gebhart/patrepeval huggingface dataset:
Growth of microvessels in serum-free matrix culture of rat aorta. A quantitative assay of angiogenesis in vitro. (1990)

We report here that rings of rat aorta embedded in gels of fibrin or collagen and cultured in MCDB 131, an optimized growth medium for microvascular endothelial cells, generate branching microvessels in the absence of serum or other soluble protein supplements. The angiogenic response is self-limited and can be quantitated by counting the newly formed microvessels daily in the living cultures. The microvascular growth curves are characteristic for each gel. Growth of microvessels in collagen gel peaks at the end of the 1st week and is followed by a rapid regression in the 2nd week. Fibrin gels, as compared with collagen, stimulate angiogenesis by 170%, support growth during the 2nd week, and protect the newly formed microvessels from early regression. Angiogenesis is inhibited by adding hydrocortisone to the culture medium. Conversely, a 230% stimulation of angiogenesis is obtained when aortic rings are cultured in collagen gels floating in serum-free medium conditioned by sarcoma 180 cells. Our results demonstrate that: (a) angiogenesis can be obtained reproducibly in serum-free culture; (b) serum-free culture is a sensitive method for testing the inhibitory or stimulatory effects of soluble or matrix factors on angiogenesis; (c) the aortic ring model can be used as a quantitative assay for the study of angiogenesis under chemically defined culture conditions.
Comparative quantitative fatty acid analysis of triacylglycerols using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and gas chromatography (2001)

Quantitative analyses of fatty acids from five triacylglycerol products, coconut oil, palm kernel oil, palm oil, lard and cocoa butter, were carried out using two analytical methods: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and gas chromatography (GC), in an effort to validate the application of MALDI-TOFMS in quantitative fatty acid analysis. For the GC analysis, transmethylated products were used, whereas, for the MALDI-TOF analysis, saponified products were used. Under MALDI-TOF conditions, the acids were detected as sodiated sodium carboxylates [RCOONa + Na]+ consistent with the mode of ionization that was previously reported. Thus, the MALDI-TOF mass spectrum of saponified coconut oil showed the presence of sodiated sodium salts of caprylic acid (7.5 ± 0.67, m/z 189), capric acid (6.9 ± 0.83, m/z 217), lauric acid (47.8 ± 0.67, m/z 245), myristic acid (20.4 ± 0.51, m/z 273), palmitic acid (9.8 ± 0.47, m/z 301), linoleic acid (0.9 ± 0.07, m/z 325), oleic acid (4.8 ± 0.42, m/z 327) and stearic acid (2.0 ± 0.13, m/z 329). Saponified palm kernel oil had a fatty acid profile that included caprylic acid (3.5 ± 0.59), capric acid (4.7 ± 0.82), lauric acid (58.6 ± 2.3), myristic acid (20.9 ± 1.5), palmitic acid (7.2 ± 1.1), oleic acid (3.8 ± 0.62) and stearic acid (1.2 ± 0.15). Saponified palm oil gave myristic acid (0.83 ± 0.18), palmitic acid (55.8 ± 1.7), linoleic acid (4.2 ± 0.51), oleic acid (34.5 ± 1.5), stearic acid (3.8 ± 0.26) and arachidic acid (0.80 ± 0.22). Saponified lard showed the presence of myristic acid (1.5 ± 0.24), palmitic acid (28.9 ± 1.3), linoleic acid (13.7 ± 0.67), oleic acid (38.7 ± 1.4), stearic acid (12.8 ± 0.64) and arachidic acid (2.4 ± 0.35). Finally, for saponified cocoa butter, the fatty acid distribution was: palmitic acid (32.3 ± 1.0), linoleic acid (2.6 ± 0.35), oleic acid (34.9 ± 1.7) and stearic acid (30.3 ± 1.6). Quantitative gas chromatographic analysis of the corresponding methyl esters from these triacylglycerol products yielded data that were mostly in agreement with the MALDI-TOFMS data. The MALDI-TOF experiment, however, proved to be superior to the GC experiment, particularly with regard to baseline resolution of unsaturated acids. Furthermore, the ability of MALDI-TOFMS to detect low concentrations of fatty acids rendered it more sensitive than the GC methodology. Copyright © 2001 John Wiley & Sons, Ltd.
Alteration of homeobox gene expression by N-ras transformation of PA-1 human teratocarcinoma cells. (1991)

We used a series of cell clones from a human teratocarcinoma cell line, PA-1, to study the effect of transformation by an activated N-ras oncogene on the expression of genes involved in retinoic acid (RA)-induced differentiation and growth regulation. Recently, it has been shown that expression of human HOX 2 genes is sequentially activated by RA beginning from Hox 2.9 at the 3' end of the HOX 2 cluster (A. Simeone, D. Acampora, L. Arcioni, P. W. Andrews, E. Boncinelli, and F. Mavilio, Nature [London] 346:763-766, 1990). We now report that six different genes of the cluster HOX 1 are sequentially induced by RA in a similar temporal pattern, beginning with genes at the 3' end of the cluster. However, in N-ras-transformed cell clones, RA-induced expression of these homeobox genes is delayed. Hox 1.4 and Hox 1.3, genes abundantly induced in nontransformed clones after 3 days of RA treatment, are expressed in N-ras-transformed cells only after 10 days of RA treatment. At this time, the cells' growth is arrested at very high density, and no differentiated morphologic characteristics are observed. Constitutive expression of a transfected Hox 1.4 gene under the control of a simian virus 40 promotor leads to differentiated cell morphology similar to that of the RA-induced phenotype and restores the growth-inhibitory effects of RA in N-ras-transformed cells. These observations provide evidence that enhanced proliferation in N-ras-transformed cells compromises teratocarcinoma cell differentiation by a mechanism that transiently suppresses homeobox gene induction and implies a central role for homeobox genes in RA-induced cell differentiation. We conclude that stimulation of a putative growth factor signal pathway, associated with ras-induced proliferation, transiently suppresses the induction of transcription factors functionally involved in cell growth and differentiation.
PHOTON COUNTING SPECTRAL ANALYZING SYSTEM OF EXTRA‐WEAK CHEMI‐ AND BIOLUMINESCENCE FOR BIOCHEMICAL APPLICATIONS (1979)

Abstract— The systematic study of the method for measuring the spectral distribution of extra‐weak light signals, such as from biochemical systems and living tissues involving chemi‐ and bio‐energized processes, led to the design and construction of a new type of spectrometer, called the filter spectral analyzer system, incorporated with the high‐sensitivity photon counting technique. Experimental tests to examine the operational characteristics of this filter spectral analyzer system and comparisons of the signal‐to‐noise ratio with a conventional grating spectrometer were made by accomplishing the spectral analysis of low‐level light sources. The measurement of the spectra of very weak chemilumines‐cence accompanying various kinds of chemical and biological processes, including autoxidation and enzymatic reaction were performed successfully.
Focused ultrasound disruption of the blood-brain barrier: a new frontier for therapeutic delivery in molecular neurooncology (2011)

Recent advances in molecular neurooncology provide unique opportunities for targeted molecular-based therapies. However, the blood-brain barrier (BBB) remains a major limitation to the delivery of tumor-specific therapies directed against aberrant signaling pathways in brain tumors. Given the dismal prognosis of patients with malignant brain tumors, novel strategies that overcome the intrinsic limitations of the BBB are therefore highly desirable. Focused ultrasound BBB disruption is emerging as a novel strategy for enhanced delivery of therapeutic agents into the brain via focal, reversible, and safe BBB disruption. This review examines the potential role and implications of focused ultrasound in molecular neurooncology.
Plasma membrane structure and remodelling during sperm maturation in the epididymis. (1998)

All mammalian spermatozoa are surrounded by a limiting plasma membrane that mediates many of the early events during fertilization. The membrane is derived originally from spermatogonia/spermatocytes in the testis but is then modified considerably during spermiogenesis, epididymal maturation and capacitation. It is characterized by an unusually high proportion of polyunsaturated phospholipids that give it special physical characteristics and compartmentalization of many of its component proteins and lipids into discrete domains on the head and tail. During passage of spermatozoa through the epididymis remodelling of the plasma membrane is commensurate with acquisition of motility and fertilizing capacity. Remodelling processes include uptake of secreted epididymal glycoproteins, removal or utilization of specific phospholipids from the inner leaflet of the bilayer, processing of existing or acquired glycoproteins by endoproteolysis and re-positioning of both protein and lipid components to different membrane domains. These modifications are carefully coordinated at different zones of the epididymis and indirectly affect intracellular membranes, organelles and even nucleoprotein. Maturation changes are described and appraised within the context of current concepts of membrane structure and fertilization.
Development of a transformation and selection system for the glycolipid‐producing yeast Candida bombicola (2008)

Sophorolipids are surface-active compounds synthesized by the non-pathogenic yeast Candida bombicola. Over recent decades much effort has been spent to optimize culture conditions in order to improve the yield and production process. As far as we know, however, hardly any attention has been given to the genetics of the producing yeast strain itself and there are no published results available on the genetic engineering of C. bombicola. Nevertheless, this can be a useful tool for the study of the sophorolipid synthesis pathway and open up perspectives for improved production. A first step is the development of a suitable transformation and selection method. This article describes the creation and selection of an uracil auxotrophic C. bombicola mutant, which can be transformed back to prototrophy with the species' own orotidine 5'-phosphate decarboxylase or URA3 gene. Successful transformation was confirmed by a PCR-based method discriminating between the wild-type and mutated URA3 gene.
Point mutations confer loss of ATP‐induced human P2X7 receptor function (2002)

Residues considered essential for ATP binding to the human P2X(7) receptor (hP2X(7)R) were investigated. HEK293 cells or Xenopus oocytes were transfected with wild-type or site-directed mutants of hP2X(7)R constructs and channel/pore activity measured in the presence of ATP or 2',3'-O-(4-benzoylbenzoyl)-ATP (BzATP). Barium uptake and ethidium influx into HEK293 cells were abolished in cells expressing K193A and K311A mutants, and were partially reduced in cells expressing mutant P210A. K193A and K311A mutations also completely abolished responses to ATP and BzATP in Xenopus oocytes as measured by electrophysiology. These results indicate that K193 and K311 are essential residues in ATP binding in the hP2X(7)R.
The cyclophilin inhibitor Debio-025 shows potent anti–hepatitis C effect in patients coinfected with hepatitis C and human immunodeficiency virus (2008)

Debio-025 induced a strong drop in CypB levels, coinciding with the decrease in hepatitis C viral load. These are the first preliminary human data supporting the hypothesis that CypB may play an important role in hepatitis C virus replication and that Cyp inhibition is a valid target for the development of anti-hepatitis C drugs.
Speaker adaptation from a speaker-independent training corpus (2002)

A technique for using the speech of multiple reference speakers as a basis for speaker adaptation in large-vocabulary continuous-speech recognition is introduced. In contrast to other methods that use a pooled reference model, this technique normalizes the training speech from multiple reference speakers to a single common feature space before pooling it. The normalized and pooled speech is then treated as if it came from a single reference speaker for training the reference hidden Markov model (HMM). The usual probabilistic spectrum transformation can be applied to the reference HMM to model a new speaker. Preliminary experimental results are reported from applying this approach to over 100 reference speakers from the speaker-independent portion of the DARPA 1000-Word Resource Management Database.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fabrication of 1 ㎛ Thickness Lead Zirconium Titanate Films Using Poly(N-vinylpyrrolidone) Added Sol-gel Method (2011)

Lead zirconate titanate (PZT) films were fabricated on Pt/Ti/<TEX>$SiO_2$</TEX>/Si substrate by the sol-gel method using a sol containing poly(N-vinylpyrrolidone) (PVP). PVP in alkoxide solutions can suppress the condensation reaction in gel films during heat treatment, and increase the viscosity of alkoxide solutions. Single-phase PZT films as thick as 1 <TEX>${\mu}m$</TEX> were deposited by repetitive coating with successive third-step heat treatments at 150<TEX>$^{\circ}C$</TEX>, 350<TEX>$^{\circ}C$</TEX> and 650<TEX>$^{\circ}C$</TEX>. After heat treatment, the films were crack free, and optically transparent. As a result, we demonstrated a PZT film with a PVP molar ratio of 0.5, which has a permittivity of 734, a dielectric loss of 0.042, a <TEX>$P_r$</TEX> of 40.5 <TEX>${\mu}C/cm^2$</TEX> and an <TEX>$E_c$</TEX> of 156 kV/cm.
Delays in the administration of antibiotics are associated with mortality from adult acute bacterial meningitis (2005)

There is an independent incremental association between delays in administrating antibiotics and mortality from adult acute bacterial meningitis. Inappropriate diagnostic-treatment sequences were significant predictors of such treatment delays.
A 2.5 V 333 Mb/s/pin 1 Gb double data rate SDRAM (2003)

While on-chip data flight times approach a few tens of nanoseconds for gigabit-scale DRAMs, a bandwidth over 250 MHz requires data input and output timing accuracy within 0.3 ns. Although a high-speed data interface can be achieved using precise clock generators such as delay locked loop (DLL), skews due to a long data access path may cause loss of internal timing margins. Diminished timing margin may be detrimental to wave pipelining for high-bandwidth. This 1 Gb double data rate (DDR) SDRAM featuring ODIC chip with nonODIC package (OCNOP), cycle-time-adaptive wave pipelining (CTAWP), and variable stage analog DLL achieves high performance despite stringent processing variations in 0.14 /spl mu/m design rules.
Development of a vascular niche platform for expansion of repopulating human cord blood stem and progenitor cells (2012)

Transplantation of ex vivo expanded human umbilical cord blood cells (hCB) only partially enhances the hematopoietic recovery after myelosuppressive therapy. Incubation of hCB with optimal combinations of cytokines and niche cells, such as endothelial cells (ECs), could augment the efficiency of hCB expansion. We have devised an approach to cultivate primary human ECs (hECs) in serum-free culture conditions. We demonstrate that coculture of CD34(+) hCB in direct cellular contact with hECs and minimal concentrations of thrombopoietin/Kit-ligand/Flt3-ligand resulted in a 400-fold expansion of total hematopoietic cells, 150-fold expansion of CD45(+)CD34(+) progenitor cells, and 23-fold expansion of CD45(+) Lin(-)CD34(hi+)CD45RA(-)CD49f(+) stem and progenitor cells over a 12-day period. Compared with cytokines alone, coculture of hCB with hECs permitted greater expansion of cells capable of multilineage engraftment and serial transplantation, hallmarks of long-term repopulating hematopoietic stem cells. Therefore, hECs establish a cellular platform for expansion of hematopoietic stem and progenitor cells and treatment of hematologic disorders.
The Arabidopsis Transcription Factor MYB12 Is a Flavonol-Specific Regulator of Phenylpropanoid Biosynthesis (2005)

Comprehensive functional data on plant R2R3-MYB transcription factors is still scarce compared to the manifold of their occurrence. Here, we identified the Arabidopsis (Arabidopsis thaliana) R2R3-MYB transcription factor MYB12 as a flavonol-specific activator of flavonoid biosynthesis. Transient expression in Arabidopsis protoplasts revealed a high degree of functional similarity between MYB12 and the structurally closely related factor P from maize (Zea mays). Both displayed similar target gene specificity, and both activated target gene promoters only in the presence of a functional MYB recognition element. The genes encoding the flavonoid biosynthesis enzymes chalcone synthase, chalcone flavanone isomerase, flavanone 3-hydroxylase, and flavonol synthase were identified as target genes. Hence, our observations further add to the general notion of a close relationship between structure and function of R2R3-MYB factors. High-performance liquid chromatography analyses of myb12 mutant plants and MYB12 overexpression plants demonstrate a tight linkage between the expression level of functional MYB12 and the flavonol content of young seedlings. Quantitative real time reverse transcription-PCR using these mutant plants showed MYB12 to be a transcriptional regulator of CHALCONE SYNTHASE and FLAVONOL SYNTHASE in planta, the gene products of which are indispensable for the biosynthesis of flavonols.
Identification of fluorescent beads using a coded aperture snapshot spectral imager (2010)

We apply a coded aperture snapshot spectral imager (CASSI) to fluorescence microscopy. CASSI records a two-dimensional (2D) spectrally filtered projection of a three-dimensional (3D) spectral data cube. We minimize a convex quadratic function with total variation (TV) constraints for data cube estimation from the 2D snapshot. We adapt the TV minimization algorithm for direct fluorescent bead identification from CASSI measurements by combining a priori knowledge of the spectra associated with each bead type. Our proposed method creates a 2D bead identity image. Simulated fluorescence CASSI measurements are used to evaluate the behavior of the algorithm. We also record real CASSI measurements of a ten bead type fluorescence scene and create a 2D bead identity map. A baseline image from filtered-array imaging system verifies CASSI's 2D bead identity map.
Fe65, a Ligand of the Alzheimer's β-Amyloid Precursor Protein, Blocks Cell Cycle Progression by Down-regulating Thymidylate Synthase Expression (2002)

The functions of the Alzheimer's beta-amyloid precursor protein (APP) and of its complex with the adaptor protein Fe65 are still unknown. We have demonstrated that Fe65 is also a nuclear protein and APP functions as an extranuclear anchor, thus preventing Fe65 nuclear translocation. According to this finding, it was also demonstrated that Fe65 could play a role in the regulation of transcription. In the present paper we show that the overexpression of Fe65 prevents G(1) --> S cell cycle progression of serum-stimulated fibroblasts and that the contemporary overexpression of APP abolishes this effect of Fe65. The overexpression of Fe65 completely abolishes the activation of a key S phase gene, the thymidylate synthase (TS) gene, driven by the transcription factor LSF/CP2/LBP1 (LSF). This phenomenon is observed only in experimental conditions leading to the accumulation of Fe65 in the nucleus. Similarly, the two other members of the Fe65 protein family, Fe65L1 and Fe65L2, have been found to translocate into the nucleus and to prevent the activation of the TS gene promoter induced by LSF. Two results support the hypothesis that the inhibitory effect of Fe65 on cell cycle progression in fibroblasts is the result of the inhibition of TS gene expression: (i) Fe65 overexpression, but not Fe65 and APP co-expression, prevents the accumulation of endogenous TS upon the exposure of cells to serum, and (ii) thymidine addition to the culture medium completely overcomes the growth arrest caused by Fe65. In neuronal PC12 cells, the overexpression of Fe65 or of Fe65L1 and Fe65L2 blocks cell cycle, as observed in fibroblasts, but thymidine supplementation to culture medium does not revert this block, thus suggesting that Fe65 proteins induce in neuronal cells a gene expression program different from that activated in fibroblasts.
Kinetics and Specificity of a H+/Amino Acid Transporter from Arabidopsis thaliana (1996)

The amino acid transporter AAP1/NAT2 recently cloned from Arabidopsis thaliana was expressed in Xenopus oocytes, and we used electrophysiological, radiotracer flux, and electron microscopic methods to characterize the biophysical properties, kinetics, and specificity of the transporter. Uptake of alanine was H(+)-dependent increasing from 14 pmol/oocyte/h at 0.032 microM H+ to 370 pmol/oocyte/h at 10 microM H+. AAP1 was electrogenic; there was an amino acid-induced depolarization of the oocyte plasma membrane and net inward currents through the transporter due to the transport of amino acids favoring neutral amino acids with shortside chains. The maximal current (imax) for alanine, proline, glutamine, histidine, and glutamate was voltage and [H+]o-dependent. Similarly, the imaxH was voltage and [amino acid]o-dependent. The imax for both H+ and amino acid were dependent on the concentrations of their respective cosubstrates, suggesting that both ligands bind randomly to the transporter. The K0.5 of the transporter for amino acids decreased as [H+]o increased and was lower at negative membrane potentials. The K0.5 for H+ was relatively voltage-independent and decreased as [amino acid]o increased. This positive cooperativity suggests that the transporter operates via a simultaneous mechanism. The Hill coefficients n for amino acids and H+ were > 1, suggesting that the transporter has more than one binding site for both H+ and amino acid. Freeze-fracture electron microscopy was used to estimate the number of transporters expressed in the plasma membrane of oocytes. The density of particles on the protoplasmic face of the plasma membrane of oocytes expressing AAP1 increased approximately 5-fold above water-injected controls and corresponded to a turnover number 350 to 800 s-1.
QoS guarantees for multimedia services on a TDMA-based satellite network (1997)

This article describes a proposed network architecture for both the ground and space segments of a satellite network supporting multimedia services with quality of service (QoS) guarantees. The space segment proposal is geared toward a TDMA-based satellite network comprising many nongeostationary satellites, while the ground segment proposal does not put any restriction an the satellite network. The ground segment proposal is based on the new ATM adaptation layer 2 (AAL2) which we consider to have a major role to play in offering an efficient way to provide multimedia services over ATM networks. Indeed, it allows easy encapsulation of the complete set of media component sessions which forms a multimedia transaction into a single ATM virtual channel connection. An additional advantage of AAL2 is that it can run over any arbitrary slotted access system independent of the ATM format (i.e., without transporting the ATM cell headers). This is important for efficient interfacing of the ground and space segments. The space segment proposal aims at providing a robust, easily managed and controlled architecture to guarantee QoS by using a combination of connectionless and connection-oriented techniques. This is achieved by: defining a fixed logical network architecture (i.e., independent of the motion of the satellites); limiting the functionality of the switches in the sky; and using adequate addressing and routing procedures.