gebhart/patrepeval huggingface dataset:
In Vivo and In Vitro Analysis of Age-Associated Changes and Somatic Cellular Senescence in Renal Epithelial Cells (2014)

Acute kidney injury is a major clinical problem and advanced age is associated with ineffective renal regeneration and poor functional outcome. Data from kidney injury models suggest that a loss of tubular epithelial proliferation contributes to a decrease in renal repair capacity with aging, but aging can also lead to a higher severity of inflammation and damage which may influence repair. In this study we tested intrinsic age-dependent changes in tubular epithelial proliferation in young and old mice, by injecting low-dose lead acetate as a non-injurious mitogen. In parallel, we explored in vitro techniques of studying cellular senescence in primary tubular epithelial cells (PTEC). Lead acetate induced tubular epithelial proliferation at a significantly higher rate in young as compared to old mice. Old kidneys showed significantly more senescence as demonstrated by increased p16 (INK4a), senescence associated β-galactosidase, and γH2AX(+)/Ki-67(-) cells. This was paralleled in old kidneys by a higher number of Cyclin D1 positive tubular cells. This finding was corroborated by a positive correlation between Cyclin D1 positivity and age in human renal biopsies. When tubular cells were isolated from mouse kidneys they rapidly lost their age-associated differences under culture conditions. However, senescence was readily induced in PTEC by γ-irradiation representing a future model for study of cellular senescence in the renal epithelium. Together, our data indicate that the tubular epithelium of aged kidney has an intrinsically reduced proliferative capacity probably due to a higher load of senescent cells. Moreover, stress induced models of cellular senescence are preferable for study of the renal epithelium in vitro. Finally, the positive correlation of Cyclin D1 with age and cellular senescence in PTEC needs further evaluation as to a functional role of renal epithelial aging.
Vitamin D: Marker or Mechanism of Action? (2011)

The field of vitamin D and cancer research has been moving forward quickly. However, some challenges remain regarding the interpretation and integration of data collected from epidemiological investigations and laboratory experiments. These include consideration of vitamin D biology, a better understanding of characteristics that affect concentrations of the biomarker of vitamin D status, 25(OH)D, and elucidation of variation in response to vitamin D supplementation. To further the field of vitamin D and cancer prevention, future studies will need to bridge the gap between the epidemiology and molecular biology of vitamin D activity in carcinogenesis.
Some identities for the higher-order q-Bernoulli polynomials of the second kind under the third dihedral group D_3 (2014)

In this paper, we consider the higher-order q-Bernoulli polynomials of the second kind and investigate some symmetric identities under the third Dihedral group D 3 which are derived from multivariate p-adic invariant integral on Z p .
Simultaneous Multi-Source Integrated Energy Harvesting System for IoE Applications (2019)

This paper presents an integrated modular multi-source energy harvesting system based on the Dickson charge pump and hill-climbing algorithm. The proposed maximum output power extraction is optimizing the system’s end-to-end efficiency. It collects the power simultaneously from multiple energy sources and boosts their DC voltages to a regulated output voltage that can be used for Internet of Everything (IoE) applications. The proposed implementation utilizes the whole capacitance on-chip regardless of the number of stages in use. A demonstration system using the proposed techniques is implemented for two sources in 0.18 μm CMOS technology and utilizes a total of 900 pF MIM capacitance. The simulation results shows that the proposed system achieves a peak MPPT efficiency of 90%, charge pump efficiency of 70% and end-to-end efficiency of 55% at a regulated output voltage of 1.5 V.
The Two Tumor Necrosis Factor Receptors Mediate Opposite Effects on Differentiation and Glucose Metabolism in Human Adipocytes in Primary Culture (2000)

Tumor necrosis factor-α (TNF) inhibits fat cell differentiation and may also mediate insulin resistance in adipocytes. Both TNF receptors are expressed in adipose tissue, but it is unknown how both receptors are involved in these biological functions. We therefore studied the effect of receptor-specific TNF muteins on adipose differentiation and insulin-stimulated glucose transport of in vitro differentiated human adipocytes in primary culture. Adipocyte precursor cells exposed to the 60-kDa TNF receptor (p60-TNFR)-specific TNFR32W-S86T showed a marked decrease in the percentage of differentiating cells in response to adipogenic factors as well as a reduction in peroxisome proliferator-activated receptor-γ2 (PPARγ2) messenger RNA (mRNA) and glycerophosphate dehydrogenase (GPDH) activity, but increased endogenous TNF mRNA expression. When cells were incubated with the p80-TNFR-specific TNFD143N-A145R, adipogenesis and PPARγ2 mRNA expression were stimulated, GPDH activity was unchanged, and TNF mRNA was completely suppressed. Insulin-stimulated 2-deoxy-d-glucose transport was inhibited by both muteins. The p60-TNFR-mediated inhibition increased continuously during 6 h of treatment and was associated with a down-regulation of glucose transporter-4 (GLUT4) mRNA and GLUT4 protein, whereas the p80-TNFR-specific mutein caused a transient increase in GLUT4 mRNA, but did not alter GLUT4 protein expression after a 24-h incubation. We conclude that p60-TNFR mediates the antiadipogenic effect as well as the down-regulation of GLUT4 by TNF, thereby leading to long-term inhibition of insulin-stimulated glucose transport. In contrast, activation of the p80-TNFR induces an adipogenic effect and transiently up-regulates GLUT4 expression. Here, the acute inhibition of insulin-stimulated glucose transport may be induced by interference with the insulin signaling pathway.
Design and Manufacturing Methodology for Mechanical Systems Using Virtual Product Simulator (2002)

In mechanical systems development, it is well known that verification tests covering all aspects of mechanics, software, and hardware cannot be performed until a working prototype of the product is completed. As a result, serious flaws may be not discovered until the final stages of development, resulting in delays and extra work, mainly on the embedded software (known as firmware). We propose a new design and manufacturing methodology for mechanical systems that is based on a 3D real-time simulator, called “VPS” (Virtual Product Simulator). This simulator enables the development of virtual mechanical models on computers, allowing engineers to work on the model without seeing the actual device. It provides more time to thoroughly test the whole system, thereby, making the development process more efficient.
Interfaces as design tools for short-period InAs/GaSb type-II superlattices for mid-infrared detectors (2006)

Abstract The effect of interface anisotropy on the electronic structure of InAs/GaSb type-II superlattices is exploited in the design of thin-layer superlattices for mid-IR detection threshold. The design is based on a theoretical envelope function model that incorporates the change of anion and cation species across InAs/GaSb interfaces, in particular, across the preferred InSb interface. The model predicts that a given threshold can be reached for a range of superlattice periods with InAs and GaSb layers as thin as a few monolayers. Although the oscillator strengths are predicted to be larger for thinner period superlattices, the absorption coefficients are comparable because of the compensating effect of larger band widths. However, larger intervalence band separations for thinner-period samples should lead to longer minority electron Auger lifetimes and higher operating temperatures in p-type SLs. In addition, the hole masses for thinner-period samples are on the order the free-electron mass rather than being effectively infinite for the wider period samples. Therefore, holes should also contribute to photoresponse. A number of superlattices with periods ranging from 50.6 to 21.2 Å for the 4 μm detection threshold were grown by molecular beam epitaxy based on the model design. Low temperature photoluminescence and photoresponse spectra confirmed that the superlattice band gaps remained constant at 330 meV although the period changed by the factor of 2.5. Overall, the present study points to the importance of interfaces as a tool in the design and growth of thin superlattices for mid-IR detectors for room temperature operation.
Performance of a Sensitive Micromachined Accelerometer With an Electrostatically Suspended Proof Mass (2014)

A three-axis micromachined accelerometer with a proof mass suspended electrostatically in six degrees of freedom was designed and tested to evaluate its performance of this sensitive sensor for potential microgravity space applications. The device is based on a glass/silicon/glass bonding structure, fabricated by bulk micromachining process, and operated with force-balance technology. The motion of the proof mass with respect to each side is fully servo-controlled by capacitive position sensing and electrostatic force feedback. The design and simulation of multiaxis suspension control loops are presented based on the stiffness requirements for different full-scale ranges. The ground test of this sensitive accelerometer is facilitated by setting the vertical axis at a relatively high measurement range to counteract the one-g gravity, whereas the range in two lateral axes can be set as low as possible to achieve high sensitivity. Detailed experimental results of electrostatic suspension, threeaxis accelerometer, and its cross-axis sensitivity are presented with the device operated initially in an atmospheric environment. The preliminary test results of a prototype accelerometer show that a sensitivity up to 688.8 V/g and a noise density down to 3 μg/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> can be achieved by setting an extremely low full-scale range of ±2.90 mg. The results also show that much different stiffness levels in the design of three-axis suspension is a major source of cross coupling effects in the prototype accelerometer.
Free Radical Scavenging and Antioxidant Activities of Substituted Hexahydropyridoindoles. Quantitative Structure−Activity Relationships (2006)

New synthetic substituted hexahydropyridoindoles were studied for their radical scavenging ability in a system of an ethanolic solution of alpha,alpha'-diphenyl-beta-picrylhydrazyl and for their lipid peroxidation inhibitory properties in a suspension of unilamellar dioleoylphosphatidylcholine liposomes. The activities in both in vitro systems were correlated with several structural parameters. In the homogeneous system of alpha,alpha'-diphenyl-beta-picrylhydrazyl, the sum of aromatic substitution constants (sigma(+)) and the hydration energy were shown to be effective predictors of the radical scavenging activity of the hexahydropyridoindole derivatives. Moreover, in the heterogeneous system comprising a model liposomal membrane, the overall antioxidant activity of the compounds was affected by their lipid-phase availability governed by the lipophilicity and basicity of the molecules.
What makes a simulation useful? [TRANSIMS] (2003)

Modern computers make possible a new blending of systems, man, and cybernetics in the detailed simulation of large sociotechnical systems. Several such simulations are currently under development at Los Alamos National Laboratory and elsewhere. When deployed, they will affect the daily lives of hundreds of millions of people and the allocation of billions of dollars. Whether they are deployed depends entirely on their perceived usefulness, which in turn depends on answers to the following: What kinds of questions does the simulation address and what kinds of solutions does it provide? How can the solutions be validated? Is simulation more cost-effective than other methods? Answers to these questions lead us to define a useful simulation as one which efficiently provides correct, robust estimates required by decision-making needs, together with well understood variability for the outcomes in hypothetical situations. The paper examines the implications of this criterion for the design of TRANSIMS, a regional transportation network simulation system, and by extension, for simulations of other sociotechnical systems.
Association between c-Met and lymphangiogenic factors in patients with colorectal cancer. (2013)

e22199 Background: Lymphangiogenesis plays an important role in cancer metastasis. Although animal models show a strong relationship between lymphangiogenesis and lymph node metastasis and survival, the clinical significance of lymphangiogenesis in colorectal cancer (CRC) remains uncertain. The goal of this study was to evaluate the association between c-Met and lymphangiogenic factors and to elucidate their prognostic significance for patients with CRC. Methods: A total of 379 tissue samples were obtained from surgically resected specimens from patients with CRC in Soonchunhyang University Cheonan Hospital between January 2002 and December 2010. The expressions of c-Met, vascular endothelial growth factor (VEGF)-C, VEGF-D, VEGF receptor (VEGFR)-3, and podoplanin were examined by immunohistochemistry. The expression of each marker and clinical factors were analyzed. Results: Three hundred and one of 379 (79.4%) tissues had c-Met expression. High expression of c-Met in tumor cells was significantly associated with high expression of VEGF-C (P &lt; .001) and VEGFR-3 (P = .001). But, there was no statistically significant association with podoplanin (P = .587) and VEGF-D (P = .096). Of the 103 evaluable patients, expression of c-Met in tumor cells was significantly associated with advanced clinical stage (P = .020), positive lymph node status (P = .038), and high expression of VEGF-C (P = .020). But, there was no statistically significant association with podoplanin (P = .518), VEGFR-3 (P = .085), VEGF-D (P = .203), and overall survival (P = .360). Conclusions: Our results provide indirect evidence for an association and possible regulatory link of c-Met with the lymphangiogenic factors. But, c-Met expression in patients with CRC are not prognostic indicator for overall survival in this retrospective study.
Acidity of Organic Molecules in the Gas Phase and in Aqueous Solvent (2000)

Using a combination of ab initio, DFT and continuum solvation methods, the gas phase and aqueous acidities for a set of weak organic acids with high pKa values, which cannot be measured experimentally in aqueous solvent, have been calculated. Comparison of the computed and experimental data for different terms used in the thermodynamic cycle for the calculation of pKa values allowed us to estimate that the errors in the pKa calculations are of order of 2 pKa units, i.e., less than 10% of the expected pKa values for the studied weak organic acids. It is shown that inclusion of explicit water molecules in the solute cavity of compounds with pKa values over 40 could lead to dubious results due to the inappropriate description of the corresponding anion solvation. Acidity trends for compounds in the gas phase and in aqueous solvent were found to be different, due to the effects of aqueous solvation.
Abstract 4643: Epstein-Barr virus infection (EBV) and expression of B-cell oncogenic markers in HIV+ diffuse large B-cell lymphoma (DLBCL) (2011)

Abstract Background: Lymphomagenicity of EBV in the setting of HIV infection has been widely accepted. However, the underlying carcinogenic mechanism of EBV is largely unknown and warrants further study. We sought to investigate the hypothesis that EBV infection is associated with expression of specific B-cell oncogenic markers in HIV+ DLBCL. Methods: HIV+ DLBCL cases diagnosed between 1996-2007 within the Kaiser Permanente California Health Plan were identified. Archived tumor specimens were retrieved and H&amp;E slides were reviewed to identify representative tumor blocks for tissue microarray (TMA) construction. Immunohistochemistry staining was performed on TMA cores to analyze the expression of selected B-cell oncogenic markers in the following categories: (1) mutagenic molecule (that induce mutation/translocation), (2) cell cycle promoter, (3) B-cell activator and (4) anti-apoptotic protein. Percent of DLBCL cells with visible marker staining was scored on a scale from 0-4 (0-9%, 10-24%, 25-49%, 50-74% and ≥75%). EBV infection was determined by in situ hybridization of EBV encoded RNA and was considered positive if ≥10% of the DLBCL cells had detectable EBV. Correlations between EBV and marker expression were examined using Spearman's correlation coefficient. Results: We identified 194 HIV+ DLBCL cases. Of these, 117 lacked sufficient tissue; another 7 had undetermined EBV status; and 70 were included in the study. Marker expressions are shown in the table: Conclusion: There was a suggestion that Cyclin E and PKC-β2 were more commonly expressed in EBV+ DLBCL, and that FOXP1, BCL2, and Survivin were more commonly expressed in EBV- DLBCL. However, none of these associations reached statistical significance. These findings provide limited support that the underlying carcinogenic mechanism of EBV involves the mediation of the expression of oncogenic markers examined here. However, our study power was limited, thus requiring confirmation in larger studies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4643. doi:10.1158/1538-7445.AM2011-4643
Aggression and personality: association with amino acids and monoamine metabolites (1996)

Associations in 52 normal individuals were examined between plasma and cerebrospinal fluid (CSF) concentrations of tryptophan (Trp) and tyrosine, and concentrations of monoamine metabolites in the CSF, and scores on an aggression questionnaire, the Kinsey Institute Reaction List II, and the Eysenck Personality Questionnaire. There was a significantly positive correlation between CSF 5-hydroxyindoleacetic acid (5-HIAA) levels and extroverted aggression scores, and a significantly negative correlation between CSF 5-HIAA levels and introverted aggression scores. Males showed higher plasma Trp concentrations than females, and significantly positive correlations between plasma Trp concentrations and scores on extroverted aggression and the Eysenck E scale. Males, furthermore, showed a significantly negative correlation between CSF Trp levels and scores on the Eysenck P scale, and a significantly positive correlation between concentrations of 3-methoxy-4-hydroxy-phenylglycol in CSF and scores on moral aggression. These results suggest that central serotonin influences aggression in normal individuals through effects on personality.
Endothelial Dysfunction in Sleep Apnea Patients Assessed by Reactive Hyperemia Peripheral (2004)

11:38 AM Objectives: Obstructive sleep apnea (OSA) is associated with increased cardiovascular morbidity and mortality. One potential mechanism to explain this association may be endothelial dysfunction (ED) in these patients. Recently, changes in the peripheral arterial tone during reactive hyperemia (RH-PAT) have been suggested to assess ED. In the present study, we used the RH-PAT technique to investigate endothelial function in OSA patients. Methods: Twenty-eight patients with suspected OSA participated. In the morning following the PSG, all underwent assessment of their endothelial function using the Endo PAT 2000 (Itamar-Medical, Caesarea, Israel). The RH-PAT hyperemic ratio was defined as the ratio of the average arterial pulse wave amplitude after occlusion release, relative to average preocclusion amplitude. Results: The average morning PAT hyperemia ratio was 1.77 ± 0.42 (range, 1.18-2.84; median, 1.81) and it tended to be lower in the 9 patients with cardiovascular morbidity (1.58 ± 0.3 vs 1.86 ± 0.45, P < 0.06, 2-tailed t test). The PAT hyperemia ratio was significantly inversely correlated (Spearman correlation) with RDI (r = −.42, P < 0.02) and tended to be inversely correlated with percent time below 90% arterial oxygen saturation (r = −.28, P < 0.13) and BMI (r = −.31, P < 0.10). Conclusions: Our results demonstrate that changes in the peripheral arterial tone during reactive hyperemia as measured by the PAT technology were significantly correlated with the severity of sleep apnea syndrome. Endothelial function was diminished with increased sleep apnea severity, and sleep apnea patients with cardiovascular disease tended to have lower PAT ratios than patients free of cardiovascular morbidity.
Autofocus algorithms for digital-holographic microscopy (2007)

Digital-holographic metrology enables quantitative phase contrast microscopy of reflective and (partially) transparent samples. In this way, new application fields are opened up for nondestructive investigations of technical samples as well as for marker-free and time-resolved analysis of cell biological processes. Studies on long-term biological processes require permanent focus position readjustment to maintain an optimum image quality. Digital holographic microscopy permits subsequent numerical focusing by variation of the propagation distance. Here, the determination of the optimal propagation distance for a sharply focused image is of particular importance. At the Laboratory of Biophysics image definition quantification algorithms were adapted to the requirements of digital holographic microscopy. In order to obtain robust and reliable algorithms, the object-dependent optical absorption properties were taken into consideration.Automatic focus tracking is demonstrated on investigations with digital holographic microscopy on both technical amplitude objects and cytological pure phase objects.
Optimization for Passive Design of Large Scale Housing Projects for Energy and Thermal Comfort in a Hot and Humid Climate (2014)

Rapid urbanization in emerging economies, like Vietnam, is commonly realized via the multiplication of stereotype projects consisting of high-rise apartment blocks, terraced, semi-detached and detached houses. For these types of dwellings, in the hot and humid Vietnamese climate, individual air conditioning systems are typically used. This requires a large share of the country energy resources. Until recently comfortable traditional housing has however been built without using such energy intensive cooling. This paper focuses on the energy consumption and thermal comfort in residential buildings if only natural ventilation is used, taking into account the urban environment. Via a parametric simulation several building types are optimized, looking at the urban layout, building orientation and size, window design and internal wind permeability. A two-step procedure is followed for the analysis. Firstly, a simplified model is used to analyse a large range of design alternatives and secondly, dynamic energy and thermal comfort simulations with EnergyPlus are made for a selected number of design options. Results reveal that the average life cycle cost of the optimal cases is 34% lower than the reference cases. The window sizes, building layouts and urban forms are crucial parameters to compensate with orientations at the early design stages. One optimization procedure was developed to make maximum use of passive design measures in large scale housing projects.