gebhart/patrepeval huggingface dataset:
Prospects for beta 3-adrenoceptor agonists in the treatment of obesity and diabetes. (1996)

beta 3-Adrenoceptor (beta 3-AR) agonists were first identified more than twelve years ago and were found to be remarkably effective in animal models of obesity and Type II (non-insulin dependent) diabetes. Those that have been taken forward to clinical studies have not, however, proved so effective in humans: they have either been of limited efficacy, or their activities have been accompanied by significant side-effects. Reasons for the failure of some beta 3-AR agonists in humans have included a poor pharmacokinetic profile and, possibly, a failure of prodrugs to be metabolised to selective beta 3-AR agonists. A more fundamental problem, however, is that the human and rat beta 3-AR differ pharmacologically, and those compounds that have been evaluated in humans have much lower efficacy at the human than the rat receptor. This problem may be compounded by there being a low number of beta 3-AR relative to beta 1-AR and beta 2-AR in those tissues that mediated thermogenesis in humans, so that low efficacy compounds tend to exhibit mainly beta 1-AR or beta 2-AR-, rather than beta 3-AR-mediated effects, despite their having selective affinity for human beta 3-AR. Nevertheless, studies using CGP 12177, which is an agonist at beta 3-AR but an antagonist at beta 1-AR and beta 2-AR, demonstrate that functional beta 3-AR are present in human adipose tissue. Moreover, the association of a polymorphism in the human beta 3-AR with obesity and diabetes demonstrates that this receptor is relevant to these diseases in humans. Thus the true potential of beta 3-AR agonists in humans can only be evaluated when a compound with good selectivity and efficacy at the human beta 3-AR, coupled with a long duration of action in vivo, has been identified.
beta-Lipotropin as a prohormone for the morphinomimetic peptides endorphins and enkephalins. (1976)

The hypophysial homomeric peptide beta-lipotropin (beta-LPH-[1-91]) has no morphinomomimetic activity in a bioassay (myenteric plexus-longitudinal muscle of the guinea pig's ileum) or binding assays with stereospecific opiate-receptors of rat brain synaptosome preparations. Incubating beta-LPH-[1-91] at neutral pH with the supernatant aqueous extracts of rat brain generates (fragments of beta-LPH with) morphinomimetic activity in the same assay systems. These results are related to the recently recognized structural relationships between beta-LPH, the newly isolated peptides met-enkephalin (beta-LPH-[61-65]) and alpha-endorphin (beta-LPH-[61-76]) and also to the biologically active fragments of analogs: beta-LPH-[61-64], beta-LPH-[61-65[-NH2, (Met(O)65)-BETA-LPH-[61-65], beta-LPH-[61-69], and beta-LPH-[61-69]. Enzymatic biogenesis of these morphinomimetic peptides would preclude localizing them as such in cellular or subcellular elements with currently available methodology.
Thermal Conductance across Phosphonic Acid Molecules and Interfaces: Ballistic versus Diffusive Vibrational Transport in Molecular Monolayers (2015)

The influence of planar organic linkers on thermal boundary conductance across hybrid interfaces has focused on the organic/inorganic interaction energy rather than on vibrational mechanisms in the molecule. As a result, research into interfacial transport at planar organic monolayer junctions has treated molecular systems as thermally ballistic. We show that thermal conductance in phosphonic acid (PA) molecules is ballistic, and the thermal boundary conductance across metal/PA/sapphire interfaces is driven by the same phononic processes as those across metal/sapphire interfaces without PAs, with one exception. We find a more than 40% reduction in conductance across henicosafluorododecylphosphonic acid (F21PA) interfaces, independent of metal contact, despite similarities in structure, composition, and terminal group to the variety of other PAs studied. Our results suggest diffusive scattering of thermal vibrations in F21PA, demonstrating a clear path toward modification of interfacial thermal transport based on knowledge of ballistic and diffusive scattering in single monolayer molecular interfacial films.
Immediate and Late Airway Response of Allergic Rhinitis Patients to Segmental Antigen Challenge: Characterization of Eosinophil and Mast Cell Mediators (1991)

Segmental antigen bronchoprovocation was used to define the nature of the inflammatory process in allergic airway disease. Bronchoalveolar lavage fluid obtained from allergic rhinitis patients 12 min after segmental antigen instillation (immediate response) revealed a significant increase in histamine and tryptase, but no cellular response. Repeat segmental lavage 48 h later (late response) showed marked and significant increases in both low and normal density eosinophils as well as striking elevations of eosinophil granular protein levels (major basic protein, eosinophil-derived neurotoxin, eosinophil cationic protein, and eosinophil peroxidase). Leukotriene C4, but not tryptase, concentrations were also consistently elevated in late lavage samples. Further, the late lavage samples showed a significant increase in interleukin-5 concentrations that correlated with the presence of eosinophils and eosinophil granular proteins. Neither eosinophils nor soluble mediators of eosinophils increased when normal subjects were similarly challenged with antigen. These data suggest that eosinophils are attracted to the airway during the late-phase allergic reaction and that IL-5 may produce changes in airway eosinophil density and promote the release of granular proteins to cause airway injury.
Quantitative MRI of the brain : measuring changes caused by disease (2003)

Contributors.Reviewers.Foreward.Introduction.Section A: The Measurement Process.1. Concepts: Measurement and MR (Paul S. Tofts).2. The Measurement Process: MR Data Collection and Image Analysis (Paul S. Tofts).3. QA: Quality Assurance, Accuracy, Precision and Phantoms (Paul S. Tofts).Section B: Windows into the Brain: Measuring MR Parameters.4. PD: Proton Density of Tissue Water (Paul Tofts).5. T1: the Longitudinal Relaxation Time (Penny A. Gowland and Valerie L. Stevenson).6. T2: the Transverse Relaxation Time (Philip A. Boulby and Fergus J. Rugg-Gunn).7. D: the Diffusion of Water (Claudia A.M. Wheeler-Kingshott, Gareth J. Barker, Stefan C.A. Steens and Mark A. van Buchem).8. MT: Magnetisation Transfer (Paul S. Tofts, Stefan C.A. Steens and Mark A. van Buchem).9. Spectroscopy: 1H Metabolite Concentrations (Paul S. Tofts and Adam D. Waldman).10. T1-w DCE-MRI: T1-weighted Dynamic Contrast-enhance d MRI (Geoff J.M. Parker and Anwar Padhani).11. T2- and T2-w DCE-MRI: Blood Perfusion and Volume Estimation using Bolus Tracking (Richard P. Kennan and H. Rolf Ja ger).12. Functional MRI (Peter Jezzard and Nick F. Ramsay).13. ASL: Blood Perfusion Measurements using Arterial Spin Labelling (Laura M. Parkes, John A. Detre).Section C: The Biology.14. Biology: The Significance of MR Parameters in Multiple Sclerosis (Bruno Brochet, Klaus G. Petry and Vincent Dousset).Section D: Analysing Images.15. Spatial Registration of Images (John Ashburner and Catriona D. Good).16. Volume and Atrophy (Geoff J.M. Parker and Declan T. Chard).17. Shape and Texture (William R. Crum).18. Histograms: Measuring Subtle Diffuse Disease (Paul S. Tofts, Gerard R. Davies and Jamshid Dehmeshki ).Section E: Where are we going?19. The Future of qMRI: Conclusions and Speculation (Paul S. Tofts).Appendix 1: Greek Alphabet for Scientific Use.Index.
Identification of universal selectivity‐determining positions in cytochrome P450 monooxygenases by systematic sequence‐based literature mining (2015)

Cytochrome P450 monooxygenases (CYPs) are a large, highly diverse protein family with a common fold. The sequences, structures, and functions of CYPs have been extensively studied resulting in more than 53,000 scientific articles. A sequence-based literature mining algorithm was designed to systematically analyze this wealth of information on SNPs, designed mutations, structural interactions, or functional roles of individual residues. Structurally corresponding positions in different CYPs were compared and universal selectivity-determining positions were identified. Based on the Cytochrome P450 Engineering Database (www.CYPED.BioCatNet.de) and a standard numbering scheme for all CYPs, 4000 residues in 168 CYPs mentioned in 2400 articles could be assigned to 440 structurally corresponding standard positions of the CYP fold, covering 96% of all standard positions. Seventeen individual standard positions were mentioned in the context of more than 32 different CYPs. The majority of these most frequently mentioned positions are located on the six substrate recognition sites and are involved in control of selectivity, such as the well-studied position 87 in CYP102A1 (P450(BM-3)) which was mentioned in the articles on 63 different CYPs. The recurrent citation of the 17 frequently mentioned positions for different CYPs suggests their universal functional relevance.
Exposing document context in the personal web (2002)

Reconnaissance agents show context by displaying documents with similar content to the one(s) the user currently has open. Research paper search engines show context by displaying documents that cite or are cited by the currently open document(s). We present a tool that applies such ideas to the personal web, that is, the space rooted in user documents but tightly connected to web documents as well. The tool organizes the personal web with a single topic hierarchy based on direct links, instead of the traditional file, bookmark, and (hidden) direct link hierarchies. The tool allows a user to easily navigate through related user and web documents, no matter whether the documents are related by directory-document, bookmark-document, direct-link, or even similar content relationships.
Adapted NOD/SCID model supports development of phenotypically and functionally mature T cells from human umbilical cord blood CD34+ cells (2002)

The NOD-LtSZ scid/scid (NOD/SCID) repopulation assay is the criterion for the study of self-renewal and multilineage differentiation of human hematopoietic stem cells. An important shortcoming of this model is the reported absence of T-cell development. We studied this aspect of the model and investigated how it could be optimized to support T-cell development. Occasionally, low-grade thymic engraftment was observed in NOD/SCID mice or Rag2(-/-)gamma(c)(-/-) mice. In contrast, the treatment of NOD/SCID mice with a monoclonal antibody against the murine interleukin-2R beta, (IL-2R beta) known to decrease natural killer cell activity, resulted in human thymopoiesis in up to 60% of the mice. T-cell development was phenotypically normal and resulted in polyclonal, mature, and functional CD1(-) TCR alpha beta (+) CD4(+) or CD8(+) single-positive T cells. In mice with ongoing thymopoiesis, peripheral T cells were observed. TREC analysis showed that T cells with a naive phenotype (CD45RA(+)) emerged from the thymus. In approximately half of these mice, the peripheral T cells included a pauciclonal outgrowth of CD45RO(+) cells. These data suggest that all elements of a functional immune system were present in these animals.
CCR5+and CXCR3+T cells are increased in multiple sclerosis and their ligands MIP-1α and IP-10 are expressed in demyelinating brain lesions (1999)

Multiple sclerosis (MS) is a T cell-dependent chronic inflammatory disease of the central nervous system. The role of chemokines in MS and its different stages is uncertain. Recent data suggest a bias in expression of chemokine receptors by Th1 vs. Th2 cells; human Th1 clones express CXCR3 and CCR5 and Th2 clones express CCR3 and CCR4. Chemokine receptors expressed by Th1 cells may be important in MS, as increased interferon-gamma (IFN-gamma) precedes clinical attacks, and IFN-gamma injection induces disease exacerbations. We found CXCR3(+) T cells increased in blood of relapsing-remitting MS, and both CCR5(+) and CXCR3(+) T cells increased in progressive MS compared with controls. Furthermore, peripheral blood CCR5(+) T cells secreted high levels of IFN-gamma. In the brain, the CCR5 ligand, MIP-1alpha, was strongly associated with microglia/macrophages, and the CXCR3 ligand, IP-10, was expressed by astrocytes in MS lesions but not unaffected white matter of control or MS subjects. Areas of plaque formation were infiltrated by CCR5-expressing and, to a lesser extent, CXCR3-expressing cells; Interleukin (IL)-18 and IFN-gamma were expressed in demyelinating lesions. No leukocyte expression of CCR3, CCR4, or six other chemokines, or anti-inflammatory cytokines IL-5, IL-10, IL-13, and transforming growth factor-beta was observed. Thus, chemokine receptor expression may be used for immunologic staging of MS and potentially for other chronic autoimmune/inflammatory processes such as rheumatoid arthritis, autoimmune diabetes, or chronic transplant rejection. Furthermore, these results provide a rationale for the use of agents that block CCR5 and/or CXCR3 as a therapeutic approach in the treatment of MS.
Chromatin accessibility, p300, and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia (2012)

Chromatin accessibility plays a key role in regulating cell type specific gene expression during hematopoiesis but has also been suggested to be aberrantly regulated during leukemogenesis. To understand the leukemogenic chromatin signature, we analyzed acute promyelocytic leukemia, a subtype of leukemia characterized by the expression of RARα-fusion proteins, such as PML-RARα. We used nuclease accessibility sequencing in cell lines as well as patient blasts to identify accessible DNA elements and identified > 100 000 accessible regions in each case. Using ChIP-seq, we identified H2A.Z as a histone modification generally associated with these accessible regions, whereas unsupervised clustering analysis of other chromatin features, including DNA methylation, H2A.Zac, H3ac, H3K9me3, H3K27me3, and the regulatory factor p300, distinguished 6 distinct clusters of accessible sites, each with a characteristic functional makeup. Of these, PML-RARα binding was found specifically at accessible chromatin regions characterized by p300 binding and hypoacetylated histones. Identifying regions with a similar epigenetic make up in t(8;21) acute myeloid leukemia (AML) cells, another subtype of AMLs, revealed that these regions are occupied by the oncofusion protein AML1-ETO. Together, our results suggest that oncofusion proteins localize to accessible regions and that chromatin accessibility together with p300 binding and histone acetylation characterize AML1-ETO and PML-RARα binding sites.
Graphene Plasmonics for Terahertz to Mid-Infrared Applications (2014)

In recent years, we have seen a rapid progress in the field of graphene plasmonics, motivated by graphene's unique electrical and optical properties, tunability, long-lived collective excitation and its extreme light confinement. Here, we review the basic properties of graphene plasmons: their energy dispersion, localization and propagation, plasmon-phonon hybridization, lifetimes and damping pathways. The application space of graphene plasmonics lies in the technologically significant, but relatively unexploited terahertz to mid-infrared regime. We discuss emerging and potential applications, such as modulators, notch filters, polarizers, mid-infrared photodetectors, and mid-infrared vibrational spectroscopy, among many others.
Progress In The Development Of A High Data Rate, High Capacity Optical Disk Buffer (1989)

Development of high data rate, high capacity optical disk buffer technology has reached demonstration of the basic modular breadboard. Test and operational data are presented.
Identifizierung und Charakterisierung von Bitterrezeptoren (2003)

Menschen nehmen Tausende von Stoffen als bitter wahr. Die chemische Struktur der verschiedenen Bitterstoffe ist sehr vielfältig: Sie reicht von kleinen Molekülen wie Kaliumchlorid oder Harnstoff, bis zu sehr komplexen organischen Verbindungen. Die Größe der einzigen bekannten menschlichen Familie von Bitterrezeptoren (TAS2Rs) wurde auf nur ca. 80-120 Mitglieder geschätzt. In Anbetracht der hohen Zahl und Komplexität der Bitterstoffe erscheint die Zahl von Rezeptoren als sehr gering. Dies führt natürlich zu einer Reihe von Fragen: Wie viele Mitglieder hat die menschliche TAS2R-Genfamilie? Wie viele verschiedene Substanzen können denselben Rezeptor aktivieren? Scheint die Zahl der TAS2R-Rezeptoren ausreichend, alle Bitterstoffe wahrnehmen zu können oder muss es noch andere Bitterrezeptorfamilien geben? Diese Fragen zu beantworten, ist das Ziel der vorliegenden Arbeit. Hier durchgeführte Analysen des menschlichen Genomprojektes zeigen, dass Menschen ca. 25 TAS2R-Rezeptoren besitzt, die eine sehr divergente Aminosäurestruktur aufweisen. Diese Rezeptoren wurden in eine neu entwickelte Expressionskassette kloniert, die den Transport des Rezeptors an die Zelloberfläche ermöglicht. Um Liganden für die menschliche TAS2R-Rezeptoren zu identifizieren, wurden die Rezeptoren in HEK293 Zellen exprimiert und mit verschiedenen Bitterstoffen stimuliert. Der Nachweis der Rezeptoraktivierung erfolgte durch Calcium-Imaging. Es konnte gezeigt werden, dass hTAS2R16 der menschliche Rezeptor zur Wahrnehmung von Salicin und verwandten bitteren Pyranosiden ist. So wird hTAS2R16 in HEK293 Zellen durch Salicin und chemisch verwandte Substanzen aktiviert. Ein Vergleich der in diesem Messsystem erhaltenen Daten mit psychophysikalisch ermittelten Geschmackswahrnehmungen beim Menschen, ergab eine hohe Übereinstimmung. Die Ergebnisse deuten auch darauf hin, dass die Desensitiverung einzelner Rezeptoren die Ursache für die Adaption des Bittergeschmacks ist. Der Nachweis der Expression des Rezeptors in menschlichen Geschmackspapillen, sowie die festgestellte Assoziation des G/A Polymorpphismus an Position 665 des hTAS2R16 Gens mit einer reduzierten Salicinwahrnehmung, sind weitere unabhängige Beweise für diese These. Ein anderer menschlicher Rezeptor, hTAS2R10, wird durch die Bitterstoffe Strychnin, Brucin und Denatonium aktiviert. Dies sowie die Tatsache, dass die zur Aktivierung benutzten Konzentrationen eine sinnvolle Korrelation zu dem menschlichen Geschmacksschwellwert von Strychnin zeigen, sind starke Hinweise, dass hTAS2R10 der menschliche Rezeptor zur Wahrnehmung von Strychnin und verwandten Substanzen ist. Die vorliegenden Daten zeigen eindeutig, dass die TAS2R-Rezeptoren auch beim Menschen Bitterrezeptoren darstellen. Sowohl hTAS2R16, als auch hTAS2R10 werden durch ein Spektrum strukturell sehr unterschiedlicher Bitterstoffe aktiviert. Falls die anderen Mitglieder der TAS2R-Familie ebenfalls dieses Verhalten zeigen, wäre es möglich, dass die nur ca. 25 Mitglieder umfassende TAS2R-Rezeptorfamilie des Menschen tatsächlich zur Wahrnehmung aller Bitterstoffe ausreicht.
Androgen insufficiency in women: diagnostic and therapeutic implications (2004)

The proposed key symptoms of the female androgen insufficiency syndrome (FAIS) include reduced libido, diminished well being and lowered mood. The diagnosis of FAIS is made on the basis of these symptoms in the setting of a low serum free testosterone level. However, there is currently no readily available inexpensive assay which reliably measures free testosterone levels in the female range. The diagnosis of FAIS is further complicated by the lack of data demonstrating a minimum serum free testosterone level which, if below this, correlates with the symptoms of FAIS. Despite the complexities involved with defining FAIS, the symptoms have been reported to respond well to testosterone replacement. There is a need for formulations of testosterone therapy specifically designed for use in women, along with clear guidelines regarding optimal therapeutic doses and long-term safety data.
Cystathionine γ-Lyase Overexpression Inhibits Cell Proliferation via a H2S-dependent Modulation of ERK1/2 Phosphorylation and p21Cip/WAK-1 (2004)

Cystathionine gamma-lyase (CSE) is a key enzyme in the trans-sulfuration pathway. CSE uses L-cysteine as a substrate to produce hydrogen sulfide (H2S). The CSE/H2S system has been shown to play an important role in regulating cellular functions in different systems. In the present study, we used CSE stably overexpressed HEK-293 cells to explore the effect of the CSE/H2S system on cell growth and proliferation. The overexpression of CSE resulted in increases in CSE mRNA levels, CSE proteins, and intracellular H2S production rates, as well as the inhibition of cell proliferation and DNA synthesis. These effects were accompanied by a sustained ERK activation and up-regulation of the cyclin-dependent kinase inhibitor p21Cip/WAK-1. Blocking the action of ERK with U0126 inhibited the induction of p21Cip/WAK-1, suggesting that ERK activation functions upstream of p21Cip/WAK-1 activation to initiate the CSE overexpression-induced cell growth inhibition. The antiproliferative effect of CSE is likely mediated by endogenously produced H2S because the H2S scavenger methemoglobin (10 microm) significantly decreased the H2S production rate and reversed the antiproliferative effect afforded by CSE. Exogenous H2S (100 microm) also inhibited cell proliferation. However, the other CSE-catalyzed products, ammonium and pyruvate, failed to inhibit cell proliferation. Methemoglobin also abolished the inhibitory effect of exogenous H2S on cell proliferation. Moreover, exogenous H2S induced a sustained ERK and p21Cip/WAK-1 activation. These findings support the hypothesis that endogenously produced H2S may play a fundamental role in cell proliferation and survival.
Cytotoxic activity of a recombinant fusion protein between insulin-like growth factor I and Pseudomonas exotoxin. (1991)

A chimeric toxin in which the cell binding domain of Pseudomonas exotoxin was replaced with mature human insulin-like growth factor I (IGF-I) was produced in Escherichia coli. This protein, IGF-I-PE40, was cytotoxic to human cell lines derived from a variety of tumor types, with a breast carcinoma line (MCF-7) and two hepatoma lines (HEP3B and HEPG2) showing the highest sensitivity to the toxin. The specificity of IGF-I-PE40 cytotoxicity was confirmed through competition with excess IGF-I and through blockage of toxin binding using an antibody specific to the type I IGF receptor. A potential interaction between the toxin and soluble IGF-binding proteins was also demonstrated. IGF-I-PE40 may be useful in the selective elimination of cells bearing the type I IGF receptor.
Proteolysis in Bacterial Regulatory Circuits (2003)

Proteolysis by cytoplasmic, energy-dependent proteases plays a critical role in many regulatory circuits, keeping basal levels of regulatory proteins low and rapidly removing proteins when they are no longer needed. In bacteria, four families of energy-dependent proteases carry out degradation. In all of them, substrates are first recognized and bound by ATPase domains and then unfolded and translocated to a sequestered proteolytic chamber. Substrate selection depends not on ubiquitin but on intrinsic recognition signals within the proteins and, in some cases, on adaptor or effector proteins that participate in delivering the substrate to the protease. For some, the activity of these adaptors can be regulated, which results in regulated proteolysis. Recognition motifs for proteolysis are frequently found at the N and C termini of substrates. Proteolytic switches appear to be critical for cell cycle development in Caulobacter crescentus, for proper sporulation in Bacillus subtilis, and for the transition in and out of stationary phase in Escherichia coli. In eukaryotes, the same proteases are found in organelles, where they also play important roles.