gebhart/patrepeval huggingface dataset:
Abstract 2004: Nucleation of transcriptional super-enhancers at tumor oncogenes by small insertions (2016)

Abstract Transcriptional super-enhancers drive expression of oncogenes in many cancers and are being targeted with novel transcriptional and epigenetic therapeutics[1,2,3,4]. Super-enhancers are acquired by cancers through multiple mechanisms, including DNA translocation of an extant super-enhancer and focal amplification. We recently discovered a novel mechanism by which super-enhancers are nucleated in T cell acute lymphoblastic leukemias (T-ALLs)[5]. In this case, a small, monoallelic insertion creates a DNA binding site for a master transcription factor protein, which binds and recruits additional factors to nucleate the super-enhancer, which in turn drives high levels of the TAL1 oncogene. We describe here a method for unbiased identification of similar genomic insertions that nucleate potentially oncogenic regulatory elements in cancers. This approach uses data from genome-wide ChIP-Seq studies that map locations of enhancer-binding proteins to identify short DNA sequences missing from reference genomes. We have found and catalogued many additional genomic insertions in 80 additional cancers. An additional insertion has been functionally characterized and determined to be a bona fide enhancer-nucleating insertion that exists in patient genomes. I will describe new insights into the regulation of cancer that occur due to nucleation of novel regulatory elements. [1] Hnisz, Abraham, Lee, et al., Cell 2013 [2] Loven, Hoke, Lin, et al., Cell 2013 [3] Kwiatkowski, et al., Nature, 2014 [4] Wang, et al., Cell, 2015 [5] Mansour et al., Science 2014 Citation Format: Brian J. Abraham, Denes Hnisz, Abraham S. Weintraub, Nicholas Kwiatkowski, Charles H. Li, Sunniyat Rahman, Zhaodong Li, Tong Ihn Lee, A Thomas Look, Marc Mansour, Richard A. Young. Nucleation of transcriptional super-enhancers at tumor oncogenes by small insertions. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2004.
DETAILED MECHANICS OF FLEXURAL RC COLUMN DEFORMATION UP TO REBAR YIELDING (2023)

Yield displacement is an important parameter in appropriately evaluating a seismic capacity of a building. To understand the detailed mechanics of flexural column deformation up to yielding of flexural rebar, deformation characteristics are measured with high resolution in a static loading test of five column specimens. Measured horizontal displacements are, then, separated into three displacement components, i.e., flexural displacement, shear displacement, and anchorage displacement, to find they are well simulated by classical flexural theory based on Bernoulli-Euler assumption, elastic shear theory considering uncracked horizontal section, and elastic deformation theory of stub considering flexural stress transferred from the column, respectively.
Optimal Design of Energy-Efficient Cell-Free Massive Mimo: Joint Power Allocation and Load Balancing (2020)

A large-scale distributed antenna system that serves the users by coherent joint transmission is called Cell-free Massive MIMO (multiple input multiple output). For a given user set, only a subset of the access points (APs) is likely needed to satisfy the users' performance demands. To find a flexible and energy-efficient implementation, we minimize the total power consumption at the APs in the downlink, considering both the hardware and transmit powers, where APs can be turned off. Even though this is a non-convex optimization problem, a globally optimal solution is obtained by solving a mixed-integer second-order cone program. We also propose a low-complexity algorithm that exploits group-sparsity in the problem formulation. Numerical results manifest that our optimization framework can greatly reduce the power consumption compared to keeping all APs turned on and only minimizing the transmit powers.
Huygens absorbing boundary condition (2014)

The Finite Difference Time Domain (FDTD) method is popular for solving Maxwell's equations in time domain. The FDTD domains are usually open regions. For practical applications, since no computer can store infinite data, the FDTD method had to introduce Absorbing Boundary Conditions (ABCs). The ABCs should be able to absorb the outgoing waves and simulate the extension to infinity. The Complex Frequency-Shifted Perfectly Matched Layer (CFS-PML) ABCs (M. Kuzuoglu and R. Mittra. Frequency Dependence of the Constitutive Parameters of Causal Perfectly Matched Absorbers. IEEE Micr. Guid. Wave Let., 6(12):447449, Dec. 1996) has been the most widely used and effective ABC since it perfectly absorbs the outgoing waves. However, the implementation of the CFS-PML is complicated and requires more computational resources. The Huygens Absorbing Boundary Condition (HABC) (J.-P. Bérenger. On the Huygens Absorbing Boundary Conditions for Electromagnetics. J. Comp. Phys., 226:354378, 2007) was recently introduced by Jean-Pierre Bérenger. The HABC is simpler to implement than the CFS-PML. Also, the HABC is proofed to be comparable in accuracy with the CFS-PML.
Optical phased arrays with evanescently-coupled antennas (2023)

An optical phased array formed of a large number of nanophotonic antenna elements can be used to project complex images into the far field. These nanophotonic phased arrays, including the nanophotonic antenna elements and waveguides, can be formed on a single chip of silicon using complementary metal-oxide-semiconductor (CMOS) processes. Directional couplers evanescently couple light from the waveguides to the nanophotonic antenna elements, which emit the light as beams with phases and amplitudes selected so that the emitted beams interfere in the far field to produce the desired pattern. In some cases, each antenna in the phased array may be optically coupled to a corresponding variable delay line, such as a thermo-optically tuned waveguide or a liquid-filled cell, which can be used to vary the phase of the antenna's output (and the resulting far-field interference pattern).
Monoclonal Antibody Production using Free-suspended and Entrapped Hybridoma Cells (1994)

(1994). Monoclonal Antibody Production using Free-suspended and Entrapped Hybridoma Cells. Biotechnology and Genetic Engineering Reviews: Vol. 12, No. 1, pp. 509-534.
Movie Review of The Immortal Life of Henrietta Lacks (2017)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Autopsy findings in HIV-infected inner-city patients. (1992)

To assess the importance of the autopsy in HIV-1 infection, we retrospectively reviewed the autopsy reports of 70 HIV-1-seropositive patients at Howard University Hospital. Of the 58 patients with AIDS, the diagnosis of AIDS was made after autopsy in 24 (41%) cases. The lung was the most common site of AIDS-diagnostic diseases, and was affected in 90% of patients. Pneumocystis carinii infection was the most common AIDS-diagnostic disease, and was present in 50% of the AIDS patients. Thirty-eight percent of AIDS diagnostic diseases were diagnosed antemortem, including 15 of the 29 Pneumocystis carinii infections. Most of the AIDS-diagnostic diseases were disseminated at autopsy and two or more diseases were found in some organs. Overall, Pneumocystis carinii pneumonia was the most common cause of death, accounting for a mortality of 43% among AIDS patients. Bacterial infections were common and contributed to the mortality and morbidity of both AIDS and non-AIDS patients. Bacterial infection was the cause of death in 15 AIDS and 9 non-AIDS patients. The clinical cause of death concurred with the pathological cause in 53% of our cases.
Nominal group technique to select attributes for discrete choice experiments: an example for drug treatment choice in osteoporosis (2013)

Background: Attribute selection represents an important step in the development of discrete-choice experiments (DCEs), but is often poorly reported. In some situations, the number of attributes identified may exceed what one may find possible to pilot in a DCE. Hence, there is a need to gain insight into methods to select attributes in order to construct the final list of attributes. This study aims to test the feasibility of using the nominal group technique (NGT) to select attributes for DCEs. Methods: Patient group discussions (4–8 participants) were convened to prioritize a list of 12 potentially important attributes for osteoporosis drug therapy. The NGT consisted of three steps: an individual ranking of the 12 attributes by importance from 1 to 12, a group discussion on each of the attributes, including a group review of the aggregate score of the initial rankings, and a second ranking task of the same attributes. Results: Twenty-six osteoporotic patients participated in five NGT sessions. Most (80%) of the patients changed their ranking after the discussion. However, the average initial and final ranking did not differ markedly. In the final ranking, the most important medication attributes were effectiveness, side effects, and frequency and mode of administration. Some (15%) of the patients did not correctly rank from 1 to 12, and the order of attributes did play a role in the ranking. Conclusion: The NGT is feasible for selecting attributes for DCEs. Although in the context of this study, the NGT session had little impact on prioritizing attributes, this approach is rigorous, transparent, and improves the face validity of DCEs. Additional research in other contexts (different decisional problems or different diseases) is needed to determine the added value of the NGT session, to assess the optimal ranking/rating method with control of ordering effects, and to compare the attributes selected with the different approaches. Keywords: discrete choice experiment, nominal group technique, patient preference, medication attributes, osteoporosis
Oxidative Removal of Self-Assembled Monolayers for Selective Atomic Layer Deposition (2008)

Using atomic force microscopy (AFM) lithography and self-assembled monolayer (SAM), selective atomic layer deposition (ALD) of ZrO2 was performed to fabricate nanostructures. SAM layer was used for a chemical mask for ZrO2 ALD process and AFM lithography for a nano-scale patterning method. AFM anodic oxidation process was applied to create oxide patterns on ODTS-coated silicon substrates. Subsequent HF etching locally removes oxide, exposing silicon layer underneath. After 100 cycles of ZrO2 ALD process and an oxygen plasma etching, ZrO2 ALD nanostructure of 4~7 nm in height and ~130 nm in line width were fabricated. A growth rate of 0.4~0.7 Aå per cycle is estimated from the AFM scanning at each step, which is slightly less than the typical ALD growth rates of ZrO2.
Unique Design Strategy for Laser‐Driven Color Converters Enabling Superhigh‐Luminance and High‐Directionality White Light (2019)

Abstract Robust ceramic color converters withstanding strong laser irradiations have recently drawn great attention for laser‐driven white lighting. However, the local emission within the incident laser spot usually expands to the whole surface area of the ceramics, which definitely makes it hard to achieve white light with high luminance and high directionality. Herein, a new strategy is proposed to solve the problem by elaborately introducing uniform spherical pores (diameter of ≈2 µm) into the phosphor ceramics with controlled contents from 8 to 24.6 vol%. The well‐distributed pores, acting as light scattering centers, enable reduction of the luminescent spot size greatly but without any losses in conversion efficiency. By using the high‐scattering ceramic color converters with 15% porosity, the light spot diameter is decreased by 46% and the central illuminance is increased by 156%. Moreover, laser‐driven white light with an enhanced beam directionality and uniformity is also achieved. A superhigh luminous flux of 7199 lm is realized by using this promising color converter in a rotary mode. The designed high‐scattering ceramics with controllable microstructures show great potential for use in extra‐high luminance laser‐driven lighting and projection.
Guidelines for Implementation of Cable Median Barrier (2009)

A detailed examination of accidents in Kansas evaluated the need for a cable median barrier. Hard copies of all accident reports from Kansas controlled-access freeways from 2002 to 2006 were reviewed. A total of 525 cross-median events and 115 cross-median crashes were identified. Cross-median encroachment rates were linearly related to traffic volume and cross-median crash rates appeared to have a second-order relationship to volume. Cross-median crashes were much more frequent in winter months and the severity of wintertime crashes was lower. This finding indicates that median barrier warranting criteria may need to be adjusted to accommodate regional climate differences, especially for warranting guidelines based on cross-median crash rates. A relationship was found between cross-median crash rate and traffic volume for Kansas freeways with median widths of 60 ft (18.3 m). This relationship was combined with encroachment rate and lateral extent of encroachment data from the Roadside Safety Analysis Program to develop general guidelines on the use of cable median barriers along Kansas freeways.
Decreased apopto-phagocytic gene expression in the macrophages of systemic lupus erythematosus patients (2013)

The clearance of apoptotic cells has an important role in the maintenance of tissue homeostasis and in the protection of tissues from the inflammatory and immunogenic contents of dying cells. A defect in the recognition and phagocytosis of apoptotic cells contributes to the development of chronic inflammation and autoimmune disorders. We have observed that compared with healthy donors, differentiated macrophages from patients with untreated systemic lupus erythematosus (SLE) showed decreased phagocytosis of apoptotic neutrophils. A TaqMan Low Density Array was designed to determine the mRNA expression levels of 95 apopto-phagocytic genes in differentiated non-phagocytosing and phagocytosing macrophages. In the macrophages of clinically and immunoserologically active SLE patients, 39 genes were expressed at lower levels than in the control macrophages. When inactive patients were compared with those with minor immunoserological abnormalities or patients in an immunoserologically active state, a relationship was observed between the altered gene expression profile and the disease state. In the macrophages of patients with engulfing apoptotic cells, an upregulation of genes involved in inflammation, autophagy, and signaling was observed. These results indicate that novel immune-pathological pathways are involved in SLE and suggest targets for potential therapeutic modulation.
Decreasing Test Qualification Time in AMS and RF Systems (2008)

The test cost of heterogeneous ICs has significantly increased. So, the definition of relevant test methods and efficient test stimuli are becoming critical research orientations for semiconductor manufacturers. The authors of this article propose decreasing the manufacturing test cost of analog and mixed-signal (AMS) and RF SoCs by automatically qualifying and optimizing the existing test set. Their computer-aided test (CAT) tool, Plasma, uses fault injection and a fault simulation technique to perform test qualification and generation. This tool reduces both test time and test equipment cost using a high-level fault model. After discussing the advantages using behavioral fault models, the authors present a method that lets them decrease overall simulation time. This method reduces the number of simulated fault-free models, thanks to a normal estimation.
New type of ordering process with volume change of molecules in the spin-crossover transition, and its new aspects of dynamical processes (2009)

Bistability between the high- and low-spin states in spin-crossover materials provides a complex temperature dependence of the ordering processes. Thermodynamic properties of the ordering phenomena were studied in a unified way, and a generic structure of the ordering processes was proposed. The origin of the interaction among the spins was also discussed, and a new mechanism based on an elastic interaction among distortions due to the volume of a molecule depending on its spin state was also proposed. With this mechanism, the typical pressure dependence of the ordering processes can be reproduced. Moreover, we studied the type of criticality of the phase transition and pointed out that the present model possesses critical behaviour belonging to the mean-field universality class. There, the spin-spin correlation function is constant at long distances and does not show an exponential decay in contrast to short-range models. It is also pointed out that the model with periodic boundary conditions does not show ordering clusters, even near the critical point or in the process of spinodal decomposition. This indicates that critical opalescence would not be observed in this model. No cluster appears, either in photo-excitation process from the low-spin state at low temperatures. On the other hand, with open boundary conditions, the system shows a cluster structure. The effects of the boundary conditions are also discussed.
A dual stable isotope method by LC-MS/MS to define patterns of androgen metabolism in localized versus advanced prostate cancer. (2016)

40 Background: Prior work has shown that androstenedione (AD) rather than testosterone (T) is the preferred substrate of 5α-reductase for dihydrotestosterone (DHT) synthesis in castration-resistant prostate cancer. However, patterns of metabolism in hormone-naive prostate cancer are still poorly defined. Previously, we reported on the utility of dual radioisotope labeling of steroid precursors to characterize androgen metabolism in localized prostate tissue. We now describe an alternative approach via stable isotope labeling and analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS), which has unique advantages over the former method. Methods: LNCaP cell lines and prostate tissue from patients undergoing radical prostatectomy for localized cancer were incubated in serum-free media, spiked with 13 C-labeled AD and 2 H-labeled T. Media was collected at 7, 24, and 48 hours of incubation. Steroids were extracted, separated, and then analyzed by way of LC-MS/MS to identify labeled metabolites of AD and T. Results: Incubation of labeled AD and T resulted in conversion over time to both 13 C-labeled and 2 H-labeled downstream metabolites, 5α-dione and DHT. Although both precursors contributed to 5α-dione and DHT formation, the steroid of origin could be determined on the basis of differential labeling. In ex-vivo tissue incubations, unlabeled 5α-dione was also observed, which was distinguishable from its stable isotopic form and most likely represents endogenous steroid. Conclusions: Both cell lines and tissue appear to metabolize labeled AD and T, and formation of DHT occurs through both precursors. Furthermore, the presence of endogenous 5α-dione suggests that alternative pathways of DHT synthesis, which bypass T, may be naturally accessible in the hormone-naïve setting. We propose a robust ex-vivo technique to readily track simultaneous pathways of DHT synthesis in prostate cancer. Future work will focus on defining metabolic phenotypes of localized prostate cancer and specific patterns of flux under different hormonal and pharmacologic conditions.
Future Directions for Mobile Agent Research (2002)

During a discussion in September 2000 the authors examined the future of research on mobile agents and mobile code. (A mobile agent is a running program that can move from host to host in network at times and to places of its own choosing.) In this paper we summa- rize and reflect on that discussion. It became clear that the field should shift its emphasis toward mobile code, in all its forms, rather than to continue its narrow focus on mobile agents. Furthermore, we encourage the development of modular components, so that application designers may take advantage of code mobility without needing to rewrite their application to fit in a monolithic mobileagent system. There are many potential applications that may productively use mobile code, but there is no &amp;quot;killer application&amp;quot; for mobile agents. Finally, we note that although security is an important and challenging problem, there are many applications and environments with security requirements well within the capability of existing mobile-code and mobile-agent frameworks.
PPP-based Ionospheric Activity Monitoring (2007)

ABSTRACT The ionosphere is inherently associated with GPS, because the refraction it causes on space radiometric measurements is one of the main effects which have to be mitigated in order to determine reliable positions using GPS signals. The ionosphere is a dispersive medium, which means the value of the group delay or phase advance of a radio signal depends on the frequency of the signal. Consequently, GPS signals are broadcast on more than one frequency and, using receivers capable of tracking GPS signals on more than one frequency, we can mathematically eliminate the first order effect of the ionospheric refraction. If on the one hand the ionosphere impacts GPS signals, on the other hand GPS can be used as a sensor of the ionosphere. In this paper we introduce a novel approach for using GPS as an ionospheric sensor. GPS receiver networks have been used for monitoring the ionosphere for a long time, but our method was created to be suitable for single-receiver operation, as one of the outputs of enhanced precise point positioning (PPP) data processing. The package in which this new technique is implemented is called GPS Analysis and Positioning Software (GAPS), a PPP package developed at the University of New Brunswick. Another characteristic of the novel approach is that only carrier-phase measurements are used, in order to avoid the contaminating effects of pseudorange measurements, such as code multipath. The filter in which the ionospheric delays are estimated is connected to the PPP filter inside GAPS, as we will discuss in this paper. In this paper we will also explain how the ionospheric delay estimation filter work. The goal of this development was to create a procedure for ionospheric delay estimation which would be suitable for single-receiver operation, as mentioned before, and also to be suitable for either static or kinematic scenarios, and eventually real-time applications. 2849