gebhart/patrepeval huggingface dataset:
Organ dysfunction following hemorrhage and sepsis: mechanisms and therapeutic approaches (Review). (1999)

Despite significant advances in the management of trauma victims, sepsis and the ensuing multiple organ failure remain the leading causes of death in the surgical intensive care unit. Although much effort has been focused on the mediators released in large quantities following shock and sepsis, blockade of mediators such as proinflammatory cytokines has not yet resulted in a successful therapy. However, as more studies are forthcoming, the mechanisms responsible for cell and organ dysfunctions following trauma-hemorrhage and sepsis are becoming better understood, and promising new therapeutic approaches are currently being evaluated. In order to understand the precise mechanisms responsible for cellular dysfunction and consequently irreversible organ damage and multiple organ failure, it is important to correlate various pathophysiological changes with mediators and signal transduction pathways at the cellular and subcellular level. In this review we focus first on factors and mediators responsible for producing cell and organ dysfunctions, especially hepatocellular dysfunction, following trauma, hemorrhagic shock, and sepsis. The changes in signaling transduction pathways will also be discussed, specifically the role of mitogen-activated protein kinases, transcription factors, nitric oxide, heat shock proteins, and inflammatory cytokines in the development of cell and organ dysfunctions following trauma-hemorrhage and sepsis. Moreover, potential therapeutic approaches for improving cell and organ functions under adverse circulatory conditions are included.
Modified Indirect Porcine Circovirus (PCV) Type 2-Based and Recombinant Capsid Protein (ORF2)-Based Enzyme-Linked Immunosorbent Assays for Detection of Antibodies to PCV (2002)

Postweaning multisystemic wasting syndrome of swine associated with porcine circovirus (PCV) is a recently reported and economically important disease. Simple and reliable diagnostic methods are needed for detecting antibodies to PCV type 2 (PCV2) for monitoring of PCV infection. Here, we report the development of two modified indirect enzyme-linked immunosorbent assays (ELISAs): a PCV2 ELISA based on cell-culture-propagated PCV2 and an ORF2 ELISA based on recombinant major capsid protein. PCV2 and ORF2 ELISA detected antibodies to PCV2 and the capsid protein, respectively, in sera from pigs experimentally infected with PCV2 as early as 14 and 21 days postinoculation (dpi). The kinetics of the antibody response to PCV2 and the major capsid protein were similar. Repeatability tests revealed that the coefficients of variation of positive sera within and between runs for both assays were less than 30%. To validate the assays, PCV2 and ORF2 ELISAs were performed with 783 serum samples of young and adult pigs collected from different herds in the Midwestern United States and compared with an indirect immunofluorescent assay (IIF). Six out of 60 samples collected from nursery and growing pigs in 1987 were positive by both ELISA and IIF. Compared with IIF, the diagnostic sensitivity, specificity, and accuracy of PCV2 and ORF2 ELISAs were similar (>90%). The tests showed no cross-reactivity with antibodies to porcine parvovirus and porcine reproductive and respiratory syndrome virus. There was good agreement between the two ELISAs and between the ELISAs and IIF. The availability of the two ELISAs should accelerate our understanding of the host immune response to PCV2 and facilitate the development of prevention and control strategies by elucidating the ecology of PCV2 within swine populations.
Numerical study on the generation of downgoing S-waves by a vertical force acting close to a step-like topography (1996)

Abstract I present detailed numerical experiments on a recently proposed S-wave generation method and show the excitation characteristics of the downgoing S-wave caused by a vertical impact acting close to a step-like topography. The geophysicists' group of Akita University recently studied and confirmed this phenomenon by in-situ measurements and named it the "pit effect." The numerical simulation is performed in 2-D space by the indirect boundary-element method using the Green's function for a homogeneous unbounded medium. The results show that the pit effect is a practical S-wave generator vertical seismic profiling (VSP) and refraction surveys. The generation of a vertical downgoing S-wave does not require any special machinery, so the pit effect can be used in many situations and especially in remote areas and difficult enviroments such as swamps and steep mountain ranges.
A single nucleotide polymorphism in the matrix metalloproteinase-1 promoter creates an Ets binding site and augments transcription. (1998)

Matrix metalloproteinases (MMPs) facilitate cellular invasion by degrading the extracellular matrix, and their regulation is partially dependent on transcription. Binding sites for members of the Ets family of transcription factors are present within MMP promoters and are potent positive regulators. We report a single nucleotide polymorphism at -1607 bp in the MMP-1 promoter, where an additional guanine (G) creates an Ets binding site, 5'-GGA-3'. This polymorphism displays significantly higher transcription in normal fibroblasts and in melanoma cells than the 1 G polymorphism, and it binds substantially more nuclear extract and recombinant ETS-1. Analysis of control DNAs from the Center d'Etude du Polymorphisme Humain pedigrees reveals that this polymorphism is not a mutation, with a frequency of the 2 G polymorphism at 30%. In contrast, in eight tumor cell lines, this frequency increased to 62.5% (P < 0.0001). Thus, this MMP-1 polymorphism contributes to increased transcription, and cells expressing the 2 G polymorphism may provide a mechanism for more aggressive matrix degradation, thereby facilitating cancer progression.
Masquerade Detection Augmented With Error Analysis (2004)

A masquerade attack, in which one user impersonates another, may be one of the most serious forms of computer abuse. Automatic discovery of masqueraders is sometimes undertaken by detecting significant departures from normal user behavior, as represented by a user profile formed from system audit data. A major obstacle for this type of research is the difficulty in obtaining such system audit data, largely due to privacy concerns. An immense contribution in this regard has been made by Schonlau et al., who have made available UNIX command-line data from 50+ users collected over a number of months. Most of the research in this area has made use of this dataset, so this paper takes as its point of departure the Schonlau et al. dataset and a recent series of experiments with this data framed by the same researchers . In extending that work with a new classification algorithm, a 56% improvement in masquerade detection was achieved at a corresponding false-alarm rate of 1.3%. In addition, encouraging results were obtained at a more realistic sequence length of 10 commands (as opposed to sequences of 100 commands used by Schonlau et al.). A detailed error analysis, based on an alternative configuration of the same data, reveals a serious flaw in this type of data which hinders masquerade detection and indicates some steps that need to be taken to improve future results. The error analysis also demonstrates the insights that can be gained by inspecting decision errors, instead of concentrating only on decision successes.
Electromagnetic wave absorbers and anechoic chambers through the years (1973)

A historical summary of the development of microwave absorbing materials and anechoic chambers is presented.
Low Light CMOS Contact Imager with an Integrated Poly-Acrylic Emission Filter for Fluorescence Detection (2010)

This study presents the fabrication of a low cost poly-acrylic acid (PAA) based emission filter integrated with a low light CMOS contact imager for fluorescence detection. The process involves the use of PAA as an adhesive for the emission filter. The poly-acrylic solution was chosen due its optical transparent properties, adhesive properties, miscibility with polar protic solvents and most importantly its bio-compatibility with a biological environment. The emission filter, also known as an absorption filter, involves dissolving an absorbing specimen in a polar protic solvent and mixing it with the PAA to uniformly bond the absorbing specimen and harden the filter. The PAA is optically transparent in solid form and therefore does not contribute to the absorbance of light in the visible spectrum. Many combinations of absorbing specimen and polar protic solvents can be derived, yielding different filter characteristics in different parts of the spectrum. We report a specific combination as a first example of implementation of our technology. The filter reported has excitation in the green spectrum and emission in the red spectrum, utilizing the increased quantum efficiency of the photo sensitive sensor array. The thickness of the filter (20 μm) was chosen by calculating the desired SNR using Beer-Lambert's law for liquids, Quantum Yield of the fluorophore and the Quantum Efficiency of the sensor array. The filters promising characteristics make it suitable for low light fluorescence detection. The filter was integrated with a fully functional low noise, low light CMOS contact imager and experimental results using fluorescence polystyrene micro-spheres are presented.
Nanoelectrospray Ionization of Protein Mixtures:  Solution pH and Protein pI (2004)

Solutions consisting of single proteins and mixtures of proteins at different pH values have been subjected to both positive ion and negative ion nanoelectrospray ionization to study the influence of solvent pH and protein pI on the ionization responses of proteins. As has been noted previously, it is possible to form protein ions of one polarity despite the fact that the proteins are present as the opposite polarity in solution. However, total response under this condition tends to be at least an order of magnitude less than the condition in which the nanoelectrospray ionization polarity is the same as the net charge of the proteins in solution. Furthermore, maximum signals in positive ion mode were noted when the pH value of the solution was 4-5 units lower than the protein pI. In the negative ion mode, maximum protein anion signals were observed when the pH was roughly 5 units higher than the protein pI. While only small changes in the abundance-weighted average charge were noted as a function of solution conditions, the extent of sodium ion incorporation was seen to depend strongly on the relationship between net protein charge in solution and gas-phase ion polarity. Sodium ion incorporation was minimized under conditions of maximum signal (i.e., low pH positive ion mode and high pH negative ion mode). Sodium ion incorporation was highest when the protein ion polarities in solution and the gas phase were opposite. These observations are consistent with the charged residue model for electrospray ionization and suggest that a degree of selectivity for electrospray ionization applied to protein mixtures can be realized via judicious selection of solution pH and ionization polarity. Furthermore, the relative extent of sodium ion incorporation under a given set of conditions appears to correlate, at least qualitatively, with protein pI.
Androgen receptor phosphorylation and stabilization in prostate cancer by cyclin-dependent kinase 1 (2006)

Androgen receptors (ARs) are phosphorylated at multiple sites in response to ligand binding, but the kinases mediating AR phosphorylation and the importance of these kinases in AR function have not been established. Here we show that cyclin-dependent kinase 1 (Cdk1) mediates AR phosphorylation at Ser-81 and increases AR protein expression, and that Cdk1 inhibitors decrease AR Ser-81 phosphorylation, protein expression, and transcriptional activity in prostate cancer (PCa) cells. The decline in AR protein expression mediated by the Cdk inhibitor roscovitine was prevented by proteosome inhibitors, indicating that Cdk1 stabilizes AR protein, although roscovitine also decreased AR message levels. Analysis of an S81A AR mutant demonstrated that this site is not required for transcriptional activity or Cdk1-mediated AR stabilization in transfected cells. The AR is active and seems to be stabilized by low levels of androgen in "androgen-independent" PCas that relapse subsequent to androgen-deprivation therapy. Significantly, the expression of cyclin B and Cdk1 was increased in these tumors, and treatment with roscovitine abrogated responses to low levels of androgen in the androgen-independent C4-2 PCa cell line. Taken together, these findings identify Cdk1 as a Ser-81 kinase and indicate that Cdk1 stabilizes AR protein by phosphorylation at a site(s) distinct from Ser-81. Moreover, these results indicate that increased Cdk1 activity is a mechanism for increasing AR expression and stability in response to low androgen levels in androgen-independent PCas, and that Cdk1 antagonists may enhance responses to androgen-deprivation therapy.
Detection of antibody-accessible proteins on the cell surface of Haemophilus influenzae type b (1981)

A radioimmunoprecipitation method has been devised which permits the direct identification of those proteins which are both exposed on the cell surface of Haemophilus influenzae type b and accessible to antibody. Both extrinsically and intrinsically radiolabeled cells of this organism were employed as the sources of antigen in radioimmunoprecipitation experiments which involved incubation of intact bacterial cells with antisera. Several different proteins, ranging in apparent molecular weight from 33,000 to 160,000, were shown to be accessible to antibody on the cell surface of this pathogen.
Optical multi-mode interference devices based on self-imaging: principles and applications (1995)

This paper presents an overview of integrated optics routing and coupling devices based on multimode interference. The underlying self-imaging principle in multimode waveguides is described using a guided mode propagation analysis. Special issues concerning the design and operation of multimode interference devices are discussed, followed by a survey of reported applications. It is shown that multimode interference couplers offer superior performance, excellent tolerance to polarization and wavelength variations, and relaxed fabrication requirements when compared to alternatives such as directional couplers, adiabatic X- or Y-junctions, and diffractive star couplers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ethylene is an endogenous stimulator of cell division in the cambial meristem of Populus (2009)

The plant hormone ethylene is an important signal in plant growth responses to environmental cues. In vegetative growth, ethylene is generally considered as a regulator of cell expansion, but a role in the control of meristem growth has also been suggested based on pharmacological experiments and ethylene-overproducing mutants. In this study, we used transgenic ethylene-insensitive and ethylene-overproducing hybrid aspen (Populus tremula x tremuloides) in combination with experiments using an ethylene perception inhibitor [1-methylcyclopropene (1-MCP)] to demonstrate that endogenous ethylene produced in response to leaning stimulates cell division in the cambial meristem. This ethylene-controlled growth gives rise to the eccentricity of Populus stems that is formed in association with tension wood.
Trastuzumab after Adjuvant Chemotherapy in HER2-Positive Breast Cancer (2005)

One year of treatment with trastuzumab after adjuvant chemotherapy significantly improves disease-free survival among women with HER2-positive breast cancer. (ClinicalTrials.gov number, NCT00045032.)
Improving the Health of Workers in Indoor Environments: Priority Research Needs for a National Occupational Research Agenda (2002)

Indoor nonindustrial work environments were designated a priority research area through the nationwide stakeholder process that created the National Occupational Research Agenda. A multidisciplinary research team used member consensus and quantitative estimates, with extensive external review, to develop a specific research agenda. The team outlined the following priority research topics: building-influenced communicable respiratory infections, building-related asthma/allergic diseases, and nonspecific building-related symptoms; indoor environmental science; and methods for increasing implementation of healthful building practices. Available data suggest that improving building environments may result in health benefits for more than 15 million of the 89 million US indoor workers, with estimated economic benefits of $5 to $75 billion annually. Research on these topics, requiring new collaborations and resources, offers enormous potential health and economic returns.
Keratinocyte-specific Pten deficiency results in epidermal hyperplasia, accelerated hair follicle morphogenesis and tumor formation. (2003)

PTEN is a tumor suppressor gene mutated in many human cancers. We used the Cre-loxP system to generate a keratinocyte-specific null mutation of Pten in mice (k5Pten(flox/flox) mice). k5Pten(flox/flox) mice exhibit wrinkled skin because of epidermal hyperplasia and hyperkeratosis and ruffled, shaggy, and curly hair. Histological examination revealed that skin morphogenesis is accelerated in k5Pten(flox/flox) mice. Within 3 weeks of birth, 90% of k5Pten(flox/flox) mice die of malnutrition possibly caused by hyperkeratosis of the esophagus. All k5Pten(flox/flox) mice develop spontaneous tumors within 8.5 months of birth, and chemical treatment accelerates the onset of tumors. k5Pten(flox/flox) keratinocytes are hyperproliferative and resistant to apoptosis and show increased activation of the Pten downstream signaling mediators Akt/protein kinase B (PKB) and extracellular signal-regulated kinase. Pten is thus an important regulator of normal development and oncogenesis in the skin.
PTK1, a novel protein kinase required for proliferation of human melanocytes. (1994)

We have identified and characterized PTK1, a novel human non-receptor protein kinase. Partial PTK1 cDNA was initially isolated by RT-PCR from mRNA of normal human melanocytes. Northern blot hybridization detected a 3.8-kb PTK1 mRNA in all tissues and cell types studied. Nucleotide sequence analysis of a full-length PTK1 cDNA showed it to encode an 847-amino acid polypeptide with an amino-terminal SH3 domain, a kinase catalytic domain, a leucine zipper-like domain, and a carboxyl proline-rich domain. The PTK1 kinase domain contains motifs generally considered diagnostic of serine/threonine kinases but also contains amino acids highly conserved among the tyrosine kinases. This suggests that PTK1 is a serine/threonine kinase, but one very closely related to the tyrosine kinase superfamily. When normal human melanocytes were exposed to antisense PTK1 oligonucleotide, cell growth was inhibited, whereas a corresponding sense oligonucleotide had no inhibitory effect. These data indicate that PTK1 plays an important role in the proliferation of normal human melanocytes.
Isolation and characterization of the human nucleophosmin/B23 (NPM) gene: identification of the YY1 binding site at the 5' enhancer region (1997)

NPM (nucleophosmin/B23) is a major nucleolar protein which is 20 times more abundant in tumor or proliferating cells than in normal resting cells. Recently, it was found that NPM gene is located at the breakpoints of the t(2:5), t(3:5) and t(5:17) chromosome translocation. To understand the human NPM gene's structure and regulation, four genomic clones were isolated from the human chromosome 5 library and their DNA sequences analyzed. The human NPM gene has 12 exons of sizes ranging from 58 to 358 bp. The chromosome breakpoint for t(2:5) and t(5:17) translocation is within intron 4 and the breakpoint for t(3:5) translocation is within intron 6. The initiation site is located 96 bp upstream from the ATG site. A typical TATA box (at -25 nt) and a GC box (at -65 nt) were identified in the promoter region. We identified two gel-shift bands (A and B) with DNA fragment E (-741/-250 nt) by EMSA. A DNA footprint was observed at (-371/-344 nt) with the nuclear extract. A double stranded DNA with the footprint sequence (-371/-344 nt) competed the formation of gel-shift bands A and B in EMSA suggesting that proteins A and B bind to the footprint region. We confirmed that protein A is transcription factor YY1. These results suggest that YY1 may play a role in NPM gene expression. This is the first report on human NPM gene structure and sequence.
Self-Assembling Cages from Coiled-Coil Peptide Modules (2013)

An ability to mimic the boundaries of biological compartments would improve our understanding of self-assembly and provide routes to new materials for the delivery of drugs and biologicals and the development of protocells. We show that short designed peptides can be combined to form unilamellar spheres approximately 100 nanometers in diameter. The design comprises two, noncovalent, heterodimeric and homotrimeric coiled-coil bundles. These are joined back to back to render two complementary hubs, which when mixed form hexagonal networks that close to form cages. This design strategy offers control over chemistry, self-assembly, reversibility, and size of such particles.
Efficacy and Safety of Intranasal Peptide YY3–36 for Weight Reduction in Obese Adults (2007)

Intranasal PYY(3-36) as administered at these intervention doses and preprandial timing is not efficacious in inducing weight loss in obese patients after 12 wk of treatment.