gebhart/patrepeval huggingface dataset:
The Nature and Absolute Hydration Free Energy of the Solvated Electron in Water (2003)

We report the first first-principles solvation-included electronic structure study to energetically compare a variety of candidate structures of the hydrated electron and to determine its absolute hydration free energy ΔGhyd298(e-). The calculated results show that both the thermal motion and bulk solvent effects can qualitatively change the relative thermodynamic stability of different structures of the hydrated electron on the basis of a cluster of a given size, and that the most stable structure in solution is not necessarily the most stable one in the gas phase. For a given number of explicitly included solvent water molecules, the most stable structure in solution reveals a unique feature of the chemical nature of the solvated electron in water, i.e., the electron forms two strong electron−hydrogen bonds of the e-···HO type with the hydrogen-bonded water cluster and two of the hydrogen bonds in the neutral water cluster are broken. On the basis of the most stable structures, the calculated electronic excitation energies are within the observed absorption range of the hydrated electron in water. The absolute hydration free energy of the solvated electron in water has been calculated to be −35.5 kcal/mol by using a reliable computational protocol of first-principles solvation-included electronic structure calculations. This value is in excellent agreement with a recently obtained value of −34.6 kcal/mol. The predicted ΔGhyd298(e-) value of −35.5 kcal/mol, when combined with our previously predicted ΔGhyd298(H+) value of −262.4 kcal/mol and ΔGhyd298(HO-) value of −104.5 kcal/mol by using the same computational protocol, gives ΔGhyd298(e-) + ΔGhyd298(H+) = −297.9 kcal/mol and ΔGhyd298(e-) − ΔGhyd298(HO-) = 69.0 kcal/mol, in excellent agreement with the corresponding values derived from experimental data.
Dietary Fat Elevates Hepatic ApoA-I Production by Increasing the Fraction of Apolipoprotein A-I mRNA in the Translating Pool (1995)

Elevated plasma high density lipoprotein cholesterol (HDL-C) levels are associated with a decreased risk for coronary heart disease. Ironically, diets enriched in saturated fat and cholesterol (HF/HC diets), which tend to accelerate atherosclerotic processes by increasing LDL cholesterol levels, also raise HDL-C. We have recently reported, using a human apoA-I (hapoA-1) transgenic mouse model, that the elevation of HDL-C by a HF/HC diet is attributable, in part, to an increase in the hepatic production of hapoA-1. To further define the hepatocellular processes associated with this induction, we have prepared primary hepatocytes from hapoA-1 transgenic mice. Rates of hapoA-1 secretion were 40% greater from cells prepared from animals fed the HF/HC relative to a low fat-low cholesterol (LF/LC) control diet. The abundance of hapoA-1 mRNA in these cells was similar between hepatocytes prepared from the HF/HC and LF/LC diet fed animals, suggesting a post-transcriptional mechanism that does not involve mRNA stability. Inhibition of secretion using brefeldin A revealed an increase in cellular hapoA-1 accumulation. Thus, the HF/HC diet apparently affects hepatic hapoA-1 production via a mechanism that is manifest prior to the exit of newly synthesized hapoA-1 from the Golgi. Pulse-chase experiments revealed a 39% greater peak hapoA-1 synthesis, with no difference in the degradation of total labeled hapoA-1 protein, as a result of the HF/HC diet feeding. Finally, resolution of liver S10 extracts via sucrose density sedimentation and metrizamide density equilibrium gradient centrifugation analyses both revealed similar increases (31 and 24%, respectively) in the relative percentage of hapoA-1 mRNA associated with the translating polysomal fractions as a result of the HF/HC feeding. Together, these data suggest that the HF/HC diet affects hepatic hapoA-1 production via a specific modulation in the relative amount of hapoA-1 mRNA in the polysomal pool. These observations provide an opportunity to explore a new mechanism regulating apoA-1 production and might lead to the development of novel therapies to elevate plasma HDL-C levels.
Rates of reductive elimination of substituted nitrophenols from the (indol-3-yl)methyl position of indolequinones (2001)

A series of indolequinones bearing substituted nitrophenols on the (indol-3-yl)methyl position was synthesised. The nitrophenol leaving groups were appropriately substituted to give a wide range (4 units) in phenolic pKa value. The rate of reductive elimination of phenoxide anions from the (indol-3-yl)methyl position of semiquinone radicals was dependent upon this pKa, with a decrease in 3.8 pK units shortening the half-life from 28 to 1.5 ms. Only 2,4-dinitrophenol (pKa = 3.9) was eliminated from an unsubstituted (indol-3-yl)methyl position at a rate that would compete with reoxidation of the radical by oxygen. A nitrothiophenol leaving group was eliminated comparatively slowly and only from the hydroquinone. These studies demonstrate the dependence upon leaving group pKa of the rate of reductive elimination from the (indol-3-yl)methyl position of indolequinones.
Chutney and relish (2010)

We report on designing augmented reality (AR) applications to support the practices of going shopping, using an accompanied shopping and reflection technique to assess the key points of engagement among shoppers and producers at a farmers' market. Our goal was to deploy innovative mobile technology in a low-tech context so that it supported everyday behaviour. The paper documents how a short research intervention was decisive in shaping the applications designed for the AR tool and explores how stories told as part of the market and in interview were used to help organise our insights.
Phytoestrogens Modulate Binding Response of Estrogen Receptors α and β to the Estrogen Response Element (2003)

Binding of estrogen receptor (ER) to estrogen response element (ERE) induces gene activation and is an important step in estrogen-induced biological effects. Here, we investigated the effects of some dietary phytoestrogens such as the isoflavones genistein and daidzein, its metabolite equol, and the coumestane coumestrol on the binding rate of ERalpha and ERbeta to ERE by a nonradioactive real-time method, the Biacore Technology. ERalpha and ERbeta were able to bind to ERE immobilized on the surface of a sensor chip even in the absence of estrogens. 17beta-Estradiol and phytoestrogens induced an increase in ER binding to ERE in a concentration-dependent manner. 17beta-Estradiol was a more potent activator of binding than the phytoestrogens studied. The concentrations of 17beta-estradiol inducing an increase in the binding response of ERalpha and ERbeta to ERE by 50% (EC(50)) as compared to unliganded ER were 0.03 and 0.01 microM, respectively. Regarding the efficacy of activation of ERalpha, from the most to the least effective compound, the sequence and the EC(50) were as follows: 17beta-estradiol (0.03 microM) > coumestrol (0.2 microM) > equol (3.5 microM) > genistein (15 microM) > daidzein (>300 microM) and for ERbeta 17beta-estradiol (0.01 microM) > coumestrol (0.025 microM) > genistein (0.03 microM) > daidzein (0.35 microM) > equol (0.4 microM). The ratios EC(50)alpha/EC(50)beta were calculated to be for 17beta-estradiol, 3; coumestrol, 8; equol, 8.8; genistein, 500; daidzein > 850. These ratios indicate that genistein and daidzein preferentially activate the binding of ERbeta to ERE. The endogenous hormone 17beta-estradiol as well as coumestrol and daidzein metabolite equol activate the binding of ERbeta to ERE only slightly more effectively than the binding of ERalpha to ERE. Thus, the effect of daidzein can be changed from a specific activator of ERbeta to an activator of both ER isotypes alpha and beta in humans who are able to convert daidzein to equol. While the results of the measurements with ERalpha were in line with the binding affinities of compounds tested for ER, there was a distinct difference between our results and the binding affinities of phytoestrogens for the ERbeta. This leads to the conclusion that phytoestrogens differ not only in their binding affinities for the ER, but also in their potential to increase the rate of receptor binding to the ERE.
Structural and Functional Analysis of Domains Mediating Interaction Between the Bagpipe Homologue, Nkx3.1 and Serum Response Factor (2008)

Nkx3.1 is a member of the NK2 class of homeodomain proteins and is expressed in development, being an early marker of the sclerotome and prostate gland. It has been shown to be a critical factor for prostate differentiation and function. Previous studies suggested that Nkx3.1 interacts with Serum Response Factor (SRF) to transactivate the Smooth Muscle gamma-Actin (SMGA) promoter. In studies presented here, we examined the molecular mechanisms underlying the functional synergy of these factors upon SMGA transcription. We demonstrate that full length Nkx3.1 physically interacts with SRF in the absence of DNA and that these factors are able to co-associate in cellular context using a mammalian two-hybrid system. The segment of SRF responsible for Nkx3.1 interaction was mapped to a approximately 30 amino acid region (AAs 142-171) at the N-terminal segment of the MADS box. Two separate regions of Nkx3.1 were found to mediate interactions with SRF. Interestingly, recognized domains of NK2 proteins, namely the TN, homeodomain DNA binding segment, and the NK2-SD do not participate in SRF interactions. One of the Nkx3.1 SRF binding domains was mapped to the N-terminal of the protein consistent with recent studies of these proteins using NMR spectroscopy by Gelmann and colleagues (1). A second SRF binding region was mapped to amino acids C-terminal to the homeodomain. Structural predictions indicate that both of the SRF interacting segments are largely hydrophobic in character and beta-strand in structure. With co-transfection transcriptional analyses we found that interaction between SRF and Nkx3.1 as well as DNA binding by both factors was required for the observed transcriptional synergy. Thus our studies have identified novel protein-protein interacting domains within Nkx3.1 and SRF that operate in concert with their respective DNA binding domains to mediate functional transcriptional synergy of these factors to regulate SMGA gene activation.
Tracking errors in a prototype real-time tumour tracking system (2004)

In motion-compensated radiation therapy, radio-opaque markers can be implanted in or near a tumour and tracked in real-time using fluoroscopic imaging. Tracking these implanted markers gives highly accurate position information, except when tracking fails due to poor or ambiguous imaging conditions. This study investigates methods for automatic detection of tracking errors, and assesses the frequency and impact of tracking errors on treatments using the prototype real-time tumour tracking system. We investigated four indicators for automatic detection of tracking errors, and found that the distance between corresponding rays was most effective. We also found that tracking errors cause a loss of gating efficiency of between 7.6 and 10.2%. The incidence of treatment beam delivery during tracking errors was estimated at between 0.8% and 1.25%.
Insulin glargin — ein langwirksames Insulinanalogon: Bessere Blutzuckerwerte beim Diabetiker (2001)

Insulin glargin (HOE 901,Lantus®)ist ein gentechnisch hergestelltes Analogon des Humaninsulins, bei dem die B-Kette am Carboxylende um zwei Arginine verlängert und das Asparagin in Position 21 der A-Kette durch Glycin ersetzt wurde. Bedingt durch diese Strukturvariationen ist Insulin glargin im physiologischen pH-Bereich (pH =7.4) schwer, in schwach saurer Lösung (pH =4) jedoch vollständig löslich. Nach Injektion der klaren Lösung in das Subkutangewebe präzipitiert Insulin glargin und bildet stabilisierte Hexamer-Assoziate. Die Schwerlöslichkeit des Mikropräzipitats ist eine erste Voraussetzung für die verzögerte Aufnahme des Insulinanalogons in den Blutkreislauf. Für die stark verlängerte Wirkung von Insulin glargin sind jedoch zusätzliche Faktoren ausschlaggebend, die sich aus der Kristallstruktur im subkutanen Depot ergeben.
Performance evaluation of wavelength assignment methods for WDM networks (2010)

In most of the research on the wavelength allocation in Wavelength Division Multiplexing (WDM) networks, the connection setting delay time is not considered. However, the entire bandwidth increases because of an increase in the transmission capacity of one wavelength. Therefore, the connection setting delay time should be considered because the data transmission time is shortened relatively. In this paper, we propose a new connection setting method, considering connection setting delay. The performance evaluation via simulations shows that the proposed method gives a better performance than the conventional forward and Backward Reservation (BR) methods.
Erbium-Doped Fiber Amplifiers: Fundamentals and Technology (1999)

INTRODUCTION 1.1 Long Haul Fiber Networks 1.2 Historical Development of Erbium-Doped Fiber Amplifiers 1.3 From Glass to Systems 2 OPTICAL FIBER FABRICATION 2.1 Introduction 2.2 Conventional Communication Fiber 2.3 Rare Earth Doped Fibers 2.4 Pump-Signal Interaction Methods 2.5 Compositions 2.6 Physical Properties 3 COMPONENTS AND INTEGRATION 3.1 Introduction 3.2 Fiber Connectors 3.3 Fusion Splicing 3.4 Pump and Signal Combiners 3.5 Isolators 3.6 Circulators 3.7 Filters 3.8 Fiber Gratings 3.9 Signal Multiplexers and Demultiplexers 3.10 Signal Add/Drop Components 3.11 Dispersion Compensation Components 3.12 Integrated Components 3.13 Pump Lasers 4 RARE EARTH IONS--INTRODUCTORY SURVEY 4.1 Introduction 4.2 Atomic Physics of the Rare Earths 4.3 Optical Spectra of Rare Earth Ions 4.4 Fundamental Properties 4.5 Spectroscopy of the Er3 Ion 4.6 Er3 -Er3 Interaction Effects 5 ERBIUM-DOPED FIBER AMPLIFIERS--AMPLIFIER BASICS 5.1 Introduction 5.2 Amplification in Three-Level Systems 5.3 Reduction of the Three-Level System to the Two-Level System 5.4 Amplified Spontaneous Emission 5.5 Analytical Solutions to the Two-Level System 6 ERBIUM-DOPED FIBER AMPLIFIERS--MODELING AND COMPLEX EFFECTS 6.1 Introduction 6.2 Absorption and Emission Cross Sections 6.3 Gain and ASE Modeling 6.4 Amplifier Simulations 6.5 Transverse Mode Models--Erbium Confinement Effect 6.6 Excited State Absorption Effects 6.7 Er3 -Er3 Interaction Effects 7 OPTICAL AMPLIFIERS IN FIBER OPTIC COMMUNICATION SYSTEMS--THEORY 7.1 Introduction 7.2 Optical Noise: Device Aspects 7.3 Optical Noise: System Aspects 8 AMPLIFIER CHARACTERIZATION AND DESIGN ISSUES 8.1 Introduction 8.2 Basic Amplifier Measurement Techniques 8.3 Amplifier Design Issues 9 SYSTEM IMPLEMENTATIONS OF AMPLIFIERS 9.1 Introduction 9.2 System Demonstrations and Issues 9.3 Soliton Systems 10 FOUR LEVEL FIBER AMPLIFIERS FOR 13 MM AMPLIFICATION 10.1 Introduction 10.2 Pr3 -doped Fiber Amplifiers 10.3 Nd3 -doped Fiber Amplifiers Appendix Subject Index
A peptide derived from the non-receptor-binding region of urokinase plasminogen activator inhibits glioblastoma growth and angiogenesis in vivo in combination with cisplatin (2000)

The urokinase plasminogen activator system is involved in angiogenesis and tumor growth of malignant gliomas, which are highly neovascularized and so may be amenable to antiangiogenic therapy. In this paper, we describe the activity of A6, an octamer capped peptide derived from the non-receptor-binding region of urokinase plasminogen activator. A6 inhibited human microvascular endothelial cell migration but had no effect on the proliferation of human microvascular endothelial cells or U87MG glioma cells in vitro. In contrast, A6 or cisplatin (CDDP) alone suppressed subcutaneous tumor growth in vivo by 48% and 53%, respectively, and, more strikingly, the combination of A6 plus CDDP inhibited tumor growth by 92%. Such combination treatment also greatly reduced the volume of intracranial tumor xenografts and increased survival of tumor-bearing animals when compared with CDDP or A6 alone. Tumors from the combination treatment group had significantly reduced neovascularization, suggesting a mechanism involving A6-mediated inhibition of endothelial cell motility, thereby eliciting vascular sensitivity to CDDP-mediated toxicity. These data suggest that the combination of an angiogenesis inhibitor that targets endothelial cells with a cytotoxic agent may be a useful therapeutic approach.
Immune function of microglia (2001)

During the past decade, mechanisms involved in the immune surveillance of the central nervous system (CNS) have moved to the forefront of neuropathological research mainly because of the recognition that most neurological disorders involve activation and, possibly, dysregulation of microglia, the intrinsic macrophages of the CNS. Increasing evidence indicates that, in addition to their well-established phagocytic function, microglia may also participate in the regulation of non specific inflammation as well as adaptive immune responses. This article focuses on the signals regulating microglia innate immune functions, the role of microglia in antigen presentation, and their possible involvement in the development of CNS immunopathology.
The Endothelial Prolyl-4-Hydroxylase Domain 2/Hypoxia-Inducible Factor 2 Axis Regulates Pulmonary Artery Pressure in Mice (2016)

Hypoxia-inducible factors 1 and 2 (HIF-1 and -2) control oxygen supply to tissues by regulating erythropoiesis, angiogenesis and vascular homeostasis. HIFs are regulated in response to oxygen availability by prolyl-4-hydroxylase domain (PHD) proteins, with PHD2 being the main oxygen sensor that controls HIF activity under normoxia. In this study, we used a genetic approach to investigate the endothelial PHD2/HIF axis in the regulation of vascular function. We found that inactivation of Phd2 in endothelial cells specifically resulted in severe pulmonary hypertension (∼118% increase in right ventricular systolic pressure) but not polycythemia and was associated with abnormal muscularization of peripheral pulmonary arteries and right ventricular hypertrophy. Concurrent inactivation of either Hif1a or Hif2a in endothelial cell-specific Phd2 mutants demonstrated that the development of pulmonary hypertension was dependent on HIF-2α but not HIF-1α. Furthermore, endothelial HIF-2α was required for the development of increased pulmonary artery pressures in a model of pulmonary hypertension induced by chronic hypoxia. We propose that these HIF-2-dependent effects are partially due to increased expression of vasoconstrictor molecule endothelin 1 and a concomitant decrease in vasodilatory apelin receptor signaling. Taken together, our data identify endothelial HIF-2 as a key transcription factor in the pathogenesis of pulmonary hypertension.
Implementation of conservation voltage reduction at Commonwealth Edison (1990)

The implementation of a conservation voltage reduction program is described. Such a program involves the calibration of substation voltage-regulating equipment so that distribution system voltages are maintained at as low a level as possible within the standard acceptable range. Initial distribution system voltmeter data were used to estimate potential voltage reductions. Program results show that an average reduction of 1.6 V was achieved. Comparison of this result with the initial estimate indicates that the feasibility of additional voltage reductions depends on the definition of acceptable service quality.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Predictors of Conversion to Multiple Sclerosis in Patients with Clinical Isolated Syndrome Using the 2010 Revised McDonald Criteria (2012)

Background. Clinically isolated syndrome (CIS) is the first neurologic episode of multiple sclerosis (MS). Magnetic resonance imaging (MRI) and clinical features are used to predict risk of conversion to MS. Objectives. The aim of this prospective study is to evaluate predictors of conversion of CIS to McDonald MS. Method. 97 patients with CIS have been followed for 2 years. Age of onset, gender, initial clinical presentation, and MRI brain and spine were assessed. The 2010 revised McDonald criteria were applied. Results. Fifty-nine patients (60.8%) with CIS converted to McDonald MS after 10.1 + 4.2 months. Thirty-seven (38.1%) of the convertors satisfied the diagnostic criteria based on the radiological parameters, while 21.7% sustained their second clinical events. A multivariate regression analysis revealed that high number of lesions in MRI (P = 0.001) and earlier age of onset (P = 0.043) predicted the conversion of CIS to McDonald MS. Gender (P = 0.5) and initial clinical presentation (optic pathway (P = 0.4), supratentorial (P = 0.91), brain stem/ cerebellum (P = 0.97), and spinal (P = 0.76)) were not statistically significant. Conclusion. Age of onset and MRI parameters can be used as predictors of CIS conversion to McDonald MS. Application of the 2010 revised McDonald criteria allows an earlier MS diagnosis.
Human myeloma cells promote the production of interleukin 6 by primary human osteoblasts (2000)

Interleukin-6 (IL-6) is an important growth and survival factor for myeloma cells. However, the identity of the cells producing IL-6 in vivo remains unclear. Myeloma cells are found closely associated with sites of active bone turnover, and cells of the osteogenic lineage, including bone marrow osteoprogenitors, osteoblasts and bone lining cells, may therefore be ideally placed to synthesize IL-6. We have examined the possibility that human osteogenic cells may produce IL-6 in response to stimulation by myeloma cells. Primary human osteoblasts (hOBs) were isolated from normal donors, co-cultured with the human myeloma cell lines, JJN-3, RPMI-8226 and NCI-H929, and the amount of IL-6 released was determined by enzyme-linked immunosorbent assay (ELISA). All myeloma cells stimulated a significant increase in the production of IL-6 when cultured with hOBs (P < 0.05). Prior fixation of hOBs completely abrogated release of IL-6 in the co-cultures. In contrast, fixed myeloma cells retained the ability to induce IL-6 production, suggesting that hOBs were the principal source of IL-6. Physical separation of myeloma cells from hOBs using transwell inserts caused a partial inhibition of IL-6 release (P < 0.05), whereas the addition of media conditioned by myeloma cells to cultures of hOBs stimulated a significant increase in IL-6 production (P < 0.05). hOBs secreted greater amounts of IL-6 than human bone marrow stromal cells (hBMSCs) (2.2- to 3.5-fold, P < 0.05), but incubating hBMSCs with dexamethasone to stimulate osteoblastic differentiation resulted in an increase in their ability to produce IL-6 (1.7- to 4. 8-fold, P < 0.05) and to respond to myeloma cells (P < 0.05). These data clearly indicate that cells of the osteoblast lineage release significant amounts of IL-6 in response to stimulation by myeloma cells and may contribute to the IL-6 that promotes the proliferation and survival of myeloma cells in vivo.
Directional Lapped Transforms for Image Coding (2009)

In this paper, we present the design of directional lapped transforms for image coding. A lapped transform, which can be implemented by a prefilter followed by a discrete cosine transform (DCT), can be factorized into elementary operators. The corresponding directional lapped transform is generated by applying each elementary operator along a given direction. The proposed directional lapped transforms are not only nonredundant and perfectly reconstructed, but they can also provide a basis along an arbitrary direction. These properties, along with the advantages of lapped transforms, make the proposed transforms appealing for image coding. A block-based directional transform scheme is also presented and integrated into HD Phtoto, one of the state-of-the-art image coding systems, to verify the effectiveness of the proposed transforms.