transcriptional activation of genes encoding an adaptive response. Yeast Ire1p requires both protein kinase and site-specific endoribonuclease (RNase) activities to signal the UPR. In mammalian cells, two homologs, Ire1 alpha and Ire1 beta, are implicated in signaling the UPR. To elucidate the RNase requirement for mammalian Ire1 function, we have identified five amino acid residues within IRE1 alpha that are essential for RNase activity but not kinase activity. These mutants were used to demonstrate that the RNase activity is required for UPR activation by IRE1 alpha and IRE1 beta. In addition, the data support that IRE1 RNase is activated by dimerization-induced trans-autophosphorylation and requires a homodimer of catalytically functional RNase domains. Finally, the RNase activity of wild-type IRE1 alpha down-regulates hIre1 alpha mRNA expression by a novel mechanism involving cis-mediated IRE1 alpha-dependent cleavage at three specific sites within the 5' end of Ire1 alpha mRNA.
Renal embolization for ablation of function in renal failure and hypertension (1989)

The results of transcatheter renal artery embolization are presented in a small group of patients with end-stage renal disease. Five of the patients were suffering from severe drug-resistant hypertension, one from rejection of a renal transplant and one had heavy haematuria from a transplant kidney. All seven patients benefited from the procedure with no significant morbidity. The procedure of renal artery embolization and its potential complications are discussed. It is concluded that renal ablation by transcatheter embolization is not only effective, but also has a significantly lower morbidity and mortality than surgical nephrectomy in this group of patients with end-stage renal disease and associated problems.
Experimental performance evaluation of a virtual software router (2011)

Software routers (SRs) are an alternative low-cost and moderate-performance router solutions implemented with general-purpose workstations able to host multiple network interface cards (NICs). Workstations can be programmed to forward packets between different NICs and to participate in routing functions. Virtualization can be used to model new protocols or hardware systems in software and without modifying the host's kernel. However virtualized routers are expected to suffer from performance degradation because of software execution overhead. In this paper, we investigate the performance impact of a virtual software router (VSR) in comparison to that of a SR. We present the performance of VSRs hosted by different workstations - with different number of processing cores.
RNA Structure: Reading the Ribosome (2005)

The crystal structures of the ribosome and its subunits have increased the amount of information about RNA structure by about two orders of magnitude. This is leading to an understanding of the principles of RNA folding and of the molecular interactions that underlie the functional capabilities of the ribosome and other RNA systems. Nearly all of the possible types of RNA tertiary interactions have been found in ribosomal RNA. One of these, an abundant tertiary structural motif called the A-minor interaction, has been shown to participate in both aminoacyl-transfer RNA selection and in peptidyl transferase; it may also play an important role in the structural dynamics of the ribosome.
Wettability Alteration of Low-permeable Carbonate Reservoir Rocks in Presence of Mixed Ionic Surfactants (2011)

Abstract Altering the wettability of the carbonate reservoir rocks from oil-wet to water-wet has figured prominently as one of the enhanced oil recovery methods in recent years. The authors measured the effect of different ionic surfactants on the wettability alteration of the rock, saturated with crude oil, and the consequent improvement in oil production was investigated by spontaneous imbibitions of solutions containing cationic, anionic, and cationic-anionic surfactant mixtures. A very low-permeable carbonate rock from one of the Iranian oil reservoirs was selected for this study. The results of imbibition tests were furthermore supported by measuring IFT, taking pictures of producing oil drops from different exterior core plug surfaces and also observing the distribution of the remaining oil in cores at the end of experiments. The results show that cationic surfactants at concentrations higher than CMC can cause a remarkable oil production through alteration of wettability and, moreover, the extent of oil production increases with temperature. In contrast, it is observed that the anionic surfactants are not able to change the wettability of an oil-wet surface and their combination with the cationic type would reduce the oil production potential of cationic surfactants.
Oral cancer detection using diffuse reflectance spectral ratio R540∕R575 of oxygenated hemoglobin bands (2006)

A low-cost, fast, and noninvasive method for early diagnosis of malignant lesions of oral mucosa based on diffuse reflectance spectral signatures is presented. In this technique, output of a tungsten halogen lamp is guided to the tissue through the central fiber of a reflection probe whose surrounding six fibers collects tissue reflectance. Ex vivo diffuse reflectance spectra in the 400 to 600-nm region is measured from surgically removed oral cavity lesions using a miniature fiber optic spectrometer connected to a computer. Reflectance spectral intensity is higher in malignant tissues and shows dips at 542 and 577 nm owing to absorption from oxygenated hemoglobin (HbO2). Measurements carried out, within an hour of surgical excision, on malignant lesion and adjoining uninvolved mucosa show that these absorption features are more prominent in neoplastic tissues owing to increased microvasculature and blood content. It is observed that reflectance intensity ratio of hemoglobin bands, R540/R575, from malignant sites are always lower than that from normal sites and vary according to the histological grade of malignancy. The diffuse reflectance intensity ratio R540/R575 of the hemoglobin bands appears to be a useful tool to discriminate between malignant lesions and normal mucosa of the oral cavity in a clinical setting.
Microwave-induced amplitude- and phase-tunable qubit-resonator coupling in circuit quantum electrodynamics (2015)

In the circuit quantum electrodynamics architecture, both the resonance frequency and the coupling of superconducting qubits to microwave field modes can be controlled via external electric and magnetic fields to explore qubit-photon dynamics in a wide parameter range. Here, we experimentally demonstrate and analyze a scheme for tuning the coupling between a transmon qubit and a microwave resonator using a single coherent drive tone. We treat the transmon as a three-level system, with the qubit subspace defined by the ground and the second excited states. If the drive frequency matches the difference between the resonator and the qubit frequencies, a Jaynes-Cummings-type interaction is induced, which is tunable in both amplitude and phase. We show that coupling strengths of about 10 MHz can be achieved in our setup, limited only by the anharmonicity of the transmon qubit. This scheme has been successfully used to generate microwave photons with a controlled temporal shape [M. Pechal et al., Phys. Rev. X 4, 041010 (2014)] and can be directly implemented with superconducting quantum devices featuring larger anharmonicity for higher coupling strengths.
Histone deacetylase inhibition modulates indoleamine 2,3-dioxygenase–dependent DC functions and regulates experimental graft-versus-host disease in mice (2008)

Histone deacetylase (HDAC) inhibitors are antitumor agents that also have antiinflammatory properties. However, the mechanisms of their immunomodulatory functions are not known. We investigated the mechanisms of action of 2 HDAC inhibitors, suberoylanilide hydroxamic acid (SAHA) and ITF 2357, on mouse DC responses. Pretreatment of DCs with HDAC inhibitors significantly reduced TLR-induced secretion of proinflammatory cytokines, suppressed the expression of CD40 and CD80, and reduced the in vitro and in vivo allostimulatory responses induced by the DCs. In addition, injection of DCs treated ex vivo with HDAC inhibitors reduced experimental graft-versus-host disease (GVHD) in a murine allogeneic BM transplantation model. Exposure of DCs to HDAC inhibitors increased expression of indoleamine 2,3-dioxygenase (IDO), a suppressor of DC function. Blockade of IDO in WT DCs with siRNA and with DCs from IDO-deficient animals caused substantial reversal of HDAC inhibition-induced in vitro suppression of DC-stimulated responses. Direct injection of HDAC inhibitors early after allogeneic BM transplantation to chimeric animals whose BM-derived cells lacked IDO failed to protect from GVHD, demonstrating an in vivo functional role for IDO. Together, these data show that HDAC inhibitors regulate multiple DC functions through the induction of IDO and suggest that they may represent a novel class of agents to treat immune-mediated diseases.
<title>Prototype optically interconnected multichip module based on computer-generated hologram technology</title> (1993)

The development of an optical interconnected multichip module (MCM) is underway at UNC- Charlotte. The approach is to use optical interconnects within a digital multichip module for connections that are longer than a certain length (break even line length). For these connections the optical link dissipates less power than the corresponding electrical link. One of the main goals of this project is to develop a technology for optical interconnects that can be implemented with minimal modification to current devices. We are currently in the process of developing a series of MCM systems. System 1 will be a testbed that enables testing of hologram encoding techniques, alignment tolerances, optical link efficiency, and thermal properties. System 2 will use the knowledge gained in the development of system 1 to build a small functional system to demonstrate the technology.
Uit de literatuur (1998)

Het voormalige Institut fur Quartarpalaontologie (tegenwoordig “Bereich Quartarpalaontologie Weimar, Institut fur Geowissenschaften der Friedrich-Schiller-Universitat, Jena”, geheten) in Weimar startte in 1978 een zoogdierpaleontologisch onderzoek in een zandgroeve in Untermassfeld bei Meiningen, in het dal van de rivier de Werra, in het zuiden van de deelstaat Thuringen. In rivierafzettingen van de Oer-Werra zijn grote hoeveelheden fossiele zoogdierresten met een Vroeg-Pleistocene ouderdom (van het Laat Waalien tot het Laat Bavelien) aangetroffen. Deze zijn door het instituut uit Weimar zeer nauwkeurig opgegraven en gedocumenteerd. Het betreft een zeer rijke zoogdierfauna met onder andere nijlpaard ( Hippopotamus amphibius antiquus) een zeer groot wild zwijn (Sus scrofa priscus), herten (onder andere van het geslacht Eucladoceros), mammoet (Mammuthus meridionalis) en neushoorn ( Dicerorhinus etruscus) en veel verschillende soorten roofdieren waaronder sabeltandtijger (Homotherium) en een grote hyena (Pachycrocuta brevirostris). Verder twaalf knaagdieren, zes soorten insecteneters, een makaak en overblijfselen van mollusken, vissen, amfibieen en reptielen (onder andere schildpad). Door de jaarlijkse, maanden durende veldcampagnes in Untermassfeld, is een zeer goed gedocumenteerde verzameling bijeengebracht. Deze zeer omvangrijke collectie is in het instituut in Weimar ondergebracht. Er zijn in verschillende publicaties al diverse onderdelen kort behandeld en Dr. Ralf Dietrich Kahlke, de huidige directeur van de genoemde instelling sprak een aantal jaren geleden uitvoerig op een bijeenkomst van de Werkgroep Pleistocene Zoogdieren te Utrecht over zijn onderzoeksproject. De heer Kahlke promoveerde in 1987 aan de universiteit van Greifswald op een proefschrift getiteld “Die unterpleistozanen Hippopotamus-Reste von Untermassfeld bei Meiningen (Bezirk Suhl, DDR) – Ein Beitrag zur Forschungs-, Entwicklungs- und Verbreitungsgeschichte fossiler Hippopotamiden in Europa”. In Untermassfeld is een indrukwekkende hoeveelheid overblijfselen in situ opgegraven van het Vroeg-Pleistocene nijlpaard. Overblijfselen van zeer jonge tot zeer oude individuen zijn gevonden. Kahlke behandelde in zijn dissertatie de vindplaats uitgebreid, beschreef en beeldde heel veel materiaal van het nijlpaard af. Helaas verscheen zijn werk niet in druk. Dat was erg jammer, want velen zouden dit werk als een standaardwerk kunnen gebruiken bij de bestudering van fossielen nijlpaarden.
Overexpression of the neutral amino acid transporter ASCT2 in human colorectal adenocarcinoma. (2003)

Cancer cells have increased amino acid transport and retention. Our aim was to determine whether the neutral amino acid transporter ASCT2 is expressed in colorectal adenocarcinomas (CRC), and whether its expression is of biological significance. Western blot analysis was performed on 4 cases of CRC. Immunohistochemical staining was performed on sections of 63 CRC, and the percent of positive cells was determined. Survival analysis was performed using the Kaplan-Meier method. Western blot analysis showed a 50 kDa protein, corresponding to ASCT2, in 3 of the 4 CRC samples. Immunohistostaining showed lack of ASCT2 immunoreactivity in 41% of the cases. ASCT2 immunoreactivity was present in 1-25% of the cancer cells in 24% of the cases, 26-50% of the cells in 13%, and in > 50% of the cells in 22% of the cases. Patient survival decreased with increased percentage of ASCT2-positive cancer cells (p = 0.0002). These results indicate that ASCT2 is expressed in a significant number of CRC, and that ASCT2 expression is associated with aggressive biological behavior. Larger studies with multivariate analysis are needed to determine whether ASCT2 expression is an independent prognostic marker in CRC.
Classification of human placental stem villi: Review of structural and functional aspects (1997)

The stem villi of the human placenta represent the central branches of the villous trees. They are characterized by a condensed fibrous stroma in which the fetal arteries and veins as well as the arterioles and venules are embedded. Functionally they are accepted as the mechanically supporting structures of the villous trees, and they are supposed to control fetal blood flow to the maternofetal exchange area, which is located in the peripheral villi. To obtain further insights into the functions of the stem villi, the recent literature has been reviewed, and some immunohistochemical, ultrastructural, and reconstruction studies have been added. These new studies were aimed at identifying immunohistochemically different subtypes of stem villi, their branching patterns, the distribution of macrophages, the stromal proliferation patterns, and the differentiation of extravascular stromal cells. Our findings demonstrate that the stem villi and their precursors, the immature intermediate villi, can selectively be identified by anti-γ-smooth muscle (sm) actin staining. Furthermore, the existence of three different subtypes of stem villi is shown; these differ regarding the presence and distribution of γ-sm actin-positive cells. These cells were immunohistochemically and ultrastructurally identified as smooth muscle cells and myofibroblasts. Increasingly complex coexpression patterns of cytoskeletal proteins reflect a clearly defined differentiation gradient of extravascular stromal cells, which covers the whole range of an undifferentiated germinative layer beneath the trophoblast to highly differentiated myofibroblasts surrounding the medias of the stem vessels. Possible functions of the extravascular contractile system include the regulation of villous turgor and the control of intervillous blood flow impedance. Microsc. Res. Tech. 38:29–41, 1997. © 1997 Wiley-Liss, Inc.