gebhart/patrepeval huggingface dataset:
Abstract 380: Discovery of new epigenetic drugs among FDA-approved drug libraries (2014)

Abstract Targeting epigenetic pathways to induce tumor suppressor gene reactivation is a promising approach for cancer therapy. Epigenetic drugs produce impressive responses in some patients; however, treatment options are limited to a small number of drugs. We screened drug libraries for epigenetic activity using a live cell-based assay. We found that around 1% of US-FDA approved drugs have significant epigenetic activity detected by GFP reactivation of a DNA methylated and silenced promoter in colon cancer cells. Newly identified drugs, most prominently cardiac glycosides, induced tumor suppressor gene reactivation and showed selective anticancer apoptosis induction. These drugs did not change DNA methylation or histone acetylation globally but induced gene reactivation and cancer cell killing through calcium signaling leading to nuclear exclusion of chromatin repressors. Our data identify new epigenetic drugs that can be rapidly repurposed for cancer clinical trials and raise questions about the safety of commonly used medications. Citation Format: Noël J. Raynal, Justin T. Lee, Youjun Wang, Judith Garriga, Gabriel Malouf, Sarah Dumont, Elisha J. Dettman, Vazganush Gharibyan, Saira Ahmed, Woonbok Chung, Wayne E. Childers, Magid Abou-Gharbia, Ryan A. Henry, Andrew Andrews, Jaroslav Jelinek, Ying Cui, Stephen B. Baylin, Donald L. Gill, Jean-Pierre J. Issa. Discovery of new epigenetic drugs among FDA-approved drug libraries. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 380. doi:10.1158/1538-7445.AM2014-380
Gas separation using polymer membranes: an overview (1994)

Abstract This overview article discusses fundamental principles of gas sorption and transport in rubbery and glassy polymers and material selection guidelines for gas separation membranes. Comparisons between the performance of membrane‐based gas separation systems and more conventional technologies in key commercial applications are provided. Companion articles in this special edition focus on state‐of‐the‐art reviews and descriptions of theoretical and experimental developments important in the technology of gas separations using polymeric membranes.
Estimation of Crystallinity in Isotropic Isotactic Polypropylene with Raman Spectroscopy (2005)

The Raman spectrum of isotactic polypropylene (iPP) has been found to exhibit vibrational peaks in the region of 750 to 880 cm(-1) that are sensitive to the degree of crystallinity. These features are broadly assigned to various modes of methyl group rocking, rho(CH2), and there have been various attempts to assess crystallinity based on the integrated intensities of these bands. Various vibrational analyses performed in the past in combination with experimental studies have concluded that the presence of crystalline order with trans-gauche conformation gives rise to a peak at 809 cm(-1), which is assigned to a rho(CH2) mode coupled with the skeletal stretching mode. However, the presence of additional peaks at 830 cm(-1), 841 cm(-1), and 854 cm(-1), within the same envelope, have been the subject of controversy. In this work isotropic films of iPP derived from the same precursor of identical tacticity have been subjected to various degrees of annealing and the integrated intensities of the Raman bands were measured. The results showed that true 3d crystallinity in isotropic iPP can only be expressed by the 809 cm(-1) band whereas the band at 841 cm(-1) corresponds to an uncoupled rho(CH2) fundamental mode and thus is a measure of the amorphous content. The less intense satellite bands at 830 cm(-1) and 854 cm(-1) of solid iPP cannot be distinguished from the 841 cm(-1) band in the melt and are generally considered as intermediate phases possibly related to non-crystalline components with 3(1)-helical conformations. Independent differential scanning calorimetry (DSC) crystallinity measurements were in broad agreement with the Raman measurements based on the normalized intensity of the 809 cm(-1) Raman band. By comparing the Raman with the DSC data a new value for the theoretical heat of fusion for the 100% crystalline iPP has been proposed.
Learning in Agent-Based Manufacturing Systems (1998)

Agent-based technology has been taken as an important approach for developing advanced manufacturing systems. Learning is one of the key techniques for implementing such systems. This paper proposes some learning issues in agent-based manufacturing systems for further discussion in the working group. As examples, the paper describes two implemented learning mechanisms and presents some experimental results in an agent-based manufacturing system. Keywords: Learning, multi-agent learning, intelligent manufacturing, distributed manufacturing systems, mediator. 1 Introduction Recently, agent-based technology has been taken as a promising approach for developing advanced manufacturing systems (Cutkosky et al 1996; Maturana and Norrie 1996; Park et al 1993; Parunak et al 1997; Shen et al 1998). Such an approach provides rapid responsive and dynamic reconfigurable structures to facilitate flexible and efficient use of manufacturing resources in a rapidly changing environment. For most app...
Optimization of hybrid JJ/CMOS memory operating temperatures (1997)

A major drawback of present superconducting electronics is the lack of suitable large scale memory. One approach to circumvent this problem is to use semiconducting CMOS memory in conjunction with the fast Josephson junction (JJ) logic. This requires operating the CMOS memory at cryogenic temperatures. The speed of CMOS circuits has been shown to increase at cryogenic temperatures. Further increase in speed can be obtained by using JJ sense circuits in the CMOS memory. Preliminary results show that access time of 1.5 ns should be possible with this hybrid JJ/CMOS approach using 1.2 micron CMOS, and JJ sense and interface circuits. We also report the results of an analysis of the optimal operating temperature of such hybrid memories in conjunction with refrigeration requirements in light of the emerging cryocooler technologies.
Computer-aided diagnosis in medical imaging : proceedings of the First International Workshop on Computer-Aided Diagnosis, Chicago, U.S.A., 20-23 September 1998 (1999)

Hardbound. Over the last decade or so, many investigators have carried out basic studies and clinical applications toward the development of modern computerized schemes for detection and characterization of lesions in radiologic images, based on computer vision and artificial intelligence. These methods and techniques are generally called computer-aided diagnosis (CAD) schemes. The development of CAD has now reached a new phase, since the first commercial unit of detection of breast lesion in mammograms was approved in June 1998 by the FDA for marketing and sale for clinical use.This book, Computer-Aided Diagnosis in Medical Imaging, presents papers from the First International Workshop on Computer-Aided Diagnosis held on September, 1998 at the University of Chicago Downtown Center. The meeting provided a forum for leading researchers and practitioners in this rapidly expanding field, encompassing automated image analysis, quantitation of im
PAVM: a framework for policy‐aware virtual machine management (2016)

Summary The problem of efficient placement of virtual machines (VMs) in cloud computing infrastructure is well studied in the literature. VM placement decision involves selecting a physical machine in the data center to host a specific VM. This decision could play a pivotal role in yielding high efficiency for both the cloud and its users. Also, reallocation of VMs could be performed through migrations to achieve goals like higher server consolidation or power saving. VM placement and reallocation decisions may consider affinities such as memory sharing, CPU processing, disk sharing, and network bandwidth requirements between VMs defined in multiple dimensions. Considering the NP‐hard complexity associated with computing an optimal solution for this VM placement decision problem, existing research employs heuristic‐based techniques to compute an efficient solution. However, most of these approaches are restricted to only a single attribute at a time. That is, a given technique of using heuristics to compute VM placement considers only a single attribute, while completely ignoring the impact of other dimensions of placing VMs. While this approach may improve the efficiency with respect to the affinity attribute in consideration, it may yield degraded performance with respect to other affinities. In addition, the criteria for determining VM‐placement efficiency may vary for different applications. Hence, the overall goal of achieving VM placement efficiency becomes difficult and challenging. We are motivated by this challenging problem of efficient VM placement and propose policy‐aware virtual machine management (PAVM), a generic framework that can be used for efficient VM management in a cloud computing platform based on the service provider‐defined policies to achieve the desired system‐wide goals. This involves efficient means to profile different VM affinities and to use profiled information effectively by intelligent and efficient VM migrations at run time considering multiple attributes at a time. By conducting extensive evaluation through simulation and real experiments that involve VM affinities on the basis of network and memory, we confirmed that the PAVM architecture is capable of improving the efficiency of a cloud system. We elaborate the architecture of a PAVM system, describe its implementation, and present details of our experiments. Copyright © 2016 John Wiley &amp; Sons, Ltd.
Auckland face simulator (2015)

The Auckland Face Simulator has been developed to create realistic, autonomously interactive, highly expressive human faces for use in applications from perceptual psychology research to new human-computer-interface technologies. The face models can represent the full range of facial muscle actions and can be precisely controlled to allow creation of novel static and dynamic stimuli for perceptual experiments. The models can also be driven by cognitive architectures in an interactive integrated system to create synthetic muscle activations. Or they can be driven by motion capture or by animation controls or any combination to achieve a high degree of realism and a full range of expression in real time.
Stereotactic helium-ion radiosurgery for the treatment of intracranial arteriovenous malformations (1989)

This work reports probing the Moiré effect directly at the nanometer scale via near-field scanning optical microscopy (NSOM). Periodic metal nanostructures of Au and Cu have been produced sequentially using particle lithography, and the overlapped regions serve as Moiré patterns at nanometer scale. The Moiré effect in these regions can be directly visualized from NSOM images, from which periodicity and structural details are accurately determined. In addition, the near-field Moiré effect was found to be very sensitive to structural changes, such as lateral displacement and/or rotations of the two basic arrays with respect to each other. Further, nanostructures of Cu exhibited higher photon transmission than Au from NSOM images. Collectively, NSOM enables direct visualization of the Moiré effect at nanoscale levels, from optical read out, and without enhancements or modification of the structures. The results demonstrate the feasibility to extend applications of the Moiré effect-based techniques to nanometer levels.
Cells as biologics for cardiac repair in ischaemic heart failure (2010)

The epidemic of heart failure due to coronary artery disease is a leading cause of morbidity and mortality worldwide. The hallmark of this pathology is maladaptive ventricular remodelling that precipitates contractile dysfunction, and ultimately leads to the overt syndrome of congestive heart failure. The central feature in this malignant cascade is the massive loss of cardiomyocytes, followed by replacement with fibrotic scar; this ultimately leads to organ failure which is further accelerated by haemodynamic overload, inflammatory–oxidative stress, and/or impaired vascularisation. Despite continuous advances in disease management, the available medical, interventional or surgical treatments fall short of addressing the root cause of disease and are typically limited to palliative strategies mitigating disease symptomatology.

The rationale for stem cell based regenerative medicine applied to the treatment of heart diseases is based on the realisation that natural self renewing processes innate to the myocardium, while sufficient to sustain normal homeostasis, fall short of salvaging heart muscle following massive injury—as in the setting of myocardial infarction.1 Accordingly, boosting the cardiac reparative capacity through supplementation of stem cell pools has been increasingly considered as a novel therapeutic approach. Indeed, it is now recognised that extracardiac (eg, bone marrow) in addition to intracardiac progenitor cells are mobilised and home to the site of the myocardial injury to participate in the compensatory healing response.1 w1 Furthermore, there is growing evidence that such cells participate in the maturation and induction of collateral vascular growth and neovasculogenesis, and may acquire phenotypic properties of neighbouring cardiac myocytes.1 These findings, propelled by recent progress in developmental biology, offer an unprecedented opportunity to achieve repair of damaged myocardium using stem cells as new therapeutic tools. Here, we focus on the current clinical experience as well needs for successful translation of the emergent field of cell based therapy from proof-of-concept …
A Digital Reference Object to Analyze Calculation Accuracy of PET Standardized Uptake Value (2015)

The variability of computed SUV(BW) between different software packages is substantial enough to warrant the introduction of a reference standard for medical image viewing workstations.
The Sirtuin 2 microtubule deacetylase is an abundant neuronal protein that accumulates in the aging CNS (2011)

Sirtuin 2 (SIRT2) is one of seven known mammalian protein deacetylases homologous to the yeast master lifespan regulator Sir2. In recent years, the sirtuin protein deacetylases have emerged as candidate therapeutic targets for many human diseases, including metabolic and age-dependent neurological disorders. In non-neuronal cells, SIRT2 has been shown to function as a tubulin deacetylase and a key regulator of cell division and differentiation. However, the distribution and function of the SIRT2 microtubule (MT) deacetylase in differentiated, postmitotic neurons remain largely unknown. Here, we show abundant and preferential expression of specific isoforms of SIRT2 in the mammalian central nervous system and find that a previously uncharacterized form, SIRT2.3, exhibits age-dependent accumulation in the mouse brain and spinal cord. Further, our studies reveal that focal areas of endogenous SIRT2 expression correlate with reduced α-tubulin acetylation in primary mouse cortical neurons and suggest that the brain-enriched species of SIRT2 may function as the predominant MT deacetylases in mature neurons. Recent reports have demonstrated an association between impaired tubulin acetyltransferase activity and neurodegenerative disease; viewed in this light, our results showing age-dependent accumulation of the SIRT2 neuronal MT deacetylase in wild-type mice suggest a functional link between tubulin acetylation patterns and the aging brain.
Plasma -Lysin and Lysozyme Following Endotoxin Administration and the Generalized Shwartzman Reaction (1971)

A single iv injection of from 10 to 1000 μg of endotoxin/kg into rabbits did not alter the plasma β-lysin levels, but did cause a marked decrease in platelet number. The same endotoxin injections resulted in a 4- to 5-fold increase in plasma lysozyme and a dramatic drop in circulating leukocytes. Both β-lysin and lysozyme were released during generalized Shwartzman reaction. These increases in β-lysin and lysozyme were accompanied by corresponding decreases in platelets and leukocytes, respectively. In vitro studies revealed that leukocytes in citrated whole blood, obtained from animals primed for the Shwartzman reaction, released lysozyme following the addition of endotoxin; whereas leukocytes in blood taken from normal animals did not.
MyocardialT2mapping with respiratory navigator and automatic nonrigid motion correction (2012)

Quantitative T₂ mapping was recently shown to be superior to T₂-weighted imaging in detecting T₂ changes across myocardium. Pixel-wise T₂ mapping is sensitive to misregistration between the images used to generate the parameter map. In this study, utility of two motion-compensation strategies-(i) navigator gating with prospective slice correction and (ii) nonrigid registration-was investigated for myocardial T₂ mapping in short axis and horizontal long axis views. Navigator gating provides respiratory motion compensation, whereas registration corrects for residual cardiac and respiratory motion between images; thus, the two strategies provided complementary functions. When these were combined, respiratory-motion-induced T₂ variability, as measured by both standard deviation and interquartile range, was comparable to that in breath-hold T₂ maps. In normal subjects, this combined motion-compensation strategy increased the percentage of myocardium with T₂ measured to be within normal range from 60.1% to 92.2% in short axis and 62.3% to 92.7% in horizontal long axis. The new motion-compensated T₂ mapping technique, which combines navigator gating, prospective slice correction, and nonrigid registration to provide through-plane and in-plane motion correction, enables a method for fully automatic and robust free-breathing T₂ mapping.
Identifying Risks and Mitigating Disruptions in the Automotive Supply Chain (2015)

Firms are exposed to a variety of low-probability, high-impact risks that can disrupt their operations and supply chains. These risks are difficult to predict and quantify; therefore, they are difficult to manage. As a result, managers may suboptimally deploy countermeasures, leaving their firms exposed to some risks, while wasting resources to mitigate other risks that would not cause significant damage. In a three-year research engagement with Ford Motor Company, we addressed this practical need by developing a novel risk-exposure model that assesses the impact of a disruption originating anywhere in a firm’s supply chain. Our approach defers the need for a company to estimate the probability associated with any specific disruption risk until after it has learned the effect such a disruption will have on its operations. As a result, the company can make more informed decisions about where to focus its limited risk-management resources. We demonstrate how Ford applied this model to identify previously unrecognized risk exposures, evaluate predisruption risk-mitigation actions, and develop optimal postdisruption contingency plans, including circumstances in which the duration of the disruption is unknown.
Effects of growth conditions on the incorporation of oxygen in AlGaN layers grown by plasma assisted molecular beam epitaxy (2000)

Using secondary ion mass spectroscopy we have shown that oxygen incorporation in AlGaN films is dependent upon the III/V growth conditions and the growth temperature of the films. AlGaN films grown under excess group III conditions (Ga-rich) exhibited step flow growth and at least a factor of 3 less oxygen incorporation than films grown under excess group V (N-rich conditions). We found that oxygen incorporation into AlGaN decreases as the growth temperature is increased. The lowest oxygen levels were achieved by growing at 750 °C under Ga-rich growth conditions. Possible sources of unwanted oxygen are discussed.
Recent Advances in Bayesian Optimization (2023)

Bayesian optimization has emerged at the forefront of expensive black-box optimization due to its data efficiency. Recent years have witnessed a proliferation of studies on the development of new Bayesian optimization algorithms and their applications. Hence, this article attempts to provide a comprehensive and updated survey of recent advances in Bayesian optimization that are mainly based on Gaussian processes and identify challenging open problems. We categorize the existing work on Bayesian optimization into nine main groups according to the motivations and focus of the proposed algorithms. For each category, we present the main advances with respect to the construction of surrogate models and adaptation of the acquisition functions. Finally, we discuss the open questions and suggest promising future research directions, in particular with regard to heterogeneity, privacy preservation, and fairness in distributed and federated optimization systems.
Two New Flavonol Glycosides from Sedum aizoon L. (2010)

Two new flavonol glycosides, Sedacins C (1) and D (2), and two known compounds (3-4), have been isolated from the whole plant of Sedum aizoon L. Their structures have been established as 6''-O-(E)-feruloylquercetin (1) and 6''-O-(E)-feruloylisorhamnetin (2) by means of spectroscopic analysis and chemical methods.Sedum aizoon L. is an endemic plant, named as 'tusanqi' in folk medicine.It is useful in tranquilization and arresting bleeding and relieving stasis and decoction for counteracting toxicity, which has been used to treat pain or traumatic, various hemorrhage and palpitation. [1]2] There are about 150 Sedum species distributed in China, it has light green leaves on thick stems and a yellow flower blooming in the summer.4][5][6] In our recent research on this plant, The repeated column chromatographic separation of the ethyl acetate and BuOH fractions of the MeOH extract resulted in the isolation of two new flavonol glycosides (1-2), as well as two known flavonol glycosides (3-4), The structures of the known compounds were determined to kaempferol-7-O-β-D-glucoside (3), 7 luteolin-7-O-β-D-glucoside (4) 8 by comparing their spectroscopic data with those in the literatures.
Medial fetal ventral mesencephalon (1997)

Currently, fetal tissue transplantation into patients with Parkinson's disease utilizes the entire ventral mesencephalon (VM) as donor tissue. However, the resulting mixture of cell types contains a relatively low proportion of therapeutically relevant dopamine (DA) neurons. We show that differential dissection of a medial region of embryonic day 14 rat VM yields a significantly higher proportion of DA neurons (8-10%) than is found in lateral VM (2%) or whole VM (4-5%). Medial VM also contained a larger number of the specific subpopulation of DA neurons (aldehyde dehydrogenase-positive; AHD) that project to dorsolateral motor region of the striatum. Selective dissection of fetal medial VM selectively enriches DA neurons in cell preparations useful for transplantation in Parkinson's disease.