gebhart/patrepeval huggingface dataset:
Mitochondrial ATP synthase. cDNA cloning, amino acid sequence, overexpression, and properties of the rat liver alpha subunit. (1990)

The predicted amino acid sequence of the alpha subunit of the rat liver mitochondrial ATP synthase has been obtained by sequencing a cDNA for the alpha subunit. Analysis of the sequence shows that it contains the A and B consensus sequences found in many nucleotide-binding proteins. Twelve amino acids of the rat liver alpha subunit differ from the sequence of the bovine heart alpha subunit; four of these involve differences in charge. The rat liver alpha subunit, from arginine 15 to the C-terminal proline 510, has been overexpressed in Escherichia coli using the alkaline phosphatase promoter (phoA) and leader peptide to direct the export of the expressed protein to the bacterial periplasm. By treating the cells with lysozyme, osmotic shock, and alkaline pH washes, the alpha subunit can be extracted in high yield (greater than 25 mg/liter) and in a high state of purity. The expressed alpha subunit remains soluble at pH 9.5 or greater and precipitates when treated with Mg2+ ions at low millimolar concentration. The bacterially expressed alpha subunit interacts with 2'(3')-O-(2,4,6-trinitrophenyl)adenosine 5'-triphosphate (TNP-ATP), resulting in a marked fluorescence enhancement upon binding. An enhancement of fluorescence is also observed upon the interaction of the alpha subunit with TNP-ADP. Preincubating the alpha subunit with 1.5 mM ATP significantly reduces the fluorescence enhancement seen with TNP-ATP. The alpha subunit binds TNP-ATP with an apparent Kd in the low micromolar range (1-5 microM) and binds TNP-ADP with an affinity at least 10-fold lower. This work shows that the rat liver alpha subunit can be overexpressed in E. coli to yield a large amount of functional protein. With the acquisition of the overexpressed alpha subunit, it is now possible to test the reconstitution of ATPase activity from a mixture of recombinant and rat liver-derived subunits and to test the formation of complexes by the overexpressed alpha and beta subunits of the rat liver F1-ATPase.
Blue Luminescence from (CdS)ZnS Core–Shell Nanocrystals (2004)

Out of the blue: (CdS)ZnS nanocrystals suitable for display applications have been prepared and exhibit a narrow, blue luminescence from 460 to 480 nm (FWHM ≤28 nm; see picture), with quantum efficiencies of 20–30 %. It is possible to demonstrate blue electroluminescence from these core–shell nanocrystals by embedding them in an organic thin-film device.
Starter Cultures for Kimchi Fermentation (2015)

Kimchi is a traditional Korean vegetable product that is naturally fermented by various microorganisms present in the raw materials. Among these microorganisms, lactic acid bacteria dominate the fermentation process. Natural fermentation with unsterilized raw materials leads to the growth of various lactic acid bacteria, resulting in variations in the taste and quality of kimchi, which may make it difficult to produce industrial-scale kimchi with consistent quality. The use of starter cultures has been considered as an alternative for the industrial production of standardized kimchi, and recent trends suggest that the demand for starter cultures is on the rise. However, several factors should be carefully considered for the successful application of starter cultures for kimchi fermentation. In this review, we summarize recent studies on kimchi starter cultures, describe practical problems in the application of industrial-scale kimchi production, and discuss the directions for further studies.
A novel biotin protein required for reductive carboxylation of 2‐oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK‐6 (2003)

Isocitrate dehydrogenase was purified from Hydrogenobacter thermophilus, and the corresponding gene was cloned and sequenced. The enzyme had similar structural properties to the isocitrate dehydrogenase of Escherichia coli, but differed in its catalytic properties, such as coenzyme specificity, pH dependency and kinetic parameters. Notably, the enzyme catalysed the oxidative decarboxylation of isocitrate, but not the reductive carboxylation of 2-oxoglutarate. The carboxylation reaction required the addition of cell extract and ATP-Mg, suggesting the existence of additional carboxylation factor(s). Further analysis of the carboxylation factor(s) resulted in the purification of two polypeptides. N-terminal amino acid sequencing revealed that the two polypeptides are homologues of pyruvate carboxylase with a biotinylated subunit, but do not catalyse pyruvate carboxylation. Pyruvate carboxylase was also purified, but was not active in stimulating isocitrate dehydrogenase. Isocitrate dehydrogenase, the novel biotin protein, ATP-Mg and NADH were essential for the reductive carboxylation of 2-oxoglutarate. These observations indicate that the novel biotin protein is an ATP-dependent factor, which is involved in the reverse (carboxylating) reaction of isocitrate dehydrogenase.
Semantic pointing (2004)

We introduce semantic pointing, a novel interaction technique that improves target acquisition in graphical user interfaces (GUIs). Semantic pointing uses two independent sizes for each potential target presented to the user: one size in motor space adapted to its importance for the manipulation, and one size in visual space adapted to the amount of information it conveys. This decoupling between visual and motor size is achieved by changing the control-to-display ratio according to cursor distance to nearby targets. We present a controlled experiment supporting our hypothesis that the performance of semantic pointing is given by Fitts' index of difficulty in motor rather than visual space. We apply semantic pointing to the redesign of traditional GUI widgets by taking advantage of the independent manipulation of motor and visual widget sizes.
A possible mechanism for the inhibition of ribosomal RNA gene transcription during mitosis. (1995)

When cells enter mitosis, RNA synthesis ceases. Yet the RNA polymerase I (pol I) transcription machinery involved in the production of pre-rRNA remains bound to the nucleolus organizing region (NOR), the chromosome site harboring the tandemly repeated rRNA genes. Here we examine whether rDNA transcription units are transiently blocked or "frozen" during mitosis. By using fluorescent in situ hybridization we were unable to detect nascent pre-rRNA chains on the NORs of mouse 3T3 and rat kangaroo PtK2 cells. Appropriate controls showed that our approach was sensitive enough to visualize, at the light microscopic level, individual transcriptionally active rRNA genes both in situ after experimental unfolding of nucleoli and in chromatin spreads ("Miller spreads"). Analysis of the cell cycle-dependent redistribution of transcript-associated components also revealed that most transcripts are released from the rDNA at mitosis. Upon disintegration of the nucleolus during mitosis, U3 small nucleolar RNA (snoRNA) and the nucleolar proteins fibrillarin and nucleolin became dispersed throughout the cytoplasm and were excluded from the NORs. Together, our data rule out the presence of "frozen Christmas-trees" at the mitotic NORs but are compatible with the view that inactive pol I remains on the rDNA. We propose that expression of the rRNA genes is regulated during mitosis at the level of transcription elongation, similarly to what is known for a number of genes transcribed by pol II. Such a mechanism may explain the decondensed state of the NOR chromatin and the immediate transcriptional reactivation of the rRNA genes following mitosis.
Real-Time PCR Quantification of Human Adenoviruses in Urban Rivers Indicates Genome Prevalence but Low Infectivity (2005)

Real-time PCR was applied to quantify the abundance of human adenoviruses in two southern California urban rivers, the San Gabriel and Los Angeles. A total of 114 river samples from five different locations were collected over a 1-year period and analyzed for human adenoviruses, along with fecal indicator bacteria and coliphages. Adenoviruses were detected by real-time PCR in approximately 16% of the samples, with concentrations ranging from 10(2) to 10(4) genomes per liter. However, a plaque assay using two human tissue culture cell lines, HEK-293A and A549, yielded negative results, suggesting that adenoviruses detected by real-time PCR are likely noninfectious. Enterovirus genome was detected in approximately 7% of the samples by reverse transcription-PCR. Analysis by Spearman's rho rank order correlation showed significant correlations between fecal indicator bacteria and indicator virus (total coliform, fecal coliform, enterococcus, and coliphage values). However, no significant correlations were found between human adenoviruses quantified by real-time PCR and culturable coliphages or fecal indicator bacteria. Kruskal-Wallis chi-square analysis showed significant seasonal variability of all fecal indicator bacteria and coliphages, while no significant variability was observed for adenoviruses or enteroviruses. This study presents the first quantitative measurement of human adenovirus genomes in urban rivers and their statistical relationship to fecal indicator bacteria and coliphages. The uncoupling between high-number genome copies of adenoviruses detected by real-time PCR and the absence of infectivity detected by tissue culture suggests that genome-based detection methods are inadequate for direct assessment of human health risk.
The Aglycone Specificity-determining Sites Are Different in 2,4-Dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA)-glucosidase (Maize β-Glucosidase) and Dhurrinase (Sorghum β-Glucosidase) (2000)

The maize beta-glucosidase isozyme Glu1 hydrolyzes a broad spectrum of substrates in addition to its natural substrate DIMBOAGlc (2-O-beta-d-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-on e), whereas the sorghum beta-glucosidase isozyme Dhr1 hydrolyzes exclusively its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-d-glucose). To study the mechanism of substrate specificity further, eight chimeric beta-glucosidases were constructed by replacing peptide sequences within the C-terminal region of Glu1 with the homologous peptide sequences of Dhr1 or vice versa, where the two enzymes differ by 4 to 22 amino acid substitutions, depending on the length of the swapped regions. Five Glu1/Dhr1 chimeras hydrolyzed substrates that are hydrolyzed by both parental enzymes, including dhurrin, which is not hydrolyzed by Glu1. In contrast, three Dhr1/Glu1 chimeras hydrolyzed only dhurrin but with lower catalytic efficiency than Dhr1. Additional domain-swapping within the C-terminal domain of Glu1 showed that replacing the peptide (466)FAGFTERY(473) of Glu1 with the homologous peptide (462)SSGYTERF(469) of Dhr1 or replacing the peptide (481)NNNCTRYMKE(490) in Glu1 with the homologous peptide (477)ENGCERTMKR(486) of Dhr1 was sufficient to confer to Glu1 the ability to hydrolyze dhurrin. Data from various reciprocal chimeras, sequence comparisons, and homology modeling suggest that the Dhr1-specific Ser-462-Ser-463 and Phe-469 play a key role in dhurrin hydrolysis. Similar data suggest that DIMBOAGlc hydrolysis determinants are not located within the extreme 47-amino acid-long C-terminal domain of Glu1.
From studies of biochemical mechanism to novel biological mediators: Prostaglandin endoperoxides, thromboxanes, and leukotriences (1983)

Research Article| September 01 1983 From studies of biochemical mechanism to novel biological mediators: Prostaglandin endoperoxides, thromboxanes, and leukotriences: Nobel Lecture, 8 December 1982 Bengt Samuelsson Bengt Samuelsson 1Department of Physiological Chemistry, Karolinska Institutet, S-104 05 Stockholm, Sweden Search for other works by this author on: This Site PubMed Google Scholar Biosci Rep (1983) 3 (9): 791–813. https://doi.org/10.1007/BF01133779 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Bengt Samuelsson; From studies of biochemical mechanism to novel biological mediators: Prostaglandin endoperoxides, thromboxanes, and leukotriences: Nobel Lecture, 8 December 1982. Biosci Rep 1 September 1983; 3 (9): 791–813. doi: https://doi.org/10.1007/BF01133779 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 ContentAll JournalsBioscience Reports Search Advanced Search This content is only available as a PDF. © 1983 The Biochemical Society1983 Article PDF first page preview Close Modal You do not currently have access to this content.
Osteoarticular allografts for reconstruction in the proximal part of the humerus after excision of a musculoskeletal tumor. (1990)

An osteoarticular allograft was used to replace the proximal end of the humerus in twenty patients who had had a wide excision of a bone tumor. Three patients needed a second allograft because the first became infected. All patients were followed for at least two years except for two patients who died. The functional results and complications of the twenty-three index procedures were evaluated. Function was excellent in one patient, good in eleven, fair in one, and poor in five. The allografts had advantages compared with other options for reconstruction (for example, prosthetic implants); these included restoration of the length of the bone, replacement of the articular surface, and sites for reattachment of the deltoid muscle and rotator cuff. We concluded that the complications do not preclude use of this procedure.
Effect of Growth Temperature on the Cryopreservation of Prototheca (1976)

The temperature at which Prototheca spp. were grown determined their response to freezing to -196 degrees C and subsequent thawing. Cells cultured at 35 degrees C were the most sensitive to freezing injury; at lower growth temperatures, resistance to freezing damage was seen. At all culture temperatures examined, the freezing tolerance varied with the age of the culture.
Evaluation of human and non‐human primate antibody binding to pig cells lacking GGTA1/CMAH/β4GalNT2 genes (2015)

Inactivation of the β4GalNT2 gene reduces human and non-human primate antibody binding resulting in diminished porcine xenoantigenicity. The increased humoral immunity of non-human primates toward GGTA1-/CMAH-deficient cells compared to pigs lacking either GGTA1 or GGTA1/CMAH/β4GalNT2 highlights the complexities of carbohydrate xenoantigens and suggests potential limitations of the non-human primate model for examining some genetic modifications. The progressive reduction of swine xenoantigens recognized by human immunoglobulin through inactivation of pig GGTA1/CMAH/β4GalNT2 genes demonstrates that the antibody barrier to xenotransplantation can be minimized by genetic engineering.
Cell-Free Protein Expression and Functional Assay in Nanowell Chip Format (2004)

The expression and characterization of large protein libraries requires high-throughput tools for rapid and cost-effective expression and screening. A promising tool to meet these requirements is miniaturized high-density plates in chip format, consisting of an array of wells with submicroliter volumes. Here, we show the combination of nanowell chip technology and cell-free transcription and translation of proteins. Using piezoelectric dispensers, we transferred proteins into nanowells down to volumes of 100 nL and successfully detected fluorescence using confocal laser scanning. Moreover, we showed cell-free expression of proteins on a nanoliter scale using commercially available coupled transcription and translation systems. To reduce costs, we demonstrated the feasibility of diluting the coupled in vitro transcription and translation mix prior to expression. Additionally, we present an enzymatic inhibition assay in nanowells to anticipate further applications, such as the high-throughput screening of drug candidates or the identification of novel enzymes for biotechnology.
Chemical self-assembly of graphene sheets (2009)

Chemically derived and noncovalently functionalized graphene sheets (GS) were found to self-assemble onto patterned gold structures via electrostatic interactions between the functional groups and the gold surfaces. This afforded regular arrays of single graphene sheets on large substrates, which were characterized by scanning electron microscopy (SEM), Auger microscopy imaging, and Raman spectroscopy. This represents the first time that self-assembly has been used to produce on-substrate and fully-suspended graphene electrical devices. Molecular coatings on the GS were removed by high current “electrical annealing”, which restored the high electrical conductance and Dirac point of the GS. Molecular sensors for highly sensitive gas detection using the self-assembled GS devices are demonstrated.
Model Predictive Control of Type 1 Diabetes: An in Silico Trial (2007)

The proposed in silico trial shows the potential of MPC for artificial pancreas design. The main features are a capability to consider meal announcement information, delay compensation, and simplicity of tuning and implementation.
Combined Antitumor Effect of Suramin Plus Irradiation in Human Prostate Cancer Cells: The Role of Apoptosis (1993)

Suramin has recently surfaced as a potential antineoplastic agent on the basis of its ability to exert a cytostatic effect on human prostate carcinoma cells. Radiotherapy for the treatment of prostate cancer has long been known as an alternative medical therapeutic approach, but the molecular mechanism involved in radiation-induced toxicity in prostatic tumors is poorly defined. In these studies, the antitumor effect of suramin and irradiation, either as individual treatments or in combination, was investigated in human prostate cancer cells. Two androgen-independent prostate cancer cell lines, DU-145 and PC-3, were used as in vitro model systems to study the underlying molecular mechanisms of these two therapeutic modalities. A cytostatic effect on cell growth was observed when cells were exposed to suramin alone, while treatment with irradiation alone resulted in significant cell death as determined by the Trypan blue exclusion assay. Suramin treatment prior to irradiation inhibited this radiation-induced cell death. In contrast, exposure of cells to suramin following irradiation enhanced the cytotoxic effect of ionizing radiation. Temporal analysis of the molecular events involved in radiation-induced toxicity revealed the characteristic fragmentation of DNA into a nucleosomal ladder (a hallmark of apoptosis) and enhanced expression of specific programmed cell death-associated genes (TRPM-2 and TGF-beta), preceding the dramatic decrease in cell number. These results indicate that radiation-induced cell death proceeds via the apoptotic pathway. Further studies have demonstrated that activation of programmed cell death by ionizing radiation is substantially inhibited by pretreatment of the cells with suramin. This study suggests that the relative timing of this combination treatment may have significant therapeutic implications in the treatment of advanced prostate cancer.
Evolution of glycosaminoglycans and their glycosyltransferases: Implications for the extracellular matrices of animals and the capsules of pathogenic bacteria (2002)

Glycosaminoglycans (linear polysaccharides with a repeating disaccharide backbone containing an amino sugar) are essential components of extracellular matrices of animals. These complex molecules play important structural, adhesion, and signaling roles in mammals. Direct detection of glycosaminoglycans has been reported in a variety of organisms, but perhaps more definitive tests for the glycosyltransferase genes should be utilized to clarify the distribution of glycosaminoglycans in metazoans. Recently, glycosyltransferases that form the hyaluronan, heparin/heparan, or chondroitin backbone were identified at the molecular level. The three types of glycosyltransferases appear to have evolved independently based on sequence comparisons and other characteristics. All metazoans appear to possess heparin/heparan. Chondroitin is found in some worms, arthropods, and higher animals. Hyaluronan is found only in two of the three main branches of chordates. The presence of several types of glycosaminoglycans in the body allows multiple communication channels and adhesion systems to operate simultaneously. Certain pathogenic bacteria produce extracellular coatings, called capsules, which are composed of glycosaminoglycans that increase their virulence during infection. The capsule helps shield the microbe from the host defenses and/or modulates host physiology. The bacterial and animal polysaccharides are chemically identical or at least very similar. Therefore, no immune response is generated, in contrast to the vast majority of capsular polymers from other bacteria. In microbial systems, it appears that in most cases functional convergent evolution of glycosaminoglycan glycosyltransferases occurred, rather than direct horizontal gene transfer from their vertebrate hosts.
Generation of a chemical gradient across an array of 256 cell cultures in a single chip (2013)

A microfluidic diffusion diluter to create stable chemical gradients across an array of cell cultures was demonstrated. The device enabled concentration based studies to be conducted at 256 different concentrations across individual, low shear cell cultures. A gradient of staurosporine on cells stained with Mitotracker Deep Red (MTDR) showed a concentration-based effect on cell apoptosis across the cell culture array.
Gamma Camera Dual Imaging with a Somatostatin Receptor and Thymidine Kinase after Gene Transfer with a Bicistronic Adenovirus in Mice (2002)

The hSSTr2 and TK proteins were simultaneously imaged following dual gene transfer with an adenovirus vector.
Robust Controller for Vertical-Longitudinal-Lateral Dynamics Control of Small Helicopter (2014)

The problem of stabilization of vertical, lateral and longitudinal dynamics for hover flight mode of an unmanned autonomous helicopter (UAH) in a gusty environment is considered. The controller design is based on a generic linear model which successfully describes the behavior of most small scale helicopters. A recursive (backstepping) design procedure is used to design the robust controller for vertical, longitudinal and lateral dynamics based on the Lyapunov’s method. For comparison purposes we design another controller based on the linear quadratic regulator (LQR) criteria. The simulation results demonstrate that the proposed controllers can effectively attenuate the gust effects and achieve rapid and accurate vertical, longitudinal and lateral position tracking when gusts occur.