gebhart/patrepeval huggingface dataset:
A thermoelectricity-lamp based integrated bake/chill system for photoresist processing (2005)

The design of an integrated bake/chill module for photoresist processing in microlithography is presented, with emphasis on the spatial and temporal temperature uniformity of the substrate. The system consists of multiple radiant heating zones for heating the substrate, coupled with an array of thermoelectric devices (TEDs) which provide real-time dynamic and spatial control of the substrate temperature. The TEDs also provide active cooling for chilling the substrate to a temperature suitable for subsequent processing steps. The use of lamp for radiative heating also provide fast ramp-up and ramp-down rates during thermal cycling operations. The feasibility of the proposed approach is demonstrate via simulations based on first principle heat transfer modeling. The distributed nature of the design also means that a simple decentralized control scheme can be used to achieve tight spatial and temporal temperature uniformity specifications.
The CI-FLOW Project: A System for Total Water Level Prediction from the Summit to the Sea (2021)

Kildow et al. (2009) reported that coastal states support 81% of the U.S. population and generate 83 percent [$11.4 trillion (U.S. dollars) in 2007] of U.S. gross domestic product. Population trends show that a majority of coastal communities have transitioned from a seasonal, predominantly weekend, tourist-based economy to a year-round, permanently based, business economy where industry expands along shorelines and the workforce commutes from inland locations. As a result of this transition, costs associated with damage to the civil infrastructure and disruptions to local and regional economies due to coastal flooding events are escalating, pushing requirements for a new generation of flood prediction technologies and hydrologic decision support tools.
NeRP: Neural Rearrangement Planning for Unknown Objects (2021)

Robots will be expected to manipulate a wide variety of objects in complex and arbitrary ways as they become more widely used in human environments. As such, the rearrangement of objects has been noted to be an important benchmark for AI capabilities in recent years. We propose NeRP (Neural Rearrangement Planning), a deep learning based approach for multi-step neural object rearrangement planning which works with never-before-seen objects, that is trained on simulation data, and generalizes to the real world. We compare NeRP to several naive and model-based baselines, demonstrating that our approach is measurably better and can efficiently arrange unseen objects in fewer steps and with less planning time. Finally, we demonstrate it on several challenging rearrangement problems in the real world.
Interactions between T Cells Responding to Concurrent Mycobacterial and Influenza Infections (2006)

CD4(+) T cells are central in mediating granuloma formation and limiting growth and dissemination of mycobacterial infections. To determine whether T cells responding to influenza infection can interact with T cells responding to Mycobacterium bovis bacille Calmette-Guérin (BCG) infection and disrupt granuloma formation, we infected mice containing two monoclonal T cell populations specific for the model Ags pigeon cytochrome c (PCC) and hen egg lysozyme (HEL). These mice were chronically infected with PCC epitope-tagged BCG (PCC-BCG) and acutely infected with HEL epitope-tagged influenza virus (HEL-flu). In these mice, PCC-BCG infection is much more abundant in the liver than the lung, whereas HEL-flu infection is localized to the lung. We observe that both T cells have access to both inflammatory sites, but that PCC-specific T cells dominate the PCC-BCG inflammatory site in the liver, whereas HEL-specific T cells dominate the HEL-flu inflammatory site in the lung. Influenza infection, in the absence of an influenza-specific T cell response, is able to increase the activation state and IFN-gamma secretion of PCC-BCG-specific T cells in the granuloma. Activation of HEL-specific T cells allows them to secrete IFN-gamma and contribute to protection in the granuloma. Ultimately, infection with influenza has little effect on bacterial load, and bacteria do not disseminate. In summary, these data illustrate complex interactions between T cell responses to infectious agents that can affect effector responses to pathogens.
Empowering authors to diagnose comprehension burden in textbooks (2012)

Good textbooks are organized in a systematically progressive fashion so that students acquire new knowledge and learn new concepts based on known items of information. We provide a diagnostic tool for quantitatively assessing the comprehension burden that a textbook imposes on the reader due to non-sequential presentation of concepts. We present a formal definition of comprehension burden and propose an algorithmic approach for computing it. We apply the tool to a corpus of high school textbooks from India and empirically examine its effectiveness in helping authors identify sections of textbooks that can benefit from reorganizing the material presented.
In Vitro Characterization of the Anti-Hepatitis B Virus Activity and Cross-Resistance Profile of 2′,3′-Dideoxy-3′-Fluoroguanosine (2006)

The fluorinated guanosine analog 2',3'-dideoxy-3'-fluoroguanosine (FLG) was shown to inhibit wild-type (wt) hepatitis B virus (HBV) replication in a human hepatoma cell line permanently expressing HBV. Experiments performed in the duck model of HBV infection also showed its in vivo antiviral activity. In this study, we investigated the mechanism of inhibition of FLG on HBV replication and its profile of antiviral activity against different HBV or duck hepatitis B virus (DHBV) drug-resistant mutants. We found that FLG-triphosphate inhibits weakly the priming of the reverse transcription compared to adefovir-diphosphate in a cell-free system assay allowing the expression of an enzymatically active DHBV reverse transcriptase. It inhibits more potently wt DHBV minus-strand DNA synthesis compared to lamivudine-triphosphate and shows a similar activity compared to adefovir-diphosphate. FLG-triphosphate was most likely a competitive inhibitor of dGTP incorporation and a DNA chain terminator. In Huh7 cells transiently transfected with different HBV constructs, FLG inhibited similarly the replication of wt, lamivudine-resistant, adefovir-resistant, and lamivudine-plus-adefovir-resistant HBV mutants. These results were consistent with those obtained in the DHBV polymerase assay using the same drug-resistant polymerase mutants. In conclusion, our data provide new insights in the mechanism of action of FLG-triphosphate on HBV replication and demonstrate its inhibitory activity on drug-resistant mutant reverse transcriptases in vitro. Furthermore, our results provide the rationale for further clinical evaluation of FLG in the treatment of drug-resistant virus infection and in the setting of combination therapy to prevent or delay drug resistance.
Secondary Structure of Uracil-DNA Glycosylase Inhibitor Protein (1995)

The Bacillus subtilis bacteriophage PBS2 uracil-DNA glycosylase inhibitor (Ugi) is an acidic protein of 84 amino acids that inactivates uracil-DNA glycosylase from diverse organisms (Wang, Z., and Mosbaugh, D. W. (1989) J. Biol. Chem. 264, 1163-1171). The secondary structure of Ugi has been determined by solution state multidimensional nuclear magnetic resonance. The protein adopts a single well defined structure consisting of five anti-parallel beta-strands and two alpha-helices. Six loop or turn regions were identified that contain approximately one half of the acidic amino acid residues and connect the beta-strands sequentially to one another. The secondary structure suggests which regions of Ugi may be involved in interactions with uracil-DNA glycosylase.
Atomic resolution strain analysis in highly textured FePt thin films (2016)

In this work, we present a detailed investigation of FePt-substrate interfaces and their influence towards the microstructural and magnetic configurations of the resulting metallic films. Discontinuous FePt films of roughly 15 nm thickness are deposited at 750 °C on MgO, MgAl2O4, SrTiO3, and (La,Sr)(Al,Ta)O3 single-crystalline substrates. All of these films mainly show out-of-plane textured FePt islands; however, fractions of L12 and in-plane oriented crystals are observed for the films on substrates with reduced lattice mismatch. Reduced easy axis coercivities and enhanced hard axis remanence values affirm this observation. Moreover, quantitative high-resolution transmission electron microscope analysis reveals that the reduced lattice mismatch results in a decreased density of dislocations, especially misfit dislocations, at the FePt-substrate interface. To further extend the research, carbon-doped FePt+32%C films are deposited on single-crystalline and sputtered MgO at 750 °C and 650 °C, respectively, to characterize the influence of a segregating media and reduced grain size. A comparison to the pure FePt sample reveals that the presence of seed layer grain boundaries leads to an increased fraction of in-plane oriented material, while the density of misfit dislocations solely depends on the degree of lattice mismatch.
Effects of Electrical Stimulation on Retinal Morphology as Seen with Optical Coherence Tomography (2020)

Retinal prostheses provide blind patients with the ability to detect motion and locate large objects. Future implants will require
 smaller electrodes to improve resolution, but increased charge density may result, creating a safety concern. We developed a
 novel in vivo method to study the effects of electrical stimulation in the retina using real time Optical Coherence Tomography
 (OCT) imaging combined with micropositioning a stimulating electrode. We observed that electrical stimulation settings with
 both pulse rates at and greater than 100 Hz as well as charge density 1.22 mC/cm2 and above resulted in retinal thickening
 within minutes of stimulation, that affected several retinal layers. We showed with statistical significance that the median
 difference between the retinal thickness before and after stimulation was different from zero. In summary, both high rate and
 high charge density were required to create retinal thickening. The stimulus levels at which thickening was noted in our study
 were significantly higher than the parameters currently used in humans.
Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments (2013)

Recent evidence suggests that corals can acclimatize or adapt to local stress factors through differential regulation of their gene expression. Profiling gene expression in corals from diverse environments can elucidate the physiological processes that may be responsible for maximizing coral fitness in their natural habitat and lead to a better understanding of the coral's capacity to survive the effects of global climate change. In an accompanying paper, we show that Porites astreoides from thermally different reef habitats exhibit distinct physiological responses when exposed to 6 weeks of chronic temperature stress in a common garden experiment. Here, we describe expression profiles obtained from the same corals for a panel of 9 previously reported and 10 novel candidate stress response genes identified in a pilot RNA-Seq experiment. The strongest expression change was observed in a novel candidate gene potentially involved in calcification, SLC26, a member of the solute carrier family 26 anion exchangers, which was down-regulated by 92-fold in bleached corals relative to controls. The most notable signature of divergence between coral populations was constitutive up-regulation of metabolic genes in corals from the warmer inshore location, including the gluconeogenesis enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase and the lipid beta-oxidation enzyme acyl-CoA dehydrogenase. Our observations highlight several molecular pathways that were not previously implicated in the coral stress response and suggest that host management of energy budgets might play an adaptive role in holobiont thermotolerance.
ChemInform Abstract: Resveratrol Dimers with an Oxabicyclo Ring in Vatica albiramis. (2011)

Abstract Albiraminol C (Ia), D (IIb) and vatalbinosides G (Ib), H (Ic), I (IIa), and J (III) are isolated from the stem of the title plant.
Impact of Fuel Quality Regulation and Speed Reductions on Shipping Emissions: Implications for Climate and Air Quality (2011)

Atmospheric emissions of gas and particulate matter from a large ocean-going container vessel were sampled as it slowed and switched from high-sulfur to low-sulfur fuel as it transited into regulated coastal waters of California. Reduction in emission factors (EFs) of sulfur dioxide (SO₂), particulate matter, particulate sulfate and cloud condensation nuclei were substantial (≥ 90%). EFs for particulate organic matter decreased by 70%. Black carbon (BC) EFs were reduced by 41%. When the measured emission reductions, brought about by compliance with the California fuel quality regulation and participation in the vessel speed reduction (VSR) program, are placed in a broader context, warming from reductions in the indirect effect of SO₄ would dominate any radiative changes due to the emissions changes. Within regulated waters absolute emission reductions exceed 88% for almost all measured gas and particle phase species. The analysis presented provides direct estimations of the emissions reductions that can be realized by California fuel quality regulation and VSR program, in addition to providing new information relevant to potential health and climate impact of reduced fuel sulfur content, fuel quality and vessel speed reductions.
Safety Performance Evaluation of Minnesota's Temporary Rigid Panel Sign Stand Systems (2007)

A wide variety of traffic controlling devices are used in work zones, some of which are not normally found on the roadside or in the traveled way outside of the work zones. These devices are used to enhance the safety of the work zones by controlling the traffic through these areas. Due to the placement of the traffic control devices, the devices themselves may be potentially hazardous to both workers and errant vehicles. The impact performance of many work-zone traffic control devices remains unknown, even though previous crash testing on work-zone traffic control devices has been conducted under the criteria of National Cooperative Highway Research Program (NCHRP) Report No. 350, Recommended Procedures for the Safety Performance Evaluation of Highway Features. The objective of the study was to evaluate the safety performance of various work-zone traffic control devices through dynamic bogie testing according to the Test Level 3 (TL-3) criteria set forth in the NCHRP Report No. 350. The impacts on the temporary rigid panel sign supports presented within resulted in acceptable safety performances. Following the analysis of these crash tests as well as the test results from other testing programs, it has been found that slight variations in design features of the work-zone traffic control devices can lead to very different performance results. Therefore, extreme care should be taken in applying crash test results from one work-zone traffic control device to similar work-zone traffic control devices with slight variations. The results of the crash tests were documented, and conclusions and recommendations pertaining to the safety performance of the work-zone traffic control devices were made.
Measurement of arterial viscoelastic properties using a foil-type pressure sensor and a photoplethysmography (2011)

This paper proposes a noninvasive method for estimating the dynamic characteristics of arterial walls using pulse waves measured in various parts of the body by a foil-type pressure sensor (FPS) and a photoplethysmography. The FPS not only has high sensitivity and flexibility but also features the ability to continuously measure the alternating-current component of pulse waves, and was employed to measure pulse waves based on the tonometry approach. Then a method of estimating changes in arterial viscoelastic indices was proposed based on the measured pulse waves and photoplethysmograms. First, in order to measure amplitude variation of the blood pressure wave shape accurately, we examined suitable mechanical forces externally applied to the FPS, and found that values of 5 - 25 [N] yielded the best performance. Next, in order to verify the time characteristics of the pulse waves, the brachial-ankle Pulse Wave Velocity (baPWV) was measured and found that baPWVs measured by the FPS and the noninvasive vascular screening device are quite similar. We then estimated the arterial viscoelastic indices of a radial artery and a dorsal pedis artery when mechanical pain stimuli were applied to the subjects. The results suggested the estimated indices could be used to quantitatively assess vascular response caused by sympathicotonia. We thus concluded the proposed method enabled noninvasive measurement of pulse waves and estimation of viscoelastic indices.
Future of multiple-e-beam direct-write systems (2012)

The crossover of high-speed digital electronics, MEMS, and cost reduction presents an exciting opportunity to extend optical lithography with multiple e-beam direct write systems. Massive parallelism overcomes the throughput limitation of e-beam direct write systems. Many innovative concepts on multiple e-beam imaging have been conceived and are being developed for various applications, such as maskwriting, prototyping, writing critical layers in high volume manufacturing (HVM), and writing all layers in HVM. MEB DW systems are capable to do all of the above. For maskwriting, the writing time can be saved by between a factor of 5 and 10 but it takes similar efforts to develop the maskwriting technology as direct wafer writing. There is insufficient demand for maskwriting and prototyping tools to warrant the development efforts. Writing critical layers in HVM makes economic sense for wafer production and makes economic sense to develop the imaging tool. However, using MEB DW for critical and non-critical layers, especially for 450-mm wafers, presents a unique opportunity to save lithography cost for the 450-mm wafer technology. This is the most desirable application for MEB DW. Once this application is established, all other applications easily follow.
Helicobacter pylori binding to new glycans based on N-acetyllactosamine (2008)

Previously we reported binding of Helicobacter pylori to various nonacid and sialylated neolacto carbohydrate structures using a wide range of natural and chemically modified sequences. A novel nonsialylated neolacto-based binding epitope, GlcNAc beta 3Gal beta 4GlcNAc, and analogous structures carrying terminal GalNAc beta 3, GalNAc alpha 3, or Gal alpha 3 showed the binding activity (Miller-Podraza H, Lanne B, Angström J, Teneberg S, Abul-Milh M, Jovall P-A, Karlsson H, Karlsson K-A. 2005. Novel binding epitope for Helicobacter pylori found in neolacto carbohydrate chains. J Biol Chem. 280:19695-19703). The present work reports two other H. pylori-binding nonsialylated neolacto-based structures, GlcA beta 3Gal beta 4GlcNAc beta 3-R and Glc beta 3Gal beta 4GlcNAc beta 3-R, and two amide derivatives (N-methyl and N-ethyl) of GlcA beta 3Gal beta 4GlcNAc beta 3-R which were bound by H. pylori. The latter structures turned out to be more effective as H. pylori binders than the parent saccharide. New reducing-end variants of the neolacto epitope including species containing N-acetyllactosamine linked beta 6 to GlcNAc or Gal with similarity to branched polylactosamines and mucins were prepared and tested. The results extend our previous findings on binding specificities of H. pylori and show that this pathogen is able to interact with an array of N-acetyllactosamine/neolacto structures, which may be of importance for the in vivo interaction of the bacterium with human cells. The information gained in this work may also be of value for rational design of anti-H. pylori drugs.
Blocking VEGF as a potential approach to improve cartilage healing after osteoarthritis. (2009)

angiogenesis. Therefore, in the current study, we used a gain- and loss-of-function approach based on tissue engineering techniques to assess the role of VEGF in MDSCmediated cartilage repair.
Dendritic cells (DC) promote natural killer (NK) cell functions: dynamics of the human DC/NK cell cross talk. (2002)

Dendritic cells (DC) were originally found critical in the setting of cognate immune responses. We first demonstrated that DC can also induce mouse NK cell activation and NK cell dependent-antitumor effects in mice. Here we analyzed the dynamics between DC and NK cells in human in vitro model systems. In the absence of LPS, DC do not trigger resting NK cells. Conversely, in the presence of LPS, resting bulk NK cells interacting with DC acquire CD25 and CD69 surface expression, produce high levels of IFN-gamma and lyse DAUDI cells. On activated IL-2 dependent NK cell lines, regardless of their differentiation stage, DC maintain or enhance NK cell proliferation and effector functions in the absence of exogenous cytokines. While IL-12, IL-15 and IL-18 are not critical, a direct cell-to-cell contact is mandatory for NK activation by DC and required for optimal proliferation. These data imply that DC also modulate human NK cell innate effector functions.
CCR Translation for This Article from CTLA-4 Blockade with Ipilimumab: Long-term Follow-up of 177 Patients with Metastatic Melanoma (2023)

CCR Translation for This Article from CTLA-4 Blockade with Ipilimumab: Long-term Follow-up of 177 Patients with Metastatic Melanoma
Tables of Glycosidase Inhibitors with Nitrogen in the Sugar Ring and Their Inhibitory Activities: Section 3.2.7–3.2.10 (1998)

This appendix contains sections titled: 3.2.7. 1-Deoxymannojirimycin and Analogs 3.2.7.1 N-Modified 3.2.7.2 O-Glycosylated or Ether 3.2.7.3 Other Modifications 3.2.8 talo-, rhamno-, D-gulo-Configurations 3.2.9 Isofagomine and Analogs 3.2.10 Siastatins and Analogs
Low-Complexity Pupil Tracking for Sunglasses-Wearing Faces for Glasses-Free 3D HUDs (2021)

This study proposes a pupil-tracking method applicable to drivers both with and without sunglasses on, which has greater compatibility with augmented reality (AR) three-dimensional (3D) head-up displays (HUDs). Performing real-time pupil localization and tracking is complicated by drivers wearing facial accessories such as masks, caps, or sunglasses. The proposed method fulfills two key requirements: low complexity and algorithm performance. Our system assesses both bare and sunglasses-wearing faces by first classifying images according to these modes and then assigning the appropriate eye tracker. For bare faces with unobstructed eyes, we applied our previous regression-algorithm-based method that uses scale-invariant feature transform features. For eyes occluded by sunglasses, we propose an eye position estimation method: our eye tracker uses nonoccluded face area tracking and a supervised regression-based pupil position estimation method to locate pupil centers. Experiments showed that the proposed method achieved high accuracy and speed, with a precision error of &lt;10 mm in &lt;5 ms for bare and sunglasses-wearing faces for both a 2.5 GHz CPU and a commercial 2.0 GHz CPU vehicle-embedded system. Coupled with its performance, the low CPU consumption (10%) demonstrated by the proposed algorithm highlights its promise for implementation in AR 3D HUD systems.