gebhart/patrepeval huggingface dataset:
Retinoic acid rewires the adrenergic core regulatory circuitry of childhood neuroblastoma (2020)

Abstract Neuroblastoma cell identity depends on a core regulatory circuit (CRC) of transcription factors that collaborate with MYCN to drive the oncogenic gene expression program. For neuroblastomas dependent on the adrenergic CRC, treatment with retinoids can inhibit cell growth and induce differentiation. Here we show that when MYCN -amplified neuroblastomas cells are treated with retinoic acid, histone H3K27 acetylation and methylation become redistributed to decommission super-enhancers driving the expression of PHOX2B and GATA3 , together with the activation of new super-enhancers that drive high levels of MEIS1 and SOX4 expression. These findings indicate that treatment with retinoids can reprogram the enhancer landscape, resulting in downregulation of MYCN expression, while establishing a new retino-sympathetic CRC that causes proliferative arrest and sympathetic differentiation. Thus, we provide mechanisms that account for the beneficial effects of retinoids in high-risk neuroblastoma and explain the rapid downregulation of expression of MYCN despite massive levels of amplification of this gene.
Advancements in the Development of a Plasma-Driven Electromagnetic Launcher (2009)

The Institute for Advanced Technology (IAT) is developing a plasma-driven railgun to launch low-mass projectiles of 5-10 g to a velocity in excess of 7 km/s. Accomplishing this goal requires overcoming the problem of bore ablation, which has been linked to an observed velocity ceiling of about 6 km/s in plasma-armature launchers. Bore ablation is a direct consequence of the intense heat radiated by plasma armatures. Controlling bore ablation requires a coordinated approach that includes magnetic augmentation to reduce power dissipation in the plasma, high-purity alumina insulators to raise the ablation resistance of the bore, and pre-acceleration to prevent ablation of the bore materials at low velocity. This paper describes the consequences of excessive bore ablation, the rationale for the IAT experiment, and results obtained from the hardware that has been designed and tested to date.
The Effect of Pressure on the Index of Refraction of Paraffin Oil and Glycerine (1932)

A refractometer for measuring the index of refraction of liquids under very high pressure is described. The values obtained for glycerine and a paraffin oil together with the constants for the Lorenz-Lorentz relation are tabulated.
INFERRING GENE REGULATORY NETWORKS FROM RAW DATA – A MOLECULAR EPISTEMICS APPROACH (2003)

Biopathways play an important role in the functional understanding and interpretation of gene function. In this paper we present the results of an iterative algorithm for automatically generating gene regulatory networks from raw data. The algorithm is based on an epistemics approach of conjecture (hypothesis formation) and refutation (hypothesis testing). These operations are performed on a matrix representation of the gene network. Our approach also provides a way of incorporating external biological knowledge into the model. This is done by pre-assigning portions of the matrix--which represent previously known background knowledge. This background knowledge helps make the results closer to a human's rendition of such networks. We illustrate our approach by having the computer replicate a gene regulatory network generated by human scientists at an academic lab.
Wireless Information and Power Transfer: Issues, Advances, and Challenges (2017)

Simultaneous Information and Power Transfer (SWIPT) for wireless communication systems presents a new paradigm, allowing wireless nodes to recharge their rechargeable batteries from RF signals (instead of fixed line or traditional energy sources) while decoding information. In this approach, the energy is harvested from ambient electromagnetic sources available within the communication system or from sources that directionally transmit RF energy. This work presents an overview, and advancement to date, as well as identifies research issues and challenges in SWIPT and RF Wireless Power Transfer (WPT) assisted technologies. The paper, in principal, addresses innovative 5G communications and Internet of Things (IoT) technologies associated with SWIPT/WPT. The paper finally presents recommendations and future trends associated with this emerging future electricity technique. This provides a valuable reference and new avenues for the future research in this direction.
CCDC 1038892: Experimental Crystal Structure Determination (2015)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
FPGAs with 28Gb/s transceivers built with heterogeneous stacked-silicon interconnects (2012)

This article consists of a collection of slides from the author's conference presentation on Xilinx's field programmable gate arrays (FPGA) that deploy 28 Gb/s transceivers built with heterogeneous stacked silicon interconnects. Some of the specific topics discussed include: key applications for use; the special features and specifications of the FPGA family of Xilinx products; stacked-silicon packaging; and the two major types of stacked silicon interconnects and applications for their use.
Aneurysm Treatment With Woven EndoBridge in the Cumulative Population of 3 Prospective, Multicenter Series: 2-Year Follow-Up (2019)

This analysis confirms the high safety profile of WEB treatment at 2 yr. Aneurysm occlusion is generally stable at 2 yr, and the retreatment rate between 1 yr and 2 yr is low (2.0%).
HDinHD: A Rich Data Portal for Huntington’s Disease Research (2021)

HDinHD (Huntington's Disease in High Definition; HDinHD.org) is an open online portal for the HD research community that presents a synthesized view of HD-related scientific data. Here, we present a broad overview of HDinHD and highlight the newly launched HDinHD Explorer tool that enables researchers to discover and explore a wide range of diverse yet interconnected HD-related data. We demonstrate the utility of HDinHD Explorer through data mining of a single collection of newly released in vivo therapeutic intervention study reports alongside previously published reports.
Design of polarization-independent optical couplers composed of three parallel slot waveguides (2008)

The characteristics of directional couplers and power splitters based on three-guide optical couplers in slot waveguide structures are analyzed in detail by a three-dimensional full-vectorial beam propagation method. The numerical results show the achievement of a compact three-guide directional coupler operating as polarization independent with a length of 58.0 microm and having almost evenly spaced propagation constants of the three lowest order modes for quasi-TE and quasi-TM modes. Thus, a high coupling efficiency from one outside waveguide to the other outside waveguide is demonstrated and is over 99.5% for both polarization states. For a three-guide power splitter, multiple sets of waveguide parameters for achieving polarization-independent operation are presented. Tolerances to operating wavelength and structural parameters are also analyzed, and the evolution of the injected field along the propagation distance through the proposed devices is demonstrated.
Controlled electron and hole trapping inYPO4:Ce3+,Ln3+andLuPO4:Ce3+,Ln3+(Ln=Sm, Dy, Ho, Er, Tm) (2009)

A detailed and systematic electron trapping study was conducted in the scientifically important wide band-gap materials ${\text{LuPO}}_{4}$ and ${\text{YPO}}_{4}$ doubly doped with ${\text{Ce}}^{3+}$ and ${\text{Ln}}^{3+}$ ($\text{Ln}=\text{Sm}$, Dy, Ho, Er, Tm). By using vacuum-ultraviolet luminescence spectroscopy and detailed thermoluminescence spectroscopy it was possible to establish by two independent methods that the observed electron traps can be assigned to the ${\text{Ln}}^{3+}$ codoping ions. It is shown that the associated electron trap depths are determined by the energy separation between the ${\text{Ln}}^{2+}$ ground states and the bottom of the conduction band. Both methods reveal a systematic behavior of electron trap depths as a function of the type of ${\text{Ln}}^{3+}$ codoping ion that can be explained by recently developed empirical models. Small differences in trap depths obtained by the two methods are discussed in the context of charge-transfer induced relaxation processes and uncertainties in glow peak analysis. Our experiments provide valuable information on $4{f}^{n}\ensuremath{\leftrightarrow}4{f}^{n}$, $4{f}^{n}\ensuremath{\rightarrow}4{f}^{n\ensuremath{-}1}5d$, ${\text{O}}^{2\ensuremath{-}}\ensuremath{\rightarrow}{\text{Ln}}^{3+}$ charge transfer and the lowest-energy ${\text{PO}}_{4}^{3\ensuremath{-}}$ group transitions as well as electron trap depths. These transition energies allowed us to construct a complete energy-level diagram for ${\text{LuPO}}_{4}:{\text{Ln}}^{3+/2+}$ and ${\text{YPO}}_{4}:{\text{Ln}}^{3+/2+}$.
Influenza-Associated Hospitalizations for Cardiovascular Diseases in the Tropics (2017)

Influenza is a major cause of mortality and morbidity. We aimed to examine the influenza-associated hospitalization rates and proportions for cardiovascular disease (CVD) in tropical Singapore. Hospital admissions for ischemic heart disease (IHD), congestive heart failure (CHF), and overall CVD were obtained from the national inpatient database for the period of 2010-2014. We used, as the key indicator of influenza virus activity, the overall proportion of specimens from outpatients with influenza-like illness in the community that tested positive for influenza as part of the national influenza surveillance program. The annual influenza-associated hospitalization rates per 100,000 person-years ranged from 9.5 to 12.2 for IHD, 7.7 to 9.1 for CHF, and 15.8 to 19.2 for overall CVD. The influenza-associated hospitalization rates increased with increasing age. Influenza was significantly associated with excess hospitalizations in elderly persons aged ≥80 years, with an excess hospitalization rate per 100,000 person-years of 242.7 for IHD (P = 0.02), 271.8 for CHF (P = 0.01), and 497.2 for overall CVD (P < 0.001). In the tropics, influenza accounts for excess cardiovascular-related hospitalizations, especially in the elderly.
Immunogenic variants obtained by mutagenesis of mouse mastocytoma P815. III. Clonal analysis of the syngeneic cytolytic T lymphocyte response (1982)

The cytolytic T lymphocyte (CTL) response of syngeneic mice to antigenic variants obtained by mutagenesis of mastocytoma P815 was analyzed at the clonal level. Estimates of the frequency of CTL precursor cells in spleens from mice immunized with P815 variants ranged from 10(-4) to 2 X 10(-3). This frequency could be increased approximately 100 times by stimulating immune spleen cells in mass culture for 6-8 days with the immunizing variant. Specificity analysis of a large number of individual CTL clones demonstrated the existence of two distinct populations of CTL. Some CTL clones lysed exclusively the immunizing variant, while others lysed equally well all P815 targets, but not syngeneic tumor L1210. These results provide direct evidence for the existence of new, individual specificities on P815 variants in addition to a common antigen already present on the original P815 cells. This confirms that a variety of new antigens can be induced by mutagenesis on the same background cell. Stable, highly active CTL clones specific for either individual variant antigens or common P815 antigens could be maintained in long-term culture.
Quasi-phase-matched (QPM) difference frequency generation in a mirrorless counterpropagating configuration (2001)

We present a theoretical analysis of second-order nonlinear difference frequency generation (DFG) in a generalized mirrorless quasi-phase-matching (QPM) frame, aimed at a comparison of counterpropagating DFG configuration (CDFG) to other DFG schemes, in view of all-optical processing applications. Field nonlinear coupling equations have been numerically solved under the hypothesis of phase-matched interaction. The evolution of propagating fields within the material and the wavelength conversion efficiency have been calculated in dependence of operating parameters. The increased complexity in the evolution of amplitude and phase for fields interacting in CDFG with respect to forward-propagating DFG (FDFG) is at the basis of a dramatic increase in the wavelength conversion efficiency under particular settings of device parameters.
Cardiotoxic Effects and the Influence on the β‐Adrenoceptor Function of Doxorubicin (Adriamycin®) in the Rat (1989)

The possible relationship between the effect of the anthracycline-cytostatic doxorubicin (Dox) on the cardiac beta-adrenoceptor function in vitro and the development of delayed cardiotoxicity in vivo has been investigated in the rat. Dox (10(-5)-10(-4) M) blocked the chronotropic effect of isoprenaline on isolated atria in a competitive manner. Treatment with a single dose of Dox 5 mg/kg intravenously caused marked ECG changes manifested by progressive prologations of the Q alpha T and S alpha T-intervals, which amounted to 37% and 58% respectivity 5 weeks after the medication. At this time no beta-blocking action was detectable when tested on the isolated atria in the same rats. The results indicate that the delayed cardiotoxicity induced by Dox is not mediated by an interference with the cardiac beta-adrenoceptor function.
Landau-Khalatnikov Switching Kinetics in the Ferroelectric Copolymer Nanostructures (2006)

In 1994 the first ultrathin Langmuir-Blodgett (LB) ferroelectric films were prepared from ferroelectric vinylidene fluoride and trifluoroethylene copolymer P(VDF-TrFE) [1 Palto, S., Blinov, L., Bune, A., Dubovik, E., Fridkin, V., Petukhova, N., Verkhovskaya, K. and Yudin, S. 1995. Ferroelectric Letters, 19: 65 [CSA][Taylor & Francis Online], [Web of Science ®] , [Google Scholar]]. It was shown that ferroelectricity exists even in two monolayers [2 Bune, A. V., Fridkin, V. M., Ducharme, S., Blinov, L. M., Palto, S. P., Sorokin, A. V., Yudin, S. G. and Zlatkin, A. 1998. Nature (London), 391: 874 [CROSSREF][CSA][Crossref], [Web of Science ®] , [Google Scholar]]. Later was shown, that these LB ferroelectric films do not reveal the critical size and ferroelectricity and polarization switching exist even in one monolayer with thickness 5 Å [3 Ducharme, S., Fridkin, V., Ievlev, A. and Verkhovskaya, K. 2004. Ferroelectrics, to be published[CSA] [Google Scholar]]. These films show typical phase transition of the first order with Curie temperature and phase transition temperature, which do not depend on the film thickness in the interval 1–30 ML [2 Bune, A. V., Fridkin, V. M., Ducharme, S., Blinov, L. M., Palto, S. P., Sorokin, A. V., Yudin, S. G. and Zlatkin, A. 1998. Nature (London), 391: 874 [CROSSREF][CSA][Crossref], [Web of Science ®] , [Google Scholar], 3 Ducharme, S., Fridkin, V., Ievlev, A. and Verkhovskaya, K. 2004. Ferroelectrics, to be published[CSA] [Google Scholar], 4 Ducharme, S. and Fridkin, V. M. 2001. Phys. Rev. Lett., 87: 019702 [CROSSREF][CSA][Crossref], [Web of Science ®] , [Google Scholar], 5 Blinov, L. M., Fridkin, V. M., Palto, S. P., Bune, A. V., Dowben, P. A. and Ducharme, S. 2000. Usp. Fiz. Nauk, 170: 247 [CSA][Crossref], [Web of Science ®] , [Google Scholar]]. In contrast with usual well-known thick ferroelectric copolymer films, prepared by the spinning method, the Langmuir-Blodgett films do not contain amorphous phase and show perfect crystal structure of orthorhombic (or monoclinic) symmetry. Recently were obtained the experimental evidence of the existence of ferroelectricity in the perovskite films with thickness 1.2–5 nm [6 Tybell, T., Ahn, C. H. and Triskone, J.-M. 1999. Appl. Phys. Lett., 75: 856 [CROSSREF][CSA][Crossref], [Web of Science ®] , [Google Scholar], 7 Fong, Dillon D., Stephenson, Brian G., Streiffer, Stephen, Eastman, Jeffrey A., Auciello, Orlando, Fuoss, Paul H. and Thompson, Carol. 2004. Science, 304: 1650 [INFOTRIEVE][CROSSREF][CSA][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. In this paper we show interesting peculiarities in switching kinetics of the ultrathin ferroelectric copolymer films.
Manipulation of lymphoid microenvironments in nonhuman primates by an inhibitor of the lymphotoxin pathway (2002)

Reticular networks in lymphoid organs play critical roles in the organization of local microenvironments. A number of these elements are maintained by continual signaling through the lymphotoxin system. Evaluation of the lymphotoxin (LT) pathway in primates using a fusion protein decoy provides a unique opportunity to assess modulation of splenic microenvironments in a species with considerably greater background immunological activity compared with rodents. Within the germinal center microenvironment, treatment resulted in a collapse of follicular dendritic cell (FDC) networks and in the disappearance of a ringlike network of immune complex-carrying cells, although some other attributes of the germinal center appeared to be unaltered. Treatment also resulted in changes in the splenic marginal zone, a microenvironment where the architecture is notably different from that of the rodent. Cessation of treatment and recovery allowed us to monitor reemergence of these cell types and revealed that FDCs rely on LT-dependent signals to recompact into appropriately positioned tight networks. Despite the loss of FDC networks, the primary Ab response to keyhole limpet hemocyanin was unaltered over a 20-day period. Manipulation of these microenvironments may represent a novel approach to modulating immune function in human disease.
Ultrastructural localization of DREADD s in monkeys (2019)

Abstract Designer receptors exclusively activated by designer drugs ( DREADD s) are extensively used to modulate neuronal activity in rodents, but their use in primates remains limited. An essential need that remains is the demonstration that DREADD s are efficiently expressed on the plasma membrane of primate neurons. To address this issue, electron microscopy immunogold was used to determine the subcellular localization of the AAV vector‐induced DREADD s hM 4Di and hM 3Dq fused to different tags in various brain areas of rhesus monkeys and mice. When hM 4Di was fused to mC herry, the immunogold labelling was mostly confined to the intracellular space, and poorly expressed at the plasma membrane in monkey dendrites. In contrast, the hM 4Di‐ mC herry labelling was mostly localized to the dendritic plasma membrane in mouse neurons, suggesting species differences in the plasma membrane expression of these exogenous proteins. The lack of hM 4Di plasma membrane expression may limit the functional effects of systemic administration of DREADD ‐actuators in monkey neurons. Removing the mC herry and fusing of hM 4Di with the haemagglutinin ( HA ) tag resulted in strong neuronal plasma membrane immunogold labelling in both monkeys and mice neurons. Finally, hM 3Dq‐ mC herry was expressed mostly at the plasma membrane in monkey neurons, indicating that the fusion of mC herry with hM 3Dq does not hamper membrane incorporation of this specific DREADD . Our results suggest that the pattern of ultrastructural expression of DREADD s in monkey neurons depends on the DREADD /tag combination. Therefore, a preliminary characterization of plasma membrane expression of specific DREADD /tag combinations is recommended when using chemogenetic approaches in primates.
Is the ACPA a Safe Haven for Trademark Infringers? - Rethinking the Unilateral Application of the Lanham Act, 22 J. Marshall J. Computer & Info. L. 655 (2004) (2004)

The Anticybersquatting Consumer Protection Act (ACPA) was enacted in 1999 as a response to international disputes over Internet domain names because according to the Congress’ point of view, courts could not successfully protected American businesses in cases where nothing more that the registration of a trademark or its variation in a domain name had occurred. This article analyzes recent court decisions regarding domain name disputes after the enactment of ACPA focusing on reverse domain name hijacking in international, trademark related and gTLD disputes. The author argues that the in rem jurisdiction provided by the ACPA and the consequent extraterritorial effect of U.S. Trademark law is problematic and is likely to cause tension and conflict with other countries in the context of international jurisdiction because while it subjects to U.S. law all foreign infringers, it fails to give same amount of protection to foreign trademark rights infringed by U.S. registrants in the U.S. courts. Therefore it is argued that the ACPA in rem jurisdiction should be restrictively and possible ways to minimize conflicts with other countries are suggested.
Perivascular adipose tissue modulates neurogenic vasorelaxation in rat mesenteric arteries (2013)

We have demonstrated that palmitic acid methyl ester (PAME) is the major perivascular adipose tissue (PVAT)‐derived relaxing factor. PAME also was shown to inhibit nicotinic acetylcholine receptor (nAChR)‐mediated inward currents on the superior cervical ganglionic neurons. The present study, therefore, was designed to determine if PAME released from the PVAT inhibited nicotine‐induced neurogenic relaxation of isolated endothelium‐denuded small mesenteric arterial (sMA) rings of 8‐week old male Sprague‐Dawley rats. In tissue bath myography study, nicotine (100 μM) induced small, basal relaxation in sMA rings with PVAT. The relaxation was significantly enhanced in arteries without PVAT. Transmural nerve stimulation (TNS) also elicited tetrodotoxin‐sensitive relaxation of sMA rings with or without PVAT. The relaxations in both ring preparations, however, were not significantly different. In sMA preparations with PVAT, TNS‐elicited relaxation or nicotine‐induced small, basal relaxation was not significantly affected by 4‐propargylglycine (10 mM, an inhibitor for H2S synthesis). These results suggest that PVAT, most likely via release of PAME but not H2S, modulates the neurogenic control of the sMA tone. (supported by Tzu Chi Univ &amp; Foundation, NSC and NHRI of Taiwan).
dSimpleGraph: A Novel Distributed Clustering Algorithm for Exploring Very Large Scale Unknown Data Sets (2010)

Some of the major challenges in current clustering applications include: some data sets are so huge that it is difficult to load the entire data sets into memory for clustering, the data sets are often distributed over different locations for various reasons, which makes it impossible to process them centrally, and when lacking prior knowledge of the unknown data sets, it is troublesome to choose the appropriate parameters to feed into existing clustering algorithms. Therefore, a distributed clustering algorithm without too many parameters becomes rather appealing. Although some distributed clustering algorithms have been proposed, it is still a challenge for them to solve all of these problems. In this paper, we propose and implement a novel micro-cluster based distributed clustering algorithm called dSimpleGraph. An equivalence relation on two micro-clusters is defined. Relying on the relation, dSimpleGraph can efficiently cluster data on the local machines, moreover, it can easily generate a determined global view from local views. Only two scalar parameters are needed and the generated clusters can be any shape. Its MapReduce-style structure allows it to be easily implemented on existing distributed computing platforms. Extensive experimental studies show that dSimpleGraph is very fast and very suitable for exploring very large scale unknown data sets.