gebhart/patrepeval huggingface dataset:
Performance engineering and topological design of metro WDM optical networks using computer simulation (2002)

This paper demonstrates the use of computer simulation for topological design and performance engineering of transparent wavelength-division multiplexing metropolitan-area networks. Engineering of these networks involves the study of various transport-layer impairments such as amplifier noise, component ripple, chirp/dispersion, optical crosstalk, waveform distortion due to filter concatenation, fiber nonlinearities, and polarization effects. A computer simulation methodology composed of three main simulation steps is derived and implemented. This methodology obtains performance estimations by applying efficient wavelength-domain simulations on the entire network topology, followed by time-/frequency-domain simulations on selected paths of the network and finally Q-budgeting on an identified worst case path. The above technique provides an efficient tool for topological design and network performance engineering. Accurate simulation models are presented for each of the performance impairments, and the computer simulation methodology is used for the design and engineering of a number of actual metro network architectures.
RETRACTED: Inside the CVD “Black Box”: A Physics-Driven Exploration of Reactor Conditions during Graphene Growth (2023)

Though more than a decade has passed since the first report of the chemical vapor deposition (CVD) of graphene on metal substrates, the CVD reactor resembles something of a black-box. The process flow conditions, and, temperature and reactant distribution profiles are poorly understood which causes significant repeatability and reproducibility issues. This also affects studies on the growth mechanism of graphene and the synthesis of completely defect free products. To address these challenges, the open source computational fluid dynamics toolbox OpenFOAM is used for the first systematic exploration of reactor conditions for the synthesis of single crystal and single layer graphene (SLG) in a tube reactor that is typically used in the laboratory. It is found that the reactor flow conditions are in the turbulent regime, and, the temperatures of the 50-100 μm thick copper foils on which graphene is grown are not uniform but have large temperature gradients with a sensitivity to the system pressure, the total mass flow rate and the process gas composition that increases with decreasing foil thickness. Furthermore, both the foil and gas temperatures can be manipulated by modifying the mass flow rates of Ar and H2 in the process gas mix. Based on this new-found knowledge, a process window was identified where the amount of Ar gas in the reactor was optimized to mimic cold-wall like conditions inside the hot-wall reactor and that favored the synthesis of pristine SLG films (while hotter reactor conditions produced films with numerous unwanted adlayers).
OS2.2 Highly personalized peptide vaccination for patients with newly diagnosed glioblastoma: the GAPVAC trial (2018)

There is a need for treatment personalization as every cancer is molecularly unique. In addition glioblastoma (GB) are immunologically regarded as resistant, “cold” tumor with few targetable antigens available from mutations, thus demanding new personalized immunotherapies. So far outside Neuro-Oncology, T cells orchestrate impressive anti-tumor effects with checkpoint inhibitors, but also vaccines. The GAPVAC consortium established an immunotherapy, for which personalized selection of 2 peptide-based actively personalized vaccines (APVAC) per patient for treatment of newly diagnosed GB was based not only on whole-exome sequencing but also on human leukocyte antigen (HLA)-ligandome analyses providing insight into the actual presentation of relevant epitopes in the tumor. GAPVAC-101 (NCT02149225) enrolled 16 patients in a European phase I feasibility, safety and immunogenicity trial integrated into standard of care. For APVAC1, up to 7 peptides were selected from a trial specific warehouse based on individual biomarker data. Vaccination (i.d.) with GM-CSF and poly-ICLC in 15 patients started with the 1st adjuvant cycle of temozolomide (TMZ). For APVAC2, analyses revealed a median of 36 somatic, non-synonymous mutations in the patients’ tumors. From the 4th TMZ cycle, 11 patients received APVAC2 with usually 2 de novo antigens per patient selected according to mutation, actual or putative HLA presentation and immunogenicity. Overall 20 APVAC2 antigens incl. 14 mutated were vaccinated. Adverse events were largely reversible injection site reactions and two anaphylactic reactions and one increase in cerebral edema. Short, non-mutated APVAC1 antigens induced sustained CD8 responses with memory phenotype. Mutated APVAC2 antigens induced predominantly CD4 responses of favorable TH1 type. Median PFS and OS were 14.2 and 29 months from diagnosis, respectively, in patients that received ≥1 APVAC vaccination (N=15). Overall, GAPVAC displayed expected safety profiles and high biological activity indicating further development.
Diffraction phase microscopy (2006)

We developed diffraction phase microscopy as a new technique for quantitative phase imaging of biological structures. It combines common path interferometry with single shot phase imaging, which provides stability and speed
Cumin Prevents 17β-Estradiol-Associated Breast Cancer in ACI Rats (2021)

Breast cancer (BC) is a leading cause of cancer deaths in women in less developed countries and the second leading cause of cancer death in women in the U.S. In this study, we report the inhibition of E2-mediated mammary tumorigenesis by <i>Cuminum cyminum</i> (cumin) administered via the diet as cumin powder, as well as dried ethanolic extract. Groups of female ACI rats were given either an AIN-93M diet or a diet supplemented with cumin powder (5% and 7.5%, <i>w</i>/<i>w</i>) or dried ethanolic cumin extract (1%, <i>w</i>/<i>w</i>), and then challenged with subcutaneous E2 silastic implants (1.2 cm; 9 mg). The first appearance of a palpable mammary tumor was significantly delayed by both the cumin powder and extract. At the end of the study, the tumor incidence was 96% in the control group, whereas only 55% and 45% animals had palpable tumors in the cumin powder and extract groups, respectively. Significant reductions in tumor volume (660 ± 122 vs. 138 ± 49 and 75 ± 46 mm<sup>3</sup>) and tumor multiplicity (4.21 ± 0.43 vs. 1.16 ± 0.26 and 0.9 ± 0.29 tumors/animal) were also observed by the cumin powder and cumin extract groups, respectively. The cumin powder diet intervention dose- and time-dependently offset E2-related pituitary growth, and reduced the levels of circulating prolactin and the levels of PCNA in the mammary tissues. Mechanistically, the cumin powder diet resulted in a significant reversal of E2-associated modulation in ERα, CYP1A1 and CYP1B1. Further, the cumin powder diet reversed the expression levels of miRNAs (miR-182, miR-375, miR-127 and miR-206) that were highly modulated by E2 treatment. We analyzed the composition of the extract by GC/MS and established cymene and cuminaldehyde as major components, and further detected no signs of gross or systemic toxicity. Thus, cumin bioactives can significantly delay and prevent E2-mediated mammary tumorigenesis in a safe and effective manner, and warrant continued efforts to develop these clinically translatable spice bioactives as chemopreventives and therapeutics against BC.
Estimating a Survival Distribution with Current Status Data and High-Dimensional Covariates (2004)

We consider the inverse problem of estimating a survival distribution when the survival times are only observed to be in one of the intervals of a random bisection of the time axis. We are particularly interested in the case that high-dimensional and/or time-dependent covariates are available, and/or the survival events and censoring times are only conditionally independent given the covariate process. The method of estimation consists of regularizing the survival distribution by taking the primitive function or smoothing, estimating the regularized parameter by using estimating equations, and finally recovering an estimator for the parameter of interest.
Sources and transformations of anthropogenic nitrogen along an urban river–estuarine continuum (2016)

Abstract. Urbanization has altered the fate and transport of anthropogenic nitrogen (N) in rivers and estuaries globally. This study evaluates the capacity of an urbanizing river–estuarine continuum to transform N inputs from the world's largest advanced (e.g., phosphorus and biological N removal) wastewater treatment facility. Effluent samples and surface water were collected monthly along the Potomac River estuary from Washington D.C. to the Chesapeake Bay over a distance of 150 km. In conjunction with box model mass balances, nitrate stable isotopes and mixing models were used to trace the fate of urban wastewater nitrate. Nitrate concentrations and δ15N-NO3− values were higher down-estuary from the Blue Plains wastewater outfall in Washington D.C. (2.25 ± 0.62 mg L−1 and 25.7 ± 2.9 ‰, respectively) compared to upper-estuary concentrations (1.0 ± 0.2 mg L−1 and 9.3 ± 1.4 ‰, respectively). Nitrate concentration then decreased rapidly within 30 km down-estuary (to 0.8 ± 0.2 mg L−1), corresponding to an increase in organic nitrogen and dissolved organic carbon, suggesting biotic uptake and organic transformation. TN loads declined down-estuary (from an annual average of 48 000 ± 5000 kg day−1 at the sewage treatment plant outfall to 23 000 ± 13 000 kg day−1 at the estuary mouth), with the greatest percentage decrease during summer and fall. Annually, there was a 70 ± 31 % loss in wastewater NO3− along the estuary, and 28 ± 6 % of urban wastewater TN inputs were exported to the Chesapeake Bay, with the greatest contribution of wastewater TN loads during the spring. Our results suggest that biological transformations along the urban river–estuary continuum can significantly transform wastewater N inputs from major cities globally, and more work is necessary to evaluate the potential of organic nitrogen and carbon to contribute to eutrophication and hypoxia.
InAlGaN/GaN-HEMT device technologies for W-band high-power amplifier (2016)

We demonstrated an excellent output power (P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">out</inf> ) density performance using a novel InAlGaN/GaN-HEMT with an 80-nm gate for a W-band amplifier. To eliminate current collapse, a unique double-layer silicon nitride (SiN) passivation film with oxidation resistance was adopted. The developed discrete GaN-HEMT achieved a P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">out</inf> density of 3.0 W/mm at 96 GHz, and we fabricated W-band amplifier MMIC using the air-bridge wiring technology. The P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">out</inf> density of the MMIC reached 3.6 W/mm at 86 GHz. We proved the potential of the developed InAlGaN/GaN-HEMT experimentally using our unique device technology. With the aim of future applications, we developed a novel wiring-inter-layer technology. It consists of a cavity structure and a moisture-resistant dielectric film technology. We demonstrated excellent high-frequency performances and low current collapse originating in humidity-degradation using AlGaN/GaN-HEMT. This is also a valuable technology for InAlGaN/GaN-HEMT.
Overview of Low Plasticity Burnishing for Mitigation of Fatigue Damage Mechanisms (2005)

Surface enhancement technologies such as shot peening (SP), laser shock peening (LSP), and low plasticity burnishing (LPB) can provide substantial fatigue life improvement. However, to be effective, the compressive residual stresses that increase fatigue strength must be retained in service. LPB provides thermally stable compression and can be performed in conventional machine shop environments on CNC machine tools. LPB enables the extension of component service lives fatigue limited by various damage mechanisms including foreign object damage (FOD), corrosion fatigue, pitting, and fretting. The thermal and mechanical stability of the compressive layer are briefly reviewed. The LPB process, tooling, and control system are briefly described. Four representative applications are presented: thermal stability in IN718, improved damage tolerance in Ti-6-4 fan blades, mitigation of fretting fatigue damage in Ti-6-4, and improved corrosion fatigue in 17-4PH stainless steel.
Search for high-mass states with one lepton plus missing transverse momentum in proton–proton collisions at s=7 TeV with the ATLAS detector (2011)

The ATLAS detector is used to search for high-mass states, such as heavy charged gauge bosons (W′,W⁎), decaying to a charged lepton (electron or muon) and a neutrino. Results are presented based on the analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 36 pb−1. No excess beyond standard model expectations is observed. A W′ with sequential standard model couplings is excluded at 95% confidence level for masses below 1.49 TeV, and a W⁎ (charged chiral boson) for masses below 1.35 TeV.
TS-MULE: Local Interpretable Model-Agnostic Explanations for Time Series Forecast Models (2021)

Time series forecasting is a demanding task ranging from weather to failure forecasting with black-box models achieving state-of-the-art performances. However, understanding and debugging are not guaranteed. We propose TS-MULE, a local surrogate model explanation method specialized for time series extending the LIME approach. Our extended LIME works with various ways to segment and perturb the time series data. In our extension, we present six sampling segmentation approaches for time series to improve the quality of surrogate attributions and demonstrate their performances on three deep learning model architectures and three common multivariate time series datasets.
Endoscopic transesophageal vs. thoracoscopic removal of mediastinal lymph nodes: a prospective randomized trial in a long term animal survival model (2011)

ELR proved to be feasible in this limited sample size and complications were not observed more frequently in this group than in the TLR group.
Hexokinase Isozymes in Human Erythrocytes (1968)

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ChemInform Abstract: SYNTHESIS OF PIRETANIDE ANALOGS 1,3,4‐TRIAZOLES (1983)

Abstract Die Umsetzung des Aminobenzoesäureesters (I) mit Diformylhydrazin (II) liefert nach alkalischer Verseifung die Piretanid‐ Analoga (III).
Membrane-tethered mucin-like polypeptides sterically inhibit binding and slow fusion kinetics of influenza A virus (2020)

The mechanism(s) by which cell-tethered mucins modulate infection by influenza A viruses (IAVs) remain an open question. Mucins form both a protective barrier that can block virus binding and recruit IAVs to bind cells via the sialic acids of cell-tethered mucins. To elucidate the molecular role of mucins in flu pathogenesis, we constructed a synthetic glycocalyx to investigate membrane-tethered mucins in the context of IAV binding and fusion. We designed and synthesized lipid-tethered glycopolypeptide mimics of mucins and added them to lipid bilayers, allowing chemical control of length, glycosylation, and surface density of a model glycocalyx. We observed that the mucin mimics undergo a conformational change at high surface densities from a compact to an extended architecture. At high surface densities, asialo mucin mimics inhibited IAV binding to underlying glycolipid receptors, and this density correlated to the mucin mimic's conformational transition. Using a single virus fusion assay, we observed that while fusion of virions bound to vesicles coated with sialylated mucin mimics was possible, the kinetics of fusion was slowed in a mucin density-dependent manner. These data provide a molecular model for a protective mechanism by mucins in IAV infection, and therefore this synthetic glycocalyx provides a useful reductionist model for studying the complex interface of host-pathogen interactions.
GPR101 drives growth hormone hypersecretion and gigantism in mice via constitutive activation of G s and G q/11 (2021)

Growth hormone (GH) is a key modulator of growth and GH over‐secretion can lead to gigantism. One form is X‐linked acrogigantism (X‐LAG), in which infants develop GH secreting pituitary tumors over‐expressing the orphan G‐protein coupled receptor, GPR101. The role of GPR101 in GH secretion remains obscure. We studied GPR101 signaling pathways and their effects in HEK293 and rat pituitary GH3 cell lines, human tumors and in transgenic mice with elevated somatotrope Gpr101 expression driven by the rat Ghrhr promoter ( Ghrhr Gpr101 ). We report that Gpr101 causes elevated GH/prolactin secretion in transgenic Ghrhr Gpr101 mice. We also show that GPR101 promotes GH secretion through the activation of not only G s , but also G q/11 , in a PKA and PKC‐dependent manner, respectively. Interestingly, in stark contrast with other G s ‐coupled receptors, GPR101 activation did not lead to the proliferation of somatotrope cells. These signatures of GPR101 signaling, notably PKC activation, are also present in human X‐LAG pituitary tumors with high GPR101 expression. These results underline a role for GPR101 in the regulation of somatotrope axis function.
Dietary restriction slows age pigment accumulation in the retinal pigment epithelium. (1993)

Dietary restriction provides a relatively simple means by which RPE age pigment content can be modulated. This should prove useful in assessing the role of RPE lipofuscin accumulation in age-related retinal disorders. That the oat fiber diet fed ad libitum was almost as effective as restriction of total food intake in slowing RPE age pigment accumulation indicates that the effect of restricted caloric intake is not mediated by almost constant hunger.
Carbon Nanotubes: Photon‐Pair Generation with a 100 nm Thick Carbon Nanotube Film (Adv. Mater. 24/2017) (2017)

The performance of nonlinear optical devices is largely limited by the small nonlinear coefficient of traditional optical materials. In article number 1605978, Kim Fook Lee, Zhipei Sun, and co-workers report a nanoscale nonlinear optical device for efficient generation of photon pairs. They design an optical device based on a 100-nm-thick carbon nanotube film, which is 1000 times thinner than the current existing devices, achieved through careful control of the nanotube diameter to significantly enhance the optical nonlinearity.
Improved Blood Substitute (1998)

The authors have previously documented that appropriate chemical and pharmacologic modification of the hemoglobin molecule are required to attenuate certain pathophysiologic reactions of the reticuloendothelium. The current study further investigates the molecular responses of human coronary artery endothelial cells to a high concentration (0.4 mmol) of 1) unmodified bovine hemoglobin; and 2) an improved blood substitute that comprises hemoglobin cross-linked intramolecularly with o-adenosine triphosphate and intermolecularly with o-adenosine, and conjugated with reduced glutathione. In this study, the scavenging effect of hemoglobins toward nitric oxide (NO) was evaluated by the measurement of nitrite (NO2-) and nitrate (NO3-) formation. The pro-oxidant effect of hemoglobin on endothelial cells was examined by the measurement of intracellular reduced glutathione, and by monitoring the formation of lipid hydroperoxides and 8-iso prostaglandin F2alpha, a novel potent vasoconstrictor, which is produced by a noncyclooxygenase mechanism involving free radical catalyzed peroxidation of arachidonic acid. The inflammatory reactions of endothelial cells were evaluated by the expression of the adhesion molecule, intracellular adhesion molecule-1, and the activation of nuclear transcription factor, nuclear factor kappaB. In additional, endothelial cell responses were investigated by analysis of intracellular ionized calcium concentrations. Results indicate that unmodified hemoglobin in a concentration of 0.4 mmol/L can aggravate endothelial cell oxidative and inflammatory responses. This hemoglobin produced a significant (p < 0.01) depletion of reduced glutathione, acceleration of lipid peroxidation, and a greater influx of Ca2+. The formation of 8-iso prostaglandin F2alpha increased compared with the control cells (p < 0.01). Unmodified hemoglobin was found to be a potent scavenger of NO, great activator of nuclear factor kappaB, and a stimulator of intracellular adhesion molecule-1 expression. Contrarily, the improved blood substitute did not appear to induce oxidative stress nor to increase the intracellular Ca2+. The concentration of 8-iso prostaglandin F2alpha was similar to that in the control cells, whereas the formation of NO2-/NO3- was much lower (p < 0.05) than in the unmodified hemoglobin group. The effect of an improved blood substitute can be linked with the anti-inflammatory and cytoprotective properties of adenosine, which is used as a cross-linker and surface modifier, and the type of the chemical modification procedure that lowers hemoglobin pro-oxidant potential.
Silica nanocone array as a template for fabricating a plasmon induced hot electron photodetector (2019)

Plasmon induced hot electrons have attracted a great deal of interest as a novel route for photodetection and light-energy harvesting. Herein, we report a hot electron photodetector in which a large array of nanocones deposited sequentially with aluminum, titanium dioxide, and gold films can be integrated functionally with nanophotonics and microelectronics. The device exhibits a strong photoelectric response at around 620 nm with a responsivity of 180 μA/W under short-circuit conditions with a significant increase under 1 V reverse bias to 360 μA/W. The increase in responsivity and a red shift in the peak value with increasing bias voltage indicate that the bias causes an increase in the hot electron tunneling effect. Our approach will be advantageous for the implementation of the proposed architecture on a vast variety of integrated optoelectronic devices.
The Role of Anesthetic Induction Agents and Neuromuscular Blockade in the Endotracheal Intubation of Trauma Victims (1992)

Department of Anesthesiology and Critical Care Medicine, and Department of Surgery, Adult Trauma Service, The Johns Hopkins University School of Medicine, Baltimore, Maryland
Dendritic cell CNS recruitment correlates with disease severity in EAE via CCL2 chemotaxis at the blood–brain barrier through paracellular transmigration and ERK activation (2012)

CNS recruitment of DCs correlates with disease severity in EAE via CCL2 chemotaxis and paracellular transmigration across the BBB, which is facilitated by ERK activation. Overall, these comprehensive studies provide a state-of-the-art view of DCs within the CNS, elucidate their path across the BBB, and highlight potential mechanisms involved in CCL2-mediated DC trafficking.