gebhart/patrepeval huggingface dataset:
Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking (2023)

Abstract Proteolysis targeting chimeras (PROTACS) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACS currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated dataset of 13 ternary complex crystals, we achieved accuracy of 92% when starting from bound structures, and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate and highly efficient, with the ability to impact early stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.
Abstract 266: Role of Marine Long-chain Monounsaturated Fatty Acid in Cardiovascular Disease Prevention and Possible Mechanism to Reduce the Atherosclerosis (2016)

Numerous studies have shown cardiovascular benefits of fish oil, and most of these favorable effects have been attributed to omega-3 fatty acids. Fish oils, however, also contain varying amounts of other unusual types of fatty acids, such as long-chain monounsaturated fatty acids (LCMUFA; i.e., C20:1 and C22:1 isomers combined). Compared with well-studied omega-3, limited information is available on the role of LCMUFA on cardiovascular disease. In the current study, we examined the effect of saury fish oil-derived LCMUFA concentrate on the pathogenesis of atherosclerosis in ApoE-deficient and LDLR-deficient mice. Male ApoE-deficient mice were fed a western diet supplemented with 5% LCMUFA concentrate or not (control) for 12 weeks. En face Sudan IV staining of the aorta revealed that LCMUFA significantly suppressed the development of atherosclerotic lesions, and down-regulated inflammatory gene expression. In LDLR-deficient female mice, we also observed that 12-week supplementation of 2% LCMUFA on a western diet significantly decreased atherosclerosis lesion areas and accumulation of macrophages, compared with western diet (control) or western diet supplemented with 2% olive oil enriched in shorter-chain MUFA oleic acid (C18:1). There were no differences, however, in plasma or hepatic lipid profiles between the three groups. LCMUFA, but not olive oil, also significantly suppressed several plasma inflammatory cytokine levels. RNA sequencing and subsequent qPCR analyses revealed that LCMUFA upregulated PPAR signaling pathways in liver. In cell culture studies, apoB-depleted plasma from the LCMUFA group promoted cholesterol efflux from macrophage-like THP-1 cells and ABCA1-overexpressing BHK cells. LCMUFA also suppressed LPS-induced inflammatory cytokine production by macrophages. In conclusion, our research showed for the first time that LCMUFA consumption could protects against atherosclerosis, possibly by upregulating the PPAR signaling pathway. Omega-3 fatty acids are generally considered the major active components in fish lipids, but our findings provide new insights into potential health effect of LCMUFA-rich fish oil and suggest that LCMUFA-rich fish oil may also be beneficial for reducing cardiovascular disease risk.
Ablation Analysis for Multi-Device Deep Learning-Based Physical Side-Channel Analysis (2023)

The use of deep learning-based side-channel analysis is an effective way of performing profiling attacks on power and electromagnetic leakages, even against targets protected with countermeasures. While many research papers have reported successful results, they typically focus on profiling and attacking a single device, assuming that leakages are similar between devices of the same type. However, this assumption is not always realistic due to variations in hardware and measurement setups, creating what is known as the portability problem. Profiling multiple devices has been proposed as a solution, but obtaining access to these devices may pose a challenge for attackers. This paper proposes a new approach to overcome the portability problem by introducing a neural network layer assessment methodology based on the ablation paradigm. This methodology evaluates the sensitivity and resilience of each layer, providing valuable knowledge to create a Multiple Device Model from Single Device (MDMSD). Specifically, it involves ablating a specific neural network section and performing recovery training. As a result, the profiling model, trained initially on a single device, can be generalized to leakage traces measured from various devices. By addressing the portability problem through a single device, practical side-channel attacks could be more accessible and effective for attackers.
Effect of 24-Epicastasterone and Its Monosalicylate on Salt Resistance of Arabidopsis thaliana Wild Type and the Salicylate-Deficit NahG Transformants (2022)

The effects of 24-epicastasterone (EC) and those of its conjugate with a salicylic acid residue—24‑epicastasterone 2-monosalicylate (MSEC)—on the resistance of Arabidopsis thaliana L. plants to 24-h contact with 175 mM NaCl were assessed. The wild type Col-0 plants and those transformed with the bacterial NahG gene of salicylate hydroxylase were compared in this respect. The pretreatment of the wild plants with 0.01–1 µM EC elevated their salt resistance, which was expressed as the decrease in their LPO rate, stabilization of the chlorophyll pool, and increase in the carotenoid level after the plants’ exposure to NaCl. MSEC also afforded a protective and more pronounced effect on the Col-0 plants. In the salt-stressed wild type plants, EC enhanced the activities of antioxidant enzymes catalase and guaiacol peroxidase; the treatment with MSEC significantly activated superoxide dismutase and catalase. Meanwhile, neither EC nor MSEC influenced the activities of the antioxidant enzymes in the NahG plants that are unable to accumulate salicylic acid. In addition, neither EC nor MSEC changed the LPO intensity and the level of photosynthetic enzymes under salt stress. It was inferred that salicylic acid is involved in the mechanism of the protective action of brassinosteroids against consequences of the strong salinization. MSEC is considered to be a practically prospective agent promoting salt resistance of plants.
Fluorescein Isothiocyanate Specifically Modifies Lysine 338 of Cytochrome P-450scc and Inhibits Adrenodoxin Binding (1989)

Treatment of cytochrome P-450scc with fluorescein isothiocyanate (FITC) resulted in covalent labeling with 1.0 +/- 0.1 eq of FITC. Reverse-phase high performance liquid chromatography of tryptic and chymotryptic digests of the labeled protein revealed that a single FITC-labeled peptide accounted for 75% of the label. This peptide was found to be specifically labeled at lysine 338 by amino acid sequencing. The modification of lysine 338 with FITC resulted in 85 +/- 15% inhibition of adrenodoxin binding to cytochrome P-450scc. In a complementary experiment it was found that if a complex between adrenodoxin and native cytochrome P-450scc was formed in the presence of cholesterol and then treated with FITC, there was almost no labeling of lysine 338. The modification of lysine 338 by FITC was not inhibited by 22(R)-hydroxycholesterol, the first intermediate in the side chain cleavage reaction which binds to the active site 300 times more tightly than cholesterol itself. These experiments suggest that lysine 338 is located at the binding site for adrenodoxin and electrostatically interacts with one of the carboxylate groups on adrenodoxin that has been implicated in binding. The fluorescence emission of the FITC label on cytochrome P-450scc was only 14% as large as that of an equivalent concentration of FITC-labeled bovine serum albumin, suggesting that it was quenched by Forster energy transfer to the heme group.
Computational Complexity Reduction in a Cognitive Radio Receiver for Green Communications (2012)

The work presented in this paper concerns the cognitive and green communications. It consists of developing a decision making method, based on statistical modeling, that makes the receiver radio able to dynamically adapt to the change of its environment. Also, we try to use this adaptability to obtain green communication by treating scenarios of reconfiguration that contribute to the reduction of energy consumption. For this goal, we treat the scenario of adapting the use of the equalizer to the state of the environment. It is to decide dynamically to turn off or to keep this component in the receiver chain. This action of turning off the equalizer should reduce the computational complexity of the receiver.
Formic acid-assisted synthesis of highly efficient Cu/ZnO catalysts: effect of HCOOH/Cu molar ratios (2016)

Metallic Cu/ZnO catalysts were directly prepared by a formic acid-assisted solid-state combustion method without further reduction.
The Kautz mesh: A new topology for SoCs (2008)

Nowadays networks-on-chip are emerging as a hot topic in IC designs with high integration. In addition to popular mesh topologies, other structures can also be considered especially in 3D VLSI design. The Kautz topology is one of the interconnection architectures for multiprocessors. In this paper we propose an efficient three dimensional layout for a novel 2D mesh structure based on the Kautz topology. Simulation results show that by using the third dimension, performance and latency can be improved compared to the 2D VLSI implementation.
WebCompanion: a friendly client-side Web prefetching agent (1999)

Accessing remote sites of the World Wide Web is often a frustrating experience for users because of long Web page retrieval times even over relatively fast Internet connections. Users are more likely to embrace the further expansion of the role of the Web into a major infrastructure for electronic commerce and for information, application, and multimedia delivery if Web accesses can be accelerated. One technique that attempts this is prefetching. We built a client-side Java-implemented prefetching agent, WebCompanion, which employs a novel adaptive, fast, and selective online prefetching strategy based on estimated round-trip times for Web resources. This strategy efficiently hides the access latencies for slow resources while at the same time limiting the network and server overhead and local resource consumption to moderate levels. Our extensive experiments show an average access speedup of greater than 50 percent and an average network byte overhead of less than 150 percent using WebCompanion over a fast Internet connection. We measured a slight acceleration in accessing the Web through WebCompanion even in a pessimistic scenario where the user never requests a prefetched document.
Refinement of RE211 particles in melt-textured RE$ndash$Ba$ndash$Cu$ndash$O bulk superconductors (2002)

The formation mechanism of fine Gd211 particles was studied by observing the size and morphology of Gd211 in the Gd–Ba–Cu–O melt-quenched from 1100 °C with various Gd211 particle sizes. The size and distribution of Gd211 particles at the partial melting stage depended on the size of initially added Gd211 particles. The precursor with fine Gd211 starting powder formed fine needle-shaped Gd211 particles after melting. The Gd211 refinement is ascribable to the increased number of Gd211 nucleation sites and growth inhibition by Pt addition. We also studied the refinement of RE211 (Nd422) particles in other RE–Ba–Cu–O (RE: Y, Dy, Eu, Sm, Nd) systems. In the cases of Y-, Dy- and Nd-systems, the size of RE211 (Nd422) particles could be reduced by decreasing the size of RE211 (Nd422) starting powders. In contrast, the employment of fine RE211 starting powder was not so effective for the size reduction of RE211 particles in the Eu- and Sm-systems.
The Body Responds (2020)

The first author uses a hermeneutic approach to reflect on her somatic experiences with clients diagnosed with Anorexia Nervosa. Using poetry, imagery, and metaphor, as well as understandings drawn from the psychodynamic literature, she attempts to convey something of the nature of her journey towards making sense of her experiences. The second author was the supervisor of the first author’s dissertation, from which this article arose.
Monoclonal antibodies generated by DNA immunization recognize CD2 from a broad range of primates (2009)

Using heterologous prime-boost (DNA immunization followed by immunization with transfected cells), we have generated depleting mouse anti-baboon CD2 monoclonal antibodies (mAb). These anti-CD2 mAb recognized a diverse range of primate CD2 from New World monkeys and Old World monkeys to humans and have potent immunosuppressive activity for human allo-MLR responses and anti-tetanus-toxoid recall responses. There was no upregulation of activation markers or release of cytokines when the mAb were incubated with human peripheral blood mononuclear cells. Using chimeric NOD-SCID IL2rgamma(null) mice, the mAb were shown to deplete human and cynomolgus monkey T cells in vivo. These anti-CD2 mAb may therefore be important immunological tools in allo- and xenotransplantation.
Correction: A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana (2022)

[This corrects the article DOI: 10.1371/journal.ppat.1008147.].
Duration of protection from live attenuated vs. sub unit HSV-2 vaccines in the guinea pig model of genital herpes: Reassessing efficacy using endpoints from clinical trials (2019)

While both the live attenuated vaccine, VC2, and the gD2 subunit vaccine provided protection, the duration of protection appeared to be greater for VC2. Using the same evaluation criteria as used in human trials provided unique insights into the utility of the guinea pig model.
Parameters required to maximize a thermoset hydro-generator stator winding life. Part I-design, manufacture, installation (1994)

This paper describes the parameters required for a thermoset hydro-generator stator winding to achieve a service life of 50 years. Such parameters covering design, manufacture, installation, online monitoring and maintenance functions have been found to be relevant based on 36 years of design and operation experience. The database includes North American, European and Far Eastern hydro generators up to 20.5 kV-500 MVA. Parameters covered can be simply stated as design, installation and manufacture: the DIM rule.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Quantum state transfer between motion and light (1999)

We describe schemes for transferring quantum states between light fields and the motion of a trapped atom. Coupling between the motion and the light is achieved via Raman transitions driven by a laser field and the quantized field of a high-finesse microscopic cavity mode. By cascading two such systems and tailoring laser field pulses, we show that it is possible to transfer an arbitrary motional state of one atom to a second atom at a spatially distant site.
Column Chromatographic Analysis of Barbiturates in Their Dosage Forms. IV. Combinations with Parabens (1977)

Abstract The nature of the alkaline hydrolysis of some barbiturates in combinations with parabens (p-hydroxybenzoates) was studied with controlled variables, including temperature, viscosity, and concentrations of sodium hydroxide, barbiturate, and parabens. The kinetic studies showed that parabens could be completely hydrolyzed in strong base at 40°C in 1 hr, while the barbiturate remained intact and was readily isolated by partition chromatography. Based on the theoretical results, a partition chromatographic procedure for butabarbital with parabens was devised. Standard recoveries averaged 100.7 % with a standard deviation of 0.89. Kinetic data indicate that the hydrolysis of parabens could also be applied to analyze combinations with amo-, seco-, and pentobarbitals. Phenobarbital and parabens are readily separated by partition chromatographic methods without prior hydrolysis of the parabens. The low extraction constant for phenobarbital allowed its retention on a column against relatively strong solvents while the intact parabens are eluted. A slightly modified method was applied to the separation of phenobarbital from parabens. Standard recoveries average 99.9% with a standard deviation of 0.69.
Empirical evidence for taxi customer-search model (2010)

A mutinomial logit model of urban taxi services has been developed for the study of the operational characteristics of the taxi industry, in which it is hypothesised that the customer-searching behaviour of vacant taxis follows a multinomial logit choice model. Although the model is commonly used, little empirical evidence exists to validate the choice mechanism and determine the set of important factors that affect the choice. In the present study, a stated preference survey of 400 taxi drivers was conducted to analyse the customer-searching behaviour of vacant taxis. The results explain how the considered parameters of waiting time, journey time, travel distance and toll affect the driver behaviour when searching for customers. In addition, market segmentation analysis was carried out to study the effects of driver demographics and operational characteristics on the searching behaviour. The parameters that were considered in this section of the study were the age of the driver, taxi ownership, driver experience and marital status.
Flat Mesomorphic Metal Organyls (1996)

Abstract Large-sized flat tetrametallomesogens containing palladium or platinum in their macroheterocyclic cores show wide ranging liquid crystalline properties, both thermotropic and lyotropic in apolar organic solvents. Here, we briefly summarise recent work from our laboratory concerning these novel metallomesogens and related bis-metal analogues.
Analysis and Modeling of a Platform with Cantilever Beam using SMA Actuator - Experimental Tests based on Computer Supported Education (2015)

This paper presents a test platform with cantilever beam that uses a SMA (Shape Memory Alloy) as actuator

and strain gauges as sensors to study of the beam deformation. From the data acquired by means of heating

and cooling processes, the engineering students can observe the hysteresis behavior of the SMA wire.

Besides, the study of this platform provide to the students can put in practice their knowledge about data

acquisition, system identification, modeling and programming based on computer supported education.
Diastereoselective synthesis of (−)-N-acetylneuraminic acid (Neu5Ac) from a non-carbohydrate source (1998)

M. Banwell, C. De Savi and K. Watson, J. Chem. Soc., Perkin Trans. 1, 1998, 2251 DOI: 10.1039/A804524K
Medium-size droplets of methyl ricinoleate are reduced by cell-surface activity in the gamma-decalactone production by Yarrowia lipolytica (2000)

Size of methyl ricinoleate droplets during biotransformation into gamma-decalactone by Yarrowia lipolytica was measured in both homogenized and non-homogenized media. In non-homogenized but shaken medium, droplets had an average volume surface diameter d32 of 2.5 microm whereas it was 0.7 microm in homogenized and shaken medium. But as soon as yeast cells were inoculated, both diameters became similar at about 0.7 microm and did not vary significantly until the end of the culture. The growth of Y. lipolytica in both media was very similar except for the lag phase which was lowered in homogenized medium conditions.
Synthesis of a phthalocyanine derivative containing easily oxidised sterically-hindered phenolic substituents (1997)

A novel phthalocyanine containing four redox-active 3,5-di-tert-butyl-4-hydroxyphenyl substituents is readily oxidised in aerated, basified solution to give a complex product mixture; the oxidation is apparently localised on the phenolic moieties without disturbing the structure of the phthalocyanine core.
Comment on “Spaser Action, Loss Compensation, and Stability in Plasmonic Systems with Gain” (2011)

A Comment on the Letter by Mark I. Stockman, Phys. Rev. Lett. 106, 156802 (2011). The author of the Letter offers a Reply.Received 17 May 2011DOI:https://doi.org/10.1103/PhysRevLett.107.259703© 2011 American Physical Society
Editorial: The Origin of Plant Chemodiversity – Conceptual and Empirical Insights (2020)

EDITORIAL article Front. Plant Sci., 30 June 2020 | https://doi.org/10.3389/fpls.2020.00890
Analysis of the gB promoter of herpes simplex virus type 1: high-level expression requires both an 89-base-pair promoter fragment and a nontranslated leader sequence (1992)

To investigate the cis-acting sequences involved in regulation of a herpes simplex virus gamma 1 gene, deletion analyses of the glycoprotein B (gB) gene promoter were performed. In transfection assays with gB-chloramphenicol acetyltransferase plasmids, high-level constitutive expression from the gB promoter was found with an 89-bp sequence (-69 to +20). Additional sequences in the 5'-transcribed noncoding leader region (+20 to +136) were required for full stimulation by herpes simplex virus infection. Plasmids with progressive deletions of the gB leader sequence demonstrated that chloramphenicol acetyltransferase expression in infected cells was proportional to the length of the leader region retained. In recombinant viruses containing a gB-gC gene fusion, a similar 83-bp (-60 to +23) region of the gB gene was found to promote accurately initiated gC mRNA from the viral genome with the same kinetics as the wild-type gB gene. Although the kinetics of expression remained the same, RNA abundance was greater with a 298-bp (-260 to +38) promoter than with the 83-bp promoter.
Sampling code clones from program dependence graphs with GRAPLE (2016)

We present GRAPLE, a method to generate a representative sample of recurring (frequent) subgraphs of any directed labeled graph(s). GRAPLE is based on frequent subgraph mining, absorbing Markov chains, and Horvitz-Thompson estimation. It can be used to sample any kind of graph representation for programs. One of many software engineering applications for finding recurring subgraphs is detecting duplicated code (code clones) from representations such as program dependence graphs (PDGs) and abstract syntax trees. To assess the usefulness of clones detected from PDGs, we conducted a case study on a 73 KLOC commercial Android application developed over 5 years. Nine of the application's developers participated. To our knowledge, it is the first study to have professional developers examine code clones detected from PDGs. We describe a new PDG generation tool jpdg for JVM languages, which was used to generate the dependence graphs used in the study.