gebhart/patrepeval huggingface dataset:
Proinflammatory Responses to Lipo‐oligosaccharide ofNeisseria meningitidisImmunotype Strains in Relation to Virulence and Disease (2002)

Inflammatory responses to lipo-oligosaccharide (LOS) contribute to the severity of meningococcal disease. Strains that express the L(3,7,9) LOS immunotypes are isolated from the majority of patients, but other immunotypes are isolated predominantly from carriers. Inflammatory responses elicited from a human monocytic cell line (THP-1) that had been pretreated with vitamin D3 (VD3) were compared after stimulation with purified LOSs from standard immunotype strains. The neutralizing effects of normal human serum and serum from mice immunized with strain B:2a:P1.5,2:L3 were compared. LOSs of immunotypes L3, L7, L8, and L9 induced significantly higher levels of tumor necrosis factor-alpha and interleukin-6, compared with other immunotypes. Normal human serum neutralized the proinflammatory responses to LOSs of all immunotypes tested. Immune mouse serum neutralized inflammatory responses against LOSs from immunotypes with epitopes cross-reactive with L(3,7,9) moieties. Antibodies found in normal human serum and immune mouse serum to the oligosaccharide, core, and lipid A moieties of meningococcal endotoxin contribute to neutralizing activity.
Experimental determination of acoustic properties using a two-microphone random-excitation technique (1977)

An experimental technique is presented for the determination of normal acoustic properties in a tube, including the effect of mean flow. An acoustic source is driven by Gaussian white noise to produce a randomly fluctuating sound field in a tube terminated by the system under investigation. Two stationary, wall-mounted microphones measure the sound pressure at arbitrary but known positions in the tube. Theory is developed, including the effect of mean flow, showing that the incident- and reflected-wave spectra, and the phase angle between the incident and reflected waves, can be determined from measurement of the auto- and cross-spectra of the two microphone signals. Expressions for the normal specific acoustic impedance and the reflection coefficient of the tube termination are developed for a random sound field in the tube. Three no-flow test cases are evaluated using the two-microphone random-excitation technique: a closed tube of specified length, an open, unbaffled tube of specified length, and a prototype automotive muffler. Comparison is made between results using the present method and approximate theory and results from the traditional standing-wave method. In all cases agreement between the two-microphone random-excitation method and comparison data is excellent. The two-microphone random-excitation technique can be used to evaluate acoustic properties very rapidly since no traversing is necessary and since random excitation is used (in each of three test cases only 7 sec of continuous data was needed). In addition, the bandwidth may be made arbitrarily small, within limits, so that the computed properties will have a high degree of frequency resolution.
Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution (2012)

5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. We introduce oxidative bisulfite sequencing (oxBS-Seq), the first method for quantitative mapping of 5hmC in genomic DNA at single-nucleotide resolution. Selective chemical oxidation of 5hmC to 5-formylcytosine (5fC) enables bisulfite conversion of 5fC to uracil. We demonstrate the utility of oxBS-Seq to map and quantify 5hmC at CpG islands (CGIs) in mouse embryonic stem (ES) cells and identify 800 5hmC-containing CGIs that have on average 3.3% hydroxymethylation. High levels of 5hmC were found in CGIs associated with transcriptional regulators and in long interspersed nuclear elements, suggesting that these regions might undergo epigenetic reprogramming in ES cells. Our results open new questions on 5hmC dynamics and sequence-specific targeting by TETs.
Ibopamine, an orally active dopamine-like drug: metabolism and pharmacokinetics in dogs. (1986)

Ibopamine (SB-7505), the 3,4-diisobutyrylester of N-methyldopamine (epinine), was rapidly hydrolyzed to epinine by plasma esterases of rat as well as of other animal species and man. Ibopamine was rapidly and extensively metabolized after oral administration to rat. Plasma levels of free epinine peaked at 30-60 min from the administration; conjugated epinine was present in larger amount, with a maximum at 3 h. Both free and conjugated epinine were still detectable at 6 h, but not at 24 h. Epinine 4-O-glucuronide, 4-hydroxy-3-methoxyphenylacetic acid and 3,4-dihydroxyphenylacetic acid appeared as main urinary metabolites; epinine 3-O-sulphate, epinine 3-O-methylether and its glucuronide, and trace amounts of epinine 4-O-sulphate were also detected.
Quantifying Point-Prediction Uncertainty in Neural Networks via Residual Estimation with an I/O Kernel (2019)

Neural Networks (NNs) have been extensively used for a wide spectrum of real-world regression tasks, where the goal is to predict a numerical outcome such as revenue, effectiveness, or a quantitative result. In many such tasks, the point prediction is not enough: the uncertainty (i.e. risk or confidence) of that prediction must also be estimated. Standard NNs, which are most often used in such tasks, do not provide uncertainty information. Existing approaches address this issue by combining Bayesian models with NNs, but these models are hard to implement, more expensive to train, and usually do not predict as accurately as standard NNs. In this paper, a new framework (RIO) is developed that makes it possible to estimate uncertainty in any pretrained standard NN. The behavior of the NN is captured by modeling its prediction residuals with a Gaussian Process, whose kernel includes both the NN's input and its output. The framework is evaluated in twelve real-world datasets, where it is found to (1) provide reliable estimates of uncertainty, (2) reduce the error of the point predictions, and (3) scale well to large datasets. Given that RIO can be applied to any standard NN without modifications to model architecture or training pipeline, it provides an important ingredient for building real-world NN applications.
Generation of effective antitumor vaccines using photodynamic therapy. (2002)

Preclinical studies have shown that photodynamic therapy (PDT) of tumors augments the host antitumor immune response. However, the role of the PDT effect on tumor cells as opposed to the host tissues has not been determined. To test the contribution of the direct effects of PDT on tumor cells to the enhanced antitumor response by the host, we examined the immunogenicity of PDT-generated murine tumor cell lysates in a preclinical vaccine model. We found that the PDT-generated tumor cell lysates were potent vaccines and that PDT-generated vaccines are more effective than other modes of creating whole tumor vaccines, i.e., UV or ionizing irradiation, and unlike other traditional vaccines, PDT vaccines do not require coadministration of an adjuvant to be effective. PDT vaccines are tumor specific and appear to induce a cytotoxic T-cell response. We have demonstrated that although both UV and PDT-generated tumor cell lysates are able to induce phenotypic DC maturation, only PDT-generated lysates are able to activate DCs to express IL-12, which is critical to the development of a cellular immune response. Our results show that PDT effects on tumor cells alone are sufficient to generate an antitumor immune response, indicating that the direct tumor effects of PDT play an important role in enhancing that host antitumor immune response. These studies also suggest that in addition to the role of PDT as a therapeutic modality, PDT-generated vaccines may have clinical potential as an adjuvant therapy.
One-Pot Colorimetric Differentiation of Polynucleotides with Single Base Imperfections Using Gold Nanoparticle Probes (1998)

Selective colorimetric polynucleotide detection based on Au nanoparticle probes which align in a “tail-to-tail” fashion onto a target polynucleotide is described. In this new nanoparticle-based detection system, Au particles (∼13 nm diameter), which are capped with 3‘- and 5‘-(alkanethiol)oligonucleotides, are used to complex a 24-base polynucleotide target. Hybridization of the target with the probes results in the formation of an extended polymeric Au nanoparticle/polynucleotide aggregate, which triggers a red to purple color change in solution. The color change is due to a red shift in the surface plasmon resonance of the Au nanoparticles. The aggregates exhibit characteristic, exceptionally sharp “melting transitions” (monitored at 260 or 700 nm), which allows one to distinguish target sequences that contain one base end mismatches, deletions, or an insertion from the fully complementary target. When test solutions are spotted onto a C18 reverse-phase thin-layer chromatography plate, color differentiation is enhanced and a permanent record of the test is obtained, thereby providing a better method for distinguishing the aforementioned target sequences. Significantly, one-pot colorimetric detection of the target in the presence of four strands with single base imperfections can be accomplished with this new probe system.
Cannabidivarin‐rich cannabis extracts are anticonvulsant in mouse and rat via a CB1 receptor‐independent mechanism (2013)

CBDV BDSs exerted significant anticonvulsant effects in three models of seizure that were not mediated by the CB1 cannabinoid receptor and were of comparable efficacy with purified CBDV. These findings strongly support the further clinical development of CBDV BDSs for the treatment of epilepsy.
Special Edition Using Microsoft Office 2000 (1999)

From the Publisher:
All-star author Ed Bott (PC Computing senior editor) understands business users and how they want to be productive without becoming hard core computer geeks. In this book, you'll quickly find all of the information you need to be productive in Word, Excel, PowerPoint, Publisher, and Outlook, without extra information that you won't use. With this you'll easily create professional documents in Word, build powerful Excel spreadsheets, prepare killer PowerPoint presentations, and get your time and email organized with Outlook. 
Tame pesky Office 2000 features like the Office Assistant and clipboard to make Office 2000 applications work quickly and efficiently for you See how to detect and avoid dangerous and destructive macro viruses that destroy your data and waste your time Step up to the new features of Office 2000 that will be the most useful for you including better web publishing in all Office applications
Codon usage in plant genes (1989)

We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general.
Added-Mass Effect in Modeling of Cilia-Based (Vibrating Cantilever-Type) Devices for Microfluidic Systems (2007)

This article shows that the added mass due to fluid structure interaction significantly affects the vibrational dynamics of cilia-based (vibrating cantilever-type) devices for handling micro/nano-scale fluid flows. Commonly, the hydrodynamic interaction between the cilia-based actuator and fluid is modeled as a Stokes drag force that is proportional to the velocity. Our main contribution is to show that such a drag effect cannot explain the substantial reduction in the resonant frequency of the cilia actuator operating in liquid when compared to the natural frequency of the cilia in air. It is shown that an added-mass approach can explain this reduction in the resonant frequency when operating cantilever-type devices in fluid. Thus, this article shows the need to model the added-mass effect, both, theoretically and by using experimental results.
Phenotypic and functional characteristics of in vivo-activated Langerhans cells. (1990)

After short term culture (2 to 3 days), Langerhans cells (LC) exhibit increased class II MHC Ag and become more potent APC than freshly obtained LC in primary allogeneic and syngeneic T cell activation. To determine whether in vivo LC undergo changes similar to cultured LC, we examined the phenotypic and functional characteristics of LC harvested from ear skin of naive mice painted with various haptens and primary irritants. At 24 h after application of 3% trinitrochlorobenzene, LC appear larger and exhibit more intense staining in epidermal sheets using anti-I-A antibodies, and there was a two- to threefold increase in I-A and I-E expression by LC using flow microfluorimetry analysis. CD45 Ag expression was not altered. Flow microfluorimetry profiles showed the presence of two different LC populations based on fluorescence intensity, i.e., one with the same Ia density as nontreated LC and the other (representing 22 to 50% of all LC) with a markedly enhanced Ia density, (i.e., a 10-fold increase in I-A and I-E). This phenotypic change was observed only with haptens, such as trinitrochlorobenzene, dinitrofluorobenzene, oxazolone, and cinnamic aldehyde. In contrast, application of 10 to 30% sodium lauryl sulfate or vehicle controls did not induce this change. Functionally, LC obtained from hapten-painted mice induced a two- to fivefold increase in 3[H]-TdR incorporation by syngeneic or allogeneic T cells, compared to equal numbers of LC from nontreated or vehicle-treated or sodium lauryl sulfate-treated mice. These phenotypic and functional changes that occur in vivo are therefore analogous to those seen when LC are cultured for short periods of time. Thus, activated LC appear in vivo in response to the epicutaneous application of haptens and may represent an essential step in hapten-specific sensitization.
The clinical significance of soluble CD86 levels in patients with acute myeloid leukemia and myelodysplastic syndrome (2003)

The presence in patients with AML of elevated levels of circulating sCD86 were associated with lower CR rates and poor survival. The prognostic significance of sCD86 was independent of cytogenetics but was modulated by age, in that it was independently significant only in younger patients. The results suggest that sCD86 may play a role in modulating immune responses associated with the progression of AML.
Impact of electroosmosis on isotachophoresis in open‐tubular fused‐silica capillaries: Analysis of the evolution of a stationary steady‐state zone structure by computer simulation and experimental validation (1995)

A dynamic computer model for simulation of open-tubular capillary electrophoresis that includes in situ calculation of electroosmosis along the fused-silica capillary column has been applied to the characterization of an anionic isotachophoretic system in presence of a cathodic electroosmotic flow. For each column segment, electroosmosis is calculated with the use of a wall mobility, the voltage gradient and the degree of dissociation of the silanol surface groups of the capillary wall. Then, the bulk capillary flow is taken to be the average of all of the segment flows and considered to represent a plug flow. This simple approach enables the combined simulation of the temporal behavior of an isotachophoretic zone structure in presence of electroosmosis. For a model anionic isotachophoretic configuration at pH 6, simulation data reveal the asymptotic formation of a stationary steady-state zone configuration in which electrophoretic and electroosmotic zone displacements are opposite and of equal magnitude. The position of the stationary boundaries are predicted to be dependent on the selected wall pK and mobility values. For two different instruments, qualitative agreement between experimental data and simulation results obtained with a wall pK between 5 and 6 is demonstrated. However, for the two experimental setups, significant differences in electroosmotic pumping (i.e. wall mobility values) are noted.
The mass spectra of some s‐triazolo[4,3‐a]pyrazines (1971)

Abstract s ‐Triazolo[4,3‐a]pyrazine underwent decomposition by loss of nitrogen from its molecular ion whereas in the 3‐alkyl derivatives the corresponding alkyl cyanide was eliminated from the 5‐membered ring. The introduction of a carbonyl or thiocarbonyl group into the 3‐position resulted in predominant loss of the triazole ring in the fragmentation process; however, with a 3‐amino substituent, the first fragment eliminated from the molecular ion was cyanamide. Methyl substitution in the 6‐membered ring resulted in the formation of ring expanded ions. On phenyl substitution, however, an interesting 1,2‐phenyl migration was observed. The mass spectra of several analogous s ‐triazolo[1,5‐a]pyrazines are also described.
Dual Regulation of a Chimeric Plant Serine/Threonine Kinase by Calcium and Calcium/Calmodulin (1996)

A chimeric Ca2+/calmodulin-dependent protein kinase (CCaMK) gene characterized by a catalytic domain, a calmodulin-binding domain, and a neural visinin-like Ca2+-binding domain was recently cloned from plants (Patil, S., Takezawa, D., and Poovaiah, B. W. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 4797-4801). The Escherichia coli-expressed CCaMK phosphorylates various protein and peptide substrates in a Ca2+/calmodulin-dependent manner. The calmodulin-binding region of CCaMK has similarity to the calmodulin-binding region of the alpha-subunit of multifunctional Ca2+/calmodulin-dependent protein kinase (CaMKII). CCaMK exhibits basal autophosphorylation at the threonine residue(s) (0.098 mol of 32P/mol) that is stimulated 3.4-fold by Ca2+ (0.339 mol of 32P/mol), while calmodulin inhibits Ca2+-stimulated autophosphorylation to the basal level. A deletion mutant lacking the visinin-like domain did not show Ca2+-stimulated autophosphorylation activity but retained Ca2+/calmodulin-dependent protein kinase activity at a reduced level. Ca2+-dependent mobility shift assays using E. coli-expressed protein from residues 358 520 revealed that Ca2+ binds to the visinin-like domain. Studies with site-directed mutants of the visinin-like domain indicated that EF-hands II and III are crucial for Ca2+-induced conformational changes in the visinin-like domain. Autophosphorylation of CCaMK increases Ca2+/calmodulin-dependent protein kinase activity by about 5-fold, whereas it did not affect its Ca2+-independent activity. This report provides evidence for the existence of a protein kinase in plants that is modulated by Ca2+ and Ca2+/calmodulin. The presence of a visinin-like Ca2+-binding domain in CCaMK adds an additional Ca2+-sensing mechanism not previously known to exist in the Ca2+/calmodulin-mediated signaling cascade in plants.
Overview of the GSM system and protocol architecture (1993)

The global system for mobile telecommunications (GSM), which provides terminal mobility, with personal mobility provided through the insertion of a subscriber identity module (SIM) into the GSM network, is discussed. Cellular mobile communications, the cellular network infrastructure, and the specification of network databases and standards are described. The GSMs, numbering plan, radio channel structure, mobility management, call routing and signaling, protocol layering architecture, signaling transport protocols, and paging messaging systems are also described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The angiogenesis inhibitor endostatin impairs blood vessel maturation during wound healing (2000)

Endostatin is a cleavage product of collagen XVIII that strongly inhibits tumor angiogenesis. To determine if endostatin affects other angiogenic processes, we generated full-thickness excisional wounds on the back of mice that were systemically treated with recombinant murine endostatin. No macroscopic abnormalities of the wound healing process were observed. Histological analysis revealed normal wound contraction and re-epithelialization, but a slight reduction in granulation tissue formation and reduced matrix deposition at the wound edge. The blood vessel density in the wounds of endostatin-treated mice was not affected. However, ultrastructural analysis demonstrated severe abnormalities in blood vessel maturation. The wound vessels in the endostatin-treated mice were narrowed or closed with an irregular luminal surface, resulting in a severe reduction in the number of functional vessels and extravasation of erythrocytes. Endostatin treatment did not affect the expression level and localization of collagen XVIII mRNA and protein. Furthermore, the angiogenesis regulators vascular endothelial growth factor, angiopoietin-1, and angiopoietin-2 were normally expressed in the wounds of endostatin-treated mice. However, expression of the major wound matrix proteins fibronectin and collagens I and III was significantly reduced. This reduction is likely to explain the reduced density of the wound matrix. Our results demonstrate that endostatin treatment reduces the number of functional blood vessels and the matrix density in the granulation tissue, but does not significantly affect the overall wound healing process.
Systemic Delivery of Dysferlin Overlap Vectors Provides Long-Term Gene Expression and Functional Improvement for Dysferlinopathy (2017)

Dysferlinopathies comprise a family of disorders caused by mutations in the dysferlin (DYSF) gene, leading to a progressive dystrophy characterized by chronic muscle fiber loss, fat replacement, and fibrosis. To correct the underlying histopathology and function, expression of full-length DYSF is required. Dual adeno-associated virus vectors have been developed, defined by a region of homology, to serve as a substrate for reconstitution of the full 6.5 kb dysferlin cDNA. Previous work studied the efficacy of this treatment through intramuscular and regional delivery routes. To maximize clinical efficacy, dysferlin-deficient mice were treated systemically to target all muscles through the vasculature for efficacy and safety studies. Mice were evaluated at multiple time points between 4 and 13 months post treatment for dysferlin expression and functional improvement using magnetic resonance imaging and magnetic resonance spectroscopy and membrane repair. A systemic dose of 6 × 10<sup>12</sup> vector genomes resulted in widespread gene expression in the muscles. Treated muscles showed a significant decrease in central nucleation, collagen deposition, and improvement of membrane repair to wild-type levels. Treated gluteus muscles were significantly improved compared to placebo-treated muscles and were equivalent to wild type in volume, intra- and extramyocellular lipid accumulation, and fat percentage using magnetic resonance imaging and magnetic resonance spectroscopy. Dual-vector treatment allows for production of full-length functional dysferlin with no toxicity. This confirms previous safety data and validates translation of systemic gene delivery for dysferlinopathy patients.
Documenting Fire: A Profile of Brian Benfer’s Industrial Series (2010)

Residue is defined as being, "something that remains after a part is taken, separated or designated or after the completion of a process". For artist Brian Benfer, the concept of residue has long been the impetus for his body of work.