gebhart/patrepeval huggingface dataset:
Co-Construction of Hybrid Spaces (2005)

When computational systems become increasingly mobile and ubiquitous, digital information and the use of computational systems may increasingly be immersed into the physical and social world of objects, people and practices. However, the digital, physical and social materials that make up these hybrid spaces have different characteristics and are hard to understand for users. In addition, users are themselves part in constructing and re-constructing the hybrid spaces. The main question addressed in this thesis is whether making aspects of the digitally mediated hybrid spaces observable and accessible provides support to users. The observability may provide support for the specific task at hand or help in building an understanding for what the system does and how, an understanding that is needed to explain system output and to cope with service breakdowns. The fundament of the approach is to empower users of computational systems to actively make sense of the system themselves. Two prototype services are described, Socifer and MobiTip. Their common denominator was to make digitally mediated parts of the hybrid spaces observable to users. Without disqualifying other kinds of information, the work focussed on digitally mediated social trails of other users. Building on experience from the prototype work and an investigation into in seamful design, observability and awareness, I have investigated the effects of making a computational system’s social context observable to users in a way that - is separated from the service’s main functionality in the interface, allowing it to become peripheral and non-obtrusive; - uses simple models and little interpretation; - to some extent opens up the service to allow for user appropriation of both service content and functionality; and - is informative rather than proactive in order to empower the user rather than acting on the user’s behalf. By designing systems that fulfil these criteria I claim that the user will be supported in performing the task at hand, with or without the service, and that with service use, the user will become more and more aware of the possibilities and limitations of the underlying technology. In addition, the digitally mediated hybrid spaces where physical, social and digital contexts meet constitute application domains in themselves, domains that users may enjoy exploring.
Opposing Effects of Jun Kinase and p38 Mitogen-Activated Protein Kinases on Cardiomyocyte Hypertrophy (1998)

c-Jun N-terminal protein kinase (JNK) and p38, two distinct members of the mitogen-activated protein (MAP) kinase family, regulate gene expression in response to various extracellular stimuli, yet their physiological functions are not completely understood. In this report we show that JNK and p38 exerted opposing effects on the development of myocyte hypertrophy, which is an adaptive physiological process characterized by expression of embryonic genes and unique morphological changes. In rat neonatal ventricular myocytes, both JNK and p38 were stimulated by hypertrophic agonists like endothelin-1, phenylephrine, and leukemia inhibitory factor. Expression of MAP kinase kinase 6b (EE), a constitutive activator of p38, stimulated the expression of atrial natriuretic factor (ANF), which is a genetic marker of in vivo cardiac hypertrophy. Activation of p38 was required for ANF expression induced by the hypertrophic agonists. Furthermore, a specific p38 inhibitor, SB202190, significantly changed hypertrophic morphology induced by the agonists. Surprisingly, activation of JNK led to inhibition of ANF expression induced by MEK kinase 1 (MEKK1) and the hypertrophic agonists. MEKK1-induced ANF expression was also negatively regulated by expression of c-Jun. Our results demonstrate that p38 mediates, but JNK suppresses, the development of myocyte hypertrophy.
Five Specific Protein-Transfer RNA Interaction (1980)

(1980). Five Specific Protein-Transfer RNA Interaction. Critical Reviews in Biochemistry: Vol. 9, No. 3, pp. 207-251.
Detect and track latent factors with online nonnegative matrix factorization (2007)

Detecting and tracking latent factors from temporal data is an important task. Most existing algorithms for latent topic detection such as Nonnegative Matrix Factorization (NMF) have been designed for static data. These algorithms are unable to capture the dynamic nature of temporally changing data streams. In this paper, we put forward an online NMF (ONMF) algorithm to detect latent factors and track their evolution while the data evolve. By leveraging the already detected latent factors and the newly arriving data, the latent factors are automatically and incrementally updated to reflect the change of factors. Furthermore, by imposing orthogonality on the detected latent factors, we can not only guarantee the unique solution of NMF but also alleviate the partial-data problem, which may cause NMF to fail when the data are scarce or the distribution is incomplete. Experiments on both synthesized data and real data validate the efficiency and effectiveness of our ONMF algorithm. 1
THE MESOZOIC RADIATION OF EUKARYOTIC ALGAE: THE PORTABLE PLASTID HYPOTHESIS1 (2003)

Although all chloroplasts appear to have been derived from a common ancestor, a major schism occurred early in the evolution of eukaryotic algae that gave rise to red and green photoautotrophic lineages. In Paleozoic and earlier times, the fossil record suggests that oceanic eukaryotic phytoplankton were dominated by the green (chl b ‐containing) algal line. However, following the end‐Permian extinction, a diverse group of eukaryotic phytoplankton evolved from secondary symbiotic associations in the red (chl c ‐containing) line and subsequently rose to ecological prominence. In the contemporary oceans, red eukaryotic phytoplankton taxa continue to dominate marine pelagic food webs, whereas the green line is relegated to comparatively minor ecological and biogeochemical roles. To help elucidate why the oceans are not dominated by green taxa, we analyzed and compared whole plastid genomes in both the red and green lineages. Our results suggest that whereas all algal plastids retain a core set of genes, red plastids retain a complementary set of genes that potentially confer more capacity to autonomously express proteins regulating oxygenic photosynthetic and energy transduction pathways. We hypothesize that specific gene losses in the primary endosymbiotic green plastid reduced its portability for subsequent symbiotic associations. This corollary of the plastid “enslavement” hypothesis may have limited subsequent evolutionary advances in the green lineage while simultaneously providing a competitive advantage to the red lineage.
Three-Dimensional Surround Sound Systems Based on Spherical Harmonics (2005)

The theory of recording and reproduction of three-dimensional sound fields based on spherical harmonics is reviewed and extended. Free-field, sphere, and general recording arrays are reviewed, and the mode-matching and simple source approaches to sound repro-duction in anechoic environments are discussed. Both methods avoid the need for both monopole and dipole loudspeakers—as required by the Kirchhoff–Helmholtz integral. An error analysis is presented and simulation examples are given. It is also shown that the theory can be extended to sound reproduction in reverberant environments. 0
In first presentation adolescent anorexia nervosa, do cognitive markers of underweight status change with weight gain following a refeeding intervention? (2009)

Cognitive impairments in adolescent AN appear to normalize with refeeding and weight gain.
Down-regulation of transcripts for Na channel α-SNS in spinal sensory neurons following axotomy (1996)

Spinal sensory (dorsal root ganglion; DRG) neurons display slowly inactivating, tetrodotoxin-resistant (TTX-R), and rapidly inactivating, TTX-sensitive (TTX-S) Na currents. Attenuation of the TTX-R Na current and enhancement of TTX-S Na current have been demonstrated in cutaneous afferent DRG neurons in the adult rat after axotomy and may underlie abnormal bursting. We show here that steady-state levels of transcripts encoding the alpha-SNS subunit, which is associated with a slowly inactivating, TTX-R current when expressed in oocytes, are reduced significantly 5 days following axotomy of DRG neurons, and continue to be expressed at reduced levels, even after 210 days. Steady-state levels of alpha-III transcripts, which are present at low levels in control DRG neurons, show a pattern of transiently increased expression. In situ hybridization using alpha-SNS- and alpha-III-specific riboprobes showed a decreased signal for alpha-SNS, and an increased signal for alpha-III, in both large and small DRG neurons following axotomy. Reduced levels of alpha-SNS may explain the selective loss of slowly inactivating, TTX-R current. The abnormal electrophysiological properties of DRG neurons following axonal injury thus appear to reflect a switch in Na channel gene expression.
Inflammation due to intra-cutaneous implantation of stratum corneum. (1984)

Fragments of sterile heel callus and suspensions of human corneocytes were implanted or injected intra-cutaneously into flank skin of guinea pigs. A mixed cellular type of inflammation was produced characterized by the accumulation of polymorphonuclear leucocytes in the early stages and a more granulomatous picture in the later stages. Epithelial hypertrophy and follicular distortion with transepidermal elimination was a frequent accompaniment. Immunoglobulins and the complement component C3 were found scattered irregularly in the inflammation produced and were not thought to be important in the process. The inflammation produced closely emulated the changes observed in acne inflammation and after rupture of horn containing cysts. It is suggested that inflammation caused by the implantation of horn may be suitable for study of human skin disease in which horny debris is released into the dermis, such as acne.
Further evidence that ribavirin interacts with eIF4E (2005)

This commentary discusses the recent reports in RNA by Yan and colleagues and Westman and colleagues of the apparent failure of ribavirin to bind to recombinant eIF4E and inhibit 7-methyl guanosine cap-dependent exogenous mRNA translation of cell extracts in vitro. Measuring binding by using affinity chromatography of matrix-immobilized proteins and by using protein emission fluorescence spectroscopy in the presence of nucleotide ligands, as well as limitations of using cell extracts for the assessment of mechanisms of mRNA translation are discussed. Possible reasons for the discordant findings of Yan and colleagues and Westman and colleagues are suggested, and direct observation of the specific binding of ribavirin to eIF4E by using mass spectrometry is presented.
Mechanisms of immune-mediated myocyte injury. (1994)

Much progress has been made in defining the mechanisms by which altered systolic and diastolic function of the heart may be produced by components of the immune system activated during allograft rejection and myocarditis and in patients with dilated cardiomyopathy. It is clear that injury of the vascular bed can occur via both humoral and cellular mediators and probably accounts for the acute alterations in ventricular compliance that occur during allograft rejection, as well as the accelerated development of graft atherosclerosis. Altered myocyte function and lysis can be produced by CTL in vitro, but the importance of this injury process in vivo remains uncertain. Other cells present in the inflammatory infiltrate can also affect myocyte function and survival. Neutrophils may cause lysis of myocytes, and cytokines produced by infiltrating macrophages and HtL may reach a sufficient concentration in the interstitial microenvironment to decrease myocyte catecholamine responsiveness and/or directly depress myocyte contractility. Humoral antibodies to myocyte cell surface antigens may cause cell damage by an antibody-dependent cytotoxic cell mechanism or by directly binding to and altering sarcolemmal receptor and/or ion channel function. Further elucidation of the extent of involvement of these different mechanisms in specific clinical settings may provide a basis for improved therapy of immune-mediated cardiac injury and dysfunction.
Variable capacity of L3T4+ T cells to cause lethal graft-versus-host disease across minor histocompatibility barriers in mice. (1987)

Highly purified populations of L3T4+ and Lyt-2+ T cell subsets were compared for their capacity to cause lethal GVHD in six different H-2-compatible, multiple minor histocompatibility antigen-different murine strain combinations. In four of these combinations (C3H.SW----B6, DBA/2----B10.D2, B10.BR----CBA, and B10.S----SJL), lethal GVHD appeared to be caused almost entirely by Lyt-2+ cells; the injection of L3T4+ cells resulted in low mortality even when these cells were presensitized to the recipient antigens. In the remaining two combinations (B10.D2----DBA/2 and B10.D2----BALB/c), L3T4+ T cells were able to cause a high incidence of GVHD and were more potent than the Lyt-2+ cells. The implications of these findings are discussed.
The influence of ion scattering on dry etch profiles (1989)

A simulation study is presented using a new version of the simulation program ADEPT (advanced simulation of dry-etching process technology), which is a subset of the process simulator COMPOSITE. Based on some aspects of plasma physics, a model was developed that allows for the calculation of important properties of a collisional sheath by Monte Carlo methods. These properties have great influence on the anisotropy of dry-etch processes. Angle/energy spectra of ions and fast neutrals can be gained from the model and can be used as input data for profile simulation. A simulation study is presented showing several profile phenomena. A short discussion is included on sidewall protection by polymer deposition, and on surface diffusion.
Increased nuclease activity in cells treated with pppA2'p5'A2'p5' A. (1979)

A series of 2'-5'-linked oligo(adenylic acid) triphosphate (2'-5' A) inhibitors of protein synthesis were described recently. These inhibitors are synthesized from ATP by an enzyme activated in interferon-treated cell extracts or rabbit reticulocyte lysates by double-stranded RNA. We show here that 2'-5' A is a potent inhibitor of protein synthesis in intact cells of different origin (human, monkey, hamster, and mouse). At a concentration of 10 nM (in AMP equivalents), protein synthesis is inhibited by 50-85%. There is also a secondary effect on the total RNA synthesis which becomes evident several hours after inhibition of protein synthesis. All of these effects, however, are transient and, after a recovery period, both RNA and protein synthesis resume rates comparable to the appropriate controls. A nuclease activity is detected in cells after treatment with 2'-5'A. The total polyadenylylated RNA is much reduced in comparison to that from untreated cells, and electrophoretic analysis in polyacrylamide slab gels provides evidence for its degradation. Similarly, there is an apparent degradation of ribosomal RNA. Consistent with these results, extracts from cells that had been treated with 2'-5'A manifest an enhanced nuclease activity in vitro on incubation with exogenous RNA. Here, we propose that, as in cell-free systems, the mechanism of action of 2'-5'A in intact cells involves activation of a nuclease. This activation is transient, but the nuclease remains sensitive to further activation by the inhibitor.
Diabetes Mellitus in the Sand Rat Induced by Standard Laboratory Diets (1964)

During an attempt to establish a laboratory colony of the sand rat (Psammomys obesus) we found that this animal invariably became obese and developed severe diabetes mellitus when fed on commercial laboratory rat feed, but remained normal when fed on fresh vegetables only. The signs of diabetes included elevated blood glucose, excessive glucose and ketone bodies in the urine, and cataracts. The diabetic animals showed degeneration of the pancreatic insulin producing tissue (beta-cells).
Large-scale synthesis of arrays of high-aspect-ratio rigid vertically aligned carbon nanofibres (2003)

We report on techniques for catalytic synthesis of rigid, high-aspect-ratio, vertically aligned carbon nanofibres by dc plasma enhanced chemical vapour deposition that are tailored for applications that require arrays of individual fibres that feature long fibre lengths (up to 20 µm) such as scanning probe microscopy, penetrant cell and tissue probing arrays and mechanical insertion approaches for gene delivery to cell cultures. We demonstrate that the definition of catalyst nanoparticles is the critical step that enables growth of individual, long-length fibres and discuss methods for catalyst particle preparation that allow the growth of individual isolated nanofibres from catalyst dots with diameters as large as 500 nm. This development enables photolithographic definition of catalyst and therefore the inexpensive, large-scale production of such arrays.
Autoxidation of semicrystalline polyethylene (1966)

Abstract Thermal oxidation in linear polyethylene is mainly confined to disordered regions in which scission reactions cause crystallization and eventual deterioration of mechanical properties. Gel formation is negligible at 100°C. As degradation proceeds, comparable changes occur in the intrinsic viscosities of melt and solution‐crystallized liner polymers, indicating that chain folds are regularly arranged and are resistant to oxidative scission. Breakdown is much more extensive in branched and crosslinked polymers since crosslinking retards oxidative crystallization and branching increases the volume fraction of substrate ultimately accessible to oxygen.
Glycolytic inhibitor 2-deoxyglucose simultaneously targets cancer and endothelial cells to suppress neuroblastoma growth (2015)

Neuroblastoma is characterized by a wide range of clinical manifestations and associated with poor prognosis when there is amplification of MYCN oncogene or high expression of Myc oncoproteins. In a previous in vitro study, we found that the glycolytic inhibitor 2-deoxyglucose (2DG) could suppress the growth of neuroblastoma cells, particularly in those with MYCN amplification. In this study, we established a mouse model of neuroblastoma xenografts with SK-N-DZ and SK-N-AS cells treated with 2DG by intraperitoneal injection twice a week for 3 weeks at 100 or 500 mg/kg body weight. We found that 2DG was effective in suppressing the growth of both MYCN-amplified SK-N-DZ and MYCN-non-amplified SK-N-AS neuroblastoma xenografts, which was associated with downregulation of HIF-1α, PDK1 and c-Myc, and a reduction in the number of tumor blood vessels. In vitro study showed that 2DG can suppress proliferation, cause apoptosis and reduce migration of murine endothelial cells, with inhibition of the formation of lamellipodia and filopodia and disorganization of F-actin filaments. The results suggest that 2DG might simultaneously target cancer cells and endothelial cells in the neuroblastoma xenografts in mice regardless of the status of MYCN amplification, providing a potential therapeutic opportunity to use 2DG or other glycolytic inhibitors for the treatment of patients with refractory neuroblastoma.
Characterization of Outer Retinal Morphology with High-Speed, Ultrahigh-Resolution Optical Coherence Tomography (2008)

High-speed UHR OCT enables quantification of scattering layers in the outer retina. An interpretation of these features is presented and supported by quantitative measurements in normal subjects and comparison with known anatomy. The thick scattering region of the outer retina previously attributed to the retinal pigment epithelium (RPE) is shown to consist of distinct scattering bands corresponding to the photoreceptor outer segment tips, RPE, and Bruch's membrane. These results may advance understanding of the outer retinal appearance in OCT images. The normative measurements may also aid in future investigations of outer retinal changes in age-related macular degeneration and other diseases.
The allyl ether as a protecting group in carbohydrate chemistry. Part VI. The allyl ether as a ‘temporary’ protecting group in oligosaccharide synthesis (1974)

Allyl 2,3,4-tri-O-benzyl-6-O-but-2-enyl-α-D-galactopyranoside was treated with chloro(tristriphenylphosphine)rhodium(I) to give predominantly the corresponding prop-1-enyl glycoside. The prop-1-enyl group was removed by hydrolysis and the free sugar was converted into 2,3,4-tri-O-benzyl-6-O-but-2-enyl-α-D-galactopyranosyl chloride, which was condensed with benzyl 2,3,4-tri-O-benzyl-α-D-galactopyranoside to give an α-linked disaccharide in high yield. The but-2-enyl group was removed to give benzyl 6-O-(2,3,4-tri-O-benzyl-α-D-galactopyranosyl)-2,3,4-tri-O-benzyl-α-D-galactopyranoside, a suitable intermediate for the synthesis of trisaccharides. The fully benzylated derivatives of benzyl 6-O-(α- and β-D-galactopyranosyl)-α-D-galactopyranose were also prepared. 6-O-Allyl-2,3,4-tri-O-benzyl-D-glucopyranose was prepared and the allyl group was removed by isomerisation with chloro(tristriphenylphosphine)rhodium(I) and subsequent acidic hydrolysis.
Interaction of ostreolysin, a cytolytic protein from the edible mushroom Pleurotus ostreatus, with lipid membranes and modulation by lysophospholipids (2003)

Ostreolysin is a 16-kDa cytolytic protein specifically expressed in primordia and fruiting bodies of the edible mushroom Pleurotus ostreatus. To understand its interaction with lipid membranes, we compared its effects on mammalian cells, on vesicles prepared with either pure lipids or total lipid extracts, and on dispersions of lysophospholipids or fatty acids. At nanomolar concentrations, the protein lysed human, bovine and sheep erythrocytes by a colloid-osmotic mechanism, compatible with the formation of pores of 4 nm diameter, and was cytotoxic to mammalian tumor cells. A search for lipid inhibitors of hemolysis revealed a strong effect of lysophospholipids and fatty acids, occurring below their critical micellar concentration. This effect was distinct from the capacity of ostreolysin to bind to and permeabilize lipid membranes. In fact, permeabilization of vesicles occurred only when they were prepared with lipids extracted from erythrocytes, and not with lipids extracted from P. ostreatus or pure lipid mixtures, even if lysophospholipids or fatty acids were included. Interaction with lipid vesicles, and their permeabilization, correlated with an increase in the intrinsic fluorescence and alpha-helical content of the protein, and with aggregation, which were not detected with lysophospholipids. It appears that either an unknown lipid acceptor or a specific lipid complex is required for binding, aggregation and pore formation. The inhibitory effect of lysophospholipids may reflect a regulatory role for these components on the physiological action of ostreolysin and related proteins during fruiting.