gebhart/patrepeval huggingface dataset:
Novel effect of the high risk-HPV E7 CKII phospho-acceptor site on polarity protein expression (2022)

The present study sheds light into the mechanisms behind the misexpression of PDZ-polarity proteins during HPV infections. Our findings stress the relevance of the CKII-mediated regulation of E7 activities, providing novel insights into the joint action of HPV oncoproteins and further indicating a conserved and most likely crucial mechanism during the viral life cycle and the associated transformation.
Optimizing performance in cross-linking negative-tone molecular resists (2015)

Many different types of non-traditional resist designs have shown promise for future generations of patterning, but there is a greater need for understanding and developing additives and ancillary materials for these novel resists compared to traditional polymeric positive tone systems which are quite mature. With the goal of meeting some of these needs, we carried out multiple different studies of negative tone molecular resists based on epoxide cross-linking. We have developed methods for controlling cross-linking in these materials using photo-decomposable nucleophiles (PDNs) which have shown resolution improvements in one resist from 26 nm down to 18 nm so far. Aqueous base developed systems have been made by introducing phenol groups to these resists. Although the first molecule designed successfully patterns in aqueous base, its performance is limited compared to organic solvent development. A series of di-functional epoxide molecular resists have been made and generally show much worse sensitivity than a fourfunctional epoxide resist. Underlayers (ULs) have been designed specifically to leverage the high reactivity of epoxides to create ULs that can cross-link to the resist. These ULs improve the adhesion of some of these molecular resists, but also show significant sensitivity improvements compared to imaging on bare silicon. Sensitivity in one resist was improved by 5-12 mJ/cm<sup>2</sup> simply by using the UL.
Time scale analysis and scalability issues for explicit rate allocation in ATM networks (1996)

End-to-end rate based congestion management has been extensively studied for control of computer communication networks. We examine some of the properties of end-to-end rate based algorithms for congestion management using explicit rate feedback, to achieve maxmin fair rate allocation in the network. We formulate a requirement on a switch's local rate allocation computation sufficient to ensure convergence of the distributed algorithm to the global maxmin fair rate allocation. We provide an upper bound on the convergence time when the switch algorithm satisfies this requirement. We propose a requirement of feasibility of the transmission rates, maintaining which results in oscillation-free operation of the algorithm while maintaining small queues at the switches. Feasibility implies that the capacity of any of the resources is not exceeded at any time. We suggest a source policy to ensure feasibility of transmission rates, the essence of which is to delay a rate increase by a certain time, while decreasing the transmission rate immediately upon receiving the appropriate feedback. Finally, we seek ways of improving scalability of the computation of maxmin fair rates in the presence of a large number of flows. We suggest using a discrete set of rates, which as we show, reduces the computational complexity and the state requirement at the switches.
Upstream sequences of rice proliferating cell nuclear antigen (PCNA) gene mediate expression of PCNA-GUS chimeric gene in meristems of transgenic tobacco plants (1991)

The transgenic tobacco plants have been generated that express the E. coli beta-glucuronidase (GUS) gene under control of the promoter from the rice proliferating cell nuclear antigen (PCNA, DNA polymerase auxiliary protein) gene. GUS expression detected in situ by staining with the chromogenic substrate, 5-bromo-4-chloro-3-indolyl-beta-D-glucuronide (X-Gluc), was restricted to meristems in the organs of the transgenic tobacco plants. This expression responded to the phytohormones which promote callus formation. Furthermore, in situ thymidine uptake showed that the GUS expression pattern corresponded well to the active sites of DNA synthesis. Deletion analysis of the 5' upstream sequence confined the GUS expression pattern to a fragment extending 263 bp upstream of the transcription start site of the rice PCNA gene. Thus, we have identified this fragment as a main regulatory element of the rice PCNA gene promoter.
AMPA antagonist LY293558 blocks the development, without blocking the expression, of behavioral sensitization to morphine (1999)

Morphine (3.0 mg/kg, s.c.) stimulates locomotor activity in rats, and this effect sensitizes with repeated intermittent treatment. We examined the ability of the AMPA antagonist LY293558, administered systemically over a range of doses (0.1-3.0 mg/kg), to alter morphine sensitization. Pretreatment with 3.0 mg/kg LY293558 attenuated the acute (session 1) locomotor-stimulating actions of morphine, whereas 1.0, 0.3, and 0.1 mg/kg were without effect. No sensitization was observed after repeated morphine treatment (3.0 mg/kg, s.c., every other day for 9 days) when morphine injections were preceded by 0.3, 1.0, or 3.0 mg/kg LY293558, whereas significant sensitization was observed when morphine injections were preceded by vehicle or 0.1 mg/kg of the antagonist. When all rats were challenged with morphine (3.0 mg/kg, s.c.) alone on day 11, the locomotor activity of rats previously exposed to LY293558 at 3.0, 1.0, or 0.3 mg/kg--but not at 0.1 mg/kg--was significantly lower than that of rats previously given morphine preceded by vehicle. On day 13, pretreatment with 1.0 mg/kg LY293558 failed to alter preestablished morphine sensitization in rats previously pretreated with vehicle. These data indicate that LY293558 blocks the development but not the expression of morphine sensitization, confirming a role for AMPA receptors in the initiation of neurobiological adaptations that occur with chronic morphine treatment.
Adaptive Concurrent Non-Malleability with Bare Public-Keys (2009)

Concurrent non-malleability (CNM) is central for cryptographic protocols running concurrently in environments such as the Internet. In this work, we formulate CNM in the bare public-key (BPK) model, and show that round-efficient concurrent non-malleable cryptography with full adaptive input selection can be established, in general, with bare public-keys (where, in particular, no trusted assumption is made). Along the way, we clarify the various subtleties of adaptive concurrent non-malleability in the bare public-key model.
Oral SMAD7 Antisense Drug for Crohn's Disease (2015)

Crohn's disease is characterized by relapsing inflammation leading to ulcers in the ileum and colon. Crohn's disease also affects the perianal region in more than half of patients. The disease is caused by a defective recognition, tolerance, or elimination of microbiota in a person who is genetically susceptible. An inappropriately overrobust reaction of the adaptive immune system leads to chronic transmural inflammation and is the cause of progressive intestinal damage, which occurs in more than two thirds of patients. In their landmark paper in 1932, Burrill Crohn and colleagues described the consequences of the disease: “a disproportionate connective tissue reaction . . .
Planning of hepatectomy for tumor resection: Resection surface construction and optimization (2013)

An interactive liver surgery planning system has been developed to construct and optimize the resection plan. With this system, the segmentation results of the liver and its components (such as tumors and vessels) are comprehensively visualized for surgeons to have an intuitive understanding of the internal anatomical structure of the liver. This system will also allow surgeons to interactively create and modify a resection plan on the virtual liver model. The resection surface, whose boundary is a closed curve, will be automatically constructed with the safe resection margins of tumors. Different from other systems, our developed system is able to generate the safety margins to all tumors. During surgery, a larger resection surface may cause potentially more bleeding and other complications. Therefore, area minimization is applied during the resection surface construction by adopting the minimal area mesh, which is a smooth surface with minimal area. After these virtual modifications, the resultant resection surface indicates the route to cut the liver for tumor removal. The volumes for both resected liver and residual liver are calculated for clinical decision making.
Tn5 insertion in the polynucleotide phosphorylase (pnp) gene in Escherichia coli increases susceptibility to antibiotics (1987)

A Tn5 insertional mutation on the Escherichia coli chromosome which caused a severalfold increase in susceptibility to structurally and functionally diverse antibiotics was found to map within the gene for polynucleotide phosphorylase (pnp) and to inactivate this enzyme, which is involved in RNA breakdown. The mutation also decreased the growth rate 10 to 25% and increased the rate of tetracycline uptake about 30%. The hypersensitivity due to the insertion was only partially complemented by a cloned pnp gene.
Shortest-Path Kernels on Graphs (2006)

Data mining algorithms are facing the challenge to deal with an increasing number of complex objects. For graph data, a whole toolbox of data mining algorithms becomes available by defining a kernel function on instances of graphs. Graph kernels based on walks, subtrees and cycles in graphs have been proposed so far. As a general problem, these kernels are either computationally expensive or limited in their expressiveness. We try to overcome this problem by defining expressive graph kernels which are based on paths. As the computation of all paths and longest paths in a graph is NP-hard, we propose graph kernels based on shortest paths. These kernels are computable in polynomial time, retain expressivity and are still positive definite. In experiments on classification of graph models of proteins, our shortest-path kernels show significantly higher classification accuracy than walk-based kernels.
Experimental Demonstration of Optical Metamaterials with Isotropic Negative Index (2016)

The critical challenge to the successful implementation of ‘perfect lens’ and ‘optical cloaking’ is to achieve isotropic negative index metamaterials. Here we experimentally demonstrate isotropic negative index metamaterials at optical frequency by proper design and scalable self-assembly.
In vivo butyrylcholinesterase activity is not increased in Alzheimer's disease synapses (2005)

Failure to observe increased [(11)C]BMP hydrolysis in vivo makes it less likely that incremental BuChE contributes importantly to acetylcholine hydrolysis in AD. The findings do not support the premise that inhibitor therapy should target BuChE so as to prevent increased levels of BuChE from hydrolyzing acetylcholine in AD cerebral cortex.
A prototype driftless gas proportional scintillation counter for muonic hydrogen X-ray spectroscopy under strong magnetic fields (1999)

Experiments for muonic atom X-ray spectrometry require detectors having large areas, working under very strong magnetic fields with good energy and timing resolution. A compact, driftless gas proportional scintillation counter (GPSC) capable of operating under such magnetic fields and having a time resolution of some tens of ns is investigated. This GPSC uses a CsI photocathode deposited onto a microstrip plate as the UV scintillation readout photosensor. This photocathode has the advantage of operating it in direct contact with the scintillation gas. The detector is filled with pure xenon at atmospheric pressure and it is designed to have high detection efficiency for 2 keV X-rays. A limited pulse amplitude-to-noise ratio is achieved with the present prototype. Photosensor positive feedback is a major drawback for improved detector performance. Energy resolutions of 33% and 34% were obtained for 1.75 and 2.3 keV X-rays, respectively.
ARM: Ka ARM Zenith Radar (KAZR): moderate sensitivity mode (2011)

Ka ARM Zenith Radar (KAZR): moderate sensitivity mode
An Electro-Osmotic Knife for Slicing Large Box Cores (1977)

ABSTRACT Large box cores can be sliced vertically or horizontally on board ship with a knife that has an electrified metal blade. The knife operates on the principle of electro-osmosis, which reduces drag along the blade during slicing and minimizes distortion of the sediment. The slices are useful for subsampling the core and for studying physical and biogenic sedimentary structures. Making slices helps solve the problems of handling, storing, and shipping the large volumes of sediment recovered in box cores.
Preface (2013)

The International Conference on Formal Methods in Computer-Aided Design, FMCAD, is a series of conferences on the theory and application of formal methods to the computer-aided design and verification of hardware and systems. The thirteenth conference in the series, FMCAD 2013, was held in Portland, OR, USA, October 20–23.
AgVO3-anchored 2D CeO2 nanocrystals prepared by solution process for visible-light-driven photooxidation of ciprofloxacin antibiotic in water (2023)

• Surfactant-assisted sol–gel-based synthesis of 2D CeO 2 nanocrystals . • AgVO 3 /CeO 2 nanocomposite enhances visible light harvesting and charge separation. • Visible-light-driven photooxidation of CIPF over 16% AgVO 3 /CeO 2 in 90 min. • Sustainable efficiency for five runs at 96%. Visible light oxidative mineralization of antibiotics over semiconducting nanostructured photocatalysts demonstrated a promising approach for preventing possible antimicrobial resistance. The design strategy of recyclable and effectual compound photocatalysts is yet under advance to avoid such impediments like fast carrier recombination and instability in solution. Herein, two-dimensional (2D) CeO 2 nanocrystals were synthesized via a modified sol–gel process in the presence of a copolymer surfactant. The 2D CeO 2 were combined with different amounts (4.0 ∼ 20.0 wt%) of nanocrystalline AgVO 3 by coprecipitation to construct p-n AgVO 3 /CeO 2 heterojunction. The formed nanostructures exposed the consistent coupling of monoclinic AgVO 3 to the cubic CeO 2 phase, as proved by XRD, XPS, and TEM depictions. The produced materials also revealed mesostructured surfaces with 149 ∼ 187 m 2 g −1 of surface area. Incorporating AgVO 3 into CeO 2 has also extended the visible-light harvesting and minimized bandgap energy (E g ) down to 2.53 eV at 16 wt%. The fast photooxidation of ciprofloxacin (CPIF), as an emergent antibiotic contaminant in water, was established after 90 min over the tuned dose of 16% AgVO 3 /CeO 2 . This innovative heterojunction photocatalyst also showed 96% sustainable recyclability after the fifth reusable run. The superb performance of 16% AgVO 3 /CeO 2 is attributed to the precise coupling of 16% AgVO 3 to CeO 2, resulting in resourceful charge separation and enhanced mobilities that lead to the oxidation of CPIF.
Trilayered Morphology of an ABC Triple Crystalline Triblock Terpolymer (2017)

Triple crystalline triblock terpolymers are materials with remarkable semicrystalline superstructures. In this work, we report for first time the alternating triple lamellar morphology that self-assembles inside spherulites of a triblock terpolymer composed of poly(ethylene oxide) (PEO), poly(ε-caprolactone) (PCL), and poly(l-lactide) (PLLA). The morphology of the PEO-b-PCL-b-PLLA triblock terpolymer is compared to an analogous PCL-b-PLLA diblock copolymer. Both diblock and triblock form a single phase in the melt. Two crystallization protocols were employed to create particular crystalline morphologies. In both cases, the isothermal crystallization of the PLA block is induced first (at 81 °C, a temperature above the melting points of both PCL and PEO blocks) and PLLA spherulites form a template, whereupon cooling the other two blocks can crystallize within the PLLA interlamellar spaces. WAXS analysis demonstrated the double crystalline and triple crystalline nature of the materials. The lamellar structure was evaluated by AFM observations and SAXS measurements. Moreover, theoretical SAXS curves of one-dimensional structural models were calculated. AFM micrographs of the triblock terpolymer evidenced the three different lamellae of PLLA, PCL and PEO that coexist together within the same spherulite. Three different lamellar thickness were determined, and their dimensions suggested that all blocks crystallized in chain-folded conformations. The evolution of the triple lamellar morphology during heating of tricrystalline samples was followed by in situ synchrotron SAXS measurements. The theoretical analysis of the SAXS curves of the triblock terpolymer allowed us to propose a stacking morphological model, in which a particular trilayer structure exists, where one lamella of PCL or one lamella of PEO is inserted randomly between two adjacent PLLA lamellae.
Characterization of tyrocidine synthetase 1 (TY1): Requirement of posttranslational modification for peptide biosynthesis (1995)

Tyrocidine synthetase 1 (TY1), produced by Bacillus brevis ATCC 8185, consists of a single multifunctional polypeptide chain catalyzing the activation, thioesterification, and epimerization of phenylalanine. Because we were concerned about possible posttranslational issues, a comparative study between the wild-type isolate and the in Escherichia coli overexpressed protein was performed. Analysis by matrix assisted laser desorption mass spectrometry (MALDI) provided a molecular mass of 122,516 +/- 120 Da for the recombinant protein, which is in agreement with the value of 122,590 Da calculated from the gene sequence. MALDI analysis of the tryptic fragments revealed that in the recombinant TY1 the putative 4'-phosphopantetheine binding site (562Ser) is not modified by the cofactor. The substrate specificity profiles of the amino acid dependent ATP[32P]PPi exchange reactions were identical, including activation of L-phenylserine, L-tyrosine, and L-methionine. However, the rates of the reverse adenylation reaction for the recombinant protein were only 22% relative to those of the wild-type enzyme. The aminoacylation levels of about 60% for TY1 from Bacillus brevis reduced to 1.4% in the overexpressed protein. A similar distribution of the D- and the L-isomer was detected at the thioester attachment site. The pI values of the wild-type and expressed TY1 are 4.9 and 5.0, respectively. In conclusion, it could be established that apo- and holo-TY1 differ in their amino acid activating properties. Posttranslational modification by 4'-phosphopantetheine is an essential requirement for aminoacylation, epimerization, and thus the functioning of the multienzyme in peptide synthesis.
Approaches for Service Deployment (2005)

Traditional IT service-deployment technologies are based on scripts and configuration files, but their limited ability to express dependencies and verify configurations results in hard-to-use and erroneous system configurations. Emerging language- and model-based tools promise to address these deployment challenges, but their benefits aren't yet clearly established. The authors compare manual, script-, language-, and model-based deployment solutions in terms of scale, complexity, expressiveness, and barriers to first use.
One‐Pot Synthesis of Substituted Quinolines by Iridium‐Catalyzed Three‐Component Coupling Reaction. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Investigation of DNA Repair Pathway Activity (2013)

DNA is constantly being damaged from endogenous and exogenous sources and efficient repair of different types of DNA lesions is essential for the survival of the organism. Dictyostelium is highly resistant to DNA damage and its genome sequence has revealed the presence of multiple repair pathways conserved with vertebrates but lost in other genetically tractable invertebrate models. As such, Dictyostelium is a powerful model organism to study selected human DNA repair pathways and may provide insights into the molecular basis of how cells become resistant to DNA damage. Here we describe a range of assays used to study DNA repair in Dictyostelium. Genes required for repair of DNA damage can be identified and analyzed by comparing the ability of control or mutant cells to survive exposure to genotoxic agents that induce different types of DNA lesion. We also describe assays that assess the presence of markers for DNA repair within chromatin either in the form of posttranslational modification of proteins at sites of damage or the recruitment of repair factors to DNA lesions. Finally, we also describe more direct assays to assess repair of DNA double-strand breaks by either homologous recombination or non-homologous end joining.
Human-like informative conversations: Better acknowledgements using conditional mutual information (2021)

This work aims to build a dialogue agent that can weave new factual content into conversations as naturally as humans. We draw insights from linguistic principles of conversational analysis and annotate human-human conversations from the Switchboard Dialog Act Corpus to examine humans strategies for acknowledgement, transition, detail selection and presentation. When current chatbots (explicitly provided with new factual content) introduce facts into a conversation, their generated responses do not acknowledge the prior turns. This is because models trained with two contexts -new factual content and conversational history -generate responses that are non-specific w.r.t. one of the contexts, typically the conversational history. We show that specificity w.r.t. conversational history is better captured by pointwise conditional mutual information (pcmi h ) than by the established use of pointwise mutual information (pmi). Our proposed method, Fused-PCMI, trades off pmi for pcmi h and is preferred by humans for overall quality over the Max-PMI baseline 60% of the time. Human evaluators also judge responses with higher pcmi h better at acknowledgement 74% of the time. The results demonstrate that systems mimicking human conversational traits (in this case acknowledgement) improve overall quality and more broadly illustrate the utility of linguistic principles in improving dialogue agents.
Thermal conductivity of oriented crystalline polymers (1980)

Abstract Thermal conductivities of six oriented semicrystalline polymers which range from 0.37 to 0.63 in crystallinity and 1 to 5 in draw ratio λ (up to about 15 for two polymers) have been measured between 100 and 340 K. It was found that for increasing λ the conductivity K ∥ (along the draw direction n̂ ) increases rapidly while K ⊥ (normal to n̂ ) decreases slightly; K ∥ also increases with temperature, but K ⊥ shows no simple pattern in temperature dependence. These general features can be reproduced reasonably well at low draw ratio (λ &lt; 5) by the modified Maxwell model, and the discrepancy in details may be attributed to the fact that the model does not take into account the possible anisotropy of the amorphous phase of the oriented polymers. At high draw ratio the intercrystalline bridge effect becomes important, and one must resort to the Takayanagi model, but the lack of corroborating x‐ray data has rendered a detailed comparison impossible.