gebhart/patrepeval huggingface dataset:
Epigenetic control of plant stress response (2007)

Living organisms have the clearly defined strategies of stress response. These strategies are predefined by a genetic make-up of the organism and depend on a complex regulatory network of molecular interactions. Although in most cases, the plant response to stress based on the mechanisms of tolerance, resistance, and avoidance has clearly defined metabolic pathways, the ability to acclimate/adapt after a single generation exposure previously observed in several studies (Boyko A et al. [2007]: Nucleic Acids Res 35:1714-1725; Boyko and Kovalchuk, unpublished data), represents an interesting phenomenon that cannot be explained by Mendelian genetics. The latest findings in the field of epigenetics and the process of a reversible control over gene expression and inheritance lead to believe that organisms, especially plants, may have a flexible short-term strategy of the response to stress. Indeed, the organisms that can modify gene expression reversibly have an advantage in evolutionary terms, since they can avoid unnecessary excessive rearrangements and population diversification. This review covers various epigenetic processes involved in plant stress response. We focus on the mechanisms of DNA methylation and histone modifications responsible for the protection of somatic cells and inheritance of stress memories.
Retraction notice (2014)

The following article has been included in a multiple retraction: Karimi A, Navidbakhsh M, Yousefi H et al. An experimental study on the elastic modulus of gelatin hydrogels using different stress–strain definitions . J Thermoplast Compos Mater, first published on 29 April 2014, DOI: 10.1177/0892705714533377. In 2015 SAGE became aware of author misconduct concerning the suspected fabrication of identities, as well as the impersonation of legitimate individuals, to manipulate the peer review process across three separate journal publications. SAGE and the journal Editors immediately launched an investigation and have decided to retract the following articles for reasons of author misconduct. Alireza Karimi was the submitting author on 12 of the articles. SAGE regrets the academic record was compromised by manipulation of the peer review process and apologises to readers.
Nutzen von Parkhaus-Leitsystemen : Einsatzbereiche und wirtschaftliche Betrachtungen (2001)

Beschrieben wird das Parkhausleitsystem SIPARK von Siemens. Es stellt ein System zur Ueberwachung von Einzelstellplaetzen in Parkhaeusern und Tiefgaragen auf der Basis des SIMATIC-Automatisierungssystems dar. Die Stellplatzueberwachung erfolgt mittels Ultraschall-Sensor, der den Belegungszustand an eine Zentraleinheit meldet. Vorgestellt werden die Komponenten des Systems und dessen praktische Funktionsweise. Ferner werden die Nutzen fuer Parkhauskunden und Parkhausbetreiber behandelt und die Wirtschaftlichkeit des Systems analysiert. Eine Einbindung von Parkhaus-Leitsystemen mit Einzelplatzueberwachung in staedtische oder regionale Parkleit- oder Verkehrsleitsysteme ist moeglich. Titel in Englisch: Guidance systems for car parks - their potential use and economic considerations.
DNA Vaccines − A Modern Gimmick or a Boon to Vaccinology? (1997)

The reports in 1993 that naked DNA encoding viral genes conferred protective immunity came as a surprise to most vaccinologists. This review analyses the expanding number of examples where plasmid DNA induces immune responses. Issues such as the type of immunity induced, mechanisms of immune protection, and how DNA vaccines compare with other approaches are emphasized. Additional issues discussed include the likely means by which DNA vaccines induce CTL, how the potency and type of immunity induced can be modified, and whether DNA vaccines represent a practical means of manipulating unwanted immune response occurring during immunoinflammatory diseases. It seems doubtful if DNA vaccines will replace currently effective vaccines, but they may prove useful for prophylactic use against some agents that at present lack an effective vaccine. DNA vaccines promise to be valuable to manipulate the immune response in situations where responses to agents are inappropriate or ineffective.
High resolution audio synchronization using chroma onset features (2009)

The general goal of music synchronization is to automatically align the multiple information sources such as audio recordings, MIDI files, or digitized sheet music related to a given musical work. In computing such alignments, one typically has to face a delicate tradeoff between robustness and accuracy. In this paper, we introduce novel audio features that combine the high temporal accuracy of onset features with the robustness of chroma features. We show how previous synchronization methods can be extended to make use of these new features. We report on experiments based on polyphonic Western music demonstrating the improvements of our proposed synchronization framework.
Crystal and molecular structure of two seven-co-ordinate distorted pentagonal bipyramidal complexes of tantalum(V) (1975)

Crystals of (I)[TaCl3L12](L1=NN′-dicyclohexylacetamidinate) are tetragonal, space group I, with cell dimensions: a= 26.328(9), c= 10.368(5)Å, Z= 8. Crystals of (II)[TaCl3L1L2][L2=(probably)NN′-dicyclohexylureate] are monoclinic, space group Cc with cell dimensions a= 12.209(8), b= 23.464(15), c= 12.324(11)Å, β= 115.34(9)°, Z= 4. Both structures were solved by Patterson and Fourier methods from diffractometer data and refined by least-squares methods to R 0.075 [(I), 2 017 reflections] and 0.060 [(II), 2 232 independent reflections]. They are both distorted pentagonal bipyramidal structures with two of the chlorine atoms in axial positions and the other equatorial. The two bidentate ligands complete the pentagonal girdle.
Energy scavenging from insect flight (2011)

This paper reports the design, fabrication and testing of an energy scavenger that generates power from the wing motion of a Green June Beetle (Cotinis nitida) during its tethered flight. The generator utilizes non-resonant piezoelectric bimorphs operated in the d31 bending mode to convert mechanical vibrations of a beetle into electrical output. The available deflection, force, and power output from oscillatory movements at different locations on a beetle are measured with a meso-scale piezoelectric beam. This way, the optimum location to scavenge energy is determined, and up to ∼115 µW total power is generated from body movements. Two initial generator prototypes were fabricated, mounted on a beetle, and harvested 11.5 and 7.5 µW in device volumes of 11.0 and 5.6 mm3, respectively, from 85 to 100 Hz wing strokes during the beetle's tethered flight. A spiral generator was designed to maximize the power output by employing a compliant structure in a limited area. The necessary technology needed to fabricate this prototype was developed, including a process to machine high-aspect ratio devices from bulk piezoelectric substrates with minimum damage to the material using a femto-second laser. The fabricated lightweight spiral generators produced 18.5–22.5 µW on a bench-top test setup mimicking beetles' wing strokes. Placing two generators (one on each wing) can result in more than 45 µW of power per insect. A direct connection between the generator and the flight muscles of the insect is expected to increase the final power output by one order of magnitude.
New Avenues for Nanoparticle-Related Therapies (2018)

Development of nanoparticle-based drug delivery systems has been attempted for the treatment of cancer over the past decade. The enhanced permeability and retention (EPR) effect is the major mechanism to passively deliver nanodrugs to tumor tissue. However, a recent systematic review demonstrated limited success of these studies, with the clearance of nanoparticles by the mononuclear phagocytic system (MPS) being a major hurdle. Herein, we propose that nanotechnologists should reconsider their research focuses, aiming for therapeutic targets other than cancer. Treatments for diseases that do not (or less) rely on EPR should be considered, such as active targeting or MPS evasion systems. For example, systemic delivery of drugs through intravenous injection can be used to treat sepsis, multi-organ failure, metabolic disorders, blood diseases, immune and autoimmune diseases, etc. Local delivery of nanodrugs to organs such as the lung, rectum, or bladder may enhance the local drug concentration with less clearance via MPS. In transplant settings, ex vivo organ perfusion provides a new route to repair injury of isolated organs in the absence of MPS. Based on a similar concept, chemotherapy with in vivo lung perfusion techniques and other isolated organ perfusion provides opportunities for cancer therapy.
Comparative antitumor activities of halichondrins and vinblastine against human tumor xenografts. (1996)

Halichondrin B and homohalichondrin B are novel tubulin-interacting agents isolated from marine sponges. The in vivo antitumor activities of these compounds were examined in human tumor models in immunodeficient mice and rats. In nude mice, regression or pronounced delay of subcutaneous tumor growth was obtained with both halichondrins, at a maximum tolerable dose of 20 micrograms/kg Q2Dx5, in three of four vinblastine-sensitive tumors, including two melanomas and one osteosarcoma; one small-cell lung cancer line was resistant. The halichondrins as well as vinblastine showed only marginal activity against KM20L colon carcinoma xenografts. In a LOX melanoma lung colony formation assay in groups of six nude mice, all control animals were sacrificed because of respiratory symptoms 38 days after cell injection, and likewise one vinblastine-treated mouse after 53 days. All halichondrin-treated mice in the lung colony assay appeared healthy throughout an observation period of 112 days (p = 0.002). Upon necropsy all vinblastine-treated animals, and two of six mice in the halichondrin group, had macroscopic lung tumor colonies. In a nude rat model for LOX bone marrow metastases, the mean lifespan of untreated control animals was 15 days. Whereas vinblastine had only a marginal effect (17 days) in this model, halichondrin B prolonged the lifespan of the animals to 32 days, representing a significant (p = 0.0016) difference between the two compounds. In conclusion, the halichondrins, which comprise a subtype of tubulin-interactive anti-mitotic agents, showed distinct antitumor activity profiles in human tumor models, thereby encouraging their further preclinical development and possible clinical evaluation.
Ionic Liquid–Mediated Selective Conversion of CO 2 to CO at Low Overpotentials (2011)

Electroreduction of carbon dioxide (CO(2))--a key component of artificial photosynthesis--has largely been stymied by the impractically high overpotentials necessary to drive the process. We report an electrocatalytic system that reduces CO(2) to carbon monoxide (CO) at overpotentials below 0.2 volt. The system relies on an ionic liquid electrolyte to lower the energy of the (CO(2))(-) intermediate, most likely by complexation, and thereby lower the initial reduction barrier. The silver cathode then catalyzes formation of the final products. Formation of gaseous CO is first observed at an applied voltage of 1.5 volts, just slightly above the minimum (i.e., equilibrium) voltage of 1.33 volts. The system continued producing CO for at least 7 hours at Faradaic efficiencies greater than 96%.
Evaluation of Blue Gene/Q hardware support for transactional memories (2012)

This paper describes an end-to-end system implementation of the transactional memory (TM) programming model on top of the hardware transactional memory (HTM) of the Blue Gene/Q (BG/Q) machine. The TM programming model supports most C/C++ programming constructs on top of a best-effort HTM with the help of a complete software stack including the compiler, the kernel, and the TM runtime.
Reactivity of cloned, expressed human FcγRIII isoforms with monoclonal antibodies which distinguish cell-type-specific and allelic forms of FcγRIII (1990)

We have isolated and expressed a cDNA encoding human NK cell Fc gamma RIII. The NK cell cDNA differs from the neutrophil Fc gamma RIII cDNA by a number of point mutations and encodes an additional 21 amino acids at its C-terminus. When transiently expressed neutrophil and NK cell Fc gamma RIII were digested with N-glycanase, deglycosylated neutrophil Fc gamma RIII had a more rapid electrophoretic mobility than NK cell Fc gamma RIII, as is observed for the human Fc gamma RIII isoforms on normal cells. The neutrophil and NK cell Fc gamma RIII isoforms apparently result from cell-type specific expression of different forms of Fc gamma RIII mRNA. A TaqI RFLP was also found for human Fc gamma RIII. Monoclonal antibodies which have been used to distinguish the neutrophil and NK cell Fc gamma RIII isoforms and the NA1 and NA2 alleles of human neutrophil Fc gamma RIII were employed to study the expression of two Fc gamma RIII cDNA clones derived from neutrophils and NK cells. Fc gamma RIII encoded by the neutrophil-derived cDNA reacts with the monoclonal antibody CLBgran11, while the NK-cell Fc gamma RIII cDNA expresses the Fc receptor which carries an antigenic determinant recognized by the antibody GRM1. Characterization of hybrid Fc gamma RIII constructed by interchange of restriction fragments between the neutrophil and NK cell cDNAs allowed localization of antigenic determinants recognized by the monoclonal antibodies.
HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. (1992)

The two subunits of the human class I histocompatibility antigen (HLA)-A2 have been expressed at high levels (20-30 mg/liter) as insoluble aggregates in bacterial cells. The aggregates were dissolved in 8 M urea and then refolded to form an HLA-A2-peptide complex by removal of urea in the presence of an antigenic peptide. Two peptides from the matrix protein and nucleoprotein of influenza virus are known to bind to HLA-A2, and both support the refolding of the recombinant HLA-A2 molecule. An additional peptide, a nonamer from the gp120 envelope protein of human immunodeficiency virus type 1, also supported refolding. Yields of purified recombinant HLA-A2 are 10-15%. In the absence of an HLA-A2-restricted peptide, a stable HLA-A2 complex was not formed. Monoclonal antibodies known to bind to native HLA-A2 also bound to the recombinant HLA-A2-peptide complex. Three purified HLA-A2-peptide complexes refolded from bacterially produced protein aggregates crystallize under the identical conditions as HLA-A2 purified from human lymphoblastoid cells. Crystals of the recombinant HLA-A2 molecule in complex with the influenza matrix nonamer peptide, Mp(58-66), diffract to greater than 1.5-A resolution.
Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice (2012)

Relapsing C. difficile disease in humans is linked to a pathological imbalance within the intestinal microbiota, termed dysbiosis, which remains poorly understood. We show that mice infected with epidemic C. difficile (genotype 027/BI) develop highly contagious, chronic intestinal disease and persistent dysbiosis characterized by a distinct, simplified microbiota containing opportunistic pathogens and altered metabolite production. Chronic C. difficile 027/BI infection was refractory to vancomycin treatment leading to relapsing disease. In contrast, treatment of C. difficile 027/BI infected mice with feces from healthy mice rapidly restored a diverse, healthy microbiota and resolved C. difficile disease and contagiousness. We used this model to identify a simple mixture of six phylogenetically diverse intestinal bacteria, including novel species, which can re-establish a health-associated microbiota and clear C. difficile 027/BI infection from mice. Thus, targeting a dysbiotic microbiota with a defined mixture of phylogenetically diverse bacteria can trigger major shifts in the microbial community structure that displaces C. difficile and, as a result, resolves disease and contagiousness. Further, we demonstrate a rational approach to harness the therapeutic potential of health-associated microbial communities to treat C. difficile disease and potentially other forms of intestinal dysbiosis.
Multiplexing holograms in the photopolymer with equal diffraction efficiency (2005)

Photopolymer is an optimum material for practical holographic storage because of low cost and good characteristics. A new epoxy resin-photopolymer is reported. Polymeric binder is epoxy resin whose refractive index is high, but the monomer’s refractive index is relatively low. The design can make monomer transfer freely in rigid frame, so we can realize no-shrinking recording and stabilize the recorded hologram. Simple grating is recorded in films, then we obtained the relationship curve between the exposure energy and diffraction efficiency by sending a single beam into the photopolymer film. According to the exposure curve, there is a recording delay, so the pre-exposure is needed to sensitize the material. In order to avoid cross-talk between contiguous holograms, angle selectivity of the material is measured. Then we investigate how diffraction efficiency is distributed in all multiplexed holograms with equal-time exposure. One method of calculating exposure schedule for multiplexing holograms in photopolymer with equal efficiency is presented. By using such exposure schedule, holograms are recorded at a single location by angle multiplexing, and the uniformity of their diffraction efficiency is remarkably improved. After iterating the procedure, it is possible to achieve much more uniform diffraction efficiency.
Granulomatous inflammation--a review. (1983)

The granulomatous inflammatory response is a special type of chronic inflammation characterised by often focal collections of macrophages, epithelioid cells and multinucleated giant cells. In this review the characteristics of these cells of the mononuclear phagocyte series are considered, with particular reference to the properties of epithelioid cells and the formation of multinucleated giant cells. The initiation and development of granulomatous inflammation is discussed, stressing the importance of persistence of the inciting agent and the complex role of the immune system, not only in the perpetuation of the granulomatous response but also in the development of necrosis and fibrosis.
Overexpression of cyclin D2 in chronic B-cell malignancies (1995)

Tumor progression in B-cell chronic lymphocytic leukemia (B-CLL) is thought to result from the gradual accumulation of small resting G0/G1 phase lymphoid cells rather than the proliferation of actively dividing cells. The recent identification of G1 cyclins that are likely to control both the progression through G0 and G1 phase and the G1/S transition prompted us to study the mRNA expression of D-type cyclins in the peripheral blood lymphocytes from 34 patients with B-CLL, 7 patients with lymphoplasmacytic lymphoma (LPL), and 2 patients with mantle cell lymphoma (MCL). Cyclin D2 mRNA was, on average, 5- to 10-fold overexpressed in most of the samples studied (B-CLL, 29/34; LPL, 7/7; MCL, 0/2) as compared with normal resting B lymphocytes, in which cyclin D2 mRNA was barely detectable. In situ hybridization with cyclin D2 digoxigenin-labeled mRNA probe showed that all the cells from a given sample were stained with approximately the same intensity. Cyclin D3 was never detected in any of the samples tested, whereas cyclin D1 was expressed in only the 3 cases (1 LPL and 2 MCL) bearing a t(11;14) translocation. A trisomy 12 was found in 4 of 19 (21%) B-CLL or LPL cases for which cytogenetic analysis was available. Although the cyclin D2 gene has been mapped to chromosome 12p13, there was no apparent correlation between trisomy 12 and the level of cyclin D2 expression. Cell cycle analysis by flow cytometry after staining with propidium iodide consistently showed that more than 96% of the cells were in G0/G1 phase, whatever the importance of cyclin D2 overexpression was, and that cyclin D2 overexpression in B-CLL was not associated with any modifications of the cell cycle repartition. No consistent overexpression of cyclin D2 was found in acute myeloid leukemias. In conclusion, overexpression of cyclin D2 mRNA was found to be an almost constant feature in B-CLL and LPL. Therefore, it led us to hypothesize, with the support of data from some transfection experiments previously reported in murine hematopoietic cell lines, that cyclin D2 might play a role in B-CLL pathogenesis, possibly by preventing cells from programmed cell death.
Granulocyte macrophage colony stimulating factor stimulates in vitro proliferation of astrocytes derived from simian mature brains (1996)

In the brain, granulocyte-macrophage colony stimulating factor (GM-CSF) may be released by infiltrated cells of the immune system including T and B lymphocytes and mononuclear phagocytes, but also by nervous system resident cells such as microglia and astrocytes. Astrocyte-secreted GM-CSF may play an important role in enhancing the local inflammatory response to central nervous system (CNS) injury and in recruting microglia and activated macrophages. In this study, we demonstrated that GM-CSF, as TNF alpha and IL 6, stimulates in vitro proliferation of simian astrocytes in primary cultures. Results were confirmed by blocking experiments performed with a specific neutralizing mAb directed against GM-CSF. Furthermore, we demonstrated that GM-CSF mediates its effect on these cells through the alpha subunit of the GM-CSF receptor which is constitutively expressed at the membrane of the cultured simian astrocytes as assessed by immunofluorescence. GM-CSF effects on astrocytes could be involved in astrocytosis, a hallmark of various neurological injuries and in inflammatory processes in an autocrine manner.
Signal Transduction and Ligand Specificity of the Human Monocyte Chemoattractant Protein-1 Receptor in Transfected Embryonic Kidney Cells (1995)

We have examined the ligand specificity and signal transduction pathways of a recently cloned receptor for monocyte chemoattractant protein-1 (MCP-1). In human 293 cells stably transfected with the MCP-1 receptor, MCP-1 bound specifically with high affinity (Kd = 260 pM) and induced a rapid mobilization of calcium from intracellular stores. The closely related chemokines MIP-1 alpha, MIP-1 beta, RANTES, interleukin 8 (IL-8), and Gro-alpha were inactive at concentrations as high as 300 nM. Activation of the MCP-1 receptor potently inhibited adenylyl cyclase with an IC50 = 90 pM. Activation of the MIP-1 alpha/RANTES receptor also mediated inhibition of adenylyl cyclase activity but with a different pharmacological profile: MIP-1 alpha (110 pM, IC50), RANTES (140 pM), MIP-1 beta (10 nM), and MCP-1 (820 nM). Mobilization of intracellular calcium and inhibition of adenylyl cyclase were blocked by pertussis toxin, suggesting that the MCP-1 receptor coupled to G alpha i. These results demonstrate that the MCP-1 receptor binds and signals in response to picomolar concentrations of MCP-1 in a highly specific manner. Signaling was manifested as mobilization of intracellular calcium and inhibition of adenylyl cyclase and was mediated by a pertussis toxin-sensitive G-protein(s).