gebhart/patrepeval huggingface dataset:
Data Warehousing with Microsoft SQL Server 7.0 Technical Reference (2000)

A book/CD-ROM showing how to take advantage of features of SQL Server 7.0 to design, build, and manage a data warehouse. Introduces basic concepts of data warehousing, then looks at online analytical processing services, data transformation services, advanced query processor and the MDX query langua
Focusing and scanning light through a multimode optical fiber using digital phase conjugation (2012)

We demonstrate for the first time to our knowledge a digital phase conjugation technique for generating a sharp focus point at the end of a multimode optical fiber. A sharp focus with a contrast of 1800 is experimentally obtained at the tip of a 105 μm core multimode fiber. Scanning of the focal point is also demonstrated by digital means. Effects from illumination and fiber bending are addressed.
CYPs, SNPs, and molecular diagnosis in the postgenomic era. (1998)

Advances in the Human Genome Project have profoundly influenced not only the search for new genes, but also the molecular diagnosis of genetic disorders. In the early 1980s, the first generation of the human genome map was based on restriction fragment length polymorphisms (RFLPs) identified by Southern analysis (1). Linkage analysis by RFLP became a very powerful tool for molecular diagnosis. The early 1990s saw the rise of the second generation of mapping, based on microsatellite markers and PCR amplification (2). These multiallelic polymorphisms are much more informative than RFLPs and simpler to study. We are now witnessing the third generation of genome mapping, based on single-nucleotide polymorphisms (SNPs), and analyzed by PCR and chip-based microarrays (3).

An SNP involves any nucleotide of the human genome in which two different bases can be found in the population. SNPs are the most common type of human genetic variation. Because they have only two alleles, they are less informative than microsatellites. This drawback is overcome by their high density throughout the genome and the simplicity and possible automation of their analysis. They may become one of the most powerful tools in human genetics for identifying disease genes and …
CD133 Expression Defines a Tumor Initiating Cell Population in Primary Human Ovarian Cancer (2009)

Evidence is accumulating that solid tumors contain a rare phenotypically distinct population of cells, termed cancer stem cells (CSC), which give rise to and maintain the bulk of the tumor. These CSC are thought to be resistant to current chemotherapeutic strategies due to their intrinsic stem-like properties and thus may provide the principal driving force behind recurrent tumor growth. Given the high frequency of recurrent metastasis associated with human ovarian cancer, we sought to determine whether primary human ovarian tumors contain populations of cells with enhanced tumor-initiating capacity, a characteristic of CSC. Using an in vivo serial transplantation model, we show that primary uncultured human ovarian tumors can be reliably propagated in NOD/SCID mice, generating heterogeneous tumors that maintain the histological integrity of the parental tumor. The observed frequency of tumor engraftment suggests only certain subpopulations of ovarian tumor cells have the capacity to recapitulate tumor growth. Further profiling of human ovarian tumors for expression of candidate CSC surface markers indicated consistent expression of CD133. To determine whether CD133 expression could define a tumor-initiating cell population in primary human ovarian tumors, fluorescence-activated cell sorting (FACS) methods were employed. Injection of sorted CD133(+) and CD133(-) cell populations into NOD/SCID mice established that tumor-derived CD133(+) cells have an increased tumorigenic capacity and are capable of recapitulating the original heterogeneous tumor. Our data indicate that CD133 expression defines a NOD/SCID tumor initiating subpopulation of cells in human ovarian cancer that may be an important target for new chemotherapeutic strategies aimed at eliminating ovarian cancer.
Effects of carbamide peroxide whitening agents on enamel surfaces and caries-like lesion formation: an SEM and polarized light microscopic in vitro study. (1997)

Whitening enamel with carbamide peroxide (CP) to remove cosmetically displeasing stains has become common-place in dental practice. This in vitro study evaluated CP treatment effects on enamel surface morphology and caries-like lesion susceptibility. Tooth quarters were prepared from 10 caries-free human molars following a fluoride-free prophylaxis. The tooth quarters were assigned to the following treatment groups: 1) Distobuccal-10 percent NW gel (Nite White, Discus Dental); 2) Distolingual-10 percent PL paste (Platinum, Colgate); 3) Mesiobuccal-16 percent NW gel; and 4) Mesiolingual-Control. Following the manufacturers' recommended treatment, each quarter was sectioned with one portion prepared for SEM and the other portion for caries-like lesion formation. Intact enamel surfaces were present with all treatments. Enamel prism markings with exaggerated prism peripheries and mild to moderate prism core loss were seen with both 10 percent NW and 16 percent NW gels, but was more prominent with 16 percent NW gel. Amorphous surface layers with occasional exposure of indistinct prism markings occurred with 10 percent PL paste. Body of lesion mean depths were 135 microns control, 159 microns 16 percent NW, 144 microns 10 percent NW, and 122 microns 10 percent PL. Lesion depths were significantly different (p < 0.05 DMR paired design) between 10 percent PL and 16 percent NW, and between control and 16 percent NW. Whitening enamel surfaces in vitro with 10 percent carbamide peroxide paste containing dicalcium phosphate dihydrate (Colgate-Platinum) produced an amorphous surface layer and reduced caries susceptibility when compared with 16 percent carbamide peroxide gel (Nite White).
Sequential paraformaldehyde and methanol fixation for simultaneous flow cytometric analysis of DNA, cell surface proteins, and intracellular proteins (1992)

A cell fixation and permeabilization procedure consisting of sequential paraformaldehyde and methanol was evaluated and found suitable for concomitant flow cytometric quantification of total cellular DNA, immunofluorescence measurements of cell surface proteins, and immunofluorescence measurements of intracellular proteins. Paraformaldehyde/methanol-fixed cells exhibited significantly greater intracellular antitubulin immunofluorescence than cells fixed with paraformaldehyde or methanol alone (p less than 0.002) and significantly greater intracellular antitubulin immunofluorescence than cells fixed with methanol followed by paraformaldehyde (p less than 0.006). With paraformaldehyde/methanol fixation, cell morphology was well preserved and forward and right angle light scatter properties were sufficiently well maintained to permit gating on these parameters. Cell surface marker staining with fluorescent anti-leukocyte antibodies was unaffected by fixation with paraformaldehyde/methanol. Paraformaldehyde effects on the intensity of DNA staining with propidium iodide were dependent on paraformaldehyde concentration and fixation temperature; these effects were least pronounced at low paraformaldehyde concentrations (0.25% or less), and at temperatures lower than 37 degrees C. Paraformaldehyde fixation may result in differences in propidium iodide staining of DNA in some diploid cells, which may produce small spurious aneuploid peaks in normal peripheral blood leukocytes. Paraformaldehyde fixation also produces an apparent increase in the DNA index of aneuploid cell populations in comparison with methanol fixation, particularly when the DNA index exceeds 1.5. Occasionally, this paraformaldehyde fixation-induced effect is useful in identifying biologically distinct near-diploid subpopulations in tumors.
Activation of actin polymerization by phosphatidic acid derived from phosphatidylcholine in IIC9 fibroblasts. (1993)

alpha-Thrombin induced a change in the cell morphology of IIC9 fibroblasts from a semiround to an elongated form, accompanied by an increase in stress fibers. Incubation of the cells with phospholipase D (PLD) from Streptomyces chromofuscus and exogenous phosphatidic acid (PA) caused similar morphological changes, whereas platelet-derived growth factor (PDGF) and phorbol 12-myristate 13-acetate (PMA) induced different changes, e.g., disruption of stress fibers and cell rounding. alpha-Thrombin, PDGF, and exogenous PLD increased PA by 20-40%, and PMA produced a smaller increase. alpha-Thrombin and exogenous PLD produced rapid increases in the amount of filamentous actin (F-actin) that were sustained for at least 60 min. However, PDGF produced a transient increase of F-actin at 1 min and PMA caused no significant change. Dioctanoylglycerol was ineffective except at 50 micrograms/ml. Phospholipase C from Bacillus cereus, which increased diacylglycerol (DAG) but not PA, did not change F-actin content. Down-regulation of protein kinase C (PKC) did not block actin polymerization induced by alpha-thrombin. H-7 was also ineffective. Exogenous PA activated actin polymerization with a significant effect at 0.01 microgram/ml and a maximal increase at 1 microgram/ml. No other phospholipids tested, including polyphosphoinositides, significantly activated actin polymerization. PDGF partially inhibited PA-induced actin polymerization after an initial increase at 1 min. PMA completely or largely blocked actin polymerization induced by PA or PLD. These results show that PC-derived PA, but not DAG or PKC, activates actin polymerization in IIC9 fibroblasts, and indicate that PDGF and PMA have inhibitory effects on PA-induced actin polymerization.
Nucleocapsid-glycoprotein interactions required for assembly of alphaviruses (1994)

We have studied interactions between nucleocapsids and glycoproteins required for budding of alphaviruses, using Ross River virus-Sindbis virus chimeras in which the nucleocapsid protein is derived from one virus and the envelope glycoproteins are derived from the second virus. A virus containing the Ross River virus genome in which the capsid protein had been replaced with that from Sindbis virus was almost nonviable. Nucleocapsids formed in normal numbers in the infected cell, but very little virus was released from the cell. There are 11 amino acid differences between Ross River virus and Sindbis virus in their 33-residue E2 cytoplasmic domains. Site-specific mutagenesis was used to change 9 of these 11 amino acids in the chimera from the Ross River virus to the Sindbis virus sequence in an attempt to adapt the E2 of the chimera to the nucleocapsid. The resulting mutant chimera grew 4 orders of magnitude better than the parental chimeric virus. This finding provides direct evidence for a sequence-specific interaction between the nucleocapsid and the E2 cytoplasmic domain during virus budding. The mutated chimeric virus readily gave rise to large-plaque variants that grew almost as well as Ross River virus, suggesting that additional single amino acid substitutions in the structural proteins can further enhance the interactions between the disparate capsid and the glycoproteins. Unexpectedly, change of E2 residue 394 from lysine (Ross River virus) to glutamic acid (Sindbis virus) was deleterious for the chimera, suggesting that in addition to its role in nucleocapsid-E2 interactions, the N-terminal part of the E2 cytoplasmic domain may be involved in glycoprotein-glycoprotein interactions required to assemble the glycoprotein spikes. The reciprocal chimera, Sindbis virus containing the Ross River virus capsid, also grew poorly. Suppressor mutations arose readily in this chimera, producing a virus that grew moderately well and that formed larger plaques.
A functional map of the nopaline synthase promoter (1984)

This paper describes the first functional map of a promoter expressed from the plant chromosome. We have constructed a series of overlapping deletion mutants within the region upstream of the Ti-plasmid encoded nopaline synthase (nos) gene. By monitoring nos expression in tumour tissue we have inferred a functional map of the nos promoter. The maximum length of sequence upstream of the transcription initiation point required to express wild type levels of nopaline synthase is 88 bp. Within this region, the "CAAT" box is essential for maximal activity; deletion of this sequence reduced apparent nos expression by over 80%. Presence of an intact or partial "TATA" box in the absence of the "CAAT" box supports a barely detectable level of nopaline synthase. Removal of all sequences upstream of the nos coding sequence results in no detectable activity.
Nuclear size control in fission yeast (2007)

A long-standing biological question is how a eukaryotic cell controls the size of its nucleus. We report here that in fission yeast, nuclear size is proportional to cell size over a 35-fold range, and use mutants to show that a 16-fold change in nuclear DNA content does not influence the relative size of the nucleus. Multi-nucleated cells with unevenly distributed nuclei reveal that nuclei surrounded by a greater volume of cytoplasm grow more rapidly. During interphase of the cell cycle nuclear growth is proportional to cell growth, and during mitosis there is a rapid expansion of the nuclear envelope. When the nuclear/cell (N/C) volume ratio is increased by centrifugation or genetic manipulation, nuclear growth is arrested while the cell continues to grow; in contrast, low N/C ratios are rapidly corrected by nuclear growth. We propose that there is a general cellular control linking nuclear growth to cell size.
IL-2–induced CD4+ T-cell expansion in HIV-infected patients is associated with long-term decreases in T-cell proliferation (2004)

Administration of interleukin 2 (IL-2) leads to selective and sustained CD4+ T-cell expansions in patients infected with HIV. It has been hypothesized that persistent CD4+ T-cell proliferation is the primary mechanism maintaining these expansions. T-cell proliferation was studied by ex vivo bromodeoxyuridine (BrdU) incorporation and intracellular Ki67 staining in HIV-infected patients treated with antiretroviral therapy (ART) with or without IL-2. In contrast to the tested hypothesis, HIV-infected patients treated with IL-2 had lower CD4+ T-cell proliferation compared to patients treated with ART alone. Independently of viral load changes, administration of IL-2 led to a decrease in basal CD4+ T-cell proliferation. Total numbers of CD4+ T cells with naive and recall, but not effector, memory phenotype were increased. The degree of CD4+ T-cell expansion correlated with the decreases in proliferation and a strong association was seen between these decreases and the expansion of the CD4+/CD25+ subset. Intermittent IL-2 in HIV-infected patients leads to expansions of CD4+/CD25+ T cells with naive and recall memory phenotypes that strongly correlate with decreases in proliferation. These data suggest that decreased T-cell proliferation is central in the CD4+ T-cell expansions induced by IL-2.
Elemental Diet-Induced Bacterial Translocation Can Be Hormonally Modulated (1993)

Elemental diet-induced bacterial translocation can be modulated hormonally and the beneficial effects of fiber on diet-induced BT appears to be hormonally mediated.
Non-lithographic method of forming ordered arrays of silicon pillars and macropores (2005)

Micrometre-scale Si pillars are formed by chemically enhanced laser ablation using nanosecond excimer laser irradiation of a Si single crystal in the presence of SF6. We demonstrate the importance of precursor holes in determining the positioning of the pillars and show that we can control the initiation of precursor holes by ruling a grating into the Si substrate prior to irradiation. A rule defines an edge from which the laser light diffracts. Near-field amplification of the laser intensity enhances the formation of the precursor holes and aligns them parallel to the rule. The pillars can be thinned and eventually removed by wet chemical etching in aqueous KOH, resulting first in ordered arrays of extremely high aspect ratio pillars (e.g. tens of micrometres in length, with ∼ 10 nm tips) and then macropores. The shape of the macropore is determined by crystallography and the anisotropy of the wet etchant.
Mosquito Larvicidal and Pupicidal Activity of Aminimides1 (1978)

Aminimides (amino-imides) are a relatively new class of fatty acid derivatives, of general formula R1-CO-N−-+N(CH3)2-R2. that are surface-active and exist as bipolarions. They have been found to be active against microorganisms (Kabara, McKillip & Sedor, 1975, J. Am. Oil Chem. Soc. 52: 316–17; Kabara & Haitsma, 1975, J. Am. Oil Chem. Soc. 52: 444–47). Since biological activity against mosquito larvae and pupae has been shown by amines (Mulla, 1967, J. Econ. Entomol. 60: 515–22; Mulla & Darwazeh, 1975, Mosq. News 35: 57–62) and by amides (Alexander & Beroza, 1963, J. Econ. Entomol. 56: 58–60), tests were made of 34 aminimides on larvae and pupae of Aedes aegypti and Culex pipiens.
Development of a Continuous Fluorescence Assay for Rhinovirus 14 3C Protease Using Synthetic Peptides (1997)

Rhinovirus 3C protease is an attractive target for therapeutic intervention owing to its important role in virion maturation and infectivity. In order to facilitate the identification of potential 3C protease inhibitors, we have developed a continuous fluorescence assay using 5-[(2-aminoethyl)amino]naphthalene-1-sulphonic acid (Edans) as a fluorescent donor and 4-(4-dimethylaminophenylazo)benzoic acid (Dabcyl) as a quenching acceptor. Several fluorogenic peptide substrates for 3C protease were synthesized by both solution chemistry and solid phase peptide synthesis. One of the synthetic Edans/Dabcyl substrates, with an amino acid sequence derived from the 2C/3A site of the virus polyprotein, yielded a 24-fold increase in fluorescence intensity after 3C cleavage. Data regarding substrate cleavage kinetics, assay sensitivity and optimization are presented. The application of this assay to the evaluation of 3C protease inhibitors is also shown.
Conditional Protein Splicing:  A New Tool to Control Protein Structure and Function in Vitro and in Vivo (2003)

Protein splicing is a naturally occurring process in which an intervening intein domain excises itself out of a precursor polypeptide in an autocatalytic fashion with concomitant linkage of the two flanking extein sequences by a native peptide bond. We have recently reported an engineered split VMA intein whose splicing activity in trans between two polypeptides can be triggered by the small molecule rapamycin. In this report, we show that this conditional protein splicing (CPS) system can be used in mammalian cells. Two model constructs harboring maltose-binding protein (MBP) and a His-tag as exteins were expressed from a constitutive promoter after transient transfection. The splicing product MBP-His was detected by Western blotting and immunoprecipitation in cells treated with rapamycin or a nontoxic analogue thereof. No background splicing in the absence of the small-molecule inducer was observed over a 24-h time course. Product formation could be detected within 10 min of addition of rapamycin, indicating the advantage of the posttranslational nature of CPS for quick responses. The level of protein splicing was dose dependent and could be competitively attenuated with the small molecule ascomycin. In related studies, the geometric flexibility of the CPS components was investigated with a series of purified proteins. The FKBP and FRB domains, which are dimerized by rapamycin and thereby induce the reconstitution of the split intein, were fused to the extein sequences of the split intein halves. CPS was still triggered by rapamycin when FKBP and FRB occupied one or both of the extein positions. This finding suggests yet further applications of CPS in the area of proteomics. In summary, CPS holds great promise to become a powerful new tool to control protein structure and function in vitro and in living cells.
A decentralized AI system for transcript applications (2002)

A working expert system for assessing a student's course requirements for graduation in various departments of a university is presented. The system draws on artificial intelligence (AI) techniques of expert systems and natural language processing to facilitate interaction with both intermediate- and end-user. Expertise is expressed in rules that take the form of English sentences. The flexibility of the AI approach allowed substantial benefit from an earlier related system for admission of transfer students. A key feature with respect to the workplace is the system's transparency or non-disruptiveness, achieved by using an existing database. A special editor for output that looks like a filled-in form of the type that has traditionally been prepared by hand is provided. Transparency and ease of use have enhanced acceptability of the system for the people in the registrar's office, who have enthusiastically collaborated in design and testing. Acceptability should also make decentralization to the departments, the university's counterpart to the government field office, possible.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New class of transforming growth factors potentiated by epidermal growth factor: isolation from non-neoplastic tissues. (1981)

Proteins potentiated by epidermal growth factor (EGF) to induce a transformed phenotype in non-neoplastic rat kidney fibroblasts in cell culture have been isolated from many non-neoplastic tissues of the adult mouse, including submaxillary gland, kidney, liver, muscle, heart, and brain. They resemble previously described transforming growth factors (TGFs) isolated from neoplastic cells as follows: they are extractable by acid/ethanol and are acid-stable, low molecular weight (6000-10,000) polypeptides requiring disulfide bonds for activity; and they cause anchorage-independent growth of non-neoplastic indicator cells that will not grow in soft agar in their absence. Partial purification of these TGFs from submaxillary glands of male mice shows that they are distinct from EGF. Unlike previously described extracellular TGFs, but like certain cellular TGFs from neoplastic cells, they are potentiated by EGF in their ability to promote anchorage-independent growth. The isoelectric point of the submaxillary gland TGF protein is near neutrality. Chromatography on Bio-Gel P-30 followed by high-pressure liquid chromatography has resulted in a 22,000-fold overall purification. The most purified protein is active in inducing growth in soft agar at 1 ng/ml when assayed in the presence of EGF. The data add further evidence to the concept that neoplasia may result from a quantitative, rather than qualitative, alteration in non-neoplastic biochemical processes.