gebhart/patrepeval huggingface dataset:
Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440 (2021)

Poly(ethylene terephthalate) (PET) is the most abundantly consumed synthetic polyester and accordingly a major source of plastic waste. The development of chemocatalytic approaches for PET depolymerization to monomers offers new options for open-loop upcycling of PET, which can leverage biological transformations to higher-value products. To that end, here we perform four sequential metabolic engineering efforts in Pseudomonas putida KT2440 to enable the conversion of PET glycolysis products via: (i) ethylene glycol utilization by constitutive expression of native genes, (ii) terephthalate (TPA) catabolism by expression of tphA2<sub>II</sub>A3<sub>II</sub>B<sub>II</sub>A1<sub>II</sub> from Comamonas and tpaK from Rhodococcus jostii, (iii) bis(2-hydroxyethyl) terephthalate (BHET) hydrolysis to TPA by expression of PETase and MHETase from Ideonella sakaiensis, and (iv) BHET conversion to a performance-advantaged bioproduct, β-ketoadipic acid (βKA) by deletion of pcaIJ. Using this strain, we demonstrate production of 15.1 g/L βKA from BHET at 76% molar yield in bioreactors and conversion of catalytically depolymerized PET to βKA. Overall, this work highlights the potential of tandem catalytic deconstruction and biological conversion as a means to upcycle waste PET.
SPHEREx: an all-sky NIR spectral survey (2018)

SPHEREx, a mission in NASA’s Medium Explorer (MIDEX) program recently selected for Phase-A implementation, is an all-sky survey satellite that will produce a near-infrared spectrum for every 6 arcsecond pixel on the sky. SPHEREx has a simple, high-heritage design with large optical throughput to maximize spectral mapping speed. While the legacy data products will provide a rich archive of spectra for the entire astronomical community to mine, the instrument is optimized for three specific scientific goals: to probe inflation through the imprint primordial non-Gaussianity left on today’s large-scale cosmological structure; to survey the Galactic plane for water and other biogenic ices through absorption line studies; and to constrain the history of galaxy formation through power spectra of background fluctuations as measured in deep regions near the ecliptic poles. The aluminum telescope consists of a heavily baffled, wide-field off-axis reflective triplet design. The focal plane is imaged simultaneously by two mosaics of H2RG detector arrays separated by a dichroic beamsplitter. SPHEREx assembles spectra through the use of mass and volume efficient linear variable filters (LVFs) included in the focal plane assemblies, eliminating the need for any dispersive or moving elements. Instead, spectra are constructed through a series of small steps in the spacecraft attitude across the sky, modulating the location of an object within the FOV and varying the observation wavelength in each exposure. The spectra will cover the wavelength range between 0.75 and 5.0 µm at spectral resolutions ranging between R=35 and R=130. The entire telescope is cooled passively by a series of three V-groove radiators below 80K. An additional stage of radiative cooling is included to reduce the long wavelength focal plane temperature below 60K, controlling the dark current. As a whole, SPHEREx requires no new technologies and carries large technical and resource margins on every aspect of the design.
Time-resolved measurements of reflectivity, plasma formation, and damage of hafnia/silica multilayer mirrors at 1064 nm (2002)

High damage threshold hafnia/silica HR mirrors were damage tested. The transient reflectivity of these mirrors was studied during laser irradiation and particularly during catastrophic damage by top layer chipping. The tests were performed in R/1 mode on 50 sites in order to correctly assess the statistical behavior of the damage threshold. During the ramp, we observed the formation of a first plasma coupled to a modification of the reflected pulse without formation of any pit or chipping damage. For further irradiations at higher fluences, the optical properties of the mirror were unchanged up to the creation of a catastrophic chipping damage coming with a more intense plasma. The statistical distributions of fluences obtained in the two cases were different. For the moment, there is no proven correlation between first plasma and chipping: plasma detection cannot be used as a nondestructive quality control.
A small‐RNA‐mediated negative feedback loop controls quorum‐sensing dynamics in Vibrio harveyi (2008)

The bioluminescent marine bacterium Vibrio harveyi uses a cell-to-cell communication process called quorum sensing (QS) to co-ordinate behaviours in response to changes in population density. QS is accomplished through the secretion and detection of extracellular signalling molecules called autoinducers. At the centre of the V. harveyi QS circuit are five small regulatory RNAs called Qrr1-5 which destabilize the mRNA of luxR, encoding LuxR, the master transcriptional regulator of QS target genes. Here we show that LuxR directly activates transcription of qrr2, qrr3 and qrr4, leading to the rapid downregulation of luxR. The LuxR-binding sites in the promoters of qrr2, qrr3 and qrr4 were identified and mutated to determine the consequences of this regulatory loop on QS dynamics. Disruption of the loop delays the transition from high to low cell density, and more significantly, decreases the cell density at which the population reaches a quorum. Our results suggest that feedback is essential for optimizing the dynamics of the transitions between individual and group behaviours.
The Oxidative Metabolism of Glutamine (1996)

Treatment of the mouse fibrosarcoma cell line L929 with tumor necrosis factor (TNF) induces necrotic cell death. A crucial step in the cytotoxic action mechanism of TNF involves perturbation of mitochondrial functions leading to the formation of reactive oxygen intermediates (ROI). L929 cells have energy requirements adapted to a high proliferation rate. Glutamine (Gln) is utilized as a major energy source and drives mitochondrial ATP formation, while glucose is mainly converted to lactate through glycolysis. We investigated the role of the bioenergetic pathways involved in substrate utilization on the cytotoxic action of TNF and established a link between Gln oxidation and TNF-induced mitochondrial distress. Omission of Gln from the medium desensitizes the cells to TNF cytotoxicity, while the lack of glucose in the medium does not alter the TNF response. Sudden depletion of Gln from the culture medium results in a sharp decline in mitochondrial respiration in the cells, which might explain the decreased TNF responsiveness. However, when L929 cells are adapted to long term growth under conditions without Gln, these so-called L929/Gln- cells have restored respiration, but they still display a decreased sensitivity to TNF cytotoxicity. Thus the TNF responsiveness of L929 cells depends on bioenergetic reactions that are specifically involved in the oxidation of Gln. This is further confirmed by the desensitizing effect of specific inhibitors of these Gln-linked enzyme reactions on TNF cytotoxicity in the parental cells, but not in the L929/Gln- cells. Analysis of the induction of mitochondrial ROI formation by TNF in parental and L929/Gln- cells suggests that the effect of Gln on the sensitivity to TNF cytotoxicity involves a mechanism that renders the mitochondria more susceptible to TNF-induced mediators, resulting in enhanced ROI production and accelerated cytotoxicity.
Cervical teratoma in a dog : case report (2001)

A young adult boxer dog was examined for a painless swelling in the left cranial cervical area that was refractory to antibiotic therapy. Ultrasound examination revealed a hypoechoic mass abutting the rostrolateral aspect of the left mandibular salivary gland. The cystic mass was excised and was found to extend through the capsule of the salivary gland and appeared to be confluent with the glandular tissue at this point. Histopathological examination of the excised tissue demonstrated tissue from all 3 germinal layers. There was no indication of malignancy and the mass was diagnosed as a benign cervical teratoma. Hypotheses regarding the origin of teratomas in general are discussed and the origin of the teratoma in this case is suggested.
Novel Prostate-Specific Promoter Derived from PSA and PSMA Enhancers (2002)

The expression of prostate-specific membrane antigen (PSMA) and prostate-specific antigen (PSA), two well characterized marker proteins, remains highly active in the hormone refractory stage of prostate cancer. In this study, an artificial chimeric enhancer (PSES) composed of two modified regulatory elements controlling the expression of PSA and PSMA genes was tested for its promoter activity and tissue specificity using the reporter system. As a result, this novel PSES promoter remained silent in PSA- and PSMA-negative prostate and non-prostate cancer cell lines, but mediated high levels of luciferase in PSA- and PSMA-expressing prostate cancer cell lines in the presence and absence of androgen. To determine whether PSES could be used for in vivo gene therapy of prostate cancer, a recombinant adenovirus, Ad-PSES-luc, was constructed. Luciferase activity in prostate cancer cell lines mediated by Ad-PSES-luc was 400- to 1000-fold higher than in several other non-prostate cell lines, suggesting the high tissue-specificity of the PSES promoter in an adenoviral vector. Finally, recombinant virus Ad-PSES-luc was injected into mice to evaluate the tissue-discriminatory promoter activity in an experimental animal. Unlike Ad-CMV-luc, the luciferase activity from systemic injection of Ad-PSES-luc was fairly low in all major organs. However, when injected into prostate, Ad-PSES-luc drove high luciferase activity almost exclusively in prostate and not in other tissues. Our results demonstrated the potential use of PSES for the treatment of androgen-independent prostate cancer patients.
Graphitic Carbon Nitride Nanostructures as Potent Catalysts for Water Splitting: Theoretical Insights (2021)

The water-splitting reaction is a highly promising green and sustainable energy source. However, finding effective catalysts for both water reduction and oxidation is an unnerving challenge. Graphitic carbon nitride (gCN) is among the most auspicious electrodes for water splitting due to its unique physicochemical properties (i.e., thermal-physical-chemical stability, electron density, and active sites) and semiconducting merits (i.e., small band gap energy of 2.7 eV, high visible light absorption, and high photocurrent density at lower potential). Unlike previous article reviews and book chapters, this book chapter emphasizes the recent advances in gCNs as electrodes for water-splitting reactions from a theoretical or fundamental perspective rooting from self-standing gCNs to transition metals/gCNs, noble metals/gCNs, and doped gCNs for water splitting. In addition, this work presents the mechanisms of water-splitting reactions on gCN materials along with their challenges and future perspectives.
AACR Cancer Progress Report 2013 (2013)

### AACR Staff

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On April 8, 2013, in an unprecedented effort to highlight the critical importance of biomedical research, the American Association for Cancer Research (AACR) joined with more than 200 organizations representing a broad spectrum of research interests and diseases
Cross-entropy motion planning (2012)

This paper is concerned with motion planning for non-linear robotic systems operating in constrained environments. A method for computing high-quality trajectories is proposed building upon recent developments in sampling-based motion planning and stochastic optimization. The idea is to equip sampling-based methods with a probabilistic model that serves as a sampling distribution and to incrementally update the model during planning using data collected by the algorithm. At the core of the approach lies the cross-entropy method for the estimation of rare-event probabilities. The cross-entropy method is combined with recent optimal motion planning methods such as the rapidly exploring random trees (RRT*) in order to handle complex environments. The main goal is to provide a framework for consistent adaptive sampling that correlates the spatial structure of trajectories and their computed costs in order to improve the performance of existing planning methods.
MEMS process compatibility of multiwall carbon nanotubes (2011)

While carbon nanotubes (CNT) have been proposed and used as structural elements (e.g., cantilevers, bearings, nanofluidic channels, etc.) in microsystems, knowledge of the compatibility of CNTs with a broad range of standard microelectromechanical system (MEMS) fabrication processes is incomplete. This work investigates the effect of 23 common MEMS processes and chemicals on catalytically-grown and arc-discharge-produced multiwall nanotubes (MWNT) and compares the observed effects with those reported in the literature. Specific individual nanotubes are observed using scanning-electron microscopy (SEM) and transmission-electron microscopy (TEM) before and after the application of each process. This allows detection of process-induced changes to the nanotube from the bulk scale down to the nanometer and even atomic scales. Various thin-film deposition techniques are used to deposit common MEMS materials on MWNTs. A variety of wet chemicals and dry etching techniques are applied to MWNTs. Many processes prove compatible with the MWNTs, which suggests that they are robust for integration into MEMS devices.
Elevation directional channel properties at BS to evaluate 3D beamforming (2013)

This paper investigates the elevation directional channel properties at a base station (BS) based on ray-tracing simulation to evaluate the performance of 3D beamforming that controls the main beam direction of a BS antenna over both the azimuth dimension and elevation dimension. Results show that the average power elevation spectrum (PES) and the distribution of the elevation angular spread at BS do not depend on the BS antenna height. Moreover, we confirmed that when a mobile station (MS) exists in the vicinity of a BS in a line of sight (LOS) situation, the more the BS antenna height decreases, the more the elevation angular spread increases. Furthermore, the dispersion of the elevation median angle at BS is small compared to that for the azimuth case.
Catalytic effect of nickel(II) chloride and palladium(II) acetate on chromium(II)-mediated coupling reaction of iodo olefins with aldehydes (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic effect of nickel(II) chloride and palladium(II) acetate on chromium(II)-mediated coupling reaction of iodo olefins with aldehydesHaolun. Jin, Junichi. Uenishi, William J. Christ, and Yoshito. KishiCite this: J. Am. Chem. Soc. 1986, 108, 18, 5644–5646Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://doi.org/10.1021/ja00278a057Request reuse permissionsArticle Views5290Altmetric-Citations472LEARN 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 InReddit PDF (421 KB) Get e-Alertsclose Get e-Alerts
Modeling and Parametric Design of Permanent-Magnet AC Machines Using Computationally Efficient Finite-Element Analysis (2011)

Computationally efficient finite-element analysis (FEA) (CE-FEA) fully exploits the symmetries of electric and magnetic circuits of sine-wave current-regulated synchronous machines and yields substantial savings of computational efforts. Motor performance is evaluated through Fourier analysis and a minimum number of magnetostatic solutions. The major steady-state performance indices (average torque, ripple and cogging torque, back-electromotive-force waveforms, and core losses) are satisfactorily estimated as compared with the results of detailed time-stepping (transient) FEA. In this paper, the CE-FEA method is presented and applied to a parametric design study for an interior-permanent-magnet machine. Significant reduction of simulation times is achieved (approximately two orders of magnitude), permitting a comprehensive search of large design spaces for optimization purposes. In this case study, the influence of three design variables, namely, stator tooth width, pole arc, and slot opening, on three performance indices, namely, average torque, efficiency, and full-load torque ripple, is examined, and design trends are derived. One hundred candidate designs are simulated in less than 20 minutes on a state-of-the-art workstation.
Novel mutations in three families confirm a major role of COL4A1 in hereditary porencephaly (2005)

This observation confirms COL4A1 as a major locus for genetic predisposition to perinatal cerebral haemorrhage and porencephaly and suggests variable expression of COL4A1 mutations.
Web Search Using Small Cores: Quantifying the Price of Efficiency (2009)

The commoditization of hardware, data center economies of scale, and Internet-scale workload growth all demand greater power efficiency to sustain scalability. Traditional enterprise workloads, which are typically memory and I/O bound, have been well served by chip multiprocessors comprising of small, power-efficient cores. While small cores deliver performanceper-Watt efficiency for such data center workloads, small cores impact application quality-of-service robustness, flexibility, and reliability for emerging Internet-scale applications, which increasingly invoke computationally intensive kernels. These challenges constitute the price of efficiency, which we quantify for an industry-strength, production-quality, nextgeneration online web search engine. Specifically, we evaluate search on server- and mobile-class architectures using Xeon and Atom processors, quantifying search efficiency at the microarchitecture- and system-level. Our findings prompt us toward re-thinking small core designs for a new breed of data center workloads in order to continue reaping the benefits of small-core power efficiency. 1.
Nonmonotonic dynamics in Lifshitz-Slyozov-Wagner theory: Ostwald ripening in nanoparticle catalysts (2012)

Nanoparticle catalysts dispersed on high-surface-area electronic support materials are used in a wide range of applications. Nano-sized particles afford a high active surface area per unit volume of an electrocatalytic medium. However, the gain in active surface area for desired surface reactions is offset in part by enhanced rates of degradation processes that cause losses in catalyst mass, catalyst surface area, and electrocatalytic activity. A dynamic model of surface-area-loss phenomena based on the theories of Lifshitz and Slyozov [J. Phys. Chem. Solids 19, 35 (1961)], Wagner [Z. Elektrochem. 65, 581 (1961)], and Smoluchowski [Z. Phys. Chem. 92, 129 (1917)] is presented. A population balance equation in particle space accounts for nanoparticle dissolution, redeposition, and coagulation. It relates kinetic rates of these processes to the evolution of the particle-size distribution and its moments. Our analysis of the temporal dynamics of the number density, mean radii, surface area, and mass moments focuses on the important case of reaction-limited Ostwald ripening. Transient solutions reveal unique scaling relationships between the moments of the evolving distribution. Diagnostic criteria established from the scaling relationships are applied to previously published experimental degradation data for supported nanoparticle catalysts in polymer electrolyte fuel cells.
Avalanche decision schemes to improve pediatric rib fracture detection (2022)

Rib fractures are a sentinel injury for physical abuse in young children. When rib fractures are detected in young children, 80-100% of the time it is the result of child abuse. Rib fractures can be challenging to detect on pediatric radiographs given that they can be non-displaced, incomplete, superimposed over other structures, or oriented obliquely with respect to the detector. This work presents our efforts to develop an object detection method for rib fracture detection on pediatric chest radiographs. We propose a method entitled “avalanche decision” motivated by the reality that pediatric patients with rib fractures commonly present with multiple fractures; in our dataset, 76% of patients with fractures had more than one fracture. This approach is applied at inference and uses a decision threshold that decreases as a function of the number of proposals that clear the current threshold. These contributions were added to two leading single stage detectors: RetinaNet and YOLOv5. These methods were trained and tested with our curated dataset of 704 pediatric chest radiographs, for which pediatric radiologists labeled fracture locations and achieved an expert reader-to-reader F2 score of 0.76. Comparing base RetinaNet to RetinaNet+Avalanche yielded F2 scores of 0.55 and 0.65, respectively. F2 scores of base YOLOv5 and YOLOv5+Avalanche were 0.58 and 0.65, respectively. The proposed avalanche inferencing approaches provide increased recall and F2 scores over the standalone models.
Negative regulation of type I interferon signaling: facts and mechanisms. (2006)

Initially described for their antiviral activities, type I Interferons are now recognized as central regulatory elements of the immune response, primarily for their effect on the differentiation of monocytes into dendritic cells and osteoclasts. They are routinely used in clinic for the treatment of several diseases, including viral hepatitis, multiple sclerosis and several forms of cancer. Interferons are however not devoid of toxic effects when high doses are administered to patients, indicating that interferon action must be timely and spatially down regulated. We review here the molecular mechanisms which have been described to shut off the interferon initiated signals.