gebhart/patrepeval huggingface dataset:
Performance-based modeling for distributed object-oriented software (2004)

Information systems are basically distributed while object oriented brings new issues in software engineering. Pairing distributed systems with object paradigms results in a distributed object model. Choosing the appropriate distributed object model is a multi-criteria decision problem. Performance is a key criterion that makes software developers be able to select the object-oriented system that best fit their requirements. Classical techniques and methodologies of performance analysis are either unsuitable or unnatural to capture performance behavior of object-oriented (OO) systems. In this paper, we present performance-based model for distributed object-oriented software (DOOS) and a methodology to analyze and evaluate its performance. The new model evaluates the overall time cost of DOOS system considering the communication overheads while preserving the OO features such as encapsulations, information hiding, inheritance, etc.
The role of C-type natriuretic peptide in cardiovascular medicine (2001)

Receptors and signalling (Fig.
Wireless Power Transfer and Energy Harvesting: Current Status and Future Prospects (2019)

The rechargeable battery is the conventional power source for mobile devices. However, limited battery capacity and frequent recharging requires further research to find new ways to deliver power without the hassle of connecting cables. Novel wireless power supply methods, such as energy harvesting and wireless power transfer, are currently receiving considerable attention. In this article, an overview of recent advances in wireless power supply is provided, and several promising applications are presented to show the future trends. In addition, to efficiently schedule the harvested energy, an energy scheduling scheme in the EH-powered D2D relay network is proposed as a case study. To be specific, we first formulate an optimization problem for energy scheduling, and then propose a modified two stage directional water filling algorithm to resolve it.
Establishment and characterization of five new human renal tumor xenografts. (1992)

Ten different human renal cell carcinoma (RCC) primary tumors were xenografted into BALB/c nu/nu mice. Five of the tumors (NU-10, NU-12, NU-20, NU-22, and NU-28) gave rise to serially transplantable tumors that were further characterized. Histology, DNA index, immunohistochemical characteristics, growth rate, and clonogenic potential were followed from primary tumor to the 5th to 15th transplant passage. Only one of the tumors (NU-20) showed remarkable instability for all tested parameters in the first five transplant passages. Histology of the other tumors was essentially the same to the histology of the primary tumors, although differences between human and host-derived vessels were apparent. DNA index values in general showed a trend toward an aneuploid character of the xenografts. Immunohistochemical analyses showed a loss of intensity of staining but a concomitant rise in the fraction of positively staining cells with antibodies against cytokeratins, vimentin, tumor-associated antigens, and human leukocyte antigen (HLA) class I antigens. Human leukocyte antigen class II antigen expression showed a loss of intensity as well as a decrease in the fraction of positive cells. Tumor doubling time was lowest in transplant passage number 0, and stable growth was noticed in transplant passages 1 through 4. Clonogenic potential of four of the lines was higher for the xenografts than for the primary tumors. The authors conclude that, on xenografting, histologic characteristics of the primary tumor are essentially conserved. Progression in the first transplant passages, however, results in tumors with a more aggressive character.
FK506 and a nonimmunosuppressant derivative reduce axonal and myelin damage in experimental autoimmune encephalomyelitis: Neuroimmunophilin ligand‐mediated neuroprotection in a model of multiple sclerosis (2004)

Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) in which demyelination and axonal loss result in permanent neurologic disability. We examined the neuroprotective property of the immunosuppressant FK506 (tacrolimus), FK1706 (a nonimmunosuppressant FK506 derivative) and cyclosporin A (CsA) in a chronic relapsing experimental autoimmune encephalomyelitis (EAE) model of MS. Female SJL/J mice were immunized by subcutaneous (s.c.) injection with proteolipid protein 139-151 peptide in complete Freund's adjuvant. At the onset of paralysis, 12-14 days after immunization, mice received daily s.c. injections of FK506 (0.2, 1, and 5 mg/kg), FK1706 (5 mg/kg), CsA (2, 10, and 50 mg/kg), saline or vehicle (30% dimethylsulfoxide) for 30 days. FK506 (at a dose of 5 mg/kg) reduced the severity of the initial disease and suppressed relapses. FK1706 did not significantly alter the clinical course and CsA (at a dose of 50 mg/kg) lessened the severity of the initial episode of EAE but did not alter relapses. In the thoracic spinal cord, FK506 (5 mg/kg), FK1706 (5 mg/kg), and CsA (50 mg/kg) significantly (P < 0.001) reduced the extent of damage in the dorsal, lateral, and ventral white matter by a mean of up to 95, 68, and 30%, respectively. A nonimmunosuppressant dose of FK506 (0.2 mg/kg) also significantly (P < 0.001) reduced the extent of damage in the spinal cord by a mean of up to 45%. Other dosages of these compounds were ineffective. FK506 markedly protects against demyelination and axonal loss in this MS model through immunosuppression and neuroprotection.
Leukemia-Associated Mutations within the NOTCH1 Heterodimerization Domain Fall into at Least Two Distinct Mechanistic Classes (2006)

The NOTCH1 receptor is cleaved within its extracellular domain by furin during its maturation, yielding two subunits that are held together noncovalently by a juxtamembrane heterodimerization (HD) domain. Normal NOTCH1 signaling is initiated by the binding of ligand to the extracellular subunit, which renders the transmembrane subunit susceptible to two successive cleavages within and C terminal to the heterodimerization domain, catalyzed by metalloproteases and gamma-secretase, respectively. Because mutations in the heterodimerization domain of NOTCH1 occur frequently in human T-cell acute lymphoblastic leukemia (T-ALL), we assessed the effect of 16 putative tumor-associated mutations on Notch1 signaling and HD domain stability. We show here that 15 of the 16 mutations activate canonical NOTCH1 signaling. Increases in signaling occur in a ligand-independent fashion, require gamma-secretase activity, and correlate with an increased susceptibility to cleavage by metalloproteases. The activating mutations cause soluble NOTCH1 heterodimers to dissociate more readily, either under native conditions (n = 3) or in the presence of urea (n = 11). One mutation, an insertion of 14 residues immediately N terminal to the metalloprotease cleavage site, increases metalloprotease sensitivity more than all others, despite a negligible effect on heterodimer stability by comparison, suggesting that the insertion may expose the S2 site by repositioning it relative to protective NOTCH1 ectodomain residues. Together, these studies show that leukemia-associated HD domain mutations render NOTCH1 sensitive to ligand-independent proteolytic activation through two distinct mechanisms.
Peptide-based PET imaging of the tumor restricted IL13RA2 biomarker (2017)

Peptides that target cancer cell surface receptors are promising platforms to deliver diagnostic and therapeutic payloads specifically to cancer but not normal tissue. IL13RA2 is a tumor-restricted receptor found to be present in several aggressive malignancies, including in the vast majority of high-grade gliomas and malignant melanoma. This receptor has been successfully targeted for diagnostic and therapeutic purposes using modified IL-13 ligand and more recently using a specific peptide, Pep-1L. In the current work, we establish the <i>in vitro</i> and <i>in vivo</i> tumor binding properties of radiolabeled Pep-1L, designed for tumor imaging. We radiolabeled Pep-1L with Copper-64 and demonstrated specific cell uptake in the IL13RA2-over expressing G48 glioblastoma cell line having abundant IL13RA2 expression. [<sup>64</sup>Cu]Pep-1L binding was blocked by unlabeled ligand, demonstrating specificity. To demonstrate <i>in vivo</i> tumor uptake, we intravenously injected into tumor-bearing mice and demonstrated that [<sup>64</sup>Cu]Pep-1L specifically bound tumors at 24 hours, which was significantly blocked (3-fold) by pre-injecting unlabeled peptide. To further demonstrate specificity of Pep-1L towards IL13RA2 <i>in vivo</i>, we exploited an IL13RA2-inducible melanoma tumor model that does not express receptor at baseline but expresses abundant receptor after treatment with doxycycline. We injected [<sup>64</sup>Cu]Pep-1L into mice bearing IL13RA2-inducible melanoma tumors and performed <i>in vivo</i> PET/CT and post-necropsy biodistribution studies and found that tumors that were induced to express IL13RA2 receptor by doxycycline pretreatment bound radiolabeled Pep-1L 3-4 fold greater than uninduced tumors, demonstrating receptor specificity. This work demonstrates that [<sup>64</sup>Cu]Pep-1L selectively binds hIL13RA2-expressing tumors and validates Pep-1L as an effective platform to deliver diagnostics and therapeutics to IL13RA2-expressing cancers.
Evaluation of alternative measures of pork carcass composition. (2001)

Carcass and live measurements of 203 pigs representing seven genetic populations and four target live weights (100, 114, 128, and 152 kg) were used to evaluate alternative measures of carcass composition. Measures of carcass lean (fat tissue-free lean, FFLM; lipid-free soft tissue, LFSTIS; and dissected lean in the four lean cuts, DL), fat (total carcass fat tissue, TOFAT), and lipid mass (soft tissue lipid, STLIP) were evaluated. Overall, LFSTIS was 22.8% greater than FFLM (47.8 vs 38.9 kg) and TOFAT was 30% greater than STLIP (38.5 vs 29.6 kg). The allometric growth coefficients relative to carcass weight were different for the measures: b = 0.776, 0.828, 0.794, 1.37, and 1.49 for FFLM, LFSTIS, DL, TOFAT, and STLIP, respectively. At 90 kg carcass weight, the predicted growth of FFLM, LFSTIS, TOFAT, and STLIP was 0.314, 0.420, 0.553, and 0.446 kg/kg increase in carcass weight. The difference between FFLM and LFSTIS, representing nonlipid components of the carcass fat tissue, was greater for barrows than for gilts (9.2 vs 8.6 kg). Lipid-free soft tissue mass was predicted more accurately from carcass or live animal measurements than FFLM with smaller relative RSD (4.6 vs 6.5% of their mean values). The alternative measures of carcass composition were evaluated as predictors of empty body protein (MTPRO) and lipid (MTLIP) mass. Empty body protein was predicted with similar accuracy (R2 = 0.74 to 0.81) from either DL, FFLM, LFSTIS, or ribbed carcass measurements. Empty body lipid was predicted more accurately from TOFAT (R2 = 0.92) or STLIP (R2 = 0.93) than ribbed carcass measurements (R2 = 0.88). Although the alternative measures of lean mass (LFSTIS vs FFLM) and lipid mass (TOFAT vs STLIP) were highly related to each other (r = 0.93 to 0.98), they had different relative growth rates (allometric coefficients) and thus cannot be predicted as linear functions of the similar alternative variable without significant weight group biases. From the 100- to 152-kg target weight groups, gilts gained 12.9% greater FFLM and 12.1% greater MTPRO but only 4.4% greater LFSTIS than barrows. Fat-free lean mass is more precise as a measure of muscle growth and as a predictor of lysine requirements. Lipid-free soft tissue can be obtained more quickly and predicted more accurately from carcass or live animal measurements.
A digitally compensated 1.5 GHz CMOS/FBAR frequency reference (2010)

A temperature-compensated 1.5 GHz film bulk acoustic wave resonator (FBAR)-based frequency reference implemented in a 0.35 microm CMOS process is presented. The ultra-small form factor (0.79 mm x 1.72 mm) and low power dissipation (515 microA with 2 V supply) of a compensated FBAR oscillator present a promising alternative for the replacement of quartz crystal frequency references. The measured post-compensation frequency drift over a 0-100 degrees C temperature range is < +/- 10 ppm. The measured oscillator phase noise is -133 dBc/Hz at 100 kHz offset from the 1.5 GHz carrier.
Diffusing-wave spectroscopy: dynamic light scattering in the multiple scattering limit (1990)

Dynamic light scattering is extended to optically thick (opaque) media which exhibit a very high degree of multiple scattering. This new technique, called diffusing-wave spectroscopy (DWS), exploits the diffusive nature of the transport of light in strongly scattering media to relate the temporal fluctuations of the multiply scattered light to the motion of the scatterers. A simple theory of DWS, based on the diffusion approximation for the transport of light, is developed to calculate the temporal electric field autocorrelation functions of the multiply scattered light. Two important scattering geometries are treated : transmission and backscattering. The theory is compared to experimental measurements of Brownian motion of submicron-diameter polystyrene spheres in aqueous suspension. The agreement between theory and experiment is excellent. The limitations of the photon diffusion approximation and the polarization dependence of the autocorrelation functions are discussed for the backscattering measurements. The effects of absorption of light and particle polydispersity are also incorporated into the theory and verified experimentally. It is also shown how DWS can be used to obtain information about the mean size of the particles which scatter light.
Interaction between c-Rel and the Mitogen-activated Protein Kinase Kinase Kinase 1 Signaling Cascade in Mediating B Enhancer Activation (1996)

The Rel family of transcription factors are important mediators of various cytokine stimuli such as interleukin (IL)-1, tumor necrosis factor (TNF)-alpha, and CD28 costimulation in T cell effector responses. These stimuli induce Rel family DNA-binding activity to the kappaB enhancer and CD28 response elements of many cytokine gene promoters leading to cytokine production. Consistent with the importance of Rel family induction during immune responses, c-Rel knockout mice exhibit profound defects in T cell functions including IL-2 secretion and T cell proliferative responses to CD28 plus T cell receptor costimulation. The novel protein kinases, c-Jun NH2-terminal kinases (JNKs)/stress-activated protein kinases, are also activated by TNF-alpha, IL-1, and CD28 costimulation. Because of the common regulation of c-Rel and JNK1 by these agents in T cells, we investigated the role of JNK1 in c-Rel activation. We found that MAP kinase kinase kinase (MEKK) 1, a JNK1 activator, induced transcription from the human immunodeficiency virus-1 long terminal repeat and IL-2R alpha promoters in a kappaB-dependent manner. Coexpression of IkappaBalpha, a c-Rel inhibitor, inhibited the MEKK1-induced transcriptional activity. JNK1 synergized with MEKK1 in activating transcription from a kappaB-driven heterologous promoter. Furthermore, JNK1 associated with c-Rel in vivo in Jurkat T cells by coimmunoprecipitation assays and bound directly to c-Rel in a yeast two-hybrid assay. c-Rel also competed with c-Jun in in vitro kinase assays. However, JNK1 did not phosphorylate c-Rel, NF-kappaB, and IkappaB alpha in vitro, indicating that c-Rel may serve as a docking molecule to allow JNK1 phosphorylation of certain Rel-associated proteins. Transactivation of the IL-2Ralpha and HIV-kappaB-driven promoters by c-Rel was augmented by coexpression of MEKK1. These results demonstrate the first significant role for the MEKK1 kinase cascade module in c-Rel-mediated transcription.
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities (1993)

301 glycosyl hydrolases and related enzymes corresponding to 39 EC entries of the I.U.B. classification system have been classified into 35 families on the basis of amino-acid-sequence similarities [Henrissat (1991) Biochem. J. 280, 309-316]. Approximately half of the families were found to be monospecific (containing only one EC number), whereas the other half were found to be polyspecific (containing at least two EC numbers). A > 60% increase in sequence data for glycosyl hydrolases (181 additional enzymes or enzyme domains sequences have since become available) allowed us to update the classification not only by the addition of more members to already identified families, but also by the finding of ten new families. On the basis of a comparison of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined. This classification has been implemented in the SWISS-PROT protein sequence data bank.
Antigen presentation to HLA class II-restricted measles virus-specific T-cell clones can occur in the absence of the invariant chain. (1988)

A human fibroblast line expressing HLA-DR1 antigen on its surface was generated by transfection with DR alpha and DR beta cDNAs. Expression of the invariant chain gene was not detectable in the transfected fibroblasts and was not induced by infection with measles virus. Lysis of measles virus-infected cells occurred with DR1- but not with DR4-restricted measles virus-specific cytotoxic T-lymphocyte (CTL) clones and was inhibited by a monoclonal antibody specific for DR antigen. Therefore, the invariant chain is not required for DR-restricted presentation of measles virus antigens by this fibroblast line. Transfected fibroblasts were lysed as efficiently as an autologous B-cell line even though they expressed much less surface DR antigen. Lysis of both the transfected fibroblasts and the B-cell line was insensitive to treatment with chloroquine. These results demonstrate that expression of a DR alpha beta heterodimer at the surface of this fibroblast line is necessary and sufficient for presentation of measles virus antigens to specific CTL clones.
Mortality in rheumatoid arthritis. (1988)

Rheumatoid arthritis (RA) is often regarded as a non-fatal disease. Yet patients with RA have a substantially reduced life expectancy. Increased mortality in RA is associated with a long disease duration, with severe disabling arthritis and with systemic involvement. Patients with chronic RA are particularly at risk of death from bacterial infection and renal disease. The influence of treatment on mortality remains unclear. In patients with mild RA, the treatments may be more toxic than the disease.
Coupling Light Emitting Diodes with Photocatalyst-Coated Optical Fibers Improves Quantum Yield of Pollutant Oxidation (2017)

A photocatalyst-coated optical fiber was coupled with a 318 nm ultraviolet-A light emitting diode, which activated the photocatalysts by interfacial photon-electron excitation while minimizing photonic energy losses due to conventional photocatalytic barriers. The light delivery mechanism was explored via modeling of evanescent wave energy produced upon total internal reflection and photon refraction into the TiO<sub>2</sub> surface coating. This work explores aqueous phase LED-irradiated optical fibers for treating organic pollutants and for the first time proposes a dual-mechanistic approach to light delivery and photocatalytic performance. Degradation of a probe organic pollutant was evaluated as a function of optical fiber coating thickness, fiber length, and photocatalyst attachment method and compared against the performance of an equivalent catalyst mass in a completely mixed slurry reactor. Measured and simulated photon fluence through the optical fibers decreased as a function of fiber length, coating thickness, or TiO<sub>2</sub> mass externally coated on the fiber. Thinner TiO<sub>2</sub> coatings achieved faster pollutant removal rates from solution, and dip coating performed better than sol-gel attachment methods. TiO<sub>2</sub> attached to optical fibers achieved a 5-fold higher quantum yield compared against an equivalent mass of TiO<sub>2</sub> suspended in a slurry solution.
Optical constants of conjugated polymer/fullerene based bulk-heterojunction organic solar cells (2002)

The performance of organic solar cells consisting of multiple layers, which are a few hundred nanometers thick, is determined by strong optical interference effects. In order to model their optical and photoelectrical behavior, we determined the optical constants of all components of this system. This was done by fitting model dielectric functions to reflection and transmission spectra of all layers in the solar cell device. We put a special emphasis on understanding the optical behavior of the photoactive bulk heterojunction film, which consists of a composite of semiconducting polymers with fullerenes.
Caveolin-1 Gene Disruption Promotes Mammary Tumorigenesis and Dramatically Enhances Lung Metastasis in Vivo (2004)

Caveolin-1 (Cav-1) is the principal structural component of caveolae membrane domains in non-muscle cells, including mammary epithelia. There is now clear evidence that caveolin-1 influences the development of human cancers. For example, a dominant-negative mutation (P132L) in the Cav-1 gene has been detected in up to 16% of human breast cancer samples. However, the exact functional role of caveolin-1 remains controversial. Mechanistically, in cultured cell models, Cav-1 is known to function as a negative regulator of the Rasp42/44 MAP kinase cascade and as a transcriptional repressor of cyclin D1 gene expression, possibly explaining its in vitro transformation suppressor activity. Genetic validation of this hypothesis at the in vivo and whole organismal level has been prevented by the lack of a Cav-1 (-/-)-null mouse model. Here, we examined the role of caveolin-1 in mammary tumorigenesis and lung metastasis using a molecular genetic approach. We interbred a well characterized transgenic mouse model of breast cancer, MMTV-PyMT (mouse mammary tumor virus-polyoma middle T antigen), with Cav-1 (-/-)-null mice. Then, we followed the onset and progression of mammary tumors and lung metastases in female mice over a 14-week period. Interestingly, PyMT/Cav-1 (-/-) mice showed an accelerated onset of mammary tumors, with increased multiplicity and tumor burden ( approximately 2-fold). No significant differences were detected between PyMT/Cav-1 (+/+) and PyMT/Cav-1 (+/-) mice, indicating that complete loss of caveolin-1 is required to accelerate both tumorigenesis and metastasis. Molecularly, mammary tumor samples derived from PyMT/Cav-1 (-/-) mice showed ERK-1/2 hyperactivation, cyclin D1 up-regulation, and Rb hyperphosphorylation, consistent with dys-regulated cell proliferation. PyMT/Cav-1 (-/-) mice also developed markedly advanced metastatic lung disease. Conversely, recombinant expression of Cav-1 in a highly metastatic PyMT mammary carcinoma-derived cell line, namely Met-1 cells, suppressed lung metastasis by approximately 4.5-fold. In vitro, these Cav-1-expressing Met-1 cells (Met-1/Cav-1) demonstrated a approximately 4.8-fold reduction in invasion through Matrigel-coated membranes. Interestingly, delivery of a cell permeable peptide encoding the caveolin-1 scaffolding domain (residues 82-101) into Met-1 cells was sufficient to inhibit invasion. Coincident with this decreased invasive index, Met-1/Cav-1 cells exhibited marked reductions in MMP-9 and MMP-2 secretion and associated gelatinolytic activity, as well as diminished ERK-1/2 signaling in response to growth factor stimulation. These results demonstrate, for the first time, that caveolin-1 is a potent suppressor of mammary tumor growth and metastasis using novel in vivo animal model approaches.