gebhart/patrepeval huggingface dataset:
Degradation of black tea theaflavin through C-ring cleavage by gut microbiota (2022)

Increasing evidence has shown that gut microbiota plays important roles in metabolizing large molecular polyphenols to bioavailable and bioactive microbial metabolites. Theaflavin (TF) is one of the major color compounds in black tea and has demonstrated anti-inflammation, antioxidant, and anticancer effects properties. However, little is known about the metabolism of TF by gut microbiota in vivo. In this study, following the administration of TF to mice, the C-ring cleavage metabolites, dihydro- and tetrahydro-theaflavin (DH-TF and TH-TF) were detected in mouse feces by LC-MS and validated by authentic standards from in situ chemical reaction. The observation of the C-ring cleavage metabolites in TF-treated conventionalized mice but not in germ-free (GF) mice confirmed the role of gut microbiota in cleaving the C-rings of TF. The detection of DH-TF from the anaerobic incubation of TF with catechin-converting gut bacteria, Eggerthella lenta (Eggerth), suggested that the microbes with the capacity to cleave the C-ring of catechins were able to metabolize TF following the same mechanism. Additionally, three small phenolic metabolites were detected in mouse feces, and one of them was primarily detected in SPF mice not GF mice, which revealed that TF, subsequent to the cleaved C-ring, can be further metabolized into smaller phenolic metabolites by gut microbiota. Dose-dependent production of these metabolites were observed from the administration of 100 mg/kg to 400 mg/kg body weight of TF. In conclusion, gut microbiota can metabolize TF to the open-ring metabolites and the phenolic metabolites through the C-ring cleavage in mice.
Case Study on Evacuation Rates within the World Trade Center Towers on September 11, 2001 (2005)

While movement of people in crowds and fire drills has been studied by numerous investigators, little data exist for real fire evacuations. This is largely due to the difficulty in establishing an accurate position-time history for the evacuees. The evacuation of the World Trade Center North and South Towers on September 11, 2001 was unique in that major, catastrophic events occurred at distinct times during the evacuation. In this paper, 14 evacuation case studies are presented in which the evacuee reported their position at these known points in time to the media. From this position-time history, the descent rate of these evacuees could be determined. These descent rates are not necessarily representative of the evacuation population in general, but they do provide some distinct data points which are of value to the fire protection and building evacuation community in assessing evacuation from high-rise buildings.
Analysis of Electrical Characteristics of AlGaN/GaN on Si Large SBD by Changing Structure (2017)

We investigated the improvement in electrical characteristics of large AlGaN/GaN on Si Schottky barrier diode (SBD) induced by structural change to achieve a better trade-off between the forward and reverse performance to obtain high power conversion efficiency in PFC converter. Using an optimized dry etch condition for a large device, we fabricated three-types of SBD with 63 mm channel width: conventional, recessed, recessed dual-anodemetal SBD. The recessed dual-anode-metal SBD exhibited a very low turn-on voltage of 0.34 V, a high forward current of 1.63 A at 1.5 V, a leakage current of 114 ㎂ at -15 V, a breakdown voltage of 794 V.
Reassignment of a rare sense codon to a non-canonical amino acid inEscherichia coli (2015)

The immutability of the genetic code has been challenged with the successful reassignment of the UAG stop codon to non-natural amino acids in Escherichia coli. In the present study, we demonstrated the in vivo reassignment of the AGG sense codon from arginine to l-homoarginine. As the first step, we engineered a novel variant of the archaeal pyrrolysyl-tRNA synthetase (PylRS) able to recognize l-homoarginine and l-N6-(1-iminoethyl)lysine (l-NIL). When this PylRS variant or HarRS was expressed in E. coli, together with the AGG-reading tRNAPylCCU molecule, these arginine analogs were efficiently incorporated into proteins in response to AGG. Next, some or all of the AGG codons in the essential genes were eliminated by their synonymous replacements with other arginine codons, whereas the majority of the AGG codons remained in the genome. The bacterial host's ability to translate AGG into arginine was then restricted in a temperature-dependent manner. The temperature sensitivity caused by this restriction was rescued by the translation of AGG to l-homoarginine or l-NIL. The assignment of AGG to l-homoarginine in the cells was confirmed by mass spectrometric analyses. The results showed the feasibility of breaking the degeneracy of sense codons to enhance the amino-acid diversity in the genetic code.
Realization of Negative Permeability in Vertical Double Split-Ring Resonators with Normal Incidence (2020)

With the rapid development of optoelectronics, methods for manipulating light–matter interactions are urgently required. In this work, three-dimensional double split-ring resonators (3D-DSRRs) have been designed via a metal-stress-driven self-folding method. The 3D-DSRRs eliminate the electric response from the meta-atoms and exhibit a magnetic dipole moment radiation power that is 1244.6-fold greater than that of two-dimensional metamaterials. By tailoring of the 3D-DSRR periodicity, the permeability is shown to vary from positive to zero, even reaching negative values under normal incidence. This strain engineering strategy provides an efficient method for designing and fabricating three-dimensional metamaterials and for increasing the variety of light–matter interactions in the mid-infrared region.
Multiplex ligation-dependent probe amplification (MLPA) on-chip (2013)

Polymerase chain reaction (PCR) has become an indispensable technique in clinical diagnostics. For integrated, lab-on-a-chip (LoC) solutions, multiplexed implementations of PCR are especially attractive; we describe the transfer and optimization of multiplex ligation-dependent probe amplification (MLPA) directly onto a silicon-based microfluidic chip. A standard, commercially-available MLPA protocol involves discrete steps: (1) probe hybridization, (2) ligation and (3) standard PCR amplification. Size separation can then be performed on the products to identify the different fragments. We describe the optimization of all MLPA reaction steps for use on-chip and show the fabrication of a single, integrated silicon fluidic chip for performing an entire MLPA protocol. These results describe a clear route towards a complete lab-on-a-chip system that integrates sample preparation, multiplex DNA amplification and detection onto a single disposable piece of silicon.
Label-Free Evaluation of Myocardial Infarction and Its Repair by Spontaneous Raman Spectroscopy (2014)

Raman spectroscopy, which provides information about molecular species and structures of biomolecules via intrinsic molecular vibrations, can analyze physiological and pathological states of tissues on the basis of molecular constituents without staining. In this study, we analyzed Raman spectra of myocardial infarction and its repair in rats using the hypothesis that the myocardium in the course of myocardial infarction and its repair could be recognized by spontaneous Raman spectroscopy on the basis of chemical changes in myocardial tissues. Raman spectra were acquired from unfixed frozen cross sections of normal and infarcted heart tissues upon excitation at 532 nm. Raman spectra of the infarcted tissues were successfully obtained at characteristic time points: days 2, 5, and 21 after coronary ligation, at which the main components of the infarcted region were coagulation necrosis, granulation tissue, and fibrotic tissue, respectively. The latent variable weights calculated by a multivariate classification method, partial least-squares-discriminant analysis (PLS-DA), revealed fundamental information about the spectral differences among the types of tissues on the basis of molecular constituents. A prediction model for the evaluation of these tissue types was established via PLS-DA. Cross-validated sensitivities of 99.3, 95.3, 96.4, and 91.3% and specificities of 99.4, 99.5, 96.5, and 98.3% were attained for the discrimination of normal, necrotic, granulation, and fibrotic tissue, respectively. A two-dimensional image of a marginal area of infarction was successfully visualized via PLS-DA. Our results demonstrated that spontaneous Raman spectroscopy combined with PLS-DA is a novel label-free method of evaluating myocardial infarction and its repair.
Tandem Hetero Diels−Alder Reaction:  Synthesis of Oxygenated Macrocycles (2001)

[structure: see text]. C2-symmetric, oxygenated macrocycles have been synthesized from simple acyclic precursors in a single step by a tandem hetero Diels-Alder reaction. Thermolysis and Lewis acid catalysis can effect this novel transformation. The tandem reaction product is formed in preference to the intramolecular cycloaddition product, and an explanation for this result is proposed.
Predatory Pricing (1991)

It has long been part of the popular folklore of business that firms sometimes engage in predatory actions against their competitors. For example, a firm might cut its price so low in some local market where it faces competition that neither the firm nor its competitor can earn a profit there. Such price-cutting would be called 'predatory' (by some) because it is inconsistent with short-run profit maximization by the firm and it appears to benefit the firm in the long run only by bankrupting or otherwise weakening its rival. Of course, predatory actions are not limited to pricing decisions — for example, a choice of store locations by a grocery chain too near its competitors could be predatory — but our discussion in this short note will focus on predatory pricing and the theoretical controversy surrounding it.KeywordsLimit PriceIncumbent FirmPotential EntrantPrice CuttingPredatory PriceThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Layered Belief Propagation for Low-complexity Large MIMO Detection Based on Statistical Beams (2018)

This paper proposes a novel layered belief propagation (BP) detector with a concatenated structure of two different BP layers for low-complexity large multi-user multi-input multi-output (MU-MIMO) detection based on statistical beams. To reduce the computational burden and the circuit scale on the base station (BS) side, the two-stage signal processing consisting of slow varying outer beamformer (OBF) and group-specific MU detection (MUD) for fast channel variations is effective. However, the dimensionality reduction of the equivalent channel based on the OBF results in significant performance degradation in subsequent spatial filtering detection. To compensate for the drawback, the proposed layered BP detector, which is designed for improving the detection capability by suppressing the intra- and inter-group interference in stages, is introduced as the post-stage processing of the OBF. Finally, we demonstrate the validity of our proposed method in terms of the bit error rate (BER) performance and the computational complexity.
U.S. Department of Energy, National Energy Technology Laboratory Solid-State Lighting Core Technologies Light Emitting Diodes on Semipolar Bulk GaN Substrate with IQE > 80% at 150 A/cm2 and 100 0C (2015)

GaN is a crucial material for light-emitting diodes (LEDs) emitting in the violet-to-green range. Despite its good performance, it still suffers from significant technical limitations. In particular, the efficiency of GaN-based LEDs decreases at high current (“current droop”) and high temperature (“temperature droop”). This is problematic in some lighting applications, where a high-power operation is required. This program studied the use of particular substrates to improve the efficiency of GaN-based LEDs: bulk semipolar (SP) GaN substrates. These substrates possess a very high material quality, and physical properties which are distinctly different from legacy substrates currently used in the LED industry. The program focused on the development of accurate metrology to quantify the performance of GaN-based LEDs, and on improvement to LED quality and design on SP substrates. Through a thorough optimization process, we demonstrated violet LEDs with very high internal quantum efficiency, exceeding 85% at high temperature and high current. We also investigated longer-wavelength blue emitters, but found that the limited strain budget was a key limitation.
RecombinantPseudomonasexoenzyme S and exoenzyme S fromPseudomonas aeruginosaDG1 share the ability to stimulate T lymphocyte proliferation (1999)

Exoenzyme S from P. aeruginosa DG1 and recombinant exoenzyme S derived from strain 388 have distinct characteristics, which has led to a controversy about their homology and their pathophysiologic consequences. We have been investigating the ability of exoenzyme S to activate T lymphocytes, and therefore performed studies to determine whether exoenzyme S from P. aeruginosa DG1 and recombinant exoenzyme S derived from strain 388 and expressed in Pseudomonas aeruginosa PA103 or in E. coli BL21(DE3), could induce T lymphocyte activation and proliferation. Both preparations were able to activate T cells and induce lymphocyte proliferation at similar levels as measured by flow cytometry of surface-activation markers and DNA synthesis, respectively. Further, a monoclonal antibody raised against exoenzyme S from strain DG1 partially neutralized T cell activation induced by recombinant exoenzyme S and bound to it in an immunoblot suggesting that the epitope responsible for T cell activation is shared by exoenzyme S from strain DG1 and recombinant exoenzyme S. These data suggest that the two different preparations of exoenzyme S, despite biochemical differences, share the characteristic that is responsible for T lymphocyte activation.Key words: exoenzyme S, Pseudomonas aeruginosa, T lymphocyte, cystic fibrosis.
Data driven respiratory signal detection in PET taking advantage of time-of-flight data (2016)

Respiratory gating is a powerful tool for tackling motion-related issues in chest PET imaging. On current scanners the respiratory signal is obtained from external devices, whereas with Data-Driven methods it can be extracted directly from the data. The aim of this work is to show the increased potential of the application of Principal Component Analysis (PCA) on TOF data. We propose a methodology that retains the TOF information and compare it to the non-TOF method. We tested the method on 16 FDG oncology patients, monitored with an RPM camera. To further investigate the benefit of TOF, PCA was selectively applied to sets of TOF bins equidistant from the center. The correlation with the RPM, the level of noise and the respiratory-likeness were analysed for all the obtained respiratory signals. The results of our analysis showed that retaining the TOF information into the sinograms considerably increased the quality of the extracted respiratory signals.
Quantifying drug-induced structural toxicity in hepatocytes and cardiomyocytes derived from hiPSCs using a deep learning method (2020)

Cardiac and hepatic toxicity result from induced disruption of the functioning of cardiomyocytes and hepatocytes, respectively, which is tightly related to the organization of their subcellular structures. Cellular structure can be analyzed from microscopy imaging data. However, subtle or complex structural changes that are not easily perceived may be missed by conventional image-analysis techniques. Here we report the evaluation of PhenoTox, an image-based deep-learning method of quantifying drug-induced structural changes using human hepatocytes and cardiomyocytes derived from human induced pluripotent stem cells. We assessed the ability of the deep learning method to detect variations in the organization of cellular structures from images of fixed or live cells. We also evaluated the power and sensitivity of the method for detecting toxic effects of drugs by conducting a set of experiments using known toxicants and other methods of screening for cytotoxic effects. Moreover, we used PhenoTox to characterize the effects of tamoxifen and doxorubicin-which cause liver toxicity-on hepatocytes. PhenoTox revealed differences related to loss of cytochrome P450 3A4 activity, for which it showed greater sensitivity than a caspase 3/7 assay. Finally, PhenoTox detected structural toxicity in cardiomyocytes, which was correlated with contractility defects induced by doxorubicin, erlotinib, and sorafenib. Taken together, the results demonstrated that PhenoTox can capture the subtle morphological changes that are early signs of toxicity in both hepatocytes and cardiomyocytes.
Are Retinal Examinations Useful in Assessing Cardiovascular Risk? (2008)

10.1038/ajh.2008.201
Rate-Splitting assisted Massive Machine-Type Communications in Cell-Free Massive MIMO (2022)

This letter focuses on integrating rate-splitting multiple-access (RSMA) with time-division-duplex Cell-free Massive MIMO (multiple-input multiple-output) for massive machine-type communications. Due to the large number of devices, their sporadic access behaviour and limited coherence interval, we assume a random access strategy with all active devices utilizing the same pilot for uplink channel estimation. This gives rise to a highly pilot-contaminated scenario, which inevitably deteriorates channel estimates. Motivated by the robustness of RSMA towards imperfect channel state information, we propose a novel RSMA-assisted downlink transmission framework for cell-free massive MIMO. On the basis of the downlink achievable spectral efficiency of the common and private streams, we devise a heuristic common precoder design and propose a novel max-min power control method for the proposed RSMA-assisted scheme. Numerical results show that RSMA effectively mitigates the effect of pilot contamination in the downlink and achieves a significant performance gain over a conventional cell-free massive MIMO network.
Bridging and spasming. (2012)

The application of investigative techniques to evaluate the coronary vasoreactivity of myocardial bridging has been previously described. In one case-control study of 29 patients with myocardial bridging,1 the results of testing for endothelium-dependent and endothelium-independent changes in coronary arterial dimensions, blood flow, and wall shear stress were compared with test values in 58 patients without myocardial bridging. In that study, which used a graded infusion of acetylcholine, the authors concluded that “myocardial bridging is characterized by enhanced wall shear rate and impairment in endothelial dependent vasorelaxation.” A subsequent study involving 128 patients with myocardial bridging and 231 patients without merely yielded confirmatory results on a larger scale.2

These data, plus other information on the importance of evaluating endothelial function in other settings (for example, chest pain and ischemia after drug-eluting stent implantation), have set the stage for analyzing the cases of the 2 patients described by Angelini and colleagues.3 One had takotsubo cardiomyopathy and the other had vasospastic symptoms brought on by the administration of desmopressin. Upon acetylcholine challenge, both patients were found to have profound coronary vasospasm. Of interest is that nicardipine infusion dramatically improved the response to acetylcholine in the first patient, although the segment of the myocardial bridge was less sensitive to the effect. In the second patient, acetylcholine administration caused the obstruction of a 1.5-cm segment of the left anterior descending coronary artery, which reproduced the patient's symptoms and electrocardiographic changes. Intracoronary nitroglycerin improved the angiographic appearance of the left anterior descending obstruction, and only systolic bridging appeared in the same segment.

These case reports led the authors to conclude that acetylcholine testing can be very useful in evaluating disorders of coronary vascular tone in the context of takotsubo cardiomyopathy or Prinzmetal angina. This conclusion is amply supported by other published information. It is crucial in recommendations such as these to make sure that specific protocols are used reliably and reproducibly to evaluate the effect of endothelium-dependent and endothelium-independent changes in coronary vasoreactivity. The protocols should be implemented and the data should be collected in a prospective fashion so that the appropriate questions can be asked and answered as we continue to evaluate and identify optimal treatment approaches for an increasingly broad and diverse group of patients.


Joerg Herrmann, MD

David R. Holmes, Jr., MD

Cardiovascular Diseases & Internal Medicine, Mayo Clinic, Rochester, Minnesota
Single molecule correlation spectroscopy in continuous flow mixers with zero-mode waveguides (2008)

Zero-Mode Waveguides were first introduced for Fluorescence Correlation Spectroscopy at micromolar dye concentrations. We show that combining zero-mode waveguides with fluorescence correlation spectroscopy in a continuous flow mixer avoids the compression of the FCS signal due to fluid transport at channel velocities up to approximately 17 mm/s. We derive an analytic scaling relationship [equation: see text] converting this flow velocity insensitivity to improved kinetic rate certainty in time-resolved mixing experiments. Thus zero-mode waveguides make FCS suitable for direct kinetics measurements in rapid continuous flow.
In-vitro-Experimente zur flüssigkeitsmodulierten Mikrowellenablation (2010)

By additionally administering a carefully chosen fluid, enhancing or protecting effects during microwave ablation can be observed. Especially Gastrografin, Magnograf and HES 10 % can be used to enhance ablation effects, whereas protective effects can be observed particularly when using Lipiodol, distilled water and Glucose 5 %-solution.
Development of a new correlation to determine the static Young’s modulus (2017)

The estimation of the in situ stresses is very crucial in oil and gas industry applications. Prior knowledge of the in situ stresses is essential in the design of hydraulic fracturing operations in conventional and unconventional reservoirs. The fracture propagation and fracture mapping are strong functions of the values and directions of the in situ stresses. Other applications such as drilling require the knowledge of the in situ stresses to avoid the wellbore instability problems. The estimation of the in situ stresses requires the knowledge of the Static Young’s modulus of the rock. Young’s modulus can be determined using expensive techniques by measuring the Young’s modulus on actual cores in the laboratory. The laboratory values are then used to correlate the dynamic values derived from the logs. Several correlations were introduced in the literature, but those correlations were very specific and when applied to different cases they gave very high errors and were limited to relating the dynamic Young’ modulus with the log data. The objective of this paper is to develop an accurate and robust correlation for static Young’s modulus to be estimated directly from log data without the need for core measurements. Multiple regression analysis was performed on actual core and log data using 600 data points to develop the new correlations. The static Young’s modulus was found to be a strong function on three log parameters, namely compressional transit time, shear transit time, and bulk density. The new correlation was tested for different cases with different lithology such as calcite, dolomite, and sandstone. It gave good match to the measured data in the laboratory which indicates the accuracy and robustness of this correlation. In addition, it outperformed all correlations from the literature in predicting the static Young’s modulus. It will also help in saving time as well as cost because only the available log data are used in the prediction.