gebhart/patrepeval huggingface dataset:
A Critical Cell-Intrinsic Role for Serum Response Factor in Glial Specification in the CNS (2012)

Astrocytes and oligodendrocytes play crucial roles in nearly every facet of nervous system development and function, including neuronal migration, synaptogenesis, synaptic plasticity, and myelination. Previous studies have widely characterized the signaling pathways important for astrocyte differentiation and unveiled a number of transcription factors that guide oligodendrocyte differentiation in the CNS. However, the identities of the transcription factors critical for astrocyte specification in the brain remain unknown. Here we show that deletion of the stimulus-dependent transcription factor, serum response factor (SRF), in neural precursor cells (NPCs) (Srf-Nestin-cKO) results in nearly 60% loss in astrocytes and 50% loss in oligodendrocyte precursors at birth. Cultured SRF-deficient NPCs exhibited normal growth rate and capacity to self-renew. However, SRF-deficient NPCs generated fewer astrocytes and oligodendrocytes in response to several lineage-specific differentiation factors. These deficits in glial differentiation were rescued by ectopic expression of wild-type SRF in SRF-deficient NPCs. Interestingly, ectopic expression of a constitutively active SRF (SRF-VP16) in NPCs augmented astrocyte differentiation in the presence of pro-astrocytic factors. However, SRF-VP16 expression in NPCs had an inhibitory effect on oligodendrocyte differentiation. In contrast, mice carrying conditional deletion of SRF in developing forebrain neurons (Srf-NEX-cKO) did not exhibit any deficits in astrocytes in the brain. Together, our observations suggest that SRF plays a critical cell-autonomous role in NPCs to regulate astrocyte and oligodendrocyte specification in vivo and in vitro.
Space Interface Device for Artificial Reality – SPIDAR – (1997)

In order to realize a human interface for the efficient modeling of three-dimensional shapes over the computer, it is necessary to create an environment in which shape models can be manipulated in the same way as their actual three-dimensional objects. Such an environment is called a virtual work space. In case that a human manipulates an object with his or her own hands, that person unconsciously uses the sensations, such as those of sight, touch, and force. In order to compose a virtual work space, it is important that information on such sensations be given comprehensively to a human. Moreover, it is necessary that all this information be generated artificially through computer processing. On the basis of these observations, the present paper newly proposes a space interface device SPIDAR as an input/output device necessary for composing a virtual work space. This device can not only obtain information on the positions of end-effectors but also provide information concerning the sensation of force to the end-effectors. Furthermore, an experiment is carried out for investigating the effect of information concerning the sensation of force on the direct manipulability of three-dimensional shapes in this virtual work space, and its effectiveness is verified.
Impact of SOI, Si<inf>1-x</inf>Ge<inf>x</inf>OI and GeOI substrates on CMOS compatible Tunnel FET performance (2008)

We report for the first time experimental investigations on SOI, Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Ge <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> OI & GeOI Tunnel FET (TFET). These devices were fabricated using a Fully Depleted SOI CMOS process flow with high k-metal gate stack, enabling 2 decades lower IOFF (~30fA/µm) compared to co-processed CMOS. We successfully solve the TFET bipolar parasitic conduction by a novel TFET architecture, the Drift Tunnel FET (DTFET), with improved OFF state control. Concerning the ON current issue, we improve the SOI p (resp. n) TFET I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</inf> by a factor 55 (resp. 8) by source-drain profiles optimization (via spacers & extensions). Moreover, we demonstrate for the first time functional TFET & CMOS devices on Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Ge <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> OI (x=15-30-100%) co-integrated with the same SOI process flow, enabling TFET ION continuous improvement with Ge content increase: I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</inf> x2700 for GeOI (compared to SOI).
A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing (2007)

The existence of a large number of proteins for which both nuclear magnetic resonance (NMR) and X-ray crystallographic coordinates have been deposited into the Protein Data Bank (PDB) makes the statistical comparison of the corresponding crystal and NMR structural models over a large data set possible, and facilitates the study of the effect of the crystal environment and other factors on structure. We present an approach for detecting statistically significant structural differences between crystal and NMR structural models which is based on structural superposition and the analysis of the distributions of atomic positions relative to a mean structure. We apply this to a set of 148 protein structure pairs (crystal vs NMR), and analyze the results in terms of methodological and physical sources of structural difference. For every one of the 148 structure pairs, the backbone root-mean-square distance (RMSD) over core atoms of the crystal structure to the mean NMR structure is larger than the average RMSD of the members of the NMR ensemble to the mean, with 76% of the structure pairs having an RMSD of the crystal structure to the mean more than a factor of two larger than the average RMSD of the NMR ensemble. On average, the backbone RMSD over core atoms of crystal structure to the mean NMR is approximately 1 A. If non-core atoms are included, this increases to 1.4 A due to the presence of variability in loops and similar regions of the protein. The observed structural differences are only weakly correlated with the age and quality of the structural model and differences in conditions under which the models were determined. We examine steric clashes when a putative crystalline lattice is constructed using a representative NMR structure, and find that repulsive crystal packing plays a minor role in the observed differences between crystal and NMR structures. The observed structural differences likely have a combination of physical and methodological causes. Stabilizing attractive interactions arising from intermolecular crystal contacts which shift the equilibrium of the crystal structure relative to the NMR structure is a likely physical source which can account for some of the observed differences. Methodological sources of apparent structural difference include insufficient sampling or other issues which could give rise to errors in the estimates of the precision and/or accuracy.
The roles of eighteen baculovirus late expression factor genes in transcription and DNA replication (1995)

A set of 18 plasmid subclones of the Autographa californica nuclear polyhedrosis virus genome supports expression from a late viral promoter in transient expression assays (J. W. Todd, A. L. Passarelli, and L. K. Miller, J. Virol. 69:968-974, 1995). Using this set of plasmids, we have assigned a role for each of the 18 genes required for optimal late gene expression with respect to its involvement at the levels of transcription, translation, and/or DNA replication. RNase protection analyses demonstrated that all of the known late expression factor genes (lefs) affected the steady-state level of reporter gene RNA. Thus, none of the lefs appeared to be specifically involved in translation. A subset of the lefs supported plasmid replication; ie-1, lef-1, lef-2, lef-3, p143, and p35 were essential for plasmid replication, while ie-n, lef-7, and dnapol had stimulatory effects. The predicted sequence of lef-7 suggests that it is a homolog of herpesvirus single-stranded DNA-binding protein (UL29). The role of p35 in plasmid replication appears to be suppression of apoptosis, because p35 could be functionally replaced in the replication assay by either Cp-iap or Op-iap, two heterologous baculovirus genes which suppress apoptosis by a mechanism which appears to differ from that of p35. Thus, one or more of the replication-related lefs or the process of plasmid replication appears to induce cellular apoptosis. Our results indicate that the remaining lefs, lefs 4 through 11, p47, and 39K (pp31), function either at the level of transcription or at that of mRNA stabilization.
Generation of Calcium Oscillations in Fibroblasts by Positive Feedback Between Calcium and IP 3 (1991)

A wide variety of nonexcitable cells generate repetitive transient increases in cytosolic calcium ion concentration ([Ca2+]i) when stimulated with agonists that engage the phosphoinositide signalling pathway. Current theories regarding the mechanisms of oscillation disagree on whether Ca2+ inhibits or stimulates its own release from internal stores and whether inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DG) also undergo oscillations linked to the Ca2+ spikes. In this study, Ca2+ was found to stimulate its own release in REF52 fibroblasts primed by mitogens plus depolarization. However, unlike Ca2+ release in muscle and nerve cells, this amplification was insensitive to caffeine or ryanodine and required hormone receptor occupancy and functional IP3 receptors. Oscillations in [Ca2+]i were accompanied by oscillations in IP3 concentration but did not require functional protein kinase C. Therefore, the dominant feedback mechanism in this cell type appears to be Ca2+ stimulation of phospholipase C once this enzyme has been activated by hormone receptors.
NF-κB, and not MYCN, Regulates MHC Class I and Endoplasmic Reticulum Aminopeptidases in Human Neuroblastoma Cells (2010)

Neuroblastoma (NB) is the most common solid extracranial cancer of childhood. Amplification and overexpression of the MYCN oncogene characterize the most aggressive forms and are believed to severely downregulate MHC class I molecules by transcriptional inhibition of the p50 NF-kappaB subunit. In this study, we found that in human NB cell lines, high MYCN expression is not responsible for low MHC class I expression because neither transfection-mediated overexpression nor small interfering RNA suppression of MYCN affects MHC class I and p50 levels. Furthermore, we identified NF-kappaB as the immediate upstream regulator of MHC class I because the p65 NF-kappaB subunit binds MHC class I promoter in chromatin immunoprecipitation experiments, and MHC class I expression is enhanced by p65 transfection and reduced by (a) the chemical NF-kappaB inhibitor sulfasalazine, (b) a dominant-negative IKBalpha gene, and (c) p65 silencing. Moreover, we showed that the endoplasmic reticulum aminopeptidases ERAP1 and ERAP2, which generate MHC class I binding peptides, are regulated by NF-kappaB, contain functional NF-kappaB-binding elements in their promoters, and mimic MHC class I molecules in the expression pattern. Consistent with these findings, nuclear p65 was detected in NB cells that express MHC class I molecules in human NB specimens. Thus, the coordinated downregulation of MHC class I, ERAP1, and ERAP2 in aggressive NB cells is attributable to a low transcriptional availability of NF-kappaB, possibly due to an unknown suppressor other than MYCN.
Structural heterogeneity of sugar chains in immunoglobulin G. Conformation of immunoglobulin G molecule and substrate specificities of glycosyltransferases. (1990)

The heterogeneous asparagine-linked sugar chains of bovine and human immunoglobulins G were separated into 12 components by reversed-phase high performance liquid chromatography, and their structures were determined by 1H NMR spectroscopy. Both immunoglobulin (Ig) G sources contained eight non-bisected biantennary complexes and four bisected biantennary complexes. In the non-bisected sugar chains of bovine IgG, galactosylation of the Man alpha 1-3 branch predominated over that of the Man alpha 1-6, whereas in the bisected complexes galactosylation of the Man alpha 1-6 branch predominated. This difference can be explained by the substrate specificities of the galactosyl-transferases and of the N-acetylglucosaminyltransferase III involved in their synthesis. The sugar chains of human IgG1 differs in the distribution of its galactose residues from bovine IgG and human IgG2. The Man alpha 1-6 branch of all IgG1s was more highly galactosylated than the Man alpha 1-3 branch even in the non-bisected complexes. Such findings are in conflict with the substrate specificities of galactosyltransferases. Whereas these enzymes derivatized more of the Man alpha 1-6 branch of native human IgG1, in denatured protein more of the Man alpha 1-3 branch was galactosylated. Thus, protein conformation may influence the structure of its sugar chains.
Geophone ground coupling (1984)

Abstract For frequencies much lower than the coupling resonant frequency, the geophone accurately follows the ground motion, but for higher frequencies the coupling can alter both the amplitude and phase of the seismic signal. The normal planting of vertical geophones in the field results in coupling adequate for conventional recording that uses frequencies less than 100 Hz. However, for very loose soils or for high-frequency seismic recording, I recommend that the geophones be buried to place the geophones in firmer soil. The coupling resonant frequency for vertical geophones is determined by the firmness of the soil, and I have measured resonant frequency ranging from 100 to 500 Hz at different locations. Because the firmness of the soil increases with depth, the coupling resonant frequency can be increased by burial of the geophones or by the use of longer spikes. The rocking of horizontal geophones causes a low-frequency coupling resonance. It is crucial that horizontal geophones be planted with their bases firmly contacting the soil. Geophones so planted have a resonance around 130 Hz, whereas those 1 cm off the ground can have a resonance of 30 Hz or lower. Soil conditions have little effect on the resonant frequency. Horizontal geophones with 1-inch spikes are as well coupled as those with longer spikes, but the best coupling is achieved by burial of the geophones.--Modified journal abstract.
The copy/DF approach to signal-specific emitter location (2002)

A general approach for performing signal-specific superresolution direction finding (DF) of cochannel emitter waveforms is reported. This approach, referred to as the copy/DF approach, uses the signal copy vectors provided by a blind or nonblind signal extraction algorithm to construct a spatial spectrum for each signal captured by a narrowband antenna array, where each spectrum has a global maximum in the direction of the signal captured by that copy vector. The approach can be used with any signal extraction algorithm, and is particularly effective in environments containing strong cochannel interference. Two classes of techniques are presented: ARMA-like (autoregressive moving average) techniques, which form spatial spectra with zeroes in the direction of the received interferers and poles in the directions of the copied signals; and ML-like (maximum likelihood) techniques, which approximate the nonblind maximum-likelihood estimate of the direction-of-arrival of the copied emitter waveforms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Historical perspective on airway smooth muscle: the saga of a frustrated cell (2001)

Despite the lack of a clearly defined physiological function, airway smooth muscle receives substantial attention because of its involvement in the pathogenesis of asthma. Recent investigations have turned to the ways in which the muscle is influenced by its dynamic microenvironment. Ordinarily, airway smooth muscle presents little problem, even when maximally activated, because unending mechanical perturbations provided by spontaneous tidal breathing put airway smooth muscle in a perpetual state of "limbo," keeping its contractile machinery off balance and unable to achieve its force-generating potential. The dynamic microenvironment affects airway smooth muscle in at least two ways: by acute changes associated with disruption of myosin binding and by chronic changes associated with plastic restructuring of contractile and cytoskeletal filament organization. Plastic restructuring can occur when dynamic length changes occur between sequential contractile events or within a single contractile event. Impairment of these normal responses of airway smooth muscle to its dynamic environment may be implicated in airway hyperresponsiveness in asthma.
Modelling LPC-residue by components for good quality speech coding (2003)

A hybrid speech coding scheme is proposed based on the properties of the linear predictive coding (LPC)-residual. It is shown that the residual comprises characteristically different components, namely, high-energy pulses, a low-energy smooth component, and a random component. It is proposed that residue coding, as a composite of the respective functions corresponding to the components, is more effective and economical than the existing coding techniques which use only a single function to represent the entire residue. Results of simulating a hybrid coder with full quantization and also subjective evaluation of its performance are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hepatic macrophages in liver fibrosis: pathogenesis and potential therapeutic targets (2016)

Hepatic macrophages account for the largest non-parenchymal cell population in the liver. Recent studies have found that hepatic macrophages have different functions in different stages of experimental liver fibrosis. Some studies found that there are different types of hepatic macrophages in the liver, although others have suggested that hepatic macrophages could switch to different phenotypes in different environments. Many studies demonstrated that while hepatic macrophages promoted fibrosis through the recruitment of proinflammatory immune cells, and the secretion of proinflammatory cytokines and chemokines in the early stages, these also promoted the resolution of hepatic fibrosis through the secretion of matrix metalloproteinases in the late stages. This article will review the current role played by hepatic macrophages in liver fibrosis and the potential therapeutic targets that modulate hepatic macrophages.
Scope and Limitations of the Pd/BINAP-Catalyzed Amination of Aryl Bromides (2000)

Mixtures of Pd(2)(dba)(3) or Pd(OAc)(2) and BINAP catalyze the cross-coupling of amines with a variety of aryl bromides. Primary amines are arylated in high yield, and certain classes of secondary amines are also effectively transformed. The process tolerates the presence of several functional groups including methyl and ethyl esters, enolizable ketones, and nitro groups provided that cesium carbonate is employed as the base. Most reactions proceed to completion with 0.5-1.0 mol % of the palladium catalyst; in some cases, catalyst levels as low as 0.05 mol % Pd may be employed. Reactions are considerably faster if Pd(OAc)(2) is employed as the precatalyst, and the order in which reagents are added to the reaction has a substantial effect on reaction rate. It is likely that the catalytic process proceeds via bis(phosphine)palladium complexes as intermediates. These complexes are less prone to undergo undesirable side reactions which lead to diminished yields or catalyst deactivation than complexes of the corresponding monodentate triarylphosphines.
[Synthesis of derivatives of 2,4-bis(arylmethino)-8-butyl-8- azabicyclo[3.2.1]octan-3-one]. (1989)

In the frame-work of continued search for novel compounds with potential cholagogic or antitumour activity, some derivatives of 2,4-bis-(arylmethino)-8-butyl-8-azabicyclo[3.2.1]octan-3-one were synthesized. 8-Butyl-8-azabicyclo[3.2.1]octan-3-one was condensed with selected tolualdehydes, methoxybenzaldehydes and chlorobenzaldehydes, as well as with piperonal, furfural, dimethylaminobenzaldehyde, 3-pyridine-carboxaldehyde and 4-pyridine-carboxaldehyde. Products of these reactions were isolated in the form of free bases or their hydrochlorides. The obtained compounds were subjected to pharmacological studies. Two as yet investigated compounds failed to induce statistically significant increase in the volume of secreted bile, but one of them was found to display cholinergic activity.
Recent developments in understanding the pathophysiology of elevated intraocular pressure. (2006)

These findings represent advances in understanding physiological and pathogenic mechanisms within the trabecular meshwork that are relevant to intraocular pressure regulation in health and glaucoma. They pave the way for future research on the pathogenesis of glaucoma and new targets for glaucoma therapy.
Parallel algorithms for on-line dynamic data compression (2003)

The authors consider parallel algorithms for online (real-time) data compression that use dynamic (adaptive) learning by textual substitution. The author's model of computation is a systolic pipe, in which processors are arranged in a linear array (each processor connected only to its left and right neighbors). He first considers an array of processors that is large enough to accommodate one dictionary entry per processor. He then discusses using an existing parallel machine where the number of available processors might be limited.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Flow cytometric enumeration of micronucleated reticulocytes: High transferability among 14 laboratories (2001)

This laboratory previously described a single-laser flow cytometric method, which effectively resolves micronucleated erythrocyte populations in rodent peripheral blood samples. Even so, the rarity and variable size of micronuclei make it difficult to configure instrument settings consistently and define analysis regions rationally to enumerate the cell populations of interest. Murine erythrocytes from animals infected with the malaria parasite Plasmodium berghei contain a high prevalence of erythrocytes with a uniform DNA content. This biological model for micronucleated erythrocytes offers a means by which the micronucleus analysis regions can be rationally defined, and a means for controlling interexperimental variation. The experiments described herein were performed to extend these studies by testing whether malaria-infected erythrocytes could also be used to enhance the transferability of the method, as well as control intra- and interlaboratory variation. For these studies, blood samples from mice infected with malaria, or treated with vehicle or the clastogen methyl methanesulfonate, were fixed and shipped to collaborating laboratories for analysis. After configuring instrumentation parameters and guiding the position of analysis regions with the malaria-infected blood samples, micronucleated reticulocyte frequencies were measured (20,000 reticulocytes per sample). To evaluate both intra- and interlaboratory variation, five replicates were analyzed per day, and these analyses were repeated on up to five separate days. The data of 14 laboratories presented herein indicate that transferability of this flow cytometric technique is high when instrumentation is guided by the biological standard Plasmodium berghei.