gebhart/patrepeval huggingface dataset:
Dual Templating for AFX/LEV Intergrowth Zeolite (2021)

Abstract Zeolite composed of an intergrowth structure based on AFX and LEV framework types was successfully synthesized by dual-templating strategy using 1,1′-(1,4-butanediyl)bis(1-azonia-4-azabicyclo[2,2,2]octane) and dimethylpiperidinium hydroxides. DIFFaX simulation and 13C NMR results indicated that the AFX framework-type is the main component of the intergrowth structure. The intergrowth material obtained was characterized using XRD, SEM, 27Al and 29Si NMR, and N2 adsorption measurements.
User-Centered Evaluation of an Augmented Reality-based Assistance System for Maintenance (2020)

Mobile Augmented Reality solutions are a promising technology for supporting service technicians in maintenance. The possibilities of augmenting the technicians’ field of vision with virtual information are confronted with the challenges of new forms of interaction and thus changing requirements for the design of user interfaces compared to desktop applications. The optimal interaction between humans and technology remains the decisive criterion for the development of usable interactive systems. Therefore, we have conducted a user-centered evaluation study in this paper and collected both quantitative and qualitative data. In two consecutive laboratory studies and a final field study we could show that user participation has a significant impact on the usability of the developed AR-based assistance system for the maintenance of heating, air conditioning, and cooling systems.
On the Way to Glycoprocessing Inhibitors − Synthesis of an Imidazolo‐Nectrisine‐Phosphono Acid Derivative: A Potential Glycosyltranferase Inhibitor (2003)

Abstract Assuming the transition state of glycosyltransferase inhibitors to be similar to those encountered with potent glycosidase inhibitors − i.e. a flattened conformation with a positively charged anomeric centre − we worked out a synthesis of the D ‐ arabino ‐configured phosphonic acid target molecule 2 derived from an imidazolo‐sugar. The key synthetic intermediate is the linear imidazolo L ‐ xylo compound 10 which could be obtained, either from L ‐ threo precursor 6 by a coupling reaction with imidazole derivative 5 , or from L ‐sorbose. A multi‐step and site specific iodination of 10 gave the mono‐iodo‐ L ‐ xylo derivative 14 which was cyclised to the D ‐ arabino ‐configured bicyclic azasugar 15 . Phosphorylation of the Grignard derivative of the latter, followed by mono‐esterification with citronellol along with some protection‐deprotection steps led to target molecule 2 . The potential inhibitor 2 is supposed to be protonated at its most basic N atom by a carboxylic acid residue in the arabinosyl‐transferase active site. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Accounting for Elastic Energy Storage in McKibben Artificial Muscle Actuators (1998)

The McKibben artificial muscle is a pneumatic actuator whose properties include a very high force to weight ratio. This characteristic makes it very attractive for a wide range of applications such as mobile robots and prosthetic appliances for the disabled. In this paper, we present a model that includes a nonlinear, Mooney–Rivlin mathematical description of the actuator’s internal bladder. Experimental results show that the model provides improvement in the ability to predict the actuator’s output force. However, a discrepancy between model and experiment, albeit smaller than previous models, still exists. A number of factors are identified that may be responsible for this discrepancy. [S0022-0434(00)00902-3]
Nickel-rich Nickel Manganese Cobalt (NMC622) Cathode Lithiation Mechanism and Extended Cycling Effects Using Operando X-ray Absorption Spectroscopy (2020)

Ni-rich NMC materials are a particularly promising class of Li-ion cathodes for various applications. LiNi0.6Mn0.2Co0.2O2 (NMC622) offers a unique balance of thermal stability and energy density, thus attracting attention for electric vehicle implementation. However, upon extended cycling, capacity fade is prevalent due to structural degradation, which is a major drawback for layered oxide cathodes. Therefore, exploring the underlying phenomena that drive detrimental structural response can lead to future improvements. For the first time, operando X-ray absorption spectroscopy (XAS) was performed on NMC622 pouch cells at three different stages. An extensive description of the first cycle (de)lithiation mechanisms was achieved through X-ray absorption near-edge structure analyses and extended X-ray absorption fine structure modeling. Transition metal specific electrochemical participation and structural variation revealed that much of the delivered capacity and distortion is a result of Ni redox behavior, while the local structure of Co and Mn are impacted due to their interdependencies. Key mechanistic components were identified, as the local structural variation from redox processes and Ni3+ Jahn–Teller distortion were decoupled. Further, operando XAS was used to investigate the structural response of NMC622 to extended cycling and was supported by X-ray diffraction, X-ray photoelectron spectroscopy, and electrochemical impedance spectroscopy analyses. Reduced capacity was found in the cell after 100 cycles and is attributed to structural degradation and cathode–electrolyte interphase buildup from repeated Li (de)insertion processes, which limit the electrochemical reversibility of Ni and Co through increased polarization. These results expand the understanding of a Ni-rich NMC material under extended cycling, which is vital to the future design of electrode materials.
Figure S1-S8 from Chemogenomic Landscape of <i>RUNX1</i>-mutated AML Reveals Importance of <i>RUNX1</i> Allele Dosage in Genetics and Glucocorticoid Sensitivity (2023)

&lt;p&gt;Supplementary Figure 1. Additional examples of genes most correlated (&gt; 0.50 or &lt;-0.50) to RUNX1 mutation type and VAF, as described in Figure 2C. Supplementary Figure 2. (a) Waterfall plot showing Pearson correlation coefficients calculated between all compounds tested in viability screen (n=5,068) and Dexamethasone. Supplementary Figure 3. Dose response curves for Flumethasone (Flu), representative of the Glucocorticoid cluster, for RUNX1mut and RUNX1wt specimens. Supplementary Figure 4. Heat map showing response profile of 32 AML cell lines to compounds of the GC cluster (n=24) and 6-thioguanine. Supplementary Figure 5. Response to GC Mometasone Furoate (MF) observed in Kasumi-1 and OCI-AML3 cells in the presence of increasing concentrations of GR full antagonist RU486. Supplementary Figure 6. (a) Infection of OCI-AML3 cells with shRNAs targeting NR3C1 (sh1 to sh4) and assessment of GR knockdown efficiency in GFP+ sorted cells by western blotting. Supplementary Figure 7. (a) Top. Expression profile of lymphoid markers and of the NR3C1 gene (encoding the GR) in AML specimens of the Leucegene cohort. Supplementary Figure 8. (a) Dose response curves and associated IC50s for Flumethasone (Flu) and Budesonide (Bude) upon RUNX1 knockdown in OCI-AML5 cells.&lt;/p&gt;
Sh-Lie algebras Induced by Gauge Transformations (2000)

The physics of ``particles of spin $\leq 2$'' leads to representations of a Lie algebra $Ξ$ of gauge parameters on a vector space $Φ$ of fields. Attempts to develop an analogous theory for spin $&gt;2$ have failed; in fact, there are claims that such a theory is impossible (though we have been unable to determine the hypotheses for such a `no-go' theorem). This led BBvD [burgers:diss,BBvd:three,BBvD:probs] to generalize to `field dependent parameters' in a setting where some analysis in terms of smooth functions is possible. Having recognized the resulting structure as that of an sh-lie algebra ($L_\infty$-algebra), we have now reproduced their structure entirely algebraically, hopefully shedding some light on what is going on.
A Spectrometer for Dynamic Nuclear Polarization and Electron Paramagnetic Resonance at High Frequencies (1995)

A high-frequency dynamic nuclear polarization (DNP)/electron paramagnetic resonance spectrometer operating at 211 MHz for1H and 140 GHz forg= 2 paramagnetic centers (5 T static field) is described. The salient feature of the instrument is a cyclotron-resonance maser (gyrotron) which generates high-frequency, high-power microwave radiation. This gyrotron, which under conventional operation produces millisecond pulses at kilowatt powers, has been adapted to operate at ∼100 W for 1 to 20 s pulses and in the continuous wave mode at the 10 W power level. Experiments combining DNP with magic-angle spinning (MAS) nuclear magnetic resonance were performed on samples consisting of 2% by weight of the free radical BDPA doped into polystyrene. Room-temperature DNP enhancement factors of 10 for1H and 40 for13C were obtained in the NMR-MAS spectra. Static DNP NMR has also been performed on samples containing nitroxides dissolved in water:glycerol solvent mixtures. Enhancements of approximately 200 have been obtained for low-temperature (14 K)1H NMR. A pulsed/CW EPR spectrometer operating at 140 GHz has been developed in conjunction with the DNP spectrometer. Microwave sources include Gunn-diode oscillators which provide low-power (20 mW) radiation, and the gyrotron, which has been used to deliver higher power levels in pulsed experiments. Results using this spectrometer are presented for continuous-wave and echo-detected EPR, electron spin-echo-envelope modulation (ESEEM), and Fourier-transform EPR.
Electronic transitions in a SimGen strained monolayer superlattice measured by photoreflectance (1990)

The first photoreflectance spectrum from a short-period strain-symmetrized SimGen superlattice has been measured at 87 K. Fifteen electronic transitions were measured between 1.1 and 2.7 eV and fit well to a third derivative functional form. Most of the transition energies were calculated using a one-band envelope-function model, adding strain and spin orbit shifts as first-order corrections. Additional transitions were observed near the expected interband energies in an unstrained Si0.2Ge0.8 random alloy. All of the calculated transition energies were found to agree to within 80 meV of the measured values.
Solving constraints on the invisible bits of the intermediate result for floating-point verification (2005)

Test generation for datapath floating-point verification involves targeting intricate corner cases, which can often be solved only through complex constraint solving. In the process of calculating the result, we use an intermediate result whose significand comprises a finite number of bits and a sticky bit that is 0 if and only if the intermediate result is exact. We refer to all the bits beyond those represented in the final result as the invisible bits. We deal with corner cases that can only be defined via constraints on the intermediate result. Our work investigates the following problem: given a floating-point operation, and constraints on the invisible bits and the sticky bit, find two inputs for the operation that yield an intermediate result compatible with the constraints. The paper supplies a deterministic solution for addition and subtraction, and probabilistic solutions for multiplication and division. It also discusses the application of these algorithms to the verification of floating-point implementations.
The transient effect of jasmonic acid feeding along with ORCA3 overexpression in catharanthus roseus hairy roots (2006)

Jasmonic acid is an important signaling molecule in plants that regulates a wide variety of cellular responses including the responses to abiotic and biotic stresses. The external application of jasmonic acid has been shown to increase the accumulation of the monomeric terpenoid indole alkaloids, TIAs, in Catharanthus roseus seedlings and hairy root cultures (1-3). Jasmonic acid regulates the expression of the ORCA3 (Octadecanoid-Responsive Catharanthus AP2/ERF-domain) transcription factor (4). The overexpression of ORCA3 in C. roseus cell suspension cultures resulted in an increase of the mRNA levels of the following TIA biosynthetic genes: anthranilate synthase, ASα, tryptophan decarboxylase, TDC, 1-deoxy-Dxylulose synthase, DXS, NADPH:cytochrome P-450 reductase, CPR, secologanin synthase, SLS, strictosidine synthase, STR, strictosidine beta-glucosidase, SGD, and desacetoxyvindoline 4-hydroxylase, D4H (5). The accumulation of mRNA transcripts did not result in an increase in TIA compounds which could be explained by the lack of an observed increase in the transcripts of geraniol 10 hydroxylase, G10H, and deacetyl vindoline 4-O-acetyl transferase, DAT (5).
Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5′-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies (1989)

1H- and 31P-n.m.r. spectroscopy were used to characterize the solution structure of the 1:1 complex formed between the antitumour antibiotic luzopeptin and the self-complementary hexanucleotide d(5'-GCATGC)2. Eighteen nuclear Overhauser effects between antibiotic and nucleotide protons, together with ring-current-induced perturbations to base-pair and quinoline 1H resonances, define the position and orientation of the bound drug molecule. Luzopeptin binds in the minor groove of the DNA with full retention of dyad symmetry, its quinoline chromophores intercalating at the 5'-CpA and 5'-TpG steps and its depsipeptide ring spanning the central two A.T base-pairs. The chromophores stack principally on the adenine base with their carbocyclic rings pointing towards the deoxyribose of the cytosine. There is no evidence for Hoogsteen base-pairing in the complex, all glycosidic bond angles and sugar puckers being typical of B-DNA as found for the free hexanucleotide. The 'breathing' motions of the A.T and internal G.C base-pairs are substantially slowed in the complex compared with the free DNA, and the observation that two phosphate resonances are shifted downfield by at least 0.5 p.p.m. in the 31P-n.m.r. spectrum of the complex suggests pronounced local helix unwinding at the intercalation sites. The data are consistent with a model of the complex in which luzopeptin bisintercalates with its depsipeptide essentially in the conformation found in the crystal of the free antibiotic [Arnold & Clardy (1981) J. Am. Chem. Soc. 103, 1243-1244]. We postulate only one conformational change within the peptide ring, which involves rotation of the pyridazine-glycine amide group linkage by 90 degrees towards the DNA surface. This manoeuvre breaks the glycine-to-glycine transannular hydrogen bonds and enables the glycine NH groups to bond to the thymine O-2 atoms of the sandwiched A.T base-pairs. It also shortens the major axis of the depsipeptide so that the interchromophore distance is more suitable for spanning two base-pairs. The model further implies that the carboxy and hydroxy groups of the L-beta-hydroxyvaline residue are appropriately positioned for hydrogen-bonding to the 2-amino group of guanine and the O-2 atom of cytosine of the adjacent G.C base-pair.
Recent developments in modeling and measuring scattering from trabecular bone (2008)

Laboratories at the US Food and Drug Administration, the University of Paris and elsewhere have investigated scattering from trabecular bone. Recent analysis of data from 23 human femur samples in vitro suggests that the Faran Cylinder Model and the Weak Scattering Model accurately predict frequency dependence of backscatter coefficient. Shear mode conversion of incident longitudinal waves may be a significant source of scattering loss. Other recent work involves the effect of errors of attenuation measurements on backscatter coefficient estimates. Backscatter measurements must be compensated for attenuation in order to estimate backscatter coefficient. However, attenuation is often overestimated because it is often measured using phase sensitive receivers that exhibit phase cancellation artifacts. Recent analysis of data from 16 human calcaneus samples in vitro suggests that backscatter coefficient estimates that are based on phase sensitive attenuation compensation tend to overestimate 1) average magnitude of backscatter coefficient at 500 kHz by a factor of about 1.6 ± 0.3 (mean ± standard deviation) and 2) average exponent (n) of frequency dependence by about 0.34 ± 0.12 (where backscatter coefficient is assumed to be proportional to frequency to the nth power).
Clinical Characteristics and Surgical Outcomes of Patients Presenting With Meningiomas Arising Predominantly From the Floor of the Middle Fossa (2010)

We present the clinical characteristics and surgical outcome of a series of patients presenting with meningiomas primarily arising from the concave floor of the middle cranial fossa. Given the relatively uncommon nature of these lesions, more investigation into the clinical behavior of this entity is warranted.
THz Hyperspectral Images Analyzed by Multivariate Statistical Methods (2018)

Images recorded using Terahertz Time-Domain Spectroscopy contain huge amounts of data, of which only a part may contain chemical and structural information. Using powerful hyperspectral image analysis, we extract both information efficiently.
Giant induced magnetic anisotropy In strain annealed Co-based nanocomposite alloys (2012)

Low loss switching of soft magnetic materials at high frequencies benefits from tuning the induced anisotropy. We show induced anisotropies,K<sub>u</sub>, as large as 1.89×10<sup>4</sup> J/m<sup>3</sup>, developed by strain annealing of Co-rich nanocompositealloys. Crystalline phases in this alloy system have large negative magnetostrictive coefficients, leading to anisotropy fields per unit stress over twice those developed in FINEMET. Tunable permeability and reduced thicknesses achieved in this process can mitigate eddy-current losses. Giant induced magnetic anisotropies are discussed in light of models for the micromechanisms of amorphous metal deformation, stress-assisted transformations in the crystallites, and directional pair ordering.
Electron Tomography of Gold Nanoparticles in Titania Composite Aerogels: Probing Structure to Understand Photochemistry (2013)

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
PDZ Domain-Mediated Interactions of G Protein-Coupled Receptors with Postsynaptic Density Protein 95: Quantitative Characterization of Interactions (2013)

G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome. Their signaling is regulated by scaffold proteins containing PDZ domains, but although these interactions are important for GPCR function, they are still poorly understood. We here present a quantitative characterization of the kinetics and affinity of interactions between GPCRs and one of the best characterized PDZ scaffold proteins, postsynaptic density protein 95 (PSD-95), using fluorescence polarization (FP) and surface plasmon resonance (SPR). By comparing these in vitro findings with colocalization of the full-length proteins in cells and with previous studies, we suggest that the range of relevant interactions might extend to interactions with K i = 450 mM in the in vitro assays. Within this range, we identify novel PSD-95 interactions with the chemokine receptor CXCR2, the neuropeptide Y receptor Y 2 , and four of the somatostatin receptors (SSTRs). The interaction with SSTR1 was further investigated in mouse hippocampal neurons, where we found a clear colocalization between the endogenously expressed proteins, indicating a potential for further investigation of the role of this interaction. The approach can easily be transferred to other receptors and scaffold proteins and this could help accelerate the discovery and quantitative characterization of GPCR-PDZ interactions.
Mucosal immunization with a delta-inulin adjuvanted recombinant spike vaccine elicits lung-resident immune memory and protects mice against SARS-CoV-2 (2022)

Multiple SARS-CoV-2 vaccine candidates have been approved for use and have had a major impact on the COVID-19 pandemic. There remains, however, a significant need for vaccines that are safe, easily transportable and protective against infection, as well as disease. Mucosal vaccination is favored for its ability to induce immune memory at the site of infection, making it appealing for SARS-CoV-2 vaccine strategies. In this study we performed in-depth analysis of the immune responses in mice to a subunit recombinant spike protein vaccine formulated with the delta-inulin adjuvant Advax when administered intratracheally (IT), versus intramuscular delivery (IM). Both routes produced robust neutralizing antibody titers (NAb) and generated sterilizing immunity against SARS-CoV-2. IT delivery, however, produced significantly higher systemic and lung-local NAb that resisted waning up to six months post vaccination, and only IT delivery generated inducible bronchus-associated lymphoid tissue (iBALT), a site of lymphocyte antigen presentation and proliferation. This was coupled with robust and long-lasting lung tissue-resident memory CD4<sup>+</sup> and CD8<sup>+</sup> T cells that were not observed in IM-vaccinated mice. This study provides a detailed view of the lung-resident cellular response to IT vaccination against SARS-CoV-2 and demonstrates the importance of delivery site selection in the development of vaccine candidates.
Monitoring response to therapy in melanoma by quantifying circulating tumour DNA with droplet digital PCR for BRAF and NRAS mutations (2015)

We assessed the utility of droplet digital PCR (ddPCR) to evaluate the potential of using circulating tumour DNA (ctDNA) as a post therapy monitoring tool in melanoma by comparing it to serum LDH levels and RECIST scores. ddPCR was shown to be reliable in distinguishing mutant from wild type alleles with no false positives. Subsequently, we quantified ctDNA ((V600E)BRAF,(V600K)BRAF or (Q61H)NRAS) in 6 stage IV melanoma patients across several time points during their treatment course. All tested patients had detectable ctDNA, which exhibited dynamic changes corresponding to the changes in their disease status. The ctDNA levels fell upon treatment response and rose with detectable disease progression. In our group of patients, ctDNA was more consistent and informative than LDH as a blood-based biomarker. In addition, BRAF mutant ctDNA as detected by ddPCR could be used diagnostically where the tumour block was unavailable. In conclusion, this study demonstrates the applicability of using ddPCR to detect and quantify ctDNA in the plasma of melanoma patients.
6-Aryl-8H-indeno[1,2-d]thiazol-2-ylamines:  A1 Adenosine Receptor Agonist Allosteric Enhancers Having Improved Potency (2005)

Allosteric enhancers (AEs) of the A(1) adenosine receptor (A(1)AR) have potential as drugs for treating neurological, cardiovascular, and renal diseases. This report describes the synthesis and evaluation of a series of 6-aryl-8H-indeno[1,2-d]thiazol-2-ylamines that exhibited AE activity at the A(1)AR. Palladium-mediated condensation of arylboronic acids with 5-bromoindan-1-one generated arylindanones 2a-aj for iodine-catalyzed condensation with thiourea, generating 2-aminothiazolium salts 3a-aj. Binding studies using membranes from cells stably expressing human A(1)ARs, A(2A)ARs, or A(3)ARs evaluated AE activity and receptor subtype selectivity. The EC(50) of the AE activities of compounds 3m-o, 3x, and 3ae were 2.2, 1.5, 0.9, 1.0, and 3.0 muM, respectively, substantially lower than that of the well characterized 2-amino-3-aroylthiophene (PD 81,723), >10 microM. The new compounds also have substantially higher maximal AE activity. These compounds had no AE activity at the A(2A)AR and only minimal activity at the A(3)AR.
Concept neighbourhoods in knowledge organisation systems. (2010)

Abstract. This paper discusses the application of concept neighbourhoods (in the sense of Formal Concept Analysis) to Knowledge Organisation Systems. Examples are provided using Roget’s Thesaurus, WordNet and Wikipedia categories. 1