gebhart/patrepeval huggingface dataset:
Cell-Type-Specific Responses to Chemotherapeutics in Breast Cancer (2004)

Recent microarray studies have identified distinct subtypes of breast tumors that arise from different cell types and that show statistically significant differences in patient outcome. To gain insight into these differences, we identified in vitro and in vivo changes in gene expression induced by chemotherapeutics. We treated two cell lines derived from basal epithelium (immortalized human mammary epithelial cells) and two lines derived from luminal epithelium (MCF-7 and ZR-75-1) with chemotherapeutics used in the treatment of breast cancer and assayed for changes in gene expression using DNA microarrays. Treatment doses for doxorubicin and 5-fluorouracil were selected to cause comparable cytotoxicity across all four cell lines. The dominant expression response in each of the cell lines was a general stress response; however, distinct expression patterns were observed. Both cell types induced DNA damage-response genes such as p21(waf1), but the response in the luminal cells showed higher fold changes and included more p53-regulated genes. Luminal cell lines repressed a large number of cell cycle-regulated genes and other genes involved in cellular proliferation, whereas the basal cell lines did not. Instead, the basal cell lines repressed genes that were involved in differentiation. These in vitro responses were compared with expression responses in breast tumors sampled before and after treatment with doxorubicin or 5-fluorouracil/mitomycin C. The in vivo data corroborated the cell-type-specific responses to chemotherapeutics observed in vitro, including the induction of p21(waf1). Similarities between in vivo and in vitro responses help to identify important response mechanisms to chemotherapeutics.
Characterization of Synthetic Polymers Using Matrix-Assisted Laser Desorption/Ionization−Time of Flight Mass Spectrometry Volume 29, Number 6, March 11, 1996, pp 2213−2221 (1996)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionCharacterization of Synthetic Polymers Using Matrix-Assisted Laser Desorption/Ionization−Time of Flight Mass Spectrometry Volume 29, Number 6, March 11, 1996, pp 2213−2221Apurva K. Chaudhary, Glenn Critchley, Abderhammane Diaf, Eric J. Beckman, and Alan J. RussellCite this: Macromolecules 1996, 29, 18, 6080Publication Date (Web):August 26, 1996Publication History Published online26 August 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ma9520151https://doi.org/10.1021/ma9520151correctionACS PublicationsCopyright © 1996 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views334Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Get e-Alertsclose Get e-Alerts
Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation (2023)

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon-carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of <i>erythro</i>-1,2-diguaiacylpropane-1,3-diol (<i>erythro</i>-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in <i>Novosphingobium aromaticivorans</i>. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts <i>erythro</i>-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the <i>N. aromaticivorans</i> LdpA and another homolog identified in <i>Sphingobium</i> sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C<sub>1</sub> reaction product, and we further demonstrated that both enantiomers of <i>erythro</i>-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.
Activation of Electron-Transfer Reduction of Oxygen by Hydrogen Bond Formation of Superoxide Anion with Ammonium Ion (2006)

A hydrogen bond formed between the superoxide anion and the ammonium ion (NH4+) accelerates electron transfer from the C60 radical anion to oxygen significantly, whereas the tetra-n-butylammonium ion has no ability to form a hydrogen bond with the superoxidie anion, exhibiting no acceleration of the electron-transfer reduction of oxygen. The second-order rate constant of electron transfer from C60*- to O2 increases linearly with increasing concentration of NH4+. This indicates that O2*- produced in the electron transfer from C60 to O2 is stabilized by 1:1 complex formation between O2*- and NH4+. The 1:1 complex formed between O2*- and NH4+ was detected by ESR. The binding of O2*- with NH4+ results in a positive shift of the reduction potential of O2 with increasing concentration of NH4+, leading to the acceleration of electron transfer from C60*- to O2.
Inhibition of prolyl 4-hydroxylase decreases muscle fibrosis following chronic rotator cuff tear (2017)

GSK1120360A resulted in improved enthesis mechanics with variable effects on muscle function. PHD inhibition may be beneficial for connective tissue injuries in which muscle atrophy has not occurred.Cite this article: J. P. Gumucio, M. D. Flood, A. Bedi, H. F. Kramer, A. J. Russell, C. L. Mendias. Inhibition of prolyl 4-hydroxylase decreases muscle fibrosis following chronic rotator cuff tear. Bone Joint Res 2017;6:57-65. DOI: 10.1302/2046-3758.61.BJR-2016-0232.R1.
Improving the In Vivo Efficacy of an Anti-Tac (CD25) Immunotoxin by Pseudomonas Exotoxin A Domain II Engineering (2018)

Tac (CD25) is expressed on multiple hematologic malignancies and is a target for cancer therapies. LMB-2 is an extremely active anti-Tac recombinant immunotoxin composed of an Fv that binds to Tac and a 38-kDa fragment of <i>Pseudomonas</i> exotoxin A (PE38). Although LMB-2 has shown high cytotoxicity toward Tac-expressing cancer cells in clinical trials, its efficacy was hampered by the formation of anti-drug antibodies against the immunogenic bacterial toxin and by dose-limiting off-target toxicity. To reduce toxin immunogenicity and nonspecific toxicity, we introduced six point mutations into domain III that were previously shown to reduce T-cell immunogenicity and deleted domain II from the toxin, leaving only the 11aa furin cleavage site, which is required for cytotoxic activity. Although this strategy has been successfully implemented for mesothelin and CD22-targeting immunotoxins, we found that removal of domain II significantly lowered the cytotoxic activity of anti-Tac immunotoxins. To restore cytotoxic activity in the absence of PE domain II, we implemented a combined rational design and screening approach to isolate highly active domain II-deleted toxin variants. The domain II-deleted variant with the highest activity contained an engineered disulfide-bridged furin cleavage site designed to mimic its native conformation within domain II. We found that this approach restored 5-fold of the cytotoxic activity and dramatically improved the MTD. Both of these improvements led to significantly increased antitumor efficacy <i>in vivo</i> We conclude that the next-generation anti-Tac immunotoxin is an improved candidate for targeting Tac-expressing malignancies. <i>Mol Cancer Ther; 17(7); 1486-93. ©2018 AACR</i>.
Assessment of the interactions between pea and salivary proteins in aqueous dispersions (2023)

To understand and limit the unpleasant oral sensation of astringency felt during the consumption of pea-based drinks, we investigated the interaction between mixtures of salivary and pea proteins, as compared to mixtures where HEPES buffer (at pH 6.8) was used as a negative control for saliva. Since astringent compounds have the ability to bind with salivary proteins, mixes of freshly collected whole unstimulated saliva and a pea protein isolate (PPI) (a dispersion at 3.5% w/v) were prepared in ratios 95:5 and 1:1 saliva:PPI, to allow different stoichiometries to occur in the mouth. Samples were incubated at 37 °C during 30 min, after centrifugation at 16000g during 20 min to separate pellet from supernatant. Using techniques such as SEC, Native-PAGE and LC-MS, 7 pea proteins were identified as being capable of forming aggregates with at least 7 saliva proteins, some of which have been previously connected to astringency.
Advantages Of Using Personal Response System Technology To Evaluate Abet And Mechanical Engineering Program Outcomes (2020)

Personal Response System (PRS) is a tool typically employed to promote active learning in class, to increase participation, to measure conceptual comprehension, and to support Millennial Learners. At Gannon University, the evaluation and assessment activities of various Engineering programs' outcomes, including those related to ABET outcomes, have been done in the last 5 years through a web-based exit survey. This presents the challenge that students are not forced to take the survey and typically a 100% response is never achieved. By introducing PRS as a means of assessing the outcomes, a 100% feedback is obtained through an immediate evaluation process. To conduct the study, seven courses in the Mechanical Engineering program were selected in order to insure a representation of the four years of undergraduate studies. Once the outcomes assessments are reviewed, action items are created for each class. These action items are implemented closing the loop. This paper describes the implementation of PRS as an outcomes evaluation tool and the advantages of this technique over the ones employed at the moment. Finally, the lessons learned and challenges experienced will be discussed.
Understanding the Effect of Water in Polyamides: A Review (2020)

Polyamides (PAs) are repeatedly exposed to environments of varying humidity throughout their service life. Due to their hygroscopic nature, moisture diffusion can alter the polymer properties, sometimes irreversibly. It has been previously found that the effect of transport of water on the structure, morphology, and physical properties of polymers is not negligibly small. In certain semi-crystalline polyamides, the diffusion coefficient has been shown to be governed by the local chain dynamics (β relaxation). The final molecular weight of PAs achieved after melt processing is a result of the equilibrium between the forward and reverse polycondensation depending on the water concentration. With the growing demand for unreinforced and reinforced polyamides as well as polyamide fibers in high-performance applications, it is critical to understand the physics of the interaction between water molecules and polymer or composite systems. This article reviews the existing literature about polyamide-water interactions with a focus on the governing physical laws of moisture transport within the polyamide matrix, drying kinetics, and dynamics of water in the polymer system. The implications of moisture on the processing and properties of the polyamides class of materials are also discussed, suggesting the need for best practices in instrumentation and control.
Adaptive Digital Back-Propagation for Optical Communication Systems (2014)

We propose an adaptive digital back-propagation method (A-DBP) to self-determine unknown fiber nonlinear coefficient gamma. Performance is experimentally verified with 10×224-Gb/s POLMUX-16QAM over 656km. Optimal DBP performance, without knowledge of gamma, is obtained by A-DBP.
Paraspinal muscle morphology and composition in adolescent idiopathic scoliosis: A histological analysis (2021)

This study demonstrates that although muscle fibers are larger on the convex side of the scoliotic curve in AIS, muscles on both sides are atrophic compared to non-scoliotic individuals, and demonstrate levels of collagen similar to severe degenerative spinal pathologies. These findings provide insight into biological maladaptations occurring in paraspinal muscle in the presence of AIS.
The Role of Stacking Faults in the Enhancement of the a-b Plane Peak in Silver Ion-Irradiated Commercial MOD REBCO Wires (2022)

The magnetic-field anisotropy of the critical current is an extrinsic property of superconducting wires that is of greatest relevance to the design of high temperature superconducting (HTS) devices. It is also a highly useful diagnostic tool to understand the dominant flux-pinning mechanisms active in different temperature and field regimes. REBa <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sub> (REBCO) coated conductors typically exhibit a large peak in critical current when the field is aligned with the REBCO <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> - <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</i> plane. The commercial pinning-enhanced American Superconductor Corporation (AMSC) REBCO coil wire used for this study is unusual in having a relatively small <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> - <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</i> plane peak at higher temperatures due to an inherently low density of stacking faults. Stacking faults can then be introduced by annealing the wire in oxygen to create the more commonly observed strong <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> - <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</i> plane peak. Complementary <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</i> -axis columnar defects can be added by silver ion-irradiation producing an additional peak in the critical current at 0°. The resulting complex critical current anisotropy is studied using transport critical current measurements over a temperature range from 20 K to 77.5 K and under magnetic fields up to 7 T. Through systematic studies on pristine and annealed samples, in the presence and absence of columnar defects created by silver irradiation, we investigated the flux-pinning interactions between stacking faults and columnar defects.
Data from MAP9 Loss Triggers Chromosomal Instability, Initiates Colorectal Tumorigenesis, and Is Associated with Poor Survival of Patients with Colorectal Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Chromosomal instability (CIN) is a common phenomenon in colorectal cancer, but its role and underlying cause remain unknown. We have identified that mitotic regulator microtubule-associated protein 9 (MAP9) is a critical regulator of CIN in colorectal cancer. We thus studied the effect of MAP9 loss on colorectal cancer in &lt;i&gt;Map9&lt;/i&gt;-knockout mice and in cell lines.&lt;/p&gt;Experimental Design:&lt;p&gt;We generated colon epithelial–specific &lt;i&gt;Map9&lt;/i&gt;-knockout mice and evaluated colorectal cancer development. Effect of &lt;i&gt;Map9&lt;/i&gt; knockout on colorectal cancer progression was determined in chemical or &lt;i&gt;Apc&lt;sup&gt;Min&lt;/sup&gt;&lt;sup&gt;/+&lt;/sup&gt;&lt;/i&gt;-induced colorectal cancer. Molecular mechanism of MAP9 was determined using spectral karyotyping, microtubule assays, and whole-genome sequencing (WGS). Clinical significance of MAP9 was examined in 141 patients with CRC.&lt;/p&gt;Results:&lt;p&gt;Spontaneous colonic tumors (9.1%) were developed in colon epithelium–specific &lt;i&gt;Map9&lt;/i&gt;-knockout mice at 17 months, but none was observed in wild-type littermates. &lt;i&gt;Map9&lt;/i&gt; deletion accelerated colorectal cancer formation both in &lt;i&gt;Apc&lt;sup&gt;Min&lt;/sup&gt;&lt;sup&gt;/+&lt;/sup&gt;&lt;/i&gt; mice and azoxymethane-treated mice, and reduced survival in &lt;i&gt;Apc&lt;sup&gt;Min&lt;/sup&gt;&lt;/i&gt;&lt;sup&gt;/+&lt;/sup&gt; mice. Mechanistically, MAP9 stabilized microtubules and mediated mitotic spindle assembly. MAP9 also maintained the spindle pole integrity and protected K-fiber from depolymerization at spindle poles. MAP9 loss induced severe mitosis failure, chromosome segregation errors, and aneuploidy, leading to transformation of normal colon epithelial cells. WGS confirmed enhanced CIN in intestinal tumors from &lt;i&gt;Map9&lt;/i&gt; knockout &lt;i&gt;Apc&lt;sup&gt;Min&lt;/sup&gt;&lt;/i&gt;&lt;sup&gt;/+&lt;/sup&gt; mice. In patients with colorectal cancer, &lt;i&gt;MAP9&lt;/i&gt; was frequently silenced and its downregulation was associated with poor survival.&lt;/p&gt;Conclusions:&lt;p&gt;MAP9 is a microtubule stabilizer that contributes to spindle stability and inhibits colorectal tumorigenesis, supporting the role of MAP9 as a tumor suppressor for preventing CIN in colorectal cancer.&lt;/p&gt;&lt;/div&gt;
Stochastic FDTD for Analysis of Statistical Variation in Electromagnetic Fields (2012)

This paper describes a new stochastic finite difference time domain (S-FDTD) method for calculating the variance in the electromagnetic fields caused by variability or uncertainty in the electrical properties of the materials in the model. Details of the 1D derivation using truncated Taylor series approximations are given. The S-FDTD analysis is then compared to Monte Carlo analysis for a 1D bioelectromagnetic example. The accuracy of the method is controlled by the approximations for the cross correlations of the fields and electrical properties. In this paper, we are able to bound the variance using cross correlations of 1 (overestimate) and the reflection coefficient (underestimate).
A data‐mining framework for large scale analysis of dose‐outcome relationships in a database of irradiated head and neck cancer patients (2015)

Prospective collection of clinical data has enabled large-scale analysis of dose-outcome relationships. The current data-mining framework revealed both known and novel dosimetric and clinical relationships, underscoring the potential utility of this analytic approach in hypothesis generation. Multivariate models and advanced, 3D dosimetric features may be necessary to further evaluate the complex relationship between neighboring OAR and observed outcomes.
H2-functions and infinite dimensional realization theory (1972)

In this paper the realization question for infinite dimensional linear systems is examined for both bounded and unbounded operators. In addition to obtaining realizability criteria covering the basic cases, we discuss the relationship between canonical realizations of the same system. What one finds is that the set of transfer functions which are realizable by triples (A,b,c) with A bounded is related in a close way, to the space of complex functions analytic and square integrable on the disk |s| < 1 and that the set of transfer functions which are realizable by triples (A,b,c) with A unbounded but generating a strongly continuous semigroup is related in a close way to functions analytic and square Integrable on a half-plane.
Accuracy of several alternative forms of the operator expansion solution for scattering from 1-D randomly rough Dirichlet surfaces (2002)

We have examined the operator expansion (OE) method in computing scattering over a wide range of scattering regimes, for l-D Dirichlet surfaces with Gaussian spectra, and with Pierson-Moskowitz spectra (used to model the ocean surface). We give a brief review of a derivation of the standard OE solution, and show how the short series are obtained. Numerical examples are presented illustrating the rapid convergence and wide accuracy of the various forms of the OE solution in several scattering regimes. Our results indicate that the short series provide efficient and accurate alternatives to the standard solution, a finding which is of significant practical value in treating scattering from 2-D surfaces. In general, our results for scattering from l-D surfaces suggest that the OE is a very attractive method for computing scattering from a wide range of realistic 2-D rough surfaces with a Dirichlet boundary condition. We also present the alternative forms of the OE solution and give one example for scattering from surfaces with a Gaussian spectrum.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Materials and Methods and Supplementary Figure Legends from Targeting Calcium Signaling Induces Epigenetic Reactivation of Tumor Suppressor Genes in Cancer (2023)

&lt;p&gt;Supplementary Materials and Methods and Supplementary Figure Legends&lt;/p&gt;
Using Pressure Analysis, Well Logs and Core Analysis for Better Understanding of the Geological Models - Cases of Berkine Basin TAGI Reservoir (2000)

In many places throughout the world hydrocarbons are being found in vertically stacked reservoirs. The Triasic reservoir might belong to a discontinuous sedimentary system, so reservoir characteristics may differ locally.