gebhart/patrepeval huggingface dataset:
Function and regulation of the cyanobacterial genes <i>lexA</i>, <i>recA</i> and <i>ruvB</i>: LexA is critical to the survival of cells facing inorganic carbon starvation (2004)

The cyanobacterial genes lexA, recA and ruvB were analysed in Synechocystis PCC6803, which is shown here to be more radiation resistant than the other unicellular model strain Synechococcus PCC7942. We found that cyanobacteria do not have an Escherichia coli-type SOS regulon. The Synechocystis lexA and recA promoters were found to be strong and UV insensitive, unlike the ruvB promoter, which is weak and UV-C inducible. Yet, lexA and recA are regulated by UV-C, but the control is negative and occurs at the post-transcriptional level. Two novel conserved elements were characterized in the lexA promoter: (i) an unusually long crucial box 5'-TAAAATTTTGTATCTTTT-3' (-64, -47); and (ii) a negatively acting motif 5'-TAT GAT-3' (-42, -37). These elements were not found in the recA promoter, which appeared to be unusually simple in harbouring only a single crucial element (i.e. the canonical -10 box). RuvB, operating in recombination-dependent cellular processes, was found to be dispensable to cell growth, whereas LexA and RecA appeared to be critical to cell viability. Using DNA microarrays, we have identified 57 genes with expression that is altered, at least twofold, in response to LexA depletion. None of these genes is predicted to operate in DNA metabolism, arguing against the involvement of LexA in the regulation of DNA repair. Instead, most of the LexA-responsive genes were known to be involved in carbon assimilation or controlled by carbon availability. Consistently, the growth of the LexA-depleted strain was found to be strongly dependent on the availability of inorganic carbon.
Three-Dimensional Photodetectors in 3-D Silicon-On-Insulator Technology (2007)

We report on the design and measurement results of three-dimensional (3-D) photodetectors in a 0.18-mum silicon-on-insulator technology. The device measurements reported here show that the photodetectors can be used for the design of high-density imaging arrays in 3-D CMOS fabrication processes. The photodiodes respond to light in the range of 1-200 000 lx with currents of 2 fA to 300 pA and can be arranged in a 3-D stack. The phototransistors respond to light intensities of 5-200 000 lx with currents from 50 fA to 2.3 muA
On the Development of New Poly(styrene-oxyethylene) Graft Copolymer Resin Supports for Solid-Phase Organic Synthesis (1998)

With the aim of creating new, improved solid supports for organic synthesis, a series of poly(styrene-oxyethylene) graft copolymers 6a - d was synthesized by anionic polymerization of ethylene oxide from a polystyrene-supported 1,3-diol 5b. Graft lengths were varied from 29 to 58 repeat units (67-82 wt % polyoxyethylene). The so-formed alcohols 6a - d were further transformed into chlorides 7a - d, amines 8a - d, and two commonly used linkers, Wang 9a - d and HMPB 10a - d. These functional group interconversions were efficiently monitored using gel-phase 13C NMR, and the solid-state properties of all copolymers were characterized by differential scanning calorimetry. Thermal properties of these materials were found to be dominated by the polyoxyethylene composition. A correlation between the melting point associated with the graft lengths and the physical properties of the resins was observed. The optimum graft copolymer composition, determined by balancing the degree of functional group loading with resin crystallinity and swelling, was found to be in the 0.4-0.5 mmol g-1 range.
C6-Ceramide Nanoliposomes Target the Warburg Effect in Chronic Lymphocytic Leukemia (2013)

Ceramide is a sphingolipid metabolite that induces cancer cell death. When C6-ceramide is encapsulated in a nanoliposome bilayer formulation, cell death is selectively induced in tumor models. However, the mechanism underlying this selectivity is unknown. As most tumors exhibit a preferential switch to glycolysis, as described in the "Warburg effect", we hypothesize that ceramide nanoliposomes selectively target this glycolytic pathway in cancer. We utilize chronic lymphocytic leukemia (CLL) as a cancer model, which has an increased dependency on glycolysis. In CLL cells, we demonstrate that C6-ceramide nanoliposomes, but not control nanoliposomes, induce caspase 3/7independent necrotic cell death. Nanoliposomal ceramide inhibits both the RNA and protein expression of GAPDH, an enzyme in the glycolytic pathway, which is overexpressed in CLL. To confirm that ceramide targets GAPDH, we demonstrate that downregulation of GAPDH potentiates the decrease in ATP after ceramide treatment and exogenous pyruvate treatment as well as GAPDH overexpression partially rescues ceramide-induced necrosis. Finally, an in vivo murine model of CLL shows that nanoliposomal C6-ceramide treatment elicits tumor regression, concomitant with GAPDH downregulation. We conclude that selective inhibition of the glycolytic pathway in CLL cells with nanoliposomal C6-ceramide could potentially be an effective therapy for leukemia by targeting the Warburg effect.
Design, synthesis and in vitro characterization of fluorescent and paramagnetic CXCR4-targeted imaging agents. (2013)

The G-protein coupled C-X-C chemokine receptor type 4 (CXCR4) is highly overexpressed in a range of cancers and is therefore an excellent biomarker for cancer imaging. To this end targeted iron oxide nanoparticles were developed and utilised for in vitro imaging of MDA-MB-231 breast cancer cells overexpressing the CXCR4 receptor. Nanoparticles comprising an iron oxide core, encapsulated in a stabilising epichlorohydrin crossed-linked dextran polymer, were conjugated to a cyclopentapeptide with affinity to the CXCR4 receptor. The particles were characterized for their size, surface charge and r2 relaxivity at 4.7 T. MR imaging of the CXCR4 receptor with targeted iron oxide nanoparticles revealed an approximately 3-fold increase in T2 signal enhancement of MDA-MB-231 cells compared to non-targeted controls. Prussian blue staining of labeled MDA-MB-231 cells revealed darker and more intense staining of the cellular membrane. This study demonstrates the potential of targeted iron oxide nanoparticles for the imaging of the CXCR4 receptor by magnetic resonance imaging (MRI).
Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents (2012)

Since the September 11, 2001, terrorist attacks in the United States, the specter of a chemical threat against civilian populations has renewed research interest in chemical warfare agents, their mechanisms of action, and treatments that reverse their effects. In this Account, we focus specifically on organophosphorus nerve agents (OPNAs). Although some OPNAs are used as pest control, the most toxic chemicals in this class are used as chemical warfare agents in armed conflicts. The acute toxicity of OPNAs results from the irreversible inhibition of acetylcholinesterase (AChE, EC 3.1.1.7) via the formation of a covalent P-O bond at the serine hydroxyl group in the enzyme active site. AChE breaks down the neurotransmitter acetylcholine at neuronal synapses and neuromuscular junctions. The irreversible inhibition of AChE causes the neurotransmitter to accumulate in the synaptic cleft, leading to overstimulation of cholinergic receptors, seizures, respiratory arrest, and death. The current treatment for OPNA poisoning combines an antimuscarinic drug (e.g., atropine), an anticonvulsant drug (e.g., diazepam), and an AChE reactivator of the pyridinium aldoxime family (pralidoxime, trimedoxime, obidoxime, HI-6, HLö-7). Because of their high nucleophilicity, oximes can displace the phosphyl group from the catalytic serine, thus restoring the enzyme's catalytic activity. During 50 years of research in the reactivator field, researchers have synthesized and tested numerous structural modifications of monopyridinium oximes and bispyridinium oximes. In the past decade, medicinal chemists have focused their research on the more efficient bispyridinium reactivators, but all known reactivators have several drawbacks. First, due to their permanent positive charge, they do not cross the blood-brain barrier (BBB) efficiently and do not readily reactivate AChE in the central nervous system. Second, no single oxime is efficient against a wide variety of OPNAs. Third, oximes cannot reactivate "aged" AChE. This Account summarizes recent strategies for the development of AChE reactivators capable of crossing the BBB. The use of nanoparticulate transport and inhibition of P-glycoprotein efflux pumps improves BBB transport of these AChE reactivators. Chemical modifications that increased the lipophilicity of the pyridinium aldoximes, the addition of a fluorine atom and the replacement of a pyridyl ring with a dihydropyridyl moiety, enhances BBB permeability. The glycosylation of pyridine aldoximes facilitates increased BBB penetration via the GLUT-1 transport system. The development of novel uncharged reactivators that can move efficiently across the BBB represents one of the most promising of these new strategies.
Intrusion Detection System (IDS): Anomaly Detection Using Outlier Detection Approach (2015)

An Intrusion Detection System (IDS) is a software application or device that monitors the system or activities of network for policy violations or malicious activities and generates reports to the management system. A number of systems may try to prevent an intrusion attempt but this is neither required nor expected of a monitoring system. The main focus of Intrusion detection and prevention systems (IDPS) is to identify the possible incidents, logging information about them and in report attempts. In addition, organizations use IDPS for other purposes, like identifying problems with security policies, deterring individuals and documenting existing threats from infringing security policies. IDPS have become an essential addition to the security infrastructure of nearly every organization. Various methods can be used to detect intrusions but each one is specific to a specific method. The main goal of an intrusion detection system is to detect the attacks efficiently. Furthermore, it is equally important to detect attacks at a beginning stage in order to reduce their impacts. This research work proposed a new approach called outlier detection where, the anomaly dataset is measured by the Neighborhood Outlier Factor (NOF). Here, trained model consists of big datasets with distributed storage environment for improving the performance of Intrusion Detection system. The experimental results proved that the proposed approach identifies the anomalies very effectively than any other approaches.
Synthesis of carboranes containing nucleoside bases (1992)

Abstract The carboranes containing uridine derivatives ( 9a,b,c ), and purine base ( 8 ) were prepared by the reaction of decaborane with the corresponding acetylene precursors ( 3a, 3b, 2c and 5b , respectively).
Application scenarios of Nautical Ad-Hoc Network for maritime communications (2009)

In terrestrial wireless communications, high data-rate transmission can be readily achieved by installing base stations on the ground. However, the same system may not be adapted to maritime communication due to the geographically restricted nature of the sea, and therefore, MF/HF modems, capable of long-distance transmission, with low data-rate are frequently employed in maritime communication. Maritime satellite communication through Inmarsat is conventionally used to compensate for the low data-rate transmission of MF/HF modems, but its high cost still remains as a main drawback. In order to enhance the transmission speed with a fairly low price, in general, a network whose architecture is similar to Vehicular Ad-hoc Network (VANET), that allows peer-to-peer communications without base stations, i.e., ad-hoc network, is crucial. Herein, we propose an ad-hoc network for nautical environment, which is named as Nautical Ad-hoc Network (NANET). In this paper, scenarios toward NANET development are described and analysis of multiple access and duplexing schemes for corresponding NANET scenarios is discussed. A guideline for further research and developmental strategies on NANET is also suggested.
INFERCNMR: A <sup>13</sup>C NMR Interpretive Library Search System (2012)

INFERCNMR is an automated (13)C NMR spectrum interpretation aid for use either as a stand-alone program or as a component of a comprehensive, computer-based system for the characterization of chemical structure. The program is an interpretive library search which requires a database of assigned (13)C NMR spectra. An interpretive library search does not require overall structural similarity between an unknown and a library entry in order to retrieve a substructure common to both. Input consists of the chemical shift and one-bond proton-carbon multiplicity of each signal in the spectrum, and the molecular formula of the unknown. Program output is one or more substructures predicted to be present in the unknown, each of which is assigned an estimated prediction accuracy.
Age‐related changes of regional pulse wave velocity in the descending aorta using Fourier velocity encoded M‐mode (2010)

Aortic pulse wave velocity (PWV) is an independent determinant of cardiovascular risk. Although aortic stiffening with age is well documented, the interaction between aging and regional aortic PWV is still a debated question. We measured global and regional PWV in the descending aorta of 56 healthy subjects aged 25-76 years using a one-dimensional, interleaved, Fourier velocity encoded pulse sequence with cylindrical excitation. Repeatability across two magnetic resonance examinations (n = 19) and accuracy against intravascular pressure measurements (n = 4) were assessed. The global PWV was found to increase nonlinearly with age. The thoracic aorta was found to stiffen the most with age (PWV [thoracic, 20-40 years] = 4.7 ± 1.1 m/s; PWV [thoracic, 60-80 years] = 7.9 ± 1.5 m/s), followed by the mid- (PWV [mid-abdominal, 20-40 years] = 4.9 ± 1.3 m/s; PWV [mid-abdominal, 60-80 years] = 7.4 ± 1.9 m/s) and distal abdominal aorta (PWV [distal abdominal, 20-40 years] = 4.8 ± 1.4 m/s; PWV [distal abdominal, 60-80 years] = 5.7 ± 1.4 m/s). Good agreement was found between repeated magnetic resonance measurements and between magnetic resonance PWVs and the gold-standard. Fourier velocity encoded M-mode allowed to measure global and regional PWV in the descending aorta. There was a preferential stiffening of the thoracic aorta with age, which may be due to progressive fragmentation of elastin fibers in this region.
25 Gbps and beyond: VCSEL development at Philips (2013)

In comparison to widely used InGaAs Quantum Wells (QW) in high speed VCSELs operating at 25 Gbps and beyond, we present an investigation on the use of GaAs QWs, which have proven their ability to serve reliably in 10 Gbps and 14 Gbps VCSEL products and allow for an evolutionary extension of data rates based on mature technology. As data centers continuously increase in size, the demand for longer reach optical links within these data centers is addressed by the proposal of using small spectral width single-mode VCSELs that offer the potential of significantly reduced chromatic dispersion along optical fibers of several 100 m length. Performance and modeling parameters of single-mode VCSELs are being compared to those of typical multi-mode VCSELs built from identical epitaxy and process technology.
Chimeric Gα<sub>q</sub> mutants harboring the last five carboxy‐terminal residues of Gα<sub>i2</sub> or Gα<sub>o</sub> are resistant to pertussis toxin‐catalyzed ADP‐ribosylation (1998)

Three widely-used Galpha(q) chimeras harboring the last five residues of Galpha(i), Galpha(o) and Galpha(z) (qi5, qo5 and qz5) were examined for their ability to serve as substrates for pertussis toxin (PTX)-catalyzed ADP-ribosylation. In COS-7 cells coexpressing one of the three opioid receptors (mu, delta, and kappa) and a Galpha(q) chimera, agonist-induced stimulation of phosphoinositide-specific phospholipase C (PI-PLC) was largely insensitive to PTX treatment. Only the qi5-mediated stimulation of PI-PLC by kappa-opioids was partially inhibited by PTX. In betagamma-release assays, PTX treatment did not affect the ability of opioid receptors to activate these chimeras. [32P]ADP-ribosylation labeled Galpha(i/o) but not qi5 or qo5, although the expression of these chimeras was confirmed by immunodetection. Thus, Galpha(q) chimeras with a Galpha(i/o)-like tail are insensitive to PTX treatment.
ChemInform Abstract: PREPARATION AND SYNTHETIC APPLICATIONS OF LITHIUM DI(ALPHA‐METHOXYVINYL)CUPRATE (1975)

Abstract Das aus dem Äther (I) mit tert‐Butyllithium gewonnene Li‐Derivat (II) reagiert bei tiefen Temperaturen mit CuJ in Dimethylsulfid zur Titelverbindung (III).
A Faster, Better Approximation Algorithm for the Minimum Latency Problem (2008)

We give a 7.18-approximation algorithm for the minimum latency problem that uses only $O(n \log n)$ calls to the prize-collecting Steiner tree (PCST) subroutine of Goemans and Williamson. This improves the previous best algorithms in both performance guarantee and running time. A previous algorithm of Goemans and Kleinberg for the minimum latency problem requires an approximation algorithm for the k-minimum spanning tree (k-MST) problem which is called as a black box for each value of k. Their algorithm can achieve an approximation factor of 10.77 while making $O(n (n+\log C) \log n)$ PCST calls, a factor of 8.98 using $O(n^3(n+\log C) \log n)$ PCST calls, or a factor of $7.18+\epsilon$ using $n^{O(1/\epsilon)}\log C$ PCST calls, via the k-MST algorithms of Garg, Arya and Ramesh, and Arora and Karakostas, respectively. Here n denotes the number of nodes in the instance, and C is the largest edge cost in the input. In all cases, the running time is dominated by the PCST calls. Since the PCST subroutine can be implemented to run in $O(n^2)$ time, the overall running time of our algorithm is $O(n^3 \log n)$. We also give a faster randomized version of our algorithm that achieves the same approximation guarantee in expectation, but uses only $O(\log^2 n)$ PCST calls, and derandomize it to obtain a deterministic algorithm with factor $7.18+\epsilon$, using $O(\frac{1}{\epsilon} \log^2 n)$ PCST calls. The basic idea for our improvement is that we do not treat the k-MST algorithm as a black box. This allows us to take advantage of some special situations in which the PCST subroutine delivers a 2-approximate k-MST. We are able to obtain the same approximation ratio that would be given by Goemans and Kleinberg if we had access to 2-approximate k-MSTs for all values of k, even though we have them only for some values of k that we are not able to specify in advance. We also extend our algorithm to a weighted version of the minimum latency problem.
X-ray diffuse scattering from alkali, silver, and europium<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>β</mml:mi></mml:math>-alumina (1978)

Crystals of varying compensation mechanism (extra oxygen bridges or ${\mathrm{Co}}^{2+}$ substitution) and phase ($\ensuremath{\beta}$ or ${\ensuremath{\beta}}^{\ensuremath{'}\ensuremath{'}}$) have been grown by adding cobalt oxide to a melt containing NaC${\mathrm{O}}_{3}$, ${\mathrm{Al}}_{2}$${\mathrm{O}}_{3}$, and ${\mathrm{Bi}}_{2}$${\mathrm{O}}_{3}$ in the proportion 2.9:4.4:100. In $(1+x){\mathrm{Na}}_{2}\mathrm{O}\ifmmode\cdot\else\textperiodcentered\fi{}11{\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ the value of $x$ is \ensuremath{\sim}0.16(3) for crystals grown from the melt and \ensuremath{\sim}0.38(3) for crystals grown from the flux. Diffuse x-ray scattering measurements confirm the formation of Al Frenkel defects which lock the extra oxygen ions in the diffusing plane. Rods of diffuse scattering are observed in $\ensuremath{\beta}$-alumina grown from the flux with Ag, K, Rb, and Eu substituted for Na in the diffusing plane. The rods are at ($h+\frac{1}{3},k+\frac{1}{3}$) and ($h+\frac{2}{3},k+\frac{2}{3}$) but not at integral ($\mathrm{hk}$). A two-dimensional short-range-order model consisting of three types of cells: (i) containing one diffusing ion, (ii) two ions, and (iii) 2 ions plus an extra bridge [cells (ii) and (iii) have no diffusing ions in the Eu case] agrees semiquantitatively with the observed data. The conditional probability for doubly occupied cells or defect cells being nearest neighbors is ${P}_{22}(1)={P}_{33}(1)\ensuremath{\sim}0.05$ (random value is 1/6) and the correlations are assumed to fall off as $\frac{{e}^{\frac{\ensuremath{-}R}{\ensuremath{\xi}}}}{{R}^{\frac{1}{2}}}$ with the signs of the coefficients given by a superlattice which isolates cell (ii) and (iii). The correlation lengths in the plane and the activation energy for ionic conductivity both vary linearly with the concentration of extra bridges for K $\ensuremath{\beta}$-alumina. The correlation lengths in units of ${a}_{0}$ are 0.9(1), 1.2(1), 2.5(1), and 6.1(5) for Na, Ag, K, and Rb from the flux and 1.0(1), 1.2(1), 1.3(1) for Ag, K, and Rb from melt-grown crystals.
An Application of White Light Interferometry in Thin Film Measurements (1972)

An application of the white light interferometry technique has been developed for measuring the thickness of thin films. The technique is used in the development of sliders which serve as carriers for the magnetic transducers (read/write elements) that operate in close proximity to magnetic disks. With the proper design of a surface contour and the applied load on the slider, a self-acting air bearing is created under the slider due to the boundary layer existing on a rotating disk.
Effective Exon Skipping and Dystrophin Restoration by 2′-O-Methoxyethyl Antisense Oligonucleotide in Dystrophin-Deficient Mice (2013)

Antisense oligonucleotide (AO)-mediated exon-skipping therapy is one of the most promising therapeutic strategies for Duchenne Muscular Dystrophy (DMD) and several AO chemistries have been rigorously investigated. In this report, we focused on the effect of 2'-O-methoxyethyl oligonucleotides (MOE) on exon skipping in cultured mdx myoblasts and mice. Efficient dose-dependent skipping of targeted exon 23 was achieved in myoblasts with MOE AOs of different lengths and backbone chemistries. Furthermore, we established that 25-mer MOE phosphorothioate (PS) AOs provided the greatest exon-skipping efficacy. When compared with 2'O methyl phosphorothioate (2'OmePS) AOs, 25-mer MOE (PS) AOs also showed higher exon-skipping activity in vitro and in mdx mice after intramuscular injections. Characterization of uptake in vitro corroborated with exon-skipping results, suggesting that increased uptake of 25-mer MOE PS AOs might partly contribute to the difference in exon-skipping activity observed in vitro and in mdx mice. Our findings demonstrate the substantial potential for MOE PS AOs as an alternative option for the treatment of DMD.