gebhart/patrepeval huggingface dataset:
1681. Female Urinary Metagenomic Analysis and Natural Language Processing Enhances the Infectious Diagnostic Yield in Precision Medicine (2020)

Abstract Background In this study, we assessed the diagnostic yield of metagenomics urine sample testing in patients with urological symptoms. Methods We conducted metagenomic analysis on 69 consecutive unbiased female patients, by sequencing their DNA using the KAPA HyperPlus library construction with next-generation sequencing (Nextseq500, Illumina) and reads were analyzed using Xplore-Patho®, an analytical system that permits the detection of 37,000+ microorganisms, including over 12,000 known pathogens, and examined report summaries written by infectious disease experts to obtain a diagnostic yield. In addition, infectious disease expert analysis was contrasted with a natural language (NLP) pathogen detection system to investigate its accuracy. Results In the expert data summaries, a total of 95% of the patients tested had at least one pathogen identified by metagenomics as a potential explanation of their urological symptoms and these results were binned into four categories: 1) 51% of infection likely, 2) 4% of infection possible, 3) 26% of low-grade infection likely and 4) 14% of low-grade infection possible. Data from healthy controls was used in conjunction with an NLP pathogen detection pipeline and compared to infectious disease expert summaries. The NLP pathogen algorithm detected that at least 97% of samples had one pathogen which was more than 5 standard deviations from the abundance of that pathogen in healthy controls, and least 84% had 2 or more pathogens. These diagnostic percentages were consistent with the infectious disease expert summaries. The NLP algorithm had access to a large database derived from PubMed articles and it was found that several relevant uropathogens were not mentioned in report summaries. For example, one well-documented uropathogen was present in 13 samples, but was not mentioned in any report summaries. Conclusion In conclusion, this study demonstrated the high diagnostic yield in females with urological symptoms following metagenomic analysis and the ability of NLP to enhance the sensitivity of reportable pathogens. Disclosures All Authors: No reported disclosures
Contributions to the Chemistry of Anionic Water‐Soluble Tetraarylporphyrins and Their Metal Complexes (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Enhanced anti-tumor immunotherapy by dissolving microneedle patch loaded ovalbumin (2019)

The skin is a very suitable organ for the induction of immune responses to vaccine antigens. Antigen delivery systems to the skin by needle and syringe directly deposit the antigen into the epidermal-dermal compartment, one of the most immunocompetent sites due to the presence of professional antigen-presenting cells aimed at the induction of antigen-specific T cells. In this study, we analyzed the amount of ovalbumin as an antigen delivered to the skin by a microneedle. When ovalbumin protein as an antigen was delivered to the skin of mice using a dissolving microneedle, it induced an immune response through the enhanced proliferation and cytokines production by the splenocytes and lymph nodes. Also, it effectively increased the ovalbumin-specific CD8+ T cell and CD4+ T cell population and induced an ovalbumin-specific CTL response against the graft of ovalbumin-expressing EG7 tumor cells in the immunized mice. Also, we identified the inhibition of tumor growth and prevention of tumor formation in the context of the therapeutic and prophylactic vaccine, respectively through EG-7 tumor mouse model. Finally, these data show the potential of patches as attractive antigen delivery vehicles.
NanoCluster Beacons Enable Detection of a Single N6-Methyladenine (2015)

While N(6)-methyladenine (m(6)A) is a common modification in prokaryotic and lower eukaryotic genomes and has many biological functions, there is no simple and cost-effective way to identify a single N(6)-methyladenine in a nucleic acid target. Here we introduce a robust, simple, enzyme-free and hybridization-based method using a new silver cluster probe, termed methyladenine-specific NanoCluster Beacon (maNCB), which can detect single m(6)A in DNA targets based on the fluorescence emission spectra of silver clusters. Not only can maNCB identify m(6)A at the single-base level but it also can quantify the extent of adenine methylation in heterogeneous samples. Our method is superior to high-resolution melting analysis as we can pinpoint the location of m(6)A in the target.
Examination of Aflatoxin B1 in Leaf Tobacco and in Cigarette Smoke Condensate (1967)

An examination of several samples of leaf tobacco, including three types of good-grade tobaccos and heavily molded flue-cured tobacco, and of cigarette smoke condensate, failed to detect aflatoxin B1. Pure aflatoxin B1 added to cigarettes was not recovered in the smoke condensate indicating that aflatoxin B1, when present, was changed or decomposed during the smoking process.
IL-5 Promotes Eosinophil Trafficking to the Esophagus (2002)

Eosinophil infiltration into the esophagus occurs in a wide range of diseases; however, the underlying pathophysiological mechanisms involved are largely unknown. We now report that the Th2 cytokine, IL-5, is necessary and sufficient for the induction of eosinophil trafficking to the esophagus. We show that transgenic mice overexpressing IL-5 under the control of a T cell (CD2) or a small intestinal enterocyte (fatty acid-binding protein) promoter have markedly increased eosinophil numbers in the esophagus. For example, esophageal eosinophil levels are 1.9 +/- 0.9 and 121 +/- 14 eosinophils/mm(2) in wild-type and CD2-IL-5-transgenic mice, respectively. Consistent with this effect being mediated by a systemic mechanism, pharmacological administration of IL-5 via a miniosmotic pump in the peritoneal cavity resulted in blood and esophageal eosinophilia. To examine the role of IL-5 in oral Ag-induced esophageal eosinophilia, eosinophilic esophagitis was induced by allergen exposure in IL-5-deficient and wild-type mice. Importantly, IL-5-deficient mice were resistant to eosinophilic esophagitis. Finally, we examined the role of eotaxin when IL-5 was overproduced in vivo. Esophageal eosinophil levels in CD2-IL-5-transgenic mice were found to decrease 15-fold in the absence of the eotaxin gene; however, esophageal eosinophil numbers in eotaxin-deficient IL-5-transgenic mice still remained higher than wild-type mice. In conclusion, these studies demonstrate a central role for IL-5 in inducing eosinophil trafficking to the esophagus.
Efficacy of ethinylestradiol 20 µg/drospirenone 3 mg in a flexible extended regimen in women with moderate-to-severe primary dysmenorrhoea: an open-label, multicentre, randomised, controlled study (2012)

Compared with the conventional regimen, the flexible extended regimen of EE/DRSP with MIB was associated with a significantly greater reduction in days with dysmenorrhoeic pain in women with moderate-to-severe primary dysmenorrhoea. The flexible(MIB) regimen was also associated with greater improvements in dysmenorrhea according to the Clinical Global Impression rating scale and was generally well tolerated.
On the use of contextual time-frequency information for full-band clustering-based convolutive blind source separation (2014)

In this paper we propose to incorporate contextual time-frequency information for clustering-based blind source separation. Previous clustering-based approaches have successfully used clustering techniques to estimate time-frequency separation masks; however, these approaches generally do not consider the contextual information of each time-frequency slot. Motivated by the homogenous behavior of speech signals, we modify the fuzzy c-means clustering to bias the results in favor of cluster membership homogeneity within localized neighborhoods in the time-frequency space. Experimental evaluations in both simulated and real-world underdetermined environments demonstrate improvement in source separation performance over previous clustering approaches.
<title>Er-doped LiNbO<formula><inf><roman>3</roman></inf></formula> waveguide lasers</title> (1997)

The state-of-the-art of Er-doped integrated optical lasers in LiNbO<SUB>3</SUB> is reviewed. They are fabricated in Er- diffusion doped substrates with Ti-diffused channel guides of high quality. The laser resonators are formed by dielectric mirrors vacuum-deposited on the polished waveguide end faces. Five different types of Ti:Er:LiNbO<SUB>3</SUB> waveguide lasers are presented.Among them are free running Fabry-Perot lasers of six different wavelengths in the range 153nm < (lambda) < 1610nm with a cw-output power up to 63mW. They have a shot noise limited relative intensity noise at frequencies above 50MHz. Tunable lasers have been developed by the intracavity integration of an acoustooptical amplifying wavelength filter yielding a tuning range up to 31nm. With an intracavity electrooptic phase modulator modelocked laser operation has been obtained with pulse repetition frequencies up to 10GHz; pulses of only a few ps width could be generated. With an intracavity amplitude modulator Q-switched laser operation has been achieved with up to 2.4W pulse peak power at 2kHz repetition frequency. Moreover, distributed Bragg reflector lasers of emission linewidth < 8kHz have been developed using a dry- etched surface grating as one of the mirrors of the laser cavity.
Three dimensional printed calcium phosphate and poly(caprolactone) composites with improved mechanical properties and preserved microstructure (2017)

Biphasic calcium phosphate scaffolds formed via three dimensional (3D) printing technology to exhibit porosity and chemical resorbability to promote osseointegration often lack the strength and toughness required to withstand loading in bone tissue engineering applications. Herein, sintering and CaP:poly(caprolactone) (PCL) composite formation were explored to improve 3D printed scaffold strength and toughness. Hydroxyapatite and α-tricalcium phosphate (α-TCP) biphasic calcium powders were printed using phosphoric acid binder, which generated monetite and hydroxyapatite scaffolds. Upon sintering, evolution of β-TCP was observed along with an increase in flexural strength and modulus but no effect on fracture toughness was observed. Furthermore, scaffold porosity increased with sintering. Additionally, two techniques of PCL composite formation were employed: postprint precipitation and 3D print codeposition to further augment scaffold mechanical properties. While both techniques significantly improved flexural strength, flexural modulus, and fracture toughness under most conditions explored, precipitation yielded more substantial increases in these properties, which is attributed to better continuity of the PCL phase. However, precipitation also compromised surface porosity due to PCL passivation of the calcium phosphate surface, which may subsequently hinder scaffold integration and bone regeneration. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 663-672, 2018.
A Hough transform system based on neural networks (1992)

Neural-like analog circuitry is suggested for image-to-parameter-space mapping, and a modified Hopfield optimization network is proposed for the parameter space peak detection. Solution time under 50 mu s is obtainable with general-purpose operational amplifiers. Example system applications include autonomous navigation, tracking multiple targets, curve following, mensuration, and image recognition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expressively actuated percussion instruments and interfaces (2013)

Percussion instruments and interfaces can be extended by incorporating actuation with motors. While many prior designs have employed actuation to simply trigger notes, this work emphasizes the importance of the musician's gesture using expressively controlled actuators. This is achieved by implementing force-feedback control of the actuators. For example, the Haptic Drum essentially consists of a drum pad attached to a woofer. Every time that a drumstick strikes the drum pad, the woofer briefly pushes it upward again, adding energy to the motion of the drumstick. In this manner, the Haptic Drum enables musicians to play one-handed drum rolls at optionally superhuman speeds and with arbitrarily complex dynamics. Furthermore, because the musician and the drumstick are inside the feedback control loop, the musician can change the rate of the drum roll by modulating the stiffness of his or her muscles or changing the downward force applied to the drumstick. Conversely, borrowing on technology for remote surgery, expressively actuated percussion instruments can be designed using force-feedback teleoperation. Simply by recording the position of the master haptic device during teleoperation, generalized motor programs can be created for expressively playing percussion instruments. This technology was employed in the composition “When the Robots Get Loose."
Influence of Prior Influenza Vaccination on Antibody and B-Cell Responses (2008)

Currently two vaccines, trivalent inactivated influenza vaccine (TIV) and live attenuated influenza vaccine (LAIV), are licensed in the USA. Despite previous studies on immune responses induced by these two vaccines, a comparative study of the influence of prior influenza vaccination on serum antibody and B-cell responses to new LAIV or TIV vaccination has not been reported. During the 2005/6 influenza season, we quantified the serum antibody and B-cell responses to LAIV or TIV in adults with differing influenza vaccination histories in the prior year: LAIV, TIV, or neither. Blood samples were collected on days 0, 7-9 and 21-35 after immunization and used for serum HAI assay and B-cell assays. Total and influenza-specific circulating IgG and IgA antibody secreting cells (ASC) in PBMC were detected by direct ELISPOT assay. Memory B cells were also tested by ELISPOT after polyclonal stimulation of PBMC in vitro. Serum antibody, effector, and memory B-cell responses were greater in TIV recipients than LAIV recipients. Prior year TIV recipients had significantly higher baseline HAI titers, but lower HAI response after vaccination with either TIV or LAIV, and lower IgA ASC response after vaccination with TIV than prior year LAIV or no vaccination recipients. Lower levels of baseline HAI titer were associated with a greater fold-increase of HAI titer and ASC number after vaccination, which also differed by type of vaccine. Our findings suggest that the type of vaccine received in the prior year affects the serum antibody and the B-cell responses to subsequent vaccination. In particular, prior year TIV vaccination is associated with sustained higher HAI titer one year later but lower antibody response to new LAIV or TIV vaccination, and a lower effector B-cell response to new TIV but not LAIV vaccination.
Multicenter clinical trial of ultrasonic circular cyclo coagulation in glaucoma patients naive of filtering surgery. Preliminary results at 6 months (2014)

Abstract Purpose To evaluate the efficacy and safety of the Ultrasonic Circular Cyclo Coagulation (UC3) procedure in patients naive of previous filtering glaucoma surgery. Methods Prospective non comparative interventional clinical study performed in 5 French glaucoma centers. Thirty eyes of 30 patients (24 primary open‐angle glaucoma and 6 secondary glaucoma), with intraocular pressure (IOP) &gt; 21 mmHg, naïve of previous filtering glaucoma surgeries, were insonified with a therapy probe comprising 6 piezoelectric transducers. The 6 transducers were activated with a 6 seconds exposure time. Complete ophthalmic examinations were performed before the procedure, and at 1 day, 1 week, 1, 2, 3, 6 and 12 months after. Primary outcomes were surgical success (defined as IOP reduction from baseline ≥ 20% and IOP &gt; 5mmHg) at the last follow‐up visit, and vision‐threatening complications. Secondary outcomes were mean IOP at each follow‐up visits compared to baseline, medication use, and complications. Results IOP was significantly reduced (p&lt;0.05), from a mean preoperative value of 28.3 ± 7.0 mmHg to a mean value of 19.5 ± 7.2 mmHg at 6 months. Success (IOP reduction &gt;20%) was achieved in 63% of eyes at 6 months after one HIFU procedure, with a mean IOP decrease of 39%. No major intra‐ or post‐operative complications occurred. Conclusion Ultrasonic Circular Cyclo Coagulation seems to be an effective and well tolerated method to reduce intraocular pressure in glaucoma patients naïve of previous glaucoma surgery. Commercial interest
Directed Evolution of the α-l-Fucosidase from Thermotoga maritima into an α-l-Transfucosidase (2006)

The alpha-L-fucosidase from Thermotoga maritima (Tm alpha fuc) was converted into alpha-L-transfucosidase variants by directed evolution. The wild-type enzyme catalyzes oligosaccharide synthesis by transfer of a fucosyl residue from a pNP-fucoside donor to pNP-fucoside (self-condensation) with alpha-(1-->3) regioselectivity or pNP-galactoside (transglycosylation) with alpha-(1-->2) regioselectivity at low yields (7%). The wild-type enzyme was submitted to one cycle of mutagenesis, followed by rational recombination of the selected mutations, which allowed identification of variants with improved transferase activity. The transferase and hydrolytic kinetics of all the mutants were assessed by NMR methods and capillary electrophoresis. It was shown that the best mutant exhibited a dramatic 32-fold increase in the transferase/hydrolytic kinetic ratio, while keeping 60% of the overall wild-type enzyme activity. Accordingly, the maximum yield of a specific transglycosylation product [pNP-Gal-alpha-(1-->2)-Fuc] reached more than 60% compared to 7% with WT enzyme at equimolar and low concentrations of donor and acceptor (10 mM). Such an improvement was obtained with only three mutations (T264A, Y267F, L322P), which were all located in the second amino acid shell of the fucosidase active site. Molecular modeling suggested that some of these mutations (T264A, Y267F) cause a reorientation of the amino acids that are in direct contact with the substrates, resulting in a better docking energy. Such mutants with high transglycosidase activity may constitute novel enzymatic tools for the synthesis of fucooligosaccharides.
Synthesis and Comparative Cytostatic Activity of the New N-7 Acyclic Purine Nucleoside Analogues with Natural N-9 Regioisomers (2005)

The synthesis of the purine derivatives alkylated at N-7 (2a) and N-9 (2b) with 2-acetoxyethoxymethyl side chain, and chemical transformations of keto to chloro (5a), chloro to thio (6a) at C-6, and amino to fluoro (7a) at C-2 position of the purine ring were described.Structures of compounds were elucidated by analysis of their 1 H and 13 C NMR spectra, MS spectra and elemental analyses.N-7 Regioisomers (2a-7a) were evaluated for their cytostatic activities and their inhibitory effects were compared with those of the corresponding N-9 isomers.The 2-aminopurin-6-thione derivative (6a) showed the highest cytostatic activity, particularly against murine leukemia (L1210).
Inversion-based control of modular high frequency inverters (2016)

Inversion-based control for modular high frequency (MHF) inverters in a two-degree-of-freedom structure is presented in this paper. This establishes a state-space average model of MHF inverters. The results of this paper are illustrated using simulation and experiment based on an MHF3P inverter with four submodules.
An improved method for culturing myotubes on laminins for the robust clustering of postsynaptic machinery (2019)

Abstract Motor neurons form specialized synapses with skeletal muscle fibers, called neuromuscular junctions (NMJs). Cultured myotubes are used as a simplified in vitro system to study the postsynaptic specialization of muscles. The stimulation of myotubes with the glycoprotein agrin or laminin-111 induces the clustering of postsynaptic machinery that contains acetylcholine receptors (AChRs). When myotubes are grown on laminin-coated surfaces, AChR clusters undergo developmental remodeling to form topologically complex structures that resemble mature NMJs. Needing further exploration are the molecular processes that govern AChR cluster assembly and its developmental maturation. Here, we describe an improved protocol for culturing muscle cells to promote the formation of complex AChR clusters. We screened various laminin isoforms and showed that laminin-221 was the most potent for inducing AChR clusters, whereas laminin-121, laminin-211, and laminin-221 afforded the highest percentages of topologically complex assemblies. Human primary myotubes that were formed by myoblasts obtained from patient biopsies also assembled AChR clusters that underwent remodeling in vitro . Collectively, these results demonstrate an advancement of culturing myotubes that can facilitate high-throughput screening for potential therapeutic targets for neuromuscular disorders.
Effect of Sulfur Impurities on Li / TiS2 Cells (1981)

Conditions leading to the generation of sulfur and hydrogen sulfide from can occur with uncontrolled handling of the active material during the fabrication of cells. These impurities affect the storage behavior of the ambient temperatures rechargeable organic electrolyte cells. An increase in the lithium anode polarization and self‐discharge of the cells is witnessed in the presence of these impurities. A mechanism of film formation and redox shuttle is discussed to account for the observed results.
Anthropometry and bioelectrical impedance inconsistently predicts fatness in women with regional adiposity (1999)

We conclude that ANTHRO and some BIA equations are accurate for predicting %BF in LB fat "shaped" women but are not appropriate for women with primarily abdominal fat patterning.
Exploring the Mechanisms Underlying the Therapeutic Effect of Salvia Miltiorrhiza Against Diabetic Nephropathy Using Network Pharmacology and Molecular Docking (2020)

Abstract BackgroundThe mechanisms underlying the therapeutic effect of Salvia Miltiorrhiza (SM) against diabetic nephropathy (DN) using systematic network pharmacology and molecular docking methods were examined.MethodsTCMSP database was used to screen the active ingredients of SM. Gene targets were obtained using Swiss Target Prediction and TCMSP databases. Related targets of DN were retrieved from the Genecards and DisGeNET databases. Next, a PPI network was constructed using the common targets of SM-DN in the STRING database. The Metascape platform was used for GO function analysis and Cytoscape plug-in ClueGO was used for KEGG pathway enrichment analysis. Molecular docking was performed using iGEMDOCK and AutoDock Vina software. Pymol and LigPlos were used for mapping the network. ResultsSixty-six active ingredients and 189 targets were screened from SM. Among them, 64 targets overlapped with DN targets. The PPI network diagram revealed that AKT1, VEGFA , IL6 , TNF , MAPK1 , TP53 , EGFR , STAT3 , MAPK14 , and JUN were the top 10 relevant targets. GO and KEGG analyses mainly focused on advanced glycation end products, oxidative stress, inflammatory response, and immune regulation. Molecular docking revealed that the potential target genes closely related to DN, including TNF , NOS2 , and AKT1 , were more stable in combination with salvianolic acid B, and their stability was better than that of tanshinone IIA.ConclusionThis study reveals the active components and potential molecular mechanisms involved in the therapeutic effect of SM against DN and provides a reference for the wide application of SM in clinically managing DN.