gebhart/patrepeval huggingface dataset:
Quantitative structure-metabolism relationships for substituted benzoic acids in the rabbit: prediction of urinary excretion of glycine and glucuronide conjugates (1996)

1. Quantitative relationships between molecular physicochemical properties of 24 substituted benzoic acids and their metabolic fate in the rabbit have been investigated using computational chemistry and multivariate statistical methods. 2. A total of 34 molecular properties were calculated for each compound using computational chemistry and were related statistically to the % molar recovery of glycine and glucuronide conjugates excreted in the urine of rabbits for the 24 compounds. 3. Compounds were successfully classified according to their dominant metabolic fate based on urinary excretion data, where stepwise linear regression analysis of the theoretical property data achieved good predictive fits for observed versus predicted % molar urinary recovery as glucuronide conjugates (r2 = 0.79) and % molar urinary recovery as glycine conjugates (r2 = 0.66). 4. Quantitative prediction of the urinary excretion of glucuronide and glycine conjugates of the parent compounds was achieved based on a statistical model using calculated molecular physicochemical parameters. Interpretation of the molecular properties, which are important for predicting the metabolic class, should give new insights into basic mechanisms of drug metabolism and underlying molecular recognition events that determine disposition and metabolism.
Association of asymptomatic hemorrhage after endovascular stroke treatment with outcomes (2021)

aICH was not associated with worse outcomes in patients with large-vessel stroke treated with EVT. aICH was more frequent in patients with successful recanalization. Further validation of our findings in large cohort studies of EVT-treated patients is warranted.
Multi-kilowatt, all-fiber integrated chirped-pulse amplification system yielding 40� pulse compression using air-core fiber and conventional erbium-doped fiber amplifier (2004)

We present a totally fiber integrated chirped-pulse amplification system using air-core photonic bandgap fiber and a conventional erbium-doped fiber amplifier. ~40-ps input pulses, generated in a Mach-Zehnder modulator, were stretched and spectrally broadened in a dispersion-shifted fiber before being amplified and subsequently compressed in 10 m of anomalously-dispersive photonic bandgap fiber to yield ~960 fs pulses. The system gives multi-kilowatt peak powers while the amplifier nonlinearity threshold is as low as ~150 W. Higher peak powers could be obtained by the use of an amplifier with higher nonlinearity threshold.
Differential delay-doppler estimation using second and higher-order ambiguity functions (1993)

Estimation of differential delay-Doppler parameters in passive sonar and radar applications is addressed. Without assuming Gaussianity it is shown that the conventional ambiguity function is asymptotically chi-squared and yields consistent delay-Doppler estimates for narrowband signals observed in uncorrelated sensor noises. Related asymptotic covariance expressions and their computable forms are also derived. It is further shown that the performance of the ambiguity function degrades severely when the sensor noises are correlated. To deal with such noises a novel third-order ambiguity function is proposed and is shown to be consistent and theoretically immune to Gaussian and symmetrically distributed disturbances. Further, to take into account the errors due to variances of sample statistics, alternative delay-Doppler estimators are defined to minimise a cumulant matching criterion and related issues are discussed. The case of wideband signals is also addressed and, finally, extensions to kth-order ambiguity functions are proposed. Computer simulations are performed to confirm the theory. Throughout the paper the analysis treats both deterministic and stochastic signals on a common framework. Connections with active sonar and radar problems are also shown as a special case.
Columnar distribution of activity dependent gabaergic depolarization in sensorimotor cortical neurons (2012)

These results demonstrate that the well-known inhibitory transmitter GABA rapidly switches from hyperpolarization to depolarization upon synaptic activity in adult somatosensory cortical neurons.
Measurement of analytes in human serum and whole blood samples by near-infrared Raman spectroscopy (1998)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 1998.
The prevalence of oral glucocorticoid use in doses associated with risk of tertiary adrenal insufficiency (2019)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Structural and magnetic properties of the (001) and (111) surfaces of the half-metal NiMnSb (2005)

Abstract. Using the full potential linearised augmented planewave method we study the electronic and magnetic properties of the (001) and (111) surfaces of the half-metallic Heusler alloy NiMnSb from first-principles. We take into account all possible surface terminations including relaxations of these surfaces. Special attention is paid to the spin-polarization at the Fermi level which governs the spin-injection from such a metal into a semiconductor. In general, these surfaces lose the half-metallic character of the bulk NiMnSb, but for the (111) surfaces this loss is more pronounced. Although structural optimization does not change these features qualitatively, specifically for the (111) surfaces relaxations can compensate much of the spin-polarization at the Fermi surface that has been lost upon formation of the surface.
Mobile Computing Innovations for Safeguards Inspections. (2014)

Abstract not provided.
Physical and chemical properties of hypersaline Lago Enriquillo, Dominican Republic (2005)

Click to increase image sizeClick to decrease image sizeKey words: CaribbeanLago Enriquillomicrobenthossaline lakesstable isotopes
Fluoride Induces a Volume Reduction in CA1 Hippocampal Slices Via MAP Kinase Pathway Through Volume Regulated Anion Channels (2020)

Regulation of cell volume is an important aspect of cellular homeostasis during neural activity. This volume regulation is thought to be mediated by activation of specific transporters, aquaporin, and volume regulated anion channels (VRAC). In cultured astrocytes, it was reported that swelling-induced mitogen-activated protein (MAP) kinase activation is required to open VRAC, which are thought to be important in regulatory volume decrease and in the response of CNS to trauma and excitotoxicity. It has been also described that sodium fluoride (NaF), a recognized G-protein activator and protein phosphatase inhibitor, leads to a significant MAP kinase activation in endothelial cells. However, NaF's effect in volume regulation in the brain is not known yet. Here, we investigated the mechanism of NaF-induced volume change in rat and mouse hippocampal slices using intrinsic optical signal (IOS) recording, in which we measured relative changes in intracellular and extracellular volume as changes in light transmittance through brain slices. We found that NaF (1~5 mM) application induced a reduction in light transmittance (decreased volume) in CA1 hippocampus, which was completely reversed by MAP kinase inhibitor U0126 (10 µM). We also observed that NaF-induced volume reduction was blocked by anion channel blockers, suggesting that NaF-induced volume reduction could be mediated by VRAC. Overall, our results propose a novel molecular mechanism of NaF-induced volume reduction via MAP kinase signaling pathway by activation of VRAC.
IgA Potentiates NETosis in Response to Viral Infection (2021)

ABSTRACT IgA is the second most abundant antibody present in circulation and is enriched at mucosal surfaces. As such, IgA plays a key role in protection against a variety of mucosal pathogens, including viruses. In addition to neutralizing viruses directly, IgA can also stimulate Fc-dependent effector functions via engagement of Fc alpha receptors (FcαRI) expressed on the surface of certain immune effector cells. Neutrophils are the most abundant leukocyte, express FcαRI, and are often the first to respond to sites of injury and infection. Here, we describe a novel function for IgA:virus immune complexes (ICs) during viral infections. We show that IgA:virus ICs potentiate NETosis – the programmed cell death pathway through which neutrophils release neutrophil extracellular traps (NETs). Mechanistically, IgA:virus ICs potentiated a suicidal NETosis pathway via engagement of FcαRI on neutrophils through a toll-like receptor (TLR)-independent, NADPH oxidase complex-dependent pathway. NETs also were capable of trapping and inactivating viruses, consistent with an antiviral function.
A study of clinical, pathological, and electroencephalographic features in 137 full-term babies with a long-term follow-up. (1970)

The authors report on their experience gained through a prospective study of 144 infants who developed seizures during the first 3 weeks of life. Only full-term neonates weighing 2,500 gm or more were included. Follow-up averaged 4 years. Seven subjects were lost on follow-up, leaving a total of 137. The clinical features of the convulsive episode are described, and a classification is presented of the most common seizure types, which differ significantly from those met in older babies. Observation of these different types of neonatal seizures may assist in discovering etiological factors and in formulating a prognosis. While no etiological clues were found in one fourth of the neonates, factors of probable etiological importance were established in three-fourths. High in the list of presumptive etiology were metabolic disturbances; intracerebral birth injuries and perinatal anoxia, once considered main causes for neonatal seizures, were considerably less frequent in this series. Central nervous system infection or malformation were met with about equal incidence. The only factor in common in eight babies was a marked postmaturity, and there was a history of pre-eclamptic toxemia in five. More than one factor of potential etiological significance was present in several babies. The study showed that mortality and morbidity run high for neonates with seizure states, the outcome being poor for about half of the cases. In contrast, the other half of the convulsing babies did quite well, often with spontaneous remission and normal psychic and motor development. We found that prognosis based on abnormal (or normal) neurological signs in a convulsing neonate show poor correlation with the state of the child when reevaluated years later. Certain etiological factors, as well as certain types of seizures, seem to carry better prognostic significance. Electroencephalographic investigation carried out along careful criteria during the newborn period has been found helpful for this series of convulsing babies. Neonates with seizures and a normal EEG had an 86% chance of normal development at age 4 years, regardless of other clinical data. In contrast, neonates with either a flat, periodic, or multifocal EEG had only a 7% chance of normal development. Unifocal EEG abnormalities showed more equivocal correlations. At the end of the study, about 50% of the subjects were found to be normal, while about 30% had survived with some serious neurological defect and 20% had died. There were 23 complete neuropathological examinations. The most helpful clinical and laboratory procedures for the work-up of a convulsing neonate are outlined, including a method for the rapid detection of metabolic disorders through diagnostic intravenous infusions.
How annealing conditions influence the fluctuation of step edges of step bunching on vicinal GaAs(100) formed by annealing in AsH3 and H2 ambient (1997)

We report how annealing conditions influence the degree of fluctuation of step edges of step bunching formed by annealing a vicinal GaAs(001) surface in AsH3 and H2 and ambient. At 700 °C, when the partial pressure is high, B steps are straighter than A steps as reported before, however, as the AsH3 partial pressure is decreased, A steps becomes straighter, finally, than the B steps at a partial pressure of 1×10−2 Torr. This reversal of the type of straight step edges can be explained by considering the (2×4)–c(4×4) phase transition. We will also apply the electron counting model established by Pashley in order to explain the experimental results, and by discussing its usefulness and limitations, finally conclude that we cannot determine the stability of steps only by this model.
Structure determination of a KSR protein domain (2011)

The crystal structure of the membrane-associated [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum (A. vinosum) has been determined at 2.1 resolution [1]. The oxidation state (Ni-A) of the enzyme was confirmed by EPR and FTIR on dissolved crystals. The overall structure of the A. vinosum [NiFe] hydrogenase resembles that of the [NiFe] hydrogenase structures derived from the sulfate-reducing bacteria, Desulfovibrio species [2].
Identifying Double Bond Positions in Phospholipids Using Liquid Chromatography-Triple Quadrupole Tandem Mass Spectrometry Based on Oxygen Attachment Dissociation (2019)

Lipids, a class of biomolecules, play a significant role in the physiological system. In this study, gas-phase hydroxyl radicals (OH·) and atomic oxygens (O) were introduced into the collision cell of a triple quadruple mass spectrometer (TQ-MS) to determine the positions of the double bond in unsaturated phospholipids. A microwave-driven compact plasma generator was used as the OH·/O source. The reaction between OH·/O and the precursor ions passing through the collision cell generates product ions that correspond to the double bond positions in the fatty acyl chain. This double bond position specific fragmentation process initiated by the attachment of OH·/O to the double bond of a fatty acyl chain is a characteristic of oxygen attachment dissociation (OAD). A TQ-MS incorporating OAD, in combination with liquid chromatography, permitted a high throughput analysis of the double bond positions in complex biomolecules. It is important to know the precise position of double bonds in lipids, since these molecules can have widely different functionalities based on the position of the double bonds. The assignment of double bond positions in a mixture of eight standard samples of phosphatidylcholines (phospholipids with choline head groups) with multiple saturated fatty acyl chains attached was successfully demonstrated.
Afferent inputs to cortical fast-spiking interneurons organize pyramidal cell network oscillations at high-gamma frequencies (60–200 Hz) (2014)

High-gamma activity, ranging in frequency between ∼60 Hz and 200 Hz, has been observed in local field potential, electrocorticography, EEG and magnetoencephalography signals during cortical activation, in a variety of functional brain systems. The origin of these signals is yet unknown. Using computational modeling, we show that a cortical network model receiving thalamic input generates high-gamma responses comparable to those observed in local field potential recorded in monkey somatosensory cortex during vibrotactile stimulation. These high-gamma oscillations appear to be mediated mostly by an excited population of inhibitory fast-spiking interneurons firing at high-gamma frequencies and pacing excitatory regular-spiking pyramidal cells, which fire at lower rates but in phase with the population rhythm. The physiological correlates of high-gamma activity, in this model of local cortical circuits, appear to be similar to those proposed for hippocampal ripples generated by subsets of interneurons that regulate the discharge of principal cells.
Interfered technology: A radiant future: A look forward to EMC in 2023, five years from now (2018)

In 1973, a three-part full-page article was published in the local newspaper describing our society in the region of Twente, the Netherlands, in 1923, 1973, and 2023 [1]. The author of this article was only 11 years old at the time, but the predictions made were interesting enough to keep that article for 45 years. The article [1] predicted several innovations for 2023, 50 years ahead, such as a magnetic levitation monorail from Twente to Amsterdam reducing the travel time from 2 hours to less than 30 minutes, as shown in Figure 1. However, all we got after 45 years was a new motorway, with lots of traffic jams, and a train that still takes 2 hours. Despite over a century of research and development, maglev trains are currently operated in just three countries: Japan, South Korea, and China. Other innovations predicted in 1973 for 2023 were clothes made by printers (yes, nearly), no cars in city centres (yes), products made in Shanghai (yes), European regions instead of European countries (no, although Catalonia would like this), no manufacturing but only research and development (no), Holec and Signaal merged (no, Holec split up into several divisions now owned by Siemens, Eaton, and General Electric, and Signaal was sold by Philips to Thomson-CSF, now THALES). And the announcement that the University of Twente will be organizing a conference on communication technology, including electronics. This was a very good prediction: communication technology will be a key issue in 2023.
Exciton energy recycling from ZnO defect levels: towards electrically driven hybrid quantum-dot white light-emitting-diodes (2016)

An electrically driven quantum-dot hybrid white light-emitting diode is fabricated via spin coating CdSe quantum dots onto a GaN/ZnO nanorod matrix. For the first time, quantum dots are excited by fluorescence resonance energy transfer from the carriers trapped at surface defect levels. The prototype device exhibits achromatic emission, with a chromaticity coordinate of (0.327, 0.330), and correlated color temperature similar to sunlight.
Reply (2016)

We thank Drs. Gupta and Ram for their interest in our paper and will address each of the issues they raised. In response to their first question, 4 (6.8%) survey respondents did not choose an available option with regard to their preference when faced with inadequate capsule support but rather offered free-text responses indicating that their preference would depend on the clinical situation. Two of these respondents also mentioned using capsular tension rings or segments depending on intraoperative factors. Drs. Gupta and Ram correctly observed a discrepancy between the text and Table 1 regarding the number of respondents who completed a fellowship. We confirm that the table is correct, accurately reflecting that 42 respondents completed fellowship. With regard to questions raised about AC IOLs, although our survey did not capture whether respondents felt equally comfortable with both options (AC IOLs and scleral-fixated PC IOLs), all respondents who indicated they felt comfortable placing scleral-fixated PC IOLs independently also indicated comfort with AC IOL placement. As indicated in Table 3, 17 (47.2%) of these respondents favored primary AC IOL placement in the setting of inadequate capsule support. Although our survey did not inquire specifically about shorter surgical times as a reason for IOL preference, of the 17 respondents who indicated comfort with both IOL types and favored AC IOL placement, 8 (47.1%) indicated a decreased risk for intraoperative complications, 5 (29.4%) indicated avoidance of a second surgery, 2 (11.8%) did not select an available answer, 1 (0.1%) indicated decreased risk for long-term complications, and 1 (0.1%) indicated best visual outcome as their reason for choosing primary AC IOL placement. Last, with regard to the third and fifth points raised by Drs. Gupta and Ram, we respectfully remind our readers that our study reports survey data rather than actual surgical outcomes. The hypothetical clinical scenarios posed in our survey were crafted to identify patient characteristics that surgeons might consider when determining their intraoperative approach to inadequate capsule support. Phacoemulsification versus extracapsular cataract extraction was not included in the clinical scenarios contained in our survey; however, we agree this distinction would be of interest for further study. Similarly, we believe that fixation technique, IOL type, and delay after primary surgery represent additional factors worthy of further study on this topic. As indicated in our introduction, clinical outcome data regarding AC IOLs versus scleral-fixated PC IOLs have been mixed to date, without a strong consensus in the literature favoring the superiority of either IOL type. The results of our survey provide information regarding current practice patterns among cataract surgeons as well as the surgical training background and patient characteristics that influence these patterns.
Chemically‐controlled orthogonal regulation of multiple endogenous genes (2018)

Genome editing platforms are powerful tools for gene manipulation. These platforms offer a wide variety of promising applications in medical science and biotechnology. Induction of protein domain associations by stimuli such as light or chemicals has been widely used for the temporal control of biomolecular function such as enzymatic activity. Further, the DNA binding specificity of genome editing tools can be applied in gene regulation systems by combining them with transcription‐activator or transcription‐repressor domains. Targeting the gene promoter sequence using multiple artificial transcription factors enables synergistic and efficient regulation of gene expression. In addition, the use of these platforms in combination can expand the scope of targetable sequences by avoiding DNA‐binding issues, such as PAM recognition for CRISPR‐Cas9, 5′‐T recognition for TALE domain, and complementary strand recognition for ZF domain. Furthermore, the guide RNA for Cas9 cannot distinguish alleles because of the commonly used gRNA sequence recognized by Cas9, thereby limiting the utility of this approach for orthogonal regulation of multiple genes. In this study, the rapamycin‐ (R‐) or gibberellin‐ (G‐) inducible system was applied for gene regulation using multiple TALEs and dCas9 to enable orthogonally inducible regulation of endogenous genes. For the R‐inducible system, FKBP‐tagged TALEs, and dCas9, the effector domains with FRB, VP64 for activation and SID×4 for repression, were constructed. GID‐tagged TALEs and dCas9 as well as GAI‐fused VP64 were constructed for the G‐inducible system. The fold change in gene expression was evaluated by luciferase reporter assays. The results showed that gene expression was regulated by addition of chemicals, indicating rapamycin‐induced FKBP‐FRB association and gibberellin‐induced GID‐GAI association. The systems were further utilized for controlling endogenous gene expression in 293A cells. The results revealed that the expression of two genes could be differentially regulated by rapamycin and gibberellin in a time‐dependent manner. This system could achieve the control of gene function in cellular phenomena owing to the programmable timing of expression and differential expression of multiple genes. Support or Funding Information This work was supported in part by the New Energy and Industrial Technique Development Organization (NEDO) of Japan, JSPS KAKENHI (25410171), Grant‐in‐Aid for Scientific Research on Innovative Areas (24119506 and 26119703) to W. N. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .