gebhart/patrepeval huggingface dataset:
Structural basis for DNA cleavage by the potent antiproliferative agent (–)-lomaiviticin A (2016)

(-)-Lomaiviticin A (1) is a complex antiproliferative metabolite that inhibits the growth of many cultured cancer cell lines at low nanomolar-picomolar concentrations. (-)-Lomaiviticin A (1) possesses a C2-symmetric structure that contains two unusual diazotetrahydrobenzo[b]fluorene (diazofluorene) functional groups. Nucleophilic activation of each diazofluorene within 1 produces vinyl radical intermediates that affect hydrogen atom abstraction from DNA, leading to the formation of DNA double-strand breaks (DSBs). Certain DNA DSB repair-deficient cell lines are sensitized toward 1, and 1 is under evaluation in preclinical models of these tumor types. However, the mode of binding of 1 to DNA had not been determined. Here we elucidate the structure of a 1:1 complex between 1 and the duplex d(GCTATAGC)2 by NMR spectroscopy and computational modeling. Unexpectedly, we show that both diazofluorene residues of 1 penetrate the duplex. This binding disrupts base pairing leading to ejection of the central AT bases, while placing the proreactive centers of 1 in close proximity to each strand. DNA binding may also enhance the reactivity of 1 toward nucleophilic activation through steric compression and conformational restriction (an example of shape-dependent catalysis). This study provides a structural basis for the DNA cleavage activity of 1, will guide the design of synthetic DNA-activated DNA cleavage agents, and underscores the utility of natural products to reveal novel modes of small molecule-DNA association.
Taxonomic Status of Micrococcus agilis Ali-Cohen 1889 (1975)

An amended description of Micrococcus agilis Ali-Cohen 1889 is proposed on the basis of a taxonomic study of five strains. Strain ATCC 966 (= CCM 2390 = NCTC 7509) is designated as the neotype strain of M. agilis Ali-Cohen 1889.
Complexity Reduction of Volterra Nonlinear Equalization for Optical\n Short-Reach IM/DD Systems (2020)

We investigate approaches to reduce the computational complexity of Volterra\nnonlinear equalizers (VNLEs) for short-reach optical transmission systems using\nintensity modulation and direct detection (IM/DD). In this contribution we\nfocus on a structural reduction of the number of kernels, i.e. we define rules\nto decide which terms need to be implemented and which can be neglected before\nthe kernels are calculated. This static complexity reduction is to be\ndistinguished from other approaches like pruning or L1 regularization, that are\napplied after the adaptation of the full Volterra equalizer e.g. by\nthresholding. We investigate the impact of the complexity reduction on 90 GBd\nPAM6 IM/DD experimental data acquired in a back-to-back setup as well as in\ncase of transmission over 1 km SSMF. First, we show, that the third-order VNLE\nterms have a significant impact on the overall performance of the system and\nthat a high number of coefficients is necessary for optimal performance.\nAfterwards, we show that restrictions, for example on the tap spacing among\nsamples participating in the same kernel, can lead to an improved tradeoff\nbetween performance and complexity compared to a full third-order VNLE. We show\nan example, in which the number of third-order kernels is halved without any\nappreciable performance degradation.\n
Differentiation of Pathogenic and Saprophytic Leptospires I. Growth at Low Temperatures (1967)

The minimal growth temperature of the pathogenic leptospires is between 13 and 15 C. The saprophytic leptospires have a minimal growth temperature between 5 and 10 C, or approximately 5 C below that of the pathogens. The capability of the saprophytic leptospires to grow at temperatures below those which allow the growth of the pathogenic leptospires provides a simple method of discrimination. With an inoculum yielding approximately 8 x 10(7) cells per ml in the test medium and an incubation temperature of 13 C, the saprophytic leptospires were easily differentiated from the pathogenic leptospires. All 13 saprophytic leptospires tested grew in the 10% rabbit serum medium at 13 C, whereas none of the 20 pathogens grew during the 30-day incubation period.
A 600 GHz low-noise amplifier module (2014)

A compact WR-1.5 (500-750 GHz) low-noise amplifier (LNA) circuit has been developed, based on a grounded coplanar waveguide (GCPW) technology utilizing 20 nm metamorphic high electron mobility transistors (mHEMTs). The realized six-stage LNA TMIC achieved a maximum gain of 15.4 dB at 576 GHz and more than 10 dB in the frequency range from 555 to 619 GHz. For low-loss packaging of the circuit, a waveguide-to-microstrip transition has been fabricated on a 20 ¼m thick GaAs substrate, demonstrating an insertion loss of only 1 dB between 500 and 720 GHz. The realized LNA module achieved a small-signal gain of 14.1 dB at 600 GHz and a room temperature (T = 293 K) noise figure of 15 dB at the frequency of operation.
On constructing correct and scalable iBGP configurations (2006)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.
Hydrodynamic model for ultrashort-pulse albation of hard dental tissue (1996)

A computational model for the ablation of tooth enamel by ultra-short laser pulses is presented. The role of simulations using this model in designing and understanding laser drilling systems is discussed. Pulses of duration 300 fsec and intensity greater than 10<SUP>12</SUP> W/cm<SUP>2</SUP> are considered. Laser absorption proceeds via multi-photon initiated plasma mechanism. The hydrodynamic response is calculated with a finite difference method, using an equation of state constructed from thermodynamic functions including electronic, ion motion, and chemical binding terms. Results for the ablation efficiency are presented. An analytic model describing the ablation threshold and ablation depth is presented. Thermal coupling to the remaining tissue and long-time thermal conduction are calculated. Simulation results are compared to experimental measurements of the ablation efficiency. Desired improvements in the model are presented.
Utilization of Numerical Optimization to Model Gas Condensate Flow Through Chokes in a Rich Gas Condensate Reservoir in Saudi Arabia (2015)

Abstract Production metering of a Saudi Arabian rich gas condensate reservoir with an average condensate to gas ratio (CGR) of 330 stock tank barrels/million standard cubic feet (STB/MMscf) is under evaluation. Inapplicability of Venturi meters, due to high liquid production, accompanied by the absence of multiphase flow meters and dedicated permanent test separator facility for individual testing, has resulted in a major metering challenge during the production life of this field. Infrequent deliverability tests with costly portable test separators are the only way to obtain direct and accurate gas and condensate rate measurements, which has severely affected the rate allocation accuracy. In this study, an alternative solution was employed to improve gas rate allocation and target rate compliance. Understanding the nature of multiphase flow through chokes and the principals of flow calculations to derive accurate correlations and models is the only alternative to mitigate the lack of surface metering devices in such a high CGR environment. Choke equations rely heavily on choke parameters, surface measurements, and fluid properties with some assumed empirical constants. The majority of the published choke correlations have their unique empirical constants that fit the flow conditions and fluid properties of the studied fields. In this study, a numerical optimization technique was implemented to develop and brand two empirical choke correlations, which model the gas condensate flow through chokes under critical flow conditions in the subject field. An iterative methodology was performed by capitalizing on a nonlinear algorithm to analyze 64 well test data points, collected from 16 different separator tests, to identify the unique values of the empirical constants, which would yield the most accurate flow rate estimations. Statistical evaluation results indicate the developed empirical choke models yielded encouraging results. The models successfully matched the measured gas flow rates, from 26 well tests, with less than 5% average absolute error, proving the high accuracy of these models in estimating the flow rates. In addition, back allocation task was greatly simplified by utilizing these developed choke equations. Comparison between the total field choke equation estimated rate and measured field gas rate at the gas plant for a period of 3 months showed an outstanding agreement with less than 5% average error and 1.02 average allocation factor. Moreover, the investigated empirical constants were examined in a different field with similar fluid properties and obtained excellent matching outcomes as well, reconfirming the precision of these correlations in estimating the gas rates in a high CGR environment. The applications of these correlations will allow field operators to accurately estimate the flow rates without the necessity of conducting frequent costly separator tests, or installing expensive permanent multiphase flow meters.
Growth and molecular characterization of dental plaque microcosms (2003)

This study demonstrates the utility of DGGE for the analysis of dental plaque, especially with respect to unculturable bacteria. Results question the assumptions of reproducibility of plaque microcosms established in non-replicated CDFFs made on the basis of selective media. Feeding regimes, particularly those involving complex nutrients, will dramatically affect population dynamics.
Stable High‐Efficiency CsPbI2Br Solar Cells by Designed Passivation Using Multifunctional 2D Perovskite (2022)

Abstract CsPbI 2 Br perovskite is known for its advantages over its organic‐inorganic hybrid counterpart including better thermal stability and appropriate bandgap for the front sub‐cell of tandem solar cell. However, its lower‐than‐satisfactory efficiency, problematic phase stability and sensitivity to moisture hinder its further advancement. Here, three kinds of glycine halides (Gly‐ X : X = Cl, Br, and I) are strategically deigned to improve the performance of CsPbI 2 Br perovskite solar cells (PSCs). Systematic experimental and calculated results prove that a 2D/3D hybrid structure is formed, wherein the Gly‐X‐based 2D perovskite is mainly located at the CsPbI 2 Br grain boundaries, and the A‐sites of the 2D perovskite form strong bonds with the 3D perovskite to suppress ion migration by increasing its activation energy. As a result, a power conversion efficiency (PCE) of 17.26% was obtained with an open‐circuit voltage ( V OC ) of 1.33 V, which is among the best PCE values for the CsPbI 2 Br PSCs. In addition, the efficiency of encapsulated device decrease only by 14.1% after 340 h continuous illumination in ambient conditions, representing one of the most‐stable inorganic PSCs reported so far. This work provides important insights into designing passivating agents to address the issue of phase segregation for the development of highly stable perovskite optoelectronic devices.
A High-Throughput Method For Zebrafish Sperm Cryopreservation and <em>In Vitro</em> Fertilization (2009)

This is a method for zebrafish sperm cryopreservation that is an adaptation of the Harvey method (Harvey et al., 1982). We have introduced two changes to the original protocol that both streamline the procedure and increase sample uniformity. First, we normalize all sperm volumes using freezing media that does not contain the cryoprotectant. Second, cryopreserved sperm are stored in cryovials instead of capillary tubes. The rates of sperm freezing and thawing (delta degrees C/time) are probably the two most critical variables to control in this procedure. For this reason, do not substitute different tubes for those specified. Working in teams of 2 it is possible to freeze the sperm of 100 males per team in approximately 2 hrs. Sperm cryopreserved using this protocol has an average of 25% fertility (measured as the number of viable embryos generated in an in vitro fertilization divided by the total number of eggs fertilized) and this percent fertility is stable over many years.
Update on Glioma Treatments in the United States (2013)

従来の放射線化学療法をもってしても予後不良である神経膠芽腫に対する新たな治療として, 分子標的薬が注目されている. 腫瘍発生・進展の分子生物学的メカニズムが明らかになるにつれ, さまざまな薬剤が開発され臨床治験が行われてきた. しかし腫瘍細胞内シグナル伝達異常の多様性などのため, 高い奏効率を示し認可に至った分子標的薬はいまだない. 神経膠芽腫という組織学的診断のみでなく, ターゲットシークエンスなどによる分子病理学的診断が実臨床に導入されつつあり, 個々の腫瘍の遺伝子異常に即した分子標的薬の選択, すなわちテーラーメイドな癌治療が有望視されている. 本稿では, アメリカにおける神経膠芽腫の治療戦略の現状を概説する.
Design issues of a core-less transformer for a contact-less application (2003)

A set of rules for designing coreless transformers for contactless applications is presented in this paper. In contactless transference of energy, there is a relative big separation distance between the coils, so coupling is low. Several simulations have been performed with an FEA tool studying different technologies and winding strategies in order to quantify the improvements in coupling and resistance for different gaps. The analysis has been done for the transcutaneous transformer of a human-body implant, but the conclusions can be extended to any kind of coreless transformer for a contact-less application. The results are consistent with the measurements.
Prestin topology: localization of protein epitopes in relation to the plasma membrane (2001)

Computer modeling of the outer hair cell (OHC) motor protein prestin produces ambiguous results regarding transmembrane regions and localization of its termini. To determine the location of prestin's N- and C-termini, we created prestin constructs with synthetic epitopes located immediately upstream or downstream of prestin. The spatial distribution of these epitopes was studied in prestin-transfected cells using immunofluorescence. In permeabilized cells, antibodies label the plasma membrane of 30% of the cells, reflecting transfec- tion efficiency. Under non-permeabilizing conditions, the few labeled cells also displayed a lack of plasma membrane integrity. These data suggest that prestin's N-and C-termini are cytoplasmic. Furthermore, prestin staining in OHCs was observed only under permeabilizing conditions. These results implicate prestin's N- and C-termini as portions that may interact with other cytoplasmic proteins. A model of prestin membrane topology is also considered based on the results.
Unconventional metabolites in chromatin regulation (2022)

Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
An Arabidopsispex10Null Mutant Is Embryo Lethal, Implicating Peroxisomes in an Essential Role during Plant Embryogenesis (2003)

Peroxisomes participate in many important functions in plants, including seed reserve mobilization, photorespiration, defense against oxidative stress, and auxin and jasmonate signaling. In mammals, defects in peroxisome biogenesis result in multiple system abnormalities, severe developmental delay, and death, whereas in unicellular yeasts, peroxisomes are dispensable unless required for growth of specific substrates. PEX10 encodes an integral membrane protein required for peroxisome biogenesis in mammals and yeast. To investigate the importance of PEX10 in plants, we characterized a Ds insertion mutant in the PEX10 gene of Arabidopsis (AtPEX10). Heterozygous AtPEX10::dissociation element mutants show normal vegetative phenotypes under optimal growth conditions, but produce about 20% abnormal seeds. The embryos in the abnormal seeds are predominantly homozygous for the disruption allele. They show retarded development and some morphological abnormalities. No viable homozygous mutant plants were obtained. AtPEX10 fused to yellow fluorescent protein colocalized with green fluorescent protein-serine-lysine-leucine, a well-documented peroxisomal marker, suggesting that AtPEX10 encodes a peroxisomal protein that is essential for normal embryo development and viability.
Demonstration of Fast Restorable All-Optical WDM Network (2001)

We report on the demonstration of a fast restorable all-optical WDM network. This network consisted of four 4× 4 optical cross-connects (OXC’s) and four in-line optical amplifiers. These OXC’s monitored not only the status of various network elements and quality of optical signals but also the optical path of each channel continuously. Thus, this network could automatically identify the causes of most network failures. For the fast restoration, we implemented these OXC’s by using thermo-optic polymer switches (switching time: < 1.5ms) and used hardware interrupt when LOS was detected. In addition, we used a pre-planned routing table made by using a simple heuristic routing and wavelength assignment algorithm. The results show that this network could be restored from any single link failure within 6ms even when the restoration path was 400 km. key words: all-optical network, restoration, wavelength-
Embryonic stem cell-derived extracellular vesicles enhance the therapeutic effect of mesenchymal stem cells (2019)

<b>Background:</b> Embryonic stem cells (ES) have a great potential for cell-based therapies in a regenerative medicine. However, the ethical and safety issues limit its clinical application. ES-derived extracellular vesicles (ES-EVs) have been reported suppress cellular senescence. Mesenchymal stem cells (MSCs) are widely used for clinical cell therapy. In this study, we investigated the beneficial effects of ES-EVs on aging MSCs to further enhancing their therapeutic effects. <b>Methods:</b><i>In vitro</i>, we explored the rejuvenating effects of ES-EVs on senescent MSCs by senescence-associated β-gal (SA-β-gal) staining, immunostaining, and DNA damage foci analysis. The therapeutic effect of senescent MSC pre-treated with ES-EVs was also evaluated by using mouse cutaneous wound model. <b>Results:</b> We found that ES-EVs significantly rejuvenated the senescent MSCs <i>in vitro</i> and improve the therapeutic effects of MSCs in a mouse cutaneous wound model. In addition, we also identified that the IGF1/PI3K/AKT pathway mediated the antisenescence effects of ES-EVs on MSCs. <b>Conclusions:</b> Our results suggested that ES cells derived-extracellular vesicles possess the antisenescence properties, which significantly rejuvenate the senescent MSCs and enhance the therapeutic effects of MSCs. This strategy might emerge as a novel therapeutic strategy for MSCs clinical application.
ChemInform Abstract: Phosphorus‐Containing Macrocyclic “Host”‐Molecules. Synthesis, Structure and Properties (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Solid‐Phase N‐Glycopeptide Synthesis Using Allyl Side‐Chain Protected Fmoc‐Amino Acids. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Clotrimazole Binds to Heme and Enhances Heme-dependent Hemolysis (2002)

Two recent studies have demonstrated that clotrimazole, a potent antifungal agent, inhibits the growth of chloroquine-resistant strains of the malaria parasite, Plasmodium falciparum, in vitro. We explored the mechanism of antimalarial activity of clotrimazole in relation to hemoglobin catabolism in the malaria parasite. Because free heme produced from hemoglobin catabolism is highly toxic to the malaria parasite, the parasite protects itself by polymerizing heme into insoluble nontoxic hemozoin or by decomposing heme coupled to reduced glutathione. We have shown that clotrimazole has a high binding affinity for heme in aqueous 40% dimethyl sulfoxide solution (association equilibrium constant: K(a) = 6.54 x 10(8) m(-2)). Even in water, clotrimazole formed a stable and soluble complex with heme and suppressed its aggregation. The results of optical absorption spectroscopy and electron spin resonance spectroscopy revealed that the heme-clotrimazole complex assumes a ferric low spin state (S = 1/2), having two nitrogenous ligands derived from the imidazole moieties of two clotrimazole molecules. Furthermore, we found that the formation of heme-clotrimazole complexes protects heme from degradation by reduced glutathione, and the complex damages the cell membrane more than free heme. The results described herein indicate that the antimalarial activity of clotrimazole might be due to a disturbance of hemoglobin catabolism in the malaria parasite.
ELECTROMAGNETIC COMPATIBILITY OF A DC POWER DISTRIBUTION SYSTEM FOR THE ATLAS LIQUID ARGON CALORIMETER COMPATIBILIDAD ELECTROMAGNÉTICA EN EL SISTEMA DE DISTRIBUCIÓN DE CORRIENTE CONTINUA PARA EL CALORÍMETRO DE ARGÓN LÍQUIDO EN ATLAS (2008)

The front-end electronics of the ATLAS Liquid Argon Calorimeter is powered by DC/DC converters nearby the front-end crates. They are fed by AC/DC converters located in a remote control room through long power cables. The stability of the power distribution scheme is compromised by the impedance of the long interconnection cable, and proper matching of the converters dynamic impedances is required. Also, the long power cable fed by a powerful AC/DC converter is a source of electromagnetic interferences in the experimental area. The optimal grounding and shielding configuration to minimize these EMI is discussed.<br>El Calorímetro de Argón Líquido en ATLAS es alimentado por convertidores DC/DC localizados cerca de sus compartimientos. Ellos son alimentados por convertidores AC/DC localizados en una sala de control lejana conectados mediante cables largos de poder. La estabilidad del sistema de distribución es sensible a la impedancia del cable largo de interconexión y son requeridos los convertidores apropiados para estabilizar la dinámica de la impedancia. También, el cable largo alimentado por el convertidor AC/DC es una fuente de interferencia electromagnética en el área experimental. En este trabajo se analiza La óptima configuración de aterrizamiento y blindaje para minimizar los efectos de EMI.