gebhart/patrepeval huggingface dataset:
Preparation and Properties of Silica-Coated Cobalt Nanoparticles (2003)

The synthesis of monodispersed, amorphous cobalt nanoparticles coated with silica in aqueous/ethanolic solution is described. Both the core size and the silica shell thickness can be controlled through the synthetic conditions. Furthermore, the transformation of the cobalt cores into crystalline, metallic cobalt upon annealing in air is demonstrated through X-ray diffraction data. Both the initial, amorphous nanoparticles and their crystalline counterpart are magnetic, which promises important applications for ferrofluid preparation and for magnetic recording media.
The highly O-glycosylated glycoprotein gp2 of equine herpesvirus 1 is encoded by gene 71 (1996)

There have been conflicting reports regarding the gene assignment of the high-molecular-mass envelope glycoprotein gp2 (gp300) of equine herpesvirus 1. Here, we provide an unequivocal demonstration that gp2 is encoded by gene 71. gp2 that was purified with a defining monoclonal antibody was cleaved internally to yield a 42-kDa protein encoded by gene 71. Amino acid composition data and N-terminal sequence analysis of a tryptic peptide identified gp2 as the product of equine herpesvirus 1 gene 71 with the SWISS-PROT database. Analysis of gp2's monosaccharide composition and the 42-kDa subunit showed that the high level of O glycosylation occurs on the serine/threonine-rich region upstream of the cleavage site.
Recombinant Toxins Containing Human Granulocyte-Macrophage Colony-Stimulating Factor and Either Pseudomonas Exotoxin or Diphtheria Toxin Kill Gastrointestinal Cancer and Leukemia Cells (1997)

The granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR) is a potential target for toxin-directed therapy, because it is overexpressed on many leukemias and solid tumors and apparently not on stem cells. To investigate the potential therapeutic use of GM-CSF toxins, we fused human GM-CSF to truncated forms of either Pseudomonas exotoxin (PE) or diphtheria toxin (DT) and tested the cytotoxicity of the resulting GM-CSF–PE38KDEL and DT388–GM-CSF on human gastrointestinal (GI) carcinomas and leukemias. Toward gastric and colon cancer cell lines, GM-CSF–PE38KDEL was much more cytotoxic than DT388–GM-CSF, with IC50s (concentration resulting in 50% inhibition of protein synthesis) of 0.5 to 10 ng/mL compared with 4 to 400 ng/mL, respectively. In contrast, toward leukemia lines and fresh bone marrow cells DT388–GM-CSF was more cytotoxic than GM-CSF–PE38KDEL. The cytotoxicity of both GM-CSF–PE38KDEL and DT388–GM-CSF toward the human cells was specific, because it could be competed by an excess of GM-CSF. Binding studies indicated that human GM-CSF receptors were present on all of the human GI and leukemic cell lines tested, at levels of 540 to 3,700 sites per cell (kd = 0.2 to 2 nmol/L), and the number of sites per cell did not correlate with the cell type. A similar pattern of cytotoxicity was found with recombinant immunotoxins binding to the transferrin receptor, in that anti-TFR(Fv)–PE38KDEL was much more cytotoxic than DT388–anti-TFR(Fv) toward GI cells, but both were similar in their cytotoxic activity toward leukemia cells. The fact that PE is more effective than DT in killing GI but not leukemic tumor cells targeted by GM-CSF indicates a fundamental difference in the way PE or DT gains access to the cytosol in these cells. GM-CSF–PE38KDEL and DT388–GM-CSF deserve further evaluation as possible treatments for selected tumors.
Electrically Switchable Bragg Gratings (2003)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Gregory P. Crawford, "Electrically Switchable Bragg Gratings," Optics & Photonics News 14(4), 54-59 (2003) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations (2014)

We present a simple molecular indexing method for quantitative targeted RNA sequencing, in which mRNAs of interest are selectively captured from complex cDNA libraries and sequenced to determine their absolute concentrations. cDNA fragments are individually labeled so that each molecule can be tracked from the original sample through the library preparation and sequencing process. Multiple copies of cDNA fragments of identical sequence become distinct through labeling, and replicate clones created during PCR amplification steps can be identified and assigned to their distinct parent molecules. Selective capture enables efficient use of sequencing for deep sampling and for the absolute quantitation of rare or transient transcripts that would otherwise escape detection by standard sequencing methods. We have also constructed a set of synthetic barcoded RNA molecules, which can be introduced as controls into the sample preparation mix and used to monitor the efficiency of library construction. The quantitative targeted sequencing revealed extremely low efficiency in standard library preparations, which were further confirmed by using synthetic barcoded RNA molecules. This finding shows that standard library preparation methods result in the loss of rare transcripts and highlights the need for monitoring library efficiency and for developing more efficient sample preparation methods.
Treatment of Vinorelbine-Associated Tumor Pain (2001)

Vinorelbine is a synthetic vinca alkaloid used for the treatment of Hodgkin's disease and metastatic breast, non-small-cell lung, and ovarian cancers. Vinorelbine-associated tumor pain can be so severe that patients are unable to complete therapy. We present a series of three patients who were premedicated with ketorolac in an attempt to control infusion-related pain. Two of our patients responded well and were able to complete their courses of vinorelbine therapy. The third had persistently severe pain, and therapy was terminated because of pain and lack of response to vinorelbine treatment. These three cases support the hypothesis that surgery or radiation therapy before the use of vinorelbine may increase the likelihood of experiencing associated tumor pain. Premedication with ketorolac and morphine before vinorelbine infusion is proposed as a reasonable prophylactic treatment for associated tumor pain.
An Overview of Geophysical and Non-Destructive Methods for Characterization of Roads and Bridges (2000)

A variety of remote sensing, surface geophysical, borehole geophysical and other non-destructive methods can be used to determine conditions of roads and bridges. Some of these methods can be utilized to determine subsurface conditions prior to construction. Some can be applied to QC measurements during construction and many can be applied after construction to determine as-built conditions, as well as degradation. The benefit of such measurements are that they are non-destructive, provide in-situ measurements of a wide range of physical properties, sample larger areas or volumes, provide continuous measurements in some cases, and provide faster measurements. All of this results in a greater sample density, which can more readily identify uniform conditions as well as locate anomalous conditions. Once anomalies conditions are identified, those areas requiring further tests, borings or repairs can be accurately and quickly located. These methods can also provide temporal measurements (detecting changes in conditions with time). Such data can be used in a database to guide management decisions for maintenance and repairs. Maintenance and repairs on roads, bridge decks and bridge scour is becoming ever important as our infrastructure ages. A variety of methods can be used to increase the efficiency and technical effectiveness of such inspections. This paper provides an overview of those methods that can and have been applied to characterizing conditions of roads and bridges.
Testis-Specific and Ubiquitous Proteins Bind to Functionally Important Regions of the Mouse Protamine-1 Promoter1 (1994)

To understand the spermatid-specific regulation of the protamine-1 (Prm-1) gene, we examined the nuclear proteins that bind to regions of the Prm-1 promoter known to regulate transcription. We focused on the Prm-1 promoter region between bp -224 and -37 because this region directs spermatid-specific expression of a heterologous reporter gene in transgenic mice and because regulatory function has been demonstrated for several subregions of this fragment. Testis nuclear proteins that bind to this promoter region were identified by means of gel mobility shift assays, and the tissue distribution of these proteins was examined through nuclear extracts derived from several mouse tissues. Nuclear extracts prepared from prepubertal and mutant mouse testes were used to demonstrate the developmental appearance of these DNA-binding proteins during spermatogenesis. These studies indicate that a testis-specific protein that appears after Day 12 interacts with a sequence (between bp -37 and -77) shown to be essential for Prm-1 transcription in vivo. In addition, a number of proteins that are not restricted to the testis interact with other functionally important regions of the Prm-1 promoter.
High level expression and secretion of Fc-X fusion proteins in mammalian cells (1998)

We have developed a general expression system that enhances the production and secretion of proteins in mammalian cells. The protein of interest is expressed as a fusion to a signal peptide and the Fc fragment of immunoglobulin as the N-terminal fusion partner, which can direct the cellular processes into expressing and secreting high levels of many different types of proteins. These include secretory proteins, enzymes and soluble domains of membrane proteins, as well as nuclear and regulatory proteins. Typical expression levels of these proteins from stable cell lines ranged from several to 100 microg/ml in conditioned media. The Fc domain helps to solubilize hydrophobic proteins and provides a handle for easy detection and purification of the fusion proteins; and it can be cleaved off by treatment with protease if desired.
Transform-ratio ternary phase-amplitude filter formulation for improved correlation discrimination (1988)

A method of formulating ternary-valued (-1,0,1) correlation filters based on the ratio of spectral energies of target and nontarget patterns is proposed, and performance of such filters is investigated by computer simulations of correlation. The results confirm the intuitive expectation that such filters can enhance signalto- clutter and discrimination performance for target recognition in the presence of large amounts of input noise. These filters may be viewed as an extension of binary phase-only filters and similarly are motivated by the prospect of near-term real-time implementation.
Tissue Distribution of PACAP as Determined by RIA: Highly Abundant in the Rat Brain and Testes (1991)

A heterologous RIA method for pituitary adenylate cyclase activating polypeptide with 38 residues (PACAP38) and a homologous RIA method for a shorter form of PACAP with 27 residues (PACAP27) were established to determine PACAP content in central and peripheral tissues in rats. The highest concentration of radioimmunoassayable PACAP38 was found in the hypothalamus, but other brain regions also contained considerable amounts of PACAP38. PACAP38 concentration in the posterior pituitary was comparable with that in the extrahypothalamic brain, but its concentration in the anterior pituitary was very low. Unexpectedly, the testis contained a high abundance of PACAP38, and the total amount of PACAP in both testes exceeded its content in the whole brain. Reverse phase HPLC suggested that the major testicular PACAP38 immunoreactivity represents PACAP38. Among peripheral tissues, adrenal gland contained the second highest concentration of PACAP. Smaller amounts of PACAP were widely distributed in the digestive tract and other peripheral tissues. The concentration of PACAP in stomach, duodenum and jejunum appeared to be greater than in other portions of the gut. In all tissues, PACAP27 represented only a minor portion of total PACAP immunoreactivity.
MEMS Laser Scanners: A Review (2014)

Laser scanners have been an integral part of MEMS research for more than three decades. During the last decade, miniaturized projection displays and various medical-imaging applications became the main driver for progress in MEMS laser scanners. Portable and truly miniaturized projectors became possible with the availability of red, green, and blue diode lasers during the past few years. Inherent traits of the laser scanning technology, such as the very large color gamut, scalability to higher resolutions within the same footprint, and capability of producing an always-in-focus image render it a very viable competitor in mobile projection. Here, we review the requirements on MEMS laser scanners for the demanding display applications, performance levels of the best scanners in the published literature, and the advantages and disadvantages of electrostatic, electromagnetic, piezoelectric, and mechanically coupled actuation principles. Resonant high-frequency scanners, low-frequency linear scanners, and 2-D scanners are included in this review.
Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes (2012)

Viruses are the most abundant biological entities on earth and encompass a vast amount of genetic diversity. The recent rapid increase in the number of sequenced viral genomes has created unprecedented opportunities for gaining new insight into the structure and evolution of the virosphere. Here, we present an update of the phage orthologous groups (POGs), a collection of 4,542 clusters of orthologous genes from bacteriophages that now also includes viruses infecting archaea and encompasses more than 1,000 distinct virus genomes. Analysis of this expanded data set shows that the number of POGs keeps growing without saturation and that a substantial majority of the POGs remain specific to viruses, lacking homologues in prokaryotic cells, outside known proviruses. Thus, the great majority of virus genes apparently remains to be discovered. A complementary observation is that numerous viral genomes remain poorly, if at all, covered by POGs. The genome coverage by POGs is expected to increase as more genomes are sequenced. Taxon-specific, single-copy signature genes that are not observed in prokaryotic genomes outside detected proviruses were identified for two-thirds of the 57 taxa (those with genomes available from at least 3 distinct viruses), with half of these present in all members of the respective taxon. These signatures can be used to specifically identify the presence and quantify the abundance of viruses from particular taxa in metagenomic samples and thus gain new insights into the ecology and evolution of viruses in relation to their hosts.
Transcription factor Fos-related antigen 1 is an effective target for a breast cancer vaccine (2003)

Protection against breast cancer was achieved with a DNA vaccine against murine transcription factor Fos-related antigen 1, which is overexpressed in aggressively proliferating D2F2 murine breast carcinoma. Growth of primary s.c. tumor and dissemination of pulmonary metastases was markedly suppressed by this oral DNA vaccine, carried by attenuated Salmonella typhimurium, encoding murine Fos-related antigen 1, fused with mutant polyubiquitin, and cotransformed with secretory murine IL-18. The life span of 60% of vaccinated mice was tripled in the absence of detectable tumor growth after lethal tumor cell challenge. Immunological mechanisms involved activation of T, natural killer, and dendritic cells, as indicated by up-regulation of their activation markers and costimulatory molecules. Markedly increased specific target cell lysis was mediated by both MHC class I-restricted CD8+ T cells and natural killer cells isolated from splenocytes of vaccinated mice, including a significant release of proinflammatory cytokines IFN-gamma and IL-2. Importantly, fluorescence analysis of fibroblast growth factor 2 and tumor cell-induced vessel growth in Matrigel plugs demonstrated marked suppression of angiogenesis only in vaccinated animals. Taken together, this multifunctional DNA vaccine proved effective in protecting against growth and metastases of breast cancer by combining the action of immune effector cells with suppression of tumor angiogenesis.
Statistical Methods for the Reliability of Repairable Systems (2000)

Terminology and Notation for Repairable Systems. Probabilistic Models: The Poisson Process. Probabilistic Models: Renewal and Other Processes. Analyzing Data from a Single Repairable System. Analyzing Data from Multiple Repairable Systems. Appendix. References.
Antimicrobial activity and mechanisms of Salvia sclarea essential oil (2015)

Salvia sclarea essential oil damaged the cell membrane and changed the cell membrane permeability, leading to the release of some cytoplasm such as macromolecular substances, ATP and DNA. In general, the antimicrobial action of Salvia sclarea essential oil is not only attributable to a unique pathway, but also involves a series of events both on the cell surface and within the cytoplasm. Therefore, more experiments need to be done to fully understand the antimicrobial mechanism of Salvia sclarea essential oil.
Fungicidal effect of human lactoferrin against Candida albicans (1992)

Human lactoferrin (LF) in its iron-free state (apo LF), killed Candida albicans in a time- and dose-dependent way. The lethal effect was stronger at pH 7.0 than at pH 5.5 and maximum inhibition at neutral pH was achieved in 25 min when the fungal cells were exposed to LF in 0.05 mM KCl at 37 degrees C. Fe(3+)-saturated LF had no fungicidal activity. Apo LF-mediated killing was also temperature-dependent with enhanced inhibition at higher temperatures (37 degrees, 42 degrees C). The presence of 1 mM D-glucose did not affect the candidacidal activity of apo LF but both phosphate and bicarbonate ions at physiological salivary concentrations completely blocked the anti-fungal effect. Therefore it seems unlikely that LF belongs to the major host defence factors against oral candidosis.
Blood-brain barrier disruption in multiple sclerosis (2003)

The blood-brain barrier (BBB) is a complex organization of cerebral endothelial cells (CEC), pericytes and their basal lamina, which are surrounded and supported by astrocytes and perivascular macrophages. Collectively these cells separate and form the compartments of the cerebral vascular space and the cerebral interstitium under normal conditions. Without the BBB, the 'interior milieu' of the central nervous system (CNS) would be flooded by humoral neurotransmitters and formed blood elements that upset normal CNS functions and lead to vascular/neural injury. Dysregulation of the BBB and transendothelial migration of activated leukocytes are among the earliest cerebrovascular abnormalities seen in multiple sclerosis (MS) brains and parallel the release of inflammatory cytokines/chemokines. Mechanisms for breakdown of the BBB in MS are incompletely understood, but appear to involve direct effects of these cytokines/ chemokines on endothelial regulation of BBB components, as well as indirect cytokine/chemokine-dependent leukocyte mediated injury. Unique endothelial structural features of the BBB include highly organized endothelial tight junctions, the absence of class II major histocompatibility complex, abundant mitochondria and a highly developed transport system in CEC. Exposure of endothelium to proinflammatory cytokines (IFN-gamma, TNF-alpha and IL-1beta) interrupts the BBB by disorganizing cell-cell junctions, decreases the brain solute barrier, enhances leukocyte endothelial adhesion and migration as well as increases expression of class II MHC and promotes shedding of endothelial 'microparticles' (EMP). In this review we examine interactions between cytokines/chemokines, activated leukocytes, adhesion molecules and activated CEC in the pathogenesis of BBB failure in MS.
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters (2001)

The genomic organization of the human protocadherin alpha, beta, and gamma gene clusters (designated Pcdh alpha [gene symbol PCDHA], Pcdh beta [PCDHB], and Pcdh gamma [PCDHG]) is remarkably similar to that of immunoglobulin and T-cell receptor genes. The extracellular and transmembrane domains of each protocadherin protein are encoded by an unusually large "variable" region exon, while the intracellular domains are encoded by three small "constant" region exons located downstream from a tandem array of variable region exons. Here we report the results of a comparative DNA sequence analysis of the orthologous human (750 kb) and mouse (900 kb) protocadherin gene clusters. The organization of Pcdh alpha and Pcdh gamma gene clusters in the two species is virtually identical, whereas the mouse Pcdh beta gene cluster is larger and contains more genes than the human Pcdh beta gene cluster. We identified conserved DNA sequences upstream of the variable region exons, and found that these sequences are more conserved between orthologs than between paralogs. Within this region, there is a highly conserved DNA sequence motif located at about the same position upstream of the translation start codon of each variable region exon. In addition, the variable region of each gene cluster contains a rich array of CpG islands, whose location corresponds to the position of each variable region exon. These observations are consistent with the proposal that the expression of each variable region exon is regulated by a distinct promoter, which is highly conserved between orthologous variable region exons in mouse and human.
Prognostic value of tumor infiltrating lymphocytes in the vertical growth phase of primary cutaneous melanoma (1996)

We demonstrated that when categories of tumor infiltrating lymphocytes are strictly defined, they indeed have very strong predictive value for primary cutaneous melanomas with a vertical growth phase. This work confirms the work of Clark et al. and fully illustrates the brisk, nonbrisk, and absent categories of infiltration. Finally, a multivariate analysis comparing thickness, mitotic rate and presence of tumor infiltrating lymphocytes showed that only thickness and presence of tumor infiltrating lymphocytes are significant and independent positive histologic prognostic factors.
Relationship between LAT1 expression and response to platinum-based chemotherapy in non-small cell lung cancer patients with postoperative recurrence. (2011)

LAT1 expression may be useful for predicting response and outcome after systemic chemotherapy.