gebhart/patrepeval huggingface dataset:
Carbon nanotube p-n junction diodes (2004)

We demonstrate a single-walled carbon nanotube p-n junction diode device. The p-n junction is formed along a single nanotube by electrostatic doping using a pair of split gate electrodes. By biasing the two gates accordingly, the device can function either as a diode or as an ambipolar field-effect transistor. The diode current–voltage characteristics show forward conduction and reverse blocking characteristics, i.e., rectification. For low bias conditions, the characteristics follow the ideal diode equation with an ideality factor close to one.
Improved Aptazyme Design and In Vivo Screening Enable Riboswitching in Bacteria (2008)

Switch-hitter: A new strategy to control gene expression relies on a ligand-dependent, ribozyme-based RNA switch. The key feature of this setup is that the ribozyme liberates the ribosome binding site upon cleavage of the message. The design made it possible to screen in vivo for an inducible aptazyme by attaching an aptamer to stem III of the ribozyme, thus preserving naturally occurring stem I/stem II contacts. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z703700_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Application of affinity chromatography for separation and quantitation of glycosylated hemoglobins. (1983)

The use of m-aminophenylboronic acid immobilized on agarose as the affinity matrix for the separation and quantitation of Glyco Hb has been investigated. The glyco fraction isolated from the affinity columns contained about 10% Hb A1a + b, 52% Hb A1c, and 38% Hb A0-like glyco components. The nonglyco fraction had major portions of Hb A1a + b and Hb A0 and a small amount of Hb A1c (also contained Hb F). In normals and diabetic patients, the comparison of the affinity method with the ion-exchange chromatographic, fluorometric, and colorimetric methods showed good correlation. The affinity method also showed acceptable precision and reproducibility. The presence of labile aldimine did not influence the affinity method because it seems that only the stable ketoamine was bound to the affinity gel and thus separated by this method. Moreover, this method was less sensitive to variations in column temperature and sample age. Glyco Hb levels were determined in newborn infants and in adults with various hemoglobinopathies. The results indicated that the presence of Hb F, Hb S, and Hb C did not affect the glyco Hb determinations. Thus the affinity chromatographic approach has wider application than ion-exchange chromatography and is, at the same time, much simpler and faster than the chemical methods.
A new tetracycline antibiotic from a Dactylosporangium species. Fermentation, isolation and structrure elucidation. (1987)

An actinomycete identified as a Dactylosporangium sp. produces a new tetracycline, 4a-hydroxy-8-methoxychlortetracycline (Sch 34164). The addition of magnesium ions to complex fermentation media increased the antibiotic titers. Sch 34164 was isolated by solvent extraction and Sephadex G-25 column chromatography. The novel structure was proposed based on spectroscopic analysis. The shift of C-4a (35 to 77 ppm) and C-8 (140 to 163 ppm) in the 13C NMR as compared to chlortetracycline was indicative of the novel hydroxyl and methoxy substituents, respectively.
A Single Flux Quantum cross-bar switch and demultiplexer (1995)

A Single Flux Quantum (SFQ) demultiplexer and a cross-bar switch for a high speed data switch are described. Both circuits were error-free in simulation to 15 Gbps. The cross-bar switch was two input, two output (2/spl times/2) and used /spl sim/400 /spl mu/A control signals to set the data path. The switch has been demonstrated at over 15 Gbps/line using average voltage measurements. The correct routing of a bit stream was demonstrated at 2.488 Gbps.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Binding of mutants of human insulin-like growth factor II to insulin-like growth factor binding proteins 1-6 (1993)

A family of six specific insulin-like growth factor binding proteins (IGFBPs) modulates the biological actions of the insulin-like growth factors, IGF-I and IGF-II. In the present study, we determined the binding affinity of purified human IGFBPs 1-6 for recombinant human IGF-II mutants whose binding to IGF-I, IGF-II/mannose 6-phosphate, and insulin receptors was previously reported (Sakano, K., Enjoh, T., Numata, F., Fujiwara, H., Marumoto, Y., Higashihashi, N., Sato, Y., Perdue, J. F., and Fujita-Yamaguchi, Y. (1991) J. Biol. Chem. 266, 20626-20635). Of the regions studied, the most important determinants of IGF-II binding to the IGFBPs were A-domain residues 48-50 and B-domain residue 26. Substitution of residues 48-50 with the analogous residues from human insulin (Thr-Ser-Ile) reduced binding to IGFBP-1, -5, and -6 more than 50-fold and to IGFBP-4 by 15-50-fold; binding to IGFBP-2 and -3 was reduced 6-12-fold. The same substitution markedly reduced binding to the IGF-II/mannose 6-phosphate receptor but not to IGF-I or insulin receptors. Although substitution of residues 54 and 55 with the analogous residues from IGF-I (Arg-Arg) abolished binding to the IGF-II/mannose 6-phosphate receptor, binding to IGFBPs was not substantially affected. Substitution of Phe26 with Ser or Leu, which decreased binding to the IGF-I and insulin receptors, reduced binding to IGFBP-1 and -6 up to 80-fold, but had lesser effects on the other IGFBPs. [Leu27]IGF-II and [Leu43]IGF-II, which had a more markedly reduced affinity for the IGF-I and insulin receptors than did [Ser26]IGF-II, were bound by the IGFBPs with relatively unchanged affinity compared with IGF-II. Thus, the determinants of IGF-II binding to IGFBPs partially overlap those for the IGF-II/mannose 6-phosphate receptor and overlap those for the IGF-I receptor to a lesser extent. IGFBP-1 and IGFBP-6 are most sensitive to changes in IGF-II structure, although IGFBP-1 binds IGF-I and IGF-II with equal affinity, whereas IGFBP-6 has a marked preferential binding affinity for IGF-II. IGF-II mutants with selective impairment in recognition by specific IGFBPs or receptors will provide a useful tool for dissecting the role of the different IGF binding macromolecules in the mediation of IGF-II actions.
miR-200b mediates post-transcriptional repression of ZFHX1B (2007)

MicroRNAs have important functions during animal development and homeostasis through post-transcriptional regulation of their cognate mRNA targets. ZFHX1B is a transcriptional repressor involved in the TGFbeta signaling pathway and in processes of epithelial to mesenchymal transition via regulation of E-cadherin. We show that Zfhx1b and miR-200b are regionally coexpressed in the adult mouse brain and that miR-200b represses the expression of Zfhx1b via multiple sequence elements present in the 3'-untranslated region. Overexpression of miR-200b leads to repression of endogenous ZFHX1B, and inhibition of miR-200b relieves the repression of ZFHX1B. In accordance with these findings, miR-200b regulates the activity of the E-cadherin promoter.
Galactomannan Antigenemia and Antigenuria in Aspergillosis: Studies in Patients and Experimentally Infected Rabbits (1987)

Purified galactomannan (GM) from Aspergillus fumigatus was used in both a radioimmunoassay and an enzyme-linked immunoassay for antigen detection. Results of the two tests seemed interchangeable. By one or both assays, GM was detected in serum from four of 12 rabbits lethally infected with A. fumigatus in concentrations ranging from 108 to 356 ng/ml. Serum antigen was detected in only two of 12 patients with invasive aspergillosis. Results of assay for GM in urine were far more encouraging. Urinary GM was detectable throughout the course of lethal aspergillosis in all 16 rabbits, in concentrations of 24-1,900 ng/ml. Urine from seven of 13 patients with invasive aspergillosis had GM concentrations of 1-83 ng/ml. Antigen excretion roughly paralleled extent of disease.
Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover (2013)

The p160 steroid receptor coactivators (SRCs) SRC-1, SRC-2 [nuclear receptor coactivator (NCOA)2], and SRC-3 [amplified in breast cancer 1 (AIB1)/NCOA3] are key pleiotropic "master regulators" of transcription factor activity necessary for cancer cell proliferation, survival, metabolism, and metastasis. SRC overexpression and overactivation occur in numerous human cancers and are associated with poor clinical outcomes and resistance to therapy. In prostate cancer (PC), the p160 SRCs play critical roles in androgen receptor transcriptional activity, cell proliferation, and resistance to androgen deprivation therapy. We recently demonstrated that the E3 ubiquitin ligase adaptor speckle-type poxvirus and zinc finger (POZ) domain protein (SPOP) interacts directly with SRC-3 and promotes its cullin 3-dependent ubiquitination and proteolysis in breast cancer, thus functioning as a potential tumor suppressor. Interestingly, somatic heterozygous missense mutations in the SPOP substrate-binding cleft recently were identified in up to 15% of human PCs (making SPOP the gene most commonly affected by nonsynonymous point mutations in PC), but their contribution to PC pathophysiology remains unknown. We now report that PC-associated SPOP mutants cannot interact with SRC-3 protein or promote its ubiquitination and degradation. Our data suggest that wild-type SPOP plays a critical tumor suppressor role in PC cells, promoting the turnover of SRC-3 protein and suppressing androgen receptor transcriptional activity. This tumor suppressor effect is abrogated by the PC-associated SPOP mutations. These studies provide a possible explanation for the role of SPOP mutations in PC, and highlight the potential of SRC-3 as a therapeutic target in PC.
Molecular Imaging of CXCR4 Receptor Expression in Human Cancer Xenografts with [64Cu]AMD3100 Positron Emission Tomography (2010)

The chemokine receptor CXCR4 and its cognate ligand CXCL12 are pivotal for establishing metastases from many tumor types. Thus, CXCR4 may offer a cell surface target for molecular imaging of metastases, assisting diagnosis, staging, and therapeutic monitoring. Furthermore, noninvasive detection of CXCR4 status of a primary tumor may provide an index of the metastatic potential of the lesion. Here, we report the development and evaluation of [(64)Cu]AMD3100, a positron-emitting analogue of the stem cell mobilizing agent plerixafor to image CXCR4 in human tumor xenografts preselected for graded expression of this receptor. This imaging method was evaluated in lung metastases derived from human MDA-MB-231 breast cancer cells. Ex vivo biodistribution studies, performed to validate the in vivo imaging data, confirmed the ability of [(64)Cu]AMD3100 to image CXCR4 expression. Our findings show the feasibility of imaging CXCR4 by positron emission tomography using a clinically approved agent as a molecular scaffold.
A minimum clipping power loss scheme for mitigating the clipping noise in ofdm (2004)

The paper proposes a new method, minimum clipping power loss scheme (MCPLS), to control the clipping noise based on the relationship between the power of clipped portion and the clipping noise power of OFDM signals. First, the transmitter generates multi-route signals that carry the same information then estimates the clipping noise power of every route under the same clipping threshold. The transmitter then selects the signal with the lowest clipping noise power to clip and transmits the signal. The simulation results proved that this method can mitigate clipping noise and improve the performance of the system. The signal-to-noise ratio is gained 8 dB to achieve 10/sub -3/ symbol-error-rate when the number of subcarriers is 256, the modulation mode is 16-QAM, the clipping threshold is 1.5 and the redundancy of system is 0.59%. The floor of symbol-error-rate is reduced from 10/sub -3/ to 3/spl middot/10/sub -5/. The arithmetic achieves better effect if the threshold is lower.
Corneal Wound Healing in an Osteopontin-Deficient Mouse (2008)

OPN modulates wound healing-related fibroblast behavior and is required to restore the physiological structure of the cornea after wound healing.
Smalltalk-80: The Language and its Implementation (1983)

Smalltalk-80 is the classic standard Smalltalk language as described in Smalltalk-80: The Language and Its Implementation by Goldberg and Robson. This book is commonly called “the Blue Booki. Squeak implements the dialect of Smalltalk described in this book, but has a different implementation. Overview of the Smalltalk Language Smalltalk is a general purpose, high level programming language. It was the first original “purei object oriented language, but not the first to use the object oriented concept, which is credited to Simula 67. The explosive growth of Object Oriented Programming (OOP) technologies began in the early 1980's, with Smalltalk's introduction. Behind it was the idea that the individual human user should be the most important component of any computing system, and that programming should be a natural extension of thinking, and also a dynamic and evolutionary process consistent with the model of human learning activity. In Smalltalk, these ideas are embodied in a framework for human-computer communication. In a sense, Smalltalk is yet another language like C and Pascal, and programs can be written in Smalltalk that have the look and feel of such conventional languages. The difference lies * in the amount of code that can be reduced, * less cryptic syntax, * and code that is easier to handle for application maintenance and enhancement. But Smalltalk's most powerful feature is easy code reuse. Smalltalk makes reuse of programs, routines, and subroutines (methods) far easier. Though procedural languages allow reuse too, it is harder to do, and much easier to cheat. It is no surprise that Smalltalk is relatively easy to learn, mainly due to its simple syntax and semantics, as well as few concepts. Objects, classes, messages, and methods form the basis of programming in Smalltalk. The general methodology to use Smalltalk The notion of human-computer interface also results in Smalltalk promoting the development of safer systems. Errors in Smalltalk may be viewed as objects telling users that confusion exists as to how to perform a desired function.
Endotracheal cuff pressure and tracheal mucosal blood flow: endoscopic study of effects of four large volume cuffs. (1984)

Large volume, low pressure endotracheal tube cuffs are claimed to have less deleterious effect on tracheal mucosa than high pressure, low volume cuffs. Low pressure cuffs, however, may easily be overinflated to yield pressures that will exceed capillary perfusion pressure. Various large volume cuffed endotracheal tubes were studied, including Portex Profile, Searle Sensiv, Mallinkrodt Hi-Lo, and Lanz. Tracheal mucosal blood flow in 40 patients undergoing surgery was assessed using an endoscopic photographic technique while varying the cuff inflation pressure. It was found that these cuffs when overpressurised impaired mucosal blood flow. This impairment of tracheal mucosal blood flow is an important factor in tracheal morbidity associated with intubation. Hence it is recommended that a cuff inflation pressure of 30 cm H2O (22 mm Hg) should not be exceeded.
r-VKORC1 Expression in Factor IX BHK Cells Increases the Extent of Factor IX Carboxylation but Is Limited by Saturation of Another Carboxylation Component or by a Shift in the Rate-Limiting Step (2006)

Carboxylation of vitamin K-dependent (VKD) proteins is required for their activity and depends on reduced vitamin K generated by vitamin K oxidoreductase (VKOR) and a redox protein that regenerates VKOR activity. VKD protein carboxylation is inefficient in mammalian cells, and to understand why carboxylation becomes saturated, we developed an approach that directly measures the extent of intracellular VKD protein carboxylation. Analysis of factor IX (fIX)-expressing BHK cells indicated that slow egress of fIX from the endoplasmic reticulum and preferential secretion of the carboxylated form contribute to secreted fIX being more fully carboxylated. The analysis also revealed the first reported in vivo VKD protein turnover, which was 14-fold faster than that which occurs in vitro, suggesting facilitation of this process in vivo. r-VKORC1 expression increased the rate of fIX carboxylation and the extent of secreted carboxylated fIX approximately 2-fold, which shows that carboxylation is the rate-limiting step in fIX turnover and which was surprising because turnover in vitro is limited by release of carboxylated fIX. Interestingly, the increases were significantly smaller than the amount of VKOR overexpression (15-fold). However, when cell extracts were tested in single-turnover experiments in vitro, where redox protein is functionally substituted with dithiothreitol, VKOR overexpression increased the fIX carboxylation rate 14-fold, showing r-VKORC1 is functional for supporting fIX carboxylation. These data indicate that the effect of VKOR overexpression is limited in vivo, possibly because a carboxylation component like the redox protein becomes saturated or because another step is now rate-limiting. The studies illustrate the complexity of carboxylation and potential importance of component stoichiometry to overall efficiency.
Identification of Program Similarity in Large Populations (1990)

Various techniques for detecting similar programs in large classes have been proposed previously, but research in this area is hampered by the lack of a means for evaluating their performance. To address this deficiency, new concepts are introduced that permit the effectiveness of competing systems to be quantified and enable realistic comparisons to be made. Using these criteria, popular approaches to plagiarism detection based on counting program attributes are shown to be inadequate. A two-stage method of identifying similar pairs based on structural features is proposed, and the superior performance of this technique is established.
Tetrazine Ligation: Fast Bioconjugation Based on Inverse-Electron-Demand Diels−Alder Reactivity (2008)

Described is a bioorthogonal reaction that proceeds with unusually fast reaction rates without need for catalysis: the cycloaddition of s-tetrazine and trans-cyclooctene derivatives. The reactions tolerate a broad range of functionality and proceed in high yield in organic solvents, water, cell media, or cell lysate. The rate of the ligation between trans-cyclooctene and 3,6-di-(2-pyridyl)-s-tetrazine is very rapid (k2 2000 M-1 s-1). This fast reactivity enables protein modification at low concentration.
Toxicological and Pharmacokinetic Properties of QPI-1007, a Chemically Modified Synthetic siRNA Targeting Caspase 2 mRNA, Following Intravitreal Injection (2014)

We report the toxicological and pharmacokinetic properties of the synthetic, small interfering RNA (siRNA), QPI-1007, following intravitreal administration. QPI-1007 is a chemically modified siRNA designed to act via the RNA interference (RNAi) pathway to temporarily inhibit expression of the caspase 2 protein and is being developed as a neuroprotectant for the treatment of nonarteritic anterior ischemic optic neuropathy and other optic neuropathies such as glaucoma that result in the death of retinal ganglion cells. The half-life of QPI-1007 in the vitreous and retina/choroid in the Dutch Belted rabbit was about 2 days, and there was no sign of accumulation after repeated administrations at either 2- or 4-week dosing intervals in the rabbit. QPI-1007 was well tolerated in Dutch Belted rabbits following single or repeated intravitreal administrations of up to 11 doses over 9 months. Test-article-related effects were limited to the eyes, with minimal to mild vitreal cellular infiltration being the major finding, which was reversible. In repeated-dose studies, a modest reduction in B-wave amplitude obtained by electroretinography was observed in animals treated with the highest dose level tested (3 mg, which is equivalent to a 12 mg/eye human dose) that was not considered to be clinically meaningful. Administration in the rat of either a single bolus intravenous (i.v.) injection of 100 mg/kg or daily bolus i.v. injections of 75 mg/kg/day for 28 days failed to elicit any macroscopic or microscopic changes, suggesting a low risk for systemic toxicity. QPI-1007 was negative in three genetic toxicity studies. Overall, the nonclinical studies support the further development of QPI-1007.
Improved Cartilage Repair After Treatment With Low-Intensity Pulsed Ultrasound (2001)

Low-intensity pulsed ultrasound accelerates bone healing via upregulation of cartilage formation and maturation phases of endchondral bone formation. The current authors evaluated the effect of ultrasound therapy on the repair of full-thickness osteochondral defects. Bilateral, 3.2 mm diameter by 5.0 mm deep osteochondral defects were created in the patellar groove of 106 adult male New Zealand rabbits. The defects were treated with daily low-intensity pulsed ultrasound therapy on the right knee. The left knee was not treated. In Part I, the effect of ultrasound therapy was evaluated at 4, 8, 12, 24, and 52 weeks after surgery. In Part II, the effect of the length of treatment (5, 10, or 40 minutes of daily ultrasound therapy) compared with standard 20 minute therapy was evaluated. The repair cartilage was evaluated and graded on a standard scale for the gross and histologic appearance. Ultrasound treatment significantly improved the morphologic features and histologic characteristics of the repair cartilage compared with nontreated controls. Earlier, better repair with less degenerative changes at later times was observed in defects treated with ultrasound. Doubling the treatment time to 40 minutes daily significantly increased the histologic quality of the repair cartilage. In the current animal model, daily low-intensity pulsed ultrasound had a significant positive effect on the healing of osteochondral defects.
Biosynthesis and degradation both contribute to the regulation of coenzyme A content in Escherichia coli (1988)

Escherichia coli mutants [coaA16(Fr); Fr indicates feedback resistance] were isolated which possessed a pantothenate kinase activity that was refractory to feedback inhibition by coenzyme A (CoA). Strains harboring this mutation had CoA levels that were significantly elevated compared with strains containing the wild-type kinase and also overproduced both intra- and extracellular 4'-phosphopantetheine. The origin of 4'-phosphopantetheine was investigated by using strain SJ135 [panD delta(aroP-aceEF)], in which synthesis of acetyl-CoA was dependent on the addition of an acetate growth supplement. Rapid degradation of CoA to 4'-phosphopantetheine was triggered by the conversion of acetyl-CoA to CoA following the removal of acetate from the media. CoA hydrolysis under these conditions appeared not to involve acyl carrier protein prosthetic group turnover since [acyl carrier protein] phosphodiesterase was inhibited equally well by acetyl-CoA or CoA. These data support the view that the total cellular CoA content is controlled by modulation of biosynthesis at the pantothenate kinase step and by degradation of CoA to 4'-phosphopantetheine.