gebhart/patrepeval huggingface dataset:
Plasma and Hepatic Concentrations of Chemicals after Virtual Oral Administrations Extrapolated Using Rat Plasma Data and Simple Physiologically Based Pharmacokinetic Models (2018)

Only a small fraction of chemicals possesses adequate in vivo toxicokinetic data for assessing potential hazards. The aim of the present study was to model the plasma and hepatic pharmacokinetics of more than 50 disparate types of chemicals and drugs after virtual oral administrations in rats. The models were based on reported pharmacokinetics determined after oral administration to rats. An inverse relationship was observed between no-observed-effect levels after oral administration and chemical absorbance rates evaluated for cell permeability ( r = -0.98, p < 0.001, n = 17). For a varied selection of more than 30 chemicals, the plasma concentration curves and the maximum concentrations obtained using a simple one-compartment model (recently recommended as a high-throughput toxicokinetic model) and a simple physiologically based pharmacokinetic (PBPK) model (consisting of chemical receptor, metabolizing, and central compartments) were highly consistent. The hepatic and plasma concentrations and the hepatic and plasma areas under the concentration-time curves of more than 50 chemicals were roughly correlated; however, differences were evident between the PBPK-modeled values in livers and empirically obtained values in plasma. Of the compounds selected for analysis, only seven had the lowest observed effect level (LOEL) values for hepatoxicity listed in the Hazard Evaluation Support System Integrated Platform in Japan. For these seven compounds, the LOEL values and the areas under the hepatic concentration-time curves estimated using PBPK modeling were inversely correlated ( r = -0.78, p < 0.05, n = 7). This study provides important information to help simulate the high hepatic levels of potent hepatotoxic compounds. Using suitable PBPK parameters, the present models could estimate the plasma/hepatic concentrations of chemicals and drugs after oral doses using both PBPK forward and reverse dosimetry, thereby indicating the potential value of this modeling approach in predicting hepatic toxicity as a part of risk assessments of chemicals absorbed in the human body.
Stereotactic body radiotherapy for benign spinal tumors: Meningiomas, schwannomas, and neurofibromas. (2019)

Stereotactic body radiation therapy (SBRT) is a relatively new technology, and its use among patients with benign spinal tumors has limited prospective data. Similar to intracranial benign tumors treated successfully with SBRT, benign spinal tumors of the same histology can also develop, and SBRT may be an effective treatment alternative in inoperable or recurrent cases. Outcomes in patients with neurofibromatosis type 1, neurofibromatosis type 2, or schwannomatosis treated with SBRT have also been reported. Single institution reports have shown local control rates over 90% and improvement in clinical symptoms. The optimum dose and fractionation to maximize local control and minimize toxicity is unknown, with few incidences of radiation treatment-related toxicities. Given the location and benign nature of these tumors, careful management of dose to critical organs is essential. With continued follow-up, the optimum use of SBRT in patients with benign spinal tumors can be better defined.
Does vitamin C act as a pro‐oxidant under physiological conditions? (1999)

Vitamin C readily scavenges reactive oxygen and nitrogen species and may thereby prevent oxidative damage to important biological macromolecules such as DNA, lipids, and proteins. Vitamin C also reduces redox active transition metal ions in the active sites of specific biosynthetic enzymes. The interaction of vitamin C with 'free', catalytically active metal ions could contribute to oxidative damage through the production of hydroxyl and alkoxyl radicals; whether these mechanisms occur in vivo, however, is uncertain. To examine this issue, we reviewed studies that investigated the role of vitamin C, both in the presence and absence of metal ions, in oxidative DNA, lipid, and protein damage. We found compelling evidence for antioxidant protection of lipids by vitamin C in biological fluids, animals, and humans, both with and without iron cosupplementation. Although the data on protein oxidation in humans are sparse and inconclusive, the available data in animals consistently show an antioxidant role of vitamin C. The data on vitamin C and DNA oxidation in vivo are inconsistent and conflicting, but some of the discrepancies can be explained by flaws in experimental design and methodology. These and other important issues discussed here need to be addressed in future studies of the role of vitamin C in oxidative damage.
N-Nitrosation of secondary amines effected by electrochemical oxidation of nitrite ion in weakly basic media. (1988)

Constant current electrolysis of sodium nitrite in aqueous acetonitrile containing secondary amines at ambient temperature resulted in the formation of the corresponding N-nitrosamines in good yields.
The Hantzsch thiazole synthesis under acidic conditions: change of regioselectivity (1987)

The condensation of α-halogeno ketones with N-monosubstituted thioureas in neutral solvent leads exclusively to 2-(N-substituted amino)thiazoles. In the present work it was shown that under acidic conditions mixtures of 2-(N-substituted amino)thiazoles and 3-substituted 2-imino-2,3-dihydrothiazoles are formed. (The isomers were distinguished by characteristic differences between their 5-H 1H n.m.r. signals and the i.r. CO bands of their trifluoroacetate derivatives.) The proportions of the 2-imino-2,3-dihydrothiazoles in the mixtures are influenced by experimental features and by the structures of the starting materials. Reactions in 10M-HCl-EtOH (1 :2) at 80 °C for 20 min were found to be the most efficient for generating 2-imino-2,3-dihydrothiazoles; in the most favourable case 2-imino-3,4-dimethyl-2,3-dihydrothiazole was obtained in 73% yield.A possible explanation of the results is discussed.
Login to UA HPC v2 (2019)

This describes setting up ssh keys and configuration to avoid having to useyour NetID+ 2-factor authentication every time you log into the HPC. Windows users will needto install a free Unix-like environment that provides a terminal so as to avoid using an ssh client like Putty (for example: Cygwin (http://www.cygwin.com)). Cygwin users must be sure to install the 'ssh' tools which are not installed by default.
Van der Waals Density Functional for General Geometries (2004)

A scheme within density functional theory is proposed that provides a practical way to generalize to unrestricted geometries the method applied with some success to layered geometries [Phys. Rev. Lett. 91, 126402 (2003)]]. It includes van der Waals forces in a seamless fashion. By expansion to second order in a carefully chosen quantity contained in the long-range part of the correlation functional, the nonlocal correlations are expressed in terms of a density-density interaction formula. It contains a relatively simple parametrized kernel, with parameters determined by the local density and its gradient. The proposed functional is applied to rare gas and benzene dimers, where it is shown to give a realistic description.
The chemical parameters and oxidative resistance to heat treatment of refined and extra virgin Moroccan Picholine olive oil (2015)

This paper presents the influence of heating on the content of saturated and unsaturated fatty acids and tocopherols of extra virgin and refined olive oil as well as some parameters describing the oxidative states of these oils. The results show that heat treatment causes a decrease in the nutritional quality of the two types of olive oil. The content of unsaturated fatty acids decreased significantly (p < 0.05) from 87.4% to 84.5% for refined olive oil, while no change was found for extra virgin olive oil. The content of saturated fatty acid did not change substantially for either type of oil. The heat treatment also caused a decrease in the tocopherol content that was more evident for the refined olive oil. This heat treatment results in an increase in free fatty acids that was more pronounced for refined olive oil. A similar result was found for the peroxide value.
Stability of Whey Proteins during Thermal Processing: A Review (2014)

Abstract Whey proteins have many benefits due to their high nutritional value and their various applications in food products. A drawback of whey proteins is their instability to thermal processing, which leads to their denaturation, aggregation, and, under some conditions, gelation. As thermal processing is a major treatment in the processing of milk and milk products, its influence on whey proteins has been extensively studied. Understanding the mechanisms involved during each stage of denaturation and aggregation of whey proteins is critical to devising ways of improving their stability. These aspects are reviewed in this paper. Also covered are approaches to preventing or reducing heat‐induced aggregation of whey proteins. Inhibition of aggregate formation has considerable potential for alleviating the problems that arise from the instability of whey proteins.
New Strategies for the Synthesis of Pyrimidine Derivatives (2008)

Recent advances in pyrimidine synthesis are described. Modification of conventional strategies involving N-C-N fragment condensation with 1,3-dicarbonyl derivatives remains a common theme in current literature. Other methods, including N-C fragment condensation strategies, provide reactive intermediates capable of intramolecular cyclization and formation of pyrimidine derivatives. These recently developed methodologies offer a valuable addendum to azaheterocycle synthesis.
What Is a Knowledge Representation (1993)

Although knowledge representation is one of the central and, in some ways, most familiar concepts in AI, the most fundamental question about it -- What is it? -- has rarely been answered directly. Numerous papers have lobbied for one or another variety of representation, other papers have argued for various properties a representation should have, and still others have focused on properties that are important to the notion of representation in general. In this article, we go back to basics to address the question directly. We believe that the answer can best be understood in terms of five important and distinctly different roles that a representation plays, each of which places different and, at times, conflicting demands on the properties a representation should have. We argue that keeping in mind all five of these roles provides a usefully broad perspective that sheds light on some longstanding disputes and can invigorate both research and practice in the field.
Seeded Supercontinuum Generation - Modulation Instability Gain, Coherent and Incoherent Rogue Waves (2012)

Deterministic supercontinuum can be generated by seeding the modulation instability-induced pulse break-up. We investigate the influence of the modulation instability gain on seeding and demonstrate the generation of coherent and incoherent rogue waves.
Adapting Learning by Demonstration for Robot Based Part Feeding Applications (2020)

Feeding parts in automated manufacturing processes lack the adaptation flexibility to rapid production changes, which are typical for small to medium enterprises. In this paper we present a novel application approach for feeding parts, which can be incorporated in small and medium production facilities. The approach relies on a scoop like tool that is attached to a collaborative robot. With the adoption of learning by demonstration methods, part feeding skills can be set-up fast and easy directly on the factory floor by a non-expert user. The approach exploits dynamic movement primitives as an underlying method for representation of trajectories. In the execution phase, we use admittance control with switching force control parameters, defined during the demonstration, for reliable execution of the part feeding skill in contact with the environment. The proposed approach is tested on on several part feeding cases with a Universal Robot UR10e.
Self-diffusion of Si in thermally grown SiO2 under equilibrium conditions (2003)

Self-diffusion coefficients of Si in thermally grown SiO2 on a semiconductor-grade silicon wafer have been determined at temperatures between 1150 and 1300 °C under equilibrium conditions using isotope heterostructures (natSiO2/28SiO2). Si self-diffusion was induced by appropriate heat treatments, and the diffusion depth profiles of Si30 isotope from SiO2nat to SiO228 layers were determined by secondary ion mass spectrometry (SIMS). The diffusion coefficients found in the present study for 1150–1300 °C are more than two orders of magnitude smaller than the values measured with semiconductor-grade SiO2 in the presence of excess silicon, i.e., in nonequilibrium conditions, and agree very well with previously reported values of Si self-diffusion in fused silica under equilibrium conditions.
BaCe 0.7 Zr 0.1 Y 0.2-x Nd x O 3- Proton Conducting Electrolyte for Intermediate Temperature Solid Oxides Fuel Cells (2010)

The sinterability, conductivity and chemical stability in CO2 atmosphere are compared for a series of doped barium cerate perovskite oxides BaCe0.7Zr0.1Y0.2-xNdxO3- (0 ≤ x ≤ 0.2) which synthesized using a solid state reaction method. Among the series of electrolytes doped with various amounts of Nd and Y, BaCe0.7Zr0.1Y0.15Nd0.05O3- has the optimal combination of sinterability and conductivity, and shows high CO2 resistance. A solid oxide fuel cell using the BaCe0.7Zr0.1Y0.15Nd0.05O3- proton conducting electrolyte at 650-700 o C efficiently co-produces electrical power and value-added ethylene from ethane.
Asynchronous algorithms for approximate distributed constraint optimization with quality bounds (2010)

Distributed Constraint Optimization (DCOP) is a popular framework for cooperative multi-agent decision making. DCOP is NP-hard, so an important line of work focuses on developing fast incomplete solution algorithms for large-scale applications. One of the few incomplete algorithms to provide bounds on solution quality is k-size optimality, which defines a local optimality criterion based on the size of the group of deviating agents. Unfortunately, the lack of a general-purpose algorithm and the commitment to forming groups based solely on group size has limited the use of k-size optimality.This paper introduces t-distance optimality which departs from k-size optimality by using graph distance as an alternative criteria for selecting groups of deviating agents. This throws open a new research direction into the tradeoffs between different group selection and coordination mechanisms for incomplete DCOP algorithms. We derive theoretical quality bounds for t-distance optimality that improve known bounds for k-size optimality. In addition, we develop a new efficient asynchronous local search algorithm for finding both k-size and t-distance optimal solutions --- allowing these concepts to be deployed in real applications. Indeed, empirical results show that this algorithm significantly outperforms the only existing algorithm for finding general k-size optimal solutions, which is also synchronous. Finally, we compare the algorithmic performance of k-size and t-distance optimality using this algorithm. We find that t-distance consistently converges to higher-quality solutions in the long run, but results are mixed on convergence speed; we identify cases where k-size and t-distance converge faster.
Scaling relations for crack-tip plasticity (2002)

The fracture toughness of semibrittle materials such as bcc transition metals or semiconductor crystals strongly depends on loading rate and temperature. If crack-tip pasticity is considered to be thermally activated, a strong correlation between these quantities is expected. An Arrthenius-like scaling relation between the loading rate and the brittle-to-ductile transition temperature has already been reported. In the present work, two-dimensional discrete dislocation dynamics simulations of crack-tip plasticity are employed to show that the different combinations of loading rates and termperatures which yield the same fracture toughness are indeed correlated by a scaling relation. This scaling relation is closely related to the law used to describe dislocation motion. A strong correlation between loading rate and temperature is found in the entiere temperature regime in which crack-tip plasticity is controlled by dislocation mobility. This shows the importance of dislocation mobility for fracture thoughness below the brittle-to-ductile transition and for the transition itself. The findings of our simulations are consistent with experimental data gathered on tungsten single crystals and suggest that non-screw dislocations are dominating crack-tip plasticity in the semibrittle regime of this material.
The conjugate gradient method in the presence of clustered eigenvalues (1993)

We present the conjugate gradient method, CG method, to solve large dense linear systems whose associated matrix has clustered eigenvalues, and we give the implementation of the algorithm using MATLAB, an interactive programming language for scientific computing.
Application of 0.1 M quadrol to the microsequence of proteins and the sequence of tryptic peptides (1975)

In an effort to extend automated Edman degradation to nanomole quantities of protein, the method of sequenator analysis described by Edman and Begg (Edman, P., and Begg, G. (1967), Eur. J. Biochem. 1, 80) was modified to permit long degradations in the absence of carrier proteins. By using an aqueous 0.1 M Quadrol program with limited, combined benezene-ethyl acetate solvent extractions, as well as a change in the delivery system for heptafluorobutyric acid, it was possible to recover and identify the first 30 amino acid residues from a sequenator run on 7 nmol of myoglobin. For 3 nmol of myoglobin, 20 steps could be identified. PTH-amino acids were identified by gas-liquid chromatography and thin-layer chromatography on polyamide sheets. Without using a carrier protein the cup to prevent mechanical losses (Niall, H. D., Jacobs, J. W., Van Rietshoten, J., and Tregear, G. W. (1974), FEBS Lett. 41, 62), the repetitive yield using this program was 93-96%. The same program has been applied successfully to peptides of 14 or more residues with or without modification by Braunitzer's reagent and to a number of larger peptides and proteins including a 216 residue segment of rabbit antibody heavy chain in which a sequence of 35 steps was accomplished on 25 nmol.
The CMU Submission for the Shared Task on Language Identification in Code-Switched Data (2014)

We describe the CMU submission for the 2014 shared task on language identification in code-switched data. We participated in all four language pairs: Spanish‐English, Mandarin‐English, Nepali‐English, and Modern Standard Arabic‐Arabic dialects. After describing our CRF-based baseline system, we discuss three extensions for learning from unlabeled data: semi-supervised learning, word embeddings, and word lists.
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0 (2021)

Abstract Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into GEMs was first enabled by the GECKO method, allowing the study of phenotypes constrained by protein limitations. Here, we upgraded the GECKO toolbox in order to enhance models with enzyme and proteomics constraints for any organism with an available GEM reconstruction. With this, enzyme-constrained models (ecModels) for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus were generated, aiming to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions revealed that upregulation and high saturation of enzymes in amino acid metabolism were found to be common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO was further developed by the implementation of an automated framework for continuous and version-controlled update of ecModels, which was validated by producing additional high-quality ecModels for Escherichia coli and Homo sapiens. These efforts aim to facilitate the utilization of ecModels in basic science, metabolic engineering and synthetic biology purposes.
The neurula stage mouse embryo in control of neuroblastoma. (1984)

The purpose of this study was to determine whether the neurula stage mouse embryo can regulate tumor formation of C-1300-3 neuroblastoma cells. Five neuroblastoma cells were injected into the second somite of neurula stage embryos, and their ability to form tumors was tested, 24 hr later, by transplanting the portion of the embryo containing the cancer cells into the testes of adult mice. Only one-third the number of tumors was obtained in comparison with controls in which (i) five neuroblastoma cells were injected into blocks of liver tissue that were then transplanted into the testes of adult animals or (ii) five C-1300-3 neuroblastoma cells were injected directly into the testes. When five C-1300-3 cells were injected into somites, which had been dissected from embryos, and the injected somites were placed in animals, significantly fewer tumors were obtained in relationship with controls. Although it is not known whether the neuroblastoma cells are induced to differentiate or are killed by the embryonic tissue, the effect appeared to be specific because the tumor-forming ability of L1210 leukemia, B-16 melanoma, embryonal carcinoma 247, and a parietal yolk sac carcinoma was unaffected by somites.
Identification of evolutionary trajectories shared across human betacoronaviruses (2021)

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, whilst the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), whilst a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1 and SARS-CoV-2), we developed a methodological pipeline to classify shared non-synonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection, and draw upon protein structure data to identify potential biological implications. We find 30 mutations, with four of these [codon sites 18121 (nsp14/residue 28), 21623 (spike/21), 21635 (spike/25) and 23948 (spike/796); SARS-CoV-2 genome numbering] displaying evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity.