gebhart/patrepeval huggingface dataset:
Application of DNA typing methods to epidemiology and taxonomy of Candida species (1987)

Methods are described for extraction of DNA from the yeast form of Candida spp., followed by digestion and electrophoresis of DNA fragments. The resulting gel patterns (greater than 100 bands) were used to type Candida isolates. Four intense bands identified, three of which are present in each isolate (6 to 7, 3.7 or 4.2, and 2.5 to 3 kilobases), appear to be DNA encoding the rRNA. The methods proved to be both simple and reproducible. The patterns were shown to be stable through several hundred doublings from multiple single colonies. A survey of isolates showed that, on the basis of similarity of gel patterns, several Candida species could be sorted into mutually exclusive groups, and subgroups could be created. Analyses of this survey suggested the possible epidemiologic and taxonomic applications of these methods. DNA typing methods appear to offer important potential advantages over phenotyping methods. The methods provide a base for further epidemiologic studies and for further development of techniques, such as the use of cloned probes for studies of DNA homology.
Obesity and Type 2 Diabetes: The Twin Epidemic: Preface (2003)

In the past decade, we have witnessed an epidemic of both type 2 diabetes and obesity. The prevalence of type 2 diabetes has increased by 33% in the United States, and 62% of Americans are classified as obese (BMI ≥ 30 kg/m2) or overweight (BMI 25–29.9 kg/m2). The recent increase in the prevalence of obesity is closely paralleled by the increase in the prevalence of diabetes. Indeed, this new unprecedented phenomenon has been referred to as “diabesity.” There is a clear strong relationship between obesity and the risk for diabetes.

This From Research to Practice section provides an up-to-date review about advances …
Nationalism and Integration in Plural Society (2010)

This paper is with reference to both areas of research of an understanding of the political concept of nationalism and the social problems of integration inherent in plural societies. The political concept of nationalism is concerned with the term ‘integration’ in the fields of political and social geography respectively. The integration generally presumes the existence of an ethnically plural society in which each group is characterized by its own language or other self-conscious cultural qualities but the problem may also exist in a political system which is made up of once distinct independent political units with which people identified. Man’s diversity, however, is not always permitted self-expression within on political unit. If a society displays a largely homogenous identity within a given state area the problem of cultural pluralism is eliminated; on the other hand, due to accidents of history, to migration policies of the past or to the misguided concepts of boundary-drawing some states are forced to accommodate a heterogeneous society. Within the pluralist framework, a transaction pattern in the socio-economic and political system to a most probable voluntary incremental development of input conditions would be suggested for respective communities and creating a distinct political nationalism. The and improved oral and written communications in the plural societies are also suggested to engender mutual advantage, and to alter their unfriendly relation to be friendly, given the differences in ideologies, political and economic systems, considering societies of Switzerland or Singapore. Throughout these approaches, the degree of internal and, indeed, international tension and conflict could be significantly reduced, which gives lessons and benefits to the entire world community including the two divided Koreas in the peninsula.
Transformation of glucocorticoid and progesterone receptors to the DNA‐binding state (1987)

This brief review explores some recent observations relating to the structure of untransformed glucocorticoid and progesterone receptors and the mechanism by which the receptors are transformed to the DNA-binding state. In their molybdatestabilized, untransformed state, progesterone and glucocorticoid receptors exist as a heteromeric 8-9S complex containing one unit of steroid binding phosphoprotein and one or two units of the 90 kD heat shock protein hsp90. When the receptors are transformed, the steroid-binding protein dissociates from hsp90. In cytosol preparations, temperature-mediated dissociation proceeds much more rapidly in the presence of hormone. The dissociated receptor binds to DNA with high affinity, regardless of whether it is in the hormone-bound or the hormone-free state. These observations raise the possibility that the primary, and perhaps the only, role for the hormone is to promote dissociation of the receptor-hsp90 complex. Molybdate, vanadate, and tungstate inhibit receptor transformation to the DNA-binding form, an effect that appears to reflect the ability of these transition metal oxyanions to stabilize the complex between the steroid receptor and hsp90. By promoting the formation of disulfide bonds, hydrogen peroxide also stabilizes the glucocorticoid receptor-hsp90 complex and prevents receptor transformation. A small, heat-stable factor present in all cytosol preparations inhibits receptor transformation, and, when the factor is removed, glucocorticoid receptors are rapidly transformed. This ubiquitous factor has the physical properties of a metal anion, and it is proposed that molybdate and vanadate affect steroid receptor complexes by interacting with a metal anion-binding site that is normally occupied by this endogenous receptor-stabilizing factor.
Corticotropin-Releasing Hormone Induces Skin Mast Cell Degranulation and Increased Vascular Permeability, A Possible Explanation for Its Proinflammatory Effects* (1998)

Mast cells are involved in atopic disorders, often exacerbated by stress, and are located perivascularly close to sympathetic and sensory nerve endings. Mast cells are activated by electrical nerve stimulation and millimolar concentrations of neuropeptides, such as substance P (SP). Moreover, acute psychological stress induces CRH-dependent mast cell degranulation. Intradermal administration of rat/human CRH (0.1-10 microM) in the rat induced mast cell degranulation and increased capillary permeability in a dose-dependent fashion. The effect of CRH on Evans blue extravasation was stronger than equimolar concentrations of the mast cell secretagogue compound 48/80 or SP. The free acid analog of CRH, which does not interact with its receptors (CRHR), had no biological activity. Moreover, systemic administration of antalarmin, a nonpeptide CRHR1 antagonist, prevented vascular permeability only by CRH and not by compound 48/80 or SP. CRHR1 was also identified in cultured leukemic human mast cells using RT-PCR. The stimulatory effect of CRH, like that of compound 48/80 on skin vasodilation, could not be elicited in the mast cell deficient W/Wv mice but was present in their +/+ controls, as well as in C57BL/6J mice; histamine could still induce vasodilation in the W/Wv mice. Treatment of rats neonatally with capsaicin had no effect on either Evans blue extravasation or mast cell degranulation, indicating that the effect of exogenous CRH in the skin was not secondary to or dependent on the release of neuropeptides from sensory nerve endings. The effect of CRH on Evans blue extravasation and mast cell degranulation was inhibited by the mast cell stabilizer disodium cromoglycate (cromolyn), but not by the antisecretory molecule somatostatin. To investigate which vasodilatory molecules might be involved in the increase in vascular permeability, the CRH injection site was pretreated with the H1-receptor antagonist diphenhydramine, which largely inhibited the CRH effect, suggesting that histamine was involved in the CRH-induced vasodilation. The possibility that nitric oxide might also be involved was tested using pretreatment with a nitric oxide synthase inhibitor that, however, increased the effect of CRH. These findings indicate that CRH activates skin mast cells at least via a CRHR1-dependent mechanism leading to vasodilation and increased vascular permeability. The present results have implications for the pathophysiology and possible therapy of skin disorders, such as atopic dermatitis, eczema, psoriasis, and urticaria, which are exacerbated or precipitated by stress.
Alzheimer's Disease: Environmental Factors and Etiologic Hypotheses (1989)

A review of published reports on conventional and unconventional viruses, aluminum, neurotoxic metals and trace elements, neurotoxins of biological origin and immune systems, suggest that environmental factors, possibly multiple ones, play a significant role in the etiology of Alzheimer's disease. A complex interaction between genetic predisposition to this illness, natural aging processes, environmental factors over a life-time exposure and pathological alterations of the host immune system is proposed.
A transient association of γ-tubulin at the midbody is required for the completion of cytokinesis during the mammalian cell division (1995)

gamma-Tubulin, a relatively new member of the tubulin gene family, is localized primarily at the centrosome throughout the mammalian cell cycle and may play a key role in nucleation of cellular microtubule assembly. A transient association of gamma-tubulin at the cytoplasmic bridge of telophase mammalian cells, the midbody, is recently documented. Using immunogold electron microscopy and serial section reconstruction analysis, we show here that the transiently associated midbody gamma-tubulin is localized at the minus ends of microtubules in the midbody structure. Using antisense RNA methods we also demonstrate that a selective depletion of transiently associated midbody gamma-tubulin causes an abortive cytokinesis due to a failure in the morphogenesis of the midbody structure.
Whole-field visualisation and velocity measurement of an instantaneous transonic turbine flow (2002)

The work described in this paper represents a premiere in the application of Particle Image Velocimetry (PIV) to turbomachinery flows. This technique allowed the visualisation of the instantaneous transonic flow in the inter-blade passage of a rotating annular cascade at engine conditions. By means of photographic recording of flow tracers and specialised image processing, the instantaneous velocity over the whole field was measured with estimated accuracy between 2 and 5%. Furthermore, the vorticity map was created by means of differentiation and linear interpolation on a Delaunay triangular grid. From the superposition of sequential frames, a steady state velocity map was reconstructed.
Biotransformation in Double-Phase Systems: Physiological Responses of Pseudomonas putida DOT-T1E to a Double Phase Made of Aliphatic Alcohols and Biosynthesis of Substituted Catechols (2004)

Pseudomonas putida strain DOT-T1E is highly tolerant to organic solvents, with a logP(ow) (the logarithm of the partition coefficient of a solvent in a two-phase water-octanol system of > or =2.5. Solvent tolerant microorganisms can be exploited to develop double-phase (organic solvent and water) biotransformation systems in which toxic substrates or products are kept in the organic phase. We tested P. putida DOT-T1E tolerance to different aliphatic alcohols with a logP(ow) value between 2 and 4, such as decanol, nonanol, and octanol, which are potentially useful in biotransformations in double-phase systems in which compounds with a logP(ow) around 1.5 are produced. P. putida DOT-T1E responds to aliphatic alcohols as the second phase through cis-to-trans isomerization of unsaturated cis fatty acids and through efflux of these aliphatic alcohols via a series of pumps that also extrude aromatic hydrocarbons. These defense mechanisms allow P. putida DOT-T1E to survive well in the presence of high concentrations of the aliphatic alcohols, and growth with nonanol or decanol occurred at a high rate, whereas in the presence of an octanol double-phase growth was compromised. Our results support that the logP(ow) of aliphatic alcohols correlates with their toxic effects, as octanol (logP(ow) = 2.9) has more negative effects in P. putida cells than 1-nonanol (logP(ow) = 3.4) or 1-decanol (logP(ow) = 4). A P. putida DOT-T1E derivative bearing plasmid pWW0-xylE::Km transforms m-xylene (logP(ow) = 3.2) into 3-methylcatechol (logP(ow) = 1.8). The amount of 3-methylcatechol produced in an aliphatic alcohol/water bioreactor was 10- to 20-fold higher than in an aqueous medium, demonstrating the usefulness of double-phase systems for this particular biotransformation.
Role of Kruppel-Like Transcription Factors in Endothelial Biology (2007)

Krüppel-like factors are members of the zinc finger family of transcription factors that have been implicated as playing key roles in regulating cellular differentiation and tissue development. Studies over the past several years support an important role for this family of factors in vascular biology. This review summarizes the role of Krüppel-like factors in endothelial cell biology.
HiHCoHP-Toward a realistic communication model for hierarchical hyperclusters of heterogeneous processors (2002)

A parameterized model of hyperclusters of processors-clusters of clusters of... of clusters of processors-is formulated under which a hypercluster enjoys generality along three orthogonal axes: (1) Its processors are heterogeneous: they may have different computational powers (speed of computation and memory access). (2) Its constituent clusters are interconnected via a hierarchy of networks of possibly differing bandwidths and speeds. (3) Its clusters at each level of the hierarchy are heterogeneous: they may differ in size. The model accounts for architectural details such as the bandwidths and transit costs of both networks and their ports. The algorithmic tractability of the model is demonstrated via broadcast and reduction algorithms, which are predictably efficient in general and actually optimal in special circumstances.
Automatic Web API Composition for Semantic Data Mashups (2012)

Data mashups enable users to create new applications by combining Web APIs from several data sources. Although data mashups have become very popular over the last few years, there are several challenging issues when combining Web APIs into data mashups, especially when compatible APIs are manually discovered and composed by mash up developers. In this paper, we propose an approach for automatic discovery and composition of Web APIs using their semantic descriptions. This approach can be described as that of generating directed a cyclic graphs (DAGs) that can produce output satisfying a desired goal. We rapidly filter out APIs that are guaranteed not to involve the composition in order to produce the DAGs efficiently.
Sequential crosslinking to control cellular spreading in 3-dimensional hydrogels (2009)

With advanced understanding of how manipulations in material chemistry and structure influence cellular interactions, material control over cellular behavior (e.g., spreading) is becoming increasingly possible. In this example, we developed a novel process that utilizes different crosslinking mechanisms to provide gel environments that are either permissive or inhibitory to cellular spreading. To accomplish this, a multi-acrylated macromer (i.e., acrylated hyaluronic acid) was first crosslinked with an addition reaction using a matrix metalloprotease (MMP) cleavable peptide containing thiol groups. When an adhesive peptide was also coupled to the network, this environment permitted the spreading of encapsulated human mesenchymal stem cells (hMSCs), whereas control systems did not. If all acrylates were not consumed during the initial crosslinking step, a photoinitiated radical polymerization could be used to crosslink the remaining acrylates and inhibit cellular spreading with the production of covalent barriers. Variations in the ratio of the two crosslink types in individual constructs controlled the degradation and mechanical properties of the hydrogels, as well as the degree of spreading of encapsulated cells. Cell spreading was further controlled spatially with the use of photomasks. Overall, this new technology is an exciting and potentially valuable tool, both to provide new insights into the relationships between gel structure and cell behavior, and for eventual tissue-engineering applications where spatial control over cells is desired.
The Saccharomyces cerevisiae Checkpoint Gene BUB1 Encodes a Novel Protein Kinase (1994)

Normal cell multiplication requires that the events of mitosis occur in a carefully ordered fashion. Cells employ checkpoints to prevent cycle progression until some prerequisite step has been completed. To explore the mechanisms of checkpoint enforcement, we previously screened for mutants of Saccharomyces cerevisiae which are unable to recover from a transient treatment with a benzimidazole-related microtubule inhibitor because they fail to inhibit subsequent cell cycle steps. Two of the identified genes, BUB2 and BUB3, have been cloned and described (M. A. Hoyt, L. Totis, and B. T. Roberts, Cell 66:507-517, 1991). Here we present the characterization of the BUB1 gene and its product. Genetic evidence was obtained suggesting that Bub1 and Bub3 are mutually dependent for function, and immunoprecipitation experiments demonstrated a physical association between the two. Sequence analysis of BUB1 revealed a domain with similarity to protein kinases. In vitro experiments confirmed that Bub1 possesses kinase activity; Bub1 was able to autophosphorylate and to catalyze phosphorylation of Bub3. In addition, overproduced Bub1 was found to localize to the cell nucleus.
The role of neurotensin in physiologic and pathologic processes (2011)

The review highlights the wide array of biological processes in which neurotensin has a role, and summarizes the most recent advances in various fields of neurotensin research. The knowledge gained through this research has led to the development of first-in-class drugs for the treatment of various medical conditions, and it is clear that in the coming years some of these agents will be ready to move from the bench to the bedside in clinical trials.
RF power amplifiers for wireless communications (2000)

Linear PA Design. Conventional High-Efficiency Amplifier Modes. Class AB PAs at GHz Frequencies. Practical Design of Class AB PAs. Overdrive and the Class F Mode. Switching Mode Amplifiers for RF Applications. Switching PA Modes at GHz Frequencies. Signals, Modulation Systems, and PA Nonlinearities. Efficiency Enhancement Techniques. Power Amplifier Bias Circuit Design. Power Amplifier Architecture. PA Linearization Techniques.
Synthesis of Two Stable Nitrogen Analogues of S-Adenosyl-l-methionine (1999)

Homochiral syntheses of two stable nitrogen analogues of S-adenosyl-l-methionine (AdoMet) are described. In the first analogue, AzaAdoMet, the sulfonium center of AdoMet, is replaced by an N-methyl moiety whose pKa is 7.08. This provides a charge-switchable analogue of AdoMet whose ionic state is a function of the pH. A second analogue, MeAzaAdoMet, has a quaternary dimethylammonium group in place of the methylsulfonium center of AdoMet: thus, its ionic state is independent of pH.
Antitumor effect and potentiation of cytotoxic drugs activity in human cancer cells by ZD-1839 (Iressa), an epidermal growth factor receptor-selective tyrosine kinase inhibitor. (2000)

Transforming growth factor alpha (TGF-alpha) is an autocrine growth factor for human cancer. Overexpression of TGF-alpha and its specific receptor, the epidermal growth factor receptor (EGFR), is associated with aggressive disease and poor prognosis. The EGFR has been proposed as a target for anticancer therapy. Compounds that block ligand-induced EGFR activation have been developed. ZD-1839 (Iressa) is a p.o.-active, quinazoline derivative that selectively inhibits the EGFR tyrosine kinase and is under clinical development in cancer patients. The antiproliferative activity of ZD-1839 alone or in combination with cytotoxic drugs differing in mechanism(s) of action, such as cisplatin, carboplatin, oxaliplatin, paclitaxel, docetaxel, doxorubicin, etoposide, topotecan, and raltitrexed, was evaluated in human ovarian (OVCAR-3), breast (ZR-75-1, MCF-10A ras), and colon cancer (GEO) cells that coexpress EGFR and TGF-alpha. ZD-1839 inhibited colony formation in soft agar in a dose-dependent manner in all cancer cell lines. The antiproliferative effect was mainly cytostatic. However, treatment with higher doses resulted in a 2-4-fold increase in apoptosis. A dose-dependent supra-additive increase in growth inhibition was observed when cancer cells were treated with each cytotoxic drug and ZD-1839. The combined treatment markedly enhanced apoptotic cell death induced by single-agent treatment. ZD-1839 treatment of nude mice bearing established human GEO colon cancer xenografts revealed a reversible dose-dependent inhibition of tumor growth because GEO tumors resumed the growth rate of controls at the end of the treatment. In contrast, the combined treatment with a cytotoxic agent, such as topotecan, raltitrexed, or paclitaxel, and ZD-1839 produced tumor growth arrest in all mice. Tumors grew slowly for approximately 4-8 weeks after the end of treatment, when they finally resumed a growth rate similar to controls. GEO tumors reached a size not compatible with normal life in all control mice within 4-6 weeks and in all single agent-treated mice within 6-8 weeks after GEO cell injection. In contrast, 50% of mice treated with ZD-1839 plus topotecan, raltitrexed, or paclitaxel were still alive 10, 12, and 15 weeks after cancer cell injection, respectively. These results demonstrate the antitumor effect of this EGFR-selective tyrosine kinase inhibitor and provide a rationale for its clinical evaluation in combination with cytotoxic drugs.
A PNA4 Quadruplex (2004)

A tetrameric PNA, TGGG, has been shown to form an intermolecular G-quadruplex. Nanoelectrospray mass spectrometry, combined with solution-phase H/D exchange, established formation of a specific tetramolecular complex. UV melting studies show that this complex undergoes a quadruplex melting transition. This is a novel four-stranded structure that offers the gross structural features of a DNA quadruplex, but without the negatively charged backbone.
Director structure around a colloid particle suspended in a nematic liquid crystal (1996)

We analyze the director field around a spherical colloid particle with radial (homeotropic) anchoring on its surface. Depending on the relative strength of anchoring W, controlled by the parameter WR/K with K the Frank constant and R the particle radius, the director distribution may possess a singular ring of a -1/2 disclination in the equatorial plane. The equilibrium radius of this ring, at rigid radial anchoring, is ${\mathit{a}}^{\mathrm{*}}$\ensuremath{\approxeq}1.25R and only weakly depends on the disclination core energy. At small anchoring the director field is regular and weakly disturbed by the particle, there is a characteristic crossover ${\mathit{W}}^{\mathrm{*}}$ between the two regimes. We obtain the analytical expression for n( r), which decays as ${\mathit{r}}^{\mathrm{\ensuremath{-}}3}$sin2\ensuremath{\theta} away from the particle, and compare it with the exact numerical solution in the highly distorted nonlinear regime. \textcopyright{} 1996 The American Physical Society.