gebhart/patrepeval huggingface dataset:
Cogenerating Synthetic Parts toward a Self-Replicating System (2017)

To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when coexpressed in batch format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in coexpression pool varied from ∼1.5 to 5-fold compared to the batch mode, with up to ∼2.4 μM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ∼13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. This work also points to what is still needed to obtain self-replicating synthetic ribosomes in situ in the PURE system.
Figure S7 from Arginine Depletion Therapy with ADI-PEG20 Limits Tumor Growth in Argininosuccinate Synthase–Deficient Ovarian Cancer, Including Small-Cell Carcinoma of the Ovary, Hypercalcemic Type (2023)

&lt;p&gt;Mouse models of SCCOHT cell lines. A, Representative histology of kidney and liver from COV434-implanted mouse in the control group, and in the 30mg/kg ADI-PEG20 group which exhibited abnormal organs upon macroscopic examination at necropsy. B, BRG1 IHC for the masses above the heart found in 2 mice in the treatment groups. Top image: mass only (mouse DGH12-2-14); bottom image, mass adjacent to normal heart (mouse DGH12-2-15). C, tumor volume and weight of SCCOHT1 mouse model. Significance was calculated using ANOVA, followed by a post-hoc Tukey's test. Error bars represent standard error of mean. D, ASS1 re-expression in SCCOHT1 cells in both saline control group and 30mg/kg treated groups. E, Representative tunnel assay images from each treatment group indicating no significant increase in apoptosis in tumors from the ADI-PEG20 treated compared to saline-treated groups, and F, COV434 subcutaneous xenograft showing foci of ASS1 re-expression in treated groups. G, average mouse weight of each mouse model, and H, plots reflecting the tumour weight adjusted by mouse weight (tumour weight/mouse weight).&lt;/p&gt;
Testing the Vascular Invasive Ability of Cancer Cells in Zebrafish (<em>Danio Rerio</em>) (2016)

Cancer cell vascular invasion and extravasation is a hallmark of metastatic progression. Traditional in vitro models of cancer cell invasion of endothelia typically lack the fluid dynamics that invading cells are otherwise exposed to in vivo. However, in vivo systems such as mouse models, though more physiologically relevant, require longer experimental timescales and present unique challenges associated with monitoring and data analysis. Here we describe a zebrafish assay that seeks to bridge this technical gap by allowing for the rapid assessment of cancer cell vascular invasion and extravasation. The approach involves injecting fluorescent cancer cells into the precardiac sinus of transparent 2-day old zebrafish embryos whose vasculature is marked by a contrasting fluorescent reporter. Following injection, the cancer cells must survive in circulation and subsequently extravasate from vessels into tissues in the caudal region of the embryo. Extravasated cancer cells are efficiently identified and scored in live embryos via fluorescence imaging at a fixed timepoint. This technique can be modified to study intravasation and/or competition amongst a heterogeneous mixture of cancer cells by changing the injection site to the yolk sac. Together, these methods can evaluate a hallmark behavior of cancer cells and help uncover mechanisms indicative of malignant progression to the metastatic phenotype.
Identification of Region-Specific Myocardial Gene Expression Patterns in a Chronic Swine Model of Repaired Tetralogy of Fallot (2015)

Surgical repair of Tetralogy of Fallot (TOF) is highly successful but may be complicated in adulthood by arrhythmias, sudden death, and right ventricular or biventricular dysfunction. To better understand the molecular and cellular mechanisms of these delayed cardiac events, a chronic animal model of postoperative TOF was studied using microarrays to perform cardiac transcriptomic studies. The experimental study included 12 piglets (7 rTOF and 5 controls) that underwent surgery at age 2 months and were further studied after 23 (+/- 1) weeks of postoperative recovery. Two distinct regions (endocardium and epicardium) from both ventricles were analyzed. Expression levels from each localization were compared in order to decipher mechanisms and signaling pathways leading to ventricular dysfunction and arrhythmias in surgically repaired TOF. Several genes were confirmed to participate in ventricular remodeling and cardiac failure and some new candidate genes were described. In particular, these data pointed out FRZB as a heart failure marker. Moreover, calcium handling and contractile function genes (SLN, ACTC1, PLCD4, PLCZ), potential arrhythmia-related genes (MYO5B, KCNA5), and cytoskeleton and cellular organization-related genes (XIRP2, COL8A1, KCNA6) were among the most deregulated genes in rTOF ventricles. To our knowledge, this is the first comprehensive report on global gene expression profiling in the heart of a long-term swine model of repaired TOF.
Photophysics of Intrinsic Single-Photon Emitters in Silicon Nitride at Low Temperatures (2023)

A robust process for fabricating intrinsic single-photon emitters in silicon nitride has been recently established. These emitters show promise for quantum applications due to room-temperature operation and monolithic integration with the technologically mature silicon nitride photonics platform. Here, the fundamental photophysical properties of these emitters are probed through measurements of optical transition wavelengths, linewidths, and photon antibunching as a function of temperature from 4.2K to 300K. Important insight into the potential for lifetime-limited linewidths is provided through measurements of inhomogeneous and temperature-dependent homogeneous broadening of the zero-phonon lines. At 4.2K, spectral diffusion was found to be the main broadening mechanism, while time-resolved spectroscopy measurements revealed homogeneously broadened zero-phonon lines with instrument-limited linewidths.
Energy diverting converter topologies for HVDC transmission systems (2013)

Grid codes imposed by utilities regulate the operation of Voltage Source Converter - High Voltage Direct Current (VSC-HVDC) interconnected offshore wind farms. Fault ride-through (FRT) specifications require the adoption of specific measures to avoid over-voltages of the HVDC link during faults in order to protect the HVDC equipment. Implementing Energy Diverting Converters (EDC), for instance Dynamic Braking Resistor (DBR) circuits, at the DC link is an established method to comply with the grid codes, where the excess energy of the wind farm is diverted into the parallel circuit during the fault. In this paper an evaluation of three different state-of-the-art DBR circuits is performed in order to establish the advantages and disadvantages of each circuit. The evaluation has shown that although the three solutions meet the FRT requirements, the modular topologies generate reduced slope current and voltage step changes during their operation, while being larger in size and requiring a higher number of semiconductors as compared to the traditional DC chopper circuit employing hard switched series connected semiconductor arrangements.
Paper #171: Validation of a Virtual Reality Knee Arthroscopy Simulator for Surgical Training (2013)

Virtual reality knee simulators can successfully replicate knee arthroscopy (to the satisfaction of experienced arthroscopy surgeons) and can effectively discriminate between subjects based on arthroscopic experience.
Probing the longitudinal electric field of Bessel beams using second-harmonic generation from nano-objects (2017)

Non-diffractive Bessel beams are receiving significant interest in optical microscopy due to their remarkably large depth of field. For example, studies have shown the superiority of Bessel beams over Gaussian beams for volumetric imaging of three-dimensionally thick or extended samples. However, the vectorial aspects of the focal fields of Bessel beams are generally obscured when traditional methods are used to characterize their three-dimensional point-spread function in space, which contains contributions from all optical field components. Here, we show experimentally the three-dimensional spatial distribution and enhanced depth of field of the longitudinal electric field components of a focused linearly-polarized Bessel beam. This is done through second-harmonic generation from well-defined vertically-aligned gallium-arsenide nanowires, whose second-order response is primarily driven by the longitudinal fields at the beam focus.
Design of cyclic peptides with biological activities from biologically active peptides: the case of peptide modulators of melanocortin receptors (2016)

Design of biologically active peptides is of critical importance for the development of potent, selective, nontoxic bioavailable drugs. A major approach that has been developed to accomplish this is the development of methods for the design and synthesis of a wide variety of cyclic peptides and peptidomimetics. In this short and general review, we outline the methods that have been developed for cyclization of peptides and how these have been used for peptide and peptidomimetic design using the melanotropin peptides and melanocortin receptors MC1R, MC3R, MC4R, and MC5R to illustrate aspects of this approach.
Microbiological Production of Surfactant from Agricultural Residuals for IOR Application (2002)

Abstract Utilization of surfactants for IOR is an accepted technique with high potential. However, technology application is frequently limited by cost. Biosurfactants (surface-active molecules produced by microorganisms) are commonly used in specialty markets such as food and textiles and have potential for IOR application. Currently, biosurfactants are not widely utilized in the petroleum industry due to high production costs associated with use of expensive substrates and inefficient product recovery methods. The economics of biosurfactant production could be significantly impacted through use of media optimization and application of inexpensive carbon substrates such as agricultural process residuals. Utilization of biosurfactants produced from agricultural residuals may 1) result in an economic advantage for surfactant production and technology application, and 2) convert a substantial agricultural waste stream to a value-added product for IOR. A biosurfactant with high potential for use is surfactin, a lipopeptide biosurfactant, produced by Bacillus subtilis. Reported here is the production and potential IOR utilization of surfactin produced by Bacillus subtilis (American Type Culture Collection (ATCC) 21332) from starch-based media. Production of surfactants from microbiological growth media based on simple sugars, chemically pure starch medium, simulated liquid and solid potato-process effluent media, a commercially prepared potato starch in mineral salts, and process effluent from a potato processor is discussed. Additionally, the effect of chemical and physical pretreatments on starchy feedstocks is discussed. This paper presents an overview of previous work. This effort details the progress of research from initial observation of surfactin production from simple growth media through production of surfactin from process effluents from a local potato processor, and finally, potential reactor design for continuous operation.1,2,3,4
Spherical harmonic domain noise reduction using an MVDR beamformer and DOA-based second-order statistics estimation (2013)

Most beamformers used for noise reduction rely on the accurate estimation of the second-order statistics of the noise, and in some cases, of the desired signal. Speech presence probability (SPP) based statistics estimators seek to update the estimates only when speech is absent/present, however, when used with a fixed a priori SPP, they cannot distinguish between a coherent desired source and coherent noise sources. We propose to distinguish between desired and noise sources by estimating the second-order statistics with a direction of arrival dependent a priori SPP, which we then use to compute the weights of a spherical harmonic domain minimum variance distortionless response filter.
T-cell Acute Leukemia 1 (TAL1) Regulation of Erythropoietin Receptor and Association with Excessive Erythrocytosis (2012)

During erythropoiesis, erythropoietin stimulates induction of erythroid transcription factors that activate expression of erythroid genes including the erythropoietin receptor (EPO-R) that results in increased sensitivity to erythropoietin. DNA binding of the basic helix-loop-helix transcription factor, TAL1/SCL, is required for normal erythropoiesis. A link between elevated TAL1 and excessive erythrocytosis is suggested by erythroid progenitor cells from a patient that exhibits unusually high sensitivity to erythropoietin with concomitantly elevated TAL1 and EPO-R expression. We found that TAL1 regulates EPO-R expression mediated via three conserved E-box binding motifs (CAGCTG) in the EPO-R 5' untranslated transcribed region. TAL1 increases association of the GATA-1·TAL1·LMO2·LDB1 transcription activation complex to the region that includes the transcription start site and the 5' GATA and 3' E-box motifs flanking the EPO-R transcription start site suggesting that TAL1 promotes accessibility of this region. Nucleosome shifting has been demonstrated to facilitate TAL1 but not GATA-1 binding to regulate target gene expression. Accordingly, we observed that with induced expression of EPO-R in hemotopoietic progenitor cells, nucleosome phasing shifts to increase the linker region containing the EPO-R transcription start site and TAL1 binds to the flanking 5' GATA and 3' E-box regions of the promoter. These data suggest that TAL1 binds to the EPO-R promoter to activate EPO-R expression and provides a potential link to elevated EPO-R expression leading to hypersensitivity to erythropoietin and the resultant excessive erythrocytosis.
Background service QoS in a UMTS network (2010)

This paper presents a methodology for evaluating the quality of service provided by a cellular network for background services, such as e-mail and text messaging. Data collected from drive testing were used as the means to evaluate different drive routes on a Universal Mobile Telecommunications System (UMTS) network. Although one type of cellular network was tested, this methodology may be readily adapted to fit other types of cellular networks.
d-alpha-tocopherol inhibits collagen alpha 1(I) gene expression in cultured human fibroblasts. Modulation of constitutive collagen gene expression by lipid peroxidation. (1991)

Ascorbic acid stimulates collagen gene transcription in cultured fibroblasts, and this effect is mediated through the induction of lipid peroxidation by ascorbic acid. Quiescent cultured fibroblasts in the absence of ascorbic acid have a high constitutive level of collagen production, but the mechanisms of collagen gene regulation in this unstimulated state are not known. Because lipid peroxidation also occurs in normal cells, we wondered if lipid peroxidation plays a role in the regulation of basal collagen gene expression. Inhibition of lipid peroxidation in cultured human fibroblasts with d-alpha-tocopherol or methylene blue decreased the synthesis of collagen, the steady-state levels of procollagen alpha 1(I) mRNA and the transcription of the procollagen alpha 1(I) gene. This effect on collagen gene expression was selective and not associated with cellular toxicity. Thus, these experiments suggest a role for lipid peroxidation in the modulation of constitutive collagen gene expression.
First evidence of subclinical renal tubular injury during sickle-cell crisis (2014)

These results demonstrated that subclinical ischemia-reperfusion tubular injury is common during VOC and highlight the importance of hydroelectrolyte monitoring and correction during VOC.
Deep UV light generation by a fiber/bulk hybrid amplifier at 199 nm (2009)

A high-pulse-repetition-frequency (PRF) pulsed light source in the deep ultraviolet region has been realized by a multiple wavelength conversion technique using a hybrid fiber/bulk amplifier system. Output of 199 nm with a power of 50 mW was achieved at 2.4 MHz PRF. The 1 microm amplifier consisted of a Yb-doped fiber amplifier and a Nd-doped YVO(4) amplifier. A 1.5 microm fiber master-oscillator power amplifier was employed as the other fundamental source. The amplifiers exhibited good amplification properties in pulse energy, polarization extinction ratio, and spectrum for nonlinear wavelength conversion.
ChemInform Abstract: TOTAL SYNTHESIS OF RACEMIC SESBANINE (1980)

Abstract Aus 4‐Carbomethoxy‐nicotinsäure (I) erhält man über Homologisierung durch Reduktion, Halogenierung, Nitrilaustausch und Veresterung den Nitrilester (II), der mit 1,4‐Dichlor‐2‐buten zu (III) substituiert wird.
Pharmacokinetics of high-titer anti–SARS-CoV-2 human convalescent plasma in high-risk children (2021)

BACKGROUNDWhile most children who contract COVID-19 experience mild disease, high-risk children with underlying conditions may develop severe disease, requiring interventions. Kinetics of antibodies transferred via COVID-19 convalescent plasma early in disease have not been characterized.METHODSIn this study, high-risk children were prospectively enrolled to receive high-titer COVID-19 convalescent plasma (>1:320 anti-spike IgG; Euroimmun). Passive transfer of antibodies and endogenous antibody production were serially evaluated for up to 2 months after transfusion. Commercial and research ELISA assays, virus neutralization assays, high-throughput phage-display assay utilizing a coronavirus epitope library, and pharmacokinetic analyses were performed.RESULTSFourteen high-risk children (median age, 7.5 years) received high-titer COVID-19 convalescent plasma, 9 children within 5 days (range, 2-7 days) of symptom onset and 5 children within 4 days (range, 3-5 days) after exposure to SARS-CoV-2. There were no serious adverse events related to transfusion. Antibodies against SARS-CoV-2 were transferred from the donor to the recipient, but antibody titers declined by 14-21 days, with a 15.1-day half-life for spike protein IgG. Donor plasma had significant neutralization capacity, which was transferred to the recipient. However, as early as 30 minutes after transfusion, recipient plasma neutralization titers were 6.2% (range, 5.9%-6.7%) of donor titers.CONCLUSIONConvalescent plasma transfused to high-risk children appears to be safe, with expected antibody kinetics, regardless of weight or age. However, current use of convalescent plasma in high-risk children achieves neutralizing capacity, which may protect against severe disease but is unlikely to provide lasting protection.Trial registrationClinicalTrials.gov NCT04377672.FundingThe state of Maryland, Bloomberg Philanthropies, and the NIH (grants R01-AI153349, R01-AI145435-A1, K08-AI139371-A1, and T32-AI052071).
Leads for Development of New Naphthalenesulfonate Derivatives with Enhanced Antiangiogenic Activity (2003)

Inhibition of angiogenesis-promoting factors such as fibroblast growth factors is considered to be a potential procedure for inhibiting solid tumor growth. Although several peptide-based inhibitors are currently under study, the development of antiangiogenic compounds of small molecular size is a pharmacological goal of considerable interest. We have already shown that certain naphthalene sulfonates constitute minimal functional substitutes of the antiangiogenic compounds of the suramin and suradista family. Using those data as a lead, we have carried out a rational search for new angiogenesis inhibitors that could provide new pharmacological insights for the development of antiangiogenic treatments. The results of the study strongly underline the relevance of the stereochemistry for an efficient inhibition of acidic fibroblast growth factor mitogenic activity by the naphthalene sulfonate family and allow us to formulate rules to aid in searching for new inhibitors and pharmaceutical developments. To provide further leads for such developments and acquire a detailed insight into the basis of the inhibitory activity of the naphthalene sulfonate derivatives, we solved the three-dimensional structure of acidic fibroblast growth factor complexed to 5-amino-2-naphthalenesulfonate, the most pharmacologically promising of the identified inhibitors. The structure shows that binding of this compound would hamper the interaction of acidic fibroblast growth factor with the different components of the cell membrane mitogenesis-triggering complex.
Traveltime-based microseismic event location using artificial neural network (2022)

Location of earthquakes is a primary task in seismology and microseismic monitoring, essential for almost any further analysis. Earthquake hypocenters can be determined by the inversion of arrival times of seismic waves observed at seismic stations, which is a non-linear inverse problem. Growing amounts of seismic data and real-time processing requirements imply the use of robust machine learning applications for characterization of seismicity. Convolutional neural networks have been proposed for hypocenter determination assuming training on previously processed seismic event catalogs. We propose an alternative machine learning approach, which does not require any pre-existing observations, except a velocity model. This is particularly important for microseismic monitoring when labeled seismic events are not available due to lack of seismicity before monitoring commenced (e.g., induced seismicity). The proposed algorithm is based on a feed-forward neural network trained on synthetic arrival times. Once trained, the neural network can be deployed for fast location of seismic events using observed P-wave (or S-wave) arrival times. We benchmark the neural network method against the conventional location technique and show that the new approach provides the same or better location accuracy. We study the sensitivity of the proposed method to the training dataset, noise in the arrival times of the detected events, and the size of the monitoring network. Finally, we apply the method to real microseismic monitoring data and show that it is able to deal with missing arrival times in efficient way with the help of fine tuning and early stopping. This is achieved by re-training the neural network for each individual set of picked arrivals. To reduce the training time we used previously determined weights and fine tune them. This allows us to obtain hypocenter locations in near real-time.