gebhart/patrepeval huggingface dataset:
Quantitative Structure Activity Relationship for Inhibition of Human Organic Cation/Carnitine Transporter (2010)

Organic cation/carnitine transporter (OCTN2; SLC22A5) is an important transporter for L-carnitine homeostasis, but can be inhibited by drugs, which may cause L-carnitine deficiency and possibly other OCTN2-mediated drug-drug interactions. One objective was to develop a quantitative structure-activity relationship (QSAR) of OCTN2 inhibitors, in order to predict and identify other potential OCTN2 inhibitors and infer potential clinical interactions. A second objective was to assess two high renal clearance drugs that interact with OCTN2 in vitro (cetirizine and cephaloridine) for possible OCTN2-mediated drug-drug interactions. Using previously generated in vitro data of 22 drugs, a 3D quantitative pharmacophore model and a Bayesian machine learning model were developed. The four pharmacophore features include two hydrophobic groups, one hydrogen-bond acceptor, and one positive ionizable center. The Bayesian machine learning model was developed using simple interpretable descriptors and function class fingerprints of maximum diameter 6 (FCFP_6). An external test set of 27 molecules, including 15 newly identified OCTN2 inhibitors, and a literature test set of 22 molecules were used to validate both models. The computational models afforded good capability to identify structurally diverse OCTN2 inhibitors, providing a valuable tool to predict new inhibitors efficiently. Inhibition results confirmed our previously observed association between rhabdomyolysis and C(max)/K(i) ratio. The two high renal clearance drugs cetirizine and cephaloridine were found not to be OCTN2 substrates, and their diminished elimination by other drugs is concluded not to be mediated by OCTN2.
Microbiological Transformations 57. Facile and Efficient Resin-Based in Situ SFPR Preparative-Scale Synthesis of an Enantiopure “Unexpected” Lactone Regioisomer via a Baeyer−Villiger Oxidation Process (2004)

[reaction: see text] The microbiological Baeyer-Villiger oxidation of (-)-bicyclo[3.2.0]hept-2-en-6-one allowed exclusive formation of the "unexpected" lactone regioisomer in 84% yield, high chemical purity, and enantiopure form. Substrate (25 g) was transformed in a 1 L bubble column reactor, following a in situ substrate feeding/product removal methodology, which afforded high volumetric productivity (1.2 g L(-)(1) h(-)(1)). This illustrates the high "sustainable chemistry" advantages of such a process, simply conducted in aqueous medium, at room temperature and using atmospheric oxygen.
Isolation of Amino Acid — Requiring Lines by Negative Selection in Haploid Protoplasts of N. Plumbaginifolia (1983)

Setting up strategies in the isolation of auxotrophs with plant cell systems requires some understanding of regulatory, biosynthetic and degradative, loops and availability of efficient cell culture systems. It is generally assumed that plants accumulate important nutrient pools(1). We have previously shown that plant cells in culture behave more like animal cells, and that similar enrichment techniques for mutant selection could eventually be extrapolated from one system to the other(2). Amino acid auxotrophs described so far in leaf protoplast cultures(3,4) were isolated with total selection procedures, and resulted in the following spectrum of amino acid defficiency: ileu-, his-, trp-. Enrichment with BUdR has recently been reported with protoplasts of H. muticus(5); one his line was isolated, but the procedure could not be reproduced within the same experimental system.
New Methods and Results in the Study of Polyacids (1966)

Abstract The present status of research on condensed vanadic, molybdic, and tungstic acids is reviewed. Information about the structure and formation of polyanions can be obtained by X‐ray analysis and from nuclear magnetic resonance, infrared, and Raman spectra, as well as from complex formation in aqueous solution. Salts of the polyacids can be prepared in organic solvents by hydrolysis of esters of the metal oxoacids.
Iron Age Shipwrecks in Deep Water off Ashkelon, Israel (2002)

In 1997, two shipwrecks were first discovered in the Mediterranean Sea west of Israel by the U.S. Navy's research Submarine NR-1. Further investigation in 1999 with the remotely operated vehicle system Medea/Jason found the wrecks to be from the eighth century B.C., the earliest known shipwrecks to be found in the deep sea. Both ships appear to be of Phoenician origin, laden with cargoes of fine wine destined for either Egypt or Carthage, when they were lost in a storm on the high seas. The ships lie upright on the seafloor at a depth of 400 m in a depression formed by the scour of bottom currents. Their discovery suggests that ancient mariners took direct routes to their destinations even if it meant traveling beyond sight of land.
Photonic Generation of Frequency-Tunable Microwave Signals Using an Array of Uniformly Spaced Optical Combs (2012)

We show analytically as well as experimentally a photonic technique for generation of frequency-tunable microwave signals. The technique involves propagating an array of uniformly spaced optical combs with identical comb profile into a length of dispersive single-mode fiber (SMF) prior to photodetection. A new scheme that involves a supercontinuum source and a Fourier-domain programmable optical processor as a spectral filter is proposed to generate the required array of optical combs. For an initial optical comb with a fixed repetition rate and a given length of standard SMF, our scheme shows that by choosing appropriate values of the number of optical combs, the number of comb lines in each optical comb, as well as the frequency spacing between the adjacent optical combs, we can generate a microwave signal whose frequency can be tuned to any integer multiple of the optical comb's repetition frequency that lies within the bandwidth of the photodetector. Based on the proposed scheme, using a 2 GHz supercontinuum source as an initial optical comb, we demonstrate the generation of stable microwave signals tunable to 8, 10, and 12 GHz.
A parallel network for the computation of structure from long-range motion (2003)

The authors propose a parallel architecture for computing the 3-D structure of a moving scene from a long image sequence, using a principle known as the incremental rigidity scheme. At each instant an internal model of the 3-D structure is updated, based upon the observations accumulated until that time. The updating process favors rigid transformations but tolerates a limited deviation from rigidity. This deviation eventually leads the internal model to converge towards the actual 3-D structure of the scene. The main advantage of this architecture is its ability to accurately estimate the 3-D structure of the scene at a low computational cost. Testing has been successfully performed on synthetic data as well as real image sequences.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
K<sub>2</sub>S<sub>2</sub>O<sub>8</sub>-mediated coupling of 6-amino-7-aminomethyl-thiazolino-pyridones with aldehydes to construct amyloid affecting pyrimidine-fused thiazolino-2-pyridones (2021)

We herein present the synthesis of diversely functionalized pyrimidine fused thiazolino-2-pyridones <i>via</i> K<sub>2</sub>S<sub>2</sub>O<sub>8</sub>-mediated oxidative coupling of 6-amino-7-(aminomethyl)-thiazolino-2-pyridones with aldehydes. The developed protocol is mild, has wide substrate scope, and does not require transition metal catalyst or base. Some of the synthesized compounds have an ability to inhibit the formation of Amyloid-β fibrils associated with Alzheimer's disease, while others bind to mature amyloid-β and α-synuclein fibrils.
APOE and cognitive decline in preclinical Alzheimer disease and non-demented aging (2004)

Although possession of the APOE epsilon4 allele is a risk factor for AD in old age, it does not modify the progression of the disease during the preclinical period. Further, in the absence of preclinical dementia, APOE did not influence global cognitive change in nondemented persons.
Reference list of 265 sources used for the discovery of relationships between data clusters and metadata properties (2012)

Visual cluster analysis provides valuable tools that help analysts to understand large data sets in terms of representative clusters and relationships thereof. Often, the found clusters are to be understood in context of belonging categorical, numerical or textual metadata which are given for the data elements. While often not part of the clustering process, such metadata play an important role and need to be considered during the interactive cluster exploration process. Traditionally, linked-views allow to relate (or loosely speaking: correlate) clusters with metadata or other properties of the underlying cluster data. Manually inspecting the distribution of metadata for each cluster in a linked-view approach is tedious, specially for large data sets, where a large search problem arises. Fully interactive search for potentially useful or interesting cluster to metadata relationships may constitute a cumbersome and long process. To remedy this problem, we propose a novel approach for guiding users in discovering interesting relationships between clusters and associated metadata. Its goal is to guide the analyst through the potentially huge search space. We focus in our work on metadata of categorical type, which can be summarized for a cluster in form of a histogram. We start from a given visual cluster representation, and compute certain measures of interestingness defined on the distribution of metadata categories for the clusters. These measures are used to automatically score and rank the clusters for potential interestingness regarding the distribution of categorical metadata. Identified interesting relationships are highlighted in the visual cluster representation for easy inspection by the user. We present a system implementing an encompassing, yet extensible, set of interestingness scores for categorical metadata, which can also be extended to numerical metadata. Appropriate visual representations are provided for showing the visual correlations, as well as the calculated ranking scores. Focusing on clusters of time series data, we test our approach on a large real-world data set of time-oriented scientific research data, demonstrating how specific interesting views are automatically identified, supporting the analyst discovering interesting and visually understandable relationships.
"Breaking the code", moving between private and public work in collaborative software development[12] (abstract only) (2003)

Software development is typically cooperative endeavor where a group of engineers need to work together to achieve a common, coordinated result. As a cooperative effort, it is especially difficult because of the many interdependencies amongst the artifacts created during the process. This has lead software engineers to create tools, such as configuration management tools, that isolate developers from the effects of each other's work. In so doing, these tools create a distinction between private and public aspects of work of the developer. Technical support is provided to these aspects as well as for transitions between them. However, we present empirical material collected from a software development team that suggests that the transition from private to public work needs to be more carefully handled. Indeed, the analysis of our material suggests that different formal and informal work practices are adopted by the developers to allow a delicate transition, where software developers are not largely affected by the emergent public work. Finally, we discuss how groupware tools might support this transition.
Dimethylamine as a Carbon Remover in Atomic Layer Epitaxy of AlAs (1995)

We have investigated a novel method of reducing impurity incorporation in atomic layer epitaxy (ALE), by the introduction of impurity-removing gas species. The concept is experimentally tested in ALE–AlAs, in which carbon concentrations in the AlAs layers are reduced by one order of magnitude by supplying dimethylamine in between the supplies of the Al (dimethylaluminum hydride) and As (arsine) sources.
Prevalence of Postoperative Pain Following Hospital Discharge: Protocol for a Systematic Review (2020)

PRR1-10.2196/22437.
Three dimensional mask effects in OPC process model development from first principles simulation (2008)

32 nm half-pitch node processes are rapidly approaching production development, but most tools for this process are currently in early development. This development state means that significant data sets are not yet readily available for OPC development. However, several printing effects are thought to become more prominent at the 32 nm half-pitch node. One of the most significant effects is the three dimensional (3D) mask effect where the mask transmittance and phase are impacted by the mask topography. For the 32nm node it is essential that this effect is correctly captured by the OPC model. As wafer data for the 32nm half-pitch is difficult to obtain, the use of rigorous lithography process simulation has proven to be invaluable in studying this effect. Using rigorous simulation, data for OPC model development has been generated that allows the specific study of 3D mask effect calibration. This study began with Kirchhoff based simulations of 32 nm node features which were calibrated into Hopkin's based OPC process models. Once the standard Kirchhoff effects were working in the OPC model, 3D mask effects were included for the same data by performing fully rigorous electromagnetic field (EMF) simulations on the mask. New EMF compensation methodologies were developed to approximate 3D mask effects in a fast OPC process simulation. These methodologies modify the phase and transmission of features to compensate for 3D mask effects in a fast OPC model. The OPC model was then refit including the 3D mask effect and found to generate as much as 5 nm differences between the fit Kirchhoff data and the fit 3D mask data. In addition, the Hopkin's based OPC model with new EMF compensation methodologies has been able to fit the 3D mask data with an RMSE value of 0.52 nm and a range of 2.76 nm. These data were compared to 32 nm half pitch node data from IMEC. In addition the data process models were used for OPC correction with first principles validation to understand the impact of the 3D mask effect on OPC.
Oak Ridge National Laboratory Annual Progress Report for the Powers Electronics and Electric Motors Program (2014)

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Interactions of Microcarriers in Simulated Microgravity (1999)

Abstract In this study, we developed a numerical model that simulated the simultaneous motion of several microcarriers in the simulated microgravity environment of the NASA HARV bioreactor. Simulations were used to predict the interaction and collision of these multiple particles under different initial seeding densities. In addition, the quasi-steady particle distribution for beads which are lighter than the surrounding fluid is presented. Results show that the frequency of particle collision increases significantly only when the initial seeding density is close to the maximum density. In addition, a stable particle density, with a relatively constant number of particle interactions, is achieved with all seeding densities using beads that are lighter than the surrounding fluid. These results are similar to those measured experimentally for light beads — beads co-locate within a sub-region of the HARV bioreactor, and achieve a consistent final bead density that is independent of the starting seeding density.
Asymmetric synthesis of substituted chromanones via C–H insertion reactions of α-diazoketones catalysed by homochiral rhodium(<scp>II</scp>) carboxylates (1992)

High levels of regio-, stereo- and enantio-selectivity are achieved in the asymmetric synthesis of six-membered oxygen heterocycles via intramolecular C–H insertion reactions of α-diazoketones catalysed by chiral rhodium(II) carboxylates.
Differential growth and residual stress in cylindrical elastic structures (2009)

Cylindrical forms are among one of Nature's fundamental building blocks. They serve many different purposes, from sustaining body weight to carrying flows. Their mechanical properties are generated through the often complex arrangements of the walls. In particular, in many structures that have elastic responses, such as stems and arteries, the walls are in a state of tension generated by differential growth. Here, the effect of differential growth and residual stress on the overall mechanical response of the cylindrical structure is studied within the framework of morpho-elasticity.
Tissue-Specific Regulation of Retinal and Pituitary Precursor Cell Proliferation (2002)

Mammalian organogenesis requires the expansion of pluripotent precursor cells before the subsequent determination of specific cell types, but the tissue-specific molecular mechanisms that regulate the initial expansion of primordial cells remain poorly defined. We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. These data reveal a molecular mechanism by which a tissue-specific transcriptional repressor-corepressor complex can provide an organ-specific strategy for physiological expansion of precursor populations.
Self-association of N-Syndecan (Syndecan-3) Core Protein Is Mediated by a Novel Structural Motif in the Transmembrane Domain and Ectodomain Flanking Region (1995)

We expressed domains of the core protein of the transmembrane heparan sulfate proteoglycan N-syndecan (syndecan-3) either individually or as maltose-binding protein fusion proteins. Biochemical characterization of the purified proteins revealed that some of them were capable of self-association and formed stable, noncovalent multimeric complexes. The formation of N-syndecan core protein complexes was also demonstrated in mammalian cells by in situ cross-linking. Identification of structural motifs in the core protein of N-syndecan responsible for the formation of these complexes was accomplished by analyzing a series of constructs comprising different regions of the protein as well as site-directed mutants. Self-association was assayed by SDS-polyacrylamide gel electrophoresis, glutaraldehyde cross-linking, and size-exclusion high pressure liquid chromatography. Our results indicated that (i) the transmembrane domain of the N-syndecan core protein was required but not sufficient for the formation of stable complexes; (ii) the minimal amino acid sequence that conferred the ability of the N-syndecan core protein to form multimeric complexes included the last four amino acids (ERKE) of the extracellular domain plus the transmembrane domain; (iii) point mutations that changed the basic residues in this sequence to alanine residues either partially or completely abolished the ability of the N-syndecan core protein to form complexes; and (iv) replacement of conserved glycine residues in the transmembrane domain with leucines abolished complex formation. This property is similar to the oligomerization activity of other transmembrane receptors and suggests that regulated self-association may be important for the biological activity of transmembrane proteoglycans.
Performance evaluation of IAS on the PDP-11/70 (1976)

Digital Equipment Corporation has recently developed a new PDP-11 operating system called IAS—Interactive Application System. Since the system was to be significantly different from existing PDP-11 systems, customers and DEC field personnel had little information about the kinds of load it would handle or what level of performance could be expected. The work reported in this paper had the objective of producing such information prior to the release of the product. The major goal was to produce a set of guidelines indicating the kinds of loads that could be handled within limits of acceptable performance by various IAS configurations. The guidelines had to be in terms understandable to salesmen and customers. At the same time they had to be based on technically sound performance measurements that could be precisely explained and repeated.
Scalable leader election (2006)

In the leader election problem, there are n processors of which (1 - b)n are good. The problem is to design a distributed protocol to elect a good leader from the set of all processors. In this paper, we present a scalable leader election protocol. Our protocol is scalable in the sense that each good processor sends and processes a number of bits which is only polylogarithmic in n. (We assume no limit on the number of messages sent by bad processors.) For b < 1/3, our protocol elects a good leader with constant probability and ensures that a 1 - o(1) fraction of the good processors know this leader.We assume a point-to-point full information model. This is similar to the full information model, but harder in the sense that in a given round, a bad processor may send different messages to different processors, rather than having to broadcast the same message to every processor.To the best of our knowledge, we present the first leader election protocol that ensures that each good processor sends and processes a sublinear number of bits. Having reduced the problem of leader election to one of informing all good processors of a bit held by 1 − o(1) fraction of good processors, we conjecture that the solution to this problem is not possible within polylogarithmic message bounds.Our techniques can be used to provide scalable solutions to Byzantine agreement and other problems.
Resource management system for a broadband multipoint bridge (2002)

The use of a bridge (also known as a multipoint central unit) to enable multipoint communications over point to point narrowband-ISDN connections is well established. We deal with multipoint bridging for a broadband network environment. We explain the benefits of employing a bridge in that context and highlight the new design problems and challenges. Of particular importance is the need for a bridge resource management system which can be used in conjunction with end to end contracts for quality of service. We describe a model for managing bridge resources based on the estimated requirements of audio and video processing functions. Aspects of the initial system design are presented.
STUDIES OF V<sub>K</sub> CENTERS IN CsI BY OPTICAL AND EPR TECHNIQUES (1973)

VK centers have been observed in CsI doped with Na+ and Tl+ after X ray irradiation at LHeT using optical and EPR techniques. Their main optical transition is located at 410 nm and they are oriented in [100] directions. Two types of thermal migration have been found : a linear displacement along the cubic axis (0° jumps) and a migration with 90° jumps. They are related to two glow peaks at 60 K and 90 K respectively and which correspond to the radiative recombination of mobile VK centers at the site of the electron traps (Na0 λ = 420 nm, Tl0 λ = 560 nm). Similar experiments have been done in CsI additively colored. The radiative recombination VK-F gives rise to a new luminescence at 495 nm.