gebhart/patrepeval huggingface dataset:
The path to developing a cervical cancer vaccine (2010)

The path that led me to where I am today in my career as a vaccinologist was not a straight one: it was riddled with twists and turns, opportunities and obstacles and full of decisions that could have taken me down very different avenues. Working and interacting with many dedicated and brilliant scientists and taking apprenticeships to become a better and more versatile scientist have been rewarding experiences and more than once luck has come into play.
Multi‐centre randomised trial of invasive and less invasive surfactant delivery methods showed similar spirometry results at 5–9 years of age (2022)

The proportion of children aged 5-9 years with subnormal FEV<sub>1</sub> was not significantly different between the groups.
Carrier-envelope frequency stabilization of a Ti:sapphire oscillator using different pump lasers (2012)

We investigate the suitability of various commercially available pump lasers for operation with a carrier-envelope offset frequency stabilized Ti:sapphire oscillator. Although the tested pump lasers differ in their setup and properties (e.g., single vs. multi-mode), we find that they are all well-suited for the purpose. The residual rms phase noise (integrated between 20 Hz and 5 MHz) of the stabilized oscillator is found to be below 160 mrad with each pump laser, corresponding to less than 1/40 of an optical cycle. Differences in performance vary slightly. In particular, our results indicate that the latest generation of multi-mode pump lasers can be used for applications where precise phase control of the oscillator is strictly required.
Motorcycle dynamics library in Modelica (2006)

This paper presents a Modelica library developed for the dynamic simulation of a motorcycle, developed within the Dymola environment (see [1], [2], [3]) and tailored to test and validation of active control systems for motorcycle dynamics. As a matter of fact, as a complete analytical model for two-wheeled vehicles is not directly available due to the complexity of their dynamic behavior, a reliable model should be based on multibody modeling tools endowed with automated symbolic manipulation capabilities. In this work we illustrate the modular approach to motorcycle modeling and discuss the tire-road interaction model, which is the crucial part of the simulator. Moreover, we propose a virtual driver model which allows to perform all possible maneuvers.
Management of Digital Video Broadcasting services in open delivery platforms (2006)

The future of digital broadcasting is moving towards solutions for the efficient delivery of interactive IP multimedia services over digital broadcasting networks, to handheld terminals. One of the most promising technologies is Digital Video Broadcasting-Handheld (DVB-H), at present under standardisation. Services deployed via this type of DVB technology should enjoy reliability comparable to TV services and high quality standards. However, the market does not at present provide effective and economical solutions for the delivery of such services to DVB-H transmitters over multi-domain IP networks due to the high level of unreliability of such networks.
A viscoelastic model for human myocardium (2021)

Understanding the biomechanics of the heart in health and disease plays an important role in the diagnosis and treatment of heart failure. The use of computational biomechanical models for therapy assessment is paving the way for personalized treatment, and relies on accurate constitutive equations mapping strain to stress. Current state-of-the art constitutive equations account for the nonlinear anisotropic stress-strain response of cardiac muscle using hyperelasticity theory. While providing a solid foundation for understanding the biomechanics of heart tissue, most current laws neglect viscoelastic phenomena observed experimentally. Utilizing experimental data from human myocardium and knowledge of the hierarchical structure of heart muscle, we present a fractional nonlinear anisotropic viscoelastic constitutive model. The model is shown to replicate biaxial stretch, triaxial cyclic shear and triaxial stress relaxation experiments (mean error ∼7.68%), showing improvements compared to its hyperelastic (mean error ∼24%) counterparts. Model sensitivity, fidelity and parameter uniqueness are demonstrated. The model is also compared to rate-dependent biaxial stretch as well as different modes of biaxial stretch, illustrating extensibility of the model to a range of loading phenomena. STATEMENT OF SIGNIFICANCE: The viscoelastic response of human heart tissues has yet to be integrated into common constitutive models describing cardiac mechanics. In this work, a fractional viscoelastic modeling approach is introduced based on the hierarchical structure of heart tissue. From these foundations, the current state-of-the-art biomechanical models of the heart muscle are transformed using fractional viscoelasticity, replicating passive muscle function across multiple experimental tests. Comparisons are drawn with current models to highlight the improvements of this approach and predictive responses show strong qualitative agreement with experimental data. The proposed model presents the first constitutive model aimed at capturing viscoelastic nonlinear response across multiple testing regimes, providing a platform for better understanding the biomechanics of myocardial tissue in health and disease.
Protein kinase Cα–mediated phosphorylation of Twist1 at Ser-144 prevents Twist1 ubiquitination and stabilizes it (2019)

Twist1 is a basic helix-loop-helix transcription factor that plays a key role in embryonic development, and its expression is down-regulated in adult cells. However, Twist1 is highly expressed during cancer development, conferring a proliferative, migratory, and invasive phenotype to malignant cells. Twist1 expression can be regulated post-translationally by phosphorylation or ubiquitination events. We report in this study a previously unknown and relevant Twist1 phosphorylation site that controls its stability. To identify candidate phosphorylation sites in Twist1, we first conducted an <i>in silico</i> analysis of the Twist1 protein, which yielded several potential sites. Because most of these sites were predicted to be phosphorylated by protein kinase C (PKC), we overexpressed PKCα in several cell lines and found that it phosphorylates Twist1 on Ser-144. Using a combination of immunoblotting, immunoprecipitation, protein overexpression, and CRISPR/Cas9-mediated PKCα knockout experiments, we observed that PKCα-mediated Twist1 phosphorylation at Ser-144 inhibits Twist1 ubiquitination and consequently stabilizes it. These results provide evidence for a direct association between PKCα and Twist1 and yield critical insights into the PKCα/Twist1 signaling axis that governs cancer aggressiveness.
Deep Circumflex Iliac Artery Perforator Flap without Iliac Crest (2008)

Worcester, Mass. From the Division of Plastic Surgery, University of Massachusetts Medical School. Received for publication November 23, 2007; accepted May 9, 2008. Presented in part at the 20th Annual Meeting of the American Society for Reconstructive Microsurgery, in Tucson, Arizona, January 14 through 17, 2006. Disclosure:None of the authors has a financial interest in any of the products, devices, or drugs mentioned in this article. Mustafa Akyurek, M.D.; Division of Plastic Surgery; University of Massachusetts Memorial Medical Center; 281 Lincoln Street; Worcester, Mass. 01605-2192; [email protected]
New Chemistry and Pyrethroid Combinations for Lepidopterous Pest Control in Broccoli (2000)

Success, Proclaim, and Avaunt were efficacious when applied alone or in combination with the pyrethroids, Warrior or Mustang. Warrior and Mustang alone also provided excellent control of the cabbage looper (Trichoplusia ni, CL) and diamondback moth (Plutella xylostella, DBM) at all rating dates for 3 weeks after a single application. Low infestation levels of the pests were attributed to the effectiveness of the insecticides.
Silicon verification of flare model & application to real chip for long range proximity correction (2007)

Optical proximity correction (OPC) plays a vital role in the lithography process for critical dimension (CD) control. With the shrinking of the design rule, CD is more sensitive to lithography process, so the task for OPC becomes more challenging. Flare, or stray light, is an added incoherent background intensity that will detract from lithography system performance, CD control and process latitude. The impact of flare on lithographic imaging and its correction through OPC has been the subject of increased investigation. In this paper, the flare effects on CD variation by changing the total image intensity are discussed. The flare map is obtained by running the flare model on the mask layout. Based on the flare map, flare test patterns are designed and flare test reticle is written. After collecting wafer silicon data with CD SEM, flare model is verified and the flare impacts on the across chip line width variation (ACLV) are presented. With the existence of flare, CD bias across different areas of the cell could be measured. As CD varies by a comparatively wider range than optical proximity range, it could not be corrected by existing OPC model. Based on the analysis of flare model and the experiment results, applications on flare correction are discussed by using OPC.
Techno-economic analysis and life cycle assessment of a biorefinery utilizing reductive catalytic fractionation (2021)

Reductive catalytic fractionation (RCF) is a promising approach to fractionate lignocellulose and convert lignin to a narrow product slate. To guide research towards commercialization, cost and sustainability must be considered. Here we report a techno-economic analysis (TEA), life cycle assessment (LCA), and air emission analysis of the RCF process, wherein biomass carbohydrates are converted to ethanol and the RCF oil is the lignin-derived product. The base-case process, using a feedstock supply of 2000 dry metric tons per day, methanol as a solvent, and H<sub>2</sub> gas as a hydrogen source, predicts a minimum selling price (MSP) of crude RCF oil of $1.13 per kg when ethanol is sold at $2.50 per gallon of gasoline-equivalent ($0.66 per liter of gasoline-equivalent). We estimate that the RCF process accounts for 57% of biorefinery installed capital costs, 77% of positive life cycle global warming potential (GWP) (excluding carbon uptake), and 43% of positive cumulative energy demand (CED). Of $563.7 MM total installed capital costs, the RCF area accounts for $323.5 MM, driven by high-pressure reactors. Solvent recycle and water removal <i>via</i> distillation incur a process heat demand equivalent to 73% of the biomass energy content, and accounts for 35% of total operating costs. In contrast, H<sub>2</sub> cost and catalyst recycle are relatively minor contributors to operating costs and environmental impacts. In the carbohydrate-rich pulps, polysaccharide retention is predicted not to substantially affect the RCF oil MSP. Analysis of cases using different solvents and hemicellulose as an <i>in situ</i> hydrogen donor reveals that reducing reactor pressure and the use of low vapor pressure solvents could reduce both capital costs and environmental impacts. Processes that reduce the energy demand for solvent separation also improve GWP, CED, and air emissions. Additionally, despite requiring natural gas imports, converting lignin as a biorefinery co-product could significantly reduce non-greenhouse gas air emissions compared to burning lignin. Overall, this study suggests that research should prioritize ways to lower RCF operating pressure to reduce capital expenses associated with high-pressure reactors, minimize solvent loading to reduce reactor size and energy required for solvent recovery, implement condensed-phase separations for solvent recovery, and utilize the entirety of RCF oil to maximize value-added product revenues.
A Heterologous Prime/Boost Vaccination Strategy Enhances the Immunogenicity of Therapeutic Vaccines for Hepatitis C Virus (2013)

We provide a proof-of-concept that immunogenicity of 2 HCV therapeutic vaccines can be improved using their combination, which merits further clinical development.
B-(E)-γ-Methoxyallyldiisopinocampheylborane (2009)

[116376-27-3] C24H41BO (MW 356.39) InChI = 1S/C24H41BO/c1-15-11-17-13-20(24(17,5)6)22(15)25(9-8-10-26-7)21-14-18-12-19(16(21)2)23(18,3)4/h8,10,15-22H,9,11-14H2,1-7H3/b10-8+/t15-,16-,17+,18+,19-,20+,21-,22?/m1/s1 InChIKey = JHWYUEHMXDKYGU-DOKKHLRJSA-N (alkoxyallylborating agent used for the reaction with aldehydes and imines to provide the (α-alkoxyhomoallylic alcohols and amines, respectively, in a highly stereoselective fashion) Alternate Name: B-γ-Alkoxyallyldiisopinocampheylborane. Analysis of Reagent Purity: 11B NMR (δ 80.0,s). Form Supplied in: not available commercially. Handling, Storage, and Precaution: Prepared and used in situ. Physical Data: unstable at higher temperatures and undergoes scrambling of the double bond. Preparative Methods: The (E)-alkoxyallylborane 1 is prepared via the reduction of (E)-1-methoxy-3-(phenylthio)propene 3 with potassium naphthalenide and subsequent treatment with Ipc2BOMe to generate the “ate” complex that upon Lewis acid (BF3·Et2O) treatment releases the free allylborane 1.1 The thiopropene 3 in turn is prepared by the reaction of methoxyallene 2 with benzenethiol in the presence of catalytic fluoroboric acid (eq 1).2 (1) Purification: none (air-and moisture-sensitive and unstable at higher temperatures, hence prepared and used in situ). Solubility: soluble in ether, THF, CH2Cl2, and other organic solvents.
Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway (2020)

The paraherquamides are potent anthelmintic natural products with complex heptacyclic scaffolds. One key feature of these molecules is the spiro-oxindole moiety that lends a strained three-dimensional architecture to these structures. The flavin monooxygenase PhqK was found to catalyze spirocycle formation through two parallel pathways in the biosynthesis of paraherquamides A and G. Two new paraherquamides (K and L) were isolated from a Δ<i>phqK</i> strain of <i>Penicillium simplicissimum</i>, and subsequent enzymatic reactions with these compounds generated two additional metabolites, paraherquamides M and N. Crystal structures of PhqK in complex with various substrates provided a foundation for mechanistic analyses and computational studies. While it is evident that PhqK can react with various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxepin-containing paraherquamide L is the favored substrate. Through this effort, we have elucidated a key step in the biosynthesis of the paraherquamides and provided a rationale for the selective spirocyclization of these powerful anthelmintic agents.
Nachweis zentral-auditiver Kompensationsvorgänge bei einseitiger Ertaubung mit funktioneller Magnetresonanztomographie (2000)

Central-auditory compensation by bilateral cortical activation was demonstrated in unilateral deaf patients. Moreover, a tendency towards a dominance of the left primary auditory cortex was found, although the difference between both hemispheres was not significant. The lateralization ratio in unilateral deaf patients is similar to findings after binaural stimulation in normally hearing subjects.
An optimized dosing regimen of cimaglermin (neuregulin 1β3, glial growth factor 2) enhances molecular markers of neuroplasticity and functional recovery after permanent ischemic stroke in rats (2015)

Cimaglermin (neuregulin 1β3, glial growth factor 2) is a neuregulin growth factor family member in clinical development for chronic heart failure. Previously, in a permanent middle cerebral artery occlusion (pMCAO) rat stroke model, systemic cimaglermin treatment initiated up to 7 days after ischemia onset promoted recovery without reduced lesion volume. Presented here to extend the evidence are two studies that use a rat stroke model to evaluate the effects of cimaglermin dose level and dose frequency initiated 24 hr after pMCAO. Forelimb- and hindlimb-placing scores (proprioceptive behavioral tests), body-swing symmetry, and infarct volume were compared between treatment groups (n = 12/group). Possible mechanisms underlying cimaglermin-mediated neurologic recovery were examined through axonal growth and synapse formation histological markers. Cimaglermin was evaluated over a wider dose range (0.02, 0.1, or 1.0 mg/kg) than doses previously shown to be effective but used the same dosing regimen (2 weeks of daily intravenous administration, then 1 week without treatment). The dose-frequency study used the dose-ranging study's most effective dose (1.0 mg/kg) to compare daily, once per week, and twice per week dosing for 3 weeks (then 1 week without treatment). Dose- and frequency-dependent functional improvements were observed with cimaglermin without reduced lesion volume. Cimaglermin treatment significantly increased growth-associated protein 43 expression in both hemispheres (particularly somatosensory and motor cortices) and also increased synaptophysin expression. These data indicate that cimaglermin enhances recovery after stroke. Immunohistochemical changes were consistent with axonal sprouting and synapse formation but not acute neuroprotection. Cimaglermin represents a potential clinical development candidate for ischemic stroke treatment.
A New Fundamental Understanding of Gas in the Drilling Riser (2021)

Abstract The work described here originated from the tragic and ultimately environmentally catastrophic event at the Macondo well in April 2010. The first part of the paper addresses the causes for the sudden and often destructive ejection of hydrocarbons from a riser when a gas kick escapes timely detection. The approach differs from previous work on the subject and provides a realistic understanding of the sequence of events responsible for the phenomenon. The focus is on the crucial few minutes and seconds prior to the sudden eruption of gas and provides a quantitative illustration of the extreme rapidity of the ejection which leaves no time for a drill crew to adopt mitigation measures. It is shown that, in many cases, a back-pressure applied at the top of the well can be beneficial. The second part of the paper describes a novel method for the detection of gas which relies on the measurement of pressure differences along sections of the riser. These data are sensitive to the mean density of the fluid in the section and can therefore detect the presence of free gas. Laboratory experiments supporting the idea are described. Proper signal processing can be developed which may be able to allow for automatic mitigation measures to be taken in the event of an otherwise undetected gas influx approaching the surface.
Linguistic Coordination as an Unobtrusive, Dynamic Indicator of Rapport, Prosocial Team Processes, and Performance in Team Communication (2017)

Language style matching ( LSM; the extent to which individuals match others’ function or “filler” words in communication) has been investigated as a potential predictor of rapport and team processes (e.g., trust). We examined the potential of LSM as an unobtrusive bottom-up indicator of rapport, trust, cohesion, and performance using a distributed, team problem-solving task. We found a dynamic relationship between LSM and performance. The relationship changes over time as team interaction progresses, but LSM also interacts with trust and rapport to affect performance. We introduce a model to explain the relationship between LSM, rapport, trust, and performance in this context.
Anionic nanoparticle-induced perturbation to phospholipid membranes affects ion channel function (2020)

Understanding the mechanisms of nanoparticle interaction with cell membranes is essential for designing materials for applications such as bioimaging and drug delivery, as well as for assessing engineered nanomaterial safety. Much attention has focused on nanoparticles that bind strongly to biological membranes or induce membrane damage, leading to adverse impacts on cells. More subtle effects on membrane function mediated via changes in biophysical properties of the phospholipid bilayer have received little study. Here, we combine electrophysiology measurements, infrared spectroscopy, and molecular dynamics simulations to obtain insight into a mode of nanoparticle-mediated modulation of membrane protein function that was previously only hinted at in prior work. Electrophysiology measurements on gramicidin A (gA) ion channels embedded in planar suspended lipid bilayers demonstrate that anionic gold nanoparticles (AuNPs) reduce channel activity and extend channel lifetimes without disrupting membrane integrity, in a manner consistent with changes in membrane mechanical properties. Vibrational spectroscopy indicates that AuNP interaction with the bilayer does not perturb the conformation of membrane-embedded gA. Molecular dynamics simulations reinforce the experimental findings, showing that anionic AuNPs do not directly interact with embedded gA channels but perturb the local properties of lipid bilayers. Our results are most consistent with a mechanism in which anionic AuNPs disrupt ion channel function in an indirect manner by altering the mechanical properties of the surrounding bilayer. Alteration of membrane mechanical properties represents a potentially important mechanism by which nanoparticles induce biological effects, as the function of many embedded membrane proteins depends on phospholipid bilayer biophysical properties.
Wet-Chemical Silicon Wafer Thinning Process for High Chip Strength (2012)

We proposed the wet-chemical Si wafer-thinning process and evaluated the damage caused by this process. For the damage evaluation, we measured the die fracture stress and fracture energy, and compared various wafer-thinning processes (backgrinding, wet-chemical Si wafer-thinning, backgrinding + chemical mechanical polishing, backgrinding + wet etching). The result of comparative study shows that wet-chemical wafer-thinning process has very high fracture stress/energy and demonstrates that the damage of wet-chemical Si wafer-thinning process is very small.
Identification of Iron(III) Peroxo Species in the Active Site of the Superoxide Reductase SOR from Desulfoarculus baarsii (2002)

The active site of superoxide reductase SOR consists of an Fe2+ center in an unusual [His4 Cys1] square-pyramidal geometry. It specifically reduces superoxide to produce H2O2. Here, we have reacted the SOR from Desulfoarculus baarsii directly with H2O2. We have found that its active site can transiently stabilize an Fe3+-peroxo species that we have spectroscopically characterized by resonance Raman. The mutation of the strictly conserved Glu47 into alanine results in a stabilization of this Fe3+-peroxo species, when compared to the wild-type form. These data support the hypothesis that the reaction of SOR proceeds through such a Fe3+-peroxo intermediate. This also suggests that Glu47 might serve to help H2O2 release during the reaction with superoxide.
Implementation of heuristic search strategies for distribution feeder reconfiguration (1990)

A method for feeder reconfiguration with the potential for handling realistic operating constraints is presented. The approach taken is to set up a decision tree to represent the various switching operations available. A best-first tree searching strategy, based on heuristics, is used to evaluate the various alternatives. Switching options which could result in overloads, voltage problems, or other operating constraints, such as those associated with system protection, are quickly eliminated as possibilities. The development of a rule-based system aimed at the reduction of the search space is presented as a means of implementing the above strategy. An example is used to illustrate the concepts described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>