gebhart/patrepeval huggingface dataset:
DNA Damage Is a Prerequisite for p53-Mediated Proteasomal Degradation of HIF-1α in Hypoxic Cells and Downregulation of the Hypoxia Marker Carbonic Anhydrase IX (2004)

We investigated the relationship between the tumor suppressor p53 and the hypoxia-inducible factor-1 (HIF-1)-dependent expression of the hypoxia marker, carbonic anhydrase IX (CAIX). MCF-7 (wt p53) and Saos-2 (p53-null) cells displayed similar induction of CAIX expression and CA9 promoter activity under hypoxic conditions. Activation of p53 by the DNA damaging agent mitomycin C (MC) was accompanied by a potent repression of CAIX expression and the CA9 promoter in MCF-7 but not in Saos-2 cells. The activated p53 mediated increased proteasomal degradation of HIF-1alpha protein, resulting in considerably lower steady-state levels of HIF-1alpha protein in hypoxic MCF-7 cells but not in Saos-2 cells. Overexpression of HIF-1alpha relieved the MC-induced repression in MCF-7 cells, confirming regulation at the HIF-1alpha level. Similarly, CA9 promoter activity was downregulated by MC in HCT 116 p53(+/+) but not the isogenic p53(-/-) cells. Activated p53 decreased HIF-1alpha protein levels by accelerated proteasome-dependent degradation without affecting significantly HIF-1alpha transcription. In summary, our results demonstrate that the presence of wtp53 under hypoxic conditions has an insignificant effect on the stabilization of HIF-1alpha protein and HIF-1-dependent expression of CAIX. However, upon activation by DNA damage, wt p53 mediates an accelerated degradation of HIF-1alpha protein, resulting in reduced activation of CA9 transcription and, correspondingly, decreased levels of CAIX protein. A model outlining the quantitative relationship between p53, HIF-1alpha, and CAIX is presented.
ASAP: An Aggressive SpeculAtive Protocol for Actively Replicated Transactional Systems (2012)

Recent advances in the field of replicated, fault tolerant transactional systems make systematic use of Optimistic Atomic Broadcast (OAB) group communication primitives in order to coordinate the replicas. According to this scheme, the replicas gain information on the existence of transactional requests before a final and global agreement is reached on the transaction serialization order. Hence, speculative processing schemes can be exploited in order to maximize the overlap between local computation and distributed coordination activities. In this article we present ASAP, an innovative Aggressive SpeculAtive Protocol, which exhibits the following two peculiarities: (A) it allows speculating along different transaction serialization orders, thus increasing the likelihood of successful overlap between local processing and coordination in case of mismatches between the optimistic and the final delivery sequence of incoming requests, (B) it speculates along chains of conflicting transactions, tracking data dependencies among transactions via an innovative concurrency control mechanism, which allows determining in a timely fashion the alternative serialization orders to be speculatively explored. Via a simulation study in the context of Software Transactional Memory systems we show ASAP can achieve robust performance independently of the likelihood of reorder between optimistic and final deliveries, providing remarkable performance improvements (enhancing the maximum sustainable throughput up to a 2x factor) with respect to state of the art speculative replication protocols.
High Specific and Ultrasensitive Isothermal Detection of MicroRNA by Padlock Probe-Based Exponential Rolling Circle Amplification (2013)

In this paper, a padlock probe-based exponential rolling circle amplification (P-ERCA) assay is developed for highly specific and sensitive detection of microRNA (miRNA). The padlock probe is composed of a hybridization sequence to miRNA and a nicking site for nicking endonuclease. Using the miRNA as a template, specific ligation to the padlock probe and linear rolling circle reaction (LRCA) are achieved under isothermal conditions. After multiple nicking reactions, many copies of short DNA products are successively produced and then used as triggers in next circle amplification. Thus, a small amount of miRNAs are converted to a large number of triggers to initiate the rolling circle amplification reaction, and circular exponential signal amplification is achieved. This padlock probe-based exponential rolling circle amplification assay exhibits a remarkable sensitivity of 0.24 zmol using optimized sequences of the padlock probe. The target-dependent circularization of the padlock probe and the ligation reaction could improve the specificity effectively, leading to single-nucleotide difference discrimination between miRNA family members. The miRNA analysis in human lung cells was performed with this method. The result indicates this highly sensitive P-ERCA strategy will become a promising miRNA quantification method in early clinical diagnostics.
Bioeffects Considerations for Diagnostic Ultrasound Contrast Agents (2008)

Diagnostic ultrasound contrast agents have been developed for enhancing the echogenicity of blood and for delineating other structures of the body. Approved agents are suspensions of gas bodies (stabilized microbubbles), which have been designed for persistence in the circulation and strong echo return for imaging. The interaction of ultrasound pulses with these gas bodies is a form of acoustic cavitation, and they also may act as inertial cavitation nuclei. This interaction produces mechanical perturbation and a potential for bioeffects on nearby cells or tissues. In vitro, sonoporation and cell death occur at mechanical index (MI) values less than the inertial cavitation threshold. In vivo, bioeffects reported for MI values greater than 0.4 include microvascular leakage, petechiae, cardiomyocyte death, inflammatory cell infiltration, and premature ventricular contractions and are accompanied by gas body destruction within the capillary bed. Bioeffects for MIs of 1.9 or less have been reported in skeletal muscle, fat, myocardium, kidney, liver, and intestine. Therapeutic applications that rely on these bioeffects include targeted drug delivery to the interstitium and DNA transfer into cells for gene therapy. Bioeffects of contrast-aided diagnostic ultrasound happen on a microscopic scale, and their importance in the clinical setting remains uncertain.
SYNTHETIC STUDIES ON BLOOD COMPATIBLE BIOMATERIALS III. SYNTHESIS, CHARAC-TERIZATION AND ANTITHROMBOGENICITY OF DIMETHYLDIPHEN YLPOLYSILOXANE/POLY (OXYTETRAM ETHYLENE)-POLYUREA SEGMENTED COPOLYMERS (1992)

A novel class of segmented copolymers, dimethyldiphenylpolysiloxane/poly (oxytetramethylene)-polyurea (PSPEU), was synthesized from α, ω-bis (γ-aminopropyl) dimethyldiphenylpolysiloxane (APMPS), which was prepared by means of basic ring-opening copolymerization of octamethylcyclotetrasiloxane, hexaphenylcyclotrisiloxane and 1, 3-bis (γ-aminopropyl) tetramethyl disiloxane. The relationships between the diphenylsiloxy contents and the properties of APMPS, including refractive index, glass transition temperature, solubility parameter as well as thermal stability, were investigated; meanwhile, the thermal stability, dynamic mechanical properties, mechanical properiesas well as the antithrombogenicity in vitro of the PSPEU were also revealed.
Simple and Versatile Route to High Yield Face-to-Face Dimeric Assembly of Ag Nanocubes and Their Surface Plasmonic Properties (2011)

We have demonstrated the higher yield dimerization of single-crystalline Ag nanocubes through preciously controlled face-selective functionalization. With the achievement of the higher yield dimerization, we could thus observe some interesting optical properties of the dimer. Both experimental and theoretical studies revealed that the 50-nm-diameter Ag nanocubes dimers with a ca. 3.3 nm gap at their junction exhibited two plasmon peaks centered at 446 nm and 600 nm, which contributed to transverse and longitudinal plasmon resonances, respectively. Elctromagnetic calculations based on the FDTD method clearly showed that a greater enhancement of the local field occurred, with an average amplitude of the electric field of 22, at the fractal space between the aggregated Ag nanocubes when the dimer was illuminated under longitudinally polarized light.
Network discovery: An estimation based approach (2011)

We consider the unaddressed problem of network discovery, in which, an agent attempts to formulate an estimate of the global network topology using only locally available information. We show that under two key assumptions, the network discovery problem can be cast as a parameter estimation problem. Furthermore, we show that some form of excitation must be present in the network to be able to converge to a solution. The performance of two methods for solving the network discovery problem is evaluated in simulation.
An In-memory Embedding of CPython for Offensive Use (2021)

We offer an embedding of CPython that runs entirely in memory without “touching” the disk. This in-memory embedding can load Python scripts directly from memory instead these scripts having to be loaded from files on disk. Malware that resides only in memory is harder to detect or mitigate against. We intend for our work to be used by security researchers to rapidly develop and deploy offensive techniques that is difficult for security products to analyze given these instructions are in bytecode and only translated to machine-code by the interpreter immediately prior to execution. Our work helps security researchers and enterprise Red Teams who play offense. Red Teams want to rapidly prototype malware for their periodic campaigns and do not want their malware to be detected by the Incident Response (IR) teams prior to accomplishing objectives. Red Teams also have difficulty running malware in production from files on disk as modern enterprise security products emulate, inspect, or quarantine such executables given these files have no reputation. Our work also helps enterprise Hunt and IR teams by making them aware of the viability of this type of attack. Our approach has been in use in production for over a year and meets our customers’ needs to quickly emulate threat-actors’ tasks, techniques, and procedures (TTPs).
Comprehensive pre-design studies of workplaces : the case of the twin cities, Minnesota (2003)

During the last two decades pre-design studies have become an integral part of design phases required for successful creation of built environments. Now, they are taking place as part of contemporary architectural design practices. Pre-design can be regarded as a phase that precedes the detailed architectural programming and space planning stages. It may include tasks and activities that range from defining functional needs and adjacency analyses to establishing design imperatives and prioritizing design recommendations, and from cost analysis and financial modeling to establishing urban design criteria for locating new buildings. This paper reports on a pre-design study conducted over the past three years for the Minnesota Departments of Agriculture (MDA), Health (MDH), and Human Services (DHS), toward developing new office facilities and laboratories. The methodology of the study is based on establishing a rigorous collaborative process that includes five major procedures. The major components of the study are programming the workplace environment, defining functional needs and relationship analyses, establishing principles for urban intervention and developing financial modeling. The paper concludes by outlining how emerging opportunities can be stemmed from pre-design studies, how employees’ productivity and comfort can be addressed, and how urban and environmental resources can be preserved and conserved.
Ca2+-Induced Increased Lipid Packing and Domain Formation in Submitochondrial Particles. A Possible Early Step in the Mechanism of Ca2+-Stimulated Generation of Reactive Oxygen Species by the Respiratory Chain (1999)

Ca2+ and P(i) accumulation by mitochondria triggers a number of alterations leading to nonspecific increase in inner membrane permeability [Kowaltowski, A. J., et al. (1996) J. Biol. Chem. 271, 2929-2934]. The molecular nature of the membrane perturbation that precedes oxidative damage is still unknown. EPR spectra of spin probes incorporated in submitochondrial particles (SMP) and in model membranes suggest that Ca(2+)-cardiolipin (CL) complexation plays an important role. Ca(2+)-induced lipid domain formation was detected in SMP but not in mitoplasts, in SMP extracted lipids, or in CL-containing liposomes. The results were interpreted in terms of Ca2+ sequestration of CL tightly bound to membrane proteins, in particular the ADP-ATP carrier, and formation of CL-enriched strongly immobilized clusters in lipid shells next to boundary lipid. The in-plane lipid and protein rearrangement is suggested to cause increased reactive oxygen species production in succinate-supplemented, antimycin A-poisoned SMP, favoring the formation of carbon-centered radicals, detected by EPR spin trapping. Removal of tightly bound CL is also proposed to cause protein aggregation, facilitating intermolecular thiol oxidation. Lipid peroxidation was also monitored by the disappearance of the nitroxide EPR spectrum. The decay was faster for nitroxides in a more hydrophobic environment, and was inhibited by butylated hydroxytoluene, by EGTA, or by substituting Mg2+ for Ca2+. In addition, Ca2+ caused an increase in permeability, evidenced by the release of carboxyfluorescein from respiring SMP. The results strongly support Ca2+ binding to CL as one of the early steps in the molecular mechanism of Ca(2+)-induced nonspecific inner mitochondrial membrane permeabilization.
Heme Oxygenase-2 Interaction with Metalloporphyrins: Function of Heme Regulatory Motifs (2001)

Heme oxygenase-2 (HO-2) degrades heme [Fe-protoporphyrin IX (Fe-PP)] to CO and bilirubin. The enzyme is a hemoprotein and interacts with nitric oxide. HO-2 has two copies of heme regulatory motif (HRM) with a conserved core of Cys264-Pro265 and Cys281-Pro282. We examined interaction of HO-2 HRMs with Fe-PP, Zn-protoporphyrin IX (Zn-PP; HO-2 inhibitor), and protoporphyrin IX (PP IX). Spectral analyses, using 1:4 or 1:1 molar ratio of the heme to 10-residue peptides, corresponding to HRM containing HO-2 sequences, revealed specific interactions as indicated by a shift in the absorption spectrum of heme. Five residue peptides qualitatively produced similar results. Substitution of cysteine with alanine in either peptide eliminated interactions, and substitution of proline with alanine reduced the peptides' affinity for heme. Neither Zn-PP nor PP IX absorption spectrum was affected by HRM peptides. The circular dichroism spectra confirmed heme-HRM peptides interactions. An astounding 4,000-6,000-fold higher concentrations of KCN were required at pH 7.5 to displace HRM peptides from heme. Data suggest (a) each HRM can contribute to HO-2-heme interaction, (b) heme iron interacts with cysteine thiol, (c) charged residues upstream of Cys264-Pro265 result in its high-affinity heme binding, and (d) inhibition of HO-2 activity by synthetic metalloporphyrins does not involve HRMs. We suggest that heme bound to HRMs may serve as a binding site/reservoir for gaseous signal molecules.
SiGe HBT-based active cold load: Design, characterization and stability measurements (2011)

We report experimental results concerning the noise performance and the stability of an active cold load (ACL) realized with an SiGe heterojunction bipolar transistor at microwave frequency (1.4 GHz). The ACL exhibits return loss higher than 35 dB and a noise temperature less than 66 K. Stability measurements performed over 4 months with a dedicated noise injection radiometer indicates that this active load is very stable.
DIMENSION REDUCTION OF MICROARRAY GENE EXPRESSION DATA: THE ACCELERATED FAILURE TIME MODEL (2009)

The construction of the components of Partial Least Squares (PLS) is based on the maximization of the covariance/correlation between linear combinations of the predictors and the response. However, the usual Pearson correlation is influenced by outliers in the response or in the predictors. To cope with outliers, we replace the Pearson correlation with the Spearman rank correlation in the optimization criteria of PLS. The rank-based method of PLS is insensitive to outlying values in both the predictors and response, and incorporates the censoring information by using an approach of Nguyen and Rocke (2004) and two approaches of reweighting and mean imputation of Datta et al. (2007). The performance of the rank-based approaches of PLS, denoted by Rank-based Modified Partial Least Squares (RMPLS), Rank-based Reweighted Partial Least Squares (RRWPLS), and Rank-based Mean-Imputation Partial Least Squares (RMIPLS), is investigated in a simulation study and on four real datasets, under an Accelerated Failure Time (AFT) model, against their un-ranked counterparts, and several other dimension reduction techniques. The results indicate that RMPLS is a better dimension reduction method than other variants of PLS as well as other considered methods in terms of the minimized cross-validation error of fit and the mean squared error of fit in the presence of outliers in the response, and is comparable to other variants of PLS in the absence of outliers. Supplementary Materials are available at http://www.worldscinet.com/jbcb/
Review of Renewable Energy Potentials in Indonesia and Their Contribution to a 100% Renewable Electricity System (2021)

Indonesia has an increasing electricity demand that is mostly met with fossil fuels. Although Indonesia plans to ramp up Renewable Energy Technologies (RET), implementation has been slow. This is unfortunate, as the RET potential in Indonesia might be higher than currently assumed given the archipelago’s size. However, there is no literature overview of RET potentials in Indonesia and to what extent they can meet current and future electricity demand coverage. This paper reviews contemporary literature on the potential of nine RET in Indonesia and analyses their impact in terms of area and demand coverage. The study concludes that Indonesia hosts massive amounts of renewable energy resources on both land and sea. The potentials in the academic and industrial literature tend to be considerably larger than the ones from the Indonesian Energy Ministry on which current energy policies are based. Moreover, these potentials could enable a 100% renewables electricity system and meet future demand with limited impact on land availability. Nonetheless, the review showed that the research topic is still under-researched with three detected knowledge gaps, namely the lack of (i) economic RET potentials, (ii) research on the integrated spatial potential mapping of several RET and (iii) empirical data on natural resources. Lastly, this study provides research and policy recommendations to promote RET in Indonesia.
Stacking Versatility in Alkali-Mixed Honeycomb Layered NaKNi2TeO6 (2021)

The reaction between P2-type honeycomb layered oxides Na<sub>2</sub>Ni<sub>2</sub>TeO<sub>6</sub> and K<sub>2</sub>Ni<sub>2</sub>TeO<sub>6</sub> enables the formation of NaKNi<sub>2</sub>TeO<sub>6</sub>. The compound is characterized by X-ray diffraction and <sup>23</sup>Na solid-state nuclear magnetic resonance spectroscopy, and the structure is discussed through density functional theory calculations. In addition to the honeycomb Ni/Te cationic ordering, NaKNi<sub>2</sub>TeO<sub>6</sub> exhibits a unique example of alternation of sodium and potassium layers instead of a random alkali-mixed occupancy. Stacking fault simulations underline the impact of the successive position of the Ni/Te honeycomb layers and validate the presence of multiple stacking sequences within the powder material, in proportions that evolve with the synthesis conditions. In a broader context, this work contributes to a better understanding of the alkali-mixed layered compounds.
Kglove Dbpedia Page Rank Frequency Embeddings (2017)

This dataset contains the vectors from computing KGloVe embeddings from a Page Rank frequency weighted DBpedia 2016-04 graph. For each entity in the graph, the text file in the zip archive contains a line with the entity name and the embedded vector. The parameter settings for the embedding are as specified in the paper: Michael Cochez, Petar Ristoski, Simone Paolo Ponzetto, and Heiko Paulheim. 2017. Global RDF Vector Space Embeddings. In The Semantic Web – ISWC 2017: 16th International Semantic Web Conference, Vienna, Austria, October 21–25, 2017, Proceedings, Part I.
ChemInform Abstract: Electroreductive Cyclization of 4‐Phenylsulfonylthioazetidinones. A New Access to 3‐Hydroxycephem and 2‐exo‐Methylenepenam. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Microstructural characterization of ion assisted SiO2 thin films by visible and infrared ellipsometry (1998)

The complex dielectric function of SiO2 films deposited on silicon substrates by electron-beam evaporation under ion bombardment is determined by infrared ellipsometry between 700 and 5000 cm−1. Analysis of the absorption band associated with the Si–O–Si stretching mode at about 1040 cm−1, the water absorption band at about 3300 cm−1, and knowledge of the visible refractive index determined by visible ellipsometry (in situ and after venting to atmosphere) enable us to model the complex structure of the films, as a densified silica matrix with pores. Depending on the ion assistance conditions, the pores are either mostly connected (allowing water penetration) or largely isolated (no water adsorption). The refractive index of the silica matrix, the pore volume fraction and the pore water filling rate are evaluated as a function of the assistance conditions.
Automatic Optimization of a Klystron Interaction Structure (2013)

The design of klystrons has long been a manual process guided by experience. However, with well-defined specifications and sufficiently rapid simulation methods, it is a good candidate process for automatic optimization techniques. In this paper, such a technique is evaluated and refined using klystron specific techniques, leading to several designs (with different tradeoffs between efficiency and size) each of a structure comparable with the SLAC B-factory klystrons. The most efficient of which, while only 1% more efficient, is 17.1% shorter.
Anosmia and dysgeusia among COVID-19 patients are associated with low levels of serum Glucagon-like peptide 1 (GLP-1) (2021)

Purpose: Anosmia and dysgeusia (AD) are common among COVID-19 patients. These symptoms are not frequently associated with rhinorrhea or nasal congestion and the underlying mechanism is unclear. Previous reports suggested that Glucagon-like peptide-1 (GLP-1) signaling plays a role in the modulation of olfaction and geusia. We aimed to assess the correlation between GLP-1 and COVID-19-associated AD. Methods: Blood samples obtained from COVID-19 patients with and without AD were tested for serum GLP-1 levels using enzyme-linked immunosorbent assay (ELISA). A second control group comprised of COVID-19-negative volunteers. Results: Forty-nine subjects were included in the study. Nineteen were positive for COVID-19. Of the 19 patients, ten had AD and nine declined such complaints. Age and basic metabolic rate were similar among all study groups. Serum GLP-1 levels were significantly lower among patients with AD as compared with patients without AD and COVID-19-negative individuals (1820 pg/ml vs 3536 pg/ml vs 3014 pg/ml, respectively, p&lt;0.02). Conclusion: COVID-19 patients who reported of AD had lower serum levels of GLP-1 as compared with those lacking AD symptoms and COVID-19-negative individuals. These results suggest that GLP-1 may be involved in the pathogenesis of AD. However, further larger scale studies should corroborate our findings