gebhart/patrepeval huggingface dataset:
EVOLUTION OF GENOME SIZE IN PINES (PINUS) AND ITS LIFE-HISTORY CORRELATES: SUPERTREE ANALYSES (2004)

Genome size has been suggested to be a fundamental biological attribute in determining life-history traits in many groups of organisms. We examined the relationships between pine genome sizes and pine phylogeny, environmental factors (latitude, elevation, annual rainfall), and biological traits (latitudinal and elevational ranges, seed mass, minimum generation time, interval between large seed crops, seed dispersal mode, relative growth rate, measures of potential and actual invasiveness, and level of rarity). Genome sizes were determined for 60 pine taxa and then combined with published values to make a dataset encompassing 85 species, or 70% of species in the genus. Supertrees were constructed using 20 published source phylogenies. Ancestral genome size was estimated as 32 pg. Genome size has apparently remained stable or increased over evolutionary time in subgenus Strobus, while it has decreased in most subsections in subgenus Pinus. We analyzed relationships between genome size and life-history variables using cross-species correlations and phylogenetically independent contrasts derived from supertree constructions. The generally assumed positive relation between genome size and minimum generation time could not be confirmed in phylogenetically controlled analyses. We found that the strongest correlation was between genome size and seed mass. Because the growth quantities specific leaf area and leaf area ratio (and to a lesser extent relative growth rate) are strongly negatively related to seed mass, they were also negatively correlated with genome size. Northern latitudinal limit was negatively correlated with genome size. Invasiveness, particularly of wind-dispersed species, was negatively associated with both genome size and seed mass. Seed mass and its relationships with seed number, dispersal mode, and growth rate contribute greatly to the differences in life-history strategies of pines. Many life-history patterns are therefore indirectly, but consistently, associated with genome size.
Hyperresponsive febrile reactions to interleukin (IL) 1α and IL-1β, and altered brain cytokine mRNA and serum cytokine levels, in IL-1β-deficient mice (1997)

IL-1beta is an endogenous pyrogen that is induced during systemic lipopolysaccharide (LPS)- or IL-1-induced fever. We have examined the fever and cytokine responses following i.p. injection of IL-1 agonists, IL-1alpha and IL-1beta, and compared these with response to LPS (i.p.) in wild-type and IL-1beta-deficient mice. The IL-1beta deficient mice appear to have elevated body temperature but exhibit a normal circadian temperature cycle. Exogenously injected IL-1beta, IL-1alpha, or LPS induced hyperresponsive fevers in the IL-1beta-deficient mice. We also observed phenotypic differences between wild-type and IL-1beta-deficient mice in hypothalamic basal mRNA levels for IL-1alpha and IL-6, but not for IL-1beta-converting enzyme or IL-1 receptor type I or type II. The IL-1alpha mRNA levels were down-regulated, whereas the IL-6 mRNA levels were up-regulated in the hypothalamus of IL-1beta-deficient mice as compared with wild-type mice. The IL-1beta-deficient mice also responded to LPS challenge with significantly higher serum corticosterone and with lower serum tumor necrosis factor type alpha levels than the wild-type mice. The data suggest that, in the redundant cascade of proinflammatory cytokines, IL-1beta plays an important but not obligatory role in fever induction by LPS or IL-1alpha, as well as in the induction of serum tumor necrosis factor type alpha and corticosterone responses either by LPS or by IL-1alpha or IL-1beta.
Security engineering of lattice-based policies (2002)

Describes an algebraic approach to the security engineering of lattice policies. The approach has two main goals. First, it seeks to model access control policies with anti-symmetry, reflexivity and transitivity exceptions using a lattice, and to propose an information flow security definition for the resulting set of policies (POL). Second, it supports a constructive approach to policy specification through an algebraic structure (POL, AND, OR, NOT, /spl equiv/, /spl les/). This structure is homomorphic to Boolean algebra. The approach's goals and design decisions are influenced by the context in which it is being used: a library of reusable security components with tools to facilitate their reuse for securing application systems.
Purification and Functional Characterization of Factor I (2013)

Factor I (FI) is a soluble, 88 kDa glycoprotein present in plasma at a concentration of approximately 35 mg/L. FI inhibits all complement pathways as it degrades activated C4b and C3b when these are bound to a cofactor such as C4b-binding protein or factor H. Here, we describe a method for purification of FI from human plasma, which is based on affinity chromatography followed by anion exchange chromatography. We also describe a functional assay, in which activity of FI can be assessed.
Conditional suicide system of Escherichia coli released into soil that uses the Bacillus subtilis sacB gene (1993)

The sacB gene from Bacillus subtilis confers sucrose sensitivity upon gram-negative bacteria. The gene was investigated for use as a potential conditional suicide system for Escherichia coli released into soil. To ensure against the loss of the cell death function encoded under nonselective conditions, the nptI-sacR-B suicide cassette was inserted into the E. coli chromosome by using a circular nonreplicative integration vector. Stability studies yielded no loss of the suicide cassette in the integrated E. coli EL1026 strain. sacB induction in the absence of a selective pressure resulted in a lysis efficiency of up to 99.9%. The microcosm experiments confirmed the ability of the suicide cassette to limit the growth and reduce the survival of E. coli strains released into soil. Sucrose addition to sterile soil resulted in a 10(-3)-fold reduction of the final E. coli population density. sacB induction prevented the proliferation and triggered the rapid disappearance of E. coli from natural soil. Mutation to sucrose tolerance occurred at a frequency of 10(-5), making E. coli EL1026 a potential counterselectable donor strain for gene transfer studies. Specificity and potential adaptability to a wide range of gram-negative bacteria are additional conveniences of this conditional suicide system for the containment and counterselection of engineered microorganisms.
Copy number variation in the genome; the human <i>DMD</i> gene as an example (2006)

Recent developments have yielded new technologies that have greatly simplified the detection of deletions and duplications, i.e., copy number variants (CNVs). These technologies can be used to screen for CNVs in and around specific genomic regions, as well as genome-wide. Several genome-wide studies have demonstrated that CNV in the human genome is widespread and may include millions of nucleotides. One of the questions that emerge is which sequences, structures and/or processes are involved in their generation. Using as an example the human DMD gene, mutations in which cause Duchenne and Becker muscular dystrophy, we review the current data, determine the deletion and duplication profile across the gene and summarize the information that has been collected regarding their origin. In addition we discuss the methods most frequently used for their detection, in particular MAPH and MLPA.
Inferring Activities from Interactions with Objects (2004)

A key aspect of pervasive computing is using computers and sensor networks to effectively and unobtrusively infer users' behavior in their environment. This includes inferring which activity users are performing, how they're performing it, and its current stage. Recognizing and recording activities of daily living is a significant problem in elder care. A new paradigm for ADL inferencing leverages radio-frequency-identification technology, data mining, and a probabilistic inference engine to recognize ADLs, based on the objects people use. We propose an approach that addresses these challenges and shows promise in automating some types of ADL monitoring. Our key observation is that the sequence of objects a person uses while performing an ADL robustly characterizes both the ADL's identity and the quality of its execution. So, we have developed Proactive Activity Toolkit (PROACT).
Light-induced electron transfer of porphyrin triad for photoelectric conversion (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLight-induced electron transfer of porphyrin triad for photoelectric conversionXiang Dong Wang, Bao Wen Zhang, Jian Wei Bai, Yi Cao, Xu Rui Xiao, and Jing Mei XuCite this: J. Phys. Chem. 1992, 96, 7, 2886–2891Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/j100186a020https://doi.org/10.1021/j100186a020research-articleACS PublicationsRequest reuse permissionsArticle Views244Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
CD73 Expression Is an Independent Prognostic Factor in Prostate Cancer (2015)

Our study revealed that CD73 is an independent prognostic factor in prostate cancer. Our data support a model in which CD73 expression in the prostate epithelium suppresses immunosurveillance by CD8(+) T cells, whereas CD73 expression in the tumor stroma reduces NF-κB signaling in tumor cells via A2B adenosine receptor signaling. CD73 expression, including in normal adjacent prostate epithelium, can thus effectively discriminate between aggressive and indolent forms of prostate cancer.
Functional Polymer Brushes in Aqueous Media from Self-Assembled and Surface-Initiated Polymers (2008)

This review focuses on the behavior of single-component, water-soluble neutral and charged brushes. Selected examples illustrate how solvation effects, hydrophobic interactions, and electrostatic interactions create complex behaviors not easily captured in mean-field treatments. In particular, we distinguish between two classes of polymer brushes: those that can be described classically within the context of generalized van der Waals potentials and those that can be described by model-dependent potentials arising from specific interactions. In classical systems, only a few global parameters are needed to predict behavior. Nonclassical systems, in contrast, necessitate several local details, which do not necessarily lead to universal scaling laws. Although these nonclassical interactions present unique opportunities for engineering functional surfaces, they also present new challenges for designing well-defined systems with precise control over distributions in the degree of polymerization and tethering density.
Targeting antigen to CD40 reinforces dendritic cells to cross-prime antigen-specific CD8+ T cells (APP3P.110) (2015)

Abstract Dendritic cells are major antigen-presenting cells that can efficiently cross-prime antigen-specific CD8+ T cells. Thus, targeting antigen to dendritic cells via surface receptors is an appealing strategy to mount CD8+ T cell-mediated immunity against intracellular pathogens and cancers. Nonetheless, which targeted receptor is the most efficient at priming CD8+ T cells remains elusive. Herein, we report the superior function of CD40 over nine different lectins and scavenger receptors at priming antigen-specific CD8+ T cells. A quantitative analysis of intracellular trafficking of antibody-bound receptors revealed that αCD40 monoclonal antibody localized mainly at the plasma membrane and subsequently accumulated at early endocytic compartments whereas αLOX-1 and αDectin-1 monoclonal antibodies localized at both early and late endocytic compartments in dendritic cells. Regardless of the differences in their subcellular localizations, targeting antigen to CD40 and lectins resulted in the same pattern of peptide epitope-specific IFNg+CD8+ T cell responses. We also report that poly(I:C) can significantly enhance both CD8+ and CD4+ T cell responses elicited by targeting antigen to CD40 in both human in vitro and in human CD40 transgenic mouse in vivo settings. This study provides key information for the rational design of DC-targeting vaccines against cancers and intracellular pathogens.
Binding of G-Quadruplex-interactive Agents to Distinct G-Quadruplexes Induces Different Biological Effects in MiaPaCa Cells (2005)

Our previous studies have demonstrated the preference of telomestatin for intramolecular, rather than the intermolecular, G-quadruplex structures, while TiMPyP4 has selectivity for intermolecular over intramolecular G-quadruplex structures. However, it was not clear whether the difference in the selectivity between two different G-quadruplex-interactive agents could determine the corresponding biological effects in cultured human tumor cells. Here we evaluated the biological effects of both TMPyP4 and telomestatin in the human pancreatic carcinoma cell line (MiaPaCa) using subtoxic and cytotoxic concentrations. The cytotoxicity of these agents against MiaPaCa cells is quite different, and the IC50 of telomestatin (0.5 microM) is about 100 times less than that of TMPyP4 (50 microM). At IC50 concentrations, TMPyP4 induced anaphase bridge formation in MiaPaCa cells, while telomestatin failed to induce anaphase bridge formation. At subtoxic concentrations, TMPyP4 induced MiaPaCa cell growth arrest, senescence, apoptosis, and telomere length shortening within 5 weeks, while similar biological effects were evident after 12 weeks following treatment with telomestatin. Our data suggest that binding of G-quadruplex-interactive agents to distinct G-quadruplexes could induce different biological effects in human cancer cells.
Two user location strategies for personal communications services (1994)

The vision of nomadic personal communications is the ubiquitous availability of services to facilitate the exchange of information between nomadic end users independent of time, location, on access arrangements. To realize this, it is necessary to locate users who move from place to place. The strategies commonly proposed are two-level hierarchical strategies, which maintain a system of home and visited databases/spl mdash/home location register (HLR) and visitor location register (VLR)/spl mdash/to keep track of user locations. Two standards exist for carrying out two-level hierarchical strategies using HLRs and VLRs. The standard commonly used in North America is the Electronics Industry Association/Telecommunications Industry Association (EIA/TIA) Interim Standard 41 (IS-41), and in Europe the Global System for Mobile Communications (GSM). The authors introduce these two strategies for locating users and provide a tutorial on their usage. Different forms of mobility in the context of PCS and a reference model for a PCS architecture are discussed. The user location strategies specified in the IS-41 and GSM standards are described, and then, using a simple example, a simplified analysis of the database loads generated by each strategy is presented. Also briefly discussed are possible modifications to these protocols that are likely to result in significant benefits by reducing query and update rate to databases and/or reducing the signaling traffic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Potential antimalarials. II. N4-Substituted 2-Methoxy(and 2-hydroxy)-1,5-naphthyridin-4-amines (1984)

Several new N4-substituted 2-methoxy(and 2-hydroxy)-1,5-naphthyridin-4-amines have been prepared from ethyl 3-aminopyridine-2-carboxylate. 2,4-Dichloro-1,5-naphthyridine with methanolic sodium methoxide gave 4-chloro-2-methoxy-1,5-naphthyridine but with methanolic hydrogen chloride afforded 4-chloro-1,5-naphthyridin-2-ol. The N4-substituted 1,5-naphthyridin-4-amines showed no significant antimalarial activity compared to chloroquine or primaquine in a preliminary in vivo screen against Plasmodium vinckei vinckei in mice.
Autonomous Appliance Scheduling for Household Energy Management (2013)

The advancement of renewable energy technologies has seen the emergence of customer owned grid tied wind and solar microgrids. These microgrids offer an opportunity to energy users to lower their energy costs as well as enabling the power suppliers to regulate the utility grid. However, the integration of the renewable energy based sources into the smart grid increases the complexity of the main grid. The success of this scheme will be heavily reliant on accurate real-time information exchange between the microgrid, the main grid, and the consumers. The communication between these agents will be critical in implementation of intelligent decisions by the smart grid. The microgrids will be required to relay energy forecasts information to the utility grid. Similarly, customers will be expected to submit energy demand schedules, to actively monitor energy price signals, to participate in energy bids, and to respond to energy management signals in real time. This kind of grid-user interaction will be overwhelming and could result in consumer apathy. There is therefore a need to develop smart systems that will autonomously execute all these tasks without the prompting of the customers. This paper presents one such approach. In this study, we proposed a demand side energy management for a grid connected household with a locally generated photovoltaic energy. To ensure efficient household energy management, smart scheduling of electrical appliances has also been presented.
Several Mutations in the Melanocortin-4 Receptor Gene Including a Nonsense and a Frameshift Mutation Associated with Dominantly Inherited Obesity in Humans (1999)

The melanocortin-4 receptor gene (MC4-R) has been implicated in weight regulation. Recently, two independent groups reported frameshift mutations associated with a dominant form of obesity (1, 2). We screened the coding region of the MC4-R in 306 extremely obese children and adolescents (mean body mass index: BMI 34.4 +/- 6.6 kg/m2), 25 healthy underweight students (mean BMI 17.1 +/- 0.8 kg/m2), 52 normal weight individuals (mean BMI 22.0 +/- 1.0 kg/m2), 51 inpatients with anorexia nervosa (AN, DSM IV criteria, mean BMI 14.3 +/- 1.5 kg/m2) and 27 patients with bulimia nervosa (BN, DSM IV criteria, mean BMI 21.7 +/- 5.8 kg/m2) by single strand conformation polymorphism analysis (SSCP). Several mutations were identified, including the frameshift mutation described (1). The mutations were as follows: a) The deletion of 4 bp (delta of CTCT at codon 211) results in a frameshift, thus rendering a truncated protein. This mutation has been assumed to be associated with dominantly-inherited morbid obesity in humans (1). Both the index patient (BMI 42.06 kg/m2, height 171 cm, age 19.6 years) and her mother (BMI 37.55 kg/m2, height 164 cm, age 42.5 years) were heterozygous for the deletion. b) A nonsense mutation at position 35 of the MC4-R was detected in two obese probands (BMI 31.29 kg/m2 and BMI 45.91 kg/m2). This mutation leads to a truncated protein that encompasses the N-terminal extracellular domain. Both carriers additionally showed (c) a missense mutation (Asp-37-Val). In both of these cases Tyr-35-Stop and Asp-37-Val were maternally transmitted, thus these variations form a haplotype. d) e) A male obese proband harbored two missense mutations (Ser-30-Phe, Gly-252-Ser). f)-i) Four different missense mutations (Pro-78-Leu, Thr-112-Met, Arg-165-Trp, Ile-317-Thr) were detected in four different male probands, respectively. All of these mutations (a to i) were found solely in extremely obese individuals whose BMIs were all above the 99th percentile. j) A silent mutation (C-579-T, Val-193-Val) was detected in a male underweight individual. k) A previously described polymorphism (Val-103-Ile; 3) was detected with similar frequencies in all different study groups. 1) We identified a novel polymorphism (Ile-251-Leu) with similar allele frequencies in all groups under study. In conclusion, our data indicate that mutations in the MC4-R are not uncommon. Whereas our data support the evidence for dominantly inherited obesity as revealed by the three obese probands with haplo-insufficiency, the functional significance of the missense mutations remains to be determined.
Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum (1991)

The lysC/asd gene cluster of Corynebacterium glutamicum ATCC 13032 was cloned and sequenced. The lysC locus coding for aspartokinase consists of two in-frame overlapping genes, lysC alpha encoding a protein of 421 amino acids (Mr 44,300) and lysC beta encoding a protein of 172 amino acids (Mr 18,600). The C. glutamicum aspartokinase was purified and found to contain two proteins of Mr 47,000 and Mr 18,000. A C. glutamicum mutant expressing a feedback-resistant aspartokinase was shown to be changed in a single base pair of the lysC beta gene, leading to an amino acid exchange in the beta-subunit of the aspartokinase. In addition, the identified mutation was found to be responsible for the enhanced expression of the asd gene located downstream of lysC.
Tumor Necrosis Factor-α and Angiostatin Are Mediators of Endothelial Cytotoxicity in Bronchoalveolar Lavages of Patients with Acute Respiratory Distress Syndrome (2002)

Acute respiratory distress syndrome (ARDS) is characterized by an extensive alveolar capillary leak, permitting contact between intra-alveolar factors and the endothelium. To investigate whether factors contained in the alveolar milieu induce cell death in human lung microvascular endothelial cells, we exposed these cells in vitro to bronchoalveolar lavage fluid (BALF) supernatants from control patients, patients at risk of developing ARDS, and patients with early- and late-phase ARDS. In contrast to BALF from control patients, a significant cytotoxicity was found in BALF from patients at risk of developing ARDS, with late-phase ARDS, and especially from patients with early-phase ARDS. Subsequently, we determined the levels of factors known to exert cytotoxicity in endothelial cells, i.e., tumor necrosis factor (TNF)-alpha, transforming growth factor (TGF)-beta1, and angiostatin. BALF from patients at risk of developing ARDS, with early-phase ARDS, and with late-phase ARDS, contained increased levels of TNF-alpha and angiostatin, but not of TGF-beta1, as compared with BALF from control patients. Whereas inhibition of TGF-beta1 had no effect in this setting, neutralization of TNF-alpha or angiostatin inhibited the cytotoxic activity on endothelial cells of part of the early-phase ARDS BALF. These results indicate that TNF-alpha and angiostatin may contribute to ARDS-related endothelial injury.