gebhart/patrepeval huggingface dataset:
Exploiting the Tr3 Interaction with Bcl-2 as a Novel Therapeutic Strategy of Cancer and Leukemia Therapy. (2006)

Abstract TR3 (Nur77) is an orphan member of the retinoid/steroid family of nuclear receptors, which translocates from nucleus to mitochondria where it binds Bcl-2 and converts Bcl-2 from an anti-apoptotic to a pro-apoptotic protein (Li, et al. Science289: 1159, 2000; Lin, et al CELL116: 527, 2004). Because Bcl-2 is pathologically over-expressed in many ca cancers and leukemias, contributing to chemoresistance, we sought to exploit the TR3 interaction with Bcl-2 as a novel therapeutic approach. Mutagenesis studies identified a 9 amino-acid peptide from TR3 that mimics the effects of the full-length protein in terms of binding Bcl-2 and inducing conformational changes that covert Bcl-2 into a killer. A cell-permeable version of this TR3 peptide induced apoptosis of cultured leukemia cell lines (CEM; Jurkat), such that gene transfer-mediated over-expression of Bcl-2 enhanced sensitivity to the TR3 peptide. In contrast, Bcl-2 over-expression rendered these leukemia cells resistant to other inducers of apoptosis, such as the broad-spectrum kinase inhibitor Staurosporine. Mutant TR3 peptides that fail to bind Bcl-2 did not induce apoptosis. To identify chemical compounds that mimic the pro-apoptotic TR3 peptide, a Fluorescence Polarization Assay (FPA) was developed in which FITC-conjugated TR3 peptide binding to Bcl-2 or other appropriate anti-apoptotic Bcl-2-family proteins was measured in high-throughput mode. This high-throughput screening (HTS) assay performs well in 384 well format, with Z′ &gt; 0.75. A chemical library of ~70,000 compounds was screened to identify compounds that displace the TR3 peptide, thus yielding hits that may serve as a potential starting point for drug discovery. Characterization of the properties of these compounds and their analogs will be described. (Supported by NIH grants R01-GM60554 and U54-HG003916).
Toward Highly Dispersed Mesoporous Bioactive Glass Nanoparticles With High Cu Concentration Using Cu/Ascorbic Acid Complex as Precursor (2019)

Copper (Cu) ions have a variety of advantageous biological functionalities, such as proangiogenic and bactericidal activities. Given the intrinsic biodegradability and biocompatibility, silicate-based mesoporous bioactive glass nanoparticles (MBGNs) are considered as promising platforms for the delivery of Cu ions. However, effective incorporation of Cu into MBGNs still faces challenges, e.g., particle aggregation, the formation of insoluble crystalline Cu-based nanoparticles, and a low loading amount of Cu. We report a novel method to synthesize chemically homogenous and highly dispersed Cu-containing MBGNs (Cu-MBGNs) with tunable Cu concentration by using ascorbic acid/Cu complexes as the precursor of Cu in a microemulsion-assisted sol-gel approach. Cu-MBGNs exhibited a sphere-like shape with a particle size between 100 and 300 nm while their pore size varied from 2 to 10 nm. The inclusion of Cu, regardless of the incorporated concentration, did not significantly affect the morphology of particles. ICP-AES results indicated that the concentration of Cu in the particles could be conveniently tuned from 0 to ~6 mol% by controlling the amount of ascorbic acid/Cu complexes added, while the formation of crystalline Cu-based nanoparticles was avoided. The amorphous feature of Cu-MBGNs was proved by XRD, while the predominant oxidation state of Cu was evidenced to be Cu<sup>2+</sup> by XPS. The incorporation of Cu did not inhibit the apatite-forming ability (bioactivity) of the particles in contact with simulated body fluid. Cu-MBGNs exhibited the capability of releasing Cu, Si, and Ca ions over time in the physiological fluid. The concentration of released Cu ions could be controlled by selecting specific Cu-MBGNs of different Cu contents. The dissolution products of most Cu-MBGNs at the dosage of 1, 0.1, and 0.01 mg/mL did not exhibit cytotoxicity, while only 7Cu-MBGN was cytotoxic at the dosage of 1 mg/mL. This study provided a feasible strategy to synthesize highly dispersed amorphous Cu-MBGNs with high Cu concentrations for biomedical applications. The particles exhibit great potential as building blocks for developing composite 3D scaffolds, coatings, and drug carriers, particularly when a large amount of particles incorporated may compromise the properties of (polymer) matrix materials while a relatively high concentration of released Cu ions is still required.
Characterization of Nb films for superconducting qubits using phase boundary measurements (2022)

Continued advances in superconducting qubit performance require more detailed understandings of the many sources of decoherence. Within these devices, two-level systems arise due to defects, interfaces, and grain boundaries and are thought to be a major source of qubit decoherence at millikelvin temperatures. In addition to Al, Nb is a commonly used metallization layer in superconducting qubits. Consequently, a significant effort is required to develop and qualify processes that mitigate defects in Nb films. As the fabrication of complete superconducting qubits and their characterization at millikelvin temperatures is a time and resource intensive process, it is desirable to have measurement tools that can rapidly characterize the properties of films and evaluate different treatments. Here, we show that measurements of the variation of the superconducting critical temperature Tc with an applied external magnetic field H (of the phase boundary Tc−H) performed with very high-resolution show features that are directly correlated with the structure of the Nb films. In combination with x-ray diffraction measurements, we show that one can even distinguish variations in the size and crystal orientation of the grains in a Nb film by small but reproducible changes in the measured superconducting phase boundary.
Agent Degradation via Catalytic and Photocatalytic Reactions on Surfaces and in Organized Assemblies (1989)

Research pursued under Contract no. DAJA45-87-C-005 has concentrated on the catalytic and photocatalytic destruction of simulants for V-agents in oxide semiconductor systems, in particular titanium dioxide. Near UV irradiation of TiO2 semiconductor particles suspended in solution generates electrons and holes in the conduction and valence bands, respectively, free charge carriers that are highly reactive reductants and oxidants. We have previously shown that all the simulants employed underwent complete oxidation and mineralization in the presence of light activated TiO2. In addition, surface adsorbed hydroxide and peroxide ions act as powerful nucleophiles promoting ester hydrolysis. These thin films were formed by a sol-gel type procedure yielding layers with a specific surface texture and a high porosity, the roughness factor being 100 to 200. Hydrolysis and oxidative decontamination were tested with agents deposited on the surface which, due to the fractal-type pore geometry, shows a very high capacity for uptake of adsorbent.
Probing bacterial pathogenesis with genetics, genomics, and chemical biology: past, present, and future approaches (2011)

Classical genetic approaches for studying bacterial pathogenesis have provided a solid foundation for our current understanding of microbial physiology and the interactions between pathogen and host. During the past decade however, advances in several arenas have expanded the ways in which the biology of pathogens can be studied. This review discussed the impact of these advances on bacterial genetics, including the application of genomics and chemical biology to the study of pathogenesis.
Theophylline as a therapy for chronic lymphocytic leukemia: a case report and review of literature (2000)

We herein, report that theophylline which can induce apoptosis in chronic lymphocytic leukemia (CLL) cells both in vitro and in vivo, also appears to be effective when used clinically to treat an advanced CLL patient.
Managing eBusiness on demand SLA contracts in business terms using the cross-SLA execution manager SAM (2003)

It is imperative for a competitive e-business service provider to be positioned to manage the execution of its service level agreement (SLA) contracts in business terms (e.g., minimizing financial penalties for service-level violations, maximizing service-level measurement based customer satisfaction metrics). This paper briefly describes the design rationale of an integrated set of business-oriented service level management (SLM) technologies under development in the SAM project at IBM TJ Watson Research Center. The e-business SLA execution manager SAM, (1) enables the provider to deploy an effective means of capturing and managing contractual SLA data as well as provider-facing non-contractual SLM data; (2) assists service personnel to prioritize the processing of action-demanding quality management alerts as per the provider's SLM objectives; and (3) automates the prioritization and execution management Of approved SLM processes on behalf of the provider, including assigning SLM tasks to service personnel.
Cost-effective safety treatments for low-volume roads. (2012)

The majority of roadside safety guidance pertains to high-volume roads.Very little guidance exists to assist engineers in treating common obstacles found alongside low-volume roads.In general, it is assumed that low traffic volumes can effectively mitigate the risks associated with vehicle impacts into fixed objects and other geometric features to a point where they do not significantly increase the accident costs relative to high-volume roads.However, a single crash on a low-volume road may result in a fatality or a severe injury, effectively making low-volume roads competitive in severity scale with high-volume roads.As a result, the possibility of a fatal or severe injury crash needs to be mitigated on low-volume roads.Common roadside features were observed in a field study and included culverts, trees, slopes, ditches, and bridges.A probability-based encroachment tool, known as the Roadside Safety Analysis Program (RSAP), was used to determine impact frequencies and severities for each feature.Treatment options, like removing the fixed object or installing W-beam guardrail, were considered for each feature.Finally, acceptable ranges in traffic volume were recommended for each safety treatment option.In these recommendations, the "do nothing" option was often considered to be the most cost-effective safety treatment for the existing configuration.However, this was not always the case.17.
Reactive crystalline molecular assemblies (2008)

thus bypassing the wavelength dependence of the Laue intensities. A monochromatic reference structure is then used to recover the 'light-on' intensities. Using polychromatic radiation time-resolution becomes limited only by the larger of the width of the synchrotron and laser pulses. In addition to allowing studies of much shorterlived excited states, this should make it possible to monitor the initial steps of chemical reactions in solids. The suitability for this purpose of a number of solid-state reactions have been explored by steady state methods [1][2][3]. We find that trans-cis, cis-trans isomerizations and [2+2] cycloadditions in solids are highly stereospecific and activation-energy-controlled, so that their rate can be manipulated by adjustment of the temperature. A number of examples will be presented.
007 Wound Healing Stimulation by Low-Level Light (2008)

It has been known for many years that low levels of laser or noncoherent light (LLLT) accelerate some phases of wound healing. LLLT can stimulate fibroblast and keratinocyte proliferation and migration. It is thought to work via light absorption by mitochondrial cytochromes, increase in reactive oxygen species and consequent gene transcription. However, despite many reports about the positive effects of LLLT on wound healing, its use remains controversial. Our laboratory has developed a model of a full thickness excisional wound in mice that allows quantitative and reproducible light dose healing response curves to be generated. We have found a biphasic dose response curve with a maximum positive effect at 2 J/cm2 of 635-nm light and successively lower beneficial effects from 3–25 J/cm2, the effect is diminished at doses below 2 J/cm2 and gradually reaches control healing levels. At light doses above 25 J/cm2 healing is actually worse than controls. Although analysis of action spectra revealed the most effective light to be 635 nm, dose response curves are likely to be of similar shape for different wavelengths of light but at different absolute fluences. We found no difference between filtered 635 ± 15-nm light from a lamp and 633-nm HeNe laser. Light alone (or a combination with other agents such as photosensitive dyes or matrix degrading enzymes) could be used for stimulation of wound healing. Our future work will be focused on understanding the mechanisms underlying effects of light on wound healing processes. We propose to examine various knockout and overexpressing mice to determine the precise mechanisms operating and to study mouse models of impaired wound healing to more closely define which patients might most benefit from LLLT.
Nanocrystal Plasma Polymerization: From Colloidal Nanocrystals to Inorganic Architectures (2008)

Nanocrystal superstructures are increasingly becoming a subject of intense study. Such materials could constitute a new class of nanocomposites of designed structure, of homogeneous composition, and with unique properties. New phenomena are observed in these materials because of the interaction at such diminutive length scales. A common problem in the development of devices relying on colloidal nanocrystal assemblies is that the individual nanocrystal building blocks require organic molecules to control their size. These ligands are responsible for the colloidal stability of the individual nanocrystal building blocks and are thus necessary for their solution processibility. Because of the ligands' incompatibility with many solid state applications, it is important to develop post-processing techniques that mildly remove them from these nanocomposites, while maintaining the size-dependent properties of the building blocks. This Account highlights a new strategy, nanocrystal plasma polymerization (NPP), for processing colloidal nanocrystal assemblies. This technique exposes the nanocomposite to a mild air plasma and allows for the removal of the nanocrystals' capping ligands while preserving their size-dependent and material properties. As a result, the process yields a nearly all-inorganic flexible solid-state material with unprecedented characteristics. We describe early experiments, in which NPP was used to create arbitrarily complex 1D, 2D, and 3D inorganic free-standing architectures entirely composed of nanocrystals, as well as future directions and challenges. We expect this platform will be useful for the design of new materials and will be a valuable new addition to the nanoscientist's toolbox.
Ground states of stealthy hyperuniform potentials: I. Entropically favored configurations (2015)

Systems of particles interacting with "stealthy" pair potentials have been shown to possess infinitely degenerate disordered hyperuniform classical ground states with novel physical properties. Previous attempts to sample the infinitely degenerate ground states used energy minimization techniques, introducing algorithmic dependence that is artificial in nature. Recently, an ensemble theory of stealthy hyperuniform ground states was formulated to predict the structure and thermodynamics that was shown to be in excellent agreement with corresponding computer simulation results in the canonical ensemble (in the zero-temperature limit). In this paper, we provide details and justifications of the simulation procedure, which involves performing molecular dynamics simulations at sufficiently low temperatures and minimizing the energy of the snapshots for both the high-density disordered regime, where the theory applies, as well as lower densities. We also use numerical simulations to extend our study to the lower-density regime. We report results for the pair correlation functions, structure factors, and Voronoi cell statistics. In the high-density regime, we verify the theoretical ansatz that stealthy disordered ground states behave like "pseudo" disordered equilibrium hard-sphere systems in Fourier space. The pair statistics obey certain exact integral conditions with very high accuracy. These results show that as the density decreases from the high-density limit, the disordered ground states in the canonical ensemble are characterized by an increasing degree of short-range order and eventually the system undergoes a phase transition to crystalline ground states. In the crystalline regime (low densities), there exist aperiodic structures that are part of the ground-state manifold but yet are not entropically favored. We also provide numerical evidence suggesting that different forms of stealthy pair potentials produce the same ground-state ensemble in the zero-temperature limit. Our techniques may be applied to sample the zero-temperature limit of the canonical ensemble of other potentials with highly degenerate ground states.
Causal Relations of Upscaled Urban Aquaponics and the Food-Water-Energy Nexus—A Berlin Case Study (2021)

Aquaponics, the water-reusing production of fish and crops, is taken as an example to investigate the consequences of upscaling a nature-based solution in a circular city. We developed an upscaled-aquaponic scenario for the German metropolis of Berlin, analysed the impacts, and studied the system dynamics. To meet the annual fish, tomato, and lettuce demand of Berlin’s 3.77 million residents would require approximately 370 aquaponic facilities covering a total area of 224 hectares and the use of different combinations of fish and crops: catfish/tomato (56%), catfish/lettuce (13%), and tilapia/tomato (31%). As a predominant effect, in terms of water, aquaponic production would save about 2.0 million m3 of water compared to the baseline. On the supply-side, we identified significant causal link chains concerning the Food-Water-Energy nexus at the aquaponic facility level as well as causal relations of a production relocation to Berlin. On the demand-side, a ‘freshwater pescatarian diet’ is discussed. The new and comprehensive findings at different system levels require further investigations on this topic. Upscaled aquaponics can produce a relevant contribution to Berlin’s sustainability and to implement it, research is needed to find suitable sites for local aquaponics in Berlin, possibly inside buildings, on urban roofscape, or in peri-urban areas.
Monitoring technology trends with podcasts, RSS and Twitter (2008)

Purpose This paper describes how information professionals can keep up with current technology news by incorporating podcasts, RSS feed readers, and the social messaging service Twitter into their daily routines. Design/methodology/approach A general review of technologies and news sources. Findings The rapid pace of technology innovation requires librarians to look for simple ways to monitor new trends that may affect library services. Podcasts, RSS readers and messaging networks like Twitter each represent low‐threshold tools that can serve as resources for breaking news, reviews, and technology journalism. Originality/value The tools offered in this article provide simple strategies for information professionals to stay abreast of technology innovations as the revelations first emerge. Provides descriptions of technologies and reviews several technology podcasts, blogs, and journalists worth following.
Aspergillus fumigatusSecreted Proteases (2014)

This chapter establishes a catalog of the proteases secreted by Aspergillus fumigatus, briefly describes their various properties, and examines their biological functions, ranging from protein digestion into short peptides and assimilable amino acids to specific proteolysis during infection. The proteases include all enzymes that catalyze the cleavage of peptide bonds (CO-NH) of proteins, digesting them into peptides or free amino acids. The proteases can be further divided into endoproteases and exoproteases. From a physiological point of view, Aspergillus secreted proteases can be classified as either acidic, neutral, or basic. Efficient protein degradation of hard keratin by hydrolytic enzymes has to be accompanied by simultaneous reduction of cysteine disulfide bridges. Although it can be stated that individual proteases such as Alp1, Mep, and Pep1 are not essential for tissue invasion, it cannot be ruled out that secreted proteases do not contribute to the establishment of invasive aspergillosis. A. fumigatus also does not possess specific large gene families encoding secreted proteases. Aspartic proteases of the A1 family and carboxypeptidases of the S10 family are multiple in many fungi. The emergence of multigenic families is most frequently due to ancient gene duplication processes allowing organisms to better adapt to different environmental conditions, and marked differences occur from one pathogenic species to another.
Linewidth, tunability, and VHF-millimeter wave frequency synthesis of vertical-cavity GaAs quantum-well surface-emitting laser diode arrays (1991)

The authors report the measurement of the laser linewidth, wavelength tunability, and generation of microwave frequencies between individually addressable elements of a vertical-cavity GaAs quantum-well surface-emitting laser diode array (lasing in the wavelength range 850-865 nm). Using heterodyne techniques, the authors obtain a deconvolved 65 MHz laser linewidth from the 109 MHz beat signal. The laser linewidth corresponds to a semiconductor laser linewidth enhancement factor alpha =5.7, which is in excellent agreement with that obtained independently from optical gain measurements and corresponding calculated refractive index changes. The authors measured heterodyne beat frequencies of 2-20 GHz. The bandwidth was limited by the microwave amplifiers. A simple calculation shows that a tuning range of 65 MHz to 3 THz can be achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Table S1 from The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints (2023)

&lt;p&gt;Supplementary Table S1. Patient Demographics.&lt;/p&gt;