gebhart/patrepeval huggingface dataset:
Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells (2013)

Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 (± 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell's ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.
SARS-CoV-2 Infection among Nursing Home Residents (2021)

Infection among Nursing Home ResidentsTo the Editor: White et al. (July 29 issue) 1 provided interesting data on the effectiveness of messenger RNA vaccines in reducing the incidence of SARS-CoV-2 infection in a vulnerable nursing home population.The study showed that there were similar decreases in SARS-CoV-2 infection (asymptomatic and symptomatic) in the vaccinated population and in the unvaccinated population.The authors attributed the decrease in infection in the vaccinated group to vaccine protection and attributed the similar decrease in the unvaccinated group to robust vaccine coverage among residents and staff, together with the use of masks and infection-control measures.This appears to be in contradiction to the authors' description of Table S3 in the Supplementary Appendix of their letter (available at NEJM .org),which indicated that they found no consistent relationship between the incidence of infection among residents and vaccination rates among the staff (a finding also acknowledged in the text of their letter).The fact that the residents in the vaccinated group were also using masks and following infection-control measures and the fact that the decline in infection was similar in the two groups raise the question of how much added protective effect was provided by vaccines in this study.The efficacy of masks in providing protection against infection and death is well documented. 2-4It is of note that both hospitalizations mentioned in the footnote of Table 1 in their letter were in the vaccinated group.
The multitumor (sausage) tissue block: novel method for immunohistochemical antibody testing. (1986)

We describe a method of embedding 100 or more different tissue samples in a normal-sized paraffin block, the multitumor tissue block (MTTB). MTTBs allow the simultaneous immunohistologic testing of numerous tissue samples on a single slide with one drop of antibody. Because all of the tissue samples are treated equally during immunostaining, most sources of variation are removed and comparative studies are facilitated. MTTBs containing miscellaneous neoplasms are suitable for screening of hybridoma supernatants during the early phases of monoclonal antibody production. This permits economical and rapid screening for tissue-specific monoclonal antibodies and simultaneous selection of those that perform well in tissue sections. MTTBs are also useful for the routine monitoring of sensitivity in immunohistochemistry because they can be prepared to include tissues with a broad spectrum of antigen densities. Because a large number of nearly identical sections can be obtained from a single MTTB, these sections could be useful for large scale interlaboratory quality control studies.
Sterol-dependent repression of low density lipoprotein receptor promoter mediated by 16-base pair sequence adjacent to binding site for transcription factor Sp1. (1988)

A 42-base pair sequence from the 5' flanking region of the low density lipoprotein receptor gene was shown previously to confer sensitivity to sterol-mediated repression when inserted into the herpes simplex virus thymidine kinase promoter. This sequence contains two contiguous 16-base pair repeats, designated repeats 2 and 3, which differ from each other at four positions. In the current study we have analyzed separately the functions of repeats 2 and 3 by altering their sequences, inserting them into the -60 position of the thymidine kinase promoter, and introducing the hybrid promoters into hamster cells by transfection. These studies show that repeat 3 is a constitutive positive transcriptional element that acts in the absence or presence of sterols. Repeat 2 confers strong repression upon repeat 3 when sterols are present. In vitro DNase footprinting and gel retardation assays show that repeat 3, but not repeat 2, binds purified Sp1, a positive transcription factor. Mutants of repeat 3 that abolish transcriptional activity in vivo abolish Sp1 binding in vitro. We suggest that the low density lipoprotein receptor is regulated by a push-pull mechanism in which sterol-regulated binding of a protein to repeat 2 silences the activity of the adjacent Sp1-binding site in repeat 3.
Effects of Fusion Temperature and Metal Ion Variation on Crystallization of Lightly Ionized Poly(butylene succinate) (2007)

Abstract Crystallization behavior was investigated for poly(butylene succinate)‐based ionomers (PBSIs) with very small amounts of metal sulfosuccinate units. The PBSI samples, precipitated by adding their chloroform solutions into an excess volume of hexane, showed not only higher overall crystallization rates than the parent PBS but also strong fusion temperature dependences of the crystallization kinetics. In the early stage of film‐hydrolysis experiments, the center region of PBSI spherulites was found to be easily eroded. A putative internal structure of PBSI spherulites, that is, relatively ion‐rich centers and ion‐poor outskirts, was proposed. PBSIs with K ions were found to show higher crystallization temperatures than those with Na ions in the non‐isothermal crystallization from the melts. These results indicate that the crystallization behavior of PBSIs is dominated by the ionic aggregates which induce the crystal nucleation around themselves. magnified image
CRC 675—Current Trends in Phytosynthesis of Metal Nanoparticles (2008)

Nanotechnology is emerging as a field of applied science and technology. Synthesis of nanoparticles is done by various physical and chemical methods but the biological system is gaining attention as an eco-friendly technique. The biosynthetic method employing plant parts is proving as a simple and cost-effective method for the synthesis of nanoparticles. The present mini review focuses on the different systems utilized for the synthesis of nanoparticles with special emphasis on the use of plants for the synthesis process, its applications and future directions.
Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging (1999)

The relationship between brain structure and complex behavior is governed by large-scale neurocognitive networks. The availability of a noninvasive technique that can visualize the neuronal projections connecting the functional centers should therefore provide new keys to the understanding of brain function. By using high-resolution three-dimensional diffusion magnetic resonance imaging and a newly designed tracking approach, we show that neuronal pathways in the rat brain can be probed in situ. The results are validated through comparison with known anatomical locations of such fibers.
Studies on Absorption, Distribution, Excretion and Metabolism of Ginseng Saponins. VII. Comparison of the Decomposition Modes of Ginsenoside-Rb1 and -Rb2 in the Digestive Tract of Rats. (1991)

In order to clarify some similarities and differences of decomposition modes between 20(S)-protopanaxadiol (20(S)-ppd) saponins, represented by ginsenoside Rb1 (Rb1) and ginsenoside Rb2 (Rb2), the decompositions of Rb1 and Rb2 in the rat gastrointestinal tract, 0.1 N HCl and crude hesperidinase were investigated in detail. As in the case of Rb2 reported previously, Rb1 was hydrolyzed to 20(R,S)-ginsenoside Rg3 in 0.1 N HCl. On the other hand, hydroperoxidation of Rb1 occurred in rat stomach; the major hydroperoxide was separated and identified as the 25-hydroperoxy-23-ene derivative of Rb1 (VIII) by 1H- and 13C-nuclear magnetic resonance and fast atom bombardment mass spectrometry. The decomposition modes of 20(S)-ppd saponins (Rb1 and Rb2) differed from that of 20(S)-protopanaxatriol saponin (Rg1) in rat stomach. In rat large intestine, five decomposition products of Rb1 were observed by thin-layer chromatography, and these were identified as gypenoside XVII (G-XVII), ginsenoside Rd (Rd), ginsenoside F2 (F2), compound K (C-K) and VIII. The decomposition modes of Rb1 and Rb2, both 20(S)-ppd saponins, are considered to be different because of the hydrolysis rate in the terminal sugar moiety at the C-20 hydroxyl group in the rat large intestine. Using crude hesperidinase, Rb1 was decomposed to G-XVII, F2 and C-K, and Rb2 was decomposed to 3-O-beta-D-glucopyranosyl-20-O-[alpha-L-arabinopyranosyl(1----6)-b eta-D- glucopyranosyl]-20-(S)-ppd, F2 and C-K. Consequently, it appears that hydrolysis by beta-glucosidase, which is present in the rat large intestine, is distinct from that by crude hesperidinase.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis and Antitumor Activity of 2-Aryl-7-fluoro-6-(4-methyl-1-piperazinyl)-4(3H)-quinazolinones (2005)

A series of new 2-aryl-7-fluoro-6-(4-methyl-1-piperazinyl)-4(3H)quinazolinones were prepared by the oxidative cyclization of the corresponding 2-arylidineamino-4-fluoro-5-(4-methyl-1-piperazinyl)benzamides.The new quinazolinones were evaluated for their antitumor activity.
Printing gold nanoparticles with an electrohydrodynamic direct-write device (2006)

A dispersion containing 15nm gold particles in ethanol was subjected to electrohydrodynamic atomization, producing droplets with an average size of ≈26μm as measured by laser diffraction. An electrohydrodynamic direct-write device was used to deposit the dispersion onto silicon wafers with the intention of printing gold tracks. Immediately after deposition ethanol evaporated, leaving the gold particles organised in a ≈75μm wide central region surrounded by two regions, each ≈50μm wide, at the edge of which two further gold tracks, each ≈7μm existed.
Minimally Invasive Treatment of Moderate Lumbar Spinal Stenosis with the Superion® Interspinous Spacer (2011)

Preliminary results with the Superion Interspinous Spacer suggest that it is an effective and safe treatment option for patients with moderate LSS who are unresponsive to conservative care.
Frontal Sinus Stents (2000)

The Freeman frontal sinus stent prevented blockage of the outflow tract in patients who had removal of disease in the sinus or duct or treatment of frontal stenosis.
Unimolecular micelles and globular amphiphiles: dendritic macromolecules as novel recyclable solubilization agents (1993)

The synthesis of dendritic polyether macromolecules based on a 3, 5-dihydroxybenzyl alcohol building block and having carboxylate groups as chain-ends is described. These novel macromolecules behave as unimolecular micelles and their ability to solvate hydrophobic molecules has been investigated by UV–VIS spectroscopy. A dramatic increase in the saturation concentration of various polycyclic aromatic compounds in water was observed which was of a magnitude similar to that observed for micelles derived from sodium dodecyl sulfate. A relationship between the solubilizing power of the dendrimer and the electron density of the polycyclic aromatic was found. A linear relationship between the solubilizing ability and the concentration of the dendrimer, even at concentrations as low as 5 × 10–7 mol dm–3, indicates that these materials do not have a critical micelle concentration. Increases in the ionic strength of an aqueous solution of the dendrimer caused an increase in the saturation concentration of the hydrophobic molecules. A recyclable solubilization and extraction system is discussed. The synthesis of a globular dendritic macromolecular amphiphile designed to reside at the interface of an organic solvent and water is also described. This ‘hybrid’ dendritic amphiphile consisting of two distinct sectors, one hydrophilic and the other hydrophobic is prepared by stepwise alkylation of a core molecule, 4,4′-dihydroxybiphenyl with the two dissimilar dendritic fragments.
Gene Structure, Chromosomal Localization, and Expression of the Murine Homologue of Human Proteinase Inhibitor 6 (PI-6) Suggests Divergence of PI-6 from the Ovalbumin Serpins (1995)

Human proteinase inhibitor 6 (PI-6) is a recently described protein belonging to the serine proteinase inhibitor (serpin) superfamily. Sequence similarity suggests that PI-6 most resembles the ovalbumin (ov) serpins which include plasminogen activator inhibitor-2, the squamous cell carcinoma antigen, monocyte/neutrophil elastase inhibitor, and maspin. Although these proteins are associated with carcinomas and inflammation, they appear to have diverse functions and little is known of their physiological roles. In this study we have characterized cDNA and genomic clones encoding mouse PI-6 in order to analyze the localization, structure, and expression of the gene. The reactive center residues (Arg-Cys) are conserved in the mouse molecule, and recombinant mouse PI-6 was shown to bind thrombin, indicating that it has similar inhibitory properties to its human counterpart. Using reverse transcriptase-polymerase chain reaction assays on RNA isolated from 15-day-old embryos and adult mice, we have shown that mouse PI-6 expression is developmentally regulated, and that, unlike human PI-6, it is absent from the placenta. The mouse homologue of the human PI-6 gene has been designated Spi3 and was mapped to chromosome 13 between the Pl1 and ctla2 alpha genes. It spans 20 kilobases, consists of 7 exons and 6 introns, and contains a TATA motif 24 nucleotides upstream of the transcriptional start site. A 680-base pair DNA fragment containing this motif and 31 nucleotides of the 5'-untranslated region of the structural gene directed transcription of a bacterial cat gene, demonstrating the presence of a functional promoter. The PI-6 gene lacks an intron present in the ovalbumin and PAI-2 genes; otherwise it is identical in terms of the numbers, position, and phasing of the intron/exon boundaries. These results suggest that PI-6 and the ov-serpin genes have diverged and do not belong to the same subgroup.
Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification (2006)

Rolling-circle amplification (RCA) and ramification amplification (RAM, also known as hyperbranched RCA) are isothermal nucleic acid amplification technologies that have gained a great application in in situ signal amplification, DNA and protein microarray assays, single nucleotide polymorphism detection, as well as clinical diagnosis. Real-time detection of RCA or RAM products has been a challenge because of most real-time detection systems, including Taqman and Molecular Beacon, are designed for thermal cycling-based DNA amplification technology. In the present study, we describe a novel fluorescent probe construct, termed molecular zipper, which is specially designed for quantifying target DNA by real-time monitoring RAM reactions. Our results showed that the molecular zipper has very low background fluorescence due to the strong interaction between two strands. Once it is incorporated into the RAM products its double strand region is opened by displacement, therefore, its fluorophore releases a fluorescent signal. Applying the molecular zipper in RAM assay, we were able to detect as few as 10 molecules within 90 min reaction. A linear relationship was observed between initial input of targets and threshold time (R2 = 0.985). These results indicate that molecular zipper can be applied to real-time monitoring and qualification of RAM reaction, implying an amenable method for automatic RAM-based diagnostic assays.
Stretch-mediated release of angiotensin II induces myocyte apoptosis by activating p53 that enhances the local renin-angiotensin system and decreases the Bcl-2-to-Bax protein ratio in the cell. (1998)

Physical forces activate apoptosis and gene expression, but the mechanism is unknown. For this purpose, adult myocytes were stretched in an equibiaxial stretch apparatus and the magnitude of cell death was examined 4 and 24 h later. The possibility of stretch-mediated activation of p53 and p53-dependent genes was evaluated at 30 min, 2, 4, 8, and 24 h. Myocyte apoptosis increased by 4.4- and 7.6-fold at 4 and 24 h after stretch. p53 binding to the promoter of angiotensinogen, AT1 receptor, and Bax also increased. Expression of angiotensinogen, AT1 receptor, p53, and Bax increased and Bcl-2 decreased in stretched myocytes. The changes in AT1 receptor, p53, Bax, and Bcl-2 became more apparent with the duration of stretch. Angiotensin II concentration in the medium increased at 10 min, reaching maximal levels at 1 and 20 h. The AT1 blocker, losartan, abolished apoptosis in stretched myocytes. Myocyte volume was not influenced by stretch. In conclusion, stretch-mediated release of angiotensin II is coupled with apoptosis and the activation of p53 which may be responsible for the prolonged upregulation of the local renin-angiotensin system and the increased susceptibility of myocytes to undergo apoptosis.
Gly389Arg polymorphism of β1-adrenergic receptor is associated with the cardiovascular response to metoprolol (2003)

The Arg389 variant of the beta(1)-adrenergic receptor was associated with a greater response to metoprolol than that of Gly389 in young, male Chinese subjects. These data suggested that the beta(1)-adrenergic receptor Gly389Arg polymorphism is of major functional importance in vivo.
L-4F, an Apolipoprotein A-1 Mimetic, Dramatically Improves Vasodilation in Hypercholesterolemia and Sickle Cell Disease (2003)

These data show that L-4F protects endothelium-dependent vasodilation in hypercholesterolemia and SCD. Our findings suggest that L-4F restores vascular endothelial function in diverse models of disease and may be applicable to treating a variety of vascular diseases.
A critical role for the histidine residues in the catalytic function of acyl‐CoA:cholesterol acyltransferase catalysis: Evidence for catalytic difference between ACAT1 and ACAT2 (2006)

To investigate a role for histidine residues in the expression of normal acyl-CoA:cholesterol acyltransferase (ACAT) activity, the histidine residues located at five different positions in two isoenzymes were substituted by alanine, based on the sequence homology between ACAT1 and ACAT2. Among the 10 mutants generated by baculovirus expression technology, H386A-ACAT1, H460A-ACAT1, H360A-ACAT2, and H399A-ACAT2 lost their enzymatic activity completely. A reduction in catalytic activity is unlikely to result from structural changes in the substrate-binding pocket, because their substrate-binding affinities were normal. However, the enzymatic activity of H386A-ACAT1 was restored to <37% of the level of the wild-type activity when cholesterol was replaced by 25-hydroxycholesterol as substrate. H527A-ACAT1 and H501A-ACAT2, termed carboxyl end mutants, exhibit activities of approximately 96% and approximately 75% of that of the wild-type. Interestingly, H425A-ACAT1 showed 59% of the wild-type activity, in contrast to its equivalent mutant, H399A-ACAT2. These results demonstrate that the histidine residues located at the active site are very crucial both for the catalytic activity of the enzyme and for distinguishing ACAT1 from ACAT2 with respect to enzyme catalysis and substrate specificity.
Visualization of Large Point Cloud in Unity (2019)

Large point cloud rendering has become a very relevant topic on 3D graphics as scanners and other sources of 3D point data are nowadays available to companies and the general public. In this project, we propose an implementation of a point cloud viewer, designed for the full-detail visualization of virtually unlimited point clouds for their inspection on short ranges. This work presents the data structure and the LoD technique to achieve a real-time rendering of the model, making emphasis on the details of an initial prototype based on Unity.
Low‐dose Ketamine Improves Pain Relief in Patients Receiving Intravenous Opioids for Acute Pain in the Emergency Department: Results of a Randomized, Double‐blind, Clinical Trial (2014)

Low-dose ketamine is a viable analgesic adjunct to morphine for the treatment of moderate to severe acute pain. Dosing of 0.3 mg/kg is possibly more effective than 0.15 mg/kg, but may be associated with minor adverse events. Future studies should evaluate additional outcomes, optimum dosing, and use in specific populations.
Solid-state metathesis reactions under pressure: A rapid route to crystalline gallium nitride (1998)

High pressure chemistry has traditionally involved applying pressure and increasing temperature until conditions become thermodynamically favorable for phase transitions or reactions to occur. Here, high pressure alone is used as a starting point for carrying out rapid, self-propagating metathesis reactions. By initiating chemical reactions under pressure, crystalline phases, such as gallium nitride, can be synthesized which are inaccessible when initiated from ambient conditions. The single-phase gallium nitride made by metathesis reactions under pressure displays significant photoluminescence intensity in the blue/ultraviolet region. The absence of size or surface-state effects in the photoluminescence spectra show that the crystallites are of micron dimensions. The narrow lines of the x-ray diffraction patterns and scanning electron microscopy confirm this conclusion. Brightly luminescent thin films can be readily grown using pulsed laser deposition.
Monoclonal anti‐biotin antibodies simulate avidin m the recognition of biotin (1993)

The sequence of the VH gene of a monoclonal anti-biotin antibody was determined. Biotin-binding motifs, similar to those in avidin and streptavidin, were identified in complementary determining regions 2 and 3, suggesting that natural selection of functional motifs may occur in unrelated protein types.