gebhart/patrepeval huggingface dataset:
Characterization and Disruption of A Gene in the Maize PathogenCochliobolus carbonumEncoding a Cellulase Lacking a Cellulose Binding Domain and Hinge Region (1995)

A gene, CEL1, in the maize pathogen Cochliobolus carbonum was identified using the cbh1-3 gene of Phanerochaete chrysosporium as a heterologous probe. The predicted product of CEL1, Cel1, is 62% identical and 71% similar to the product of cbh1-3 and 54 to 62% identical to five cellobiohydrolases from other filamentous fungi. The location of the polyadenylation site 221 bp downstream of the stop codon and the location of a single intron of 55 bp were identified by comparison of the sequences of genomic and cDNA copies of CEL1. The transcriptional start site was determined by rapid amplification of cDNA ends (RACE) to be 39 bp upstream of the putative translational start site. CEL1 mRNA abundance is high when C. carbonum is grown on cellulose or maize cell walls but is undetectable when grown on 2% sucrose or cellulose plus sucrose. Cel1 has a predicted signal peptide of 18 amino acids and therefore a mature size of 46.4 kDa. Like the product of cbh1-1 of P. chrysosporium, but unlike most other endoglucanases and cellobiohydrolases (including the predicted product of cbh1-3), Cel1 does not have a putative cellulose binding domain or associated hinge region. The codon bias of CEL1 is stronger than the bias of cbh1-1 and comparable to that of cbh1-3 and that of the C. carbonum genes PGN1 and XYL1, (encoding endopolygalacturonase and endo-xylanase, respectively). A strain of C. carbonum specifically mutated at CEL1 was produced by transformation with a truncated copy of CEL1. Integration and disruption of CEL1 in the mutant was confirmed by DNA and RNA blotting. Pathogenicity of the CEL1 mutant was indistinguishable from the wild-type, indicating that CEL1 by itself is not a critical disease determinant. Culture filtrates of C. carbonum grown on cellulose or maize cell walls had several cellobiohydrolase, endoglucanase, and beta-glucosidase activities that were separable by chromatofocusing, hydrophobic interaction, or ion-exchange high-performance liquid chromatography.(ABSTRACT TRUNCATED AT 250 WORDS)
Pollen–Pistil Interactions Result in Reproductive Isolation between Sorghum bicolor and Divergent Sorghum Species (2005)

Sorghum [ Sorghum bicolor (L.) Moench] breeders have long recognized the importance of exotic germplasm and noncultivated sorghum races as sources of valuable genes for genetic improvement. The genus Sorghum consists of 25 species classified as five sections: Eu‐sorghum , Chaetosorghum , Heterosorghum , Para‐sorghum , and Stiposorghum Species outside the Eu‐sorghum section are sources of important genes for sorghum improvement, including those for insect and disease resistance, but these have not been used because of the failure of these species to cross with sorghum. An understanding of the biological nature of the incompatibility system(s) that prevent hybridization and/or seed development is necessary for the successful hybridization and introgression between sorghum and divergent Sorghum species. The objectives of this study were to determine the reason(s) for reproductive isolation between Sorghum species. The current study utilized 14 alien Sorghum species and established that pollen–pistil incompatibilities are the primary reasons that hybrids with sorghum are not obtained. The alien pollen tubes showed major inhibition of growth in sorghum pistils and seldom grew beyond the stigma. Pollen tubes of only three species grew into the ovary of sorghum. Fertilization and subsequent embryo development were not common. Seeds with developing embryos aborted before maturation, apparently because of breakdown of the endosperm.
The World Economy (2000)

Global economic activity has continued to gain momentum in recent months and a cyclical upturn is now clearly underway. The rate of growth of world GDP is projected to rise to just under 4¼ per cent this year, from an estimated outturn of 3.4 per cent last year. Growth is expected to accelerate in all the major regional markets for the first time since 1994. The improving economic prospects are already apparent in the trade statistics for the latter part of last year. World trade growth, measured in terms of merchandise trade volumes, is expected to rise by 9 per cent this year from 5½ per cent in 1999.
The development of equivalent system technique for deriving an energy function reflecting transfer conductances (1999)

This paper shows that a well-defined energy function can be developed to reflect the transfer conductances for multi-machine power systems under an assumption that all transmission lines have uniform R/X ratios. The energy function is derived by introducing a pure reactive equivalent system for the given system. In this study, a static energy function reflecting transfer conductances is also derived as well as the transient energy function. The proposed static energy function is applied to voltage stability analysis and tested for various sample systems. The test results show that the accuracy of voltage stability analysis can be considerably improved by reflecting transfer conductances into the energy function.
IL-12 Rapidly Alters the Functional Profile of Tumor-Associated and Tumor-Infiltrating Macrophages In Vitro and In Vivo (2007)

Tumor-associated macrophages (TAMs) play a major role in promoting tumor growth and metastasis and in suppressing the antitumor immune response. Despite the immunosuppressive environment created by the tumor and enforced by tumor-associated macrophages, treatment of tumor-bearing mice with IL-12 induces tumor regression associated with appearance of activated NK cells and activated tumor-specific CTLs. We therefore tested the hypothesis that IL-12 treatment could alter the function of these tumor-associated suppressor macrophages. Analysis of tumor-infiltrating macrophages and distal TAMs revealed that IL-12, both in vivo and in vitro, induced a rapid (<90 min) reduction of tumor supportive macrophage activities (IL-10, MCP-1, migration inhibitory factor, and TGFbeta production) and a concomitant increase in proinflammatory and proimmunogenic activities (TNF-alpha, IL-15, and IL-18 production). Similar shifts in functional phenotype were induced by IL-12 in tumor-infiltrating macrophages isolated from the primary tumor mass and in TAMs isolated from lung containing metastases, spleen, and peritoneal cavity. Therefore, although TAMs display a strongly polarized immunosuppressive functional profile, they retain the ability to change their functional profile to proinflammatory activities given the appropriate stimulus. The ability of IL-12 to initiate this functional conversion may contribute to early amplification of the subsequent destructive antitumor immune response.
Universal DNA Tag Systems: A Combinatorial Design Scheme (2000)

Custom-designed DNA arrays offer the possibility of simultaneously monitoring thousands of hybridization reactions. These arrays show great potential for many medical and scientific applications, such as polymorphism analysis and genotyping. Relatively high costs are associated with the need to specifically design and synthesize problem-specific arrays. Recently, an alternative approach was suggested that utilizes fixed, universal arrays. This approach presents an interesting design problem-the arrays should contain as many probes as possible, while minimizing experimental errors caused by cross-hybridization. We use a simple thermodynamic model to cast this design problem in a formal mathematical framework. Employing new combinatorial ideas, we derive an efficient construction for the design problem and prove that our construction is near-optimal.
Germination of Bacillus anthracis spores within alveolar macrophages (1999)

The fatal character of the infection caused by inhalation of Bacillus anthracis spores results from a complex pathogenic cycle involving the synthesis of toxins by the bacterium. We have shown using immunofluorescent staining, confocal scanning laser microscopy and image cytometry analysis that the alveolar macrophage was the primary site of B. anthracis germination in a murine inhalation infection model. Bacillus anthracis germinated inside murine macrophage-like RAW264.7 cells and murine alveolar macrophages. Germination occurred in vesicles derived from the phagosomal compartment. We have also demonstrated that the toxin genes and their trans-activator, AtxA, were expressed within the macrophages after germination.
CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences (2015)

Genome engineering has been revolutionized by the discovery of clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated system genes (Cas) in bacteria. The type IIB Streptococcus pyogenes CRISPR/Cas9 system functions in many species and additional types of CRISPR/Cas systems are under development. In the type II system, expression of CRISPR single guide RNA (sgRNA) targeting a defined sequence and Cas9 generates a sequence-specific nuclease inducing small deletions or insertions. Moreover, knock-in of large DNA inserts has been shown at the sites targeted by sgRNAs and Cas9. Several tools are available for designing sgRNAs that target unique locations in the genome. However, the ability to find sgRNA targets common to several similar sequences or, by contrast, unique to each of these sequences, would also be advantageous. To provide such a tool for several types of CRISPR/Cas system and many species, we developed the CRISPR MultiTargeter software. Similar DNA sequences in question are duplicated genes and sets of exons of different transcripts of a gene. Thus, we implemented a basic sgRNA target search of input sequences for single-sgRNA and two-sgRNA/Cas9 nickase targeting, as well as common and unique sgRNA target searches in 1) a set of input sequences; 2) a set of similar genes or transcripts; or 3) transcripts a single gene. We demonstrate potential uses of the program by identifying unique isoform-specific sgRNA sites in 71% of zebrafish alternative transcripts and common sgRNA target sites in approximately 40% of zebrafish duplicated gene pairs. The design of unique targets in alternative exons is helpful because it will facilitate functional genomic studies of transcript isoforms. Similarly, its application to duplicated genes may simplify multi-gene mutational targeting experiments. Overall, this program provides a unique interface that will enhance use of CRISPR/Cas technology.
Sulphide Impairment of Substrate Oxidation in Rat Colonocytes: A Biochemical Basis for Ulcerative Colitis? (1993)

1. Isolated colonic epithelial cells of the rat were incubated for 40 min with [6-14C]glucose and n-[1-14C]butyrate in the presence of 0.1-2.0 mmol/l NaHS, a concentration range found in the human colon. Metabolic products, 14CO2, acetoacetate, beta-hydroxybutyrate and lactate, were measured and injury to cells was judged by diminished production of metabolites. 2. Oxidation of n-butyrate to CO2 and acetoacetate was reduced at 0.1 and 0.5 mmol/l NaHS, whereas glucose oxidation remained unimpaired. At 1.0-2.0 mmol/l NaHS, n-butyrate and glucose oxidation were dose-dependently reduced at the same rate. 3. To bypass short-chain acyl-CoA dehydrogenase activity necessary for butyrate oxidation, ketogenesis from crotonate was measured in the presence of 1.0 mmol/l NaHS. Suppression by sulphide of ketogenesis from crotonate (-10.5 +/- 6.1%) compared with control conditions was not significant, whereas suppression of ketogenesis from n-butyrate (-36.00 +/- 5.14%) was significant (P = < 0.01). Inhibition of FAD-linked oxidation was more affected by NaHS than was NAD-linked oxidation. 4. L-Methionine (5.0 mmol/l) significantly redressed the impaired beta-oxidation induced by NaHS. Methionine equally improved CO2 and ketone body production, suggesting a global reversal of the action of sulphide. 5. Sulphide-induced oxidative changes closely mirror the impairment of beta-oxidation observed in colonocytes of patients with ulcerative colitis. A hypothesis for the disease process of ulcerative colitis is that sulphides may form persulphides with butyryl-CoA, which would inhibit cellular short-chain acyl-CoA deHydrogenase and beta-oxidation to induce an energy-deficiency state in colonocytes and mucosal inflammation.
Structure−Activity Relationships of a Novel Class of Endothelin-A Receptor Antagonists and Discovery of Potent and Selective Receptor Antagonist, 2-(Benzo[1,3]dioxol-5-yl)-6-isopropyloxy-4-(4-methoxyphenyl)-2H-chromene-3- carboxylic Acid (S-1255). 1. Study on Structure−Activity Relationships and Basic Structure Crucial for ETA Antagonism (2002)

A novel series of endothelin-A (ET(A)) selective receptor antagonists having a 2H-chromene skeleton are described. A lead compound, 2-(benzo[1,3]dioxol-5-yl)-2H-chromene-3-carboxylic acid (3), was found by modifications of our own angiotensin II antagonist. A structure-activity relationship (SAR) study of 3 reveals that the structural requirements essential for potent and selective ET(A) receptor binding affinity are the m,p-methylenedioxyphenyl, carboxyl, and isopropoxy groups at the 2-, 3-, and 6-positions, respectively, on the (R)-2H-chromene skeleton. The substituent at the 4-position is also important for improving the activity, and various hydrophobic functional groups of 6-9 A such as liner, branched, and cyclic aliphatic groups, unsubstituted and substituted aryl groups, and even halogen atoms were acceptable. These results suggest that (R)-2-(benzo[1,3]dioxol-5-yl)-6-isopropoxy-2H-chromene-3-carboxylic acid, formula 108, is the crucial basic structure to be recognized by the ET(A) receptor. The most potent compound is (R)-48 (S-1255), which binds to the ET(A) receptor with an IC(50) value of 0.19 nM and is 630-fold selective for the ET(A) receptor than for the ET(B) receptor. This compound has 55% oral bioavailability in rats. On the basis of the SAR, the roles of each substituent in the receptor binding are discussed.
Isolation of the human PC6 gene encoding the putative host protease for HIV-1 gp160 processing in CD4+ T lymphocytes. (1996)

Production of infectious HIV-1 virions is dependent on the processing of envelope glycoprotein gp160 by a host cell protease. The protease in human CD4+ T lymphocytes has not been unequivocally identified, yet members of the family of mammalian subtilisin-like protein convertases (SPCs), which are soluble or membrane-bound proteases of the secretory pathway, best fulfill the criteria. These proteases are required for proprotein maturation and cleave at paired basic amino acid motifs in numerous cellular and viral glycoprotein precursors, both in vivo and in vitro. To identify the gp160 processing protease, we have used reverse transcription-PCR and Northern blot analyses to ascertain the spectrum of SPC proteases in human CD4+ T cells. We have cloned novel members of the SPC family, known as the human PC6 genes. Two isoforms of the hPC6 protease are expressed in human T cells, hPC6A and the larger hPC6B. The patterns of SPC gene expression in human T cells has been compared with the furin-defective LoVo cell line, both of which are competent in the production of infectious HIV virions. This comparison led to the conclusion that the hPC6 gene products are the most likely candidates for the host cell protease responsible for HIV-1 gp160 processing in human CD4+ T cells.
BORIS/CTCFL expression is insufficient for cancer-germline antigen gene expression and DNA hypomethylation in ovarian cell lines. (2010)

Expression of the cancer-germline (CG) (or cancer-testis) antigen gene BORIS/CTCFL has been proposed to mediate activation of CG antigen genes in cancer. Consistent with this idea, we have observed that BORIS is frequently expressed in ovarian cancer, often in conjunction with other CG genes. Here we assessed the role of BORIS in CG antigen gene regulation and DNA methylation using normal and cancerous ovarian cell lines, and the CG genes MAGE-A1, NY-ESO-1, and XAGE-1 as models. Adenoviral vectored BORIS was expressed at robust levels and exhibited predominant nuclear localization in ovarian cells. However, BORIS expression in immortalized ovarian surface epithelial cells or ovarian cancer cell lines did not induce CG antigen gene expression or lead to CG antigen promoter DNA hypomethylation. BORIS overexpression also did not alter global DNA methylation, as assessed by genomic 5-methyl-deoxycytidine levels and LINE-1 methylation. We used decitabine to further assess the role of BORIS in CG gene activation and found that decitabine treatment induced BORIS and other CG genes with similar kinetics, suggesting that BORIS induction does not account for the induction of other CG genes by decitabine in ovarian cancer cells. In agreement, siRNA knockdown of BORIS did not block decitabine-mediated induction of CG genes or DNA hypomethylation in ovarian cancer cells treated with this agent. We conclude that BORIS is insufficient for CG antigen gene expression and DNA hypomethylation in ovarian cell lines, and that additional factors are likely required for CG antigen expression in ovarian cancer.
Shaping Inputs to Reduce Vibration in Flexible Space Structures (1992)

A theoretical background of impulse shaping is presented along with some insight into the methods of calculating multiple mode sequences. The Middeck Active Control Experiment (MACE), an MIT/NASA space shuttle experiment, is then described as the testbed for the experiments. A nonlinear simulation is used to verify the effectiveness of these shapers on a model of MACE. Finally, hardware, experimental results are presented and analyzed. Some conclusions were derived from the results of testing. First, it was found that the shaper was effective in canceling the slowest frequency of the structure, but was less successful in the higher modes. Second, large angle movements decreased the effective vibration cancellation. Third, although methods exist which can increase the robustness of an impulse shaper, none were found to aid in canceling the effects of nonlinearities caused by large angle moves. Fourth, the bandwidth of the controller was found to be closely associated with the effectiveness of the shaper. Shaping, Mace, Vibration, Discos Modes,
Detection and serotyping of herpes simplex virus in MRC-5 cells by use of centrifugation and monoclonal antibodies 16 h postinoculation (1985)

Monoclonal antibodies (Syva Co., Palo Alto, Calif.) were used for the detection and serotyping of herpes simplex virus (HSV) isolates by immunofluorescence 16 h after inoculation of MRC-5 monolayers in 3.7-ml shell vials and after low-speed centrifugation. A total of 119 specimens were inoculated into conventional tube cell cultures and shell vials. Of 98 specimens inoculated on the same day of receipt in the laboratory (fresh specimens), all 23 (23.5%) HSV-positive specimens were identified by serotype in 16 h in shell vials by immunofluorescence, whereas only 8 of 23 HSV-positive specimens (34.8%) produced cytopathic effects in conventional tube cell cultures in this time period. Similarly, of 21 original specimen extracts previously determined to be culture positive for HSV (stored specimens), all were detected and serotyped by the immunofluorescence test with monoclonal antibodies 16 h postinoculation compared with the recognition of only 8 of these isolates (38.1%) by cytopathic effect that soon. This technique of centrifugal inoculation of HSV in shell vials containing MRC-5 cells permitted detection of this virus in all positive specimens with serotype determination within 16 h postinoculation.
Topical polyphenolic antioxidants reduce the adverse effects of intense pulsed light therapy (2009)

In this study, the concurrent pneumatic topical application of polyphenolic antioxidants reduced lipid peroxidation and skin dehydration in IPL-treated skin. Polyphenolic antioxidants may confer a protective effect on facial skin and enhance the effects of IPL therapy.
Tumor cell instability, diversification, and progression to the metastatic phenotype: from oncogene to oncofetal expression. (1987)

It is proposed that tumor cell instability and the expression of cellular diversification mechanisms ensure that malignant neoplasms contain heterogeneous, phenotypically diverse tumor cell subpopulations. In such potentially unstable cellular mixtures of tumor cell phenotypes, some malignant cells may ultimately evolve with the most favorable properties for their progression to metastatic cells. Rates of cellular phenotypic instability and phenotypic diversification as well as their underlying causes appear to vary greatly among different tumor cells, and they are probably modulated by further genetic and chromosome changes and more frequently by intra- and extracellular epigenetic events that also differ, depending on the nature of the tumor cells and their cellular and microenvironmental interactions. Diversified malignant cells are characterized by quantitative and perhaps a few qualitative differences in gene expression, which may explain their abilities to undergo rapid changes in phenotypic properties. As tumor diversification and selection proceed uniquely in vivo, highly malignant cell subpopulations may eventually become dominant and gradually and independently lose their cellular and microenvironmental responsiveness. Tumor cell diversification mechanisms may be similar or identical to normal developmentally regulated diversification mechanisms that are used during embryonic and postembryonic cell diversification and development.
Glutaredoxins Grx3 and Grx4 regulate nuclear localisation of Aft1 and the oxidative stress response inSaccharomyces cerevisiae (2006)

Grx3 and Grx4, two monothiol glutaredoxins of Saccharomyces cerevisiae, regulate Aft1 nuclear localisation. We provide evidence of a negative regulation of Aft1 activity by Grx3 and Grx4. The Grx domain of both proteins played an important role in Aft1 translocation to the cytoplasm. This function was not, however, dependent on the availability of iron. Here we demonstrate that Grx3, Grx4 and Aft1 interact each other both in vivo and in vitro, which suggests the existence of a functional protein complex. Interestingly, each interaction occurred independently on the third member of the complex. The absence of both Grx3 and Grx4 induced a clear enrichment of G1 cells in asynchronous cultures, a slow growth phenotype, the accumulation of intracellular iron and a constitutive activation of the genes regulated by Aft1. The grx3grx4 double mutant was highly sensitive to the oxidising agents hydrogen peroxide and t-butylhydroperoxide but not to diamide. The phenotypes of the double mutant grx3grx4 characterised in this study were mainly mediated by the Aft1 function, suggesting that grx3grx4 could be a suitable cellular model for studying endogenous oxidative stress induced by deregulation of the iron homeostasis. However, our results also suggest that Grx3 and Grx4 might play additional roles in the oxidative stress response through proteins other than Aft1.