gebhart/patrepeval huggingface dataset:
Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing (2020)

National Institutes of Health (Grants 1F31-MH117886, 1R01-MH110049 and 1DP1-HL141201)
Cover Feature: Formation of Iron (III) Trimesate Xerogel by Ultrasonic Irradiation (Eur. J. Inorg. Chem. 15/2022) (2022)

The Cover Feature shows the ultrasound-assisted formation of Fe-BTC gels, iron carboxylate metal-organic frameworks (MOFs) constructed from iron ions and 1,3,5 benzenetricarboxylic acid linkers. The gels were obtained by two different procedures: ultrasonic irradiation (US) of different water solutions containing the linker and iron nitrate, with or without the additive tetramethylammonium hydroxide. Gelation was observed regardless of the duration of the irradiation, the precursor concentration, the additive, or the US apparatus used. While drying, the wet gels underwent shrinking and cracked into tiny fractions of transparent solid xerogels consisting of interconnected spherical, thermally stable nanoparticles with a permanent microporous structure. The authors acknowledge Prof. Christoph Hartl for gently assisting with the cover′s graphic layout. More information can be found in the Research Article by G. Mannias, M. Pilloni and co-workers.
ChemInform Abstract: Synthesis of gem‐Difluorinated Heterocycles Using a Difluoropropargyl Molecular Scaffold (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Clinical Proton MR Spectroscopy in Central Nervous System Disorders (2014)

A large body of published work shows that proton (hydrogen 1 [(1)H]) magnetic resonance (MR) spectroscopy has evolved from a research tool into a clinical neuroimaging modality. Herein, the authors present a summary of brain disorders in which MR spectroscopy has an impact on patient management, together with a critical consideration of common data acquisition and processing procedures. The article documents the impact of (1)H MR spectroscopy in the clinical evaluation of disorders of the central nervous system. The clinical usefulness of (1)H MR spectroscopy has been established for brain neoplasms, neonatal and pediatric disorders (hypoxia-ischemia, inherited metabolic diseases, and traumatic brain injury), demyelinating disorders, and infectious brain lesions. The growing list of disorders for which (1)H MR spectroscopy may contribute to patient management extends to neurodegenerative diseases, epilepsy, and stroke. To facilitate expanded clinical acceptance and standardization of MR spectroscopy methodology, guidelines are provided for data acquisition and analysis, quality assessment, and interpretation. Finally, the authors offer recommendations to expedite the use of robust MR spectroscopy methodology in the clinical setting, including incorporation of technical advances on clinical units.
New method removing SEM image noise to characterize CD and LWR (2019)

It is important to remove image noise properly to measure critical dimension (CD) and roughness values from scanning electron microscope (SEM) images. In order to reduce image noise, the number of electron beam (EB) scans, or frame number, is increased. However, this excess EB irradiation damages the objects being measured and changes their size. In this paper, a new image analysis method is introduced to remove image noise without a typical noise filter. In this method, each image frame is used in a four dimensional array, and several artificial images are generated and edge coordinates are calculated. As a result of this new method, we can separate the line width roughness (LWR) components into process roughness and image noise, and analyze images with lower number of frames with minimal EB damage. The impact of image noise on the accuracy of CD extraction is explained in the section on analysis of variance (ANOVA). The variation is separated as wafer to wafer (WTW), field to field (FTF), die to die (DTD), pattern to pattern (PTP), line width roughness (LWR), and stochastic pattern noise (SPN; which is random variation per a pattern) at this ANOVA. Roughness component from image noise is included in SPN. It is possible to remove the image noise component from SPN by applying this new image analysis method, and it is also possible to discuss the SPN from shot noise of exposure tool or variation of resist material component. ANOVA can put an end to discussion of measurement length of line pattern to know the state of low frequency roughness. LWR component of long wavelength is distributed to PTP and SPN when short patterns are measured. It is important to remove image nose properly and to compare the statistical analysis processed SPN value.
Numerical simulations of an antenna-amplifier-Cherenkov maser with a rod slow-wave structure operating in a non-axisymmetric mode (2004)

It has been recently proposed that a traveling wave tube could be combined with a surface wave antenna if a relativistic electron beam propagates near and along the antenna's slow-wave structure, i.e., the TWT rf drive would simultaneously serve as the antenna feed signal. In the simplest geometry of such an antenna-amplifier, an annular beam propagates outside a dielectric rod antenna, and the drive signal is in the fundamental non-axisymmetric HE/sub 11/ mode. We present the first antenna-amplifier simulation results obtained using the 3-D version of the MAGIC particle-in-cell (PIC) code. Gain and beam bunching have been demonstrated for an X-band signal entering into the system in the TE/sub 11/, mode of a circular waveguide. The linear amplifier response was observed as well as saturation at increased interaction length. In addition, the effects of the generation of harmonics of the main frequency, found earlier in one-dimensional modeling, have been verified. Furthermore, the possibility of controlling the harmonic content in the output spectrum by means of input frequency variation, also studied earlier in 1-D simulations, has been confirmed. As the frequency changes within the amplification band, the output power remains the same, and spectral peaks shift to the new frequency and its harmonics, but the harmonic content in the spectrum changes significantly.
A Vibration Resistant Nanopositioner for Mobile Parallel-Probe Storage Applications (2007)

We describe a planar microelectromechanical systems (MEMS)-based x/y nanopositioner designed for parallel-probe storage applications. The nanopositioner is actuated electromagnetically and has x/y motion capabilities of plusmn60 mum. The mechanical components are fabricated from a single-crystal silicon wafer using a deep-trench-etching process. To render the system robust against vibration, we utilize a mass-balancing concept that makes the system stiff against linear shock, but still compliant for actuation, and therefore results in low power consumption. We present details of the finite-element model used to design the device as well as experimental results for the frequency response, actuation, and vibration-rejection properties of the nanopositioner
Fecal Viral Load and Norovirus-associated Gastroenteritis (2006)

We report the median cDNA viral load of norovirus genogroup II is >100-fold higher than that of genogroup I in the fecal specimens of patients with norovirus-associated gastroenteritis. We speculate that increased cDNA viral load accounts for the higher transmissibility of genogroup II strains through the fecal-oral route.
Accelerating Machine Learning Inference with Probabilistic Predicates (2018)

Classic query optimization techniques, including predicate pushdown, are of limited use for machine learning inference queries, because the user-defined functions (UDFs) which extract relational columns from unstructured inputs are often very expensive; query predicates will remain stuck behind these UDFs if they happen to require relational columns that are generated by the UDFs. In this work, we demonstrate constructing and applying probabilistic predicates to filter data blobs that do not satisfy the query predicate; such filtering is parametrized to different target accuracies. Furthermore, to support complex predicates and to avoid per-query training, we augment a cost-based query optimizer to choose plans with appropriate combinations of simpler probabilistic predicates. Experiments with several machine learning workloads on a big-data cluster show that query processing improves by as much as 10x.
Validation and analysis of a mathematical model of a replication-competent oncolytic virus for cancer treatment: implications for virus design and delivery. (2003)

Motivated by the rapid expansion in the development of replication-competent viral agents for the treatment of solid tumors, we formulated and analyzed a three-dimensional mathematical model of a tumor that is infected by a replication-competent virus. We initially considered three patterns of intratumoral injection in which a fixed fraction of cells are initially infected with the virus throughout (a) the entire tumor, (b) the tumor core, and (c) the tumor rim, respectively. For each injection pattern, an approximate analysis of the model provides a simple and accurate condition for whether the virus will eradicate the tumor. The model was then generalized to incorporate nutrient-limited necrosis and an innate immune response against virus-infected tumor cells. Recent preclinical and clinical data were used to validate the model and estimate key parameter values. Our analysis has the following implications: even in the absence of an immune response, tumor eradication requires widespread distribution of the virus within the tumor at the time of infection; core or rim injections alone may result in tumor escape, particularly in a well-vascularized tumor; the more rapidly a virus lyses infected cells the more effective it will be at controlling the tumor; and the innate immune response to the virus can potentially prevent the virus from controlling the tumor, even with repeat injections. Therefore, in addition to diffuse intratumoral infection, tumor eradication by oncolytic adenovirus will probably require potent suppression of innate immune clearance mechanisms (e.g., by replacement of adenovirus E3 genes), combinations with traditional (chemotherapy, radiotherapy) treatments, and/or concomitant therapeutic gene expression with resultant bystander effects.
Supplementary Methods , Table 1 from Dual Roles of PARP-1 Promote Cancer Growth and Progression (2023)

&lt;p&gt;PDF file - 91K&lt;/p&gt;
Solar-driven water splitting (2014)

Investigators in our NSF CCI Solar Fuels Program are working on catalysts for both water oxidn. to dioxygen (OER) and proton redn. to dihydrogen (HER). Promising HER heterogeneous catalysts include Ni-Mo and CoP, which reduce protons in aq. solns. with catalytic efficiencies near that of platinum. We also are investigating sol. iron, cobalt, and nickel complexes that catalyze dihydrogen prodn. from protic solns. at relatively low overpotentials. Employing laser flash/quench and NMR methods, we have shown that the active intermediate in cobalt-catalyzed dihydrogen evolution is a Co(II)-hydride. Among several new photoanode materials synthesized at Caltech, one that is esp. promising is dinitrogen-intercalated tungsten oxide. This 1.9 eV band gap oxide exhibits photocurrent under illumination out to 640 nm with a faradaic efficiency near unity for OER in perchloric acid solns. In other work of note, we have shown that robust metal-oxide water oxidn. catalysts can be made by pulsed laser ablation of precursors in liqs.
Inkjet-Printed Monolayers as Platforms for Tethered Polymers (2005)

Combining inkjet printing and atom-transfer radical polymerization (ATRP) provides a straightforward and versatile method for producing patterned polymer surfaces that may serve as platforms for a variety of applications. We report the use of drop-on-demand technology to print binary chemical gradients and simple patterns onto solid substrates and, by using surface-confined ATRP, amplify these patterns and gradients. Chemically graded monolayers prepared by inkjet printing dodecanethiol and backfilling with 11-mercaptoundecanol showed continuous changes in the water contact angle along the gradient. These samples also exhibited a distinct change in the intensity of methyl group and C-O stretching modes along the gradient. Graded or patterned polymer layers were produced by growing, with ATRP, tethered poly(methyl methacrylate) (PMMA) layers from gradient or patterned printed monolayers that contained a bromo-capped initiator. Atomic force microscopy and optical microscopy confirmed that the PMMA layers amplified the underlying printed initiator layer with remarkable fidelity.
A Novel Synthesis of 4-Hydroxy-3-phenylcoumarins by Titanium(III)-Mediated Reductive C-C Bond Formation (1993)

4-Hydroxy-3-phenylcoumarins (4-hydroxy-3-phenyl-2H-1-benzopyran-2-ones) were readily synthesized in two steps by the titanium(III)-mediated reaction of methyl benzoylformate and substituted salicylaldehydes followed by lactonization, under acidic conditions, of the resulting methyl 2,3-dihydroxy-3-(2-hydroxyaryl)-2-phenylpronanoates.
Low voltage hot-carrier programming of ultra-scaled SOI finflash memories (2007)

In this paper, we present a deep investigation of ultra-scaled Finflash memories, fabricated on Silicon on Insulator (SOI) substrate, with Silicon NanoCrystal (Si-NC) or nitride layers acting as storage nodes. Electrical characteristics of devices with channel length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ) as short as 30 nm, and fin width (W <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FIN</sub> ) as narrow as 10 nm are shown. Effective Channel Hot Electron (CHE) writing with sub-3.2 V drain biases (i.e. DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</sub> =3V at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> /V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> /t <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">stress</sub> =9V/2.5V/100 mus), as well as Hot Hole Injection (HHI) erasing with sub-4.5V drain biases are demonstrated. Finally, fully three dimensional Monte Carlo simulations, coupled with an original semi-analytical approach, allow us to give a qualitative explanation of the obtained experimental data.
ChemInform Abstract: KOMPLEXE VON EISEN(II) UND EISEN(III) MIT DEM VIERZAEHNIGEN MAKROCYCLUS 5,7,7,12,14,14‐HEXAMETHYL‐1,4,8,11‐TETRAAZACYCLOTETRADECADIEN‐(4,11) (1972)

Abstract Die Reaktion von F e(II)‐Salzen mit dem makrocyclischen Liganden in Acetonitril liefert das Komplexion (Ia), das als Perchlorat, Jodid, Tetraphenylborat oder Hexafluorophosphat isoliert wurde.
Paramagnetic NMR spectroscopy and coordination structure of cobalt(II) Cys112Asp azurin (1995)

Paramagnetic ^1H-NMR spectra of Co(II)-substituted Cys112Asp azurin from Pseudomonas aeruginosa have been&#13;\nanalyzed and compared with those of the Co(II) wild-type (WT) protein. Hyperfine-shifted signals (including&#13;\nAsp112 β-CH_2 signals in the mutant as well as previously unobserved Cys112 β-CH_2 signals in WT) from all the&#13;\nmetal-coordinated residues have been detected and unambiguously assigned. Notably, the spectra indicate that&#13;\nvery little if any unpaired spin density is located on the Met121 protons in the Cys112Asp protein. A computer-generated&#13;\nmodel of the mutant Co(II) structure consistent with electronic absorption as well as the NMR data&#13;\nincludes a Gly45 carbonyl, His46, an unusually coordinated Asp112, and His117 in the ligation sphere.
Non-Methylated CpG Motif Packaged into Fusogenic Liposomes Enhance Antigen-Specific Immunity in Mice (2006)

DNA rich in non-methylated CG motifs (CpGs) enhances induction of immune responses against co-administered antigen encoding genes. CpGs are therefore among the promising adjuvants known to date. However, naked plasmid DNA, even which contains CpG motifs, are taken up by antigen presenting cells via the endocytosis pathway. Endocytosed DNAs are thus degraded and their gene expression levels are inefficient. In this context, an effective plasmid delivery carrier is required for DNA vaccine development. We show in the present study that packaging plasmids containing CpGs into fusogenic liposomes (FL) derived from conventional liposomes and Sendai virus-derived active accessory proteins is an attractive method for enhancing the efficacy of a DNA vaccine. These CpG-enhanced plasmids (possessing 16 CpG repeats) that were packaged into FL, enhanced ovalbumin (OVA)-specific T cell proliferation and cytotoxic T cell activity after immunization. In fact, vaccination with CpG enhanced plasmid-loaded FL induced effective prophylactic effects compared with 13 repeats CpG containing plasmid in a tumor challenge experiment. Thus, the development of a CpG-enhanced DNA-FL genetic immunization system represents a promising tool for developing candidate vaccines against some of the more difficult infectious, parasitic, and oncologic disease targets.
PCI-31523: An irreversible inhibitor of Bruton’s tyrosine kinase (Btk) that disrupts B cell receptor (BCR) signaling, is cytotoxic to B cell lymphomas, and is active in an animal arthritis model (2007)

5398 Many lymphomas require an intact BCR for survival and, therefore, should be uniquely sensitive to drugs that target the BCR pathway. The kinase Btk is activated by stimulation of the BCR and it in turn phosphorylates and activates Phospholipase C-gamma (PLCg) to transmit BCR signaling further downstream. We have designed PCI-31523, a selective and irreversible inhibitor that covalently binds to Cys-481 in the active site of Btk. In purified enzyme assays, PCI-31523 inhibits Btk with an IC50 of 200-fold selectivity over the structurally related kinase Lck. In normal human B cells, PCI-31523 inhibits anti-IgM induced signaling and proliferation at concentrations as low as 10nM. To confirm that PCI-31523 acts as a selective inhibitor in cells, we used phospho-specific antibodies that detect known phosphorylation events downstream of BCR stimulation. We found that PCI-31523 does not significantly inhibit the Src-family proximal kinases that trans-phosphorylate Btk at Tyr-551. In contrast, at 10nM, PCI-31523 completely blocks the Btk-dependent phosphorylation of PLCg. In addition, PCI-31523 leads to a significant decrease in Ca++ flux and phosphorylation of Erk. Lastly, PCI-31523 has no effect on PMA/Ionomycin induced phosphorylation of Erk. Thus, as predicted for a selective Btk inhibitor, PCI-31523 acts downstream of the Src-family kinases and upstream of PLCg. We tested the effects of PCI-31523 on a variety of BCR expressing lymphoma cell lines. The diffuse large B cell lymphoma lines DHL-4 and DHL-6 as well as the follicular lymphoma line DoHH2 are sensitive to PCI-31523, with growth arrest and apoptosis occurring at concentrations as low as 0.5uM. In contrast, the lymphoma cell lines Ramos, Raji, and DB are resistant to PCI-31523 cytotoxicity. To investigate this differential sensitivity, we used phospho-flow cytometry to quantitate basal and anti-IgM-induced phosphorylation of Erk. PCI-31523 is more potent at reducing phospho-Erk in a sensitive cell line (DHL-6) than in a resistant cell line (Ramos). Thus the amount of inhibition of phospho-Erk appears to be correlated with the degree of cytotoxicity and this biomarker may function as a predictor of clinical responsiveness. PCI-31523 has been tested in vivo in a mouse collagen antibody arthritis model. Oral dosing of PCI-31523 (10mg/kg qd) results in almost complete inhibition of inflammation, indicating that this compound may be effective in both autoimmune disease and lymphoma.
Numerical Analysis of A Hydrogen Jet Diffusion Flame Using a PDF Method Considering a Detailed Chemical Mechanism (2003)

本研究では, 乱流噴流拡散火災を対象に, 流れ場についてはk-ε2方程式モデルを用い, またスカラー場については, 有限反応速度を考慮したスカラーPDF (F-PDF)法による解析を試みた。また, F-PDF法の精度評価のために, 反応速度無限大を仮定し, 混合分率(Z)のみをPDF法で解析するスカラーPDF (I-PDF)法, また従来のFlamelet Model (F. M.)法による解析結果および実験結果と比較を行ない, F-PDF法の有効性を検討した。
Arginine‐induced conformational change in the c‐ring/a‐subunit interface of ATP synthase (2008)

The rotational mechanism of ATP synthases requires a unique interface between the stator a subunit and the rotating c-ring to accommodate stability and smooth rotation simultaneously. The recently published c-ring crystal structure of the ATP synthase of Ilyobacter tartaricus represents the conformation in the absence of subunit a. However, in order to understand the dynamic structural processes during ion translocation, studies in the presence of subunit a are required. Here, by intersubunit Cys-Cys cross-linking, the relative topography of the interacting helical faces of subunits a and c from the I. tartaricus ATP synthase has been mapped. According to these data, the essential stator arginine (aR226) is located between the c-ring binding pocket and the cytoplasm. Furthermore, the spatially vicinal residues cT67C and cG68C in the isolated c-ring structure yielded largely asymmetric cross-linking products with aN230C of subunit a, suggesting a small, but significant conformational change of binding-site residues upon contact with subunit a. The conformational change was dependent on the positive charge of the stator arginine or the aR226H substitution. Energy-minimization calculations revealed possible modes for the interaction between the stator arginine and the c-ring. These biochemical results and structural restraints support a model in which the stator arginine operates as a pendulum, moving in and out of the binding pocket as the c-ring rotates along the interface with subunit a. This mechanism allows efficient interaction between subunit a and the c-ring and simultaneously allows almost frictionless movement against each other.
Front Matter: Volume 8652 (2013)

A unique, consistent, permanent citation identifier (CID) number is assigned to each article at the time of
Formation of 3-Dimensional Structure by Electroforming (2007)

[in Japanese]
The fluid dynamics of canine olfaction: unique nasal airflow patterns as an explanation of macrosmia (2009)

The canine nasal cavity contains hundreds of millions of sensory neurons, located in the olfactory epithelium that lines convoluted nasal turbinates recessed in the rear of the nose. Traditional explanations for canine olfactory acuity, which include large sensory organ size and receptor gene repertoire, overlook the fluid dynamics of odorant transport during sniffing. But odorant transport to the sensory part of the nose is the first critical step in olfaction. Here we report new experimental data on canine sniffing and demonstrate allometric scaling of sniff frequency, inspiratory airflow rate and tidal volume with body mass. Next, a computational fluid dynamics simulation of airflow in an anatomically accurate three-dimensional model of the canine nasal cavity, reconstructed from high-resolution magnetic resonance imaging scans, reveals that, during sniffing, spatially separate odour samples are acquired by each nostril that may be used for bilateral stimulus intensity comparison and odour source localization. Inside the nose, the computation shows that a unique nasal airflow pattern develops during sniffing, which is optimized for odorant transport to the olfactory part of the nose. These results contrast sharply with nasal airflow in the human. We propose that mammalian olfactory function and acuity may largely depend on odorant transport by nasal airflow patterns resulting from either the presence of a highly developed olfactory recess (in macrosmats such as the canine) or the lack of one (in microsmats including humans).