gebhart/patrepeval huggingface dataset:
The Role of Platelet‐Derived RANTES in Large Vessel Dysfunction Associated with Acute Hypercholesterolemia (2007)

Hypercholesterolemia, a risk factor for the development of atherosclerosis, elicits inflammation and endothelial cell dysfunction in large arteries. Multiple blood cell populations have been implicated in the development of lesions, but it remains unclear what mediators and cytokines are involved in disease pathogenesis. Although the cytokine, RANTES, has been implicated in acute HC-induced vascular disease, its role still remains unclear. Our hypothesis is that platelet derived-RANTES contributes to large vessel dysfunction in the setting of acute hypercholesterolemia. Wire myography was employed to assess endothelial-independent and endothelial-dependent vasomotor responses of aortic rings in four groups of mice: wild-type mice (WT) on a normal diet (ND), WT mice on a high cholesterol diet for 2 weeks (HC), RANTES-deficient mice (RANTES−/−) on HC, and RANTES−/− →WT-HC chimera mice. Endothelium-independent contraction to phenylephrine did not differ between the groups. Aortic rings from each group also exhibited similar endothelial-independent dilation responses to sodium nitroprusside. In contrast, HC led to an impaired endothelium-dependent vasodilation response to acetylcholine in WT mice. This hypercholesterolemia-induced dysfunction was absent in the RANTES−/− group on HC and the RANTES−/− →WT-HC chimera group. These findings appear to indicate that platelet derived-RANTES contributes to hypercholesterolemia-induced vascular dysfunction in large arteries long before the development of atherosclerotic plaques. (Supported by R01 HL26441)
The Influence of Compressibility on the Aerodynamics of an Inverted Wing in Ground Effect (2011)

For inverted wings in close ground proximity, such as race car configurations, the aerodynamic ground effect can produce local velocities significantly greater than the freestream and the effects of compressibility may occur sooner than would be expected for a wing that is not close to a ground plane. A three-dimensional computational fluid dynamics study was conducted, involving a modified NASA GA(W)-2 LS [1]-0413 MOD inverted wing with an endplate, to investigate the onset and significance of compressibility for low subsonic Mach numbers. With the wing angle of incidence fixed, Mach numbers from 0.088 to 0.4 were investigated, at ground clearances ranging from infinite (free flight) to a height-to-chord clearance of 0.067. The freestream Mach number at which flow compressibility significantly affects the predicted aerodynamic coefficients was identified to be as low as 0.15. Beyond this point, as the compressible flow conditions around the wing result in changed pressure distribution and separation behavior, treating the flow as incompressible becomes inappropriate and leads to consistent underprediction of lift and drag. The influence on primary vortex behavior of density changes around the wing was found to be relatively inconsequential even at the higher end of the Mach scale investigated. By a freestream Mach number of 0.4 and at low clearances, local supersonic flow regions were established close to the suction peak of the lower wing surface in compressible simulations; the formation of a normal shock wave between the wing and the ground was shown to result in significant increases in separation and therefore overall drag, as well as a distinct loss of downforce.
Static and Dynamic Disorder in Formamidinium Lead Bromide Single Crystals (2023)

We show that formamidinium-based crystals are distinct from methylammonium-based halide perovskite crystals because their inorganic sublattice exhibits intrinsic local static disorder that coexists with a well-defined average crystal structure. Our study combines terahertz-range Raman scattering with single-crystal X-ray diffraction and first-principles calculations to probe the evolution of inorganic sublattice dynamics with temperature in the range of 10-300 K. The temperature evolution of the Raman spectra shows that low-temperature, local static disorder strongly affects the crystal structural dynamics and phase transitions at higher temperatures.
Imaging of human tooth enamel using ultrasound (2003)

This paper reports the results of a complete circumferential scan of a human tooth and its underlying dentino-enamel junction using ultrasound at frequencies in the 10-MHz range. The imagery shows clearly a two-dimensional contour of the dentinoenamel junction with a depth and lateral resolution of approximately 100 microm and 750 microm, respectively. The resulting sonograph is compared with an optical micrograph of the same tooth to verify the accuracy of the ultrasonic technique. The results are a significant step toward the biolocation of submillimeter size features within the tooth volume.
A General Framework of Mechatronic Modular Architecture (2013)

The independent designs guided by domain technologies of mechatronic system lead to the problem of hard compatibility and the difficulty to reuse resources between the systems. This paper presents an approach based on the reuse for modular mechatronic system, and a general framework for modular mechatronic system is designed. After the analysis of related characteristics of the mechatronic system, the modular principle of mechatronic system is proposed. Secondly, a general framework (F-Model) based on reusability of software and hardware in mechatronic system is developed. Following is to elaborate in details on the parts of software, hardware, and infrastructure of mechatronic system. Finally, 6-DOF industrial robot arm and medical accompany robot are taken as our experiment platform to design system based on F-Model. Results in practical application confirm the value of F-Model for reusing modules in designing mechatronic systems.
Effect of Storage Temperature on Cultured Epidermal Cell Sheets Stored in Xenobiotic-Free Medium (2014)

Cultured epidermal cell sheets (CECS) are used in regenerative medicine in patients with burns, and have potential to treat limbal stem cell deficiency (LSCD), as demonstrated in animal models. Despite widespread use, short-term storage options for CECS are limited. Advantages of storage include: flexibility in scheduling surgery, reserve sheets for repeat operations, more opportunity for quality control, and improved transportation to allow wider distribution. Studies on storage of CECS have thus far focused on cryopreservation, whereas refrigeration is a convenient method commonly used for whole skin graft storage in burns clinics. It has been shown that preservation of viable cells using these methods is variable. This study evaluated the effect of different temperatures spanning 4°C to 37°C, on the cell viability, morphology, proliferation and metabolic status of CECS stored over a two week period in a xenobiotic-free system. Compared to non-stored control, best cell viability was obtained at 24°C (95.2±9.9%); reduced cell viability, at approximately 60%, was demonstrated at several of the temperatures (12°C, 28°C, 32°C and 37°C). Metabolic activity was significantly higher between 24°C and 37°C, where glucose, lactate, lactate/glucose ratios, and oxygen tension indicated increased activation of the glycolytic pathway under aerobic conditions. Preservation of morphology as shown by phase contrast and scanning electron micrographs was best at 12°C and 16°C. PCNA immunocytochemistry indicated that only 12°C and 20°C allowed maintenance of proliferative function at a similar level to non-stored control. In conclusion, results indicate that 12°C and 24°C merit further investigation as the prospective optimum temperature for short-term storage of cultured epidermal cell sheets.
Are seeds suitable for flow cytometric estimation of plant genome size? (2005)

The genome size of species that do not contain compounds that influence fluorochrome accessibility appears to be the same when estimated using specific seed tissues and young leaves. Seeds can be more suitable than leaves, especially for species containing staining inhibitors in the leaf cytosol. Thus, use of seeds for FCM nuclear DNA content estimation is recommended, although for some species a specific seed tissue (usually the radicle) should be used. Protocols for preparation of samples from endospermic and endospermless seeds have been developed.
Introduction to Nonlinear Science (1995)

The aim of this book is to develop a unified approach to nonlinear science, which does justice to its multiple facets and to the diversity and richness of the concepts and tools developed in this field over the years. Nonlinear science emerged in its present form following a series of closely related and decisive analytic, numerical and experimental developments that took place over the past three decades. It appeals to an extremely large variety of subject areas, but, at the same time, introduces into science a new way of thinking based on a subtle interplay between qualitative and quantitative techniques, topological and metric considerations and deterministic and statistical views. Special effort has been made throughout the book to illustrate both the development of the subject and the mathematical techniques, by reference to simple models. Each chapter concludes with a set of problems. This book will be of great value to graduate students in physics, applied mathematics, chemistry, engineering and biology taking courses in nonlinear science and its applications.
Fatty acid accumulation in the yeast Sporidiobolus salmonicolor during batch production of γ-decalactone (2006)

This paper provides new information about the metabolism of various fatty acids and gamma-decalactone production by yeast. An analysis of the fatty acid composition of the yeast Sporidiobolus salmonicolor during batch production of lactone with ricinoleic acid methyl ester as a precursor showed an accumulation of the gamma-decalactone precursor inside the cells. Electron microscopy of the yeasts showed the presence of large internal inclusions leading to membrane and organelle lysis and, consequently, death of the yeast. S. salmonicolor cultivated with methyl oleate did not produce gamma-decalactone and is viable during the whole culture. Analysis of the long chain fatty acid fraction showed incorporation of methyl oleate.
64.3L: Late‐News Paper : Aerial Imaging by Retro‐Reflection (AIRR) (2013)

Abstract We propose a new method to realize aerial display that enables three‐dimensionally floating transparent signage without physical hardware on the sign position. The proposed aerial imaging method is based on retro‐reflection. An aerial image of the LED panel has been successfully formed with a mirror window and retro‐reflective material.
Immunologically unrelated Heliothis sp. and Spodoptera sp. midgut membrane‐proteins bind Bacillus thuringiensis CryIA(b) δ‐endotoxin (1993)

The Bacillus thuringiensis toxins, CryIA(a), CryIA(b), CryIA(c) and CryIC were used in a ligand-blot assay to detect specific toxin-binding proteins in the brush-border membranes of Heliothis virescens, Helicoverpa zea, Spodoptera littoralis, Spodoptera exigua and Spodoptera litura. While CryIA(a) and CryIA(b) always recognize the same protein(s) in a given species, CryIA(c) and CryIC were found to bind to other proteins. Polyclonal antibodies directed against the CryIA(b) binding protein of H. virescens and polyclonal anti-idiotype antibodies recognizing some determinants of the CryIA(b)-binding protein involved in the interaction with the toxin, were used to analyse immunological relationships among the toxin-binding proteins. The results showed that the 170-kDa toxin-binding proteins from the H. virescens and H. zea are immunologically related. However, the toxin-binding proteins from the Spodoptera species did not cross-react with either type of antibodies. Therefore, we conclude that the CryIA(b) toxin has different binding determinants on the toxin molecules itself which can interact with specific binding sites on the toxin-binding proteins from Heliothis sp. and Spodoptera sp.
Novel approach of power electronics for efficient DC fast charging systems (2018)

Increasing sales of electric vehicles demand a comprehensive density of car charging infrastructure. Therefore, market analysts predict that the worldwide car charger market will grow at a CAGR of 33.61% during the period 2018-2023. High Power DC chargers provide up to 350kW and allow charging the EV battery within 5 minutes, which is a prerequisite for long-distance travel and hence required for consumer acceptance and wide-reach EV adoption. Cost and reliability will become major drivers for the EV charging hardware and require special attention. This paper describes a novel approach, which addresses needs on competitive cost, efficiency and availability to fulfil market demand. The presented 50kW power cell has an input rectifier with phase factor correction to rectify and boost the AC voltage and a DC/DC converter with galvanic isolation for safety. The cell runs with optimal performance at 40 kHz switching frequency using standard 650V IGBTs. The modular approach allows installing the 50kW power cell in chargers with 50kW as well as 350kW due to easy paralleling. This paper describes the challenges to power electronics, the different possible approaches and a new way of a highly performant power electronics for an efficient DC fast charging solution. Simulation of the final topology will be presented.
Gene Fitness Landscapes of Vibrio cholerae at Important Stages of Its Life Cycle (2013)

Vibrio cholerae has evolved to adeptly transition between the human small intestine and aquatic environments, leading to water-borne spread and transmission of the lethal diarrheal disease cholera. Using a host model that mimics the pathology of human cholera, we applied high density transposon mutagenesis combined with massively parallel sequencing (Tn-seq) to determine the fitness contribution of >90% of all non-essential genes of V. cholerae both during host infection and dissemination. Targeted mutagenesis and validation of 35 genes confirmed our results for the selective conditions with a total false positive rate of 4%. We identified 165 genes never before implicated for roles in dissemination that reside within pathways controlling many metabolic, catabolic and protective processes, from which a central role for glycogen metabolism was revealed. We additionally identified 76 new pathogenicity factors and 414 putatively essential genes for V. cholerae growth. Our results provide a comprehensive framework for understanding the biology of V. cholerae as it colonizes the small intestine, elicits profuse secretory diarrhea, and disseminates into the aquatic environment.
Evidence of Antibodies to Spotted Fever Group Rickettsiae in Small Mammals and Quail from Mississippi (2012)

Rickettsia parkeri is a recently recognized human pathogen primarily associated with the Gulf Coast tick Amblyomma maculatum, with immature stages of this tick reported from wild vertebrates. To better understand the role of vertebrates in the natural history of this bacterium, we evaluated small mammals and ground-dwelling birds for evidence of infection with R. parkeri or exposure to the organism. We sampled small mammals (n=39) and passerines (n=47) in both north-central and southeast Mississippi, while northern bobwhite (Colinus virginianus) samples (n=31) were obtained from farms in central Mississippi. Blood from all sampled animals was tested using polymerase chain reaction (PCR) for spotted fever group rickettsiae (SFGR), and for antibodies to SFGR using R. parkeri antigen. Ectoparasite samples were removed from animals and included mites, lice, fleas, and immature ticks. Of 39 small mammal samples collected, 7 were positive for antibodies to SFGR; none tested positive by PCR for DNA of SFGR. Of 47 passerine blood samples collected, none were positive for DNA of SFGR by PCR, nor did any show serological evidence of exposure. Finally, none of 31 northern bobwhite samples tested were positive for SFGR DNA, while 7 were seropositive for rickettsial antibodies. Detection of seropositive rodents and quail suggests a role for these host species in the natural history of SFGR, possibly including R. parkeri, but the extent of their role has not yet been elucidated.
Application of Bioaffinity Mass Spectrometry for Analysis of Ligands (2005)

Bioaffinity mass spectrometry is a novel technology for analysis of binding proteins and their ligands. In this review, we introduce the concepts and principles of bioaffinity surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS). Various preactivated chip types and several approaches for binding of ligands or their binders to the chips are discussed. We also provide specific examples for the use of this technology for screening antibodies, analyzing ligands, glycoconjugates, protein-protein inter-actions, and DNA (RNA) binding proteins. In pursuit of developing new tests or studies of mechanism of drug action in therapeutic drug monitoring practice, this technology may provide a more rapid approach for ligand-binder studies.
Anatomical Brain Barriers to Cancer Spread: Segmentation from CT and MR Images (2020)

This is the challenge design document for the "Anatomical Brain Barriers to Cancer Spread: Segmentation from CT and MR Images" Challenge, accepted for MICCAI 2020. The goal of this challenge is to identify best methods to segment brain structures that serve as barriers to cancer spread, for use in computer assisted target definition for radiotherapy plan optimization. Target delineation is a major task in the radiotherapy workflow since it influences the overall outcome of the treatment. Accurate delineation of structures for treatment planning is associated with better local tumor control and reduced radiation dose to non-target tissues leading to improved therapeutic index. Accuracy can be improved through automation of target definition by identifying natural anatomical barriers to tumor spread. The barriers are brain structures that are not routinely outlined during the treatment planning for radiotherapy plan optimization. Advanced expertise and time is required to identify anatomy on computed tomography images used for treatment planning. Automation of the barrier delineation will make the treatment planning workflow more efficient leading to improved scheduling and potentially increasing the size of patient panels. With improving precision of radiation dose delivery and increasing number of patients treated in the<br> cancer centers worldwide, algorithmic assistance for the target definition is becoming a necessity. Creating standardized definition of the target and normal anatomy will also create an excellent educational resource for clinicians working at centers with low patient volume, and for medical residents. Segmentation of the brain structures is a challenging task as different structures can be appreciated more or less favorably on different imaging modalities. For example, the skull is typically segmented using a CT image, whereas falx cerebri is better seen on an MR T1-weighted image. Furthermore, as multi-modality images are usually acquired at different time points they could present with subtle differences even for brain imaging. This presents a unique technological challenge as information from multi-modality imaging is used by the radiation oncologist to define the clinical target volume for each individual patient's disease. The proposed challenge will provide participants with 60 cases, each consisting of a planning CT scan and two MR scans (post-contrast T1-weighted and T2-weighted FLAIR volumes) with 12 normal structures previously contoured using co-registered CT and MR at a single institution using an imaging protocol defined for glioma radiotherapy treatment planning. This dataset is valuable to the medical imaging and radiation oncology communities as it could advance algorithm development for automated segmentation of these structures, which in turn could be used for automated radiotherapy target definition.
A numerical study of the auto-ignited laminar lifted methane/hydrogen mixtures in heated co-flow air (2017)

In the present study, the liftoff characteristics of a laminar HCNG flame are investigated using 2-D numerical simulations by varying the fuel jet velocity. It is observed that the liftoff height decreases with increasing fuel jet velocity. Gradual transition from the tribrachial flame to the MILD combustion is also observed. From both Da analysis and transport budget analysis, it is verified that auto-ignition is the main stabilization mechanism of the lifted flame. Additional simulations are carried out with modified hydrogen diffusivity, showing that the decrease of liftoff height is mainly attributed to the high diffusivity of hydrogen molecule. Preferential diffusion effect of hydrogen is clarified by revising the ignition delay time term in the liftoff height relation. It is also shown that the revised ignition delay time increases as the fuel jet velocity decreases since hydrogen ratio RH decreases at the upstream of flame front with decreasing fuel jet velocity. The high diffusive nature of hydrogen molecule increases the ignition delay time at lower fuel jet velocity, which, in turn, leads to the increase of the liftoff height.
DNA damage response (DDR) variants and effects on the tumor transcriptome and microenvironment in east Asian (EA) prostate cancers (PCa). (2023)

75 Background: Aberrations of the DDR pathway have been shown to be prognostic of survival and predictive of PARP inhibition in PCa. We have previously reported on the prevalence of germline DDR mutations based on a 32-gene set in localized PCa in EA men, and observed comparable rates with that of White men. Here, we performed additional analyses investigating for associations between DDR variants to the somatic transcriptome of localized PCa. Methods: We utilized a prospectively recruited cohort of 172 EA patients, with centrally assessed Gleason’s score (GS) by an expert pathologist. Germline profiling was performed by whole exome sequencing (100X) using the Illumina Novaseq (CA). Joint genotyping was performed to annotate variants that were deemed to be pathogenic (P)/likely pathogenic (LP)/conflict of interest pathogenic (CIP) based on the CADD and REVEL scores. Tumor transcriptome was profiled using the Decipher Genomic Classifier (GC, Veracyte, CA) based on the Affymetrix ST array (ThermoFisher, CA). Results: Among the subset of 172 EA men, we observed DDR variants in 26 (15%) patients, which was comparable to the larger cohort of 890 men from the same institution. Among the DDR mutations, 2 (7.7%) were classified as P/LP, while 24 (92.3%) were CIP. Decipher GC scores were comparable between patients with and without DDR mutations (median GC score 0.87 vs 0.53, Mann-Whitney U P=0.10). For luminal-basal subtyping by either the PAM50 and Prostate specific subtyping models, we did not observe a difference for the basal (P=0.48) and luminal subtypes (P=0.21). Interestingly, DNA repair gene-set expression were comparable between patients with DDR mutations versus those without (median score -0.2 vs -0.17). However, we observed microenvironment differences for immune-related genes, where patients harboring DDR mutations manifested a less immune-suppressive environment versus those without (PDL2: -0.15 vs 0.2; Treg: 0.09 vs 0.13; MDSC: 0.03 vs 0.07, respectively). Conclusions: Herein, we report an extension of our previous work (Lua, et al. ASCO GU, 2023), where we show potential linkages between the germline DDR variant status and the tumor transcriptome. Our findings suggest the influence of germline DDR variants that extends beyond tumorigenesis.
Properdin has an ascendancy over factor H regulation in complement-mediated renal tubular damage (2014)

In the pathogenesis of renal tubular damage, P can directly bind to PTECs and may accelerate AP activation by surpassing fH regulation.