gebhart/patrepeval huggingface dataset:
Monitoring the Chemical Assembly of a Transmembrane Bradykinin Receptor Fragment: Correlation Between Resin Solvation, Peptide Chain Mobility, and Rate of Coupling (2002)

A combined resin solvation-peptide chain motion and kinetics of coupling reaction approach was applied to monitor details of the synthesis of TM-34, a 34-residue transmembrane segment of the bradykinin receptor. The dynamics of resin-bound peptide fragments attached to a stable free radical amino acid were examined by EPR spectroscopy. In agreement with an abrupt decrease (from 83 to 43%) in peptide purity occurring in the 12−16 region when DMF was used, a much more strongly immobilized chain population was detected, especially at the 12-mer stage. Conversely, faster couplings and improved synthesis were observed in 20% DMSO/NMP, probably due to the higher chain mobility in this mixed solvent. In addition, findings relating to solvation of peptide resins seemed to corroborate the previously advanced proposition that the 1:1 sum of electron acceptor and electron donor properties of a solvent can be considered to be an alternative and more appropriate parameter for its polarity. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
ChemInform Abstract: How Does Tyrosinase Work? Recent Insights from Model Chemistry and Structural Biology (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Wear and fatigue behavior of nano‐structured dental resin composites (2006)

Theoretically, nano-structured dental resin composites are purported to have increased wear and fatigue resistance compared with microfill composites and may favor the achievement of restoratives with better long-term performance. This study sought to assess the behavior of nano-structured composites resulting from either abrasion and fatigue loading. Ten specimens (12 x 5 x 2.5 mm) were prepared from each of five composites: Ceram-X mono, Filtek Supreme, Grandio, Premise, and Heliomolar (serving as the microfill control). A surface profile was recorded using a three-dimensional profiling system, and the specimens were subjected to 10(5) cycles of three-body abrasion in the new OHSU oral wear simulator. A second profile was generated and the before and after profiles were fit and analyzed. The volume loss and maximum depth of the wear facet on each specimen were calculated. Another 30 specimens (25 x 2 x 2 mm) were tested for flexural fatigue limit (FFL) in four-point bending via the staircase method. The test was carried out until 10(4) cycles were completed or until fracturing the specimen. One-way ANOVA and Tukey's test demonstrated greater volumetric loss for Grandio and Ceram-X than that observed for the remaining composites. Kruskal-Wallis and the least significant difference test ascertained that Heliomolar, Grandio, and Supreme showed significantly higher FFL than Ceram-X and Premise. In terms of wear and fatigue resistance, nano-structured composites may perform either similarly or comparatively worse than a microfilled composite.
Differentiation of regioisomers at 15N natural abundance using gradient‐enhanced 1H/15N HMBC NMR spectroscopy (1998)

The 1H/15N HMBC experiment at 15N natural abundance using pulsed field gradients is a useful tool for chemical shift assignment and structure elucidation. This experiment assisted in the identification of regioisomers that could not be distinguished with conventional 1H/1H nuclear Overhauser or 1H/13C correlation NMR experiments. The natural abundance 15N gradient-enhanced HMBC experiment was easily implemented, provided high-quality spectra and readily distinguished nitrogen-containing regioisomers. This experiment can aid in structure elucidation when traditional 1H and 13C experiments fail to provide unique structural assignment. © 1998 John Wiley & Sons, Ltd.
An object-oriented data framework for virtual environments with hierarchical modeling (1999)

Virtual reality technology, which is cyberspace composed of multimedia, is a field of comprehensive technology. It is of three basic feathers, namely, interaction, immersion and imagination so that we have to cope with the need for extremely large data sets, massive amounts of computation, and high-throughput networking. This paper presents an approach for object-oriented data modeling framework of complicated virtual environments. The paper discusses the hierarchical decomposition of objects in virtual environments and reuse of these object data libraries to constitute model of virtual environments. This modeling approach used in the paper makes sure that modeling data can be inherited, modularized, maintained easily so as to control redundant data and reduce the software development time, at the same time, realizes dynamic behaviors of objects to meet the needs of some changes of virtual environments.
Globosides but Not Isoglobosides Can Impact the Development of Invariant NKT Cells and Their Interaction with Dendritic Cells (2012)

Recognition of endogenous lipid Ag(s) on CD1d is required for the development of invariant NKT (iNKT) cells. Isoglobotrihexosylceramide (iGb3) has been implicated as this endogenous selecting ligand and recently suggested to control overstimulation and deletion of iNKT cells in α-galactosidase A-deficient (αGalA(-/-)) mice (human Fabry disease), which accumulate isoglobosides and globosides. However, the presence and function of iGb3 in murine thymus remained controversial. In this study, we generate a globotrihexosylceramide (Gb3)-synthase-deficient (Gb3S(-/-)) mouse and show that in thymi of αGalA(-/-)/Gb3S(-/-) double-knockout mice, which store isoglobosides but no globosides, minute amounts of iGb3 can be detected by HPLC. Furthermore, we demonstrate that iGb3 deficiency does not only fail to impact selection of iNKT cells, in terms of frequency and absolute numbers, but also does not alter the distribution of the TCR CDR 3 of iNKT cells. Analyzing multiple gene-targeted mouse strains, we demonstrate that globoside, rather than iGb3, storage is the major cause for reduced iNKT cell frequencies and defective Ag presentation in αGalA(-/-) mice. Finally, we show that correction of globoside storage in αGalA(-/-) mice by crossing them with Gb3S(-/-) normalizes iNKT cell frequencies and dendritic cell (DC) function. We conclude that, although detectable in murine thymus in αGalA(-/-)/Gb3S(-/-) mice, iGb3 does not influence either the development of iNKT cells or their interaction with peripheral DCs. Moreover, in αGalA(-/-) mice, it is the Gb3 storage that is responsible for the decreased iNKT cell numbers and impeded Ag presentation on DCs.
FLAIR, T1 contrast enhancement, MR perfusion, and FDG PET following hypofractionated stereotactic radiotherapy (HFSRT), bevacizumab (BEV), and temozolomide (TMZ) for glioblastoma (GBM). (2011)

2048 Background: In GBM, VEGF inhibition decreases vascular permeability and MRI contrast enhancement (CE), which may or may not reflect meaningful anti-tumor activity. We sought to evaluate the relationships between different imaging modalities and anti-tumor activity in a prospective phase II trial of BEV, TMZ and HFSRT in GBM. Methods: Newly diagnosed GBM pts (N=40) received HFSRT with concomitant/ adjuvant BEV and TMZ. All pts underwent dynamic susceptibility contrast MR perfusion (DSC) at baseline, after HFSRT and every 2m. An FDG-PET scan was done at cycle 6. McDonald and RANO response criteria were applied. Results: DSC showed early/progressive decreases in relative cerebral blood volume (rCBV): baseline mean rCBV: 2.77; 6 weeks: 1.65 (p=0.014); 2m: 1.07 (p<0.001); 4m: 0.98 (p<0.001). Conversely, the extent of FLAIR hypersignal progressively increased (mean diameter product: 953, 1165, 1145, 1384 at 6 wks, 2m, 4m and 6m). Response rates per McDonald vs RANO were: complete response (27 vs 10%), partial (63 vs 63%), stable disease (3% vs 20%), progression (7 vs 7%). Because progressive FLAIR occurred within the RT port, time to radiographic progression per McDonald and RANO were identical: median 13m. Residual hypermetabolism seen at the 6m PET (N=6/31) predicted poor survival (p<0.001). Three pts with progressive FLAIR but not CE underwent re-resection; two had true PD and one had mainly radionecrosis. Conclusions: As treatment failure was mostly local, RANO criteria did not shorten time to progression compared to McDonald. DSC depicted early changes in rCBV linked to VEGF modulation, validating DSC as a reliable tool to evaluate anti-VEGF properties of new drugs in vivo. However, VEGF modulation was not predictive of durable anti-tumor activity. A positive PET at 6m predicted poor survival, indicating treatment failure even if other imaging modalities suggested otherwise. However, tumor progression may still be present despite negative PET and DSC, particularly in the setting of increasing non-enhancing FLAIR within the RT port. New imaging tools and improved response criteria are needed to guide management of these pts.
Europa Clipper Mission: Road from System Integration Review to Launch (2023)

Jupiter's icy moon Europa is a prime target in our exploration of potentially habitable worlds beyond Earth. The combination of a subsurface liquid water layer in contact with a rocky seafloor may yield an ocean rich in the elements and energy needed for the emergence of life, and for potentially sustaining life through time. Europa may hold the clues to one of NASA's long-standing quests - to determine whether or not we are alone in the universe. The Europa Clipper mission will characterize Europa's habitability as the first step in the search for potential life at the Jovian moon by conducting approximately four dozen flybys. While the Clipper project is entering into the heart of its testing and validation program, some critical updates have been in work to ensure mission success. This paper will summarize changes to the mission plan and science measurement requirements from the mission's System Integration Review (SIR) baseline. It will outline the Verification and Validation (V&V) approach and how key technical challenges like power management in the presence of extreme changes in temperature and illumination, and science robustness in the presence of spacecraft and instrument faults and cyber-security are being addressed. Since SIR, Europa Clipper's Propulsion Module has arrived at JPL along with the Plasma Instrument for Magnetic Sounding (PIMS), Europa Ultraviolet Spectrograph (Europa-UVS), Europa Thermal Emission Imaging System (E-THEMIS). Europa Imaging System (EIS) Wide Angle Camera (WAC), Surface Dust Analyzer (SUDA) and boxes from the GNC, Avionics, Propulsion, Power and Thermal subsystems. Some science requirements have been relaxed while the mission plan has been updated to improve robustness and increase the number of data collection opportunities per flyby. Gaining confidence that such a large, complex spacecraft will operate as intended in the extreme temperature and radiation environments is accomplished through a combination of piecewise system level testing, and modeling where testing is not possible. Solar array power management in the presence of extreme temperature variation, from the inner solar system to seeing first light after the cold soaks of up to nine-hour Jupiter eclipses, has been improved to address the dynamic current-voltage (IV) curve behavior. Probabilistic risk assessments are regularly used to understand how changes in science observation schedule, science measurement requirements, and expected frequency of interruptions due to radiation and other causes affect robustness of the mission as a whole to achieve its intended science. In the cyber-security realm, increasing threats and vulnerability concerns have necessitated higher levels of protective actions by sponsoring agencies and projects. The Clipper project has implemented new cybersecurity requirements from NASA and other government agencies to protect project assets, and has been actively engaged with institutional efforts to standardize the set of responses and controls which projects will utilize in the future.
Sex versus gender-related differences in new-onset heart failure with preserved and reduced left ventricular ejection fraction (2022)

Abstract Aims Sex refers to genetic and biological characteristics, whereas gender reflects psychosocial norms, roles and behaviors. Sex differences in new-onset heart failure are well described, but gender differences in new-onset heart failure with preserved (HFpEF) and reduced left ventricular ejection fraction (HFrEF) are unknown. Methods A total of 6830 participants (50.3% women, mean age of 54 years) from the Prevention of Renal and Vascular End-Stage Disease (PREVEND) observational Dutch cohort were enrolled in the study. Gender-related characteristics were assessed using self-administered questionnaires. LASSO regression analysis selected the psychosocial variables related to sex, whose coefficient estimates were used to calculate the gender-related scores for each subject [1–2]. The participants were grouped by sex and further analyzed according to tertiles of the gender-related score. Competing-risk regression analysis was used to assess whether sex and gender were associated with new-onset HFrEF (LVEF ≤40%) and HFpEF (LVEF ≥50%). Results Women with predominantly masculine gender had lower BMI, were more often Caucasian and had higher total cholesterol and high-density lipoprotein (HDL) levels than women with a predominantly feminine gender. Men with predominantly feminine gender were less often Caucasian with lower total cholesterol and HDL cholesterol levels than men with a predominantly masculine gender. During a median follow-up of 8.3 years, 227 (3.3%) subjects were diagnosed with heart failure (57.3% HFrEF and 43.7% HFpEF). In the total population including both men and women, feminine gender was significantly and independently associated with a higher risk of new-onset HFpEF compared with masculine gender (HR per 10 point: 1.17, 95% CI: 1.06–1.30; p=0.003). However, sex was not associated with new-onset HFpEF (HR: 1.09, 95% CI: 0.73–1.62; p=0.670). Separately in men, feminine gender was associated with a higher risk of new-onset HFpEF (HR: 1.37, 95% CI: 1.06–1.78; p=0.017), but not in women (HR: 1.13, 95% CI: 0.90–1.41; p=0.310). Conclusions Gender and sex are different constructs and feminine gender was associated with an increased risk of new-onset HFpEF, whereas sex was not associated with new-onset HFpEF. Funding Acknowledgement Type of funding sources: Foundation. Main funding source(s): Dutch Kidney Foundation
Design and Preparation of a Core–Shell Metal–Organic Framework for Selective CO2 Capture (2013)

The design of a core-shell metal-organic framework comprising a porous bio-MOF-11/14 mixed core and a less porous bio-MOF-14 shell is reported. The growth of the MOF shell was directly observed and supported by SEM and PXRD. The resulting core-shell material exhibits 30% higher CO2 uptake than bio-MOF-14 and low N2 uptake in comparison to the core. When the core-shell architecture is destroyed by fracturing the crystallites via grinding, the amount of N2 adsorbed doubles but the CO2 adsorption capacity remains the same. Finally, the more water stable bio-MOF-14 shell serves to prevent degradation of the water-sensitive core in aqueous environments, as evidenced by SEM and PXRD.
Dependence of liver R2* on the fat spectral model. (2023)

Using MRS, we examined whether the assumed fat spectral model (6-, or 9-peak) altered liver R2* estimation in vivo . We found that liver R2* estimation was model-independent, and liver R2*was not significantly different from water R2* (p = 0.07). However, fat R2* values estimated for these models were different (p &amp;lt; 0.0001), suggesting that fat R2* estimation in high-fat tissues may be model dependent.
Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide (2018)

Sal-like 4 (SALL4) is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in hepatocellular carcinoma, a malignancy with no effective treatment. In cancer cells, SALL4 associates with nucleosome remodeling deacetylase (NuRD) to silence tumor-suppressor genes, such as PTEN. Here, we determined the crystal structure of an amino-terminal peptide of SALL4(1-12) complexed to RBBp4, the chaperone subunit of NuRD, at 2.7 Å, and subsequent design of a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. FFW peptide disruption of the SALL4-NuRD complex resulted in unidirectional up-regulation of transcripts, turning SALL4 from a dual transcription repressor-activator mode to singular transcription activator mode. We demonstrate that FFW has a target affinity of 23 nM, and displays significant antitumor effects, inhibiting tumor growth by 85% in xenograft mouse models. Using transcriptome and survival analysis, we discovered that the peptide inhibits the transcription-repressor function of SALL4 and causes massive up-regulation of transcripts that are beneficial to patient survival. This study supports the SALL4-NuRD complex as a drug target and FFW as a viable drug candidate, showcasing an effective strategy to accurately target oncogenes previously considered undruggable.
A Scaling Study of Excess OFF-State Current in InGaAs Quantum-Well MOSFETs (2019)

A scaling study of excess OFF-state current in planar InGaAs quantum-well MOSFETs is reported. We find that pure band-to-band tunneling (BTBT) dominates the drain OFF-state current in devices with channel length above ~1 μm. In this regime, the drain-gate voltage sets the rate of BTBT. In devices with channel lengths below 1 μm, a parasitic bipolar transistor effect becomes relevant. The bipolar current gain is found to scale inversely with the effective channel length for Lg between 70 nm and 1 μm, as expected from simple bipolar transistor theory. For Lg below ~70 nm, the OFF-state current increases rapidly due to an enhancement in bipolar current gain as a result of strong short-channel effects and punchthrough. Current gains in excess of 104 have been observed. A reduction in channel thickness decreases both BTBT and the bipolar gain effect.
A Practical Transistor-Level Dual Threshold Voltage Assignment Methodology (2005)

Leakage power has become one of the most critical design concerns for the system-level chip designer. Multi-threshold techniques have been used to reduce runtime leakage power without sacrificing performance. In this paper we present an effective and scalable transistor-level V/sub th/ assignment approach and show leakage reduction over standard cell-level V/sub th/ assignment. The main disadvantage of transistor-level V/sub th/ assignment is increased cell library size and characterization effort. In comparison to previous approaches, our approach yields better solution quality, requires smaller cell library, is more accurate in considering the impact of V/sub th/ assignment on propagation delay, slew (transition delay) and capacitance, and is significantly faster.
A New Subcarrier Demodulator of Satellite Telemetry Approaching to the Ideality Based on the Digital Signal (2009)

In the deep space communication under the USB (unified S-band) system, the channel coding is generally used in the telemetry down-link. To get the coding gain, the subcarrier demodulation model needs to work reliably under the low Es/No. In this paper, a new BPSK subcarrier demodulation model of digital signal is introduced. This demodulation model is able to work well when the E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> is up to 1 dB, also its demodulation loss is very low. So it is applicable for the bad telemetry channel.
Competitive Structure of Mobile TV in Korea (2009)

본 연구는 모바일 VOD, 지상파 DMB, 위성 DMB 로 구성된 국내 모바일 TV시장의 경쟁 관계를 분석한다. 이 세 매체간의 경쟁관계를 분석하기 위해 한정된 자원을 두고 매체들이 경쟁하는 개념인 적소이론 (Niche Theory)을 이용하였다. 매체들의 경쟁상황은 적소 척도인 적소폭(niche breadth), 적소중복(niche overlap), 경쟁적 우위성 (niche superiority) 을 적용한다. 나아가 적소이론을 바탕으로 매체간의 보완, 대체, 배제의 관계를 설명하기 위한 통합 모델을 제안하였다. 분석결과 위성 DMB와 지상파 DMB는 치열한 경쟁관계를 나타냈으며 지상파 DMB의 우월성에 의한 위성 DMB의 대체관계를 도출하였으며 성공적인 국내 모바일 TV의 전략으로 방송기반 DMB와 모바일 VOD의 듀얼모드 비즈니스 전략을 강조하였다.
A new route to the imidazole-2-thiones from 2-thiohydantoins. Implications in the study of ergothioneine (1968)

1. 2-Thiohydantoins are reduced by borohydrides to 4(5)-hydroxyimidazolidine-2-thiones, which eliminate water in acid to form imidazole-2-thiones. Both steps take place in mild conditions, in high yield. A number of imidazole-2-thiones have been synthesized by this sequence of steps, with one, two or three substituents in the 1-, 3- and 4(5)-positions. 2. 4(5)-Hydroxyimidazolidine-2-thiones are ammonium pseudo-bases, giving rise to an equilibrium mixture of amino aldehyde, carbinolamine and mesomeric ammonium cationic forms. The elimination of water is suggested to be a property of the mesomeric ammonium cation. 3. The mild conditions in which imidazole-2-thiones are formed from 4(5)-hydroxyimidazolidine-2-thiones are similar to those in which ergothioneine, a naturally occurring imidazole-2-thione of uncertain function, is normally released and measured. It is suggested that the occurrence in vivo of a precursor to ergothioneine, in the form of a 4(5)-hydroxyimidazolidine-2-thione, would explain many otherwise conflicting published data.
Deep learning‐based classification and structure name standardization for organ at risk and target delineations in prostate cancer radiotherapy (2021)

Radiotherapy (RT) datasets can suffer from variations in annotation of organ at risk (OAR) and target structures. Annotation standards exist, but their description for prostate targets is limited. This restricts the use of such data for supervised machine learning purposes as it requires properly annotated data. The aim of this work was to develop a modality independent deep learning (DL) model for automatic classification and annotation of prostate RT DICOM structures. Delineated prostate organs at risk (OAR), support- and target structures (gross tumor volume [GTV]/clinical target volume [CTV]/planning target volume [PTV]), along with or without separate vesicles and/or lymph nodes, were extracted as binary masks from 1854 patients. An image modality independent 2D InceptionResNetV2 classification network was trained with varying amounts of training data using four image input channels. Channel 1-3 consisted of orthogonal 2D projections from each individual binary structure. The fourth channel contained a summation of the other available binary structure masks. Structure classification performance was assessed in independent CT (n = 200 pat) and magnetic resonance imaging (MRI) (n = 40 pat) test datasets and an external CT (n = 99 pat) dataset from another clinic. A weighted classification accuracy of 99.4% was achieved during training. The unweighted classification accuracy and the weighted average F1 score among different structures in the CT test dataset were 98.8% and 98.4% and 98.6% and 98.5% for the MRI test dataset, respectively. The external CT dataset yielded the corresponding results 98.4% and 98.7% when analyzed for trained structures only, and results from the full dataset yielded 79.6% and 75.2%. Most misclassifications in the external CT dataset occurred due to multiple CTVs and PTVs being fused together, which was not included in the training data. Our proposed DL-based method for automated renaming and standardization of prostate radiotherapy annotations shows great potential. Clinic specific contouring standards however need to be represented in the training data for successful use. Source code is available at https://github.com/jamtheim/DicomRTStructRenamerPublic.