gebhart/patrepeval huggingface dataset:
Ca2+/calmodulin-dependent protein kinase II. Identification of a regulatory autophosphorylation site adjacent to the inhibitory and calmodulin-binding domains. (1988)

Ca2+/calmodulin-dependent protein kinase II (CaM-kinase II) autophosphorylated under limiting conditions (7 microM [gamma-32P]ATP, 500 microM magnesium acetate, 4 degrees C) was analyzed by CNBr cleavage and peptide mapping to determine the site of autophosphorylation that brings about transition of the kinase to the Ca2+-independent form. Reverse phase high performance liquid chromatography (HPLC) (C3) revealed one major CN-Br 32P-peptide (CB1) that eluted at about 6% propanol. This peptide contained [32P]threonine, but almost no [32P]serine, and migrated as a single band (Mr = 3000-3500) in polyacrylamide gels run in the presence of urea and sodium dodecyl sulfate. The properties of CB1 were compared to the properties of a 26-residue synthetic peptide containing the CaM-binding and inhibitory domains as well as a consensus phosphorylation sequence (-Arg-Gln-Glu-Thr-) of rat brain CaM-kinase II (residues 282-307 and 283-308 of the alpha and beta subunits, respectively). CB1 and the synthetic peptide comigrated in urea/sodium dodecyl sulfate gels, co-eluted from reverse phase HPLC (C3 and C18) and from Sephadex G-50, and exhibited Ca2+-dependent calmodulin-binding properties. When the two peptides were subjected to automated Edman sequence analysis, both exhibited a burst of 32P release at cycle 5, which is consistent with the expected amino-terminal sequence of the two peptides, i.e. His-Arg-Gln-Glu-Thr(PO4)-. These findings indicate that autophosphorylation of Thr286 (alpha subunit) and Thr287 (beta subunit) is responsible for transition of CaM-kinase II to the Ca2+-independent form.
ADAM13 Disintegrin and Cysteine-rich Domains Bind to the Second Heparin-binding Domain of Fibronectin (2002)

ADAM13 is a member of the disintegrin and metalloprotease protein family that is expressed on cranial neural crest cells surface and is essential for their migration. ADAM13 is an active protease that can cleave fibronectin in vitro and remodel a fibronectin substrate in vivo. Using a recombinant secreted protein containing both disintegrin and cysteine-rich domains of ADAM13, we show that this "adhesive" region of the protein binds directly to fibronectin. Fibronectin fusion proteins corresponding to the various functional domains were used to define the second heparin-binding domain as the ADAM13 binding site. Mutation of the syndecan-binding site (PPRR --> PPTM) within this domain abolishes binding of the recombinant disintegrin and cysteine-rich domains of ADAM13. We further show that the adhesive disintegrin and cysteine-rich domain of ADAM13 can promote cell adhesion via beta(1) integrins. This adhesion requires integrin activation and can be prevented by antibodies to the cysteine-rich domain of ADAM13 and beta(1) integrin. Finally, wild type, but not the E/A mutant of ADAM13 metalloprotease domain, can be shed from the cell surface, releasing the metalloprotease domain associated with the disintegrin and cysteine-rich domains. This suggests that ADAM13 shedding may involve its own metalloprotease activity and that the released protease may interact with both integrins and extracellular matrix proteins.
A Fair Fast Scalable Rea,der-Writer Lock (1993)

A reader-writer (RW) lock allows either multiple readers to inspect shared data or a single writer exclusive access for modifying that data. On shared memory multiprocessors,cost of acquiring and releasing these locks can have a large impact on the performance of parallel applications. A major problem with naive implementations of these locks, where processors spin on a global lock variable waiting for the lock to become available, is that the memory containing the lock and the interconnection network to that memory will also become contended when the lock is contended.
Myocardial Insulin-Like Growth Factor-I Gene Expression During Recovery From Heart Failure After Combined Left Ventricular Assist Device and Clenbuterol Therapy (2005)

The data suggest involvement of elevated myocardial IGF-I mRNA in recovery. IGF-I may act to limit atrophy and apoptosis during reverse remodeling and to promote repair and regeneration in concert with stromal cell derived factor.
Ultrashort echo time spectroscopic imaging (UTESI) of cortical bone (2007)

Cortical bone in the mature skeleton has a short T(2)* and produces no detectable signal with conventional MR sequences. A two-dimensional ultrashort echo time (UTE) sequence employing half radio frequency (RF) pulse excitations and radial ramp sampling reduces the effective TE to 8 micros and is capable of detecting signals from cortical bone. We propose a time-efficient UTE spectroscopic imaging (UTESI) technique based on an interleaved variable TE acquisition, preceded by long T(2)* signal suppression using either a 90 degrees pulse and gradient dephasing or an inversion pulse and nulling. The projections were divided into multiple groups with the data for each group being collected with progressively increasing TE and interleaved projection angles. The undersampled projections within each group sparsely covered k-space. A view sharing and sliding window reconstruction algorithm was implemented to reconstruct images at each TE, followed by Fourier transformation in the time domain to generate spectroscopic images. T(2)* was quantified through either exponential fitting of the time domain images or line fitting of the magnitude spectrum. Relative water content and the resonance frequency shift due to bulk susceptibility were also evaluated. The feasibility of this technique was demonstrated with phantom and volunteer studies on a clinical 3T scanner.
Antitumor Activity and Pharmacology of 1‐β‐D‐Arabinofuranosylcytosine‐5′‐stearylphosphate: An Orally Active Derivative of 1‐β‐D‐Arabinofuranosylcytosine (1989)

The antitumor activity of 1-beta-D-arabinofuranosylcytosine-5'-alkylphosphates (CnPCAs) against L1210 leukemia in mice after oral administration was demonstrated. The optimum length of the alkyl group on the phosphate moiety of CnPCA for exhibiting a high antitumor activity was found to be between tetradecyl (C14) and tricosyl (C23). The most active alkyl derivative in this system was found to be 1-beta-D-arabinofuranosylcytosine-5'-stearylphosphate (C18PCA). The optimum and minimum effective doses of C18PCA were 100 and 6.25 mg/kg/day (q1d, day 1 to day 5), respectively. The maximum T/C% of C18PCA was approximately 220. The antitumor activity of C18PCA was not greatly dependent on the treatment schedule and route. Plasma concentration of 1-beta-D-arabinofuranosylcytosine (ara-C) remained in the range of 0.4 to 0.75 nmol/ml [corrected] for 24 h after oral administration of 100 mg/kg (170 mumol/kg) of C18PCA. These results indicate that C18PCA administered per orally is absorbed intact through the gastrointestinal tract and area-C is released of long period of time. C18PCA is regarded as an orally active depot form of ara-C.
Combinatorial effects ofFlk1andTal1on vascular and hematopoietic development in the mouse (2003)

Mouse embryos mutant for the VEGF receptor, VEGFR2, Flk-1, or Kdr, fail to form both endothelial and hematopoietic cells, suggesting a possible role in a common progenitor to both lineages. The transcription factor Tal1 (Scl), is not expressed in Flk1(-/-) embryos, consistent with a downstream role in the Flk1 pathway. We tested whether expression of Tal1 under the Flk1 promoter was sufficient to rescue the loss of endothelial and hematopoietic cells in Flk1 mutants. Only partial rescue of hematopoiesis and endothelial development was observed in vivo. However, Flk1(-/Tal1) embryonic stem (ES) cells were capable of blast colony formation in vitro at levels equivalent to Flk1(+/-) heterozygotes. Ectopic expression of Tal1 under the Flk1 promoter in Flk1(+/-) mouse embryos or ES cells caused no obvious pathology but increased the number of blast colony forming cells (BL-CFCs) and enhanced their hematopoietic potential. These single-cell-derived BL-CFCs also produced smooth muscle cells in vitro. Increased Tal1 expression inhibited smooth muscle differentiation in this assay, whereas loss of Tal1 promoted smooth muscle formation. We propose a model in which the combinatorial effects of Flk1 and Tal1 act to regulate cell fate choice in early development into hematopoietic, endothelial, and smooth muscle lineages.
Amino acids at the N‐ and C‐termini of human glutamate carboxypeptidase II are required for enzymatic activity and proper folding (2004)

Human glutamate carboxypeptidase II (GCPII) is a co-catalytic metallopeptidase and its putative catalytic domain is homologous to the aminopeptidases from Vibrio proteolyticus and Streptomyces griseus. In humans, the enzyme is expressed predominantly in the nervous system and the prostate. The prostate form, termed prostate-specific membrane antigen, is overexpressed in prostate cancer and is used as a diagnostic marker of the disease. Inhibition of the form of GCPII expressed in the central nervous system has been shown to protect against ischemic injury in experimental animal models. Human GCPII consists of 750 amino acids, and six individual domains were predicted to constitute the protein structure. Here, we report the analysis of the contribution of these putative domains to the structure/function of recombinant human GCPII. We cloned 13 mutants of human GCPII that are truncated or extended at one or both the N- and C-termini of the GCPII sequence. The clones were used to generate stably transfected Drosophila Schneider's cells, and the expression and carboxypeptidase activities of the individual protein products were determined. The extreme C-terminal region of human GCPII was found to be critical for the hydrolytic activity of the enzyme. The deletion of as few as 15 amino acids from the C-terminus was shown to completely abolish the enzymatic activity of GCPII. Furthermore, the GCPII carboxypeptidase activity was abrogated upon removal of more than 60 amino acid residues from the N-terminus of the protein. Overall, these results clearly show that amino acid segments at the N- and C-termini of the ectodomain of GCPII are essential for its carboxypeptidase activity and/or proper folding.
Large‐Area, Selective Transfer of Microstructured Silicon: A Printing‐ Based Approach to High‐Performance Thin‐Film Transistors Supported on Flexible Substrates (2005)

The selective transfer and accurate registration of microstructured silicon (μs-Si) across large areas is demonstrated using a printing-based procedure applicable to both rigid (i.e., glass) and flexible plastic substrates (see Figure). The utility of this technique to construct macroelectronic systems that incorporate high-performance μs-Si thin-film transistors on flexible substrates is also demonstrated.
[Associations between hepatitis B virus x gene mutations and hepatocellular carcinoma]. (2015)

Incidence of the T1674C mutation in the X region and of the T1753C mutation and the A1762T/G1764A double mutation in the BCP region was higher for patients with HBV-related HCC; the T1753C mutation and the A1762T/G1764A double mutation may inhibit the formation of HBeAg.
MicroRNAs in Cancer (2009)

MicroRNAs (miRNAs) are small, noncoding RNAs with important functions in development, cell differentiation, and regulation of cell cycle and apoptosis. MiRNA expression is deregulated in cancer by a variety of mechanisms including amplification, deletion, mutation, and epigenetic silencing. Several studies have now shown that miRNAs are involved in the initiation and progression of cancer. In this review, we briefly describe miRNA biogenesis and discuss how miRNAs can act as oncogenes and tumor suppressors. We also address the role of miRNAs in the diagnosis, prognosis, and treatment of cancer.
Challenges associated with the targeted delivery of gelonin to claudin-expressing cancer cells with the use of activatable cell penetrating peptides to enhance potency (2011)

We conclude that while a claudin-3 and -4 ligand serves to deliver rGel into 2008 cells the delivered molecules were entrapped in intracellular vesicles. Incorporation of R9 non-specifically increased rGel cytotoxicity and this effect could be masked by inclusion of an E9 sequence. However, the putative protease cleavable sequences tested were inadequate for release of R9-rGel from CPE-E9-G4S-R9-rGel.
Transcranial focused ultrasound neuromodulation of the human primary motor cortex (2018)

Abstract Transcranial focused ultrasound is a form of non-invasive neuromodulation that uses acoustic energy to affect neuronal excitability. The effect of ultrasound on human motor cortical excitability is currently unknown. We apply ultrasound to the primary motor cortex in humans using a novel transcranial ultrasound and magnetic stimulation (TUMS) paradigm that allows for concurrent and concentric ultrasound stimulation with transcranial magnetic stimulation (TMS). This allows for non-invasive inspection of the effect of ultrasound on motor neuronal excitability using the motor evoked potential (MEP) generated by TMS. We test the effect of ultrasound on single pulse MEP recruitment curves and paired pulse protocols including short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). We also test the longevity of the effect and the effect of ultrasound on the cortical silent period in a small sub-sample of participants. In addition, we test the effect of ultrasound to motor cortex on a stimulus response reaction time task. Results show ultrasound inhibits the amplitude of single-pulse MEPs and attenuates intracortical facilitation but does not affect intracortical inhibition. Early evidence suggests that ultrasound does not affect cortical silent period duration and that the duration of inhibition may be related to the duration of stimulation. Finally, ultrasound reduces reaction time on a simple stimulus response task. This is the first report of the effect of ultrasound on human motor cortical excitability and motor behavior and confirms previous results in the somatosensory cortex that ultrasound results in effective neuronal inhibition that confers a performance advantage.
Peripheral nerve regeneration through guidance tubes (2004)

Biological nerve grafts have been extensively utilized in the past to repair peripheral nerve injuries. More recently, the use of synthetic guidance tubes in repairing these injuries has gained in popularity. This review focuses on artificial conduits, nerve regeneration through them, and an account of various synthetic materials that comprise these tubes in experimental animal and clinical trials. It also lists and describes several biomaterial considerations one should regard when designing, developing, and manufacturing potential guidance channel candidates. In the future, it it likely that the most successful synthetic nerve conduit will be one that has been fabricated with some of these strategies in mind.
The Effective Production of Shikonin by Cultures with an Increased Cell Population (1985)

We have studied the efficient production of shikonin derivatives by suspension cultures of Lithospermum erythrorhizon with an increased cell population. The yield of shikonin derivatives was highest (800 mg/liter) when 2.8 g dry wt/liter of the cells was inoculated into the M-2 medium which we had developed for the production, but the excess inoculum lowered the yield. We investigated suitable conditions for production with the increased cell population. The optimum amount of inoculum rose to 4.9 g dry wt/liter when the concentrations of all the components contained in the M-8 medium, which we developed for increasing the productivity by modification of the M-2 medium, were increased in proportion to the amount of inoculum, and consequently we could increase the yield of the shikonin derivatives from 1400 mg/liter to 1900 mg/liter. Moreover, the increased rate of oxygen supply in addition to the enrichment of the medium made it possible to produce 2300 mg/liter of the shikonin derivatives from a culture for which 5.6 g dry wt/liter of the cells was inoculated.
CHO DUKX cell lineages preadapted to growth in serum-free suspension culture enable rapid development of cell culture processes for the manufacture of recombinant proteins (1996)

Using an adaptive strategy, Chinese hamster ovary (CHO) cell lines were developed that are capable of robust growth in serum-free suspension culture. These preadapted derivatives of the commonly used strain of CHO cells (CHO DUKX), termed PA-DUKX, were used for the introduction and stable expression of several heterologous human genes. A significant advantage of recombinant PA-DUKX cells was their ability to readily resume growth in serum-free suspension culture after transfection and amplification of heterologous genes. Expression of recombinant human proteins in PA-DUKX cells was quantitatively similar to that of lineages generated using conventional CHO DUKX cells. In addition, recombinant human proteins expressed by transfected PA-DUKX lineages were shown to be biochemically and structurally similar to those expressed in CHO DUKX cells, PA-DUKX host cell technology provides an opportunity for reducing the time and resources required to develop large-scale, suspension culture-based manufacturing processes employing serum-free medium. (c) 1996 John Wiley & Sons, Inc.
Theoretical Analysis of View Interpolation With Inaccurate Depth Information (2011)

A problem of view interpolation from a pair of rectified stereo images with inaccurate depth information is addressed. Errors in geometric information greatly affect the quality of the resulting images since inaccurate geometry causes miscorrespondences between the input images. A new theory for quantitatively analyzing the effect of depth errors and providing a principled optimization scheme based on the mean-squared error metric is proposed. The theory clarifies that, if the probabilistic distribution of the depth errors is given, an optimized view-interpolation scheme that outperforms conventional linear interpolation can be derived. It also reveals that, under specific conditions, linear interpolation is acceptable as an approximation of the optimized-interpolation scheme. Furthermore, band limitation combined with linear interpolation is also analyzed, leading to an optimal cutoff frequency, which achieves better results than the antialias scheme proposed in previous studies. Experimental results using real scenes are also presented to confirm this theory.
The methylation patterns of chromosomal integration regions influence gene activity of transferred DNA in Petunia hybrida (1992)

The regions of integration of a transferred DNA-fragment from three transgenic Petunia hybrida plants were analysed for their influence on the expression of the foreign DNA. Each of the three transformants, lines 16, 17 and 24, contained a fragment of a plasmid on which two genes were located, an npt-II gene which renders the plants resistant to kanamycin and the A1 gene from Zea mays, a visible marker gene that leads to the production of a brick red anthocyanin pigment in the flowers. Inactivation of both genes in line 16 is associated with integration into a region of highly repetitive DNA, while the integration sites of the other two lines were essentially unique. The integration regions of lines 17 and 24, both of which show expression of the foreign genes at characteristically different intensities, showed a distinct methylation pattern that was stably conserved for these regions in both transgenic and wild-type plants. The characteristic methylation pattern of the two integration regions was also imposed on the border region of the integrated fragments and might thus be responsible for the differences in the intensity of gene expression observed among the two lines.
AN ECONOMIC MODEL OF U.S. IMPORTS OF BUTTER AND MILK FAT PRODUCTS (2005)

This study developed a model to explain monthly imports of butter and butter substitutes. The U.S. imports butter and other high milk fat products that can substitute for a strict definition of butter. These products include dairy spreads, butter substitutes, anhydrous milk fat, and food preparations. The U.S. imports these high milk fat products under a tariff-rate quota system (TRQ) implemented by the World Trade Organization (WTO). This study quantified all the milk fat contained in U.S. butter and butter substitute imports. A conceptual model was developed to explain imports of these products under a TRQ system. And an econometric model was estimated to analyze the economic factors that drive over-quota imports. The model found that the wedge between U.S. and world butter prices explains much of the incentive to import overquota butter and butter substitutes.
Purification and Properties of a Bacteriocin-Like Substance (Acnecin) of Oral Propionibacterium acnes (1978)

Propionibacterium acnes CN-8, isolated from human dental plaque, was grown in a liquid medium, and its bacteriocin-like substance (acnecin) was extracted from the cells by ultrasonic treatment. Acnecin was purified to a homogeneous state with recovery of 47%. Specific activity increased 72-fold in comparison with the crude extract. The properties of acnecin were as follows. (i) Acnecin may consist of five subunits with a molecular weight of about 12,000. (ii) Its isoelectric point was 5.5. (iii) In amino acid composition, aspartic acid, glutamic acid, glycine, and alanine were predominant, whereas cystine was not present. (iv) Acnecin contained 3.3% carbohydrate but was substantially free from lipid. (v) The activity was lost by heating at 60 degrees C or by protease and lysozyme treatments. Acnecin acted bacteriostatically on the indicator strain without killing it. The action spectrum of acnecin was very narrow; it was effective only against strains of non-acnecin-producing P. acnes and Corynebacterium parvum, a species closely related to P. acnes.
Gene Mutations and Genomic Rearrangements in the Mouse as a Result of Transposon Mobilization from Chromosomal Concatemers (2006)

Previous studies of the Sleeping Beauty (SB) transposon system, as an insertional mutagen in the germline of mice, have used reverse genetic approaches. These studies have led to its proposed use for regional saturation mutagenesis by taking a forward-genetic approach. Thus, we used the SB system to mutate a region of mouse Chromosome 11 in a forward-genetic screen for recessive lethal and viable phenotypes. This work represents the first reported use of an insertional mutagen in a phenotype-driven approach. The phenotype-driven approach was successful in both recovering visible and behavioral mutants, including dominant limb and recessive behavioral phenotypes, and allowing for the rapid identification of candidate gene disruptions. In addition, a high frequency of recessive lethal mutations arose as a result of genomic rearrangements near the site of transposition, resulting from transposon mobilization. The results suggest that the SB system could be used in a forward-genetic approach to recover interesting phenotypes, but that local chromosomal rearrangements should be anticipated in conjunction with single-copy, local transposon insertions in chromosomes. Additionally, these mice may serve as a model for chromosome rearrangements caused by transposable elements during the evolution of vertebrate genomes.
Two Controlled Trials of Antibiotic Treatment in Patients with Persistent Symptoms and a History of Lyme Disease (2001)

There is considerable impairment of health-related quality of life among patients with persistent symptoms despite previous antibiotic treatment for acute Lyme disease. However, in these two trials, treatment with intravenous and oral antibiotics for 90 days did not improve symptoms more than placebo.