gebhart/patrepeval huggingface dataset:
Estrogen affects levels of Bcl‐2 protein and mRNA in medial amygdala of ovariectomized rats (2008)

The survival factor Bcl-2 is a cyclic AMP response element-binding protein (CREB) gene product implicated in mediating some of estrogen's effects on neuroprotection. Previously, we showed an effect of estradiol benzoate (E) on numbers of neuron-specific protein (NeuN)- and phosphorylated CREB (pCREB)-positive cells in medial (MeA), but not central (CeA), amygdala of ovariectomized rats. To determine whether these effects are accompanied by an E-induced increase in Bcl-2, we examined the effects of E on levels of Bcl-2 protein and mRNA in MeA and CeA of ovariectomized rats treated with E regimens resulting in moderate (2.5 microg E for 4 or 14 days) or high (10 microg E for 14 days) plasma estradiol levels. As a physiological control, we showed that all E treatments increased uterine wet weight relative to vehicle; 10 microg E for 14 days also increased uterine weight compared with that seen with lower E levels. Western blot analysis revealed that all E groups displayed an increase in uterine Bcl-2 protein levels compared with vehicle. We found that 2.5 microg and 10 microg E for 14 days increased levels of Bcl-2 gold immunolabeling compared with vehicle and 2.5 microg E for 4 days in MeA, but not CeA. We measured Bcl-2 mRNA levels in vehicle and 2.5 microg E-treated 14-day groups. There was a significant increase in Bcl-2 mRNA levels in MeA, but not CeA, of E-treated ovariectomized rats compared with vehicle controls. The E-induced increase in protein and mRNA levels of Bcl-2 in MeA may be important for neuroprotection in this region.
Alkali Metal Fluorides in Organic Synthesis (1983)

Some applications of alkali metal fluorides in organic synthesis are reviewed. The use of alkali metal fluorides as catalysts in the reactions of fluorine-containing compounds is also discussed. 1. Introduction 2. Elimination of Hydrogen Halides 3. Michael and Knoevenagel Reactions 4. Decarboxylation 5. Reactions of Fluorine-Containing Compounds 5.1. Reactions of Polyfluoroolefins 5.2. Polymerisation 5.3. Reactions of Carbonyl-Containing Compounds 5.4. Reactions with Halogens
Lifetime Prediction of All-ceramic Bridges by Computational Methods (2003)

There has been limited use of ceramic materials for all-ceramic posterior bridges. Major reasons are the low strength, the strength scatter, and the time-dependent strength decrease of ceramics due to slow crack growth. The objective of this study was to predict the long-term failure probability and loading capability of all-ceramic bridges (Empress 1, Empress 2, In-Ceram Alumina, and ZrO(2)) by computational techniques. The lifetimes of different bridge model designs were predicted by means of the NASA post-processor CARES. Bridges made of zirconia showed a very high mechanical long-term reliability. Empress I and InCeram Alumina seem to be insufficient as posterior bridge materials based on this prediction. The lifetime of the all-ceramic bridges can be significantly increased by improving the design in the connector area. We conclude that computational techniques can help to judge a ceramic material and a specific ceramic bridge design with respect to mechanical reliability before clinical use.
The Neural Autoregressive Distribution Estimator (2011)

We describe a new approach for modeling the distribution of high-dimensional vectors of dis-crete variables. This model is inspired by the restricted Boltzmann machine (RBM), which has been shown to be a powerful model of such distributions. However, an RBM typi-cally does not provide a tractable distribution estimator, since evaluating the probability it assigns to some given observation requires the computation of the so-called partition func-tion, which itself is intractable for RBMs of even moderate size. Our model circumvents this difficulty by decomposing the joint dis-tribution of observations into tractable condi-tional distributions and modeling each condi-tional using a non-linear function similar to a conditional of an RBM. Our model can also be interpreted as an autoencoder wired such that its output can be used to assign valid probabilities to observations. We show that this new model outperforms other multivari-ate binary distribution estimators on several datasets and performs similarly to a large (but intractable) RBM. 1
Mutagenesis of the hairpin ribozyme (1994)

Extensive in vitro mutagenesis studies have been performed on the hairpin ribozyme and substrate in an effort to refine the overall secondary structure of the molecule and provide further insight into what elements are essential for activity. A secondary structure consisting of four helices and five loop regions remains the basic model as originally proposed. Two helices, helix 1 and 2, form between the substrate and ribozyme while helices 3 and 4 are within the ribozyme itself. Our results suggest that helices 3 and 4 are smaller than previously proposed, consisting of four base pairs and three base pairs respectively. Helix 4 can be extended without loss of activity and loop 3 at the closed end of the hairpin model can be varied in sequence with retention of activity. There is an unpaired nucleotide between helices 2 and 3 consisting of a single A base, suggesting the opportunity for flexibility within the tertiary structure at this point. Comparisons are made between the new data and previously published mutagenesis and phylogenetic data. Substrate targeting rules require base pairing between helices 1 and 2 with cleavage (*) occurring in a preferred 5'(g/c/u)n*guc3' sequence of the substrate.
Engineering Fundamentals of the Internal Combustion Engine (1997)

This applied thermoscience book covers the basic principles and applications of various types of internal combustion engines. Explores the fundamentals of most types of internal combustion engines with a major emphasis on reciprocating engines. Covers both spark ignition and compression ignition engines as well as those operating on four-stroke cycles and on two-stroke cycles ranging in size from small model airplane engines to the larger stationary engines. Examines recent advancements, such as, Miller cycle analysis, lean burn engines, 2-stroke cycle automobile engines, variable valve timing, and thermal storage.
Aberrant repair and fibrosis development in skeletal muscle (2011)

The repair process of damaged tissue involves the coordinated activities of several cell types in response to local and systemic signals. Following acute tissue injury, infiltrating inflammatory cells and resident stem cells orchestrate their activities to restore tissue homeostasis. However, during chronic tissue damage, such as in muscular dystrophies, the inflammatory-cell infiltration and fibroblast activation persists, while the reparative capacity of stem cells (satellite cells) is attenuated. Abnormal dystrophic muscle repair and its end stage, fibrosis, represent the final common pathway of virtually all chronic neurodegenerative muscular diseases. As our understanding of the pathogenesis of muscle fibrosis has progressed, it has become evident that the muscle provides a useful model for the regulation of tissue repair by the local microenvironment, showing interplay among muscle-specific stem cells, inflammatory cells, fibroblasts and extracellular matrix components of the mammalian wound-healing response. This article reviews the emerging findings of the mechanisms that underlie normal versus aberrant muscle-tissue repair.
Living planktonic foraminifera from the Gulf of California (1973)

Vertical, horizontal and surface plankton tows, distribution and depth concentration discussed
PERK and GCN2 Contribute to eIF2α Phosphorylation and Cell Cycle Arrest after Activation of the Unfolded Protein Response Pathway (2005)

Exposure of cells to endoplasmic reticulum (ER) stress leads to activation of PKR-like ER kinase (PERK), eukaryotic translation initiation factor 2alpha (eIF2alpha) phosphorylation, repression of cyclin D1 translation, and subsequent cell cycle arrest in G1 phase. However, whether PERK is solely responsible for regulating cyclin D1 accumulation after unfolded protein response pathway (UPR) activation has not been assessed. Herein, we demonstrate that repression of cyclin D1 translation after UPR activation occurs independently of PERK, but it remains dependent on eIF2alpha phosphorylation. Although phosphorylation of eIF2alpha in PERK-/- fibroblasts is attenuated in comparison with wild-type fibroblasts, it is not eliminated. The residual eIF2alpha phosphorylation correlates with the kinetics of cyclin D1 loss, suggesting that another eIF2alpha kinase functions in the absence of PERK. In cells harboring targeted deletion of both PERK and GCN2, cyclin D1 loss is attenuated, suggesting GCN2 functions as the redundant kinase. Consistent with these results, cyclin D1 translation is also stabilized in cells expressing a nonphosphorylatable allele of eIF2alpha; in contrast, repression of global protein translation still occurs in these cells, highlighting a high degree of specificity in transcripts targeted for translation inhibition by phosphorylated eIF2alpha. Our results demonstrate that PERK and GCN2 function to cooperatively regulate eIF2alpha phosphorylation and cyclin D1 translation after UPR activation.
Dimensioning of self-healing rings and their interconnections (2002)

A new hierarchical self-healing ring (H-SHR) architecture for survivability is proposed and dimensioned. First, the dimensioning of single SHRs (unidirectional and bidirectional) is considered. Closed form expressions of required capacity are presented for single SHRs under three uniform demand patterns. For general demand, a new routing algorithm which complements the shortest path routing algorithm in attempt to reduce the capacity requirement is proposed. Then it is shown that the dimensioning of H-SHRs can be converted into the dimensioning of each single rings inside it by performing translation of original demand. Thus the new routing algorithm can be used in dimensioning of H-SHR networks. Closed form expressions for uniform H-SHRs using shortest path routing are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hepatic microsome studies are insufficient to characterize in vivo hepatic metabolic clearance and metabolic drug-drug interactions: studies of digoxin metabolism in primary rat hepatocytes versus microsomes. (2004)

The effects of hepatic uptake and efflux transporters on metabolism of digoxin were examined in isolated rat hepatocytes versus microsomes. The metabolic clearance estimated from microsomes was 4.59 +/- 0.69 ml/min/kg. However, the metabolic clearance estimated from hepatocytes was 15.9 +/- 3.0 ml/min/kg. The former did not correlate with in vivo clearance (12.9 ml/min/kg) for digoxin. Rifampin (an organic anion-transporting peptide 2 inhibitor) or GG918 [GF120918 (N-(4-[2-(1,2,3,4-tetrahydro-6,7-dimethoxy-2-isoquinolinyl)ethyl]-phenyl)-9,10-dihydro-5-methoxy-9-oxo-4-acridine carboxamide)] (a potent P-glycoprotein inhibitor) were used to estimate effects of uptake or efflux transporters on digoxin metabolism. Whereas both inhibitors exerted minimal effects on metabolism in microsomes, rifampin and GG918 significantly decreased and increased digoxin metabolism in hepatocytes, respectively. Concentration-time course studies further demonstrated that, compared with the area under the curve (AUC) of control (15.6 +/- 0.1 microM . min), an increase of AUC (20.1 +/- 0.5 microM . min, p < 0.005) was observed when digoxin was coincubated with rifampin and a decrease of AUC (14.1 +/- 0.1 microM . min, p < 0.01) when GG918 was also present. Digoxin primary metabolite concentrations changed directionally in an inverse manner with parent drug concentrations, as would be expected. These results strongly suggest that the hepatic uptake and efflux transporters that are found in hepatocytes, but not in microsomes, modulate intracellular concentration of digoxin and thus affect metabolism. We conclude that the interplay of transporters and enzymes must be considered in defining the intrinsic metabolic clearance of the liver and in evaluating potential drug-drug interactions.
An immunodominant cytotoxic T cell epitope on the VP7 rotavirus protein overlaps the H2 signal peptide (1993)

C57BL/6 (1-1-2 b) mice were primed with the bovine RF strain of rotavirus to study the induction of CD8 + cytotoxic T lymphocytes (CTLs). These rotavirus-specific CTLs were detected only after in vitro restimula-tion with the virus. Using a recombinant vaccinia virus we identified the RF VP7 protein as a major target of these CTLs. The response against this protein was obtained also after in vitro restimulation with simian SA11 and human WA strains of rotavirus. Using published D b and K b allele-specific motifs to predict possible CTL epitopes in the RF VP7 protein, we synthesized and tested 18 predicted peptides of VP7. Only one peptide was able to sensitize target cells at a concentration below 5 × 10-7 M. This CTL epitope was also induced by immunization with the RF VP7 expressed with a baculovirus vector, and was shown to be immunodominant byits capacity to inhibit, in an unlabelled target assay, the bulk response against ceils infected with recombinant vaccinia virus expressing VP7. This CTL epitope overlaps the H2 signal peptide of the protein.
Correction of MFG-E8 Resolves Inflammation and Promotes Cutaneous Wound Healing in Diabetes (2016)

Milk fat globule epidermal growth factor-factor 8 (MFG-E8) is a peripheral glycoprotein that acts as a bridging molecule between the macrophage and apoptotic cells, thus executing a pivotal role in the scavenging of apoptotic cells from affected tissue. We have previously reported that apoptotic cell clearance activity or efferocytosis is compromised in diabetic wound macrophages. In this work, we test the hypothesis that MFG-E8 helps resolve inflammation, supports angiogenesis, and accelerates wound closure. MFG-E8(-/-) mice displayed impaired efferocytosis associated with exaggerated inflammatory response, poor angiogenesis, and wound closure. Wound macrophage-derived MFG-E8 was recognized as a critical driver of wound angiogenesis. Transplantation of MFG-E8(-/-) bone marrow to MFG-E8(+/+) mice resulted in impaired wound closure and compromised wound vascularization. In contrast, MFG-E8(-/-) mice that received wild-type bone marrow showed improved wound closure and improved wound vascularization. Hyperglycemia and exposure to advanced glycated end products inactivated MFG-E8, recognizing a key mechanism that complicates diabetic wound healing. Diabetic db/db mice suffered from impaired efferocytosis accompanied with persistent inflammation and slow wound closure. Topical recombinant MFG-E8 induced resolution of wound inflammation, improvements in angiogenesis, and acceleration of closure, upholding the potential of MFG-E8-directed therapeutics in diabetic wound care.
Enabling Continuous‐Flow Chemistry in Microstructured Devices for Pharmaceutical and Fine‐Chemical Production (2008)

Abstract Microstructured devices offer unique transport capabilities for rapid mixing, enhanced heat and mass transfer and can handle small amounts of dangerous or unstable materials. The integration of reaction kinetics into fluid dynamics and transport phenomena is essential for successful application from process design in laboratory to chemical production. Strategies to implement production campaigns up to tons of pharmaceutical chemicals are discussed, based on Lonza projects.
Self-esteem in patients with rheumatic diseases : The role of body-self unity (2008)

Background: Maintaining positive self-esteem is one of the challenges for patients with chronic diseases. Limitations in physical functioning, often associated with having a rheumatic disease, can influence the perception of the body as belonging to the person (or as detached from the self) and might thereby finally affect the self-esteem of patients. The concept of body-self unity has been investigated in a phenomenological research tradition that works with qualitative methodology and small samples. Objectives: To develop a questionnaire to measure body-self unity quantitatively and to investigate the predictive value of body-self unity for self-esteem in patients with rheumatic diseases. Methods: The Body Experience Questionnaire was developed for the measurement of body-self unity. Besides this questionnaire, illness cognitions, pain intensity, functional limitations and self-esteem were measured via computers with touchscreen. 168 patients (mean age = 54,2 years, 62% female) with a rheumatic disease participated in this study consecutive visiting the rheumatology clinic. To analyse predictors of self-esteem, hierarchical regression analyses were employed (first step demographic characteristics, second step disease related variables (disease duration, functional limitations, pain), final step psychological constructs (body-self unity, illness cognitions)). Results: The Body Experience Questionnaire revealed a two factor structure with good reliability (subscale harmony, Cronbachs alpha=.76; subscale alienation, Cronbachs alpha = 0.84). The final model of the hierarchical regression analyses showed that self-esteem can be predicted by helplessness, acceptance, harmony of body and self and most strongly by the alienation of body and self. R2 of the final model was 0.50 (delta R for psychological variables in the final step was 0.28). The relation between functional limitations and self-esteem was fully mediated by the psychological constructs body self unity and illness cognitions. Conclusion: This study showed the importance of psychological characteristics and particularly the experience of the body for self-esteem in patients with a rheumatic disease. Further research should explore therapies to increase the body-self unity.
Computer animation programming methods and techniques (1995)

Dynamics of computer graphics graphics structures and manipulation image acquisition and encoding animation techniques programming user-animated objects background animation object animation modelled animation animation programming in Windows.
Interrelationships: International Economic Law and Developing Countries (2004)

This Article is an introduction to six articles that were presented at a symposium entitled Interrelationships: International Economic Law and Developing Countries, held in Washington, D.C. in October 2002 by the American Society for International Law's International Economic Law Group. What should be done to further development? All nations,1 international economic organizations,2 and most major non-governmental * Professor of Law, South Texas College of Law; Chair of the International Economic Law Group of the American Society of International Law (2001-2003). Professor Taylor was also the Chair of the 2002 Conference. 1 Every country devotes itself to development simply by seeking to improve the standard ofliving of its population. In the international arena, for example, each country seeks to not only manage its own economy but also to attract investors from outside. See generally VNCTAD, WoRLD INVESTMENT REPORT 2003: FDI PoLICIES FOR DEVELOPMENT: NATIONAL AND INTERNATIONAL PERSPECTIVES (2003), available at http:/ /www.unctad.org/en/docs/ /wir 2003_en.pdf. This report addresses the need governments feel to seek out international investment agreements (such as bilateral investment agreements), even though they appear to curtail their ability to control their own policy choices. The report focuses on how such agreements should be written, structured, and implemented in order to focus on countries' development objectives. Countries also seek to improve their economic situation by entering into regional trading arrangements. According to the World Trade Organization (VITO), by 2005, there may be 300 regional trade agreements (assuming that those planned and being negotiated come into being). See WTO, Regional Trade Agreements, at http:/ /www.wto.org/ english/tratop_e/region_e/region_e.htm (last visited Apr. 29, 2004). 2 The most obvious examples are the WTO and the World Bank. The WTO is currently in the midst of the Doha Round of negotiations. The Doha Declaration established development as the theme of this set of negotiations. Ministerial Conference, 4th Sess., Ministerial Declaration, WT/MIN(01)/DEC/1 (Nov. 20, 2001), para. 2 (International trade can play a major role in the promotion of economic development and the alleviation of poverty. We recognize the need for all our peoples to benefit from the increased opportunities and welfare gains that the multilateral trading system generates. The majority of WTO Members are developing countries. We seek to place their needs and interests at the heart ofthe Work Programme adopted in this Declaration.). WTO Members are currently struggling to restart the Doha negotiations after the inconclusive end to the Canc(m meeting in late 2003. According to WTO Director General Supachai Panitchpakdi:
Modeling human tumor angiogenesis in a three-dimensional culture system (2013)

The intrinsic complexity of the process of vessel formation limits the efficacy of cellular assays for elucidation of its molecular and pharmacologic mechanisms. We developed an ex vivo three-dimensional (3D) assay of sprouting angiogenesis with arterial explants from human umbilical cords. In this assay, human arterial rings were embedded in basement membrane extract gel, leading to a network of capillarylike structures upon vascular endothelial growth factor (VEGF) A stimulation. The angiogenic outgrowth consisted of endothelial cells, which actively internalized acetylated-low-density lipoprotein, surrounded by pericytes. Computer-assisted quantification of this vascular network demonstrated considerable sensitivity of this assay to several angiogenic inhibitors, including kinase inhibitors and monoclonal antibodies. We also performed targeted gene knockdown on this model by directly infecting explanted umbilical arteries with lentiviruses carrying short-hairpin RNA. Downregulation of VEGFR2 resulted in a significant reduction of the sprouting capability, demonstrating the relevance of human vascular explants for functional genomics studies. Furthermore, a modification of this assay led to development of a 3D model of tumor-driven angiogenesis, in which angiogenic outgrowth was sustained by spheroids of prostate cancer cells in absence of exogenous growth factors. The human arterial ring assay bridges the gap between in vitro endothelial cell and animal model, and is a powerful system for identification of genes and drugs that regulate human angiogenesis.
Direct machine parameter optimization for intensity modulated radiation therapy (IMRT) of oropharyngeal cancer – a planning study (2009)

The purpose of the study was to investigate the potential of direct machine parameter optimization (DMPO) to achieve parotid sparing without compromising target coverage in IMRT of oropharyngeal cancer as compared to fluence modulation with subsequent leaf sequencing (IM) and forward planned 2-step arc therapy (IMAT). IMRT plans were generated for 10 oropharyngeal cancer patients using DMPO and IM. The resulting dose volume histograms (DVH) were evaluated with regard to compliance with the dose volume objectives (DVO) and plan quality. DMPO met the DVO for the targets better than IM but violated the DVO to the parotids in some cases. DMPO provided better target coverage and dose homogeneity than IM and comparable to IMAT. Dose to the parotids (23Gy) was significantly lower than for IMAT (48Gy), but somewhat higher than for IM (20Gy). Parotid sparing with IM was, however, only achieved at the cost of target coverage and homogeneity. DMPO allows achieving parotid sparing in the treatment of oropharyngeal cancer without compromising target coverage and dose homogeneity in the target as compared to 2-step IMAT. Better overall plan quality can be delivered with less monitor units than with IM.