gebhart/patrepeval huggingface dataset:
Efficient Transfection and Expression of Heterologous Genes in PC12 Cells (1990)

The PC12 pheochromocytoma cell line has been a favorite model system for cell and neurobiologists, but has proven relatively refractory to standard DNA transfection methods. We have found that the cationic lipid "lipofectin" provides a simple, gentle, and nontoxic procedure that vastly improves transfection efficiencies in PC12 cells. Transient expression of chloramphenicol acetyl transferase (CAT) driven by a Rous sarcoma virus long terminal repeat (LTR) is much more efficient using lipofectin when compared with calcium phosphate as a transfection procedure. Additionally, transient transfection of nerve growth factor (NGF)-differentiated PC12 cells proceeds with equal efficiency relative to naive, uninduced cells. Using the lipofectin procedure, the frequency of stable transfection is 100-fold higher than that reported with standard calcium phosphate precipitation protocols. To examine the effectiveness of different promoters for efficient expression of heterologous DNA in PC12 cells, three different promoter-bearing constructs were utilized. Each construct contains a different promoter sequence upstream from a chicken calsequestrin cDNA. A human cytomegalovirus (CMV) immediate early promoter construct produced the highest level of expression, followed by a human beta-actin promoter construct. Expression from a mouse Moloney sarcoma virus LTR construct could not be detected. These results overcome the previous transfection problems of low efficiency and low viability that have plagued many PC12 cell investigations.
Promoter Structure and Transcriptional Activation with Chromatin Templates Assembled In Vitro (1998)

To gain a better understanding of the role of chromatin in the regulation of transcription by RNA polymerase II, we examined the relation between promoter structure and the ability of Gal4-VP16 to function with chromatin templates assembled in vitro. First, to investigate whether there are synergistic interactions among multiple bound factors, we studied promoter constructions containing one or five Gal4 sites and found that a single recognition site is sufficient for Gal4-VP16 to bind to chromatin, to induce nucleosome rearrangement, and to activate transcription. Notably, we observed that Gal4-VP16 binds to a single site in chromatin with affinity comparable with that which it binds to naked DNA, even in the absence of ATP-dependent nucleosome remodeling activity. Second, to explore the relation between translational nucleosome positioning and transcriptional activation, we analyzed a series of promoter constructions in which nucleosomes were positioned by Gal4-VP16 at different locations relative to the RNA start site. These experiments revealed that the positioning of a nucleosome over the RNA start site is not an absolute barrier to transcriptional activation. Third, to determine the contribution of core promoter elements to transcriptional activation with chromatin templates, we tested the ability of Gal4-VP16 to activate transcription with TATA box- versus DPE-driven core promoters and found that the TATA box is not required to achieve transcriptional activation by Gal4-VP16 with chromatin templates. These results suggest that a single protomer of a strong activator is able to bind to chromatin, to induce nucleosome remodeling, and to activate transcription in conjunction with a broad range of chromatin structures and core promoter elements.
Synthesis of new bile salt analogues, sodium 3 alpha, 7 alpha-dihydroxy-5 beta-cholane-24-sulfonate and sodium 3 alpha, 7 beta-dihydroxy-5 beta-cholane-24-sulfonate. (1990)

This report describes the chemical synthesis of two new bile salt analogues, namely sodium 3 alpha,7 alpha-dihydroxy-5 beta-cholane-24-sulfonate and sodium 3 alpha,7 beta-dihydroxy-5 beta-cholane-24-sulfonate from chenodeoxycholic acid and ursodeoxycholic acid, respectively. Each common bile acid was converted into the corresponding 5 beta-cholane-3,7,24-triol by treatment with ethyl chloroformate in the presence of triethylamine followed by sodium borohydride reduction. Reaction of the cholanetriol with p-toluenesulfonyl chloride at 4 degrees C afforded the partially tosylated product, 24-p-toluenesulfoxy-5 beta-cholane-3,7-diol, which was then treated with sodium iodide to produce 24-iodo-5 beta-cholane-3,7-diol. The 24-iodide was refluxed with sodium sulfite in aqueous ethanol to give the desired sulfonate analogue of the naturally occurring bile acid, chenodeoxycholic acid or ursodeoxycholic acid.
Secreted Respiratory Syncytial Virus G Glycoprotein Induces Interleukin-5 (IL-5), IL-13, and Eosinophilia by an IL-4-Independent Mechanism (1999)

The attachment glycoprotein G of respiratory syncytial virus (RSV) is produced as both membrane-anchored and secreted forms by infected cells. Immunization with secreted RSV G (Gs) or formalin-inactivated alumprecipitated RSV (FI-RSV) predisposes mice to immune responses involving a Th2 cell phenotype which results in more severe illness and pathology, decreased viral clearance, and increased pulmonary eosinophilia upon subsequent RSV challenge. These responses are associated with increased interleukin-4 (IL-4) production in FI-RSV-primed mice, and the responses are IL-4 dependent. RNase protection assays demonstrated that similar levels of IL-4 mRNA were induced after RSV challenge in mice primed with vaccinia virus expressing Gs (vvGs) or a construct expressing only membrane-anchored G (vvGr). However, upon RSV challenge, vvGs-primed mice produced significantly greater levels of IL-5 and IL-13 mRNA and protein than vvGr-primed mice. Administration of neutralizing anti-IL-4 antibody 11.B11 during vaccinia virus priming did not alter the levels of vvGs-induced IL-5, IL-13, pulmonary eosinophilia, illness, or RSV titers upon RSV challenge, although immunoglobulin G (IgG) isotype profiles revealed that more IgG2a was produced. vvGs-priming of IL-4-deficient mice demonstrated that G-induced airway eosinophilia was not dependent on IL-4. In contrast, airway eosinophilia induced by FI-RSV priming was significantly reduced in IL-4-deficient mice. Thus we conclude that, in contrast to FI-RSV, the secreted form of RSV G can directly induce IL-5 and IL-13, producing pulmonary eosinophilia and enhanced illness in RSV-challenged mice by an IL-4-independent mechanism.
Advances in the Management of Sepsis and the Understanding of Key Immunologic Defects (2011)

Anesthesiologists are increasingly confronting the difficult problem of caring for patients with sepsis in the operating room and in the intensive care unit. Sepsis occurs in more than 750,000 patients in the United States annually and is responsible for more than 210,000 deaths. Approximately 40% of all intensive care unit patients have sepsis on admission to the intensive care unit or experience sepsis during their stay in the intensive care unit. There have been significant advances in the understanding of the pathophysiology of the disorder and its treatment. Although deaths attributable to sepsis remain stubbornly high, new treatment algorithms have led to a reduction in overall mortality. Thus, it is important for anesthesiologists and critical care practitioners to be aware of these new therapeutic regimens. The goal of this review is to include practical points on important advances in the treatment of sepsis and provide a vision of future immunotherapeutic approaches.
The green fluorescent protein as a marker to visualize plant mitochondria in vivo (1997)

To determine how to utilize the green fluorescent protein (GFP) as a marker for subcellular localization and as a label for plant mitochondria in vivo, transgenic suspension cells and tobacco plants expressing GFP with and without a mitochondrial localization signal were generated. The first GFP form used, GFP1, is easily observable in cells with low autofluorescence, such as suspension cells or trichomes, but masked in green tissue. For the visualization of GFP in cells and tissues with high autofluorescence, such as leaf, the use of a very strong promoter (35S35SAMV), a highly expressed modified mGFP4 coding region and a brighter mutant form of GFP (S65T) was necessary. Confocal or two-photon laser scanning microscopy reveal a distinct subcellular localization of the fluorescence in cells expressing GFP or coxIVGFP. In cells expressing untargeted GFP, fluorescence accumulates in the nucleoplasm but is also distributed throughout the cytoplasm. It is excluded from vacuoles, nucleoli and from round bodies that are likely to be leucoplasts. In contrast, fluorescence is localized specifically to mitochondria in cells expressing coxIVGFP fusion protein as shown by co-localization with a mitochondrial-specific dye. This permits the direct observation of mitochondria and mitochondrial movements in living plant cells and tissues throughout plant development. Three-dimensional reconstruction of individual cells can give additional information about the distribution and numbers of mitochondria.
A Community of Maths Learners and the Role of the Ego (2008)

The manner in which mathematical concepts can be taught in classrooms in the form of conversations among a community of maths learners is discussed. The ways in which conjectures put forth by diverse students can be analysed by giving all a chance to put forth their answers, and thereby also involving their ego in a positive way are described.
Subjective Evaluation of Dedicated Multiple-Hop Satellite Communications for Government and Military Users (1970)

Acceptability of telephone communications over a circuit which included two synchronous orbit satellite links in tandem is the primary subject presented. Round trip delay in the order of 1100 ms was caused by such a circuit, and the question studied was this: wall this phenomenon cause actual users to rate the circuit unacceptable? The users consisted of military and civilian government personnel who were experienced in world-wide telephone communications over military networks. The statistics of almost 200 users revealed that with 99-percent certainty, less than 2 percent of the users will rate the circuit including two synchronous orbit satellite links in tandem unacceptable. The circuit used was equipped with Western Electric Company 3A echo suppressors at both ends. Tests were also performed with circuits including three and four synchronous orbit satellite links in tandem of which the third and fourth satellite links were provided by simulation circuitry. The results in these cases yielded a surprisingly small number of users who rated the circuit unacceptable. A definite change from the normal conversational mode to accomodate the delay accounts for this fact.
Molecular Imprinting in Cross‐Linked Materials with the Aid of Molecular Templates— A Way towards Artificial Antibodies (1995)

Abstract Can binding sites be produced in organic or inorganic polymers—similar to those in antibodies—which are able to recognize molecules and which may have catalytic action? In this article we review a method, analogous to a mechanism of antibody formation proposed earlier, by which in the presence of interacting monomers a cross‐linked polymer is formed around a molecule that acts as a template. After removal of the template, an imprint containing functional groups capable of chemical interaction remains in the polymer. The shape of the imprint and the arrangement of the functional groups are complementary to the structure of the template. If chiral templates are used, the success of the imprinting process can be assessed by the ability of the polymer to resolve the racemate of the template molecule. Through optimization of the process has led to chromatographic separation factors of α = 4–8, and to base line separations. There is also great interest in the surface imprinting of solid materials and monolayers. In all cases, the structure of the polymeric matrix in the imprinted materials and the function of the binding groups are of crucial importance. The mechanisms of imprinting and molecular recognition of substrates are by now well understood. A large number of potential applications for this class materials are being intensively developed, for example in the chromatogrphic resolution of recemates, and as artificial antibodies, chemosensors, and selective catalysts. The use of similarly produced materials as enzyme models is also of great interest.
Identification of a genetic locus required for biosynthesis of the lipopeptide antibiotic surfactin in Bacillus subtilis (1988)

Surfactin is a lipopeptide antibiotic produced by the cells of Bacillus subtilis ATCC 21332. A genetic locus responsible for surfactin production (sfp) was transferred from ATCC 21332 to JH642, a derivative of the standard B. subtilis 168. To study the sfp locus at the molecular level, a Tn917 insertion mutant that was blocked in surfactin production (srf) was isolated. The srf::Tn917 mutation was found to be closely linked to sfp, and both loci mapped by PBS1 phage transduction to the chromosomal region between aroI and mtlB. These studies suggest that JH642, a strain which is not a producer of surfactin (genotypically sfp0), contains at least some of the genes encoding surfactin production. Expression of the srf gene(s) was examined in both sfp and sfp0 cells by assaying beta-galactosidase activity encoded by a promoterless lacZ gene that was fused to the srf::Tn917 insertion. In cells of both strains, srf-directed beta-galactosidase activity increased when cells entered the stationary phase of the growth curve, but the activity in sfp cells was higher than that in sfp0 cells. srf-lacZ expression was partially impaired by a mutation in spo0A. In sfp0 cells, this dependence on the spo0A gene product could be entirely bypassed by an abrB suppressor mutation. In the sfp cells, the abrB mutation could not restore the defect conferred by the spo0A mutation. These data suggest that the sfp locus, which is responsible for surfactin production, alters the transcriptional regulation of srf in JH642 cells.
Prospective Tractography-Based Targeting for Improved Safety of Focused Ultrasound Thalamotomy (2018)

This is the first report of prospective VIM targeting with tractography for FUS-T. These results suggest that tractography-guided targeting is safe and has satisfactory short-term clinical outcomes.
Electrical stimulation facilitates rat facial nerve recovery from a crush injury (2008)

Electrical stimulation initiates and accelerates facial nerve recovery in the rat model as it significantly reduces recovery time for the semi-eyeblink reflex, a marker of early recovery. It also hastens recovery of other functions.
CJ-15,801, a Novel Antibiotic from a Fungus, Seimatosporium sp. (2001)

A novel antibiotic, CJ-15,801 (I), was isolated from the fermentation broth of a fungus, Seimatosporium sp. CL28611. The structure was determined to be a pantothenic acid analog having an alpha,beta-unsaturated carboxylic acid moiety by spectroscopic analyses. The compound inhibits the growth of multi-drug resistant (MDR) Staphylococcus aureus strains with MIC ranging from 6.25 to 50 microg/ml.
Structural Variation of the Human Genome (2006)

There is growing appreciation that the human genome contains significant numbers of structural rearrangements, such as insertions, deletions, inversions, and large tandem repeats. Recent studies have defined approximately 5% of the human genome as structurally variant in the normal population, involving more than 800 independent genes. We present a detailed review of the various structural rearrangements identified to date in humans, with particular reference to their influence on human phenotypic variation. Our current knowledge of the extent of human structural variation shows that the human genome is a highly dynamic structure that shows significant large-scale variation from the currently published genome reference sequence.
Assigning confidence to conditional branch predictions (1996)

Many high performance processors predict conditional branches and consume processor resources based on the prediction. In some situations, resource allocation can be better optimized if a confidence level is assigned to a branch prediction; i.e. if the quantity of resources allocated is a function of the confidence level. To support such optimizations, we consider hardware mechanisms that partition conditional branch predictions into two sets: those which are accurate a relatively high percentage of the time, and those which are accurate a relatively low percentage of the time. The objective is to concentrate as many of the mispredictions as practical into a relatively small set of low confidence dynamic branches. We first study an ideal method that profiles branch predictions and sorts static branches into high and low confidence sets, depending on the accuracy with which they are dynamically predicted. We find that about 63 percent of the mispredictions can be localized to a set of static branches that account for 20 percent of the dynamic branches. We then study idealized dynamic confidence methods using both one and two levels of branch correctness history. We find that the single level method performs at least as well as the more complex two level method and is able to isolate 89 percent of the mispredictions into a set containing 20 percent of the dynamic branches. Finally, we study practical, less expensive implementations and find that they achieve most of the performance of the idealized methods.
Deformable Templates for Face Recognition (1991)

We describe an approach for extracting facial features from images and for determining the spatial organization between these features using the concept of a deformable template. This is a parameterized geometric model of the object to be recognized together with a measure of how well it fits the image data. Variations in the parameters correspond to allowable deformations of the object and can be specified by a probabilistic model. After the extraction stage the parameters of the deformable template can be used for object description and recognition.
Failure of Anterior Cingulate Activation and Connectivity With the Amygdala During Implicit Regulation of Emotional Processing in Generalized Anxiety Disorder (2010)

These data demonstrate that patients with generalized anxiety disorder show significant deficits in the noninstructed and spontaneous regulation of emotional processing. Conceptualization of anxiety as importantly involving abnormalities in emotion regulation, particularly a type occurring outside of awareness, may open up avenues for novel treatments, such as by targeting the medial prefrontal cortex.
A DnaB intein in Rhodothermus marinus : Indication of recent intein homing across remotely related organisms (1997)

A dnaB gene encoding a homologue of the Escherichia coli DNA helicase DnaB was cloned and sequenced in the thermophilic eubacterium Rhodothermus marinus, predicting a DnaB protein that harbors an intein. This DnaB intein is 428 amino acid residues long, has several putative intein sequence motifs (including two putative endonuclease motifs), and is capable of protein splicing when produced in E. coli cells. The R. marinus DnaB intein is a close homologue of a DnaB intein in the cyanobacterium Synechocystis sp. strain PCC6803. The two inteins are positioned identically in their respective DnaB proteins. They also share a 54% sequence identity (74% sequence similarity) that is markedly higher than the 37% sequence identity shared by the extein sequences of the two DnaB proteins. Horizontal intein transfer (homing) is therefore invoked to relate these two DnaB inteins. The codon usage of R. marinus DnaB intein coding sequence differs markedly from the codon usages of its flanking extein coding sequences and other genes in the same genome, suggesting more recent acquisition of the DnaB intein in this organism.
A General Method for the Formation of Aryl−Sulfur Bonds Using Copper(I) Catalysts (2002)

[reaction: see text] We report a mild, palladium-free synthetic protocol for the cross-coupling reaction of aryl iodides and thiols using 10 mol % CuI and 10 mol % neocuproine, with NaOt-Bu as the base, in toluene at 110 degrees C. Using this protocol, we have shown that a variety of aryl sulfides can be synthesized in excellent yields from readily available iodides and thiols.
Tracking the mechanisms of deep brain stimulation for neuropsychiatric disorders (2008)

Deep brain stimulation (DBS) has recently emerged as a potential treatment for medically intractable neuropsychiatric disorders. Pilot clinical studies with encouraging results have been performed with DBS of the ventral anterior internal capsule (VAIC) and subgenual cingulate white matter (Cg25WM) for the treatment of obsessive-compulsive disorder and depression. However, little is known about the underlying response of individual neurons, or the networks they are connected to, when DBS is applied to the VAIC or Cg25WM. This review summarizes current understanding of the response of axons to DBS, and discusses the general brain network architectures thought to underlie neuropsychiatric disorders. We also employ diffusion tensor imaging tractography to better understand the axonal trajectories surrounding DBS electrodes implanted in the VAIC or Cg25WM. Finally, we attempt to reconcile various data sets by presenting generalized hypotheses on potential therapeutic mechanisms of DBS for neuropsychiatric disease.
DEMONSTRATION OF AN ADVANCED PUBLIC TRANSPORTATION SYSTEM IN THE CONTEXT OF AN IVHS REGIONAL ARCHITECTURE (1994)

This paper describes the systems architecture of the prototype Advanced Public Transport System (APTS) called APTS BusView. This system displays the following information on a single Geographical Information System (GIS) screen: 1) real time bus locations from an Advanced Vehicle Location (AVL) system operated by Seattle Metro; and 2) real time motorway congestion data obtained from the Traffic Systems Management Centre (TSMC) operated by Washington State Department of Transport. The systems architecture is presented first, followed by a description of how the system works. The benefits which are expected to accrue from the system are then listed. For the covering abstract see IRRD 868006.
Effect of phospholipase A2 inhibitors on mouse T lymphocytes. I. Phospholipase A2 inhibitors exert similar immunological activities as glycosylation inhibiting factor (1989)

Since our previous experiments suggested that glycosylation-inhibiting factor (GIF) is a phosphorylated derivative of a phospholipase inhibitory protein, we determined whether other well-known phospholipase inhibitors may have similar biological activities. The results showed that phospholipase A2 (PLA2) inhibitors, such as recombinant human lipocortin I and ONO-RS-082, could switch T cell hybridoma 12H5 cells from the formation of glycosylated IgE-binding factors (IgE-BF) to the formation of unglycosylated IgE-BF, whereas neomycin, a phospholipase C inhibitor, failed to affect the nature of IgE-BF formed by the cells. The minimum concentrations of lipocortin I and ONO-RS-082 required for switching the 12H5 cells to the formation of unglycosylated IgE-BF were comparable to or less than IC50 of the inhibitors for PLA2. The ability of partially purified GIF to switch the 12H5 cells to the formation of unglycosylated IgE-BF was markedly enhanced by treatment of the preparation with alkaline phosphatase. It was also found that lipocortin I and ONO-RS-082, but not neomycin, facilitated the generation of GIF-producing T cells. When spleen cells of ovalbumin (OVA)-primed BDF1 mice were stimulated with homologous antigen and the activated T cells were propagated by recombinant IL-2 in the presence of GIF, lipocortin I, or ONO-RS-082, T cells obtained in the cultures constitutively produced their own GIF. Antigenic stimulation of the T cells induced the formation of unglycosylated IgE-BF and GIF with an affinity for OVA.(ABSTRACT TRUNCATED AT 250 WORDS)