gebhart/patrepeval huggingface dataset:
Programmed line width roughness metrology by multitechniques approach (2018)

At modern manufacturing geometries, roughness control presents a huge challenge for the lithography step. For advanced nodes, this morphological aspect reaches the same order of magnitude as the critical dimension (CD). Hence, the control of roughness needs an adapted metrology. Specific samples with designed roughness have been manufactured using e-beam lithography. These samples have been characterized with three different methodologies: CD-scanning electron microscopy, optical critical dimension, and small angle x-ray scattering. The main goal is to compare the capability of each of these techniques in terms of reliability, type of information obtained, time to obtain the measurements, and level of maturity for the industry. The next step will be to develop a hybrid metrology approach for roughness determination with these techniques.
Neural precursor cell cultures from GM2 gangliosidosis animal models recapitulate the biochemical and molecular hallmarks of the brain pathology (2009)

In this work we showed that genotype-related patterns of hexosaminidase activity, isoenzyme composition, gene expression and ganglioside metabolism observed during embryonic and postnatal brain development are recapitulated during the progressive stages of neural precursor cell (NPC) differentiation to mature glia and neurons in vitro. Further, by comparing NPCs and their differentiated progeny established from Tay-Sachs (TS) and Sandhoff (SD) animal models with the wild-type counterparts, we studied the events linking the accumulation of undegraded substrates to hexosaminidase activity. We showed that similarly to what observed in brain tissues in TS NPCs and progeny, the stored GM2 was partially converted by sialidase to GA2, which can be then degraded in the lysosomes to its components. The latter can be used in a salvage pathway for the formation of GM3. Interestingly, results obtained from ganglioside feeding assays and from measurement of lysosomal sialidase activity suggest that a similar pathway might work also in the SD model.
Potential Mechanisms behind Physical Exercise vs. Epigenetic Regulation for Preventing Breast Cancer (2017)

Breast cancer is the most commonly diagnosed cancer and has been the second leading cause of death due to cancer among women worldwide. It is a disease in which malignant (cancer) cells form in the tissues of the breast and become deadly when they metastasize, spreading to other organs or bones. Breast cancer is one of the major cancer diseases, occurring in both men and women, but it is rare in men. Though risk for breast cancer is affected by genetic factors, age, and other factors or personal habits; recent studies have suggested that physical exercise induces positive effects for lowering these risks as well as reducing the incidence rate. In the current review, we will look at previous studies, which have investigated links between physical exercise and breast cancer in the last decade. Meanwhile, we will discuss potential mechanisms by which physical exercise may play a role in preventing breast cancer, with special emphasis on a recent study on epigenetic regulations during physical exercise.
Active Control of Separation from the Flap of a Supercritical Airfoil (2006)

Zero-mass-flux periodic excitation was applied at several regions on a simplified high-lift system to delay the occurrence of flow separation. The NASA Energy Efficient Transport (EET) supercritical airfoil was equipped with a 15% chord simply hinged leading edge flap and a 25% chord simply hinged trailing edge flap. Detailed flow features were measured in an attempt to identify optimal actuator placement. The measurements included steady and unsteady model and tunnel wall pressures, wake surveys, arrays of surface hot-films, flow visualization, and particle image velocimetry (PIV). The current paper describes the application of active separation control at several locations on the deflected trailing edge flap. High frequency (F(+) approximately equal to 10) and low frequency amplitude modulation (F(+) sub AM approximately equal to 1) of the high frequency excitation were used for control. It was noted that the same performance gains were obtained with amplitude modulation and required only 30% of the momentum input required by pure sine excitation.
OF MUTAGENESIS IN MAMMALIAN CELLS IN CULTURE (1989)

frequ~fcy ~sually re~orded per mamma11an gene of 1x10 - 1x10. Th1S observat10n was a serious obstacle to the use of shuttle vectors for the study of untill the use of certain mammalian cell lines such as the human 293 cells and EBV-derived shuttle vectors (1-3) provided acceptable background mutation of 10-~ The low spontaneous background of these systems facilated, and in many cases made possible, the observation of mutations induced by radiation and chemical agents (1-3,6). Analysis of the mutational spectra within target genes elucidated the mechanisms by which DNA photoproducts and alkyl adducts are processed into mutations in cultured mammalian cells. However, mainly in the case of alkylating agents, the multitude of induced DNA chemical modification products did not allow the identification of the precise lesions responsible for the mutagenic effects evident in the mutational spectra of these agents. In order to establish this relationship, we have constructed a shuttle vector containing a model DNA lesion at a known genome site. A simplified scheme of a lesion-specific mutagenesis study is depicted in Fig. 1. The shuttle vector is mod!fied to contain a 6 specific DNA adduct, in the example 0 -methylguanine (0 MeGua). The recombinant DNA genome is transfected into
Live-seq enables temporal transcriptomic recording of single cells (2022)

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity<sup>1</sup>. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy<sup>2,3</sup>, thus allowing to couple a cell's ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell transcriptome read-outs to demonstrate that Live-seq can accurately stratify diverse cell types and states without inducing major cellular perturbations. As a proof of concept, we show that Live-seq can be used to directly map a cell's trajectory by sequentially profiling the transcriptomes of individual macrophages before and after lipopolysaccharide (LPS) stimulation, and of adipose stromal cells pre- and post-differentiation. In addition, we demonstrate that Live-seq can function as a transcriptomic recorder by preregistering the transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure. This enabled the unsupervised, genome-wide ranking of genes on the basis of their ability to affect macrophage LPS response heterogeneity, revealing basal Nfkbia expression level and cell cycle state as important phenotypic determinants, which we experimentally validated. Thus, Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.
An exploratory, randomised, placebo-controlled, 14 day trial of the soluble guanylate cyclase stimulator praliciguat in participants with type 2 diabetes and hypertension (2019)

This trial was funded by Cyclerion Therapeutics.
Unique Catalytic Mechanism for Ru-Loaded Ternary Intermetallic Electrides for Ammonia Synthesis (2022)

Intermetallic electrides have recently shown their priority as catalyst components in ammonia synthesis and CO<sub>2</sub> activation. However, their function mechanism has been elusive since its inception, which hinders the further development of such catalysts. In this work, ternary intermetallic electrides La-TM-Si (TM = Co, Fe, and Mn) were synthesized as hosts of ruthenium (Ru) particles for ammonia synthesis catalysis. Although they have the same crystal structure and possess low work functions commonly, the promotion effects on Ru particles rather differ from each other. The catalytic activity follows the sequence of Ru/LaCoSi > Ru/LaFeSi > Ru/LaMnSi. Furthermore, Ru/LaCoSi exhibits much better catalytic durability than the other two. A combination of experiments and first-principles calculations shows that apparent N<sub>2</sub> activation energy on each catalyst is much lower than that over conventional Ru-based catalysts, which suggests that N<sub>2</sub> dissociation can be conspicuously promoted by the concerted actions of the specific electronic structure and atomic configuration of intermetallic electride-supported catalysts. The NH<sub><i>x</i></sub> formations proceeded on La are energetically favored, which makes it possible to bypass the scaling relations based on only Ru as the active site. The rate-determining step of Ru/La-TM-Si was identified to be NH<sub>2</sub> formation. The transition metal (TM) in La-TM-Si electrides has a significant influence on the metal-support interaction of Ru and La-TM-Si. These findings provide a guide for the development of new and effective catalyst hosts for ammonia synthesis and other hydrogenation reactions.
Comparative evaluation of hydrolytic efficiency toward microcrystalline cellulose of Penicillium and Trichoderma cellulases (1995)

Composition, stability at different pH and temperatures and hydrolytic efficiency toward microcrystalline cellulose (MCC) of Penicillium cellulase were evaluated. The pH optimum (4·5-5·0) of filter paper activity (FPA) and temperature optimum (50–55°C) were determined. Maximum stability of FPA was observed at pH 4·0–5·0 and temperature 40–50°C. A minor contribution of stirring (3–4%) in inactivation of Penicillium preparation was shown. Kinetic parameters of MCC hydrolysis by Penicillium cellulase were determined at optimal conditions (pH 4·5, 50°C): Km = 50 g/l, Vmax = 330 μM/min per gram of protein. More effective saccharification of MCC by Penicillium preparations compared to Trichoderma reesei cellulases with the same level of total cellulolytic activity (FPA=1·0 U/ml) was demonstrated. Glucose concentration in 24 h hydrolysate was 41 g/l for Penicillium cellulase, 15 g/l for T. reesei (Privolzhski Fermentation Plant) and 26 g/l for T. reesei (Genencor). Hydrolysates of Penicillum cellulase contained only 9% of cellobiose compared to 24–40% of cellobiose for T. reesei cellulases. Factors contributing to superior properties of Penicillium cellulase — higher level of cellobiase activity and higher operational stability — are discussed.
Operation of Naturally Sampled Current Regulators in the Transition Mode (1987)

A fundamental component model of current-regulated naturally sampled PWM inverters operating in the pulse-dropping mode is proposed. Analytical and test results are compared for purposes of model verification and regulator evaluation. The results demonstrate the problems with the classical (stationary reference frame) current regulator that occur in this region of operation. In contrast, the synchronous reference frame regulator is shown to have ideal steady-state response in this region.
A Facile Entry to Bicyclic Systems from L-Glutamic Acid (2001)

An efficient synthesis of bicyclic heterocycles has been realized from L-glutamic acid.The key step is the construction of the pyrrole ring in a single step, using tosylmethyl isocyanide (TosMIC) methodology.Structures of reaction intermediates and final products were investigated using density functional theory calculations.
4-Substituted Cubylcarbinylamines:  A New Class of Mechanism-Based Monoamine Oxidase B Inactivators (1997)

Cubylcarbinylamine (1a), (4-cyclopropylcubyl)carbinylamine (1b), and (4-phenylcubyl)carbinylamine (1c) were synthesized and shown to be time-dependent, irreversible inactivators of monoamine oxidase B (MAO B). Substrate protects the enzyme from inactivation, but beta-mercaptoethanol does not, suggesting that these compounds are mechanism-based inactivators. All three compounds were also substrates for MAO B with partition ratios ranging from 152 to 536. The 4-substituted analogues were more potent inactivators than the unsubstituted analogue, indicating a benefit to 4-substitution in this class of inactivators.
On the use of Artificial Neural Networks in Topology Optimisation (2022)

The question of how methods from the field of artificial intelligence can help improve the conventional frameworks for topology optimisation has received increasing attention over the last few years. Motivated by the capabilities of neural networks in image analysis, different model-variations aimed at obtaining iteration-free topology optimisation have been proposed with varying success. Other works focused on speed-up through replacing expensive optimisers and state solvers, or reducing the design-space have been attempted, but have not yet received the same attention. The portfolio of articles presenting different applications has as such become extensive, but few real breakthroughs have yet been celebrated. An overall trend in the literature is the strong faith in the "magic" of artificial intelligence and thus misunderstandings about the capabilities of such methods. The aim of this article is therefore to present a critical review of the current state of research in this field. To this end, an overview of the different model-applications is presented, and efforts are made to identify reasons for the overall lack of convincing success. A thorough analysis identifies and differentiates between problematic and promising aspects of existing models. The resulting findings are used to detail recommendations believed to encourage avenues of potential scientific progress for further research within the field.
Structure−Activity Relationship of Uridine 5‘ - Diphosphoglucose Analogues as Agonists of the Human P2Y 14 Receptor (2020)

UDP-glucose (UDPG) and derivatives are naturally-occurring agonists of the Gi protein-coupled P2Y14 receptor, which occurs in the immune system. We synthesized and characterized pharmacologically novel analogues of UDPG modified on the nucleobase, ribose, and glucose moieties, as the basis for designing novel ligands in conjunction with modeling. The recombinant human P2Y14 receptor expressed in COS-7 cells was coupled to phospholipase C through an engineered Gα-q/i protein. Most modifications of the uracil or ribose moieties abolished activity; this is among the least permissive P2Y receptors. However, a 2-thiouracil modification in 15 (EC50 49 ± 2 nM) enhanced the potency of UDPG (but not UDP-glucuronic acid) by 7-fold. 4-Thio analogue 13 was equipotent to UDPG, but S-alkylation was detrimental. Compound 15 was docked in a rhodposin-based receptor homology model, which correctly predicted potent agonism of UDP-fructose, UDP-mannose, and UDP-inositol. The hexose moiety of UDPG interacts with multiple H-bonding and charged resides and provides a fertile region for agonist modification.
Non-Submodular Maximization via the Greedy Algorithm and the Effects of Limited Information in Multi-Agent Execution (2022)

We provide theoretical bounds on the worst case performance of the greedy algorithm in seeking to maximize a normalized, monotone, but not necessarily submodular ob-jective function under a simple partition matroid constraint. We also provide worst case bounds on the performance of the greedy algorithm in the case that limited information is available at each planning step. We specifically consider limited information as a result of unreliable communications during distributed execution of the greedy algorithm. We utilize notions of curvature for normalized, monotone set functions to develop the bounds provided in this work. To demonstrate the value of the bounds provided in this work, we analyze a variant of the benefit of search objective function and show, using real-world data collected by an autonomous underwater vehicle, that theoretical approximation guarantees are achieved despite non-submodularity of the objective function.
Overall statistical analysis of saliva samples comparing periodontal cohorts from diabetics and non-diabetics. (2015)

&lt;p&gt;*25 metabolites were increased in saliva from subjects with gingivitis, 10 metabolites were increased in saliva from diabetic, non-gingivitis subjects.&lt;/p&gt;&lt;p&gt;**12 metabolites were increased in saliva from diabetic subjects with periodontitis, 42 metabolites were increased in saliva from diabetic, periodontally healthy subjects.&lt;/p&gt;&lt;p&gt;***17 metabolites were increased in saliva from non-diabetic gingivitis subjects without diabetes, 3 metabolites were increased in saliva from non-diabetic, periodontally healthy subjects.&lt;/p&gt;&lt;p&gt;****62 metabolites were increased in saliva from non-diabetic periodontitis subjects, 2 metabolites were increased in saliva from non-diabetic, periodontally healthy subjects.&lt;/p&gt;
Suppression of Hedgehog signalling promotes pro‐tumourigenic integrin expression and function (2014)

Aberrant Hedgehog (Hh) signalling has been reported in a number of malignancies, particularly basal cell carcinoma (BCC) of the skin. Clinical trials of Hh inhibitors are underway in many cancers, and these have produced significant clinical benefit in BCC patients, although regrowth of new, or clinically aggressive, variants, as well as development of secondary malignancies, has been reported. αvβ6 integrin is expressed in many cancers, where it has been shown to correlate with an aggressive tumour phenotype and poor prognosis. We have previously reported αvβ6 up-regulation in aggressive, morphoeic BCC variants, where it modulates the stromal response and induces invasion. To examine a possible link between Hh and αvβ6 function, we generated BCC models, overexpressing Gli1 in immortalized keratinocytes (NTert1, HaCaT). Unexpectedly, we found that suppressing Gli1 significantly increased αvβ6 expression. This promoted tumour cell motility and also stromal myofibroblast differentiation through integrin-dependent TGF-β1 activation. Gli1 inhibited αvβ6 expression by suppressing TGF-β1-induced Smad2/3 activation, blocking a positive feedback loop maintaining high αvβ6 levels. A similar mechanism was observed in AsPC1 pancreatic cancer cells expressing endogenous Gli1, suggesting a common mechanism across tumour types. In vitro findings were supported using human clinical samples, where we showed an inverse correlation between αvβ6 and Gli1 expression in different BCC subtypes and pancreatic cancers. In summary, we show that expression of Gli1 and αvβ6 inversely correlates in tumours in vivo, and Hh targeting up-regulates TGF-β1/Smad2/3-dependent αvβ6 expression, promoting pro-tumourigenic cell functions in vitro. These results have potential clinical significance, given the reported recurrence of BCC variants and secondary malignancies in patients treated by Hh targeting.
Effective Bronchodilator Resuscitation of Children in the Emergency Room: Device or Interface? (2011)

Aerosol therapy is a vital component in the treatment of children with asthma, and inhaled β-agonists are the first-line therapy for bronchospasm in acute asthma. In the emergency department, bronchodilators are commonly administered to children via small-volume jet nebulizer (SVN) or large-volume
Visualization of C. elegans transgenic arrays by GFP (2006)

The GFP-LacI*lacO transgene detection system works in C. elegans for visualization of chromosomes and extrachromosomal transgenes. It can be used as a marker for genetic mosaic analysis. The lacO repeat sequence as an extrachromosomal array becomes a valuable technique allowing rapid, accurate determination of spontaneous loss of the array, thereby allowing high-resolution mosaic analysis. The lin-3 gene is required in the anchor cell to induce the epidermal vulval precursors cells to undergo vulval development.
Faculty Opinions recommendation of p62 links the autophagy pathway and the ubiqutin-proteasome system upon ubiquitinated protein degradation. (2017)

The ubiquitin-proteasome system (UPS) and autophagy are two distinct and interacting proteolytic systems. They play critical roles in cell survival under normal conditions and during stress. An increasing body of evidence indicates that ubiquitinated cargoes are important markers of degradation. p62, a classical receptor of autophagy, is a multifunctional protein located throughout the cell and involved in many signal transduction pathways, including the Keap1-Nrf2 pathway. It is involved in the proteasomal degradation of ubiquitinated proteins. When the cellular p62 level is manipulated, the quantity and location pattern of ubiquitinated proteins change with a considerable impact on cell survival. Altered p62 levels can even lead to some diseases. The proteotoxic stress imposed by proteasome inhibition can activate autophagy through p62 phosphorylation. A deficiency in autophagy may compromise the ubiquitin-proteasome system, since overabundant p62 delays delivery of the proteasomal substrate to the proteasome despite proteasomal catalytic activity being unchanged. In addition, p62 and the proteasome can modulate the activity of HDAC6 deacetylase, thus influencing the autophagic degradation.
Establishing a Biofilm Co-culture of Pseudomonas and Aspergillus for Metabolite Extraction (2015)

Filamentous fungi and bacteria form mixed-species biofilms in nature and diverse clinical contexts (Frey-Klett <i>et al.</i>, 2011; Peleg <i>et al.</i>, 2010). The interactions between fungi and bacteria, often mediated by secreted metabolites, have important ramifications for the biology of the interacting partners (Frey-Klett <i>et al.</i>, 2011). This is particularly true for the bacterium <i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) and the fungus <i>Aspergillus fumigatus</i> (<i>A. fumigatus</i>) which often reside in the same niche such as lungs of cystic fibrosis (CF) patients. Some studies have reported that co-infection with <i>P. aeruginosa</i> and <i>A. fumigatus</i> could lead to a decrease in lung function relative to their respective single species infection (Amin <i>et al.</i>, 2010; Peleg <i>et al.</i>, 2010). Metabolite extraction and analysis allow for the characterization of specific microbial metabolites in the polymicrobial biofilm. This protocol describes how to prepare the <i>Pseudomonas-Aspergillus</i> co-culture biofilm on solid medium in preparation for metabolite extraction.
Excited-state proton transfer of equilenin and dihydroequilenin: interaction with bilayer vesicles (1986)

The two-state excited-state proton-transfer process for d-equilenin [d-3-hydroxyestra-1,3,-5(10),6,8-pentaen-17-one] and dihydroequilenin is found to depend both on pH and on proton acceptor concentration. Both the protonated and deprotonated forms of the excited molecule are fluorescent. As is the case for 2-naphthol, the excited-state pKa (pKa*) is substantially lower than the ground-state pKa. Fluorescence decay studies have been performed as a function of emission wavelength in aqueous solutions at pH 6.9 in the presence of acetate anion (0.1 M). At this pH, both back-reaction from the excited-state and ground-state heterogeneity are minimal. A monoexponential decay is found in the blue region of the spectrum and a biexponential decay on the red edge. The lifetimes measured across both regions are constant, with a negative preexponential term, characteristic of an excited-state reaction, evident at longer wavelengths. Decay-associated spectra (DAS), the preexponential terms associated with the measured lifetimes, have been acquired for these aqueous solutions. Equilenin and dihydroequilenin are found to adsorb to dimyristoyllecithin (DML) vesicles. Rates for excited-state proton transfer are greatly reduced when dihydroequilenin adsorbs to vesicles. The accessibility of the bound probe to acetate as a proton acceptor depends on the cholesterol content of the vesicles.