gebhart/patrepeval huggingface dataset:
Combined Experimental and Computational Approach toward the Structural Design of Borosilicate-Based Bioactive Glasses (2020)

Transitioning beyond a trial-and-error based approach for the compositional design of next-generation borosilicate-based bioactive glasses requires a fundamental understanding of the underlying compositional and structural drivers controlling their degradation and ion release in vitro and in vivo. Accordingly, the present work combines magic-angle spinning (MAS) NMR techniques, MD simulations, and DFT calculations based on GIPAW and PAW algorithms, to build a comprehensive model describing the short-to-medium-range structure of potentially bioactive glasses in the Na2O–P2O5–B2O3–SiO2 system over a broad compositional space. P2O5 preferentially tends to attract network modifier species, thus resulting in a repolymerization of the silicate network and a restructuring of the borate component. 11B{31P} and 31P{11B} dipolar recoupling experiments suggest that the ability of glasses to incorporate P2O5 without phase separation is related to the formation of P–O–B(IV) linkages integrated into the borosilicate glass network. An analogous approach is used for elucidating the local environments of the Na+ network modifiers. This work, along with future studies aimed at elucidating composition–structure–solubility/bioactivity relationships, will lay the foundation for the development of quantitative structure–property relationship (QSPR) models, thus representing a leap forward in the design of functional borosilicate bioactive glasses with controlled ionic release behavior.
Decorin is an early CSF biomarker of Alzheimer’s Aβ amyloidosis (2021)

Abstract Background Alzheimer’s disease (AD) brains are characterized by extracellular amyloid‐beta (Aβ) deposition and autophagy dysregulation. Here we aimed at deepening the understanding of these brain pathologies and how they translate to the CSF using App knock‐in mice. Method AD postmortem brain tissues and App knock‐in mouse models ( App NL‐F and App NL‐G‐F ) were used for autophagy characterization. The cerebrospinal fluid (CSF) from App knock‐in mice was analyzed by label‐free mass spectrometry (MS) and compared with previously reported CSF MS results from patients. The expression of decorin in the mouse brains was analyzed by immunohistochemistry and western blot. The autophagy‐activating effect of decorin was measured in the mouse primary neurons. Result p62 and LC3 II levels were increased in App NL‐G‐F mice similar to the marked accumulation of p62 in AD brains. Several extracellular matrix (ECM) proteins, including decorin, were significantly increased in the CSF of both App NL‐F mice and amyloid‐positive/tau‐negative subjects with normal cognition. Decorin was decreased in parvalbumin‐positive interneurons but increased in choroideus plexus of App NL‐F mice, both of which correlated with Aβ pathology. Decorin‐treated mouse primary neurons exhibited lowered p62 and LC3 II levels. Conclusion Autophagy is similarly inhibited in the brains of App NL‐G‐F mice and AD patients. The similar increase of decorin in CSF of App NL‐F mice and amyloid‐positive/tau‐negative subjects with normal cognition indicates a potential of decorin as an early biomarker of Aβ amyloidosis. In addition, decorin activates neuronal autophagy by increasing autophagosomal‐lysosomal degradation linking changes in ECM to autophagy.
Characterization Procedure for Stand-Alone Merging Units Based on Hardware-in-the-Loop Technology (2021)

The digitalization of a medium voltage network requires huge efforts from distributed system operators and electric utilities. The main reason is attributed to the costs associated with the replacement or introduction of new intelligent electronic devices capable of collecting and digitalizing current and voltage measurements. To this purpose, this paper introduces a new idea of a stand-alone merging unit (SAMU), which features real-time and hardware-in-the-loop technology, completed with accurate voltage and current sensors. Furthermore, the characterization procedure that allows an evaluation of the metrological performance of a complex device, such as a SAMU, is fully described. From the results, it is highlighted that (i) the developed SAMU is capable of performing highly accurate voltage, current, and power measurements; (ii) the characterization procedure is simple and exploitable for all kinds of SAMUs and other synchronized measurement devices.
Structural Basis of Mitochondrial Receptor Binding and GTP-Driven Conformational Constriction by Dynamin-Related Protein 1 (2017)

Abstract Mitochondrial inheritance, genome maintenance, and metabolic adaptation all depend on organelle fission by D ynamin- R elated P rotein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogs M itochondrial D ynamics 49 and 51 (MID49/MID51) and M itochondrial F ission F actor (MFF), but the mechanisms by which these proteins recruit DRP1 and regulate its activities are unknown. Here we present a cryoEM structure of human, full-length DRP1 bound to MID49 and an analysis of structure- and disease-based mutations. We report that GTP binding allosterically induces a remarkable elongation and rotation of the G-domain, Bundle-Signaling Element (BSE) and connecting hinge loops of DRP1. In this nucleotide-bound conformation, a distributed network of multivalent interactions promotes DRP1 copolymerization into a linear filament with MID49, MID51 or both. Subsequent GTP hydrolysis and exchange within the filament leads to receptor dissociation, shortening through disassembly, and concomitant curling of DRP1 oligomers into closed rings. The dimensions of the closed DRP1 rings are consistent with DRP1-constricted mitochondrial tubules observed in human cells. These structures are the first views of full-length, receptor- and nucleotide-bound dynamin-family GTPases and—in comparison with nucleotide-free crystal structures—teach us how these molecular machines perform mechanical work through nucleotide-driven allostery.
Motor Vehicle Emissions Variability (1996)

Abstract Test-to-test variability has been observed by many current testing methods, including the Federal Test Procedure, the IM240 dynamometer test, the idle test common to many Inspection and Maintenance programs, and on-road remote sensing. The variability is attributable to the vehicle, not to the testing procedure. Because the vehicles are the dominant source of variability, the only way such vehicles can be reliably identified is through the use of multiple tests. The emissions variability increases with increasing average emissions, and it appears to be prevalent among the few newer technology vehicles with defective, but untampered, closed-loop emissions control systems (1981 and newer models). In one fleet the variable emitters constitute 2.2% to 4.8% of the vehicles and contribute 8.5% to 22% of the total carbon monoxide emissions. Scheduled I/M programs that fail to ensure repair of these vehicles allow a significant portion of vehicles with excess emissions to escape reduction measures.
Reduction of Nitrate, Bromate, and Chlorate by Zero Valent Iron (Fe0) (2002)

Oxo-anions occur in drinking waters, pose potential health risks, and should be controlled. It may be possible to incorporate zero-valent iron (Fe0) into water treatment processes to remove oxo-anions. Under near neutral pH (∼7) and aerobic conditions, the three oxo-anions studied (NO3-,BrO3-,ClO3-) were electrochemically reduced by Fe0 in batch and continuous-flow packed column experiments. Mass balances provided strong evidence that ammonia is the primary reduction by-product from nitrate, chloride from chlorate, and bromide from bromate. Protons were consumed during the reaction, resulting in an increase in pH (i.e., production of hydroxide). Oxo-anion removal rates decreased as follows: BrO3->ClO3->NO3-. Differing rates of oxo-anion removal between batch and continuous flow column tests suggested that higher solid (Fe0) to liquid ratios increase oxo-anion electrochemical reduction, and scaling up of batch kinetic data to larger scale must consider the solid–liquid ratios. The atomic structure (atomic radii, electron orbital configuration, electron affinity) of nitrogen, chlorine, and bromine elements of the oxo-anions, and the bond dissociation energy between these elements and oxygen, were good indicators for the relative rates of reduction by Fe0.
<title>Penetrating radiation impact on NIF final optic components</title> (1997)

The principal technical goal of the National Ignition Facility (NIF) is to achieve thermonuclear ignition in a laboratory environment via inertial confinement fusion. This will enable NIF to service the DOE stockpile stewardship management program, inertial fusion energy goals, and advance scientific frontiers. All of these applications will make use of the extreme conditions that the facility will create in the target chamber. In the case of a projected 20 MJ yield scenario, NIF will produce approximately 10<SUP>19</SUP> neutrons with a characteristic DT fusion 14 MeV energy per neutron. There will also be a substantial amount of high energy x-rays as well as solid, liquid and gaseous target debris produced with directly or indirectly by the inertial confinement fusion process. A critical design issue is the protection of the final optical components as well as sophisticated target diagnostics in such a harsh environment.
Design and optimization of a lowimpedance pulsed power marx generator to drive a relativistic x-band magnetron (2006)

Summary form only given. The relativistic magnetron provides a low-impedance (10-20 U) load that inherently needs matching to a low-impedance pulsed-power supply (gigawatt or greater power) to operate with maximum efficiency. One of the most common and reliable pulsed-power drivers used to accomplish this is a Marx generator. The University of New Mexico previously used a modified Pulseradreg 110 A electron beam accelerator to produce high-power microwaves from a backward wave oscillator (BWO), which was a high-impedance load (130 U). This driver will be used for planned experiments driving an X-band relativistic magnetron. The main part of the Pulserad's assembly is a Marx generator composed of capacitors, spark gaps and resistors electrically arranged in an 11-stage Marx circuit. The output impedance of the Marx generator is about ~35 U (which is why a shunt resistor was required to facilitate operation with the BWO), maximum charging voltage of each single stage is <100 kV, and total stored energy is about 600 Joules. In this presentation results of the design and optimization efforts aimed at reducing the intrinsic impedance of the Marx generator are discussed. In order to provide power from the Marx generator to an X-band relativistic magnetron, a coaxial transmission line and a vacuum-insulator interface will be used and their design will be discussed
Electrospun Platinum Group Metal Free Catalyst Powder/Nafion/PEO Cathodes for Hydrogen/Air Fuel Cells (2020)

In recent years, there has been considerable research on platimum-group-metal-free (PGM-free) catalysts as the cathode material for proton-exchange membrane (PEM) fuel cells [1]. Although the oxygen reduction activity of these type of catalysts is lower than Pt or Pt-based alloys, a higher loading of these inexpensive catalysts may be a good way to balance sluggish oxygen reduction kinetics. One serious draw back of all PGM-free catalysts is their poor durability in a fuel cell. Pintauro and coworkers have shown the the durability issue can be solved using a cathode binder of Nafion ® and poly(vinylidene fluoride), but the fuel cell power output was low [2]. In the present study, PGM-free cathode fabrication and performance are presented using particle/polymer electrospinning. Nanofiber mat cathodes with a catalyst loading of 1.0, 2.0, and 3.0 mg/cm 2 were prepared using an iron based Fe-N-C catalyst (Pajarito Powder, NPC-2000), Nafion ionomer and poly (ethylene oxide) (PEO) as a carrier polymer for elelctrospinning. An SEM of one catalyst/Nafion fiber is shown in Figure 1 . After removing PEO from a fiber mat by soaking in hot water, the nanofiber-based cathodes were incorporated into H 2 /air fuel cell membrane-electrode assemblies (MEAs) and their performance (power output and durability) was compared to that of conventional sprayed-cathode MEAs (with neat Nafion binder). The effects of fiber composition, thickness and the choice of solvent for electrospinning on fuel cell performance were also examined. The maximum power density of a PGM-free nanofiber-cathode MEA, was found to be 252 mW/cm 2 at 80 ° C for H 2 and air at 2 atm backpressure. References: 1) Thompson, S.T.; Papageorgopoulos, D. Nat Catal 2 , 558-561 (2019). 2) Slack, J.; Halevi, B.; McCool, G.; Li, J.; Pavlicek, R.; Wycisk, R.; Mukerjee, S.; Pintauro P. ChemElectroChem 5 , 1537–1542 (2018) Figure 1
Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo (2015)

In E. coli, robust transcriptional pausing involves RNAP interaction with G-dC at the upstream end of the RNA-DNA hybrid, which interferes with translocation. CpG DNA sequences induce transcriptional pausing and G-to-A errors.
Sodium Channel Blockers. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Hemozoin is a key factor in the induction of malaria‐associated immunosuppression (1999)

Infection-associated immunoincompetence during malaria might result from macrophage dysfunction. In the present study, we investigated the role of macrophages as target for immunosuppression during infection, using the murine Plasmodium c. chabaudi model. Special attention has been paid to the analysis of processing/presentation of protein antigens and presentation of peptides, using cocultures of peritoneal exudate cells (PECs) from infected mice and antigen-specific T-cell hybridomas. The results obtained indicate a defective processing of protein antigens that becomes maximal at acute parasitemias. In addition, macrophages from acutely infected mice suppress the interleukin-2 production by the antigen-activated T-cell hybridomas. This effect was independent of prostaglandin and nitric oxide production by the macrophage. The possible role of parasite components in the impaired accessory cell function of PECs was investigated and hemozoin, the end-product of the hemoglobin catabolism by intraerythrocytic malaria parasites, was found to induce similar infection-associated deficiencies in vitro. Moreover, hemozoin, was shown to mimic the immunosuppressive effects induced in PECs during in-vivo infections with P. chabaudi. In conclusion, we propose that hemozoin is a key factor in the malaria-associated immunosuppression, affecting both the antigen processing and immunomodulatory functions of macrophages.
Severe Adenovirus Pneumonia Followed by Bacterial Septicaemia: Relevance of Co-Infections in Allogeneic Hematopoietic Stem Cell Transplantation (2016)

Infections are one of the major complications after allogeneic stem cell transplantation (allo-SCT). Disseminated infections with human adenoviruses species A, B or C are associated with a lethality of 24 to 36 %. Fatal outcome is usually observed with high viral loads in blood (median peak HAdV DNAemia 10(8) copies/mL). Here we report two adult patients with disseminated infection with human adenovirus C2 after allo-SCT. Interestingly, both patients developed bacterial septicaemia following the disseminated HAdV infection. Despite lower peak adenoviral loads in blood (<106 copies/mL) than usually reported for fatal cases of HAdV infection and broad spectrum antimicrobial therapy both patients experienced a rapidly fatal outcome. These cases shared the following similarities: disseminated adenovirus infection, adenovirus pneumonia, neurological symptoms and bacterial septicaemia. This suggests that in patients undergoing allo-SCT, viral bacterial co-infections worsen the clinical outcomes.
Platelet nitrate responsiveness in fasting and postprandial type 2 diabetes (2005)

Vascular responsiveness to exogenous nitrates in type 2 diabetes (T2DM) is attenuated in brachial and coronary vessels. We determined platelet responsiveness to nitric oxide (NO) in T2DM and control subjects. We examined whether the postprandial (PP) state affected platelet sensitivity to NO donors in T2DM patients and the extent of correlation between this and measures of oxidative stress, compared to changes in endothelial function. Twelve T2DM subjects were studied fasting and four hours after a test meal and compared with 15 healthy controls. We assessed the inhibitory effects of NO donors on adenosine 5'-diphosphate (ADP)-induced platelet aggregation. Oxidative stress was assessed by lipid-derived free radicals, ex vivo by electron paramagnetic resonance spectroscopy and markers of lipid peroxidation. Endothelial function was assessed by flow-mediated vasodilatation (FMD) of the brachial artery. Results are expressed as (mean +/- SEM). Fasting platelet aggregation was increased in diabetics versus controls (14.86 +/- 1.1 Ohms vs. 10.76 +/- 1.1 Ohms, p < 0.05). Sodium nitroprusside (SNP) and glyceryl trinitrate (GTN) inhibited ADP-induced aggregation by 73.1 +/- 5.9% and 50.3 +/- 7.7% in healthy controls compared to 15.4 +/- 7% and 19.5 +/- 8.2% in T2DM (p < 0.05). Fasting and postprandial inhibition of platelet aggregation with NO donors in T2DM was similar. T2DM patients had higher levels of oxidative stress in the fasting state and postprandially. There were no PP correlations with platelet NO resistance. In conclusion, there is platelet hyporesponsiveness to NO donors (SNP/GTN) in T2DM compared to controls, with increased ADP-induced platelet aggregation. Platelet abnormalities were associated with increased oxidative stress.
HeartMate II Left Ventricular Assist Device Implantation in Patients with Advanced Hepatic Dysfunction (2014)

Continuous-flow LVAD support may significantly improve hepatic function, allowing patients with poor preimplant liver function to become better candidates for heart transplantation.
Evaluation of Interactive Virtual Reality as a Preoperative Aid in Localizing Renal Tumors (2020)

<b><i>Introduction:</i></b> A detailed understanding of renal tumor anatomy is required to perform partial nephrectomy. We evaluated the utility of a CT-based interactive virtual reality (iVR) display to assist surgeons' understanding of the precise location of the renal tumor. <b><i>Methods:</i></b> CT scans and iVR models of 11 patients with a mean R.E.N.A.L. nephrometry score of 6.9 were evaluated. Seven faculty urologists and six urology residents reviewed CT scans and positioned each tumor onto a digital three-dimensional model of the same kidney, although without the tumor present. A week later, participants repeated the session using both iVR models and CT scans. For both time points, the overlap between the surgeon-inserted tumor and the actual tumor location was calculated. Participants answered a 1 to 10 Likert scale survey to gauge their understanding of renal and tumor anatomy based on CT alone <i>vs</i> CT+iVR. <b><i>Results:</i></b> Median tumor overlap for the entire cohort was 28% after CT review and 42% after CT+iVR (<i>p</i> = 0.05); among faculty urologists, for CT+iVR <i>vs</i> CT alone, percentage overlap improved (47% <i>vs</i> 33%, <i>p</i> = 0.033) and the incidence of 0% overlap decreased (19%-4%, <i>p</i> = 0.024), respectively. Among residents, there was no significant difference for either percentage overlap or 0% overlap for CT <i>vs</i> CT+iVR. The percentage overlap for the two tumors with high R.E.N.A.L. nephrometry scores (i.e., 10) increased from 51% to 67% after using CT+iVR (<i>p</i> = 0.039). The combination of CT+iVR was an independent predictor of improved overlap <i>vs</i> CT alone (odds ratio 2.22, 95% confidence interval 1.04-4.78, <i>p</i> = 0.039). Faculty surgeons' survey responses showed an improved understanding of the tumor location and shape with the addition of iVR (<i>p</i> < 0.05). <b><i>Conclusions:</i></b> The addition of patient-specific iVR models to standard CT imaging improved the ability of faculty urologists to accurately configure the location of a renal tumor, and improved their understanding of tumor anatomy.
Finding new information via robust entity detection (2010)

Journalists and editors work under pressure to collect relevant details and background information about specific events. They spend a significant amount of time sifting through documents and finding new information such as facts, opinions or stakeholders (i.e. people, places and organizations that have a stake in the news). Spotting them is a tedious and cognitively intense process. One task, essential to this process, is to find and keep track of stakeholders. This task is taxing cognitively and in terms of memory. Tell Me More offers an automatic aid to this task. Tell Me More is a system that, given a seed story, mines the web for similar stories reported by different sources and selects only those stories which offer new information with respect to that original seed story. Much like a journalist, the task of detecting named entities is central to its success. In this paper we briefly describe Tell Me More and, in particular, we focus on Tell Me More’s entity detection component. We describe an approach that combines off-the-shelf named entity recognizers (NERs) with WPED, a publicly available NER that uses Wikipedia as its knowledge base. We show significant increase in precision scores with respect to traditional NERs. Lastly, we present an overall evaluation of Tell Me More using this approach.
Effect of the class of switching-mode power amplifiers on the efficiency of band-pass delta-sigma architectures (2011)

This paper studies the impact of using a non-50-% duty cycle square-wave as an input signal, on the efficiency performance of different types of switching-mode power amplifiers (SMPAs). This investigation is important when the power amplifier (PA) is fed with bi-level pulses with a duty cycle different from the typical value of 50 %. This is the case in bandpass delta-sigma (BPDS) modulation where the duty cycle of the output pulses may vary from 0 % to 100 % based on the type of modulation and signal statistics. Simulation results show that the class-E PA is less sensitive to the variation of the duty cycle than the class-F and the class-D modes of operation. Therefore class-E PA is the best choice to be employed in band-pass delta-sigma based transmitter designs. Besides the PAs performance comparison, a correction on the efficiency calculation of the SMPAs driven by a duty cycle varying signal, is proposed in this paper.
Rapid interrogation of cancer cell of origin through CRISPR editing (2021)

The increasing complexity of different cell types revealed by single-cell analysis of tissues presents challenges in efficiently elucidating their functions. Here we show, using prostate as a model tissue, that primary organoids and freshly isolated epithelial cells can be CRISPR edited ex vivo using Cas9-sgRNA (guide RNA) ribotnucleoprotein complex technology, then orthotopically transferred in vivo into immunocompetent or immunodeficient mice to generate cancer models with phenotypes resembling those seen in traditional genetically engineered mouse models. Large intrachromosomal (∼2 Mb) or multigenic deletions can be engineered efficiently without the need for selection, including in isolated subpopulations to address cell-of-origin questions.