gebhart/patrepeval huggingface dataset:
Textbook of Pharmacology (1991)

This authoritative, timely textbook succintly describes the actions of drugs that are essential for their rational therapuetic use. Emphasizes prototypical drugs, drugs or processes that demonstrate pharmacological principles, most commonly prescribed drugs, and toxicological apsects and common environmental toxins. Chapters on specific drugs address mechanisms of action, actions on organ systems, pharmacokinetics, therapeutic indications, adverse effects, and interactions with other drugs, foods, or conditions.
Purification of Synthetic Lipopeptide Conjugates by Liquid Chromatography (1995)

Abstract Conventional normal phase liquid chromatography (LC) was implemented for the purification of a synthetic lipid-peptide conjugate and its electrophilic lipid precursor. N-bromoacetic distearoylphosphatidylethanolamine (DSPE-COCH2Br) was extracted from the crude reaction mixture and purified in a single chromatographic step with a gradient of chloroform, methanol, and 50% aqueous acetic acid. This compound was covalently linked to Ser-Phe-Leu-Leu-Arg-Asn-(βAla)3-Tyr-NHCH2CH2SH, a hydrophilic decapeptide, and the conjugate was both extracted and purified in a single step by normal phase gradient LC using a hand-packed 3 mL Sep-Pak™ column. The eluent was a mixture of hexane, chloroform, 2-propanol, acetic acid, and water. Runs were monitored by thin layer chromatography and the plates developed with iodine and ninhydrin.
Synthesis and applications of nano-structured iron oxides/hydroxides – a review (2011)

The nano iron oxides have been synthesized by almost all the known wet chemical methods which include precipitation at ambient/elevated temperatures, surfactant mediation, emulsion/micro-emulsion, electro-deposition etc. Iron oxides in nano-scale have exhibited great potential for their applications as catalytic materials, wastewater treatment adsorbents, pigments, flocculants, coatings, gas sensors, ion exchangers, magnetic recording devices, magnetic data storage devices, toners and inks for xerography, magnetic resonance imaging, bioseparation and medicine. Nano sized magnetite Fe3O4, and maghemite &#947-Fe2O3 exhibiting excellent magnetic properties find applications for biomedical purposes and as soft ferrites. Iron hydroxides and oxyhydroxides such as ferrihydrite, goethite, akaganeite, lepidocrocite are being evaluated for their applications in water purification for the removal of toxic ions. Hematite, &#947-Fe2O3 in the nano range has been used to obtain transparent paints. In catalysis both iron oxides and hydroxides find application in numerous synthesis processes. This review outlines the work being carried out on synthesis of iron oxides in nano form and their various applications. Keywords: nano iron oxides, synthesis, catalysts, magnetic properties, biomedical application International Journal of Engineering, Science and Technology, Vol. 2, No. 8, 2010, pp. 127-146
Augmentation of hypoxic pulmonary vasoconstriction in the isolated perfused rat lung by in vitro antagonists of endothelium-dependent relaxation. (1988)

The role of the endothelium in hypoxic constriction of the intact pulmonary vascular bed has not been clearly elucidated. To test for a possible role for endothelium-derived relaxing factor(s) (EDRF) in the hypoxic pressor response, isolated, whole blood-perfused rat lungs from male Sprague-Dawley rats treated with meclofenamate were prepared. Three protocols were performed, including: (a) normal saline (control); (b) the putative EDRF inhibitors, eicosatetraynoic acid (ETYA, 1 X 10(-4) M) or nordihydroguaiaretic acid (NDGA, 1 X 10(-4) M) versus vehicle DMSO; and (c) the putative EDRF inhibitor hydroquinone (HQ, 1 X 10(-4) M) versus vehicle ethyl alcohol (ETOH). The pulmonary pressor response to angiotensin II (Ang II, 0.25 micrograms) injections alternated with 6-min periods of hypoxic ventilation (3% O2, 5% CO2) was measured before and after the administration of saline, inhibitors, or vehicles. The administration of the EDRF inhibitors ETYA, NDGA, and HQ resulted in a marked accentuation of the hypoxic pressor response that was not seen in the controls (P less than 0.05). In separate experiments, lungs precontracted with norepinephrine (1 X 10(-6) M) were pretreated with edrophonium (1 X 10(-4) M) and then observed for endothelium-dependent vasodilator responses to acetylcholine at increasing doses (1 X 10(-7)-1 X 10(-4) M). Administration of ETYA, NDGA, or HQ abrogated the observed vasodilatation to acetylcholine, which was not seen with vehicles alone (P less than 0.01). These studies suggest an important role for the endothelium in pulmonary vascular responsiveness to alveolar hypoxia through possible release of a relaxing factor(s) that attenuates the degree of pulmonary arterial constriction.
Evaluating the ε-Domination Based Multi-Objective Evolutionary Algorithm for a Quick Computation of Pareto-Optimal Solutions (2005)

Since the suggestion of a computing procedure of multiple Pareto-optimal solutions in multi-objective optimization problems in the early Nineties, researchers have been on the look out for a procedure which is computationally fast and simultaneously capable of finding a well-converged and well-distributed set of solutions. Most multi-objective evolutionary algorithms (MOEAs) developed in the past decade are either good for achieving a well-distributed solutions at the expense of a large computational effort or computationally fast at the expense of achieving a not-so-good distribution of solutions. For example, although the Strength Pareto Evolutionary Algorithm or SPEA (Zitzler and Thiele, 1999) produces a much better distribution compared to the elitist non-dominated sorting GA or NSGA-II (Deb et al., 2002a), the computational time needed to run SPEA is much greater. In this paper, we evaluate a recently-proposed steady-state MOEA (Deb et al., 2003) which was developed based on the epsilon-dominance concept introduced earlier(Laumanns et al., 2002) and using efficient parent and archive update strategies for achieving a well-distributed and well-converged set of solutions quickly. Based on an extensive comparative study with four other state-of-the-art MOEAs on a number of two, three, and four objective test problems, it is observed that the steady-state MOEA is a good compromise in terms of convergence near to the Pareto-optimal front, diversity of solutions, and computational time. Moreover, the epsilon-MOEA is a step closer towards making MOEAs pragmatic, particularly allowing a decision-maker to control the achievable accuracy in the obtained Pareto-optimal solutions.
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction (2000)

The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences and metabolic modules from the EMP/MPW family of databases. This system contains data derived from about 40 completed or nearly completed genomes. Sequence homologies, various ORF-clustering algorithms, relative gene positions on the chromosome and placement of gene products in metabolic pathways (metabolic reconstruction) can be used for the assignment of gene functions and for development of overviews of genomes within WIT. The integration of a large number of phylogenetically diverse genomes in WIT facilitates the understanding of the physiology of different organisms.
In vitro studies of the interaction of poly(NIPAm/MAA) nanoparticles with proteins and cells (2000)

The pH- and temperature-responsive poly(N-isopropylacrylamide-co-methacrylic acid) (PNIPAm/MAA) nanoparticles are of potential application in targeted drug delivery. Their responsive properties in the presence of human serum albumin were investigated using dynamic light scattering (DLS), protein assay, and electron spin resonance (ESR) spectroscopy. Their interaction with human monocytes and polymorphonuclear leukocytes (PMNLs) was studied using scanning electron microscopy (SEM) and oxygen consumption method. The nanoparticles exhibited a volume phase transition at 35-40 degrees C in Hanks balanced salt solution (HBSS) and in phosphate buffer solution (PBS) of pH 7.4. The diameter of the nanoparticles decreased slightly in the presence of HSA at 25 degrees C at neutral pH, whereas an increase in the diameter in pH 6 PBS at 40 degrees C was revealed. The amount of albumin adsorbed onto the nanoparticles decreased with increasing temperature. The ESR spectra of spin labeled HSA indicated a more restricted environment in the nanoparticles at elevated temperatures. The stimulation of PMNL oxygen consumption by PNIPAm based nanoparticles, an indication of phagocytosis of the particles, was not observed regardless whether the nanoparticles were incubated in plasma or serum. In contrast, the more hydrophobic polystyrene (PSt) particles induced a significant increase in the rate of oxygen consumption after the incubation. PNIPAm/MAA-grafted-PSt particles behaved similarly to the PNIPAm/MAA nanoparticles, suggesting that surface properties dictate the recognition of colloids by PMNLs.
Cigarette smoke condensate stimulates urokinase production through the generation of reactive oxygen species and activation of the mitogen activated protein kinase pathways in human gingival fibroblasts (2009)

Cigarette smoke condensate stimulates urokinase production and plasmin activation in gingival fibroblasts. Moreover, cigarette smoke condensate-stimulated urokinase production depends on both the activation of ERK/JNK pathways and on the generation of intracellular reactive oxygen species. These results show that cigarette smoke may alter connective tissue remodeling by inducing production of the urokinase-type plasminogen activator through specific signaling pathways.
A Physical Unclonable Function with Redox-based Nanoionic Resistive Memory (2016)

A unique set of characteristics are packed in emerging nonvolatile reduction-oxidation (redox)-based resistive switching memories (ReRAMs) such as their underlying stochastic switching processes alongside their intrinsic highly nonlinear current-voltage characteristic, which in addition to known nano-fabrication process variation make them a promising candidate for the next generation of low-cost, low-power, tiny and secure Physically Unclonable Functions (PUFs). This paper takes advantage of this otherwise disadvantageous ReRAM feature using a combination of novel architectural and peripheral circuitry. We present a physical one-way function, nonlinear resistive Physical Unclonable Function (nrPUF), potentially applicable in variety of cyber-physical security applications given its performance characteristics. We experimentally verified performance of Valency Change Mechanism (VCM)-based ReRAM in nano-fabricated crossbar arrays across multiple dies and runs. In addition to a massive pool of Challenge-Response Pairs (CRPs), using a combination of experimental and simulation, our proposed PUF shows a reliability of 98.67%, a uniqueness of 49.85%, a diffuseness of 49.86%, a uniformity of 47.28%, and a bit-aliasing of 47.48%.
Overview and Evaluation of Bluetooth Low Energy: An Emerging Low-Power Wireless Technology (2012)

Bluetooth Low Energy (BLE) is an emerging low-power wireless technology developed for short-range control and monitoring applications that is expected to be incorporated into billions of devices in the next few years. This paper describes the main features of BLE, explores its potential applications, and investigates the impact of various critical parameters on its performance. BLE represents a trade-off between energy consumption, latency, piconet size, and throughput that mainly depends on parameters such as connInterval and connSlaveLatency. According to theoretical results, the lifetime of a BLE device powered by a coin cell battery ranges between 2.0 days and 14.1 years. The number of simultaneous slaves per master ranges between 2 and 5,917. The minimum latency for a master to obtain a sensor reading is 676 µs, although simulation results show that, under high bit error rate, average latency increases by up to three orders of magnitude. The paper provides experimental results that complement the theoretical and simulation findings, and indicates implementation constraints that may reduce BLE performance.
Suppression of epithelial apoptosis and delayed mammary gland involution in mice with a conditional knockout of Stat3 (1999)

Mammary gland involution is characterized by extensive apoptosis of the epithelial cells. At the onset of involution, Stat3 is specifically activated. To address the function of this signaling molecule in mammary epithelial apoptosis, we have generated a conditional knockout of Stat3 using the Cre-lox recombination system. Following weaning, a decrease in apoptosis and a dramatic delay of involution occurred in Stat3 null mammary tissue. Involution is normally associated with a significant increase in IGFBP-5 levels. This was observed in control glands, but not in the absence of Stat3. IGFBP-5 has been suggested to induce apoptosis by sequestering IGF-1 to casein micelles, thereby inhibiting its survival function. Our findings suggest that IGFBP-5 is a direct or indirect target for Stat3 and its upregulation is essential to normal involution. No marked differences were seen in the regulation of Stat5, Bcl-x(L), or Bax in the absence of Stat3. Precocious activation of Stat1 and increases in levels of p53 and p21 occurred and may act as compensatory mechanisms for the eventual initiation of involution observed in Stat3 null mammary glands. This is the first demonstration of the importance of a Stat factor in signaling the initiation of physiological apoptosis in vivo.
A Novel Acidophilic RNA Motif That Recognizes Coenzyme A (1998)

Specific recognition of nucleotide cofactors by RNA may be important in engineering new RNA enzymes (ribozymes). Although in vitro selections (SELEX) have identified nucleic acid motifs ("aptamers") that bind a variety of adenosine cofactors, none of these recognizes coenzyme A (CoA), the primary biological cofactor used in acyltransfer reactions. We used SELEX experiments with two random RNA pools to identify aptamers that bind CoA. Functional boundary determination and extensive comparative sequence analysis (including reselection of a mutagenized, circularly permuted RNA) led to the identification of a 52 nucleotide minimal aptamer ("min52"). The RNA structural motif contains a large internal loop with 26 unpaired nucleotides flanked by helices of any base-paired sequence. Twenty loop nucleotides are specifically required for binding activity, 12 of which are derived from the original primer binding sequences. Specificity studies with CoA analogues demonstrated that the aptamer recognizes many adenosine analogues, including ATP, and that recognition is predominantly through the Höogsteen face of adenine. Binding activity is greatest at acidic pH (optimum near 5.0), in low or no monovalent salt, and at high concentrations of either Mg2+ or Mn2+. Strong binding activity (86% of maximum) is observed at pH 4.0, suggesting that at least some extreme conditions (acidic pH) may be compatible with RNA World theories of the origin and early evolution of life. In the presence of 10 mM Mg2+, binding is unaffected by the addition of 1 mM Ca2+, but it is mildly inhibited by 1 mM Zn2+ or Co2+ or by 0.1 mM Cu2+ or Ni2+. The dissociation constant (Kd) for the association of min52 RNA with ATP in solution was measured to be 2.4 +/- 0.4 microM under the conditions of the selection and 0.5 +/- 0.1 microM under optimized conditions. Finally, we show that the selected CoA aptamer populations contain other RNAs at low frequencies that preferentially recognize intact CoA and are not eluted from the resin by AMP alone.
Addendum to “Radio Propagation Over Plane Earth-Field Strength Curves” (1937)

In the paper of the above title in the January 1937 issue of the Bell System Technical Journal, an approximation which was not explicitly pointed out was made in deriving equation (17). A note from Mr. K. A. Norton∗ of the Federal Communications Commission points out that equation (17) does not give a reasonable result when τ = 1. The explanation is that two terms which are unimportant except near the transmitter when the ground is a perfect dielectric were deleted.
Simple method for accurate alignment in toric phakic and aphakic intraocular lens implantation (2008)

A simple technique for the accurate surgical alignment of toric phakic and aphakic intraocular lenses (IOLs) is described. The mathematical relationship between toric misalignment and cylinder error is reviewed to demonstrate the importance of toric lens alignment in the setting of increased rotational stability with newer generation lenses. A formula for calculating the exact lens misalignment given a manifest cylinder is also presented.
Proinflammatory Cytokines Lowering Erythropoietin Production (1998)

The plasma level of erythropoietin (Epo) in anemic patients suffering from inflammation is often low in relation to the blood hemoglobin concentration. Various proinflammatory cytokines have been tested for their action on the synthesis of Epo. Interleukin 1 (IL-1) and tumor necrosis factor-alpha(TNF-alpha) suppress Epo gene expression in isolated perfused rat kidneys and in human hepatoma cell cultures. IL-6 inhibits in the kidney, and conflicting results have been reported for its effect on Epo synthesis in hepatic cells. Several other cytokines tested were without effect. Thus, mainly IL-1 and TNF-alpha seem to be responsible for the defect in Epo production in severe systemic and renal inflammatory diseases.
Three‐dimensional method for comparing in vivo interventional MR images of thermally ablated tissue with tissue response (2003)

Our results suggest that our methodology can be used to achieve three-dimensional registration of histology and in vivo MR images. In MR lesion images, the inner border of the hyperintense region corresponds to the border of irreversible cell damage. This is good evidence that during RF ablation treatments, iMRI lesion images can be used for real-time feedback.
Control of adenovirus E1B mRNA synthesis by a shift in the activities of RNA splice sites. (1984)

The primary transcript from adenovirus 2 early region 1B (E1B) is processed by differential RNA splicing into two overlapping mRNAs, 13S and 22S. The 22S mRNA is the major E1B mRNA during the early phase of infection, whereas the 13S mRNA predominates during the late phase. In previous work, it has been shown that this shift in proportions of the E1B mRNAs is influenced by increased cytoplasmic stability of the 13S mRNA at late times in infection. Two observations presented here demonstrate that the increase in proportion of the 13S mRNA at late times is also regulated by a change in the specificity of RNA splicing. First, the relative concentrations of the 13S to 22S nuclear RNAs were not constant throughout infection but increased at late times. Secondly, studies with the mutant, adenovirus 2 pm2250 , provided evidence that there was an increased propensity to utilize a 5' splice in the region of the 13S 5' splice site at late times in infection. Adenovirus 2 pm2250 has a G----C transversion in the first base of E1B 13S mRNA intron preventing splicing of the 13S mRNA but not of the 22S mRNA. During the early phase of a pm2250 infection, the E1B primary transcripts were processed into the 22S mRNA only. However, during the late phase, when the 13S mRNA normally predominates, E1B primary transcripts were also processed by RNA splicing at two formerly unused or cryptic 5' splice sites. Both cryptic splice sites were located much closer to the disrupted 13S 5' splice site than to the 22S 5' splice site. Thus, the temporal increase in proportion of the 13S mRNA to the 22S mRNA is regulated by two processes, an increase in cytoplasmic stability of the 13S mRNA and an increased propensity to utilize the 13S 5' splice site during the late phase of infection. Adenovirus 2 pm2250 was not defective for productive infection of HeLa cells or for transformation of rat cells.
"Lift Slab Construction: its History, Methodology, Economics, and Applications" (1988)

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Platinum(iv) anticancer prodrugs – hypotheses and facts (2016)

In this manuscript we focus on Pt(iv) anticancer prodrugs. We explore the main working hypotheses for the design of effective Pt(iv) prodrugs and note the exceptions to the common assumptions that are prevalent in the field. Special attention was devoted to the emerging class of "dual action" Pt(iv) prodrugs, where bioactive ligands are conjugated to the axial positions of platinum in order to obtain orthogonal or complementary effects that will increase the efficacy of killing the cancer cells. We discuss the rationale behind the design of the "dual action" prodrugs and the results of the pharmacological studies obtained. Simultaneous release of two bioactive moieties inside the cancer cells often triggers several processes that together determine the fate of the cell. Pt(iv) complexes provide many opportunities for applying new concepts in targeting, synergistic cell killing and exploiting novel nanodelivery systems.
A Common Regulator for the Operons Encoding the Enzymes Involved in d -Galactarate, d -Glucarate, and d -Glycerate Utilization in Escherichia coli (2000)

Genes for D-galactarate (gar) and D-glucarate (gud) metabolism in Escherichia coli are organized in three transcriptional units: garD, garPLRK, and gudPD. Two observations suggested a common regulator for the three operons. (i) Their expression was triggered by D-galactarate, D-glucarate, and D-glycerate. (ii) Metabolism of the three compounds was impaired by a single Tn5 insertion mapped in the yaeG gene (proposed name, sdaR), outside the D-galactarate and D-glucarate systems. Expression of the sdaR gene is autogenously regulated.
Hourglass schemes: how to prove that cloud files are encrypted (2012)

We consider the following challenge: How can a cloud storage provider prove to a tenant that it's encrypting files at rest, when the provider itself holds the corresponding encryption keys? Such proofs demonstrate sound encryption policies and file confidentiality. (Cheating, cost-cutting, or misconfigured providers may bypass the computation/management burdens of encryption and store plaintext only.) To address this problem, we propose hourglass schemes, protocols that prove correct encryption of files at rest by imposing a resource requirement (e.g., time, storage or computation) on the process of translating files from one encoding domain (i.e., plaintext) to a different, target domain (i.e., ciphertext). Our more practical hourglass schemes exploit common cloud infrastructure characteristics, such as limited file-system parallelism and the use of rotational hard drives for at-rest files. For files of modest size, we describe an hourglass scheme that exploits trapdoor one-way permutations to prove correct file encryption whatever the underlying storage medium. We also experimentally validate the practicality of our proposed schemes, the fastest of which incurs minimal overhead beyond the cost of encryption. As we show, hourglass schemes can be used to verify properties other than correct encryption, e.g., embedding of "provenance tags" in files for tracing the source of leaked files. Of course, even if a provider is correctly storing a file as ciphertext, it could also store a plaintext copy to service tenant requests more efficiently. Hourglass schemes cannot guarantee ciphertext-only storage, a problem inherent when the cloud manages keys. By means of experiments in Amazon EC2, however, we demonstrate that hourglass schemes provide strong incentives for economically rational cloud providers against storage of extra plaintext file copies.