gebhart/patrepeval huggingface dataset:
TU-AB-303-12: Towards Inter and Intra Fraction Plan Adaptation for the MR-Linac (2015)

Purpose: To develop a new sequencer for IMRT that during treatment can account for anatomy changes provided by online and real-time MRI. This sequencer employs a novel inter and intra fraction scheme that converges to the prescribed dose without a final segment weight optimization (SWO) and enables immediate optimization and delivery of radiation adapted to the deformed anatomy. Methods: The sequencer is initially supplied with a voxel-based dose prescription and during the optimization iteratively generates segments that provide this prescribed dose. Every iteration selects the best segment for the current anatomy state, calculates the dose it will deliver, warps it back to the reference prescription grid and subtracts it from the remaining prescribed dose. This process continues until a certain percentage of dose or a number of segments has been delivered. The anatomy changes that occur during treatment require that convergence is achieved without a final SWO. This is resolved by adding the difference between the prescribed and delivered dose up to this fraction to the prescription of the subsequent fraction. This process is repeated for all fractions of the treatment. Results: Two breast cases were selected to stress test the pipeline by producing artificial inter and intra fraction anatomy deformations using a combination of incrementally applied rigid transformations. The dose convergence of the adaptive scheme over the entire treatment, relative to the prescribed dose, was on average 8.6% higher than the static plans delivered to the respective deformed anatomies and only 1.6% less than the static segment weighted plans on the static anatomy. Conclusion: This new adaptive sequencing strategy enables dose convergence without the need of SWO while adapting the plan to intermediate anatomies, which is a prerequisite for online plan adaptation. We are now testing our pipeline on prostate cases using clinical anatomy deformation data from our department. This work is financially supported by Elekta AB, Stockholm, Sweden.
Copper-Catalyzed [<sup>18</sup>F]Fluorination of (Mesityl)(aryl)iodonium Salts (2014)

A practical, rapid, and highly regioselective Cu-catalyzed radiofluorination of (mesityl)(aryl)iodonium salts is described. This protocol utilizes [(18)F]KF to access (18)F-labeled electron-rich, -neutral, and -deficient aryl fluorides under a single set of mild conditions. This methodology is applied to the synthesis of protected versions of two important radiotracers: 4-[(18)F]fluorophenylalanine and 6-[(18)F]fluoroDOPA.
Magnetoelectric Characterization of Multiferroic Nanostructure Materials (2014)

AbstractIn the last decade, a tremendous amount of research works have been carried out in the area of multiferroic nanostructure materials in order to meet the requirement of science and technology for the future microelectronic industries. The potential functionalities of any kind nanostructure materials lies in the vicinity of large surface to volume ratio compare to the bulk counterpart. The new technology for microelectronics require small dimension, robust mechanical properties, higher degree of electrical and electronic properties and finally high output power with low dissipation energy. The area of ferroelectric and multiferroic nanostructures are vast, this chapter deals with the different variety of multiferroic nanostructure with different dimensionality (D) 0D 1D, 2D and 3D and their state of art characterization process. Possible and feasible theoretical modeling and related experimental facts of already established multiferroics nanostructures will be described. It will also cover the advantages and the limitations of these nanostructures in design, development, and particularly for device applications.Keywords: Multiferroicsnanoparticlesmagnetoelectricheterostructuresnanocomposites
Multifusion, Multispectral, Optical Polarimetric Imaging Sensing Principles (2006)

The goal of this study is to present novel, multifusion optical imaging sensing principles, based on active-multispectral polarimetric imaging of targets surrounded by scattered media. Specifically, the novelty of this study consists in the fusion of multispectral images, with polarimetric imaging principles, forming image differences. The experimental results indicate clearly that, high-contrast multispectral Mueller polarimetric image differences, as well as Degree of Linear Polarization (DOLP) images can be obtained from transmitted or backscattered photons, from targets embedded in turbid media
Understanding network failures in data centers (2011)

We present the first large-scale analysis of failures in a data center network. Through our analysis, we seek to answer several fundamental questions: which devices/links are most unreliable, what causes failures, how do failures impact network traffic and how effective is network redundancy? We answer these questions using multiple data sources commonly collected by network operators. The key findings of our study are that (1) data center networks show high reliability, (2) commodity switches such as ToRs and AggS are highly reliable, (3) load balancers dominate in terms of failure occurrences with many short-lived software related faults,(4) failures have potential to cause loss of many small packets such as keep alive messages and ACKs, and (5) network redundancy is only 40% effective in reducing the median impact of failure.
Unraveling the Molecular Pathophysiology of Myelodysplastic Syndromes (2011)

Somatically acquired genetic abnormalities lead to the salient features that define myelodysplastic syndromes (MDS): clonal hematopoiesis, aberrant differentiation, peripheral cytopenias, and risk of progression to acute myeloid leukemia. Although specific karyotypic abnormalities have been linked to MDS for decades, more recent findings have demonstrated the importance of mutations within individual genes, focal alterations that are not apparent by standard cytogenetics, and aberrant epigenetic regulation of gene expression. The spectrum of genetic abnormalities in MDS implicates a wide range of molecular mechanisms in the pathogenesis of these disorders, including activation of tyrosine kinase signaling, genomic instability, impaired differentiation, altered ribosome function, and changes in the bone marrow microenvironment. Specific alterations present in individual patients with MDS may explain much of the heterogeneity in clinical phenotype associated with this disease and can predict prognosis and response to therapy. Elucidation of the full complement of genetic causes of MDS promises profound insight into the biology of the disease, improved classification and prognostic scoring schemes, and the potential for novel targeted therapies with molecular predictors of response.
Fabrication and characterization of germanium-on-insulator through epitaxy, bonding, and layer transfer (2014)

A scalable method to fabricate germanium on insulator (GOI) substrate through epitaxy, bonding, and layer transfer is reported. The germanium (Ge) epitaxial film is grown directly on a silicon (Si) (001) donor wafer using a “three-step growth” approach in a reduced pressure chemical vapour deposition. The Ge epilayer is then bonded and transferred to another Si (001) wafer to form the GOI substrate. The Ge epilayer on GOI substrate has higher tensile strain (from 0.20% to 0.35%) and rougher surface (2.28 times rougher) compared to the Ge epilayer before transferring (i.e., Ge on Si wafer). This is because the misfit dislocations which are initially hidden along the Ge/Si interface are now flipped over and exposed on the top surface. These misfit dislocations can be removed by either chemical mechanical polishing or annealing. As a result, the Ge epilayer with low threading dislocations density level and surface roughness could be realized.
Deep-Learning-Based Imaging through Glass-Air Disordered Fiber with Transverse Anderson Localization (2018)

We demonstrate for the first time that deep neural networks (DNNs) can be trained to recover images transported through a 90 cm-long silica-air disordered optical fiber at variable working distances without any distal optics.
Cervical Cytokines Associated With Chlamydia trachomatis Susceptibility and Protection (2019)

Cytokines involved in humoral, type I interferon, and T-helper (Th) 17 responses were associated with susceptibility to C. trachomatis, whereas cytokines involved in Th1 polarization, recruitment, and activation were associated with protection against ascension and reinfection.
Manipulation of living cells by atomic force microscopy (2004)

Currently there is a great interest in using atomic force microscopy (AFM) to study living cells under biophysiological conditions. It has been shown that problems invoked by the deformation and destruction of soft biological materials can be solved by using tapping mode AFM. Besides the capability of AFM to characterize the membrane surface of living cells, it can be employed to modify surfaces and manipulate nano sized structures. By feeding force information measured from AFM to a haptic joystick, an augmented reality is developed. Under the assistance of the augmented virtual reality, the operator can monitor the tip position and feel the three dimensional forces which are proportional to the actual forces acting on the cantilever during nanomanipulation. The experimental study shows the effectiveness of the proposed scheme.
Abstract 4404: Comparative <i>in vivo</i> pharmacokinetic properties of antibody-maytansinoid conjugates with alternative non-cleavable linkers (2010)

Abstract Antibody-maytansinoid conjugates (AMCs) are targeted anticancer agents that deliver a highly potent cytotoxic maytansinoid agent (DM1 or DM4) specifically to tumor cells displaying their target antigen. Multiple AMCs are now in clinical testing for treatment of an array of cancers. AMCs can employ either a reducible (“cleavable”) disulfide linkage or a non-reducible (“non-cleavable”) thioether linkage to tether the thiol-containing maytansinoid agent to the antibody. The most advanced AMC, trastuzumab-DM1 (T-DM1), employs a maleimide based thioether bond made using SMCC (N-succinimidyl-4-(N-maleimido-methyl)-cyclohexane-1-carboxylate) linker to tether DM1 to the trastuzumab antibody. Given the interest in AMC's with non-cleavable linkers we initiated a study to evaluate alternative non-cleavable antibody-maytansinoid linkages in vivo. This report describes the results of a pharmacokinetic study to evaluate the relative in vivo stability of antibody maytansinoid conjugates with three different non-cleavable linkers: (1) a maleimido-based thioether linkage between the antibody and the thiol-containing maytansinoid DM1 (huC242-MCC-DM1), (2) an iodoacetamido-based thioether linker (huC242-SIA-DM1), or (3) a non sulfur containing link where the maytansinoid is covalently bound directly to the antibody via an amide bond (huC242-Maytansinoid). The three well characterized conjugates were administered intravenously (10 mg/kg) to CD1 mice and plasma samples were withdrawn via retro-orbital plexus at various time points post injection for determination of concentration of intact conjugate by ELISA methods. The pharmacokinetic data describing conjugate clearance were essentially indistinguishable for all three conjugates, each of which had β phase terminal half-lives of approximately 7.5 days. We did not observe any enhanced instability of the maleimido-based thioether-linked conjugate (huC242-MCC-DM1) compared to the iodoacetamido-based thioether-linked conjugate (huC242-SIA-DM1), as has been reported for auristatin conjugates (Alley et. al. Bioconj. Chem. 2008, 19(3), 759-765). In a separate study, we show that the in vivo half-life of the tritiated conjugate, huC242-MCC-[3H]-DM1, in mouse plasma is similar to the half-life for clearance of total antibody from plasma as measured by ELISA (t1/2,β = 10.5 d vs. 12.6 d, respectively), demonstrating that the huC242-MCC-DM1 conjugate has excellent stability in vivo. We conclude that all three of the non-cleavable conjugate linkages examined here for AMCs (maleimido thioether, acetamido thioether and amide linkage) behave similarly in vivo in terms of plasma stability. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4404.
Characterization of imaging threshold detectors employing a phase-conjugate resonator (1986)

We have previously reported resolution of 40 Ip/mm in an imaging threshold detector using a phase conjugate resonator (PCR),1 This device, which is a combination of the conventional BaTiO3 PCR2 with the incoherent-to-coherent spatial light modulator concept3,4, is intended to produce an output when one element of an n × n pixel array is above a preset threshold. This performance is obtained by using a separate spatially encoded erase beam to erase all transverse modes of the resonator except those of the desired element. Since the erasure is not complete, but only sufficient to keep undesirable pixels from resonating, it is necessary to avoid crosstalk, i.e., partial reflections from one element assisting the oscillation of another, for the device to operate as intended.
Further Structure–Activity Relationships Study of Hybrid 7-{[2-(4-Phenylpiperazin-1-yl)ethyl]propylamino}-5,6,7,8-tetrahydronaphthalen-2-ol Analogues: Identification of a High-Affinity D3-Preferring Agonist with Potent in Vivo Activity with Long Duration of Action (2007)

This paper describes an extended structure-activity relationships study of aminotetralin-piperazine-based hybrid molecules developed earlier for dopamine D2/D3 receptors. Various analogues as positional isomers have been developed where location of the phenolic hydroxyl group has been varied on the aromatic ring. Between two catechol derivatives, compound 6e with a two methylene linker length exhibited higher affinity and selectivity for D3 over D2 receptors over compound 6f with four methylene linkers (D2/D3 = 50.6 vs 7.51 for 6e and 6f, respectively). In general, the (-)-isomer was more potent than the (+)-isomeric counterpart. Binding results indicated highest selectivity for D3 receptors in compound (-)- 10 ( K i = 0.35 nM; D2/D3 = 71). In the 5-hydroxy series, highest selectivity for D3 receptors was exhibited by compound (-)- 25 ( K i = 0.82 nM; D2/D3 = 31.5). Most potent compounds exhibited binding and functional affinities at the sub-nanomolar level for the D3 receptor. Binding assays were carried out with HEK-293 cells expressing either D2 or D3 receptors by using tritiated spiperone as radioligand for competition studies to evaluate inhibition constants ( K i). A functional assay of selected compounds for stimulating GTPgammaS binding was carried out with CHO cells expressing human D2 receptors and AtT-20 cells expressing human D3 receptors. The functional assay results indicated partial to full agonist characteristics of test compounds. Compound (-)- 25 was selected further for in vivo study to evaluate its potency in producing contralateral rotations in rats with unilateral lesion in the nigrostriatal region induced by neurotoxin 6-OHDA, a Parkinsonian animal model. Compound (-)- 25 at 5 micromol/kg exhibited rotational activity that lasted beyond 12 h, whereas at a 1 micromol/kg dose the rotations lasted beyond 8 h.
Chemoselective hydrosilations. I. Synthesis and photopolymerization of 1‐propenyl ether functionalized siloxanes (1995)

Abstract The synthesis of 1‐propenyl ether‐functionalized siloxanes (PFS) has been achieved by the controlled, rhodium‐catalyzed, chemoselective hydrosilation of 1‐allyloxy‐4(1‐propen‐oxy) butane with various H‐functional siloxanes. It was shown that the hydrosilation pro‐ceeds exclusively at the allyl ether group of 1‐allyloxy‐4(1‐propenoxy) butane without par‐ticipation at the 1‐propenyl ether group. The photoinduced cationic polymerization of these monomers was studied using various analytical techniques and found to take place very rapidly. © 1995 John Wiley & Sons, Inc.
Ultrathin nonlinear metasurfaces (2016)

We present a novel class of ultrathin metasurfaces operating in a nonlinear regime, simultaneously providing generation efficiencies that are many orders of magnitude larger than in other nonlinear setups, and, at the same time, capable of controlling the local phase of the nonlinear signal with high precision and subwavelength resolution. The key to achieving such outstanding performance is combining a strong local field enhancement and polarization selectivity of plasmonic nano-antennas with extremely high nonlinearity of multi-quantum well semiconductor stacks. In this work, we discuss the operation principles of such metasurfaces and provide experimental and numerical results. We also show how a savvy application of Lorentz reciprocity principle allows for fast and efficient analysis and modeling of such metasurfaces consisting of thousands of elements.
Quantitative Microbial Ecology through Stable Isotope Probing (2015)

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
FPGA programmable logic block evaluation using quantified Boolean satisfiability (2006)

A novel field programmable gate array (FPGA) logic synthesis technique that determines if a logic function can be implemented in a given programmable circuit is presented, and how this problem can be formalised and solved using quantified Boolean satisfiability is described. This technique is general enough to be applied to any type of logic function and programmable circuit; thus, it has many applications to FPGAs. The application demonstrated is the FPGA programmable logic block evaluation and the results show that this tool allows radical new features of FPGA logic blocks to be evaluated in a rigorous scientific way.
A Novel Mechanism of Cell Killing by Anti-topoisomerase II Bisdioxopiperazines (2000)

Bisdioxopiperazines are a unique class of topoisomerase II inhibitors that lock topoisomerase II at a point in the enzyme reaction cycle where the enzyme forms a closed clamp around DNA. We examined cell killing by ICRF-187 and ICRF-193 in yeast cells expressing human topoisomerase II alpha (htop-IIalpha). Expression of htop-IIalpha in yeast cells sensitizes them to both ICRF-187 and ICRF-193, compared with cells expressing yeast topoisomerase II. ICRF-193 is still able to exert growth inhibition in the presence of genes encoding both ICRF-193-resistant and ICRF-193-sensitive htop-IIalpha enzymes, indicating that sensitivity to bisdioxopiperazines is dominant. Killing by ICRF-193 occurs more rapidly, than the killing in yeast cells due to a temperature-sensitive yeast topoisomerase II incubated at the non-permissive temperature. These results are reminiscent of a top-II poison such as etoposide. However, the killing caused by ICRF-193 and ICRF-187 is not enhanced by mutations in the RAD52 pathway. The levels of drug-induced DNA cleavage observed with htop-IIalpha in vitro is insufficient to explain the sensitivity induced by this enzyme in yeast cells. Finally, arrest of cells in G(1) does not protect cells from ICRF-193 lethality, a result inconsistent with killing mechanisms due to catalytic inhibition of top-II or stabilization of a cleavable complex. We suggest that the observed pattern of cell killing is most consistent with a poisoning of htop-II by ICRF-193 by a novel mechanism. The accumulation of closed clamp conformations of htop-II induced by ICRF-193 that are trapped on DNA might interfere with transcription, or other DNA metabolic processes, resulting in cell death.
Seaweed-Derived Nontoxic Functionalized Graphene Sheets as Sustainable Materials for the Efficient Removal of Fluoride from High Fluoride Containing Drinking Water (2017)

Herein we present a sustainable and cost-effective approach for the preparation of functionalized graphene nanosheets (GNs) directly from seaweed and deep eutectic solvents (DESs). The seaweed granules remained after the recovery of juice from fresh brown seaweed, Sargassum tenerrimum, was utilized as a raw material and DESs generated by the complexation of choline chloride and metal salts were employed as solvent and catalyst for the large scale and facile production of metal oxide functionalized GNs. Moreover considering the biological application of such GNs, where nontoxic nature of substrates is desirable, we have also evaluated the cytotoxicity of the functionalized GNs (Fe3O4/Fe, SnO2/SnO/Sn, or ZnO/Zn-functionalized GNs), and most of them were found to be nontoxic against human lung carcinoma cells (A549). Thereafter, efficiency of these GNs was assessed for the removal of F– from fluoride contaminated groundwater (2.72–6.71 mg L–1) used for drinking purposes. After treatment with GNs, the concentration of fluoride was found to reduce to 0.36–1.69 mg L–1 (75–87% removal efficiency). Moreover, after recovery of GNs from the water, no significant contamination of metal ions was found in the remaining water. Thus, seaweed-derived nontoxic GNs can be utilized to produce safe drinking water with permissible fluoride content as per World Health Organization (WHO) norms.
A Short and Efficient Synthesis of Mono-substituted 1,4,7-Triazacyclononanes (2003)

Abstract A convenient synthesis of 1,4,7-Triazacyclononane (tacn) derivatives substituted with a single pendant donor group is described. Mono-substituted tacns with a hydroxylalkyl, an aminoalkyl, or a benzyl group are synthesized via efficient cyclization of inexpensive starting materials followed by detosylation.
Mining Trajectories for Spatio-temporal Analytics (2012)

Mining high resolution trajectories from moving vehicles can provide insightful analytics and enable location based decision making. In this paper, we introduce a trajectory mining prototype system to generate the trajectory heat map at aggregated level for the online spatial-temporal analytics. The proposed method is scalable and efficient since we develop a mechanism using a small subset of trajectory points to capture all trajectory patterns. We experimentally verified the applicability and scalability of this system with large scale real world dataset.