gebhart/patrepeval huggingface dataset:
Influence of impurity and phonon scattering effects in resonant tunneling structures (1993)

Tunneling properties and their temperature variations of molecular bean epitaxy grown symmetric AlAs/GaAs/AlAs resonant tunneling diodes with thin barriers are studied theoretically and experimentally. The measured peak and valley current densities show strong dependences on temperature. A Monte Carlo simulation including impurity and optical-phonon scatterings is developed for the calculation of the current-voltage behavior of the double barrier structures. This approach reveals pronounced temperature dependent tunneling features which agree well with measured results.
521. Similarities and Differences in Transcriptomic Host Response between SARS-CoV-2 and Other Viral Infections (2020)

Abstract Background COVID-19 is a pandemic caused by the SARS-CoV-2 virus that shares and differs in clinical characteristics of known viral infections. Methods We obtained RNAseq profiles of 62 prospectively enrolled COVID-19 patients and 24 healthy controls (HC). We collected 23 independent studies profiling 1,855 blood samples from patients covering six viruses (influenza, RSV, HRV, Ebola, Dengue and SARS-CoV-1). We studied host whole-blood transcriptomic responses in COVID-19 compared to non-COVID-19 viral infections to understand similarities and differences in host response. Gene signature threshold was absolute effect size ≥1, FDR ≤ 0.05%. Results Differential gene expression of COVID-19 vs HC are highly correlated with non-COVID-19 vs HC (r=0.74, p&amp;lt; 0.001). We discovered two gene signatures: COVID-19 vs HC (2002 genes) (COVIDsig) and non-COVID-19 vs HC (635 genes) (nonCOVIDsig). Pathway analysis of over-expressed signature genes in COVIDsig or nonCOVIDsig identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection and cytokine production. Conversely, for under-expressed genes, pathways indicated repression of lymphocyte differentiation and activation (Fig1). Intersecting the two gene signatures found two genes significantly oppositely regulated (ACO1, ATL3). We derived a third gene signature using COCONUT to compare COVID-19 to non-COVID-19 viral infections (416 genes) (Fig2). Pathway analysis did not result in significant enrichment, suggesting identification of novel biology (Fig1). Statistical deconvolution of bulk transcriptomic data found M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells and total B cells changed in the same direction across COVID-19 and non-COVID-19 infections. Cell types that increased in COVID-19 relative to non-COVID-19 were CD56bright NK cells, M2 macrophages and total NK cells. Those that decreased in non-COVID-19 relative to COVID-19 were CD56dim NK cells &amp; memory B cells and eosinophils (Fig3). Figure 1 Figure 2 Figure 3 Conclusion The concordant and discordant responses mapped here provide a window to explore the pathophysiology of COVID-19 vs other viral infections and show clear differences in signaling pathways and cellularity as part of the host response to SARS-CoV-2. Disclosures Simone A. Thair, PhD, Inflammatix, Inc. (Employee, Shareholder) Yudong He, PhD, Inflammatix Inc. (Employee) Yehudit Hasin-Brumshtein, PhD, Inflammatix (Employee, Shareholder) Suraj Sakaram, MS in Biochemistry and Molecular Biology, Inflammatix (Employee, Other Financial or Material Support, stock options) Rushika R. Pandya, MS, Inflammatix Inc. (Employee, Shareholder) David C. Rawling, PhD, Inflammatix Inc. (Employee, Shareholder) Purvesh Khatri, PhD, Inflammatix Inc. (Shareholder) Timothy Sweeney, MD, PHD, Inflammatix, Inc. (Employee, Shareholder)
Novel Series of Potent Glucokinase Activators Leading to the Discovery of AM-2394 (2016)

Glucokinase (GK) catalyzes the phosphorylation of glucose to glucose-6-phosphate. We present the structure-activity relationships leading to the discovery of AM-2394, a structurally distinct GKA. AM-2394 activates GK with an EC50 of 60 nM, increases the affinity of GK for glucose by approximately 10-fold, exhibits moderate clearance and good oral bioavailability in multiple animal models, and lowers glucose excursion following an oral glucose tolerance test in an ob/ob mouse model of diabetes.
Pyramidal motion estimation techniques exploiting intra-level motion correlation (2003)

The conventional pyramidal motion estimation technique, although capable of reducing the heavy computational load as required by the full search block matching algorithm, has the problem of propagating false motion vectors. In this work, pyramidal motion estimation techniques that exploit the intra-level motion correlation to overcome this serious drawback are presented. Instead of scaling the motion vectors from the corresponding positions at the adjacent lower pyramidal level as the prediction motion vectors for the current pyramidal level as is done in the conventional technique, the prediction motion vectors are generated through either median filtering or linear prediction of a set of neighboring motion vectors. Various pyramidal data structures are employed to test the proposed techniques. Simulation results show that the proposed techniques not only improve the prediction performance, but also result in a more consistent motion field. It is further shown that this improvement in the performance is achieved with negligible extra computational load.
Structure and Expression of Mitochondrial Citrate Synthases from Higher Plants (1996)

Mitochondrial citrate synthase (EC 4.1.3.7) represents the first enzyme of the tricarboxylic acid cycle, catalyzing the condensation of acetyl-CoA and oxaloacetate, finally yielding citrate and CoA. We report here the isolation of cDNA clones encoding citrate synthase from Nicotiana tabacum, Beta vulgaris and Populus. Nucleotide and deduced amino acid sequences were compared with previously published sequences of mitochondrial citrate synthases from Arabidopsis thaliana and potato, as well as with the sequence of glyoxysomal citrate synthase from pumpkin. Homologies between the various plant mitochondrial enzymes were in the range from 77.2% (potato vs. Arabidopsis) to 94.2% (potato vs. tobacco) on the nucleotide level (coding regions only), and in the range from 70.1% to 90.4% (potato vs. Arabidopsis, and potato vs. tobacco, respectively) on the amino acid level. Identities of the mitochondrial isozymes to the pumpkin glyoxysomal enzyme were below 30% on the nucleotide and amino acid level. In Northern blot experiments citrate synthase mRNA was detected in all tissues analyzed. However, levels of expression showed tissue dependency despite the fact that citrate synthase is usually considered a house-keeping enzyme. Whether these different levels of expression reflect tissue-specific variations with respect to basic metabolism awaits further analysis.
Disfunción ventricular en pacientes con cirrosis hepática (2006)

background: Cardiopulmonary abnormalities are frequent in patients with advanced stages of liver and lung diseases. Several studies have shown some degree of increased ventricular wall thickness, diastolic dysfunction, and abnormal systolic response to stress, without any relation to the etiology of the hepatic disease. Objective: To know the echocardiographic profile of patients with hepatic cirrhosis and its relation with the etiology, the Child-Pugh classification and the hepatopulmonary syndrome frequency. Patients and method: 120 patients with liver disease were consecutively included in four groups of 30 patients each one: alcoholic-nutritional hepatic cirrhosis, primary biliary cirrhosis, autoimmune cirrhosis, and post-necrotic cirrhosis. They were divided accordingly to the Child-Pugh classification. A contrast echocardiogram was obtained in all cases. Results: An increase in the end systolic diameter “E” wave-interventricular septum distance of the left ventricle and the higher mitral valve opening correlated with the worst functional Child-Pugh classification. In alcoholic nutritional hepatic cirrhosis we found the biggest left ventricle end systolic dimensions, as well as right ventricle diastolic diameter and right/left ventricle rate. Hepatopulmonary syndrome was found in 20 patients (16.7%). Conclusion: Right cardiac chamber enlarged in cirrhosis is probably the consequence of an increased preload. Left ventricle ejection fraction at rest is preserved, however, the increased left ventricle end systolic diameter could mean a reduction of the contractile reserve, as can be observed in our cases.
ChemInform Abstract: Access to Imidazole Derivatives by Silver(I) Carbonate Mediated Coupling of Vinyl Azides with Secondary Amines. (2016)

Abstract An operationally simple protocol for preparation of a set of imidazole derivatives via formation of three new C—N bonds in a cascade process is developed.
New trialkylsilyl enol ether chemistry: direct 1,2-bis-azidonation of triisopropylsilyl enol ethers: an azido-radical addition process promoted by TEMPO (1995)

Treatment of triisopropylsilyl enol ethers with PhIO/TMSN3/TEMPO (cat.)–45 °C results in 1,2-bis-azidonation, which appears to occur through a radical addition process; the 1-azido group can be replaced by carbon nucleophiles such as allyl, methyl, cyano, acetylene and acetonyl.
Packaging for Spacecraft and Its Commercial Implications (1997)

This paper discusses aspects of electronic packaging which are critical to MEMS devices and in particular, of extreme importance to packaging devices which are intended for use aboard spacecraft.
Durable Goods Monopoly with Incomplete Information (1992)

This article reconsiders the durable goods monopoly problem when the monopolist's marginal cost is private information. We show that the Coase Conjecture implies the No Trade Theorem: In any equilibrium in which the lowest-cost seller's initial offer approaches her marginal cost, the aggregate probability of trade must vanish. However, we also construct non-Coasean equilibria which approximate the unique outcome of the rental version of the same model. These (stationary) equilibria are comparatively efficient. The results are equally applicable to the mathematically-equivalent problem of sequential bargaining with two-sided incomplete information where one party makes all the offers.
Versatile Tetrablock Copolymer Scaffold for Hierarchical Colloidal Nanoparticle Assemblies: Synthesis, Characterization, and Molecular Dynamics Simulation (2017)

A unique combination of molecular dynamics (MD) simulation and detailed size exclusion chromatography-multiangle light scattering (SEC-MALS) analysis is used to provide important a priori insights into the solution self-assembly of a well-defined and symmetric tetrablock copolymer with two acrylic acid (AA) outer blocks, two polystyrene (PS) inner blocks, and a trithiocarbonate (TTC) central group, prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization. SEC-MALS experiments show that the copolymer forms aggregates in both tetrahydrofuran and N,N-dimethylformamide (DMF), even in the presence of different salts, but not in 1,4-dioxane (dioxane). Combined with MD simulations, these results indicate that the AA units are the main cause of aggregation through intermolecular hydrogen bonding, with additional stabilization by the central TTC. The block copolymer chains self-assemble in dioxane by adding cadmium acetate, originating flowerlike inverse micelles with a cadmium acrylate core and the TTC groups in the outer surface of the PS corona. The micelles were used as nanoreactors in the templated synthesis of a single cadmium selenide (CdSe) quantum dot (QD) in the core of each micelle, whereas the shell TTC groups can be converted into thiol functions for further use of these units in hierarchical nanostructures. Only in dioxane where simulations and SEC-MALS suggest an absence of copolymer aggregates prior to cadmium acetate addition do well-dispersed and highly luminescent CdSe QDs form by templated synthesis. These results provide valuable insights into the self-assembly of RAFT copolymers in different solvent systems as it relates to the preparation of emissive QDs with polymer-spaced thiol functionality for binding to gold nanostructures.
Probing the acceptor substrate binding site of Trypanosoma cruzi trans-sialidase with systematically modified substrates and glycoside libraries (2011)

Systematically modified octyl galactosides and octyl N-acetyllactosamines were assessed as inhibitors of, and substrates for, T. cruzi trans-sialidase (TcTS) in the context of exploring its acceptor substrate binding site. These studies show that TcTS, which catalyses the α-(2→3)-sialylation of non-reducing terminal β-galactose residues, is largely intolerant of substitution of the galactose 2 and 4 positions whereas substitution of the galactose 6 position is well tolerated. Further studies show that even the addition of a bulky sugar residue (glucose, galactose) does not impact negatively on TcTS binding and turnover, which highlights the potential of 'internal' 6-substituted galactose residues to serve as TcTS acceptor substrates. Results from screening a 93-membered thiogalactoside library highlight a number of structural features (notably imidazoles and indoles) that are worthy of further investigation in the context of TcTS inhibitor development.
Pulmonary aspergillosis masquerading as progressive post-transplant lymphoma (1996)

Abstract We report a patient with post-transplant lymphoma who was treated by renal allograft nephrectomy, discontinuation of immuno-suppressive therapy, and initiation of acyclovir administration. Despite these measures he appeared to have progressive lymphoma. Had a biopsy and cultures not been done, the diagnosis of aspergillosis would have been missed and the patient might have been treated with chemotherapy, with a potentially lethal outcome. Data from the Cincinnati Transplant Tumor Registry indicate that of 662 patients treated for post-transplant lymphoma, 277 patients died of cancer and 137 died of other causes, of which infection was a major factor. This case emphasizes the importance of proper work-up of patients with apparently progressive lymphomas.
A search for $$ {\Xi}_{\mathrm{cc}}^{++} $$→ D+pK−π+ decays (2019)

A bstract A search for the $$ {\Xi}_{cc}^{++} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>Ξ</mml:mi><mml:mi>cc</mml:mi><mml:mrow><mml:mo>+</mml:mo><mml:mo>+</mml:mo></mml:mrow></mml:msubsup></mml:math> baryon through the $$ {\Xi}_{cc}^{++} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>Ξ</mml:mi><mml:mi>cc</mml:mi><mml:mrow><mml:mo>+</mml:mo><mml:mo>+</mml:mo></mml:mrow></mml:msubsup></mml:math> → D + pK − π + decay is performed with a data sample corresponding to an integrated luminosity of 1 . 7 fb − 1 recorded by the LHCb experiment in pp collisions at a centre-of-mass energy of 13 TeV. No significant signal is observed in the mass range from the kinematic threshold of the decay to 3800 MeV/ c 2 . An upper limit is set on the ratio of branching fractions $$ \mathrm{\mathcal{R}}=\frac{\mathrm{\mathcal{B}}\left({\Xi}_{cc}^{++}\to {D}^{+}{pK}^{-}{\pi}^{+}\right)}{\mathrm{\mathcal{B}}\left({\Xi}_{cc}^{++}\to {\Lambda}_c^{+}{K}^{-}{\pi}^{+}{\pi}^{+}\right)} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>ℛ</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>ℬ</mml:mi><mml:mfenced><mml:mrow><mml:msubsup><mml:mi>Ξ</mml:mi><mml:mi>cc</mml:mi><mml:mrow><mml:mo>+</mml:mo><mml:mo>+</mml:mo></mml:mrow></mml:msubsup><mml:mo>→</mml:mo><mml:msup><mml:mi>D</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msup><mml:mi>pK</mml:mi><mml:mo>−</mml:mo></mml:msup><mml:msup><mml:mi>π</mml:mi><mml:mo>+</mml:mo></mml:msup></mml:mrow></mml:mfenced></mml:mrow><mml:mrow><mml:mi>ℬ</mml:mi><mml:mfenced><mml:mrow><mml:msubsup><mml:mi>Ξ</mml:mi><mml:mi>cc</mml:mi><mml:mrow><mml:mo>+</mml:mo><mml:mo>+</mml:mo></mml:mrow></mml:msubsup><mml:mo>→</mml:mo><mml:msubsup><mml:mi>Λ</mml:mi><mml:mi>c</mml:mi><mml:mo>+</mml:mo></mml:msubsup><mml:msup><mml:mi>K</mml:mi><mml:mo>−</mml:mo></mml:msup><mml:msup><mml:mi>π</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msup><mml:mi>π</mml:mi><mml:mo>+</mml:mo></mml:msup></mml:mrow></mml:mfenced></mml:mrow></mml:mfrac></mml:math> with ℛ &lt; 1 . 7 (2 . 1) × 10 − 2 at the 90% (95%) confidence level at the known mass of the $$ {\Xi}_{cc}^{++} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>Ξ</mml:mi><mml:mi>cc</mml:mi><mml:mrow><mml:mo>+</mml:mo><mml:mo>+</mml:mo></mml:mrow></mml:msubsup></mml:math> state.
Performance of multitone and multicarrier direct sequence spread spectrum in the presence of partial-band pulse jamming/interference (2003)

Variations on single-carrier (SC) direct-sequence spread spectrum (DS-SS) signaling schemes have seen much study, especially the multicarrier (MC) approach, and to a lesser degree the multitone (NIT) approach. A comparison of the techniques in the presence of partial band jamming has not yet been done. This impairment is of interest in the spectral overlay of narrowband and DS-SS systems, and in military anti-jam systems. We provide new analytical and computer simulation results for performance of NIT and MC DS-SS in the presence of partial band pulsed jamming. We investigate performance as a function of the number of subcarriers, per-subcarrier processing gain, and jammer bandwidth and center frequency for two different types of interfering signals. Comparisons between simulations and analysis show good agreement, and show that for some cases the NIT approach can be more robust than MC.
Enhanced hydroxyapatite nanorods formation on graphene oxide nanocomposite as a potential candidate for protein adsorption, pH controlled release and an effective drug delivery platform for cancer therapy (2016)

Creatine phosphate used as a phosphorus source for synthesis of a HAp/GO nanocomposite toward protein/anti-cancer drug loading and selective pH dependent drug delivery platforms.
Comparison of Cas9 activators in multiple species (2016)

Several programmable transcription factors exist based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare Cas9 activator systems and examine their ability to induce robust gene expression in several human, mouse, and fly cell lines. We also explore the potential for improved activation through the combination of the most potent activator systems, and we assess the role of cooperativity in maximizing gene expression.
Shot-filling effects in nanometer-scale electron-beam lithography (2021)

Photonic nanocavities achieve tight temporal and spatial confinement of light through the quality factor, Q, and the mode volume, V, respectively. This results in local enhancements of the electric field, E , which is central to a number of applications requiring enhanced light-matter interaction [1], such as nonlinearities [2] or efficient optical interconnects [3]. Previously, it was believed that the mode volume in dielectrics was bound by the diffraction limit [4], and therefore field enhancements were achieved by large quality factors [5]. With the recent discovery of dielectric bowtie cavities, however, mode volumes deep below the diffraction limit are possible in devices with nanometer-scale features [2,6]. Such features, in turn, pose challenges to the resolution of fabrication at the deep nanoscale. Here we investigate the importance of precise pattern design and the effects of rasterization (shot-filling) in electron-beam lithography when pushing the resolution limit. We consider a novel nanocavity design obtained by inverse design using tolerance-constrained topology optimization [6] in which the local density of optical states (LDOS) is optimized at the very center of a silicon cavity to have Q = 1100, V = 0.08 (λ/2n)3, and λ = 1551 nm. To illustrate the importance of shot-filling for high-resolution electron-beam lithography, we first consider the test structure shown in Fig. 1. The contours between material boundaries are used to define a set of polygons as shown in Fig. 1a. Individual patterns are well separated to be isolated from long-range proximity effects [7]. Figures 1b and d show the fracturing of the polygon as well as the discretization into individual shots separated by a pitch, p, and exposed with a uniform dose density, D. This means that the impinging charge dose of each shot (in coulomb) is q = p2D. Electron-scattering through the material broadens the point-like exposures along with the other process steps, here development and etching, to yield an effective deposited dose density, Deff, shown on the grayscale map in Figs. 1c and e [7-8]. The regions that receive an effective dose density greater than the dose to clear, D0, will be developed as indicated by the green contour. Figure 1c, shows visible line-edge roughness caused by the coarse discretization and poor dose uniformity, which, for a cavity, can cause substantial optical loss through scattering (reduction in Q) [5], while the finer discretization in Fig. 1e produces much smoother edges and a higher fidelity in the pattern transfer due to the finer discretization. Figure 2 shows three nanocavities fabricated with the same process on the same chip where the current, and therefore pitch, is varied. Already when the pitch is increased from 1 nm to 3.5 nm, several of the small features cannot be resolved, and with p = 6 nm the central part becomes disconnected, thus charging up under SEM inspection. We will report on our latest progress towards realizing structures with extreme confinement of light.
Pulse energy scaling of multi-pass cells for nonlinear spectral broadening applications (2022)

We discuss basic pulse energy scaling principles for multi-pass cells (MPCs) and introduce a novel multi-pass cell type which we employ to numerically predictpost-compression of 125 mJ pulses using a 2 m setup.
Merging enzymatic and synthetic chemistry with computational synthesis planning (2022)

Synthesis planning programs trained on chemical reaction data can design efficient routes to new molecules of interest, but are limited in their ability to leverage rare chemical transformations. This challenge is acute for enzymatic reactions, which are valuable due to their selectivity and sustainability but are few in number. We report a retrosynthetic search algorithm using two neural network models for retrosynthesis-one covering 7984 enzymatic transformations and one 163,723 synthetic transformations-that balances the exploration of enzymatic and synthetic reactions to identify hybrid synthesis plans. This approach extends the space of retrosynthetic moves by thousands of uniquely enzymatic one-step transformations, discovers routes to molecules for which synthetic or enzymatic searches find none, and designs shorter routes for others. Application to (-)-Δ<sup>9</sup> tetrahydrocannabinol (THC) (dronabinol) and R,R-formoterol (arformoterol) illustrates how our strategy facilitates the replacement of metal catalysis, high step counts, or costly enantiomeric resolution with more elegant hybrid proposals.
Diskrete Silber(I)‐Palladium(II)‐Oxo‐Nanocluster, {Ag4Pd13} und {Ag5Pd15}, sowie die Rolle der Metall‐Metall‐Bindung induziert durch Kationen‐Einschluss (2016)

Abstract Die beiden diskreten Silber(I)‐Palladium(II)‐Oxo‐Nanocluster {Ag 4 Pd 13 } und {Ag 5 Pd 15 } sind die ersten Beispiele von edelmetallverkappten Polyoxoedelmetallaten mit einem neuartigen Wirt‐Gast‐Bindungsmodus, der hetero‐ und homometallische Ag‐Pd‐ und Ag‐Ag‐Wechselwirkungen beinhaltet. Umfassende theoretische Studien deuten darauf hin, dass die Ag‐Pd‐Metallbindungen teilweise von einem Polyanion‐Oberflächeneffekt auf die Ag I ‐Gastionen herrühren, der durch starke elektrostatische Kräfte induziert wird. Diese Arbeit eröffnet ein Gebiet komplett anorganischer Silber‐Palladium‐Oxo‐Nanocluster, die als Vorstufen für die Bildung monodisperser Kern‐Schale‐Nanopartikel angesehen werden können, welche eine hohe Relevanz im Bereich der Katalyse haben.