gebhart/patrepeval huggingface dataset:
Abstract 4013: A novel multifunctional protein tag enables simple and sensitive bioluminescent quantification of tagged proteins (2017)

Abstract Dysregulation of protein expression is a key mechanism of tumorigenesis. The most commonly used approach to monitor changes in expression is to perform SDS-PAGE, followed by immunoblotting, a labor-intensive process that requires high-quality antibodies to detect proteins at endogenous levels of expression. We have developed a novel protein tag utilizing NanoLuc Binary Technology (NanoBiT), a binary complementation system based on NanoLuc luciferase. The tag, designated High BiT (HiBiT), is only 11 amino acids in length, which minimizes potential interference with protein function. The amount of HiBiT-tagged protein is measured using a lytic detection reagent containing Large BiT (LgBiT), which binds with high affinity to HiBiT (KD~1 nM) to reconstitute a bright, luminescent enzyme. HiBiT-tagged proteins can be quantified in cell lysates over 7 orders of magnitude of linear dynamic range with a limit of detection of less than 10-19 moles (3 fg of 30 kDa protein). The simple add-mix-read assay protocol can be completed in minutes, providing an assay that is compatible with high-throughput applications. The sensitivity of the assay allows quantification of expression at endogenous levels, and the small tag size is ideal for CRISPR-mediated genome editing. HiBiT-tagged proteins separated by SDS-PAGE can be detected on blots at sub-picogram levels with a detection reagent containing LgBiT. By eliminating the multiple steps of blocking, binding, and washing of traditional blotting techniques, the protocol takes minutes instead of hours. Additionally, the cell surface expression, internalization, or secretion of HiBiT-tagged proteins can be measured in minutes using a non-lytic detection reagent containing the cell-impermeable LgBiT protein. HiBiT represents a next-generation protein tag that allows simple quantification of proteins of interest in their cellular context or following SDS-PAGE. Citation Format: Christopher Eggers, Braeden Butler, Robin Hurst, Mary Hall, Brock Binkowski, Lance Encell, Marie Schwinn, Thomas Machleidt, Keith Wood, Frank Fan. A novel multifunctional protein tag enables simple and sensitive bioluminescent quantification of tagged proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4013. doi:10.1158/1538-7445.AM2017-4013
Research on production, performance and fibre dispersion of PVA engineering cementitious composites (2008)

Polyvinyl alcohol (PVA) fibre is considered as one of the most suitable polymeric fibres to be used as the reinforcement of engineered cementitious composites (ECCs). Research and application have shown that PVA–ECC can significantly counteract the deficiency of ordinary concrete. In the present paper, micromechanics based design theory and fracture mechanics formulation leading to energy and strength criteria to achieve strain hardening and multiple cracking are described. Engineered cementitious composites showing pseudo strain hardening behaviour with over 6% of strain capacity under tension is produced. Uniaxial tensile tests of PVA–ECC are conducted and the results support the validity of the proposed theory. Also viscosity modifying agent plays an important role in the dispersion of the fibres in the matrix. It is shown that a uniform distribution of fibres throughout the bulk of the composite material is crucial to its excellent workability, tight crack width and reduction in the autogenous and drying shrinkage strains.
Pre-proparathyroid Hormone: A Direct Translation Product of Parathyroid Messenger RNA (1974)

An 8-15S RNA fraction from calf parathyroid glands stimulated the incorporation of radioactive lysine and methionine into protein by 15- to 30-fold in a wheat germ extract. The major product, representing 25% of the total protein synthesized, could be bound to an antiserum to parathyroid hormone and binding was inhibited by parathyroid hormone. The chromatographic mobilities of the two tryptic peptides of the cell-free product that contained methionine were identical to the corresponding peptides of parathyroid hormone. Upon electrophoresis in acidic or sodium dodecyl sulfate-acrylamide gels, the cell-free product migrated more slowly than either parathyroid hormone or its biosynthetic precursor, proparathyroid hormone. Analysis of cyanogen bromide products indicated that the cell-free product contained an additional sequence of amino acids at the amino-terminal end. A protein corresponding to the cell-free product could not be detected in intact cells even during incubations with [(3)H]leucine as short as 2 min, which suggests the protein may be a transient precursor to proparathyroid hormone.
Thyrotropin-releasing hormone (TRH) is not thyrotropic but somatotropic in fed and starved adult chickens (1991)

Adult fed and starved Warren chickens, 2 yr of age, and approaching the end of the second laying year, were injected iv with 1 of the following products: 10 micrograms of thyrotropin releasing hormone (TRH); 100 micrograms of bovine thyrotropin (bTSH); 100 micrograms of ovine growth hormone (oGH); saline. The influence on plasma concentrations of thyroxine (T4), triiodothyronine (T3) or chicken GH (cGH) were followed. Prior to injection, it was clear from the control values that starvation for 3 d decreased plasma levels of T3 and increased cGH, whereas 7 d of fasting increased T4 and cGH. The plasma levels of cGH were elevated greater than 10-fold at 15 min following the TRH challenge in food-deprived chickens compared to a less than 4-fold increase in normal fed hens. This increase was followed by a rise in T3 after 1 h, which was also more pronounced in the starved animals, whereas T4 decreased or remained unaffected. Increases in T4 can, however, be obtained with 100 micrograms TSH in normal fed (2-fold) or starved animals (greater than 3-fold). Following injection of 100 micrograms oGH, a significant increase in T3 levels was observed which in fed animals was already present at 30 min, but the higher levels persisted for 1 and 2 h in fed and starved hens. At the same time, a decrease in T4 was observed in both groups of GH-treated chickens. It is concluded that TRH at the dose used is not thyrotropic but has a somatotropic effect and is responsible for the peripheral conversion of T4 into T3.
VHP: Vibrotactile Haptics Platform for On-body Applications (2021)

Wearable vibrotactile devices have many potential applications, including sensory substitution for accessibility and notifications. Currently, vibrotactile experimentation is done using large lab setups. However, most practical applications require standalone on-body devices and integration into small form factors. Such integration is time-consuming and requires expertise.
Establishment of a Mouse Macula Densa Cell Line with an nNOS Promoter Driving EGFP Expression (2005)

We describe a unique method for establishing a functionally intact macula densa cell line from immortalized renal cells in culture. The macula densa is involved in the tubuloglomerular feedback (TGF) system in the kidney and specifically expresses neuronal nitric oxide synthase (nNOS). A 347 bp portion of the nNOS promoter was used to drive the expression of enhanced green fluorescence protein (EGFP). An immortalized distal tubule (DT) cell line was derived from distal tubules microdissected from the kidneys of SV40 large T antigen transgenic mice. Immunofluorescence labeling using an antibody against nNOS revealed no specific EGFP expression in immunofluorescence-negative DT cells. The established cell line (NE-MD) showed a time-dependent increase in signals of the nNOS protein when they were incubated with 12 microM furosemide (an inhibitor of Na(+)-K(+)-2Cl(-) symporter) for 5 h. In conclusion, this newly developed macula densa cell line will be useful in studies of the TGF stem.
Bragg gratings photoinduced in ZBLAN fibers by femtosecond pulses at 800 nm (2007)

Fiber Bragg gratings were written in thulium-doped and undoped single-mode ZBLAN fibers by focusing femtosecond laser pulses on the fiber core through a phase mask. Maximum index modulation of the order of 1 x 10(-3) was induced in both types of fibers. Measurements of the transverse refractive index changes across the core and cladding regions indicate that the grating formation originates from a negative index change.
Determination of the activation range of passive UHF RFID transponders by radar cross-section measurements (2009)

The relationship among the radar cross-section (RCS), the antenna gain and the activation range of passive UHF radio frequency identification (RFID) transponders was determined in this paper. The originality of our paper is that we have proposed to determine the antenna gain and the reading range of an inlay tag by a non-destructive way and with conventional radio frequency measuring devices. We first introduced a theoretical approach to calculate power backscattered by the tag and founded a relationship with the power transmitted to its chip. Two different methods to measure the activation range were proposed. The first one is based on the RCS measurement using only a vector network analyzer and a reference antenna. In the second one, we considered the “transmitter-tag-receiver” link, consisting of a vector signal generator for the transmitter and a signal analyzer for the receiver. A number of measurements were conducted; the results obtained with both methods were found to be in good agreement with those obtained in simulation.
Continuing five or more locoregional therapies before living donor salvage liver transplantation for hepatocellular carcinoma is related to poor recurrence-free survival (2018)

Continuing five or more locoregional therapies for recurrent HCC after LR is related to poor recurrence-free survival after SLT.
Therapeutic Implications of GIPC1 Silencing in Cancer (2010)

GIPC1 is a cytoplasmic scaffold protein that interacts with numerous receptor signaling complexes, and emerging evidence suggests that it plays a role in tumorigenesis. GIPC1 is highly expressed in a number of human malignancies, including breast, ovarian, gastric, and pancreatic cancers. Suppression of GIPC1 in human pancreatic cancer cells inhibits in vivo tumor growth in immunodeficient mice. To better understand GIPC1 function, we suppressed its expression in human breast and colorectal cancer cell lines and human mammary epithelial cells (HMECs) and assayed both gene expression and cellular phenotype. Suppression of GIPC1 promotes apoptosis in MCF-7, MDA-MD231, SKBR-3, SW480, and SW620 cells and impairs anchorage-independent colony formation of HMECs. These observations indicate GIPC1 plays an essential role in oncogenic transformation, and its expression is necessary for the survival of human breast and colorectal cancer cells. Additionally, a GIPC1 knock-down gene signature was used to interrogate publically available breast and ovarian cancer microarray datasets. This GIPC1 signature statistically correlates with a number of breast and ovarian cancer phenotypes and clinical outcomes, including patient survival. Taken together, these data indicate that GIPC1 inhibition may represent a new target for therapeutic development for the treatment of human cancers.
Cover Picture: Diazirines as Potential Molecular Imaging Tags: Probing the Requirements for Efficient and Long‐Lived SABRE‐Induced Hyperpolarization (Angew. Chem. Int. Ed. 40/2017) (2017)

Diazirines are an attractive class of potential molecular tags for magnetic resonance imaging owing to their biocompatibility and ease of incorporation into a large variety of molecules. In their Communication on page 12112 ff., W. S. Warren, S. J. Malcolmson, Q. Wang, and co-workers show with a 15N2-diazirine-containing choline derivative that 15N2-diazirine motifs are capable of supporting long-lasting polarization by the simple SABRE-SHEATH hyperpolarization method, making then promising as tags for NMR/MRI imaging. Diazirines are an attractive class of potential molecular tags for magnetic resonance imaging owing to their biocompatibility and ease of incorporation into a large variety of molecules. In their Communication on page 12112 ff., W. S. Warren, S. J. Malcolmson, Q. Wang, and co-workers show with a 15N2-diazirine-containing choline derivative that 15N2-diazirine motifs are capable of supporting long-lasting polarization by the simple SABRE-SHEATH hyperpolarization method, making then promising as tags for NMR/MRI imaging. Polymeric Vesicles Natural Product Synthesis Nitrile Synthesis
Controlling the plasmonic properties of ultrathin TiN films at the\n atomic level (2017)

By combining first principles theoretical calculations and experimental\noptical and structural characterization such as spectroscopic ellipsometry,\nX-ray spectroscopy, and electron microscopy, we study the dielectric\npermittivity and plasmonic properties of ultrathin TiN films at an atomistic\nlevel. Our results indicate a remarkably persistent metallic character of\nultrathin TiN films and a progressive red shift of the plasmon energy as the\nthickness of the film is reduced. The microscopic origin of this trend is\ninterpreted in terms of the characteristic two-band electronic structure of the\nsystem. Surface oxidation and substrate strain are also investigated to explain\nthe deviation of the optical properties from the ideal case. This paves the way\nto the realization of ultrathin TiN films with tailorable and tunable plasmonic\nproperties in the visible range for applications in ultrathin metasurfaces and\nflexible optoelectronic devices.\n
ChemInform Abstract: TRANSITION METAL METHYLENE COMPLEXES, IV. NOVEL METHYLENE COBALT COMPLEXES (1978)

Abstract Der Co‐Komplex (I) reagiert mit den Diazoestern (II) in siedendem Benzol unter Bildung der zweikernigen diamagnetischen Titelkomplexe (III), in denen die den , Verbindungen (II) entsprechenden Carbene als Brückenliganden stabilisiert sind.
Readout characteristics of a minute aperture-mounted optical head slider flying above a submicron wide metal patterned medium track (2004)

Advances in a digital network society require both higher densities and higher transfer rates in all sorts of storage devices. In optical recording, the trend toward higher recording density and larger storage capacity requires novel surface recording technologies that would drastically improve recording density. To satisfy these severe requirements, we have already proposed a compact integrated optical head slider assembly for proximity optical recording based on the "near field principle". Using the optical head slider, we have successfully demonstrated readout signals from 200 to 150-nm-long bit patterns at frequency bands up to approximately 10 MHz. However, from the practical point of view, it is quite necessary to evaluate readout signals from patterns of smaller (sub-micron to sub-sub-micron) track width in order to prove high-density recording potential. In this paper, we have investigated tracking accuracy characteristics utilizing sub-micron sized alternate patterns of 1-mm length formed in a straight line in the circumferential direction of the medium. Arranging precisely the head's relative position to these recorded patterns, we have successfully obtained readout signals just crossing the sub-micron line-and-space pattern's boundaries. Assuming that an aperture runs along an accurate trajectory of the arc of a circle, readout signal amplitude variations when crossing the pattern edge at a right angle have precisely predicted. Also, the influences of track width on maximum readout signal intensity and tracking sensitivity are discussed in detail.
Development of a Lower Temperature SOFC (2009)

A major impediment to commercialization of solid oxide fuel cell (SOFC) technology has been high operating temperature. Higher conductivity, and thus lower temperature, oxide electrolytes have existed for some time (ranging from gallates and ceria to bismuth oxide based materials). However, each of these materials has it's own specific issues. Moreover, transitioning from a zirconia electrolyte to one of these alternate electrolytes requires development of an entirely new cell material set. Over the last 20 years we have focused on using the most conductive, and hence lowest temperature, electrolytes. To overcome inherent instability in reducing environments we developed a bilayer bismuth-oxide/ceria electrolyte. To overcome reactivity with more conventional cathode materials we developed a bismuth-ruthenate/bismuth-oxide composite cathode. Finally, these materials were integrated into an anode supported cell resulting in power densities of ~2 W/cm2 at 650{degree sign}C. The materials issues, how they were addressed, and the ultimate performance achieved are discussed.
OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations (2021)

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM's Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM's Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen's early Nobel prize winning experiments by using OpenMM's Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.
The host exocyst complex is targeted by a conserved bacterial type III effector protein that promotes virulence (2020)

ABSTRACT For most Gram-negative bacteria, pathogenicity largely depends on the type-III secretion system that delivers virulence effectors into eukaryotic cells. The subcellular targets for the majority of these effectors remain unknown. Here, we show that Xanthomonas campestris , the causal agent of black rot disease, delivers the highly conserved effector XopP that interacts with host’s EXO70 protein. EXO70 is an essential component of the exocyst complex with a role in plant immunity. The XopP/EXO70 interaction is specific and inhibits exocyst-dependent exocytosis without activating a specific plant NLR receptor that guards EXO70. In this way, Xanthomonas efficiently inhibits the host’s PAMP-triggered immunity (PTI) by blocking exocytosis of PR1, callose deposition and the FLS2 immunity-receptor translocation to the plasma membrane, promoting successful infection.
Abstract B53: Selective BET bromodomains epigenetic signaling inhibition as a therapeutic strategy in primary bone tumors (2013)

Abstract Osteosarcoma is the most frequent primary bone tumor that develops mainly in young adults. Despite recent improvements of the therapeutic advances, the survival rate at 5 years is below 30% for patients with poor response to treatment or with metastasis. The histones modifications are of critical importance in maintaining of the transcription program of both normal and tumor cells. The bromodomain and extra-terminal domain (BET) protein family is an important class of “histone reading protein” capable to recognize the N-acetylation of lysine residues on histone tails. BET bromain proteins have recently been described as regulators of MYC expression in various tumors. In this study, we present the therapeutic opportunity to pharmacologically target the BET bromodomain family in primary bone tumors. The consequence of this pharmacologic inhibition of bromodomains is a wide gene expression alteration, but it is believed to selectively target malignant cells by disrupting transcription at intense activity, most notably MYC and Runx2 in our model. Considering MYC and Runx2 are of particular importance for the oncogenic potential of primary bone tumors, a therapeutic strategy targeting those networks might be extremely relevant and potent. In osteosarcoma tumor cell lines, BET inhibitor reduced cell growth in a dose-dependent manner and induced apoptosis with an increase of sub-G1 fraction and PARP cleavage. These biological events were accompanied by decreased expression and activity of both MYC and Runx-2, and by an expression modulation of their target genes. Moreover, BET inhibitor affects bone remodeling process by disrupting both osteoclast and osteoblast differenciation. In vivo, BET inhibitor (IP; 50mg/kg) significantly inhibits tumor growth by 70% and prolongs survival in both POS-1 syngenic and HOS xenograft models compared to control. Additionnally, these results were accompanied by a decrease of associated bone lesions. These findings demonstrate that dual pharmacologic inhibition of MYC and Runx-2 is achievable through targeting BET bromodomains to treat osteosarcoma. Note: This abstract was not presented at the conference. Citation Format: Francois Lamoureux, Marc Baud'huin, Lidia Rodriguez, Camille Jacques, Martine Berreur, Francoise Rédini, James E. Bradner, Dominique Heymann, Benjamin Ory. Selective BET bromodomains epigenetic signaling inhibition as a therapeutic strategy in primary bone tumors. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B53.
An Interleave Principle for Demonstrating concurrent Programs (1984)

Although they want to know whether their concurrent programs are working properly, programmers may not need a rigorous proof of correctness.
Nonprecious‐metal Fe/N/C Catalysts Prepared from π‐Expanded Fe Salen Precursors toward an Efficient Oxygen Reduction Reaction (2018)

Abstract The front cover artwork for issue 4/2018 represents research conducted in a collaboration between Osaka University (Japan) and Nippon Shokubai Co., Ltd. (Japan). The image illustrates the preparation of the Fe/N/C catalysts by pyrolysis of π ‐expanded Fe(Salen) precursors for the oxygen reduction reaction. See the Full Paper itself at https://doi.org/10.1002/cctc.201701629 .