gebhart/patrepeval huggingface dataset:
Effect of intense x-ray free-electron laser transient gratings on the magnetic domain structure of Tm:YIG (2023)

In ferromagnets, domain patterns can be controlled globally using magnetic fields or spin-polarized currents. In contrast, the local control of the magnetization on the nanometer length scale remains challenging. Here, we demonstrate how magnetic domain patterns in a Tm-doped yttrium iron garnet (Tm:YIG) thin film with perpendicular magnetic anisotropy can be permanently and locally imprinted by high intensity photon pulses of a hard x-ray transient grating (XTG). Micromagnetic simulations provide a qualitative understanding of the observed changes in the orientation of magnetic domains in Tm:YIG and XTG-induced changes. The presented results offer a route for the local manipulation of the magnetic state using hard XTG.
Data from Epigenetic Inactivation of Galanin Receptor 1 in Head and Neck Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; One copy of the galanin receptor 1 (&lt;i&gt;GALR1&lt;/i&gt;) locus on 18q is often deleted and expression is absent in some head and neck squamous cell carcinoma (HNSCC) cell lines. To determine if loss of heterozygosity and hypermethylation might silence the &lt;i&gt;GALR1&lt;/i&gt; gene, promoter methylation status and gene expression were assessed in a large panel of HNSCC cell lines and tumors.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Promoter methylation of &lt;i&gt;GALR1&lt;/i&gt; in 72 cell lines and 100 primary tumor samples was analyzed using methylation-specific PCR. GALR1 expression and methylation status were analyzed further by real-time PCR and bisulfite sequencing analysis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The &lt;i&gt;GALR1&lt;/i&gt; promoter was fully or partially methylated in 38 of 72 (52.7%) HNSCC cell lines but not in the majority 18 of 20 (90.0%) of nonmalignant lines. &lt;i&gt;GALR1&lt;/i&gt; methylation was also found in 38 of 100 (38%) primary tumor specimens. Methylation correlated with decreased &lt;i&gt;GALR1&lt;/i&gt; expression. In tumors, methylation was significantly correlated with increased tumor size (&lt;i&gt;P&lt;/i&gt; = 0.0036), lymph node status (&lt;i&gt;P&lt;/i&gt; = 0.0414), tumor stage (&lt;i&gt;P&lt;/i&gt; = 0.0037), &lt;i&gt;cyclin D1&lt;/i&gt; expression (&lt;i&gt;P&lt;/i&gt; = 0.0420), and &lt;i&gt;p16&lt;/i&gt; methylation (&lt;i&gt;P&lt;/i&gt; = 0.0494) and survival (&lt;i&gt;P&lt;/i&gt; = 0.045). Bisulfite sequencing of 36 CpG sites upstream of the transcription start site revealed that CpG methylation within transcription factor binding sites correlated with complete suppression of &lt;i&gt;GALR1&lt;/i&gt; mRNA. Treatment with trichostatin A and 5-azacytidine restored &lt;i&gt;GALR1&lt;/i&gt; expression. In UM-SCC-23 cells that have total silencing of &lt;i&gt;GALR1&lt;/i&gt;, exogenous &lt;i&gt;GALR1&lt;/i&gt; expression and stimulation with galanin suppressed cell proliferation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Frequent promoter hypermethylation, gene silencing, association with prognosis, and growth suppression after reexpression support the hypothesis that &lt;i&gt;GALR1&lt;/i&gt; is a tumor suppressor gene in HNSCC.&lt;/p&gt;&lt;/div&gt;
Cognitive support during high-consequence episodes of care in cardiovascular surgery (2017)

Despite significant efforts to reduce preventable adverse events in medical processes, such events continue to occur at unacceptable rates. This paper describes a computer science approach that uses formal process modeling to provide situationally aware monitoring and management support to medical professionals performing complex processes. These process models represent both normative and non-normative situations, and are validated by rigorous automated techniques such as model checking and fault tree analysis, in addition to careful review by experts. Context-aware Smart Checklists are then generated from the models, providing cognitive support during high-consequence surgical episodes. The approach is illustrated with a case study in cardiovascular surgery.
Combination of artesunate and WNT974 induces KRAS protein degradation by upregulating E3 ligase ANACP2 and β-TrCP in the ubiquitin–proteasome pathway (2022)

Our data clearly show that the combination treatment significantly enhances KRAS protein degradation via the ubiquitination ubiquitin-proteasome pathway, which is also demonstrated in xenograft mouse model. The study provides strong scientific evidence for the development of the combination of WNT974 and ART as KRAS-targeting therapeutics for CRC treatment. Video Abstract.
Complete genome sequence of Cohnella sp. HS21 isolated from Korean fir ( Abies koreana ) rhizospheric soil (2019)

The genus Cohnella, which belongs to the family Paenibacillaceae, inhabits a wide range of environmental niches. Here, we report the complete genome sequence of Cohnella sp. HS21, which was isolated from the rhizospheric soil of Korean fir (Abies koreana) on the top of Halla Mountain in the Republic of Korea. Strain HS21 features a 7,059,027 bp circular chromosome with 44.8% GC-content. Its genome contains 5,939 protein-coding genes, 78 transfer RNA (tRNA) genes, 27 ribosomal RNA (rRNA) genes, 4 noncoding RNA genes (ncRNA), and 90 pseudogenes. The bacterium contains antibiotic-related gene clusters and genes encoding plant cell wall-degrading enzymes.
Discovery of T Cell Receptor β Motifs Specific to HLA–B27–Positive Ankylosing Spondylitis by Deep Repertoire Sequence Analysis (2016)

We identified TCRβ motifs that are enriched in B27-positive AS patients as compared to B27-positive healthy controls. This suggests that a common antigen, presented by HLA-B27 and detected by CD8+ T cells, may be associated with AS disease pathogenesis.
Metrology target design simulations for accurate and robust scatterometry overlay measurements (2016)

Overlay metrology target design is an essential step prior to performing overlay measurements. This step is done through the optimization of target parameters for a given process stack. A simulation tool is therefore used to improve measurement performances. This work shows how our Metrology Target Design (MTD) simulator helps significantly in the target design process. We show the role of film and Optical CD measurements in improving significantly the fidelity of the simulations. We demonstrate that for various target design parameters we are capable of predicting measured performance metrics by simulations and correctly rank various designs performances.
Down-regulation of Chondrocyte Aggrecan and Type-II Collagen Gene Expression Correlates with Increases in Static Compression Magnitude and Duration (2000)

The goal of this study was to examine the simultaneous effects of mechanical compression of chondrocytes on mRNA expression and macromolecular synthesis of aggrecan and type-II collagen. Bovine cartilage explants were exposed to different magnitudes and durations of applied mechanical compression, and levels of aggrecan and type-IIa collagen mRNA normalized to glyceraldehyde-3-phosphate dehydrogenase were measured and quantified by Northern blot analysis. Synthesis of aggrecan and type-II collagen protein was measured by radiolabel incorporation of [35S]sulfate and [3H]proline into macromolecules. The results showed a dose-dependent decrease in mRNA levels for aggrecan and type-II collagen, with increasing compression relative to physiological cut thickness applied for 24 hours. Radiolabel incorporation into glycosaminoglycans and collagen also decreased with increasing compression in a dose-related manner similar to the changes seen in mRNA expression. The modulation of aggrecan and type-II collagen mRNA and protein synthesis were dependent on the duration of the compression. Aggrecan and type-II collagen mRNA expression increased during the initial 0.5 hours of static compression; however, 4-24 hours after compression was applied total mRNA levels had significantly decreased. The synthesis of aggrecan and collagen protein decreased more rapidly than did mRNA levels after the application of a step compression. Together, these results suggest that mechanical compression rapidly alters chondrocyte aggrecan and type-II collagen gene expression on application of load. However, our results indicate that the observed decreases in biosynthesis may not be related solely to changes in mRNA expression. The mechanisms by which mechanical forces affect different segments of the biosynthetic pathways remain to be determined.
T Cell Immunity in Acute HIV‐1 Infection (2010)

Exceedingly high viral loads and rapid loss of CD4(+) T cells in all tissue compartments are a hallmark of acute human immunodeficiency virus type 1 (HIV-1) infection, which is often accompanied by clinical symptoms such as fever, maculopapular rash, and/or lymphadenopathy. The resolution of the clinical symptoms and the subsequent decrease in plasma viremia are associated with the emergence of HIV-1-specific CD4(+) and CD8(+) T cell responses. The remarkable early inhibition of viremia by CD8(+) T cells appears to be precipitated by only a limited number of specific CD8(+) T cell responses, and the plasma viremia is reduced to a "set point" level. Over time, the breadth and magnitude of CD8(+) T cell responses increase, but without a change in the control of viral replication or further reduction in the viral set point. Moreover, the early viral set point, consequent on the first CD8(+) T cell responses, is highly predictive of the later course of disease progression. Thus, HIV-1-specific CD8(+) T cell responses in acute HIV-1 infection appear uniquely able to efficiently suppress viral replication, whereas CD8(+) T cell responses generated in the chronic phase of infection appear often impaired.
Future plans for CMB anisotropy measurements with the MAXIMA array (1997)

The Millimeter-Wave Anisotropy eXperiment Array (MAXIMA) experiment is an evolution of the degree-scale CMB anisotropy experiment MAX. MAXIMA is also based on a balloon-borne telescope and Adiabatic Demagnetization Refrigerator (ADR) cooled bolometers operated at 100 mK. The new experiment is designed to dramatically increase the amount of CMB anisotropy power spectrum information gathered compared to MAX. There are three main components to this improvement: (1) A large increase in sky coverage per flight is made possible by a large increase in the instrument sensitivity and an efficient observation strategy. (2) High resolution in l-space and sensitivity to high values of l is achieved by the total power mode observation strategy and small (11' FWHM) beams. (3) Robust checks for instrumental systematics and foregrounds are made by repeated measurements of the same area of sky on several time scales and wide frequency coverage.
Deep Sequential Models for Task Satisfaction Prediction (2017)

Detecting and understanding implicit signals of user satisfaction are essential for experimentation aimed at predicting searcher satisfaction. As retrieval systems have advanced, search tasks have steadily emerged as accurate units not only to capture searcher's goals but also in understanding how well a system is able to help the user achieve that goal. However, a major portion of existing work on modeling searcher satisfaction has focused on query level satisfaction. The few existing approaches for task satisfaction prediction have narrowly focused on simple tasks aimed at solving atomic information needs.
Optical fiber atomic force microscope with photonic crystal force sensor (2015)

An atomic force microscope (AFM) integrated directly on the facet of a standard single-mode optical fiber is designed, fabricated, and tested. High resolution force sensing is achieved with a Fabry-Perot interferometer made of two photonic crystal (PC) mirrors separated by silicon springs. The device is fabricated with standard MEMS techniques and assembled on the facet of a single mode optical fiber by focus ion beam (FIB) welding and OmniProbe manipulation. We demonstrate that topographic and tip-sample interaction force information can be extracted from its reflected light. The force curve measurement has a resolution of 10pN/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.5</sup> in a drastically smaller footprint than traditional AFMs, which can enable in-vivo AFM imaging.
Étude en laboratoire de l'adhérence béton de resurfaçage - dalle de chaussée (1992)

This paper presents a laboratory study on the bonding of a concrete overlay to an old slab. The main variables of the study were the bonding agents and the initial slab temperature when the overlay was placed. A flexure test setup, based on the theory of beams of elastic foundation, was developed. The results obtained were compared with those of the slant–shear test. Key words: bonding agent, debonding, elastic foundation, interface, beam.
TH-C-17A-05: Cherenkov Excited Phosphorescence Oxygen (CEPhOx) Imaging During Multi-Beam Radiation Therapy (2014)

Purpose: Cherenkov radiation is created during external beam radiation therapy that can excite phosphorescence in tissue from oxygen-sensitive, bio-compatible probes. Utilizing the known spatial information of the treatment plan with directed multiple beam angles, Cherenkov Excited Phosphorescence Oxygen (CEPhOx) imaging was realized from the reconstructions of Cherenkov excited phosphorescence lifetime. Methods: Platinum(II)-G4 (PtG4) was used as the oxygen-sensitive phosphorescent probe and added to a oxygenated cylindrical liquid phantom with a oxygenated/deoxygenated cylindrical anomaly. Cherenkov excited phosphorescence was imaged using a time-gated ICCD camera temporallysynchronized to the LINAC pulse output. Lifetime reconstruction was carried out in NIRFAST software. Multiple angles of the incident radiation beam was combined with the location of the prescribed treatment volume (PTV) to improve the tomographic recovery as a function of location. The tissue partial pressure of oxygen (pO2) in the background and PTV was calculated based on the recovered lifetime distribution and Stern-Volmer equation. Additionally a simulation study was performed to examine the accuracy of this technique in the setting of a human brain tumor. Results: Region-based pO2 values in the oxygenated background and oxygenated/deoxygenated PTV were correctly recovered, with the deoxygenated anomaly (15.4 mmHg) easily distinguished from the oxygenated background (143 mmHg). The data acquisition time could be achieved within the normal irradiation time for a human fractionated plan. The simulations indicated that CEPhOx would be a sufficient to sample tumor pO2 sensing from tumors which are larger than 2cm in diameter or within 23mm depth from the surface. Conclusion: CEPhOx could be a novel imaging tool for pO2 assessment during external radiation beam therapy. It is minimally invasive and should work within the established treatment plan of radiation therapy with multiple beams in situations where tumor pO2 measurement is a pertinent radiotherapy efficiency and dosimetric need.
Mutual Valorization of 5-Hydroxymethylfurfural and Glycerol into Valuable Diol Monomers with Solid Acid Catalysts (2018)

Biomass platform molecules such as glycerol and 5-hydroxymethylfurfural have been valorized into diol monomers by acetalization reaction in the presence of tridirectional large pore zeolites (HY and Beta), a laminar zeolite (ITQ-2) and a mesoporous aluminosilicate (MCM-41), and a conventional homogeneous acid catalyst (p-toluenesulfonic acid). The influence of the solvent polarity, pore structure, hydrophobic character, and acidity of the catalyst on the activity and selectivity to 5-hydroxymethylfurfural (HMF) glyceryl acetals has been studied. Results showed that, while the homogeneous catalyst mainly promotes polymerization reactions, tridirectional zeolites are more active catalysts but less selective and deactivate more rapidly than mesoporous MCM-41 and delaminated two-dimensional zeolites. ITQ-2 and MCM-41 catalysts with smaller confinement effects, easy diffusion, and adequate surface polarity provide high yield (98%) and selectivity (100%) to the target compound. These catalysts are stable and allow regeneration and reuse.
Longitudinal exposure of human T lymphocytes to weak oxidative stress suppresses transmembrane and nuclear signal transduction. (1994)

Products of polyamine oxidase activity, at micromolar levels and during a period of 2 to 3 days, down-regulate IL-2 mRNA levels and activity in human lymphocytes. We studied whether this suppression was associated with signal transduction abnormalities. We found that polyamine oxidase activity suppresses both anti-CD3-induced IL-2 production and protein tyrosine phosphorylation. Polyamine oxidase activity also caused a reduction in intracellular calcium mobilization after mitogenic stimulation. The most distal step of CD3-mediated signal transduction is dependent upon transcription factors that regulate a set of genes, including IL-2. We found that polyamine oxidase-treated cells exhibited very low DNA binding activity of two such factors: NFAT and NF-kappa B. On the other hand, AP-1 DNA binding activity was enhanced in polyamine oxidase-treated cells, suggesting a possible role for AP-1 in the human lymphocyte stress response. In accordance with the oxidation dependence of this suppressive mechanism, N-acetylcysteine (NAC; an antioxidant) significantly reversed the polyamine oxidase effects on lymphokine production and signal transduction. These results suggest that NAC contributes, under oxidizing conditions, to the preservation of immune function. In summary, our data suggest that chronic low-level oxidative stress, via suppression of mitogen-induced transmembrane signaling (protein-tyrosine phosphorylation and calcium mobilization), causes a decrease in the DNA binding activity of transcription factors that regulate the IL-2 gene. This results in decreased IL-2 production.
Thermoelectric properties of epitaxial ScN films deposited by reactive magnetron sputtering onto MgO(001) substrates (2013)

Epitaxial ScN(001) thin films were grown on MgO(001) substrates by dc reactive magnetron sputtering. The deposition was performed in an Ar/N2 atmosphere at 2 × 10−3 Torr at a substrate temperature of 850 °C in a high vacuum chamber with a base pressure of 10−8 Torr. In spite of oxygen contamination of 1.6 ± 1 at. %, the electrical resistivity, electron mobility, and carrier concentration obtained from a typical film grown under these conditions by room temperature Hall measurements are 0.22 mΩ cm, 106 cm2 V−1 s−1, and 2.5 × 1020 cm−3, respectively. These films exhibit remarkable thermoelectric power factors of 3.3–3.5 × 10−3 W/mK2 in the temperature range of 600 K to 840 K. The cross-plane thermal conductivity is 8.3 W/mK at 800 K yielding an estimated ZT of 0.3. Theoretical modeling of the thermoelectric properties of ScN calculated using a mean-free-path of 23 nm at 300 K is in very good agreement with the experiment. These results also demonstrate that further optimization of the power factor of ScN is possible. First-principles density functional theory combined with the site occupancy disorder technique was used to investigate the effect of oxygen contamination on the electronic structure and thermoelectric properties of ScN. The computational results suggest that oxygen atoms in ScN mix uniformly on the N site forming a homogeneous solid solution alloy. Behaving as an n-type donor, oxygen causes a shift of the Fermi level in ScN into the conduction band without altering the band structure and the density of states.
Low-Power Frequency-Locked Loop Circuit with Short Settling Time (2022)

A phase-locked loop (PLL) is an important and commonly used electronic circuit in various electronic systems. Its main drawback is the use of an RC low-pass filter which takes up the majority of the PLL area on the chip. The RC low-pass filter is necessary to ensure the PLL stability. To mitigate this issue, a frequency-locked loop (FLL) is used because the stability of an FLL system depends on the Miller capacitance inside of the operational amplifier, which drastically reduces the capacitor size and thus the chip area. This paper presents the design of a fully integrated FLL based on a frequency-to-voltage converter (FVC). FVC is optimised so that it stabilises in just three clock cycles, which reduces the settling time of the entire FLL circuit. The voltage-controlled oscillator (VCO) is optimised for low power in all corners and for a wide input signal range. The circuit is implemented in a 180-nm CMOS process. Simulations show that the FLL circuit is functional in all voltage, temperature and technology corners. It has a short settling time while using a small amount of power and chip area compared to the conventional PLL designs.
Semi-automated extraction of research topics and trends from NCI funding in radiological sciences from 2000-2020 (2023)

Investigators, funders, and the public desire knowledge on topics and trends in publicly funded research but current efforts in manual categorization are limited in scale and understanding. We developed a semi-automated approach to extract and name research topics, and applied this to \$1.9B of NCI funding over 21 years in the radiological sciences to determine micro- and macro-scale research topics and funding trends. Our method relies on sequential clustering of existing biomedical-based word embeddings, naming using subject matter experts, and visualization to discover trends at a macroscopic scale above individual topics. We present results using 15 and 60 cluster topics, where we found that 2D projection of grant embeddings reveals two dominant axes: physics-biology and therapeutic-diagnostic. For our dataset, we found that funding for therapeutics- and physics-based research have outpaced diagnostics- and biology-based research, respectively. We hope these results may (1) give insight to funders on the appropriateness of their funding allocation, (2) assist investigators in contextualizing their work and explore neighboring research domains, and (3) allow the public to review where their tax dollars are being allocated.
The Adrenal Life Cycle: The Fetal and Adult Cortex and the Remaining Questions (2006)

Article The Adrenal Life Cycle: The Fetal and Adult Cortex and the Remaining Questions was published on November 1, 2006 in the journal Journal of Pediatric Endocrinology and Metabolism (volume 19, issue 11).
Proteus: Control and management system (2002)

The Proteus is a highly parallel MIMD, multiple instruction, multiple-data machine, optimized for large granularity tasks. The system is designed to use 256 to 1024 RISC processors. Computer vision algorithms consist of sub-algorithms, which can be executed in parallel. Advanced software system for partitioning, scheduling, development, and execution of tasks can utilize this fact in a data flow programming paradigm to increase throughput. The authors describe how these modules interact with each other such that permit the efficient control of large grained parallelism without having to handle the general concurrency problem.