gebhart/patrepeval huggingface dataset:
Magnetic Resonance Imaging Overestimates Ferumoxide-Labeled Stem Cell Survival After Transplantation in the Heart (2008)

The persistence of significant iron-dependent MRI signal derived from ferumoxide-containing macrophages despite few or no viable stem cells 3 weeks after transplantation indicates that MRI of ferumoxide-labeled cells does not reliably report long-term stem cell engraftment in the heart.
British Telecom TPON application in the US network (2003)

The authors discuss the cost modeling against copper of various forms of TPON (telephony over a passive optical network) in a typical US environment. Passive optical networks such as TPON, with their lean use of fiber and low-fixed costs, are shown to be less sensitive to distance than copper. This leads to he conclusion that the approach can be a cost-effective method of delivering POTS while providing an effective platform for future wideband or broadband upgrades. Although TPON has been used as a role model for this costing, several approaches should be capable of similar results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Self-Assembly of Tunable Intrinsically Disordered Peptide Amphiphiles (2022)

Abstract Intrinsically disordered peptide amphiphiles (IDPAs) present a novel class of synthetic conjugates that consist of short hydrophilic polypeptides anchored to hydrocarbon chains. These hybrid polymer-lipid block constructs spontaneously self-assemble into dispersed nanoscopic aggregates or ordered mesophases in aqueous solution due to hydrophobic interactions. Yet, the possible sequence variations and their influence on the self-assembly structures is vast and have hardly been explored. Here, we measure the nanoscopic self-assembled structures of four IDPA systems that differ by their amino acid sequence. We show that permutations in the charge pattern along the sequence remarkably alter the headgroup conformation and consequently alters the pH-triggered phase transitions between spherical, cylindrical micelles and hexagonal condensed phases. We demonstrate that even a single amino acid mutation is sufficient to tune structural transitions in the condensed IDPA mesophases, while peptide conformations remain unfolded and disordered. Furthermore, alteration of the peptide sequence can render IDPAs to become susceptible to enzymatic cleavage and induces enzymatically activated phase transitions. These results hold great potential for embedding multiple functionalities into lipid nanoparticle delivery systems by incorporating IDPAs with desired properties.
ChemInform Abstract: Superacidic Cyclization of All‐trans‐ω‐acetoxyfarnesyl Benzyl Ether. (2000)

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.
Potassium Ethenyl Trifluoroborate (2006)

[13682-77-4] C2H3BF3K (MW 133.99)





InChI = 1S/C2H3BF3.K/c1-2-3(4,5)6;/h2H,1H2;/q-1;+1



InChIKey = ZCUMGICZWDOJEM-UHFFFAOYSA-N



(an organometallic reagent that participates in palladium-catalyzed cross-coupling reactions with aryl- or alkenyl halides or triflates and with arenediazonium electrophiles. Thus, it is a capable vinylating agent when using palladium catalysts. Rhodium-catalyzed asymmetric conjugate addition to enones. Rhodium-catalyzed addition to dehydroamino esters to give alanine derivatives)



Physical Data: mp 241 °C.



Solubility: soluble in acetone,1 acetonitrile.



Form Supplied in: highly stable, easily prepared white solid.



Analysis of Reagent Purity: 1H NMR, 13C NMR, 19F NMR, 11B NMR.



Preparative Methods:2 to a solution of trimethyl borate (1.5 equiv) in anhydrous THF is added dropwise a 15% solution of vinylmagnesium chloride (1 equiv) in THF at –60 °C. The mixture is stirred under argon for 30 min at –60 °C, raised to room temperature and stirred another 30 min. Potassium hydrogen fluoride (6 equiv) is added at once at 0 °C followed by the slow addition of water which results in a white precipitate. The suspension is stirred for 30 min at room temperature after which the solvents are removed. The resulting powder is thoroughly dried under vacuum, extracted several times with acetone, and the solvent is removed under vacuum. The product is purified by dissolving in a minimum amount of boiling acetone and reprecipitating by addition of diethyl ether to give the vinyl trifluoroborate.



Purification: purified by reprecipitation with diethyl ether from acetone.
Roles of microtubules, cell polarity and adhesion in electric-field-mediated motility of 3T3 fibroblasts (2004)

Direct-current electric fields mediate motility (galvanotaxis) of many cell types. In 3T3 fibroblasts, electric fields increased the proportion, speed and cathodal directionality of motile cells. Analogous to fibroblasts' spontaneous migration, we initially hypothesized that reorientation of microtubule components modulates galvanotaxis. However, cells with intact microtubules did not reorient them in the field and cells without microtubules still migrated, albeit slowly, thus disproving the hypothesis. We next proposed that, in monolayers wounded and placed in an electric field, reorientation of microtubule organizing centers and stable, detyrosinated microtubules towards the wound edge is necessary and/or sufficient for migration. This hypothesis was negated because field exposure mediated migration of unoriented, cathode-facing cells and curtailed migration of oriented, anode-facing cells. This led us to propose that ablating microtubule detyrosination would not affect galvanotaxis. Surprisingly, preventing microtubule detyrosination increased motility speed, suggesting that detyrosination inhibits galvanotaxis. Microtubules might enhance adhesion/de-adhesion remodeling during galvanotaxis; thus, electric fields might more effectively mediate motility of cells poorly or dynamically attached to substrata. Consistent with this hypothesis, incompletely spread cells migrated more rapidly than fully spread cells. Also, overexpression of PAK4, a Cdc42-activated kinase that decreases adhesion, enhanced galvanotaxis speed, whereas its lack decreased speed. Thus, electric fields mediate fibroblast migration via participation of microtubules and adhesive components, but their participation differs from that during spontaneous motility.
Pulmonary Hemosiderosis Due to Mitral Valvular Heart Disease (1999)

We report a case of biopsy-proven secondary hemosiderosis of the lung in a 58-year-old patient with mitralvalvular heart disease. Both chest radiography and high-resolution CT demonstrated patchy areas of ground-glassopacity; the former indicated that it was in both lungs, while the latter showed inter- and intralobular septalthickening. These findings were reversible when pulmonary venous hypertension was corrected.
Fairness Through Robustness: Investigating Robustness Disparity in Deep Learning (2020)

Deep neural networks (DNNs) are increasingly used in real-world applications (e.g. facial recognition). This has resulted in concerns about the fairness of decisions made by these models. Various notions and measures of fairness have been proposed to ensure that a decision-making system does not disproportionately harm (or benefit) particular subgroups of the population. In this paper, we argue that traditional notions of fairness that are only based on models' outputs are not sufficient when the model is vulnerable to adversarial attacks. We argue that in some cases, it may be easier for an attacker to target a particular subgroup, resulting in a form of \textit{robustness bias}. We show that measuring robustness bias is a challenging task for DNNs and propose two methods to measure this form of bias. We then conduct an empirical study on state-of-the-art neural networks on commonly used real-world datasets such as CIFAR-10, CIFAR-100, Adience, and UTKFace and show that in almost all cases there are subgroups (in some cases based on sensitive attributes like race, gender, etc) which are less robust and are thus at a disadvantage. We argue that this kind of bias arises due to both the data distribution and the highly complex nature of the learned decision boundary in the case of DNNs, thus making mitigation of such biases a non-trivial task. Our results show that robustness bias is an important criterion to consider while auditing real-world systems that rely on DNNs for decision making. Code to reproduce all our results can be found here: \url{https://github.com/nvedant07/Fairness-Through-Robustness}
Magnetism and Its Structural Coupling Effects in 2D Ising Ferromagnetic Insulator VI<sub>3</sub> (2021)

van der Waals (vdW) magnets have emerged as a tunable platform for exploring a variety of layer-dependent magnetic phenomena. Here we probe the thickness-dependent magnetism of vanadium triiodide (VI3), a material known as a layered ferromagnetic Mott insulator in its bulk form, using magnetic circular dichroism microscopy. Robust ferromagnetism is observed in all thin layers, down to the monolayer limit with large coercive fields. In contrast to known vdW magnets, the Curie temperature shows an anomalous increase as the layer number decreases, reaching a maximum of 60 K in monolayers. Second harmonic generation measurements reveal broken inversion symmetry in exfoliated flakes, down to trilayers. This observation demonstrates that the exfoliated flakes take a layer stacking arrangement that differed from the inversion-symmetric parent bulk counterpart. Our results suggest a coupling effect between magnetic and structural degrees of freedom in VI<sub>3</sub> and its potential for engineering layer and twist angle-dependent magnetic phenomena.
A Single Amino Acid That Determines the Sensitivity of Progesterone Receptors to RU486 (1992)

The progesterone analog RU486, an abortifacient, inhibits the action of progestins in humans but not in chickens or hamsters. Substitution of cysteine at position 575 by glycine in the hormone binding domain (HBD) of the chicken progesterone receptor (cPR) generated a cPR that binds RU486 and whose activity is antagonized by that compound. In fact, all receptors that bind RU486 have a glycine at the corresponding position. The hamster PR, like cPR, has a cysteine. Only glycine--not methionine or leucine--at position 575 allowed binding of RU486 to cPR. Substitution of this glycine by cysteine in the human PR (hPR) abrogated binding of RU486 but not that of an agonist. The corresponding mutation in the human glucocorticoid receptor resulted in a loss of binding of both dexamethasone and RU486. Examination of a series of 11 beta-substituted steroids showed that antagonism is not an intrinsic property of an antihormone, because one hPR antagonist acted as an agonist for a mutated hPR. The positioning of an aromatic 11 beta-substitution in the PR HBD appears to be critical for generating agonistic or antagonistic activity.
Cyclopentenone prostaglandins: New insights on biological activities and cellular targets (2001)

The cyclopentenone prostaglandins PGA2, PGA1, and PGJ2 are formed by dehydration within the cyclopentane ring of PGE2, PGE1, and PGD2. PGJ2 is metabolized further to yield Δ12-PGJ2 and 15-deoxy-Δ12,14-PGJ2 (15d-PGJ2). Various compounds within the cyclopentenone prostaglandin family possess potent anti-inflammatory, anti-neoplastic, and anti-viral activity. Most actions of the cyclopentenone prostaglandins do not appear to be mediated by binding to G-protein coupled prostanoid receptors. Rather, the bioactivity of these compounds results from their interaction with other cellular target proteins. 15-deoxy-Δ12,14-PGJ2 is a high affinity ligand for the nuclear receptor PPARγ and modulates gene transcription by binding to this receptor. Other activities of the cyclopentenone prostaglandins are mediated by the reactive α,β-unsaturated carbonyl group located in the cyclopentenone ring. The transcription factor NF-κB and its activating kinase are key targets for the anti-inflammatory activity of 15d-PGJ2, which inhibits NF-κB-mediated transcriptional activation by PPARγ-dependent and independent molecular mechanisms. Other cyclopentenone prostaglandins, such as Δ7-PGA1 and Δ12-PGJ2, have strong anti-tumor activity. These compounds induce cell cycle arrest or apoptosis of tumor cells depending on the cell type and treatment conditions. We review here recent progress in understanding the mechanisms of action of the cyclopentenone prostaglandins and their possible use as therapeutic agents. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 3, 185–210, 2001
Rare variants in GABA(A) receptor genes in Rolandic epilepsy and related syndromes (2015)

Objective: To test whether mutations in gamma-aminobutyric acid type A receptor (GABA(A)-R) subunit genes contribute to the etiology of Rolandic epilepsy (RE) or its atypical variants (ARE). Methods: We performed exome sequencing to compare the frequency of variants in 18 GABA(A)-R genes in 204 European patients with RE/ARE versus 728 platform matched controls. Identified GABRG2 variants were functionally assessed for protein stability, trafficking, postsynaptic clustering and receptor function. Results: Out of 18 screened GABA(A)-R genes, we detected an enrichment of rare variants in the GABRG2 gene in RE/ARE patients (5/204, 2.45%) in comparison to controls (1/723, 0.14%) (OR = 18.07, 95% CI = 2.01 - 855.07, p = 0.0024, pcorr = 0.043). We identified a GABRG2 splice variant (c.549-3T>G) in two unrelated patients as well as three nonsynonymous variations in this gene (p.G257R, p.R323Q, p.I389V). Functional assessment showed reduced surface expression of p.G257R and decreased GABA-evoked currents for p.R323Q. The p.G257R mutation displayed diminished levels of palmitoylation, a posttranslational modification crucial for trafficking of proteins to the cell membrane. Enzymatically raised palmitoylation levels restored the surface expression of the p.G257R variant {Gamma}2-subunit. Interpretation: The statistical association and the functional evidence suggest that mutations of the GABRG2 gene may increase the risk of RE/ARE. Restoring the impaired membrane trafficking of some GABRG2 mutations by enhancing palmitoylation might be an interesting therapeutic approach to reverse the pathogenic effect of such mutants.
Hamiltonian Engineering with Multicolor Drives for Fast Entangling Gates and Quantum Crosstalk Cancellation (2022)

Quantum computers built with superconducting artificial atoms already stretch the limits of their classical counterparts. While the lowest energy states of these artificial atoms serve as the qubit basis, the higher levels are responsible for both a host of attractive gate schemes as well as generating undesired interactions. In particular, when coupling these atoms to generate entanglement, the higher levels cause shifts in the computational levels that lead to unwanted ZZ quantum crosstalk. Here, we present a novel technique to manipulate the energy levels and mitigate this crosstalk with simultaneous off-resonant drives on coupled qubits. This breaks a fundamental deadlock between qubit-qubit coupling and crosstalk. In a fixed-frequency transmon architecture with strong coupling and crosstalk cancellation, additional cross-resonance drives enable a 90 ns CNOT with a gate error of (0.19±0.02)%, while a second set of off-resonant drives enables a novel CZ gate. Furthermore, we show a definitive improvement in circuit performance with crosstalk cancellation over seven qubits, demonstrating the scalability of the technique. This Letter paves the way for superconducting hardware with faster gates and greatly improved multiqubit circuit fidelities.
Celiprolol Increases Coronary Blood Flow and Reduces Severity of Myocardial Ischemia via Nitric Oxide Release (2003)

Celiprolol is a selective beta(1)-adrenoceptor antagonist with antihypertensive actions, which causes renal vasodilation by increasing tissue nitric oxide (NO) levels. The authors tested whether celiprolol increases coronary blood flow (CBF) by increasing cardiac NO release in the ischemic heart in vivo. In open-chest dogs, coronary perfusion pressure of the left anterior descending coronary artery was reduced so that CBF decreased to 60% of control levels, and thereafter, coronary perfusion pressure was maintained constant. Ten minutes after the reduction of coronary perfusion pressure, we infused celiprolol into the left anterior descending coronary artery and measured fractional shortening and lactate extraction ratio as indices of regional myocardial contractility and metabolism. CBF significantly increased from 51.5 mL/100 g/min +/- 1.9 to 67.0 mL/100 g/min +/- 5.1 20 minutes after celiprolol infusion without changes in coronary perfusion pressure, while fractional shortening and lactate extraction ratio increased. Celiprolol also increased cardiac NO release. The L omega-nitroarginine methyl ester, the inhibitor of NO synthase, attenuated the increases in CBF, fractional shortening, lactate extraction ratio, and cardiac NO release due to celiprolol. ICI 118551, a beta(2)-adrenoceptor antagonist, did not blunt the effects of celiprolol and a nonselective beta-adrenoceptor antagonist, propranolol, increased neither CBF nor cardiac NO release, indicating that the effect of celiprolol is independent of beta-adrenoceptor blockade. It was concluded that celiprolol mediates coronary vasodilation and improves myocardial ischemia through NO-dependent mechanisms.
Molecular Design of Photocathode Materials for Hydrogen Evolution and Carbon Dioxide Reduction (2019)

Storage of solar energy in the form of readily available easy-to-handle fuels is the main bottleneck towards the development of a carbon-neutral alternative energy. Taking inspiration from natural systems, artificial photosynthesis is a technology to-be for efficiently converting the tremendous solar energy received every day on Earth into chemical energy, that is, fuels. We focus here on the construction of photocathodes, as components of photoelectrochemical (PEC) cells. In such devices, H 2 evolution or CO 2 reduction at the photocathode is combined with water oxidation to oxygen at an anode or photoanode. We review here the various molecular-based materials developed in this context.
Cytokine release and expression induced by OmpA proteins from the Gram-negative anaerobes,<i>Porphyromonas asaccharolytica</i>and<i>Bacteroides fragilis</i> (2008)

OmpA proteins from Gram-negative anaerobes Porphyromonas asaccharolytica and Bacteroides fragilis induced release and expression of IL-1alpha, tumor necrosis factor (TNF)-alpha, IFN-gamma, IL-6, and IL-10 from murine splenocytes in vitro in a dose-dependent fashion. The release of the cytokines induced by B. fragilis Bf-OmpA was at much lower levels compared with P. asaccharolytica Omp-PA; Bf-OmpA did not induce release of IL-10. Omp-PA and Bf-OmpA were able to upregulate mRNA expression of the tested cytokines. The results obtained with refolded Bf-OmpA were similar to those with native Bf-OmpA. The data presented in this research demonstrate for the first time that Omps from anaerobic bacteria can induce the release of cytokines, suggesting that Omp-PA and Bf-OmpA may play important roles in the pathogenic processes of these bacteria.
Antimicrobial Activity of 5-membered Nitroheteroaromatic Compounds beyond Nitrofurans and Nitroimidazoles: Recent Progress (2021)

The last decade has been characterized by the development and approval of pretomanid and delamanid, which are nitroimidazole based drugs for multidrug -resistant tuberculosis. This attracted renewed attention to the nitroheterocyclic scaffolds as a source of safe and efficient antimicrobial agents. While the primary focus is still on nitrofurans and nitroimidazoles, well known as bioreducible prodrugs, a number of studies have been published on other 5-membered nitroheteroaromatic compounds. The latter not only show promising antimicrobial activity but also demonstrate modes of action different from the conventional reductive activation of the nitro group. Considering the potential of these efforts to impact the continuing race against drug-resistant pathogens, herein we review non-furan/imidazole-based 5-membered nitroheteroaromatics investigated as antimicrobial agents in 2010-2020.
Detecting Sex-Biased Gene Flow in African-americans Through the Analysis of Intra- and Inter-Population Variation at Mitochondrial DNA and Y- Chromosome Microsatellites (2012)

This study reports on variations at the mitochondrial DNA (mtDNA) hypervariable region 1 (HVR-1) and at seven Y-chromosome microsatellites in an African-American population sample from Chicago, IL, USA. Our results support the hypothesis that the population studied had undergone a European male-biased gene flow. We show that comparisons of intra-and inter-population diversity parameters between African-Americans, Europeans and Africans may help detect sex-biased gene flow, providing a complement to quantitative methods to estimate genetic admixture.
Highly Ordered Mesoporous Crystalline MoSe<sub>2</sub> Material with Efficient Visible‐Light‐Driven Photocatalytic Activity and Enhanced Lithium Storage Performance (2012)

Abstract Highly ordered mesoporous crystalline MoSe 2 is synthesized using mesoporous silica SBA‐15 as a hard template via a nanocasting strategy. Selenium powder and phosphomolybdic acid (H 3 PMo 12 O 40 ) are used as Se and Mo sources, respectively. The obtained products have a highly ordered hexagonal mesostructure and a rod‐like particle morphology, analogous to the mother template SBA‐15. The UV‐vis‐NIR spectrum of the material shows a strong light absorption throughout the entire visible wavelength region. The direct bandgap is estimated to be 1.37 eV. The high surface area MoSe 2 mesostructure shows remarkable photocatalytic activity for the degradation of rhodamine B, a model organic dye, in aqueous solution under visible light irradiation. In addition, the synthesized mesoporous MoSe 2 possess a reversible lithium storage capacity of 630 mAh g −1 for at least 35 cycles without any notable decrease. The rate performance of mesoporous MoSe 2 is much better than that of analogously synthesized mesoporous MoS 2 , making it a promising anode for the lithium ion battery.