gebhart/patrepeval huggingface dataset:
In VitroCharacterization of the Microglial Inflammatory Response toStreptococcus suis, an Important Emerging Zoonotic Agent of Meningitis (2010)

Streptococcus suis is an important swine and human pathogen responsible for septicemia and meningitis. In vivo research in mice suggested that in the brain, microglia might be involved in activating the inflammatory response against S. suis. The aim of this study was to better understand the interactions between S. suis and microglia. Murine microglial cells were infected with a virulent wild-type strain of S. suis. Two isogenic mutants deficient at either capsular polysaccharide (CPS) or hemolysin production were also included. CPS contributed to S. suis resistance to phagocytosis and regulated the inflammatory response by hiding proinflammatory components from the bacterial cell wall, while the absence of hemolysin, a potential cytotoxic factor, did not have a major impact on S. suis interactions with microglia. Wild-type S. suis induced enhanced expression of Toll-like receptor 2 by microglial cells, as well as phosphotyrosine, protein kinase C, and different mitogen-activated protein kinase signaling events. However, cells infected with the CPS-deficient mutant showed overall stronger and more sustained phosphorylation profiles. CPS also modulated inducible nitric oxide synthase expression and further nitric oxide production from S. suis-infected microglia. Finally, S. suis-induced NF-κB translocation was faster for cells stimulated with the CPS-deficient mutant, suggesting that bacterial cell wall components are potent inducers of NF-κB. These results contribute to increase the knowledge of mechanisms underlying S. suis inflammation in the brain and will be useful in designing more efficient anti-inflammatory strategies for meningitis.
Antimicrobial resistance and the role of vaccines (2018)

> Stanley Falkow (Fig. 1) dedicated his life’s work to the study of bacteria and infectious disease. He was a leader in the discovery of the mechanisms of antibiotic resistance and among the first to recognize and raise the alarm about the problem of multidrug resistance. The articles of this Special Feature on Antimicrobial Resistance and the Role of Vaccines are dedicated to his memory (Box 1).



Fig. 1. 
Stanley Falkow, January 24, 1934–May 5, 2018, a pioneer in the fight to understand and address AMR. Image courtesy of Manuel R. Amieva (photographer).



Box 1 #### Dedication

This Special Feature on Antimicrobial Resistance and the Role of Vaccines is dedicated to the memory of microbiologist Stanley Falkow. Professor Falkow was a pioneer in understanding how bacteria cause disease and discovered how antibiotic resistance spreads among bacteria. In 1964, Falkow was the first to physically isolate a distinct band of DNA comprising the episome (plasmid) with the genetic material coding for antibiotic resistance in a cesium chloride gradient. As early as 1975, he wrote a book entitled Infectious Multiple Drug Resistance (17) and noted that while “we owe to chemotherapy [antibiotics] the debt of reducing the high mortality rate of many bacterial infections [and to hygiene and vaccines the debt of preventing them], in helping to solve some of the problems of infectious diseases, chemotherapy created some problems of its own.” The “problems” Falkow refers to were, of course, the multidrug-resistant bacterial strains generated as a natural consequence of the drugs’ use.

Falkow received numerous honors in recognition of his work, including election to the National Academy of Sciences in 1984, the Royal Society in Britain in 2007, and presentation of the National Medal of Science in 2014. Stanley Falkow died at his home in Portola Valley, California, on May 5, 2018, at the age of 84. … 

[↵][1]1To whom correspondence should be addressed. Email: rino.r.rappuoli{at}gsk.com.

 [1]: #xref-corresp-1-1
TEM and AEM study of polycrystalline CdS/CdTe heterostructures for photovoltaic applications (1993)

CdTe-based solar cells are attracting increasing attention due to their potential for lowcost, large-area high-efficiency photovoltaic applications. Recently, conversion efficiencies exceeding 15% have been reproducibly demonstrated for small area devices. However, the morphology, microstructure and interface properties have not been studied in a systematic manner. Additionally, these structures are normally subjected to at least one heat treatment step prior to device fabrication. The effects of such heat treatment on the microstructure and the CdS/CdTe interface are not well understood. In this work TEM, AEM and secondary ion mass spectrometry (SIMS) were used to study the morphology, microstructure and the CdS/CdTe interface as a function of deposition parameters and post deposition heat treatment. The solar cells used have the following structure: The CdS and CdTe films were grown by physical vapor deposition. The thickness of these films is 0.5μm for CdS and 2-3μm for CdTe. In some cases, the CdS was heat treated at 400°C for 20-30 min prior to the deposition of CdTe. After the deposition of the latter, the samples were heat treated in the presence of CdCl 2 at 400°C for 20-30 min in air.
Calcul des contraintes de retrait gene par frottement dans les dallages : Influence des fibres vis a vis des risques de fissuration (2000)

On presente un modele permettant de prevoir, en fonction du dosage en fibres, des dimensions de la structure et de la nature du support, le nombre et l'ouverture des fissures qui vont eventuellement apparaitre suite au developpement des mecanismes de retrait. Celui-ci prend en compte les differentes origines des deformations de retrait : auto-dessiccation, exothermie des reactions, sechage. Outre les parametres caracteristiques du materiau permettant de calculer ces deformations et les parametres d'echanges imposes par le milieu exterieur, un parametre caracterisant l'interface entre la structure et le support est introduit. L'allure du champ de contraintes obtenu montre la capacite des fibres a substituer a des fissures traversantes un reseau de microfisssures peu ouvertes. (A)
Uncertainty quantification in the calibration of numerical elements in nonlinear seismic analysis (2022)

Abstract Modeling uncertainty in structural models can greatly affect the reliability of nonlinear time history results, which are central to performance‐based earthquake engineering. A crucial source of modeling uncertainty is the uncertainty in the parameters of constitutive models, which simulate the hysteretic behavior of key structural components. In current research and engineering practice, it is assumed that the accuracy of a nonlinear structural model is achieved by component calibration, which is conducted by trying to best match the response of a numerical model of a component to test results under a standardized quasi‐static loading regime. However, previous research has shown that even a very well‐fitted component‐level calibration might result in considerable errors in the system‐level structural dynamic response. This study is an initial attempt to investigate calibration relevance incorporating a rigorous uncertainty quantification framework. In the proposed framework, parameters of a constitutive model are considered as random inputs. Calibration error at the component level and global error at the system level are quantified based on the discrepancies between the simulation models with probabilistic inputs and reference models. Polynomial chaos expansions (PCEs) metamodels are implemented to conduct sensitivity analysis and investigate calibration relevance. Three buckling restrained braced frames (BRBFs) with different heights are investigated using the proposed framework. Four calibration methods’ relevance with global errors based on three engineering demand parameters (EDPs) are studied. The results allow for the identification of optimum hyperparameters to achieve peak calibration relevance and to evaluate different calibration methods for several EDPs for the three BRBFs.
Observer variation in immunohistochemical analysis of protein expression, time for a change? (2006)

We have demonstrated that ICCC is a consistent method to assess observer variation when a continuous scoring system is used, compared with kappa statistics, which depends on a categorical system. Given the importance of accurate assessment of protein expression in diagnostic and experimental medicine, we suggest raising thresholds for observer variation: ICCC of 0.7 should be regarded as the minimum acceptable standard, ICCC of 0.8 as good and ICCC of > or = 0.9 as excellent.
Towards Unbiased BFS Sampling (2011)

Breadth First Search (BFS) is a widely used approach for sampling large graphs. However, it has been empirically observed that BFS sampling is biased toward high-degree nodes, which may strongly affect the measurement results. In this paper, we quantify and correct the degree bias of BFS. First, we consider a random graph RG(pk) with an arbitrary degree distribution pk. For this model, we calculate the node degree distribution expected to be observed by BFS as a function of the fraction f of covered nodes. We also show that, for RG(pk), all commonly used graph traversal techniques (BFS, DFS, Forest Fire, Snowball Sampling, RDS) have exactly the same bias. Next, we propose a practical BFS-bias correction procedure that takes as input a collected BFS sample together with the fraction f. Our correction technique is exact (i.e., leads to unbiased estimation) for RG(pk). Furthermore, it performs well when applied to a broad range of Internet topologies and to two large BFS samples of Facebook and Orkut networks.
Measurement of cerebral oxygen pressure in living mice by two-photon phosphorescence lifetime microscopy (2022)

The ability to quantify partial pressure of oxygen (pO<sub>2</sub>) is of primary importance for studies of metabolic processes in health and disease. Here, we present a protocol for imaging of oxygen distributions in tissue and vasculature of the cerebral cortex of anesthetized and awake mice. We describe <i>in vivo</i> two-photon phosphorescence lifetime microscopy (2PLM) of oxygen using the probe Oxyphor 2P. This minimally invasive protocol outperforms existing approaches in terms of accuracy, resolution, and imaging depth. For complete details on the use and execution of this protocol, please refer to Esipova et al. (2019).
Highly Conductive Nucleotide Analogue Facilitates Base-Calling in Quantum-Tunneling-Based DNA Sequencing (2019)

Quantum-tunneling-based DNA sequencing is a single molecular technology that has great potential for achieving facile and high-throughput DNA sequencing. In principle, the sequence of DNA could be read out by the time trace of the tunnel current that can be changed according to molecular conductance of nucleobases passing through nanosized gap electrodes. However, efficient base-calling of four genetic alphabets has been seriously impeded due to the similarity of molecular conductance among canonical nucleotides. In this article, we demonstrate that replacement of canonical 2'-deoxyadenosine (dA) with a highly conductive dA analogue, 7-deaza dA, could expand the difference of molecular conductance between four genetic alphabets. Additionally, systematic evaluation of molecular conductance using a series of dA and dG analogues revealed that molecular conductance of the nucleotide is highly dependent on the HOMO level. Thus, the present study demonstrating that signal characteristics of the nucleotide can be modulated based on the HOMO level provides a widely applicable chemical approach and insight for facilitation of single molecular sensing as well as DNA sequencing based on quantum tunneling.
Pulsed-Field Capillary Electrophoresis: Optimizing Separation Parameters with Model Mixtures of Sulfonated Polystyrenes (1994)

The electrophoretic transport of high molecular weight charged solutes, both flexible and stiff polymers, has been studied by capillary electrophoresis under constant-field and pulsed-field conditions. Sulfonated polystyrenes were used as model solutes in different entangled polymer solutions. First, changes of the end-to-end distance vectors of flexible polymers were examined through the mobility/potential-gradient curves. Under pulsed-field conditions, the influence of different pulse shapes, frequencies, and amplitudes of forward and backward pulses on the electrophoretic mobilities of model solutes was studied. Resolution of the mixture components was strongly affected by changes in frequency of both sine-wave and square-wave pulses. The experimental results obtained under pulse-field conditions are roughly in agreement with the existing theories of electrophoretic transport.
Transcriptional Adaptation of Drug-tolerantMycobacterium tuberculosisDuring Treatment of Human Tuberculosis (2015)

Transcriptional patterns suggest that drug-tolerant bacilli in sputum are in a slow-growing, metabolically and synthetically downregulated state. Absence of the isoniazid stress signature in drug-tolerant bacilli indicates that physiological state influences drug responsiveness in vivo. These results identify novel drug targets that should aid in development of novel shorter tuberculosis treatment regimens.
Notes on a New Coherence Estimator (2016)

This document discusses some interesting features of the new coherence estimator in [1] . The estimator is d erived from a slightly different viewpoint. We discuss a few properties of the estimator, including presenting the probability density function of the denominator of the new estimator , which is a new feature of this estimator . Finally, we present an appr oximate equation for analysis of the sensitivity of the estimator to the knowledge of the noise value. ACKNOWLEDGEMENTS The preparation of this report is the result of an unfunded research and development activity. Sandia National Laboratories is a multi - program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE - AC04 - 94AL85000.
MDP is effective for removing residual polycarboxylate temporary cement as an adhesion inhibitor (2020)

The effect of cleaner containing 10-methacryloyloxydecyl dihydrogen phosphate (MDP) for removing temporary cement remnants on dentin surface was evaluated. Flat dentin surfaces were wet-polished (Co) and HY-BOND temporary cement hard (Shofu) was applied to the surface. This temporary cement was removed using an air-scaler (Sc), brush (Br), or phosphoric acid and NaOCl (NC). A prototype cleaner containing MDP (Kuraray Noritake Dental, Tokyo, Japan) was used with agitation mode (MC+AG). KATANA Avencia block (Kuraray Noritake Dental) was luted with SA Cement Plus Automix (Kuraray Noritake Dental). Co showed significantly higher bond strength than Sc or Br (p<0.001 each). Bond strengths with NC (p=0.99) and MC+AG (p=0.38) did not differ significantly from that with Co. Transmission electron microscopy revealed sufficient interaction of MC+AG. Cleaner containing MDP can effectively remove temporary cement by agitation, and can be expected to improve the chemical bonding ability by binding more MDP to dentin.
Oxidative Ring Opening of 2,5‐Diarylfurans by Selectfluor®. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
02-TW laser system at 1  kHz (1997)

We have developed a 1-kHz repetition-rate Ti:sapphire laser system that can simultaneously generate high peak and average powers of 0.2TW and 4W, respectively. The laser system generates 4-mJ energy pulses with a 20-fs pulse width. We eliminated thermal lensing in the system by cooling the Ti:sapphire crystal to 125K. The output 20-fs pulses were fully characterized by use of the new technique of transient-grating frequency-resolved optical gating. We demonstrate experimentally that the pulse duration at the output is limited only by fifth-order dispersion.
Data from Silencing the Snail-Dependent RNA Splice Regulator ESRP1 Drives Malignant Transformation of Human Pulmonary Epithelial Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Epithelial-to-mesenchymal transition (EMT) is organized in cancer cells by a set of key transcription factors, but the significance of this process is still debated, including in non–small cell lung cancer (NSCLC). Here, we report increased expression of the EMT-inducing transcription factor Snail in premalignant pulmonary lesions, relative to histologically normal pulmonary epithelium. In immortalized human pulmonary epithelial cells and isogenic derivatives, we documented Snail-dependent anchorage-independent growth &lt;i&gt;in vitro&lt;/i&gt; and primary tumor growth and metastatic behavior &lt;i&gt;in vivo&lt;/i&gt;. Snail-mediated transformation relied upon silencing of the tumor-suppressive RNA splicing regulatory protein ESRP1. In clinical specimens of NSCLC, ESRP1 loss was documented in Snail-expressing premalignant pulmonary lesions. Mechanistic investigations showed that Snail drives malignant progression in an ALDH&lt;sup&gt;+&lt;/sup&gt;CD44&lt;sup&gt;+&lt;/sup&gt;CD24&lt;sup&gt;−&lt;/sup&gt; pulmonary stem cell subset in which ESRP1 and stemness-repressing microRNAs are inhibited. Collectively, our results show how ESRP1 loss is a critical event in lung carcinogenesis, and they identify new candidate directions for targeted therapy of NSCLC.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; This study defines a Snail-ESRP1 cancer axis that is crucial for human lung carcinogenesis, with implications for new intervention strategies and translational opportunities. &lt;i&gt;Cancer Res; 78(8); 1986–99. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
NDE techniques for detecting grout defects in cable stays (1993)

Problems with corrosion of steel strands in grouted bridge cable stays have raised concern about the integrity of the grout layer protecting the strands. Bleed water that may accumulate in the grout layer if voids or bubbles are trapped during the grouting process can lead to corrosion of the cables. This research study was undertaken to evaluate various nondestructive evaluation (NDE) methods for inspection of this grout layer. Methods which were studied include ultrasonics, film radiography, computed tomography (CT), and neutron radiography. The feasibility of using computed tomography for inspection of the grout layer has been demonstrated. Voids as small as 0.04 in. (1mm) in diameter were identified in both the annular region of grout and inside the steel cable bundle. Although some of these voids were manufactured, many of those found were a result of the grouting operation during fabrication of the specimens, an observation which lends urgency to the need for an inspection system. Laboratory experiments were conducted with a prototype ultrasonic inspection unit which utilizes two rolling contact probes with 500 kHz transducers. A digital signal subtraction technique was found to be particularly useful in analyzing the received signals. The ultrasonic system was successful in identifying the location of defects, but information regarding the size and content of the defects was inconclusive. Three distinct regions exist along the cable which will most likely require different inspection schemes. It is envisioned that the main section of cable will be inspected by one technique, possible ultrasonics, while the lower regions of cable, where extra layers are added for fire and crash protection, will require a radiographic technique. The third region, which includes the saddles and anchorages, will likely require a third inspection technique, such as a portable linear accelerator.
Prediction and analysis of nonisothermal crystallization of polymers (1997)

The crystallization behavior of polyetheretherketone (PEEK), polyoxymethylene (POM), polyethyleneterephtalate (PET), and polypropylene (PP) under nonisothermal conditions has been studied. Differential scanning calorimetry was used to monitor crystallization from the melt and a kinetic model has been proposed to describe three-dimensional spherulitic crystal growth. The model, which accounts for crystalline growth rate, uses two modified Avrami equations to represent both heterogeneous and homogeneous nucleation and growth processes. The model parameters are all associated with physical constants. The predicted evolution of absolute crystallinity showed good agreement with experimentally obtained values for a wide range of cooling rates. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 875–888, 1997
Topological Transformation of π‐Conjugated Molecules Reduces Resistance to Crystallization (2017)

Abstract Two electronically delocalized molecules were designed as models to understand how molecular shape impacts the tradeoff between solubility and crystallization tendencies in molecular semiconductors. The more soluble compound TT contains a non‐planar bithiophene central fragment, whereas CT has a planar cyclopentadithiophene unit. Calorimetry studies show that CT can crystallize more easily than TT . However, absorption spectroscopy shows that the initially amorphous TT film can eventually form crystals in which the molecular shape is significantly more planar. Two thermally reversible polymorphs for TT were observed by XRD and grazing‐incidence wide‐angle X‐ray scattering (GIWAXS) measurements. These findings are relevant within the context of designing soft semiconductors that exhibit high solubility and a tendency to provide stable organized structures with desirable electronic properties.
Automatic Intent-Based Secure Service Creation Through a Multilayer SDN Network Orchestration (2018)

Growing traffic demands and increasing security awareness are driving the need for secure services. Current solutions require manual configuration and deployment based on the customer's requirements. In this work, we present an architecture for an automatic intent-based provisioning of a secure service in a multilayer - IP, Ethernet, and optical - network while choosing the appropriate encryption layer using an open-source software-defined networking (SDN) orchestrator. The approach is experimentally evaluated in a testbed with commercial equipment. Results indicate that the processing impact of secure channel creation on a controller is negligible. As the time for setting up services over WDM varies between technologies, it needs to be taken into account in the decision-making process.