gebhart/patrepeval huggingface dataset:
From Wind to the Electric Grid: Comprehensive Modeling of Wind Turbine Systems (2016)

A detailed model of a full-conversion wind turbine (WT) is presented in this article. The developed model uses cosimulation by several freeware WT simulation tools-such as the turbulent wind simulator (TurbSim) and Fatigue, Aerodynamics, Structures, and Turbulence (FA ST), both from the National Renewable Energy Laboratory (NREL)-and commercial software to perform a detailed analysis of all WT components. An optimal level of model complexity is achieved to allow the design, analysis, and simulation of the controls and subsystem interactions within a turbine under various conditions. The article introduces a maximum power point tracking (MPPT) control for a variable-speed WT with stall power regulation and analyzes its influence on flexible blades and the drivetrain. The proposed simulation tools and the developed model reveal some stability issues and subsystem interaction complexities that are not visible in simpler models. In this article, modeling results are presented that detail the performance of the WT system.
MORE THAN MONEY: THE EXPONENTIAL IMPACT OF ACADEMIC TECHNOLOGY TRANSFER (2014)

Academic technology transfer in its current form began with the passage of the Bayh-Dole Act in 1980, which allowed universities to retain ownership of federally funded intellectual property. Since that time, a profession has evolved that has transformed how inventions arising in universities are treated, resulting in significant impact to US society. While there have been a number of articles highlighting benefits of technology transfer, now, more than at any other time since the Bayh-Dole Act was passed, the profession and the impacts of this groundbreaking legislation have come under intense scrutiny. This article serves as an examination of the many positive benefits and evolution, both financial and intrinsic, provided by academic invention and technology transfer, summarized in Table 1.
Unraveling the Correlation between Raman and Photoluminescence in Monolayer MoS2 through Machine‐Learning Models (2022)

2D transition metal dichalcogenides (TMDCs) with intense and tunable photoluminescence (PL) have opened up new opportunities for optoelectronic and photonic applications such as light-emitting diodes, photodetectors, and single-photon emitters. Among the standard characterization tools for 2D materials, Raman spectroscopy stands out as a fast and non-destructive technique capable of probing material's crystallinity and perturbations such as doping and strain. However, a comprehensive understanding of the correlation between photoluminescence and Raman spectra in monolayer MoS<sub>2</sub> remains elusive due to its highly nonlinear nature. Here, the connections between PL signatures and Raman modes are systematically explored, providing comprehensive insights into the physical mechanisms correlating PL and Raman features. This study's analysis further disentangles the strain and doping contributions from the Raman spectra through machine-learning models. First, a dense convolutional network (DenseNet) to predict PL maps by spatial Raman maps is deployed. Moreover, a gradient boosted trees model (XGBoost) with Shapley additive explanation (SHAP) to bridge the impact of individual Raman features in PL features is applied. Last, a support vector machine (SVM) to project PL features on Raman frequencies is adopted. This work may serve as a methodology for applying machine learning to characterizations of 2D materials.
SPCR-01 RAPIDPLAN HIPPOCAMPAL SPARING WHOLE BRAIN MODEL VERSION 2 - HOW FAR CAN WE REDUCE THE DOSE? (2022)

Abstract BACKGROUND Whole-brain radiotherapy (WBRT) has been the standard palliative treatment for patients with brain metastases due to its effectiveness, availability, and ease of administration. Recent clinical trials have shown that limiting radiation dose to the hippocampus is associated with decreased cognitive toxicity. In this study, we updated an existing Knowledge Based Planning (KBP) model to further reduce dose to the hippocampus and improve other dosimetric plan quality characteristics. METHODS 42 clinical cases were contoured according to NRG-CC001 guidelines. A new dosimetric scorecard was created as an objective measure for plan quality. The new Hippocampal Sparing Whole Brain Version 2 (HSWBv2) model adopted a complex recursive training process and was validated with five additional cases. HSWBv2 treatment plans were generated on the Varian HalcyonTM and TrueBeamTM systems and compared against plans generated from the existing (HSWBv1) model released in 2016. RESULTS On the HalcyonTM platform, 42 cases were re-planned. Hippocampal D100% from HSWBv2 and HSWBv1 models had an average dose of 5.75 Gy and 6.46 Gy, respectively (p&amp;lt;0.001). HSWBv2 model also achieved a hippocampal Dmean of 7.49 Gy, versus 8.10 Gy in HSWBv1 model (p&amp;lt;0.001). Hippocampal D0.03CC from HSWBv2 model was 9.86 Gy, in contrast to 10.57 Gy in HSWBv1 (p&amp;lt;0.001). For PTV_3000, D98% and D2% from HSWBv2 model were 28.27 Gy and 31.81 Gy, respectively, compared to 28.08 Gy (p=0.020) and 32.66 Gy from HSWBv1 (p&amp;lt;0.001). Among several other dosimetric quality improvements, there was a significant reduction in PTV_3000 V105% from 35.35% (HSWBv1) to 6.44% (HSWBv2) (p&amp;lt;0.001). On five additional validation cases, dosimetric improvements were also observed on TrueBeamTM. CONCLUSION In comparison to published data in addition to the HSWBv1 model, the HSWBv2 model achieved higher quality HA-WBRT treatment plans through further reductions in hippocampal dose while improving target coverage and dose conformity/homogeneity. HSWBv2 model is shared publicly.
Engineering 3D cell instructive microenvironments by rational assembly of artificial extracellular matrices and cell patterning (2011)

Engineered artificial microenvironments hold enormous potential as models to study developmental, physiological, pathological, and regenerative processes under highly defined conditions. Such platforms aim at bridging the gap between traditional in vitro 2D culture systems and animal models. By dissecting the biological complexity into an amenable number of parameters, systemic manipulation and study in controllable environments closely resembling the in vivo situation is possible. Novel strategies that address the evaluation of either ECM components, growth factors or cell-cell interactions on cellular behaviour are being developed. However, reliable methods that simultaneously recapitulate the natural instructive microenvironments in terms of cell and matrix composition, biological cues, heterogeneity and geometry are not yet available. Such spatially-defined microenvironments may be necessary to initiate and guide the formation of artificial tissues by morphogenetic processes. In this work, we introduce a flexible strategy that relies on the combination of artificial extracellular matrices with patterning techniques as well as a layer-by-layer approach to mimic rationally-designed instructive milieus. By a rational arrangement of cells and defined biochemical and biophysical extracellular cues, we report control of cell migration and generation of an artificial vascularized bone tissue-like construct.
A critical analysis of experimental spinal cord injury models (1985)

This critical review examines the several models which have been proposed to study mechanisms of acute spinal cord injury. From a physiologic point of view, each model offers particular advantages and is useful to address specific questions about the pathophysiology. From a biomechanics point of view, however, adequate simulation of clinically occurring spinal cord injuries requires control of impact parameters which are important to injury outcome, such as amount of compression and velocity of loading. A controlled contusion technique developed by the authors provides this control and results in clinically relevant experimental injury. Both transient and maintained compression are important in determining the neurologic outcome of injury. When combined with an improved understanding of vertebral failure kinematics, neurologic injury potential may be estimated from specific vertebral loading (and failure) parameters. Beyond the biomechanics of injury, physiology must be carefully considered in the experimental protocol. The effects of alternative anesthetics, respiratory parameters, adjunctive agents and laminectomy will be reviewed. Standardized protocol would facilitate communication and comparability between laboratories. Also, the severity and outcome of clinical injury may be affected by factors such as high blood alcohol and hemorrhagic shock. Experimental study of these factors requires particular attention to baseline physiologic parameters in the experimental setting. (Author/TRRL)
Pharmacokinetics, safety and tolerability of the novel, selective mineralocorticoid receptor antagonist finerenone – results from first‐in‐man and relative bioavailability studies (2015)

The safety, tolerability and pharmacokinetics of the selective nonsteroidal mineralocorticoid receptor antagonist finerenone were evaluated in healthy male volunteers in two randomized, single-centre studies. Study 1 was a first-in-man, single-blinded, placebo-controlled, parallel-group, dose-escalation study. Fasted participants (n = 45) received single oral doses of finerenone 1-40 mg polyethylene glycol (PEG) solution or placebo. Study 2 was a relative bioavailability study comparing a finerenone 10 mg immediate-release (IR) tablet with finerenone 10 mg PEG solution in the fasted state, investigating the effect of a high-fat/high-calorie meal on the pharmacokinetics of the IR tablet and assessing a further dose escalation to finerenone 80 mg (eight × finerenone 10 mg IR tablets), in an open-label, fourfold crossover design (n = 15). Finerenone was rapidly absorbed from PEG solution (median time to maximum plasma concentration [tmax ]: 0.500-1.00 h), exhibited dose-linear pharmacokinetics and was rapidly eliminated from plasma (geometric mean terminal half-life [t½ ]: 1.70-2.83 h). Finerenone IR tablets demonstrated similar pharmacokinetics (median tmax : 0.750-2.50 h; geometric mean t½ : 1.89-4.29 h) with, however, enhanced bioavailability versus PEG solution (least-squares mean tablet/solution ratio of 187% for area under the plasma-concentration curve [AUC] and maximum plasma concentration [Cmax ]). High-fat/high-calorie food affected the rate but not the extent of finerenone absorption. Finerenone was well tolerated and did not influence clinical laboratory parameters, blood pressure, heart rate, urinary electrolytes or neurohormones, including serum aldosterone and angiotensin II. In conclusion, finerenone has favourable pharmacokinetics and tolerability in healthy men, and is suitable for dosing independent of food intake.
The critical velocity in pipeline flow of slurries (1980)

Abstract In slurry transport, the critical velocity is defined as the minimum velocity demarcating flows in which the solids form a bed at the bottom of the pipe (bed load flows) from fully suspended flow. An analysis based on balancing the energy required to suspend the particles with that derived from dissipation of an appropriate fraction of the turbulent eddies is used to develop a correlation for prediction of the critical velocity. Comparison of the results with available experimental critical velocity data, relating to a rather wide variety of slurry systems, confirms that the present correlation does a superior job of prediction than all previously proposed critical velocity correlations.
Australian funnel-web spiders evolved human-lethal δ-hexatoxins for defense against vertebrate predators (2020)

Australian funnel-web spiders are infamous for causing human fatalities, which are induced by venom peptides known as δ-hexatoxins (δ-HXTXs). Humans and other primates did not feature in the prey or predator spectrum during evolution of these spiders, and consequently the primate lethality of δ-HXTXs remains enigmatic. Funnel-web envenomations are mostly inflicted by male spiders that wander from their burrow in search of females during the mating season, which suggests a role for δ-HXTXs in self-defense since male spiders rarely feed during this period. Although 35 species of Australian funnel-web spiders have been described, only nine δ-HXTXs from four species have been characterized, resulting in a lack of understanding of the ecological roles and molecular evolution of δ-HXTXs. Here, by profiling venom-gland transcriptomes of 10 funnel-web species, we report 22 δ-HXTXs. Phylogenetic and evolutionary assessments reveal a remarkable sequence conservation of δ-HXTXs despite their deep evolutionary origin within funnel-web spiders, consistent with a defensive role. We demonstrate that δ-HXTX-Ar1a, the lethal toxin from the Sydney funnel-web spider <i>Atrax robustus</i>, induces pain in mice by inhibiting inactivation of voltage-gated sodium (Na<sub>V</sub>) channels involved in nociceptive signaling. δ-HXTX-Ar1a also inhibited inactivation of cockroach Na<sub>V</sub> channels and was insecticidal to sheep blowflies. Considering their algogenic effects in mice, potent insecticidal effects, and high levels of sequence conservation, we propose that the δ-HXTXs were repurposed from an initial insecticidal predatory function to a role in defending against nonhuman vertebrate predators by male spiders, with their lethal effects on humans being an unfortunate evolutionary coincidence.
Negative effect of deep cochlear implant electrode insertion on speech perception. (2010)

This case study details the evaluation, explantation, and subsequent reimplantation of a cochlear implant (CI) recipient with an unusually deep electrode array insertion. Although the positive value of sufficiently deep insertion and the effect of insertion variability have been researched, there are few data available that illustrate the detrimental effects on speech recognition when deep insertion corrupts optimal use of the CI. This unique case report challenges the assumption that deeper insertion will result in improved speech understanding and demonstrates the importance of fully evaluating recipients' complaints and recognizing the impact of frequency-to-place mismatch.
The robustness of an admittance control law designed for force guided assembly to the disturbance of contact friction (2003)

The design of an admittance control law for reliable force-guided assembly is addressed. The overall objective is to design the manipulator's mechanical performance so that, at each possible bounded part misalignment, the contact force always leads to a motion that alleviates the misalignment. The implementation of such an approach using a single nominal velocity and a single admittance function is referred to as force-assembly. Previous work addressing force-assembly of a workpiece into a fixture has shown that when workpiece/fixture contact is frictionless there always exists an admittance control law that ensures the proper insertion of a workpiece into a deterministic future. The authors discuss the identification of the condition that must be satisfied for force-assembly with friction and the optimization of the admittance control law to obtain the maximum value of friction that satisfies the force-assembly conditions for a given workpiece-fixture combination.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hierarchic models of hearing for sound separation and reconstruction (2002)

In building a machine to detect and segregate individual components in sound mixtures, the best example to copy is the human auditory system. Several models of auditory organization implement various rules of psychoacoustic grouping. We propose in addition to model auditory inference as exhibited in the well-known 'phonemic restoration illusion' of Warren (1970). A hierarchy of abstracted features and source hypotheses similar to that of Nawab (1992) allows reconstruction of obliterated detail which can then be used to recreate an 'idealized' sound without corruption. A preliminary example of fitting a harmonic model to a noisy recording of a clarinet gives a very convincing resynthesis with the interference totally removed. However, there are many issues including the design of the representation and the control architecture still to be addressed in building a more general system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Scratch Lithography of 10 nm Silicon Structures (1995)

A new lithography method, scratch lithography, is proposed for fabrication of silicon nanostructures. When a poly(methylmethacrylate) (PMMA) layer coated on a Si substrate is scratched by a needle, some of the PMMA molecules adhere to the substrate and cannot be removed by rinsing in acetone. The individual PMMA molecules thus fixed to the surface can be used as etch masks for electron cyclotron resonance microwave plasma etching (ECR etching) with SF 6 at a low temperature (-130° C), which leads to formation of Si pillars of 10 nm diameter with a high aspect ratio (∼10). A 10-nm-wide line was also formed unintentionally, probably owing to the microroughness of the tip, suggesting that it may be possible to fabricate well-controlled nanostructures if the scratching tip is reduced to nanometer dimensions.
Spirocyclic Products via Carbene Intermediates from Thermolysis of 1,2-Dialkynylpyrrole and 1,2-Diethynylimidazole (2022)

Abstract The thermal rearrangements of 1,2-dialkynylimidazoles have been shown to lead to trapping products of cyclopenta[b]pyrazine carbene intermediates. Here we show that a similar rearrangement also occurs in the case of 1,2-diethynyl-1H-pyrrole, and that trapping the intermediate cyclopenta[b]pyridine carbene with solvent THF affords an ylide that undergoes a Stevens rearrangement to a spirocyclic product. An analogous rearrangement and trapping is observed for thermolysis of 1,2-dialkynylimidazoles in THF or 1,4-dioxane.
Data from Clonal Spreading of Tumor-Infiltrating T Cells Underlies the Robust Antitumor Immune Responses (2023)

&lt;div&gt;Abstract&lt;p&gt;The repertoire of tumor-infiltrating T cells is an emerging method for characterizing effective antitumor T-cell responses. Oligoclonal expansion of the tumor T-cell repertoire has been evaluated; however, their association with antitumor effects is unclear. We demonstrate here that the polyclonal fraction of the tumor-reactive T-cell repertoire, consisting of relatively minor clones, increased in tumor-bearing mice treated with monoclonal anti–programmed death-ligand 1 (PD-L1) or anti-CD4, which correlated with antitumor effects. Meanwhile, the size of the oligoclonal fraction consisting of major clones remained unchanged. Moreover, the polyclonal fraction was enriched in progenitor exhausted T cells, which are essential for a durable antitumor response, and was more dependent on CCR7&lt;sup&gt;+&lt;/sup&gt; migratory dendritic cells, which are responsible for priming tumor-reactive T cells in the tumor-draining lymph nodes. These results suggest that the expansion of diverse tumor-reactive clones (“clonal spreading”) represents characteristics of antitumor T-cell responses induced by anti-CD4 and anti–PD-L1 treatment.&lt;/p&gt;&lt;/div&gt;
Genetics of structural and functional brain changes in autism spectrum disorder (2020)

Autism spectrum disorder (ASD) is a neurological and developmental disorder characterized by social impairment and restricted interactive and communicative behaviors. It may occur as an isolated disorder or in the context of other neurological, psychiatric, developmental, and genetic disorders. Due to rapid developments in genomics and imaging technologies, imaging genetics studies of ASD have evolved in the last few years. Increased risk for ASD diagnosis is found to be related to many specific single-nucleotide polymorphisms, and the study of genetic mechanisms and noninvasive imaging has opened various approaches that can help diagnose ASD at the nascent level. Identifying risk genes related to structural and functional changes in the brain of ASD patients provide a better understanding of the disease's neuropsychiatry and can help identify targets for therapeutic intervention that could be useful for the clinical management of ASD patients.
Inhibition of Tumor Invasion by Genomic Down-regulation of Matriptase through Suppression of Activation of Receptor-bound Pro-urokinase (2004)

Urokinase-type plasminogen activator (uPA) degrades the extracellular matrix and plays critical roles in tumor invasion and metastasis. Matriptase, a membrane-bound serine protease, was shown to activate uPA in a uPA receptor-free, solution-based study. We now investigate whether matriptase affects activation of receptor-bound uPA and contributes to the invasiveness of HRA human ovarian cancer cells in vitro and tumor behavior in nude mice. Here we show the following. 1) uPA expression was effectively stimulated by TGF-beta1 in HRA cells. 2) Antisense (AS)-matriptase transfection achieved a marked inhibition of receptor-bound pro-uPA activation without altering expression of uPA and uPA receptor mRNA and proteins, irrespective of whether cells were stimulated with TGF-beta1. 3) Tumor cell receptor-bound pro-uPA could be efficiently cleaved by matriptase to generate enzymatically active two-chain uPA. Thus, matriptase can substitute for plasmin in the proteolytic activation of pro-uPA to enzymatically active uPA. 4) The AS-matriptase-treated cells had a decreased ability to invade an extracellular matrix layer, as compared with control cells. 5) When the AS-matriptase-treated cells were injected intraperitoneally into nude mice, the mice developed smaller tumors. Our data identify a novel role for matriptase for activation of receptor-bound uPA.
Exposure During Pancreatic Surgery. Do We Have to Examine the Falciform and Round Ligaments for Pancreatic Cancer Metastasis? (2015)

We concluded that routine pathological examination of the falciform and round ligaments is not justified if the surgeon elects to remove the structures for ease of exploration and retraction during surgery. This may lighten the workload and reduce costs in a busy pathology laboratory.
Preparation of nucleotide mimics with potent inhibitory activity against HIV reverse transcriptase (1991)

D. M. Coe, D. C. Orr, S. M. Roberts and R. Storer, J. Chem. Soc., Perkin Trans. 1, 1991, 3378 DOI: 10.1039/P19910003378
Heating mechanisms of LDMOS and LIGBT in ultrathin SOI (1997)

Temperature rises due to self-heating in silicon-on-insulator (SOI) power devices may lead to performance degradation and reliability problems. This letter investigates the mechanisms and spatial distribution of heat generation in linearly graded SOI LDMOS and LIGBT devices. While Joule heating dominates in LDMOS devices, hole collection at the p-well-drift region junction contributes strongly to the heating of LIGBT's. Also, the presence of both Joule and recombination heating makes the heating profile more uniform in LIGBT's. These effects combine to yield a temperature rise in LIGBT's that is more uniform and lower on average than that in LDMOS devices.