gebhart/patrepeval huggingface dataset:
Acute lung inflammation induced in the rabbit by local instillation of 1-0-octadecyl-2-acetyl-sn-glyceryl-3-phosphorylcholine or of native platelet-activating factor. (1983)

The intratracheal instillation into rabbits of 1-0-octadecyl-2-acetyl-sn-glyceryl-3-phosphorylcholine (AGEPC) or native platelet-activating factor (PAF) was shown to induce a dose-dependent acute pulmonary inflammation characterized by accumulation of macrophages in the alveolar space, degenerative and necrotic changes of alveolar epithelium, and accumulation of polymorphonuclear leukocytes (PMNs) and platelets in the alveolar capillary lumens with degenerative changes of endothelial cells. Infiltration of alveolar septa by inflammatory cells and, in a later stage, pulmonary fibrosis were also observed. Intrabronchial instillation of lysoglyceryl ether phosphorylcholine (lyso-GEPC) produced no inflammatory changes or only mild ones. In comparison with acute inflammation induced by intratracheal instillation of C5a des Arg, which is mainly characterized by the presence of neutrophils, red blood cells, and fibrin in the alveolar space, AGEPC and native PAF seem to induce a more severe accumulation of macrophages in the alveolar space and septa and of platelet and PMNs in the lumens of alveolar capillaries. These results are compatible with the concept that during inflammatory reaction an intraalveolar release of PAF contributes to the development of pulmonary injury.
On the possibility of extending the lifetime of lithium-ion batteries through optimal V2G facilitated by an integrated vehicle and smart-grid system (2017)

Renewable energies are a key pillar of power sector decarbonisation. Due to the variability and uncertainty they add however, there is an increased need for energy storage. This adds additional infrastructure costs to a degree that is unviable: for an optimal case of 15 GW of storage by 2030, the cost of storage is circa: £1000/kW. A promising solution to this problem is to use the batteries contained within electric vehicles (EVs) equipped with bi-directional charging systems to facilitate ancillary services such as frequency regulation and load balancing through vehicle to grid (V2G) technologies. Some authors have however dismissed V2G as economically unviable claiming the cost of battery degradation is larger than arbitrage. To thoroughly address the viability of V2G technologies, in this work we develop a comprehensive battery degradation model based on long-term ageing data collected from more than fifty long-term degradation experiments on commercial C6/LiNiCoAlO2 batteries. The comprehensive model accounts for all established modes of degradation including calendar age, capacity throughput, temperature, state of charge, depth of discharge and current rate. The model is validated using six operationally diverse real-world usage cycles and shows an average maximum transient error of 4.6% in capacity loss estimates and 5.1% in resistance rise estimates for over a year of cycling. This validated, comprehensive battery ageing model has been integrated into a smart grid algorithm that is designed to minimise battery degradation. We show that an EV connected to this smart-grid system can accommodate the demand of the power network with an increased share of clean renewable energy, but more profoundly that the smart grid is able to extend the life of the EV battery beyond the case in which there is no V2G. Extensive simulation results indicate that if a daily drive cycle consumes between 21% and 38% state of charge, then discharging 40%–8% of the batteries state of charge to the grid can reduce capacity fade by approximately 6% and power fade by 3% over a three month period. The smart-grid optimisation was used to investigate a case study of the electricity demand for a representative University office building. Results suggest that the smart-grid formulation is able to reduce the EVs' battery pack capacity fade by up to 9.1% and power fade by up to 12.1%.
Physiological Ecology of <i>Stenoxybacter acetivorans</i> , an Obligate Microaerophile in Termite Guts (2007)

Stenoxybacter acetivorans is a newly described, obligately microaerophilic beta-proteobacterium that is abundant in the acetate-rich hindgut of Reticulitermes. Here we tested the hypotheses that cells are located in the hypoxic, peripheral region of Reticulitermes flavipes hindguts and use acetate to fuel their O(2)-consuming respiratory activity in situ. Physical fractionation of R. flavipes guts, followed by limited-cycle PCR with S. acetivorans-specific 16S rRNA gene primers, indicated that cells of this organism were indeed located primarily among the microbiota colonizing the hindgut wall. Likewise, reverse transcriptase PCR of hindgut RNA revealed S. acetivorans-specific transcripts for acetate-activating enzymes that were also found in cell extracts (acetate kinase and phosphotransacetylase), as well as transcripts of ccoN, which encodes the O(2)-reducing subunit of high-affinity cbb(3)-type cytochrome oxidases. However, S. acetivorans strains did not possess typical enzymes of the glyoxylate cycle (isocitrate lyase and malate synthase A), suggesting that they may use an alternate pathway to replenish tricarboxylic acid cycle intermediates or they obtain such compounds (or their precursors) in situ. Respirometric measurements indicated that much of the O(2) consumption by R. flavipes worker larvae was attributable to their guts, and the potential contribution of S. acetivorans to O(2) consumption by extracted guts was about 0.2%, a value similar to that obtained for other hindgut bacteria examined. Similar measurements obtained with guts of larvae prefed diets to disrupt major members of the hindgut microbiota implied that most of the O(2) consumption observed with extracted guts was attributable to protozoans, a group of microbes long thought to be "strict anaerobes."
Video summarization with supervised learning (2008)

We present a video summarization technique based on supervised learning. Within a class of videos of similar nature, user provides the desired summaries for a subset of videos. Based on this supervised information, the summaries for other videos in the same class are generated. We derive frame-transitional features and subsequently represent each frame transition as a state. We then formulate a loss functional to quantify the discrepency between state transitional probabilities in the original video and that in the intended summary video, and optimize this functional. We experimentally validate the performance of the technique using cross-validation scores on two different class of videos, and demonstrate that the proposed technique is able to produce high quality summarization capturing the user perception.
Characterization of Two Distinct Dual Specificity Phosphatases Encoded in Alternative Open Reading Frames of a Single Gene Located on Human Chromosome 10q22.2 (2004)

Dual specificity phosphatases (DSPs) are members of the protein-tyrosine phosphatase superfamily that dephosphorylate both phosphotyrosine and phosphoserine/threonine residues in vitro. Many DSPs have been found to play important roles in various aspects of cellular function and to be involved in human disease. We have identified a gene located on human chromosome 10q22.2, which utilizes alternative open reading frames (ORFs) to encode the following two distinct DSPs: the previously described testis and skeletal muscle-specific dual specificity phosphatase (TMDP) and a novel DSP, muscle-restricted dual specificity phosphatase (MDSP). Use of alternative ORFs encoding distinct proteins from a single gene is extremely rare in eukaryotes, and in all previously reported cases the two proteins produced from one gene are unrelated. To our knowledge this is the first example of a gene from which two distinct proteins of the same family are expressed using alternative ORFs. Here we provide evidence that both MDSP and TMDP proteins are expressed in vivo and are restricted to specific tissues, skeletal muscle and testis, respectively. Most interestingly, the protein expression profiles of both MDSP and TMDP during mouse postnatal development are strikingly similar. MDSP is expressed at very low levels in myotubes and early postnatal muscle. TMDP is not detectable in testis lysate in the first 3 weeks of life. The expression of both MDSP and TMDP proteins was markedly increased at approximately the 3rd week after birth and continued to increase gradually into adulthood, implying that the physiological functions of both DSPs are specific to the mature/late-developing organs. The conserved gene structure and the similarity in postnatal expression profile of these two proteins suggest biological significance of the unusual gene arrangement.
Lanthanide-induced relaxation anisotropy (2018)

Lanthanide ions accelerate nuclear spin relaxation by two primary mechanisms: dipolar and Curie. Both are commonly assumed to depend on the length of the lanthanide-nucleus vector, but not on its direction. Here we show experimentally that this is wrong - careful proton relaxation data analysis in a series of isostructural lanthanide complexes (Ln = Tb, Dy, Ho, Er, Tm, Yb) reveals angular dependence in both Curie and dipolar relaxation. The reasons are: (a) that magnetic susceptibility anisotropy can be of the same order of magnitude as the isotropic part (contradicting the unstated assumption in Guéron's theory of the Curie relaxation process), and (b) that zero-field splitting can be much stronger than the electron Zeeman interaction (Bloembergen's original theory of the lanthanide-induced dipolar relaxation process makes the opposite assumption). These factors go beyond the well researched cross-correlation effects; they alter the relaxation theory treatment and make strong angular dependencies appear in the nuclear spin relaxation rates. Those dependencies are impossible to ignore - this is now demonstrated both theoretically and experimentally, and suggests that a major revision is needed of the way lanthanide-induced relaxation data are used in structural biology.
Pharmacological effects of nalorphine and nalorphine-7,8-oxide (nalorphine-epoxide): interaction of the intrinsic activity, affinity and pharmacological responses. (1986)

We examined the relationship between the pharmacological effects and the interactions of the receptors of nalorphine and its epoxide. The abilities of nalorphine-epoxide to displace [3H]-dihydromorphine (mu-site) and [3H]-ethylketocyclazocine (kappa-site) were practically equal to those of the parent compound, nalorphine, using binding assay to the rat brain membrane preparations. Furthermore, the affinities of mu- and kappa-receptors are virtually uninfluenced by epoxidation of the 7,8-double bond of nalorphine using electrically stimulated mouse and rabbit vasa deferentia. The intrinsic activity of nalorphine, however, is considerably decreased by epoxidation. Moreover, the antagonistic effect of nalorphine to the morphine-induced antinociception (via mu-receptors) was little influenced by epoxidation, but the antinociceptive effect of nalorphine using the acetic acid writhing test was considerably reduced by epoxidation. These results suggest the presence of a higher receptor capacity for the antinociception mediated through kappa-receptors and that the differences between the pharmacological responses of nalorphine and its epoxide are due to the differences of their intrinsic activities.
Maximizing neotissue growth kinetics in a perfusion bioreactor: An in silico strategy using model reduction and Bayesian optimization (2017)

In regenerative medicine, computer models describing bioreactor processes can assist in designing optimal process conditions leading to robust and economically viable products. In this study, we started from a (3D) mechanistic model describing the growth of neotissue, comprised of cells, and extracellular matrix, in a perfusion bioreactor set-up influenced by the scaffold geometry, flow-induced shear stress, and a number of metabolic factors. Subsequently, we applied model reduction by reformulating the problem from a set of partial differential equations into a set of ordinary differential equations. Comparing the reduced model results to the mechanistic model results and to dedicated experimental results assesses the reduction step quality. The obtained homogenized model is 10<sup>5</sup> fold faster than the 3D version, allowing the application of rigorous optimization techniques. Bayesian optimization was applied to find the medium refreshment regime in terms of frequency and percentage of medium replaced that would maximize neotissue growth kinetics during 21 days of culture. The simulation results indicated that maximum neotissue growth will occur for a high frequency and medium replacement percentage, a finding that is corroborated by reports in the literature. This study demonstrates an in silico strategy for bioprocess optimization paying particular attention to the reduction of the associated computational cost.
Tumor-Associated Macrophages Regulate Murine Breast Cancer Stem Cells Through a Novel Paracrine EGFR/Stat3/Sox-2 Signaling Pathway (2012)

The cancer stem cell (CSC) hypothesis has gained significant recognition as a descriptor of tumorigenesis. Additionally, tumor-associated macrophages (TAMs) are known to promote growth and metastasis of breast cancer. However, it is not known whether TAMs mediate tumorigenesis through regulation of breast CSCs. Here, we report that TAMs promote CSC-like phenotypes in murine breast cancer cells by upregulating their expression of Sox-2. These CSC-like phenotypes were characterized by increased Sox-2, Oct-4, Nanog, AbcG2, and Sca-1 gene expression, in addition to increased drug-efflux capacity, resistance to chemotherapy, and increased tumorigenicity in vivo. Downregulation of Sox-2 in tumor cells by siRNA blocked the ability of TAMs to induce these CSC-like phenotypes and inhibited tumor growth in vivo. Furthermore, we identified a novel epidermal growth factor receptor (EGFR)/signal transducers and activators of transcription 3 (Stat3)/Sox-2 paracrine signaling pathway between macrophages and mouse breast cancer cells that is required for macrophage-induced upregulation of Sox-2 and CSC phenotypes in tumor cells. We showed that this crosstalk was effectively blocked by the small molecule inhibitors AG1478 or CDDO-Im against EGFR and Stat3, respectively. Therefore, our report identifies a novel role for TAMs in breast CSC regulation and establishes a rationale for targeting the EGFR/Stat3/Sox-2 signaling pathway for CSC therapy.
Lupus-related myelitis: serial MR findings. (1994)

Spinal cord widening and signal abnormalities are common MR findings during episodes of transverse myelitis related to systemic lupus erythematosus, and contrast enhancement is less frequently seen. Improvement or resolution of these findings correlates with clinical improvement.
Interaction Between Primary Alveolar Macrophages and Primary Alveolar Type II Cells Under Basal Conditions and After Lipopolysaccharide Or Quartz Exposure (2006)

Intercellular communications between alveolar macrophages (AM) and alveolar epithelial type II (TII) cells have been suggested to be important in cellular responses. The main objective of this study was to improve our understanding of the interactions between AM and TII cells that might occur in the lung. In the present investigation, this interaction was studied under different interaction conditions (transwell or mixed coculture) and different exposure conditions (basal, lipopolysaccharide [LPS] exposure, or silica exposure). Studies also attempted different approaches to identify specific mediator(s) involved in this interaction. The following findings were made: (1) Surfactant released from TII cells appears to exert an inhibitory effect on AM activity. (2) Basal transwell coculture conditions are better than mixed coculture conditions to study AM/TII cell interactions, since the inhibitory effect of the surfactant in the transwell coculture is minimized. (3) AM/TII cell interaction is dependent on cell culture (transwell vs mixed) and exposure conditions. (4) Oxidants, tumor necrosis factor (TNF)-alpha, interleukin (IL)-1beta, prostaglandins, and leukotrienes probably do not independently affect the AM/TII intercellular interaction; instead, they appear to indirectly modulate the complex pathways of AM/TII communication.
The Tumor Metastasis Suppressor Gene <i>Drg-1</i> Down-regulates the Expression of Activating Transcription Factor 3 in Prostate Cancer (2006)

The tumor metastasis suppressor gene Drg-1 has been shown to suppress metastasis without affecting tumorigenicity in immunodeficient mouse models of prostate and colon cancer. Expression of Drg-1 has also been found to have a significant inverse correlation with metastasis or invasiveness in various types of human cancer. However, how Drg-1 exerts its metastasis suppressor function remains unknown. In the present study, to elucidate the mechanism of action of the Drg-1 gene, we did a microarray analysis and found that induction of Drg-1 significantly inhibited the expression of activating transcription factor (ATF) 3, a member of the ATF/cyclic AMP-responsive element binding protein family of transcription factors. We also showed that Drg-1 attenuated the endogenous level of ATF3 mRNA and protein in prostate cancer cells, whereas Drg-1 small interfering RNA up-regulated the ATF3 expression. Furthermore, Drg-1 suppressed the promoter activity of the ATF3 gene, indicating that Drg-1 regulates ATF3 expression at the transcriptional level. Our immunohistochemical analysis on prostate cancer specimens revealed that nuclear expression of ATF3 was inversely correlated to Drg-1 expression and positively correlated to metastases. Consistently, we have found that ATF3 overexpression promoted invasiveness of prostate tumor cells in vitro, whereas Drg-1 suppressed the invasive ability of these cells. More importantly, overexpression of ATF3 in prostate cancer cells significantly enhanced spontaneous lung metastasis of these cells without affecting primary tumorigenicity in a severe combined immunodeficient mouse model. Taken together, our results strongly suggest that Drg-1 suppresses metastasis of prostate tumor cells, at least in part, by inhibiting the invasive ability of the cells via down-regulation of the expression of the ATF3 gene.
ChemInform Abstract: HERST. VON 2,4,6‐TRIPHENYL‐1,3,5‐TRIAZIN (1973)

Abstract Benzonitril (I) läßt sich durch Chlorsulfonsäure bei 0‐5°C während 12 ‐ 24 Stdn. zu 2,4,6‐Triphenyl‐1,3,5‐triazin (II) trimerisieren (Ausbeute 85 ‐ 88%).
Air Flow and Heat Transfer in a Temperature-Controlled Open Top Enclosure (2012)

A large 12-meter-diameter open top enclosure (OTE) equipped with two unique belowground and above ground heating systems was built and intensively tested in Oak Ridge, TN, USA. The OTE is a prototype for use within an environmental change experiment, in which replica units will be built in Minnesota to assess the response of northern peatland ecosystems to increases in temperature and elevated atmospheric CO2. For several months, temperatures, energy, wind speed and relative humidity were monitored throughout the enclosure space to assess the enclosure performance and efficiency. In parallel, Computational Fluid Dynamics (CFD) simulations were performed with ANSYS-CFX to investigate the impacts of external wind, buoyancy, and OTE design on the temperatures achieved within the enclosure. The addition of a frustum that partially reduced the top opening was also investigated experimentally and numerically. The OTE is capable of achieving a temperature differential of at least +6°C for air using a combination of 8 electrical heaters. Differential temperatures were sustained for several months. The experimental data and the numerical results showed that the addition of a frustum dramatically decreases the operating cost of the OTE and leads to better control over the differential air temperature in the enclosure. Buoyancy forces and winds heavily impacted enclosure performance. It was also found that the heating efficiency of the OTE depends mainly on the wind speed, and that there exists a critical wind speed at which the heating efficiency is the highest.
Shiga Toxin 2-Converting Bacteriophages Associated with Clonal Variability in <i>Escherichia coli</i> O157:H7 Strains of Human Origin Isolated from a Single Outbreak (2003)

Shiga toxin 2 (Stx2)-converting bacteriophages induced from 49 strains of Escherichia coli O157:H7 isolated during a recent outbreak of enterocolitis in Spain were examined in an attempt to identify the variability due to the stx(2)-converting phages. The bacterial isolates were divided into low-, medium-, and high-phage-production groups on the basis of the number of phages released after mitomycin C induction. Low- and medium-phage-production isolates harbored two kinds of phages but released only one of them, whereas high-phage-production isolates harbored only one of the two phages. One of the phages, phi SC370, which was detected only in the isolates with two phages, showed similarities with phage 933W. The second phage, phi LC159, differed from phi SC370 in morphology and DNA structure. When both phages were present in the same bacterial chromosome, as occurred in most of the isolates, only phi SC370 was detected in the supernatants of the induced cultures. If phi LC159 was released, its presence was masked by phi SC370. When phi SC370 was absent, large amounts of phi LC159 were released, suggesting that there was some regulation of phage expression between the two phages. To our knowledge, this is the first description of clonal variability due to phage loss. The higher level of phage production was reflected in the larger amounts of Stx2 toxin produced by the cultures. Some relationship between phage production and the severity of symptoms was observed, and consequently these observations suggest that the virulence of the isolates studied could be related to the variability of the induced stx(2)-converting phages.
Fully Automated Production of 68Ga-DOTA-NOC with a Trasis miniAIO® Synthesizer (2013)

GaGe
Evolutionary computation in bioinformatics (2007)

Bioinformatics has never been as popular as it is today. The genomics revolution is generating so much data in such rapid succession that it has become difficult for biologists to decipher. In particular, there are many problems in biology that are too large to solve with standard methods. Researchers in evolutionary computation (EC) have turned their attention to these problems. They understand the power of EC to rapidly search very large and complex spaces and return reasonable solutions. While these researchers are increasingly interested in problems from the biological sciences, EC and its problem-solving capabilities are generally not yet understood or applied in the biology community. This book offers a definitive resource to bridge the computer science and biology communities. Gary Fogel and David Corne, well-known representatives of these fields, introduce biology and bioinformatics to computer scientists, and evolutionary computation to biologists and computer scientists unfamiliar with these techniques. The fourteen chapters that follow are written by leading computer scientists and biologists who examine successful applications of evolutionary computation to various problems in the biological sciences. * Describes applications of EC to bioinformatics in a wide variety of areas including DNA sequencing, protein folding, gene and protein classification, drug targeting, drug design, data mining of biological databases, and biodata visualization.* Offers industrial and academic researchers in computer science, biology, and bioinformatics an important resource for applying evolutionary computation.* Includes a detailed appendix of biological data resources.