gebhart/patrepeval huggingface dataset:
Expression of fluorescent proteins in Lactobacillus rhamnosus to study host–microbe and microbe–microbe interactions (2017)

Probiotic Lactobacillus strains are widely used to benefit human and animal health, although the exact mechanisms behind their interactions with the host and the microbiota are largely unknown. Fluorescent tagging of live probiotic cells is an important tool to unravel their modes of action. In this study, the implementation of different heterologously expressed fluorescent proteins for the labelling of the model probiotic strains Lactobacillus rhamnosusGG (gastrointestinal) and Lactobacillus rhamnosusGR-1 (vaginal) was explored. Heterologous expression of mTagBFP2 and mCherry resulted in long-lasting fluorescence of L. rhamnosusGG and GR-1 cells, using the nisin-controlled expression (NICE) system. These novel fluorescent strains were then used to study in vitro aspects of their microbe-microbe and microbe-host interactions. Lactobacillus rhamnosusGG and L. rhamnosusGR-1 expressing mTagBFP2 and mCherry could be visualized in mixed-species biofilms, where they inhibited biofilm formation by Salmonella Typhimurium-gfpmut3 expressing the green fluorescent protein. Likewise, fluorescent L. rhamnosusGG and L. rhamnosusGR-1 were implemented for the visualization of their adhesion patterns to intestinal epithelial cell cultures. The fluorescent L. rhamnosus strains developed in this study can therefore serve as novel tools for the study of probiotic interactions with their environment.
Non Nucleic Acid Inhibitors of Protein·DNA Interactions Identified through Combinatorial Chemistry (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNon Nucleic Acid Inhibitors of Protein·DNA Interactions Identified through Combinatorial Chemistry†Shawn Y. Stevens, Barry A. Bunin, Matthew J. Plunkett, Patrick C. Swanson, Jonathan A. Ellman, and Gary D. GlickView Author Information Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109-1055 Department of Chemistry University of California-Berkeley Berkeley, California 94720 Cite this: J. Am. Chem. Soc. 1996, 118, 43, 10650–10651Publication Date (Web):October 30, 1996Publication History Received17 July 1996Published online30 October 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja962452ahttps://doi.org/10.1021/ja962452arapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views238Altmetric-Citations20LEARN 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 Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Biopolymers,Immunology,Inhibitors,Peptides and proteins Get e-Alerts
Factors that predict weight loss success differ by diet intervention type (2023)

These data provide evidence to inform more precise and personalized approaches to diet intervention for weight loss and cardiometabolic health.
c-Kit inhibitors prevent respiratory viral infection-induced acute asthma via the blockade of innate lymphoid cell activation (2016)

Abstract Asthma is a major public health problem that affects nearly 10% of the general population and is thought to be mediated by allergen-specific Th2 cells, adaptive immunity and allergic inflammation. Current treatments for asthma generally focus on minimizing the Th2-driven eosinophilic inflammation with the use of anti-inflammatory therapies such as corticosteroids. However, this approach, targeting the adaptive Th2 cell immunity with corticosteroids, has not reduced the high rates of hospitalizations for acute asthma, most often caused by acute viral infection, including influenza. Recently, type 2 innate lymphoid cells (ILC2) expressing c-Kit have been shown to expand during influenza infection and directly caused airway hyper reactivity (AHR), a cardinal feature of asthma. We now show that the treatment of influenza-infected mice with c-Kit kinase inhibitors blocked the development of AHR and airway inflammation and greatly reduced the number and function of ILC2 cells, whereas the treatment with corticosteroids, commonly used to treat acute asthma, failed to prevent the influenza-induced AHR. We also demonstrated that c-Kit function is required for normal ILC2 cell function and for influenza-induced AHR, and that c-Kit kinase inhibitor inhibits murine lung ILC2 cell proliferation and cytokine productions in vitro and in vivo. Furthermore, the treatment of c-Kit inhibitor did not affect in vivo viral clearance. Our study demonstrated the crucial role of c-Kit in modulating the ILC2 activation in the lungs, particularly in respiratory viral infection induced acute asthma.
Introspection-based Explainable Reinforcement Learning in Episodic and Non-episodic Scenarios (2022)

With the increasing presence of robotic systems and human-robot environments in today's society, understanding the reasoning behind actions taken by a robot is becoming more important. To increase this understanding, users are provided with explanations as to why a specific action was taken. Among other effects, these explanations improve the trust of users in their robotic partners. One option for creating these explanations is an introspection-based approach which can be used in conjunction with reinforcement learning agents to provide probabilities of success. These can in turn be used to reason about the actions taken by the agent in a human-understandable fashion. In this work, this introspection-based approach is developed and evaluated further on the basis of an episodic and a non-episodic robotics simulation task. Furthermore, an additional normalization step to the Q-values is proposed, which enables the usage of the introspection-based approach on negative and comparatively small Q-values. Results obtained show the viability of introspection for episodic robotics tasks and, additionally, that the introspection-based approach can be used to generate explanations for the actions taken in a non-episodic robotics environment as well.
An As-P(n+-n-)double diffused drain MOSFET for VLSI's (1983)

An As-P(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> ) double diffused drain is characterized as one of the most feasible device structures for VLSI's from the overall viewpoint of device design. This device makes good use of both As, suitable for microfabrication, and P, in realizing a graded junction. The feasibility of this double diffused drain is investigated comparing it with a conventional As drain over the wide range of effective channel length from 0.5 to 5 µm. We have also succeeded in directly measuring hot-hole gate current as low as on the order of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-15</sup> A. This current seems to have an important influence on the hot-carrier effects. On the basis of the experiments and simulations using the two-dimensional process/device analysis programs SUPREM and CADDET, it is shown that this device structure provides remarkable improvements, not only in terms of channel hot-electron effects, but also avalanche hot-carrier effects, which are more responsible for hot-carrier related device degradation due to impact ionization at the drain. In addition, this structure has almost the same short channel effect characteristics, for example threshold-voltage lowering as a conventional MOSFET.
Phase I/II study of transcatheter arterial chemoembolization with cisplatin powder and degradable starch microspheres for unresectable hepatic metastases from colorectal cancer refractory to systemic standard chemotherapy. (2011)

577 Background: We conducted a phase I/II study of novel transcatheter arterial chemoembolization with cisplatin powder and degradable starch microspheres (DSM) to determine the recommended dose (RD) and to assess the efficacy and safety. Methods: Cisplatin powder and DSM mixing solution was administered followed by the injection of DSM alone via hepatic artery every 4 weeks. In phase I, cohorts of 3 patients received escalating dose of cisplatin (50, 65 and 80mg/m 2 ), and RD was estimated during the first cycle. In the phase II, more RD patients were added to assess tumor response, toxicity, hepatic progression free survival (H-PFS) and 6-month overall survival (OS) rate. Results: A total of 24 patients (male 16, female 8; mean age 63.0, range 45-79; colon 15, rectal 9) were enrolled in this study. FOLFOX had previously been administered to all patients, irinotecan-containing regimen to 12 and bevacizumab and/or cetuximab to 14. During phase I (n= 9 patients), maximum tolerated dose was not reached and cisplatin 80 mg/m 2 was recommended for a phase II. Phase II enrolled 15 patients. The following grade 3 toxicities were observed: platelets reduction 16.6%, aspartate transaminase elevation 38.8%, alanine transaminase elevation 16.6%, hyponatremia 11.1%, cholecystitis 5.5%. The tumor response rate was 53.3% (CR 0, PR 8, SD 6, and PD 1). The median H-PFS was 6.3 months (95% CI; 2.71 to 9.88) and 6 -month OS rate was 86.7%. Conclusions: This phase I/II study demonstrates that novel transcatheter arterial chemoembolization with 80 mg/m 2 cisplatin powder and DSM is well tolerable, and can produce a high response rate with encouraging survival duration. Further clinical trials are warranted. No significant financial relationships to disclose.
Synthese des Colchicins (1959)

Abstract Diese Totalsynthese geht von Purpurogallin aus und führt in 20 Stufen über Desacetylaminocolchicein und (±)‐Desacetyl‐isocolchicinamid zum natürlichen (−)‐Colchicin.
Medicaid Patients Have Greater Difficulty Scheduling Health Care Appointments Compared With Private Insurance Patients: A Meta-Analysis (2019)

Medicaid patients are known to have reduced access to care compared with privately insured patients; however, quantifying this disparity with large controlled studies remains a challenge. This meta-analysis evaluates the disparity in health services accessibility of appointments between Medicaid and privately insured patients through audit studies of health care appointments and schedules. Audit studies evaluating different types of outpatient physician practices were selected. Studies were categorized based on the characteristics of the simulated patient scenario. The relative risk of appointment availability was calculated for all different types of audit scenario characteristics. As a secondary analysis, appointment availability was compared pre- versus post-Medicaid expansion. Overall, 34 audit studies were identified, which demonstrated that Medicaid insurance is associated with a 1.6-fold lower likelihood in successfully scheduling a primary care appointment and a 3.3-fold lower likelihood in successfully scheduling a specialty appointment when compared with private insurance. In this first meta-analysis comparing appointment availability between Medicaid and privately insured patients, we demonstrate Medicaid patients have greater difficulty obtaining appointments compared with privately insured patients across a variety of medical scenarios.
In Situ Generation of Surface Plasmon Polaritons Using a Near-Infrared Laser Diode (2012)

We demonstrate a semiconductor laser-based approach which enables plasmonic active devices in the telecom wavelength range. We show that optimized laser structures based on tensile-strained InGaAlAs quantum wells-coupled to integrated metallic patternings-enable surface plasmon generation in an electrically driven compact device. Experimental evidence of surface plasmon generation is obtained with the slit-doublet experiment in the near-field, using near-field scanning optical microscopy measurements.
Predicting Fall Risks in an Elderly Population: Computer Dynamic Posturography Versus Electronystagmography Test Results (2001)

For this population, CDP was determined to be a more sensitive test for identifying patients who have fallen, with limits of stability testing the most significant part of the CDP battery; for ENG studies, the best falls indicator was the ocular motor battery.
Molecular cloning and expression of the Candida albicans beta-N-acetylglucosaminidase (HEX1) gene (1994)

beta-N-Acetylglucosaminidase was purified from the spent culture medium of Candida albicans A72 grown in the presence of N-acetylglucosamine (GlcNAc). The N-terminal amino acid sequence of the protein was determined, two degenerate oligonucleotide probes were constructed, and a 3.9-kb BamHI fragment of DNA that hybridized to both probes was subcloned from a lambda EMBL4 library of C. albicans A72 genomic DNA. This fragment of DNA contained the entire beta-N-acetylglucosaminidase (HEX1) gene, which consisted of an open reading frame coding for a polypeptide precursor of 562 amino acids with a putative 22-amino-acid leader sequence. The deduced HEX1 amino acid sequence showed similarity to hexosaminidases from a variety of organisms. Growth of C. albicans on GlcNAc induced transcription of HEX1, resulting in increased specific beta-N-acetylglucosaminidase activity. HEX1 mRNA (2.35 kb) from GlcNAc-grown cells was approximately 200 bp larger than HEX1 mRNA from cells grown on glucose. This size difference was suggested to result from the use of alternative transcription termination sites. The cloned HEX1 gene introduced into C. albicans SGY-243 on a plasmid also responded to GlcNAc induction.
A Speech Quality Evaluation Method Based on Auditory Characteristic (2016)

In this paper, an objective measurement for speech quality evaluation based on auditory characteristics is proposed. Firstly, the features are extracted by the Gammatone auditory filter bank to calculate the Gammatone Frequency Cepstrum Coefficient (GFCC) of the original speech and the distortion. After getting the GFCC, the average distortion distance is obtained. Then, in order to get an objective estimator for the objective Mean Opinion Score (MOS), it is necessary to map the normalized average distortion distance to the MOS scale. Experiments show that the proposed algorithm can greatly reduce the algorithm complexity. At the same time, the relevancy between the subjective MOS and the objective MOS is close to the Perceptual Evaluation of Speech Quality (PESQ). It is proved that the new algorithm is useful for the real-time online monitoring of the speech quality.
Chemische Synthese an Oberflächen mit Präzision in atomarer Größenordnung: Beherrschung von Komplexität und Genauigkeit (2019)

Abstract Rastersondenmikroskopische (SPM‐)Verfahren sind leistungsfähige Hilfsmittel, um die Struktur und Dynamik von Molekülen an Oberflächen und Grenzflächen zu untersuchen sowie Atome und Moleküle durch äußere Krafteinwirkung, durch inelastisches Elektronentunneln oder durch ein elektrisches Feld präzise zu steuern. Die schnelle Entwicklung dieser SPM‐Manipulationsmodi ermöglichte es, eine Feinsteuerung der grundlegenden Prozesse in der Physik der Grenzflächen und der chemischen Reaktivität, darunter Adsorption, Diffusion, Bindungsbildung sowie ‐dissoziation, mit einer Präzision auf Einzelatom‐/Molekülebene zu erreichen. Ihre kontrollierte Anwendung zur Herstellung atomskaliger Strukturen und die Synthese neuer, auch außergewöhnlicher Moleküle mit programmierten Eigenschaften werden vorgestellt. Es werden die Möglichkeiten und Herausforderungen bezüglich der Entwicklung komplexer chemischer Systeme diskutiert, indem mögliche zukünftige Auswirkungen auf die Nanowissenschaften und die industrielle Nanotechnologie analysiert werden.
Strain induced coupling and quantum information processing with hexagonal boron nitride quantum emitters (2021)

We propose an electromechanical scheme where the electronic degrees of freedom of boron vacancy color centers hosted by a hexagonal boron nitride nanoribbon are coupled for quantum information processing. The mutual coupling of color centers is provided via their coupling to the mechanical motion of the ribbon, which in turn stems from the local strain. The coupling strengths are computed by performing ab-initio calculations. The density functional theory (DFT) results for boron vacancy centers on boron nitride monolayers reveal a huge strain susceptibility. In our analysis, we take into account the effect of all flexural modes and show that despite the thermal noise introduced through the vibrations one can achieve steady-state entanglement between two and more number of qubits that survives even at room temperature. Moreover, the entanglement is robust against mis-positioning of the color centers. The effective coupling of color centers is engineered by positioning them in the proper positions. Hence, one is able to tailor stationary graph states. Furthermore, we study the quantum simulation of the Dicke-Ising model and show that the phonon non-equilibrium phase transition occurs even for a finite number of color centers. Given the steady-state nature of the proposed scheme and accessibility of the electronic states through optical fields, our work paves the way for the realization of steady-state quantum information processing with color centers in hexagonal boron nitride membranes.
PNAG exopolysaccharide eradication gives neutrophils access to Staphylococcus aureus biofilm infections (2023)

Abstract Staphylococcus aureus ( S. aureus ) can form biofilms on biotic or abiotic surfaces making biofilm infections a relevant clinical problem. Biofilms can evade immunity and resist antimicrobial treatment, and as such an understanding of biofilm infection in vivo is necessary to inform new therapeutics. Using a mouse model of S. aureus foreign-body skin infection and intravital microscopy, we imaged the interactions between neutrophils and S. aureus biofilm. We observed that neutrophils were separated from bacteria by a biofilm matrix composed of the polysaccharide intercellular adhesin (PIA), an exopolysaccharide chemically designated as poly-N-acetylglucosamine (PNAG) that is produced by enzymatic machinery encoded by the icaADBC operon. Infection with icaADBC-deficient S. aureus strains led to increased neutrophil infiltration and access to bacteria and resulted in full clearance of infection by 7 days. Moreover, enzymatic treatment with PgaB, which hydrolyzes partially deacetylated PNAG, was shown to disaggregate the biofilm giving neutrophils access into the infection site to improve clearance. Taken together, our results show that PNAG shelters S. aureus biofilms from innate host defense, and that targeting the biofilm matrix with glycoside hydrolases is a promising therapeutic avenue to treat S. aureus biofilm infections. Author Summary Staphylococcus aureus is a major cause of biofilm-associated infections, which pose a major threat to human health. A biofilm is difficult to treat since bacteria are protected from antimicrobials within an extracellular matrix. This study is the first to show that the PgaB enzyme, a glycoside hydrolase, can disrupt the S. aureus biofilm matrix in vivo. Disrupting the biofilm matrix with PgaB gives neutrophils access to bacteria for elimination.
The Light Field Camera: Extended Depth of Field, Aliasing, and Superresolution (2011)

Portable light field (LF) cameras have demonstrated capabilities beyond conventional cameras. In a single snapshot, they enable digital image refocusing and 3D reconstruction. We show that they obtain a larger depth of field but maintain the ability to reconstruct detail at high resolution. In fact, all depths are approximately focused, except for a thin slab where blur size is bounded, i.e., their depth of field is essentially inverted compared to regular cameras. Crucial to their success is the way they sample the LF, trading off spatial versus angular resolution, and how aliasing affects the LF. We show that applying traditional multiview stereo methods to the extracted low-resolution views can result in reconstruction errors due to aliasing. We address these challenges using an explicit image formation model, and incorporate Lambertian and texture preserving priors to reconstruct both scene depth and its superresolved texture in a variational Bayesian framework, eliminating aliasing by fusing multiview information. We demonstrate the method on synthetic and real images captured with our LF camera, and show that it can outperform other computational camera systems.
Capacity and Gain Analysis of a Reconfigurable MEMS Antenna (2008)

This paper presents the investigation results on therecon¯gurable properties of an antenna array compris-ing of four feed elements and four parasitic elementsplaced on a ¯nite ground plane. This antenna is in-tended to improve the diversity gain for a Multiple In-put Multiple Output (MIMO) communication system.We intend to use a recon¯gurable antenna to com-bat the problem of signal deterioration in a handhelddevice so that it can get optimum signal strength inany orientation. With our presented antenna, we canachieve up to sixteen di®erent con¯gurations depend-ing on the requirement. The di®erent con¯gurationsare controlled with the help of RF switches which areimplemented using micro-electromechanical systems(MEMS). The recon¯gurable antenna was fabricatedand tested for its impedance and radiation character-istics and the results were found to be in reasonable agreement with the simulations. Channel measure-ments were made with the help of a MIMO test setup.
Measurement of the Attention Effect of the Fraser-Wilcox Illusion Applied to Caution Making by Pre-cueing Task (2019)

The caution making is used in various daily situations as a preventive measure of tumble accident which is one of the labor accidents. The purpose of this study is to propose a display that incorporates the Fraser-Wilcox illusion and has a higher attention effect. Fraser-Wilcox illusion is a type of visual illusion in which a part of a still image appears to be moving. We compare the attention effects of shapes that induce the Fraser-Wilcox illusion and those that do not. As an evaluation method of attention recall effect, the pre-cueing task which was an experimental technique to measure the characteristics of visual attention was used. The correlation between the amount of visual illusion and the target reaction time was examined. As a result, a strong negative correlation was observed. The larger the amount of visual illusion, the faster the detection of the target. These results suggest that the Fraser-Wilcox illusion has an alerting effect on visual illusion.