gebhart/patrepeval huggingface dataset:
2D NMR-Based Metabolomics Uncovers Interactions between Conserved Biochemical Pathways in the Model OrganismCaenorhabditis elegans (2012)

Ascarosides are small-molecule signals that play a central role in C. elegans biology, including dauer formation, aging, and social behaviors, but many aspects of their biosynthesis remain unknown. Using automated 2D NMR-based comparative metabolomics, we identified ascaroside ethanolamides as shunt metabolites in C. elegans mutants of daf-22, a gene with homology to mammalian 3-ketoacyl-CoA thiolases predicted to function in conserved peroxisomal lipid β-oxidation. Two groups of ethanolamides feature β-keto functionalization confirming the predicted role of daf-22 in ascaroside biosynthesis, whereas α-methyl substitution points to unexpected inclusion of methylmalonate at a late stage in the biosynthesis of long-chain fatty acids in C. elegans. We show that ascaroside ethanolamide formation in response to defects in daf-22 and other peroxisomal genes is associated with severe depletion of endocannabinoid pools. These results indicate unexpected interaction between peroxisomal lipid β-oxidation and the biosynthesis of endocannabinoids, which are major regulators of lifespan in C. elegans. Our study demonstrates the utility of unbiased comparative metabolomics for investigating biochemical networks in metazoans.
Rearrangement During Sintering in Two‐Dimensional Arrays (1986)

Densification of two‐dimensional arrays of nearly monosized copper spheres was examined by hot‐stage optical microscopy. The evolution of the particle arrangement was studied with computer methods, and statistical correlations were sought. Color graphics were found useful for displaying the spatial relationship of the local sintering parameters. It was found that differential densification was the major cause of rearrangement, rather than asymmetric neck formation.
Quality-of-Life Change Associated With Robotic-Assisted Therapy to Improve Hand Motor Function in Patients With Subacute Stroke: A Randomized Clinical Trial (2010)

Robotic-assisted therapy may be an effective alternative or adjunct to the delivery of intensive task practice interventions to enhance hand function recovery in patients with stroke.
An Unusual Pathway to Cyclobutane Formation via Desulfurative Intramolecular Photocycloaddition of an Enone Benzothiazoline Pair (2009)

Irradiation of the enone benzothiazoline 3 leads to the formation of cyclobutane 5. Preliminary mechanistic studies establish the intermediacy of an enecarbamate 14 in this photochemical transformation, which could be the result of sulfur extrusion from an episulfide intermediate. Photocycloaddition of the enecarbamate intermediate 14 leads to the formation of "crossed" photoadducts, i.e., 5, in excellent yield, with high levels of regio- and stereochemical control.
Enhancing Thin Dielectric Remaining Detection Under Polysilico Plug of Advanced DRAM by Electron Beam Inspection ISSM Paper: YE-P-022 (2007)

We’ve studied using negative mode e-beam inspection (EBI) to detect a thin layer of dielectric remain at the bottom of storage node contact (SNC) hole. A thin layer (~15 nm) of nitride at the bottom of some SNC holes was intentionally created, EBI were performed at two stages: post etch clean and after silicon nitride cap of SNC plug. Negative mode EBI after SNC nitride cap deposition successfully captured these contact open defects as bright voltage contrast (BVC) defects. The cross-section scanning electron microscope (SEM) confirmed the results. The inspection mechanism is also discussed in the paper. We found that negative mode EBI is very useful for in-line defect monitoring.
Immunization of mice withLactobacillus caseiexpressing intimin fragments produces antibodies able to inhibit the adhesion of enteropathogenicEscherichia colito cultivated epithelial cells (2008)

Enteropathogenic Escherichia coli (EPEC) are frequently isolated as a cause of infantile diarrhea in developing countries. Its pathogenicity is distinguished by histopathological alterations at the site of infection, known as attaching and effacing (A/E) lesions, in which bacterial virulence factors and host proteins participate. Intimin, a bacterial adhesin expressed by all EPEC described to date, is responsible for the intimate adherence of the bacteria to host cells and is essential for the formation of A/E lesions. Mucosal vaccination may represent an efficacious intervention to prevent EPEC infection and lower morbidity and mortality rates. Strategies for mucosal vaccinations that use lactic acid bacteria for the delivery of heterologous antigens rely on their safety profile and ability to stimulate the immune system. In the present work, we have constructed Lactobacillus casei strains expressing different fragments of intimin beta, a subtype that is frequently expressed by EPEC strains. Mucosal immunization of mice with L. casei expressing intimin fragments induced specific systemic and mucosal antibodies. These antibodies were able to recognize native intimin on the surface of EPEC and to inhibit in vitro EPEC binding to epithelial cells.
Photoacoustic determination of the optical absorptance of highly transparent solids (1978)

A photoacoustic method has been applied to the quantitative measurement of optical absorption at 10.6 μm in coated and uncoated alkali halide samples having a spatially varying optical absorption. Photoacoustic signals were measured as a function of the chopping frequency of a CO2 laser source. The dependence of the signals on chopping frequency and an absolute electrical calibration of the cell were used to interpret the data. The results are in good agreement with laser calorimetry or infrared transmission measurements on the same samples. Signal fluctuations identified with thermal and source-coherence effects are reported and discussed. The experiments reported here confirm the utility of the photoacoustic technique in the general investigation of optical properties of highly transparent materials.
Temporally-Consistent Surface Reconstruction using Metrically-Consistent Atlases (2021)

We propose a method for unsupervised reconstruction of a temporally-consistent sequence of surfaces from a sequence of time-evolving point clouds. It yields dense and semantically meaningful correspondences between frames. We represent the reconstructed surfaces as atlases computed by a neural network, which enables us to establish correspondences between frames. The key to making these correspondences semantically meaningful is to guarantee that the metric tensors computed at corresponding points are as similar as possible. We have devised an optimization strategy that makes our method robust to noise and global motions, without a priori correspondences or pre-alignment steps. As a result, our approach outperforms state-of-the-art ones on several challenging datasets. The code is available at https://github.com/bednarikjan/temporally_coherent_surface_reconstruction.
Ligand Anatomy:  Probing Remote Substituent Effects in Asymmetric Catalysis through NMR and Kinetic Analysis (2006)

A series of structurally related beta-amino alcohols only differing in the steric bulk of a remote alkoxy group exhibit striking differences in kinetic behavior when used as ligands in the asymmetric diethylzinc addition to benzaldehyde (R = Trityl, much more active). A combination of NMR titration studies and kinetic analysis allows the quantitative decomposition of the remote substituent effect into a lower dimerization constant of the active species and a much faster ethyl addition step.
Thioether Profragrances: Parameters Influencing the Performance of Precursor‐Based Fragrance Delivery in Functional Perfumery (2014)

A series of thioether profragrances was prepared by reaction of different sulfanylalkanoates with δ-damascone and tested for their release efficiencies in a fabric-softener and an all-purpose cleaner application. Dynamic headspace analysis on dry cotton and on a ceramic plate revealed that the performance of the different precursors depended on the structure, but also on the particular conditions encountered in different applications. Moreover, profragrances derived from other α,β-unsaturated fragrance aldehydes and ketones were synthesized analogously and evaluated using the same test protocol. Thioethers were found to be suitable precursors to release the corresponding fragrances, but neither the quantity of profragrance deposited from an aqueous environment onto the target surface, nor the amount of fragrance released after deposition could be linearly correlated to the hydrophilicity or hydrophobicity of the compounds. Different sets of compounds were found to be the best performers for different types of applications. Only one of the compounds evaluated in the present work, namely the thiolactic acid derivative of δ-damascone, efficiently released the corresponding fragrance in both of the tested applications. Profragrance development for functional perfumery thus remains a partially empirical endeavour. More knowledge (and control) of the various application conditions are required for an efficient profragrance design.
CoScribe: Integrating Paper and Digital Documents for Collaborative Knowledge Work (2009)

This paper presents CoScribe, a concept and prototype system for the combined work with printed and digital documents, which supports a large variety of knowledge work settings. It integrates novel pen-and-paper-based interaction techniques that enable users to collaboratively annotate, link and tag both printed and digital documents. CoScribe provides for a very seamless integration of paper with the digital world, as the same digital pen and the same interactions can be used on paper and displays. As our second contribution, we present empirical results of three field studies on learning at universities. These motivated the design of CoScribe and were abstracted to a generic framework for the design of intuitive pen-and-paper user interfaces. The resulting interaction design comprising collaboration support and multiuser visualizations has been implemented and evaluated in user studies. The results indicate that CoScribe imposes only minimal overhead on traditional annotation processes and provides for a more efficient structuring and retrieval of documents.
TD-03 Convolutional neural networks identify in situ adaptive immune cell architectures in human lupus (2018)

<h3>Background</h3> Adaptive immunity is driven by antigen-restricted cell:cell interactions. In mice, two-photon excitation microscopy (TPEM) has revolutionized our understanding of immune cell architectures. However, TPEM has several limitations: most notably it can only be used to study manipulated animal model systems and not human disease. Previously, we demonstrated that by quantifying the distance between B cells and T cells in multichannel confocal images of human tissue (Cell Distance Mapping, CDM) we could identify cognate interactions. However, CDM used fixed filters and could not accurately capture cell shape. We postulated that this might be important as T cells adopt different shapes when scanning for antigen and after recognizing MHC class II-restricted peptides. <h3>Methods</h3> We implemented a deep convolutional neural network (DCNN) that accurately identified both cell position and shape. The DCNN output was then analyzed with a tuned convolutional neural network (TNN) to identify distance and cell shape features that best discriminated between different T cell populations relative to dendritic cells (DCs). We refer to this analysis pipeline as CDM<sup>3</sup>. <h3>Results</h3> In mice, CDM<sup>3</sup> discriminated between cognate and non-cognate T cell interactions with DCs with a sensitivity and specificity similar to most TPEM measures. In human lupus nephritis, CDM<sup>3</sup> both confirmed that myeloid DCs present antigen to CD4<sup>+</sup> T cells <i>in situ</i> and identified plasmacytoid DCs as an important antigen presenting cell in severe inflammation. <h3>Conclusions</h3> CDM<sup>3</sup> provides a novel tool for quantifying <i>in situ</i> adaptive immune cell networks broadly applicable to the study of human diseases including autoimmunity and cancer. <h3>Acknowledgements</h3> Funded by the NIH including the Autoimmunity Centers of Excellence.
FIXATION ABILITY OF CHLORIDE ION BY HARDENED CEMENT ADDED WITH CaO・2Al<sub>2</sub>O<sub>3</sub> (2010)

CaO・2Al2O3を混和した普通ポルトランドセメントを水和させると、セメント水和物としてCaO・2Al2O3・Ca（OH）2・12H2Oが多量に生成した。セメント中のCa（OH）2生成量はCaO・2Al2O3の混和が多いほど少なくなった。CaO・2Al2O3を混和し、水和させたセメント硬化体中のCa（OH）2量はCaO・2Al2O3混和量の増加に伴って減少した。CaO・2Al2O3を混和し、水和させたセメント硬化体中を塩水に浸漬すると、固定化塩化物イオン量は増加し、可溶性塩化物が占める割合が減少した。これは、フリーデル氏塩の生成による塩化物固定化の化学的な作用によると考察した。
Impedance spectroscopy of H and OH adsorption on stepped single-crystal platinum electrodes in alkaline and acidic media (2010)

The adsorption kinetics of hydrogen and hydroxyl on Pt(111) and stepped Pt[n(111) × (110)] electrodes with n = 29, 9, and 4 in acidic and alkaline electrolytes have been studied using impedance spectroscopy. We found a potential dependent charge transfer resistance, R(ct), (∼30 Ω cm(2) to ∼1 kΩ cm(2)) for hydrogen underpotential deposition in alkaline media (0.05 M NaOH), whereas in acidic media (0.025 M HClO(4)) R(ct) was too low to be determined accurately. Assuming simple (mean field) isotherms to fit our data, we obtain repulsive interactions between H(upd) at the (111) terrace and effective attractive interactions at the steps. The adsorption of OH on (111) terraces is fast in both acidic and alkaline media.
Canadian National Electrophysiology Ablation Registry Report 2011-2016 (2021)

Abstract Background/Purpose : Interventional cardiac electrophysiology (EP) is a rapidly evolving field in Canada; a nationwide registry was established in 2011 to conduct a periodic review of resource allocation. Methods: The registry collects annual data on EP lab infrastructure, imaging, tools, human resources, procedural volumes, success rates, and wait times. Leading physicians from each EP lab were contacted electronically; participation was voluntary. Results: All Canadian EP centres were identified (n=30); 50% and 45% of active centres participated in the last 2 instalments of the registry. A mean of 508±270 standard and complex catheter ablation procedures were reported annually for 2015-2016 by all responding centres. The most frequently performed ablation targets atrial fibrillation (PVI) arrhythmia accounting for 36% of all procedures (mean=164±85). The number of full time physicians ranges between 1 and 7 per centre, (mean=4). The mean wait time to see an electrophysiologist for an initial non-urgent consult is 23 weeks. The wait time between an EP consult and ablation date is 17.8 weeks for simple ablation, and 30.1 weeks for AF ablation. On average centres have 2 (range: 1-4) rooms equipped for ablations; each centre uses the EP lab an average of 7 shifts per week. While diagnostic studies and radiofrequency ablations are performed in all centres, point-by-point cryoablation is available in 85% centres; 38% of the respondents use circular ablation techniques. Conclusion: This initiative provides contemporary data on invasive electrophysiology lab practices. The EP registry provides activity benchmarks on national trends and practices.
PHOTOELECTRON SPECTRA OF 1,3-CYCLOHEXADIENE (2002)

The photoelectron spectra of 1,3-cyclohexadiene (CHD) have been investigated to probe the electrocyclic ring opening reaction in the gas phase. The molecules are ionized by exciting through the intermediate 1B2 state by ultraviolet femtosecond laser pulses. The observed features were explained based on two-photon and three-photon absorption processes. A doubly excited valence superexcited state is observed around 9eV. A detailed pump-probe experiment is underway to explore the dynamics of the observed superexcited state as well the isomerization reactions in CHD.
Enhancement of interleukin 1 and interleukin 2 releases by ubenimex. (1987)

The effect of ubenimex on the release of interleukin 1 (IL-1) and interleukin 2 (IL-2) from immuno-competent cells was studied. Ubenimex enhanced release of IL-1 from mouse peritoneal macrophages at 1.0 and 100 micrograms/ml in vitro and the release at 1.0 microgram/ml was larger. When ubenimex was administered to mice IL-1-releasing activity of the peritoneal macrophages was enhanced 3 and 5 days after the administration but not enhanced 1 day after the administration. Ubenimex also enhanced IL-2 release from rat spleen cells at 0.1 and 10 micrograms/ml, when concanavalin A (Con A) was added in the IL-2-releasing system. The enhancement was still observed with mouse spleen cells, when serum was further added. Moreover, thymocyte-proliferating activity was attained in the broths which rat spleen cells were incubated with ubenimex from 0.1 to 10 micrograms/ml in the absence and presence of Con A.
Interpretation of electron spin resonance parameters for transition metal complexes (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInterpretation of electron spin resonance parameters for transition metal complexesJeffrey I. Zink and Russell S. DragoCite this: J. Am. Chem. Soc. 1972, 94, 13, 4550–4554Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/ja00768a023https://doi.org/10.1021/ja00768a023research-articleACS PublicationsRequest reuse permissionsArticle Views163Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
COUNTING ELEMENTS IN THE SYMMETRIC GROUP (2009)

By using simple ideas from subgroup growth of pro-finite groups we deduce some combinatorial identities on generating functions counting various elements in symmetric groups.
A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence (2010)

Certain environmental microorganisms can cause severe human infections, even in the absence of an obvious requirement for transition through an animal host for replication ("accidental virulence"). To understand this process, we compared eleven isolate genomes of Burkholderia pseudomallei (Bp), a tropical soil microbe and causative agent of the human and animal disease melioidosis. We found evidence for the existence of several new genes in the Bp reference genome, identifying 282 novel genes supported by at least two independent lines of supporting evidence (mRNA transcripts, database homologs, and presence of ribosomal binding sites) and 81 novel genes supported by all three lines. Within the Bp core genome, 211 genes exhibited significant levels of positive selection (4.5%), distributed across many cellular pathways including carbohydrate and secondary metabolism. Functional experiments revealed that certain positively selected genes might enhance mammalian virulence by interacting with host cellular pathways or utilizing host nutrients. Evolutionary modifications improving Bp environmental fitness may thus have indirectly facilitated the ability of Bp to colonize and survive in mammalian hosts. These findings improve our understanding of the pathogenesis of melioidosis, and establish Bp as a model system for studying the genetics of accidental virulence.
Multilayered Magnetic Gelatin Membrane Scaffolds (2015)

A versatile approach for the design and fabrication of multilayer magnetic scaffolds with tunable magnetic gradients is described. Multilayer magnetic gelatin membrane scaffolds with intrinsic magnetic gradients were designed to encapsulate magnetized bioagents under an externally applied magnetic field for use in magnetic-field-assisted tissue engineering. The temperature of the individual membranes increased up to 43.7 °C under an applied oscillating magnetic field for 70 s by magnetic hyperthermia, enabling the possibility of inducing a thermal gradient inside the final 3D multilayer magnetic scaffolds. On the basis of finite element method simulations, magnetic gelatin membranes with different concentrations of magnetic nanoparticles were assembled into 3D multilayered scaffolds. A magnetic-gradient-controlled distribution of magnetically labeled stem cells was demonstrated in vitro. This magnetic biomaterial-magnetic cell strategy can be expanded to a number of different magnetic biomaterials for various tissue engineering applications.
Origins of the Scalp-Recorded Frequency-Following Response in the Cat (1979)

The frequency-following response (FFR) is a short-latency scalp-recorded evoked potential elicited by the presentation of low-frequency acoustic stimuli. It is thought to be the result of the synchronous electrical activity in brain stemauditory nuclei to each wave in the acoustic signal. The present investigation constitutes an attempt to determine the generators of the FFR in the cat by analysis of the response and by section of brain stem auditory nuclei and tracts. Among the results were the following: (1) the cochlear nuclei contribute approximately 50% of the amplitude of the scalp-recordedFFR in the cat. (2) The cochlea also makes a significant contribution, accounting for an average of nearly 25% of the response amplitude. (3) The superior olivary nuclei (and/or the nuclei of the lateral lemnisci) account for about 20% of the response amplitude. (4) The contributions from the inferior colliculi (contrary to earlier studies) were found to be relatively insignificant. (5) As a consequence of the existence of multiple generators, the FFR ample area of hair cell excitation for each stimulus frequency involved in the mediation of the FFR, suggestion that scalp-recorded FFRs could be used to ascertain low-frequency hearingsensitivity in uncooperative human subjects.
Commentary: Landmark articles on copper in the field of human health (2001)

In deciding on an appropriate paper for this topic, we had to first choose between copper deficiency and copper toxicity. Copper deficiency is a common problem in some animals species, but is rare in the human. It occasionally occurs on a dietary basis, bowel surgery basis, or overtreatment with anticopper drugs. It is also a major clinical problem in the rare inherited condition, Menke's disease. Progress has been made in the understanding of Menke's disease, particularly with the cloning of the gene responsible, known as ATP7A [1-3]. Thus, a landmark article could have reasonably been selected from the Menke's disease area.
Virtual focus of a ray data source (2023)

Ray data files are a common way to model light sources, such as light emitting diodes (LEDs), in optical design software. Often, when an LED shall be placed at the focal point of a collimating lens, it is desirable to know the coordinates of just a single point, which is representative of the light source location, similar to the center of mass for a distribution of matter. In some communities, this point is known as the “virtual focus,” and some LED vendors publish the virtual focus coordinates with their ray data sources. However, it is hard to find a clear and precise definition of the virtual focus, and it is not clear how it can be computed in an efficient way. We explain our definition and provide an efficient algorithm and its MATLAB® implementation.