gebhart/patrepeval huggingface dataset:
Cell Type-Specific Expression of Transforming Growth Factor-β 1 in the Mouse Uterus during the Periimplantation Period (1990)

Immunohistochemistry and in situ and Northern blot hybridization were employed to determine temporal and spatial expression of transforming growth factor-beta 1 (TGF beta 1) in the mouse uterus during the periimplantation period. The polyclonal antisera anti-LC-(1-30) and anti-CC-(1-30), raised against two different preparations of a peptide corresponding to the amino-terminal 30 amino acids of TGF beta 1, were used for histochemical analyses because of their distinct staining patterns. Anti-LC shows intracellular staining, while staining by anti-CC is primarily extracellular. The colocalization of intracellular staining by anti-LC with in situ hybridization of TGF beta 1 mRNA in the luminal and glandular epithelia on days 1-4 of pregnancy (day 1 = vaginal plug) indicates that the epithelial cells are the primary sites of TGF beta 1 synthesis during the preimplantation period. On the other hand, staining of the extracellular matrix of the stroma by anti-CC during this period suggests an active accumulation of TGF-beta 1 that is synthesized in and secreted from the epithelia. While intracellular staining and accumulation of TGF-beta 1 mRNA in the epithelia were clearly evident on days 1-4, the extracellular staining showed temporal fluctuations. The clear extracellular staining of the stroma that was observed on day 1 was absent on day 2; moderate staining was again visualized in the stroma on day 3 and was markedly increased on day 4.(ABSTRACT TRUNCATED AT 250 WORDS)
Role of a solvent‐exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo‐β‐lactamase (2003)

Numerous X-ray crystal structures of the metallo-beta-lactamase from Bacteroides fragilis and related organisms show a beta-hairpin loop immediately adjacent to the active-site zinc atom(s). Both crystallographic and NMR information show that the end of this beta-hairpin loop, which contains a solvent exposed tryptophan residue, Trp49, is highly flexible in the absence of substrates or other ligands, giving rise in some of the X-ray structures to a lack of observable electron density in this region. We report an investigation of the role of this mobile, solvent-exposed tryptophan using site-directed mutagenesis, steady state kinetics measurements and characterization by NMR. Trp49 appears to have a role both in substrate binding and in promotion of catalysis. Substitution of this residue with a number of different side chains indicates that the binding interaction depends on the bulky hydrophobic and aromatic nature of the indole ring, which can provide relatively non-specific interactions with a variety of antibiotic substrates. In this way, the tryptophan at this position provides a large degree of the breadth of substrate specificity for the metallo-beta-lactamase. Previous studies established that the antibiotic binding site was sufficiently plastic that the derivatization of existing antibiotics is unlikely to result in the successful treatment of bacterial infections incorporating this resistance element. Rather, a more productive approach may be to design therapeutics directed towards this solvent-exposed tryptophan residue.
Excited state absorption spectra and intersystem crossing kinetics in the naphthaldehydes (1984)

Picosecond time resolved, excited state absorption spectra following excitation at 355 nm are reported for 1-naphthaldehyde (1-NA) and 2-naphthaldehyde (2-NA) in room temperature solutions. The kinetics of the lowest excited singlet state (S1) decay are determined for each. The S1 lifetimes in cyclohexane are ∼26 ps for 1-NA and ∼55 ps for 2-NA. Both Sn←S1 and Tn←T1 spectra are reported. Molecular orbital model calculations based on the INDO formalism predict excited state singlet–singlet spectra and spin-orbit coupling matrix elements that are consistent with the observed spectra and kinetics.
Physics of growing biological tissues: the complex cross-talk between cell activity, growth and resistance (2019)

For many organisms, shapes emerge from growth, which generates stresses, which in turn can feedback on growth. In this review, theoretical methods to analyse various aspects of morphogenesis are discussed with the aim to determine the most adapted method for tissue mechanics. We discuss the need to work at scales intermediate between cells and tissues and emphasize the use of finite elasticity for this. We detail the application of these ideas to four systems: active cells embedded in tissues, brain cortical convolutions, the cortex of Caenorhabditis elegans during elongation and finally the proliferation of epithelia on extracellular matrix. Numerical models well adapted to inhomogeneities are also presented. This article is part of the theme issue 'Rivlin's legacy in continuum mechanics and applied mathematics'.
Trophoblastäre Funktionen werden durch Protein Inhibitors of Activated STATs (PIAS) reguliert (2009)

Hintergrund: Signal Transducer und Activator of Transcription 3 (STAT3) ist ein intrazelluläres Signal-Molekül in trophoblastären Zellen, das durch Leukämie Inhibitorische Factor (LIF)-Rezeptor-Bindung an seinem tyr705-Rest phosphoryliert werden kann. Diese Phosphorylierung korreliert mit der Invasivität. Protein Inhibitors of Activated STATs (PIAS) wirken der STAT-Aktivierung entgegen. Deswegen wird erwartet, dass sie die Trophoblast-Invasion regulieren.
Continuous Removal of SO2 in the Model Flue Gas over PAN-ACF with Recovering Aqueous H2SO4 (1993)

Abstract SO2 was adsorbed, oxidized, hydrated, and recovered continuously as aq. H2SO4 at 30–100 °C on a polyacrylonitrile based active carbon fiber (PAN-ACF-FE-300). SO2 of 1000 ppm in a model flue gas was removed completely for longer than 60 h at 30 and 50 °C by W/F = 5.0 × 10−3 g min ml−1 by supplying sufficient humidity of 10 and 20 vol%, respectively. The heat-treatment of the ACF at 800 °C was found very effective to enhance the catalytic activity.
Perception of Nonverbal Cues After Right Brain Damage (1984)

TBA
ChemInform Abstract: Pushing Flow Chemistry to New Limits: Development of a Flow Process Towards Spirangien A (2014)

Abstract Review: 12 refs.
Functional Clustering of Metastasis Proteins Describes Plastic Adaptation Resources of Breast-Cancer Cells to New Microenvironments (2008)

To examine the molecular mechanisms underlying breast cancer metastasis in liver and search for potential markers of metastatic progression in soft-tissue, we analyzed metastatic variants developed from the highly metastatic MDA-MB 435 cell line through in vivo stepwise selection in the athymic mice. Comparative proteomic analysis using two-dimensional electrophoresis (2DE-DIGE) revealed that 74 protein spots were reproducibly more than doubled in liver metastatic cells compared to parental counterpart. From 22 proteins identified by MALDI-TOF, belonging to intermediate filaments, intracellular transport and ATP synthesis, we generated a protein-protein interaction network containing 496 nodes, 12 of which interacted. GRP 75 was connected with four other proteins: prohibitin, HSP 27, elongin B and macropain delta chain. After functional classification, we found that pathways including hepatocyte growth factor receptor (p = 0.014), platelet-derived growth factor (p = 0.018), vascular endothelial growth factor (p = 0.021) and epidermal growth factor (p = 0.050) were predominant in liver metastatic cells, but not in lung metastatic cells. In conclusion, we suggest that GRP 75 is involved in cell proliferation, tumorigenesis and stress response in metastatic cells by recruiting signals in which the transmembrane receptor protein tyrosine kinase signaling pathway (p-value FDR = 1.71 x 10(-2)) and protein amino acid phosphorylation (p-value FDR = 3.28 x 10(-2)) might be the most significant biological process differentially increased in liver metastasis.
Interactions of hydrogen with native defects in GaN (1997)

The atomic and electronic structure of hydrogen-vacancy complexes in GaN is investigated with pseudopotential-density-functional calculations. Calculated formation energies provide information about the likelihood of incorporation of these complexes in $n$-type and $p$-type material, and binding energies provide a measure for the dissociation energy. Vibrational frequencies yield a signature of the complex that should facilitate experimental identification. The behavior of hydrogenated nitrogen vacancies during annealing of acceptor-doped GaN is discussed, and a correlation with the frequently observed luminescence band around 420 nm is proposed.
Supplementary Table 2 from Novel Associations between Common Breast Cancer Susceptibility Variants and Risk-Predicting Mammographic Density Measures (2023)

&lt;p&gt;Supplementary Table 2. Associations (95% Confidence Interval (CI) in brackets) between all 77 breast cancer susceptibility variants and percent dense area, dense area, and non-dense area&lt;/p&gt;
Criteria for evaluation of open source cloud computing solutions (2011)

Cloud computing promises on- demand scalability and flexibility for the enterprise environment and open source products have a large presence in this area. We have devised an elaborate set of criteria for evaluation and comparison of open source IaaS cloud computing solutions which can be used for ranking and choosing between the available products. We explain each criteria group and give both the rationale and the estimated impact of the criteria. We also briefly introduce several of the most common open source cloud computing IaaS solutions to be evaluated using the created criteria.
Functional significance of individual variations in callosal area (1995)

We considered the hypothesis that the richness of callosal interhemispheric connections has a role in determining the degree of behavioural laterality and time-sharing ability in dual-task performance. Behavioural laterality as measured by dichotic word listening, line bisection and turning bias tests correlated inversely with the midsagittal cross-sectional area of the corpus callosum, as seen on MRI. The amount of dual task interference was strongly inversely correlated with the callosal area in both within-hemisphere and between-hemispheres conditions. These relationships between normal variations in callosal area, and outcomes on tests both of laterally and time-sharing capacity in normal adults suggest that the corpus callosum assumes a cross-excitatory role when subjects perform these tasks.
Sustainable blockchain-enabled services: Smart contracts (2017)

This paper introduces some of the interdependent components within the multifaceted solution our team is developing towards accelerating the functionality, complexity and versatility of blockchain-enabled services. The focus here is particularly on introducing and bringing together selected individual components of the solution to achieve a synergistic effect in expanding the functionality of blockchain-enforced smart contracts. The contributions of this paper include: (i) proposing a method for automated management of contracts with hierarchical conditionality structures through an hierarchy of intelligent agents and the use of hierarchical cryptographic key-pairs; (ii) proposing a method for efficient and secure matching and transfer of smart-contract underlyings (entities) among disparate smart contracts/subcontracts; (iii) proposing a method for producing an hierarchy of common secrets to facilitate hierarchical communication channels of increased security, and applying this method both in the context of method (i) and method (ii); and (iv) proposing the use of distributed hash tables DHT in building secure and optimized repositories in the context of method (i) and in the context method (ii), where the former involves a DHT repository of smart contracts and the latter involves a DHT repository of entities underlying smart contracts that are being exchanged among different smart contracts and subcontracts. The smart-contract focused methods introduced in this paper contribute to the overall goal towards a sustainable adaptive mechanism for processing evolving volumes, versatility, and complexity of blockchain transactions, traffic, and services. Blockchain-enabled services are efficient, secure, automated, and allowing worldwide distribution of resources. They present a more efficient and sustainable alternative to current service infrastructures within a range of domains, particularly the legal and financial domains. They also set a sustainable infrastructure for emerging Internet-of-things services.
A within‐subject between‐apparatus comparison of impulsive choice: T‐maze and two‐lever chamber (2015)

Whereas intertemporal choice procedures are a common method for examining impulsive choice in nonhuman subjects, the apparatus used to implement this procedure varies across studies. The purpose of the present study was to compare impulsive choice between a two-lever chamber and a T-maze. In Experiment 1, rats chose between a smaller, immediate reinforcer and a larger, delayed reinforcer, first in a two-lever chamber and then in a T-maze. Delay to the larger reinforcer changed in an ascending and descending order (0-32 s) across sessions. Experiment 2 examined the same between-apparatus comparison but under steady-state conditions with the delay fixed at 32 s. In Experiment 1, choice for the larger, delayed reinforcer was generally higher in the T-maze than in the two-lever chamber. Similarly in Experiment 2, steady-state choice for the larger, delayed reinforcer was higher in the T-maze. Choice for the 32-s delayed reinforcer was also greater in Experiment 2 than in Experiment 1, suggesting that extended exposure to the delay is required for the T-maze to yield reliable impulsive choice data. While the reasons for the between-apparatus discrepancies are at present unknown, results from both experiments clearly demonstrate that the apparatus matters when assessing overall level and reliability of impulsive choice data.
Proximity effect of spin orbit coupling in Pt/Co2FeAl and Pt/Permalloy bilayers_810571 (2013)

Proximity effect of spin orbit coupling is investigated through anomalous Hall effect in Pt/Co2FeAl and Pt/Permalloy bilayers. A series of nontrivial magnetotransport behaviors, resulting from a strong impact of phonons on skew scattering, is observed in these films with ultrathin ferromagnetic layers. The parameters representing skew scattering, side jump and intrinsic contributions are dramatically enhanced when the ferromagnetic layer is very thin, and they have clear linear dependences on the reciprocal of ferromagnetic layer thickness, indicating a powerful influence of Pt/Ferromagnet interface. Further study on Cu/Co2FeAl and Ta/Co2FeAl bilayers reveals that a simple interface scattering without intense spin orbit coupling is not sufficient to trigger such a phenomenon. The proximity effect of spin orbit coupling is thus suggested to occur at the Pt/Ferromagnet interface, and as a result quite large anomalous Hall angle (0.036) and Nernst angle (0.23) are confirmed in the Pt/CFA films at room temperature.
Abstract 415: The characterization of in vitro models demonstrating a significant delay of acquired resistance to ulixertinib (ERK1/2) (2022)

Abstract Ulixertinib (BVD-523) is a first-in-class small molecule inhibitor of ERK1/2 currently being investigated in several oncology clinical trials, both as a single agent and in combination with other anti-cancer therapeutics. Clinical acquired resistance has been described by others for numerous efficacious small molecule agents. Relevant to the MAPK pathway, emergence of resistance to BRAF and MEK inhibitors limits their clinical efficacy. In vitro models of ulixertinib resistance were generated in an endeavor to characterize and predict potential clinical mechanisms of resistance and guide rational combination therapies. The BRAF-V600E mutant melanoma cell line, A375, was cultured in progressively increasing concentrations of ulixertinib or other MAPK pathway inhibitors (dabrafenib and/or trametinib). Drug-resistant A375 clones were readily obtained following growth in high concentrations of dabrafenib or trametinib. In contrast, developing resistance to ulixertinib proved challenging. Eventually, ulixertinib resistant clones emerged and demonstrated varying degrees of cross-resistance to other MAPK pathway inhibitors and displayed bell-shaped dose-response curves indicative of drug addiction for optimal proliferation. To elucidate potential mechanisms of resistance, Reverse Phase Protein Array profiling of 306 proteins was performed on parental A375 and ulixertinib-resistant clones following treatment with ulixertinib at varying concentrations and treatment times. Principal component analysis revealed clustering of resistant clones by ulixertinib treatment conditions (concentrations and duration). Differences between parental A375 and ulixertinib resistant clones were revealed, including components of MAPK, HER2, and autophagy markers. This work begins to tease out potential mechanisms of resistance to ulixertinib and guide potential combination partners that could circumvent acquired resistance. Citation Format: Deborah Knoerzer, Anupama Reddy, David Sorrell, Caroline M. Emery. The characterization of in vitro models demonstrating a significant delay of acquired resistance to ulixertinib (ERK1/2) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 415.
Supplementary Figures from Mesenchymal CD44 Expression Contributes to the Acquisition of an Activated Fibroblast Phenotype via TWIST Activation in the Tumor Microenvironment (2023)

&lt;p&gt;PDF file, 1638K, Transgenic bone marrow transplantation into GFP+ recipient mice resulted in mice with two labeled cell populations (S1); Fewer activated myofibroblast incorporation in tumors engrafted in CD44-/- BMT mice compared to WT BMT (S2); Human and murine MSC phenotype shows no difference between knockdown MSC and naive MSC (S3); Protein and RNA expression of CD44 ligands in tumor cell lines and MSC (S4); Blocking CD44 expression on MSC inhibits migration in vitro and in vivo (S5).&lt;/p&gt;
Application of momentary Fourier transform to SAR processing (1999)

A common technique in signal and image processing is to extract a portion of the signal by windowing, and then perform the DFT on the window contents. The momentary Fourier transform (MFT) applies to the particular case where the window is moved one data sample along the signal between successive transforms. An alternative derivation of the recursive form of the MFT using general matrix transforms is given. How DFTs and IDFTs are used in the SPECAN and SIFFT methods of synthetic aperture radar (SAR) processing is described. The MFT and inverse MFT are applied to these methods and the advantages and disadvantages they have compared to the FFT/IFFT algorithms are shown.
A chemical model of coal devolatilization using percolation lattice statistics (1988)

The authors have developed a model for coal devolatilization that incorporates the diversity of coal structure in such a way that the analytical data obtained from solid state NMR provides the initial input data. Using an experimentally determined kinetic rate parameters, it is possible to fit the gas, tar and char production of a lignite and high volatile bituminous coal. The authors have employed percolation theory to provide analytical expressions for the lattice statistics required in devolatilization modeling. The percolation theory allows one to avoid the more time consuming Monte Carlo technique with no loss of generality or important statistical features. Percolation theory analytically describes the size distribution of finite clusters of sites joined by intact bridges but isolated from all remaining sites by broken bridges. The theory specifies a critical bridge population, depending only on the site coordination number, above which infinite arrays will coexist with clusters of finite size. It is a simple matter to adapt the structural features of percolation theory to both the tar and gas obtained in coal pyrolysis. The infinite arrays of percolation theory are interpreted as the macroscopic lattice of unreacted coal and/or char while the relatively small tar molecules may be identifiedmore » with the fine clusters of percolation theory. The details of the model are discussed together with the results obtained in modeling devolatilization behavior of coals of various ranks.« less
Accurate measurement of the optical constants for modeling organic and organophosphorous liquid layers and drops (2018)

We present accurate measurements for the optical constants for a series of organic liquids, including organophosphorous compounds. Bulk liquids are rarely encountered in the environment, but more commonly are present as droplets of liquids or thin layers on various substrates. Providing reference spectra to account for the plethora of morphological conditions that may be encountered under different scenarios is a challenge. An alternative approach is to provide the complex optical constants, n and k, which can be used to model the optical phenomena in media and at interfaces, minimizing the need for a vast number of laboratory measurements. In this work, we present improved protocols for measuring the optical constants for a series of liquids that span from 7800 to 400 cm-1. The broad spectral range means that one needs to account for both strong and weak spectral features that are encountered, all of which can be useful for detection, depending on the scenario. To span this dynamic range, both long and short cells are required for accurate measurements. These protocols are presented along with experimental and modeling results for thin layers of silicone oil on aluminum.
STATISTICAL PROCESS CONTROL AND MACHINE CAPABILITY IN THREE DIMENSIONS (1995)

Key word: Multivariate statistical process controlMultivariate machine acceptance testing T 2control chartsMultivariate machine capability
Net Shape Spin Formed Cryogenic Aluminum Lithium Cryogenic Tank Domes for Lower Cost Higher Performance Launch Vehicles (2013)

With the goal of lower cost (simplified manufacturing and lower part count) and higher performance (higher strength to weight alloys) the NASA Technical Maturation Program in 2006 funded a proposal to investigate spin forming of space launch vehicle cryogenic tank domes. The project funding continued under the NASA Exploration Technology Development Program through completion in FY12. The first phase of the project involved spin forming of eight, 1 meter diameter path finder domes. Half of these were processed using a concave spin form process (MT Aerospace, Augsburg Germany) and the other half using a convex process (Spincraft, Boston MA). The convex process has been used to produce the Ares Common Bulkhead and the concave process has been used to produce dome caps for the Space Shuttle light weight external tank and domes for the NASDA H2. Aluminum Lithium material was chosen because of its higher strength to weight ratio than the Aluminum 2219 baseline. Aluminum lithium, in order to obtain the desired temper (T8), requires a cold stretch after the solution heat treatment and quench. This requirement favors the concave spin form process which was selected for scale up. This paper describes the results of processing four, 5.5 meter diameter (upper stage scale) net shaped spin formed Aluminum Lithium domes. In order to allow scalability beyond the limits of foundry and rolling mills (about 12 foot width) the circular blank contained one friction stir weld (heavy lifter scales require a flat blank containing two welds). Mechanical properties data (tensile, fracture toughness, stress corrosion, and simulated service testing) for the parent metal and weld will also be discussed.