gebhart/patrepeval huggingface dataset:
Induction of interferon gamma production by natural killer cell stimulatory factor: characterization of the responder cells and synergy with other inducers. (1991)

We previously reported that natural killer cell stimulatory factor (NKSF), a heterodimeric lymphokine purified from the conditioned medium of human B lymphoblastoid cell lines, induces interferon gamma (IFN-gamma) production from resting peripheral blood lymphocytes (PBL) and synergizes with interleukin 2 in this activity. In this study, we show that human NKSF induces IFN-gamma production from both resting and activated human PBL and from freshly isolated murine splenocytes. Human T and NK cells produce IFN-gamma in response to NKSF, but resting PBL require the presence of nonadherent human histocompatibility leukocyte antigens DR+ (HLA-DR+) accessory cells to respond to NKSF. The mechanism(s) by which NKSF induces IFN-gamma production results in accumulation of IFN-gamma mRNA, is insensitive to cyclosporin A, and synergizes with those mediated by phytohemagglutinin, phorbol diesters, anti-CD3 antibodies, and allogeneic antigens, but not by Ca2+ ionophores. The ability of NKSF to directly induce IFN-gamma production and to synergize with other physiological IFN-gamma inducers, joined with the previously described ability to enhance lymphocyte cytotoxicity and proliferation, indicates that this lymphokine is a powerful immunopotentiating agent.
Nucleotide sequence analysis of a 10.5 kbp HindIII fragment of fowlpox virus: relatedness to the central portion of the vaccinia virus HindIII D region (1990)

The nucleotide sequence of a 10465 bp HindIII genomic fragment from fowlpox virus (FPV) is presented. Analysis of the nucleotide sequence revealed 10 potential major open reading frames (ORFs). Five of these ORFs are predicted to encode polypeptides with significant homology to hypothetical polypeptides derived from nucleotide sequence analysis of the vaccinia virus (VV) HindIII D region. Interestingly, these homologous ORFs do not occur in the same tandem arrangement in the FPV genome as they do in the VV genome. These results are discussed.
Computational Alanine Scanning of Protein-Protein Interfaces (2004)

Protein-protein interactions are key components of all signal transduction processes, so methods to alter these interactions promise to become important tools in dissecting function of connectivities in these networks. We have developed a fast computational approach for the prediction of energetically important amino acid residues in protein-protein interfaces (available at http://robetta.bakerlab.org/alaninescan), which we, following Peter Kollman, have termed "computational alanine scanning." The input consists of a three-dimensional structure of a protein-protein complex; output is a list of "hot spots," or amino acid side chains that are predicted to significantly destabilize the interface when mutated to alanine, analogous to the results of experimental alanine-scanning mutagenesis. 79% of hot spots and 68% of neutral residues were correctly predicted in a test of 233 mutations in 19 protein-protein complexes. A single interface can be analyzed in minutes. The computational methodology has been validated by the successful design of protein interfaces with new specificity and activity, and has yielded new insights into the mechanisms of receptor specificity and promiscuity in biological systems.
Fat in flames: influence of cytokines and pattern recognition receptors on adipocyte lipolysis (2015)

Adipose tissue has the largest capacity to store energy in the body and provides energy through the release of free fatty acids during times of energy need. Different types of immune cells are recruited to adipose tissue under various physiological conditions, indicating that these cells contribute to the regulation of adipose tissue. One major pathway influenced by a number of immune cells is the release of free fatty acids through lipolysis during both physiological (e.g., cold stress) and pathophysiological processes (e.g., obesity, type 2 diabetes). Adipose tissue expansion during obesity leads to immune cell infiltration and adipose tissue remodeling, a homeostatic process that promotes inflammation in adipose tissue. The release of proinflammatory cytokines stimulates lipolysis and causes insulin resistance, leading to adipose tissue dysfunction and systemic disruptions of metabolism. This review focuses on the interactions of cytokines and other inflammatory molecules that regulate adipose tissue lipolysis during physiological and pathophysiological states.
The ligand binding site of the platelet integrin receptor GPIIb-IIIa is proximal to the second calcium binding domain of its alpha subunit. (1990)

The extreme carboxyl-terminal amino acid sequence of the gamma chain of fibrinogen is involved in the binding of this adhesive protein to the platelet integrin glycoprotein (GP) IIb-IIIa, and synthetic peptides corresponding to this region inhibit fibrinogen as well as fibronectin and von Willebrand factor binding to platelets. A chemical cross-linking approach was used to characterize the interaction of a 16-amino acid fibrinogen gamma chain peptide with platelets and to localize the site of its binding to GPIIb-IIIa. This peptide became specifically cross-linked to GPIIb, and platelet stimulation selectively enhanced its cross-linking to this alpha subunit. The cross-linking reaction was specifically inhibited by fibrinogen and an Arg-Gly-Asp peptide but not by an unrelated protein or a substituted peptide. Utilizing a combination of immunochemical mapping, enzymatic and chemical digestions, and amino acid sequencing, the cross-linking site of the gamma chain peptide in GPIIb was localized to a stretch of 21 amino acids. The identified region, GPIIb 294-314, contains the second putative calcium binding domain within GPIIb. The primary structure of this region is highly conserved among alpha subunits of other integrin adhesion receptors. These results identify a discrete region of GPIIb that resides in close proximity to a ligand binding site within GPIIb-IIIa. The homologous region may be involved in the functions of other integrin receptors.
[The relative importance of different oxidants in the degradation process of quinoline using O3/UV]. (2003)

In this paper the relative importance of different oxidants in the degradation process of quinoline using O3/UV was studied. O3 and .OH played the most important roles in removing quinoline. Their concentrations were measured using indigo method and .OH-probe compound (p-CBA) method respectively, and the relative importance of these two oxidants was quantitatively determined. The second-order reaction rate constant between quinoline and hydroxyl radical was calculated as 6.65 x 10(9) mol.(L.s)-1. In the present experimental condition, .OH and O3 oxidations contributing to the total degradation rate of quinoline were 88% and 12% respectively. Increasing the hydroxyl radical concentration will help to improve the total removal rate of quinoline.
Structural Characterization of Follistatin: A Novel Follicle-Stimulating Hormone Release-Inhibiting Polypeptide from the Gonad (1987)

Follistatin, a novel, single chain, glycosylated polypeptide bearing no homology with previously characterized inhibins but exhibiting potent and specific pituitary FSH-release inhibition has been structurally characterized by protein microsequencing, cDNA cloning, and DNA sequencing. Two populations of clones differing in their 3'-untranslated sequences were found to encode a 344 amino acid precursor protein and an identical but carboxyl terminal truncated 317 amino acid precursor, respectively. Additionally, one clone, FS18, contained two introns and probably resulted from reverse transcription of heterogeneous nuclear RNA during cDNA library construction. Follistatin is unusually cysteine-rich, containing 36 cysteines in the mature coding sequence of 315 amino acids and an extremely acidic carboxyl terminal region, FS(292-304), comprised of Glu-Asp-Thr-Glu-Glu-Glu-Glu-Glu-Asp-Glu-Asp-Gln-Asp which probably resides outside a tightly cross-linked protein sphere. The heparin-binding ability of follistatin can probably be ascribed to the basic region specified by FS(75-86), Lys-Lys-Cys-Arg-Met-Asn-Lys-Lys-Asn-Lys. Overall, follistatin is organized into three homologous domains, FS(66-135), FS(139-210), and FS(216-287) containing 70, 72, and 72 amino acids, respectively, which show a 52% homology among themselves and a 57% homology with the 56 amino acid human pancreatic secretory trypsin inhibitor protein when aligned for maximum homology.
SMERS: Music Emotion Recognition Using Support Vector Regression (2009)

Music emotion plays an important role in music retrieval, mood detection and other music-related applications. Many issues for music emotion recognition have been addressed by different disciplines such as physiology, psychology, cognitive science and musicology. We present a support vector regression (SVR) based music emotion recognition system. The recognition process consists of three steps: (i) seven distinct features are extracted from music; (ii) those features are mapped into eleven emotion categories on Thayer’s two-dimensional emotion model; (iii) two regression functions are trained using SVR and then arousal and valence values are predicted. We have tested our SVR-based emotion classifier in both Cartesian and polar coordinate system empirically. The result indicates the SVR classifier in the polar representation produces satisfactory result which reaches 94.55% accuracy superior to the SVR (in Cartesian) and other machine learning classification algorithms such as SVM and GMM.
Overproduction of corticotropin-releasing factor in transgenic mice: a genetic model of anxiogenic behavior (1994)

Corticotropin-releasing factor (CRF) is released in response to various stressors and regulates adrenocorticotropin secretion and glucocorticoid production. In addition to its endocrine functions, CRF acts as a neuromodulator in extra-hypothalamic systems and has been shown to play a role in behavioral responses to stress. CRF overproduction has been implicated in affective disorders such as depression and anorexia nervosa. A transgenic mouse model of CRF overproduction has been developed in order to examine the endocrine and behavioral effects of chronic CRF excess. CRF transgenic animals exhibit endocrine abnormalities involving the hypothalamic-pituitary-adrenal axis such as elevated plasma levels of ACTH and glucocorticoids. The present series of experiments tested the hypothesis that chronic overproduction of CRF throughout the life-span of these animals may lead to an anxiogenic behavioral state. CRF transgenic mice and normal littermate controls were tested by measuring locomotor activity in a novel environment and through the use of an elevated plus-maze as indices of anxiety. CRF transgenic animals exhibited an increase in anxiogenic behavior, an effect known to occur following central administration of CRF in mice and rats. Injection of the CRF antagonist alpha-helical CRF 9-41 into the lateral cerebral ventricles reversed the anxiogenic state observed in the CRF transgenics. This finding supports the possibility that central CRF overproduction may mediate the anxiogenic behavior exhibited in this animal model. Thus, CRF transgenic mice represent a genetic model of CRF overproduction that provides a valuable tool for investigating the long-term effects of CRF excess and dysregulation in the CNS.
Couette membrane filtration with constant shear stress. (1989)

Recent developments in the field of blood component separation have revealed the usefulness of membrane filtration using couette type configurations and Taylor vortices as an efficient and effective method. The authors have analyzed in detail the physical and chemical effects on whole blood separated into protein rich plasma, and concentrated red blood cell suspensions, using this technique. The authors also have calculated and demonstrated the technical specifications required to provide laminar flow with Taylor Vortex formation throughout the device, as well as those required to retain constant shear stress on the blood components as viscosity changes. By maintaining constant shear stress below a critical level, it is possible to avoid shear induced hemolysis and to maintain maximal separation efficiency throughout the procedure. The device has further been designed to alter the filtration velocity along the membrane so that the critical filtration velocity is nowhere exceeded, i.e., concentration polarization effects are prevented.
Inferring the most important types of a query (2008)

In this paper we present a technique for ranking the most important types or categories for a given query. Rather than trying to find the category of the query, known as query categorization, our approach seeks to find the most important types related to the query results. Not necessarily the query category falls into this ranking of types and therefore our approach can be complementary.
Trapped Photons Induced Ultrahigh External Quantum Efficiency and Photoresponsivity in Hybrid Graphene/Metal‐Organic Framework Broadband Wearable Photodetectors (2018)

Abstract Metal‐organic frameworks (MOFs) have recently emerged as attractive materials for their tunable properties, which have been utilized for diverse applications including sensors, gas storage, and drug delivery. However, the high porosity and poor electrical conductivity of MOFs restrict their optoelectronic applications. Owing to the inherent tunability, a broadband photon absorbing MOF can be designed. Combining the superior properties of the MOFs along with ultrahigh carrier mobility of graphene, for the first time, this study reports a highly sensitive, broadband, and wearable photodetector on a polydimethylsiloxane substrate. The external quantum efficiency of the hybrid photodetector is found to be &gt;5 × 10 8 %, which exceeds all the reported values of similar devices. The porosity of the MOF and ripple structure graphene can assist the trapping of photons at the light‐harvesting layer. The device photoresponsivity is found to be &gt;10 6 A W −1 with a response time of &lt;150 ms, which is approximately ten times faster than the current standards of the graphene‐organic hybrid photodetectors. In addition, utilizing the excellent flexibility of the graphene layer the wearability of the devices with stretchability up to 100% is demonstrated. The unique discovery of MOF‐based high‐performance photodetectors opens up a new avenue in organic–inorganic hybrid optoelectronics.
Differentiation of Human U937 Promonocytic Cells is Impaired by Moderate Copper Deficiency (2001)

Copper (Cu) deficiency suppresses macrophage activities in animals and humans. Our previous studies indicated that the induction of Cu deficiency in differentiated U937 monocytic cells impairs respiratory burst and bactericidal activities and lipopolysaccharide-mediated secretion of inflammatory mediators. The current investigation examined the roles of Cu in the monocytic differentiation process. Human U937 promonocytic cells were exposed to a high affinity Cu chelator (5 microM 2,3,2-tetraamine [tet]) for 24 hr before inducing differentiation by treatment with 1,25-dihydroxyvitamin D3 plus interferon-gamma (DI). This procedure decreased cell Cu by 55% without compromising cellular Zn, Fe, or general metabolic activities. Lower Cu status significantly attenuated the expression of maturation markers Mac-1 (CD11b), ICAM-1 (CD54), and LPS-R (CD14). This change was associated with a marked suppression in respiratory burst activity and killing of Salmonella. To examine if the adverse effect of inadequate Cu on the DI-induced differentiation represented a more general defect, U937 cells were treated with phorbol 12-myristate 13-acetate (PMA). Lower Cu status also suppressed PMA-mediated differentiation of U937 cells. Supplemental Cu, but not Zn or Fe, blocked the tet-induced declines in cell Cu, expression of maturation markers, and respiratory burst and bactericidal activities. These results demonstrate that Cu is essential for the monocytic differentiation process that contributes to the competency of the host's defense system.
Designer genes: recombinant antibody fragments for biological imaging. (2000)

Monoclonal antibodies (MAbs), with high specificy and high affinity for their target antigens, can be utilized for delivery of agents such as radionuclides, enzymes, drugs, or toxins in vivo. However, the implementation of radiolabeled antibodies as "magic bullets" for detection and treatment of diseases such as cancer has required addressing several shortcomings of murine MAbs. These include their immunogenicity, sub-optimal targeting and pharmacokinetic properties, and practical issues of production and radiolabeling. Genetic engineering provides a powerful approach for redesigning antibodies for use in oncologic applications in vivo. Recombinant fragments have been produced that retain high affinity for target antigens, and display a combination of rapid, high-level tumor targeting with concomitant clearance from normal tissues and the circulation in animal models. An important first step was cloning and engineering of antibody heavy and light chain variable domains into single-chain Fvs (molecular weight, 25-27 kDa), in which the variable regions are joined via a synthetic linker peptide sequence. Although scFvs themselves showed limited tumor uptake in preclinical and clinical studies, they provide a useful building block for intermediate-sized recombinant fragments. Covalently linked dimers or non-covalent dimers of scFvs (also known as diabodies) show improved targeting and clearance properties due to their higher molecular weight (55 kDa) and increased avidity. Further gains can be made by generation of larger recombinant fragments, such as the minibody, an scFv-CH3 fusion protein that self-assembles into a bivalent dimer of 80 kDa. A systematic evaluation of scFv, diabody, minibody, and intact antibody (based on comparison of tumor uptakes, tumor:blood activity ratios, and calculation of an Imaging Figure of Merit) can form the basis for selection of combinations of recombinant fragments and radionuclides for imaging applications. Ease of engineering and expression, combined with novel specificities that will arise from advances in genomic and combinatorial approaches to target discovery, will usher in a new era of recombinant antibodies for biological imaging.
Pharmacokinetic assessment of irinotecan, SN-38, and SN-38-glucuronide: a substudy of the FIRIS study. (2013)

No alterations in CPT-11 pharmacokinetics after repeated IRIS or FOLFIRI administration were observed. Neutropenia was more frequent in the FOLFIRI group than in the IRIS group because exposure to SN-38 was greater in the former group.
Stress signaling in yeast (1995)

In the yeast Saccharomyces cerevisiae three positive transcriptional control elements are activated by stress conditions: heat shock elements (HSEs), stress response elements (STREs) and AP-1 responsive elements (AREs). HSEs bind heat shock transcription factor (HSF), which is activated by stress conditions causing accumulation of abnormal proteins. STREs mediate transcriptional activation by multiple stress conditions. They are controlled by high osmolarity via the HOG signal pathway, which comprises a MAP kinase module and a two-component system homologous to prokaryotic signal transducers. AREs bind the transcription factor Yap1p. The three types of control elements seem to have overlapping, but distinct functions. Some stress proteins encoded by HSE-regulated genes are necessary for growth of yeast under moderate stress, products of STRE-activated genes appear to be important for survival under severe stress and ARE-controlled genes may mainly function during oxidative stress and in the response to toxic conditions, such as caused by heavy metal ions.
Leukotriene production in gerbil brain after ischemic insult, subarachnoid hemorrhage, and concussive injury (1985)

A leukotriene-like immunoreactivity was measured by radioimmunoassay in the gerbil forebrain following ischemia and reperfusion, subarachnoid hemorrhage (SAH), or nonlethal concussive brain injury. In each paradigm an increase in immunoreactivity levels was found. Peak levels were reached 15 to 30 minutes after each insult, and slowly returned to baseline over the next 24 hours. The study supports the suggestion that cerebral vessels and circulating blood are capable of producing leukotrienes, and that a major source of production is a nonvascular component within gray matter, possibly the cortical neuron. Leukotrienes may play a role in the pathophysiology of cerebral edema formation, cerebral vasospasm, seizure activity, and other central nervous system abnormalities. These studies are the first to demonstrate leukotriene production in gerbil brain following SAH or concussive brain injury.
Monolithic coaxial transmission lines for mm-wave ICs (2002)

A transmission line with potential application to terahertz ICs has been fabricated and characterized. The transmission line is a coaxial (shielded) line which is integrable and compatible with existing monolithic microwave integrated circuit (MMIC) technology. The structure is composed of a center conductor surrounded by a homogeneous dielectric (probimide), covered entirely by a gold plated ground plane. The coaxial lines are terminated to coplanar waveguide pads for on-wafer microwave measurements. The loss and other lumped transmission line parameters were extracted from the measured S-parameter data. The simulation results based on initial experimental data suggest the usefulness of coaxial line in the frequency range above 200 GHz. The shielded coaxial lines have the following characteristics: no radiation losses, no crosstalk between adjacent lines which enables denser IC design, compatible with existing MMIC technology, and easy transition to microstrip and coplanar waveguides.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improving Localization Robustness in Monocular SLAM Using a High-Speed Camera (2008)

In the robotics community localization and mapping of an unknown environment is a well-studied problem. To solve this problem in real-time using visual input, a standard monocular Simultaneous Localization and Mapping (SLAM) algorithm can be used. This algorithm is very stable when smooth motion is expected, but in case of erratic or sudden movements, the camera pose typically gets lost. To improve robustness in Monocular SLAM (MonoSLAM) we propose to use a camera with faster readout speed to obtain a frame rate of 200Hz. We further present an extended MonoSLAM motion model, which can handle movements with significant jitter. In this work the improved localization and mapping have been evaluated against ground truth, which is reconstructed from off-line vision. To explain the benefits of using a high frame rate vision input in MonoSLAM framework, we performed repeatable experiments with a high-speed camera mounted onto a robotic arm. Due to the dense visual information MonoSLAM can faster shrink localization and mapping uncertainties and can operate under fast, erratic, or sudden movements. The extended motion model can provide additional robustness against significant handheld jitter when throwing or shaking the camera.