gebhart/patrepeval huggingface dataset:
Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor (2002)

The ability of Pseudomonas syringae pv. tomato DC3000 to parasitize tomato and Arabidopsis thaliana depends on genes activated by the HrpL alternative sigma factor. To support various functional genomic analyses of DC3000, and specifically, to identify genes involved in pathogenesis, we developed a draft sequence of DC3000 and used an iterative process involving computational and gene expression techniques to identify virulence-implicated genes downstream of HrpL-responsive promoters. Hypersensitive response and pathogenicity (Hrp) promoters are known to control genes encoding the Hrp (type III protein secretion) machinery and a few type III effector proteins in DC3000. This process involved (i) identification of 9 new virulence-implicated genes in the Hrp regulon by miniTn5gus mutagenesis, (ii) development of a hidden Markov model (HMM) trained with known and transposon-identified Hrp promoter sequences, (iii) HMM identification of promoters upstream of 12 additional virulence-implicated genes, and (iv) microarray and RNA blot analyses of the HrpL-dependent expression of a representative subset of these DC3000 genes. We found that the Hrp regulon encodes candidates for 4 additional type III secretion machinery accessory factors, homologs of the effector proteins HopPsyA, AvrPpiB1 (2 copies), AvrPpiC2, AvrPphD (2 copies), AvrPphE, AvrPphF, and AvrXv3, and genes associated with the production or metabolism of virulence factors unrelated to the Hrp type III secretion system, including syringomycin synthetase (SyrE), N(epsilon)-(indole-3-acetyl)-l-lysine synthetase (IaaL), and a subsidiary regulon controlling coronatine production. Additional candidate effector genes, hopPtoA2, hopPtoB2, and an avrRps4 homolog, were preceded by Hrp promoter-like sequences, but these had HMM expectation values of relatively low significance and were not detectably activated by HrpL.
Purification and Characterization of polκ, a DNA Polymerase Encoded by the Human DINB1 Gene (2001)

The Escherichia coli dinB gene encodes DNA polymerase (pol) IV, a protein involved in increasing spontaneous mutations in vivo. The protein-coding region of DINB1, the human ortholog of DNA pol IV, was fused to glutathione S-transferase and expressed in insect cells. The purified fusion protein was shown to be a template-directed DNA polymerase that we propose to designate pol kappa. Human pol kappa lacks detectable 3' --> 5' proofreading exonuclease activity and is not stimulated by recombinant human proliferating cell nuclear antigen in vitro. Between pH 6.5 and 8.5, human pol kappa possesses optimal activity at 37 degrees C over the pH range 6.5-7.5, and is insensitive to inhibition by aphidicolin, dideoxynucleotides, or NaCl up to 50 mm. Either Mg(2+) or Mn(2+) can satisfy a metal cofactor requirement for pol kappa activity, with Mg(2+) being preferred. Human pol kappa is unable to bypass a cisplatin adduct in the template. However, pol kappa shows limited bypass of an 2-acetylaminofluorene lesion and can incorporate dCTP or dTTP across from this lesion, suggesting that the bypass is potentially mutagenic. These results are consistent with a model in which pol kappa acts as a specialized DNA polymerase whose possible role is to facilitate the replication of templates containing abnormal bases, or possessing structurally aberrant replication forks that inhibit normal DNA synthesis.
Detectable Concentrations of Urinary Trypsin Inhibitor in Cerebrospinal Fluid (2000)

Urinary trypsin inhibitor (UTI) is a physiological protease inhibitor produced in the liver and excreted into urine. Urinary trypsin inhibitor-like antigen has been demonstrated on glial cells in the brain. This study measured cerebrospinal UTI levels in various conditions. Seven subjects in each of the following groups were studied: patients undergoing spinal anesthesia for minor surgery, spinal anesthesia for cesarean section, removal of meningioma, or at postoperative day 3 after ruptured intracranial aneurysm clipping. Cerebrospinal fluid was collected from a spinal needle, a needle puncturing the sylvian fissure, or a drainage tube from the optical carotid cistern. Urine was collected from a urinary catheter. Cerebrospinal and urinary UTI concentrations were measured by radioimmunoassay, and the urinary UTI concentration was divided by urinary creatinine concentration to give the systemic UTI concentration. The cerebrospinal UTI concentration in the brain tumor and postoperative state groups was significantly higher than in the spinal anesthesia and cesarean section groups. The systemic UTI concentration in the cesarean section and postoperative state groups was significantly higher than in the spinal anesthesia and brain tumor groups. The present results demonstrate that UTI can be detected in the cerebrospinal fluid, and suggest that cerebrospinal UTI increases in patients with a brain tumor or inflammation and is not affected by systemic UTI.
A 3D integral imaging optical see-through head-mounted display (2014)

An optical see-through head-mounted display (OST-HMD), which enables optical superposition of digital information onto the direct view of the physical world and maintains see-through vision to the real world, is a vital component in an augmented reality (AR) system. A key limitation of the state-of-the-art OST-HMD technology is the well-known accommodation-convergence mismatch problem caused by the fact that the image source in most of the existing AR displays is a 2D flat surface located at a fixed distance from the eye. In this paper, we present an innovative approach to OST-HMD designs by combining the recent advancement of freeform optical technology and microscopic integral imaging (micro-InI) method. A micro-InI unit creates a 3D image source for HMD viewing optics, instead of a typical 2D display surface, by reconstructing a miniature 3D scene from a large number of perspective images of the scene. By taking advantage of the emerging freeform optical technology, our approach will result in compact, lightweight, goggle-style AR display that is potentially less vulnerable to the accommodation-convergence discrepancy problem and visual fatigue. A proof-of-concept prototype system is demonstrated, which offers a goggle-like compact form factor, non-obstructive see-through field of view, and true 3D virtual display.
Macromol. Rapid Commun. 8/2010 (2010)

Back Cover: The picture presents examples for recent progress in the photonic properties of conjugated organometallic polymers derived from trans-bis(para-ethynylbenzene)bis(phosphine)platinum(II). Their intriguing optical and electronic properties render these polymers important for optical power limiting, light-emitting, photovoltaic, and nanotechnological applications. Further details can be found in the article by W.-Y. Wong* and P. D. Harvey on page 671.
Heterogeneity and progesterone-receptor distribution in endometrial adenocarcinoma (1984)

Objective response to progestin therapy occurs in 30% to 35% of patients with recurrent or metastatic endometrial carcinoma. Measurement of progesterone receptor (PR) in these tumors has been suggested as a method for distinguishing between responders and nonresponders. However, studies on steroid receptor measurements in endometrial carcinoma may be subject to complexities of tumor, tissue, and cellular heterogeneity. The authors provide evidence for the existence of various types of heterogeneity and address the problem of cellular heterogeneity by determination of PR concentrations in the glandular and stromal cells of the endometrium. It is concluded that until the problem of tumor and tissue heterogeneity is resolved, PR concentrations in endometrial carcinoma must be interpreted with caution.
Aerosolized nanogram quantities of plasmid DNA mediate highly efficient gene delivery to mouse airway epithelium (2005)

The lung is an important target of gene therapeutic interventions. In contrast to intratracheal instillation, inhalation would be the most practical route of administration in clinical applications. Here we show that aerosolized nanogram quantities of pDNA complexed to PEI (350 ng) yielded transfection levels 15-fold higher than a 140-fold higher dose (50 microg) of the same vector applied directly to the lungs of mice via intratracheal intubation. An important efficacy parameter is the osmolarity of the aerosol and not biophysical properties of the nebulized vector. Vectors formulated and nebulized in hypoosmotic distilled water yielded 57- and 185-fold higher expression levels than those in isotonic 5% glucose or Hepes-buffered saline, respectively. Pretreatment of mice with nebulized indomethacin, which prevents water-induced airway alteration, resulted in lower gene expression, whereas pretreatment with EGTA or polidocanol, which modulate tight-junction activity, had no effect. These results, together with histological analysis of regional lung deposition and gene expression, suggest that a temporary water-induced hypoosmotic shock permeabilizes the epithelium sufficiently to allow vector uptake. The so far observed inefficiency of nonviral gene delivery to the airways may be the result of an inappropriate method of vector administration.
Coordinative peptide recognition. Making intermolecular processes intramolecular (2006)

The design of synthetic receptors that function under physiological conditions is still a challenge. A successful strategy is the use of reversible coordination of Lewis-basic guest molecules to Lewis-acidic metal complexes to provide high and selective binding affinities in water. A screening experiment using potentiometric titration was used to find suitable metal complex � side chain interactions. Imidazol showed affinities towards NTA and IDA complexes of Cu(II) and Ni(II). Zn(II) and Cd(II) cyclen interestingly showed the same affinities. A modular approach of receptor synthesis was established and used to synthesise a large variety of receptor building blocks. One of the NTA receptors was successfully linked with beta-sheet recognition units (MOPAS). Using this receptor a pentapeptide conformation was controlled in DMSO. The combination of a IDA receptor and a fluorescenting crown ether resulted in a histidine selective receptor. The binding event was monitored by emission spectroscopy. The receptor showed excellent selectivity towards histidine among all 20 natural amino acids.
Novel Cytotoxic Diterpenes, Excavatolides A−E, Isolated from the Formosan Gorgonian Briareum excavatum (1998)

The chemistry of Briareum excavatum, a Formosan gorgonian coral, was investigated. This study has led to the isolation of five novel marine natural products, excavatolides A-E (1-5), together with brianolide (6). The structures of the above compounds were established by spectral and chemical methods. The relative configuration of excavatolide B (2) was further confirmed by a single-crystal X-ray structure analysis. Cytotoxicity of these compounds toward various cancer cell lines also is described.
Severity of Basal Cell Hyperplasia Differs in Reflux Versus Eosinophilic Esophagitis (2006)

Basal cell hyperplasia is more severe in children with eosinophilic esophagitis than in those with reflux esophagitis. The finding of basal cell hyperplasia is a powerful clue into the underlying etiology of pediatric esophagitis and, along with epithelial eosinophil count, can be used as information to guide therapy.
A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal (2009)

We performed a genome-wide siRNA screen in mouse embryonic stem (ES) cells to identify genes essential for self-renewal, and found 148 genes whose down-regulation caused differentiation. Many of the identified genes function in gene regulation and/or development, and are highly expressed in ES cells and embryonic tissues. We further identified target genes of two transcription regulators Cnot3 and Trim28. We discovered that Cnot3 and Trim28 co-occupy many putative gene promoters with c-Myc and Zfx, but not other pluripotency-associated transcription factors. They form a unique module in the self-renewal transcription network, separate from the core module formed by Nanog, Oct4, and Sox2. The transcriptional targets of this module are enriched for genes involved in cell cycle, cell death, and cancer. This supports the idea that regulatory networks controlling self-renewal in stem cells may also be active in certain cancers and may represent novel anti-cancer targets. Our screen has implicated over 100 new genes in ES cell self-renewal, and illustrates the power of RNAi and forward genetics for the systematic study of self-renewal.
Cloning and Functional Expression of a Novel Geranylgeranyl Pyrophosphate Synthase Gene from Arabidopsis thaliana in Escherichia coli (1997)

A gene encoding a novel geranylgeranyl pyrophosphate (GGPP) synthase from Arabidopsis thaliana has been identified and termed GGPS5. The gene has been sequenced and expressed in Escherichia coli. The deduced amino acid sequence showed 64.5% and 57.5% identify with a putative GGPP synthase from Arabidopsis and Capsicum annuum, respectively. GGPP enzymatic activity was detected in E. coli cells expressing the GGPS5 gene in two different ways. One was the direct measurement of GGPP synthase activity in cell extracts and the other was the yellow color production of cells when the GGPS5 gene was co-expressed with crtB, crtI, crtY and crtZ genes derived from Erwinia uredovora.
Functional evidence for three distinct and independently inhibitable adhesion activities mediated by the human integrin VLA-4. Correlation with distinct alpha 4 epitopes (1991)

The human integrin VLA (very late activation antigens)-4 (CD49d/CD29), the leukocyte receptor for both the CS-1 region of plasma fibronectin (Fn) and the vascular cell surface adhesion molecule-1 (VCAM-1), also mediates homotypic aggregation upon triggering with specific anti-VLA-4 monoclonal antibody (mAb). Epitope mapping of this integrin on the human B-cell line Ramos, performed with a wide panel of anti-VLA-4 mAb by both cross-competitive cell binding and protease sensitivity assays, revealed the existence of three topographically distinct epitopes on the alpha 4 chain, referred to as epitopes A-C. By testing this panel of anti-VLA-4 mAb for inhibition of cell binding to both a 38-kDa Fn fragment containing CS-1 and to VCAM-1, as well as for induction and inhibition of VLA-4 mediated homotypic cell adhesion, we have found overlapping but different functional properties associated with each epitope. Anti-alpha 4 mAb recognizing epitope B inhibited cell attachment to both Fn and VCAM-1, whereas mAb against epitope A did not block VCAM-1 binding and only partially inhibited binding to Fn. In contrast, mAb directed to epitope C did not affect cell adhesion to either of the two VLA-4 ligands. All mAb directed to site A, as well as a subgroup of mAb recognizing epitope B (called B2), were able to induce cell aggregation, but this effect was not exerted by mAb specific to site C and by a subgroup against epitope B (called B1). Moreover, although anti-epitope C and anti-epitope B1 mAb did not trigger aggregation, those mAb blocked aggregation induced by anti-epitope A or B2 mAb. In addition, anti-epitope A mAb blocked B2-induced aggregation, and conversely, anti-epitope B2 mAb blocked A-induced aggregation. Further evidence for multiple VLA-4 functions is that anti-Fn and anti-VCAM-1 antibodies inhibited binding to Fn or to VCAM-1, respectively, but did not affect VLA-4-mediated aggregation. In summary, we have demonstrated that there are at least three different VLA-4-mediated adhesion functions, we have defined three distinct VLA-4 epitopes, and we have correlated these epitopes with the different functions of VLA-4.
Cryolipolysis for Noninvasive Fat Cell Destruction (2009)

Cryolipolysis is worthy of further study because it has been shown to significantly decrease subcutaneous fat and change body contour without causing damage to the overlying skin and surrounding structures or deleterious changes in blood lipids.
Selective Inhibition of Aβ Fibril Formation (1996)

We describe here an inhibitor of in vitro fibril formation, hexadecyl-N-methylpiperidinium (HMP) bromide, which is selective for the Alzheimer's disease peptide Abeta. At 10 microM, its IC50 for inhibiting Abeta aggregation at pH 5.8, HMP bromide does not inhibit fibril formation by other amyloidogenic polypeptides nor does it affect the folding stability of the beta-sheet-rich immunoglobulin VL domain REI. In addition, small structural modifications of HMP bromide reduce or eliminate its ability to inhibit pH 5.8 aggregation of Abeta. These indications of specificity, plus the ability of the molecule to inhibit A beta aggregation at concentrations almost an order of magnitude below its critical micelle concentration, suggest a mechanism of inhibition other than micellar solubilization of Abeta. HMP bromide is required in approximately a 1:1 stoichiometry for effective inhibition at pH 5.8. Although stoichiometric amounts of HMP bromide with respect to total Abeta inhibit Abeta fibril formation at pH 7.4, the molecule is incapable, at lower concentrations, of blocking the seeding of fibril formation by small amounts of added Abeta fibrils. The results suggest the existence of a binding surface on A beta capable of binding amphipathic molecules such as HMP bromide and which, when occupied, precludes assembly of A beta into amyloid fibrils. Molecules that bind to this site with high specificity may prove to be useful therapeutic agents for preventing or retarding the cerebral amyloid plaque formation implicated in Alzheimer's disease pathology.
LFA-1 Adhesion Molecules Are Not Involved in the Early Stages of HIV-1 env -Mediated Cell Membrane Fusion (1992)

A recently developed sensitive assay to examine the early stages of HIV-1 env-mediated cell fusion is based on the redistribution of fluorescent dyes between membranes and cytoplasm of adjacent cells, monitored by fluorescence video microscopy. This assay demonstrated that membrane fusion can occur under conditions where no syncytia are formed. Fusion started earlier than syncytia formation and was not very sensitive to HIV-1 env+/CD4+ cell ratios. In the current study, this assay was used to determine the role of LFA-1 in HIV-1 env-mediated membrane fusion and syncytia formation. CD4- LFA-1- Epstein-Barr virus transformed lines from two leukocyte adhesion deficiency patients were infected with recombinant vaccinia expressing gp120/41 (HIV-IIIB), and cocultured with CD4+ subclones of the human T cell line CEM, which were generated by chemical mutagenesis and express either normal (LFA-1+), or low levels of LFA-1 (LFA-1lo). It was found that the LFA-1lo T-cell clone formed much smaller and fewer syncytia compared to the LFA-1+ subclones, but both clones fused equally well with the gp120/41 expressing LFA-1- B cells as monitored by redistribution of fluorescent dyes. Furthermore, monoclonal antibodies against the LFA-1 molecules reduced the number of syncytia formed but had no effect on membrane fusion. These findings demonstrate that the adhesion molecule LFA-1 does not play a crucial role in the early events of HIV-1 env-mediated cell membrane fusion, but may contribute to the later events leading to giant cell formation.
Synthesis of Paclitaxel‐Conjugated β‐Cyclodextrin Polyrotaxane and Its Antitumor Activity (2013)

Cap it all: A β-cyclodextrin polyrotaxane was synthesized by using poly(propylene glycol) as the axle and β-cyclodextrin as the end cap. An antitumor agent, paclitaxel, was conjugated to it. The drug-conjugated polyrotaxane penetrates deep into tumors, impedes tumor growth, and prolongs the life of tumor-bearing mice better than Taxol. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Communication Tools Can Control the Interview (1986)

This article describes basic techniques to help individuals become more interesting and effective communicators in front of any kind of audience. Topics covered include: audience reaction, communication tools (mind, face, body, voice), and practice. The author summarizes the main points of a presentation by Arch Lustberg at the 1985 AWWA annual conference in Washington, D.C.
徐熙娣（小S）：悦己，才能悦人 (2010)

提到小S，首先映入你脑海的是哪些词语？鬼马、精灵、搞笑、花痴、时尚、麻辣……似乎哪一个都和贤妻良母搭不上边。也难怪，近期关于她婚姻变故的传闻一波接着一波，对此小S高调回应：造这种谣的人是疯子，对疯子说的话不需要在意，我和我老公不知道多恩爱，我的家庭不知道多和睦，我幸福还来不及，哪有闲心搭理这些谣言!
The prothrombinase-catalyzed activation of prothrombin proceeds through the intermediate meizothrombin in an ordered, sequential reaction. (1986)

The activation of bovine prothrombin by prothrombinase (Factor Xa, Factor Va, synthetic phospholipid vesicles, and calcium ion) was studied in the presence of the fluorescent, reversible thrombin inhibitor dansylarginine-N-(3-ethyl-1,5-pentanediyl) amide (DAPA). Recordings of fluorescence intensity during prothrombin activation exhibited maxima that decreased to stable limiting values. These data suggested the transient appearance of the meizothrombin-DAPA complex, which exhibits fluorescence with 1.5-fold greater intensity than the thrombin-DAPA complex. At substrate concentrations well below Km, progress curves could be fitted by equations describing an ordered, sequential conversion of prothrombin to thrombin through the intermediate meizothrombin via two pseudo-first order steps. The pseudo-first order rate constants for both steps varied linearly with enzyme concentration, indicating that both steps are catalyzed by prothrombinase. The progress of the reaction was also monitored by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and densitometry analyses of aliquots removed at intervals spanning the reaction. These analyses confirmed both the existence of meizothrombin and its time course as predicted from the equations used to analyze fluorescence intensity profiles. Meizothrombin levels peaked at about 0.3 mol/mol initial prothrombin under the conditions typically studied. In addition, prethrombin 2, which is the intermediate expected from cleavages occurring in the order opposite that required to form meizothrombin, was not observed under any of the conditions examined. These data indicate that prothrombin activation catalyzed by the fully assembled prothrombinase complex proceeds via an ordered, sequential reaction with meizothrombin as the sole intermediate.
Human Cathepsin O2, a Matrix Protein-degrading Cysteine Protease Expressed in Osteoclasts (1996)

Cathepsin O2, a human cysteine protease predominantly present in osteoclasts, has been functionally expressed in Spodoptera frugiperda Sf9 cells using the Autographa californica nuclear polyhedrosis virus. Following in vitro activation at pH 4.0 with pepsin, active enzyme with an apparent molecular weight of 29,000 was obtained. N-terminal sequencing revealed the typical processing site for cysteine proteases of the papain family with a proline in the position adjacent to the N-terminal alanine residue. The S2P2 subsite specificity of human cathepsin O2 is similar to cathepsin S but distinguished from cathepsins L and B. Similar to cathepsin S, cathepsin O2 is characterized by a bellshaped pH activity profile and is stable at pH 6.5 for 30 min at 37 degrees C. Cathepsin O2 is further distinguished by its potent collagenolytic activity against Type I collagen between pH 5 and 6, and elastinolytic activity against insoluble elastin at pH 7.9. Its capacity to efficiently degrade Type I collagen and its high expression in osteoclasts suggest that cathepsin O2 may play a major role in human osteoclastic bone resorption.