gebhart/patrepeval huggingface dataset:
Hepatic VLDL Production in ob/ob Mice Is Not Stimulated by Massive De Novo Lipogenesis but Is Less Sensitive to the Suppressive Effects of Insulin (2003)

Type 2 diabetes in humans is associated with increased de novo lipogenesis (DNL), increased fatty acid (FA) fluxes, decreased FA oxidation, and hepatic steatosis. In this condition, VLDL production is increased and resistant to suppressive effects of insulin. The relationships between hepatic FA metabolism, steatosis, and VLDL production are incompletely understood. We investigated VLDL-triglyceride and -apolipoprotein (apo)-B production in relation to DNL and insulin sensitivity in female ob/ob mice. Hepatic triglyceride (5-fold) and cholesteryl ester (15-fold) contents were increased in ob/ob mice compared with lean controls. Hepatic DNL was increased approximately 10-fold in ob/ob mice, whereas hepatic cholesterol synthesis was not affected. Basal rates of hepatic VLDL-triglyceride and -apoB100 production were similar between the groups. Hyperinsulinemic clamping reduced VLDL-triglyceride and -apoB100 production rates by approximately 60% and approximately 75%, respectively, in lean mice but only by approximately 20% and approximately 20%, respectively, in ob/ob mice. No differences in hepatic expression of genes encoding apoB and microsomal triglyceride transfer protein were found. Hepatic expression and protein phosphorylation of insulin receptor and insulin receptor substrate isoforms were reduced in ob/ob mice. Thus, strongly induced hepatic DNL is not associated with increased VLDL production in ob/ob mice, possibly related to differential hepatic zonation of apoB synthesis (periportal) and lipid accumulation (perivenous) and/or relatively low rates of cholesterogenesis. Insulin is unable to effectively suppress VLDL-triglyceride production in ob/ob mice, presumably because of impaired insulin signaling.
Antigen-selective modulation of AAV immunogenicity with tolerogenic rapamycin nanoparticles enables successful vector re-administration (2018)

Gene therapy mediated by recombinant adeno-associated virus (AAV) vectors is a promising treatment for systemic monogenic diseases. However, vector immunogenicity represents a major limitation to gene transfer with AAV vectors, particularly for vector re-administration. Here, we demonstrate that synthetic vaccine particles encapsulating rapamycin (SVP[Rapa]), co-administered with AAV vectors, prevents the induction of anti-capsid humoral and cell-mediated responses. This allows successful vector re-administration in mice and nonhuman primates. SVP[Rapa] dosed with AAV vectors reduces B and T cell activation in an antigen-selective manner, inhibits CD8<sup>+</sup> T cell infiltration in the liver, and efficiently blocks memory T cell responses. SVP[Rapa] immunomodulatory effects can be transferred from treated to naive mice by adoptive transfer of splenocytes, and is inhibited by depletion of CD25<sup>+</sup> T cells, suggesting a role for regulatory T cells. Co-administration of SVP[Rapa] with AAV vector represents a powerful strategy to modulate vector immunogenicity and enable effective vector re-administration.
Agitation in cognitive disorders: International Psychogeriatric Association provisional consensus clinical and research definition (2014)

A provisional consensus definition of agitation has been developed. This definition can be used to advance interventional and non-interventional research of agitation in patients with cognitive impairment.
Functions of Eukaryotic Factors in Initiation of Translation (2001)

Initiation of protein synthesis in both eukaryotes andprokaryotes involves the assembly by initiation factors ofseparated large and small ribosome subunits into a ribosomal initiation complex in which initiator tRNA is positioned in the ribosomal P site so that it is base-paired withthe initiation codon of the mRNA. In prokaryotes, thesmall (30S) ribosomal subunit binds directly to the initiation codon region, and initiation involves only three single-subunit initiation factors termed IF1, IF2, and IF3.The initiation process in eukaryotes is significantly morecomplex than this; it may involve more than ten eukaryotic initiation factors (eIFs), and on most mRNAs, thesmall (40S) ribosomal subunit first binds to the 5′ end ofan mRNA and then scans downstream searching for theinitiation codon...
Ray tracing complex scenes (1986)

A new algorithm for speeding up ray-object intersection calculations is presented. Objects are bounded by a new type of extent, which can be made to fit convex hulls arbitrarily tightly. The objects are placed into a hierarchy. A new hierarchy traversal algorithm is presented which is efficient in the sense that objects along the ray are queried in an efficient order.Results are presented which demonstrate that our technique is several times faster than other published algorithms. Furthermore, we demonstrate that it is currently possible to ray trace scenes containing hundreds of thousands of objects.
Formation of stable cationic lipid/DNA complexes for gene transfer. (1996)

Stable cationic lipid/DNA complexes were formed by solubilizing cationic liposomes with 1% octylglucoside and complexing a DNA plasmid with the lipid in the presence of detergent. Removal of the detergent by dialysis yielded a lipid/DNA suspension that was able to transfect tissue culture cells up to 90 days after formation with no loss in activity. Similar levels of gene transfer were obtained by mixing the cationic lipid in a liposome form with DNA just prior to cell addition. However, expression was completely lost 24 hr after mixing. The transfection efficiency of the stable complex in 15% fetal calf serum was 30% of that obtained in the absence of serum, whereas the transient complex was completely inactivated with 2% fetal calf serum. A 90-day stability study comparing various storage conditions showed that the stable complex could be stored frozen or as a suspension at 4 degrees C with no loss in transfection efficiency. Centrifugation of the stable complex produced a pellet that contained approximately 90% of the DNA and 10% of the lipid. Transfection of cells with the resuspended pellet and the supernatant showed that the majority of the transfection activity was in the pellet and all the toxicity was in the supernatant. Formation of a stable cationic lipid/DNA complex has produced a transfection vehicle that can be stored indefinitely, can be concentrated with no loss in transfection efficiency, and the toxicity levels can be greatly reduced when the active complex is isolated from the uncomplexed lipid.
Alveolar epithelial cell death adjacent to underlying myofibroblasts in advanced fibrotic human lung (1998)

Earlier work from this laboratory showed that abnormal fibroblast phenotypes isolated from fibrotic human lung produce factor(s) capable of inducing apoptosis and necrosis of alveolar epithelial cells in vitro [B. D. Uhal, I. Joshi, A. True, S. Mundle, A. Raza, A. Pardo, and M. Selman. Am. J. Physiol. 269 (Lung Cell. Mol. Physiol. 13): L819-L828, 1995]. To determine whether epithelial cell death is associated with proximity to abnormal fibroblasts in vivo, the spatial distribution of epithelial cell loss, DNA fragmentation, and myofibroblasts was examined in the same tissue specimens used previously for fibroblast isolation. Paraffin sections of normal and fibrotic human lung were subjected to in situ end labeling (ISEL) of fragmented DNA and simultaneous immunolabeling of alpha-smooth muscle actin (alpha-SMA); replicate samples were subjected to electron microscopy and detection of collagens by the picrosirius red technique. Normal human lung exhibited very little labeling except for positive alpha-SMA immunoreactivity of smooth muscle surrounding bronchi and vessels. In contrast, fibrotic human lung exhibited moderate to heavy ISEL of interstitial, cuboidal epithelial, and free alveolar cells. ISEL of the alveolar epithelium was not distributed uniformly but was most intense immediately adjacent to underlying foci of alpha-SMA-positive fibroblast-like interstitial cells. Both electron microscopy and picrosirius red confirmed epithelial cell apoptosis, necrosis, and cell loss adjacent to foci of collagen accumulation surrounding fibroblast-like cells. These results demonstrate that the cuboidal epithelium of the fibrotic lung contains dying as well as proliferating cells and support the hypothesis that alveolar epithelial cell death is induced by abnormal lung fibroblasts in vivo as it is in vitro.
Hierarchical Patterns of Global Human Y-Chromosome Diversity (2001)

We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.
Procedural Generation of Videos to Train Deep Action Recognition Networks (2017)

Deep learning for human action recognition in videos is making significant progress, but is slowed down by its dependency on expensive manual labeling of large video collections. In this work, we investigate the generation of synthetic training data for action recognition, as it has recently shown promising results for a variety of other computer vision tasks. We propose an interpretable parametric generative model of human action videos that relies on procedural generation and other computer graphics techniques of modern game engines. We generate a diverse, realistic, and physically plausible dataset of human action videos, called PHAV for Procedural Human Action Videos. It contains a total of 39,982 videos, with more than 1,000 examples for each action of 35 categories. Our approach is not limited to existing motion capture sequences, and we procedurally define 14 synthetic actions. We introduce a deep multi-task representation learning architecture to mix synthetic and real videos, even if the action categories differ. Our experiments on the UCF101 and HMDB51 benchmarks suggest that combining our large set of synthetic videos with small real-world datasets can boost recognition performance, significantly outperforming fine-tuning state-of-the-art unsupervised generative models of videos.
On small antenna impedance in weakly dissipative media (1978)

Based on antenna modeling theory, a simple formula is established relating antenna impedance in a dissipative medium to that in free space. The approximation is shown to be valid for small losses ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\alpha/\beta \leq 0.1</tex> ) and is restricted to bare perfectly conducting small antennas. An application to a conical unipole is presented, and a simple graphical construction is proposed to derive the required impedance curve in the complex plane from that in free space.
Role of xanthine oxidase in thermal injury of skin. (1989)

These studies were designed to assess pathophysiologic factors responsible for increased vascular permeability occurring in rat skin that has been thermally injured in vivo. Under the conditions employed, permeability changes and edema formation progressed over time, with peak changes occurring 60 minutes after thermal trauma. The plasma of thermally injured rats showed dramatic increases in levels of xanthine oxidase activity, with peak values appearing as early as 15 minutes after thermal trauma. Excision of the burned skin immediately after thermal injury significantly diminished the increase in plasma xanthine oxidase activity. The skin permeability changes were attenuated by treatment of animals with antioxidants (catalase, superoxide dismutase [SOD], dimethyl sulfoxide [DMSO], dimethylthiourea [DMTU]) or an iron chelator (deferoxamine), supporting the role of oxygen radicals in the development of vascular injury as defined by greatly increased vascular permeability. Studies employing laser Doppler velocimetry in thermally injured skin revealed a pronounced and sustained decrease in blood flow after thermal trauma, a pattern not affected by protective interventions. The failure of neutrophil depletion to protect against the vascular permeability changes and the protective effects of the xanthine oxidase inhibitors (allopurinol and lodoxamide tromethamine) suggest that xanthine oxidase is the most likely source of the oxygen radicals involved in edema formation. Lodoxamide was found to have some hydroxyl radical (HO.) scavenging ability (greater than that of allopurinol) but no iron chelating activity. Some of the protective effects of lodoxamide and allopurinol may be linked to their HO. scavenging ability. These data suggest that, in this model of thermal trauma, vascular injury defined by increased vascular permeability is, in part, related to the activation of xanthine oxidase and the generation of toxic oxygen metabolites that damage microvascular endothelial cells.
The Efficiency of Motion-Compensating Prediction for Hybrid Coding of Video Sequences (1987)

Performance bounds for generalized hybrid coding of video sequences with motion-compensating prediction are derived based on rate-distortion theory. It is shown that the spatial power spectrum of the motion-compensated prediction error can be calculated from the signal power spectrum and the displacement estimation error p.d.f.. A spatial Wiener filter can improve the efficiency of motion-compensating prediction. Memoryless encoding of the motion-compensated prediction error and intraframe encoding of the motion-compensated prediction error are compared. An evaluation of the rate-distortion functions for a typical videoconference sampling format shows that for integer pel accuracy of the displacement estimate the additional gain by motion-compensating prediction over pure intraframe coding is limited to ∼ 0.8 bits/sample in moving areas. Required accuracies of the displacement estimate for a gain of motion-compensating interframe coding over intraframe coding are given.
Cyclodehydration of N- and C-substituted .beta.-amino alcohols to the corresponding aziridines with diethoxytriphenylphosphorane (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclodehydration of N- and C-substituted .beta.-amino alcohols to the corresponding aziridines with diethoxytriphenylphosphoraneJeffery W. Kelly, Nita L. Anderson, and Slayton A. Evans Jr.Cite this: J. Org. Chem. 1986, 51, 1, 95–97Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://doi.org/10.1021/jo00351a020RIGHTS & PERMISSIONSArticle Views1953Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (433 KB) Get e-Alerts Get e-Alerts
Introns increase transcriptional efficiency in transgenic mice. (1988)

Experiments were designed to test the effect of introns on gene expression in transgenic mice. Four different pairs of gene constructs, which were identical except that one member of each pair lacked all introns, were compared for expression of mRNA after introduction into the murine germ line by microinjection of fertilized eggs. The expression of two chimeric genes, made by fusing either the mouse metallothionein I or the rat elastase 1 promoter/enhancer to the rat growth hormone gene, was assayed in fetal liver or pancreas, respectively, while two natural genes, an oligonucleotide-marked mouse metallothionein I gene and the human beta-globin gene, were assayed in fetal liver. In each case there was, on average, 10- to 100-fold more mRNA produced from the intron-containing construct. Moreover, mRNA levels were proportional to the relative rates of transcription that were measured in isolated nuclei. However, when the expression of the two mouse metallothionein I gene-based constructs was tested after transfection into cultured cells, little difference was observed. These observations suggest that introns play a role in facilitating transcription of microinjected genes and that this effect may be manifest only on genes exposed to developmental influences.
DL‐homoserinehydroxamic Acid, DL‐homo‐cystinedihydroxamic Acid, and Derivatives by Hydroxylaminolysis of γ‐Hydroxy‐ and γ‐Thio‐Lactones (1970)

Abstract The reaction of α‐amino‐, α‐carbamoylamino‐, α‐benzamido‐, and α‐benzyloxycarbonyl‐amino‐γ‐butyrolactone with hydroxylamine led to the formation of DL‐homoserinehydroxamic acid and α‐N‐acyl derivatives. α‐N‐Benzoyl‐DL‐homoserine‐N‐methyl‐hydroxamic acid and O‐benzylhydroxamic acid ester were prepared by reacting α‐benzamido‐γ‐butyrolactone with N‐methylhydroxylamine and with O‐benzylhydroxylamine, respectively. Hydroxyl‐aminolysis of DL‐homocysteinethiolactone and of N‐acyl‐DL‐homocysteinethiolactones gave homocystinedihydroxamic acid and N,N′‐disubstituted derivatives. Relative reactivities of O‐ and S‐lactones were compared.
Cloning and identification of the Escherichia coli murB DNA sequence, which encodes UDP-N-acetylenolpyruvoylglucosamine reductase (1992)

The murB gene, which complemented the UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.1.1.158) mutation in Escherichia coli ST5, was cloned from an E. coli chromosomal library. murB was subcloned on a 2.8-kb PvuII fragment into pUC19 and sequenced. A 1,029-bp open reading frame encoded a 342-amino-acid polypeptide of 37,859 Da. A DNA sequence homology search revealed that murB had almost 100% homology with a previously reported unidentified open reading frame, ORFII, at 89.9 min. Physical and genetic mapping results were consistent with this map position, and minicell analyses of murB subclones showed a plasmid-encoded protein of approximately 37,000 Da, which closely matched the calculated size of the murB protein.
CT-2576, an inhibitor of phospholipid signaling, suppresses constitutive and induced expression of human immunodeficiency virus. (1995)

Viruses such as human immunodeficiency virus (HIV) require cellular activation for expression. Cellular activation in lymphoid cells is associated with augmented accumulation of certain phosphatidic acid (PA) species derived from the hydrolysis of glycan phosphatidylinositol (GPI). This suggests that activation of a phospholipid pathway may play a role in initiation of viral replication. To test this hypothesis, we examined the effect of tat gene expression on the production of cellular PA species, as the Tat protein is essential for HIV expression and has been implicated in activating the expression of multiple host cellular genes. Expression of tat increased the expression of PA. We then tested whether synthetic inhibitors of PA metabolism would inhibit activation of the HIV long terminal repeat by Tat and tumor necrosis factor alpha (TNF-alpha). CT-2576 suppressed both PA generation induced by Tat and HIV long terminal repeat-directed gene expression in response to Tat or TNF-alpha at a posttranscriptional step. CT-2576 also inhibited constitutive as well as TNF-alpha- and interleukin 6-induced expression of HIV p24 antigen in chronically infected U1 cells and in peripheral blood lymphocytes acutely infected with a clinical isolate of HIV. Pharmacological inhibition of synthesis of selected PA species may therefore provide a therapeutic approach to suppression of HIV replication.
A Time-Based Analog-to-Digital Converter Using a Multi-Phase Voltage-Controlled Oscillator (2006)

A time-based analog-to-digital converter(ADC) employing a multi-phase voltage-controlled oscillator(VCO) is presented. The VCO is based on a ring oscillator which converts analog input voltage to phase information. Digital output is produced by a phase quantizer which consists of a counter for coarse quantization and phase detector for fine quantization. Using this technique, an 8-bit 100Msamples/s ADC is designed and simulated. Impact of jitter and VCO linearity on the ADC performance is analyzed and verified.
Structural Insights of Stereospecific Inhibition of Human Acetylcholinesterase by VX and Subsequent Reactivation by HI-6. (2018)

Over 50 years ago, the toxicity of irreversible organophosphate inhibitors targeting human acetylcholinesterase (hAChE) was observed to be stereospecific. The therapeutic reversal of hAChE inhibition by reactivators has also been shown to depend on the stereochemistry of the inhibitor. To gain clarity on the mechanism of stereospecific inhibition, the X-ray crystallographic structures of hAChE inhibited by a racemic mixture of VX (P <sub>R/S</sub>) and its enantiomers were obtained. Beyond identifying hAChE structural features that lend themselves to stereospecific inhibition, structures of the reactivator HI-6 bound to hAChE inhibited by VX enantiomers of varying toxicity, or in its uninhibited state, were obtained. Comparison of hAChE in these pre-reactivation and post-reactivation states along with enzymatic data reveals the potential influence of unproductive reactivator poses on the efficacy of these types of therapeutics. The recognition of structural features related to hAChE's stereospecificity toward VX shed light on the molecular influences of toxicity and their effect on reactivators. In addition to providing a better understanding of the innate issues with current reactivators, an avenue for improvement of reactivators is envisioned.