gebhart/patrepeval huggingface dataset:
Simultaneous Perception of Forces and Motions Using Bimanual Interactions (2012)

When teaching physical skills, experts or robotic assistants commonly move a novice through a task. However, this guiding motion is only partially effective at portraying the full experience because the guided person is only performing the task passively and the guidance and task forces can become ambiguously intertwined. The interaction evaluated in this paper separates the task and guidance forces by guiding one hand so the user can actively recreate the motion with their other hand that receives task-related forces. This method is based on the ability of humans to easily move their hands through similar paths, such as drawing circles, compared to the difficulty of simultaneously drawing a square with one hand and a circle with the other. Several experiments were first performed to characterize the reference frames, interaction stiffnesses, and trajectories that humans can recreate. Visual Symmetry and Joint-Space Symmetry proved to be easier than Point Mirror Symmetry and participants' recreated motions typically lagged by approximately 50-100 ms. Based on these results, participants used bimanual guidance to identify the orientation of a hard rod embedded in a soft material. The results show that participants could identify the orientation of the rod equally well when working independently compared to being bimanually guided through a desired motion.
Postmortem Forensic Toxicology of Selective Serotonin Reuptake Inhibitors: A Review of Pharmacology and Report of 168 Cases (2000)

This paper reviews the complex pharmacology of the new class of antidepressant medications exhibiting selective inhibition of serotonin reuptake. The four selective serotonin reuptake inhibitors (SSRIs) considered--fluoxetine, fluvoxamine, sertraline and paroxetine--can result in toxicity and death through contributing to serotonergic excess resulting in serotonin syndrome, inhibiting the metabolism of other centrally acting drugs, leading to accumulation of toxic concentrations, and exerting complex vasoactive effects on the vascular smooth muscle. This latter feature is of particular concern in patients with preexisting heart disease. An analytical method involving isolation of the drugs by liquid/liquid extraction at alkaline pH into n-butyl chloride, and analysis by gas chromatography/mass spectrometry (GC/MS) is described, together with some of its limitations. Toxicologic and cause and manner of death data were examined in 60 deaths involving fluoxetine, 5 involving fluvoxamine, 75 involving sertraline, and 28 involving paroxetine. Deaths involving drug toxicity were generally a result of ingestion of multiple drugs, and in only a small number of the cases was death attributed principally to the SSRI involved. The potential for drug interactions between members of this class of drugs is discussed as well as their metabolites and a variety of other therapeutic and abused drugs which can contribute to their toxicity. In the absence of other risk factors, the lowest concentrations determined to have resulted in death were 0.63 mg/L for fluoxetine, 0.4 mg/L for paroxetine, and 1.5 mg/L for sertraline. We had insufficient data to make even this crude assessment for fluvoxamine. Drug-induced elevation of serotonin concentrations may be a significant risk factor for patients with atherosclerotic cardiovascular disease (ASCVD). Other factors including preexisting disease and the presence of other drugs and their pharmacology need to be carefully considered before determining the appropriate cause and manner of death in these cases.
Collaborative Systems and Multi-user Interfaces (1986)

A collaborative system is a real-time computer-based environment of cooperative work. Computer systems have been available for some time to assist individuals with their work, but the use of computers by groups is underdeveloped. The thesis of this dissertation is that a collaborative system can be built in a principled way using network-connected workstations and that such a system can enhance group work. Previous systems to support group work have generally either avoided computers, as in teleconferencing, or have relied on long-haul networks to support asynchronous message-passing, as in computer conferencing. This dissertation focuses on real-time software tools to support groups working together in the same room. The Colab system and its tools explore the following properties of computer-based cooperation: the structure of the problem-solving process, the design of multi-user interfaces, social coordination, simultaneous activity, maintenance of consistent views of shared objects, and uses for digitally captured meetings. To better understand and evaluate computer-based collaborative tools and their uses, the Colab system and the Cognoter presentation tool were implemented and used for both real and posed idea organization tasks. To test the system design and its effect on structured problem-solving, many early Colab/Cognoter meetings were monitored and a series of preliminary experiments were performed. These early observations indicated that people can and do work more efficiently and in parallel if they are given tools that help them stay focused and that help manage the added complexity of multi-user interactions.
Gold microspheres: a selective technique for producing biologically effective dose enhancement (2000)

An increased biologically effective dose can be produced by gold microspheres suspended in cell culture or distributed in tumour tissue exposed to kilovoltage photon beams. With the increasing use of interstitial brachytherapy with isotopes that produce low-energy photons, high-Z particles might find a role for significantly improving the therapeutic ratio.
Functionalization of Surfaces by Water-Accelerated Atom-Transfer Radical Polymerization of Hydroxyethyl Methacrylate and Subsequent Derivatization (2002)

We report the synthesis of unusually thick poly(2-hydroxyethyl methacrylate) (PHEMA) films on gold surfaces by surface-initiated atom transfer radical polymerization (ATRP). Polymerization from the surface occurs rapidly at room temperature in aqueous media, resulting in the formation of 700 nm thick polymer films in just 12 h. Control experiments using neat monomer and catalyst (no water) yield films with thicknesses of only 6 nm, demonstrating the accelerating effect of water on surface-initiated ATRP. Kinetic studies reveal a nearly linear increase in thickness with reaction time, indicating that chain growth from the surface is a controlled process with some “living” character. A second block can be grown from dormant initiators at the end of PHEMA chains, providing further evidence of “living” chain ends. Derivatization of the hydroxyl groups of grafted PHEMA with a variety of molecules allows dense functionalization of these films. Reflectance FTIR spectroscopy shows a virtually quantitative yield in derivatization reactions, and the increase in film thickness after surface derivatization correlates with the molecular mass of the newly formed repeat unit.
Sinogram Interpolation Method for Sparse-Angle Tomography (2014)

In sparse-angle X-ray tomography reconstruction, where only a small number of projection images are taken around the object, appropriate sinogram interpolation has a significant impact on image quality. A novel sinogram interpolation method is introduced for extreme sparse tomographic reconstruction where only nine measured projection images are available. The sinogram is interpolated by solving characteristics of the so-called warps, which can be considered as approximation sine waves in a limited region. The numerical evidence suggests that this approach gives superior results over standard interpolation methods when the tomographic data are extremely sparse and noisy.
Palmitoylation at Cys 574 is essential for MT1‐MMP to promote cell migration (2005)

MT1-MMP is a type I transmembrane proteinase that promotes cell migration and invasion. Here, we report that MT1-MMP is palmitoylated at Cys574 in the cytoplasmic domain, and this lipid modification is critical for its promotion of cell migration and clathrin-mediated internalization. The palmitoylation-defective mutant (C574A) failed to promote cell migration and was not internalized through clathrin pathway like wild-type, but it was internalized through the caveolae pathway. Reintroducing a cysteine at different positions in the cytoplasmic tail of the C574A mutant revealed that the position of the palmitoylated cysteine relative to LLY573, a motif that interacts with mu2 subunit of adaptor protein 2, is critical for the cell motility-promoting activity of MT1-MMP and its clathrin-mediated internalization. Taken together, palmitoylation of MT1-MMP is one of the key posttranslational modifications that determines MT1-MMP-dependent cell migration.
Paper and Flexible Substrates as Materials for Biosensing Platforms to Detect Multiple Biotargets (2015)

The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant interest in clinical applications for disease diagnosis and treatment monitoring at the point-of-care (POC) settings. Rapid, accurate POC diagnostic assays play a crucial role in developing countries, where there are limited laboratory infrastructure, trained personnel, and financial support. However, current diagnostic assays commonly require long assay time, sophisticated infrastructure and expensive reagents that are not compatible with resource-constrained settings. Although paper and flexible material-based platform technologies provide alternative approaches to develop POC diagnostic assays for broad applications in medicine, they have technical challenges integrating to different detection modalities. Here, we address the limited capability of current paper and flexible material-based platforms by integrating cellulose paper and flexible polyester films as diagnostic biosensing materials with various detection modalities through the development and validation of new widely applicable electrical and optical sensing mechanisms using antibodies and peptides. By incorporating these different detection modalities, we present selective and accurate capture and detection of multiple biotargets including viruses (Human Immunodeficiency Virus-1), bacteria (Escherichia coli and Staphylococcus aureus), and cells (CD4(+) T lymphocytes) from fingerprick volume equivalent of multiple biological specimens such as whole blood, plasma, and peritoneal dialysis effluent with clinically relevant detection and sensitivity.
Towards a learning optimizer for shared clouds (2018)

Query optimizers are notorious for inaccurate cost estimates, leading to poor performance. The root of the problem lies in inaccurate cardinality estimates, i.e., the size of intermediate (and final) results in a query plan. These estimates also determine the resources consumed in modern shared cloud infrastructures. In this paper, we present C ARD L EARNER , a machine learning based approach to learn cardinality models from previous job executions and use them to predict the cardinalities in future jobs. The key intuition in our approach is that shared cloud workloads are often recurring and overlapping in nature, and so we could learn cardinality models for overlapping subgraph templates. We discuss various learning approaches and show how learning a large number of smaller models results in high accuracy and explainability. We further present an exploration technique to avoid learning bias by considering alternate join orders and learning cardinality models over them. We describe the feedback loop to apply the learned models back to future job executions. Finally, we show a detailed evaluation of our models (up to 5 orders of magnitude less error), query plans (60% applicability), performance (up to 100% faster, 3x fewer resources), and exploration (optimal in few 10s of executions).
ISOMERS OF 3,7,11‐TRIMETHYLDODECA‐2,4,6,8,10‐ PENTAENAL (A LINEAR ANALOGUE OF RETINAL) and LOWER HOMOLOGUES IN THEIR INTERACTION WITH BOVINE OPSIN and BACTERIOOPSIN (1985)

Abstract— The all‐trans and 3 mono‐cir isomers of the title linear pentaenal have been prepared. Results of their interaction with bovine opsin and bacterioopsin are presented. Likewise, the negative results on two lower member homologs are described. Implications on the specificity of the binding sites are discussed.
Analysis of the aphthovirus 2A/2B polyprotein ‘cleavage’ mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal ‘skip’ (2001)

The 2A region of the aphthovirus foot-and-mouth disease virus (FMDV) polyprotein is only 18 aa long. A 'primary' intramolecular polyprotein processing event mediated by 2A occurs at its own C terminus. FMDV 2A activity was studied in artificial polyproteins in which sequences encoding reporter proteins flanked the 2A sequence such that a single, long, open reading frame was created. The self-processing properties of these artificial polyproteins were investigated and the co-translational 'cleavage' products quantified. The processing products from our artificial polyprotein systems showed a molar excess of 'cleavage' product N-terminal of 2A over the product C-terminal of 2A. A series of experiments was performed to characterize our in vitro translation systems. These experiments eliminated the translational or transcriptional properties of the in vitro systems as an explanation for this imbalance. In addition, the processing products derived from a control construct encoding the P1P2 region of the human rhinovirus polyprotein, known to be proteolytically processed, were quantified and found to be equimolar. Translation of a construct encoding green fluorescent protein (GFP), FMDV 2A and beta-glucuronidase, also in a single open reading frame, in the presence of puromycin, showed this antibiotic to be preferentially incorporated into the [GFP2A] translation product. We conclude that the discrete translation products from our artificial polyproteins are not produced by proteolysis. We propose that the FMDV 2A sequence, rather than representing a proteolytic element, modifies the activity of the ribosome to promote hydrolysis of the peptidyl(2A)-tRNA(Gly) ester linkage, thereby releasing the polypeptide from the translational complex, in a manner that allows the synthesis of a discrete downstream translation product to proceed. This process produces a ribosomal 'skip' from one codon to the next without the formation of a peptide bond.
Temperature dependence of type I-IA dual-fibre Bragg gratings (2004)

Fibre Bragg gratings (FBGs) of a new IA type have been reported to show thermal behaviour that is different from that of conventional type I gratings. Given a sufficiently large temperature coefficient difference between the two grating types, a dual-grating sensor formed by both types of gratings could allow simultaneous temperature and strain measurement. Such dual-grating sensors were prepared for the 830 nm wavelength region and tested at temperatures of up to 300°C. As far as the variation of the different temperature coefficients is concerned, the temperature coefficient of type IA FBGs and the temperature coefficient of type I FBGs have been found to converge as the temperature increases. The difference in temperature coefficients drops to 1% after annealing at 300°C.
Flow cytometric detection of apoptosis: Comparison of the assays of in situ DNA degradation and chromatin changes (1994)

The aim of this study was to compare three methods of detection of apoptotic cells: (1) the method based on elution of low molecular weight DNA from the ethanol fixed cells followed by cell staining with DAPI (diamidino-2-phenylindole) or propidium iodide as the DNA fluorochromes, (2) the method of in situ labeling of DNA strand breaks with biotinylated dUTP, utilizing exogenous terminal deoxyribonucleotide transferase, and (3) the method of analysis of DNA denaturation in situ using acridine orange to differentially stain denatured and double-stranded DNA sections following cell exposure to 0.1 M HCl. Cells of the human promyelocytic HL-60 line, treated in vitro with the DNA topoisomerase I inhibitor camptothecin, which selectively triggers apoptosis of S-phase cells, were chosen as a model. The method based on analysis of changes in DNA denaturability was the most sensitive in terms of detection of the earliest changes in chromatin of cells undergoing apoptosis; the increased sensitivity of DNA to denaturation in S-phase cells was measured as early as 100 min after addition of camptothecin. DNA cleavage, assayed either by the univariate measurement of DNA content following extraction of low molecular weight DNA, or by labeling DNA strand breaks with biotinylated dUTP, was detected in S-phase cells after 120 min incubation with camptothecin. The percentage of apoptotic cells at the late stage of apoptosis, the kinetics of cell transition to apoptosis, and kinetics of the loss of S phase cells were all essentially similar when measured by any method.(ABSTRACT TRUNCATED AT 250 WORDS)
Cytokines, adhesion molecules (E-selectin and VCAM-1) and graft-versus-host disease. (1995)

Analysis of skin biopsy specimens for the presence of adhesion molecules, composition of cellular infiltrates, Ki-67 antigen expression, and examination of serum for interleukin 6 (IL-6) and tumor necrosis factor alpha (TNF-alpha) levels, wes performed in patients after allogeneic bone marrow transplantation (alloBMT), to study the pathomechanism of acute graft-versus-host disease (aGvHD). It was found that: 1) early hematological recovery constitutes a risk factor for grade IV GvHD, 2) vascular cell adhesion molecule-1 (VCAM-1) is present in the matrix organizing the cells in the bone marrow and in aGvHD infiltrates, 3) HLA DR antigens aberrant expression in epithelial cells, as well as 4) strong expression of Ki-67 is seen in early stages of aGvHD. These immunopathomorfological lesions are cytokine-dependent. High levels of IL-6 and TNF-alpha were found in sera of patients affected with the aGvHD process and infectious complications. An increase of IL-6 in the course of aGvHD is a sign of poor prognosis. These data support the notion that cytokines facilitate the cell accumulation at the site of aGvHD at the beginning of this process and again, at the final stage of the disease, cytokines high levels are associated with the organ damage.
AN OVERVIEW OF THE OMNeT++ SIMULATION ENVIRONMENT (2008)

The OMNeT++ discrete event simulation environment has been publicly available since 1997. It has been created with the simulation of communication networks, multiprocessors and other distributed systems in mind as application area, but instead of building a specialized simulator, OMNeT++ was designe
Proximity Mapping of the Tet Repressor-Tetracycline-Fe2+ Complex by Hydrogen Peroxide Mediated Protein Cleavage (1995)

We demonstrate in a quantitative in vitro induction assay that tetracycline-Fe2+ is a more than 1000-fold stronger inducer of Tet repressor compared to tetracycline-Mg2+. Oxidative cleavage of the Tet repressor-tetracycline-Fe2+ complex with H2O2 and ascorbate results in an Fe(2+)-dependent specific fragmentation of the protein. The maximal yield of about 15% and a reaction time of less than 30 s are only observed in the presence of the drug, whereas about 1% cleavage is obtained after 30 min in the presence of Fe2+ without tetracycline. Cleavage is not inhibited by several radical scavengers, suggesting a highly localized reactivity of the redox-active oxo intermediates in the proximity of the Fe(2+)-tc chelater where they are generated. The products can be separated by HPLC only after denaturation, indicating that the complex is not disrupted by cleavage. Residues at which the cleavage takes place are identified using the masses of the fragments determined by electrospray mass spectrometry and their N-terminal sequences. The major cleavage site maps to residues 104 and 105 of Tet repressor. Less efficient cleavages occur at residues 56 and 136, and the least efficiently cleaved sites are around residues 144 and 147. The cleavage efficiencies correlate to the distances and orientations of the respective peptide bonds to Mg2+ in the crystal structure of the Tet repressor-tetracycline-Mg2+ complex. We discuss potential reaction mechanisms leading to protein cleavage.
The UL45 gene product is required for herpes simplex virus type 1 glycoprotein B-induced fusion (1994)

Herpes simplex virus type 1 (HSV-1) syncytial (syn) mutants cause formation of giant polykaryocytes and have been utilized to identify genes promoting or suppressing cell fusion. We previously described an HSV-1 recombinant, F1 (J.L. Goodman, M. L. Cook, F. Sederati, K. Izumi, and J. G. Stevens, J. Virol. 63:1153-1161, 1989), which has unique virulence properties and a syn mutation in the carboxy terminus of glycoprotein B (gB). We attempted to replace this single-base-pair syn mutation through cotransfection with a 379-bp PCR-generated fragment of wild-type gB. The nonsyncytial viruses isolated were shown by DNA sequencing not to have acquired the expected wild-type gB sequence. Instead, they had lost their cell-cell fusion properties because of alterations mapping to the UL45 gene. The mutant UL45 gene is one nonsyncytial derivative of F1, A4B, was found to have a deletion of a C at UL45 nucleotide 230, resulting in a predicted frame shift and termination at 92 rather than 172 amino acids. Northern (RNA) analysis showed that the mutant UL45 gene was normally transcribed. However, Western immunoblotting showed no detectable UL45 gene product from A4B or from another similarly isolated nonsyncytial F1 derivative, A61B, while another such virus, 1ACSS, expressed reduced amounts of UL45. When A4B was cotransfected with the wild-type UL45 gene, restoration of UL45 expression correlated with restoration of syncytium formation. Conversely, cloned DNA fragments containing the mutant A4B UL45 gene transferred the loss of cell-cell fusion to other gB syn mutants, rendering them UL45 negative and nonsyncytial. We conclude that normal UL45 expression is required to allow cell fusion induced by gB syn mutants and that the nonessential UL45 protein may play an important role as a mediator of fusion events during HSV-1 infection.
The current status and portability of our sequence handling software (1986)

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.