gebhart/patrepeval huggingface dataset:
DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells (2008)

DNA double-strand breaks (DSBs) are dangerous lesions that can lead to potentially oncogenic genomic rearrangements or cell death. The two major pathways for repair of DSBs are nonhomologous end joining (NHEJ) and homologous recombination (HR). NHEJ is an intrinsically error-prone pathway while HR results in accurate repair. To understand the origin of genomic instability in human cells it is important to know the contribution of each DSB repair pathway. Studies of rodent cells and human cancer cell lines have shown that the choice between NHEJ or HR pathways depends on cell cycle stage. Surprisingly, cell cycle regulation of DSB repair has not been examined in normal human cells with intact cell cycle checkpoints. Here we measured the efficiency of NHEJ and HR at different cell cycle stages in hTERT-immortalized diploid human fibroblasts. We utilized cells with chromosomally-integrated fluorescent reporter cassettes, in which a unique DSB is introduced by a rare-cutting endonuclease. We show that NHEJ is active throughout the cell cycle, and its activity increases as cells progress from G1 to G2/M (G1 < S < G2/M). HR is nearly absent in G1, most active in the S phase, and declines in G2/M. Thus, in G2/M NHEJ is elevated, while HR is on decline. This is in contrast to a general belief that NHEJ is most active in G1, while HR is active in S, G2 and M. The overall efficiency of NHEJ was higher than HR at all cell cycle stages. We conclude that human somatic cells utilize error-prone NHEJ as the major DSB repair pathway at all cell cycle stages, while HR is used, primarily, in the S phase.
Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. (1994)

The wx-K mutation results from the insertion of a copia-like retrotransposon into exon 12 of the maize waxy gene. This retrotransposon, named Hopscotch, has one long open reading frame encoding all of the domains required for transposition. Computer-assisted database searches using Hopscotch and other plant copia-like retroelements as query sequences have revealed that ancient, degenerate retrotransposon insertions are found in close proximity to 21 previously sequenced plant genes. The data suggest that these elements may be involved in gene duplication and the regulation of gene expression. Similar searches using the Drosophila retrotransposon copia did not reveal any retrotransposon-like sequences in the flanking regions of animal genes. These results, together with the recent finding that reverse-transcriptase sequences characteristic of copia-like elements are ubiquitous and diverse in plants, suggest that copia-like retrotransposons are an ancient component of plant genomes.
Rhamnolipids mediate detachment of Pseudomonas aeruginosa from biofilms (2005)

The process of detachment, through which bacteria use active mechanisms to leave biofilms and return to the planktonic (free-living) state, is perhaps the least understood aspect of the biofilm life cycle. Like other stages of biofilm development, detachment is a dynamic, regulated process, controlled by specific genes, and induced by particular environmental cues. In previous work we discovered Pseudomonas aeruginosa variants that exhibit accelerated biofilm detachment. These hyper-detaching variants arise spontaneously from biofilms at a high frequency, and they exhibit robust detachment under different biofilm growth conditions. Here we show that these variants detach by a mechanism requiring the biosurfactant rhamnolipid and that this detachment mechanism rapidly restores antibiotic sensitivity to separating bacteria. We also show that rhamnolipids can bring about detachment in wild-type P. aeruginosa biofilms. These findings raise the possibility that this detachment mechanism may be useful as a treatment to disrupt established biofilms. Interestingly, the rhamnolipid-mediated detachment mechanism involves the formation of cavities within the centre of biofilm structures. Our data suggest a model to explain detachment that occurs via this pattern.
An adaptive subdivision method for surface-fitting from sampled data (1986)

A method is developed for surface-fitting from sampled data. Surface-fitting is the process of constructing a compact representation to model the surface of an object based on a fairly large number of given data points. In our case, the data is obtained from a real object using an automatic three-dimensional digitizing system. The method is based on an adaptive subdivision approach, a technique previously used for the design and display of free-form curved surface objects. Our approach begins with a rough approximating surface and progressively refines it in successive steps in regions where the data is poorly approximated. The method has been implemented using a parametric piecewise bicubic Bernstein-B&amp;eacute;zier surface possessing G 1 geometric continuity. An advantage of this approach is that the refinement is essentially local reducing the computational requirements which permits the processing of large databases. Furthermore, the method is simple in concept, yet realizes efficient data compression. Some experimental results are given which show that the representation constructed by this method is faithful to the original database.
Optimization of waveguide bends and bent mode converters using a genetic algorithm (2002)

Waveguide bends must be designed such that they have only a little mode conversion. A small spurious mode content inside the bend can be tolerated if the modes are converted back to the main mode at the end of the curved section. A program was developed to optimize bends and bent mode converters for oversized waveguides using a genetic algorithm.
Evaluation of the metS and murB Loci for Antibiotic Discovery Using Targeted Antisense RNA Expression Analysis in Bacillus anthracis (2007)

The biowarfare-relevant bacterial pathogen Bacillus anthracis contains two paralogs each of the metS and murB genes, which encode the important antibiotic target functions methionyl-tRNA synthetase and UDP-N-acetylenolpyruvoylglucosamine reductase, respectively. Empirical screens were conducted to detect and characterize gene fragments of each of these four genes that could cause growth reduction of B. anthracis when inducibly expressed from a plasmid-borne promoter. Numerous such gene fragments that were overwhelmingly in the antisense orientation were identified for the metS1 and murB2 alleles, while no such orientation bias was seen for the metS2 and murB1 alleles. Gene replacement mutagenesis was used to confirm the essentiality of the metS1 and murB2 alleles, and the nonessentiality of the metS2 and murB1 alleles, for vegetative growth. Induced transcription of RNA from metS1 and murB2 antisense-oriented gene fragments resulted in specific reduction of mRNA of their cognate genes. Attenuation of MetS1 enzyme expression hypersensitized B. anthracis cells to a MetS-specific antimicrobial compound but not to other antibiotics that affect cell wall assembly, fatty acid biosynthesis, protein translation, or DNA replication. Antisense-dependent reduction of MurB2 enzyme expression caused hypersensitivity to beta-lactam antibiotics, a synergistic response that has also been noted for the MurA-specific antibiotic fosfomycin. These experiments form the basis of mode-of-action detection assays that can be used in the discovery of novel MetS- or MurB-specific antibiotic drugs that are effective against B. anthracis or other gram-positive bacterial pathogens.
Selection Pressure on HIV-1 Envelope by Broadly Neutralizing Antibodies to the Conserved CD4-Binding Site (2012)

The monoclonal antibody (MAb) VRC01 was isolated from a slowly progressing HIV-1-infected donor and was shown to neutralize diverse HIV-1 strains by binding to the conserved CD4 binding site (CD4bs) of gp120. To better understand the virologic factors associated with such antibody development, we characterized HIV-1 envelope (Env) variants from this donor and five other donors who developed broadly neutralizing antibodies. A total of 473 env sequences were obtained by single-genome amplification, and 100 representative env clones were expressed and tested for entry and neutralization sensitivity. While VRC01 neutralizes about 90% of the genetically diverse heterologous HIV-1 strains tested, only selective archival Env variants from the VRC01 donor were sensitive to VRC01 and all of the Env variants derived from the donor plasma were resistant, indicating strong antibody-based selection pressure. Despite their resistance to this broadly reactive MAb that partially mimics CD4, all Env variants required CD4 for entry. Three other CD4bs MAbs from the same donor were able to neutralize some VRC01 escape variants, suggesting that CD4bs antibodies continued to evolve in response to viral escape. We also observed a relatively high percentage of VRC01-resistant Env clones in the plasma of four of five additional broadly neutralizing donors, suggesting the presence of CD4bs-directed neutralizing antibodies in these donors. In total, these data indicate that the CD4bs-directed neutralizing antibodies exert ongoing selection pressure on the conserved CD4bs epitope of HIV-1 Env.
Dispatch of direct load control using dynamic programming (1991)

An approach based on dynamic programming is presented for the dispatch of direct load control (DLC). The objective is to coordinate DLC strategies with system unit commitment such that the system production cost is minimized. To achieve this goal, the DLC dispatch is first integrated into the unit commitment problem. An optimization technique based on dynamic programming is then developed to reach the optimal DLC dispatch strategy and system generation schedule. To demonstrate the effectiveness of the approach, results from a sample study performed on the Taiwan power system are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mild Traumatic Brain Injury (Concussion) During Combat (2010)

Blast mechanism of concussion was inconsistently associated with PCS, depending on the definition of concussion utilized. A self-reported history of blast mechanism was not associated with persistent PCS for the majority of US soldiers with concussions.
A Hybrid Drug Limits Resistance by Evading the Action of the Multiple Antibiotic Resistance Pathway (2015)

Hybrid drugs are a promising strategy to address the growing problem of drug resistance, but the mechanism by which they modulate the evolution of resistance is poorly understood. Integrating high-throughput resistance measurements and genomic sequencing, we compared Escherichia coli populations evolved in a hybrid antibiotic that links ciprofloxacin and neomycin B with populations evolved in combinations of the component drugs. We find that populations evolved in the hybrid gain less resistance than those evolved in an equimolar mixture of the hybrid's components, in part because the hybrid evades resistance mediated by the multiple antibiotic resistance (mar) operon. Furthermore, we find that the ciprofloxacin moiety of the hybrid inhibits bacterial growth whereas the neomycin B moiety diminishes the effectiveness of mar activation. More generally, comparing the phenotypic and genotypic paths to resistance across different drug treatments can pinpoint unique properties of new compounds that limit the emergence of resistance.
Retrobiosynthetic analysis of carbon fixation in the phototrophic eubacterium Chloroflexus aurantiacus (1993)

The phototrophic bacterium Chloroflexus aurantiacus does not use any of the known autotrophic CO2 fixation pathways. There is evidence for a new cyclic autotrophic pathway in which acetyl-CoA is converted to 3-hydroxypropionate and further to succinate and malate. This hypothesis was tested by feeding growing cultures during several generations with 3-hydroxy[1-13C]propionate, [1-13C]acetate, or [2-13C]acetate, in addition to unlabeled CO2. The relative 13C content of individual carbon atoms in biosynthetic amino acids and nucleosides was determined by 1H- and 13C-NMR spectroscopy. 13C coupling patterns were analyzed by two-dimensional 13C-TOCSY experiments which were optimized for the analysis of multiply 13C-labeled biosynthetic samples. From the 13C enrichments of amino acids and nucleosides, the labeling patterns of central metabolic intermediates were evaluated by a retrobiosynthetic approach. Both 3-hydroxypropionate and acetate were incorporated into all central metabolic pools. The 13C labeling and coupling patterns suggest a novel carbon fixation pathway via 3-hydroxypropionate. Specifically, we propose that acetyl-CoA is carboxylated to malonyl-CoA which is reduced under formation of 3-hydroxypropionyl-CoA. Dehydration and reduction yield propionyl-CoA which is converted to succinate by a second carboxylation reaction. The net product of autotrophic carbon fixation appears to be glyoxylate. However, it is not yet known how glyoxylate is channeled into anabolic metabolism. Assimilation of acetate can proceed via the CO2 fixation pathway, but also via the glyoxylate pathway.
Generation of cytotoxic T-cell responses with synthetic melanoma-associated peptidesin vivo: Implications for tumor vaccines with melanoma-associated antigens (1996)

Peptide epitopes derived from differentiation antigens of the melanocyte lineage have been identified in human melanomas and normal cultured melanocytes as targets for MHC-restricted cytotoxic T lymphocytes (CTL). Characterization of multiple CTL-defined antigenic determinants and the presence of corresponding precursor CTL open perspectives for the development of antigen-based vaccines. In the present study, we determined the CTL reactivity against melanoma-associated peptides derived from Melan A/MART-1, tyrosinase and gp100/Pmel17 in 10 HLA-A2+ melanoma patients and 10 healthy individuals. Then, we examined the immunological effects and toxicity of intradermal inoculation of synthetic melanoma-associated peptides. Six patients with advanced melanoma received weekly intradermal injections of 6 melanoma-associated peptides and the influenza matrix peptide as a control for 4 consecutive weeks. DTH reactions were observed in 5/6 patients at the injections sites of the tyrosinase signal peptide and of the influenza matrix peptide. No toxic side effects were observed. Changes in CTL reactivity after peptide vaccination were assessed by an MLPC assay for each peptide. Generation of peptide-specific CTL was documented against Melan A/MART-1-derived peptide epitopes, the tyrosinase signal peptide and the influenza matrix peptide after vaccination. A decreasing CTL response against the internal tyrosinase peptide was documented in 1 patient through the course of vaccination and a decrease in DTH reactions. No major tumor regressions were observed. Two patients with rapidly progressive disease before vaccination have shown disease stabilization since vaccinations started. In conclusion, our results demonstrate that peptide alone injected intradermally may generate antigen-specific DTH reactions and an increase of antigen-specific CTL reactivity.
Pseudomorphically Grown Ultraviolet C Photopumped Lasers on Bulk AlN Substrates (2011)

Optically pumped ultraviolet lasers were fabricated on low-defect-density bulk (0001) AlN substrates. AlxGa1-xN/AlyGa1-yN heterostructures were grown by metal–organic vapor phase epitaxy near atmospheric pressure. Time-resolved photoluminescence studies of the multiple quantum well emission show long decay times of 900 ps at room temperature and confirm the high structural quality of the epitaxial layers. Laser resonators with a length of about 1 mm were formed by cleaving the AlN crystal to obtain m-plane mirror facets. Lasing is demonstrated at a wavelength of 267 nm with a threshold power density as low as 126 kW/cm2 at room temperature. The laser emission was transverse electrically polarized.
Macrophage Inhibitory Cytokine-1 (MIC-1/GDF15) Slows Cancer Development but Increases Metastases in TRAMP Prostate Cancer Prone Mice (2012)

Macrophage inhibitory cytokine-1 (MIC-1/GDF15), a divergent member of the TGF-β superfamily, is over-expressed by many common cancers including those of the prostate (PCa) and its expression is linked to cancer outcome. We have evaluated the effect of MIC-1/GDF15 overexpression on PCa development and spread in the TRAMP transgenic model of spontaneous prostate cancer. TRAMP mice were crossed with MIC-1/GDF15 overexpressing mice (MIC-1(fms)) to produce syngeneic TRAMP(fmsmic-1) mice. Survival rate, prostate tumor size, histopathological grades and extent of distant organ metastases were compared. Metastasis of TC1-T5, an androgen independent TRAMP cell line that lacks MIC-1/GDF15 expression, was compared by injecting intravenously into MIC-1(fms) and syngeneic C57BL/6 mice. Whilst TRAMP(fmsmic-1) survived on average 7.4 weeks longer, had significantly smaller genitourinary (GU) tumors and lower PCa histopathological grades than TRAMP mice, more of these mice developed distant organ metastases. Additionally, a higher number of TC1-T5 lung tumor colonies were observed in MIC-1(fms) mice than syngeneic WT C57BL/6 mice. Our studies strongly suggest that MIC-1/GDF15 has complex actions on tumor behavior: it limits local tumor growth but may with advancing disease, promote metastases. As MIC-1/GDF15 is induced by all cancer treatments and metastasis is the major cause of cancer treatment failure and cancer deaths, these results, if applicable to humans, may have a direct impact on patient care.
Structural Basis for Accommodation of Nonsteroidal Ligands in the Androgen Receptor (2005)

The mechanism by which the androgen receptor (AR) distinguishes between agonist and antagonist ligands is poorly understood. AR antagonists are currently used to treat prostate cancer. However, mutations commonly develop in patients that convert these compounds to agonists. Recently, our laboratory discovered selective androgen receptor modulators, which structurally resemble the nonsteroidal AR antagonists bicalutamide and hydroxyflutamide but act as agonists for the androgen receptor in a tissue-selective manner. To investigate why subtle structural changes to both the ligand and the receptor (i.e. mutations) result in drastic changes in activity, we studied structure-activity relationships for nonsteroidal AR ligands through crystallography and site-directed mutagenesis, comparing bound conformations of R-bicalutamide, hydroxyflutamide, and two previously reported nonsteroidal androgens, S-1 and R-3. These studies provide the first crystallographic evidence of the mechanism by which nonsteroidal ligands interact with the wild type AR. We have shown that changes induced to the positions of Trp-741, Thr-877, and Met-895 allow for ligand accommodation within the AR binding pocket and that a water-mediated hydrogen bond to the backbone oxygen of Leu-873 and the ketone of hydroxyflutamide is present when bound to the T877A AR variant. Additionally, we demonstrated that R-bicalutamide stimulates transcriptional activation in AR harboring the M895T point mutation. As a whole, these studies provide critical new insight for receptor-based drug design of nonsteroidal AR agonists and antagonists.
A Common Palette Creation Algorithm for Multiple Images with Transparency Information (2009)

In this paper, we present a novel common palette creation algorithm for multiple images with transparency information. The proposed algorithm supports creation of a common palette for multiple images, transparent alpha images and flexibility to the user to add a color in the palette. This method was extensively tested for natural and synthetic images and the results are reported here. The experimental results show that the proposed method produces excellent results and outperforms existing state-of-the-art color reduction methods.
An improved immunocytochemical procedure for high‐sensitivity detection of incorporated bromodeoxyuridine (1987)

This report describes an improved immunochemical procedure to stain cells in suspension for incorporated bromodeoxyuridine (BrdUrd) and total DNA content. The procedure consists of five steps: chromatin proteins are extracted by treating with 0.1 M HCl and 0.7% Triton X-100 to facilitate DNA denaturation and to minimize nonspecific staining; cellular DNA is denatured by heating to 100 degrees C in distilled water; BrdUrd in single-stranded DNA (ssDNA) is stained using an immunochemical procedure; autofluorescence is reduced using sodium borohydride (NaBH4); and DNA is stained with the fluorescent dye propidium iodide. With this procedure, the BrdUrd incorporated by CHO cells during periods as short as a few seconds can be detected using flow cytometry. In addition, the stoichiometry of the immunofluorescent staining procedure is high.
The protooncogeneMYCcan break B cell tolerance (2005)

The protooncogene MYC has been implicated in both the proliferation and programmed cell death of lymphoid cells, and in the genesis of lymphoid tumors. Here, we report that overexpression of MYC, as found in many lymphomas, can break immune tolerance. Mice that would otherwise be tolerant to a transgenic autoantigen mounted an immune response to the antigen if MYC was vigorously expressed in the B cell lineage. The responsive B cells converted to an activated phenotype and produced copious amounts of autoantibody that engendered immune complex disease of the kidney. MYC was required to both establish and maintain the breach of tolerance. These effects may be due to the ability of MYC to serve as a surrogate for cytokines. We found that the gene could mimic the effects of cytokines on both B cell proliferation and survival and, indeed, was required for those effects. These findings demonstrate a critical role for MYC in the response of B cells to antigen and expand the potential contributions of MYC to the genesis of lymphomas.
Building blocks for data flow prototypes (1980)

A variety of proposed architectures for data flow computers have been advanced. Evaluation of the practical potential of these proposals is being studied through analysis and simulation, but these techniques cannot be used to study a machine design in sufficient detail to make accurate predictions of performance. As a basis for extrapolating cost/performance of these architectures, and for developing a methodology for data flow program preparation, the construction of prototype machines is needed. In this paper we present our plan for realizing experimental data flow machines as packet communication systems using two types of hardware elements: a microprogrammed processing element with provision for packet transmission and reception; and a router unit used to build networks to support packet communication among processing elements.
Electrostatic-Force-Directed Assembly of Ag Nanocrystals onto Vertically Aligned Carbon Nanotubes (2007)

A facile dry route electrostatic-force-directed assembly (ESFDA) was used to deposit silver nanocrystals onto the external surface of vertically aligned multiwalled carbon nanotubes (MWCNTs). Charged and nonagglomerated aerosol silver nanocrystals were first produced using a mini-arc plasma source. The nanocrystals were then assembled onto the electrically biased MWCNT array through the enhanced electric field near the CNT surface. The electrostatic field plays a crucial role in the assembly process. Gradients of the nanocrystal size and the nanocrystal areal density along the length of the CNT have been observed, and these are likely due to the variation of the electric field near the CNT surface. The ESFDA technique enables the in situ coating of CNT arrays with nanocrystals to create novel hybrid nanomaterials with tailored properties.