gebhart/patrepeval huggingface dataset:
Periostin in Allergic Inflammation (2014)

Periostin, an extracellular matrix protein belonging to the fasciclin family, has been shown to play a critical role in the process of remodeling during tissue/organ development or repair. Periostin functions as a matricellular protein in cell activation by binding to their receptors on cell surface, thereby exerting its biological activities. After we found that periostin is a downstream molecule of interleukin (IL)-4 and IL-13, signature cytokines of type 2 immune responses, we showed that periostin is a component of subepithelial fibrosis in bronchial asthma, the first formal proof that periostin is involved in allergic inflammation. Subsequently, a great deal of evidence has accumulated demonstrating the significance of periostin in allergic inflammation. It is of note that in skin tissues, periostin is critical for amplification and persistence of allergic inflammation by communicating between fibroblasts and keratinocytes. Furthermore, periostin has been applied to development of novel diagnostics or therapeutic agents for allergic diseases. Serum periostin can reflect local production of periostin in inflamed lesions induced by Th2-type immune responses and also can predict the efficacy of Th2 antagonists against bronchial asthma. Blocking the interaction between periostin and its receptor, αv integrin, or down-regulating the periostin expression shows improvement of periostin-induced inflammation in mouse models or in in vitro systems. It is hoped that diagnostics or therapeutic agents targeting periostin will be of practical use in the near future.
Complete Regeneration of Bone in the Baboon by Recombinant Human Osteogenic Protein-1 (hOP-1, Bone Morphogenetic Protein-7) (1996)

We examined the efficacy of a single application of recombinant human osteogenic protein-1 (hOP-1, bone morphogenetic protein-7) for its ability to regenerate large calvarial defects in adult male baboons (Papio ursinus). Recombinant hOP-1, in conjunction with baboon or bovine guanidinium-extracted insoluble collagenous bone matrix (0.1, 0.5 and 2.5 mg per g of collagenous matrix as carrier), was implanted in 46 calvarial defects surgically prepared in 14 baboons, whilst 18 defects were implanted with the carrier matrix without hOP-1. Specimens were harvested on d 15, 30, 90 and 365 and subjected to histomorphometry on serial undecalcified sections cut at 7 pm to study the temporal sequence of tissue morphogenesis after the single application of hOP-1. Histological analysis indicated that the induction of new bone formation proceeded from the periphery to the central core of hOP-1 treated specimens after rapid angiogenesis and mesenchymal cell migration in apposition to the collagenous matrix. Whilst chondrogenesis was limited, newly formed bone has already filled with fully differentiated bone marrow elements as early as d 15, even with the 0.1 mg dose of hOP-1. On d 30 and 90, doses of 0.1 and 0.5 mg of hOP-1 showed greater amounts of bone than controls, and on d 90, they induced complete regeneration of the defects. Doses of 2.5 mg hOP-1 per g of matrix induced extensive osteogenesis initially with heterotopic ossification and displacement of the temporalis muscle above the defects. One year after implantation of hOP-1 there was restoration of the internal and external cortices of the calvaria. These results show that hOP-1 induces complete regeneration of calvarial bone in the adult primate, and suggest that the optimal activity of hOP-1 to achieve regeneration is between 100 and 500 pg of hOP-1 per g of matrix. These results in the primate may form the scientific basis for future clinical applications of hOP-1.
Finite-difference modelling of wavefield constituents (2015)

The finite-difference method is among the most popular methods for modelling seismic wave propagation. Although the method has enjoyed huge success for its ability to produce full wavefield seismograms in complex models, it has one major limitation which is of critical importance for many modelling applications; to naturally output up-and downgoing and P-and S-wave constituents of synthesized seismograms. In this paper, we show how such wavefield constituents can be isolated in finite-difference-computed synthetics in complex models with high numerical precision by means of a simple algorithm. The description focuses on up-and downgoing and P-and S-wave separation of data generated using an isotropic elastic finitedifference modelling method. However, the same principles can also be applied to acoustic, electromagnetic and other wave equations.
Chromatic Aberration-Free Grating-Lens Pair (1989)

We have developed a high numerical aperture grating-lens pair with large wavelength allowance. It has a new &quot;center cross&quot; structure, in which all rays cross the optical axis between the two grating lenses. Grating-lenses have concentric grating rings with radii set to cancel the diffraction angle changes caused by wavelength change. Wavelength allowance was estimated using RMS of wavefront aberration. An example calculation showed a wavelength allowance of 20 nm for a numerical aperture of 0.7. This value is sufficient for use with laser diodes with mode hopping or multimode.
A "one channel" spectral colour prediction model for transparent fluorescent inks on a transparent support (1997)

A color prediction model meant for computing the transmittance spectra of uniform color samples was presented. The study involved the prediction of color spectra produced with one fluorescent ink at different concentrations. In regard with it, the measurements of quantum yields, absorbtion bands, and emission spectra were also presented.
Generation of random arrays using clipped laser speckle (1986)

A technique for generating 2-D arrays of random numbers using clipped laser speckle is presented. A 2-D detector array is exposed to a fully developed laser speckle pattern. When the output of the array is clipped, the elements with value above threshold are set to unity while the others are set to zero. The result is an array of randomly positioned elements of unit value. The spatial coordinates of the elements above threshold are taken as the random deviates. By controlling the clipping threshold for each element, one can dictate the probability that the clipped output from each element will be above threshold. Any distribution can be produced by varying the probability that the output from each element is above threshold. We present experiments performed on a 256 × 256-element detector array for which the elements were individually addressable. The integration time for each detector can be adjusted to obtain various distributions. Applications of random arrays include Monte Carlo calculations and coherent pattern recognition.
Pippi: Practical Protocol Instantiation (2022)

A protocol specifies interactions between roles, which together constitute a multiagent system (MAS). Enacting a protocol presupposes that agents are bound to the its roles. Existing protocol-based approaches, however, do not adequately treat the practical aspects of how roles bindings come about. Pippi addresses this problem of MAS instantiation. It proposes the notion of a metaprotocol, enacting which instantiates a MAS suitable for enacting a given protocol. Pippi demonstrates the subtleties involved in instantiating MAS arising from protocol composition, correlation, and decentralization. To address these subtleties and further support practical application patterns, we introduce an enhanced protocol language, with support for parameter types (including role and protocol typed parameters, for metaprotocols), interface flexibility, and binding constraints. We discuss the realization of our approach through an extended agent architecture, including the novel concept of a MAS adapter for contact management. We evaluate Pippi's expressiveness by demonstrating common patterns for agent discovery.
Monomer Names (2017)

IUPAC recommendations on source-based nomenclature for single-strand polymers have so far addressed its application mainly to copolymers, non-linear polymers and polymer assemblies, and within generic source-based nomenclature of polymers. In this document, rules are formulated for devising a satisfactory source-based name for a polymer, whether homopolymer or copolymer, which are as clear and rigorous as possible. Thus, the source-based system for naming polymers is presented in a totality that serves as a user-friendly alternative to the structure-based system of polymer nomenclature. In addition, because of their widespread and established use, recommendations for the use of traditional names of polymers are also elaborated.
ChemInform Abstract: Synthesis of Bifunctional Au—Sn Organic—Inorganic Catalysts for Acid‐Free Hydroamination Reactions. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Molecular Population Genetics and Evolution of a Prion-like Protein in Saccharomyces cerevisiae (2001)

The prion-like behavior of Sup35p, the eRF3 homolog in the yeast Saccharomyces cerevisiae, mediates the activity of the cytoplasmic nonsense suppressor known as [PSI(+)]. Sup35p is divided into three regions of distinct function. The N-terminal and middle (M) regions are required for the induction and propagation of [PSI(+)] but are not necessary for translation termination or cell viability. The C-terminal region encompasses the termination function. The existence of the N-terminal region in SUP35 homologs of other fungi has led some to suggest that this region has an adaptive function separate from translation termination. To examine this hypothesis, we sequenced portions of SUP35 in 21 strains of S. cerevisiae, including 13 clinical isolates. We analyzed nucleotide polymorphism within this species and compared it to sequence divergence from a sister species, S. paradoxus. The N domain of Sup35p is highly conserved in amino acid sequence and is highly biased in codon usage toward preferred codons. Amino acid changes are under weak purifying selection based on a quantitative analysis of polymorphism and divergence. We also conclude that the clinical strains of S. cerevisiae are not recently derived and that outcrossing between strains in S. cerevisiae may be relatively rare in nature.
Bayesian adaptive alignment and inference. (1997)

Sequence alignment without the specification of gap penalties or a scoring matrix is attained by using Bayesian inference and a recursive algorithm. This procedure's recursive algorithm sums over all possible alignments on the forward step to obtain normalizing constants essential to Bayesian inferences, and samples from the exact posterior distribution on the backward step. Since both terminal and intervening unrelated subsequences will often be excluded from an alignment, the resulting alignments may be seen as extensions of local alignments. An alignment's significance is assessed using the Bayesian evidence. A shuffling simulation shows that Bayesian evidence against the null hypothesis tends to be a conservative measure of significance compared to classical p-values. An application to proteins from the GTPase superfamily shows that the posterior distribution of the number of gaps is often flat and that the posterior distribution of the evolutionary distance is often flat and sometimes bimodal. An alignment of 1GIA with 1ETU shows good correspondence with a structural alignment.
Digital Video Recording Techniques Using 1/2 Inch Metal Particle Tape (1985)

During the past ten years, rapid progress has been made in development of recording techniques for home use VTR. Nevertheless, a limit has now been reaches to improvement in such functional areas as SN ratio, resolution, and dubbing. It is now expected that digital recording techniques will be introduced into the video field in the future to assure even further development.
Evaluating complexity and resilience trade-offs in emerging memory inference machines. (2021)

Abstract not provided.
Bacteriophage Inactivation by UV-A Illuminated Fullerenes: Role of Nanoparticle-Virus Association and Biological Targets (2012)

Inactivation rates of the MS2 bacteriophage and (1)O(2) generation rates by four different photosensitized aqueous fullerene suspensions were in the same order: aqu-nC(60) < C(60)(OH)(6) ≈ C(60)(OH)(24) < C(60)(NH(2))(6). Alterations to capsid protein secondary structures and protein oxidation were inferred by detecting changes in infrared vibrational frequencies and carbonyl groups respectively. MS2 inactivation appears to be the result of loss of capsid structural integrity (localized deformation) and the reduced ability to eject genomic RNA into its bacterial host. Evidence is also presented for possible capsid rupture in MS2 exposed to UV-A illuminated C(60)(NH(2))(6) through TEM imagery and detection of RNA infrared fingerprints in ATR-FTIR spectra. Fullerene-virus mixtures were also directly visualized in the aqueous phase using a novel enhanced darkfield transmission optical microscope fitted with a hyperspectral imaging (HSI) spectrometer. Perturbations in intermolecular extended chains, HSI, and electrostatic interactions suggest that inactivation is a function of the relative proximity between nanoparticles and viruses and (1)O(2) generation rate. MS2 log survival ratios were linearly related to CT (product of (1)O(2) concentration C and exposure time T) demonstrating the applicability of classical Chick-Watson kinetics for all fullerenes employed in this study. Results suggest that antiviral properties of fullerenes can be increased by adjusting the type of surface functionalization and extent of cage derivatization thereby increasing the (1)O(2) generation rate and facilitating closer association with biological targets.
Use of Expression Profiles of HBV-DNA Integrated Into Genomes of Hepatocellular Carcinoma Cells to Select T Cells for Immunotherapy (2019)

HCC cells contain short segments of integrated HBV-DNA that encodes epitopes that are recognized by and activate T cells. HBV transcriptomes of these cells could be used to engineer T cells for personalized immunotherapy. This approach might be used to treat a wider population of patients with HBV-associated HCC.
KAUSTat: A Wireless, Wearable, Open-Source Potentiostat for Electrochemical Measurements (2019)

Advanced technology is needed every day for wireless, wearable sensors/potentiostats to record real-time measurements and monitor the chemical processes and physiological signals of the human body. Most of the potentiostats present on the market work as "black boxes" without access to their internal structure and their limited information of circuitry makes it challenging to develop new measurement methods and further integration with other instruments. Despite high resolution (e.g., measure low currents with high precision and low noise) of commercial potentiostats, the potentiostats used in laboratories are heavy, non-portable, and expensive. To fill this void, we introduce KAUSTat, a wireless, wearable, open-source potentiostat. The KAUSTat device interfaces with a smartphone to generate cyclic voltammetry curves using a Bluetooth Low Energy (BLE) protocol. Experiments with buffer and hexacyanoferrate solutions were conducted to assess the efficiency of the device. The results generated by KAUSTat are in agreement with those of the commercial potentiostat "Emstat." Considering wireless and wearable features of KAUSTat, it represents a convenient portable device for on-site sensing with low-power requirements.
Chapter 5. Catalysis's Role in Bioproducts Update (2015)

The goal for catalyst development, both homogeneous and heterogeneous, using bio-based feedstocks is designing new and robust materials for the dehydration, decarboxylation, decarbonylation, hydrogenolysis, esterification, and ketonization reactions that are required for converting these renewable, generally oxygenated feedstocks to desirable and renewable products. This chapter summarizes the work done on developing bio-based products in the last decade using the seminal US Department of Energy report on the top twelve bio-based chemicals as a starting point to assess catalyst improvement, novel process options, commercialization potential, and market penetration when possible.
A cost-effective WDM-PON using a multiple contact Fabry-P&#x00E9;rot laser diode (2010)

We demonstrated a WDM-PON using a multiple contact Fabry-Pérot laser diode without seed light. The electrical envelope tuning of the laser enables colour-free operation at 1.25 Gb/s with 100-GHz channel spacing.
Robust Cell-Load Learning With a Small Sample Set (2019)

Learning of the cell-load in radio access networks (RANs) has to be performed within a short time period. Therefore, we propose a learning framework that is robust against uncertainties resulting from the need for learning based on a relatively small training set. To this end, we incorporate prior knowledge about the cell-load in the learning framework. For example, an inherent property of the cell-load is that it is monotonic in downlink (data) rates. To obtain additional prior knowledge we first study the feasible rate region, i.e., the set of all vectors of user rates that can be supported by the network. We prove that the feasible rate region is compact. Moreover, we show the existence of a Lipschitz function that maps feasible rate vectors to cell-load vectors. With these results in hand, we present a learning technique that guarantees a minimum approximation error in the worst-case scenario by using prior knowledge and a small training sample set. Simulations in the network simulator NS3 demonstrate that the proposed method exhibits better robustness and accuracy than standard learning techniques, especially for small training sample sets.
Metal-free Michael addition initiated multicomponent oxidative cyclodehydration route to polysubstituted pyridines from 1,3-dicarbonyls (2008)

A simple metal-free, step-economic and selective access to pyridines from readily available substrates is reported, involving a flexible 4 A molecular sieves promoted Michael addition initiated domino three-component reaction between a 1,3-dicarbonyl, a Michael acceptor and a synthetic equivalent of ammonia.
Recycling trash in cache (2015)

The disparity between processing and storage speeds can be bridged in part by reducing the traffic into and out of the slower memory components. Some recent studies reduce such traffic by determining dead data in cache, showing that a significant fraction of writes can be squashed before they make the trip toward slower memory. In this paper, we examine a technique for eliminating traffic in the other direction, specifically the traffic induced by dynamic storage allocation. We consider recycling dead storage in cache to satisfy a program's storage-allocation requests. We first evaluate the potential for recycling under favorable circumstances, where the associated logic can run at full speed with no impact on the cache's normal behavior. We then consider a more practical implementation, in which the associated logic executes independently from the cache's critical path. Here, the cache's performance is unfettered by recycling, but the operations necessary to determine dead storage and recycle such storage execute as time is available. Finally, we present the design and analysis of a hardware implementation that scales well with cache size without sacrificing too much performance.
Balancing Efficacy and Safety of an Anti-DLL4 Antibody through Pharmacokinetic Modulation (2015)

PK modulation has potentially broad implications for development of antibody-based therapeutics. Our safety studies with anti-DLL4 F(ab')2 also provide new evidence reinforcing the notion that the DLL4 pathway is extremely sensitive to pharmacologic perturbation, further underscoring the importance of exercising caution to safely harness this potent pathway in humans.
A petabit photonic packet switch (P/sup 3/S) (2004)

This paper presents a new petabit photonic packet switch (P/sup 3/S) architecture that is highly scalable both in dimension and capacity while maintaining high system performances. Using a new multidimensional photonic multiplexing scheme that includes space, time, wavelength, and subcarrier domains, we propose a photonic switch fabric based on a 3-stage Clos network to provide scalable large-dimension photonic interconnections with nanosecond reconfiguration speed. Packet buffering is implemented electronically at the input and output port controllers, allowing the central photonic switch fabric to transport high-speed optical signals without electrical-to-optical conversion. Optical time division multiplexing (OTDM) technology further scales port speed beyond electronic speed up to 160 Gbits/s to minimize the fiber connections. To solve output contention, we propose a new arbitration scheme, called frame-based exhaustive matching (FEM), using extended frames to aggregate cells from different incoming lines. The extended frame relaxes the stringent arbitration time constraint at a 160 Gbit/s port speed. Based on the FEM scheme in the proposed architecture, a 6400 /spl times/ 6400 switch with a total capacity of 1.024 petabit/s can be achieved with throughput close to 100% under various traffic conditions.
Determining &#x201C;mixedness&#x201D; and an application of finite-gain stability results to &#x201C;mixed&#x201D; system interconnections (2010)

A loss of passivity in the face of certain frequency dynamics (eg: high frequency dynamics) given an otherwise passive system leads to the notion of a “mixed” system. A “mixed” system is one that has a concept of small gain associated with it over those frequency intervals where passivity is lost. In this paper, a test for determining “mixedness” for linear, time-invariant systems is provided and several finite-gain stability results for interconnections of such systems are presented. The “mixedness” test involves examining the spectral characteristics of two Hamiltonian matrices, one associated with the passive aspects of the system and one associated with the notion of small gain. The finite-gain stability results are derived using a dissipative systems framework.
Supplementary Table S1 from Elesclomol induces cancer cell apoptosis through oxidative stress (2023)

Supplementary Table S1 from Elesclomol induces cancer cell apoptosis through oxidative stress
Solid State NMR Investigations of Chain Dynamics and Network Order in Model Poly(dimethylsiloxane) Elastomers (2010)

This work is at a relatively early stage, however it has been demonstrated that we can reliably probe basic network architectures using the MQ-NMR technique. The initial results are in good agreement with what is known from standard network theory and will serve as a basis for the study of progressively increasing structural complexity in Siloxane network systems.