gebhart/patrepeval huggingface dataset:
Establishment of the Mesodermal Cell Line QCE-6 (1996)

The QCE-6 cell line was derived from precardiac mesoderm of the Japanese quail. As previously reported, these cells are able to differentiate into two distinct cardiac cell types with myocardial or endocardial endothelial cell properties. This present communication describes in detail the derivation of this cell line and further characterizes the nontreated and induced myocardial and endothelial phenotypes of these cells. The QCE-6 cells exhibit an epithelial morphology, as well as the pattern of protein expression, that is characteristic of precardiac mesoderm. Treatment with retinoic acid, basic fibroblast growth factor (bFGF), transforming growth factor (TGF)-beta 2, and TGF-beta 3 induces these cells to differentiate and produce mixed cultures of epithelial and mesenchymal cells. The epithelial cells express myosin, desmin, and cardiac troponin I in a punctate pattern throughout the cytoplasm. These sarcomeric proteins become organized in a premyofibrillar pattern when TGF-beta 1, platelet-derived growth factor (PDGF)-BB, and insulin-like growth factor (IGF) II are added in combination along with retinoic acid, bFGF, TGF-beta 2, and TGF-beta 3. Also, these treatments induce Na+,K(+)-ATPase expression. When the QCE-6 cells are cultured on collagen type I, the mesenchymal cells that are promoted by retinoic acid, bFGF, TGF-beta 2, and TGF-beta 3 will invade the gel. These mesenchymal cells are positive for QH1 and JB3, which are both markers for presumptive endocardial cells within the early cardiogenic mesoderm. The addition of both PDGF-BB and IGF II to QCE-6 cell cultures will inhibit the ability of retinoic acid, bFGF, TGF-beta 2, and TGF-beta 3 to induce both the mesenchymal morphology and QH1 and JB3 expression. Collectively, these results suggest that the proces of cardiac cell differentiation is regulated by multiple signals and that early cardiogenic mesoderm contains a bipotential stem cell that can give rise to both the myocardial and endocardial lineages. More important, since the QCE-6 cells are representative of early cardiogenic cells, this cell line offers a unique model system to study cardiac cell differentiation.
Ultrahigh resolution optical biopsy with endoscopic optical coherence tomography (2004)

Optical coherence tomography (OCT) is an emerging medical imaging technology that can generate high resolution, cross-sectional images of tissue in situ and in real time. Although endoscopic OCT has been used successfully to identify certain pathologies in the gastrointestinal tract, the resolution of current endoscopic OCT systems has been limited to 10-15 microm for in vivo studies. In this study, in vivo imaging of the rabbit gastrointestinal tract is demonstrated at a three-fold higher resolution (< 5 microm), using a broadband Cr(4+):Forsterite laser as the optical light source. Images acquired from the esophagus, trachea, and colon reveal high resolution details of tissue architecture. Definitive correlation of architectural features in OCT images and histological sections is shown. The ability of ultrahigh resolution endoscopic OCT to image tissue morphology at an unprecedented resolution in vivo advances the development of OCT as a potential imaging tool for the early detection of neoplastic changes in biological tissue.
Leucine catabolism during the differentiation of 3T3-L1 cells. Expression of a mitochondrial enzyme system. (1983)

Leucine can be utilized efficiently as a precursor for lipid biosynthesis by adipose tissue, especially in the presence of glucose or glucose and insulin. During the differentiation of 3T3-L1 fibroblasts to adipocytes, the rate of lipid biosynthesis from L-[U-14C]leucine increases at least 30-fold and lipogenesis, with [U-14C] acetate as the precursor, increases by 10- to 15-fold. The specific activities of two mitochondrial dehydrogenases in the leucine oxidative pathway, the branched chain alpha-ketoacid dehydrogenase and isovaleryl-CoA dehydrogenase, as well as of leucine:alpha-ketoglutarate transaminase, increase at least 20-fold during the adipose conversion. Isovaleryl-CoA dehydrogenase was assayed in crude extracts using a specific fluorimetric method employing electron transfer flavoprotein as the electron acceptor for the flavoprotein dehydrogenase. The specific activity of 3-hydroxy-3-methylglutaryl-CoA lyase, the mitochondrial enzyme catalyzing the terminal reaction in the leucine degradation pathway, increases 4-fold during differentiation. The increases in the specific activities of the mitochondrial enzymes occur without a change in the specific activity of cytochrome oxidase, indicating that the increases do not simply reflect proliferation of mitochondria. The biosynthesis of at least 20 soluble mitochondrial polypeptides is enhanced during the adipose conversion of the fibroblasts as determined by polyacrylamide gel electrophoresis following incubation of the cells with [35S] methionine. The results provide a conservative estimate of the extent of changes in mitochondrial soluble proteins during the adipose conversion. They also establish that differentiated 3T3-L1 adipocytes metabolize leucine like mature adipose tissue and illustrate the roles of the branched chain alpha-ketoacid dehydrogenase and isovaleryl-CoA dehydrogenase in lipogenesis.
Genistein, a dietary ingested isoflavonoid, inhibits cell proliferation and in vitro angiogenesis. (1995)

Consumption of a plant-based diet can prevent the development and progression of chronic diseases that are associated with extensive neovascularization. To determine whether prevention might be associated with dietary derived angiogenesis inhibitors, we have fractionated urine of healthy human subjects consuming a plant-based diet and examined the fractions for their abilities to inhibit the proliferation of vascular endothelial cells. One of the most potent fractions contained several isoflavonoids, which we identified by gas chromatography-mass spectrometry and subsequently synthesized. Of all synthetic compounds, the isoflavonoid genistein was the most potent and inhibited endothelial cell proliferation and in vitro angiogenesis at half maximal concentrations of 5 and 150 mumol/L, respectively. Moreover, genistein inhibited the proliferation of various tumor cells. Genistein excretion in urine of subjects consuming a plant-based diet is in the micromolar range, which is 30-fold higher than that of subjects consuming a traditional Western diet. The high concentrations of genistein in urine of vegetarians and our present results suggest that genistein may contribute to the preventive effect of plant-based diet on chronic diseases, including solid tumors, by inhibiting neovascularization and tumor cell proliferation. Thus genistein may have important applications in the treatment of solid tumors and angiogenic diseases.
Design and Testing of a New Injection Approach for Liquid Composite Molding (2004)

Resin Transfer Molding (RTM) is used to manufacture advanced fiber-reinforced composite parts. In this process, a fiber preform is placed into the mold cavity and sealed shut. Then, a liquid thermoset resin is injected into the mold through the injection gates and the gates are not closed until the resin arrives at the vent locations. One expects the resin to arrive last at the vents after having saturated the complete preform to obtain a successful part. However, the resin path to impregnate the preform is usually not repeatable due to the inherent nature of not being able to place the fiber preform exactly in the same location in the mold. A micron-size gap between the preform and the mold edge will introduce flow deviations and alter the flow pattern causing the resin to arrive prematurely at the vent locations. Thus, it is desirable to have multiple gate and vent locations, to aid in distributing the resin throughout the mold effectively and efficiently. In this paper, we present the design and validations of an automated RTM intelligent workstation. The workstation will have distributed injection gates and vents that will be triggered by the control methodology selected based on the on-line flow pattern of the resin during the impregnation process. Point sensors placed in the mold walls that will monitor the arrival of the resin will detect the on-line flow pattern. To automate and control the fluid flow during the RTM process it is also necessary to individually open or close various injection locations. A new method, which can deliver the resin to various locations within the mold, while still allowing any individual gate to be opened or closed at any time during the filling, was designed and tested. Development of such versatile injection scheme provides the potential to have better control on the distribution of the resin during impregnation and will lead to successful mold filling without any dry regions despite the presence of disturbances created by the quality and the placement of the perform.
Suppression by glutamate of proliferative activity through glutathione depletion mediated by the cystine/glutamate antiporter in mesenchymal C3H10T1/2 stem cells (2007)

Although previous studies including ours have demonstrated the functional expression of different glutamate (Glu) signaling machineries such as Glu receptors (GluRs) and transporters in osteoblasts and chondrocytes, little attention has been paid to the role of Glu in their ancestral mesenchymal stem cells to date. In the present study, we have evaluated the possible functionality of Glu in cultured mouse mesenchymal stem cell line C3H10T1/2 cells endowed to proliferate for the self-renewal and to differentiate toward osteoblast, chondrocyte, adipocyte, and myocyte lineages. Expression of mRNA was for the first time shown with the cystine/Glu antiporter composed of xCT and 4F2hc subunits, in addition to particular excitatory amino acid transporter (EAAT) isoforms and ionotropic GluRs, in undifferentiated C3H10T1/2 cells. Glu significantly suppressed the proliferation activity at a concentration over 500 microM without inducing cell death or differentiation, while the suppression occurred in a manner sensitive to the prevention by cystine and reduced glutathione (GSH), but not by EAAT inhibitors. A significant decrease was seen in intracellular GSH levels in C3H10T1/2 cells cultured with Glu, whereas the cellular proliferation activity was drastically decreased by the addition of the GSH depleter cyclohexene-1-one and the GSH biosynthesis inhibitor L-buthionine-[S,R]-sulfoximine, respectively. Transient overexpression of both xCT and 4F2hc subunits led to an increased basal proliferative activity in C3H10T1/2 cells. These results suggest that Glu could suppress the cellular proliferation toward self-renewal through a mechanism associated with the depletion of intracellular GSH after promoting the retrograde operation of the cystine/Glu antiporter in C3H10T1/2 cells.
Quantification of endothelial permeability, leakage space, and blood volume in brain tumors using combined T1 and T2* contrast-enhanced dynamic MR imaging (2000)

This study describes a method for imaging brain tumors that combines T1-weighted (T1W) and T2*-weighted (T2*W) dynamic contrast-enhanced acquisitions. Several technical improvements have been made to produce high-quality three-dimensional mapping of endothelial permeability surface area product (k) and leakage space (vl), based on T1W data. Tumor blood volume maps are obtained from T2*W images with a complete removal of residual relaxivity effects. The method was employed in 15 patients with brain tumors (5 gliomas, 5 meningioma, and 5 acoustic schwannoma). Mean values of vl were significantly greater in acoustic schwannomas (53% +/- 9%) than in meningiomas (34% +/- 7%) or gliomas (22% +/- 4%). Mean values of vl in meningioma were significantly greater than those of gliomas. Mean values of rCBV correlated closely with k. There was also a positive correlation between k and vl for pixels with low k values. This relationship was weaker in areas of high k. The highest mean ratios of k to vl (k(ep)) were seen in two patients with glioblastoma, one patient with transitional cell meningioma, and one patient with angioblastic meningioma. Pixel-by-pixel comparison showed a strong correlation between rCBV and k in 11 of 15 patients. However, decoupling between pixel-wise rCBV and k was found in four patients who had lesions with moderate k and vl elevation but no increase of rCBV. Results from this study suggest that in assessing the angiogenic activities in brain tumors it is advisable to monitor simultaneously changes in tumor blood volume, vessel permeability, and leakage space of tumor neovasculature.
Infection by verocytotoxin-producing Escherichia coli (1989)

Verocytotoxin (VT)-producing Escherichia coli (VTEC) are a newly recognized group of enteric pathogens which are increasingly being recognized as common causes of diarrhea in some geographic settings. Outbreak studies indicate that most patients with VTEC infection develop mild uncomplicated diarrhea. However, a significant risk of two serious and potentially life-threatening complications, hemorrhagic colitis and the hemolytic uremic syndrome, makes VTEC infection a public health problem of serious concern. The main reservoirs of VTEC appear to be the intestinal tracts of animals, and foods of animal (especially bovine) origin are probably the principal sources for human infection. The term VT refers to a family of subunit exotoxins with high biological activity. Individual VTEC strains elaborate one or both of at least two serologically distinct, bacteriophage-mediated VTs (VT1 and VT2) which are closely related to Shiga toxin and are thus also referred to as Shiga-like toxins. The holotoxins bind to cells, via their B subunits, to a specific receptor which is probably the glycolipid, globotriosyl ceramide (Gb3). Binding is followed by internalization of the A subunit, which, after it is proteolytically nicked and reduced to the A1 fragment, inhibits protein synthesis in mammalian cells by inactivating 60S ribosomal subunits through selective structural modification of 28S ribosomal ribonucleic acid. The mechanism of VTEC diarrhea is still controversial, and the relative roles of locally acting VT and "attaching and effacing adherence" of VTEC to the mucosa have yet to be resolved. There is increasing evidence that hemolytic uremic syndrome and possibly hemorrhagic colitis result from the systemic action of VT on vascular endothelial cells. The role of antitoxic immunity in preventing the systemic complications of VTEC infection is being explored. Antibiotics appear to be contraindicated in the treatment of VTEC infection. The most common VTEC serotype associated with human disease is O157:H7, but over 50 different VT-positive O:H serotypes have now been identified. The best strategies for diagnosing human VTEC infection include testing for the presence of free VT in fecal filtrates and examining fecal cultures for VTEC by means of deoxyribonucleic acid probes that specify genes encoding VT1 and VT2. Both methods are currently confined to specialized laboratories and await commercial development for wider use. In the meantime, most laboratories should continue to screen for the most common human VTEC serotype, O157:H7, using a sorbitol-containing MacConkey medium.
Scanning near-field optical microscope using cantilever integrated with light emitting diode, waveguide, aperture, and photodiode (2002)

The integrated probe is advantageous for reducing the system size and the alignment labor and for improving the reliability of the SNOM. Even when a multi-functional probe is used, the SNOM system requires to set additional bulky elements. The further integration of the SNOM system is still a great challenge. In this study, a highly integrated cantilever for SNOM is described. All components necessary for the SNOM system (LED light source, waveguide, nanometer size aperture tip, and photodiode) are integrated on the cantilever.
Designing Macromolecules for Therapeutic Applications:  Polyester DendrimerPoly(ethylene oxide) “Bow-Tie” Hybrids with Tunable Molecular Weight and Architecture (2002)

The design and preparation of new polyester dendrimer, poly(ethylene oxide) hybrid systems for drug delivery and related therapeutic applications, are described. These systems consist of two covalently attached polyester dendrons, where one dendron provides multiple functional handles for the attachment of therapeutically active moieties, while the other is used for attachment of solubilizing poly(ethylene oxide) chains. By varying the generation of the dendrons and the mass of the poly(ethylene oxide) chains, the molecular weight, architecture, and drug loading can be readily controlled. The "bow-tie" shaped dendritic scaffold was synthesized using both convergent and divergent methods, with orthogonal protecting groups on the periphery of the two dendrons. Poly(ethylene oxide) was then attached to the periphery of one dendron using an efficient coupling procedure. A small library of eight carriers with molecular weights ranging from about 20 kDa to 160 kDa were prepared and characterized by various techniques, confirming their well-defined structures.
A tunable, femtosecond pulse source operating in the range 1.06-1.33 microns based on an Yb doped holey fiber amplifier (2001)

Summary form only given. Wavelength tunable femtosecond optical pulse sources have applications in areas as diverse as ultrafast spectroscopy, materials processing, optoelectronics, nonlinear optics and optical chemistry. In the past, such sources have been available only in limited wavelength ranges and were realized using solid state lasers with complex, high precision cavities. More recently, the soliton self frequency shift (SSFS) in silica fibers has been exploited to obtain tunable femtosecond pulses; tuning from 1.55-2.2 /spl mu/m was previously reported in conventional silica fiber, and tuning from 1.3-1.6 /spl mu/m has been demonstrated using tapered microstructured fiber. Here we report what we believe is the first demonstration of a continuously tunable soliton source in the wavelength range 1.06-1.33 /spl mu/m, a wavelength range that is difficult to access using conventional solid state laser technology. The system is based on diode pumped Yb/sup 3+/ doped silica fiber components, and operates at mW average input power levels in a 4.7 m length of fiber.
Combining Adoptive Cellular and Immunocytokine Therapies to Improve Treatment of B-Lineage Malignancy (2007)

Currently, the lineage-specific cell-surface molecules CD19 and CD20 present on many B-cell malignancies are targets for both antibody- and cell-based therapies. Coupling these two treatment modalities is predicted to improve the antitumor effect, particularly for tumors resistant to single-agent biotherapies. This can be shown using an immunocytokine, composed of a CD20-specific monoclonal antibody fused to biologically active interleukin 2 (IL-2), combined with ex vivo expanded human umbilical cord blood-derived CD8(+) T cells, that have been genetically modified to be CD19 specific, for adoptive transfer after allogeneic hematopoietic stem-cell transplantation. We show that a benefit of targeted delivery of recombinant IL-2 by the immunocytokine to the CD19(+)CD20(+) tumor microenvironment is improved in vivo persistence of the CD19-specific T cells, and this results in an augmented cell-mediated antitumor effect. Phase I trials are under way using anti-CD20-IL-2 immunocytokine and CD19-specific T cells as monotherapies, and our results warrant clinical trials using combination of these two immunotherapies.
Precursor-Directed Biosynthesis of Erythromycin Analogs by an Engineered Polyketide Synthase (1997)

A genetic block was introduced in the first condensation step of the polyketide biosynthetic pathway that leads to the formation of 6-deoxyerythronolide B (6-dEB), the macrocyclic precursor of erythromycin. Exogenous addition of designed synthetic molecules to small-scale cultures of this null mutant resulted in highly selective multimilligram production of unnatural polyketides, including aromatic and ring-expanded variants of 6-dEB. Unexpected incorporation patterns were observed, illustrating the catalytic versatility of modular polyketide synthases. Further processing of some of these scaffolds by postpolyketide enzymes of the erythromycin pathway resulted in the generation of novel antibacterials with in vitro potency comparable to that of their natural counterparts.
Cell Culture of Sporadic Hepatitis E Virus in China (1999)

The isolation and identification of the 87A strain of epidemic hepatitis E virus (HEV) by means of cell culturing have been described previously. This paper reports the successful isolation of a sporadic HEV strain (G93-2) in human lung carcinoma cell (A549) cultures. The etiology, molecular and biological properties, and serological relationship of this new strain to other, epidemic HEV strains are described. The propagation of both sporadic and epidemic HEV strains in a cell culture system will facilitate vaccine research.
Deadline-Based Scheduling for GPU with Preemption Support (2018)

Modern automotive-grade embedded computing platforms feature high-performance Graphics Processing Units (GPUs) to support the massively parallel processing power needed for next-generation autonomous driving applications (e.g., Deep Neural Network (DNN) inference, sensor fusion, path planning, etc). As these workload-intensive activities are pushed to higher criticality levels, there is a stronger need for more predictable scheduling algorithms that are able to guarantee predictability without overly sacrificing GPU utilization. Unfortunately, the real-rime literature on GPU scheduling mostly considered limited (or null) preemption capabilities, while previous efforts in broader domains were often based on programming models and APIs that were not designed to support the real-rime requirements of recurring workloads. In this paper, we present the design of a prototype real-time scheduler for GPU activities on an embedded System on a Chip (SoC) featuring a cutting edge GPU architecture by NVIDIA adopted in the autonomous driving domain. The scheduler runs as a software partition on top of the NVIDIA hypervisor, and it leverages latest generation architectural features, such as pixel-level preemption and threadlevel preemption. Such a design allowed us to implement and test a preemptive Earliest Deadline First (EDF) scheduler for GPU tasks providing bandwidth isolations by means of a Constant Bandwidth Server (CBS). Our work involved investigating alternative programming models for compute APIs, allowing us to characterize CPU-to-GPU command submission with more detailed scheduling information. A detailed experimental characterization is presented to show the significant schedulability improvement of recurring real-time GPU tasks.