gebhart/patrepeval huggingface dataset:
Detection of Circulating Tumor Necrosis Factor after Endotoxin Administration (1988)

Cytokines, products of stimulated macrophages, are thought to mediate many host responses to bacterial infection, but increased circulating cytokine concentrations have not been detected consistently in infected patients. We measured plasma concentrations of circulating tumor necrosis factor alpha (cachectin), interleukin-1 beta, and gamma interferon, together with physiologic and hormonal responses, in 13 healthy men after intravenous administration of Escherichia coli endotoxin (4 ng per kilogram of body weight) and during a control period of saline administration. Eight additional subjects received ibuprofen before receiving endotoxin or saline. Plasma levels of tumor necrosis factor were generally less than 35 pg per milliliter throughout the control period, but increased 90 to 180 minutes after endotoxin administration to mean peak concentrations of 240 +/- 70 pg per milliliter, as compared with 35 +/- 5 pg per milliliter after saline administration. Host responses were temporally associated with the increase in circulating tumor necrosis factor at 90 minutes, and the extent of symptoms, changes in white-cell count, and production of ACTH were temporally related to the peak concentration of tumor necrosis factor. Ibuprofen pretreatment did not prevent the rise in circulating tumor necrosis factor (mean peak plasma level, 170 +/- 70 pg per milliliter) but greatly attenuated the symptoms and other responses after endotoxin administration. Concentrations of circulating interleukin-1 beta and gamma interferon did not change after endotoxin administration. We conclude that the response to endotoxin is associated with a brief pulse of circulating tumor necrosis factor and that the resultant responses are effected through the cyclooxygenase pathway.
Text data acquisition for domain-specific language models (2006)

The language modeling community is showing a growing interest in using large collections of text mined from the World Wide Web (WWW) to supplement sparse in-domain text resources. However, in most cases the style and content of the text harvested from these corpora differs significantly from the specific nature of these domains. In this paper we present a relative entropy (r.e.) based method to select relevant subsets of sentences whose distribution in an n-gram sense matches the domain of interest. Using simulations, we provide an analysis of how the proposed scheme outperforms filtering techniques proposed in recent language modeling literature on mining text from the web. A comparative study is presented using a text collection of over 800M words collected from the WWW. Experimental results show that by using the proposed subset selection scheme we can get performance improvement in both Word Error Rate (WER) and Perplexity (PPL) over the models built from the entire collection by using just 10% of the data. Improvements in data selection also translated to a significant reduction in the vocabulary size as well as the number of estimated parameters in the adapted language model.
On dynamical Poisson groupoids. I (2005)

Introduction A class of biequivariant Poisson groupoids Duality An explicit case study of duality Coboundary dynamical Poisson groupoids - the constant $r$-matrix case Appendix Bibliography.
Liver-Specific Alpha 2 Interferon Gene Expression Results in Protection from Induced Hepatitis (2000)

The current therapy for hepatitis B and C is based on systemic administration of recombinant human alpha interferon (r-hIFN-alpha). However, systemic delivery of r-hIFN-alpha is associated with severe side effects, but more importantly, it is effective in only a small percentage of patients. In an effort to maximize IFN-alpha antiviral efficacy, we have explored the therapeutic potential of murine IFN-alpha2 (mIFNalpha2) selectively expressed in the liver. To this end, we have developed a helper-dependent adenovirus vector (HD) containing the mIFN-alpha2 gene under the control of the liver-specific transthyretin promoter (HD-IFN). Comparison with a first-generation adenovirus carrying the same mIFN-alpha2 expression cassette indicates that at certain HD-IFN doses, induction of antiviral genes can be achieved in the absence of detectable circulating mIFN-alpha2. Challenge of injected mice with mouse hepatitis virus type 3 showed that HD-IFN provides high liver protection. Moreover, liver protection was also observed in acute nonviral liver inflammation hepatitis induced by concanavalin A at 1 month postinfection. These results hold promise for the development of a gene therapy treatment for chronic viral hepatitis based on liver-restricted expression of IFN-alpha2.
Leucine-enriched essential amino acid and carbohydrate ingestion following resistance exercise enhances mTOR signaling and protein synthesis in human muscle (2007)

We recently showed that resistance exercise and ingestion of essential amino acids with carbohydrate (EAA+CHO) can independently stimulate mammalian target of rapamycin (mTOR) signaling and muscle protein synthesis in humans. Providing an EAA+CHO solution postexercise can further increase muscle protein synthesis. Therefore, we hypothesized that enhanced mTOR signaling might be responsible for the greater muscle protein synthesis when leucine-enriched EAA+CHOs are ingested during postexercise recovery. Sixteen male subjects were randomized to one of two groups (control or EAA+CHO). The EAA+CHO group ingested the nutrient solution 1 h after resistance exercise. mTOR signaling was assessed by immunoblotting from repeated muscle biopsy samples. Mixed muscle fractional synthetic rate (FSR) was measured using stable isotope techniques. Muscle protein synthesis and 4E-BP1 phosphorylation during exercise were significantly reduced (P < 0.05). Postexercise FSR was elevated above baseline in both groups at 1 h but was even further elevated in the EAA+CHO group at 2 h postexercise (P < 0.05). Increased FSR was associated with enhanced phosphorylation of mTOR and S6K1 (P < 0.05). Akt phosphorylation was elevated at 1 h and returned to baseline by 2 h in the control group, but it remained elevated in the EAA+CHO group (P < 0.05). 4E-BP1 phosphorylation returned to baseline during recovery in control but became elevated when EAA+CHO was ingested (P < 0.05). eEF2 phosphorylation decreased at 1 and 2 h postexercise to a similar extent in both groups (P < 0.05). Our data suggest that enhanced activation of the mTOR signaling pathway is playing a role in the greater synthesis of muscle proteins when resistance exercise is followed by EAA+CHO ingestion.
A Framework for Computing the Privacy Scores of Users in Online Social Networks (2010)

A large body of work has been devoted to address corporate-scale privacy concerns related to social networks. Most of this work focuses on how to share social networks owned by organizations without revealing the identities or the sensitive relationships of the users involved. Not much attention has been given to the privacy risk of users posed by their daily information-sharing activities. In this article, we approach the privacy issues raised in online social networks from the individual users’ viewpoint: we propose a framework to compute the privacy score of a user. This score indicates the user’s potential risk caused by his or her participation in the network. Our definition of privacy score satisfies the following intuitive properties: the more sensitive information a user discloses, the higher his or her privacy risk. Also, the more visible the disclosed information becomes in the network, the higher the privacy risk. We develop mathematical models to estimate both sensitivity and visibility of the information. We apply our methods to synthetic and real-world data and demonstrate their efficacy and practical utility.
Stem cell biology of the central nervous system (2002)

Neural stem cells (NSCs) are multipotential progenitor cells that have self-renewal activities. A single NSC is capable of generating various kinds of cells within the central nervous system (CNS), including neurons, astrocytes, and oligodendrocytes. Because of these characteristics, there is increasing interest in NSCs and neural progenitor cells from the aspects of both basic developmental biology and therapeutic applications to the damaged brain. This special issue, dedicated to understanding the nature of the NSCs present in the CNS, presents an introduction to several avenues of research that may lead to feasible strategies for manipulating cells in situ to treat the damaged brain. The topics covered by these studies include the extracellular factors and signal transduction cascades involved in the differentiation and maintenance of NSCs, the population dynamics and locations of NSCs in embryonic and adult brains, prospective identification and isolation of NSCs, the induction of NSCs to adopt particular neuronal phenotypes, and their transplantation into the damaged CNS.
Eicosapentaenoic acid metabolism in brain microvessel endothelium: effect on prostaglandin formation. (1989)

Mouse brain microvessel endothelial cells convert eicosapentaenoic acid (EPA) to prostaglandin (PG) E3, PGI3, and several hydroxy fatty acid derivatives. Similar types of products are formed by these microvessel endothelial cells from arachidonic acid. The formation of PGI2 and PGE2 is reduced, however, when the brain microvessel endothelial cultures are incubated initially with EPA. Exposure to linolenic or docosahexaenoic acid also decreased the capacity of these microvessel endothelial cells to form PGI2 and PGE2, but the reductions were smaller than those produced by EPA. Like the endothelial cultures, intact mouse brain microvessels convert EPA into eicosanoids, and incubation with EPA reduces the subsequent capacity of the microvessels to produce PGI2 and PGE2. Brain microvessel endothelial cells took up less EPA than arachidonic acid, primarily due to lesser incorporation into the inositol, ethanolamine, and serine glycerophospholipids. By contrast, considerably more EPA than arachidonic acid was incorporated into triglycerides. These findings suggest that the microvessel endothelium may be a site of conversion of EPA to eicosanoids in the brain and that EPA availability can influence the amount of dienoic prostaglandins released by the brain microvasculature. Furthermore, the substantial incorporation of EPA into triglyceride suggests that this neutral lipid may play an important role in the processing and metabolism of EPA in brain microvessels.
An Internal Regulatory Element Controls Troponin I Gene Expression (1989)

During skeletal myogenesis, approximately 20 contractile proteins and related gene products temporally accumulate as the cells fuse to form multinucleated muscle fibers. In most instances, the contractile protein genes are regulated transcriptionally, which suggests that a common molecular mechanism may coordinate the expression of this diverse and evolutionarily unrelated gene set. Recent studies have examined the muscle-specific cis-acting elements associated with numerous contractile protein genes. All of the identified regulatory elements are positioned in the 5'-flanking regions, usually within 1,500 base pairs of the transcription start site. Surprisingly, a DNA consensus sequence that is common to each contractile protein gene has not been identified. In contrast to the results of these earlier studies, we have found that the 5'-flanking region of the quail troponin I (TnI) gene is not sufficient to permit the normal myofiber transcriptional activation of the gene. Instead, the TnI gene utilizes a unique internal regulatory element that is responsible for the correct myofiber-specific expression pattern associated with the TnI gene. This is the first example in which a contractile protein gene has been shown to rely primarily on an internal regulatory element to elicit transcriptional activation during myogenesis. The diversity of regulatory elements associated with the contractile protein genes suggests that the temporal expression of the genes may involve individual cis-trans regulatory components specific for each gene.
Procholeragenoid: An Aggregated Intermediate in the Formation of Choleragenoid (1971)

Abstract A high molecular weight polymer, designated “procholeragenoid,” is an intermediate in the heat-mediated conversion of the cholera exo-enterotoxin, choleragen, to the natural toxoid, choleragenoid. The demonstration of this polymer offers an explanation for the conversion of the toxin, ca. 90,000 m.w., to the antigenically identical toxoid, ca. 60,000 m.w., without apparent loss of a fragment. Isolated procholeragenoid has little residual toxicity and is immunogenic for mice.
Endotoxin Removed from Hemoglobin Solution using Polymyxin-B Immobilized Fibre (PMX-F) Followed by a new Tdrbidohetric Endotoxin Assay (1992)

Endotoxin contamination in modified hemoglobin can result in side effects. Accurate measurement and effective elimination of endotoxin are important in producing safe hemoglobin preparation. A new turbidometric endotoxin assay (Toxinometer) was studied, in which absorbance of wavelength was applied at 660 nm. This method is not affected by the presence of hemoglobin in solution. This way, toxinometer can accurately measure endotoxin concentration in hemoglobin solution. For the elimination of endotoxin, polymyxin-B immobilized fiber (PMX-F) was studied in-vitro and compared with commercial materials. The PMX-F was found to be a convenient and less expensive approach.
Neutrophil functional responses depend on immune complex valency (1995)

Ligand-induced cross-linking of Fc gamma receptors (Fc gamma R) on neutrophils plays a significant role in their stimulation, shown here by contrasting the responses induced by low valency immune complexes (LICs) and high valency immune complexes (HICs) and by cross-linking LICs in situ (L/Ab) after their addition to the cells. Multiparameter flow cytometry was used to measure immune complex (IC)-elicited changes in cytoplasmic Ca2+ concentration and initiation of the oxidative burst simultaneously in the same cell and to correlate these with Fc gamma R occupancy. We have previously shown that subpopulations of neutrophils respond maximally to subsaturating concentrations of HIC; saturating dosages stimulate the entire population. This discrepancy was not due to differences in receptor occupancy. The magnitude of the transient Ca2+ increase was independent of the dose of HIC but depended on the dose when an LIC was used. As shown here, L/Ab cross-linking elicited Ca2+ responses similar to those observed in HIC-stimulated cells. In contrast, LIC elicited only minimal intracellular delta pH and no oxidative burst or membrane potential changes at all unless Fc gamma R was cross-linked, accomplished by HIC or by L/Ab. However, azurophilic degranulation, as determined by elastase release, was not observed in cells stimulated by the in situ cross-linking method, whereas the HIC preparation triggered azurophilic degranulation. Thus, some Fc gamma R-mediated neutrophil effector functions such as azurophilic degranulation and oxidative burst initiation have an absolute requirement for Fc gamma R cross-linking, whereas signaling functions such as changes in membrane potential, intracellular pH, and intracellular Ca2+ concentration can occur, albeit more slowly and to a lesser extent, if single Fc gamma R are occupied.
Fundamentals of the capacitive resistivity technique (2006)

Abstract Capacitive resistivity (CR) is an emerging geophysical technique designed to extend the scope of the conventional methodology of dc resistivity to environments where galvanic coupling is notoriously difficult to achieve — for example, across engineered structures (roads, pavements), hard rock, dry soil, or frozen ground. Conceptually, CR is based on a four-point array capacitively coupled to the ground. Under certain conditions, capacitive measurements of resistivity are equivalent to those obtained with the dc technique, thus making dc interpretation schemes applicable to CR data. The coupling properties of practical sensor realizations are shown to be a function of their geometrical arrangement. Separate bodies of theory are associated with two complementary but distinct sensor types: the capacitive-line antenna and the plate-wire combination. The use of plate-wire combinations results in localized coupling, which, in conjunction with a quasi-static (low-frequency) formulation of the transfer impedance, provides a valid emulation of the dc measurement with point electrodes. A parametric study of the complex, quasi-static transfer impedance reveals the existence of a restricted range of practical parameters that permits successful operation of CR instruments at low induction numbers. Theory predicts that emulating the dc measurement is compromised if low-induction-number operation is not maintained throughout a survey area, as in a zone of high conductivity. Validation of the theory is achieved using specially designed field-scale experiments carried out with a CR instrument capable of measuring the full complex transfer impedance. At intermediate dipole separations, the results are consistent with the predictions of quasi-static theory. Deviations observed in the near and far separation zones can be explained by geometric effects or the breakdown of quasi-static conditions, respectively. Finally, under suitable conditions the phase-sensitive expression for apparent resistivity as a function of the complex transfer impedance is shown to reduce to the classical dc formula for the in-phase component. CR, while capable of emulating dc resistivity, also can be regarded as a physical complement of the inductively coupled ground-conductivity method.
A Trivalent Virus-Like Particle Vaccine Elicits Protective Immune Responses against Seasonal Influenza Strains in Mice and Ferrets (2009)

There is need for improved human influenza vaccines, particularly for older adults who are at greatest risk for severe disease, as well as to address the continuous antigenic drift within circulating human subtypes of influenza virus. We have engineered an influenza virus-like particle (VLP) as a new generation vaccine candidate purified from the supernatants of Sf9 insect cells following infection by recombinant baculoviruses to express three influenza virus proteins, hemagglutinin (HA), neuraminidase (NA), and matrix 1 (M1). In this study, a seasonal trivalent VLP vaccine (TVV) formulation, composed of influenza A H1N1 and H3N2 and influenza B VLPs, was evaluated in mice and ferrets for the ability to elicit antigen-specific immune responses. Animals vaccinated with the TVV formulation had hemagglutination-inhibition (HAI) antibody titers against all three homologous influenza virus strains, as well as HAI antibodies against a panel of heterologous influenza viruses. HAI titers elicited by the TVV were statistically similar to HAI titers elicited in animals vaccinated with the corresponding monovalent VLP. Mice vaccinated with the TVV had higher level of influenza specific CD8+ T cell responses than a commercial trivalent inactivated vaccine (TIV). Ferrets vaccinated with the highest dose of the VLP vaccine and then challenged with the homologous H3N2 virus had the lowest titers of replicating virus in nasal washes and showed no signs of disease. Overall, a trivalent VLP vaccine elicits a broad array of immunity and can protect against influenza virus challenge.
Asymmetric Synthesis and Biological Evaluation of Glycosidic Prodrugs for a Selective Cancer Therapy (2008)

A severe limitation in cancer therapy is the often insufficient differentiation between malign and benign tissue using known chemotherapeutics. One approach to decrease side effects is antibody-directed enzyme prodrug therapy (ADEPT). We have developed new glycosidic prodrugs such as (-)-(1S)-26 b based on the antibiotic (+)-duocarmycin SA ((+)-1) with a QIC(50) value of 3500 (QIC(50)=IC(50) of prodrug/IC(50) of prodrug+enzyme) and an IC(50) value for the corresponding drug (prodrug+enzyme) of 16 pM. The asymmetric synthesis of the precursor (-)-(1S)-19 was performed by arylation of the enantiomerically pure epoxide (+)-(S)-29 (> or = 98 % ee).
Synergistic Substrate Inhibition of ent-Copalyl Diphosphate Synthase: A Potential Feed-Forward Inhibition Mechanism Limiting Gibberellin Metabolism (2007)

Gibberellins (GAs) or gibberellic acids are ubiquitous diterpenoid phytohormones required for many aspects of plant growth and development, including repression of photosynthetic pigment production (i.e. deetiolation) in the absence of light. The committed step in GA biosynthesis is catalyzed in plastids by ent-copalyl diphosphate synthase (CPS), whose substrate, (E,E,E,)-geranylgeranyl diphosphate (GGPP), is also a direct precursor of carotenoids and the phytol side chain of chlorophyll. Accordingly, during deetiolation, GA production is repressed, whereas flux toward these photosynthetic pigments through their common GGPP precursor is dramatically increased. How this is accomplished has been unclear because no mechanism for regulation of CPS activity has been reported. We present here kinetic analysis of recombinant pseudomature CPS from Arabidopsis (Arabidopsis thaliana; rAtCPS) demonstrating that Mg(2+) and GGPP exert synergistic substrate inhibition effects on CPS activity. These results suggest that GA metabolism may be limited by feed-forward inhibition of CPS; in particular, the effect of Mg(2+) because light induces increases in plastid Mg(2+) levels over a similar range as that observed here to affect rAtCPS activity. Notably, this effect is most pronounced in the GA-specific AtCPS because the corresponding activity of the resin acid biosynthetic enzyme abietadiene synthase is 100-fold less sensitive to [Mg(2+)]. Furthermore, Mg(2+) allosterically activates the plant porphobilinogen synthase involved in chlorophyll production. Hence, Mg(2+) may have a broad role in regulating plastidial metabolic flux during deetiolation. Finally, the observed synergistic substrate/feed-forward inhibition of CPS also seems to provide a novel example of direct regulation of enzymatic activity in hormone biosynthesis.
Optimizing codes for compressed ultrafast photography by the genetic algorithm (2018)

&lt;p&gt;The compressed ultrafast photography (CUP) technique, providing the fastest receive-only camera so far, has shown to be a well-established tool to capture the ultrafast dynamical scene. This technique is based on random codes to encode and decode the ultrafast dynamical scene by a compressed sensing algorithm. The choice of random codes significantly affects the image reconstruction quality. Therefore, it is important to optimize the encoding codes. Here, we develop a new scheme to obtain the optimized codes by combining a genetic algorithm (GA) into the CUP technique. First, we measure the dynamical scene by the CUP system with random codes and obtain the dynamical scene image at each moment. Second, we use these reconstructed dynamical scene images as the optimization target and optimize the encoding codes based on the GA. Finally, we utilize the optimized codes to recapture the dynamical scene and improve the image reconstruction quality. We validate our optimization scheme by the numerical simulation of a moving double-semielliptical spot and the experimental demonstration of a time-and space-evolving pulsed laser spot. (c) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement&lt;/p&gt;\n\n&lt;p&gt;&amp;nbsp;&lt;/p&gt;