gebhart/patrepeval huggingface dataset:
Total Ion Current Chromatogram (TICC) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Lp82 calpain during rat lens maturation and cataract formation (1998)

Lp82 is a proteolytic enzyme likely functioning in early lens development and maturation. The rapid loss of Lp82 activity during lens maturation is probably caused by three factors: autodegradation associated with the proteolysis of soluble and insoluble proteins occurring in the rat lens nucleus, association of Lp82 with the lens insoluble fraction, and loss of Lp82 mRNA. Lp82 may function early in lens maturation along with m-calpain, which then is predominant in the latter stages of maturation. Proteolysis in selenite cataract is partially caused by over-activation of Lp82.
Efficiently Computing Piecewise Flat Embeddings for Data Clustering and\n Image Segmentation (2016)

Image segmentation is a popular area of research in computer vision that has\nmany applications in automated image processing. A recent technique called\npiecewise flat embeddings (PFE) has been proposed for use in image\nsegmentation; PFE transforms image pixel data into a lower dimensional\nrepresentation where similar pixels are pulled close together and dissimilar\npixels are pushed apart. This technique has shown promising results, but its\noriginal formulation is not computationally feasible for large images. We\npropose two improvements to the algorithm for computing PFE: first, we\nreformulate portions of the algorithm to enable various linear algebra\noperations to be performed in parallel; second, we propose utilizing an\niterative linear solver (preconditioned conjugate gradient) to quickly solve a\nlinear least-squares problem that occurs in the inner loop of a nested\niteration. With these two computational improvements, we show on a publicly\navailable image database that PFE can be sped up by an order of magnitude\nwithout sacrificing segmentation performance. Our results make this technique\nmore practical for use on large data sets, not only for image segmentation, but\nfor general data clustering problems.\n
Time course of the effect of ferumoxytol on T1-relaxation times of blood, liver, myocardium, and acute infarction (2012)

Background Intravenous iron-supplementation drugs are frequently used for treatment of iron-deficiency anemia in chronic kidney disease. Some iron-agents alter tissue T1-relaxation times (T1) for days after administration, and could obscure MRI diagnosis. Conversely, these agents may have the potential to delineate pathology. We sought to investigate the T1-shortening effect of ferumoxytol and iron-dextran, determine how T1 of blood, liver, and myocardium change over time in-vivo after iron administration, and explore the utility of these agents for imaging acute myocardial infarction (MI). Methods We determined in-vitro T1 of ferumoxytol and irondextran (20mg Fe ad 500ml 0.9%NaCl). Seven dogs with acute, reperfused MI were scanned five days later on a 3.0T MRI-scanner, at which time ferumoxytol (n=5) or iron-dextran (n=2) was administered in clinically used doses (approx. 130mg iron). Inversion-recovery, gradient-echo images with various inversion-times (1151600ms) were acquired prior to and serially after ironinjection at multiple time-points on day 1 (n=7), 2 (n=5), 3 (n=2), and 7 (n=7). T1 was determined by standard curve-fitting. Results In-vitro T1 of ferumoxytol and iron-dextran were 13% and 89% of 0.9%NaCl, respectively. T1 of blood, myocardium, and liver were 2027±421ms, 1384±143ms, and 806±74ms, respectively. Results for ferumoxytol were: T1 of blood dropped to 7% (p 0.05). Conclusions Ferumoxytol may affect cardiovascular MR beyond 2 days and liver MR beyond 1 week after administration of doses used clinically for iron-deficiency anemia. Unless recognized, this could affect MRI diagnosis. The differential kinetics suggest a potential use of ferumoxytol for delineation of acute MI.
DNA damage assessment by comet assay of human lymphocytes exposed to jet propulsion fuels (2002)

Exposure to jet fuel damages DNA and results in a number of physiological changes in liver, lung, immune, and neurological tissue. In this study the single-cell gel electrophoresis assay or comet assay was used to compare the DNA damage in human peripheral lymphocytes produced by three jet propulsion fuels: JP-8, JP-5, and JP-8+100. These fuels consist of complex mixtures of aliphatic, aromatic, and substituted naphthalene hydrocarbons. Two exposure times were investigated which correspond to estimated occupational exposure times and concentrations of fuels were used that were based on previous fuel toxicity studies. Analysis of samples for the extent of DNA damage as determined by tail moment and percent tail DNA was performed on exposed cells following a brief recovery time. All fuels produced significant increases in DNA damage; however, only JP-8+100 was genotoxic at the lowest exposure concentration (1:500). At the highest exposure concentration (1:75), the mean tail moments for JP-8 and JP-8+100 (32.041 +/- 2.599 and 45.774 +/- 4.743, respectively) were significantly greater than for JP-5 (1.314 +/- 0.474). These results indicate that JP-8+100 is the most potent inducer of DNA damage in human peripheral lymphocytes and that both JP-8+100 and JP-8 are capable of damaging lymphocyte DNA to a greater extent than JP-5.
Using Real Options to Estimate the Pre-commercialisation Value of a Drought Tolerant Wheat Trait (2020)

Uncertainty, sunk investment costs and managerial flexibility means standard investment budgeting methods such as net present value are ineffective and undervalue risky investments. Real options attains a more accurate and comprehensive assessment of investments. In this study, we apply a real options analytical framework to investment decisions during the research and development (R&amp;D) process of a drought tolerant wheat trait. The results suggest the option value for investment is positive at each R&amp;D stage and that investors should continue to invest. Biotechnology firms should use a real options analytical framework like the one applied in this paper for investment strategy development and for investment decisions involving uncertainty, sunk costs and decision flexibility.
The essential role of oxygen in activation the blue emitting light from cerium doped Aluminum nitride thin films (2017)

Oral presentation given at the 2017 E-MRS Spring Meeting, held in Strasbourg (France) on May 22-26, 2017.
Spinal cord quantitative MRI discriminates between disability levels in multiple sclerosis (2013)

In this cross-sectional study of patients with MS, quantitative MRI reflects clinically relevant differences beyond what can be detected by conventional MRI. Our findings support the utility of quantitative MRI in clinical settings, where accurate measurement of disease burden is becoming increasingly critical for assessing treatment efficacy.
Synthesis and characterization of pH‐and salt‐sensitive hydrogel based on chemically modified poultry feather protein isolate (2009)

Abstract Hydrogels were synthesized from poultry feather protein by crosslinking ethylene diamine tetraacetic dianhydride (EDTAD)‐modified feather protein isolate (FPI) with glutaraldehyde (Glu). Different molar ratios of EDTAD/FPI were used to obtain FPI of different degrees of acylate modification. Differential scanning calorimeter measurements of glass transition temperature suggested that hydrogel formation was based on the hydrogen bond between EDTAD‐modified FPI segments. The swelling properties of modified FPI hydrogel were investigated in deionized water and in solutions of different salt contents (i.e., ionic strengths) and pH. An optimal swelling ratio (SR) of 63 g/g was obtained when molar ratios of EDTAD/FPI and Glu/FPI were 0.12 and 0.008, respectively. SR decreased substantially with increase in ionic strength, and at a given ionic strength, SR increased with solution pH in 4.0 to 10.0 range. The water transport mechanism of the hydrogel was also pH dependent and was controlled by Fickian diffusion and polymer relaxation. At higher pH value, the water transport profile became more dependent on polymer relaxation than at lower pH. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Improved thermal conductivity and AC dielectric breakdown strength of silicone rubber/BN composites (2020)

The present study demonstrates a synergistic effect with the addition of low loading levels of boron nitride filler in silicone rubber that resulted in significant improvement in both ac breakdown strength and thermal conductivity of silicone rubber composites. Our results show that addition of 2.5 vol% and 7 vol% of h-BN platelets improved thermal conductivity of silicone rubber composites by 25% and 65% respectively. The ac breakdown strength of silicone rubber composites was investigated by varying surface area and particle size of hexagonal boron nitride (h-BN) platelets. The breakdown strength of composites with only 2.5 vol% of low surface area boron nitride (0075) was enhanced by 20% and with high surface area boron nitride (7HS) was improved by 30%. The improvement in ac breakdown strength was primarily attributed to effective heat dissipation in the composite as well as low dielectric loss performance of the composite and was dependent upon the textural properties of boron nitride fillers.
Acute upregulation of CCR-5 expression by CD4+ T lymphocytes in HIV-infected patients treated with interleukin-2 (1999)

Chemokine receptors are involved in trafficking of lymphocytes. The IL-2-induced upregulation of chemokine receptors in TH cells may thus play a role in the acute effects of this cytokine in TH lymphocyte redistribution.
INGR Roadmap Optics Chapter (2022)

Optical networks have long played a central role in telecommunication networks, forming the fiber backbone of the Internet. Over time fiber optic systems have evolved and found deployment increasingly closer to the network edge. Today, optical systems extend to the server network interface cards and home access networks. New application areas have emerged such as the use of free space communications using LiFi technologies, space communication networks between satellites and ground stations. Looking ahead, optical systems in many areas will continue to be driven by the need for higher speeds and capacity in order to keep up with traffic demands. In addition to faster interfaces speeds, parallel fiber or spatial division multiplexing will be used for future capacity growth. In several application areas, new functionality is expected such as low latency in Xhaul networks and optical switching and co-packaged optics in data centers. LiFi will become critical for mitigating RF interference for in-building networks. Intense research is underway to develop quantum networks to connect quantum computers. This general trend toward new functionalities for optical systems, moving beyond capacity growth in fiber networks, is driven in large part by the increasing performance and demands of today's user equipment and applications. From the network edge to the data centers, components are reliant on optics. The integration of optics into these new applications and the higher levels of functionality demanded of optics motivate the use of roadmaps to guide research and development and overcome future roadblocks.
Dynamic lumbar pedicle screw-rod stabilization: in vitro biomechanical comparison with standard rigid pedicle screw-rod stabilization (2010)

In a 1-level pedicle screw-rod construct, hinged-dynamic screws allowed a quantity of motion that was substantially closer to normal motion than that allowed by rigid pedicle screws. Both systems altered kinematics similarly. Less load was borne by the hinged screw construct, indicating that the hinged-dynamic screws allow less stress shielding than standard rigid screws.
Donor‐derived organ transplant transmission of coccidioidomycosis (2011)

Coccidioidomycosis in solid organ transplant recipients most often occurs as a result of primary infection or reactivation of latent infection. Herein, we report a series of cases of transplant-related transmission of coccidioidomycosis from a single donor from a non-endemic region whose organs were transplanted to 5 different recipients. In all, 3 of the 5 recipients developed evidence of Coccidioides infection, 2 of whom had disseminated disease. The degree of T-cell immunosuppression and timing of antifungal therapy initiation likely contributed to development of disease and disease severity in these recipients. This case series highlights the importance of having a high index of suspicion for Coccidioides infection in solid organ transplant recipients, even if the donor does not have known exposure, given the difficulties of obtaining a detailed and accurate travel history from next-of-kin.
Field Demonstration of Durable Link Slabs for Jointless Bridge Decks Based on Strain-Hardening Cementitious Composites (2005)

The research presented herein describes the development of durable link slabs for jointless bridge decks based on strainhardening cementitious composite - engineered cementitious composite (ECC). Specifically the superior ductility of ECC was utilized to accommodate bridge deck deformations imposed by girder deflection, concrete shrinkage, and temperature variations, providing a cost-effective solution to a number of deterioration problems associated with bridge deck joints. Based on the findings within, the implementation of a durable ECC link slab is possible in a standard bridge deck reconstruction scenario. This report includes development of theoretical guidelines for compete design of an ECC link slab, example calculations, desk references, sample design drawings, material specifications, and contractual special provisions. In addition to these documents, the results of full scale mixing trials and demonstrations are summarized and recommendations are made along with batching sequences and mix designs for large scale mixing. A summary of construction practices and procedures is also included, followed by the results of full scale load testing on the completed ECC link slab demonstration bridge. Conclusions within the report reveal that with the aid of design documents provided within, the design of an ECC link slab element can be completed with little difficulty by Department of Transportation design engineers. The mixing of ECC material at commercial concrete plants can also produce a large scale version of the material similar in mechanical performance to laboratory grade material. The construction of an ECC link slab can be completed by a general contractor with some additional care when working with this new material. Finally, load tests conclude that the ECC link slab functions as designed under bending loads.
Performance analysis of monolithic RF transformers by experimental characterization (2003)

Electrical performances of 4-port n:n dual-spiral transformers fabricated in a thick plated copper on silicon process are analyzed. Multiport data analysis techniques and compact modeling are used to study the relationships between the physical and the electrical attributes of the devices. Analytical models, based on measurements from 50 MHz to 20 GHz, are used to explore achievable device performance under different design constraints.
Can a reverse shoulder arthroplasty be used to revise a failed primary reverse shoulder arthroplasty? (2018)

Revision RSA, when used to salvage a failed primary RSA, can be a successful procedure. At intermediate follow-up, survival rates are reasonable, but dislocation and glenoid lucency remain a concern, particularly in smokers. Cite this article: Bone Joint J 2018;100-B:1493-98.
Flexible Electronics: The Next Ubiquitous Platform (2012)

Thin-film electronics in its myriad forms has underpinned much of the technological innovation in the fields of displays, sensors, and energy conversion over the past four decades. This technology also forms the basis of flexible electronics. Here we review the current status of flexible electronics and attempt to predict the future promise of these pervading technologies in healthcare, environmental monitoring, displays and human-machine interactivity, energy conversion, management and storage, and communication and wireless networks.
Interference mitigation based on precoded SRS (2016)

This paper illustrates an interference mitigation method based on the estimation of an equivalent channel using Sounding Reference Signal (SRS) sequences in Time Division Duplex (TDD) multi-cell systems. The key idea is to precode the SRS sequence with a pre-coder that is computed based on the choice made by the User Equipment (UE) of its preferred signal subspace. Assuming channel reciprocity in TDD systems, the interfering Base Stations (BSs) can estimate the equivalent precoded channels and avoid sending signal to their own UE in that direction, thus reducing interference, without any need for feedback. We investigate this method with varying degrees of available perfect channel state information at the transmitter and show that it can surpass a Maximum-Ratio-Transmission (MRT) transceiver.
Transient activation of topoisomerase I in leukotriene D4 signal transduction in human cells (1990)

U937 human monoblast cells incubated with leukotriene D4 (LTD4) rapidly released arachidonic acid metabolites into the culture medium. Release was suppressed by the high-affinity LTD4 receptor antagonist SK&F 104353. Arachidonic acid release induced by LTD4 has been linked to a rapid induction of gene expression, and the propagation of the receptor binding signal is probably associated with enzymes that regulate gene expression. We have studied the participation of DNA topoisomerase I in LTD4 signal transduction. LTD4-specific release of arachidonic acid metabolites was inhibited (60-80%) by the topoisomerase I inhibitor camptothecin. LTD4 increased protein-linked DNA strand breakage induced by camptothecin in U937 cells; this enhancement was prevented by coincubation of the cells with LTD4 plus the receptor antagonist SK&F 104353. In addition, LTD4 produced a rapid transient increase in extractable topoisomerase I activity, which was maximum within the first 10 min after addition of LTD4 to the culture medium. Incubation of cultures for greater than 10 min with LTD4 before the addition of camptothecin resulted in no enhancement of camptothecin-induced DNA strand breakage, consistent with a reversal of topoisomerase I activation. Staurosporine, an inhibitor of protein kinase C, blocked LTD4-induced arachidonic acid release and attenuated the effect of LTD4 on camptothecin-induced DNA strand breakage. These results are consistent with the view that the regulation of topoisomerase I activity is involved in the propagation of LTD4-mediated signals in U937 cells.
A RAC-GEF network critical for early intestinal tumourigenesis (2021)

RAC1 activity is critical for intestinal homeostasis, and is required for hyperproliferation driven by loss of the tumour suppressor gene Apc in the murine intestine. To avoid the impact of direct targeting upon homeostasis, we reasoned that indirect targeting of RAC1 via RAC-GEFs might be effective. Transcriptional profiling of Apc deficient intestinal tissue identified Vav3 and Tiam1 as key targets. Deletion of these indicated that while TIAM1 deficiency could suppress Apc-driven hyperproliferation, it had no impact upon tumourigenesis, while VAV3 deficiency had no effect. Intriguingly, deletion of either gene resulted in upregulation of Vav2, with subsequent targeting of all three (Vav2<sup>-/-</sup> Vav3<sup>-/-</sup> Tiam1<sup>-/-</sup>), profoundly suppressing hyperproliferation, tumourigenesis and RAC1 activity, without impacting normal homeostasis. Critically, the observed RAC-GEF dependency was negated by oncogenic KRAS mutation. Together, these data demonstrate that while targeting RAC-GEF molecules may have therapeutic impact at early stages, this benefit may be lost in late stage disease.
Towards Precision Measurements of Radiation Reaction (2019)

We find the long-time dynamics of charges in electromagnetic fields, revealing that charge energy loss to radiation leads to counter-intuitive acceleration. Using this phenomenon, we propose a method to observe radiation reaction with weak fields. © 2019 The Author(s)
Architecting ambient intelligence systems (2008)

Ambient Intelligence (AmI) systems refer to ubiquitous computing with focus on human experiences. The AmI ideas are based on the premise that if environment around individuals can be personalized for the current needs of an individual, then the lives can be more productive and enjoyable. New and existing technologies will be used to personalize spaces and experiences in AmI environments. The goal of AmI is to make computing and technology transparent and invisible to the individual. AmI is characterized by unobtrusive and mostly invisible technologies working together, anticipating the needs, and personalizing the environment and experiences for individuals. This paper presents new ideas in developing AmI infrastructure for deploying AmI services. The proposed system architecture is based on characterizing the roles and rights of individuals in the current environment and designing components and services that respond to these roles. The generalized architecture can be used to adapt physical as well as virtual spaces to fit individual preferences. A general architecture is necessary to move AmI from a collection of "cool gadgets" to an ambient and aware service focused on personalization for individuals.