gebhart/patrepeval huggingface dataset:
Development and performance evaluation of a single-ring OpenPET prototype (2012)

One of the challenging applications of PET is implementing it for in-beam PET, which is an in situ monitoring method for charged particle therapy. For this purpose, we have previously proposed an open-type PET scanner, OpenPET. The original OpenPET had a physically opened field of view (FOV) between two detector rings through which irradiation beams pass. This dual-ring OpenPET (DROP) had a wide axial FOV including the gap. This geometry was not necessarily the most efficient for application to in-beam PET in which only a limited FOV around the irradiation field is required. Therefore, we have proposed a new single-ring OpenPET (SROP) geometry which can provide an accessible and observable open space with higher sensitivity and a reduced number of detectors than the DROP. The proposed geometry was a cylinder shape with its ends cut at a slant, in which the shape of each cut end became an ellipse. In this work, we developed and evaluated a small prototype of the SROP geometry for proof-of-concept. The SROP prototype was designed with 2 ellipse-shaped detector rings of 16 depth of interaction (DOI) detectors. The DO! detectors consisted of 1024 GSOZ crystals which were arranged in 4 layers of 16 × 16 arrays, coupled to a 64-ch FP-PMT. Each ellipse-shaped detector ring had a major axis of 281.6 mm and a minor axis of 207.5 mm. For the slant mode, the rings were placed at a 45-deg slant from the axial direction and for the nonslant mode (used as a reference) they were at 90 deg from the axial direction with no gap. The system sensitivity and average spatial resolution were measured from a <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">22</sup> Na point source and were 5.0 % and 2.5 mm, respectively, for the slant mode. Comparison between the slant mode and the non-slant mode showed no remarkable difference in terms of the sensitivity distribution and spatial resolution performance. Therefore, we concluded that the SROP geometry has a good potential as an open geometry especially suitable for in-beam imaging.
Covalently cyclized agonist and antagonist analogues of bombesin and related peptides. (1991)

During a search for possible cyclization points in shortened, potent bombesin agonists and antagonists, it was found that the joining of amino acid residues in positions 6 and 14 by various means resulted in retention of significant binding affinity for rat pancreatic acini and murine Swiss 3T3 cells. In one series of analogues, Cys residues in these positions were used for bridging via a disulfide bond. (D)-C-Q-W-A-V-G-H-L-C-NH2 retained significant binding affinity for rat pancreatic acini cells and was a full amylase releasing agonist (EC50 187 nM). Potency was markedly increased by substituting D-Ala for Gly (EC50 67 nM compared to 10 nM for its linear counterpart) and was decreased by substituting L-Cys for D-Cys in this analogue (EC50 214 nM), thus strongly suggesting stabilization of peptide folding by the D residues. Elimination of the COOH-terminal amino acid produces competitive antagonists in the linear analogues; however, (D)-C-Q-W-A-V-G-H-C-NH2 was devoid of activity. Likewise, cyclization to position 13 with the 14 amino acids intact to give (D)-C-Q-W-A-V-G-H-C-L-NH2 resulted in an almost inactive peptide. On the other hand, as in the linear series, the reduced peptide bond analogue, (D)-C-Q-W-A-V-(D)-A-H-L-psi (CH2NH)-C-NH2, was a receptor antagonist (IC50 5.7 mM), albeit much weaker than the corresponding linear analogues, but with no residual agonist activity. Direct head-to-tail cyclization was also tried. Both cyclo[(D)-F-Q-W-A-V-G-H-L-L] (EC50 346 nM) and the shorter cyclo [Q-W-A-V-G-H-L-L] (EC50 1236 nM) were full agonists. Elimination of the COOH-terminal residue in cyclo[(D)-p-Cl-F-Q-W-A-V-(D)-A-H-L] produced an agonist (EC50 716 nM) rather than an antagonist. These results provide support for the proposal that both bombesin agonists and antagonists adopt a folded conformation at their receptor(s). Furthermore, the retention of appreciable potencies using several cyclization strategies and chain lengths suggests that further optimization of these structures both in terms of potency and ring size is possible. Since these peptides have increased conformational restriction, they should begin to serve as useful substrates for NMR and molecular modeling studies aimed at comparing the obviously subtle differences between agonist and antagonist structures.
Improved Thin, Flexible Heat Pipes (2004)

Flexible heat pipes of an improved type are fabricated as layers of different materials laminated together into vacuum- tight sheets or tapes. In comparison with prior flexible heat pipes, these flexible heat pipes are less susceptible to leakage. Other advantages of these flexible heat pipes, relative to prior flexible heat pipes, include high reliability and greater ease and lower cost of fabrication. Because these heat pipes are very thin, they are highly flexible. When coated on outside surfaces with adhesives, these flexible heat pipes can be applied, like common adhesive tapes, to the surfaces of heat sinks and objects to be cooled, even if those surfaces are curved.
Use of homotopy-based approaches in finding Controlling Unstable Equilibrium Points in transient stability analysis (2016)

This paper introduces the use of homotopy-based approaches in computing the Controlling Unstable Equilibrium Points (controlling UEPs) in transient stability analysis using direct methods. It is well known that the regions of convergence of the controlling UEPs are very sensitive to the initial guesses, and traditional iterative methods fail to find the correct controlling UEPs if the initial guesses lie outside their regions of convergence. On the other hand, homotopy-based approaches are very reliable in finding solutions because they are globally convergent. However, homotopy-based approaches are intrinsically slow if the initial point is far from the desired solution because these methods map the trajectory of the solution from an easy and known solution to the desired solution. This paper proposes an algorithm that uses a homotopy-based approach with the exit point as an initial point to reliably find the correct controlling UEP. To reduce computational effort, the proposed method uses an approximate exit point rather than computing an accurate exit point as is common practice in finding controlling UEPs. Further, this method eliminates the necessity of computing the Minimum Gradient Point (MGP), which makes the homotopy-based approaches comparable with the other iterative methods in terms of the speed of computation. An explicit characterization of the region of convergence of a controlling UEP and its boundary starting from an exit point for a typical power system is derived. The method is applied on the WECC and the NE 39 test systems to demonstrate its effectiveness in finding the controlling UEPs.
Multispectral Enhancement Method to Increase the Visual Differences of Tissue Structures in Stained Histopathology Images (2012)

In this paper we proposed a multispectral enhancement scheme in which the spectral colors of the stained tissue-structure of interest and its background can be independently modified by the user to further improve their visualization and color discrimination. The colors of the background objects are modified by transforming their N -band spectra through an NxN transformation matrix, which is derived by mapping the representative samples of their original spectra to the spectra of their target colors using least mean square method. On the other hand, the color of the tissue structure of interest is modified by modulating the transformed spectra with the sum of the pixel’s spectral residual-errors at specific bands weighted through an NxN weighting matrix; the spectral error is derived by taking the difference between the pixel’s original spectrum and its reconstructed spectrum using the first M dominant principal component vectors in principal component analysis. Promising results were obtained on the visualization of the collagen fiber and the non-collagen tissue structures, e.g., nuclei, cytoplasm and red blood cells (RBC), in a hematoxylin and eosin (H&E) stained image.
Phenylethanolamine N‐methyltransferase (<i>PNMT</i>) gene and early‐onset Alzheimer disease (2001)

The activity of human phenylethanolamine N-methyltransferase (PNMT) is reduced in the neurons of those cells in many subcortical areas of the brain that are known to undergo neurodegeneration in Alzheimer disease (AD). Others have reported that PNMT is decreased in brains of persons with AD and that the decrease in enzymatic activity is due to a reduced amount of the enzyme protein. We have previously described two polymorphisms, G-353A and G-148A, in the promoter region of the gene coding for PNMT. These markers were tested for their association with the occurrence of sporadic AD. Genotyping of 131 necropsy confirmed AD cases, and 947 adult nondemented controls were completed. We observed a significant association between both of the PNMT gene polymorphisms and early-onset AD (EOAD) (P < or = 0.007), but not in late-onset AD (LOAD). These data suggest that genetic variation in the promoter of the PNMT gene is associated with increased susceptibility to the sporadic form of EOAD.
Selective boron delivery to murine tumors by lipophilic species incorporated in the membranes of unilamellar liposomes. (1995)

The nido-carborane species K[nido-7-CH3(CH2)15-7,8-C2B9H11] has been synthesized for use as an addend for the bilayer membrane of liposomes. Small unilamellar vesicles, composed of distearoylphosphatidylcholine/cholesterol, 1:1, and incorporating K[nido-7-CH3(CH2)15-7,8-C2B9H11] in the bilayer, have been investigated in vivo. The time-course biodistribution of boron delivered by these liposomes was determined by inductively coupled plasma-atomic emission spectroscopy analyses after the injection of liposomal suspensions in BALB/c mice bearing EMT6 mammary adenocarcinomas. At the low injected doses normally used (approximately 5-10 mg of boron per kg of body weight), peak tumor boron concentrations of approximately 35 micrograms of boron per g of tissue and tumor/blood boron ratios of approximately 8 were achieved. These values are sufficiently high for the successful application of boron neutron capture therapy. The bilayer-embedded boron compound may provide the sole boron source or, alternatively, a concentrated aqueous solution of a hydrophilic boron compound may also be encapsulated within the liposomes to provide a dose enhancement. Thus, the incorporation of both K[nido-7-CH3(CH2)15-7,8-C2B9H11] and the hydrophilic species, Na3[1-(2'-B10H9)-2-NH3B10H8], within the same liposomes demonstrated significantly enhanced biodistribution characteristics, exemplified by maximum tumor boron concentrations of approximately 50 micrograms of boron per g of tissue and tumor/blood boron ratios of approximately 6.
Diastereoselective and Enantioselective Cyclopropanation of Alkenes Catalyzed by Cobalt Porphyrins (2003)

Cobalt(II) porphyrin complexes were shown to be general and efficient catalysts for selective cyclopropanation of alkenes with ethyl diazoacetate (EDA). The catalytic system can operate with alkenes as limiting reagents, requiring only stoichiometric amounts of EDA. The protocol is performed in one-pot fashion without the need of slow addition of EDA. The diastereoselectivity of the current system can be tuned by using different porphyrin ligands or additives, giving either trans- or cis-dominant cyclopropanes. The asymmetric cyclopropanation was also demonstrated with the use of chiral cobalt porphyrin complexes.
Flexible wavelength division multiplexing (FWDM) networks (2011)

Flexible wavelength division multiplexing improves resource utilization in optical networks. In this paper, we review the recent progresses in FWDM research on both the physical layer and the control plane aspects. (2 pages)
Mesenchymal Stem Cells Prevent Hydrocephalus After Severe Intraventricular Hemorrhage (2013)

Intraventricular transplantation of umbilical cord blood-derived mesenchymal stem cells significantly attenuated the posthemorrhagic hydrocephalus and brain injury after IVH. This neuroprotective mechanism appears to be mediated by the anti-inflammatory effects of these cells.
Identity-Based Internet Protocol Networking (2012)

The Identity-Based Internet Protocol (IBIP) Network project is experimenting with a new enterprise oriented network architecture using standard Internet Protocol to encode identity (ID) information into the IP packet by a new edge security device referred to as the IBIP policy enforcement point (PEP). This is a variant of a network admission control process that establishes user and host identities as well as provides optional information on host visibility, organizational affiliation, current role, and trust metric (associated with the user and host endpoints). Our motivation is to increase our security posture by leveraging identity, reducing our threat exposure, enhancing situational understanding of our environment, and simplifying network operations. In addition to authentication, we leverage strong anti-spoofing technology to improve accountability. We reduce our threat surface by “hiding” our client hosts and making all infrastructure devices inaccessible. Any attempt to access a hidden host or infrastructure device results in a policy violation attributable to the user/host that caused the violation and provides enhanced situational awareness of such activities. Our servers can also have a “permissible use” policy that ensures that the server only operates across the network per that policy. Finally, as users log in and servers are added to the network all dynamic configurations for access control initiated by such changes are automatically carried out without manual intervention, thereby reducing potential vulnerabilities caused by human errors.
Compressed-leaf bounding volume hierarchies (2018)

We propose and evaluate what we call Compressed-Leaf Bounding Volume Hierarchies (CLBVH), which strike a balance between compressed and non-compressed BVH layouts. Our CLBVH layout introduces dedicated compressed multi-leaf nodes where most effective at reducing memory use, and uses regular BVH nodes for inner nodes and small, isolated leaves. We show that when implemented within the Embree ray tracing framework, this approach achieves roughly the same memory savings as Embree's compressed BVH layout, while maintaining almost the full performance of its fastest non-compressed BVH.
Immunological Characterization and Neutralizing Ability of Monoclonal Antibodies Directed Against Botulinum Neurotoxin Type H (2016)

This 3-mAb combination potently neutralized BoNT/H and represents a potential human antitoxin that could be developed for the prevention and treatment of type H botulism.
Binary antidotes for organophosphate poisoning: aprophen analogs that are both antimuscarinics and carbamates (1989)

Prophylaxis against organophosphate poisoning can be achieved by pretreatment with physostigmine or pyridostigmine, which are carbamates, and aprophen, which is an anticholinergic agent. Thus, a series of aprophen analogues was synthesized with carbamyl substitutions on the phenyl rings (carbaphens). The rationale behind this design is that such compounds might exhibit most of the therapeutic characteristics of aprophen, as well as the ability to protect prophylactically by chemically masking cholinesterase enzymes. Compounds 4 (dimethylhydroxycarbaphen), 15 (dimethylcarbaphen), and 16 (monomethylcarbaphen) were found to inactivate human butyrylcholinesterase in a time-dependent manner with potencies similar to those of physostigmine or pyridostigmine, and the latter two exhibited almost the same antimuscarinic profile as aprophen. In contrast to the potent inactivation of butyrylcholinesterase by these compounds, marginal inactivation of acetylcholinesterase activity was observed, and only at much higher drug concentrations. The noncarbamylated analogues had no effect on the activity of either cholinesterase. The carbaphen compounds are hence prototype drugs that can interact with either muscarinic receptors or butyrylcholinesterase. Furthermore, these compounds are prodrugs, since after carbamylation of the cholinesterase, the leaving group 14 (hydroxyaprophen) is a potent antimuscarinic itself.
Processing of Nanometer-Scale CeO<sub>2</sub> Particles (2002)

A semi-batch reactor method was developed for directly synthesizing undoped and doped nanometer-scale CeO2 particles at room temperature. Powders exhibited a surface area of ≈170 m2/g. Control over the particle size, size distribution, and state of agglomeration could be achieved through variation of the mixing conditions and oxidation pathway.
Three-dimensional tumor localization in thick tissue with the use of diffuse photon-density waves (1997)

A new approach to three-dimensional tumor localization in turbid media with the use of measurements in a single plane is presented. Optical diffuse photon-density waves are used to probe the turbid medium. Relative amplitudes and phases are measured in the detection plane. Lateral localization is accomplished in the detection plane. With a Fourier optics approach, the scattered wave is reconstructed throughout the volume to provide depth localization. Computer-simulation results that validate this technique are presented. Applications of this technique to multiple tumors and to optical mammography are discussed.
A database encryption system with subkeys (1981)

A new cryptosystem that is suitable for database encryption is presented. The system has the important property of having subkeys that allow the encryption and decryption of fields within a record. The system is based on the Chinese Remainder Theorem.
Helper-independent retrovirus vectors with Rous-associated virus type O long terminal repeats (1988)

We have constructed nonpermuted replication-competent avian retrovirus vectors that derive from Rous sarcoma virus (S. H. Hughes, J. J. Greenhouse, C. J. Petropoulos, and P. Sutrave, J. Virol. 61:3004-3012, 1987). We describe here the construction and properties of corresponding vectors in which the long terminal repeats (LTRs) of the parental virus have been replaced by the LTRs of the endogenous chicken virus Rous-associated virus type O. The Rous-associated virus type O LTR vectors replicated approximately 1/10 as well as the parental vectors and expressed a test gene, chloramphenicol acetyltransferase, approximately 1/30 to 1/50 as well.
Magnetic Tape Recording (1999)

Abstract The sections in this article are History Manufacturing and Structure of Tapes and Floppy Disks Magnetic Properties of Tapes Magnetization Reversal of Fine Particles Recording Physics Recording Systems Magnetic Tape Recording: Outlook
Dendronized Cellulose Nanocrystals as Templates for Preparation of ZnS and CdS Quantum Dots (2014)

Cellulose nanocrystals (CNC) isolated from bleached bagasse pulp were modified with a second-generation isocyanate dendron (G2-dendron) to prepare dendronized cellulose nanocrystals (DCN). Transmission electron microscopy (TEM), elemental analysis for nitrogen, Fourier transform infrared (FTIR) and 13C magic angle spinning nuclear magnetic resonance (13C MAS NMR) proved occurrence of the modification of cellulose nanocrystals surfaces. The dendronized cellulose nanocrystals were used as templates for formation of ZnS and CdS quantum dots with uniform diameter at low temperature in water. The prepared DCN/QDs were highly soluble in water. TEM images showed that the size of the prepared quantum dots was about 5 nm in diameter. UV-Visible and fluorescence spectroscopy showed absorption and emission at wavelength values lower than that reported for bulk ZnS and CdS.
FAME (2016)

Fault attacks are a known serious threat to embedded software security. We propose FAME, a low-cost and flexible approach to defend embedded software against fault attacks.
Litz: elastic framework for high-performance distributed machine learning (2018)

Machine Learning (ML) is an increasingly popular application in the cloud and data-center, inspiring new algorithmic and systems techniques that leverage unique properties of ML applications to improve their distributed performance by orders of magnitude. However, applications built using these techniques tend to be static, unable to elastically adapt to the changing resource availability that is characteristic of multi-tenant environments. Existing distributed frameworks are either inelastic, or offer programming models which are incompatible with the techniques employed by high-performance ML applications.

Motivated by these trends, we present Litz, an elastic framework supporting distributed ML applications. We categorize the wide variety of techniques employed by these applications into three general themes -- stateful workers, model scheduling, and relaxed consistency -- which are collectively supported by Litz's programming model. Our implementation of Litz's execution system transparently enables elasticity and low-overhead execution.

We implement several popular ML applications using Litz, and show that they can scale in and out quickly to adapt to changing resource availability, as well as how a scheduler can leverage elasticity for faster job completion and more efficient resource allocation. Lastly, we show that Litz enables elasticity without compromising performance, achieving competitive performance with state-of-the-art non-elastic ML frameworks.
Glucotypes reveal new patterns of glucose dysregulation (2018)

Diabetes is an increasing problem worldwide; almost 30 million people, nearly 10% of the population, in the United States are diagnosed with diabetes. Another 84 million are prediabetic, and without intervention, up to 70% of these individuals may progress to type 2 diabetes. Current methods for quantifying blood glucose dysregulation in diabetes and prediabetes are limited by reliance on single-time-point measurements or on average measures of overall glycemia and neglect glucose dynamics. We have used continuous glucose monitoring (CGM) to evaluate the frequency with which individuals demonstrate elevations in postprandial glucose, the types of patterns, and how patterns vary between individuals given an identical nutrient challenge. Measurement of insulin resistance and secretion highlights the fact that the physiology underlying dysglycemia is highly variable between individuals. We developed an analytical framework that can group individuals according to specific patterns of glycemic responses called "glucotypes" that reveal heterogeneity, or subphenotypes, within traditional diagnostic categories of glucose regulation. Importantly, we found that even individuals considered normoglycemic by standard measures exhibit high glucose variability using CGM, with glucose levels reaching prediabetic and diabetic ranges 15% and 2% of the time, respectively. We thus show that glucose dysregulation, as characterized by CGM, is more prevalent and heterogeneous than previously thought and can affect individuals considered normoglycemic by standard measures, and specific patterns of glycemic responses reflect variable underlying physiology. The interindividual variability in glycemic responses to standardized meals also highlights the personal nature of glucose regulation. Through extensive phenotyping, we developed a model for identifying potential mechanisms of personal glucose dysregulation and built a webtool for visualizing a user-uploaded CGM profile and classifying individualized glucose patterns into glucotypes.