gebhart/patrepeval huggingface dataset:
Prevention of tissue damage by water jet during cavitation (2003)

Cavitation bubbles accompany explosive vaporization of water following pulsed energy deposition in liquid media. Bubbles collapsing at the tip of a surgical endoprobe produce a powerful and damaging water jet propagating forward in the axial direction of the probe. We studied interaction of such jet with tissue using fast flash photography and modeled the flow dynamics using a two-dimensional Rayleigh-type hydrodynamic simulation. Maximal velocity of the jet generated at pulse energies of up to 1 mJ was about 80 m/s. The jet can produce tissue damage at a distance exceeding the radius of the cavitation bubble by a factor of 4. We demonstrate that formation of this flow and associated tissue damage can be prevented by application of the concave endoprobes that slow down the propagation of the back boundary of the bubble. Similar effect can be achieved by positioning an obstacle to the flow, such as a ring behind the tip.
Experimental Approaches for Controlling Current Flowing through Metal–Molecule–Metal Junctions (2006)

Abstract Two experimental approaches that enable control of current flow through metal–molecules–metal junctions are described. A number of studies using two‐electrode metal–molecules–metal junctions have shown that the current between the electrodes depends on the structures of the incorporated molecules. When a tunneling mechanism dominates electron transport through organic molecules, the molecules behave similar to resistors with resistivities that can be controlled by changing the structure. Incorporation of molecules with increasing conjugation into Hg‐based junctions increases the current flow dramatically. Alternatively, by using four‐electrode electrochemical junctions that allow the potential of the electrodes to be controlled with respect to the energy levels of the incorporated molecules, it is possible to change the mechanism of electron transfer and produce abrupt increases in the current flow. These signals, analogous to solid‐state diodes, are particularly significant for molecular electronics. Electrochemical junctions also permit prediction of the value of the applied potential at which the current will start taking off and to identify the mechanism of charge transport. New and recently published results obtained using junctions based on Hg electrodes in an “electrochemical” mode show that two junctions incorporating redox centers by different interactions behave as current switches, with the current flow dominated by different charge‐transport mechanisms.
Evidence for the Stochastic Integration of Gene Trap Vectors into the Mouse Germline (1997)

A large scale insertional mutagenesis experiment was performed in embryonic stem (ES) cells by introducing two types of gene trap vectors into the genome. These cell lines carrying mutations were introduced into the mouse germline. In order to assess the feasibility of a large scale cloning of the targeted genes from these lines, we have isolated and characterized 55 trapped exons from the corresponding ES cells. Analysis of the data has revealed that vectors containing or lacking an internal ribosome entry site (IRES) can integrate into the ES cell genome stochastically. The targeted genes comprise 30% known genes, 20% expressed sequence tags (ESTs) and 50% novel or unknown genes. The known genes belong to several major classes and represent complete or partial knockouts. Using currently available methods or modifications of them, it should be feasible to do a large scale cloning of trapped genes from the mouse ES cell lines.
SBS limitation on a spectrum-sliced fiber-amplifier light source (1995)

Recently, we proposed a spectrum-sliced fiber-amplifier light source for multichannel WDM systems.1 The high-power ASE from an EDFA, which is already in the single-mode fiber, could be efficiently divided into many channels by using integrated-optic WDM demultiplexers.2 Thus, this spectrum-sliced ASE could be used as a light source for WDM systems in place of several wavelength-selected DFB lasers. To demonstrate the principle, we showed that the spectrum-sliced ASE source could be used for transmission of 1.7-Gbit/s data. The application of these light sources is not limited to local-loop networks. In this paper we show that when the spectrum-sliced fiber-amplifier light source is used, it is possible to launch high optical power (&gt;22 dBm) into the single-mode optical fiber without the limitation imposed by stimulated Brillouin scattering (SBS)
Projector-based three dimensional graphics (2002)

Light projectors can be arranged into electronic displays that offer large, bright, and high resolution images. However, despite their unique characteristics, projectors have been treated like any other two-dimensional display devices, e.g. CRT monitors or LCD panels, to create flat and usually rectangular images. Even the growth of three dimensional computer graphics has followed this limitation. To improve and widen the range of applications of projectors, in this dissertation I present a single unified geometric framework for projector-based graphics. It is based on the notion of the projector as the dual of a camera. The geometric framework is based on (i) the analytical projection model, (ii) the geometric representation of the display surface and (iii) the viewer location. The framework can be used for practically all the projector-based applications. For classic projectorbased systems, such as tiled displays or immersive panoramic displays, the framework provides a fundamentally different approach that allows greater freedom and flexibility. In addition, it enables a new class of projector-based visualization methods.
Understanding chemical and physical mechanisms in atomic layer deposition (2020)

Atomic layer deposition (ALD) is a powerful tool for achieving atomic level control in the deposition of thin films. However, several physical and chemical phenomena can occur which cause deviation from "ideal" film growth during ALD. Understanding the underlying mechanisms that cause these deviations is important to achieving even better control over the growth of the deposited material. Herein, we review several precursor chemisorption mechanisms and the effect of chemisorption on ALD growth. We then follow with a discussion on diffusion and its impact on film growth during ALD. Together, these two fundamental processes of chemisorption and diffusion underlie the majority of mechanisms which contribute to material growth during a given ALD process, and the recognition of their role allows for more rational design of ALD parameters.
Oral eltanexor treatment of patients with higher-risk myelodysplastic syndrome refractory to hypomethylating agents (2022)

Patients with higher-risk myelodysplastic syndromes (MDS) refractory to hypomethylating agents (HMAs) have limited therapeutic options and an expected overall survival (OS) of 3-5 months. Eltanexor is an investigational oral selective inhibitor of nuclear export with low central nervous system penetrance and an acceptable tolerability profile. Preclinical studies suggest that myeloid malignancies are sensitive to nuclear export inhibition. Eltanexor exhibited efficacy in hematologic models, supporting exploration in a clinical trial. This phase 1/2 study (NCT02649790) assessed single-agent activity of eltanexor in patients with higher-risk MDS and 5-19% myeloblasts. Two starting doses of eltanexor were evaluated: 20 mg (n = 15), 10 mg (n = 5), both administered on days 1-5 each week of a 28-day cycle. Twenty patients with primary HMA-refractory MDS, with a median age of 77 years (range 62-89), and a median of two prior treatment regimens (range 1-4) were enrolled. Of these, 15 were evaluated for efficacy and 20 for safety. The overall response rate (ORR) was 53.3%, with seven patients (46.7%) achieving marrow complete remission (mCR) and one additional patient achieving hematologic improvement (HI). In the 10 mg group, three patients (60%) reached mCR and two (40%) stable disease (SD), while for 20 mg, four patients (40%) had mCR and two (20%) SD. A total of three patients (20%) had HI and became transfusion independent ≥ 8 weeks. Median OS for the efficacy-evaluable patients (n = 15) was 9.86 months (7.98, NE). Overall, the most frequently reported treatment-related adverse events were nausea (45%), diarrhea (35%), decreased appetite (35%), fatigue and neutropenia (both 30%). Single-agent oral eltanexor was active, safe, and well tolerated in patients with higher-risk, primary HMA-refractory MDS.
Recombinant T cell receptors specific for HLA-A*02:01-restricted neoepitopes containing KRAS codon 12 hotspot mutations (2020)

Abstract KRAS codon 12 mutations are among the most common hotspot mutations in human cancer. Using a functional screening platform we set out to identify αβ T-cell receptors (TCRs) as potential targeting reagents for KRAS G12D and/or KRAS G12V neoepitopes presented by the prevalent HLA-A*02:01 allele. Here we describe isolation and characterization of three distinct CD8 + T cell clones from a pre-treated 76 year old patient with pancreatic ductal adenocarcinoma (PDAC). One clone was KRAS G12V reactive and two clones were KRAS G12D reactive. Tetramer staining showed high specificity of each T cell clone for its cognate HLA-A*02:01 restricted KRAS G12V or KRAS G12D neoepitope (&gt;98% tetramer positive) without appreciable cross-reactivity to wild-type KRAS (&lt;2% tetramer positive). We amplified and sequenced the full-length TCR alpha and beta chains from each of the three T cell clones and determined that these three TCRs comprised distinct combinations of two different TCR alpha chains and two distinct TCR beta chains. We resynthesized these TCR alpha and beta chain nucleotide sequences and reconstituted the original pairs in healthy donor CD8 + T cells by lentiviral transduction, substituting the human αβ TCR constant gene segments with murine αβ TCR constant gene segments to prevent mispairing with endogenous TCR subunits. Tetramer analysis and IFN-γ ELISpot analysis confirmed the specificity of each reconstituted TCR for its cognate HLA-A*02:01 restricted KRAS neoepitope. To test cytolytic activity TCR-transduced healthy donor CD8 + T cells were co-cultured with KRAS G12V , KRAS G12D or KRAS wt peptide-pulsed K562-HLA-A*02:01 antigen presenting cells at an effector to target cell ratio of 4:1. Under these conditions we observed neoepitope-specific killing of 16.5% to 19.0% of target cell populations. To assess in vivo activity we developed a KRAS G12V /A*02:01 patient-derived xenograft (PDX) mouse model. Over a 56-day period, PDX bearing mice infused with human TCR-transduced T cells had significantly reduced tumor growth and longer survival compared to mice infused with non-transduced control T cells. In conjunction with other therapeutic approaches, immune effector cell therapies expressing these TCRs may improve outcomes for HLA-A*02:01 patients with KRAS G12V and/or KRAS G12D positive tumors.
Space-borne optical communications - a challenging reality (2003)

Optical inter-satellite links (ISLs) have recently become operational reality. We outline potential commercial applications, focusing on broadband mobile communication networks with global coverage, and discuss some design issues and trade-offs for optical ISLs.
Temporal and sequential changes of glial cells and cytokine expression during neuronal degeneration after transient global ischemia in rats (2011)

Ischemic stress in 4VO activated glial cells in areas beyond CA1 in the lag phase. Pyramidal neurons were injured in CA1 from the end of the lag phase and then neuronal cells reduced in CA1 in the exponential phase. After neuronal death began, the influence of dead cells on glial cells and cytokine expression gradually became stronger than the influence by ischemic stress. Therefore, from the deceleration phase, changes in glial cells and cytokine production were likely caused by dead cells. Cytokine interaction in the microenvironment may determine the functions of IL-1α, IL-1β, IL-4, IL-6 and IFN-γ in all four phases. The function of GM-CSF and TNF-α in the deceleration phase may be neurotrophic.
Supplementary Table 1 from Somatic <i>ERCC2</i> Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma (2023)

&lt;p&gt;Treatment information and sequencing metrics for all patients The treatment information and raw sequencing metrics, including mean target coverage, for each case is listed here. In addition, the mutation rate data referred to in the Results and represented in Supplementary Figure 1 is listed here by synonymous rate, non-synonymous rate, and total number of mutations per patient. *Cases that were included in the TCGA effort (UC-0296 and UC-0234). (dd = dose dense, GC = gemcitabine/cisplatin, MVAC = methotrexate, vinblastine, doxorubicin, cisplatin). Unavailable cases for Fluidigm Validation (due to inadequate remaining DNA or technical failure) are also denoted (n = 15).&lt;/p&gt;
Role of tautomerism in RNA biochemistry (2014)

Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solvent-exchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.
Performance and Reliability of Deep-Ultraviolet Light-Emitting Diodes Fabricated on AlN Substrates Prepared by Hydride Vapor Phase Epitaxy (2013)

The reliability and output power of AlGaN-based deep-ultraviolet light-emitting diodes (DUV-LEDs) fabricated on AlN substrates prepared by hydride vapor phase epitaxy are reported. TEM analysis revealed that dislocation density in LED layers, except the p-GaN layer, was below 106 cm-2. DUV-LEDs emitting at 261 nm exhibited an output power of 10.8 mW at 150 mA. The lifetime of these LEDs was estimated to be over 10,000 h for cw operation at 50 mA. No significant acceleration of output power decay at higher operation currents was observed. The estimated lifetime at the operation current of 150 mA was over 5,000 h.
Classifying Music-Related Actions (2012)

Our research on music-related actions is based on the conviction that sensations of both sound and body motion are inseparable in the production and perception of music. The expression "musicrelated actions" is here used to refer to chunks of combined sound and body motion, typically in the duration range of approximately 0.5 to 5 seconds. We believe that chunk-level music-related actions are highly significant for the experience of music, and we are presently working on establishing a database of music-related actions in order to facilitate access to, and research on, our fast growing collection of motion capture data and related material. In this work, we are confronted with a number of perceptual, conceptual and technological issues regarding classification of musicrelated actions, issues that will be presented and discussed in this paper.\nProceedings of the ICMPC-­ESCOM 2012 Joint Conference: 12th Biennial International Conference for Music Perception and Cognition, 8th Triennial Conference of the European Society for the Cognitive Sciences of Music. 2012 Thessaloniki, Greece, July 23–28.
Potential antitumor agents. 41. Analogs of amsacrine with electron-donor substituents in the anilino ring (1984)

The preparation and antitumor activity of a series of 3'-alkylamino and 3'-dialkylamino analogues of amsacrine are reported. The results support previous work suggesting that the presence of electron-donating groups in the 3'-position of the anilino ring substantially enhance the antitumor activity of amsacrine analogues, possibly by the provision of high levels of electron density at the 6'-position. The alkylamino derivatives generally possess tighter DNA binding, higher levels of in vitro and in vivo antileukemic activity, and greater aqueous solubility than the corresponding amsacrine analogues.
Repetitive surge current test of SiC MPS diode with load in bipolar regime (2018)

The reliability of power diodes under surge current is an important factor that has to be taken into account for power electronic applications. In this work, latest generation SiC MPS (Merged Pin Schottky) diodes (650V, 1200V, 1700V) with different current classes from Infineon are exposed to repetitive high surge current stress. Furthermore, the temperature was estimated using different methods including direct measurement, Sentaurus TCAD simulation, Cauer network and an analytical model using temperature dependent mobility. It was found that the diodes could withstand a high number of high-current pulses. However, before reaching final destruction, different ageing phenomenon were observed at the unipolar and bipolar regime of the MPS diode. A detailed investigation on the aging mechanisms including failure analysis was performed.
Multi-hole Defect Photonic Crystals with Enhanced Surface Area for Biosensing Applications (2013)

Multi-hole defect (MHD) photonic crystal cavities functionalized with in situ synthesized DNA bioreceptors are demonstrated for biosensing applications. By significantly increasing light interaction with target biomolecules in the MHD region, improved detection sensitivity is achieved.
Max-min Fair Resource Allocation in SD-RAN (2022)

Software-Defined Radio Access Networks (SD-RANs), introduced for the first time in 5G networks, symbolize a paradigm shift in the way the allocation of cellular network resources is performed. The main feature of SD-RAN is the possibility to decouple the control plane from the data plane, and associating the former with a controller that is located away from the Base Stations (BSs). This enables an increased flexibility in the allocation of network resources, resulting in considerable performance improvements compared to the classical pre-5G resource allocation in cellular networks. However, it is not yet clear to what extent this enhancement ranges in terms of different metrics of interest and optimization objectives. One such objective is to allocate resources so that the minimum value of the data rate in the network is maximized, i.e., to provide max-min fairness. Therefore, in this paper, we consider analytically the problem of max-min fairness in an SD-RAN environment by deriving the policy which accomplishes that along with the achievable performance, of interest to users and cellular operators. We do this for two scenarios; one in which we provide max-min fairness across all users in the network, and the other in which the goal is to provide max-min fairness in throughput across BSs, and within users of each BS. We evaluate the performance with input parameters from real data sets. Results show that the introduction of SD-RAN improves the minimum rate by up to 4× compared to the case with no SD-RAN controller.
Any-time clustering of high frequency news streams (2007)

We describe a large scale system for clustering a stream of news articles that was developed as part of the Geospace &amp;amp; Media Tool (GMT). The GMT integrates the news feed with geospatial, census, and human network information to provide a research tool for members of Congress and their staffs. News articles covering the same event are summarized for the user through the clustering component. The clustering result is available to the user at any time without additional on-demand clustering steps. The documents are grouped into clusters on-the-fly without any assumptions on the number of clusters and without retrieving previous documents. High efficiency is achieved by utilizing locality sensitive hashing (LSH) as a means to determine a small set of candidate clusters for each document. This way a large number of clusters can be considered while keeping the number of expensive document to cluster comparisons low. Our experiments with the system reveal interesting aspects of large-scale text processing in general and news clustering in particular. We demonstrate how the LSH based approximation achieves a large speedup at the cost of only few and small errors. On a high-frequency benchmark data set a clustering quality comparable to one of the best non-streaming document clustering algorithms is obtained.
Reconstructing Loopy Curvilinear Structures Using Integer Programming (2013)

We propose a novel approach to automated delineation of linear structures that form complex and potentially loopy networks. This is in contrast to earlier approaches that usually assume a tree topology for the networks. At the heart of our method is an Integer Programming formulation that allows us to find the global optimum of an objective function designed to allow cycles but penalize spurious junctions and early terminations. We demonstrate that it outperforms state-of-the-art techniques on a wide range of datasets.
Cognitive neuropsychology is more than single-case studies. (1993)

S. M. Sokol et al. (1991) claim that "The Cognitive Neuropsychology Approach" (p. 355) is limited to the single-case study design. The present article takes issue with this claim. Contrary to the beliefs of Sokol et al., we argue (a) that cognitive modularity is best studied by group design, (b) that the possibility of neural reorganization in patients should be tested through converging evidence from different populations using various methods, and (c) that cognitive neuropsychology can benefit from being a part of cognitive neuroscience where both neural and cognitive mechanisms underlying normal cognition are relevant.
Nitridation Kinetics and Thermodynamics of Silicon Powder Compacts (1991)

The nitridation kinetics of Si powder compacts were studied by measuring the flow rate dependence of N 2 and N 2 –H 2 gas mixtures during slow heating of Si compacts while simultaneously monitoring the oxygen partial pressure of the egress gas. The reaction was found to occur in two distinct stages. In pure nitrogen the initial stage was interpreted in terms of devitrification of the native silica layer, catalyzed by Fe impurities, and the exposure of the underlying Si. The reaction sequence at that point has been unequivocally shown to be image followed by the formation of oxynitride according to image as evidenced by a large increase in the oxygen partial pressure simultaneously with the onset of the initial stage. In the absence of hydrogen, both reactions are rapidly suppressed as the oxygen liberated competes with the nitrogen for the exposed silicon surface and reoxidizes it. However, in the presence of hydrogen, the oxygen liberated reacts with the hydrogen and prevents the reoxidation of the Si. The net reaction in this case is image and/or image with the second reaction being thermodynamically favored. The main nitridation reaction occurring between 1300° and 1400°C appears to be diffusion controlled and depends on the nature of the passivating layer that forms during the initial stage.