gebhart/patrepeval huggingface dataset:
Aporphines: 25—Trimethylsilyl derivatives ofN-methyl andN-propyl aporphines: Gas chromatographic and mass spectrometric properties (1979)

A series of synthetic, semisynthetic and naturally occurring aporphine alkaloids were converted to the O-trimethylsilyl derivatives, and analyzed by gas chromatography mass spectrometry. A discussion of structurally informative fragment ions along with gas chromatographic data is presented. Their applicability to the analysis of biological metabolites of apomorphine, a CNS active structural analog of dopamine, is discussed.
A Search for Reliable Molecular Markers of Prognosis in Prostate Cancer (2012)

Most prostate cancers are treated, although more than 80% remain clinically insignificant and fewer than 3% are fatal. This retrospective study of 240 radical prostatectomy cases with comprehensive follow-up was a search for reliable markers of prostate cancer prognosis evaluable on biopsy specimens to enable minimization of unnecessary treatment, morbidity, and costs. Representative cancer and benign tissue from each prostatectomy specimen was made into tissue microarrays and stained with antibodies targeting 20 gene sequences. Traditional clinical and pathologic prognosticators and the 20 antibody stains were correlated with patient outcomes. By univariable analysis 4 of 20 antibodies (STMN1/stathmin 1, CYP4Z1/cytochrome p450-4z1, CDH1/E-cadherin, and Hey2), Gleason score, perineural invasion, and apical involvement were statistically significant outcome predictors for biopsy tissue. By multivariate analysis, Gleason score, Hey2, and CYP4Z1 were independently predictive. STMN1 and CDH1 were not independent of Gleason score but remain useful because marker interpretation is objective and Gleason scores often differ for biopsy and prostatectomy specimens.
ChemInform Abstract: A Convenient Synthesis of 2‐Alkyl‐5,10,15,20‐tetraphenylporphyrins: Reaction of Metallo‐2‐nitro‐5,10,15,20‐tetraphenylporphyrins with Grignard and Organolithium Reagents. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Nitric oxide participates in calcium-mediated regulation of renin release. (1994)

The regulation of renin release is unusual in that intracellular calcium reportedly acts as an inhibitory second messenger. Increased calcium not only inhibits renin release but is a cofactor in nitric oxide synthesis. Also, nitric oxide can inhibit renin release. This study was done in vitro using rat renal cortical slices to determine whether calcium-mediated renin inhibition could be in part due to the concurrent production of nitric oxide. Renin concentration in the incubation medium was determined by radioimmunoassay for angiotensin I (Ang I) generation (in nanograms Ang I per hour per milligram per 30 minutes of incubation). In all studies, n = 6 to 17. In normal-calcium incubation medium (2.6 mmol/L), 10(-4) mol/L NG-monomethyl L-arginine, which blocks nitric oxide synthesis, caused an 18% increase in basal renin release (78.6 +/- 8.9 versus 66.7 +/- 5.8 [ng Ang I/h]/mg per 30 minutes incubation, P &lt; .05). When calcium was eliminated from the incubation medium, basal renin release doubled (to 133.1 +/- 15.2 [ng Ang I/h]/mg per 30 minutes incubation, P &lt; .001). Without calcium, inhibiting nitric oxide synthesis had no further effect on renin release (126.8 +/- 17.7 [ng Ang I/h]/mg per 30 minutes incubation). High-calcium medium (7.8 mmol/L) reduced basal renin release by half (30.8 +/- 4.8 [ng Ang I/h]/mg per 30 minutes incubation, P &lt; .001), but inhibiting nitric oxide synthesis in high-calcium medium stimulated renin release by 50% (46.9 +/- 6.2 [ng Ang I/h]/mg per 30 minutes incubation, P &lt; .005). Addition of the calmodulin inhibitor W-7 completely reversed the inhibition of renin by high-calcium medium.(ABSTRACT TRUNCATED AT 250 WORDS)
Tandem Aromatization of Oxygenated Furans by Framework Zinc In Zeolites. A Computational Study (2017)

We have performed electronic structure calculations to characterize the active site of the zeolite CIT-6 (isomorphically substituted Zn-Beta) and to study the Diels–Alder dehydrative aromatization of methyl-5-(methoxymethyl)-furoate (MMFC) and of the dimethyl ester of 2,5-furan-dicarboxylic acid (DMFDC) with ethylene. Three types of active sites have been investigated: a site where the framework charge was balanced by two protons (Z0); a site with an H+ and a Li+ as counter-cations (Z1); and an active site with two Li+ counter-cations (Z2). Using NBO and Bader analysis, we conclude that Zn incorporation into the zeolite framework is not through covalent bonding to framework oxygen atoms but rather is through ionic bonding. Despite the ionic character of the active site and the generally strong Lewis acidic nature of Zn(II) cations, we find no catalysis of the Diels–Alder reaction for the two furans tested. On the other hand, the dehydration of the Diels–Alder cycloadduct can be either Brønsted or Lewis acid catalyzed depending on the active site type. The Z0-type sites are found to be more active than the Z1- and Z2-type sites. Furthermore, the Z0-type sites exhibit both Lewis and Brønsted acid characters with similar catalytic activities. In full agreement with experiment, we find that the conversion of MMFC to (4-methoxymethyl) benzenecarboxylate via Diels–Alder dehydrative aromatization is easier than the conversion of DMFDC to dimethyl terephthalate as the two electron withdrawing groups in DMFDC stabilize the corresponding cycloadduct against dehydration.
The Nature of Personal Identity in the Near-Death Experience: Paul Brunton and the Ancient Tradition (1984)

"In this paper the nature of personal identity is examined from two perspectives: observations reported by selected near-death experiencers (NDErs) and the viewpoint represented by the late English writer Paul Brunton (1898-1981)" (abstract). The paper explores the implications of these two perspectives.
Hydrogen Induced Si Surface Segregation on Ge-Covered Si(001) (1998)

Using Fourier transform infrared-attenuated total reflectance spectroscopy in conjunction with hydrogen adsorption to probe surface layer composition, we observe a reversible place exchange between Ge and Si on Ge-covered Si(001) when the surface is dosed with atomic H at elevated temperatures. First-principles calculations confirm a thermodynamic driving force for this place exchange. To explain the intriguing kinetics of the place exchange, which shows no time dependence, we propose a dimer-vacancy diffusion-assisted mechanism limited by vacancy interactions.
Conditions for the Selective Conversion of Quaternary 3‐Anilino‐1,5‐dimethylpyrazolium Salts into 3‐Anilino‐1,5‐dimethylpyrazole. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Deep ultraviolet Raman scattering characterization of ion-implanted SiC crystals (2005)

Multiple energy phosphorous ions were implanted into 4H-SiC at room temperature and at an elevated temperature (500 °C) followed by annealing at various temperatures. Deep ultraviolet Raman microscopy was used to analyze the effect of the implantation dose and postannealing temperature on the recovery of surface layers damaged by the implantation. The Raman analysis showed that the recovery rate of the crystallinity increased with an increase in the annealing temperature. However, for highly dosed samples, recovery was not complete even with annealing temperatures up to 1700 °C. With room-temperature implantation, part of the implanted layer was converted into a 3C structure with heavy stacking faults. New Raman bands were observed at below 500cm−1 in samples heavily dosed with 4.0×1016cm−2 after annealing, which revealed that excess phosphorus precipitates. A downshift of the phonon Raman bands and a reduction in the LO–TO-phonon frequency splitting were observed in as-implanted samples and ones that are not completely recovered by annealing. This feature is discussed based on several mechanisms.
Establishment and Characterization of a Novel Anti-DNAM-1 Monoclonal Antibody (2013)

DNAM-1 (CD226) is expressed on the majority of NK cells, CD8(+) T cells, and CD4(+) T cells and mediates an activating signal in these cells upon binding to the ligands CD155 or CD112 expressed on target cells or antigen-presenting cells. DNAM-1 plays an important role in tumor immunity mediated by NK cells and CD8(+) T cells and the development of graft-versus-host disease (GVHD) in mice. We previously generated a monoclonal antibody against mouse DNAM-1, TX42, which inhibited DNAM-1 binding to its ligands CD155 and CD112 and inhibited activation of NK cells and CD8(+) T cells in vitro. Injection of mice with TX42 ameliorated the development of GVHD in mice. Here, we generated a new clone of anti-DNAM-1 MAb, TX92. TX92 similarly stained primary spleen cells, including CD8(+) and CD4(+) T cells and NK cells. TX92 as well as TX42 interfered with the interaction between DNAM-1 and ligands CD155 and CD112. However, TX92 recognizes a different epitope and, unlike TX42 partially, but not completely, depleted peripheral blood (PB) CD8(+) T cells in vivo. Thus, TX92 is a unique MAb that is characterized not only by inhibitory function of DNAM-1 binding to the ligands but also by function of partial depletion of PB CD8(+) T cells.
New Method for the Orthogonal Labeling and Purification of Toxoplasma gondii Proteins While Inside the Host Cell (2015)

Studying how T. gondii modifies the host cell to permit its survival is complicated by the complex protein environment of the host cell. The approach presented in this article provides the first method for specific labeling of T. gondii proteins while the parasite grows inside the host cell. We show that this approach is useful for pulse-chase labeling of parasite proteins during in vitro growth. It should also be applicable during in vivo infections and in other apicomplexan parasites, including Plasmodium spp.
Internal cell manipulation using infrared laser traps. (1989)

The ability of infrared laser traps to apply controlled forces inside of living cells is utilized in a study of the mechanical properties of the cytoplasm of plant cells. It was discovered that infrared traps are capable of plucking out long filaments of cytoplasm inside cells. These filaments exhibit the viscoelastic properties of plastic flow, necking, stress relaxation, and set, thus providing a unique way to probe the local rheological properties of essentially unperturbed living cells. A form of internal cell surgery was devised that is capable of making gross changes in location of such relatively large organelles as chloroplasts and nuclei. The utility of this technique for the study of cytoplasmic streaming, internal cell membranes, and organelle attachment was demonstrated.
ChemInform Abstract: FORMATION OF A NONCHEMILUMINESCENT EXCITED‐STATE SPECIES IN THE DECOMPOSITION OF 4A‐(ALKYLPEROXY)FLAVINS (1981)

Abstract Der sich unter Chemilumineszenz vollziehende Zerfall der Alkylperoxy?avine (I) führt zu Quantenausbeuten (I), die von der Verdünnung unabhängig sind, bei Deuterierung im Alkylrest einen Isotopieeffekt (PH/CDU von 1.7‐2.0 aufweisen und durch Zusatz fluoreszenzfähiger Substanzen wie z.B. (II) oder Rhodamin Bbis zu einem Sättigungswert gesteigert werden.
Oxidative Stress and Nanotechnology (2013)

The emergence of nanotechnology has had a profound effect on almost every aspect of the 21st century's daily life. It has had a revolutionary impact from stain-resistant clothing and cosmetics to envi
Modulation of Kinin B2 Receptor Signaling Controls Aortic Dilatation and Rupture in the Angiotensin II–Infused Apolipoprotein E–Deficient Mouse (2016)

B2R signaling promotes aortic rupture within a mouse model associated with the ability to stimulate inflammatory phenotypes of neutrophils and vascular smooth muscle cells. B2R antagonism could be a potential therapy for AAA.
Cost Aware Resource Sizing and Scaling of Microservices (2019)

Microservices are small, independent, loosely coupled components which provide flexibility, agility, and scalability to an application. While these are aimed for scalability, achieving it needs judicious trade-offs between size, number and cost of provisioning. In this architecture, sizing in both homogeneous and heterogeneous resources plays a key role to balance application performance and resource requirement, as workload demand varies. This paper provides insights where the importance of considering workload characterization to decide a homogeneous or heterogeneous scaling strategy for a microservice is discussed. The work exploits the correlation of workload characterization, predicted workload demand and selection of right-sized microservice to minimize resource costs. Size of microservice is referred with respect to the amount of resources allocated to the microservice. This work also evaluates trade-offs between considering the entire predicted workload demand for resource cost optimization against algorithmic computational complexity and designs a heuristic to reduce such complexity. Evaluation of results demonstrate two important outcomes. Firstly, workload characterization helps to choose between homogeneous or heterogeneous sizing for different microservices. And secondly, by considering workload demand prediction beyond the current scheduling interval, allows to make scaling decision in the current cycle keeping in view whether the demand is going to increase or decrease. The paper also details on how to use the insights of application characterization and workload trend for choosing an appropriate scaling strategy.
Lewis Adducts of the Side‐On End‐On Dinitrogen‐Bridged Complex [{(NPN)Ta}2(μ‐H)2(μ‐η1:η2‐N2)] with AlMe3, GaMe3, and B(C6F5)3: Synthesis, Structure, and Spectroscopic Properties (2004)

Reaction of the side-on end-on dinitrogen complex [{(NPN)Ta}(2)(mu-H)(2)(mu-eta(1):eta(2)-N(2))] (1; in which NPN=(PhNSiMe(2)CH(2))(2)PPh), with the Lewis acids XR(3) results in the adducts [{(NPN)Ta}(2)(mu-H)(2)(mu-eta(1):eta(2)-NNXR(3))], XR(3)=GaMe(3) (2), AlMe(3) (3), and B(C(6)F(5))(3) (4). The solid-state molecular structures of 2, 3, and 4 demonstrate that the N-N bond length increases relative to those found in 1 by 0.036, 0.043, and 0.073 A, respectively. In solution complexes 2-4 are fluxional as evidenced by variable-temperature (1)H NMR spectroscopy. The (15)N{(1)H} NMR spectra of 2-4 are reported; furthermore, their vibrational properties and electronic structures are evaluated. The vibrational structures are found to be closely related to that of the parent complex 1. Detailed spectroscopic analysis on 2-4 leads to the identification of the theoretically expected six normal modes of the Ta(2)N(2) core. On the basis of experimental frequencies and the QCB-NCA procedure, the force constants are determined. Importantly, the N-N force constant decreases from 2.430 mdyn A(-1) in 1 to 1.876 (2), 1.729 (3), and 1.515 mdyn A(-1) (4), in line with the sequence of N-N bond lengths determined crystallographically. DFT calculations on a generic model of the Lewis acid adducts 2-4 reveal that the major donor interaction between the terminal nitrogen atom and the Lewis acid is mediated by a sigma/pi hybrid molecular orbital of N(2), corresponding to a sigma bond. Charge analysis performed for the adducts indicates that the negative charge on the terminal nitrogen atom of the dinitrogen ligand increases with respect to 1. The lengthening of the N-N bond observed for the Lewis adducts is therefore explained by the fact that charge donation from the complex fragment into the pi* orbitals of dinitrogen is increased, while electron density from the N-N bonding orbitals p(sigma) and pi(h) is withdrawn due to the sigma interaction with the Lewis acid.
ChemInform Abstract: STUDIES ON PEPTIDES. APPLICATION OF TRIFLUOROMETHANESULPHONIC ACID AS A DEBLOCKING REAGENT TO THE SYNTHESIS OF NEUROTENSIN (1976)

Abstract Das hypotensiv wirksame Tridecapeptid Neurotensin (I) wird ′ach konventionellen Methoden dargestellt.
Sparse Modeling for Image and Vision Processing (2014)

In recent years, a large amount of multi-disciplinary research has been conducted on sparse models and their applications. In statistics and machine learning, the sparsity principle is used to perform model selection-that is, automatically selecting a simple model among a large collection of them. In signal processing, sparse coding consists of representing data with linear combinations of a few dictionary elements. Subsequently, the corresponding tools have been widely adopted by several scientific communities such as neuroscience, bioinformatics, or computer vision. Sparse Modeling for Image and Vision Processing provides the reader with a self-contained view of sparse modeling for visual recognition and image processing. More specifically, the work focuses on applications where the dictionary is learned and adapted to data, yielding a compact representation that has been successful in various contexts. It reviews a large number of applications of dictionary learning in image processing and computer vision and presents basic sparse estimation tools. It starts with a historical tour of sparse estimation in signal processing and statistics, before moving to more recent concepts such as sparse recovery and dictionary learning. Subsequently, it shows that dictionary learning is related to matrix factorization techniques, and that it is particularly effective for modeling natural image patches. As a consequence, it has been used for tackling several image processing problems and is a key component of many state-of-the-art methods in visual recognition. Sparse Modeling for Image and Vision Processing concludes with a presentation of optimization techniques that should make dictionary learning easy to use for researchers that are not experts in the field.
Blink rate in ALS (2012)

The French neurologist, Charcot, first described amyotrophic lateral sclerosis (ALS) in the middle of the 19th century. ALS is as a multisystem disorder that causes upper and lower motor neuron dys...
Triplet Waves in a Quantum Spin Liquid (2000)

We report a neutron scattering study of the spin- 1/2 alternating bond antiferromagnet Cu(NO3)(2);2.5D(2)O for 0.06<k(B)T/J1<1.5. For k(B)T/J1<<1 the excitation spectrum is dominated by a coherent singlet-triplet mode centered at J1 = 0.442(2) meV with sinusoidal dispersion and a bandwidth of J2 = 0.106(2) meV. A complete description of the zero temperature contribution to the scattering function from this mode is provided by the single mode approximation. At finite temperatures we observe exponentially activated band narrowing and damping. The relaxation rate is thermally activated and wave vector dependent with the periodicity of the reciprocal lattice.
Adaptive constraint reduction for training support vector machines. (2008)

A support vector machine (SVM) determines whether a given observed pattern lies in a particular class. The decision is based on prior training of the SVM on a set of patterns with known classification, and training is achieved by solving a convex quadratic programming problem. Since there are typically a large number of training patterns, this can be expensive. In this work, we propose an adaptive constraint reduction primal-dual interior-point method for training a linear SVM with ℓ1 penalty (hinge loss) for misclassification. We reduce the computational effort by assembling the normal equation matrix using only a well-chosen subset of patterns. Starting with a large portion of the patterns, our algorithm excludes more and more unnecessary patterns as the iteration proceeds. We extend our approach to training nonlinear SVMs through Gram matrix approximation methods. We demonstrate the effectiveness of the algorithm on a variety of standard test problems.
Predicting Kinase-Substrate Interactions in Medulloblastoma Subtypes (2020)

Medulloblastoma (MB), the most common malignant pediatric brain cancer, has four subtypes based on genomics profiling: Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4. However, subtype heterogeneity and low mutation rates hinder the identification of actionable molecular targets within each group. Studies thus suggest a phosphoproteomics (study of protein phosphorylation), instead of a genomics approach, to better distinguish the MB subgroups. Thus, this research will measure MB's irregular protein activity via protein phosphorylation patterns. Protein kinases phosphorylate proteins on specific amino acids, also known as substrates, to regulate their functions. Given that less than 5% of substrates have annotated kinase associations, it is difficult to identify the kinases in MB which irregularly phosphorylate their substrates in order to determine the most effective kinases for drugs to target. As a result, the publicly-available tool NetworKIN was employed to predict novel kinase-substrate interactions in this study to expand the currently limited annotated interactions. For a given dataset of substrates, NetworKIN will output kinase-substrate predictions, each receiving a confidence score (higher score = higher confidence) ranging from zero to the hundreds. To identify a score threshold for high confidence predictions, NetworKIN was run on the substrates in the Human PhosphoSite Plus Database (PSP), the largest curated database of experimentally verified kinase-substrate interactions in humans. Three statistical thresholding methods were tested and the optimal cutoff score was determined to lie at 5.88. This threshold was applied to the predictions for the MB dataset, resulting in 774 novel high confidence kinase-substrate interactions. To understand how these interactions altered the enriched kinases across the MB subgroups, kinase activity scores before and after adding the predictions were calculated for all 20 samples using the tool Inference of Kinase Activities from Phosphoproteomics. Subgroup classification based on these activity scores revealed that, with the addition of high-confidence interactions to PSP, there are two smaller subgroups of Group 3 and one of those subgroups more closely resembled the Group 4 samples. The alignment of these findings with current literature increases our confidence in the prediction algorithm and elucidates novel phosphorylation patterns to more accurately portray the phosphosignaling pathways driving MB tumorigenesis. Future cancer phosphoproteomics studies can also employ this robust prediction tool to continue expanding our understanding of aberrant kinase-substrate interactions in human diseases.
Carbon sources effect on pectinase production from Aspergillus japonicus 586 (2000)

The effect of different carbon sources on the pectinesterases, endo- and exo-polygalacturonase activities from Aspergillus japonicus 586 was evaluated in liquid media (Manachini solutions) supplemented with different substrate concentrations. The culture medium was inoculated with 5.10(6) spores/ml and mantained under agitation (140 rpm), at 30°C, during 122 h. The enzyme evaluation was carried out 24 h after filtration. The crude extract from A. japonicus 586 indicated that the best enzymatic activities were afforded in the presence of 0.5% pectin (pectinesterease), 0.2% pectin and 0.2% glycerol (endopolygalacturonase), and 0.5% pectin associated to 0.5% glucose (exopolygalacturonase). Carbon sources concentration, isolated or associated, significantly affects the pectinesterase, and endo- and exopolygalacturonase activities. Pectin, glucose and saccharose, when added to the culture medium in high concentrations, exhibited a repression effect on all the analyzed enzymes.