gebhart/patrepeval huggingface dataset:
Multi‐planar plenoptic displays (2013)

Abstract Multi‐planar plenoptic displays consist of multiple spatially varying light‐emitting and light‐modulating planes. In this work, we introduce a framework to display light field data on this new type of display device. First, we present a mathematical notation that describes each of the layers in terms of the corresponding light transport operators. Next, we explain an algorithm that renders a light field with depth into a given multi‐planar plenoptic display and analyze the approximation error. We show two different physical prototypes that we have designed and built: The first design uses a dynamic parallax barrier and a number of bi‐state (translucent/opaque) screens. The second design uses a beam splitter to co‐locate two pairs of parallax barriers and static image projection screens. We evaluate both designs on a number of different 3D scenes. Finally, we present simulated and real results for different display configurations.
‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets (2018)

The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.
Oxygen-Regulated β <sub>2</sub> -Adrenergic Receptor Hydroxylation by EGLN3 and Ubiquitylation by pVHL (2009)

Agonist-induced ubiquitylation and degradation of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) play an essential role in surface receptor homeostasis, thereby tuning many physiological processes. Although beta-arrestin and affiliated E3 ligases mediate agonist-stimulated lysosomal degradation of the beta(2)-adrenergic receptor (beta(2)AR), a prototypic GPCR, the molecular cues that mark receptors for ubiquitylation and the regulation of receptor degradation by the proteasome remain poorly understood. We show that the von Hippel-Lindau tumor suppressor protein (pVHL)-E3 ligase complex, known for its regulation of hypoxia-inducible factor (HIF) proteins, interacts with and ubiquitylates the beta(2)AR, thereby decreasing receptor abundance. We further show that the interaction of pVHL with beta(2)AR is dependent on proline hydroxylation (proline-382 and -395) and that the dioxygenase EGLN3 interacts directly with the beta(2)AR to serve as an endogenous beta(2)AR prolyl hydroxylase. Under hypoxic conditions, receptor hydroxylation and subsequent ubiquitylation decrease dramatically, thus attenuating receptor degradation and down-regulation. Notably, in both cells and tissue, the abundance of endogenous beta(2)AR is shown to reflect constitutive turnover by EGLN3 and pVHL. Our findings provide insight into GPCR regulation, broaden the functional scope of prolyl hydroxylation, and expand our understanding of the cellular response to hypoxia.
Alignment of a nematic liquid crystal on nano‐grooved material (2010)

Abstract We demonstrate the alignment characteristics of a nematic liquid crystal on the surface of a nanoimprinted material that is a functionally graduated composite suitable for the alignment of a liquid crystal on a groove surface processed by nanoimprinting lithography. With the electro‐optic characteristics shown in twisted nematic and in‐plane switching modes, the potential liquid crystal applications are examined. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Two molecular forms of the human interferon-gamma receptor. Ligand binding, internalization, and down-regulation. (1988)

The receptors for human interferon-gamma (IFN-gamma) on peripheral blood monocytes and various cells of nonhematopoietic origin were thoroughly characterized and compared. The receptors of all cell types exhibited a similar affinity for IFN-gamma (Kd approximately 1 x 10(-10) M), and in all cases receptor-mediated endocytosis and ligand degradation were demonstrated. However, the receptors differed in their molecular weights (95,000 in HeLa cells and 140,000 in monocytes, assuming a 1:1 ligand to receptor ratio) as concluded from experiments of cross-linking to 125I-IFN-gamma. Lower molecular weight species were obtained as well, particularly in monocytes. Such species could represent either degradation products or subunit structures. The monocyte and HeLa receptor responded differently to an excess of ligand. A significant receptor down-regulation was observed when monocytes were incubated with an excess of 125I-IFN-gamma, whereas no such down-regulation was observed in HeLa cells or in normal fibroblasts. This differential response was observed both in the presence or in the absence of a protein synthesis inhibitor. The receptor on monocytes was found to be acid-labile whereas that on HeLa cells was resistant to acid treatment. These and additional experiments indicate that the monocyte receptor is inactivated following internalization, whereas the HeLa receptor retains its structure and recycles back to the cell surface. The difference in the properties and fate of these two receptor subtypes is probably related to the differential functions of IFN-gamma in various cell types.
Performance study and system optimization on sleep mode operation in IEEE 802.16e (2009)

Energy efficiency in mobile devices remains a critical issue in the design of wireless communication system. In order to provide a high quality of service (QoS), the IEEE 802.16e-2005 standard supports three unique power saving classes (PSCs) which aim to reduce the power consumption of mobile devices based on the different types of traffic. Our goal is to design an optimal sleep mode selection scheme so as to maximize the energy efficiency in a mobile WiMAX system while providing a certain QoS guarantee. In this paper, we propose a theoretical framework based on the semi-Markov decision process along with a performance evaluation on the sleep mode operation. Based on this model, we formulate a stochastic optimization problem and solve it through our novel policy optimization algorithm, which is capable of finding the optimal policy for the selection of different PSCs. The numerical and simulation results demonstrate the validity of our proposed scheme under different QoS requirements such as the packet delay and energy consumption level. We believe that our scheme has achieved a high energy efficiency and is best fit to the IEEE 802.16e mobile system.
Anthropometric Studies of the Human Sacrum Relating to Dorsal Transsacral Implant Designs (1986)

The sacrum offers several possibilities for fixation that, when combined, appear to provide a secure foundation for a dorsally-placed, transsacrally-fixed implant. The dorsal sacral landmarks, particularly the first and second dorsal foramina, are readily identifiable and relate in a consistent manner both qualitatively and quantitatively to the major mass of sacral bone, which is located ventrally to the vital structures of the sacrum. The authors have utilized these findings in the design of a new implant for direct sacral fixation.
A Framework for Development of Risk-Informed Autonomous Adaptive Cyber Controllers (2019)

This article details a framework and methodology to risk-inform the decisions of an unsupervised cyber controller. A risk assessment methodology within this framework uses a combination of fault trees, event trees, and attack graphs to trace and map cyber elements with business processes. The methodology attempts to prevent and mitigate cyberattacks by using adaptive controllers that proactively reconfigure a network based on actionable risk estimates. The estimates are based on vulnerabilities and potential business consequences. A generic enterprise-control system is used to demonstrate the wide applicability of the methodology. In addition, data needs, implementation, and potential pitfalls are discussed.
A Stereoselective Process for the Manufacture of a 2′-Deoxy-β-<scp>d</scp>-Ribonucleoside Using the Vorbrüggen Glycosylation (2013)

A practical and scalable process for the manufacture of cladribine (1) is described. Vorbrüggen glycosylation of doubly silylated 2-chloroadenine 2 with protected 1-O-acetyl-2-deoxy-α,β-d-ribofuranose 3 under reversible conditions in the presence of 20 mol % triflic acid in a solvent that selectively precipitated the desired β-anomer β-4a whilst leaving the unwanted α-anomer α-4a in solution to isomerise allowed good overall stereoselectivity with exclusive regioselectivity. An aging step allowed anomerisation of α-4a to β-4a, thereby improving the isolable yield of the β-anomer. Direct filtration of the product mixture without a catalyst quench or aqueous workup furnished the crude β-anomer β-4a in good yield (up to 68%) and purity (>95% by HPLC) with no regioisomers detected and only ∼1–3% (by HPLC) of the undesired α-anomer. Deprotection of the crude, unpurified intermediate β-4a followed by recrystallisation provided drug-grade cladribine (1). The process includes three isolation steps and was demonstrated on kilogram scales using cGMP providing 99.8–99.9% pure cladribine in up to an overall 43% yield based on 2-chloroadenine (5). In contrast to previous methods, column chromatography and/or bulky directing groups were not required in the glycosylation step, a high pressure vessel was not needed in the deprotection step, and only one dedicated recrystallisation step was necessary.
Low-Crosstalk Designs For Integrated Optical Crossbar Switches (1990)

Integrated optical matrix switches can process optical signals whose data rate exceeds 100 Gbit/s, which might be very useful in a multi-computer environment. This paper describes a hybrid design which uses combinations of the conventional switch and a new 2-stage switch for crosstalk suppression in the integrated optical rectangular crossbar matrix switches. Using the hybrid design, we believe that low-crosstalk integrated optical crossbar switches can be fabricated with much relief to the stringent process control.
Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels (2018)

Drug discovery campaigns directly targeting the voltage-gated sodium channel NaV1.7, a highly prized target in chronic pain, have not yet been clinically successful. In a differentiated approach, we demonstrated allosteric control of trafficking and activity of NaV1.7 by prevention of SUMOylation of collapsin response mediator protein 2 (CRMP2). Spinal administration of a SUMOylation incompetent CRMP2 (CRMP2 K374A) significantly attenuated pain behavior in the spared nerve injury (SNI) model of neuropathic pain, underscoring the importance of SUMOylation of CRMP2 as a pathologic event in chronic pain. Using a rational design strategy, we identified a heptamer peptide harboring CRMP2's SUMO motif that disrupted the CRMP2-Ubc9 interaction, inhibited CRMP2 SUMOylation, inhibited NaV1.7 membrane trafficking, and specifically inhibited NaV1.7 sodium influx in sensory neurons. Importantly, this peptide reversed nerve injury-induced thermal and mechanical hypersensitivity in the SNI model, supporting the practicality of discovering pain drugs by indirectly targeting NaV1.7 via prevention of CRMP2 SUMOylation. Here, our goal was to map the unique interface between CRMP2 and Ubc9, the E2 SUMO conjugating enzyme. Using computational and biophysical approaches, we demonstrate the enzyme/substrate nature of Ubc9/CRMP2 binding and identify hot spots on CRMP2 that may form the basis of future drug discovery campaigns disrupting the CRMP2-Ubc9 interaction to recapitulate allosteric regulation of NaV1.7 for pain relief.
Draft Genome Sequence of Bifidobacterium animalis subsp. <i>lactis</i> Strain CECT 8145, Able To Improve Metabolic Syndrome <i>In Vivo</i> (2014)

Bifidobacterium animalis subsp. lactis strain CECT 8145 is able to reduce body fat content and improve metabolic syndrome biomarkers. Here, we report the draft genome sequence of this strain, which may provide insights into its safety status and functional role.
Brittle System Analysis (1999)

The goal of this paper is to define and analyze systems which exhibit brittle behavior. This behavior is characterized by a sudden and steep decline in performance as the system approaches the limits of tolerance. This can be due to input parameters which exceed a specified input, or environmental conditions which exceed specified operating boundaries. An analogy is made between brittle commmunication systems in particular and materials science.
Single-Crystalline Germanium Thin Films by Electrodeposition and Solid-Phase Epitaxy (2007)

Single-crystal germanium films on silicon were prepared by electrodeposition and solid-phase epitaxy. The germanium films were amorphous as-deposited and crystallized into single crystals or polycrystals, depending on the cleanliness of the Si substrates. The low deposition temperature, the ease of thickness control, and the inherit advantage of spatial selectivity of the electrodeposition process make this method a promising way to selectively grow high-quality germanium for device applications.
The Use of Pulp Fibres for the Production of Wood/Plastic Composites (2011)

Natural fibres can enhance the performance of a plastic component in a manner similar to glass fibre. Compared with glass fibres natural fibres have the advantage that the whole composite material remains carbon based which brings benefits in terms of (energy-) recycling, machine abrasion and a 'green' image. They are also usually cheaper than their synthetically produced counterparts. The disadvantage of natural fibres is a propensity to take up water, variable quality and uncertainty of supply. Quality and supply issues of natural fibres arise as the currently used natural fibres are predominately agricultural fibres such as hemp or sisal which are harvested on a seasonal basis. The pulping of wood on the other hand creates fibres with very consistent quality and supply can be guaranteed for many years ahead. This makes wood fibres an ideal candidate for composite products. Scion is undertaking research that looks at the suitability of various types of pulp fibres for composite production. Composites made from polypropylene and incorporating several common pulp types were prepared. The composites show substantially increased performance similar and in some cases superior to agricultural fibres. High-yield pulps such as TMP or MDF show good reinforcement potential. This paper gives an introduction to pulp based wood/plastic composites, describes some composite forming techniques using pulp fibres and compares the performance of several pulps when used for composite manufacture.
Molecular cloning and characterization of a conserved nuclear serine(threonine) protein kinase. (1995)

Human, Drosophila melanogaster, and Caenorhabditis elegans cDNA clones encoding homologues of a serine(threonine) protein kinase (EC 2.7.1.37) (designated Ndr protein kinase) have been isolated and sequenced. The human and Drosophila cDNAs predict polypeptides of 54 kDa and 52 kDa, respectively, which share approximately 80% amino acid similarity. Northern analysis of human tissues revealed a ubiquitously expressed 3.9-kb transcript. Recombinant GST-Ndr underwent intramolecular autophosphorylation on serine and threonine residues in vitro but failed to transphosphorylate several standard protein kinase substrates. Transfection of the human cDNA into COS-1 cells resulted in the appearance of an intense nuclear staining in cells analyzed by indirect immunofluorescence; deletion mutagenesis identified a short basic peptide, KRKAETWKRNRR, responsible for the nuclear accumulation of Ndr. Thus, Ndr is a conserved and widely expressed nuclear protein kinase. The closest known relative of this previously uncharacterized kinase is Dbf2, a budding yeast protein kinase required for the completion of nuclear division.
Wide-field smartphone fundus photography using trans-pars-planar illumination and miniaturized indirect ophthalmoscopy (Conference Presentation) (2018)

It is known that wide-field fundus photography is essential for screening, diagnosis and treatment evaluation of eye diseases such as diabetic retinopathy (DR), age-related macular degeneration (AMD), retinopathy of premature (ROP), etc. However, the high equipment cost of existing devices is a limiting factor for clinical deployment of wide-field fundus photography, particularly in rural and underserved areas where both expensive instruments and skilled operators are not available. Low-cost smartphone fundus cameras promise convenient assessment of eye diseases at point-of-care environments, and may also enable affordable telemedicine screening to foster the access to medical cares in rural and underserved areas. However, practical application of existing smartphone fundus cameras is limited by the small field of view (FOV) in single-shot images. We have recently demonstrated the feasibility of trans-pars-planar illumination, i.e., delivering illuminating light through pars plana outside of the pupil. By freeing the whole pupil for image purpose only, the trans-pars-planar illumination provides one unique opportunity to develop snapshot, low-cost, but high-quality wide-field fundus camera. Using all off-the-shelf parts, a smartphone-based prototype fundus camera was constructed to achieve a 152-degree FOV in single-shot images, without the need for pharmacological pupil dilation. Moreover, we have also explored miniaturized indirect ophthalmoscopy to achieve wide-field fundus video photography. A totally wireless smartphone fundus camera was constructed, with a whole weight of 255 g. This device allowed both snapshot fundus photography and continuous video recording.
Probe Electrospray Ionization (2014)

Probe electrospray ionization (PESI) is an electrospray-based atmospheric-pressure surface sampling and ionization technique for mass spectrometry that uses a solid needle instead of a capillary. While ionization occurs in a fashion similar to that involved in electrospray ionization, the novel aspect of PESI is discontinuous sampling. The needle is driven up and down along the vertical axis to the apex of the ion-sampling orifice. At the highest position, the liquid trapped at the needle tip is electrosprayed. PESI is applicable to analyze the biological samples, imaging, real-time reaction monitoring, etc. The most unique feature of PESI is the sequential and exhaustive ionization of the analytes that cannot be accomplished by the capillary-based electrospray.
Reduction of β‐amyloid peptide<sub>42</sub> in the cerebrospinal fluid of patients with Alzheimer's disease (1995)

Abstract In this clinical study, the cerebrospinal fluid (CSF) level of a Novemberel form of the β‐amyloid peptide (Aβ) extending to position 42 (Aβ 42 ) was determined in patients with Alzheimer's disease (AD) as well as controls. In addition to measurement of CSF Aβ 42 levels, total Aβ peptides, microtubule‐associated protein τ, and apolipoprotein E (ApoE) genotype were also assessed. It is interesting that CSF Aβ 42 levels were found to be significantly lower in AD patients relative to controls, whereas total Aβ levels were not. Aβ 42 has recently been shown to preferentially deposit in the brain tissue of patients with AD, suggesting that diminished clearance may account for its reduction in CSF. As previously reported, τ levels were increased in AD patients; however, neither Aβ 42 nor τ levels were apparently influenced by the ApoE genotype.
Process control in a high-noise environment using a limited number of measurements (2004)

In this paper, we develop a hybrid control algorithm that produces control values for processes where only a limited number of function evaluations are available for the control law generation. This situation arises, for example, in stencil printing processes in printed circuit board manufacturing, where the cost associated with multiple function evaluations is prohibitive: The proposed control algorithm is given by a modified version of a constrained conjugated-gradient method, transitioned into a windowed-smoothed block-form of the least-squares affine estimator.
ChemInform Abstract: Enantioselective Synthesis of R‐(+)‐α‐Lipoic Acid. (1987)

Abstract The dilithio compound (II) is alkylated and then reduced to give the allylic alcohol (III) which yields the epoxyalcohol (IV) by catalytic enantioselective epoxidation.
Wall++ (2018)

Human environments are typified by walls, homes, offices, schools, museums, hospitals and pretty much every indoor context one can imagine has walls. In many cases, they make up a majority of readily accessible indoor surface area, and yet they are static their primary function is to be a wall, separating spaces and hiding infrastructure. We present Wall++, a low-cost sensing approach that allows walls to become a smart infrastructure. Instead of merely separating spaces, walls can now enhance rooms with sensing and interactivity. Our wall treatment and sensing hardware can track users' touch and gestures, as well as estimate body pose if they are close. By capturing airborne electromagnetic noise, we can also detect what appliances are active and where they are located. Through a series of evaluations, we demonstrate Wall++ can enable robust room-scale interactive and context-aware applications.
Bioactive Metabolites of the Endophytic Fungi of Pacific Yew, <i>Taxus brevifolia</i> (1994)

The endophytic microbes associated with the Pacific yew tree, Taxus brevifolia, were examined as potential alternative sources of the anticancer drug taxol, a secondary metabolite of the host organism. A novel fungus, Taxomyces andreanae, isolated from the inner bark of a yew tree growing in northwestern Montana, appears to produce taxol and other taxanes, in de novo fashion when grown in semi-synthetic liquid media. The presence of taxol in the fungal extract was confirmed by mass spectrometry, comparative chromatographic behavior with yew taxol, reactivity with taxol-specific monoclonal antibodies, and 9KB cytotoxicity studies. Both acetate-1-14C and phenylalanine UL-14C served as precursors of taxol-14C in fungal culture labeling studies, confirming the de novo synthesis of taxol by the fungus. Immunoassay techniques are currently being used to screen extracts of Taxomyces andreanae for new taxanes, and to determine if other endophytic fungi are taxol producers. Fungal endophytes used in this study are further screened for additional biological activity following taxol/taxane analysis.