gebhart/patrepeval huggingface dataset:
Tripod amphiphiles for membraneprotein manipulation (2009)

Integral membrane proteins (IMPs) are crucial biological components, mediating the transfer of material and information between cells and their environment. Many IMPs have proven to be difficult to isolate and study. High-resolution structural information on this class of proteins is limited, largely because of difficulties in generating soluble forms of such proteins that retain native folding and activity, and difficulties in generating high-quality crystals from such preparations. Isolated IMPs typically do not dissolve in aqueous solution, a property that arises from the large patches of hydrophobic surface necessary for favorable interactions with the core of a lipid bilayer. Detergents are generally required for IMP solubilization: hydrophobic segments of detergent molecules cluster around and shield from water the hydrophobic protein surfaces. The critical role played by detergents in membrane protein manipulation, and the fact that many IMPs are recalcitrant to solubilization and/or crystallization with currently available detergents, suggest that it should be valuable to explore new types of amphiphiles for these purposes. This review constitutes a progress report on our long-term effort to develop a new class of organic molecules, collectively designated "tripod amphiphiles," that are intended as alternatives to conventional detergents for membrane protein manipulation. One long-range goal of this research is to identify new types of amphiphiles that facilitate IMP crystallization. This review should help introduce an important biochemical need to organic chemists, and perhaps inspire new approaches to the problem.
The Rational Design of Selective Benzoxazepin Inhibitors of the α-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of ( <i>S</i> )-2-((2-(1-Isopropyl-1 <i>H</i> -1,2,4-triazol-5-yl)-5,6-dihydrobenzo[ <i>f</i> ]imidazo[1,2- <i>d</i> ][1,4]oxazepin-9-yl)oxy)propanamide (GDC-0326) (2016)

Inhibitors of the class I phosphoinositide 3-kinase (PI3K) isoform PI3Kα have received substantial attention for their potential use in cancer therapy. Despite the particular attraction of targeting PI3Kα, achieving selectivity for the inhibition of this isoform has proved challenging. Herein we report the discovery of inhibitors of PI3Kα that have selectivity over the other class I isoforms and all other kinases tested. In GDC-0032 (3, taselisib), we previously minimized inhibition of PI3Kβ relative to the other class I insoforms. Subsequently, we extended our efforts to identify PI3Kα-specific inhibitors using PI3Kα crystal structures to inform the design of benzoxazepin inhibitors with selectivity for PI3Kα through interactions with a nonconserved residue. Several molecules selective for PI3Kα relative to the other class I isoforms, as well as other kinases, were identified. Optimization of properties related to drug metabolism then culminated in the identification of the clinical candidate GDC-0326 (4).
Polyamine dendrimer‐based MRI contrast agents for functional kidney imaging to diagnose acute renal failure (2004)

DAB-G2 was found to be the best candidate for functional kidney imaging and enabled early diagnosis of acute renal injury.
A New Fabrication Approach For Planar, Ion-Implanted InP JFETs (1989)

A new, planar, fully ion-implanted indium phosphide (InP) junction field-effect transistor (JFET) fabrication process is described which utilizes n* source-drain implantation, Be and Be/P p+ gate implantation, a AuZn/Ni/TiW/Au gate metallization and proximity rapid thermal annealing. The JFETs exhibit a gate leakage current of approximately 40 nA at -8 V for a 1 pm x 150 μm gate, a reverse breakdown voltage of 17.5 V at 25 μA, and a maximum transconductance of 140 mS/mm. The addition of a Ni layer in the gate metallization significantly improves its adhesion. The specific contact resistance of the new gate structure is measured to be as low as 2 x 10<sup>5</sup> ohm-cm2,which is the lowest value reported to date for contacts to p-type InP.
Simple, effective countermeasures to P300‐based tests of detection of concealed information (2004)

We found countermeasures to protocols using P300 in concealed information tests. One, the "six-probe" protocol, in Experiment 1, uses six different crime details in one run. The countermeasure: generate covert responses to irrelevant stimuli for each probe category. Hit rates were 82% in the guilty group; 18% in the countermeasure group. The average reaction time (RT) distinguished these two groups, but with overlap in RT distributions. The "one-probe" protocol, in the second experiment, uses one crime detail as a probe. Here, one group was run in 3 weeks as a guilty group, a countermeasure group, and again as in Week 1. COUNTERMEASURE: Covert responses to irrelevant stimuli. In Week 1, hit rate was 92%. In Week 2, it was 50%. In Week 3, 58%. There was no overlap in the irrelevant RT distribution in Week 2: Countermeasure use was detectable. However, in Week 3, the RT distributions resembled those of Week 1; test-beaters could not be caught. These studies have shown that tests of deception detection based on P300 amplitude as a recognition index may be readily defeated with simple countermeasures that can be easily learned.
Fusion nuclear science facilities and pilot plants based on the spherical tokamak (2016)

Abstract A fusion nuclear science facility (FNSF) could play an important role in the development of fusion energy by providing the nuclear environment needed to develop fusion materials and components. The spherical torus/tokamak (ST) is a leading candidate for an FNSF due to its potentially high neutron wall loading and modular configuration. A key consideration for the choice of FNSF configuration is the range of achievable missions as a function of device size. Possible missions include: providing high neutron wall loading and fluence, demonstrating tritium self-sufficiency, and demonstrating electrical self-sufficiency. All of these missions must also be compatible with a viable divertor, first-wall, and blanket solution. ST-FNSF configurations have been developed simultaneously incorporating for the first time: (1) a blanket system capable of tritium breeding ratio TBR ≈ 1, (2) a poloidal field coil set supporting high elongation and triangularity for a range of internal inductance and normalized beta values consistent with NSTX/NSTX-U previous/planned operation, (3) a long-legged divertor analogous to the MAST-U divertor which substantially reduces projected peak divertor heat-flux and has all outboard poloidal field coils outside the vacuum chamber and superconducting to reduce power consumption, and (4) a vertical maintenance scheme in which blanket structures and the centerstack can be removed independently. Progress in these ST-FNSF missions versus configuration studies including dependence on plasma major radius R 0 for a range 1 m–2.2 m are described. In particular, it is found the threshold major radius for TBR = 1 is <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mstyle displaystyle="false"> <mml:mstyle displaystyle="false"> <mml:msub> <mml:mrow> <mml:mi>R</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>0</mml:mn> </mml:mrow> </mml:msub> </mml:mstyle> <mml:mo>⩾</mml:mo> <mml:mn>1.7</mml:mn> </mml:mstyle> </mml:math> m, and a smaller R 0 = 1 m ST device has TBR ≈ 0.9 which is below unity but substantially reduces T consumption relative to not breeding. Calculations of neutral beam heating and current drive for non-inductive ramp-up and sustainment are described. An A = 2, R 0 = 3 m device incorporating high-temperature superconductor toroidal field coil magnets capable of high neutron fluence and both tritium and electrical self-sufficiency is also presented following systematic aspect ratio studies.
Starch-Based Blown Films (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStarch-Based Blown FilmsFelix H. Otey, Richard P. Westhoff, and William M. DoaneCite this: Ind. Eng. Chem. Prod. Res. Dev. 1980, 19, 4, 592–595Publication Date (Print):December 1, 1980Publication History Published online1 May 2002Published inissue 1 December 1980https://pubs.acs.org/doi/10.1021/i360076a021https://doi.org/10.1021/i360076a021research-articleACS PublicationsRequest reuse permissionsArticle Views423Altmetric-Citations168LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Cyclolinear polysiloxanes. II. Crosslinking and characterization (2006)

Abstract The synthesis and characterization of two groups of novel networks prepared from cyclolinear polysiloxanes are described. The first group of networks from cyclolinear polysiloxanes (N‐CLPSs) was synthesized by the hydrosilation of vinyl‐terminated cyclolinear polyorganosiloxanes [prepared from diacetoxydiethyltetramethylcyclotetrasiloxane (D 4 Et 2 OAc 2 ) or diacetoxytriethylpentamethylcyclopentasiloxane (D 5 Et 3 OAc 2 )] with a copolymer of dimethylsiloxane and methylhydrosiloxane as the crosslinking agent. Hydrosilation was effected with a platinum carbonyl catalyst with a cyclovinylsiloxane moderator. The second group of networks (N‐eCLPSs) was prepared similarly with extended cyclolinear polysiloxanes. The mechanical properties of the novel networks were comparable to those of polydimethylsiloxane networks (N‐PDMS). The oxygen permeabilities were similar to or slightly higher than that of N‐PDMS. The glass‐transition temperatures of D 4 Et 2 OAc 2 ‐ and D 5 Et 3 OAc 2 ‐based N‐CLPSs were −67.8 and −90.8 °C, respectively, whereas the incorporation of polydimethylsiloxane spacers into similar N‐eCLPSs lowered their glass‐transition temperatures to −109.7 and −115.0 °C. Upon heating to 800 °C in air, N‐CLPSs yielded more residue than N‐eCLPSs, which in turn yielded more residue than N‐PDMS. These results may have been due to the presence of T units in the cyclic siloxane units, which may have inhibited chain degradation or the formation of volatile products. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4053–4062, 2006
High repetition rate ultrashort pulse picosecond laser amplifier (2007)

We demonstrate a directly diode-pumped Yb-doped high repetition rate ultrashort pulse laser amplifier. The chosen amplifier geometry allows for avoiding chirped pulse amplification which results in a simple and robust ultrashort pulse source that is well suited for industrial micro- and nanomachining applications. The laser system produces average powers on the 10-W-level for pulse repetition rates between 50 and 100 kHz. The pulse duration out of the amplifier is below 2 ps which is about one order of magnitude shorter than that of state-of-the-art picosecond amplifiers based on Nd:YVO. If wanted, the slightly chirped amplified picosecond pulses can be compressed down to about 500 fs pulse duration by using a compact and high efficiency transmission grating compressor.
Role of FOXC1 in regulation of basal-like/triple-negative breast cancer (2009)

11016 Background: Class identification studies have proposed 3 prognostically relevant molecular subtypes of breast cancer: luminal, HER2 and basal-like. The latter is associated with poor prognosis but its molecular basis is not clear. We hypothesized a direct correlation between FOXC1 expression and basal-like breast cancer. Methods: Expression of FOXC1, CK5, CK14, EGFR, c-Kit, αB-crystallin, ITGB4 and FOXC2 in basal-like breast cancer was examined using publicly available microarray datasets. A molecular signature of 40 genes sharing co-ordinate up or down regulation with FOXC1 was identified on one microarray (49 patients) and validated on 5 other microarrays (1,232 patients). The clinical significance of FOXC1 gene expression and the FOXC1 gene signature was evaluated using censored survival data. FOXC1 protein expression was assessed by immunohistochemistry (IHC) of a 96-sample breast cancer tissue microarray. Normal breast epithelial, luminal and basal breast cancer cells transfected with FOXC1 vectors were evaluated for cell proliferation, migration and invasion. Results: FOXC1 was found to be consistently and exclusively upregulated in basal-like triple negative breast cancer and was associated with poor overall survival (p<0.0001). The FOXC1 gene signature accurately predicted the basal-like phenotype. IHC analysis of FOXC1 protein expression in human breast cancers confirmed its potential to be used as a clinical biomarker of basal-like breast cancer. Normal breast epithelial cells and luminal breast cancer cells with low or no FOXC1 expression underwent epithelial-to-mesenchymal transition and displayed increased cellular proliferation, migration, invasion, and expression of basal cell markers when FOXC1 was overexpressed. In contrast, knockdown of FOXC1 by shRNA in basal-like breast cancer cells conferred luminal phenotype. Breast cancer progression-linked signaling pathways like NF-κB and p38MAPK were significantly stimulated in basal-like breast cancer as well as by in vitro FOXC1 overexpression. Conclusions: FOXC1 is a dominant determinant of the basal-like phenotype of breast cancer. We propose FOXC1 to be the single best molecular marker of and a potential therapeutic target for basal-like / triple negative breast cancer. No significant financial relationships to disclose.
Characterization of efficient dual-wavelength (1050 + 800 nm) pumping scheme for thulium-doped fiber amplifiers (2003)

We report on the characterization of a recently introduced dual-wavelength pumping scheme for thulium-doped fiber amplifiers using 800 and 1050 nm. Using a counterpropagating pump configuration, 180 mW of total pump power yielded 27-dB small-signal gain and less than 5-dB noise figure. Furthermore, using optical frequency domain reflectometry, the distributed gain in this configuration was evaluated, allowing for optimization of the doped fiber length.
"Alcove" Holograms For Computer-Aided Design (1987)

A new concave semi-cylindrical holographic stereogram format, called the "alcove" hologram, offers 3-D real images that project to the viewer's fingertips with an angle of view of nearly 180 degrees. The hologram is area-multiplexed in a way that is extendable to large holograms that can be quickly and automatically produced, perhaps by a computer peripheral "3-D hard copy" device. In order to produce undistorted images, the input images must be intensively processed, or derived from a digital data base, so that the method for hologram production is particularly suited to a digital imaging and design environment.
An in Vitro Reducing System for the Enzymic Conversion of Cobalamin to Adenosylcobalamin (2001)

Homogeneous ferredoxin (flavodoxin):NADP(+) reductase and flavodoxin A proteins served as electron donors for the reduction of co(III)rrinoids to co(I)rrinoids in vitro. The resulting co(I)rrinoids served as substrates for the ATP:co(I)rrinoid adenosyltransferase (CobA) enzyme of Salmonella enterica serovar Typhimurium LT2 and were converted to their respective adenosylated derivatives. The reaction products were isolated by reverse phase high performance liquid chromatography, and their identities were confirmed by UV-visible spectroscopy, mass spectrometry, and in vivo biological activity assays. Adenosylcobalamin generated by this system supported the activity of 1,2-propanediol dehydratase as effectively as authentic adenosylcobalamin. This is the first report of a protein system that can be coupled to the adenosyltransferase CobA enzyme for the conversion of co(III)rrinoids to their adenosylated derivatives.
Thermal Device Design for a Carbon Nanotube Terahertz Camera (2018)

Terahertz (THz) wave detectors are increasingly expected to serve as key components of powerful nondestructive and noncontact inspection tools in a large variety of fields. In contrast to conventional THz detectors based on rigid solid materials, we previously developed an uncooled and bendable THz camera based on the THz-induced photothermoelectric effect of carbon nanotube (CNT) array devices and demonstrated omnidirectional THz imaging of three-dimensional curved samples. Although this development opened a pathway to flexible THz electronics, the physical parameters that determine the performance of the CNT THz camera have not been fully investigated. As a result, the thermal device design has not been optimized in terms of the camera sensitivity and spatial resolution. In this work, we studied the underlying mechanism of the THz-induced photothermoelectric effect of the CNT camera and found physical factors related to the detector performance. Through simulation and experiments, we observed that the detection sensitivity and response time strongly depend on the CNT channel width and film thickness. We further identified that the irradiated wave penetration into the CNT film through the electrode materials deteriorates the detection area, which is directly linked to the camera spatial resolution. By utilizing the improved CNT device design fabricated based on these findings, we eliminated undesired signals generated via thermal diffusion and THz wave penetration and achieved higher-sensitivity THz detection and higher imaging resolution compared to our previously reported THz camera. The presented technologies are expected to contribute to future flexible THz imaging applications and will also be applicable to other types of photothermoelectric devices.
MPL Mutation Profile in JAK2 Mutation-Negative Patients with Myeloproliferative Neoplasms. (2009)

Abstract Abstract 1891 Poster Board I-914 Myeloproliferative neoplasms (MPNs) are multipotent hematopoietic stem cell neoplasms characterized by excess production of various blood cells. Mutations in the thrombopoietin receptor gene (MPL) have been reported in JAK2 V617F-negative patients with MPNs. We evaluated the prevalence of MPL mutations relative to those of JAK2 mutations at V617 or in exons 12 through 15 in a large number of patients with suspected MPNs. A total of 2790 patients with suspected MPNs referred to our institution were first screened for JAK2 V617F and exon 12–15 mutations. Patients with no JAK2 mutations detected were then tested for MPL mutations in exons 10 and 11 by means of a sensitive MPL reverse-transcription-PCR-based assay with direct bidirectional sequencing. All JAK2 and MPL mutation assays were performed on plasma RNA, rather than DNA isolated from blood or bone marrow cells. Of the 2790 patients, 529 (18.96%) had a V617F mutation; 12 (0.43%) had small insertion/deletions in exon 12; and 7 (0.25%) had other JAK2 mutations, including point mutations in exons 13–15 and an exon 14 splice mutation. MPL mutations were identified in 66 of the 2242 (2.94%) JAK2 mutation-negative patients (2.37% of all tested patients). W515L was the dominant MPL mutant detected in 46 patients (70%) including two patients with homozygous W515L mutation. The other W515 variants (W515K, W515R, W515S, W515G, W515A, W515*) comprised 16% (N=11) of the MPL mutations. The remaining MPL mutations (n =9, 14%) were detected at other locations in exon 10 and 11. Two of these were novel exon 10 deletion/insertion mutations and two were unreported exon 11 point mutations. The exon 10 T496-A497ALVI (4AA) homozygous insertion was detected in one patient with a confirmed diagnosis of idiopathic myelofibrosis and the W515-P518 del/ins (KT) mutation was detected in another patient with unspecified MPN. The two novel MPL exon 11 point mutations were D545G and D545N. The S505N mutation (n=2) and V507I (n=1), R514K (n=1), and A519V (n=1) were also detected. Furthermore, three unreported silent polymorphisms/mutations (T496, L543, and D534) were detected. In conclusion, our results demonstrate that for every 100 V617F mutations detected in patients with MPNs, there are 2.3 JAK2 exon 12 mutations, 1.3 JAK2 exon 13–15 mutations, and 12.5 MPL mutations. Thus, MPL mutation detection should be performed on all JAK2 V617F-negative patients with suspected MPNs. In addition, our findings indicate that >20% of MPL mutations would have been missed if only W515L and W515K were analyzed; thus, sequencing of both exon 10 and 11 may be beneficial. Disclosures: No relevant conflicts of interest to declare.
Recombinant mumps virus as a cancer therapeutic agent (2016)

Mumps virus belongs to the family of Paramyxoviridae and has the potential to be an oncolytic agent. Mumps virus Urabe strain had been tested in the clinical setting as a treatment for human cancer four decades ago in Japan. These clinical studies demonstrated that mumps virus could be a promising cancer therapeutic agent that showed significant antitumor activity against various types of cancers. Since oncolytic virotherapy was not in the limelight until the beginning of the 21(st) century, the interest to pursue mumps virus for cancer treatment slowly faded away. Recent success stories of oncolytic clinical trials prompted us to resurrect the mumps virus and to explore its potential for cancer treatment. We have obtained the Urabe strain of mumps virus from Osaka University, Japan, which was used in the earlier human clinical trials. In this report we describe the development of a reverse genetics system from a major isolate of this Urabe strain mumps virus stock, and the construction and characterization of several recombinant mumps viruses with additional transgenes. We present initial data demonstrating these recombinant mumps viruses have oncolytic activity against tumor cell lines in vitro and some efficacy in preliminary pilot animal tumor models.
Spatially resolved standoff trace chemical sensing using backwards transient absorption spectroscopy (2018)

A technique for the spatially resolved and molecule-specific detection of chemical vapors is presented. The chemical specificity arises from a transient absorption spectrum where an ultraviolet (UV) pulse excites the molecule to a Rydberg state, and a near-infrared (NIR) or visible probe pulse records a transient absorption spectrum. By recording the NIR pulse reflected off a random, distant object and measuring the elapsed time between the emission of the UV pulse and the absorption of a counter-propagating NIR pulse, the distance to the absorber is obtained. The feasibility of the approach is demonstrated by detecting acetone plumes with millimeter scale spatial resolution.
An Aza-Diels–Alder Approach to Crowded Benzoquinolines (2015)

Graphene nanoribbons (GNRs) are promising candidate materials for the next generation of nanoscale electronics. Described herein is the synthesis of 2,4,6-substituted benzoquinolines, which constitute building blocks for nitrogen-doped GNRs. The presented facile and modular aza-Diels-Alder chemistry accommodates the installation of diverse functionalities at the crowded benzoquinolines' 2 positions. Given the general utility of the benzoquinoline motif, these findings hold relevance not only for carbon-based electronics but also for a range of chemical disciplines.