gebhart/patrepeval huggingface dataset:
Measuring Protein Shapes in Living Cells (2021)

ADVERTISEMENT RETURN TO ISSUEHighlightsNEXTMeasuring Protein Shapes in Living CellsNikolai Slavov*Nikolai SlavovDepartment of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United StatesBarnett Institute, Northeastern University, Boston, Massachusetts 02115, United States*Email: [email protected]; [email protected]More by Nikolai Slavovhttps://orcid.org/0000-0003-2035-1820Cite this: J. Proteome Res. 2021, 20, 6, 3017Publication Date (Web):May 14, 2021Publication History Published online14 May 2021Published inissue 4 June 2021https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00376https://doi.org/10.1021/acs.jproteome.1c00376in-briefACS PublicationsCopyright © Published 2021 by American Chemical SocietyRequest reuse permissionsArticle Views606Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Conformation,Labeling,Mass spectrometry,Monomers,Peptides and proteins Get e-Alerts
Growth inhibitory effects of quercetin on bladder cancer cell (2006)

Quercetin, a flavonoid found in many fruits and vegetables, belongs to an extensive class of polyphenolic compounds. Previous studies reported that quercetin inhibits the proliferation of various cancer cells and tumor growth in animal models. We investigated the growth inhibition and colony formation of quercetin on three bladder cancer cells (EJ, J82 and T24). The expression of tumor suppressor genes and oncogenes such as P53, Survivin, PTEN, as well as the methylation status of these genes was also evaluated. We observed that quercetin induced apoptosis in bladder cancer cells in a time- and dose-dependent manner. Quercetin (100 micromolars) significantly inhibited EJ, T24 and J82 cell growth accompanied by an increase in the G0/G1 phase. In all cell lines, quercetin decreased the expression of mutant P53 and Survivin proteins. However, there was no change in the level of PTEN protein. Moreover, the DNA methylation levels of the estrogen receptor (Er-beta), P16INK4a and RASSF1A were strongly decreased (from 35 to 70%) in the quercetin-treated group compared to the control. In conclusion, our study suggested that quercetin inhibits growth, colony formation and hypermethylation of bladder cancer cell lines. Quercetin-induced apoptosis might be associated with a decrease in mutant P53 and Survivin proteins.
One-Stage Synthesis of Cagelike Porous Polymeric Microspheres and Application as Catalyst Scaffold of Pd Nanoparticles (2011)

One-stage synthesis of cagelike porous polymeric microspheres and their application as catalyst scaffold of Pd nanoparticles are discussed. The synthesis of cagelike porous polymeric microspheres is achieved by W/O/W emulsion polymerization of a surfactant monomer of N-(4-vinylbenzyl)-N,N-dibutylamine hydrochloride and a hydrophobic monomer of styrene in water. Ascribed to the surfactant monomer, convenient one-stage synthesis of cagelike porous polymeric microspheres is afforded, and cagelike porous polymeric microspheres with size ranging from 300 to 600 nm and pore volume as large as 0.31 cm3/g are fabricated. The porous character and the inherent quaternary ammonium moieties make the cagelike porous polymeric microspheres to be the promising catalyst scaffold of Pd nanoparticles, and up to 10 wt % Pd catalyst with the metal particle size ranging from 2.1 to 5.7 nm is loaded. The catalytic hydrogenation of nitrobenzene by H2 demonstrates that the heterogeneous Pd catalyst is efficient and reusable.
Acute promyelocytic leukemia can be treated successfully without cytotoxic chemotherapy. (2011)

In their scholarly article, Dr. Park and Dr. Tallman review the important clinical trials for treating patients with APL reported over the last two decades and argue the case for further reduction and perhaps elimination of conventional cytotoxic chemotherapy in the frontline treatment of this disease.[1]
Identifying the Older Person Likely to Require Long‐Term Care Services (1987)

The purpose of this study is to determine the accuracy of predictions in identifying older persons who subsequently require long-term care such as home services or institutionalization. Eighty-six individuals undergoing geriatric evaluation between May 1983 and April 1984 were evaluated using a series of commonplace tasks such as opening doors, stacking checkers, and copying a simple sentence. Predictions of an individual's use of long-term care services were made during the initial evaluation and were based on whether the person could complete all the manual tasks and on the amount of time required to do so. Outcomes were determined by telephone interviews by a trained social worker in Dec 1984. A statistically significant association (P less than 0.005) was observed between the predictions and actual outcomes. Analysis of variance confirmed that the mean times for each outcome were different (F = 2.6, P less than 0.05). The results suggest that timing manual performance offers a useful way to prospectively identify older persons at risk of requiring additional long-term care services.
Performance of a Solar Absorption Cooling System Using Nanofluids and a Membrane-Based Microchannel Desorber (2020)

In this work, the performance of a single effect absorption cooling system fed by solar thermal energy is evaluated. The absorption chiller includes a membrane-based microchannel desorber using three types of nanoparticles: Al2O3, CuO, or carbon nanotubes (CNT). Correlations available in the open literature to calculate the thermal conductivity of nanofluids are reviewed. Using experimental data for the water-lithium bromide solution (H2O-LiBr) with Al2O3 and CNT nanoparticles, the most appropriate correlation for thermal conductivity is selected. Nanofluid properties are evaluated using a concentration of nanoparticles of up to 5% in volume. The largest increase in the desorption rate (7.9%), with respect to using pure H2O-LiBr solution, is obtained using CNT nanoparticles and the maximum concentration of nanoparticles simulated. The performance of the chiller is evaluated and the daily solar coefficient of performance (SCOP) for the solar cooling facility is obtained. The best improvement with respect to the conventional system (without nanoparticles) represents an increase in the cooling effect of up to 6%. The maximum number of desorber modules recommended, always lower than 50, has been identified.
Views from the top : new product competition (2015)

The numbers are in, scores have been tallied, and the judges' decisions will be revealed soon. Until then, here is an overview what went down during our judging day for the 2015 Pharmaceutical & Cosmetic Review/Symrise New Product Competition (NPC).
Kinetics of protein adsorption and immunological reactions at a liquid/solid interface by ellipsometry (1977)

The adsorption of bovine serum albumin and the subsequent reaction with it of rabbit anti-bovine serum albumin at a saline solution/gold interface are observed in vitro by ellipsometry. By suitable choice of protein concentrations, the processes of adsorption and immunological reaction can be followed in detail by an ordinary null ellipsometer. A simple kinetic model for the formation of a monolayer of protein at the saline solution/gold interface provides adequate explanation for the experimental results. It is shown that ellipsometry is capable of providing information on molecular dimensions, molecular diffusion velocities and adsorption rates.
Differentially-private network trace analysis (2010)

We consider the potential for network trace analysis while providing the guarantees of "differential privacy." While differential privacy provably obscures the presence or absence of individual records in a dataset, it has two major limitations: analyses must (presently) be expressed in a higher level declarative language; and the analysis results are randomized before returning to the analyst.
Einleitung (1986)

Man spricht oft über „Gastarbeiter“ und „Gastarbeiterkinder“, doch kaum jemand assoziiert mit diesen Begriffen die koreanischen Arbeitnehmer und deren Kinder. Über diese Menschen ist so gut wie nichts bekannt, denn das Interesse an dieser Gruppe ist sehr gering. Die Zahl der Koreaner in der Bundesrepublik ist — verglichen mit „Gastarbeitern“ anderer Ethnien — relativ niedrig, was jedoch nicht bedeutet, daß die damit gegebene Problematik hier nicht existent wäre; sie scheint sogar größer zu sein, da sich niemand dieser Problematik annimmt.
Development of an Adaptive and a Switched Beam Smart Antenna System for Wireless Communications (2006)

Abstract This study concentrates on the development of two separate Smart Antenna Systems for the 2.45 GHz ISM band. Both systems incorporate the RF-beamforming method. Each system has the ability to point the beam in a three dimensional space, both in azimuth and in elevation direction. The Switched Beam System adopts a passive network-based beamforming approach, using 2-D Butler matrix topologies. The Adaptive System utilizes the vector modulator method, but only in the azimuth direction, increasing beam-steering accuracy, whereas introducing complexity and cost. The system design is presented for both cases, along with some module design and testing examples. A comparison of the two systems will be also discussed.
Solution Structure of the Two-Iron Rubredoxin of <i>Pseudomonas oleovorans</i> Determined by NMR Spectroscopy and Solution X-ray Scattering and Interactions with Rubredoxin Reductase<sup>,</sup> (2004)

Here we provide insights into the molecular structure of the two-iron 19-kDa rubredoxin (AlkG) of Pseudomonas oleovorans using solution-state nuclear magnetic resonance (NMR) and small-angle X-ray scattering studies. Sequence alignment and biochemical studies have suggested that AlkG comprises two rubredoxin folds connected by a linker region of approximately 70 amino acid residues. The C-terminal domain (C-Rb) of this unusual rubredoxin, together with approximately 35 amino acid residues of the predicted linker region, was expressed in Escherichia coli, purified in the one-iron form and the structure of the cadmium-substituted form determined at high-resolution by NMR spectroscopy. The structure shows that the C-Rb domain is similar in fold to the conventional one-iron rubredoxins from other organisms, whereas the linker region does not have any discernible structure. This tandem "flexible-folded" structure of the polypeptide chain derived for the C-Rb protein was confirmed using solution X-ray scattering methods. X-ray scattering studies of AlkG indicated that the 70-amino acid residue linker forms a structured, yet mobile, polypeptide segment connecting the globular N- and C-terminal domains. The X-ray scattering studies also showed that the N-terminal domain (N-Rb) has a molecular conformation similar to that of C-Rb. The restored molecular shape indicates that the folded N-Rb and C-Rb domains of AlkG are noticeably separated, suggesting some domain movement on complex formation with rubredoxin reductase to allow interdomain electron transfer between the metal centers in AlkG. This study demonstrates the advantage of combining X-ray scattering and NMR methods in structural studies of dynamic, multidomain proteins that are not suited to crystallographic analysis. The study forms a structural foundation for functional studies of the interaction and electron-transfer reactions of AlkG with rubredoxin reductase, also reported herein.
Modelling Context with User Embeddings for Sarcasm Detection in Social Media (2016)

We introduce a deep neural network for automated sarcasm detection.
Esterification of Carboxylic Acids with Dicyclohexylcarbodiimide/4‐Dimethylaminopyridine:<i>tert</i>‐Butyl Ethyl Fumarate (2003)

Abstract Esterification of carboxylic acids with dicyclohexylcarbodiimide/4‐dimethylaminopyridine: tert ‐butyl ethyl fumarate reactant: 45.59 g (0.22 mol) of dicyclohexylcarbodiimide product: tert‐butyl ethyl fumarate
Effect of Increased Glucose Levels on Na<sup>+</sup>/K<sup>+</sup>‐Pump Activity in Cultured Neuroblastoma Cells (1988)

Neuroblastoma cells were used to analyze the effect of elevated glucose levels on myo-inositol metabolism and Na+/K+-pump activity. The activity of the Na+/K+ pump in neuroblastoma cells is almost totally sensitive to ouabain inhibition. Culturing neuroblastoma cells in 30 mM glucose caused a significant decrease in Na+/K+-pump activity, myo-inositol metabolism, and myo-inositol content, compared to cells grown in the presence of 30 mM fructose. Glucose supplementation also caused a large intracellular accumulation of sorbitol. The aldose reductase inhibitor sorbinil prevented the abnormalities in myo-inositol metabolism and partially restored Na+/K+-pump activity in neuroblastoma cells cultured in the presence of elevated glucose levels. These results suggest that the accumulation of sorbitol by neuroblastoma cells exposed to elevated concentrations of extracellular glucose causes a decrease in myo-inositol metabolism and these abnormalities are associated with a reduction in Na+/K+-pump activity.
Single barrier varactors for submillimeter wave power generation (1993)

Theoretical work on single barrier varactor (SBV) diodes indicates that the efficiency of a tripler with a SBV diode has a maximum for a considerably smaller capacitance variation than previously thought. SBV diodes based on GaAs, InGaAs and InAs have been fabricated and their DC properties have been tested. Detailed modeling of the carrier transport properties of the SBV device is carried out in two steps. First, the semiconductor transport equations are solved simultaneously, using a finite difference scheme in one dimension. Second, the calculated I-V and C-V characteristics are used by a multiplier simulator to calculate the optimum impedances and output powers at the frequencies of interest. The authors have developed an analysis technique which complements the harmonic balance technique. Simulations for a case study of a 750-GHz multiplier show that InAs diodes perform favorably compared to GaAs diodes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Overview of persistent pain in older adults. (2014)

With the shifting age demographics of the U.S. population, more psychologists will be asked to provide clinical services to older adults. Given the high prevalence of persistent pain in aging, in many cases this will mean providing empirically supported interventions for pain and the interference it creates. The purpose of this review is to provide a broad overview of the scope and impact of persistent pain in older people and to discuss mechanisms by which persistent geriatric pain can lead to suffering and disability. We consider the unique context of pain in older adulthood and review differences between older and younger people in terms of pain perception, the social network, beliefs about pain, pain-related coping, and adherence to pain medication. Finally, we discuss special issues affecting pain management in older adults, including dementia, polypharmacy, and barriers to accessing adequate pain care. This review also highlights a need for greater provider training in pain management to meet the needs of a changing U.S. population.
Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition (2016)

Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections (UTIs) worldwide, causing over 150 million clinical cases annually. There is currently no specific treatment addressing the asymptomatic carriage in the gut of UPEC before they initiate UTIs. This study investigates the efficacy of virulent bacteriophages to decrease carriage of gut pathogens. Three virulent bacteriophages infecting an antibiotic-resistant UPEC strain were isolated and characterized both in vitro and in vivo. A new experimental murine model of gut carriage of E. coli was elaborated and the impact of virulent bacteriophages on colonization levels and microbiota diversity was assessed. A single dose of a cocktail of the three bacteriophages led to a sharp decrease in E. coli levels throughout the gut. We also observed that microbiota diversity was much less affected by bacteriophages than by antibiotics. Therefore, virulent bacteriophages can efficiently target UPEC strains residing in the gut, with potentially profound public health and economic impacts. These results open a new area with the possibility to manipulate specifically the microbiota using virulent bacteriophages, which could have broad applications in many gut-related disorders/diseases and beyond.
Lidar determination of winds by aerosol inhomogeneities: motion velocity in the planetary boundary layer (1988)

The paper presents results from lidar measurements of wind velocity in the planetary boundary layer using correlation data processing. Two lidars are used in our experiments: a ruby lidar operating along slant paths and a YAG:Nd lidar operating for near vertical sounding used by us for the first time. On the basis of our experience the optimal sizes of aerosol inhomogeneities (30-300 m), the duration of the experiments (2-10 min), and the repetition rate of laser shots (fractions of hertz to several hertz) are determined. The results are compared to independent data obtained from anemometer measurements, theodolite- and radar-tracked pilot balloons. The range of differences is ~1-2 m/s in speed and 10-15 degrees in direction. Preliminary results from the use of lidar data to remotely sound the wind speed for various atmospheric stratifications and synoptic situations are described as well.
Frequent value locality and its applications (2002)

By analyzing the behavior of a set of benchmarks, we demonstrate that a small number of distinct values tend to occur very frequently in memory. On an average, only eight of these frequent values were found to occupy 48% of memory locations for the benchmarks studied. In addition, we demonstrate that the identity of frequent values remains stable over the entire execution of the program and these values are scattered fairly uniformly across the allocated memory. We present three different algorithms for finding frequent values and experimentally demonstrate their effectiveness. Each of these algorithms is designed to suit a different application scenario. Since the contents of memory exhibit frequent value locality, it is expected that frequent values will be observed in data streams that flow across different points in the memory hierarchy. We exploit this observation for developing two low-power designs: a low-power level-one data cache and a low-power external data bus. In each of these applications a different form of encoding of frequent values is employed to obtain a low-power design. We also experimentally demonstrate the effectiveness of these designs.
IQ-imbalance and its compensation for non-ideal analog receivers comprising frequency-selective components (2006)

Abstract. Within current implementations of mobile terminals, more and more analog components are replaced by appropriate digital processing. On the one hand, the analog front-ends become less complex. On the other hand, more digital signal processing is required to compensate for the spurious effects of the front-end. In this article, the frequency-selective imbalance of the in-phase and quadrature-phase signals is addressed. A closed representation of arbitrary signals being processed by an arbitrary imbalanced analog front-end is provided. The analysis is valid for both, direct conversion and intermediate frequency (IF) reception. With the consideration of practical variations of amplitude and phase impairments, the influence of only the frequency-dependent portions of the impairments is investigated. It is shown, that the compensation of the quasi-linear impairments is sufficient and complex deconvolutive IQ-regeneration procedures are not stringently required to obtain sufficient signal qualities.
Nonthermal Irreversible Electroporation: Fundamentals, Applications, and Challenges (2013)

Tissue ablation is an essential procedure for the treatment of many diseases. In the last decade, a nonthermal tissue ablation using intensive pulsed electric fields, called nonthermal irreversible electroporation (NTIRE), has rapidly emerged. The exact mechanisms responsible for cell death by NTIRE, however, are currently unknown. Nevertheless, the technique's remarkable ability to ablate tissue in the proximity of larger blood vessels, to preserve tissue architecture, short procedure duration, and shortened postoperative recovery period rapidly moved NTIRE from bench to bed side. This work provides an overview on the development of NTIRE, its current state-of-the-art, challenges, and future needs.
Large-Scale Production of Natural Cytokines During Activation and Expansion of Human T Lymphocytes in Hollow Fiber Bioreactor Cultures (1999)

We studied the large-scale production of a variety of natural cytokines during the activation and expansion of human T lymphocytes in a hollow fiber bioreactor culture system. Peripheral blood mononuclear cells (PBMC) were activated using phytohemagglutinin plus recombinant interleukin-2 (IL-2). Phytohemagglutinin was either present in the hollow fiber bioreactor during the entire 15-16-day culture period or only during the 20-h preactivation of the PBMC in culture bags. The expanding T lymphocytes were mainly CD3+,8+ and exerted maximal natural, activated, bispecific monoclonal antibody-redirected and lectin-dependent cytolytic activities between days 9 and 13 of culture. IL-1 and IL-4 were only produced in low amounts. IL-8 and lymphotoxin were primarily produced during the first week of culture. Harvest of the hollow fiber bioreactor culture supernatant at the time of peak cytokine concentration would have yielded per 10(8) PBMC input between 3.7 and 4.9 micrograms of IL-8 (at days 2 or 3), and between 0.02 and 0.5 microgram of lymphotoxin (at days 6 or 7). Tumor necrosis factor-alpha and IL-6 were produced during the entire culture period of 15 or 16 days: per 10(8) PBMC input, between 0.1 and 0.4 microgram of tumor necrosis factor-alpha (at days 2 or 3) and between 0.03 and 0.5 microgram of IL-6 (at days 15 or 16). Production of interferon-gamma and granulocyte-macrophage colony-stimulating factor started from initiation of cultures onwards to reach peak levels at the end of the 15- or 16-day culture period, yielding at that time between 2.1 and 17.7 micrograms/ml of interferon-gamma and between 0.4 and 4.2 micrograms of granulocyte-macrophage colony-stimulating factor per 10(8) PBMC input. The production of tumor necrosis factor-alpha, IL-6, interferon-gamma, and granulocyte-macrophage colony-stimulating factor was proportional to the extent of lymphocyte multiplication. These results demonstrate the usefulness of hollow fiber bioreactor cultures to produce natural cytokines during the activation and expansion of predominantly CD3+,8+ T lymphocytes.