gebhart/patrepeval huggingface dataset:
Fragmentation trees for the structural characterisation of metabolites (2012)

Metabolite identification plays a crucial role in the interpretation of metabolomics research results. Due to its sensitivity and widespread implementation, a favourite analytical method used in metabolomics is electrospray mass spectrometry. In this paper, we demonstrate our results in attempting to incorporate the potentials of multistage mass spectrometry into the metabolite identification routine. New software tools were developed and implemented which facilitate the analysis of multistage mass spectra and allow for efficient removal of spectral artefacts. The pre-processed fragmentation patterns are saved as fragmentation trees. Fragmentation trees are characteristic of molecular structure. We demonstrate the reproducibility and robustness of the acquisition of such trees on a model compound. The specificity of fragmentation trees allows for distinguishing structural isomers, as shown on a pair of isomeric prostaglandins. This approach to the analysis of the multistage mass spectral characterisation of compounds is an important step towards formulating a generic metabolite identification method.
ANX7 as a Bio‐Marker in Prostate and Breast Cancer Progression (2001)

The ANX7 gene codes for a Ca2+-activated GTPase, which has been implicated in both exocytotic secretion in cells and control of growth. In this review, we summarize information regarding increased tumor frequency in the Anx7 knockout mice, ANX7 growth suppression of human cancer cell lines, and ANX7 expression in human tumor tissue micro-arrays. The loss of ANX7 is significant in metastatic and hormone refractory prostate cancer compared to benign prostatic hyperplasia. In addition, ANX7 expression has prognostic value for predicting survival of breast cancer patients.
Antifungal hydrogels (2007)

Fungi are increasingly identified as major pathogens in bloodstream infections, often involving indwelling devices. Materials with antifungal properties may provide an important deterrent to these infections. Here we describe amphogel, a dextran-based hydrogel into which amphotericin B is adsorbed. Amphogel kills fungi within 2 h of contact and can be reused for at least 53 days without losing its effectiveness against Candida albicans. The antifungal material is biocompatible in vivo and does not cause hemolysis in human blood. Amphogel inoculated with C. albicans and implanted in mice prevents fungal infection. Amphogel also mitigates fungal biofilm formation. An antifungal matrix with these properties could be used to coat a variety of medical devices such as catheters as well as industrial surfaces.
Human Tracking and Vital Sign Monitoring with a Switched Phased-Array Self-Injection-Locked Radar (2020)

This paper presents a switched phased-array (SPA) radar that uses self-injection-locking (SIL) and digital beamforming (DBF) technologies to provide high sensitivity of vital sign detection and accurate azimuthal tracking of a mobile person. Advantageously, the complexity of RF transmission and reception in the proposed SPA radar is very low compared to the conventional phased array radar. In the experiment, a prototype SPA-SIL radar was implemented to operate in the 2.4 GHz ISM band. This radar can automatically track the azimuth angle of a subject and successfully detect his vital signs over a wide azimuth and distance range,
Laparoscopic Excision of Suspected Extra-Adrenal Pheochromocytoma Located in the Mesenteric Root (2002)

A 35-year-old woman presented with symptoms consistent with pheochromocytoma. Biochemical evaluation was equivocal. An MRI scan demonstrated an extra-adrenal high-intensity lesion on a T2-weighted sequence, which supported the suspicion of an extra-adrenal pheochromocytoma. Laparoscopically discovered to be located in the root of the small bowel mesentery, the 5-cm mass was excised along with a segment of small bowel. Pathology examination demonstrated fibromatosis, a benign lesion.
PEGylated Liposomes Accumulate in the Areas Relevant to Skin Toxicities via Passive Extravasation across “Leaky” Endothelium (2022)

PEGylated liposome is the cornerstone platform for modern drug delivery. Unfortunately, as exemplified by PEGylated liposomal doxorubicin (aka Doxil), altered doxorubicin pharmacokinetics causes off-target accumulation in the skin, including the palms and feet, leading to severe dose-limiting toxicity. In addition to Doxil, other nanoparticles and PEGylated liposomes exhibit significant deposition in the skin, but mechanisms of accumulation are poorly understood. Using <i>ex vivo</i> imaging and <i>ex vivo</i> confocal microscopy, we show that PEGylated liposomes in mice accumulate predominantly in the areas subject to mechanical stress/pressure. Blood vessels in foot skin appear to be especially leaky, exhibiting burst-like extravasations. Using high-resolution confocal microscopy and liposomes labeled with different dyes in the membrane and/or interior, two modes of extravasation were observed: (1) as intact liposomes; (2) as separated liposomal components. On the other hand, stable cross-linked iron oxide nanoworms extravasated only as intact nanoparticles. There was no colocalization between liposomes and exosomal marker CD81, excluding the role of exocytosis. Also, <i>in situ</i> perfusion of formalin-fixed foot skin with labeled liposomes revealed that the extravasation is mediated by passive, energy-independent diffusion and not by leukocyte "hitchhiking". These findings improve our understanding of extravasation pathways of nanocarriers in the areas relevant to skin pathologies and could lead to strategies to prevent and treat liposome-induced skin toxicities.
A search for new anti-herpes virus compounds. (1987)

This study reports on the synthesis and the activity of a series of new compounds of nucleoside-type structure. They are characterized for being differently substituted in the aromatic ring of the base (deazoadenosine derivatives) or by bearing a dansyl group in the sugar moiety (dansylthymidine). One molecule belonging to this latter class of compounds (the 3'-0-dansylthymidine) is showing an anti-herpesvirus potential while being active in inhibiting the virus-encoded enzyme thymidine kinase. This finding may represent an important step for the synthesis of new enzyme inhibitors and it is discussed in terms of future developments of more active congeners.
Der Einfluss rekonstruktionsbedingter Bewegungsartefakte auf den koronaren Kalziumscore bei der Mehrschicht-Spiral-CT (2001)

The influence of motion artifacts conditioned by reconstruction, on the coronary calcium score in multislice spiral CT.A major problem of the quantification of coronary calcifications is a high variability of the coronary calcium score between recurrent examinations and different observers. Aim of our study is to evaluate the influence of different RR-intervals on the coronary calcium score utilizing retrospectively gated Multislice Spiral CT (MSCT) data sets.50 consecutive patients underwent MSCT examination (Somatom Volume Zoom, Siemens, Forchheim, G) utilizing a standardized scan protocol (4 x 2.5 mm collimation, 3 mm increment, tube current 133 mAs, tube voltage 120 kV). Retrospectively gated image reconstruction was performed every 10 % of the RR interval. Coronary calcification was evaluated by the Agatston score. Coronary risk assessment was performed in all patients with image reconstruction beginning at 80 % of the RR interval. The reconstruction intervals with the least motion artifacts were identified and chosen as reference for a reevaluation of the coronary risk. The results of different reconstruction times were compared.The mean calcium score was 551.6. The calcium score varied between 512.2 (90 %) and 571.7 (70 %), depending on the image reconstruction interval. Compared to the mean calcium score a new classification of the coronary risk was necessary in 7/50 of the patients at 80 % reconstruction interval, and in 2/50 of the patients at 50 % of the RR interval, respectively.Movement of the coronary arteries at different image reconstruction intervals has an important influence on the coronary calcium score. Based on our data, we propose image reconstruction at 50 % of the RR interval for evaluation of the coronary calcium score by MSCT.
Field-Deployable, High-Resolution, Time-of-Flight Aerosol Mass Spectrometer (2006)

The development of a new high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is reported. The high-resolution capabilities of this instrument allow the direct separation of most ions from inorganic and organic species at the same nominal m/z, the quantification of several types of organic fragments (CxHy, CxHyOz, CxHyNp, CxHyOzNp), and the direct identification of organic nitrogen and organosulfur content. This real-time instrument is field-deployable, and its high time resolution (0.5 Hz has been demonstrated) makes it well-suited for studies in which time resolution is critical, such as aircraft studies. The instrument has two ion optical modes: a single-reflection configuration offers higher sensitivity and lower resolving power (up to approximately 2100 at m/z 200), and a two-reflectron configuration yields higher resolving power (up to approximately 4300 at m/z 200) with lower sensitivity. The instrument also allows the determination of the size distributions of all ions. One-minute detection limits for submicrometer aerosol are <0.04 microg m(-3) for all species in the high-sensitivity mode and <0.4 microg m(-3) in the high-resolution mode. Examples of ambient aerosol data are presented from the SOAR-1 study in Riverside, CA, in which the spectra of ambient organic species are dominated by CxHy and CxHyOz fragments, and different organic and inorganic fragments at the same nominal m/z show different size distributions. Data are also presented from the MIRAGE C-130 aircraft study near Mexico City, showing high correlation with independent measurements of surrogate aerosol mass concentration.
Viscoelasticity Imaging of Biological Tissues and Single Cells Using Shear Wave Propagation (2021)

Changes in biomechanical properties of biological soft tissues are often associated with physiological dysfunctions. Since biological soft tissues are hydrated, viscoelasticity is likely suitable to represent its solid-like behavior using elasticity and fluid-like behavior using viscosity. Shear wave elastography is a non-invasive imaging technology invented for clinical applications that has shown promise to characterize various tissue viscoelasticity. It is based on measuring and analyzing velocities and attenuations of propagated shear waves. In this review, principles and technical developments of shear wave elastography for viscoelasticity characterization from organ to cellular levels are presented, and different imaging modalities used to track shear wave propagation are described. At a macroscopic scale, techniques for inducing shear waves using an external mechanical vibration, an acoustic radiation pressure or a Lorentz force are reviewed along with imaging approaches proposed to track shear wave propagation, namely ultrasound, magnetic resonance, optical, and photoacoustic means. Then, approaches for theoretical modeling and tracking of shear waves are detailed. Following it, some examples of applications to characterize the viscoelasticity of various organs are given. At a microscopic scale, a novel cellular shear wave elastography method using an external vibration and optical microscopy is illustrated. Finally, current limitations and future directions in shear wave elastography are presented.
Mechanism of Decomposition of Surface Ethoxy Species to Ethene and Acidic OH Groups on H-ZSM-5 (2015)

The reaction mechanism of the decomposition of ethoxy species to ethene and acidic OH groups on H-ZSM-5 was studied by IR spectroscopy using isotope-labeled ethanol. The concerted mechanism occurring on both the ethoxy (acid) site and the counterpart lattice oxygen was suggested by GC-MS analysis of evolved d2-ethene and IR observation of the recovery of OH s groups on acid sites from the decomposition of CH3CD2O- ethoxy species. The concerted mechanism was further confirmed by the estimation of activation energy for decomposition of CH3CH2O-, CH3CD2O-, and CD3CD2O- ethoxy species, 122 ± 3, 125 ± 3, and 140 ± 5 kJ mol(-1), respectively, where the kinetic isotope effect was observed for the cleavage of the CH or CD bond of the methyl group of the ethoxy species.
Signal Enhancement in a Nonlinear Transfer Characteristic (1998)

We study nonlinear behavior in a model of a periodically modulated, overdamped rf SQUID loop operating in the dispersive (i.e., nonhysteretic) mode. In the presence of correlated noise we find an enhancement of the output signal-to-noise ratio (SNR) as a function of the nonlinearity parameter of the device. The calculation involves knowledge only of the input-output transfer characteristic of the device. These signal enhancement properties appear to be generic to devices characterized by nonlinear transfer characteristics. We also use our transfer characteristic approach to explain recent experimental results showing SNR enhancement in dc SQUIDs as a function of dc bias current and flux.
NKG2D ligands are expressed on stressed human airway epithelial cells (2006)

Immune surveillance of the airways is critical to maintain the integrity and health of the lung. We have identified a family of ligands expressed on the surface of stressed airway epithelial cells whose function is to bind the NKG2D-activating receptor found on several pulmonary lymphocytes, including natural killer cells, gammadelta(+) T cells, and CD8(+) T cells. We employed real-time PCR and flow cytometry in normal and transformed airway epithelial cell to demonstrate that major histocompatibility complex class I chain-related (MIC) B and the UL-16 binding protein (ULBP) ligands (ULBP1-4) are ubiquitously expressed at the mRNA level in all cell lines. MICA/B surface expression was present on 70% of transformed cell lines but was undetectable on primary cells. We demonstrate that MICA/B and ULBP 1, 2, 3, and 4 expression is rare or absent on the cell surface of unstimulated normal human bronchial epithelial cells although transcripts and intracellular proteins are present. Normal human bronchial epithelial cells exposed to 0.3 mM hydrogen peroxide exhibit an induction of all ligands examined on the cell surface. Surface expression is independent of changes in transcript level or total cellular protein and is mediated by the ERK family of mitogen-activated protein kinases. The induction of NKG2D ligands on stressed airway epithelial cells represents a potentially important mechanism of immune cell activation in regulation of pulmonary health and disease.
Panorama of boron nitride nanostructures via lamp ablation (2018)

A diverse range of remarkable boron nitride (BN) nanostructures subsuming nano-horns, nano-rods, nano-platelets, and clusters of hollow nanospheres (nano-onions, arguably of greatest applied and fundamental interest) have been produced exclusively from crystalline BN precursor powder via lamp ablation. The procedure is safe, devoid of toxic reagents, simple, rapid and scalable—generating some genres of nanoparticles that had previously proved elusive. Product structure and composition were unambiguously assessed by high-resolution transmission electron microscopy, energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy.
Techniques for the decoding of low density parity check codes: efficient simulation, algorithm improvement and implementation (2007)

After the introduction of iterative coding, Low Density Parity Check (LDPC) codes have received a lot of attention due to their remarkable near Shannon-limit performance and practical decoder implementation. However, when employing an LDPC code for various applications, multiple issues do arise at the simulation, algorithm and implementation levels. The first issue is the performance evaluation of the iterative LDPC decoder in the very low Bit Error Rate (BER) regions. So far, no analytical tool has been developed to evaluate the performance of LDPC codes. Unfortunately standard Monte Carlo (MC) simulations cannot be used for performance estimation in these low BER regions due to prohibitive execution times. The second issue is the efficiency of the decoding algorithm. Due to the presence of short cycles in the bipartite graph, sum-product decoding algorithms lead to considerable performance loss for short block-length LDPC codes and produce error floors for longer codes. In addition, the iterative processing and estimation of soft probabilistic values with these algorithms result in very high computational complexity, which in turn impedes the adoption of LDPC codes for power constrained systems. Another prime objective is to design a high throughput decoder architecture which is capable of supporting multiple rates and variable code lengths within minimal area. 
This work aims to address and provide solutions to the above problems. As a solution to the performance estimation problem of LDPC codes, a highly efficient and novel fast BER simulation technique is developed. At the algorithm level, a performance improvement and error floor avoidance method is introduced, and a computationally efficient algorithm is developed for the sum-product decoding of LDPC codes. And finally, at the architecture level, a high throughput multi-rate variable code length implementation is presented which, when implemented, efficiently minimizes device resources while alleviating the routing complexity of the decoder.
Pharmacokinetics of oligodeoxynucleotides encapsulated in liposomes: effect of lipid composition and preparation method (1999)

1. The effect of the method employed to prepare liposomes and their lipid composition were evaluated in terms of the encapsulation efficiency and pharmacokinetic features of two oligodeoxynucleotides of a 21 mer: the normal (N-Odn) and the phosphorothioate (S-Odn) oligodeoxynucleotide. 2. Liposomes were prepared by the classical method of multilamellar vesicles (MV) and by the dehydration-rehydration method (DR). Two lipid mixtures were used to prepare liposomes--the predominant lipid being phosphatidylcholine (PC) and sphingomyelin (SM) respectively. 3. The DR method for liposome preparation provided the highest encapsulation efficiency, regardless of liposome lipid composition and the type of oligodeoxynucleotide involved (N-Odn or S-Odn). 4. The pharmacokinetics of free and liposome encapsulated oligodeoxynucleotides was studied in mouse following i.v. administration. Liposome encapsulated oligodeoxynucleotides exhibited a significantly lower plasma clearance and longer half-life and residence time than free oligodeoxynucleotides. The method used to obtain the liposomes affected plasma clearance, which was lower for liposomes elaborated by the DR method than for liposomes prepared with the MV method. The use of S-Odn in place of N-Odn decreased the plasma clearance of oligodeoxynucleotide when administered encapsulated in liposomes, regardless of the lipid composition and method used to obtain the liposomes.
Magic-Factor 1, a Partial Agonist of Met, Induces Muscle Hypertrophy by Protecting Myogenic Progenitors from Apoptosis (2008)

Because of these features Magic-F1 represents a novel molecular tool to counteract muscle wasting in major muscular diseases such as cachexia or muscular dystrophy.
ChemInform Abstract: Potential Antitumor Agents. Part 61. Structure‐Activity Relationships for in vivo Colon 38 Activity Among Disubstituted 9‐Oxo‐9H‐xanthene‐4‐ acetic Acids. (1991)

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.
A real options framework for space mission design (2005)

A real options framework for use in space mission design is presented. Such a framework has potential application in architecting flexibility in certain mission designs with the objective of maximizing mission utility. It integrates economic principles of cost, return, risk, flexibility, and other concepts from Black-Scholes option pricing theory and the multiplicative binomial process. Options pricing theory provides an objective method for valuing flexibility in making future investment decisions based on new information becoming available; such flexibility may have great value in certain risky ventures. This flexibility in the future may or may not exist without additional investment. The development of investment strategies to create flexibility must include answering the question ''how much can be invested to create the desired flexibility?'' The answer must include a priori estimation of the value that the flexibility provides; in this application the real options framework becomes a powerful tool. The utility of this tool is demonstrated through conceptual examples; these examples also illustrate some limitations of the method. This work is by no means a comprehensive study. At best it attempts to demonstrate that there are techniques and ways of thinking - frameworks - that offer benefits for the complex process of mission design for an uncertain and often risky future.
Experimental Comparison of RF Waveform Designs for Wireless Power Transmission (2021)

The possibility to harvest energy from ambient radio-frequency (RF) sources has intrigued humankind for the past several decades. In this context, there has been a tremendously growing research interest in the field of wireless power transfer (WPT) using the RF range of the electromagnetic (EM) spectrum. In this paper, we experimentally investigate the aspect of real-time energy harvesting (EH) via different types of waveform designs such as orthogonal frequency division multiplexing (OFDM), square, triangular, sinusoidal, and sawtooth. We make use of a Software Defined Radio (SDR) and a Powercast P21XXCSR-EVB EH module to carry out the experiments on the practical device to assess performance. Specifically, we are interested in obtaining insights based on the comparison between the aforementioned waveform designs from the perspectives of the separation distance between the USRP and P21XXCSR-EVB EH module, and power emission via USRP. In this vein, some additional experiments are subsequently performed after a suitable candidate waveform has been reported. The demonstration of the EH is provided in terms of the abovementioned investigation metrics while seeking the best waveform to support WPT.