gebhart/patrepeval huggingface dataset:
Eyes wide shut: Protein kinase C isozymes are not the only receptors for the phorbol ester tumor promoters (2000)

In addition to the well-characterized interaction with classical and novel protein kinase C (PKC) isozymes, the phorbol ester tumor promoters bind to other receptors lacking kinase activity. Among these novel phorbol ester receptors, two families of proteins may play a role in the regulation of cell growth and malignant transformation: chimaerins and ras guanyl-releasing protein (ras-GRP). These proteins possess a single copy of the C1 domain that is involved in binding of phorbol esters and the lipid second messenger diacylglycerol. Four isoforms of chimaerins (alpha1-, alpha2-, beta1-, and beta2-chimaerins) have been isolated to-date, all of them possessing GTPase-activating protein activity for Rac, a small GTP-binding protein that controls actin cytoskeleton organization, cell-cycle progression, adhesion, and migration. Ras-GRP is a guanine nucleotide exchange factor for ras and promotes malignant transformation in fibroblasts in a phorbol ester-dependent manner. The C1 domain in Ras-GRP may, therefore, have a dominant role in Ras-GRP activation and is essential for phorbol ester-dependent activation of downstream effectors of ras, i.e., the mitogen-activated protein kinase cascade. Thus, a novel concept emerges in which phorbol esters may exert cellular responses through pathways not involving phorbol ester-responsive PKC isozymes. The discovery of "nonPKC" phorbol ester receptors adds an additional level of complexity to the understanding of phorbol ester effects and the molecular mechanisms of carcinogenesis.
Fibril specific, conformation dependent antibodies recognize a generic epitope common to amyloid fibrils and fibrillar oligomers that is absent in prefibrillar oligomers (2007)

Since the fibril specific antibodies are conformation dependent, sequence-independent, and recognize epitopes that are distinct from those present in prefibrillar oligomers, they may have broad utility for detecting and characterizing the accumulation of amyloid fibrils and fibrillar type oligomers in degenerative diseases.
The involvement of the sigma-1 receptor in neurodegeneration and neurorestoration (2014)

The sigma-1 receptor (Sig-1R) is a single 25 kD polypeptide and a chaperone protein immersed in lipid rafts of the endoplasmic reticulum (ER) where it interacts with mitochondria at the mitochondria-associated ER membrane domain (MAM). Upon activation, the Sig-1R binds to the inositol trisphosphate receptor (IP3R), and modulates cellular calcium (Ca(2+)) homeostasis. Also, the activated Sig-1R modulates plasma membrane receptor and ion channel functions, and may regulate cellular excitability. Further, the Sig-1R promotes trafficking of lipids and proteins essential for neurotransmission, cell growth and motility. Activation of the Sig-1R provides neuroprotection and is neurorestorative in cellular and animal models of neurodegenerative diseases and brain ischaemia. Neuroprotection appears to be due to inhibition of cellular Ca(2+) toxicity and/or inflammation, and neurorestoration may include balancing abberant neurotransmission or stimulation of synaptogenesis, thus remodelling brain connectivity. Single nucleotide polymorphisms and mutations of the SIGMAR1 gene worsen outcome in Alzheimer's disease and myotrophic lateral sclerosis supporting a role of Sig-1R in neurodegenerative disease. The combined neuroprotective and neurorestorative actions of the Sig-1R, provide a broad therapeutic time window of Sig-1R agonists. The Sig-1R is therefore a strong therapeutic target for the development of new treatments for neurodegenerative diseases and stroke.
Reaction kinetics of a high pressure helium fast discharge afterglow (1982)

This work reports the study of elementary processes which govern the relaxation of the afterglow of a 3 kA 7 ns duration discharge in helium at atmospheric pressure. Populations of the dominant energy storing species were monitored as functions of time through measurements of the emission asnd absorption of radiation from the plasma. The atomic helium spectral lines, radiated during the discharge pulse, were found to rapidly transform into molecular helium bands in the visible and far ultraviolet (600–1000 Å) regions during the afterglow. The observed features of this He2 radiation were consistent with a collisional-radiative scheme of electronic recombination of molecular He2+ ions, the concentration of which was inferred from Hβ line broadening. A significant fraction of the He+2 recombination events were found to result in helium atoms in the metastable 2 3S state, and the time dependence of this dissociation process correlated with that of He2 populations characterized by quantum number n = 4. The concentration of 2 3S atoms was comparable to the electron density, ranging from 1014 to 1015 cm−3. The concentration of molecular a 3Σ+u metastables was found to be one order of magnitude lower, suggesting a collisional coupling to the radiating A 1Σ+u state. From the data rate coefficients have been extracted for the processes of electron–ion recombination, ionizing collisions between atomic metastables, and superelastic electron–metastable collisions.
[Trial of the safety, reactivity and therapeutic effectiveness of an ointment containing swine leukocytic interferon]. (1981)

An ointment containing porcine leucocytic interferon (PLI) with the use of lanolin as the base and addition of human serum albumin for stabilization of the antiviral activity and Tris-or Hepes-buffer solutions for stabilization of the medium pH value was studied. The trials on volunteers with herpetic affections of the face and genitalia showed absolute safety of the drug, its areactivity and sufficiently high therapeutic efficacy as compared to an ointment containing human leucocytic interferon. The positive effect was observed in 52 out of 78 patients. On the basis of these data the PLI may be recommended for further clinical trials.
Hydrogen Bonding Effects on the Surface Structure and Photoelectrochemical Properties of Nanostructured SnO2 Electrodes Modified with Porphyrin and Fullerene Composites (2005)

Hydrogen bonding effects on surface structure, photophysical properties, and photoelectrochemistry have been examined in a mixed film of porphyrin and fullerene composites with and without hydrogen bonding on indium tin oxide and nanostructured SnO2 electrodes. The nanostructured SnO2 electrodes modified with the mixed films of porphyrin and fullerene composites with hydrogen bonding exhibited efficient photocurrent generation compared to the reference systems without hydrogen bonding. Atomic force microscopy, infrared reflection absorption, and ultraviolet-visible absorption spectroscopies and time-resolved fluorescence lifetime and transient absorption spectroscopic measurements disclosed the relationship between the surface structure and photophysical and photoelectrochemical properties relating to the formation of hydrogen bonding between the porphyrins and/or the C60 moieties in the films on the electrode surface. These results show that hydrogen bonding is a highly promising methodology for the fabrication of donor and acceptor composites on nanostructured semiconducting electrodes, which exhibit high photoelectrochemical properties.
Vaccinia DNA topoisomerase I promotes illegitimate recombination in Escherichia coli. (1989)

Vaccinia virus encapsidates a Mr 32,000 type IDNA topoisomerase. Although the vaccinia gene encoding the topoisomerase is essential for virus growth, the role of the enzyme in vivo remains unclear. In the present study, the physiologic consequences of vaccinia topoisomerase action have been examined in a heterologous system, Escherichia coli. The vaccinia topoisomerase gene was inducibly expressed in an int-lambda lysogen BL21(DE3) using a T7 RNA polymerase-based transcription system. Expression of active topoisomerase in this context resulted in recA-dependent lysogenic induction as well as cell lysis. Surprisingly, topoisomerase expression also effected a 200-fold increase in the titer of infectious lambda phage, apparently by promoting int-independent prophage excision. This effect was not observed during lysogenic induction with nalidixic acid. Restriction analysis of genomic DNA from plaque-purified excisants revealed (in 10 of 10 cases) gross alterations of the DNA structure around the att site relative to the structure of the parental phage DE3. It is construed therefore that vaccinia DNA topoisomerase I acts to promote illegitimate recombination in E. coli.
Stereoselective Favorskii rearrangement of carvone chlorohydrin; expedient synthesis of (+)-dihydronepetalactone and (+)-iridomyrmecin (1994)

E. Lee and C. H. Yoon, J. Chem. Soc., Chem. Commun., 1994, 479 DOI: 10.1039/C39940000479
REOVIRUS-LIKE SEQUENCES ISOLATED FROM ADULT ASIAN CITRUS PSYLLID, (HEMIPTERA: PSYLLIDAE: DIAPHORINA (2009)

The Asian citrus psyllid, Diaphorina citri Kuwayama, (Insecta: Hemiptera: Psyllidae), has been identified as a damaging pest and an efficient vector of the plant infecting bacterium ( Candidatus Liberibacter asiaticus ) which is strongly associated with the disease Huanglongbing (HLB), known as ‘Citrus greening disease’. Huanglongbing has caused extensive economic losses in the citrus industries worldwide. Traditional control measures of the psyllid have proven to be ineffective and costly. Biological control measures have been shown to provide environmentally friendly management tools for insect pests. In this study, an expression library was prepared from adult psyllids in search of new pathogens that can be use as biological control agents. We identified 2 viral sequences: one 616 base pairs and a second, 792 base pairs. Both had significant similarity to viruses within the insect Reovirus group. Phylogenetic and homology comparisons indicated that the viral sequences were most closely related to the viruses in the Family Reoviridae , Genus Fijivirus , specifically Nilaparvata lugens reovirus, NLRV.
Vaccination with multiple antigen peptide as rejection antigen peptide in murine leukemia. (1998)

pRL1a (IPGLPLSL) is the Ld-binding tumor rejection antigen peptide recognized by CTLs on BALB/c radiation leukemia RL(male)1. We demonstrated that in vivo and in vitro sensitization with pRL1a multiple antigen peptide (MAP), but not with the pRL1a peptide itself, generated pRL1a-specific CTLs in the spleen cells of BALB/c mice. No enhancement of cytotoxicity was observed by emulsifying pRLla MAP in incomplete Freund's adjuvant or in complete Freund's adjuvant for in vivo sensitization. Selective depletion of CD4+ T cells in mice by treatment with anti-L3T4 (CD4) monoclonal antibody and that of macrophages by treatment with carrageenan on in vivo sensitization with pRL1a MAP abrogated CTL generation. The findings suggest that CD4+ T cells and antigen-presenting cells were necessary for the in vivo priming of CD8+ T cells with pRL1a MAP. Furthermore, we demonstrated that in vivo sensitization of BALB/c mice with pRL1a MAP, but not with pRL1a peptide, showed an inhibitory effect on RL(male)1 tumor growth. No growth-inhibitory effect was observed on control RVA, RVD, or Meth A tumors.
Opioid growth factor-opioid growth factor receptor axis is a physiological determinant of cell proliferation in diverse human cancers (2009)

The opioid growth factor (OGF) regulates cell proliferation of human cancer cells through the cyclin-dependent kinase inhibitory pathway, with mediation of this action by the OGF receptor (OGFr). The ubiquity of the OGF-OGFr axis in human cancer is unknown. We used 31 human cancer cell lines, representative of more than 90% of neoplasias occurring in humans, and found that OGF and OGFr were detected in the cytoplasm and nucleus by immunohistochemistry. The addition of OGF to cultures depressed cell number up to 41%, whereas naltrexone (NTX) increased cell proliferation by up to 44%, a total of 85% in the modulating capacity for the OGF-OGFr axis. Neutralization of OGF by specific antibodies led to a marked increase in cell number. Knockdown of OGFr by OGFr-siRNA resulted in a significant increase in the number of cells, even in the face of the addition of exogenous OGF. The cultures to which NTX was added and subjected to OGFr-siRNA were similar to those with OGF-siRNA alone. The OGF-OGFr axis, a physiological determinant of cell-proliferative activity, is a ubiquitous feature of human cancer cells. The identification of this native biological system in neoplasia may be important in understanding the pathophysiology of neoplasia, and in designing treatment modalities that utilize the body's own chemistry.
15 Years of Clinical Experience With Bupropion HCl (2005)

Bupropion has played and will continue to play an important role as a treatment for major depressive disorder in adults, as well as for other related disorders.
Criticality and Parallelism in Combinatorial Optimization (1996)

Local search methods constitute one of the most successful approaches to solving large-scale combinatorial optimization problems. As these methods are increasingly parallelized, optimization performance initially improves but then abruptly degrades to no better than that of random search beyond a certain point. The existence of this transition is demonstrated for a family of generalized spin-glass models and the traveling salesman problem. Finite-size scaling is used to characterize size-dependent effects near the transition, and analytical insight is obtained through a mean-field approximation.
Multi-View Stereo for Community Photo Collections (2007)

We present a multi-view stereo algorithm that addresses the extreme changes in lighting, scale, clutter, and other effects in large online community photo collections. Our idea is to intelligently choose images to match, both at a per-view and per-pixel level. We show that such adaptive view selection enables robust performance even with dramatic appearance variability. The stereo matching technique takes as input sparse 3D points reconstructed from structure-from-motion methods and iteratively grows surfaces from these points. Optimizing for surface normals within a photoconsistency measure significantly improves the matching results. While the focus of our approach is to estimate high-quality depth maps, we also show examples of merging the resulting depth maps into compelling scene reconstructions. We demonstrate our algorithm on standard multi-view stereo datasets and on casually acquired photo collections of famous scenes gathered from the Internet.
Erythropoietin Is a Novel Vascular Protectant Through Activation of Akt1 and Mitochondrial Modulation of Cysteine Proteases (2002)

The present work serves to illustrate that EPO can offer novel cytoprotection during ischemic vascular injury through direct modulation of Akt1 phosphorylation, mitochondrial membrane potential, and cysteine protease activity.
Structured illumination for tomographic X-ray diffraction imaging (2013)

Tomographic imaging of the molecular structure of an object is important for a variety of applications, ranging from medical and industrial radiography to security screening. X-ray diffraction imaging is the preeminent technique for performing molecular analysis of large volumes. Here we propose and demonstrate a new measurement architecture to improve the source and detector efficiency for diffraction imaging. In comparison with previous techniques, our approach reduces the required overall scan time by 1-2 orders of magnitude, which makes possible real-time scanning of a broad range of materials over a large volume using a table-top setup. This method, which relies on structuring spatially the illumination incident on an object moving relative to the X-ray source, is compatible with existing systems and has the potential to significantly enhance performance in an array of areas, such as medical diagnostic imaging and explosives detection.
Cloning and sequence analysis of the Saccharomyces cerevisiae RAD9 gene and further evidence that its product is required for cell cycle arrest induced by DNA damage. (1989)

Procaryotic and eucaryotic cells possess mechanisms for arresting cell division in response to DNA damage. Eucaryotic cells arrest division in the G2 stage of the cell cycle, and various observations suggest that this arrest is necessary to ensure the completion of repair of damaged DNA before the entry of cells into mitosis. Here, we provide evidence that the Saccharomyces cerevisiae RAD9 gene, mutations of which confer sensitivity to DNA-damaging agents, is necessary for the cell cycle arrest phenomenon. Our studies with the rad9 delta mutation show that RAD9 plays a role in the cell cycle arrest of methyl methanesulfonate-treated cells and is absolutely required for the cell cycle arrest in the temperature-sensitive cdc9 mutant, which is defective in DNA ligase. At the restrictive temperature, cell cycle progression of cdc9 cells is blocked sometime after the DNA chain elongation step, whereas cdc9 rad9 delta cells do not arrest at this point and undergo one or two additional divisions. Upon transfer from the restrictive to the permissive temperature, a larger proportion of the cdc9 cells than of the cdc9 rad9 delta cells forms viable colonies, indicating that RAD9-mediated cell cycle arrest allows for proper ligation of DNA breaks before the entry of cells into mitosis. The rad9 delta mutation does not affect the frequency of spontaneous or UV-induced mutation and recombination, suggesting that RAD9 is not directly involved in mutagenic or recombinational repair processes. The RAD9 gene encodes a transcript of approximately 4.2 kilobases and a protein of 1,309 amino acids of Mr 148,412. We suggest that RAD9 may be involved in regulating the expression of genes required for the transition from G2 to mitosis.
Aggressive Maneuvering of Small Autonomous Helicopters: A Human-Centered Approach (2001)

Unmanned small autonomous helicopters can perform aggressive maneuvers that will be useful for operations in challenging conditions. This paper presents an analysis of the pilot’s execution of aggressive maneuvers from flight test data, collected on an instrumented small-scale acrobatic helicopter. A full-envelope nonlinear dynamic model of the helicopter was developed and validated for aggressive maneuvering. This model was used as part of the hardware-in-the-loop simulation environment to demonstrate intuitive control strategies that were determined from the analysis of flight data. This insight will be helpful in determining closed-loop strategies for autonomous aggressive maneuvering on MIT’s platform.
Erratum to: Quality Characteristics and Antioxidants of Mavrolia cv. Virgin Olive Oil (2012)

There was an error in both the abstract and in Table 3. The correct value for the Tyrosol concentration is 21.88 ± 4.48 mg/kg.
Control of the 1,2-rearrangement process by oxidosqualene cyclases during triterpene biosynthesis (2015)

Oxidosqualene cyclases (OSCs) catalyze the cyclization of an acyclic substrate into various polycyclic triterpenes through a series of cation-π cyclization and 1,2-rearrangement processes. The mechanisms by which OSCs control the fate of intermediate carbocation to generate each specific triterpene product have not yet been determined. The formation of ubiquitous sterol precursors in plants, cycloartenol and Cucurbitaceae-specific cucurbitadienol, only differs by the extent of the 1,2-rearrangement of methyl and hydride. In the present study, we identified critical residues in cycloartenol synthase and cucurbitadienol synthase that were primarily responsible for switching product specificities between the two compounds. The mutation of tyrosine 118 to leucine in cycloartenol synthase resulted in the production of cucurbitadienol as a major product, while the mutation of the corresponding residue leucine 125 to tyrosine in cucurbitadienol synthase resulted in the production of parkeol. Our discovery of this "switch" residue will open up future possibilities for the rational engineering of OSCs to produce the desired triterpenes.
An unusual strain of human keratinocytes which do not stratify or undergo terminal differentiation in culture. (1988)

We have characterized an unusual cell phenotype in third passage cultures of a human keratinocyte strain derived from newborn foreskin epidermis. The cells had the same DNA fingerprint pattern as the second passage, morphologically normal, keratinocytes; they formed desmosomes and expressed the keratin profile characteristic of normal keratinocytes in culture. However, unlike normal keratinocytes, the cells did not grow as compact colonies and did not stratify or undergo terminal differentiation, even after TPA treatment or suspension culture. For these reasons we named them ndk for "nondifferentiating keratinocytes." The ndk cells also differed from normal keratinocytes in that they did not require a feeder layer and were not stimulated by cholera toxin to proliferate. The ndk cells had an absolute requirement for hydrocortisone and their growth rate was increased when epidermal growth factor was added to the medium. Although ndk failed to undergo terminal differentiation in culture, they were not transformed, since they were still sensitive to contact inhibition of growth, did not proliferate in soft agar, and had a limited lifespan in culture. The appearance of the ndk phenotype was correlated with a doubling of chromosome number and the presence of a lp marker chromosome. We suggest that these cells are a useful experimental adjunct to cultures of normal keratinocytes, in which proliferation and terminal differentiation are tightly coordinated, because in ndk cells there appears to be a block in terminal differentiation.
RF MEMS switches and switch circuits (2001)

MEMS switches are devices that use mechanical movement to achieve a short circuit or an open circuit in the RF transmission line. RF MEMS switches are the specific micromechanical switches that are designed to operate at RF-to-millimeter-wave frequencies (0.1 to 100 GHz). The forces required for the mechanical movement can be obtained using electrostatic, magnetostatic, piezoelectric, or thermal designs. To date, only electrostatic-type switches have been demonstrated at 0.1-100 GHz with high reliability (100 million to 10 billion cycles) and wafer-scale manufacturing techniques. It is for this reason that this article will concentrate on electrostatic switches.
Covalent Inhibition of Bacterial Quorum Sensing (2009)

Chemical coordination of gene expression among bacteria as a function of population density is regulated by a mechanism known as 'quorum sensing' (QS). QS in Pseudomonas aeruginosa, an opportunistic pathogen that causes disease in immunocompromised patients, is mediated by binding of the transcriptional activator, LasR, to its ligand, 3-oxo-C(12)-HSL, leading to population-wide secretion of virulence factors and biofilm formation. We have targeted QS in P. aeruginosa with a set of electrophilic probes designed to covalently bind Cys79 in the LasR binding pocket, leading to specific inhibition of QS-regulated gene expression and concomitant reduction of virulence factor secretion and biofilm formation. This first example of covalent modification of a QS receptor provides a new tool to study molecular mechanisms of bacterial group behavior and could lead to new strategies for targeting bacterial virulence.