gebhart/patrepeval huggingface dataset:
Ligand and solvent effects on the absorption spectra of CdS magic-sized clusters (2023)

The absorption spectra of congenetic wurtzite (WZ) and zincblende (ZB) CdS magic-sized clusters are investigated. We demonstrate that the exciton peak positions can be tuned by up to 500 meV by varying the strong coupling between X-type ligands and the semiconductor cores, while the addition of L-type ligands primarily affects cluster midgap states. When Z-type ligands are displaced by L-type ligands, red shifts in the absorption spectra are observed, despite the fact there is a small decrease in cluster size. Density functional theory calculations are used to explain these findings and they reveal the importance of Cd and S dangling bonds on the midgap states during the Z- to L-type ligand exchange process. Overall, ZB CdS clusters show higher chemical stability than WZ clusters but their optical properties exhibit greater sensitivity to the solvent. Conversely, WZ CdS clusters are not stable in a Lewis base-rich environment, resulting in various changes in their spectra. Our findings enable researchers to select capping ligands that modulate the optical properties of semiconductor clusters while maintaining precise control over their solvent interactions.
Direct adaptive neural network control of nonlinear systems (1997)

This paper addresses the tracking control problem for a general class of nonlinear systems using neural networks (NN). The proposed controller ensures that the output of the system tracks any given reference signal which belongs to a known compact set. It is proven that the closed-loop system is semi-globally uniformly ultimately bounded type. In addition, if the approximate accuracy of the neural networks is high enough, an arbitrarily small tracking error can be achieved.
EI-1941-1 and -2, Novel Interleukin-1.BETA. Converting Enzyme Inhibitors Produced by Farrowia sp. E-1941: I. Biochemical Characterization of EI-1941-1 and -2 (2003)

EI-1941-1 and -2 isolated from the culture broths of Farrowia sp. selectively inhibited the human recombinant ICE activity with IC50 values of 0.086 and 0.006 microM, respectively, without inhibiting elastase and cathepsin B. EI-1941-1 and -2 also inhibited mature interleukin-1beta secretion from THP-1 cells induced by LPS with IC50 values of 5.0 and 10.3 microM, respectively. Biochemical characterizations of EI-1941-1 and -2 are described in this article.
Accurate Double-Height Micromolding Method for Three-Dimensional PolyDiMethylSiloxane Structures (2003)

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(R)-(-)- and (S)-(+)-Adenallene: synthesis, absolute configuration, enantioselectivity of antiretroviral effect, and enzymic deamination. (1992)

Synthesis of optically pure (-)- and (+)-adenallene 2 and 3 is described. Racemic adenallene (1a) was subjected to deamination with adenosine deaminase monitored by HPLC using a Chiralcel CA-1 column to give (-)-adenallene (2) and (+)-hypoxallene (4). The latter compound was converted to acetate 5. The reaction of 5 with trifluoromethanesulfonic anhydride and pyridine followed by ammonolysis furnished acetate 6 or (+)-adenallene (3) depending on the solvent used in the last step. Acetate 5 was smoothly transformed to the 6-chloro derivative 7, but an attempted ammonolysis led only to racemization and decomposition. Single crystal X-ray diffraction established the R-configuration of (-)-enantiomer 2. The latter forms a pseudosymmetric dimer in the lattice with the adenine moiety in an anti-like conformation. The torsional angles of the allenic bonds show departures from 90 degrees (91 and 97 degrees, respectively) and rotameric preference of the hydroxymethyl groups is different in both molecules of the dimer. The R-enantiomer 2 inhibited the replication and cytopathic effect of human immunodeficiency virus (HIV-1) in ATH8 cell culture with an IC50 of 5.8 microM, whereas the S-enantiomer 3 was less active (IC50 > 200 microM). The enantioselectivity of the anti-HIV effect is significantly lower than that of 2',3'-dideoxyadenosine. Kinetics of deamination of R- and S-enantiomers 2 and 3 catalyzed by adenosine deaminase gave the following parameters: Km values of S-form 3 and R-form 2 were 0.41 and 0.52 mM with Vmax being 530 and 18.5 mumol/min, respectively [corrected]. Again,, a much lower level of enantioselectivity of deamination was observed than that of D- and L-adenosine. These results indicate (i) different enantioselectivity of enantiomers 2 and 3 as HIV inhibitors and adenosine deaminase substrates and (ii) both R- and S-enantiomers 2 and 3 can function as nucleoside analogues with varied enantioselectivity for different enzymes or receptors.
Influence of temperature on a carbon nanotube resonator by molecular dynamics simulations (2011)

Phonon related multi-scale problems are very challenging but worthy of study to predict the thermal characteristics of nanomaterial composites on the continuum scale. For this reason, we have studied the interaction between mechanical and thermal characteristics in a carbon nanotube resonator by observing the phase space trajectories, strain-stress distributions, and lattice vibrational spectra. The calculation was based on molecular dynamics simulations using the REBO potential, where a carbon nanotube was excited by sinusoidal mechanical forcing at a tube end with constant-temperature boundary condition. The result confirms that the localized strain distribution is in agreement with previous high-resolution transmission electron microscopy results [1]. Particularly notable is the excitation near the 1st mode of resonance frequency which shows transient vibration with the beating frequency. Based on the simulations, the dynamic Young’s modulus and the damping coefficient will be extracted in the frequency domain for different nanotube length and chirality, and will be compared with the continuum theories. In addition, by carrying out the calculations for various temperatures, the interaction between the first resonance mode and the background phonons will be discussed based on the obtained dissipated thermal energy and the phonon energy spectra.
Supplemental Table 1 from A Synthetic Lethal Screen Reveals Enhanced Sensitivity to ATR Inhibitor Treatment in Mantle Cell Lymphoma with ATM Loss-of-Function (2023)

&lt;p&gt;Supplemental Table 1. DiscoveRx ATR inhibitor profile&lt;/p&gt;
Development of targeted radiotherapy for triple negative breast cancer. (2018)

e13112 Background: Breast cancer (BC) remains a leading cause of cancer-related deaths worldwide. Triple negative breast cancer (TNBC) is an aggressive phenotype that comprises only 15-20% of all new BC cases but is responsible for a majority of related deaths. Chemotherapy is the current mainstay treatment for TNBC but side effects and drug-resistance remain an issue, so development of targeted therapies for TNBC is critical. Tumor associated mucin 1 (tMUC1), an aberrantly glycosylated transmembrane glycoprotein, is overexpressed in > 90% of TNBCs. We’ve developed a humanized, tMUC1-specific antibody (hTAB004) and radiolabeled it to allow for targeted TNBC treatment. Methods: hTAB004 was conjugated to DOTA-NHS, purified, formulated in a metal free buffer and radiolabeled with Indium-111 or Actinium-225 to produce 111In-DOTA-hTAB004 and 225Ac-DOTA-hTAB004, respectively. In vivo and ex vivo biodistribution studies of 111In-DOTA-hTAB004 were performed in HCC70 xenograft tumor-bearing female NSG mice (n = 3) using SPECT/CT imaging. Therapeutic efficacy of 225Ac-DOTA-hTAB004 was determined in HCC70 xenograft tumor-bearing female nude mice (n = 5/group) and monitoring body weight and tumor sizes. Results: Radiolabeling efficiency of hTAB004 with Indium-111 and Actinium-225 was > 97%. In vivo biodistribution data revealed increased accumulation of 111In-DOTA-hTAB004 in the tumor over 120 hrs. Ex vivo biodistribution data showed 46% ID/g uptake of 111In-DOTA-hTAB004 in the tumor, > 3-fold higher than in the next highest uptake organ, the spleen. Tumor volumes decreased by > 89% in mice treated with a single injection of 225Ac-DOTA-hTAB004 (18kBq), but continued to grow in the control group that received DOTA-hTAB004 alone. Based on Invicro IACUC criteria, 100% of treated mice survived until the end of the study while all mice in control group died by day 35. Conclusions: 111In-DOTA-hTAB004 biodistribution data indicates the excellent tumor targeting capabilities of hTAB004 and 225Ac-DOTA-hTAB004 therapy data shows exceptional clinical benefit in mice bearing human tumors. Given this data, radiolabeled hTAB004 is a promising targeted treatment and imaging option for TNBC. Acknowledgment Funded by NCI SBIR Contract No HHSN261201600013C
Neuronal glucose but not lactate utilization is positively correlated with NMDA‐induced neurotransmission and fluctuations in cytosolic Ca<sup>2+</sup>levels (2009)

Although the brain utilizes glucose for energy production, individual brain cells may to some extent utilize substrates derived from glucose. Thus, it has been suggested that neurons consume extracellular lactate during synaptic activity. However, the precise role of lactate for fueling neuronal activity is still poorly understood. Recently, we demonstrated that glucose metabolism is up-regulated in cultured glutamatergic neurons during neurotransmission whereas that of lactate is not. Here, we show that utilization of glucose but not lactate correlates with NMDA-induced neurotransmitter glutamate release in cultured cerebellar neurons from mice. Pulses of NMDA at 30, 100, and 300 microM, leading to a progressive increase in both cytosolic [Ca2+] and release of glutamate, increased uptake and metabolism of glucose but not that of lactate as evidenced by mass spectrometric measurement of 13C incorporation into intracellular glutamate. In this manuscript, a cascade of events for the preferential neuronal utilization of glucose during neurotransmission is suggested and discussed in relation to our current understanding of neuronal energy metabolism.
Degradation of chondroitin sulfate A by a PUL-like operon in Tannerella forsythia (2022)

Advanced periodontitis has been shown to have strong association with the residence of the bacterial consortia known as the red complex comprised by Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. T. forsythia shares a distant genetic linkage to Bacteroidetes thetaiotaomicron and may therefore produce analogous polysaccharide utilization loci (PUL) which enable complex carbohydrate degradation, import, and use, although this capacity has yet to be demonstrated. Chondroitin sulfate A is a linear, sulfated carbohydrate linked to periodontal disease as the principal species of glycosaminoglycan appended on the surface of cortical bone of teeth and in supporting dental ligaments. Through genomic comparisons with B. thetaiotaomicron, a new PUL-like operon (Bfo2285-Bfo2295, and Bfo3043) was identified in T. forsythia and the crystal structure of two proteins from this PUL-like operon, Bfo2290 and Bfo2294, were reported using X-ray crystallography. Enzyme kinetics for Bfo2290 were reported using a pH-dependent assay and suggested a Km of 0.75 mg/ml ± 0.60 mg/ml, Kcat of 3.74 min-1 ± 0.88 min-1, and Vmax of 7.48 μM/min ± 1.76 μM/min with partially degraded chondroitin sulfate A. Fluorophore-assisted carbohydrate electrophoresis was used to show the processive degradation of chondroitin sulfate A by the proteins encoded in T. forsythia PUL-like operon, and revealed Bfo2291 and Bfo2290 to be an endolytic chondroitin sulfate A lyase and exolytic ΔDi-4S chondroitin sulfate A sulfatase, respectively.
Sulfatides are endogenous ligands for the TLR4–MD-2 complex (2021)

Many endogenous molecules, mostly proteins, purportedly activate the Toll-like receptor 4 (TLR4)-myeloid differentiation factor-2 (MD-2) complex, the innate immune receptor for lipopolysaccharide (LPS) derived from gram-negative bacteria. However, there is no structural evidence supporting direct TLR4-MD-2 activation by endogenous ligands. Sulfatides (3-<i>O</i>-sulfogalactosylceramides) are natural, abundant sulfated glycolipids that have variously been shown to initiate or suppress inflammatory responses. We show here that short fatty acid (FA) chain sulfatides directly activate mouse TLR4-MD-2 independent of CD14, trigger MyD88- and TRIF-dependent signaling, and stimulate tumor necrosis factor α (TNFα) and type I interferon (IFN) production in mouse macrophages. In contrast to the agonist activity toward the mouse receptor, the tested sulfatides antagonize TLR4-MD-2 activation by LPS in human macrophage-like cells. The agonistic and antagonistic activities of sulfatides require the presence of the sulfate group and are inversely related to the FA chain length. The crystal structure of mouse TLR4-MD-2 in complex with C16-sulfatide revealed that three C16-sulfatide molecules bound to the MD-2 hydrophobic pocket and induced an active dimer conformation of the receptor complex similar to that induced by LPS or lipid A. The three C16-sulfatide molecules partially mimicked the detailed interactions of lipid A to achieve receptor activation. Our results suggest that sulfatides may mediate sterile inflammation or suppress LPS-stimulated inflammation, and that additional endogenous negatively charged lipids with up to six lipid chains of limited length might also bind to TLR4-MD-2 and activate or inhibit this complex.
Investigating the relationship between driver's sense of agency and EEG: Mu-rhythm is more suppressed in higher SoA case (2017)

The present study investigated the relationship between driver's SoA and relative power of alpha band in EEG. The SoA rating results suggest that driver has less SoA under driving assistance or disturbance generally, while inexperienced driver may have enhanced SoA under driving assistance. In EEG results, although not significant, some electrodes showed greater alpha band power in automated or delayed condition, implying that driver's SoA could be evaluated by measuring the alpha band activity over certain area of brain. In future plans, more experiment should be conducted to include both experienced and inexperienced drivers, to increase the number of EEG data, and to evaluate the effect of ERD by body movement. Phase coherence analysis should be done as well.
Analytic models of high-temperature hohlraums (2001)

A unified set of high-temperature-hohlraum models has been developed. For a simple hohlraum, P(S)=[A(S)+(1-alpha(W))A(W)+A(H)]sigmaT(4)(R)+(4Vsigma/c)(dT(4)(R)/dt), where P(S) is the total power radiated by the source, A(S) is the source area, A(W) is the area of the cavity wall excluding the source and holes in the wall, A(H) is the area of the holes, sigma is the Stefan-Boltzmann constant, T(R) is the radiation brightness temperature, V is the hohlraum volume, and c is the speed of light. The wall albedo alpha(W) identical with(T(W)/T(R))(4) where T(W) is the brightness temperature of area A(W). The net power radiated by the source P(N)=P(S)-A(S)sigmaT(4)(R), which suggests that for laser-driven hohlraums the conversion efficiency eta(CE) be defined as P(N)/P(Laser). The characteristic time required to change T(4)(R) in response to a change in P(N) is 4V/c[(1-alpha(W))A(W)+A(H)]. Using this model, T(R), alpha(W), and eta(CE) can be expressed in terms of quantities directly measurable in a hohlraum experiment. For a steady-state hohlraum that encloses a convex capsule, P(N)=[(1-alpha(W))A(W)+A(H)+[(1-alpha(C))A(C)(A(S)+alpha(W)A(W))/A(T)]]sigmaT(4)(RC), where alpha(C) is the capsule albedo, A(C) is the capsule area, A(T) identical with(A(S)+A(W)+A(H)), and T(RC) is the brightness temperature of the radiation that drives the capsule. According to this relation, the capsule-coupling efficiency of the baseline National Ignition Facility hohlraum is 15-23 % higher than predicted by previous analytic expressions. A model of a hohlraum that encloses a z pinch is also presented.
Discovery and validation of novel methylated DNA markers of cervical cancer. (2021)

5526 Background: HR-HPV DNA testing, with or without cervical cytology, provides excellent sensitivity for detection of cervical cancer (CC) and its precursors; negative test results indicate that risk of disease is extremely low and enable women to undergo reduced screening with safety. However, management of women who screen positive remains challenging as many will prove to have self-limited HR-HPV infections. DNA methylation is an early event in carcinogenesis that could enhance CC screening specificity. Methods: For discovery, DNA from 70 FFPE CC (36 squamous, 34 adenocarcinoma) tissues that were reviewed microscopically, 18 fresh frozen benign cervicovaginal (BCV) tissues collected at the time of benign hysterectomy, and 18 buffy coats from cancer-free women underwent reduced representation bisulfite sequencing (RRBS) to identify MDMs associated with CC. Candidate MDM selection was based on area under the receiver operating characteristic curve (AUC) discrimination, methylation fold change, and low background methylation among benign controls. Candidate MDMs were re-tested using methylation-specific PCR (MSP) to confirm performance. Blinded biological validation was performed using MSP on DNA extracted from independent FFPE CC (38 squamous, 43 adenocarcinoma) and BCV (40) tissues. The performance of CC MDMs was also tested in DNA extracted from cervical dysplasia (36 adenocarcinoma in situ (AIS), 32 cervical intraepithelial neoplasia (CIN) 2/3, 11 CIN 1) FFPE tissues. Results: From RRBS discovery and technical validation via MSP, 30 candidate MDMs showed marked methylation fold changes (10 to &gt;1000) across both CC histologies compared to BCV tissue from cancer-free women. Each of the 30 MDMs highly discriminated CC from BCV tissue with 9 MDMs having an AUC &gt;0.90 (Table). CC MDMs also highly discriminated AIS from BCV but did not perform well in CIN 2/3 and CIN 1 (Table). Conclusions: Whole methylome sequencing, stringent filtering criteria, and biological validation have yielded outstanding candidate MDMs for CC that highly discriminate CC from BCV, notably with high specificity. Performance in cervical dysplasias varied with higher positivity rates in AIS than in CIN 2/3 and CIN 1. Translation to testing these novel MDMs in lower genital tract biospecimens and the addition of HR-HPV to the CC panel are warranted.[Table: see text]
Identification and detection of three new F17 fimbrial variants in Escherichia coli strains isolated from cattle (2014)

F17 fimbriae are produced by pathogenic Escherichia coli involved in diarrhea and septicemia outbreaks in calves and lambs. These proteins result from the expression of four different clustered genes, namely f17A, f17D, f17C and f17G, encoding a pilin protein, a periplasmic protein, an anchor protein and an adhesin protein, respectively. Several variants of f17A and f17G genes have been reported and found genetically associated with typical virulence factors of bovine pathogenic E. coli strains. In this study, a new F17e-A variant, closely related to F17b-A, was identified from a collection of 58 E. coli isolates from diarrheic calves in Iran. While highly prevalent in Iranian F17-producing clinical isolates from calves, this variant was rare among E. coli from a French healthy adult bovine population, suggesting a possible association with virulence. The f17Ae gene was also found in the genome of the Shiga-like toxin variant Stx1d-producing bovine E. coli strain MHI813, and belonged to a gene cluster also encoding a new F17-G3 variant, which greatly differed from F17-G1 and F17-G2. This gene cluster was located on a pathogenicity island integrated in the tRNA pheV gene. The gene coding for a third new F17f-A variant corresponding to a combination of F17c-A and F17d-A was also identified on the pVir68 plasmid in the bovine pathogenic E. coli strain 6.0900. In conclusion, we identified three new F17-A and F17-G variants in cattle E. coli, which may also have significant impact on the development of new diagnostics and vaccination tools.
A comparison between lipase‐catalyzed esterification of oleic acid with glycerol in monolayer and microemulsion systems (1994)

Abstract Lipase‐catalyzed synthesis‐esterification of oleic acid with glycerol‐was carried out in L2 microemulsions and in monolayers. The microemulsions were based on isooctane as a nonpolar component and various water‐glycerol mixtures as polar component. The substrate, oleic acid/sodium oleate, constituted the microemulsion surfactant. The lipase resides mainly in the water pools. Monolayers of oleic acid/sodium oleate were formed on subsolutions of glycerol and water, and the enzyme solution was injected under the compressed monolayers. Thus, the arrangement of the reactants at the oil‐water interface of the microemulsion can be regarded as analogous to that at the airwater interface of the monolayer. The microemulsion structure was characterized by self‐diffusion nuclear magnetic resonance. It was found that the higher the glycerol‐to‐water ratio, the lower are the water D‐values. The reactions in microemulsions generally gave a low degree of oleic acid conversion. The yield increased with increasing glycerolto‐water ratio. Monoglycerides were the main product, and no triglyceride could be detected. The monolayer experiments gave a somewhat higher degree of conversion, with tri‐ and diglycerides being the major reaction products. The reason why triglycerides are formed in monolayer experiments but not in microemulsions is believed to be due to an unfavorable partitioning of the diglyceride in the microemulsion systems. Once formed, the diglyceride will partition into the hydrocarbon domain and become inaccessible for reaction with the enzyme‐O‐acyl intermediate at the oil‐water interface. In addition, the interfaces in the two systems are different. The monolayer interface is static, whereas the microemulsion interface is highly dynamic, and this difference may also influence the product patterns.
Quantifying Individual Losses in a Direct Methanol Fuel Cell (2011)

Studying the performance of a direct methanol fuel cell (DMFC) is complicated by the complex interactions of kinetic and transport processes. As a result, changes in one aspect of the cell have consequences in other aspects, which are difficult to elucidate from full-cell polarization (i.e., voltage versus current) behavior. This study outlines a strategy to use current and voltage relationships from anode half-cells, cathode half-cells, and hydrogen pump coupled with methanol crossover data and a mathematical model. In this way, all the kinetic and transport processes have been quantified, and the cell voltage was deconstructed (i.e., individual voltage losses were quantified). This data analysis accounts for all of the voltage losses observed during the operation of the full cell. As expected, the anode and cathode overpotentials accounted for most of the losses (i.e., 92% on average). Also, the cathode flow rate has been shown to affect the methanol crossover by diffusion. Cells operated at constant stoichiometry or where the cathode flow rate is small can show a parabolic shape in the methanol crossover because the electroosmotic drag dominates over diffusion as the primary transport mechanism for methanol through the membrane. Decrease in the methanol crossover was observed for cells with high compression and thicker cathode electrodes. The one-dimensional model, developed previously (García et al., 2004, “Mathematical Model of a Direct Methanol Fuel Cell,” J. Fuel Cell Sci. Technol., 1(1), pp. 43–48), was improved by: (1) including methanol transport from the anode flow channel to the backing layer using a mass transfer resistance and (2) accounting for the unreacted methanol transport through the cathode. The model was able to reasonably predict the anode, cathode, full-cell polarization, and methanol crossover data for methanol concentrations between 0.05 M and 2 M at all operating currents.