gebhart/patrepeval huggingface dataset:
Butadiene-induced Intrastrand DNA Cross-links: A Possible Role in Deletion Mutagenesis (2000)

To initiate studies designed to identify the mutagenic spectrum associated with butadiene diepoxide-induced N(2)-N(2) guanine intrastrand cross-links, site specifically adducted oligodeoxynucleotides were synthesized in which the adducted bases were centrally located within the context of the human ras 12 codon. The two stereospecifically modified DNAs and the corresponding unmodified DNA were ligated into a single-stranded M13mp7L2 vector and transfected into Escherichia coli. Both stereoisomeric forms (R, R and S,S) of the DNA cross-links resulted in very severely decreased plaque-forming ability, along with an increased mutagenic frequency for both single base substitutions and deletions compared with unadducted DNAs, with the S,S stereoisomer being the most mutagenic. Consistent with decreased plaque formation, in vitro replication of DNA templates containing the cross-links by the three major E. coli polymerases revealed replication blockage by both stereoisomeric forms of the cross-links. The same DNAs that were used for replication studies were also assembled into duplex DNAs and tested as substrates for the initiation of nucleotide excision repair by the E. coli UvrABC complex. UvrABC incised linear substrates containing these intrastrand cross-links with low efficiency, suggesting that these lesions may be inefficiently repaired by the nucleotide excision repair system.
Cooperative/distributed localization and characterization of GNSS jamming interference (2013)

Interference is the major threat to integrity of navigation systems. In this paper, we provide new approaches to localization and characterization operations of GNSS jamming signals in both cooperative and distributed architectures. As for localization, Differential Received Signal Strength (DRSS) and an Extended Kalman Filter (EKF) are exploited. With respect to characterization, two approaches are envisaged, both based on exploiting the Karhunen-Loève Expansion (KLE). In the first, the nodes estimate and reconstruct the received jamming signal and share this data between themselves or with a Fusion Center (FC), which exploits KLE for data aggregation. In the second approach, signal estimation and reconstruction are performed at the FC, thus decreasing the nodes' complexity. The performance of the localization and characterization algorithms are analyzed in terms of Mean Localization Error (MLE) and Mean Square Error (MSE), respectively. Simulation results show that the proposed algorithms provide good performance.
Animal models of alcoholic liver disease--focus on the intragastric feeding model. (2003)

The use of animal models has contributed to greater understanding of how alcoholic liver disease (ALD) develops, and of how the severity of liver injury is influenced by factors other than alcohol, such as nutrition, oxygen deprivation (as occurs with sleep apnea or smoking), and gene regulation. This article focuses on the use of one animal model in particular, the intragastric feeding model in rats. This model allows scientists to rigorously control an animal's consumption of both alcohol and dietary nutrients and is providing important information on the mechanisms of injury of alcoholic liver disease.
Glucose-Based Amphiphilic Telomers Designed to Keep Membrane Proteins Soluble in Aqueous Solutions: Synthesis and Physicochemical Characterization (2008)

A novel class of nonionic amphipols (NAPols) designed to handle membrane proteins in aqueous solutions has been synthesized, and its solution properties have been examined. These were synthesized through free radical cotelomerization of glucose-based hydrophilic and amphiphilic monomers derived from tris(hydroxymethyl)acrylamidomethane using azobisisobutyronitrile as the initiator and thiol as the transfer agent. The molecular weight and the hydrophilic/lipophilic balance of the cotelomers were modulated by varying the thiol/monomers and the hydrophilic monomer/amphiphilic monomer ratios, respectively, and were characterized by 'H NMR, UV, gel permeation chromatography, and Fourier transform infrared spectroscopy. Their physicochemical properties in aqueous solution were studied by dynamic light scattering, aqueous size-exclusion chromatography, analytical ultracentrifugation, and surface-tension measurements. NAPols are highly soluble in water and form, within a large concentration range, well-defined supramolecular assemblies with a diameter of approximately 6-7 nm, a narrow particle size distribution, and an average molecular weight close to 50 x 10(3) g x mol(-1). Varying the hydrophilic/amphiphilic monomer ratio of NAPols in the range of 3.0-4.9, the degree of polymerization in the range of 51-78, and the resulting average molar mass in the range of 20-29 x 10(3) g x mol(-1) has little incidence on their solution properties. Glucose-based NAPols efficiently kept soluble in aqueous solutions two test membrane proteins: bacteriorhodopsin and the transmembrane domain of Escherichia coli's outer membrane protein A.
Defatting heptocytes under flow (2014)

There is a critical shortage of transplantable livers in both the US and the world. One method to increase the donor pool is to develop methodology to recondition extended criteria donor grafts, a large portion of which are moderate to severe macrosteatotic livers. Transplantation of these livers often leads to primary nonfunction caused by an increased susceptibility to the effects of ischemia reperfusion injury that result from the harvesting, transportation, and transplantation of the liver. Our lab has developed a novel cocktail of defatting reagents that can, over a period of two days, render hepatocytes lean and with good cell viability and function. Despite this accomplishment, in order to be feasibly performed in a clinical setting, the defatting process must be completed in a matter of hours. The current project focuses on understanding the differences between defatting in a static versus flow environment and then using this information to develop the ideal parameters for defatting whole organs. Our hypothesis in the current work is that using flow and the appropriate defatting agents, steatotic hepatocytes can be defatted in a clinically relevant time of hours, without decreasing cell viability or function. In order to test this hypothesis, a perfusion reactor was constructed which holds microscope slides that can be seeded with fatty hepatocytes. Perfusion of defatting media was performed at different flow rates over a six hour period. Results showed that within a six hour period, significant defatting (as compared to static cultures) was observed at both 2.0 and 4.0 ml/min as indicated by oil red O staining. Current experiments are focused on further evaluation of hepatocyte viability and function (e.g. albumin, urea, and cytochrome P450 function). These types of parametric experiments will form the basis for future perfusions with whole organs from obese rats.
A description of the electronic computer at the institute for advanced studies (1952)

In June, 1946 John von Neumann, Herman H. Goldstine, and Arthur W. Burks set forth logical principles on the basis of which they proposed to construct a general purpose computing machine at the Institute for Advanced Study in Princeton, New Jersey.
A Pharmacologic “Stress Test” for Assessing Select Antioxidant Defenses in Patients with CKD (2020)

A Study with RBT-1, in Healthy Volunteers and Subjects with Stage 3-4 Chronic Kidney Disease, NCT0363002 and NCT03893799.
Clinical translation of interventions that target ageing: towards a longevity dividend (2017)

Abstract Exciting advances have been made recently in understanding the mechanistic underpinnings of ageing. Mounting evidence suggests that progression of ageing changes can be modulated. Interventions that extend healthspan and lifespan in model organisms have been developed. The time is approaching for translation of these interventions into clinical treatments. By targeting fundamental ageing mechanisms, it may be possible to delay, prevent, or alleviate chronic diseases as a group, rather than individually, and enhance healthspan. Such a compression of morbidity would have profound clinical and economic benefits, with reductions in life-years spent with chronic disease and age-related dysfunction. However, barriers remain, including lack of clinical and regulatory paradigms for translating agents that target fundamental ageing processes into clinical interventions, and a shortage of personnel trained to do so. Here we consider research findings that support the potential value of translational ageing research and strategies to move these findings from bench to bedside.
Review: Novel Nonviral Delivery Approaches for Interleukin-12 Protein and Gene Systems: Curbing Toxicity and Enhancing Adjuvant Activity (2006)

It has become increasingly apparent that the ability to generate an optimal host immune response requires effective cross talk between the innate and adaptive components of the immune system. Pro-inflammatory cytokines, in particular those that can induce a danger signal, often called signal 3, are crucial in this role of initiating and augmenting the presentation of exogenous antigen to T cells by dendritic cells. Interleukin-12 (IL-12) in particular has been defined as a "signal 3" cytokine required for the antigen cross priming. Given this unique interactive function, a significant amount of work has been performed to define possible therapeutic applications for IL-12. Systemic IL-12 administration can clearly act as a potent adjuvant for postvaccination T cell responses in a variety of diseases. As an example, in the cancer setting, systemic IL-12 is capable of suppressing tumor growth, metastasis, and angiogenesis in vivo. IL-12, however, has been associated with significant dose- and schedule-dependent toxicity in early clinical trials, results that have proven to be a major obstacle to its clinical application. Recent research has focused on decreasing the toxicity of IL-12 using different delivery approaches, including virus-based and gene-modified cell-based delivery. Although effective, these approaches also have limitations, including the generation of neutralizing antibodies, in addition to lacking the simplicity and versatility required for universal clinical application. Thus, there is a significant interest in the development of alternative delivery approaches for IL-12 administration that can overcome these issues. Several nonviral delivery approaches for IL-12 protein or gene expression vectors are being defined, including alum, liposomes, and polymer-based delivery. These developing approaches have shown promising adjuvant effects with significantly lessened systemic toxicity. This article discusses the potential capabilities of these nonvirus-based IL-12 delivery systems in different disease settings, including allergy, infection, and cancer.
Chemical Protective Textiles of UiO-66-Integrated PVDF Composite Fibers with Rapid Heterogeneous Decontamination of Toxic Organophosphates (2018)

Metal-organic frameworks (MOFs) are a new and growing area of materials with high porosity and customizability. UiO-66, a zirconium-based MOF, has shown much interest to the military because of the ability of the MOF to catalytically decontaminate chemical warfare agents (CWAs). Unfortunately, the applications for MOFs are limited because of their powder form, which is difficult to incorporate into protective clothing. As a result, a new area of research has developed to functionalize fabrics with MOFs to make a wearable multifunctional fabric that retains the desired properties of the MOF. In this work, UiO-66 was incorporated into poly(vinylidene) fluoride/Ti(OH)<sub>4</sub> composite fabric using electrospinning and evaluated for its use in chemical protective clothing. The base triethanolamine (TEA) was added to the composite fabric to create a self-buffering system that would allow for catalytic decontamination of CWAs without the need for a buffer solution. The fabrics were tested against the simulants methyl-paraoxon (dimethyl (4-nitrophenyl) phosphate, DMNP), diisopropyl fluorophosphate (DFP), and the nerve agent soman (GD). The results show that all of the samples have high moisture vapor transport and filtration efficiency, which are desirable for protective clothing. The incorporation of TEA decreased air permeation of the fabric, but increased the catalytic activity of the composite fabric against DMNP and DFP. Samples with and without TEA have rapid half-lives ( t<sub>1/2</sub>) as short as 35 min against GD agent. These new catalytically active self-buffering multifunctional fabrics have great potential for application in chemical protective clothings.
Caspase-dependent Activation of Calpain during Drug-induced Apoptosis (1999)

We have previously demonstrated that calpain is responsible for the cleavage of Bax, a proapoptotic protein, during drug-induced apoptosis of HL-60 cells (Wood, D. E., Thomas, A., Devi, L. A., Berman, Y., Beavis, R. C., Reed, J. C., and Newcomb, E. W. (1998) Oncogene 17, 1069-1078). Here we show the sequential activation of caspases and calpain during drug-induced apoptosis of HL-60 cells. Time course experiments using the topoisomerase I inhibitor 9-amino-20(S)-camptothecin revealed that cleavage of caspase-3 substrates poly(ADP-ribose) polymerase (PARP) and the retinoblastoma protein as well as DNA fragmentation occurred several hours before calpain activation and Bax cleavage. Pretreatment with the calpain inhibitor calpeptin blocked calpain activation and Bax cleavage but did not inhibit PARP cleavage, DNA fragmentation, or 9-amino-20(S)-camptothecin-induced morphological changes and cell death. Pretreatment with the pan-caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (Z-VAD-fmk) inhibited PARP cleavage, DNA fragmentation, calpain activation, and Bax cleavage and increased cell survival by 40%. Interestingly, Z-VAD-fmk-treated cells died in a caspase- and calpain-independent manner that appeared morphologically distinct from apoptosis. Our results suggest that excessive or uncontrolled calpain activity may play a role downstream of and distinct from caspases in the degradation phase of apoptosis.
Développement de carbures de molybdène supportés pour l’hydrogénation de l’acide succinique en phase aqueuse (2018)

SSCI-VIDE+CDFA+NPR:MAB:CPI
Antitumor efficacy and local distribution of doxorubicin via intratumoral delivery from polymer millirods (2006)

The purpose of this study was to evaluate the antitumor efficacy and local drug distribution from doxorubicin-containing poly(D,L-lactide-co-glycolide) (PLGA) implants for intratumoral treatment of liver cancer in a rabbit model. Cylindrical polymer millirods (length 8 mm, diameter 1.5 mm) were produced using 65% PLGA, 21.5% NaCl, and 13.5% doxorubicin. These implants were placed in the center of VX2 liver tumors (n = 16, 8 mm in diameter) in rabbits. Tumors were removed 4 and 8 days after millirod implantation, and antitumor efficacy was assessed using tumor size measurements, tumor histology, and fluorescent measurement of drug distribution. The treated tumors were smaller than the untreated controls on both day 4 (0.17 +/- 0.06 vs. 0.31 +/- 0.08 cm(2), p = 0.048) and day 8 (0.14 +/- 0.04 vs. 1.8 +/- 0.8 cm(2), p = 0.025). Drug distribution profiles demonstrated high doxorubicin concentrations (>1000 microg/g) at the tumor core at both time points and drug penetration distances of 2.8 and 1.3 mm on day 4 and 8, respectively. Histological examination confirmed necrosis throughout the tumor tissue. Biodegradable polymer millirods successfully treated the primary tumor mass by providing high doxorubicin concentrations to the tumor tissue over an eight day period.
Face flips in origami tessellations (2019)

Given a flat-foldable origami crease pattern $G=(V,E)$ (a straight-line drawing of a planar graph on a region of the plane) with a mountain-valley (MV) assignment $\mu:E\to\{-1,1\}$ indicating which creases in $E$ bend convexly (mountain) or concavely (valley), we may flip a face $F$ of $G$ to create a new MV assignment $\mu_F$ which equals $\mu$ except for all creases $e$ bordering $F$, where we have $\mu_F(e)=-\mu(e)$. In this paper we explore the configuration space of face flips for a variety of crease patterns $G$ that are tilings of the plane, proving examples where $\mu_F$ results in a MV assignment that is either never, sometimes, or always flat-foldable for various choices of $F$. We also consider the problem of finding, given two foldable MV assignments $\mu_1$ and $\mu_2$ of a given crease pattern $G$, a minimal sequence of face flips to turn $\mu_1$ into $\mu_2$. We find polynomial-time algorithms for this in the cases where $G$ is either a square grid or the Miura-ori, and show that this problem is NP-hard in the case where $G$ is the triangle lattice.
MicroRNA miR-7 regulates synthesis and secretion of insulin-like peptides (2019)

Abstract The insulin/IGF pathway is essential for linking nutritional status to growth and metabolism. MicroRNAs (miRNAs) are short RNAs that are players in the regulation of this process. The miRNA miR-7 shows highly conserved expression in insulin-producing cells across the animal kingdom, however, its conserved functions in regulation of insulin-like peptides (ILPs) remains unknown. Using Drosophila as a model, we demonstrate that miR-7 limits ILP availability by inhibiting its production and secretion. Increasing miR-7 alters body growth and metabolism in an ILP-dependent manner, elevating circulating sugars and total body triglycerides, while decreasing animal growth. These effects are not due to direct targeting of ILP mRNA, but instead arise through alternate targets that affect the function of ILP-producing cells. The Drosophila F-actin capping protein, CPA, is a direct target of miR-7, and knockdown of CPA in IPCs phenocopies the effects of miR-7 on ILP secretion. This regulation of CPA is conserved in mammals, with the mouse ortholog Capza1 also targeted by miR-7 in β-islet cells. Taken together, these results support a role for miR-7 regulation of an actin capping protein in insulin regulation, and highlight a conserved mechanism of action for an evolutionarily ancient microRNA. Disclosure Statement PA, JB, AJ and RWC have nothing to declare. JJC is an employee of Sg2, LLC, a healthcare consulting company.
10 Gb/s 1.95 mW active cascode transimpedance amplifier for high speed optical receivers (2016)

This paper presents the design and performance of a transimpedance amplifier (TIA) for optical receivers integrated in a 130nm CMOS technology. The proposed TIA is based on common source (CS) voltage amplifier with a shunt-shunt feedback resistor using active cascode technique (CSAC-TIA). The CSAC technique succeeds to extend the bandwidth without scarifying the gain and power consumption. The presented CSAC-TIA shows a post layout simulated transimpedance gain of 56.65 dBΩ with bandwidth 7 GHz for 0.2 pF photodiode capacitance and optical sensitivity of -20.5 dBm at a BER= 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> . The presented CSAC-TIA consumes 1.95 mW from single voltage supply of 1.5 V.
Spasticity: pathophysiology, evaluation and management (2012)

Spasticity is common in many neurological disorders, such as stroke and multiple sclerosis. It is part of the upper motor neurone syndrome manifesting as increased tone, clonus, spasms, spastic dystonia and co-contractions. The impact of spasticity varies from it being a subtle neurological sign to severe spasticity causing pain and contractures. Existing spasticity can be worsened by external factors such as constipation, urinary tract infections or pressure ulcers. Its management involves identification and elimination of triggers; neurophysiotherapy; oral medications such as baclofen, tizanidine and dantrolene; focal injection of botulinum toxin, alcohol or phenol, or baclofen delivered intrathecally through a pump; and surgical resection of selected dorsal roots of the spinal cord. This article reviews the current understanding of pathophysiology, clinical features and management of spasticity.
Does cyclodextrin affect penetration of diclofenac sodium through amniotic membrane? (2013)

Abstract Purpose To investigate permeability of amniotic membrane (AM) to diclofenac sodium containing eye drops with or without cyclodextrin (CD) Methods Cryopreserved AM pieces on cellulose acetate filter membranes were mounted in the previously established vertical Franz‐diffusion cell system equipped with autosampler. In vitro penetration of two commercially available eyedrops containing 0.1% diclofenac sodium was examined. Voltaren Ophtha CD (VO, with CD) and Uniclophen (UN, without CD) were compared. Drug release was determined by quantitative absorbance measurement carried out with a high performance liquid chromatography (HPLC). Results The initial two hours, release of diclofenac from VO was lower than penetration of diclofenac from UN. At 30 minutes only 6.6% of diclofenac penetrated AM from VO vs 11.5% from UN. At 2 hours difference between two eyedrops was not siginificant (25.69% for VO and 27.39% for UN; p&gt;0.05). After two hours, greater concentration of VO could be measured in the acceptor phase than that of UN and this difference remained significant over the study period. Seven and half hour after instillation we detected 56.26% for VO versus 35.62% for UN of baseline concentrations Conclusion Drug penetration of diclofenac sodium was affected by CD. Until 120 minutes following instillation, CD decreased drug release from eyedrop containing CD compared to eyedrop without CD. After 2 hours, however drug penetration became significantly greater from solution with CD compared to solution without CD.
Acoustic wave propagation in air-bubble curtains in water; Part I, History and theory (1982)

Abstract Air bubbles in water increase the compressibility several orders of magnitude above that in bubble-free water, thereby greatly reducing the velocity and increasing attenuation of acoustic waves. The effect of air bubbles in water on acoustic wave propagation was studied extensively during World War II as part of an overall effort to apply underwater sound in submarine warfare. Currently, air bubble curtains are used to prevent damage of submerged structures (e.g., dams) by shock waves from submarine explosives. Also, air-bubble curtains are used to reduce damage to water-filled tanks in which metals are formed by explosives.Since World War II, research has progressed less feverishly in government and university laboratories. Published results of laboratory experiments generally confirm theoretical velocity and attenuation functions and demonstrate that these quantities are dependent principally upon frequency, bubble size, and fractional volume of air. Below the bubble resonant frequency and in the frequency range of marine energy sources, acoustic wave velocity is essentially independent of frequency and bubble radius, being well below the velocity in bubble-free water. In this frequency range, attenuation increases with increasing frequency, decreasing bubble radius, and increasing fractional air volume.
Enhanced Birefringence of Inhomogeneous Slabs (2009)

We show that the presence of an interface changes the local field distributions in inhomogeneous materials. The loss of field symmetry leads to a significant surface-induced birefringence of an inhomogeneous medium.