gebhart/patrepeval huggingface dataset:
Integrin binding specificity regulates biomaterial surface chemistry effects on cell differentiation (2005)

Biomaterial surface chemistry has profound consequences on cellular and host responses, but the underlying molecular mechanisms remain poorly understood. Using self-assembled monolayers as model biomaterial surfaces presenting well defined chemistries, we demonstrate that surface chemistry modulates osteoblastic differentiation and matrix mineralization independently from alterations in cell proliferation. Surfaces were precoated with equal densities of fibronectin (FN), and surface chemistry modulated FN structure to alter integrin adhesion receptor binding. OH- and NH(2)-terminated surfaces up-regulated osteoblast-specific gene expression, alkaline phosphatase enzymatic activity, and matrix mineralization compared with surfaces presenting COOH and CH(3) groups. These surface chemistry-dependent differences in cell differentiation were controlled by binding of specific integrins to adsorbed FN. Function-perturbing antibodies against the central cell binding domain of FN completely inhibited matrix mineralization. Furthermore, blocking antibodies against beta(1) integrin inhibited matrix mineralization on the OH and NH(2) surfaces, whereas function-perturbing antibodies specific for beta(3) integrin increased mineralization on the COOH substrate. These results establish surface-dependent differences in integrin binding as a mechanism regulating differential cellular responses to biomaterial surfaces. This mechanism could be exploited to engineer materials that control integrin binding specificity to elicit desired cellular activities to enhance the integration of biomaterials and improve the performance of biotechnological culture supports.
Self-actuating biosensor using a piezoelectric cantilever and its optimization (2006)

This paper presents a self-actuating biosensor based on the piezoelectric cantilever optimized by Taguchi method for the label-free detection of specific biomoleculars. Until now, even though the optimisation of the cantilever-based biosensors have been performed by changing dimensions one by one, few researches have performed the geometric optimisation considering the overall configuration of the piezoelectric cantilever. This paper suggests a method of optimising the piezoelectric cantilever by the Taguchi method. The first resonance frequency, the separation factor, and the sensing signal of the piezoelectric cantilever were selected as the object functions. The resonator driving circuit will keep the cantilever resonance on the binding of the antigen with antibody. By real-time monitoring of the resonance frequency shift by the frequency sensing circuit, the effects of the protein binding on the change of the cantilever stiffness and mass will be investigated.
Hdr Cfa Image Rendering (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
Multimodality Therapy for Large and Giant Intracavernous Internal Carotid Artery Aneurysms (2008)

Most patients with intracavernous large and giant aneurysms show cranial nerve signs, and a variety of surgical treatments have been developed. From the viewpoint of multimodality therapy, a combination of bypass and IC ligation or a combination of intravascular therapy and surgery has been performed. We studied 29 consecutive patients with intracavernous large and giant aneurysms during the past 15 years. All the patients presented with cranial nerve signs. Therapeutic modalities for each patient were selected depending on anatomical features of the aneurysm on radiological examinations and neurological/hemodynamic conditions during balloon test occlusion (BTO). ICAs were occluded surgically or endovascularly in 6 patients without bypass surgery. ICA ligation was simultaneously combined with high-flow bypass in 4 patients or with STA-MCA anastomosis in 14 patients, in which 2 patients developed delayed ischemic neurological symptoms due to emboli from the thrombosed aneurysms. STA-MCA anastomosis followed by internal coil trapping of the aneurysm under antiplatelet and anticoagulant therapy was successfully performed in 2 recent patients. Pre-operative neurological symptoms ameliorated when treatment was initiated within 3 months after the onset of symptoms. Favorable clinical outcomes can be expected for patients with an intracavernous large or giant ICA aneurysm treated surgically or endovascularly based on adequate pre-operative radiological, neurological and hemodynamic evaluations. The treatment algorithm for the management of intracavernous large or giant aneurysms of ICA should be reviewed and revised according to the development of new devices and techniques.
Flexible functional split in 5G networks (2017)

5G networks are expected to support various applications with diverse requirements in terms of latency, data rates and traffic volume. Cloud-RAN and densely deployed small cells are two of the tools at disposal of Mobile Network Operators to cope with such challenges. In order to mitigate the fronthaul requirements imposed by the Cloud-RAN architecture, several functional splits, each characterized by a different demarcation point between the centralized and the distributed units, have emerged. However, the selection of the appropriate centralization level (i.e., the functional split) still remains a challenging task, since a number of parameters have to be considered in order to make such a decision. In this paper, a virtual network embedding (VNE) algorithm is proposed to flexibly select the appropriate functional split. The VNE is formulated as an Integer Linear Programming problem whose objective is to minimize the intercell interference and the fronthaul bandwidth utilization by dynamically selecting the appropriate functional split. Finally, a scalable VNE heuristic is also proposed.
Characteristics of the Membrane Permeability of Temperature-Sensitive Liposome (1991)

Abstract The relationship between the temperature-sensitivity of the release of an entrapped drug from liposome as well as the type of drug or liposome is discussed. The drug release from DPPC liposome (dipalmitoylphosphatidylcholine liposome) has been confirmed to increase abruptly near its phase-transition temperature for both low-molecular-weight compouds (such as calcein) and high-molecular-weight compounds (such as dextran). The amount of temperature-sensitive calcein released from the liposomes was dependent on the method of liposome preparation: that is, the release from REV (reverse phase evaporated vesicle) was the highest; next was that from LUV (large unilamellar vesicle prepered by detergent removal method), and lowest was from SUV (small unilamellar vesicle prepared by an ultrasonication method). In order to examine the size effect of liposomes on temperature-sensitive drug release, REV was fractionated into three groups according to their average sizes and calcein release for each group was investigated. The temperature at which calcein release showed a maximum was almost the same in each of three groups; while as the average liposome size of a group was larger, the initial rate of calcein release became higher and the temperature at which calcein release began became lower. The amount of release of a entrapped drug was primarily dependent on the molecular weight of the drug, in spite of the variety of drugs investigated.
BIOCATALYTIC SYNTHESES OF AROMATICS FROM D-GLUCOSE: Renewable Microbial Sources of Aromatic Compounds (1995)

Chemistry is moving into a new era in which renewable resources and starting materials such as D-glucose will likely be prominent features of industrial chemical manufacture. The keys to this progress are the design, development, and use of microbial biocatalysts. Aromatic biosynthesis serves as a paradigm for how biocatalysts can be manipulated to achieve the yield, rate, and purity criteria central to chemical manufacture. A disproportionate amount of the metabolic carbon flow of the biocatalyst must first be directed into the common pathway of aromatic amino acid biosynthesis. This review describes ways of achieving this goal through the traditional strategy of manipulating the catalytic activity of the first enzyme in the common pathway, as well as the amelioration of limitations in the in vivo availability of common-pathway enzyme substrates. The inability of individual enzymes to convert their substrate to product fast enough to avoid substrate accumulation further impedes carbon flow through the common pathway. This review also discusses identification and removal of these rate-limiting enzymes. Finally, we examine the creation of heterologous biocatalysts and how biocatalysis could be integrated with traditional chemical transformations to expand the number of organic chemicals that can be synthesized from glucose.
Structured illumination microscopy artifacts caused by illumination scattering (2021)

Abstract Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artifacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index (RI) from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artifacts caused by scattering in thick samples.
Metabolic effects of propionate, hexanoate and propionylcarnitine in normoxia, ischaemia and reperfusion (1994)

It has been suggested that propionyl-L-carnitine administration to ischaemic hearts facilitates the restoration of cardiac function upon reperfusion, but it is still a matter of dispute whether its effect is conveyed via the metabolic effect of the propionyl moiety, the carnitine moiety or other mechanisms involving membrane receptor interactions. The metabolism of propionylcarnitine involves the formation of succinyl-CoA, which causes an increase in the total amount of tricarboxylic acid cycle intermediates. According to the current paradigm, anaplerosis ensures rapid restoration of tricarboxylic acid cycle activity during reperfusion. To evaluate the contribution of anaplerosis to the protective effect of propionylcarnitine during ischaemia and reperfusion, isolated rat hearts were perfused with Krebs-Henseleit bicarbonate buffer containing 5 mM glucose+insulin (12 IU per litre), to which 1 mM propionate, 0.8 mM hexanoate or 1 mM propionylcarnitine were added. Global 20 or 24 min no-flow ischaemia was followed by 10 min reperfusion. The flavoprotein redox state, myoglobin oxygenation, oxygen consumption and mechanical functioning of the heart were recorded and metabolites determined in freeze-trapped tissue. In parallel experiments, the cellular energy state was studied with phosphorus nuclear magnetic resonance spectrometry. The addition of 1 mM propionylcarnitine failed to cause an anaplerotic effect, but did bring about an oxidation of flavins, probably due to citrate synthase inhibition. Propionate showed similar but stronger effects and a marked anaplerosis, but still failed to improve the recovery of the heart upon reperfusion. The addition of hexanoate caused marked anaplerosis upon reperfusion and flavin reduction. The results failed to demonstrate that propionylcarnitine had any beneficial effect on the ischaemic myocardium.
Synthesis and Characterization of Fatty Acid Methyl Ester by In-Situ Transesterification in Capparis Deciduas Seed (2008)

(FAME) Fatty acid methyl ester is made virgin or used vegetable oils (both edible and non-edible) and animal fats. Fatty acid methyl ester operates in compression ignition engines like petro-diesel. Fatty acid methyl ester can be blended in any ratio with petroleum diesel fuels. It can be stored just like the petroleum diesel fuel. Petrodiesel can be replaced by biodiesel due to its superiority. It has various advantages. The seeds of Capparis deciduas are found to contain non-edible oil in the range of about 63.75 %. The percentage of biodiesel yield increases with concentration of KOH as a catalyst. The aim of this article is to demonstrate the cost effective new source of energy by single step reaction i.e. production of oil by combining extraction and reaction of extract with the mixture of alcohols. In this article the effect of catalyst concentration, time, water content and temperature on in-situ transesterification is studied to obtain optimum yield and Fatty acid methyl ester (Biodiesel) Fuel characterization tests show the striking similarity of various physical & chemical properties and campers to ASTM standards.
The Effect of Reduced Barometric Pressure on Fracture Healing in Rats (1967)

Fracture healing in a series of fractures of the fibula in Fischer rats was studied at a simulated altitude of 18,000 feet in both acclimatized and unacclimatized animals. The acclimatized animals healed their fractures as well as control animals did, but there was significant retardation of fracture healing in the unacclimatized animals, up to thirty and forty days.
On fast Construction of SAH-based Bounding Volume Hierarchies (2007)

With ray <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">traversal</i> performance reaching the point where real-time ray tracing becomes practical, ray tracing research is now shifting away from faster traversal, and towards the question what has to be done to use it in truly interactive applications such as games. Such applications are problematic because when geometry changes every frame, the ray tracer's internal index data structures are no longer valid. Fully rebuilding all data structures every frame is the most general approach to handling changing geometry, but was long considered impractical except for grid-based grid based ray tracers, trivial scenes, or reduced quality of the index structure. In this paper, we investigate how some of the fast, approximate construction techniques that have recently been proposed for kd-trees can also be applied to bounding volume hierarchies (BVHs). We argue that these work even better for BVHs than they do for kd-trees, and demonstrate that when using those techniques, BVHs can be rebuilt up to 10x faster than competing kd-tree based techniques.
The WUSCHEL gene promotes vegetative‐to‐embryonic transition in Arabidopsis (2002)

Formation of somatic embryos in plants is known to require high concentrations of auxin or 2,4-dichlorophenoxyacetic acid (2,4-D), which presumably acts to trigger a signalling cascade. However, very little is known about the molecular mechanism that mediates the vegetative-to-embryogenic transition. We have employed a genetic approach to dissect the signal transduction pathway during somatic embryogenesis. In a functional screen using a chemical-inducible activation-tagging system, we identified two alleles of Arabidopsis gene PGA6 whose induced overexpression caused high-frequency somatic embryo formation in all tissues and organs tested, without any external plant hormones. Upon inducer withdrawal, all these somatic embryos were able to germinate directly, without any further treatment, and to develop into fertile adult plants. PGA6 was found to be identical to WUSCHEL (WUS), a homeodomain protein previously shown to be involved in specifying stem cell fate in shoot and floral meristems. Transgenic plants carrying an estradiol-inducible XVE-WUS transgene can phenocopy pga6-1 and pga6-2. Our results suggest that WUS/PGA6 also plays a key role during embryogenesis, presumably by promoting the vegetative-to-embryogenic transition and/or maintaining the identity of the embryonic stem cells.
Superior efficacy of secreted over somatic antigen display in recombinant Salmonella vaccine induced protection against listeriosis. (1996)

Vaccination provides the most potent measure against infectious disease, and recombinant (r) viable vaccines expressing defined pathogen-derived antigens represent powerful candidates for future vaccination strategies. In a new approach we constructed r-aroA- Salmonella typhimurium displaying p60 or listeriolysin (Hly) antigen of Listeria monocytogenes in secreted or somatic form in the host cell. Vaccination of mice with r-aroA- S. typhimurium induced protection against the intracellular pathogen L. monocytogenes only with secreted and not with somatic antigen. Secreted Hly was slightly more potent in inducing protective immunity than secreted p60. Both r-aroA- S. typhimurium secreting p60 in the endosome and r-aroA- S. typhimurium secreting Hly in the cytosol induced protective CD4+ and CD8+ T-cells suggesting CD8+ T-cell stimulation independent from intracellular residence of r-aroA- S. typhimurium carriers. Hence, not only the type of antigen but also its display by the r-carrier within the host cell critically influences vaccine efficacy.
Efficient radiative recombination from ⟨112¯2⟩ -oriented InxGa1−xN multiple quantum wells fabricated by the regrowth technique (2004)

In x Ga 1 − x N multiple quantum wells (QWs) with [0001], ⟨112¯2⟩, and ⟨112¯0⟩ orientations have been fabricated by means of the regrowth technique on patterned GaN template with striped geometry, normal planes of which are (0001) and {112¯0}, on sapphire substrates. It was found that photoluminescence intensity of the {112¯2} QW is the strongest among the three QWs, and the internal quantum efficiency of the {112¯2} QW was estimated to be as large as about 40% at room temperature. The radiative recombination lifetime of the {112¯2} QW was about 0.38ns at low temperature, which was 3.8 times shorter than that of conventional [0001]-oriented InxGa1−xN QWs emitting at a similar wavelength of about 400nm. These findings strongly suggest the achievement of stronger oscillator strength owing to the suppression of piezoelectric fields.
Fibroblast growth factors as angiogenesis factors: New insights into their mechanism of action (1997)

Angiogenesis is critical for physiological processes such as embryonic development and wound repair (D’Amore and Thompson, 1987; Folkman and Shing, 1992). Angiogenesis also contributes to several pathologies either directly, as in diabetic retinopathy, or indirectly by supporting the growth of pathological tissues, as in rheumatoid arthritis and tumor growth (Folkman, 1995). During angiogenesis, new capillaries arise as sprouts from preexisting capillaries or post-capillary venules. This phenomenon is accomplished by a series of sequential steps. In the initial phase of capillary sprouting, the basement membrane of endothelial cells in the parent blood vessel is degraded. Degradation of the basement membrane is mediated by endothelial cell proteinases, most notably plasminogen activators (PAs) and a variety of matrix-degrading metalloproteinases (MMPs). Once the basement membrane is degraded, endothelial cells bud out from the preexisting vessel and migrate into the perivascular space. Cells at the base of the sprout proliferate and replace migrated cells. Initially, the tubes or cords contain no lumen; a new basement membrane is formed, and after two contiguous sprouts have fused to form a loop, a lumen forms and blood begins to flow (Ausprunk and Folkman, 1977).
The effect of fasting or desmopressin before treatment on the concentration of mitomycin C during intravesical administration (2000)

Unprepared patients produce variable and often substantial volumes of urine during intravesical chemotherapy. There was a significant reduction in urine output after fasting or by administering desmopressin before instillation. These measures increase the area under the concentration-time curve for mitomycin C and potentially increase the efficacy of treatment.
Signaling through JAK2‐STAT5 pathway is essential for IL‐3‐induced activation of microglia (2003)

Microglia, the resident macrophage of the brain, mediates immune and inflammatory responses in the central nervous system (CNS). Activation of microglia and secretion of inflammatory cytokines associate with the pathogenesis of CNS diseases, including multiple sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease, prion disease, and AIDS dementia. Microbial pathogens, cytokines, chemokines, and costimulatory molecules are potent inducers of microglial activation in the CNS. Signaling through its receptor, IL-3 induces the activation of JAK-STAT and MAP kinase pathways in microglial cells. In this study, we found that in vitro treatment of EOC-20 microglial cells with tyrphostin AG490 blocked IL-3-induced tyrosine phosphorylation of JAK2, STAT5A, and STAT5B signaling proteins. Stable transfection of EOC-20 cells with a dominant negative JAK2 mutant also blocked IL-3-induced tyrosine phosphorylation of JAK2, STAT5A, and STAT5B in microglia. The blockade of JAK2-STAT5 pathway resulted in a decrease in IL-3-induced proliferation and expression of CD40 and major histocompatibility complex class II molecules in microglia. These findings highlight the fact that JAK2-STAT5 signaling pathway plays a critical role in mediating IL-3-induced activation of microglia.
Focal accumulation of an apolipoprotein B-based synthetic oligopeptide in the healing rabbit arterial wall. (1990)

The functions of surface-accessible domains of apolipoprotein (apo) B, the protein moiety of low density lipoprotein (LDL), are unknown, aside from the LDL receptor-binding domain, which lies toward the carboxyl-terminal end of apoB. Since LDL accumulation in arterial lesions does not depend on recognition of LDLs by a cell-surface receptor, we synthesized an oligopeptide with the sequence of the trypsin-accessible domain of apoB that lies closest to the amino-terminal end of the protein and compared its biological activity to that of another synthetic oligopeptide with the sequence of the heparin- and apoB/apoE receptor-binding domains of apoE. (Tyrosine was added at the amino-terminal end of each peptide to facilitate radiolabeling.) The 18-amino acid apoB-based peptide included residues 1000-1016 of apoB, for which no function has been previously described. In radioautographs, the 125I-labeled peptide accumulated focally at the healing edges of regenerating endothelial islands in the balloon-catheter deendothelialized rabbit aorta. In contrast, the 21-residue apoE-based peptide, which included residues 129-148 of apoE, accumulated diffusely and uniformly throughout the deendothelialized areas of the aorta. The data show that focal binding of the apoB-based peptide can delineate arterial lesions and suggest that this arterial wall-binding domain of apoB mediates accumulation of LDLs in arterial lesions.