gebhart/patrepeval huggingface dataset:
Abstract 2743: Accelerating the exploration of novel gene fusion events in prostate cancer (2010)

Abstract Gene fusions are regarded as cancer defining and often proven causative for cancer development. Up to 50% of prostate cancers harbor recurrent gene fusions, most often the TMPRSS2-ERG fusion. Other ETS gene fusions have been described involving ETV1, ETV4, and ETV5. The remaining prostate cancers are considered gene fusion negative based on fluorescence in-situ hybridization (FISH) or RT-PCR for known fusion specific transcripts. Paired-end RNA-sequencing is a novel approach to systematically interrogate for fusion transcripts in a global and un-biased manner. Herein, we exploit FusionSeq, a computational tool specifically developed to nominate chimeric transcripts from paired-end RNA-seq data, with the goal of identifying new gene fusions. Using FusionSeq we identified the androgen-induced genes FKBP5 and KLK2 as two novel 5′ fusion partners for the ETS genes ERG and ETV1, respectively. General transcriptional chimerism (e.g. read-through transcripts) without evidence of underlying genomic rearrangements is not restricted to prostate cancer but also occurs in the patient's matched benign prostate tissue, providing evidence for an extended complexity of the cellular transcriptome and supporting the notion that a gene's definition might have to be considered flexible. Finally, we report the identification and the validation of two novel gene fusions: i) the tumor suppressor and cell cycle regulator CDKN1A (p21WAF, CIP1) is fused to CD9; besides down-regulating p21 gene expression, the CDKN1A-CD9 fusion also alters the CD9 protein. ii) by fusing IKBKB (IKK2, IκB kinase beta subunit) to TNPO1 (transportin 1), IKBKB gene expression increases over other prostate cancers, suggesting a pronounced activation of the NFκB complex. Our results show that a small subset of prostate cancers may harbor private gene fusions involving tumor suppressors and regulators of pathways implicated in cancer development. 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 2743.
Protection against Oxidative Damage by Iron Chelators:  Effect of Lipophilic Analogues and Prodrugs of N,N‘-Bis(3,4,5-trimethoxybenzyl)ethylenediamine- N,N‘-diacetic Acid (OR10141) (2000)

N,N'-Bis(3,4,5-trimethoxybenzyl)ethylenediamine-N,N'-diacetic acid (1) was recently described as a new type of iron chelator for protection against oxidative damage. It has a low affinity for iron, but the corresponding iron complex undergoes a site-specific oxidation by hydrogen peroxide through intramolecular aromatic hydroxylation into a highly stable iron phenolato complex, which does not catalyze hydroxyl radical formation. The purpose of this local activation process is to minimize toxicity compared to strong iron chelators, which may interfere with normal iron metabolism. 1 efficiently protects biological molecules against oxidative damage in vitro but not intact cells because of poor membrane permeability. We show here that, among a series of prodrug esters and lipophilic analogues, membrane-permeant N,N'-bis(3,4,5-trimethoxybenzyl)ethylenediamine-N,N'-diacetic acid diacetoxymethyl ester (7) protects human skin fibroblasts against hydrogen peroxide toxicity with an IC(50) of 3 microM. These results thus demonstrate that, providing sufficient intracellular chelator concentration is reached, 1 efficiently protects cells against the deleterious effects of hydrogen peroxide. This strategy of oxidative activation should help the design of new chelators with better safety margins, which may be useful against oxidative damage under conditions where a prolonged administration is needed.
Kinetics and 28-day test–retest repeatability and reproducibility of [11C]UCB-J PET brain imaging (2020)

[<sup>11</sup>C]UCB-J is a novel radioligand that binds to synaptic vesicle glycoprotein 2A (SV2A). The main objective of this study was to determine the 28-day test-retest repeatability (TRT) of quantitative [<sup>11</sup>C]UCB-J brain positron emission tomography (PET) imaging in Alzheimer's disease (AD) patients and healthy controls (HCs). Nine HCs and eight AD patients underwent two 60 min dynamic [<sup>11</sup>C]UCB-J PET scans with arterial sampling with an interval of 28 days. The optimal tracer kinetic model was assessed using the Akaike criteria (AIC). Micro-/macro-parameters such as tracer delivery (K<sub>1</sub>) and volume of distribution (V<sub>T</sub>) were estimated using the optimal model. Data were also analysed for simplified reference tissue model (SRTM) with centrum semi-ovale (white matter) as reference region. Based on AIC, both 1T2k_V<sub>B</sub> and 2T4k_V<sub>B</sub> described the [<sup>11</sup>C]UCB-J kinetics equally well. Analysis showed that whole-brain grey matter TRT for V<sub>T</sub>, DVR and SRTM BP<sub>ND</sub> were -2.2% ± 8.5, 0.4% ± 12.0 and -8.0% ± 10.2, averaged over all subjects. [<sup>11</sup>C]UCB-J kinetics can be well described by a 1T2k_V<sub>B</sub> model, and a 60 min scan duration was sufficient to obtain reliable estimates for both plasma input and reference tissue models. TRT for V<sub>T</sub>, DVR and BP<sub>ND</sub> was <15% (1SD) averaged over all subjects and indicates adequate quantitative repeatability of [<sup>11</sup>C]UCB-J PET.
(DURIP-95) Nano-Kelvin Cooling of Dense Atoms for an Ultra-Stable Fountain Atomic Clock. (1997)

Abstract : With the funding provided under this grant, we have procured equipments for creating a sample of 87Rb atoms with ultracold temperature (35 nano-Kelvin) and high density (10(exp 12 /sq cm), using Raman cooling via velocity selective coherent population trapping. We have already been able to create a magneto-optic trap (MOT) of 87Rb atoms, loaded from background rubidium vapor inside the trap chamber. We have achieved a density close to 10(exp 12) /sq cm, at a temperature of 80 mu-K, which is typical of such a trap. The next step is to load the trap from a chirp-slowed atomic beam, and use a repumping beam which is dark at the center. This is expected to increase the density to about 10(exp 12) /sq cm. We will then Raman- cool the sample to about 35 nano-Kelvin, thus yielding a sample for a rubidium fountain clock. The fountain clock loaded from this source is expected to have a short term accuracy that is more than two orders of magnitude better than existing cesium fountain, which are already a factor of two better than existing cesium beam clocks used as primary frequency standards.
Supplementary Figure S1 from CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer (2023)

&lt;p&gt;LDL enhances PC cell growth and assessment of CYP27A1 expression levels in different stages of PC&lt;/p&gt;
Coordination of Autonomous Vehicles and Dynamic Traffic Rules in Mixed Automated/Manual Traffic (2022)

We consider the coordination of multiple connected automated vehicles (CAVs) by a central coordinator (CC) in mixed traffic where also non-controlled vehicles (NCVs) are present. The CC directly provides motion target commands to the CAVs and affects the behavior of NCVs by controlling dynamic traffic rules, such as changing traffic lights. We model the traffic rules for these scenarios by mixed-logical constraints, and the response of the NCVs to the changing traffic rules by a switched system with switches triggered by logic conditions. The proposed approach is implemented as a mixed-integer programming (MIP) problem to be solved in the central coordinator, which also handles timing constraints.
OS0107 Measurement of the friction force between PVA roller brushes and semiconductor wafers with various films in chemicals (2016)

Polyvinyl acetal (PVA) brushes have been widely used in the post CMP cleaning. To better understanding the cleaning mechanisms of PVA brushes, we measured the friction force between PVA roller brushes and semiconductor wafers with various films in chemicals. As a result, the friction force was decreased with increase of pH of chemicals. On the other hand, combinations of W or Cu and NH_4OH only showed large friction force. Furthermore, the friction force was decreased with the increase of the rotation speed in citric acid or ultra pure water. In contrast, the friction force was increased with the increase of the rotation speed in NH_4OH.
Visualizing myosin–actin interaction with a genetically-encoded fluorescent strain sensor (2008)

Many proteins have been shown to undergo conformational changes in response to externally applied force in vitro, but whether the force-induced protein conformational changes occur in vivo remains unclear. To reveal the force-induced conformational changes, or strains, within proteins in living cells, we have developed a genetically encoded fluorescent “strain sensor,” by combining the proximity imaging (PRIM) technique, which uses spectral changes of 2 GFP molecules that are in direct contact, and myosin–actin as a model system. The developed PRIM-based strain sensor module (PriSSM) consists of the tandem fusion of a normal and circularly permuted GFP. To apply strain to PriSSM, it was inserted between 2 motor domains of Dictyostelium myosin II. In the absence of strain, the 2 GFP moieties in PriSSM are in contact, whereas when the motor domains are bound to F-actin, PriSSM has a strained conformation, leading to the loss of contact and a concomitant spectral change. Using the sensor system, we found that the position of the lever arm in the rigor state was affected by mutations within the motor domain. Moreover, the sensor was used to visualize the interaction between myosin II and F-actin in Dictyostelium cells. In normal cells, myosin was largely detached from F-actin, whereas ATP depletion or hyperosmotic stress increased the fraction of myosin bound to F-actin. The PRIM-based strain sensor may provide a general approach for studying force-induced protein conformational changes in cells.
NP Bracketing by Maximum Entropy Tagging and SVM Reranking (2004)

We perform Noun Phrase Bracketing by using a local, maximum entropy-based tagging model, which produces bracketing hypotheses. These hypotheses are subsequently fed into a reranking framework based on support vector machines. We solve the problem of hierarchical structure in our tagging model by modeling underspecified tags, which are fully determined only at decoding time. The tagging model performs comparably to competing approaches and the subsequent reranking increases our system’s performance from an f-score of 81.7 to 86.1, surpassing the best reported results to date of 83.8. 1 Introduction and Prior Work Noun Phrase Bracketing (NP Bracketing) is the task of identifying any and all noun phrases in a sentence. It is a strictly more difficult problem than
JAMES D. DRAKE. The Nation's Nature: How Continental Presumptions Gave Rise to the United States of America. (2012)

James D. Drake's new book offers a valuable and neglected perspective on early America by trying to recapture eighteenth-century understandings of the North American continent. Drake provides an engagingly written narrative that should appeal both to scholars and to some readers outside of the academy. Because most early American historians employ a range of geographic categories that have been imposed by modern scholarship, it is tempting to forget that early Americans participated in their own sophisticated discussions of geography. Drake not only demonstrates an avid contemporary interest in knowledge and theories about the continent, but he also builds a persuasive case for the importance of their implications. Ideas about the North American continent provided a rationale for the expansion of the British Empire, helped to forge an identity for citizens of the new republic, structured debates about federalism in the Constitution, and emboldened American expansionists. These metageographies often revealed more about the aspirations and interests of settlers and authorities than about actual geographic conditions, and at times the contrast between eighteenth-century metageographies and modern understandings of geography could be striking. Before the American Revolution, British colonists viewed the North American continent as particularly well-suited to the expansion of the British Empire and, by extension, less appropriate for others. (At that time, the term “continent” designated a less precise and often smaller piece of land than it does now, enabling British colonists to participate in the process of defining and constructing North America.) Perhaps not surprisingly, the colonists came to view this continent as a space contained enough to be occupied by one power or empire but not vast enough to share. Even earlier than this, however, colonists developed a number of arguments that dismissed Native American claims to the continent, contending, in essence, that the British newcomers were in fact more naturally suited to rule North America than the continent's indigenous peoples. While British colonists emphasized that the continent was especially well-made for the British character, the Seven Years' War made clear that Britain and not France would rule it.
Serial Time Encoded Amplified Microscopy (2009)

We present an imaging method that maps a 2D image into a serial time-domain waveform and simultaneously amplifies it optically. Continuous real-time images at a record frame rate of 6.1 MHz are captured using an oscilloscope.
Elementary Problems: E1243, E2440, E2652, E2665-E2670 (1977)

Sidney Penner, Peter Frankl, John R. Samborski, Ron Evans, I. Martin Isaacs, I. J. Schoenberg, Shyam Johari, Stanley L. Sclove, Elementary Problems: E1243, E2440, E2652, E2665-E2670, The American Mathematical Monthly, Vol. 84, No. 7 (Aug. - Sep., 1977), pp. 567-568
A Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial of the Efficacy and Safety of the Oral Soluble Guanylate Cyclase Stimulator (2017)

This trial sought to evaluate whether vericiguat, a novel oral soluble guanylate cyclase (sGC) stimulator, was superior to placebo, on a background of standard of care, in increasing the time to the first occurrence of the composite endpoints of cardiovascular (CV) death and heart failure (HF) hospitalization in patients with HF with reduced ejection fraction (HFrEF). Deficiency in sGC-derived cyclic guanosine monophosphate (cGMP) causes both myocardial dysfunction and impaired endothelium-dependent vasomotor regulation that includes the myocardial microcirculation. Experimental studies have suggested multiple potential benefits of sGC stimulators including prevention, or even reversal, of left ventricular hypertrophy and fibrosis, as well as reduction of ventricular afterload through both systemic and pulmonary vasodilation. Hence, restoration of sufficient nitric oxide (NO)-sGC-cGMP signaling has been proposed as an important treatment target in HF. Vericiguat has been shown to directly stimulate sGC and enhance sGC sensitivity to endogenous NO. Available phase IIb data in HFrEF patients indicate vericiguat is safe and well-tolerated, and exploratory analyses indicate that it results in a dose-dependent, clinically significant reduction in N-terminal pro-B-type natriuretic peptide (NT-proBNP) at the highest tested dose. VICTORIA (Vericiguat Global Study in Subjects With Heart Failure With Reduced Ejection Fraction) is a randomized, placebo-controlled, parallel group, multicenter, double-blind, event-driven phase 3 trial of vericiguat in subjects with HFrEF. Approximately 4,872 subjects will be randomized to evaluate the efficacy and safety of vericiguat compared with placebo on a background of standard of care. After a screening phase of up to 30 days, eligible subjects will be treated until the required number of cardiovascular deaths is observed. The estimated median follow-up duration is approximately 18 months. All subjects will be followed until study completion to assess for the occurrence of endpoint events. VICTORIA will establish the efficacy and safety of vericiguat on cardiovascular death and HF hospitalization in patients with HFrEF. (A Randomized Parallel-Group, Placebo-Controlled, Double-Blind, Event-Driven, Multi-Center Pivotal Phase III Clinical Outcome Trial of Efficacy and Safety of the Oral sGC Stimulator Vericiguat in Subjects With Heart Failure With Reduced Ejection Fraction [HFrEF]-VerICiguaT Global Study in Subjects With Heart Failure With Reduced Ejection Fraction [VICTORIA]; NCT02861534).
The evaluation of speckle contrast with variable speckle generator (2011)

Abstract— While laser projection has many advantages, there is a problem with speckle patterns generated as a result of interference of the laser beam and results in bad effects to observers. In 2010, a variable speckle generator, which produces an angular shift of incident light to the screen and generates variable speckle patterns, was suggested. In this study, the performance of a variable speckle generator by using a volume phase holographic beam shaper and scanning mirror was investigated in detail by evaluating both the objective and subjective speckle contrast. The morphology of the speckle pattern was also investigated when the variable speckle generator was activated. With a scanning VPH beam shaper, the objective speckle was effectively reduced because each point of the VPH beam shaper generated different speckle patterns and coherency among each pattern disappeared by using the scan process. On the other hand, subjective speckle was also dramatically reduced by changing the incident angle on the screen, which resulted in generating variable subjective speckle. It was also shown that the speckle reduction rate by using a variable speckle generator did not depend on the coherent length of a laser by evaluating the normalized speckle contrast against the angular shift on the screen.
Dihydroxyboryldeoxyuridine (DBDU); can a borated nucleoside deceive the DNA molecule (1985)

The possibility of using a boronated analog of thymidine for Neutron Capture Therapy (NCT) is intriguing, as the boron is targeted to the cell's most sensitive location. Such an analog has been synthesized in the form of dihydroxyboryldeoxyuridine (DBDU). Data are presented indicating that DBDU is indeed incorporated in the nucleus, and that significant radiosensitization is produced in cell cultures as a consequence of this uptake. The results demonstrate that cells exposed to DBDU for 1 cell cycle incorporate an amount of boron such that the resultant biological effect is equivalent to a boron concentration of 6 ..mu..g /sup 10/B/g cell. Other studies have shown that it should be possible to effect successful BNCT with a boron concentration of approx.15 ..mu..g /sup 10/B/g cell (with an epithermal neutron beam; thermal beams would require more; reference 1). Thus it would appear that DBDU is capable of delivering boron concentrations approaching that which should be useful for therapy. 7 refs.
Toward the Digital Design Studio: Large Display Explorations (2009)

ABSTRACT Inspired by our automotive and product design customers using large displays in design centers, visualization studios, and meeting rooms around the world, we have been exploring the use and potential of large display installations for almost a decade. Our research has touched on many aspects of this rich design space, from individual tools to complete systems, and has generally moved through the life cycle of a design artifact: from the creation phase, through communication and collaboration, to presentation and dissemination. As we attempt to preserve creative flow through the phases, we introduce social structures and constraints that drive the design of possible point solutions in the larger context of a digital design studio trail environment built in the lab. Although many of the interactions presented are viable across several design phases, this article focuses primarily on facilitating collaboration. We conclude with critical lessons learned of both what avenues have been fruitful and which roads to avoid. This article lightly covers the whole design process and attempts to inform readers of key factors to consider when designing for designers.
Tetrahedral Oxyanions in Halogen-Bonded Coordination Networks (2011)

The deliberate construction of (6,3) networks via halogen bond-driven self-assembly of tetra-n-butylammonium perchlorate, periodate, and perrhenate with 1,4-diiodotetrafluorobenzene is reported. The mononegative oxyanions sit at network nodes and work as tridentate halogen bond (XB) acceptors, the diiodobenzene derivative spaces the nodes and function as a bidentate XB donor, while the ammonium cations occupy the space encircled by the supramolecular (6,3) frames. Mixed crystals wherein two different oxyanions statistically occupy the network nodes have also been obtained and show geometrical parameters intermediate to the corresponding pure crystals containing only one of the two oxyanions. Mononegative tetrahedral oxyanions are thus demonstrated to behave as general and effective tectons in anion coordination and anion-templated assembly driven by halogen bonding.
One-Year Feasibility Study of Replenish MicroPump for Intravitreal Drug Delivery: A Pilot Study (2014)

The results of this study in a Beagle dog model are supportive of the biocompatibility of Replenish MicroPump and pave the way to the use of these devices for ocular automated drug delivery after further testing in larger animal models.
Influence of surface modification and long-term exposure on mechanical creep properties of γ-TiAl G4 (2009)

An investigation of the corrosion processes were performed for coated and uncoated γ-TiAl G4, an alloy designed to work in the temperature range 750 – 800°C, where oxidation and corrosion phenomena occur. An aluminising pack cementation treatment was used to improve the oxidation resistance of this γ-TiAl G4 alloy. Cyclic corrosion tests were performed at 800°C in air for up to 800 1-hour cycles with a Na2SO4/NaCl mixture. The influence of both aluminisation and the corrosion phenomena on the creep behaviour was investigated. The cyclic corrosion resistance of the coated γ- TiAl G4 was shown to be improved by aluminising. The pack cementation treatment had no detrimental effect on the creep behaviour. Moreover, neither is creep affected by the corrosion of coated specimens. As corroded uncoated specimen exhibited good creep behaviour, it can be concluded that this alloy is suitable, even without coating, for turbine applications in hot corrosion atmospheres at least up to 800°C.
Method for modeling decoherence on a quantum-information processor (2003)

We develop and implement a method for modeling decoherence processes on an N-dimensional quantum system that requires only an ${N}^{2}$-dimensional quantum environment and random classical fields. This model offers the advantage that it may be implemented on small quantum-information processors in order to explore the intermediate regime between semiclassical and fully quantum models. We consider in particular ${\ensuremath{\sigma}}_{z}{\ensuremath{\sigma}}_{z}$ system-environment couplings which induce coherence (phase) damping, although the model is directly extendable to other coupling Hamiltonians. Effective, irreversible phase damping of the system is obtained by applying an additional stochastic Hamiltonian on the environment alone, periodically redressing it and thereby irreversibliy randomizing the system phase information that has leaked into the environment as a result of the coupling. This model is exactly solvable in the case of phase damping, and we use this solution to describe the model's behavior in some limiting cases. In the limit of small stochastic phase kicks the system's coherence decays exponentially at a rate that increases linearly with the kick frequency. In the case of strong kicks we observe an effective decoupling of the system from the environment. We present a detailed implementation of the method on a nuclear magnetic resonance quantum-information processor.