gebhart/patrepeval huggingface dataset:
Abstract 1986: RAS signaling is the key factor determining differential response to PI3K and MAPK targeting compounds in a panel of breast cancer cell lines (2010)

Abstract We have tested PI3K and MAPK targeting compounds in a panel of 69 breast cancer cell lines. Following the molecular stratification of breast cancer tumors, we have used ER and HER2 biomarkers to stratify cell lines into HER2 positive (HER2+), ER positive (ER+), and triple negative (TN; ER-, PR- and HER2-) subgroups. Both gene expression and response to compounds showed significant differences among the subtypes. Response to mTOR and AKT inhibition was the greatest in ER+ and HER2+ groups (86%, 85% for mTORi and 64%, 77% for AKTi response rates, respectively), whereas TN cell lines showed preferential sensitivity to MEK inhibition (30%). The combination of AKT plus MEK and mTOR plus MEK inhibitors showed synergy in TN tumors (56% and 80% response rates, respectively), particularly in the epithelial subgroup. We believe that RAS pathway deregulation, as reported by a gene expression signature of RAS activation, is the key latent variable that explains the difference in responses. This conclusion is based on pathway activation differences between subtypes. We observe that the TN group has both elevated PI3K and MAPK signaling, evident by high levels of RAS, pERK, and pMEK signatures, whereas the ER+/GGI+ group only has high levels of PI3K signaling. Thus, mTOR, AKT, or MEK alone is insufficient to inhibit the TN lines, whereas the combos are very effective. Finally, we have assessed the prevalence of the EMT and RAS signatures across subtypes of breast tumors. Similar to cell lines, the RAS signature is markedly higher in TN compared to ER+/GGI+ and, to a lesser extent, compared to HER2+ tumors. The EMT signature on the other hand is not significantly different among subtypes. This would suggest that the response patterns observed in ER+/GGI+ and TN/E subtypes of this breast panel will be applicable to a substantial subpopulation of breast tumors (∼38%). Importantly, these breast subtypes represent the largest unmet need and are a high priority for the clinical oncology. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1986.
ChemInform Abstract: Terpenoid Chirons: Preparation and Transformations of 2‐Hydroxy‐1,1,4a( R),6‐tetramethyl‐trans‐δ5,6‐octalin. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage–fusion–bridge cycle events in osteosarcoma (2005)

Osteosarcoma (OS) is characterized by chromosomal instability and high-copy-number gene amplification. The breakage-fusion-bridge (BFB) cycle is a well-established mechanism of genomic instability in tumors and in vitro models used to study the origins of complex chromosomal rearrangements and cancer genome amplification. However, until now, there have been no high-resolution cytogenetic or genomic array studies of BFB events in OS. In the present study, multicolor banding (mBAND) FISH and submegabase resolution tiling set (SMRT) array comparative genomic hybridization (CGH) were used to identify and map genomic signatures of BFB events in four OS cell lines and one patient tumor. The expected intermediates associated with BFB-dicentric chromosomes, inverted duplications, and intra- and interchromosomal amplifications-were identified. mBAND analysis provided detailed mapping of rearrangements in 1p, 6p, and 8q and showed that translocation junctions were often in close proximity to fragile sites. More detailed mBAND studies of OS cell line MG-63 revealed ladderlike FISH signals of equally spaced interchromosomal coamplifications of 6p21, 8q24, and 9p21-p22 in a homogeneously staining region (hsr). Focal amplifications that concordantly mapped to the hsr were localized to discrete genomic intervals by SMRT array CGH. The complex amplicon structure in this hsr suggests focal amplifications immediately adjacent to microdeletions. Moreover, the genomic regions in which there was deletion/amplification had a preponderance of fragile sites. In summary, this study has provided further support for the role of the BFB mechanism and fragile sites in facilitating gene amplification and chromosomal rearrangement in OS.
IgE-Mediated Disorders: Current Therapeutics and New Strategies Involving Synthetic Peptides (2008)

Most of the current therapies for the treatment of atopic diseases are based on drugs that inhibit or suppress components of the allergic inflammatory response. Antihistamines, bronchodilators, antiallergic drugs and corticosteroids remain by far the most effective therapeutic response to allergic diseases in reducing symptoms and concomitant inflammatory reactions. The last two decades witnessed a large number of works aimed at identifying medications targeting specific steps in the allergic cascade. Because the binding of IgE to mast cells via the high affinity surface mast cell receptor (FcεRI) is the central event in allergic manifestations, its inhibition seems the best approach for designing innovative antiallergic drugs. Progress has been made on the molecular level by using anti-IgE and anti-FcεRI antibodies, or chimeric proteins targeting Fc receptors. Nevertheless, validation of IgE and FcεRI as crucial targets for allergic disorders is provided by a wealth of studies where the antiallergic activity of small molecules, such as peptides, able to inhibit IgE/FcεRI interaction, was assessed. D-PAM, a tetrameric IgE-binding tripeptide, derived through combinatorial chemistry, represents a new and innovative mechanism for atopy treatment. Due to its polycationic structure, this peptide is active in in vitro (β- hexosaminidase release) and in vivo (passive and active cutaneous anaphylaxis) models of allergy, without interfering with IgE/FcεRI or IgE/Ag interaction, thus opening the way to development of new antiallergic drugs. Keywords: Allergic disorders, IgE, FcεRI, antiallergic drugs, mast cell degranulation
Evaluating anesthetic protocols for functional blood flow imaging in the rat eye (2017)

The purpose of this study is to evaluate the suitability of five different anesthetic protocols (isoflurane, isoflurane–xylazine, pentobarbital, ketamine–xylazine, and ketamine–xylazine–vecuronium) for functional blood flow imaging in the rat eye. Total retinal blood flow was measured at a series of time points using an ultrahigh-speed Doppler OCT system. Additionally, each anesthetic protocol was qualitatively evaluated according to the following criteria: (1) time-stability of blood flow, (2) overall rate of blood flow, (3) ocular immobilization, and (4) simplicity. We observed that different anesthetic protocols produced markedly different blood flows. Different anesthetic protocols also varied with respect to the four evaluated criteria. These findings suggest that the choice of anesthetic protocol should be carefully considered when designing and interpreting functional blood flow studies in the rat eye.
Fusion of bone marrow–derived stem cells with striated muscle may not be sufficient to activate muscle genes (2004)

Several studies have demonstrated the existence of pluripotent bone marrow-derived stem cells capable of homing to injured cardiac and skeletal muscle; however, there has been little evidence demonstrating the induction of tissue-specific endogenous genes in donor stem cells following engraftment. A new study in this issue reports an intriguing finding that raises additional concerns relating to stem cell plasticity and stem cell therapy in an already heated and controversial field. The study demonstrates that wild-type bone marrow-derived side population stem cells are indeed readily incorporated into both skeletal and cardiac muscle when transplanted into mice that lack delta-sarcoglycan -- a model of cardiomyopathy and muscular dystrophy. However, these cells fail to express sarcoglycan and thus to repair the tissue, which suggests that this stem cell population has limited potential for cardiac and skeletal muscle regeneration.
Comparison of Direct and Mediated Electron Transfer for Cellobiose Dehydrogenase from Phanerochaete sordida (2009)

Direct and mediated electron transfer (DET and MET) between the enzyme and electrodes were compared for cellobiose dehydrogenase (CDH) from the basidiomycete Phanerochaete sordida (PsCDH). For DET, PsCDH was adsorbed at pyrolytic graphite (PG) electrodes while for MET the enzyme was covalently linked to a low potential Os redox polymer. Both types of electrodes were prepared in the presence of single walled carbon nanotubes (SWCNTs). DET requires the oxidation of the heme domain, while MET occurs partially via the heme and the flavin domain at pH 3.5. At pH 6 MET occurs solely via the flavin domain. Most probably, the interaction of the domains decreases from pH 3.5 to 6.0 due to electrostatic repulsion of deprotonated amino acid residues, covering the surfaces of both domains. MET starts at a lower potential than DET. The midpoint potentials at pH 3.5 for the flavin (40 mV) and the heme domain (170 mV) were determined with spectroelectrochemistry. The electrochemical and spectroelectrochemical measurements presented in this work are in conformity. The pH dependency of DET and MET was investigated for PsCDH. The optimum was observed between pH 4 and 4.5 pH for DET and in the range of pH 5-6 for MET. The current densities obtained by MET are 1 order of magnitude higher than by DET. During multicycle cyclic voltammetry experiments carried out at different pHs, the PsCDH modified electrode working by MET turned out to be very stable. In order to characterize a PsCDH modified anode working by MET with respect to biofuel cell applications, this electrode was combined with a Pt-black cathode as model for a membraneless biofuel cell. In comparison to DET, a 10 times higher maximum current and maximum power density in a biofuel cell application could be achieved by MET. While CDH modified electrodes working by DET are highly qualified for applications in amperometric biosensors, a much better performance as biofuel cell anodes can be obtained by MET. The use of CDH modified electrodes working by MET for biofuel cell applications results in a less positive onset of the electrocatalytic current (which may lead to an increased cell voltage), higher current and power density, and much better long-term stability over a broad range of pH.
Decreased Cardiac Output in Infants of Mothers Who Abused Cocaine (1990)

Cocaine increases the level of circulating catecholamines by blocking the catecholamine reuptake receptors. The effect of intrauterine cocaine exposure on cardiac output was studied in 15 full-term newborn infants whose mothers used cocaine during pregnancy. A total of 22 healthy nonexposed full-term infants served as a control group. On the first day of life, cardiac output (183 +/- 12 vs 235 +/- 13 mL/kg per minute, mean +/- SD; P less than .05) and stroke volume (1.3 +/- 0.1 vs 1.9 +/- 0.1 mL/kg, mean +/- SD; P less than .005) were lower and arterial blood pressure (60 +/- 2 vs 41 +/- 2 mmHg, mean +/- SD; P less than .001) higher in the infants exposed to cocaine. On day 2, cardiac output, stroke volume, and mean arterial blood pressure were similar, probably because of the gradual excretion of cocaine and its metabolites by the infant. It was speculated that an increase in plasma norepinephrine levels is responsible for the cardiovascular effects of intrauterine cocaine exposure.
Antileishmanial Activity of Natural Diterpenes from Cistus sp. and Semisynthetic Derivatives Thereof (2006)

Eleven cis-clerodane diterpenes, seven labdane type diterpenes and one triterpene isolated from Cistus monspeliensis and the resin "Ladano" of Cistus creticus subsp. creticus were evaluated against Leishmania donovani promastigotes, the causative agent for visceral leishmaniasis. In addition, eleven semisynthetic manoyl oxide, seventeen labdane type derivatives and a triterpene were also evaluated for their antileishmanial activity. 18-Acetoxy-cis-clerod-3-en-15-ol, 15,18-diacetoxy-cis-clerod-3-ene and 13-(E)-8a-hydroxylabd-13-en-15-ol 2-chloroethylcarbamate exhibited the most potent and selective leishmanicidal activity with IC50 values of 3.3 microg/ml, 3.4 microg/ml and 3.5 microg/ml, respectively.
Effect of Refining Conditions for Ultra Low Carbon Steel on Decarburization Reaction in RH Degasser. (1992)

On the basis of a mixed-control mechanisminvolving the mass transfer of carbon and oxygen in the molten steel in the vacuum vessel and the transport of carbon and oxygen by the circulation flow, a new reaction model for RH decarburization has been developed to clarify the effect of oxygen concentration on the decarburization rate. The model can also predict the effect of the KTBmethod, in which oxygen gas is blown onto the molten steel in the vacuum vessel, on the decarburization rate.
Neuroprotection in Glaucoma Using Calpain-1 Inhibitors: Regional Differences in Calpain-1 Activity in the Trabecular Meshwork, Optic Nerve and Implications for Therapeutics (2008)

Glaucoma is a group of irreversible blinding eye diseases affecting over 70 million people worldwide. Systemic delivery of calpain-1 inhibitors was proposed as a neuroprotection strategy for the prevention of progressive optic nerve damage in glaucoma. We present a general review of calpain-1 and an account of vast differences in processing of calpain-1 in the trabecular meshwork (TM) and the optic nerve. Calpain-1 accumulates in the glaucomatous TM tissues in vivo. However, calpain-1 activity is substantially lower in the glaucomatous TM compared to controls, apparently owing to partial degradation, and modification by lipid oxidation products such as iso [4]levuglandin E2 (iso [4]LGE(2)). Treatment of calpain-1 with iso [4]LGE(2) in vitro results in covalent modification, inactivation, and resistance to protease digestion. Iso [4]LGE(2)-modified calpain-1 appeared to undergo ubiquitination in the TM by cellular degradation machinery mediated by ubch1-2, ubch5,6 and E6-AP, E2 and E3 enzymes respectively. In the TM, iso [4]LGE(2)-modified calpain-1 loading impairs the cellular proteasome activity consistent with competitive inhibition and formation of suicidal high molecular weight aggregates. In contrast, higher calpain-1 activity, that appears to be under translational control, was observed in glaucomatous optic nerve compared to control. Therapeutic neuroprotection strategies using calpain-1 inhibitors will require consideration of such anatomic differences in its activity and biosynthesis.
Friction free bilateral system based on twin drive control system considering resonant frequency for haptics (2004)

This paper proposes a new friction free bilateral system based on twin drive control system considering resonant frequency for haptics. The twin drive system consists of two motors, which are coupled by the differential gear. The output torque becomes a different torque of both motors. The nonlinear friction torque of twin drive system can be easily compensated. However, as this system is constructed by the planetary gear and the differential gear, this system has the mechanical resonant frequency. Hence, it often has the tensional vibration. In order to overcome this problem, this paper proposes a new two-mass-model of twin drive system, and identifies these mechanical parameters and the friction torque. Moreover, this paper realizes a fine friction free bilateral control system considering its resonant frequency.
High-Modulation-Efficiency, Integrated Waveguide Modulator–Laser Diode at 448 nm (2016)

To date, solid-state lighting (SSL), visible light communication (VLC) and optical clock generation functionalities in the blue-green color regime have been demonstrated based on discrete devices, including light-emitting diodes, laser diodes, and transverse-transmission modulators. This work presents the first integrated waveguide modulator-laser diode (IWM-LD) at 448 nm, offering the advantages of small-footprint, high-speed, and low power-consumption. A high modulation efficiency of 2.68 dB/V, deriving from a large extinction ratio of 9.4 dB and a low operating voltage range of 3.5 V, was measured. The electroabsorption characteristics revealed that the modulation effect, as observed from the red-shifting of the absorption edge, was resulted from the external-field-induced quantum-confined-Stark-effect (QCSE). A comparative analysis of the photocurrent versus wavelength spectra in semipolar- and polar-plane InGaN/GaN quantum wells (QWs) confirmed that the IWM-LD based on semipolar (20¯2 ¯1) QWs was able to operate in a manner similar to other III-V materials typically used in optical telecommunications, due to the reduced piezoelectric field. Utilizing the integrated modulator, a -3dB bandwidth of ~1 GHz was measured, and a data rate of 1 Gbit/s was demonstrated using on-off keying (OOK) modulation. Our experimental investigation highlighted the advantage of implementing the IWM-LD on the same semipolar QW epitaxy in enabling a high-efficiency platform for SSL-VLC dual-functionalities.
Broadband Mode Converters by Femtosecond-Laser-Light Refractive-Index Tailoring (2014)

Possible designs for a new type of mode converters based on microstructuring the refractive-index profile of an optical fiber with ultrashort laser pulses are proposed and characterized numerically. Both LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> -LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">02</sub> and LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> -LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> converters exhibit in excess of 20-dB extinction ratio over more than 200-nm bandwidth with moderate losses. The length of the converters is only a few hundred micrometers, making them some of the shortest mode converters available.
A planar cascading architecture for a ceramic Knudsen micropump (2009)

This paper describes a 9-stage Knudsen pump with planar architecture that uses nanoporous ceramic for thermal transpiration. While operating at 55 K above room temperature, the pump provides a maximum pressure head exceeding 12 kPa at a sealed outlet, or a gas flow rate of ap3.8 muL/min. against a pressure head of 160 Pa. Experiments also demonstrate the capability of the pump to steer water droplets at speeds exceeding 1200 mum/s through a 250 mum fluorinated ethylene propylene capillary. The packaged volume for the 9-stage pump discussed here is 25times25times7.25 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . These characteristics indicate that the pump is potentially useful in microfluidic systems intended for both gas and liquid phase chemical sensing.
Evaluation of Phenetic Species and Phylogenetic Relationships in the Genus Trichoderma by Cladistic Analysis of Isozyme Polymorphism (1989)

Taxonomy in Trichoderma is problematic because of the lack of reliable morphological characters. This study evaluates five morphological species using methods of isozyme analysis that allow determination of allozyme polymorphism. One hundred nine alleles were resolved at 16 putative enzyme loci among 71 strains tested. Morphological species were not characterized either by specific alleles at single loci or by specific patterns of alleles at multiple loci. Rather, most alleles were distributed among most species, and each species included several different alleles at most loci. Allele patterns were analysed by phylogenetic analysis using parsimony (PAUP). A strict consensus tree was derived from 20 equally parsimonious, shortest cladograms using Gliocladium virens as an outgroup. In the resulting cladogram, T. harzianum included a main group of strains adjacent to the outgroup and other strains distributed throughout the cladogram; this species appears to be paraphyletic. A core group of T. pseudokoningii strains appears to be monophyletic and derived directly from a T. harzianum-like ancestral group. Trichoderma hamatum included three isozymically distinct strains with close affinity to Gliocladium virens and a main group which appears to have been derived from a T. harzianum-like ancestral group independently of the core group of T. pseudokoningii. Trichoderma koningii and T. viride are not well distinguished from each other, but T. viride appears to be more derived and may have arisen from a more ancestral T. koningii type. Phylogenetic analysis of allozyme data identified isozymically similar core groups of strains within morphological species, clusters of strains from various species, and isozymically distinct strains for further study. Wide distribution of numerous aUeles among morphological species suggests that extensive genetic exchange occurs among these taxa.
Report of the Exhibition: &#x201C;Digital Public Art in HANEDA AIRPORT &#x201C;AIR HARBOR&#x201D; - Technology Meets Air: A Sensation of a New World&#x201D; (2010)

We produced an exhibition “Digital Public Art in HANEDA AIRPORT `AIR HARBOR' - Technology Meets Air: A Sensation of a New World” in October, 2009 at the Haneda Airport which is public space and is the biggest airport in Japan. This exhibition aims to show the new concept “Digital Public Art” which tries to evolve media art to public art. This exhibition is also an experiment to bring information technology into public spaces as an interactive art works. In this exhibition, we combined virtual reality technologies, human interface methods, and signal processing techniques with art for developing public art artworks. From the view point of technology, we have developed display technologies such as projecting to real objects display, sensing technologies for large area such as carbon dioxide (CO2) sensing for people's congestion, interface technologies such as public interface, especially for the public spaces. We have solved problems that occur when we set information technologies in to the public space. In this paper, we propose the “Digital Public Art” and introduce the exhibition “AIR HARBOR” and its technologies that are suitable in the public space.