gebhart/patrepeval huggingface dataset:
Characterization of Multiple Regions Involved in Replication and Mobilization of Plasmid pNZ4000 Coding for Exopolysaccharide Production in Lactococcus lactis (1998)

We characterized the regions involved in replication and mobilization of the 40-kb plasmid pNZ4000, encoding exopolysaccharide (EPS) production in Lactococcus lactis NIZO B40. The plasmid contains four highly conserved replication regions with homologous rep genes (repB1, repB2, repB3, and repB4) that belong to the lactococcal theta replicon family. Subcloning of each replicon individually showed that all are functional and compatible in L. lactis. Plasmid pNZ4000 and genetically labeled derivatives could be transferred to different L. lactis strains by conjugation, and pNZ4000 was shown to be a mobilization plasmid. Two regions involved in mobilization were identified near two of the replicons; both included an oriT sequence rich in inverted repeats. Conjugative mobilization of the nonmobilizable plasmid pNZ124 was promoted by either one of these oriT sequences, demonstrating their functionality. One oriT sequence was followed by a mobA gene, coding for a trans-acting protein, which increased the frequency of conjugative transfer 100-fold. The predicted MobA protein and the oriT sequences show protein and nucleotide similarity, respectively, with the relaxase and with the inverted repeat and nic site of the oriT from the Escherichia coli plasmid R64. The presence on pNZ4000 of four functional replicons, two oriT sequences, and several insertion sequence-like elements strongly suggests that this EPS plasmid is a naturally occurring cointegrate.
Machine Scoring of Student Essays: Truth and Consequences (2006)

The current trend toward machine-scoring of student work, Ericsson and Haswell argue, has created an emerging issue with implications for higher education across the disciplines, but with particular importance for those in English departments and in administration. The academic community has been silent on the issue—some would say excluded from it—while the commercial entities who develop essay-scoring software have been very active. Machine Scoring of Student Essays is the first volume to seriously consider the educational mechanisms and consequences of this trend, and it offers important discussions from some of the leading scholars in writing assessment.
Biochemical Identification of a Mutated Human Melanoma Antigen Recognized by CD4+ T Cells (1999)

CD4(+) T cells play a critical role in generating and maintaining immune responses against pathogens and alloantigens, and evidence suggests an important role for them in antitumor immunity as well. Although major histocompatibility complex class II-restricted human CD4(+) T cells with specific antitumor reactivities have been described, no standard method exists for cloning the recognized tumor-associated antigen (Ag). In this study, biochemical protein purification methods were used in conjunction with novel mass spectrometry sequencing techniques and molecular cloning to isolate a unique melanoma Ag recognized by a CD4(+) tumor-infiltrating lymphocyte (TIL) line. The HLA-DRbeta1*0101-restricted Ag was determined to be a mutated glycolytic enzyme, triosephosphate isomerase (TPI). A C to T mutation identified by cDNA sequencing caused a Thr to Ile conversion in TPI, which could be detected in a tryptic digest of tumor-derived TPI by mass spectrometry. The Thr to Ile conversion created a neoepitope whose T cell stimulatory activity was enhanced at least 5 logs compared with the wild-type peptide. Analysis of T cell recognition of serially truncated peptides suggested that the mutated amino acid residue was a T cell receptor contact. Defining human tumor Ag recognized by T helper cells may provide important clues to designing more effective immunotherapies for cancer.
Last Findings on Dual Inhibitors of Abl and Src Tyrosine-Kinases (2007)

Chronic myelogenous leukemia (CML) is a myeloproliferative disease characterized by the presence of the Philadelphia chromosome that expresses the constitutively activated tyrosine kinase Bcr-Abl; this enzyme causes hyperproliferation of the stem cells and the consequent pathology of the disease. Targeted inhibitors of Bcr-Abl have antiproliferative effects on the leukemic cells and induce apoptosis, favouring a regression of the CML chronic phase, but in the successive blast crisis phase cancer cells frequently develop resistance to Bcr-Abl inhibitors. Src is a family of non-receptor tyrosine kinases, fundamental for cell development, growth, replication, adhesion, motility and is overexpressed in a wide number of human cancers. Recently it was demonstrated that Src is increased in hematopoietic cells expressing Bcr-Abl and is involved in the oncogenic pathway that causes CML. For this reason and also for the development of resistance to classical Bcr-Abl inhibitors, various dual Src/Abl inhibitors have been recently synthesized and tested. This mini review will be focused on the latest finding on this matter.
Systemic p53 Gene Therapy of Cancer with Immunolipoplexes Targeted by Anti-Transferrin Receptor scFv (2001)

This is the first report using scFv-targeting immunolipoplexes for systemic gene therapy. The TfRscFv has a number of advantages over the transferrin (Tf) molecule itself: (1) scFv has a much smaller size than Tf producing a smaller immunolipoplex giving better penetration into solid tumors; (2) unlike Tf, the scFv is a recombinant protein, not a blood product; (3) large scale production and strict quality control of the recombinant scFv, as well as scFv-immunolipoplex, are feasible. The sensitization of tumors to chemotherapy by this tumor-targeted and efficient p53 gene delivery method could lower the effective dose of the drug, correspondingly lessening the severe side effects, while decreasing the possibility of recurrence. Moreover, this approach is applicable to both primary and recurrent tumors, and more significantly, metastatic disease. The TfRscFv-targeting of cationic immunolipoplexes is a promising method of tumor targeted gene delivery that can be used for systemic gene therapy of cancer with the potential to critically impact the clinical management of cancer.
Manipulation of lignin quality by downregulation of cinnamyl alcohol dehydrogenase (1994)

The composition of lignin in tobacco stems has been altered by genetic engineering. Antisense expression of sequences encoding cinnamyl alcohol dehydrogenase (CAD), the enzyme catalysing the final step in lignin precursor synthesis, leads to the production of a modified lignin in otherwise normal plants. Although Klason and acetyl bromide lignin determinations show little quantitative change in lignin deposition in CAD antisense plants, a number of qualitative changes have been identified. The lignin is altered in both composition and structure and is more susceptible to chemical extraction. Consistent with a block in CAD activity, antisense plants incorporate less cinnamyl alcohol monomers and more cinnamyl aidehyde monomers into lignin than corresponding control plants. Antisense plants with very low levels of CAD activity also show a novel phenotype with the appearance of a red‐brown colour in xylem tissues. A similar phenotype is correlated with altered lignification and improved digestibility in brownmidrib mutants of maize and sorghum. The improved chemical extractability of lignin in CAD antisense plants supports a role for this technology in improving the pulp and paper‐making value of forest trees while the similarity with brown‐midrib mutants suggests a route to more digestible forage crops.
Galectin-9 Controls CD40 Signaling through a Tim-3 Independent Mechanism and Redirects the Cytokine Profile of Pathogenic T Cells in Autoimmunity (2012)

While it has long been understood that CD40 plays a critical role in the etiology of autoimmunity, glycobiology is emerging as an important contributor. CD40 signaling is also gaining further interest in transplantation and cancer therapies. Work on CD40 signaling has focused on signaling outcomes and blocking of its ligand, CD154, while little is known about the actual receptor itself and its control. We demonstrated that CD40 is in fact several receptors occurring as constellations of differentially glycosylated forms of the protein that can sometimes form hybrid receptors with other proteins. An enticing area of autoimmunity is differential glycosylation of immune molecules leading to altered signaling. Galectins interact with carbohydrates on proteins to effect such signaling alterations. Studying autoimmune prone NOD and non-autoimmune BALB/c mice, here we reveal that in-vivo CD40 signals alter the glycosylation status of non-autoimmune derived CD4 T cells to resemble that of autoimmune derived CD4 T cells. Galectin-9 interacts with CD40 and, at higher concentrations, prevents CD40 induced proliferative responses of CD4(lo)CD40(+) effector T cells and induces cell death through a Tim-3 independent mechanism. Interestingly, galectin-9, at lower concentrations, alters the surface expression of CD3, CD4, and TCR, regulating access to those molecules and thereby redirects the inflammatory cytokine phenotype and CD3 induced proliferation of autoimmune CD4(lo)CD40(+) T cells. Understanding the dynamics of the CD40 receptor(s) and the impact of glycosylation status in immunity will gain insight into how to maintain useful CD40 signals while shutting down detrimental ones.
Dicistronic Tagging of Genes Active in Embryonic Stem Cells of Mice (1997)

A gene-trap vector, pWH14, has been developed to tag genes expressed in embryonic stem (ES) cells of the mouse. The approach relies on the ability of the endogenous promoter to drive promoterless neo-IRES-lacZ construct producing a dicistronic mRNA consisting of the neomycin-resistance (neo) gene and the beta-galactosidase gene sequence. The neo gene produces a chimeric protein with the truncated product of the tagged gene and serves as a selectable marker for an insertion into an expressed gene. The internal ribosome entry site (IRES) sequence from murine encephalomyocarditis virus allows the translation of the second cistron, lacZ, to produce beta-galactosidase that can be used as a reporter for the expression of the tagged gene. The pWH14 vector was introduced into ES cells by electroporation, and the cells were selected for G418-resistance. About 50% of the G418-resistant colonies were stained positive for the beta-galactosidase activity. Southern analysis showed that each clone had one or more vector sequences integrated. Northern blot analysis of the clones positive for beta-galactosidase indicated that the fused RNAs containing the neo and the beta-gal genes were derived from the endogenous promoters of the tagged genes. Seven clones were chosen and injected into blastocysts, and chimeras were obtained. Two of the gene-trap insertions (wh14.1 and wh14.3) were transmitted through germ-line. In these two lines, the pattern of lacZ expression was restricted to early stages of embryos. This gene-trap vector may provide a means for tagging and studying the active genes in vivo in early embryogenesis.
Evaluation of monoclonal antibodies for the development of breast cancer immunotoxins. (1985)

Eighty-five antibodies recognizing breast cancer-selective antigens were conjugated to ricin toxin A-chain using a disulfide linkage. The cytotoxicities of the resulting immunotoxins were determined on breast cancer cells and normal human fibroblasts. Twenty-four antibodies formed immunotoxins that were toxic to at least one breast cancer cell line at concentrations of 10 nM or less but were nontoxic to human fibroblast lines used as negative controls. Some of the breast tumor-selective immunotoxins were as toxic as a conjugate between monoclonal anti-transferrin receptor and ricin toxin A-chain (50% inhibition of cellular protein synthesis at approximately 0.1 nM). Another set of four immunotoxins were indiscriminately toxic to human breast tumor cell lines, two human fibroblast cell lines, and a human lymphoblastoid line. Several of the antibodies the toxin conjugates of which specifically killed breast cancer cell lines may be useful in cancer therapy, since they show a wide range of binding to individual breast tumors and cell lines and a limited range of binding to normal tissue types.
Adaptive block matching motion estimation algorithmfor video coding (1995)

A simple adaptive block matching algorithm is proposed for motion estimation. The proposed method exploits the motion correlation of spatially neighbouring blocks to determine the search origin and adjusts the search range according to different motion content of the block. Simulation results show that the proposed algorithm achieves nearly the same MSE performance as the full-search method but requires ~80% less computation.
Neomycin inhibits angiogenin-induced angiogenesis (1998)

A class of angiogenesis inhibitor has emerged from our mechanistic study of the action of angiogenin, a potent angiogenic factor. Neomycin, an aminoglycoside antibiotic, inhibits nuclear translocation of human angiogenin in human endothelial cells, an essential step for angiogenin-induced angiogenesis. The phospholipase C-inhibiting activity of neomycin appears to be involved, because U-73122, another phospholipase C inhibitor, has a similar effect. In contrast, genistein, oxophenylarsine, and staurosporine, inhibitors of tyrosine kinase, phosphotyrosine phosphatase, and protein kinase C, respectively, do not inhibit nuclear translocation of angiogenin. Neomycin inhibits angiogenin-induced proliferation of human endothelial cells in a dose-dependent manner. At 50 microM, neomycin abolishes angiogenin-induced proliferation but does not affect the basal level of proliferation and cell viability. Other aminoglycoside antibiotics, including gentamicin, streptomycin, kanamycin, amikacin, and paromomycin, have no effect on angiogenin-induced cell proliferation. Most importantly, neomycin completely inhibits angiogenin-induced angiogenesis in the chicken chorioallantoic membrane at a dose as low as 20 ng per egg. These results suggest that neomycin and its analogs are a class of agents that may be developed for anti-angiogenin therapy.
MicroRNA regulation of homeostatic synaptic plasticity (2011)

Homeostatic mechanisms are required to control formation and maintenance of synaptic connections to maintain the general level of neural impulse activity within normal limits. How genes controlling these processes are co-coordinately regulated during homeostatic synaptic plasticity is unknown. MicroRNAs (miRNAs) exert regulatory control over mRNA stability and translation and may contribute to local and activity-dependent posttranscriptional control of synapse-associated mRNAs. However, identifying miRNAs that function through posttranscriptional gene silencing at synapses has remained elusive. Using a bioinformatics screen to identify sequence motifs enriched in the 3'UTR of rapidly destabilized mRNAs, we identified a developmentally and activity-regulated miRNA (miR-485) that controls dendritic spine number and synapse formation in an activity-dependent homeostatic manner. We find that many plasticity-associated genes contain predicted miR-485 binding sites and further identify the presynaptic protein SV2A as a target of miR-485. miR-485 negatively regulated dendritic spine density, postsynaptic density 95 (PSD-95) clustering, and surface expression of GluR2. Furthermore, miR-485 overexpression reduced spontaneous synaptic responses and transmitter release, as measured by miniature excitatory postsynaptic current (EPSC) analysis and FM 1-43 staining. SV2A knockdown mimicked the effects of miR-485, and these effects were reversed by SV2A overexpression. Moreover, 5 d of increased synaptic activity induced homeostatic changes in synaptic specializations that were blocked by a miR-485 inhibitor. Our findings reveal a role for this previously uncharacterized miRNA and the presynaptic protein SV2A in homeostatic plasticity and nervous system development, with possible implications in neurological disorders (e.g., Huntington and Alzheimer's disease), where miR-485 has been found to be dysregulated.
Calibration of Coulter Counters for Particles ∼1 μ in Diameter (1966)

A linear relationship between particle volume and instrument response is confirmed for particles between 0.75 and 2.5 μ3, but this relationship may not hold for smaller particles. The implicit assumption of negligible surface conductance in derivations of this relationship is found acceptable for polystyrene spheres about 1 μ in diameter. A potential source of error in calibration is identified and allowed for. A relationship is developed between observed count and true count which allows coincident passage correction to be based on all available experimental points. The critical volume is found experimentally to be a function of particle volume.
Are cannabinoids an effective and safe treatment option in the management of pain? A qualitative systematic review (2001)

Cannabinoids are no more effective than codeine in controlling pain and have depressant effects on the central nervous system that limit their use. Their widespread introduction into clinical practice for pain management is therefore undesirable. In acute postoperative pain they should not be used. Before cannabinoids can be considered for treating spasticity and neuropathic pain, further valid randomised controlled studies are needed.
Recombinant human extracellular superoxide dismutase reduces concentration of oxygen free radicals in the reperfused rat heart (1990)

In isolated rat heart, rh-EC-SOD C reduces free radical concentrations at least to the same extent as Cu-Zn superoxide dismutase.
Prostaglandin D2-induced bronchoconstriction is mediated only in part by the thromboxane prostanoid receptor (1995)

Prostaglandin D2 (PGD2) is a potent bronchoconstrictor, and is thought to have a role in the pathogenesis of asthma. PGD2 causes vasodilation acting via the prostaglandin (DP) receptor on vascular smooth muscle, and myocontraction acting via the thromboxane (TP) receptor on bronchial smooth muscle. To determine the relative contribution of these mechanisms we have studied the degree to which a potent TP receptor antagonist inhibits PGD2-induced bronchoconstriction. Twelve atopic asthmatic subjects underwent baseline PGD2 bronchial challenges to determine the cumulative concentration of PGD2 required to reduce forced expiratory volume in one second (FEV1) by 20%. At four subsequent randomized visits, subjects received this concentration of PGD2 90 min after dosing with placebo or 20, 50 or 100 mg of BAY u 3405, a potent competitive TP receptor antagonist. Serum was taken for drug assay at 90 min. After each dose of PGD2, FEV1 was measured for 30 min, and the area under the percentage fall in the FEV1/time curve (AUC) was calculated. The mean +/- SEM AUC for placebo was 414 +/- 68, and for the 20, 50 and 100 mg doses of BAY u 3405 was 169 +/- 33, 173 +/- 59 and 135 +/- 63, respectively. There were no significant differences between the AUCs for any of the drug doses, whilst all three doses were significantly different from placebo. The plateau response achieved with increasing doses of the antagonist suggests complete blockade of the TP receptor. These data demonstrate that thromboxane receptor blockade only partially inhibits the airway narrowing response to PGD2, and support the existence of a vascular component to PGD2-induced acute airway narrowing in asthma.
(N-Pyrrolyl)B(C6F5)2-A New Organometallic Lewis Acid for the Generation of Group 4 Metallocene Cation Complexes (2000)

Treatment of the (C6F5)2BF x OEt2 (3) complex with N-pyrrolyl lithium gives bis(pentafluorophenyl)(N-pyrrolyl)borane (2), a strong organometallic Lewis acid, which was characterized by X-ray diffraction (B-N bond length: 1.401(5) A). It exhibits a columnar superstructure in the crystal and contains pi-stacks of pyrrolyl units. Compound 2 readily abstracts alkyl anions from a variety of alkyl Group 4 metallocene-type complexes and leads to the clean formation of the respective metallocene ions or ion pairs. For example, the treatment of Cp3ZrCH3 (9) with 2 transfers a methyl anion to yield the ion pair [Cp3Zr]+[(C4H4N)B(CH3)(C6F5)2]- (12). The X-ray crystal structure analysis of 12 shows a close contact between zirconium and the pyrrolyl-beta-carbon (2.641(2) A). The borane 2 adds to (butadiene)zirconocene (13) to yield the betaine system [Cp2Zr]+[(C4H6)B- (NC4H4)(C6F)2]- (15). Complex 15 contains a distorted eta3-allyl moiety inside the metallacyclic framework and it features an internal Zr+...(pyrrolyl)B- ion pair interaction with a Zr...pyrrolyl-alphacarbon separation of 2.723(3) A (determined by X-ray diffraction). From the dynamic NMR spectra of 15 the bond strength of the internal ion pair interaction was estimated to be deltaGdiss (223 K) approximately = to15 kcalmol(-1). Treatment of dimethylzirconocene (16) with 2 yields the metallocene borate salt [Cp2ZrCH3]+[(C4H4N)B(CH3)(C6F5)2]- (17), which is an active catalyst for the polymerization of ethene.
Theory of the Prism–Film Coupler by Plane-Wave Analysis (1970)

A laser beam can be coupled with high efficiency into a light-guiding thin film by means of a prism–film coupler. Basically this device is a totally reflecting prism, the light-guiding film being separated from the reflecting prism face by a narrow gap of reduced refractive index. This coupling scheme is analyzed in detail by the method of plane-wave expansion. It is shown how the coupling efficiency is determined by the competition between the desired coupling effect and the reverse effect of leakage. A general condition is derived under which the transverse profile of the input beam continues undistorted into the guide. The theory is illustrated for a gaussian beam, which allows a maximum coupling efficiency of 0.80.
Accelerating t-SNE using tree-based algorithms (2014)

The paper investigates the acceleration of t-SNE--an embedding technique that is commonly used for the visualization of high-dimensional data in scatter plots--using two tree-based algorithms. In particular, the paper develops variants of the Barnes-Hut algorithm and of the dual-tree algorithm that approximate the gradient used for learning t-SNE embeddings in O(N log N). Our experiments show that the resulting algorithms substantially accelerate t-SNE, and that they make it possible to learn embeddings of data sets with millions of objects. Somewhat counterintuitively, the Barnes-Hut variant of t-SNE appears to outperform the dual-tree variant.