gebhart/patrepeval huggingface dataset:
Sensory Properties of Under‐Roasted Coffee Beverages (2013)

Conditions milder than standard roasting (under-roasting: 140 to 170 °C for 20 to 12 min) have been proposed to reduce the formation of potentially harmful compounds developing during standard coffee roasting. In the present study, sensory properties of brews prepared with under-roasted coffees (140 to 165 °C for 20 min) were described by descriptive analysis. Two meta-attributes were defined: "coffee" consisting of attributes positively related to the increasing of process temperature and "no-coffee" consisting of those negatively related to temperature. The progressive lowering of "no-coffee" and the corresponding increasing of "coffee" mean values were induced by temperature increasing in under-roasting conditions. The processing temperature of 150 °C seems to represent the changing point between the 2 meta-attributes with "no-coffee" prevailing at lower and "coffee" at higher temperatures. Consumer responses indicate the positive effect of both product processing temperature and "coffee" attribute intensity on liking. Brews from coffee treated at temperature lower than 150 °C showed a sensory profile characterized by "no-coffee" attributes and resulted the less preferred by regular coffee consumers.
Tetrasphaera elongata sp. nov., a polyphosphate-accumulating bacterium isolated from activated sludge. (2002)

A new meso-diaminopimelic acid-containing, gram-positive bacterium was isolated from an activated sludge reactor showing enhanced biological phosphorus removal activity. The isolate was an asporogenous oval to rod-shaped bacterium, but occasionally formed clumps. The Neisser staining was positive, suggesting intracellular polyphosphate granules. The isolate was an aerobic chemoheterotroph which was capable of utilizing various sugars, sugar alcohols and organic acids. It contained anteiso-C15:0, iso-C15:0, iso-C14:0 and C16:0 as the major cellular fatty acids, and menaquinone-8(H4) as the major quinone. The G+C content of the genomic DNA was 69.6 mol%. Analysis of the 16S rDNA sequence revealed that the isolate is a new member of the family Intrasporangiaceae. The closest relatives were Tetrasphaera species. On the basis of the phenotypic and phylogenetic distinctiveness of the isolate, it was concluded that the organism represents a new species in the genus Tetrasphaera, for which the name Tetrasphaera elongata sp. nov. is proposed. The type strain is strain Lp2T (= JCM 11141T = DSM 14184T).
Effect of Optical Coherence Tomography Resolution on the Assessment of Dental Enamel Indications (2018)

We have implemented optical coherence tomography with different light sources and imaging optics to provide varying spatial resolution and field-of-view. We examined the impact of these parameters on visualization and quantification of dental enamel indications.
Effectiveness of CHIKV vaccine VLA1553 demonstrated by passive transfer of human sera (2022)

Chikungunya virus (CHIKV) is a reemerging mosquito-borne alphavirus responsible for numerous outbreaks. Chikungunya can cause debilitating acute and chronic disease. Thus, the development of a safe and effective CHIKV vaccine is an urgent global health priority. This study evaluated the effectiveness of the live-attenuated CHIKV vaccine VLA1553 against WT CHIKV infection by using passive transfer of sera from vaccinated volunteers to nonhuman primates (NHP) subsequently exposed to WT CHIKV and established a serological surrogate of protection. We demonstrated that human VLA1553 sera transferred to NHPs conferred complete protection from CHIKV viremia and fever after challenge with homologous WT CHIKV. In addition, serum transfer protected animals from other CHIKV-associated clinical symptoms and from CHIKV persistence in tissue. Based on this passive transfer study, a 50% micro-plaque reduction neutralization test titer of ≥ 150 was determined as a surrogate of protection, which was supported by analysis of samples from a seroepidemiological study. In conclusion, considering the unfeasibility of an efficacy trial due to the unpredictability and explosive, rapidly moving nature of chikungunya outbreaks, the definition of a surrogate of protection for VLA1553 is an important step toward vaccine licensure to reduce the medical burden caused by chikungunya.
Coronary Artery Disease Risk and Lipidomic Profiles Are Similar in Hyperlipidemias With Family History and Population‐Ascertained Hyperlipidemias (2019)

Background We asked whether, after excluding familial hypercholesterolemia, individuals with high low-density lipoprotein cholesterol ( LDL -C) or triacylglyceride levels and a family history of the same hyperlipidemia have greater coronary artery disease risk or different lipidomic profiles compared with population-based hyperlipidemias. Methods and Results We determined incident coronary artery disease risk for 755 members of 66 hyperlipidemic families (≥2 first-degree relatives with similar hyperlipidemia) and 19 644 Finnish FINRISK population study participants. We quantified 151 circulating lipid species from 550 members of 73 hyperlipidemic families and 897 FINRISK participants using mass spectrometric shotgun lipidomics. Familial hypercholesterolemia was excluded using functional LDL receptor testing and genotyping. Hyperlipidemias ( LDL -C or triacylglycerides >90th population percentile) associated with increased coronary artery disease risk in meta-analysis of the hyperlipidemic families and the population cohort (high LDL -C: hazard ratio, 1.74 [95% CI, 1.48-2.04]; high triacylglycerides: hazard ratio, 1.38 [95% CI, 1.09-1.74]). Risk estimates were similar in the family and population cohorts also after adjusting for lipid-lowering medication. In lipidomic profiling, high LDL -C associated with 108 lipid species, and high triacylglycerides associated with 131 lipid species in either cohort (at 5% false discovery rate; P-value range 0.038-2.3×10<sup>-56</sup>). Lipidomic profiles were highly similar for hyperlipidemic individuals in the families and the population ( LDL -C: r=0.80; triacylglycerides: r=0.96; no lipid species deviated between the cohorts). Conclusions Hyperlipidemias with family history conferred similar coronary artery disease risk as population-based hyperlipidemias. We identified distinct lipidomic profiles associated with high LDL -C and triacylglycerides. Lipidomic profiles were similar between hyperlipidemias with family history and population-ascertained hyperlipidemias, providing evidence of similar and overlapping underlying mechanisms.
Photoreceptor Structure and Function in Patients with Congenital Achromatopsia (2011)

The current approach of using high-resolution techniques to assess photoreceptor structure and function in patients with achromatopsia should be useful in guiding selection of patients for future therapeutic trials as well as monitoring therapeutic response in these trials.
PROXECCO—Proximity effect correction by convolution (1993)

In electron-beam lithography the proximity effect limits achieved resolution. A possible approach for proximity effect correction is the transform based method which uses deconvolution. This method requires high computing power and data reduction algorithms because of the small grid size. The fine grid is mainly needed for preserving pattern, not for the resolution of the correction. The new method called PROXECCO avoids this disadvantage by separating the calculation into correction related and pattern related steps. The grid size is spatially independent from pattern and can be as coarse as needed for correction. This results in a quadratical gain in computing time for the transformation. The pattern dimensions are kept exactly maintained and data reduction is not needed anymore.
Comparison of Nonlinear to Linear Thermoacoustic Stability Analysis of a Gas Turbine Combustion System (2012)

Gas turbines offer a high operational flexibility and a good turn down ratio to meet future requirements of power production. In this context stable operation over a wide range and for different blends of fuel is requested. Thermoacoustic stability assessment is crucial for accelerating the development and implementation of new combustion systems. The results of nonlinear and linear thermoacoustic stability assessments are compared on basis of recent measurements of flame describing functions and thermoacoustic stability of a model swirl combustor operating in the fully turbulent regime. The different assessment methods are outlined. The linear thermoacoustic stability assessment yields growth rates of the thermoacoustic instability whereas the limit cycle amplitude is predicted by the nonlinear stability method. It could be shown that the predicted limit cycle amplitudes correlate well with the growth rates of excitation obtained from linear modeling. Hence for screening the thermoacoustic stability of different design approaches a linear assessment may be sufficient while for detailed prediction of the dynamic pressure amplitude more efforts have to be spent on the nonlinear assessment including the analysis of the nonlinear flame response.
Characterization of Critical Determinants of ACE2–SARS CoV-2 RBD Interaction (2021)

Despite sequence similarity to SARS-CoV-1, SARS-CoV-2 has demonstrated greater widespread virulence and unique challenges to researchers aiming to study its pathogenicity in humans. The interaction of the viral receptor binding domain (RBD) with its main host cell receptor, angiotensin-converting enzyme 2 (ACE2), has emerged as a critical focal point for the development of anti-viral therapeutics and vaccines. In this study, we selectively identify and characterize the impact of mutating certain amino acid residues in the RBD of SARS-CoV-2 and in ACE2, by utilizing our recently developed NanoBiT technology-based biosensor as well as pseudotyped-virus infectivity assays. Specifically, we examine the mutational effects on RBD-ACE2 binding ability, efficacy of competitive inhibitors, as well as neutralizing antibody activity. We also look at the implications the mutations may have on virus transmissibility, host susceptibility, and the virus transmission path to humans. These critical determinants of virus-host interactions may provide more effective targets for ongoing vaccines, drug development, and potentially pave the way for determining the genetic variation underlying disease severity.
Retrieving Time-Dependent Green’s Functions in Optics with Low-Coherence Interferometry (2015)

We report on the passive measurement of time-dependent Green's functions in the optical frequency domain with low-coherence interferometry. Inspired by previous studies in acoustics and seismology, we show how the correlations of a broadband and incoherent wave field can directly yield the Green's functions between scatterers of a complex medium. Both the ballistic and multiple scattering components of the Green's function are retrieved. This approach opens important perspectives for optical imaging and characterization in complex scattering media.
Performance evaluation of energy-efficient high-speed tiered-storage system (2010)

Large-scale high-performance storage in high-performance computing systems consists of numerous HDDs and consumes a large amount of energy. To reduce the energy consumed by these storage systems, we previously proposed a high-speed tiered-storage system with a power-aware proactive method of storage-tiering management, which we named the energy-efficient high-speed tiered-storage system (eHiTS). eHiTS consists of a high-speed online storage component as the first tier and a large capacity nearline storage component as the second tier. The first-tier online storage is used as a data cache. For reducing energy consumption, it is necessary to reduce the online storage capacity, but this decreases performance. We derive the relationship between performance and online storage capacity by analytical calculation and simulation with an actual HPC system. The results show that with a 1% of decrease in performance, online capacity could be reduced to the capacity which can hold about 1.4 times as many volumes as the maximum number of volumes required by jobs running in parallel. In this case, energy consumption was reduced by an estimated 38% with eHiTS compared with conventional tiered-storage systems.
Preparative Linear Ion Trap Mass Spectrometer for Separation and Collection of Purified Proteins and Peptides in Arrays Using Ion Soft Landing (2004)

A preparative mass spectrometer for microarray fabrication is reported. The instrument includes an atmospheric pressure ionization source, a linear ion trap mass analyzer, an ion collection surface positioning system, and a surface loading chamber with independent vacuum pumping. It was designed for the production of protein arrays using the ion soft-landing technique to collect ions on a surface after separation by mass/charge ratio. Small microarrays have been prepared by isolating and soft landing individual protein or peptide ions after electrospray ionization of mixtures. The composition and purity of the separated materials has been confirmed using independent external mass spectrometric analysis of rinse solutions of the collected spots, either by the new method of electrosonic spray ionization MS or by nanospray ionization MS. The ability to retain bioactivity in the mass-selected and collected biomolecules has been demonstrated in particular cases. The reported instrument has also been characterized as an analytical mass spectrometer.
Measurement of strain hardening exponent n-value by additional rolling strain for aluminum alloy sheets (2009)

The combined method of rolling and simple tension to obtain the strain hardening exponent n-value by Hollomon's equation in wide strain range has been compared with the simple tension method in commercial pure aluminum alloy sheets. The n-value by simple tension method is measured to be 0.32, 0.36 or 0.25 respectively in the three stages of growing strain. The third and last stage is the strain range of 0.06~0.23 that is just before the necking. In comparison, the n-value by combined method is obtained to be 0.24 in the wide strain range of 0.06~2.2 in which the rolling strain up to 90% of thickness reduction is changed to the equivalent strain and added to the tensile strain. This n-value is recognized to be almost equal to the value by simple tension method. The changes of crystal orientation due to the deformation are different in these two methods, however, the similar dislocation cell structures are observed when the nearly equal n-values are obtained. These results support the utility of combined method standing on the assumption of plastic uniformity of material to obtain the n-value for wide strain range and suggest that n-value depends rather on the dislocation structures than the crystal structures.
Central role of mitochondrial aldehyde dehydrogenase and reactive oxygen species in nitroglycerin tolerance and cross-tolerance (2004)

Recent studies suggest that mitochondrial aldehyde dehydrogenase (ALDH-2) plays a central role in the process of nitroglycerin (glyceryl trinitrate, GTN) biotransformation in vivo and that its inhibition accounts for mechanism-based tolerance in vitro. The extent to which ALDH-2 contributes to GTN tolerance (impaired relaxation to GTN) and cross-tolerance (impaired endothelium-dependent relaxation) in vivo remain to be elucidated. Rats were treated for three days with GTN. Infusions were accompanied by decreases in vascular ALDH-2 activity, GTN biotransformation, and cGMP-dependent kinase (cGK-I) activity. Further, whereas in control vessels, multiple inhibitors and substrates of ALDH-2 reduced both GTN-stimulation of cGKI and GTN-induced vasodilation, these agents had little effect on tolerant vessels. A state of functional tolerance (in the GTN/cGMP pathway) was recapitulated in cultured endothelial cells by knocking down mitochondrial DNA (ρ(0) cells). In addition, GTN increased the production of reactive oxygen species (ROS) by mitochondria, and these increases were associated with impaired relaxation to acetylcholine. Finally, antioxidants/reductants decreased mitochondrial ROS production and restored ALDH-2 activity. These observations suggest that nitrate tolerance is mediated, at least in significant part, by inhibition of vascular ALDH-2 and that mitochondrial ROS contribute to this inhibition. Thus, GTN tolerance may be viewed as a metabolic syndrome characterized by mitochondrial dysfunction.
The dual-gain mode: a way to enhance the dynamic range of X-ray detectors (2006)

Varian Medical Systems has manufactured and recently put into operation a clinically-applicable solution for image-guided radiation therapy. Cone-beam CT imaging, one of the operation modes of the imaging unit of this device, aims at high-quality volumetric reconstruction. To boost the image quality, the dual-gain mode, a successful means for enhancing the dynamic range of the flat-panel detectors and obtaining better results in the contrast of the reconstructed image, was developed and successfully tested during the last few years. The important steps in the calibration of this mode involve a correction to the pulse widths associated with the X-ray production, the assessment of the detector signal above which nonlinear effects become significant and the determination of some properties of the detector pixels, namely, of dark fields, flatness corrections, etc. Finally, the defect-pixel map is obtained, containing dead and flickering pixels, as well as pixels with properties which are sufficiently `out of range'. An effect observed in the offset correction of raw images seems to originate in the mismatch between the measured and extrapolated values of the dark field; a correction scheme is proposed to take account of this effect. In the data processing, which is achieved on the basis of the files produced in the calibration of the mode, the high-gain signal is used whenever meaningful; otherwise, it is substituted by the low-gain signal, properly scaled. Defect pixels are interpolated from their good neighbours; a procedure achieving a correction in case of small defect-pixel clusters is outlined.
Evidence that a non-RGD domain in rat osteopontin is involved in cell attachment (1993)

The bone sialoprotein osteopontin (OPN) promotes cell attachment and spreading through its RGD (Arg-Gly-Asp) sequence. To study additional regions of OPN involved in cell attachment, peptides of rat OPN were evaluated for their capacity to mediate cell binding to wells in vitro. Human gingival fibroblasts were incubated on microtiter plates coated with either OPN or OPN peptides. A peptide of M(r) 28 kD, obtained after digestion with endoproteinase Arg-C and isolated by reversed-phase HPLC, enhanced cell attachment to a similar degree as OPN. Sequence analysis showed that the amino terminus of the 28 kD peptide starts at Ser142 and therefore does not contain the RGD cell attachment sequence (residues 128-130). Cell attachment mediated through both OPN and the 28 kD peptide was blocked by the addition of GRGDSPA peptides or LM-609, a monoclonal antibody to the integrin alpha V beta 3, a receptor for vitronectin. A variant peptide, GRG-ESPA, did not alter cell attachment. Based on these observations, we conclude that (1) binding of OPN and the 28 kD peptide to fibroblasts involves binding to alpha V beta 3, (2) a site other than the RGD sequence on OPN is also involved in binding to integrins, and (3) the binding of this second site to alpha V beta 3 is inhibited by RGD-containing peptides.
Activating WASP mutations associated with X-linked neutropenia result in enhanced actin polymerization, altered cytoskeletal responses, and genomic instability in lymphocytes (2010)

X-linked neutropenia (XLN) is caused by activating mutations in the Wiskott-Aldrich syndrome protein (WASP) that result in aberrant autoinhibition. Although patients with XLN appear to have only defects in myeloid lineages, we hypothesized that activating mutations of WASP are likely to affect the immune system more broadly. We generated mouse models to assess the role of activating WASP mutations associated with XLN (XLN-WASP) in lymphocytes. XLN-WASP is expressed stably in B and T cells and induces a marked increase in polymerized actin. XLN-WASP-expressing B and T cells migrate toward chemokines but fail to adhere normally. In marked contrast to WASP-deficient cells, XLN-WASP-expressing T cells proliferate normally in response to cell-surface receptor activation. However, XLN-WASP-expressing B cells fail to proliferate and secrete lower amounts of antibodies. Moreover, XLN-WASP expression in lymphocytes results in modestly increased apoptosis associated with increased genomic instability. These data indicate that there are unique requirements for the presence and activation status of WASP in B and T cells and that WASP-activating mutations interfere with lymphocyte cell survival and genomic stability.
Variation in the Etch Rate of LIBWE Fabricating Deep Microtrenches (2012)

Variation in the etch rates for fabricating single deep microtrenches by laser-induced backside wet etching (LIBWE) employing a KrF excimer laser and acetone solution of pyrene is investigated. Microtrenches with widths of 5, 8, 10, 15, and 20 m, a length of 1 mm, and depths up to 90 m were fabricated with a fluence of 1.3 J/cm 2 , a pulse repetition of 80 Hz, and various pulse numbers. Special care was directed to maintaining in-focus conditions for etching. In the fabrication of 5-mwide microtrenches, etch rates of 5.3 nm/pulse evaluated for trenches with depths of less than 4 m increased by a factor of 2.55 to 13.5 nm/pulse when the trenches became deeper than 16 m. Such variation in the etch rate reduced with width and became negligibly small for 20-m-wide microtrenches. Based on a similar dependence on width, the variation in etch rate with depth can be related to the size effect observed in LIBWE. As a factor causing the size effect as well as the variation in etch rate with depth, the interaction between the laser-heated surface and the solution in an early time region of the laser-induced phenomena is proposed.
Supplementary Figure Legends from Nature of Tumor Control by Permanently and Transiently Modified GD2 Chimeric Antigen Receptor T Cells in Xenograft Models of Neuroblastoma (2023)

Supplementary Figure Legends from Nature of Tumor Control by Permanently and Transiently Modified GD2 Chimeric Antigen Receptor T Cells in Xenograft Models of Neuroblastoma