gebhart/patrepeval huggingface dataset:
Accuracy of Pneumocystis jirovecii Plasma Cell-Free DNA PCR for Noninvasive Diagnosis of Pneumocystis Pneumonia (2022)

Pneumocystis pneumonia (PCP) caused by Pneumocystis jirovecii is a serious infection in immunocompromised hosts which requires prompt diagnosis and treatment. The recommended specimen for diagnosis of PCP is bronchoalveolar lavage (BAL) fluid, which is invasive and may not be possible in unstable patients. The aim of this study was to evaluate the accuracy of noninvasive P. jirovecii plasma cell-free DNA (cfDNA) PCR using recently optimized preanalytical and analytical methods. Adult patients undergoing clinical testing for PCP with direct fluorescent antibody stain (DFA), respiratory PCR, and/or β-d-glucan were included in this study. Sensitivity and specificity P. jirovecii plasma cfDNA PCR was determined in PCP suspects categorized as proven and probable. A total of 149 patients were included in this study, of which 10 had proven and 27 had probable PCP. Most patients (95.9%, 143/149) were immunocompromised, including hematological malignancies (30.1%), bone marrow transplant (11.2%), solid organ transplantation (47.6%), and HIV/AIDS (4.2%). P. jirovecii plasma cfDNA PCR showed sensitivity and specificity of 100% (10/10; 95% confidence interval [CI], 69.2 to 100) and 93.4% (127/136; 95% CI, 87.8 to 96.9), and 48.6% (18/37; 95% CI, 31.9 to 65.6) and 99.1% (108/109; 95% CI, 94.9 to 100) in proven and proven/probable cases, respectively. P. jirovecii cell-free DNA PCR was similar in sensitivity but with substantially improved specificity over β-d-glucan (sensitivity, 60.0% [18/30; 95% CI, 40.6 to 77.3]); specificity, 66.7% [22/33; 95% CI, 48.2 to 82.0]) in patients with proven/probable PCP. Plasma cfDNA PCR offers a noninvasive testing option for early and accurate diagnosis of PCP, particularly in patients who cannot tolerate bronchoscopy.
<title>UV routes for approaching low-temperature dielectrics deposition in III-V technology</title> (1994)

As a `cold process' photochemical deposition enables us to obtain insulator and dielectric thin films on III-V compounds. To sustain the remarkable progress in the performance of electronic and optical devices may necessitate the utilization of this innocuous processing for novel applications. Possible areas of interest range from simply optically protective coating to layers for highly sophisticated optoelectronic integration of III-V and Si on the same chip.
Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial (2022)

Patients with rheumatoid arthritis (RA) receive highly targeted biologic therapies without previous knowledge of target expression levels in the diseased tissue. Approximately 40% of patients do not respond to individual biologic therapies and 5-20% are refractory to all. In a biopsy-based, precision-medicine, randomized clinical trial in RA (R4RA; n = 164), patients with low/absent synovial B cell molecular signature had a lower response to rituximab (anti-CD20 monoclonal antibody) compared with that to tocilizumab (anti-IL6R monoclonal antibody) although the exact mechanisms of response/nonresponse remain to be established. Here, in-depth histological/molecular analyses of R4RA synovial biopsies identify humoral immune response gene signatures associated with response to rituximab and tocilizumab, and a stromal/fibroblast signature in patients refractory to all medications. Post-treatment changes in synovial gene expression and cell infiltration highlighted divergent effects of rituximab and tocilizumab relating to differing response/nonresponse mechanisms. Using ten-by-tenfold nested cross-validation, we developed machine learning algorithms predictive of response to rituximab (area under the curve (AUC) = 0.74), tocilizumab (AUC = 0.68) and, notably, multidrug resistance (AUC = 0.69). This study supports the notion that disease endotypes, driven by diverse molecular pathology pathways in the diseased tissue, determine diverse clinical and treatment-response phenotypes. It also highlights the importance of integration of molecular pathology signatures into clinical algorithms to optimize the future use of existing medications and inform the development of new drugs for refractory patients.
Resonant regeneration in the sub-quantum regime – A demonstration of fractional quantum interference (2011)

Light shining through wall experiments (in the optical as well as in the microwave regime) are a powerful tool to search for light particles coupled very weakly to photons such as axions or extra hidden sector photons. Resonant regeneration, where a resonant cavity is employed to enhance the regeneration rate of photons, is one of the most promising techniques to improve the sensitivity of the next generation of experiments. However, doubts have been voiced if such methods work at very low regeneration rates where on average the cavity contains less than one photon. In this Letter we report on a demonstration experiment using a microwave cavity driven with extremely low power, to show that resonant amplification works also in this regime. In accordance with standard quantum mechanics this is a demonstration that interference also works at the level of less than one quantum. As an additional benefit this experiment shows that thermal photons inside the cavity cause no adverse effects.
[Separation and purification of alkaloids from radix of Zanthoxylum nitidum by macroporous adsorption resin]. (2008)

This method is simple, feasible and fit for industry production.
Simulation analysis of structures on the reaction pathway of RNAse A (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSimulation analysis of structures on the reaction pathway of RNAse AKaren Haydock, Carmay Lim, Axel T. Brunger, and Martin KarplusCite this: J. Am. Chem. Soc. 1990, 112, 10, 3826–3831Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/ja00166a016https://doi.org/10.1021/ja00166a016research-articleACS PublicationsRequest reuse permissionsArticle Views134Altmetric-Citations45LEARN 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-Alertsclose Get e-Alerts
A comparative analysis of current mode control techniques used in high power factor boost rectifier for electric/hybrid vehicle (2011)

This project proposes current mode control techniques for high power factor operation of boost rectifier. The current mode control techniques are linear peak current mode control (LPCM),non-linear carrier (NLC) and predictive switching modulator (PSM). The steady state stability analysis of the boost rectifier with the proposed switching modulators is analyzed and compared in this paper. The proposed modulators are realized by using a single-phase diode rectifier bridge with a Boost dc-dc converter for active power factor correction (PFC). The three current mode control techniques are simulated in MATLAB/ Simulink. Based on results, Predictive Switching Modulator(PSM)is considered as better modulator for improving power factor of Boost D.C- D.C converter.
Industrial Application of IEEE P1687 for an Automotive Product (2013)

This paper focuses on an industrial application of the proposed 1687 standard to significantly improve the test development effort and quality of test patterns for mixed signal IPs of an automotive design. The P1687 standard will enable the industry to develop test patterns for IPs on the IP level without having to know how the IP will be embedded within different designs. To measure the impact of P1687, we are applying a commercial P1687 EDA tool on an industrial 65nm automotive design. The presented results underline the significant advantages of P1687 over the current IEEE Std 1149.1-based test methodology, in both, automation of test pattern development as well as reduction of test setup data volume by more than 50%.
Newborn Rabbit Responsiveness to the Mammary Pheromone is Concentration-dependent (2004)

The effect of the intensity of odour signals has rarely been investigated in the regulation of odour-guided behaviour in young mammals. This series of experiments used the mammary pheromone (MP) of the female rabbit to assess the influence of stimulus concentration on neonatal pup responsiveness. The MP is a single compound isolated from rabbit milk that releases in pups the typical head searching and oral seizing behaviour. The pups (n = 621) were exposed to graded concentrations of the MP in bioassays varying in stimulus delivery conditions. Experiment 1 demonstrated that in aqueous dilutions the MP efficiently elicits behavioural responses only within a limited range of concentrations (from 2.5 x 10(-9) to 2.5 x 10(-5) g/ml). Experiment 2 yielded the same outcome with highly purified MP delivered in dynamic conditions with a gas chromatograph. Finally, Experiment 3 used deodorized milk as the solvent of the MP; despite this change in the physico-chemical context of stimulation, similar results were reached.
Blended foods for tube-fed children: a safe and realistic option? A rapid review of the evidence (2016)

With the growing number of children and young people with complex care needs or life-limiting conditions, alternative routes for nutrition have been established (such as gastrostomy feeding). The conditions of children and young people who require such feeding are diverse but could relate to problems with swallowing (dysphagia), digestive disorders or neurological/muscular disorders. However, the use of a blended diet as an alternative to prescribed formula feeds for children fed via a gastrostomy is a contentious issue for clinicians and researchers. From a rapid review of the literature, we identify that current evidence falls into three categories: (1) those who feel that the use of a blended diet is unsafe and substandard; (2) those who see benefits of such a diet as an alternative in particular circumstances (eg, to reduce constipation) and (3) those who see merit in the blended diet but are cautious to proclaim potential benefits due to the lack of clinical research. There may be some benefits to using blended diets, although concerns around safety, nutrition and practical issues remain.
Regional differences in quantities of histochemically detectable mucosubstances in nasal, paranasal, and nasopharyngeal epithelium of the bonnet monkey. (1987)

Inhaled irritants induce secretory cell hyperplasia in nasal epithelium of animals. To characterize this response histochemically it is first important to know the histochemical character and distribution of epithelial mucosubstance in the normal nasal cavity. An automated image analyzing method was used to detect and quantitate acidic, neutral, and sulfated mucosubstances in the epithelium lining the nasal and paranasal airways of eight bonnet monkeys. Tissue sections 2 micron thick from defined regions of these airways were stained with either alcian blue/periodic acid-Schiff to demonstrate acid and neutral mucosubstances or high iron diamine to demonstrate sulfated mucins. Respiratory epithelium covering maxilloturbinates had the largest volume of stainable mucosubstance per unit surface area of basal lamina, whereas the maxillary sinus epithelium had the least. There was a general anteroposterior increase in the quantity of total epithelial mucosubstance along the septal and lateral walls of the nasal cavity, and there was more acidic than neutral mucosubstance in the posterior nasal airway than in the anterior. Epithelial mucosubstance in the maxillary sinus was predominantly neutral. Therefore, we conclude that there are substantial regional quantitative differences in stainable mucosubstances in the primate nasal epithelium which must be considered when examining nasal mucosa for irritant-induced changes in epithelial mucins.
Effect of phase encoding steps on 1D chemical shift imaging of lactate during brain activation (1994)

Lactate is a unique indicator of brain activation and is detectable in vivo by proton magnetic resonance spectroscopy. Previous brain activation studies have been confined to single-voxel localization of lactate. To extend this work to 1D chemical shift imaging, computer simulation and test-object studies were conducted to examine tradeoffs among the number of phase encoding steps, signal-to-noise ratio (SNR) and resolution. An iterative algorithm was developed to reduce truncation artifacts arising from a limited number of phase encoding steps. The results indicate that the resolution and SNR attained with 8 phase encoding steps and 16 averages per step after applying the truncation reduction algorithm are approximately equal to those attained with 32 encoding steps and 4 averages per step. Thus, 32 steps would be preferred since contamination is minimized with increasing steps.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A study of ultrasonic property variations within jet-engine nickel alloy billets (2002)

A summary is presented of an ongoing project to measure the UT properties of jet-engine nickel alloy billets and to correlate their properties with the local billet microstructure. To date, measurements have been performed on four “strip” coupons cut from three different Nickel alloy billets (IN718 and Waspaloy). Longitudinal-wave velocities, attenuation, backscattered noise capacity (FOM) have been measured at selected sites for two propagation directions. The UT results are consistent with equiaxed microstructures in which the mean grain diameter varies with radial depth. The grain diameter at selected sites is determined from detailed metallographic studies and compared with that estimated from the measured attenuation.
Caribbean Quarterly Bulletin: Volume 9: Issue 2, July 2020 (2020)

Governments in the Caribbean region have been relatively successful in flattening the infection curve of the coronavirus in their countries. Geographical isolation is a contributing factor, but decisive and determined government action has been effective in reducing community transmission. Many potential deaths have been avoided. Yet this accomplishment has yet to be compensated with an economic reward. As these countries begin to open their domestic economies, they are still battered by external shocks. This is particularly the case for the tourism-dependent economies that experienced a virtual shutdown of the sector during the second quarter of the year. The natural-resource-based economies are also suffering from the lingering effects of the decline in commodity prices and related external demand. This second special edition of the IDB Caribbean Quarterly Bulletin provides an update of economic conditions in the region. It also focuses on important evolving issues, including the potential impact of the corona virus crisis on countries balance of payments, and on new data from the IDB on the real-time social effects of the crisis.
BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology (2020)

Prokaryotic cells display a striking subcellular organization. Studies of the underlying mechanisms in different species have greatly enhanced our understanding of the morphological and physiological adaptation of bacteria to different environmental niches. The image analysis software tool BacStalk is designed to extract comprehensive quantitative information from the images of morphologically complex bacteria with stalks, flagella, or other appendages. The resulting data can be visualized in interactive demographs, kymographs, cell lineage plots, and scatter plots to enable fast and thorough data analysis and representation. Notably, BacStalk can generate demographs and kymographs that display fluorescence signals within the two-dimensional cellular outlines, to accurately represent their subcellular location. Beyond organisms with visible appendages, BacStalk is also suitable for established, non-stalked model organisms with common or uncommon cell shapes. BacStalk, therefore, contributes to the advancement of prokaryotic cell biology and physiology, as it widens the spectrum of easily accessible model organisms and enables highly intuitive and interactive data analysis and visualization.
ChemInform Abstract: Generation of Nitrile Oxides from Oxime Derivatives by the Oxidation with Ammonium Hexanitratocerate(IV). (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Measurement of turbulent water vapor fluxes using a lightweight unmanned aerial vehicle system (2011)

Abstract. We present here the first application of a lightweight unmanned aerial vehicle (UAV) system designed to measure turbulent properties and vertical latent heat fluxes (λE). Such measurements are crucial to improve our understanding of linkages between surface moisture supply and boundary layer clouds and phenomena such as atmospheric rivers. The application of UAVs allows for measurements on spatial scales complimentary to satellite, aircraft, and tower derived fluxes. Key system components are: a turbulent gust probe; a fast response water vapor sensor; an inertial navigation system (INS) coupled to global positioning system (GPS); and a 100 Hz data logging system. We present measurements made in the continental boundary layer at the National Aeronautics and Space Administration (NASA) Dryden Research Flight Facility located in the Mojave Desert. Two flights consisting of several horizontal straight flux run legs up to ten kilometers in length and between 330 and 930 m above ground level (m a.g.l.) are compared to measurement from a surface tower. Surface measured λE ranged from −53 W m−2 to 41 W m−2, and the application of a Butterworth High Pass Filter (HPF) to the datasets improved agreement to within ± 12 W m−2 for 86 % of flux runs, by removing improperly sampled low frequency flux contributions. This result, along with power and co-spectral comparisons and consideration of the differing spatial scales indicates the system is able to resolve vertical fluxes for the measurement conditions encountered. Challenges remain, and the outcome of these measurements will be used to inform future sampling strategies and further system development.
Neuroimaging for detecting covert awareness in patients with disorders of consciousness: reinforce the place of clinical feeling! (2015)

GENERAL COMMENTARY article Front. Hum. Neurosci., 17 February 2015Sec. Cognitive Neuroscience https://doi.org/10.3389/fnhum.2015.00078
Semipermeable Cellulose Beads Allow Selective and Continuous Release of Small Extracellular Vesicles (sEV) From Encapsulated Cells (2020)

The clinical benefit of therapies using Mesenchymal Stem Cells (MSCs) is attributable to their pleiotropic effect over cells and tissues, mainly through their secretome. This paracrine effect is mediated by secreted growth factors and extracellular vesicles (EV) including small EV (sEV). sEV are extra-cellular, membrane encompassed vesicles of 40 to 200 nm diameter that can trigger and signal many cellular responses depending on their cargo protein and nucleic acid repertoire. sEV are purified from cell culture conditioned media using several kits and protocols available that can be tedious and time-consuming, involving sequences of ultracentrifugations and density gradient separations, making their production a major challenge under Good Manufacturing Practices (GMP) conditions. We have developed a method to efficiently enrich cell culture media with high concentrations of sEV by encapsulating cells in semipermeable cellulose beads that allows selectively the release of small particles while offering a 3D culture condition. This method is based on the pore size of the capsules, allowing the release of particles of ≤ 200 nm including sEV. As a proof-of-principle, MSCs were encapsulated and their sEV release rate (sEV-Cap) was monitored throughout the culture and compared to sEV isolated from 2D seeded cells (sEV-2D) by repetitive ultracentrifugation cycles or a commercial kit. The isolated sEV expressed CD63, CD9, and CD81 as confirmed by flow cytometry analysis. Under transmission electron microscopy (TEM), they displayed the similar rounded morphology as sEV-2D. Their corresponding diameter size was validated by nanoparticle tracking analysis (NTA). Interestingly, sEV-Cap retained the expected biological activities of MSCs, including a pro-angiogenic effect over endothelial cells, neuritic outgrowth stimulation in hippocampal neurons and immunosuppression of T cells <i>in vitro</i>. Here, we successfully present a novel, cost, and time-saving method to generate sEV from encapsulated MSCs. Future applications include using encapsulated cells as a retrievable delivery device that can interact with the host niche by releasing active agents <i>in vivo</i>, including sEV, growth factors, hormones, and small molecules, while avoiding cell clearance, and the negative side-effect of releasing undesired components including apoptotic bodies. Finally, particles produced following the encapsulation protocol display beneficial features for their use as drug-loaded delivery vehicles.
Tagging and Cloning of a Petunia Flower Color Gene with the Maize Transposable Element Activator (1993)

George Chuck, Tim Robbins, Charanjit Nijjar, Ed Ralston, Neal Courtney-Gutterson, Hugo K. Dooner, Tagging and Cloning of a Petunia Flower Color Gene with the Maize Transposable Element Activator, The Plant Cell, Vol. 5, No. 4 (Apr., 1993), pp. 371-378
Prevention of biofilm formation on titanium surfaces modified with conjugated molecules comprised of antimicrobial and titanium-binding peptides (2009)

Specific binding of antimicrobial peptides to titanium (Ti) surfaces may serve to prevent biofilm formation, leading to a reduction in peri-implantitis. This study evaluated the binding behavior of conjugated molecules consisting of antimicrobial and hexapeptidic Ti-binding peptides (minTBP-1) using the quartz crystal microbalance (QCM-D) technique, and investigated the effect of modification of Ti surfaces with these peptides on the bioactivity of Porphyromonas gingivalis. Four kinds of peptide were prepared: histatin 5 (DSHAKRHHGYKRKFHEKHHSHRGY), minTBP-1 + histatin 5 (RKLPDAPDSHAKRHHGYKRKFHEKHHSHRGY), lactoferricin (FQWQRNMRKVR), and minTBP-1 + lactoferricin (RKLPDAPGGFQWQRNMRKVR). The QCM-D analysis demonstrated that significantly larger increases in peptide adsorption were observed in the conjugated peptides than in antimicrobial peptides alone. In addition, ATP activity in P. gingivalis in peptide-modified specimens significantly decreased compared to that in the Ti control. These results indicate that surface modification with conjugated molecules consisting of antimicrobial and Ti-binding peptides is a promising method for reduction of biofilm formation on Ti surfaces.