gebhart/patrepeval huggingface dataset:
Magnon softening in a ferromagnetic monolayer: A first-principles spin dynamics study (2010)

We study the Fe/W(110) monolayer system through a combination of first-principles calculations and atomistic spin dynamics simulations. We focus on the dispersion of the spin-waves parallel to the [001] direction. Our results compare favorably with the experimental data of Prokop et al. [Phys. Rev. Lett. 102, 177206 (2009)] and correctly capture a drastic softening of the magnon spectrum, with respect to bulk bcc Fe. The suggested shortcoming of the itinerant electron model, in particular that given by density functional theory, is refuted. We also demonstrate that finite-temperature effects are significant, and that atomistic spin dynamics simulations represent a powerful tool with which to include these.
Blind Identification Using Second-Order Statistics: a Nonstationarity and Nonwhiteness Approach (2006)

We consider an approach to the blind identification problem of instantaneous mixtures using second-order statistics through the nonstationarity and nonwhiteness properties of signals. We propose the use of natural gradient learning to form off-line/block processing (BP) and on-line processing (OP) algorithms suitable respectively for blind identification with batch data and on-line data and show that the proposed algorithms can be considered as a class of algorithms offering quasi-uniform performance. The identifiability conditions are presented which provide a key insight into these algorithms. The paper shows simulation results and concludes with some connections of the proposed algorithms to other existing algorithms.
Ultrasound Lesion Detectability as a Distance Between Probability Measures (2021)

Lesion detectability (LD) quantifies how easily a lesion or target can be distinguished from the background. LD is commonly used to assess the performance of new ultrasound imaging methods. The contrast-to-noise ratio (CNR) is the most popular measure of LD; however, recent work has exposed its vulnerability to manipulations of dynamic range. The generalized CNR (gCNR) has been proposed as a robust histogram-based alternative that is invariant to such manipulations. Here, we identify key shortcomings of CNR and strengths of gCNR as LD metrics for modern beamformers. Using the measure theory, we pose LD as a distance between empirical probability measures (i.e., histograms) and prove that: 1) gCNR is equal to the total variation distance between probability measures and 2) gCNR is one minus the error rate of the ideal observer. We then explore several consequences of measure-theoretic LD in simulation studies. We find that histogram distances depend on bin selection that LD must be considered in the context of spatial resolution and that many histogram distances are invariant under measure-preserving isomorphisms of the sample space (e.g., dynamic range transformations). Finally, we provide a mathematical interpretation for why quantitative values such as contrast ratio (CR), CNR, and signal-to-noise ratio should not be compared between images with different dynamic ranges or underlying units and demonstrate how histogram matching can be used to reenable such quantitative comparisons.
ChemInform Abstract: Novel Aromatic Fluoroolefins via Fluoro‐Julia—Kocienski Olefination. (2011)

Abstract The methodology, previously developed by Gosh and Zajc, is modified and allows a high diversity of products which are of interest in medicinal chemistry.
Metal-Binding Pharmacophore Library Yields the Discovery of a Glyoxalase 1 Inhibitor (2019)

Anxiety and depression are common, highly comorbid psychiatric diseases that account for a large proportion of worldwide medical disability. Glyoxalase 1 (GLO1) has been identified as a possible target for the treatment of anxiety and depression. GLO1 is a Zn<sup>2+</sup>-dependent enzyme that isomerizes a hemithioacetal, formed from glutathione and methylglyoxal, to a lactic acid thioester. To develop active inhibitors of GLO1, fragment-based drug discovery was used to identify fragments that could serve as core scaffolds for lead development. After screening a focused library of metal-binding pharmacophores, 8-(methylsulfonylamino)quinoline (8-MSQ) was identified as a hit. Through computational modeling and synthetic elaboration, a potent GLO1 inhibitor was developed with a novel sulfonamide core pharmacophore. A lead compound was demonstrated to penetrate the blood-brain barrier, elevate levels of methylglyoxal in the brain, and reduce depression-like behavior in mice. These findings provide the basis for GLO1 inhibitors to treat depression and related psychiatric illnesses.
Helicobacter pylori -Induced Interleukin-12 p40 Expression (2010)

Interleukin-12 (IL-12) is a heterodimeric cytokine produced by antigen-presenting cells that promotes the development of T-helper lymphocyte 1 (Th1). Chronic gastritis induced by Helicobacter pylori is considered a Th1-mediated process. IL-12 levels in gastric biopsy samples of H. pylori-infected patients are higher than in those of uninfected individuals, but the cellular source of IL-12 remains elusive. IL-12 staining was detected in mucosal epithelial cells, lymphocytes, and macrophages in specimens of patients with H. pylori-positive gastritis. Therefore, we investigated IL-12 p40 mRNA induction by H. pylori in gastric epithelial cells and T cells. Although cag pathogenicity island (PAI)-positive H. pylori induced IL-12 p40 mRNA expression, an isogenic mutant of the cag PAI failed to induce it in both cell types. Supernatants from H. pylori cultures and H. pylori VacA induced IL-12 p40 mRNA expression in T cells but not in epithelial cells. The activation of the IL-12 p40 promoter by H. pylori was mediated through NF-κB. The transfection of IκB kinase and NF-κB-inducing kinase dominant-negative mutants inhibited H. pylori-induced IL-12 p40 activation. Inhibitors of NF-κB, phosphatidylinositol 3-kinase, p38 mitogen-activated protein kinase, and Hsp90 suppressed H. pylori- and VacA-induced IL-12 p40 mRNA expression. The results indicate that H. pylori induces IL-12 p40 expression by the activation of NF-κB, phosphatidylinositol 3-kinase, and p38 mitogen-activated protein kinase. Hsp90 is also a crucial regulator of H. pylori-induced IL-12 p40 expression. In addition to the cag PAI, VacA might be relevant in the induction of IL-12 expression and a Th1-polarized response only in T cells.
The Power Conscious Synergistic Processor Element of a Cell Processor (2005)

A 4-way SIMD streaming processor of a cell processor is developed in a 90nm SOI technology. CMOS static gates implement the majority of the logic. Dynamic circuits are used in critical areas, occupying 19% of the non-SRAM area. ISA, microarchitecture, and physical implementation are co-optimized to achieve a compact and power efficient design
The B1-fragment Ion from Protonated Glycine is an Electrostatically-bound Ion/Molecule Complex of CH2=NH+2 and CO (1996)

The stability of the B1-ion from glycylglycine dipeptides was studied using collision-induced dissociation experiments and ab initio calculations. This study reveals that the B1-type ion from glycine should be considered as an electrostatically bound ion/moecule complex, which dissociates into a glycine immonium ion (A1) and a carbon monoxide molecule. The stability of this complex has been calculated at various levels of the theory. At the highest level of theory (#RHF/6-311G**) it is found that the energy requirement, including zero-point vibrational energy correction, for dissociation into a glycine immonium A1 ion and a neutral carbon monoxide CO molecule is −4.0 kJ mol−1. Furthermore it could be concluded that B1-ions from glycine are stable if they are present as N-acylated species. The formation of stable B ions requires at least two carbonyl groups in the peptide backbone moiety.
Synthesis and Characterization of Poly(isobenzofuran) Films by Chemical Vapor Deposition (2006)

This paper describes the synthesis and properties of poly(isobenzofuran) (PIBF) films prepared by a thermal chemical vapor deposition (CVD) process. The synthesized precursor monomer, 1,2,3,4-tetrahydro-1,4-epoxynaphthalene, is pyrolyzed by flowing it through a tube furnace at temperatures of 600−750 °C. A reactive intermediate, isobenzofuran (IBF) monomer, is produced by this pyrolysis and deposited onto a silicon substrate where it polymerizes to form a thin coating of poly(isobenzofuran) (PIBF) on the surface. The chemical structure and composition of the PIBF films are supported by nuclear magnetic resonance (NMR) spectroscopy, Fourier transform infrared spectroscopy (FT-IR), and X-ray photoelectron spectroscopy (XPS). The weight-average molecular weight of the PIBF films range from 5500 to 9400 by varying the deposition (stage), pyrolysis (furnace), and vaporization (source) temperatures. With the variation of deposition temperature (5, 10, 15, 20, 25 °C) and pyrolysis temperature (600, 650, 700, 750 °C), significant changes are observed in deposition (growth) rate, molecular weight, and morphology while the chemical structure of the PIBF films remain the same as probed by FT-IR and XPS analysis. On the other hand, variation of the vaporization temperature (40, 45, 50, 55, 60 °C) leads to significant changes in the chemical structure as well as in the deposition rate, molecular weight, film uniformity, and morphology. By exploring several operating conditions, we have obtained optimal conditions for deposition temperature (10 °C), pyrolysis temperature (750 °C), and vaporization temperature (60 °C) that provide good film properties as well as fast film growth. To investigate the possible role of cationic initiation in IBF polymerization, PIBF films were deposited on several surfaces tailored with self-assembled monolayers (SAMs) of thiols that have functional groups of different acidities, including a carboxylic acid (−COOH), a phenol (−PhOH), an alcohol (−OH), an amine (−NH2), and a methyl group (−CH3). We observed the fastest growth of PIBF (k = 2.5 Å/s) on the carboxylic acid-terminated surfaces whereas the slowest growth was on the methyl-terminated surfaces (k = 0.02 Å/s). On the basis of the experimental observations, we proposed a growth mechanism for the PIBF films by the CVD process.
Machine Learning Enabled Image Classification for Automated Data Acquisition in the Electron Microscope (2023)

Journal Article Machine Learning Enabled Image Classification for Automated Data Acquisition in the Electron Microscope Get access Carolin B Wahl, Carolin B Wahl Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United StatesInternational Institute for Nanotechnology, Northwestern University, Evanston, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Alexandra Day, Alexandra Day Department of Electrical and Computer Engineering, Northwestern University, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Vishu Gupta, Vishu Gupta Department of Electrical and Computer Engineering, Northwestern University, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Roberto R dos Reis, Roberto R dos Reis Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United StatesThe NUANCE Center, Northwestern University, Evanston, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Wei-keng Liao, Wei-keng Liao Department of Electrical and Computer Engineering, Northwestern University, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Chad A Mirkin, Chad A Mirkin Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United StatesInternational Institute for Nanotechnology, Northwestern University, Evanston, IL, United StatesDepartment of Chemistry, Northwestern University, Evanston, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Alok Choudhary, Alok Choudhary Department of Electrical and Computer Engineering, Northwestern University, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Vinayak P Dravid, Vinayak P Dravid Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United StatesInternational Institute for Nanotechnology, Northwestern University, Evanston, IL, United StatesThe NUANCE Center, Northwestern University, Evanston, IL, United States Corresponding authors: v-dravid@northwestern.edu, ankit-agrawal@northwestern.edu Search for other works by this author on: Oxford Academic Google Scholar Ankit Agrawal Ankit Agrawal Department of Electrical and Computer Engineering, Northwestern University, IL, United States Corresponding authors: v-dravid@northwestern.edu, ankit-agrawal@northwestern.edu Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Pages 1909–1910, https://doi.org/10.1093/micmic/ozad067.986 Published: 22 July 2023
The Prevalence of Persistent Prostate Cancer after Radiotherapy Detected at Radical Cystoprostatectomy for Bladder Cancer (2013)

After radiotherapy 45% of men had persistent prostate cancer (37% of men with no evidence of disease). A decreased prostate cancer rate was associated with later treatment year and combined brachytherapy/external beam radiation regimens. Similar to men treated with radical cystoprostatectomy for muscle invasive bladder cancer, meticulous attention should be paid during prostate removal in men treated with radiotherapy because many may have persistent prostate cancer. In addition, markers other than prostate specific antigen should be studied in men treated with radiotherapy to better identify those with biochemical recurrence.
Lessons learned from the semantic translation of healthcare data (2014)

Healthcare data provides a wealth of information that can be used to study and improve patient outcomes. Electronic Medical Records and other sources of healthcare data are often managed in relational database system and archived using modern data warehousing techniques. Contemporary semantic database technology has many advantages over traditional database systems; however, the utility of the semantic data can be limited if the data is not converted properly from a tabular representation. There are a variety of tools which will naively convert tabular data into a Resource Description Format semantic graph. Without proper guidance from the operator, the tools will generate a semantically weak database which doesn't have the necessary richness for semantic analysis. This paper describes the conversion process for two healthcare databases, with the goal of creating a robust dataset for semantic analysis. The “lessons learned” from this process are detailed in order to serve as a resource for other biomedical researchers and clinicians interested in generating a useful semantic dataset from their own relational databases.
Reply to ‘‘Comment on ‘Transient kinetics of nucleation’ ’’ (1991)

The results obtained in our previous paper [Phys. Rev. A 41, 2101 (1990)] are extended to obtain N(${\mathit{g}}_{\mathit{d}}$,t), the total accumulated number concentration of nucleated clusters at the detectable size, ${\mathit{g}}_{\mathit{d}}$. It is shown that N(${\mathit{g}}_{\mathit{d}}$,t) obtained by Shneidman [preceding Comment, Phys. Rev. A 44, 8441 (1991)] is incorrect since the time lag associated with N(${\mathit{g}}_{\mathit{d}}$,t) suffers a singularity at ln(-1).
Bombesin-like Peptides Modulate Alveolarization and Angiogenesis in Bronchopulmonary Dysplasia (2007)

Early bombesin-like peptide overproduction in 125-day PRN animals predicted alveolarization defects weeks later. Bombesin-like peptide blockade improved septation, with the greatest effects at P21. This could have implications for preventing BPD in premature infants.
KINETIC STUDIES OF SEMI-BATCH EMULSION CO-POLYMERIZATION OF 80:20 VINYL ACETATE-BUTYL ACRYLATE (1984)

ABSTRACT
Differentiable Rendering of Neural SDFs through Reparameterization (2022)

We present a method to automatically compute correct gradients with respect to geometric scene parameters in neural SDF renderers. Recent physically-based differentiable rendering techniques for meshes have used edge-sampling to handle discontinuities, particularly at object silhouettes, but SDFs do not have a simple parametric form amenable to sampling. Instead, our approach builds on area-sampling techniques and develops a continuous warping function for SDFs to account for these discontinuities. Our method leverages the distance to surface encoded in an SDF and uses quadrature on sphere tracer points to compute this warping function. We further show that this can be done by subsampling the points to make the method tractable for neural SDFs. Our differentiable renderer can be used to optimize neural shapes from multi-view images and produces comparable 3D reconstructions to recent SDF-based inverse rendering methods, without the need for 2D segmentation masks to guide the geometry optimization and no volumetric approximations to the geometry.
Stereoelectronically controlled cyclization reactions on the way to peri‐fused tetrahydropyrazolo[1,5‐a]pyridines as aza analogs of ergoline partial structures (1991)

Abstract The synthesis of the 3‐substitued tetrahydropyrazolopyridin‐4‐ylalkyl iodides 7a, 7b, 8a and 8b as well as their behavior towards anionic cyclization conditions have been investigated. An (enol endo )‐ exo ‐tet‐type ring closure only proceeds when a seven‐membered ring is annulated ( 9b, 10b ). Otherwise, treatment of the β‐keto ester 7a with NaH results in O‐alkylation to yield the stereoelectronically favored ( Z )‐enol ether 13a , which can be isomerized to the thermodynamically more stable ( E ) isomer 13b . Various attemps to achieve ring closure of the methyl ketone 8a failed; instead, β‐elimination is observed. Annulation of a six‐membered carbocycle is acchieved when the triester 17 is treated by a Dieckmann condensation to give the tricyclic products 18 and 19 .
Performance of Atrial Fibrillation Detection in a New Single‐Chamber ICD (2016)

This RR interval-based AF detection algorithm performs well with high sensitivity and specificity. Integration of this algorithm into single-chamber ICDs will help monitor and detect AF, thus facilitating optimal therapy to prevent AF-related sequelae.
Linked Parallel Synthesis and MTT Bioassay Screening of Substituted Chalcones (2001)

A 644-membered library of chalcones was prepared by parallel synthesis using the Claisen−Schmidt base-catalyzed aldol condensation of substituted acetophenones and benzaldehydes. The cytotoxicity of these chalcones was conveniently determined upon the crude products directly in 96-well microtiter test plates by the conventional MTT assay. This method revealed seven chalcones of IC50 less than 1 μM of which 4‘-hydroxy-2,4,6,3‘-tetramethoxychalcone (5a) was the most active [IC50 (K562), 30 nM]; it causes cell cycle arrest at the G2/M point and binds to tubulin at the colchicine binding site.
Asymmetric Baylis-Hillman Reaction: An Enchanting Expedition (2008)

The development of new strategies for realizing the asymmetric Baylis-Hillman reaction remains at the forefront of research into this important organic reaction. This review gives a comprehensive account of the work that has emanated from our group on the asymmetric Baylis-Hillman reaction. Herein, the use of homochiral electrophiles, Michael acceptors, and bases and double asymmetric induction protocols as tools for the asymmetric Baylis-Hillman reaction is discussed. The account also covers the application of such protocols in natural product synthesis.
Forced evaporative cooling in a holographic atom trap (2003)

Summary form only given. We present progress on evaporative cooling of rubidium atoms in a holographic atom trap. Adiabatically decreasing the intensity of our YAG laser results in phase space densities greater than 1/2.
Alcohol Inhibits Odontogenic Differentiation of Human Dental Pulp Cells by Activating mTOR Signaling (2020)

Long-term heavy alcohol consumption could result in a range of health, social, and behavioral problems. People who abuse alcohol are at high risks of seriously having osteopenia, periodontal disease, and compromised oral health. However, the role of ethanol (EtOH) in the biological functions of human dental pulp cells (DPCs) is unknown. Whether EtOH affects the odontoblastic differentiation of DPCs through the mechanistic target of rapamycin (mTOR) remains unexplored. The objective of this study was to investigate the effects of EtOH on DPC differentiation and mineralization. DPCs were isolated and purified from human dental pulps. The proliferation and odontoblastic differentiation of DPCs treated with EtOH were subsequently investigated. Different doses of EtOH were shown to be cytocompatible with DPCs. EtOH significantly activated the mTOR pathway in a dose-dependent manner. In addition, EtOH downregulated the alkaline phosphatase activity, attenuated the mineralized nodule formation, and suppressed the expression of odontoblastic markers including ALP, DSPP, DMP-1, Runx2, and OCN. Moreover, the pretreatment with rapamycin, a specific mTOR inhibitor, markedly reversed the EtOH-induced odontoblastic differentiation and cell mineralization. Our findings show for the first time that EtOH can suppress DPC differentiation and mineralization in a mTOR-dependent manner, indicating that EtOH may be involved in negatively regulating the dental pulp repair.
On the convergence analysis of a variable step-size LMF algorithm of the quotient form (2010)

The least-mean fourth (LMF) algorithm is best known for its fast convergence and low steady-state error especially in non-Gaussian noise environments. Recently, there has been a surge of interest in the LMF algorithm with different variants being proposed. The fact that different variable step-size least-mean square algorithms have shown to outperform its fixed step-size counterpart, a variable step-size least-mean fourth algorithm of the quotient form (VSSLMFQ) is proposed here. Therefore in this work, the proposed algorithm is analysed for its performance in the steady-state and it is shown to achieve a lower steady-state error then the traditional LMF algorithm. Finally, a number of computer simulations are carried out to substantiate the theoretical findings.
Biomarkers of Operational Tolerance After Liver Transplantation: Are We There Yet? (2021)

Over the past 15 years, many studies have attempted to describe the immunophenotypic traits of patients reaching spontaneous operational tolerance (SOT) after liver transplantation (LT) [reviewed in (1)]. The majority of them have been cross-sectional retrospective studies, limited by small sample sizes and by the difficulty of adequately adjusting for clinical confounders, in particular the effect of pharmacological immunosuppression. Over the same period of time, three prospective multi-center trials of immunosuppression discontinuation that included sequential protocolized liver biopsies have revealed that not all recipients who maintain stable allograft function in the absence of immunosuppression can be considered as having reached SOT (2-5).