gebhart/patrepeval huggingface dataset:
Genetic Modulation of the Overexpression of Tailoring Genes <i>eryK</i> and <i>eryG</i> Leading to the Improvement of Erythromycin A Purity and Production in <i>Saccharopolyspora erythraea</i> Fermentation (2008)

Erythromycin A (Er-A) is the most potent and clinically important member in the Er family produced by Saccharopolyspora erythraea. Er-B and Er-C, which are biologically much less active and cause greater side effects than Er-A, serve as the intermediates for Er-A biosynthesis and impurities in fermentation processes of many industrial strains. In this study, systematical modulation of the amounts of tailoring enzymes EryK (a P450 hydroxylase) and EryG (an S-adenosylmethionine-dependent O-methyltransferase) was carried out by genetic engineering in S. erythraea, including alterations of gene copy number ratio and organization and integrating the locus on the chromosome by homologous recombination. Introduction of additional eryK and eryG genes into S. erythraea showed significant impacts on their transcription levels and enhanced the biotransformation process from Er-D to Er-A with gene dose effects. At the eryK/eryG copy number ratio of 3:2 as well as their resultant transcript ratio of around 2.5:1 to 3.0:1, Er-B and Er-C were nearly completely eliminated and accordingly converted to Er-A, and the Er titer was improved by around 25% in the recombinant strain ZL1004 (genotype PermK*-K-K-G + PermE*-K + PermA*-G) and ZL1007 (genotype PermK*-K-G-K + PermE*-K + PermA*-G). This study may contribute to the continuous efforts toward further evaluation of the Er-producing system, with the aims of improving Er-A purity and production at the fermentation stage and lowering the production costs and environmental concerns in industry.
A comparison of intravenous and intradiscal delivery of multipotential stem cells on the healing of injured intervertebral disk (2014)

A major hurdle of cellular therapy for biological treatment of intervertebral disk (IVD) degeneration is the delivery method where current delivery methods are limited to intradiscal injection which can potentially cause further degeneration. Recent studies indicated that multipotential stem cells (MPSCs) from human umbilical cord blood home to injured sites and induce local therapeutic changes, thereby potentially addressing the drawbacks of direct delivery. We tested the effects of these cells on injured IVD using a mouse model of puncture-induced degeneration via two delivery methods. Caudal IVD underwent needle puncture, and MPSCs were injected indirectly (intravenously), or directly (intradiscally) into the nucleus pulposus. IVD were harvested for histological, gene and protein analysis after 14 weeks. Our finding showed limited homing ability of the MPSCs. However, regardless of delivery method, no engraftment or expansion of MPSCs was observed at the injured site. Contrasting to direct injection, intravenous injection neither improved the degeneration status, nor preserve disk height, however, both delivery methods increased glycosaminoglycan (GAG) protein and Acan gene expression relative to controls, suggesting possible paracrine effects. Identifying the mechanisms by which MPSCs act on endogenous IVD cells would provide insights into the potential of these cells to treat IVD injuries and degeneration.
Natural estolides produced by <i>Pseudomonas</i> sp. 42A2 grown on oleic acid: Production and characterization (2003)

Abstract Estolides are a group of FA polyesters resulting from ester bond formation between a hydroxyl or olefinic group of one FA and the terminal carboxyl group of a second FA. These products are commonly found in trace amounts, forming tetraglycerides in several oil seed plants, and have been produced by acid clay and enzymatic catalysis in vitro . In this study, natural estolides produced by a bacterial culture are presented for the first time. Pseudomonas sp. 42A2 produced ( E )‐10‐hydroxy‐8‐octadecenoic acid and ( E )‐7,10‐dihydroxy‐8‐octadecenoic acid when grown on oleic acid. It is suggested that these FA were polymerized in culture by a lipase produced by the bacterial strain, resulting in a mixture of estolides. These compounds amounted to 3.8 g/L after 72 h of incubation. LC‐MS analysis indicated that the types of estolides formed were dimers ( m/z 560–610), trimers ( m/z 845–906), tetramers ( m/z 1122–1202), pentamers ( m/z 1328–1424), and hexamers ( m/z 1554–1788), with a relative abundance of 27.5, 19.4, 15, 9.7, and 11%, respectively. This is the first report in which hexamers were detected in a bacterial culture.
Stereo panorama with a single camera (2003)

Full panoramic images, covering 360 degrees, can be created either by using panoramic cameras or by mosaicing together many regular images. Creating panoramic views in stereo, where one panorama is generated for the left eye, and another panorama is generated for the right eye is more problematic. Earlier attempts to mosaic images from a rotating pair of stereo cameras faced severe problems of parallax and of scale changes. A new family of multiple viewpoint image projections, the Circular Projections, is developed. Two panoramic images taken using such projections can serve as a panoramic stereo pair. A system is described to generates a stereo panoramic image using circular projections from images or video taken by a single rotating camera. The system works in real-time on a PC. It should be noted that the stereo images are created without computation of 3D structure, and the depth effects are created only in the viewer's brain.
Titanium aluminum nitride sputtered by HIPIMS (2012)

TiAlN was sputtered reactively by HIPIMS in the target compositions Ti/Al 33/67 and 50/50 using a modified OC Oerlikon Balzers INNOVA coating equipment. The resulting film properties like deposition rate, surface roughness, hardness, Young's modulus, wear, and film stress were analyzed as function of the nitrogen gas flow, pressure, target-substrate distance, and substrate bias. Furthermore, the films were characterized by X-ray diffraction and secondary electron microscopy of the cross section and the surface appearance. The process characteristics and film properties were compared with pulsed DC sputtering under the same conditions.
Collision-Induced Dissociation for Mass Spectrometric Analysis of Biopolymers: High-Resolution Fourier Transform Ion Cyclotron Resonance MS4 (1994)

Efficient collision-induced dissociation multistage tandem high-resolution mass spectrometry of peptide ions is demonstrated for the first time. Specifically, four-stage Fourier transform ion cyclotron resonance collision-induced dissociation tandem-in-time MS4 is demonstrated for bradykinin quasimolecular ions, MH+, produced by matrix-assisted laser desorption/ionization. We combine off-resonant excitation and ion axialization to improve the efficiency of parent ion dissociation and product ion collection and detection at every MS stage. We observe successive loss of water/ammonia from the C-terminus to leave an (MH-NH3/H2O)+ ion in the second stage, followed by successive losses of the next two amino acids, arginine and phenylalanine. High mass resolving power is achieved throughout all four MS stages, in an experiment that consumes approximately 10 pmol of peptide and takes only approximately 5 min. We project that it should be possible to automate this experiment for high-speed sequencing of biopolymers.
V<sup>III</sup>(OH){O<sub>2</sub>C–C<sub>6</sub>H<sub>4</sub>–CO<sub>2</sub>}.(HO<sub>2</sub>C–C<sub>6</sub>H<sub>4</sub>–CO<sub>2</sub>H)x(DMF)<sub>y</sub>(H<sub>2</sub>O)z (or MIL-68), a new vanadocarboxylate with a large pore hybrid topology : reticular synthesis with infinite inorganic building blocks? (2004)

V(III)(OH)[O(2)C-C(6)H(4)-CO(2)].(HO(2)C-C(6)H(4)-O(2)H)(x)(DMF)(y)(H(2)O)(z) or MIL-68 was solvothermally synthesised in a non-aqueous medium. Its structure, built up from octahedral chains connected by terephthalate linkers, exhibits large hexagonal channels containing different occluded moieties. Their irreversible removal releases a specific surface area of 603(22) m(2).g(-1)(BET).
Biocompatible Chemotherapy for Leukemia by Acid-Cleavable, PEGylated FTY720 (2020)

Targeting the inability of cancerous cells to adapt to metabolic stress is a promising alternative to conventional cancer chemotherapy. FTY720 (Gilenya), an FDA-approved drug for the treatment of multiple sclerosis, has recently been shown to inhibit cancer progression through the down-regulation of essential nutrient transport proteins, selectively starving cancer cells to death. However, the clinical use of FTY720 for cancer therapy is prohibited because of its capability of inducing immunosuppression (lymphopenia) and bradycardia when phosphorylated upon administration. A prodrug to specifically prevent phosphorylation during circulation, hence avoiding bradycardia and lymphopenia, was synthesized by capping its hydroxyl groups with polyethylene glycol (PEG) via an acid-cleavable ketal linkage. Improved aqueous solubility was also accomplished by PEGylation. The prodrug reduces to fully potent FTY720 upon cellular uptake and induces metabolic stress in cancer cells. Enhanced release of FTY720 at a mildly acidic endosomal pH and the ability to substantially down-regulate cell-surface nutrient transporter proteins in leukemia cells only by an acid-cleaved drug were confirmed. Importantly, the prodrug demonstrated nearly identical efficacy to FTY720 in an animal model of BCR-Abl-driven leukemia without inducing bradycardia or lymphopenia in vivo, highlighting its potential clinical value. The prodrug formulation of FTY720 demonstrates the utility of precisely engineering a drug to avoid undesirable effects by tackling specific molecular mechanisms as well as a financially favorable alternative to new drug development. A multitude of existing cancer therapeutics may be explored for prodrug formulation to avoid specific side effects and preserve or enhance therapeutic efficacy.
Enhancing Effect of Daidzein on the Differentiation and Mineralization in Mouse Osteoblast-like MC3T3-E1 Cells (2006)

The effect of daidzein, an important isoflavone, on the differentiation and mineralization in MC3T3-E1 cells, a mouse calvaria osteoblast-like cell line, was investigated. The MTT assay, the alizarin red S and von Kossa staining, the measurement of calcium (Ca) and phosphorus (P) concentrations by inductively coupled plasma-atomic emission spectrometry and the nitrophenol liberation method were used to determine the cell proliferation, mineralization and intracellular alkaline phosphatase (ALP) activity, respectively. Daidzein enhanced the cell proliferation after the culture for 2 days and the effect reached maximum on day 6. ALP activity and cellular Ca and P contents were increased time- and dose-dependently when the cells were treated with daidzein in the presence of disodium beta-glycerophosphate and L-ascorbic acid. Differentiation of the cells to the mature osteoblasts was prompted under incubation in the presence of daidzein for 21 days, by the time the mineralized nodules formed. The calcium depositions of the cells by alizarin red S staining were increased significantly after the culture with daidzein as long as 28 days. It has been demonstrated that daidzein may be able to enhance the bone differentiation and mineralization and prompt the bone formation in the early growing stage and the late growing stage of osteoblasts.
Application of foresight's technology to implement a waveform development environment (2002)

To achieve interconnection of disparate waveforms and radio architectures, a mechanism must be available to efficiently develop and test waveforms, to prototype new software definable radio (SDR,) architectures, and to download waveforms in the field. At present, such SDR applications are developed using disparate traditional SW and HW tools that do not support a HW/SW co-design process for a total system synthesis. Foresight Systems, Inc. has developed several tools that address a methodology for this waveform development environment, how to model functions and architectures for the environment, mapping functions to architectures, simulation and performance calculations, and automatic code generation for systems in an integrated development environment (IDE). In the SDR field, waveform and control domain libraries must exist as well as architecture libraries with a rich variety of multi-processor models, operating systems (OS), protocols, and I/O drivers. Such libraries are necessary in order for the designer to perform HW/SW co-design and system trade-offs to construct various instantiations of communication waveforms dynamically downloadable to a software mobile radio. The application of Foresight Systems' technology to the development of a waveform development environment for software definable radios is currently under active discussion between Foresight Systems and commercial firms.
Dissolution mechanism of cellulose in N2O4-DMSO system. (1986)

The dissolution mechanism of cellulose in the N204-DMSO system was studied by comparing 1H-NMR spectra of cellulose/N204-DMSO solutions with those of methanol/N204-DMSO solutions. In the dissolved state, cellulose was found to form trinitrite ester, and this formation reaction was irreversible in DMSO.
Efficient generation of shared RSA keys (2001)

We describe efficient techniques for a number of parties to jointly generate an RSA key. At the end of the protocol an RSA modulus N = pq is publicly known. None of the parties know the factorization of N . In addition a public encryption exponent is publicly known and each party holds a share of the private exponent that enables threshold decryption. Our protocols are efficient in computation and communication. All results are presented in the honest but curious scenario (passive adversary).
Methotrexate diffusion from acrylic cement. Local chemotherapy for bone tumours (1989)

We investigated the possible use of acrylic cement containing chemotherapeutic drugs in the treatment of malignant lesions in bone. The diffusion of methotrexate (MTX) from methylpolymethacrylate implants was studied in vitro: polymerisation of the cement did not destroy the drug; liberation began immediately and about 10% was released by 18 hours. Some release continued for as long as six months. In vivo experiments on rats with induced osteosarcoma showed that MTX in cement had both local and general effects which were dependent on the dosage. A series of 17 large dogs with spontaneous osteosarcoma were then treated by local resection and cement containing MTX. General chemotherapeutic effects were detectable from 2 hours to 5 days, survival was increased and local recurrence was reduced, but there were four cases of delayed wound healing. Preliminary studies in human patients confirm the possibility that this method of local chemotherapy could be a useful addition to the treatment of malignant tumours of bone.
Crystal Structure of Haloalkane Dehalogenase LinB from <i>Sphingomonas paucimobilis</i> UT26 at 0.95 Å Resolution:  Dynamics of Catalytic Residues<sup>,</sup> (2004)

We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in conformation B was mainly in the C(alpha)-C(beta)-C(gamma) angle (126 degrees ) that deviated by 13.4 degrees from the "ideal" bond angle of 112.6 degrees. On the basis of these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that protonation of the His272 side-chain nitrogen atoms does indeed reduce the distance between the side-chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in the Asp108 C(alpha)-C(beta)-C(gamma) angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at N(delta)(1) and Asp108 in conformation A gave the most exothermic reaction (DeltaH = -22 kcal/mol). With His272 doubly protonated at N(delta)(1) and N(epsilon)(2), the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in conformation B, the Asp108 C(alpha)-C(beta)-C(gamma) angle changed during the reaction and the Asp108 moved to conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.
A scalable approach for subscription-based information commerce (2002)

We consider an information commerce environment where clients subscribe to information objects sent via a broadcast onto a shared network (e.g., wireless, LAN, the Internet). In this context, a client should only be able to access its objects of interest for its subscription period, and the security system used must not be easily broken. Existing systems fail to perform well with increased client loads. We propose a new system, Drop Groups, and show that it is scalable.
Centrality-Based Anomaly Detection on Multi-Layer Networks Using Many-Objective Optimization (2020)

Anomaly detection on complex network is receiving increasing attention, e. g., for finding illegal financial transactions, or for understanding the behavior of people via analyzing social network data. This paper presents a novel method for recognizing and finding anomalies in complex networks. Specifically, it targets multi-layer social network data aiming at finding abnormal behavior of some (groups of) nodes in the network. The method starts by measuring the centrality of all nodes in each layer of the multi-layer network, continues by applying many-objective optimization with full enumeration based on minimization, and obtains the Pareto Front. Objective functions to be optimized simultaneously are the centrality of each layer in the network and thus, the number of objective function are the numbers of existing layers of a multi-layer networks. After the Pareto Front settles, the set of nodes in the Pareto Front are considered as a basis for finding the set of suspected anomaly nodes, using the novel ACE-Score. The ACE-Score is calculated by considering the centrality of a node in the i - th layer, the mean of the centrality in that layer, the standard deviation, and the edge density of each layer. A high ACE-Score then indicates candidate anomalous nodes. We evaluate the approach on generated synthetic network as well as real-world complex networks, demonstrating the effectiveness of the proposed approach. A key feature of our proposed approach is its interpretability and explainability, since we can directly assess anomalous nodes with respect to the network topology.
Position Locationing for Millimeter Wave Systems (2018)

The vast amount of spectrum available for millimeter wave (mmWave) wireless communication systems will support accurate real-time positioning concurrent with communication signaling. This paper demonstrates that accurate estimates of the position of an unknown node can be determined using estimates of time of arrival (ToA), angle of arrival (AoA), as well as data fusion or machine learning. Real-world data at 28 GHz and 73 GHz is used to show that AoA-based localization techniques will need to be augmented with other positioning techniques. The fusion of AoA-based positioning with received power measurements for RXs in an office which has dimensions of 35 m by 65.5 m is shown to provide location accuracies ranging from 16 cm to 3.25 m, indicating promise for accurate positioning capabilities in future networks. Received signal strength intensity (RSSI) based positioning techniques that exploit the ordering of the received power can be used to determine rough estimates of user position. Prediction of received signal characteristics is done using 2-D ray tracing.
Cell damage by cytolysin. Spontaneous recovery and reversible inhibition by divalent cations. (1988)

Cytolysin-induced membrane damage (which requires low Ca2+) has been studied 1) in E by assay of hemolysis, 2) in Lettre cells by measurement of transmembrane potential, intracellular content of K+ and Na+, leakage of phosphoryl[3H]choline or 51Cr from [3H]choline-labeled or 51CrO4(2-)-labeled cells and leakage of lactate dehydrogenase, and 3) in phospholipid bilayers by measurement of electrical conductivity changes. In Lettre cells, damage is restricted and reversible: little lactate dehydrogenase leaks from cells that leak substantial amounts of Na+, K+, and phosphoryl[3H]choline; at low amounts of cytolysin, membrane potential and intracellular content of Na+ and K+ recover within minutes. In E and Lettre cells, membrane damage is inhibited by Zn2+, by high Ca2+, or by low pH. Inhibition is reversible: addition of EGTA to Zn2+-protected E or Lettre cells (incubated in the presence of cytolysin, low Ca2+ and Zn2+) initiates leakage; removal of Zn2+ (and cytolysin and Ca2+) by washing also initiates leakage; such leakage is again sensitive to Zn2+, high Ca2+, or H+. In phospholipid bilayers, channels induced by cytolysin (at low Ca2+) are partially closed by negative voltage; Ca2+, Zn2+, or H+ promote channel closure. Channels are re-opened (only partially in the case of Zn2+) by positive voltage. From all these results it is concluded that the action of cytolysin on membranes is similar to that of other pore-forming agents: damage does not necessarily lead to lysis of nucleated cells, and can be prevented by Ca2+, Zn2+, or H+.
Optimal design of a coreless stator axial flux permanent-magnet generator (2005)

This paper describes a hybrid method for calculating the performance of a coreless stator axial flux permanent-magnet (AFPM) generator. The method uses a combination of finite-element analysis and theoretical analysis. The method is then incorporated into a multidimensional optimization procedure to optimally design a large power coreless stator AFPM generator. The measured performance of the manufactured prototype compares favorably with the predicted results. The design approach can be applied successfully to optimize the design of the coreless stator AFPM machine.
State Observer for Grid-Voltage Sensorless Control of a Converter Under Unbalanced Conditions (2017)

This paper deals with grid-voltage sensorless synchronization and control under unbalanced grid conditions. A three-phase grid-connected converter equipped with an LCL filter is considered, and no signals other than the converter currents and the dc-link voltage are measured for control. An augmented adaptive state observer is proposed for estimation of the positive- and negative-sequence components of the grid voltage. Dynamic performance limitations of the proposed method and effects of parameter errors are analyzed. The proposed observer is tested as part of a sensorless control system. Experimental results show that the proposed method works well even under highly unbalanced grid conditions.