gebhart/patrepeval huggingface dataset:
Hierarchically structured bicontinuous polymeric microemulsions (2010)

We recently described the synthesis and phase behavior of a new type of CECEC–P multiblock copolymer composed of glassy poly(cyclohexylethylene) (C), semicrystalline poly(ethylene) (E), and elastomeric poly(ethylene-alt-propylene) (P) with symmetric (equal volume) CECEC and P sequences (G. Fleury and F. S. Bates, Macromolecules, 2009, 42, 3598–3610). Here we report the formation and characterization of a multicontinuous structure based on the blending of CEC triblock copolymer and P homopolymer with such a hexablock copolymer along the 50 : 50 (CEC/P) isopleth. These materials produce a sequence of phases that are correlated with the volume fraction of CECEC–P as evidenced by SAXS and TEM measurements. A percolating bicontinuous mesostructure was identified at volume fractions of hexablock copolymer, fCECEC–P = 0.10 and 0.125, within the composition range known to result in a bicontinuous morphology in A–B/A/B systems. A solid product was formed by cooling the initially homogeneous ternary mixture from above the melting temperature of the E blocks to room temperature. Crystallization of E leads to microphase separation of C and E and simultaneous ejection of P from CEC (and CECEC) at a larger length scale. The mechanical properties of these materials are inferior to what is anticipated based on pure CEC triblock copolymer, attributable to the low molecular weight and irregular structure of the C/E region sequences. Nevertheless, this study establishes a procedure for producing bicontinuous yet structurally asymmetric materials based on the microemulsion process and extends the concept of a microemulsion to multiblock copolymers.
Liouville’s theorem and concentrator optics (1986)

We formulate a version of Liouville’s theorem, which is well suited for discussing the performance of optical systems in any geometry. The formalism is applied to an optical concentrator with spherical symmetry.
Abstract 5140: Discovery of biomarkers predicting response to radiation and anti PD1 therapy in head and neck squamous cell cancer (2019)

Introduction: Treatment of head and neck squamous cell cancer (HNSCC) frequently includes surgery, radiation, chemotherapy, targeted agents, and increasingly combination of the former with immune checkpoint inhibition. An understanding of the mechanisms mediating response to these therapies as well as biomarkers that can better tailor therapy on an individualized basis and reduce treatment-related toxicity would benefit patients.Methods: To uncover these mechanisms and biomarkers, we analyzed whole transcriptome RNA-Seq data of two different cohorts of head and neck squamous cell cancer patients: pre and post-treatment samples from radiation therapy and pre-treatment samples from anti-PD1 therapy. We evaluated the abundance of eight immune and two stromal cell populations and pathway activity changes by using Gene Set Variation Analysis (GSVA).Results and Conclusions: Following radiation genes involved in epithelial to mesenchymal transition, extracellular matrix remodeling, and wound healing are upregulated. Additionally, there is evidence of tumor microenvironment remodeling post-radiation consistent with increased fibroblast abundance and decreased immune cell infiltration. Furthermore, innately resistant tumors to anti-PD1 also display similar signatures of gene regulation, suggesting a common mechanism mediating response to both types of treatment. Notably, these signatures are strongly correlated to activation of the transforming growth factor (TGF-β) signaling pathway and suggest that attenuating its signaling may improve anti-PD-1 response and also response to radiation treatment in head and neck squamous cell cancer.Citation Format: Joon Sang Lee, Michele Sanicola-Nadel, Alexei Protopopov, Emma Wang, Joachim Theilhaber, Tun Tun Lin, Michael Korrer, Sohini Roy, Young Jun Kim, Jack Pollard. Discovery of biomarkers predicting response to radiation and anti PD1 therapy in head and neck squamous cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5140.
An Innovative Method to Enable Well Kick-Off and Liquid Unloading Using Dry Ice (2022)

Abstract Gas production can be enhanced by the unloading of liquid accumulated in the wellbore. Conventionally, it is addressed by dropping soap sticks into a gas well. The foamability of soap sticks tends to decrease in the presence of condensate. Alternativity, well can be kicked-off by using N2 lifting but it is an expensive method that involves coil tubing operation. In this paper, an innovative and simple method of unloading a condensate-bearing gas well using dry ice is described. Gas wells accumulated with liquid or condensate can be unloaded by displacing it with CO2 gas. It also helps to reduce hydrostatic pressure during kick-off well. Dry ice pellets can be inserted inside the wellbore, which can be settled down by gravity and CO2 gas formation inside the wellbore due to dry ice sublimation. The dry ice sublimation rate can be restricted by encapsulating it with self-degradable polymers that can be hydrolyzed inside the wellbore. Cylindrical dry ice pellets from the food industry having a half-inch diameter and a couple of inches long were used in this work. Dry ice is the solid form of CO2 having an expansion ratio of 1 to 554 for solid to gas at sublimation point −78.5 °C and atmospheric pressure. The density of dry ice is 1.562 gm/cm3. A series of lab experiments were conducted to show CO2 gas generation from dry ice in the water. After inserting a dry ice pellet into the water column, it settled down at the bottom and started releasing CO2 gas with a sudden expansion in volume. CO2 foam was also generated by inserting dry ice pallets with foaming agents inside the water column. The release of CO2 gas in the wellbore and foam generation can assist in decreasing hydrostatic pressure and lifting liquid inside the wellbore. At the well site, a simple modification is required to insert dry ice into the wellbore. The cylindrical chamber needs to be installed above the master value of the Christmas tree. This is described in the paper with the procedure to follow during the operation. A mathematical tool has been developed to estimate the amount of dry ice pallets required for a given well geometry. For 4.5 inch, 1000 ft long production tubing, 1000 kg dry ice can release 51.7 bbl of CO2 gas, which can generate a 495 psi increase in pressure. Well intervention operations are complex and expensive processes. It is preferred to use simpler, quicker, safer, and more cost-effective methodologies. The use of dry ice to unload gas well is simple, cheaper and an innovative solution. The release of CO2 gas from dry ice can offer additional benefits such as better and faster cleanup and the removal of condensate blockage in the near-wellbore area.
Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2 (2019)

CRISPR-Cas adaptive immune systems function to protect bacteria from invasion by foreign genetic elements. The CRISPR-Cas9 system has been widely adopted as a powerful genome-editing tool, and phage-encoded inhibitors, known as anti-CRISPRs, offer a means of regulating its activity. Here, we report the crystal structures of anti-CRISPR protein AcrIIC2<sub>Nme</sub> alone and in complex with Nme1Cas9. We demonstrate that AcrIIC2<sub>Nme</sub> inhibits Cas9 through interactions with the positively charged bridge helix, thereby preventing sgRNA loading. In vivo phage plaque assays and in vitro DNA cleavage assays show that AcrIIC2<sub>Nme</sub> mediates its activity through a large electronegative surface. This work shows that anti-CRISPR activity can be mediated through the inhibition of Cas9 complex assembly.
Diffusion Processes on Power-Law Small-World Networks (2005)

We consider diffusion processes on power-law small-world networks in different dimensions. In one dimension, we find a rich phase diagram, with different transient and recurrent phases, including a critical line with continuously varying exponents. The results were obtained using self-consistent perturbation theory and can also be understood in terms of a scaling theory, which provides a general framework for understanding processes on small-world networks with different distributions of long-range links.
An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules (2008)

Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into DNA. This system can be applied to conventional PCR protocols employing DNA templates containing unnatural bases, natural and unnatural base triphosphates, and a 3'-->5' exonuclease-proficient DNA polymerase. For highly faithful and efficient PCR amplification involving the unnatural base pairing, we identified the natural-base sequences surrounding the unnatural bases in DNA templates by an in vitro selection technique, using a DNA library containing the unnatural base. The system facilitates the site-specific incorporation of a variety of modified unnatural bases, linked with functional groups of interest, into amplified DNA. DNA fragments (0.15 amol) containing the unnatural base pair can be amplified 10(7)-fold by 30 cycles of PCR, with <1% total mutation rate of the unnatural base pair site. Using the system, we demonstrated efficient PCR amplification and functionalization of DNA fragments for the extremely sensitive detection of zeptomol-scale target DNA molecules from mixtures with excess amounts (pmol scale) of foreign DNA species. This unnatural base pair system will be applicable to a wide range of DNA/RNA-based technologies.
Cover Picture: Molybdenum and Tungsten Imido Alkylidene Complexes as Efficient Olefin‐Metathesis Catalysts (Angew. Chem. Int. Ed. 38/2003) (2003)

Molybdenum imido alkylidenes along with the corresponding tungsten complexes have played a critical role in the emergence of catalytic olefin metathesis as one of the key transformations in chemical synthesis. R. R. Schrock and A. H. Hoveyda recount on page 4592 ff the journey that began with the discovery of tantalum alkylidenes and eventually led to the development of highly effective chiral catalysts, and even supported chiral catalysts (shown in the vials), for asymmetric metathesis.
Reliability and capacity efficiency of restoration strategies for telecommunication networks (2004)

Traditional restoration strategies are designed to provide 100% restoration in the event of any single failure. The impact of simultaneous failures in the network is not frequently studied. Simultaneous failure scenarios become an important consideration when the network is subject to stringent reliability requirements. We examine and compare the robustness of two familiar restoration strategies, 1+1 and shared mesh, and two new proposals, enhanced shared mesh and enhanced shared mesh "plus", with respect to the resilience to simultaneous failures. We propose and utilize efficient algorithms to evaluate demand-pair availabilities for each restoration strategy. Our algorithms for the shared mesh and enhanced shared mesh designs represent new work in this area. We check the accuracy of our availability algorithms with a Monte Carlo simulation. We use the algorithms in conjunction with two real networks to compare the restoration strategies.
ChemInform Abstract: Concise Route to a Series of Novel 3‐(Tetrazol‐5‐yl)quinoxalin‐2(1H)‐ones. (2012)

Abstract A three‐step sequence is developed for the synthesis of compounds (V) via Ugi‐azide multi‐component reaction, simultaneous N‐deprotection followed by intramolecular cyclization and oxidation.
Urinary TMPRSS2:ERG and PCA3 in an Active Surveillance Cohort: Results from a Baseline Analysis in the Canary Prostate Active Surveillance Study (2013)

For men on active surveillance, both PCA3 and TMPRSS2:ERG seem to stratify the risk of having aggressive cancer as defined by tumor volume or Gleason score.
Aneugen Molecular Mechanism Assay: Proof-of-Concept With 27 Reference Chemicals (2019)

A tiered bioassay and data analysis scheme is described for elucidating the most common molecular targets responsible for chemical-induced in vitro aneugenicity: tubulin destabilization, tubulin stabilization, and inhibition of mitotic kinase(s). To evaluate this strategy, TK6 cells were first exposed to each of 27 presumed aneugens over a range of concentrations. After 4 and 24 h of treatment, γH2AX, p53, phospho-histone H3 (p-H3), and polyploidization biomarkers were evaluated using the MultiFlow DNA Damage Assay Kit. The assay identified 27 of 27 chemicals as genotoxic, with 25 exhibiting aneugenic signatures, 1 aneugenic and clastogenic, and 1 clastogenic. Subsequently, a newly described follow-up assay was employed to investigate the aneugenic agents' molecular targets. For these experiments, TK6 cells were exposed to each of 26 chemicals in the presence of 488 Taxol. After 4 h, cells were lysed and the liberated nuclei and mitotic chromosomes were stained with a nucleic acid dye and labeled with fluorescent antibodies against p-H3 and Ki-67. Flow cytometric analyses revealed that alterations to 488 Taxol-associated fluorescence were only observed with tubulin binders-increases in the case of tubulin stabilizers, decreases with destabilizers. Mitotic kinase inhibitors with known Aurora kinase B inhibiting activity were the only aneugens that dramatically decreased the ratio of p-H3-positive to Ki-67-positive nuclei. Unsupervised hierarchical clustering based on 488 Taxol fluorescence and p-H3: Ki-67 ratios clearly distinguished compounds with these disparate molecular mechanisms. Furthermore, a classification algorithm based on an artificial neural network was found to effectively predict molecular target, as leave-one-out cross-validation resulted in 25/26 agreement with a priori expectations. These results are encouraging, as they suggest that an adequate number of training set chemicals, in conjunction with a machine learning algorithm based on 488 Taxol, p-H3, and Ki-67 responses, can reliably elucidate the most commonly encountered aneugenic molecular targets.
Solvatochromism of Distyrylbenzene Pairs Bound Together by [2.2]Paracyclophane:  Evidence for a Polarizable “Through-Space” Delocalized State (2005)

A series of compounds were designed and synthesized to examine how through-space and through-bond electron delocalization respond to solvent effects. The general strategy involves the study of “dimers” of the distyrylbenzene chromophore held in close proximity by the [2.2]paracyclophane core and a systematic dissection of the chromophore into components with through-space and through-bond electronic delocalization. Steady state and time-resolved fluorescence spectroscopy in a range of solvents reveals a red-shift in emission and an increase in the intrinsic fluorescence lifetime for the emitting state in polar solvents when donor substituents are absent. We propose that through-space delocalization across the [2.2]paracyclophane core is more polarizable in the excited state, relative to the through-bond (distyrylbenzene based) excited state. When strong donors are attached to the distyrylbenzene chromophore, the charge transfer character of the distyrylbenzene-based excited state dominates fluorescence properties.
15 μm solder bonding of GaAs/AlGaAs MQW devices to MOSIS 0.8 μm CMOS for 1 Gb/s two-beam smart-pixel receiver/transmitter (2002)

A two-beam optical repeater circuit operates to 1 Gb/s, consumes 10 mW, occupies about 1100 /spl mu/m/sup 2/, and is realized with a technology capable of providing thousands of optical inputs and outputs to foundry-grade VLSI silicon CMOS circuitry. The technology provides this capability by attaching GaAs/AlGaAs multiple-quantum-well (MQW) modulators and detectors to VLSI CMOS with flip-chip solder bonding. The main unique features are summarized.
Characterization of SiGe Layer during Ge Condensation Process by X-ray Diffraction Methods (2011)

We fabricated a Ge-on-insulator (GOI) structure by the Ge condensation method and characterized the SiGe layer during the condensation process by X-ray reciprocal space mapping and synchrotron microbeam X-ray diffraction. The crystalline quality of the SiGe layer degraded during the initial 1 h of oxidation at 1050 °C and it also rapidly degraded during 1 h of oxidation at 900 °C immediately before the formation of GOI structures. The slight degradation was caused by annealing in Ar, indicating that the degradation during the initial 1-h condensation is accelerated by Ge atoms being ejected from the oxidized interface.
Optical Control of DNA Helicase Function through Genetic Code Expansion (2017)

Nucleotide excision repair (NER) is a general DNA repair mechanism that is capable of removing a wide variety of DNA lesions induced by physical or chemical insults. UvrD, a member of the helicase SF1 superfamily, plays an essential role in bacterial NER by unwinding the duplex DNA in the 3' to 5' direction to displace the lesion-containing strand. In order to achieve conditional control over NER, we generated a light-activated DNA helicase. This was achieved through a site-specific incorporation of a genetically encoded hydroxycoumarin lysine at a crucial position in the ATP-binding pocket of UvrD. The resulting caged enzyme was completely inactive in several functional assays. Moreover, enzymatic activity of the optically triggered UvrD was comparable to that of the wild-type protein, thus demonstrating excellent OFF to ON switching of the helicase. The developed approach provides optical control of NER, thereby laying a foundation for the regulation of ATP-dependent helicase functions in higher organisms. In addition, this methodology is applicable to the light-activation of a wide range of ATPases.
Abstract 5526: Inhibition of the histone methyl transferase EZH2 causes viability defects in multiple myeloma (2014)

Abstract Histone lysine methylation, which is dynamically regulated by methyltransferases and demethylases, plays an important role in the establishment and maintenance of chromatin structure and thereby contributes to the control of gene expression. The development of small molecule methyltransferase and demethylase inhibitors provides an approach to manipulate transcriptional programs, and thus potentially allow interference with aberrant cellular states as observed in cancer. The histone methyltransferase Enhancer of Zeste Homologue 2 (EZH2) is a component of the Polycomb Repressive Complex 2. It mediates trimethylation of lysine 27 on histone 3 (H3K27me3), which leads to transcriptional repression. EZH2 has been widely implicated in cancer and inhibition of its catalytic activity provides a novel therapeutic approach to treat human cancers. Constellation has identified, characterized and optimized potent, selective and reversible EZH2 small molecule inhibitors as well as studied the biological impact of such inhibition. We have previously shown that pharmacological inhibition of EZH2 causes selective lymphoma cell viability defects with cell lines harboring EZH2 mutations being the most sensitive. The discovery of small molecules that specifically inhibit EZH2 has enabled us to look for other disease indications that might be dependent on EZH2 for survival. We carried out a long term cell viability screen in ∼75 cell lines across several different hematological malignancies using an EZH2 inhibitor. About 30% of all tested Mutliple Myeloma and Plasmacytoma cell lines showed a time-dependent phenotypic response. In these cell lines H3K27me3 levels were effectively reduced in a dose dependent manner within 4 days of compound treatment which was followed by the induction of apoptotsis at later time points. EZH2 inhibitors also achieved tumor growth inhibition in a Multiple Myeloma subcutaneous xenograft model. To understand the underlying molecular mechanism of EZH2 inhibitor sensitivity in Multiple Myeloma, genome-wide mapping of EZH2 and H3K27me3 sites in the absence and presence of the compound have been performed in conjunction with gene expression profiling and the results will be discussed. In conclusion, we identified Multiple Myeloma as a disease modality where EZH2 inhibition leads to cell viability defects both in vitro and in vivo. Citation Format: Shilpi Arora, Vidya Balasubramanian, Kaylyn Williamson, Victor Gehling, Chris Nasveschuk, Rishi Vaswani, Jennifer Busby, Shivani Garapaty, Priya Iyer, Feng Zhao, Robert Campbell, Richard Cummings, Jim Audia, JC Harmange, Brian Albrecht, Andrew Cook, Les Dakin, Emmanuel Normant, Patrick Trojer. Inhibition of the histone methyl transferase EZH2 causes viability defects in multiple myeloma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5526. doi:10.1158/1538-7445.AM2014-5526
Ih Tunes Theta/Gamma Oscillations and Cross-Frequency Coupling In an In Silico CA3 Model (2013)

Ih channels are uniquely positioned to act as neuromodulatory control points for tuning hippocampal theta (4-12 Hz) and gamma (25 Hz) oscillations, oscillations which are thought to have importance for organization of information flow. contributes to neuronal membrane resonance and resting membrane potential, and is modulated by second messengers. We investigated oscillatory control using a multiscale computer model of hippocampal CA3, where each cell class (pyramidal, basket, and oriens-lacunosum moleculare cells), contained type-appropriate isoforms of . Our model demonstrated that modulation of pyramidal and basket allows tuning theta and gamma oscillation frequency and amplitude. Pyramidal also controlled cross-frequency coupling (CFC) and allowed shifting gamma generation towards particular phases of the theta cycle, effected via 's ability to set pyramidal excitability. Our model predicts that in vivo neuromodulatory control of allows flexibly controlling CFC and the timing of gamma discharges at particular theta phases.
<title>Fusion of multiview interferometric and slant range SAR data for building reconstruction</title> (2000)

Modern very high resolution interferometric SAR sensors deliver slant range magnitude and ground range interferometric height and coherence measurements at pixel sizes of 30cm to 10cm from a single flight path. Detection and reconstruction of buildings get feasible from this kind of data. Single data sources are corrupted by blur, speckle noise and other view dependent effects as e.g., layover and shadows. Especially in case of buildings, these phenomenological features provide also valuable information about the underlying building structure. In this paper we use information from the interferometric height and coherency channel to detect buildings. Shadow information from slant range magnitude images is then used to delimit the exact boundaries of the buildings further and rectangles are fit to the selected points. The resulting building models are input into a simulator to produce slant range magnitude images and interferometric height information. The layover and shadow regions from these simulated images are compared with the corresponding regions in the original data to detect occlusions of adjacent buildings and to further refine the building structure. The results are compared to ground truth data available from optical imagery. Accuracies achieved in the measurement of building dimensions are in the range of 3 pixels.