gebhart/patrepeval huggingface dataset:
Real-time method for motion-compensated MR thermometry and MRgHIFU treatment in abdominal organs (2013)

The presented method demonstrated in moving phantoms and breathing sheep accurate motion-compensated MR thermometry and precise HIFU focal point lock-on target using only real-time pencil-beam navigator tracking information, making it applicable without any pretreatment data acquisition or organ motion modeling.
Cancer Phototherapy: Multimodal‐Imaging‐Guided Cancer Phototherapy by Versatile Biomimetic Theranostics with UV and γ‐Irradiation Protection (Adv. Mater. 17/2016) (2016)

On page 3273, P. Huang, X. Chen, and co-workers report a versatile biomimetic theranostic agent based on magnetic melanin nanoparticles (MMNs). This agent enables guided photothermal cancer therapy combining positron-emission tomography (PET), magnetic resonance (MR), photoacoustic (PA), and photothermal (PT) for multimodal-imaging. MMNs also exhibit efficient shielding against UV- and γ-irradiation.
Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS) (2012)

In conclusion, the large number of cir genes and their expression throughout the intraerythrocytic cycle of development indicates that CIR proteins are likely to be important for parasite survival. In particular, the detection of dominant cir transcripts at the peak of P. chabaudi infection supports the idea that CIR proteins are expressed, and could perform important functions in the biology of this parasite. Further application of the methodologies described here may allow the elucidation of CIR sub-family A and B protein functions, including their contribution to antigenic variation and immune evasion.
Inhibition of HIF-prolyl-4-hydroxylases prevents mitochondrial impairment and cell death in a model of neuronal oxytosis (2016)

Mitochondrial impairment induced by oxidative stress is a main characteristic of intrinsic cell death pathways in neurons underlying the pathology of neurodegenerative diseases. Therefore, protection of mitochondrial integrity and function is emerging as a promising strategy to prevent neuronal damage. Here, we show that pharmacological inhibition of hypoxia-inducible factor prolyl-4-hydroxylases (HIF-PHDs) by adaptaquin inhibits lipid peroxidation and fully maintains mitochondrial function as indicated by restored mitochondrial membrane potential and ATP production, reduced formation of mitochondrial reactive oxygen species (ROS) and preserved mitochondrial respiration, thereby protecting neuronal HT-22 cells in a model of glutamate-induced oxytosis. Selective reduction of PHD1 protein using CRISPR/Cas9 technology also reduced both lipid peroxidation and mitochondrial impairment, and attenuated glutamate toxicity in the HT-22 cells. Regulation of activating transcription factor 4 (ATF4) expression levels and related target genes may mediate these beneficial effects. Overall, these results expose HIF-PHDs as promising targets to protect mitochondria and, thereby, neurons from oxidative cell death.
Reference values for respiratory impedance in adult men and women: data from the Austrian LEAD Study. (2022)

<b>Background</b> Determination of reference values of respiratory impedance (Zrs) measured by forced oscillation technique (FOT) is of utmost importance in its clinical use. The aim of our study was to present reference values for whole-breath FOT measurements for adults (18-80 years). <b>Methods</b> 1264 adult healthy asymptomatic never-smokers of the Austrian LEAD Study cohort were included in the analysis. Nearly all participants had normal weight (BMI ≤ 35) and had normal lung volumes (total lung capacity (TLC) ≥ lower limit of normal). Data were collected with the Resmon Pro FULL device using a multiple frequency mode of 5-11-19 Hz. Sex-specific prediction equations were developed for Resistance (R) 5 Hz (5) expiratory (exp.), R5 inspiratory (insp.), R5 total (tot.), Reactance (X) 5 exp., X5 insp. and X5 tot. using the LMS (lambda, mu, sigma) method. Body height only showed a significant influence on the parameters chosen. Therefore, it was used as a single covariate. <b>Results</b> We created percentile curves and look up tables including reference values for a height from 143cm to 204cm. While R values in men decrease with height between 150cm and 180cm and flattened at higher length (&gt;180cm), R values in females progressively declined with higher height. X showed a progressive increase with height in men and a flattening of X at higher length (&gt;180cm) in women. <b>Conclusion</b> Our study provides highly accurate reference values for clinically useful Zrs parameters in the form of look up tables. Beside the establishment of reference values further research is required for the optimal positioning of Zrs in respiratory diagnostics.
Gene Variation of Endoplasmic Reticulum Aminopeptidase 1 and Risk of Incident Type 2 Diabetes Mellitus amongst 22,718 Initially Healthy Women (2018)

Objective: Recent studies have demonstrated the importance of Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) gene variants in inflammatory conditions, including Type 1 diabetes mellitus. However, to date, no large prospective, genetic-epidemiological data are available on the relevance of ERAP1 genetic variation in the risk of non-insulin dependent diabetes. Methods: The association between 33 tag-SNPs (tSNPs) of ERAP1 and incident Type 2 Diabetes mellitus (T2D) was investigated in 22,718 Caucasian female participants of the prospective Women's Genome Health Study. All were free of known cancer, cardiovascular disease, and diabetes mellitus at baseline. During an 18-year follow-up period, 1,927 newly diagnosed first ever T2D were identified. Multivariable Cox regression analysis was performed to investigate the relationship between genotypes and T2D risk assuming an additive genetic model. Results: None of the gene variants evaluated were associated with T2D risk. Conclusions: If corroborated in other large prospective studies, the present findings suggest that genetic variation within the ERAP1 gene locus may not be useful prognostic indicators for risk assessment of type 2 diabetes mellitus. Keywords: Type 2 Diabetes Mellitus, genetic epidemiology, single nucleotide polymorphisms, ERAP1, risk assessment, gene Variation.
Numerical simulations for impact damage detection in composites using vibrothermography (2010)

Composite materials are widely used in many engineering applications due to their high strength-to-weight ratios. However, it is well known that composites are susceptible to impact damage. Detection of impact damage is an important issue in maintenance of composite structures. Various non-destructive image-based techniques have been developed for damage detection in composite materials. These include vibrothermography that detects surface temperature changes due to heating associated with frictional energy dissipation by damage. In the present paper numerical simulations are used to investigate heat generation in a composite plate with impact damage in order to support damage detection analysis with vibrothermography. Explicit finite elements are used to model ultrasonic wave propagation in the damaged plate. Simulated delamination and cracks induce frictional heating in the plate. Coupled thermo-mechanical simulations are performed in high frequencies using commercial LS-Dyna finite element code. Very good qualitative agreement between measurements and simulations has been obtained. The area of increased temperature corresponds very well with the damaged area in both experiments and simulations. Numerical model has to be further refined in order to quantitatively match the experiments. The main issues of concern are frictional and thermal properties of composites. The final goal of these research efforts is to predict damage detection sensitivity of vibrothermography in real engineering applications based on numerical models.
Digital Color Imaging Handbook (2011)

Color Fundamentals for Digital Imaging, Gaurav Sharma, Xerox Corporation Visual Psychophysics and Color Appearance, Garrett M. Johnson and Mark D. Fairchild, Rochester Institute of Technology Physical Models for Color Prediction, Patrick Emmel, Clariant International Color Management for Digital Imaging Systems, Edward J. Giorgianni, Thomas E. Madden and Kevin E. Spaulding, Eastman Kodak Company Device Characterization, Raja Bala, Xerox Corporation Digital Color Halftones, Charles M Hains, Shen-ge Wang, and Keith T. Knox, Xerox Corporation Human Visual Model Based Color Halftoning, A. Ufuk Agar, Hewlett Packard Company, Farhan A. Baqai, Sony Electronics, and Jan P. Allebach, Purdue University Compression of Color Images, Ricardo de Queiroz, Xerox Corporation Color Quantization, Luc Brun, Universite Reims, Champagne Ardenne and Alain Tremeau, Universite Jean Monnet de Saint-Etienne Gamut Mapping, Jan Morovic, University of Derby Efficient Color Transformation Implementation, Raja Bala and R. Victor Klassen, Xerox Corporation Color Image Processing for Digital Cameras, Ken Parulski and Kevin E. Spaulding, Eastman Kodak Company
Metabolism of p-aminobenzoic Acid in the Perfused Livers of Chronically Uraemic Rats (1979)

1. Chronic renal failure was induced in rats by surgical removal of thirteen-sixteenths of renal tissue. 2. The metabolism of p-amino[14C]benzoic acid was studied in the isolated perfused livers of control and chronically uraemic rats. There was a slower rate of clearance and decreased overall metabolism of the compounds in the uraemic rats. 3. Conjugation of p-amino[14C]benzoic acid with glycine and the formation of p-aminobenzoic acid glucuronide were both significantly decreased in the uraemic rats, but there was a significant increase in acetylation of both p-aminobenzoic acid and its glycine conjugate.
PHRONESIS: A One‐Shot Approach for Sequential Assignment of Protein Resonances by Ultrafast MAS Solid‐State NMR Spectroscopy (2022)

Solid-state NMR (ssNMR) spectroscopy has emerged as the method of choice to analyze the structural dynamics of fibrillar, membrane-bound, and crystalline proteins that are recalcitrant to other structural techniques. Recently, <sup>1</sup> H detection under fast magic angle spinning and multiple acquisition ssNMR techniques have propelled the structural analysis of complex biomacromolecules. However, data acquisition and resonance-specific assignments remain a bottleneck for this technique. Here, we present a comprehensive multi-acquisition experiment (PHRONESIS) that simultaneously generates up to ten 3D <sup>1</sup> H-detected ssNMR spectra. PHRONESIS utilizes broadband transfer and selective pulses to drive multiple independent polarization pathways. High selectivity excitation and de-excitation of specific resonances were achieved by high-fidelity selective pulses that were designed using a combination of an evolutionary algorithm and artificial intelligence. We demonstrated the power of this approach with microcrystalline U-<sup>13</sup> C,<sup>15</sup> N GB1 protein, reaching 100 % of the resonance assignments using one data set of ten 3D experiments. The strategy outlined in this work opens up new avenues for implementing novel <sup>1</sup> H-detected multi-acquisition ssNMR experiments to speed up and expand the application to larger biomolecular systems.
THE INFLUENCE OF NITROGEN, PHOSPHORUS AND POTASSIUM ON THE COLD ACCLIMATION OF WINTER WHEAT (Triticum aestivum L.) (1981)

Mineral nutrition influenced the rate of cold acclimation and the level of hardiness attained by winter wheat plants grown in modified Hoagland’s solution. Plants grown in modified Hoagland’s solution at (a) one-half strength (control), (b) low potassium and (c) low phosphorus acclimated the fastest and were the hardiest. Plants grown in high and very high levels of nitrogen and a high level of phosphorus were the least hardy. For the acclimation period, significant correlation coefficients existed between the LT 50 and osmotic potential, crown moisture content and crown dry weight for all nutrient regimes. However, when differences due to nutrient regimes were considered, there were no significant correlations with LT 50 .
High efficacy of saliva in detecting SARS-CoV-2 by RT-PCR in adults and children (2020)

Abstract Background RT-PCR of nasopharyngeal swabs (NPS) is the acknowledged gold standard for the detection of SARS-CoV-2 infection. Rising demands for repetitive screens and mass-testing necessitate, however, the development of additional test strategies. Saliva may serve as an alternative to NPS as its collection is simple, non-invasive and amenable for mass- and home-testing but rigorous validation of saliva particularly in children is missing. Methods We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and nasopharyngeal swab (NPS) of 1270 adults and children reporting to outpatient test centers and an emergency unit for an initial SARS-CoV-2 screen. The saliva collection strategy developed utilizes common, low-cost plastic tubes, does not create biohazard waste at collection and was tailored for self-collection and suitability for children. Results In total, 273 individuals were tested SARS-CoV-2 positive in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (Overall Percent Agreement = 97.8%). Despite lower viral loads in saliva of both adults and children, detection of SARS-CoV-2 in saliva compared well to NPS (Positive Percent Agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (Positive Predictive Value = 84.8%), underlining that NPS sampling in children can be challenging. Conclusions The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2 with particular advantages for testing children that is readily applicable to increase and facilitate repetitive and mass-testing in adults and children. Article Summary Main Points Comparison with nasopharyngeal swabs in a large test center-based study confirms that saliva is a reliable and convenient material for the detection of SARS-CoV-2 by RT-PCR in adults and increases detection efficacy in children.
The Role of Crowdsourcing in the Emerging Internet-Of-Things (2017)

In this position paper we wish to propose and discuss several open research questions associated with the IoT. In particular, we wish to consider how crowdsourcing can be used as a scalable, reliable, and sustainable approach to support various computationally difficult and ambiguous tasks recognised in IoT research. We illustrate our work by examining a number of use cases related to healthcare and smart cities, and finally consider the future development of the IoT eco-system with respect to the socio-technical philosophy and implementation of the Web Observatory.
Purification, crystallization and preliminary X-ray diffraction analysis of the Kelch-like motif region of mouse Keap1 (2004)

Keap1 (Kelch-like ECH-associating protein 1) is a negative regulator of the Nrf2 transcription factor in the cytoplasm. The Kelch/DGR (double-glycine repeat) domain of Keap1 associates with Nrf2 as well as with actin filaments. A recombinant protein containing both the Kelch/DGR domain and the C-terminal region of mouse Keap1 was expressed in Escherichia coli, purified to near-homogeneity and crystallized by the sitting-drop vapour-diffusion method. The crystal belongs to space group P6(1) or P6(5), with unit-cell parameters a = b = 102.95, c = 55.21 A, and contains one molecule in the asymmetric unit. A complete diffraction data was collected to 2.25 A resolution using an R-AXIS IV++ imaging plate mounted on an RA-Micro7 Cu Kalpha rotating-anode X-ray generator.
A dual optic accommodating foldable intraocular lens (2003)

A dual optic intraocular lens design can increase the optical effect of a given displacement and suggests improvements for accommodating intraocular lenses.
p-Channel Ge MOSFET by Selectively Heteroepitaxially Grown Ge on Si (2009)

We successfully demonstrate Ge pMOSFET integrated on Si. In this process, Ge is grown selectively on Si on patterned SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> by heteroepitaxy, and pMOSFET is fabricated with gate dielectric stack consisting of thin GeO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and Al metal gate electrode. Fabricated devices show ~80% enhancement over the Si universal hole mobility. These results are promising toward monolithically integrating Ge MOSFETs with Si CMOS VLSI platform.
Cardioprotective 3′,4′-dihydroxyflavonol attenuation of JNK and p38MAPK signalling involves CaMKII inhibition (2013)

DiOHF (3',4'-dihydroxyflavonol) is cardioprotective against I/R (ischaemia/reperfusion) injury. The biological activities of flavonols are associated with kinase modulation to alter cell signalling. We thus investigated the effects of DiOHF on the activation of MAPKs (mitogen-activated protein kinases) that regulate the cardiac stress response. In an ovine model of I/R, JNK (c-Jun N-terminal kinase), p38(MAPK), ERK (extracellular-signal-regulated kinase) and Akt were activated, and NP202, a pro-drug of DiOHF, reduced infarct size and inhibited JNK and p38(MAPK) activation, whereas ERK and Akt phosphorylation were unaltered. Similarly, in cultured myoblasts, DiOHF pre-treatment preserved viability and inhibited activation of JNK and p38(MAPK), but not ERK in response to acute oxidative and chemotoxic stress. Furthermore, DiOHF prevented stress-activation of the direct upstream regulators MKK4/7 (MAPK kinase 4/7) and MKK3/6 respectively. We utilized small-molecule affinity purification and identified CaMKII (Ca(2+)/calmodulin-dependent protein kinase II) as a kinase targeted by DiOHF and demonstrated potent CaMKII inhibition by DiOHF in vitro. Moreover, the specific inhibition of CaMKII with KN-93, but not KN-92, prevented oxidative stress-induced activation of JNK and p38(MAPK). The present study indicates DiOHF inhibition of CaMKII and attenuation of MKK3/6→p38(MAPK) and MKK4/7→JNK signalling as a requirement for the protective effects of DiOHF against stress stimuli and myocardial I/R injury.
Computer Science and Biology: An Unlikely Pair (2002)

from the first installment (IEEE Intelligent Systems, Nov./Dec. 2001, vol. 16, no. 6) to this second one, and several accepted manuscripts will spill over to future issues of IEEE Intelligent Systems. This outstanding community support reflects the interest and excitement that permeates the field. In a very real and immediate sense, our biomedical colleagues today are running the experiments and generating the data that will unlock the deepest secrets of biology and medicine. As indicated by the cover illustration and its image of harvesting the fruits of knowledge, intelligent systems will play a crucial role in transforming these into tangible biomedical benefits that will improve the lot of all mankind. To some, there is a deep irony in the fact that computational intelligence has such a crucial role in the understanding of life. Computer science and biology are, at first blush, an unlikely pairing: abstract, symbolic–numeric computation and wet, evolved living things. But the depth of the relationship between computing and life has only begun to be plumbed, and already the marriage has changed both fields forever. One day, the relationship between biology and computer science might be seen to be as deep and abiding as the relationship between mathematics and physics.
The Crucible in its time (1991)

It has sometimes been assumed that The Crucible emerged directly and solely from the McCarthy hysteria of the USA in the 1950s: this is untrue, for Miller had long been fascinated by the witch-trials of Puritan Massachusetts in the seventeenth century. But there is equally no doubt that 'McCarthyism', as it came to be called, resurrected his interests and directed them to a dramatic gesture, especially when he became personally involved. A little generalized background information may thus be useful.KeywordsWalk AwayReligious PersecutionDrama CompetitionLoyalty OathTrade Union OfficialThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Exon skipping through the creation of a putative exonic splicing silencer as a consequence of the cystic fibrosis mutation R553X (2007)

Nonsense mutations that occur more than 50 bases upstream of terminal spliced junctions are generally thought to lead to degradation of the corresponding transcripts by the process of nonsense-mediated mRNA decay. It has also been proposed that some nonsense mutations may affect splicing by the process of nonsense-associated altered splicing (NAS), or by the disruption of a splicing regulatory element. In this study, the effect of the R553X mutation on the splicing of exon 11 of the cystic fibrosis transmembrane conductance regulator gene was investigated. Evidence that R553X causes exon 11 to skip through the creation of a putative exonic splicing silencer (ESS) was provided. The putative ESS appears to be active when located immediately upstream of a 5' splice site. These findings argue against the possibility that R553X-associated exon 11 skipping is caused by NAS. The study further suggests that aminoglycoside antibiotic treatment would not be effective for patients with the R553X mutation, owing to the skipping of exon 11, and further emphasises the need for detailed mechanistic characterisation of the consequences of nonsense disease mutations.
Controlled depolymerisation assessed by analytical ultracentrifugation of low molecular weight chitosan for use in archaeological conservation (2018)

The heterogeneity and molecular weight of a chitosan of low molecular weight (molar mass) and low degree of acetylation (0.1) for potential use as a consolidant for decayed archaeological wood were examined by sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge before and after depolymerisation. Sedimentation velocity before depolymerisation revealed a uniform distribution of sedimentation coefficient with little concentration dependence. SEDFIT-MSTAR analysis revealed a weight average molecular weight M<sub>w</sub> of (14.2 ± 1.2) kDa, and polydispersity index of ~ 1.2. Further analysis using MULTISIG revealed a distribution of material between 2 and 20 kDa and consistent with the weight average M<sub>w</sub>. Controlled depolymerisation using hydrogen peroxide and ultra-violet radiation in an acetic acid medium reduced this to (4.9 ± 0.7) kDa, with a similar polydispersity. The depolymerised material appears to be within the range that has been predicted to fully penetrate into archaeological wood. The consequences for this finding and the use of the analytical ultracentrifuge in wood conservation strategies are considered.
Use of prototype two-channel endoscope with elevator enables larger lift-and-snare endoscopic mucosal resection in a porcine model (2014)

The increased lift of the mucosal epithelium, through use of the dual-channel elevator scope, allows for larger EMR when using a lift-grasp-cut technique. Noting the thin nature of the porcine colonic wall, use of the elevator may also make this technique safer.