gebhart/patrepeval huggingface dataset:
Rab5 and Rab7, but Not ARF6, Govern the Early Events of HIV-1 Infection in Polarized Human Placental Cells (2005)

Trophoblasts, the structural cells of the placenta, are thought to play a determinant role in in utero HIV type 1 (HIV-1) transmission. We have accumulated evidence suggesting that HIV-1 infection of these cells is associated with uptake by an unusual clathrin/caveolae-independent endocytic pathway and that endocytosis is followed by trafficking through multiple organelles. Furthermore, part of this trafficking involves the transit of HIV-1 from transferrin-negative to EEA1 and transferrin-positive endosomes, suggesting a merger from nonclassical to classical endocytic pathways in these cells. In the present article, the relationship between the presence of HIV-1 within specific endosomes and infection was studied. We demonstrate that viral infection is virtually lost when endosome inhibitors are added shortly after exposure to HIV-1. Thus, contrary to what is seen in CD4+ T lymphocytes, the initial presence of HIV-1 within the endosomes is mandatory for infection to take place. Importantly, this process is independent of the viral envelope proteins gp120 and gp41. The Rab family of small GTPases coordinates the vesicular transport between the different endocytic organelles. Experiments performed with various expression vectors indicated that HIV-1 infection in polarized trophoblasts relies on Rab5 and Rab7 without the contribution of Arf6 or Rab11. Furthermore, we conclude that Rab5 drives movements from raft-rich region to early endosomes, and this transit is required for subsequently reaching late endosomes via Rab7. This complex trafficking is mandatory for HIV-1 infection to proceed in human polarized trophoblasts.
Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics (2005)

Abstract Pyrophyllite is the precursor to other smectite-group minerals which exhibit swelling. The mineral structure of pyrophyllite can lead to other minerals in the smectite group, including montmorillonite, through appropriate isomorphous substitutions. In this work, an atomic model of the pyrophyllite interlayer was constructed. The response of the interlayer was evaluated using steered molecular dynamics simulations. In steered molecular dynamics, external forces were applied to individual atoms to study the response of the model to applied forces. In this work, forces are applied to the surface clay atoms to evaluate the displacement vs. applied stress in the interlayer between clay layers. This paper describes the construction of the model, the simulation procedure, and the results of the simulations which show that under the applied loading, deformation occurs mainly in the interlayer. The clay layers show relatively little deformation. The results show that the relationship between applied stress and displacement of the interlayer is linear. The stress-deformation relationship for the interlayer is presented.
Trimer Stabilization, Oligomerization, and Antibody-Mediated Cell Surface Immobilization Improve the Activity of Soluble Trimers of CD27L, CD40L, 41BBL, and Glucocorticoid-Induced TNF Receptor Ligand (2009)

For many ligands of the TNF family, trimer stability and oligomerization status are crucial determinants of receptor activation. However, for the immunostimulatory ligands CD27L, CD40L, 41BBL, and glucocorticoid-induced TNF receptor ligand (GITRL) detailed information regarding these requirements is lacking. Here, we comprehensively evaluated the effect of trimer stability and oligomerization on receptor activation by these ligands. Treatment with soluble Flag-tagged CD27L, 41BBL, and GITRL minimally activated receptor signaling, while Flag-CD40L was highly active. Oligomerization with anti-Flag Abs further enhanced the specific activity of Flag-CD40L 10-fold and of Flag-41BBL more than 200-fold, but it failed to activate Flag-CD27L and Flag-GITRL. We next investigated the relevance of trimer stability by introducing the tenascin-C (TNC) trimerization domain, yielding stabilized Flag-TNC-ligand trimers. Oligomerization with anti-Flag Ab potently activated signaling by Flag-TNC-CD27L and Flag-TNC-GITRL and, albeit to a lesser extent, Flag-TNC-CD40L and Flag-TNC-41BBL. Forced hexamerization, by introducing an Ig Fc domain, revealed that hexameric derivatives of Flag-TNC-41BBL, Flag-CD40L, and Flag-TNC-GITRL all activate receptor signaling with high efficiency, whereas hexameric Flag-CD27L variant left inactive. Finally, we attempted to selectively activate receptor signaling on targeted cells, by using Ab fragment (single-chain fragment variable region, scFv)-ligand fusion proteins, an approach previously applied to other TNF ligands. Target cell surface Ag-selective activation was achieved for scFv-41BBL, scFv-CD40L, and scFv-GITRL, although the latter two displayed already significant activity toward Ag-negative cells. In conclusion, our data establish that trimeric CD40L is active, 41BBL requires hexamerization, GITRL requires trimer stabilization, and CD27L requires trimer stabilization and oligomerization. Furthermore, surface immobilization might be exploited to gain locally enhanced ligand activity.
PINE OIL PROTECTS LIVING TREES FROM ATTACK BY THREE BARK BEETLE SPECIES, DENDROCTONUS SPP. (COLEOPTERA: SCOLYTIDAE) (1981)

Abstract Pine oil, a by-product of sulphate wood pulping, protected pheromone-baited, living Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco), lodgepole pine ( Pinus contorta Dougl.), and spruce ( Picea glauca (Moench) Voss - P . engelmannii Parry hybrids) from attack by Douglas-fir beetle ( Dendroctonus pseudotsugae Hopk.), mountain pine beetle ( D . ponderosa Hopk.), and spruce beetle ( D . rufipennis (Kirby)), respectively. Pine oil also protected surrounding trees and reduced attack incidence on Douglas-fir, lodgepole pine, and spruce within at least a 10 m radius. α-Terpineol, one of the constituents of the pine oil mixture, was less effective.
Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2 (2013)

The Cox protein from bacteriophage P2 is a small multifunctional DNA-binding protein. It is involved in site-specific recombination leading to P2 prophage excision and functions as a transcriptional repressor of the P2 Pc promoter. Furthermore, it transcriptionally activates the unrelated, defective prophage P4 that depends on phage P2 late gene products for lytic growth. In this article, we have investigated the structural determinants to understand how P2 Cox performs these different functions. We have solved the structure of P2 Cox to 2.4 Å resolution. Interestingly, P2 Cox crystallized in a continuous oligomeric spiral with its DNA-binding helix and wing positioned outwards. The extended C-terminal part of P2 Cox is largely responsible for the oligomerization in the structure. The spacing between the repeating DNA-binding elements along the helical P2 Cox filament is consistent with DNA binding along the filament. Functional analyses of alanine mutants in P2 Cox argue for the importance of key residues for protein function. We here present the first structure from the Cox protein family and, together with previous biochemical observations, propose that P2 Cox achieves its various functions by specific binding of DNA while wrapping the DNA around its helical oligomer.
Seven Novel Macrocyclic Polypeptides fromViolaarvensis (1999)

Seven novel macrocyclic polypeptides, designated as varv peptides B-H, have been isolated from the aerial parts of Viola arvensis. Their primary structures have been elucidated by automated Edman degradation and mass spectrometry. They all consist of 29 or 30 amino acid residues, covalently cyclized via the amide backbone and by three internal disulfide bridges. Their amino acid sequences are as follows: varv peptide B, cyclo-(TCFGGTCNTPGCSCDPWPMCSRNGLPVCGE); varv peptide C, cyclo-(TCVGGTCNTPGCSCSWPVCTRNGVPICGE); varv peptide D, cyclo-(TCVGGSCNTPGCSCSWPVCTRNGLPICGE); varv peptide E, cyclo-(TCVGGTCNTPGCSCSWPVCTRNGLPICGE); varv peptide F, cyclo-(TCTLGTCYTAGCSCSWPVCTRNGVPICGE); varv peptide G, cyclo-(TCFGGTCNTPGCSCDPWPVCSRNGVPVCGE); and varv peptide H, cyclo-(TCFGGTCNTPGCSCETWPVCSRNGLPVCGE). The varv peptides B-H exhibited high degrees of homology with the hitherto known macrocyclic peptides varv peptide A, kalata B1, violapeptide I, circulins A and B, and cyclopsychotride A.
Newer insights into the mechanism of action of Psidium guajava L. leaves in infectious diarrhoea (2010)

Collectively, the results indicate that the decoction of P. guajava leaves is an effective antidiarrhoeal agent and that the entire spectrum of its antidiarrhoeal activity is not due to quercetin alone.
The Cockcroft-Walton Voltage Multiplying Circuit (1953)

The conventional Cockcroft-Walton voltage multiplying circuit is studied considering it as a transmission line. It is shown that, even when no direct current is drawn from the high voltage electrode, there is an important loss in output voltage caused by circulating currents in the stray capacitances. This loss of voltage is independent of the supply frequency. Formulas are developed for the voltage efficiency resulting from a given choice of capacitor size and number of stages. Two modifications of the Cockcroft-Walton circuit which improve the voltage efficiency are suggested and analyzed. The first of these involves a loading coil at the high voltage end of the line. The second involves the addition of inductors in series with each of the capacitors of the circuit.
Imaging plasma membranes without cellular internalization: multisite membrane anchoring reagents based on glycol chitosan derivatives (2015)

Plasma membrane imaging has received substantial attention due to its capability for dynamically tracing significant biological processes including cell trafficking, vesicle transportation, apoptosis, etc. However, cellular internalization of staining molecules poses challenges to the development of fluorescent dyes to specifically label plasma membranes rather than intracellular organelles. In this work, glycol chitosan, a multifunctional biomaterial derived from natural polymers, was used for the first time to image the plasma membranes based on a strategy of multisite membrane anchoring. A glycol chitosan derivative, glycol chitosan-cholesterol-FITC (Chito-Chol-FITC), was synthesized by using glycol chitosan as the backbone, and PEG-cholesterols and FITC molecules as side chains. The cholesterol groups and FITC molecules serve as hydrophobic anchoring units and fluorescent units, respectively. Benefitting from the strategy, this molecular probe could rapidly stain the cell membrane within 5 min as well as effectively restrain the cellular uptake process-it could tolerate an incubation time of 6 h without substantial cellular internalization. Its imaging performance far exceeds that of the current commercial plasma membrane imaging reagents based on small molecules (such as DiD and FM families), which will be easily internalized by the cells within 10-15 min. The present work shows the biomacromolecular assembly of the glycol chitosan derivative on the cell surface, which may shed new light on the interactions of biomaterials with biological systems. Besides, the multisite membrane anchoring strategy developed herein also provides a novel platform for future cell surface engineering studies.
On Distributed Communications Networks (1962)

A discussion of the problem of building digital communication networks using links with less than perfect reliability. The redundancy level used is defined as a measure of connectivity. The systems planner must choose that form of redundancy so that the form of the noise or interference appears to be somewhat statistically independent for each redundant element added. If this goal is completely met, there can be an exponential payoff for a linear increase of added elements. As an example, the paper examines the synthesis of a system in which the form of the disturbance or noise is the simultaneous destruction of many geographically separated installations. The system considered is a high-speed digital data transmission network composed of unreliable links, but which exhibits any arbitrarily desired level of systems reliability or survivability.
Synthesis and inhibitory activities on platelet aggregation of some flavonoid analogues. (1995)

A series of 26 benzodioxan and benzodioxol derivatives of flavone have been prepared. The activity of the compounds on washed human platelet aggregation induced by adenosine diphosphate (ADP, 5 mumol/l), collagen (10 micrograms/ml) and calcimycin (20 mumol/l) was evaluated. The alkoxycarbonyl side chain derivatives inhibited all three types of aggregation inducers. Among the tested compounds Ia is the most potent inhibitor of collagen-induced aggregation but possesses a weak activity against the other two used inducers. The esters IIIb and in particular, IIIc are active against all the three used inducers. These results suggest that ethoxycarbonyl group is a potent substituent to provide the antiplatelet action in this series of flavonoids.
Modulation of the antigenic phenotype of early‐passage human melanoma cells derived from multiple autologous metastases by recombinant human leukocyte, fibroblast and immune interferon (1990)

We have investigated the relationship between in vitro cultivation of autologous melanoma metastases derived from different patients and their levels of expression of class-I and -II major histocompatibility complex (MHC) antigens and melanoma-associated antigens (MAAs). Cell cultures were established from 23 individual metastatic melanoma lesions from 10 patients and were tested early after isolation (between 3rd and 10th passages) for both constitutive expression and modulation by recombinant human leukocyte (IFN-alpha), fibroblast (IFN-beta) or immune (IFN-gamma) interferon of MHC antigens and MAA. All of the melanoma cell lines displayed altered antigen expression following IFN treatment. While in vitro cultures derived from different individuals varied in both constitutive and IFN-modified antigenic expression, cultures of autologous metastases derived from the same patient were very similar. In addition, differences in antigenic profile were apparent when early-passage in vitro cultures were compared with the same melanoma lesion, not established in culture, from which they were derived. The unique de novo and IFN-modified antigenic phenotype of cultures derived from different patients indicates that the antigenic phenotype displayed by melanoma cultures grown in vitro is genetically determined. The differences found between in vitro cultures and their corresponding in vivo lesions, as well as the antigenic heterogeneity displayed by multiple autologous melanoma lesions in vivo, suggest that the in vivo antigenic phenotype may be determined, at least in part, at an epigenetic level.
Aqua ammonia process for simultaneous removal of CO<SUB align=right>2, SO<SUB align=right>2 and NO<SUB align=right>x (2004)

Experimental research work in applying aqueous ammonia solution for the simultaneous reduction of acidic gaseous emission from fossil fuel-fired utility plants is currently being performed at the National Energy Technology Laboratory. The traditional monoethanolamine process for CO2 removal suffers the disadvantages of low carbon dioxide loading capacity, equipment corrosion, amine degradation by SO2 and O2 in flue gas, and high energy penalty during absorbent regeneration. The aqueous ammonia process can simultaneously remove CO2, SO2, NOx, plus HCl and HF that may exist in the flue gas. There could be oxidation of SO2 and NO prior to contacting the aqueous ammonia absorbent. Test results pertaining to the ammonia/carbon dioxide reaction in a semi-continuous reactor system are presented. The parametric effects of sparger design, reaction temperature, and ammonia concentration on gas loadings and absorption rates are discussed. Regeneration test results, including solution-cycling between the regeneration and absorption steps to determine a realistic loading capacity for the ammonia solutions are also presented.
Croup (2014)

Chapter 2 covers croup, and includes information on definition, demographics, clinical features, anatomy, imaging modalities and features, imaging algorithm, applied physics, differential diagnoses and pitfalls, and a bulleted summary of key points.
Form-finding with polyhedral meshes made simple (2014)

We solve the form-finding problem for polyhedral meshes in a way which combines form, function and fabrication; taking care of user-specified constraints like boundary interpolation, planarity of faces, statics, panel size and shape, enclosed volume, and last, but not least, cost. Our main application is the interactive modeling of meshes for architectural and industrial design. Our approach can be described as guided exploration of the constraint space whose algebraic structure is simplified by introducing auxiliary variables and ensuring that constraints are at most quadratic. Computationally, we perform a projection onto the constraint space which is biased towards low values of an energy which expresses desirable "soft" properties like fairness. We have created a tool which elegantly handles difficult tasks, such as taking boundary-alignment of polyhedral meshes into account, planarization, fairing under planarity side conditions, handling hybrid meshes, and extending the treatment of static equilibrium to shapes which possess overhanging parts.
Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants. (1994)

A near-full-length casbene synthase cDNA clone, pCS7, was isolated by using a partial cDNA clone, pCS4, to probe a lambda gt10 library constructed from poly(A)+ RNA from elicited castor bean seedlings. The cDNA insert had a length of 1983 bases with a polyadenylate tail of 19 bases. Translation of the cDNA sequence revealed an open reading frame encoding a 601-aa protein with a predicted M(r) of 68,960. Search of the GenBank data base with the deduced translation product revealed 42% identity and 65% similarity with 5-epi-aristolochene synthase from tobacco and 31% identity and 53% similarity with limonene synthase from spearmint. Each of the three proteins catalyzes an intramolecular cyclization of a prenyl diphosphate substrate to a specific cyclic terpenoid hydrocarbon product. The proposed reaction mechanisms for the three catalytic processes share common chemical features, even though the products being formed are members of three different classes of terpenoid compounds. Analysis of the alignment of the three proteins suggests that both primary and secondary structural elements are conserved. These similarities suggest that the genes that encode terpenoid cyclization enzymes of this type in angiosperms have undergone divergent evolution from an ancestral progenitor gene. In support of this proposition, the locations of five of the six introns in the casbene synthase gene align very closely with those of the five introns in the 5-epi-aristolochene synthase gene.
Parallel Epigenomic and Transcriptomic Responses to Viral Infection in Honey Bees (Apis mellifera) (2015)

Populations of honey bees are declining throughout the world, with US beekeepers losing 30% of their colonies each winter. Though multiple factors are driving these colony losses, it is increasingly clear that viruses play a major role. However, information about the molecular mechanisms mediating antiviral immunity in honey bees is surprisingly limited. Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers. One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss. Uninfected control and infected, symptomatic bees were collected within 20-24 hours after infection. Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection. There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans. There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections.
Maintaining intraoperative normothermia: a meta-analysis of outcomes with costs. (1999)

The present study used a meta-analysis to examine 4 questions about intraoperative hypothermia. The questions addressed were as follows: (1) Is the difference in adverse patient outcomes between normothermic and mildly hypothermic patient groups significant across studies and within studies? (2) What is the magnitude of the difference in adverse patient outcomes across studies? (3) What are the costs resulting from the difference in adverse patient outcomes? (4) Does a significant difference exist in effectiveness of modality for maintaining intraoperative normothermia? The results of this meta-analytic study provide evidence that the difference in adverse patient outcomes between the normothermic and mildly hypothermic patients is significant across studies for all adverse outcomes examined. The magnitude of this difference and the costs resulting from these adverse outcomes are presented. In addition, a significant difference in effectiveness between warming modalities for maintaining intraoperative normothermia was found. A significant increase in the risk of costly complications occurred when patient temperatures dropped a mean of 1.5 degrees C. For example, patients who become mildly hypothermic are much more likely to receive blood transfusions and to develop infections; both of these outcomes result in increased costs. Minimizing adverse outcomes is critical to cost-effective patient care in today's competitive healthcare environment. The cost of preventing intraoperative hypothermia is much less than the cost of treating the adverse outcomes that affect patients experiencing intraoperative hypothermia. Meta-analytic results allowed us to conclude that hypothermia averaging only 1.5 degrees C less than normal resulted in cumulative adverse outcomes adding between $2,500 and $7,000 per surgical patient to hospitalization costs across a variety of surgical procedures. In conclusion, patients whose temperatures have been maintained at normal levels during the intraoperative period experience fewer adverse outcomes, and their overall hospital costs are lower. Intraoperative normothermia is maintained more effectively with the use of forced air warming.
A graphical user interface to theCCP4 program suite (2003)

CCP4i is a graphical user interface that makes running programs from the CCP4 suite simpler and quicker. It is particularly directed at inexperienced users and tightly linked to introductory and scientific documentation. It also provides a simple project-management system and visualization tools. The system is readily extensible and not specific to CCP4 software.