gebhart/patrepeval huggingface dataset:
A Comparison of C3a and C5a-Mediated Stable Adhesion of Rolling Eosinophils in Postcapillary Venules and Transendothelial Migration In Vitro and In Vivo (1999)

The comparative ability of the complement anaphylatoxins C3a and C5a to mediate leukocyte adhesion and transendothelial migration in vivo and in vitro was investigated. Superfusion of IL-1beta-stimulated rabbit mesentery with C3a resulted in a rapid and stable adhesion of rolling eosinophils, but not neutrophils, to postcapillary venules. However, C3a failed to evoke subsequent transmigration of the adherent eosinophils. In contrast, C5a induced both the rapid activation-dependent firm adhesion and transmigration of eosinophils and neutrophils through venular endothelium. C3a induced selective shedding of L-selectin and an increase in alphaMbeta2 integrin expression on eosinophils but not neutrophils, while C5a induced shedding of L-selectin and up-regulation of alphaMbeta2 integrin on both eosinophils and neutrophils. Both C3a- and C5a-dependent adhesion to venular endothelium was blocked by ex vivo treatment of eosinophils with anti-alpha4 and anti-beta2 integrin mAbs. In vitro, both C3a (but not C3a(desArg)) and C5a (including C5a(desArg))-dependent transmigration of eosinophils across IL-1beta-stimulated endothelial monolayer was mediated by alpha4beta1 and alphaMbeta2 integrins. Overall these studies suggest that C3a is eosinophil-specific chemotactic mediator that influences selectively eosinophil adhesion but not transmigration in vivo. C5a in contrast is a complete activator of integrin-dependent adhesion as well as transmigration of eosinophils and neutrophils.
Neurogenic Orthostatic Hypotension (2008)

A 65-year-old man reports a 6-month history of dizziness, light-headedness, weakness, and fatigue while upright. He takes no medication and has no personal or family history of neurologic disease. On physical examination, his supine blood pressure is 160/100 mm Hg, with a heart rate of 72 beats per minute; on standing, his blood pressure falls to 70/40 mm Hg, with no change in heart rate. The results of the remainder of the examination, including neurologic examination, are normal. How should he be evaluated and treated?
Coulometric Electrode Array Detectors for HPLC (2024)

Part 1 An introduction to HPLC-based electrochemical detection - from single electrode to multi-electrode arrays, I.N. Acworth and M. Bowers. Part 2 Qualitative utility of coulometric array detection - theoretical and applied aspects, J.K. Cullison and P.H. Gamache. Part 3 HPLC with electrcde array detection and its application in analytical food chemistry, G. Sontag et al. Part 4 The measurement of markers of oxidative damage, anti-oxidants and related compounds using HPLC and coulometric array analysis, P.H. Gamache et al. Part 5 CEAS generation of large multi-parameter metabolic databases for determining categorical process involvement of biological molecules, P.E. Milbury. Part 6 The application of n-EC-HPLC to the analysis of insect biogenic amines , T.C. Sparks et al. Part 7 A phylogenetic analysis of biogenic monoamines in the central nervous systems of various organisms and application to the fields of medical biochemistry, N. Takeda. Part 8 Multicomponent quantitations of monoamines and related compounds in biological fluids and CNS tissues by HPLC coupled with multi-electrode electrochemical detection, P. Huettl and G.A. Gerhardt. Part 9 The application of the multi-electrode detection system to neurochemistry - in-vivo microanalysis studies, M. Naoi et al. Part 10 HPLC-multi-electrochemical detection system - application to neurochemical studies in paediatrics, Y. Takeuchi et al. Part 11 neurotransmitter disturbances in Alzheimer's disease with Lewy bodies, P.J. Langlais. Part 12 Determination of illicit drugs and related substances by using HPLC with an electrochemical coulometric array detector, G. Achilli and G.P. Cellerino. Part 13 Enantioseparation of biologically-active compounds by HPLC, Y. Deng et al. Part 14 Analysis of endogenous enantiomers of neurotoxins in clinical samples by a multi-electrode detection systems with a chiral column, W. Maruyama et al. Part 15 Electrochemical measurement of electrochemically unreactive compounds - an examination of the use of derivatives and photolysis with a HPLC and coulometric detection, I.N. Acworth and J. Waraska.
Sterol 27-Hydroxylase– and ApoAI/Phospholipid–Mediated Efflux of Cholesterol From Cholesterol-Laden Macrophages (1998)

Cholesterol-laden, human monocyte-derived macrophages were found to contain 27-hydroxycholesterol in proportion to their content of cholesterol ester. In accordance with previous work with human lung alveolar macrophages, there was a significant efflux of 27-hydroxycholesterol and 3beta-hydroxy-5-cholestenoic acid from the cultured cells. The efflux of 27-hydroxycholesterol was proportional to the cellular content of this steroid. Incubation of cholesterol-laden macrophages with reconstituted discoidal complexes made from apolipoprotein A-I and phospholipids resulted in a decrease in total cellular cholesterol, an increase in the efflux of free cholesterol, and a concomitant decrease in the total production and efflux of 27-oxygenated steroids, in particular, 3beta-hydroxy-5-cholestenoic acid. Reconstituted discoidal complexes with the Milano variant of apolipoprotein A-I gave virtually identical results, whereas high density lipoprotein was less efficient. These results suggest that cultured cholesterol-laden cells can export some of their excess cholesterol in the form of 27-hydroxycholesterol, 3beta-hydroxy-5-cholestenoic acid, and free cholesterol. In the presence of exogenous cholesterol acceptors, export of free cholesterol becomes more effective, resulting in less cholesterol exported via the 27-hydroxylase pathway. The balance between the two mechanisms for removal of cholesterol from macrophages may be of importance for formation of foam cells and development of atherosclerosis.
Single-site mutations in the conserved alternating-arginine region affect ionic channels formed by CryIAa, a Bacillus thuringiensis toxin (1997)

The role of the third domain of CryIAa, a Bacillus thuringiensis insecticidal toxin, in toxin-induced membrane permeabilization in a receptor-free environment was investigated. Planar lipid bilayer experiments were conducted with the parental toxin and five proteins obtained by site-directed mutagenesis in block 4, an arginine-rich, highly conserved region of the protein. Four mutants were constructed by replacing the first arginine in position 21 by a lysine (R521K), a glutamine (R521Q), a histidine (R521H), or a glutamic acid (R521E). A fifth mutant was obtained by replacing the fourth arginine by a lysine (R527K). Like CryIAa, the mutants formed cation-selective channels. A limited but significant reduction in channel conductance was observed for all mutants except R521H. The effect was more dramatic for the voltage dependence of the channels formed by R521K and R521Q, which was reversed compared to that of the parental toxin. This study provides the first direct evidence of a functional role for domain III in membrane permeabilization. Our results suggest that residues of the positive arginine face of block 4 interact with domain I, the putative pore-forming region of CryIAa.
Blind Separation of Event-Related Brain Responses into Independent Components (1996)

Abstract : Functional imaging of brain activity based on changes in blood flow does not supply information about the relative timing of brief bursts of neural activity in different brain areas. Multichannel electric or magnetic recordings from the scalp provide high temporal resolution, but are not easily decomposed into the separate activities of multiple brain networks. We report here a method for the blind separation of event-related brain responses into spatially stationary and temporally independent subcomponents using an Independent Component Analysis algorithm. Applied to electroencephalographic responses from an auditory detection task, each of the most active identified sources accounted for all or part of a previously identified response component. This spatiotemporal decomposition was robust to changes in sensors and input data length, and was stable within subjects. The method can be used to assess the timing, strength, and stability of event-related activity in brain networks during cognitive tasks, regardless of source location.
Analysis of ChIP-Seq Data (2007)

The arrival of next-generation sequencing (NGS) technologies has revolutionized the field of molecular biology. This is especially apparent in the field of genome-wide ChIP studies, where early successful applications to identification of transcription factor (TF) binding sites, regions of RNA Pol II activity and locations of histone modifications (Barski et al (2007), Mikkelsen et al (2007), Johnson et al (2007), Robertson et al (2007)) coupled with cost-effectivenes of the technology led to NGS supplanting microarrays (ChIP-Chip) as the tool of choice for these assays. The change in technology has led to the demand for new statistically-sound data analysis tools to determine genomic locations where protein-DNA interactions of interest occurred from raw data. Many such tools, often called peak-finders, are now openly available to researchers, and they approach the problem of region identification and assessing significance in numerous different ways. This large number of analysis approaches is partly due to complex biases the data exhibits and the need to account for them as well as lack of convincing data-generating model that would allow for straightforward calculation of statistical significance. In this talk we will give overview of ChIP-Seq assays and some properties of the data that affect downstream analysis. We note here that we will restrict ourselves to discussing the Illumina sequencing technology, the most widely used one in the field. We will then discuss some general features of current peak-finding tools and propose our own approach to peak-finding in the context of TF binding site identification.
Malaria vaccine: Immunization of mice with a synthetic T cell helper epitope alone leads to protective immunity (1993)

The immunogenicity of the non-repetitive sequences of the Plasmodium berghei circumsporozoite (CS) protein was studied using synthetic peptides. Two CS sequences (residues 20-39 and 57-70) exhibiting T cell helper activity were identified. Immunization of BALB/c mice with a branched peptide containing either the 20-39 or the 57-70 sequence and two repeats (B epitope) in a linear sequence induced high titers of anti-repeat and anti-sporozoite antibodies. Mice immunized with the T-B construct (high antibody titers) or with the 57-70 epitope alone (no serum anti-repeat or anti-peptide antibodies) were protected to a similar degree after challenge with infective sporozoites. No protection was obtained in mice immunized with the 20-39 epitope. These results indicate that BALB/c mice can be protected either by effector T cells or by high levels of anti-repeat antibodies. Thus, in the same strain, a double mechanism of protection can be obtained by a synthetic peptide vaccine.
Electron Acceptor Materials Engineering in Colloidal Quantum Dot Solar Cells (2011)

Lead sulfide colloidal quantum dot (CQD) solar cells with a solar power conversion efficiency of 5.6% are reported. The result is achieved through careful optimization of the titanium dioxide electrode that serves as the electron acceptor. Metal-ion-doped sol-gel-derived titanium dioxide electrodes produce a tunable-bandedge, well-passivated materials platform for CQD solar cell optimization.
Molecular cloning and characterization of two genes encoding sigma factors that direct transcription from a Bacillus thuringiensis crystal protein gene promoter (1991)

Two sigma factors, sigma 35 and sigma 28, direct transcription from the Bt I and Bt II promoters of the cryIA(a) gene of Bacillus thuringiensis; this gene encodes a lepidopteran-specific crystal protoxin. These sigma factors were biochemically characterized in previous work (K. L. Brown and H. R. Whiteley, Proc. Natl. Acad. Sci. USA 85:4166-4170, 1988; K. L. Brown and H. R. Whiteley, J. Bacteriol. 172:6682-6688, 1990). In this paper, we describe the cloning of the genes encoding these two sigma factors, as well as their nucleotide and deduced amino acid sequences. The deduced amino acid sequences of the sigma 35 and sigma 28 genes show 88 and 85% identity, respectively, to the sporulation-specific sigma E and sigma K polypeptides of Bacillus subtilis. Transformation of the sigma 35 and sigma 28 genes into B. subtilis shows that the respective B. thuringiensis sigma factor genes can complement spoIIG55 (sigma E) and spoIIIC94 (sigma K) defects. Further, B. thuringiensis core polymerase reconstituted with either the sigma 35 or sigma 28 polypeptide directs transcription from B. subtilis promoters recognized by B. subtilis RNA polymerase containing sigma E and sigma K, respectively. Thus, sigma 35 and sigma 28 of B. thuringiensis appear to be functionally equivalent to sigma E and sigma K of B. subtilis. However, unlike the situation for sigma K in B. subtilis, the homologous sigma 28 gene in B. thuringiensis does not result from a late-sporulation-phase chromosomal rearrangement of two separate, partial genes.
Recombinant Gene Expression Protocols (1997)

The current explosive progress in molecular biological research can be definitively traced to the development of molecular cloning technology. The ability to insert specific gene sequences into cloning vectors and their subse­ quent expansion is the cornerstone of modem molecular biology. A direct practical outcome of molecular cloning technology is its application to ex­ press specific recombinant genes. Currently, recombinant gene products are used in a wide spectrum of applications, including gene therapy, production of bioactive pharmaceuticals, synthesis of novel biopolymers, in agriculture and animal husbandry, and so on. A fundamental requirement for successful recombinant gene expression is the design of the cloning vector and the choice of the host organism for expression. Recombinant Gene Expression Protocols grows out of the need for a laboratory manual that provides the reader the background and rationale, as well as the practical protocols for the preparation of "expression constructs" and their introduction into appropriate host cells and/or organisms. The chap­ ters in this book are grouped by their expression hosts, including E. coli, yeast, mammalian cells, nonmammalian eukaryotes such as plants, Xenopus, and insects, as well as in transgenic organisms. In-depth information is presented on the important characteristics of expression cloning vectors and the various methods for efficiently introducing expression constructs into target cells and/ or organisms. Throughout Recombinant Gene Expression Protocols, the authors have consistently striven for a balanced presentation of both background informa­ tion and actual laboratory details
An Outbreak of Enterically Transmitted non-A, non-B Hepatitis in Pakistan (1989)

An epidemic of enterically transmitted non-A, non-B hepatitis occurred at a college in Sargodha, Pakistan in early 1987. There were 133 clinical cases, an attack rate of approximately 20%. Though the disease was relatively mild, all clinical cases required hospitalization and prolonged convalescence. Nearly all cases were associated with a single water source. The epidemic ended when the water supply was improved. This is the 4th described epidemic of non-A, non-B hepatitis in Pakistan.
Insulin-Mediated Regulation of Neuronal Maturation (1984)

Exposure to insulin increased stimulus-evoked transmission at synapses formed in culture by cholinergic retinal neurons derived from fetal rats. This effect occurred at physiological concentrations and was long lasting. The findings support the hypothesis that insulin may serve as a developmental signal to regulate the emergence of effective neurotransmission across nascent synapses.
Synthesis and Characterization of Truncated Triangular Silver Nanoplates (2002)

Truncated triangular silver nanoplates have been synthesized in large quantities using a solution phase method in the presence of cetyltrimethylammonium bromide micelles. The obtained particles have an average edge size of 68 nm, thickness of 24 nm, and the degree of truncation of 0.35. They are single crystals, with a (111) lattice plane as the basal plane. The aqueous solution of these particles displays a clear red color due to a strong in-plane dipole plasmon resonance peaked at 552 nm. These particles can self-assemble into chainlike nanostructures through either partial or close stacking of neighborhood nanoplates.
Detection of occult metastatic breast cancer cells in blood by a multimolecular marker assay: correlation with clinical stage of disease. (2001)

Currently, molecular markers offer the unique opportunity to identify occult metastasis in early stage cancer patients not otherwise detected with conventional staging techniques. To date, well-characterized molecular tumor markers to detect occult breast cancer cells in blood are limited. Because breast tumors are heterogeneous in tumor marker expression, we developed a "multimarker" reverse transcription-PCR assay combined with the highly sensitive electrochemiluminescence automated detection system. Breast cancer cell lines (n = 7), primary breast tumors (n = 25), and blood from normal donors (n = 40) and breast cancer patients [n = 65; American Joint Committee on Cancer (AJCC) stages I-IV] were assessed for four mRNA tumor markers: beta-human chorionic gonadotropin (beta-hCG), oncogene receptor (c-Met), beta 1-->4-N-acetylgalactosaminyl-transferase, and a tumor-associated antigen (MAGE-A3). None of the tumor markers were expressed in any normal donor bloods. Breast cancer cell lines and primary breast tumors expressed beta-hCG, c-Met, beta 1-->4-N-acetylgalactosaminyl-transferase, and MAGE-A3 mRNA. Of the 65 breast cancer patient blood samples assessed, 2, 3, 15, 49, and 31% expressed 4, 3, 2, 1, and 0 of the mRNA tumor markers, respectively. At least two markers were expressed in 20% of the blood specimens. The addition of a combination of markers enhanced detection of systemic metastasis by 32%. In patient blood samples, the MAGE-A3 marker correlated significantly with tumor size (P = 0.0004) and AJCC stage (P = 0.007). The combination of beta-hCG and MAGE-A3 mRNA markers correlated significantly with tumor size (P = 0.04), and the marker combination c-Met and MAGE-A3 showed a significant correlation with tumor size (P = 0.005) as well as AJCC stage (P = 0.018). A multimarker reverse transcription-PCR assay that correlates with known clinicopathological prognostic parameters may have potential clinical utility by monitoring tumor progression with a blood test.
Gene Flow and Natural Selection in the Origin of Drosophila pseudoobscura and Close Relatives (1997)

The divergence of Drosophila pseudoobscura and close relatives D. persimilis and D. pseudoobscura bogotana has been studied using comparative DNA sequence data from multiple nuclear loci. New data from the Hsp82 and Adh regions, in conjunction with existing data from Adh and the Period locus, are examined in the light of various models of speciation. The principal finding is that the three loci present very different histories, with Adh indicating large amounts of recent gene flow among the taxa, while little or no gene flow is apparent in the data from the other loci. The data were compared with predictions from several isolation models of divergence. These models include no gene flow, and they were found to be incompatible with the data. Instead the DNA data, taken together with other evidence, seem consistent with divergence models in which natural selection acts against gene flow at some loci more than at others. This family of models includes some sympatric and parapatric speciation models, as well as models of secondary contact and subsequent reinforcement of sexual isolation.
Stability of poliovirus RNA in cell-free translation systems utilizing two initiation sites. (1981)

The stability of purified poliovirus RNA in cell-free translation systems prepared from HeLa cells or rabbit reticulocytes has been examined. Degradation of the RNA occurs with a t1/2 of approximately 35 min at 30 degrees C under conditions used for in vitro translation. Degradation is due in part to activity in the cell lysate, and in part to contaminants in the commercial preparations of creatine phosphokinase used in the energy-regenerating system. Addition of crude preparations of initiation factors significantly slows degradation, presumably as a result of protein-RNA interactions which confer resistance to nuclease action. Prior treatment of RNA with methylmercury hydroxide has no effect on degradation rates. On the other hand, endogenous mRNA, present as a messenger ribonucleoprotein particle in extracts from poliovirus-infected HeLa cells, remains completely intact during in vitro translation. These infected cell extracts synthesize the normal complement of viral proteins and utilize two different initiation sites for translation. Treatment of the infected cell extract with micrococcal nuclease destroys the endogenous mRNA. Subsequent addition of exogenous RNA to the same extract results in the formation of a protein-associated RNA particle with sedimentation properties slightly different from the endogenous messenger ribonucleoprotein, and the added RNA is unstable. We conclude that two initiation sites can be utilized on intact poliovirus mRNA, and fragmentation of the RNA is not prerequisite for generation of a second site in this RNA.
In vivo measurements of the elastic mechanical properties of human skin by indentation tests (2007)

Knowledge about the human skin mechanical properties is essential in several domains, particularly for dermatology, cosmetic or to detect some cutaneous pathology. This study proposes a new method to determine the human skin mechanical properties in vivo using the indentation test. Usually, the skin mechanical parameters obtained with this method are influenced by the mechanical properties of the subcutaneous layers, like muscles. In this study, different mechanical models were used to evaluate the effect of the subcutaneous layers on the measurements and to extract the skin elastic properties from the global mechanical response. The obtained results demonstrate that it is necessary to take into account the effect of the subcutaneous layers to correctly estimate the skin Young's modulus. Moreover, the results illustrate that the variation of the measured Young's modulus at low penetration depth cannot be correctly described with usual one-layer mechanical models. Thus a two-layer elastic model was proposed, which highly improved the measurement of the skin mechanical properties.
Evaluating Speech, Face, Emotion and Body Movement Time-series Features for Automated Multimodal Presentation Scoring (2015)

We analyze how fusing features obtained from different multimodal data streams such as speech, face, body movement and emotion tracks can be applied to the scoring of multimodal presentations. We compute both time-aggregated and time-series based features from these data streams--the former being statistical functionals and other cumulative features computed over the entire time series, while the latter, dubbed histograms of cooccurrences, capture how different prototypical body posture or facial configurations co-occur within different time-lags of each other over the evolution of the multimodal, multivariate time series. We examine the relative utility of these features, along with curated speech stream features in predicting human-rated scores of multiple aspects of presentation proficiency. We find that different modalities are useful in predicting different aspects, even outperforming a naive human inter-rater agreement baseline for a subset of the aspects analyzed.